title: BET protein-dependent E2F pathway confers bell-shaped type resistance to tankyrase inhibitors in APC-mutated colorectal cancer [CUT&RUN]

city: Tokyo

first: Shun

last: Morino

address: 3-8-31, Ariake, Koto-ku

institute: JFCR

summary: In colorectal cancer (CRC), WNT/β-catenin signaling is aberrantly activated mainly by loss-of-function mutations in adenomatous polyposis coli (APC) and is involved in tumor progression. Tankyrase inhibitors, which suppress WNT/β-catenin signaling, are under pre-clinical and clinical trials, while their resistance mechanisms remain unclear. In this study, we established tankyrase inhibitor-resistant CRC cells, JC73-RK100, from APC-mutated patient-derived CRC cells. JC73-RK100 cells and several CRC cells were sensitive to tankyrase inhibitors at low concentrations but were resistant at high concentrations (i.e., bell-shaped dose response: BSDR). Mechanistically, tankyrase inhibitors at high concentrations promoted BRD3/4-dependent E2F target gene transcription and over-activated cell cycle progression in the BSDR cells. BET inhibitors canceled the bell-shaped dose response to tankyrase inhibitors. Taken together, these observations suggest that combination of tankyrase and BET inhibitors would be a useful therapeutic approach to overcome a subset of resistance to tankyrase inhibitors.

overall_design: Examination of histone modification (H3K27ac) and chromatin associated proteins (BRD3, BRD4) using CUT&RUN in colorectal cancer PDC JC73, JC73-RK100 and JC21 cells treated with or without tankyrase inhibitor RK-582.

first: Tetsuo

last: Mashima

first: Hiroyuki

last: Seimiya


title: RNAseq analysis of blood from influenza infected patients and healthy controls, project SIG_combined, subset 1

status: Public on Jul 30 2024

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

country: Germany

institute: University Münster

type: Expression profiling by high throughput sequencing

summary: Study responses in peripheral blood of patients infected with influenza virus and compared to healthy control. Results: Strong differential host reponse after infection was observed.

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overall_design:
This record  represents a subset of the combined data from four records submitted at the GEO-IDs: GSE155635, GSE158592, GSE196350, GSE213168, unique samples, day 1 only

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The table below lists GEO accessions reused/reanalyzed for this study.
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title: AP-3-84 effects on gene expression in thioglycollate-induced, ID8 ascites or bone-marrow derived macrophages

status: Public on Jul 26 2024

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

country: USA

institute: The Wistar Institute

summary: Here we studied the effects of AP-3-84 treatment on gene expression in different types of macrophages: thioglycollate-induced macrophages, ascites macrophages from ID8 ovarian cancer-bearing mice, bone marrow-derived macrophages. We also studied whether AP-3-84 effects are mediated by p53 using bone marrow-derived macrophages from p53 KO mice. We found the dramatic changes in gene expression upon AP-3-84 treatment in all types of macrophages with the induction of major stress response programs and apoptosis signaling.

overall_design: We isolated thioglycollate-induced macrophages, ascites macrophages from ID8 ovarian cancer-bearing mice. We also generated M0, M1 or M2-polarized macrophages using hematopoietic bone marrow stem cells from wild-type B6 or p53 KO B6 mice. We then treated these different types of macrophages with 10 uM AP-3-84 for 4 hours and analyzed gene expression changes by bulk RNA Sequencing.

first: Evgenii

middle: N

last: Tcyganov

first: Taekyoung

last: Kwak

first: Luis

last: Montaner


title: Different stage of iPSC reprogramming

status: Public on Jul 29 2024

city: Harbin

first: Yuchen

last: Sun

state: Heilongjiang

address: Baojian road 157

department: Department of histology and embryology

country: China

institute: Harbin Medical University

summary: RNA seq data during different point of ipsc reprogramming from Dox TetOn OSKM system

overall_design: DOX was added in D0, the total RNA of 4F2A MEFs was harvested by using TRIzol reagent (Invitrogen). Each group was prepared with two parallel replicates. Then, all the samples were sent to BGI Corporation (China) for further RNA-seq analysis via BGISEQ-500 sequencer.The PCA, GO and KEGG pathway and other analyses were performed by R.

first: Xinglin

last: Hu

first: Lei

last: Lei


title: Mechanical stretch exacerbates imiquimod-induced dermatitis associated with increased IL-1β and IL-6 production.

city: Tainan City

first: Yi-Kai

last: Hong

state: Please select an option below

address: No.1, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

summary: Psoriasis vulgaris is a chronic inflammatory skin disease which tends to affect the extensor surface of the body. IL-17A and IL-23 antagonists are currently the main and powerful therapeutic choices but the skin areas which are subject to stretching, namely knees, elbows and the lower back, are often reluctant to treatments. ; Hence, we hypothesize that stretching has a dominant effect on psoriasis development. First, we found that, in imiquimod-treated psoriasis-like mouse model, mechanical stretch promotes a significant increase in clinical severity, epidermal thickness, and inflammatory cell infiltration of psoriasis. Transcriptomics profiling revealed that Il6 and Il1b genes are significantly upregulated and play a major role in the activation and recruitment of neutrophils, macrophages, and T cells in stretching group. Upstream analysis further identifies NF-κB as a critical transcription factor to drive pro-inflammatory cytokine expression during stretch application. Immunofluorescence staining confirmed the increased expression of IL-1β and IL-6. In summary, our findings uncover that the mechanical biology contributes to psoriasis progression mainly through enhancing the production of IL-1β and IL-6.

overall_design: To comprehensively and systemically identify the main molecular signal pathways involved in stretch-enhanced skin inflammation, the transcriptomes of the IMQ-treated skin tissues with skin stretch (n=5) or without skin stretch (n=4), were profiled and compared (FS/IMQ+ vs. NS/IMQ+) by mRNA microarray.

first: Chaw-Ning

last: Lee

first: Wei-Chen

last: Lin

first: Chao-Kai

last: Hs

first: Yu-Chen

first: Shu-Yi

last: Cheng

first: Ming-Jer

last: Tang

first: Chao-Chun

last: Yang


title: Maternal adipose tissue DNA methylation and gene expression associated with excessive gestational weight gain

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

type: Methylation profiling by high throughput sequencing

summary: Omental adipose tissue was obtained from 24 women aged 25-40 years with a healthy singleton pregnancy and a pre-pregnancy BMI of 18.5-26 kg/m2. Genomic DNA was extracted for promoter DNA methylation analysis of candidate genes LEP, TNF, NPY, POMC and SOCS3 using bisulfite amplicon sequencing.

overall_design: In a sample of 24 participants, we used a non-parametric regression to identify CpG sites with a methylation state that associates with

first: Yen

middle: T

last: Wong

first: Martha

last: Lappas

first: Jeffrey

last: Craig

first: Ratana

last: Lim

first: Caitlyn

last: Nguyan-Ngo

first: Priya

last: Sumithran


title: Dysfunctional BCAAs catabolism protests from diet-induced obesity via IRF4/BCATm pathway in skeletal muscle

city: Shanghai

first: Kong

last: Xingxing

state: Shanghai

address: Songhu Road 2005

department: School of Life Sciences

institute: Fudan University

summary: It is well established that obese animals and humans show deficiencies in skeletal muscle content and metabolism. However, the mechanisms under how skeletal muscle metabolism affects systemic energy homeostasis is not well-defined. Here, we compared the skeletal muscle transcriptome from obese and lean controls in different species. We found an immune-responsive transcription factor interferon regulatory factor 4 (IRF4) was conserved to be increased in obese subjects from the three species (humans, non-human primates and mice). Thus, we demonstrated that loss of IRF4 specifically in skeletal muscle of mice showed protection against the metabolic effects of high-fat diet, with unexpected increased plasma and muscle branched-chain amino acid (BCAA) levels. Conversely, overexpression of skeletal muscle IRF4 caused obesity and insulin resistance, with decreased BCAA contents. Mechanistically, IRF4 can transcriptionally regulate branched-chain aminotransferase isozyme (BCATm) expression, and that overexpression of BCATm can reverse the effects of IRF4 depletion regarding to metabolic phenotypes. Further, we demonstrated ablation of IRF4 in skeletal muscle increased mitochondrial activity and glycogen synthesis in a BCATm- dependent manner. These studies establish IRF4 as a novel driver of BCAA metabolism via BCATm in skeletal muscle and may interpret the BCAAs paradox in obesity.

overall_design: Examination of different gene expression in skeletal muscle tissue near knee joint of lean and obesity male subjects.

first: Xingxing

last: Kong

first: Tiemin

last: Liu


title: Nuclear MTHFD2 secures centromere methylation, chromosome stability and correct mitosis progression [RNA-seq]

city: Barcelona

first: Luca

last: Cozzuto

state: Barcelona

address: Carrer Dr. Aiguader 88

department: Bioinformatics facility

country: Spain

institute: Centre for genomic regulation (CRG)

summary: Subcellular compartmentalization of metabolic enzymes may elicit specific cellular functions by establishing a unique metabolic environment. Indeed, the nuclear translocation of certain metabolic enzymes is required for epigenetic regulation and gene expression control. Here, we reveal that, in cancer cells, the mitochondrial enzyme methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) localizes in the nucleus during the G2-M phase of the cell cycle to secure mitosis progression. Nuclear MTHFD2 interacts with proteins involved in mitosis regulation and centromere stability, including the methyltransferases KMT5A and DNMT3B. Loss of MTHFD2 induces centromere overexpression and severe methylation defects, and impedes correct mitosis completion. As a consequence, MTHFD2 deficient cells accumulate chromosomal aberrations arising from chromosome congression and segregation defects. Blocking the catalytic nuclear function of MTHFD2 recapitulates the phenotype observed in MTHFD2 deficient cells, attributing to nuclear MTHFD2 an enzymatic active role in controlling mitosis. Our discovery uncovers a nuclear moonlighting role for the cancer target MTHFD2, and emphasizes that cancer metabolism rewiring may encompass the relocation of metabolic enzymes to alternative subcellular compartments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 MTHFD2 wild-type and knock-out cells at two different time points (initial, final). There are 3 biological replicates per condition.

