title: Maternal Exercise Prior to and During Gestation Induces Sex-Specific Alterations in the Mouse Placenta

status: Public on Jan 31 2024

city: Little Rock

first: Meghan

middle: Lynne

last: Ruebel

state: AR

address: 15 Children's Way

institute: USDA-ARS/Arkansas Childrens Hospital

summary:
Examined the role of maternal voluntary wheel running commencing 10 weeks prior to gestation, and throughout pregnancy, on placental transcriptome in late gestation
While exercise (EX) is beneficial during pregnancy for both mother and child, little is known about the mechanisms by which maternal (MAT EX) mediates changes in utero. We hypothesized that effects of MAT EX prior to and during gestation will be evident in transcriptomic signatures in the placenta and will be sexually dimorphic.  Six-week-old female C57BL/6 mice were divided into 2 groups; with (exercise, EX; N = 7) or without (sedentary, SED; N = 8) access to voluntary running wheels. EX was provided via 24-hour access to wheels for 10 weeks prior to conception until late pregnancy (18.5 days post coitum).  Sex-stratified placenta and fetal livers were collected.  Mi-croarray analysis of SED and EX placenta revealed that MAT EX affected gene transcript expression of 283 and 661 transcripts in male and female placenta (±1.4-fold, p < 0.05).  Gene-set enrichment and Ingenuity Pathway analyses of male placenta showed that MAT EX led to inhibition of sig-naling pathways, biological functions, and down regulation of transcripts related to lipid and steroid, while MAT EX in female placentas led to activation of pathways, biological functions, and gene expression related to muscle growth, brain, vascular development, and growth factors. Overall, our results suggest that effects of MAT EX on the placenta and presumably on the offspring are influenced by maternal habitus and are sexually dimorphic.

overall_design: Six microarrays  were used for each group (Sedentary vs Exercise), representing six placentas per group. A n=3 microarrays per sex/group were used (ie n=3 male_SED, n=3 female_SED, n=3 Male_EX, N=3 female_EX)

first: Sarah

last: Borengessar

first: Kartik

last: Shankar


title: Role of ATP-dependent chromatin remodellers in regulating global gene expression in Saccharomyces cerevisiae

status: Public on Feb 08 2024

city: Srinagar

first: Ajaz ul Hamid

last: Wani

state: Jammu and Kashmir

address: Hazratbal

department: Biotechnology

country: India

institute: University of Kashmir

type: Expression profiling by high throughput sequencing

summary: We report change in the gene expression levels and this change is associated with the change in higher order folding upon deletion of ATP-dependent chromatin remodellers.

overall_design: RNA was extracted from both wildtype and triple deletion (ISW1, ISW2 and CHD1) strain using acidic phenol: chloroform method, ribosomal RNA was depleted by ribozero kit, cDNA was generated by kit, and cDNA library were prepared for NGS and sequenced.

first: Ajazul

last: Hamid Wani

first: Fouziya

last: Rashid


title: Analysis of transcriptomes from filling endosperms of zmnac128 zmnac130 mutants

status: Public on Jan 10 2024

city: Hefei

first: Di

last: Peng

address: Huangshan Road 443

country: China

institute: University of Science and Technology of China

summary: TO explore the transcriptional role of ZmNAC128 and ZmNAC130 and to explore core genes in their regulatory network combined with previous transcriptomes

overall_design: The 16-DAP endosperm of wild type (F2 offsprings of B73 and KN5585) and zmnac128 zmnac130 mutant(F2 offsprings of B73 and KN5585) are used to perform RNA-seq.


title: Tumor-infiltrating Monocytic Myeloid-derived suppressor cells play a key role in forming immunosuppressive microenvironment in  human gastric cancer

status: Public on Jan 22 2024

city: Fukuoka

first: Chikanori

last: Tsutsumi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Surgery and Oncology, Graduate School of Medical Sciences

country: Japan

institute: Kyushu University

summary: The present data suggest that M-MDSC, play a predominant role in forming the immunosuppressive microenvironment in GC.

overall_design: We performed scRNA-seq analysis from 17 gastric cancers, 8 esophageal squamous cell carcinoma, 10 normal gastric mucosae, and 5 normal esophageal mucosae.

first: Kenoki

last: Ohuchida


title: CD8+ T cell-derived Fgl2 regulates immunity in a cell-autonomous manner

status: Public on Jan 05 2024

city: Atlanta

first: Kelsey

last: Bennion

state: Georgia

address: 201 Dowman Drive

department: Surgery

country: USA

institute: Emory University

summary: The regulatory circuits dictating CD8+ T cell responsiveness vs. exhaustion during anti-tumor immunity are incompletely understood. Here, we report that tumor-infiltrating antigen-specific PD-1+ TCF-1- CD8+ T cells express the immunosuppressive cytokine Fgl2. Conditional deletion of Fgl2 from antigen-specific CD8+ T cells prolonged CD8+ T cell persistence, decreased phenotypic and transcriptomic signatures of T cell exhaustion, and improved tumor control. Melanoma patients who died of their disease exhibited increased expression of Fgl2 in tumor-infiltrating CD8+ T cells as compared to those who survived. PD-1+CD8+ T cell-derived Fgl2 also negatively regulated virus-specific T cell responses in a model of chronic viral infection. Mechanistically, the enhanced responsiveness of Fgl2-deficient CD8+ T cells is underpinned by the interaction of Fgl2 with CD8+ T cell-expressed FcγRIIB, ligation of which results in caspase 3/7-mediated apoptosis. These data illuminate a novel cell-autonomous regulatory axis by which PD-1+ CD8+ T cell responses are regulated in vivo.

overall_design:
WT or Fgl2-/- OT-I tumor-specific CD8+ T cells were given to mice a day prior to B16-OVA challenge. On day 14 post tumor challenge, the spleens of the mice were harvested, and OT-I T cells were isolated by sorting on CD3+CD8+Thy1.1+ (congenic marker) for subsequent bulk RNA-sequencing
Emory NPRC Genomics Core (contributor)

first: Mandy

last: Ford

first: Danya

last: Liu


title: GQIcombi application to subdue glioma via differentiation therapy

status: Public on Jan 09 2024

city: Moscow

first: Varvara

last: Kolesnikova

state: Russian Federation

address: Moscow, Butlerova st., 5A

country: Russia

institute: IHNA&NPh RAS

summary: Modern therapy approaches fail to prevent high grade glioma recurrence. So, alternative ways need to be developed. Changing glioma cells’ fate is an alternative way to prevent tumor growth. Two-step protocol based on an antiproliferative G-quadruplex and small molecules triggering neural differentiation showed to be effective on glioblastoma cell cultures. This approach was named a differential therapy. In this paper, we broaden the spectrum of cell cultures to gliomas of II, III and IV grades, showing the universality of suggested protocol on a variety of cancer cells. We checked the reasonability of consistent addition of factors to the glioma cells. Moreover, we demonstrated a significant inhibition of tumor growth after injection of GQIcombi into 101/8 tumor in glioma rat model. Thus, the proposed strategy of influencing on cancer cell growth is applicable to be further translated for therapy use.

overall_design: To investigate the influence of combination of an antiproliferative aptamer and neuroinducing small molecules - GQIcombi - on glioma cell culture of IV Grade, we sequentially added these factors to cells and collected cells for transcriptomic analisys on the 10th day of the experiment.

first: Galina

last: Pavlova

first: Dmitry

last: Usachev


title: Disease modifying therapy impacts on miRNA expression profiling in peripheral blood from Relapsing-Remitting Multiple Sclerosis patients

status: Public on Jan 03 2024

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

summary: Multiple sclerosis (MS) is a chronic and progressive neurological disease. MS is characterized by early-stage neuroinflammation, neurodegeneration, and demyelination, with a spectrum of heterogeneous clinical manifestations in terms of disease course and response to therapy. The currently unsatisfied availability of diagnostic and prognostic biomarkers concerning disease progression and treatment response represents an important requirement for therapy individualization and drug efficacy. Specific Disease Therapies (DMTs) are available to prevent MS-related brain damage; however, the specific drug choice is still under debate and needs further characterization. Since differentially expressed miRNAs have been proposed as diagnostic tools in neurodegenerative/neuro-inflammatory diseases, such as multiple sclerosis, amyotrophic lateral sclerosis, and Alzheimer's disease, we characterized the miRNA expression profiling in peripheral blood mononuclear cells (PBMC) of subjects with relapsing-remitting MS treated with high efficacy DMTs: Cladribine (CLA, n=11 patients) or Ocrelizumab (OCRE, n=14 patients). The treated patients were compared to control (CTR) untreated subjects (n=15). Blood samples were collected from patients before treatment (time t0) and 6 months post-treatment (time t1), but just once from control subjects.  CLA drug tablets were administered to the selected relapsing-remitting MS patients with a dosage of 1.75 mg/kg given for 5 days. OCRE drug was administered to the other relapsing-remitting MS patients by infusion with a dosage of 300 mg, twice in two weeks.

overall_design: We measured miRNA expression profile, using Agilent microarray, in MS patients and control subjects without MS.  Patients were treated either with Cladribine (CLA, n=11 patients) or with Ocrelizumab (OCRE, n=14 patients). Peripheral blood samples were collected from patients before treatment (time t0) and 6 months post-treatment (time t1), but just once at time t0 from control subjects.

first: Leonardo

last: Malimpensa

first: Valeria

last: Manzini

first: Rossella

last: Brandi

first: Chiara

last: D’Amelio

first: Tommaso

last: Gosetti di Sturmeck

first: Sebastiano

last: Crisafulli

first: Gina

last: Ferrazzano

first: Daniele

last: Belvisi

first: Francesca

last: Malerba

first: Rita

last: Florio

first: Esterina

last: Pascale

first: Marco

last: Salvetti

first: Antonino

last: Cattaneo

first: Mara

last: D’Onofrio

first: Antonella

last: Conte


title: Targeting Valine Catabolism for Selective Inhibition of Metabolic Reprogramming in Prostate Cancer

status: Public on Jan 18 2024

city: Brisbane

first: Charles

middle: Liam

last: Bidgood

state: QLD

address: Translational Research Institute, 37 Kent Street, Woolloongabba

department: School of Biomedical Sciences

country: Australia

institute: Queensland University of Technology

summary: Metabolic reprogramming and energetic rewiring are hallmarks of cancer which fuel disease progression and facilitate evasion to the rising anti-tumour pressures introduced by therapy. The remodelling of oxidative phosphorylation and enhanced lipogenesis have previously been characterised as key metabolic features of prostate cancer (PCa). Recently, succinate-dependent mitochondrial reprogramming was identified in high-grade PCa tumours, as well as upregulation of the enzymes associated with branched-chain amino acid (BCAA) catabolism. In this study, we hypothesised that the degradation of the BCAAs, particularly valine, may play a critical role in anapleurotic refuelling of the mitochondrial succinate pool, as well as the maintenance of intracellular lipids in PCa.

overall_design: To investigate the global transcriptomic implications of valine catabolism inhibition on LNCaP prostate cancer cells by siRNA knockdown of 3-hydroxyisobutyryl-CoA hydrolase (HIBCH).

