title: Prenatal fetal head and placental gene expression in a mouse model of advanced maternal age

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

country: Poland

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

summary: Advanced maternal age is a risk factor for neurodevelopmental disorders in offspring. The present study aimed to investigate differences in placental and fetal head gene expression between old and young C57BL6/J female mice. Conceptuses were collected at E12.5 and processed for transcriptomic mRNA gene expression microarray analyses. The most significant differences between old and young females were found in gene expression of the fetal heads (398 differentially expressed genes, DEG) as compared with the placenta (51 DEG).

overall_design: Fetuses with their placentas were collected from pregnant BTBR and B6 advanced maternal aged females (42-65 weeks old, AMA) and young (10-23 weeks old, YMA) females. RNA for transcriptomic analyses was extracted from placentas and fetal heads following the manufacturers’ instructions. Total RNA extraction was conducted using the Universal RNA Purification Kit (Eurx, Poland), and included a DNase treatment (Eurx, Poland). The quantity and purity of isolated nucleic acids were validated using a Nanodrop 1000 spectrophotometer (Thermo Fisher Scientific, USA). RNA integrity of selected samples was additionally validated using a Bioanalyzer 2100 microcapillary electrophoresis device (Agilent, USA). Genome-wide transcriptomic analysis was performed using SurePrint G3 Mouse GE v2 8x60K microarrays (GPL21163, Agilent Technologies, USA) and Agilent Technologies Reagent Set according to the manufacturer’s instructions. 100 ng of RNA of each sample (n=4 fetuses and placentas per maternal age group per tissue, only male offspring were selected for microarrays purposes) was labeled using Low Input QuickAmp Labeling Kit One-Color (Agilent Technologies, USA) and hybridized on the microarrays according to the manufacturer’s protocol. Statistical analysis of raw data was carried out using the default protocol of the Partek Genomics Suite. Microarrays analyses were conducted in n=4 conceptuses per maternal age group, obtained from 4 different litter of old and young mothers.

first: Marta

middle: M

last: Ziętek

first: Aneta

last: Jaszczyk

first: Silvestre

last: Sampino

first: Joanna

last: Gościk


title: Effect of vehicle or drug treatment on gene expression in BxPC3 cell line

status: Public on Sep 26 2024

city: New York

first: Tiphaine

middle: Christiane

last: Martin

address: 1470 Madison Ave

department: Oncological Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

type: Expression profiling by high throughput sequencing

summary: To investigate the effect of mutant p53 Y220C acetylation in gene expression, we treated BxPC3 (p53Y220C/-) cell lines with either DMSO, or PK9328 or MS172.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DMSO vs MS172 treatment in BxPC3 cell line

first: Kabir

last: Md

first: Martin

last: Tiphaine


title: mRNAseq in control and siQk in mouse primary OPC cells

status: Public on Sep 27 2024

city: Niigata

first: Masato

last: Yano

address: 757, Ichibancho, Asahimachidori, Chuo-ku, Niigata-shi,

department: Division of Neurobiology and Anatomy

country: Japan

institute: Niigata University

summary: We sequenced mRNA from mouse primary OPC cells to compare gene expression level and alternative splicing events between 3 control and 3 siQk.

overall_design: mRNA profiles obtained from 3 different control and 3 siQk were generated by deep sequencing using Illumina NextSeq.

first: Yoshika

last: Hayakawa-Yano


title: Downregulation of MED12 via siRNA in prostate cancer cell lines (3’ tag DGE)

city: Innsbruck

first: Florian

last: Handle

address: Müllerstrasse 44

department: Institute of Pathology, Neuropathology and Molecular Pathology

country: Austria

institute: Medical University of Innsbruck

summary: The Mediator complex is a multi-subunit protein that modulates gene expression on a genome-wide scale. MED12 and cyclin-dependent kinase 8 (CDK8) or its paralog CDK19 are components of its kinase module that regulate the proliferation of prostate cancer cells. In this study, we investigated how MED12 and CDK8/19 influence cancer-driven processes in prostate cancer cell lines, focusing on AR activity and enzalutamide resistance.

overall_design: To investigate the relevance of MED12 in enzalutamide sensitive and resistant prostate cancer cells, we performed siRNA mediated knockdown and analyzed the response using high-throughput 3’ tag differential gene expression analysis.

first: Chiara

last: Andofi

first: Zoran

last: Culig


title: Hematopoietic cells emerging from hemogenic endothelium exhibit lineage-specific oxidative stress responses

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we sought to understand how low oxygen levels affect hematopoietic populations deriving from HE. We investigated the role of NRF2, glutathione metabolism and canonical/non-canonical TCA cycle pathways in specifying erythroid and non-erythroid populations. Here, we uncover striking differences in how oxidative stress affects and is dealt with by different hematopoietic populations following their emergence from HE.

overall_design: We performed a Multiome analysis with combined single-cell RNAseq and ATAC-seq on HE-derived populations following 72 hours of subculture at 4% O2 (termed hypoxia for simplicity) or ambient oxygen levels (normoxia). Samples are HE-derived cells cultured in hypoxia (H) or normoxia (N).

first: Leal

last: Oburoglu

first: Harmke

last: Biezeman


title: Twin study identifies early immunological and metabolic dysregulation of CD8+ T cells in multiple sclerosis

city: Planegg

first: Vladyslav

last: Kavaka

address: Großhaderner Str. 9

country: Germany

institute: Institute for Clinical Neuroimmunology, Biomedical Center, University Hospital of the Ludwig-Maximilians University Munich

summary: Multiple sclerosis (MS) is an inflammatory neurological disease of the central nervous system with a subclinical phase preceding frank neuroinflammation. CD8+ T cells are abundant within MS lesions, but their potential role in disease pathology remains unclear. Using high-throughput single-cell RNA sequencing and single-cell T cell receptor analysis, we compared CD8+ T cell clones from the blood and cerebrospinal fluid (CSF) of monozygotic twin pairs in which the co-twin had either no or subclinical neuroinflammation (SCNI). We identified peripheral MS-associated immunological and metabolic alterations indicative of an enhanced migratory, pro-inflammatory, and activated CD8+ T cell phenotype, which was also evident in co-twins with SCNI and in an independent validation cohort of people with MS (pwMS). Together, our in-depth single-cell analysis indicates a disease-driving pro-inflammatory role of infiltrating CD8+ T cells and identifies potential immunological and metabolic therapeutic targets in both prodromal and definitive stages of the disease.

overall_design:
CD8+ T cells from PBMCs of the MS twin cohort (n = 12; 6 healthy twins, 6 twins with SCNI, and 12 twins with MS; 193,771 cells) and the validation cohort (n = 17; 5 individuals with IIH and 12 individuals with MS; 89,859 cells) were isolated via FACS and processed using the 10X manufacturer's protocol to generate single-cell transcriptome and TCR libraries. The corresponding TCR sequences are included within the metadata of the uploaded objects. --------------------- Author state: Fastq raw data files from humans are not updated due to data protection concerns.
---------------------
Author states that fastq raw data files from humans are not provided due to data protection concerns.

first: Eduardo

last: Beltrán


title: Neoadjuvant cabozantinib restores CD8+ T cells in patients with locally advanced non-metastatic clear cell renal cell carcinoma: a phase 2 trial

city: Atlanta

first: Donald

last: McGuire

state: GA

address: 1462 Clifton Road room 412

institute: Emory University School of Medicine

summary: Cabozantinib is an oral multikinase inhibitor approved for treatment in metastatic renal cell carcinoma (RCC). We hypothesized that neoadjuvant cabozantinib could downstage localized tumors, facilitating partial nephrectomy, and facilitating surgery in patients with locally advanced tumors that would require significant adjacent organ resection.  We, therefore, conducted a phase 2, single-arm trial of cabozantinib treatment for 12 weeks in 17 patients with locally advanced biopsy-proven non-metastatic clear cell RCC before surgical resection. Six patients (35%) experienced a partial response, and 11 patients (65%) had stable disease. We identified that plasma cell-free DNA (cfDNA), VEGF, c-MET, Gas6, and AXL were significantly increased while VEGFR2 decreased during cabozantinib treatments. CD8+ T cells were activated in the blood, expressing the proliferation marker Ki67 and activation markers HLA-DR and CD38. Cabozantinib treatment depleted myeloid populations acutely. Importantly, immune niches made up of the stem-like CD8+ T cells and antigen presenting cells were increased in every patient. These data suggest that cabozantinib treatment was clinically active and safe in the neoadjuvant setting in patients with locally advanced non-metastatic clear cell RCC and activated the anti-tumor CD8+ T cell response. The trial is registered at ClinicalTrials.gov under registration no. NCT04022343.

overall_design: We conducted a phase 2, single-arm trial of cabozantinib treatment for 12 weeks in 17 patients with locally advanced biopsy-proven non-metastatic clear cell RCC before surgical resection. Patients’ tumor samples from surgery were formalin-fixed paraffin embedded (FFPE). Tumor areas were macrodissected from the slides for RNA-Seq.

first: Mehmet

middle: A

last: Bilen

first: BaoHan

middle: T

last: Vo

first: Yuan

last: Liu

first: Rachel

last: Greenwald

first: Amir

middle: H

last: Davarpanah

first: Rakesh

last: Shiradkar

first: Liping

last: Li

first: Bassel

last: Nazha

first: Jacqueline

last: Brown

first: Sierra

last: Williams

first: Wilena

last: Session

first: Greta

last: Russler

first: Sarah

last: Caulfield

first: Shreyas

middle: S

last: Joshi

first: Vikram

last: Narayan

first: Christopher

middle: P

last: Filson

first: Kenneth

last: Ogan

first: Omer

last: Kucuk

first: Bradley

middle: C

last: Carthon

first: Luke

middle: D

last: Balzo

first: Athena

last: Cohen

first: Adriana

last: Boyanton

first: Nataliya

last: Prokhnevska

first: Maria

last: Cardenas

first: Ewelina

last: Sobierajska

first: Caroline

last: Jansen

first: Dattatraya

last: Patil

first: Edouard

last: Nicaise

first: Adeboye

middle: O

last: Osunkoya

first: Haydn

last: Kissick

first: Viraj

last: Master


title: Inhibition of CDK8/CDK19 with the small molecule inhibitor SEL120-34A in prostate cancer cell lines (3’ tag DGE)

first: Florian

last: Handle

overall_design: To investigate if CDK8/CDK19 inhibition has similar effects as downregulation of MED12 in enzalutamide sensitive and resistant prostate cancer cells, we treated the cells with SEL120-34A and analyzed the response using high-throughput 3’ tag differential gene expression analysis.

first: Chiara

last: Andofi

first: Zoran

last: Culig


title: Effect of oral gavage of Fusobacterium nucleatum on the development of the placenta in mice

city: Guangzhou

first: Shanshui

last: Zeng

address: Bsogao Road

country: China

institute: Southern medical university

summary: Placental Fusobacterium nucleatum localization may be associated with pregnancy complications, including preeclampsia (PE), but nothing is known about its specific pathobiology. We aimed to perform transcriptomic analysis of the placentas of mice that were orally gavaged with Fusobacterium nucleatum or saline during pregnancy to further elucidate placental dysfunction in these conditions.

