title: Gene expression of daughter CD8+ T cells that inherited or not pre-mitotic mitochondria

city: Oxford

first: Mariana

last: Borsa

address: Roosevelt Drive

department: NDORMS

institute: University of Oxford

summary: T cell immunity is impaired during ageing, particularly in memory responses needed for efficient vaccination. Autophagy and asymmetric cell division (ACD) are cell biological mechanisms key to memory formation, which undergo a decline upon ageing. However, despite the fundamental importance of these processes in cellular function, the link between ACD and in vivo fate decisions has remained highly correlative in T cells and in the field of mammalian ACD overall. Here we provide robust causal evidence linking ACD to in vivo T cell fate decisions and our data are consistent with the concept that initiation of asymmetric T cell fates is regulated by autophagy. Analysing the proteome of first-daughter CD8+ T cells following TCR-triggered activation, we reveal that mitochondrial proteins rely on autophagy for their asymmetric inheritance and that damaged mitochondria are polarized upon first division. These results led us to evaluate whether mitochondria were asymmetrically inherited and to functionally address their impact on T cell fate. For this we used a novel mouse model that allows sequential tagging of mitochondria in mother and daughter cells, enabling their isolation and subsequent in vivo analysis of CD8+ T cell progenies based on pre-mitotic cell cargo. Autophagy-deficient CD8+ T cells showed impaired clearance and symmetric inheritance of old mitochondria, suggesting that degradation events promote asymmetry and are needed to generate T cells devoid of old organelles. Daughter cells inheriting old mitochondria are more glycolytic and upon adoptive transfer show reduced memory potential, whereas daughter cells that have not inherited old mitochondria from the mother cell are long-lived and expand upon cognate-antigen challenge. Proteomic and single-cell transcriptomic analysis of cells inheriting aged mitochondria suggest that their early fate divergence relies on one carbon metabolism as a consequence of poor mitochondrial quality and function. These findings increase our understanding of how T cell diversity is early-imprinted during division and will help foster the development of strategies to modulate T cell function.

overall_design: CD8+ T cells isolated from murine spleens and expressing a SnapTag on the outer membrane protein 25 (OMP25) of the mitochondria (MitoSnap) were activated for 36h, aiming to generate daughter cells, and had their SnapTag labelled with fluorescent substrates before and after mitosis. Two cell populations were sorted depending on the maintenance of MitoSnap labelling: MitoSnap+ kept both pre-mitotic and post-mitotic SnapTag labelling and MitoSnap- cleared them up. Cells from 4 mice were cultured and sorted separately. Before encapsulation for scRNAseq, cells were pooled in equal numbers. Thus, each single MitoSnap+ and MitoSnap- sample results from the equal contribution of 4 biological samples.

first: Amir

last: Kayvanjoo

first: Anna

last: Simon


title: Topoisomerase I (TOP1) is a functional mitotic interactor of the bookmarking factor HNF1B [BTBD2_KO]

status: Public on Dec 01 2025

city: Paris

first: Pontoglio

last: Marco

address: 160 rue de Vaugirard

country: France

institute: Institut Necker Enfants Malades

type: Expression profiling by high throughput sequencing

summary: HNF1B (Hepatocyte Nuclear Factor 1-Beta) is a POU-homeobox transcription factor expressed in kidney and frequently mutated in patients suffering from Congenital Anomalies of the Kidney and the Urinary Tract (CAKUT). HNF1B is a bookmarking factor, able to bind mitotic chromatin and necessary for the post-mitotic reactivation of gene expression. In order to characterize the molecular functions of HNF1B as a bookmarking factor, we performed ChIPseq on asynchronous and mitotic renal cells. We developed a novel ChIP method with a non-aqueous crosslinking (NAQC) to circumvent the well-known artefactual effects of formaldehyde crosslinking of mitotic chromosomes. NAQC-ChIP allowed the retention of the mitotic signal that was lost with a regular ChIP. With this novel methodology, we show that the vast majority HNF1B binding sites detected in asynchronous cells are also bound in mitosis.

overall_design: In order to assess the transcriptional biological impact of the loss of HNF1B we performed RNAseq on HNF1B-depleted 786-O (HNF1B siRNA).

first: Alessia

last: Bagattin

first: Salvina

last: Tammaccaro

first: Magali

last: Chiral

first: Munevver

middle: P

last: Makinistoglu

first: Jonathan

last: Lerner

first: Serge

last: Garbay

first: Nicolas

last: Kuperwasser

first: Marco

last: Pontoglio


title: H4K16 acylations fine-tune transcriptional response during metabolic perturbations (ATAC-seq)

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We studied the concerted effects of the H4K16 acylations in vivo using a mouse model of the metabolic disorder propionic acidemia (PA), which causes metabolic challenges and systemic shifts in acyl-CoA ratios. Our findings indicate that H4K16 acylations act in vivo in a coordinated manner, allowing fine-tuning of transcriptional responses to metabolic stresses. Our work provides insights into the adaptive mechanisms of chromatin regulation in response to metabolic challenges.

overall_design: ATAC-seq on WT and PA female mouse livers in 2 biological replicates.

first: Sandra

last: Nitsch

first: Eva

last: Richard

first: Lourdes

middle: R

last: Desviat

first: Robert

last: Schneider


title: H4K16 acylations fine-tune transcriptional response during metabolic perturbations (RNA-seq)

overall_design: RNA-seq on WT and PA female mouse livers in 2 biological replicates.


title: Identification of perturbation-responsive regions and genes in comparative spatial transcriptomics atlases

city: Geneve

first: Alan Yue Yang

last: Teo

address: Chem. des Mines 9, Campus Biotech

department: SV

country: Switzerland

institute: EPFL

summary: This submission is a dataset of single-nucleus transcriptomics in the spinal cords of mice. The single-nuclei transcriptomics data is harvested and profiled using Visium Spatial Gene Expression.

overall_design: We used spatial transcriptomics to profile the mid thoracic spinal cord in young SCI mice, old SCI mice and old mice treated with regeneration therapy.

first: Alan

middle: Y

first: Matthieu

last: Gautier

first: Laurent

last: Brock

first: Jennifer

last: Tsai

first: Thomas

middle: H

last: Hutson

first: Alexandra

last: de Coucy

first: Achilleas

last: Laskaratos

first: Nicola

last: Regazzi

first: Quentin

last: Barraud

first: Michael

middle: V

last: Sofroniew

first: Mark

middle: A

last: Anderson

first: Grégoire

last: Courtine

first: Jordan

middle: W

last: Squair

last: Skinnider


title: Developmental exposure to methyl ester sulfonate induces autism-like behavioral  deficits in mice by dysregulation of the Notch/Hes signaling pathway disrupting  neuronal differentiation

city: Nanjing

first: Liehai

last: Hu

address: 22 Hankou Road, Nanjing 210093, P. R. China

department: Medical school

country: China

institute: Nanjing University

summary:
 Developmental exposure to environmental pollutants is increasingly recognized as a
 significant risk factor for autism spectrum disorder (ASD), yet the specific mechanisms
 by which individual toxicants contribute to this neurodevelopmental disorder remain
 largely unknown. Methyl ester sulfonate (MES), a widely used anionic surfactant with
 widespread environmental detection, lacks comprehensive evaluation for
 developmental neurotoxicity. Here, we exposed pregnant mice to environmentally
 relevant MES doses (0.06–6 mg/L) from gestational day 8.5 (GD8.5) to postnatal day
 21.5 (PND21.5) and assessed their offspring for neurodevelopmental changes. Results
 showed dose-dependent ASD-like behavioral deficits, including impaired social
 interactions, heightened anxiety-like behaviors, and increased repetitive/stereotypic
 patterns. These behavioral anomalies were accompanied by neuropathological
 alterations, including blood-brain barrier (BBB) disruption, neuronal loss, and reduced
 dendritic spine density, indicative of impaired synaptogenesis. Integrative
 transcriptomic analysis of hippocampal tissue revealed significant dysregulation of key
 pathways involved in neurodevelopment, prominently featuring the Notch/Hes signaling
 pathway. Molecular docking simulations suggested that MES could directly interactwith Notch receptors, potentially disrupting ligand-receptor interactions. Further in vitro
 experimental validation demonstrated that MES exposure suppressed neural stem cell
 differentiation. Collectively, these findings provided evidence that early-life MES
 exposure acts as a neurodevelopmental toxicant by disrupting Notch/Hes signaling,
 thereby impairing neuronal differentiation and synaptogenesis, which underlied the
 observed ASD-like behavioral deficits in mice. This study offers novel mechanistic
 insights into how environmental factors contribute to ASD pathogenesis and highlights
 the need for toxicological assessment of widely distributed surfactants.

overall_design: Mice were continuously exposed to MES from embryonic stage to adulthood using a free-drinking method, and genes significantly differentially expressed in the hippocampus were detected using RNA-seq and mechanistically validated in a cellular model.

first: Ke

last: Ren

first: Yunhui

last: Xia

first: Dongmei

last: Li


title: Deletion of SWI/SNF ATPase activity in hepatocytes of adult liver disrupts circadian gene expression and central liver functions [ChIPseq]

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: The circadian rhythm in the murine liver governs the activity of numerous enhancers which in turn coordinates diurnal gene expression. This process is controlled by oscillating activities of specific transcription factors (TFs) and recruitment of co-regulators, including histone modifying enzymes and chromatin remodeling complexes. Several circadian controlled TFs interact with the SWI/SNF family of chromatin remodeling complexes to control chromatin accessibility. To unravel the significance of SWI/SNF ATPase subunits in circadian chromatin remodeling, we mapped chromatin accessibility, SWI/SNF occupancy, and gene expression throughout a day in murine liver. We found remarkable remodeling during fasting-to-fed transitions, and a third of circadian enhancers exhibited circadian SWI/SNF occupancy and accessibility. Intriguingly, genetic disruption of either of the two mutually exclusive ATPases of SWI/SNF had minor effects on chromatin accessibility in circadian enhancers, indicating redundancy. However, simultaneous disruption of both ATPases caused a collapse of the chromatin landscape, liver damage and inflammation. This disruption abolishes rhythmic expression of metabolic genes without affecting oscillation of the core circadian clock. In summary, this suggests an indispensable role of SWI/SNF-mediated chromatin remodeling of enhancers for circadian transcriptomic rhythms and basic liver function.

overall_design:
To investigate the role of SWI/SNF chromatin remodeling complexes in circadian chromatin remodeling we mapped chromatin accessibility (ATAC-seq), SWI/SNF occupancy (Brg1 ChIP-seq), and gene expression (RNA-seq) throughout a day in murine liver. All mice were housed at ~23 °C and 12-hour light/dark cycle. Circadian experiments were performed in mice trained to night restricted feeding (NRF) for 4 days.
Mice were sacrificed by cervical dislocation at different timepoints during the day (ZT 2, 6, 10, 14, 18, and 22). Wild type mice were C57BL/6N background and Smarca2-/- 44 and Smarca4fl/fl mice in a 129/Sv background were backcrossed with C57BL/6N mice and subsequently intercrossed. At age 8-10 weeks, the resulting Smarca2-/- mice, Smarca4fl/fl mice, and Smarca2-/-;smarca4fl/fl mice were tail vein injected AAV-TBG-GFP or AAV-TBG-CRE. Ten days after injection the mice were trained to NRF for another 4 days. Three mice per time point were used for RNA-seq and ATAC-seq of WT mice. Two mice per time point for Brg1 ChIP-seq in WT mice. Four mice were used for RNA-seq and ATAC-seq at ZT10 of mice with the different genotypes.

