title: Single-cell analysis of Tgfbr2-KO pulmonary monocytes and interstitial macrophages

city: Montpellier

first: Qiang

last: BAI

address: 371 Avenue du Doyen Gaston Giraud

institute: PhyMedExp INSERM U1046

summary: Lung interstitial macrophages (IMs) inhabit the lung parenchyma and are thought to contribute to lung immunoregulation and homeostasis. While recent progress has been made about the development, diversity and transcriptional regulation of lung IMs, the microenvironmental signals responsible for their tissue-specific identity remain unidentified. Here we found, in mice, that lung endothelial cell-derived Tgf 1 specifically triggered a core Tgf receptor-dependent lung IM signature in bone marrow-derived monocytes and macrophages (Macs). In vivo, myeloid-specific ablation of Tgf receptor signaling severely impaired monocyte-to-IM development, resulting in the accumulation of perivascular monocytes, decreased IM numbers and a severe loss of IM-intrinsic identity. Of note, monocyte-to-IM development was similarly impaired in the absence of endothelial-specific Tgf 1. Functionally, mice selectively lacking Tgf receptor in IMs exhibited a severe impairment of the lung immunoregulatory environment and prematurely developed lung hyperinflation, increased compliance and decreased elastance, changes classically associated with ageing. Our work identifies a novel endothelial - IM axis involving Tgf 1-Tgf r interactions that shapes IM identity and thereby sustains lung tissue integrity, thus providing foundations for IM-targeted interventions in the context of lung ageing and other chronic inflammatory disorders.

overall_design: Lung CD45.1-CD45.2+Ly6G-SiglecF-CD11b+SSCloCD64+ cells were FACS-sorted from lung single-cell suspensions pooled from 5 chimeric mice established by adoptively transferring CD45.1-CD45.2+ LyzM-Cre Tgfbr2 fl/fl bone marrow (Tgfbr2-KO) or CD45.1-CD45.2+ Tgfbr2 fl/fl bone marrow (control) to irradiated CD45.1+CD45.2+ IM-DTR mice. Cells from each group were then labelled with BioLegend TotalSeq anti-mouse hastags (TotalSeq-B0301 for control group and TotalSeq-B0303 for Tgfbr2-KO group) before being pooled and subjected to library preparation with Chromium Controller and Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (10X Genomics). The two samples were then demultiplexed, separated by barcode and UMI were counted with cellranger (10X Genomics).

first: Wen

last: Peng

last: Bai

first: Joan

last: Abinet

first: Thomas

last: Marichal


title: Identification of Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma. [ChIP-Seq]

status: Public on Mar 06 2025

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

department: Pathology

country: USA

institute: University of Michigan Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: High expression of MYC and its target genes define a subset of germinal center B-cell diffuse large B-cell lymphoma (GCB-DLBCL) associated with poor outcomes. Half of these high-grade cases show chromosomal rearrangements between the MYC locus and heterologous enhancer-bearing loci, while focal deletions of the adjacent non-coding gene PVT1 are enriched in MYC-intact cases. To identify genomic drivers of MYC activation, we used high-throughput CRISPR-interference (CRISPRi) profiling of candidate enhancers in the MYC locus and rearrangement partner loci in GCB-DLBCL cell lines and mantle cell lymphoma (MCL) comparators that lacked common rearrangements between MYC and immunoglobulin (Ig) loci. Rearrangements between MYC and non-Ig loci were associated with unique dependencies on specific enhancer subunits within those partner loci. Notably, fitness dependency on enhancer modules within the BCL6 super-enhancer (BCL6-SE) cluster regulated by a transcription factor complex of MEF2B, POU2F2, and POU2AF1 was higher in cell lines bearing a recurrent MYC::BCL6-SE rearrangement. In contrast, GCB-DLBCL cell lines without MYC rearrangement were highly dependent on a previously uncharacterized 3’ enhancer within the MYC locus itself (GCBME-1), that is regulated in part by the same triad of factors. GCBME-1 is evolutionarily conserved and active in normal germinal center B cells in humans and mice, suggesting a key role in normal germinal center B cell biology. Finally, we show that the PVT1 promoter limits MYC activation by either native or heterologous enhancers and demonstrate that this limitation is bypassed by 3’ rearrangements that remove PVT1 from its position in cis with the rearranged MYC gene.

overall_design:
ChIP-Seq datasets were aligned to hg19
***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

middle: J

first: Aishwarya

last: Gurumurthy

first: Ashwin

last: Iyer


title: MyD88-mediated signaling in intestinal fibroblasts regulates macrophage antimicrobial defense and prevents dysbiosis in the gut II

status: Public on Mar 05 2025

city: Hershey

first: Marina

last: Chulkina

state: Pennsylvania

address: 500 University dr department of medicine

department: Medicine

institute: Penn State Health Medical Center

type: Expression profiling by high throughput sequencing

summary: Fibroblasts that reside in the gut mucosa are among the key regulators of innate immune cells, but their role in the regulation of the defense functions of macrophages remains unknown. MyD88 is suggested to shape fibroblast responses in the intestinal microenvironment. We found that mice lacking MyD88 in fibroblasts showed a decrease in the colonic antimicrobial defense, developing dysbiosis and aggravated DSS-induced colitis. These pathological changes were associated with accumulation of Arginase 1+ macrophages with low antimicrobial defense capability. Mechanistically, production of IL-6 and CCL2 downstream of MyD88 was critically involved in fibroblast-mediated support of macrophage antimicrobial function, and IL-6/CCL2 neutralization resulted in the generation of macrophages with decreased production of antimicrobial peptide cathelicidin and impaired bacterial clearance. Collectively, these findings revealed a critical role of fibroblast-intrinsic MyD88 signaling in regulating macrophage antimicrobial defense under colonic homeostasis, and its disruption results in dysbiosis, predisposing host to the development of intestinal inflammation.

overall_design: Gene expression profiling based on RNA-seq data from enriched colonic mucosal tissue of mice with or without conditional fibroblast-specific MyD88 knockout in DSS colitis.

first: Iryna

middle: V

last: Pinchuk


title: Spatial control of m6A deposition on enhancer and promoter RNAs through co-acetylation of METTL3 and H3K27 on chromatin

city: GuangZhou

first: meijun

last: ye

state: -- Please Select --

address: Room 418, Science and Technology Building, North Campus, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, Guangdong, China.

country: China

institute: SUN YAT-SEN UNIVERSITY

type: Non-coding RNA profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: A hollow fiber membrane-based liver organoid-on-a-chip model for examining drug metabolism and transport

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

summary: Liver-on-a-chip models predictive for both metabolism and transport of drug candidates in humans are lacking. Here, we have established an advanced, bioengineered and animal-free hepatocyte-like millifluidic system based on 3D hollow fiber membranes (HFMs), recombinant human laminin 332 and adult human stem cell-derived organoids. Organoid cells formed polarized and tight monolayers on HFMs, which displayed improved hepatocyte-like maturation over standard organoid cultures in Matrigel from matched donors. mRNA sequencing and immunofluorescence revealed that HFM cultures exhibited the expression of broad panel of phase I and II drug metabolizing enzymes, and of drug transporters. Functionally, in both static conditions and under flow circulation, HFM monolayers metabolized a cocktail of drugs that are targets for most important phase I and II enzymes. In addition, we were able to study disposition of those parental compounds and their metabolites in the basal circulation and apical compartment of the chip. Moreover, we demonstrated that our system can be used to study drug disposition in a modular setting with other PK/ADME-relevant organ systems. In conclusion, we have generated a proof-of-concept liver organoid-on-a-chip model for examining both metabolism and transport of drugs, which can be further developed towards prediction of PK/ADME profiles in humans.

overall_design:
RNA-seq of liver tissue, liver organoids and organoids cultured on 3D hollow fiber membranes

HFM: hollow fiber membrane
EM/DM: expansion and differentiation medium
1-5: donor number
P: passage
D: day

first: Adam

last: Myszczyszyn

first: Anna

last: Münch

first: Vivian

last: Lehmann

first: Theo

last: Sinnige

middle: G

first: Manon

last: Bouwmeester

first: Roos-Anne

last: Samsom

first: Marit

last: Keuper-Navis

middle: K

last: van der Made

first: Sarah

last: Braem

first: Daniel

last: Kogan

first: Hossein

last: Eslami Amirabadi

first: Evita

last: van de Steeg

first: Rosalinde

last: Masereeuw

first: Bart

last: Spee


title: Spatial control of m6A deposition on enhancer and promoter RNAs through co-acetylation of METTL3 and H3K27 on chromatin [CRISPR_screen]

summary: Interaction between the m6A methyltransferase METTL3 and METTL14 is critical for METTL3 to deposit m6A on various types of RNAs. It is still intriguing whether there is spatial control of m6A deposition on different types of RNAs. Here, through genome-wide CRISPR/Cas9 screening based on a bimolecular fluorescence complementation (BIFC) reporter, we find the H3K27ac acetylase p300 and PAK2 inhibit the interaction between METTL3 and METTL14. We further find that p300-catalyzed acetylation of METTL3 specifically occurs on H3K27ac marked chromatin. METTL3 acetylation suppresses the binding of METTL3 on H3K27ac-marked chromatin by inhibiting its interaction with METTL14. Disruptive K-to-R mutations on the three METTL3 acetylation sites promote the m6A of chromatin-associated RNAs transcribed from p300 bound enhancers and promoters marked by H3K27ac and H3K4me1-3 other than those regions marked by H3K36me3 and H3K9me3, resulting in degradation of eRNAs and paRNAs and transcription inhibition of ferroptosis-inhibition related genes. In addition, PAK2 promotes METTL3 acetylation by phosphorylating METTL3. Inhibition of PAK2 promotes the ferroptosis induced by RSL3, ML162, as well as the chemotherapy drug CDDP in a manner that depends on the acetylation of METTL3. Our study reveals a spatial-selective way to specifically regulate the deposition of m6A on enhancer and promoter RNAs.

overall_design: CRISPR sgRNA sequencing was performed on A549 cells expressing the highest and lowest 5% of TETon-BIFC signal.

first: Xiang

last: Huang

first: Jinkai

last: Wang

first: Zhijun

last: Ren

first: Meijun

last: Ye


title: Programmable mRNA Therapeutics for Controlled Epigenomic Modulation of Single and Multiplexed Gene Expression in Diverse Diseases (human data)

status: Public on Mar 04 2025

city: Cambridge

first: Charles

last: O'Donnell

state: MA

address: 140 First Street, Suite 501

institute: Omega Therapeutics

summary: Pathogenic gene dysregulation can be attributed to chromatin state change that pre-transcriptionally regulates expression. Recent breakthroughs elucidating the rules governing this DNA control layer, an epigenetic code, unlock a new modality in precision medicine to target gene dysregulation across myriad diseases. Leveraging these natural mechanisms, we developed a modular platform to design programmable mRNA therapeutics, Epigenomic Controllers (EC), that control gene expression through directed epigenetic change. ECs tune expression levels of one or multiple genes with durable effect of weeks-to-months in vivo following a single dose. We characterized ECs across multiple targets and designed an EC effectively inhibiting the cancer- and inflammatory-disorder-associated multi-gene cluster CXCL1-8. With precision targeting of NF-kB signaling and novel identification of homologous murine surrogates, ECs significantly reduced neutrophil migration in vivo during acute lung inflammation. A platform approach to EC design for epigenomic modulation opens new treatment frontiers for diverse gene targets, including those considered "undruggable."