overall_design: For F. nucleatum-induced PE model, female mice were first gavaged with antibiotics combination (vancomycin, 100 mg/kg; neomycin sulfate, metronidazole and ampicillin, 200 mg/kg) for five consecutive days to remove gut microbiota, and then gavaged with 10^8 colony forming unit (CFU) of F. nucleatum every day for one-week, followed by mating. Next, pregnant mice received everyday gavage of F. nucleatum (10^8 CFU) until GD17.5. PBS was used as blank control.

first: Bingyu

last: Li

first: Dongxin

last: Zhang

first: Hongwei

last: Zhou


title: Downregulation of MED12 via siRNA in 22Rv1 prostate cancer cells (full transcriptome)

overall_design: To investigate the relevance of MED12 in de novo enzalutamide resistant 22Rv1 cells, we performed siRNA mediated knockdown and analyzed the response using differential gene expression analysis.


title: Downregulation of MED12 via siRNA in SPHEROIDS derived from prostate cancer cell lines (3’ tag DGE)

overall_design: To investigate the relevance of MED12 in spheroids derived from enzalutamide sensitive and resistant prostate cancer cells, we performed siRNA mediated knockdown, generated spheroids and analyzed the response using high throughput 3' tag differential gene expression analysis.


title: Expanded ATXN1 alters transcription and calcium signaling in SCA1 human motor neurons derived from induced pluripotent stem cells

city: Minneapolis

first: Ying

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Dysfunction and loss of motor neurons (MNs) in the brain stem and spinal cord is hypothesized to contribute to premature lethality in spinocerebellar ataxia type 1 (SCA1) by affecting the swallowing and breathing. Despite the usefulness of SCA1 mouse models in studying pathogenesis, they have important limitations including species differences and extreme size of repeats in comparison to the repeat length present in adult SCA1 patients. Thus, to study early stages of SCA1 pathogenesis that have been shown to be most therapeutically effective in human cells, we have created a human motor neuron model of SCA1. We differentiated MNs patient and unaffected control-donated iPSCs to assess the effect of mutant ATXN1 on this vulnerable cell population with the goal to provide insight to human cellular pathology in this cell type and facilitate the development of therapies to limit pathogenesis in SCA1.

overall_design: To investigate molecular mechanisms underlying SCA1 pathogenesis, we used RNA sequencing of iPSC-derived MN progenitors (pMNs) and MNs to investigate transcriptional changes.

first: Carrie

last: Sheeler

first: Marija

last: Cvetanovic


title: Targeting the CLK2/SRSF9 splicing axis in prostate cancer leads to decreased ARV7 expression in an rs5918762 allele-dependent manner (ONT long read sequencing)

summary: The  Cdc2-like kinase (CLK)-family is a regulator of the splicing process. Here, we report the effect of Lorecivivint (SM04690), a CLK/DYRK inhibitor,  on alternative splicing in the prostate cancer cell line 22Rv1. Lorecivivint treatment lead to impaired growth and  disruption of several oncogenic pathways, including the androgen response, MYC, and Wnt/β-catenin hallmark pathways. Taken together, this data shows that alternative splicing is a pivotal process in prostate cancer and is suitable to be targeted.

overall_design: Gene expression analysis of long-read RNA-seq data of 22Rv1 prostate cancer cells treated with 50 nM Lorecivivnt for three days vs. vehicle (DMSO).

first: Jasper

last: Van Goubergen

first: Frédéric

last: R Santer


title: Targeting the CLK2/SRSF9 splicing axis in prostate cancer leads to decreased ARV7 expression in an rs5918762 allele-dependent manner

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

overall_design: Refer to individual Series


title: Targeting the CLK2/SRSF9 splicing axis in prostate cancer leads to decreased ARV7 expression in an rs5918762 allele-dependent manner (Illumina short read)

overall_design: Differential gene expression analysis of short-read RNA-seq data of 22Rv1 prostate cancer cells treated with 50 nM Lorecivivnt for three days vs. vehicle (DMSO).

middle: R

last: Santer


title: Gene expression profile of human monocyte-derived macrophage stimulated with CRP (20 microg/mL)

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

institute: Graduate School of Medical Sciences, Kumamoto University

summary: Macrophages are immune cells in contributing to several kinds of diseases, and activation status of macrophages are considered to be regulated by several stimulations.

overall_design: To test the gene expression change in activated macrophages, human monocyte-derived macrophages were stimulated with CRP (20 microg/mL). The mRNA expression in control, stimulated, infected macrophages were analysed. Macrophages (200000 cells/well in 6-well plate) were stimulated with CRP. Based culture madium was DMEM/HamF12 medium supplemented with 10% FBS.


title: Gene expression analysis of enzalutamide resistant MDA PCa 2b prostate cancer cells

summary: MDA PCa 2b is an androgen-responsive, AR-positive prostate cancer cell line.  Here, we report the generation of an Enzalutamide-resistant derivative, MDA PCa 2b-EnzaR. Gene expression of MDA PCa 2b-EnzaR compared to its parental counterpart were assessed by short-read RNA sequencing.

overall_design: Differential gene expression analysis of RNA-seq data from enzalutamide sensitive (vehicle treated) and enzalutamide resistant MDA PCa 2b prostate cancer cells.


title: Glutaminase-1 Inhibition Alleviates Senescence of Wharton’s Jelly-derived Mesenchymal Stem Cells via Senolysis.

city: seoul

first: Eun Joo

last: Lee

address: 81, Irwon-ro

country: South Korea

institute: encellinc

summary:
we attempted to identify the genetic changes in the remaining MSCs after BPTES treatment and identified senescence-related candidate genes that recovered after BPTES treatment.
The transcriptomes of U-MSCs and rS-MSCs were analyzed to determine the genetic significance of replicative senescence in WJ-MSCs

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for U-MSCs and rS-MSCs with BPTES treatment
Comparative gene expression profiling analysis of RNA-seq data for 3lots of U-MSCs and rS-MSCs

first: Eun

middle: J

first: Sun

last: Kim


title: The effect of Uphill and Downhill treadmill Running on the transcription of peripheral blood mononuclear cells in young male SD rats

city: Ji’nan ,China

first: jie

middle: -yong

last: yang

address: 山东省济南市世纪大道10600号

institute: Human Movement Science

summary:
Using  Affymetrix GeneChip® Rat Genome 230 2.0 Array chip to screen the effect of Uphill and Downhill treadmill exercise on the key genes that affect bone mass in the peripheral blood mononuclear cells (PBMCs) of  young male  rats.
Thirty-six male Sprague-Dawley rats were randomly assigned to a control group and both running groups of uphill and downhill (n = 12). Bone mineral density (BMD), bone mineral content (BMC) and bone microstructure of the femur were measured. PBMCs were extracted and the gene expression profile of mRNA detected.Gene Ontology and KEGG pathway analysis were used.The results showed exercise mainly activated the biological processes and cellular pathways involved in immune, inflammation and osteoclast differentiation.

overall_design: the effect of Uphill and Downhill treadmill exercise on the mRNA profiles  in the peripheral blood mononuclear cells (PBMCs) of young male SD rats.

first: Jie-yong

last: Yang


title: Effect of abrogated DNA-binding of thyroid hormone receptor alpha on the gene expression in CD25- CD4+ naive T cells and CD25+ CD4+ regulatory T cells

city: Essen

first: Christina

last: Wenzek

address: Hufelandstr. 55

department: Department of Endocrinology

institute: University Hospital Essen, University Duisburg-Essen

summary: Thyroid hormones (TH) have emerged as important regulators of the immune system, mediating pro- and anti-inflammatory actions. However, the role of TH in T cells, which are central players of protective immunity has remained largely elusive. To address the impact TH on CD4 T cell immunity, we used RNA-sequencing analysis of naive CD4 T cells and Treg isolated from spleens of mice with a mutation in the DNA binding domain of TRα (TRαGS) or WT littermates. In absence of canonical TRα signaling gene expression profile of naive CD4 T cells was altered with enriched differential expression of genes involved in T cell homeostasis and migration. In TRαGS Treg increased expression of activation and migratory markers was found. Moreover, abrogated canonical TRα signaling was also related to changes in NFκB signaling pathway in Treg, which has been previously related to Treg induction and function. Hence, our findings provide new insight in the effect of canonical TRα singlaing in CD4 T cell immunity.

overall_design: To investigate the impact of TRα signaling on differentiation and function of Treg we isolated CD25- CD4+ naive T cells as well as CD25+ CD4+ Treg from spleen of TRαGS mice and WT littermates by FACS. Gene expression profile of isolated cells was determined and gene expression profiles of genotypes wihtin both T cell subsets were compared.

first: Devon

last: Siemes

first: Sebastian

middle: G

last: Hönes

first: Lars

last: Moeller

first: Daniel

last: Engel

first: Astrid

last: Westendorf

first: Dagmar

last: Führer

first: Ludger

last: Klein-Hitpass


title: Controlling DNA-deletionsizes in CRISPR-edited human T cells by the strength of TCR stimulation and pifithrin-α

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: CRISPR/Cas9-engineered human T cells hold great promise in improving T cell effector functions for adoptive T cell therapies. To ensure safety during CRISPR/Cas9-editing optimized gRNAs, novel variants or prediction tools for indel outcomes have been developed. Still, several reports describe the occurrence of chromosomal truncations or loss of large DNA fragments of up to several kbs after CRISPR/Cas9 editing. So far, the measures to increase the safety of T cell products focused on the CRISPR Cas9 system. However, T cell-intrinsic features such as their massive expansion after TCR stimulation have not been taken into consideration. Here, we describe driving forces of indel formation in primary human T cells. Increased T cell activation and proliferation speed correlate with higher knock-out rates and larger deletions. Editing of non-activated T cells reduces the risk of unwanted large deletions but with the downside of reduced knock-out efficiencies. An alternative strategy to reduce the risk of large deletions is the addition of the small molecule pifithrin-α after CRISPR/Cas9 editing. Pifithrin-α treatment results in a smaller, more defined deletion pattern. PFT-a furthermore reduces the risk of unwanted chromosomal translocations and aneuploidy while maintaining the functionality of CRISPR-engineered T cells. Controlling T cell activation and the addition of pifithrin-α are easily accessible strategies for safer CRISPR/Cas9-engineering for adoptive T cell therapies.

overall_design: CD4 and PDCD1 gene loci were simultaneously targeted with Cas9 RNPs in activated and non-activated T cells. Genotoxicity was assesed via CAST-Seq.

first: Laurenz

last: Ursch

first: Jule

last: Müschen

first: Julia

last: Ritter

first: Kathrin

last: Schumann

last: Klermund

first: Toni

last: Cathomen


title: Enhancer activation from transposable elements in extrachromosomal DNA

status: Public on Sep 25 2024

city: Stanford

first: Matthew

last: Jones

state: MA

address: 500 Main Street (Building 76)

department: Biology

institute: Massachusetts Institute of Technology

summary: Extrachromosomal DNA (ecDNA) is a hallmark of aggressive cancer, contributing to both oncogene amplification and tumor heterogeneity. Here, we used Hi-C, super-resolution imaging, and long-read sequencing to explore the nuclear architecture of MYC-amplified ecDNA in colorectal cancer cells. Intriguingly, we observed frequent spatial proximity between ecDNA and 68 repetitive elements which we called ecDNA-interacting elements or EIEs. To characterize a potential regulatory role of EIEs, we focused on a fragment of the L1M4a1#LINE/L1 which we found to be co-amplified with MYC on ecDNA, gaining enhancer-associated chromatin marks in contrast to its normally silenced state. This EIE, in particular, existed as a naturally occurring structural variant upstream of MYC, gaining oncogenic potential in the transcriptionally permissive ecDNA environment.  This EIE sequence is sufficient to enhance MYC expression and is required for cancer cell fitness. These findings suggest that silent repetitive genomic elements can be reactivated on ecDNA, leading to functional cooption and amplification. Repeat element activation on ecDNA represents a mechanism of accelerated evolution and tumor heterogeneity and may have diagnostic and therapeutic potential.

