title: Association between gut microbiota and CpG island methylator phenotype in colorectal cancer [DREAM]

first: Jean-Pierre

last: Issa

overall_design: DNA was isolated from human colorectal cancer tumor and adjacent normal tissue samples and performed Digital Restriction Enzyme Analysis of Methylation (DREAM) for methylation profiling.

first: Pyoung Hwa

last: Park

first: Kelsey

last: Keith

first: Gennaro

last: Calendo

first: Jaroslav

last: Jelinek

first: Jozef

last: Madzo

first: Raad

last: Gharaibeh

first: Jayashri

last: Ghosh

first: Carmen

last: Sapienza

first: Christian

last: Jobin


title: Conserved intronic secondary structures with concealed branch sites regulate alternative splicing of poison exons

status: Public on Jun 12 2024

city: Shanghai

first: Zhan

last: Ding

address: 300 Feng Lin Road

country: China

institute: CAS Center for Excellence in Molecular Plant Sciences

type: Expression profiling by high throughput sequencing

summary: Alternative splicing (AS) generates large amounts of RNA isoforms and dramatically increases the complexities of transcriptomes and proteomes. However, it remains unclear how RNA structures contribute to AS regulation. Here, we systematically search transcriptomes for secondary structures with concealed branch-sites (BSs) in the alternatively spliced introns and predict thousands from six organisms, of which many are evolutionarily conserved. Intriguingly, a highly conserved stem-loop structure with concealed BSs is found in animal SF3B3 genes and colocalizes with a downstream poison exon (PE). Destabilization of this structure allows increased usage of the branch sites and results in enhanced PE inclusion in both human and Drosophila cells, leading to decreased expression of SF3B3. Through an RNAi screen of 28 RNA-binding proteins, we find that this stem-loop structure is sensitive to U2 and U2-associated proteins. Furthermore, we find that SF3B3 also facilitates DNA repair and protects genome stability by enhancing interaction between ERCC6/CSB and arrested RNA polymerase II. Importantly, both Drosophila and human cells with the secondary structure mutated by genome editing exhibit altered DNA repair in vivo. This study provides a novel and common mechanism for AS regulation of PEs and reveals a physiological function of SF3B3 in DNA repair.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design:
To investigate the differernce of gene expression and splicing between SF3B3-MMS1 overexpression cell line and contral cell line, we established  SF3B3-MMS1 overexpression cell and performed RNA-seq.
To investigate the structure in target region of SF3B3, we incubated 293T cells with NAI-N3 and then  performed RNA-seq to detect the mutation rate of target region between contral and NAI-N3 treated cell lines.

first: Hao

last: Li

first: Yong-Zhen

last: Xu


title: Transgenerational effects of exercise on mouse brain and cognition

city: Madrid

first: José Luis

middle: Trejo

last: Pérez

state: Madrid

address: Av. Dr. Arce, 37

department: Neurociencia Traslacional

country: Spain

institute: Instituto Cajal, CSIC

summary: Lifestyle induces long lasting effects on the brain and cognition, with some interventions like stress including transgenerational inheritance on the next generations mediated by epigenetic mechanisms. Physical exercise is one potent intervention driving robust improvements of cognition and brain health, also inducing intergenerational transmission to the litter. However, little is known about whether exercise effects may be transgenerationally transmitted. Here we analyzed the adult hippocampal neurogenesis (AHN) and the behavioral phenotype of sedentary adult male mice of the F2 generation of exercised grandfathers (F0, patrilineal design). Both F1 and F2 were sedentary, while F0 performed a moderate exercise training. We found that the F2 mice from exercised F0 acquired and recalled both spatial and non-spatial information better than F2 from sedentary F0. Contextual fear conditioning resulted not affected, together with no differences in the AHN markers. These results demonstrate that the transgenerational transmission of the effects of exercise on specific cognitive tasks persists after two generations, even though some of the cellular changes induced in F1 disappear in F2, and suggest that moderate exercise training has a longer-lasting effect than previously thought, and this aspect is worth taking into account in public health programs.

overall_design: Comparative profiling analysis of miRNA-seq data of F2 generation of exercised grandfathers (F0, patrilineal design) vs F2 generation of sedentary grandfathers.

first: Elisa

last: Cintado

first: Patricia

last: Tezanos

first: Manuela

last: De las Casas

first: Pablo

last: Muela

first: Kerry

middle: R

last: McGreevy

first: Ángela

last: Fontán-Lozano

first: Eva

last: Sacristán-Horcajada

first: Jaime

last: Pignatelli

first: María

last: Jesús del Hierro

first: Julia

last: Fernández-Punzano

first: Lluis

last: Montoliu

first: José

middle: L

last: Trejo


title: Transcriptome analysis revealed the genes involved in cold stress during flowering from Prunus sibirica

city: shenyang

first: quangang

last: liu

state: liao ning

address: maguanqiao

department: Forestry College

institute: Shenyang Agricultural University

summary: Through transcriptome sequencing analysis of clones with strong freezing resistance (CR_453) and weak freezing resistance (NC_371) of Prunus sibirica，a total of 15,228significantly differentially expressed genes were obtained. Among them, there are 6,630 up-regulated genes and 8,598 down-regulated genes. Differential genes are compared and screened, and B3, MYB, AAA, zf-GRF,  bHLH, TCP, WD40, HSP, PPR, Zim, AP2, CBF, etc, Freeze-related gene family.It is also found that a large number of gene families are regulated by hormones, including GST_N、Auxin_inducible， Abhydrolase_1，P450，AP2，ADH_N，Zim，HATPase_c，2OG-FeII_Oxy，IPPT，C2，RRM_1and so on.

overall_design: Using Prunus sibirica flower organs with strong frost resistance clone No. 453 (treatment group) and weak frost resistance clone No. 371 (control group) as the test materials, flowers were collected  at 0 h, 15min, 30min, 1h, 2h  when the flower organs were subjected to frost (-4 °C). The clones were repeated 3 times, placed in liquid nitrogen, stored in an ultra-low temperature refrigerator (-80 °C), and transcriptome sequencing was completed by Nuovo Zhiyuan (Beijing) Co., Ltd.

first: Liu

last: Quangang

first: Dong

last: Shengjun

first: Zhao

last: Shuo


title: MR1 presents sulfated bile acid as a self antigen for MAIT cells [PBMC]

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

summary: To investigate the effect of cholic acid sulfate to MAIT cells, PBMCs were stimulated with each antigen (5-OP-RU, cholic acid sulfates; CA3S and CA7S) and scRNA sequencing was performed. the homeostatic related genes expressed in cholic acid sulfate stimulation, while the inflammatory related gene expressed in 5-OP-RU stimulation. This analysis showed that cholic acid sulfate contributes to maintenance of MAIT cells.

overall_design:
PBMCs were stimulated with 5-OP-RU, CA3S and CA7S. 17 days later, CD161+MR1-5-OP-RU tetramer+ cells were sorted and analyed using single-cell TCR- and RNA-seq.

Hashtag sample definitions:
Hash_tag_1, non-stimulated
Hash_tag_2, 5-OP-RU (5-(2-oxo-propylidenamino)6-D-ribitylaminouracil) 10  M
Hash_tag_3, Cholic acid 3-sulfate 1000  M
Hash_tag_4, Cholic acid 3-sulfate 300  M
Hash_tag_5, Cholic acid 7-sulfate 1000  M
Hash_tag_6, Cholic acid 7-sulfate 300  M
Hash_tag_7, Cholic acid 7-sulfate 100  M

first: Emi

last: Ito

first: Yu-Chen

last: Liu

last: Okuzaki

first: Sho

last: Yamasaki


title: Bone Marrow-Derived Mesenchymal Stem Cell Secretome Alters Gene Expression and Upregulates Motility of Human Endometrial Stromal Cells

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

country: USA

institute: Rutgers

summary: Cyclic regeneration of the endometrium, and its repair after parturition or injury, are crucial for successful reproduction.  Mesenchymal stem cells (MSCs) derived from bone marrow (BM-MSC) facilitate tissue repair via their secretome, which contains growth factors and cytokines that promote wound healing.  Despite the implication of MSCs in endometrial regeneration and repair, the mechanisms remain unclear.  This study tested the hypothesis that the secretome of MSCs from human BM upregulates human endometrial stromal cell (HESC) proliferation, migration and invasion, and activates pathways to increase HESC motility.  MSCs were purchased from ATCC (BM-MSC-1) and cultured from the BM aspirate of a healthy female donor (BM-MSC-2). Indirect co-culture of MSCs and hTERT-immortalized HESCs via a transwell system studied the effect of the BM-MSC secretome on HESC proliferation, migration, and invasion. To study the effect of the MSC secretome on HESC gene expression, HESCs were exposed to the BM-MSC secretome via indirect co-culture for 24 h. Total RNA was extracted from HESCs for RNA sequencing (RNA-Seq). Differentially expressed genes (DEG) and significantly altered pathways were identified.    Indirect co-culture of HESCs with BM- MSCs resulted in significant increase in HESC migration and invasion regardless of the source of MSCs. Effects on cellular proliferation varied among the BM-MSC source. Exposure of HESCs to the secretome of BM-MSCs changed the expression of 10,141 genes with FDR  < 0.05. There was overlap among 4351 genes between HESCs exposed to BM-MSC-1 and BM-MSC-2, including upregulated expression of cell motility genes common to both BM-MSC exposures.  Increased HESC motility by the secretome of BM-MSC appears to be mediated by paracrine and autocrine mechanisms, in part by modifying HESC gene expression.  These data support the potential for leveraging the MSC secretome as a novel cell-free therapy in the treatment of disorders of endometrial regeneration.

overall_design: 9 hTERT-immortalized human endometrial stromal cell (HESC) samples were analyzed; n=3 replicate samples for HESC exposed to BM-MSC purchased from ATCC (BM-MSC-1) (HESC+BM-MSC-1-1, HESC+BM-MSC-1-2, HESC+BM-MSC-1-3), n=3 replicate samples for HESC exposed to BM-MSC isolated from healthy female donor BM (BM-MSC-2) (HESC+BM-MSC-2-1, HESC+BM-MSC-2-2, HESC+BM-MSC-2-3), and n=3 replicate samples for the control group exposed to control media without MSCs (HESC-1, HESC-2, HESC-3).

first: Qingshi

last: Zhao

first: Karla

last: Larios

first: Lauren

last: Sherman

first: Kennisha

last: Okereke

first: Pranela

last: Rameshwar

first: Nataki

middle: C

last: Douglas

first: Sara

middle: S

last: Morelli


title: The small non-coding RNA Vaultrc5 is dispensable to mouse development

status: Public on Jun 11 2024

city: Bethesda

first: Joana

middle: A

last: Vidigal

state: MD

address: 37 Convent Dr, Room 6056

department: LBMB

institute: NIH/NCI

summary: Vault RNAs (vRNAs) are evolutionarily conserved small non-coding RNAs transcribed by RNA polymerase lll. Initially described as components of the vault particle, they have since also been described as noncanonical miRNA precursors and as riboregulators of autophagy. As central molecules in these processes, vRNAs have been attributed numerous biological roles including regulation of cell proliferation and survival, response to viral infections, drug resistance, and animal development. Yet, their impact to mammalian physiology remains largely unexplored. To study vault RNAs in vivo, we generated a mouse line with a conditional Vaultrc5 loss of function allele. Because Vaultrc5 is the sole murine vRNA, this allele enables the characterization of the physiological requirements of this conserved class of small regulatory RNAs in mammals. Using this strain, we show that mice constitutively null for Vaultrc5 are viable and histologically normal but have a slight reduction in platelet counts pointing to a potential role for vRNAs in hematopoiesis. This work paves the way for further in vivo characterizations of this abundant but mysterious RNA molecule. Specifically, it enables the study of the biological consequences of constitutive or lineage-specific Vaultrc5 deletion and of the physiological requirements for an intact Vaultrc5 during normal hematopoiesis or in response to cellular stresses such as oncogene expression, viral infection, or drug resistance.

