title: A single cell transcriptomic map of the developing Atoh1-lineage uncovers neural fate decisions and neuronal diversity in the hindbrain. [CUT&RUN]

first: Huda

last: Zoghbi

summary: Proneural transcription factors set up the molecular cascade to orchestrate neuronal diversity. One such transcription factor, Atoh1, gives rise to cerebellar excitatory neurons and over 30 distinct nuclei in the brainstem critical for hearing, breathing, and balance. Although the neurons that arise from the Atoh1-lineage have been qualitatively described, the transcriptional programs that drive their fate decisions and the full extent of their diversity remain unknown. Here, we analyzed single-cell RNA-sequencing and ATOH1 DNA binding in Atoh1-lineage neurons of the developing mouse hindbrain. This high-resolution dataset revealed new markers for specific brainstem nuclei and demonstrated transcriptionally heterogeneous progenitors require ATOH1 for proper migration. Moreover, we identified a sizable proliferating unipolar brush cell progenitor in the mouse Atoh1-lineage that was described in humans as the origin of one medulloblastoma subtype. Collectively, our data reveal unprecedented insight into the developing mouse hindbrain and provide markers for functional assessment of less studied neuronal populations.

overall_design: Atoh1 binding profiles in the hindbrain of Atoh1GFP/GFP E12.5 and E14.5 mouse embryos. Atoh1-lineage neurons labeled by GFP as well as GFP-negative cells in mouse hindbrains were enriched by FACS, followed by CUT&RUN and sequencing on the NovaSeq 6000.

first: Jessica

last: Butts

first: Zoghbi

last: Huda

first: Durham

last: Mark


title: Determinants of selectivity in the dicing mechanism

status: Public on Jun 01 2024

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

type: Expression profiling by high throughput sequencing

summary: The RNase III enzyme, DICER, is instrumental in the production of small RNAs, including miRNAs and siRNAs, by cleaving their precursors, such as pre-miRNAs, shRNAs, and long duplex RNAs. Utilizing High-throughput (HT) cleavage assays, our study delves into the cleavage activity of DICER. We challenge the widely accepted 2-nt loop counting rule in the previous study, revealing a divergent mechanism, the bipartite base pairing rule. This rule directs DICER's cleavage sites via the RNase III domain. Moreover, we demystify the recognition mechanism of the previously identified YCR motif. Building on this understanding, a secondary YCR motif that also influences DICER's cleavage sites has been discovered. We also address a long-debated issue concerning DICER's cleavage sites on long stem RNAs, such as pre-siRNAs or long shRNAs/pre-miRNAs. Our study shows that the dsRBD plays a crucial role in determining the cleavage sites of DICER in long-stem RNAs. In sum, our research provides a comprehensive understanding of several fundamental DICER mechanisms, challenging the long-standing model of the loop counting rule. This newfound knowledge reshapes our understanding of DICER's mechanisms, providing a robust foundation for future studies investigating the vast number of DICER mutations linked to various diseases.

overall_design: We overexpressed different DICER proteins in human cells, including  DICER-WT, DICER-delta-Helicase, DICER-delta-dsRBD. We then conducted in vitro assays using the purified DICER proteins and synthetic RNA substrates. The terms "Control" and "double cleavage" in the sample names refer to the original shRNA substrates and the RNA cleavage products by one of the DICER proteins, respectively. They are then cloned by adapter ligation, RT-PCR to obtain the libraries.

first: Thi

middle: N

last: Le

first: Cong-Truc

first: Tuan-Anh

last: Nguyen


title: RNA Sequencing Analysis of Monocytes Exposed to Airway Fluid from Children with Pediatric Acute Respiratory Distress Syndrome

city: Atlanta

first: Min

last: Huang

address: WMB, 101 Woodruff Circle

country: USA

institute: Emory University

summary: Importance: Monocytes are plastic cells that assume different polarization states that can either promote inflammation or tissue repair and inflammation resolution. Polarized monocytes are partially defined by their transcriptional profiles that are influenced by environmental stimuli. The airway monocyte response in pediatric acute respiratory distress syndrome (PARDS) is undefined. Objectives: To identify differentially expressed genes and networks using a novel transcriptomic reporter assay with donor monocytes exposed to the airway fluid of intubated children with and at-risk for PARDS. To determine differences in gene expression at two time points using the donor monocyte assay exposed to airway fluid from intubated children with PARDS obtained 48-96 hours following initial tracheal aspirate sampling. Design, Setting and Participants: In vitro pilot study carried out using airway fluid supernatant from 57 children: 44 children with PARDS and 13 children at-risk for PARDS. Main Outcomes and Measures: We performed bulk RNA sequencing using a transcriptomic reporter assay of monocytes exposed to airway fluid from intubated children to discover gene networks differentiating PARDS from at-risk for PARDS. We also report differences in gene expression in children with PARDS 48-96 hours following initial tracheal aspirate sampling. Results: We found that interleukin (IL)-10, -4, and -13, cytokine/chemokine signaling, and the senescence-associated secretory phenotype are upregulated in monocytes exposed to airway fluid from intubated children with PARDS compared to those at-risk for PARDS. Signaling by NOTCH, histone deacetylation/acetylation, DNA methylation, chromatin modifications (B-WICH complex), and RNA polymerase I transcription and its associated regulatory apparatus were upregulation in children with PARDS 48-96 hours following initial tracheal aspirate sampling. Conclusions and Relevance: We identified gene networks important to the PARDS airway immune response using bulk RNA sequencing from a monocyte reporter assay that exposed monocytes to airway fluid from intubated children with and at-risk for PARDS. Mechanistic investigations are needed to validate our findings.

overall_design: Human donor monocytes were exposed to airway trachael aspirate lavage fluid from intubated children at risk for and who met criteria for pediatric acute respiratory distress syndrome (PARDS) within 72 hours of intubation (Sample 1) and again 48-96 hours after the first sampling timepoint (Sample 2). Network analysis of the differentially expressed transcripts for the childen with and at risk for PARDS was performed. Network analysis of the differentially expressed transcripts for children with severe PARDS at sample timepoint 2 versus 1 was also performed.

first: Jocelyn

middle: R

last: Grunwell

first: Rishikesan

last: Kamaleswaran


title: Exploring the role of TAGLN in the pathogenesis of pathological scarring

city: Shanghai

first: Jia

last: Zhou

state: --- Select One ---

address: 639 Zhizaoju Road, Shanghai

country: China

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

summary: Pathological scarring is a fibroproliferative disorder characterised by abnormal fibroblast function and excessive deposition of extracellular matrix. In this study, based on the results of preliminary single-cell sequencing, we identified an enriched fibroblast subpopulation in keloids, which highly expresses TAGLN. In this study, we investigated the roles of TAGLN in the pathogenesis of pathological scars, respectively. And functional assays revealed that downregulation of TAGLN inhibited the motility activity and secretory functions of pathological scar fibroblasts, including invasion, migration, contraction and collagen secretion. We identified downstream targets of TAGLN by RNA-seq results analysis and further validation in. This study provides new perspectives for understanding pathological scarring and possible targets for clinical treatment.

overall_design: To elucidate the potential mechanisms of TAGLN in pathological scarring, we performed RNA-seq sequencing of HPSF after treatment with si-TAGLN and si-NC. We first analysed the gene expression of each group in the RNA sequencing data and identified differentially expressed genes based on a P value less than or equal to 0.01. And we combined GO enrichment analysis and KEGG analysis to screen potential downstream targets.

first: Xinwei

last: Cheng

first: Zhen

last: Gao


title: A type 2 cytokine Fc–IL-4 revitalises exhausted CD8+ T cells against cancer

status: Public on May 31 2024

city: New Haven

first: Rong

last: Fan

state: Connecticut

address: 55 Prospect St.

department: Biomedical Engineering

institute: Yale University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Current cancer immunotherapy predominately focuses on eliciting type 1 immune responses fighting cancer; however, long-term complete remission remains uncommon. A pivotal question arises whether type 2 immunity can be orchestrated alongside type 1-centric immunotherapy to achieve enduring response against cancer. Here, we show that an interleukin-4 fusion protein (Fc–IL-4), a typical type 2 cytokine, directly acts on CD8+ T cells and enriches functional terminally exhausted CD8+ T (CD8+ TTE) cells in the tumour. Consequently, Fc–IL-4 remarkably enhances anti-tumour efficacy of type 1 immunity-centric adoptive T cell transfer (ACT) or immune checkpoint blockade (ICB) therapies and induces durable remission across multiple syngeneic and xenograft tumour models. Mechanistically, we uncovered that Fc–IL-4 signals through both signal transducer and activator of transcription 6 (STAT6) and mammalian target of rapamycin (mTOR) pathways, augmenting the glycolytic metabolism and nicotinamide adenine dinucleotide (NAD+) level of CD8+ TTE cells in a lactate dehydrogenase A (LDHA)-dependent manner. The metabolic modulation mediated by Fc–IL-4 is indispensable for reinvigorating intratumoural CD8+ TTE cells. These findings underscore Fc–IL-4 as a potent type 2 cytokine-based immunotherapy that synergizes effectively with type 1 immunity to elicit long-lasting responses against cancer. Our study not only sheds light on the synergy between these two types of immune responses but also unveils an innovative strategy for advancing next-generation cancer immunotherapy by integrating type 2 immune factors.