overall_design: ChIP-seq profiling of Untreated and EC-treated IMR90 cells for P65, H3K9me3, CXCL, and HA at 24 and 48 hours

first: Odonnell

last: Charles


title: Translational profiling reveals novel gene expression changes in the direct and indirect pathways in a mouse model of Levodopa induced dyskinesia

city: Toronto

first: Naomi

middle: P

last: Visanji

state: ON

address: Tanz CRND, 60 Leonard Ave

country: Canada

institute: University of Toronto

summary: Here we employ two transgenic mouse lines, combining translating ribosomal affinity purification (TRAP) with bacterial artificial chromosome expression (Bac), to selectively isolate RNA from either DRD1A expressing striatonigral, or DRD2 expressing striatopallidal medium spiny neurons (MSNs) of the direct and indirect pathways respectively, to study changes in translational gene expression following repeated LDOPA treatment. 195 significantly varying transcripts were identified among the 4 treatment groups. Pathway analysis revealed an overrepresentation of calcium signaling and long-term potentiation in the DRD1A expressing MSNs of the direct pathway, with significant involvement of long-term depression in the DRD2 expressing MSNs of the indirect pathway following chronic treatment with LDOPA. Several MAPK associated genes (NR4A1, GADD45G, STMN1, FOS and DUSP1) differentiated the direct and indirect pathways following both acute and chronic LDOPA treatment. However, the MAPK pathway activator PAK1 was downregulated in the indirect pathway and upregulated in the direct pathway, strongly suggesting a role for PAK1 in regulating the opposing effects of LDOPA on these two pathways in dyskinesia. Future studies will assess the potential of targeting these genes and pathways to prevent the development of LDOPA-induced dyskinesia.

overall_design:
Here we employ two transgenic mouse lines, combining translating ribosomal affinity purification (TRAP) with bacterial artificial chromosome expression (Bac). The striatum was dissected and subject to TRAP. Extracted ribosomal RNA was amplified, purified and gene expression was quantified using microarray.

>>>Submitter states that raw data IDAT files are no longer available for this study<<<

first: N

first: M

last: Ghani


title: Natural killer cells’ functional impairment drives the immune escape of pre-malignant clones in early-stage myelodysplastic syndromes

city: Los Angeles

first: Yiqian

last: Gu

state: CA

address: 5000D Terasaki Life Sciences Building

institute: University of California Los Angeles

summary: Early therapeutic interventions following cancer detection are known to extend patient survival. A key challenge is dissecting preneoplastic disease states' biological mechanisms that precede tumorigenesis to slow down disease progression and/or mitigate disease-related comorbidities.

overall_design: Myelodysplastic syndromes (MDS) cannot be cured by currently available pharmacological therapies, which fail to eradicate aberrant hematopoietic stem cells (HSCs), most of which are mutated by the time of diagnosis. Developing early intervention strategies for MDS patients requires a better understanding of aberrant HSC expansion mechanisms. Here, we sought to elucidate how MDS HSCs evade immune surveillance and expand in patients with clonal cytopenias of undetermined significance (CCUS), the pre-malignant stage of MDS. Using multi-omic single-cell approaches and functional in vitro studies, we showed that immune escape at disease initiation is mainly mediated by mutant, dysfunctional natural killer (NK) cells with impaired cytotoxic capability against cancer cells. Preclinical in-vivo studies demonstrated that NK cells infusion from healthy donors efficiently depleted CCUS mutant cells while allowing normal cells to regenerate hematopoiesis. Our findings suggest that early intervention with adoptive cell therapy can prevent or delay the development of MDS.

first: Simona

last: Colla

first: May

last: Daher

first: Bijender

last: Kumar

first: Abhinav

last: Jain


title: Characterization of dsRNA Binding Proteins through Solubility Analysis Identifies ZNF385A as a dsRNA Homeostasis Regulator

city: Tianjin

last: Jiang

state: Tianjin

address: Weijin Road

institute: Tianjin university

summary: Double-stranded RNA (dsRNA) binding proteins (dsRBPs) play crucial roles in various cellular processes, especially in the innate immune response. Comprehensive characterization of dsRBPs is essential to understand the intricate mechanisms for dsRNA sensing and response. Traditional methods have predominantly relied on affinity purification, favoring the isolation of strong dsRNA binders. Here, we adopted the proteome integral solubility alteration (PISA) workflow for characterizing dsRBPs, resulting in the observation of 18 known dsRBPs and the identification of 200 novel potential dsRBPs. Next, we focused on zinc finger protein 385A (ZNF385A) and discovered that its knockout activated the transcription of interferon-β in the absence of immunogenic stimuli. The knockout of ZNF385A elevated the level of endogenous dsRNAs, especially transcripts associated with retroelements, such as short interspersed nuclear element (SINE), long interspersed nuclear element (LINE), and long terminal repeat (LTR). Moreover, loss of ZNF385A enhanced the bioactivity of 5-Aza-2'-deoxycytidine (5-AZA-CdR) and tumor-killing effect of NK cells. Our findings greatly expand the dsRBP reservoir and contribute to the understanding of cellular dsRNA homeostasis.

overall_design: dsRIP-seq profiling of wild type HeLa cells and ZNF385A knockout cells.


title: Spatial control of m6A deposition on enhancer and promoter RNAs through co-acetylation of METTL3 and H3K27 on chromatin [GLORI]

first: meijun

last: ye

overall_design: Chromatin-associated RNA m6A profiles of METTL3-WT or METTL3-3KR A549 cells were generated by deep sequencing, in diplicate, using SURFSeq 5000 platform on PE100 mode.


title: Liver TET1 promotes metabolic dysfunction-associated steatotic liver disease

city: New Orleans

first: Chiung-Kuei

state: Louisiana

address: 1430 Tulane Ave

department: Department of Pathology and Laboratory Medicine

institute: Tulane University School of Medicine

summary: DNA demethylation is regulated by the TET family proteins, whose enzymatic activity requires 2-oxoglutarate (2-OG) and iron that both are elevated in MASLD. We aimed to investigate liver TET1 in MASLD progression. Depleting TET1 substantially alleviated  MASLD progression. Whole body Knockout of TET1 (TKO) slightly improved diet induced obesity and glucose homeostasis. Intriguingly, hepatic cholesterols, triglycerides, were significantly decreased upon TET1 depletion. Moreover, targeting TET1 with a small molecule inhibitor significantly suppressed MASLD progression. Liver TET1 plays a deleterious role in MASLD, suggesting the potential of targeting TET1 in hepatocytes to suppress MASLD.

overall_design: RNA-seq profiling of WT (C57BL/6J) and its coresponding whole body TET-1 knock out, fed with High fat Diet (HFD) for 16 weeks.

first: Hongze

last: Chen

first: Muhammad Azhar

last: Nisar

first: Joud

last: Mulla

first: Xinjian

last: Li

first: Kevin

last: Cao

first: Katsuya

last: Nagaoka

first: Shang

last: Wu

first: Peng-Sheng

last: Ting

first: Tung-Sung

last: Tseng

first: Hui-Yi

last: Lin

first: Xiao-Ming

last: Yin

first: Wenke

last: Feng

first: Zhijin

first: Zhixiang

last: Cheng

first: William

last: Mueller

first: Amalia

last: Bay

first: Layla

last: Schechner

first: Xuewei

last: Bai


title: EGFR controls transcriptional and metabolic rewiring in KRASG12D colorectal cancer [MRTX1133]

city: Vienna

first: Dana

last: Krauß

address: Borschkegasse 8a

department: Center for Cancer Research

country: Austria

institute: Medical University of Vienna

summary: We used RNA-Seq to profile APCmin, KRASG12D, TP53 murine organoids in the presence and absence of EGFR in combination with control or MRTX1133 (100 nM) treatment.


title: EGFR controls transcriptional and metabolic rewiring in KRASG12D colorectal cancer [WNT_INH]

summary: We used RNA-Seq to profile APCmin, KRASG12D, TP53 murine organoids in the presence and absence of EGFR in combination with control or 2 µM ICG-001 or 3 µM CHIR99021 treatment.


title: EGFR controls transcriptional and metabolic rewiring in KRASG12D colorectal cancer [BPTES]

summary: We used RNA-Seq to profile APCmin, KRASG12D, TP53 murine organoids in the presence and absence of EGFR in combination with control or 10 µM BPTES treatment.


title: EGFR controls transcriptional and metabolic rewiring in KRASG12D colorectal cancer [SMOC2]

summary: We used RNA-Seq to profile APCmin, KRASG12D, TP53 murine organoids in the presence and absence of EGFR and additional deletion of SMOC2.

overall_design: Expression profiling by high throughput sequencing


title: Multidimensional OMICs reveal ARID1A orchestrated control of DNA damage, splicing, and cell cycle in normal and malignant urothelial cells [RNA-seq]

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

summary: Epigenetic regulators, such as the SWI/SNF complex, play an important role in tissue development and homeostasis, and are frequently mutated in cancer. ARID1A, a subunit of the SWI/SNF complex, is mutated in approximately 20% of all bladder tumors, however, our understanding of the consequences thereof remains limited. Here, we generated various loss- and gain-of-function models to conduct Omni-ATAC-Seq, RNA-Seq, interactome analyses, and first functional studies to characterize ARID1A-affected pathways potentially suitable for the treatment of ARID1A-deficient bladder cancers. We observed decreased cell proliferation and deregulation of stress-regulated pathways including DNA repair in ARID1A-deficient cells. Furthermore, ARID1A was linked to alternative splicing and translational regulation on RNA and interactome levels. The absence of ARID1A drastically impacted the accessibility of chromatin, displaying significantly less accessible chromatin especially around distal, but not proximal, enhancers. Less accessible chromatin areas were mapped to pathways such as DNA damage response and cell proliferation. Indeed, the G2/M checkpoint appeared impaired after DNA damage in ARID1A-deficient cells. Together, this highlights the broad impact of ARID1A and the possibility of targeting proliferative and DNA repair pathways.

overall_design: To investigate the impact of ARID1A-deficiency in four bladder cell lines, mRNA-Seq was performed. T24 and UROtsa with and without a CRISPR/Cas9-mediated ARID1A Knockout, HBLAK with or without siRNA against ARID1A, and JMSU-1 (carrying a homozygous ARID1A mutation) were transformed to re-express ARID1A, were tested.

first: Rebecca

middle: M

last: Schloesser

first: Florian

last: Krumbach

first: Eyleen

last: Corrales

first: Christian

last: Preisinger

first: Franziska

last: Liss

first: Melanie

last: Boerries

first: Kerstin

last: Becker

first: Ruth

last: Knüchel-Clarke

first: Stefan

last: Garczyk

first: Bernhard

last: Lüscher


title: Multidimensional OMICs reveal ARID1A orchestrated control of DNA damage, splicing, and cell cycle in normal and malignant urothelial cells [ATAC-seq]

overall_design: To understand more about the deregulation of ARID1A in bladder cancer, generated ARID1A-knockout UROtsa cells were submitted for an Omni-ATAC-Seq and tested against ARID1A-proficient UROtsa (n=5 per group).


title: Multidimensional OMICs reveal ARID1A orchestrated control of DNA damage, splicing, and cell cycle in normal and malignant urothelial cells


title: Single cell RNA sequencing of E0771 Control and Foxm1 knockout xenograft tumors from the mammary fat pad of C57BL6/J mice

