title: EIF6 conditions drug-tolerant persister-like transdifferentiation in small cell lung carcinoma (SCLC cell lines)

first: Haoning

last: Peng

summary: Drug-tolerant persister cells withstand treatments by adapting their identity through lineage-dependent plasticity during systemic anti-cancer therapies. This phenomenon is evident in small-cell lung carcinoma (SCLC), a lethal neuroendocrine cancer initially responsive (60-80%) to platinum-based chemotherapy but succumbing to resistance within 6 months in advanced stages. This resistance associates with the transdifferentiation of residual tumour cells into a non-neuroendocrine state, a process intricately tied to SCLC's chemotolerance, yet molecular mechanisms governing this lineage conversion remain completed understood. Here we use paired cytoplasmic RNA-seq and polysomal RNA-seq to compare gene expression between NE and non-NE SCLC cell lines on both transcriptional and translational level. We report that first-line chemotherapy induces translation initiation factor eIF6 in drug-tolerant persister-like cells in SCLC, correlating with the non-neuroendocrine state in SCLC. Intervening eIF6 inhibits non-neuroendocrine transdifferentiation, thus enhancing SCLC responsiveness to chemotherapy. This study sheds light on eIF6's potential therapeutic interventions to mitigate treatment resistance in SCLC.

overall_design:
We performed RNA-sequencing for paired cytoplasmic mRNA and polysomal mRNA in H196 cells vs. H69 cells and H69M cells vs.H69 cells for comparing their gene expression on both transcriptional and translational level.
We performed RNA-sequencing for paired cytoplasmic mRNA and polysomal mRNA in H196 cells vs. H69 cells, H69M cells vs.H69 cells, H82R cells vs. H82 cells and H209A cells vs.H209 cells for comparing their gene expression on both transcriptional and translational level.

first: Zhile

last: Wang

first: Mengyao

first: Lunxu

last: Liu

first: Shensi

last: Shen


title: Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome [CUT&RUN]

status: Public on Dec 21 2023

city: St. Louis

first: Jennifer

middle: E.

last: Phillips-Cremins

state: MO

address: 4515 McKinley Ave

department: Bioengineering

country: USA

institute: Washington University in St. Louis

summary: Short tandem repeat (STR) instability causes transcriptional silencing in several repeat expansion disorders. In fragile X syndrome (FXS), mutation-length expansion of a CGG STR represses FMR1 via local DNA methylation. Here, we find Megabase-scale H3K9me3 domains on autosomes and encompassing FMR1 on the X-chromosome in induced pluripotent stem cell (iPSC)-derived neural progenitors, B-cells, and fibroblasts with mutation-length CGG expansion. H3K9me3 domains connect via inter-chromosomal interactions and demarcate severe misfolding of TADs and loops. They harbor long synaptic genes replicating at the end of S phase, replication stress-induced double strand breaks, and STRs prone to stepwise somatic instability. CRISPR engineering of the full-mutation CGG to premutation-length reverses H3K9me3 domains on the X-chromosome and multiple autosomes, refolds TADs, and restores expression. H3K9me3 domains also arise in a subset of normal-length iPSCs with increased STR instability burden. Our results reveal Mb-scale heterochromatinization and trans interactions among chromosomes susceptible to repeat genetic instability.

overall_design: Hi-C, H3K9me3 ChIP-seq, CTCF ChIP-seq, RNA-seq, H3K9me3 CUT&RUN, and short and long read genome sequencing were used in multiple cell types to interrogate epigenetic changes in cell lines with normal, premutation, and disease level repeat expansions in FMR1.

first: Thomas

last: Malachowski

first: Keerthivasan

middle: R

last: Chandradoss

first: Linda

last: Zhou

first: Ravi

last: Boya

first: Ashley

last: Cook

middle: E


title: Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome [RNA-seq]

type: Expression profiling by high throughput sequencing


title: Spatially resolved human kidney multi-omics single cell atlas highlights the key role of fibrotic microenvironment in kidney disease progression.

status: Public on Jan 17 2024

city: Philadelphia

first: Jonathan

last: Levinsohn

state: PA

address: 3400 Civic Center Blvd, Smilow 12-188

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Kidneys possess come one of the most intricate three-dimensional cellular structures in the body, yet the spatial molecular principles of kidney health and disease remain inadequately understood. Here we generated high-quality single cell (sc), single nuclear (sn), spatial (sp) RNA expression and sn open chromatin datasets for 79 samples, capturing half a million cells from healthy, diabetic, and hypertensive diseased human kidneys. By combining the sn/sc and sp RNA data, we identify over 100 cell types and states and successfully map them back to their spatial locations. Computational deconvolution of spRNA-seq helps to identifies glomerular, tubular, immune, and fibrotic spatial microenvironments (FMEs). Although injured proximal tubule cells appear to be the nidus of fibrosis, we reveal the complex, heterogenous cellular and spatial organization of human FMEs, including the highly intricate and organized immune environment. We demonstrate the clinical utility of the FME spatial gene signature for the classification of a large number of human kidneys for disease severity and prognosis. We provide a comprehensive spatially-resolved molecular roadmap for the human kidney and the fibrotic process and demonstrate the clinical utility of spatial transcriptomics.

overall_design:
We provided human kidney atlas by generating the following datasets: (i) scRNA-seq (16 Control + 13 Disease), (ii) snRNA-seq (7 control + 11 Disease), (iii) snATAC-seq (10 Control + 8 Disease), (iv) Spatial Transcriptomics (3 Control + 11 Disease).

**Raw data were not provided due to privacy concerns**

Susztak_SC_SN_ATAC_merged_preSCVI_final.h5ad: merged object of snRNA/scRNA/snATAC
Susztak_SC_SN_ATAC_merged_PostSCVI_final.h5ad: integrated object via SCVI
Susztak_KPMP_SC_SN_ATAC_merged_PostSCVI_final.h5ad: integrated object via SCVI with KPMP samples as well
7_13_23_slide0_annotated_iPTsubclusters.h5ad: Annotated CosMx Object

first: Amin

last: Abedini

first: Konstantin

last: Kloetzer

first: Ziyuan

last: Ma

first: Julia

last: Frederick

first: Poonam

last: Dhillon

first: Michael

last: Balzer

first: Rojesh

last: Shrestha

first: Kishor

last: Devalaraja-Narashimha

first: Gurmannat

last: Kalra

first: Tanmoy

last: Bhattacharyya

first: Erding

last: Hu

first: Steven

last: Pullen

first: Carine

middle: M

last: Boustany-Kari

first: Paolo

last: Guarnieri

first: John

last: Liles

first: Hanyung

last: Yu

first: Kyle

last: Coleman

first: Anil

last: Karihaloo

first: Daniel

last: Traum

first: Matthew

last: Palmer

last: Vitale

first: Lea

last: Sarov-Blat

first: Lori

last: Morton

first: Christopher

last: Hunter

first: Klaus

middle: H

last: Kaestner

first: Mingyao

last: Li

first: Katalin

last: Susztak


title: The Hippo kinase LATS1 controls CTCF chromatin occupancy and the hormonal response of three-dimensionally grown breast cancer cells

status: Public on Nov 19 2023

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

summary: The cancer epigenome has been studied in cells cultured in 2D monolayers on plastic surfaces, but recent studies highlight the impact of the extracellular matrix (ECM) and the 3D environment on multiple cellular functions. Here, we report the physical, biochemical and genomic differences between T47D breast cancer cells cultured in 2D monolayer and as 3D spheroids in Matrigel. Cells within 3D spheroids exhibit a rounder nucleus with less accessible, more compacted chromatin, and altered expression of over 2,000 genes, the majority of which become repressed. Hi-C analysis reveals that cells grown in 3D exhibit enrichment in regions belonging to the B compartment, decrease on chromatin bound CTCF and increased fusion of Topologically Associating Domains (TADs). Upregulation of the Hippo pathway in 3D spheroids results in the activation of the LATS1 kinase, which promotes phosphorylation and displacement of CTCF from DNA, likely responsible for the observed TAD fusions. Cells grown in 3D exhibit higher progesterone receptor (PR) binding to chromatin, leading to an increase in the number hormone-regulated genes. This effect is in part mediated by the LATS1 activation, which favors cytoplasmic retention of YAP and CTCF removal.

overall_design: Epigenomic analysis of LATS1 kinase in controlling CTCF for 3D growth of breast cancer cells

first: Julieta

last: Cuellar

first: Rosario

middle: T

last: Sanz

first: A

middle: S

last: Nach

first: David

last: Castillo

first: Francois

last: Le Dily

first: Maria

middle: V

last: Neguembor

first: Marco

last: Malatesta

first: Marc

middle: A

last: Marti-Renom

first: Miguel

last: Beato

first: Guillermo

middle: P

last: Vicent


title: mTORC2-mediated cell-cell interaction promote BMP4-induced WNT activation and mesoderm differentiation

status: Public on Nov 06 2023

city: London

first: Li

last: Tong

address: Du Cane Road

department: Metabolism, Digestion & Reproduction

country: United Kingdom

institute: Imperial College London

summary: The mechanistic target of rapamycin complex 2 (mTORC2) is essential for embryonic development but the underlying molecular mechanisms remain unclear. Here we show that disruption of mTORC2 in human embryonic stem cells (hESCs) considerably alters the balance of Rho/Rac signaling and reduces cell adhesion. Although these changes have no clear effect on their self-renewal and the expression of pluripotent markers, they significantly impede BMP-induced activation of canonical WNT genes, leading to impaired mesendoderm differentiation. Direct activation of the downstream WNT pathway by inhibiting GSK3 dramatically improves mesendoderm differentiation in mTORC2-deficient hESCs. Our studies uncover a new mechanism by which mTORC2 regulates cell fate determination and link the intercellular contacts with the activation of WNT genes.

overall_design: To investigate the function of mTORC2 in the regulation of embryonic development and cell fate determination, we disrupted RICTOR gene in human embryonic stem cells (hESCs) by CRISPR/Cas9. We then performed differential expression analysis using RNA-seq from two WT and two KO hESC lines.

first: Faiza

last: Batool

first: Yueh-Ho

last: Chiu

first: Yudong

last: Zhou

first: Xiaolun

last: Ma

first: Santosh

last: Atanur

first: Wei

last: Cui


title: K6-Linked Ubiquitylation Signals Reactive Aldehyde-Induced RNA-Protein Crosslink Resolution

status: Public on Nov 03 2023

city: Würzburg

first: Julian

last: Konig

address: Am Hubland

country: Germany

institute: Würzburg University

summary: Reactive aldehydes induce the formation of RNA-protein crosslinks (RPCs), RPCs in the mRNA stall the ribosome and inhibit translation, RPCs are K6-linked ubiqutylated by RBR-type E3 ligase RNF14, RPCs are resolved in a UBXN1-VCP/p97-dependent manner

overall_design: Proteome-wide iCLIP to detect the distribution of RPC across RNAs; RPCs were introduced with 5 uM 4sU + 0.5 J/cm² UVA (365 nm); protein cleanup with SP3 beads; 2 replicates

first: Anna

last: Orekhova

first: Rebecca

last: Hobrecht

first: Anke

last: Busch

first: Stefanie

last: Ebersberger

last: König

first: Petra

last: Beli


title: Cell network in mouse liver regeneration

status: Public on Feb 23 2024

city: Portland

first: Bin

last: Li

state: OR

address: 3181 SW Sam Jackson Pk Rd

department: Oregon Stem Cell Center

institute: Oregon Health and Science University

summary: In this study, we compared different liver cell populations in normal and partial hepatectomy mouse model.

