title: TRMT1L-catalyzed m22G27 on tyrosine tRNA is required for efficient mRNA translation and cell survival under oxidative stress. [Nano-tRNAseq]

status: Public on May 08 2024

city: Houston

first: Catherine

last: Denicourt

address: 6431 Fannin St

department: Integrative Biology and Pharmacology

institute: The University of Texas HSC Houston

summary: Mapping of the epitranscriptome has revealed the chemical diversity of RNA modifications and their functional importance in regulating gene expression. Transfer RNAs (tRNAs) are one of the most modified cellular RNAs, containing on average 10-13 modifications per molecule. These modifications have been shown to be critical for several aspects of tRNA functions, such as decoding, folding, and stability. Here we report that the human RNA methyltransferase TRMT1L associates with components of the Rix1 ribosome biogenesis complex and co-sediments with pre-60S ribosomes. Using eCLIP-Seq, we show that TRMT1L binds to a subset of tRNAs and to the 28S rRNA. Additionally, we demonstrate that TRMT1L is responsible for catalyzing N2, N2-dimethylguanosine (m22G) solely at position 27 of tRNA-Tyr-GUA by Nano-tRNAseq and RNA LC-MS. Surprisingly, TRMT1L depletion also impaired the deposition of acp3U and dihydrouridine on tRNA-Tyr-GUA, Cys-GCA, and Ala-CGC. TRMT1L knockout cells have a marked decrease in tRNA-Tyr-GUA levels, coinciding with a reduction in global translation rates and hypersensitivity of oxidative stress. Our results establish TRMT1L as the elusive methyltransferase catalyzing the m22G27 modification on tRNA Tyr, resolving a long-standing gap of knowledge and highlighting its potential role in a tRNA modification circuit crucial for translation regulation and stress response.

overall_design: Purified tRNAs isolated from WT and TRMT1L KO HCT116 cells were processed for Nano-tRNAseq to identify TRMT1L regulated tRNA modifications. The base calling errors (base mismatch, insertion and deletion) for each nucleotide position and tRNA iso-decoder reference were calculated for each duplicate sample.

first: Sseu-Pei

last: Hwang

first: Han

last: Liao

first: Katherine

last: Barondeau

first: Xinyi

last: Han

first: Cassandra

last: Herbert

first: Hunter

last: McConie

first: Amirtha

last: Shekar

first: Dimitri

last: Pestov

first: Patrick

last: Limbach

first: Jeffrey

middle: T


title: Single Cell Sequencing of Human Langerhans Cells Identifies Altered Gene Expression Profiles in Patients with Atopic Dermatitis

status: Public on May 03 2024

city: Amsterdam

first: Nina

last: van Sorge

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

type: Expression profiling by high throughput sequencing

summary: Atopic dermatitis (AD) is characterized by dysregulated T cell immunity and skin microbiome dysbiosis with predominance of Staphylococcus aureus (S. aureus). Emerging evidence suggests a role for S. aureus in exacerbating AD skin inflammation. Interestingly, specific glycosylation of S. aureus cell wall structures amplifies skin inflammation through interaction with Langerhans cells (LCs). However, the role of LCs in AD remains poorly characterized. Here, we performed single cell RNA-sequencing of primary epidermal LCs and dermal T cells isolated from skin biopsies of AD patients and healthy controls, alongside specific glycoanalysis of S. aureus strains isolated from the AD lesions. Our findings reveal four LC subpopulations, including two steady-state clusters (LC1 and LC1H) and two pro-inflammatory/matured subsets (LC2 and migratory LCs). The latter two subsets were enriched in AD skin. AD LCs showed enhanced expression of C-type lectin receptors, the high-affinity IgE receptor (FcεR1), and activation of prostaglandin and leukotrienes biosynthesis pathways, as well as upregulated transcriptional signatures related to T cell activation pathways and increased expression of CCL17 (specifically LC2) compared to healthy LCs. Correspondingly, T helper 2 and regulatory T cell populations were increased in AD lesions. Our study provides proof-of-concept for an active role of LCs in connecting the S. aureus-T cell axis in the AD inflammatory cycle.

overall_design: Single cell RNA sequencing (sort-seq) of human epidermal Langerhans cells and dermal T cells from atopic dermatitis patients (n=4 for LCs n=3 for T cells) and healthy controls (n=3)

first: Sara

middle: M

last: Tamminga

first: Marlot

last: van der Wal

first: Femke

last: van Wijk


title: Haploinsufficient phenotypes promote selection of PTEN and ARID1A deficient clones in human colon.

status: Public on May 13 2024

city: Cambridge

first: Nefeli

last: Skoufou-Papoutsaki

address: Robinson Way

country: United Kingdom

institute: University of Cambridge

summary: Normal human tissues are known to be composed of a pactchwork of mutant clones but with limited implications on cancer risk. PTEN and ARID1A deficient clones were detected in the human colon using immunohistrochemistry and were found to be the product of monoallelic loess. They were associated with a bias in clone dynamics which resulted in positive selection in the tissue. Heterozygous mutations were introduced in intestinal organoids which were subjected to bulk RNA-seq to describe the molecular mechanisms behind their positive selection. Although PTEN het organoids were associated with an advantageous phenotype in organoids, which was recapitulated in the transcriptomic analysis with increase proliferation and upregulation of developmental/regenerative processes and metabolic reprogramming, the ARID1A het organoids showed reduced growth which was seen as upregulation of apoptosis and downregulation of DNA replication. The discrepancy between the tissue and organoid phenotype for ARID1A was later explained due to the impact on stromal cells which are found in the tissue and are mediating the selective advantage. Importantly these molecular alterations and behaviours arise due to haploinsufficiency of these tumour suppressors in a pre-neoplastic context.

overall_design: We subjected the generated heterozygous organoids to bulk RNA-seq to study the molecular effects of the monoallelic gene loss. PTEN het, ARID1A het, WT and PTEN KO- 4 replicates each that were different isogenic clones


title: Nitric oxide inhibits ten-eleven translocation DNA demethylase activity to regulate 5mC and 5hmC across the genome [RNA-seq]

status: Public on May 01 2024

city: Chicago

first: Douglas

middle: David

last: Thomas

state: Illinois

address: 900 S Ashland Ave

department: Pharmaceutical Sciences

country: USA

institute: University of Illinois Chicago

summary: DNA methylation at cytosine bases of eukaryotic DNA (5-methylcytosine, 5mC) is a heritable epigenetic mark that can regulate gene expression in health and disease. Enzymes that metabolize 5mC have been well-characterized yet the discovery of endogenously produced signaling molecules that regulate DNA methyl-modifying machinery have not been described. Herein, we report that the free radical signaling molecule nitric oxide (NO) can directly inhibit the Fe(II)/2-OG-dependent DNA demethylases ten-eleven translocation (TET) and Human AlkB homolog 2 (ALKBH2). Physiologic NO concentrations reversibly inhibited TET and ALKBH2 demethylase activity by binding to the mononuclear non-heme iron atom in place of O2 to form a dinitrosyliron complex (DNIC). In cancer cells treated with exogeneous NO, or cells endogenously synthesizing NO, there was a global increase in DNA 5mC, a substrate for TET, that could not be attributed to increased DNA methyltransferase activity. 5mC was also elevated in NO-producing mouse xenograft and patient derived xenograft tumors. Genome-wide DNA methylome analysis of cells chronically treated with NO (10 days) demonstrated enrichment of 5mC at gene-regulatory loci which correlated to the expression of NO-regulated tumor-associated genes. Regulation of DNA methylation is distinctly different from canonical NO-signaling and represents a novel epigenetic regulatory mechanism of NO.

overall_design: To assess whether nitric oxide (NO) altered gene expression patterns, we conducted RNA sequencing (RNA-seq) on cells treated with 100 uM DETA/NO or untreated for 10 days. For this study we used two triple-negative breast cancer cell lines, MDA-MB-231 and MDA-MB-468.


title: Nitric oxide inhibits Ten-eleven translocation DNA demethylase activity to regulate 5mC and 5hmC across the genome

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: TRMT1L-catalyzed m22G27 on tyrosine tRNA is required for efficient mRNA translation and cell survival under oxidative stress. [eCLIP-seq]

first: Catherine

state: TX

overall_design: RNAs binding to TRMT1L in HCT116 and HeLa cells were analyzed by eCLIP-seq to identify the potential RNA substrates of TRMT1L. The experiment was done in biological duplicates. Each biological replicate has a IP sample and a control size-matched input (SMInput) sample.

middle: A

last: Chang


title: Nitric oxide inhibits Ten-eleven translocation DNA demethylase activity to regulate 5mC and 5hmC across the genome [oxRRBS]

overall_design: To assess whether nitric oxide (NO) altered DNA methylation and/or hydroxymethylation patterns, we conducted oxidative reduced representation bisulfite sequencing (oxRRBS) on cells treated with 100 uM DETA/NO or untreated for 10 days. For this study we used two triple-negative breast cancer cell lines, MDA-MB-231 and MDA-MB-468.


title: The Effect of Adolescent Environmental Enrichment and Social Defeat on the Nucleus Accumbens and Hippocampus in a Selectively Bred Model with Anxious Phenotype (bLR Rats): RNAseq data

city: Ann Arbor

first: Megan

middle: Hastings

last: Hagenauer

state: MI

address: 205 Zina Pitcher Pl.

department: MBNI

institute: University of Michigan

summary: Stress is a major influence on mental health status; the ways that individuals respond to or copes with stressors determine whether they are negatively affected in the future. Stress responses are established by an interplay between genetics, environment, and life experiences. Psychosocial stress is particularly impactful during adolescence, a critical period for the development of mood disorders. In this study we compared two established, selectively-bred Sprague Dawley rat lines, the “internalizing” bred Low Responder (bLR) line versus the “externalizing” bred High Responder (bHR) line, to investigate how genetic temperament and adolescent environment impact future responses to social interactions and psychosocial stress, and how these determinants of stress response interact. Animals were exposed to social and environmental enrichment in adolescence prior to experiencing social defeat and were then assessed for social interaction and anxiety-like behavior. Adolescent enrichment caused bLR rats to display less social avoidance, more social interaction, less submission during defeat, and resilience to the prolonged effects of social stress on corticosterone, while enrichment caused bHR animals to show greater aggression during defeat and during a neutral social encounter, and decreased anxiety-like behavior. To gain insight into the development of social resilience in the anxious phenotype bLRs, RNA-seq was conducted on the hippocampus and nucleus accumbens, two brain regions that mediate stress regulation and social behavior. Gene sets previously associated with stress, social behavior, aggression and exploratory activity were enriched with differential expression in both regions, with a particularly large effect on gene sets that regulate social behaviors. These findings provide further evidence that adolescent enrichment can serve as an inoculating experience against future stressors. The ability to induce social resilience in a usually anxious line of animals by manipulating their environment has translational implications, as it underscores the feasibility of intervention strategies targeted at genetically vulnerable adolescent populations.

overall_design: The RNA-sequencing component of this study examined gene expression in the nucleus accumbens (NACC) and hippocampus (HC) in male bLR rats that had either experienced social and environmental enrichment (EE) or standard housing (NIL) during adolescence (P35-P60), and then received either four days of social defeat (SD: P61-64) or a no defeat control condition (NIL). All animals then received behavioural testing (P65-67) to measure social interaction and anxiety-like behavior (elevated plus maze). On P68, the animals were sacrificed. Brain tissue from the nucleus accumbens and hippocampus was collected for RNA-Sequencing, and blood was collected for plasma hormone measurements (corticosterone, testosterone). When reusing this data, please note that many of the batch-related or technical variables (generation, dissection date, RNA extraction date, RNA concentration) were found to influence behavioral, hormonal, or gene expression findings and should be included as co-variates in models when applicable.