overall_design: To interrogate the conformational state of circular extrachromosomal DNA (ecDNA), we performed Hi-C on COLO 320DM colorectal cancer cells.

first: Katerina

last: Kraft

first: Sedona

middle: E

last: Murphy

first: Quanming

last: Shi

first: Aarohi

last: Bhargava-Shah

first: Christy

last: Luong

first: King

middle: L

last: Hung

first: Britney

last: He

first: Rui

last: Li

first: Seung

middle: K

last: Park

first: Natasha

last: Weiser

first: Jens

last: Luebeck

first: Vineet

last: Bafna

first: Jef

last: Boeke

first: Paul

last: Mischel

first: Alistair

middle: N

last: Boettiger

first: Howard

middle: Y

last: Chang


title: Upregulation of SNAP25 by HDAC inhibition ameliorates NPC disease phenotypes via autophagy induction

city: Seoul

first: SeungEun

last: Lee

address: 1 Gwanak-Ro, Gwanak-gu

department: Veterinary

institute: Seoul National University

summary: Niemann-Pick Type C disease (NPC) is a rare fatal neurodegenerative disorder caused by mutations in NPC1 and NPC2 gene leading to abnormal accumulation of unesterified cholesterol in lysosomes. There have been no available treatments and FDA approved drugs for treating NPC. SAHA, a HDAC inhibitor (HDACi), was shown to ameliorate NPC disease phenotypes and considered as a therapeutics candidate but its mechanism of action is not fully clarified yet. Here, we investigated whether SAHA and HNHA, a new derivative of SAHA, reduced cholesterol level and then performed NGS analysis for these two compounds in NPC-iNSCs. Intracellular trafficking, secretion, and vesicular transport factors were highly enriched by two compounds treatment in NPC-iNSCs. Notably, SNAP25, a subunit of SNARE complex was significantly upregulated. Since autophagic flux is impaired in NPC cells due to SNARE complex deficiency, we hypothesized that increasing SNAP25 could contribute to form autolysosomes. When SNAP25 was overexpressed in NPC cells, it compensated deficient Vamp8-SNAP29-STX17 complexes to Vamp8-SNAP25-STX17 complexes then it restores autolysosomes leading to reduce accumulated LC3, LAMP1a, and p62. Consistently, SNAP25 was upregulated by HDAC inhibitors treatment and recovered deficient autophagic flux in vitro, and in vivo. Therefore, upregulation of SNAP25 by HDAC inhibition ameliorated NPC phenotypic and behavioral disorder in 2D culture system and NPC-/- mouse model. These results demonstrated a key role of SNAP25 to ameliorate NPC disease phenotypes and provided HDAC inhibitors as new therapeutic candidates for NPC treatment

overall_design: NPC-iNSCs were treated with HDAC inhibitors, SAHA, HNHA  and analyzed. Whole transcriptome from each samples were performed as single-end 75 sequencing using NextSeq 500  (Illumina, Inc., USA).

first: Seung-Eun

first: Yooju

last: Jung


title: Evaluation of the evolution of aged vs young  lung tumor cells derived from ex vivo transformation

first: ZHUXUAN

last: LI

state: NY

address: 417 E 68th St

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: Aging is one of the most important risk factor for cancer. However, next to nothing is known about how the age of the cell of origin impacts the evolution of tumor cells. Here we interrogated the cell-intrinsic forces that drive the progression of aged vs young cell of origin for lung cancer by using ex vivo transformation approaches

overall_design: Normal type 2 alveolar epithelial cells from aged vs young Kras-LSL-G12D/+; Trp53 fl/fi; Rosa26-LSL-EGFP-Cas9 (KPCas9) mice were isolated by FACS and transformed ex vivo. These tumor cells were maintained in 3D culture (tumor organoid)  for 8 passages and samples from each passage, including untransformed alveolar organoids.

first: Xueqian

last: Zhuang

first: Simon

last: Joost

first: Tuomas

last: Tammela


title: Reduction in olfactory ability in aging Mitf mutant mice without evidence of neurodegeneration

city: Reykjavik

first: Thorarinn

last: Gudjonsson

address: Vatnsmyrarvegur 16

department: Faculty of Medicine

country: Iceland

institute: University of Iceland

summary: Age-related decline occurs in most brain structures and sensory systems. An illustrative case is olfaction, where the olfactory bulb (OB) undergoes deterioration with age, resulting in reduced olfactory ability. A decline in olfaction is also associated with early symptoms of neurodegenerative diseases, including Alzheimer’s disease (AD) and Parkinson’s disease (PD). However, the underlying reasons are unclear. The microphthalmia-associated transcription factor (MITF) is expressed in the projection neurons (PNs) of the OB – the mitral and tufted (M/T) cells. Primary M/T cells from Mitf mutant mice show hyperactivity, potentially attributed to reduced expression of a key potassium channel subunit, Kcnd3/Kv4.3. This influences intrinsic plasticity, an essential mechanism involving the non-synaptic regulation of neuronal activity. As neuronal hyperactivity often precedes neurodegenerative conditions, the current study aimed to determine whether the absence of Mitf has degenerative effects during aging. Aged Mitf mutant mice showed reduced olfactory ability without inflammation. However, an increase in the expression of potassium channel subunit genes in the OBs of aged Mitfmi-vga9/mi-vga9 mice suggests that during aging compensatory mechanisms lead to stabilization.

overall_design: To investigate differentially expressed genes in the olfactory bulb (OB) in the absence of Mitf, we performed RNA-seq analysis between aged Mitfmi-vga9/mi-vga9 (Mitf mutant) and C57BL/6J (WT) OBs. We then compared three aged Mitf mutant OBs to WT OBs.

first: Mechmet

last: Fatich

first: Steingrímsson

last: Eiríkur

first: Petersen

last: Pétur Henry


title: TGF-β and RAS jointly unmask primed enhancers to drive metastasis

first: Jun Ho

institute: MSKCC

first: Richard

last: Koche

first: Joan

last: Massagué


title: The gene expression profiling among normal chondrocyte, osteoarthritis chondrocyte and chondrosarcoma

city: Taichung

first: Ya

middle: Huey

last: Chen

address: No. 100號, Section 1, Jingmao Road, Beitun District, Taichung City, 406

department: Cancer Center

country: Taiwan

institute: China Medical University

summary: To investigate the gene expression profiling in bone diseases including osteoathritis (OA) and bone cancer (chondrosarcoma), different chondrocytes were isolated and assessed. For OA, the paired normal and OA chondrocytes were isolated from patient with total knee replacement surgery.  Identification and delineation of dys-regulated genes between normal and OA chondrocytes and the regulatory mechanisms may provide the opportunity to treat OA. Also, the comparison with normal chondrocyte and chondrosarcoma cell lline (JJ012) gene expression profiling to identify the novel targets for chondrosarcoma therapies.

overall_design: Primary isolation of normal and OA chondrocytes from cartilages of OA patient with total knee replacement surgery. Chondrosarcoma cell line, JJ012, was  maintain in the sutiable medium for the further studies. These three cells cDNA microarray was performed and analyzed.

first: Ya-Huey

first: Chiao-Chen

last: Chung


title: Transcriptomic analyses reveal the effects of herbicides on the mycelium of Morchella sextelata

city: Lanzhou

first: Yongxiang

last: Dang

state: Gansu province

address: Peili street

institute: Northwest Normal University

summary: Morchella sextelata, recognized for its medicinal properties and distinctive taste, is a highly valued edible mushroom. Despite its commercial importance, the mushroom's susceptibility to environmental factors and its reactions to herbicides commonly used in cultivation have not been extensively studied. This research aimed to explore how four prevalent herbicides—Trifluralin, Pendimethalin, S-metolachlor, and Acetochlor—affect the mycelial growth of Morchella sextelata. The study involved cultivating the mycelium in a Potato Dextrose Agar (PDA) medium with concentrations of herbicides at ten times the standard application rate, followed by measuring the degree of mycelial growth inhibition. Employing transcriptomic analysis, RNA sequencing was conducted on the mycelium exposed to the herbicides. The subsequent transcriptome profiling indicated that the application of these herbicides impacted various biological pathways within Morchella sextelata, with a notable influence on glycolysis/gluconeogenesis and the glyoxylate cycle, which are crucial for energy production and metabolic processes. While Trifluralin and Pendimethalin demonstrated a less pronounced negative impact on mycelial growth, the study concluded that all tested herbicides were detrimental to Morchella sextelata. It is thus recommended that, in agricultural practice, the use of herbicides be approached with caution, and that application rates be strictly adhered to in order to ensure the healthy cultivation of Morchella sextelata and minimize potential pesticide residue issues.

overall_design: PDA medium was applied with 10 times the normal application concentration of T, P, S, A herbicides, respectively, inoculated with Morchella sextelata, placed in culture at 20°C for 5 days, the growth length of the mycelium was measured and recorded, and three replications were set up for each group, and CK was inoculated with PDA medium without added herbicides. The percentage of mycelial growth inhibition (MGI) was determined as follows: MGI (%) =[(dc-dt)/dc]*100%, where Dc and Dt are the mean diameters (cm) in the control and treatment groups, respectively.

first: Xuetai

last: Zhu

first: Lijuan

last: Liu

first: Xiaoxue

last: Zhao


title: Evaluation of the impact of genetically suppression of DNA methyltransferase 1 (DNMT1) in aged vs young type 2 alveolar epithelial cells (AT2).

city: New York

first: ZHUXUAN

summary: Using somatic genetic approaches, we aim for investigating the role of DNMT1 suppression in the regulation of transcriptom of young AT2 cells, in comparing with the effect of aging.

overall_design: Aged (> 2 years old) and young (12-16 weeks old) Rosa26-mTmG mice were infected by either control shRNA (Ren713) or shRNAs targeting DNMT1. Due to the Cre recombinase, cells bearing shRNAs were turned green (GFP positive). Eleven days post-infection,  lungs were harvested and GFP+ epithelial cells or other cells were collected for scRNA-Seq.

first: Xueqian

first: Qing

last: Wang

first: Emily

last: Wong


title: Evaluation of the impact of genetically suppression of Nupr1 in aged vs young type 2 alveolar epithelial cells (AT2).

last: LI

summary: Our data demonstrated that Nupr1 has an age-specific function in the proliferation and differentiation of lung adenocarcinoma cells that are derived from AT2 cells. However, how Nupr1 impact AT2 cells in vivo has not been tested. Using somatic genetic approaches, we performed single-cell mRNA sequencing with primary AT2 cells with control or shRNAs targeting Nupr1.

overall_design: Aged (> 2 years old) and young (12-16 weeks old) Rosa26-mTmG mice were infected by either control shRNA (Ren713) or shRNAs targeting Nupr1. Due to the Cre recombinase, cells bearing shRNAs were turned green (GFP positive). Five days post-infection, mice were exposed to hyperoxia-induced alveolar injury. Four weeks after injury (when lung injury healedin general), lungs were harvested and GFP+ epithelial cells or other cells were collected for scRNA-Seq.

