title: Anti-NY-ESO-1 TCR T-cells show a potent anti-tumour activity in the Sk-Mel-37 Melanoma Murine Xenograft Model

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

country: Russia

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

summary: In this work, we compared the expression profiles of CD3+ T-cells with anti-NY-ESO-1-transduced T-cells.

overall_design: We profiled total RNA from the Anti-NY-ESO-1-transduced TCR T-cells on NanoString Sprint Platform using Immunology V2 panel.


title: Liver-specific matrin-3 knockout alters the chromatin accessibility in the liver of mice [ATAC-seq]

status: Public on Oct 01 2024

city: Lincoln

first: Xinghui

last: Sun

state: NE

address: 1901 Vine Street

department: Biochemistry

country: USA

institute: University of Nebraska - Lincoln

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Matrin-3 is an RNA-binding protein involved in the pathogenesis of human diseases. Here we examined its previously uncharacterized role in regulating chromatin accessibility in the liver of mice. Bulk ATAC-seq and bioinformatics analysis identified 523 and 829 differential peaks (FDR < 0.05), respectively, in the liver of female mice fed a chow diet or 60% HFD for 16 weeks. Peak annotation by HOMER and ChIPseeker identified 183 and 444 genes, respectively, that are associated with the differential peaks. Enrichr analysis of these genes revealed that Hallmark terms such as "Xenobiotic metabolism" was enriched in the liver of chow-fed and HFD-fed mice. TRRUST database analysis from Metascape uncovered that Hnf4α is the main transcription factor regulating these peak-associated genes in the liver of chow-fed mice, and Hnf4α and Nr1i3 are the main transcription factors regulating these peak-associated genes in the liver of HFD-fed mice. Our data demonstrated that liver-specific matrin-3 deficiency alters chromatin accessibility likely affecting the action of two transcription factors Hnf4α and Nr1i3 in the liver of mice.

overall_design: Matrin-3 floxed mice were bred with Albumin-Cre mice (The Jackson Laboratory, #003574) to produce liver-specific matrin-3 knockout mice (LKO).  Mice were housed on a normal 12/12 light-dark cycle. Mice had ad libitum access to a normal chow diet (Envigo, cat# 2016) and water, or a HFD with 60 kcal% fat (Research Diets, D12492) and water. Female matrin-3 floxed mice and littermate LKO  mice were fed a HFD at 7 weeks of age for 16 weeks. Sixteen weeks post-HFD, mice were fasted for 12 hours for euthanasia and tissue collection. Nuclei from 50 mg frozen liver were isolated following the Chang Lab protocol (Corces et al, 2017; PMID: 28846090) for ATACseq library construction.

first: Xiao

last: Cheng


title: A single rare  sigma 70 variant establishes a different gene expression pattern in the E.coli pathobiont LF82

status: Public on Sep 30 2024

city: Bethesda

first: Melissa

last: Arroyo-Mendoza

state: MD

address: 8 CENTER DR RM 2A11

department: LBG

institute: NIDDK

type: Expression profiling by high throughput sequencing

summary: LF82, an adherent invasive Escherichia coli (AIEC) pathobiont, is associated with Crohn’s disease, an inflammatory bowel disease of unknown etiology. No genetic features have been identified that distinguish AIEC strains, such as LF82, from “commensal” or pathogenic E. coli. We investigated an extremely rare single nucleotide polymorphism (SNP) within the highly conserved rpoD gene, encoding sigma70 [primary sigma factor, RNA polymerase (RNAP)]. We demonstrate that sigma70 D445V results in transcriptome and phenotypic changes consistent with LF82 phenotypes, including increased biofilm formation and antibiotic resistance. The position of D445V within RNAP is predicted to affect spacer interaction; in vitro transcriptions reveal that the variant increases transcription from several promoters with a 16 bp spacer and a -14G:C. Our work demonstrates that a single SNP within the bacterial primary sigma can lead to myriad gene expression changes/ new phenotypes and suggests an underrecognized mechanism by which pathobionts and other strain variants can emerge.

overall_design:
To investigate the effect of a rare mutation found in the sigma 70 of E. coli LF82, isogenic LF82 WT and rpoD V445D mutant were created.
Gene expresion profilling analysis was performed using the data that was obtained from the RNA-seq of the isogenic pairs that were grown in triplicate. Comparative gene expression profilling analysis of the RNA-seq data for the LF82 isogenic pairs and E.coli MG1655 isogenic pairs (WT and rpoD D445V mutant) grown at 37o C was performed
Comparative gene expression profilling analysis of the RNA-seq data for the LF82 isogenic pairs and E.coli MG1655 isogenic pairs (WT and rpoD D445V mutant , GEO: GSE222248, Bioproject: PRJNA918682) grown at 37o C was performed

first: Alexandra

last: Proctor

first: Abraham

last: Correa-Medina

first: Sarah

last: DeWolf

first: Meghan

last: Wymore Bran

first: Virginia

last: Rosas

first: Hernan

last: Lorenzi

first: Michael

middle: J

last: Wannemuhler

first: Gregory

last: Phillips

first: Deborah

middle: M

last: Hinton


title: Mutant NPM1 marginally impacts ribosome footprint in acute myeloid leukemia cells

city: Perugia

first: Brunangelo

last: Falini

address: Piazza Università, 1

country: Italy

institute: University of Perugia

summary: Combining RNA-seq, Ribo-seq and selective NPM1c degradation through dTAG-13, we explored for the first time the impact of NPM1c on ribosome footprint in the two available NPM1-mutated cell lines. Analysis of translatome showed that NPM1c only marginally impacts ribosome abundance and positioning on mRNA in NPM1-mutated cells.

overall_design: We performed ribosome footprint profiling and bulk RNA sequencing in two NPM1-mutated cell lines (i.e. OCI-AML3 and IMS-M2), engineered to express endogenous NPM1c fused to the FKBP(F36V) degron domain. Incubation of degron cells with the small compound dTAG-13 enables highly specific degradation of >85% of NPM1c within 4h.

first: Lorenzo

last: Brunetti

first: Giulia

last: Pianigiani

middle: C

last: Gundry

first: Margaret

middle: A

last: Goodell


title: Increased CCL2/CCR2 axis in MYC/BCL2 double-expressor DLBCL promotes tumor progression by increasing M2 macrophages

city: Seoul

first: Yoon Kyung

last: Jeon

address: 101 Daehak-ro, Jongno-gu

department: Pathology

country: South Korea

institute: Seoul National University College of Medicine

summary: The pathogenesis of c-MYC and BCL2 double-expressor diffuse large B cell lymphoma (DE DLBCL) remains unclear, particularly in terms of the tumor microenvironment. We aimed to analyze the immune microenvironment of DE DLBCLs to understand the basis of DE-DLBCL's aggressiveness and identify potential therapeutic targets. To discover the key features of DE-DLBCL, fourteen non-DE and 14 DE DLBCL samples underwent RNA-seq analysis. For validation, formalin-fixed paraffin-embedded tissues from 126 patients were immunostained for CD3, CD4, CD8, FOXP3, CD68 and CD163. Two c-MYClow/BCL2low DLBCL (SU-DHL-10 and HT) and 2 c-MYChigh/BCL2high DLBCL cell lines (DOHH2 and OCI-LY8) were used for in vitro assays. The prognostic impact of differential chemokine secretion and immune profiles was evaluated in a mouse tumor model. RNA-seq analysis revealed significantly higher CCL2 and CCR2 mRNA in DE DLBCLs (Padj < 0.05). Public datasets showed higher M2/macrophage ratio and lower T cell infiltration in DE DLBCLs (P < 0.05). Immunohistochemistry confirmed higher M2 macrophages and M2/total macrophage ratio in DE DLBCL (P=0.010 and P=0.098, respectively). In vitro, c-MYChigh/BCL2high cell lines exhibited increased CCL2 secretion, as seen in RNA-seq analysis. Knockdown and overexpression studies identified that MYC and BCL2 overexpression increased CCL2 secretion by upregulation of NF-κB p65 subunit, and the increased CCL2 secretion was crucial for M2 polarization. In mouse tumor models, CCL2 was related to aggressive tumor growth and an immunosuppressive tumor microenvironment. In conclusion, the increased CCL2/CCR2 axis confers aggressiveness of DE DLBCLs by increasing M2 polarization.

overall_design: Nodal DLBCL samples, excluding primary mediastinal large B-cell lymphoma, primary central nervous system lymphoma, Epstein-Barr virus-positive DLBCL, T-cell/histiocyte-rich large B-cell lymphoma, and immunodeficiency-associated DLBCL. The cohort is composed of 14 c-MYC/BCL double expressor lymphomas (DELs) and 14 non-DELs.

first: Yoon

middle: K

first: Sehui

last: Kim

first: Hyein

last: Jeong


title: Zebrafish reveal new roles for Fam83f in hatching and DNA damage-mediated autophagic responses

city: Princeton

first: Rebecca

middle: Ann

last: Jones

state: New Jersey

address: Lewis Thomas Laboratory

department: Molecular Biology

institute: Princeton University

summary: The FAM83 (Family with sequence similarity 83) family is highly conserved in vertebrates, yet little is known of the functions of these proteins beyond a correlation with oncogenesis. Of the family, FAM83F is of particular interest because it is the only membrane targeted FAM83 protein. FAM83F has been shown to activate the canonical Wnt signalling pathway and bind to and stabilize p53 when overexpressed, two pathways often dysregulated in disease.  Insights into gene function can often be gained by studying the roles they play during development, and here we report the generation of fam83f knock-out (fam83f-/-) zebrafish, which we have used to elucidate the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the proteolytic enzyme containing hatching gland of developing zebrafish embryos, and that fam83f-/- embryos hatch earlier than WT counterparts, despite developing at a comparable temporal rate. We demonstrate that fam83f-/- embryos are more sensitive to ionizing radiation than WT embryos, a finding that contrasts with the previously reported role of FAM83F as a stabilizer of p53. Transcriptomic analysis shows that loss of fam83f causes downregulation of phosphatidylinositol-3-phosphate (PI(3)P) binding proteins and impairment of cellular degradation pathways, particularly autophagy, which is a crucial component of the DNA damage response. Finally, we show that Fam83f protein is itself targeted to the lysosome when expressed in cultured cells, and that this localization is dependent upon a C’ terminal signal sequence.  The zebrafish lines we have generated here suggest for the first time that Fam83f plays an important role in autophagic/lysosomal processes, resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo.

overall_design:
fam83fa-/- zebrafish are more sensitive to ionizing radiation (IR) than WT counterparts. We conducted bulk RNA-seq on WT vs two different fam83fa-/- (K1 and K2) zebrafish lines by subjecting 24 hpf embryos from each genotype to IR then extracting total RNA at 2 and 10 hours following treament (t1 and t2).  Three biological replicates of a minimum of 10 embryos per replicate were sequenced by bulk RNA-seq to to identify any differences in the DNA damage response between WT and fam83fa-/- mutants.

