title: Protein-mediated stabilization and nicking of the nontemplate DNA strand dramatically affect R-loop formation in vitro

city: DAVIS

first: FREDERIC

last: CHEDIN

state: CA

address: 1 shields avenue

department: MCB

institute: UC DAVIS

summary: R-loops are an important class of non-B DNA structures that form co-transcriptionally. Using in vitro transcription and unbiased quantitative sequencing readouts, we show that the addition of single-strand DNA binding proteins co-transcriptionally can drive a 3- to 5-fold increase of R-loop frequency without significant changes to R-loop distribution. We propose that this is caused by stabilizing and preventing the collapse of short nascent R-loops. This suggests that R-loop formation is highly dynamic and highlights single strand binding proteins as players in cellular R-loop regulation. We further show that non-template strand DNA nicks are powerful initiators of R-loop formation, increasing R-loop frequencies by up to two orders of magnitude. Atomic force microscopy (AFM) revealed that the non-template strand in nick-initiated structures is often flayed away from the RNA:DNA hybrid and engaged in self-pairing, creating unique forked R-loop features. DNA nicks, one of the most frequent DNA lesions in cells, are therefore potential hotspots for opportunistic R-loop initiation and may cause the formation of a novel class of R-loops. Overall, this work highlights the importance of the displaced single-strand on R-loop initiation and dynamics.

overall_design: R-loop footprinting (SMRF-seq) of in-vitro transcribed plasmids with/without ssDNA nick (CRISPR/Cas9 or NtBspQI) in the presence/absence of ssDNA binding protein (SSB) added during or post-transcription. Untranscribed plasmids and transcribed + RNaseH1 plasmids were used as controls.

first: Ethan

last: Holleman

first: Thomas

last: Catley

first: Tadas

last: Sereiva

first: Stella

last: Hartono

first: Alice L

last: Pyne

first: Frédéric

last: Chédin


title: Combined use of FoxM1 inhibitor, thiostrepton and the PI3K/mTOR dual inhibitor, GSK458, synergistically promotes an anticancer effect in ovarian clear cell carcinoma

status: Public on Sep 26 2025

city: SUITA

first: WANG

last: YAN

state: OSAKA

address: 2-2 YAMADAOKA

country: Japan

institute: Osaka University

type: Expression profiling by high throughput sequencing

summary: Activating mutations in PIK3CA encoding p110α, the catalytic subunit of PI3K, have been described to occur in 33%–40% of OCCC. To testify whether Thiostrepton and GSK458 could exert synergistic anti-tumor effects against OCCC, we use RNA sequence from TOV21G cell line therapy groups.

overall_design: The groups were divided into four groups-Control group, thiostrepton (1uM) monotherapy, GSK458 (0.1uM) monotherapy, thiostrepton combined with GSK458 group for 48h. Total RNA was extracted using the Qiagen RNeasy Mini Kit (Qiagen, Venlo, Netherlands). RNA integrity was evaluated using the Agilent 2100 Bioanalyzer RNA Nano Chip (Agilent Technologies, Santa Clara, CA, USA). There is one sample for each group. Totally there are four samples from each therapy group.

first: Yan

last: Wang

first: Yasuto

last: Kinose


title: Bulk RNAseq of ex vivo salt treated isolated human monocytes

city: Nashville

first: Ashley

last: Mutchler

address: 1005 Dr. D.B. Todd Jr. Boulevard

country: USA

institute: Meharry Medical College

summary: Salt sensitivity of blood pressure (SSBP) is associated with persistent immune activation after sodium normalization, suggesting immune “salt memory.” Prior work identified that sodium entry into antigen-presenting cells (APCs) via epithelial sodium channels triggers NLRP3 inflammasome activation through the formation of isolevuglandins (IsoLGs), highly reactive lipid aldehydes. IsoLG scavenging with 2-hydroxybenzylamine (2-HOBA) reduces NLRP3 expression and attenuates salt-induced hypertension, implicating IsoLGs as upstream immune regulators. This study tested whether IsoLGs also act as epigenetic modifiers by covalently modifying histone H1, thereby altering chromatin accessibility at inflammatory loci such as NLRP3. PBMCs from 10 hypertensive adults classified as salt-sensitive (SS) or salt-resistant (SR) were collected at baseline, after salt loading, and after depletion. Integrated single-cell RNA-seq and ATAC-seq revealed that SS monocytes exhibited salt-induced enhancer activation and increased chromatin accessibility at the NLRP3 locus. IsoLG–protein adducts correlated with blood pressure changes and were most prominent in CD14⁺ monocytes. In murine APCs, high salt induced IsoLG adduction of histone H1, attenuated by 2-HOBA. Knockdown of H1F0 reduced high salt–induced NLRP3 expression, supporting a role for H1.0 in transcriptional regulation. These findings identify IsoLG modification of histone H1 as a potential mechanism linking extracellular sodium exposure to persistent chromatin remodeling and sustained inflammatory gene expression in SS individuals. IsoLG–histone adducts may represent novel therapeutic targets for immune-driven hypertension.

overall_design: Heparinized blood was obtained from 11 volunteers, and peripheral blood  mononuclear cells (PBMCs) were isolated by Ficoll gradient. Briefly, collected blood was diluted 4-fold with PBS+2mM EDTA buffer then carefully layered over 15 mL of Ficoll-PaqueTM  in a 50 mL conical tube. After centrifugation at 400xg for 30 minutes at 20°C, carefully aspirate the top plasma layer. Next, carefully remove the next layer containing PBMCs and tranfer to another 50 mL conical tube. Fill with buffer and centrifuge again at 300xg for 10 minutes at 20°C. Resuspend the cell pellet and proceed to monocyte isolation. Isolation of monocytes was achieved by magnetic labeling and negative selection using the Miltenyi monocyte isolation kit  (Miltenyi Biotec, Cat# 130-091-151), according to manufacturer’s protocol using LS columns. Monocytes were then cultured in 12-well plates at 1 x 10^6 /mL density in either normal salt RPMI media (150 mM) or high salt RPMI media (190 mM) for 72 hr. RPMI media 1640 (Gibco) was supplemented with 10% FBS, 1% pen/strep, 1% HEPES, and 2-Mercaptoethanol (0.05 mM). For total RNA isolation, we used the RNEasy Midi Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocol. Targeted analysis of polyadenylated transcripts was performed using the Illumina Tru-seq RNA sample prep kit, and paired-end sequencing was done on the Illumina HiSeq2500. Using the R package, the FASTQ data files from the paired-end sequencing analysis were aligned with TopHat 2 for each sample against the human GRCh38 reference genome assembly. Quality control for the RNAseq data occurred during the following stages: 1) RNA quality; 2) raw read data (FASTQ); 3) alignment; 4) gene expression. Quality control for the raw data and alignment were performed using QC3 , and the MultiRankSeq method was used for expression analysis. Raw data false discovery rate (FDR < 0.05) was used to correct for multiple hypothesis testing.

first: Jeremiah

middle: M

last: Afolabi

first: Mohammad

last: Saleem

first: Annet

last: Kirabo

middle: L


title: ID2 downregulation promotes tumor cell proliferation via elevated TCF3 activity in Multiple Myeloma [RNA-Seq]

city: Boston

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Multiple myeloma (MM) is characterized by rewired transcriptional circuits. Transcription factors and their cofactors are major and selective non-oncogene dependencies in MM cells. By performing a gain-of-function (GOF) perturbation screen in MM cell lines, we identified the Inhibitor of DNA binding (ID) proteins as putative suppressors of MM cell fitness. Among the ID genes, ID2 was found to be downregulated in MM patient cells and acted as a tumor suppressor by directly binding and repressing the transcription factor TCF3. Lower ID2 expression in MM cells conferred a proliferative advantage by allowing higher TCF3 activity in tumor cells, resulting in a striking dependency on this TF. To the contrary, ID2 overexpression reduced TCF3 binding to DNA and rewired the MM transcriptome, leading to cell-cycle arrest and senescence. The myeloma bone marrow milieu participates in this process by further decreasing the expression of ID2 and enhancing TCF3 activity, revealing a novel mechanism by which the tumor microenvironment controls MM cell behavior.

overall_design: RNA-seq profiling was performed on three myeloma cell lines (AMO1, H929, and KMS20) and their ID2-overexpressing derivatives (ID2-OE) after 24 hours of incubation with 0.25 µg/ml doxycycline.

first: Mariateresa

last: Fulciniti

first: Yao

last: Yao

first: Tommaso

last: Perini

first: Raphael

last: Szalat

first: Nikhil

middle: C

last: Munshi


title: Transient RORβ Knockdown by Cell-penetrating siRNA Alleviates Retinal Degeneration Caused by Proteotoxicity

city: Ulsan

first: Hyo Kyung

last: Lee

address: UNIST-gil 50

department: Biomedical engineering

country: South Korea

institute: UNIST

summary: Retinitis pigmentosa (RP) is characterized by rod photoreceptor degeneration-driven apoptosis, which secondarily triggers cone photoreceptor loss and eventual blindness. Preserving rod function remains a primary therapeutic objective. Inspired by prior studies demonstrating that neural retina leucine zipper (Nrl) knockdown conferred resistance to rod mutations and induced in vivo rod-to-cone conversion with therapeutic effects in inherited retinal degeneration (IRD) models, we hypothesized that knockdown of retinoid-related orphan receptor beta (RORβ), an upstream regulator of Nrl, could yield similar or superior outcomes. To test this, we developed a cell-penetrating asymmetric siRNA (cp-asiRNA) targeting RORβ (cp-asiRORB), designed to overcome conventional siRNA limitations, including inefficient cellular delivery, off-target effects, and immune activation. Intravitreal administration of cp-asiRORB in RhoP23H mice—an autosomal dominant RP model harboring the P23H rhodopsin mutation—successfully reduced RORβ expression in rod photoreceptors. Contrary to our initial expectation of observing an in vivo reprogramming effect, RORβ knockdown did not seem to induce rod-to-cone conversion. Instead, transient RORβ suppression effectively mitigated apoptosis by enhancing proteostasis, leading to improved rod survival, reduced degeneration, and preserved visual function.  Furthermore, single-cell RNA sequencing of retinas treated with cp-asiRORB in RhoP23H mice revealed significant upregulation of proteasomal subunits in RORβ-reduced rod photoreceptors. Consistent with these findings, in HEK293T cells under proteotoxic stress, RORβ knockdown reduced apoptosis, improved cell viability, and diminished aggresome formation. These results demonstrate that transient RORβ suppression alleviates RP progression by augmenting proteasomal activity to resolve proteotoxicity, offering a novel therapeutic avenue for RP patients.

overall_design: All animal experiments were performed in accordance with the guidelines approved by the Institutional Animal Care and Use Committee (IACUC) of Konkuk University (Approval No. KU24219). The mice were housed under a 12-hour light/dark cycle at a temperature of 22 ± 2°C and humidity of 50 ± 10%, with free access to food and water. Two- and eight-week-old C57BL/6J mice were obtained from DBL (Incheon, Korea), while RhoP23H mice and rd10 mice were purchased from Jackson Laboratory (Bar Harbor, Maine, USA) and bred under Specific Pathogen-Free (SPF) conditions at the Konkuk University Laboratory Animal Research Center. Genotyping was performed using PCR with specific primers (primer sequences in Supplementary Table S1). Experiments involving RhoP23H mice utilized heterozygous animals, while those involving rd10 mice used homozygous animals. All experimental groups were randomly assigned. Two-week-old RhoP23H and rd10 mice were carefully administered an intravitreal injection of cp-asiRORβ (1 μg/μL), followed by analysis three weeks later. The same procedure was performed on two- and eight-week-old C57BL/6J mice.