last: Zhuang

first: Tuomas


title: The pore-forming apolipoprotein APOL7C drives phagosomal rupture and antigen cross-presentation by dendritic cells

city: Calgary

first: Paul

last: Gordon

state: AB

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

summary: Conventional dendritic cells (cDCs) generate protective cytotoxic T lymphocyte (CTL) responses against pathogens and tumours. This is achieved through a process known as cross-presentation (XP) and, despite its obvious biological importance, the mechanism(s) driving XP remain unclear. Here, we show that a cDC-specific pore-forming protein called apolipoprotein L 7C (APOL7C) is upregulated in response to innate immune stimuli and is recruited to phagosomes. Strikingly, its association with phagosomes leads to phagosomal rupture. This allows for the escape of engulfed antigens to the cytosol where they can be processed via the endogenous MHC class I antigen processing pathway.  Accordingly, mice deficient in APOL7C do not efficiently prime CD8+ T cells in response to immunization with bead-bound and cell-associated antigens.  Altogether, our data indicate the presence of dedicated apolipoproteins that mediate the delivery of phagocytosed proteins to the cytosol of activated cDCs to facilitate XP.

overall_design: To investigate genes upregulated in MuTuDC1940 cells upon stimulation with poly(I:C). MuTuDC1940 cells were treated with or without poly(I:C) at 5 ug/ml (micrograms per millilitre) for 18 hours before RNA extraction and analysis.

first: Johnathan

last: Canton

first: Song

last: Huang

first: Gerone

last: Gonzales

first: Liam

last: Wilkinson


title: Exploring TSA-Induced Haploid Embryogenesis in Brassica napus

city: Wageningen

first: Anneke

last: Horstman

state: Nederland

address: Droevendaalsesteeg,

department: Plant Science Group

country: Netherlands

institute: Wageningen University and Research

summary: Haploid embryos can be induced from cultured immature pollen following stress treatment. In Brassica napus, the application of the histone/lysine deacetylase (HDAC/KDAC) inhibitor trichostatin A (TSA) to pollen cultures enhances the production of differentiated embryos and embryogenic callus when applied together with heat stress (Li et al., 2014). To identify genes associated with the induction of haploid embryogenesis and to investigate which genes may be responsible for TSA-induced lipid and starch accumulation in the embryogenic structures, we compared the transcriptomes of pollen cultures treated with heat stress and 0.05 µM TSA to those of untreated pollen cultures, both at two days.

overall_design: 6 samples were analyzed. For each condition, three biological replicates were analyzed (1 genotype, 2 treatments)

first: Kim

last: Boutilier


title: Anti-necroptotic effects of human Wharton’s jelly-derived mesenchymal stem cells in skeletal muscle cell death model via secretion of GRO-α

first: Sun Jeong

last: Kim

address: 701, Yeongdong-daero, Gangnam-gu

institute: ENCell Co. Ltd.

summary: Human mesenchymal stem cells (hMSCs) have therapeutic applications and potential for use in regenerative medicine. However, the use of hMSCs in research and clinical medicine is limited by a lack of information pertaining to their donor-specific functional attributes. In this study, we compared the characteristics of same-donor derived placenta (PL) and Wharton’s jelly (WJ)-derived hMSCs, we also compared their mechanism of action in a skeletal muscle disease in vitro model. The effects of GRO-α were also investigated in a Duchenne muscular dystrophy (DMD) mouse model. The same-donor-derived hWJ- and hPL-MSCs exhibited typical hMSC characteristics. GRO-α was differentially expressed in hWJ- and hPL-MSCs. However, when the secretion of GRO-α was considered, hWJ-MSCs displayed a higher ability to inhibit necroptosis in skeletal muscle cells than hPL-MSCs. This demonstrates the anti-necroptotic therapeutic effect of GRO-α in the skeletal muscle cell death model. Furthermore, considering their potential to inhibit necroptosis in skeletal muscle cells, hWJ-MSCs and the derived GRO-α are novel treatment options for skeletal muscle diseases such as DMD.

sample_organism:
Homo sapiens
Mus musculus

overall_design: To identify the secreted anti-necroptosis soluble factor from hWJ-MSCs, the conditioned media from each sample group, comprising hWJ- and hPL-MSCs from the same donor co-cultured with C2C12 cells, were analyzed using antibody arrays. We collected the conditioned media from the following groups to perform the array: C2C12 alone, hWJ-MSCs alone (A, B, C), hPL-MSCs alone (A, B, C), and C2C12 cells co-cultured with hWJ-MSCs (A, B, C), or hPL-MSCs (A, B, C). To identify the secreted anti-necroptosis soluble factor from hWJ-MSCs, the conditioned media from each sample group, comprising hWJ- and hPL-MSCs from the same donor co-cultured with C2C12 cells, were analyzed using antibody arrays.

first: Sang Eon

last: Park

first: Soo Jin

last: Kwon

first: Jang Bin

last: Jeong

first: Min-Jeong

first: Suk-joo

last: Choi

first: Soo-young

last: Oh

first: Gyu Ha

last: Ryu

first: Hong Bae

last: Jeon

first: Jong Wook

last: Chang


title: Effects of Hsd11b1 overexpressing in mc3T3-e1 pre-osteoblastic cell lines under glucocorticoid excess (ATAC-Seq)

city: Hong Kong

first: CHUANXIN

last: ZHONG

state: Hong Kong

address: ACC205, Hong Kong Baptist University, 15 Baptist University Road Kowloon Tong

institute: HONG KONG BAPTIST UNIVERSITY

summary: To explore the mechanism by which osteoblastic 11β-HSD1 regulates bone formation and glucose handling, we transfected the mouse MC3T3-E1 osteoblastic cells with a plasmid carrying the exogenous Hsd11b1 or EGFP gene to construct the 11β-HSD1-overexpressed and control osteoblastic cells (hereafter MC3T3-HSD1 and MC3T3-GFP cells), respectively. After incubating with 11-DHC,we then employed  assay for transposase-accessible chromatin with sequencing (ATAC-seq) to examine the gene expression profile between MC3T3-HSD1 and MC3T3-GFP cells.

first: Zhong

last: Chuanxin

first: Liu

last: Jin

first: Zhang

last: Ge


title: A longevity-specific bank of induced pluripotent stem cells from centenarians and their offspring

city: Boston

first: George

last: Murphy

address: 670 Albany Street

department: Department of Medicine

institute: Boston University / Boston Medical Center

summary: Centenarians provide a unique lens through which to study longevity, healthy aging, and resiliency. Moreover, models of human aging and resilience to disease that allow for the testing of potential interventions are virtually non-existent. We obtained and characterized over 86 centenarian and offspring peripheral blood samples including those connected to functional independence data highlighting resistance to disability and cognitive impairment. Targeted methylation arrays were used in molecular aging clocks to compare and contrast differences between biological and chronological age in these specialized subjects. Isolated peripheral blood mononuclear cells (PBMCs) from 20 of these subjects were then successfully reprogrammed into high-quality induced pluripotent stem cell (iPSC) lines which were functionally characterized for pluripotency, genomic stability, and the ability to undergo directed differentiation. The result of this work is a one-of-a-kind resource for studies of human longevity and resilience that can fuel the discovery and validation of novel therapeutics for aging-related disease.

overall_design: In this resource paper, a large cohort of centenarians with extreme longevity (EL) and their offspring had their peripheral blood profiled via Illumina EPICv2 methylation arrays to compare biological and chronological age. In addition, 20 of these subjects were reprogrammed into iPSC lines as a resource for studies on longevity and resilience.

first: Todd

middle: W

last: Dowrey

first: Samuel

middle: F

last: Cranston

first: Nicholas

last: Skvir

first: Yvonne

last: Lok

first: Brian

last: Gould

first: Bradley

last: Petrowitz

first: Daniel

last: Villar

first: Jidong

last: Shan

first: Marianne

last: James

first: Mark

last: Dodge

first: Anna

last: Belkina

first: Richard

middle: M

last: Giadone

first: Sofiya

last: Milman

first: Paola

last: Sebastiani

first: Thomas

middle: T

last: Perls

first: Stacy

last: Andersen


title: Gene expression analysis of lung tissue transferred bone marrow cells with low and high aldehyde dehydrogenase activity (ALDHdim and ALDHbr).

city: Hiroshima-shi

first: Shugo

last: Inada

state: Hiroshima

address: 5-17-5 Midorii

institute: Hiroshima University

summary: To investigate the kinetics of bone marrow ALDHbr cells for antifibrotic effect, gene expression analysis was performed using murine model of bleomycin-induced pulmonary fibrosis.

overall_design: Gene expression analysis of fibrotic lung sections transferred bone marrow ALDHdim and ALDHbr cells.

first: Taku

last: Nakashima


title: Effects of Hsd11b1 overexpressing in mc3T3-e1 pre-osteoblastic cell lines under glucocorticoid excess

first: CHUANXIN

last: ZHONG

summary: To explore the mechanism by which osteoblastic 11β-HSD1 regulates bone formation and glucose handling, we transfected the mouse MC3T3-E1 osteoblastic cells with a plasmid carrying the exogenous Hsd11b1 or EGFP gene to construct the 11β-HSD1-overexpressed and control osteoblastic cells (hereafter MC3T3-HSD1 and MC3T3-GFP cells), respectively. After incubating with 11-DHC,we then employed RNA sequencing (RNA-seq) to examine the gene expression profile between MC3T3-HSD1 and MC3T3-GFP cells.

first: Zhong

last: Chuanxin

first: Liu

last: Jin

first: Zhang

last: Ge


title: Neddylation Signaling Inactivation by Tetracaine Hydrochloride Suppresses Cell Proliferation and Vemurafenib-resistance of Melanoma

city: luzhou

first: yi

last: peng

address: xianglinlu

institute: 西南医科大学

summary: This study aimed to investigate the transcriptomic changes in A375 cells upon treatment with 400μM tetracaine hydrochloride (TTC) for 24 hours.  RNA-seq data were generated from TTC-treated and untreated control A375 cells to identify differentially expressed genes and pathways involved in the cellular response to TTC exposure.  The findings may provide insights into the molecular mechanisms underlying the effects of TTC on A375 cells.

overall_design: The experiment involved two conditions: 1) A375 cells treated with 400μM TTC for 24 hours, and 2) A375 cells treated with an equivalent dose of PBS as a control. Three biological replicates were prepared for each condition. Total RNA was extracted, and RNA-seq libraries were constructed and sequenced using Illumina technology.

first: Jianguo

last: Feng

first: Xiang

last: Huang


title: Latent EBV enhances the efficacy of anti-CD3 mAb in Type 1 Diabetes

city: New Haven

first: Ana

last: Lledo Delgado

state: CONNECTICUT

address: 300 George St

department: Immunobiology

institute: Yale University

summary: Teplizumab is approved for delay of diagnosis of type 1 diabetes and modulates new onset disease. Compared to EBV seronegative patients, those who were EBV seropositive prior to treatment had a more robust response to drug in two clinical trials. We compared the phenotypes, transcriptomes, and development of peripheral blood cells before and after teplizumab treatment. Higher number of Tregs and “partially exhausted” CD8+ T cells were found in EBV seropositive individuals at the baseline in the TN10 and AbATE trials. Single cell transcriptomics and functional assays identified downregulation of NFB and other pathways after treatment in treated EBV seropositive patients. Among diabetes antigen specific CD8+ T cells, T cell receptor and mTOR signaling were also reduced. Impairments in function of adaptive immune cells were enhanced by teplizumab treatment in EBV seropositive individuals. Our data indicate that EBV can impair signaling pathways in immune cells, that broadly redirect cell differentiation.