overall_design:
1. For the in vivo study, B16F10 tumor-bearing CD45.2+Thy1.2+ C57BL/6 mice received i.v. adoptive transfer of activated Thy1.1+ PMEL CD8+ T cells (5 × 106 per mouse), followed by four doses of peritumoral (p.t.) administration of Fc–IL-4 (20 μg per mouse) or PBS control every other day. After the above treatment, tumors were collected and digested, and tumor-infiltrating PMEL T cells were enriched and sorted out for scRNA-seq.
2. For the in vitro study, single-cell co-profiling of epigenomic landscape and gene expression in the same single nuclei was performed on the ex vivo-induced CD8+ terminally exhausted T cells in the presence or absence of 20ng/mL IL-4.

first: Zhiliang

last: Bai

first: Bing

last: Feng

first: Li

last: Tang


type: Non-coding RNA profiling by high throughput sequencing

overall_design: RNA sequencing


title: Transcriptome-wide gene expression outlier analysis pinpoints therapeutic vulnerabilities in colorectal cancer

city: Candiolo

first: Federica

last: Di Nicolantonio

state: Torino

address: Candiolo Cancer Institute FPO-IRCCS, SP142, km 3.95

department: Department of Oncology

country: Italy

institute: University of Torino

summary: Multiple strategies are continuously being explored to expand the drug target repertoire in solid tumors. We devised a novel computational workflow for transcriptome-wide gene expression outlier analysis that allows the systematic identification of both overexpression and underexpression events in cancer cells. Here, it was applied to expression values obtained through RNA sequencing in 226 colorectal cancer (CRC) cell lines that were also characterized by whole-exome sequencing and microarray-based DNA methylation profiling. We found cell models displaying an abnormally high or low expression level for 3533 and 965 genes, respectively. Gene expression abnormalities that have been previously associated with clinically relevant features of CRC cell lines were confirmed. Moreover, by integrating multi-omics data, we identified both genetic and epigenetic alternations underlying outlier expression values. Importantly, our atlas of CRC gene expression outliers can guide the discovery of novel drug targets and biomarkers. As a proof of concept, we found that CRC cell lines lacking expression of the MTAP gene are sensitive to treatment with a PRMT5-MTA inhibitor (MRTX1719). Finally, other tumor types may also benefit from this approach.

overall_design: DNA methylation profiles were obtained for 88 parental CRC cell lines grown in vitro without any treatment

first: Elisa

last: Mariella

first: Ludovic

last: Barault

first: Giulia

last: Gionfriddo


title: Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver -Spatial Transcriptomics

status: Public on May 28 2024

city: Singapore

first: jinghe

last: xie

address: 21 Lower Kent Ridge Road

country: Singapore

institute: nuh

summary: ADAR1 is thought to be an immune suppressor maintaining self-tolerance to endogenous nucleic acids. Lack of ADAR1 results in MDA5 (Ifih1) activation and MDA5 deletion rescues ADAR1 null embryonic lethality. We generated liver specific ADAR1; MDA5 double KO mice and performed high throughput sequencing to investigate hepatic inflammation in these mice. Spatial transcriptomics (Visium, 10x Genomics) was performed on FFPE mice liver tissues. Constructed libraries were sequenced on the Novaseq 6000 platform. Over 250 million pairs of mappable reads for each sample were obtained.

overall_design: Examination of spatially resolved transcriptomes of Ifih1-/- Adar1wt/wt Alb-Cre+, Ifih1-/- Adar1wt/flox Alb-Cre+, and Ifih1-/- Adar1flox/flox Alb-Cre+ mice liver tissues to investigate  the effects of Adar1 depletion against Ifih1 null background.

first: Leilei

last: Chen

first: Wei

middle: L

last: Gan

first: Xi

last: Ren


title: Defective N-Glycosylation of IL6 Induces Metastasis and Tyrosine Kinase Inhibitor Resistance in Lung Cancer

status: Public on Jul 16 2024

city: Tainan

first: Chun-Hua

last: Hung

address: No. 138, Sheng-Li Rd., North Dist.

country: Taiwan

institute: National Cheng Kung University

summary: The biological consequences of various IL-6 glycoforms are unknown. To uncover the function of N-glycosylation of IL-6 in lung cancer, we compare the gene expression profiles in NSCLC cells induced by conditioned medium containing IL-6 with complete N-glycosylation (NG-IL6) or defective N-glycosylation (deNG-IL6).

overall_design: NG-IL6- or deNG-IL6- induced gene expression in human lung adenocarcinoma cells AS2-vec (with empty vector) was measured at 3 hours after exposure to the IL-6 glycoforms 1 ng/mL. Three independent experiments were performed.

first: Wu-Chou

last: Su


first: Truc

last: LE

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

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver -scRNAseq

summary: ADAR1 is thought to be an immune suppressor maintaining self-tolerance to endogenous nucleic acids. Lack of ADAR1 results in MDA5 (Ifih1) activation and MDA5 deletion rescues ADAR1 null embryonic lethality. We generated liver specific ADAR1; MDA5 double KO mice and performed high throughput sequencing to investigate hepatic inflammation in these mice. Single cell RNA sequencing was performed on cells isolated from mice livers. Constructed libraries were sequenced on the HiSeq X platform. Over 100 million pairs of mappable reads for each sample were obtained.

overall_design: Transcriptomes of single cells isolated from Ifih1-/- Adar1wt/wt Alb-Cre+, Ifih1-/- Adar1wt/flox Alb-Cre+, and Ifih1-/- Adar1flox/flox Alb-Cre+ mice livers were compared to examine the effects of Adar1 depletion against Ifih1 null background.

first: Vanessa

middle: H

last: Ng

first: Yangyang

last: Song

first: Omer

last: An


title: Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver -HCC scRNAseq

summary: ADAR1 is thought to be an immune suppressor maintaining self-tolerance to endogenous nucleic acids. ADAR1 is often overexpressed in hepatocellular carcinoma tumors, and might contribute to immunosuppression and immune evasion of cancer cells. We performed single cell RNA sequencing on non-tumor and tumor HCC samples. Constructed libraries were sequenced on the HiSeq X platform. Over 150 million pairs of mappable reads for each sample were obtained.

overall_design: Transcriptomes of single cells isolated from non-tumor and tumor HCC samples were examined to investigate immunosuppression and association with cellular crosstalk mechanisms.

first: Dan

middle: Y

last: Young


title: Human airway epithelial cells co-treated with IL-4 and IL-13 for seven days.

status: Public on May 29 2024

city: Boston

first: Nora

last: Barrett

state: Massachussetts

address: 60 Fenwood Rd

department: Allergy and Clinical Immunology

institute: Brigham and Women’s Hospital

summary: Nasal basal epithelial cells from 6 healthy adult donors were grown in air-liquid interface (ALI) cultures for fourteen days. Cells were then treated with 10 ng/mL of IL-4 and 10 ng/mL of IL-13 for seven additional days. Next, cell lysates were used for low-input RNA-seq library preparation (Smart-seq2) and sequencing.

overall_design: To investigate the effect of cytokine stimulation on epithelial cells we generated gene expression profiles using RNA-seq from 5 healthy donors under in vitro co-stimulation with IL-4 and IL-13 or under resting condition.

first: Maria

last: Gutierrez-Arcelus

first: Nils

last: Hallen

first: George

last: Huang

first: Sarah

last: Djeddi

first: Daniela

last: Fernandez-Salinas


title: Single-cell CAR T atlas reveals type 2 function in 8-year leukaemia remission

status: Public on May 27 2024

first: Rong

last: Fan

summary: Despite a high response rate in chimeric antigen receptor (CAR) T therapy for acute lymphocytic leukemia (ALL), approximately 50% of patients relapse within the first year, representing an urgent question to address in the next stage of cellular immunotherapy. To investigate the molecular determinants of ultra-long CAR T persistence, we obtained single-cell multi-omics sequencing data from 695,819 pre-infusion CAR T cells at the basal level or upon CAR-specific stimulation from 82 pediatric ALL patients enrolled in the first two CAR T ALL clinical trials and 6 healthy donors. We identified that elevated type-2 functionality in CAR T infusion products was significantly associated with patients maintaining a median B-cell aplasia duration of 8.4 years. Analysis of ligand-receptor interactions unveiled that type-2 cells regulate a distinct dysfunctional population, and the addition of IL-4 during antigen-specific activation alleviates CAR T cell dysfunction while enhancing functional fitness at both transcriptomic and epigenomic levels. Serial proteomic profiling of post-infusion sera revealed a higher level of circulating type-2 cytokines in 5-year or 8-year relapse-free responders. In a leukemic mouse model, type-2 high CAR T products demonstrated superior expansion and antitumor activity particularly upon leukemia rechallenge. Restoring antitumor efficacy in type-2 low CAR T cells was attainable by enhancing their type-2 functionality, either through incorporating IL-4 into the manufacturing process or priming manufactured CAR T products with IL-4 prior to infusion. Our findings provide key insights into the mediators of CAR T longevity and suggest potential therapeutic strategies to sustain long-term remission by boosting type-2 functionality in CAR T cells.

