title: Control of neuronal excitation-inhibition balance by BMP-SMAD1 signaling [Smad1cKOvsctrl_RNAseq]

city: Basel

first: Peter

last: Scheiffele

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

summary: Throughout life, neuronal networks in the mammalian neocortex maintain a balance of excitation and inhibition which is essential for neuronal computation. Deviations from a balanced state have been linked to neurodevelopmental disorders and severe disruptions result in epilepsy. To maintain balance, neuronal microcircuits composed of excitatory and inhibitory neurons sense alterations in neural activity and adjust neuronal connectivity and function. Here, we identified a signaling pathway in the adult mouse neocortex that is activated in response to elevated neuronal network activity. Over-activation of excitatory neurons is signaled to the network through the elevation of BMP2, a growth factor well-known for its role as morphogen in embryonic development. BMP2 acts on parvalbumin-expressing (PV) interneurons through the transcription factor SMAD1, which controls an array of glutamatergic synapse proteins and components of peri-neuronal nets. PV interneuron-specific disruption of BMP2-SMAD1 signaling is accompanied by a loss of PV cell glutamatergic innervation, underdeveloped peri-neuronal nets, and decreased excitability. Ultimately, this impairment of PV interneuron functional recruitment disrupts cortical excitation – inhibition balance with mice exhibiting spontaneous epileptic seizures. Our findings suggest that developmental morphogen signaling is re-purposed to stabilize cortical networks in the adult mammalian brain.

overall_design: RNA-seq

first: Zeynep

last: Okur

first: Nadia

last: Schlauri

first: Vassilis

last: Bitsikas

first: Myrto

last: Panopoulou

first: Raul

last: Ortiz

first: Michaela

last: Schwaiger

first: Kajari

last: Karmakar

first: Dietmar

last: Schreiner


title: Control of neuronal excitation-inhibition balance by BMP-SMAD1 signaling [RNA-seq]

status: Public on Feb 16 2024

type: Expression profiling by high throughput sequencing


title: Control of neuronal excitation-inhibition balance by BMP-SMAD1 signaling [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq


title: Control of neuronal excitation-inhibition balance by BMP-SMAD1 signaling


title: Imeglimin Improves Systemic Metabolism by Targeting Brown Adipose Tissue and Gut Microbiota in Obese Model Mice

city: Tokyo

first: Motoharu

last: Awazawa

address: 1-21-1 Toyama, Shinjuku

country: Japan

institute: National Institute for Global Health and Medicine

summary: Imeglimin is a recently developed anti-diabetic drug that could concurrently promote insulin secretion and insulin sensitivity, while its mechanisms of action are not fully understood. Here we show that imeglimin administration could protect mice from high fat diet-induced weight gain with enhanced energy expenditure and attenuated whitening of brown adipose tissue. Imeglimin administration led to significant alteration of gut microbiota, which included an increase of Akkermansia genus, with attenuation of obesity-associated gut pathologies. Ablation of microbiota by antibiotic treatment partially abrogated the insulin sensitizing effects of imeglimin, while not affecting its actions on body weight gain or brown adipose tissue. Collectively, our results characterize imeglimin as a potential agent promoting energy expenditure and gut integrity, providing new insights into its mechanisms of action.

overall_design: 4 HFD vs 4 HFD+Imeglimin

first: Maya

last: Matsushita

first: Ikumi

last: Nomura

first: Kohijiro

last: Ueki


title: tRNA epitranscriptome determines pathogenicity of the opportunistic pathogen Pseudomonas aeruginosa

status: Public on Feb 17 2024

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

country: Germany

institute: Twincore

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

sample_organism:
Pseudomonas aeruginosa
Pseudomonas aeruginosa UCBPP-PA14

overall_design: Refer to individual Series


title: Next Generation Sequencing Quantitative Analysis of altered expression of genes in BCa cells-induced PDGFRα+ITGA11+ CAFs and other CAFs

city: Guangzhou

first: Changhao

last: Chen

state: Guangdong

address: 107 Yanjiangxi Road, Yuexiu District, Guangzhou, Guangdong Province, P. R. China

department: Urology

country: China

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: The cellular diversity of stromal compartment within the tumor microenvironment might change dynamically as tumors evolve that allowing distant dissemination of tumor cells and informing the treatment options. We used single cell RNA sequencing (scRNA-seq) to provide a detailed insight of cellular components feature in bladder cancer and identify that PDGFRα+ITGA11+ CAFs were essential for lymphatic metastasis of bladder cancer. To identify molecular mechanism of PDGFRα+ITGA11+ CAFs formation, next generation sequencing (NSG) was performed to explore the upregulated genes in bladder cancer-induced PDGFRα+ITGA11+ CAFs.

overall_design: To detect the precise mechanism of bladder cancer in inducing the formation of PDGFRα+ITGA11+ CAFs, the total RNAs of bladder cancer-induced PDGFRα+ITGA11+ CAFs and control CAFs were extracted and the next generation sequencing was conducted to explore the expressing profile difference between different groups. The results were obtained from three independent experiments.

first: Tianxin

last: Lin

first: Hanhao

last: Zheng


title: Spatial transcriptomic reveals the cellular landscape of bladder cancer

summary: The cellular diversity of stromal compartment within the tumor microenvironment might change dynamically as tumors evolve that allowing distant dissemination of tumor cells and informing the treatment options. Importantly, the localization of cells in tumor microenvironment indicates the biological function of cells. Thus, we used spatial transcriptomic to reveal the cellular landscape and corresponding cellular localization in bladder cancer.

overall_design: The xx-case paraffin sections of bladder cancer were obtained from Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University. Then, the tissue sections were subjected to the Visium Spatial Tissue Optimization Slide kit to fit the time for permeabilization by generating fluorescently labeled cDNA tissue prints. Subsequently, the permeabilization processes were conducted and the spatially barcoded, full-length cDNA is amplified via PCR to generate sufficient mass for library construction. The library sequencing was performed on the Illumina novaseq 6000.


title: Defining the activity of pro-reparative extracellular vesicles in wound healing based on miRNA payloads and cell type-specific lineage mapping

city: La Jolla

first: Brian

last: Eliceiri

state: CA

address: 9500 Gilman Drive MC 8236

department: Surgery

country: USA

institute: University of California San Diego Health

type: Non-coding RNA profiling by high throughput sequencing

summary: Small extracellular vesicles (EVs) are released by cells and deliver biologically active payloads important in the intercellular signaling that coordinates the response of multiple cell types in cutaneous wound healing.  Here we focus on the use of EV reporters to address cell type specificity and central questions regarding EV source cells, target cells, heterogeneity, payload, and activity using a combination of molecular approaches to address some of the barriers to translation in the use of engineered EVs.  We identify a role for EVs released by resident macrophages present in adipose tissue and dermis to stimulate proliferation of overlying basal layer of keratinocytes.  For these studies we use an allograft model, where donor EVs are harvested from subcutaneous implants, then purified for transplantation into the wound bed of recipient mice with a defined impaired wound healing phenotype.  We demonstrate that EVs isolated from diabetic obese mice decreased keratinocyte proliferation and delayed wound closure, and that EVs loaded with specific miRNAs like miR-425-5p increased proliferation and accelerated wound closure.  Utilizing a CD9-GFP reporter system, we show that fibroblasts uptake macrophage-derived EVs.  In this work, we show that cell type-specific approaches can be used to unravel the biochemical activity of EVs in the complex microenvironment of the wound bed and form the basis for developing targeted pro-reparative EV payloads.

overall_design: miRNA-Seq

first: Dong Jun

last: Park

middle: P


title: Accelerated cystogenesis by dietary protein load is dependent on, but not initiated by, kidney macrophages

city: Birmingham

first: Takamitsu

middle: at

last: Saigusa

state: AL

address: 1720 2nd Ave. South. MCLM533

department: Medicine

institute: University of Alabama at Birmingham

summary:
Background: Disease severity of autosomal dominant polycystic kidney disease  (ADPKD) is influenced by diet. Dietary protein, a recognized cyst-accelerating factor, is  catabolized into amino acids (AA) and delivered to the kidney leading to renal  hypertrophy. Injury-induced hypertrophic signaling in ADPKD results in increased  macrophage (MФ) activation and inflammation followed by cyst growth. We hypothesize  that the cystogenesis-prompting effects of HP diet are caused by increased delivery of  specific AA to the kidney, ultimately stimulating MФs to promote cyst progression.
Methods: Pkd1 flox/flox mice with and without Cre (CAGG-ER) were given tamoxifen to  induce global gene deletion (Pkd1KO). Pkd1KO mice were fed either a low (LP; 6%),  normal (NP; 18%), or high (HP; 60%) diet for 1 week (early) or 6 weeks (chronic). Mice  were then euthanized and tissues were used for histology, immunofluorescence and  various biochemical assays. One week fed kidney tissue was cell sorted to isolate  tubular epithelial cells for RNA sequencing.
Results: Chronic dietary protein load in Pkd1KO mice increased kidney weight, number  of kidney infiltrating and resident MФs, chemokines, cytokines and cystic index  compared to LP diet fed mice. Accelerated cyst growth induced by chronic HP were  attenuated by liposomal clodronate-mediated MФ depletion. Early HP diet fed Pkd1KO  mice had larger cystic kidneys compared to NP or LP fed counterparts, but without  increases in the number of kidney MФs, cytokines, or markers of tubular injury. RNA  sequencing of tubular epithelial cells in HP compared to NP or LP diet group revealed  increased expression of sodium-glutamine transporter Snat3, chloride channel Clcnka,  and gluconeogenesis marker Pepck1, accompanied by increased excretion of urinary  ammonia, a byproduct of glutamine.
Conclusion: Chronic dietary protein load-induced renal hypertrophy and accelerated  cyst growth in Pkd1KO mice is dependent on both infiltrating and resident MФ  recruitment and subsequent inflammatory response. Early cyst expansion by HP diet,  however, is relient on increased delivery of glutamine to kidney epithelial cells, driving  downstream metabolic changes prior to inflammatory provocation.

overall_design: Kidneys from Pkd1KO mice fed low, normal, and high protein diets (2.8 g/day) for 1 week were collected for flow sorting of the epithelial cell population.

first: Randee

last: Sedaka

first: Shinobu

last: Yamaguchi

first: Jifeng

last: Huang

first: David

middle: K

last: Crossman


title: Gene expression profile at the single cell level of splenic LCMV-specific B cells in acute versus chronic LCMV infection [scRNA-seq, CITE-seq]

city: Clayton

first: Kim

last: Good-Jacobson

state: Victoria

address: Gr Fl Reception (Bldg 77) 23 Innovation Walk

country: Australia

institute: Monash University

summary: Chronic viral infection disrupts memory B cell development. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of antigen-specific B cells responding to acute versus chronic LCMV infection.

overall_design:
Splenic LCMV-specific B cells from LCMV-infected mice were isolated by fluorescence-activated cell sortings (FACS) and analysed using scRNA-seq.