Treatments:
AD = Actinomycin D in DMSO vehicle
IR = ionizing radiation (20 Grays gamma radiation)
unDMSO = untreated AD control (vehicle only i.e. DMSO)
un = untreated IR control

first: Gavin

last: Kelly

first: Nourdine

last: Bah

first: James

last: Smith


title: MAIT cells in experimental autoimmune encephalomyelitis (EAE)

city: Hamburg

first: Jan Broder

last: Engler

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

summary: Multiple sclerosis (MS) is the most common inflammatory disease of the central nervous system (CNS) most likely caused by autoreactive T cells. Mucosal-associated invariant T (MAIT) cells are characterized by a semi-invariant T cell receptor (TCR) with which they recognize 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil (5-OP-RU), a metabolite of the riboflavin (vitamin B2) pathway only present in yeast and bacteria. MAIT cells have been detected in inflamed brain lesions of MS patients. However, functional analyses of CNS-infiltrating MAIT cells are lacking and require a characterisation in the MS animal model experimental autoimmune encephalomyelitis (EAE).

overall_design: Murine MAIT cells (living CD45+CD11b–CD45R–TCR-β+MR1tetramer(5-OP-RU)+ cells) were sorted from spleens and central nervous system of healthy mice and mice on day 14 of experimental autoimmune encephalomyelitis (EAE). Five animals were pooled per sample. All EAE mice had a score >= 3.

first: Mark

last: Walkenhorst

first: Jan

middle: B

first: Manuel

last: Friese

first: Willing

last: Anne


title: Innate protection against intrarectal SIV acquisition by a live Simian-Human immunodeficiency virus vaccine

first: Kimia

last: Dadkhah

address: Rockville Pike

department: NCI

institute: NIH

summary: Identifying immune correlates of protection is a major challenge in AIDS vaccine development. Anti-Envelope antibodies have been considered critical against SIV/HIV acquisition. Here, we evaluated the efficacy of a SHIV vaccine against SIVmac251 challenge, where the role of antibody was excluded as there was no cross-reactivity between SIV and SHIV Envelope antibodies. After eight low-dose rectal challenges with SIVmac251, 12 SHIV-vaccinated animals demonstrated 83% efficacy, compared to six naïve controls, suggesting protection could be achieved in the absence of anti-Envelope antibodies. Interestingly, CD8+ T cells (and some NK cells) were not essential for the preventing viral acquisition, as none of the CD8-depleted macaques were infected by SIVmac251 challenges. Initial investigation of protective innate immunity revealed that protected animals had elevated pathways related to platelet aggregation/activation, and reduced pathways related to interferon and responses to virus. Moreover, higher expression of platelet factor 4 (PF4) on circulating platelet-leukocyte aggregates was associated with reduced viral acquisition. Our data highlighted the importance of innate immunity and may provide new opportunities for novel HIV vaccines or therapeutic strategy development.

overall_design: To define the biomarkers on the CD41+CD14+ monocyte-platelet aggregates (MPAs), single-cell RNAseq analysis was performed on two PBMC samples (one vaccinated V56 and one naïve N2).

first: Michael

first: Yongjun

last: Sui

first: Jay

last: Berzofsky


title: Role of USP39 in HeLa and HEK293T cells

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

institute: Goethe University Frankfurt

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

overall_design: Refer to individual Series


title: Expression of serum EV microRNAs in aging mice

status: Public on Sep 29 2024

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

country: Japan

institute: Hirosaki University

summary: In Japan in recent years, the population has been aging and the risk of contracting various age-related diseases has increased with age, so there is a need to analyze components characteristic of aging and examine their association with diseases to detect age-related diseases at an early stage. In this study, miRNAs in serum EVs of 82-102-week-old aged mice were analyzed to look for microRNAs (miRNAs) characteristic of aging, and increased expression of mmu-miR-21a-5p was found.

overall_design: Eight-week-old (8w) (n = 5), 82-week-old (82w) (n = 5) and 102-week-old (102w) (n = 3) mice were used in this study. In this study, mice of various ages were used to search for microRNAs whose expression changes in serum with aging.

first: Keisuke

last: Yamamoto


title: Heterogeneous enhancer states orchestrate β cell responses to metabolic stress

city: SCOTTSDALE

first: Zong

last: Wei

state: Arizona

address: 13400 E Shea Blvd

institute: Mayo Clinic

summary: Obesity-induced β cell dysfunction is a significant contributor to the onset of type 2 diabetes. Metabolic stress triggers expansive enhancer and gene expression dynamics in islet endocrine cells. However, identifying the precise gene regulatory network and the corresponding epigenetic mechanisms driving the islet dysfunction remains challenging. Here we utilize Paired-Tag, a combinatorial index-based multi-omic platform, to concurrently profile single-nuclei RNA with H3K4me1 or H3K27ac, two distinct histone modifications defining enhancer states, in lean and obese islets. Our study revealed gene expression, distinct enhancer states, RNA-enhancer links, and intra-islet paracrine communications that align with amplified unfolded protein responses and decreased insulin secretion function at a single-cell level.

overall_design: We use Paired-Tag to investigate the multifaceted cellular trajectories defined by the integration of transcriptome and epigenome of H3K27Ac or H3K4Me1, in islets of mice under normal chow (NC) or high-fat diet (HFD).

first: Liu

last: Wang

first: Jie

last: Wu


title: Holliday junction resolvase RuvC targets biofilm eDNA to facilitate pathogen spread in plants

city: Wuhan

first: Xinya

last: Du

state: Hubei

address: Huazhong Agricultural University, No. 1, Shishishan Street, Hongshan District

country: China

institute: Huazhong Agricultural University

summary: Biofilm lifestyle is critical for bacterial pathogens to colonize and protect themselves from host immunity and antimicrobial chemicals in plants and animals. The formation and regulation mechanism of phytobacterial biofilm are still obscure. Here, we found that Ralstonia solanacearum Resistance to ultraviolet C (RuvC) is highly abundant in biofilm and positively regulates pathogenicity by governing systemic movement in tomato xylem. RuvC protein accumulates at the later stage of biofilm and specifically targets the Holliday junction (HJ) like structures to disrupt biofilm extracellular DNA (eDNA) lattice, thus facilitating biofilm dispersal. Recombinant RuvC protein can resolve extracellular HJ prevent bacterial biofilm formation. Heterologous expression of R. solanacearum or Xanthomonas oryzae pv. oryzae RuvC with plant secretion signal in tomato or rice confers resistance to bacterial wilt or bacterial blight disease, respectively. Plant chloroplast localized HJ resolvase monokaryotic chloroplast 1 (MOC1) which is structural similar to bacterial RuvC shows a strong inhibit effect on bacterial biofilm formation. Re-localization of SlMOC1 to apoplast in tomato roots leads to increase resistance to bacterial wilt. Our novel finding reveals a critical pathogenesis mechanism of R. solanacearum and provides an efficient biotechnology strategy to improve plant resistance to bacteria vascular disease.

overall_design: The sample names were GMI1000 and ΔRuvC, and the source of the sample species was R.solanacearum. The wild-type GMI1000 or ΔRuvC mutant was cultured to OD600=1 at 28℃. Different single colonies were as 1 biological replicate, and total of 3 biological replicates were performed.

first: Changqiu

last: Fan

first: Pengyue

last: Li

first: Jingjing

last: Tian

first: Yang

last: Lin

first: Jiatao

last: Xie

first: Jiangsen

last: Cheng

first: Yanping

last: Fu

first: Daohong

last: Jiang

first: Meng

last: Yuan

first: Xiao

last: Yu

first: Kenichi

last: Tsuda

first: Bo


title: Transcriptome differences between mature luminal and luminal progenitor cells of the breast

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

summary: In this study, we grew primary breast epithelial cells from breast biopsies of healthy donors, five each of African Ancestry, European ancestry and those who identify as Hispanic using epithelial cell reprogramming assay growth method. Cells grown were sorted into luminal progenitors (CD49F+/EpCAM+, labelled as PP cells) and mature luminal (CD49F-/EpCAM+, labelled as NP cells) by flow cytometry. Flow sorted cells were subjected to RNA-seq.

overall_design: Step1: grow primary cells from breast tissues of healthy donors, Step 2: Sort grown cells into mature luminal and luminal progenitor cells by flow cytometry, step 3: prepare RNA directly from the flow sorted cells and subject to RNA-seq

first: Fang

last: Fang

first: Kenneth

middle: P

last: Nephew

first: Manjushree

last: Anjanappa


title: The Effect of Spt5p on Transcriptional Directionality [ChIP-seq]

status: Public on Sep 28 2024

city: Daejeon

first: Hae Jin

last: An

address: 291 Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

summary: SPT5 is a well-conserved factor which manipulates multiple stages of transcription including promoter-proximal pausing (PPP). Furthermore, recent studies have reported an unidentified increase of antisesne transcripts near promoters in SPT5 mutations. Here, we have identified Spt5p-restricted intragenic antisense transcripts which are in close relationship with sense transcription. The antisense highly-restricted genes have common properties: endogenously strong sense transcription and weak antisense transcription, which is also conserved in humans. We identified that Spt5p depletion reduce H3K36me3 and H3K79me3 and lead to histone hyperacetylation, which might be the intermediate stage to induce antisense transcription. We additionaly found possible termination factors that are involved in the antisense restriction with Spt5p. By unveiling the new role of SPT5 in finely balancing the transcription bidirections, we revealed that transcription machinery can determine the direction cotranscriptionally.

overall_design:
ChIP-seq libraries were generated using Bur1p-IS strain presented by S. Bratowski's group (Chun et al., 2019) and Spt5p-AID strain. S. pombe is used for spike-in control. Two biological replicates are merged. Every libraries are normalized by spike-in. Histone ChIP-seq libraries are additionally normalized by H3 values.
Please note that processed data file generated from both replicates is linked to the corresponding rep1 sample records.

first: Haejin

first: Hyeokjun

last: Yang

first: Daeyoup

last: Lee


title: Resistance to age-related hearing loss in the echolocating big brown bat (Eptesicus fuscus)

city: College Park

first: Gerald

last: Wilkinson

address: Biology-Psychology Building

department: Department of Biology

institute: University of Maryland

summary: Hearing mediates many behaviors critical for survival in echolocating bats, including foraging and navigation. Although most mammals are susceptible to progressive age-related hearing loss, the evolution of biosonar, which requires the ability to hear low-intensity echoes from outgoing sonar signals, may have selected against the development of hearing deficits in bats. Many echolocating bats exhibit exceptional longevity and rely on acoustic behaviors for survival to old age; however relatively little is known about the aging bat auditory system. In this study, we used DNA methylation to estimate the ages of wild-caught big brown bats (Eptesicus fuscus) and measured hearing sensitivity in young and aging bats using auditory brainstem responses (ABRs) and distortion product otoacoustic emissions (DPOAEs). We found no evidence for hearing deficits in bats up to 12.5 years of age, demonstrated by comparable thresholds and similar ABR and DPOAE amplitudes across age groups. We additionally found no significant histological evidence for cochlear aging, with similar hair cell counts, afferent, and efferent innervation patterns in young and aging bats. Here we demonstrate that big brown bats show minimal evidence for age-related hearing loss and therefore represent informative models for investigating mechanisms that may preserve hearing function over a long lifetime.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We ran bisulphite converted DNA from wing skin biopsies on a custom Illumina methylation array to estimate their ages based on existing methylation clock sfrom Wilkinson et al. 2021 (PMC7955057)

first: Grace

last: Capshaw

first: Amanda

last: Lauer

first: Clarice

last: Diebold

first: Danielle

last: Adams

first: Jack

last: Rayner

first: Cynthia

last: Moss


title: Sex-biased ZRSR2 mutations in myeloid malignancies impair plasmacytoid dendritic cell activation and apoptosis [PDX]

city: Boston

first: Christopher

last: Booth

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive leukemia of plasmacytoid dendritic cells (pDCs). BPDCN occurs at least three times more frequently in men than women, but the reasons for this sex bias are unknown. Here, studying genomics of primary BPDCN and modeling disease-associated mutations, we link acquired alterations in RNA splicing to abnormal pDC development and inflammatory response through Toll-like receptors. Loss-of-function mutations in ZRSR2, an X chromosome gene encoding a splicing factor, are enriched in BPDCN and nearly all mutations occur in males. ZRSR2 mutation impairs pDC activation and apoptosis after inflammatory stimuli, associated with intron retention and inability to upregulate the transcription factor IRF7. In vivo, BPDCN-associated mutations promote pDC expansion and signatures of decreased activation. These data support a model in which male-biased mutations in hematopoietic progenitors alter pDC function and confer protection from apoptosis, which may impair immunity and predispose to leukemic transformation.