middle: L

first: Lisa

middle: K

last: Philp

first: Anja

last: Rockstroh

first: Melanie

last: Lehman

first: Colleen

middle: C

last: Nelson

first: Martin

last: Sadowski

first: Jennifer

middle: H

last: Gunter


title: Homeobox regulator Wilms tumour 1 (WT1) is displaced by androgen receptor at cis-regulatory sites in the endometrium of PCOS patients.

status: Public on Feb 16 2024

city: Swansea

first: David

last: James

address: Swansea University, Singleton Park

department: Medical School

country: United Kingdom

institute: Swansea University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Polycystic ovary syndrome (PCOS) is a common gynaecological disorder, characterised by elevated circulating androgens and increased expression of androgen receptor (AR) and by downregulation of Wilms Tumour 1 in the endometrium, The objectives of this study are: 1) Understand the functional role of WT1 in regulating decidualization response in healthy endometrial tissue, and 2) understand how interactions between aberrant WT1 and AR expression in PCOS patients result in dysregulation of deciduallization processes

overall_design: Endometrial stromal cells isolated from 3 healthy patients were pooled together, grown to confluency and treated with cAMP. One chromatin sample (containing genetic background from 3 different patients) was immunoprecipitated with an anti-WT antibody and subsequently submitted to ChIP-Seq

middle: W

first: Robert

middle: S

last: Conlan

first: Marcos

last: Quintella


title: Tumor-infiltrating monocytic myeloid-derived suppressor cells contribute to the development of an immunosuppressive tumor microenvironment in gastric cancer

status: Public on Jan 19 2024

first: Chikanori

last: Tsutsumi

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

overall_design: Refer to individual Series


title: m6A RIP-seq for Cytokine-treated Islets and Beta-cells or T1D Islets

status: Public on Jan 01 2024

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

type: Methylation profiling by high throughput sequencing

summary: Type 1 Diabetes (T1D) is characterized by autoimmune-mediated destruction of insulin-producing beta-cells. Recent research has focused on the role of the innate immune system in initiating this process. To investigate this further, we used m6A-profiling of human islets from non-diabetic individuals and the human beta-cell line EndoC-bH1 treated with PBS or interleukin 1 beta and interferon alpha, as well as established T1D patients. Our findings reveal that N6-Methyladenosine (m6A) is a mechanism that helps protect beta-cells by accelerating the decay of mRNA from the 2'-5'-oligoadenylate synthetase (OAS) genes, which controls the antiviral innate immune response at the onset of T1D. These results provide insight into the adaptive safeguarding mechanisms of beta-cells and the role of m6A in T1D development, highlighting potential targets for therapeutic interventions.

overall_design: RNA-seq and m6A RIP-seq  were performed on cytokine-treated human islets and beta-cell line EndoC-bH1, or islets from control and T1D patients.

first: Dario

last: DeJesus

first: Rohit

last: Kulkarni


title: Analysis of extracellular vesicle microRNA profiles reveals distinct blood and lymphatic endothelial cell origins

status: Public on Jan 17 2024

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

type: Non-coding RNA profiling by high throughput sequencing


title: Differential gene expression in beta cells and non-beta cells from islets of NOD mice

summary: Diabetes (T1D) is a disease in which the immune system destroys the insulin-producing beta cells. Recently, researchers have become interested in the role of the innate immune system in initiating this process. To further investigate this, we used RNA-seq to analyze sorted beta cells from non-diabetic and pre-diabetic female non-obese models of diabetes (NOD). These results shed light on the potential involvement of m6A mediators in the development of T1D, highlighting a promising avenue for future research.

overall_design: RNA-seq was performed on FACS sorted islet cells by autofluorescence beta and non-beta cells from NOD female mice.


title: NCoR1 limits angiogenic capacity by altering Notch signaling [RNA]

status: Public on Feb 12 2024

city: Frankfurt

first: Simonida

last: Zehr

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

country: Germany

institute: Goethe University, Frankfurt am Main, Germany,

summary: Corepressors negatively regulate gene expression by chromatin compaction. Targeted regulation of gene expression could provide a means to control endothelial cell phenotype. We hypothesize that by targeting corepressor proteins, endothelial angiogenic function can be improved. To study this, the expression and function of nuclear corepressors in human umbilical vein endothelial cells (HUVEC) and in murine organ culture was studied. RNA-seq revealed that nuclear receptor corepressor 1 (NCoR1), Silencing Mediator of Retinoid and Thyroid hormone receptors (SMRT) and repressor element-1 silencing transcription factor (REST) are the highest expressed corepressors in HUVECs. Knockout and knockdown strategies demonstrated that the depletion of NCoR1 increased the angiogenic capacity of endothelial cells, whereas depletion of SMRT or REST did not. Interestingly, the effect was VEGF signaling independent. NCoR1 depletion significantly upregulated angiogenesis-associated genes, especially tip cell genes, including ESM1, DLL4 and NOTCH4, as observed by RNA- and ATAC-seq. Confrontation assays comparing cells with and without NCoR1-deficiency revealed that loss of NCoR1 promotes a tip-cell position during spheroid sprouting. Moreover, a proximity ligation assay identified NCoR1 as a direct binding partner of the Notch-signaling-related transcription factor RBPJk. Luciferase assays showed that siRNA-mediated knockdown of NCoR1 promotes RBPJk activity. Furthermore, NCoR1 downregulation prompts upregulation of several elements in the Notch signaling cascade. Downregulation of NOTCH4, but not NOTCH1, prevented the positive effect of NCoR1 knockdown on spheroid outgrowth. Collectively, these data indicate that decreasing NCOR1 expression is an attractive approach to promote angiogenic function.

overall_design: RNA sequencing (n = 3) of human umbilical vein endothelial cells (HUVEC) treated with either negative control siRNA #12935300 or siRNA #HSS114352, which knocks down NCoR1  expression.

first: Tom

last: Teichmann

first: Pedro

last: Malacarne

first: Stefan

last: Günther

first: Beatrice

last: Pflüger-Müller

first: Timothy

last: Warwick

first: Ralf

middle: P

last: Brandes


title: Body-wide genetic deficiency of poly(ADP-ribose) polymerase 14 sensitizes mice to colitis

status: Public on Jan 13 2024

city: Turku

first: Madhukar

last: Vedantham

address: Kiinamyllynkatu 10-D

country: Finland

institute: University of Turku

summary: Inflammatory bowel disease (IBD) is a debilitating and relapsing chronic disease of the gastrointestinal tract affecting millions of people. Here, we investigated the expression and functions of poly (ADP-ribose) polymerase 14 (Parp14), an important regulator of immune cells functions, using a biobank IBD patient cohort as well as the oral dextran sulfate sodium (DSS) exposure mouse IBD colitis, and, in parallel, the oral Salmonella exposure mouse colitis models. Parp14 was expressed in the human colon, by cells in the lamina propria, but, in particular, by the epithelial cells with a typical granular staining pattern in the cytosol. The same Parp14 staining pattern was evidenced in both mouse models. Body-wide genetic deficiency of Parp14 in C57BL/6N background sensitized mice to DSS colitis, i.e., the Parp14-deficient mice displayed increased rectal bleeding as well as stronger epithelial erosion, Goblet cell loss and immune cell infiltration. The absence of Parp14 did not cause mouse colon bacterial dysbiosis based on PacBio long read sequencing. Also, the colon leukocyte populations of Parp14-deficient mice appeared nominal based on flow cytometry. In contrast, we witnessed an altered transcriptional signature in Parp14-deficient mice with bulk tissue RNA-Seq. Gene Ontology (GO)-based classification of differentially expressed genes demonstrated that the colon transcriptional signature of Parp14-deficient mice was dominated by abnormalities in inflammation and infection response both prior and after the DSS exposure. The data indicate that Parp14 has an important role in the maintenance of epithelial barrier integrity in colitis, and that Parp14 may have functions also outside the immune cell compartment. The prognostic and predictive biomarker potential of Parp14 as well as its mutational landscape in IBD merits further investigation.

overall_design: To investigate the transcriptome changes in colon of Parp14-deficient mice when compared to wt mice in resting state and post DSS-induced colitis, we performed bulk tissue RNA-Seq analysis of the mouse colon distal sections post-DSS treatment at day 8.

first: Arto

last: Pulliainen


title: Analysis of extracellular vesicle microRNA profiles reveals distinct blood and lymphatic endothelial cell origins [small RNA]

summary: Extracellular Vesicles (EVs) are crucial mediators of cell-to-cell communication in physiology but also in pathological conditions. Specifically, EVs released from the vasculature into blood were found to be quantitatively and qualitatively different in diseases versus healthy states. However, our understanding on EVs derived from the lymphatic system is still scarce. In this study we compared the mRNA and miRNA expression in blood vascular (BEC) and lymphatic (LEC) endothelial cells.  After characterization of the EVs by fluo-triggered flow cytometry, nanoparticle tracking analysis and cryo-EM we utilized small RNA-sequencing to characterize miRNA signatures in the EVs and thereof identify cell-type specific miRNAs in BEC and LEC. We believe that our data provide a solid basis for further functional in vitro and in vivo studies addressing the role of EVs in the blood and lymphatic vasculature.

overall_design: Different endothelial cells (especially lymphatic and blood endothelial cells) were used to derive Extracellular vesicles. Conditioned cells were collected after EVs were harvested. Intracellular RNA as well as RNA isolated from Evs was used to perform smallRNA sequencing. Quantification of miRNA transcriptome was performed.

first: Marianne

last: Pultar

first: Johannes

last: Oesterreiche

first: Jaana

last: Hartmann

first: Moritz

last: Weigl

first: Katharina

last: Schimek

first: Thomas

last: Heuser

first: Marlene

last: Brandstetter

last: Grillari

first: Peter

last: Sykacek

first: Matthias

last: Hackl

first: Wolfgang

last: Holnthoner


title: Analysis of extracellular vesicle microRNA profiles reveals distinct blood and lymphatic endothelial cell origins [mRNA]

first: Andreas

last: Diendorfer

overall_design: Different endothelial cells (especially lymphatic and blood endothelial cells) were used to derive Extracellular vesicles. Conditioned cells were collected after EVs were harvested. Intracellular RNA was used to perform mRNA and smallRNA sequencing.


title: Investigating the role of telomere length in 3D spatiotemporal gene regulation in cardiomyocytes [CUT&Tag]

status: Public on Dec 31 2023

city: Shanghai

first: Bin

last: Li

address: Jinzun Road

institute: Shanghai jiaotong University

type: Genome variation profiling by high throughput sequencing

summary: Telomeres, TTAGGGn DNA repeat sequences located at the ends of eukaryotic chromosomes, play a pivotal role in ageing and are targets of DNA damage and DNA damage response. Although short telomeres have been implicated in heart failure, little is known about the role of telomeres in cardiomyocytes.To fill this gap in knowledge, we studied myocardial ageing in the form of telomere lengths under isogenic background.

overall_design: CUT&Tag for FOXC1 in CONTROL and FOXC1 OE hiPSCs-derived cardiomyocytes.