overall_design: Total RNA sequencing of livers and brains of 7-9 week old male mice wild-type or ko for vaultrc5

first: Mahendra

last: Prajapat


title: MR1 presents sulfated bile acid as a self antigen for MAIT cells [single-cell RNA-seq]

summary: To investigate the contribution of novel antigen for MAIT cells; Cholic acid sulfate, we established Sult2a KO mice lacking antigen-producing the enzyme. We performed scRNA sequencing of whole thymocyte and liver cells from these and wild type mice. Sult2a was deficient in hepatocytes, whereas there was no change in other genes or cell proportions, suggesting that deficient of Sult2a did not affect to other genes. The analysis of thymocye implied that cholic acid sulfate may have affected the MAIT subsets.

overall_design: Whole thymocyte and density fractionated-liver cells from 5-week-old wild type and Sult2aΔ1-8/Δ1-8 mice were analyzed using scRNA sequencing.


title: Transcriptomic responses in the host during mosquito-transmitted  and blood passaged Plasmodium chabaudi infections.

city: London

first: Jean

last: Langhorne

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: Plasmoidium chabuadi AS infections initiated by mosquito transmitted infections give rise to an attenuated blood-stage infection when compared to serially blood passaged parasites. Furthermore, Plasmoidium chabuadi CB infections have an increased virulence as compared with Plasmoidium chabuadi AS. We compared the immune response in the spleens induced by these two types of parasites and two types of infection routes in order to determine what may cause this attenuation.  Spleens were taken at several timepoints during the blood-stage infection and RNA-seq analysis was performed.

overall_design: 6 Time points - (Days post blood cycle infection 3,6,9,12,30, 60)  2 infection conditions (MT and SBP) and two parasite strains (P.chaubadi AS and P.chabaudi CB). Each group used age/sex matched C57BL/6 mice, with at least 3 replicates in infection groups. Controls/Naïve mouse with no infection were age/sex matched.

first: Jingwen

last: Lin

first: Chris

last: Alder

first: Caroline

last: Hosking

first: Sarah

last: Manni


title: Whole transcriptomes analyses of HGC-27 cell line treated with control DMSO, disulfiram, thiram or CX-6258

city: shanghai

first: yang

last: tang

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: Purpose: To figure out the molecular function of disulfiram, thiram and CX-6258, RNA sequencing was performed to analyze the geome-wide change of disulfiram, thiram and CX-6258 treated HGC-27 cells compared to those of control DMSO treated cells.         Methods: Total mRNA was extracted from HGC-27 cells. Then RNA quality was assessed using an Agilent Bioanalyzer 2100 and the sample reads were sequenced using Illumina Hiseq 4000 platform. As a reasult, we got the transcript data using Hisat2 followed by Stringtie. qRT–PCR validation was performed using TaqMan and SYBR Green assays.    Conclusion: The results showed disulfiram, thiram and CX-6258 may target distinct combinations of various pathways including Hippo pathway. The Hippo signaling indeed can be targeted by disulfiram, thiram and CX-6258 even though these compounds also interfere with other biological processes.

overall_design: Total mRNA was extracted from HGC-27 cells treated with control DMSO, disulfiram, thiram or CX-6258. The quality was assessed using Agilent 2100, and the profiles were sequenced on the Illumina NovaSeq 6000.

first: Yang

last: Tang

first: Shi

last: Jiao

first: Zhaocai

last: Zhou


title: Effect of lincRNA-p21 knockout (KO) in ventricles 8 weeks after sham/Transverse aortic restriction (TAC) surgeries

city: Boston

first: Yi

last: Wang

state: MA

address: 320 Longwood Avenue

institute: Boston Children's Hospital

summary: Cardiac hypertrophy is an adaptive response to pressure overload aimed at maintaining cardiac function. However, prolonged hypertrophy significantly increases the risk of maladaptive cardiac remodeling and heart failure. The role of cardiac long non-coding RNAs in cardiac hypertrophy and cardiomyopathy is not well understood. lincRNA-p21 was induced in mouse and human cardiomyopathy tissue. Global and cardiac-specific lincRNA-p21 knockout significantly suppressed pressure overload-induced ventricular wall thickening, stress marker elevation, and deterioration of cardiac function. Genome-wide transcriptome analysis and transcriptional network analysis revealed that lincRNA-p21 acts in trans to stimulate the NFAT/MEF2 pathway. Mechanistically, lincRNA-p21 bound to the scaffold protein KAP1. lincRNA-p21 cardiac-specific knockout suppressed stress-induced nuclear accumulation of KAP1, and KAP1 knockdown attenuated cardiac hypertrophy and NFAT activation. KAP1 positively regulated pathological hypertrophy by physically interacting with NFATC4 to promote the overactive status of NFAT/MEF2 signaling. Importantly, GapmeR ASO depletion of lincRNA-p21 similarly inhibited cardiac hypertrophy and adverse remodeling, highlighting the therapeutic potential of inhibiting lincRNA-p21.

overall_design: To measure transcriptomic changes genome-wide, we performed RNA sequencing using ventricular apexes of lincRNA-p21 global KO mice and littermate controls at 8 weeks after sham or TAC surgery.

first: Dazhi


title: Effect of lincRNA-p21 knockdown on neonatal mouse cardiomyocytes (CMs) treated with phenylephrine (PE)

overall_design: To elucidate the mechanisms underlying the salutary effect of lincRNA-p21 inhibition, we used cultured neonatal mouse cardiomyocytes (CMs) treated with the hypertrophic agonist phenylephrine (PE) for 24 hours to simulate the short-term hypertrophic response in CMs. To avoid the potential effect on cis regulatory elements and nascent RNA products resulting from genomic DNA manipulation, we utilized  GapmeR antisense oligonucleotide (ASO) to knockdown the linRNA-p21 level (gr-Lp21) through RNase H-dependent degradation mechanisms.


title: PFOS exposure/diet effects on intestinal tissue

city: Lexington

first: Yekaterina

last: Zaytseva

state: KY

address: 760 Press ave

department: Toxicology and Cancer Biology

institute: University of Kentucky

summary: PFOS, a member of the chemical group known as per- and polyfluoroalkyl substances (PFAS), is a well-documented environmental contaminant. Its high bioaccumulation potential and long elimination half-life can disrupt multiple biological pathways negatively affecting human health. The gastrointestinal tract (GI) is directly exposed to environmental pollutants via contaminated drinking water and food, potentially influencing intestinal homeostasis under both physiological and pathological conditions. Although some studies have highlighted the potential role of PFOS in tumor development, scientific literature on PFOS exposure in the GI is limited and the association between this environmental pollutant and GI-associated diseases remains to be determined. Therefore, this study aims to delineate the effects of PFOS on normal intestinal cells. The effect of PFOS on gene expression profiles was assessed through RNAseq analysis conducted on the intestinal tissue of C57BL/6 mice. Through RNAseq analysis, we identified the top pathways upregulated by PFOS as cancer, lipid metabolism and immune system. The KEGG analysis further highlighted significant gene enrichment in pro-oncogenic signaling pathways, including NOTCH, WNT/β-catenin and TGF-β. The RNAseq, q-RT-PCR and western blot analyses of normal intestinal tissues revealed that PFOS exposure leads to downregulation of 3-hydroxy-3-methylglutaryl-Coa synthase 2 (HMGCS2), a key enzyme in the synthesis of β-hydroxybutyrate (βHB), a critical ketogenic molecule.  In summary, our data suggests that PFOS may induce GI pathological changes that can increase the risk of CRC development. We identified that downregulation of ketogenesis and upregulation of lipid metabolism are the major effects of PFOS exposure in intestinal epithelium.

overall_design: To investigate the effect of PFOS in gene expression profile in normal intestinal tissues, we used 7-week-old C57BL/6 male mice. The mice were placed on an irradiated diet supplemented with one of three fibers: cellulose (control), inulin, or pectin.  The mice were exposed to PFOS at 3μg/Kg BW per day by drinking water and maintained on the diet for 7 weeks. The composition of the diets was the following: Fiber: 8% wt/wt, Fat: 35% kcal, protein: 20% kcal and carbohydrate: 45% kcal.

first: Josiane

middle: W

last: Tessmann

first: Jerika

last: Durham

first: Ryan

last: Goettl

first: Daheng

last: He

first: Chi

first: Pan

last: Deng

first: Bernhard

last: Hennig

middle: Y


title: Development of MDM2-targeting PROTAC technology for advancing bone regeneration

city: Seoul

first: Sol

last: Jeong

address: Gwanakgu, Gwanakro1

country: South Korea

institute: SNU

summary: MDM2 inhibitor remarkably induced biomineralization in hDPSCs but it remained the problem that p53 activation is insufficient due to MDM2-p53 autoregulatory feedback loop. To overcome the limitation of the MDM2 inhibitors, we applied proteolysis targeting chimera (PROTAC), a technology that degrades a protein of interest (POI) by intracellular ubiquitin-proteasome system. Hence, we propose a strategy to induce hard tissue regeneration by MDM2-targeting PROTAC technology. We selected Nutlin-3 of POI ligand among various MDM2 inhibitors based on the screening process, and the selected CRBN of E3 ligase ligand. The MDM2-PROTAC synthesis platform was designed by each ligand combination. By performing the degradation test for selected compounds, we evaluated the characteristics of the developed MDM2 PROTAC such as the maximal degradation concentration (DCmax), the half of maximal degradation concentration (DC50), and half-lifetime. To investigate gene expression profiling of MDM2-targeting small molecules, we conducted RNA-sequencing under MDM2 PROTAC and Nutlin-3 (POI ligand) treated conditions. We not only confirmed a robust effect on biomineralization by MDM2-targeting small molecules but also demonstrated the potent osteogenic differentiation ability of MDM2 PROTAC when compared to an MDM2 inhibitor. MDM2-PROTAC significantly increased mRNA levels of osteogenic differentiation marker genes. Also, the significant bone generation effect of MDM2 PROTAC was validated in an ovariectomy (OVX)-induced osteoporosis animal model. Through these results, it is expected that a new therapeutic modality for hard tissue regeneration will be possible, and the application range of the PROTAC system can be expanded.

overall_design: RNA-sequencing was performed to comparative gene profiling of developed MDM2-targeting PROTACs, Nutlin-3 (POI ligand) and Control group in osteoinductive condition in hBMSCs.

first: Jinman

last: Kim


title: Effect of CRY2 stabilizer and proteasome inhibitor on MDA-MB-231 cells

city: Los Angeles

first: Yuanzhong

last: Pan

state: California

address: 1002 Childs Way

institute: University of Southern California

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

overall_design: Refer to individual Series


title: Gene expression profiling of lung tissues comparing between Ism1-/- and Wildtype mice at postnatal day 7 (P7) stage

city: Singapore

first: Mahalakshmi

last: Shanmugasundaram

state: Singapore

address: 16, Science Drive 4, Blk S3, Level 6

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

summary: Isthmin 1 (ISM1) is a secreted protein of 60 kDa which has known functions of anti-apoptosis and anti-angiogenesis. To understand the physiological functions of ISM1, we generated Ism1 knockout (Ism1-/-) mice in C57BL/6J background through CRISPR gene editing technology. Under normal conditions, Ism1-/- mice presented spontaneous and progressive lung emphysema with enhanced immune cell infiltration compared to wildtype mice suggesting the role of ISM1 in pulmonary inflammation. In order to understand the pathways perturbed in the Ism1-/- mice, bulk RNA-sequencing analysis was performed using total RNA isolated from the lungs of WT and Ism1-/- mice at post-natal day 7 (P7) stage, when the process of alveolarization occurs.