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 gain a comprehensive understanding of the alterations in the tumor microenvironment following FOXM1 depletion in breast cancer cells, we employed single-cell RNA sequencing (scRNA-seq) on tumor samples from control and FOXM1 knockout groups.

overall_design: E0771 Control, Foxm1 KO sg1, and Foxm1 KO sg3 tumors were harvested and digested at 37 degrees. Dead cells were removed from the samples before they were counted and loaded onto the 10X Chromium controller, targeting 10,000 cells for capture per well.

first: Nourhan

last: Abdelfattah

first: Santosh

last: Timilsina

first: Manjeet

last: Rao


title: Histone H3 cysteine 110 enhances iron metabolism and modulates replicative life span in Saccharomyces cerevisiae

first: Siavash

last: Kurdistani

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

summary: The discovery of histone H3 copper reductase activity provides a novel metabolic framework for understanding the functions of core histone residues, which, unlike N-terminal residues, have remained largely unexplored. We previously demonstrated that histone H3 cysteine 110 (H3C110) contributes to Cu2+ binding and its reduction to Cu1+. However, this residue is absent in Saccharomyces cerevisiae, raising questions about its evolutionary and functional significance. Here, we report that H3C110 has been lost in many fungal lineages despite near-universal conservation across eukaryotes. Introduction of H3C110 into S. cerevisiae increased intracellular Cu1+ levels and ameliorated the iron homeostasis defects caused by inactivation of the Cup1 metallothionein or glutathione depletion. Enhanced histone copper reductase activity also extended replicative lifespan under oxidative growth conditions but reduced it under fermentative conditions. Our findings suggest that a tradeoff between histone copper reductase activity, iron metabolism, and lifespan may underlie the loss or retention of H3C110 across eukaryotes.

overall_design: mRNA profiles of yeast with the histone H3 A110C mutation and/or cup1F8* or gsh1Δ grown in fermentative or oxidative medium

first: Chen

last: Cheng


title: Total RNAseq from fly heads at different ages - circRNAs are extremely stable in the brain and can serve as age and experience markers [Temp_Stress_circ]

city: Waltham

first: Sebastian

last: Kadener

state: Massachusetts

address: 415 South Street

institute: Brandeis University

summary: Circular RNAs are a large class of stable RNAs generated by backsplicing that accumulate with age in neural tissue. To determine the reason for this accumulation, we profiled circRNAs from fly heads at six timepoints during their lifespan. We found that the global levels of circRNAs increase linearly with age and that circRNAs are excellent age-markers. At the individual level, we found that most circRNAs increase their levels with age, and this increase does not correlate with changes on overall transcription, the levels of the mRNA counterparts, changes in intron retention, or splicing of the host gene, demonstrating that the increase is not due to biogenesis. In addition, a sustained stimulus, like transient exposure to higher or lower temperatures, leads to increases (but no decreases) in the levels of specific circRNAs further demonstrating the stability of these molecules in vivo. This unusually high stability suggests that circRNAs can be used as experience markers. Indeed, flies that were treated for ten days at 29°C display high levels of specific temperature-induced circRNAs even six weeks after being returned to standard conditions. Together, our data demonstrates that circRNAs are extremely stable in vivo and that they can be utilized as stress/life experience markers.

overall_design: CantonS, wild-type, flies were grown at 25C in 12:12 light:dark conditions, allowed to mate for 3 days prior to separating males. Flies were then given a day to recover from CO2 exposure and placed at 18, 25, or 29 °C for 10 days to assess the effect of temperature treatment. Flies were flash frozen in liquid nitrogen just before (pre-treatment sample) or right after the temperature exposures. Samples were collected in triplicates. RNA from the fly brains was extracted using TRIzol reagent (Sigma, T9424) and treated with DNaseI (NEB, M0303L). We used 1 ug of RNA as input for ribodepletion (with a protocol based on Adiconis et al. 2013). Total RNA libraries were prepared with NEXTFLEX Rapid Directional RNA-Seq Kit 2.0 (PerkinElmer) as recommended by the manufacturer. Samples were sequenced by Novogene (Novogene Corporation Inc 8801 Folsom BLVD, Suite 290, Sacramento, CA) with HiSeq-4000.

first: Ken

last: Kirio

first: Ines

last: Patop

first: Ane

last: Martin Anduaga

first: Jenna

last: Harris

first: Nagarjuna

last: Pamudurti

first: Claire

last: Martel


title: Chromothripsis orchestrates leukemic transformation in blast phase MPN through targetable amplification of DYRK1A

city: Oxford

first: Charlotte

last: Brierley

address: University of Oxford, Headley Way

country: United Kingdom

institute: MRC WIMM


title: Deciphering the role of IRF4 and its interacting proteins in differentiated regulatory and T helper 17 cells

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

summary: The transcription factor interferon regulatory factor 4 (IRF4) is crucial for the differentiation and fate determination of pro-inflammatory Th17 and the functionally opposing group of immunomodulatory regulatory T cells.Despite its central role in Th lineage determination, molecular mechanisms of IRF4-mediated gene expression in fully differentiated Th17/Treg cells are still not fully understood. In the present study, we integrated data derived from affinity-purification and full mass spectrometry-based proteome analysis with chromatin immune precipitation sequencing (ChIP-Seq)to unveil IRF4-driven lineage determination in Treg and Th17 cells.This allowed the characterization of IRF4-steered expression of proteins generally involved in the T cell development as well as subtype-specific differentiation and identification of novel, yet uncharted IRF4 interactors. To out knowlede no other study investigated the molecular mechanisms of IRF4-steered gene expression and IRF4 interactions in an unbiased approach, directly comparing fully differentiated T helper 17 and regulatory T cells.

overall_design: Naive CD4+ T cells from splenocytes of IRF4bio (IRF4-Bio.Rosa26BirA) and control (Rosa26BirA) animals were in vitro differentiated into Th17 and Treg cells. IRF4-Bio.Rosa26BirA mice express a fusion protein of IRF4 with a short BirA-recognition site (Avi-Tag, Driegen et al, 2015, PMID: 16201414) and co-express the enzyme BirA, thereby IRF4 gets in vivo biotinylated. Control animals express only the enzyme BirA and have no biotinylated IRF4. After 3 days of cell differentiation with respective cytokines, the cells were harvested and crosslinked with formaldehyde. After cell lysis and sheering of the chromatin, magnetic streptavidin-coated beads (M280 Dynabeads) were added to the lysate and all IRF4-unbound chromatin fragments were washed away. After these extensive washing steps, only sequence-specific IRF4-bound chromatin fragments are eluted and sent for sequencing. As the target protein IRF4 is in vivo biotinylated, the IRF4bio-ChIP approach makes advantage of the strong non-covalent biotin-streptavidin interaction and does not require any IRF4-specific antibodies.

first: Anna

last: Gabele

first: Maximilan

last: Sprang

first: Tobias

last: Bopp

first: Ute

last: Distler


title: High mobility group A1 (HMGA1) promotes esophageal squamous cell carcinoma progression by inhibiting STING-mediated anti-tumor immunity

city: Kaifeng

first: Kaiyue

last: He

state: Henan

address: North section of Jinming Avenue, Longting District, Kaifeng City, Henan Province

institute: Henan University

summary: Esophageal squamous cell carcinoma (ESCC) is a common and aggressive cancer with limited responses to immunotherapy. High mobility group A1 (HMGA1), a chromatin remodeling protein, plays a key role in tumor progression, but its impact on anti-tumor immunity in ESCC remains unclear. Here we show that HMGA1 suppresses the stimulator of interferon genes (STING), inhibiting type I interferon secretion, downregulating interferon-stimulated genes, and impairing tumor-infiltrating lymphocyte (TIL) recruitment. HMGA1 inhibits STING transcription by competing with the coactivator CBP/p300 for binding to CREB. ESCCs from genetically modified mouse models with altered HMGA1 and STING expression exhibit varying TIL levels and sensitivity to STING agonists. Additionally, we design and synthesize a series of HMGA1 inhibitors, including a perylene-based nanoparticle, PDIC-DPC, which effectively inhibits HMGA1 and enhances TIL infiltration. Our findings identify HMGA1 as a critical immune checkpoint in ESCC and suggest that targeting HMGA1 could improve immunotherapy outcomes.

overall_design: To investigate the regulatory effect of HMGA1 on whole genome gene expression, we analyzed the gene expression profiles of KYSE-30 cells which were stable knockdown of HMGA1 by using RNA seq data. The aim of this study is to reveal that HMGA1 affects tumor malignant progression by regulating Innate immunity.


title: EGFR controls transcriptional and metabolic rewiring in KRASG12D colorectal cancer

first: Dana

last: Krauß

summary: We used RNA-Seq to profile APCmin, KRASG12D, TP53 murine organoids in the presence and absence of EGFR.

overall_design: Expression profiling by high throughput sequencing.


title: Chromothripsis orchestrates leukemic transformation in blast phase MPN through targetable amplification of DYRK1A [RNA]

summary: Investigating the impact of chr21 amplification in primary patient Lin-Cd34+ cells

overall_design: RNA-sequencing was performed in 5 primary patient chr21amp cells, 4 non-chr21amp primary patient cells and 5 age-matched controls

first: Giulia

last: Orlando

first: Adam

last: Mead

first: Beth

last: Psaila


title: Molecular fingerprints for bone marrow cells, acute lymphoblastic leukemia [ATAC-seq]

city: Munich

first: Carolin

last: Prexler

address: Kölner Platz 1, Haus 11

department: School of Medicine and Health, Department of Pediatrics

institute: Technical University of Munich, TUM University Hospital

summary: The overall goal of this study was to characterize bone marrow cells based on their transcriptome, epigenome, surface protein expression and BCR-VDJ-profile for accurate identification of clinically relevant cell states. This submission includes B-cell acute lymphoblastic (pre-)leukemia samples from mice. This project has received funding from ERA perMed JTC2018 under the title „Genomics-based tools for personalized treatment to reduce chemotherapy burden in paediatric cancer” (Acronym “GEPARD”)

overall_design: WT control vs. Pre-leukemia and Leukemia; Duplikates

first: Julia

last: Hauer

first: Franziska

last: Auer


title: Blocking the TCA Cycle in Cancer Cells Potentiates CD36+ T-cell-Mediated Antitumor Immunity by Suppressing ER Stress-Associated THBS2 Signaling

city: ATLANTA

first: Teng

last: Yong

state: Georgia

address: 1701 Uppergate Drive

department: Whinship Cancer INST

institute: Emory University

summary: The aim of this study is to investigate the influence of CPI-613 treatment on the transcriptome profile of human head and neck squamous cell carcinoma

overall_design: Investigation of mRNA profiles of CPI-613 treatment in human head and neck squamous cell carcinoma cells.

first: Yong

last: Teng

first: Fanghui

last: Chen

first: Fan

last: Yang


title: B cell convergence to distinct broadly reactive epitopes following vaccination with chimeric influenza virus hemagglutinins

city: New York

first: Patrick

last: Wilson

state: NY

address: 413 E. 69th Street

department: gale and Ira Drukier Institute for Children's Health

institute: Weill Cornell Medicine

summary: In a phase I clinical trial, the chimeric hemagglutinin (cHA) immunogen induced antibody responses against the conserved HA stalk domain. However, the landscape of the B cell specificities and subsets induced by this vaccine remain undetermined. Here, we paired single cell RNA-sequencing and B cell receptor repertoire sequencing to analyze the relationship between transcriptome and B cell specificity following cHA immunization. We show that the cHA inactivated vaccine with a squalene-based adjuvant induced a robust activated B cell and memory B cell phenotype against two broadly neutralizing epitopes of the stalk domain. The overall specificities of the acute plasmablast and memory B cell responses were distinct, with the plasmablast compartment largely targeting non-neutralizing epitopes of the HA stalk. Altogether, these data indicate the B cell landscape following cHA vaccination includes diverse B cell subsets that are differentially induced by distinct vaccine formulations, including memory and de novo B cell responses against diverse broadly conserved epitopes.