first: Alex

last: Chang

first: Qian

last: Bian

first: Wu

last: zuo


title: P. falciparum-specific Genomic Context Protein-Binding Microarray

city: State College

first: Manuel

last: Llinás

state: Pennsylvania

address: W122 Millennium Science Complex, Pollock Road

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary: Development of the human malaria parasite, Plasmodium falciparum is regulated by a limited number of sequence-specific transcription factors (TFs). However, the mechanisms by which these TFs recognize genome-wide binding sites to regulate target genes is still largely unknown. To address TF target specificity, we investigated the binding of two TF subsets that either bind CACACA or GTGCAC and further characterized PfAP2-G and PfAP2-EXP which bind unique DNA motifs (GTAC and TGCATGCA). We interrogated the impact of DNA sequence context and the chromatin landscape on P. falciparum TF binding using high-throughput in vitro and in vivo binding assays, DNA shape predictions, epigenetic post-translational modifications, and chromatin accessibility. We determined that DNA sequence context does not greatly impact binding site selection for CACACA-binding TFs, while chromatin accessibility, epigenetic patterns, co-factor recruitment, and dimerization contribute to differential binding. In contrast, GTGCAC-binding TFs prefer different sequence contexts, DNA shape profiles, and chromatin dynamics. Finally, we find that TFs that preferentially bind divergent DNA motifs may bind overlapping genomic regions in vivo due to low-affinity binding to other sequence motifs. Our results demonstrate that TF binding site selection relies on a combination of DNA sequence and chromatin features, thereby contributing to the complexity of P. falciparum gene regulatory mechanisms.

overall_design: 4x180k high-density Genomic Context Protein-Binding Microarray (gcPBM) representing over 24,000 unique genomic regions from the P. falciparum genome. This array design was used to test eight specific DNA-binding domains (DBDs) against motif-containing sites from the P. falciparum genome. Using position weight matrix (PWM) data from published work (De Silva et al. 2008 & Campbell et al. 2010), all instances of each motif of interest (i.e., CACACA, GTGCAC, GTAC, and TGCATGCA) were identified in the P. falciparum genome (Plasmodium falciparum 3D7 strain genome release v38), using a motif E-score cutoff of >0.45. Only intergenic regions (excluding telomeric regions) were used for this gcPBM design. The numbers of probes found containing each motif recognized by the eight DBDs are as follows: 2848 probes with putative sites for PF3D7_0420300_D1 (500 negative controls), 4251 probes with putative sites for AP2-LT_D1 (500 negative controls), 3864 probes with putative sites for PF3D7_1305200_D1 (500 negative controls), 4321 probes with putative sites for AP2-HC_D1 (500 negative controls), 1459 probes with putative sites for SIP2_D1 (500 negative controls), 3742 probes with putative sites for AP2-I_D3 (500 negative controls), 8998 probes with putative sites for AP2-G_D1 (1000 negative controls), and 1059 probes with putative sites for AP2-EXP_D1 (1000 negative controls). Any sequence containing another instance of the centered motif in the left or right flanks was mutated to prevent multiple binding sites per 36-bp window. The number of 36-bp genomic regions designed for each TF. HDP1 motif-specific genomic sequences were not initially included in the gcPBM design due to its identification and characterization after the initial design of the gcPBM experiment, and was included after the fact. Due to the similarities between the CACACA and GTGCAC PWMs, there were genomic DNA sequences that led to redundant probe designs, which were discarded, leaving only one instance of the sequence. After discarding redundant probe designs with motif types, the total number of probes per motif group is as follows: 9388 probes with putative CACACA sites (1834 CACACA negative controls), 1394 probes with putative GTGCAC sites (736 GTGCAC negative controls), 8998 probes with putative GTAC sites (620 GTAC negative controls), and 1059 probes with putative TGCATGCA sites (612 TGCATGCA negative controls). Overall, the P. falciparum gcPBM design reached a total of 24,641 unique genomic regions. Each DNA probe was replicated in random areas of the microarray surface (CACACA/GTGCAC with 8 replicates per sequence and GTAC/TGCATGCA with 6 replicates per sequence), which brought the total number of DNA probes to 174,550 spots for a 4x180k microarray (Agilent Technologies). Additional spots on the array were set aside for control grid alignment, microarray scanning, and downstream analysis.

first: Victoria

middle: A

last: Bonnell

first: Yuning

last: Zhang

first: John

last: Horton

first: Raluca

last: Gordân


title: MNase titration-Seq of Saccharomyces cerevisiae.

first: Ajaz ul Hamid

last: Wani

summary: We report change in the nucleosome occupancy and accessibility upon deletion of ATP-dependent chromatin remodellers (ISW1, ISW2 & CHD1) in Saccharomyces cerevisiae.

overall_design: Both wildtype and triple deletion strains chromatin was crosslinked, digested with increasing concentrations of MNase, and after DNA purification NGS library was prepared and sequenced.

first: Ajazul

first: Fouziya

last: Rashid


title: Investigating the role of telomere length in 3D spatiotemporal gene regulation in cardiomyocytes [RNA-Seq]

overall_design: Whole transcriptomic analyses of of nTL- and sTL- hiPSCs-derived cardiomyocytes.

last: Zuo


title: Investigating the role of telomere length in 3D spatiotemporal gene regulation in cardiomyocytes [Hi-C]

overall_design: In this study, the dynamics of chromatin structure of nTL-CMs and sTL-CMs were depicted.


title: Expression of profilin 2 isoforms was associated with lung metastasis of colorectal cancer as revealed by a comprehensive gene expression study using mice model

city: Utsunomiya

first: Naoyuki

last: Toyota

state: Tochigi

institute: Tochigi Cancer Center

summary: Cell lines that were highly metastatic to the lung  were sequenced to explore the difference of gene expression.

overall_design: In a mouse model, cell lines that were highly metastatic to the lung were established by injecting colorectal cancer cells through the tail vein and recovering them from the lungs. Differential gene expression was investigated using DNA microarrays by comparing the cells with their parental cells.

first: Y

last: Tajima


title: Effect of miR-939 overexpression on gene expression in heat-killed S. aureus-stimulated keratinocytes

status: Public on Dec 11 2023

city: nanjing

first: wang

last: jiating

state: jiangsu

address: 12 Jiang Wangmiao Street

institute: Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Atopic dermatitis (AD) is a common, chronic inflammatory skin disease that seriously affects quality of life and is a major cause of skin diseases worldwide. Staphylococcus aureus (S. aureus) colonization on the skin plays an important role in the pathogenesis of AD; however, the mechanism of how it modulates skin immunity to exacerbate AD remains unclear. MicroRNAs are short non-coding RNAs that act as post-transcriptional regulators of genes. They are involved in the pathogenesis of various inflammatory skin diseases. In this study, we established miRNA expression profiles for keratinocytes stimulated with heat-killed S. aureus (HKSA). We found that miR-939 was highly upregulated in HKSA-stimulated keratinocytes and AD lesions. In vitro studies revealed that miR-939 increased the expression of matrix metalloproteinase genes, including MMP1, MMP3, and MMP9, as well as the cell adhesion molecule ICAM1 in human primary keratinocytes. In vivo studies indicated that miR-939 increased the expression of matrix metalloproteinases to promote the colonization of S. aureus and exacerbated S. aureus-induced AD-like skin inflammation. Taken together, these findings suggest that miR-939 is an important regulator of skin inflammation in AD.

overall_design: To perform an unbiased study of miR-939 function in keratinocytes, we performed a global transcriptomic analysis in keratinocytes with miR-939 overexpression followed by HKSA stimulation. Keratinocytes transfected with hsa-miR-939-5p mimic or the corresponding negative control, followed by treatment with HKSA or PBS for 8 h were subject to RNA sequencing.

first: Jiating

last: Wang

first: Xinfeng

last: Wu

first: Dongqing


title: The interferon-rich skin environment regulates Langerhans cell ADAM17 to promote photosensitivity in lupus

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

summary: The autoimmune disease lupus erythematosus (lupus) is characterized in part by photosensitivity, where patients can develop inflammatory skin lesions with even ambient ultraviolet radiation (UVR) exposure. Evidence points to a role for type I interferon (IFN-I) in photosensitivity, but mechanistic understanding remains limited. We have shown that photosensitivity in lupus models is at least in part attributable to Langerhans cell (LC) dysfunction. Healthy LCs limit photosensitivity via a disintegrin and metalloprotease 17 (ADAM17), a sheddase that normally limits UVR-induced skin inflammation by releasing soluble epidermal growth factor receptor (EGFR) ligands to support keratinocyte survival. On the other hand, LCs from lesional and even non-lesional lupus model skin show reduced ADAM17 activity and mRNA expression. Non-lesional human lupus skin also showed evidence of LC dysfunction, and, here, we asked how the lupus skin environment contributes to this dysfunction. We show that non-lesional skin in human CLE and multiple photosensitive lupus models share gene expression patterns consistent with a high IFN environment and LC dysfunction. IFN-I inhibits murine and human LC ADAM17 activity, and anti-IFNAR1 in lupus models restores LC ADAM17 function and reduces photosensitivity in EGFR and LC ADAM17-dependent manners. Reactive oxygen species (ROS) are a mediator of ADAM17 activity, and we show that lupus models have reduced UVR-induced LC ROS generation that is restored by anti-IFNAR1. Our findings suggest shared pathogenic mechanisms of photosensitivity in human and murine lupus skin and a model whereby the IFN-I-rich microenvironment in non-lesional lupus skin inhibits UVR-induced ADAM17 activity, predisposing to photosensitivity. Our data also suggest that the beneficial effects of the recently FDA-approved anifrolumab (anti-IFNAR1) on human lupus skin could act in part by restoring LC function.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from non-lesional ears of MRL/+ vs MRL/lpr mice and B6 vs B6.Sle1yaa mice.

first: Thomas

middle: M

last: Li

first: Noa

last: Schwartz

first: Yurii

last: Chinenov

first: Andrea

middle: R

last: Daamen

first: David

middle: J

last: Oliver

first: Theresa

middle: T

last: Lu


title: BCR repertoire of B cells with distinct developmental timings

status: Public on Dec 17 2023

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

institute: Nihon University

summary: B cells are known to have different properties and BCR repertoires depending on the time of development. Our objective is to investigate the BCR repertoire of B cells across embryonic, neonatal, and adult stages, particularly in cells with a RAG2 expression history. We focus on sequencing and analyzing the immunoglobulin heavy chain (IGH) genes of these cells to understand their BCR diversity and specificity. Additionally, we explore the relationship between B-1a cells and bone marrow IgM+ plasmablasts/plasma cells, aiming to shed light on the development and function of B-1a cells in the immune system.

overall_design: We generated a novel RAG2-based doxycycline-inducible/repressible temporal lymphoid-lineage labeling system, which avoids the potentially toxic effects of tamoxifen on embryos and enables noninvasive labeling to track B cells developed at embryonic, neonatal, and adult periods under native hematopoietic conditions. Utilizing this system in combination with LC1 and Rosa-tdTomato mice, we sorted and analyzed BCR repertoire sequences in B cells developed at these distinct developmental stages.