overall_design: Total RNA extracted from whole lung tissue of WT and Ism1-/- mice at postnatal day 7 (P7) stage in triplicates

first: G

middle: E

last: Ruowen


title: H3K9me3 and H3K27me3 genomic occupancy on neonatal mouse cardiomyocytes (CMs) treated with PBS/phenylephrine (PE) and lincRNA-p21 WT/knockdown

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: To examine changes in H3K9me3 and H3K27me3 genomic occupancy upon lincRNA-p21 inhibition under hypertrophy condition, we performed chromatin immunoprecipitation followed by sequencing in cultured neonatal mouse CMs treated with lincRNA-p21 or negative control (NC) GapmeR under either PE or vehicle (PBS) treatment.


title: Chronic and acute exposure to rotenone lead to distinct Parkinson’s disease-related phenotypes in human iPSC-derived peripheral neurons

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary: Peripheral autonomic nervous system (P-ANS) dysfunction is a critical non-motor phenotype of Parkinson's disease (PD). While the majority of PD cases are sporadic with no identified PD-associated genes involved, epidemiological and animal model studies suggest an association with pesticides and other environmental toxins but underlying cellular mechanisms affecting the human P-ANS is unclear. Here, we mapped the global transcriptome changes in human induced-pluripotent stem cell (iPSC) derived P-ANS sympathetic neurons followed by exposure to the PD-related pesticide, rotenone. Surprisingly, we revealed distinct transcriptome profiles between acute and chronic exposure to rotenone. In the acute stage, there was a down regulation of specific cation channel genes mediating action potential signaling, while in the chronic stage, the human P-ANS neurons exhibited dysregulation of anti-apoptotic and Golgi apparatus-related pathways. Moreover, we identified the sodium voltage-gated channel subunit SCN3A/Nav1.3 as a potential biomarker in human P-ANS neurons associated with PD. Our analysis of the rotenone-altered coding and non-coding genome of human P-ANS neurons may thus provide insight into the pathological signaling events that occur in the sympathetic neurons during PD progression.

overall_design: Here we established a model of human P-ANS in PD by utilizing the pesticide, rotenone that is associated with increased PD risk, inhibits complex I of the mitochondrial respiratory chain, and reproduces PD pathological staging as found in patients.  By applying transcriptomics approach, we uncover molecular mechanisms by which rotenone causes pathology in human P-ANS neurons involving both functional abnormalities and specific neurodegeneration signaling.

first: Mahmood

last: Saleh

first: Fatima

last: Amer-Sarsour

first: Hila

last: Kobo

first: Gad

middle: D

last: Vatine

first: Avraham

last: Ashkenazi


title: The adhesin RadD enhances Fusobacterium nucleatum tumor colonization and colorectal carcinogenesis

first: Lu

last: Zhang

address: 145 Middle Shandong Road

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

summary: Fusobacterium nucleatum can bind to host cells and potentiate intestinal tumorigenesis. Here, we used a genome-wide screen to identify an adhesin, RadD, which facilitates the attachment of F. nucleatum to CRC cells in vitro. RadD directly binds to CD147, a receptor overexpressed on CRC cell surfaces, which initiated a PI3K-AKT-NF-κB-MMP9 cascade, subsequently enhancing tumorigenesis in mice. Clinical specimen analysis showed that elevated radD gene levels in CRC tissues correlated positively with activated oncogenic signaling and poor patient outcomes. Finally, blockade of the interaction between RadD and CD147 in mice effectively impaired F. nucleatum attachment and attenuated F. nucleatum-induced oncogenic response. Together, our study provides insights into an oncogenic mechanism driven by F. nucleatum RadD and suggests that the RadD-CD147 interaction could be a potential therapeutic target for CRC.

overall_design: To explore the downstream signaling pathway mediated by the RadD, we performed gene expression profiling of human colorectal camcer cell line HCT116 cells co-incubated with Fn WT and Fn ∆radD. Sample C_1, C_2 and C_3 were from PBS-treated cell; Sample WT100_1, WT100_2 and WT100_3 were from Fn WT-treated cell with MOI100; Sample Delta100_1, Delta100_2 and Delta100_3 were from Fn ∆radD-treated cell with MOI100.

first: Xiao-Xu

last: Leng

first: Jing-Yuan

last: Fang


title: Microglia contribute to methamphetamine reinforcement and reflect persistent transcriptional and morphological adaptations to the drug

city: Miami

first: Alexander

middle: Ve

last: Margetts

state: FL

address: 1600 NW 10th Ave, Rosenstiel Med Sci 7014A

department: Psychiatry and Behavioral Sciences

institute: University of Miami

summary: Methamphetamine use disorder (MUD) is a chronic, relapsing disease that is characterized by repeated drug use despite negative consequences for which there are currently no FDA approved cessation therapeutics. Repeated methamphetamine (METH) use induces long-term gene expression changes in brain regions associated with reward processing and drug-seeking behavior, and recent evidence suggests that methamphetamine-induced neuroinflammation may also shape behavioral and molecular responses to the drug. Microglia, the resident immune cells in the brain, are principal drivers of neuroinflammatory responses and contribute to the pathophysiology of substance use disorders. Here, we investigated transcriptional and morphological changes in striatal microglia in response to methamphetamine-taking and during methamphetamine abstinence, as well as their functional contribution to drug-taking behavior. We show that methamphetamine self-administration induces transcriptional changes related to protein folding, mRNA processing, immune signaling, and neurotransmission in striatal microglia. Importantly, many of these transcriptional changes persist through abstinence, a finding supported by morphological analysis. Functionally, we report that microglial ablation increases methamphetamine-taking, possibly involving neuroimmune and neurotransmitter regulation. In contrast, microglial depletion did not alter methamphetamine-seeking behavior following 21 days of abstinence, highlighting the complexity of drug-seeking behaviors. Taken together, these results suggest that methamphetamine induces both short and long-term changes in striatal microglia that contribute to altered drug-taking behavior and may be leveraged for preclinical development of methamphetamine cessation therapeutics.

overall_design: Mice were permitted to intravenously self-administer methamphetamine (0.05 mg/kg/inf dissolved in 0.9% saline) or saline during 15 daily 2-hr sessions. After 15 days of IVSA (Acquisition and Maintenance), mice underwent 21 days of forced home cage abstinence. Striatal microglia were isolated immediately after the final maintenance session (MN and SAL) and following abstinence (ABS).

first: Samara

middle: J

last: Vilca

middle: V

first: Leon

last: Höglund

first: Isabella

last: Fleites

first: Lauren

last: Bystrom

first: Tate

last: Pollock

first: Florence

last: Bourgain-Guglielmetti

first: Claes

last: Wahlestedt

first: Luis

middle: M

last: Tuesta


title: DNMT1 promotes cyst growth and epigenetic age acceleration in autosomal dominant polycystic kidney disease

city: Rochester

first: Xiaogang

last: Li

state: Minnesota

address: 200 1st Street, SW

institute: Mayo Clinic

summary: Alteration of DNA methylation leads to diverse diseases, and the dynamic changes of DNA methylation (DNAm) on sets of CpG dinucleotides in mammalian genomes, named as “DNAm age” and “epigenetic clocks” that can predict chronological age. However, whether and how dysregulation of DNA methylation promotes cyst progression and epigenetic age acceleration in ADPKD remains elusive. In this study, we show that DNA methyltransferase 1 (DNMT1) is upregulated in cystic renal epithelial cells and tissues, and that knockout of Dnmt1 and targeting DNMT1 with hydralazine, a safe demethylating agent, delays cyst growth in Pkd1 mutant kidneys and extends life span of Pkd1 conditional knockout mice. With methyl-CpG binding domain (MBD) protein-enriched genome sequencing (MBD-seq), DNMT1 chromatin immunoprecipitation (ChIP)-sequencing and RNA-sequencing analysis, we identify two novel DNMT1 targets, PTPRM and PTPN22 (members of the protein tyrosine phosphatase family), which function as mediators of DNMT1 and the phosphorylation and activation of PKD associated signaling pathways, including ERK, mTOR and STAT3. With whole genome bisulfide sequencing (WGBS) in ADPKD kidneys versus normal individuals, we found that the methylation of epigenetic clock associated genes were dysregulated, supporting that epigenetic age was accelerated in ADPKD kidneys. We further identify four epigenetic clock associated genes, including Hsd17b14, Mbnl1, Rassf5 and Plk2. The diverse biological roles of these four genes suggest that their methylation status may not only predict epigenetic age acceleration but also contribute to disease progression in ADPKD.

overall_design: We wanted to explore the association between the DNA methylation, cyst progression and aging acceleration in ADPKD. We performed DNMT1-ChIP-Seq and MBD-Seq in Pkd1 heterozygous PH2 cells or homozygous PN24 cells.

first: Julie

middle: X

last: Zhou

first: Xiaoyan


title: An inducible genetic tool for tracking and manipulating specific microglial states in development and disease

city: St. Louis

first: Kia

middle: Marie

last: Barclay

email: kbarclay@wustl.edu, qingyunli@wustl.edu

state: MO

address: 4370 Duncan Ave

department: Neuroscience

institute: Washington University in St. Louis

summary: Recent single-cell RNA sequencing studies have revealed distinct microglial states in development and disease. These include proliferative region-associated microglia (PAM) in developing white matter and disease-associated microglia (DAM) prevalent in various neurodegenerative conditions. PAM and DAM share a similar core gene signature and other functional properties. However, the extent of the dynamism and plasticity of these microglial states, as well as their functional significance, remains elusive, partly due to the lack of specific tools. Here, we report the generation of an inducible Cre driver line, Clec7a-CreERT2, designed to target PAM and DAM in the brain parenchyma. Utilizing this tool, we isolate and profile labeled cells during development and in several disease models, uncovering convergence and context-dependent differences in PAM/DAM gene expression. Through long-term tracking, we demonstrate surprising levels of plasticity in these microglial states. Lastly, we specifically deplete DAM in cuprizone-induced demyelination, revealing their roles in disease progression and recovery.

overall_design: Single microglia or myeloid cells from a given region were FACS sorted from female animal samples (Clec7aCreERT2;tdTomato) into 96-well plates. Libraries were prepared with a semi-automated Smart-seq2 protocol. Each Novaseq sequencing run was done by pooling ~350 cells with the unique Illumina 384 indexes.

first: Nora

last: Abduljaward

first: Zuolin

last: Cheng

first: Jin

last: Yang

first: Dvita

last: Kapadia

first: Tristan


title: Chronic treatment with glucagon-like peptide-1/glucagon receptor co-agonist causes weight-loss independent improvements in hepatic steatosis

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: Co-agonists at the glucagon-like peptide-1/glucagon receptors (GLP1R/GCGR) show promise as treatments for metabolic dysfunction-associated steatotic liver disease (MASLD). Unlike GLP1, glucagon directly acts on the liver to reduce fat content. To date most metabolic studies have looked at heavily GLP1R-biased co-agonists and have not distinguished weight-loss versus weight loss-independent effects. We demonstrate that 24 days’ treatment with Dicretin, a GLP1/GCGR co-agonist with high potency at the GCGR, in mice with hepatic steatosis secondary to diet-induced obesity leads to superior reduction of hepatic lipid content when compared to Semaglutide or equivalent weight loss by calorie restriction. Hepatic transcriptomic and metabolomic profiling demonstrated many changes that were unique to Dicretin-treated mice: some known targets of glucagon signalling and others with as yet unclear physiological significance. Our study supports the development of GLP1/GCGR co-agonists for treatment of MASLD and related conditions.