first: Natalia

last: Pardo-Lorente

first: Sara

last: Sdelci


title: Single-cell RNA sequencing reveals the gonadal dynamic changes of sex differentiation in hermaphroditic protogynous orange-spotted grouper, Epinephelus coioides

city: Haizhu district, Guangzhou

first: wang

last: tong

state: GD

address: School of Life Sciences，Sun Yat-Sen University East Campus

institute: School of Life Sciences, Sun Yat-Sen University

summary: Sex differentiation is a complex process that requires many factors to regulate proliferation, differentiation, development, and organization of the gonads. In teleosts, the molecular mechanisms of sex differentiation are diverse and unclear, especially in hermaphrodite fish. In the present study, 15 cell types, including germ cells, follicle cells, and theca cells, and so on, were identified using single-cell RNA sequencing (scRNA-seq) in the gonads during sex differentiation in a hermaphrodite fish, orange-spotted grouper (Epinephelus coioides). Two pre-follicle cell types were defined, and the differentiating trajectories of the follicle cells were outlined. Notably, both pre-follicle and follicle cells highly expressed male-related genes synchronously, such as amh, sox9, and dmrt3 in pre-follicle cells, as well as dmrt1 in follicle cells. Oocyte possessed two distinct states, with high expression of oocyte development related genes in one state and spermatogenesis related genes in the other state, respectively. Our results provide novel insights into cell types and lineage tracing in the gonads during sex differentiation in hermaphrodite species.

overall_design: Single-cell suspensions from mixed and freshly dissected gonads at 80 days post-hatching (dph) (n=30), 120 dph (n=20), and 180 dph (n=5), were prepared with two biological duplicates.

first: Xi

last: Wu

first: Chaoyue

last: Zhong

first: Yang

first: Tong

last: Wang


title: Impaired oxysterol-liver X receptor signaling underlies aberrant cortical neurogenesis in a stem cell model of neurodevelopmental disorder

city: Cardiff

first: Daniel

last: de la Fuente

address: Maindy Road

country: United Kingdom

institute: Cardiff University

summary: The mechanisms by which genomic risks contribute to the onset of neuropsychiatric conditions remain a key challenge and a prerequisite for successful development of effective therapies. 15q11.2 copy number variation (CNV) containing the CYFIP1 gene is associated with autism and schizophrenia. Using stem cell models, we show that 15q11.2 deletion (15q11.2del) and CYFIP1 loss of function (CYFIP1-LoF) lead to premature neuronal differentiation, while CYFIP1 gain of function (CYFIP1-GoF) favors neural progenitor maintenance. CYFIP1 dosage changes led to dysregulated cholesterol metabolism and altered levels of 24S,25-epoxycholesterol, which can mimic the 15q11.2del and CYFIP1-LoF phenotypes by promoting cortical neuronal differentiation and can restore the impaired neuronal differentiation of CYFIP1-GoF neural progenitors. Moreover, the neurogenic activity of 24S,25-epoxycholesterol is lost following genetic deletion of liver X receptor (LXRβ), while compound deletion of LXRβ in CYFIP1-/- background rescued their premature neurogenesis. This work delineates LXR-mediated oxysterol regulation of neurogenesis as a pathological mechanism in neural cells carrying 15q11.2 CNV and provides a potential target for therapeutic strategies for associated disorders.

overall_design: Three biological replicates were produced for each sample and time-points of differentiation. Paired-end sequencing and a depth of approximately 33 million reads per sample were used for all sequencing experiments.

last: Cabezas de la Fuente

first: Claudia

last: Tamburini

first: Meng

last: Li


title: Myeloid Cell Adhesion Molecule 1 (CADM1) promotes pro-inflammatory signaling during Inflammatory Bowel Disease.

status: Public on Jul 28 2024

city: Ithaca

first: Praveen

last: Sethupathy

email: as3999@cornell.edu, pr46@cornell.edu

state: NY

address: T7 006D Veterinary Research Tower, Box 17

department: Department of Biomedical Sciences

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing

summary: Background and aims: Cytotoxic T cells have long been postulated to facilitate autoimmune destruction of intestinal epithelium; and the precise causal events leading to inflammatory bowel diseases (IBDs) remain unresolved. CADM1, a membrane adhesion protein which can shed its extracellular ectodomain enters the systemic circulation as well as bind the receptor CRTAM present on CD8+ T cells. Methods: We performed RNA and small RNA sequencing on colon tissue from IBD and non-IBD (NIBD) control patients. We performed spatial transcriptomics and stimulated lamina propria mononuclear cells (LPMCs) with the soluble form of CADM (sCADM1) in these patients. Dextran Sulfate Sodium (DSS) was used to induced colitis in a conditional myeloid Cadm1 loss-of-function mouse. Results: MicroRNA-375 was significantly decreased while its direct target CADM1 was markedly up-regulated in UC patients compared to NIBD control subjects. Single cell proteomics data identified CADM1 enrichment in multiple clusters including macrophages and dendritic cells from colonic tissue of human subjects with IBD. An increased number of CADM1+CD68+ cells was detected adjacent to CD8+ T-cells within the intestinal epithelium of colon sections from patients with ulcerative colitis (UC) compared to NIBD subjects. Myeloid Cadm1 conditional knockout mice were protected against DSS-induced colitis indicating Cadm1 may facilitate binding/localization of cytotoxic cell populations within the gut epithelium. Furthermore, we observed that serum levels of the cleaved extracellular ectodomain of CADM1 (sCADM1) are elevated in medically refractory UC patients compared to non-IBD and UC donors in remission and treatment of LPMCs with recombinant sCADM1 enhanced STAT3 phosphorylation. Conclusions: Together these results identify CADM1 as a potent mediator of pro-inflammatory signaling pathways and demonstrate its potential as a diagnostic and therapeutic target for preventing the IBDs.

overall_design: We performed small RNA sequencing on colon tissue from IBD and non-IBD (NIBD) control patients.

first: Shehzad

last: Sheikh

first: Matthew

last: Poy

first: Terrence

last: Furey

first: Chandhan

last: Sona

first: Kimberly

last: Darlington

first: Alexandria

last: Shumway


title: Human Somitoids Generated by Reprogramming Pax8+ Urine Cells [ChIP-seq]

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: we used chip-seq data to find the mechanism of CDX2 function on maintaining UiPSM features, based on the characteristic change when CDX2

overall_design: Examination of CDX2 transcription factor action site and H3k27ac modifications in UiPSM and CDX2-/- UiPSM


title: Mis-splicing Drives Loss of Function of p53E224D Point Mutation

city: Durham

first: Ian

middle: C

last: Lock

state: North Carolina

address: 438 research Drive

department: Radiation Oncology

institute: Duke University

summary:
Background: Tp53 is the most commonly mutated gene in cancer. Canonical Tp53 DNA damage response pathways are well characterized and classically thought to underlie the tumor suppressive effect of Tp53. Challenging this dogma, mouse models have revealed that p53 driven apoptosis and cell cycle arrest are dispensable for tumor suppression. Here, we investigated the inverse context of a p53 mutation predicted to drive expression of canonical targets, but is detected in human cancer.
Methods: We established a novel mouse model with a single base pair mutation (GAG>GAC, p53E221D) in the DNA-Binding domain that has wild-type function in screening assays, but is paradoxically found in human cancer in Li Fraumeni syndrome. Using mouse p53 E221D and the the analogous human p53E224D mutant, we evaluated expression, transcriptional activation, and tumor suppression in vitro and in vivo.
Results: Expression of human p53E224D from cDNA translated to a fully functional p53 protein. However, p53 E221D/E221D RNA transcribed from the endogenous locus is mis-spliced resulting in nonsense mediated decay. Moreover, fibroblasts derived from p53 E221D/E221D mice do not express a detectable protein product. Mice homozygous for p53 E221D exhibited increased tumor penetrance and decreased life expectancy compared to p53 WT animals.
Conclusions: Mouse p53 E221D and human p53 E224D mutations lead to splice variation and a biologically relevant p53 loss of function in vitro and in vivo.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Wild-Type and homozygous P53E221D/E221D mutant  mouse embryonic fibroblasts were sequenced without perturbation in triplicate. NCI-H716 and HCT116 cells were similarly sequenced in triplicate.

first: Nathan

middle: H

last: Leisenring

first: Warren

last: Floyd

first: Eric

last: Xu

first: Lixia

last: Luo

first: Yan

last: Ma

first: Erin

last: Mansell

first: Diana

middle: M

last: Cardona

first: Chang-Lung

last: Lee

first: David

middle: G

last: Kirsch


title: Human Somitoids Generated by Reprogramming Pax8+ Urine Cells [ATAC-seq]

summary: Compared chromatin dynamical changes between UiPSM and CDX2-/- UiPSM using genome-wide ATAC seq

overall_design: Examination of chromatin dynamical changes in UiPSM and CDX2-/- UiPSM


title: Monomeric EGFR-mediated activation of STAT3 promotes triple-negative breast cancer progression

city: Xiamen

first: Jing

last: Bi

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District, Xiamen, Fujian Province, China

institute: Xiamen University

summary: Dimerization is believed necessary for receptor tyrosine kinases (RTKs) activation. Here we report that monomeric epidermal growth factor receptor (EGFR) directly phosphorylates the signal transducer and activator of transcription-3 (STAT3) in the absence of transmembrane protein TMEM25 (hereafter referred to as TAMER (Transmembrane protein Antagonizing Monomeric EGF Receptor signaling) to reflect its molecular function). We identified TAMER as a checkpoint for the monomeric-EGFR/STAT3 signaling, and downregulation of TAMER in triple-negative breast cancer (TNBC) results in a persistent activation of STAT3 that is required for TNBC progression, which gives a good explanation why targeting EGFR dimerization by antibodies showed no significant benefit to TNBC patients in clinical trials. Remarkably, supply of TAMER strongly suppressed TNBC progression, presenting a promising targeted therapy for TNBC. Hence, our study demonstrated the first RTK monomer-mediated signaling pathway, introducing an unprecedented pattern of RTK signaling that may play key roles in certain physiological or pathological contexts, which might need to be inspected for therapeutically targeting RTKs in the future.In this paper, RNA-seq were used to identify different gene expression in WT and TMEM25 knockout  MDA-MB-231 cells.

overall_design: mRNA profiles of  WT and TMEM25 knockout MDA-MB-231 cells.

first: Hong-Rui

last: Wang

first: Taoling

last: Zeng

first: Tong-Jin

last: Zhao


title: Cxcl10 and Cxcr3 regulate self-renewal and differentiation of hematopoietic stem cells

status: Public on Jul 25 2024

city: Guangzhou

first: Fangshu

last: Liu

address: he First Affiliated Hospital of Jinan University, 613W Huangpu Rd, Guangzhou, Guangdong,

institute: Department of Hematology, the First Affiliated Hospital of Jinan University

summary: Background: The function of hematopoietic stem cells (HSC) is regulated by HSC internal signaling pathways and their microenvironment. Chemokines and chemokine ligands play important roles in the regulation of HSC function. Yet, their functions in HSC are not fully understood.  Methods: We established Cxcr3 and Cxcl10 knockout mouse models (Cxcr3-/- and Cxcl10-/-) to analyze the roles of Cxcr3 or Cxcl10 in regulating HSC function. The cell cycle distribution of LT-HSC was assessed via flow cytometry. Cxcr3-/-and Cxcl10-/-stem/progenitor cells showed reduced self-renewal capacity as measured in serial transplantation assays. To study the effects of Cxcr3 or Cxcl10 deficient bone marrow microenvironment, we transplanted CD45.1 donor cells into Cxcr3-/-or Cxcl10-/- recipient mice (CD45.2) and examined donor-contributed hematopoiesis. Results: Deficiency of Cxcl10 and its receptor Cxcr3 led to decreased BM cellularity in mice, with a significantly increased proportion of LT-HSC. Cxcl10-/- stem/progenitor cells showed reduced self-renewal capacity in the secondary transplantation assay. Notably, Cxcl10-/- donor-derived cells preferentially differentiated into B lymphocytes, with skewed myeloid differentiation ability. Meanwhile, Cxcr3-deficient HSCs demonstrated a reconstitution disadvantage in secondary transplantation, but the lineage bias was not significant. Interestingly, the absence of Cxcl10 or Cxcr3 in bone marrow microenvironment did not affect HSC function.  Conclusions: The Cxcl10 and Cxcr3 regulate the function of HSC, including self-renewal and differentiation, adding to the understanding of the roles of chemokines in the regulation of HSC function.