overall_design: Combining scRNA-seq and CITE-seq, we performed multi-omics profiling of both basal unstimulated CAR T cells and the activated CAR+ cells.

first: Zhiliang

last: Bai


title: Temporal effects of BMP4 on mouse embryonic and extraembryonic development

status: Public on May 21 2024

city: Rehovot

first: Markus

last: Mittnenzweig

state: Shfela

address: 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

summary: The developing placenta, originated in the mouse through the extra-embryonic ectoderm (ExE), is essential for mammalian embryonic development. Yet, unbiased characterization of ExE differentiation dynamics and interaction with the embryo proper remains incomplete. Here, we develop a temporal single-cell model of mouse gastrulation that maps continuous and parallel differentiation in embryonic and extraembryonic lineages. This is matched with a 3-way perturbation approach to target signaling from the embryo proper, the ExE alone, or both. We show that ExE specification involves early spatial and transcriptional bifurcation of uncommitted ectoplacental cone cells (EPCs) and chorion progenitors. Early BMP4 signaling from chorion progenitors is required for proper differentiation of uncommitted EPCs and later for their specification towards trophoblast giant cells. We also find bi-phasic regulation by BMP4 in the embryo. The early ExE-originating BMP4 signal is necessary for proper endo-mesoderm bifurcation, allantois, and primordial germ cells (PGCs) specification. However, commencing at E7.5, embryonic-derived BMP4 source restricts PGC pool size by favoring differentiation of their extraembryonic mesoderm precursors towards an allantois fate. ExE and embryonic tissues are therefore entangled in time, space, and signaling axes, highlighting the importance of their integrated understanding and modeling in vivo and in vitro.

overall_design: We individually imaged each embryo and performed index-sorting for them with subsequent plate-based scRNA-seq (MARS-seq). For ex utero cultured embryos, we pooled 5 embryos and performed 10x single-cell RNA-seq on them for two time points (late streak and head fold stage embryos). For further analysis of mutant/perturbation data, query data was compared to an already established dataset [Mittnenzweig et al. Cell 2021] that was further enriched in this study. The projection of query cells over the atlas resulted in best matching WT embryos that were used to calculate time, cell state composition and differential gene expression between query and atlas cells.

first: Ron

last: Hadas

first: Hernan

last: Rubinstein

first: Raz

last: Ben-Yair

first: Saifeng

last: Cheng

first: Alejandro

last: Aguilera-Castrejon

first: Netta

last: Reines

first: Ayelet-Hashahar

last: Orenbuch

first: Aviezer

last: Lifshitz

first: Dong-Yuan

last: Chen

first: Michael

middle: B

last: Elowitz

first: Magdalena

last: Zernicka-Goetz

first: Jacob

last: Hanna

first: Amos

last: Tanay

first: Yonatan

last: Stelzer


title: Development of a novel non-invasive biomarker panel for hepatic fibrosis in individuals with MASLD

status: Public on May 17 2024

city: Zeist

first: Lars

last: Verschuren

address: Utrechtseweg 48

department: Microbiology and Systems Biology

country: Netherlands

institute: TNO

summary:
- Background & Aims: Considering the escalating prevalence of metabolic dysfunction-associated steatotic liver disease (MASLD) and MASLD-related fibrosis, accurate non-invasive biomarkers for diagnosis and staging of fibrosis are urgently needed. This study Aims to develop a blood-based biomarker panel for fibrosis detection in individuals with MASLD.
- Approach & Results: Using a translational diet-induced LDLr-/-.Leiden MASLD mouse model, candidate biomarkers were identified focused on the mechanism of collagen deposition, by integrating hepatic gene expression and new extracellular matrix deposition, as detected by dynamic D2O-labeling. To translate these findings to humans, gene expression profiles and biomarkers were analyzed in liver biopsies and serum samples from 67 individuals with histologically characterized MASLD and variable degrees of fibrosis. This led to the selection of three biomarkers   for a blood-based fibrosis biomarker panel: IGFBP7, SSc5D and Sema4D. The accuracy of the biomarker panel was tested in a separate cohort of 128 individuals with histologically characterized MASLD across different stages of fibrosis. A Light Gradient Boosting Machine (LGBM) model was applied to predict fibrosis stage in MASLD (F0/F1: AUC = 0.90; F2: AUC = 0.91; F3/F4: AUC = 0.87).
- Conclusion & Discussion: Using a translational Approach to identify collagen turnover related proteins indicative of fibrosis, we developed an accurate blood-based biomarker panel to detect and stage hepatic fibrosis in individuals with MASLD.

overall_design:
- Selection of translation cohort
To translate the murine findings to humans, 74  individuals with MASLD were selected of whom stored liver biopsy material was available at the pathology department of the Erasmus Medical Center and Utrecht Medical Center, the Netherlands. A patient list was generated with the following search criteria: “steatosis OR steatohepatitis OR NASH OR NAFLD” from 1997 onwards. Patient records were reviewed and patients diagnosed with HBV, HCV, alcoholic steatohepatitis and auto-immune hepatitis were excluded. In addition, patients with other comorbidities, treated with steroids, hormonal therapy including anticonception and with benign liver tumors were excluded. Then, biobanked stained liver tissue slides were collected and reviewed by an external pathologists (JV& MD) resulting in a Fibrosis score for each individual liver biopsy. All patients that passed this review and were diagnosed as true MASLD patients were then included. Fibrosis is assessed on a scale from stages 0-4. Stage 0 denotes no fibrosis, stage 1 indicates perisinusoidal or periportal fibrosis, stage 2 reflects perisinusoidal and (peri)portal fibrosis, stage 3 signifies bridging fibrosis, and stage 4 represents cirrhosis. Stored tissue blocks containing the biopsy sample was than requested from the tissue biobank and further processed for RNA isolation and next generation sequencing. Out of the 74 samples of human formalin-fixed paraffin-embedded (FFPE) liver, a subset of 67 samples passed Quality Control (QC) and was selected for RNA sequencing.

first: Anne Linde

last: Mak

first: Arianne

last: van Koppen

first: Serdar

last: Özsezen

first: Sonia

last: Difrancesco

first: Martien

middle: P

last: Caspers

first: Jessica

last: Snabel

first: Anne-Marieke

last: van Dijk

first: Koen

last: van Son

first: Robert

last: Kleemann

first: Amanda

middle: J

last: Kiliaan

first: Eric

last: Hazebroek

first: André

last: Boonstra

first: Michail

last: Doukas

first: Max

last: Nieuwdorp

first: Joanne

last: Verheij

first: Adriaan

middle: G

last: Holleboom

first: Maarten

middle: E

last: Tushuizen

first: Roeland

last: Hanemaaijer


title: Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver -bulk RNA-seq

first: jinghe

last: xie

summary: ADAR1 is thought to be an immune suppressor maintaining self-tolerance to endogenous nucleic acids. Lack of ADAR1 results in MDA5 (Ifih1) activation and MDA5 deletion rescues ADAR1 null embryonic lethality. We generated liver specific ADAR1; MDA5 double KO mice and performed high throughput sequencing to investigate hepatic inflammation in these mice. Bulk RNA was sequenced on the HiSeq X platform. Over 100 million pairs of mappable reads for each sample were obtained.

overall_design: Transcriptomes of Ifih1-/- Adar1wt/wt Alb-Cre+ (n=3), Ifih1-/- Adar1wt/flox Alb-Cre+ (n=2), and Ifih1-/- Adar1flox/flox Alb-Cre+ (n=2) mice livers were compared to examine the effects of Adar1 depletion against Ifih1 null background.

first: Leilei

last: Chen

first: Wei

last: Gan

first: Xi

last: Ren

first: Vanessa

last: Ng

first: Yangyang

last: Song

first: Omer

last: An


title: Theophylline derivatives promote the activation of primordial follicles and ameliorate fertility deficits in naturally aged mice

status: Public on May 30 2024

city: Guangzhou

first: wenbo

last: zhang

state: Guangdong

address: Outer Ring East Road

institute: South China University of Technology

summary: The residual dormant primordial follicles in aged women and patients with premature ovarian insufficiency (POI) are difficult to activate in vivo. In this study, we found that PDE1A, PDE2A and PDE6D were expressed mainly in mouse primordial follicle oocytes and that PDE1A and PDE2A levels were significantly decreased during the activation of primordial follicles. The specific inhibitors of PDE1 (nimodipine), PDE2 (EHNA) and PDE5/6 (zaprinast) and the nonspecific PDE inhibitors theophylline derivatives (including aminophylline, dyphylline, enprofylline, choline theophyllinate, doxofylline, arofylline and lisofylline) activated mouse primordial follicles. These inhibitors also increased the levels of cyclic adenosine monophosphate (cAMP) and phosphorylated protein kinase B (p-Akt) in cultured mouse ovaries. Moreover, the administration of aminophylline, dyphylline and enprofylline to neonatal mice by intraperitoneal injection and to adolescent mice by oral treatment increased the number of growing follicle and the levels of p-Akt in the ovaries. Importantly, the oral administration of aminophylline increased the quantity and quality of ovulated oocytes and the number of offspring in naturally aged mice. In addition, aminophylline, dyphylline and enprofylline activated human primordial follicles and increased p-Akt levels. Thus, theophylline derivatives activate primordial follicles by increasing cAMP levels and activating the PI3K/Akt pathway, and the oral administration of aminophylline increases fertility in naturally aged female mice. As oral medications, theophylline derivatives may be used to increase fertility in aged women and patients with POI.