first: Angela

last: O'Connor

middle: H

first: Pamela

last: Maras

first: Elaine

middle: K

last: Hebda-Bauer

first: Fan

last: Meng

first: Stanley

middle: J

last: Watson

first: Huda

last: Akil


title: To Be or Not to Be - Decoding the Trabecular Meshwork Cell Identity

status: Public on Apr 26 2024

first: Alice

middle: Yuxuan

last: Tian

email: ayt2@rice.edu, alicet.3993@gmail.com

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: The trabecular meshwork within the conventional outflow apparatus is critical in maintaining intraocular pressure homeostasis. In vitro studies employing primary cell cultures of the human trabecular meshwork (hTM) have conventionally served as surrogates for investigating the pathobiology of TM dysfunction. Despite its abundant use, translation of outcomes from in vitro studies to ex vivo and/or in vivo studies remains a challenge. Given the cell heterogeneity, performing single-cell RNA sequencing comparing primary hTM cell cultures to hTM tissue may provide important insights on cellular identity and translatability, as such an approach has not been reported before. In this study, we assembled a total of 14 primary hTM in vitro samples across passages 1-4, including 4 samples from individuals diagnosed with glaucoma. This dataset offers a comprehensive transcriptomic resource of primary hTM in vitro scRNA-seq data to study global changes in gene expression in comparison to cells in tissue in situ. We have performed extensive preprocessing and quality control, allowing the research community to access and utilize this public resource.

overall_design: 14 human eye trabecular meshwork primary cell culture sc-RNA-seq samples were compared to 3 post-mortem sc-RNA-seq samples

first: Hasna

last: Baidouri

first: Sangbae

last: Kim

first: Jin

last: Li

first: Xuesen

last: Cheng

first: Yumei

first: Rui

last: Chen

first: VijayKrishna

last: Raghunathan


title: Transcriptomic and lipidomic analysis of the differential pathway contribution for the incorporation of erucic acid to triacylglycerol during pennycress seed maturation

status: Public on Apr 25 2024

city: Zaragoza

first: Miguel

last: Alfonso

state: Aragón

address: Avda. Montañana 1005

department: Plant Biology

country: Spain

institute: CSIC

summary: Thlaspi arvense (Pennycress) is an emerging feedstock for biofuel production because of its high seed oil content enriched in erucic acid. A transcriptomic and a lipidomic study were performed to analyze the dynamics of gene expression, glycerolipid content and acyl-group distribution during seed maturation. Genes involved in fatty acid biosynthesis were expressed at the early stages of seed maturation. Genes encoding enzymes of the Kennedy pathway like TaDGAT1, TaLPAT or TaGPAT increased their expression with maturation, coinciding with the increase in TAG species containing 22:1. Positional analysis showed that the most abundant TAG species contained 18:2 at sn-2 position in all maturation stages, suggesting no specificity of the TaLPAT for VLCFAs. TaDGAT2 mRNA was more abundant at the initial maturation stages, coincident with the rapid incorporation of 22:1 to TAG, suggesting a coordination between DGAT enzymes for TAG biosynthesis. Genes encoding TaPDAT1, TaLPCAT or TaPDCT, involved in acyl-editing or PC-derived DAG/TAG biosynthesis showed also higher expression at the early maturation stages, coinciding with a higher proportion of TAG species containing C18 fatty acids. These results suggested a higher contribution of these two pathways at the early stages of seed maturation. LC-MS analysis of the content and acyl-group distribution of DAG and PC pools was compatible with the acyl content in TAG at the different maturation stages. Our data point to a model in which a strong temporal coordination between pathways and isoforms in each pathway, both at the expression and acyl-group incorporation, contributes to high erucic TAG accumulation in Pennycress.

overall_design:
Seeds from five developmental stages corresponding to GREEN (G, 12 days after flowering, DAF), GREENYELLOW (GY, 19 DAF), YELLOWGREEN (YG, 26 DAF), YELLOW (Y, 33DAF) and MATURE (M, 45 DAF), were chosen for analysis. Seeds separated from the pods, corresponding to these different maturation stages, harvested, frozen in liquid nitrogen, and stored at -80 ºC for further analysis.
RNA-Seq libraries were prepared and sequenced on an Illumina NovaSeq6000 at Novogene Ltd (www.novogene.uk). Ten libraries, corresponding to two biological replicates of the five different seed developmental stages
Comparative gene expression analysis of the RNA-Seq data for the GREEN, GREENYELLOW, YELLOWGREEN, YELLOW and MATURE seed maturation stages was performed.

first: Ana

last: Claver

first: Luján

last: María de los Ángeles

first: M

middle: V

last: López


title: Moderate Endurance Exercise increases Arrhythmia Susceptibility and modulates Cardiac Structure and Function in a Sex Dimorphic manner.

city: Pittsburgh

first: Sharon Ann

last: George

state: PA

address: 200 Lothrop Street W1355

institute: University of Pittsburgh

summary: While moderate endurance exercise has been reported to improve cardiovascular health , its effects on cardiac structure and function are not fully characterized, especially with respect to sex dimorphism. We aimed to assess the effects of moderate endurance exercise on cardiac physiology in male versus female mice.

overall_design: C57BL/6J mice of both sexes were run on a treadmill for six weeks. ECG and echocardiography were performed every two weeks. After six weeks of exercise, mice were euthanized, and RNA sequencing was performed to determine exercise-induced transcriptional changes.    and RNA sequencing was performed to determine exercise-induced transcriptional changes.

first: Sharon


title: SETD2 Mutations Do Not Contribute to Clonal Fitness in Response to Chemotherapy in Childhood B Acute Lymphoblastic Leukemia

city: New York

first: Sonali

last: Narang

state: NY

address: 435 east 30th street

institute: NYU Langone

type: Genome binding/occupancy profiling by high throughput sequencing


title: MECHANISMS UNDERLYING THE DIRECT PROGRAMMING OF MOUSE EMBRYONIC FIBROBLASTS TO THYMIC EPITHELIAL CELLS BY FOXN1 [RNA-seq]

status: Public on Apr 22 2024

city: Nashville

first: Seung Woo

last: Kang

state: TN

address: MRBIV 10475, 2215 Garland Avenue

department: Department of Cell and Developmental Biology

institute: Vanderbilt University

summary: Thymic epithelial cells (TECs) are a critical functional component of the thymus’s ability to generate T cells for the adaptive immune system in vertebrates. However, no in vitro system for studying TEC function exists. Overexpressing the transcription factor FOXN1 initiates transdifferentiation of fibroblasts into TEC-like cells (iTECs) that support T cell differentiation in culture or after transplant. In this study, we characterized iTEC programming at the cellular and molecular level to determine how it proceeds and identified mechanisms that can be targeted for improving this process. These data showed that iTEC programming consisted of discrete gene expression changes that differed early and late in the process, and that iTECs upregulated markers of both cortical and medullary TEC (cTEC and mTEC) lineages. We demonstrated that promoting proliferation enhanced iTEC generation, and that Notch inhibition allowed induction of mTEC differentiation. Finally, we showed that MHCII expression was the major difference between iTECs and fetal TECs. MHCII expression was improved by co-culturing iTECs with fetal double-positive T-cells. This study supports future efforts to improve iTEC generation for both research and translational uses.

overall_design: Programming process including MEF negative control, fetal TEC positive control, iTECs 2, 10 days post-programming. Additionally, we added iTECs 12 days post-reprogramming that are sorted based on an epithelial cell marker (Epcam) expression.

first: Zhongyao

last: Ma

first: Seung

middle: W


title: SETD2 Mutations Do Not Contribute to Clonal Fitness in Response to Chemotherapy in Childhood B Acute Lymphoblastic Leukemia (WES)

summary:
To investigate the impact of SETD2 mutations on clonal fitness in B actue lymphoblastic leukemia we generated cells lines with SETD KO using CRISPR/Cas9 system.
We then performed phenotypic based assays as well as gene expression profiling, mutation burden, and chromtain accessibilty analysis using data obtained from RNA-seq, Whole exom sequencing following drug traetment, and ATAC-seq.

overall_design: Mutation calling between pretreated and treated clone for KOPN-8 KO and WT clone. 3 clones of each cell line was subjected to treatment and sequences before and after treatment with chemotherap.

first: Gloria

middle: C

last: Yametti

first: Gabriel

last: Robbins

first: Ashfiyah

last: Chowdhury

first: Talia

last: Ostrow

first: Harrison

last: Kilberg

first: Josh

last: Greenberg

first: Lindsay

last: Kramer

first: Elizabeth

last: Raetz

first: Nikki

last: Evensen

first: William

middle: L

last: Carroll


title: Identifying suitable experimental designs to determining differentially expressed genes and benchmark doses from transcriptomic dose-response studies in zebrafish embryos

status: Public on Apr 17 2024

city: Ottawa

first: John

last: Stead

state: ON

address: 1125 Colonel By Drive

department: Department of Neuroscience

country: Canada

institute: Carleton University

summary: To identify suitable experimental designsfor toxicology experiments (i.e., sample size, pool size, number of biological replicates, and number of doses), we exposed zebrafish embryos to 0.1% dimethyl sulfoxide for 4-120 hours post fertilization. We then created 96 samples to examine the impact of pool size comprised of 1, 5, 10, and 20 zebrafish embryos each (n = 24). From these, total RNA extraction was extracted and transcriptomic analyses were done using the TempO-Seq S1500+ Surrogate Assay platform. Samples were sequencing on an Illumina NextSeq 2000. The data were simulated to conduct power analyses exploring suitable study designs for identification of differentially expressed genes and for benchmark dose analysis. The aim was to identify a feasible pool size and sample size that would yield an acceptable false discovery rate for these analyses.

overall_design: Samples were comprised of different pool sizes of embryos (i.e., 1, 5, 10, and 20 embryos per sample, indicated by Z1, Z5, Z10, and Z20) to identify optimal experimental designs for the dose-response study. Each pool size included 24 samples and a total of 96 samples were sequenced on the TempO-Seq S1500+ Surrogate assay platform. This study consisted of 12 extraction batches with 8 samples per batch and 3 batches per pool size.

first: Hyojin

last: Lee

first: Andrew

last: Williams

first: Ella

last: Atlas

first: Jan

last: Mennigen

first: Jason

last: O'Brien

first: Carole

last: Yauk


title: Identification of differential circRNA expression profiles in human macrophages induced by viru-lent and avirulent Mycobacterium tuberculosis strains

status: Public on Apr 10 2024

city: Wuhan

first: Yifan

last: Zhu

address: Huazhong Agricultural University, Wuhan, China

country: China

institute: HZAU

type: Non-coding RNA profiling by high throughput sequencing

summary: Tuberculosis is a chronic infectious disease caused by Mycobacterium tuberculosis (M.tb) infection, remains a leading cause of morbidity and mortality world-wide. Circular RNAs are non-coding RNAs with diverse functions. However, most M.tb related circRNAs remain undiscovered. We used circRNA-seq technology to sequence the THP-1 cells infected with virulent and avirulent M.tb strains for 12 h.

overall_design: circRNA-seq for THP-1 cells infected with virulent M.tb ( 1458 strain, clinic strain isolated from diseased cattle with TB) and avirulent M.tb ( H37Ra) strains for 12 h.