first: Nicolaj

middle: I

last: Toft

first: Victor

middle: E

last: Goitea


title: Deletion of SWI/SNF ATPase activity in hepatocytes of adult liver disrupts circadian gene expression and central liver functions [RNAseq]


title: Deletion of SWI/SNF ATPase activity in hepatocytes of adult liver disrupts circadian gene expression and central liver functions [ATACseq]


title: TCF3::HLF Orchestrates an Enhancer-Promoter Network with Activation of MEF2C to Promote Immature HSC Gene Expression in Leukemia [RNA-seq]

city: Zürich

first: Valdemar

middle: Jacob Sven-Åke

last: Priebe

address: Lengghalde 5

institute: Kindersptal Zürich/University of Zurich

summary: Oncogenic fusion transcription factors (TFs) frequently drive hematopoietic malignancies by altering gene expression in key developmental programs. TCF3::HLF is a fusion TF that characterizes a rare, treatment-resistant subtype of B-cell acute lymphoblastic leukemia (t(17;19) TCF3::HLF-positive B-ALL). Despite its clinical significance, the mechanisms by which TCF3::HLF induces leukemia are unclear. We used HiChIP mapping and genetic interference to analyze TCF3::HLF at the 3D-genome level, revealing enhancer-promoter interactions that control gene activation or repression. Notably, TCF3::HLF directly regulates MEF2C expression through its enhancer, as interference disrupted MEF2C transcription and inhibited leukemia propagation. This disruption also diminished embryonal hematopoietic stem cell (HSC) gene signatures and restored mature HSC and B-lymphoid markers. These findings highlight MEF2C as a critical component of the transcriptional network reprogrammed by TCF3::HLF. Our study provides insight into how TCF3::HLF rewires the 3D genome to drive leukemia and serves as a resource for further exploration of the TCF3::HLF regulome.

overall_design:
To directly assess the regulatory impact of the TCF3::HLF-bound MEF2C enhancer, we employed CRISPR editing to eliminate the HLF binding site within the enhancer in Cas9GPF expressing HAL-01 cells.
Comperative gene expression profiling was done on Day13 samples  for MEF2C enhancer KO (sgRNA_96, sgRNA_97) and scrambled controls (sgRNA_SCR1)


title: Dynamics of Tumor Heterogeneity from Primary to Metastatic Dissemination in Prostate Cancer

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

summary: Identifying drivers of cancer progression to guide treatment selection is hindered by limited abilities to understand tumor heterogeneity’s impact on evolution. Here, we delineated the phenotypic variability across ~300,000 prostate tumor cells collected from multi-loci in primary and matched locoregional metastases. We found inter-patient heterogeneity to be confined to malignant populations. While malignant populations exhibit intra-locus heterogeneity, they maintain inter-loci phenotypic similarity within a patient’s prostate gland. Furthermore, the inter-loci malignant population similarity is paired with a shared clonal architecture. Lastly, we show that malignant populations disseminating to locoregional lymph nodes mirror the clonal architecture and phenotypic heterogeneity observed across primary tumor loci while showcasing cell state transition to inflammatory phenotypes. These findings provide insights into four distinct measures of tumor heterogeneity, revealing diverse evolutionary paths across patients converging to common phenotypic adaptations in early prostate cancer progression.

overall_design:
38 prostate cancer specimens derived from five human patients with ISUP > 3 pathology who underwent radical prostatectomy and pelvic lymph node dissection at surgery as part of the International Cancer Genome Consortium (ICGC) late-onset cohort. Using single-cell multiome (expression and chromatin accessibility from RNA and ATAC, respectively) sequencing assay, we characterized 282,956 nuclei/cells, with a median of 6 primary tumor foci from the prostate gland and 3 locoregional lymph node metastases across all patients.

***************************************************************
These dataset are coming from patients hence we have opted to submit the raw fastq files to EGA.
***************************************************************

first: Kira

last: Furlano

first: Tina

last: Keshavarzian

first: Clarissa

last: Gerhäuser

first: Christoph

last: Plass

first: Thorsten

last: Schlomm


title: TCF3::HLF Orchestrates an Enhancer-Promoter Network with Activation of MEF2C to Promote Immature HSC Gene Expression in Leukemia [HiChIP]

overall_design:
To delineate the 3D-genomic interactions orchestrated by the fusion protein TCF3::HLF in t(17;19) ALL cells, we performed MNase-HiChIP with two independent replicates using the TCF3::HLF positive cell line HAL-01, with the TCF3 wild-type allele knocked out, thereby enabling selective immunoprecipitation of the fusion protein when using antibodies against TCF3.
We performed the HiChIP following the Dovetail®-HiChIP-MNase-Kit-User-Guide-Version-1.3. with modefications using E2A (CST #12258) antibody for pull-down.
Interaction events were analyzed using FitHiChIP.


title: Phosphorylated RB represses the transcriptional activity of ETS1 to modulate the sensitivity of prostate cancer cells to CDK4/6 inhibitors [RNA-seq]

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

summary: CDK4/6 inhibitors are potential drugs for PCa treatment. Exploring underlying mechanism of cquired resistance to CDK4/6 inhibitors a is very important for the clinical application of these drugs. In the present study, we found that inhibiton of EGFR increased the sensitivity of PCa to CDK4/6 inhibitors in an RB-dependent manner. Mechanically, we demonstrate that the RB 249SPRT252 motif phosphorylated by CDK4/6 bound with ETS1 to transcriptionally decreased the expression of ZNF783, which inactivated the EGFR tyrosine kinase inhibitor resistance pathway. While, treatment with CDK4/6 inhibitors de-phosphorylated RB and diminished the interaction between RB and ETS1 to activated the EGFR tyrosine kinase inhibitor resistance pathway through enhancing the expression of ZNF783, which resulted in the acquired resistance of PCa to CDK4/6 inhibitors. Furthermore, we employed RB 249SPRT252 motif derived the phospho-mimic plasmid or PROTAC to verify the these findings. Collectively, this study not only revealed a new mechanism by which phosphorylated RB suppresses the transcriptionally function of ETS1 but also provided a novel strategy for enhancing the antitumor effect of CDK4/6 inhibitors on PCa.

overall_design: Comparative gene expression profiling of RNA-seq data from 22RV1 cells treated with the indicated constructs

first: Xin

last: Jin

last: zeng


title: Phosphorylated RB represses the transcriptional activity of ETS1 to modulate the sensitivity of prostate cancer cells to CDK4/6 inhibitors [CUT&Tag]

overall_design: CUT&Tag data from 22RV1 cells treated with the indicated constructs


title: Skeletal muscle transcriptional dysregulation of genes involved in senescence is associated with prognosis in severe heart failure

city: Stockholm

first: Alen

last: Lovric

address: Nobels väg 5

country: Sweden

institute: Karolinska Institutet

summary: The skeletal muscle hypothesis refers to a vicious cycle of successive deterioration of left ventricular function, skeletal muscle remodeling, and functional capacity in patients with heart failure. Although some underlying processes have been characterized, the regulatory mechanisms and their associations with clinical status and prognosis are still largely unclear. To identify mechanisms and characterize plausible key processes involved in the disease pathophysiology, we performed RNA sequencing and network analysis using human skeletal muscle samples from 66 patients with severe symptomatic heart failure (HFrEF; NYHA III-IV, left ventricular ejection fraction ≤ 30). A co-expression network consisting of 14 communities, involved in well-established biological processes within human skeletal muscle was identified and validated in two independent cohorts. Network communities related to mitochondrial beta-oxidation, extracellular matrix remodeling, oxidative phosphorylation, and contractile elements were shown to have lower expression in HFrEF patients compared with age-matched controls. This is consistent with the known muscle phenotype in patients with HRrEF. Based on the strong correlation with clinical features and prognosis, extracellular matrix remodeling, mitochondrial beta-oxidation, and p53 signaling communities were identified as key processes. The former two communities were highly enriched with genes regulated by physical (in)activity, i.e., bed rest and exercise, and weak association with prognosis. Community related to p53 signaling, with CDKN1A as a key regulator, was increased in HFrEF patients compared to age-matched controls and associated with worse prognosis. The current work differentiates previously proposed factors underlying heart failure-induced skeletal muscle dysfunction, emphasizes the p53 signaling community and importance of biological age in this process. The distinct association with clinical status and prognosis furthermore supports pathophysiological significance and clinical potential of the p53 signaling community.

overall_design: Transcriptional profiling of vastus lateralis muscle between heart failure patients and healthy individuals.

first: Eric

last: Rullman

first: Michael

last: Melin

first: Rodrigo

last: Fernandez-Gonzalo

first: Thomas

last: Gustafsson


title: Effect of recombinant human Annexin A5 on gene expression of bone marrow-derived macrophages differentiating into osteoclasts

city: Shanghai

first: Zhuoxuan

last: Jia

state: Shanghai

institute: Shanghai 9th People’s  Hospital, Shanghai Jiao Tong University School of Medicine

summary: Primary BMMs were obtained from male C57BL/6 miceaged 4-6 weeks. The mice were euthanized, and femurs and tibias were removed. BMMs were flushed out of the bones using a cold culture medium, filtered through a 70-um cell strainer , and centrifuged at 1500 rpm for 5 min. The cells were suspended in cold culture medium supplemented with 20 ng/ml M-CSF and cultured for five days, with half of the medium being replaced on day three and full replacement on day 5 before being used for subsequent experiments.The culture medium was alpha-MEM supplemented with 10% FBS and 1% penicillin-streptomycin-gentamicin solution. Mature BMDMs were double-stained using flow cytometry antibodies CD16/32 and F4/80 for identification. The recombinant protein AnxA5 used in this study was produced by SEME Cell Technology Co., Ltd, China. To investigate the role of AnxA5 in osteoclast differeation, 100000 BMDMs were seeded in 12 well plates. After 24 hours of cell seeding, the regular medium was replaced with culture medium (30ng/ml m-csf, control group, A-1, A-2,A-3 and A-4), culture medium containing  50 ng/mL RankL (model group, B-1, B-2, B-3 amd B-4), culture medium containing  50 ng/mL RankL and 2 ug/mL of Annexin A5 (Treat group, C-1, C-2,C-3 and C-4) for 5 days.

overall_design: Total RNA was extracted using Trizol from BMMs after m-CSF and RANKL treatment with or without Annexin A5 (n = 4) for 5 days.

first: Wenjie

last: Zhang


title: Comprehensive drug repurposing approach identifies Bavisant as a compound for regenerative therapeutics in multiple sclerosis

first: Nadjet

last: Gacem

address: 47 BD de l'Hôpital, Hôpital de la Pitié Salpêtrière

institute: Paris Brain Institute

summary: To assess the pro-myelinating and neuroprotective effects of the histamine H3 recepetor antagonist, we conducted bulk RNAseq on rat primary OPCs.

overall_design: Comparative gene expression profiling and differentially regulated pathways analysis of RNA-seq data from rat primary OPCs cultures, in basal condition or after treatment with Bavisant at 1 µM and 10µM.