first: Chanok

last: Son

first: Hyoik

last: Jang

first: Chul-Woo

last: Park

first: Dong Ki

first: Semin

first: Hyewon

last: Chung


title: Characterization of the Effects of Oxymatrine on Myocardial Hypertrophy in SHR Through Metabolome and Transcriptome

city: Chongqing

first: Chaohong

last: Li

address: Yuzhong Road

country: China

institute: Chongqing Medical University

summary: Cardiac hypertrophy is a cardiac structural remodeling and dysfunction resulting from chronic hypertension and is an independent risk factor for cardiovascular morbidity and mortality. Study have implicated the protect role of oxymatrine (OMT) on the ventricular remodeling in spontaneously hypertensive rats (SHRs). However, the underlying mechanisms of remains unclear. In this study, we investigated investigates the potential of OMT in improving myocardial hypertrophy in SHRs through integrated analysis of transcriptomics and metabolomics. The results show that OMT significantly alleviates myocardial hypertrophy in SHRs and improves heart function by reducing the myocardial enlargement and collagen deposition. Transcriptomic analysis revealed that OMT reversed the expression of 10 genes associated with linoleic acid/arachidonic acid metabolism, cytochrome P450, steroid hormone biosynthesis, and myocardial adrenergic signaling. Metabolomic analysis indicated that OMT reversed the levels of 16 metabolites related to steroid hormone biosynthesis, aldosterone synthesis and secretion, and tryptophan metabolism. Integrated analysis revealed that Integrated analysis identified Cyp2e1 and desoxycortone (also known deoxycorticosterone, DOC) as key genes and metabolites involved in the transcriptional and metabolic interactions through which OMT improves myocardial hypertrophy in SHR. In summary, our study underscores the potential molecular and metabolic mechanisms of OMT against pressure overload-induced myocardial hypertrophy and provides theoretical support for its exploration in other indications.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the left ventricle in spontaneously hypertensive rats (SHR) with or without oxymatrine.

first: Xingyu

first: Jie

last: Tan

first: Qinghua

last: Fang

first: Muzi

last: Zhang

first: Jing

last: Huang


title: Discovery of circulating cell-free DNA 5hmC  biomarkers for peritoneal metastasis in colorectal and appendiceal cancer

city: Chicago

first: Lu

last: Gao

state: IL

institute: University of Chicago

summary: Peritoneal metastasis (PM) is associated with a poor prognosis in patients with colorectal cancer (CRC) or appendiceal adenocarcinoma (AA). Detection of PM remains challenging due to the low sensitivity of current imaging modalities and the invasiveness of tissue pathology-based diagnostics. Here, we demonstrate for the first time the feasibility of using 5-hydroxymethylcytosine (5hmC) signatures derived from circulating cell-free DNA (cfDNA) as minimally biomarker s for PM. Using nano-hmC-Seal on plasma-derived cfDNA and next-generation sequencing, we obtained genome-wide 5hmC profiles from 112 CRC or AA patients   (n = 71 PM+ and n = 41 PM–) and 73 non-cancer controls. Predictive models trained on genomic region  5hmC levels distinguished PM status with an area under the curve of 0.827  (92.4% sensitivity, 46.1% specificity). Pathway enrichment analysis identified epigenetically dysregulated cancer, cell migration, adhesion and immune-related pathways in PM. This study lays a foundation for future clinical assay development for PM.

overall_design:
Case-control study: Differential 5hmC features were identified by comparing PM+ patients, PM− patients, and non-cancer controls

Access to demographic information requires contacting the corresponding author and will only be provided upon reasonable request.

first: Yuri

last: Malina

first: Ankit

last: Dhiman

first: Diana

last: West-Szymanski

first: Yaniv

last: Berger

first: Xiaolong

last: Cui

first: Zhou

first: Urszula

last: Dougherty

first: Hunter

last: Witmer

first: Marco

last: Rivas

first: Chang

last: Ye

first: Biren

last: Reddy

first: Alex

last: Luna

first: Akushika

last: Kwesi

first: Zifeng

last: Deng

first: Alana

last: Beadell

first: Philip

last: Hsu

first: Chuan

last: He

first: Wei

first: Marc

last: Bissonnette

first: Kiran

last: Turaga


title: Iron-sensitive RNA regulation by poly C binding proteins

city: Chapel Hill

first: Maria

last: Aleman

state: NC

address: 120 Mason Farm Rd.

institute: University of North Carolina at Chapel Hill

summary: Iron is important for normal cellular function and posttranscriptional mechanisms regulate the cellular response to iron deficiency. In this study we explore how RNA binding proteins, PCBP1 and PCBP2, exhibit iron-sensitive RNA regulation.

overall_design: Stable K562 cells were treated with or without doxycycline to induce overexpression of flag-tagged PCBP1

first: Daniel

last: Dominguez


title: Iron-sensitive RNA regulation by poly C binding proteins [P1KD]

overall_design: K562 cells were transduced to express short hairpin RNAs targeting luciferase (shCtrl) or PCBP1 (shPCBP1).


title: Gene expression profile at single cell level of CD45+ lymphocytes in B16 tumors treated with or without SPOP inhibitor SPOP-IN-6b

first: Pengda

middle: P.

last: Lie

address: 21-246 Lineberger Cancer Center

department: Biochemistry and Biophysics

summary: SPOP inhibitor stabilize STING protein and activate STING signaling in vitro, which may enhance anticancer immunity. We used single cell RNA sequencing (scRNA-seq) to analyze the effect of SPOP inhibitor on the composition of different types of infiltrated CD45+ immune cells in B16 melanoma tumors

overall_design: B16 tumor-beraring C57BL/6J mice were daily treated with or without 60 mg/kg of SPOP-IN-6b from day 5 to day 13. On day 14, tumor-infiltrating CD45+ cells in B16 tumors were enriched through positive selection via anti-CD45 biotinylated antibody and streptavidin pulldown, followed by scRNAseq.

first: Xin

last: Zhou

first: Zhichuan

last: Zhu

first: Mark

last: G. Woodcock

first: Gatphan

last: Atassi


title: Iron-sensitive RNA regulation by poly C binding proteins [chelator]

overall_design: K562 cells were treated overnight with DMSO (control) or iron chelator (21H7) with three biological replicates per condition.


title: Transcriptional landscape of asymmetric gonadal development in female chicken embryos [scRNA-seq]

city: University Park

first: Tae Hyun

last: Kim

state: PA

address: 317 AVBS

institute: Penn State University

summary: Asymmetrical gonadal development is an intriguing phenomenon observed in the majority of female birds. In chickens, the left gonad of female embryos develops into a functional ovary, while the right gonad undergoes degeneration during embryogenesis. This sexually dimorphic trait is primarily induced by the spatial differential expression of the PITX2 gene. However, a comprehensive understanding of the transcriptional profile of the developing gonads during asymmetric development is still lacking. To elucidate the molecular mechanism of asymmetric gonadal development in chickens, we compared the transcriptomes between left and right gonads of female chickens using bulk- and single cell (sc) -RNA sequencing (RNA-seq) approaches. Our bulk RNA-seq analysis of the female chicken gonads at E5 (HH26), E6.5 (HH30), E8 (HH34), and E9.5 (HH36) revealed significant differential gene expression between the left and right female chicken gonads, particularly in signaling pathways, cell cycle, and metabolic processes. Moreover, scRNA-seq analysis revealed that coelomic epithelial, interstitial, and pre-granulosa cells of the left gonads share a highly proliferative status, contributing to the asymmetric gonadal cell proliferation, which may be regulated by the TGFβ signaling pathway. Our findings demonstrate that dynamic cell-type-specific transcriptional profiles during embryogenesis play a vital role in the asymmetric gonadal development of female chickens.

overall_design: To investigate the asymmetrical development of female gonads at the single-cell level during early differentiation, we separately collected the left and right gonads at embryonic day 5 (E5) and performed 10x single-cell RNA sequencing (scRNA-seq).

first: Hongjo

last: Lee


title: Study on the mechanism of macrophage PTEN inhibiting intestinal neurogenesis and inflammation progression

city: Zhengzhou

first: chen

last: lin

state: Henan

address: Erqi District, University North Road

institute: ZHENGZHOU University

summary: Chronic stress can promote nerve progression and aggravate intestinal inflammation. We found that stress can induce the downregulation of cellular PTEN, thus promoting the proliferation of intestinal nerve cells and inducing increased inflammation

overall_design: Comparative gene expression profiling analysis of RNA-seq data for macrophages from WT mice and macrophages  PTEN knockout mice

first: Ming

last: Wang

first: Lin

last: Chen

first: Zhenzhen

last: Pan

first: Yan

last: Yan


title: Transcriptional landscape of asymmetric gonadal development in female chicken embryos

overall_design: To investigate the female asymmetrical gonad development in avian species, we collected left and right embryonic gonads separately at four different time points during embryonic development and performed RNA-seq analysis


title: E2F1 induces a G0-G1 re-entry transcriptional program without changing chromatin accessibility [RNA-seq]

city: Santa Cruz

first: Ali

last: Shariati

address: 1156 High St

department: Biomolecular Engineering

institute: University of California Santa Cruz

summary: Many cells in our body reside in a reversible nondividing state termed G0 or quiescence. Precise regulation of entry and exit from G0 is critical for maintaining tissue homeostasis. G0 entry can occur when cells do not receive the required signals for cell cycle progression, leading to active repression of cell cycle genes through several mechanisms, including formation of repressor complexes to restrict chromatin accessibility for transcriptional activators. G0 cells can re-enter the G1 phase of the cell cycle upon receiving growth factor signals, resulting in activation of the Mitogen-Activated Protein Kinase pathway, converging on E2F transcription factors. Ectopic expression of E2F1 alone, a transcriptional activator, is sufficient to promote G0 exit without requiring the upstream signals, but it is unclear how E2F1 can overcome the chromatin lockdown in G0 cells to activate cell cycle genes. To better understand this mechanism, we compared dynamics, gene regulation and chromatin accessibility state between E2F1-mediated and growth factor (serum)-induced cell cycle reentry. Using live cell single cell tracking, we observe that E2F1 induction leads to accelerated cell cycle progression compared to regular serum-induced cell cycle re-entry. This accelerated cell cycle re-entry by E2F1 is accompanied by faster upregulation of cell cycle genes. Interestingly, we find that E2F1 preferentially binds to gene promoters that remain in a poised chromatin state after G0 induction, suggesting that G0 cells are prepared for cell cycle re-entry via regulating chromatin states in essential cell cycle genes.

overall_design: Constucts for doxycycline inducible expression of E2F1 or empty-vector (EV) control were stably integrated into 3T3 cells. The E2F1 and EV 3T3 cells were serum starved for 48 hours to induce a G0-like state, followed by E2F1 induction, EV induction or 10% serum addition, to induce G1/S phase reentry. Samples were collected at 0, 2, 6 and 12 hours after induction or serum addition. RNA was extracted for RNA-sequencing and nuclei were extracted for ATAC-Seq. In addition, cells were prepared for E2F1 ChIP-Seq at the 12 hour time point only. Together the RNA-Seq, ATAC-Seq and ChIP-Seq were used to identify E2F1 gene regulatory network involved in cell cycle reentry from G0.