overall_design: 10 cell population from normal and partial hepatectomy liver were isolated and FACS sorted into Trizol to extract RNA for RNA-seq

first: Carl

last: Pelz

first: Markus

last: Grompe


title: Cabozantinib and IL-27 Combinatorial Therapy for Bone-Metastatic Prostate Cancer

status: Public on Oct 25 2023

city: West Lafayette

first: Marxa

middle: Leao

last: Figueiredo

state: IN

address: 625 Harrison St

department: Basic Medical Sciences

institute: Purdue University

summary: Prostate cancer is the second leading cause of cancer-related death among American men. Prostate tumor cells exhibit significant tropism for the bone and once metastasis occurs, survival rates fall significantly. Current treatment options are not curative and focus on symptom management. Immunotherapies are rapidly emerging as a possible therapeutic option for a variety of cancers including prostate cancer, however, variable patient response remains a concern. Chemotherapies, like cabozantinib, can have immune-priming effects which sensitize tumors to immunotherapies. Additionally, lower doses of chemotherapy can be used in this context which can reduce patient side effects. We hypothesized that a combination of chemotherapy (cabozantinib) and immunotherapy (Interleukin-27 (IL-27)) could be used to treat bone-metastatic prostate cancer and exert pro-osteogenic effects. IL-27 is a multi-functional cytokine, which promotes immune cell recruitment to tumors, while also promoting bone repair. To test this hypothesis, in vivo experiments were performed where syngeneic C57BL/6J mice were implanted intratibially with TRAMP-C2ras-Luc cells that are able to form tumors in bone. Immunotherapy was administered in the form of intramuscular gene therapy, delivering plasmid DNA encoding a reporter gene (Lucia), and/or a therapeutic gene (IL-27). Sonoporation was used to aid gene delivery. Following immunotherapy, the animals received either cabozantinib or a vehicle control by oral gavage. Bioluminescence imaging was used to monitor tumor size over time. Combinatorial therapy inhibited tumor growth and improved survival. Further, RNA sequencing was used to investigate the mechanisms involved. Microcomputed tomography and differentiation assays indicated that the combination therapy improved bone quality by enhancing osteoblast differentiation and inhibiting osteoclast differentiation. Our conclusion is that a chemo-immunotherapy approach such as the one examined in this work has potential to emerge as a novel therapeutic strategy for treating bone-metastatic prostate cancer. This approach will enable a significant reduction in chemotherapy-associated toxicity, enhance sensitivity to immunotherapy, and improve bone quality.

overall_design: Mouse adenocarcinoma cell line TC2Ras was cultured in Dulbecco’s modified Eagle’s medium–nutrient mixture F-12 (DMEM-F12) (Gibco, Waltham, Massachusetts) supplemented with 10% FBS (Hyclone, Cytiva, Marlborough, MA) and 1% antibiotic-antimycotic (Anti-Anti) (Gibco). Male C57/BL6 mice (8-10 weeks of age) were obtained from Envigo. Mice were handled in accordance with an approved study protocol by the Purdue Animal Care and Use Committee (PACUC). TC2ras cells were prepared for implantation by adding trypsin (0.25% Trypsin-EDTA, Gibco, Billings, MT) to the cells and washing with sterile 1x DPBS. The pellet was resuspended in 1x DPBS at an appropriate concentration. For the intratibial model, 105 TC2Ras-Luc cells were injected in each tibia in 10ul sterile 1xDPBS. For the subcutaneous model, 3x105 TC2Ras cells were injected in each flank in 50uL sterile 1xDPBS. Implantation was performed under 2% inhaled isoflurane anesthesia delivered by high-flow vaporizer (VetFlo, Kent Scientific, Torrington, CT). In the subcutaneous model, tumors were harvested one week post implantation for RNA-sequencing analysis. In the intratibial model, three mice per group were euthanized 14 days post implantation, whereas the rest of the mice (n=4) were allowed to progress to the ethical endpoint. Post-euthanasia, tumors were collected in RNAlater (Invitrogen, Waltham, MA) and preserved for further RNA isolation and analysis. In short, RNA was isolated using RNeasy kit (Qiagen) according to manufacturer's protocol. Poly(A) RNA sequencing library was prepared following Illumina's TruSeq-stranded-mRNA protocol and conducted by LC Sciences (Houston, TX, USA). Poly(A) tail-containing mRNAs were purified using oligo-dT Briefly, magnetic beads with two rounds of purification, and fragmented using divalent cation buffer at elevated temperature. Quality control analysis and quantification of the sequencing library were performed using an Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000. For transcript assembly and estimating transcript expression levels, software is described by Figueiredo et al. (2020) (21). For differential expression analysis of mRNAs, StringTie was used by calculating fragments per kilobase million (FPKM). The differentially expressed mRNAs were selected with log2 (fold change) > 1.5 or log2 (fold change) < -1.5 and with statistical significance (p < 0.05) by edgeR.

first: Shreya

last: Kumar

first: Grace

last: Mulia


title: Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome [ChIP-seq]

first: Jennifer

last: Phillips-Cremins

first: Thomas

last: Malachowski

first: Keerthivasan

last: Chandradoss

first: Linda

last: Zhou

first: Ravi

last: Boya

first: Ashley

last: Cook


title: Mechanoresponsive genomic enhancers potentiate the cellular response to matrix stiffness [Bulk RNA-seq]

status: Public on Jan 31 2024

city: Durham

first: Charles

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

summary: Epigenetic control of gene regulation and cell phenotype is influenced by changes in the mechanical microenvironment. Yet how mechanical forces precisely influence epigenetic state to regulate transcriptional responses remains largely unmapped. Here, we combine genome-wide epigenome profiling, epigenome editing, and phenotypic and single-cell RNA-seq screening to identify a sub-class of genomic enhancers that is responsive to the mechanical microenvironment. These enhancers regulate genes that act as key drivers for a variety of functional behaviors including apoptosis, mechanotransduction, proliferation, and migration. We find distinct patterns wherein subsets of mechano-enhancers can be preferentially active on either soft or stiff extracellular matrix (ECM) contexts. Epigenetic editing of these mechano-enhancers on rigid materials precisely tunes mechanically-induced gene expression to levels observed on softer materials, and broadly enables reprogramming of cellular response to the mechanical microenvironment. These mechanically-activated enhancers act as key signal transducers and may constitute a new class of targets that can be modulated to alter mechanically-driven disease states.

overall_design:
To determine the genes regulated by the pREs identified in the proliferation and migration screens, we made a sub-library of gRNAs targeting 87 of the pREs (10 gRNAs/pRE) with the largest effect sizes in either or both of the previous screens. This library also included positive controls of promoter-targeting and known enhancer-targeting gRNAs, and 100 non-targeting negative control gRNAs, for a total of 1,005 gRNAs in the sub-library. We transduced HFFs expressing dCas9KRAB cultured on TCP with this gRNA library at 0.33 MOI, and eight days post-transduction we profiled 103,440 quality single cell transcriptomes. We recovered a median of 1 gRNA per cell and identified an average of 159 cells containing each gRNA. To identify significant gene linkages to each pRE, we tested cells that had each gRNA versus all cells that did not receive that gRNA, and compared expression for all genes within +/- 1Mb from the targeted pRE.
Human fibroblasts and A549 lung adenocarcinoma cells grown on soft (1 kPa) or stiff (50 kPa) hydrogels showed widespread differences in gene expression and chromatin accessibility by RNA-seq and ATAC-seq. CRISPRi was used to perturb differentially accessible regions surrounding stiffness-responsive genes such as MYH9, BMF, and FZD2 and identify distal mechanoenhancers that influenced gene expression. Functional high-throughput CRISPRi screening was performed to discover ~100 putative regulatory regions that influenced cell growth or migration. CRISPRi screening with single-cell RNA-seq identified 201 functional connections of these mechanoenhancers to their gene targets, including CTGF, CYR61, NF2, RFLNB, RANGAP1, SKP2 and others. Epigenetic editing of mechanoenhancers with CRISPRi in cells cultured on stiff substrates, including activated human donor-derived fibroblasts from healthy and idiopathic pulmonary fibrosis (IPF) lung tissue, resulted in gene expression patterns similar to those observed on soft substrates. Epigenetic modulation of these mechanoenhancers also resulted in functional changes in mechanosensing, migration, growth, and apoptosis.

first: Brian

middle: D

last: Cosgrove

first: Lexi

last: Bounds

first: Carson

middle: K

last: Taylor

first: Alan

middle: L

last: Su

first: Anthony

middle: J

last: Rizzo

first: Alejandro

last: Barrera

first: Gregory

last: Crawford

first: Brenton

last: Hoffman


title: A unique active role for HOTAIR to promote transcription in prostate cancer progression

status: Public on Mar 26 2024

city: Tianjin

first: Yuyang

last: Qian

state: Tianjin

address: 94 Weijin Road

department: cell and genetic department

country: China

institute: Nankai university

summary:
Previous research has predominantly focused on the regulatory role of lncRNA HOTAIR in gene silencing through its interaction with the Polycomb repressive complex 2 (PRC2). Here, our study uncovers a novel regulatory mechanism of HOTAIR, which facilitates prostate cancer (PCa) progression by sustaining transcription elongation. Using ChIRP-seq, RNA-seq, and ChIP-seq, we successfully mapped the binding sites of HOTAIR across the genome and determined their interplay with the epigenetic landscape. We discovered that the co-localization of HOTAIR with the androgen receptor (AR) can activate gene transcription. In the context of AR binding, we discovered that HOTAIR maintains transcription elongation by facilitating the formation of the CDK9/Pol2S2 complex. We revealed a unique capacity of HOTAIR to promote transcriptional activation on gene promoters/bodies with low H3K27me3 enrichment, a function contrasting to its established PRC2-related transcriptional inhibitory roles in regions with high H3K27me3 signal. Finally, we identified two direct target genes of HOTAIR (MMP14 and TNFAIP2), which contribute to the progression of PCa. Collectively, our research sheds new light on HOTAIR's role in transcriptional regulation, offering potential therapeutic strategies and expand our understanding of HOTAIR's roles in PCa progression.
In this study, we used ChIRP-seq to identify HOTAIR binding sites on genome-wide of PCa cells. Then, for purpose of associating chromatin location of HOTAIR to epigenetic landscape, we profiled repressed histone mark (H3K27me3) and active histone mark (H3K27ac). Finally, we integrated data of ChIRP-seq, RNA-seq and ChIP-seq for a complete analysis. We identified that HOTAIR can co-locate with AR to enhance transcription elongation on low H3K27m3 enrichment gene body/promoter, which differs from the function of HOTAIR on high H3K27me3 enrichment region.

overall_design:
The project include RNA-seq, ChIRP-seq, ChIP-seq and Cut and Tag between the 22Rv1 WT cells and two HOTAIR poly-A Knock-in cells.
The project include ChIRP-seq between the 22Rv1 WT cells and two HOTAIR poly-A Knock-in cells.

