title: Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape [MSC_hyperL_D11_RNA-seq]

overall_design: We analyzed transcriptomic changes with targeted epigenetic editing. Human mesenchymal stromal cells were electroporated with gRNA and dCAS9-DNMT3A/3L. Controls were transfected with plasmids expressing scramble guide RNAs and dCAS9-DNMT3A/3L. Timepoint of isolation is denoted in "time point".


title: Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape [HEK_FHL2]

status: Public on Feb 11 2025

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

type: Methylation profiling by genome tiling array

summary: Aging is reflected by genome-wide DNA methylation changes, but it is largely unclear how these epigenetic modifications are regulated. In this study, we explored the possibility to interfere with epigenetic clocks by epigenetic editing at individual CpG sites. CRISPR-guided approaches (dCas9-DNMT3A and CRISPRoff) facilitated targeted methylation at age-associated genomic regions that remained stable for up to three months. Furthermore, epigenetic editing evoked many genome-wide off-target effects, which were highly reproducible and enriched at other age-associated CpGs – thus, they are not random off-target effects but seem to resemble co-regulated epigenetic bystander modifications. 4C chromatin conformation analysis at age-associated sites revealed increased interactions with bystander modifications and other age-associated CpG sites. Subsequently, we multiplexed epigenetic modifications in HEK293T, mesenchymal stromal cells, and T cells at five genomic regions that become either hypermethylated or hypomethylated upon aging. While epigenetic editing at age-hypomethylated CpGs appeared less stable, it also resulted preferentially in bystander modifications at CpGs with highest correlation with chronological age. Notably, modifications were simultaneously observed at CpGs that gain and lose methylation with age. These results demonstrate that targeted epigenetic editing can modulate the epigenetic aging network in its entirety and thereby interfere with epigenetic clocks.

overall_design: We analyzed genome-wide DNA-methylation changes with targeted epigenetic editing. HEK293T cells were transfected with plasmids expressing guide RNAs and epigenetic editors. Composition of controls are indicated by "title" and "treatment". Timepoint of isolation is noted in "time point".

first: Sven

last: Liesenfelder

first: Mohamed

middle: H

last: Elsafi Mabrouk

first: Jessica

last: Iliescu

first: Monica

last: Varona Baranda

first: Athanasia

last: Mizi

first: Juan

middle: F

last: Perez-Correa

first: Martina

last: Wessiepe

first: Argyris

last: Papantonis


title: Spatial Gene Expression of Human Coronary Arteries Revealed the Molecular Features of Diffuse Intimal Thickening in Explanted Hearts

city: Vancouver

first: Ying

last: Wang

state: British Columbia

address: 166-1081 Burrard St

department: Pathology and Laboratory Medicine, UBC

country: Canada

institute: Centre for Heart Lung Innovation - St. Paul's Hospital

summary: Diffuse intimal thickening (DIT) is a preclinical stage of atherogenesis in humans that does not exist in commonly used mouse models of atherosclerosis. Vascular smooth muscle cells (SMCs) are the predominant cell type that occupies the intimal and medial layers of human coronary arteries. The intimal layer of DIT is particularly prone to developing atherosclerosis later in life. Differences in the molecular features between the intimal and medial layers of DIT regions may represent the earliest changes that promote atherogenesis in humans, and can be studied by spatial molecular phenotyping.

overall_design: With six coronary artery  samples (three from autopsies, three from freshly explanted hearts) from formalin-fixed paraffin-embedded (FFPE) tissue sections, Visium was used to obtain whole transcriptome profiles of the intimal and medial layers of these blood vessels. Post Visium-sequencing, one sample (Sample2d1) was removed from downstream analysis as it failed to pass our quality control.

first: Leung

last: Samuel

first: Li

last: Boaz

first: Elishaev

last: Maria

first: Cheng

last: Wan-Hei

first: Mocci

last: Giuseppe

first: Björkegren

last: Johan

first: Lai

last: Chi

first: Singh

last: Amritpal

first: Wang

last: Ying


title: Broad rim lesions are a novel pathological / morphologicaland imaging biomarker for rapid disease progression in Multiple Sclerosis (part 1)

status: Public on Feb 12 2025

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

summary: Current Multiple Sclerosis (MS) treatments reduce relapse activity but have limited impact on disease progression. Clinical trials targeting progression often fail due to insufficient understanding of its underlying mechanisms. This study analyzes a clinically well-characterized MS autopsy cohort comparing selected individuals with opposite disease trajectories of slow versus rapid progression by extensive unbiased histology and spatial transcriptomics. It unveils a novel lesion type marked by an extensive myeloid cell rim with cellular and transcriptional signatures of inflammation, enhanced antigen presentation and lymphocyte activation that is strongly linked to rapid progression. Validation through an independent TSPO-PET study confirms the association between lesions with a broad myeloid cell rim and disease progression. These findings offer crucial insights into the mechanisms behind MS progression, identifying broad rim lesions as a biomarker for rapid disease progression and potentially guiding patient selection for future therapeutic trials targeting CNS intrinsic inflammation.

overall_design: Samples from broad rim lesions were investigated using spatial transcriptomics. For each sample 4 ROIs at the rim and 4 in the NAWM were selected and segmented into AOIs using CD68 as morphology marker.

first: Luisa

last: Klotz

first: Joost

last: Smolders

first: Jussi

last: Lehto

first: Markus

last: Matilainen

first: Luzia

last: Buchholz

first: Stefanie

last: Albrecht

first: Aletta

middle: M

last: van den Bosch

first: Laura

last: Airas

first: Inge

last: Huitinga

first: Tanja

last: Kuhlmann


title: Tracking and mitigating imprint erasure during induction of naïve human pluripotency at single-cell resolution [RNA-Seq]

city: St. Louis

first: Thorold

middle: W.

last: Theunissen

state: MO

address: 4515 McKinley Ave, Room 3313

country: USA

institute: Washington University in St. Louis

type: Expression profiling by high throughput sequencing

summary: Naïve human pluripotent stem cells (hPSCs) model the pre-implantation epiblast. However, parent-specific epigenetic marks (imprints) are eroded in naïve hPSCs, which represents an important deviation from the epiblast in vivo. To track the dynamics of imprint erasure during naïve resetting in real time, we established a dual-colored fluorescent reporter at both alleles of the imprinted SNRPN locus. During primed-to-naïve resetting, SNRPN expression becomes biallelic in most naïve cells and biallelic SNRPN expression is irreversible upon re-priming. We utilized this live-cell reporter to evaluate chemical and genetic strategies to minimize imprint erasure. Decreasing the level of MEK/ERK inhibition or overexpressing the KRAB zinc finger protein ZFP57 protected a subset of imprints during naïve resetting. Combining these two strategies protected imprint levels to a further extent than either strategy alone. This study offers an experimental tool to track and enhance imprint stability during transitions between human pluripotent states in vitro.

overall_design: Bulk RNA-seq analysis of H9 and H9-SRG primed, naïve, and alternative hESCs.

middle: A

last: Fischer

middle: W

first: Sabine

last: Dietmann


title: Epileptic phenotypes in slc13a5 loss-of-function zebrafish are rescued by blocking NMDA receptor signaling

city: Calgary

first: Deepika

last: Dogra

state: Alberta

address: 3330 Hospital Dr NW

department: Department of Medical Genetics

institute: University of Calgary

summary: SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra- and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures, developmental delays, behavioral deficits, poor motor progression, and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here, we used CRISPR/Cas9 to create loss-of-function mutations in slc13a5a and slc13a5b, the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances, consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum, a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy, including an imbalance in glutamatergic and GABAergic excitatory-inhibitory gene expression, disrupted neurometabolism, and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically, we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy-like phenotypes. Slc13a5 protein co-localizes with excitatory NMDA receptors in wild-type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics, hyperexcitable calcium events, and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over-chelates the ions needed to regulate NMDA receptor function, leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery.

overall_design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls, 5a mutants, 5b mutants and 5a/5b double mutants


title: Emerin Dysregulation Drives the Very-Small-Nuclear Phenotype and Lineage Plasticity that Associates with a Clinically Aggressive Subtype of Prostate Cancer

city: Los Angeles

first: Edwin

last: Posadas

state: CA

address: 8700 Beverly Blvd, Davis Building, Room 5094C

department: urology

institute: Cedars-Sinai Medical Center

summary: Background: Circulating tumor cells (CTCs) with a very-small-nuclear phenotype (vsnCTCs) in prostate cancer (PCa) are characterized by nuclei smaller than 8.5 μm. Our previous studies established an association between vsnCTCs and visceral metastasis. Reduction of emerin (EMD), a nuclear envelope protein, contributes to PCa metastasis and nuclear shape instability. Here we investigated the correlation between EMD expression and the vsnCTC phenotype and its clinical impact. Methods: We analyzed CTCs from 93 mCRPC patients and categorized them as either vsnCTC+ or vsnCTC- and compared overall survival (OS) and progression-free survival (PFS). C4-2B, 22Rv1, and DU145 with EMD knockdown were developed and characterized by nuclear size and gene expression by GSEA analysis. Abiraterone- and enzalutamide-resistant (Abi-R/Enza-R) C4-2B cells were also characterized by nuclear size and EMD expression. Results: vsnCTC+ patients had significantly worse OS and PFS compared to vsnCTC- patients. EMD expression was markedly reduced in CTCs from vsnCTC+ patients compared to vsnCTC- patients, with a significant positive correlation between EMD expression and CTC nuclear size. EMD knockdown in PCa cells resulted in smaller nuclei, enhanced invasion, and the upregulation of genes associated with lineage plasticity. Additionally, C4-2B Abi-R/Enza-R cells had smaller nuclei and lower EMD expression. vsnCTC+ cells also showed enhanced platinum sensitivity. Conclusions: The presence of vsnCTCs represents a novel hallmark of an aggressive subtype of mCRPC, closely linked to EMD loss and lineage plasticity. These findings highlight the importance of EMD dysregulation in the vsn phenotype, disease progression, and therapeutic resistance in patients with PCa.

overall_design: C4-2B (RRID: CVCL_4784), DU145 (RRID: CVCL_0105), and 22Rv1 (RRID: CVCL_1045) cells were purchased from ATCC. C4-2B, 22Rv1 and DU145 cells were transfected with EMD siRNA (sc-35296, Santa Cruz) and control scramble siRNA (sc-37007, Santa Cruz) using Lipofectamine 3000 (Fisher Scientific), as described by the manufacturer. Then, 24 h after the addition of the transfection mix, liposomes were removed, and fresh medium was added. Total RNA was extracted with the RNeasy Plus Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. All the RNA-seq experiments were performed in triplicate. RNA library and transcriptome sequencing were performed by Novogene (Sacramento, CA, USA).