first: Gerrald

middle: A

last: Lodewijk

first: Benjamin

middle: R

last: Topacio

first: Silvart

last: Arabian

first: Seungho

first: Abolfazl

last: Zargari

first: Znala

last: Williams

first: Edward

last: Wu

first: Sayaka

last: Kozuki

first: Rana

last: Rahimi

first: Neda

last: Bidoki

first: Vanessa

last: Jonsson

first: Eric

last: Malekos

first: Susan

last: Carpenter

first: Gerd

last: Muller

first: Seth

last: Rubin

middle: S


title: LSD1 inhibition promotes CD8+ T cells mediated anti-tumor immunity by MHC-I upregulation and enhanced infiltration of dendritic cells through IFNγ-CXCL9-CXCR3 axis

first: Manish

middle: V.

last: Bais

address: W216, 700 Albany street

department: Translational Dental Medicine

institute: Boston University

summary: Poor infiltration of CD8+ cells and dysregulated MHC-I provide resistance to anti-cancer clinical therapies. This study aimed to uncover mechanisms of lysine-specific demethylase 1 (Kdm1a or LSD1) in antitumor immunity in Head and Neck Squamous cell carcinoma (HNSCC). LSD1 inhibition in syngeneic and chronic tobacco carcinogen-induced HNSCC mice recruited an activated dendritic cell (DCs), CD4+, and CD8+ T cells, enriched IFNγ in T cells, CXCL9 in DCs, and CXCR3 in T cells, evaluated by single cell RNA-seq analysis. Humanized HNSCC mice and TCGA data validate inverse correlation of Kdm1a with markers of DCs, CD8+ T cells, and their activating chemokines. LSD1 knockout or inhibitors in mouse HNSCC and co-culture showed MHC-I upregulation in tumors for efficient antigen presentation. Overall, LSD1 inhibition promoted DCs through IFNγ-CXCL9-CXCR3 axis and MHC-I upregulation in tumors to induce CD8+ T cell medicated antitumor immunity, which has implications for poorly immunogenic and immunotherapy-resistant cancers therapy.

overall_design: The 4NQO exposed mice were treated with either vehicle (n=4) or SP2509 (n=6) and subjected to RNA sequencing.

middle: V

first: Amit

middle: K

last: Chakraborty

first: Rajnikant

middle: D

last: Raut


title: Gene regulatory network analysis on snRNAseq revealed key regulators for hepatocellular carcinoma progression

city: Seoul

first: Taehong

last: Min

address: 369, Sangdo-ro, Dongjak-gu, Seoul, Republic of Korea

department: School of Systems Biomedical Science

institute: Soongsil University

summary: Many clinical researchers have developed targeted therapy and immunotherapy for the case of advanced stage of hepatocellular carcinoma (HCC). However, the molecular mechanisms of HCC development still need to be investigated to improve the response rate of those therapies. Here, we generated single nucleus RNA sequencing (snRNAseq) data from biopsy samples of six patients with Barcelona Clinic Liver Cancer (BCLC) advanced C stage. We first found that the gene expression heterogeneity in hepatocytes was mainly dissected by vascular invasion. To identify the key regulators of malignant progression of hepatocytes, we applied TENET, a gene regulatory network (GRN) inference tool based on pseudotime-ordered single cell expression. TENET predicts that MLXIPL and CUX1 are the top two regulators and regulate each other. This prediction was comprehensively validated by overexpression and knockdown of CUX1 in two HCC cell lines. This study suggested that GRN analysis with single cell transcriptomics provides new therapeutic targets for HCC.

overall_design: Single nucleus sequencing of HCC was conducted to elucidate genes associated with a poor response to treatment and disease progression, leading to an unfavorable prognosis and to to discover new biomarkers for HCC.


title: Genome-wide transcriptome analysis of whole brain (Except for the cerebellum and olfactory bulb) in CBA/N mouse (Mus musculus)

city: Nagoya

first: Takashi

last: Yoshimura

address: Furo-cho, Chikusa-ku

institute: Nagoya University

summary: We compared the gene expression of whole brain (Exclusion of cerebellum and olfactory bulb) in CBA/N mouse (Mus musculus) between 4-week-feeding under winter-like condition and summer-like condition using RNA-seq.

overall_design: To compare expression profile between winter and summer, we collected whole brain from CBA/N male and female mice (Mus musculus) kept under winter-like condition (Light: Dark=8:16, 10℃) and summer-like condition (Light: Dark=16:8, 30℃) for 4 weeks, and performed RNA-seq analysis.


title: PHF3 binds G-rich RNAs and regulates RNA stability through its TFIIS-like domain (TLD) and plant homeodomain (PHD)

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

country: Germany

institute: Max-Planck-Institut für molekulare Genetik

summary: Transcription and RNA processing are tightly coupled and precisely coordinated to ensure appropriate levels of mature transcripts. The C-terminal domain (CTD) of RNA polymerase II (Pol II) is phosphorylated differentially during the transcription cycle and serves as a landing pad for a variety of transcriptional regulators and RNA processing proteins. PHD finger protein 3 (PHF3) binds to the serine-2 phosphorylated Pol II CTD with its Spen Paralogue and Orthologue C-terminal (SPOC) domain and regulates transcription elongation and mRNA stability. Here we show that PHF3 is an RNA-binding protein that recognizes a G-rich motif prone to form G-quadruplexes (G4s) within RNAs required for  neurogenesis. We identify PHF3 TFIIS-like domain (TLD) as an RNA-binding domain, which shows nanomolar affinity for G-rich RNAs. TLD recruits PHF3 onto target RNAs and acts in concert with the plant homeodomain (PHD) to promote target RNA destabilization. PHF3 SPOC and PHD-TLD domains mediate interactions with various RNA-binding proteins (RBPs) that regulate mRNA stability. While PHF3 SPOC-dependent interactions with the m6A writer complex, splicing and elongation factors do not impact m6A RNA modification, alternative splicing or polyadenylation, PHF3 PHD-TLD domains interact with the PAF1 complex as a positive regulator of mRNA stability and interfere with its binding to Pol II. Our results establish PHF3 as an RNA-binding protein that binds G-rich RNAs through its TLD domain and destabilizes RNAs through PHD-TLD domains.

overall_design: FLASH libraries of N-terminally tagged PHF3 in Flp-In T-Rex HEK293 cells

first: Ibrahim

last: Ilik

first: Xué

last: Strobl

first: Dea

last: Slade

first: Tugce

last: Aktas


title: RNA-seq analysis of the impact of intermediate passaging on cell fate determination of mesendoderm progenitors [Day 12 & 16]

city: Macau

first: Guokai

last: Chen

address: University of Macau Avenida da Universidade Taipa, Macau, China

institute: University of Macau

summary: To investigate the impact of intermediate passaging on cell fate determination, cells were passaged during mesendoderm differentiation, and samples collected at different time points were subjected to bulk RNA-seq. We report here that intermediate passaging alters cell fate and directs mesendodermal progenitors toward cardiac cell fate.

overall_design: Bulk RNA-seq on samples were collected on Day 12 and Day 16 of differentiation, comparing non-passaged cells differentiated in the presence and absence of WNT inhibitor versus cells that differentiated following intermediate passaging.

first: Weiwei

last: Liu

first: Chuyu

first: Ningyi

last: Shao


title: MeRIP-seq and RNA-seq Reveals RNA m6A Methylation Patterns and Gene Expression Profile of Arabidopsis Plants in Response to CMV Infection

city: Shenzhen

first: yujing

last: lin

address: No. 1088 Xueyuan Avenue, Nanshan District, Shenzhen City, Guangdong Province

institute: Southern University of Science and Technology

type: Methylation profiling by high throughput sequencing

summary: We reported that m6A plays a positive role in plant defense against virus pathogen Cucumber mosaic virus (CMV). CMV genomic RNAs can be m6A modified during plant infection, leading to reduced stability of viral RNAs. Dysfunctions of m6A writers and some readers led to increased susceptibility to CMV. Intriguingly, the increased susceptibility was only observed in the absence of 2b protein encoded by CMV. Our data demonstrated that CMV-2b can inhibit the deposition of m6A at viral RNAs through interfering with the assembly of m6A catalytic complexes. Expression of 2b protein can also antagonize plant m6A deposition. Moreover, CMV-2b was also found to interact with m6A reader proteins to disrupt its recognition of m6A-marked viral RNAs. Our findings unraveled an antagonistic mechanism of m6A-mediated plant antiviral defense.

overall_design: The Arabidopsis Col-0 plants were inoculated by wild-type cucumber mosaic virus (CMV) and the mutated virus deficient in 2b protein (CMVΔ2b). At 14 days post infection, CMV and CMVΔ2b-infected plants as well as uninfected mock plants were subjected to MeRIP-seq and RNA-seq analysis.

first: Jiahui

first: Yujing

last: Lin

first: Chengguo

last: Duan


title: RNA-seq analysis of the impact of intermediate passaging on cell fate determination of mesendoderm progenitors

overall_design: Bulk RNA-seq on samples collected on Day 0,1,2,3,5,7,10 of differentiation, comparing non-passaged cells differentiated in the presence and absence of WNT inhibitor versus cells that differentiated following intermediate passaging.

last: LIU

last: SHAO

last: CHEN


title: Resolving the 4D chromatin dynamics during early random X chromosome inactivation

city: Beijing

first: Hao

last: Xie

address: No.5 Yiheyuan Road

institute: Peking University

summary: X chromosome inactivation (XCI) is a process that compensates X-linked gene dosage in mammalian female cells. The silencing of a randomly selected chromosome is accompanied by dramatic three-dimensional (3D) reorganization across the entire chromosome. To investigate the 4D chromatin dynamics during early inactivation stages, we applied the multi-omics sequencing technique HiRES, which simultaneously detects 3D genome and transcriptome in single cells, in a mouse embryonic stem cell line with induced random XCI. The 3D genome and transcriptome dual-omics data allowed us to identify XCI lineages at single-cell resolution. We characterized multiple layers of chromosome reorganization during random XCI and discovered a transient structural inactivation state for both X chromosomes resulted from biallelic Xist expression. By constructing single-cell inactivation trajectories, we found that a vast majority of chromatin remodeling either accompanied or followed gene silencing. Further analysis of interaction decay kinetics revealed that TAD attenuation began from loss of interactions on TAD anchors. This study thus drew a detailed depiction of fine-scale chromatin reorganization during the initiation of random XCI.

overall_design: To initiate random X-chromosome inactivation (rXCI), we induced the differentiation of female hybrid mouse embryonic stem cells (mESCs) obtained from a cross between the C57B6/J and CAST/EiJ mouse strains by removing 2i/Lif. Subsequently, we harvested cells at multiple time points during the differentiation process, spanning from day 0 to day 4. We then utilized HiRES technology to simultaneously obtain 3D genome and transcriptome data at the single-cell level.

first: Xiaowen

first: Zhiyuan


title: IL-4-mediates Pro-Regenerative Cellular Reprogramming in 3D Liver Culture

city: Toronto

first: Diana

last: Nakib

state: ON

address: 101 College Street

country: Canada

institute: University of Toronto

summary: This study highlights the proregenerative effects of interleukin-4 in a 3-dimensional liver tissue culture platform. Interleukin-4 supplementation induces a myeloid cell phenotype shift, expands hepatocyte and cholangiocyte progenitors and inhibits fibroblast activation. Our findings open new avenues for cytokine-based therapies to stimulate immune-driven liver regeneration.