first: Bo

last: Wang

first: Wange

last: Lu


title: Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome

first: Jennifer

last: Phillips-Cremins

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

overall_design: Refer to individual Series


title: The impact of Tbet and/or Runx3 deficiency on Tle3 binding pattern in early effector CD8 T cells

status: Public on Oct 10 2023

city: Nutley

first: Hai-Hui

last: Xue

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation

institute: Hackensack University Medical Center

summary: The goal of this study is to determine if central memory (Tcm) and effector memory (Tem) CD8 T cells can be reprogrammed to change their fate. We demonstrate that genetic ablation of Tle3 can promote generation of Tcm cells at the expense of Tem cells, and this can occur during the effector phase of the immune response.

overall_design: Genome-wide mapping of transcriptomic, chromatin accessibility, and Tle3 binding profiles of WT naïve and effector cells, WT and Tle3-deficient central/effector memory CD8+ T cells.

first: Shaoqi

last: Zhu


title: Impact of Tle3 induced deletion on transcriptomes of effector memory CD8 cells


title: Reprogramming fate of central memory CD8+T cells by targetig the transcriptional coregulator Tle3 [scRNA-seq]

overall_design: Single cell RNAseq analysis of WT or Tle3-deficient antigen-specific memory CD8 T cells isolated on day 30 after infection with LCMV-Armstrong.

first: Sung

last: Park


title: Impact of Tle3 deficiency on memory T cell transcriptome


title: Mapping dynamic Tle3 distribution during CD8 T cell responses


title: Impact of Tle3 deficiency on memory T cell chromatin accessbility landscape


title: Reprogramming fate of central memory CD8+T cells by targetig the transcriptional coregulator Tle3


title: Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome [Hi-C]

first: Thomas

last: Malachowski

first: Keerthivasan

last: Chandradoss

first: Linda

last: Zhou

first: Ravi

last: Boya

first: Ashley

last: Cook


title: RNA catabolism restricts ERV expression and functionalization [KD RNA-Seq]

status: Public on Oct 01 2023

city: New York

first: Robert

last: Sebra

state: New York

address: 1 Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

summary: Endogenous retroviruses (ERVs) are remnants of ancient parasitic viral integrations and comprise a sizable portion of the genome in most organisms. Deregulated expression of ERVs in human is associated with a plethora of disease conditions, such as cancer and neurodegeneration. Epigenetic mechanisms silence most ERVs by generating a local repressive environment (heterochromatin) to prevent their expression. However, the mechanisms controlling the fate of ERVs residing in euchromatic regions of the genome (e.g. MERVL elements) are not well understood. Here, by integrating multidimensional epigenetic and genomic analyses, we demonstrate that silencing of euchromatic MERVL elements is achieved via transcription-coupled RNA degradation. Disrupting RNA catabolism promotes RNAPII elongation from MERVL promoters, increases MERVL expression and exonization, creating novel chimeric gene isoforms, and directing embryonic stem (ES) cells toward a terminal undifferentiated state.  Our results indicate that RNA catabolism is a core regulatory module of gene networks that safeguards cell identity and potency, restricts MERVL functionalization and suppresses gene birth.

overall_design: Total RNA-Seq of mESCs undergoing siRNA-mediated KD of Exosc3, Ints11, Rbm7, Cpsf2 and Zcchc8. Three separate KD experiments were performed, each with respective siCtrl samples (see "experiment" column for metadata detail).

first: D

last: Torre

first: Y

last: Fstkchyan

first: I

last: Marazzi


title: Enhancer grammar of liver cell types and hepatocyte zonation states [multiome_validation]

status: Public on Sep 07 2023

city: Leuven

first: Carmen

last: Bravo Gonzalez-Blas

address: Herestraat 49

country: Belgium

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

summary: Cell type identity is encoded by gene regulatory networks (GRN), in which transcription factors (TFs) bind to enhancers to regulate target gene expression. In the mammalian liver, lineage TFs have been characterized for the main cell types, including hepatocytes. Hepatocytes cover a relatively broad cellular state space, as they differ significantly in their metabolic state, and function, depending on their position with respect to the central or portal vein in a liver lobule. It is unclear whether this spatially defined cellular state space, called zonation, is also governed by a well-defined gene regulatory code. To address this challenge, we have mapped enhancer-GRNs (eGRNs) across liver cell types at high resolution, using a combination of single-cell multi-omics, spatial omics, GRN inference, and deep learning. We found that zonated variation in gene expression in hepatocytes, liver sinusoidal endothelial cells and hepatocellular stellate cells corroborate cell state changes in transcription and chromatin accessibility with spatial transcriptomics. eGRN mapping suggests that zonation states in hepatocytes are driven by the repressors Tcf7l1 and Tbx3, that modulate the core hepatocyte GRN, controlled by Hnf4a, Cebpa, Hnf1a, Onecut1 and Foxa1, among others. To investigate how these TFs cooperate with cell type TFs, we performed an in vivo Massively Parallel Reporter Assay (MPRA) on 12,000 hepatocyte enhancers and used these data to train a hierarchical deep learning model (called DeepLiver) that exploits both enhancer accessibility and activity. DeepLiver confirms Cebpa, Onecut, Foxa1, Hnf1a and Hnf4a as drivers of enhancer specificity in hepatocytes; Tcf7l1/2 and Tbx3 as regulators of the zonation state; and Hnf4a, Hnf1a, AP-1 and Ets as activators. Finally, taking advantage of in silico mutagenesis predictions from DeepLiver and MPRA, we confirmed that the destruction of Tcf7l1/2 or Tbx3 motifs in zonated enhancers abrogates their zonation bias. Our study provides a multi-modal explanation of the regulatory code underlying hepatocyte identity and their zonation state, that can be exploited to engineer enhancers with desired activity levels and zonation patterns.

overall_design: 10x single cell multiome on the mouse liver

middle: B

last: González-Blas

first: Stein

last: Aerts


title: Transcriptional profiling of the developing murine intestine

status: Public on Sep 11 2023

city: Los Angeles

first: Dario

last: Boffelli

state: CA

address: 700 N San Vicente Blvd

department: Pediatrics

institute: Cedars Sinai

summary: To identify transcriptional changes during the development of the small intestine, we performed scRNAseq using MULTI-seq on 86,845 cells collected from embryos at E13.5-E18.5. We additionally identified transcriptional changes along the proximal-distal axis of the small intestine by isolating RNA from 2.5mm fragments of the tissue that had been cut along this axis. Mice were collected from Pdgfra-H2BGFP mice to enrich for mesenchymal populations.

overall_design: Single-cell RNA sequencing was performed using MULTI-seq on mouse embryonic intestinal tissues from Pdgfra-H2BGFP mice across five developmental time points with pooled replicates (E13.5, 4 replicates; E14.5, 3 replicates; E15.5, 2 replicates; E16.5, 2 replicates; and E18.5, 2 replicates). The intestines were divided into 2.5mm-length pieces along its proximal-distal axis (E13.5, 3 segments; E14.5, 5 segments; E15.5, 10 segments; E16.5, 15 segments; E18.5, 20 segments). We enriched for rare cell populations (PdgfraHigh, or Epcam+, or CD31+ or CD45+).

first: Tyler

last: Huycke

first: Hikaru

last: Miyazaki

first: Christopher

last: McGinnis

first: Dedeepya

last: Vaka

first: Ophir

last: Klein

first: Zev

last: Gartner


title: Global Endometrial DNA Multi-omics Analysis Reveals Insights into mQTL Regulation and Associated Endometriosis Disease Risk and Endometrial Function

status: Public on Sep 12 2023

city: Herston

first: Sally

last: Mortlock

state: QLD

address: School of Public Health

department: School of Public Health

country: Australia

institute: University of Queensland

summary: Endometriosis is a leading cause of pain and infertility affecting millions of women globally. Biological and genetic effects on DNA methylation (DNAm) can influence gene regulation and contribute to complex disease. Herein, we characterize variation in endometrial DNAm and its association with menstrual cycle phase, endometriosis, and genetic variants through analysis of genome-wide genotype data and methylation at 759,345 DNAm sites in endometrial samples from 984 deeply-phenotyped participants. We estimate that 15.4% of the variation in endometriosis is captured by DNAm and identify significant differences in DNAm profiles and DNAm networks, associated with endometriosis, endometriosis sub-phenotypes and menstrual cycle phase, including opening of the window for embryo implantation. DNAm quantitative trait locus (mQTL) analysis identified 118,185 independent cis-mQTLs including 51 associated with risk of endometriosis highlighting candidate genes contributing to disease risk. Our work provides functional evidence for epigenetic targets contributing to endometriosis risk and pathogenesis. Data generated serve as a valuable resource for understanding tissue-specific effects of methylation on endometrial biology in health and disease.

overall_design: Bisulphite converted DNA from the 984 endometrial samples were hybridised to the Illumina Infinium MethylationEPIC Beadchip

last: Giudice


title: Enhancer grammar of liver cell types and hepatocyte zonation states [chip-seq]


title: Enhancer grammar of liver cell types and hepatocyte zonation states [AML12_MPRA]


title: Enhancer grammar of liver cell types and hepatocyte zonation states [12K_MPRA]

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: 10x single cell multiome on the mouse liver.

last: Bravo González-Blas


title: Enhancer grammar of liver cell types and hepatocyte zonation states [FACS_MPRA]


title: RNA catabolism restricts ERV expression and functionalization

last: Sebra

type: Methylation profiling by high throughput sequencing


title: Early-life stress and ovarian hormones alter transcriptional regulation in the nucleus accumbens resulting in sex-specific responses to cocaine [RNA-Seq]

status: Public on Sep 05 2023

city: Bronx

first: Marija

last: Kundakovic

state: NY

address: 441 E. Fordham Road

department: Biological Sciences

institute: Fordham University

summary: Cocaine use disorder affects people across genders, although women are reported to be more sensitive than men to cocaine’s addictive properties. Our study highlights that cocaine use in women and other menstruating individuals may involve complex effects of ovarian hormones that interact with internal factors (such as negative affective state) and external risk factors such as stress and, for the first time, we reveal the molecular substrates through which female-specific factors can induce stronger and longer-lasting, sex-specific responses to cocaine.

overall_design: RNA-seq experiments were designed to determine differential RNA expression in the nucleus accumbens of male and female mice, among both controls and animals subjected to early life stress in the form of 2 weeks maternal separation for 2 hours per day from postnatal day 1-14. Six biological replicates (each composed of bilateral nucleus accumbens) were tested per group. Female groups were balanced by the estrous cycle containing and equal number for proestrus/estrus animals and metestrus/diestrus animals.

first: Devin

last: Rocks

first: Ivana

last: Jaric

first: Fabio

last: Bellia

first: Heining

last: Cham

first: John

last: Greally

first: Masako

last: Suzuki


title: Impact of Tle3 induced deletion on chromatin accessibility profile of effector memory CD8 cells

first: Hai-Hui

last: Xue

first: Shaoqi

last: Zhu


title: Gene expression profile at single cell level of tumor cells and immune cells from mouse SCLC tumors and preSC allograft samples.

status: Public on Aug 08 2023

city: Houston

first: Shengzhe

last: Zhang

state: TX

address: 6565 MD Anderson Blvd

department: Experimental Radiation Oncology

institute: MD Anderson Cancer Center

summary: Small cell lung carcinoma (SCLC) is a lethal neuroendocrine type of lung cancer with limited therapeutic options. We used single cell RNA sequencing (scRNA-seq) to study SCLC tumogenesis.

overall_design: We used a gene knockout induced SCLC mouse model and a mouse cell line allograft model. Collect the fresh tissue and analyzed using scRNAseq.