overall_design: cH5/1+ MBCs (CD19+CD27+HA+) from cHA vaccine recipients were sort purified for analysis of transcriptome and V(D)J gene usage

first: Jenna

last: Guthmiller

first: Linda

last: Lan

first: Lei

last: Li


title: Transcriptional profiling of microglia lacking Smad2/3

city: Rancagua

first: Nicolas

last: Santander

address: Libertador Bernardo O'Higgins 611

country: Chile

institute: Universidad de O´Higgins

summary: Smad2/3 are canonical effector of TGFb signaling. This pathway is essential for microglial differentiation. We isolated Smad2/3-deficient microglia from mice and determined their transcriptional profiles. By comparing to control microglia, we observed changes in the expression of genes involved in macrophage function and lipid metabolism, which is consistent with the importance of these processes in microglial homeostasis. since microglia lacking Smad2/3 show an activated phenotype, these results provide insights into the transcriptional regulation of microglial function.

overall_design: We FACS-sorted microglia from brains of 4 mice lacking Smad2/3 in microglia and 4 wild-type littermates at P60.

first: Carlos

last: Lizama

first: Thomas

last: Arnold


title: EGFR controls transcriptional and metabolic rewiring in KRASG12D colorectal cancer [scRNA]

first: Dana

last: Krauß

summary: We used scRNA-Seq to profile APCmin, KRASG12D, TP53 murine organoids in the presence and absence of EGFR.

overall_design: Expression profiling by high single-cell throughput sequencing.


title: Characterization of a novel zebrafish model of MTMR5-associated Charcot-Marie-Tooth disease type 4B3

status: Public on Mar 03 2025

first: Jordan

last: Lindzon

state: Ontario

address: 686 Bay St.

department: Genetics & Genome Biology

institute: Peter Gilgan Centre for Research and Learning

summary: Biallelic loss of expression/function variants in MTMR5/SBF1 cause the inherited peripheral neuropathy Charcot-Marie-Tooth (CMT) Type 4B3. There is an incomplete understanding of the disease pathomechanism(s) underlying CMT4B3, and despite its severe clinical presentation, currently no disease modifying therapies. A key barrier to the study of CMT4B3 is the lack of pre-clinical models that recapitulate the clinical and pathologic features of the disease. To address this barrier, we generated a zebrafish CRISPR/Cas9 mutant line with a full gene deletion of mtmr5. Resulting homozygous deletion zebrafish are born at normal Mendelian ratios and have preserved motor function. However, starting by 10 days-post-fertilization, mutant zebrafish develop obvious morphometric changes in head size and brain volume. These changes are accompanied at the pathological level by abnormal axon outgrowths and by the presence of dysmyelination, changes reminiscent of the nerve pathology in human CMT4B3. Importantly, RNA sequencing from brain-enriched samples identifies novel disease pathways including transcriptional changes in genes responsible for neurogenesis, chromatin remodeling/organization, and synaptic membrane homeostasis. Overall, our mtmr5 knockout zebrafish mirror genetic, clinical, and pathologic features of human CMT4B3. As such, it represents a first pre-clinical model to phenocopy the disease, and an ideal tool for future studies on disease pathomechanism(s) and therapy development.

overall_design: Bulk RNA-sequencing of 7 days-post-fertilization mtmr5-knockout and wild-type brain-enriched zebrafish samples. Four biological replicates were included from different breeding pairs over time.

first: Maia

last: List

first: Salma

last: Geissah

first: Atai

last: Ariaz

first: Mo

last: Zhao

first: James

last: Dowling


title: Analysis of amygdala astrocytes as a function of stress and fear

city: Boston

first: Michael

last: Wheeler

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

summary: Neuroimmune interactions—signals transmitted between immune and brain cells—regulate many aspects of tissue physiology including responses to psychological stress, which can predispose individuals to develop neuropsychiatric diseases. Still, the interactions between hematopoietic and brain-resident cells that influence complex behaviors are poorly understood. Here, we used a combination of genomic and behavioral screens to demonstrate that astrocytes in the amygdala limit stress-induced fear behavior through EGFR. Mechanistically, amygdala astrocyte EGFR expression inhibits a stress-induced pro-inflammatory signal transduction cascade that facilitates neuro-glial cross-talk and stress-induced fear behavior through the orphan nuclear receptor NR2F2 in amygdala neurons. We uncovered that, in turn, decreased EGFR signaling and fear behavior were associated with meningeal monocyte recruitment during chronic stress. This set of neuroimmune interactions was therapeutically targetable by psychedelic administration, which reversed monocyte accumulation in the brain meninges along with fear behavior. Together with validation in clinical samples, these data suggest that psychedelics can be used to target neuroimmune interactions relevant to neuropsychiatric disorders and potentially other inflammatory diseases.

overall_design:
To investigate the transcriptional responses of astrocytes to chronic stress and fear, we performed bulk RNA-sequencing on astrocytes from the amygdala of mice exposed or not to chronic stress with or without fear conditioning/extinction
We performed gene expression profiling analysis using data obtained from RNA-seq of astrocytes (n=5 per group) from the amygdala of mice exposed or not to chronic stress with or without fear conditioining and extinction

middle: A

first: Elizabeth

middle: N

last: Chung

first: Jinsu

last: Lee


title: Bacterial immunotherapy leveraging IL-10R hysteresis for both phagocytosis evasion and tumor immunity revitalization [RNA-seq]

city: shenzhen

first: zhiguang

last: chang

address: No. 1068, Xueyuan Avenue, Shenzhen University Town, Xili, Nanshan District

department: Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology

institute: Chinese Academy of Sciences

summary: Bacterial immunotherapy holds promising cancer-fighting potential. However, unlocking its power requires a mechanistic understanding of how bacteria both evade antimicrobial immune defenses and stimulate antitumor immune responses within the tumor microenvironment (TME). Here, by harnessing an engineered Salmonella enterica strain with this dual proficiency, we unveiled a singular mechanism underlying. Specifically, the hysteretic nonlinearity of interleukin-10 receptor (IL-10R) expression drives tumor-infiltrated immune cells into a tumor-specific IL-10Rhi state. Bacteria leverage this to enhance tumor-associated macrophages producing IL-10, evade phagocytosis by tumor-associated neutrophils, and coincidently expand and stimulate the preexisting exhausted tumor-resident CD8+ T cells. This effective combination eliminated tumors, prevented recurrence, and inhibited metastasis across multiple tumor types. Analysis of human samples suggested that IL-10Rhi state might be a ubiquitous trait across human tumor types. Our study unveils the unsolved mechanism behind bacterial immunotherapy's dual challenge in solid tumors and provides a framework for intratumor immunomodulation.

overall_design: Workflow for isolating and treating primary CD8 T cells from mouse spleens. Briefly, isolated CD8+ T cells were stimulated with anti-mouse CD3ε and CD28 antibodies for 12 h, followed by antibody removal and washing. Cells were divided into four groups: Pre-exposure (direct sample collection), Initial exposure (stimulated with 10 ng/ml IL-10 for 6 h), Rest (stimulated with 10 ng/ml IL-10 for 6 h, washed, and cultured for 48 h in 0.5 ng/ml IL-10 with medium changes every 12 h), and Subsequent exposure (same as Rest, with an additional 6-h stimulation with 10 ng/ml IL-10)

first: Zhiguang

last: Chang

first: Xuan

last: Guo

first: Xuefei

first: Yan

last: Wang

first: Zhongsheng

last: Zang

first: Yichuan

last: Xiao

first: Chenli

last: Liu


title: Mandibular monocytes have enhanced osteoclast differentiation and differentially regulated gene expression compared to femur derived monocytes

city: Minneapolis

first: Kim

last: Mansky

state: MN

address: 515 Delaware St SE

institute: University of Minnesota

summary: To determine if there are differences between osteoclasts from the mandible and femur of 1-year-old mice we evaluated gene expression and differentiation potential of osteoclast precursors. Osteoclasts from the mandible of 1-year-old mice were larger in size compared to those in the femur, but significantly less in number. The differentially regulated genes with increased expression in the mandible are associated with osteoclast lineage commitment, proliferation, and inflammation; similar to those in the 2-month old mice. Bulk RNA sequencing demonstrated that the mandible had more upregulated genes compared to the femur, and the pathways enriched in the mandible were distinct from those in the femur. Changes in osteoclast precursors due to again may be regulated by different mechanisms in the craniofacial and appendicular regions of the skeleton.

overall_design: Bulk RNA-SEQ of femur and mandible derived monocytes from 1 year old C57BL/6 mice

first: Juan E.

last: Abrahante Llorens

first: Emilyn

last: Aisnas

first: Rachel

last: Clark

first: Amy

last: Tasca

first: Jaydn

last: Nelson


title: Analysis of amygdala astrocytes following monocyte adoptive transfer during stress

first: Michael

overall_design:
To investigate the transcriptional responses of astrocytes to monocyte adoptive transfer, we performed bulk RNA-sequencing on astrocytes from the amygdala of mice exposed to a combination of 7-day restraint stress that and transferred intravenously with vehicle or monocytes for 7 days.
We performed gene expression profiling analysis using data obtained from RNA-seq of astrocytes from the amygdala of mice exposed to 7-day restraint stress that were transferred intravenously with saline or monocytes for 7 days.


title: Defective endomembrane dynamics in Rab27a deficiency impairs nucleic acid sensing and cytokine secretion in immune cells

city: La Jolla

first: Mouad

last: Ait Kbaich

state: California

address: 10550 N Torrey Pines Rd

institute: Scripps Research

summary: We collected gene expression data (RNAseq) from mature Ly6G+ neutrophils isolated from mice bone marrow. The samples were obtained from both Wild-Type and RAB27A knockout mice. These neutrophils were either treated with CpG, a TLR9 agonist, for 6 hours or left untreated. The transcriptional data complement the study of the role of Rab27a-mediated vesicular trafficking on signaling pathways downstream of TLR9 activation and cytokine secretion in immune cells.

overall_design: Neutrophils from wild type and Rab27aKO mature neutrophils were isolated using Ly6G positive selection. The cells were stimulated with 5 µM CpG-B or left untreated and incubated for 6h at 37C. RNA was isolated using Qiagen RNeasy Mini Kit and sequenced by BGI Genomics using Illumina HISEQ4000

first: Juan

last: Yu

first: Elsa

last: Meneses-Salas

first: Jennifer

middle: L

last: Johnson

first: Susanna

last: Manenti

first: Danni

last: Chen

first: Kasra

last: Askari

first: Jing

last: He

first: Aparna

last: Shukla

first: Binchu

last: Shaji

first: Rosana

last: Gonzalez-Quintial

first: Ben

last: Croker

first: Jinzhong

last: Zhang

first: Hal

last: Hoffman

first: William

middle: B

last: Kiosses

first: Catherine

last: Hedrick

first: Kersi

last: Pestonjamasp

first: Nathan

last: Wineinger

first: Roberto

last: Baccala

first: Sergio

middle: D

last: Catz


title: Analysis of amygdala astrocytes following monocyte depletion

first: Michael

last: Wheeler

overall_design:
To investigate the role of monocytes in driving behavioral phenotypes associated with chronic stress, we treated tamoxifen-conditioned CCR2-DTR mice with saline (n=3) or DTx (n=3) and performed bulk RNA-sequencing on astrocytes from the basolateral amygdala following 18 days of chronic stress and fear conditioning.
We performed gene expression profiling analysis using data obtained from RNA-seq of amygdala astrocytes following chronic stress, fear conditioning, and monocyte depletion in CCR2-DTR mice.