overall_design: Single nucleus RNA sequencing of live nuclei in murine precision cut liver slices by high throughput sequencing

first: Damra

last: Camat

first: Ian

last: McGilvray

first: Sonya

last: MacParland


title: Pharmacological Targeting of RIG-I Selectively Activates the Integrated Stress Response

city: La Jolla

first: Jeffery

last: Kelly

state: California

address: 10550 North Torrey Pines Road

department: Chemistry

institute: The Scripps Research Institute

summary: The integrated stress response (ISR) is a eukaryotic pathway that attenuates global protein synthesis while allowing selective translation of specific mRNAs, which together can reestablish homeostasis following an acute stress. Diverse pathologic insults activate one or more of the four ISR kinases, which selectively phosphorylate eIF2a to induce translational and transcriptional adaptation of multiple biological functions. Recent results suggest that enhancing ISR kinase activity could ameliorate pathologies linked to numerous diseases, including many neurodegenerative disorders. However, few pharmacological strategies exist to selectively activate ISR kinases and downstream adaptive signaling. Here, we describe compound A8 and its cyclized metabolite CC81 as highly-selective ISR activators that activate the heme-regulated inhibitor (HRI) ISR kinase through a mechanism involving binding of the cytosolic pattern recognition receptor RIG-I. Our results establish a pharmacological strategy to selectively activate HRI-dependent ISR signaling by targeting RIG-I, revealing new mechanistic options for ameliorating etiologically diverse diseases through ISR activation.

overall_design: Total RNASequencing of A8 treated HEK293T cells to determine mechanism of action. RNA was submitted to BGI Genomics Co., Ltd. for strand-specific mRNA sequencing on their DNBSEQ platform with three biological replicates per condition.

first: Caroline

last: Cuoco

first: Leonard

last: Yoon

first: Jessica

last: Rosarda

first: Evan

middle: T

last: Powers

first: R

last: Wiseman

middle: W


title: Gene expression profile of cholangiocarcinoma（CCA）cells by overexpressing miR-182/183-5p

city: Jinan

first: Shu

middle: Li

last: zhuang

state: China/Shandong

address: Department of General Surgery, Qilu Hospital, Shandong University, 107, Jinan Culture Road, Jinan, 250012, China.

department: Qilu Hospital

institute: Shandong University

summary: Cholangiocarcinoma (CCA) is a type of highly aggressive cancer arising from the biliary system. Through miRNA sequencing, we screened that miR-182/183-5p was highly expressed in bile exosomes. miRNA affects gene expression by binding to mRNA or otehr. Here we profile the transcriptome of CCA cells following miR-182/183-5p overexpressing.

overall_design: We overexpressed NC, miR-182-5p and miR-183-5p in cholangiocarcinoma cell line QBC-939, respectively. Cell total mRNA expression profiling was dected by high throughput sequencing.

first: Zongli

last: Zhang

first: Yunfei

last: Xu

first: Lizhuang

last: Shu


title: Single cell analysis of the impact of intermediate passaging on cell fate determination of mesendoderm progenitors

first: Guokai

last: Chen

summary: To investigate the impact of intermediate passaging on cell fate determination, cells were passaged during mesendoderm differentiation, and samples collected at different time points were subjected to single cell RNA sequencing. We report here that intermediate passaging alters cell fate and directs mesendodermal progenitors toward cardiac cell fate.

overall_design: Single cell RNA sequencing on samples collected on Day 2, 3 and 10 of differentiation, comparing passaged and non-passaged cells in the presence and absence of WNT inhibitor.

first: Weiwei

last: LIU

first: Chuyu

first: Ningyi

last: SHAO


title: Methylation profiling of PDX-AML samples using Illumina Infinium MethylationEPIC BeadChips

status: Public on Sep 25 2025

city: Munich

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

department: Research Unit Apoptosis in Hematopoietic Stem Cells

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany

summary: We established serially transplantable and robust, genetically engineered patient derived xenograft (PDX) models of acute myeloid leukemia (AML).

overall_design: Patients'  primary AML cells were transplanted into NSG mice. Models which engrafted were serially passaged and isolated from murine bone marrow. Methylation profiling was done with Illumina Infinium MethylationEPIC BeadChips.

first: Binje

last: Vick

first: Tobias

last: Herold

first: Sebastian

last: Vosberg

first: Philipp

last: Greif


title: Promoter competition and Polycomb Response Elements govern transvection efficiency between co-regulated engrailed and invected genes in Drosophila.

city: Los Angeles

first: Natalie

middle: Dianna

last: Gehred

address: 650 Charles E Young Dr

department: Anesthesiology & Perioperative Medicine

institute: University of California, Los Angeles

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transvection is a phenomenon where gene regulatory elements interact between different chromosomes, adding an additional layer of regulatory control beyond traditional cis-interactions. Although transvection effects have been characterized for many individual genes in Drosophila, it remains unclear how trans-interactions occur among multiple co-regulated genes where enhancers are shared. Here we demonstrate that transvection is supported at the engrailed-invected (en-inv) locus, where transcription of the two developmental patterning genes is coordinated by common enhancers. Our data show that the presence of the en promoter in cis to the enhancers prevents trans-activation of inv, but removal of this promoter enables robust transvection, demonstrating competition between heterologous promoters in trans. We also find that local Polycomb Response Elements (PREs) enhance transvection reliability but are not strictly required for trans-activation. Furthermore, our analysis reveals that transvection at this locus is developmentally regulated, occurring efficiently in third instar larval tissues and late-stage embryos but not in early embryonic stages. Finally, we show that en-inv transvection can be reconstituted using transgenic constructs at an ectopic chromosomal location where it produces a striking reciprocal expression pattern between en in cis and inv in trans, suggesting that these enhancers can choose to activate one promoter or the other in a stochastic manner.

overall_design: ChIP-seq of H3K27me3 histone post-translational modification in Drosophila melanogaster 3rd instar larval brains and wing imaginal discs from homozygotes of the HAinv84-invdel45 and invdel45 lines.

first: Yuzhong

last: Cheng

first: Adrienne

last: Perkins

first: Fountane

last: Chan

first: Jack

last: Bateman

first: Judith

last: Kassis


title: Translatome of Dorsal Striatum Parvalbumin interneurons revisited: insights across diverse experimental paradigms [RiboTag]

city: Bellaterra (Cerdanyola del Vallès)

first: Laura

last: Cutando Ruiz

state: Barcelona

address: Facultat de Medicina, M1/125, Av. de Can Domènech Campus de la UAB · 08193 Bellaterra

department: Department of Cellular Biology, Physiology and Immunology - Institute of Neurosciences

country: Spain

institute: Universitat Autònoma de Barcelona

summary: Parvalbumin (PV) interneurons in the dorsal striatum (DS) are fast-spiking GABAergic cells critical for feedforward inhibition and synaptic integration within basal ganglia circuits. Despite their well-characterized electrophysiological roles, their molecular identity remains incompletely defined. Using the Ribotag approach in Pvalb-Cre mice, we profiled the translatome of DS PV interneurons and identified over 2,700 transcripts significantly enriched (fold-change > 1.5) in this population. Our data validate established PV markers and reveal a distinct molecular signature of DS PV neurons compared to PV interneurons from the nucleus accumbens. Gene ontology analyses highlight prominent expression of genes related to extracellular matrix components, cell adhesion molecules, synaptic organization, ion channels, and neurotransmitter receptors, particularly those mediating glutamatergic and GABAergic signaling. Notably, perineuronal net markers were robustly expressed in DS PV interneurons and confirmed by immunofluorescence. Transcriptomic analysis of DS PV neurons following repeated d-amphetamine exposure identified Gm20683 as the only differentially expressed transcript between treated groups. Furthermore, RNAseq analysis of mice subjected to an operant behavior paradigm with two types of food reward (high-palatable diet or standard chow) identified over 1,000 and 100 genes enriched in DS PV neurons from standard and high-palatable masters, respectively. These findings provide a comprehensive molecular profile of DS PV interneurons, distinguishing them from other striatal PV populations, and reveal specific gene expression changes associated with psychostimulant exposure and reward-driven behaviors. Our findings deepen insight into the molecular mechanisms of PV interneuron activity in striatal circuits and their potential roles in neuropsychiatric, motor and reward-related disorders.

overall_design: Whole striata were extracted from adult Pvalb-Ribotag mice, as previously described (Puighermanal et al., 2020). Striatal tissue from two to three mice was pooled to generate a single sample for polyribosome immunoprecipitation and subsequent RNAseq. Punches containing striata of Pvalb-Cre:RiboTag mice were homogenized and incubated with anti-hemagglutin (HA) antibodies and protein A/G magnetic beads to isolate the polysome-associated mRNAS in PV neurons.

first: Emmanuel

last: Valjent

last: Cutando


title: Translatome of Dorsal Striatum Parvalbumin interneurons revisited: insights across diverse experimental paradigms [RNA-Seq]


title: Fat cadherin cleavage releases a transcriptionally active nuclear fragment to regulate target gene expression

city: St. Louis

first: Helen

last: McNeill

state: Missouri

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine in St. Louis

summary: The atypical cadherin fat (ft) controls growth, planar cell polarity (PCP) tissue organization, and mitochondrial function, in organisms ranging from fruit flies to mammals.  Working at the apical-junctional plasma membrane, the intracellular domain of the Ft protein, FtICD binds to and regulates components of the Hippo and PCP pathways.  Unexpectedly, we find that a fragment of the FtICD is present in the nucleus in cultured cells as well as in embryonic and larval tissues and identify nuclear localization and nuclear export signals in FtICD required for this localization.  We show membrane-bound FtICD is cleaved and enters nuclei in vivo.  Using endogenously tagged Ft as well as overexpressed FtICD we conducted ChIP-seq experiments and identified putative Ft targets including genes involved in signaling pathways, chromatin organization, pattern formation, and neural development.  RNAseq demonstrates that some of these genes are dysregulated in ft mutants.  We observe strong co-localization of Ft binding regions with peaks for other factors such as DREF and BEAF-32, as well as the Hippo pathway components Yorkie (Yki) and Scalloped (Sd), suggesting that Ft may act in conjunction with these factors to regulate gene expression.  Supporting this hypothesis, we found that Ft physically interacts with both Yki and Sd in co-immunoprecipitation experiments in S2 cells.  We propose that the modulation of Hippo pathway activity constitutes one of the nuclear functions of Ft, complementing its established function as an upstream regulator of Hippo signaling.

overall_design: RNA-seq profiling of Drosophila 16-20 h embryo. This dataset is used to compare w^1118 (wild-type) and ft^fd5-5/ft^X13 (Ft null mutants).

first: Jannette

last: Rusch

first: Nattapon

last: Thanintorn

last: Mcneill


title: Fatty acid-activated proton transporter SR4 prevents hepatic steatosis and metabolic alterations in diabetic mice by improving mitochondria function, energy balance and oxidative stress

city: Duarte

first: Yate-Ching

last: Yuan

address: 1500 East Duarte

institute: City of Hope

summary: Type 2 diabetes (T2D) is a growing global health crisis, largely driven by rising obesity rates. Untreated T2D leads to severe complications such as cardiovascular disease, nephropathy, retinopathy, neuropathy, and hepatic dysfunction. Current therapies primarily manage hyperglycemia but often fail to address core pathophysiological drivers like insulin resistance and obesity. This highlights an urgent need for novel therapeutics with distinct mechanisms, particularly those targeting energy metabolism and insulin sensitivity, to improve long-term T2D outcomes. Modulating mitochondrial respiration through mild uncoupling has emerged as a promising strategy to promote negative energy balance. SR4, a small-molecule mitochondrial uncoupler, represents a novel class of fatty acid-activated proton transporters. In this study, we investigated the metabolic effects of oral SR4 administration in male db/db mice model of T2D. SR4 significantly reduced body weight gain and improved body composition by selectively decreasing fat mass without affecting lean mass. Indirect calorimetry confirmed that SR4 treatment increased oxygen consumption and total energy expenditure, independent of food intake. Importantly, SR4 substantially improved glycemic control, reduced insulin resistance, and prevented dyslipidemia, hepatic steatosis, and liver injury. Mechanistically, SR4 activated hepatic AMP-activated protein kinase (AMPK), enhanced mitochondrial respiration, and mitigated oxidative stress. Liver transcriptomic profiling further demonstrated broad metabolic reprogramming, including downregulation of lipogenesis and peroxisome proliferator-activated receptor γ (PPARγ) signaling, concurrently with upregulation of genes involved in energy metabolism and antioxidant defense. Collectively, these findings demonstrate that SR4 ameliorates multiple aspects of metabolic dysfunction in an obese T2D mouse model by targeting key pathways in energy regulation and lipid metabolism. Our results provide additional mechanistic insights into the effects of mitochondrial uncouplers in the liver and support further investigation of SR4 and related fatty acid anion transporters as a novel therapeutic class for metabolic diseases.