overall_design: We studied the effects of nonspecific phosphodiesterase inhibitors theophylline derivatives on primordial follicle activation and their possible mechanism by in vitro and in vivo mouse models, human ovarian tissue culture models. In addition, we studied the effects of theophylline derivatives on aged mice fertility by the naturally aged mice model. The possible mechanism of aminophylline improving oocyte quality was studied through metabolome of granulosa cells and transcriptome sequencing of oocytes.


title: Differential analysis of gene expression in liver tissues of patients with nonalcoholic fatty liver disease and controls.

status: Public on May 15 2024

city: Changsha

first: xiaohua

last: luo

state: hunan

address: 139 Renmin Road

institute: The Second Xiangya Hospital of Central South University

summary: Non-alcoholic fatty liver disease (NAFLD) comprises a collection of chronic liver disorders distinguished by the excessive accumulation of lipids within hepatocytes and the presence of steatosis. It covers a range of liver conditions that vary from simple steatosis (non-alcoholic fatty liver, NAFL) to non-alcoholic steatohepatitis (NASH). In this study, hepatic gene expression was compared among 6 patients with NAFL, 4 with NASH, and 6 healthy controls. All of these samples were collected prior to the liver transplantation procedure. Subsequently, differential genes were identified through comparative analysis of sequencing results, and target genes potentially related to the pathogenesis of NAFLD were further investigated. Numerous potential target genes and pathways have been identified in NAFLD, providing potential targets for therapeutic interventions.

overall_design: RNA-seq data of liver tissues of 10 NAFLD patients and 6 controls.


title: A dynamic subpopulation of CRISPR-Cas overexpressers allows Streptococcus pyogenes to rapidly respond to phage [RNA-seq]

status: Public on May 14 2024

city: Baltimore

first: Joshua

last: Modell

state: MD

address: 725 N Wolfe St, PCTB 614

institute: Johns Hopkins University School of Medicine

summary: Cas9 is a transcriptional autoregulator in many strains of S. pyogenes. A natural single guide RNA (tracr-L) directs Cas9 to bind to and repress its promoter. In this study, we aimed to determine whether tracr-L, crRNAs, or other noncanonical guide RNAs direct Cas9 to bind to other regions of the genome and potentially regulate the expression of additional genes.

overall_design: To determine whether CRISPR-Cas overexpression or loss leads to changes in gene expression, we generated strains of S. pyogenes that overexpress (∆tracr-L) or lack (∆CRISPR-Cas) the CRISPR-Cas system and performed RNA-Seq along with the WT strain.

first: Marie

last: Stoltzfus

first: Rachael

last: Workman

first: Nicholas

middle: C

last: Keith

middle: W


title: Novel anti-virulence compounds disrupt exotoxin expression in MRSA

city: High Point

first: Heather

middle: Bennett

last: Miller

state: NC

address: One University Parkway

department: Chemistry

institute: High Point University

summary: Hemolysins are lytic exotoxins expressed in most strains of S. aureus, but hemolytic activity varies between strains. We have previously reported several novel anti-virulence compounds that disrupt the S. aureus transcriptome, including hemolysin gene expression. This report delves further into our two lead compounds, loratadine and a structurally related brominated carbazole, and their effects on hemolysin production in methicillin-resistant S. aureus (MRSA). To gain understanding into how these compounds affect hemolysis, we analyzed these exotoxins at the DNA, RNA, and protein level after in vitro treatment. While lysis of red blood cells varied between strains, DNA sequence variation did not account for it. We hypothesized that our compounds would modulate gene expression of multiple hemolysins in two hospital-acquired strains of MRSA, both with staphylococcal cassette chromosome mec (SCCmec) type II. RNA-seq analysis of differential gene expression in untreated and compound-treated cultures revealed hundreds of differentially expressed genes, with a significant enrichment in genes involved in hemolysis. The brominated carbazole and loratadine both displayed the ability to reduce hemolysis in strain 43300 but displayed differential activity in strain USA100. These results corroborate gene expression studies as well as western blots of alpha hemolysin. Together, this work suggests that small molecules may alter exotoxin production in MRSA but that the directionality and/or magnitude of the difference are likely strain dependent.

overall_design: Differential gene expression was examined between MRSA cultures either untreated, treated with oxacillin only, treated with compound 8 or loratadine alone, or cotreated with oxacillin and loratadine or compound 8. Each of the six treatments was performed with biological triplicates.


title: Genome-wide screen of Mycobacterium tuberculosis-infected macrophages revealed GID/CTLH complex-mediated modulation of bacterial growth

status: Public on May 08 2024

city: Ithaca

first: Nelson

middle: Victor

last: Simwela

state: NY

address: 930 Campus Rd

department: Microbiology and Immunology

institute: Cornell University

summary: The eukaryotic GID/CTLH complex is a highly conserved E3 ubiquitin ligase involved in a broad range of biological processes. However, a role of this complex in host antimicrobial defenses has not been described. We exploited Mycobacterium tuberculosis (Mtb) induced cytotoxicity in macrophages in a FACS based CRISPR genetic screen to identify host determinants of intracellular Mtb growth restriction. Our screen identified 5 (GID8, YPEL5, WDR26, UBE2H, MAEA) of the 10 predicted members of the GID/CTLH complex as determinants of intracellular growth of both Mtb and Salmonella serovar Typhimurium. We show that the antimicrobial properties of the GID/CTLH complex knockdown macrophages are mediated by enhanced GABAergic signaling, activated AMPK, increased autophagic flux and resistance to cell death. Meanwhile, Mtb isolated from GID/CTLH knockdown macrophages are nutritionally starved and oxidatively stressed. Our study identifies the GID/CTLH complex activity as broadly suppressive of host antimicrobial responses against intracellular bacterial infections.

sample_organism:
Mycobacterium tuberculosis
Mus musculus

platform_organism:
Mycobacterium tuberculosis
Mus musculus

overall_design: Analysis of the transcriptional profile of both the host and Mtb in  Mtb infected GID/CTLH knockdown macrophages (Scramble (SC), GID8, WDR26 and MAEA)

first: N

middle: V

first: L

last: Johnston

first: P

last: Bita

first: C

last: Altier

middle: M

last: Sassetti

first: D

last: Russell


title: Comprehensive transcriptome analysis of lung tissues in the sugen/hypoxia rats with/without treatment of chrysin or trimetazidine

status: Public on May 16 2024

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

summary: Pulmonary arterial hypertension (PAH) is a debilitating progressive disease characterized by high blood pressure in the pulmonary artery. Chrysin (5,7-dihydroxyflavone) is a phytochemical, which is a flavonoid widely present in plant sources. It is known that right ventricular dysfunction is the worst mortality predictor in patient with PAH. Recent studies have shown that chrysin improves hemodynamic parameters including right ventricular pressure, right ventricular hypertrophy, and pulmonary vascular remodeling in a rat model of chronic hypoxia-induced pulmonary hypertension. On the other hand, trimetazidine (TMZ) is an anti-ischemic agent widely used in the treatment of coronary artery disease. It has been reported that trimetazidine therapy for 3 months on top of standard PAH regime significantly improve right ventricular ejection fraction and functional capacity in patient with PAH. However, the effects of chrysin or trimetazidine on gene expression in lung of patient with PAH. Here, we performed that a comprehensive analysis of gene expression changes in lung tissues of sugen-received rats under hypoxic conditions, which is a model of PAH with chrysin or trimetazidine treatment using RNA sequencing (RNA-seq).

overall_design: mRNA profiles of lung tissues  were generated by RNA sequencing using the NextSeq 500 (Illumina).

first: Asako

last: Yanagisawa

first: Takayuki

last: Kobayashi

first: Yoshitoshi

last: Kasuya

first: Koichiro

last: Tatsumi


title: Expansion of profibrotic monocyte-derived alveolar macrophages in patients with persistent respiratory symptoms and radiographic abnormalities after COVID-19

status: Public on May 12 2024

city: Chicago

first: Alexander

middle: V.

last: Misharin

state: IL

address: 303 E Superior

institute: Northwestern University


title: The genetic architecture of protein interaction affinity and specificity

status: Public on May 02 2024

city: Basel

first: Guillaume

last: Diss

address: 66 Maulbeerstrasse

country: Switzerland

institute: FMI

summary: Proteins function in crowded cellular environments in which they must bind to specific target proteins but also avoid binding to many other off-target proteins. In large protein families this task is particularly challenging because many off-target proteins have very similar structures. How this specificity of physical protein-protein interactions in cellular networks is encoded and evolves is not very well understood. Here we address the question of specificity-encoding by comprehensively quantifying the effects of all mutations in one protein, JUN, on its binding to all other members of a protein family, the 54 human basic leucine zipper transcription factors. Fitting a global thermodynamic model to the data reveals that most affinity changing mutations equally affect JUN’s propensity to bind to all its interaction partners. Mutations that alter the specificity of binding are much rarer. These specificity-altering mutations are, however, distributed throughout the JUN interaction interface. JUN’s interaction specificity is encoded by both positive determinants that promote on-target interactions and negative determinants that prevent off-target interactions. Indeed, about half of the specificity-defining residues in JUN have dual functions and both promote on-target binding and prevent off-target binding. Whereas nearly all mutations that alter specificity are pleiotropic and also alter the affinity of binding to all interaction partners, the converse is not true with mutations outside of the interface able to tune affinity without affecting specificity. Our results provide the first global view of how mutations in a protein affect binding to all its potential interaction partners and reveal the distributed encoding of specificity and affinity in an interaction interface. They also show how the modular architecture of coiled-coils provides an elegant solution to the challenge of optimising specificity and affinity in a large protein family.

