title: Plasma proteomics and organ dysfunction in COVID-19 ARDS

city: COLUMBUS

first: Joseph

middle: S

last: Bednash

state: OH

address: 473 W 12th Avenue, DHLRI 509

department: Medicine

institute: Ohio State University

summary: Fatal COVID-19 is often complicated by hypoxemic respiratory failure and acute respiratory distress syndrome (ARDS). Mechanisms governing lung injury and repair in ARDS remain poorly understood because there are no biomarker-targeted therapeutics for patients with ARDS. We hypothesized that plasma proteomics may uncover unique biomarkers that correlate with disease severity in COVID-19 ARDS. We analyzed the circulating plasma proteome from 32 patients with ARDS and COVID-19 using an aptamer-based platform, which measures 7289 proteins, and correlated protein measurements with sequential organ failure assessment (SOFA) scores at 2 time points (Days 1 and 7 following ICU admission). We compared differential protein abundance and SOFA scores at each individual time point and identified 119 proteins at Day 1 and 46 proteins at Day 7 that correlated with patient SOFA scores. We modeled the relationship between dynamic protein abundance and changes in SOFA score between Days 1 and 7 and identified 39 proteins that significantly correlated with changes in SOFA score. Using Ingenuity Pathway Analysis, we identified increased ephrin signaling and acute phase response signaling correlated with increased SOFA scores over time, while pathways related to pulmonary fibrosis signaling and wound healing had an inverse relationship with SOFA scores between Days 1 and 7. These findings suggest that persistent inflammation may drive worsened disease severity, while repair processes correlate with improvements in organ dysfunction over time. This approach is generalizable to more diverse ARDS cohorts for identification of protein biomarkers and disease mechanisms as we strive towards targeted therapies in ARDS.

overall_design: Proteomic profiles via SomaLogic aptamer-based microarray (SomaScan 7k v.4) from plasma from ARDS patients with COVID-19 with variable degrees of organ dysfunction.

first: Moemen

last: Eltobgy

first: Brett

last: Klamer

first: Joshua

last: Englert

first: Guy

last: Brock


title: NAD Depletion in Skeletal Muscle does not Compromise Muscle Function or Accelerate Aging

status: Public on Apr 09 2025

city: Copenhagen N

first: NNF CBMR

last: Single-Cell Omics Platform

address: Blegdamsvej 3B

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

summary: NAD is a ubiquitous electron carrier essential for energy metabolism and the post-translational modification of numerous regulatory proteins. Perturbation of NAD metabolism is considered detrimental to health, with NAD depletion commonly thought to promote aging. However, the extent to which cellular NAD concentration can be decreased without deleterious repercussions is unclear. We generated a mouse model where nicotinamide phosphoribosyltransferase (NAMPT)-mediated NAD+ biosynthesis is disrupted in adult skeletal muscle. The resulting 85% decrease in muscle NAD+ abundance was associated with preserved tissue integrity and functionality, as demonstrated by its unchanged morphology, contractility, and exercise tolerance. This lack of defects was corroborated by intact mitochondrial respiratory capacity and unaffected muscle transcriptomic and proteomic profiles. Furthermore, lifelong NAD depletion did not accelerate muscle aging or impair whole-body metabolism. Collectively, these findings indicate that NAD depletion does not contribute to age-related decline in skeletal muscle function.

platform_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus

overall_design: We profiled DNA methylation in 48 samples. The experiment is a two-way factorial design with 23 old and 25 young mice, 25 of which were wild-type and 23 of which where NAMPT was knocked out in adult skeletal muscle.

first: Sabina

last: Chubanava

first: Iuliia

last: Karavaeva

first: Amy

middle: M

last: Ehrlich

first: Roger

last: Justicia

first: Astrid

middle: L

last: Basse

first: Ivan

last: Kulik

first: Emilie

last: Dalbram

first: Danial

last: Ahwazi

first: Samuel

middle: R

last: Heaselgrave

first: Kajetan

last: Trošt

first: Ben

last: Stocks

first: Ondřej

last: Hodek

first: Raissa

middle: N

last: Rodrigues

first: Jesper

middle: F

last: Havelund

first: Farina

last: Schlabs

first: Steen

last: Larsen

first: Carlos

last: Henriquez-Olguín

first: Daniela

last: Giustarini

first: Ranieri

last: Rossi

first: Zachary

last: Gerhart-Hines

first: Thomas

last: Moritz

first: Juleen

last: Zierath

first: Kei

last: Sakamoto

middle: E

last: Jensen

first: Nils

middle: J

last: Færgeman

first: Gareth

middle: G

last: Lavery

first: Atul

last: Deshmukh

first: Jonas

middle: T

last: Treebak


title: Engineering a novel HSV-1 strain for oncolytic therapy of solid tumors

city: Augusta

first: Balveen

last: Kaur

state: GA

address: CN-3205, 1410 Laney-Walker Blvd

department: Pathology

country: USA

institute: Augusta University

type: Expression profiling by high throughput sequencing

summary: Oncolytic HSV-1 derived viruses are being developed for cancer treatment. Here we describe the isolation of a novel strain of HSV-1, and its engineering to safely harness it as an oncolytic therapeutic. This strain (UT1a) was isolated from a de-identified consented patient biorepository. CRISPR-Cas9-based recombination was utilized to insert bacterial artificial chromosome (BAC) genes into the viral UL39 and UL40 locus resulting in the deletion of both large and small subunits of the viral ribonucleotide reductase (RR). Subsequent deletion of viral RL1 genes encoding the neurovirulence factor ɣ34.5, resulted in OncoDelta (OncoD), a virus deleted for UL39, UL40 and both copies of RL1. OncoD retained tumor cell specific cytotoxicity and replication, was safe and non-toxic in intracranial injections in naïve mice up to doses of (5 x 106), maximal injectable dose OncoD and showed significant anti-tumor immune activating potential in multiple tumor models. Transcriptome profiling of OncoD showed that it impaired DNA damage repair pathways and hence synergized with radiation to improve therapeutic response in vitro and in vivo.

overall_design: RNA-seq profiling of human glioblastoma GBM12 cells treated with PBS or infected with oncolytic HSV-1 OncoD for 24h at 0.01 MOI

first: Karina

last: Vazquez-Arreguin

first: Alex

last: Gonzalez

first: Amy

last: Webb

first: Xiaokui

last: Mo

first: Yoshihiro

last: Otani


title: The mechanism of LDO on Macrophages in transcriptome level

city: xi'an

first: Wei

last: Gaofei

state: Shaanxi

address: beilin

country: China

institute: Northwestern Polytechnical University

summary: The mechanism of LDO on BMDM was analyzed based by RNA-seq

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BMDM after treatment of LPS and LPS+LDO

first: Junyan

last: Zhuang

first: Gaofei

last: Wei


title: Single-nuclei transcriptome analysis of IgM+ cells isolated from channel catfish spleen

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

summary: Channel catfish, Ictalurus punctatus, are the primary cultured species of the catfish industry. Significant losses in production are attributed to bacterial diseases which are challenging to control and new interventions need to be developed. To gain insight into the in situ catfish immune system, we used single-nuclei RNAseq. We produced two single-nuclei atlases from three individual catfish using flow cytometry sorted IgM+ splenic cells. Libraries were prepared using the 10X Genomics system and sequenced on an Illumina sequencer. The reads were aligned to the reference genome (Ip Coco_2.0) using Cell Ranger (v8.0.0).

overall_design: Spleen samples from three adult catfish were collected and sorted for IgM+ cells to generate a channel catfish IgM+ cell transcriptome atlas.

first: Johanna

last: Aldersey

middle: W

first: Benjamin

middle: H

last: Beck

first: Miles

middle: D

last: Lange


title: HIF1α deletion promotes mitochondrial repurposing in bone marrow-derived macrophages, but not in tissue-resident alveolar macrophages

city: Chicago

first: Rengul

last: Cetin-Atalay

address: 5841 S. Maryland Avenue

institute: The University of Chicago

summary: RNA-Seq data investigates the impact of HIF-1α deletion on the transcriptome of tissue-resident alveolar macrophages (TR-AMs) and bone marrow-derived macrophages (BMDMs) both at baseline and following treatment with the HIF-1α stabilizer FG-4592

overall_design: Mouse inducible HIF-1α knockout (Hif1a-/-) TR-AMs and BMDMs

first: Gokhan M

last: Mutlu

first: Woods S

last: Parker

first: Atalay

last: Rengul

first: Angelo Y

last: Meliton

first: Hamanaka B

last: Robert


title: Integrated transcriptomic and metabolomic analysis reveals that cathepsin D regulates the phenotypic transition of vascular smooth muscle cells by inhibiting glycolysis

city: Fenyang

first: Songhao

last: Tian

address: No. 16 College Road

institute: Fenyang College of Shanxi Medical University

summary: This study investigates the role of Cathepsin D (CTSD) in diabetic vascular complications, particularly its impact on the phenotypic transformation of vascular smooth muscle cells (VSMCs) induced by advanced glycation end-products (AGEs), and explores its potential molecular mechanisms. CTSD was overexpressed in VSMCs using lentiviral vectors. Various methods, including CCK-8, immunofluorescence, SA-β-Gal staining, EdU assay, scratch assay, cell cycle analysis, and Western blotting, were employed to assess VSMC viability, proliferation, migration, senescence, and apoptosis. Additionally, transcriptomic and metabolomic analyses were conducted to investigate the molecular mechanisms underlying CTSD overexpression in VSMCs. AGEs treatment significantly inhibited CTSD expression in VSMCs, leading to reduced cell viability, enhanced proliferation and migration, increased senescence, and apoptosis. In contrast, overexpression of CTSD effectively inhibited AGEs-induced VSMC proliferation, migration, senescence, and apoptosis. Combined transcriptomic and metabolomic analyses suggested that CTSD may affect VSMC phenotypic transformation by inhibiting the glycolysis pathway. This study highlights the critical role of CTSD in the phenotypic transformation of VSMCs induced by AGEs and provides a new perspective for cardiovascular and cerebrovascular disease treatment. CTSD may emerge as a novel therapeutic target, though its specific molecular mechanisms and clinical application prospects in VSMC phenotypic transformation require further investigation.