overall_design: PBMCs from the TN10 trial were obtained and stained with hashtag antibodies to analyze using scRNAseq

first: Kevan

last: Herold


title: Comparative Transcriptomics of Broad-Spectrum and Synthetic Cannabidiol Treated Skeletal Myotubes

city: Liverpool

first: Daniel

middle: John

last: Owens

address: Byrom Street

department: Research Institute for Sport and Exercise Science

country: United Kingdom

institute: Liverpool John Moores University

summary: Cannabidiol (CBD), a cannabinoid from the cannabis plant, is widely used in sports for recovery, pain management, and sleep improvement, yet its effects on muscle are not well understood. This study aimed to determine the transcriptional response of murine skeletal muscle myotubes to broad-spectrum CBD and synthetic CBD (sCBD), hypothesizing significant changes in metabolism, myogenesis, and inflammation, with unique gene expression profiles for broad-spectrum CBD due to its additional compounds. Differentiated C2C12 myotubes were treated with 10 µM CBD, sCBD, or vehicle control (DMSO) for 24 hours before RNA extraction. Poly-A tail enriched mRNA libraries were constructed and sequenced using 2x50 bp paired-end sequencing.  CBD and sCBD treatment induced 4489 and 1979 differentially expressed genes (DEGs; p <0.001, FDR step-up <0.05), respectively, with common upregulation of 857 genes and common downregulation of 648 genes. Common upregulated DEGs were associated with “response to unfolded protein”, “cell redox homeostasis”, “endoplasmic reticulum stress”, “oxidative stress” and “cellular response to hypoxia”. Common downregulated DEGs were linked to “sarcomere organization”, “skeletal muscle tissue development”, “regulation of muscle contraction”, “skeletal muscle contraction” and “muscle contraction”. CBD treatment induced 1342 unique upregulated DEGs and 1137 unique downregulated DEGs, compared to 154 and 152 unique up- and downregulated DEGs in sCBD.  The transcriptional data indicate that CBD may induce mild cellular stress, activating pathways associated with altered redox balance, unfolded protein response, and endoplasmic reticulum stress. We hypothesize that CBD interacts with muscle and may elicit a ‘mitohormetic’ effect that warrants further investigation.

overall_design: Our aim was to investigate the global transcriptional response of C2C12 skeletal muscle myotubes following exposure to broad-spectrum CBD and synthetic CBD. We aimed to ascertain if 1) skeletal muscle is responsive to broad spectrum CBD and synthetic CBD and 2) whether these effects are attributable solely to CBD or the vast array of other compounds in commercially available broad-spectrum CBD. We therefore exposed C2C12 myotubes to a vehicle control (DMSO), 10uM broad spectrum CBD or 10uM synthetic CBD for 24 hours.

first: Scott

last: Gillham

first: Mark

last: Viggars

first: Paige

last: Cole

first: Andy

last: Nolan

first: Graeme

last: Close


title: Activation of Piezo1-mediated mechanotransduction by LOX promotes neuronal ferroptosis leading to HIBD and discovery of LOX inhibitor TA

city: NanJing

first: Jiang

middle: Dong

last: ya

state: 江苏省

address: 12 Xuefu Road, Nanjing, Jiangsu, China

institute: NanJing university

summary: Neonatal hypoxic-ischemic brain damage (HIBD) is initiated by perinatal asphyxia, leading to brain injury triggered by reduced blood and oxygen flow, resulting in neurological impairments such as cerebral palsy, epilepsy, cognitive deficits, and behavioral disorders.Recent insights collectively suggest the important roles of lysyl oxidase (LOX) in the pathological processes of several acute and chronic neurological diseases, but the molecular regulatory mechanisms in HIBD remain elusive.In this study, we found through the study of HIBD rat models and the  oxygen-glucose deprivation/re-oxygenation (OGD/R) cell models that LOX significantly increased after HIBD or OGD/R. RNA seq results showed a significant increase in piezo1 after primary neuron OGD/R, and iron death data was also enriched. Moreover, inhibiting LOX or piezo1 can rescue neuronal ferroptosis and further improve cognitive function in rats. In addition, we also found that traumatic acid can inhibit the enzyme activity of LOX and improve a series of pathological features of neuronal damage caused by increased LOX.

overall_design: To detect the transcriptional changes of primary neurons after OGD/R, we extracted rat primary neurons for OGD/R post sequencing. Afterwards, we will compare the RNA seq of the OGD/R group with the control group to find the data of interest.

first: Dongya

last: Jiang

first: Xiaohua

last: Dong


title: Gene expression analysis of bone marrow cells with high aldehyde dehydrogenase activity (ALDHbr) obtained from male and female mice.

first: Shugo

last: Inada

summary: To investigate the difference of male and female murine bone marrow ALDHbr cells collected by fluorescence activated cell sorting, gene expression analysis was performed.

overall_design: Gene expression analysis of bone marrow ALDHbr cells obtained from male and female C57BL/6 mice.

first: Taku

last: Nakashima


title: Effect of FTO-KD on m6A modification in GH3 cell line [MeRIP-seq]

city: Guangzhou

first: Zhixiang

last: Zuo

address: No. 651 Dongfeng Dong road

institute: Sun Yat-sen University

type: Methylation profiling by high throughput sequencing

summary: Growth hormone-secreting pituitary adenomas account for approximately 10% of endocrine pituitary tumors and are pathologically classified into densely granulated adenomas (DGGH) and sparsely granulated adenomas (SGGH). m6A has been reported to play an important role in tumorigenesis and development, but its potential role in the pathogenesis of these two subtypes has not yet been thoroughly investigated. Consequently, we performed MeRIP-seq analysis of pituitary adenomas and the GH3 cell line. We observed that the expression of FTO was significantly increased in SGGH, leading to a reduction in m6A modification and a disruption of desmosome organization.

overall_design: To explore the effect of FTO on gene expression and m6A modification, we established FTO-KD GH3 cell lines.

first: Xiaobing


title: Blocking antibodies against integrin-α3, -αM, and -αMβ2 de-differentiate myofibroblasts, and improve lung fibrosis and kidney fibrosis

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

institute: University of Illinois at Chicago

summary: Fibrosis is involved in 45% of deaths in the United States, and no treatment exists to reverse the progression of lung or kidney fibrosis. Myofibroblasts are key to the progression and maintenance of fibrosis. We investigated features of cell adhesion necessary for monocytes to differentiate into myofibroblasts, seeking to identify pathways key to myofibroblast differentiation. Blocking antibodies against integrins α3, αM, and αMβ2 de-differentiate myofibroblasts in vitro, lower the pro-fibrotic secretome of myofibroblasts, and treat lung fibrosis and inhibit kidney fibrosis in vivo. Decorin’s collagen-binding peptide can be used to direct functionalized blocking antibodies (against integrins-α3, -αM, -αMβ2) to both fibrotic lungs and fibrotic kidneys, reducing the dose of antibody necessary to treat fibrosis. This targeted immunotherapy blocking key integrins may be an effective therapeutic for the treatment of fibrosis.

overall_design: lung tissue from (1-3) healthy lungs, (4-6) fibrotic lungs, (7-9) fibrotic lungs treated with targeted anti-a3 antibody, and (10-12) fibrotic lungs treated with targeted anti-amb2 antibody were sectioned and processed to isolate the mRNA, then converted to cDNA and sequenced.

first: Michael

last: White


title: Meningeal-derived retinoic acid regulates neurogenesis via suppression of Notch and Sox2 [Spatial Transcriptomics]

city: Aurora

first: Christina

last: Como

state: CO

institute: University of Colorado

summary: During development, the meninges act as a regulator of neocortical development by secreting ligands that act on neural cells to regulate neurogenesis and neuronal migration.  Meninges-derived retinoic acid (RA) promotes neocortical progenitor cell cycle exit however the underlying mechanism is unknown. Here, we use Foxc1-mutant embryos that lack meninges-derived ligands, spatial transcriptomics, and profiling of retinoic-acid receptor-a (RARa) DNA binding to identify the neurogenic transcriptional mechanisms of RA signaling in cortical neural progenitors. We determined that meningeal-derived RA controls neurogenesis by suppressing self-renewal pathways Notch signaling and the transcription factor Sox2. We show that RARα binds in the Sox2ot promoter, a long non-coding RNA that regulates Sox2 expression, and RA promotes Sox2ot expression in neocortical progenitors. Our findings elucidate a previously unknown mechanism of howmeningeal RA coordinates neocortical development and insight into how defects in meningeal develop can cause neurodevelopmental disorders.

overall_design: Spatial transcriptomics data from E14 mouse coronal sections including 2 controls and 2 Foxc1 Mutants

first: Julie

last: Siegenthaler


title: Meningeal-derived retinoic acid regulates neurogenesis via suppression of Notch and Sox2 [CUT&Run]

overall_design: CUT&RUN DNA sequencing for Myctag-Rar alpha in E14 Prom1+ magnetically separated cortical cells


title: 3D spheroid culture synchronizes heterogeneous mesenchymal stem cells into an immunomodulatory phenotype with enhanced suppressive effect on inflammation

city: Shenzhen

first: Ruiqing

last: Lu

state: Guangdong

address: Taoyuan Street, Nanshan District

institute: Tsinghua University

summary: Mesenchymal stem cells (MSC) are heterogeneous in morphology and transcriptome, resulting in varying therapeutic outcomes. In this study, we found that 3D spheroid culture of heterogeneous MSC, which have undergone conventional 2D monolayer culture for 5-6 passages, synchronized the cells into a uniform cell population with dramatically reduced cell size, and considerably increased levels of immunosuppressive genes and growth factors. Sc-RNA-Seq analysis of the cells revealed that 3D MSC consisted of 2 major cell subpopulations and both expressed high levels of immunosuppressive factors, compared to 6 subpopulations in 2D MSC. In addition, 3D MSC showed a greater suppressive effect on T cells. Moreover, intravenous infusion of a large dose of 3D MSC prior to Imiquimod (IMQ) treatment significantly improved psoriatic lesion. Thus, our results indicate that 3D spheroid culture reprograms heterogeneous mesenchymal stem cells into a uniform immunosuppressive phenotype and promises a novel therapeutic potential for inflammatory diseases.

overall_design: The mesenchymal stem cells were isolated from human placenta and cultured in vitro to passage 5. The mesenchymal stem cells produced by two-dimensional adhesion culture and three-dimensional spherical culture  were digested with trypsin and analyzed by single cell sequencing.

first: Ke

last: Zheng

first: Yongjie

last: Zhou

first: Weibu

last: Wang

first: Yanan

last: Zhang

first: Yu

last: Chen

first: Miaohua

last: Mo

first: Xiaosong

last: Li

first: Yankai

first: Jundong

last: Xie

first: Haiji

first: Qingyang

last: Yang

first: Guoliang

first: Yi

last: Zhao

first: Yaojiong

last: Wu


title: Transcriptomic analysis of bacterial vaginosis-associated bacteria living in single or multispecies biofilms