overall_design: Mice with hepatic steatosis and Diet Induced Obesity were treated with vehicle, Dicretin (a GLP1/GCGR co-agonist), Semaglutide (GLP1R agonist), or equivalent weight loss by calorie restriction. Four samples from each treatment group were selected for NGS sequencing, followed by Gene Set Enrichment Analysis.

first: Marian

last: Dore


title: Direct Reprogramming of Fibroblasts into Functional Mammary Epithelial cells by small molecules (bulk miRNA-seq)

city: Guangxi

first: ben

last: huang

address: NO.100. DAXUE EAST RD, Nanning

institute: School of Animal Science and Technology, Guangxi University

type: Non-coding RNA profiling by high throughput sequencing

summary: Mammary epithelial cells (MECs), the only cell type which could be capable of secreting milk in mammary gland, can be applied for the generation of transgenic mammary cell/gland bioreactor. However, continuously achieving large amount of high-quality goat MECs by non-invasion method, especially prepuberal MECs, in vitro has been a challenge. Here, we show that a small molecules cocktail enables the in vitro generation of chemically-induced mammary epithelial cells (CiMECs) with milk-secreting properties from goat ear fibroblasts. The properties of CiMECs were highly similar to those of naturally isolated MECs. Notably, the CiMECs lineage reprogramming process may partially imitate the MECs developmental process from embryonic to milk-secreting stages. Interestingly, fibroblasts were firstly reversed back to embryonic ectoderm/surface ectoderm-like state. Our findings constitute a substantial step toward further promoting the application of transgenic mammary bioreactors, moreover, also offer a new strategy for obtaining other cell types by reprogrammed fibroblasts.

overall_design: The six samples are analyzed. BERTV0d are control group with three replicates. BFRTV8d are treatment group with three replicates.

first: Dandan

last: Zhang

first: Ben

last: Huang


title: RNA-Seq of fibrillin 1 (Fbn1) tight-skin (Tsk) mice

first: Sandra

last: Orsulic

state: CA

address: 10833 Le Conte Ave

department: Obstetrics and Gynecology

institute: David Geffen School of Medicine at UCLA

summary: A fibrotic environment supports cancer growth. Our aim is to assess the transcriptomic differences by performing RNA sequencing in a fibrosis mouse model to provide insight into the increased growth of ovarian cancer in Fbn1 Tsk mice. Elucidating the targets important in fibrosis could provide potential clues to the mechanism of preferential cancer growth in fibrotic environments.

overall_design: Dermal mRNA profiles of 6-week old wild type (WT) and Fbn1+/- mice

first: Barbie

last: Taylor-Harding


title: mDRIP-seq: a high-throughput method for R-loop mapping and quantitative assessment

city: Shenzhen

first: Changbin

last: Sun

address: Dapeng

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

summary: Current methods for R-loop mapping need to perform DNA:RNA immunoprecipitation for each sample individually, with consequent limitations in throughput. Here, we develop and validate mDRIP-seq, a multi-sample barcoding and pooling method for R-loop mapping. We show mDRIP-seq performs equivalently as conventional methods, but with the merits of high throughput and cost-efficiency. We also show the simplicity of mDRIP-seq for relative and absolute quantitation of genomic R-loop fractions for multiple samples. Together, mDRIP-seq is a high-throughput and cost-efficient method for R-loop mapping and quantitative assessment and can be widely applied to large-scale dynamic profiles of these important structures for diverse organisms.

sample_organism:
Escherichia coli
Arabidopsis thaliana
Oryza sativa
Saccharomyces cerevisiae
Homo sapiens
Mus musculus

overall_design: mDRIP-seq development, and R-loop mapping in multiple samples

first: Wei

last: Xu


title: Differential gene expression in SK-MEL-5 and MALME-3M cell lines following IFN-γ treatment

status: Public on Jun 10 2024

city: Gent

first: Ramiro

last: Martinez

state: Flaanders

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: UGENT-OncoRNAlab

summary: This study explores the effects of IFN-γ treatment on gene expression in two melanoma cell lines, SK-MEL-5 and MALME-3M. Using RNA sequencing, we aimed to identify differentially expressed lncRNA genes that respond to IFN-gamma, which could illuminate pathways involved in immune response modulation in melanoma cells.

overall_design: We conducted an RNA sequencing experiment on both cell lines, both treated and non-treated with IFN-γ. Cells were seeded in 6-well plates in triplicates, and treatment was initiated at the time of seeding. IFN-gamma was administered for 24 hours, after which RNA was extracted using the miniRNAeasy kit (Qiagen, Cat# 217604) according to manufacturer’s instructions. Library preparation followed and RNAseq was performed with NovaSeq SP 200 kit (2 x 100 cycles).


title: Transcriptomes of individual Amphimedon queenslandica larvae and settled post-larvae that were presented with one of three different settlement cues at different times (hours) post emergence from the adult sponge

city: Brisbane

first: Tahsha

last: Say

state: QLD

address: The University of Queensland

department: School of Biological Sciences

country: Australia

institute: The University of Queensland

summary: To assess how larvae of different ages vary in their responses to different settlement cues, we induced individual Amphimedon queenslandica larvae with one of three different settlement cues at 1.5, 3, 5, and 8 hours post emergence (hpe) from the adult sponge. The settlement cues were (1) the articulated coralline algae Amphiroa fragilissima, (2) the crustose coralline algae Mesophyllum sp., and (3) the filtered seawater (FSW) negative control. We used CEL-Seq2, an RNA-Sequencing approach (Hashimshony et al., 2016), to generate transcriptome data for a total of 144 individuals (larvae and settled post-larvae) at 2 hours post induction (hpi) to the different settlement cues.

overall_design: Transcriptomic data for a total of 144 individual larvae and settled post-larvae of the sponge Amphimedon queenslandica that were exposed to one of three different settlement cues at 1.5, 3, 5 and 8 hours post emergence (hpe). The settlement cues were (1) the articulated coralline algae Amphiroa fragilissima (2) the crustose coralline algae Mesophyllum sp., and (3) the filtered seawater (FSW) negative control. To ensure that no behavioural interactions or conspecific cues would affect larval settlement responses, each larva was induced with a single piece of the inductive cue (~5 mm length A. fragilissima and ~5mm2 for Mesophyllum sp.) in a separate well of 12-well sterile polycarbonate tissue culture plates with 5 ml of 0.22 μm FSW. Settlement plates were placed on a dark surface under a natural day-night regime and were semi-submerged in flowing water from the reef to mimic ambient temperature fluctuations.    Swimming larvae and settled post-larvae were sampled for RNA-sequencing at 2 hours post induction (hpi) to a settlement cue (corresponding to larval ages of 3.5, 5, 7 and 10 hpe). Individual larvae (n = 9) were collected for gene expression analyses at 2 hpi to one of three different settlement cues (A. fragilissima, Mesophyllum sp. and the FSW negative control). Post-larvae (n = 7; but one treatment had 6) were sampled at 2 hpi to the coralline algae A. fragilissima and Mesophyllum sp., but only at 5 and 8 hpe as there was insufficient settled post-larvae at all other induction times. All settled post-larvae had attached to a substrate and were not dislodged by agitation (swirling) of the plate. We also collected larvae (n = 9) aged 0.5 hpe that had not been induced with a settlement cue, to act as the developmental controls.    Upon collection, larvae and post-larvae were immediately rinsed in a 50:50 sea water:RNAlater wash, and fixed in 100% RNA later (Invitrogen) at 4°C for 24 hours to allow the solution to thoroughly penetrate the tissue before being transferred to -80°C until processing as per manufacturer’s recommendations. RNA was isolated from individual larvae and settled post-larvae using TRIzol (Sigma) (Jindrich et al., 2017) and stored at -80°C in UltraPure™ DNase/RNase-free water (ThermoFisher) until further processing. PolyA libraries were prepared according to the CEL-Seq2 protocol (Hashimshony et al., 2016) and sequenced across three runs on two lanes of Illumina HiSeq2500 on rapid mode using HiSeq Rapid SBS v2 reagents (Illumina) at the Ramaciotti Centre for Genomics (University of New South Wales, NSW, Australia). CEL-Seq2 reads were processed using a publicly available pipeline (https://github.com/yanailab/CEL-Seq-pipeline). Read counts were obtained from demultiplexed reads mapped to A. queenslandica Aqu2.1 gene models (Fernandez-Valverde, Calcino, & Degnan, 2015).

first: Sandie

last: Degnan


title: Prediction of Non-Coding sRNAs and Screening of Virulence-Related sRNAs of Salmonella Pullorum

city: Haikou

first: HE

last: Ting

address: Hainan University, Meilan District, Haikou City, Hainan Province, China

institute: Hainan University

summary: Purpose: Searching for sRNAs in Salmonella pullorum by RNA sequencing and exploring their functions.Methods: High-throughput sequencing of RNA extracted from Salmonella pullorum under normal growth conditions to detect newly discovered sRNAs, followed by experiments to verify their functions.Results: The proportion of Clean Reads of this sequencing was >65%, and the base Q30s were all above 85%, indicating that the sequencing quality is good and can be used for subsequent analysis. The sRNAscanner software predicted that 148 new sRNAs might exist on the reference genome of Salmonella fowl dysentery, and the reads obtained from sequencing were compared to the genome, and it was found that 110 out of the 148 newly predicted sRNAs could be detected.Conclusions: sRNAs are widely found in bacteria and are involved in many physiological processes. In this study, we detected new sRNAs in Salmonella pullorum by RNA-seq, which lays the foundation for the subsequent investigation of the regulatory functions of sRNAs in bacteria.

sample_organism: Salmonella enterica subsp. enterica serovar Pullorum

overall_design: Salmonella pullorum were cultured to logarithmic growth in LB medium, total RNA was extracted ，in triplicate, and 150 bp bipartite sequencing was performed using an Illumina NovaSeq 6000 high-throughput sequencer.

first: Ting

last: He

first: Tiansen

last: Li


title: Bulk RNA-seq of siGFPT2 and NC grouped H1975 cells

city: Nanjing

first: Jiawen

last: Cui

state: Jiangsu

address: TongJiaXiang #24

institute: China Pharmaceutical University

summary: In the evolving field of cancer immunotherapy, EGFR-mutated NSCLC presents a significant challenge, demonstrating marked resistance to established treatments. An effective method to counter this resistance remains elusive. Through comprehensive genetic and pharmacological analyses across various models, we have identified glutamine fructose-6-phosphate transaminase 2 (GFPT2) as a key facilitator of immune evasion in EGFR-mutated NSCLC.

overall_design: In this experiment, we analyzed NC and siGFPT2 grouped H1975 cells on Illumina Novaseq 6000 platform to investigate the differential gene expression.

first: Luyao

last: Ao

first: Wenjing

last: Jia

first: Liu

last: Jiali


title: Bulk RNA-seq of H1975 cells treated with Almonertinib, EGF and EGFR-knockdown

summary: Through comprehensive genetic and pharmacological analyses across various models, we have identified glutamine fructose-6-phosphate transaminase 2 (GFPT2) as a key facilitator of immune evasion in EGFR-mutated NSCLC. Mechanistically, under EGFR mutation condition, GFPT2 expression, which is typically low in normal tissues, is highly induced via EGFR/IRE1α/Xbp1s signaling axis, leading to a significant increase in intracellular UDP-GlcNAc and consequently, an altered N-glycosylation profile.

