title: Valbenazine promotes body growth via growth hormone signaling during zebrafish embryonic development

city: Wenzhou

first: Guan

last: Kaiyu

state: Zhejiang Sheng

address: 128 Xueshiqian Road, Ouhai District

institute: Wenzhou Seventh People's Hospital

summary: To study the embryonic developmental toxicity of a VMAT-2 inhibitor Valbenazine (VBZ).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control group (zebrafish larvae exposed to solvent control DMSO) and experimental group (zebrafish larvae exposed to 10 uM Valbenazine).

first: Zhenkang

last: Su

first: Fengqing

last: Qin

first: Miaomiao

last: Zheng

first: Hai

last: Zhang


title: Extracellular vesicles from early- and late-passage endothelial cells differentially regulate cerebrovascular and brain aging in mice via changes in a miR-17-5p-dependent pathway

status: Public on May 12 2024

city: Zhanjiang

first: Huiting

state: Guangdong

address: No. 57 People's Road South, Xiashan District

department: Neurological department

country: China

institute: The Affiliated Hospital of Guangdong Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Vascular aging, which is characterized by brain endothelial cell (EC) senescence and dysfunction, is known to contribute to various age-related cerebrovascular and neurodegenerative diseases. However, the underlying mechanisms remain unclear. EC-derived microvesicles (EMVs) and exosomes (EEXs) retain the characteristics of parent cells and transfer their contents to modulate the functions of recipient cells, showing potential for evaluation or regulation of vascular aging. Here, as indicated by analyses of senescence-associated beta-galactosidase (SA-β-gal) staining, cerebral blood flow, blood–brain barrier function, aging-related markers and cognitive ability, we found that young primary EC (passage 2-4) released EMVs alleviated mouse cerebrovascular and brain aging more effectively than EEXs. Aged EC (passage 15-16) released EMVs were more effective than their released EEXs at exacerbating mouse cerebrovascular and brain aging. We further revealed that these EMVs regulated cerebrovascular and brain aging by transferring miR-17-5p and modulated EC senescence and function via the miR-17-5p/PI3K/Akt pathway. Clinically, the levels of plasma EMVs and their associated miR-17-5p (EMV-miR-17-5p) were significantly increased or decreased in elderly individuals and were closely correlated with reactive oxygen species (ROS) and vascular aging. Receiver operating characteristic (ROC) analysis revealed that the area under the curve (AUC) was 0.724 for EMVs, 0.77 for EMV-miR-17-5p and 0.815 for their combination for distinguishing vascular aging. Our results identified novel roles for EMVs and showed that these vesicles more effectively modulated vascular and brain aging than did EEXs by regulating EC functions through the miR-17-5p/PI3K/Akt pathway; thus, EMVs and EMV-miR-17-5p are promising biomarkers and therapeutic targets for vascular aging.

overall_design: To investigate the mechanism of different effects of EMV from young and old endothelial cells (y.EMVs and o.EMVs). MiRNA sequencing was applied to identify the functional miRNAs in EMVs. Comparative gene expression profiling analysis of RNA-seq data for y.EMVs (derived from passage 2-5 primary endothelial cells) and o.EMVs (derived from passage 15-16 primary endothelial cells))


title: The effect of G-quadruplex on gene expression by treating S2 cell with different concentration of TMPyP4

status: Public on May 13 2024

city: Wuhan

first: Zhen-Xia

last: Chen

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

institute: Huazhong Agricultural University

type: Expression profiling by high throughput sequencing

summary: In this study, G-quadruplex ligand TMPyP4 was utilized to treat S2 cell and DMSO was served as control. The stabilization role of TMPyP4 will promote the formation of G-quadruplex and then affect gene expression. Identifying whether the effect is positive or negative is important for our understanding of the functionality of non-coding element.

overall_design: We treated S2 cell with different concentration of TMPyP4 (25μmol/L, 50μmol/L, 100μmol/L). We designed three experimental groups and one control group.  The experimental group 1 was treated with 25μmol/L alone, the experimental group 2 was treated with 50μmol/L alone, and the experimental group 3 was treated with 100μmol/L alone. The drug solvent DMSO-treated group served as a control group, with 3 replicates per treatment in each group.

first: Sheng

middle: H

last: Qian

first: Yi-Xuan

last: Tu

first: Lu


title: Secreted Clusterin Inhibits Tumorigenesis by Modulating Tumor Cell and Macrophage in Human Meningioma

city: Guangzhou

first: by

last: h

address: Guangzhou, Guangdong Province

institute: Jinan University

summary: Our single-cell transcriptomic dataset exceeds the scale of previous efforts to systematically characterize meningioma. We identified CLU is tumor suppresser, also promote the anti-tumor capability of macrophage, that why CLU decreased in meningioma malignancy. HDACi may inhibit meningioma by increasing CLU expression. Therefore, promoting CLU expression maybe a great strategy for meningioma therapeutics.

overall_design:
Single-cell analysis of 18 specimens from 13 patients: 2 with meningeal, 8 with grade I, 4 with grade II and 4 with grade III.

**Raw data are not provided due to patient privacy concerns**

first: Hongyi

first: Oscar

middle: J

last: Luo

first: Chao

last: Ke


title: Impact of triphenyl phosphate on sperm quality reduction: evidence from human, mice and cells

city: Nanjing

first: Yuhan

last: Ma

state: Jiangsu

address: Hankou Road 22

institute: Nanjing University

summary: In this study, we identified that reduced T production in Leydig cells after TPhP exposure was attributed to impaired cholesterol metabolism. Collectively, these data indicated that TPhP exposure could reduce male reproductive quality, which provided insights into the adverse effects of TPhP on human reproductive health and also provided a basis for the formulation of policy on TPhP usage by relevant government agencies.

overall_design: To investigate the key events in mouse primary Leydig cells after TPhP or DPhP exposure, RNA-seq was performed to find the differentially expressed genes.

first: Dihui

last: Xu

first: Xiaodong

last: Han

first: Yabing


title: Spermine-induced gene expression change in human macrophages

city: Hangzhou

first: Hongde

last: Li

state: Zhejiang

address: 150 Fucheng Road

institute: Hangzhou Institute of Medicine, Chinese Academy of Sciences

summary: Polyamines, crucial molecules involved in cell proliferation and growth, play a pivotal role in cancer development and progression. Within the tumor microenvironment, macrophages, key components of the immune system, exhibit a complex relationship with polyamines. Evidence suggests that polyamines can modulate macrophage polarization, influencing their functional phenotypes. Here, we detected the gene expression changes in spermine-stimulated human macrophages isolated from PBMCs.

overall_design: Macrophage isoloated from human PBMCs were devided into two groups: one is Control, the other is spermine-treated group (Spermine). Total RNAs were extracted, and RNA-seq were performed

last: Hu

first: Yinghua

last: Zhu


title: Differences in gene expression between multicellular spheres and adherent cell of tongue cancer cell lines CAL27 and HSC3

first: Jiong

last: Lyu

address: Rd.Yuhangtang  866

institute: Zhejiang University

summary: To investigate the differences in gene expression between multicellular spheres and adherent cell of tongue cancer cell, We compared the difference in gene expression between CAL27 and HSC3 cultured in suspension culture and adherent culture.

overall_design: CAL27 and HSC3 cell lines cultured in suspended culture (DMEM/F12 with 2% B27, 10ng/ml EGF and 10ng/ml bFGF in low adhesion culture plate, at 7th day) and under adherent conditions (DMEM/F12 with 10% FBS, at logarithmic period) were collected. Gene expression profiling were analyzed in these cells.

first: Yuwen

last: Miao

first: Pan

last: Wang


title: Multi-Omics Integration Highlights the Role of Ubiquitination in Endometriosis Fibrosis

city: xiamen

first: Mengjie

last: Yang

state: Fujian

address: 66 Zhenhai Road, Siming District, Xiamen City, Fujian Province, China

department: National Institute for Data Science in Health and Medicine

institute: School of Medicine, Xiamen University

summary: An in-depth conjoint analysis of transcriptome and proteome abundance atlas on endometrial tissues was generated from 6 control females and 10 patients with endometriosis.

first: MengJie

first: Hong

last: Jiang

first: XinYu

last: Ding

first: HuaYing

first: JiaHao

first: LiJun

first: Xinqin

last: He

first: ZhiXiong

last: Huang

first: QiongHua


title: CDC7 inhibition impairs neuroendocrine transformation in lung and prostate tumors through MYC degradation

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

country: USA

institute: Memorial SLoan-Kettering Cancer Center

summary: Neuroendocrine (NE) transformation is a mechanism of resistance to targeted therapy in lung and prostate adenocarcinomas leading to poor prognosis. Upregulation of the cell cycle kinase CDC7 occurred in tumors undergoing NE transformation, after TP53/RB1 co-inactivation, leading to induced sensitivity to the CDC7 inhibitor simurosertib. CDC7 inhibition suppressed NE transdifferentiation and extended response to targeted therapy in in vivo models of NE transformation by inducing the proteasome-mediated degradation of MYC, implicated in stemness and histological transformation. Ectopic overexpression of a degradation-resistant MYC isoform reestablished the NE transformation phenotype observed on targeted therapy, even in the presence of simurosertib. CDC7 inhibition also markedly extended response to standard cytotoxics in lung and prostate small cell carcinoma models. These results nominate CDC7 inhibition as a strategy to constrain lineage plasticity and to effectively treat NE tumors. As simurosertib clinical efficacy trials are ongoing, this concept could be readily translated for patients at risk.

overall_design: 4-10 male 6-week-old NOD.Cg-Prkdc<scid> Il2rg<tm1Wjl>/SzJ (NSG) mice were subcutaneously engrafted per treatment arm and until tumors reached 100-150 mm3. At that point, mice were randomized into groups and treated with either vehicle, simurosertib (40 mg/kg p.o. QDx3), enzalutamide (10 mg/kg p.o. QDx5), osimertinib (25 mg/kg p.o. QDx5) or their combination. Mice weights and tumor volumes were measured twice a week and mice were sacrificed when tumors reached humane endpoint (volume = 1000 mm3). The number of mice per treatment arm were selected according to previous experience with the models and response to treatments. Blinding was not performed. All animal experiments were approved by the Memorial Sloan Kettering Cancer Center (MSKCC) Animal Care and Use Committee (#13-07-007).

first: Alvaro

last: Quintanal-Villalonga

first: Charles

middle: M

last: Rudin

first: Nicholas

middle: D

last: Socci


title: Identification of hepatocyte-primed biliary epithelial cells in the homeostatic liver by in vivo lentiviral gene transfer to mice and non-human primates [2]

status: Public on May 11 2024

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

summary: To investigate the differences in the trascriptome of mouse cholangiocytes transduced in vivo by lentiviral vector compared to the untransduced counterpart

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse cholangiocytes transduced or not in vivo by lentiviral vector administration

first: Alessio

last: Cantore

first: Michela

last: Milani

first: Stefano

last: Beretta


title: Mosaic RBD nanoparticle elicits immunodominant antibody responses across sarbecoviruses