overall_design: RNA sequence profiling of livers from  db/db mouse after 5 weeks treatment via  vehicle control versus after 5 weeks of SR4 treatment

first: James

last: Figarola

first: Jyotsana

last: Singhal

first: Sharad


title: Enhanced Trained Immunity in Peripheral Monocytes in Unstable Angina With Elevated High-Sensitivity C-Reactive Protein

city: Wuhan

first: Jiyu

last: Zhang

state: Hubei

address: 1277 Jiefang Road, Jianghan District, Wuhan 430022, Hubei, China

institute: Huazhong University of Science and Technology

summary: Despite effective secondary prevention for coronary heart diseases, recurrent events remain high. Elevated high-sensitivity C-reactive protein (hsCRP) indicates increased inflammation risk. This study aimed to investigate the trained immunity of circulating monocytes in unstable angina (UA) patients with elevated hsCRP. We analyzed CD14+ monocytes from UA patients, comparing high-risk (hsCRP ≥3 mg/L) and low-risk (hsCRP <1 mg/L) groups. We assessed cytokine production and conducted metabolic, transcriptional, and epigenetic profiling. Patients with elevated hsCRP exhibited enhanced proinflammatory responses, glycolytic activity, and altered immune profiles, indicating sustained monocyte trained immunity, which contributes to residual inflammation risk in cardiovascular disease.

overall_design: RNA-seq profiling of CD14+ monocytes from UA patients, comparing high-risk (hsCRP ≥3 mg/L, n=6) and low-risk (hsCRP <1 mg/L, n=6) groups. Monocytes were magnetically purified from blood and profiled either immediately after sorting or after LPS stimulation (10 ng/mL, 6 hours).

first: Fen

last: Yang

first: Yuhan

last: Liao

first: Xinyi

last: Xia

first: Miao

last: Yu

first: Xiang


title: The impact of hsa_circ_0001910 on downstream gene expression changes in breast cancer cells

city: Shijiazhuang

first: Fei

last: Liu

state: China

address: No. 12 Jiankang Road

institute: The Fourth Hospital of Hebei Medical University Cancer Institute

summary: To investigate the impact of hsa_circ_0001910 on downstream genes in breast cancer cells, we knocked down the expression of hsa_circ_0001910 in MDA-MB-231 cells and observed the changes in downstream gene expression.

overall_design: MDA-MB-231 cells were transfected with hsa_circ_0001910 siRNA and siNC. Three independent experiments were performed.

first: Yang

last: Sang


title: VEGF-mediated signaling is required and sufficient for the rejuvenation of aged human skin in vivo

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

summary: While the rejuvenation of aged human organs remains one of the most ambitious goals in medicine, it is known that tissue aging can be modulated by circulating systemic factors. Previously, we had shown that transplantation of aged human skin onto immunocompromised mice results in epidermal rejuvenation. However, the underlying mechanisms remained unknown. Therefore, to disclose such mechanisms, aged human skin xenotransplants were analyzed transplated in SCID/Beige young mice and analyzed by RNA-Seq in pre-transplanted, one, two and  four  weeks after transplantation.

overall_design: RNA-seq of old (mean age 82±7 years) human skin xenotransplants from young SCID/Beige mice

first: Aviad

last: Keren

first: Ander

last: Izeta

first: Marta

last: Bertolini

first: Yaniv

first: Yehuda

last: Ullmann

first: Laura

last: Yndriago

first: Daniela

last: Gerovska

middle: J

last: Arauzo-Bravo

first: Ralf

last: Paus

first: Amos

last: Gilhar


title: Isogenic Wild Type and iPSC-Derived CTBP1 Mutant Neuronal Cells Exhibit Neurodevelopmental Defects

city: Saint Louis

first: Elliott

last: Klotz

state: MO

address: 1Brookings Dr

institute: Washington University

summary: Hypotonia, ataxia, developmental delay and tooth enamel defect syndrome (HADDTS) is a recently identified syndrome linked to a heterozygous mutation in the C-Terminal Binding Protein 1 (CTBP1) transcriptional corepressor. The mutation is located within the major binding cleft (PXDLS), crucial for CtBP1’s interaction with proteins that regulate gene expression. We generated isogenic induced pluripotent cell lines (iPSCs) with the CTBP1 mutation in heterozygous and homozygous using CRISPR/Cas9 editing method. The transcriptional profile of iPSC-derived early neurons from isogenic wild-type and CTBP1 heterozygous and homozygous mutants was determined by RNA sequencing. The RNA-Seq data revealed downregulation of several key transcriptional factors, with homozygous mutations causing more pronounced downregulation than heterozygous mutations. Isogenic mutant neural stem cells (NSCs) exhibited less adhesion, migration, and calcium dysregulation, and mutant neurons showed premature neurite outgrowth. Our transcriptome and biological results provide novel insight into the mechanism of CTBP1 p.R342W mutation's role in the defective neurodevelopmental process.

overall_design: Total RNA of isogenic iPSC cell line samples that have heterozygous and homozygous CTBP1 mutations were isolated and analyzed using high-throughput RNA sequencing.


title: A multi-omics analysis of chondrocyte allometry

city: Hung Hom, Kowloon

first: Lanlan

last: Zhang

address: 11 Yuk Choi Road

country: Hong Kong

institute: The Hong Kong Polytechnic University

summary: Transcriptomic analysis on SHR chondrocytes supported enhanced glycolysis and aberrant mTOR signalling. The insulin-like growth factor (IGF) family is linked with chondrocyte development and homeostasis. We observed that SHR chondrocytes expressed a lower level of IGF1 at neonatal age. During chondrocyte development, we identified IGF2 as one of the most significantly downregulated genes in WKY, while genes involved in rheumatoid arthritis and glycolysis were prominently enriched in SHR.

overall_design: Primary culture chondrocytes were harvested from femorotibial cartilage of spontaneous hypertensive rats (SHR) and its normotensive control Wistar Kyoto rats at 5 days or 3 months old. Cartilage condyles were isolated, thoroughly washed, then placed in cell culture medium supplemented with 0.5 or 3 mg/mL Collagenase D. The cartilage pieces were incubated at 37°C with 5% CO2 until a monolayer culture of chondrocytes was obtained.

first: Man Ting

last: Au

first: Yuqi


title: Fat cadherin cleavage releases a transcriptionally active nuclear fragment to regulate target gene expression [ChIP-Seq]

first: Helen

last: McNeill

summary: The atypical cadherin fat (ft) controls growth, planar cell polarity (PCP) tissue organization, and mitochondrial function, in organisms ranging from fruit flies to mammals.  Working at the apical-junctional plasma membrane, the intracellular domain of the Ft protein, FtICD, binds to and regulates components of the Hippo and PCP pathways.  Unexpectedly, we find that a fragment of the FtICD is present in the nucleus in cultured cells as well as in embryonic and larval tissues, and we identify nuclear localization and nuclear export signals in FtICD required for this localization.  We show that membrane-bound FtICD is cleaved and enters nuclei in vivo.  Using endogenously tagged Ft as well as overexpressed FtICD, we conducted ChIP-seq experiments and identified putative Ft targets, including genes involved in signaling pathways, chromatin organization, pattern formation, and neural development.  RNAseq demonstrates that some of these genes are dysregulated in ft mutants.  We observe strong co-localization of Ft binding regions with peaks for other factors such as DREF and BEAF-32, as well as the Hippo pathway components Yorkie (Yki) and Scalloped (Sd), suggesting that Ft may act in conjunction with these factors to regulate gene expression.  Supporting this hypothesis, we found that Ft physiclly interacts with both Yki and Sd in co-immunoprecipitation experients in S2 cells.  We propose that the modulation of Hippo pathway activity constitutes one of the nuclear functions of Ft, complementing its estalished function as an upstream regulator of Hippo signaling.

overall_design:
GFP ChIP-seq of 16-20 hr Drosophila embryos using two separate fly strains with endogenously GFP-tagged ft gene
FLAG ChIP-seq of 3rd instar larval eye-brain complexes of Drosophila overexpressing FLAG-tagged Ft intracellular domain (FtICD)

first: Jannette

last: Rusch

first: Nattapon

last: Thanintorn

first: Chikin

last: Kuok


title: The transaminase-ω-amidase pathway is a redox switch in glutamine metabolism that generates α-ketoglutarate [RNA-seq_NIT2-GLS1-KO]

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

institute: Goethe Universität Frankfurt am Main

summary: Oxidative stress is caused by short-lived molecules and metabolic changes are fast cellular responses. Here we studied how the endothelial cell metabolome reacts to oxidative challenges to identify redox-sensitive metabolic enzymes. H2O2 selectively increased α-ketoglutaramate (αKGM), a largely uncharacterized metabolite produced by glutamine transamination and an unrecognized intermediate of endothelial glutamine catabolism. The enzyme nitrilase-like 2 ω-amidase (NIT2) converts αKGM to α-ketoglutarate (αKG). Reversible oxidation of specific cysteine in NIT2 inhibited its catalytic activity. Furthermore, a variant in the NIT2 gene that decreases its expression is associated with increased plasma αKGM in humans. Endothelial-specific knockout mice of NIT2 exhibited increased levels of αKGM and impaired angiogenesis. Knockout of NIT2 impaired endothelial cell proliferation, sprouting and induced senescence. In conclusion, we show that the glutamine transaminase-ω-amidase pathway is a metabolic switch where NIT2 is the redox-sensitive enzyme. The pathway is modulated in humans and functionally important for endothelial glutamine metabolism.

overall_design: RNA-seq of human umbilical vein endothelial cells after knockout of NIT2 or GLS1, compared to non-targeting control.

first: Niklas

last: Heerle

first: Pedro Felipe

last: Malacarne

first: Flávia

last: Rezende


title: MIAT-DHX9 spatiotemporal expression drives venous neointimal hyperplasia through nucleolar homeostasis and mitotic progression

city: shanghai

first: yue

last: lou

address: No. 393 HuaxiaCentral Road

institute: Shanghai Jiao Tong University

summary: Venous neointimal hyperplasia, characterized by the abnormal proliferation of smooth muscle cells (SMCs), represents a critical contributor to vascular stenosis and therapeutic failure in vascular interventions. Here, we identified a novel role of spatiotemporal nucleolar expression of DExH-box helicase 9 (DHX9) and its binding partner, the long non-coding RNA (lncRNA) MIAT in venous neointimal pathogenesis. In normal SMCs, DHX9 transiently localized to nucleoli during the early S phase. Pathologically, endogenous-activated MIAT facilitated nucleolar DHX9 location and its interaction with PARP1. Activated-MIAT induced mitotic spindle pole location of DHX9 which was destroyed by PARP inhibitor. MIAT also drove SMCs proliferation by accelerating cell cycle progression. While depleting MIAT or DHX9 led to remarkable nucleolar subphase disruption, mitotic breakage-fusion-bridge, and DNA damage. Of note, nucleolar-associated morphology phenotypes analyzed with deep learning are determined to be valuable biomarkers for assessing cellular status and disease progress. MIAT was repressed in cultured human veins, reducing SMCs proliferation and vascular intimal hyperplasia. These results establish the MIAT-DHX9 axis as the central regulator of venous SMCs in arteriovenous fistula and venous graft models. Our study may provide a new avenue to destroy the pathologic spatiotemporal function of DHX9 by targeting MIAT in intimal hyperplasia.

overall_design: RNA-seq data for rat VSMCs with lncRNA MIAT overexpression, n = 3 each group.

first: Yue

last: Lou

first: Wen-hao

last: Tian

first: Jia-long

last: Cui

first: Guo-zhu

last: Sun

first: Fan

last: Lv

first: Xian-hui

last: Liang

first: Kai

last: Huang

first: Qing-ping

last: Yao

first: Ying-xin

last: Qi


title: The transaminase-ω-amidase pathway is a redox switch in glutamine metabolism that generates α-ketoglutarate.