first: Elizabeth

last: Chung

first: Jinsu

last: Lee


title: CTCF depletion uncouples the role of enhancer-promoter interactions and higher-order chromatin hubs in gene regulation during cellular differentiation [RNA-seq]

city: Goettingen

first: Yi

last: Zhu

address: Am Fassberg 11

institute: Max Planck Insitute for Multidisciplinary Sciences

summary: Enhancers and promoters interact in 3D chromatin structures to regulate gene expression. The mechanisms that drive the formation of these structures and their function during cellular differentiation are incompletely understood. Here, we study the structure-function relationship of the genome in a lymphoid-to-myeloid differentiation system at very high resolution. We demonstrate a close correlation between binding of regulatory proteins, formation of chromatin interactions, and gene expression. By integrating analysis of single-allele topologies and computational modeling, we show that tissue-specific gene loci are organized into chromatin hubs, characterized by cooperative interactions between multiple enhancers, promoters, and CTCF-binding sites. Depletion of CTCF leads to a near-complete loss of these structures, which indicates that CTCF-mediated interactions provide a scaffold for chromatin hub formation. In contrast, the effects of CTCF depletion on gene expression are relatively mild and can be explained by rewired enhancer-promoter interactions. Together, our results demonstrate an instructive role for enhancer-promoter interactions in gene regulation during cellular differentiation, which does not depend on cooperative interactions in chromatin hubs.

overall_design: RNA-seq. Studies of gene expression dynamic during human B cell to macrophage transdifferentiation with and without CTCF.

first: Magdalena

last: Karpinska

first: A

last: Oudelaar


title: CTCF depletion uncouples the role of enhancer-promoter interactions and higher-order chromatin hubs in gene regulation during cellular differentiation [Tri-C]

overall_design:
Tri-C experiments. Studies of multiway cis-element interactions during human B cell to macrophage transdifferentiation.
Please note that processed data file generated from all replicates is linked to the corresponding *rep1 sample records.


title: Repeat Ascaris challenge reduces worm intensity through gastric cellular reprogramming

city: Houston

first: Jill

middle: E

last: Weatherhead

state: TX

address: 1102 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

summary: Ascariasis (roundworm) is the most prevalent parasitic nematode infection worldwide, impacting approximately 500 million people predominantly in low- and middle-income countries (LMICs). While people of all ages are infected with Ascaris, infection intensity (defined by worm burden) paradoxically peaks in pre-school and school aged children but then declines with age. The cause of age-dependent Ascaris worm intensity is not well understood but may be dependent on cellular changes in mucosal barrier sites. We have previously found that the gastric mucosa is a critical barrier site for Ascaris infection. Following oral ingestion of Ascaris eggs, larvae use AMCase secreted by gastric chief cells and acid secreted by gastric parietal cells to hatch. Once hatched, larvae translocate across the gastric mucosa to initiate the larval migratory cycle. However, inducing mucosal injury with administration of Tamoxifen induces mucosa cellular changes that impairs Ascaris hatching and reduces larval translocation across the gastric mucosa. In this study we established a repeated Ascaris suum challenge mouse model and evaluated if repeated Ascaris challenge also lead to cellular changes in the gastric mucosal barrier. We found that repeated Ascaris challenge caused cellular changes in the gastric mucosa which reduced worm intensity in the liver independent of the adaptive immune response. Thus, in endemic regions, where individuals experience recurrent infection throughout their lives, gastric cellular changes may be a key mechanism leading to the observed age-dependent Ascaris worm intensity changes from childhood to adulthood.

overall_design: RNAseq profiling of gastric tissue from female BALB/c mice either repeatedly infected with Ascaris suum or gavaged with PBS.

first: Yifan

last: Wu

first: Charlie

last: Suarez-Reyes

first: Nina

last: Tang

first: Alexander R.

last: Kneubehl

first: Jill E.


title: CTCF depletion uncouples the role of enhancer-promoter interactions and higher-order chromatin hubs in gene regulation during cellular differentiation.

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

overall_design: Refer to individual Series


title: Inflammatory memory in macrophages emerges from coordinated transcription factor and chromatin dynamics

city: Chicago

first: Savas

last: Tay

state: IL

address: 5640 South Ellis Avenue

department: Pritzker School of Molecular Engineering

institute: University of Chicago

summary: RNA seq for murine bone marrow derived macrophages stimulated with either polyI:C (1000 ng/mL) or CPG (300 nM/mL) for 4 hours followed by TNF (10 ng/mL) or LPS (1 ng/mL) for 4 hours. Controls are 4 hours media followed by polyI:C/CpG/LPS/TNF or polyI:C/CpG followed by media.

overall_design: Comparison of triplicate bone marrow derived macrophages (homozygous mvenus tagged RelA mice) with indicated stimulation patterns. Approximately 150K macrophages per condition.

first: Andrew

last: Wang

first: Minjun

last: Son


title: CTCF depletion uncouples the role of enhancer-promoter interactions and higher-order chromatin hubs in gene regulation during cellular differentiation [Capture-C]

overall_design:
Capture-C experiments. Studies of cis-element interactions during human B cell to macrophage transdifferentiation.
Please note that processed data file generated from both replicates is linked to the corresponding *rep1 sample records.


title: Comparative single-cell analysis reveals tendon progenitor dysfunction by age-associated oxidative-sress and its restoration by antioxidant treatment

first: Dongsu

last: Park

address: One Baylor Plaza

department: Molecular and Human Genetics

summary: Impaired healing of adult tendons with fibrosis remains clinical challenges while neonatal tendons have full functional restoration. However, age-associated cellular and molecular changes in tendon cells and tendon stem/progenitor cells (TSPCs) remain unknown. Here, comparative single cell transcriptomics of early postnatal (2-week-old) and adult (20-week-old) mouse tendons revealed that adult tendons have reduced number of TSPCs, decreased gene expression in tendon and cartilage development, and a greater population of fibro-tenogenic cells. Notably, adult TSPCs and tenocytes exhibit increased expression of immune-response and oxidative-stress genes with higher EGFR but decreased IGF signaling. Adult tendon cells show increased levels of intracellular reactive oxygen species (ROS) in vivo. In contrast, antioxidant treatment of adult tendons significantly reduces intracellular ROS of TSPCs and improves tendon strength in vivo. Hence, these findings suggest that increased inflammation and ROS during tendon aging deteriorates tendon function and regeneration that can be mitigated by antioxidant treatment.

overall_design: Non-hematopoietic and non-endothelial cells from 2-week and 20-week-old mouse patellar tendons were isolated by Fluorescence-activated cell sorting and analyzed by 10x scRNA-seq

first: Youngjae

last: Jeong


title: Analysis of amygdala neurons in chronic stress by EGFR+ astrocytes

first: Michael

overall_design: To investigate the role of Egfr in chronic stress, we knocked down Egfr or Rosa (control) in astrocytes using an AAV with Cas9 expression driven by the GfaABC1D promoter and performed bulk RNA-sequencing on neurons. We performed gene expression profiling analysis using data obtained from RNA-seq of amygdala neurons following knockdown of Egfr (n=3) or Rosa control (n=3) in amygdala astrocytes.


title: CTCF depletion uncouples the role of enhancer-promoter interactions and higher-order chromatin hubs in gene regulation during cellular differentiation [Micro-Capture-C]

overall_design:
Micro-Capture-C experiments. Studies of cis-element interactions during human B cell to macrophage transdifferentiation.
Please note that processed data files generated from all replicates are linked to the corresponding *rep1 sample records.


title: The pro-inflammatory cytokine IL6 suppresses mitochondrial function via the gp130-JAK1/STAT1/3-HIF1α/ERRα axis

city: Tarrytown

first: Kun

last: Xiong

address: 777 Old Saw Mill River Road

department: Molecular Profiling and Data Science

institute: Regeneron Pharmaceuticals

summary: Chronic inflammation and a decline in mitochondrial function are hallmarks of aging. Here, we show that the two mechanisms may be linked. We found that interleukin-6 (IL6) suppresses mitochondrial function in settings where PGC1 (both PGC1α and PGC1β) expression is low. This suppression is mediated by the JAK1/STAT1/3 axis, which activates HIF1α through non-canonical mechanisms involving upregulation of HIF1A and ERRα transcription, and subsequent stabilization of the HIF1A protein by ERRα. HIF1α, in turn, inhibits ERRα, which is a master regulator of mitochondrial biogenesis, thus contributing to the inhibition of mitochondrial function. When expressed at higher levels, PGC1 rescues ERRα to boost baseline mitochondrial respiration, including under IL6-treated conditions. Our study suggests that inhibition of the IL6 signaling axis could be a potential treatment for those inflammatory settings where mitochondrial function is compromised.

overall_design: We found IL6+IL6R but not TNFa could reduce mitochondrial function in RPE-1 hTERT cells. To explore the underlying mechanism, we treated RPE-1 hTERT cells (n=5 in each treatment) with IL6(100ng/ml)+soluble IL6R(100ng/ml), or TNFa(100ng/ml), or mock treatment (vehicle dH2O control) for 3 days. Samples were harvested for bulk RNA sequencing profiling.

first: Xu

last: Jianing

first: Wakai

last: Matthew

first: Xiong

last: Kun

first: Yang

last: Yanfeng

first: Prabakaran

last: Adithya

first: Wu

last: Sophia

first: Ahrens

last: Diana

first: Molia

last: Pilar

first: Ni

last: Min

first: Bai

last: Yu

first: Shavlakadze

last: Tea

first: David

last: Glass


title: Spatial transcriptomic mapping of the mouse brain in chronic stress

last: Wheeler

overall_design:
To investigate the localization of subpopulations of astrocytes and neurons associated with chronic stress and fear behavior in amygdala nuclei, we performed STEREO-seq on mice exposed to chronic stress.
We performed spatial transcriptomics analysis using data obtained from STEREO-seq of the brains of mice following exposure to chronic stress.

first: Elizabeth

last: Chung

first: Jinsu

last: Lee


title: Analysis of amygdala neuron control by NR2F2 in chronic stress

overall_design:
To investigate the role of Nr2f2 in chronic stress, we knocked down Nr2f2 or Rosa (control) in neurons using an AAV with Cas9 expression driven by the Hsyn promoter.
We performed gene expression profiling analysis using data obtained from RNA-seq of amygdala neurons with Nr2f2 (n=3) or Rosa (n=4) knocked down.


title: Analysis of amygdala neuron chromatin accessibility by NR2F2

overall_design:
To investigate Nr2f2 regulation of chromatin accessibility, we performed ATAC-seq on amygdala neurons from neuron-targeting sgRosa26 (n=4) and sgNr2f2 (n=4) mice knockdown that were exposed to 7D restraint stress.
We performed Chromatin Accessibility profiling analysis using data obtained from ATAC-seq of neurons from mice following exposure to  stress with or without Nr2f2 knocked down.