title: Early-life stress and ovarian hormones alter transcriptional regulation in the nucleus accumbens resulting in sex-specific responses to cocaine [ATAC-Seq]

overall_design: ATAC-seq experiments were designed to determine chromatin accessibility profiles of nucleus accumbens neurons in young adult females in two different stages of the estrous cycle  (proestrus and diestrus) and in age-matched males between controls and animals that received 10mg/kg of cocaine (i.p.) and were sacrificed 1 hour after injection. 2-3 biological replicates (each pooled from three animals) were tested per group.


title: Enhancer grammar of liver cell types and hepatocyte zonation states [multiome]

first: Carmen

last: Bravo Gonzalez-Blas

first: Stein

last: Aerts


title: Enhancer grammar of liver cell types and hepatocyte zonation states [FACS_ATAC]


title: Acute resistance to BET inhibitors remodels compensatory transcriptional programmes via p300 co-activation

city: Mainz

first: Daniel

last: Sasca

address: Langenbeckstr 1

department: Department of Hematology and Oncology

institute: University Medical Center Mainz

summary: Aiming to discover anticipatory combination treatments for better and longer disease response rates, we here explore immediate epigenetic and transcriptional reactions after BET inhibition. BET inhibitor-driven decommissioning of BRD4 from chromatin is followed by an acute compensatory feedback loop intended to attenuate the loss of transcription. Critically, this adaptation occurs almost exclusively at key AML maintenance genes and is co-mediated by p300. However, this also provides a rationale therapeutic opportunity, with BET- followed by p300 inhibition. Of note, the transcriptional programs that p300 regulates to induce resistance to BET inhibition differ between AML subtypes. In some AMLs, p300 regulates transitional transcriptional patterns that allow homeostatic adjustments during earlier stages of resistance to BET inhibition, so that the importance of p300 is highest during initial resistance stages. In other AMLs, p300 leads to a linear induction of resistance to BET inhibition and, therefore, remains crucial throughout all stages of acquisition of resistance.

overall_design: SLAM-Seq performed in monocytic leukemia cell line SKNO-1 at two timepoints (4h and 24h). At 4h, cells were studied under treatment of BETi or dCBP; At 24h, BETi and Combo (BETi+dCBP).

first: Viral

last: Shah

first: Aarón

last: Gallego-Crespo


title: SETD2 loss in renal epithelial cells drives epithelial to mesenchymal transition in a TGFβ-independent manner [ChIP-Seq]

status: Public on Jul 12 2023

city: Rochester

first: Keith

middle: Darrell

last: Robertson

state: MN

address: 200 First Street SW, Stabile 12-70

department: Pharmacology

institute: Mayo Clinic

summary: SETD2 is one of most frequently mutated genes in renal cell carcinoma. It is generally known as the only histone methyltransferase that catalyze the trimethylation of lysine 36 on histone H3 (H3K36me3). Mutation of this gene and/or loss of its mark have been linked to metastasis and worse patient outcomes in kidney cancer. In this paper, we will examine the mechanism by which SETD2 loss induces epithelial-to-mesenchymal transition (EMT), which is a major pathway that drives invasion and early metastasis in various cancer types. To achieve the goals, we performed several omics analysis including RNA-seq, ChIP-seq and ATAC-seq to characterize how SETD2 deletion alters transcriptome and epigenome.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K36me3 in SETD2 WT, KO and rescue cells. Each sample is run in duplicates.

first: Tianchu

last: Wang

first: Ryan

last: Wagner

last: Hlady

first: Liguo

first: Jeong-Heon

last: Lee


title: The Genetic Architecture of Dietary Iron Overload and Associated Pathology in Mice

status: Public on Aug 11 2023

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Tissue iron (Fe) overload is a frequent pathologic finding in multiple disease states including non-alcoholic fatty liver disease (NAFLD), neurodegenerative disorders, cardiomyopathy, diabetes, and some forms of cancer. The role of iron, as a cause or consequence of disease progression and observed phenotypic manifestations, remains controversial. In addition, the impact of genetic variation on iron overload related phenotypes is unclear, and the identification of genetic modifiers is incomplete. Here, our aim was to characterize the genetic architecture of dietary iron overload and pathology using the Hybrid Mouse Diversity Panel (HMDP), a panel of over 100 genetically distinct mouse strains optimized for genome-wide association studies and systems genetics. Dietary iron overload was induced by feeding male mice (114 strains, 6-7 mice per strain on average) a high iron diet for six weeks, and then tissues were collected at 10-11 weeks of age. Liver metal levels and gene expression were measured by ICP-MS and RNASeq, and lipids were measured by colorimetric assays. FaST-LMM was used for genetic mapping, and Metascape, WGCNA, and Mergeomics were used for pathway, module, and key driver bioinformatics analyses. Mice on the high Fe diet accumulated Fe in the liver, with a 6.5-fold difference across strain means. The iron loaded diet also led to a spectrum of copper deficiency and anemia, with liver copper levels highly correlated with red blood cell count, hemoglobin, and hematocrit. Hepatic steatosis of various severity was observed histologically, with 52.5-fold variation in triglyceride (TG) levels across the strains. TG and Fe mapped most significantly to an overlapping locus on chromosome 7 that has not been previously associated with either trait. Based on network modeling, significant key drivers for both Fe and TG accumulation are involved in cholesterol biosynthesis and oxidative stress management. To make the full data set accessible and useable by others, we have made our data and analyses available on a resource website.

overall_design: Expression profiling by RNA-Seq for liver in 114 inbred mouse strains following 4 weeks on chow diet and 6 weeks on high-iron diet

first: Brie

last: Fuqua

first: Aldons

last: Lusis


title: SETD2 loss in renal epithelial cells drives epithelial to mesenchymal transition in a TGFβ-independent manner [RNA-Seq]

overall_design: We performed RNA-seq in renal proximal tubule epithelial cells (RPTEC) to characterize transcriptome change caused by SETD2 deletion. We further analyzed differential gene expression data in RPTEC SETD2 WT, KO, rescue, and TGF-β-treated/untreated WT. Each sample is run in duplicates.

first: Xiaoyu


title: Early-life stress and ovarian hormones alter transcriptional regulation in the nucleus accumbens resulting in sex-specific responses to cocaine

first: Marija

last: Kundakovic


title: TET2 lesions enhance the aggressiveness of CEBPA-mutant AML by re-balancing GATA2 expression

status: Public on Aug 28 2023

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

summary: The myeloid transcription factor CEBPA is recurrently biallelically mutated (i.e., double mutated; CEBPADM) in acute myeloid leukemia (AML); with a combination of hypermorphic N-terminal mutations (CEBPANT), promoting expression of the leukemia-associated p30 isoform, and amorphic C-terminal mutations. CEBPADM AML features recurrent co‑occurring mutations; however, insight into the underlying mechanisms for the co-mutational spectra is incomplete. By combining transcriptomic and epigenomic analyses of data from CEBPA-TET2-co-mutant patients with experimental models thereof, we identify GATA2 as a conserved target of the CEBPA-TET2 mutational axis, providing a rationale for the mutational spectra in CEBPADM AML. Mechanistically, we suggest that elevated CEBPA levels, driven by the CEBPANT, mediate recruitment of TET2 to the GATA2 distal hematopoietic enhancer and thereby increase GATA2 expression. Conversely, CEBPADM AML gains a competitive advantage by loss of TET2; decreasing GATA2 promoter demethylation and re-balancing GATA2 levels. Further, demethylating treatment of CEBPA-TET2-co-mutant AML restores GATA2 levels, and prolongs disease latency.

overall_design: Epigenomic (ATAC-seq) and transcriptomic (QUANT-seq) profiling of murine Cebpap30/p30 Tet2WT and Tet2MUT cells

first: Elizabeth

last: Heyes

first: Gabriele

last: Manhart

first: Florian

last: Grebien


title: Enhancer grammar of liver cell types and hepatocyte zonation states [scRNA-seq]

first: Carmen

last: Bravo Gonzalez-Blas

last: Bravo González-Blas

first: Stein

last: Aerts


title: Enhancer grammar of liver cell types and hepatocyte zonation states [scATAC-seq]


title: SETD2 loss in renal epithelial cells drives epithelial to mesenchymal transition in a TGFβ-independent manner


title: Enhancer grammar of liver cell types and hepatocyte zonation states

sample_organism:
Homo sapiens
Mus musculus
synthetic construct


title: Immune Escape after Allogeneic Hematopoietic Cell Transplantation in Pediatric Patients with Acute Myeloid Leukemia

status: Public on Jun 26 2023

first: Sanam

last: Shahid

address: 1275 York Avenue

department: Department of Pediatrics

institute: Memorial Sloan Kettering Cancer Center

summary: Although allogeneic hematopoietic cell transplantation (allo-HCT) is curative for high-risk pediatric acute myeloid leukemia (AML), disease relapse remains the primary cause of post-transplant mortality. To identify pressures imposed by allo-HCT on AML cells that escape the graft-versus-leukemia effect, we evaluated immune signatures in bone marrow samples from four pediatric patients using a multimodal single-cell approach. Downregulation of MHC class II (MHC-II) expression observed at post-transplant relapse was most profound in progenitor-like blasts and was accompanied by correlative changes in transcriptional regulation. Dysfunction of activated NK cells and CD8+ T cell subsets at the time of relapse was evidenced by the loss of IFN-γ response, TNF-a signaling via NF-kB, and IL-2/STAT5 signaling. Clonotype analysis of post-transplant relapse samples revealed expansion of dysfunctional T cells and enrichment of T regulatory and T helper cells. Using novel computational methods, our results illustrate a diverse immune-related transcriptional signature in post-transplantation relapses not previously reported in pediatric AML.

overall_design: scRNA/TCR sequencing with feature barcoding

first: Nicholas

last: Ceglia

first: Jean-Benoît

last: Le Luduec

first: Andrew

last: McPherson

first: Barbara

last: Spitzer

first: Viktoria

last: Bojilova

first: Mohammad

last: Panjwani

first: Mikhail

last: Roshal

first: Sohrab

last: Shah

first: Omar

last: Abdel-Wahab

first: Benjamin

last: Greenbaum

first: Katharine

middle: C

last: Hsu


title: SETD2 loss in renal epithelial cells drives epithelial to mesenchymal transition in a TGFβ-independent manner [ATAC-Seq]

first: Keith

last: Robertson

overall_design: Assay for transposase-accessible chromatin DNA-sequencing (ATAC-seq) in SETD2 WT, KO and rescue cells. Each sample is run in duplicates.

first: Tianchu

last: Wang

first: Ryan

last: Hlady

first: Liguo

first: Jeong-Heon

last: Lee


title: Transcriptional profiling of canine osteosarcoma identifies of prognostic gene expression signatures with translational value for humans.

status: Public on Aug 01 2023

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

summary: Osteosarcoma is a rare maligancy seen in pediatric human patients but frequently seen in canine patients. Because of the increased frequecy of osteosarcoma in canines it is becoming  recognized as an informative model for human osteosarcoma. Therefore in a better effort to understand the moclular features common to both human and canine osteosracoma a transcriptional mRNA seq dataset of 186 canine osteosarcoma primary tumors

overall_design: Primary tumor samples were collected from 186 primary canine osteosarcoma tumors and subsquently sent for transcriptionally profiled using next generation sequencing.