first: Le

last: Zhang

first: Pai-Chi

last: Teng

first: Karen

last: Cavassani

first: Jasmine

middle: J

last: Wang

first: Catherine

middle: S

last: Grasso

first: Joshua

last: Watson

first: Zijing

last: Chen

first: Kai-Han

last: Tu

first: Brenda

middle: C

last: Salumbides

first: Krizia

last: Rohena-Rivera

first: Lilit

last: Gevorkian

first: Minhyung

last: Kim

first: Sungyong

last: You

first: Dolores

last: Di Vizio

first: Howard

last: Sandler

first: Timothy

last: Daskivich

first: Neil

last: Bhowmick

first: Michael

middle: R

last: Freeman

first: Hsian-Rong

last: Tseng

first: Jie-Fu


title: The ALS-associated co-chaperone DNAJC7 mediates neuroprotection against proteotoxic stress by modulating HSF1 activity

city: Chicago

first: Evangelos

last: Kiskinis

state: IL

address: 303 E. Superior Street

department: Neurology

institute: Northwestern University Feinberg School of Medicine

summary: The degeneration of neurons in patients with amyotrophic lateral sclerosis (ALS) is commonly associated with accumulation of misfolded, insoluble proteins. Heat shock proteins (HSPs) are central regulators of protein homeostasis as they fold newly synthesized proteins and refold damaged proteins. Heterozygous loss-of-function mutations in the DNAJC7 gene that encodes an HSP co-chaperone were recently identified as a cause for rare forms of ALS, yet the mechanisms underlying pathogenesis remain unclear. Using mass spectrometry, we found that the DNAJC7 interactome in human motor neurons (MNs) is enriched for RNA binding proteins (RBPs) and stress response chaperones. MNs generated from iPSCs with the ALS-associated mutation R156X in DNAJC7 exhibit increased insolubility of its client RBP HNRNPU and associated RNA metabolism alterations. Additionally, DNAJC7 haploinsufficiency renders MNs increasingly susceptible to proteotoxic stress and cell death as a result of an ablated HSF1 stress response pathway. Critically, expression of HSF1 in mutant DNAJC7 MNs is sufficient to rescue their sensitivity to proteotoxic stress, while postmortem ALS patient cortical neurons exhibit a reduction in the expression of HSF1 pathway genes. Taken together, our work identifies DNAJC7 as a crucial mediator of HNRNPU function and stress response pathways in human MNs and highlights HSF1 as a therapeutic target in ALS.

overall_design: RNA-Seq profiling of iPSC-derived motor neurons expressing either homozygous WT DNAJC7 (+/+), or heterozygous mutant DNAJC7 (R156X/+)

first: Andrew

last: Fleming

first: Nalini

last: Rao

first: Matthew

last: Wright

first: Jeffrey

middle: N

last: Savas


title: Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape [HEK_HypoL_D3]

first: Wolfgang

last: Wagner

summary: Aging is reflected by genome-wide DNA methylation changes, but it is largely unclear how these epigenetic modifications are regulated. In this study, we explored the possibility to interfere with epigenetic clocks by epigenetic editing at individual CpG sites. CRISPR-guided approaches (dCas9-DNMT3A and CRISPRoff) facilitated targeted methylation at an age-associated genomic region in PDE4C that remained stable for more than three months. Furthermore, epigenetic editing evoked many genome-wide off-target effects, which were highly reproducible and enriched at other age-associated CpGs - thus, they are not random off-target effects, but seem to resemble coregulated epigenetic bystander modifications. 4C chromatin conformation analysis at age-associated sites revealed increased interactions with bystander modifications and other age-associated CpG sites. Subsequently, we multiplexed epigenetic modifications in HEK293T and primary T cells at five genomic regions that become either hypermethylated or hypomethylated upon aging. While epigenetic editing at age-hypomethylated CpGs appeared less stable, it also resulted in a clear enrichment of bystander modifications at other age-associated CpGs. Conversely, epigenetic clocks tend to be accelerated up to ten years after targeted DNA methylation, particularly at hypermethylated CpGs. These results demonstrate that targeted epigenome editing can modulate the epigenetic aging network in its entirety and thereby interfere with epigenetic clocks.

overall_design: We analyzed genome-wide DNA-methylation changes with targeted epigenetic editing. HEK293T cells were transfected with plasmids expressing guide RNAs and epigenetic editors. Composition of controls are indicated by "title" and "treatment". Timepoint of isolation is noted in "description".

first: Sven

last: Liesenfelder

first: Mohamed

last: Elsafi Mabrouk

first: Jessica

last: Iliescu

first: Monica

last: Varona Baranda

first: Athanasia

last: Mizi

first: Martina

last: Wessiepe

first: Argyris

last: Papantonis


title: Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape [T_cell_hyper]

overall_design: We analyzed genome-wide DNA-methylationchanges with targeted epigenetic editing. Human primary T-cells were transfected with plasmids expressing guide RNAs and dCAS9-DNMT3A/3L. Controls were transfected with plasmids expressing scramble guide RNAs and dCAS9-DNMT3A/3L. Timepoint of isolation is noted in "time point".


title: Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape [HEK_HyperL_D7]


title: Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape [4C-seq]

overall_design: We analyze chromatin interaction of 3 age-associated CpG regions in HEK cells using i4C-sequencing: PDE4C, FHL2, and MEIS1-AS3 (each viewpoint in triplicates). Sequencing was performed in 2-3 runs and there are up to 6 fastq.gz files for each sample.


title: Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape

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

overall_design: Refer to individual Series


title: Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape [RNA-seq]

overall_design: We analyzed gene expression changes with targeted epigenetic editing at age-hypermethylated CpGs (PDE4C, FHL2, KLF14, ELOVL2, TEAD1). HEK293T cells were transfected with plasmids expressing guide RNAs and dCAS9-DNMT3A/3L (experiment) or scramble guide and dCAS9-DNMT3A/3L (control).


title: Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape [HEK_HypoL_D15]


title: Anti-tumor CD4Th1 cells controls the migration and outgrowth of disseminated cancer cells

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: Comparison of gene expression profiles of disseminated cancer cells with primary tumors and metastatic tumors

overall_design: To investigate the gene expression profiles of disseminated cancer cells compared to primary tumors and metastatic tumors in breast cancer and role of anti-tumor CD4Th1 immune response on the gene expression profiles, we performed RNA sequencing.

first: Ganesan

last: Ramamoorthi

first: Brian

last: Czerniecki


title: Alterations in the hepatocyte epigenetic landscape in steatosis

city: Saarbruecken

first: Gilles

last: Gasparoni

state: Saarland

address: Campus

department: Genetics Department

institute: Saarland University

type: Methylation profiling by high throughput sequencing

summary: Fatty liver disease or the buildup of fat in the liver, has been reported to affect the global population. This comes with an increased risk for the development of fibrosis, cirrhosis, and hepatocellular carcinoma. Yet, little is known about the effects of a diet containing high fat and alcohol towards epigenetic aging, with respect to changes in transcriptional and epigenomic profiles. In this study, we took up a multi-omics approach and integrated gene expression, methylation signals, and chromatin signals to study the epigenomic effects of a high-fat and alcohol-containing diet on mouse hepatocytes. We identified four relevant protein-protein interaction network clusters that were associated with relevant pathways that promote steatosis. Using a machine learning approach, we predict specific transcription factors that might be responsible to modulate the functionally relevant clusters. Finally, we discover four additional CpG loci and validate aging-related differential CpG methylation. Differential CpG methylation linked to aging showed minimal overlap with altered methylation in steatosis.

overall_design: Reduced representation bisulfite sequencing (RRBS): Library preparation was conducted as described previously in a one-tube reaction [19]. Briefly, 500 ng genomic DNA was digested with MspI, repaired and A-tailed using Klenow fragment enzyme (NEB), subsequently Illumina TruSeq universal adaptors were ligated (T4 ligase, NEB). Bisulfite treatment was performed using the EZ DNA Methylation-Gold Kit (Zymo Res.) according to the manufacturer's protocol. Library preparation was accomplished by amplification with indexed TruSeq adaptor sequences (12 cycles) to add sample-specific 6bp identifiers. Sequencing was conducted on the HiSeq2500 (Illumina) on a 100 bp single-read flow cell aiming at 25-30 Mio reads per sample.

first: Ranjan

middle: K

last: Maji

first: Beate

last: Czepukojc

first: Michael

last: Scherer

first: Sascha

last: Tierling

first: Cristina

last: Cadenas

first: Kathrin

last: Gianmoena

first: Nina

first: Karl

last: Nordström

first: Stephan

last: Laggai

first: Xinyi

last: Yang

first: Anupam

last: Sinha

first: Peter

last: Ebert

first: Maren

last: Falk-Paulsen

first: Sarah

last: Kinkley

first: Ho-Ryun

last: Chung

first: Philip

last: Rosenstiel

first: Jan

middle: G

last: Hengstler

first: Jörn

last: Walter

first: Marcel

last: Schulz

first: Sonja

last: Kessler

first: Alexandra

last: Kiemer


title: Lucicebtide (ST101) effect on hPBMCs-derived M2-type macrophages.

status: Public on Feb 10 2025

city: Tarrytown

first: Claudio

last: Scuoppo

state: NY

address: 500 White Plains Rd Fl 2

institute: Sapience Therapeutics

summary: Reprogramming immunosuppressive M2-like macrophage to immune-active M1-like macrophage represents a promising strategy to improve responses to immunotherapy. Lucicebtide (previously referred to as ST101) is a peptide antagonist of the transcription factor C/EBPβ, a key activator of the transcriptional program in immunosuppressive macrophages. We show that Lucicebtide exposure reprograms human Perypheral Blood Mononuclear cells (hPBMSc)-derived M2-like macrophage to the pro-inflammatory M1-like phenotype. RNAseq tracriptional profiling of M2-like macrophages untreated or treated with Lucicebtide induces a substantial dowregulation of the M2-program and a subset of known C/EBPβ targets. Taken togheter, these data highlight the ability of Lucicebtide to rewire the M2-like immunosuppressive program and support combinatorial stategies to potentiate immunotherapy approaches.

overall_design: RNA-seq profiling of hPMBCs-derived M2-like cultures untreated or treated with 10 μM Lucicebtide.

first: Jim

last: Rotolo

first: Lila

last: Ghamsari

first: Barry

last: Kappel


title: Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape [T_cell_hypo]

first: Wolfgang

last: Wagner

overall_design: We analyzed genome-wide DNA-methylationchanges with targeted epigenetic editing. Human primary T-cells were transfected with plasmids expressing guide RNAs and dCAS9-DNMT3A/3L.Controls were transfected with plasmids expressing scramble guide RNAs and dCAS9-DNMT3A/3L. Timepoint of isolation is noted in "description".

first: Sven

last: Liesenfelder

first: Mohamed

last: Elsafi Mabrouk

first: Jessica

last: Iliescu

first: Monica

last: Varona Baranda

first: Athanasia

last: Mizi

first: Martina

last: Wessiepe

first: Argyris

last: Papantonis


title: Differential expression of RhoA gene in SMART-Cas9 knockout macrophages

city: Shenzhen

first: Jingqin

last: Chen

country: China

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

summary: We have identified that Ras homolog gene family member A (RhoA) is a pivotal target in inducing osteoclastogenesis in macrophages. Subsequently, we developed a strategy termed Specific Macrophage RhoA Targeting (SMART). In this strategy, phosphatidylserine-enriched macrophage membranes are engineered to deliver CRISPR-Cas9 plasmids containing a macrophage-specific promoter (SMART-Cas9), thereby enabling targeted editing of the RhoA gene in RAW264.7 macrophages. High-throughput transcriptome sequencing was then performed. Transcriptome analysis revealed that ablation of the macrophage RhoA gene significantly inhibited key signaling pathways associated with bone destruction.