first: Brahim

last: Nait-Oumesmar


title: The aged environment alters the differentiation and myelination of grafted human oligodendrocytes

summary: To assess the effect of age on the differentiation/myelination potential of human oligodendrocytes grafted in the demyelinating central nervous system, we conducted bulk RNAseq on hiOL engrafted in LPC lesion.

overall_design: Comparative gene expression profiling and differentially regulated pathways analysis of RNA-seq data from hiOL grafted in LPC lesion in aged and young groups.

first: Anne

last: Baron Van Evercoorren

first: Marion

last: Levy


title: Bypass of blocking lesions by RNAPII reveals key insights into DNA damage resistance [PRO-seq]

city: Miami

first: Carolina

middle: Paula

last: Banuelos

state: Florida

address: 1580 NW 10th Ave

department: Medicine

country: USA

institute: University of Miami

summary: Ultraviolet (UV) irradiation or platinum-based drugs generate bulky DNA lesions that impede transcription elongation by RNA Polymerase II (RNAPII). This unscheduled transcription elongation block triggers a stress response, which includes initiating transcription-coupled DNA repair, removing and degrading the halted RNAPII, and a global transcriptional shutdown. However, the molecular and cellular consequences of RNAPII successfully bypassing these blocking lesions have remained unknown. Here, we have identified the acetyltransferase p300 as a regulator of the stress response when RNAPII stalls at blocking lesions. Indeed, p300 interacts with the halted RNAPII and controls its removal and degradation in a USP7-dependent mechanism. Notably, in p300-deficient cells, transcription persists despite DNA damage, as RNAPII bypasses blocking lesions, leading to mutant mRNAs and splicing variants accumulation. This persistent transcription activity is particularly detrimental post DNA damage as it results in toxic translation activity and higher DNA damage levels. These observations provide the first evidence that bypass of blocking lesions by RNAPII inhibits DNA repair as well as the cellular stress response. Our findings offer essential insights into the mechanisms of resistance to DNA damage and suggest strategies to enhance the efficacy of platinum-based drugs, such as cisplatin, in anti-tumor therapies.

overall_design: To characterize the impact of p300 deficiency on transcription control post DNA damage, Precision Run-On Sequencing (PRO-Seq) was conducted in both WT and p300-deficient cells. PRO-Seq maps the location of actively engaged, non-arrested, or paused RNA polymerases with base-pair resolution


title: Novel culture systems for naive human embryonic stem cells  based on chemical molecule screening

first: Tao

last: Wu

address: Tongji University Siping Road Campus

department: school of life science and technology

institute: Tongji University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Novel culture systems for naive human embryonic stem cells  based on chemical molecule screening [RNA-seq]

summary: We systematically screened novel culture systems designed for naïve human embryonic stem cells via high-content screening and small molecule combinations. Our findings indicate that the cell lines established through this innovative system closely mimic the in vivo Inner Cell Mass (ICM) concerning both transcriptome profiles and methylation patterns. Additionally, we observed an elevated level of methylation specifically on transposable elements within these cell lines. Furthermore, our investigations suggest that the genomic stability of this novel system may exhibit superior qualities.

overall_design: Analyzing gene expression profile of naïve hESCs maintained and induced from primed-to-naïve transition under alternative conditions

first: Jindian

last: Hu

first: Yixuan

last: Wang


title: Genetic Mapping of Monocyte Fate Decisions Following Myocardial Infarction

city: Saint Louis

first: Kory

last: Lavine

state: Missouri

address: 660 S. Euclid Ave

department: Internal Medicine - Cardiology

institute: Washington University School of Medicine

summary: Inflammation contributes to the pathogenesis of cardiac disease and represents a viable therapeutic target for heart failure. Cardiac injury elicits recruitment of neutrophils, monocytes, and T-cells. Monocytes and their progeny represent are highly abundant, display incredible functional diversity, and are key determinants of myocardial inflammation. Much remains to be learned regarding mechanisms and signaling events that instruct monocyte fate decisions. We devised a genetic lineage tracing strategy using Ccr2crERT2Rosa2LSL-tdTomato mice in combination with single cell RNA-sequencing to map the fate and differentiation trajectories of monocytes that infiltrate the heart after reperfused myocardial infarction (MI). We observe that monocyte recruitment is restricted to the first 5 days following MI. Infiltrating monocytes give rise to transcriptionally distinct and spatially restricted macrophage and dendritic cell-like subsets, dynamically shift over time, and chronically persist within the myocardium. Pseudotime analysis predicted two differentiation trajectories of monocyte-derived macrophages that are initially partitioned into the border and infarct zones, respectively. Among these trajectories, we show that macrophages expressing a type I IFN responsive signature are an intermediate population localized within the border zone and promote myocardial protection. Collectively, these data uncover new complexities of monocyte differentiation in the infarcted heart and suggest that modulating monocyte fate decisions may have clinical implications.

overall_design: We performed 90 minutes of closed chest ischemia of the left anterior descending coronary artery followed by reperfusion. For Ccr2:CreERT2,Rosa26:tdTomato mice, a single IP dose of 60mg/kg tamoxifen was given 1 day prior to injury. Hearts were collected at indicated timepoints and cells flow sorted for monocytes and macrophages for single cell RNA sequencing. For Cx3cr1:CreERT2,Rosa26:tdTomato mice, tamoxifen was injected IP daily for 5 days beginning on the day of instrumentation followed by 9 days of chase. Hearts were collected 2 days after injury and flow sorted for monocytes and macrophages and separated into tomato positive and negative libraries for single cell RNA sequencing. n=3 mice pooled for each library.

first: Andrew

middle: L

last: Koenig

first: Farid

middle: F

last: Kadyrov

first: Junedh

middle: M

last: Amrute

first: Steven

last: Yang

first: Carla

middle: J

last: Weinheimer

first: Jessica

last: Nigro

first: Attila

last: Kovacs

first: Gabriella

last: Smith


title: Isoleucyl-tRNA synthetase 1 novel mutation promotes deposition of pulmonary surfactant through stabilizing Cathepsin Z [scRNA-seq]

first: Weitao

last: Zhou

state: Minhang district

address: Block 8, Children's Hospital of Fudan University, Wanyuan Road, Minhang District, Shanghai, China

institute: Children's Hospital of Shanghai Jiaotong University

summary: Isoleucyl-tRNA synthetase 1(IARS1) disorder is a recently identified multi-organ disease, only a limited cases have been reported so far; furthermore, the mechanisms underlying IARS1 mutation and the symptoms remain unknown. In this report, we present four families with seven distinct IARS1 variants, associated with growth retardation, fatty liver, mental development disorder, and severe pulmonary alveolar proteinosis. IARS1-Tyr148Cys/Arg444* mice are established and exhibited pulmonary alveolar proteinosis and other multi-organ disorders that closely mimic human phenotype. Analysis of single cell RNA sequencing of peripheral blood mononuclear cells from patients and lung metabolomics of lung in IARS1-Tyr148Cys/Arg444* mice analysis indicated disruption in phagosome, lysosome and fatty acid metabolism, cholesterol metabolism pathways. IARS1 mutations results in accumulation of surfactant in alveolar macrophages and alveoli in compound heterozygous mouse model, while IARS1 deficiency impairs the post-translation of Cathepsin Z(CTSZ) by inhibiting ubiquitin-mediated degradation. CTSZ depleted also shows abnormal cholesterol degradation and deposition of pulmonary surfactant associated proteins and overexpression CTSZ could rescue IARS1 deficiency related alveolar macrophage disfunction in vitro. These finding suggest that biallelic IARS1 deficiency impair alveolar macrophage, partly by impair CTSZ -dependent degeneration; and IARS1 could consider as a candidate gene in inherit pulmonary alveolar proteinosis.

overall_design: mRNA profile of PBMCs from IARS1 mutation patient 4 and his fraternal twin brother (healthy control)

first: Dan

last: Dai

first: Libo

first: Liling

last: Qian


title: Isoleucyl-tRNA synthetase 1 novel mutation promotes deposition of pulmonary surfactant through stabilizing Cathepsin Z

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Novel culture systems for naive human embryonic stem cells  based on chemical molecule screening [WGBS]

overall_design: Analyzing  whole-genome methylation level of naïve hESCs maintained and induced from primed-to-naïve transition under alternative conditions


title: Study on the mechanism of DLX5 interaction with MYCN in the occurrence and development of neuroblastoma

city: Wuhan

first: Xiao

middle: si

last: Yu

address: Jiefang Avenue

department: Pediatric Surgery

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Neuroblastoma is the most common childhood tumor, which has high malignant degree and low survival rate, and seriously threatens the life and health of children. MYCN is a member of the MYC family and is closely associated with the development of neuroblastoma. In addition, DLX5 (Distal-Less Homeobox 5) also promotes cell proliferation by upregulating MYC promoter activity, but the role of DLX5 in neuroblastoma remains unclear. The aim of this study was to reveal the mechanism of DLX5 in the occurrence and development of neuroblastoma and to explore the targeted treatment strategy of neuroblastoma.

overall_design: Neuroblastoma cell line SY5Y was constructed with DLX5 overexpression cell line, and cells in control group and overexpression group were harvested with Trizol reagent and sent to RNAseq.

first: Yi

last: He

first: Xiaosi

first: Chenzhao

last: Feng

first: Xvyong

last: chen

first: Lei

last: Xiang

first: Luyao

first: Ke

last: Chen

first: Jinyi

last: You

first: Shiming

first: Jiaxin

last: Zhang

first: Jiexiong


title: Breast cancer cells can recognize and respond to different levels of progestins to achieve different phenotypic outputs [RNA-seq]

city: Boston

first: Yingtian

last: Xie

state: MA

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

summary: The steroid hormone progesterone, acting through its nuclear progesterone receptor (PR), has complex physiologic activities with different levels of hormones manifesting distinct and sometimes opposing phenotypic responses in target tissues. However, most of what is currently known about the transcriptional activity of PR comes from studies performed using progestins at levels that are in the high physiologic range (>10nM), relevant only in the luteal phase of the reproductive cycle and pregnancy in humans. These studies do not consider the non-linearity of responses to progestins that exist in physiology and are not informative as to the mechanisms by which low levels of progestins, as occurs during menopause (0.1-0.3nM), exert their biological activities. Thus, we undertook to define the mechanisms which enable cells to recognize and respond to different levels of progestins.

overall_design: T47D cells were plated 2.5x10^5 cells per well in 6-well culture plates. Cells were allowed to attach overnight in phenol red-free RPMI 1640 supplemented with 8% charcoal-stripped FBS (CFS), NEAA, and NaPyr. Synchronization was achieved by 24-48hr serum starvation in phenol red-free RPMI 1640 supplemented with 0.1% CFS, NEAA, and NaPyr. Synchronized T47D cells were treated with the relevant assay compounds. Cell plates were incubated at 37*C in the presence of 5% CO2 for the noted amount of time. Upon treatment completion, media was removed by aspiration, and cells were gently washed with sterile PBS. Isolation of total RNA was performed using the Aurum™ Total RNA Mini-Kit according to the manufacturer’s instructions (Bio-Rad, Hercules, CA). Total RNA concentration and quality were determined using a Nanodrop 1000 (ThermoFisher).