title: Total RNAseq from fly heads at different ages - circRNAs are extremely stable in the brain and can serve as age and experience markers [CSaging]

first: Sebastian

last: Kadener

address: 415 South Street

institute: Brandeis University

summary: Circular RNAs are a large class of stable RNAs generated by backsplicing that accumulate with age in neural tissue. To determine the reason for this accumulation, we profiled circRNAs from fly heads at six timepoints during their lifespan. We found that the global levels of circRNAs increase linearly with age and that circRNAs are excellent age-markers. At the individual level, we found that most circRNAs increase their levels with age, and this increase does not correlate with changes on overall transcription, the levels of the mRNA counterparts, changes in intron retention, or splicing of the host gene, demonstrating that the increase is not due to biogenesis. In addition, a sustained stimulus, like transient exposure to higher or lower temperatures, leads to increases (but no decreases) in the levels of specific circRNAs further demonstrating the stability of these molecules in vivo. This unusually high stability suggests that circRNAs can be used as experience markers. Indeed, flies that were treated for ten days at 29°C display high levels of specific temperature-induced circRNAs even six weeks after being returned to standard conditions. Together, our data demonstrates that circRNAs are extremely stable in vivo and that they can be utilized as stress/life experience markers.

overall_design: CantonS, wild-type, flies were grown at 25C in 12:12 light:dark conditions, allowed to mate for 3 days prior to separating males and females for aging. After that, flies were flash frozen in liquid nitrogen 0, 10, 20, 30, 40, or 50 days later. Samples were collected in duplicate or triplicates. RNA from the fly brains was extracted using TRIzol reagent (Sigma, T9424) and treated with DNaseI (NEB, M0303L). We used 1 ug of RNA as input for ribodepletion (with a protocol based on Adiconis et al. 2013). Total RNA libraries were prepared with NEXTFLEX Rapid Directional RNA-Seq Kit 2.0 (PerkinElmer) as recommended by the manufacturer. Samples were sequenced by Novogene (Novogene Corporation Inc 8801 Folsom BLVD, Suite 290, Sacramento, CA) with HiSeq-4000.

first: Ken

last: Kirio

first: Ines

last: Patop

first: Ane

last: Martin Anduaga

first: Jenna

last: Harris

first: Nagarjuna

last: Pamudurti

first: Claire

last: Martel


title: Analysis of amygdala astrocyte responses during chronic stress by EGFR

first: Michael

overall_design:
To investigate the role of Egfr in chronic stress, we knocked down Egfr or Rosa (control) in astrocytes using an AAV with Cas9 expression driven by the GfaABC1D promoter.
We performed gene expression profiling analysis using data obtained from RNA-seq of amygdala astrocytes with Egfr (n=3) or Rosa (n=4) knocked down.


title: Analysis of psychedelic control of primary human monocytes

overall_design:
To investigate the anti-inflammatory properties of MDMA and psilocybin in human monocytes, we treated human monocytes in vitro with 10uM psilocybin, 10uM MDMA, and 100 ng/mL LPS and performed bulk RNA-sequencing.
We performed gene expression profiling analysis using data obtained from RNA-seq of human monocytes following treatment with PBS, 100 ng/mL LPS, 10uM psilocybin, 10uM MDMA, or combination treatments.


title: Analysis of Aldh1l1-tdTomato+ cells during chronic stress by scRNA-seq

overall_design: To identify responses of Aldh1l1-tdTomato+ cells associated with chronic stress, we exposed mice to 0 or 18D of tube restraint, sorted tdTomato+ cells from Aldh1l1-tdTomato reporter mice and performed Drop-seq. We then performed gene expression profiling analysis.


title: Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity informing a looping-mediated therapeutic avenue

city: Milwaukee

first: Victor

last: Jin

state: WI

address: 8701 Watertown Plank Rd.

institute: Medical College of Wisconsin

summary: Current knowledge in three-dimensional (3D) chromatin regulation in normal and disease states was mostly accumulated through Hi-C profiling in in vitro cell culture system. The limitations include failing to recapitulate disease-specific physiological properties and often lacking clinically relevant disease microenvironment. In this study, we conduct tissue-specific Hi-C profiling in a pilot cohort of 12 breast tissues comprising of two normal tissues (NTs) and ten ER+ breast tumor tissues (TTs) including five primary tumors (PTs), and five tamoxifen-treated recurrent tumors (RTs). We find largely preserved compartments, highly heterogeneous topological associated domains (TADs) and intensively variable chromatin loops among breast tumors, demonstrating 3D chromatin-regulated breast tumor heterogeneity. Further cross-examination identifies RT-specific looping-mediated biological pathways and suggests CA2, an enhancer-promoter looping (EPL)-mediated target gene within the bicarbonate transport metabolism pathway, might play a role in driving the tamoxifen resistance. Remarkably, the inhibition of CA2 not only impedes tumor growth both in vitro and in vivo, but also reverses chromatin looping. Our study thus yields significant mechanistic insights into the role and clinical relevance of 3D chromatin architecture in breast cancer endocrine resistance.

overall_design: Hi-C experiment of 12 tissue sample, including 2 normal tissues, 5 primary breast tumor and 5 tamoxifen recurrent breast tumor tissues

first: Lavanya

last: Choppavarapu

first: Tianxiang

last: Liu

first: Kun

last: Fang


title: Analysis of mouse monocytes in chronic stress

overall_design:
To investigate the responses of monocytes to chronic stress and psychedelics, we performed bulk RNA-sequencing on monocytes from the deep cervical lymph nodes and meninges from mice exposed to chronic stress and psychedelics.
We performed gene expression profiling analysis using data obtained from RNA-seq of monocytes from mice following exposure to chronic stress with or without psilocybin or MDMA.


title: Lag3 and PD-1 pathways regulate NFAT-dependent TCR signalling programmes during early CD4+ T cell activation

city: Birmingham

last: Bending

address: IBR

department: Institute of Immunology and Immunotherapy

institute: University of Birmingham

summary: Here we perform QuantSeq 3' mRNA sequencing of RNA extracted from flow sorted splenic CD4+ T cell from Tg4 Nr4a3-Tocky Tiger mice that been reactivated in the presence of Isotype, anti-PD-L1, anti-Lag3 or combination therapy. Transcriptional analysis reveals strong T cell receptor signalling, T helper cell bias and metabolic priming in response to combination therapy.

overall_design: Tg4 Nr4a3-Tocky Il10-GFP mice were immunized through subcutaneous injection of 4 mg/kg [4Y] MBP peptide PBS into the flank. 24 hrs later antibodies were administrated via the intraperitoneal (i.p.) route with isotype control (pool or rat IgG1 and rat IgG2a), 0.5 mg of anti-PD-L1 antibody (clone MIH5 73), in vivo grade anti-Lag3 (clone C9B7W) or r combination therapy (anti-PD-L1 and anti-Lag3 pooled at 1:1 ratios).  30 minutes after immunotherapy administration a second dose of 0.4 mg/kg [4Y]-MBP peptide in PBS was administered subcutaneously to the contralateral flank. Mice were then euthanized 12 hours later and CD4+ Nr4a3-Timer Red+ Nr4a3-Timer Blue+ T cells isolated and RNA extracted for 3' mRNA sequencing. 3 biological replicate mice were obtained for the 4 experimental groups. Each sample was run on 4 lanes, resulting in 48 FASTQ files (4 per experimental replicate).


title: Analysis of MDD and control patients by snRNA-seq

overall_design:
To investigate the amygdala in MDD, we performed snRNA-seq on amygdala samples from control (n=6) and MDD (n=6) patients.
We performed gene expression profiling analysis using nuclei obtained from snRNA-seq of amygdala samples from control (n=6) and MDD (n=6) patients.


title: Analysis of amygdala astrocytes in stress after meningeal monocyte depletion

overall_design:
To investigate the transcriptional responses of astrocytes to meningeal monocytes, we injected by intra-cisterna magna injection (ICM) anti-Ccr2 antibody or isotype, and performed bulk RNA-sequencing on astrocytes from the amygdala of mice after being exposed to 7-d chronic stress.
We performed gene expression profiling analysis using data obtained from RNA-seq of astrocytes (n=5 per group) from the amygdala of mice exposed to chronic stress and treated ICM with anti-CCR2 or anti-IgG antibody.


title: Single cell sequencing shows that Sox9-expressing cells populate most mesenchymal lineages postnatally in mouse bone

city: Charlestown

first: Neal

middle: Patrick

last: Smith

address: 149 13th Street

institute: Massachusetts General Hospital

summary: In growing bones of mice, multiple cell types contribute to the osteoblast lineage, including growth plate chondrocytes, perichondrial cells and CXCL12-abundant reticular (CAR) marrow stromal cells.  Here we use single cell RNA sequencing and lineage tracing to show that all these osteoblast precursors, even postnatally, derive from Sox9-expressing progenitors. We also characterize a distinct group of chondrocytes between the perichondrium and the columns of growth plate chondrocytes that contribute to the osteoblast lineage.

overall_design: Sox9-CreERT2;tdTomato transgenic mice received a single, 2mg dose of tamoxifen. At days 2, 7, 13 and 35 post-tamoxifen administration, Isolated hindlimbs were mechanically crushed into 2mL of Hank’s Balanced Salt Solution (Sigma Aldrich, H6648). Supernatant was filtered through a 70µm filter (Corning, 352350) into a 50mL Falcon tube. The remaining tissue was further incubated with 2 Wunsch units of LiberaseTM (Sigma Aldrich, 5401127001) and 0.25% Trypsin-EDTA (Fisher Scientific, 15400054) at 37°C for 30 min with agitation. The supernatant was again filtered through a 70µm filter into a 50mL Falcon tube. Cells were then stained with CD45-APC (ThermoFisher, MCD4505), Ter119-APC (ThermoFisher, 17-5921-82) and DAPI (Invitrogen, D1306) for 30min on ice. Cells were washed with FACS Buffer (Phosphate Buffered Solution plus 2% fetal bovine serum). Flow cytometry and sorting was performed with a 4-laser BD LSR II and FACSDivia. TdTomato+/DAPI-/APC- cells were sorted into FACS Buffer.

first: Alexandra-Chloe

last: Villani

first: Henry

last: Kronenberg


title: Hepatic stellate cells control liver zonation and function via R-spondin 3 [bulkRNAseq_mouse_HSCdepleted]

first: Atsushi

last: Sugimoto

address: 1130 Saint Nicholas Avenue

institute: Columbia University

summary: Hepatic stellate cells (HSCs) exert a central pathogenic role in the development of liver fibrosis. However, the fibrosis-independent and homeostatic functions of these specialized liver pericytes remain poorly understood. Here, we demonstrate that genetic depletion of HSCs alters Wnt target gene expression in hepatocytes and liver zonation, leading to profound alterations of regeneration, cytochrome P450 metabolism and injury. HSC-selective deletion of Rspondin-3, a modulator of Wnt signalling with high enrichment in HSCs, phenocopies the effects of HSC depletion on hepatocyte gene expression, zonation, regeneration and cytochrome P450-mediated detoxification and increases alcohol-associated and metabolic dysfunction-associated steatotic liver injury. Rspondin-3 expression decreases with HSC activation and is associated with disease progression in patients with alcohol-associated and metabolic dysfunction-associated steatotic liver disease. These hitherto unknown protective and hepatocyte-regulating functions of HSCs via Rspondin-3, resembling the R-spondin-expressing stromal niche of other organs, should be integrated into therapeutic concepts for liver fibrosis.