overall_design: RNA sequencing of 11 BPDCN PDX samples and 3 normal pDC samples, either untreated or treated with 1 µg/ml R848 for 24 hours

first: Andrew

last: Lane

first: Katsuhiro

last: Togami


title: The Effect of Spt5p on Transcriptional Directionality [RNA-seq]

overall_design:
RNA-seq libraries were generated using Bur1p-IS strain presented by S. Bratowski's group (Chun et al., 2019) and several auxin-inducible degron (AID) strains. S. pombe is used for spike-in control. Two biological replicates are merged. Every libraries are normalized by spike-in.
Please note that processed data file generated from both replicates is linked to the corresponding rep1 sample records.


title: Deferasirox, an iron chelator, impacts myeloid differentiation by modulating NF-kB activity via mitochondrial ROS

status: Public on Sep 27 2024

first: Nathan

middle: Elias

last: Jeffries

address: 185 Cambridge St MCPZN 4400

department: CRM

institute: Massachusetts General Hospital

summary: Deferasirox (DFX) can improve erythropoiesis in patients with MDS. We sought to test how these changes occur and whether myelopoiesis broadly is affected by analyzing neutrophils and neutrophil precursors treated with DFX.

overall_design: We cultured human, LIN- bone marrow and peripheral blood cells in media containing GCSF for 5 days while treating with either DMSO, 1.5 uM DFX, or 3 uM DFX.

middle: E

first: Kashish

last: Chetal

first: Ruslan

middle: I

last: Sadreyev

first: David

last: Sykes


title: Remodeling of Il4-Il13-Il5 locus underlies selective gene expression (ChIP-seq)

first: Hiroyuki

last: Nagashima

state: Maryland

address: 10 Center Dr, Room 13C120

summary: The type 2 cytokines, interleukin (IL)-4, IL-5 and IL-13 reside within a multi-gene cluster in mammals. These cytokines represent the hallmark of type 2 immune responses controlling parasites and promoting tissue repair, as well as causing allergic diseases. Both innate and adaptive lymphocytes secrete type 2 cytokines with discordant production spectra. We took a holistic structural and functional view of the type 2 cytokine locus before and after activation, comparing innate (ILC2) and adaptive (Th2) lymphocytes to understand mechanisms underlying their distinctive programs. Rapid induction of IL-5 dominates in ILC2, whereas IL-4 does so in Th2 cells. Using high-resolution chromatin conformation capture we found that global cellular chromatin architecture remained constant, whereas the type 2 cytokine locus rapidly remodeled. In ILC2, Il13 and Il5 loci were aligned in proximity whereas Il4 locus was insulated. In Th2 cells, Il4 and Il13 positioned in proximity while the Il5 locus remained distal. Select REs were individually deleted in mice to confirm cell-type specific and activation-dependent roles in type 2 responses in vivo. Thus, contrary to the premise that chromatin architecture plays a minimal role in steady-state gene induction, signal-dependent remodeling of 3D configuration underlies the discordant cytokine outputs in ILC2s versus Th2 cells.

overall_design: ChIP-seq for transcription factors using mouse ILC2s and Th2 cells.

first: Nagashima

last: Hiroyuki

first: Jiang

last: Kan


title: 3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes [Cut&Tag]

city: Nancy Cedex

first: Guillermo

last: Barreto

address: 9, Avenue de la Forêt de Haye ‐ BP 20199

department: Campus Biologie-Santé. Faculté de Médecine

country: France

institute: CNRS Director of Research

summary: Studying the dynamics of three-dimensional (3D) chromatin structure is essential to the understanding of biological processes in the nucleus. Integrative analysis of multi-omics data in recent publications have provided comprehensive and multilevel insight into 3D genome organization emphasizing its role for transcriptional regulation. While enhancers are regulatory elements that play a central role in the spatiotemporal control of gene expression, chromatin looping has been broadly accepted as a means for enhancer-promoter interactions yielding cell-type-specific gene expression signatures. On the other hand, G-quadruplexes (G4s) are non-canonical DNA secondary structures that are enriched at promoters and related to increased gene expression. However, the role of G4s in promoter-distal regulatory elements, such as super-enhancers (SE), as well as in 3D genome organization and chromatin looping mediating long-range enhancer-promoter interactions has remained elusive. Here we show that mature microRNA 9 (miR-9) is enriched at promoters and SE of genes that are inducible by tissue growth factor beta 1 (TGFB1) signaling. Further, we find that nuclear miR-9 is required for chromatin features related to increased transcriptional activity, such as broad domains of the euchromatin histone mark H3K4me3 (histone 3 tri-methylated lysine 4) and G4s. Moreover, we show that nuclear miR-9 is required for promoter-super-enhancer looping. Our study places a nuclear microRNA in the same structural and functional context with G4s and promoter-enhancer interactions during 3D genome organization and transcriptional activation induced by TGFB1 signaling, a critical regulator of proliferation programs in cancer and fibrosis.

overall_design: MLg or MLE12 cells were transfected with antagomiR probes (Ambion) using Lipofectamine 2000 (Invitrogen) following the manufacturer’s instructions and after 48 h cells were harvested. Followed Cut&Tag protocol was performed to obtained DNA associated to the Histone mark or  G-quadruplexes structure

first: Julio

last: Cordero


title: Remodeling of Il4-Il13-Il5 locus underlies selective gene expression [Hi-C]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: HiC for mouse ILC2s, mouse Th2 and human Th2 cells.

first: Kan

last: Jiang


title: Remodeling of Il4-Il13-Il5 locus underlies selective gene expression (fHiC)

overall_design: Focused HiC for mouse ILC2s


title: A  Mobile  miR160-Triggered  Transcriptional  Axis  Controls  Root  Stem  Cell  Niche  Maintenance and Regeneration in Arabidopsis

first: Limin

last: Pi

state: Hubei province

address: No.299 Bayi Road, Wuchang District

institute: Wuhan University

summary: In  multicellular  organisms,  communication  between  cells  is  vital  for  their  fate determination. In plants, the quiescent center (QC) signals to adjacent stem cells to maintain them undifferentiated. However, how surrounding stem cells instruct the QC remains poorly understood. Here we show that in the Arabidopsis root, microRNA160 (miR160)  moves  from  vascular  stem  cells  to  the  QC,  where it degrades the mRNAs of two auxin response factors, ARF10 and ARF17. This degradation relieves BRAVO from direct transcriptional repression, maintaining QC quiescence. We further identify that blocking miR160 movement due to DNA damage-induced vascular stem cell death and restricted symplastic transport reduces BRAVO and WOX5 expression, leading to QC division to replenish damaged stem cells during root regeneration. Together, our results demonstrate that a transcriptional axis initiated by mobile miR160 regulates the QC and stem cell behavior, advancing our understanding of the communication between stem cells and their surrounding cellular environment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Col-0, arf10-3 arf16-3, 35S:MIR160c anf pARF10:mARF10-GFP; each genotype has three replicates; 12 samples in Total.

first: Xixi

last: Cai

first: Yanjun

last: Chen


title: Single-cell RNA sequencing of thymic EC and TEC from control and RANKL treated aged mice

city: Marseille

first: Magali

last: Irla

address: 163 Av. de Luminy

institute: Centre d’Immunologie de Marseille-Luminy (CIML)

summary: Age-related thymic involution, leading to reduced T cell production, is one of the major causes of immunosenescence. This results in an increased susceptibility to cancers, infections, and autoimmunity and in reduced vaccine efficacy. Here, we identified that the receptor activator of nuclear factor κB (RANK)-RANK ligand (RANKL) axis in the thymus is altered during aging. Using a conditional transgenic mouse model, we demonstrated that endothelial cells depend on RANK signaling for their cellularity and functional maturation. Decreased RANKL availability during aging resulted in a decline in cellularity and function of both endothelial cells and thymic epithelial cells, contributing to thymic involution. We then found that, whereas RANKL neutralization in young mice mimicked thymic involution, exogenous RANKL treatment in aged mice restored thymic architecture as well as endothelial cell and epithelial cell abundance and functional properties. Consequently, RANKL improved T cell progenitor homing to the thymus and boosted T cell production. This cascade of events resulted in peripheral T cell renewal and effective antitumor and vaccine responses in aged mice. Furthermore, we conducted a proof-of-concept study that showed that RANKL stimulates endothelial cells and epithelial cells in human thymic organocultures. Overall, our findings suggest that targeting the RANK-RANKL axis through exogenous RANKL administration could represent a therapeutic strategy to rejuvenate thymic function and improve T cell immunity during aging.

overall_design: Expression profiling by high throughput sequencing. CD31+ EC were sorted 3 weeks after GST and RANKL treatment in aged mice and mixed in equal ratios. Five hundred WT splenic B cells were added to each pool to ease batch correction if necessary. Cells were individually loaded onto a Chromium Next GEM chip K (10X Genomics), and cells were droplet-encapsulated with a Chromium Controller (10X Genomics). Libraries were prepared with the Chromium single cell 5′ v2 kit (10X Genomics) according to the manufacturer’s instructions with dual index. The concentration and quality of cDNA libraries were determined using the Qubit dsDNA HS assay kit (Thermo Fisher Scientific) for the Qbit fluorometer and the High Sensitivity DNA Analysis Kit (Agilent) for the bioanalyzer, respectively. Libraries were sequenced on an Illumina NextSeq 2000 platform with a 100-cycles P2 flow cell.

first: Jessica

last: Chevallier

first: Jérémy

last: Santamaria


title: 3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes [CHiP-seq]

overall_design: Cells were transfected with antagomiR probes (Ambion) using Lipofectamine 2000 (Invitrogen) following the manufacturer’s instructions, and harvested 24 h later for further analysis. Anti-hsa-miR-Mir9-5p (Ambion, #17000). Following 20 h after transfection, TGFB1 signaling was induced with 5 ng/ml final concentration of human recombinant TGFB1 (Sigma-Aldrich) for 4 h. After ChIP-seq for H3k4me3 was performed to obtain associated DNA to that modificaiton.