overall_design: To investigate the effects of AGEs on rat thoracic aortic VSMCs, the cells were incubated with 200 μg/mL for 24 h.To examine the impact of CTSD over-expression on AGEs-induced VSMCs, five cell groups were established: normal VSMCs treated with BSA (C-B group), empty vector-transfected VSMCs treated with BSA (N-B group), normal VSMCs treated with AGEs (C-A group), empty vector-transfected VSMCs treated with AGEs (N-A group), and overexpression-transfected VSMCs treated with AGEs (T-A group).We then performed gene expression profiling using data obtained from RNA-seq of cells from three different treatment groups (N-B, N-A, T-A).Comparative analysis of gene expression profiles of RNA-seq data of VSMCs cells from T-A and N-B groups, respectively, with those from N-A group, reveals the function of CTSD

first: Xingmin

last: He

first: Mingfeng

last: Ma


title: Immunotherapy alongside IL-15 promote intratumoral cytotoxic CD4+T cell activation against MHC-II-expressing tumors

city: Wuhan

first: wang

last: boyu

address: No. 1095 Jiefang Dadao, Hubei Province, Jiaokou District, Wuhan City

department: Tongji Hospital

institute: Huazhong University of Science and Technology

summary: By killing tumor cells, cytotoxic CD8+ T cells are the major effectors in antitumor immunity. A subset of CD4+ T cells also possesses cytotoxic activity by expressing perforin and granzymes and is associated with immunotherapy efficacy. Despite the progress made in characterizing cytotoxic CD4+ T cells in various diseases, the status of cytotoxic CD4+ T cells in non-small cell lung cancer (NSCLC) and the driving mechanisms and forces involved in reviving intratumoral cytotoxic CD4+ T cells remain unclear. Here, we showed that CD4+GzmB+ T cells obtained from patients with NSCLC expressed increased levels of SLC7A5 compared with their counterparts. Upregulation of SLC7A5 was essential for the differentiation of CD4+GzmB+ T cells from naïve CD4+ T cells stimulated with TCR and IL-2. Both T-bet and Eomes are required for the differentiation of CD4+GzmB+ T cells. Interestingly, IL-15 can further increase SLC7A5 expression in differentiated CD4+GzmB+ T cells. Moreover, through activation of the AKT-FOXO1-T-bet axis, IL-15 increased the effector function of intratumoral CD4+GzmB+ T cells. In addition to IL-15, owing to the unique expression profile of PD-1 and CD85j in tumor-infiltrating CD4+GzmB+ T cells, using patient-derived lung cancer explants, we showed that simultaneous blockade of PD-1 and CD85j promoted the effector function of CD4+GzmB+ T cells by activating the AKT pathway. Importantly, using a mouse model of lung cancer, we demonstrated that intrinsic MHC II expression in cancer cells determines the significance of CD4+GzmB+ T-cell-mediated antitumor immunity in response to immunotherapy.

overall_design: Purified CD4+T cells were enriched from peripheral blood of four healthy donors.Then CD4+T cells were treated with anti-CD3/28 plus IL-15(-com group) or not（-b group) to analyse for RNA-seq.

first: Boyu

last: Wang


title: Medicago Mting1 Mting2 double knockout mutants are extremely dwarfed and never flower implicating essential MtING functions in growth and flowering

city: Auckland

first: Yongyan

last: Peng

state: Auckland

address: 120 Mt Albert Road

department: Kiwifruit New Cultivars

country: New Zealand

institute: Plant and Food Research

summary: The regulation of flowering time to synchronise with external environmental signals is critical to plant reproductive success and agricultural productivity. Previously, we used CRISPR-Cas9 gene editing to show the INHIBITOR OF GROWTH 2 gene (MtING2) promotes flowering and growth in the model temperate legume Medicago truncatula, especially under inductive vernalized long days. A second ING gene, MtING1, did not appear to regulate flowering. To further dissect the genetic function of the two ING genes in flowering and growth, we cross-pollinated selected Mting1 and Mting2 single mutants to create two different double mutants;  Mting1-7 Mting2-2 double knockout mutant and Mting1-1 Mting2-11 double PHD finger mutant. The growth and flowering of these mutants was assessed in vernalized long-day conditions. We also used fluorescence confocal microscopy and in vitro protein biophysical analysis to investigate the subcellular localization and oligomerization of the proteins. Finally we carried out gene expression analysis by both RNA-seq and RT-qPCR to determine how the two genes affect transcript accumulation to influence flowering.

overall_design: We carried out RNA-seq on single Mting mutants and double Mting mutant and compared to the relative wildtype. Leaf and shoot apex tissue was harvested from plants grown under VLD conditions, 4 h after dawn on day 14 (WT, Mting1-7, Mting1-1, Mting2-11 and Mting1-1 Mting2-11), day 15 (Mting2-2) and day 21 (Mting1-7 Mting2-2) when plants had 2-3 fully expanded trifoliate leaves. Three biological replicates were harvested per tissue type per genotype, each consisting of 1 to 2 fully expanded trifoliate leaves from the same plant, or 3 to 4 primary apices from different plants. Harvested tissue was snap-frozen in liquid nitrogen and homogenised by metal beads in a Geno/Grinder® 2010 (New Jersey, USA). Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Germany) according to the user manual. RNA quantity and quality were checked by a NanoPhotometer® N60 (Implen, Germany) and a Bioanalyzer 2100 (Agilent Technologies, USA).

first: Matthew

last: Mayo-Smith

first: Axel

last: Poulet

first: Lulu

last: Zhang

first: David

last: Goldstone

first: Joanna

last: Putterill


title: TLDR (True Length of Diverse capped RNAs)-seq: a method for 5’-to-3’ end sequencing of capped full-length RNAs with or without 3’ polyadenylation

city: Copengagen

first: Albin

last: Sandelin

address: Ole Maaløes Vej 5

department: Department of Biology, Section for Computational and RNA Biology

summary: Analysis and understanding of transcript functions is greatly helped by knowing the full-length sequence of individual RNAs. New long-read sequencing devices such as Oxford Nanopore and Pacbio have the potential to sequence full-length transcripts, but standard methods lack the ability to capture true RNA 5’ ends and selects for poly-adenylated (pA+) transcripts. We present a method that, by utilizing cap-trapping and 3’ end adapter ligation, can sequence transcripts from the exact 5’ end to 3’ end regardless of whether they are poly-adenylated, with no need for ribosomal RNA depletion. We show that the method can faithfully detect 5’ ends, splice junctions and 3’ ends, has high reproducibility between runs and gene expression estimates from the method correlate well with short-read sequencing methods. We also demonstrate that the method can detect and sequence full-length pA- RNAs, including lncRNAs, promoter upstream transcripts (PROMPTs) and enhancer RNAs. TLDR-seq is therefore useful for the characterization of diverse capped RNA species.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA was extracted from WT HeLa S3 cells, WT mouse embryonic stem cells (mES) and knock down mES cells (of either RBM7 or ZCCHC8) and analyzed by TLDR-seq on MinION flow cells

first: Jamie

last: Auxillos

first: Arnaud

last: Stigliani

first: Christian

last: Vaagensø

first: Will

last: Garland

first: Adnan

last: Niazi

first: Eivind

last: Valen

first: Torben

last: Jensen


title: A Cellular and Molecular Basis of Leptin Resistance

city: New York

first: Wei

state: New York

address: 1230 York Ave.

department: Bioinformatics Resource Center

institute: The Rockefeller University

summary: Humans with obesity and diet-induced obese mice (DIO) have high leptin levels and fail to respond to the exogenous hormone suggesting that obesity is caused by leptin resistance, the pathogenesis of which is unknown. We found that leptin treatment reduced plasma levels of leucine and methionine, mTOR-activating ligands, leading us to hypothesize that chronic mTOR activation might inhibit leptin signaling. Rapamycin, an mTOR inhibitor, reduced fat mass and increased leptin sensitivity in DIO mice but not in mice with defects in leptin signaling. Rapamycin restored leptin’s actions on POMC neurons and failed to reduce the weight of mice with defects in melanocortin signaling. mTOR activation in POMC neurons caused leptin resistance while POMC specific mutations in mTOR activators decreased weight gain of DIO mice. Thus, increased mTOR activity in POMC neurons is necessary and sufficient for the development of leptin resistance in DIO mice establishing a key pathogenic mechanism leading to obesity.

overall_design: Chow-fed, diet-induced-obese (DIO), and chow-fed ob/ob mice were treated with rapamycin or vehicle. Hypothalamic nuclei from these mice were dissociated and Fluorescient-activated sorted to enrich NeuN+ nuclei.

first: Bowen

last: Tan

first: Kristina

last: Hedbacker

first: Ji-Dung

last: Luo

first: Jeffrey

last: Friedman


title: mRNA sequencing analysis of fresh resected lung tissues from tuberculosis patients

city: Shanghai

first: Zilu

last: Wen

address: No. 2901, Caolang Road, Jinshan District, Shanghai

institute: SHANGHAI PUBLIC HEALTH CLINICAL CENTER

type: Non-coding RNA profiling by high throughput sequencing

summary: Fresh resected lung tissues were obtained from nine tuberculosis patients with elevated pulmonary 18F-FDG avidity. Lung tissues with 18F-FDG avidity and nearby uninvolved tissues were profiled with mRNA sequencing.

overall_design: Fresh resected human lung tissues with high 18F-FDG avidity and nearby uninvolved tissues with background or low 18F-FDG avidity were profiled with mRNA sequencing.

first: Yanzheng

last: Song

first: Ka-Wing

last: Wong

first: Lin

last: Wang


title: BARD1 is an exploitable therapeutic target for homologous repair proficient pancreatic ductal adenocarcinomas [MiaPaCa-2]

city: Philadelphia

first: Aditi

last: Jain

state: PA

address: 1015 Walnut Street

department: Surgery

institute: Thomas Jefferson University

summary: The overall 5-year survival rate of patients with pancreatic ductal adenocarcinoma (PDAC) is only 13% and there is an unmet need for better therapies. For the minority (5-10%) of patients with homologous recombination repair (HRR) deficient  PDAC tumors (BRCA1/2, PALB2 mutations), poly (ADP-ribose) polymerase (PARP) inhibitor (PARPi) and platinum-based therapies offer the best-personalized treatment approach. However, the efficacy of these treatments is often limited due to inherent (HRR proficient tumors) or acquired drug resistance. We have previously shown that expression of BARD1 or BRCA1- Associated- Ring- Domain- 1, a DNA repair protein and an obligate binding partner of BRCA1, is post-transcriptionally upregulated by the pro-survival RNA binding protein HuR (ELAVL-1), in PDAC. Here, we evaluated BARD1’s functional role in PDAC cell biology and evaluated its potential as a therapeutic target in HRR-proficient PDAC. BARD1 expression was silenced in HRR- proficient PDAC cells using both small interfering RNAs and CRISPR/Cas9 deletion. Silencing BARD1 decreased cell proliferation and 3D matrigel invasion in vitro. Tumor growth of BARD1KO mouse xenografts was markedly impaired. Mechanistically, using RNA sequencing of BARD1 silenced cells, we found a de-enrichment of the epithelial-mesenchymal-transition (EMT) pathway and global downregulation of c-Myc-target genes, which control diverse cell signaling events in PDAC. BARD1 stabilized the c-Myc protein through inhibition of the ubiquitin–proteasome system. Further, to evaluate if BARD1 loss is synergistic with DNA damage agents, we employed a focused DNA damage drug library in BARD1 silenced cells and found that cells were uniquely sensitized to the PARP inhibitors class of drugs. Our proof-of-concept study implicates BARD1 as an attractive, exploitable therapeutic target for HRR proficient PDAC patients and presents a unique opportunity to expand the PDAC patient population that could benefit from PARP inhibitors in the clinical setting.

overall_design: To investigate the effects of targeting BARD1 in PDAC cell lines, we transiently silenced BARD1 using BARD1 siRNA in MiaPaCa-2 cell line

first: Sohum

last: Patel


title: BARD1 is an exploitable therapeutic target for homologous repair proficient pancreatic ductal adenocarcinomas [PANC-1]

overall_design: To investigate the effects of targeting BARD1 in PDAC cell lines, we transiently silenced BARD1 using BARD1 siRNA in Panc-1 cell line


title: T-cell receptor repertoire alterations drive pathological gut immunological and microbial signatures in humans and mice with hypomorphic RAG deficiency

city: BETHESDA

first: Cihan

last: Oguz

state: MD

address: NIHBC 29B BG RM 1NN20, 9000 ROCKVILLE PIKE

institute: NIH

summary: Mechanistic knowledge about the homeostatic interplay between T cell-mediated immunity and gut microbiota is still limited. We aimed to investigate how restriction of the T-cell receptor (TCR) repertoire (VDJ region) may influence gut microbiota composition, causing tissue inflammation and disruption of peripheral immune tolerance. Based on the clinical observation of colonic inflammation in patients with partial RAG deficiency (pRD), we applied a multi-omics strategy to study a mouse model of hypomorphic Rag1 deficiency (Rag1 mutant mice) with spontaneous development of colitis.