The only raw data which was used was the *.fastq.gz samples (6 pairs, 12 samples all together; out of them two pairs are for RNA-Seq - one for mice 24 and 44 and one for mice 36 and 59, 2 pairs for VDJ, again one for 27_44 and one for 36_59, and 2 pairs for HTO, again one for 27_44 and one for 36_59) and also the belo feature_reference.csv :
id,name,read,pattern,sequence,feature_type
C0301,C0301_TotalSeqC,R2,5PNNNNNNNNNN(BC),ACCCACCAGTAAGAC,Antibody Capture
C0302,C0302_TotalSeqC,R2,5PNNNNNNNNNN(BC),GGTCGAGAGCATTCA,Antibody Capture
Each of the 27_44 files contains a mixture of Acute replicate 1 and Chronic replicate 1, and the two can be distinguished by their HTO (C0301 representing acute and C0302 chronic). Similarly, each 36_59 file contains a mixture of Acute replicate 2 and Chronic replicate 2, and they again can be distinguished by HTO. The 10X software tool (Cellranger) created the not de-multiplexedCSP_27-44_filtered_feature_bc_matrix.h5 andCSP_36-59-filtered_feature_bc_matrix.h5 files. Since for each cell there we have its HTOwe know which one is acute and which one is chronic and based on this we can do the analysis

The files linked to the Series records are the aggregation of the two sequencing runs (since after all the two replicates were analysed together).

middle: L

first: Lucy

last: Cooper

first: Adele

last: Barugahare

first: Katherine

middle: J

last: Jackson

first: Luciano

middle: G

last: Martelotto


title: Sperm-borne tsRNAs and microRNA analysis in relation to  dairy cattle fertility

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

summary:
Purpose: Screening the sperm sncRNAs that are responsible for dairy cattle fertility is of great interest, however, exploring the fertility-associated sncRNAs in sperm and linking them with the epigenetic inheritance in bovine has not been performed yet.  Here in this study, we hypothesized that some sncRNAs in bovine sperm have a great potential to be linked with direct and immediate bull fertility data and could later influence the embryo and possibly impacting the daughter fertility.
Methods: 12 bovine cryopreserved semen (high bull fertility, n=3 VS low bull fertility, n=3; high daughter fertility, n=3 vs low daughter fertility, n=3) that came from a pre-filtered 100 bull list (Figure 1) had been selected to extract total sperm RNA, the somatic cell lysis buffer had been added during the RNA extraction process to avoid the somatic cell pollution. The maternal and other confounding factors had been taken into consideration during the calculation of the phenotype criteria index.After the library construction, the library size that was smaller than 200 base pairs (adapter size around 125 nt) had been cut and sent for next-generation sequencing
Results: bull fertility and daughter fertility related sncRNAs had been identified.
Conclusions: providing promising epigenetic biomarker for cattle fertility improvement in the future, although these small non-coding RNAs need to be validated in larger sample sizes before being used as biomarkers.

overall_design: 10 sperm sncRNAs from bull for sequencing

first: Ying

last: Zhang

first: Patricia

last: Tremblay

first: Clément

last: Plessis

first: Pascal

last: Dufour

first: Hélène

last: Martin

first: Marc

middle: A

last: sIrard


title: Nfe2l3 promotes neuroprotection and long-distance axon regeneration after injury in vivo [Third party: scRNA-seq]

status: Public on Feb 22 2024

city: Farmington

first: Ephraim

middle: F

last: Trakhtenberg

state: CT

address: 263 Farmington Ave. RM L4005

department: Neuroscience

institute: University of Connecticut School of Medicine

summary: Nuclear factor erythroid 2 like (Nfe2l) gene family members 1-3 mediate cellular response to oxidative stress, including in the central nervous system (CNS). However, neuronal functions of Nfe2l3 are unknown. Here, we comparatively evaluated expression of Nfe2l1, Nfe2l2, and Nfe2l3 in singe cell RNA-seq (scRNA-seq)-profiled cortical and retinal ganglion cell (RGC) CNS projection neurons, investigated whether Nfe2l3 regulates neuroprotection and axon regeneration after CNS injury in vivo, and characterized a gene network associated with Nfe2l3 in neurons. We showed that, Nfe2l3 expression transiently peaks in developing immature cortical and RGC projection neurons, but is nearly abolished in adult neurons and is not upregulated after injury. Furthermore, within the retina, Nfe2l3 is enriched in RGCs, whereas Nfe2l1 and Nfe2l2 are expressed robustly in other retinal cell types as well, and are also upregulated after injury. We also found that, expressing Nfe2l3 in injured RGCs through localized intralocular viral vector delivery promotes neuroprotection and long-distance axon regeneration after optic nerve injury in vivo. Moreover, Nfe2l3 treatment provided a similar extent of neuroprotection and axon regeneration as viral vector-targeting of Pten and Klf9, which are prominent regulators of neuroprotection and long-distance axon regeneration. Finally, we bioinformatically characterized a gene network associated with Nfe2l3 in neurons, which revealed the association of Nfe2l3 with established mechanisms of neuroprotection and axon regeneration. Thus, Nfe2l3 is a novel neuroprotection and axon regeneration-promoting factor with a therapeutic potential for treating CNS injury and disease.

relation:
SubSeries of: GSE253840
Reanalysis of: GSM3500947
Reanalysis of: GSM3500948
Reanalysis of: GSM3500949
Reanalysis of: GSM3500950
Reanalysis of: GSM3500951
Reanalysis of: GSM3500952
Reanalysis of: GSM3500953
Reanalysis of: GSM3500954
Reanalysis of: GSM3500955
Reanalysis of: GSM4277166
Reanalysis of: GSM4277167
Reanalysis of: GSM4277168
Reanalysis of: GSM4277169
Reanalysis of: GSM4277170
Reanalysis of: GSM4277171
Reanalysis of: GSM4277172
Reanalysis of: GSM4277173
Reanalysis of: GSM4277174
Reanalysis of: GSM4277175
Reanalysis of: GSM4277176
Reanalysis of: GSM4277177
Reanalysis of: GSM4277178
Reanalysis of: GSM4277179
Reanalysis of: GSM4277180
Reanalysis of: GSM4277181
Reanalysis of: GSM3239586
Reanalysis of: GSM3239587
Reanalysis of: GSM3239588
Reanalysis of: GSM3239589
Reanalysis of: GSM3239590
Reanalysis of: GSM3239591
Reanalysis of: GSM3239592
Reanalysis of: GSM3239593
Reanalysis of: GSM3239594
Reanalysis of: GSM3239595
Reanalysis of: GSM3239596
Reanalysis of: GSM3239597
Reanalysis of: GSM3239598
Reanalysis of: GSM3239599
Reanalysis of: GSM3239600
Reanalysis of: GSM3239601
Reanalysis of: GSM3239602
Reanalysis of: GSM3239603
Reanalysis of: GSM3239604
Reanalysis of: GSM3239605
Reanalysis of: GSM3239606
Reanalysis of: GSM5969851
Reanalysis of: GSM5969852
Reanalysis of: GSM5969853
Reanalysis of: GSM5969854
Reanalysis of: GSM5969855
Reanalysis of: GSM5969856
Reanalysis of: GSM5969857
Reanalysis of: GSM5969858
Reanalysis of: GSM5969859
Reanalysis of: GSM5969860
Reanalysis of: GSM5969861
Reanalysis of: GSM5969862
Reanalysis of: GSM5969863
Reanalysis of: GSM5969864
Reanalysis of: GSM5969865
Reanalysis of: GSM5969866
Reanalysis of: GSM5969867
Reanalysis of: GSM5969922
Reanalysis of: GSM5969882
Reanalysis of: GSM5969883
Reanalysis of: GSM5969884
Reanalysis of: GSM5969885
Reanalysis of: GSM5969886
Reanalysis of: GSM5969887
Reanalysis of: GSM5969888
Reanalysis of: GSM5969889
Reanalysis of: GSM5969890
Reanalysis of: GSM5969891
Reanalysis of: GSM5969914
Reanalysis of: GSM5969915
Reanalysis of: GSM5969916
Reanalysis of: GSM5969917
Reanalysis of: GSM5969918
Reanalysis of: GSM5969919
Reanalysis of: GSM5621465
Reanalysis of: GSM5621466
Reanalysis of: GSM5621467
Reanalysis of: GSM5621468
Reanalysis of: GSM5621469
Reanalysis of: GSM5621470
Reanalysis of: GSM5621471
Reanalysis of: GSM5621472
Reanalysis of: GSM5621473
Reanalysis of: GSM5621474
Reanalysis of: GSM5621475
Reanalysis of: GSM5621476
Reanalysis of: GSM5621477
Reanalysis of: GSM5621478
Reanalysis of: GSM3907320
Reanalysis of: GSM3907321
Reanalysis of: GSM3907322
Reanalysis of: GSM3907323
Reanalysis of: GSM3907324
Reanalysis of: GSM3907325
Reanalysis of: GSM3907326
Reanalysis of: GSM3907327
Reanalysis of: GSM3907328
Reanalysis of: GSM3907329
Reanalysis of: GSM4078555
Reanalysis of: GSM4078556
Reanalysis of: GSM4078557
Reanalysis of: GSM4078558

overall_design:
Normalized matrices and cell metadata (e.g., type assignment) was obtained from the GEO accession numbers as follows: for cortical embryonic, postnatal, and adult projection neurons from GSE143949, GSE123335, and GSE116470; for RGC embryonic, postnatal, adult projection neurons, and injured adult RGCs from GSE185671 and GSE137400; and for all adult normal and injured retinal cell types from GSE199317. Seurat v4.3.0 was used to merge and normalize the datasets mapped to the mm10 genome. Datasets were batch adjusted and integrated using Harmony. Cell type identity of cells that passed scRNA-seq QCs was confirmed based on established cell type markers.
Data processing details:
Cell-counts matrices were obtained from the GEO submissions from the previously published data. Matrices were loaded as Seurat objects in R.
Seurat objects were merged and expression was normalized. A cell counts matrix for the merged dataset was then generating by extracting counts matrix from Seurat object.
The condition each cell belongs to was appended to the cell ID in the columns of the matrix
genome assembly: mm10
RDS files: Containing cortical or RGC embryonic, postnatal, adult projection neurons, injured adult RGCs, and all adult normal and injured retinal cell types, with cells' normalized expression values for each gene.

first: Agnieszka

last: Lukomska

first: Matthew

last: Frost


title: PRPF8-mediated dysregulation of hBrr2 helicase disrupts human spliceosome kinetics and 5'-splice-site selection causing tissue-specific defects

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

country: United Kingdom

institute: University of Leeds

summary: The carboxy-terminus of the spliceosomal protein PRPF8, which regulates the RNA helicase Brr2, is a hotspot for mutations causing retinitis pigmentosa-type 13, with unclear role in human splicing and tissue-specificity mechanism. We used patient induced pluripotent stem cells-derived cells, carrying the heterozygous PRPF8 c.6926A>C (p.H2309P) mutation to demonstrate retinal-specific endophenotypes comprising photoreceptor loss, apical-basal polarity and ciliary defects. Comprehensive molecular, transcriptomic, and proteomic analyses revealed a role of the PRPF8/Brr2 regulation in 5’-splice site (5’SS) selection by spliceosomes, for which disruption impaired alternative splicing and weak/suboptimal 5’SS selection, and enhanced cryptic splicing, predominantly in ciliary and retinal-specific transcripts. Altered splicing efficiency, nuclear speckles organisation, and PRPF8 interaction with U6 snRNA, caused accumulation of active spliceosomes and poly(A)+ mRNAs in unique splicing clusters located at the nuclear periphery of photoreceptors. Collectively these elucidate the role of PRPF8/Brr2 regulatory mechanisms in splicing and the molecular basis of retinal disease, informing therapeutic approaches.

overall_design: Gene expression profiling on iPSC-derived retinal organoids, retinal pigment epithelium (RPE) and kidney organoids from four patients carrying the pathogenic PRPF8 RP type 13 c.6926A>C (p.H2309P) heterozygous missense mutation.