overall_design: To investigate the effect of macrophage RhoA deficiency on bone destruction in rheumatoid arthritis (RA), we employed a targeted macrophage-specific RhoA knockout strategy using SMART-Cas9. One untreated macrophage cell line was used as the control group. Subsequently, total RNA was extracted from the cells, and high-throughput transcriptome sequencing was performed. Gene expression profiling was then conducted using the data obtained from RNA-seq. Each sample was replicated three times to ensure robustness and reproducibility of the results.

first: Jianhai

first: Jianwei

last: Tan


title: Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape [HEK_PDE4C]

overall_design: We analyzed genome-wide DNA-methylation changes with targeted epigenetic editing. HEK293T cells were transfected with plasmids expressing guide RNAs and epigenetic editors. Composition of controls are indicated by "title", "treatment" and "Timepoint of isolation".

middle: V

last: Baranda


title: Transfer RNA acetylation regulates in vivo mammalian stress signaling

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transfer RNA acetylation regulates in vivo mammalian stress signaling [tissues]

summary: Transfer RNA (tRNA) modifications are crucial for protein synthesis, but their position-specific physiological roles remain poorly understood. Here, we investigate the impact of N4-acetylcytidine (ac4C), a highly conserved tRNA modification catalyzed by the essential acetyltransferase Nat10. By targeting Thumpd1, a nonessential adapter protein required for Nat10-catalyzed tRNA acetylation, we determine that loss of tRNA acetylation leads to reduced levels of tRNALeu, increased ribosome stalling, and activation of eIF2α phosphorylation. Thumpd1 knockout mice exhibit growth defects and sterility. Concurrent knockout of Thumpd1 and the stress-sensing kinase Gcn2 causes penetrant postnatal lethality in mice, indicating a critical genetic interaction. Our findings demonstrate that a modification restricted to a single position within type II cytosolic tRNAs can regulate ribosome-mediated stress signaling in mammalian organisms, with implications for our understanding of translational control and therapeutic interventions.

overall_design: RNA-Seq samples from mouse tissues in which Thumpd1 gene has been knocked out (Thumpd1 KO) vs control (WT).

first: Gamage

last: Supuni Thalalla

first: Khoogar

last: Rhoxane

first: Manage

last: Shereen Howpay

first: Crawford

last: McKenna C.

first: Georgeson

last: Joe

first: Sanders

last: Chelsea

first: Polevoda

last: Bogdan V.

first: Nance

last: Kellie D.

first: Perez

last: Minervo

first: Thu

last: Chu T.

first: Evans

last: Christine N.

first: Das

last: Sudipto

first: DaRos

last: Judey T.

first: Hunter

last: Kent

first: Amin

last: Ruhul

first: Holewinski

last: Ronald J.

first: Meyer

last: Thomas J.

first: Yang

last: Acong

first: Jailwala

last: Parthav

first: Nguyen

last: Joe T.

first: Andressen

last: Thorkell

first: Mock

last: Beverly A.

first: Gu

last: Shuo

first: Edmondson

last: Elijah F.

first: Difilippantonio

last: Simone

first: Chari

last: Raj

first: Schwartz

last: Schraga

first: O’Connell

last: Mitchell R.

first: Wu

last: Colin Chih-Chien

first: Meier

last: Jordan L.


title: Transfer RNA acetylation regulates in vivo mammalian stress signaling [cells]

first: Thomas

last: Meyer

overall_design: RNA-Seq samples from human embryonic kidney cells (HEK-293T) cells in which THUMPD1 gene has been knocked out (THUMPD1 KO) vs control (WT).

first: Supuni Thalalla

last: Gamage

first: Rhoxane

last: Khoogar

first: Shereen Howpay

last: Manage

first: McKenna C.

last: Crawford

first: Joe

last: Georgeson

first: Chelsea

last: Sanders

first: Bogdan V.

last: Polevoda

first: Kellie D.

last: Nance

first: Minervo

last: Perez

first: Chu T.

last: Thu

first: Christine N.

last: Evans

first: Sudipto

last: Das

first: Judey T.

last: DaRos

first: Kent

last: Hunter

first: Ruhul

last: Amin

first: Ronald J.

last: Holewinski

first: Thomas J.

first: Acong

last: Yang

first: Parthav

last: Jailwala

first: Joe T.

last: Nguyen

first: Thorkell

last: Andressen

first: Beverly A.

last: Mock

first: Shuo

last: Gu

first: Elijah F.

last: Edmondson

first: Simone

last: Difilippantonio

first: Raj

last: Chari

first: Schraga

last: Schwartz

first: Mitchell R.

last: O’Connell

first: Colin Chih-Chien

last: Wu

first: Jordan L.

last: Meier


title: KLRG1 identifies regulatory T cells with mitochondrial alterations that accumulate with aging

city: Madrid

first: María

last: Mittelbrunn

state: Madrid

address: C/ Nicolás Cabrera, 1

country: Spain

institute: Centro de Biología Molecular Severo Ochoa

summary: Recent works using single cell RNA sequencing (scRNAseq) technology have uncovered several subpopulations of CD4+ T cells that accumulate with aging, including activated regulatory T cells, effector memory T cells, exhausted T cells or cytotoxic T cells. These age-associated T cells are emerging as relevant players in the control of inflammaging and tissue senescence. Herein, based on information provided by scRNAseq data, we present a flow cytometry panel that allows the identification of age-associated T cell subsets in systematic larger analysis in mice. We use this panel to evaluate at single cell level mitochondrial and senescence marks in the different age-associated CD4 T cell subpopulations. Our analysis identifies a subpopulation of regulatory T cells (Tregs) that is characterized by the extracellular expression of the co-inhibitory molecule Killer cell lectin-like receptor subfamily G member 1 (KLRG1) and accumulates with aging in humans and mice. KLRG1-expressing Tregs display features of senescence such as mitochondrial alterations, increased expression of cell-cycle regulators and genomic DNA damage. Functionally, KLRG1+ Treg cells show a reduced suppressive activity in vivo accompanied by a pro-inflammatory phenotype in which FOXP3 expression is preserved but accompanied by the engagement of an inflammatory program.

overall_design: To investigate a new Treg subset, we analysed the transcriptome of three different splenic Treg subsets (resting Tregs, activated Tregs and KLRG1+Tregs) sorted from 4 young and 4 old mice

first: Gonzalo

last: Soto-Heredero

first: Enrique

last: Gabandé-Rodríguez

first: Elisa

last: Carrasco

first: José I

last: Escrig-Larena

first: Manuel M.

last: Gómez de las Heras

first: Sandra

last: Delgado-Pulido

first: Isaac

last: Francos-Quijorna

first: Eva M.

last: Blanco

first: Álvaro

last: Fernández-Almeida

first: David

last: Abia

first: María Josefa

last: Rodríguez

first: Cristina M

last: Fernández-Díaz

first: María Beatriz

last: Álvarez-Flores

first: Ana

last: Ramírez de Molina

first: Sascha

last: Jung

first: Antonio

last: del Sol

first: Virginia

last: Zorita

first: Fátima

last: Sánchez-Cabo

first: Carlos

last: Torroja


title: Crosstalk signaling between the epithelial and non-epithelial compartments of the mouse inner ear

city: Nashville

first: Taha

last: Jan

state: TN

address: 2220 Pierce Ave, PRB 752

department: Otolaryngology

institute: VUMC

summary: The otolith organs of the inner ear consist of the utricle and saccule that detect linear acceleration. These organs rely on mechanosensitive hair cells for transduction of signals to the central nervous system. In the murine utricle, about half of the hair cells are born during the first postnatal week. Here, we report diverse cell-cell crosstalk among the 12 annotated cell populations in the developing neonatal utricle, including epithelial and non-epithelial cellular signaling. The mesenchymal cells are the dominant signal senders during the postnatal period. Epithelial to mesenchymal signaling, as well as mesenchymal to epithelial signaling, are quantitatively shown through the TGFβ and Pleiotrophin pathways. This study highlights the dynamic process of postnatal vestibular organ development that relies not only on epithelial cells, but also on crosstalk between spatial compartments and among different cell groups.

overall_design: This dataset contains FACS sorted utricle cells that underwent single cell RNA sequencing using the Smart-seq2 method. The mouse utricles were harvested at the indicated ages (postnatal day 4 and 6) and the sensory epithleium was peeled away from the non-sensory epithelium. The two cellular compartments (sensory epitheilum and non-sensory epithelium) were then separated and underwent FACS sorting and plate based sequencing separately. The sensory epithelial cells were previously published by our group (GSE155966) but have been reanalyzed here and included for copmleteness sake.

first: Alan

last: Cheng

first: Stefan

last: Heller


title: Single cell deletion of the transcription factors Sox9 and Trps1 reveals novel functions in adult cortical astrocytes [RNA-seq]

city: Planegg-Martinstied

first: Giacomo

last: Masserdotti

address: Groshaderner Strasse 9

department: ISF

institute: Helmholtz Zentrum

summary: Purpose of the study is to evaluate the impact of Sox9 and Trps1 knock-down in vivo at single cell level

overall_design: Astrocyte-specific lentiviral constructs carrying gRNAs targeting Sox9, Trps1 and or both were injected in the cerebral cortex of adult transgenic mice expressing Cas9 protein. Transduced cells were retrived from the cortex 7 and 21 days post injection and subjected to SmartSeq2 for single cell sequencing

first: Poornemaa

last: Natarajan

first: Christina

last: Koupourtidou

first: Thibault

last: de Resseguier

first: Manja

last: Thorwirth

first: Riccardo

last: Bocchi

first: Judith

last: Fischer-Sternjak

first: Sarah

last: Gleiss

first: Diana

last: Rodrigues

first: Mike

last: Myoga

first: Jovica

last: Ninkovic

first: Magdalena

last: Götz


title: ATRX mutations mediate an immunogenic phenotype and macrophage infiltration in neuroblastoma.