overall_design: To characterize the transcriptomic and immune repertoire differences between the wild-type and Rag1 mutant mice at 3 weeks and 12 weeks of age, with and without ANMV (ampicillin, neomycin, metronidazole and vancomycin) treatment (only at 12 weeks for the Rag1 mutant mice), we performed scRNA-seq and TCR repertoire (VDJ region) sequencing of colonic lamina propria-specific CD4+ T cells. The scRNA-seq and TCR libraries were coupled with hashtag oligo (HTO) libraries for labeling the samples in order to demultiplex the pooled libraries into wild-type and Rag1 mutant mice at 3/12 weeks of age and with/without ANMV treatment cell populations for downstream analysis. The number of libraries sequenced is six for scRNA-seq, six for TCR (VDJ) repertoire, and six for HTOs.

first: Riccardo

last: Castagnoli

first: Francesca

last: Pala

first: Poorani

last: Subramanian

first: Benjamin

last: Schwarz

first: Ai Ing

last: Lim

first: Andrew

last: Burns

first: Elena

last: Fontana

first: Marita

last: Bosticardo

first: Cristina

last: Corsino

first: Angelina

last: Angelova

first: Ottavia

last: Delmonte

first: Heather

last: Kenney

first: Deanna

last: Riley

first: Grace

last: Smith

first: Lisa

last: Ott de Bruin

first: Vasileios

last: Oikonomou

first: Lucas

last: Dos Santos Dias

first: Danielle

last: Fink

first: Eric

last: Bohrnsen

first: Cole

last: Kimzey

first: Gian Luigi

last: Marseglia

first: Guisela

last: Alva-Lozada

first: Jenna

last: Bergerson

first: Ana

last: Brett

first: Karlla

last: W Brigatti

first: Dimana

last: Dimitrova

first: Cullen

last: Dutmer

first: Alexandra

last: Freeman

first: Ale

last: Hanadys

first: Steven

last: Holland

first: Francesco

last: Licciardi

first: Srdjan

last: Pasic

first: Laura

last: Poskitt

first: David

last: Potts

first: Joseph

last: Dasso

first: Svetlana

middle: O

last: Sharapova

first: Kevin

middle: A

last: Strauss

first: Brant

last: Ward

first: Melis

last: Yilmaz

first: Douglas

middle: B

last: Kuhns

first: Michail


title: miRNA sequencing analysis of fresh resected lung tissues from tuberculosis patients

first: Zilu

last: Wen

summary: Fresh resected lung tissues were obtained from nine tuberculosis patients with elevated pulmonary 18F-FDG avidity. Lung tissues with 18F-FDG avidity and nearby uninvolved tissues were profiled with miRNA sequencing.

overall_design: Fresh resected human lung tissues with high 18F-FDG avidity and nearby uninvolved tissues with background or low 18F-FDG avidity were profiled with miRNA sequencing.

first: Yanzheng

last: Song

first: Ka-Wing

last: Wong

first: Lin

last: Wang


title: CTCF point mutation at R567 disrupts mouse heart development via 3D genome rearrangement and transcription dysregulation [RNA-seq]

city: Guangzhou

first: HongXin

last: Zhong

address: No. 190, Open Source Avenue, Luogang District, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: In this study, we analyzed gene expression change in heart tissues from 8-week-old wild-type and Ctcf heterozygous mutant mice by using RNA-seq.

overall_design: Comparative gene expression analysis of RNA-seq data for 8-week-old wild-type and Ctcf heterozygous mutant samples.

first: Hongxin

first: Hongjie

last: Yao


title: Parasite and vector circadian clocks mediate efficient malaria transmission

city: Berkeley

first: Filipa

last: Rijo-Ferreira

state: CA

address: Koshland Hall

institute: UC Berkeley

summary: Malaria transmission begins when Anopheles mosquitos deposit saliva and Plasmodium parasites during a bloodmeal. As Anopheles mosquitos are nocturnal, we investigated whether their   salivary glands are under circadian control, anticipating bloodmeals and   modulating parasite biology for host encounters. Here we show that   approximately half of the mosquito salivary gland transcriptome, particularly   genes essential for efficient bloodmeals such as anti-blood clotting factors,   exhibits circadian expression. Furthermore, measuring hemoglobin levels, we   demonstrate that mosquitos prefer to feed and ingest more blood at nighttime.   Notably, we show a substantial subset of the salivary gland-resident parasite   transcriptome cycling throughout the day, indicating that this stage is not   transcriptionally quiescent. Among the sporozoite genes undergoing rhythmic   expression are those involved in parasite motility, potentially modulating   the ability to initiate infection at different times of day. Our findings   suggest a circadian tripartite relationship between the vector, parasite and   mammalian host that together modulate malaria transmission.

sample_organism:
Plasmodium berghei
Anopheles stephensi

platform_organism:
Plasmodium berghei
Anopheles stephensi

overall_design: mRNA-seq circadian profiles generated for female Anopheles stephensi mosquitoes kept under 2 different light conditions. Salivary glands were harvested starting day 19 post bloodfeeding at every 4 hours for 3 days.

first: Inês

last: Bento

first: Brianna

last: Parrington

first: Rushlenne

last: Pascual

first: Alexander

last: Goldberg

first: Eileen

first: Hani

last: Liu

first: Helene

last: Borrmann

first: Mira

last: Zelle

first: Nicholas

last: Coburn

last: Takahashi

first: Joshua

last: Elias

first: Maria

last: Mota


title: CTCF point mutation at R567 disrupts mouse heart development via 3D genome rearrangement and transcription dysregulation [4C-seq]

summary: In this study, we performed 4C sequencing to investigate alterations in chromatin interactions mediated by the Lmod2 promoter and its potential enhancer.

overall_design: 4C-seq was performed using wild-type and Ctcf homozygous mutation in heart tissues from E18.5 mouse embryos. The region for Lmod2 promoter and its potential enhancer was used as a viewpoint.

first: Gongcheng

last: Hu


title: EED inhibitor impedes dendritic cell inflammatory functions

city: Hangzhou

first: Jiajia

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: Dendritic cells (DCs), the main antigen-presenting cells, are at the forefront of the immunity in response to autoimmune diseases. Epigenetic histone H3 lysine K27 trimethylation (H3K27me3) modification by embryonic ectoderm development (EED) is tightly associated with restrained transcriptional programs and has important functions in diverse biological processes and diseases, but its role in DC functionality remains elusive. In this study, we show that EED inhibitors block the activation especially migration of DCs, thus emphasizing EED as a pivotal regulator in DC homeostasis, which may be of great value for autoimmune disorders.

overall_design: LPS and LPS+EED inhibitor treated DC2.4

first: Wenxiang

last: Hong

first: Han

last: Huang

first: Qinjie

last: Weng


title: Elucidation of the substrate specificity of the ABC transporter Tba uncovers an unsuspected role in the biosynthesis of glycopeptide antibiotics

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

country: Germany

institute: Institute for Bioinformatics and Medical Informatics

summary: Glycopeptide antibiotics (GPA) such as vancomycin and teicoplanin are essential last-resort antibiotics produced by actinomycetes. Their biosynthesis is encoded within biosynthetic gene clusters, also harboring genes for regulation, and transport. Diverse types of GPAs have been characterized that differ in peptide backbone composition and modification patterns. However, little is known about the ATP-binding cassette (ABC) transporters facilitating GPA export. Employing cutting-edge techniques, we investigated the substrate specificity of GPA ABC-transporters towards the type-I GPA, balhimycin. Phylogenetic analysis and trans-complementation experiments revealed that balhimycin can only be exported by the related type I GPA transporters Tba and Tva (transporter of vancomycin). Molecular dynamics simulations and mutagenesis experiments showed that Tba exhibits specificity towards the peptide backbone rather than the attached modifications. Unexpectedly, deletion or functional inactivation of Tba halted balhimycin biosynthesis. Combined with proximity dependent biotinylation experiments this suggested that the interaction of the active transporter with the biosynthetic machinery is required for compound production.

overall_design: To investigate the differential expression of genes from the type I gylcopeptide biosynthetic gene cluster of balhimycin in a mutant lacking the correspoding ABC transporter (Tba) we analyzed RNA-seq samples from this mutant and compared the expression levels to the wildtype. As a control, we used a mutant lacking an StrR-regulator, Bbr, which regulates the overexpression of the biosynthetic genes.

first: Dardan

last: Beqaj

first: Nicola

last: Gericke

first: Theresa

last: Harbig

first: Samuel

last: Wagner

first: Evi

last: Stegmann


title: Vitamin C promotes epidermal proliferation by enhancing the DNA demethylation of proliferation-related genes in human epidermal equivalents (Microarray)

city: Kizugawa

first: Akari

last: Kuwano

state: Kyoto

address: 6-5-4 Kunimidai

country: Japan

institute: Rohto Pharmaceutical Co., Ltd.

summary:
The stratified structure of the epidermis, the outermost layer of the skin, is highly regulated through the differentiation of keratinocytes. Vitamin C act as a cofactor for DNA demethylation enzyme ten-eleven translocation (TET) in epigenetic mechanism. Previous study revealed that VC deficiency causes epidermal atrophy in hairless mice unable to synthesize VC.
We used microarrays to examine in detail the differences in gene expression in keratinocytes with and without VC addition.

overall_design: Total RNA was extracted from a half portion of human epidermal equivalents treated with or without 1.0 mM VC for 14 days using an miRNeasy Mini Kit (Qiagen, Inc.) according to the manufacturer’s instructions.

first: Yasunori

last: Sato


title: FABP4 as a critical mediator in osteoporosis: inhibition strategies and therapeutic potential

city: Shenzhen

first: jianhui

last: liang

state: Guangdong

address: 1068 Xueyuan Avenue, Nanshan District

institute: Shenzhen Institute of Science and Technology

summary: Fatty acid-binding protein 4 (FABP4), a key lipid protein in metabolism and inflammation, has been suggested to be linked to osteoporosis (OP), though direct evidence is scarce. Here, we present the first clear evidence of FABP4's significant role in OP, supported by clinical data and comprehensive in vivo and in vitro experiments. Elevated serum FABP4 in OP patients inversely correlates with bone mineral density (BMD), with similar trends observed in OVX mice. While FABP4 does not influence osteoblast differentiation, it promotes osteoclast formation and bone resorption. The FABP4 inhibitor BMS309403, with an IC50 of 0.89 μM, inhibits osteoclast differentiation by modulating calcium ions and suppressing the Ca2+-Calcineurin-NFATc pathway. Oral BMS309403 increased BMD in OVX mice, albeit less effectively than alendronate, whereas bone-targeted PLGA nanoparticles showed comparable efficacy to alendronate. This research identifies FABP4 as a promising therapeutic target for OP, with significant clinical implications.

overall_design: Bone marrow-derived macrophageswere divided into four groups: one group was cultured with MCSF for an additional 2 days, another group with MCSF and RANKL for 2 days, a third group with MCSF, RANKL, and 1 μM BMS309403 for 2 days, and the final group with MCSF, RANKL, and 1 μM RHC80267 for 2 days.