sample_organism:
Escherichia coli
Saccharomyces cerevisiae

overall_design: Deep mutational scanning of the interaction JUN's leucine zipper domain and all other human bZIP

first: Alexandra

last: Bendel

first: André

last: Faure

first: Dominique

last: Klein

first: Kenji

last: Shimada

first: Georg

last: Kempf

first: Simone

last: Cavadini

first: Benjamin

last: Lehner


title: AntimiR  blocking of miR-23b and -218 corrects myotonic dystrophy primary cell defects over a wide range of CTG repeat expansions.

status: Public on May 01 2024

city: Burjassot

first: Ruben

last: Artero

state: Valencia

address: C/ Doctor Moliner, 50

department: Genetics

country: Spain

institute: Universidad de Valencia

summary: This study tested candidate therapeutic antimiRs in a comprehensive new collection of primary myoblasts derived from myotonic dystrophy type 1 (DM1) patients. DM1 is caused by genetically unstable CTG repeat expansions in the DMPK gene and has multiple clinical presentations, likely because of variable repeat sizes at the tissue and organ levels. Expanded DMPK transcripts deplete Muscleblind-Like Splicing Regulator protein MBNL1, which in turn causes DM1 symptoms. A promising therapeutic approach increases the expression of MBNL1 by blocking natural repressors miR-23b and miR-218 employing antimiRs with chemical modifications designed for a better pharmacological profile in humans. In untreated primary cells, we demonstrate that upregulated therapeutic targets miR-23b and miR-218 and reduced MBNL1 protein levels inversely correlate with CTG repeat size, supporting that active MBNL1 protein repression synergizes with the sequestration by CUG repeats in DM1. Upon treatment with novel antimiRs, multiple readouts of RNA toxicity associated with typical DM1 alterations improved. MBNL1-dependent exon inclusions, and myoblast fusion and myotube area defects, showed robust correction over a wide range of CTG expansions. Unexpectedly, antimiR treatment also reduced DMPK transcript levels and the number of ribonuclear aggregates. Based on these data, we selected a leading antimiR for further transcriptomics characterization and demonstrated that it reversed up to 68% of dysregulated genes. The study revealed that the candidate antimiRs could provide therapy to clinically relevant DM1 forms over a wide range of repeat sizes and genetic backgrounds by simultaneously reducing MBNL1 sequestration and derepressing protein synthesis.

overall_design: To investigate the efects of AntimiR blocking miR-23b we cultured myoblast cell lines derived from 8 DM1 patients and  9 heathy donors. We treated the DM1 cell lines with AntimiR blocking miR-23b and performed an RNA-seq with 2 replicates of the treated group.

first: Estefanía

last: Cerro-Herreros

first: Judit

last: Núñez-Manchón

first: Neia

last: Naldaiz-Gastesi

first: Marc

last: Carrascosa-Sàez

first: Andrea

last: García-Rey

first: Irene

last: González-Martínez

first: Jorge

last: Espinosa-Espinosa

first: Kevin

last: Moreno

first: Javier

last: Poyatos-García

first: Juan

last: Vilchez

first: Adolfo

last: López de Munain

first: Mònica

last: Suelves

first: Gisela

last: Nogales-Gadea

first: Beatriz

last: Llamusí

first: Rubén


title: Structural and molecular distinctions of secondary and primary spines in the sea urchin Lytechinus variegatus

city: Providence

first: Madison

last: Silvia

state: Rhode Island

address: 185 Meeting St

department: MCB

institute: Brown University

summary: Sea urchins (echinoids) are common model organisms for research in developmental biology and for their transition from a bilateral larva into their post-metamorphic adult with pentaradial body symmetry. The adult also has a calcareous endoskeleton with a multimetameric pattern of continuously added elements, among them the namesake of this phylum, spines. Nearly all echinoids have both large primary spines, and an associated set of smaller secondary spines.We hypothesize that the secondary spines of the tropical variegated urchin species, Lytechinus variegatus, are morphologically and molecularly distinct structures from primary spines and not just small spines. To test this premise, we examined both spine types using light microscopy, micro-CT imaging, lectin labeling, transcriptomics, and fluorescent in situ hybridization (FISH). Our findings reveal basic similarities between the two types in mineral and cellular anatomy, but with clear differences in growth patterns, genes expressed, and in the location of gene expression within the two types of spines. In particular, secondary spines have non-overlapping, longitudinally concentrated growth bands that lead to a blunt and straight profile, and a distinct transcriptome involving the upregulation in many genes in comparison to the primary spines. Neural, ciliary, and extracellular matrix interacting factors are implicated in the differentially expressed gene (DEG) dataset, including two genes - ONECUT2 and an uncharacterized discoidin- and thrombospondin-containing protein - that show spine type- specific localizations in FISH, and may be of interest to ongoing work in urchin spine patterning.These results demonstrate that primary and secondary spines have overlapping but distinct molecular and biomineralized characteristics, suggesting unique developmental and regenerative mechanisms, and devotion to this spiny dermal phylum.

overall_design: For transcriptomic analysis, 50 primary and 100 secondary spines each were harvested from 4 wild-caught L. variegatus individuals. All individuals chosen were of the white-and-green color morph, in order to avoid potential confounds due to genetic and transcriptomic differences between morphs (for discussion of color morph effects in this species, see (Moscoso, 2015; Pawson and Miller, 1982; Wessel et al., 2024) . Spines were immersed in TriZol and RNA was extracted following the manufacturer’s instructions. The resulting 4 primary and 4 secondary samples were sent to NovoGene for comparative RNAseq analysis, with the echinobase.org L. variegatus assembly v3.0 as the reference genome.

first: Elise

last: Hebert

first: Gary

last: Wessel


title: A dynamic subpopulation of CRISPR-Cas overexpressers allows Streptococcus pyogenes to rapidly respond to phage

first: Joshua

last: Modell

overall_design:
Chromatin immunoprecipitation and sequencing (ChIP-Seq) for Cas9 in S. pyogenes strains
Please note that *narrowPeak data file generated from both ChIP and input sample is linked to the corresponding *ChIP sample records.

first: Marie

last: Stoltzfus

first: Rachael

last: Workman

first: Nicholas

last: Keith


title: Drug Repurposing Using Molecular Network Analysis Identifies Janus Kinase as Targetable Driver in Necrobiosis Lipoidica

city: Rochester

first: Tao

last: Ma

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

summary: Drug repurposing is an attractive strategy for therapy development, particularly in rare diseases where traditional drug development approaches may be challenging due to high cost and small numbers of patients. Here we used a novel drug identification and repurposing pipeline to identify candidate targetable drivers of disease and corresponding therapies through application of causal reasoning using a combination of open-access resources and transcriptomics data. We optimized our approach on psoriasis as a disease model, demonstrating the ability to identify known and novel molecular drivers of psoriasis and link them to current and emerging therapies. Application of our approach to a cohort of tissue samples of necrobiosis lipoidica, an unrelated, rare, and to date molecularly poorly characterized cutaneous inflammatory disorder, identified a unique set of upstream regulators, particularly highlighting the role of IFNG and the JAK-STAT pathway as a likely driver of disease pathogenesis and linked it to JAK inhibitors as potential therapy. Analysis of an independent cohort of NL samples validated these findings with the overall agreement of drug matched upstream regulators above 96%. These data highlight utility of our approach in rare diseases and offer a novel opportunity for drug discovery in other rare diseases in dermatology and beyond.

overall_design: we analyzed 17 histologically typical, archival formalin-fixed paraffin-embedded (FFPE) lesions and 5 control tissues. Whole transcriptome analysis was performed, identifying 3,857 differentially expressed genes with 2,471 genes upregulated and 1,386 genes downregulated in NL (|Log2FC|>1, p<0.05).