title: Breast cancer cells can recognize and respond to different levels of progestins to achieve different phenotypic outputs


title: Divergent Redox Responses of Macular and Peripheral Müller Glia: Implications for Retinal Vulnerability

city: Hangzhou

first: penghui

last: Yang

state: Zhejiang

address: 866 Yuhangtang Road

institute: Pharmaceutical Informatics Institute

summary: The predilection of many conditions, such as macular telangiectasia type 2, for the human macula suggests it may be more susceptible to stress than the peripheral retina. In this study, we have comprehensively investigated the genetic profiling of the macula and peripheral retina in response to stress. We conducted single-cell RNA sequencing analysis on the macula and peripheral retina of four donors cultured ex vivo with or without exposure to light stress. We found that the peripheral retina generally exhibited more transcriptional changes than the macula in response to stress. Interestingly, the most pronounced changes were observed in a subgroup of Müller cells that are dominant in the peripheral retina. Genes more abundantly expressed in peripheral retinal Müller cells were mainly associated with stress responses and were more influenced by light stress. In contrast, genes that were highly expressed in Müller cells that predominate in the macula played roles in cellular function and were less influenced by light stress. We identified that Metallothionein 1 (MT1), A Kinase Anchor Protein 12 (AKAP12) and MAF BZIP Transcription Factor F (MafF) were more abundantly expressed in peripheral Müller cells than in macular Müller cells. We found that these genes were also activated in the mouse retina in the early stages of development of subretinal neovascularization. Knockdown of the MT1, AKAP12 and MafF genes in human primary Müller cells reduced cell viability in response to light stress and disrupted several stress response pathways. Taken together, our findings indicate that macular Müller cells are more directed toward maintaining retinal cell function rather than mounting a stress response when they are exposed to stress, which may contribute to the macula’s vulnerability to degenerative disease.

overall_design: We set four experimental Groups (Exposed to Intense Light).Group 1: Macular neural retinas from left donor eyes exposed to intense light (LM).Group 2: Mid-peripheral neural retinas from left donor eyes exposed to intense light (LP).Control Groups (Exposed to Dim Light). Group 3: Macular neural retinas from right donor eyes exposed to dim light (CM). Group 4: Mid-peripheral neural retinas from right donor eyes exposed to dim light (CP. Duration of Light Exposure: All groups were exposed to their respective light conditions for 4 hours.


title: Use of azithromycin may impair fetal growth via causing ER stress in placental syncytiotrophoblasts

first: Fan

last: Pan

address: Ren Ji Hospital, Shanghai Jiao Tong University School Of Medicine, Shanghai  Street Address: 845 Lingshan Road, Pudong New Area

institute: Shanghai jiaotong university

summary: Azithromycin (AZM) is widely used to treat perinatal mycoplasma infection in pregnancy. The use of AZM is thought to have few adverse consequences. However, emerging evidence indicates that AZM may have potential adverse effects on pregnancy outcomes. Here, we explored whether AZM might affect pregnancy outcomes by influencing placental function. To investigate the effects of azithromycin on human placenta trophoblast, Transcriptomic sequencing was conducted to screen the genes and biological pathways influenced by AZM in cultured human placental trophoblasts

overall_design: Comparative gene expression profling analysis of RNA-seq data for azithromycin traeted primary human placenta syncytiotrophoblasts.

first: Wang

last: Wang-sheng

first: Sun

last: Kang


title: Developmental cell type specific enhancers in orofacial morphology and disease [human]

city: Farmington

first: Emma

middle: Wentworth

last: Winchester

state: Connecticut

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

summary: The noncoding genome contains sequences called enhancers which facilitate expression of target genes through recruitment and binding of transcription factors. Enhancers are typically active in developmental stage-, tissue-, and cell type-specific patterns, whereby they control the spatiotemporal expression patterns of target genes. Sequence variation within enhancers can alter expression of their target genes where the enhancer is active, causing isolated phenotypes ranging from normal morphological differences to malformations. The role of orofacial enhancers in normal morphology and disease of the orofacial region has previously been established in bulk human assays. However, the conservation of these findings and the cell types contributing to these phenotypes are unknown, limiting work in prevention and treatment of malformations. To uncover cell type-specific enhancers whose sequence variants contribute to normal facial morphology and malformations, we performed single cell multiome (snATAC and snRNA-seq) sequencing on 17 human samples spanning 6 unique stages from 4-8 weeks gestation and 14 mouse samples spanning 6 stages from E9.5-15.5. We identified 15 distinct cell types, for which we leveraged the cell type specific chromatin accessibility and transcriptomic profiles and previously published chromatin conformation data to identify cell type specific enhancer-gene predicted interactions, which we call the ‘enhancerprints’. These enhancerprints revealed a cell type-specific enrichment pattern of common single nucleotide variants for biologically relevant phenotypes such as epithelium in orofacial clefting and mesenchyme in facial variation.

overall_design:
Aligned snMultiome-seq of a time span of human developing orofacial regions.
single cell multiome (snATAC and snRNA-seq) sequencing on 17 human samples spanning 6 unique stages from 4-8 weeks gestation.

***Submitter declares that the raw data will be added to phs002008.v1.p1 in dbGap due to subject privacy concerns.***

first: Tara

middle: N

last: Yankee

first: Kevin

last: Child

first: Sungryong

last: Oh

first: Rachael

last: Massey

first: Justin

last: Cotney


title: Comparative translating ribosome affinity purification-RNAseq (TRAPseq) by lung cell-specific drivers

city: Houston

first: Edwin

middle: Justin

last: Ostrin

state: Texas

address: 1515 Holcombe Blvd, Unit 1465

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

summary: Translating ribosome affinity purification coupled to next-generation RNA sequencing permits profiling of specific cellular compartments. Here, we used well-characterized Cre and CreER drivers to lineage trace different cell populations in the developing lung with a ribosomal L10-GFP fusion protein. Two different anti-GFP antibodies were used to pull down ribosomes. mRNA was isolated, reversed transcribed, and processed using next-generation sequencing. Profiling showed distinct clustering between alveolar cell drivers and epithelial cell drivers, which were clearly distinguishable from raw mRNA input.

overall_design: 49 samples are included here -- 3 of raw input (supernatant from purification) and 46 TRAP-seq specimens. These include 16 cell-specific Cre and CreER drivers specific to alveolar, epithelial, smooth muscle, or other cell types with two different anti-GFP  antibodies. Neonatal lungs (~P5) were dissected and stripped from surrounding tissue. Translating ribosomes were isolated per previous protocol (see for instance 10.1242/dev.160788), and pulled down using one of two anti-GFP antibodies (19C8 or Rb). cDNA libraries constructed using 300 bp inserts and submitted for next-gen reads on Illumina NextSeq 500 pipeline. Raw reads processed for QC using fastqc and poor quality reads filtered using trimmomatic. Aligned to mm10 genome using STAR aligner and counts quantitated, normalized, and all pairwise comparisons done using DESeq2.

first: Jichao


title: Developmental cell type specific enhancers in orofacial morphology and disease [mouse]

overall_design: single cell multiome (snATAC and snRNA-seq) sequencing on 14 mouse samples spanning 6 stages from E9.5-15.5.


title: TMC7 is essential for maintanance of elongated spermatids volume by regulating TGN-derived and SYPL1-defined vesicles

city: Beijing

first: Zheng

last: LV

address: State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China

institute: China Agricultural University

summary: The expression levels of trans-Golgi network related genes were abnormal in the testis after Tmc7 deletion

overall_design: Comparative gene expression profiling analysis of RNA-seq data from Tmc7 knockout and heterozygote testes

last: Lv

first: Longjie

last: Sun

first: Xuexue

first: Xiaomei

first: Xiaohong

last: Yao

first: Shuang

last: Tian

first: Chaofan

last: Wang

first: Jiali

last: Liu


title: Breast cancer cells can recognize and respond to different levels of progestins to achieve different phenotypic outputs [ATAC-seq]

first: Yingtian

last: Xie

overall_design: T47D cells were plated 2x10^5 cells per well in 10cm culture plates. Cells were allowed to attach overnight in phenol red-free RPMI 1640 supplemented with 8% charcoal-stripped FBS (CFS), NEAA, and NaPyr. Synchronization was achieved by 48hrs serum starvation in phenol red-free RPMI 1640 supplemented with 0.1% CFS, NEAA, and NaPyr. Synchronized T47D cells were then treated with 0.1nM R5020, 10nM R5020, or DMSO vehicle. Cell plates were incubated at 37*C in the presence of 5% CO2 for 6hrs or 18hrs, after which cells were washed with PBS dissociated from the culture plate using gentle trypsinization (0.05% for minimal time). Omni-ATAC was performed as previously described (PMID: 28846090).


title: Biopsy And Blood Gene Expression Distinguish Injury, Subclinical and Clinical Rejection in Kidney Transplant Recipients

city: La Jolla

first: SUNIL

last: KURIAN

state: CA

address: 10666 N Torrey Pines Rd

institute: Scripps Health

summary: Short-term kidney transplant rejection rates have vastly improved. Unfortunately, the focus is still on clinical acute rejection, whereas patients with no graft dysfunction and subclinical rejection without protocol biopsies would be treated as having no ongoing injury. Molecular diagnostic tests to detect rejection are still reliant on the current gold standard, kidney histology. Our work is the first to examine molecular profiles in matched tissue and blood samples from a prevalent kidney transplant recipient population. We show molecular evidence, in blood and tissue, that subclinical rejection is a precursor of clinical rejection and that non-alloimmune injury to the graft can be distinguished from immune activation. Our work supports consideration of tissue molecular profiling for a comprehensive understanding of noninvasive diagnostics.

overall_design: This analysis was performed on 290 (51 subAR, 23 cAR, 43 acute dysfunction- no rejection (ADNR) and 174 normal (TX) biopsy samples and 283 (50 subAR, 22 cAR, 41 ADNR and 170 TX) matched blood samples previously collected from 129 patients paired with “for cause” or surveillance kidney biopsies as part of CTOT-08 study. A total of 573 samples were profiled.

first: Sunil

last: Kurian


title: ndufs2-/- zebrafish model Leigh syndrome with shortened lifespan, developmental anomalies, altered transcriptome and disrupted metabolism

city: Philadelphia

first: Marni

last: Falk

state: PA

address: 3401 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: Mitochondrial complex I (CI) deficiency, one genetic etiology of Leigh syndrome spectrum (LSS), manifests with complex multi-system dysfunction with lactic acidemia and early mortality. To facilitate screening of therapeutic candidates for CI diseases, we used CRISPR/Cas9 to generate a ndufs2-/- zebrafish line. Ndufs2 deficient larvae displayed reduced survival, neuromuscular dysfunction, and morphological malformations. We performed transcriptomic sequencing of ndufs2-/- larvae at 6 vs 7 dpf, across and within clutches, and relative to sibling or WT controls. These results were compared to transcriptome data of ndufs2-/- missense mutant C. elegans (gas-1(fc21)) and CI disease patient fibroblasts. Transcriptome profiling revealed consistently dysregulated pathways in ndufs2-/- larvae, gas-1(fc21) worms, and human CI deficient cell lines with increased expression of the electron transport chain, TCA cycle, fatty acid beta oxidation, and one-carbon metabolism. Targeted biochemical analyses revealed a reduction in CI activity and unbiased metabolomic studies identified increased lactate, TCA cycle intermediates, and carnitine species. These changes suggest central metabolism has shunted glucose utilization towards lactate production. Additionally, we determined alterations in one-carbon metabolism associated pathways likely contribute to pathology. Our established, validated ndufs2-/- zebrafish model of CI deficiency recapitulates LSS phenotypes and will be useful for future studies of CI disease and therapeutics.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: RNA-seq profiling of human-derived fibroblast cells grown in galactose media. Patients sequenced are either healthy (n=7) or have confirmed Complex I Primary Mitochondrial Disease (n=2).