first: Qian

last: Xie

first: Xiangfu

last: Du

first: Jianhui

last: Liang

first: Yanni

last: Shen

first: Tailin

last: Wu

first: Yan

last: Wang

first: Huiren

last: Tao


title: Vitamin C promotes epidermal proliferation by enhancing the DNA demethylation of proliferation-related genes in human epidermal equivalents (WGBS)

type: Methylation profiling by high throughput sequencing

summary: The stratified structure of the epidermis, the outermost layer of the skin, is highly regulated through the differentiation of keratinocytes. Vitamin C act as a cofactor for DNA demethylation enzyme ten-eleven translocation (TET) in epigenetic mechanism. Previous study revealed that VC deficiency causes epidermal atrophy in hairless mice unable to synthesize VC.

overall_design: Genomic DNA was extracted from a half portion of human epidermal equivalents using the Monarch Genomic DNA Purification Kit (New England Biolabs, Ipswich, MA, US). The integrity and quality of the DNA were evaluated using a NanoDrop One and TapeStation (Agilent Technologies) prior to analysis. DNA methylation sequencing was performed and Chithe data analysed using a previously described WGBS methodology63. Bisulfite treatment was performed by using a Swift BiosciencesTM Accel-NGS® Methyl-Seq DNA Library Kit (Swift Biosciences, Ann Arbor, Michigan, US) to generate WGBS libraries. The amplified libraries were sequenced using an Illumina Nova Seq 6000 with 150 bp paired-end reads following standard Illumina sequencing protocols. To analyse the bisulfite sequencing results, the quality of the raw paired-end sequence reads was assessed with FastQC (version 0.11.7). Low-quality (< 20 bases) or 5'-end 10-base sequences and adapter sequences were trimmed by Trim Galore (version 0.5.0) with the options "-q 20 --phred33 --clip_R1 10 --clip_R2 10 --paired". The trimmed reads were aligned to the reference genome using methylpy (version 1.4.6) with the options "--remove-clonal True --trim-reads FALSE". Annotation was performed with in-house software. The number of methylated cytosines in the 1,000 bases of nonoverlapping windows across the whole genome was estimated by the tileMethylCounts function from the methylKit (version 1.10.0) package. Normalization was performed using the normalizeCoverage function in methylKit. Bases with less than 10× read coverage and bases with more than 99.9th percentile coverage in each sample (likely PCR artifacts with abnormally high coverage) were removed by the filterByCoverage function of methylKit. All the samples were then merged by using the unite function in methylKit with the destrand = FALSE option. To identify DMRs, differential methylation was calculated using the calculate DiffMeth function of methylKit. Regions with a q value less than 0.01 and a methylation change greater than 25% between the groups were considered significant DMRs. A cluster analysis heatmap of the DMRs and DEGs was generated with ComplexHeatmap (version 2.12.1). To perform an integrated analysis of the gene expression and DNA methylation profiles, normalization of the gene expression levels was performed using the robust multiarray average (RMA) method with oligo software, and the expression levels were corrected among the samples. The program limma was used for comparisons between the groups.


title: Targeted release of a bispecific fusion protein SIRPα/Siglec-10 by oncolytic adenovirus reinvigorates tumor associated macrophages to improve therapeutic outcomes in solid tumors

city: Nanjing

first: yenan

last: Zhang

state: Jiangsu

address: Hankou Road

institute: Medical School of Nanjing University

summary: CD47/SIRPα and CD24/Siglec-10 signaling pathways have been found to suppress macrophage phagocytosis of malignant cells. We constructed a recombinant oncolytic adenovirus expressing a fusion protein composed of the extracellular domains of murine SIRPα and Siglec-10 (SIRPα/Siglec-10), termed AdV-mSS. Intratumoral administration of AdV-SS markedly enhanced antitumor efficacy than AdV-Ctrl in multiple solid tumor models. To reveal differences in biological processes between them. subcutaneous 14-day H22-CAR -bearing BALB/c mice were intratumorally injected with PBS, 5 × 10^8 IFU AdV-Ctrl, or 5 × 10^8 IFU AdV-mSS twice. Forty-eight hours post-treatment, we harvested tumor tissue and sorted these TAMs by anti-mouse F4/80 magnetic beads. Samples were subjected to transcriptome sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TAMs from AdV-mSS (n=3) or AdV-Ctrl (n=3) or PBS (n=3) treated subcutaneous H22-CAR -bearing BALB/c mice .

first: Yenan

first: Bohao

last: He

first: Min

last: Wei

first: Chuning

last: Xu


title: CD4+ cells and pediatric obesity-related asthma - Single Cell

city: Bronx

first: Deepa

last: Rastogi

address: 3415 Bainbridge Ave

institute: Albert Einstein College of Medicine

summary: To investigate the contribution of CD4+ T cells in pediatric obesity-related asthma.

overall_design: Comparison of single cell RNA-seq footprint of CD4+ T cells in obese children with asthma (B group) to obese children without asthma (C group) and healthy weight children with (A group) or without asthma (D group).

first: David

last: Thompson


title: RNA-Seq of mGULL knockdown and hGULL rescue in C57BL6 wild-type mice

city: Bethesda

first: Haiming

last: Cao

address: 9000 Rockville Pike

department: NHLBI

summary: For determined h/mGULL have the function similarities, we employed rescue experiments in mice. We knocked down mGULL in mouse liver using shRNAs delivered by adenovirus, and subsequently co-expressed hGULL to assess its capacity to rescue for the loss of function effect of mGULL. After confirmed the mGULL knockdown or hGULL overexpression efficiency, we isolation the total RNA for RNA seq.

overall_design: Seven-weeks old C57BL/6 male were injected via intravitreal injection with adenovirus expressing Control(Lac+pAdv5 virus), shmGULL (shmGULL+pAdv5)or shmGULL+hGULL (for each group, total active viral particles is 5×108) for 7 days before sacrifice.

first: Zhe

last: Li

first: Sunmi

last: Seok

first: Chengfei

last: Jiang


title: Human mutations, altering a single tyrosine in the STAT5B SH2 domain, have opposing impacts on enhancer function and mammary development [RNA-seq]

first: Hye Kyung

last: Lee

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: Mammary gland development during pregnancy is controlled by lactogenic hormones via the JAK2-STAT5 pathway. Gene deletion studies in mice have revealed the crucial roles of both STAT5A and STAT5B in establishing the genetic programs necessary for the development of mammary epithelium and successful lactation. Several hundred single nucleotide polymorphisms (SNPs) have been identified in human STAT5B, although their pathophysiological significance remains largely unknown. The SH2 domain is vital for STAT5B activation, and this study focuses on the impact of two specific missense mutations identified in T cell leukemias, the substitution of tyrosine 665 with either phenylalanine (Y665F) or histidine (Y665H). By introducing these human mutations into the mouse genome, we uncovered distinct and opposite functions. Mice harboring the STAT5BY665H mutation failed to develop functional mammary tissue, resulting in lactation failure, while STAT5BY665F mice exhibited accelerated mammary development during pregnancy. Transcriptomic and epigenomic analyses identified STAT5BY665H as Loss-Of-Function (LOF) mutation, impairing enhancer establishment and alveolar differentiation, whereas STAT5BY665F acted as a Gain-Of-Function (GOF) mutation, elevating enhancer formation. Persistent hormonal stimulation through two pregnancies led to the establishment of enhancer structures, gene expression and successful lactation in STAT5BY665H mice. Lastly, we demonstrate that Olah, a gene known to drive life-threatening viral disease in humans, is regulated by STAT5B through a candidate four-partite super-enhancer. In conclusion, our findings underscore the role of human STAT5B variants in modulating mammary gland homeostasis and their critical impact on lactation.

overall_design: Total RNA-seq was done for the mammary tissues at at day 13 and 18 of pregnant (p13, p18) of 2-month-old age for wild-type and mutant mice carrying a point mutation in Stat5b-Y665.

first: Hye-Kyung


title: Neutrophils negatively regulate IL-17 producing γδ T cells under physiological conditions

city: Borstel

first: Sebastian

last: Marwitz

address: Parkallee 3a

department: Histology

institute: Research Center Borstel - Leibniz Lung Center

summary: In addition to serving as the primary effector cells against infections, neutrophils have been implicated in the regulation of both innate and adaptive immunity. In this study, we employed neutropenic mice to investigate the role of neutrophils in the regulation of the immune system under physiological conditions. Unexpectedly, we observed an accumulation of γδ T cells in the cervical lymph nodes of neutropenic mice. Transcriptomic analysis revealed that these accumulated γδ T cells exhibited unique expression profiles of cell surface molecules and genes involved in defense responses. Further characterization indicated that the accumulated γδ T cells were IL-17 producing CD44+CD62L−CD27− memory cells. Additionally, in vitro experiments demonstrated that neutrophils could inhibit the function of IL-17A producing γδ T cells by inducing cell death in these activated cells. Given that IL-17A is a critical cytokine for the recruitment of neutrophils to peripheral tissues, our study suggests that the crosstalk between neutrophils and IL-17A producing γδ T cells is a crucial mechanism for maintaining immune homeostasis under physiological conditions

overall_design: 8 samples in total of 4 mice each group

first: Xinhua

last: Yu


title: Intestinal stearoyl-CoA desaturase-inhibition improves obesity-associated metabolic disorders

city: Bethesda, MD

first: Frank

last: Gonzalez

address: Bldg. 37 National Institutes of Health

department: Center for Cancer Research

institute: National Institutes of Health, National Cancer Institute

summary: Stearoyl-coenzyme A desaturase 1 (SCD1) catalyzes the rate-limiting step of de novo lipogenesis and modulates lipid homeostasis. Although numerous SCD1 inhibitors have been tested in treating metabolic disorders both in preclinical and clinic studies, the tissue-specific role of SCD1 in modulating obesity-associated metabolic disorders remains unclear. Here a novel role for intestinal SCD1 in obesity-associated metabolic disorders was uncovered. Intestinal SCD1 was found to be induced during obesity progression both in humans and mice. Intestine-specific, but not liver-specific, SCD1 deficiency reduced obesity and hepatic steatosis. A939572, a SCD1-specific inhibitor, ameliorated obesity and hepatic steatosis dependent on intestinal, but not hepatic, SCD1. Mechanistically, intestinal SCD1 deficiency impeded obesity-induced oxidative stress through its novel function of inducing metallothionein 1 (MT1) in intestinal epithelial cells. These results suggest that intestinal SCD1 could be a viable target that underlies the pharmacological effect of chemical SCD1 inhibition in the treatment of obesity-associated metabolic disorders.

overall_design: Examination of gene expression change in intestine of intestine-specific SCD1 knockout mice fed an obesity-promoting 60% high fat diet using RNASeq.

first: Yangliu

last: Xia

first: Tingting

last: Yan

first: Vorthon

last: Sawaswong


title: Effect of depletion of IGF2BP3 on gene expression in LUAD

city: Linhai, Zhejiang

first: Jiapei

last: Ding

state: Zhejiang

address: Xi Men Street No.150

department: Department of Radiation Oncology

institute: Taizhou Hospital of Wenzhou Medical University

summary: IGF2BP3, an oncofetal protein and an m6A reader, is a member of the IGF2BPs family playing an important role in cell migration in early embryogenesis, oncogenesis, metabolism and metastasis. To clarify the effect of depletion of IGF2BP3 on gene expression in LUAD, we conducted IGF2BP3 knocked out experiments in the NCI-H1299 LUAD cell lines. The knockout efficiency was validated by western blot analysis, demonstrating successful silencing of IGF2BP3 at the protein levels in NCI-H1299 cells. To explore the underlying mechanisms of IGF2BP3 in LUAD development, we conducted RNA-sequencing analysis using IGF2BP3 knockout and control NCI-H1299 cells, with each group consisting of three biological replicates. The analysis revealed that IGF2BP3 knockout resulted in differential expression of 1700 genes including 621 genes upregulated and 1079 downregulated.