title: Decoding the Epigenetics and Chromatin Loop Dynamics of Androgen Receptor-Mediated Transcription [Start-seq]

city: Vancouver

last: Lack

state: BC

address: 2660 Oak S

country: Canada

institute: Vancouver Prostate Centre

summary: Androgen receptor (AR)-mediated transcription plays a critical role in normal prostate development and prostate cancer growth. AR drives gene expression by binding to thousands of cis-regulatory elements (CRE) that loop to hundreds of target promoters. With multiple CREs interacting with a single promoter, it remains unclear how individual AR bound CREs contribute to gene expression. To characterize the involvement of these CREs, we investigated the AR-driven epigenetic and chromosomal chromatin looping changes.  We collected a kinetic multi-omic dataset comprised of steady-state mRNA, chromatin accessibility, transcription factor binding, histone modifications, chromatin looping, and nascent RNA. Using an integrated regulatory network, we found that AR binding induces sequential changes in the epigenetic features at CREs, independent of gene expression. Further, we showed that binding of AR does not result in a substantial rewiring of chromatin loops, but instead increases the contact frequency of pre-existing loops to target promoters. Our results show that gene expression strongly correlates to the changes in contact frequency. We then proposed and experimentally validated an unbalanced multi-enhancer model where the impact on gene expression of AR-bound enhancers is heterogeneous, and is proportional to their contact frequency with target gene promoters. Overall, these findings provide new insight into AR-mediated gene expression upon acute androgen simulation and develop a mechanistic framework to investigate nuclear receptor mediated perturbations.

overall_design: Small Capped Nascent RNA Sequencing (Start-seq) for acute androgen treatment on LNCaP cells.

first: Umut

last: Altintas

first: Ji-Heui

last: Sao

first: Matthew

middle: L

last: Freedman


title: Riluzole Enhancing anti-PD-1 Efficacy by Activating cGAS/STING Signaling

city: Columbus

first: Jing

middle: Jenny

last: Wang

state: OH

address: 460 W. 12th Street

department: Cancer Biology and Genetics

institute: Ohio State University

summary: Colorectal cancer is the second leading cause of cancer mortality in the US. Although immune checkpoint blockade therapies such as anti-PD-1/PD-L1 have had successes in some patients, the response rate is still low. We have found that riluzole, a well-tolerated FDA-approved oral medicine for treating amyotrophic lateral sclerosis, increased intratumoral CD8+ T cells and suppressed tumor growth of colon cancer cells in syngeneic immune competent mice. Riluzole-mediated tumor suppression was dependent on the presence of CD8+ T cells. Riluzole activates the cytosolic DNA sensing cGAS/STING pathway and increases expression of interferon β (IFNβ) and IFNβ-regulated genes including CXCL10. Inhibition of ATM, but not ATR, results in a synergistic increase in IFNβ expression, suggesting that riluzole-dependent double strand breaks contribute to cGAS/STING activation. Knockout of cGAS or STING significantly attenuated expression of IFNβ and CXCL10 and nearly abolished suppression of tumor growth. Riluzole failed to increase intratumoral CD8+ T cells in STING knockout tumors. These results indicate that riluzole recruits CD8+ T cells into the tumor microenvironment through tumor cell intrinsic STING activation. When riluzole was combined with a PD-1 antibody, the treatment was more effective in suppressing tumor growth in vivo. Taken together, our studies indicate that riluzole inhibits tumor growth through the activation of cGAS/STING signaling and may increase the efficacy of anti-PD-1/PD-L1 therapies in colon cancer.

overall_design: To examine how Riluzole treatment affects the transcriptome of CT26 cultured mouse cells

first: Wang

last: Jing

first: Miles

last: Wayne


title: Decoding the Epigenetics and Chromatin Loop Dynamics of Androgen Receptor-Mediated Transcription [ATAC-seq]

first: Nathan

overall_design: Assay for transposase-accessible chromatin with sequencing (ATAC-seq) for acute androgen treatment on LNCaP cells.


title: Decoding the Epigenetics and Chromatin Loop Dynamics of Androgen Receptor-Mediated Transcription [ChIP-seq]

overall_design: Chromatin Immunoprecipitation with sequencing (ChIP-seq) for acute androgen treatment on LNCaP cells.


title: Controlling DNA-deletion sizes, chromosomal translocations and aneuploidy in CRISPR-edited human T cells by the strength of TCR stimulation and pifithrin-α

city: Munich

first: Laurenz

middle: Thomas

last: Ursch

address: Trogerstraße 30

institute: TUM

summary: CRISPR/Cas9-engineered human T cells hold great promise in improving T cell effector functions for adoptive T cell therapies. To ensure safety during CRISPR/Cas9-editing optimized gRNAs, novel variants or prediction tools for indel outcomes have been developed. Still, several reports describe the occurrence of CRISPR-induced chromosomal aberrations, such as loss of large DNA fragments or even aneuploidy. So far, the measures to increase the safety of T cell products focused on the CRISPR Cas9 system. However, T cell-intrinsic features, such as their massive expansion after TCR stimulation, have not been fully taken into consideration. Here, we describe driving forces of indel formation in primary human T cells. Increased T cell activation and proliferation speed correlate with larger deletions. Editing of non-activated T cells reduces the risk of unwanted large deletions but with the downside of reduced knock-out efficiencies. An alternative strategy to reduce the risk of large deletions is the addition of the small molecule pifithrin-α after CRISPR/Cas9 editing. Pifithrin-α treatment results in smaller, more defined deletions and reduces the risk of CRISPR-induced chromosomal translocations and aneuploidy in a p53-independent manner while maintaining the functionality of CRISPR-engineered T cells. Controlling T cell activation and the addition of pifithrin-α are easily accessible strategies for safer CRISPR/Cas9-engineering for adoptive T cell therapies.

overall_design: To investigate the effects of Pifithrin alpha on the DNA-Damage-Repair, primary human T-cells were genetically edited with CRISPR/Cas9 with or without the presence of Pifithrin alpha. The following are not used in the manuscript: GSM7967669, GSM7967672, GSM7967674, GSM7967675, GSM7967676, GSM7967677, GSM7967680, GSM7967681, GSM7967682, GSM7967683, and GSM7967686.

middle: T

first: Jule

middle: S

last: Müschen

first: Julia

last: Ritter

last: Klermund

first: Bettina

last: Bernard

first: Saskia

last: Kolb

first: Linda

last: Warmuth

first: Geoffroy

last: Andrieux

first: Gregor

last: Miller

first: Marina

last: Jiménez-Muñoz

first: Fabian

last: Theis

first: Melanie

last: Boerries

first: Dirk

middle: H

last: Busch

first: Toni

last: Cathomen

first: Kathrin

last: Schumann


title: Saturation genome Editing of BRCA2 variants from C-terminal DNA binding domain

city: Frederick

first: Shyam

last: Sharan

address: 1050 Boyles Street

department: Mouse Cancer Genetics Program

institute: National Cancer Institute

summary: Accurate interpretation of genetic variation is a critical step towards realizing the potential of precision medicine. Sequencing-based genetic tests have uncovered a vast array ofBRCA2sequence variants. Due to limited clinical, familial and/or epidemiological data, thousands of variants are considered to be variants of uncertain significance (VUS). Here we have utilized CRISPR-Cas9-based saturation genome editing (SGE) in a humanized-mouse embryonic stem cell line. We have categorized nearly all possible missense single nucleotide variants (SNVs) encompassing the C-terminal DNA binding domain ofBRCA2.We have generated the function scores for 6270 SNVs, covering 95.5% of possible SNVs in exons 15-26 spanning residues 2479-3216, including 1069 unique missense VUS, with 81% functional and 14% found to be nonfunctional. Our classification aligns strongly with pathogenicity data from ClinVar, orthogonal functional assays and computational meta predictors. Our statistical classifier exhibits 92.2% sensitivity and 96% specificity in distinguishing clinically benign and pathogenic variants recorded in ClinVar. Furthermore, we offer proactive evidence for 617 SNVs being non-functional and 3396 SNVs being functional demonstrated by impact on cell growth and response to DNA-damaging drugs like cisplatin and olaparib. This classification serves as a valuable resource for interpreting unidentified variants in the population and for physicians and genetic counselors assessingBRCA2VUSs in patients.

overall_design: Saturation genome editing (SGE) of BRCA2

first: Sounak

last: Sahu


title: Remodeling of Il4-Il13-Il5 locus underlies selective gene expression (ATAC-Seq)

city: Bethesda

first: Hiroyuki

last: Nagashima

institute: NIH

overall_design: ATAC-seq for mouse ILC2s, human naïve Th cells and human Th2 cells.

first: Kan

last: Jiang


title: Decoding the Epigenetics and Chromatin Loop Dynamics of Androgen Receptor-Mediated Transcription [RNA-seq]

first: Nathan

last: Lack

overall_design: RNA Sequencing for acute androgen treatment on LNCaP cells.

first: Umut

last: Altintas

first: Ji-Heui

last: Sao

first: Matthew

last: Freedman


title: The Effect of Spt5p on Transcriptional Directionality [PRO-seq]

first: Hae Jin

last: An

overall_design: PRO-seq and PRO-cap libraries were generated using Bur1p-IS strain presented by S. Bratowski's group (Chun et al., 2019) and several auxin-inducible degron (AID) strains. S. pombe is used for spike-in control. Two biological replicates are merged. Every libraries are normalized by spike-in.

first: Haejin

first: Hyeokjun

last: Yang

first: Daeyoup

last: Lee


title: 3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes [ChIRP_seq]

first: Guillermo

last: Barreto

summary: Chromatin is the physiological template for all biological processes in the eukaryotic cell nucleus. In addition, the structure of chromatin is intrinsically related to its function. Thus, studying the dynamics of three-dimensional (3D) chromatin structure is essential to understand these biological processes. Recent publications based on integrative analysis of multi-omics studies have provided comprehensive and multilevel insights into 3D genome organization emphasizing its role during transcriptional regulation. However, the function of nuclear microRNAs in 3D genome organization has remained elusive. Here we show that mature microRNA 9 (miR-9) is enriched at promoters and super-enhancers (SE) of genes that are inducible by tissue growth factor beta 1 (TGFB1) signaling. Further, we found that nuclear miR-9 is required for broad domains of the euchromatin histone mark H3K4me3 (histone 3 tri-methylated lysine 4), as well as the nucleic acid secondary structure G-quadruplexes (G4s), both are chromatin features related to increased transcriptional activity. Moreover, we show that nuclear miR-9 is required for promoter-super-enhancer looping. Our study places a nuclear microRNA in the same structural and functional context with G4s and promoter-enhancer interactions during 3D genome organization and transcriptional activation induced by TGFB1 signaling, a pathway that plays important role in hyperproliferative diseases, such as cancer and fibrosis.

overall_design: Mlg cells were transfected with Mir9 complementary probe and biotinalited beads were used to obtain the DNA associated to Mir9

first: Julio

last: Cordero


title: 3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes

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

overall_design: Refer to individual Series


title: Enhancer reprogramming underlies therapeutic utility of a SMARCA2 degrader in SMARCA4 mutant cancer [ChIP-Seq]

city: Houston

first: Carl

last: Gay

state: TX

address: 1515 Holcombe Blvd

department: Thoracic-Head & Neck Med Onc

institute: The University of Texas MD Anderson Cancer Center

summary: Lung cancer is the top cause of cancer mortality. Despite recent advances, the majority of patients with lung cancer still lack effective therapeutic options, underscoring the dire need for additional treatment approaches. Genomic studies have identified frequent mutations in subunits of the SWI/SNF chromatin remodeling complex including SMARCA4 and ARID1A in non-small cell lung cancer with a frequency of up to 33% in advanced stage disease, making it the most frequently mutated complex in lung cancer.  Recent reports have identified the paralogue SMARCA2 to be synthetic lethal to SMARCA4 suggesting SMARCA2 is a valuable therapeutic target. However, the discovery of selective inhibitors of SMARCA2 has been challenging. To overcome this hurdle, we have utilized iterative structure-activity relationship (SAR) studies to develop novel, potent and selective SMARCA2 degrading small molecules based on proteolysis targeting chimera (PROTAC) technology. We demonstrated that YD23, our lead SMARCA2 PROTAC, potently and selectively induces degradation of SMARCA2. Mechanistically, we show that SMARCA2 degradation in SMARCA4-mutant cells induces a profound reprograming of the enhancer landscape with marked loss of chromatin accessibility at enhancers of genes involved in cell proliferation. Furthermore, we identified nuclear effectors of the Hippo pathway, YAP/TEAD, as key co-conspirators of SMARCA2 in driving the growth of SMARCA4-mutant cancer cells that can be disrupted by our degrader.  Finally, we show that YD23 has a potent tumor growth inhibitory activity in SMARCA4-mutant xenograft tumors. These findings provide the mechanistic basis for development of SMARCA2 degraders as synthetic lethal therapeutics against SMARCA4 mutant tumors.