first: Keiko

last: Fujisaki

first: Ryo

last: Goitsuka


title: An ultra high-throughput, massively multiplexable, single-cell RNA-seq platform in yeasts

status: Public on Dec 27 2023

city: Tempe

first: Leandra

last: Brettner

state: AZ

address: 1001 S McAllister Ave

department: Biodesign Center for Mechanisms of Evolution

institute: Arizona State University

summary: Yeasts are naturally diverse, genetically tractable, and easy to grow such that researchers can investigate any number of genotypes, environments, or interactions thereof. However, studies of yeast transcriptomes have been limited by the processing capabilities of traditional RNA sequencing techniques. Here we optimize a powerful, high-throughput single-cell RNA sequencing (scRNAseq) platform, SPLiT-seq (Split Pool Ligation-based Transcriptome sequencing), for yeasts and apply it to 43,388 cells of multiple species and ploidies. This platform utilizes a combinatorial barcoding strategy to enable massively parallel RNA sequencing of hundreds of yeast genotypes or growth conditions at once. This method can be applied to most species or strains of yeast for a fraction of the cost of traditional scRNAseq approaches. Thus, our technology permits researchers to leverage “the awesome power of yeast” by allowing us to survey the transcriptome of hundreds of strains and environments in a short period of time, and with no specialized equipment. The key to this method is that sequential barcodes are probabilistically appended to cDNA copies of RNA while the molecules remain trapped inside of each cell. Thus, the transcriptome of each cell is labeled with a unique combination of barcodes. Since SPLiT-seq uses the cell membrane as a container for this reaction, many cells can be processed together without the need to physically isolate them from one another in separate wells or droplets. Further, the first barcode in the sequence can be chosen intentionally to identify samples from different environments or genetic backgrounds, enabling multiplexing of hundreds of unique perturbations in a single experiment. In addition to greater multiplexing capabilities, our method also facilitates a deeper investigation of biological heterogeneity given its single-cell nature. For example, in the data presented here we detect transcriptionally distinct cell states related to cell cycle, ploidy, metabolic strategies, etc. all within clonal yeast populations grown in the same environment. Hence, our technology has two obvious and impactful applications for yeast research: the first is the general study of transcriptional phenotypes across many strains and environments, and the second is investigating cell-to-cell heterogeneity across the entire transcriptome.

sample_organism:
Saccharomyces cerevisiae
Candida albicans

overall_design: Diploid s288c, genetically naive haploid BY4741, MATa ura3A0 his3∆1 met17∆0 P ACT1-GAL3::SpHIS5 gall1∆gal10∆::LEU2 leu2∆0::P PGK1 -mCherry-KanMX6 ybr209w∆::B103-HphMX6, and MATa ura3A0 his3∆1 met17∆0 P ACT1-GAL3::SpHIS5 gall1∆gal10∆::LEU2 leu2∆0::P GAL1 -YFP-KanMX6 ybr209w∆::BC3-HphMX6, and ATCC 3147 C. albicans strains were used. Cells were streaked on YP plus 2% dextrose agar plates from frozen -80C glycerol stocks and grown at 30C for 48 hours. In experiments 1 and 2, single colonies of s288c and ATCC 3147 were picked into YP plus 2% dextrose liquid media (YPD). The YFP and mCherry engineered cells were picked into Synthetic Complete minus glucose (Sunrise) plus 2.5% sucrose, 1.25% raffinose, and 0.625% galactose media to induce YFP expression in experiment 2. In experiment 3, diploid s288c cells and haploid BY4741 cells were picked into Synthetic Complete (Sunrise) plus 2% glucose media (SCD). All cultures were grown with shaking at 30C for 24 hours. For experiments 1 and 2, cells were then transferred into fresh YPD media at a 1:250 dilution and grown until cultures reached approximately 2-4*10^7 cells/mL, or early mid log phase. For experiment 3, approximately 15,000 total cells were transferred into 50 mL of fresh SCD and sampled at 17, 19, 21, and 23 hours after inoculation which correspond to approximately 0.9*10^7, 2.7*10^7, 5.7*10^7, and 8.6*10^7 cells/mL.

first: Kerry

last: Geiler-Samerotte


title: Integrin b1 acetylation-induced transcriptomic reprograming of mouse embryonic endothelial cells and functions

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: Reciprocal regulation of integrin-dependent cell-matrix adhesions and cell-cell junctions is critical for controlling endothelial permeability and proliferation in cancer and inflammatory diseases, but remain poorly understood. Here, we investigated how acetylation of the distal NPKY-motif of b1-integrin influences endothelial cell physiology and barrier function. Expression of an acetylation-mimetic B1A-K794Q-GFP mutant induced transcriptomic reprograming of embryonic endothelial cells particularly in genes responsible for cell adhesion, proliferation, polarity and barrier function. B1A-K794Q-GFP induced a constitutive activation of MAPK signaling, an impairment of junctions, increased proliferation and an altered contact inhibition at confluency. Structural analysis of integrin b1 interaction with KINDLIN-2, biochemical pulldown assay and molecular dynamic analysis showed that acetylation of K794 increases KINDLIN-2 binding to the integrin b1 cytoplasmic tail. Accordingly, altering KINDLIN-2 levels modified Claudin-5 expression and endothelial barrier function. Revealing how integrin b1 acetylation regulates endothelial cell junctions offers new therapeutic possibilities for controlling vascular permeability.

overall_design: To understand the influence of integrin b1 acetylation on gene transcription in endothelial cells, we have expressed a chimeric form of human integrin 1 with an extracellular eGFP tag in mouse embryonic endothelial eEnd2 cells. The integrin b1 was used either as wildtype (WT) or carrying the acetyl-mimetic mutation (lysine-to-glutamin at Lys794 or K794Q). For expression of human integrin 1, we used the previously (Vega, Kastberger et al. 2020) generated pCDNA3 plasmid with the CMV promoter replaced by a fragment of matrix attachment region of chicken lysozyme (MAR) and a small fragment of human actin  promoter (SAP), and encoding for human integrin b1A containing an extracellular tagging after the K107 with the green fluorescence protein.  Mouse embryonic endothelial cell line eEnd2 was transfected with this pcDNA-SAPMAR-ITGB1AK107-GFP encoding for human integrin 1A (wildtype or K794Q mutant)-eGFP chimera, by using Neon nucleofector (Thermo Fisher Scientific) according to the manufacturer recommendation. Two populations of GFP positive cells (GFPlow and GFPhigh) were sorted by fluorescence-activated cell sorting (FACS) and sub-cultured until use. Sorted cells were cultured in DMEM supplemented with 10% fetal calf serum (FCS) in humidified atmosphere with 5% CO2 at 37°C. Confluent cells in 10-cm dishes were lysed and the total mRNA were extracted with the RNA and protein extraction kit (Macherey-Nagel). Total RNA of three different cultures of each sorted cells were sequenced, aligned and the differential expression of genes analysed at the iGE3 Genomics Platform (University of Geneva, Geneva, Switzerland). Reference: Vega, M. E., et al. (2020). "Stimulation of Fibronectin Matrix Assembly by Lysine Acetylation." Cells 9(3): 655.

first: Adama

last: Sidibé

first: Bernhard

last: Wehrle-Haller


title: The potential role of drug transporters and amikacin modifying enzymes in M. avium

city: Nijmegen

first: Jodie

last: Schildkraut

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: Radboudumc

summary:
Background: Mycobacterium avium complex (MAC) bacteria cause opportunistic infections in humans. Treatment yields cure rates of 60% and is comprised of a macrolide, a rifamycin and ethambutol; and in severe cases amikacin. Mechanisms of antibiotic tolerance remain mostly unknown. To elucidate these mechanisms, we studied the transcriptomic response to antibiotics and investigated the contribution of efflux and amikacin modification to susceptibility.
Methods: M. avium was subjected to subinhibitory concentrations of clarithromycin, amikacin, ethambutol and rifampicin followed by RNA sequencing. Based thereupon, we characterized M. avium efflux pumps and performed time-kill kinetic analysis using each antibiotic in combination with the efflux pump inhibitors (EPIs) berberine, verapamil and CCCP to study the role of efflux on susceptibility. Finally, we studied the modification of amikacin by M. avium using metabolomic analysis.
Results: Changes in respiratory state and changes in ribosome binding and protein folding likely contribute to clarithromycin and amikacin tolerance, respectively. No clear drug-specific mechanisms of tolerance are found for ethambutol and rifampicin. Of the EPIs, only berberine increased the susceptibility to rifampicin and clarithromycin. Finally, we show that M. avium, in contrast to M. abscessus, is not able to modify amikacin.
Conclusion: M. avium likely relies on a combination of drug-specific and generic mechanisms of antibiotic tolerance including changes in respiratory and metabolic state in addition to drug efflux and target modification. Efflux inhibition can increase susceptibility but this effect is EPI and antibiotic specific. Finally, the lack of amikacin modifying activity in M. avium is important for its activity.

overall_design: M. avium was subjected to subinhibitory concentrations of clarithromycin, amikacin, ethambutol and rifampicin followed by RNA sequencing at 24 and 72h to study the transcriptomic response to antibiotic stress

last: Schidkraut

first: Jordy

last: Coolen

first: Jakko

last: van Ingen


title: MicroRNA signatures associated with basal cell carcinoma subtypes

city: Salt Lake City

first: Doug

last: Grossman

state: Utah

address: Huntsman Cancer Institute, 2000 Circle of Hope

department: Dermatology

institute: Huntsman Cancer Institute

summary: In summary, we have validated differential expression of several miRs, namely two that are downregulated in all BCC subtypes compared to control skin (miR.383.5p, miR.145.5p), two that are downregulated in superficial BCC (miR.181c.5p, miR.181b.5p) relative to nodular and infiltrative BCC, and several that are upregulated in infiltrative BCC relative to superficial BCC (miR.22.5p, miR.18a.3p, miR.708.5p, miR.758.3p, miR.30c.5p), and two that are upregulated in infiltrative BCC relative to nodular BCC (miR.22.5p, miR.758.3p). To our knowledge, this study has investigated and validated the largest number of BCC tumors representing the different subtypes.

overall_design: Tumors were identified in the University of Utah Dermatopathology (PowerPath®) database and corresponding H&E-stained slides were reviewed by a dermatopathologist (S.R.F.) to confirm diagnosis and tumors were selected that constituted >80% of the tissue specimen. Sections (20 mm) were cut, dried on glass slides, and then scraped into microfuge tubes. Whole RNA was isolated using a RecoverAll kit (Thermo Fisher Scientific, AM1975), quantitated by ScreenTape Assay (Agilent), converted to cDNA (Qiagen QIAseq miRNA Library Prep) for miRNA sequencing.