first: Robert

last: Atkinson

first: Maria

last: Georgiou

first: Chunbo

last: Yang

first: Katarzyna

last: Szymanska

first: Albert

last: Lahat

first: Elton

middle: R

last: Vasconcelos

first: Avril

last: Watson

first: Joseph

last: Collin

first: Birthe

last: Dorgau

first: Marina

middle: M

last: Molina

first: Ji

last: Yanlong

first: Ross

last: Laws

first: Chia

last: ShyanBeh

first: Rachel

last: Queen

last: Elliott

first: Chileleko

last: Siachisumo

first: Martin

last: McKibbin

first: Tracey

last: Davey

first: Chris

last: Inglehearn

first: Marzena

last: Kurzawa-Akanbi

first: Abhijit

last: Saxena

middle: H

last: Steel

first: Magda

last: Karwatka

first: Henning

last: Urlaub

first: Robin

last: Ali

first: Sushma

middle: N

last: Grellscheid

first: Colin

last: Johnson

first: Sina

last: Mozaffari-Jovin

first: Majlinda

last: Lako


title: Aggressive human MenG C meningiomas have a molecular counterpart in canines

city: Houston

first: Akdes

last: Serin Harmanci

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: We found that canine meningiomas can be classified molecularly, and the aggressive group of tumors in canines is similar to human MenG C tumors. This aggressive class exhibits chromosomal instability, cell cycle activation, and increased MKI67 expression. Further studies of canine meningiomas in larger cohorts might help advance treatment options for both canines and humans.

overall_design: canine meningioma

first: Beth

last: Boudreau

first: Tiemo

last: Klisch

first: Jonathan

last: Levine

first: Akash

last: Patel


title: Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy gene

status: Public on Feb 14 2024

city: Ames

first: Ravindra

last: Singh

state: IA

address: 2034 Veterinary Medicine

department: Biomedical Sciences

institute: Iowa State University

summary: Spinal muscular atrophy (SMA) genes, SMN1 and SMN2, produce multiple circular RNAs (circRNAs), including C2A-2B-3-4 that encompasses early exons 2A, 2B, 3 and 4. Here we report the transcriptome- and proteome-wide effects of overexpression of C2A-2B-3-4 in inducible HEK293 cells. Our RNA-Seq analysis revealed altered expression of ~15% genes (4,172 genes) by C2A-2B-3-4. About half of the affected genes by C2A-2B-3-4 remained unaffected by L2A-2B-3-4, a linear transcript encompassing exons 2A, 2B, 3 and 4 of SMN1/SMN2. These findings underscore the unique role of the structural context of C2A-2B-3-4 in gene regulation. A surprisingly high number of upregulated genes by C2A-2B-3-4 were located on chromosomes 4 and 7, whereas many of the downregulated genes were located on chromosomes 10 and X. Supporting a cross-regulation of SMN1/SMN2 transcripts, C2A-2B-3-4 and L2A-2B-3-4 upregulated and downregulated SMN1/SMN2 mRNAs, respectively. Proteome analysis revealed 61 upregulated and 57 downregulated proteins by C2A-2B-3-4 with very limited overlap with those affected by L2A-2B-3-4. Independent validations confirmed the effect of C2A-2B-3-4 on expression of genes associated with chromatin remodeling, transcription, spliceosome function, ribosome biogenesis, lipid metabolism, cytoskeletal formation, cell proliferation and neuromuscular junction formation. Our findings reveal a broad role of C2A-2B-3-4, a universally expressed circRNA produced by SMN1/SMN2.

overall_design: We induced overexpression of a circular RNA produced by the SMN gene to study its function, followed by characterization of the transcriptome and proteome

first: Diou

last: Luo

first: Eric

last: Ottesen

first: JiHeon

last: Lee


title: Mouse Smartseq3 Data from Mold et al. Clonally Heritable Gene Expression Imparts a Layer of Diversity in Cell Types

city: Solna

first: Carl-Johan

middle: Wilheard Torkel

last: Eriksson

state: Stockholm

address: Solnavägen 9

department: CMB

country: Sweden

institute: Karolinska Institute

summary: Mouse cells harvested from the central nervous system of two different mice injected at post-coital day 9.5 with lentivirus encoding barcodes that allow for clonal tracking and gene expression in single cell RNAseq measurements (TREX, Ratz et al 2022).  Cells are isolated from the cortex 14 days after birth and profiled by scRNA-seq using the Smartseq3 method.

overall_design:
Smartseq3 libraries were prepared on single cells isolated from the mouse cortex and FACS sorted based on GFP expression (indicating lentiviral expression of clonal barcodes) according to the standard protocol (https://www.protocols.io/view/smart-seq3-protocol-36wgq5rjxgk5/v3).

Please note that Series supplementary files include an example of how the .yaml file for the zumis-run looks like, the expected barcodes and the .fa file for lentiviral barcodes within the samples, which are needed to accurately regenerate the entire pipeline.

first: Jeff

middle: E

last: Mold

last: Erickson

first: Michael

last: Ratz

first: Jonas

last: Frisén


title: Brown adipose tissue histone proteoform analysis reveals an epigenetic response to cold stress

status: Public on Feb 15 2024

city: Houston,

first: Hari Krishna

last: Yalamanchili

address: 1250 Moursund St #1125,

type: Methylation profiling by high throughput sequencing

summary: Regulation of the thermogenic response by brown adipose tissue (BAT) is an important mechanism in the basic biology and treatment of obesity and diabetes. Consensus transcriptional regulatory analysis of a publicly-available RNA-seq dataset uncovered a large number of nodes representing epigenetic modifiers that were altered in BAT in response to chronic thermogenic activation. Thus, we hypothesized that chronic activation of BAT results in epigenetic modifications of DNA and histones that affect the tissue function. To test our hypothesis, wildtype male C57BL/6J mice were housed under chronic conditions of thermoneutral temperature (TN, 28.8°C), mild cold/room temperature (RT, 22°C), or severe cold (SC, 8°C). Reduced representation bisulfite sequencing (RRBS) revealed a marked decrease in methylation of promoters and intragenic regions in BAT genomic DNA in response to varying degrees of chronic cold exposure. Integration of our RRBS and the publicly available RNA-Seq dataset suggested a role for epigenetic modification of DNA in gene regulation in response to cold. To analyze histone modifications, we developed a robust method for the isolation and quantitation of histone proteoforms, which enabled the first comparison of histone H3.2 and H4 proteoforms in BAT.  We report distinct on/off histone signals that are observed with histone H3.2 in BAT, but not in the liver, when mice are acclimated to severe cold in comparison with mild cold. Specifically, we observe a larger percentage of histone H3.2 with the K9 dimethylation mark coupled with K36 mono- or di-methylation and K23 acetylation, suggesting strong repression of previously active chromatin. Taken together, our results provide novel findings supporting global epigenetic modification in murine BAT in response to varying degrees of chronic cold stimuli and establish a methodology to quantitatively study histones in BAT, allowing for direct comparisons to decipher mechanistic changes during the thermogenic response.

overall_design: To investigate the effect of housing temperature on DNA methylation in brown adipose tissue (BAT), male C57BL/6J mice were housed at thermoneutral (TN, 28oC) or standard room temperatures (RT, 22oC) beginning at weaning (3 weeks of age). At 8 weeks of age, a cohort of RT-housed mice were housed under severe cold (SC, 8oC) for two weeks. BAT was dissected when mice were 10 weeks old. n=4 per TN, RT, or SC-housed group.

first: Bethany

last: Taylor

first: Loic

last: Steinthal

first: Michelle

last: Dias

first: Hari

first: Scott

last: Ochsner

first: Gladys

last: Zapata

first: Nitesh

last: Mehta

first: Neil

last: McKenna

first: Nicolas

last: Young

first: Alli

last: Nuotio-Antar


title: Sex-dependent Effects of AHR Activation in Endothelial Cells in Hypoxic  Conditions

city: Gainesville

first: Terence

last: Ryan

address: 1864 Stadium Rd

institute: University of Florida

summary: Chronic kidney disease (CKD) is a risk factor for peripheral arterial disease, however the molecular mechanisms linking the pathobiologies are ill-defined. The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor, has been previously shown to regulate angiogenesis. Notably, CKD results in the accumulation of metabolites that are endogenous ligands for the AHR. Results from animal work showed in male mice with CKD, AHRecKO lead to improvements in limb perfusion without improvements in muscle contractile or mitochondrial function. There was no effect of genotype observed in female mice. To assess these sex-dependent effects we cultured hypoxic endothelial cells from male and female mice and found inherent sex differences in AHR activating potential. Further to this, we performed bulk RNA sequencing and identified several angiogenic genes that were differentially expressed. In summaryn mice with CKD, endothelium-specific deletion of the AHR improved blood perfusion in muscle but did not confer improvement in mitochondrial function or muscle strength. Interestingly, these changes were observed in male, but not female, mice. Cell culture experiments revealed inherent sex-differences in gene expression.

overall_design: To asses the inherenent differenceds in gene expression in endothelial cells as a result of AHR activation and hypoia, we isolated and cultured primary CD31-positive cells from the liver of 4-week old male and female C57BL6/J mice. Cells were treated with 100uM Indoxyl Sulfate (IS) or DMSO control and incubated in hypoxia chamber.

first: Victoria

last: Palzkill


title: Chronic Stress Alters Lipid Mediator Profiles Associated with Immune-Related Gene Expressions in Mouse Bone Marrow and Spleen

city: Kobe

first: Tomoyuki

last: Furuyashiki

state: Hyogo

address: 7-5-1 Kusunoki-cho Chuo-ku

institute: Kobe University

summary: Despite the importance of lipid mediators in stress and depression and their link to inflammation, the influence of stress on these mediators and their role in inflammation is not fully understood. This study used RNA-seq, LC-MS/MS, and flow cytometry analyses in a mouse model subjected to chronic social defeat stress to explore the effects of acute and chronic stress on lipid mediators, gene expression, and cell population in the bone marrow and spleen. We observed that chronic stress in the bone marrow precipitated a persistent lymphoid-to-myeloid transition, accompanied by corresponding gene expression changes. This change was associated with decreased levels of 15-deoxy-d12,14-prostaglandin J2, a lipid mediator that inhibits inflammation. Conversely, in the spleen, chronic stress led to a transient lymphoid-to-myeloid transition, alongside gene expression patterns suggestive of extramedullary hematopoiesis. These changes were linked to lower levels of 12-HEPE and resolvins, both critical for inhibiting and resolving inflammation. Our findings highlight the significant role of anti-inflammatory and pro-resolving lipid mediators in the immune responses induced by chronic stress in the bone marrow and spleen. This study paves the way for understanding how these lipid mediators contribute to the immune mechanisms of stress and depression.

overall_design: Two to six biological replicates were analyzed for each of 10 conditions (five stress conditions; two organs per stress condition)

first: Io

last: Horikawa

first: Hirotaka

last: Nagai

first: Masayuki

last: Taniguchi

first: Guowei

last: Chen

first: Masakazu

last: Shinohara

first: Tomohide

last: Suzuki

first: Shinichi

last: Ishii

first: Yoshio

last: Katayama

first: Shiho

last: Kitaoka


title: Gene expression profile at single cell level of bladder cancer and normal adjacent tissues

first: Changhao

summary: The cellular diversity of stromal compartment within the tumor microenvironment might change dynamically as tumors evolve that allowing distant dissemination of tumor cells and informing the treatment options. Thus, we used single cell RNA sequencing (scRNA-seq) to provide a detailed insight of cellular components feature in bladder cancer.

overall_design: Fresh bladder cancer tissues and normal adjacent tissues were obtained from patients and washed with ice-cold PBS. Then, the tissues were subjected to prepare single cell suspensions with tumor dissociation kit. Subsequently, the single cell suspensions were used to generate single-cell Gel Bead-In-EMlusion (GEMs) by a 10X Genomics GemCode Single-cell instrument and construct the cDNA libraries. The library sequencing was performed on the Illumina novaseq 6000.