first: Dana

last: Mitchell

first: Donna

last: Iadarola

first: Neal

middle: D

last: Mathew

first: Kelsey

last: Keith

first: Christoph

last: Seiler

first: Sanghyeon

last: Yu

first: Man

middle: S

last: Kim

first: Niki

last: Woodard

first: Eiko

last: Nakamaru-Ogiso

first: Deanne

last: Taylor


title: Temporal gene expression profiling analysis of Clostridium boutlinum strain ATCC 19397.

city: Helsinki

first: Miia

last: Lindström

address: Agnes Sjöbergin katu 2

department: Faculty of Veterinary Medicine

country: Finland

institute: University of Helsinki

summary: Clostridium botulinum is a Gram-positive bacterium that produces highly potent botulinum neurotoxins causing botulism. The study examines the temporal gene expression profile of C. botulinum ATCC 19397 over time. Using these data, we aimed developping new transcriptomic analytical tools as understanding the regulation of neurotoxin production. The research contributes to unraveling the complexities of controlling C. botulinum and its neurotoxin in the food industry.

overall_design: Temporal gene expression profiling analysis of RNA-seq from Clostridium boutlinum strain ATCC 19397 grown in laboratory conditions.

first: François

middle: P

last: Douillard

first: Katja

last: Selby

first: Elio

last: Nushi

first: Antti

last: Honkela


title: Bulk RNA-seq analysis of nilotinib resistant JURL-MK1 cells compared against parental JURL-MK1 cells.

city: Glasgow

first: David

last: Vetrie

address: Wolfson Wohl Cancer Research Centre

department: Institute of Cancer Sciences

country: United Kingdom

institute: Glasgow University

summary: Bulk RNA-seq was performed on a monoclonal nilotinib-resistant cell line derived from parental JURL-MK1 cells and on parental JURL-MK1 cells.  The aim of the study was to identify the molecular differences between the two cell lines.

overall_design: Three different passages of nilotinib-resistant JURL-MK1 cells (also referred to here as C3 cells) and parental JURL-MK1 cells (also referred to here as WT cells)  (n = 3 replicates of each) were cultured for 72 hrs and total cellular RNA was then extracted for RNA-seq analysis.

first: Thomas

last: Stevens

first: Mary

middle: T

last: Scott


title: Single cell RNA-seq analysis of the effects of fluphenazine and/or nilotinib on primary CML CD34+CD38- cells

summary: Single cell RNA-seq was performed on primary human CML CD34+CD38- cultured in vitro for 48 hrs in the presence of fluphenazine or nilotinib alone, or a combination.

overall_design: CML CD34+CD38- cells were flow sorted from primary CD34+ cells and cultured in vitro for 48 hrs in the presence of fluphenazine  alone (5 µM) and/or with nilotinib (5 µM). Cells were then processed for single cell RNA-seq analysis (n = 1 sample).


title: Bulk RNA-seq analysis for knockdowns of dopamine receptors DRD3 or DRD4 in JURL-MK1 cells +/- TKI (nilotinib) in vitro.

summary: Bulk RNA-seq analysis was performed across a 72 hr  timecourse for JURL-MK1 cells in which the dopamine receptors DRD3 or DRD4 were knocked down by lentiviral mediated shRNAs in vitro.  Knockdown cells were also treated with and without a TKI (nilotinib.

overall_design: DRD3 was knocked down in JURL-MK1 cells using two different shRNA constructs (sh46 and sh47).  DRD4 was knocked down in JURL-MK1 cells using two different shRNA constructs (sh53 and sh55). Controls were shRNA for scrambled. Post-transduction of JURL-MK1 cells with shRNAs, total cellular RNA was harvested on days 1,2,3 of time course experiments for each knockdown construct.  sh53 DRD4 knockdown cells  were also +/- tyrosine kinase inhibitor (TKI) nilotinib (2 nM) for 2 or 3 days. Independent biological replicate experiments were performed in duplicate (n=2) or triplicate (n=3) for each knockdown condition and each timepoint.


title: METTL3 Promotes Histone H3K9 Acetylation through Recruitment of Histone Acetyltransferase 1 to Chromatin [H3K9Ac ChIP-seq]

city: Riverside

first: Yinsheng

last: Wang

state: California

address: 501 Big Springs Road

institute: UC-Riverside

summary: METTL3 constitutes the catalytic subunit of the major methyltransferase complex mediating the formation of N6-methyladenosine (m6A) in mRNA. Although the resulting m6A is known to regulate numerous cellular processes, the protein interaction network of this complex remains largely unknown. Here, we employed ascorbate peroxidase-based proximity labeling followed by LC-MS/MS analysis to examine systematically the interaction proteins of METTL3 and METTL14 in HEK293T cells. Aside from many proteins involved in mRNA splicing, a subset of histone regulatory proteins are enriched in the proximity proteome of METTL3, including histone acetyltransferase 1 (HAT1). In addition, genetic ablation of METTL3 led to reduced chromatin occupancy of HAT1 isoform-a, which is expressed exclusively in the nucleus, and diminished H3K9Ac in HEK293T cells, especially in retrotransposons. Depletion of HAT1 led to diminished H3K9Ac, which could be restored by wild-type HAT but not the one fused with the nuclear export sequence (NES) of PKI to remove it from the nucleus. Our in vitro acetylation assay further confirmed the acetylation activity of HAT1 isoform-a on nucleosome histone H3K9. The reduced retrotransposons H3K9Ac in METTL3-/- cells could be restored by ectopic expression of wild-type METTL3, but not its catalytically inactive D395A mutant. Together, we assessed the protein interactome of METTL3, uncovered a new function of HAT1 in acetylating H3K9 in chromatin, and revealed a crosstalk between METTL3-mediated formation of m6A and HAT1-catalyzed formation of H3K9Ac in chromatin.

overall_design: Genome-wide profiling analysis of H3K9Ac in HEK293T cells, FTO-/- cells, and ALKBH5-/- cells

first: Xiaomei

last: He

first: Yen-Yu

last: Yang


title: Reciprocal inflammatory signals establish profibrotic cross-feeding metabolism [young_old_bleo]

city: San Francisco

first: Javier

last: Gomez Ortega

address: 513 Parnassus Ave.

institute: UCSF

summary: When monocyte-derived macrophages are recruited to injured tissues, they can induce a maladaptive fibrotic response characterized by excessive production of fibrillar collagen from local fibroblasts. Macrophages initiate the fibrotic programming of fibroblasts via paracrine factors, but it is unclear if reciprocal responses from the fibroblasts trigger pro-fibrotic programming of macrophages to establish a collaborative feed-forward fibrotic circuit. We identify macrophage-fibroblast cross talk necessary for injury-associated fibrosis, in which macrophages induce interleukin 6 (IL-6) expression in fibroblasts via purinergic receptor P2rx4 signaling and IL-6 induces arginase 1 (Arg1) expression in macrophages. Surprisingly, Arg1 contributes to fibrotic responses by metabolizing arginine to ornithine, which fibroblasts use as a substrate to synthesize proline, a uniquely abundant constituent of fibrillar collagen Taken together, we define a bidirectional circuit between macrophages and fibroblasts that facilitates cross-feeding metabolism necessary for injury-associated fibrosis.

overall_design: Lungs were isolated after 7 days after bleomycin injury. Immune cells were obtained by positive selection by binding to CD45 microbeads and passing through MACS columns (130-049-601, Miltenyi Biotech). Primary mouse lung fibroblasts were freshly isolated after magnetic bead-based negative selection of epithelial cells (118204, Biotin anti-mouse CD326 Epcam, Clone: G8.8, BioLegend), endothelial cells (102404, Biotin anti-mouse CD31, clone: 390), immune cells (103104, Biotin anti-mouse CD45, clone: 30-F11, BioLegend), pericytes and smooth muscle cells (134716, Biotin anti-mouse CD146, clone: ME-9F1, BioLegend), and red blood cells (116204, Biotin anti-mouse Ter119, clone: TER-119, BioLegend) with biotinylated antibodies and Dynabeads (MyOne Streptavidin T1, 65601, Thermo Fisher Scientific)

first: Preeti

last: Yadav

middle: G

last: Ortega

first: Kai-chun

last: Chang

first: Charlene

last: Pan

first: Nivedita

last: Biswas

first: Xiaoyang

last: Yin

first: Aritra

last: Bhattacharyya

first: Kaveh

last: Boostanpour

first: Tatsuya

last: Tsukui

first: Dean

last: Sheppard

first: Baosheng

last: Li

first: Maishan

last: Mazharul

first: Hiroki

last: Taenaka

first: Michael

middle: A

last: Matthay

first: Rieko

last: Muramatsu

first: Mohammad

last: Naser

first: Ari

middle: B

last: Molofsky

first: Paul

last: Wolters

first: Adam

middle: R

last: Abate

first: Kevin

last: Tharp

first: Mallar

last: Bhattacharya


title: CARD11 gain of function upregulates BCL2A1 and promotes resistance to targeted therapies combination in B-cell lymphoma [scRNA-seq]

city: Nantes

first: David

last: Chiron

address: 8 quai Moncousu

institute: CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université

summary: Strategy combining targeted therapies is effective in B-cell lymphomas such as mantle celllymphoma (MCL), but acquired resistances remain a recurrent issue. Herein, we performed integrative longitudinal genomic and single-cell RNA-seq analyses of MCL patients treated with targeted therapies against CD20, BCL2 and BTK (i.e., OAsIs trial). We revealed the emergence of subclones with a selective advantage against OAsIs combination in vivo and showed that resistant cells were characterized by BCR-independent overexpression of NFkB1 target genes, especially due to CARD11 mutations. Functional studies demonstrated that CARD11 gain of function not only resulted in BCR independence, but also directly increase the transcription of the antiapoptotic BCL2A1, leading to venetoclax and OAsIs combination resistance. Based on the transcriptional profile of OAsIs-resistant subclones, we designed a 16-gene resistance signature that was also predictive for MCL patients treated with conventional chemotherapy, underlying a common escape mechanism.

overall_design: 7 bone marrow samples from 6 patients included in the OAsIs trial were analyzed in single cell RNA sequencing (scRNA-seq). Briefly, live MCL cells were first enriched by Ficoll-Paque Plus and anti-human CD19 magnetic beads. Depletion of human erythroid precursors and erythrocytes was then performed using CD235a (Glycophorin-A) magnetic beads. 15,000 cells from the resulting suspensions were loaded on a Chromium controller to generate single-cell partitions following the manufacturer’s protocol (10X genomics). scRNA-seq libraries were constructed using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 and sequenced using the NovaSeq 6000 system (Illumina).