first: Suzanne

last: Fastner

first: Hafeez

last: Rahman

first: Jose

last: Gutierrez

first: Nathan

last: Shen

first: Scott

last: Florell

first: Abigail

first: Chris

last: Stubben

first: Ken

last: Boucher

first: Dekker

last: Deacon

first: Robert

last: Judson-Torres

first: Douglas


title: Investigating the role of telomere length in 3D spatiotemporal gene regulation in cardiomyocytes

first: Bin

last: Li

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

overall_design: Refer to individual Series


title: Nucleation and spreading rejuvenate polycomb domains every cell cycle

status: Public on Dec 01 2023

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

overall_design: Cleavage under targets and tagmentation with flow sorting (CUT&Flow) for the histone modification H3K27me3 in mESCs

first: Giovana

last: Veronezi


title: Dysregulated Wnt signaling confers resistance to cuproptosis in cancer stem cells

status: Public on Nov 21 2023

city: Wuhan

first: Yuantong

last: Liu

state: Hubei

address: Luoyu road

institute: Wuhan University

summary: Cuproptosis is characterized by the aggregation of lipoylated components of the tricarboxylic acid cycle and subsequent loss of iron-sulfur cluster proteins as a unique copper-dependent form of regulated cell death. Dysregulation of copper homeostasis and resulting cuproptosis induction is an emerging area of interest for cancer therapy. However, mechanisms of cancer cell evasion of cuproptosis are not well understood. Here, we found that the cuproptosis process is accompanied by activation of the Wnt/β-catenin pathway. Mechanistically, copper binds to PDK1 and promotes its interaction with AKT, resulting in activation of the Wnt/β-catenin pathway and cancer stem cell (CSC) properties. Notably, aberrant activation of Wnt/β-catenin signaling conferred resistance of CSCs to cuproptosis. Further studies showed that the β-catenin/TCF4 transcriptional complex directly binds to the promoter region of ATP7B, a protein responsible for the efflux of copper ions from the cell, inducing its expression and reducing intracellular copper accumulation, thereby inhibiting cuproptosis. Knockdown of TCF4 or pharmacological blockade of the Wnt/β-catenin pathway increased the sensitivity of CSCs to elesclomol-Cu-induced cuproptosis. These findings reveal a link between copper homeostasis regulated by the Wnt/β-catenin pathway and cuproptosis sensitivity, and may provide a precision medicine strategy for cancer treatment by selectively inducing cuproptosis

overall_design: Cal27 sphere cells were treated with Wnt-pathway inhibitors LF3 for 24h, and the transcriptome was sequenced and analyzed.

first: Yuan-Tong


title: Dysregulated Wnt signaling confers resistance to cuproptosis in cancer cells

overall_design: To comprehensively analyze the changes in transcriptome levels during cuproptosis in cancer cells, Cal27 cells were treated with elesclomol and copper in a 1:1 ratio (elesclomol-Cu, ES-Cu), and the transcriptome was sequenced and analyzed.


title: Facemask acne attenuation through modulation of indirect microbiome interactions

status: Public on Nov 27 2023

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

summary: During the COVID-19 pandemic, facemasks have played a pivotal role in preventing person-person droplet transmission of viral particles. However, prolonged facemask wearing causes skin irritations colloquially referred to as ‘maskne’ (mask + acne), which manifests as acne and contact dermatitis and is mostly caused by pathogenic skin microbes. Previous studies revealed that the putative causal microbes were anaerobic bacteria, but the pathogenesis of facemask-associated skin conditions remains poorly defined. We therefore characterized the role of the facemask-associated skin microbiota in the development of maskne using culture-dependent and -independent methodologies. Metagenomic analysis revealed that the majority of the facemask microbiota were anaerobic bacteria that originated from the skin rather than saliva. Previous work demonstrated direct interaction between pathogenic bacteria and antagonistic strains in the microbiome. We expanded this analysis to include indirect interaction between pathogenic bacteria and other indigenous bacteria classified as either ‘pathogen helper (PH)’ or ‘pathogen inhibitor (PIn)’ strains. In vitro screening of bacteria isolated from facemasks identified both strains that antagonized and promoted pathogen growth. These data were validated using a mouse skin infection model, where we observed attenuation of symptoms following pathogen infection. Moreover, the inhibitor of pathogen helper (IPH) strain, which did not directly attenuate pathogen growth in vitro and in vivo, functioned to suppress symptom development and pathogen growth indirectly through PH inhibitory antibacterial products such as phenyl lactic acid. Taken together, our study defines a mechanism by which indirect microbiota interactions under facemasks control symptoms of maskne by suppressing a skin pathogen for the first time.

overall_design: To investigate possible biosynthesis pathways for metabolites that were highly produced by the IPH strain and showed antimicrobial activity against PH, we conducted a transcriptome analysis of the IPH strain M6 and control strain IFM15. Total RNAs were extracted from bacteria cultured for 48 hours under anaerobic conditions.

first: Sung

first: Dohyeon

last: Kim

first: Choong-Min

last: Ryu

first: Hwi

last: Seo


title: Genome-wide mapping of MEF2A binding sites by CUT&Tag-seq in chicken primary myoblasts

status: Public on Dec 05 2023

city: Chengdu

first: Xinglong

last: Wang

state: Sichuan

address: Wangjiang

department: College of Life Sciences

institute: sichuan university

summary: In this study, CUT&Tag-seq technology was employed to investigate MEF2A binding sites across the entire genome of chicken primary myoblasts. CUT&Tag was performed using CUT&Tag Assay Kit for Illumina Pro (TD904-1) from Vazyme. Antibody targeting MEF2A as well as IgG were used.The final DNA library on a HiSeq PE150 platform was subjected for the analyses. This study provides a wide landscape of MEF2A target genes from chicken primary myoblasts, which supports the active role of MEF2A in avian muscle development.

overall_design:
Cleavage under targets and tagmentation (CUT&Tag) for MEF2A in chicken primary myoblasts (CPM)

**Processed data were removed because the submitter stated that the analysis method was wrong**

first: Jiannan

last: Zhang

first: Jiancheng

last: Su

first: Yajun


title: More than the clock: distinct regulation of muscle function and metabolism by PER2 and RORα

status: Public on Jan 02 2024

city: Basel

first: Shivani

last: Mansingh

address: Spitalstrasse 41

institute: Biozentrum, University of Basel

summary: Circadian rhythms, governed by the dominant central as well as various peripheral clocks, regulate almost all biological processes, including sleep-wake cycles, hormone secretion, and metabolism. In certain contexts, regulation and function of the peripheral oscillations can be decoupled from the central clock. However, the specific mechanisms underlying muscle-intrinsic clock-dependent modulation of muscle function and metabolism remain unclear. We investigated the outcome of perturbations of the primary and secondary feedback loops of the molecular clock in skeletal muscle by specific gene ablation of Period 2 (Per2) and RAR-related orphan receptor alpha (RORα), respectively.  In both models, a dampening of core clock gene oscillation was observed, while the phase was preserved. Moreover, both loops seem involved in the homeostasis of amine groups. Very divergent outcomes were seen for overall muscle gene expression, primarily affecting circadian rhythmicity in the Per2, and non-oscillating genes in the RORα knockouts, leading to distinct outcomes in terms of metabolome and phenotype. These results highlight the entanglement of the molecular clock and muscle plasticity, and allude to specific functions of different clock components, i.e. the primary and secondary feedback loops, in this context. The reciprocal interaction between muscle contractility and circadian clocks might therefore be instrumental to determine a finely tuned adaptation of muscle tissue to perturbations in health and disease.

overall_design: Muscles from PER2 muscle-specific knockout mice (MKO), control (CTRL), and RORa MKO mice were collected at zeitgeber time (ZT) 0, 4, 8, 12, 16, and 20. 3-4 mice were used for seqeuencing replicated for each time-point and each genotype.

first: Geraldine

last: Maier

first: Julien

last: Delezie

first: Wandrille

last: Duchemin

first: Pal

last: Westermark

first: Christoph

last: Handschin


title: KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism.

status: Public on Nov 08 2023

city: Bronx

first: Matanel

last: Yheskel

state: NY

address: 1300 Morris Park

department: Genetics

institute: Albert Einstein College of Medicine

summary: Genes encoding the KDM5 family of transcriptional regulators are disrupted in individuals with intellectual disability (ID). To understand the link between KDM5 and ID, we generated five Drosophila strains harboring missense alleles analogous to those observed in patients. These alleles showed effects on neuroanatomical development, cognition, and other behaviors, in addition to a transcriptional signature that included the downregulation of many ribosomal protein genes. A similar transcriptional profile was observed in KDM5C knockout human glutamatergic neurons derived from induced pluripotent stem cells (iPSCs), suggesting a conserved role for KDM5 proteins in regulating ribosomal protein genes. Loss of ribosomal protein gene expression resulted in changes to neuronal ribosome composition. Moreover, we find that the translation efficiency of mRNAs required for mitochondrial metabolism was particularly affected upon reduction KDM5 in Drosophila neurons. Altered mitochondrial activity was confirmed through metabolomic studies that revealed decreased citric acid cycle activity. KDM5 therefore plays a key role in maintaining mitochondrial function that, when altered, could contribute to cognitive and behavioral phenotypes.

overall_design: To understand how patient Claes-Jensen Syndrome (CJS) associated variants in KDM5C modeled in Drosophila affect transriptional programs in neurons, we created 5 CJS variant strains as well as a synthetic demethylase-dead strain and performed paired-end RNA-Sequencing. All variants were compared to WT KDM5. We dicovered that ribosome protein genes were downregulted acorss all ID variants. To understand how loss of KDM5 function affected translation efficiency, we performed Ribo-Seq on control and kdm5-knockdown neurons.

first: Julie

last: Secombe


title: Activation domains and Coactivator direct genomic localization of fused DNA binding domains, defining the subset of activated promoters

status: Public on Dec 22 2023

city: Rehovot

first: Naama

last: Barkai

state: HaMerkaz

address: Herzl 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

sample_organism:
Saccharomyces cerevisiae
Saccharomyces cerevisiae BY4741


title: Sweat gland development requires an eccrine dermal niche and couples two epidermal programs

status: Public on Nov 10 2023

city: Philadelphia

first: Yana

middle: G

last: Kamberov

state: PA

address: 415 Curie Blvd CRB 535

institute: University of Pennsylvania Perelman School of Medicine

summary: Eccrine sweat glands are indispensable for human thermoregulation and, similar to other mammalian skin appendages, form from multipotent epidermal progenitors. Limited understanding of how epidermal progenitors specialize to form these vital organs has precluded therapeutic efforts toward their regeneration. Herein, we applied single-nucleus transcriptomics to compare the expression content of wild-type, eccrine-forming mouse skin to that of mice harboring a skin-specific disruption of Engrailed 1 (En1), a transcription factor that promotes eccrine gland formation in humans and mice. We identify two concurrent but disproportionate epidermal transcriptomes in the early eccrine anlagen: one that is shared with hair follicles and one that is En1 dependent and eccrine specific. We demonstrate that eccrine development requires the induction of a dermal niche proximal to each developing gland in humans and mice. Our study defines the signatures of eccrine identity and uncovers the eccrine dermal niche, setting the stage for targeted regeneration and comprehensive skin repair.

overall_design: Nuclei were isolated from En1-cKO and Control ventral hind limb skin at P2.5 and analyzed using snRNA-seq.

first: Heather

last: Dingwall


title: microRNA expression data from liver samples of mice fed with a high fat diet for 24 weeks

status: Public on Oct 31 2023

city: Lübeck

first: Henriette

last: Kirchner

address: Ratzeburger Allee 160

department: Institute for Human Genetics

institute: University of Lübeck

summary:
Although the global prevalence of obesity and type 2 diabetes is rising, the molecular mechanisms of dysregulated glucose and lipid metabolism are still incompletely understood. Epigenetic mechanisms were shown to have an impact in disease manifestation, but the underlying hepatic miRNA expression signature is not completely elucidated.
We used microarrays to perform a comprehensive screen of the complete microRNA transcriptome in liver samples of diet induced obese (DIO) mice in order to identify expressed microRNAs that might target genes of hepatic lipid and glucose metabolism.