first: Tianxin

last: Lin

first: Hanhao

last: Zheng


title: Renal congestion exacerbates acute kidney injury in mice

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

summary: The number of heart failure (HF) patients is increasing. HF is frequently accompanied by kidney dysfunction and such organ failure is closely related. Recent investigations revealed that increased renal venous pressure, rather than decreased cardiac output, causes the deterioration of kidney function in HF patients; however, the underlying responsible mechanisms are unknown. We demonstrated that reduced blood flow speed in peritubular capillaries (PTCs) by renal congestion and upregulation of nuclear factor-κB (NF-κB) signaling synergistically exacerbate kidney injury. We generated a novel mouse model with unilateral renal congestion by coarctation of the inferior vena cava between renal veins. Intravital imaging highlighted the notable dilatation of PTCs and decreased renal blood flow speed in the congestive kidney. Renal damage after ischemia reperfusion injury was exacerbated in the congestive kidney and accumulation of polymorphonuclear leukocytes (PMNs) within PTCs was observed at the acute phase after injury. Pharmacological inhibition of NF-κB ameliorated renal congestion-mediated exacerbation of kidney injury. In vitro, adhesion of PMNs on the TNFα-stimulated endothelial cells was accelerated by perfusion of PMNs at a slower speed, which was cancelled by the inhibition of NF-κB signaling. Our study demonstrates the importance of slower blood flow accompanying activated NF-κB signaling in the congestive kidney in the exacerbation of renal injury. These mechanisms may explain how increased renal venous pressure in HF patients causes the deterioration of kidney dysfunction. Inhibition of NF-κB signaling may be a therapeutic candidate for the vicious cycle between heart and kidney failure with increased renal venous pressure.

overall_design: RNAseq was used to profile mouse congestive kidney


title: IL-17 activates dermal reticular fibroblasts to promote neutrophil recruitment and host defense

city: San Diego

first: Kellen

last: Cavagnero

state: California

address: 9500 Gilman Dr

institute: Univeristy of California, San Diego

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: RNA-seq analysis of isogenic mouse prostate cancer cell lines with distinct sensitivity to immune checkpoint therapy

status: Public on Feb 13 2024

city: Notre Dame

first: Dailin

last: Gan

address: Holy Cross Dr.

institute: University of Notre Dame

summary: Resistant to immune checkpoint blockade (ICB) therapy, especially in a few solid tumor types including advanced prostate cancer (PCa), represents a formidable clinical challenge.  In this study, we developed a series of ICB-resistant PCa cell lines from an ICB-sensitive PCa cell line previously developed from the PB-Cre+ PtenL/L p53L/L Smad4L/L mouse model of metastatic PCa. These four cell lines were profiled with RNAseq.

overall_design: RNA-seq profiling of a series of four Pten/p53/Smad4 (PPS) mouse prostate cancer cell lines using the Illumina pipeline.

first: Sean

last: Murphy

first: Sharif

last: Rahmy

first: Xin

last: Lu


title: A scRNAseq atlas of larval Drosophila ventral cord - a resource for studying motor systems function and development

city: Bethesda

first: Mihaela

last: Serpe

state: MD

address: 35 Convent Dr, Bldg 35, Room 1C-1016

department: NICHD

institute: NIH

summary: Drosophila larval ventral nerve cord (VNC) shares many similarities with the spinal cord of vertebrates and has emerged as a major model for understanding the development and function of motor systems. We use high quality single cell RNA sequencing to create a comprehensive atlas of larval VNC cell types. Our atlas provides a high-resolution characterization of larval VNC capturing primary neurons, glia and the functional landscape that coordinates larval behavior. At the same time, this atlas offers unique insights into neurogenesis and into the strategies and signaling networks utilized for generation of the adult VNC.

overall_design: We have previously described in detail the single-cell RNA sequencing protocols that we optimized for the analysis of Drosophila larval tissues (Nguyen et al., 2021; Vicidomini et al., 2021). Here we analyzed VNCs from Drosophila third instar larvae of five different genotypes. The VNCs  were manually dissected and dissociated using a combination of mechanical and enzymatic treatments. The cell suspensions were processed using droplet microfluidics (10x Genomics Chromium platform)  and the resulting libraries were sequenced on an Illumina platform. To characterize larval motor neurons, selective neuronal populations were GFP-marked and FACS-enriched before processing. This strategy permitted separation and identification of all motor neuron bundles, linking individual neuron clusters to morphologically characterized known subtypes.

first: Tho

last: Nguyen

first: Rosario

last: Vicidomini

first: Saumitra

middle: D

last: Choudhury

first: Tae-Hee

last: Han

first: Dragan

last: Maric

first: Thomas

last: Brody


title: Intron detention tightly regulates the stemness/differentiation switch in the adult neurogenic niche

city: San Juan de Alicante

first: Angela

last: Nieto

state: Alicante

address: Av. Ramón y Cajal s/n

department: Developmental Neurobiology

country: Spain

institute: Instituto de Neurociencias (CSIC-UMH)

summary: The goal of this study is to analyze the changes in the transcriptional profile at the first stages of neural stem cell (NSC) differentiation.

overall_design: Transcriptional profiles of differentiating adult neural stem cells 0, 1 and 6 hours after the initiation of this process

first: Ainara

last: Gonzalez-Iglesias

first: Aida

last: Arcas

first: M


title: Dietary fiber is a critical determinant of pathologic ILC2 responses and intestinal inflammation - Bulk RNA-Seq

city: New York

first: Mohammad

last: Arifuzzaman

state: NY

address: 413 E 69th Street, 7th Floor

department: Department of Medicine

institute: Weill Cornell Medicine

summary: Innate lymphoid cells (ILCs) can promote host defense, chronic inflammation or tissue protection and are regulated by cytokines and neuropeptides. However, their regulation by diet and microbiota-derived signals remains unclear. We show that an inulin fiber diet promotes Tph1-expressing inflammatory ILC2s (ILC2INFLAM) in the colon which produce IL-5 but not tissue-protective amphiregulin (AREG), resulting in accumulation of eosinophils. This exacerbates inflammation in a murine model of intestinal damage and inflammation in an ILC2- and eosinophil-dependent manner. Mechanistically, inulin fiber diet elevated microbiota-derived bile acids, including cholic acid (CA) that induced expression of ILC2-activating IL-33. In IBD patients, bile acids, their receptor farnesoid X receptor (FXR), IL-33, and eosinophils were all upregulated compared to controls, suggesting relevance of this diet-ILC2 axis in human IBD pathogenesis. Together, these data reveal that dietary fiber-induced changes in microbial metabolites operate as a rheostat that governs protective versus pathologic ILC2 responses with relevance to precision nutrition for inflammatory diseases.

overall_design: Colonic biopsies from five non-IBD healthy controls and five pan-colitic IBD patients were digested into single cell suspensions and used to construct RNA-Seq libraries.

first: Jazib

last: Uddin

first: Alex

last: Grier

first: David

last: Artis


title: Systematic dissection of tumor-normal single-cell ecosystems across a thousand tumors of 30 cancer types

city: Daejeon

first: Jun Hyeong

last: Lee

address: 291 Daehak-ro, Yuseong-gu, Daejeon

country: South Korea

institute: KAIST

summary: The complexity of the tumor microenvironment poses significant challenges in cancer therapy. Here, to comprehensively investigate the tumor-normal ecosystems, we perform an integrative analysis of 4.9 million single-cell transcriptomes from 1,070 tumor and 493 normal samples in combination with pan-cancer 137 spatial transcriptomics, 8,887 TCGA, and 1,261 checkpoint inhibitor-treated bulk tumors. We define a myriad of cell states constituting the tumor-normal ecosystems and also identify hallmark gene signatures across different cell types and organs. Our atlas characterizes distinctions between inflammatory fibroblasts marked by AKR1C1 or WNT5A in terms of cellular interactions and spatial co-localization patterns. Co-occurrence analysis reveals interferon-enriched community states including tertiary lymphoid structure (TLS) components, which exhibit differential rewiring between tumor, adjacent normal, and healthy normal tissues. The favorable response of interferon-enriched community states to immunotherapy is validated using immunotherapy-treated cancers (n=1,261) including our lung cancer cohort (n=497). Deconvolution of spatial transcriptomes discriminates TLS-enriched from non-enriched cell types among immunotherapy-favorable components. Our systematic dissection of tumor-normal ecosystems provides a deeper understanding of inter- and intra-tumoral heterogeneity.

overall_design:
Bulk RNA-sequencing of immunotherapy-treated lung cancer cohorts.

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

first: SeHoon

first: Jung

last: Choi

first: Jong-Eun

last: Park


title: Gene expression profiling of acidic cell compartments from HCT116 spheroids.

city: Dijon

first: Romain

last: Boidot

address: 1, rue Pr Marion

country: France

institute: CGFL

summary: We deciphered specific traits of acidic cancer cells by comparing gene expression profiles in acidic (negative K-pHLIP and positive pHLIP cells) and buffered (negative pHLIP cells) cell compartments from HCT116 colorectal cancer 3D spheroids.

overall_design: HCT116 3D spheroids were labeled with AlexaFluor 568 pHLIP (pH low insertion peptide) and AlexaFluor 594 K-pHLIP (pH-independent control peptide) conjugated peptides, and sorted by FACS to isolate negative K-pHLIP and positive pHLIP cells (acidic) from pHLIP-negative cell population (buffered). We then subjected both cell populations to RNA-seq analysis to compare the transcriptomes acidic vs. buffered cancer cells.

first: Léo

last: Aubert

first: Estelle

last: Bastien

first: Corentin

last: Richard

first: Olivier

last: Feron


title: eIF4A1 enhances LARP1-mediated translational repression during mTORC1 inhibition

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

institute: RIKEN

summary: Eukaryotic translation initiation factor (eIF) 4A — a DEAD-box RNA-binding protein — plays an essential role in translation initiation. Recent reports have suggested helicase-dependent and helicase-independent functions for eIF4A, but the multifaceted roles of eIF4A have not been fully explored. Here, we show that eIF4A1 enhances translational repression during the inhibition of mechanistic target of rapamycin complex 1 (mTORC1), an essential kinase complex controlling cell proliferation. RNA pulldown followed by sequencing revealed that eIF4A1 preferentially binds to mRNAs containing terminal oligopyrimidine (TOP) motifs (TOP mRNAs), whose translation is rapidly repressed upon mTORC1 inhibition. This selective interaction depends on a La-related RNA-binding protein, LARP1. Ribosome profiling revealed that deletion of EIF4A1 attenuated the translational repression of TOP mRNAs upon mTORC1 inactivation. Moreover, eIF4A1 increases the affinity between TOP mRNAs and LARP1 and thus ensures stronger translational repression upon mTORC1 inhibition. Our data show the multimodality of eIF4A1 in modulating protein synthesis through an inhibitory binding partner and provide a unique example of the repressive role of a universal translational activator.

overall_design: Ribosome profiling of EIF4A1 KO and EIF4A2 KO cells with PP242 treatment, RNA-Seq of EIF4A1 KO cells, RNA pulldown-seq of SBP-EIF4A1- and SBP-EIF4A2- expressing cells, and RIP-seq of SBP-EIF4A1-expressing cells upon LARP1 knockdown.