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: ATRX is one of the most frequently mutated genes in high-risk neuroblastoma. ATRX mutations are mutually exclusive with MYCN amplification and mark a recognizable patient subgroup, presenting in older children with chemotherapy-resistant, slowly progressive disease. The mechanisms underlying how ATRX mutations drive high-risk and difficult-to-treat neuroblastoma are still largely elusive. To unravel the role of ATRX in neuroblastoma, we generated isogenic neuroblastoma cell line models of both ATRX loss of-function and ATRX in-frame multi-exon deletions, representing different types of alterations found in patients. RNA-sequencing analysis consistently showed significant upregulation of pathways implicated in inflammatory responses and epithelial-to- mesenchymal transition in the ATRX-mutant cell lines. In vivo, ATRX mutations mediate macrophage recruitment in xenograft models. This was further confirmed in patient-derived xenograft models. In support of this, bioinformatic analysis of previously published neuroblastoma patient data sets revealed an immunogenic phenotype and higher score of macrophages (with no distinction between M1 and M2 macrophage populations) and dendritic cells, but not lymphocytes, in ATRX-mutant versus ATRX wildtype tumors. Histopathological assessment of diagnostic samples from patients with ATRX mutant disease confirmed these findings with more macrophage infiltration compared to MYCN-amplified tumors. In conclusion, these results highlight that in contrast to MYCN-amplified neuroblastoma, which is associated with a cold immune microenvironment, ATRX-mutated neuroblastoma is characterized by a distinct immunogenic phenotype.

overall_design: Samples include four NBL-S P53 KO, ATRX IFF clones; two NBL-S P53 KO, ATRX WT clones; and the NBL-S P53 KO line the clones were generated from

first: Federica

last: Lorenzi

first: Sina

last: Jostes

first: Qiong

last: Gao

first: Ciaran

last: Hutchinson

first: Jennifer

last: Tall

first: Barbara

last: Martins da Costa

first: Anisha

last: Cooke

first: Dyanne

last: Rampling

first: Olumide

last: Ogunbiyi

first: Irene

last: Jiminez

first: Karen

last: Barker

first: Giuseppe

last: Barone

first: Debbie

last: Hughes

first: Michael

last: Hubank

first: Gudrun

last: Schleiermacher

first: John

last: Anderson

first: Emily

last: Bernstein

first: Louis

last: Chesler

first: Sally

middle: L

last: George


title: CHD1 Loss Hijacks SREBP2-mediated Cholesterol Biosynthesis to Fuel SPOP-deficient Prostate Cancer and Confers Resistance to Castration [scRNA-seq]

city: Houston

first: Di

last: Zhao

state: Tx

address: Zayed Building Z7. 4018

institute: MD Anderson Cancer Center

summary: Androgen receptor (AR) is an important driver in the disease progression of castration-resistant prostate cancer (CRPC). Speckle-type BTB/POZ protein (SPOP) mutations stabilize AR and frequently co-occur with the loss of chromodomain helicase DNA-binding protein 1 (CHD1). We generated a new genetically engineered mouse model and prostate cancer cells model containing CHD1 deletion and SPOP mutation to study the underlying mechanism. We found CHD1 loss–induced cholesterol production supplies intratumoral androgen biosynthesis and retains AR transcriptional activity in SPOP-mutated prostate tumors, leading to castration resistance.

overall_design: To deconvolute CHD1’s biological function and mechanism of action in SPOP-mutated tumors, we performed single-cell RNA sequencing (scRNA-seq) analysis of PSp and PCSp GEMM. To this end, we performed surgical castration on 9-month-old PSp and PCSp GEM mice (n=2 per cohort), and one month later, we collected the whole prostate tumors for scRNA-seq.

first: Yue

last: Lu

first: Feiyu

last: Chen


title: Single cell deletion of the transcription factors Sox9 and Trps1 reveals novel functions in adult cortical astrocytes [Spatial transcriptomics]

first: Giacomo

last: Masserdotti

summary: Astrocytes play key roles in brain function but it is still poorly understood how these are orchestrated by pan-astrocyte transcriptions factors (TFs). Here we examined the function of the well-known pan-astrocyte TF Sox9 and the novel astrocyte TF Trps1 (Transcriptional Repressor GATA Binding 1) by Cas9-mediated in vivo deletion using Mokola-pseudotyped lentiviral delivery into the adult cerebral cortex. The consequences of deleting either Sox9 or Trps1 alone or simultaneously were explored at single cell level (by patch-based single cell transcriptomics) and tissue level (by spatial transcriptomics). This revealed TF-specific functions in astrocytes, like synapse maintenance and immune response, as well as non-cell-autonomous effects on the surrounding cells such as on oligodendrocytes and other immune cells. Interestingly, deleting both factors cancels out some effects, suggesting that they antagonize each other’s function to some extent. Taken together, this study reveals a novel role of Trps1 and Sox9 in adult astrocytes and their communication with other glial and immune cells.

overall_design: Spatial transcriptomics of the adult mouse cortex after CRISPR mediated deletion of Sox9, Trps1 (by injection of g-Control, g-Sox9, g-Trps1 or g-Sox9+Trps1 Mok-LVs) at 7 days post injection (7dpi)

first: Poornemaa

last: Natarajan

first: Christina

last: Koupourtidou

first: Thibault

last: de Resseguier

first: Manja

last: Thorwirth

first: Riccardo

last: Bocchi

first: Judith

last: Fischer-Sternjak

first: Sarah

last: Gleiss

first: Diana

last: Rodrigues

first: Mike

last: Myoga

first: Jovica

last: Ninkovic

first: Magdalena

last: Götz


title: RNA-seq and IP-seq of Rbfox1(WT)/LASR and Rbfox1(F125A)/LASR

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA


title: CHD1 Loss Hijacks SREBP2-mediated Cholesterol Biosynthesis to Fuel SPOP-deficient Prostate Cancer and Confers Resistance to Castration

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Our rapid immunoprecipitation mass spectrometry (RIME) data showed that CHD1 had a notable interaction with chromatin remodeler sucrose non-fermenting-2 homolog (SNF2H). Then we verified the RIME data by performing co-immunoprecipitation (co-IP) assays, and we found that CHD1 forms a complex with SNF2H and ACF1 proteins in multiple PCa cells. Besides, our ChIP-sequencing data revealed that the CHD1 binds to the SREBF2 gene promoter in PCa cells.  To further dissect the impact of CHD1 and SNF2H on SREBF2 transcription, we performed Cleavage Under Targets and Release Using Nuclease Sequencing (CUT&RUN) to uncover whether SNF2H co-localized with CHD1 on the promoter region of the SREBF2 gene in SPOP-mutated LNCaP cells in low androgen conditions.

first: Haoyan

last: Li


title: IP-seq of nuclease-protected RNA associated with Rbfox1(WT)/LASR and Rbfox1(F125A)/LASR

summary: Rbfox1(WT) has a high affinity for GCAUG whereas Rbfox1(F125A) has a lower affinity for this motif. LASR associated with each protein was purified, nuclease-protected RNA was extracted, and libraries were prepared from both samples. A third control sample is the same protocol applied to cells that don't express FLAG-tagged Rbfox.

overall_design: Purification protocol outlined in Damianov et al., 2016 was applied to Flp-In 293 Rbfox2 KO#7 line without any transgenes, with FLAG-Rbfox1(WT) line, and with FLAG-Rbfox1(F125A) . Next, RNA was extracted from protein complexes and libraries were prepared with a modified version of the iCLIP protocol outlined in Damianov et al 2016. RNA isolation procedure: Purified Rbfox/LASR complexes were digested with Proteinase K and RNA was extracted using phenol-chloroform and ethanol precipitation. The sample was then treated with TurboDNAse to remove any background DNA.  cell or tissues: HEK293 Flp-In Rbfox2 KO#7

first: Parham

last: Peyda

first: Chia-Ho

first: Douglas

last: Black


title: Human MeCP2 binds to promoters and inhibits transcription in an unmethylated yeast genome

city: Vancouver

first: LeAnn

last: Howe

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry and Molecular Biology

institute: University Of British Columbia

summary: MeCP2 is a DNA-binding transcriptional regulator that is present at near-histone levels in mammalian cortical neurons. Originally identified as a DNA methylation reader, MeCP2 has been proposed to repress transcription by recruiting corepressors to methylated DNA. While some genome-wide occupancy studies support a preference for methylated DNA, others suggest that MeCP2 binding is more influenced by DNA sequence and accessibility than methylation status. Moreover, multiple studies also suggest a role for MeCP2 in gene activation. To clarify MeCP2 function we expressed MeCP2 in Saccharomyces cerevisiae, which lacks DNA methylation and known MeCP2 corepressors. We find that MeCP2 is toxic to yeast and globally inhibits transcription, indicating that MeCP2 can have significant functional impacts without DNA methylation or mammalian corepressors. A subset of MeCP2 mutations that cause the neurodevelopmental disorder Rett syndrome, specifically those that map to the DNA binding domain, alleviate the toxicity of MeCP2 in yeast. Consistent with the importance of DNA binding for toxicity in yeast, we show that MeCP2 binds to the yeast genome, with increased occupancy at GC-rich, nucleosome-depleted sequences. These findings present yeast as a useful tool for analyzing MeCP2 and reveal MeCP2 properties that are not strictly dependent on DNA methylation or mammalian corepressors.

overall_design:
ChIP-seq for wild-type and the T158M mutant of MeCP2 expressed in S. cerevisiae from an estradiol induced promoter
SLAM-seq for wild-type and the T158M mutant of MeCP2 expressed in S. cerevisiae from an estradiol induced promoter


title: Intratumoral Fusobacterium nucleatum Recruits Tumor-Associated Neutrophils to Promote Gastric Cancer Progression and Immune Evasion

city: Guangzhou

first: Tianhao

last: Zhang

state: Guangdong

address: No. 58, Zhongshan 2nd Road, Yuexiu District

department: Division of Gastrointestinal Surgery Center

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: Intratumoral microbiota can impact the development and progression of many types of cancer, including gastric cancer (GC). A better understanding of the precise mechanisms by which microbiota support GC could lead to improved therapeutic approaches. Here, we investigated the effect of intratumoral microbiota on the tumor immune microenvironment (TIME) during GC malignant progression. Analysis of human GC tissues with 16S rRNA amplicon sequencing revealed that Fusobacterium nucleatum (F. nucleatum) was significantly enriched in GC tissues with lymph node metastasis and correlated with a poor prognosis. F. nucleatum infection spontaneously induced chronic gastritis and promoted gastric mucosa dysplasia in mice. Furthermore, GC cells infected with F. nucleatum showed accelerated growth in immunocompetent mice compared to immunodeficient mice. Single-cell RNA sequencing uncovered that F. nucleatum recruited tumor-associated neutrophils (TANs) to reshape the tumor immune microenvironment. Mechanistically, F. nucleatum invaded GC cells and activated IL-17/NF-κB/RelB signaling, inducing TAN recruitment. F. nucleatum also stimulated TAN differentiation into the pro-tumoral subtype and subsequent promotion of PD-L1 expression, further facilitating GC immune evasion while also enhancing the efficacy of anti-PD-L1 antibody therapy. Together, this data uncovers mechanisms by which F. nucleatum affects GC immune evasion and immunotherapy efficacy, providing insights for developing effective treatment strategies.

overall_design: This study integrates multiple approaches, such as construction of a mouse primary GC model, 16S rRNA sequencing, Single-cell sequencing, Transcriptome sequencing, Scanning electron microscope (SEM), Transmission Electron Microscope (TEM), Multiplex immunofluorescence staining, and other in vivo and in vitro experiments, to elucidate the complex interplay between F. nucleatum and the TIME in GC.

first: Ying

first: Ertao

last: Zhai

first: Risheng

last: Zhao

first: Yan

last: Qian

first: Zhixin

last: Huang

first: Yinan

last: Liu

first: Zeyu

first: Xiang

last: Xu

first: Jianqiu

first: Zikang

first: Zhi

last: Liang

first: Ran

last: Wei

first: Linying

last: Ye

first: Jinping

last: Ma

first: Qingping

last: Wu

first: Jianhui

last: Chen

first: Shirong

last: Cai


title: A microRNA-regulated transcriptional state defines intratumoral CD8+T cells that respond to immunotherapy

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah

summary: Rising rates of advanced-stage colorectal cancer (CRC) and poor survival rates necessitate effective therapeutic options. Immune checkpoint inhibition (ICI), specifically anti-PD-1 therapy, shows potential, but clinical determinants of a positive response are suboptimal. Here, we identify microRNA-155 (miR-155) as necessary for CD8 T cell infiltrated tumors through an unbiased in vivo Crispr-Cas9 screen of tumor-antigen-specific CD8 T cell-related miRNAs. MiR-155 was necessary for a vital CD8 T cell differentiation cascade by repressing Ship-1, thereby inhibiting stemness and Tcf-1 while enhancing effector function and Cxcr6 expression, an indispensable aspect of anti-tumor and -PD-1 responses. Through a miR-155-dependent CD8 T cell transcriptional profile, we identified a gene signature that predicts anti-PD-1 responses across ten cancers. Taken together, our findings support a model whereby miR-155 serves as a central axis for CD8 T cell-dependent immunity in CRC and anti-PD-1 responses against multiple cancers that may be leveraged therapeutically or as a biomarker.