overall_design: LT-HSCs (Lin-Sca-1+c-Kit+CD135-CD150+CD48-) were isolated from bone marrow cells of three WT mice, Cxcl10-/- and Cxcr3-/- mice, respectively. 500~800 drops per mouse were sorted into 96-well plates containing 10μl buffer (2%FBS+DPBS). RNA extraction and amplification were performed with Discover-sc WTA Kit V2 following the manufacturer's instructions (Vazyme, N711-02). cDNA concentration was determined by Qubit 3.0. Sequencing libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina according to the manufacturer's protocol (Vazyme, TD503-01) and sequenced on the Illumina sequencing platform by Genedenovo Biotechnology Co., Ltd (Guangzhou, China).

first: Juan

last: Du

first: Hui


title: Single-cell RNA sequencing analysis of the effect of 4-octyl itaconate administration on gene expression in immune cells isolated from traumatic brain injury mice brain

status: Public on Jul 27 2024

city: New Orleans

first: Ning

state: LA

address: 1324 Tulane Ave. JBJ building, School of Medicine, Room 632

department: Neurosurgery

institute: Tulane University School of Medicine

summary: 4-octyl itaconate regulates immune response of brain immune cells following traumatic brain injury.

overall_design: 11-12 weeks old male mice were subjected to sham (n=8) or controlled cortical impact injury (n=20). At 1 hour later, CCI mice were randomly administrated with vehicle (40% cyclodextrin in PBS) (n=10) or 4-octyl itaconate (4-OI, 10 mg/kg) (n=10) via intraperitoneally injection. Mice were sacrificed and perfused 12 hours after CCI and ipsilateral brain hemispheres were collected. CD11b positive cells were isolated through CD11b+-magnet beads. The isolated CD11b positive cells from Sham, TBI+Vehicle, and TBI+4-OI groups were randomly divided into two samples, respectively, for single-cell RNA sequencing analysis.

first: Di

last: Zhou

first: Xiaoying


title: Endoglin regulates the integrity of the bone marrow vasculature

city: Dresden

first: Ben

last: Wielockx

address: Fetscherstrasse 74

institute: IKL, Carl Gustav Carus Universitätklinikum Dresden

summary: Patients with a heterozygous mutation in Endoglin (Eng) suffer from hereditary hemorrhagic telangiectasia (HHT), a condition characterized by the development of arteriovenous malformations (AVMs) across various organs, leading to significant bleeding, blood abnormalities, and anemia. Eng is a transmembrane protein and an accessory receptor for transforming growth factor-β (TGF-β) and is therefore essential for maintaining normal vascular architecture. Despite extensive research linking Eng deficiency to AVMs, the precise mechanisms driving this association remain poorly understood. In addition, the role of the bone marrow, a primary source of immune and other blood cells, in the context of endothelial Eng (EC-Eng) deficiency has yet to be explored. In this study, we demonstrate that bone marrow blood vessels conditionally deficient in Eng undergo a temporally orchestrated remodeling process over four weeks, characterized by distinct proliferative and resolution phases. We detail the specific phases of this remodeling, including angiogenic set points, the involvement of the beta integrin family, and modulation of vascular integrity. Furthermore, we explore the impact on the hematopoietic stem and progenitor cell (HSPC) compartment and the resultant changes in circulating blood cells. Using a conditional heterozygous deficient EC-Eng mouse model, we observe significant similarities to phenotypes described in the cKO line, which may ultimately be detrimental in patients with HHT. Taken together, using a combination of different in vivo approaches, our research proposes that very low levels of Eng expression in the endothelium may drive critical vascular remodeling in the bone marrow, sharing mechanisms with early vascular processes leading to AVM formation.

overall_design:
To analyze the effects of endothelial Endoglin deficiency, we generated the Cdh5:CreERT2-Engf/f mouse line. The Enff/f mous line has been described previously and contains loxP sites flanking exons five and six of the endoglin gene. For this project, we induced the KO by using tamoxifen injections when mice reached 8 weeks of age.
Flow cytometry and cell sorting were performed, with endothelial cells from bone marrow being defined as CD31+, CD45,ter119-. These cells were isolated directly into lysis buffer.
We performed gene expression profiling analysis using data obtained from RNAseq of WT and KO femurs at 2 different timepoints (2 and 4 weeks after KO induction)

first: Diego

last: Rodriguez

first: Mangesh

last: Jaykar

first: Deepika

last: Watts

first: Anupam

last: Sinha

last: Gaete

first: Anja

last: Krüger

first: Peter

last: Mirtschink

first: Martina

last: Rauner

first: Triantafyllos

last: Chavakis

first: Helen

last: Arthur


title: Long-lived central memory gamma delta T cells confer protection against murine cytomegalovirus reinfection

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

country: France

institute: Parean Biotechnologies

summary: The involvement of γδ TCR-bearing lymphocytes in immunological memory has gained increasing interest due to their functional duality between adaptive and innate immunity. γδ T effector memory (TEM) and central memory (TCM) subsets have been identified, but their respective roles in memory responses are poorly understood. In the present study, we used subsequent mouse cytomegalovirus (MCMV) infections of αβ T cell deficient mice in order to analyze the memory potential of γδ T cells. As for CMV-specific αβ T cells, MCMV induced the accumulation of cytolytic, KLRG1+CX3CR1+ γδ TEM that principally localized in infected organ vasculature. Typifying T cell memory, γδ T cell expansion in organs and blood was higher and more efficient after secondary viral challenge than after primary infection. Viral control upon MCMV reinfection was prevented when masking γδ T-cell receptor, and was associated with a preferential amplification of private and unfocused TCR δ chain repertoire composed of a combination of clonotypes expanded post-primary infection and, more unexpectedly, of novel expanded clonotypes. Finally, long-term-primed γδ TCM cells, but not γδ TEM cells, protected T cell-deficient hosts against MCMV-induced death upon adoptive transfer, probably through their ability to survive and to generate TEM in the recipient host. This better survival potential of TCM cells was confirmed by a detailed scRNASeq analysis of these two γδ T cell subsets which also revealed their similarity to classically adaptive αβ CD8 T cells. Overall, our study uncovered memory properties of long-lived TCM γδ T cells that confer protection in a chronic infection, highlighting the interest of this T cell subset in vaccination approaches.

overall_design: C57BL/6 TCRalpha-/- mice (n=15) were infected with mouse cytomegalovirus for 3 months. Splenocytes were pooled and used as a whole population (sample 3) or sorted into gamma delta TCM (CD44+CD62L+) (sample 1) or TEM (CD44+CD62L-) (sample 2) subpopulations. Splenocytes from age-matched control uninfected mice (n=9) were pooled (sample 4). Nuclei were prepared from samples 1-4 for scATAC and scRNASeq analysis.

first: Nathalie

last: Yared

first: Maria

last: Papadopoulou

first: Pierre

last: Barennes

first: Hang

middle: P

last: Pham

first: Valentin

last: Quiniou

first: Sonia

last: Netzer

first: Hanna

last: Kaminski

first: Laure

last: Burguet

first: Amandine

last: Demeste

first: Pacôme

last: Colas

first: Lea

last: Charrot

first: Benoit

last: Rousseau

first: Julien

last: Izotte

first: Atika

last: Zouine

first: Xavier

last: Gauthereau

first: David

last: Vermijlen

first: Julie

last: Déchanet-Merville

first: Myriam

last: Capone


title: Systematic characterization of indel variants using a yeast-based protein folding sensor

city: Copenhagen

first: Sven

last: Larsen-Ledet

state: N

address: Ole Maaloes Vej 5

country: Denmark

institute: University of Copenhagen

summary: Gene variants resulting in insertions or deletions of amino acid residues (indels) have important consequences for evolution and are often linked to disease, yet compared to missense variants the effects of indels are poorly understood and ineptly predicted. To approach this issue, we developed a sensitive protein folding sensor based on complementation of uracil auxotrophy in yeast by circular permutated orotate phosphoribosyltransferase (CPOP). The sensor accurately reports on the folding of disease-linked missense variants and artificially designed proteins. Applying the folding sensor to a saturated library of single amino acid indel variants in human DHFR revealed that most regions which tolerate indels are confined to internal loops and the N- and C-termini. Surprisingly, indels are also allowed at a central α-helix. Several indels are temperature-sensitive and the folding of most indels is rescued upon binding to the competitive DHFR inhibitor methotrexate. Predictions using Rosetta and AlphaFold2 correlate with the observed effects, suggesting that most indels operate by destabilizing the native fold and that these computational tools may be useful for classification of indels observed in population sequencing.

overall_design: The human DHFR sequence was divided into five tiles. For each tile, we generated an indel library comprising all possible single residue deletions as well as insertion of a single glycine residue at each position in that tile. The DHFR sequence outside each tile in the five libraries was wild-type. The DHFR libraries were inserted into the CPOP folding sensor and cloned into pAG415. The libraries were transformed into a ura5Δura10Δ strain. Cells were plated on medium with and without methotrexate at 30 °C and 37 °C to select for folding of DHFR indel variants. Based on the relative change in frequency, we calculated a CPOP folding score of each DHFR indel variant.