first: Alysia

middle: N

last: Hughes

first: Xing

last: Li

first: Julia

middle: S

last: Lehman

first: Steven

middle: A

last: Nelson

first: David

last: DiCaudo

first: Rekha

last: Mudapphati

first: Angelina

last: Hwang

first: Jacob

last: Kechter

first: Mark

last: Pittelkow

first: Aaron

last: Mangold

first: Aleksandar

last: Sekulic


title: Circular RNA circZFPM2 regulates cardiomyocyte hypertrophy and survival

status: Public on Apr 25 2024

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

country: Germany

institute: Hanover Medical School

summary: Hypertrophic cardiomyopathy (HCM) constitutes the most common genetic cardiac disorder. However, current pharmacotherapeutics are mainly symptomatic and only partially address underlying molecular mechanisms. Circular RNAs (circRNAs) are a recently discovered class of non-coding RNAs and emerged as specific and powerful regulators of cellular functions. By performing global circRNA-specific next generation sequencing in cardiac tissue of patients with hypertrophic cardiomyopathy compared to healthy donors, we identified circZFPM2 (hsa_circ_0003380. CircZFPM2, which derives from the ZFPM2 locus, is a highly conserved regulatory circRNA that is strongly induced in HCM tissue. In vitro loss-of-function experiments were performed in neonatal rat cardiomyocytes, human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), and HCM-patient-derived hiPSC-CMs. A knockdown of circZFPM2 was found to induce cardiomyocyte hypertrophy and compromise mitochondrial respiration, leading to an increased production of reactive oxygen species and apoptosis. In contrast, delivery of recombinant circZFPM2, packaged in lipid-nanoparticles or using AAV-based overexpression, rescued cardiomyocyte hypertrophic gene expression and promoted cell survival. Additionally, HCM-derived cardiac organoids exhibited improved contractility upon CM-specific overexpression of circZFPM2. Multi-Omics analysis further promoted our hypothesis, showing beneficial effects of circZFPM2 on cardiac contractility and mitochondrial function. Collectively, our data highlight that circZFPM2 serves as a promising target for the treatment of cardiac hypertrophy including HCM.

overall_design: To study the role of circZFPM2 signalling in cardiomyocytes, Human induced pluripotent stem cell-derived cardiomyocytes were transfected with an siRNA specifically designed against the backsplice site of circZFPM2.

first: Dimyana

last: Neufeldt

first: Arne

last: Schmidt

first: Elisa

last: Mohr

first: Dongchao

last: Lu

first: Shambhabi

last: Chatterjee

first: Ke

last: Xiao

first: Wen

last: Pan

first: Sarah

last: Cushman

first: Christopher

last: Jahn

first: Malte

last: Juchem

first: Hannah

last: Hunkler

first: Giuseppe

last: Cipriano

first: Bjarne

last: Jürgens

first: Kevin

first: Sonja

last: Groß

first: Mira

last: Jung

first: Jeannine

last: Hoepfner

first: Natalie

last: Weber

first: Roger

last: Foo

first: Andreas

last: Pich

first: Robert

last: Zweigerdt

first: Theresia

last: Kraft

first: Thomas

last: Thum

first: Christian

last: Bär


title: Analysis of gene expression in SLMAP3 knockout immortalized E14.5 mouse embryonic fibroblasts

city: Ottawa

first: Balwant

last: Tuana

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

summary: Due to the developmental abnormalities observed in SLMAP3 knockout mouse embryos, we aimed to investigated the impact of gene expression in E14.5 mouse embryonic fibroblasts (MEFs) isolated from these animals. The cells used for RNA-sequencing were previously immortalized with a transient expression of SV40 large T (SV40 1: pBSSVD2005 was a gift from David Ron - Addgene plasmid # 21826 ; http://n2t.net/addgene:21826 ; RRID:Addgene_21826). These immortalized cells express mostly the largest isoforms of SLMAP (~ 90kDa), which are the ones knocked out in the embryos, and therefore compensation because of other isoforms is negligible.

overall_design: Immortalized mouse embryonic fibroblasts from 4  different wildtype and 4 different SLMAP3 knockout E14.5  embryos were used. RNA-sequencing was performed with each sample for the quantification of differential gene expression between the knockout and wild type cells.

first: Ana

last: Dias

first: Taha

last: Rehmani


title: Expression data from neural stem cells of adult mice brains in TCQA- and TFQA- treatments

status: Public on Apr 27 2024

city: Tsukuba City

first: Hongyu

last: Lin

state: Ibaraki

address: Tennodai 1-1-1

department: Life and Earth Sciences

institute: University of Tsukuba

summary:
TCQA- and TFQA- treatments in NSCs showed the significant performance on improving neurogenesis compared with no- treatment NSCs. TCQA and TFQA‐ treatments in NSCs also had significant activation of ErbB signaling pathway, AKT and MAPK kinases. Among them, TCQA- treatment upregulated Myc gene when Jun was mediated in TFQA- treatment, which stimulated the functions of enhancing synaptic growth and neuron differentiation.
We used microarrays to detail the global programme of gene expression underlying treatment and identified distinct classes of regulated genes during this process.

overall_design: Neural stem cells of adult mice brains were selected  for RNA extraction on Affymetrix microarrays. We selected 6-8 weeks old adult male ICR mice for neural stem cell extraction. After two weeks of incubation, TCQA- and TFQA- treatments for 72 h were performed.


title: Tipifarnib Reduces Circulating Extracellular Vesicles and Protects Against Pressure Overload-mediated Cardiac Remodeling and Dysfunction

status: Public on May 07 2024

city: Philadelphia

first: Vandana

last: Mallaredy

state: Pennsylvania

address: 3500 N Broad St, MERB 983

department: Aging + Cardiovascular Discovery Center

institute: Temple University

summary:
BACKGROUND: Heart failure (HF) is one of the leading causes of mortality worldwide. Extracellular vesicles (EVs) including small EVs, or exosomes and their molecular cargo are known to modulate cell to cell communication during multiple cardiac diseases.  However, the role of systemic EV biogenesis inhibition in the models of HF is not well documented and remains unclear.
METHODS: We investigated the role of circulating exosomes during cardiac dysfunction and remodeling in a mouse transverse aortic constriction (TAC) model of HF. Importantly, we investigate the efficacy of Tipifarnib (Tip), a recently identified exosome biogenesis inhibitor that targets the critical proteins (Rab27a, nSmase2 and Alix) involved in exosome biogenesis for this mouse model of HF. In this study, 10-week-old male mice underwent TAC surgery, were randomly assigned to groups with and without Tip treatment (10 mg/kg three times/week) and monitored for 8 weeks and a comprehensive assessment was conducted through performed echocardiographic, histological, and biochemical studies.
RESULTS: TAC significantly elevated circulating plasma exosomes and markedly increased cardiac left ventricular (LV) dysfunction, cardiac hypertrophy, and fibrosis. Furthermore, injection of plasma exosomes from TAC mice induced LV dysfunction and cardiomyocyte hypertrophy in uninjured mice without TAC. On the contrary, treatment of Tip in TAC mice reduced circulating exosomes to baseline and remarkably improved LV functions, hypertrophy, and fibrosis. Tip treatment also drastically altered the miRNA profile of circulating post-TAC exosomes, including miR331-5p which was highly downregulated both in TAC circulating exosomes and in TAC cardiac tissue. Mechanistically, miR331-5p is crucial for inhibiting fibroblast-to-myofibroblast transition by targeting HOXC8, a critical regulator of fibrosis. Tipifarnib treatment in TAC mice upregulated the expression of miR331-5p that acts as potent repressor for one of the fibrotic mechanisms mediated by HOXC8.
CONCLUSIONS: Our study underscores the pathological role of exosomes in HF and fibrosis in response to pressure overload. Tipifarnib mediated inhibition of exosome biogenesis and cargo sorting may serve as a viable strategy to prevent progressive cardiac remodeling to HF.

overall_design: We investigated the role of circulating exosomes during cardiac dysfunction and remodeling in a mouse transverse aortic constriction (TAC) model of HF, and the efficacy of Tipifarnib (Tip), a recently identified exosome biogenesis inhibitor involved in exosome biogenesis for this mouse model of HF.

first: Raj

last: Kishore


title: Effect of FOSL1 and HDAC2 knockdown on gene expression in cancer cell lines

city: Beijing

first: Chengqi

last: Yi

address: Yiheyuan Road

department: School of Life Sciences

institute: Peking University

summary: We identifled FOSL1 and HDAC2 as master regulators of cancer cell metabolism. To validate their function, we knockdown FOSL1 in pancreatic adenocarcinoma cell line PANC-1 and HDAC2 in lung adenocarcinoma cell line H1299, respectively. Then RNA-seq was performed to investigate the alterations of metabolic genes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for knockdown cell lines and controls. Three replicates were included for each group.

first: Zhe

last: Zhou

first: Di

last: Dong

first: Yuxin

last: Yin


title: Mitochondria-localized MBD2c facilitates mtDNA transcription and drug resistance

status: Public on Apr 18 2024

city: Hefei

first: Yijie

last: Hao

address: Huangshan Road 443

institute: USTC

summary: Mitochondria contain a 16kb-dsDNA genome encoding 13 proteins essential for respiration, whereas its regulatory mechanism and potential role in cancer development remain elusive. Although Methyl-CpG-binding protein (MBD) proteins are essential for nuclear transcription, their role in mitochondrial DNA (mtDNA) transcription is unknown. Here, we report that the MBD2c splicing variant translocates into mitochondria to mediate mtDNA transcription and increase mitochondrial respiration in triple negative breast cancer (TNBC) cells. Specifically, MBD2c binds D-loop regions in mtDNA to recruit SIRT3, which in turn deacetylates TFAM, a primary mitochondrial transcription factor, and activates its function. TFAM activation subsequently enhances transcription of the whole mitochondrial genome. Furthermore, MBD2c overexpression recovered the decreased mtDNA-encoded RNA and protein levels induced by the DNA synthesis inhibitor, cisplatin (CDDP), in vitro and in vivo, preserving mitochondrial gene expression and respiration, consequently enhancing TNBC cells drug resistance and proliferation. These data collectively demonstrate that MBD2c positively regulates mtDNA transcription, thus connecting epigenetic regulation by deacetylation with cancer cell metabolism, suggesting druggable targets to overcome resistance.