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

summary: Universal vaccines cross-protecting against sarbecoviruses including SARS-CoV-2 are in great need under continuous emergence of SARS-CoV-2 variants and potential novel  coronavirus. Nanoparicle vaccines displaying mosaic receptor-binding domains (RBDs) or spike (S) proteins from SARS-CoV-2 and other sarbecoviruses were used for preparedness to emergent zoonotic outbreak. Here, we describe a self-assembling nanoparticle using lumazine synthase (LuS) as the scaffold to display RBDs from different sarbecoviruses. The mosaic LuS-RBD vaccines induced cross-reactive binding and neutralizing antibody responses to sarbecoviruses. Single B cell sequencing revealed that mosaic LuS-RBD elicited B-cell receptor (BCR) repertoire using an immunodominant germline gene pair of IGHV14-3: IGKV14-111 in mice. Most of the tested IGHV14-3: IGKV14-111 monoclonal antibodies (mAbs) are broadly cross-reactive to the clade 1a, 1b and 3 sarbecoviruses. By antibody binning and cryo-electron microscopy, we determined a reprensentative IGHV14-3: IGKV14-111 mAb, M2-7, bound to an conserved epitope on RBD largely overlapping with a pan-sarbecovirus mAb S2H97, which suggested that mosaic nanoparticles expended B cells recognizing the common epitopes shared by different clades of sarbecoviruses. These results provide immunological insights into the cross-reactive responses elicited by mosaic nanoparticle against emerging sarbecoviruses.

overall_design: To identify the potential mechanisms contributing to the broad-spectrum neutralization induced by the mosaic nanoparticle vaccines, we analyzed the antigen-specific antibody repertoire using single-cell BCR profiling. BALB/c mice were immunized with two doses of LuS-RBD or LuS-mRBD-B. At fourteen days post-vaccination, using RBD proteins conjugated with fluorochrome as the probe, antigen-reactive germinal center B cells (BGC) from lymph nodes were isolated and sorted by flow cytometry (GL-7+B220hiCD38loIgD−CD93−CD138−). To obtain the paired variable (V)-regions, chromium immune profiling solution (10X Genomics) was applied to these BGC cells for single-cell BCR sequencing (scBCR-seq). Sequences covering the full-length V(D)J segments for both heavy and light chains were analyzed.


title: Nucleobase adducts bind MR1 and stimulate MR1-restricted T cells

city: Basel

first: Gennaro

last: De Libero

address: Hebelstrasse 20

department: Dept of Biomedicine

country: Switzerland

institute: University of Basel

summary: MR1T cells are a recently discovered class of T cells that recognize antigens presented by the MHC-I–related molecule MR1 in the absence of microbial infection. The nature of the self-antigens that stimulate MR1T cells remains unclear, hampering our understanding of their physiological role and therapeutic potential. By combining genetic, pharmacological, and biochemical approaches, we found that carbonyl stress and changes in nucleobase metabolism in target cells promote MR1T cell activation. Stimulatory compounds formed by carbonyl adducts of nucleobases were detected within MR1 molecules produced by tumor cells and their abundance and antigenicity were enhanced by drugs that induce carbonyl accumulation. Our data reveal carbonyl nucleobase adducts as MR1T cell antigens. Recognizing cells under carbonyl stress allows MR1T cells to monitor cellular metabolic changes with physiological and therapeutic implications.

overall_design: A375-MR1-Cas9 cells were transduced by pooled part A and B GecKO v2 CRISPR library at an MOI of 0.3. Replicates of resultant APCs had a 64-fold representation of each guide within the library and underwent 4 consecutive rounds of killing by TC5A87 T cells at a E:T of 2:1, following which surviving cells were expanded for 24 hrs and genomic DNA extracted for PCR amplicon sequencing.

first: Alessandro

last: Vacchini

first: Andrew

last: Chancellor

first: Qinmei

first: Rodrigo

last: Colombo

first: Julian

last: Spagnuolo

first: Giuliano

last: Berloffa

first: Daniel

last: Joss

first: Ove

last: Øyås

first: Chiara

last: Lecchi

first: Giulia

last: De Simone

first: Aisha

last: Beshirova

first: Vladimir

last: Nosi

first: José

middle: P

last: Loureiro

first: Aurelia

last: Morabito

first: Corinne

last: De Gregorio

first: Michael

last: Pfeffer

first: Verena

last: Schaefer

last: Prota

first: Alfred

last: Zippelius

first: Jörg

last: Stelling

last: Häussinger

first: Laura

last: Brunelli

first: Peter

last: Villalta

first: Marco

last: Lepore

first: Enrico

last: Davoli

first: Silvia

last: Balbo

first: Lucia

last: Mori


title: A Lactate-induced SREBF2-dependent genetic program drives an immunotolerant dendritic cell population during cancer progression [CITEseq]

city: Durham

first: Brent

last: Hanks

state: North Carolina

address: 308 Research Dr

department: Medicine

institute: Duke University

summary: Dendritic cells (cDCs) are essential mediators of anti-tumor immunity. Cancers have developed mechanisms to render DCs dysfunctional within the tumor microenvironment. Utilizing CD63 as a unique surface marker, we demonstrate that mature regulatory DCs (mregDCs) suppress DC antigen cross-presentation while driving TH2 and regulatory T cell differentiation within tumor-draining lymph node tissues. Transcriptional and metabolic studies show that mregDC functionality is dependent upon the mevalonate biosynthetic pathway and the master transcription factor, SREBP2. Melanoma-derived lactate activates DC SREBP2 in the tumor microenvironment (TME) and drives mregDC development from conventional DCs. DC-specific genetic silencing and pharmacologic inhibition of SREBP2 promotes anti-tumor CD8+ T cell activation and suppresses melanoma progression. CD63+ mregDCs reside within the sentinel lymph nodes of melanoma patients. Collectively, this work describes a tumor-driven SREBP2-dependent program that promotes CD63+ mregDC development and function while serving as a promising therapeutic target for overcoming immune tolerance in the TME.

overall_design: scRNAseq of dendritic cells (DCs) sorted from the tumor draining lymph node or non-draining lymph node of Tyrosinase-driven Cre Recombinase BRAFV600E, PTEN-/- mice on a C57Bl6 background, as well as Dcs sorted from the inguinal lymph node of non-tumor bearing wildtype mice. Additionally, scATACseq was performed on DCs sorted from the tumor draining lymph node of Tyrosinase-driven Cre Recombinase BRAFV600E, PTEN-/- mice. scRNAseq was also performed on dendritic cells sorted from the sentinel lymph node of human melanoma patients in addition to spatial transcriptomics of the sentinel lymph node of human melanoma patients.

last: Plebanek

first: Yue

last: Xue

first: Y-Van

last: Nguyen

first: Nicholas

middle: C

last: DeVito

first: Xueying

last: Wang

first: Alisha

last: Holtzhausen

first: Georgia

last: Beasley

first: Balamayooran

last: Theivanthiran

middle: A


title: Therapeutic efficacy of antimalarial drugs targeting DosRS signaling in Mycobacterium abscessus

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: Regulation of M. abscessus gene expression in WT or dosR mutant and treated with artemisinin

overall_design: WT or DosR deletion mutant were cultured in 16 mL of Dubos browth +10% ADS and 0.05% Tween 80 starting at an OD of 0.05  in a T-25 flask (in horizontal position). The cultures were treated with 20 uM artemisinin or a DMSO control for 24 hours, RNA was extracted, llibraries generated, sequenced and differential gene expression analyzed.

first: J

last: Belardinelli

middle: T

last: Williams

first: B

middle: K

last: Johnson

first: R

middle: B

first: M

last: Jackson


title: Muscle group specific transcriptomic and DNA methylation differences related to developmental patterning influence FSHD

city: Irvine

first: Ali

last: Mortazavi

state: CA

address: 2300E Biological Sciences 3

institute: UC Irvine

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RNAseq between gestational diabetes mellitus and healthy control groups

city: Ningbo

first: Yifang

last: Hu

address: fenghua road

institute: ningbo university

summary: tsRNA profiles of gestational diabetes mellitus and healthy control groups were generated by deep sequencing using Illumina NextSeq 500.

overall_design: RNA profiles of  test and control samples

last: HU

first: Yisheng

last: Zhang


title: N-terminal tagging of RNA Polymerase II shapes transcriptomes more than C-terminal alterations

city: Coventry

first: Daniel

last: Hebenstreit

address: Gibbet Hill Rd

country: United Kingdom

institute: University of Warwick

summary: To investigate the effect of RPB1 CTD length on transcription dynamics, six mutant U2OS cell lines expressing tagged versions of α-amanitin resistant RPB1 with CTDs of varying lengths (Dendra2-RPB1-25R (D25), Dendra2-RPB1-52R (D52), Dendra2-RPB1-70R (D70), HaloTag-RPB1-25R (H25), HaloTag-RPB1-52R (H52), and HaloTag-RPB1-70R (H70)) were grown in α-amanitin to degrade endogenous RPB1, then their RNA was sequenced at single-cell resolution using a droplet-based system.

overall_design: The three HaloTag cell lines (H25, H52, and H70) were sequenced on 25-FEB-2021 but the target number of reads was not obtained, so the same libraries were sequenced again on 23-MAR-2021. Separate sequencing runs of the same library were treated as one sample when processing. The three Dendra2 cell lines (D25, D52, and D70) were sequenced on 16-JUN-2021.

first: Adam

last: Callan-Sidat


title: Retinal inflammation mediated by mineralocorticoid receptor activation depends on its ligands

status: Public on May 10 2024

city: Paris

first: Bastien

last: Leclercq

state: Ile-de-France

address: 15 Rue de l'École de Médecine

country: France

institute: INSERM

summary: Transgenic rats overexpressing human mineralocorticoid receptor (hMR) under the control of the ecologic promotor 1 (P1.hMR rats) were used as well as their WT littermates. We observed low grade inflammation, RPE abnormatilites and anatomical signs of choroidal neuropathy in these rats. Bulk-transcriptomic analysis of neuroretinas was peformed to identify potential mechanisms.

overall_design: Animals were sacrified and eyes were freshly dissected to extract RNA from neuroretinas for transcriptomic analysis.

first: Francine

last: Behar-Cohen

first: Min

last: Zhao


title: Muscle group specific transcriptomic and DNA methylation differences related to developmental patterning influence FSHD [expression]

summary: Muscle groups throughout the body are specialized in function and are specified during development by position specific gene regulatory networks. In developed tissue, myopathies affect muscle groups differently. Facioscapulohumeral muscular dystrophy, FSHD, affects upper body and tibialis anterior (TA) muscles earlier and more severely than others such as quadriceps. To investigate an epigenetic basis for susceptibility of certain muscle groups to disease, we perform DNA methylation and RNA sequencing on primary patient derived myoblasts from TA and quadricep for both control and FSHD2 as well as RNA-seq for myoblasts from FSHD1 deltoid, bicep and TA over a time course of differentiation. We find that TA and quadricep retain methylation and expression differences in transcription factors that are key to muscle group specification during embryogenesis. FSHD2 patients have differences in DNA methylation and expression related to SMCHD1 mutations and FGF signaling. Genes induced specifically in FSHD are more highly expressed in more commonly affected muscle groups. We find a set of genes that distinguish more susceptible muscle groups including developmental associated TFs and genes involved in WNT signaling. Adult muscle groups therefore retain transcriptional and DNA methylation differences associated with development, which may contribute to susceptibility in FSHD.

overall_design: Time-course of primary FSHD2 myoblasts from tibialis anterior and quadricep, control myoblasts from tibialis anterior and quadricep, FSHD1 myoblasts from bicep, deltoid and tibialis anterior

first: Katherine

middle: E

middle: S


title: A chromosome region linked to neurodevelopmental disorders acts in distinct neuronal circuits in males and females to control locomotor behavior

city: Iowa City

first: Yann

last: Vanrobaeys

state: IA

address: 169 Newton Road

department: Neuroscience and Pharmacology

institute: University of Iowa

summary: We report a single nuclei RNA-seq of mouse total striatum to identify gene expression changes in males and female between WT and 16p11.2 hemideletion.