first: Salomé

last: Decombis

first: Céline

last: Bellanger

first: Yannick

last: Le Bris

first: Candice

last: Madiot

first: Jane

last: Jardine

first: Juliana

last: Carvalho Santos

first: Delphine

last: Boulet

first: Christelle

last: Dousset

first: Audrey

last: Menard

first: Charlotte

last: Kervoelen

first: Élise

last: Douillard

first: Philippe

last: Moreau

first: Stéphane

last: Minvielle

first: Agnès

last: Moreau-Aubry

first: Benoit

last: Tessoulin

first: Gael

last: Roué

first: Nicolas

last: Bidère

first: Steven

last: Le Gouill

first: Catherine

last: Pellat-Deceunynck


title: CARD11 gain of function upregulates BCL2A1 and promotes resistance to targeted therapies combination in B-cell lymphoma

first: David

last: Chiron

summary: Strategy combining targeted therapies is effective in B-cell lymphomas such as mantle cell lymphoma (MCL), but acquired resistances remain a recurrent issue. Herein, we performed integrative longitudinal genomic and single-cell RNA-seq analyses of MCL patients treated with targeted therapies against CD20, BCL2 and BTK (i.e., OAsIs trial). We revealed the emergence of subclones with a selective advantage against OAsIs combination in vivo and showed that resistant cells were characterized by BCR-independent overexpression of NFkB1 target genes, especially due to CARD11 mutations. Functional studies demonstrated that CARD11 gain of function not only resulted in BCR independence, but also directly increase the transcription of the antiapoptotic BCL2A1, leading to venetoclax and OAsIs combination resistance. Based on the transcriptional profile of OAsIs-resistant subclones, we designed a 16-gene resistance signature that was also predictive for MCL patients treated with conventional chemotherapy, underlying a common escape mechanism. Among druggable strategies to inhibit CARD11-dependent NFkB1 transduction, we evaluated the selective inhibition of its essential partner MALT1. We demonstrated that MALT1 protease inhibition led to the reduction of genes involved in OAsIs resistance, including BCL2A1. Consequently, MALT1 inhibition induced synergistic cell death in combination with BCL2 inhibition, irrespective of CARD11 mutational status, both in vitro and in vivo. Taken together our study identified mechanisms of resistance to targeted therapies and provided a novel strategy to overcome resistance in aggressive B-cell lymphoma.

overall_design: RNA-seq expression in BCL2A1 + CARD11 WT cell lines (SP53, NTS3, REC-1) and BCL2A1+ CARD11 MUT cells (001-124, OCILY3, SUDHL16) treated 24h with the BTK inhibitor Ibrutinib (500 nM) or the MALT1 inhibitor MLT-748 (1 μM)

first: Salomé

last: Decombis

first: Céline

last: Bellanger

first: Yannick

last: Le Bris


title: METTL3 Promotes Histone H3K9 Acetylation through Recruitment of Histone Acetyltransferase 1 to Chromatin [Nascent RNA-seq]

first: Yinsheng

last: Wang

overall_design: Nascent RNA-seq data for wild-type and METTL3-/- HEK293T cells.

first: Xiaomei

last: He

first: Yen-Yu

last: Yang


title: Isoleucyl-tRNA synthetase 1 novel mutation promotes deposition of pulmonary surfactant through stabilizing Cathepsin Z [RNA-seq]

first: Weitao

last: Zhou

summary: Isoleucyl-tRNA synthetase 1(IARS1) disorder is a recently identified multi-organ disease, only a limited cases have been reported so far; furthermore, the mechanisms underlying IARS1 mutation and the symptoms remain unknown. In this report, we present four families with seven distinct IARS1 variants, associated with growth retardation, fatty liver, mental development disorder, and severe pulmonary alveolar proteinosis. IARS1-Tyr148Cys/Arg444* mice are established and exhibited pulmonary alveolar proteinosis and other multi-organ disorders that closely mimic human phenotype. Analysis of single cell RNA sequencing of peripheral blood mononuclear cells from patients and lung metabolomics of lung in IARS1-Tyr148Cys/Arg444* mice analysis indicated disruption in phagosome, lysosome and fatty acid metabolism, cholesterol metabolism pathways. IARS1 mutations results in accumulation of surfactant in alveolar macrophages and alveoli in compound heterozygous mouse model, while IARS1 deficiency impairs the post-translation of Cathepsin Z(CTSZ) by inhibiting ubiquitin-mediated degradation. CTSZ depleted also shows abnormal cholesterol degradation and deposition of pulmonary surfactant associated proteins and overexpression CTSZ could rescue IARS1 deficiency related alveolar macrophage disfunction in vitro. These finding suggest that biallelic IARS1 deficiency impair alveolar macrophage, partly by impair CTSZ -dependent degeneration; and IARS1 could consider as a candidate gene in inherit pulmonary alveolar proteinosis.

overall_design: mRNA profile of lungs from  IARS1-TYR148CYS/ARG444* and IARS1-WT mices

first: Dan

last: Dai

first: Libo

first: Liling

last: Qian


title: Single-cell Transcriptome Atlas of the uroclepsia Rat urethra with LIPUS treatment

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

summary: Single-cell transcriptomes of Rat urethra in normal,  uroclepsia and uroclepsia with LIPUS treatment.

overall_design: Single-cell transcriptomes of SD female Rat urethra in normal,  uroclepsia (ovariectomy and urethral dilatation) and uroclepsia with LIPUS treatment.


title: Generation and characterisation of a preclinical model of IDH-mutant astrocytoma

city: London

first: Sebastian

last: Brandner

address: Queen Square

department: Institute of Neurology

institute: University College London

summary: Comparison of various induced brain tumours with controls using Illumina mouse Infinium Methylation Arrays

overall_design: 52 samples from various mouse models to indice IDH-mutant Astrocytomas. Including 4 controls and 9 other conditions

first: Raquel

last: Fonseca

first: Andrew

last: Lowe

first: Stefan

last: Pusch

first: James

last: Innes

first: Ayisha

last: Shabbir

first: Joanne

last: Lau

first: Andreas

last: von Deimling


title: Integrative genome-wide analysis reveals the RNA-binding motifs of yeast Pcf11 and its role in fine-tuning terminator strength

city: Shihezi City

first: sheng

last: yue

state: Xinjiang

address: Dongcheng Street, Shihezi City

department: College of Chemistry and Chemical Engineering

institute: Shihezi University

summary: Pcf11 is a transcriptional termination factor that interferes with cell survival and mRNA 3′-end processing. However, the mechanism by which Pcf11 regulates transcriptional termination and the molecular basis of its interaction with the terminator remain unclear. Here, we performed gene expression profile, binding pattern, and RNA-binding motif studies on Pcf11. We used in vivo CLIP-seq to map thousands of Pcf11 binding sites in Saccharomyces cerevisiae and revealed the RNA-binding motifs of Pcf11 in the 3'-UTR region.

overall_design: The complete structural domains are essential for Pcf11 to perform its functions, C-terminal C2HC zinc finger defects can interfere with cell survival and influence mRNA 3′-end processing. The ΔPcf11 and Pcf11-AARR strains were constructed by directly deleting Pcf11 from the genome and mutating four conserved amino acid residues (Y575A/E577R/E578R/W582A) to investigate in-depth the biological function of Pcf11. In addition, overexpressing Pcf11 with a strong promoter (TEF1p) and terminator (GRS1t) or a weak promoter (CDC60p) and terminator (DITIt) resulted in transcription fluctuation. RNA-seq was conducted to compare the global gene expression patterns between the WT, ΔPcf11,Pcf11-AARR, Pcf11-OE1 and Pcf11-OE2 strains to investigate the effect of Pcf11 deletion on transcription.

first: Yue

last: Sheng

first: Haifeng

last: Ding

first: Chun

last: Li

first: Genlin

last: Zhang


title: Effect of depletion of Prrc2b on gene expression during oligodendrocyte development in isloated oligodendrocyte progenitor cells of C57BL/6J mice

city: beijing

first: Zhihong

last: Song

address: Taiping Road 27

institute: Beijing Institute of Basic Medical Sciences

summary: To investigate the  function  Prrc2b in the regulation of oligodendrocyte progenitor cells development, we isolated oligodendrocyte progenitor cells in brain tissues of Prrc2bf/f and Prrc2bf/f; Olig2-Cre mice at P4.

overall_design: To systemically investigate the mechanism underlying the development of hypomyelination in the context of Prrc2b deficiency, we performed RNA sequencing (RNA-seq) analysis on in brain tissues of Prrc2bf/f and Prrc2bf/f; Olig2-Cre mice at P4.

first: Ying

first: Shukun

last: Wang


title: Effect of depletion of Prrc2b on gene expression during neural development in isloated neural stem cells of C57BL/6J mice

summary: To investigate the  function m6A binding protein Prrc2b in the regulation of neural development, we isolated neural stem cells  in brain tissues of Prrc2bf/f and Prrc2bf/f; Nestin-Cre mice at E17.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in brain tissues of Prrc2bf/f and Prrc2bf/f; Nestin-Cre mice at E17.


title: Developmental cell type specific enhancers in orofacial morphology and disease

first: Emma

last: Winchester

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

overall_design: Refer to individual Series


title: Identification of stress response by multi-scale analyses of drought effect in Arabidopsis thaliana under future climate CO2

city: Antwerp

first: Hamada

last: AbdElgawad

address: Groenenborgerlaan 171

country: Belgium

institute: Antwerp University

summary:
We used a multidisciplinary approach to investigate the interaction of drought and elevated CO2 in Arabidopsis thaliana leaves. Transcriptome and subsequent metabolite analyses identified a strong induction of the aliphatic glucosinolate (GL) biosynthesis as a main effect of eCO2 in drought-stressed leaves.
We subjected Arabidopsis seedlings to a combination of two hydration (well-watered and drought) and CO2 levels (ambient (375±9 ppm; aCO2) and elevated (633±16 ppm; eCO2). To identify the molecular mechanisms involved in response to drought and eCO2, we performed a genome-wide transcriptome analysis on the developing rosette at 21 DAS, when it contains leaves in all stages of their development.

overall_design: Twenty whole rosettes of Arabidposis plants were harvested at 21 days after sowing (DAS) from four treatments: 1) aCO2, 2) aCO2 + drought (40% Soil Water Content, SWC), 3) elevated CO2, 4) aCO2 + drought stress (40% SWC). Twenty whole rosettes per each biological replicate were collected.  Three biological replicates used per each treatment (3 replicates x 4 conditions = 12 samples).

last: Gaurav Zinta

first: Johann

last: Hornbacher

first: Jutta

last: Papenbrock

first: Marios

last: Nektarios Markakis

first: Han

last: Asard

first: Gerrit

last: Beemster


title: Effects of gestational exposure to air pollution on placental methylation mark

city: los angeles

first: Shubhamoy

last: Ghosh

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

summary: We report the distribution of methylation mark by Next Generation Sequencing (RRBS) from Gestational D19 mouse exposed to Air -Pollutant material with or without prior treatment with Fish Oil.

overall_design: Examination of DNA methylation pattern in mouse placenta during gestational exposer to Air pollutant material and impact of fish oil treatment.