overall_design: Chromatin Immunoprecipitation  Sequencing  (ChIP-seq) on H3K27ac and HeK4me1 in 3 cell lines (H1693, H1975, HCC44)

first: Sasikumar

last: Kotagiri

first: Blazanin

last: Nicholas

first: Yuanxin

last: Xi

first: Md

last: Qudratullah

first: Xiaobing

last: Liang

first: Yawen

last: Wang

first: Poonam

last: Pandey

first: Anand

last: Singh

first: Jing

first: Yonathan

last: Lissanu


title: Enhancer reprogramming underlies therapeutic utility of a SMARCA2 degrader in SMARCA4 mutant cancer [ATAC-Seq]

overall_design: ATAC-seq was performed in 4 cell lines (2 SMARCA4-WT, 2 SMARCA4-mutant) each treated for DMSO, YD23, and ACBI1 (each 1µM) for 96 hr. 2 replicates each.


title: Enhancer reprogramming underlies therapeutic utility of a SMARCA2 degrader in SMARCA4 mutant cancer [RNA-Seq]

overall_design: RNA-sequencing for 6 different cell lines (3 SMARCA4-WT, 3-SMARCA4-mutant) each treated with DMSO, YD23, or ACBI1 (1µM each) for 96 hours.


title: Decoding the Epigenetics and Chromatin Loop Dynamics of Androgen Receptor-Mediated Transcription [HiChIP]

first: Nathan

last: Lack

overall_design: HiC combined with capture ChIP-seq (HiChIP) for acute androgen treatment on LNCaP cells.

first: Umut

last: Altintas

first: Ji-Heui

last: Sao

first: Matthew


title: The BAF complex enhances transcription through interaction with H3K56ac in the histone globular domain

status: Public on Sep 26 2024

first: Kim

last: Hyoungmin

address: 291, Daehak-ro, Yuseong-gu, Daejeon, 34141, Rep. of KOREA

department: Department of Biological Sciences

summary: Histone post-translational modifications play pivotal roles in eukaryotic gene expression. To date, most studies have focused on modifications in unstructured histone N-terminal tail domains and their binding proteins. However, transcriptional regulation by chromatin-effector proteins that directly recognize modifications in histone globular domains has yet to be clearly demonstrated, despite the richness of their multiple modifications. Here, we show that the ATP-dependent chromatin-remodeling BAF complex stimulates p53-dependent transcription through direct interaction with H3K56ac located on the lateral surface of the histone globular domain. Mechanistically, the BAF complex recognizes nucleosomal H3K56ac via the DPF domain in the DPF2 subunit and exhibits enhanced nucleosome-remodeling activity in the presence of H3K56ac. We further demonstrate that a defect in H3K56ac–BAF complex interaction leads to impaired p53-dependent gene expression and DNA damage responses. Our study provides direct evidence that histone globular domain modifications participate in the regulation of gene expression.

overall_design: The BAF complex harboring R350H mutation in the DPF2 subunit exhibited a defect in physical interaction with nucleosomal H3K56ac. To investigate the effect of DPF2-mediated interactions of the BAF complex with H3K56ac on gene expression in DNA-damaging conditions, we introduced the DPF2 R350H mutation into the genome of HCT116 cells using the CRISPR/Cas9 gene-editing system. We then performed RNA sequencing analyses on WT and DPF2 R350H HCT116 cells in the presence and absence of doxorubicin treatments.

first: Hyoungmin

last: Kim

first: Kwangbeom

last: Hyun

first: Jaehoon


title: 3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes [RNA-Seq]

first: Guillermo

last: Barreto

overall_design: MLg cells were transfected with 10nM of antiMir9 and total RNA was harvested 48h after transfection to perform total-RNA-seq

first: Julio

last: Cordero


title: TGF-β and RAS jointly unmask primed enhancers to drive metastasis (RNA-Seq)

city: New York

first: Jun Ho

last: Lee

address: 417 E 68th St

institute: MSKCC

summary: Epithelial-to-mesenchymal transitions (EMTs) and extracellular matrix (ECM) remodeling are distinct yet important processes during carcinoma invasion and metastasis. TGF-β and RAS, signaling through SMAD and RAS-responsive element-binding protein 1 (RREB1), jointly trigger expression of EMT and fibrogenic factors as two discrete arms of a common transcriptional response in carcinoma cells. Here we demonstrate that both arms form a program for lung adenocarcinoma pulmonary metastasis and identify chromatin determinants tying the expression of the constituent genes to TGF-β and RAS dual inputs. RREB1 binds near H4K16ac histone marks and histone H2A.Z-loaded nucleosomes at enhancers in the fibrogenic genes IL11, PDGFB, and HAS2 and the EMT transcription factor SNAI1, priming these enhancers for activation by a SMAD4-INO80 nucleosome remodeling complex in response to TGF-β. These regulatory properties set the fibrogenic EMT program apart from RAS-independent TGF-β gene responses and illuminate the operation and vulnerabilities of a transcriptional program that promotes metastatic outgrowth.

overall_design: Expression profiling by high throughput sequencing of 393T3 cells, a cell line derived from a lung tumor from a KrasG12D;p53-/- (KP) genetically engineered mouse model, treated with SB505124 or TGF-β for 1.5 h

first: Richard

last: Koche

first: Joan

last: Massagué


title: Remodeling of Il4-Il13-Il5 locus underlies selective gene expression (mRNA-Seq)

first: Hiroyuki

last: Nagashima

overall_design: mRNA-seq for mouse Th2 cells, human naïve Th cells and human Th2 cells.

first: Kan

last: Jiang


title: 3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes [HICHIP_seq]

overall_design: crosslinked chromatin from 2Million MLg cells were harvested to perform HichiP protocol.


title: Response of pulmonary mononcytes to Staphylococcus aureus infection

city: Newark

first: Dane

last: Parker

state: NJ

address: 205 South Organge Ave, G-1208

department: Pathology, Immunology and Laboratory Medicine

institute: Rutgers New Jersey Medical School

summary: To better understand the cytokines and products produced by monocytes during infection we purified monocytes from the lungs of mice infected with S. aureus and compared them to naïve cells in the bone marrow.

overall_design: Comparative gene expression analysis of naïve bone marrow monocytes with monocytes from the lungs of S. aureus infected mice


title: Overcoming amphotericin B resistance in Candida auris using the antiemetic drug, rolapitant

city: West Lafayette

first: Sagar

last: Utturkar

address: 201 S University St

department: Institute for Cancer Research

institute: Purdue University

summary: The emergence of Candida auris poses a significant health challenge that has led to a new era of multidrug-resistant fungal infections. Invasive infections caused by C. auris are usually associated with remarkable morbidity and mortality. For many years, amphotericin B (AmB) remained the most efficient and the last line of treatment against most hard-to-treat fungal infections. However, strains of C. auris possess extraordinary resistance to most antifungal agents, including AmB. In this study, we screened ~2600 FDA-approved drugs and clinical compounds to identify the antiemetic drug rolapitant as a promising enhancer to AmB against C. auris. Rolapitant exhibited potent synergistic interactions with AmB against all tested (29/29) C. auris isolates. In a time-kill assay, rolapitant restored the fungicidal activity of AmB within 4 h. Additionally, the synergistic relationship between rolapitant and AmB was observed against other medically crucial Candida, Cryptococcus and Aspergillus species with ΣFICI that ranged from 0.16 to 0.5. In a transcriptomic study, ion transporters and ATP generation were identified as primary pathways impacted in C. auris AR0390 cells exposed to rolapitant. An ATP luminescence assay confirmed that rolapitant, at sub-inhibitory concentrations, significantly interfered with ATP production in C. auris. Moreover, rolapitant enhanced the in vivo activity of AmB in a mouse model of disseminated C. auris infection, as the combination reduced the fungal burden in murine kidneys by ~1 log (~90%) colony forming units. Our findings warrant further investigation of using rolapitant to overcome AmB resistance in C. auris and other fungal species.

overall_design:
Samples GSM7806557, GSM7806558 and GSM7806559 from GSE244094 were used as the controls:
GSM7806557     DMSO sample 1 [A4] SRX21897801 SAMN37548903
GSM7806558     DMSO sample 2 [A5] SRX21897802 SAMN37548902
GSM7806559     DMSO sample 3 [A6] SRX21897803 SAMN37548901

first: Ehab

last: Salama

first: Yehia

last: Elgammal

first: Nadia

last: Lanman

first: S

first: Tony

middle: R

last: Hazbun

first: Mohamed

middle: N

last: Seleem


title: TGF-β and RAS jointly unmask primed enhancers to drive metastasis (Mnase-Seq)

overall_design: Nucleosome occupancy profiling by high throughput sequencing of 393T3 cells, a cell line derived from a lung tumor from a KrasG12D;p53-/- (KP) genetically engineered mouse model, treated with SB505124 or TGF-β for 1.5 h


title: TGF-β and RAS jointly unmask primed enhancers to drive metastasis (DRIPc-seq)

overall_design: Genome binding/occupancy profiling by high throughput sequencing of 393T3 cells, a cell line derived from a lung tumor from a KrasG12D;p53-/- (KP) genetically engineered mouse model, treated with SB505124 or TGF-β for 1.5 h


title: TGF-β and RAS jointly unmask primed enhancers to drive metastasis (ChIP-Seq)

overall_design: Chromatin accessibility profiling by high throughput sequencing of 393T3 cells, a cell line derived from a lung tumor from a KrasG12D;p53-/- (KP) genetically engineered mouse model, treated with SB505124 or TGF-β for 1.5 h


title: TGF-β and RAS jointly unmask primed enhancers to drive metastasis (ATAC-Seq)


title: Effects of Myotonic Dystrophy (DM1) models on hepatocyte transcriptomes

city: Urbana

first: Zachary

last: Dewald

state: IL

address: 506 South Mathews Ave

institute: University of Illinois Urbana Champaign

summary: Myotonic Dystrophy (DM1), a common neuromuscular disease, has been shown to have detrimental effects on the livers of patients. To study whether DM1 is directly altering liver function or whether these effects are secondary to DM1 induced functional changes in other tissues, we sequenced the transcriptomes of hepatocytes from liver-specific and whole-body murine models of DM1. We found substantial transcriptomic alteration in the liver-specific model, along with distinguishable physiological changes in the livers of both the liver-specific and whole-body models. This data serves as a survey of transcriptomic alterations in occurring in the livers of DM1 patients.