overall_design: We performed single nuclei RNA-sequencing from total striatum of 4 groups: WT males (sample 795 and 809), 16p11.2 del/+ males (sample 796 and 807), WT females (sample 798 and 803), and 16p11.2 del/+ females (sample 806 and 811).

first: Jaekyoon

last: Kim

first: Felicia

last: Davatolhagh

first: Benjamin

last: Kelvington

first: Joseph

middle: F

last: Lynch III

first: Snehajyoti

last: Chatterjee

first: Sarah

middle: L

last: Ferri

first: Christopher

last: Angelakos

first: Alea

last: Mills

first: Marc

last: Fuccillo

first: Thomas

last: Nickl-Jockschat

first: Ted

last: Abel


title: Identification of hepatocyte-primed biliary epithelial cells in the homeostatic liver by in vivo lentiviral gene transfer to mice and non-human primates [1]

first: Ivan

last: Merelli

summary: To investigate the differences in the trascriptome of mouse cholangiocytes marked with or without the Confetti reporter after induction of CreERT2-mediated recombination driven by Albumin promoter

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse cholangiocytes traced trough tamoxifen-induced activation of CreERT2-mediated recombination of the Confetti reporter

first: Alessio

last: Cantore

first: Michela

last: Milani

first: Stefano

last: Beretta


title: Cortistatin A treatment effects on umbilical cord blood-derived megakaryocytes

city: Philadelphia

last: Thom

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: These experiments treated cord blood-derived megakaryocytes with Cortistatin A for 0-8 h and analyzed resultant gene expression changes by microarray analysis.

overall_design: Effects of Cortistatin A on cord blood-derived megakaryocytes at 0-8 h and analyzed by microarray.


title: Proteogenomics analysis to identify acquired resistance-specific alterations in melanoma PDXs on MAPKi therapy [RNA-seq]

city: Little Rock

first: Stephanie

last: Byrum

state: Arkansas

address: 501 Jack Stephens Dr, Jackson T. Stephens Bldg 4th floor

institute: University of Arkansas for Medical Sciences

summary: Therapeutic approaches to treat melanoma include small molecule drugs that target activating protein mutations in pro-growth signaling pathways like the MAPK pathway. While beneficial to the approximately 50% of patients with activating BRAFV600 mutation, mono- and combination therapy with MAPK inhibitors is ultimately associated with acquired resistance. To better characterize the mechanisms of MAPK inhibitor resistance in melanoma, we utilize patient-derived xenografts and apply proteogenomic approaches leveraging genomic, transcriptomic, and proteomic technologies that permit the identification of resistance-specific alterations and therapeutic vulnerabilities. A specific challenge for proteogenomic applications comes at the level of data curation to enable multi-omics data integration. Here, we present a proteogenomic approach that uses custom curated databases to identify unique resistance-specific alternations in melanoma PDX models of acquired MAPK inhibitor resistance. We demonstrate this approach with a NRASQ61L melanoma PDX model from which resistant tumors were developed following treatment with a MEK inhibitor. Our multi-omics strategy addresses current challenges in bioinformatics by leveraging development of custom curated proteogenomics databases derived from individual resistant melanoma that evolves following MEK inhibitor treatment and is scalable to comprehensively characterize acquired MAPK inhibitor resistance across patient-specific models and genomic subtypes of melanoma.

overall_design: A patient-derived xenograft (PDX) of an NRASQ61L patient melanoma tumor was established as non-dissociated tumor fragments in NOD scid gamma (NSG) mice and serially passaged without dissociation, in vitro growth cycles, or adjunctive in vivo growth supplements such as Matrigel. To derive the acquired-resistant NRASQ61L tumors, we implanted one tumor fragment (passage #2) per NSG mouse. A cohort of tumor-bearing mice with similar tumor volumes were selected for experimentation. When the tumors reached ~500 mm3, a mouse was treated with the vehicle-chow (V), while four mice were treated with trametinib-embedded chow (R1,2,4,5) to achieve 5 mg/kg/day dosing. All trametinib-treated tumors displayed tumor regression at this chosen dosage. Tumor tissues for NRASQ61L vehicle (V) and four treated samples (R1,2,4,5) were harvested at end-points and prepared for whole exome sequencing (WES) and bulk RNA-sequencing (RNA-seq).

first: Kanishka

last: Manna

first: Prashanthi

last: Dharanipragada

first: Duah

last: Alkam

first: Nathan

last: Avaritt

first: Charity

last: Washam

first: Michael

last: Robeson

first: Ricky

last: Edmonson

first: Samuel

middle: G

last: Mackintosh

first: Zhentao

last: Yang

first: Yan

last: Wang

first: Shirley

last: Lomeli

first: Gatien

last: Moriceau

first: Roger

last: Lo

first: Alan

last: Tackett


title: Microarray comparison of adult peripheral blood megakaryocytes to umbilical cord blood-derived megakaryocytes

first: Christopher

summary: Primary adult peripheral blood (PB) megakaryocytes and umbilical cord blood (CB) megakaryocytes

overall_design: Comparison of PB and CB megakaryocytes.


title: Muscle group specific transcriptomic and DNA methylation differences related to developmental patterning influence FSHD [methylation]

first: Ali

last: Mortazavi

overall_design: Time-course of primary FSHD2 myoblasts from tibialis anterior and quadricep, control myoblasts from tibialis anterior and quadricep.

first: Katherine

last: Williams

first: S


title: Selective CAR-T cell mediated B cell depletion suppresses interferon signature in SLE [PBMC]

city: Berlin

first: Artur

last: Wilhelm

address: Virchowweg 11

department: Rheumatology and clinical immunology

country: Germany

institute: Charite Berlin

summary: Applying advanced molecular profiling together with highly specific targeted therapies offers the possibility to better dissect the mechanisms underlying immune mediated inflammatory diseases such as systemic lupus erythematosus (SLE) in humans. Here we apply a combination of single cell RNA sequencing and T/B cell repertoire analysis to perform an in-depth characterization of molecular changes in the immune-signature upon CD19 CAR T cell-mediated depletion of B cells in SLE patients. The resulting datasets do not only confirm a selective CAR T cell-mediated reset of the B cell response, but simultaneously reveal consequent changes in the transcriptional signature of monocyte and T cell subsets that respond with a profound reduction in type 1 interferon signaling. Our current data thus provide evidence for a causal relationship between the B cell response and the increased interferon signature observed in SLE and additionally demonstrate the usefulness of combining targeted therapies and novel analytic approaches to decipher molecular mechanisms of immune-mediated inflammatory diseases in humans.

overall_design: We generated single cell sequencing data of SLE patients prior to and after anti CD19 CAR-T cell therapy

first: David

last: Chambers

first: Fabian

last: Müller

first: Aline

last: Bozec

first: Ricardo

last: Grieshaber-Bouyer

first: Thomas

last: Winkler

first: Dimitrios

last: Mougiakakos

first: Andreas

last: Mackensen

first: Georg

last: Schett

first: Gerhard

last: Krönke


title: Regulation of the transcription factor CdnL promotes adaptation to nutrient stress in Caulobacter

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

institute: University of Geneva, Faculty of Medicine / CMU

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In response to nutrient deprivation, bacteria activate a conserved stress response pathway called the stringent response (SR). In Caulobacter crescentus, SpoT synthesizes the secondary messengers (p)ppGpp, which affect transcriptional reprogramming by binding to RNA polymerase to downregulate anabolic gene transcription. (p)ppGpp can also impact the expression of anabolic genes by controlling the levels and activities of their transcriptional regulators. In Caulobacter, a major regulator of anabolic genes is the conserved transcription factor CdnL. If and how CdnL is controlled during the SR and why that might be functionally important is unclear. Here, we show that CdnL is regulated post-translationally in a manner dependent on SpoT and the ClpXP protease. We find that stabilization of CdnL causes misregulation of ribosomal and metabolic genes during starvation. Functionally, we demonstrate that the combined action of SR transcriptional regulators and CdnL clearance allows for rapid adaptation to nutrient repletion. We also find that cells that are unable to clear CdnL during starvation are outcompeted by wild-type cells when subjected to fluctuations in nutrients. We hypothesize that post-transcriptional clearance of CdnL during the SR, in conjunction with direct binding of (p)ppGpp and DksA to RNAP, are critical for altering the transcriptome in order to permit cell survival during nutrient stress.

overall_design: ChIP-Seq analysis to examine the whole-genome binding/occupancy of CdnL (both the wild type and *DD mutant) in Caulobacter crescentus under normal and depleted carbon conditions.

first: Erika

last: Smith

first: Gaël

last: Panis

first: Selamawit

last: Woldemeskel

first: Peter

last: Chien

first: Erin

last: Goley


title: Proteogenomics analysis to identify acquired resistance-specific alterations in melanoma PDXs on MAPKi therapy [WES]

first: Stephanie

last: Byrum

type: Genome variation profiling by high throughput sequencing

first: Kanishka

last: Manna

first: Prashanthi

last: Dharanipragada

first: Duah

middle: H

last: Alkam

first: Nathan

last: Avaritt

first: Charity

last: Washam

first: Michael

last: Robeson

first: Ricky

last: Edmonson

first: Samuel

last: Mackintosh

first: Zhentao

last: Yang

first: Yan

last: Wang

first: Shirley

last: Lomeli

first: Gatien

last: Moriceau

first: Roger

last: Lo

first: Alan

last: Tackett


title: Gene expression of HCT-116 cell lines treated with EVs isolated using GlyExo-Capture method

city: Beijing

first: Boan

last: Li

address: Baili Street and Qingfeng West Road in Tiangongyuan Street

institute: the Fifth medical center of Chinese PLA General Hospital

summary: Extracellular vesicles (EVs) play a crucial role in facilitating intercellular communication. The microRNA profiles carried by EVs often exhibit variations between tumor patients and healthy individuals, making them promising biomarkers. These biomarkers are implicated in oncogenic processes and tumor metastasis upon uptake by recipient cells. To investigate the impact of EV biomarkers on tumorigenesis, we exposed HCT-116 cell lines to EVs isolated from the serum of both tumor patients and healthy individuals. In comparison to cell lines treated with extracellular vesicles (EVs) from healthy individuals and blank controls, cell lines treated with EVs from HCC sources exhibit significant alterations in the expression of certain genes associated with pathways related to liver cancer. Our findings shedlight on the intricate interplay between EVs and tumor progression.

overall_design: Comparative analysis of RNA-seq data: HCC-derived extracellular vesicles (EVs) treatment effects on HCT-116 cells compared to healthy EVs treatment and control cells.

first: Kun

last: Hao

first: Wenqian

last: Du

first: Ailan


title: Tanscriptomic analysis examined the specific mechanisms by which Foxm1 defects in cardiac fibroblasts prevent cardiac remodeling induced by pressure overload

first: shuai

last: song

address: No. 1609 Xietu Road, Xuhui District, Shanghai

department: Department of Cardiology

institute: Zhongshan  Hospital, Fudan University

summary: Cardiac fibroblasts (CFs) play a crucial role in cardiac remodeling, which is a common cause of heart failure (HF). However, the molecular mechanisms underlying the transformation of fibroblasts into myofibroblasts remain largely unknown. Foxm1 is well-known in various cardiovascular diseases. However, the role of Foxm1-driven CF activation in the progression of cardiac remodeling towards HF is still being investigated. In this study, we observed an upregulation of Foxm1 expression in samples obtained from patients with heart failure (HF) and in mice with transverse aortic constriction (TAC)-induced cardiac remodeling. Additionally, we discovered that inhibition of Foxm1 using the drug FDI-6 improved TAC-induced cardiac remodeling and attenuated the activation of cardiac fibroblasts (CFs). Furthermore, through our investigations, we found that Foxm1 was activated in Tcf21-Cre and PostnMCM transgenic mice subjected to TAC surgery, resulting in the activation of CFs and exerting an influence on the cardiac remodeling process.