overall_design: NCI-H1299 was obtained from the Cell Bank of the Chinese Academy of Sciences (Shanghai, China). The cells were grown and maintained at 37°C in a humid atmosphere with and 5% CO2 and were cultured in Gibco’s RPMI 1640 Medium (Thermo Fisher, Schwerte, Germany) supplemented with 10% FBS and 1% PAA. CHOPCHOP (https://chopchop.rc.fas.harvard.edu/) and CRISPR design (http://crispr.mit.edu/) were used to design two single guide RNAs (sgRNA, Supplementary Table 3) targeted to the BsmBI of IGF2BP3 (NCBI GeneID 10643).  Annealed oligonucleotides were ligated into LentiCrisprv2 (GENECARE, GC010100605). The plasmids were sequenced to confirm successful ligation. For transfection, 4*10^5 293T cells were plated overnight in antibiotic-free medium and then transfected with 4µg of LentiCrisprv2 using Lipofectamine 3000. After high speed centrifugation, supernatant was collected and frozen at -80 ° C. NCI-H1299 cells were then infected with the supernatant, and selected under puromycin (2.0 µg/ml) for 48 hours and subsequently plated onto 96 well plates (10 cells/ml). Single cell colonies were expanded for RNA extraction, protein extraction and cryopreservation. The knockout efficiency was validated by western blot analysis, demonstrating successful knockout of IGF2BP3 at the protein levels in NCI-H1299 . Total RNA was isolated from IGF2BP3 knockout and control NCI-H1299 cells using TRIzol Reagent. RNA sequencing (RNA-seq) analysis was performed at Lian Chuan Biotech Inc. (Hangzhou, China).


title: Linker histone H1-0 is a specific mediator of the ETV6::RUNX1 transcriptional landscape in preleukemia and B cell acute lymphoblastic leukemia [scRNA-seq]

city: Düsseldorf

first: Vera

middle: Helena

last: Jepsen

address: Moorenstraße 5

institute: University Hospital Düsseldorf

summary: The chimeric hematopoietic transcription factor ETV6::RUNX1 is the most common oncogenic fusion in pediatric B cell precursor acute lymphoblastic leukemia (BCP-ALL). It induces a clinically silent preleukemic state that requires secondary mutations for progression to full-blown leukemia. ETV6::RUNX1 functions primarily through repression of RUNX1 binding sites. In order to elucidate the characteristic quiescent state of ETV6::RUNX1 expressing cells, we generated preleukemic human induced pluripotent stem cell (hiPSC) models from two healthy donors using CRISPR/Cas9 gene editing. We identified upregulation of linker histone H1-0 in preleukemic hiPSCs, which was preserved upon hematopoietic differentiation and transformation to overt BCP-ALL. ETV6::RUNX1 induces activity of the H1-0 promoter whereas depletion of H1-0 specifically inhibited ETV6::RUNX1 signature genes, indicating its role as a novel key mediator of the quiescent ETV6::RUNX1 transcriptional profile. Single-cell gene expression analysis revealed that H1-0 levels strongly anti-correlate with cellular transcriptional activity, resulting in particularly high expression in quiescent cells during hematopoietic development. Pharmacologically, H1-0 protein levels correspond to susceptibility of BCP-ALL towards histone deacetylase inhibitor (HDACi) treatment and our data indicate efficacy of combinatorial drug treatment using the potent H1-0-inducing HDACi Quisinostat in BCP-ALL expressing high basal H1-0 levels.

overall_design: To delineate effects of ETV6::RUNX1 in hematopoietic cells, we performed scRNA-seq analysis of hematopoietic progenitor cells (HPCs) differentiated from ETV6::RUNX1+ and wild-type hiPSCs.

first: Ute

last: Fischer


title: Human mutations, altering a single tyrosine in the STAT5B SH2 domain, have opposing impacts on enhancer function and mammary development

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq for TFs and histone markers at day 13 and 18 of pregnant (p13, p18) of 2-month-old age for wild-type and mutant mice carrying a point mutation in Stat5b-Y665 and at day 10 of lactation (L10) after second pregnancy of Y665H mutant.


title: Expression Profiling of Cells In The Perilesional Area of Mouse Cerebral Cortex After Traumatic Brain Injury (TBI) with Immune-Modifying Particle (IMP) Treatment

city: Chicago

first: Chian-Yu

last: Peng

state: IL

address: Department of Neurology, 10-233 Ward Building, 303 E Chicago Ave.

institute: Northwestern University, Feinberg School of Medicine

summary:
To investigate the cell type specific responses to traumatic brain injury with and without PLGA-based immune-modifying nanoparticle treatments,
We performed single cell RNA sequencing of perilesion are cells from mice that received TBI with and without IMP treatment.

overall_design: we harvested 3mm cubed of perilesional cerebral cortical tissue from two mice, 24 hours after receiving controlled cortical impact TBI with and without IMP treatments two hours post injuries. Dissociated single cells were proceeded for scRNAseq via 10x Genomics Chromium platform and sequenced using a Illumina Hiseq 6000

first: John

last: Kessler


title: Single-cell gene expression profile and TyP-HIM-seq DNA barcode level of CD19 CAR-Jurkat and Ramos cells

first: Juan

last: Wei

address: 150 Dongfang Rd

institute: Hangzhou Institute of Medicine, CAS

summary: Cell–cell interactions (CCIs) are essential for tissue functionality and targeted therapies, particularly in the context of chimeric antigen receptor T (CAR T) cells. Here, we introduce TyP-HIM-seq, a barcoding approach based on tyrosinase-catalyzed proximity (TyP) labeling. This method enables the simultaneous high-throughput measurement of interacting cells and their mRNA expressions through single-cell sequencing. By translating intercellular contact into in situ chemical labeling of a DNA barcode, TyP-HIM-seq allows for a comprehensive assessment of CCIs and full deconvolution of related molecular pathways. We used TyP-HIM-seq to investigate the CCIs between CD19 CAR-Jurkat cells and Ramos tumor cells.

overall_design: CAR-J cells and Ramos cells were separately modified with tyrosinase and phenol groups to serve as bait and prey cells. Then, the two cells were mixed at 1:1 and cocultured with amine-ssDNA barcodes at 37 °C for 30 min. After stringent PBS washing, the cells with barcoded DNA tagging were profiled by scRNA-seq.

first: Hao-Ran

last: Jia

first: Qin

last: Wu


title: E-cigarette Vapor Extract Alters Human Eosinophil Gene Expression in an Effect Mediated by Propylene glycol, Glycerin, and Nicotine

city: San Diego

first: Gregory

last: Seumois

address: 9420 Athena Cir, La Jolla

institute: La Jolla Institute for immunology

summary: E-cigarette use (vaping) has become widespread, and its effects on airway inflammation and disease are not fully delineated. E-cigarette vapor extract (EVE) profoundly affects neutrophil function. We hypothesized that EVE also alters eosinophil function and thus could impact allergic airways disease. We employed RNA-sequencing to measure the ex vivo effect of EVE components on human eosinophil transcription. Eosinophils from 7 non-vaping subjects without asthma were isolated by negative selection from venous blood. Cells were incubated for 48 hours with EVE consisting of glycerin, propylene glycol and nicotine (EVE+), EVE without nicotine (“EVE-”), Extract Buffer (EB), and untreated media. Bulk RNA-sequencing was performed. Principal component analysis revealed that the EVE+ and EVE- conditions clustered closely together. Differential gene expression analysis revealed a “negative regulation of interferon gamma production” and “apoptotic mitochondrial changes” pathways for genes upregulated in EVE- samples and a down regulation of  “inflammatory response” and “chemokine signaling” in comparison to the EB control condition. 93 genes were differentially expressed genes between EVE+ and EVE-, indicating a relatively small effect of nicotine on eosinophil gene expression. These results demonstrate that EVE significantly alters eosinophil gene expression, predominantly mediated by propylene glycol and glycerin rather than by nicotine. This study motivates further research into the pathogenic effects of vaping on airway eosinophils and allergic airways disease.

overall_design: Circulating Eosinophils from 7 healthy subjects non-smokers are isolated and in vitro submitted to different E-cigarette vaping compounds including PEG, Glycerin and Nicotine. After 48 hours of treatment, cells are harvested and totRNA is extracted and sequencing libraries are prepared for whole trancriptome expression analysis.

first: Nicholas

last: Hogan

first: F

last: Castaneda-Castro

first: Howard

last: Brickner

first: Ashmitaa

last: Ramamoorthy Premlal

first: Monalisa

last: Mondal

first: Sara

last: Herrera-De La Mata

first: Pandurangan

last: Vijayanand

first: Laura

last: Crotty Alexander

first: Praveen

last: Akuthota


title: Co-culture of hepatic stellate cells and hepatic progenitor cells

city: Utrecht

first: Maya

last: Haaker

address: Yalelaan 2

country: Netherlands

institute: Utrecht University

summary: Following liver damage, ductular reaction and liver fibrosis often develop simultaneously. Activated hepatic stellate cells (HSC) are the main cell type in liver fibrosis development, while proliferation of hepatic progenitor cells is seen in ductular reaction. This study aims to gain insight on the interaction between these two cell types by an in vitro 3D co-culture system.

overall_design: HSCs were isolated from healthy wild-type mice in order to obtain quiescent HSCs. Intrahepatic cholangiocyte organoids (ICOs) with a fluorescent tag (dTomato) were used as progenitor cells. Both cell types were cultured in Matrigel (3D), either separately (3D mono-culture) or together (3D co-culture) and cells were sorted after seven days. Gene expression in each cell type was analyzed using bulk RNA sequencing.

first: Bernd

last: Helms

first: Christian

last: Wolfrum

first: Falko

last: Noé


title: Gene expression profiles of Ramos tumor cells with TNFRSF17 knockdown.

first: Juan

last: Wei

summary: TNFRSF17 in Ramos tumor cells has been found to affect their interaction with CD19 CAR T cells. We used RNA sequencing to compare the transcriptomic profiles between TNFRSF17 knockdown Ramos cells and unperturbed control cells.

overall_design: Ramos cells treated with mock or TNFRSF17 siRNAs were harvested for bulk RNA sequencing. Three biological replicates were performed for each condition.


title: The Human Cardiac “Age-OME”: Age-specific changes in myocardial molecular expression

city: Panania

first: Benjamin

middle: John

last: Hunter

state: NSW

address: 118 Horsley Rd

department: School of Medical Sciences

country: Australia

institute: The University of Sydney

summary: Ageing is one of the most significant risk factors for heart disease, however, it is still not clear how the human heart changes with age. Taking advantage of a unique set of pre-mortem, cryopreserved, non-diseased human hearts, we performed omics analyses (transcriptomics, proteomics, metabolomics, and lipidomics), coupled with biologically-informed computational modelling in younger (≤25 years old) and older hearts (≥50 years old) to describe the molecular landscape of human cardiac ageing. In older hearts, we observed a downregulation of proteins involved in calcium signalling and contractile apparatus. Furthermore, we found a potential dysregulation of central carbon generation of fuel, glycolysis and fatty acids oxidation, along with an increase in long-chain fatty acids. This study presents and analyses the first molecular data set of normal human cardiac ageing, which has relevant implications for understanding the human cardiac ageing process and the development of age-related heart disease.

overall_design: The aim of this study was to perform multi-omics analyses on cryopreserved pre-mortem human left ventricular myocardium to uncover the molecular influence of cardiac ageing.