overall_design: In this experiment, we analyzed H1975 cells treated with Almonertinib, EGF and EGFR-knockdown on Illumina Novaseq 6000 platform to investigate the differential gene expression.

first: Jiali

last: Liu


title: mDRIP-seq is a high-throughput method for quantitative R-loop landscape profiling

summary: Current methods for R-loop profiling need to perform experiments for each sample individually, with consequent limitations in throughput. Here, based on the barcoding strategy, we develop mDRIP-seq, a high-throughput method showing equivalent performance as conventional methods, but with merits of 7-fold less cost and 6-fold less hand-on time per sample. We also show the simplicity and effectiveness of mDRIP-seq for relative and absolute quantitation of genomic R-loop fractions for multiple samples. Together, mDRIP-seq is a high-throughput and cost-efficient method for R-loop mapping and quantitative assessment that can be widely applied to large-scale dynamic profiles of these important structures for diverse organisms.

platform_organism:
Escherichia coli
Arabidopsis thaliana
Oryza sativa
Saccharomyces cerevisiae
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Imbalance in Unc80 RNA Editing Disrupts Dynamic Neuronal Activity and Olfactory Perception

city: Taoyuan

first: Yi-Tung

last: Chen

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

summary: To investgate the funcitonal role of Unc80 by RNA editing mechanism

overall_design:
We performed gene expression profiling analysis using data obtained from RNA-seq of tissues (replicate)
Differentiated gene expression profiling analysis of RNA-seq data for Unc80 tissues

first: Hui-Wen

first: Chung-Pei

last: Ma


title: Transcriptomic analysis reveals the protective biomarkers of Pien Tze Huang in liver cirrhosis mice model [mRNA_lncRNA]

city: Shanghai

first: Qiange

last: Xiao

address: No. 1954 Huashan Road, Xuhui District

institute: Shanghaijiaotong University

summary: Cirrhosis has been one of the major causes of morbidity and mortality worldwide, but safe and effective therapy remains limited. A traditional Chinese medicine, Pien Tze Huang (PTH), has been reported to be effective in protecting the liver. Thus, in this study, we established a mouse cirrhosis model to investigate the effect of PTH on cirrhosis and the potential protective biomarkers using transcriptomic analysis. We identified 1689, 218, 61, and 145 differentially expressed mRNAs, lncRNAs, miRNAs, and circRNAs between the PTH treatment group and the cirrhosis group. Functional enrichment analysis demonstrated that biologically sensible GO terms, such as positive regulation of biological process and response to stimulus, and KEGG pathways, such as IL-17 signaling pathway and Steroid hormone biosynthesis, might be associated with PTH treatment. Similarity analysis based on the drug-induced gene expression profiles of Connectivity Map (version 2) suggested that PTH might have a similar effect to several drugs in clinical trials for cirrhosis. Finally, integration analysis of the competitive endogenous RNA network revealed that eight genes, i.e., P4ha1, Runx1, Inpp5d, Trp53inp1, Rrad, Pkm, Eva1a, and Jun, might be the potential protective biomarkers of PTH against cirrhosis.

overall_design: 18 male C57BL/6 mice were randomly divided into three groups, with 6 mice in each group. The groups were named as follows: the blank control group treated with corn oil and double distilled water (Control group), the liver cirrhosis model group treated with CCl4 and double distilled water (Cirrhosis group), and the PTH-treatment group treated with CCl4 and PTH (Cirrhosis-PTH group). After 12 weeks, the mice were sacrificed and their liver tissues were obtained for mRNA and lncRNA sequencing.

first: Hao

last: wu

first: Shengying

last: Qin


title: Transcriptomic analysis reveals the protective biomarkers of Pien Tze Huang in liver cirrhosis mice model [circRNA]

overall_design: 18 male C57BL/6 mice were randomly divided into three groups, with 6 mice in each group. The groups were named as follows: the blank control group treated with corn oil and double distilled water (Control group), the liver cirrhosis model group treated with CCl4 and double distilled water (Cirrhosis group), and the PTH-treatment group treated with CCl4 and PTH (Cirrhosis-PTH group). After 12 weeks, the mice were sacrificed and their liver tissues were obtained for circRNA sequencing.


title: Transcriptomic analysis reveals the protective biomarkers of Pien Tze Huang in liver cirrhosis mice model [miRNA]

overall_design: 18 male C57BL/6 mice were randomly divided into three groups, with 6 mice in each group. The groups were named as follows: the blank control group treated with corn oil and double distilled water (Control group), the liver cirrhosis model group treated with CCl4 and double distilled water (Cirrhosis group), and the PTH-treatment group treated with CCl4 and PTH (Cirrhosis-PTH group). After 12 weeks, the mice were sacrificed and their liver tissues were obtained for microRNA sequencing.


title: The cyclic-AMP binding domain of the efflux pump Rv3728 acts as a regulator of phosphatidyl-myo-inositol mannosides composition in Mycobacterium tuberculosis

city: London

first: Gerald

last: Larrouy-Maumus

address: South Kensington Campus

institute: Imperial College London

type: Genome variation profiling by high throughput sequencing

summary: Tuberculosis (TB) is an ancient disease caused by the intracellular bacterial pathogen Mycobacterium tuberculosis (Mtb). The rise of antimicrobial resistance (AMR) threatens to bring Mtb to the forefront of bacterial pathogens as the current treatments are increasingly becoming ineffective. Understanding the development of AMR and the virulence processes of Mtb is crucial for the identification of new drug targets and the rational design of anti-TB treatments. One of the established mechanisms of resistance is through the function of efflux proteins, which are transmembrane transporters that bind and remove antibiotic molecules out from the cell. Here, we determine the role of Rv3728, a major facilitator superfamily (MFS) efflux pump protein, which also predicted to bind 3',5'-cyclic adenosine monophosphate (cAMP). Using bioinformatic tools and cAMP binding assay, we confirm that Rv3728 binds to cAMP and identified E597 and R606 as important residues involved in binding. Although Rv3728 deletion has no impact on bacterial resistance and tolerance to different antibiotics, it affects membrane permeability and alters the acylation profile of phosphatidyl-myo-inositol mannosides lipids.

overall_design: Mycobacterium tuberculosis H37Rv KO and WT.

first: Vivian

last: Tounta

first: Moubani

last: Chakraborty

first: Yi

first: Nadia

last: Fernandes

first: Richard

last: Williams

first: Thomas

last: Meier

first: Julien

last: Vaubourgeix

first: Helene

last: Botella

first: Sandhya

last: Visweswariah


title: Mesenchymal stem cell-loaded hydrogel improves surgical treatment for chronic cerebral ischemia

city: Wuhan

first: Huayu

last: Kang

state: Hubei

address: Jiefang Avenue 1095,Qiaokou District

institute: Tongji Medical College, Huazhong University of Science & Technology

summary: Chronic cerebral ischemia (CCI) results in a prolonged insufficient blood supply to the brain tissue, leading to impaired neuronal function and subsequent impairment of cognitive and motor abilities. Our previous research showed that in mice with bilateral carotid artery stenosis, the collateral neovascularization post Encephalo-myo-synangiosis (EMS) treatment could be facilitated by bone marrow mesenchymal stem cells (MSCs) transplantation. Considering the advantages of biomaterials, we synthesized and modified a gelatin hydrogel for MSCs encapsulation. We then applied this hydrogel on the brain surface during EMS operation in rats with CCI, and evaluated its impact on cognitive performance and collateral circulation.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: For the rats 7 days post EMS treatment, mRNA and miRNA sequencing were performed on the temporal lobe of the brain. For RNA sequencing of rats, the control group consisted of bilateral common carotid artery occlusion (BCCAO) rats treated with EMS, while the experimental group consisted of BCCAO rats transplanted with BMSC-loaded hydrogel during EMS treatment.Besides, mRNA sequencing was conducted on stable overexpressing miR-183 and miR-96 cell lines for comparison with NC.


title: LiaR-dependent gene expression contributes to antimicrobial responses in group A Streptococcus [RNA-seq]

city: Houston

first: Anthony

last: Flores

state: TX

address: 6431 Fannin St., MSB 3.130

institute: UTHSC/McGovern Medical School

summary: The ability to sense and respond to host defenses is essential for pathogen survival. Some mechanisms involve two-component systems (TCS) that respond to host molecules, such as antimicrobial peptides (AMPs) and activate specific gene regulatory pathways to aid in survival. Alongside TCSs, bacteria coordinate cell division proteins, chaperones, cell wall sortases and secretory translocons at discrete locations within the cytoplasmic membrane, referred to as functional membrane microdomains (FMMs). In Group A Streptococcus (GAS), the FMM or “ExPortal” coordinates protein secretion, cell wall synthesis and sensing of AMP-mediated cell envelope stress via the LiaFSR three-component system. Previously we showed GAS exposure to a subset of AMPs (-defensins) activates the LiaFSR system by disrupting LiaF and LiaS co-localization in the ExPortal, leading to increased LiaR phosphorylation, expression of the transcriptional regulator SpxA2, and altered GAS virulence gene expression. The mechanisms by which LiaFSR integrates cell envelope stress with responses to AMP activity and virulence are not fully elucidated. Here, we show the LiaFSR regulon is comprised of genes encoding SpxA2 and three membrane-associated proteins: a PspC domain-containing protein (PCP), the lipoteichoic acid-modifying protein LafB and the membrane protein insertase YidC2. Our data show phosphorylated LiaR induces transcription of these genes via a conserved operator, whose disruption attenuates GAS virulence and increases susceptibility to AMPs in a manner primarily dependent on differential expression of SpxA2. Our work expands understanding of the LiaFSR regulatory network in GAS and identifies targets for further investigation of mechanisms of cell envelope stress tolerance contributing to GAS pathogenesis.

overall_design: Comparison of wild-type to mutants either lacking components of the LiaFSR two-component system, or isogenic mutants altered in ability of LiaS to phosphorylate/dephosphorylate LiaR

first: Luis

last: Vega

first: Misu

last: Sanson-Iglesias

first: Piyali

last: Mukherjee

first: Kyle

last: Buchan

first: Gretchen

last: Morrison

first: Anne

last: Hohlt


title: Interaction of solute carrier family 39 member 1 and dynamin related protein 1 to facilitate development of hepatocellular carcinoma by impairing mitochondrial quality control

city: ShenZhen

first: Rui

last: Li

state: Guangdong

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

summary: In this study, HCC samples from 12 non-relapsed and 15 relapsed HCC patients after surgically resection, were collected for RNA sequencing. Liver-specific SLC39A1 knockout mice (SLC39A1lko) were generated by crossing Alb-Cre mice and SLC39A1flox/flox mice. Liver samples from mice were analyzed for inflammation, fibrosis and proliferation. Mitochondrial dynamics, autophagy, ROS and mitochondrial membrane potential (MMP), were detected. Co-immunoprecipitation and molecular docking were used to identify protein interactions. Targeting 1-28 peptide of SLC39A1 was designed.

overall_design: Lentiviral pLKO.1-shRNA plasmids targeting SLC39A1, SLC50A1 and SLC66A3. For lentivirus packaging, pLKO.1-control, pLKO.1-shSLC39A1, pLKO.1-shSLC50A1 and pLKO.1-shSLC66A3 were transfected into HEK-293T cells using a co-transfection system (pMD2G: psPAX2: target plasmids = 1:3:4) with PEI. The culture supernatant was collected at 48 and 72 h after transfection and then filtered through a 450 nm filter. When cancer cells reached approximately 30% coverage in 6-well plates, 0.5ml of lentivirus, 0.5 ml of fresh medium were added for infection. After incubation for 24 h, puromycin (2 µg/µl) was used for three days to select cells that were successfully infected.