overall_design: To comprehensively explore the potential mechanisms underlying Foxm1-mediated cardiac remodeling, we conducted transcriptomic analyses in neonatal ventricular cardiac fibroblasts  (NVCFs) with Foxm1 knockdown or overexpression. RNA samples were collected from NVCFs in different experimental groups, including si-NC (negative control), si-Foxm1 (Foxm1 knockdown), Ang-II (angiotensin II stimulation), si-Foxm1+Ang-II (combined Foxm1 knockdown and angiotensin II stimulation), OE-NC (overexpression negative control), and OE-Foxm1 (Foxm1 overexpression).


title: Fibroblast-derived exosomal microRNA regulates NKX3-1 expression in androgen-sensitive, androgen receptor-dependent prostate cancer cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: The expression profiling of exosomal miRNAs produced by fibroblasts (human prostate stromal and three types of primary cultured prostate fibroblasts) revealed that certain fibroblast-produced exosomes may be involved in the suppression of oncogenic dedifferentiation in prostate cancer cells.

overall_design: In this study, miRNA expression profiling was obtained for exosomal miRNAs produced by fibroblasts (human prostate stroma and three types of primary cultured prostate fibroblasts).

first: Chise

last: Matsuda

first: Kenichiro

last: Ishii

first: Yasuhisa

last: Nakagawa

first: Taku

last: Shirai

first: Takeshi

last: Sasaki

first: Yoshifumi

last: Hirokawa

first: Kazuhiro

last: Iguchi

first: Masatoshi

last: Watanabe


title: METTL14 regulates neuroblastoma through the m6A modification

city: Suzhou

first: Jianwei

last: Wang

address: No.92 Zhongnan street

institute: Children's hospital of scoochow university

summary: RNA methylation is involved in the regulation of cell response and cell fate, and is closely related to the development of tumors. METTL14 is considered to be a m6A methyltransferase. Studies have found that METTL14 is associated with the occurrence and development of a variety of tumors, but the mechanism in neuroblastoma is not clear. The expression of METTL14 in high risk patients was significantly higher than that in low risk patients. Interference with METTL14 expression in SK-N-BE(2) cells significantly interfered with cell cycle and inhibited cell proliferation, migration and invasion. In neuroblastoma, METTL14 activates the PI3K/AKT signaling pathway by targeting YWHAH by upregulating m6A levels in mRNA transcripts. In all findings, it was suggested that METTL14 has a cancer-promoting function in neuroblastoma.

overall_design: The expression of METTL14 was interfered with shRNA in neuroblastoma cells SK-N-BE(2), and the alteration of m6A modification level in mRNA was analyzed.

first: Jian

last: Pan


title: RNAseq on PYMT cells  treated with TGFB2 and/or BMP4 in 3D matrigel

city: Bronx

first: Julio

last: Aguirre-Ghiso

address: 1301 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

summary:
Dormancy of disseminated tumor cells in secondary organs leads to late breast cancer-related deaths after relapse. The bone marrow is one of the primary breast cancer metastatic sites and is associated with poor prognosis. Here, we investigated the role of major factors of the bone marrow, BMP4 and TGF?2, in regulating cancer cell dormancy. Unexpectedly, we observed that TGF?2 and BMP4 have a synergistic effect that induces dormancy in both normal and transformed mammary stem cells. Several assays (3D matrigel, FUCCI Cell Cycle Indicator) showed that co-exposure to TGF?2 and BMP4 had a stronger anti-proliferative effect than each ligand alone. In addition, transformed cells fully retained this synergistic effect while they became less sensitive to individual cytokines.
Surprisingly, single-cell RNAseq analysis revealed the heterogeneity of the G0 compartment at the transcriptomic level. We identified a unique deep dormant cluster under TGF?2 and BMP4 co-exposure characterized by a blended signature from treatments by TGF?2 or BMP4 alone. These findings reveal that disseminated breast cancer cells in the bone marrow are placed in a deep dormant stage by the synergistic effect of TGF?2 and BMP4 that neither factor can achieve alone.
Lastly, our data suggest that the local BMP4 levels decrease with tissue aging and can therefore contribute to dormant cell awakening.
By providing a better understanding of BMP4/TGF?2 signaling, our results open opportunities to prevent cancer relapse.

overall_design:
We performed RNAseq to assess the differential programs inducing dormancy by TGFB2 and/or BMP4 treatment
PYMT cells were treated with 5ng/mL of TGFΒ2, BMP4, or both for 3 days.

first: Véronique

last: Maguer Satta

first: Emma

last: Risson


title: Exploration of lncRNA/circRNA-miRNA-mRNA networks in patients with chronic atrophic gastritis in plateau areas [miRNA]

city: Chengdu

first: Jinlin

last: Yang

state: Sichuan Province

address: Guoxue Lane, Wuhou District

institute: Department of Gastroenterology and Hepatology, West China Hospital of Sichuan University

summary: Higher incidence of chronic atrophic gastritis (CAG) is generally considered a precancerous lesion of gastric cancer (GC). Therefore, the early diagnosis and treatment of CAG, especially in Tibetan Plateau areas, play an important role in the prevention of GC. The atrophic and non-atrophic gastric mucosal tissue samples from 7 patients with chronic gastritis (CG) and cancer tissue samples from 3 patients with GC were collected. High-throughput sequencing was performed to identify the differentially expressed in lncRNAs, circRNAs, miRNAs, and mRNAs, followed by the construction of competitive endogenous RNA (ceRNA) regulatory networks (lncRNA/circRNA-miRNA-mRNA network) in CAG. Those differentially expressed mRNAs with the same expression trend in both CAG and GC were further identified. Two datasets (GSE153224 and GSE163416), involving data in non-Tibetan Plateau areas, were used to further screen out plateau-specific mRNAs in CAG, followed by identification of the plateau-specific and ferroptosis related mRNAs. GO and KEGG enrichment analysis were performed to investigate the biological functions of plateau-specific mRNAs in CAG. This study may provide useful information for identifying potential biomarkers for the diagnosis of CAG.

first: Wen

first: Chao

last: Liu

first: Tao

last: Ren

first: Xiaohong

last: Chen

first: Cuiting

last: Liang

first: Jin


title: Relaxin Attenuates the Genomic Actions and Biological Effects of Estrogens in the Myometrium by Reducing Estrogen Receptor Alpha Phosphorylation [ChIP-seq]

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: In this study we examine the extent and nature of functional interactions between the E2 and Rln signaling pathways in the myometrium.  In addition, we delineate the mechanisms underlying functional interplay between the E2/ERα and Rln/RXFP1 signaling pathways at the molecular and physiological levels in myometrial tissue and cells during quiescence and contractility.

overall_design: ChIP-seq was performed on purified ChIPed DNA obtained from ovariectomized mouse myometrium. Immunoprecipitation was performed using the polyclonal antibodies for ERa, H3K27ac, or H3K4me1.

first: Sudeshna

last: Tripathy

first: Anusha

last: Nagari

first: Mala

last: Mahendroo

first: W


title: Decitabine induces the expression of genes in THP-1 cells

city: shanghai

first: hezhou

last: guo

address: Shanghai, P. R. China.  No. 197 Rui Jin Er Road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Next Generation Sequencing Facilitates Quantitative Analysis of THP-1 cells treated with DMSO and Decitabine

overall_design: mRNA profiles of THP-1 cells were generated by deep sequencing, in duplicate, using Illumina Navoseq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using  SYBR Green assays.

first: Hezhou

last: Guo

first: Ruixue

last: Feng


first: Christopher

last: Thom

summary: Effects of Cortistatin A on cord blood-derived megakaryocytes at 96 h.

overall_design: Effects of Cortistatin A on cord blood-derived megakaryocytes at 96 h and analyzed by microarray.


title: A systems-level analysis of bile acids effects on rat colon epithelial cells

city: Aarhus

first: Hanne

last: Moeller

address: Wilhelm Meyers Alle 3, building 1233

department: Dept. of Biomedicine

country: Denmark

institute: Aarhus University

summary:
Bile acid diarrhoea is a chronic condition caused by increased delivery of bile acids to the colon. The underlying mechanisms remain to be elucidated.
To investigate genes involved in bile acid diarrhoea, systems-level analyses were employed on a rat bile acid diarrhoea model.
Twelve male Wistar Munich rats, housed in metabolic cages, were fed either control or bile acid-mixed (1% w/w) diets for ten days. Food intake, water intake, urine volume, bodyweight and faecal output were monitored daily. After euthanasia, colonic epithelial cells were isolated using calcium-chelation and processed for systems-level analyses, i.e. RNA-sequencing transcriptomics and mass spectrometry proteomics.
Bile acid-fed rats suffered diarrhoea, indicated by increased drinking, faeces weight and faecal water content compared with control rats. Urine output was unchanged.
With bile acid-feeding, RNA-sequencing revealed 204 increased and 401 decreased mRNAs; mass spectrometry 183 increased and 111 decreased proteins. Among the altered genes were genes associated with electrolyte and water transport (including Slc12a7, Clca4 and Aqp3) and genes associated with bile acid transport (Slc2b1, Abcg2, Slc51a, Slc51b and Fabps).
Correlation analysis showed a significant positive correlation (Pearson’s r=0.28) between changes in mRNA-expression and changes in protein-expression. However, caution must be exercised in making a direct correlation between experimentally determined transcriptomes and proteomes.
Genes associated with bile acid transport responded to bile acid-feeding, suggesting that colonic bile acid transport occur by regulated protein facilitated mechanisms rather than passive diffusion.
In addition, the study provides annotated rat colonic epithelial cell transcriptome and proteome with response to bile acid-feeding.

overall_design:
Twelve male Wistar Munich rats were housed in single-animal metabolic cages (Techniplast) with ad libitum access to water and standard rodent chow (cat. no. 1321, Altromin).
For an initial three days, the rats were acclimatized to the metabolic cages with ad libitum access to water and standard rodent chow. Subsequently, six rats were switched to standard rodent chow mixed with 1% w/w sodium cholate (Sigma Aldrich). After 10 days on the different diets rats were euthanized by cervical dislocation, their abdomens opened and the colons were dissected out and colonic epithelial cells (CECs) were processed for RNA sequencing.
Purified total RNA from distal colon CECs from the five sodium cholate treated rats with highest RNA concentration in the extract and from the five controls with highest RNA concentration in the extract was selected for sequencing. Preparation of strand-specific cDNA libraries, RNA selection using polyA purification and single channel RNA sequencing was performed by Eurofins Genomics (Germany) using HiSeq SBS Kit v4 on a HiSeq 2500 (Illumina). BWA-MEM version 0.7.12-r1039 was used to map RNA reads to reference sequences (Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2[q-bio.GN]). Normalization of reads was performed using Trimmed Mean of M values (TMM) normalization method with the edgeR-package version 3.16.2 in R. Gene expression profiling was performed and differential expression analysis was performed. Inclusion criteria included a false discovery rate (FDR) of less than 1% as recommended by the company. A fold change of more than 2 was used as the cut off value.