overall_design: To analyze the effects of miR155 on T cell states within colon cancer, we performed single-cell RNA-Seq (scRNAseq) on CD45+ immune cells isolated by FACS from MC38-challenged WT or miR-155 TKO mice with or without anti-PD-1 mAb treatment. There were 8 mouse treatment conditions. All mice, both males and females, were challenged with MC38 tumors. Half of each sex cohort contained miR155 fl/fl with a CD4-Cre driver, the other half had only the miR155 fl/fl allele. Half of the mice within each of these genotypes received anti-PD-1 injections, the other half received a PBS mock injection. Each sample set was pooled from tumors in 6 to 8 mice within each of the 8 treatment conditions.

first: William

last: Tang

first: Ben

last: Battistone

first: Kaylyn

last: Bauer

first: Allison

last: Weis

first: Cindy

last: Barba

first: Zaki

last: Wilmont

first: Arevik

last: Ghazaryan

first: Van

last: Tran

first: Soh-Hyun

last: Lee

first: Busra

last: Agir

first: Morgan

last: Nelson

first: Amber

last: Thibeaux

first: Colton

last: Hernandez

first: Aik

last: Tan

first: Dinesh

last: Rao

first: Matthew

last: Williams

first: Micah

last: Drummond

first: Ellen

last: Beswick

first: June

last: Round

first: H

last: Ekiz

first: Warren

middle: P

last: Voth

last: O’Connell


title: RNA sequencing of Flp-In 293 Rbfox2 KO#7 parental, Rbfox1(WT), and Rbfox1(F125A) expressing cells

first: Chia-ho

last: Lin

summary: How does Rbfox's binding to its canonical motif through its RRM contribute to its splicing activity? Splicing changes will be assessed in cells that don't express Rbfox versus cells that express wildtype Rbfox1, and cells that express the RNA binding mutant Rbfox1(F125A).

overall_design: FLAG-Rbfox1(WT) and FLAG-Rbfox1(F125A) were integrated into the Flp-In locus in Flp-In 293 Rbfox2 KO#7 parental line. All three lines were treated with doxycyline for 48 hrs to induce expression of the transgenes. Cells were then harvested and both RNA and protein were extracted. The protein levels were assessed with immunoblotting and were similar between FLAG-Rbfox1(WT) and FLAG-Rbfox1(F125A). RNA was extracted and submitted to UNGC sequencing core for polyA RNA-seq. Note that each line was grown in triplicate and samples for RNA-seq were submitted for each replicate resulting in a total of 9 samples sequenced: 3 replicates of Flp-In 293 Rbfox2 KO#7 line, 3 replicates of Flp-In 293 Rbfox2 KO#7 F-Rbfox1(WT) line, and 3 replicates of Flp-In 293 Rbfox2 KO#7 F-Rbfox1(F125A) line.

first: Parham

last: Peyda

first: Chia-Ho

first: Douglas

last: Black


title: An in-depth analysis on vaginal wound healing post surgery: Transcriptomic effects of autologous micrografting versus acellular grafts

city: Copenhagen

first: Tu

last: Hu

address: 5 Artillerivej

department: Infectious Disease Immunology

country: Denmark

institute: Statens Serum Institut

summary: Understanding wound healing in vaginal tissue is crucial for improving female health outcomes, particularly in the context of surgeries like pelvic organ prolapse, post-radiation stricture formation and complications resulting from vaginal childbirth. Tissue-engineered grafts have proven successful for vaginal tissue repair, however, the mechanisms that stimulate tissue repair are unknown. This study aims to explore the transcriptomic signatures during tissue repair after using autologous micrografting versus acellular grafts in a rabbit model for surgical vaginal reconstruction. During a single surgical procedure, we created a graft for vaginal reconstruction consisting of autologous micrografts and supporting biomaterials. This graft was named "perioperative, layered, autologous, tissue expansion (PLATE)." We also produced acellular grafts that lacked autologous micrografts,. Our findings revealed distinct differences in gene expression patterns associated with wound healing, extracellular matrix organization, and smooth muscle regeneration between the two graft types. Notably, our findings revealed that micrografting showed an accelerated progression towards the final stages of wound healing, as evidenced by elevated matrix metalloproteinase (MMP) expression, particularly MMP-13. Additionally, Transforming Growth Factor Beta-1 (TGF-β1) emerged as an expected vaginal wound healing regulator. This study provides valuable insights into the molecular mechanisms of PLATE grafts and opens new avenues for the development of targeted therapies to improve wound healing in vaginal tissues.

overall_design: 16 Female New Zealand White rabbits aged 17-19 weeks (juvenile) and weighing 3,1 kg (+- 0,3 kg) were used for this study. We sequenced mRNA from native rabbit vaginas (control, n=6), sham-operated rabbit vaginas (sham, n=3), acellular graft-inserted vaginas 10 mm from the graft zones (acellular n=3), and PLATE graft inserted vaginas 10 mm from the graft zones (PLATE, n=4).

first: Oliver

last: Willacy

first: Dennis

last: Rootsi

first: Nicolai

last: Juul

first: Clara

middle: I

last: Chamorro

first: Thomas

last: Litman

first: Magdalena

last: Fossum


title: ARID1A Mutations Promote Immune Evasion of Follicular Lymphoma Through Reduced FAS-Mediated Apoptosis by Hindering RUNX3-ETS1 Cooperativity.

city: Planegg

first: Maria

last: Solovey

address: Grosshadernerstr 9

department: Department of Physiological Chemistry

institute: Ludwigs Maximillians University

summary: The cell death receptor FAS and its ligand (FASLG) play a crucial role in the negative selection of B cells during the germinal center (GC) reaction. Failure to eliminate potentially harmful B cells can lead to the development B cell malignancies. Follicular lymphoma (FL) is a prototypic GC-derived B cell malignancy. Translocation and overexpression of antiapoptotic BCL2 is a hallmark of FL. Additional alterations have been shown to be clinically relevant, including mutations in ARID1A. ARID1A is part of the SWI/SNF nucleosome remodeling complex that regulates DNA accessibility (“openness”). However, the contribution of ARID1A mutations to the development and the biology of FL remains unclear. Based on a functional screen, we investigated the link between ARID1A mutations and FAS/FASLG-induced apoptosis in FL. We analyzed 151 diagnostic FL biopsies and found that ARID1A mutations were recurrent and mainly disruptive, with an overall frequency of 18%. Additionally, we observed that ARID1A mutant FL showed significantly lower FAS expression in the FL tumor cell population. Functional experiments in t(14;18)+ B lymphoma cells demonstrated that ARID1A is directly involved in the regulation of FAS, and ARID1A loss leads to decreased FAS protein and gene expression. However, ARID1A loss did not affect FAS promoter openness. Instead, we identified and experimentally validated a previously unknown co-transcriptional complex consisting of RUNX3 and ETS1 that regulates FAS expression, and ARID1A loss leads to reduced RUNX3 promotor openness and gene expression. The reduced FAS levels induced by ARID1A loss rendered lymphoma cells resistant to both soluble and T cell membrane-anchored FASLG-induced apoptosis. Furthermore, we observed an additional accumulation of ARID1A mutations in relapsed/refractory FL biopsies, indicating that we have identified a functionally and clinically relevant mechanism how FL cells can escape T cell mediated killing, which may also profoundly impact the efficacy of subsequent therapies, including CAR T cells.

overall_design: A total of fifteen single cell-derived clones was assayed in technical duplicates in OCI-Ly1 and OCI-Ly8. For each cell line three control clones (ctrl#1,ctrl#7, and ctrl#9 in OCI-Ly1, ctrl#3, ctrl#6, and ctrl#11, in OCI-Ly8) transduced with the empty pSpCas9(BB)-2A-GFP backbone, were analysed. In OCI-Ly1, two single cell clones with heterozygous ARID1A mutation (#F9 and #F10), and three ARID1A knock-out clones (#E8, #G1, and #H3), were sequenced. In OCI-Ly8, three single cell clones with heterozygous ARID1A mutation (#A9, #G5 and #G10), and one ARID1A knock-out clone (#G6), were sequenced.

first: Martina

last: Antoniolli

first: Carolin

middle: D

last: Strobl

first: Deepak

last: Bararia

first: William

last: Keay

first: Johannes

last: Hildebrand

first: Louisa

last: Adolph

first: Michael

last: Heide

first: Verena

last: Passerini

first: Lucas

middle: E

last: Wange

first: Wolfgang

last: Egart

first: Susanne

last: Thieme

first: Helmut

last: Blum

last: Rudelius

first: Julia

last: Mergener

first: Christina

last: Ludwig

first: Sebastian

last: Bultmann

first: Heinrich

last: Leonhardt

first: Marion

last: Subklewe

last: von Bergwelt-Baildon

last: Colomé-Tatché

last: Weigert


title: Transcriptional profiling of striatum and cortex from a mouse model of Huntington's disease (Q140) crossed with Mlh1 heterozygous mice [Mlh1]

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: As part of collaboration between UCLA and CHDI, UCLA is creating knockouts (KOs) of 123 genes, implicated in Huntington’s disease (HD) through various computational modeling efforts. Striatum and cortex were isolated from 6-month-old Mlh1+/- mice crossed with the Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 4 genotypes: WT, Mlh1+/-, Q140, and Q140 X Mlh1+/-, 8 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the striatum and cortex tissues of 6-month-old Mlh1+/-, Q140 KI, Q140 X Mlh1+/-, and wild-type mice. N = 8 per group (3-4F/4-5M).

first: Jim

last: Rosinski


title: Transcriptional profiling of striatum and cortex from a mouse model of Huntington's disease (Q140) crossed with Rgs9 heterozygous mice and Msh2 heterozygous or knockout mice [Msh2]

summary: As part of collaboration between UCLA and CHDI, UCLA is creating knockouts (KOs) of 123 genes, implicated in Huntington’s disease (HD) through various computational modeling efforts. Striatum and cortex were isolated from 12-month-old Msh2-/- (KO) or Msh2+/-mice crossed with the Rgs9+/- and Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 9 genotypes: WT, Msh2-/-, Rgs9+/- X Msh2-/-, Rgs9+/-, Het (Q140) KI X Msh2-/-, Het (Q140) KI X Rgs9+/- X Msh2+/-, Het (Q140) KI X Rgs9+/- X Msh2-/-, Het (Q140) KI X Rgs9+/-, and Het (Q140) KI, 6-8 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the striatum and cortex tissues of 12-month-old Msh2-/-, Rgs9+/- X Msh2-/-, Rgs9+/-, Het (Q140) KI X Msh2-/-, Het (Q140) KI X Rgs9+/- X Msh2+/-, Het (Q140) KI X Rgs9+/- X Msh2-/-, Het (Q140) KI X Rgs9+/-, Het (Q140) KI, and wild-type mice. N = 6-8 per group (2-5F/3-5M).


title: Rice specific Histone H4 Variant forecasts a stress dependent epigenetic program by virtue of distinct nucleosome properties [ChIP-Seq]