first: Amy

last: LeBlanc

first: Christina

last: Mazcko

first: Josh

last: Mannheimer


title: Multi-comparative Bioinformatic Detection of MEOX2 De Novo Motif Sites And Distal Intergenic Sequences By ChIP-Seq, Reveals MEOX2-Dependent Modulation of EGFR-Gene Sequences In A Lung Cancer Preclinical Model

status: Public on Jun 15 2023

city: Tlalnepantla

first: Armas

middle: López

last: Leonel

state: Estado de México

address: Av. de los reyes

department: UBIMED

country: Mexico

institute: Universidad Nacional Autónoma de México

summary:
Mesenchyme Homebox-2 (MEOX2) transcription factor and its role in lung malignant diseases. It is mentioned that MEOX2 has recently been proposed as a genetically amplified and overexpressed lung tumor biomarker that promotes cellular proliferation, tumor growth, pre- and clinical progression, and oncological therapy resistance.
The study used a large-scale epigenome occupancy strategy to identify novel MEOX2-related cellular pathways. It was also discovered that MEOX2 has a significant occupation on distal intergenic sequences, De Novo Moitf Sites as well as on EGFR-genetic sequences, and positively regulates EGFR-gene expression in human lung cancer cells and preclinical tumor growth.
The study concluded that overexpressed MEOX2 is negatively clinically correlated with poorer progression-free survival in lung cancer patients with early clinical stages, with or without EGFR-TKIs based therapy.

overall_design:
RNA-Seq
Pineda Villegas and Armas López contributed equally to this work.

first: P

last: Pineda Villegas

first: L

last: Armas López

first: M

last: García Jiménez

first: O

last: Trejo Villegas

first: A

middle: I

last: Peralta Arrieta

first: Q

last: Ortíz

last: Mendoza

first: C

last: González

first: J

last: Gaytan

first: H

last: Rosas Vargas

first: R

last: Rosell

last: Arrieta

first: S

last: Turcan

last: Zúñiga

first: I

last: Heijink

first: F

last: Ávila Moreno


title: Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells [ChIP-Seq]

status: Public on Jun 01 2023

first: Julian

last: Pulecio

department: Developmental Biology

summary: It remains unclear how ESCs rapidly establish enhancer regulatory elements to activate lineage-specific genes at the earliest differentiation stages. Previous studies suggest that some tissue-specific enhancers are pre-marked in ESCs with permissive features that support their competence to induce gene expression in response to the binding of lineage transcription factors (TFs). However, the absence of functional assays to identify chromatin regions with the competence to activate gene expression upon TF binding has impeded to better define any pre-marking features and their role on the transcriptional competence of the chromatin. To address this, we leveraged a CRISPR-activation(a) system to systematically interrogate the presence of chromatin regions able to induce the expression of 5 lineage-specific genes that are inactive in human ESCs (hESCs). Multiple CRISPRa screens discovered 42 regions, which we termed Competent Chromatin Regions (CCRs), that can induce the expression of the 5 lineage genes upon CRISPRa targeting. ChIP seq analyses showed that CCRs do not represent primed or active enhancers, since they are not enriched in H3K4me1 or H3K27ac histone modifications. Instead, CCRs are characterized by the enriched occupancy of OCT4, NANOG and demethylation factors TET1 and QSER1, which prevent DNA hypermethylation. Although CCRs are exclusively found at the topologically associated domains shared with their related genes, we found they do not require an enrichment in pre-established chromatin contacts to exert their function. To assess the extent of our findings, we simulated the earliest stages of lineage differentiation by inducing the expression of the lineage TF FOXA2 in undifferentiated hESCs and we found it preferentially binds to the regions predicted as CCRs. Our results suggest that the factors enriched at CCRs facilitate the binding of lineage TFs and enable ESCs to promptly activate the expression of lineage genes. This study advances our understanding of pluripotency regulation in ESCs by identifying a novel type of regulatory regions that supports their developmental plasticity.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modification H3K27ac, and the transcription factors FOXA2 (upon CRISPR activation via targeting the promoter region of the FOXA2 gene),OCT4, NANOG and SOX2 in hESCs. All the experiments were performed with n=2 biological replicates.

first: Danwei

last: Huangfu

first: Hyein

last: Cho

first: Jielin

last: Yan


title: Gene expression profile at single cell level of the enteric nervous system (ENS) of 5 days post fertilization (dpf) zebrafish

status: Public on May 31 2023

city: Rotterdam

first: Naomi

last: Kakiailatu

address: Naomi

department: Clinical Genetics

country: Netherlands

institute: Erasmus MC

summary: We used single cell RNA sequencing (scRNA-seq) to characterize the ENS in the zebrafish intestine.

overall_design: Zebrafish intestines were manually isolated at 5dpf and dissociated into a single cell suspension. Live, single cells were sorted by Fluorescence-activated cell sorting (FACS) according to the presence or absence of DAPI signal. Sorted cells were processed and analyzed using 10X scRNAseq.

middle: E

last: Kuil

first: N

last: Windster

first: E

last: Bindels

last: Zink

first: G

last: van der Zee

middle: M

last: Hofstra

last: Shepherd

first: V

last: Melotte

last: Alves


title: A tumor multi-region query reveals novel DNA methylation targets linked to ccRCC poor outcome and metastasis

status: Public on May 02 2023

first: Keith

last: Robertson

summary: DNA methylation from multi-region normal kidney and ccRCC tumors

overall_design: 169 total samples (30 Normal, 138 Primary Tumor, 1 Metastatic) from 12 patients

first: Louis

middle: Y

last: El Khoury


title: Extracellular microRNA: Novel Biomarker and Potential Therapeutic Target in Trauma

status: Public on Mar 22 2023

city: Baltimore

first: Brittney

last: Williams

state: Maryland

address: 22 South Greene St, S11C00

department: Anesthesiology

institute: University of Maryland Baltimore

type: Non-coding RNA profiling by high throughput sequencing

summary: Based on our animal studies, we propose that circulating miRNAs are released from injured tissues after trauma. We use small RNA sequencing to characteriza plasma miRNA in trauma and healthy control patients and trauma and control mice

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: noncoding extracellular RNA was isolated from cell-free plasma and was analyzed by an Agilent 2100 Bioanalyzer with the Small RNA kit and used for small RNA sequencing library preparation. Libraries were sequenced on an Illumina NextSeq 500 and analyzed by Norgen Bioteck Corp. The raw sequence data were analyzed using the exceRpt small RNAseq pipeline (Genboree Bioinformatics).

first: Wei

last: Chao

first: Andrew

last: Suen

first: Sheng

last: Wang

first: Lin

last: Zou

first: Olivia

last: Conn

first: Laurence

last: Weschler

first: Fengqian

last: Chen

first: Kerri

last: Lopez


title: Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells

first: Julian

last: Pulecio

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

overall_design: Refer to individual Series


title: Genome-wide chromatin accessibility and gene expression profiling during flatfish metamorphosis

status: Public on Feb 16 2023

city: Vigo

first: Laura

middle: Guerrero

last: Peña

state: Pontevedra

address: Eduardo Cabello, 8

department: Aquaculture and Biotecnology

country: Spain

institute: CSIC


title: Pathogenic Mutation that Dislocates GATA2 Zinc Fingers Establishes a Hematopoiesis-Disrupting Signaling Network

status: Public on Feb 27 2023

city: Madison

first: Emery

middle: H

last: Bresnick

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

summary: Although certain human genetic variants are conspicuously loss-of-function, decoding the impact of many variants is challenging. Previously, we described a leukemia predisposition syndrome (GATA2-deficiency) patient with a germline GATA2 variant that inserts nine amino acids between the two zinc fingers (9aa-Ins). Here, we conducted mechanistic analyses using genomic technologies and a genetic rescue system with Gata2 enhancer-mutant hematopoietic progenitor cells to compare how GATA2 and 9aa-Ins function genome-wide. Despite nuclear localization, 9aa-Ins was severely defective in occupying and remodeling chromatin and regulating transcription. Variation of the inter-zinc finger spacer length revealed that insertions were more deleterious to activation than repression. GATA2-deficiency generated a lineage-diverting gene expression program and a hematopoiesis-disrupting signaling network in progenitors with reduced Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) and elevated Interleukin-6 (IL-6) signaling. As insufficient GM-CSF signaling causes pulmonary alveolar proteinosis and excessive IL-6 signaling promotes bone marrow failure, GATA2-deficiency patient phenotypes, these results provide insight into mechanisms underlying GATA2-linked pathologies.

overall_design: 100000 Hoxb8-immortalized wild type hematopoietic progenitors (hi−77+/+) infected with control (empty) retrovirus, Gata2 -77 enhancer deleted mutant progenitors (hi−77−/−) infected with empty retrovirus or GATA2- or 9aa-Ins-expressing retrovirus were FACS isolated for GFP+

first: Mabel

last: Jung

first: Peng

last: Liu

first: Sean

last: McIlwain


status: Public on Feb 22 2023

city: MADISON

first: Siqi

last: Shen

state: WI

address: 425 Henry Mall

institute: University of Wisconsin - Madison

summary: While certain human genetic variants are conspicuously loss-of-function, decoding the functional impact of many variants is challenging. Previously, we described a leukemia predisposition syndrome (GATA2-deficiency) patient with a germline GATA2 variant that inserts nine amino acids between the two zinc fingers (9aa-Ins). Here, we conducted mechanistic analyses using genomic technologies in Gata2 enhancer-mutant hematopoietic progenitor cells to reveal how the insertion impacts GATA2 function genome-wide. Despite being nuclear-localized, 9aa-Ins was severely defective, with activation more impaired than repression. Variation of the inter-zinc finger spacer length revealed that repression tolerated insertions that were detrimental to activation. GATA2 deficiency generated a hematopoiesis-disrupting signaling network in progenitor cells with reduced Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) signaling and elevated Interleukin-6 (IL-6) signaling. As insufficient GM-CSF signaling causes pulmonary alveolar proteinosis and excessive IL-6 signaling causes bone marrow failure, hallmark phenotypes of GATA2-deficiency patients, these results establish molecular mechanisms underlying GATA2-linked pathologies.