overall_design: A whole-body model for DM1 was developed by Maurice Swanson (Kanadia et al., 2003) by interrupting the expression of Mbnl1, the key splicing factor thought to be responsible for the effects of DM1 in muscle tissue, globally in FVB mice. We isolated hepatocytes from these Mbnl1 KO mice as well as FVB controls and performed hi-resolution bulk RNA-Seq upon them. Additionally, we developed a liver specific model for DM1 by combining a tissue specific murine model for DM1 developed by Thomas Cooper with a liver specific ApoE promoter. This model works by utilizing the ApoE promoter to drive the expression of a reverse tetracycline trans-activator (rtTA), which when exposed to doxycycline (dox) induces the expression of a toxic, trinucleotide (CUG) repeat RNA responsible for causing DM1. By feeding these mice dox in their diet from birth, we can induce DM1 in the liver specifically. Hepatocytes from these mice as well as mice lacking the DM1 inducing allele (but still fed dox) were isolated and RNA-seq was performed upon them.

first: Dewald

last: Zachary


title: Protein tyrosine phosphatase receptor kappa regulates glycolysis, de novo lipogenesis and promotes hepatocyte metabolic reprogramming in obesity

city: Anderlecht

first: Valerie

last: Vandenbempt

state: Vlaams-Brabant

address: Lenniksebaan 808

country: Belgium

institute: Université Libre de Bruxelles

summary: Metabolic dysfunction within the liver is a major cause of human disease worldwide. Fat accumulation, de novo lipogenesis, and glycolysis are key drivers of hepatocyte reprogramming and the consequent metabolic dysfunction-associated steatotic liver disease (MASLD). The underpinning molecular mechanisms affected by steatosis and inflammation in the obese states remain unknown. Here we report that obesity leads to dysregulated expression of protein-tyrosine phosphatases (PTPs) in the liver. Protein Tyrosine Phosphatase Receptor Kappa (PTPRK) expression was increased in hepatocytes during steatosis and inflammation in humans and mice, and positively correlates with PPARγ-induced lipogenic signalling. Supporting this, PTPRK knockout mice displayed reduced fat accumulation in adipose tissue and liver after exposure to an obesogenic diet. Phosphoproteomic analysis in primary hepatocytes and hepatic metabolomics identified specific phosphotyrosine residues in fructose-1,6 bisphosphatase-1 and glycolysis regulation as targets of PTPRK. The changes in glycolysis and de novo lipogenesis revealed PTPRK was a driving force for metabolic reprogramming in hepatocytes. Moreover, hepatoma cell lines showed reduced colony-forming ability after PTPRK silencing in vitro, and PTPRK knockout mice developed smaller tumours after diethylnitrosamine-induced hepatocarcinogenesis in vivo. Through computational modelling, we identified selective PTPRK inhibitors. These compounds decreased glycolytic rates in hepatoma cell lines, PPARγ expression in primary hepatocytes and steatosis in obese mice. In conclusion, our study defines a novel mechanism for the development of MASLD, revealing a key role of PTPRK on hepatic glycolysis regulation with implications in lipid metabolism, and liver tumour development. We propose PTPRK as a potential target for metabolic liver dysfunction, and the identified inhibitors may represent promising candidates for therapy in obesity-associated liver diseases.

overall_design: Bulk RNA-Seq of mouse livers with low and high fat for wild type and PTPRK knockout mice.

first: Eduardo

last: Gilglioni

first: Ao

last: Li

first: Wadsen

last: St-Pierre-Wijckmans

first: Tzu-Keng

last: Shen

first: Israel

last: Pérez-Chávez

first: Garnik

last: Hovhannisyan

first: Michela

last: Lisjak

first: Javier

last: Negueruela

first: Julia

last: Bauzá-Martinez

first: Jose

middle: M

last: Herranz

first: Daria

last: Ezerina

first: Stephane

last: Demine

first: Zheng

last: Feng

first: Thibaut

last: Vignane

first: Lukas

last: Otero

first: Flavia

last: Lambertucci

first: Alena

last: Prašnická

first: Jacques

last: Devière

first: David

middle: C

last: Hay

last: Encinar

first: Sumeet

last: Singh

first: Joris

last: Messens

first: Milos

last: Filipovic

first: Hayley

last: Sharpe

first: Eric

last: Trépo

first: Wei

last: Wu

first: Esteban

last: Gurzov


title: BMP9 and BMP10 coordinate liver cellular crosstalk to maintain liver health

city: Beijing

first: Huan

last: Wang

address: 38 Life Science Park Road

institute: National Center for Protein Sciences, Beijing

summary: The liver is a largest solid organ in the body and is majorly composed of HCs, ECs, KCs, and HSCs, which spatially interact and cooperate each other to maintain liver homeostasis. However, the complexity and molecular mechanisms underlying the crosstalk between these different cell types remain to be revealed. Here, we generated mice with conditional deletion of Bmp9/10 in different liver cell types and demonstrated that HSCs was the major source of BMP9 and BMP10 in the liver. Using transgenic ALK1 (receptor for BMP9/10) reporter mice, we found that ALK1 is expressed on KCs and ECs other than HCs and HSCs. KCs from Bmp9/10HSC-KO (conditional deletion of Bmp9/10 from HSCs) mice lost their signature genes expression, such as ID1/3, CLEC4F, VSIG4 and CLEC2, and were replaced by monocyte-derived macrophages. ECs from Bmp9/10HSC-KO mice also lost their identity and were transdifferentiated to continuous ECs, ultimately leading to collagen IV deposition and liver fibrosis. Hepatic ECs expressed several angiocrine factors, such as BMP2, BMP6, Wnt2 and Rspo3, to regulate liver iron metabolism and metabolic zonation. We found that these angiocrine factors were significantly decreased in ECs from Bmp9/10HSC-KO mice, which further resulted in liver iron overload and disruption of HCs zonation. In addition, focal fatty liver spontaneously occurred in Bmp9/10HSC-KO mice at the age of 28W. In summary, we demonstrated that HSCs play a central role in mediating liver cell-cell crosstalk via production of BMP9/10 to maintain liver health.

overall_design:
To investigate how BMP9/10 affected  liver macrophages and endothelial cells, we performed bulk RNA-seq analysis of sorted liver macrophages and endothelial cell from Bmp9/10HSC-KO and their control mice.
To investigate how Smad4 affected  liver macrophages, we performed bulk RNA-seq analysis of sorted liver macrophages from Smad4 cKO mice and their control mice.
To investigate how livers were affected in  Bmp9/10HSC-KO mice, we performed bulk RNA-seq analysis of liver tissues from Bmp9/10HSC-KO and their control mice.

first: Dianyuan

last: Zhao

first: Li

last: Tang


title: Decoding the Epigenetics and Chromatin Loop Dynamics of Androgen Receptor-Mediated Transcription

first: Nathan

middle: A

last: Lack

overall_design: Refer to individual Series

first: Umut Berkay

last: Altintas


title: Enhancer reprogramming underlies therapeutic utility of a SMARCA2 degrader in SMARCA4 mutant cancer

first: Carl

last: Gay


title: Modulation of activated T cells by transient EZH2 inhibition [ChIP-Seq]

city: La Jolla

first: Jaroslav

last: Zak

state: CA

address: 10550 North Torrey Pines Rd

department: Immunology and Microbiology

institute: The Scripps Research Institute

summary: The histone methyltransferase enhancer of zeste homolog 2 (EZH2)-mediated epigenetic regulation of T cell differentiation in acute infection has been extensively investigated. However, the role of EZH2 in T cell exhaustion remains under-explored. Here, using in vitro exhaustion models, we demonstrate that transient inhibition of EZH2 in T cells prior to the phenotypic onset of exhaustion with a clinically approved inhibitor, Tazemetostat, delays their dysfunctional progression and preserves T cell stemness and polyfunctionality while having no negative impact on cell proliferation. Tazemetostat induces T-cell epigenetic reprogramming and increases the expression of the self-renewal T cell transcription factor TCF1 by reducing its promoter H3K27 methylation preferentially in rapidly dividing T cells. Transcriptomic profiling revealed a cell division-dependent upregulation of genes associated with thymocytes, memory and effector T cell subsets. Mapping of EZH2-associated genomic regions by ChIP-seq showed an enrichment of promoters among H2K27me3 loci reduced in abundance by tazemetostat, including those genes upregulated in taz-treated T cells.

overall_design: In brief, cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Clariostar (BMG Labtech). Extrapolation to the original chromatin volume allowed determination of the total chromatin yield.    An aliquot of chromatin (40 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of antibody against H3K27me3 (Active Motif, 39155, Lot 11822023). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.

first: Peng

first: Yingqin

last: Hou

first: Yujie

last: Shi


title: Modulation of activated T cells by transient EZH2 inhibition [RNA-Seq]

overall_design: OT-I splenocytes were activated with OVA257-264 (SIINFEKL, 500 nM) with 60 IU/mL of IL-2 for three days to obtain CD8+ T cells. The cells were further cultured with or without 1 µM Taz for 24 or 48 h before they are harvested for RNA extraction with the Arcturus™ PicoPure™ RNA Isolation Kit (KIT0204, ThermoFisher Scientific). Traces of genomic DNA were removed using RNase-Free DNase Set (79254, QIAGEN) following the on-column digesting protocol of the RNA isolation kit. Library construction and RNAseq data acquisition was done by the Novogene Corporation (Sacramento, CA) using Illumina HiSeq platform and PE150 strategy.


title: Transcriptomic changes in signaling using NCI-H358 cells treated with a KRAS G12C or a SOS1::KRASi inhibitor

status: Public on Sep 25 2024

city: Vienna

first: Malgorzata

middle: Emilia

last: Kamuda

address: Dr.Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer-Ingelheim

summary: Assessing global transcriptomic changes in signaling using RNA-seq.

overall_design: NCI-H358 cells were seeded as 1,000 cell spheroids in Aggrewells and allowed to equilibrate for 48h. Afterwards, cells were treated for either 6h (initial signaling) or 72h (rebound signaling). The respective samples, were treated with different compounds, either as monotherapy or in combination using a KRAS G12C inhibitor (MRTX849) or a SOS1::KRAS inhibitor (BI00923406).

first: Robert

last: Kortum

first: Nancy

last: Sealover

first: Daniel

last: Gerlach


title: Pathogenic Proteotoxicity of Cryptic Splicing is Alleviated by Ubiquitination and ER-Phagy

city: Frankfurt

first: Cristian

last: Prieto-Garcia

address: Theodor-Stern-Kai 7

institute: Institute of Biochemistry II

summary: RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However, the regulatory mechanisms connecting these processes remain poorly understood. Here, we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic 5′ splice sites. Importantly, disruptive cryptic variants evade mRNA surveillance pathways and are translated into misfolded proteins. These spurious isoforms disrupt proteostasis causing cytosolic protein aggregates and ER stress. Proteotoxic exons activate unfolded protein response, causing CHOP-mediated cell death. In response to impaired splicing, eukaryotic cells enhance ubiquitination and ER-phagy to alleviate the pathogenic accumulation of proteotoxic isoforms. Our findings show how cryptic splicing-induced proteotoxicity can be mitigated, and provide insight into the molecular pathogenesis of spliceosome-associated diseases such as retinitis pigmentosa.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT Zebrafish and its morpholino usp39 KD derivarive

first: Vigor

last: Matkovic

first: Thorsten

last: Mosler

first: Congxin

last: Li

first: Jie

last: Liang

first: Felix

last: Haidle

first: Igor

last: Mačinković

first: James

last: Oo

first: Alfredo

last: Cabrera-Orefice

first: Rayene

last: Berkane

first: Fenfen

last: Xu

first: Giulio

last: Giuliani

first: Anne-Claire

last: Jacomin

first: Ines

last: Tomaskovic

first: Marion

last: Basoglu

first: Marina

last: Hoffmann

first: Rajeshwari

last: Rathore

first: Ronay

last: Cetin

first: Doha

last: Boutguetait

first: Süleyman

last: Bozkurt

first: María

last: Hernández Cañás

first: Mario

last: Keller

first: Jonas

last: Busam

first: Varun

middle: J

last: Shah

first: Ilka

last: Wittig

first: Manuel

last: Kaulich

first: Petra

last: Beli

first: Wojciech

last: Galej

first: Ingo

last: Ebersberger

first: Likun

first: Christian

last: Münch

first: Alexandra

last: Stolz

first: Ralf

last: Brandes

first: William

middle: K

last: Tse

first: Stefan

last: Legewie

last: Eimar

first: Kathi

last: Zarnack

first: Michaela

last: Müller-McNicoll

first: Ivan

last: Dikic


title: Fth1-mScarlet reports monocyte state during lipopolysaccharide-induced lung inflammation

city: Pittsburgh

first: Rachel

last: Gottschalk

state: PA

address: 5051 Centre Ave.