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

summary: Bacterial vaginosis (BV) is the most common cause of vaginal discharge among women worldwide. BV is characterized by an imbalance in the vaginal microbiota with depletion of protective Lactobacillus species and overgrowth of facultative and strictly anaerobic bacteria. Although the development of a polymicrobial biofilm on the vaginal epithelium is a hallmark of BV, interactions between key BV-associated bacteria (BVAB) [i.e. Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia] present in the biofilm are still not completely understood. In this study, we aimed to analyse the transcriptome of single and triple-species biofilms growing in the rich medium, New York City III (NYCIII). A previous analysis of triple-species biofilms composition by qPCR showed that the biofilms were mainly composed of G. vaginalis, followed by F. vaginae and P. bivia. The transcriptomic analysis revealed a total of 431 (34 upregulated and 397 downregulated), 126 (36 upregulated and 90 downregulated), and 39 (31 upregulated and 8 downregulated) differentially expressed genes for G. vaginalis, F. vaginae, and P. bivia, respectively. Gene ontology only detected enrichment for the downregulated genes of G. vaginalis and 47 GO terms were associated with molecular functions, cellular components and biological processes, mainly metabolism. Hence, this work showed the adaptation of 3 BVAB when growing in a triple-species biofilm, with several genes being differentially expressed in all the species growing in a polymicrobial biofilm.

sample_organism:
Gardnerella vaginalis
Prevotella bivia
Fannyhessea vaginae

overall_design: To study the alterations that growing in single or in multispecies biofilms may have on bacterial vaginosis-associated bacteria, G. vaginalis, F. vaginae and P. bivia were grown both in single and triple-species biofilms and their transcriptomes were characterised.

first: Lúcia

last: Sousa

first: Juliano

last: Novak

first: Angela

first: Christina

middle: A

last: Muzny

first: Nuno

last: Cerca


title: The histone demethylase KDM5C regulates IRF transcriptional programming impacting dendritic cell population heterogeneity and function (CUT&RUN)

city: Grand Rapids

first: Connie

last: Krawczyk

state: MI

address: 333 Bostwick Ave

department: Metabolism and Nutritional Programming

institute: Van Andel Institute

summary: Functional and phenotypic heterogeneity of dendritic cells (DCs) plays a crucial role in facilitating the development of diverse immune responses essential for host protection. We found that KDM5C, a histone lysine demethylase, regulates conventional DC (cDC) and plasmacytoid DC (pDC) population heterogeneity and function. Mice deficient in KDM5C in DCs, have increased proportions of cDC2Bs and cDC1s, which was partly dependent on type I interferon and pDCs. Loss of KDM5C resulted in an increase in Ly6C- pDCs, which, compared to Ly6C+ pDCs, have limited ability to produce type I interferon and can more efficiently stimulate antigen-specific CD8 T cells. KDM5C-deficient DCs have increased expression of inflammatory genes, altered expression of lineage-specific genes, and reduced function. In response to Listeria infection, KDM5C-deficient mice mounted reduced CD8 responses due to decreased antigen presentation by cDC1s. Thus, KDM5C is a key regulator of DC heterogeneity and a critical driver functional properties of DCs.

overall_design: This study was done to analyze the difference between knockout and wild type KDM5C expression in dendritic cell populations with and without LCMV-Armstrong infection. Each group contains 3 biological reps and 5 DC subsets (unless there were not enough samples to sort or there was dropout due to sequencing and unsuccessful library prep).

first: Hannah

last: Guak

first: Matthew

last: Weiland


title: The histone demethylase KDM5C regulates IRF transcriptional programming impacting dendritic cell population heterogeneity and function (RNA-seq)


title: Age-related decline in pancreas regeneration is associated with an increased proinflammatory response to injury

city: Copenhagen

first: Luis

last: Arnes

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research & Innovation Centre

summary: The regenerative capacity of the pancreas diminishes with age. Understanding acinar cell responses to injury and the resolution of regenerative processes is crucial for tissue homeostasis. However, knowledge about the impact of aging on these processes remains limited. To investigate the influence of aging on pancreas regeneration, we established a cohort of young (7-14 weeks) and old (18 months) C57bl/6 mice. Experimental pancreatitis was induced using caerulein, and pancreas samples were collected at various timepoints after induction, covering acute damage response, inflammation, peak proliferation, and inflammation resolution. Our analysis involved immunohistochemistry, quantitative imaging, and gene expression analyses. Our study revealed a significant decline in the regenerative capacity of the pancreas in old mice. Despite similar morphology and transcriptional profiles between the pancreas of young and old mice under homeostasis, the aged pancreas is primed to generate an exacerbated proinflammatory reaction in response to injury. Specifically, we observed notable upregulation of Junb expression in acinar cells and aberrant myofibroblast activation in aged pancreas. The response of acinar cells to injury in the pancreas of aged mice is characterized by an increased susceptibility to inflammation and stromal reactions. Our findings uncover a pre-existing proinflammatory state in aged acinar cells, offering insights into potential strategies to prevent the onset of pancreatic insufficiency and the development of inflammatory conditions. These insights hold implications for preventing conditions such as chronic pancreatitis and pancreatic ductal adenocarcinoma.

overall_design: To investigate the effect of aging during the initiation of pancreatitis, we performed four hourly caerulein-injections in young (7w) and aged (18 months) C57BL/6JRj mice. RNA was extracted from bulk pancreas an hour after the first injection (5H).

first: Kristina

last: Høj

first: Jonathan

last: Baldan

first: Assis

last: Juliana


title: The histone demethylase KDM5C regulates IRF transcriptional programming impacting dendritic cell population heterogeneity and function

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

overall_design: Refer to individual Series


title: Individual ChIP-seq for REV-ERBα, FOXA1,BRD4 and H3K27ac

city: Sacramento

first: yatian

last: yang

state: CA

institute: UC Davis

summary: Genome-wide measurements of histone modifications and transcripton factors binding in Lucao35CR PDX tumor and cell models to study FOXA and REV-ERBα regulate the tumorigenic programs

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-seq for different histone marks and transcriptional factors in C42B cell and Lucap35CR.

first: Yatian

first: Xiong

last: Zhang

first: Demin

last: Cai

first: Hong-wu

last: Chen


title: Targeted immunoproteomics of cerebrospinal fluid in disease-modifying treatment-naïve Multiple Sclerosis patients

city: North Grafton

first: Jillian

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

summary: We performed a retrospective study on CSF from 20 DMT-naïve MS patients to investigate the correlation between intrathecal immune proteins and clinical MS phenotype.

overall_design: 92 proteins were analyzed via Olink's Target 96 Inflammation Panel from CSF of 20 patients with multiple sclerosis who had never received disease modifying therapy throughout the course of their disease. These 20 patients were run as part of a larger cohort of 70 CSF samples spread across two 96-well qPCR plates, Plate 2 was normalized to plate 1 via Olink Bridging Method. Here we have included the 20 samples post-normalization relevant to our recently published study and indicated on which plate they were found (plate 1 or plate 2).

first: Carolina

last: Ionete

first: Christopher

middle: C

last: Hemond


title: Moderate-level resistance exercise significantly improved the Sickness Impact Profile ALS-19 and muscle transcriptome of the early-stage ALS patients.

city: Itabashi-ku

first: Hiroshi

last: Nishimune

state: Tokyo

address: 35-2 Sakaecho

department: Neurobiology of Aging

institute: Tokyo Metropolitan Institute for Geriatrics and Gerontology

summary: Amyotrophic lateral sclerosis (ALS) patients lose motor and neuromuscular function but lack effective treatments. The objective of this study was to evaluate the effect of moderate-level exercise on ALS scores, neuromuscular function, and transcriptome in ALS patients. Methods: A pilot open-label, non-randomized clinical trial was conducted in seven individuals with early-stage ALS. Participants were given three months of moderate-level home-based resistance exercise focusing on the quadriceps muscles. Before and after the exercise program, participants were evaluated by quantifiable outcome measures using bilateral quadriceps strength with manual muscle testing and handheld dynamometers and functional outcome measures using five times sit-to-stand and Timed-Up-and-Go. In addition, changes in the transcriptome and mitochondrial respiration of exercised muscles were compared before and after the exercise. Results: The exercise program significantly improved the Sickness Impact Profile ALS-19 (SIP/ALS-19) and did not cause serious adverse events to the patients. ALSFRS-R, quantifiable outcome measures, functional outcome measures, and muscle respiration values did not change by the exercise program. Transcriptome analysis revealed that exercise reverted the expression level of genes decreased in ALS, including PVALB. Conclusions: Three months of moderate-level resistance exercise is not detrimental for the patients and may have a positive effect on patients’ QOL.

overall_design: To evaluate the effect of moderate-level exercise on ALS scores, neuromuscular function, and transcriptome in ALS patients.

first: Omar

last: Jawdat

first: Jason

last: Rucker

first: Tomoki

last: Nakano

first: Kotaro

last: Takeno

first: Heather

last: Wilkins

first: Jeffery

last: Statland

first: Mamatha

last: Pasnoor

first: Mazen

last: Dimachkie

first: Carla

last: Sabus

first: Yomna

last: Badawi

first: Suzanne

last: Hunt

first: Naoko

middle: H

last: Tomioka

first: Sumedha

last: Gunewardena

first: Clark

last: Bloomer

first: Laura

last: Herbelin

first: Richard

middle: J

last: Barohn


title: RNA-sequencing assay to Identify changed gene expression in gastric cancer cells with SCAMP1 knockdown

city: Tianjin

first: Gang

last: Ma

email: horsegang@163.com, horsegang@tmu.edu.cn

address: West Huan-Hu Rd, Ti Yuan Bei, Hexi District

department: Department of Gastric Surgery

institute: Tianjin Medical University Cancer Institute and Hospital

summary:
Purpose: To understand how SCAMP1 drives the proliferation of GC cells,  endogenous SCAMP1 expression was reduced using shRNA in gastric cancer cell line NCI-N87. RNA sequencing was performed to characterize differentially expressed genes (DEGs) betwenn the control (shCtrl) and the SCAMP1-depleted (shS1#1) NCI-N87 cells.
Methods: When shCtrl and shS1#1 NCI-N87 cells grew to approximately 80% confluence, these cells were washed twice using pre-chilled PBS. Total RNAs were extracted using Trizol reagents (Thermo Fisher Scientific).  Poly(A) mRNAs were isolated and enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module. Library was generated with NEBNext ® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, E7420S) following the manufacturer’s instruction, and library was then sequenced by Novogene (Beijing, China). FastQC was used to examine the quality of raw reads. Read alignment was conducted using STAR (v2.5.1b),  and R package edgeR (v3.8.5) was used to determine relative transcript abundance and differentially expressed genes (DEGs) between shCtrl and shS1#1 sample.
Results: Generally, the expressions of 495 genes increased whereas the expressions of 204 genes decreased in shS1#1 cells, compared with shCtrl cells (|log2FC| > 1 and P < 0.05). Gene Ontology (GO) analysis indicated that significant portion of these differentially expressed genes were enriched in ligand-receptor interactions, such as fibroblast growth factor receptor binding, and the downstream signaling pathways, such as PI3K-Akt pathway.
Conclusions: Reduced SCAMP1 expression attenuates the proliferation in GC cells via deactivating multiple pro-tumoral signaling pathways.