first: Yuichi

last: Shichino

first: Tomokazu

last: Yamaguchi

first: Kazuhiro

last: Kashiwagi

first: Mari

last: Mito

last: Takahashi

first: Takuhiro

last: Ito

first: Nicholas

middle: T

last: Ingolia

first: Keiji

last: Kuba


title: IL-17 activates dermal reticular fibroblasts to promote neutrophil recruitment and host defense [RNAseq]

first: Kellen

last: Cavagnero

summary: The complex system by which the skin regulates immune responses to the external environment is unclear. Here, we investigated cell-cell interactions underlying cutaneous defense against S. aureus. Single-cell transcriptomics (scRNA-Seq) and unbiased network analysis revealed unexpected, dominant IL-17-mediated dermal reticular fibroblast-to-neutrophil communication. Multi-faceted in vitro omics studies demonstrated that IL-17 synergized with several factors including TNF⍺ to induce fibroblast NFKBIZ and chemokine secretion. Cultured fibroblasts drove robust neutrophil recruitment through NFKBIZ-dependent CXCR2 and CXCR4 ligands. Mice lacking IL-17R in fibroblasts (PdgfraΔIl17ra) were generated to determine the significance of fibroblast-neutrophil communication. PdgfraΔIl17ra mice exhibited drastically reduced skin neutrophilia in multiple disease models and reduced defense against S. aureus. These findings were translated to humans by comprehensive analysis of biopsies from psoriasis patients on and off anti-IL-17 treatment. Thus, dermal fibroblasts are critical for skin type 17 inflammation and represent a novel target for treatment of infection and inflammatory disease.

overall_design: Bulk RNA-seq of fibroblasts and neutrophils stimulated in vitro


title: Cardiovascular changes in the NZB/W F1 mouse model of lupus nephritis

city: Erlangen

first: Christoph

last: Daniel

address: Krankenhausstr. 8-10

department: Nephropathology

institute: FAU Erlangen-Nürnberg

summary: Lupus nephritis with pronounced signs of chronic kidney disease leads to significant changes in the heart. It is not yet clear whether these changes are caused by the chronic kidney disease or by the autoimmune disease. It is also unclear which factors are responsible for the cardiovascular changes. Therefore, the gene expression of mice with lupus nephritis (NZB_W) will be compared with healthy controls (NZW).

overall_design: Mouse hearts were collected from NZB_W female mice with moderate kidney injury according to Austin scoring with an age of 12-15 weeks(NZB-W) and healty age matched controls (NZW), followed by mRNA isolation and hybridization on Mouse Genome 430 2.0 Array. This experiment was done as a pilot test to identify candidate genes that were differentially regulated during cardiac alterations induced by lupus nephritis.

first: Kerstin

last: Amannn

first: Romy

last: Böhme


title: scRNA-seq of 50 and 80 hpf isolated zebrafish hearts

city: Bad Nauheim

first: Noah

last: Knoppik

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max-Planck-Institute for Heart and Lung Research

summary: Seeking to identify additional transcription factors required for cardiac valve formation, we determined and explored the transcriptional landscape of endocardial cells at the time when key morphogenetic events underlying valve development take place.

overall_design: We isolated wild-type zebrafish hearts at 50 hours post-fertilization (hpf) when valve identity has just been established, and at 80 hpf when forming valves are first observed

first: Agatha

last: da Silva

first: Felix

last: Gunawan

first: Giulia

last: Boezio

first: Emilie

last: Faure

first: Alexis

last: Théron

first: Jean-François

last: Avierinos

first: SoEun

last: Lim

first: Shivam

last: Jha

first: Radhan

last: Ramadass

first: Stefan

last: Guenther

first: Mario

last: Looso

first: Stéphane

last: Zaffran

first: Thomas

last: Juan

first: Didier

last: Stainier


title: TAD boundary deletion causes PITX2-related cardiac electrical and structural defects

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

summary: Right atrial and sinoatrial node RNA-seq of Ch4q25(DelB) and control adult mice

overall_design: Whole tissue RNA-seq of adult right atria and sinoatrial nodes

first: Fernanda

last: Bosada

first: Karel

last: van Duijvenboden


title: Identification of gene expression in cells that may express micropeptide from RN7SL1

city: Suita

first: Tomoaki

last: Hara

state: Osaka

address: Yamadaoka 2-2

department: Graduate School of Medicine

institute: Osaka university

summary: RN7SL1 is a 299-base single-stranded RNA that binds to five SRP proteins and contributes to the generation of transmembrane and secretory proteins as a signal recognition particle. It theoretically possesses two small open reading frames (smORFs) and encodes a micropeptide of 7 and 16 amino acids from the 5' side. However, it is unknown if those smORFs are translated. Therefore, we constructed a plasmid vector expressing RN7SL1-GFP, in which the former sequence was replaced by AcGFP1, and examined whether GFP is expressed. In 293T cells electroporated or lipofected with the RN7SL1-GFP-expressing plasmid, GFP fluorescence was detected under the microscope in both cases, although there were a few GFP-positive cells. GFP-positive and GFP-negative cells were separated by FACS and gene expression of each sample was confirmed by RNA-seq. As a result, GFP-positive cells showed activation of cancer-related pathways compared to GFP-negative cells. These results suggest that RN7SL1 smORFs may be translated under special conditions.

overall_design: 293T cells were electroporated or lipofected with RN7SL1-GFP expression plasmid and GFP positive and GFP negative cells were separated by FACS. Total RNA was extracted from 293T cells under 4 conditions (electroporation GFP negative, electroporation GFP positive, lipofection GFP negative, lipofection GFP positive) and RNA-seq was performed.

first: Sikun

last: Meng

first: Daisuke

last: Motooka

first: Yoshiko

last: Tsuji

first: Yasuko

last: Arao

last: Saito

first: Hiromichi

last: Sato

first: Hideshi

last: Ishii


title: Human Adult Glial Progenitors Express Distinct miRNA Profiles Compared to their Fetal Counterparts

status: Public on Feb 12 2024

city: Rochester

first: Steven

last: Goldman

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

summary: Human glial progenitor cells (hGPCs) exhibit diminished expansion competence with age, as well as after recurrent demyelination. Using RNA-sequencing to compare the gene expression of fetal and adult hGPCs, we identify age-related changes in transcription consistent with the repression of genes enabling mitotic expansion, concurrent with the onset of aging-associated transcriptional programs. Adult hGPCs develop a repressive transcription factor network centered on MYC, and regulated by ZNF274, MAX, IKZF3, and E2F6. Individual over-expression of these factors in iPSC-derived hGPCs lead to a loss of proliferative gene expression and an induction of mitotic senescence, replicating the transcriptional changes incurred during glial aging. miRNA profiling identifies the appearance of an adult-selective miRNA signature, imposing further constraints on the expansion competence of aged GPCs. hGPC aging is thus associated with acquisition of a MYC-repressive environment, suggesting that suppression of these repressors of glial expansion may permit the rejuvenation of aged hGPCs.

overall_design: Adult (A2B5+; n=4) and fetal (CD140a+; n=4) hGPC cell suspensions were isolated via MACS as noted above, and their miRNA isolated using miRNeasy kits according to manufacturer instructions (QIAGEN).  Purified miRNA was then prepared and profiled on Affymetrix GeneChip miRNA 3.0 Arrays as instructed by their standard protocol.  Raw CEL files were then read into R via the oligo package and samples were normalized via robust multi-array averaging (RMA).  Probes were then filtered for only human miRNAs according to Affymetrix's annotation, and differential expression was carried out in limma where significance was established at an adjusted p-value < 0.01.

first: John

last: Mariani

first: Devin

last: Chandler-Militello


title: Identification of irradiation-induced ATM-dependent lncRNAs

city: Poznan

first: Agnieszka

last: Dzikiewicz-Krawczyk

address: Strzeszynska 32

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

summary: DNA damage response (DDR) is a complex process, essential for cell survival. Especially deleterious type of DNA damage are DNA double-strand breaks (DSB), which can lead to genomic instability and malignant transformation if not repaired correctly. The central player in DSB detection and repair is the ATM kinase which orchestrates the action of several downstream factors. Despite substantial knowledge of DNA repair processes, still several aspects of DNA damage detection and signaling are not fully understood. Recent studies have suggested that long non-coding RNAs (lncRNAs) are involved in DDR. Here, we aimed to identify lncRNAs induced upon DNA damage in an ATM-dependent manner. 7 mRNAs and 10 lncRNAs were significantly induced 1h after ionizing radiation (IR) in healthy donors, whereas none in AT patients. 447 mRNAs and 149 lncRNAs were induced 8h after IR in the control group, while only 100 mRNAs and 3 lncRNAs in AT patients.  Among IR-induced mRNAs, we found several genes with well-known functions in DDR. Gene Set Enrichment Analysis  and Gene Ontology revealed delayed induction of key DDR pathways in AT patients compared to controls. The induction and dynamics of selected 9 lncRNAs were confirmed by RT-qPCR at several time-points after IR on a larger cohort. Moreover, inhibition of ATM with a specific inhibitor (KU-60019) proved that those lncRNAs are dependent on ATM. Some of the detected lncRNAs are localized next to protein-coding genes involved in DDR. We observed that induction of lncRNAs after IR preceded changes in expression of adjacent genes. This indicates that IR-induced lncRNAs may regulate the transcription of nearby genes. Subcellular fractionation into chromatin, nuclear, and cytoplasmic fractions revealed that the majority of studied lncRNAs are localized in chromatin, which further suggests their role in regulation of gene expression. In summary, our study revealed several lncRNAs induced by IR in an ATM-dependent manner. Their co-localization and co-expression with genes involved in DDR suggest that those lncRNAs may be important players in cellular response to DNA damage.

overall_design: DNA damage was induced by ionizing radiation (1 Gy) in immortalized lymphoblastoid cell lines (LCLs) derived from 4 patients with ataxia-telangiectasia (AT) and 4 healthy donors. Cells were collected 1h and 8h after IR to allow identification of lncRNAs involved in the early and late response to DNA damage. A strand-specific RNA sequencing approach was applied to identify IR-induced lncRNAs and mRNAs.

first: Marta

last: Podralska

first: Marcin

last: Sajek

first: Antonina

last: Bielicka

first: Magdalena

last: Żurawek

first: Iwona

last: Ziółkowska-Suchanek

first: Katarzyna

last: Iżykowska

first: Tomasz

last: Kolenda

last: Kazimierska

last: Kasprzyk

first: Weronika

last: Sura

first: Barbara

last: Pietrucha

first: Bożena

last: Cukrowska

first: Natalia

last: Rozwadowska


title: Impaired VLDL secretion following Mttp deletion promotes tumorigenesis and is accelerated by Fabp1 deletion

city: Saint Louis

first: Nicholas

last: Davidson

state: Missouri

address: 425 South Euclid Ave, Box 8124

department: Internal Medicine

institute: Washington University in St Louis School of Medicine

summary: Genetic polymorphisms that impair VLDL secretion are linked to hepatic steatosis, fibrosis and hepatocellular cancer (HCC). Liver-specific deletion of microsomal triglyceride transfer protein (Mttp-LKO) impairs VLDL assembly, promoting hepatic steatosis and fibrosis, which are attenuated in Mttp-LKO mice with germline Fabp1 deletion (Fabp1/Mttp DKO) mice.  Here we examine the impact of impaired VLDL secretion in Mttp-LKO mice on HCC incidence and progression in comparison to Fabp1/Mttp DKO mice. DEN treated Mttp-LKO mice exhibited steatosis with increased tumor burden compared to flox controls, while diethylnitrosamine (DEN)- treated Fabp1/Mttp DKO mice exhibited a paradoxical increase in tumor burden and >50% mortality by 50 weeks.  Lipidomic surveys revealed progressive enrichment in distinct triglyceride species in livers from Mttp-LKO mice with further enrichment in Fabp1/Mttp DKO mice.  RNAseq analysis performed on liver tissue at 6 months revealed mRNA changes suggesting altered monocarboxylic acid utilization and increased aerobic glycolysis, while hepatocytes from Fabp1/Mttp DKO mice exhibited increased capacity to utilize glucose and glutamine. Taken together, these findings demonstrate that hepatic tumorigenesis is increased in mice with impaired VLDL secretion and further accelerated via pathways including altered fatty acid compartmentalization and shifts in hepatic energy utilization.