first: Zhe

last: Wang


title: PIK3CA inhibition in models of proliferative glomerulonephritis and lupus nephritis

city: Paris

first: Pierre

last: Isnard

address: 156-160, rue de Vaugirard

country: France

institute: INEM

summary: Proliferative glomerulonephritis is a severe condition often leading to kidney failure. There is a significant lack of effective treatment for these disorders. Here, following the identification of a somatic PIK3CA gain-of-function mutation in podocytes of a patient, we demonstrate using multiple genetically engineered mouse models, single-cell RNA sequencing and spatial transcriptomics the crucial role played by this pathway for proliferative glomerulonephritis development by promoting podocyte proliferation, dedifferentiation and inflammation. Additionally, we show that alpelisib, a PI3Kα inhibitor, improves glomerular lesions and kidney function in different mouse models of proliferative glomerulonephritis and lupus nephritis by targeting podocytes. Surprisingly, we determined that pharmacological inhibition of PI3Kα affects B and T lymphocyte population in lupus nephritis mouse models with decrease in the production of proinflammatory cytokines, autoantibodies and glomerular complement deposition, which are all characteristic features of PI3K delta (PI3Kδ) inhibition, the primary PI3K isoform expressed in lymphocytes. Importantly, PI3Kα inhibition does not impact lymphocyte function under normal conditions. These findings were then confirmed in human lymphocytes isolated from patients with active lupus nephritis. In conclusion, we demonstrate the major role played by PI3Kα in proliferative glomerulonephritis and show that in this condition, alpelisib acts on both podocytes and the immune system.

overall_design: Four µm of Alcohol Formalin and Acetic acid (AFA) fixed and paraffin embedded needle kidney biopsies from healthy control patients (n=4) and patients with severe lupus nephritis (n=4) were processed for digital spatial profiling to explore the glomerular-specific transcriptional programs of  crescentic extracapillary glomerular lesions of the selected 49 glomerular regions.

first: Junna

last: Yamaguchi

first: Guillaume

last: Canaud


title: LiaR-dependent gene expression contributes to antimicrobial responses in group A Streptococcus [ChIP-seq]


title: Investigation of molecular mechanisms of iron dependency alteration of ANKL by enviromental factors

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

institute: Saga University

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


title: Transcriptomic analysis of EPFL and Cycloheximide treated clv3 epfl1 epfl2 epfl4 epfl6 mutants

city: Philadelphia

first: Aman

middle: Yebio

last: Husbands

state: PA

address: 103B Caroline Lynch Bldg, 433 S University Ave

institute: The University of Pennsylvania

summary: Maintenance and regulation of the shoot apical meristem size and boundaries are essential for plant growth and leaf organogenesis. Canonically, CLAVATA 1, CLAVATA 3 and WUSCHEL control shoot apical meristem (SAM) size and SAM maintenance. Recently it has been shown that ERECTA (ER) family genes also control SAM size at its boundaries. The ERECTA family of receptor like protein kinases are bound by EPIDERMAL PATTERNING FACTOR LIKE (EPFL) protein ligands. Loss of the ER receptor genes or a subset of the EPFL ligands lead to an enlarged meristem. Loss of both CLAVATA genes and ER family genes synergize to produce even larger meristems with a loss of leaf production. In this experiment we perform deep sequencing to measure the transcriptome wide molecular changes in the clv3 epfl1 epfl2 epfl4 epfl6 quintuple mutant under mock, 3h ectopic EPLF6 ligand, 10 minute pretreatment with cycloheximide (CHX) and combined 10 minute CHX pretreatment followed by a 3h EPFL6 treatment. Treatment of the quintuple mutant with EPFL6 leads to a modest but targeted downregulation of MEI2 C-TERMINAL RRM ONLY LIKE 1(MCT1) RNA binding family proteins. CHX treatment was used to inhibit the translation of new proteins. By blocking new protein production, only direct signaling targets of EPFL6 would be seen. The severe toxic effects of CHX leads to a complete rearrangement of the transcriptome. However, EPFL6 still alters some CHX targets, mostly through downregulation.

overall_design: Pairwise comparisons on a two factorial design of Mock, EPFL6, cycloheximide and  EPFL6+cycloheximide treatment

first: Liang

last: Zhang

first: Ricardo

last: Urquidi Camacho

first: Elena

last: Shpak


title: Single-cell RNA sequencing reveals the evolution of immune landscape during perihematomal edema progression after intracerebral hemorrhage

city: Jining

first: Daojing

address: 89 Guhuai Road

department: Department of neurology

institute: Affiliated Hospital of Jining Medical University

summary: The complicated immune response in the post-intracerebral hemorrhage brain constitutes a crucial component of perihematomal edema pathophysiology. Here, we aimed to characterize the transcriptional profiles of immune cell populations in human PHE tissue

overall_design: A multi-stage profile was developed, comprising Group1 (n=3, 0-6 hours post-ICH, G1), Group2 (n=3, 6-24 hours post-ICH, G2), and Group3 (n=3, 24-48 hours post-ICH, G3).We employed single-cell RNA sequencing scRNA-seq to comprehensively map the immune cell populations in post-intracerebral hemorrhage samples which were resected from patients at different stages of post-ICH

first: Peng

first: Cong

last: Gao

first: Qiang

last: Guo


title: Protective function and differentiation cues of brain-resident CD8+ T cells during surveillance of latent Toxoplasma gondii infection

city: Toulouse Cedex 3

first: Nicolas

last: Blanchard

address: CHU Purpan BP3028

department: Inserm UMR1291

institute: Toulouse Institute for Infectious and Inflammatory Diseases (Infinity)

summary: Chronic Toxoplasma gondii infection induces brain-resident CD8+ T cells (bTr) but the protective functions and differentiation cues of these cells remain undefined.  Here, we used a mouse model of latent infection by T. gondii leading to effective CD8+ T cell-mediated parasite control.  Thanks to antibody depletion approaches, we found that peripheral circulating CD8+ T cells are dispensable for brain parasite control during chronic stage, indicating that CD8+ bTr are able to prevent brain parasite reactivation.  We observed that the retention markers CD69, CD49a and CD103 are sequentially acquired by brain parasite-specific CD8+ T cells throughout infection, and that a majority of CD69/CD49a/CD103 triple-positive (TP) CD8+ T cells also express Hobit, a transcription factor associated with tissue residency.  This TP subset develops in a CD4+ T cell-dependent manner, and is associated with effective parasite control during chronic stage.  Conditional invalidation of TAP-mediated MHC class I presentation showed that presentation of parasite antigens by glutamatergic neurons and microglia regulate the differentiation of CD8+ bTr into TP cells.  Single-cell transcriptomic analyses revealed that resistance to encephalitis is associated with the expansion of stem-like subsets of CD8+ bTr. In summary, parasite-specific brain-resident CD8+ T cells are a functionally heterogeneous compartment which autonomously ensure parasite control during T. gondii latent infection and which differentiation is shaped by neuronal and microglial MHC I presentation.  A more detailed understanding of local T cell-mediated immune surveillance of this common parasite is needed for harnessing brain-resident CD8+ T cells in order to enhance control of chronic brain infections.

overall_design: For 3' scRNA-seq: Facs-sorted CD103-negative vs. CD103-positive CD8+ Kb-OVA dex+ T cells from the different biological conditions were obtained in two independent experiments.  One experiment comprised an encephalitis (Tg.SAG1-OVA-infected C57BL/6) and latency (Tg.GRA6-OVA-infected C57BL/6) group analyzed at d52pi, and one comprised only the latency group analyzed at d160pi.  Single-cell libraries were generated immediately after Facs-sorting using Chromium Single Cell 3’ Library & Gel Bead Kit v3 according to the manufacturer’s protocol (10X Genomics).   For CITE-seq: CITE-seq dataset is derived from one experiment in which B6.Ld mice were infected with Tg.GRA6-OVA and analyzed at d46pi.  Brain-isolated CD8+ T cells were pooled from 4 mice and labeled with TotalSeqC CD3 and CD8 antibodies (Biolegend), and with PE-coupled dCODE Kb-OVA, Ld-GRA6 and Kb-SIYRYYGL control dextramers, to enable retrospective identification of OVA-specific and GRA6-specific cells among total CD8+ T cells.  dCODE dextramer-positive CD8+ T cells were enriched by 2 successive magnetic sorting steps.  Single-cell libraries were generated immediately with Chromium Next GEM Single Cell 5' Kit v2 and 5' Feature Barcode Kit according to the manufacturer’s protocol (10X Genomics).

first: Rémi

last: Porte

first: Marine

last: Alis


title: A synonymous mutation of rs1137070 cause the Mice Maoa gene transcription and translation to decrease

city: 郑州市

first: 凯欣

last: 李

state: 河南省

address: 郑州市高新区金梭路

institute: CTQTC

summary: Monoamine oxidase-A (MAOA) EcoRV polymorphism (rs1137070) is a unique synonymous mutation (c.1409 T >C) of the Maoa gene that plays a role in the expression and Maoa function. This study explored the relationship between the mouse Maoa rs1137070 and the differences in Maoa gene expression. The mouse with the CC genotype of rs1137070 had a lower odds ratio of 2.44 for the Maoa level compared with the T carriers. The TT wild genotype of Maoa had elevated mRNA expression and a longer half-life, significant expression and structure differences of genotype were explored. In addition, the Maoa with different aspartic acid synonymous codons affect Maoa expression and enzyme activity that underlines the association between rs1137070 and Maoa. A dual-luciferase reporter assay confirmed that GAC was more efficient than GAT binding. On the other hand, the synonymous mutation altered the Maoa gene expression in individual mice and RNA pull-down assay suggested that it could affect the interaction with RNA binding protein. The result illustrated that synonymous mutation can indeed regulate the downregulation of gene expression, leading to changes in Maoa function and neurological-related diseases.

overall_design: Transcriptome sequencing of six addiction-related brain regions in wild-type and Ki-type mice，We then performed gene expression profiling analysis using data obtained fromRNA-seg of 2 different genotypes.

first: Kaixin


title: AFF4 globally affects the release of paused RNA polymerase II in HEL cells [ChIP-seq]

city: Shang Hai

first: Zimei

last: Yang

address: Dongchuan road 800

institute: Shang Hai Jiaotong University

summary: P-TEFb, a heterodimer of kinase, CDK9, and Cyclin T1, is a critical regulator of promoter-proximal pause release of Pol II in metazoans. It is capable of forming three larger multiprotein complexes, including the super elongation complex (SEC), the BRD4/P-TEFb complex and the 7SK snRNP. In the SEC or the BRD4/P-TEFb, P-TEFb is enzymatically active, while in the 7SK snRNP, its activity is inhibited. The SEC consists of AFF1 or 4, ENL or AF9, ELL1, 2 or 3 and EAF1 or 2 in addition to P-TEFb, the only subunit with catalytic activity, and the noncatalytic subunits have been found to be able to regulate pause release through P-TEFb. One recent study showed that in human DLD-1 cells, the SEC only regulates pause release of heat shock (HS) genes, whereas the BRD4/P-TEFb complex regulates pause release of the rest of the genes. In this study, we found that AFF4 knockdown in human HEL cells decreased not only cellular level but also global chromatin occupancy of CTD serine 2 phosphorylated Pol II, and notably, increased promoter-proximal pause of Pol II on several hundred HS and thousands of non-HS genes. Mechanistically, AFF4 facilitates pause release likely by facilitating the binding of P-TEFb to Pol II. These results suggest that the extent of impact of AFF4 on pause release is likely to be context-dependent or cell-type dependent.