first: Jonathan

last: Yde

first: Qi

last: Wu

first: Johan

last: Borg

first: Robert

last: Fenton


title: Geochip data of soil microbial community of biomes from three termperature zones

city: Shanghai

first: Lantian

last: Su

address: 800 Dongchuan Rd.

department: School of Agriculture and Biology

institute: Shanghai Jiaotong University

summary: Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to examined functional gene structure of microbes in three biomes, including boreal, temperate and tropical area.

overall_design: In this study, to investigate the influence of biome, age and vegetation on microbial functional genes in forest soils, we focused on three biomes in Lahti (represents boreal area), Baltimore (temperate area) and Singapore (tropical area). 40 sampling sites were set in each biome. At each site, approximately 0.10 kg of soils was collected from surface (top 50 cm) for microbial Geochip analyses

last: Hui


title: Exploration of lncRNA/circRNA-miRNA-mRNA networks in patients with chronic atrophic gastritis in plateau areas

first: Jinlin

last: Yang

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

overall_design: Refer to individual Series


title: NR4A3耗尽对血管钙化的影响

first: Wenqi

last: Ma

state: Shanghai

address: 227 Chongqing South Road, Huangpu District, Shanghai, China


title: NR4A1 transcriptionally regulates the differentiation of stem-like CD8+ T cells in the tumor microenvironment (ChIP-Seq)

status: Public on May 09 2024

first: Jing

last: Hao

address: South Chongqing Road 227, Huangpu District

department: Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital

institute: Shanghai Immune Therapy Institute

summary: CD8+ T cells are rendered exhausted in tumor and chronic infection. Among heterogeneous exhausted T cells, a subpopulation of progenitor-like (Tpex) cells have been found important for long-term tumor or pathogen control, and are also the main responders in immunotherapy. Using a new reporter mouse for the orphan nuclear receptor NR4A1, originally characterized critical in T cell dysfunction, we discover that the reporter is highly expressed in Tpex cells in tumor and chronic infection. Enforced expression of Nr4a1 promotes Tpex cell accumulation, whereas tumor control is improved after Nr4a1 deletion, associated with increased effector function but decreased long-term maintenance of CD8+ T cells. Integrating ChIP-seq and RNA-seq analysis, NR4A1 is found to bind and promote the expression of Tpex-related genes, and suppresses terminal differentiation-associated genes. This study therefore has identified a key role of NR4A1 in Tpex regulation and provides a promising target for immunotherapy.

overall_design: NR4A1-OV/ RV-GFP virus infected CD8+ T cells re-stimulated with PMA/Ionomycin were used for RNA extraction. NR4A1 WT/KO naïve CD8+ T cells were activated with plate-bound anti-CD3/CD28 (2μg/mL) and re-stimulated with PMA/Ionomycin for RNA extraction. The tumor-infiltrating OT-I cells were isolated on day 21 post tumor cell inoculation, and the Nr4a1RFP+ and Tim-3+ OT-I cells were sorted with BD FACS Aria Cell Sorter. Tumor infiltrated Nr4a1-/- and Nr4a1+/+ Ly108+ OT-I cells were sorted out for RNA harvest. Total RNA was extracted reverse transcribed into cDNA and built library for sequencing using BGI-Hiseq500 (BGI Genomics) or Smartseq2. For ChIP-seq samples, Nr4a1-HA infected CD8+ T cells were purified and re-stimulated with PMA/Ionomycin, the the cells were fixed and digested with MNase cocktail (Active Motif). Antibodies against HA tag (3724, clone C29F4; Cell Signaling Technology) were used to precipitate the NR4A1 bounded chromatin. The immunoprecipitated DNA was purified and sent to BGI Genomics company for library building and sequencing with Illumina HiSeq 2500.

first: Ruifeng

last: Li

first: Xiaohong

last: Zhao

first: Xinwei

last: Liu

first: Xiang

last: Chen

first: Tian

last: Xie

first: Xiaoli

first: Chenjun

last: Yao

first: Qinli

last: Sun

first: Kun

last: Wei

first: Mengting

last: Gou

first: Xinxin

last: Chi

first: Wei

last: Xu

first: Ling

last: Ni

first: Chen

last: Dong


title: NR4A1 transcriptionally regulates the differentiation of stem-like CD8+ T cells in the tumor microenvironment (RNA-Seq)


title: Wybutosine hypomodification of tRNAphe activates HERVK and impairs neuronal differentiation

city: Guangzhou

first: Manqi

address: No. 135, Xingang Xi Road

institute: Sun Yat-Sen University

summary: We previously reported that loss-of-function of TYW1 led to cerebral palsy with severe intellectual disability through reduced neural proliferation. However, whether TYW1 loss affect neural differentiation is unknown. In this study, we first demonstrated that TYW1 loss blocked the formation of OHyW in tRNAphe, therefore affected the translation efficiency of UUU codon. Using the brain organoid model, we showed impaired neuron differentiation when TYW1 was depleted. Interestingly, retrotransposons were differentially regulated in TYW1-/- hESCs. In particular, one kind of human-specific endogenous retrovirus-K (HERVK/HML2), whose reactivation impaired human neurodevelopment, was significantly up-regulated in TYW1-/- hESCs. Consistently, a UUU codon enriched protein, SMARCAD1, which was a key factor in controlling endogenous retroviruses was reduced. Taken together, TYW1 loss leads to upregulation of HERVK in hESCs by down-regulated SMARCAD1, thus impairing neuron differentiation.

overall_design: To investigate the role of TYW1 in neuron differentiaiton, we generated TYW1 knockout clones in hESC

first: Chuanbo

first: Ruirui

last: Guo


title: In vivo perturbomics identifies CALHM2 as a checkpoint of NK cell therapy [AAV-CRISPR screen]

city: West Haven

first: Sidi

state: CT

address: 850 West Campus Drive

institute: Yale University

summary: Natural killer (NK) cells are an innate immune cell type that serves at the first level of defense against pathogens and cancer. NK cells have clinical potential; However, multiple current limitations exist that naturally hinder the successful implementation of NK cell therapy against cancer, including their effector function, persistence, and tumor infiltration. To unbiasedly identify genes underlying critical NK cell characteristics against cancer, we perform functional mapping of tumor infiltrating NK (TINK) cells by both in vivo AAV-CRISPR screens and single-cell sequencing. We establish a strategy with AAV-SleepingBeauty(SB)-CRISPR screening leveraging a focused  high-density sgRNA library, and perform four independent in vivo tumor infiltration screens of primary NK cells in mouse models of melanoma, breast cancer, pancreatic cancer, and glioblastoma. In parallel, we characterize single-cell transcriptomic landscapes of tumor-infiltrating NK cells, which identifies previously unexplored sub-populations of NK cells with distinct expression profiles, a shift from immature to mature NK (mNK) cells in the tumor microenvironment (TME), and decreased expression of mature marker genes in mNK cells. CALHM2, a calcium homeostasis modulator previously not linked to NK function, emerges as a convergent hit from both CRISPR screen and single-cell data. CALHM2 knockout NK cells show enhancement of in vitro cytotoxicity and in vivo tumor infiltration in both mouse primary NK and human chimeric antigen receptor (CAR)-NK cells. Re-introduction of CALHM2 mRNA reverses CALHM2 knockout phenotype of NK cytotoxicity and degranulation. Importantly, in a solid tumor model that is completely resistant to adoptive cell therapy of unmodified CAR-NK cells, CALHM2 knockout CAR-NK cells show potent in vivo anti-tumor efficacy. Human primary NK cell study with multiple donors reveals that CALHM2 knockout enhances cytotoxicity, degranulation and cytokine production of NK cells. Transcriptomics profiling of human primary NK cells reveal multiple enriched pathways of downstream genes upon CALHM2 knockout in both baseline and stimulated conditions. These data identify endogenous cellular genetic checkpoints that naturally limit NK cell function, and pinpoint CALHM2 as a key factor in which genetic modification can be engineered to enhance NK cell-based immunotherapies.

overall_design: The AAV-CRISPR screen was performed with >400x coverage, in which > 5e7 Cas9+ NK cells were transduced with an approximate ~50% infectivity rate, using the AAV-Surf-v2 viral library (0.5 infectivity * 5e7 cells / 61,911 sgRNAs > 400-fold coverage). Naïve NK cells were isolated from the spleens of Rsky/Cas9 mice. Syngeneic mouse models of melanoma, GBM, and pancreatic cancers were setup with subcutaneous injections of 2e6 B16F10, 5e6 GL261, or 4e6 Pan02 cells, respectively. Syngeneic mouse models of breast cancer were established by fat-pad injections of 2e6 E0771 cells into C57BL/6J mice. AAV-Surf-v2-infected NK cells were adoptively transferred into tumor burden mice via i.v. tail vein injections. Four screen models were used with different endpoints: B16F10 melanoma and E0771 breast cancer models were euthanized by 20 days post tumor implantation (dpi), while GL261 GBM and Pan02 pancreatic cancer models were euthanized at 27 dpi and 24 dpi, respectively. For B16F10 melanoma and E0771 breast cancer models, 4e6 AAV-Surf-v2 infected NK cells were injected into 9 and 10 tumor-burden mice, respectively; 2e6 AAV-Surf-v2 infected NK cells were injected into 7 Pan02 pancreatic cancer and 11 GL261 GBM mouse models.

first: Renauer

last: Paul

first: Peng

last: Lei


title: In vivo perturbomics identifies CALHM2 as a checkpoint of NK cell therapy [bulkRNAseq]

overall_design: CALHM2-KO and AAVS1-KO mutations were generated from primary human peripheral blood NK cells using  aCRISPR-Cas9 system. NK cells with each genotype were sequenced at baseline (unstimulated) and after coculture with HT-29 cells.


title: Multifunctional Enzyme Nanocapsules Boost T Cell Immunity and Multifunctional Enzyme Nanocapsules Boost T Cell Immunity and Efficacy of Cancer Immunotherapy

city: Los Angeles

first: Jeffrey

last: Harding

address: 405 Hilgard Avenue

institute: University of California Los Angeles

summary: Cancer immunotherapy has reshaped the landscape of cancer treatment, but its effectiveness is limited by tumor immunosuppression caused by excessive lactate production by cancer cells. While efforts to reduce lactate levels through lactate dehydrogenase inhibition have been made, such inhibitors can disrupt the metabolism of healthy cells and cause severe non-specific toxicity. Based on lactate oxidase, we report herein an enzyme therapeutic, which reduces lactate levels, releases an immunostimulatory molecule-hydrogen peroxide, averts tumor immunosuppression, and synergistically improves the efficacy of immune checkpoint blockades, as demonstrated in a murine melanoma model and a humanized mouse model of triple-negative breast cancer.

overall_design: Single-cell RNA seq of tumor cells treated with and without nanoparticles

first: Jing

last: Wen

first: Zheng

last: Cao


title: In vivo perturbomics identifies CALHM2 as a checkpoint of NK cell therapy

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Dynamic molecular signatures of acute myocardial infarction based on transcriptomics

first: Xuejiao

last: Wang

address: No.5 Beixiange, Xicheng District

institute: Guang’anmen Hospital, China Academy of Chinese Medical Sciences

summary: Peripheral blood mononuclear cells were collected from the patients. RNA-seq and analysis was performed on the collected samples. Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions(Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) is used to construct sequencing library

overall_design: We enrolled patients with AMI aged between 30 and 70. RNA-seq analysis was performed on the peripheral blood mononuclear cells collected from the patients at three time points: 1 day, 7 days, and 3 months after AMI. Differential genes and metabolites between groups were screened by bio-informatics methods to understand the dynamic changes of AMI in different periods.