first: Cassandra

last: Malecki

first: Giovanni

last: Guglielmi

first: Dylan

last: Harney

first: Yen

middle: C

last: Koay

first: Anthony

last: Don

first: Oscar

last: Han

first: Jasmine

last: Khor

first: Lisa

last: Nguyen

first: Michael

last: Pan

first: Peter

last: Gawthrop

first: Nathan

last: Isles

first: Joshua

last: Chung

first: Robert

last: Hume

first: Matthew

last: Taper

first: Mark

last: Larance

first: Fabian

last: Spill

first: Vijay

last: Rajagopal

first: John

last: O’Sullivan

first: Sean

last: Lal


title: Estrogen Intracellular Retention is Augmented by GRAM Domain Containing Protein ASTER-B in Breast Cancer Cells

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Estrogen is the primary mitogen for ER+ BC cells, but how the hormone is retained intracellularly is poorly understood. We found that the ER+ BC cell line MCF-7 retains a substantial amount of hormone even upon removal of the hormone from the culture medium. The effect of acute E2 treatment followed by washout on gene regulation was determined by RNA-seq over an E2 treatment timecourse. In agreement with intracellular hormone levels, gene exprssion was also sustained over hours after removal of the hormone. We next identified that ASTER-B, a cholesterol-binding protein, was mislocalized into the nucleus of MCF-7 cells, and was associated with retained E2. By knocking down GRAMD1B (ASTER-B), both E2 retention and its associated gene regulatory programs (ER binding and gene expression) were significantly abrogated. Taken together, this shows E2 retention is required for sustained E2 induction, and that ASTER-B supports accumulation and retention of intracellular E2.

overall_design: RNA-seq of MCF-7 cells treated either continuously or acutely with a time course of E2 treatments.

first: Kim

last: Hyung Bum

first: Nandu

last: Tulip

first: Nagari

last: Anusha

first: Kraus

last: W Lee


title: CTCF mutation at R567 affects mouse heart development via 3D genome rearrangement and transcription dysregulation [RNA-seq]

city: Guangzhou

first: HongXin

last: Zhong

address: No. 190, Open Source Avenue, Luogang District, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: In this study, we analyzed gene expression change in heart tissues from wild-type, Ctcf heterozygous and homozygous mutant mice by using RNA-seq.

overall_design: Comparative gene expression analysis of RNA-seq data for wild-type, Ctcf heterozygous and Ctcf homozygous mutant samples.

first: Hongxin

first: Hongjie

last: Yao


title: Urolithin A mitigates behavioral and synaptic deficits associated with epilepsy through VDAC-1 inhibition: A novel treatment approach

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: Supplementation of Urolithin-A, a catabolite of ellagic acid-containing precursors, has been shown to benefit the central nervous system (CNS). This study focused on deciphering the potential anti-epileptic effects of Urolithin-A, a small molecule of natural origin. To understand the primary underlying mediators of UA’s anti-epileptic efficacy, RNA sequencing was performed in the sub-acute epileptic model of Drosophila (4 hours of treatment duration with epileptic inducer-picrotoxin (PTX))  to abstain from the interference of secondary pathways. Four treatment groups were included in the study: 1) Vehicle (0.5% DMSO), 2) 1mM PTX, 3) 1mM PTX + Urolithin-A (100µM), and 4) Urolithin-A (100µM). Administration of Urolithin-A restores the PTX-induced misregulated genes of brain hemolymph and metabolic dysfunctions.

overall_design: The picrotoxin-induced sub-acute seizure model of Drosophila was included in the study. The sub-acute name is given according to the short treatment duration of 4 hours. Four treatment groups were included in the study: 1) Vehicle (0.5% DMSO), 2) 1mM PTX, 3) 1mM PTX + Urolithin-A (100µM), and 4) Urolithin-A (100µM). PTX represents the epileptic context.

first: Shefali

last: Mishra

first: Upendra

last: Nongthomba

first: Madavan

last: Vasudevan

first: Varun

last: Gowda


title: Cholesterol metabolism and neuroinflammatory changes in a non-human primate model of neuropathic pain

city: Izunokuni, Shizuoka

first: Hiroshi

last: Yamane

address: 632-1 Mifuku

department: Pharmaceuticals Research Center

institute: Asahi Kasei Pharma Corporation

summary: Neuropathic pain remains one of the major neurological conditions with high unmet medical needs. Poor translation from preclinical studies using rodent models to clinical trials is one of the major obstacles to the development of new pharmacological medications to treat neuropathic pain. The aims of this study were to establish a behavioral test to evaluate spontaneous pain in a spinal nerve ligation (SNL) model using cynomolgus monkey as a non-human primate (NHP) model, and to unravel changes in the transcriptomic profile in dorsal spinal cord in this model. After right unilateral L7 SNL surgery in cynomolgus monkeys, the percentage of weight-bearing on ipsilateral hindlimb significantly decreased. Transcriptomic analysis of RNA-seq results from the dorsal part of the spinal cord identified pathways matching those in equivalent rodent models, along with NHP-specific pathways, suggesting that neuroinflammation and cholesterol transportation/metabolism were the main pathways altered in this NHP model. Additionally, several upregulated genes observed here were previously reported uniquely in clinical studies, but not in rodent models. This study provides a potentially useful pharmacological model that can aid the development of pain relief therapies by inducing a robust behavioral phenotype and changes in gene expression resembling those in patients.

overall_design:
To investigate the molecular aspects of the pathophysiology of neuropathic pain in the monkey SNL model, we performed gene expression analysis using data obtained from RNA-seq of the dorsal part of the spinal cord.
Comparative gene expression profiling analysis of RNA-seq data for the ipsilateral (right) dorsal part of the spinal cord and the contralateral (left) one.

first: Tomoya

last: Tanaka

first: Tadahiro

last: Iimura


title: Myeloid EGFR deficiency accelerates recovery from Aki via macrophage efferocytosis and neutrophil apoptosis

city: Nashville

first: Yinqiu

last: Wang

state: TN

address: 313 Harpeth view circle

department: medicine

institute: vumc

summary: Altered expression and activation of the Epidermal Growth Factor Receptor (EGFR) is implicated in acute and chronic kidney injury. In addition to expression in intrinsic kidney cells, EGFR is expressed in myeloid cells, which play important roles to promote both acute kidney injury and subsequent fibrosis. In murine ischemic acute kidney injury (AKI), myeloid deletion of EGFR promoted a proresolving, anti-inflammatory phenotype and increased efferocytotic capacity in macrophages, accelerated recovery in response to AKI and inhibited subsequent development of tubulointerstitial fibrosis. We found that selective EGFR expression and activation in neutrophils also accelerated recovery from ischemic kidney injury and reduced subsequent fibrosis. EGFR activation played an essential role in increasing the life span of neutrophils in the injured kidney, and deletion of EGFR expression either in all murine myeloid cells or selectively in neutrophils decreased kidney neutrophil Mcl-1 expression and promoted neutrophil apoptosis, which was accompanied by accelerated recovery from organ injury and reduced subsequent fibrosis. These studies identify previously undescribed coordinated and complementary roles for EGFR activation in neutrophils and macrophages to exacerbate kidney injury.

overall_design: leukocytes were enriched with CD45 microbeads  from both EGFRf/f (WT) and CD11b-Cre: EGFRf/f (myeloid EGFR-/-) mice underwent ischemic injury for 1 and 3 days for single cell RNA-seq (scRNA-seq)

first: Raymond

last: Harris

first: Ming-Zhi

last: Zhang

first: Yu

last: Pan

first: Shirong

last: Cao


title: Linker histone H1-0 is a specific mediator of the ETV6::RUNX1 transcriptional landscape in preleukemia and B cell acute lymphoblastic leukemia [RNA-seq]

first: Vera

last: Jepsen

overall_design:
To analyze the transcriptional landscape conferred by the ETV6::RUNX1 fusion gene, we generated knock-in human induced pluripotent stem cells (hiPSCs) derived from two healthy donors (HW8 and ChiPSC12). In the generated hiPSC lines (n=3), ETV6::RUNX1 is expressed under control of the endogenous ETV6 promoter.
We performed gene expression profiling analysis using data obtained by RNA-seq of 2 wild-type hiPSC lines (HW8 WT and ChiPSC12 WT) and 3 monoclonal ETV6::RUNX1+ hiPSC lines (HW8 E::R 1, HW8 E::R 2, ChiPSC12 E::R).
To determine the contribution of H1-0 to ETV6::RUNX1+ BCP-ALL pathology, we knocked down H1-0 in the ETV6::RUNX1+ BCP-ALL cell line REH using siRNA pools.
We performed gene expression profiling analysis using data obtained by RNA-seq of REH cells treated with a non-targeting siRNA pool (siCtrl) and two H1-0-targeting siRNA pools (siH1-0_1, siH1-0_2) for 48 hours.

first: Ute

last: Fischer


title: RNA-seq  and RNC-seq of  S1K247Q, S1K247R, and S1WT

city: Shanghai

first: Sally

last: Shen

address: Meilong Road No.130

institute: East China University of Science and Technology

summary: RNC-seq experiment of the simulated acetylated mutant S1K247Q, non-acetylated mutant S1K247R, and wile-type of S1 protein S1WT.

overall_design: S1K247Q, S1K247R, and S1WT constitutive overexpression strains of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S  grown in LB medium are used for RNC-seq

first: Yi-Lin

first: Bang-Ce

last: Ye

first: Ying

last: Zhou


title: Gene expression profiles of Mock or LLC CM treated WT and Rab37 KO BMDMs.

city: Tainan

first: Yi

middle: Ching

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

summary: Rab37 is a small GTPase that plays a crucial role in tumor progression. We hypothesized that Rab37 alters gene expression profiles in macrophages, influencing macrophage polarization. To further confirm this, we conducted GeneChip expression array analyses to unveil the distinct gene profiles between wild-type (WT) and Rab37 knockout (KO) bone marrow-derived macrophages under conditions of mock or Lewis lung cancer conditional medium (LC CM) treatment.

overall_design: In this study, the BMDMs isolated from WT and Rab37 KO mice were treated with mock or  LLC CM for 24 hours. Total RNA were collected for microarray assays.

first: YANG

last: YOU-EN

first: KUO

last: I-YING

first: WANG

last: YI-CHING


title: Transcriptome analysis of Drosophila larval epidermis containing a deletion in the mitochondrial DNA

first: David

last: Pla-Martín

address: Universitätsstr. 1 Building 22.03; 4th Floor

department: Institute of Biochemistry and Molecular Biology I

institute: Medical Faculty and University Clinics. Heinrich Heine University Düsseldorf

summary: Mitochondrial DNA is exposed to multiple insults produced by normal cellular function. We found that the retromer enhances and coordinates the expulsion of mitochondrial matrix components through mitochondrial-derived vesicles and mtDNA with direct transfer to lysosomes. Using a Drosophila model carrying a long deletion on the mtDNA (ΔmtDNA), we evaluated in vivo the role of the retromer in mtDNA extraction and turnover in the larval epidermis. The presence of ΔmtDNA elicits the activation of a specific transcriptome profile related to counteract mitochondrial damage. Expression of the retromer component Vps35 is sufficient to restore mtDNA homoplasmy and mitochondrial defects associated with ΔmtDNA.