overall_design:
Study was performed on whole liver RNA isolated from 3 genotypes of mice:Mttp fl/fl mice (CON), mice with liver specific deletion of Mttp (MttpLKO) and MttpLKO mice with germline deletion of Fabp1 (Fabp1 Mttp DKO)
All mice were C57BL/6J congenic male mice injected with DEN at P14d and sacrificed at 6 months of age
Each sample represents pooled RNA from 3 mice of same genotype.  3 pools of RNA were analyzed for each genotype for a total of 9 samples.

middle: O

first: Elizabeth

middle: P

last: Newberry

middle: Q

last: Molitor


title: Dietary fiber is a critical determinant of pathologic ILC2 responses and intestinal inflammation

first: Mohammad

last: Arifuzzaman

overall_design: Single cells suspensions generated from colon biopsies from a non-IBD healthy control and a pan-colitic IBD patient were used for scRNA-seq.

first: Arifuzzaman

last: Mohammad

first: Uddin

last: Jazib

first: Grier

last: Alex

first: Artis

last: David


title: The TELOMERE REPEAT BINDING proteins TRB4 and TRB5 function as transcriptional activators of PRC2-controlled genes to regulate plant development

city: CLERMONT FERRAND

first: simon

last: amiard

address: 28 place henry dunant

institute: CNRS - UMR 6247 - GRED

summary: TELOMERE REPEAT BINDING proteins (TRBs) are plant specific transcriptional regulators that combine two DNA binding domains: the GH1 domain shared with H1 linker histones and the Myb/SANT domain that specifically recognize AAACCCT, the telomeric motif, present at telomeres, centromere-proximal Interstitial Telomeric Repeats (ITRs) and at promoters of numerous protein-coding genes. TRB1, TRB2 and TRB3 (TRB1-3) proteins collaborate with PRC2 and JMJ14 for deposition of H3K27me3 and removal of H3K4me3 to induce transcriptional repression in a functionally redundant manner.  Here we report that TRB4 and TRB5, which belong to a separate TRB clade conserved among spermatophytes, fulfill chromatin roles distinct from TRB1-3. We show that TRB4 and TRB5 are involved in the transcriptional control of several hundred genes involved in developmental responses to environmental cues and in consequence TRB4 and TRB5 loss of function plants present developmental growth defects including delayed flowering. Most of the trb4 trb5 transcriptomic defects differ from those of trb1 trb2 trb3, suggesting a distinct mode of action at the chromatin level. Indeed, TRB4 binds to several thousand sites in the genome, mainly to TSS and promoter regions of transcriptionally active and H3K4me3-marked genes, but it does not affect global H3K4me3 levels. In contrast to TRB1-3, TRB4 is not enriched at H3K27me3-marked gene bodies, and combined loss of TRB4 and TRB5 affects H3K27me3 only at a small subset of genes. Yet, TRB4 physically interacts with the catalytically active subunit of somatic PRC2 complexes CURLY LEAF (CLF). Unexpectedly, loss of TRB4 and TRB5 partially suppresses developmental defects of clf mutant plants, likely through their role as positive transcriptional regulators of the key flowering genes SOC1 and FT. We further show that TRB4 and TRB1 share multiple target genes and reveal physical and genetic interactions between TRBs of the two distinct clades, altogether unveiling that TRB proteins engage in both positive and negative interplay with other members of the family to regulate plant development through PRC2-dependent and independent mechanisms.

overall_design: To investigate the role of TRB4 and TRB5 in Arabidopsis we created two independent trb45 lines, we performed gene expression profilling of the two trb45 mutants compared to WT and to a trb123 triple mutant.

first: Simon

last: Amiard

first: Aline

last: Probst


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

overall_design: Refer to individual Series


title: Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster [Fib_KD_RiboMeth-seq]

city: Lausanne

first: Jean-Yves

last: Roignant

address: Quartier Unil Sorge, Bâtiment Génopode

department: CIG

institute: UNIL

summary:
The majority of Nm modifications in eukaryotes are placed by Fibrillarin, a conserved methyltransferase belonging to a ribonucleoprotein complex guided by C/D box small nucleolar RNAs (C/D box snoRNAs).
We built the first comprehensive map of Nm sites in Drosophila melanogaster rRNAs using two complementary approaches (RiboMethSeq and Nanopore direct RNA sequencing) and identified their corresponding C/D box snoRNAs by whole-transcriptome sequencing (TGIRT-seq).

overall_design: Comparative 2'O-methylation in rRNA by RiboMeth-seq in control (dsLacZ, n=4), Fibrillarin knockdown S2R+ cells (dsFib, n=4) as well as fly heads from individuals exposed to oxidative, heat and nutrient stress.

first: Athena

last: Sklias

first: Virginie

last: Marchand

first: Yuri

last: Motorin


overall_design:
To investigate the role of TRB4 and TRB5 in Arabidopsis we created two independent trb45 lines
We performed gene expression profilling of the two trb45 mutants compared to WT and to a trb123 triple mutant


title: Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster


title: Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster [Fib_KD_TGIRT-seq]

overall_design: Comparative gene expression analysis of TGIRT-seq data in control (dsLacZ, n=3) and Fibrillarin knockdown S2R+ cells (dsFib, n=3)


title: Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster [Tissues_TGIRT-seq]

overall_design: Gene expression analysis of TGIRT-seq data in Canton-S female head (n=3) and ovarian tissue (n=3)


title: Colon cancer treatment with BAMLET

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

institute: Lund University


title: Dual function of H2AK119ub1 on gene regulation via modulating canonical-PRC1 and H1-dependent chromatin compaction H2AK119ub1 deferentially fine-tunes gene expression by modulating canonical-PRC1 and H1-dependent chromatin compaction

status: Public on Feb 11 2024

city: Chongqing

first: Jie

last: Lan

state: Chongqing

address: No. 1 Yixueyuan Rd, Yuzhong District

institute: Chongqing medical university

summary: First, we applied ChIP-seq (Chromatin Immunoprecipitation) to measure the enrichment of Cbx7, Ring1B, and H3K27me3 on DNA in WT (wild-type), Ring1bI53A, and Rybp/Yaf2-DKO ESCs. The results suggest that accumulation of cPRC1 on chromatin isn’t caused by the mis-regulation of H3K27me3 in Ring1bI53A mESCs and Rybp/Yaf2-DKO impairs the accumulation of ncPRC1 on chromatin. Next, here we adopt ChIP-seq to investigate the dynamic of Ring1B and Cbx7 on DNA during Rybp/Yaf2 degradation after IAA treatment. We found that that H2AK119ub1 plays an important role in restricting the binding of cPRC1 on chromatin and thereby compromises cPRC1-mediated chromatin compaction. And then, we carried out mRNA-seq and identified differential expressed genes among WT and Ring1bI53A mESCs. Next, we applied ChIP-seq (Chromatin Immunoprecipitation) to measure the enrichment of Cbx7, Ring1B, Jarid2, PHC1, and PCGF2 on DNA in WT (wild-type), Ring1bI53A, and Bap1-KO ESCs . The results suggest that the binding of “all cPRC1” with nucleosomes is blocked by H2AK119ub1. Finally, here we performed MNase-seq in WT and H1-QKO mESCs. We found that H1-QKO lead to a stronger decondensation of H2Aub1_enriched TSSs compared with residual TSS regions. The result of ChIP-seq for H1 and ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing) of WT and Ring1BI53A, and mRNA-seq of WT and H1-QKO mESCs suggest H2AK119ub1 represses genes via promoting H1-mediated chromatin compaction.

overall_design: RNA-seq, ATAC-seq, ChIP-seq for WT, I53A, Rybp/Yaf2 DKO, H1QKO cells. And MNase-seq for WT and H1QKO cells.

first: Guohong

last: Li


overall_design:
To investigate the role of TRB4 and TRB5 in Arabidopsis we analysed H3K4me3 and H3K27me3 profile in trb45 mutant compared to WT
ChIP_seq experiments for H3K4me3 and H3K27me3 in WT (Col0) and in trb45 mutants


summary: TELOMERE REPEAT BINDING proteins (TRBs) are plant specific transcriptional regulators that combine two DNA binding domains: the GH1 domain shared with H1 linker histones and the Myb/SANT domain that specifically recognize AAACCCT, the telomeric motif, present at telomeres, centromere-proximal Interstitial Telomeric Repeats (ITRs) and at promoters of numerous protein-coding genes. TRB1, TRB2 and TRB3 (TRB1-3) proteins collaborate with PRC2 and JMJ14 for deposition of H3K27me3 and removal of H3K4me3 to induce transcriptional repression in a functionally redundant manner. Here we report that TRB4 and TRB5, which belong to a separate TRB clade conserved among spermatophytes, fulfill chromatin roles distinct from TRB1-3. We show that TRB4 and TRB5 are involved in the transcriptional control of several hundred genes involved in developmental responses to environmental cues and in consequence TRB4 and TRB5 loss of function plants present developmental growth defects including delayed flowering. Most of the trb4 trb5 transcriptomic defects differ from those of trb1 trb2 trb3, suggesting a distinct mode of action at the chromatin level. Indeed, TRB4 binds to several thousand sites in the genome, mainly to TSS and promoter regions of transcriptionally active and H3K4me3-marked genes, but it does not affect global H3K4me3 levels. In contrast to TRB1-3, TRB4 is not enriched at H3K27me3-marked gene bodies, and combined loss of TRB4 and TRB5 affects H3K27me3 only at a small subset of genes. Yet, TRB4 physically interacts with the catalytically active subunit of somatic PRC2 complexes CURLY LEAF (CLF). Unexpectedly, loss of TRB4 and TRB5 partially suppresses developmental defects of clf mutant plants, likely through their role as positive transcriptional regulators of the key flowering genes SOC1 and FT. We further show that TRB4 and TRB1 share multiple target genes and reveal physical and genetic interactions between TRBs of the two distinct clades, altogether unveiling that TRB proteins engage in both positive and negative interplay with other members of the family to regulate plant development through PRC2-dependent and independent mechanisms.

overall_design:
To investigate the role of TRB4 and TRB5 in Arabidopsis we created TRB4_GFP lines in WT (Col0) background
ChIP_seq experiments for TRB4_GFP using GFP Antibody  in Col0_TRB4GFP lines


title: Dysregulation of ribosome-associated quality control elicits cognitive disorders via overaccumulation of TTC3

first: Nayan

last: Suryawanshi

address: Hirosawa 2-1

department: Center for Brain Science

summary:
To investigate overaccumulated TTC3 inhibits translation initiation in Ltn1 KO neurons, we established harringtonine treated WT and Ltn1 KO mice primary cultured cortical neurons with Ttc3 RNAi or scrambled RNAi.
We then performed read (footprint) count analysis at translation initiation site using data obtained from RNA-seq (Ribo-seq).

overall_design: Comparative read count analysis of RNA-seq (Ribo-seq) data for WT and Ltn1 KO mice primary cultured cortical neurons and Tc3 KD derivatives.

first: Ryo

last: Endo

first: Yi

middle: K

last: Chen


title: Gene expression signatures in WT and Mcph1-/- hematopoietic stem cells

city: Tianjin

first: Jianwei

last: Wang

address: 10 Yuexin Street, Binhai New Area

institute: HAIHE LABORATORY OF CELL ECOSYSTEM

summary: We aimed to analyze the changes of gene expression signatures in WT and Mcph1-/- hematopoietic stem cell (lineage-, c-kit+ Sca-1+ CD150+, CD34-) usingRNA-seq. These two population of hematopoietic stem cell (HSC) were purified from the bone marrow of WT and Mcph1-/- mice. Results provide insight into the role of MCPH1 in HSC.