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

country: India

institute: National Centre for Biological Sciences - TIFR

summary: Probing the rice genome for novel histone coding genes revealed a genera specific, histone H4 variant with several variations in N-terminal tail sequence motifs, expressing in a tissue-specific manner. Genetic perturbation of the H4 variant in rice led to defects in growth and fertility. Probing the chromatin binding sites of the H4 variant with a custom antibody revealed its binding at specific genes and its knockout led to mis-expression of stress-associated genes. Stress-challenged plants showed loss of the H4 variant and re-distribution of other H4 linked histone marks. In vitro reconstituted rice nucleosomes with H4 variant histones displayed atypical properties in terms of stability, intra-nucleosome binding and structure, when compared to the canonical nucleosomes.

overall_design: We performed ChIP seq analyses to look at the binding sites of histone H4 variant in WT , h4v knockout (h4vko), overexpression of H4 variant (H4VOE) seedlings. Seedlings were also administered salt stress to evaluate the binding site differences upon salt stress. These are performed in biological replicates and plants grown uniformly were used for the analyses. For histone H4 variant, custom generated antibody was used while for other histone marks like canonical H4 and H4K5Ac, commercially available antibodies were used.

first: Padubidri

last: Shivaprasad

first: Vivek

middle: H

last: Sundar G


title: From cyst to tapeworm: Transcriptome of Taenia solium in vitro activation and growth

status: Public on Feb 09 2025

city: Lima

first: Cristina

last: Guerra-Giraldez

state: Lima

address: Honorio Delgado 430

department: Facultad de Ciencias e Ingeniería

country: Peru

institute: Universidad Peruana Cayetana Heredia

summary: The cestode Taenia solium develops as a tapeworm in the human intestine, starting from a larva (cyst). Upon maturing, it produces hundreds of thousands of infectious eggs. When ingested by pigs and humans, the eggs develop as cysts that lodge in various tissues, including the brain, leading to neurocysticercosis. Despite advances in understanding cestode biology through genomic and transcriptomic studies, particularly in model organisms, much remains unknown about the activation of T. solium cysts in the human digestive tract and the events that drive the development into adult worms—the stage responsible for dispersing the parasite. We present a transcriptome generated by Next Generation Sequencing from T. solium cysts activated in culture and collected at three different in vitro growth stages, as defined by their morphology. We identified differentially expressed genes and biological processes relevant to growth phases that can be further explored with the dataset. The information is valuable for identifying genes that regulate the molecular, metabolic, and cellular events leading to parasite maturation or elements driving its transmission.

overall_design: Bulk RNA-seq was performed on pooled T. solium cysts under four conditions: non-cultured (NC), pre-evaginated (PRE), evaginated (EV), and post-evaginated (POST). Each condition was further analyzed with or without taurocholic acid supplementation (TA+ or TA-) to assess its role in promoting evagination.

first: David

last: Castaneda-Carpio

first: Renzo

last: Gutierrez-Loli

first: Jose

last: Maravi-Jaime

first: Valeria

last: Villar-Davila

first: Segundo W

last: Del Aguila


title: Rice specific Histone H4 Variant forecasts a stress dependent epigenetic program by virtue of distinct nucleosome properties [MNase-Seq]

overall_design: In order to understand the extent of DNA wound by the canonical H4 and  H4 variant nucleosomes, MNase protection assay followed by deep sequencing was performed. In vitro reconstituted nucleosomes (NCPs) with Widom601 nucleosome positioning sequence and arbitrary sequences on either side is subjected to limited nuclease activity using MNase. Post MNase digestion the DNA fragments were purified and deep sequenced. Alignment of these fragments reveal the extent and location of histone-octamer protected zones.


title: Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition

city: Goettingen

first: Michael

last: Lidschreiber

address: Am Fassberg 11

institute: Max-Planck-Institute for Multidisciplinary Scienes

summary: Metazoan gene transcription by RNA polymerase (Pol) II is regulated in the promoter-proximal region. Pol II can undergo termination in the promoter-proximal region, but whether this can contribute to transcription regulation in cells remains unclear. Here, we extend our previous multi-omics analysis to quantify changes in transcription kinetics during a human cell type transition event. We observe that upregulation of transcription involves an increase in initiation frequency and, at a set of genes, a decrease in promoter-proximal termination. In turn, downregulation of transcription involves a decrease in initiation frequency and an increase in promoter-proximal termination. Thus, promoter-proximal termination of Pol II contributes to the regulation of human gene transcription.

first: Kseniia

last: Lysakovskaia

first: Arjun

last: Devadas

first: Björn

last: Schwalb

first: Patrick

last: Cramer


title: Rice specific Histone H4 Variant forecasts a stress dependent epigenetic program by virtue of distinct nucleosome properties [RNA-Seq]

overall_design: We performed RNA seq analyses to look at the expression of the genes in WT , h4v knockout (h4v), overexpression (OE) of H4 variant (OE_H4V), H4 canonical (OE_H4C) and chimeric H4 (OE_H4CHMR) in seedlings and leaves. Seedlings were also administered salt stress to evaluate the gene expression changes upon salt stress in WT and h4v knockout plants. These are performed in biological duplicates and plants grown uniformly were used for the analyses.


title: Effect of SOCS1 overexpression on AML gene expression in OCI-AML2 cell line

status: Public on Feb 08 2025

city: Nottingham

first: Sergio

last: Rutella

address: Clifton Campus

department: John van Geest Cancer Research Centre

country: United Kingdom

institute: Nottingham Trent University

summary: Despite the curative potential of allogeneic hematopoietic stem cell transplantation for acute myeloid leukemia (AML), its efficacy is limited by intrinsic resistance of cancer cells to donor-derived T-cell cytotoxicity. Using a genome-wide CRISPR screen, we identified the  SOCS1-JAK1-STAT1 pathway as a mediator of AML susceptibility to T cells. SOCS1 knockdown in AML cells sensitized them to killing by allogeneic T cells, whereas SOCS1 overexpression in AML cells induced resistance to T-cell anti-leukemic activity. Mechanistically, SOCS1 protected AML cells from T-cell killing by antagonizing IFNγ-JAK1-induced ICAM-1 expression. Furthermore, primary AML cells with lower SOCS1 expression correlated with better overall survival in patients, especially those with a lower exhausted CD8+ T-cell score. Thus, this study reveals SOCS1 and its downstream mediators as a potential targetable pathway to enhance T cell-based immunotherapy for AML.

overall_design: RNA-seq profiling of OCI-AML2 cells transduced with scrambled control shRNA and SOCS1 overexpressing ORF

first: Enoch

last: Tin

first: Jayakumar

last: Vadakekolathu

first: Li

last: Zhang


title: CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation II

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

summary: Although the chromatin regulator CTCF is enriched at genes escaping from X-chromosome inactivation (XCI), molecular mechanisms remain elusive. We examined CTCF and epigenetic features at escape genes on the inactive X (Xi) in mouse F1 hybrid cells and tissues. We found that escape genes are located inside topologically insulated domains limited by convergent arrays of CTCF binding sites, suggesting loop formation. Xi-specific deletion of a CTCF right boundary of the escape gene Car5b caused loss of CTCF binding and changes of histone modifications at Car5b and abolished escape, suggesting loss of insulation. This is consistent with Car5b lack of escape in mouse brain showing no CTCF binding at the boundary. Inversion of this boundary had no effect on Car5b escape, suggesting that tandem coiled looping could still function as insulation. To test whether chromatin features of the Xi could affect escape we examined mutants in which the Xi-specific compact structure is disrupted or there is loss of H3K27me3 enrichment. We found that both conditions cause an Xi-specific increase in active marks and gene expression at escape regions, suggesting that the 3D structure and heterochromatic marks of the Xi play a role in modulating escape levels of genes insulated by CTCF.

sample_organism:
Mus musculus
Mus spretus

platform_organism:
Mus musculus
Mus spretus

overall_design: CTCF, H3K27ac and H3K27me3 CUT&RUN on F1 hybrid wild-type and CRISPR/cas9-modified Patski cells

first: He

last: Fang

first: Christine

middle: M

last: Disteche


title: An Oryza-specific histone H4 variant predisposes H4 lysine 5 acetylation to modulate salt stress responses

first: Shivaprasad

last: Padubidri V.

summary: Paralogous variants of canonical histones guide accessibility to DNA and function as additional layers of genome regulation. Across eukaryotes, the mechanism of action and functional significance of several variants of core histones are well known except those of histone H4. Here we show that a variant of H4 (H4.V) expressing tissue-specifically among Oryza members mediated specific epigenetic changes contributing to salt tolerance. H4.V was incorporated into specific heterochromatic sites, where it blocked the deposition of active histone marks. Stress-dependent redistribution of H4.V enabled the incorporation of acetylated H4 lysine 5 (H4K5ac) in the gene bodies. The misexpression of H4.V led to defects in reproductive development and in mounting salt stress responses. H4.V formed homotypic nucleosomes and mediated these alterations by conferring distinct molecular properties to the nucleosomes, as seen with cryo electron microscopy structures and biochemical assays. These results reveal not only an H4 variant among plants but also a chromatin regulation that might have contributed to the adaptation of semi-aquatic Oryza members.

sample_organism:
Oryza sativa
synthetic construct

platform_organism:
Oryza sativa
synthetic construct

overall_design: Refer to individual Series


title: RNA-seq and small RNA-seq covering three genotypes of medaka gonad at three phases of gonadal differentiation [RNA-seq]

status: Public on Feb 07 2025

city: Wuhan

first: Xing

last: Lin

state: Hubei

address: No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province

institute: Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences

summary: Goal of this study is the gene expression analysis at three time points: 10 days post-hatch (D10), 30 days post-hatch (D30), and 120 days post-hatch (D120) among XYDMY- females (MT_Fe_Ov), WT females (WT_Fe_Ov) and males (WT_Ma_Te).

overall_design: We conducted transcriptional analysis at three time points: 10 days post-hatch (D10), 30 days post-hatch (D30), and 120 days post-hatch (D120) among XYDMY- females (MT_Fe_Ov), WT females (WT_Fe_Ov) and males (WT_Ma_Te).

first: Daji

last: Luo


title: RNA-seq and small RNA-seq covering three genotypes of medaka gonad at three phases of gonadal differentiation [small RNA-seq]

type: Non-coding RNA profiling by high throughput sequencing

summary: Goal of this study is the miRNA expression analysis at three time points: 10 days post-hatch (D10), 30 days post-hatch (D30), and 120 days post-hatch (D120) among XYDMY- females (MT_Fe_Ov), WT females (WT_Fe_Ov) and males (WT_Ma_Te).

overall_design: We conducted miRNA analysis at three time points: 10 days post-hatch (D10), 30 days post-hatch (D30), and 120 days post-hatch (D120) among XYDMY- females (MT_Fe_Ov), WT females (WT_Fe_Ov) and males (WT_Ma_Te).


title: Simultaneous profiling of ac4C and m5C modifications from nanopore direct RNA sequencing

city: Shanghai

first: Xiang

last: Yu

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

summary: Long-read nanopore sequencing has emerged as a potent tool for studying RNA modifications. However, the detection of N4-acetylcytidine (ac4C) based on nanopore sequencing remains largely unexplored. Here, we introduce ac4Cnet, a deep learning frame utilizing Oxford Nanopore direct RNA sequencing to accurately identify ac4C sites. Our methodology involves training ac4Cnet capable of distinguishing ac4C from unmodified cytidine and 5-methylcytosine (m5C), as well as estimating the modification rate at each ac4C site. We demonstrate the robustness of our approach through validations on independent in vitro datasets and a human cell line, highlighting its versatility and potential for advancing the study of ac4C modifications.