first: Rasmus

last: Hartmann-Petersen


title: Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors

city: Rehovot

first: Naama

last: Barkai

state: HaMerkaz

address: Herzl 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Activation domains (ADs) within transcription factors (TFs) induce gene expression by recruiting coactivators to specific regulatory regions. Within the prevailing model, TF-coactivator recruitment is independent of DNA binding, which is consistent with direct AD-coactivator interactions seen outside cells. However, this independence was not yet tested within the genomic context. Here, we targeted two Med15-interacting ADs to hundreds of budding yeast promoters through fusions with multiple DNA binding domains (DBDs), gradually controlling their abundances using libraries of synthetic promoters. Genomic profiling revealed that AD identity influences DNA binding locations and that transcription induction and Med15 recruitment are restricted to a subset of DBD-bound promoters displaying flexible expression, multiple-TFs binding, and fuzzy nucleosome architecture. Further, when fused to a DBD, Med15 redirected binding towards promoters of fuzzy nucleosomes, overcoming DBD-based preferences. Our results demonstrate that ADs and their recruited coactivators posses an inherent preference for genomic localization and, therefore, define the subset of induced promoters.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces cerevisiae BY4741

overall_design: ChEC-Seq experiments at OD600 of 0.4, all of the samples except one have at least duplicates. 30 second MNase activation. The experiments with calibration control (see description here - ARO80-MNase addition) ARO80 tf with fused MNase was added to the culture as a 10% ratio calculated by the respective OD600.

first: Vladimir

last: Mindel

first: Sagie

last: Brodsky

first: Hadas

last: Yung

first: Wajd

last: Manadre


title: UNVEILING THE MIXL1 CORE GENE REGULATORY NETWORK FOR CELL FATE DECISION DURING MOUSE GASTRULATION

city: WESTMEAD

first: PIERRE

last: OSTEIL

state: NSW

address: 214 Hawkesbury Road

department: Embryology

institute: CMRI

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

overall_design: Refer to individual Series


title: Transcriptomic changes in mouse Epiblast stem cells induced with Mixl1

summary: We performed total RNA-seq in a epiblast stem cell model of mouse gastrulation to determine the effect of Mixl1 knockout and induction.

overall_design: Total RNA-seq of Mixl1-knockout and Mixl1-inducible mouse Epiblast stem cells after 2 d of serum differentiation

first: Pierre

last: Osteil

first: Nazmus

last: Salehin

first: Patrick

last: Tam


title: Chromatin immunoprecipitation in mouse Epiblast stem cells induced with FLAG-Mixl1

summary: We performed ChIP-seq in a epiblast stem cell model of mouse gastrulation to identify the genomic binding locations of mouse MIXL1

overall_design: ChIP-seq of Mixl1-inducible mouse Epiblast stem cells after 2 d of serum differentiation using the FLAG epitope.


title: Positive regulation of Hedgehog signaling via phosphorylation of GLI2/GLI3 by DYRK2 kinase

city: Chiba

first: SAISHU

last: YOSHIDA

address: 2-2-1 Miyama, Funabashi-shi

department: Department of Biomolecular Science,

country: Japan

institute: Toho University

summary: To understand the molecular mechanisms underlying developmental abnormalities in  Dyrk2-/- mice, we performed comprehensive whole-genome RNA sequencing of the MEFs from wild-type and  Dyrk2-/- embryos

overall_design: We performed gene expression profiling analysis of RNA-seq data for wild-type and Dyrk2-/- MEFs in the presence of 100 nM SAG for 24 h as well as  MEFs treated with siDyrk2 or siNegative (siNeg) in the presence of 100 nM SAG for 24 h

first: Saishu

last: Yoshida

first: Akira

last: Kawamura

first: Katsuhiko

last: Aoki

first: Pattama

last: Wiriyasermkul

first: Shinya

last: Sugimoto

first: Junnosuke

last: Tomiyoshi

first: Ayasa

last: Tajima

first: Yamato

last: Ishida

first: Yohei

last: Katoh

first: Takehiro

last: Tsukada

first: Yousuke

last: Tsuneoka

first: Kohji

last: Yamada

first: Shushi

last: Nagamori

first: Kazuhisa

last: Nakayama

first: Kiyotsugu


title: Crosstalk between neural tissue-specific extracellular matrix and mesenchymal stem cells and their promotion of peripheral nerve regeneration in vivo

city: Beijing

first: Xiangling

last: Li

state: Beijing

address: Fucheng Road

institute: Chinese PLA General Hospital

summary: A favorable regenerative microenvironment is essential for peripheral nerve regeneration. Neural tissue-specific extracellular matrix (ECM) is a natural material that helps direct cell behavior and promote nerve regeneration. Mesenchymal stem cell (MSC) transplantation is effective in promoting peripheral nerve regeneration. In conclusion, this study summarizes the in vivo response characteristics and underlying molecular mechanisms of BMSCs and ADSCs on neural-tissue-derived ECM materials, providing new clues when selecting the optimal MSCs for repairing PNI in the clinic.

overall_design:
Here, a rat sciatic nerve deficit injury model was used to investigate in vivo response characteristics, molecular mechanisms, and effects of adipose-derived mesenchymal stem cells (ADSCs) and bone marrow-derived mesenchymal stem cells (BMSCs) on neural tissue-derived ECM materials to promote peripheral nerve repair. The results showed that BMSCs exhibited more significant immunomodulatory effects on tissue-derived ECMs, as evidenced by the up-regulation of interleukin (IL)-10, down-regulation of IL-1β and tumor necrosis factor-alpha (TNF-α) expression, promotion of M1-type macrophage polarization to M2-type, and a significant increase in the number of regulatory T cells (Tregs). However, ADSCs exhibited more pronounced features of pro-myelination and vasculogenesis on tissue-derived ECM materials. To further elucidate the underlying molecular mechanisms, changes in long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) were systematically investigated using whole transcriptome sequencing. Notably, both BMSCs and ADSCs were effective in repairing peripheral nerve injury (PNI) in the presence of neural tissue-derived ECM.
Total: 9 samples.


title: Intestinal Microbiota Composition is Predictive of Radiotherapy-induced Acute Gastrointestinal Toxicity in Prostate Cancer Patients

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: The search for factors beyond the radiotherapy dose that could identify patients more at risk of developing radio-induced toxicity is essential to establish personalised treatment protocols for improving the quality-of-life of survivors. To investigate the role of the intestinal microbiota in the development of radiotherapy-induced gastrointestinal toxicity, the MicroLearner observational cohort study characterised the intestinal microbiota of 136 (discovery) and 79 (validation) consecutive prostate cancer patients at baseline radiotherapy. Gastrointestinal toxicity was assessed weekly during RT using CTCAE. An average grade >1.3 over time points was used to identify patients suffering from persistent acute toxicity (endpoint). The intestinal microbiota of patients was quantified from the baseline faecal samples using 16S rRNA gene sequencing technology.

overall_design: Intestinal microbiota of prostate cancer patients was profiled before radiotherapy from faecal samples using 16S rRNA gene sequencing technology and processed using the Ion Reporter metagenomic pipeline


title: Misaligned feeding uncouples daily rhythms within brown adipose tissue and between peripheral clocks

city: Dallas

first: Joseph

last: Takahashi

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

summary: Extended consumption of food into the rest period perturbs the phase relationship between circadian clocks in the periphery and the brain and has deleterious effects on health through mechanisms that remain incompletely understood. Beyond the liver, how other metabolic organs respond to hypocaloric diet (amount and timing) is largely unexplored. We investigated how feeding time impacts circadian gene expression in white (eWAT) and brown (BAT) adipose tissues in comparison to liver and hypothalamus. With automated feeders, we restricted food to either daytime or nighttime in C57BL/6J male mice, with or without caloric restriction. We found tissue-specific changes in the phase and amplitude of genome-wide mRNA expression patterns induced by daytime feeding in liver and eWAT, whereas BAT exhibited resilience and remained predominately entrained to the light-dark cycle, similar to hypothalamus. We uncovered an internal split within the BAT in response to conflicting environmental cues, displaying inverted oscillations on a subset of metabolic genes without modifying its local core circadian machinery. Integrating intra- and inter-tissue disruptions in circadian clock-controlled transcriptional networks with metabolic outcomes may help elucidate the mechanism underlying the health burden of eating at the wrong time of the day.

overall_design: To address systemic influences of daytime feeding on circadian profiles of gene expression, we generated mRNA-seq for 6 months-old C57BL/6J male mice fed under different feeding conditions. We collected liver and brown adipose tissue (BAT) samples every 4h during 2 days in constant darkness. For liver (12 timepoints x 2 biological replicates x 5 feeding conditions , total 120 samples). For BAT, (12 timepoints x 2 feeding conditions , total 24 samples).

first: Victoria

middle: A

last: Acosta-Rodríguez

first: Filipa

last: Rijo-Ferreira

first: Laura

last: van Rosmalen

first: Mariko

last: Izumo

first: Noheon

last: Park

first: Chryshanthi

last: Joseph

first: Chelsea

last: Hepler

first: Anneke

middle: K

last: Thorne

first: Jeremy

last: Stubblefield

last: Bass

first: Carla

middle: B

last: Green

middle: S


title: Blocking CX3CR1+ Tumor-associated Macrophages Synergize with anti-PD-1 Therapy in Hepatocellular Carcinoma

first: Xiaonan

last: Xiang

address: No.866, Yuhangtang road Road

department: School of Medicine

institute: Zhejiang University

summary: The efficacy of immune checkpoint inhibitors (ICI) in hepatocellular carcinoma (HCC) treatment remains limited, warranting further investigation into the underlying mechanisms. Accumulating evidence indicates that myeloid cells within the tumor microenvironment (TME) play a role in immune evasion and treatment resistance. In this study, we aimed to explore the contribution of tumor-associated macrophages (TAMs) in the HCC TME. Our findings unveil the critical involvement of CX3C motif chemokine receptor 1 (CX3CR1)-positive TAMs in inducing T cell exhaustion through interleukin-27 (IL-27) secretion, providing valuable insights into the mechanisms underlying the suboptimal efficacy of anti-PD-1 therapy in HCC. Additionally, we identified prostaglandin E2 (PGE2) released by immune-attacked tumor cells as a key driver of CX3CR1+ TAM recruitment. To enhance the therapeutic response to current anti-PD-1 therapy, we propose a novel treatment strategy that combines targeted depletion of CX3CR1+ TAMs with anti-PD-1 therapy. Overall, our study contributes to the understanding of TAMs' role in cancer immunotherapy and presents potential clinical implications for HCC treatment. By targeting CX3CR1+ TAMs in conjunction with anti-PD-1 therapy, we have the potential to enhance the effectiveness of immunotherapeutic interventions in HCC patients.

overall_design: We magnetically sorted F4/80+ cells from murine liver cancer treated with IgG, anti-PD-1, anti-CX3CR1 or anti-PD-1/CX3CR1 (4 samples each group). Then we used these cells for RNAseq.