overall_design: We compare chromatin accessibility and gene expression signatures using ATAC-seq and RNA-seq in HSCs from the bone marrow of mice of two genotypes(WT and Mcph1-/-).

first: Hanqing

last: He

first: Qiongye

last: Dong


title: C19ORF84 connects piRNA and DNA methylation machineries to defend the mammalian germ line

city: Edinburgh

first: Yuka

last: Kabayama

address: 5 Little France Drive

institute: University of Edinburgh

summary: In the male mouse germline, PIWI-interacting RNAs (piRNAs) bound to the PIWI protein MIWI2 guide the DNA methylation of young active transposable elements (TEs) through SPOCD1. We identified loss-of-function variants in the human SPOCD1 gene that cause male infertility and defective TE silencing. One of the SPOCD1 pathogenic alleles encodes a truncated protein that lacks the conserved carboxy-terminus. We discovered that this deleted region interacts with C19ORF84. In mouse foetal germ cells, C19ORF84 is a nuclear protein that is required for the association of SPOCD1 with DNMT3L, an essential component of the de novo methylation machinery. In summary, we found a conserved role for SPOCD1 in safeguarding the continuity of the human germline and discovered C19ORF84, an uncharacterised protein essential for orchestrating piRNA-directed DNA methylation.

overall_design: Examination of piRNA expression profiles in control (C19orf84+/-) and C19orf84-/- foetal testes as well as RNA expression profiles in wild-type and C19orf84-/- P20 testis.

first: Ansgar

last: Zoch

first: Gabriela

last: Konieczny

first: Theresa

last: Schöpp


title: Methylation data profiling for blastic plasmacytoid dendritic cell neoplasm

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

institute: University of Lübeck

type: Methylation profiling by genome tiling array

summary: Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive malignancy assumed to originate from plasmacytoid dendritic cells (pDCs), which affects the skin and bone marrow and sequentially other organ systems. Here, we used EPIC arrays to characterize methylation profiles in 51 BPDCN cases.

overall_design: Total DNA was extracted and prepared for EPIC arrays from 51 FFPE BPDC cases following the manufacturer protocol.

first: Niklas

last: Gebauer

first: Hauke

last: Busch


title: Slam-seq reveals that miR-430 regulates zygotic mRNA during zebrafish embryogenesis [titration_data]

status: Public on Feb 10 2024

city: Kansas City

first: Ariel

middle: Alejandro

last: Bazzini

institute: Stowers Institute for Medical Research

summary: Background: Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and affecting gene function during this period is bound to affect both pools of mRNAs, it has been challenging to study their expression dynamics separately. Results: By employing Slam-seq, a nascent mRNA labeling transcriptomic approach, in a developmental time series we observe that over half of the early zebrafish embryo transcriptome consists of maternal-zygotic genes, emphasizing their pivotal role in early embryogenesis. We provide an hourly resolution of de novo transcriptional waves and follow nascent mRNA trajectories, finding that most de novo transcriptional events are stable throughout this period. Additionally, by blocking microRNA430 function, a key post-transcriptional regulator during zebrafish embryogenesis, we directly show that it destabilizes hundreds of de novo transcribed mRNAs from pure zygotic as well as maternal-zygotic genes. This unveils a novel miR-430 function during embryogenesis, fine-tuning zygotic gene expression, which highlights that Slam-seq can be used to disentangle transcriptional and post-transcriptional regulation of mRNA levels.  Conclusion: Such valuable insights into zebrafish early embryo transcriptome dynamics emphasize the significance of post-transcriptional regulators in zygotic genome activation. These findings pave the way for future investigations into the coordinated interplay between transcriptional and post-transcriptional landscapes required for the establishment of animal cell identities and functions.

overall_design: Zebrafish embryos were dechorionated and either non-injected or injected at single cell stage with ~1000pL of 25/50/75mM s4-UTP by itself or the highest dose with 200µg/µl Alpha Amanitin. Embryos were kept in the dark until collection time, shield stage (~6 hours post-injection). Total RNA was extracted, and kept away from direct light,  alkylated, used for library preparation with QuantSeq 3′ mRNA‐Seq Library Prep Kit for Illumina (FWD).

first: Danielson

last: Baia Amaral

first: Rhonda

last: Egidy

first: Anoja

last: Perera


title: Colitis associated with immune checkpoint inhibitors [tissue_cells]

city: Charlestown

first: Kamil

last: Slowikowski

state: Massachusetts

address: Mailstop CNY 149-8, 149 13th Street

institute: Massachusetts General Brigham

summary: In this study we set investigate four aspects of irColitis that are vital  to the pathogenesis of most immunotherapy related adverse events: (1) the  interactions between CD8 T cells and other immune, epithelial, and  mesenchymal cells that sustain organ specific inflammation; (2) the  contribution of circulating immune cells to disease; (3) the epithelial and  mesenchymal defects that define parenchymal organ injury and dysfunction;  (4) the transcriptional features of colitis associated with anti-PD-1  monotherapy versus anti-PD-1/CTLA-4 dual therapy. We leveraged single-cell  RNA-sequencing (scRNA-seq) and single-nuclei RNA-sequencing (snRNA-seq) of  colon mucosal biopsies and paired blood specimens collected from a  well-characterized cohort of irColitis cases and controls to define the  cellular and molecular drivers of irColitis.

overall_design:
Single-cell RNA-seq, single-nucleus RNA-seq, TCR, BCR, and CITE-seq; 28 patients
***Raw data are being deposited in dbGaP due to patient privacy concerns***

first: Molly

last: Thomas

first: Alexandra

middle: C

last: Villani


title: Selective CDK7 inhibition suppresses cell cycle progression and MYC signaling while enhancing apoptosis in therapy-resistant estrogen receptor positive breast cancer

city: Boston

first: Cristina

last: Guarducci

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary:
Purpose: Resistance to endocrine therapy (ET) and CDK4/6 inhibitors (CDK4/6i) is a clinical challenge in estrogen receptor (ER) positive (ER+) breast cancer (BC). Cyclin-dependent kinase 7 (CDK7) is a candidate target in endocrine resistant ER+ BC models and selective CDK7 inhibitors (CDK7i) are in clinical development for the treatment of ER+ BC. Nonetheless, the precise mechanisms responsible for the activity of CDK7i in ER+ BC remain elusive. Herein, we sought to unravel these mechanisms.
Experimental Design: We conducted multi-omic analyses in ER+ BC models in vitro and in vivo including models with different genetic backgrounds. We also performed genome wide CRISPR knock-out library screens to identify potential therapeutic vulnerabilities in CDK4/6i resistance models.
Results: We found that the on-target anti-tumor effects of CDK7 inhibition in ER+ BC are in part p53 dependent, involve cell-cycle inhibition and suppression of c-Myc. Moreover, CDK7 inhibition exhibited cytotoxic effects, distinctive from the cytostatic nature of ETs and CDK4/6i. CDK7 inhibition resulted in suppression of ER phosphorylation at S118, however, long-term CDK7 inhibition resulted in increased ER signaling, supporting the combination of ET with a CDK7i. Lastly, genome wide CRISPR/Cas9 screens identified CDK7 and MYC signaling as putative vulnerabilities in CDK4/6i resistance, and CDK7 inhibition effectively inhibited CDK4/6i resistant models.
Conclusions: Taken together, these findings support the clinical investigation of selective CDK7 inhibition combined with ET to overcome treatment resistance in ER+ BC. In addition, our study highlights the potential of increased c-Myc activity and intact p53 as predictors for sensitivity to CDK7 inhibitor-based treatments.

overall_design: 1. Comparative gene expression profiling analysis of RNA-seq data for ER-WT MCF7 cells and its ER-mutant derivatives  with and without CDK7 mutation and in two PDX models (WT:1415 and Mut:1526). 2. Comparative gene expression profiling analysis of RNA-seq data for Palbociclib-sensitive and -resistant T47D and MCF7 cells.

first: Rinath

last: Jeselsohn


title: CRISPRδ: dCas13-mediated translational repression for accurate gene silencing in mammalian cells

city: Wako

first: Shintaro

last: Iwasaki

address: S205 Bioscience Bldg. 2-1 Hirosawa

department: Cluster for Pioneering Research

institute: RIKEN

summary: Current gene silencing tools based on RNA interference (RNAi) or more recently the CRISPR-Cas13 systems have critical drawbacks in such as off-target effects (RNAi) or collateral mRNA cleavage (CRISPR-Cas13). Thus, a more specific method of gene knockdown has been demanded. Here we developed “CRISPRδ”, an approach for translational silencing, harnessing the catalytically inactive Cas13 proteins (dCas13). Owing to the tight association with mRNA, dCas13 serves as a physical roadblock for scanning ribosomes in translation initiation, but not for elongating ribosomes, with no effect on mRNA stability. Guide RNAs covering the start codon lead to the highest efficacy, irrespective of translation initiation mechanisms: cap-dependent, IRES-dependent, or RAN translations. Strikingly, genome-wide ribosome profiling revealed extremely high specificity of CRISPRδ in a gene knockdown. Moreover, the fusion of a translation repressor to dCas13 ensured further improvement of the knockdown efficacy. Our method provides a framework for translational repression-based gene silencing in eukaryotes.

overall_design: Ribosome profiling and RNA-Seq of HEK 293 cells

first: Apostolopoulos

last: Antonios

first: Tsuiji

last: Hitomi

first: Shichino

last: Yuichi

first: Iwasaki

last: Shintaro


title: Altered microbial bile acid metabolism exacerbates T cell-driven inflammation during graft-versus-host disease

status: Public on Feb 09 2024

city: New York

first: Oriana

last: Miltiadous

address: 1275 York Ave

department: Pediatrics

institute: Memorial Sloan Kettering

summary: Microbial transformation of bile acids affects intestinal immune homeostasis but its impact on inflammatory pathologies remains largely unknown. Using a mouse model of graft-versus-host disease (GVHD), we found that T cell-driven inflammation decreased the abundance of microbiome-encoded bile salt hydrolase (BSH) genes and reduced the levels of unconjugated and microbe-derived bile acids. Several microbe-derived bile acids attenuated farnesoid X receptor (FXR) activation, suggesting that loss of these metabolites during inflammation may increase FXR activity and exacerbate the course of disease. Indeed, mortality increased with pharmacological activation of FXR and decreased with its genetic ablation in donor T cells during mouse GVHD. Furthermore, patients with GVHD after allogeneic hematopoietic cell transplantation showed similar loss of BSH and the associated reduction in unconjugated and microbe-derived bile acids. Additionally, the FXR antagonist ursodeoxycholic acid reduced the proliferation of human T cells and was associated with a lower risk of GVHD-related mortality in patients. We propose that dysbiosis and loss of microbe-derived bile acids during inflammation may be an important mechanism to amplify T cell-mediated diseases.