first: Amit

last: Ganguly

first: Bo-Chul

last: Shin

first: Sherin

last: Devaskar


title: Effects of gestational exposure to air pollution on placental mark


title: Effects of gestational exposure to air pollution on placental 5-Hydroxymethylation mark

summary: We report the distribution of 5-Hydroxymethylation mark by Next Generation Sequencing from Gestational D19 mouse exposed to Air -Pollutant material with or without prior treatment with Fish Oil.

first: Peng

last: Jin


title: METTL3 Promotes Histone H3K9 Acetylation through Recruitment of Histone Acetyltransferase 1 to Chromatin (caRNA-m6A-seq)

first: Yinsheng

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild-type, HAT1-KD, and METTL3-/- HEK293T cells.

first: Xiaomei

last: He

first: Yen-Yu

last: Yang


title: METTL3 Promotes Histone H3K9 Acetylation through Recruitment of Histone Acetyltransferase 1 to Chromatin (ChIP-Seq)

overall_design: Genome-wide profiling analysis of H3K9Ac in HEK293T cells, the isogenic METTL3-/- cells, and the knockout cells complemented with wild-type or catalytically inactive METTL3


title: Gene expression of Mycobacterium tuberculosis and infected macrophages using bacilli log phase and NRP1/NRP2 phases

city: CDMX

first: Addy

middle: Cecilia

last: Helguera-Repetto

state: CDMX

address: Montes Urales

department: Inmunobioquímica

country: Mexico

institute: Instituto Nacional de Perinatología "Isidro Espinosa de los Reyes"

summary: In order to stablish differences between M. tuberculosis gene expression when different growth conditions are used in a macrophage infection model (Log, NRP1 and NRP2 stages), we have designed a whole M. tb genome microarray combined with 173 human genes. RNA from bacilli and macrophages was isolated at 24h and 48h post infection. Microarrays were hybridized usign a combination of mycobacterial and human RNA and expression level was assesed using the Agilent SureScan Microarray Scanner. Then, data were normalized and differential expression was analyzed.

overall_design: M. tuberculosis (bacilli either in Log phase, NRP1 phase or NRP2 phase) and macrophages gene expression obtained from the infection model  was measured at 24 h and 48 h post infection (MOI 5.0 was used for infection)  Two independent experiments were performed at each time (24 h or 48 h).

first: Samantha

last: Yong-Mendoza

first: Brayan

last: Rodriguez-Romero

first: Rodrigo

last: García-Herrera


title: Transcriptomic Changes in Mouse Trophoblast Cells Following Oxycodone Exposure

city: Columbia

first: Pallav

last: Singh

address: CE720 Clinical Support and Education

department: Institute for Data Science and Informatics

institute: University of Missouri

summary: Pregnant women are increasingly being prescribed and others are abusing opioid drugs. Neonates prenatally exposed to opioids are at risk for neonatal abstinence syndrome (NAS) that is linked with poor fetal and infant outcomes and possible diseases later in life. As the primary communication organ between mother and conceptus, the placenta is potentially vulnerable to opioid effects but may be key to understanding how these drugs affect long-term offspring health and how poor health outcomes may be ameliorated in utero. We have demonstrated maternal oxycodone (OXY) treatment in mice reduced parietal trophoblast giant cell (pTGC) area. OXY exposure affected placental gene expression profiles, including genes unique to the placenta. These gene expression patterns correlated with placental histological changes induced by OXY. We hypothesize that particular trophoblast (TB) cells of the mouse, most likely the pTGC, and probably certain TB subpopulations of the human placenta are particularly vulnerable to OXY exposure. To follow-up on these results, effects of OXY on transcriptome profiles of TB stem cells (TSC) and those differentiated into pTGC were examined and compared to control counterparts. Findings reveal OXY exposure induced distinct transcriptomic change in TSC and pTGC. Transcripts altered in TSC are generally enriched in the embryonic brain, whereas, those affected in the pTGC, including several prolactin and cathepsin forms, are associated with the placenta. Data suggest developmental exposure to OXY might alter similar gene-sets in TSC and the developing brain. Such findings may thus provide early diagnostic biomarkers and targets to prevent diseases associated with opioid-exposed NAS.

overall_design: RNA samples were collected from either undifferentiated mouse trophoblast stem cells (mTSCs) or parietal trophoblast giant cells (pTGCs); the cells were treated with either 10 ug/mL oxycodone or 0.9% saline solution; each treatment group has four replicates; the mTSCs are a control against the pTGCs, and the saline treated samples are a control against the oxycodone-treated samples

first: Cheryl

last: Rosenfeld

first: R

last: Roberts

first: Trupti

last: Joshi

first: Jessica

last: Kinkade


title: Integrated control of mitochondrial dynamics and cancer cell stemness by σ1 receptor

city: Bellinzona

first: Giada

last: Sandrini

address: Via Chiesa 5

institute: IOR

summary: Tumor cells endowed with cardinal stem cell properties are pervasively present in human cancers. Cancer stem cells (CSCs) play an essential role in metastasis, treatment resistance, and disease recurrence. Therefore, strategies to eradicate CSCs could increase the treatment efficacy and produce more durable clinical remissions in cancer patients. Mitochondrial dynamics is critical for controlling the balance between self-renewal and differentiation of stem cells. Although the underlying molecular mechanisms remain elusive, the link between mitochondria and stemness may provide opportunities for discovering innovative treatment approaches. Here, we provide evidence of a functional link between mitochondria, the Wnt/β-catenin pathway, and the σ1R receptor (σ1R), a unique ligand-activated chaperon protein residing at the endoplasmic reticulum (ER)-mitochondria contact sites. We show that the σ1R/mitochondria/β-catenin axis is crucial for executing the stem cell program and represents a vulnerability in CSCs. Inhibiting σ1R with synthetic antagonists or genetic knockdown disrupts mitochondrial dynamics and Wnt/β-catenin signaling leading to loss of self-renewal and progressive exhaustion of the CSC progeny. Activation of σ1R/mitochondria/β-catenin signaling occurs preferentially in metastatic castration-resistant prostate cancer (CRPC) compared to hormone-naïve primary tumors and is associated with clinical progression. The critical role of σ1R in controlling the tumor-initiating capability of CSCs provides novel avenues for anticancer drug discovery.mamamilan

overall_design: RNA-seq analysis of DU145 with shSigma-1 and shCtrl in two culture condition: adhesion and tumor sphere.

first: Gianluca

last: Civenni

first: Carlo

middle: V

last: Catapano


title: METTL3 Promotes Histone H3K9 Acetylation through Recruitment of Histone Acetyltransferase 1 to Chromatin

last: Wang


title: De novo methylation enforces long-term lineage-specific programing of TFH and TH1 memory cells [WGBS]

city: Salt Lake City

first: Jeffrey

middle: Scott

last: Hale

state: Utah

address: 15 North Medical Drive

department: Pathology

institute: University of Utah

summary: In this study, we used whole genome methylation analyses of naive cells and Tfh and Th1 cell subsets at the effector and memory cell stages to identify dynamic programing changes in DNA methylation. We identified lineage-specific demethylation and de novo methylation programs that were acquired during effector cell differentiation and were stably maintained in memory cells subsets.

overall_design: Mouse antigen-specific CD4 T cells (SMARTA TCR Transgenic) were sorted from spleens of non-infected mice (CD4 T cell naïve samples), LCMV Armstrong infected mice at day 7 post-infection (effector Th1 and effector Tfh samples) and at day 75-92 post-infection (memory Th1 and memory Tfh samples) for whole genome bisulfite sequencing (WGBS).

first: Camille

middle: L

last: Novis

first: Mark

middle: E

last: Wadsworth

first: Katheryne

last: Varley

first: J


title: A facile dCAS9-M. EcoGII system for targeted DNA 6mA methylation in living cell

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

summary: DNA methylation plays vital roles in multiple biological processes. N6-methyladenine (6mA), a prevalent DNA modification in prokaryotes, has recently been shown to play functional roles in eukaryotic cells with diverse distributions. However, the prevalence of 6mA and its functional roles at specific genomic regions have yet to be clearly established. Here, we developed a facile and versatile approach for locus-specific 6mA installation. We fused a nuclease dead Cas9 (dCas9) with an engineered N6‑deoxyadenine methyltransferase M. EcoGII, which could achieve rapid and efficient 6mA methylation at targeted genomic locus. By using our system, we have successfully introduced 6mA onto tested gene promoter regions. We have observed a repressive role of 6mA in gene transcription regulation. We also validated a positive correlation between 6mA and H3K9Me3 in tumor suppressor genes such as RASSF2 and AKAP6. This new approach provides a direct way for depiction of basic roles of 6mA in specific genomic locus and expands the toolkit for epigenetic regulation.

overall_design: We profiled geome-wide 6mA together with paired IgG samples.

first: Liangzhi

last: Luo

first: Ziyang

last: Hao

first: Chuan

last: He


title: High-throughput single cell RNA-sequencing of developing lens for cataract gene discovery

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

summary: The eye lens contains anteriorly localized epithelial cells (anterior epithelium of lens, AEL) and posteriorly localized fiber cells (FCs). Cells in the AEL are further distinguished based on their proliferative indexes, while FCs can be distinguished based on their differentiation stages. Thus far, lens transcriptomics has focused on whole lens tissue samples or entire populations of AEL or FCs, and has provided key insights into lens pathobiology. Now, with recent advances, single-cell RNA-sequencing (scRNA-seq) can inform on cell-specific transcript heterogeneity and lead to new insights into pathological changes in individual cells that may contribute toward cataract. To make this approach practicable for wide applicability, we developed a working protocol for lens scRNA-seq that can be applied to tissue samples subjected to short-term storage, and used it to characterize embryonic and newborn mouse lens.

overall_design: Mouse lenses were micro-dissected at embryonic day (E) 16.5 and postnatal day (P) 0 followed by dissociation with Collagenase/Dispase and TrypLE to obtain a single-cell suspension, followed by cell viability/counts estimates. The cell suspension was frozen for transport and thawed and further processed prior to scRNA-seq library preparation and automated sequencing. Data was analyzed using 10x Genomics data-analysis and Seurat tools.

first: Salil

last: Lachke


title: Integrating multi-omics data with genome scale metabolic modeling for the analysis of Pseudomonas aeruginosa persister cells

city: Charlottesville

first: Jason

last: Papin

state: Virginia

address: 415 Lane Road Room 2041

department: Biomedical Engineering

institute: University of Virginia

summary: Pseudomonas aeruginosa is a Gram-negative multi-drug resistant bacterial pathogen, capable of forming environmentally-resistant subpopulations known as persister cells. These cells are transient phenotypic variants that are able to tolerate antimicrobial treatment and have been implicated in the recalcitrant nature of chronic infections and in the resistance to disinfection. While persister cells are classically associated with reduced metabolic activity, the characteristics of their metabolism are not well understood. In this work, we performed an experimental and computational systems-level analysis to characterize the metabolic state of persister cells. To accomplish this, we deeply profiled both wildtype and persister samples of P. aeruginosa with transcriptomic sequencing and metabolomic analyses. This revealed a distinct metabolic repertoire in persister cells, marked by an increase in central metabolism activity. To aid in the analysis, integration of both the transcriptomic and metabolomic datasets with a P. aeruginosa genome-scale metabolic network reconstruction (GENRE) provided condition-specific models of the persister and untreated states. We then used the model of persister cell metabolism to hypothesize single-gene targets of persister cell viability. Experimental testing of model predictions suggested that persister cells are robust to single-gene deletions and that combinatorial targeting strategies may be necessary to completely inhibit the persister phenotype. Using this approach, we gained insight into P. aeruginosa persister cell metabolism and highlighted possible combinatorial gene targeting strategies to inhibit the development of the persister cell phenotype.