overall_design: 50000 Hoxb8-immortalized wild type hematopoietic progenitors (hi-77+/+) infected with control (empty) retrovirus, Gata2 -77 enhancer deleted mutant progenitors (hi-77-/-) infected with empty retrovirus or GATA2- or 9aa-Ins-expressing retrovirus were FACS isolated for GFP+

first: Sündüz

last: Keleş


title: Transcriptomic consequences of atfA/atfB gene deletions in Aspergillus nidulans

status: Public on Feb 15 2023

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary: The bZIP transcription factors (TFs) govern regulation of development, secondary metabolism and various stress responses in filamentous fungi. In this work, we carried out genome-wide expression studies employing Illumina RNAseq to understand the roles of the two bZIP transcription factors AtfA and AtfB in Aspergillus nidulans. Comparative analyses of transcriptomes of vegetatively grown cells (mycelia) and asexual spores (conidia) obtained from the surface cultures of control, DatfA, DatfB, DatfADatfB mutant strains with/without menadione sodium bisulfite (MSB) treatment were performed. Probable AtfA and AtfB dependent gene sets were determined by comparing transcriptomes of both single gene deletion mutants with the reference strain, and the double gene deletion mutant with the appropriate single gene deletion mutants. As AtfA is the primary bZip TF governing stress-response in A. nidulans, a significantly higher number was differentially expressed genes (DEGs) by DatfA than DatfB in both mycelial and conidial samples, and most of the AtfB dependent genes showed AtfA dependence, too. Moreover, a low number of genes showing AtfB dependence only can be a consequence of that DatfA leading to downregulation of atfB expression. The abundance of atfA and atfB mRNAs and, concurring with it the number of AtfA and AtfB affected genes were much higher in conidial than in mycelial samples. The number of AtfB- (but not of AtfA-) affected DEGs decreased markedly in the presence of MSB, which was accompanied with decreased mRNA levels of atfB in MSB treated mycelial (reference strain) and conidial (DatfA mutant) samples. The overlap between the AtfA dependent DEGs in the case of MSB treated and untreated mycelial samples was low demonstrating that distinct genes can be under AtfA control in different cell types. The AtfA-dependent DEGs were enriched with carbohydrate metabolism genes. Among them, AtfA-dependence of glycolytic genes in the case of the conidial samples was the most notable. Levels of transcripts of certain secondary metabolitic gene clusters, like the Emericellamide cluster also showed AtfA-dependent regulation. The AtfA affected DEGs under all experimental conditions include those encoding catalase and histidine-containing phosphotransfer proteins. The 23 DEGs that solely dependent on AtfB considering all transcriptomics data sets, included a putative a -glucosidase (agdB), a putative a-amylase, calA involved in early conidial germination and an alternative oxidase. In summary, there is a complex interaction between the two b-Zip TFs in which the main function of AtfB is supporting the regulatory role of the primary b-Zip TF AtfA in A. nidulans.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mycelia and conidia of Aspergillus nidulans reference strain, DatfA mutant, DatfB mutant, and DatfA-DatfB double mutant under menadione (MSB) treated and untreated conditions with three biological replicates.

first: Beatrix

last: Kocsis

first: Mi-Kyung

last: Lee

first: Jae-Hyuk

last: Yu

first: István

last: Pócsi

first: Éva

last: Leiter

first: Tamás


title: Chromatin accessibility at four key stages of turbot development, from phylotypic to post-metamorphic stages [ATAC-seq]

summary: Metamorphosis is a widely studied post-embryonic process in which many tissues undergo dramatic modifications to adapt to the new adult lifestyle. Flatfish represent a good example of metamorphosis in teleosts. During flatfish metamorphosis, organ regression and neo-formation occur, being the most remarkable change the migration of one of the eyes to the other side of the body. In order to create a useful and reliable tool to advance the molecular study of metamorphosis in flatfish, we generated a chromatin accessible atlas as well as gene expression profile during four developmental stages ranging from a phylotypic stage to a post-metamorphic stage. We identified 29,019 accessible regions of chromatin and 3,253 differentially expressed genes. We found stage-specific regulatory regions and gene expression profile, supporting the quality of the results. Our work provides strongly reproducible data for further studies to elucidate the regulatory elements that ensure successful metamorphosis.

overall_design: ATACseq experiments in different developmental stages in Scophthalmus maximus

last: Guerrero-Peña

first: Paula

last: Suarez-Bregua

first: Alejandro

last: Gil-Gálvez

first: Silvia

last: Naranjo

first: Luis

last: Méndez-Martínez

first: Ricardo

last: Tur

first: Pablo

last: García-Fernández

first: Juan

last: Tena

first: Josep

last: Rotllant


title: RNA stability controlled by m6A methylation provides X to autosome compensation in mammals

status: Public on Feb 14 2023

city: Würzburg

first: Julian

last: Konig

address: Am Hubland

institute: Würzburg University


title: RNA sequencing of wild-type liver at stage 54, stage 61, stage 66 and T3 treated liver.

status: Public on Jan 31 2023

city: Bethesda

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Conclusions: Our study represents the first detailed analysis of liver transcriptomes in wild-type tadpoles, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.

overall_design: Examination of 3 biological replicate from the different Xenopus tropicalis tadpoles.

first: Yuta

last: Tanizaki

first: Hongen

last: Zhang

first: Yun-Bo

last: Shi


title: Transcriptomic analysis of WT versus Ikzf4-/- CD4+ T cells cultured in Th2-polarizing conditions

status: Public on Feb 01 2023

city: Columbus

first: Ken

last: Oestreich

state: Ohio

address: 460 W 12th Avenue, 740 Biomedical Research Tower

institute: The Ohio State University

summary: The Ikaros zinc finger transcription factor Eos has been commonly implicated in regulatory T cells to promote their immunosuppressive functions. Paradoxically, a new role is emerging for Eos in promoting pro-inflammatory responses of conventional CD4+ T cells in the dysregulated setting of autoimmunity. Even so, the precise role of Eos in regulating the differentiation and function of healthy effector CD4+ T cell subsets remains unclear. Here, we find that Eos is a positive regulator of CD4+ T helper 2 (TH2) cells—effector T cells implicated in the induction of allergic asthma. Using murine in vitro TH2 cells and an in vivo house dust mite asthma model, we found that Eos-deficient T cells had reduced expression of key TH2 transcription factors, effector cytokines, and differentiation receptors. Mechanistically, among various TH2-polarizing pathways, the IL-2/STAT5 axis and its downstream TH2 gene targets emerged as one of the most significantly downregulated networks in Eos deficiency. Using in vitro TH2 cells and overexpression of Eos zinc-finger-domain mutants, we discovered that Eos forms a novel complex with and supports the tyrosine-phosphorylated signaling activity of STAT5. Overall, these data define a novel regulatory mechanism whereby Eos promotes IL-2/STAT5 activity to facilitate TH2 differentiation.

overall_design: Naïve WT or Ikzf4-/- CD4+ T cells were cultured in complete IMDM under Th2 (10 ug/mL anti-Ifng, 10 ng/mL IL-4) polarizing conditions on plate-bound anti-CD3 (5ug/mL) and anti-CD28 (2ug/mL) for 3 days. Total RNA was isolated and provided to Azenta Life Sciences for library preparation and downstream analysis.

first: Jasmine

middle: A

last: Tuazon


title: Whole-transcriptome quantitative analysis of WT versus Ikzf3-/- CD4+ T cells cultured in Th1-polarizing or Tfh-polarizing conditions

summary: Effective immunity to viruses such as influenza and SARS-CoV-2 requires the generation of CD4+ T cell subsets that coordinate complementary aspects of the immune response. These include T follicular helper (TFH) and T helper 1 (TH1) cells, which promote humoral and cell-mediated helper responses, respectively. A third population, CD4+ cytotoxic T lymphocytes (CD4-CTLs) facilitates clearance of infection via mechanisms normally associated with CD8+ T cells, including perforin-mediated destruction of infected cells. Here, we identify the transcription factor Aiolos as a reciprocal regulator of TFH and CD4-CTL responses. We demonstrate that Aiolos deficiency compromises TFH differentiation and antibody production during influenza infection. Conversely, we find that CD4+ T cells acquire a cytotoxic-like program in the absence of Aiolos, including increased expression of the CTL-associated transcription factors Eomes and Blimp-1. We further show that while Aiolos positively regulates the TFH transcriptional regulators Zfp831, Tcf-1 and Bcl-6, it also directly represses expression of IL-2Ra and IL-2/STAT5-driven expression of the cytotoxic gene program. Thus, our findings identify Aiolos as a pivotal regulator of TFH and CD4-CTL differentiation and highlight its potential as a therapeutic target for the manipulation of CD4+ T cell humoral and cytotoxic responses.

overall_design: Naïve WT or Ikzf3-/- CD4+ T cells were cultured in complete IMDM ((IMDM [Life Technologies], 10% FBS [26140079, Life Technologies], 1% Penicillin-Streptomycin [Life Technologies], and 50uM 2-mercapto-ethanol [Sigma-Aldrich]) under Th1 (5ug/mL anti-IL-4, 5ng/mL IL-12, 50U/mL IL-2) or Tfh (5ug/mL anti-IL-4, 100ng/mL IL-6) polarizing conditions on plate-bound anti-CD3 (5ug/mL) and anti-CD28 (2ug/mL) for 3 days (72 hrs). Total RNA was isolated and provided to Azenta Life Sciences for library preparation and downstream analysis.

first: Kaitlin

last: Read

first: Devin

last: Jones


title: ATAC-seq analysis of WT versus Ikzf3-/- CD4+ T cells cultured in Th1-polarizing or Tfh-polarizing conditions

overall_design: Naïve WT or Ikzf3-/- CD4+ T cells were cultured in complete IMDM ((IMDM [Life Technologies], 10% FBS [26140079, Life Technologies], 1% Penicillin-Streptomycin [Life Technologies], and 50uM 2-mercapto-ethanol [Sigma-Aldrich]) under Th1 (5ug/mL anti-IL-4, 5ng/mL IL-12, 50U/mL IL-2) or Tfh (5ug/mL anti-IL-4, 100ng/mL IL-6) polarizing conditions on plate-bound anti-CD3 (5ug/mL) and anti-CD28 (2ug/mL) for 3 days. For each sample, 5x10^4 cells at >95% viability were processed using the Illumina Nextera DNA Library Preparation Kit, according to the manufacturer’s instructions.


title: Depressed protein synthesis and anabolic signaling potentiate ACL tear resultant quadriceps atrophy I

status: Public on Jan 11 2023

city: Lexington

first: Alexander

middle: Romano

last: Keeble

state: KY

address: 900 S Limestone st

institute: University of Kentucky

summary: Background: An anterior cruciate ligament tear (ACLT) leads to protracted quadriceps weakness and atrophy. Protein turnover largely dictates muscle size and is highly responsive to injury and loading. Regulation of the molecular protein synthetic machinery within the quadriceps following ACLT has largely been unexplored, limiting the development of targeted therapies. Purpose: To define the effect of ACLT on 1) activation of protein synthetic and catabolic signaling within quadriceps biopsies from human participants, and 2) the time course of alterations to protein synthesis and its molecular regulation in a mouse model of ACL injury. Study Design: Descriptive laboratory studyMethods: Muscle biopsy specimens were obtained from the ACL-injured and non-injured vastus lateralis of young adults following an overnight fast (n=21, mean ± SD: 19 ± 5 years). Mice had their limbs assigned to ACLT or control, and whole quadriceps were collected 6 hours, 1, 3, or 7 days post-injury with puromycin (0.04µmol/g) injected 30 minutes before tissue collection. Muscle fiber size and expression and phosphorylation of protein anabolic signaling proteins and E3 ubiquitin ligases were assessed at the protein and transcript level. Relative protein synthesis was measured by puromycin incorporation in mice.Results: Human quadriceps showed reduced phosphorylation of ribosomal protein S6 (-41%) in the ACL-injured limb (p<0.05), in addition to elevated phosphorylation of eukaryotic initiation factor 2α (+98%, p<0.05), indicative of depressed protein anabolic signaling in the injured limb. No differences in E3 ubiquitin ligase expression were noted (p>0.05). Protein synthesis was lower at 1 and 3 days post-ACLT in mice (p<0.05 vs. control limb). Conclusions: 1) Global protein synthesis and anabolic signaling deficits occur in the quadriceps in response to ACL injury, without notable changes in measured markers of muscle protein catabolism. 2) Importantly, these deficits occur prior to the onset of significant atrophy, underscoring the need for early intervention.  Clinical Relevance: These findings suggest blunted protein anabolism as opposed to increased catabolism likely mediates the quadriceps atrophy that occurs following ACL injury. Thus, future interventions should aim to restore muscle protein anabolism rapidly following the initial injury.