overall_design: Three biological replicates for each group - shCtrl and shS1#1 - were subjected to RNA-sequencing analysis respectively, among which  shCtrl acted as the reference sample for shS1#1 .

first: Yang

last: Yang

first: Fenglin

last: Cai

first: Bing

last: Ke

first: Jingyu

last: Deng


title: Gene expression changes induced by SMPD1 or GPR64 silencing in A673 Ewing Sarcoma cells

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: We used RNA-sequencing to compare the gene expression changes induced by SMPD1 silencing and GPR64 silnecing.

overall_design: A673 cells were were transfected with either scrambled-siRNA or SMPD1-siRNA or GPR64-siRNA for 48 hours. Transfection was carried out using Lipofectamine™ RNAiMAX Transfection Reagent (Thermo Fisher) according to the manufacturer’s protocol. After 48 hours, cells were harvested and total RNA was extracted using TRIzol reagent (Invitrogen). For whole-genome transcriptome profiling, four libraries were generated from total RNA sequencing.

first: Kruthi

last: Suvarna

first: Panneerselvam

last: Jayabal

first: Yuzuru

last: Shiio

first: Zhao

last: Lai


title: Establishment of Giant Panda Induced Pluripotent Stem Cells

city: Chengdu

first: Yan

last: Li

state: Sichuan

address: 375#Panda Road,Northern Suburb

institute: Chengdu Research Base of Giant Panda Breeding

summary: The giant panda (Ailuropoda melanoleuca) stands as a flagship and umbrella species, symbolizing global biodiversity. While traditional assisted reproductive technology faces constraints in safeguarding the genetic diversity of giant pandas and bolstering the population size of giant pandas, induced pluripotent stem cells (iPSCs) known for their capacity to differentiate into diverse cells types, including germ cells, present a transformative potential for conservation of endangered animals. In our study, we isolated primary fibroblast cells from an individual giant panda and successfully generated giant panda induced pluripotent stem cells (GPiPSCs) through a non-integrating episomal vectors reprogramming method. Characterization of these GPiPSCs revealed their state of primed pluripotency and demonstrated their potential for differentiation. Furthermore, we innovatively formulated a species-specific chemically defined FACL medium and unraveled the intricate signaling pathway networks responsible for maintaining the pluripotency and fostering cell proliferation of GPiPSCs. This study provides key insights into rare species iPSCs, offering materials for panda characteristics research and laying the groundwork for in vitro giant panda gamete generation, potentially aiding endangered species conservation.

overall_design: To generate giant panda induced pluripotent stem cells (GPiPSCs) through a non-integrating episomal vectors reprogramming method. There were 25 sample used in this study. Title of the sample including the word 'rep' represented replicate. And also the title gave the detailed description of the status of each sample.

first: Yuliang

last: Liu

first: Jing


title: Location and function of TDP-43 in platelets: Alterations in neurodegenerative diseases and arising considerations for current plasma biobank protocols

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

summary: The TAR DNA Binding Protein (TDP-43) has been implicated in the pathogenesis of human neurodegenerative diseases and exhibits hallmark neuropathology in amyotrophic lateral sclerosis (ALS). Here, we explore its tractability as a plasma biomarker of disease and describe its localization and possible functions in the cytosol of platelets. Novel TDP-43 immunoassays were developed on three different technical platforms and qualified for specificity, signal-noise ratio, detection range, variation, spike recovery and dilution linearity in human plasma samples. Fractionation studies revealed that >95% of plasma TDP-43 protein [RL1] was located within the platelet cytosol, together with numerous RNAs. Platelet-derived TDP-43 exhibits TDP-43 proteoforms detected in neurodegenerative diseases, TARDBP RNA splice variants and TDP-43 RNA targets found in the central nervous system (CNS). We propose that TDP-43 serves similar functional roles in platelets and synapses, suggesting that the study of platelet TDP-43 might provide a window into TDP-43 proteinopathies within the CNS. The restricted compartmentalization of plasma TDP-43 in platelets provides a highly concentrated substrate for further biochemical analyses. Moreover, our results suggest that current plasma biobanking protocols are subject to considerable heterogeneity in platelet recovery and measurements of TDP-43 in plasma.

overall_design: TDP-43 gene expression was reduced in SH-SY5Y cells and U87 cells by gene silecing. Differential gene expression was conducted between silenced cells and their corresponding controls. Patient platelets were compared against control U87 and  control SH-SY5Y

first: Sara

last: Cappelli

first: Giulia

last: Canarutto

first: Emanuele

last: Buratti


title: Engineered cell elongation promotes extracellular electron transfer of Shewanella oneidensis

first: Huan

last: Yu

address: Weijin Road Campus: No. 92 Weijin Road, Nankai District, Tianjin

department: School of Chemical Engineering and Technology

institute: Tianjin University

summary: To investigate how cell elongation impacts extracellular electron transfer (EET) of electroactive microorganisms (EAMs), the division of model EAM Shewanella oneidensis MR-1 was engineered by reducing the formation of cell divisome. Specially, by blocking the translation of division proteins via anti-sense RNAs or expressing division inhibitors, the cellular length and output power density were all increased. Electrophysiological and transcriptomic results synergistically revealed that the programmed cell elongation reinforced EET by enhancing NADH oxidation, inner-membrane quinone pool, and abundance of c-type cytochromes. Moreover, cell elongation enhanced hydrophobicity due to decreased cell-surface polysaccharide, thus facilitated initial surface adhesion stage in biofilm formation. The output current and power density all increased in positive correction with cellular length. However, inhibition of cell division reduced cell growth, which was then restored by quorum sensing-based dynamic regulation of cell growth and elongation phases. The QS-regulated elongated strain thus enabled a cell length of 143.6 ± 40.3 µm (72.6-fold of that of S. oneidensis MR-1), which resulted in an output power density of 248.0 ± 10.6 mW m-2 (3.41-fold of that of S. oneidensis MR-1) and exhibited superior potential for pollutant treatment. Engineering cellular length paves an innovate avenue for enhancing the EET of EAMs.

overall_design: To investigate the specifc mechanisms underlying enhanced power production of cell elongation, the transcriptomes of SulA and WT were comparatively analyzed.

first: Feng

first: Baocai

last: Zhang

first: Hao

last: Song


title: Compulsive methamphetamine taking is associated with differential expression of HDAC2-regulated genes in the rat dorsal striatum

city: Baltimore

first: Atul

last: Daiwile

state: MD

address: 251 Bayview Blvd,

department: MNRB

institute: NIDA

summary: Methamphetamine (METH) use disorder (MUD) is a neuropsychiatric disorder with loss of self-control over drug intake despite of negative consequences. The behavioral consequences of long-term METH intake on compulsive and non-compulsive individuals remain unclear. Herein we trained rats to self-administered METH 1st for 22 days than 8 days of foot-shock and 15 days of abstinence. Which was followed by 12 days of reinstatement to METH self-administration then 3 days of foot-shock and 15 days of abstinence. After 1st foot-shock phase we found two phenotypes based on their METH intake i.e., shock resistance (SR, compulsive), and shock sensitive (SS, non-compulsive). Interestingly during reinstatement of METH self-administration then foot-shock, some (resurgent shock resistance, RSR) non-compulsive rats, displayed compulsive METH intake behavior. During both abstinence period rats were tested for drug seeking behavior and SR rats displayed higher METH seeking then RSR and SS. 24 hour after 2nd withdrawal day testing, we compared transcriptional and epigenetic changes in dorsal striatum.

middle: P

first: Michael

last: McCoy

first: Subramaniam

last: Jayanthi

first: Bruce

last: Ladenheim

first: Jean

last: Cadet


title: Microarray detection of m7G RNA methylation modification in human lung cancer tissues

city: Nanning

first: Aruo

address: No.22 Shuangyong Road, Qingxiu District

institute: Guangxi Medical University

summary: A microarray assay of RNA m7G methylation modification in human lung cancer tissues compared the altered RNA m7G methylation modification in cancerous and paraneoplastic tissues of lung cancer patients.

overall_design:
Two-condition experiment, cancerous tissue vs. paraneoplastic tissue, three individuals mixed samples
Please note that each raw file contains both Cy5 (IP) and Cy3 (Sup) data and is linked to the corresponding IP sample records.


title: Fenofibrate lowers cardiac lipid accumulation and attenuates diabetic cardiomyopathy in db/db mice.

city: Gwangju

first: JiWon

last: Park

address: 123, Cheomdangwagi-ro, Buk-gu

department: Biomedical Science and Technology

institute: Gwangju Institute of Science Technology

summary: In the DCM model using db/db mice, the goal of this study was to assess the therapeutic potential of fenofibrate.

overall_design: Male mice aged 8 weeks were separated into four groups, two of which received db/db treatments with fenofibrate (n=4) and corn oil (vehicle, n=4).

first: Jiwon

first: Wooju

last: Jeong

first: Yumin

last: Kim

first: Sung

last: Cho

first: Chang-Myung

last: Oh


title: Transcriptome-wide mapping of RNA:protein interactions of USP39 in HEK293T cells

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

institute: Goethe University Frankfurt

summary: We performed USP39 iCLIP2 in HEK293T WT cells

overall_design: 3 biological replicates were subjected to the iCLIP2 procedure with UV-crosslinking at 254 nm. For IPs an anti-USP39 antibody was used. No UV treatment served as negative control. For each sample 2 regions were cut from the membrane designated with L = low and H = high.


title: Identification of a transcription factor network that regulates anti-TNF mediated IL-10 expression in human CD4+ T-cells

city: London

first: Leonie

last: Taams

state: london

address: CIBCI, 1.26, New Hunts House

institute: King's College London

summary: CD4+ T-cells are key players in the pathogenesis of rheumatoid arthritis (RA) through potent production of inflammatory mediators including IL-17A, IFNg and TNF. Anti-TNF therapy has revolutionized the treatment of RA and we previously demonstrated that in vitro treatment of human CD4+ T-cells with the anti-TNF monoclonal antibody adalimumab (ADA) promotes anti-inflammatory IL-10 expression in multiple subpopulations of CD4+ T-cells. Here we investigated the transcriptional mechanisms underlying the IL-10 induction by TNF-blockade in in vitro stimulated CD4+ T-cells. CD4+ T-cells were isolated from PBMC of healthy volunteers by magnetic isolation and cultured for 3 days with anti-CD3/CD28 mAb in the absence or presence of anti-TNF. After culture, CD45RA+ cells were depleted and RNA was extracted for gene expression profiling by RNA-seq and cell nuclei were isolated for chromatin accessibility analysis by ATAC-seq. Gene expression analysis of memory CD4+ T-cells showed a distinct gene signature of 183 genes (q-value <0.05) conferred by anti-TNF treatment. Pathway enrichment analysis of the differentially expressed genes revealed multiple pathways related to cytokine signalling and regulation of cytokine production; in particular, IL10 was the most upregulated gene by anti-TNF, while the proinflammatory cytokines and chemokines IFNG, IL9, IL22 and CXCL10 were significantly downregulated (q-value <0.05). Transcription factor (TF) motif analysis at the differentially open chromatin regions after anti-TNF treatment revealed 58 TF motifs, shared by all donors, enriched at the IL10 locus. We identified 7 TF candidates for the anti-TNF mediated regulation of IL-10, which were either differentially expressed or whose locus was differentially accessible upon anti-TNF stimulation. We postulate that this TF network, which includes MAF and PRMD1, drives transcriptional regulation of IL-10 in anti-TNF treated T-cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD4+ T-cells stimulated with anti-CD3 and anti-CD28 mAb for 72h in the absence or presence of 1 ug/ml of anti-TNF (adalimumab) and subsequenly depleted of CD45RA+ cells pre-RNA isolation. Comparative chromatin accesibility analysis of ATAC-seq data for CD4+ T-cells stimulated with anti-CD3 and anti-CD28 mAb for 72h in the absence or presence of 1 ug/ml of  anti-TNF  (adalimumab) and subsequenly depleted of CD45RA+ cells pre-nuclei isolation.