first: Guang

last: Yang

first: Jun

last: Li

first: Chao

last: Meng

first: Zengming

last: Xue


title: Repurposing niclosamide in mouse models of amyotrophic lateral sclerosis

city: Rome

first: Savina

last: Apolloni

address: Via della Ricerca Scientifica, 1

department: Department of Biology

institute: University of Rome Tor Vergata

summary: ALS is a complex neurodegenerative disease influenced by genetic, epigenetic, and environmental factors, resulting in dysfunction in cellular and molecular pathways. The limited efficacy of current treatments highlights the need for combination therapies targeting multiple aspects of the disease. Niclosamide, an anthelminthic drug listed as an essential medicine, has been repurposed in clinical trials due to its anti-inflammatory and anti-fibrotic properties. Niclosamide can inhibit various molecular pathways (such as STAT3 and mTOR) that are dysregulated in ALS, suggesting its potential to disrupt these altered mechanisms associated with the pathology. Our recent findings have demonstrated that niclosamide can effectively inhibit inflammatory and fibrotic molecular pathways in ALS models. We administered niclosamide intraperitoneally to two transgenic murine models, FUS and SOD1-G93A mice, which replicate key pathologies and biological processes of ALS. The treatment was initiated at the onset of symptoms, and we assessed the progression of the disease by neurological scores, rotarod and grip tests, as well as monitoring survival. Additionally, we examined the effects of the treatment on spinal cord and muscle degeneration in the treated mice. In both models, the administration of niclosamide resulted in a slowdown of disease progression, an increase in survival rates, and an improvement in tissue pathology. This was characterized by a reduction in gliosis, motor neuron loss, muscle atrophy, and inflammatory markers. Based on these results, our findings demonstrate that niclosamide can impact multiple pathways involved in ALS. This multi-targeted approach leads to a slowdown in the progression of the disease, thereby positioning niclosamide as a promising candidate for repurposing in the treatment of ALS.

overall_design: Gene expression analysis of spinal cord from niclosamide (Nic)and control vehicle (Veh)-treated SOD1-G93A mice at the end stage and symptomatic phase of the disease. A total of n=14 samples were analysed by RNA seq: n=4 end stage Nic, n=4 end stage Veh, n=3 symptomatic Nic, n=3 symptomatic Veh.

first: Martina

last: Milani

first: Ilaria

last: Della Valle

first: Simona

last: Rossi

first: Paola

last: Fabbrizio

first: Cassandra

last: Margotta

first: Giovanni

last: Nardo

first: Mauro

last: Cozzolino

first: Nadia

last: D'Ambrosi


title: Simulated Lunar Microgravity Transiently Arrests Growth and Induces Osteocyte-Chondrocyte Lineage Differentiation in Human Wharton’s jelly stem cells.

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

summary: Human Wharton’s jelly stem cells (hWJSCs) are multipotent stem cells extensively employed in biotechnology applications and can be differentiated into distinct lineages through various culture approaches. However, the impact of simulated microgravity (sμG) on the growth, differentiation, and viability of this cell population is incompletely characterized. We aimed to determine whether acute (72 hour) exposure to lunar sμG (0.16 G) elicited changes in growth, viability and lineage differentiation in hWJSCs and if putative changes were maintained once exposure to terrestrial gravity (1.0G) was restored. Our data support earlier findings that acute sμG significantly reduces cell division potential of hWJSCs, and suggest that actute sμG-exposure induces reversible changes in cell growth accompanied by osteocyte – chondrocyte changes in lineage differentiation.

overall_design:
hWJSCs (n=7) were cultured under standard 1.0G conditions, prior to being passaged and cultured under sμG (0.16G) using a Random Positioning Machine. Separate control lines accounting for alterations in cell culture gas exchange and sμG were ran in parallel for a total of 72 hours. Cells were sampled before passage and cultured for a further 72-hour period of growth at 1.0G.
Cells were sampled for cell morphology imaging, cell counts using both an automated cell counter and trypan blue vital count, cell viability (MTS) assay, FACS analysis for CD34, CD45, CD73, CD90 and CD105, total RNA extraction for qRT-PCR and RNA sequencing.

first: Subramanian

last: ARJUNAN

first: Chelsea

last: IP

last: Oguz

first: Adaikalavan

last: Ramasamy

first: Matthew

middle: W

last: KEMP


title: Activation of feedforward wiring in adult hippocampal neurons by the bHLH transcription factor Ascl4

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

institute: University of Zurich

summary: Although evidence indicates that the adult brain retains a considerable capacity for circuit formation, adult wiring has not been broadly considered and remains poorly understood. Here, we investigated wiring activation in adult neurons. Based on bioinformatic analyses on a previously published dataset (GSE161619), we identified the basic-helix-loop-helix (bHLH) transcription factor Ascl4 as a potential regulator of adult wiring and show that the AAV-mediated overexpression of Ascl4 can cell autonomously induce wiring in different types of hippocampal neurons of adult mice. The new axons are mainly feedforward and reconfigure synaptic weights in the hippocampal circuit. Mice with rewired circuits do not display signs of pathology and solve spatial problems equally well as controls. Our results demonstrate reprogrammed connectivity by a single transcriptional factor and provide insights into the regulation of brain connectivity in adults.

overall_design: This dataset includes single-cell RNAseq data from AAV-EGFP labeled ventral hippocampal granule cells and ventral hippocampal medial CA1 pyramidal neurons of 3-4 months old adult mice. For the granule cell and pyramidal cell experiments Calb1-Cre and Nex-Cre transgenic lines were used, respectively, ensuring genetic access to these cell types. The cells were infected either with intrahippocampal microinjection of Cre-dependent AAV-EGFP and AAV-Ascl4 (experimental group, "AAV-Ascl4") or only Cre-dependent AAV-EGFP in equal amount (control group, "AAV-EGFP"). The cells were collected via electrophysiological patch pipette (patch-RNAseq) from acute brain slices 1 month after AAV injections. The partitioning of the data as follows (total number of cells sequenced / number of cells that passed quality control): (1) AAV-EGFP granule cell (“GFP GC”):60 / 53, (2) AAV-Ascl4 granule cell (“Ascl4 GC”):  56/ 52, (3) AAV-EGFP CA1 pyramidal cell (“GFP CA1”): 54 / 48, (4) AAV-Ascl4 pyramidal cell (“Ascl4 CA1”): 58 / 51.

first: Wenshu

last: Luo

first: David

last: Lukacsovich

first: Charlotte

last: Seng


title: Gene expression profiles of white bass (Morone chrysops) and hybrid striped bass (M. chrysops x M. saxatilis) gill tissue over time following Flavobacterium covae exposure

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

summary: Columnaris disease is a prevalent disease in freshwater environments worldwide caused by the ubiquitous aquatic bacterium Flavobacterium species. Adhesion to the external mucosal surfaces of fishes is the initial stage of infection, and the gills specifically have been identified as both a primary target and release site for this pathogen. Previous research has indicated that a predominant US aquaculture product, the hybrid striped bass (Morone chrysops x M. saxatilis), is more susceptible to infection with Flavobacterium columnare (covae) than the maternal white bass (M. chrysops) parental species. Therefore, to further elucidate the differences between these fish we conducted a transcriptomic profiling study examining the differences of gene expression in gill mucosal tissue over time after exposure to F. covae isolate LSU-066-04. Combined with previous work, these data provide a greater understanding of host immune response to a common pathogen in moronids.

sample_organism:
Morone chrysops x Morone saxatilis
Morone chrysops

overall_design: Gill tissues were sampled from 48 indiviudals at four timepoints prior to (t= 0 hr control) or following exposure to Flavobacterium covae (t= 1 hr, 4 hr, and 24 hr post treatment) (n=24 white bass, WB, and 24 hybrid striped bass, HB, total: 6 of each sampled at each of the four timepoints)

first: Linnea

last: Andersen


title: Single-cell profiling reveals immune aberrations in progressive idiopathic pulmonary fibrosis

city: Tel Aviv

first: Avraham

last: Unterman

address: Weizmann 6

country: Israel

institute: Tel Aviv Sourasky Medical Center

summary: Rationale: Changes in peripheral blood cell populations have been observed but not detailed at single-cell resolution in idiopathic pulmonary fibrosis (IPF).  Objectives: To provide an atlas of the changes in the peripheral immune system in stable and progressive IPF.  Methods: Peripheral blood mononuclear cells (PBMCs) from IPF patients and controls were profiled using 10x Chromium 5’ single-cell RNA sequencing (scRNA-seq). Flow cytometry was used for validation. Protein concentrations of Regulatory T-cells (Tregs) and Monocytes chemoattractants were measured in plasma and lung homogenates from patients and controls.  Measurements and Main Results: Thirty-eight PBMC samples from 25 patients with IPF and 13 matched controls yielded 149,564 cells that segregated into 23 subpopulations, corresponding to all expected peripheral blood cell populations. Classical monocytes were increased in progressive and stable IPF compared to controls (32.1%, 25.2%, 17.9%, respectively, p<0.05). Total lymphocytes were decreased in IPF vs controls, and in progressive vs stable IPF (52.6% vs 62.6%, p=0.035). Tregs were increased in progressive IPF (1.8% vs 1.1%, p=0.007), and were associated with decreased survival (P=0.009 in Kaplan-Meier analysis). Flow cytometry analysis confirmed this finding in an independent cohort of IPF patients. Tregs were also increased in two cohorts of lung scRNA-seq. CCL22 and CCL18, ligands for CCR4 and CCR8 Treg chemotaxis receptors, were increased in IPF.  Conclusions: The single-cell atlas of the peripheral immune system in IPF, reveals an outcome-predictive increase in classical monocytes and Tregs, as well as evidence for a lung-blood immune recruitment axis involving CCL7 (for classical monocytes) and CCL18/CCL22 (for Tregs).

overall_design: 38 peripheral blood mononuclear cells (PBMCs) samples from 25 patients with IPF (12 patients with progressive disease and 13 patients with stable disease) and 13 matched control subjects were profiled using 10x Genomics Chromium 5’ single-cell RNA sequencing (scRNA-seq).

first: Amy

middle: Y

last: Zhao

first: Nir

last: Neumark

first: Jonas

last: Schupp

first: Farida

last: Ahangari

first: Carlos

last: CosmeJr

first: Prapti

last: Sharma

first: Jasper

last: Flint

first: Yan

last: Stein

first: Changwan

last: Ryu

first: Genta

last: Ishikawa

first: Tomokazu

last: Sumida

first: Jose

last: Gomez

last: Herazo-Maya

first: Charles

last: DelaCruz

first: Erica

last: Herzog

first: Naftali

last: Kaminski


title: Exploration of lncRNA/circRNA-miRNA-mRNA networks in patients with chronic atrophic gastritis in plateau areas [lncRNA]

first: Jinlin

last: Yang

summary: Higher incidence of chronic atrophic gastritis (CAG) is generally considered a precancerous lesion of gastric cancer (GC). Therefore, the early diagnosis and treatment of CAG, especially in Tibetan Plateau areas, play an important role in the prevention of GC. The atrophic and non-atrophic gastric mucosal tissue samples from 7 patients with chronic gastritis (CG) and cancer tissue samples from 3 patients with GC were collected. High-throughput sequencing was performed to identify the differentially expressed in lncRNAs, circRNAs, miRNAs, and mRNAs, followed by the construction of competitive endogenous RNA (ceRNA) regulatory networks (lncRNA/circRNA-miRNA-mRNA network) in CAG. Those differentially expressed mRNAs with the same expression trend in both CAG and GC were further identified. Two datasets (GSE153224 and GSE163416), involving data in non-Tibetan Plateau areas, were used to further screen out plateau-specific mRNAs in CAG, followed by identification of the plateau-specific and ferroptosis related mRNAs. GO and KEGG enrichment analysis were performed to investigate the biological functions of plateau-specific mRNAs in CAG. This study may provide useful information for identifying potential biomarkers for the diagnosis of CAG.