overall_design: Comparative gene  expression was assessed in human quadricep tissue in non-ACL injured limbs and ACL-injured limbs pre reconstruction surgery

middle: R

first: Camille

last: Brightwell

first: Christine

last: Latham

first: Nicholas

middle: T

last: Thomas

first: C

last: Mobley

first: Kevin

last: Murach

first: Darren

last: Johnson

first: Brian

last: Noehren

first: Christopher

middle: S

last: Fry


title: WT versus Ikzf3-/- CD4+ T cells cultured in Th1-polarizing or Tfh-polarizing conditions


title: New approaches to the production of certified varieties of apple trees using NGS diagnostics of pathogens

status: Public on Dec 09 2022

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

institute: Hungarian University of Agriculture and Life Sciences

summary: Implementation and evaluation of tests (PCR, ELISA, NGS) for the presence of viruses, viroids and phytoplasma in propagation materials of apple. Research and application of new sanitation techniques using promising antiviral substances, or cryo-knife. Confirmation of health status of sanitated cultivars including use of modern diagnostic methods such as high-throughput sequencing (NGS).

overall_design: 16 sRNA libraries were prepared and used to survey viromes of apple trees - no replicate samples were prepared

first: Igor

last: Koloňuk

last: Várallyay

first: Jaroslava

last: Přibylová

first: Zsuzsanna

middle: N

last: Galbacs

first: Almash

last: Jahan

first: Josef

last: Špak

first: Ondřej

last: Lenz

first: Jiří

last: Sedlák


title: Genome-wide methylation studies in nasal epithelial cells using a custom Asthma&Allergy DNAm array.

status: Public on Dec 23 2022

city: Chicago

first: Emma

last: Thompson

state: IL

address: 920 E 58th St, CLSC Rm 501

department: Human Genetics

institute: The University of Chicago

summary: We performed an epigenome-wide association study (EWAS) of allergic sensitization using nasal epithelial cell DNA from 280 subjects.

overall_design: Nasal epithelial cell methylation patterns were assessed in 280 children at age 11 with allergic sensitization as a quantitative trait.

first: Carole

last: Ober

first: William

last: Wentworth-Sheilds


title: The gene expression signature of electrical stimulation in the human brain

status: Public on Feb 13 2023

city: Iowa City

first: Muhammad

last: Elsadany

state: IA

address: 25 S Grand Ave

department: Psychiatry

institute: University of Iowa

summary: Direct electrical stimulation (eSTIM) is widely used clinically, from neurosurgical mapping to therapeutic interventions for neurological and neuropsychiatric disorders (1-10). Despite over a century of application, its molecular and cellular underpinnings remain unknown. Here, using state-of-the-art single-nuclei multiomic profiling, we map changes in cell-type-specific gene expression and chromatin accessibility in vivo in the human cortex following eSTIM of neurosurgery patients. eSTIM impacts a network of cells that extends beyond excitatory neurons to include inhibitory neurons, astrocytes, oligodendrocytes and microglia. We observed an upregulation of canonical immediate-early genes (IEGs: FOS, NPAS4, EGR4) in excitatory and inhibitory neurons and induction of cytokine-related genes CCL3 and CCL4 in microglia. The cross-species conservation of this gene signature, together with our examination of a cohort of both epilepsy and cancer patients, underscores the fundamental role of these changes in stimulation-driven plasticity while controlling for disease and environmental confounds. Our study of changes in chromatin accessibility reveals a common code that involves a cell-type specific signature of transcription factor binding motifs for members of the EGR family. By addressing these previously unexplored questions about activity-induced gene expression in vivo in the human brain, our findings challenge the long-standing neuron-centric view of eSTIM, highlighting the broader role of non-neuronal cells, including microglia, in mediating the impact of brain stimulation.

overall_design: We performed bulk RNA-Seq on samples obtained from human subjects (n=4 pairs) and mouse cortex (n=4 pairs) before and after electrical stimulation. The human bulk RNA-seq was performed in two paradigms: stimulated (n=4 pairs) and unstimulated (n=4 pairs). Additionally, we performed sn-multi-omics sequencing on samples obtained from human subjects (n=6 pairs) before and after electrical stimulation.

first: Snehajyoti

last: Chatterjee

first: Yann

last: Vanrobaeys

first: Annie

last: Gleason

middle: J

last: Park

first: Shane

last: Heiney

first: Ariane

last: Rhone

first: Kirill

middle: V

last: Nourski

first: Budhaditya

last: Basu

first: Utsav

last: Mukherjee

first: Lucy

last: Langmack

middle: K

last: Kovach

last: Kocsis

first: Yukiko

last: Kikuchi

first: Yaneri

last: Ayala

first: Mark

last: Bowren

first: Marco

last: Hefti

first: Ethan

last: Bahl

first: Kailin

last: Yang

first: Jeremy

middle: D

last: Greenlee

first: Hiroto

last: Kawasaki

first: Hiroyuki

last: Oya

first: Matthew

last: Howard III

last: Petkov

first: Thomas

last: Nickl-Jockschat

first: Li-Chun

last: Lin

first: Jacob

last: Michaelson

first: Ted

last: Abel


title: Transcriptional Differences Between COVID-19 and Sepsis

status: Public on Nov 29 2022

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: Although some studies reported the comprehensive mRNA expression analysis of coronavirus disease 2019 (COVID-19) using blood samples to understand its pathogenesis, the characteristics of RNA expression in COVID-19 and sepsis have not been compared. We compared the transcriptome expression of whole blood samples from patients with COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and patients with sepsis caused by other bacteria who entered the intensive care unit to clarify the COVID-19-specific RNA expression and understand its pathogenesis. Transcriptomes related to mitochondria were upregulated in COVID-19, whereas those related to neutrophils were upregulated in sepsis. However, the transcriptomes related to neutrophils were upregulated in both COVID-19 and sepsis compared to in healthy controls, whereas the mitochondrial transcriptomes were upregulated in COVID-19 and downregulated in sepsis compared to in healthy controls. Moreover, sepsis showed sub-optimal intrinsic apoptotic features compared with COVID-19. The transcriptome expression of COVID-19 has been examined in vitro but has not been widely validated using human specimens. This study improves the understanding of the pathogenesis of COVID-19 and can contribute to the development of treatments.

overall_design: Comparing the mRNA levels of whole blood samples from COVID-19 patients with septic patients clarified a pathology that is specific to COVID-19.

first: Hisatake

last: Matsumoto


title: Progenitor-derived endothelin controls dermal sheath contraction for hair follicle regression

status: Public on Oct 31 2022

city: New York

first: Michael

last: Rendl

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

summary: Progenitor cell death and dermal papilla relocation during the regression phase of the hair growth cycle are essential for stem cell activation and follicle regeneration. This drastic follicle remodeling is coordinated by dermal sheath (DS) smooth muscle contraction, but how DS-generated forces are regulated is unknown. Here, we identify endothelin signaling - a potent vasoconstriction-regulating pathway - as the key activating mechanism of DS contraction. Pharmacological blocking or genetic ablation of both endothelin receptors, ETA and ETB, impedes DS contraction and halts follicle regression. Progenitors at the epithelial strand bottleneck are the main source of endothelin ligand ET-1, which is required for follicle regression. ET signaling in DS cells and downstream contraction is dynamically regulated by cytoplasmic Ca2+ levels via cell membrane and sarcoplasmic reticulum calcium channels. Together, these findings illuminate an epithelial-mesenchymal-interaction paradigm in which progenitors - before undergoing programmed cell death - control the contraction of the surrounding sheath smooth muscle to orchestrate homeostatic tissue regression and follicle reorganization.

overall_design: Bulk RNA seq was performed on FACS sorted Dermal sheath (DS), Dermal Papilla (DP) and Dermal fibroblasts (2 biological replicates x 3 populations)  from P16 (Early catagen) mice back skins using Illumina HiSeq 2000 platform at the Genome Technology Center at NYU.

first: Pieter

last: Martino

first: Raghava

last: Sunkara

first: Nicholas

last: Heitman

first: Martina

last: Rangl

first: Alexia

last: Brown

first: Nivedita

last: Saxena

first: Laura

last: Grisanti

first: Donald

last: Kohan

first: Masashi

last: Yanagisawa


title: RNA stability controlled by m6A methylation provides X to autosome compensation in mammals [miCLIP2]

first: Julian

last: Konig

summary: In therian mammals, X-chromosomal genes are expressed only from a single active X chromosome, both in males (XY) as well as females (XX). To compensate for this reduction in dosage compared to the evolutionary ancestral state on two autosomes, it has been proposed that genes from the active X chromosome exhibit dosage compensation (“Ohno’s hypothesis”). However, the existence and mechanism of X-to-autosome dosage compensation are still under debate. Here, we show that dosage compensation is achieved via differential N6-methyladenosine (m6A) RNA modification. X-chromosomal transcripts are reduced in m6A modifications and more stable compared to the autosomal counterparts. Acute depletion of m6A using a small molecule inhibitor differentially affects autosomal and X-chromosomal transcripts across sexes, cell types, tissues and species, resulting in perturbed dosage compensation. We propose that higher stability of X-chromosomal transcripts is directed by lower levels of m6A, indicating that mammalian dosage compensation occurs via epitranscriptomic RNA regulation.

overall_design: miCLIP2 experiments were performed on polyA+ RNA from female mESC, with 4 biological replicates.

first: Cornelia

last: Rücklé

first: Nadine

last: Körtel

first: Felicia

last: Basilicata

first: Anke

last: Busch

first: Kathi

last: Zarnack

first: Claudia

last: Valsecchi

last: König


title: RNAseq of 4T1 cells expressing exogenous LINC01133

status: Public on Oct 03 2022

city: Boston

first: Antoine

middle: Elias

last: Karnoub

state: MA

address: 3 Blackfan Circle

department: Pathology

institute: Beth Israel Deaconess Medical Center and Harvard Medical School

summary:
The PI3K pathway represents the most hyperactivated oncogenic pathway in triple-negative breast cancer (TNBC), a highly aggressive tumor subtype encompassing ~15% of breast cancers with no targeted therapeutics. Despite critical contributions of its signaling arms to disease pathogenesis, PI3K pathway inhibitors have not achieved expected clinical responses in TNBC owing largely to still-incomplete understanding of the compensatory cascades that operate downstream of PI3K. Here, we investigated the contributions of long non-coding RNAs (lncRNAs) to PI3K activities in clinical and experimental TNBC, and discovered a prominent role for LINC01133 as a PI3K-AKT signaling effector. We found that LINC01133 exerted pro-tumorigenic roles in TNBC, and that it governed a previously undescribed mTORC2-dependent pathway that activated AKT in a PI3K-independent manner. Mechanistically, we show that LINC01133 induced the expression of the mTORC2 component PROTOR1/PRR5 by competitively coupling away its negative mRNA regulator, the heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNPA2B1). PROTOR1/PRR5 in turn was sufficient and necessary for LINC01133-triggered functions, casting previously unappreciated roles for this Rictor-binding protein in cellular signaling and growth. Notably, LINC01133 antagonism undermined cellular growth and we show that the LINC01133-PROTOR1/PRR5 pathway tightly associated with TNBC poor patient survival. Altogether, our findings uncovered a lncRNA-driven signaling shunt that acts as a critical determinant of malignancy downstream of the PI3K pathway and as a potential RNA-based theranostic in clinical TNBC management.
We performed comparative gene expression profiling analyses using RNA-seq of triplicates of control 4T1 cells (harboring empty plasmid control) and 4T1 cell trioplicates expressing exogenous LINC01133.