overall_design: Total RNA extracted from liver samples of DIO mice that were fed with a 58 % high fat diet (HFD) for 24 weeks were used for microarray measurement in order to establish a database for the murine microRNA expression pattern.

first: Christin

last: Krause

first: Jan

last: Britsemmer

first: Paul

last: Pfluger

first: Sonja

last: Schriever


title: Effect of anti-CD20 treatment on the composition and gene expression of meningeal ectopic lymphoid tissue and CSFin a spontaneous EAE model,  using single cell gene expression .

status: Public on Nov 01 2023

city: Munich

first: Gildas

last: Lepennetier

address: Ismaninger Straße 22

department: Neurology

institute: Klinikum Rechts der Isar

summary: Objective: To investigate how anti-CD20 B cell-depleting monoclonal antibodies (ɑCD20 mAb) alter the composition and gene expression of immune cells in meningeal ectopic lymphoid tissue (mELT) and the CSF in a murine model of Multiple Sclerosis (MS). Methods: We utilized a spontaneous chronic experimental autoimmune encephalomyelitis (EAE) model of mice with mutant T and B cell receptors specific for myelin oligodendrocyte glycoprotein (MOG), which develop meningeal inflammatory infiltrates resembling those described in Multiple Sclerosis (MS).  We studied the changes in cell composition and gene expression after anti-CD20 treatment in mELT and CSF.

overall_design: single cell gene expression and Bcell receptor sequences of meningeal ectopic lymphoid tissue and CSF in 3 anti-CD20 and 3 vehicle treated Thx2D2 mice

first: Klaus

last: Lehmann-Horn

first: Jolien

last: Diddens

first: Tanja

last: Georgieva

first: Friederich

last: Verena


title: Monitoring melanoma patients on treatment reveals a distinct macrophage population driving targeted therapy resistance

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

institute: Hopitaux universitaires de Geneve

summary: Although treatment of melanoma patients with BRAF and MEK inhibitors has demonstrated impressive clinical outcomes, innate or acquired resistance to targeted therapy remains a major challenge. To uncover resistance mechanisms in patients, we performed single cell RNA sequencing of longitudinal biopsies of the same tumors from four consenting melanoma patients before the start of BRAFi/MEKi treatment and at different time points during treatment. Among the genes most differentially expressed between malignant cells from resistant vs. responding patients was POSTN encoding the secreted factor periostin. POSTN was predicted to predominantly signal to a macrophage population associated with targeted therapy resistance (TTR) in patients and was able to polarize macrophages towards a TTR phenotype. Finally, polarized TTR macrophages protected melanoma cells from MEKi-induced killing, which involved CD44 receptor expression on melanoma cells. Thus, interfering with the protective activity of TTR macrophages might represent a strategy to overcome targeted therapy resistance in melanoma.

overall_design:
Fine needle aspirates from melanoma tumors of 4 patients at baseline up to 4 during BRAF MEK inhibitor treatment, due to human data raw files will be available upon request

>>Submitter states: Raw data couldn't be included due patient privacy concerns. Requests can be made to the PI for access to the raw data.<<<

middle: F

first: Jelena

last: Vasilevska


title: Genome-wide maps of TCF4 in CAL27 sphere cells

first: Yuantong

last: Liu

summary: For the first time, we investigated the role of TCF4 in CAL27 sphere cells.

overall_design: Examination of regulatory role of TCF4 in CAL27 sphere cells.

first: Yuan-Tong


title: Gasdermin D deficiency affects mitochondrial dynamics and metabolic  to orchestrates neurogenesis during embryonic development

status: Public on Nov 13 2023

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
Purpose: To gain  futher insight into how GSDMD regulates the proliferative of neural progenitors ,RNA-seq was used to analyze the genome-wide changes resulting from the cerebral cortices of E13 GSDMD conditional knock out mice and littermate wild-type.
Methods: Total RNA from E13 telencephalic tissue of wild-type(WT) and Gsdmdfl/fl;Nestin-Cre mice was extracted. Specifically, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, total RNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics
Results: Approximately  one thousand transcripts showed differential expression between the wild-type(WT) and Gsdmdfl/fl;Nestin-Cre mice brain cortex, with a fold change ≥1.5 and p value <0.05.Geneontology analysis of the up-regulated genes showed obvious enrichment of biological processes related to development and proliferation.The down-regulated genes exhibited enrichment of biological processes related to the negative regulation of cell proliferation and developmental process. These results reflected GSDMD plays a role in cortex development.
Conclusions:  RNA-seq based transcriptome characterization would provide a overall understanding how GSDMD gene contribute to brain cortical development.

overall_design: Total mRNA profiles of E13 wild type (WT) and Gsdmdfl/fl;Nestin-Cre mice were generated by deep sequencing, in triplicate,  using Illumina HiSeq 2500.

first: HongYan

last: Ma


title: CRISPR screenings reveal neuropeptide orchestrate T helper cell fate decision

status: Public on Dec 25 2023

first: Yu

last: Hou

address: No.5 Yiheyuan Street

department: School of life sciences

institute: Peking University

summary: T helper type 1 (Th1) cells play critical roles in viral infection response and autoimmune disease. Recent studies have implicated the imbalance of T helper subtypes is correlated with outcome of COVID-19 infection, however, the underlying mechanism that balancing Th1 cells versus other T helper cells remains unknown. Here, we profiled the heterogeneity and dynamic regulation during in vivo and in vitro Th1 differentiation using scRNA-seq and defined the Th1 unique program using a Th1/Th2 dichotomous differentiation condition. To further validate the functions of defined Th1 regulators, we performed CRISPR screenings for both in vitro as well as in vivo Th1 differentiation. RAMP3 as one of the receptors for neuropeptide CGRP was defined as a novel regulator balancing Th1 and Th2 differentiation and was proved an indispensable role for Th1 response during virus infection. CGRP, RAMP3 and cAMP signaling form a positive feedback loop to enhance Th1 differentiation through activating STAT1. Together, ur work highlights the network between CGRP-mediated neuronal signaling and immune response during virus infection.

overall_design: 1. To explore the dynamic regulation during in vitro T cell differentiation, we performed temporal bulk RNAseq during in vitro T cell differnetiation under Th0, Th1 and Th2 conditions. 2. To explore the gene regulation during in vivo Th1 differentiation, we performed single cell RNA-seq of splenocyte upon LCMV Armstrong infection. 3. To further explore the interaction between Th1 and Th2 regulation networks, we performed tepmoral single cell RNA-seq under Th1-Th2 bifurcation condition. 4. To reveal the effect of CGRP, we performed RNA-seq and ATAC-seq upon CGRP treatment under both Th1 and Th2 polarization conditions.

first: Vijay

last: Kuchroo


title: Liver microRNA transcriptome reveals miR-182 as link between type 2 diabetes and fatty liver disease in obesity

first: Henriette

last: Kirchner

summary:
Although the global prevalence of type 2 diabetes is still rising, the molecular mechanisms of dysregulated glucose and lipid metabolism are still incompletely understood. Epigenetic mechanisms were shown to have an impact in disease manifestation, but still the hepatic miRNA expression signature in diabetic subjects was not completely elucidated.
We used microarrays to performe a genome wide screen of the complete noncoding RNA transcriptome in order to identify dsyregulated miRNAs which target genes of the hepatic glucose and lipid metabolism.

overall_design: Total RNA extracted from liver biopsies of 20 non-diabetic and 20 type-2-dabetic obese human subjects, matched for age and gender, were used for microarray measurement in order to establish a database for the human small noncoding RNA expression pattern in metabolic diseases.

first: Christin

first: Cathleen

last: Geißler

first: Katharina

last: Iben

first: Martina

last: Grohs

first: Meike

last: Kaehler

first: Jonas

last: Wagner

first: Stefan

last: Wolter

first: Oliver

last: Mann

first: Ingolf

last: Cascorbi

first: Hendrik

last: Lehnert


title: Epithelial aPKC deficiency leads to stem cell loss preceding metaplasia in colorectal cancer initiation

status: Public on Nov 07 2023

city: New York

first: Jorge

last: Moscat

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE


title: Effect of Zika virus (ZIKV) on gene expression in nonhuman primate (NHP) fetal brain during development

status: Public on Nov 02 2023

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: To investigate the transcriptional response in nonhuman primate fetal brain at term gestation following ZIKV exposure in utero

overall_design: Comparative gene expression analysis of RNA-seq data from different nonhuman primate fetal brain regions of mock and ZIKV-infected animals

first: Jennifer

last: Tisoncik-Go

first: Leanne

last: Whitmore

last: Gale Jr


title: β2-adrenergic receptor transcriptional response in HEK293 wild type, β-arrestin1/2 KO and Gαs KO cells upon isoproterenol stimulation.

status: Public on Oct 17 2023

city: La Jolla

first: Valeria

last: Burghi

address: 3855 Health Sciences Drive, Room 2345

department: Pharmacology

institute: University of California San Diego

summary: The role of nuclear signaling by β2-adrenergic receptor (β2AR) through β-arrestins in the absence of a functional Gαs protein has not been evaluated. This has prevented a comprehensive understanding of the relative contribution of Gαs and β-arrestins to the overall β2AR signaling, thereby limiting our appreciation of how β-arrestin- or Gαs-biased ligands may affect their therapeutic outcomes. To explore the role of Gαs and β-arrestin in nuclear transcriptional programs in a global unbiased approach, we performed RNA sequencing studies in cells lacking either of these two signaling arms downstream from β2AR, followed by detailed bioinformatics analysis of gene expression signatures. We noticed multiple genes whose individual expression levels were distinct in β-arrestin1/2 and Gαs KO cells. Rather than focusing on the individual gene level, we performed a detailed analysis of gene signatures taking advantage of large datasets that were recently compiled as part of the Molecular Signatures Database (MSigDB). This approach supported that β-arrestins are not required for the activation of PKA gene signatures, including prior datasets of forskolin and CREB1 targets, while Gαs is essential. β2AR activation also led to significant changes in multiple MAPK signatures, which clearly support the activation of MAPK nuclear transcriptional programs by these receptors. Although individual variations do exist reflecting the complexities of β-arrestin- and Gαs-mediated signaling events, stimulation of these MAPK regulated gene signatures was not significantly reduced in β-arrestin1/2 KO cells but abolished in Gαs KO cells.

overall_design: HEK293 wild type, β-arrestin1/2 KO and Gαs KO cells transiently overexpressing wild type β2-adrenergic receptor were stimulated with isoproterenol or vehicle for 1 h in triplicates. We performed differential gene expression analysis using data obtained from RNAseq. We also obtained enrichment profiles for gene sets related to PKA and MAPK pathways.

first: Adam

last: Officer

first: Xingyu

last: Wu

first: J

last: Gutkind


title: Spatial transcriptomics on Zika virus infected fetal brains of nonhuman primates

summary: Investigation of spatial transcriptomic responses of nonhuman primate fetal brains during development

overall_design:
Identification of regional transcriptomic responses to Zika virus in fetal brains of non human primates
Please note that In the count and norm matrix contains the data for the samples used for the analysis which passed the min limit of quantification of 2

first: Andrew

last: Gustin

first: Caleb

last: Stokes


title: Expression signature characteristic of Anaplastic Large Cell Lymphoma (ALCL) patients

status: Public on Dec 06 2023

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

institute: Azienda USL- IRCCS di Reggio Emilia

summary: RNA extracted from tumor biopsies of 44 patients affected by ALCL was analyzed on the nCounter system using a custom panel called VF_150921 (Nanostring Technologies).