overall_design: RNA was extracted from untreated and persister Pseudomonas aeruginosa (PA14) cells immediately before exposure, 5 and 24 hours after exposure to 10X MIC conditions.

first: Anna

last: Blazier

first: Glynis

last: Kolling

first: Joseph

middle: M

last: Ficarrotta


title: Pou5f3 and Nanog organize active chromatin in three dimensions

city: Cambridge

first: Aleksandra

last: Galitsyna

state: Massachusetts

address: 77 Massachusetts Avenue

department: IMES

institute: Massachusetts Institute of Technology

summary: Zygotic genome in zebrafish embryogenesis is activated by transcription factors Pou5f3, Sox19b and Nanog. While it  was previously demonstrated, that these factors displace nucleosomes and create the regions of open chromatin, their role in three-dimensional genome organisation was not studied. Here we show, that large-scale chromatin structures, TADs and compartments, form independently of Pou5f3, Sox19b and Nanog. However, Pou5f3 and Nanog are required for formation of small-scale 3D active chromatin structures which we call "fountains".

overall_design: To investigate if Pou5f3, Sox19b and Nanog play a role in 3D organization of chromatin , we compared 3D chromatin maps using Hi-C method in the wild-type, single, double and triple mutants by these factors. Hi-C was performed shortly before zygotic genome activation ( 2.75 hours post-fertilization, or hpf), and after zygotic genome activation, at late blastula stage ( 5.3 hpf). To characterize the developmental  changes of 3D chromatin , we also performed Hi-C on the wild-type at 11 hpf and 25 hpf.

first: Sergey

last: Ulianov

first: Daria

last: Onichtchouk


title: Microbial activation of intestinal TLRs is critical for the establishment of normal behavior

city: Hamilton

first: Premysl

last: Bercik

state: ON

address: 1280 Main St W

institute: McMaster University


title: Colonic gene expression in mice mono-colonized with E.coli HA107

summary: The gut microbiota can influence brain function and behaviour through several mechanisms. The first critical step that initiates microbial-host interaction which leads to the establishment of normal behavior is unknown. In this study, we identified that activation of the innate immune system by microbes is a critical step in the initiation of the gut-brain communication. We showed that bacterial mono-colonization was sufficient to initiate the normalization of behavior which critically depends on Toll-like receptors. To investigate the mechanisms by which immune system activation affects behavior, we assessed the colonic immune gene expression profile from germ-free Swiss Webster and MyD88-/- Ticam-/- mice before and after mono-colonization with E.coli HA107 bacterial strain. To identify the relevant pathways, we searched for genes that fulfilled the criteria based on the behavioral tests: (1) change in transcripts at 2 weeks and (2) similar expression between 2 and 4 weeks post-colonization in C57BL/6 mice; 3) unchanged expression in MyD88-/- Ticam-/- mice. These criteria were fulfilled by 26 genes, mainly related to the innate immunity. Ingenuity pathway analysis revealed that many were related both to immune function and neural development and behavior. These results raise the possibility that impaired postnatal microbiota-host cross talk could affect normal brain maturation process and lead to altered neurodevelopment and psychiatric disorders later in life.

overall_design: We extracted total RNA of colonic tissues from germ-free (GF) Swiss Webster and MyD88-/- Ticam-/- mice before and after mono-colonization with E.coli HA107 bacteria. We pooled together RNA samples from 20 GF and 20 mono-colonized group to form a representative samples. We finally ran 11 samples in total through the NanoString nCounter® Gene Expression CodeSet for mouse inflammation genes.

first: Vivek

last: Philip


title: Brain gene expression in mice mono-colonized with E.coli HA107

summary: The gut microbiota can influence brain function and behaviour through several mechanisms. The first critical step that initiates microbial-host interaction which leads to the establishment of normal behavior is unknown. In this study, we identified that activation of the innate immune system by microbes is a critical step in the initiation of the gut-brain communication. We showed that bacterial mono-colonization was sufficient to initiate the normalization of behavior which critically depends on Toll-like receptors. To investigate the mechanisms by which immune system activation affects behavior, we assessed the brain region specific (hippocampus and amygdala) gene expression from germ-free Swiss Webster mice before and after mono-colonization with E.coli HA107 bacterial strain. Gene expression analysis showed that colonization affected multiple pathways related to innate immunity and neuronal function, including canonical pathway of glucocorticoid receptor that play key role in regulating emotion and cognition. Several genes directly involved in neuronal plasticity were altered by colonization, including phenotypic switch in NMDA receptors subunits, which in conventional animals is observed after birth and possibly linked to initial exposure to microbiome. These results raise the possibility that impaired postnatal microbiota-host cross talk could affect normal brain maturation process and lead to altered neurodevelopment and psychiatric disorders later in life.

overall_design: We extracted total RNA of hippocampus and amygdala brain regions from germ-free (GF) Swiss Webster and MyD88-/- Ticam-/- mice before and after mono-colonization with E.coli HA107 bacteria. We pooled together RNA samples from 10 GF and 10 mono-colonized group to form a representative samples. We finally ran 6 samples in total through the NanoString nCounter® Mouse Gene Expression Custom CodeSet.


title: Altas of gene expression in mice liver during liver regeneration process post 2/3 partial hepatectomy using RNA-seq

city: Beijing

first: Xian

last: Liu

address: 38 Life Science Park Street

institute: Beijing Institute of Life Omics

summary:
Purpose: The goal of this study is to profile genes expression in mice liver during liver regeneration process post 2/3 partial hepatectomy using RNA-seq.
Methods: Mice aged 8~10 weeks were performed with either 70% partial hepatectomy(PH) or shamed operation. At 0.5h, 2h, 4h, 24h, 48h, 72h, 120h, 168h post PH and after shamed operation, mice (six at each time point) were killed and liver samples were harvested. Total RNA were prepared from the liver samples using TRIZOL reagent (Invitrogen), and the mRNA profiles were genenated by Illumina HiSeq 2000. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: Our study provides a realiable dataset covering the three phases of liver regeneration: primer phase(0.5h,2h,4h), proliferation phase (24h, 48h, 72h), and termination phase (120h,168h). Using this dataset, we discover some interesting facts undiscovered before, especially on the re-organization process after proliferation wave and the termination phase.

overall_design: mRNA profiles at 0.5h, 2h, 4h, 24h, 48h, 72h, 120h, 168h post hepatectomy and sham group were generated by deep sequencing, each group has two pooled samples (three samples were pooled into one).

first: Miao

last: Yu

first: Xiaoming

last: Yang


title: ISO-seq analysis during sex reversal in Monopterus albus

status: Public on Nov 30 2025

city: Wuhan

first: Yuan

last: Zhao

address: Donghu Road 7th

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: The rice field eel (Monopterus albus) is an economically important freshwater-farmed fish with natural sex reversal characteristics, which results in low egg production and seedling shortage. Limited epigenomic and transcriptomic information during sex reversal hinders research on the reproductive development of Monopterus albus. In this investigation, 9 key stages during sex reversal were collected for multi-omics experiments, including PacBio Iso-seq, RNA-seq and ATAC-seq. Through combined analysis of Iso-seq and RNA-seq, we constructed more accurate transcript annotation than those from NCBI. A total of 37,911 unannotated transcripts were obtained, including transcripts from novel genes and alternative splicing structures, etc. The noteworthy point is that our annotations have more precise polyA locations. In addition, we identified multiple potential cis-regulatory elements with high confidence based on changes in chromatin accessibility by ATAC-seq, providing precise targets for regulating gene expression and thereby modulating gonadal development. In summary, we provides a comprehensive and convenient data resource for studying sex reversal-related mechanisms from multiple perspectives.

overall_design: ISO-seq of mixture of female (PVO, VO, and MO stages), intersex ((ISE, ISM,  and ISL stage), and male ( ES, MS, and LS stage) during sex reversal in Mpnopterus albus.


title: Transcriptome analysis during sex reversal in Monopterus albus

overall_design: RNA-seq profiling of  female (PVO, VO, and MO stages), intersex (ISE, ISM,  and ISL stage), and male ( ES, MS, and LS stage) during sex reversal in Mpnopterus albus.


title: Chromatin accessibility analysis during sex reversal in Monopterus albus

overall_design: ATAC-seq profiling of  female (PVO, VO, and MO stages), intersex ((ISE, ISM,  and ISL stage), and male ( ES, MS, and LS stage) during sex reversal in Mpnopterus albus.


title: Revealing the mechanism of high altitude adaptation in poikilotherm: an intraspecific comparative transcriptomic analysis in a toad-headed lizard, Phrynocephalus vlangalii

city: Hangzhou

first: Haojie

last: Tong

address: No.258, Xueyuan St.

department: School of life Sciences

institute: China Jiliang University

summary: Background: Hypoxia, low temperature and intensive ultraviolet are three of the top ecological factors that restrict the survival of high altitude living organisms. Previous studies mainly focused on the adaption mechanisms of endothermic organisms rather than poikilotherm at high altitudes. In this work, we aimed to identify several candidate genes that may be related to high-altitude adaptation in poikilotherm by comparing the transcriptomes of Phrynocephalus vlangalii from different elevations. Results: We performed Illumina sequencing for the two populations, Madoi and Maqu, about 80 million sequence reads were obtained, respectively. A total of 60,725 and 49,638 transcripts for each population were generated by de novo assembly. We also identified 140 genes that have undergone strong positive selection (Ka/Ks>1) and 352 protein-coding genes that may have experienced potential positive selection (1≥Ka/Ks>0.5) after comparison to the orthologous transcripts. By considering their functions, among 140 genes with Ka/Ks>1, 11 genes were most possibly related to high altitude adaptation, including six genes related to hypoxia adaption, three genes associated with cold adaption, and two ultraviolet adaption related genes. In addition, fourteen genes that were associated with high altitude adaptation among 352 genes that may experience potential positive selection. Finally, we discovered similar gene expressions between the two populations, but different on all the unigenes and candidate genes (Ka/Ks>0.5).Conclusions: We preliminary studied the high altitude adaptation mechanisms of P. vlangalii. By comparing the two populations inhabiting different altitudes, we identified a series of candidate genes that may have promoted adaption for the high-elevation distributed population of P. vlangalii. And it is notable that the expression level of all the candidate genes was also relatively higher than all the unigenes. Thus, future research is necessary to better understand the impacts of these candidate genes on high altitude adaptation. We also found the evidence for convergent evolution on some genes between endothermic and poikilothemic species, but further research of ectotherm are requisite to better understand the complicated mechanisms of high altitude adaptation.

overall_design: This study employed Trinity, BLAST program and KaKs_CALCULATOR program for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 2 different populations of Phrynocephalus vlangalii (Madoi and Maqu).

first: Kailong

last: Zhang

first: Yuanting

last: Jin