first: Wen

last: Pan

first: Chao

last: Liu

first: Tao

last: Ren

first: Xiaohong

last: Chen

first: Cuiting

last: Liang

first: Jin

last: Wang


title: scChIC-seq reveals focusing of global chromatin domains during differentiation

city: Utrecht

first: Jake

last: Yeung

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: We profile single cell histone modifications using a new high-throughput scChIC-seq technique on K562 and mouse bone marrow.

overall_design: single cell histone modifications on K562 and mouse bone marrow.

first: Peter

last: Zeller

first: Buys

last: de Barbanson

first: Alexander

last: van Oudenaarden


title: Gene expression profiling of mouse CRTC1-MAML2-driven MEC-like tumors

city: Gainesville

first: Lizi

last: Wu

state: FL

address: 2033 Mowry Road

institute: University of Florida

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: We established a transgenic CRTC1-MAML2 fusion mouse model and crossed it with the MMTV-Cre transgenic mouse line  to induce Cre expression and consequently the CRTC1-MAML2 fusion transgene expression in salivary glands. We observed that Cre-induced CRTC1-MAML2 transgene expression caused the formation of salivary gland tumors resembling the histological features of human MEC. Here we performed genome-wide gene expression profiling analysis to characterize the transcriptomic feature of these murine CRTC1-MAML2-driven MEC-like tumors.

overall_design: Gene expression profiling was carried out on CRTC1-MAML2-driven MEC-like tumors (T), matched tumor adjacent normal salivary gland tissues (NAT), and normal salivary gland tissues (N) from the control non-transgene carrier littermates (N). Differentially expressed genes (DEGs) were determined in three comparison groups, including NAT vs. N, T vs. NAT, and T vs. N.


title: UBXN9 inhibits the RNA exosome function to promote T cell control of liver tumorigenesis

first: Li

last: Zhang

address: Dongchuan road 800

institute: Shanghai Cancer Institute

summary: To explore the function of UBXN9 in regulating liver tumorigenesis, we generated UBXN9-overexpressing and control LPC-HRas liver tumor cells by using lentivirus. Then, the mRNAs derived from these two groups of cells, including two replicates for each group , were subjected to  RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from UBXN9-overexpressing and control LPC-HRas liver tumor cells .

first: Zhang

last: Li

first: Kun

last: Jiao

first: Yun

first: Guiqin

last: Xu

first: Zhaojuan

first: Lvzhu

last: Xiang

first: Zehong

first: Chen

first: You

last: Zuo

first: Ningqian

last: Zhen

first: Qiang

last: Xia

first: Yongzhong


title: Disruption of the Circadian Rhythm Is Exacerbated by Aging and Partially Restored by Time-restricted Feeding

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

summary: To characterize any differences in the effects of Circadian rhythm disorders (CRD) on mice of various ages, we selected young (8-week-old),  and aged (18-month-old) mice and created a model of CRD by modifying the light/dark cycle under which they were housed.

overall_design: We performed RNA sequencing of the colon, cecum, peripheral blood mononuclear cells (PBMCs), hypothalamus, and hippocampus of 8-week-old and 18-month-old CRD and CON mice.


title: CHD2 Regulates Neuron-glioma Interactions in Pediatric Glioma

city: New York

first: Zhiguo

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

summary: High-grade gliomas (HGG) are deadly diseases for both adult and pediatric patients. Recently, it has been shown that neuronal activity promotes the progression of multiple subgroups of HGG. However, epigenetic mechanisms that govern this process remain elusive. Here we report that the chromatin remodeler CHD2 regulates neuron-glioma interactions in diffuse midline glioma (DMG) characterized by onco-histone H3.1K27M. Depletion of CHD2 in H3.1K27M DMG cells compromises cell viability and neuron-to-glioma synaptic connections in vitro, neuron-induced proliferation of H3.1K27M HGG DMG cells in vitro and in vivo, activity-dependent calcium transients in vivo, and extends the survival of H3.1K27M DMG-bearing mice. Mechanistically, CHD2 coordinates with the transcription factor FOSL1 to control the expression of axon-guidance and synaptic genes in H3.1K27M DMG cells. Together, our study reveals a mechanism whereby CHD2 controls the intrinsic gene program of the H3.1K27M DMG subtype, which in turn regulates the tumor growth-promoting interactions of glioma cells with neurons.

overall_design: The CUT&RUN experiments were conducted in WT, CHD2 KO, FOSL1 KO SU-DIPG-IV cells. The markers performed by CUT&RUN methods in DIPG cells included CHD2, FOSL1, H3K4me3, H3K27Ac and H3K27me3.  For the regulation of gene expression, we performed total RNA-seq experiments in WT, CHD2 KO SU-DIPG-IV/SU-DIPG-XVII/SU-DIPG-XXXVI, FOSL1 KO SU-DIPG-IV cells.

first: Xu

first: Shoufu

last: Duan


title: Radiation-induced upregulation of FGL1 promotes esophageal squamous cell carcinoma metastasis via IMPDH1

city: Xi’an

first: Shan

last: Huang

address: No.157, Xi Wu Road

institute: The Second Afﬁliated Hospital of Xi’an Jiaotong University

summary: This study investigates the role of fibrinogen-like protein 1 (FGL1) in driving ESCC cells

overall_design: Comprehensive RNA sequencing and functional experiments elucidated the intricate mechanism associated with FGL1.

first: Jiayi


title: In vivo perturbomics identifies CALHM2 as a checkpoint of NK cell therapy [scRNA-Seq]

first: Sidi

last: Chen

overall_design: NK cells were isolated from the spleens of C57BL/6J mice and expanded through in vitro culture. Syngeneic mouse models of melanoma and breast cancer models were established with subcutaneous injections of native B16F10 or fat pad injections of E0771 cells into C57BL/6J mice. NK cells were adoptively transferred into tumor burden mice via i.v. tail vein injections. At 7- and 15-days post NK cell transferred, one mouse was sacrificed from each tumor model. Splenocytes from spleens and tumors were collected from mice.

first: Paul

last: Renauer

first: Lei

last: Peng

last: Sidi


title: Tudor domain containing protein 5-like(Tdrd5l) identifies a novel germline body and regulates maternal RNAs during oogenesis

city: Balitmore

first: Mark

last: Van Doren

state: Maryland

address: 3400 N Charles street, Mudd Hall

department: Biology

institute: Johns Hopkins University

summary: In this study we show that Drosophila Tudor-domain containing protein 5-like (Tdrd5l) is important for post-transcriptional regulation of maternal mRNAs. Tdrd5l localizes to a novel of body in the germline and interacts with post-transcriptional regulation pathways. In mutant females we observe accumulation of Gurken and its activator Orb in nurse cells during oogenesis. Decreased orb function suppresses the Tdrd5l-mutant phenotype, indicating that this is a primary defect in these mutants.

overall_design: Gene expression comparison between Tdrd5l mutant testes and control testes. Additional gene expression analysis between Tdrd5l mutant ovaries and control ovaries

first: Caitlin

last: Pozmanter

first: Leif

last: Benner

first: Sydney

last: Kelly

first: Harrison

last: Curnutte


title: Drosophila models of dementia uncover shared and specific targets of TDP-43 proteinopathy across ALS and FTD relevant circuits

city: Hershey

first: Daniela

last: Zarnescu

address: 500 University Drive Crescent Building C4605

department: Cellular and Molecular Physiology

institute: Penn State College of Medicine

summary: We developed a fly model of TDP-43 driven dementia by over-expressing YFP tagged human TDP-43 in the mushroom body neurons of the fly brain

overall_design: We used GFP immunoprecipitation to pull down TDP-43 complexes from fly heads,  obtained RNA-seq from total input and immunoprecipitated fractions, and then compared expression to identify genes enriched in the TDP-43 fraction

first: E

last: Alsop

first: R

last: Godfrey

last: Bjork


title: Transcriptomic Responses of Cannabis sativa L. to Trichoderma hamatum Treated under Drought Conditions

status: Public on May 08 2024

city: Chuncheon-si

first: Byeong-Ryeol

last: Ryu

state: Gangwon-state

address: 1, Kangwondaehak-gil

department: Department of Bio-Health Convergence

country: South Korea

institute: Kangwon National Univsersity

summary: Cannabis sativa L., which has been reclassified as an agronomic crop, has experienced an increase in cultivation. Its interactions with a variety of environmental stressors have been extensively studied. However, the mechanisms of recovery through fungal associations remain underexplored. Trichoderma hamatum, known for its role as a biological agent, enhances plant growth and provides antagonistic defense against pathogenic microbes. This meta-dataset aims to investigate whether Th can enhance drought resistance in a Cannabis plants.

overall_design: To investigate how Trichoderma hamatum treatment manifests drought resistance mediation activities at the transcriptome level in Cannabis sativa L., adult Cannabis plants were used. Drought treatment was achieved by halting irrigation, a stress method that hemp can experience in field cultivation. Trichoderma hamatum was isolated from the soil of the cannabis cultivation area using Trichoderma Selective Medium, and then separated into a single fungal strain through the hyphal tip separation process. The fungal strain's TEF1, ITS, and Large Subunit rRNA were sequenced, and identified using NCBI BLASTn. The experimental groups were designed under four different conditions: control, drought stress, T. hamatum single treatment, and a combination of drought stress and T. hamatum treatment.

first: Ryu

last: Byeong-Ryeol

first: Park

last: Sang-Hyuck

first: Gim

last: Gyeong-Ju

first: Shin

last: Ye-Rim

first: Kim

last: Min-Jun

first: Kang

last: Min-Ji

first: Kwon

last: Tae-Hyung

first: Lim

last: Jung-Dae


title: ReDD: RNA editing detection by direct RNA sequencing and deep learning

city: Ann Arbor

first: Kin Fai

last: Au

state: MI

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

summary: Many previous studies, including the Next Generation Sequencing (NGS)-based ones, have shown the critical roles of RNA editing in biomedicine. Direct RNA sequencing emerges as another powerful technique to advance the understanding of RNA editing by new paradigms, especially in single-molecule and long-range characterization. The urgent gap is the accurate and robust identification of RNA editing at the single-molecule and single-nucleotide resolution from direct RNA sequencing. This is challenging due to the inherent nature of the context-dependence on the raw signals, which requires enormous training data with considerable diversity. Here we propose two coupled measures to address them: 1) an abductive deep learning strategy implemented as the software ReDD fully utilizes the widely accessible NGS-based RNA editing data as indirect labels of direct RNA sequencing to achieve the detection at the single-molecule level; 2) a cloud-based platform Argo-ReDD serves as a central database for assembling large and diverse data from the community to continuously train the abductive deep learning model, which also meets the community demand of a user-friendly way to perform RNA editing analyses, such as co-occurrence analysis, quantitative analysis and gene isoform-resolved analysis, based on the specific information from direct RNA sequencing.