first: Aizhen

last: Guo


title: SETD2 Mutations Do Not Contribute to Clonal Fitness in Response to Chemotherapy in Childhood B Acute Lymphoblastic Leukemia (ATAC-Seq)

first: Sonali

last: Narang

overall_design: Comparative differential peak analysis of ATAC-seq for 697 and KOPN-8 cells SETD2 KO clones compared to WT. ATAC was performed in duplicate for each cell line.

first: Gloria

last: Yametti

first: Gabriel

last: Robbins

first: Ashfiyah

last: Chowdhury


title: Single cell RNA sequencing for normal and lymphangiogenesis-inhibiting vascular allografts

status: Public on Apr 12 2024

city: Hangzhou

first: Qingbo

last: Xu

address: 79 Qingchun Road

department: Department of Cardiology

institute: the First Affiliated Hospital, Zhejiang University School of Medicine

summary: Transplant arteriosclerosis is a major limitation to long-term survival of patients with solid organ transplantation. Although lymphatic vessels have been recently reported to possess organ-specific features in allograft transplantation, the relationship between lymphangiogensis and transplant arteriosclerosis remains unknown.

overall_design: This entry contains 10x Single-cell RNA-seq data of FACS sorted CD45+/- cells from normal or MAZ51-treating  mouse vascular allografts (Recipient: wild type (C57BL6/J); Donor: wild type (BALB/c thoracic artery).

first: Kai

last: Chen

first: Rong

last: Mou

first: Pengwei


title: Unstable EBV latency drives inflammation in multiple sclerosis patient derived spontaneous B cells [Batch2]

status: Public on Apr 04 2024

city: Philadelphia

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Epidemiological studies have demonstrated that Epstein-Barr virus (EBV) is an etiologic risk factor, and perhaps prerequisite, for the development of MS. EBV establishes life-long latent infection in a subpopulation of memory B cells. Although B cells play a key role in the pathobiology of MS, EBV-associated mechanisms of B cell inflammation and disease pathogenesis in EBV (+) B cells from MS patients are not well characterized. Accordingly, we obtained lymphoblastoid lines (LCLs) and spontaneous LCLs (SLCLs), distinguished by their transformation with lab strain (B95.8) or endogenous EBV, respectively, from MS patients and healthy controls to study host-virus interactions in B cells.  Here, we use transcriptomics and genomics-based approaches to identify differences in EBV gene expression and regulation of both viral and cellular genes in LCLs compared to SLCLs and between SLCLs generated from healthy controls and MS patients during “active” or “stable” periods of disease activity. We demonstrate increased lytic gene expression in SLCLs derived from MS patient B cells, especially those generated from peripheral blood mononuclear cells (PBMCs) obtained during “active” disease.

overall_design: RNASeq of LCLs and Spontaneous LCLs from MS patients and healthy controls

first: Samantha

middle: S

last: Soldan

first: Paul

last: Lieberman


title: Micro bulk sequencing on murine Bleomycin-induced fibrotic lungs sorted on SA-β-Gal and GD3

city: Nice

first: Julien

last: Cherfils-Vicini

address: 28 Avenue de Valombrose

country: France

institute: IRCAN - CNRS - INSERM

summary: Aging is marked by a progressive decline in physiological function, leading to an increased susceptibility to age-related diseases and cancer. On the cellular level, aging correlates with an accumulation of senescent cells, which play a dual role: they are critical for tissue homeostasis, yet their over-accumulation may drive pathological aging. We recently revealed that senescent cells could overexpress immunosuppressive molecules like the ganglioside GD3 at their cell surface to evade from immune surveillance and to facilitate their tolerogenicity. We investigate which cells expressed GD3 and whether this ganglioside could be considered as a new marker associated to senescence in a model of senescence associated disease: Bleomycin-induced lung fibrosis.

overall_design: To characterize GD3 positive cells we induced lung fibrosis in young C57Bl6/J male mice by Bleomycin instillation. After 27 days, we collected the lungs, dissociated them and labeled them for GD3 as well as a know senescence marker: SA-β-Gal. We then sorted the different fractions.

first: Iryna

last: Moskalevska

first: Lyvia

last: Moudombi

first: Marie

last: Michallet

first: Maude

last: Ardin

first: Anthony

last: Ferrari


title: MECHANISMS UNDERLYING THE DIRECT PROGRAMMING OF MOUSE EMBRYONIC FIBROBLASTS TO THYMIC EPITHELIAL CELLS BY FOXN1 [scRNA-seq]

first: Seung Woo

last: Kang

overall_design: 1. Programming process including MEF control, 3 days, and 12 days post-reprogramming. 2. The effect of NOTCH signal on the iTEC repgrogramming process (No Treat, Vehicle, DAPT every 24 hours, starting at 5 days post-programming for 7 days). 3. The effect of co-culturing with E16.5 foetal thymocytes on the iTEC reprogramming process (starting at 5 days post-programming for 5 days).

first: Seung


title: SETD2 Mutations Do Not Contribute to Clonal Fitness in Response to Chemotherapy in Childhood B Acute Lymphoblastic Leukemia (RNA-Seq)

first: Sonali

last: Narang

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 697 and KOPN-8 cells SETD2 KO clones compared to WT. RNA extraction and sequencing was done in triplicate for each line.

first: Gloria

first: Gabriel

first: Talia

last: Ostrow

first: Harrison

last: Kilberg

first: Josh

last: Greenberg

first: Lindsay

last: Kramer

first: Elizabeth

last: Raetz

first: Nikki

last: Evensen

first: William

last: Carroll


title: Unstable EBV latency drives inflammation in multiple sclerosis patient derived spontaneous B cells [Batch1]

first: Priyankara

last: Wickramasinghe

first: Samantha

last: Soldan

first: Paul


title: ATAC-seq analysis  in KPC1199 murine PDAC cell line with or without glutamine starvation

status: Public on Apr 30 2024

city: Shanghai

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

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

summary: We determined if up- and/or down-regulated genes in pancreatic tumor cells cultured under low-glutamine conditions were accompanied by alterations in genome-wide chromatin accessibility and then performed ATAC-seq of KPC1199 cells treated with low glutamine concentrations versus normal-media-treated controls.  The ATAC-seq was performed according to the TruePrep Tagment Enzyme for ATACseq kit (TD501, Vazyme). DNA libraries were constructed following the manufacturer’s instructions of the Trueprep index kit v2 (TD202, Vazyme) and thereafter sequenced to an average of 20 million reads per sample.

overall_design: For library preparation, murine PDAC cell lines with Cont, Low Gln were first established. ATAC-seq and DNA library were prepared according to manufacturer’s instructions.

first: Xuqing

last: Shen

first: Jing

last: Xue


title: Synergistic induction of blood-brain barrier properties

status: Public on Apr 18 2024

city: Frankfurt am Main

first: Ricardo

middle: Mamede

last: Figueiredo

address: Altenhöferallee 3

country: Germany

institute: GenXPro GmbH

summary: Blood–brain barrier (BBB) models derived from human stem cells are powerful tools to improve our understanding of cerebrovascular diseases and to facilitate drug development for the human brain. Yet providing stem cell–derived endothelial cells with the right signaling cues to acquire BBB characteristics while also retaining their vascular identity remains challenging. Here, we show that the simultaneous activation of cyclic AMP and Wnt/β-catenin signaling and inhibition of the TGF-β pathway in endothelial cells robustly induce BBB properties in vitro. To target this interaction, we present a small-molecule cocktail named cARLA, which synergistically enhances barrier tightness in a range of BBB models across species. Mechanistically, we reveal that the three pathways converge on Wnt/β-catenin signaling to mediate the effect of cARLA via the tight junction protein claudin-5. We demonstrate that cARLA shifts the gene expressional profile of human stem cell–derived endothelial cells toward the in vivo brain endothelial signature, with a higher glycocalyx density and efflux pump activity, lower rates of endocytosis, and a characteristic endothelial response to proinflammatory cytokines. Finally, we illustrate how cARLA can improve the predictive value of human BBB models regarding the brain penetration of drugs and targeted nanoparticles. Due to its synergistic effect, high reproducibility, and ease of use, cARLA has the potential to advance drug development for the human brain by improving BBB models across laboratories.

overall_design: Gene expression profiling analysis of human stem cell-derived brain-like endothelial cells treated with cARLA and control untreated cells (4 biological replicates per group).

first: Gergő

last: Porkoláb

first: Mária

last: Mészáros

first: Anikó

last: Szecskó

first: Judit

middle: P

last: Vigh

first: Fruzsina

middle: R

last: Walter

first: Ildikó

last: Kálomista

first: Gaszton

last: Vizsnyiczai

first: Jeng-Shiung

last: Jan

first: Fabien

last: Gosselet

first: Monika

last: Vastag

first: Natalie

last: Hudson

first: Matthew

last: Campbell

first: Szilvia

last: Veszelka

last: Deli


title: Transcriptome analysis of Streptococcus mutans quorum sensing-induced cells

status: Public on Apr 28 2024

city: Toronto

first: Delphine

last: Dufour

state: Ontario

address: 124 Edward Street

institute: Faculty of Dentistry, University of Toronto

summary: In the human pathogen Streptococcus mutans, the canonical peptide-based quorum sensing system is an inducible DNA repair system that is pivotal for bacterial survival. Previous work showed that the CSP signaling peptide is a stress-signaling alarmone that controls different stress-induced phenotypes. In this study, we exposed S. mutans to the CSP pheromone to mimic DNA damage conditions. Transcriptome analysis was then performed to evaluate the differential gene expression between the normal stationary phase cells and the CSP-induced stationary phase cells. The data obtained contribute to the understanding of the CSP-induced phenotypes in S. mutans.

overall_design: S. mutans cells were induced with the CSP quorum sensing pheromone for 24 hours.  The gene expression profiling of the CSP-induced cells was compared to the one of non-induced cells.

first: Celine

last: Levesque


title: Multilayer network construction and analysis pipeline for gene expression data

status: Public on Apr 01 2024

city: Beijing

first: Yingxing

last: Li

state: Beijing

address: Peking Union Medical College Hospital (Dongdan campus), No.1 Shuaifuyuan Wa

institute: Peking Union Medical College Hospital

summary: Molecular networks are key to understanding the complexity of biological systems. Despite the advances in network construction and analysis techniques, challenges remain in incorporating multidimensional interactions into a hybrid network model and reducing the complexity of large networks into functional modules or influential nodes. Here, we introduce CREAM, a user-friendly application that empowers biologists to construct multilayer networks by integrating gene expression data with various known interactions predicted by experimental and computational techniques, and to identify functional modules and prognostic biomarkers within these networks. When applied to multiple cancer types, CREAM outperforms state-of-the-art module detection methods in identifying biologically relevant modules. Further investigation of colon adenocarcinoma revealed numerous well-known cancer regulators and a promising new therapeutic target, miR-8485. Our in vitro and in vivo experiments demonstrated its inhibitory effects on colon cancer cell proliferation and migration. Overall, CREAM is expected to significantly advance network-based precision medicine research.

overall_design: In order to investigate the regulatory effects of miR-8485 on human colorectal cancer cells, we performed transcriptome sequencing on human colorectal cancer cells HCT116 transfected with miR-8485 mimics and their control group.