first: Jianguo

last: Wang

first: Hui

last: Zhang

first: Xiao

last: Xu


title: ELMSAN1 Regulates Differentiation and Maturation of Cardiomyocytes Derived from Human Induced Pluripotent Stem Cells

city: Birmingham

first: Yang

last: Zhou

state: AL

address: 1825 University Blvd

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

summary: Background ELMSAN1 is a newly identified scaffolding protein of the mitotic deacetylase complex (MiDAC), playing a pivotal role in early embryonic development. Studies on Elmsan1 knockout mice showed that its absence results in embryo lethality and heart malformation. However, the precise function of ELMSAN1 in heart development and formation has remained elusive. To gain insights into its potential role in cardiac lineage, we employed human-induced pluripotent stem cells (hiPSCs) to model early cardiogenesis and investigated the function of ELMSAN1.  Methods and Results We generated ELMSAN1-deficient hiPSCs through both knockdown and knockout, revealing that ELMSAN1 appears to be unnecessary for hiPSC maintenance. During the process of cardiac differentiation, ELMSAN1 depletion led to a delay in pluripotency deactivation, decreased expression of cardiac-specific markers, and reduced differentiation efficiency. The impaired expression of genes associated with contractile sarcomere structure, calcium handling, and ion channels were also noted in ELMSAN1-deficient cardiomyocytes derived from hiPSCs (hiPSC-CMs). Additionally, through a series of structural and functional assessments, we found that these cells are immature, exhibiting incomplete sarcomere Z-line structure and length, decreased calcium amplitude, increased time to peak value, faster beat rate with a shorter beat period, decreased field potential duration, and prolonged propagation delay. Of note, we found that the cardiac specific role of ELMSAN1 is likely associated with histone H3K27 acetylation level. The transcriptome analysis provided additional insights, indicating maturation reduction with energy metabolism switch and restored cell proliferation in ELMSAN1 knockout cardiomyocytes.  Conclusions In this study, we address the significance of the direct involvement of ELMSAN1 in the differentiation and maturation of hiPSC-CMs. We first report the impact of ELMSAN1 on multiple aspects of hiPSC-CM generation, including cardiac differentiation, sarcomere formation, calcium handling, electrophysiological maturation and proliferation.

overall_design: To gain insight into the developmental role of ELMSAN1 in cardiac lineage commitment, we generated ELMSAN1-Knock Out (KO) human induced pluripotent stem cells (hiPSCs) using CRISPR/Cas9 system. We then differentaited the wild-type (WT) and KO hiPSCs into cardiomyocytes. We then performed gene expression profiling analysis using data obtained from RNA-seq of WT and KO cells at two time points (Day 0 and Day 9) during the cardiomyocyte differentiation process. Comparative gene expression profiling analysis of RNA-seq data was perfromed on these four samples.

first: Yu-An

last: Lu

first: Jiacheng

last: Sun


title: Systematic evaluation of GAPs and GEFs identifies ARHGAP45 as a targetable leukemia-specific RhoGAP dependency

city: New York

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

summary: GTPase-activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs) function as negative and positive regulators of small GTPases, respectively, and play key roles in cell fate determination. The aberrant function of GAPs and GEFs has long been implicated in cancer development but their vast number and potential redundancy have hindered comprehensive understanding of their roles. Here we performed functional genetic screens of GAPs and GEFs in primary AML specimens to uncover an unexpected and selective role for ARHGAP45 in AML. Depletion of ARHGAP45 impedes AML growth without affecting normal human CD34+ cells in vivo. Epistasis screens revealed RhoA as the major substrate of ARHGAP45 and that depletion of the Rho GTPase CDC42 synergized with ARHGAP45 deletion. Consistent with this, pharmacologic CDC42 inhibition enhanced the effect of ARHGAP45 deletion. ARHGAP45 gives rise to a minor histocompatibility antigen (termed HA-1), which can be recognized by antigen-specific T cells. CDC42 inhibition not only sensitized AML cells to ARHGAP45 inhibition but also promoted the activity of HA-1 antigen-specific T cells by upregulating ARHGAP45-derived epitope in AML cells.

overall_design: To gain insights into ARHGAP45-regulated transcriptomic changes at single-cell resolution, we introduced Cas9-sgRNA RNP into cells from three human AML PDX samples with diverse genotypes and two primary patient samples. These primary samples were directly isolated from patients without propagation in mice. Both samples harbored DNMT3A, FLT3-ITD, and NPM1c mutations, which are associated with poor clinical outcomes.. Each sample was subjected to Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), for multiplex sample indexing and simultaneous measurement of single-cell transcriptomics and cell surface protein expression.

first: Pu

first: Zhendong

last: Cao

first: Xiangyu

last: Pan

first: Junwei

last: Shi

first: Omar

last: Abdel-Wahab


title: Skin wounds in mice of different number of days the transcriptome sequencing

city: Hohhot

first: Jiamin

last: Zhao

address: zhaowuda road

institute: Inner Mongolia Agricultural University

summary: C57BL/6J mice wound closure areas were photographed and measured daily until day 14 post-wound. At days 1, 3, 7, 10, 12 and 14 after wound injury batches of mice were sacrificed after anesthesia and full thickness skin samples were collected from the entire wound sites (including the scab and epithelial margins) for evaluation.

overall_design: A total of 7 samples, respectively,3,5,7,10,12 0 and 14 days after mice skin damage tissue samples, each sample with 5 repeat, 0 days after injury of tissue samples in the control group.

first: Yunjie

last: Bai

first: Zhiguo

last: Gong

first: Shungyi


title: Gene expression profile of all CD4 T cells from the mesenteric lymph nodes of SPF and Nippostrongylus Brasiliensis infected mice

city: West haven

first: Antariksh

last: Tyagi

state: CT

address: 830 West Campus Dr

institute: Yale University

summary: The discovery of naïve T cell transcriptional heterogeneity in specific-pathogen-free (SPF) mice represents a paradigm shift. While the ablation of Vista can alter the proportion of naïve CD4+ T cells with unique transcriptional signatures and the ‘readiness’ of the mice to break tolerance, the effect of non-heritable environmental exposures to commensals or infections remains entirely unknown. This is especially significant since individual variance in immune response, rather than being genetically inherited, is mostly attributed to environmental factors. Here we demonstrate that transcriptional heterogeneity characterizes even the germ-free (GF) mouse naïve CD4+ T cells. Naïve CD4+ T cell transcriptional subsets and their proportions were identical between GF, SPF and conventionalized GF mice, thus commensal-independent. Notwithstanding, Nippostrongylus brasiliensis (N.b.) infection altered the proportions of these transcriptional subsets, and the appearance of cells with a unique transcriptional signature. These naïve T cell-intrinsic changes accounted for the decreased immunization response of mice to an unrelated antigen. The compositional and functional changes in the naïve CD4+ T cell pool were dependent-variables of helminth infection, regressing with N.b. clearance. Therefore, naïve T cells are not uniformly uncommitted substrates for antigen-dependent activation but actively integrate environmental cues to permute the magnitude of the immune response.

overall_design: sorted CD3+CD4+B220-TCRB+ from the mesenteric lymph nodes of SPF or Nippostrongylus Brasiliensis infected mice (1 week)

first: Carla

last: Rothlin


title: Multi-omics datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells [ATAC-Seq II]

first: Yi

last: Hu

address: No. 28 Fuxing Rd， Haidian district，Beijing

summary: we generated CUT&Tag, ATAC-seq, RNA-seq, high-resolution Hi-C and Micro-C datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells.

overall_design: ATAC-Seq profiles of normal control human bronchial epithelial cells, TP63 overexpressed human bronchial epithelial cells and radiation induced lung cancer cells

first: Z

last: pingkun

first: L

last: qiaowei


title: LncRNA-LPE binding to TCP1 activates the PI3K/AKT signaling pathway in preeclampsia

city: Shanghai

first: Yaoxi

last: Xiong

state: i

address: Jinqian Road No.1567

institute: The International Peace Maternity and Child Health Hospital, School of Medicine

summary: The role of long noncoding RNA (LncRNA) in numerous diseases was well-established. However, its pathological significance in preeclampsia (PE) remains obscure. In this investigation, a novel low-expression LncRNA (LncRNA-LPE) was identified in PE, and the regulatory mechanism in the progression of PE was examined. We found that LncRNA-LPE was downregulated in PE compared with normal plancenta, suggesting its potential relation with the development of PE. Modulation of LncRNA-LPE expression in trophoblast cells revealed its capacity to influence the migration and invasion abilities. To identify proteins that interact with LncRNA-LPE, RNA pull-down assays, mass spectrometry, and RNA immunoprecipitation (RIP) assays were employed. And we found LncRNA-LPE could interact with the RNA-binding protein T-complex protein 1 (TCP1), which might subsequently influence the PI3K/AKT signaling pathway and lead to autophagy changing. Our results demonstrated that LncRNA-LPE facilitates the development of preeclampsia by binding to TCP1 and activating PI3K/AKT signaling pathway, indicating its potential as a morbidity marker and therapeutic target for preeclampsia.

overall_design: To investigate the synergistic effect of LncRNA LPE in the regulation of preeclampsia, we established an HTR-8/SVneo cell line overexpressing LncRNA LPE.

first: Shuying

last: Wang

first: Chao

last: Chen

first: Chengrong

last: He

first: Hong

last: Shen

first: Ruling

first: Xingyu

last: Yang

first: Weiwei

last: Cheng


title: Loss of Hectd1 disrupts muscle sarcomere assembly and causes combined desmin-nemaline myopathy

city: Solna

first: Igor

last: Cervenka

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

summary: The sarcomere is the muscle contractile unit, whose assembly and disassembly are intimately linked to changes in myofiber size and function. Mutations in sarcomeric proteins are common causes of myopathies, ranging from severe neonatal to adult-onset forms. Here, we identify HECTD1 as an E3 ubiquitin ligase necessary for sarcomere maintenance. We show that silencingHectd1 in myotubesreduces the levels of proteins critical for sarcomere integrity including a-actin, titin, troponins, tropomyosins, and several myosin heavy chain isoforms. We further establish that Hectd1 ubiquitylates and stabilizes the molecular chaperones KLHL40/41, that when dysfunctional destabilize nebulin and other sarcomere thin filament proteins (causing nemaline myopathy). Consequently, skeletal muscle-specific Hectd1 knockout mice (Hectd1 mKO) show progressive muscle weakness, exercise intolerance, and unresolved tissue remodeling. Molecular and histological analysis of Hectd1 mKO muscle revealed subsarcolemmal storage of the scaffold protein desmin, mitochondrial abnormalities, and severe sarcomere disorganization. This work uncovers Hectd1 as an E3 ligase critical for sarcomere assembly, and a novel diagnostic gene for myopathy with features of nemaline and desmin myopathy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse soleus muscle from comparing wild-type and Hectd1 conditional skeletal muscle knockout (mKO) animals. Control mice were kept in conventional cages throughout the entire protocol. Experiment was performed in three replicates per condition.