overall_design: Chromatin  immunoprecipitation DNA-sequencung (ChIP-seq) for MBD2c in MDA-MB-468 cells

first: Shengqi

last: Shen

first: Linchong

last: Sun

first: Ping

last: Gao

first: Huafeng

last: Zhang


title: Cyclical transcription factor AP2XII-9 is a key activator for asexual division and apicoplast inheritance in Toxoplasma gondii tachyzoite

status: Public on May 05 2024

city: Nanning

first: Dandan

last: Hu

state: China

address: Daxue East Rd #100, College of Animal Science and Techenology, Guangxi University.

institute: Guangxi University

summary: Toxoplasma gondii is an intracellular parasitic protozoan that poses a significant risk to pregnant women and immunocompromised individuals. T. gondii tachyzoites duplicate rapidly in host cells during acute infection through endodyogeny. This highly regulated division process is accompanied by complex gene regulation networks. TgAP2XII-9 is a cyclical transcription factor, but its specific role in the parasite cell cycle is not fully understood. Here, we demonstrate that TgAP2XII-9 is identified as a nuclear transcription factor and is dominantly expressed during the S/M phase of the tachyzoite cell cycle. CUT&Tag results indicate that TgAP2XII-9 targets key genes for the moving junction machinery (RON2, 4, 8) and daughter cell inner membrane complex (IMC). TgAP2XII-9 deficiency resulted in a significant downregulation of rhoptry proteins and rhoptry neck proteins, leading to a severe defect in the invasion and egress efficiency of tachyzoites. Additionally, the loss of TgAP2XII-9 correlated with a substantial downregulation of multiple IMC and apicoplast proteins, leading to disorders of daughter bud formation and apicoplast inheritance, and further contributing to the inability of cell division and intracellular proliferation. Our study reveals that TgAP2XII-9 acts as a critical S/M-phase regulator that orchestrates the endodyogeny and apicoplast division in T. gondii tachyzoite. This study contributes to a broader understanding of the complexity of the parasite’s cell cycle and its key regulators.

overall_design:
To assess the functions of TgAP2XII-9 in T. gondii, an indole-3-acetic acid (IAA) degradation (mAID) system was used to generate an inducible knockdown (iKD) of TgAP2XII-9 parasites (iKD TgAP2XII-9). Potentially regulated genes of the transcription factor TgAP2XII-9 were investigated by RNA-seq using TgAP2XII-9 iKD parasites with or without IAA treatment for 24 hours. Three biological replicates were employed. And the raw data was already posted on SRA database under project PRJNA1070975.
To further characterize the direct target genes of TgAP2XII-9, CUT&Tag experiments were performed using the endogenously 3xHA tagged parasite and RH strain.

first: Yuehong

last: Shi

first: Xuan

last: Li

first: Yue

last: He

first: Yucong

last: Jiang

first: Xingju

last: Song


title: Capture of TAD reorganization endows variant patterns of gene transcription

status: Public on Apr 29 2024

city: Shanghai

first: He

state: Shanghai

address: Tongji University, 1239 Siping Road, Yangpu District, Shanghai

institute: School of Life Science and Technology, Tongji University

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

overall_design: Refer to individual Series


title: Neoadjuvant PARPi or Chemotherapy in Ovarian Cancer Informs Targeting Effector Treg Cells for Homologous-Recombination-Deficient Tumors

status: Public on Jul 05 2024

city: Wuhan

first: Qinglei

state: Hubei

address: Jiefang Avenue

department: Department of Gynecological Oncology

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


title: A fine kinetic balance of interactions directs transcription factor hubs to genes

status: Public on Apr 16 2024

city: philadelphia

first: Mustafa

last: Mir

state: PA

address: 3501 Civic Center Boulevard, CTRB 9030

institute: Children's Hospital of Philadelphia


title: Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis - CD45 scRNA-Seq

status: Public on Apr 12 2024

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

summary: Adult inflammatory bowel disease is incompletely understood. We combine unbiased single-cell RNA sequencing (gene expression profiling, CITE-seq derived cell surface protein data, TCR and BCR sequence data) with unbiased spatial transcriptomics to interrogate changes across immune and non-immune populations in colitis and health, across tissue and blood. We compare idiopathic ulcerative colitis with hitherto under-studied immune checkpoint therapy induced colitis, utilizing non-inflamed disease states as additional controls. We identify patterns of inflammation and response unique and common to both diseases, and infer changes in cell trafficking with potential therapeutic implications. We go on to localize disease-specific changes in tissue using spatial transcriptomics. We leverage this data to interrogate cellular interactions in an unbiased manner, allowing us to describe novel microdomains of inflammation and repair.

overall_design: Flow-cytometry (FACS) sorted CD45 positive immune cells from tissue (colon), in patients with active ulcerative colitis (UC_I), paired non-inflamed areas at the same endoscopy (UC_NI), active immune checkpoint inhibitor-induced colitis (CC_I), patients given checkpoint inhibitors without colitis (CC_NI), compared with healthy controls (HC). Patients with CC were treated with anti-PD-1 immunotherapy (Monotherapy)

first: Agne

last: Antanaviciute

first: Tarun

last: Gupta

first: Anna

last: Aulicino

first: Rosana

last: Babu

first: Chloe

last: Lee

first: Hashem

last: Koohy


title: Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis - Spatial Transcriptomics

summary: Adult inflammatory bowel disease is incompletely understood. We combine unbiased single-cell RNA sequencing (gene expression profiling, CITE-seq derived cell surface protein data, TCR and BCR sequence data) with unbiased spatial transcriptomics to interrogate changes across immune and non-immune populations in colitis and health, across tissue and blood. We compare idiopathic ulcerative colitis with hitherto under-studied immune checkpoint therapy induced colitis, utilizing non-inflamed disease states as additional controls. We identify patterns of inflammation and response unique and common to both diseases, and infer changes in cell trafficking with potential therapeutic implications. We go on to localize disease-specific changes in tissue using spatial transcriptomics, leveraging this data to interrogate cellular interactions in an unbiased manner, allowing us to describe novel microdomains of inflammation and repair.

overall_design: Colon sections from adult healthy patients (HC) and adults with actively inflamed ulcerative colitis (UC_I) and checkpoint inhibitor-induced colitis (CC_I) were subject to unbiased spatial transcriptomic analysis using the 10X visium platform. Patients with CC were either treated with anti-PD-1 immunotherapy (Monotherapy) or a combination of simultaneous anti-PD-1 and anti-CTLA4 immunotherapy (Dual therapy).


title: A fine kinetic balance of interactions directs transcription factor hubs to genes [Cut and Run]

status: Public on Apr 15 2024

summary: Eukaryotic gene regulation relies on the binding of sequence-specific transcription factors (TFs). TFs bind chromatin transiently yet occupy their target sites by forming high-local concentration microenvironments (hubs and condensates) that increase the frequency of binding events. Despite their ubiquity, such microenvironments have been difficult to study in endogenous contexts due to technical limitations. Here, we overcome these limitations and investigate how hubs drive TF occupancy at their targets. Using a DNA binding perturbation to a hub-forming TF, Zelda, in Drosophila embryos, we find that hub properties, including the stability and frequencies of associations to targets, are key determinants of TF occupancy. Our data suggest that hub targeting is driven not just by specific DNA motif recognition, but also by a fine-tuned kinetic balance of interactions between TFs and their co-binding partners.

overall_design: WT embryos were compared to embryos with the 5th Zinc Finger of Zelda deleted

first: Apratim

last: Mukherjee

first: Samantha

last: Fallacaro

first: Puttachai

last: Ratchasanmuang

first: Joseph

last: Zinski

first: Alan

last: Boka

first: Kareena

last: Shankta


title: Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis.


title: Gene expression profiles in rat alveolar macrophages exposure to cellulose nanofibrils, microcrystalline cellulose, and lipopolysaccharide.

status: Public on Mar 31 2024

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

institute: National Institute of Advanced Industrial Science and Technology

summary: To assess the biological impact of cellulose nanofibrils (CNFs) at the transcriptional level, we conducted whole-genome microarray analyses on rat alveolar macrophages (NR8383) exposed to CNFs with varying physicochemical properties. The findings were compared with those from exposure to microcrystalline cellulose (MCC) and lipopolysaccharide (LPS).

overall_design: Rat alveolar macrophages (NR8383) were exposed to six types of cellulose nanofibrils (CNFs: CNF1, CNF2, CNF3, CNF4, CNF5, and CNF6) at a concentration of 100 µg/mL, as well as MCC and LPS at concentrations of 100 µg/mL and 10 ng/mL, respectively, for 24 hours. The experiments included a vehicle control group (n=4). Cyanine-3-labeled cRNA, generated from NR8383 exposed to CNFs, MCC, and LPS was hybridized to a Whole Rat Genome Microarray. Subsequently, the scanned images of the hybridized microarray slides were subjected to numerical analysis to assess the transcriptional-level biological effects of CNFs on NR8383, compared with those from exposure to MCC and LPS.