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

overall_design: Refer to individual Series


title: The transaminase-ω-amidase pathway is a redox switch in glutamine metabolism that generates α-ketoglutarate [RNA-seq_NIT2_aKGM_4h_24h]

overall_design: RNA-seq of human umbilical vein endothelial cells treated with alpha-ketoglutaramate for either 4 or 24 hours.


title: Fumarate hydratase acetylation by ethanol orchestrates mitochondrial DNA release and cGAS-STING-IRF3 mediated Hepatic stellate cell differentiation

city: New Haven

first: Suyavaran

last: Arumugam

state: Connecticut

address: 300 Cedar Street

department: Internal Medicine

institute: Yale University

summary: Alcohol consumption is a major cause of liver fibrosis and further increases liver fibrosis due to other chronic liver diseases. Alcohol induces activation of hepatic stellate cells (HSC), the key fibrogenic cell of the liver, but the metabolic basis for this is not well understood. We identified that acetaldehyde, a metabolite of ethanol, induces lysine acetylation of mitochondrial fumarase (FH1), specifically in lysine residues K80 and K230 leading to reduced FH1 activity and accumulation of the substrate fumarate. The excess mitochondrial fumarate induced mitochondrial DNA (mtDNA) oxidation and release into the cytosol via formation of a mitochondrial permeability pore and voltage-dependent anion channel. The released mtDNA was observed to activate cGAS and subsequently the STING-IRF3 cascade. In a 6-week mouse model of alcohol diet, we observed that FH1 inhibition aggravated, while the STING inhibitor (IFM-004490-7) significantly blocked it. In conclusion, we observed that ethanol derived acetaldehyde mediated FH1 acetylation and subsequent inhibition result in the activation of HSC via the cGAS/STING/IRF3 pathway. This opens the possibility for novel therapeutic approaches to alleviate liver fibrosis by targeting FH1 acetylation and reducing its activity.

overall_design: Study groups were as follows: (1) Wild type C57BL6/J mice injected with corn oil (100ul injection, 3×per week for 4 weeks) (n=6) (2) Wild type mice injected with CCl4 0.5 ml/kg b.wt  intraperitoneally (i.p.) 1 in 4 dilution in corn oil, 3×week for 4 weeks (n=6); (3) Col1a2/STING-/- mice injected with corn oil (100ul injection, 3×per week for 4 weeks) (n-6) (4) Col1a2/STING-/- mice injected with CCl4 0.5 ml/kg b.wt  intraperitoneally 1 in 4 dilution in corn oil, 3×week for 4 weeks (n=6). Two mice from each group were subjected to single-cell isolation.

first: Wajahat

last: Mehal

first: Frhaan

last: Zahrawi


title: MIAT-DHX9 spatiotemporal expression drives venous neointimal hyperplasia through nucleolar homeostasis and mitotic progression.

overall_design: RNA-seq data for rat VSMCs with lncRNA MIAT knockdown treatment for 72 hours, n = 3 each group.

first: Wenhao

first: Jialong

first: Guozhu

first: Xianhui

first: Qingping

first: Yingxin


title: Human B cells induced by primary SARS-CoV-2 infection

city: New York

first: Patrick

last: Wilson

state: NY

address: 413 E 69th St

department: Pediatrics

institute: Weill Cornell Medicine

summary: This study was designed to capture the single cell transcriptome and BCR sequence of B cells that were bait sorted using oligo-tagged viral antigens.

overall_design: Human B cells (viable/CD19+/antigen-PE+ or viable/CD19+/antigen-APC+) were bait sorted after initial magnetic enrichment and used in downstream sequencing.

first: Siriruk

last: Changrob

first: Lei

last: Li

first: Chloe

last: Troxell


title: Spatial transcriptomic analysis of 53 pre-treatment biopsies from LARC patients using GeoMx technology

city: Geneva

first: MELIVOIA

last: RAPTI

address: Rue du Général-Dufour

department: Medicine

country: Switzerland

institute: University of Geneva

summary:
Locally Advanced Rectal cancer (LARC) is treated using neoadjuvant chemoradiotherapy (nCRT) followed by surgery. On average 15% of tumors at surgery will present a pathological complete response (pCR). Increasing pCR can be done at the cost of treatment intensification usually combining nCRT and chemotherapy which comes with higher toxicity. However, many LARC patients do not respond to the current neoadjuvant treatments while experiencing important treatment related side effects. Predicting pCR following nCRT opens the door to non-surgical management - the watch and wait strategy and avoid escalation as well as sparring non-responders from nCRT in patients not eligible for intensification. Using RNA expression data, several groups have defined predictive signatures, however, none have made it into clinical practice.
A comprehensive differential expression analysis was conducted across six Gene Expression Omnibus (GEO) datasets, followed by integration with four microarray datasets for refinement. A machine learning approach was employed to identify a 186-gene signature predictive of response to nCRT, validated using cross-validation. Gene set enrichment analysis (GSEA) was performed to explore biological pathways associated with treatment response. Spatial transcriptomic profiling of pre-treatment biopsies further examined gene expression in tumor and stroma compartments and identified eight compartment-specific genes significantly associated with response, with tumor-associated genes showing greater predictive value than stroma-associated genes.
This study identifies a novel 186-gene signature associated with nCRT response in LARC, with potential clinical utility in guiding personalized treatment. Further validation in larger cohorts and exploration of spatial biomarkers are needed to confirm its clinical relevance.

first: Petros

last: Tsantoulis

first: Thibaud

last: Koessler


title: The chromatin remodeler CHD1L controls human cortical neurogenesis  and contributes to distal 1q21.1 deletion/duplication syndrome [CUT&RUN]

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

summary: Background/objectives: Deletions and duplications of the distal 1q21.1 region are associated with syndromic forms of autism (MIM612474, 612475). Variable phenotypes have been reported, including congenital heart defects, autism, schizophrenia, head circumference and height defects. Methods: To elucidate which gene(s) are responsible for the 1q21.1 duplication/deletion- associated phenotypes, we performed gene manipulation in zebrafish and mice. We deciphered the function of candidate driver(s) by multi-omics approaches on human iPSC- derived neural progenitor cells (NPC) and cerebral organoids (CO). Results: We modeled duplication of the 1q21.1 region by overexpressing the 8 genes in the region in zebrafish. We found that only overexpression of CHD1L led to macrocephaly and increased larval body length. Conversely, deletion of the CHD1L zebrafish ortholog resulted in microcephaly and decreased larval body length. These mirror phenotypes are also observed when Chd1l expression is modulated in a mammalian model, notably with a variation in the number of mature Tbr1-positive neurons in the mouse embryo. NPCs derived from control and CHD1L Knock-out isogenic hiPSCs were subjected to transcriptomic and chromatin accessibility analyses. These approaches revealed that CHD1L regulates the expression levels and accessibility of genes involved in neuronal differentiation and synaptogenesis, including autism susceptibility genes such as UNC5D and DPP6. Strikingly, absence of CHD1L shifts the cellular identity from forebrain to retinal fate in CO. Finally, pathogenic missense and truncating variants of CHD1L were found in individuals with autism and/or height defects. Conclusion: CHD1L is a major contributor of the 1q21.1 duplication/deletion-associated microcephaly and growth defects. CHD1L dosage is required during human brain regionalization.

overall_design: Human Neural Progenictor Cells derived from hiPSC were subjected to CUT&RUN analysis targeting the proteins CHD1L and H3K4me2.

first: Marianne

last: Lemée

last: Ye

first: Christelle

last: Golzio


title: WT1-Expressing Mesenchymal Cells Promote Pancreatic Cancer Growth

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: MI

address: 1500 E Medical Center Dr

institute: University of Michigan Medical School

summary: Here, we sought to understand the functional role of WT1-Expressing cells in pancreatic ductal adenocarcinoma.

overall_design: Normal Pancreata were collected from 2 adult male mice (7 months old) and processed for sequencing. For sequencing of untreated orthotopic tumors, 2 adult female mice (6 months old) received orthotopic injections of 50,000 7940b cells (C57Bl6J strain, Ptf1acre/+;KrasLSLG12D/+;p53flox/+) into the pancreas. Orthotopic tumors grew for 3 weeks before the tumors were dissected for sequencing. For sequencing of diptheria toxin treated tumors, 3 adult male R26tdTomato/DTR mice and 2 adult male WT1-CreERT2/+; R26tdTomato/DTR mice were implanted orthotopically with 50,000 7940b cells. Four days following orthotopic injection, mice recieved 5 daily doses of oral gavage tamoxifen (4mg/daily) and were maintained on tamoxifen chow for the remaining duration of the experiment. The day after the final dose of oral gavage tamoxifen, mice recieved intraperitoneal injections of diptheria toxin every 4-7 days (25ug/kg) until mice were euthanized and tumors dissected for sequencing (3 weeks after orthotopic implantation).

first: Allison

last: Bischoff

first: Yaqing

last: Zhang


title: Peanut Allergy Oral Immunotherapy Drives Single-Cell Multi-omic Changes in Peanut-reactive T cells Associated with Sustained Unresponsiveness

city: Palo Alto

first: Xiaorui

last: Han

state: CA

address: 240 Pasteur Dr. BMI

institute: Stanford University School of Medicine

summary: Oral immunotherapy (OIT) is the only FDA-approved treatment for peanut allergy (PA). Peanut-reactive (pr) CD4+ T cells are pivotal in PA pathogenesis as well as OIT-induced desensitization (DS). However, the underlying pr CD4+ T cell immune mechanisms leading to sustained unresponsiveness (SU) after OIT discontinuation remain largely unknown. We analyzed single-cell RNA and protein immunophenotypes and TCR repertoires of pr CD4+ T cells from a phase 2 peanut OIT trial cohort. We identify increased cytotoxicity-related phenotypes and Th1 CTL (cytotoxic T lymphocytes)-like cell clonal expansion during OIT in pr T effector memory cells, while Th2-related phenotypes and Th2a-like cell clonal expansion decreased. OIT participants who achieved SU had lower baseline Th2-related phenotypes, elevated cytotoxicity-related gene signatures in pr Teff cells post-OIT and higher CD39 expression in pr Tregs (T regulatory cells) after OIT withdrawal. These findings clarify OIT-induced CD4+ T cell tolerance mechanisms and can guide effective allergen-specific OIT strategies.