overall_design: Evaluation of expression profile associated to ALK phenotype in ALCL patients.

first: Valentina

last: Fragliasso


title: Multi-omics datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells.

status: Public on Nov 04 2023

first: Yi

last: Hu

address: No. 28 Fuxing Rd， Haidian district，Beijing

institute: Chinese PLA General Hospital

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

overall_design: Refer to individual Series


title: Next Generation Sequencing and Quantitative Analysis of mRNAs in Caenorhabditis elegans fbxl-5 Mutant Animals

status: Public on Dec 01 2023

city: Chapel Hill

first: Robert

middle: Houston

last: Dowen

state: NC

address: 321 Fordham Hall, CB7100

department: Cell Biology and Physiology

institute: University of North Carolina at Chapel Hill

summary: The molecular mechanisms that govern the metabolic commitment to reproduction, which often occurs at the expense of the soma, remain poorly understood. We identified the C. elegans F-box protein FBXL-5 as a negative regulator of maternal provisioning of vitellogenin lipoproteins, which mediate the transfer of intestinal lipids to the germline. Mutations in fbxl-5 partially suppress the vitellogenesis defects observed in the heterochronic mutants lin-4 and lin-29, both of which ectopically express fbxl-5 at the adult developmental stage. FBXL-5 functions cell-autonomously to negatively regulate expression of the vitellogenin genes; and consistently, intestinal over-expression of FBXL-5 is sufficient to inhibit vitellogenesis, impair overall lipid homeostasis, and reduce lifespan. Our epistasis analyses suggest that fbxl-5 functions in concert with cul-6, a cullin gene, and the Skp1-related genes skr-3 and skr-5 to regulate vitellogenesis. Additionally, fbxl-5 acts genetically upstream of rict-1, which encodes the core mTORC2 protein Rictor, to govern vitellogenesis. Together, our results reveal an unexpected role for a SCF ubiquitin-ligase complex in controlling intestinal lipid homeostasis by tuning mTORC2 activity.

overall_design: The mRNAs of wild-type, lin-29(n333), fbxl-5(rhd43), and rict-1(mg360) day 1 adult animals were profiled by high-throughput sequencing, in triplicate.


title: Effect of depletion of FXR1 on gene expression in head and neck squamous cell carcinoma (HNSCC) cells

status: Public on Sep 30 2023

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

summary: FXR1 is an essential RNA-binding protein. This chromosome 3q26-28 gene is overexpressed in many epithelial tumors. FXR1 controls the turnover and translation of multiple mRNAs and is involved in cellular transformation. We identified critical residues in the protein that are post-translationally modified. These regulate the stability of FXR1 protein, its RNA-binding function, cell growth, and proliferation. Here we show that PRMT5-mediated arginine methylation of FXR1 increases the protein's binding to G-quadruplex RNAs in vivo and controls their expression in cancer cells. Independent point mutations of specific arginine residues in the nuclear export signal (R386, R388) and arginine-glycine rich (R453, R455, R459) domains of FXR1 abrogate the RNA-binding in vitro. Genetic and small molecule inhibition of PRMT5 minimizes methylation and levels of FXR1 and suppresses oral tumor growth and proliferation. RNA-seq analyses of FXR1 KD cells show an increase in the expression of PLK2, TCN2, and TRAF4 along with FXR1’s well-known target CDKN1A. Like CDKN1A, these targets possess strong G4 sequences. FXR1 and G4-RNA interactions provide new insights into the molecular mechanism of FXR1 and its interaction with target mRNAs. Furthermore, an increased expression of FXR1 and PRMT5 is colocalized in cancer tissues, leading to a poor patient prognosis. Thus, our data demonstrate that PRMT5-mediated arginine methylation of FXR1 arginine residues in the NES and RGG domains plays a critical role in binding and controlling G4-RNAs, which encode tumor suppressors and promote cancer cell growth and proliferation.

overall_design: To investigate the cooperative functionFXR1 in the HNSCC cell lines in which FXR1 has been knocked down by shRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of control and KD cells with Biological triplicates.

first: Mrinmoyee

last: Majumder

first: Viswanathan

last: Palanisamy


title: KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism II.

status: Public on Oct 23 2023

first: Matanel

last: Yheskel

overall_design: To understand how loss of KDM5C affected gene expression of human iPSC induced glutamatergic neurons, created two CRISPR KO lines from L

first: Julie

last: Secombe


title: PKA regulated genes in HEK293 cells

status: Public on Oct 21 2023

summary: When exploring the role of Gαs and β-arrestin in nuclear transcriptional programs downstream from β2-adrenergic receptor (β2AR), we noticed a dearth of information on PKA-regulated genes sets. Thus, we first used the tetracycline-regulated expression of wild type PKA Cα subunit in HEK293 cells to develop a PKA signature. This approach revealed multiple PKA-regulated genes, including well known PKA downstream transcriptional targets, such as PCK1 and FOS, and many new PKA transcriptional targets whose underlying mechanism can now be explored.

overall_design: HEK293 cells with tetracycline-regulated expression of wild type PKA Cα subunit and HEK293 parental cells (controls) were treated with doxycycline for 48 hours in triplicates. We performed differential gene expression analysis using data obtained from RNAseq.


title: Evolution of neuronal cell classes and types in the vertebrate retina

status: Public on Oct 01 2023

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

sample_organism:
Danio rerio
Didelphis marsupialis
Callithrix jacchus
Homo sapiens
Mustela putorius furo
Sus scrofa domesticus
Bos taurus
Ovis aries
Peromyscus maniculatus
Anolis sagrei
Ictidomys tridecemlineatus
Rhabdomys pumilio
Tupaia chinensis


title: Deep mutational scanning of the interaction of JUN's leucine zipper domain and other human bZIPs in different experimental conditions

status: Public on Oct 18 2023

first: Alexandra

middle: Michaela

last: Bendel

address: Maulbeerstr. 66

department: Genome Regulation

institute: Friedrich Miescher Institute for Biomedical Research

overall_design: Amplicon-Seq

first: Kristjana

last: Skendo

first: Kenji

last: Schimada

first: Dominique

last: Klein

first: Kotryna

last: Kauneckaite-Griguole

first: Guillaume

last: Diss


title: Multiomic Single Cell Evaluation Reveals Inflammatory Cytokines Affect Innate Lymphoid Cell Fate After Allogeneic Stem Cell Transplantation [scATAC-Seq]

status: Public on Sep 14 2023

city: CHAPEL HILL

first: SONIA

last: LAURIE

address: 125 Mason Farm Road

institute: UNC CHAPEL HILL

summary:
Although allogeneic hematopoietic stem cell transplantation (alloHSCT) is the preferred treatment for a variety of hematologic malignancies, its use is limited by the development of acute graft-versus-host disease (aGvHD).  Type II innate lymphoid cells (ILC2s) are immune cells that play an important role in maintaining homeostasis in mucosal tissues.  Previous work has shown that ILC2 cells fail to reconstitute after chemotherapy or stem cell transplantation, though the mechanism for this finding is unclear, making delineation of the mechanisms involved in their turnover and reconstitution could have a significant impact on transplant outcomes.

We evaluated the hypothesis that the loss of ILC2 cells post-transplant induced epigenetic changes that convert ILC2 cells to ILC1-like cells.  Strikingly, single-cell, multiomic analysis of donor-derived ILC2s after transplantation revealed a previously unreported population of ILC1-like cells that differentiate from ILC2s in the small intestine lamina propria (exILC2s). To recapitulate this transdifferentiation, we modeled skewing of ILC2s in vitro with IL-12, IL-1b, and IL-18 (termed proinflammatory cytokine conditioned ILC2s, pcILC2s) and observed a reduction in Type 2 lineage-defining regulatory factors and the acquisition of proinflammatory Type 1 characteristics consistent with the phenotype and function of the exILC2s recovered post-transplant. Excitingly, our approach confirms the skewed cell population expresses ILC1 associated Tbx21 and reveals Nr4a2, Foxo1, and Fli1 as additional putative drivers of the emergent ILC1-like exILC2s after alloHSCT.

To test whether ex vivo generated pcILC2s contribute to aGVHD-mediated mortality, we infused transdifferentiated donor WT or pcILC2s and measured the clinical score and survival of recipient mice after alloHSCT in a mismatched murine model. Unlike their unmanipulated WT ILC2 counterparts, our pcILC2s accelerated morbidity and mortality. Finally, peripheral blood cells from human patients with aGvHD have an altered chromatin landscape at ILC2-associated regions of accessibility compared to transplanted controls.

These data demonstrate that following transplantation ILC2s convert to a pro-pathogenic population ILC1-like cell state. These findings provide novel insights into the contribution of ILC plasticity to mucosal dysregulation and aGvHD pathogenesis after alloHSCT in a murine model and may inform new approaches for modulating innate lymphocytes in human disease.

overall_design: Adults receiving allogeneic hematopoietic stem cell transplantations consented to have blood-derived PBMCs biobanked under Duke University IRB study protocol Pro00110250. We requested samples from 3-6 patients after alloHSCT with a diagnosis of acute graft-versus-host disease and 3-6 that were stable. Additionally, we requested a pre-HSCT sample and then one drawn as close as possible to the time of the aGVHD diagnosis, as well as 3 months and 1 year where available. Biobanked buffy coat samples were  stored in liquid nitrogen prior to thawing and subsequent isolation of nuclei from viable cells.

first: Sonia

last: Laurie

first: Joseph

last: Foster II

first: Danny

last: Bruce

first: Hemamalini

last: Bommiasamy

first: Oleg

middle: V

last: Kolupaev

first: Mostafa

last: Yazdimamaghani

first: Samantha

last: Pattenden

first: Nelson

last: Chao

first: Stefanie

last: Sarantopoulos

first: Joel

last: Parker

first: Ian

last: Davis

first: Jonathan

last: Serody


title: Multiomic Single Cell Evaluation Reveals Inflammatory Cytokines Affect Innate Lymphoid Cell Fate After Allogeneic Stem Cell Transplantation

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: MIR193BHG inhibits the proliferation, migration and invasion of trophoblasts by upregulating p53

status: Public on Oct 16 2023

city: Zhengzhou

first: Ping

last: Wang

address: Kangfu Front Street

institute: The Third Affiliated Hospital of Zhengzhou University

summary: Aberrantexpression of long non-coding RNAs (lncRNAs) has been reported to play a crucial role in the biological function of trophoblasts and contribute to preeclampsia (PE). Our previous study demonstrated that MIR193BHG is increased in preeclamptic placental tissues. In this study, we further explored the effects of  MIR193BHG on the function of trophoblast cells and attempted to elucidate its underlying molecular mechanisms. Results showed that MIR193BHG was predominantly localized in the nucleus of HTR-8/SVneo cells. Overexpression of MIR193BHG significantly inhibited proliferation, migration and invasion of HTR-8/SVneo cells, while increasing apoptosis. Knockdown of MIR193BHG produced opposite effects.Furthermore, overexpression of MIR193BHG led to significant increases in both mRNA and protein levels of p53 compared with the control group. More importantly, knockdown of p53 rescued the negative effects induced by overexpressed MIR193BHG on cell proliferation, migration, and invasion while partially counteracting its apoptotic effects on HTR-8/SVneo cells. In conclusion, our findings suggest that MIR193BHG played a critical role in the progression of PE by regulating the expression of p53 and  may serve as a novel therapeutic target for PE.