first: Wenting

last: Guo

first: Mingfei

last: Han


title: Epigenetic inheritance of diet-induced and sperm-borne mitochondrial RNAs

status: Public on Apr 03 2024

city: München

first: Raffaele

last: Teperino

address: Ingolstädter Landstraße 1

department: Institute of Experimental Genetics (IEG)

institute: Helmholtz Zentrum München

summary:
Spermatozoa harbor a complex and environment sensitive pool of small non-coding RNAs (sncRNA)1, which influences offspring development and adult phenotypes1-7. Whether spermatozoa in the epididymis are directly susceptible to environmental cues is not fully understood8. We used two distinct paradigms of preconception acute high fat diet to dissect epididymal vs testicular contributions to the sperm sncRNA pool and offspring health. We show that epididymal spermatozoa, but not developing germ cells, are sensitive to the environment and identify mitochondrial tRNAs and their fragments (mt-tsRNA) as sperm-borne factors. In humans, mt-tsRNAs in spermatozoa correlate with BMI and paternal overweight at conception doubles offspring obesity risk and compromises metabolic health. Sperm sncRNA-seq of mice mutant for genes involved in mitochondrial function, and metabolic phenotyping of their wild-type offspring, suggest that alterations of mt-tsRNAs are downstream of mitochondrial dysfunction. Most importantly, single embryo transcriptomics of genetically hybrid two-cell embryos demonstrated sperm-to-oocyte transfer of mt-tRNAs at fertilisation and implied them in the control of early embryo transcription.  Our study supports the importance of paternal health at conception for offspring metabolism, shows that mt-tRNAs are diet-induced and sperm-borne and demonstrates, for the first time in a physiological setting, father-to-offspring transfer of sperm mitochondrial RNAs at fertilization.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Whole transcriptome sequencing of 6 pairs of esophageal squamous cell carcinoma and paracancerous tissues

status: Public on Apr 15 2024

city: Nanchong

first: kang

last: liu

state: State...

address: 55 Dongshun Road, Gaoping District, Nanchong city, Sichuan Province

institute: north sichuan medical college

summary: Screening and identification of novel biomarkers affecting the progression of esophageal squamous cell carcinoma by whole-transcriptome sequencing of 6 pairs of esophageal squamous cell carcinoma tissues and adjacent tissues

overall_design: We sequenced and analyzed 6 pairs of esophageal squamous cell carcinoma tissues and paracancerous tissues

first: liu

last: kang

first: song

last: guiqin


title: Effect of TIMP1 treatment on human VSMC gene expression

status: Public on Apr 09 2024

city: Cambridge

first: Helle

last: Jorgensen

address: Papworth Road

department: Cardiorespiratory section

institute: University of Cambridge

summary: Human VSMC isolates generated from aortic explants were treated in serum free media, +/- the addition of 500 ng / mL TIMP1 for 6 hours

overall_design: To investigate the potential impact of TIMP1 protein on VSMC function, we treated six independent isolates of human VSMCs with recombinant TIMP1 protein and compared gene expression profiles to control samples using bulk RNA-seq.

middle: D

last: Worssam

first: Sebnem

last: Oc

first: Jordi

last: Lambert


title: Transcriptome profiling of MRC5 cells induced in senescence by different stresses

status: Public on Mar 30 2024

first: Julien

last: Cherfils-Vicini

summary: Aging is characterized by a gradual decline of physiological functions causing age-related diseases and increasing vulnerability against cancer. At a cellular level, aging is associated with a progressive accumulation of senescent cells. Senescent cells are involved in tissue homeostasis on one hand but, on another hand, their accumulation can lead to pathological aging processes. The events regulating the elimination of senescent cells by the immune system are still poorly known. Here we want to understand the transcriptome variations between the different kinds on senescences of one same cell line to link them to their immunological properties.

overall_design: Primary human fibroblasts MRC5 were induced to senesce by exposure to Bleomycin during 24h at 50 µg/mL. Replicative senescence was induced by continuous passaging of primary human fibroblasts MRC5 at 5% O2 until they reached a plateau in their growth curve. Oncogene-Induced senescence was induced in MRC5 fibroblasts transduced with a vector expressing H-RASG12V and treated with 4-Hydroxytamoxifen at 50nm every 48h for 5 or 8 days. For all experiments, young cells have been used at pdl 30 and senescent cells have been defined as at least 90% SA-b-Galactosidase assay + and no more than 10% of EdU+ cells. RNA from young and senescent cells was extracted using the TRI reagent (Sigma-Aldrich, ref#B8416-15UN) protocol, the quality and concentration was assessed using a nanodropTM and a bioanalyzer (Agilent). Library construction, sequencing and initial data filtering including adaptor removal were performed by BGI Genomics. RNA was sequenced by the DNBSEQ platform in paired-end mode with 150 bp sequencing length. Low quality reads, adaptor contamination and excessively high levels of unknown base N reads were removed from the analysis with SOAPnuke. The reads were aligned to the GCF_000001405.39_GRCh38.p13 reference genome using HISAT2. After that, Ericscript (0.5.5-5) and rMATS (v4.1.1) were used to detect fusion genes and differential splicing genes. Bowtie2 was applied to align the clean reads to the gene set. Quantification was performed by RSEM (v1.2.28).

first: Iryna

last: Moskalevska


title: Changes in the cellular makeup of motor patterning circuits drive courtship song evolution in Drosophila

first: Justin

last: Walsh

address: 3740 Hamilton Walk

institute: University of Pennsylvania

summary: How evolutionary changes in genes and neurons encode species variation in complex motor behaviors are largely unknown. Here, we develop genetic tools that permit a neural circuit comparison between the model species Drosophila melanogaster and the closely-related species D. yakuba, who has undergone a lineage-specific loss of sine song, one of the two major types of male courtship song in Drosophila. Neuroanatomical comparison of song patterning neurons called TN1 across the phylogeny demonstrates a link between the loss of sine song and a reduction both in the number of TN1 neurons and the neurites serving the sine circuit connectivity. Optogenetic activation confirms that TN1 neurons in D. yakuba have lost the ability to drive sine song, while maintaining the ability to drive the singing wing posture. Single-cell transcriptomic comparison shows that D. yakuba specifically lacks a cell type corresponding to TN1A neurons, the TN1 subtype that is essential for sine song. Genetic and developmental manipulation reveals a functional divergence of the sex determination gene doublesex in D. yakuba to reduce TN1 number by promoting apoptosis. Our work illustrates the contribution of motor patterning circuits and cell type changes in behavioral evolution, and uncovers the evolutionary lability of sex determination genes to reconfigure the cellular makeup of neural circuits.

sample_organism:
Drosophila melanogaster
Drosophila yakuba

overall_design: Doublesex expressing neurons from male flies were isolated by FACS based on the expression of tdTomato and analyzed by scRNAseq

first: Dajia

last: Ye

first: Ian

last: Junker

first: Yun

last: Ding


title: Chronic alcohol drinking modulates synchrony between midbrain gene transcription and long-lasting changes in dopamine terminal and opioid function in macaques

status: Public on Apr 16 2024

first: Cody

last: Siciliano

address: 2222 Pierce Avenue, 410 Robinson Research Building

department: Pharmacology

summary: Alcohol use disorder is marked by disrupted behavioral and emotional states which can persist into abstinence. The enduring synaptic alterations that remain despite the absence of alcohol are of interest for interventions to prevent relapse. 28 male rhesus macaques underwent over 20 months of alcohol drinking interspersed with three 30-day forced abstinence periods. After the last abstinence period, we paired ex vivo voltammetry in nucleus accumbens slices with RNA-sequencing of the ventral tegmental area. We found persistent augmentation of dopamine transporter function, kappa opioid receptor sensitivity, and dynorphin release – all inhibitory regulators which act to decrease extracellular dopamine. Surprisingly, though transcript expression was not altered, the relationship between gene expression and functional readouts of these encoded proteins was highly dynamic and altered by drinking history. Therefore, the long-lasting synaptic impact of alcohol use suggests that assessment of transcript-function relationships may provide avenues for precision therapeutics targeted to specific synaptic pathophysiologies.

overall_design: We paired a model of chronic voluntary alcohol (ethanol) drinking and protracted abstinence with within-subject measures of dopamine terminal function and assessment of gene transcription. In an effort to maximize translational relevance and implications of gene expression quantification, rhesus macaque (macaca mulatta) subjects were used, because of the genetic and behavioral diversity in the model that mirrors individual differences in human drinkers(Grant et al., 2008), as well as the homology to humans in genetic sequence(Gibbs et al., 2007) and neural circuit architecture(Balsters et al., 2020; Haber & Knutson, 2010). Following an induction protocol, subjects were allowed to self-administer alcohol under continuous access conditions for 12 months, followed by three one-month abstinence periods interspersed with three-month periods of re-access to alcohol. At the end of the third and final abstinence period, real-time dopamine release kinetics and inhibitory regulation by axonal KORs were measured directly via ex vivo fast-scan cyclic voltammetry in the NAc of 28 rhesus macaques (17 alcohol drinkers, 11 calorically-yoked or housing controls). Bulk RNA-sequencing of the VTA taken from the same subjects was used to measure gene expression upstream of dopamine terminals.

first: Zahra

middle: Z

last: Farahbakhsh

first: Katherine

middle: M

last: Holleran

first: Jonathon

last: Sens

first: Steve

last: Fordahl

first: Madelyn

middle: I

last: Mauterer

first: Alberto

last: López

first: Verginia

last: Cuzon Carlson

first: Drew

last: Kiraly

first: Kathleen

last: Grant

first: Sara

last: Jones


title: Chromatin accessibilty profiling of SCA1+ and SCA1- lineage traced VSMCs

first: Helle

last: Jorgensen

summary: VSMCs expressing SCA1 have increased proliferative capacity (Dobnikar et al, 2018; Worssam et al, 2022; Pan et al, 2020). We therefore, mapped chromatin accessibility changes using bulk ATAC-seq for SCA1+ and SCA1- lineage traced VSMCs.

overall_design: We mapped chromatin accessibility changes using bulk ATAC-seq for SCA1+ and SCA1- lineage traced, EYFP+ VSMCs from injured animals separately, and compared these to EYFP+ VSMCs from littermate control animals that had not undergone surgery. In parallel, we also profiled EYFP-SCA1+ cells from injured animals.

first: Matthew

last: Worssam

first: Sebnem

last: Oc

first: Jordi

last: Lambert

middle: F


title: A single cell survey of CD127+ immune cells and EpCAM+ epithelial cells from wild type mice and Gabbr1-deficient mice

status: Public on Mar 27 2024

city: Chaoyang Distric

first: Nian

last: Liu

address: Institute of Biophysics,#15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: To explore the role of GABAergic signaling in regulation of ILC3 function and intestinal tissue homeostasis, we performed single cell RNA sequencing to analyze intestinal CD127+ immune cells and EpCAM+ epithelial cells

overall_design: Gabbr1flox/flox;Rorc-Cre- (Gabbr1WT)  and Gabbr1flox/flox;Rorc-Cre+ (Gabbr1ΔRorc) mice were treated with 2.5% DSS for  colitis induction. Small intestine tissues were dissociated with GEXSCOPE® Tissue Dissociation according to manufacturer's instructions. CD45+CD127+ immune cells and CD45-EpCAM+ epithelial cells were sorted using FACS, mixed at 1:1 ratio and subjected to scRNA-seq.