overall_design: To investigate the transcriptome profile activated upon mtDNA damage, we generated drosophila larvae carrying a long deletion in the mtDNA. To do that, we crossed A58-Gal4 driver with UAS-mitoT4lig, UAS-mitoAflIII (BL 84979) (∆mtDNA)

last: Pla Martin

first: Parisa

last: Kakanj

first: Belen

last: Molla


title: Fucoidan reduces NETs accumulation and alleviates chemotherapy-induced peripheral neuropathy

city: Nanjing

first: Wentao

last: Liu

state: Jiangsu Province

address: No.101 Longmian Avenue, Jiangning District, Nanjing

department: Department of Pharmacology

institute: Nanjing medical university

summary: Chemotherapy-induced peripheral neuropathy (CIPN) is a serious adverse reaction of chemotherapy with limited treatment. Previous research indicates neutrophil extracellular traps (NETs) is a critical pathogenesis of CIPN. LPS/HMGB1 serve as important inducers of NETs. Here, we aim to target inhibiting NETs formation (NETosis) to alleviate CIPN. Clinically we found the content of LPS, HMGB1 and NETs in the plasma of CIPN patients was significantly increased and positively correlated with VAS scores. Fucoidan decreased LPS/HMGB1/NETs content and relieved CIPN in mice. Mechanistically, fucoidan upregulated the scavenger receptor A1 (SR-A1) expression and promoted bone marrow derived macrophage (BMDM) to phagocytize LPS/HMGB1. Fucoidan also facilitated BMDM to engulf NETs via the recognition and localization of SR-A1 and HMGB1. The therapeutic effects of fucoidan were abolished by SR-A1 knockout. RNA-seq analysis showed that fucoidan significantly increased sqstm1 (p62) gene expression. Fucoidan promoted the competitive binding of sqstm1 and Nrf2 to Keap1, increasing Nrf2 nuclear translocation and SR-A1 transcription. Additionally, microbial diversity sequencing analysis (16S) showed that fucoidan increased gut microbiota diversity and abundance, and upregulated the Bacteroides/Firmicutes ratio. In conclusion, fucoidan promotes SR-A1-mediated phagocytosis of LPS/HMGB1/NETs and maintains gut microbial homeostasis, providing a potential therapeutic strategy for CIPN.

overall_design: The BMDM were extracted by isolating the tibia and femurs of the mice after their necks were removed. The cells within the tibia and femurs were blown into DMEM medium (10% FBS+10% L929 culture medium +1% penicillin-streptomycin solution,100×) . After they were cultured for 7 days, trypsin was used to digest them followed by centrifugation, suspension, and seeding onto petri dishes. Fucoidan (250ug/ml) was administered prior to treating with L-OHP (5uM) for 12 hours. Total cellular RNA was extracted using Trizol for high-throughput sequencing.


title: Gene expression profile at single-cell level of helped and helpless LCMV-specific CD8+ effector T cells (day 7 post acute LCMV infection)

city: New York

first: Darwin

last: D'Souza

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

summary: We used single-cell RNA sequencing (scRNA-seq) to obtain transcriptomic profiles of virus-specific CD8+ effector T cells generated in the presence (helped) or absence (helpless) of CD4+ T cells.

overall_design: Young adult B6 mice were treated with isotype control antibody (helped) or depleted of CD4+ T cells (helpless), transferred intravenuously with 5,000 naïve congenic (CD90.1+) T cell receptor transgenic (TCRtg) CD8+ T cells specific for the LCMV GP33-41 determinant (P14 cells), and challenged with LCMV Armstrong (2e5 pfu intraperitoneally). Seven days later, live P14 effector T cells (P14 TE)  were purified from spleens of P14 chimeras by fluorescence activated cell sorting  for downstream scRNA-seq processing.

first: Verena

last: van der Heide

first: Travis

last: Dawson

first: Dirk

last: Homann


title: Microarray gene expression profiling of rat cerebellar Granule Cells (GCs) before and after Lamin A-knockdown

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

summary: Nuclear lamins are nuclear type V intermediate filament proteins that form a meshwork structure underlying the inner nuclear membrane, the nuclear lamina. The nuclear lamina associates with other nuclear envelope proteins and plays numerous roles, including maintaining the nuclear shape and structure, assembly and disassembly of the nucleus, heterochromatin organisation, transcriptional regulation and other nuclear functions. Here, we studied the role of A-type lamins in the maturation of rat cerebellar GCs during normal brain development by performing the gene expression profiling of GCs knocked-down for Lamin A. We demonstrated that Lamin A/C has a key role in neural differentiation and GC maturation, also under physiological conditions.

overall_design: By using Agilent Whole Rat Genome 4x44K microarray platform (grid ID 014879), we performed the gene expression profiling of Lmna-knockdown GCs (n=2) as compared to mock GCs (n=2).

first: Mara

last: D'Onofrio

first: Rossella

last: Brandi

first: Armando

last: Felsani

first: Igea

last: D'Agnano


title: Macrophage ATF6 Accelerates Orthodontic Tooth Movement through Promoting Tnfα Transcription

first: Bin

last: Yan

address: 140Hanzhong Road

institute: Nanjing Medical University

summary: Corticotomy is a clinical procedure targeting alveolar bone to activate regional acceleratory phenomenon (RAP) and promote orthodontic tooth movement (OTM). Corticotomy involves the orchestration of inflammation by macrophages, but the underlying mechanism remains unclear. Here, we identify endoplasmic reticulum (ER) stress sensor activating transcription factor 6 (ATF6) as a critical player modulating pro- and anti-inflammatory macrophage polarization. We show that macrophage-specific ATF6 deletion blocks corticotomy-induced OTM acceleration, while macrophage ATF6 overexpression exaggerates the acceleration effect. Furthermore, the proportion of pro-inflammatory macrophages is positively correlated with ATF6 expression in vitro and in vivo. By RNA-seq and CUT&Tag, we demonstrate that ATF6 interacts with Tnfα promotor and augments its transcription, thereby mediating the effect of TNF signaling pathway in pro-inflammatory macrophage polarization. In summary, ATF6 may aggravate alveolar bone remodeling during corticotomy by promoting Tnfα transcription in macrophages, suggesting that ATF6 may represent a promising therapeutic target for non-invasive accelerating orthodontics.

overall_design: To investigate the mechanism by which ATF6 influences macrophage pro-inflammatory function, we sought to identify candidate target inflammatory cytokines of ATF6 p50 in BMDMs using Cleavage Under Targets & Tagmentation (CUT&Tag) assay. To this end, BMDMs were stimulated with alveolar bone lysates from BLANK, TM, and TM+CO models for 3 hours.

first: Zhichun

last: Jin


address: 140hanzhong road

overall_design: To dissect the mechanism by which ATF6 modulates macrophage inflammatory signals, RNA-sequencing (RNA-seq) was performed on BMDMs transfected with negative control siRNA (si-NC) and ATF6 siRNA (si-ATF6) upon TM+CO stimulation.


title: Oncofetal reprogramming of the tumor vasculature

city: Amsterdam

first: Judy

last: van Beijnum

state: Noord Holland

address: CCA rm 2.52, De Boelelaan 1118

department: Medical Oncology

institute: VUMC

summary: Certain embryonic genes, such as carcinoembryonic antigens (CEA) and oncofetal antigens, become re-expressed in malignant transformation and we hypothesized that a similar phenomenon features tumor endothelial cells as well. Therefore, we performed a systematic search for mouse embryo-specific gene expression at days E11 and E18 in comparison to adult mouse and queried for overexpression of these genes in sorted murine tumor endothelial cells.

overall_design: Whole mouse embryo (E11, N=4; E18, N=4), whole adult mouse (N=2), sorted tumor endothelial cells from murine B16F10 melanoma (N=2), sorted pooled (N=2 mice) normal endothelial cells from mouse organs (N=1)

middle: R

first: Elisabeth

last: Huijbers

first: Arjan

last: Griffioen


title: Loss function of tumor suppressor FRMD8 confers resistance to tamoxifen therapy via a dual mechanism

city: Beijing

first: Qianchen

last: Li

address: Beijing

institute: PKU

summary: Approximately 40% ERα-positive breast cancer patients suffer from therapeutic resistance to tamoxifen. Although reduced ERα level is the major cause of tamoxifen resistance, the underlying mechanisms remain elusive. Here, we report that FRMD8 raises the level of ERα at both transcriptional and post-translational layers. FRMD8 deficiency in MMTV-Cre+; Frmd8fl/fl; PyMT mice accelerates mammary tumor growth and loss of luminal phenotype, and confers tamoxifen resistance. Single-cell RNA profiling reveals that Frmd8 loss decreases the proportion of hormone-sensing differentiated epithelial cells and downregulates the levels of ERα. Mechanically, on one hand, loss of FRMD8 inhibits ESR1 transcription via suppressing the expression of FOXO3A, a transcription factor of ESR1. On the other hand, FRMD8 interacts both with ERα and UBE3A, and disrupts the interaction of UBE3A with ERα, thereby blocking UBE3A-mediated ERα degradation. In breast cancer patients, FRMD8 gene promoter is found hypermethylated and low level of FRMD8 predicts poor prognosis. Therefore, FRMD8 is an important regulator of ERα and may control therapeutic sensitivity to tamoxifen in ERα-positive breast cancer patients.

overall_design: Four mice mammary tumors at endpoint (17-18 weeks) from the MMTV-Cre- and MMTV-Cre+ models were harvested and analyzed using 10x Genomics.Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics) , according to the manufacturer’s instructions.

first: Weijie

last: Wu

first: Miao

last: Yu

first: Yiqian

last: Zhao

first: Lei

last: Zhang

first: Yi

last: Sun

first: Zhenbin

last: Wang

first: Yuqing

last: Gong

first: Jun

last: Zhan

first: Hongquan


title: The mRNA expression in the T-lymphomas of W/W mice

first: Jia

middle: bing

address: 197, Ruijin Er Street

institute: Shanghaijiaotong university

summary: Determining the mRNA expression profiles in the T-lymphomas of W/W mice before and after ATO treatment by RNA-seq.

overall_design: Compare the differences in transcriptome profiles between the T-lymphomas samples before and after ATO treatment.

first: Jiabing

first: Lu

last: Min


title: Integrated analysis of messenger RNA and microRNA in patients with community-acquired pneumonia associated sepsis

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

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

overall_design: Refer to individual Series


title: Integrated analysis of messenger RNA and microRNA in patients with community-acquired pneumonia associated sepsis (mRNA part)

summary:
Background: Community-acquired pneumonia (CAP) is defined as an acute lung infection involving the alveoli that occurs in a patient without recent health care exposure. A complication of CAP is severe sepsis, a syndrome of infection often accompanied by systemic inflammation and organ dysfunction. The aim of this study was to evaluate mRNA and miRNA in whole blood and to perform an integrative analysis to assess cellular signals that play a role in the pathogenesis of patients with CAP-associated sepsis.
Methods: This was a prospective, observational, single-center study of patients transported to the Department of Traumatology and Acute Critical Medicine, Graduate School of Medicine, Osaka University. Patients with CAP-associated sepsis were analyzed. The diagnosis of pneumonia was made according to the clinical findings, including blood samples and chest computed tomography scan, and the diagnosis of sepsis followed the Sepsis-3 guidelines.
Results: We included 14 critically ill patients with CAP-associated sepsis and 15 healthy control subjects (HCS). The median ages of the patient group and HCS were 78 and 55 years, and their body mass indexes were 22.8 and 21.7 kg/m2, respectively. All patients were treated at the critical care center, and 11 of the 14 patients received ventilatory management. All patients survived. These 14 patients met the diagnostic criteria of Sepsis-3 and were diagnosed as having CAP-associated sepsis. Of them, 6 patients met the diagnostic criteria for septic shock. RNA sequencing showed the number of genes with up:down (upregulated:downregulated) expression variation (false discovery rate [FDR] <0.05, |log2 fold change| >1.2) to be 1209:1461 for mRNA; 51:21 for microRNA; and 646:1274 for miRNA-targeted mRNA. Canonical pathway analysis using mRNA showed activation of the PD-1 and PD-L1 cancer immunotherapy signaling pathways and inhibition of the Th1 signaling pathway as well as that using miRNA-targeted mRNAs.
Conclusions: Using integrated analysis of mRNA and miRNA, we elucidated for the first time, to our knowledge, that T-cell exhaustion occurred during the acute phase of CAP-associated sepsis and that miRNA regulated Th1 signaling and PD-1 and PD-L1 cancer immunotherapy signaling through the RNA interference action of mRNA.