overall_design: HTR-8/SVneo cells transfected with MIR193BHG overexpression plasmids and mock plasmids were collected and lysed with Trizol reagent. Next, 1μg RNA was used for library preparation with TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina). The sequenced reads were then aligned to the human reference genome (GRCh38.91) using Hisat2. Differential gene expression was performed using EdgeR. The threshold used in this study to screen up- or downregulated mRNAs was logFC > 0.5 and P < 0.05.

first: Hong

last: Li

first: Zhan

last: Zhang


title: Multiomic Single Cell Evaluation Reveals Inflammatory Cytokines Affect Innate Lymphoid Cell Fate After Allogeneic Stem Cell Transplantation [ChIP-Seq]

middle: Stuart

department: Lineberger Comprehensive Cancer Center

summary: Type II innate lymphoid cells (ILC2s) maintain homeostasis and barrier integrity in mucosal tissues. Previous work has shown that in mice and humans, ILC2s fail to reconstitute after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Determining the mechanisms involved in their impaired reconstitution could improve transplant outcomes. By integrating chromatin and transcriptomic analysis of marked, transplanted ILC2s at the single cell level, we identify a previously unreported population of converted ILC1-like cells in the small intestine post-transplant. Exposure of ILC2s to proinflammatory cytokines in vitro results in a mixed ILC1-ILC2 phenotype but was able to convert only an extremely small population of ILC2s to ILC1s as observed in vivo. Whereas ILC2s protected against acute graft-versus-host disease (aGVHD) mediated-morbidity and mortality, infusion of proinflammatory cytokine-exposed ILC2s accelerated aGvHD. Finally, circulating peripheral blood mononuclear cells from patients with aGvHD have an altered ILC2-associated chromatin landscape compared to transplanted controls. These data demonstrate, for the first time, that ILC2s fail to repopulate their protective niche after allo-HSCT in part due to conversion to a pro-pathogenic population marked by an ILC1-like chromatin state, providing novel insights into the contribution of ILC plasticity to aGvHD pathogenesis after allo-HSCT.

overall_design: Following 4 days of in vivo administration of 0.4 ug IL-25, C57BL/6 mice were sacrificed and lineage (CD8α [clone 53-6.7], CD4 [RM 4.4], CD3ε [145-2C11], γδTCR [UC7-13DS], TER119 [TER-119], B220 [RA3-6B2], CD11b [M1/70], NK1.1 [PK136], CD11c [N418], CD19 [MB19-1], Ly6G [1A8], and CD49b [DX5]) negative, ST2+ cells from the peritoneum and mesenteric lymph nodes were isolated and expanded in culture for 6 days in the presence of recombinant IL-7 and IL-33 (ILC2).

first: Stephanie


title: DNA methylation restricts default deterministic fates towards neural and germline lineages during early development

status: Public on Oct 09 2023

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

summary: We investigate the impact of DNA methylation on chromatin accessibility during epiblast differentiation. To this end, we used in vitro Epiblast-like cell (EpiLC) differentiation on WT and DNA-methylation free TKO murine ESCs. We next performed ATAC seq using TDE1 Tn5 transposase (Nextera).

overall_design: ATAC-seq on WT and TKO ESCs (D0), and D2, D4 EpiLCs

first: Mathieu

last: Schulz

first: Mélanie

last: Armand

first: Aurélie

last: Teissandier

first: Déborah

last: Bourc'his


title: Deregulation of oxidative phosphorylation pathways in embryos derived in vitro from prepubertal and pubertal heifers based on whole-transcriptome sequencing

status: Public on Sep 11 2023

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

summary: Purpose: The purpose of this study was to examine whether different developmental competence of the embryos derived from prepubertal and pubertal animals is affected by the heterogeneity of their transcriptomic profiles. Moreover, the expression of molecular markers associated with mitochondrial function, expressed by the genes involved in OXPHOS, might be applied as a predictable marker for embryonic developmental capability.

overall_design:
Methods: Bovine cumulus-oocyte complexes were obtained by ovum pick- up method from pre- pubertal and pubertal heifers. After 24 hours, the mature cumulus-oocyte complexes (COCs) were fertilized in vitro using commercial bull semen. 18 hours after fertilization, the embryos were transferred to culture medium and grown for another 7 days to the blastocyst stage. Total RNA was isolated from two groups of blastocysts. The cDNA libraries were prepared according to the SMARTer Stranded Total RNA Seq Kit v3- Pico Input Mammalian (Takara Bio, USA, Inc). The quality and quantity of the obtained libraries were measured with Qubit (Invitrogen, ThermoFisher Scientific), TapeStation2200 (Agilent, Santa Clara, CA, USA) and High Sensitivity D1000 ScreenTape RNA ScreenTape (Agilent, Santa Clara, CA, USA) according to the manufacturer’s instructions. The concentrations of the libraries obtained were normalized to 10 nm, and the next samples were pooled. NGS sequencing was performed on a NextSeq500 Illumina platform in 75 single-end cycles according to the manufacturer’s instructions.  Analysis of the transcriptome profile were determined by the Database for Annotation, Visualization and Integrated Discovery (DAVID). We identified 436 differentially expressed genes (DEGs) between embryos derived from pre-pubertal and pubertal heifers.
Results: We identified 436 differentially expressed genes (DEGs) between embryos derived from pre-pubertal and pubertal heifers. Kyoto Encyclopedia of Genes (KEGG) pathway analysis suggested that the genes involved in mitochondrial function including oxidative phosphorylation were different in two researched groups. Differences of the level of expression of genes associated with mitochondrial function were found: ATP synthases (ATP5MF-ATP synthase membrane subunit f, ATP5PD- ATP synthase peripheral stalk subunit d, ATP12A- ATPase H+/K+ transporting non-gastric alpha2 subunit ), NADH dehydrogenases (NDUFS3- NADH:ubiquinone oxidoreductase subunit core subunit S3, NDUFA13- NADH:ubiquinone oxidoreductase subunit A13 , NDUFA3- NADH:ubiquinone oxidoreductase subunit A3), cytochrome c oxidase (COX17), cytochrome c somatic (CYCS) and ubiquinol cytochrome c reductase core protein 1 (UQCRC1). This study indicated that genes involved in OXPHOS could be predictive indicators for the embryo capacity, developmental competence and implantation ability.
Conclusions: Accurate knowledge of the gene expression profile in blastocysts will allow researchers to better understand the molecular mechanisms controlling early embryo development. Moreover, taking into consideration, using the in vitro embryo production provides the increase of the production efficiency and is essential for the selection and breeding of the animals with genetic potential. Additionally, the possibility of using blastocysts derived from prepubertal heifers in embryo transfer programmes will directly provide possibilities to enhance genetic gain in domestic livestock via the reduction of generation interval. Moreover, our results could be beneficial for searching for molecular indicators that could be used to develop good-quality oocytes of greater developmental ability. Taken together, these results suggest that genes involved in OXPHOS could be predictive molecular markers and indicators for embryo capacity, developmental competence and implantation ability, which in turn should result in pregnancy.
To unravel the gene expression pathways important for mitochondrial function, the transcriptomic profiles of genes involved in oxidative phosphorylation from blastocysts derived from prepubertal and pubertal heifers were compared.

first: Milena

last: Traut

first: Ilona

last: Kowalczyk-Zieba

first: Dorota

last: Boruszewska

first: Joanna

last: Jaworska

first: Sandra

last: Gąsiorowska

first: Krzysztof

last: Lukaszuk

first: Katarzyna

last: Ropka-Molik

last: Piórkowska

first: Izabela

last: Woclawek-Potocka


title: Genome-Wide CRISPR Screen Identifies Multiple Synthetic Lethal Targets That Enhance KRAS (G12C) Inhibitor Efficacy

first: Ziyan

last: Lin

department: Applied Bioinformatics Laboratories

institute: NYU Grossman School of Medicine


title: A single-cell atlas of pig gastrulation as a resource for comparative embryology

status: Public on Oct 05 2023

city: Sutton Bonington

first: Ramiro

last: Alberio

state: Leicestershire

address: Sutton Bonington Campus

department: School of Biosciences

institute: University of Nottingham

summary: The bilaminar disc of early pig embryos closely mirrors that of humans making it a powerful model for studying gastrulation. Given the difficulties obtaining embryos in non-rodents, early cell-fate decisions during mammalian gastrulation remain ill-understood. Here we present a single-cell transcriptomic atlas of pig gastrulation and early organogenesis. We uncover the dynamics of cell fate emergence during pig peri-gastrulation and reveal conserved and species-specific transcriptional programs across different mammals. Combined with investigations in embryos and embryonic stem cells, we elucidate the spatial, molecular, and temporal events during definitive endoderm (DE) formation. We show that early FOXA2+ epiblast progenitors become DE without undergoing epithelial-to-mesenchymal transition, contrasting later emerging FOXA2/TBXT+ anterior primitive streak, which form node/notochord progenitors. We demonstrate that DE fate is driven by hypoblast-derived NODAL signalling, which is extinguished upon DE differentiation. These findings highlight the interplay between temporal and topological signalling during early cell fate decisions during mammalian gastrulation.

overall_design: Single-cell RNA sequencing of 62 pig embryos at 8 different time points ranging from the beginning of gastrulation (E11.5) through to the 12 somite stage (E15) using the 10X chromium platform.

first: Luke

last: Simpson

first: Andrew

last: Strange

first: Doris

last: Klisch

first: Sophie

last: Kraunsoe

first: Takuya

last: Azami

first: Daniel

last: Goszczynski

first: Triet

last: Le

first: Beanjamin

last: Planells

first: Nadine

last: Holmes

first: Fei

last: Sang

first: Sonal

last: Henson

first: Matthew

last: Loose

first: Jenifer

last: Nichols


title: Genome-Wide CRISPR Screen Identifies Multiple Synthetic Lethal Targets That Enhance KRAS (G12C) Inhibitor Efficacy [RNA-seq-mm10]

summary: KRAS G12C inhibitors (G12Ci) alone and in various combinations are being tested in multiple tumors with over-activation of the RAS/ERK pathway. KRAS plays a critical role in normal cell signaling; hence, G12Cis could influence the signaling pathways. We found that several novel pathways including Hippo pathways are upregulated upon MRTX849 treatment. Our results argue for testing KRAS G12C and TEAD inhibitor combinations in NSCLC patients.

overall_design: Expression profiling by high throughput sequencing. To compare gene expression of  tumor cells, and associated signaling pathways changes upon  KRAS G12Ci and KRAS G12C+SHP2i drug resistance.

first: Suman

last: Mukhopadhyay

first: Alireza

last: Khodadadi-Jamayran

first: Benjamin

last: Neel