overall_design: Bulk RNA sequencing of whole liver from 8 weeks old HSC-depleted mouse by the iDTR method (control, n=3, HSC depleted, n=3), from 8-9 weeks old Rspo3 KO in HSC by Lrat-Cre (control, n=5, Rspo3?HSC, n=5), 32-34 weeks old Rspo3 KO in HSC by Lrat-Cre (Control, n=5, Rspo3?HSC, n=5), and from 8 weeks old Rspo3 KO in EC by Lyve1-Cre (control, n=4, Rspo3?EC, n=4)

first: Qiuyan

last: Sun

first: Robert

middle: F

last: Schwabe


title: Transcriptome alteration of cancer stem cells (CSCs) and non-CSCs when CSCs were depleted in HNSCC

city: Beijing

first: Zhen

last: Qin

address: 22 Zhongguancun South Avenue

institute: Peking University

summary: To investigate the  difference of signaling and  cancer stemness activation molecules in CSCs and non-CSCs  when Bmi1 was inhibited.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The data performed RNA-Seq were as follows: 1) HN6 ALDH+ CSCs treated with PTC209 and DMSO;2) K16+ tumor cells from tumor-bearing K16CreER; RosatdTomato mice treated with PTC209 versus control vehicle; 3) Epcam+ ALDH- tumor cells from PDX#3 treated with PTC209 versus control vehicle;

first: Lingfei

last: Jia


title: CTCF depletion uncouples the role of enhancer-promoter interactions and higher-order chromatin hubs in gene regulation during cellular differentiation [ChIPmentation]

first: Yi

last: Zhu

overall_design:
ChIPmentation experiments. Studies of protein occupancy dynamic during human B cell to macrophage transdifferentiation.
Please note that processed data file generated from all replicates is linked to the corresponding *rep1 sample records.

first: Magdalena

last: Karpinska

first: A

last: Oudelaar


title: Lifestyle-induced changes in alternative splicing patterns in mice

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

overall_design: Refer to individual Series


title: Circular RMST cooperates with lineage-driving transcription factors to govern neuroendocrine transdifferentiation

city: Toronto

first: Housheng

middle: Hansen

last: He

address: 101 College Street

institute: Princess Margaret Cancer Centre

summary: Circular RNA (circRNA) is a class of noncoding RNA with regulatory potentials. It is unexplored how they may be functionally involved in the transdifferentiation of prostate and lung adenocarcinoma to neuroendocrine prostate cancer (NEPC) and small cell lung cancer (SCLC). Here we identified an exceptionally abundant circRNA circRMST predominantly expressed in NEPC and SCLC and conserved between humans and mice. Using shRNA, siRNA, CRISPR-Cas13 and Cas9, we consistently showed that circRMST is essential for tumour growth and for the expression of ASCL1, a master regulator of neuroendocrine fate. Genetic knockout of Rmst in NEPC genetic engineered mouse models led to a prevention of neuroendocrine transdifferentiation and sustained tumours in adenocarcinoma state. Mechanistically, circRMST physically interacts with lineage transcription factors NKX2-1 and SOX2. Loss of circRMST induces NKX2-1 protein degradation through autophagy-lysosomal pathway and alters the genomic binding of SOX2, which collectively leads to the loss of ASCL1 transcription.

overall_design: To investigate function of circRMST, we designed two shRNAs and performed stable knockdown experiments in SHP77 small cell lung cancer cell line. shGFP was used as the negative control. Two biological replicates for each shRNA were performed. We identified that circRMST physically interacts with SOX2 and NKX2-1. To understand the interactions and the downstream target genes, we performed siRNA knockdown of SOX2 and NKX2-1 with two independent siRNAs each in SHP77. Two biological replicates were performed. In addition, we performed ChIP-seq of SOX2 and NKX2-1 in SHP77 SCLC-A cells with and without circRMST shRNAs to investigate how the cistromes for the two transcription factors are altered without circRMST. Two biological replicates were performed for each transcription factor.

first: Mona

last: Teng

first: Housheng Hansen


title: Cell cycle duration determines oncogenic transformation capacity

first: Rod

last: Bremner

address: 600 University Ave

department: Lunenfeld-Tanenbaum Research Institute

institute: Mount Sinai Hospital

summary: We present single-cell RNA sequencing data of P8 mouse retina with Rb/p107 double knockout (DKO), or Rb/p107 DKO with Skp2+/-.

overall_design: Sc RNA-seq of P8 retins of α-Cre; Rbf/f; P107-/- (DKO, tumor-prone) and α-Cre; Rbf/f; P107-/-; Skp2+/- (DKO-Skp2+/-, tumor-resistant) were compared

first: Danian

last: Chen

first: Katherine

last: Huang

first: Joel

last: Pearson


title: Role of DYRK1A in MPN

city: Memphis

first: Lance

last: Palmer

state: TN - Tennessee

address: 262 Danny Thomas Pl

department: Hematology

institute: St. Jude Children's Research Hospital

summary: We aim to investigate the role of DYRK1A gene in MPN pathogenesis by DYRK inhibitor and genetic knockout

overall_design: RNA-sequencing was performed in SET2 DYRK1A KO clone 11H1 and 14B5 generated by CRISPR/Cas9. Wild-type SET2 cells was included as a control. DYRK1A KO clones 11H1 and 14B5 were compared to wild-type SET2 cells repsectively (3x3 analysis).

first: Bon

middle: H

last: Yip

first: John

last: Crispino


title: Dehydrozingerone ameliorate renal structures compromised in diabetic nephropathy

status: Public on Mar 01 2025

city: HAJIPUR

first: NIVEDITA

last: SINGH

address: INDUSTRIAL AREA HAJIPUR

department: Pharmacology and Toxicology

country: India

institute: NATIONAL INSTITUTE OF PHARMACEUTICAL EDUCATION AND RESEARCH HAJIPUR

summary: Kidney structural integrity is critical for bodily excretory mechanism. Diabetes has been considered as one of the major risk factors for chronic kidney disease, but the underlying mechanism remains elusive. The present study investigates the transcriptomic and proteomic profiling of long-term impact of high-fat diet (HFD) on renal tissue in mice and role of dehydrozingerone (DH) in reinstating the normal kidney function. Animals were divided into four groups- healthy (NCD+Veh), diabetic (HFD-STZ+Veh), healthy+DH (NCD+Veh+DH) and treatment (HFD-STZ+DH). 65th days of HFD-fed C57BL/6 mice developed diabetes and kidney dysfunction evident by albuminuria, proteinuria, and glucotoxicity with accumulation of glucose, triglyceride, cholesterol, albumin, and total protein in blood serum. The HFD-fed kidney showed renal injuries, including prominent defects in the glomerular filtration system by downregulation of proteins involved in transport, metabolic process, energy production, anti-oxidation, etc. Downregulation of lipid metabolism is the most impacted metabolic process under diabetic condition. Downregulation of transport proteins mainly impact the functioning of podocytes, cell adhesion and cytoskeletal rearrangement. HFD feeding also increased oxidative stress and induced mitochondrial dysfunction, and thereby activating the pro-apoptotic pathway. Progression of DNA damage under diabetic condition triggered the epigenetic alteration and subsequent downstream changes which is evident by activation of HDAC1 under diseased condition. Transcriptomic study revealed the potential of dehydrozingerone in attenuating the diabetic condition by positively regulating transport system, mitochondrial function, lipid metabolism, DNA damage and epigenetic alteration, and oxidative stress, which ameliorate the kidney function.

overall_design: RNA-seq profiling of whole kidney tissue from healthy, diseased, and treatment group.

first: Nivedita

last: Singh

first: Anuradha

last: Kesarwani

first: Velayutham

last: Ravichandiran

first: Vipan Kumar

last: Parihar


title: Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant

status: Public on Mar 02 2025

city: Washington

first: Anton

last: Wellstein

state: DC

address: 3970 Reservoir Road, N.W.,

department: Oncology

institute: Georgetown University


title: Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant (LTR cell-free DNA)

summary: Molecular biomarkers to monitor changes after liver transplant are essential to reveal mechanisms of injury, guide clinical decision-making and improve patient outcomes. Current approaches have limited scope and are unable to differentiate between host and graft amongst the causes of graft injury. Here, we utilize circulating, cell-free methylated DNA released from dying cells to monitor cellular damages after liver transplant impacting the graft tissue as well as host organs. We expand existing cell-type-specific DNA methylation atlases curated from whole-genome bisulfite sequencing (WGBS) of healthy tissues to characterize liver cell-types relevant to injury progression and tissue repair. Liver cell-type-specific methylation blocks are validated through multi-omic data integration and found to be enriched in open chromatin and regulatory regions functionally important for the respective cell populations. Cell-free DNA (cfDNA) fragments were captured from patient serum by hybridization to CpG-rich DNA panels and mapped to the expanded DNA methylation atlases to inform tissue origins of cell types. We profiled 135 blood samples collected from 44 liver transplant patients at serial time points before and after transplant. We found that liver transplant initially results in multi-tissue cellular damage that subsequently recovers in patients with graft acceptance during the first post-operative week. Further, we show that sustained elevation of hepatocyte and biliary epithelial cfDNA beyond the first week is indicative of early-onset graft injury. Most notably, cfDNA composition can differentiate amongst causes of graft injury. Thus, cell-free methylated DNA can detect cellular damages and prompt early intervention.

overall_design:
Tissue-of-origin analysis of cell-free DNA (cfDNA) using identified cell-type specific methylation patterns from reference WGBS data in healthy tissues. CfDNA from serum samples was analyzed by hybridization capture sequencing for changes in methylated cfDNA to uncover cellular damages.
-----------------------------------
Authors state "Raw data for these samples are not available due to patient privacy concerns."

first: Megan

last: McNamara

first: Sidharth

middle: S

last: Jain

first: Kesha

last: Oza

first: Vinona

last: Muralidaran

first: Amber

last: Kiliti

first: A

last: McDeed

first: Digvijay

last: Patil

first: Yuki

last: Cui

first: Marcel

middle: O

last: Schmidt

first: Anna

middle: T

last: Riegel

first: Alexander

last: Kroemer


title: Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant [Reference Celltype Chromatin]

overall_design:
Tissue-of-origin analysis of cell-free DNA (cfDNA) using identified cell-type specific methylation patterns from reference WGBS data in healthy tissues. CfDNA from serum samples was analyzed by hybridization capture sequencing for changes in methylated cfDNA to uncover cellular damages.