overall_design: Prospective cohort study

first: Hisatake

last: Matsumoto


title: Integrated analysis of messenger RNA and microRNA in patients with community-acquired pneumonia associated sepsis (miRNA part)


title: Comprehensive analysis of m6A-modified circRNAs in mice model of myocardial injury induced by obstructive sleep apnea

city: 泉州

first: 清石

last: 陈

state: 福建省

address: 福建省泉州市鲤城区中山北路34号

institute: 医科大学附属第二医院

type:
Non-coding RNA profiling by array
Other

summary: The aim of this current study is to explore m6A-modified circRNAs expression profiles and reveal their potential functional roles in mouse models of CIH with the use of bioinformatics analysis.

overall_design: The mouse model of OSA treated by chronic intermittent hypoxia (CIH) was established. We assessed the expression profiles of  m6A-modified circRNAs by microarray analysis.

first: Qingshi

last: Chen


title: Epigenome analysis of HELLS in liver cancer [methylation]

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

summary: Genome wide DNA methylation profiling of shControl and shHELLS in HepG2. The Illumina Infinium MethylationEPIC BeadChip kits was used to obtain DNA methylation profiles.

overall_design: Genomic DNA from shControl and shHELLS HepG2 were hybridised to Illumina Infinium MethylationEPIC BeadChip

first: Jueng

middle: S

first: Sung

middle: K

last: Choi


title: Epigenome analysis of HELLS in liver cancer

summary:
Genome wide H3K9me3 profiling of shControl and shHELLS in HepG2
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3K9me3 in HepG2

overall_design: global change of H3K9me3 in control and HELLS knockdown liver cancer cell


title: HELLS knockdown or overexpression in liver cancer cells

summary: Transcriptome analysis after loss or gain of HELLS in HepG2.

overall_design: Generating stable HELLS knockdown or overexpressed cells using shRNA and overexpression vector in HepG2.


title: Microglia and myeloid cell populations of the developing mouse retina

status: Public on Apr 08 2025

city: Durham

first: Jeremy

last: Kay

state: NC

institute: Duke University

summary: Microglia make important contributions to central nervous system (CNS) development, but the breadth of their distinct developmental functions remain poorly understood. The mouse retina has been a key model system for understanding fundamental mechanisms controlling assembly of the CNS. To gain insight into where and how microglia might influence retinal development, here we identified molecularly unique myeloid cell populations that are selectively present during development, and characterized their anatomical locations. Development-specific transcriptional states were identified using single-cell (sc) and single-nucleus (sn) RNA-sequencing (RNA-seq) across multiple timepoints: postnatal day (P)5, P10, and P17. Transcriptional states were validated in vivo by histological staining for key RNA and/or protein markers.

overall_design: For scRNA-seq, retinal myeloid cells were purified by flow cytometry from Cx3cr1-YFP mice at three timepoints: P5, P10, and P17. Two repilcates were collected at each timepoint, although one P5 replicate failed and is not included here. Each replicate comprised all of the pups from a single litter (10-14 retinas from 5-7 mice). One of the P10 replicates included a cocktail of transcriptional/translational inhibitors to suppress ex vivo gene activation. For snRNA-seq, myeloid cell nuclei were fluorescently labeled using Cx3cr1-CreER; lox-stop-lox-Sun1GFP mice. GFP+ nuclei from P5 and P10 retinas were purified by flow cytometry. One replicate (i.e. litter) was run for each snRNA-seq timepoint.

first: Sage

last: Martineau

first: Samantha

last: Zarnick

middle: N


title: RNA sequencing for the DCA- or vehicle-treated ILC2s in vitro

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

summary: RNA sequencing was performed for the DCA- or vehicle-treated ILC2s sorted from the large intestine of C57BL/6 mice (n = 2 per group).

overall_design: Sorted large intestinal ILC2s from C57BL/6 mice were cultured in complete IMDM media containing IL-2 (10 ng/mL), IL-7 (10 ng/mL), IL-25 (10 ng/mL), and IL-33 (10 ng/mL) for 5 days, followed by treatment with DCA for 16 hours. The DCA- or vehicle-treated ILC2s were harvested by centrifugation and lysed for RNA extraction.

first: Qiuheng

last: Tian

first: Xi

last: Yuan

first: Yatai

first: Shiyang

last: Li


title: Gene expression profile at single cell level of cells from the murine small intestinal tumors

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of cells within murine colonic tumors with genetic mutations.

overall_design: Cells from mouse small intestinal tumors with mutant Braf and mutant P53, with and without Rnf43 deletion, were harvested for analysis with scRNAseq

first: Megan

last: Mills

first: Tamsin

last: Lannagan

first: Owen

last: Sansom


title: Programmable RNA acetylation with CRISPR-Cas13

city: Daejeon

first: Won Do

last: Heo

address: 291, Daehak-ro, Yuseong-gu

department: Department of Biological Sciences

institute: Korea Advanced Institute of Science and Technology (KAIST)

summary: Recent studies claim that N4-acetylcytidine (ac4C) modification of RNA confers crucial regulatory roles, such as increasing translation efficiency and prolonging its half-life. However, the absence of methods for selectively acetylating specific RNA molecules hampers linking ac4C to cell physiology. Here, we developed an efficient molecular tool that incorporates ac4C on a specific transcript of interest. Through protein engineering, we developed a hyperactive variant of N-acetyltransferase 10 (NAT10), designated eNAT10. When fused to the programmable RNA-targeting protein dCas13, eNAT10 enables robust acetylation of various target RNAs in multiple contexts. RNA acetylation by dCas13-eNAT10 was highly dependent on co-transfected guide RNA, highlighting its specificity. We also describe the first programmable RNA chemical modification in vivo using dual-AAV. Utilizing our system, we found that acetylation of RNA may modulate the subcellular localization of modified transcripts. We anticipate that our tool will facilitate numerous studies on ac4C functions across different cellular and disease contexts.

overall_design: acRIP-seq & ac4C-seq profiling of off-target RNA acetylation in HEK293T cells transfected with dCas13-eNAT10, at 2-days post-transfection. acRIP-seq profiling of off-target RNA acetylation in mouse liver tissue transduced with dCas13-eNAT10 encoding AAV, at 3-weeks post-transduction. RNA-seq profiling of HEK293T cells transfected with dCas13-eNAT10, at 2-days post-transfection. Nuclear-cytoplasmic fractionation-seq profiling of HEK293T cells transfected with dCas13-eNAT10, at 2-days post-transfection.

first: Jihwan

last: Yu

first: Juae

last: Jin

first: Eury

last: Kwon

first: Hyunsoo

last: Jang

first: Sang-kun

first: Donggyun

last: Kim

first: Chaemin

first: Seungkyu

last: Son

first: Ki-Jun

last: Yoon


title: Endometrial assembloid model reveals endometrial adenogenesis regulation by estradiol-driven WNT7B expression [bulk RNA-seq]

city: Hong Kong

first: Yimeng

address: 21 Sassoon Road, Pokfulam Hong Kong

institute: The university of Hong Kong

summary: Little is known about the adenogenesis of human endometrial glands. This study explored endometrial adenogenesis using a novel three-dimensional endometrial assembloid model that integrates human endometrial organoids (EOs) and human endometrial stromal cells (HESCs). The model effectively recapitulated endometrial tubular gland formation, underscoring the critical role of stromal-epithelial interactions. Transcriptomic analyses identified WNT7B as a key intrinsic regulator for EO-derived tubular gland formation, which is extrinsically regulated by TGFβ1-VDR interaction between HESCs and EOs. Estradiol stimulated endometrial gland development via WNT7B downregulation in EOs. This finding was validated in an estradiol-stimulated mouse model and clinical samples from women undergoing in vitro fertilization (IVF) cycles. Uterine-specific WNT7B knockout in mice further confirmed its inhibitory role in endometrial gland development. This study offers insights into endometrial adenogenesis and potential therapeutic targets for related endometrial disorders.

overall_design: As differential tubular gland development ability has been identified in different endometrial organoid samples, we tried to identify the differential gene expression patterns in EOs with and without tubular gland development capacity. EOs were collected separately that with and without tube development potential for RNA sequencing analysis.

first: Xintong

first: Jianlin

first: Cheuk

middle: L

last: Lee

first: Philip

last: Chiu


title: A high-risk osteoarthritis mutation in COL6A3 alters the mechanobiologic response of chondrocytes derived from human induced pluripotent stem cells

city: Saint Louis

first: Farshid

last: Guilak

state: MO

address: 660 S Euclid Ave, Campus Box 8233

department: Dept of Orthopedics

institute: Washington University in St. Louis

summary: Osteoarthritis (OA) is a complex disease arising from a combination of genetic, biological, and mechanical risk factors that act, in part, to alter chondrocyte homeostasis. Our recent exome sequencing studies identified a causal OA variant in COL6A3, a monomeric unit of collagen type VI that serves as a distinguishing component of the pericellular matrix (PCM), a key transducer of mechanical and biochemical signals for the chondrocyte. To study the effect of this mutation, human induced pluripotent stem cell (hiPSC)-derived chondrocytes, genetically edited to harbor the COL6A3 mutation, were used as an in vitro model to investigate chondrocyte mechanobiology and pathobiology. COL6A3 mutant chondrocytes exhibited reduced expression of key matrix proteins, suggesting altered PCM structure and composition.  Functional analyses revealed altered mechanotransduction, characterized by heightened osmotically induced calcium signaling and reduced anabolic response to TRPV4 activation, at the transcriptional level and in matrix biosynthesis. RNA sequencing identified dysregulated pathways and aberrant TRPV4 signaling in mutant chondrocytes following mechanical loading. The presence of the COL6A3 mutation resulted in disrupted circadian rhythms, with increased BMAL1 expression and a significant phase shift, suggesting a link between the PCM and the circadian clock. Finally, COL6A3 mutant chondrocytes exhibited exacerbated catabolic response to interleukin-1, a key inflammatory cytokine in OA. Our study demonstrates the utility of a human iPSC-based system for studying the pathophysiology of specific OA risk alleles. These findings highlight the impact of the COL6A3 variant on chondrocyte physiology and support targeting mechanotransduction signaling pathways as a potential strategy for OA intervention in this case.

overall_design: To investigate the impact of a high-risk osteoarthritis mutation in COL6A3 on chondrocyte mechanotransduction, human induced pluripotent stem cells (hiPSCs) were gene-edited to harbor the mutation and differentiated into chondrocytes alongside unedited, wildtype hiPSCs. Wildtype and COL6A3 mutant hiPSC-derived chondrocytes were encapsulated in an agarose hydrogel and cultured for 14 days to form tissue-engineered cartilage, and subjected to physiologic levels of dynamic, compressive mechanical loads (10% stain, 1Hz) over 3 hours, or left uncompressed to serve as a free-swelling control. Loaded samples were collected at three time-points immediatly after mechanical loading (0hrs, 3hrs, 24hrs). Tissue-engineereed cartilage was also cultured with the TRPV4 specific antagonist GSK205 (10 uM) under these specific free-swelling and loaded conditions.

first: Harissa

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