department: Immunology

institute: University of Pittsburgh

summary: Monocytes and macrophages are central to host defense but also contribute to inflammation-associated pathology. Efforts to manipulate monocyte and macrophage function are limited by our ability to effectively quantify the functional programs of these cells. We identified the gene Fth1, which encodes the Ferritin heavy chain, as highly predictive of alveolar macrophage transcriptomic states during LPS-induced lung inflammation and developed a novel Fth1-mScarlet reporter mouse. In the steady state lung, high Fth1-mScarlet expression is restricted to alveolar macrophages. In response to LPS-induced lung inflammation, Fth1 reporter activity is robustly increased in monocytes, with its expression reporting genes that are differentially expressed in monocytes versus macrophages. Consistent with this reporter associated gene profile, within the Lyz2-GFP+CD11b+Ly6C+ gate the highest Fth1 reporter expression was observed CD11c+ cells, indicative of monocyte-to-macrophage differentiation. While Fth1-mScarlet was induced in monocytes responding to either TLR4 ligation or M-CSF induced macrophage differentiation in vitro, TLR4-dependent expression occurred with greater speed and magnitude. Considering this, we suggest that Fth1-mScarlet expression reports monocyte-to-macrophage differentiation, with increased expression in pro-inflammatory states. Dissecting macrophage differentiation from inflammatory programs will be enhanced when combining Fth1-mScarlet with other reporter systems. Thus, the Fth1-mScarlet model addresses an important lack of tools to report the diverse spectrum of monocyte and macrophage states in vivo.

overall_design:
LPS (20 μg in 50 μl; E. coli 0111:B4 from InvivoGen) was instilled directly into the tracheas of Fth1-mScarlet x Lyz2GFP mice sedated with isoflurane. Three days later, mice were sacrificed using CO2 euthanasia.
Lungs were cut into 1-mm3-sized pieces and digested in DMEM containing Liberase TM (10 mg/ml) and deoxyribonuclease I (10 U/ml) in a shaker for 30 minutes at 37°C. Lungs were then further dissociated using a gentleMACS Dissociator (Miltenyi Biotec) and red blood cells were lysed with ACK Lysing Buffer (Lonza).
Lung homogenate was stained and sorted for Lyz2GFP+CD11b+Ly6C+Ly6G- cells gated on low versus high Fth1-mScarlet expression, as well as low Fth1-mScarlet cells from untreated mice. These samples were submitted for RNA-seq analysis.

first: Brandon

last: Michalides

first: Karsen

last: Shoger

first: Sonia

last: Kruszelnicki

first: Neha

last: Cheemalavagu

first: Anamarie

last: Martinez-Turak

first: Morgan

last: Jackson-Strong

first: Colin

last: Laughlin

first: Omkar

last: Betsur

first: Devon

last: Colby

first: Marlies

last: Meisel

first: Sebastien

last: Gingras


title: Modulation of activated T cells by transient EZH2 inhibition

first: Jaroslav

last: Zak


title: Beta cell-specific PAK1 enrichment ameliorates diet-induced glucose intolerance by promoting insulin biogenesis and minimizing beta cell apoptosis [RNA-Seq]

city: Duarte

first: Debbie

last: Thurmond

address: City of Hope Beckman Research Institue

department: Molecular and Cellular Endocrinology

institute: City of Hope

summary: Aims/ hypothesis: p21 (Cdc42/Rac1) activated Kinase 1 (PAK1) is depleted in type 2 diabetic human islets compared to non-diabetic (ND) human islets, and acute PAK1 restoration to type 2 diabetic human islets can restore insulin secretory function ex vivo. We hypothesized that beta cell specific PAK1 enrichment in vivo carries the capacity to mitigate high-fat diet-induced glucose intolerance by increasing the functional beta cell mass. Methods: Type 2 diabetic or ND human islets expressing exogenous PAK1 specifically in beta cells were used for bulk RNA-sequencing (RNA-seq). Human EndoC-

overall_design:
Type 2 diabetic or ND human islets expressing exogenous PAK1 specifically in beta cells were used for bulk RNA-sequencing (RNA-seq), to investigate differential gene expression.
Islets from ND and type 2 diabetes human donors were transduced at 100 MOI with Ad-RIP Ctrl or Ad-RIP-hPAK1 for 1 hr at 37 degrees C. Transduced islets were then washed twice and incubated for 48 hrs in CMRL medium.

first: Miwon

last: Ahn

first: Sangeeta

last: Dhawan

first: Erika

last: McCown

first: Pablo

last: Garcia

first: Supriyo

last: Bhattacharya

first: Roland

last: Stein


title: Transcriptome analysis of hepatocellular carcinoma and adjacent non-tumor liver tissues [II]

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: To study its expression and regulatory functions in hepatocellular carcinoma (HCC) progression, whole transcriptome RNA sequencing in paired HCC tumor and adjacent non-tumor liver tissue samples from 3 local Hispanic patients was performed.

overall_design: Three tumor-normal pairs of HCC samples were profiled using high-throughput RNA sequencing techniques and their relative gene expression levels were compared.

first: Lu-Zhe

last: Sun

first: Francisco

last: Cigarroa

first: Hakim

last: Bouamar

first: Zhao

last: Lai


title: Shivering improves metabolic health in adults with overweight or obesity

status: Public on Sep 24 2024

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Mild cold acclimation increases insulin sensitivity and previous studies indicate that some level of muscle contraction is essential for provoking this effect. Here, 15 adults with overweight or obesity, the majority of which had impaired glucose tolerance (n=9), were intermittently cold exposed for 10 consecutive days to induce 1 hour of shivering per day. Cold acclimation with shivering improved oral glucose tolerance, blood pressure, fasting glucose, triglyceride, and non-esterified free-fatty acid concentrations, and may thus represent a novel lifestyle approach for the prevention and treatment of obesity-related metabolic disorders.

overall_design: Skeletal muscle biopsies were obtained from the m. vastus lateralis from participants before (baseline) and after cold acclimation (10 days, 1 hour of shivering per day), and subjected to gene expression profiling by RNA-sequencing.

first: Adam

last: Sellers

first: Sten

last: van Beek

first: Rosalie

last: Baak

first: Sander

last: Kersten

first: Joris

last: Hoeks

first: Wouter

middle: D

last: van Marken Lichtenbelt


title: Protein O-GlcNAcylation coupled to Hippo signaling drives vascular dysfunction in diabetic retinopathy [9A]

city: Tianjin

first: Yi

last: Lei

address: Qixiangtai street NO.22

institute: Tianjin Medical University General Hospital

summary: Metabolic disorder is emerging as a crucial contributor to the pathogenesis of diabetic vascular complications including diabetic retinopathy (DR), the leading cause of blindness in the working-age population. Yet, the underlying molecular mechanisms of how the disturbed metabolic homeostasis contribute to vascular dysfunction in DR remain elusive. O-GlcNAcylation modification act as a nutrient sensor particularly sensitive to ambient glucose. Here, we observed pronounced O-GlcNAc elevation in retina endothelial cells (ECs) of DR patients and mouse models. Endothelial-specific depletion or pharmacological inhibition of O-GlcNAc transferase efficiently mitigated vascular dysfunctions. Mechanistically, we found that YAP/TAZ, key effectors of the Hippo pathway, are O-GlcNAcylated in DR. We identified Thr383 as an O-GlcNAc site on YAP, which inhibits its phosphorylation at Ser397, leading to its stabilization and activation. Consequently, highly activated YAP/TAZ, promotes vascular dysfunction by inducing a pro-angiogenic and glucose metabolic transcriptional program. These findings emphasize the critical role of O-GlcNAc-Hippo axis in DR pathogenesis and suggest its unique potential as a therapeutic target.

overall_design: To investigate the downstream effects of YAP/TAZ on regulating DR, we profiled transcriptome from siYAP/TAZ or siCtrl transfected HRCECs cultured in high (25 mM) glucose medium.


title: Single Nucleus DNA Sequencing of Flow Sorted Archived Frozen and Formalin Fixed Paraffin Embedded Solid Tumors

city: Scottsdale

first: Michael

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

summary: We applied DNA content based flow cytometry methods to interrogate the genomes of clinical samples from 8 patients with ovarian cancer. These included 6 high grade serous ovarian carcinomas, a low grade serous carcinoma, and an endometriod carcinoma. Archived samples obtained from surgical resections from a University of California San Francisco (UCSF) tissue bank. Notably for this study we distinguished and sorted diploid and aneuploid tumors. We then profiled the the whole genome copy number for each sample. These data were used to provide standards for single cell analyses of the same tissues including FFPE samples.

overall_design: We applied DNA content based flow sorting to isolate the nuclei of clonal populations from ovarian carcinoma biopsies. We coupled this strategy with oligonucleotide array CGH (aCGH) thereby obtaining high definition genomic profiles of clonal populations from each tumor.

first: Yumei

last: Zhou

first: Xianfeng

first: Jocelyn

last: Chapman


title: Role of transglutaminase 2 in promoting biglycan synthesis in idiopathic gingival fibromatosis

city: Sendai

first: Shigeki

last: Suzuki

state: Miyagi

address: 4-1, Seiryo-machi, Aoba-ku

institute: Tohoku University Graduate School of Den

summary: The mechanism of idiopathic gingival fibromatosis is still unclear. To provide new insights into the molecular and cellular differences between idiopathic gingival fibromatosis and periodontitis, we first identified the gene TGM2, which is differentially expressed between the two. We found that the expression of TGM2 is predominantly lower in idiopathic gingival fibromatosis than in periodontitis, and that the activity of SP1 due to the decreased expression of TGM2 promotes the generation of extracellular matrix-related genes in idiopathic gingival fibromatosis. We have identified biglycan, an extracellular matrix that is specifically upregulated in idiopathic gingival fibromatosis, and highlight the effects of SP1 and TGM2 on biglycan expression.

overall_design: Gingival fibroblasts were established from gingiva isolated from patients with idiopathic gingival fibromatosis and periodontitis.Using data obtained from gingival fibroblasts from two patients with idiopathic gingival fibromatosis and one patient with periodontitis, expression variation was analyzed by GO analysis and volcano plots.