overall_design:
Single cell RNA-sequencing profiling of in vitro activated T cells treated with FXR ligands, DMSO or activating signals for 24h
*** Please note that the raw data are not included due to patient privacy concerns***

first: Sarah

last: Lindner

first: Ruben

middle: J

last: Ramos

first: Jenny

last: Paredes

first: Anastasia

middle: I

last: Kousa

first: Anqi

last: Dai

first: Teng

last: Fei

first: Emma

last: Lauder

first: John

last: Frame

first: Nicholas

last: Waters

first: Keimya

last: Sadeghi

first: Gabriel

last: Armiho

first: Romina

last: Ghale

first: Kristen

last: Victor

first: Brianna

last: Gipson

first: Sebastien

last: Monette

first: Marco

middle: V

last: Russo

first: Chi

middle: L

last: Nguyen

last: Slingerland

first: Ying

last: Taur

first: Kate

middle: A

last: Markey

first: Hana

last: Andrlova

first: Sergio

last: Girald

first: Miguel-Angel

last: Perales

first: Pavan

last: Reddy

first: Jonathan

middle: U

last: Peled

first: Melody

last: Smith

first: Justin

last: Cross

first: Marina

last: Burgos da Silva

first: Clarissa

last: Campbell

first: Marcel

last: van den Brink


title: BRI2-mediated regulation of TREM2 processing in microglia and its potential implications for Alzheimer's disease and related dementias

city: newark

first: Luciano

last: D'Adamio

state: New Jersey

address: 205 s orange ave CC-H-13

department: PPN

institute: rutgers

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the expression changes in microglia association of genomic changes of Bri2 or/and Trem2

overall_design: microglia were isolated from adult mice brains using CD11b magentic beads and performed with scRNAseq analysis

first: Tao

last: Yin

first: Metin

last: Yesiltepe


title: Targeting WIP1 phosphatase promotes partial remission in experimental collapsing glomerulopathy

city: Nice

last: Shkreli

address: 28 av de Valombrose

department: Faculty of Medicine

institute: IRCAN

summary: Collapsing focal segmental glomerulosclerosis (FSGS), also known as collapsing glomerulopathy (CG), is the most aggressive variant of FSGS and is characterized by rapid progression to end-stage kidney disease (ESKD). Understanding CG pathogenesis represents a key step for the development of targeted therapies. Previous work implicated the telomerase protein component TERT in CG pathogenesis, as transgenic TERT expression in adult mice resulted in a CG resembling that seen in human primary CG and HIV-associated nephropathy (HIVAN). We used the telomerase-induced mouse model of CG (i-TERTci mice) to identify mechanisms to inhibit CG pathogenesis. We found that inactivation of WIP1 phosphatase, a p53 target acting in a negative feedback loop, blocks disease initiation in i-TERTci mice. Repression of disease initiation upon WIP1 deficiency is associated with senescence enhancement and requires TGF-b functions. We further assessed efficacy of a pharmacologic treatment to reduce disease severity in both i-TERTci mice and in a mouse model of HIVAN (Tg26 mice). We found that pharmacologic inhibition of WIP1 enzymatic activity in either telomerase mice with CG or in Tg26 mice promotes partial remission of proteinuria and ameliorates renal histopathologic features. Histological as well as high throughput sequencing methods further showed that selective inhibition of WIP1 does not promote kidney fibrosis or inflammation. Our findings suggest that targeting WIP1 may be an effective therapeutic strategy for patients with CG.

overall_design: To gain insight into the molecular factors and pathways modulated in i-TERTci mice treated with a selective inhibitor of WIP1 (GSK2830371) we performed high-throughput sequencing (bulk RNA-seq) analysis of total kidneys from DMSO- and GSK2830371-treated i-TERTci mice, and we compared transcriptomes of these mice to those of control single transgenic actin-rtTA+ mice.

first: Tynhinane

last: Hamidouche


title: Effects of BRD4 inhibitor JQ1 on the expression profile in cervical cancer HeLa cells

city: Quanzhou

first: Jianqing

last: Zheng

state: Fujian

address: No. 950, Donghai Street, Fengze District, Quanzhou 362000, Fujian Province, P.R.

institute: The Second Affiliated Hospital of Fujian Medical University

summary: The potential antitumor effects of JQ1 on cervical cancer cells and its impact on the expression profile remain unknown. To explore the mechanism of JQ1 affecting the progression of cervical cancer, this study used high-throughput sequencing technology to investigate the transcriptome changes of cervical cancer cells treated with JQ1 to reveal the signal pathway and biological function of JQ1 on cervical cancer cells and to provide transcriptome evidence for the application of cervical in the potential treatment of cervical cancer.

overall_design: To generate the expression profile of cervical cancer (CC) HeLa-cells treated with different concentrations of bromine domain protein 4 (BRD4) inhibitor (JQ1) using whole transcriptome resequencing. 1 μmol/L concentration of JQ1 treated for 72h was applied to inhibit HeLa cells in experimental group, and while the control group was incubated with a drug-free medium for 72 h. We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 HeLa cells.

first: Bifen

last: Huang

first: Lihua

last: Xiao

first: Min

last: Wu


title: MicroRNA-21 controls the circadian regulation of apoptosis in atherosclerotic lesions

city: München

first: Maliheh

last: Nazari-Jahantigh

state: --Please select--

department: LMU

institute: IPEK

summary: Atherosclerosis is a leading cause of death due to the rupture of arterial lesions characterized by a necrotic core and inflammatory activity. Although lesion vulnerability follows a diurnal pattern with a higher incidence of rupture in the morning, the role of circadian rhythms in atherosclerotic lesions is unclear. Here we show that apoptosis in lesions follows a diurnal pattern that is controlled through the circadian regulation of the pro-apoptotic XIAP associated factor 1 (Xaf1) by the Mir21 strands. The increased apoptosis during the transition from the inactive to the active phase is not matched with the efferocytic removal of dead cells resulting in increased necrotic core formation. Lack of Mir21 expression in macrophages decreases atherosclerosis and necrotic core formation in mice, suggesting that Mir21-mediated diurnal apoptosis promotes lesion growth. In human atherosclerotic lesions, apoptosis also follows a diurnal pattern with a peak in the morning and oscillates in-phase with XAF1 expression and anti-phase with miR-21 expression. Thus, diurnal apoptosis regulated by a Mir21-controlled macrophage death clock may contribute to circadian regulation of lesion vulnerability.

overall_design: Gene expression in aortic arches was compared between BM Mir21–/– mice and BM Mir21+/+ mice after 12 weeks of an HFD feeding period by microarray analysis (n=3 mice per group).

first: Andreas

last: Schober

middle: N

last: Jahantigh

first: Richard

middle: M

last: Blay


title: The early macrophage response to pathogens requires dynamic regulation of the nuclear paraspeckle

city: Bryan

first: Kristin

last: Patrick

state: Texas

address: 8447 Riverside Pkwy, MREB 3102

department: Microbial Pathogenesis and Immunology

institute: Texas A&M University, College of Medicine

summary: To ensure a robust immune response to pathogens without risking immunopathology, the kinetics and amplitude of inflammatory gene expression in macrophages need to be exqui- sitely well controlled. There is a growing appreciation for stress-responsive membraneless organelles (MLOs) regulating various steps of eukaryotic gene expression in response to extrinsic cues. Here, we implicate the nuclear paraspeckle, a highly ordered biomolecular condensate that nucleates on the Neat1 lncRNA, in tuning innate immune gene expression in murine macrophages. In response to a variety of innate agonists, macrophage paraspeckles rapidly aggregate (0.5 h poststimulation) and disaggregate (2 h poststimulation). Paraspeckle maintenance and aggregation require active transcription and MAPK signaling, whereas paraspeckle disaggregation requires degradation of Neat1 via the nuclear RNA exosome. In response to lipopolysaccharide treatment, Neat1 KO macrophages fail to properly express a large cohort of proinflammatory cytokines, chemokines, and antimicrobial mediators. Consequently, Neat1 KO macrophages cannot control replication of Salmonella enterica serovar Typhimurium or vesicular stomatitis virus. These findings highlight a prominent role for MLOs in orchestrating the macrophage response to pathogens and support a model whereby dynamic assembly and disassembly of paraspeckles reorganizes the nuclear landscape to enable inflammatory gene expression following innate stimuli.

overall_design: The goal of the experiment was to determine the contribution of Neat1 to basal and induced innate immune gene in primary bone marrow derived macrophages (BMDMs). Total RNA was isolated from WT and Neat1 KO BMDMs at rest (UN) and after 2h and 4h LPS treatment (10ng/ml) using the Zymo Direct-Zol RNA purification kit with on-column DNase treatment and elution in nuclease-free water. Library prep was done using ribodepletion by the Baylor College of Medicine Genomic and RNA Profiling (GARP) Core and sequenced on an Illumina Novaseq 6000.

first: Sikandar

last: Azam

first: Kaitlyn

last: Armijo

first: Chi

last: Weindel

first: Morgan

last: Chapman

first: Alice

last: Devigne

first: Shinichi

last: Nakagawa

first: Tetsuro

last: Hirose

first: Susan

last: Carpenter

first: Robert

last: Watson


title: Skin graft with dermis and appendages generated in vivo by cell competition

city: Bunkyo-ku

first: Naoaki

last: Mizuno

state: Tokyo

address: 1-5-45 Yushima

institute: Tokyo Medical and Dental University

summary: Autologous skin grafting is a standard treatment for skin defects such as burns. No artificial skin substitutes are functionally equivalent to autologous skin grafts. The cultured epidermis lacks the dermis and does not engraft deep wounds. Although reconstituted skin, which consists of cultured epidermal cells on a synthetic dermal substitute, can engraft deep wounds, it requires the wound bed to be well-vascularized and lacks skin appendages. In this study, we successfully generate complete skin grafts with PSC-derived epidermis with appendages on p63 knockout embryos' dermis. Donor PSC-derived keratinocytes encroach the embryos' dermis by eliminating p63 knockout keratinocytes based on cell-extracellular matrix adhesion mediated cell competition. Although the chimeric skin contains allogenic dermis, it is engraftable as long as autologous grafts. Furthermore, we could generate semi-humanized skin segments by human keratinocytes injection into the amnionic cavity of p63 knockout mice embryos. Niche encroachment opens the possibility of human skin graft production in livestock animals.

overall_design: We performed single cell RNA-seq of wild type & Trp63 knockout mouse embryos' skin at E14.5.

first: Hisato

last: Nagano

first: Hideyuki

last: Sato

first: Eiji

last: Mizutani

first: Mayuko

last: Kano

first: Mariko

last: Kasai

first: Hiromi

last: Yamamoto

first: Hiromitsu

last: Nakauchi


title: Colitis associated with immune checkpoint inhibitors [tissue_nuclei]

first: Kamil

last: Slowikowski

overall_design:
Single-nucleus RNA-seq; 26 patients
***Raw data are being deposited in dbGaP due to patient privacy concerns***

first: Molly

last: Thomas

first: Alexandra

last: Villani


title: Lysosome-coupled mRNA transport maintains mitochondrial and ribosomal homeostasis in the axon

city: Bethesda

first: Raffaella

last: De Pace

state: Maryland

address: 9000 Rockville Pike Bethesda 35A 2F242 20892

department: NICHD

institute: NIH/NICHD

summary: To understand the function of BORCS5 in mRNA tranport, RNA-seq analysis was performed on axons and neurons from WT and BORCS5-KO human i3Neurons.

overall_design: RNA-seq analysis was performed on the neuron and axonal compartments of human i3Neuron grown on microfluidic device in each genotype. The number of biological replicates were 2 WT axons, 2 WT neurons, 3 BORCS5-KO axons, and 3 BORCS5-KO neurons.

first: Saikat

last: Ghosh

first: Juan

middle: S

last: Bonifacino


title: circular Neurexin3 knockdown in rat orbitofrontal cortex

city: Philadelphia

first: Stephanie

last: Daws

state: PA

address: 3500 N Broad St

institute: Temple University

summary: We report mRNAs differentially expressed in the orbitofrontal cortex of adult male rats 7 days following knockdown of circular Neurexin 3 in the orbitofrontal cortex.

overall_design: mRNA profiles in the orbitofrontal cortex of animals selectively infused with a scrambled control siRNA or an siRNA targeted to the backsplice junction of Neurexin 3 in the orbitofrontal cortex

last: Sillivan


title: Colitis associated with immune checkpoint inhibitors [blood_cells]

overall_design:
Single-cell RNA-seq, TCR, BCR, and CITE-seq on peripheral blood mononuclear cells (PBMCs) from 21 patients.
***Raw data are being deposited in dbGaP due to patient privacy concerns***