first: Paulo

middle: R

last: Jannig

first: Serge

last: Ducommun

first: Elie

last: Naddaf

first: Eileen

last: Kokesh

first: Jorge

last: Correia

first: Marta

last: Murgia

first: Baptiste

last: Jude

first: Anastasia

last: Rumyantseva

first: Michele

last: Azzolini

first: Margareta

last: Posmyr-Palmertz

first: Matthias

last: Mann

first: Christoph

last: Freyer

first: Anna

last: Wredenberg

first: Johanna

last: Lanner

first: Andreas

last: Hahn

first: Ana

last: Töpf

first: Volker

last: Straub

middle: L

last: Ruas


title: A Self-Complementary AAV Proviral Plasmid System to Reduce Aberrant Cross-Packaging and ITR Promoter Activity in AAV Vector Preparations (Short-read)

city: Columbus

first: Scott

last: Harper

state: Ohio

address: Center for Gene Therapy, 575 Children’s Crossroads Room WC3740

institute: The Research Institute at Nationwide Children's Hospital

summary: Adeno-associated viral vectors (AAV) are a leading delivery system for gene therapy in animal models and humans.  With several FDA-approved AAV gene therapies on the market, issues related to vector manufacturing have become increasingly important. In this study, we focused on potentially toxic DNA contaminants that can arise from AAV proviral plasmids, the raw materials required for manufacturing recombinant AAV in eukaryotic cells.  Typical AAV proviral plasmids are circular DNAs containing a therapeutic gene cassette flanked by natural AAV inverted terminal repeat (ITR) sequences, and a plasmid backbone carrying prokaryotic sequences required for plasmid replication and selection in bacteria. While the majority of AAV particles package the intended therapeutic payload, some capsids instead package the bacterial sequences located on the proviral plasmid backbone.  Since ITR sequences also have promoter activity, potentially toxic bacterial open reading frames can be produced in vivo, thereby representing a safety risk.  In this study, we describe a new AAV proviral plasmid for vector manufacturing that (1) significantly decreases cross-packaged bacterial sequences; (2) increases correctly packaged AAV payloads; and (3) blunts ITR-driven transcription of cross-packaged material to avoid expressing potentially toxic bacterial sequences.  This system may help improve the safety of AAV vector products.

overall_design: Novel AAV plasmids were packaged into 1st-generation AAV serotypes. Cross-packaging of AAV backbone and other contaminants was assessed by short-read Illumina sequencing.

first: Noah

last: Taylor

first: Matthew

last: Guggenbiller

first: Pranali

last: Mistry

first: Oliver

last: King

middle: Q


title: Vascular endothelial S1PR2 aggravates cardiac ischemia/reperfusion injury through triggering mitochondrial dysfunctions and endothelial pyroptosis via RHO/ROCK1/DRP1/NLRP3 pathway [heart]

first: yunhao

last: duan

address: 150 Jimo Rd, Pudong New District

institute: Shanghai East Hospital

summary: Endothelial cell dysfunction plays an essential role in the process of cardiac ischemia-reperfusion (I/R) injury. Mitochondria damage, which can trigger inflammasome activation and subsequent pyroptosis, perturbs endothelial homeostasis, leading to aggravated cardiac I/R injury. Sphingosine 1-phosphate (S1P), a bioactive lipid molecule, exerts multifaceted effect on I/R injury via its different S1P receptors. However, the effect of EC-expressing S1P receptors on endothelial dysfunction, mitochondrial damage-induced inflammasome activation and consequent pyroptosis during cardiac I/R injury remain unclear. Our findings suggest a pivotal role of EC-expressing S1PR2 to control EC mitochondrial homeostasis and demonstrate that S1PR2-meidated mitochondrial dysfunction can trigger inflammasome activation and pyroptosis in ECs, which significantly influences inflammatory responses and heart injuries following I/R.

overall_design: We provided an RNA-seq analysis on heart tissues of WT and VECre-S1pr2-/- mouse after cardiac ischemia-reperfusion.

first: Yunhao

last: Duan

first: Lin

last: Zhang


title: Loss of Elp3 impairs the immune response to helminths by blocking intestinal tuft cell differentiation

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

summary: Intestinal tuft cells are critical in anti-helminth immunity by producing IL-25, which triggers IL-13 secretion by activated group 2 innate lymphoid cells (ILC2s) in order to ultimately expand both goblet and tuft cells. Translational reprogramming is involved in intestinal tuft cell differentiation but the role of tRNA modifications in this process is unknown. We show here that epithelial Elp3, a tRNA-modifying enzyme, promotes tuft cell differentiation and is consequently critical for IL-25 production, ILC2 activation, goblet cell expansion and control of N. brasiliensis infection in mice. Elp3 is essential for the IL-13-dependent induction of some glycolytic enzymes such as Hexokinase 1 and Aldolase A and consequently links specific metabolic pathways to tuft cell differentiation. Importantly, loss of epithelial Elp3 in the intestine blocks the translation of Nprl2, a mTORC1 inhibitor, which consequently enhances mTORC1 activation and stabilizes Atf4 in both transit amplifying and progenitor cells. Likewise, Atf4 overexpression in mouse intestinal epithelium blocks tuft cell differentiation and impairs the control of intestinal helminth infection. Collectively, our data define Atf4 as a negative regulator of tuft cell differentiation and provide insights into mechanisms through which some tRNA modifications promote a type 2 immune response to parasites in the intestine.

overall_design: To investigate the role of the tRNA-modifying enzyme Elp3 in tuft cell differentiation, we performed a Single Cell RNA-sequencing on intestinal epithelial cells from Elp3WT vs Elp3ΔIEC mice. Mice were treated overnight with rIL-13 in order to induce tuft cell differentiation.

first: Caroline

last: Wathieu

first: Latifa

last: Karim

first: Alain

last: Chariot


title: Transcriptomic evaluation of skin tape-strips in children with allergic asthma uncovers epidermal barrier dysfunction and asthma-associated biomarkers abnormalities

first: Madeline

last: Kim

address: 1 Gustave Levy Place

institute: Icahn School of Medicine at Mount Sinai

summary: Tape-strips were obtained from skin of 18 pediatric patients with moderate allergic asthma (MAA) (n=11), severe allergic asthma (SAA) (n=9), and from healthy children (n=12) and analyzed with bulk RNA-sequencing (RNA-seq). Differential expression was defined as |fold change|≥2 and false discovery rate<0.05. MAA and SAA shared downregulation of G-protein-coupled receptor- (GPCR), mitochondria-, and Wnt-signaling-related genes. Terminal differentiation (FLG/filaggrin), cell adhesion (CDH19, JAM2), lipid biosynthesis/metabolism (ACOT2, LOXL2) markers were significantly downregulated in MAA and SAA (FDR<0.05). Many of these markers additionally correlated with metrics of asthma severity (e.g. exacerbation rate per year, forced expiratory volume in 1 second [FEV1] [% predicted], impulse oscillometry [IOS] R5-20 Hz, fractional excretion of nitric oxide [FeNO]).

overall_design: Bulk RNA-seq data was profiled from tape strips collected from the skin of 18 pediatric patients with moderate allergic asthma (MAA) (n=11), severe allergic asthma (SAA) (n=9), and from healthy children (n=12).

first: Ester

last: Del Duca

first: Dante

last: Dahabreh

first: Jonathan

last: Bar

first: Joel

last: Correa Da Rosa

first: Grace

last: Rabinowitz

first: Paola

last: Facheris

first: Pedro

middle: J

last: Gómez Arias

first: Annie

last: Chang

first: Vivian

last: Utti

first: Amira

last: Chowdhury

first: Ying

last: Liu

first: Alexandru

last: Laculiceanu

first: Ioana

last: Agache

first: Emma

last: Guttman-Yassky


title: Early MicroRNA and Metabolite Changes Post-ACL Reconstruction Surgery

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

country: Canada

institute: Schroeder Arthritis Institute

summary:
Objective: To determine alterations in plasma miRNAs during early stages (2 weeks and 6 weeks) post ACL reconstruction surgery
MicroRNA libraries were prepared using the QIAseq miRNA Library Kit and sequenced on the Illumina NextSeq550. MiRNA reads were then aligned with the mature miRNAs from miRBase v22.1 and human reference genome to create counts for each sample.

overall_design: MiRNA-seq data for plasma from 129 ACL reconstruction OA patients were analyzed for comparative miRNA profiling.

first: Amit

last: Sandhu

first: Katrina

last: Hueniken

first: Chiara

last: Pastrello

first: Igor

last: Jurisica

first: Nikita

last: Looby

first: Vinod

last: Chandran

first: Starlee

last: Lively

first: Jason

last: Rockel

first: Pratibha

last: Potla

first: Anastasia

last: Sanjevic

first: Kimberly

last: Perry

first: Shenghan

last: Li

first: Shgufta

last: Docter

first: Tamara

last: Wagner

first: Darrell

last: Ogilve-Harris

first: Tim

last: Dwyer

first: Jas

last: Chahal


title: Vascular endothelial S1PR2 aggravates cardiac ischemia/reperfusion injury through triggering mitochondrial dysfunctions and endothelial pyroptosis via RHO/ROCK1/DRP1/NLRP3 pathway [endothelial cells]

first: yunhao

last: duan

overall_design: We provided an RNA-seq analysis on heart endothelial cells of WT and VECre-S1pr2-/- mouse after cardiac ischemia-reperfusion.

first: Yunhao

last: Duan

first: Lin

last: Zhang


title: iSuRe-HadCre is an essential tool for effective conditional genetics

city: Madrid

first: Rui

last: Benedito

state: Madrid

address: C. de Melchor Fernández Almagro, 3

institute: CNIC

summary: Methods to modify gene function in mice with high spatiotemporal resolution have revolutionized biomedical research, with Cre-loxP technology remaining the most widely used. We previously generated the iSuRe-Cre mouse allele, a dual Cre-reporter line that, by permanently expressing Cre in reporter-expressing cells, provides certainty that these cells recombine other floxed alleles. Here we report the generation, validation, and utility of a second-generation allele, iSuRe-HadCre. In contrast to its predecessor, the new allele is targeted to the ubiquitously expressed Rosa26 locus, shows no leakiness, is significantly brighter and more sensitive to CreERT2 activity, and has no Cre-related toxicity. iSuRe-HadCre achieves this through a novel inbuilt recombinase genetic switch that ensures that cells expressing a fluorescent reporter have transient, but sufficient, expression of Cre. This new tool will be essential for the precise, efficient, and trustworthy analysis of gene function in single cells or entire tissues of mice.

overall_design: Liver and heart Endothelial Cells of Control,  Cdh5-CreERT2 + iSuReHad-Cre or Cdh5-CreERT2 + iSureCre mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of Tomato signal and analyzed using scRNAseq.