***************************************************************
Submitter states that missing raw files are due to patient privacy concerns.
***************************************************************

middle: J


title: HNF3α targets Nckap1l and promotes renal fibrosis following ischemia-reperfusion injury [CUT&TAG]

city: Shenyang

first: Ling

last: Hou

email: 79594942@qq.com, houl@sj-hospital.org

address: No.36 Sanhao street

institute: China Medical University

summary: Ischemia-reperfusion injury-induced acute kidney injury is a major cause of chronic kidney disease, lacking effective interventions. We found elevated HNF3α (also known as FOXA1) expression in CKD patients, which correlated with collagen deposition, serum creatinine, and urea levels. Conditional knockout of HNF3α in renal tubular epithelial cells protected against IRI-induced renal fibrosis in vivo. To explore the mechanisms by which HNF3α promotes renal fibrosis, we analyse the genome-wide target sites of HNF3α using CUT&Tag sequencing.

overall_design: A total of 100,000 TKPTS cells were subjected to CUT&Tag sequencing analysis using the NovoNGS CUT&Tag4.0 High-Sensitivity Kit for Illumina (N259-YH01, Novoprotein, Suzhou, China), according to the specified protocol. The CUT&Tag libraries were sequenced by Genesky Biotechnologies Inc. (Shanghai, China) using the Illumina Novaseq platform.

first: Aihua

last: Zhang

first: Yan

last: Guo

first: Mi

last: Bai


title: Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant (LTR reference cell type)

middle: K


title: Osteopontin Reduces Foreign Body Response in Silicone-Based Implants in Humans and Mice

city: Stanford

first: Jennifer

middle: Brigitta

last: Parker

state: CA

address: 257 Campus Drive

department: Surgery

institute: Stanford University

summary: Subcutaneous implants often elicit an inflammatory foreign body response (FBR) in the shape of a capsule around the implanted material, and it is not yet clear why certain materials such as dermal matrix (ADM), clinically used in breast reconstruction, are more efficient in attenuating this chronic reaction. Here, we investigate the molecular response of human and mouse tissues implanted with silicone treated with ADM by analysing single-cell RNA and proteomics. In patient-derived implanted tissues exposed to ADM, we identify high levels of Osteopontin-1 (SPP1) together with attenuated FBR, in contrast to higher inflammatory response in implanted tissues not exposed to ADM. In a Spp1 knockout mouse model of FBR, we demonstrate that a reduction in SPP1 expression prevents the beneficial effects of ADM in the capsule formation, revealing that the protein is necessary to decrease fibrotic response. In wildtype mice, we demonstrate that a sustained release from a hydrogel of recombinant Spp1 is sufficient to reduce fibrotic encapsulation even in the absence of ADM, suggesting a therapeutic approach for reducing FBR around implants.

overall_design:
Single cell RNA sequencing of hashed mouse capsule tissue from ADM-coated and non-ADM control implant foreign body response model

Single cell RNA sequencing of hashed human capsule tissue from two-stage implant-based breast reconstruction patients.

***************************************************************
Submitter states that missing human raw files are due to patient privacy concerns.
***************************************************************

first: Michelle

last: Griffin


title: Retinoic Acid reprograms pDCs to resist the inhibitory effect of multiple myeloma

city: guangzhou

first: wanli

last: yu

address: 南方医科大学

institute: 南方医科大学

summary: Plasmacytoid dendritic cells (pDCs) are a rare subset of dendritic cells in the body, distinguished by their secretion of large amounts of IFN-α upon activation by pathogen-derived ligands. pDCs express high levels of TLR7 and TLR9 in endosomes, endoplasmic reticulum, and lysosomes, enabling them to recognize pathogen-derived RNA and DNA containing CpG sequences, as well as synthetic ligands. However, in patients with multiple myeloma, pDCs exhibit functional impairment, characterized by a loss of both IFN-α secretion capacity and their ability to perform pro-tumor functions. In our previous high-throughput drug screening study, we identified that all-trans retinoic acid (ATRA) may have the potential to enhance and restore the IFN-α secretion capacity of pDCs. Therefore, we investigated the changes in gene transcription levels in human primary pDCs treated with ATRA and CpG through RNA sequencing (RNA-seq). The RNA-seq analysis of pDCs revealed that following ATRA treatment, the expression of retinoic acid-induced gene 1 (RIG-I) and numerous related interferon-stimulated genes (ISGs) associated with the secondary response to type I interferon were significantly upregulated.

overall_design: To investigate the mechanism by which ATRA enhances the secretion of IFNA by pDCs, we isolated pDCs from human peripheral blood and stimulated them with different compounds for 6 hours. ATRA group were treated with 10nM ATRA; CpG group were treated with 1mM CpG; CpG_ATRA group were treated with 10nM ATRA and 1mM CpG and the control group was grown in the same culture conditions without the addition of any drugs.

first: Wanli

last: Yu

first: Wei

last: Lin

first: Enguang

last: Bi


title: Safety and Efficacy of Atuzabrutinib Topical Gel in Patients with Mild-to-Moderate Atopic Dermatitis: Findings from Phase 2a Trial

city: San Antonio

first: Mark

last: Lee

address: 1973 NW Loop 410 Suite 106

institute: Progressive Clinical Research

summary: This phase 2a study of atuzabrutinib (PRN473/SAR444727), a Bruton tyrosine kinase inhibitor, comprised of a double-blind placebo-controlled treatment period and an open-label uncontrolled treatment period and evaluated safety and efficacy of atuzabrutinib 5% gel vs placebo (in double-blind period) in patients with mild-to-moderate atopic. dermatitis (AD).  Patients aged 18–70 years diagnosed with mild-to-moderate AD (N=39) for at least 6 months were included in the study. During the double-blinded Period (Days 1–14), two target lesions with a difference ≤1 point in total sign score (TSS) were randomized 1:1 to atuzabrutinib or matching placebo twice daily. During open-label period (Days 15–42), patients continued to treat the assigned areas and other AD-affected lesions (except scalp, palms, soles and genitals) with atuzabrutinib BID. The objective is to evaluate the safety, tolerability, PK and preliminary efficacy of atuzabrutinib in patients with mild to moderate AD. RNA sequencing analysis was performed to understand the target immune cell expression in lesional skin biopsies versus normal skin and the effect of atuzabrutinib.

overall_design:
This study is a Phase 2a that consists of a randomized, double-blind, intra-patient placebo controlled treatment period and an open-label uncontrolled

***************************************************************
Due to legal constraints, the FASTQ files cannot be uploaded to dbGaP or EGA for this clinical study.
***************************************************************

first: Lee

last: Mark

first: Mikol

last: Vincent

first: Truong

last: Vinh

first: Attieh

last: Elham

first: Huang

last: Siying

first: Vigan

last: Marie

first: Wiekowski

last: Maria

first: Xu

last: Christine

first: Lin

last: Ben

first: Nassar

last: Dany


title: Ythdf2 Suppresses the 2C-like State in Mouse Embryonic Stem Cells via Cooperation with Cnot1 [RNA-seq_siCNOT1]

city: Nanjing

first: Xiang

last: Wu

address: 639 longmiandadao

institute: China Pharmaceutical University

summary: Mouse embryonic stem cells (ESCs) consist of a rare population of heterogeneous cells which express 2-cell-stage-specific transcripts and are referred to as 2-cell-like cells (2CLCs). Accumulating evidence has demonstrated that transcription factors and epigenetic modifications exert crucial functions in the transition of ESCs to 2CLCs. However, the roles of RNA modification in the regulation of 2C-like state remain elusive. Using Dux-induced 2CLCs system, we examine N6-methyladenosine (m6A) modification landscape in transcriptome-wide, and find that m6A is dynamically regulated during Dux-driven 2C-like reprogramming. Intriguingly, many of 2C-specific transcripts are highly methylated, including Dux and Zscan4 cluster genes. We further identify the m6A reader protein Ythdf2 as a critical regulator of 2C-like state. Depletion of Ythdf2 facilitates robust expressions of 2C transcripts and the transition of ESCs to 2CLCs. Mechanically, Ythdf2 binds to the Dux/Zscan4 transcripts and promotes their degradation through recruiting the key component of RNA deadenylase complex, Cnot1. Consistent with the phenotype of Ythdf2 deficiency, silencing of Cnot1 induces the 2C gene expressions and the transition of ESCs into the 2C-like state. Collectively, our findings reveal novel insights into the epitranscriptomic regulation of the 2C-like state in mouse ESCs.

overall_design: RNA sequencing in mouse embryonic stem cells (mESCs) treated with siCnot1 or siNT

first: Junjie

last: He

first: Wanting

last: Cai

first: Xiaomin

last: Liu


title: Ythdf2 Suppresses the 2C-like State in Mouse Embryonic Stem Cells via Cooperation with Cnot1 [RNA-seq_Ythdf2rescue]

overall_design: RNA sequencing in mouse embryonic stem cells (mESCs) with overexpression(shscr+Emptyvector,shYthdf2+Emptyvector,shYthdf2+YTHDF2widetype,shYthdf2+YTHDF2mutation)


title: Umbilical Cord Blood miRNA Profiling: Links to Maternal Metabolism and Neonatal Traits

city: Graz

first: Ursula

last: Hiden

address: Auenbruggerplatz 14

department: Obstetrics and Gynecology

institute: Medical University of Graz

summary: We performed miRNA profiling of umbilical cord plasma (UCP) to investigate the association of circulating neonatal miRNAs with maternal metabolic parameters and neonatal anthropometric, metabolic, and inflammatory characteristics in healthy pregnancies. We collected data and UCP samples from 16 pregnancies, in equal parts with normal weight and overweight mothers, and male and female neonates. We performed next-generation miRNA sequencing and analysed metabolic and inflammatory parameters in UCP. Our results revealed that the majority of UCP miRNAs are sensitive to maternal and neonatal characteristics, particularly to maternal BMI,  Our study highlights the susceptibility of UCP miRNAs to maternal metabolism, demonstrates their association with neonatal metabolic and inflammatory traits, and underscores the potential role of circulating umbilical cord blood miRNAs in fetal metabolism and development.

overall_design: miRNA sequencing in umbilical cord plasma samples after pregnancies of normal weight (n=8) and overweight (n=8) women

first: Jasmin

last: Strutz

first: Anna

last: Rieder

first: Elisa

last: Weiss


title: Lifestyle-induced changes in alternative splicing patterns in mice [skeletal muscle]

first: Heike

last: Vogel

summary: Alternative splicing diversifies the cellular protein landscape but aberrant splicing is implicated in many diseases. We aimed to investigate to which extent mis-splicing contributes to insulin resistance as the causal defect of Type 2 Diabetes and whether diet- and exercise-based lifestyle interventions can reverse mis-splicing.

overall_design: Alternative splicing analysis was conducted with Whippet and rMATS using RNA sequencing data from skeletal muscle and adipose tissue of diabetes susceptible NZO mice fed ad libitum, with intermittent fasting or caloric restriction and from healthy C57BL/6J mice subjected to exercise

first: Annette

last: Schürmann

last: Gaugel

first: Markus

last: Jähnert

first: Alexander

last: Neumann


title: Ythdf2 Suppresses the 2C-like State in Mouse Embryonic Stem Cells via Cooperation with Cnot1 [MeRIP-seq]

overall_design: MeRIP-seq in mouse embryonic stem cells (mESCs) following 24-hour treatment with Dox or DMSO

first: Xiao-Min


title: HNF3α targets Nckap1l and promotes renal fibrosis following ischemia-reperfusion injury

first: Ling

last: Hou

summary: Ischemia-reperfusion injury-induced acute kidney injury is a major cause of chronic kidney disease, lacking effective interventions. We found elevated HNF3α expression in CKD patients, which correlated with collagen deposition, serum creatinine, and urea levels. Conditional knockout of HNF3α in renal tubular epithelial cells protected against IRI-induced renal fibrosis in vivo. To explore the mechanisms by which HNF3α promotes renal fibrosis, we transfected TKPTS cells with Hnf3a overexpression plasmids or control plasmids, and then performed transcriptome sequencing.

overall_design: TKPTS cells were cultured in 6-well plates and transfected with pcDNA3.1-Hnf3a-Flag or pcDNA3.1-Flag. Twenty-four hours later, the cells were harvested for transcriptome sequencing.

first: Aihua

last: Zhang

first: Yan

last: Guo

first: Mi

last: Bai