overall_design: Nanopore direct-RNA sequencing data of ac4C-modified transcripts from rice cDNA libraries

first: You

last: Wu

first: Wenna

last: Shao


title: The effects of AMPK activator A-769662 on the transcriptome of pathological phenotypes following mitochondrial DNA depletion

city: Umea

first: Paulina

last: Wanrooij

address: Kemihuset (K), Campus, Umeå Umeå universitet, 901 87 Umeå

country: Sweden

institute: Umea University

summary: AMP-activated protein kinase (AMPK) is a master regulator of cellular energy homeostasis that also plays a role in preserving mitochondrial function and integrity. Upon a disturbance in the cellular energy state that increases AMP levels, AMPK activity promotes a switch from anabolic to catabolic metabolism to restore energy homeostasis. However, it is currently unclear how severe of a mitochondrial dysfunction is required to trigger AMPK activation, and whether stimulation of AMPK using specific agonists can improve the cellular phenotype following mitochondrial dysfunction. Using a cell model of mitochondrial disease characterized by progressive mitochondrial DNA (mtDNA) depletion and deteriorating mitochondrial metabolism, we show that mitochondria-associated AMPK becomes activated early in the course of the advancing mitochondrial dysfunction, before any quantifiable decrease in the ATP/(AMP+ADP) ratio or respiratory chain activity. Moreover, stimulation of AMPK activity using the specific small-molecule agonist A-769662 alleviated the mitochondrial phenotypes caused by the mtDNA depletion and restored normal mitochondrial membrane potential. Notably, the agonist treatment was able to partially restore mtDNA levels in cells with severe mtDNA depletion, while it had no impact on mtDNA levels of control cells. The beneficial impact of the agonist was also observed in cells from patients suffering from mtDNA depletion. However, the positive effects of A-769662 in the two experimental cell models appeared to involve at least partially different mechanisms. These findings improve our understanding of the effects of specific small-molecule activators of AMPK on mitochondrial and cellular function, and suggest a potential utility for these compounds in disease states involving mtDNA depletion.

overall_design: Uninduced and 4-day induced PolɣD1135A cells untreated or treated with 100 μM A-769662 for 72 h were grown to 80-90% confluence in 6-well plates, harvested and flash-frozen. Total RNA was extracted from cell pellets using Qiagen RNeasy Plus kit (QIAGEN) according to manufacturer’s instructions. Initial sample quality control was performed using Qubit and agarose gel electrophoresis. RNA libraries were prepared by Azenta Life Sciences using Illumina’s PolyA selection method, followed by sequencing on the Illumina NovaSeq platform with a 2x150 bp configuration, achieving a sequencing depth of approximately 20-30 million paired end reads per sample. Data files were assessed using FastQC, and read alignment was performed using STAR2.5.2b. On the WSL2 platform, featureCounts for Linux was utilized for quantification and generation of counts files.

first: Gustavo

last: Carvalho

first: Tran V. H.

last: Nguyen

first: Bruno

last: Repolês

first: Josefin M. E.

last: Forslund

first: W. M. Ruchitha Rukmal

last: Wijethunga

first: Farahnaz

last: Ranjbarian

first: Isabela C.

last: Mendes

first: Choco Michael

last: Gorospe

first: Namrata

last: Chaudhari

first: Micol

last: Falabella

first: Mara

last: Doimo

first: Sjoerd

first: Robert D. S.

last: Pitceathly

first: Anders

last: Hofer

first: Paulina H.


title: Microglial reprogramming enhances antitumor immunity and immunotherapy response in melanoma brain metastases

city: San Juan de Alicante

first: Francisco Javier

last: Rodríguez Baena

state: Alicante

address: Avenida Ramón y Cajal S/N Campus de San Juan

institute: Instituto de Neurociencias CSIC-UMH

summary: Melanoma is one of the tumor types with the highest risk of brain metastasis. However, the biology of melanoma brain metastasis and the contribution of the brain immune microenvironment to the responses to therapies remain insufficiently characterized. By using preclinical models and single-cell transcriptomics, we identify a mechanism to promote antitumor immunity in melanoma brain metastasis. We show that activation of the Rela/NF-kB pathway in microglia promotes melanoma brain metastasis and that targeting this pathway elicits microglia reprogramming towards a proinflammatory phenotype that enhances antitumor immunity and reduces brain metastatic burden. Additionally, proinflammatory microglial markers in melanoma brain metastasis correlate with better responses to immune checkpoint inhibitors in patients and we show that Rela/NF-kB targeting improves responses to these therapies in the brain. Thus, we propose targeting Rela/NF-kB in activated microglia as a strategy to promote antitumor immunity and responses to immune checkpoint inhibitors in melanoma brain metastasis.

overall_design: Single cell RNA-seq Data Analysis of CD45+/CX3CR1+ immune cells isolated in NRAS* MBMs generated in Rela WT and Rela cKO mice

first: Angel

last: Marquez-Galera

first: Francisco

last: Rodriguez-Baena

first: Jose

last: Lopez-Atalaya

first: Berta

last: Lopez Sanchez-Laorden


title: CITE-Seq analysis of FACS-sorted live human CD45+ cells isolated from the ears of huNOG-EXL mice in a model of atopic dermatitis

city: San Diego

first: Anja

last: Koester

address: 10290 Campus Point Dr

department: Immunology Research

institute: Eli Lilly and Company

summary: CD200R is an immune checkpoint receptor of the IgG family that is primarily expressed on cells of the myeloid lineage.  In vivo studies with knockout mice of either the receptor or its ligand, CD200, have demonstrated that it is an inhibitory receptor capable of negatively regulating immune responses. Previous work using agonistic antibodies to mouse CD200R showed inhibition of mast cell activation in multiple preclinical models of autoimmune diseases. We developed an agonistic antibody to the human CD200 receptor to downregulate the immune system human inflammatory conditions. Ucenprubart, is a humanized IgG4 monoclonal antibody that binds and agonizes human CD200R to suppress cellular activity in CD200R-expressing cells.The antibody was engineered to have desired properties for agonism and cross-reactivity to cyno CD200R. In vivo the antibody demonstrated efficacy in a humanized mouse model of contact hypersensitivity as well as passive cutaneous anaphylaxis in cynomolgus monkeys.

overall_design: CITE-Seq analysis of FACS-sorted live human CD45+ cells isolated from the ears of huNOG-EXL mice one day after the third oxazolone challenge in a model of atopic dermatitis. Mice were previously treated with CD200R agonist mAb (Ucenprubart), dupilumab, or an isotype control mAb (two biological replicates per treatment group).

first: Christoph

last: Preuss

first: David

last: Muench


title: pNET-seq in Arabidopsis after flavopiridol (FLA) treatment

city: Beijing

first: Jincong

last: Zhou

address: Tsinghua Yuan

institute: Tsinghua University

summary: Eukaryotic euchromatin is the less compact chromatin and modified by many histone modifications such as H3 Lysine 36 methylation (H3K36me). Here we report a new chromatin state, Transcription Resistive, which is differentiated from activation and silencing. Transcription resistive is stamped by H3K36me with almost undetectable transcription activity but open chromatin state, and occupies most documented plant essential genes. Mutating SDG8, previously known as the major H3K36 methyltransferase in Arabidopsis, surprisingly elevates 78.7% H3K36me3 marked resistive loci, which count for 39.4% of the coding genome. Genetically, SDG8 prevents H3K36me activity of SDG4 at short and intron-less genes to secure plant fertility, while SDG8 collaborates with other H3K36me methyltransferases on long and intron-rich genes. Together, our results reveal SDG8 is the primary sensor to suppress excessive H3K36me, and uncovered the resistive is the conserved H3K36me-stamped novel transcription state in plants, highlighting the regulatory diversities and biological significances of H3K36 methylation in eukaryotes.

overall_design: To test the possibility that the transcription rate of some genes is too rapid to be effectively captured by pNET-seq, we conducted the flavopiridol (FLA, 10 μM) treatment (4 hours) with the 7-day seedlings to slow down the PolII elongation rate and then performed the PolII-Ser2p pNET-seq.


title: Gene expression profiling by bulk RNAseq from the livers of wild-type mice and those with loss-of-function mutations in URI 48 hours after partial hepatectomy

city: Madrid

first: Ruth

last: Álvarez-Díaz

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

institute: Spanish National Cancer Research Center (CNIO)

summary: We used bulk RNA sequencing to examine the differentially expressed genes in the livers of URI loss-of-function mutant (specific deletion of URI in hepatocytes using serum albumin-creERT2 line) and wild-type littermate control mice 48 hours after partial hepatectomy (48H).

overall_design: Liver samples from URI loss-of-function model (specific deletion of URI in hepatocytes using serum albumin-creERT2 line; URI(+/D)Hep mouse) and wild-type littermate control mice 48 hours after partial hepatectomy (48H).

first: María del Mar

last: Rigual

first: Nabil

last: Djouder

last: Alvarez-Diaz


summary: Melanoma is one of the solid tumor types with the highest risk of brain metastasis. However, the biology of melanoma brain metastasis and the contribution of the brain immune microenvironment to the responses to therapies remain insufficiently characterized. By using preclinical models and single-cell transcriptomics, we identify microglia, as critical regulators of melanoma biology in the brain. We show that activation of the Rela/NF-kB pathway in microglia promotes melanoma brain metastasis and that targeting this pathway elicits microglia reprogramming towards a pro-inflammatory phenotype that enhances anti-tumor immunity and reduces brain metastatic burden. Additionally, canonical and pro-inflammatory microglial markers in melanoma brain metastasis correlate with better responses to immune checkpoint inhibitors in patients and we show that Rela/NF-kB targeting improves responses to these therapies in the brain. Thus, we propose targeting Rela/NF-kB in activated microglia as a strategy to promote anti-tumor immunity and to improve the response to immune checkpoint inhibitors in melanoma brain metastasis.

overall_design: Single cell RNA-seq Data Analysis of stromal cells in Nras* MBMs generated in mice.

last: Sanchez-Laorden


title: SCD1-dependant activation of GSK3β-NRF2-SLC7A11 pathway regulates lipid metabolism and suppresses ferroptosis in KRAS/STK11/KEAP1 co-mutant lung adenocarcinoma