first: Benyu

first: Zusen

last: Fan


title: A progeria-associated BAF-1 mutation modulates gene expression and accelerates aging in C. elegans II

status: Public on Mar 22 2024

city: Seville

first: Peter

last: Askjaer

address: UPO Carretera de Utrera km 1

institute: Centro Andaluz de Biología del Desarrollo

summary: Alterations in the nuclear envelope are linked to a variety of rare diseases termed laminopathies. These include both tissue specific and systemic diseases. A single amino acid substitution in human barrier to autointegration factor (BAF) at position 12 (A12T) causes Néstor-Guillermo Progeria Syndrome (NGPS). This premature ageing condition affects a variety of tissues, leading to growth retardation and severe skeletal defects, including scoliosis. Taking advantage of the conservation between human and C. elegans BAF proteins, we have modified the baf-1 locus in C. elegans to mimic the human NGPS mutation (baf-1(G12T)). In this work, we characterized the phenotypes caused by the G12T mutation at molecular, cellular, and organismal scale. We found that the mutation induced multiple phenotypes related to fertility, lifespan, and stress resistance. Importantly, nuclear morphology deteriorated faster during aging in baf-1(G12T), reproducing an important hallmark of cells from progeria patients. Nuclear envelope accumulation of lamin and emerin was reduced whereas localization of BAF-1(G12T) was similar to wild type BAF-1. We determined the chromatin binding profiles for wild type and mutant BAF-1 and performed transcriptome analyses through tissue-specific DamID. Although the global profiles for the two proteins resembled each other, we also identified many discrete regions with altered association to BAF-1(G12T). Most genes deregulated by the baf-1(G12T) mutation were characterized by a change in BAF-1 association, suggesting a direct relation between BAF-1 binding and gene expression. We propose that C. elegans can serve as a relevant model to understand how a mutation in an essential protein expressed throughout development triggers the appearance of symptoms ~2 years after birth of human patients.

overall_design: Tissue-specific DamID in hypodermis and intestine of C. elegans to determine chromatin binding profiles of BAF-1 and BAF-1(G12T).

first: Raquel

last: Romero-Bueno

first: Adrián

last: Fragoso-Luna

first: Cristina

last: Ayuso

first: Alan

last: Kavsek

first: Christian

last: Riedel

first: Jordan

last: Ward


title: Single-cell analysis reveals transcriptional dynamics in primary parathyroid tissue

status: Public on Mar 12 2024

city: New Haven

first: Diane

last: Krause

state: CT

address: 10 Amistad St.

department: Laboratory Medicine

institute: Yale University

summary: Studies on human parathyroid tissue are often limited to adenomatous tissue due to difficulty obtaining healthy tissue. We obtained nonhuman primate parathyroids to provide a suitable alternative for sequencing analysis that would bear the closest semblance to human organs as possible. We analyzed four M. mulatta normal parathyroid specimens to that show a continuous trajectory of cell states comprising the normal adult parathyroid. We calculated the predicted pseudotime progression based on transcriptomic signatures that were reflective of repopulating progenitors, progressing to chief cells, and ultimately oxyphils, and clustered genes based on their expression dynamics along this axis. As a comparator, we histologically characterized and sequenced four human adenomas with varying oxyphil and chief cell abundance to highlight similarities and differences to normal parathyroid cell expression dynamics. We noted abundant RARRES2 transcripts that were detected in both human adenoma and normal primate parathyroid cells, and provided co-immunostaining validation of Chemerin presence in PTH-expressing cells, which could play a previously unrecognized role in parathyroid endocrine function.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Comparative scRNAseq analysis of normal non-human primate parathyroid glands and human parathyroid adenomas with varying oxyphil/chief cell abundance

first: Aarthi

last: Venkat

first: Maximillian

last: Carlino

first: Betty

last: Lawton

first: Manju

last: Prasad

first: Matt

last: Amodio

first: Courtney

middle: E

last: Gibson

first: Caroline

last: Zeiss

first: Smita

last: Krishnaswamy


title: Spatio-temporal transcriptome maps in the early embryos of Halocynthia roretzi

status: Public on Mar 16 2024

first: Kaile

last: Zhang

address: No. 600 Yishan Road

department: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

institute: Shanghai Jiao Tong University

summary: The ascidia Halocynthia roretzi (Phylum: Chordata, Subphylum: Tunicata, Class: Ascidiacea) have been used as model species in development biology for over a century. It offers attractive experimental features, including a compact genome, invariant embryonic cell lineages, small embryonic cell number, and translucent embryos, which allow the description of developmental processes with a cellular level of resolution. Staged RNA-seq data has been already deposited in DDBJ (accessiton number DRA005714 and DRA005711). In the present study, we sequenced genome of H. roretzi of a southwestern Japanese population using RNA-Seq data. These RNA-Seq data covers expressions in 8 cell and 110 cell embryos of Animal(A), Vegetal(V) and whole-embryo regions. These genome assembly, transcript assembly, and transcript models are incorporated into the ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and blast searches. The genome and transcriptome resources will be useful datasets for developmental biology, evolutionary biology and molecular ecology using this model organism.

overall_design: Examination of different expressions in 8 cell and 110 cell embryos of Animal(A), Vegetal(V) and whole-embryo regions

first: Kai

last: Wang

first: Ritsuko

last: Suyama

first: Nanako

last: Mizutani

first: Masaki

last: Matsuo

first: Yu

last: Peng

first: Masahide

last: Seki

first: Yutaka

last: Suzuki

first: Nicholas

last: M. Luscombe

first: Christelle

last: Dantec

first: Patrick

last: Lemaire

first: Atsushi

last: Toyoda

first: Hiroki

last: Nishida

first: Takeshi

last: A. Onuma


title: transcriptional responses of LPS-stimulated microglia in Alzheimer's disease

status: Public on Mar 11 2024

city: Guangzhou

first: Yongyi

last: Ye

state: Guangdong

address: No.250, Changgang East Road

department: the Second Affiliated Hospital of Guangzhou Medical University

summary: Neuroimmunity is present as an important mechanism in the brains of Alzheimer's patients, and microglia are a key component of the brain's innate immune response during the development and progression of Alzheimer's disease. The interferon pathway plays an important role in the pathophysiologic mechanisms of AD. RNA-seq was performed on LPS-treated microglia(LPS) and untreated microglia(WT) to further explore.

overall_design: To further investigate the transcriptional responses in LPS-stimulated microglia, primary microglia were divided into control group and LPS-treated group, with 3 samples in each group and 6 samples in total. The LPS treatment group was treated with 1ug/ml LPS.


title: ZEB1 controls a lineage-specific transcriptional program essential for melanoma cell state transitions

status: Public on Mar 25 2024

city: LYON

first: Julie

last: CARAMEL

address: 28 Rue Laennec

institute: Cancer Research Center of Lyon

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


title: ZEB1 controls a lineage-specific transcriptional program essential for melanoma cell state transitions [ChIP-seq]

status: Public on Mar 26 2024

summary: Cell plasticity sustains intra-tumor heterogeneity and treatment resistance in melanoma. Deciphering the transcriptional mechanisms governing reversible phenotypic transitions between proliferative/differentiated and invasive/stem-like states is required. Expression of the ZEB1 transcription factor is frequently activated in melanoma, where it fosters adaptive resistance to targeted therapies. Here, we performed a genome-wide characterization of ZEB1 transcriptional targets, by combining ChIP-sequencing and RNA-sequencing, upon phenotype switching in melanoma models. We identified and validated ZEB1 binding peaks in the promoter of key lineage-specific genes crucial for melanoma cell identity. Mechanistically, ZEB1 negatively regulates SOX10-MITF dependent proliferative/melanocytic programs and positively regulates AP-1 driven invasive and stem-like programs. Comparative analyses with breast carcinoma cells revealed lineage-specific ZEB1 binding, leading to the design of a more reliable melanoma-specific ZEB1 regulon. We then developed single-cell spatial multiplexed analyses to characterize melanoma cell states intra-tumoral heterogeneity in human melanoma samples. Combined with scRNA-Seq analyses, our findings confirmed increased ZEB1 expression in Neural-Crest-like cells and mesenchymal cells, underscoring its significance in vivo in both populations. Overall, our results define ZEB1 as a major transcriptional regulator of cell states transitions and provide a better understanding of lineage-specific transcriptional programs sustaining intra-tumor heterogeneity in melanoma.

overall_design: ZEB1 ChIP-seq were performed on untreated and treated GLO cells and AS3 melanoma cells.

first: Simon

last: Durand

first: Yaqi

last: Tang

first: Roxane

last: Pommier

first: Valentin

last: Benboubker

first: Maxime

last: Grimont

first: Felix

last: Boivin

first: Laetitia

last: Barbollat

first: Eric

last: Cumunel

first: Florian

last: Dupeuble

first: Anaïs

last: Eberhardt

first: Maud

last: Plaschka

first: Stéphane

last: Dalle

last: Caramel


title: The three-dimensional structure of chromatin condensed by PRC1 is porous and accessible [ChIP-seq]

status: Public on Mar 07 2024

city: Clayton

first: Michael

last: Uckelmann

state: Victoria

address: 23 Innovation Walk

department: Biochemistry

country: Australia

institute: Monash University

summary: The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organisation and dynamics of chromatin compacted by gene-repressing factors are unknown. Using cryo-electron tomography, we solved the three-dimensional structure of chromatin condensed by the Polycomb Repressive Complex 1 (PRC1) in a complex with CBX8. Unexpectedly, PRC1-condensed chromatin is porous and forms a size-selective diffusion barrier that is stabilised through multivalent dynamic interactions. Accordingly, PRC1 remains dynamic within the condensate while maintaining the chromatin static. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of open and closed chromatin states and instead suggest that PRC1 permits size-selective accessibility of macromolecules into chromatin condensates.

overall_design: Chromatin immunoprecipitation (ChIP) using antibodies for CBX8 and H3K27me3 in J1 mouse embryonic stem cells after 48 hours of retinoic acid treatment

first: Chen

last: Davidovich


title: The three-dimensional structure of chromatin condensed by PRC1 is porous and accessible [ATAC_CP15]

overall_design: ATAC-seq for mouse embryonic stem cells that have a TetO-GFP reporter gene cassette integrated into chromosome 15 and a TetR-CBX8 construct constitutively expressed. Cells were treated with dox to induce eviction of TetR-CBX8 from the TetO array


title: The three-dimensional structure of chromatin condensed by PRC1 is porous and accessible


title: Exploring the Respective Contributions of DNA Polymerase Proofreading and Mismatch Repair in the Shaping of Spontaneous Mutation Rates.

city: JOUY-EN-JOSAS

first: Ira

last: Tanneur

address: INRAE - Unité MaIAGE  Bât 210 et 233  Domaine de Vilvert

department: MaIAGE

institute: INRAE

summary:
The spontaneous mutation rate is a crucial parameter in molecular evolution which is maintained very low.
To better characterize how proofreading activity of the DNA polymerase and Mismatch repair (MMR) which are ubiquitous in all kingdoms of life shape a mutational landscape we built B. subtilis 168-derived strains allowing conditional inactivation of either one or both of these two error reparation mechanisms.
In practice, we used an IPTG-inducible promoter to control the expression of mutant alleles selected for their ability to displace by competition their functional counterparts. The first allele, denoted here mutL*, has a mutation in the ATP hydrolysis active site of MutL. The second allele, denoted here polC* encodes an exonuclease-deficient variant of PolC.
Fluctuation tests and Mutation Accumulation experiments confirmed extremely high mutation rates, upon IPTG-induction, in the strain that combine these two deficient alleles in a synthetic operon (mutL*//polC*).
The purpose of this transcritomic study was to better characterize this inducible system. Analysis of the data did not reveal specific transcriptional responses of the bacterium to IPTG addition and extreme mutations rates.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
To investigate the potential impact on mutation rate on the transcriptional profile of B. subtilis, we performed RNA-Seq a WT-like chassis strain (CS), and three strains that are deficient in a reparation system after addition of IPTG : an MMR-deficient strain (mutL*), a proofreading-deficient strain (polC*) and a MMR- and proofreading-deficient strain (mutL*//polC*).
CS with and without IPTG, as well as mutLpolC without IPTG, were used to 1) control the absence of impact of IPTG on transcription 2) provide a transcriptional profile of B. subtilis with a WT mutation rate as a point of reference. Two biological replicates per strain x condition were made. We then performed differential expression analysis using the data from the RNA-Seq.