overall_design: The samples in this data set include total RNAs derived from three 4T1 cell replicates harboring empty pLVX vector (WT or control) and three 4T1 cell replicates harboring pLVX-LINC01133 expression plasmid.

first: Zhenbo

last: Tu


title: Radiation combined with KRAS-MEK inhibitors enhances anticancer immunity in KRAS-mutated tumor models

status: Public on Oct 01 2022

city: jinan

first: yawen

last: zheng

address: jiefang road,No105

institute: jinan central hospital

overall_design: Refer to individual Series


title: Radiation combined with KRAS-MEK inhibitors enhances anticancer immunity in KRAS-mutated tumor models [CT26 RNA-seq]

summary: KRAS mutation is a common driver in solid tumors, and KRAS-mutated tumors are relatively resistant to radiotherapy. Therefore, we investigated the combined effect of radiation and KRAS-MEK inhibitors (AMG510 and trametinib) in KRAS-mutated tumors.

overall_design: The expression of programmed death-ligand 1 (PD-L1), major histocompatibility complex (MHC) Class I molecules, and cytokines in KRAS-mutated cell lines was assessed using flow cytometry, western blot analysis, quantitative PCR, and enzyme-linked immunosorbent assay. In vivo, tumor growth, T cell infiltration, and gene sequencing analyses were conducted in two murine KRAS-mutated models.

first: Yawen

last: Zheng

first: Yanan

last: Liu

first: Fang

last: Zhang

first: Ligang

last: Xing


title: Radiation combined with KRAS-MEK inhibitors enhances anticancer immunity in KRAS-mutated tumor models [LLC RNA-seq]


title: RNA-sequencing of control (CTL), MLKL -/- (MLKL) and RIPK3-/- (RIPK3) 3T3-L1 preadipocytes (J0) or differentiated (J7) cells.

status: Public on Oct 10 2022

city: Paris

first: Jeremie

last: Gautheron

address: 27 rue chaligny

country: France

institute: Sorbonne Universite - Centre de Recherche Saint-Antoine

summary:
Purpose: Necroptosis as been implicated in various deseases. The goal of this study is to invastigate the impact of RIPK3 and MLKL in the lipid metabolism of adipocytes.
Methods: 3T3-L1 preadipocytes invalidated or not for RIPK3 or MLKL were exposed differenciated into mature adipocytes and the mRNA profiles of wild type (WT),  RIPK3-/- knockout (RIPK3-KO) or MLKL-/- knockout 3T3-L1 cells control (J0) or differenciated into mature adipocytes (J7) were generated by deep sequencing, in 3 copies, using Illumina NOVAseq 6000 plateform. Differential expression analysis between two conditions/groups (five biological replicates per condition) was performed using DESeq2 R package. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. qRT–PCR validation was performed using SYBR Green assays
Results: The DEGs were clustered using a hierarchical clustering algorithm, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis unveiled a clear reduction in the expression of genes involved in the early or late stages of adipogenesis in MLKL-KO cells
Conclusions: Taken together, these data suggest that Mlkl but not Ripk3 deficiency impaired adipogenesis of 3T3-L1 cells by reducing the expression of pro-adipogenic factors and genes involved in fatty acid metabolism.

overall_design: RNAseqencing of control (CTL), MLKL-/- (MLKL) and RIPK3-/- (RIPK3) 3T3-L1 undifferenciated (J0) or fully differenciated (J7) cells.

first: Julie

last: Magusto

first: Carine

last: Beaupere


title: Fatty acid binding protein 5 inhibition attenuates pronociceptive cytokine/chemokine expression and suppresses osteoarthritis pain: A comparative human and rat study

status: Public on Dec 31 2022

city: Stony Brook

first: David

last: Carlson

address: 100 Nicolls Rd

institute: Stony Brook University

summary: Abstract   Objective: Osteoarthritis (OA) is accompanied by severe and debilitating pain that current analgesics are unable to fully alleviate. A multitude of signaling molecules, pathways, and cells have been identified as regulators of OA pain. Fatty acid binding protein 5 (FABP5) regulates pain in other disease states and we hypothesized that it is involved in the regulation of OA pain.   Design: This was a combined clinical and pre-clinical study. Human synovial and osteochondral tissues collected during total knee arthroplasty were subjected to immunohistochemical analyses to identify the spatial expression patterns of FAB5, COX1, COX2, and macrophages. In addition, synovial specimens were cultured the presence and absence of SBFI-103, a selective FABP5 inhibitor, and cytokines and chemokines levels were measured. The rat monoiodoacetate (MIA) model of OA was then enlisted to evaluate the efficacy of SBFI-103 in alleviating OA pain. Finally, RNAseq was performed to identify alterations in synovial gene expression in vehicle and SBFI-103 treated MIA rats.  Results: FABP5 expression was present in clinical OA tissues, with higher expression seen higher grade OA and no apparent differences between genders. Furthermore, FABP5 staining colocalized with CD14+ cells, indicating a macrophage origin of FABP5. Synovial specimens secreted CCL2, IL6, IL8, CXCL1, MIF, and Serpin E1 in vitro and treatment with SBFI-103 attenuated CCL2, IL6, IL8, and CXCL1, but not MIF and Serpin E1. Twenty-eight days after MIA injection, rats exhibited histological joint degradation and significant incapacitance. Ketoprofen treatment partially reduced incapacitance and naproxen had no effect; however, SBFI-103 showed a dose dependent alleviation of incapacitance that was independent of cannabinoid or PPARα receptor activity. RNAseq analyses identified differential expression of >6,000 transcripts compared to contralateral controls in vehicle treated rats and only 513 after SBFI-103 treatment. Notably, CCL2, CCL7, CCL9, and CXCL1were upregulated in vehicle treated rats, but not those treated with SBFI-103, and this was confirmed with qPCR.  Conclusions: Our results show that FABP5 is upregulated in clinical and preclinical OA tissues and that its inhibition lowers pronociceptive signaling and reduces OA pain, indicating that FABP5 inhibitors may constitute a novel class of analgesics to treat OA.

overall_design: Comparative gene expression analysis of RNA-Seq data from rat synovial tissue, contrasting samples with monoiodoacetate (MIA) injections compared with control samples injected with saline solution

first: Chris

last: Gordon

first: James

last: Trainor

first: Rohan

last: Shah

first: Keith

last: Studholme

first: Alex

last: Gelman

first: Faniya

last: Doswell

first: Faisal

last: Sadar

first: Allessio

last: Giovannetti

first: Josh

last: Gershenson

first: Ayesha

last: Khan

last: Nicholson

first: ZeYu

last: Huang

first: Michael

last: Spurgat

first: Shao-Jun

last: Tang

first: Hehe

last: Wang

first: Iwao

last: Ojima

last: Komatsu

first: Martin

last: Kaczocha


title: Amyloid beta 42 alters cardiac metabolism and impairs cardiac function in obesity

status: Public on Sep 22 2022

city: Melbourne

first: Mark

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

institute: Burnet Institute

summary: There are epidemiological associations between obesity and type 2 diabetes, cardiovascular disease and Alzheimer’s disease. While some common aetiological mechanisms are known, the role of amyloid beta 42 (Ab42) in these diverse chronic diseases is obscure. Here we show that adipose tissue releases Ab42, which is increased from adipose tissue of obese mice and is associated with higher plasma Ab42. Increasing circulating Ab42 levels in mice had no effect on systemic glucose homeostasis but had obesity-like effects on the heart, including reduced cardiac glucose clearance and impaired cardiac function. These effects on cardiac function were not observed when circulating Ab40 levels were increased. Administration of an Ab neutralising antibody prevented obesity-induced cardiac dysfunction and hypertrophy. Furthermore, Ab neutralising antibody administration in established obesity prevented further deterioration of cardiac function. Multi-contrast transcriptomic analyses revealed that Ab42 impacted pathways of mitochondrial metabolism and exposure of cardiomyocytes to Ab42 inhibited mitochondrial function. These data reveal a role for systemic Ab42 in the development of cardiac disease in obesity and suggest that therapeutics designed for Alzheimer’s disease could be effective in combating obesity-induced heart failure.

overall_design: This series consists of two components that were conducted separately. In part 1 of this study, C57BL6 mice were treated with Aβ42, an amyloid beta peptide of 42 amino acids, or a scrambled Aβ42 sequence at a dose of 1mg/day i.p. In the second part of the study, C57BL6 mice given Aβ42 were additionally treated with a Aβ42 neutralising antibody called 3D6 or a control antibody.

first: Liam

middle: G

last: Hall

first: Juliane

last: Czeczor

first: Timothy

last: Connor

first: Javier

last: Botella

first: Kirstie

last: De Jong

middle: C

last: Renton

first: Amanda

last: Genders

first: Kylie

last: Venardos

first: Sheree

last: Martin

first: Simon

last: Bond

first: Kathryn

last: Aston-Mourney

first: Sophie

last: Hussey

first: Kirsten

middle: F

last: Howlett

last: Hargreaves

first: Roberto

last: Cappai

last: Campbell

first: Greg

last: Collier

first: Ken

last: Walder

first: Matthew

last: McKenzie

first: Sean

middle: L

last: McGee


title: Distinct microglia subsets are associated with α-synucleinopathy in multiple system atrophy

status: Public on Sep 06 2022

city: Fukuoka

first: Hiroo

last: Yamaguchi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Neurology

institute: Neurological Institute, Graduate School of Medical Sciences,  Kyushu University

summary: We developed a novel mice model of multiple system atrophy (MSA)-cerebellar type (MSA-C) by over-expression of human mutant α-synuclein (α-syn) in oligodendrocyte using Tet-off system. We identified distinct microglial subpopulations in a novel MSA-C model mice.

overall_design: mRNA profiles of  CD11b-positive microglia from the brains of Tg mice before MSA-C onset, Tg mice after MSA-C onset, and Tg mice treated with BLZ945.


status: Public on Jul 27 2022

city: San Francisco

first: Sanjeev

last: Ranade

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

summary: We performed scATAC-seq over multiple time points of heart development in WT C57Bl6/J embryos and in Tbx1 mutant mice (Tbx1 KO). We dissected primarily the cardiac region but also the regions dorsal to the heart and the pharyngeal arches to capture the progenitor cells that migrate into the heart and the neural crest cells. For time points E10.5 and E11.5, we primarily dissected the regions behind the heart and included less of the overall cardiac region. We included pharyngeal arches for all time points and, at E11.5, we excluded the first arch. For Tbx1 null embryos, we also generated scRNA-seq data for WT and mutant embryos from the same pool of dissociated cells used for scATAC-seq.

overall_design: For all embryos, we micro-dissected the tissue and dissociated using TryplE and then proceeded with a nuclei isolation method according to manufacturer's instructions (10X Genomics, https://support.10xgenomics.com/single-cell-gene-expression/sample-prep/doc/demonstrated-protocol-isolation-of-nuclei-for-single-cell-rna-sequencing-and-tissues-for-single-cell-rna-sequencing). For all samples, multiple replicates for WT and KO were used and we include all replicates below.

first: Angelo

last: Pelonero

first: Deepak

last: Srivastava