overall_design:
We generated definitive endoderm and pharyngeal endoderm, and primordial germ cell-like cells from human ESC, using the in vitro differentiation systems we have recently developed. We also generated HEK293T ADAR1(E912A/E912A) cells using the E912A mutation method we have previously developed.We further transfected the E912A cells with the ADAR2 gRNAs of "TGTAGAAACACTTATCACCT" and "ACCATCTTTACCTGGCAGTT", and selected single clone cells to create the HEK293T double mutant cells with ADAR1(E912A/E912A) and ADAR2(-/-).
We generate long-read RNA-seq data using Oxford Nanopore Technologies (ONT) direct RNA sequencing (dRNA-ONT) protocols with one replicate and short-read RNA-seq data using Illumina with three replicates.
We detects the A-to-I RNA editing sites in HEK293T, H1 and H9 cells by ReDD, our in-house software on the direct RNA sequencing data.

first: Yunhao

last: Wang

first: Roberta

last: Sala

first: Andrea

last: Cipriano

first: Vittorio

last: Sebastiano

first: Shi-Bin

last: Hu

first: Jin

last: Li

first: Kin


title: Effects of estradiol, progesterone, prolactin and oxytocin on miRNA levels in T47D human breast cells

city: Laval

first: Isabelle

last: Plante

state: Québec

address: 531 boul Des prairies

department: Armand-Frappier Santé Biotechnologie

country: Canada

institute: INRS

summary: The aim of the project was to analyse the levels of miRNA upon hormonal treatment in T47D breast cells

overall_design: T47D cells were obtained from ATCC and maintained in RPMI-1640 media without phenol red, supplemented with 10% fetal bovine serum (FBS). At 60 to 70% confluency, media was replaced with media containing hormone-stripped FBS for 16 hours. Then, cells were exposed to estradiol (10 nM, 24 hours), progesterone (10 nM, 6 hours), prolactin (8.7 nM (200 ng/mL), 8 hours) and oxytocin (100 nM, 24 hours for oxytocin) or the appropriate vehicle (0.1% ethanol for estrogen and progesterone, 4 mM hydrochloric acid for prolactin and nuclease-free water for oxytocin). miRNA were extracted and sequenced.

first: Cameron

last: Confuorti

first: Maritza

last: Jaramillo


title: Cell-type and sex-specific rhythmic gene expression in the nucleus accumbens

city: Pittsburgh

first: Colleen

middle: A.

last: McClung

address: 450 Technology Drive

institute: University of Pittsburgh

summary: Circadian rhythms are critical for human health and are highly conserved across species. Disruptions in these rhythms contribute to many diseases, including psychiatric disorders. Previous results suggest that circadian genes modulate behavior through specific cell types in the nucleus accumbens (NAc), particularly dopamine D1-expressing medium spiny neurons (MSNs). However, diurnal rhythms in transcript expression have not been investigated in NAc MSNs. In this study we identified and characterized rhythmic transcripts in D1- and D2-expressing neurons and compared rhythmicity results to homogenate as well as astrocyte samples taken from the NAc of male and female mice. We find that all cell types have transcripts with diurnal rhythms and that top rhythmic transcripts are largely core clock genes, which peak at approximately the same time of day in each cell type and sex. While clock-controlled rhythmic transcripts are enriched for protein regulation pathways across cell type, cell signaling and signal transduction related processes are most commonly enriched in MSNs. In contrast to core clock genes, these clock-controlled rhythmic transcripts tend to reach their peak in expression about 2 hours later in females than males, suggesting diurnal rhythms in reward may be delayed in females. We also find sex differences in pathway enrichment for rhythmic transcripts peaking at different times of day. Protein folding and immune responses are enriched in transcripts that peak in the dark phase, while metabolic processes are primarily enriched in transcripts that peak in the light phase. Importantly, we also find that several classic markers used to categorize MSNs are rhythmic in the NAc. This is critical since the use of rhythmic markers could lead to over- or under-enrichment of targeted cell types depending on the time at which they are sampled. This study greatly expands our knowledge of how individual cell types contribute to rhythms in the NAc.

overall_design: To sequence actively translated mRNAs, male and female Drd1- and A2a-Cre mice were crossed to RiboTag mice31, expressing a Cre-inducible HA-Rpl22. C57BL/6J mice were used to generate homogenate samples. Previously generated data was used for astrocyte analysis28 wherein the GFP-inducible alternative to HA-Rpl22, Rpl10a, was crossed to Aldh1l1-eGFP mice. Mice were over 10 weeks old and maintained on a 12:12 light-dark (LD) schedule with lights on (Zeitgeber Time (ZT0)) at 0700. Food and water were provided ad libitum and procedures were approved by the University of Pittsburgh IACUC. NAc tissue was collected from male and female mice pseudo-randomly across 6 times of day (ZT2,6,10,14,18,22). As described previously28,31, co-immunoprecipitation was used to isolate cell-type specific ribosome-associated mRNAs. Final eluted homogenate and D1 or D2 specific RNA was used for sequencing. Following quality/integrity assessment, libraries were prepared and sequenced (blinded samples). mRNA (D1/D2) or total (homogenate) RNA sequencing was performed (n>3) using the NextSeq 500 platform (Illumina) at the University of Pittsburgh Health Sciences Sequencing Core. After preprocessing and filtering of sequencing data, a parametric cosinor model32 assuming a sinusoidal relationship between the gene expression level and ZT was used to detect rhythmicity (Supp.Table.1). Six total samples were excluded, due to insufficient RNA, library preparation or raw counts.

first: Lauren

middle: M

last: DePoy

first: Kaitlyn

last: Petersen

first: Wei

last: Zong

first: Ross

last: Matthaei

first: Kyle

middle: D

last: Ketchesin

first: RuoFei

last: Yin

first: Megan

last: Perez

first: Chelsea

last: Vadnie

first: Darius

last: Becker-Krail

first: Madeline

middle: R

last: Scott

first: George

last: Tseng


title: Therapeutic targeting of PKM2 ameliorates NASH fibrosis progression in a macrophage-specific and liver-specific manner

city: Guangzhou

first: Liu

last: Junli

state: Guangdong

address: Guangzhou, Jinan university

institute: jinan university

summary: Nonalcoholic steatohepatitis (NASH) might soon become the leading cause of end-stage liver disease worldwide with limited treatment options. Liver fibrosis, driven by chronic inflammation and hepatic stellate cells (HSCs) activation, critically determines morbidity and mortality in patients with NASH. Pyruvate kinase M2 (PKM2) is involved in immune activation and inflammatory liver diseases; however, its role and therapeutic potential in NASH fibrosis remain largely unexplored. By bioinformatic screening and analysis of human and murine NASH livers, we found that PKM2 was specifically upregulated in non-parenchymal cells (NPCs) in fibrotic NASH livers, especially in macrophages. Macrophage-specific Pkm2 knockout (Pkm2fl/flLysMCre) significantly ameliorated hepatic inflammation and fibrosis severity in three distinct NASH models induced by methionine–choline-deficient (MCD) diet, high-fat high-cholesterol (HFHC) diet and western diet plus weekly carbon tetrachloride injection (WD/CCl4). Single-cell transcriptomic analysis indicated that deletion of PKM2 in macrophage reduced profibrotic Ly6Chigh macrophage infiltration. Mechanistically, PKM2-dependent glycolysis promotes NLRP3 activation in proinflammatory macrophages, thus inducing HSCs activation and fibrogenesis. Pharmacological PKM2 agonist efficiently attenuated the profibrotic crosstalk between macrophages and HSCs in vitro and in vivo. Translationally, ablation of PKM2 in NPCs by cholesterol-conjugated heteroduplex oligonucleotides, a novel oligonucleotide drug that preferentially accumulated in the liver, dose-dependently reversed NASH fibrosis without observable hepatotoxicity. Our study highlights the pivotal role of macrophage PKM2 in advancing NASH fibrogenesis. Therapeutic modulation of PKM2 in a macrophage-specific or liver-specific fashion may serve as a novel strategy to combat NASH fibrosis.

overall_design: Liver non-parenchymal cells from PKM2ΔMAC and PKM2FL/FL mice fed with MCD diet for 8 weeks were subjected to scRNA-seq

first: Hengdong

last: Qu

first: Di

last: Zhang

first: Junli

last: Liu

first: Jieping

last: Deng

first: Ruoyan

last: Xie

first: Keke

first: Hongmei

first: Ping

last: Tao

first: Genshu

last: Wang

first: Jian

last: Sun

first: Oscar

middle: J

last: Luo

first: Chen

first: Wencai

last: Ye

last: Hong


title: The oncolytic adenovirus Delta-24-RGD in combination with ONC201 induces a potent antitumor response in pediatric high-grade and diffuse midline glioma models

city: Pamplona

first: Marta

middle: Maria

last: Alonso Roldán

state: Navarra

address: CIMA building , Pio XII 55

department: Dpt of Pediatrics

country: Spain

institute: University Hospital of Navarra

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

overall_design: Refer to individual Series


title: FOXO1 enhances CAR T cell stemness, metabolic fitness and efficacy [human_FOXO1_TCF7_OE_RNAseq]

city: Melbourne

first: Kevin

middle: C

last: sek

state: VIC

address: 305 Grattan Street

department: Cancer Immunology

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Investigating the transcriptional profile of human FOXO1 or TCF7 overexpressing α-lewisY CAR T cells

overall_design: Human anti-Lewis Y CAR T cells overexpressing  mCherry (control), FOXO1 or TCF7 were generated from healthy donor peripheral blood mononuclear cells (PBMC). Control, FOXO1 or TCF7  overexpressing CD8+ CAR T cells were assessed by RNA-Sequencing

first: Paul

last: Beavis

first: Phil

last: Darcy

last: Sek

first: Isabelle

last: Munoz


title: FOXO1 enhances CAR T cell stemness, metabolic fitness and efficacy [human_FOXO1OE_stimulation/rest_RNAseq]

summary: Investigating the transcriptional profile of human FOXO1 overexpressing α-lewisY CAR T cells after stimulation or after stimulation and rest

overall_design: Human anti-Lewis Y CAR T cells overexpressing FOXO1 or mCherry (control) were generated from healthy donor peripheral blood mononuclear cells (PBMC).Control or FOXO1- expressing CD8+ CAR T cells were assessed by RNA-Sequencing prior to stimulation, after 24 h activation with 0.1 μg/ml plate bound anti-Lewis Y  or after 7 days recovery post stimulation with anti-Lewis Y.


title: RNA sequencing comparison of B7-H3.TMIGD2 and B7-H3.CD28.4-1BB CAR-T cells to CD19.CD28.4-1BB CAR-T cells in vitro

city: Bronx

first: Christopher

last: Nishimura

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

summary: We generated a new B7-H3 CAR-T cell costimulatory domain using TMIGD2 and found it was as good or better than the CD28.4-1BB costimulatory domain. Little is known about TMIGD2 signaling, so we examined how each CAR signals individually compared to CD19.CD28.4-1BB control CAR-T cells.

overall_design: We cocultured CAR-T cells with HCC827 tumor cells for 24 hours. We purified T cells, isolated T cell RNA, and finally performed RNA sequencing

first: Phillip

last: Galbo Jr.

first: Deyou

last: Zheng

first: XingXing

last: Zang