last: TANNEUR

first: Matthieu

last: JULES

first: Pierre

last: NICOLAS


title: A progeria-associated BAF-1 mutation modulates gene expression and accelerates aging in C. elegans I

status: Public on Mar 21 2024

first: Peter

last: Askjaer

overall_design: Tissue-specific RNA polymerase DamID in hypodermis and intestine of C. elegans to determine transcriptomes of wild type and baf-1(G12T) mutants.

first: Raquel

last: Romero-Bueno

first: Adrián

last: Fragoso-Luna

first: Cristina

last: Ayuso

first: Alan

last: Kavsek

first: Christian

last: Riedel

first: Jordan

last: Ward


title: Depletion of PCCB and/or PIK3CA from pancreatic tumor cells KPC influences T cells infiltrating to TME

status: Public on Mar 01 2024

city: Stony Brook

first: Richard

last: Lin

address: 1 Circle Road

institute: Stony Brook University

summary: Most human pancreatic ductal adenocarcinoma (PDAC) are not infiltrated with cytotoxic T cells and are highly resistant to immunotherapy. Our previous study demonstrated that ablation of Pik3ca in KPC (KrasG12D; Trp53R172H; Pdx1-Cre) pancreatic cancer cells induced host T cells to infiltrate and completely eliminate the tumors in a syngeneic orthotopic implantation mouse model. Here we report that implantation of Pik3ca-/- KPC (named αKO) cancer cells induces clonal expansion of cytotoxic T cells infiltrating the pancreatic tumors in this mouse model. To identify potential molecules that can regulate the activity of these anti-tumor T cells, we conducted an in vivo genome-wide gene-deletion screen using αKO cells implanted in the mouse pancreas and the result shows that deletion of propionyl-CoA carboxylase subunit B gene (Pccb) in αKO cells (named p-αKO) leads to immune evasion, tumor progression and death of host mice. Surprisingly, p-αKO tumors are still infiltrated with T cells but they are inactive against tumor cells. However, blockade of PD-L1/PD1 interaction reactivated clonally expanded T cells infiltrating p-αKO tumors, leading slower tumor progression and improve survival of host mice. These results indicate that Pccb can modulate the activity of cytotoxic T cells infiltrating some pancreatic tumors and this understanding may help to improve immunotherapy for PDAC.

overall_design: After implanting αKO and p-αKO cells to the pancreas of B6 mice, and implanting p-αKO cells to PD1-null mice, the tumors were extracted 12 days post implantaiton. CD4 and CD8 T cells were enriched and single cell RNA as well as TCR were sequenced with 10x genomics' protocol.

first: Han

last: Han


title: Experimental tests strongly challenge the evidence of a healthy human blood microbiome

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: The study critically evaluate the results of 16S targeted amplicon sequencing performed on the total DNA collected from healthy donors’ blood samples in the light of specific negative controls.

sample_organism:
Escherichia coli
Mus musculus
human blood metagenome

overall_design: Total DNA was extracted from the blood of healthy subjects and from negative controls (whose DNA concentration has been inflated through known spyke DNA), amplified to collect amplicons of variable V3–V4 regions (primers 341F and 805R) of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

first: Amedeo

last: Amedei

first: Leandro

last: Di Gloria


title: Spatio-temporal transcriptome maps in the early embryos of Oikopleura dioica

first: Kaile

last: Zhang

summary: The larvacean, Oikopleura dioica, is a planktonic chordate and belongs to tunicate that is the closest relative to vertebrates. Its simple and transparent body, invariant embryonic cell lineages and short life cycle of five days make it a promising model organism for research in developmental biology. The genome browser, OikoBase, has been established in 2013 using Norwegian O. dioica. However, genome information of other populations is not available, despite that many researchers have used local populations. In the present study, we sequenced genome of O. dioica of a southwestern Japanese population using RNA-Seq data. These RNA-Seq data covers expressions in 8 cell and 12 hours post fertilization (HPF) embryos of Animal(A), Vegetal(V) and whole-embryo regions, as well as whole embryo of 13 stages, including OD_STAGE01 (unfertilized egg), OD_STAGE02 (fertilized egg), OD_STAGE03 (2-cell), OD_STAGE04 (4-cell), OD_STAGE05 (8-cell), OD_STAGE06 (16-cell), OD_STAGE07 (32-cell), OD_STAGE08 (1.5 hours post fertilization), OD_STAGE09 (2.5 hours post fertilization, tadpole larvae), OD_STAGE10 (3 hours post fertilization, hatched larvae), OD_STAGE11 (5 hours post fertilization, early organogenesis), OD_STAGE12 (8 hours post fertilization, late organogenesis), OD_STAGE13 (10 hours post fertilization, juvenile), Adult male and Adult female. These genome assembly, transcript assembly, and transcript models are incorporated into the ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and blast searches. The genome and transcriptome resources will be useful datasets for developmental biology, evolutionary biology and molecular ecology using this model organism.

overall_design: Examination of different expressions in 8 cell and 12 hours post fertilization (HPF) embryos of Animal(A), Vegetal(V) and whole-embryo regions, as well as whole embryo of 13 stages, including OD_STAGE01 (unfertilized egg), OD_STAGE02 (fertilized egg), OD_STAGE03 (2-cell), OD_STAGE04 (4-cell), OD_STAGE05 (8-cell), OD_STAGE06 (16-cell), OD_STAGE07 (32-cell), OD_STAGE08 (1.5 hours post fertilization), OD_STAGE09 (2.5 hours post fertilization, tadpole larvae), OD_STAGE10 (3 hours post fertilization, hatched larvae), OD_STAGE11 (5 hours post fertilization, early organogenesis), OD_STAGE12 (8 hours post fertilization, late organogenesis), OD_STAGE13 (10 hours post fertilization, juvenile), Adult male and Adult female

first: Kai

last: Wang

first: Ritsuko

last: Suyama

first: Nanako

last: Mizutani

first: Masaki

last: Matsuo

first: Yu

last: Peng

first: Masahide

last: Seki

first: Yutaka

last: Suzuki

first: Nicholas

last: M. Luscombe

first: Christelle

last: Dantec

first: Patrick

last: Lemaire

first: Atsushi

last: Toyoda

first: Hiroki

last: Nishida

first: Takeshi

last: A. Onuma


title: BRG1/BRM inhibitor targets AML stem cells and exerts superior preclinical efficacy combined with BET or Menin inhibitor (scRNA-Seq)

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

summary: BRG1 (SMARCA4) and BRM (SMARCA2) are the mutually exclusive core ATPases of the chromatin remodeling BAF (BRG1/BRM-associated factor) complexes. They enable transcription factors/co-factors to access enhancers/promoter and modulate gene-expressions responsible for cell growth and differentiation of AML stem/progenitor cells. In AML with MLL1r (MLL1 rearrangement) or mutant (mt) NPM1, although Menin inhibitor (MI) treatment induces clinical remissions, most patients either fail to respond or relapse, some harboring Menin mutations. FHD-286 is an orally bioavailable, selective inhibitor of BRG1/BRM under clinical development in AML. Present studies show that FHD-286 induces differentiation and lethality in AML cells with MLL1r or mtNPM1, concomitantly causing perturbed chromatin accessibility and repression of c-Myc, PU.1 and CDK4/6. Co-treatment with FHD-286 and decitabine, BET inhibitor (BETi) or MI, or venetoclax synergistically induced in vitro lethality in AML cells with MLL1r or mtNPM1. In patient-derived xenograft (PDX) models of AML with MLL1r or mtNPM1, FHD-286 treatment reduced AML burden, improved survival, and attenuated AML-initiating potential of stem-progenitor cells. Compared to each drug, co-treatment with FHD-286 and BETi, MI, decitabine or venetoclax significantly reduced AML burden and improved survival, without inducing significant toxicity. These findings highlight the FHD-286-based combinations as promising therapy of AML with MLL1r or mtNPM1.

overall_design: Single cell RNA Seq of an MLL-AF9 expressing AML and a mutant NPM1 + FLT3-ITD AML treated with FHD-286 for 16 hours.

first: Warren

last: Fiskus

first: Kapil

middle: N

last: Bhalla


title: ATAC-seq of TNF-alpha activation in HEK cells with or without TRAFTAC against NfkB

status: Public on Mar 04 2024

city: Zürich

first: Pierre-Luc

last: Germain

address: Winterthurerstrasse 190

department: D-HEST Institute for Neuroscience

country: Switzerland

institute: ETH Zürich

summary: TRAnscription Factor TArgeting Chimeras (TRAFTACs) can downregulated specific transcription factors at the protein-level through their DNA-binding affinity. We tested a previously validated TRAFTAC (Samarasinghe et al., 2021) against NFkB in the context of TNF-alpha activation in HEK cells, and profiled DNA accessibility using ATAC-seq.

overall_design: Replicating the experiments from (Samarasinghe et al., 2021), we transfected HEK cells with the dCas9-HT7 plasmid and DNA-RNA hybrids (NFkB or scrambled TRAFTAC, in duplicates) for 6h, before treating the cells with TNF-alpha (which triggers NFkB activation) and the PROTAC against the Halo tag (HP14) for 19h. We confirmed a 37% reduction in NFkB1/p50 levels before collecting the four samples for ATAC profiling.

first: Selinar

middle: J

last: Frey

first: Vincent

last: Fischer

first: Katharina

last: Gapp


title: BRG1/BRM inhibitor targets AML stem cells and exerts superior preclinical efficacy combined with BET or Menin inhibitor (scATAC-Seq)

overall_design: Single cell ATAC Seq of patient-derived AML cells treated with FHD-286 for 16 hours.


title: BRG1/BRM inhibitor targets AML stem cells and exerts superior preclinical efficacy combined with BET or Menin inhibitor (Bulk RNA-Seq)

overall_design: Paired end RNA Seq of a leukemia cell line treated with BRG1-BRM inhibitor FHD-286  for 16 hours.


title: The three-dimensional structure of chromatin condensed by PRC1 is porous and accessible [ATAC-seq]

first: Michael

last: Uckelmann

overall_design: ATAC-seq for wildtype and CBX8 knockout J1 mouse embryonic stem cells. Samples have been treated either with 1 uM retinoic acid to induce differentiation or with an equivalent volume of DMSO (control)

first: Chen

last: Davidovich


title: BRG1/BRM inhibitor targets AML stem cells and exerts superior preclinical efficacy combined with BET or Menin inhibitor (Bulk ATAC-Seq)

overall_design: Paired end ATAC Seq of leukemia cell lines from an MLL-AF9 expressing AML treated with FHD-286 for 16 hours.