overall_design: To comprehensively characterize the heterogeneous pr CD4+ T cell, including pr Teff CD4+ T cells (CD4+CD154+) and pr Treg CD4+ T cells (CD4+CD137+CD154-), and their longitudinal responses in OIT, we used peripheral blood mononuclear cells (PBMC) from 31 POISED (Our phase 2 randomized, controlled peanut OIT trial: Peanut Oral Immunotherapy: Safety, Efficacy, Discovery; NCT 02103270) participants: 23 active participants who underwent OIT and passed DBPCFC at week 104 (14 peanut-0 participants, of whom 7 passed (SU) and 7 failed (DS) at week 117, and 9 peanut-300 participants, of whom 5 passed and 4 failed DBPCFC at week 117); 8 placebo participants; and 5 age- and gender-matched non-peanut allergic controls. We stimulated PBMCs with peanut solution for 18 hours, and sorted pr CD4+ T cells (CD4+CD137+ and/or CD4+CD154+) and non-reactive (nr) CD4+ T cells (CD4+CD154-CD137-). Sorted cells were processed using the BD Rhapsody™ platform for single cell RNA-sequencing (scRNA-seq) with a focus on 432 immune-relevant target transcripts (399 commercially pre-defined target panel complemented with 33 targets of interest), and 42 immune-relevant Ab-seq markers for protein level detection as well as single-cell paired TCRαβ sequencing.

first: Xuhuai

last: Ji

first: Kari

last: Nadeau


title: Mucus-derived glycans are inhibitory signals for Salmonella Typhimurium SPI-1-mediated invasion

city: Cambridge

first: Katharina

last: Ribbeck

state: Massachusetts

address: 21 Ames St

department: Biological Engineering

institute: Massachusetts Institute of Technology

summary: Mucus forms a critical barrier against enteric pathogens like Salmonella enterica serovar Typhimurium. While in vivo studies indicate that secreted, gel-forming mucins and specifically Core 3 glycosylation are protective against S. Typhimurium, the molecular mechanisms involved remain unclear. Here, we measure gene expression changes in Salmonella enterica serovar Typhimurium LT2 following growth in SPI-1 inducing medium (LB + 0.3M NaCl) with or without purified MUC2 (0.1%, w/v), MUC2 glycans (0.1%, w/v), a pool of monosaccharide components comprised of D-galactose, D-GalNAc, D-GlcNAc, D-fuc, and Neu5Ac (0.1%, w/v), or specific individual mucin sugars, namely N-acetyl galactosamine (GalNAc) (0.2%, w/v) and N-acetyl glucosamine (GlcNAc) (0.2%, w/v). Notably, we find MUC2, MUC2 glycans, and to a lesser extent,D-GalNAc and D-GlcNAc downregulate SPI-1 gene expression.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: S. Typhimurium LT2 overnight cultures were diluted 1:100 in 100 µL of SPI-1-inducing LB.3 medium (with or without 0.1% MUC2, 0.1% MUC2 glycans, 0.2% GalNAc, 0.2% GlcNAc, 0.1% monosaccharide pool containing equal volumes of D-galactose, D-GalNAc, D-GlcNAc, L-fucose, and Neu5AC) for 3 h at 37 °C, under static conditions. RNA was extracted with the MasterPure RNA Purification Kit (Biosearch Technologies), and DNA was eliminated using the Turbo DNA-Free Kit (Ambion). The Agilent 2100 Bioanalyzer (Agilent Technologies) was used to assess RNA integrity. rRNA was depleted with the NEBNext rRNA Depletion Kit for bacteria (NEB). The Illumina HiSeq platform was used for the sequencing mucin-, glycan-treated, and monosaccharide pool-treated samples with a single-end protocol and read lengths of 40 nucleotides. The Illumina NovaSeq platform was used for sequencing HexNAc-treated samples with a paired-end protocol and read lengths of 50 nucleotides. Reads were analyzed on the Galaxy platform with the Burrows-Wheeler algorithm, HTseq-count, and DESeq2. For all analyses of the sequencing data, we considered FDR-adjusted P values < 0.05 as significant.

first: Kelsey

last: Wheeler

first: Michaela

last: Gold

first: Corey

last: Stevens

first: Karsten

last: Tedin

first: Amanda

last: Wood

first: Deniz

last: Uzun

first: Gerardo

last: Cárcamo-Oyarce

first: Bradley

last: Turner

first: Marcus

last: Fulde

first: Jeongmin

last: Song

first: Jessica

last: Kramer


title: Multi-lineage cardiac model recapitulates human cardiogenesis and heart defects

city: Beijing

first: li

last: wang

institute: State Key Laboratory of Cardiovascular Disease, Fuwai Hospital

summary: Congenital heart defects constitute the leading cause of human fetal death, however the underlying mechanisms of most cardiac defects remain unknown. The ability to generate in vitro cardiac models mimicking significant aspects of native heart development is a prerequisite for disease modeling. Here, we established a 2D cardiac platform that equivalent of human fetal heart with pluripotent stem cells (hPSCs). Through the precise manipulation of retinoic acid (RA) signaling, we recapitulated the anterior-posterior patterning found in embryogenesis. By lineage tracing analyses and single-cell transcriptomic profiling, we described the lineage relationships between distinct populations and the developmental potentials of heart-field-specific progenitors. Comparisons of hPSC-derived and gastrulating human hearts enabled the identification of in vivo-like cardiac molecular characteristics in our platform. We used this model to unravel maternal pregestational diabetes-induced congenital heart defects. Together, the 2D cardiac platform offers a unique tool for disease modeling, drug discovery and cardiogenesis studying.

overall_design: To investigate the transcriptomic profiles of populations generated under two distinct conditions, scRNA-seq was utilized during the in vitro differentiation of human pluripotent stem cells (hPSCs) into cardiac lineages. This process encompassed six key developmental stages (days 0, 2, 4, 8, 14, 30). We captured single cells with the 10x Genomics Chromium single-cell platform followed by quality control tests, and retained 5,2575 cells for subsequent transcriptomic analysis. Additionally, we assessed the feasibility of our system to model specific aspects of pregestational diabetes-induced congenital heart disease (PGD) in vitro. To simulate PGD, we modified our differentiation protocols to replicate the glucose levels associated with maternal hyperglycemia (defined as a random plasma glucose level of ≥ 200 mg/dL) and performed scRNA-seq on populations differentiated under both PGD and control conditions.

first: Li

last: Wang

first: Qi

last: Feng

first: Yang

last: Che


title: Maternal Micronutrient Insufficiency Exacerbates Growth Restriction with Ambient Heat on Placental and Fetal Development during Pregnancy

city: College Station

first: Kartik

last: Shankar

email: kartik.shankar@cuanschutz.edu, kartikster@gmail.com, kartik.shankar@usda.gov, kartik.shankar@ag.tamu.edu

state: TX

address: 498 Olsen Blvd TAMU 2250 TAMU 2250

department: RAFSRU

institute: USDA ARS

summary: Malnutrition in women of childbearing age is associated with an increased risk of fetal growth restriction and poor infant development. Climate change, specifically the rise in ambient temperature, is thought to exacerbate the effects of malnutrition. However, few mechanistic studies exist to examine the interactions between maternal nutrition and ambient temperature on fetal growth. Here we develop a novel animal model of marginal micronutrient insufficiency and modest heat stress during pregnancy to understand interactive effects on fetal growth in mice.  Female C57BL6/J mice (8 wk old, n = 6-8/group) were given ad libitum access to either AIN-93G (CON) or a modified AIN-93 diets containing 70% mineral, micronutrient, and vitamin mix (70MMV) for 4 weeks. After breeding females were housed at either 22⁰C or 33⁰C in an environmental chamber for the duration of pregnancy while remaining on their respective diets. Mice fed 70MMV diet had significantly reduced body weight gains during pregnancy in comparison to CON diet fed group. Serum K, Fe, Zn, and Se levels showed reduced levels either by diet or temperature. A novel interaction between modest heat and micronutrient insufficiency was identified and led to an altered placenta transcriptome and fetal growth restriction in this model. Sexually dimorphic differences were observed in placental and fetal tissues in the temperature groups. In males, placenta gene expression related to vascularization, nutrient transport, and stress-related responses (i.e. ER stress and inflammation) were impacted in the combination group exposed to 70MMV diet and elevated temperature, while in females the same biological functions were affected only in the CON-33C group. Collectively, our results point to an interaction between modest heat and micronutrient insufficiency on placental dysfunction and the pathogenesis of fetal growth restriction, highlighting the emerging nexus of maternal nutrition and heat stress typically seen in resource-restrained settings.

overall_design: RNA was extracted from placenta tissue from individual mice in four groups (2 diets - control and 70MMV and 2 -temp 22C and 33C, n = 6 per group) using the RNeasy Mini Kit per manufacturer’s instructions including on-column DNase digestion. Total RNA was quantified using a Qubit RNA BR Assay Kit and RNA integrity was assessed on an RNA ScreenTape. Placental sex was identified via genotyping of fetal tails. Placental RNA was pooled to create n =3 pools for each of the 8 groups (4 groups X 3 pools X 2 sexes = 24 libraries)

first: Meghan

last: Ruebel


title: Acute Immunological Phenotypes in Individuals with Traumatic Spinal Cord Injury.

city: Manhasset

first: Ona

last: Bloom

state: New York

address: 350 Community Dr

department: Molecular Medicine

institute: Feinstein Institute

summary: Acutely after traumatic spinal cord injury (SCI), the immune system responds with an inflammatory cascade that promotes secondary damage to the spinal cord and systemic inflammation, which promotes persistent medical consequences. Here, we combined clinical and research data to evaluate cellular and molecular changes in the systemic immune system of individuals with SCI (SCI, N = 36) within 0–4 days after injury compared to uninjured individuals (CTL, N = 36). Analyzing blood samples by bulk-RNA Seq, 4752 differentially expressed (DE) gene transcripts were identified in SCI compared with CTLs, including increased expression of genes associated with inflammation and innate immunity (e.g., Neutrophil degranulation, Toll-Like Receptor signaling). Most participants with SCI had complete blood count data available, of whom 36% had elevated white blood cell and neutrophil counts, 24% had elevated monocytes, and 36% had lymphopenia. Significantly reduced expression of canonical natural killer (NK) cell, T cell and dendritic cell (DC) genes were identified, consistent with reduced frequencies of these cell types, determined by flow cytometry. Some molecular changes appeared to be influenced by motor completeness of injury. C-reactive protein, a validated clinical biomarker of inflammation, was significantly elevated after SCI, with levels higher in motor complete compared to motor incomplete injuries. This was also apparent for several other proinflammatory cytokines (e.g., High Mobility Group Box 1 protein, IL-6, IL-8). These data confirm and extend prior observations of cellular and molecular immunological changes, that may serve as potential biomarkers of injury severity, or as future therapeutic targets to improve health.