first: Irene

last: García-González

first: Álvaro

last: Regano

first: Susana

middle: F

last: Rocha


title: A common CTRB misfolding variant associated with pancreatic cancer risk  causes ER stress and inflammation in mice

first: Jaime

last: Martinez de Villarreal

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

summary: Objective: Genome wide association studies have identified an exon 6 CTRB2 deletion variant that is associated with increased PDAC risk. To acquire evidence on its causal role, we developed a new mouse strain carrying an equivalent variant in Ctrb1, the mouse orthologue of CTRB2.  Design: We used CRISPR/Cas9 to introduce a 707bp deletion in Ctrb1 encompassing exon 6 (Ctrb1Dexon6). This mutation closely mimics the human deletion variant. Mice carrying the mutant allele were extensively profiled at 3 months to assess their phenotype.   Results: Ctrb1Dexon6 mutant mice express a truncated CTRB1 that accumulates in the ER. The pancreas of homozygous mutant mice displays reduced chymotrypsin activity and total protein synthesis. The histological aspect of the pancreas is inconspicuous but ultrastructural analysis shows evidence of dramatic ER stress, and cytoplasmic and nuclear inclusions. Transcriptomic analyses of the pancreas of mutant mice reveals acinar program down-regulation and increased activity of ER stress-related and inflammatory pathways. Heterozygous mice have an intermediate phenotype. Agr2 is one of the most up-regulated genes in mutant pancreata. Ctrb1Dexon6 mice exhibit impaired recovery from acute caerulein-induced pancreatitis. Administration of TUDCA or sulindac partially alleviates the phenotype. A transcriptomic signature derived from the mutant pancreata is significantly enriched in normal human pancreas of CTRB2 exon 6 deletion variant carriers from the GTEx cohort.  Conclusions: This mouse strain provides formal evidence that the exon 6 deletion variant causes ER stress and inflammation in vivo, providing an excellent model to understand its contribution to pancreatic ductal adenocarcinoma and to identify preventive strategies.

overall_design: To gain a comprehensive understanding of the molecular mechanisms underlying the phenotype of the pancreas of 3- month -old Ctrb1Δ/Δ mice, we performed genome wide transcriptomic analysis using RNA-seq. N=6 mice/genotype sequenced as pool of two mice of the same genotype.

first: Cristina

last: Bodas

last: Felipe

last: Martínez-de-Villarreal

first: Francisco

middle: X

last: Real


title: Expression profiling of Gm1142-/-, Gm1142-/- Gm4779-/- and normal wildtype mouse testes on postnatal day 7 (P7).

status: Public on Jul 31 2024

city: Wuhan

first: ZHIYI

last: CHEN

address: WuHan

institute: WuHan University

summary: To investigate the role of Gm1142 protein in mouse reproduction, We collected Gm1142-/-, Gm1142-/- Gm4779-/- and normal wildtype mouse testes on postnatal day 7 (P7) for RNA sequencing.

overall_design: We collected Gm1142-/-, Gm1142-/- Gm4779-/- and normal wildtype mouse testes on postnatal day 7 (P7) for RNA sequencing, three replications for every group.

first: Mengcheng

last: Luo

first: Rong

last: Liu

first: Jiemin

last: Chen

first: Zhiyi


title: Single Cell Sequencing Analysis of Infiltrating Immune Cells in Orthotopically Implanted Liver Cancer in Mice Treated with Isotype or Anti-PD-1 Therapy

city: Hangzhou

first: Xiaonan

last: Xiang

summary: The anti-PD-1 mAb is a type of immunotherapy known to have a significant impact on tumor immune components. In this study, we utilized single-cell RNA sequencing (scRNAseq) to analyze infiltrating immune cells of liver cancer in mice treated with both anti-PD-1 and isotype control.

overall_design: Following treatment with either IgG or anti-PD-1, C57/BL6 mice with orthotopic liver tumors underwent Fluorescence-activated cell sorting (FACS) sorting of tumor-infiltrating CD45+ immune cells, which were subsequently subjected to scRNAseq.

first: Jianguo

last: Wang

first: Hui

first: Zhixiong

last: Shi

first: Xiao

last: Xu


title: Human Somitoids Generated by Reprogramming Pax8+ Urine Cells [RNA-seq]

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

summary: Describe the transcriptional expression profile

overall_design: Building library and sequencing the wild type and CDX2KO UiPSM samples


title: T cell intrinsic immunomodulatory effects of TAK-981 in chronic lymphocytic leukemia patient derived T cells

city: Duarte

first: Alexey

middle: V.

last: Danilov

state: CA

address: 1500 E Duarte Road

institute: City of Hope National Medical Center

summary: Transcriptome analysis of TAK981 or DMSO pre-treated chronic lymphocytic leukemia  patient derived T cells upon TCR engagement

overall_design: Peripheral blood derived and FACS sorted (CD4+CD45RA+ CD45RO-) Naïve CD4 T cells from four chronic lymphocytic leukemia patients was pre treated with TAK981 or DMSO (1hr) then stimulated with CD3/CD28.  Gene expression profiles were determined through use of Affymetrix Clariom S hybridization array. Gene expression was quantified by Transcriptome Analysis Console (v 4.0) software.  No technical replicates were performed.

middle: V

first: Nathan

middle: D

last: Pennock

first: Allison

last: Berger

first: Vi

last: Lam

first: Carly

last: Roleder

first: Nur

last: Bruss

first: Scott

last: Best

first: Xiaoguang

first: Tingting

first: Lapo

last: Alinari

first: Tanya

last: Siddiqi


title: Differences in gene expression of liver cancer cells after co-culture with activated CD8+ T cells in vitro

first: Xiaonan

address: No.866, Yuhangtang road Road

institute: Zhejiang University

summary: To investigate the difference in gene expression of liver cancer cells after co-culture with activated CD8+T cells , we established a tumor cells/activated CD8+T cells co-culture system  in which murine liver cancer cell line hepa1-6 were co-cultured and attacked directly by murine in vitro activated spleen naive CD8+T cells (effector: target=5:1)  for 48 hours. We then performed gene expression profiling analysis using data obtained from RNA-seq of two different groups (immune attacked or control) with 5 repetitions per group.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hepa1-6 cells and  hepa1-6 attacked by activated CD8+T cells.

last: Zhang


title: Roscovitinen suppresses TRIM32 nuclear translocaton via STAT3 signaling

city: Lanzhou

first: TANG

middle: JIAN

last: MING

state: Gansu

address: 1604 No.1 Donggang West Road, Chengguan District

institute: The First Clinical Medical College of Lanzhou University

summary: Next Generation Sequencing Facilitates Quantitative Analysis of MDA-MB-231 cells treated with Roscovitinen and DMSO

overall_design: mRNA profiles of MDA-MB-231 cells were generated by deep sequencing, in duplicate, using Illumina Navoseq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using  SYBR Green assays.

first: Jianming

last: Tang


title: The rRNA epitranscriptome and myonuclear SNORD landscape in skeletal muscle fibers contributes to ribosome heterogeneity and is altered by hypertrophic stimulus

status: Public on Jul 24 2024

city: Stockholm

first: Paulo

middle: R.

last: Jannig

department: Department of Physiology and Pharmacology

summary: In cell biology, ribosomal RNA (rRNA) 2'O-methyl (2'-O-Me) is the most prevalent post-transcriptional chemical modification contributing to ribosome heterogeneity. The modification involves a family of small nucleolar RNAs (snoRNAs) and is specified by box C/D snoRNAs (SNORDs). Given the importance of ribosome biogenesis for skeletal muscle growth, we asked if rRNA 2'-O-Me in nascent ribosomes synthesized in response to a growth stimulus is an unrecognized mode of ribosome heterogeneity in muscle. To determine the pattern and dynamics of 2'-O-Me rRNA, we used a sequencing-based profiling method called RiboMeth-seq. We applied this method to tissue-derived rRNA of skeletal muscle and rRNA specifically from the muscle fiber using an inducible myofiber-specific RiboTag mouse in sedentary and mechanically overloaded conditions. These analyses were complemented by myonuclear-specific small RNA sequencing to profile SNORDs and link the rRNA epitranscriptome to known regulatory elements generated within the muscle fiber. We demonstrate for the first time that mechanical overload of skeletal muscle 1) induces decreased 2'-O-Me at a subset of skeletal muscle rRNAand 2) alters the SNORD profile in isolated myonuclei. These findings point to a transient diversification of the ribosome pool via 2'-O-Me during growth and adaptation in skeletal muscle. These findings suggest changes in ribosome heterogeneity at the 2'-O-Me level during muscle hypertrophy and lay the foundation for studies investigating the functional implications of these newly identified "growth-induced" ribosomes.

overall_design:
Experiment 1: Whole skeletal muscle RNA following 3, 7, and 14 days of mechanical overload (MOV) and a sham surgery control condition in C57BL/6J (females, 5 months of age, n=12) were used for RiboMeth-seq analysis. MOV was induced by synergist ablation for which a small portion of the gastrocnemius muscle was removed (22), while sham surgery involved the same steps of synergist ablation without the removal of muscle.

Experiment 3: A skeletal muscle specific RiboTag mouse (HSA-RiboTag) was generated by crossing the HSA-mER-CRE-mER (MCM) mouse (Jax, Stock No. 025750) with the RiboTag mouse (Jax, Stock No. 029977), which enabled cre-mediated hemagglutinin (HA) epitope tagging of ribosomes at the ribosomal protein L22 locus in a skeletal muscle-specific manner. HSA-RiboTag mice (females, 4-6 months of age, n=3 overload/sham) were administered tamoxifen (75 mg /kg body weight, corn oil solution) by intraperitoneal injection for five days starting on the day of MOV. For this experiment, MOV was performed on one limb with the contralateral limb serving as sham control.

first: Minying

last: Cui

first: Maral

last: Halladjian

first: Nicolai

last: Krogh

first: Henrik

last: Nielsen

first: Ferdinand

last: von Walden


title: Nuclear MTHFD2 secures centromere methylation, chromosome stability and correct mitosis progression

city: Barcelona

first: Luca

last: Cozzuto

state: Barcelona

address: Carrer Dr. Aiguader 88

institute: Centre for genomic regulation (CRG)

summary: Subcellular compartmentalization of metabolic enzymes may elicit specific cellular functions by establishing a unique metabolic environment. Indeed, the nuclear translocation of certain metabolic enzymes is required for epigenetic regulation and gene expression control. Here, we reveal that, in cancer cells, the mitochondrial enzyme methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) localizes in the nucleus during the G2-M phase of the cell cycle to secure mitosis progression. Nuclear MTHFD2 interacts with proteins involved in mitosis regulation and centromere stability, including the methyltransferases KMT5A and DNMT3B. Loss of MTHFD2 induces centromere overexpression and severe methylation defects, and impedes correct mitosis completion. As a consequence, MTHFD2 deficient cells accumulate chromosomal aberrations arising from chromosome congression and segregation defects. Blocking the catalytic nuclear function of MTHFD2 recapitulates the phenotype observed in MTHFD2 deficient cells, attributing to nuclear MTHFD2 an enzymatic active role in controlling mitosis. Our discovery uncovers a nuclear moonlighting role for the cancer target MTHFD2, and emphasizes that cancer metabolism rewiring may encompass the relocation of metabolic enzymes to alternative subcellular compartments.