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: InactivatingSTK11/KEAP1 co-mutations are genomic drivers of primary resistance totherapies and worse outcome in KRAS-mutatedlung adenocarcinoma(LUAD), however the underlying mechanisms is still not understood.Here we provide a transcriptomic analysis of over 3800 “real-world” LUAD cases that concomitant loss of STK11 and KEAP1 in a KRAS-mutant tumorleads to significant upregulation of fatty acid metabolism, and redox signaling pathways with significantly high expression of ferroptosis evasion genes, SCD1 and SLC7A11. Global transcriptomics and kinase arrays demonstrate the role SCD1 in regulating AKT/GSK3β/NRF2 signaling mediated modulation of SLC7A11 and GSH metabolism. Furthermore, in a lipidomic assay, SCD1 knockout led to regulation of SFA-MUFA levels that promoted ferroptosis. SCD1 inhibition reverses the resistance to ferroptosis induction promoted by STK11/KEAP1 loss inmouse models. These data provide evidence that SCD1 protects ferroptosis induction and therapeutic targeting of this pathway is a promising translational strategy in KRAS mutant LUADs with concomitant loss ofSTK11 and KEAP1.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H661, H358, H1993,H2228, H2122 cells with -/+ CVT-11127 (SCD inhibitor treatment)

first: Utsav

last: Sen

first: Charles

last: Coleman

first: Nishant

last: Gandhi

first: Deniz

last: Demircioglu

first: Omar

last: Hayatt

first: Elisa

last: de Stanchina

first: Dan

last: Hasson

first: Triparna


first: Francisco Javier

last: Rodríguez Baena

overall_design:
To investigate the role of microglia in the progression of melanoma brain metastases (MBM) we developed murine B16F10 MBM in Cx3cr1-yfp reporter mice
We injected animals with saline (Sham-control animals) and animals with melanoma cell via the carotid artery to provoke brain colonisation and therefore obtain MBM. We obtained 4 different samples, composed each of a pool of three different animals with mixed genders. The samples are composed of FACS isolated subpopulations of Cx3cr1+ and double Tmem119+ or CD49D+ subpopulations within the MBM. The experimental groups are the following: CMG (Control microglia); animals injected with saline and operated via the intracarotid artery as well, isolated using CX3cr1+/Tmem119+. TMG (tumor microglia) and T-MAC (Tumor associated macrophages); animals injected with B16F10 cells via the intracarotid artery. Cells isolated using Cx3cr1+ and Tmem119+ or Cx3cr1+ and CD49D respectively.
The comparative anaysis have been perform to compare CMG vs either TMG or TA-MAC.

first: Francisco

last: Rodriguez-Baena

first: Jose

last: Lopez-Atalaya

first: Berta


title: Metformin reduces the competitive advantage of Dnmt3aR878H HSPCs [RRBS]

city: Toronto

first: Mohsen

last: Hosseini

state: Ontario

address: 101 College Street

institute: Princess Margaret Cancer Centre

summary: Through a multi-omics approach, we discovered that metformin acts by enhancing the methylation potential in Dnmt3aR878H/+ cells and reversing their aberrant DNA CpG methylation and histone H3K27 trimethylation (H3K27me3) profiles.

overall_design: To investigate DNA methylation patterns of Dnmt3a+/+ and mutant Dnmt3aR878H/+ HSPCs treated with or without metformin for 1 month, we utilized the Lineage-/c-kit+ fraction (hematopoietic stem and progenitor cells ) from mouse bone marrow. A total of 1.5ug genomic DNA extracted from LK-enriched BM cells were submitted to Novogene.

first: Steven

last: Chan

first: Veronique

last: Voisin

first: Ali

last: Chegini


title: Metformin reduces the competitive advantage of Dnmt3aR878H HSPCs [ChIP-Seq]

overall_design: We utilized magnetic beads for the purpose of isolating the Lineage-/c-kit+ fraction (hematopoietic stem and progenitor cells ) from mouse bone marrow. Afterwards, we isolated RNA and DNA from the LK population and performed several studies including bulk RNA-sequencing, CITE-Seq, RRBS, and ChIP Sequencing.


title: Foxp1 developing neocortex (scATAC-Seq)

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

summary: The transcription factor Foxp1 is expressed in the neocortex with restricted patterns across development. We used single nuclei-ATAC sequencing (snATAC-Seq) to determine the cell-type roles of Foxp1 in control and Foxp1 conditional knock-out animals generated by crossing to Emx1.Cre hemizygous mice. Samples were collected at embyonic day (E)13.5, E16.5, and post-natal day (P)0.5.

first: Ana

last: Ortiz

first: Fatma

last: Ayhan

first: Matthew

last: Harper


title: Foxp1 developing neocortex (snRNA-Seq)

summary: The transcription factor Foxp1 is expressed in the neocortex with restricted patterns across development. We used single nuclei-RNA sequencing (snRNA-Seq) to determine the cell-type roles of Foxp1 in control and Foxp1 conditional knock-out animals generated by crossing to Emx1.Cre hemizygous mice. Samples were collected at embyonic day (E)13.5, E16.5, and post-natal day (P)0.5.


title: Foxp1 developing neocortex

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


title: Metformin reduces the competitive advantage of Dnmt3aR878H HSPCs [BulkRNA]

overall_design: To investigate the mechanism of action, we performed transcriptome profiling of Dnmt3a+/+ and mutant Dnmt3aR878H/+ HSPCs treated with or without metformin for 1 month.


title: Metformin reduces the competitive advantage of Dnmt3aR878H HSPCs [CITE-Seq]

overall_design: To investigate the mechanism of action and explore the expansion of clusters, we performed single-cell RNA Seq profiling of Dnmt3a+/+ and mutant Dnmt3aR878H/+ HSPCs treated with or without metformin for 7 months.


title: ACVR2A attenuation impacts lactate production and hyperglycolytic conditions attracting regulatory T cells in hepatocellular carcinoma

city: Tokyo

first: Koya

last: Yasukawa

state: --- Select One ---

country: Japan

institute: Tokyo medical and dental university

summary: Although ACVR2A mutations are prevalent in non-viral hepatocellular carcinomas (HCC), the underlying mechanism remains unelucidated. Our molecular investigation reveals that ACVR2A impairment induces hyperglycolysis through the inactivation of the SMAD signaling pathway. Using syngeneic transplantation models and human clinical samples, we clarify that ACVR2A-deficient HCC cells produce and secrete lactate via the upregulation of LDHA and MCT4 expression levels, which promotes regulatory T (Treg) cell accumulation and then acquires resistance to immune checkpoint inhibitors. Remarkably, genetic knockdown and pharmacological inhibition of MCT4 ameliorate the high lactate milieu in ACVR2A-deficient HCC, resulting in the suppression of intratumoral Treg cell recruitment and the restoration of the sensitivity to PD-1 blockade. These findings furnish compelling evidence that lactate attenuates anti-tumor immunity, and that therapeutics targeting this pathway present a promising strategy for mitigating immunotherapy resistance in ACVR2A-deficient HCC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the Hepa1-6 NC cells and the Hepa1-6 Acvr2a KO cells subclones.

first: Shu

last: Shimada


title: Influence of GPR35 deficiency on the ileal and macrophage transcriptome

city: Cambridge

first: Gavin

last: Sewell

state: Cambridgeshire

address: Puddicombe Way

department: Jeffrey Cheah Biomedical Centre, University of Cambridge

institute: Cambridge Institute of Therapeutic Immunology and Infectious Disease

summary: Mutations in GPR35 (G protein coupled receptor 35) are linked to ulcerative colitis and primary sclerosing cholangitis. How GPR35, which interacts with the Na/K-ATPase to determine ion transport, influences the transcriptome of macrophages and the ileum is unknown. Here compare transcript expression in bone marrow-derived macrophages and isolated ileum from mice deficient in GPR35 (knockout) with wild type mice by bulk RNA sequencing.

overall_design: Ileal tissue from wild type (n=5) and GPR35-deficient mice (n=5) was isolated and RNA extracted. Bone marrow-derived macrophages were cultured from wild type (n=5) and GPR35-deficient (n-5) mice and RNA extracted as described previously.

first: Tom

last: Karlsen

first: Joshua

last: Elias

middle: W

first: Nicole

last: Kaneider


title: Human stem cells with in vivo high plasticity generated by cell-cell communication

city: Stanford

first: Jingxue

last: Xin

state: California

address: JAMES CLARK CENTER E100A

institute: Stanford University

summary: We report the discovery of a population of tiny, dormant cells from human peripheral blood, which upon activation and maturation in vitro exhibit unique transcriptome and cellular phenotypes, distinct from all known cell types. These novel cells can deliver RNA-rich granules to suitable recipient cells and provide guidance, and are thus named “mature Guide Cells” (or m-GCs) and their dormant precursors are named “pre-GCs.” When m-GCs are co-cultured with human umbilical cord-derived mesenchymal stromal cells (UC-MSCs), cell-cell communication occurs in which RNA-rich granules are transferred from m-GCs to UC-MSCs via tunneling nanotubes (TNT). As a result, a novel type of stem cells with high plasticity is generated, which can be induced to differentiate into the representative cell types from all three germ layers in vitro. The newly generated stem cells, named “guide integrated adult Stem Cells” (or giaSCs) are characterized by unique cell morphology, gene expression, and phenotypic profile. They are also observed to have a remarkable capacity to promote tissue reconstitution in vivo.

overall_design: We conducted experiments to obtain RNA-seq data for human guide cells (pre-GC and m-GC), UC-MSC, and giaSC. For each of the cell type, we extracted RNA from 2 individuals as biological replicates, with 2-3 technical replicates per individual. Single cell RNA-seq data were also generated from m-GC.

first: Shaowei

last: Li

first: Xi

last: Chen

first: Bowen

last: Liu

first: Bo

first: Min

last: Hu

first: Wing

last: Wong


title: Transcriptomic profiling of host response genes in convalescent COVID-19 donors and healthy controls using the NanoString nCounter Human Host Response V1.0 Panel

city: Brighton

first: Sarah

last: Unterberger

address: Biology Road

institute: BSMS

summary: NanoString nCounter assay was performed to measure the basal expression of host response genes in primary human monocytes from convalescent COVID-19 donors and SARS-CoV-2 naïve healthy individuals.

overall_design: In this study, RNA was isolated from primary human monocytes from convalescent COVID-19 donors who had experienced mild or severe symptoms and SARS-CoV-2 naïve healthy controls and the expression of 785 genes was measured. COVID-19 participants were recruited 3-6 months following a positive reverse transcription polymerase chain reaction (RT-PCR) test for SARS-CoV-2. These participants were categorised into two groups based on their disease severity. Participants who were symptomatic but did not require hospitalisation were classed as mild. Participants who required hospitalisation and oxygen therapy were classified as severe. RNA collected from healthy control samples prior to the emergence of SARS-CoV-2 were included in the study as the control group.

first: Sandra

last: Sacre

first: Nadia

last: Terrazzini


title: SLC13A5 plays an essential role in the energy shift to oxidative phosphorylation in cisplatin-resistant mesothelioma stem cells

status: Public on Feb 06 2025

city: Sapporo-shi

first: Marie

last: Kato-Shinomiya

state: Hokkaido

address: Kita-ku, N15W7

department: Department of Cancer Pathology, Faculty of Medicine

institute: Hokkaido University

summary: To explore new therapeutic approaches, we identified genes specifically expressed in mesothelioma stem cell-like cells derived from human mesothelioma cell lines using hydrogel-based stem cell induction method. Gene expression in ACC-MESO-4 cells cultured on double network (DN) hydrogel composed of poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (PAMPS) and poly(N,N’-dimethylacrylamide) (PDMAAm) was compared to that on control polystyrene (PS) dish and on ultra-low attachment (ULA) dish, a classical method for enriching stem cells.

overall_design: ACC-MESO-4 cells were cultured for 3 days in double network (DN) hydrogel composed of poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (PAMPS) and poly(N,N’-dimethylacrylamide) (PDMAAm), polystyrene (PS) dish, and ultra-low attachment (ULA) dish. Total RNA was extracted from these cells using the RNeasy Mini kit (Qiagen) and subjected to microarray analysis.

first: Hirokazu

last: Sugino