first: Giovanni

last: Povoleri

last: Ridley

first: Sylvine

last: Lalnunhlimi

first: Audrey

last: Kelly

first: Paul

last: Lavender

middle: S


title: Circulating MicroRNAs as Potential Biomarkers for Ischemic Stroke in Patients with Asymptomatic Intracranial Artery Stenosis

city: China

first: Qian

last: Zhang

address: No.119 South 4th Ring West Road

institute: Beijing Tiantan Hospital

summary: To investigate the differential expressed circulating microRNA (miRNA) in asymptomatic intracranial artery stenosis (ICAS) patients with incident ischemic stroke. The results showed three miRNAs were differentially down-regulated (fold change >1.3 and P <0.05).

overall_design: 716 participants with asymptomatic ICAS at baseline from the Asymptomatic Polyvascular Abnormalities Community study were enrolled in this study (2010-2011). Among patients with intracranial artery stenosis, 12 subjects who had a new-onset incident ischemic stroke and 12 without stroke during the 2014-2015 follow-up period were used to analysis. MiRNA microarrays were used to distinguish circulating microRNA expression of baseline serum samples between the two groups.


title: Tomo-Seq of Dugeisa japonica along AP axis

city: Sagamihara

first: Makoto

last: Kashima

state: Kanagawa

address: 5-1-16, Fuchinobe

institute: Aoyama Gakuinn University

summary: In order to reveal temporal gene expression pattern in intact Dugesia japonica, we conducted high-thoriughput version of Tomo-Seq along the AP, DV, and LR axis.

overall_design: The data is consist of 78, 28, and 51 sections data along AP, DV, and LR axis, respectively.

first: Daichi

last: Kawahara


title: small RNA sequencing of mature diploid strawberry

city: Nanjing

first: Tingting

last: Gu

state: Jiangsu

address: 1 Weigang

department: Horticulture

institute: Nanjing Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA sequencing was performed in woodland strawberry fruits for study of chromatin structure.

overall_design: Small RNA-seq of the immature (the preT stage) and mature (the red stage) fruits of woodland strawberry.

first: Qinwei

last: Pan


title: ChIP-seq of Fragaria.vesca

summary: Histone modifications mediate between genes and environment in plant growth and developmental events. To characterize the histone modification signatures in strawberry, we performed ChIP-seq experiments for seven histone marks in the immature and mature fruits, and leaves of the woodland strawberry F. vesca ('Ruegen'). The seven histone marks include H3K9/K14ac, H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3 and H3K9me2. In addition, to reveal the effect of the histone deacetylase FvHDA6, H3K9/K14a was profiled in FvHDA6-OE fruits.

overall_design: multi-replicates ChIP-seq of different tissues from Fragaria vesca

first: XiaoRong

last: Huang


title: L.J. could rescure the adverse effects induced by busulfan on the liver

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: We report the side-effects of busulfan on the liver, and foud that the L.J. could rescure the side-effect of busulfan in many factors,such as lipid metabolism and oxidative stress

overall_design: Exploration of the FMT effects on the damaged liver induced by busulfan

first: Y

last: Hao


title: L.J. could rescure the adverse effects induced by busulfan on the testis

summary: We report the side-effects of busulfan on the testis, and foud that the L.J. could rescure the side-effect of busulfan in many factors,such as inflammation and oxidative stress

overall_design: Exploration of the FMT effects on the damaged testis induced by busulfan


title: L.J. could rescure the adverse effects induced by busulfan on the spleen

summary: We report the side-effects of busulfan on the spleen, and foud that the L.J. could rescure the side-effect of busulfan in many factors,such as inflammation and oxidative stress

overall_design: Exploration of the FMT effects on the damaged spleen induced by busulfan


title: High-throughput sequencing of strawberry fruits

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

overall_design: Refer to individual Series


title: Evaluating Novel Therapeutic Strategies to Enhance CAR-T Cell Efficacy Using Patient-Derived Organotypic Tumor Spheroids

status: Public on Sep 24 2024

city: Boston

first: Russell

last: Jenkins

state: MA

address: 55 Fruit Street

institute: Masschussetts General Hospital

summary: Novel therapeutic strategies are needed to improve the efficacy of chimeric antigen receptor (CAR)-T cells in the treatment of solid tumors. Multiple tumor microenvironmental factors are thought to contribute to CAR-T cell therapy resistance in solid tumors, and appropriate model systems to identify and examine these factors using clinically relevant biospecimens are limited. Here, we examined the activity of B7-H3 (CD276) directed CAR-T (B7-H3.CAR-T) using 3D microfluidic cultures of patient-derived organotypic tumor spheroids (PDOTS) and confirmed activity of B7-H3.CAR-T in PDOTS. While B7-H3 expression in PDOTS was associated with B7-H3.CAR-T sensitivity, mechanistic studies revealed dynamic upregulation of co-inhibitory receptors on CAR-T cells following target cell encounter that led to CAR-T cell dysfunction and limited efficacy against B7-H3 expressing tumors. PD-1 blockade restored CAR-T activity in monotypic and organotypic tumor spheroids with improved tumor control and upregulation of effector cytokines. Given the emerging role of TANK-binding kinase 1 (TBK1) as an immune evasion gene, we examined the effect of TBK1 inhibition on CAR-T efficacy. Similar to PD-1 blockade, TBK1 inhibition restored CAR-T activity in monotypic and organotypic tumor spheroids, prevented CAR-T cell dysfunction, and enhanced T cell proliferation.  Inhibition or deletion of TBK1 also enhanced sensitivity of cancer cells to immune-mediated killing. Taken together, our results demonstrate the feasibility and utility of ex vivo profiling of CAR-T cells using PDOTS and suggest that targeting TBK1 is a novel strategy to enhance CAR-T efficacy by overcoming tumor-intrinsic and -extrinsic resistance mechanisms.

overall_design:
For scRNAseq analysis of PDOTS +/- CAR-T cell challenge, B7-H3.CAR-T cells and cryopreserved PDOTS (melanoma, 10214) were thawed and rested media to serve as baseline (0 hour) controls.  Remaining PDOTS were prepared in collagen for 3D culture.  B7-H3.CAR-T cells (E:T 1:1) were added with or without TBK1i (1 μM), 250 μg/mL pembrolizumab (Meck Sharp&Dobine, NDC 000^-3026-01), or the combination, compared to untreated control for 24 hours before PDOTS +/- CAR-T were collected for processing. Droplet-based isolation of single cells and subsequent libraries were generated with the Chromium Controller (10X Genomics) according to the manufacturer’s specifications using the 10x Chromium Next GEM single cell 5’ kit v2 (1000263). Characterization of the sequencing library was performed with the Bioanalyzer High Sensitivity DNA kit  (Agilent; 5067-4626) and Qubit (ThermoFisher) instruments. Each pair of sample libraries were were sequenced using Illumina NextSeq 500 with two paired-end reads (read1= 26; read2= 46).

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We are submitting raw data to dbGaP
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first: Jenkins

last: Russell


title: Exponential expansion of CD34+ cells in response to StemRegenin-1 occurs with minimal changes in gene expression

city: Pretoria

first: Juanita

last: Mellet

state: Gauteng

address: 5 Bophelo road

department: Immunology

country: South Africa

institute: University of Pretoria

summary: Hematopoietic stem/progenitor cell transplantation (HSCT) is a well-established treatment option for hematological and other disorders. Umbilical cord blood (UCB) is a rich source of hematopoietic stem and progenitor cells (HSPCs). Cluster of Differentiation (CD)34 is commonly used as a cell surface marker to identify and isolate HSPCs. Transplantation using a single UCB unit may be associated with delayed hematopoietic reconstitution as it may not contain a sufficient number of HSPCs required for adult transplantation. One way of overcoming this limitation is through ex vivo expansion of UCB-derived HSPCs using the aryl hydrocarbon receptor (AhR) antagonist, StemRegenin-1 (SR1), which promotes the expansion of HSPCs. Our study investigated the effects of SR1 on the transcriptome of expanded CD34+ cells from UCB, and we also report on a comparison between the transcriptome profiles of 7-day expanded and non-expanded CD34+ cells. CD34+ HSPCs expanded with SR1 for 7 days displayed two significantly downregulated genes, cytochrome P450, family 1, subfamily B, polypeptide 1 (CYP1B1) and erythrocyte membrane protein band 4.1-like 3 (EPB41L3), when compared to controls (without SR1). Transcriptome analysis of CD34+ HSPCs expanded for 7 days using SR1 revealed that 391 genes were significantly upregulated, while 456 genes were significantly downregulated when compared to non-expanded CD34+ cells. In conclusion, though hundreds of genes were differentially expressed between SR1-expanded and non-expanded CD34+ HSPCs, only two genes were significantly downregulated in cells expanded for 7 days with SR1 versus control at the same time point (without SR1).

overall_design: RNA was extracted from freshly isolated CD34+ cells (Day0, D0) and 7-day expanded CD34+ cells (Day 7, D7) with and without SR1.

first: Chrisna

last: Durandt

first: Melvin

last: Ambele

first: Michael

last: Pepper


title: Gene Expression Regulation in Brain Underlying Innate Immune Memory

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

institute: University of British Columbia

summary: As the brain’s resident immune cells, microglia upregulate inflammatory gene expression to promote immune functions. Following the response to early life infection, microglia can remain in a “primed” state in which a subsequent immune trigger produces a hyper-activation. Paradoxically, multiple repeated immune activating events can lead to tolerance, the suppression of immune gene expression and function. Both priming and tolerance represent a form of cellular memory that may be disrupted in neurodevelopmental disorders and is largely unexplored in microglia. We hypothesize that acute versus repeated immune activation engages expression of distinct sets of genes, leading to either microglial priming or tolerance. Using in vivo peripheral injections of low dose liposaccharide (LPS 500ug/kg intraperitoneal) to mimic bacterial infection in mice, we compared animals recievig 1, 2, 3, or 4 daily doses of LPS compared to Vehicle (PBS) controls. We examined tissue from three brain regions, the hippocampus, striatum and frotal cortex by RNAseq.

overall_design: 10 week old male mice were injected intraperitoneally with low-dose lipopolysaccharide (LPS, Sigma) at a daily dose of 500 ug/kg bodyweight or an equal volume of vehicle PBS. Each mouse was given a total of four injections spaced 24 hours apart. Animals received either four LPS injections on four consecutive days (4xLPS), a single vehicle injection followed by three LPS injections on the following three days (3xLPS), two vehicle injections on two consecutive days followed by two LPS injections on the following two days (2xLPS), three vehicle injections on three consecutive days followed by a single LPS injection on the fourth day (1xLPS), or four vehicle injections (PBS control).