title: BRG1/BRM inhibitor targets AML stem cells and exerts superior preclinical efficacy combined with BET or Menin inhibitor

overall_design: Refer to individual Series


title: BRG1/BRM inhibitor targets AML stem cells and exerts superior preclinical efficacy combined with BET or Menin inhibitor (ChIP-Seq)

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modification H3K27Ac, BRG1 and BRM in AML MOLM13 cell line and patient-derived AML cells.


title: New point mutations in the sodium channel gene and deciphering pyrethroid resistance using RNA-seq in Triatoma dimidiata from Colombia

status: Public on Feb 29 2024

city: Medellín

first: Sara

last: Zuluaga

department: Antioquia

country: Colombia

institute: Universidad de Antioquia

summary: This study focuses on determining resistance to different pyrethroids in populations of Triatoma dimidiata of Boyacá, Colombia. To determine the possible causes of resistance, we sequenced RNA of three populations: laboratory, field, and under pressure of lambda-cyhalothrin. Transcriptomic profile analyses of T. dimidiata revealed differentially regulated genes in both the field population and in the laboratory population under pressure from lambda-cyhalothrin. Gene enrichment analysis showed positive regulation of transcripts related to detoxifying enzymes and mitochondrial proteins, suggesting a significant role in resistance.

overall_design: To determine changes in the mRNA profiles of Triatoma dimidiata, we selected three individuals from the field population, three from the first-generation lambda-cyhalothrin pressure population, and three susceptible laboratory individuals.

first: Geysson

last: Fernandez

first: Carl

last: Lowenberger

first: Omar

last: Triana


title: RNA sequencing of neutrophils isolated from lung, spleen and bone marrow of Mycobacterium tuberculosis infected mice

city: ALBANY

first: Bibhuti

middle: B

last: Mishra

state: NEW YORK

address: 49 New Scotland Ave

department: Immunology and Microbial Disease

institute: Albany Medical College

summary: Mycobacterium tuberculosis infection of mice elicits a robust neutrophil influx that associates with poor outcome from tuberculosis (TB). However, the mechanism by which neutrophils contribute to TB disease pathogenesis is not understood. To gain insights into the pathological functions of neutrophils, the current study performs bulk mRNA sequencing from the neutrophils isolated from lung, spleen and bone marrow of  resistant (C57BL/6) and susceptible (IL-1R1 KO) mice at 28 days post M.tuberculosis HN878 infection.

overall_design: Transcriptome analysis of neutrophils sorted from the lung, spleen and bone marrow of  C57BL/6 (IL1R1+/+) and IL1R1-/- mice, at 4 weeks post Mycobacterium tuberculosis HN878 infection.

first: Mohd

last: Saqib

first: Shreya

last: Das

first: Yi

last: Cai


title: JAK-STAT signaling maintains homeostasis in T cells and macrophages (spatial transcriptomics)

status: Public on Feb 24 2024

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Immune cells need to sustain a state of constant alertness over a lifetime. Yet, little is known about the regulatory processes that control the fluent and fragile balance that is called homeostasis. Here we demonstrate that JAK-STAT signaling, beyond its role in immune responses, is a major regulator of immune cell homeostasis. We investigated JAK-STAT-mediated transcription and chromatin accessibility across 12 mouse models, including knockouts of all STAT transcription factors and of the TYK2 kinase. Baseline JAK-STAT signaling was detected in CD8+ T cells and macrophages of unperturbed mice – but abrogated in the knockouts and in unstimulated immune cells deprived of their normal tissue context. We observed diverse transcription-regulatory programs, including gene regulation by STAT2 and IRF9 independent of STAT1. In summary, our large-scale dataset and integrative analysis of JAK-STAT mutant and wildtype mice uncovered a crucial role of JAK-STAT signaling in unstimulated immune cells, where it contributes to a poised epigenetic and transcription-regulatory state and helps prepare these cells for rapid response to immune stimuli.

overall_design: 4 spatial transcriptomics samples of spleen-tissue slices  from wildtype and Stat1 mutant animals

first: Nikolaus

last: Fortelny

first: Matthias

last: Farlik

first: Victoria

last: Fife

first: Anna-Dorothea

last: Gorki

first: Caroline

last: Lassnig

first: Barbara

last: Maurer

first: Katrin

last: Meissl

first: Marlies

last: Dolezal

first: Laura

last: Boccuni

first: Aarathy

last: Geetha

first: Anzhelika

last: Karjalainen

first: Stephen

last: Shoebridge

first: Ulrike

last: Mann

first: Rohit

last: Jain

first: Shweta

last: Tikoo

first: Nina

last: Zila

first: Wolfgang

last: Esser-Skala

first: Thomas

last: Krausgruber

first: Katarzyna

last: Sitnik

first: Asma

last: Farhat

last: Penz

first: Anastasiya

last: Hladik

first: Tobias

last: Suske

first: Mojoyinola

last: Akagha

first: Sophie

last: Zahalka

first: Martin

last: Senekowitsch

first: Daniele

last: Barreca

first: Florian

last: Halbritter

first: Sabine

last: Macho-Maschler

last: Weninger

first: Heidi

middle: A

last: Neubauer

first: Richard

last: Moriggl

first: Sylvia

last: Knapp

first: Veronika

last: Sexl

first: Birgit

last: Strobl

last: Decker

first: Mathias

last: Müller


title: FKBP51 in glutamatergic forebrain neurons promotes early life stress inoculation in female mice via a Tcf4-mediated pathway

status: Public on Feb 26 2024

city: Munich

middle: V.

last: Schmidt

state: Bayern

address: Kraepelinstrasse 2-10

institute: Max Planck Institute of Psychiatry

summary: Early life stress (ELS) has often been described as a risk factor for developing psychiatric disease. However, moderate exposure to ELS can also lead to stress inoculation and consequently adaptive changes on brain and behavior. Moreover, the FKBP5 gene, encoding the FKBP51 co-chaperone, has been associated with an increased risk for developing psychiatric disorders, specifically in interaction with ELS exposure. However, the underlying mechanisms behind the interaction of FKBP51 and moderate ELS exposure are still not completely understood and particularly data in the female sex are scarce. In this study, the contribution of FKBP51 in glutamatergic forebrain neurons to the long-term consequences of moderate ELS was investigated in both sexes, by using the Fkbp5Nex conditional knockout line. In female wild-type Fkbp5lox/lox mice, ELS exposure led to an anxiolytic phenotype and improved memory performance in a stressful context, however this ELS effect was absent in in Fkbp5Nexx wild-type mice. Interactive effects of FKBP51 in glutamatergic forebrain neurons and moderate ELS exposure in female mice were also reflected on brain volume of different cortical regions, the subiculum and white matter structures. Furthermore, interactive effects were observed for structural and electrophysiological properties of CA1 pyramidal neurons of the dorsal hippocampus. RNA sequencing of the hippocampus revealed the transcription factor 4 (TCF4) as a potential regulator of these interactive effects. Cre-dependent viral overexpression of TCF4 in female Nex-Cre mice led to similar beneficial effects on behavior as the moderate ELS exposure. Taken together, this study shows that FKBP51 in glutamatergic forebrain neurons mediates adaptive effects of moderate ELS exposure on emotional regulation, cognitive behavior and neuronal structure and function. Moreover, it proposes TCF4 as an underlying target that drives the FKBP51-mediated effects of moderate ELS on brain and behavior.

overall_design: To investigate downstream molecular mechanisms of early life stress-induced beneficial effects of behavior and the involvement of FKBP51 in glutamtergic neurons in female mice, we performed RNA-seq on 6 female mice per condition (2 stress conditions (control or ELS); 2 genotypes (wildtype or FKBP51 glutamatergic knockout))

middle: V

first: Lotte

last: van Doeselaar

first: Alexandra

last: Abromeit

first: Tibor

last: Stark

first: Danusa

last: Menegaz

first: Shiladitya

last: Mitra

first: Huanqing

last: Yang

first: Ghalia

last: Rehawi

first: Rosa-Eva

last: Huettl

first: Joeri

last: Bordes

first: Sowmya

last: Narayan

first: Jan

last: Deussing

first: Michael

last: Czisch

first: Janine

last: Knauer-Arloth

first: Matthias

last: Eder

first: Juan

last: Lopez


title: Cell-mediated Immune Response Signature to AAV Capsid in Cynomolgus Monkeys

city: San Diego

first: Richard

last: Virgen-Slane

state: CA

address: 0777 Science Center Drive, CB4-2131, Pfizer La Jolla

department: Global Computational Safety Science, DSRD

institute: Pfizer

summary: Cell-mediated immune (CMI) responses to adeno-associated virus (AAV) can lead to both tissue damage and loss of therapeutic transgene expression. Identifying robust biomarkers of CMI and understanding CMI mechanisms can be help to helpful in clinical practice and in advancement of AAV gene therapies. The present work evaluated PBMCs from non-human primates (NHP) before and 14 days following immunization with AAV9 capsid. PBMCs were stimulated in vitro with AA9  capsid peptides to evaluate CMI responses by IFN- ELISPOT, intracellular cytokines and activation markers by flow cytometry, secreted cytokines by ELISAMSD,  and transcriptional responses by RNAseq. AAV peptide stimulation produced a robust IFN- ELISPOT response at 14 days. Flow cytometry revealed an increase in IFN- positive CD4 and CD8 cells,  IL2 positive CD4 cells, and TNF positive CD4 cells. An increase in the CXCR3 ligands IP-10 and I-TAC were detected both inas secreted  proteins. The most robust changes in response to AAV stimulation and strongest correlations to ELISPOT response were revealed by RNAseq, including transcripts encoding IFN- and transcripts encoding , IP-10 and I-TAC , and many downstream transcripts and several IFN-independent pathways. These data provide evidence that a gene signature, or CXCR3 ligand transcripts or protein  could serve as robust and sensitive alternatives to ELISPOT for detection of CMI, andCMI and warrant further benchmarking in human samples.

overall_design: PBMCs were isolated from cynomolgus monkeys before or 14 days after treatment with AAV9. Cells were then stimulated in vitro overnight with either DMSO, a CD3 positive control, or AAV9 capsid peptides to evalute cell-mediated immune responses to the AAV.

first: Thomas

last: Lanz

first: Sophia

middle: G

last: Lee

first: Jessie

last: Qian


title: NAT10-mediated mRNA N4-acetylation is Essential for the Translational Regulation During Oocyte Meiotic Maturation in Mice

status: Public on Feb 18 2024

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

summary: Mammalian oocyte maturation is driven by strictly translational regulation of maternal mRNAs stored in the cytoplasm. However, the function and mechanism of post-transcriptional chemical modifications especially the newly identified N4-acetylcytidine (ac4C) catalyzed by N-acetyltransferase 10 (NAT10) in this process are previously unknown. In this study, we developed a low-input ac4C sequencing technology—ac4C LACE-seq and mapped 8241 ac4C peaks at the whole transcriptome level using 50 mouse oocytes at the germinal vesicle (GV) stage. We profiled the mRNA landscapes of NAT10-interactions and ac4C modifications. The NAT10-interacted and ac4C modified transcripts displayed association with high translation efficiency in oocytes. Oocyte-specific Nat10 knockout wiped out ac4C signals in oocytes and caused severe defects in meiotic maturation and female infertility. ac4C LACE-seq results indicated that Nat10 deletion led to a failure of ac4C deposition on mRNAs encoding key maternal factors such as MAY2, ZAR1, BTG4 and cyclin B1 that regulate transcriptome stability and maternal-to-zygotic transition. Nat10-deleted oocytes had decreased mRNA translation efficiencies during meiotic maturation, partially due to the direct inhibition ac4C sites on specific transcripts. In sum, we developed low-input, high-sensitivity mRNA ac4C profiling approach and highlighted the important physiological function of ac4C in precise regulation of the oocyte meiotic maturation by enhancing translation efficiency.