overall_design: Whole-genome methylation and structural variation analysis of nanopore WGS data for HCT116 MTHFD2 wild-type and knock-out cells.

first: Pardo-Lorente

last: Natalia

first: Cozzuto

last: Luca

first: Gkanogiannis

last: Anestis

first: Sdelci

last: Sara


title: Peyer’s patches are required for Bacteroides fragilis to induce protective systemic IgA

city: Syracuse

first: Joel

last: Wilmore

state: NY

address: 766 Irving Ave

department: Microbiology and Immunology

institute: SUNY Upstate Medical University

summary: Gut-educated IgA-secreting plasma cells that disseminate beyond the mucosa and into systemic tissues can help prevent disease in several contexts. Here we show, the commensal bacteria Bacteroides fragilis (Bf), is an efficient inducer of systemic IgA responses. The generation of bone marrow IgA plasma cells and high levels of serum IgA specific to Bf requires robust intestinal colonization. Bf-specific IgA responses were severely diminished in mice lacking Peyer’s patches, but not mice lacking a cecal patch. Colonization resulted in few changes in the host transcriptional profile in the gut, suggesting a commensal relationship. High levels of Bf-specific serum IgA, but not IgG, provided protection from peritoneal abscess formation in a bowel perforation model of Bf dissemination. These findings demonstrate a critical role for bacterial colonization and Peyer’s patches in the induction of robust systemic IgA responses that confer protection from bacterial dissemination originating from the gut.

overall_design: Mice were treated with B. fragilis by oral gavage and given either 1 or 6 doses and then euthanized 2 or 4 weeks after treatment. A 2cm piece of colon or small intestine were washed to remove feces and then RNA was isolated for RNAseq analysis.

first: Joshua

last: Harris


title: Effect of the deletion of the genes involved in phospholipid synthesis pathway on gene expression (DKO)

first: Zhu

last: Yibing

state: Zhe Jiang

address: Xihu

department: Life Of Science

summary: Phospholipid and nucleotide syntheses are fundamental metabolic processes in eukaryotic organisms, with their dysregulation implicated in various disease states. However, the interplay between these pathways remains elusive. With genetic and metabolic analyses in the yeast S. cerevisiae, we elucidate how cytidine triphosphate utilization and recycling in the Kennedy pathway for phospholipid synthesis influence nucleotide metabolism and redox balance. Deficiencies in the Kennedy pathway impose constraints on nucleotide salvage, prompting compensatory co-activation of de novo nucleotide synthesis and the pentose phosphate pathway. Consequently, this metabolic shift towards alternative nucleotide and phospholipid synthesis pathways fosters the production of antioxidants such as NADPH and glutathione. Additionally, we observe that this oxidation-responsive Kennedy pathway for phospholipid synthesis is inhibited during replicative aging, highlighting its activation as an antioxidative defense mechanism in aged cells. These findings underscore the critical role of pathway choice in phospholipid synthesis in the integrative regulation of nucleotide metabolism, redox balance, and membrane biophysical properties for cellular defense.

overall_design: we knockout PAH1 and DGK1 in yeasts and perform RNA-seq in normal culturing conditions.

first: Yibing

last: Zhu

first: Xiaomeng

last: Tong

first: Jingyuan

last: Xue

first: Hong

last: Qiu

first: Dao-Qiong

last: Zheng

first: Cunqi

last: Ye


title: Single cell RNAseq profiling of Human Pancreatic Islets across sex

city: New Orleans

first: Franck

last: Mauvais-Jarvis

state: LA

address: 1430 Tulane Avenue Lab# 2301

department: Department of Medicine - Section of Endocrinology and Metabolism

institute: Tulane University

summary: Mechanisms driving sex differences across islet cells is unknown. Thus, studying sex differences in islet regulation and function represent a unique avenue to understand the sex-specific heterogeneity in β cell failure in diabetes. We examined sex and race differences in human pancreatic islets from 15 donors using an orthogonal series of experiments including single cell RNA-seq (scRNA-seq), single nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq), dynamic hormone secretion, and bioenergetics.

overall_design: Human islets (500 IEQ per condition) were cultured overnight in a humidified incubator containing 5% CO2 at 37°C. Islet cells were then dispersed using TrypLE (Thermofischer), and immediately evaluated for viability (90.61±3.04%) by Cellometer Automated Cell Counter (Nexcelom Bioscience) prior to single cell RNAseq library preparation. For 10x single cell RNAseq library preparation, 5000-6500 individual live cells per sample were targeted by using 10x Single Cell 3’ RNAseq technology provided by 10x Genomics (10X Genomics Inc). Briefly, viable single cell suspensions were partitioned into nanoliter-scale Gel Beads-In-EMulsion (GEMs). Full-length barcoded cDNAs were then generated and amplified by PCR to obtain sufficient mass for library construction. Following enzymatic fragmentation, end-repair, A-tailing, and adaptor ligation, single cell 3’ libraries comprising standard Illumina P5 and P7 paired-end constructs were generated. Library quality controls were performed by using Agilent High Sensitive DNA kit with Agilent 2100 Bioanalyzer (Agilent) and quantified by Qubit 2.0 fluorometer (ThermoFisher). Pooled libraries at a final concentration of 750pM were sequenced with paired end single index configuration by Illumina NextSeq 2000 (Illumina).

first: Mirza

last: Qadir


title: Effect of the deletion of the genes involved in phospholipid synthesis pathway on gene expression (PAH1 DGK1)


title: LARP3, LARP7, and MePCE are Involved in the Early Stage of Human Telomerase RNA Biogenesis

city: Taipei

first: Chi-Kang

last: Tseng

address: No.1 Jen Ai road section 1

department: Graduate institute of microbiology

institute: National Taiwan university, College of Medicine

summary: Human telomerase assembly is a highly dynamic process. Using biochemical approaches, we found that LARP3 and LARP7/MePCE are involved in the early stage and that their binding to hTR is destabilized when the mature hTR is produced. LARP3 plays a negative role in preventing the processing of the 3′-extended long (exL) form and binding of LARP7 and MePCE. Interestingly, the tertiary structure of the exL form prevents LARP3 binding and facilitates hTR biogenesis. Supporting this process, LARP3 at low levels promotes hTR maturation, increases telomerase activity, and elongates telomeres. LARP7 and MePCE knockdown inhibits the conversion of the 3′-extended short (exS) form into mature hTR and the cytoplasmic accumulation of hTR, resulting in telomere shortening. Our data suggest that LARP3 and LARP7/MePCE mediate the processing of hTR precursors and thus control the production of functional telomerase.

overall_design: To investigate the function of PARN, LARP7, and MePCE in hTR 3'-end processing. We isolated the RNA from PARN, LARP7, and MePCE knockdown cell lines in HeLa cells, followed by 3' RACE sequencing.

first: Tsai-Ling

last: Kao

first: Yu-Cheng

last: Huang

first: Yi-Hsuan

last: Chen

first: Peter

last: Baumann


title: Satellite glial contact enhances differentiation and maturation of human induced sensory neurons

city: Boston

first: Chelsey

last: LeBlang

state: Massachusetts

address: 360 Longwood Ave

department: Cancer Biology

institute: Dana Farber Cancer Institute

summary: Induced sensory neurons (iSNs) generated from pluripotent stem cells are used to model human peripheral neuropathies, however current differentiation protocols produce sensory neurons with an embryonic phenotype. Peripheral glial cells contact sensory neurons early in development and contribute to formation of the canonical pseudounipolar morphology, but these signals are not encompassed in current iSN differentiation protocols. Here, we show that terminal differentiation of iSNs in co-culture with rodent Dorsal Root Ganglion satellite glia (rSG) advances their differentiation and maturation. Co-cultured iSNs develop pseudounipolar morphology through contact with rSGs. This transition depends on semaphorin-plexin guidance cues and on glial gap junction signaling. In addition to morphological changes, iSNs terminally differentiated in co-culture exhibit enhanced spontaneous action potential firing, more mature gene expression, and increased susceptibility to paclitaxel induced axonal degeneration. Thus, iSNs differentiated in coculture with rSGs provide a better model for understanding human peripheral neuropathies.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: To determine the impact of iSN-rDRG glial coculture on iSN development we compared human mRNA  from iSN- rDRG glial cocultures (Glia_iSN_Co) with iSNs cultured alone (iSN only). We also explored the impact of maturation media on glial cell populations comparing rat mRNA from rDRG glial cultures maintained in baseline media (Glia Only),rDRG glial cultures treated with maturation media (Glia_NCATS), and rDRG glial cultures that were cocultured with iSNs (Glia_iSN_co).

first: Rosalind

last: Segal


title: Effect of depletion of IMPDH1 and IMPDH2 on gene expression after DNA damage in HeLa cells

city: Beijing

first: Yundong

last: Xiong

address: 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

summary: Guanosine nucleotide (GTP) serves as a pivotal purine nucleoside triphosphate, essential for DNA and RNA structure and function. Additionally, it acts as an activator for the guanine-binding protein family (G protein), participating in crucial cellular processes such as cytoskeleton rearrangement, membrane transport, protein synthesis, and signal transduction. IMPDH1 and IMPDH2 are key enzymes in the de novo synthesis of guanine nucleotides. Our research shows that they exhibit differential activities under DNA damage conditions. Specifically, IMPDH1 predominantly maintains enzymatic activity during DNA damage, facilitating GTP synthesis and cell survival. Our data indicate that following DNA damage, IMPDH1 and IMPDH2 affect distinct pathways in cells, with IMPDH1 potentially promoting the expression of homologous recombination repair proteins.

overall_design: To investigate the distinct impacts of IMPDH1 and IMPDH2 on gene expression following DNA damage, we generated stable knockdown cell lines for both IMPDH1 and IMPDH2. Subsequently, we treated wild-type (WT), IMPDH1 knockdown (KD), and IMPDH2 KD cells with the DNA damage-inducing drug TMZ. After treatment, we harvested the cells for RNA sequencing and conducted gene expression analysis based on the RNA sequencing results.


title: Effect of Itaconate in mouse macrophages cell line (RAW264.7)

city: Detroit

first: Nikhlesh

last: Singh

state: MI

address: 6135  Woodward Avenue

institute: Wayne State University School of Medicine

summary: To investigate the expression prolfile of genes regulated by Itaconate  in RAW264.7.

overall_design: RAW264.7 were exposed to Itaconate for 24 hrs and then gene expression profiling was performed using 3 prime RNA sequencing.

first: Shivantika

last: Bisen