first: Yurika

last: Ninomiya

first: Shinji

last: Matsuda

first: Shizu

last: Hirata-Tsuchiya


title: Integrative 3D Genomics with Multi-Omics Analysis and Functional Validation of Genetic Regulatory Mechanisms of Abdominal Fat Deposition in Chickens (ATAC-seq).

city: Harbin

first: Linyong

last: Shen

state: Heilongjiang

address: No.600, Changjiang Road, Xiangfang District

institute: Northeast Agricultural University

summary: Chickens are the most abundant agricultural animals globally, with controlling abdominal fat deposition (AFD) being a key objective in poultry breeding. While GWAS can identify genetic variants associated with AFD traits, the precise roles and mechanisms of these variants remain largely unclear. This study used two distinct chicken lines, selectively bred for differing AFD, as experimental models. Through the integration of genomic, epigenomic, 3D genomic, and transcriptomic data, a comprehensive chromatin 3D regulatory network map was developed to reveal the genetic regulatory mechanisms that influence AFD traits.

overall_design: Abdominal fat tissue from six randomly selected NEAUHLF individuals (three from each line) from the initial pool of 330 chickens underwent ATAC-seq sequencing by Frasergen, (Wuhan, China).


title: Beta cell-specific PAK1 enrichment ameliorates diet-induced glucose intolerance by promoting insulin biogenesis and minimizing beta cell apoptosis

first: Debbie

last: Thurmond

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


title: Exposure to benzyl butyl phthalate (BBP) leads to increased double-strand break formation and germline dysfunction in Caenorhabditis elegans

city: Boston

first: Shannan

last: Ho Sui

address: 401 Park Drive

institute: Harvard

summary: Endocrine disrupting chemicals (EDCs) have been linked to various health problems including effects on reproductive health. Benzyl butyl phthalate (BBP) is a commonly used plasticizer found in many consumer products that has been shown to act as an EDC and affect human reproduction and development. However, how it might impact the germline and affect the specialized cell division program of meiosis, which results in the formation of haploid gametes (i.e. eggs and sperm), remained unclear. Here, using the nematode C. elegans, we show that BBP exposure at levels within the range of what is detected in humans, impairs accurate chromosome segregation which can result in aneuploidy. Similar to mammals, BBP exposure in C. elegans results in a non-monotonic dose response, whereby lower doses result in the strongest effects, and BBP is efficiently metabolized, underscoring the use of this model system for gaining mechanistic insights into how this EDC impacts the germline. BBP results in increased levels of DNA double-strand breaks (DSBs), activation of a DNA damage checkpoint, and altered chromosome morphology in exposed germlines. We propose that BBP exposure alters gene expression and results in increased oxidative stress, resulting in increased DSBs, thereby compromising chromosome morphology and accurate segregation.

overall_design: Following 24-hour exposure to either 0.1% DMSO alone or BBP dissolved in DMSO, 1,200 worms per condition were washed five times with M9, then collected in 500 μl of Trizol (Invitrogen) for RNA extraction, and frozen at -80°C. There were four biological replicates per treatment. RNA purification was performed using the Direct-zol RNA Miniprep Plus kit (Zymo Research) following manufacturer’s instructions. RNA concentrations, as well as the 260/280 and 260/230 ratios, were assessed using a Nanodrop (Thermo Fisher Scientific). The RNA was prepared for sequencing with the Kapa mRNA HyperPrep kit (Roche) and sequenced on a NovaSeq 6000 using an SP 2x50bp run (Illumina) by the Bauer Core Facility at Harvard University.


title: Integrative 3D Genomics with Multi-Omics Analysis and Functional Validation of Genetic Regulatory Mechanisms of Abdominal Fat Deposition in Chickens  (Hi-C).

overall_design: Abdominal fat tissue from six randomly selected NEAUHLF individuals (three from each line) from the initial pool chickens underwent Hi-C


title: Remodeling of Il4-Il13-Il5 locus underlies selective gene expression

city: Bethesda

first: Hiroyuki

last: Nagashima

address: 10 Center Dr, Room 13C120

institute: NIH


title: Expansion effect of romiplostim on hematopoietic stem and progenitor cells versus other thrombopoietin receptor agonists

city: Machida

first: Naoki

last: Onoda

state: Tokyo

address: 3-6-6, Asahi-machi

institute: Kyowa Kirin Co., Ltd.

summary: Romiplostim, a thrombopoietin (TPO) receptor agonist, is a clinically approved drug that is clearly effective in reconstituting hematopoiesis in refractory aplastic anemia and　idiopathic thrombocytopenic purpura. However, the mechanism underlying its biological effect is unknown, and its difference with other TPO receptor agonists remains unclear. Therefore, we determined the in vitro expansion effect of romiplostim on human CD34+ hematopoietic stem and progenitor cells (HSPCs) versus recombinant human TPO (rhTPO) and another clinically available drug eltrombopag. We also performed single-cell RNA-seq to define the effect of romiplostim on CD34+ HSPCs at the molecular level. The maximum expansion effect of romiplostim on total CD34+ cells, CD34+CD38+ progenitor cells, and CD34+CD38− immature cells was comparable to that of rhTPO, but higher than that of eltrombopag, particularly on CD34+CD38− immature cells. Single-cell RNA-seq analysis revealed that both romiplostim and eltrombopag induced signatures driven by rhTPO, but romiplostim induced molecular changes related to RHOA signaling at the most primitive subsets in HSPCs that were partially or not driven by eltrombopag. Additionally, romiplostim lacked the ability to induce TFRC expression observed by eltrombopag. In conclusion, romiplostim expands and affects human HSPCs similar to rhTPO but partially different from eltrombopag in terms of induction of gene expression.

overall_design: Four batches of frozen human cord blood–derived CD34+ cells were thawed and mixed to prepare sufficient amount of cells. TPOR agonists were added to the cells, after which the cells were incubated for 2 days at 37℃ and 5% CO2, and analyzed using scRNA-seq.

first: Yuta

last: Tezuka

first: Tatsuya

last: Morishima

first: Yoshiki

last: Sumitomo

first: Keigo

last: Nishii

first: Hitoshi

last: Takizawa

first: Masayuki

last: Kai


title: Precise genetic control of ATOH1 enhances maturation of regenerated hair cells in mouse utricle

first: Amanda

middle: Joy

last: Kedaigle

address: 1325 Boylston St

department: Systems Biology - Molecular Innovation

institute: Decibel Therapeutics


title: Targeting Lysine Demethylase 5 (KDM5) in Mantle Cell Lymphoma

city: London

first: Findlay

last: Bewicke-Copley

address: John Vane Science Centre, Barts Cancer Institute

country: United Kingdom

institute: Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London

summary: Loss of function mutations in the histone methyltransferase KMT2D are common in lymphomas but difficult to target. We reported targeting KDM5 restores epigenetic balance in germinal centre (GC) lymphomas. Here, we show the KDM5 family are over-expressed in mantle cell lymphoma (MCL). GS716054, a pro-drug, increases H3K4 trimethylation (H3K4me3) and kills MCL cells including TP53 mutated cells via suppression of the MYC pathway. It can overcome ibrutinib resistance and synergises with ibrutinib. These data suggest a possible role for KDM5-inhibitors in advanced MCL.

overall_design: 3 celllines were treated with either control (DMSO) or KDM5 inhibitor (GS716054) and RNAseq was performed after 24 or 72 hours post treatment.

first: Danmei

last: Xu

first: Karina

last: Close

first: Jessica

last: Okosun

first: Robert

middle: P

last: Gale

first: Jane

last: Apperley

first: David

last: Weinstock

first: Jude

last: Fitzgibbon


title: Developmental Timecourse of Mouse Utricles

summary: Vestibular hair cells are mechanoreceptors critical for detecting head position and motion. In mammals, hair cell loss causes vestibular dysfunction as spontaneous regeneration is nearly absent. Constitutive expression of exogenous ATOH1, a hair cell transcription factor, increases regeneration of hair cells, but these cells fail to mature. With the aim of developing an optimized AAV-based ATOH1 gene therapy, we used single-cell RNA-Seq and explored the impact of defined promoters on ATOH1 transgene expression level, timing, effects in distinct cell types, and the maturity of regenerated vestibular hair cells ex vivo and in vivo.

overall_design: Utricles from WT mice were profiled at 14 timepoints from E14.5-P16.

first: Tian

last: Wang

last: Yang

first: Gabriela

last: Pregernig

first: Ryan

last: McCarthy

first: Xudong

last: Wu

first: Lars

last: Becker

first: Ning

last: Pan

first: Kathy

last: So

first: Leon

last: Chen

first: Tyler

last: Gibson

first: Kathryn

last: Ellis

first: Jonathan

last: Sellon

first: Douglas

last: Gobron

first: Monika

last: Kowalczyk

first: Noah

last: Druckenbrod

first: Alan

middle: G

last: Cheng

first: Joseph

last: Burns


title: Protein O-GlcNAcylation coupled to Hippo signaling drives vascular dysfunction in diabetic retinopathy [3A]

first: Yi

last: Lei

overall_design: To determine the mechanism of O-GlcNAcylation in regulating the function of retinal ECs, we profiled transcriptome from PUGNAc or vehicle treated HRCECs. And HRCECs were treated with DMSO or 25 μM PUGNAc for 24 hr, and total RNA was harvested for RNA-seq.


title: In Vivo and Ex Vivo Utricles treated with ATOH1 under different promoters

first: Amanda

last: Kedaigle

overall_design: Gentamicin-damaged utricle explants were transduced with AAV8-CMV-ATOH1, AAV8-GFAP-ATOH1, or AAV8-RLBP1-ATOH1 and then were maintained in culture for 7, 12, or 20 days before being processed for 10X singlecell RNA-Seq. In addition, in vivo utricles and cristae were collected from IDPN-damaged mice treated with AAV8-GFAP-ATOH1-H2B-EGFP (IDPN and GFAP-ATOH1), IDPN damaged mice (IDPN), or naive mice (Control) at 2 weeks and 4 weeks post-treatment (4 weeks and 6 weeks after IDPN administration).

first: Tian

last: Wang

last: Yang


title: Contrasting the development of larval and adult body plans during the evolution of biphasic lifecycles in sea urchins

status: Public on Sep 23 2024

city: DURHAM

first: Alejandro

last: Berrio

state: NC

address: 124 Science Dr

department: Biology

institute: Duke University

summary: Sea urchins are a unique system for studying developmental transistions because of the stark differences between their bilateral larval and pentaradial adult body plans. Here, we use single cell RNA-sequencing to analyze the development of Heliocidaris erythrogramma (He), a sea urchin species with an accelerated, non-feeding mode of larval development. The sequencing time course extends from early embryogenesis to roughly a day before the onset of metamorphosis in He larvae, which is a period that has not been covered by previous datasets. We find that the non-feeding developmental strategy of He is associated with several changes in the specification of larval cell types compared to sea urchins with feeding larvae, such as the loss of a larva-specific skeletal cell population. Furthermore, the development of the larval and adult body plans in sea urchins may utilize largely different sets of regulatory genes. These findings lay the groundwork for extending existing developmental gene regulatory networks to cover additional stages of biphasic lifecycles.

overall_design: 5 scRNA-seq samples capturing 5 time points over 14 hours of a lecithotrophic sea urchin development

first: Brennan

last: McDonald

first: Abdul

last: Massri

first: Maria

last: Byrne

first: David

last: McClay

first: Gregory

last: Wray