overall_design: The oocytes were harvested from mature WT and Gdf9-cre Nat10 conditional knockout female mice 32-48h after PMSG and washed by 0.2% containing PBS for 3 times, then 10 oocytes per sample were lysed in lysis buffer (containing 0.2% Triton X-100 and Recombination RNase Inhibitor) and prceeded for cDNA library constribution following the workflow of Smart-seq2. And for each sample, ERCC (1:1000, 0.2μl/sample) were added as spike-in for further calibration.

first: Lu

last: Chen

first: Yuke

last: Wu

first: Yunwen

first: Hengyu


title: IRF1 cooperates with ISGF3 or GAF to form de novo enhancers in murine macrophages

status: Public on Feb 14 2024

city: Los Angeles

first: Carolina

last: Chavez

address: 10833 LeConte Ave

institute: UCLA


title: Impact of Tumor Microenvironment on Efficacy of CD19 CAR T-Cell Therapy or Chemotherapy and Transplant in Large B-Cell Lymphoma

city: Santa Monica

first: Simone

last: Filosto

state: California

address: 2400 Broadway

institute: Kite Pharma

summary: The phase 3 ZUMA-7 trial in second-line large B-cell lymphoma demonstrated superiority of anti-CD19 CAR T-cell therapy (axicabtagene ciloleucel; axi-cel) over standard of care (SOC; salvage chemotherapy followed by hematopoietic transplantation). Here, we present a prespecified exploratory analysis examining the association between pretreatment tumor characteristics and the efficacy of axi-cel versus SOC. B-cell gene expression signature (GES) and CD19 expression significantly associated with improved event-free survival (EFS) for axi-cel (P=.0002 for B-cell GES; P=.0165 for CD19 expression) but not SOC (P=.9374 for B-cell GES; P=.5526 for CD19 expression). Axi-cel showed superior EFS over SOC irrespective of B-cell GES and CD19 expression (P=8.56e–9 for B-cell GES high; P=.0019 for B-cell GES low; P=3.85e–9 for CD19 gene high; P=.0017 for CD19 gene low). Low CD19 expression in malignant cells correlated with a tumor GES consisting of immune suppressive stromal and myeloid genes, highlighting the inter-relation between malignant cell features and immune contexture substantially impacting axi-cel outcomes. Tumor burden, lactate dehydrogenase, and cell-of-origin impacted SOC more than axi-cel outcomes. T-cell activation and B-cell GES, which are associated with improved axi-cel outcome, decreased with increasing lines of therapy. These data highlight differences in resistance mechanisms to axi-cel and SOC and support earlier intervention with axi-cel.

overall_design: 256 pretreatment tumor biopsies were analyzed, 134 from the Axicabtagene Ciloleucel arm and 122 from the Standard of Care Chemotherapy arm

first: Gayatri

last: Tiwari

first: Justin

last: Budka


title: Distinct ontogenetic lineages dictate cDC2 heterogeneity marrow of humans

city: London

first: Hector

last: Huerga Encabo

address: The Francis Crick Institute, 1 Midland Rd

institute: The Francis Crick Institute

summary: Type 2 pre-cDCs are considered as a homogeneous population in the bone marrow but have show that this is not the case in mice. We used single cell RNA sequencing to show that  the bone marrow  of humas, as it is the case for mice, contains two subsets of progenitors that are primed  to give rise to different cDC2 subsets in peripheral tissues.

overall_design: cDCs and their progenitors isolated  from the bone marrow of human donours were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: H

first: D

last: Bonnet


title: Spatially resolved transcriptional landscape of human knee cartilage in patients with osteoarthritis (OA) and non-OA controls

status: Public on Feb 05 2024

city: Xi'an

first: Yue

address: Yanta West Road No.76

institute: Xi'an Jiaotong University

summary: The characterization of knee articular cartilage changes with different zones -- articular surface, (AS), superficial zone (SZ), middle zone (MZ), and deep zone (DZ) -- based on the organization of the tissue and the alignment degree of collagen fibers. To comprehensively explore the spatial landscape of chondrocytes on human knee articular cartilage, we carried out the laser capture microdissection (LCM) coupled with full-length mRNA sequencing.

overall_design: 124 samples of 9 cartilage samples from 4 patients with OA and 1 non-OA control

first: Xiaogao

last: Meng

first: Guangdun

last: Peng

first: Shiquan

last: Sun


title: Response to tumor- infiltrating lymphocyte adoptive therapy is associated with preexisting CD8+T- myeloid cell networks in melanoma [CD45 scRNAseq]

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

institute: Centre hospitalier universitaire vaudois

summary: Adoptive cell therapy (ACT) using ex vivo–expanded tumor-infiltrating lymphocytes (TILs) can eliminate or shrink metastatic melanoma, but its long-term efficacy remains limited to a fraction of patients. Using longitudinal samples from 13 patients with metastatic melanoma treated with TIL-ACT in a phase 1 clinical study, we interrogated cellular states within the tumor microenvironment (TME) and their interactions. We performed bulk and single-cell RNA sequencing, whole-exome sequencing, and spatial proteomic analyses in pre- and post-ACT tumor tissues, finding that ACT responders exhibited higher basal tumor cell–intrinsic immunogenicity and mutational burden. Compared with nonresponders, CD8+ TILs exhibited increased cytotoxicity, exhaustion, and costimulation, whereas myeloid cells had increased type I interferon signaling in responders. Cell-cell interaction prediction analyses corroborated by spatial neighborhood analyses revealed that responders had rich baseline intratumoral and stromal tumor–reactive T cell networks with activated myeloid populations. Successful TIL-ACT therapy further reprogrammed the myeloid compartment and increased TIL-myeloid networks. Our systematic target discovery study identifies potential T-myeloid cell network–based biomarkers that could improve patient selection and guide the design of ACT clinical trials.

overall_design: Melanoma tumor gene expression profiling pre and post TIL adoptive cell therapy by CD45-sorted single cell RNAseq

first: Alexandre

last: Harari

first: Denarda

last: Dangaj

first: George

last: Coukos


title: Response to tumor- infiltrating lymphocyte adoptive therapy is associated with preexisting CD8+T- myeloid cell networks in melanoma [scTCRseq]

overall_design: Melanoma tumor gene expression profiling pre and post TIL adoptive cell therapy by CD45-sorted single cell TCRseq


title: JAK-STAT signaling maintains homeostasis in T cells and macrophages (RNA-seq)

first: Christoph

last: Bock

overall_design: 471 RNA-seq samples of spleen-derived immune cells with mutations of JAK-STAT signaling components

first: Nikolaus

last: Fortelny

first: Matthias

last: Farlik

first: Victoria

last: Gernedl

first: Anna-Dorothea

last: Gorki

first: Caroline

last: Lassnig

first: Barbara

last: Maurer

first: Katrin

last: Meissl

first: Marlies

last: Dolezal

first: Laura

last: Boccuni

first: Aarathy

last: Geetha

first: Anzhelika

last: Karjalainen

first: Stephen

last: Shoebridge

first: Asma

last: Farhat

first: Thomas

last: Penz

first: Anastasiya

last: Hladik

first: Tobias

last: Suske

first: Mojoyinola

last: Ola

first: Sophie

last: Zahalka

first: Martin

last: Senekowitsch

first: Daniele

last: Barreca

first: Florian

last: Halbritter

first: Sabine

last: Macho-Maschler

first: Heidi

last: Neubauer

first: Richard

last: Moriggl

first: Sylvia

last: Knapp

first: Veronika

last: Sexl

first: Birgit

last: Strobl

last: Decker

first: Mathias

last: Müller


title: Frac-seq in mESCs with and without TIP60

status: Public on Jan 30 2024

city: Illkirch

first: Manuel

last: Mendoza

address: 1 rue Laurent Fries

institute: INSTITUTE OF GENETICS AND MOLECULAR AND CELLULAR BIOLOGY

summary: Transcript buffering entails the reciprocal modulation of mRNA synthesis and degradation rates, ensuring a constant RNA concentration amidst changes in cellular conditions. While an increasing body of research supports a global, non-sequence-specific linkage between mRNA synthesis and degradation, the underlying mechanisms remain elusive. To explore this, we investigated alterations in RNA metabolism following the acute depletion of TIP60/KAT5, the transcriptional coactivator and acetyltransferase subunit of the NuA4 complex, in mouse embryonic stem cells. By combining RNA sequencing of nuclear, cytoplasmic, and newly synthesised transcript fractions with biophysical modelling, we show that TIP60 activates transcription of numerous genes, with substantially fewer genes undergoing transcriptional repression. Surprisingly, specific RNA species' transcription changes triggered by TIP60 depletion were counterbalanced by compensatory adjustments in RNA export and/or stability within the nucleus and in RNA stability within the cytoplasm. These discoveries imply that transcript buffering operates on a gene-specific level and suggest that cells continually monitor RNA molecule counts in nuclear and cytoplasmic compartments to maintain cellular homeostasis.

overall_design: Cytoplasmic and Nuclear RNA Purification. 19 samples, 2 conditions (TIP60-AID transgenic mESC line treated with auxin for 24h or DMSO), 3 fractions (cytoplasmic, nuclear, total)

first: Faezeh

last: Forouzanfar


title: Response to tumor- infiltrating lymphocyte adoptive therapy is associated with preexisting CD8+T- myeloid cell networks in melanoma

first: David

last: Barras

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


title: JAK-STAT pathways maintain homeostasis in immune cells (ATAC-Seq)

first: Christoph

last: Bock

overall_design: 496 ATAC-seq samples of spleen-derived immune cells with mutations of JAK-STAT signaling components

first: Nikolaus

last: Fortelny

first: Matthias

last: Farlik

first: Victoria

last: Gernedl

first: Anna-Dorothea

last: Gorki

first: Caroline

last: Lassnig

first: Barbara

last: Maurer

first: Katrin

last: Meissl

first: Marlies

last: Dolezal

first: Laura

last: Boccuni

first: Aarathy

last: Geetha

first: Anzhelika

last: Karjalainen

first: Stephen

last: Shoebridge

first: Asma

last: Farhat

first: Thomas

last: Penz

first: Anastasiya

last: Hladik

last: Suske


title: JAK-STAT signaling maintains homeostasis in T cells and macrophages

last: Bock

overall_design: The experimental design is described in the SubSeries listed below.


title: Target knockdown after systemic OTV administration in mice

status: Public on Feb 12 2024

city: South San Francisco

first: David

last: Tatarakis

email: tatarakis@dnli.com, genomics@dnli.com

address: 161 Oyster Point Blvd

department: Discovery Genomics

institute: Denali Therapeutics

summary: Using single nucleus RNA sequencing, we knockdown of Malat1 across all cell types upon peripheral administration of OTV:Malat1.

overall_design: TfR.KI mice received four weekly doses of 60mpk OTV:Malat1, nonTV:Malat1, Malat1 ASO (at an ASO-equivalent dose), or TV with no ASO. Tissues were harvested 72 hours after the final dose and snap frozen for molecuar analysis.

first: Scarlett

last: Barker

first: Connie

last: Ha

last: Sandmann