overall_design: Two wild type and two AFF4 knockdown with Pol II antibody

first: Ming

last: Yu

first: Ge


title: Notum Regulates the Cusp and Root Patterns in Mouse Molar

city: Seodaemun-gu

first: Sung-Won

last: Cho

state: Seoul

address: Yonsei-ro 50,

department: Department of Oral Biology

institute: Yonsei University College of Dentistry

summary: Notumis a direct target of Wnt/β-catenin signaling and plays a crucial role as a Wnt inhibitor within a negative feedback loop. In the tooth, Notum is known to be expressed in odontoblasts, and severe dentin defects and irregular tooth roots have been reported in Notum-deficient mice. However, the precise expression pattern of Notum in early tooth development, and the role of Notum in crown and root patterns remain elusive. In the present study, we identified a novel Notum expression in primary enamel knot (EK), secondary EKs, and dental papilla during tooth development. Notum-deficient mice exhibited enlarged secondary EKs, resulting in broader cusp tips, altered cusp patterns, and reduced concavity in crown outline. These alterations in crown outline led to a reduction in cervical tongue length, thereby inducing root fusion in Notum-deficient mice. Overall, these results suggest that the size of secondary EK size, regulated by the Wnt/Notum negative feedback loop, has a significant impact on the patterns of crown and root during tooth morphogenesis.

overall_design:
To investigate the gene expression pattern and the role of Notum in the developing tooth, Notum knockout mouse (Notumem1(IMPC)Tcp) generated on the C57BL/6N background strain were purchased from the international mouse phenotyping consortium (IMPC) and mated with C57BL/6N wild-type mice to get the future generations. All animal experiments were performed under approved protocols of the Intramural Animal Use and Care Committee of the Yonsei University College of Dentistry.
Notum-/- mice and the Notum+/+ control mice embryonic day (E) 14.5 and E16.5 maxillary and mandibular molar tooth germs RNA were isolated, and bulk RNA sequencing was performed.
Comparative gene expression profiling analysis of the RNA-seq data for Notum-/- mice and the Notum+/+ was performed at E14.5 and E16.5.

first: Dinuka

last: Adasooriya

first: Ju-Kyung

last: Jeong

first: Minjae

last: Kyeong

first: Shiqi

last: Kan

first: Jiwoo

last: Kim

first: Eui-Sic


title: Podocyte Epac1 promotes glycolysis and protects against glomerulonephritis

city: Toulouse

first: Maximin

last: Détrait

address: 1 avenue Jean Poulhès- BP 84225

institute: INSERM I2MC

summary: The second messenger cyclic AMP (cAMP) is involved in many aspects of renal physiology and disease. Epac is an effector of cAMP and its pathophysiological role in the development of chronic kidney diseases (CKD) has yet to be determined. Here, we show that total Epac1 isoform genetic deletion does not cause any baseline renal abnormalities but remarkably potentiates the deterioration of renal structure and function during the progression of the nephrotoxic serum (NTS)-induced glomerular nephritis (GN). Similarly, podocyte Epac1 deletion in podocytes exacerbated GN development. Global gene expression profile in mouse glomeruli using RNAseq analysis indicates a transcriptomic signature of GN related to immune system, extracellular matrix, and cytoskeleton gene dysregulation at the onset of the disease. Furthermore, glomeruli with podocyte Epac1 deletion display altered mitochondrion and metabolic processes in nephritic mice. Consistently, mechanistic analysis demonstrates that Epac1 activation increases human podocyte mitochondrial function to cope with extra energy demand in stress condition. Of particular importance, Epac1 increases aerobic glycolysis to ameliorate podocyte viability and motility. Therefore, the metabolic flexibility mediated by Epac1 constitutes a protective mechanism against podocyte injury. Altogether these data highlight the potential of Epac1 as a therapeutic approach for CKD treatment.

overall_design:
To investigate the role of podocyte Epac1 in GN progression, glomerulonephritis (GN) was induced in conditional knockdown 3-month-old female mice with specific Epac1 deletion in podocytes (NPHS2Cre: Epac1fl/fl) and in the littermate (Epac1fl/fl), by 2 consecutive days’ intravenous administration of decomplemented nephrotoxic serum (NTS; 18,5 µl/gBW), while the control mice were injected with PBS.
We examined RNA glomerular extracts from 21 female mice at two stages of the disease: early (day 4) and late (day 11).:
- PBS: 3 Epac1fl/fl; 3 NPHS2Cre: Epac1fl/fl
- NTS D4: 3 Epac1fl/fl; 4 NPHS2Cre: Epac1fl/fl
- NTS D11: 4 Epac1fl/fl; 4 NPHS2Cre: Epac1fl/fl
In order to perform comparative gene expression profilling analysis.

first: Lilia

last: Abbad

first: Christos

last: Chatziantoniou

first: Frank

last: Lezoualc'h


title: AFF4 globally affects the release of paused RNA polymerase II in HEL cells

overall_design: Refer to individual Series


title: AFF4 globally affects the release of paused RNA polymerase II in HEL cells [RNA-seq]

overall_design: Two wild type and two AFF4 knockdown

last: Zhang


title: PGE2 alters chromatin through H2A.Zvariant enhancer nucleosome modification to promote hematopoietic stem cell fate (RNA-Seq)

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: Hematopoietic stem and progenitor cells (HSPCs) need  require tight transcriptional regulation. In-depth knowledge on how epigenetic mechanisms  regulate chromatin landscape in order to control gene expression,  particularly in response to external stimuli, will be key to understand the pathogenesis of  hematologic disorders and improve blood stem cell-based therapies. Prostaglandin E2 (PGE2) and  its metabolically resistant analog 16,16-dimethyl-PGE2 (dmPGE2) were previously identified as a  potent external stimulus to enhance HSPC engraftment. PGE2 has been evaluated in various  clinical trials to improve engraftment of stem cells. To understand the mechanism of gene  expression changes, Wwe identified that dmPGE2 mediates chromatin flexibility at HSPC-specific  enhancers through histone-variant H2A.Z acetylation to promote master transcription factor (TF)  binding and reinforce expression of genes involved in stem cell fate and engraftment.

overall_design: ATAC-seq was performed, after a 2hr pulse with either dmPGE2 or DMSO on human CD34+ HSPCs

first: Audrey

last: Sporrij

first: Avik

last: Choudhuri

first: Meera

last: Prasad

first: Brejnev

last: Muhire

first: Eva

last: Fast

first: Margot

last: Manning

first: Jodi

last: Weiss

first: Michelle

last: Koh

first: Song

first: Robert

last: Kingston

first: Michael

last: Tolstorukov

first: Hans

last: Clevers

middle: I


title: PGE2 alters chromatin through H2A.Zvariant  enhancer nucleosome modification  to promote hematopoietic stem cell fate (ChIP-Seq)

last: Yang

first: Yi

last: Zhou


title: Inorganic Ions Activate Lineage-Specific Gene Regulatory Networks to Drive Stem Cells Differentiation

city: Bryan

first: Irtisha

last: Singh

address: 8447 Riverside Pkwy, Medical Research and Education Building II Suite 4344

department: Department of Molecular and Cellular Medicine

institute: Texas A&M University

summary: Bioactive aqueous inorganic ions facilitate human mesenchymal stem cell lineage commitment by directing biomolecular signaling

overall_design: Investigation of ions' impact on stem cell fate and molecular signaling cascades

first: Anna

last: Kersey

first: Akhilesh

middle: K

last: Gaharwar


title: PGE2 alters chromatin through H2A.Zvariant enhancer nucleosome modification to promote hematopoietic stem cell fate

first: Leonard

last: Zon


title: PGE2 alters chromatin through H2A.Zvariant  enhancer nucleosome modification  to promote hematopoietic stem cell fate (Mnase-Seq)

first: Audrey

last: Sporrij


title: PGE2 alters chromatin through H2A.Zvariant   enhancer nucleosome modification  to promote hematopoietic stem cell fate (ATAC-Seq)

first: Avik

last: Choudhuri


title: Quantification of salinity-induced gene expression in young AGB1-deficient roots

city: Taipei

first: Yueh

last: Cho

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

institute: Academia Sinica

summary: To further investigate the gene expression profiles in agb1 mutant seedlings responding to salt stress, we employed whole transcriptome microarray expression profiling as a discovery platform to identify genes with the potential to be regulated by AGB1-mediated signaling cascades. Arabidopsis thaliana 7-day-old wild-type and agb1-3 mutant roots were challenged by immersing in 150 mM NaCl containing MS liquid media for 0 or 4 hours, and 4,830 genes induced by high salinity were identified that distinguished between zero and four hours among wild-type and agb1-3 samples. Thirteen of the 22 gene expressions that are transcriptionally regulated by bZIP17 under salt stress were decreased in agb1-3 compared to wild-type roots. The expression of three genes (NAC019, RD20, and TSPO) from this group was quantified in the same RNA samples by real-time PCR, confirming lower expression in both agb1-3 and bzip17-4 roots.

overall_design: Salinity induced gene expression in 7-day-old Arabidopsis thaliana wild-type (Col-0 ecotype) and agb1-3 mutant root was treated with 150 mM NaCl for 0 and 4 hours in MS lipid media.  Three independent experiments were performed at each time (0 or 4 hours).


title: AFF4 globally affects the release of paused RNA polymerase II in HEL cells [PRO-seq]

first: Zimei

overall_design: One sample

first: Ming

last: Yu

first: Ge

last: Zhang


title: The neurotrophic factor neuritin impacts T cell electrical and metabolic state for the balance of tolerance and immunity.

city: Baltimore

first: Drew

last: Pardoll

state: Maryland

address: 1650 Orlean St.

department: Oncology

institute: Johns Hopkins Medical Institute

summary: In order to understand the role of Nrn1, we compared the gene expression profile of Nrn1_KO and WT iTreg cells or Th0 cells.

overall_design: We performed gene expression profile analysis on Nrn1_KO and WT iTreg in IL2 medium or stimulated with aCD3+IL2; also Nrn1_KO and WT Th0 cells.

first: Hong


title: The effect of bile acis on the transcriptome of mouse intestinal organoids

city: Jinan City

first: Yue

last: Wang

address: No. 44, Wenhua West Road

institute: Shandong University

summary: To investigate the role of bile acids in regulating intestinal epithelium differentiation, mouse small intestinal organoids cultured for 2 days were incubated with a series of bile acids at 50 mmol/L for 96 hours and lysed for RNA extraction.

overall_design: RNA-seq data for mouse small intestinal organoids treated with CA, CDCA and DCA (50 mmol/L),respectively.

first: Yanbo

first: Lixiang

last: Li

first: Mengqi

last: Zheng

first: Xiuli

last: Zuo

first: Shiyang

first: Yanqing


title: Gpcpd1-GPC metabolic pathway is dysfunctional in aging and its deficiency severely perturbs glucose metabolism