overall_design:
RNAsequencing from whole blood taken 0-4 days post injury, from participants with SCI. Inclusion and exclusion criteria was applied. Data was compared to un-injured participants as controls. Acute SCI samples ID1V0-ID10V0 and control samples ID13V0-ID21 were previously analyzed as part of a longitudinal study (GSE226238) and were included in this analysis of all acute samples.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Debra

last: Morrison

first: Camille

last: Pinpin

first: Annette

last: Lee

first: Cristina

last: Sison

first: Ashley

last: Chory

first: Peter

last: Gregersen

first: Gail

last: Forrest

first: Steven

last: Kirshblum

first: Susan

last: Harkema

first: Maxwell

last: Boakye

first: James

last: Harrop

first: Thomas

middle: N

last: Bryce

first: Jan

middle: M

last: Schwab

first: Brian

last: Kwon

first: Adam

middle: B

last: Stein

first: Matthew

last: Bank


title: Discovery of Long-Acting APOC3 siRNA for Treating Patients with Hypertriglyceridemia

city: Carlsbad

first: Sagar

last: Damle

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

summary: Apolipoprotein C-III (APOC3) plays a crucial role in triglyceride metabolism, and its high expression leads to hypertriglyceridemia, a condition associated with an increased risk of cardiovascular disease and acute pancreatitis. However, loss-of-function variants in APOC3 are linked to lower triglyceride levels and reduced incidence of coronary artery diseases. APOC3 mRNA, primarily synthesized by hepatocytes, is an ideal target for GalNAc-conjugated small interference RNA (siRNA) mediated gene silencing. Our research takes a unique approach, conducting systematic structure-activity relationship (SAR) studies to identify a long-acting APOC3 siRNA with a minimal number of 2’-F nucleotides. We evaluated the use of 5’-vinylphosphonate (5’-VP), 5’-methylene phosphonate (5’-MP), FHNA, and methane sulphonyl phosphoramidite backbone chemistry in APOC3 siRNA design and employed deoxynucleotides or 2’-O-methyl  (OMe) to replace 2’-F residues. Additionally, we utilized 2’-O-methoxyethyl (MOE) nucleotides in conjunction with phosphorothioate modification to enhance metabolic stability. To ensure the preferential loading of the antisense strand, we strategically placed MOE nucleotides at specific sites in the antisense strand.  These efforts led to the identification of APOC3 siRNA containing a novel chemical scaffold with a long duration of action (DOA) and tolerability in rodents and nonhuman primates. A comparative analysis of preclinical and clinical data of plozasiran surrogate suggests that our APOC3 siRNA may provide clinical benefits with less frequent exposure (>6 months apart), which could significantly improve the treatment of patients with hypertriglyceridemia.

first: Thazha

middle: P

last: Prakash

middle: E

last: Mullick

first: Eric

last: Swayze


title: Protective effect of Golden Bifid treatment on slow transit constipation rat

city: Fuzhou

first: Aling

last: Shen

state: Fujian

address: 1 Qiuyang road, Minhou Shangjie

institute: Fujian university of Traditional Chinese Medicine

summary: The goal of this study is to compare the differently expressed genes in colon tissue of Control and loperamide (LOP) induced slow transit constipation (STC) rat model with or without Golden Bifid (Jin Shuang Qi, JSQ) or positive control group (Prukapril Succinate Tablet, PST) treatment. The loperamide induced STC rat model were randomly divided into 3 groups: LOP, LOP + JSQ and LOP + PST groups (n=6 for each group). Control rats (n=6) were set as control. The STC rat model was induced by administering loperamide intraperitoneally at a dose of 3 mg/kg body weight twice daily for 21 days in all groups except the Control group. On the 8th day, the LOP + JSQ group was intragastrically with 0.540 g/kg/d 1 h after each loperamide administration for 14 days. The LOP + PST group was given prucalopride succinate tablets at a dose of 0.18 mg/kg/d by oral gavage 1 h after each loperamide administration for 14 days. Then the colon tissues were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with colonic rats in 4 groups: Control, LOP, LOP + JSQ and LOP + PST treated (n=6 for each group) to identify the differently expressed genes and related pathway.

first: Liya

last: Liu

first: Ying

last: Cheng


title: The chromatin remodeler CHD1L controls human cortical neurogenesis and contributes to distal 1q21.1 deletion/duplication syndrome [RNA-seq]

first: Tao

last: YE

overall_design: Human Neural Progenictor Cells derived from hiPSC controls and mutant for the gene CHD1L were subjected to ATAC-seq analysis, includes fours replicates per cell line (one control and 2 isogenic mutants).

first: Maria-Nicla

last: Loviglio

first: Céline

last: Keime

first: Christelle

last: Golzio


title: Developing a robust genome editing tool based on an endogenous Type I-B CRISPR-Cas system in Saccharopolyspora spinosa

city: Shanghai

first: Wenfang

last: Wang

address: 100 Guilin Road

institute: Shanghai Normal University

summary: Saccharopolyspora spinosa is an industrial rare actinomycete capable of producing important environmental-friendly biopesticides, spinosyns. However, exploitation of S. spinosa has been limited due to its genetic inaccessibility and lack of effective genome engineering tools. Here, we characterized the activity of an endogenous type I-B CRISPR-Cas system as well as its recognized protospacer adjacent motifs (PAMs) based on bioinformatics analysis combined with plasmid interference assay in S. spinosa. By reprogramming this endogenous CRISPR-Cas system, we achieved 100% editing efficiency for gene deletion. Using this tool, the genetic barrier composed of the Restriction-Modification (RM) systems was systematically disarmed. We showed that by disarming one type I RM system and two type II RM systems simultaneously, the transformation efficiency of foreign plasmids was significantly increased. Based on the engineered strain with simultaneous deletion of these three RM genes, we achieved the deletion of 75-kb spinosyns biosynthetic gene cluster as well as gene insertion at high efficiency. Collectively, we developed a reliable and high-efficiency genome editing tool based on the endogenous type I CRISPR-Cas system combined with the disarmament of the RM systems in S. spinosa. This is the first time to establish an endogenous CRISPR-Cas-based genome editing tool in the non-model industrial actinomycetes.

overall_design:
To investigate the transcription of the endogenous Type I-B CRISPR-Cas system, we then performed gene expression profiling analysis using data obtained from RNA-seq of cultured S. spinosa strain at three time points.

Grant ID: 2019YFA0905400
Grant title: Network Reconstruction and System Optimization of Actinomycetes Drug Synthesis Biological Systems
Funding source: National Key Research and Development Program

Grant ID: 32270095
Funding source: National Natural Science Foundation of China

first: Huiyan

last: He

first: Hewei

first: Yinhua

last: Lu


title: The chromatin remodeler CHD1L controls human cortical neurogenesis and contributes to distal 1q21.1 deletion/duplication syndrome [ATAC-seq]

first: Marianne

last: Lemée

last: Ye


title: circRNAs expression profile analysis of PK-15 cells response to transmissible gastroenteritis virus infection

city: Chongqing

first: Xiwang

last: Yang

state: Chongqing

address: 2# Tiansheng Street

institute: Southwest University

type: Non-coding RNA profiling by high throughput sequencing

summary: To analyze the effect of Transmissible gastroenteritis virus (TGEV) infection on expression profile of circular RNAs (circRNAs) in pig renal epithelial cells (PK-15), we decided to sequence the circRNAs transcriptome of control and TGEV-infected PK-15 cells based on the Illumina HiSeq 4000 platform. The source genes of the differentially expressed circRNAs were subjected to GO function and KEGG pathway enrichment analysis. Meanwhile, we built a regulatory network of DE circRNAs and predicted multiple circRNA-miRNA-mRNA regulatory axes about innate immunity and the pathogenesis of TGEV. In this study, transcriptome sequencing results revealed that a total of 1029 novel circRNAs were identified in the control and TGEV- infected PK -15 cells. In TGEV-infected PK-15 cells, the expression levels of 70 circRNAs were significantly up-regulated and 58 circRNAs were significantly down-regulated compared to control PK-15 cells. GO functional analysis of the source genes of differentially expressed circRNAs indicated that the differentially expressed circRNAs source genes in TGEV-infected PK-15 cells were mainly enriched in the intracellular part, intracellular membrane-bounded organelle and nucleus and cellular macromolecule metabolic process, nucleobase-containing compound metabolic process, nitrogen compound metabolic process, and regulation of cellular metabolic process and heterocyclic compound binding, organic cyclic compound binding and nucleic acid binding.The results of KEGG pathway enrichment analysis showed that the significantly differentially expressed circRNAs source genes in the TGEV-infected PK -15 cells were mainly enriched in the regulation of actin cytoskeleton, influenza A, hepatitis C and cAMP signaling pathway. circRNA-miRNA-mRNA interaction networks demonstrated that circRNAs regulated innate immunity and transmembrane ion transport.

overall_design: To explore the potential regulatory role of circRNAs during Transmissible gastroenteritis virus（TGEV） infection. We established a TGEV infected cell model by infecting PK-15 cells with TGEV. RNA-seq was performed on TGEV infected cell models and PK-15 cells, with three independent replicates set for each sample. Analyze and screen differentially expressed circRNAs from sequencing data. The source genes of the differentially expressed circRNAs were subjected to GO function and KEGG pathway enrichment analysis. Finally, bioinformatics analysis was used to predict and validate the circRNA-miRNA-mRNA regulatory axis associated with host immunity in viral infections.


title: The chromatin remodeler CHD1L controls human cortical neurogenesis and contributes to distal 1q21.1 deletion/duplication syndrome.


title: Nucleosome context regulates chromatin reader preference

city: Durham

first: Michael-Christopher

last: Keogh

state: NC

address: 6 Davis Dr

institute: EpiCypher, Inc

summary: Chromatin is more than a simple genome packaging system, and locally distinguished by histone post-translational modifications (PTMs) that can change nucleosome structure and / or be “read” by chromatin-associated proteins to mediate downstream events. An accurate understanding of histone PTM binding preference is vital to understanding chromatin function and disease development, and has led to the identification of multiple therapeutic targets. Such studies most often use histone peptides, even though this cannot explore the full regulatory potential of nucleosome context. Here we apply a range of complementary and easily adoptable biochemical and genomic approaches to interrogate fully defined peptide and nucleosome targets containing acyl, methyl, methyl analog and phospho PTMs with a diversity of mono- or multi- valent chromatin readers. Nucleosome context consistently refined reader binding, and was particularly informative when analyzing multivalent engagement. This included abrogating the binding of L3LBTL1 MBT to histone tails with lower methyl states (me1 or me2 at H3K4, H3K9, H3K27, H3K36 or H4K20); and demonstrating that specificity of the CBX7 chromodomain for H3K27me3 is enabled by an adjacent DNA-binding AT-hook like (ATL[MK1] ) motif. Further, the in vitro binding preferences of readers to nucleosomes was confirmed by in vivo reader-CUT&RUN genomic mapping. Such data confirms that interrogating with more representative substrates provides greater insight to chromatin reader capability and biological mechanism.

overall_design: CUT&RUN reactions performed in K562 cells.

first: Matthew

middle: R

last: Marunde

first: Irina

last: Popova

first: Nathan

last: Hall

first: Anup

last: Vaidya

first: James

last: Bone

first: Brandon

middle: A

last: Boone

first: Peter

last: Brown

first: Ryan

last: Ezell

first: Tessa

last: Firestone

first: Harrison

last: Fuchs

first: Elisa

last: Gibson

first: Zachary

last: Gillespie

first: Susan

middle: L

last: Gloor

first: Allison

last: Hickman

first: Sarah

last: Howard

first: Natalia

last: Husby

first: Victoria

last: Hsiung

first: Andrea

last: Johnstone

first: Laiba

middle: F

last: Khan

first: Krzysztof

last: Krajewski

first: Alexander

middle: S

last: Lee

first: Eileen

last: McAnarney

first: Keith

last: Maier

first: Danielle

last: Maryanski

first: Jamie

last: McCuiston

first: Kelsey

last: Noll

first: Katherine

last: Novitzky

first: Emily

last: Patteson

first: Keli

last: Rodriguez

first: Julio

middle: C

last: Sanchez

first: Luis

last: Schachner

first: Catherine

last: Smith


title: The chromatin remodeler CHD1L controls human cortical neurogenesis and contributes to distal 1q21.1 deletion/duplication syndrome [scMultiome]

first: Tao

last: YE

overall_design: 60 days in vitro-old cerebral organoïds derived from hiPSC control or isogenic mutant for the gene CHD1L were subjected to single-nucléi 10X multiome analysis (10X Genomics) for Gene expression and ATAC-seq analysis.

first: Marianne

last: Lemée

last: Ye

first: Christelle

last: Golzio