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

summary: Skeletal muscle plays a central role in the regulation of systemic metabolism during lifespan. With aging, muscle mediated metabolic homeostasis is perturbed, contributing to the onset of multiple chronic diseases. Our knowledge on the mechanisms responsible for this age-related perturbation is limited, as it is difficult to distinguish between correlation and causality of molecular changes in muscle aging. Glycerophosphocholine phosphodiesterase 1 (GPCPD1) is a highly abundant muscle enzyme responsible for the hydrolysis of the lipid glycerophosphocholine (GPC). The physiological function of GPCPD1 remained largely unknown. Here, we report that the GPCPD1-GPC metabolic pathway is dramatically perturbed in the aged muscle. Muscle-specific inactivation of Gpcpd1 resulted in severely affected glucose metabolism, without affecting muscle development. This pathology was muscle specific and did not occur in white fat-, brown fat- and liver-deficient Gpcpd1 deficient mice. Moreover, in the muscle specific mutant mice, glucose intolerance was markedly accelerated under high sugar and high fat diet. Mechanistically, Gpcpd1 deficiency results in accumulation of GPC, without any other significant changes in the global lipidome. This causes an “aged-like” transcriptomic signature in young Gpcpd1 deficient muscles and impaired insulin signaling. Finally, we report that GPC levels are markedly perturbed in muscles from both aged humans and patients with Type 2 diabetes, with a high correlation between GPC levels and increased chronological age. Our findings show the novel and critical physiological function of GPCPD1-GPC metabolic pathway to glucose metabolism, and the perturbation of this pathway with aging, which may contribute to glucose intolerance in aging.

overall_design: To investigate the function of Gpcpd1 in the muscle, we firstly generated mice with a floxed Gpcpd1 allele. Subsequently, we crossed these mice to Mck Cre transgenic mice to generate muscle specific Gpcpd1 KO mice.

first: Michael

last: Orthoffer

first: Domagoj

last: Cikes

first: Joseph

last: Penninger


title: Cerebrospinal fluid cell-free DNA methylomes recapture pediatric medulloblastoma tissue's tumor feature

city: Houston

first: Jia

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

type: Methylation profiling by high throughput sequencing

summary: Medulloblastoma (MB) is an embryonal tumor of the cerebellum and a highly malignant childhood brain tumor. Cell-free circulating tumor DNA (ctDNA) from the cerebrospinal fluid (CSF) of patients with brain tumors faithfully represent genomic alterations of brain tumors. Distinct epigenetic signatures among subgroups of MB allow us to detect epigenetic alterations in CSF to aid classify and guide therapy of MB tumors. Here, we evaluate DNA methylation of ctDNA derived from small amount of CSF (200 µL) and matched tumor DNA from four subtypes of MB patients. We find highly concordance of DNA methylation between CSF ctDNA and tumor DNA in a subtype manner. Our results show that CSF ctNDA methylation can be a minimal invasive precisely method to assess epigenetic alterations of MB in a subtype manner, which is complementary to current diagnoses of MB tumors.

overall_design: We sequenced DNA methylomes of pediatric medulloblastoma tissues and matached CSF  samples; We systematically compared DNA methylome between CSF and matched tumor samples.

first: Yun

last: Huang

first: Xiaonan


title: Sex-biased gene expression across tissues reveals unexpected differentiation in the gills of the threespine stickleback

status: Public on Jun 09 2024

city: Québec

first: Florent

last: Sylvestre

state: Québec

address: 2325, rue de l'Université

country: Canada

institute: Université Laval

summary: Sexual dimorphism can evolve through sex-specific regulation of the same gene set. However, sex chromosomes can also facilitate this by directly linking gene expression to sex. Moreover, heteromorphic sex chromosomes often exhibit different gene content, which contributes to sexual dimorphism. Understanding patterns of sex-biased gene expression across organisms is important for gaining insight about the evolution of sexual dimorphism and sex chromosomes. Moreover, studying gene expression in species with recently established sex chromosomes can help understand the evolutionary dynamics of gene loss and dosage compensation. The threespine stickleback is known for its strong sexual dimorphism, especially during the reproductive period. Sex is determined by a young XY sex chromosome pair with three non-recombining regions that have started to degenerate. Using the high multiplexing capability of 3′ QuantSeq to sequence the sex-biased transcriptome of liver, gills and brain, we provide the first characterization of sex-specific transcriptomes from ~80 stickleback (40 males and 40 females) collected from a natural population during the reproductive period. We find that the liver is extremely differentiated (36% of autosomal genes) and reflects ongoing reproduction, while the brain shows very low levels of differentiation (0.78%) with no particular functional enrichment. Finally, the gills exhibit high levels of differentiation (5%), suggesting that sex should be considered in physiological and ecotoxicological studies of gill responses in fishes. We also find that sex-biased gene expression in X-linked genes is mainly driven by a lack of dosage compensation. However, sex-biased expression of genes that have conserved copies on both sex chromosomes is likely driven by the degeneration of Y allele expression and a down-regulation of male-beneficial mutations on the X chromosome.

overall_design: 80 individuals (40 males and 40 females) were sampled from a natural population at Baie de l'Isle Verte (Québec) during reproductive period. We then harvested brain, gills and liver for total RNA-seq expression profiling, yielding 227 successfull library

first: Nadia

last: Aubin-Horth

first: Louis

last: Bernatchez


title: Next Generation Sequencing Analysis of Wild Type and hnRNPK-MKO liver transcription

city: 31上海市

first: Yangjun

last: Luo

address: 岳阳路320号

institute: 中国科学院上海营养与健康研究所

summary: we report liver fibrosis defects in hnRNPK Alb-Cre mice, in which hnRNPK is ablated in hepatocyte cells.

overall_design: The control and hnRNPK Alb-Cre gene in liver mRNA profiles were generated by deep sequencing, using Illumina NovaSeq 6000

first: Ying

last: Feng


title: TET-mediated DNA demethylation influences histone enhancers H3K4me1 and H3K27ac in breast cancer

city: Chennai

first: Samson

last: Mani

state: Tamilnadu

address: 38, Sardar Patel Road

department: Molecular Oncology

country: India

institute: Cancer Institute (WIA)

summary: The study is designed to understand the role of TET mediated demethylation and its intricate interplay with histone enhancers and loci-specific 5-hmC levels of candidate genes in breast cancer.

overall_design: TET1 and TET2 depletion have been performed using siRNA-mediated gene silencing in MCF-7 breast cancer cell lines. TET-deficient and the control cells were pulled with H3k27ac and H3K4me1 antibodies followed by ChIP bead purification, library preparation, and sequencing.

first: Deepa

last: Ramasamy

first: Arunagiri

last: Rao


title: Gene expression signatures in Ythdf3-/- and WT hematopoietic stem cells

city: Tianjin

first: Jianwei

last: Wang

address: 10 Yuexin Street, Binhai New Area

institute: HAIHE LABORATORY OF CELL ECOSYSTEM

summary: Analysis of Ythdf3-/- and WT hematopoietic stem cell (lineage-, c-kit+ Sca-1+ CD150+, CD34-). The hematopoietic stem cell (HSC) were purified from the bone marrow of WT and Ythdf3-/- mice.

overall_design: Five samples from five different mice were analyzed including two KO samples and three WT samples


title: Genome-wide maps in gastric cancer MKN-45 cells with or without the overexpression of transcriptional factor SIX2

city: Nanjing

first: Lufeng

address: Tongjia Xiang 24

department: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention

institute: China Pharmaceutical University

summary: Analysis of MKN-45 cells following SIX2 stable overexpression or not. SIX2 regulates various mRNA expression in MKN-45 cells.Results provide insight into the role of SIX2-involved mechanisms underlying SIX2-mediated effects on gastric cancer stemness.

overall_design: mRNA profiles of MKN-45 cells with or without SIX2 overexpression were generated by deep sequencing, in two repeats, using Illumina NovaSeq 6000.

first: Qianqian

last: Guo

first: Wenzhou

last: Zhang

first: Yi

last: Zhou


title: RNA-Seq analysis reveals the growth of Populus in different light qualities

city: Kunming

first: Xiaolin

address: qingyun street

institute: southwest forestry university

summary: Light plays a key role in plant growth, development and response to adversity. Plants perceive different wavelengths of light in the environment through various photoreceptors and regulate plant growth and development through light signaling. However, there are fewer studies on the effects of different light qualities on the growth and development of tree species at high altitude. In the study, the effects of blue and green light treatments on the growth and development of Populus cuttings were investigated. Blue light treatment significantly increased the high growth of Populus, while green light treatment showed the opposite trend. Consequently, blue light treatment demonstrated growth promotion by increasing the growth hormone content of Populus. This implies that Populus may benefit from blue light therapy in terms of growth and development, which may be helpful for further research into the introduction and cultivation of  poplar species in high altitude regions.

sample_organism:
Populus qamdoensis
Populus schneideri

platform_organism:
Populus qamdoensis
Populus schneideri

overall_design: To investigate the response mechanism of plants to different light bands at high altitude, we evaluated the effects of blue, green and white light on plant growth and physiological traits by treating the cuttings of Populus with white, blue and green light films. We further used RNA-seq technology to investigate the molecular basis of plant responses to different wavelengths of light at the transcriptional level.

first: ChengZhong

last: He

first: Dan

last: Zong

first: Jingmin


title: Effect of Fusobacterium nucleatum on human HUVEC cells

status: Public on Jun 08 2024

city: Guangzhou

first: Shanshui

last: Zeng

address: Bsogao Road

institute: Southern medical university

summary: Localization of Fusobacterium nucleatum in the placenta may be associated with pregnancy complications including preeclampsia (PE), but its specific pathobiology is unknown. Our aim was to analyze the effect of Fusobacterium nucleatum on HUVEC cells to further elucidate placental dysfunction in the context of Fusobacterium nucleatum infestation.

overall_design: HUVEC cells were intervened using F. nucleatum outer membrane protein FomA for 24 h. PBS was used as a control.

first: Bingyu

last: Li

first: Dongxin


title: CircPTEN-MT derived from PTEN regulates mitochondrial energy metabolism

city: Beijing

first: Danhui

last: Ruan

address: Peking University HSC 38 Xueyuan Road, Haidian District Beijing P.R.China

institute: Peking University

summary: SMMC-7721 cell lines were transfected with si-NC or si-circPTEN-MT and subjected to RNA-seq

overall_design: SMMC-7721 cell lines mRNA profiles of si-NC and si-circPTEN-MT.SMMC-7721  cell lines were transfected with si-NC or si-circPTEN-MT (GAGACAAAAAGGTTTTTGG). 48 hours later, cells were collected and subjected to RNA-seq.

first: Jiancheng

last: Xu

first: Yuxin

last: Yin


title: scRNA-Seq reveals anti-fibrotic mechanisms of TRPC6 inhibition [Spatial Transcriptomics]

city: Greifswald

first: Yao

state: State

address: Felix-Hausdorff-Straße 3

country: Germany

institute: University Medicine Greifswald

summary: Inhibition of transient receptor potential canonical 6 channels (TRPC6) alleviates tubular injury and renal fibrosis induced by unilateral ureteral obstruction (UUO).However, the exact renoprotective mechanisms are unknown. In this study, we utilized single-cell RNA sequencing (scRNA-Seq) to define the cellular and transcriptional landscape associated with renoprotection through in vivo TRPC6 inhibition, specifically using SH045 (larixyl N-methylcarbamate), in the UUO model.

overall_design: Six C57BL/6 mice underwent unilateral ureteral obstruction (UUO) surgery. Seven days post-surgery, the kidneys from Vehicle-treated (n=3) and SH045-treated (n=3) mice were harvested. The contralateral kidneys from Vehicle-treated mice (n=3) served as the control group (Ctrl group). A total of nine kidney samples were used for single-cell RNA sequencing (scRNA-seq). Additionally, two of these samples (one from the SH045 group and one from the Vehicle group) were simultaneously analyzed using spatial transcriptomics.