first: Sawae

last: Obara


title: Unlocking the power of transcriptomic biomarkers in qualitative and quantitative genotoxicity assessment of chemicals II

status: Public on Mar 27 2024

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

summary: There is a need to move from binary hazard assessment to more quantitative assessment of genotoxicity to better inform human health risk assessment and understand the relevance of positive in vitro genotoxicity findings. New approach methodologies (NAMs), including transcriptomic biomarkers combined with high-throughput technologies, enable the testing of a broad concentration range, which allows quantitative assessment of in vitro results. Initial work with the transcriptomic GENOMARK and TGx-DDI biomarkers demonstrate their potential use for hazard identification and chemical prioritization; however, no study has evaluated the concordance and complementarity of GENOMARK and TGx-DDI. The overall aim of this study is to examine if a combined approach of integrating both transcriptomic biomarkers for genotoxicity in human relevant HepaRGTM cells increases the certainty in hazard calls and potency rankings of chemicals. A sub-aim is to investigate whether GENOMARK is applicable to the TempO-Seq® high-throughput sequencing technology, to collect concentration-response data to rapidly perform hazard classification and potency ranking.  Therefore, HepaRGTM cells were exposed to 10 chemicals (i.e. eight known in vivo genotoxicants and two in vivo non-genotoxicants) in increasing concentrations over 72h. TempO-Seq® was used to obtain concentration-response data for both biomarkers. Benchmark concentration (BMC) modelling of chemicals that were classified positive was conducted to obtain BMCs and transcriptomic points of departure (tPODs) for potency ranking. The results confirm that GENOMARK is applicable to TempO-Seq® since it achieved 100% predictive accuracy. In addition, a high concordance was observed in the hazard classifications and potency rankings between both biomarkers. Overall, our findings show that in vitro transcriptomic data can be used to rapidly and effectively identify genotoxic hazards while simultaneously providing additional insights on potency that is more informative in a modern hazard assessment paradigm. The results of this case study support the high value of integrating these NAMs in a weight of evidence evaluation of genotoxicity using the important human-liver cell line.

overall_design: A total of 71 samples were sequenced using a whole human transcriptome panel for this toxicogenomics study on a qualitative and quantitative genotoxicity assessment of chemicals, including technical controls (reference RNA; and cells with no treatment). The solvent controls were comprised of 0.5% DMSO in medium. 5 concentrations of each chemical were tested in triplicate, meaning in three different batches of HepaRGTM cells.

first: Anouck

last: Thienpont

first: Eunnara

last: Cho

first: Andrew

last: Williams

last: J Meier

first: Carole

last: L Yauk

first: Vera

last: Rogiers

first: Tamara

last: Vanhaecke

first: Birgit

last: Mertens


title: A time-resolved single-cell roadmap of the logic driving anterior neural crest diversification from neural border to migration stages

status: Public on Mar 29 2024

city: Paris

first: Anne-Hélène

last: Monsoro-Burq

state: Ile-de-France

address: 26 rue d'Ulm

country: France

institute: Curie Institute

sample_organism:
Xenopus laevis
Xenopus tropicalis

platform_organism:
Xenopus laevis
Xenopus tropicalis


title: Signal-independent activation reveals two-component regulatory networks.

status: Public on Mar 25 2024

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary: Each bacterial species has specific regulatory systems to control physiology, adaptation, and host interactions. One challenge posed by this diversity is to define the evolving gene regulatory networks. This study aims to characterise two-component systems (TCS) in Streptococcus gagalactiae, the main cause of neonatal meningitis. Here we demonstrate signal-independent activation of signalling pathways by systematically targeting the conserved mechanism of phosphatase activity of the  histidine kinases of the two main TCS families. Transcriptomic analysis resolves most pathways with high resolution, encompassing specialized, connected, and global regulatory systems. The activated network notably reveals the connection between CovRS and SaeRS signaling through the adhesin PbsP, linking the main regulators of host  interactions to balance pathogenicity. Additionally, constitutive activation of the BceRS system reveals its role in cell envelope homeostasis beyond antimicrobial resistance. Overall, this study demonstrates the generalizability and versatility of TCS genetic activation to uncover regulatory logics and biological processes.

overall_design:
To investigate the activation of  regulatory networks by phosphatase-deficient histidine kinases, we generated 14 strains (called the HK+ mutants), with an alanine substitution of the predicted phosphatase catalytic residue or at the corresponding position.
We then performed differential gene expression analysis by RNA-seq between the wild-type parental strain (BM110) and the 14 HK+ mutants.
RNA are purified from exponentialy growing cultures (OD600 = 0.5) in rich media (THY) incubated at 37°C in static condition. Biological triplicate (Replicate 1, 2, and 3) are done on different days. Two wild-type controls (BM110_A and BM110_B) are included.

first: Cosme

last: CLAVERIE

first: Francesco

last: COPPOLINO

first: Maria-Vittoria

last: MAZZUOLI

first: Elise

last: JACQUEMET

last: LEGENDRE

first: Odile

last: SISMEIRO

first: Arnaud

last: FIRON


title: Effects of Antifibrotic Drugs on Transcriptome of Peripheral Blood Mononuclear Cells in Idiopathic Pulmonary Fibrosis [IPF_PBMC]

status: Public on Mar 28 2024

city: Chiba

first: Takeshi

last: Kawasaki

address: 1-8-1, Inohana, Chuoku

department: Respirology

institute: Chiba University

summary: Two antifibrotic drugs, pirfenidone (PFD) and nintedanib (NTD), are currently used to treat idiopathic pulmonary fibrosis (IPF). Peripheral blood mononuclear cells are immunocompetent cells that can predispose to those within the lungs and orchestrate cell-cell interactions associated with IPF pathogenesis. We employed RNA sequencing to examine the transcriptome signature in bulk peripheral blood mononuclear cells of patients with IPF and the effects of antifibrotic drugs on these signatures. Differentially expressed genes (DEGs) were analyzed in patients with IPF and healthy controls, before and after antifibrotic treatment. Enrichment analysis suggested that fatty acid elongation interferes with profibrotic TGF-β/ signaling and production of oxidative stress since treatment with NTD upregulated the elongation enzymes ELOVL6 and ELOVL7. Treatment with PFD downregulated COL1A1 which produces wound-healing collagens, as activated monocyte-derived macrophages during tissue damage participate in the production of collagen, type I, and alpha 1. Plasminogen activator inhibitor-1 (PAI-1) regulates wound healing by inhibiting plasmin-mediated matrix metalloproteinases activation, and inhibition of PAI-1 activity attenuates lung fibrosis. DEGs analysis suggested that both PFD and NTD upregulated SERPINE1 which in turn regulates PAI-1 activity. This study detected different DEGs as a result of PFD and NTD treatments, suggesting different mechanistic roles for the two antifibrotic drugs.

overall_design:
To investigate the pathogenesis of IPF in PBMCs, we compared IPF (n=6) and healthy control (n=6) samples by RNA-seq.
Then, to investigate the effects of antifibrotic drugs in PBMCs, we compared samples before and after administration of PFD (n=3) and NTD (n=3), respectively, by RNA-seq.

first: Daisuke

last: Ishii

first: Hironori

last: Sato

first: Koichiro

last: Tatsumi

first: Takuro

last: Imamoto

first: Keiichiro

last: Yoshioka

first: Mitsuhiro

last: Abe

first: Yoshinori

last: Hasegawa

first: Osamu

last: Ohara

first: Takuji

last: Suzuki


title: TET activity propagates transcriptional memory through embryonic dormancy [CUT&TAG]

status: Public on Mar 19 2024

city: Berlin

first: Maximilian

last: Stötzel

state: Berlin

address: Ihnestraße 65

department: Meissner

institute: Max-Planck-Institute for molecular genetics

summary: Dormancy is an essential biological process for the propagation of many life forms through generations and stressful conditions. Early embryos of many mammals are preservable for weeks to months within the uterus under dormancy, which can be induced in vitro through mTOR inhibition. Dormancy features silencing of the genome and abundant heterochromatin formation, which conflicts with the permissive and uncommitted genomic profile of pluripotent cells. Cellular strategies to maintain pluripotency in the fate of this conflict are not known. Here we probed chromatin regulation during embryonic stem cells’ (ESC) entry into dormancy to identify mechanisms that ensure nsure faithful propagation of cellular identity through dormancy. We show a global increase in DNA methylation and loss of chromatin accessibility in dormant ESCs and find that TET DNA demethylases are essential to counteract this trend at key pluripotency regulatory elements. Perturbation of TET activity compromises transcriptional programs and embryo survival through dormancy; whereas its enhancement improves survival rates. We propose that key regulatory elements are bookmarked coordinately by TETs and transcription factors in dormancy for maintenance of cellular identity. Our results reveal the first essential chromatin regulator in establishing mammalian dormancy and paves the way to building its temporal regulatory code in embryonic and adult tissues.

overall_design: Either wild-type or TET1/2 double-knock out embryonic stem were cultured with or without mTOR inhibition using Ink128

first: Aydan

last: Bulut-Karslioglu


title: Unlocking the power of transcriptomic biomarkers in qualitative and quantitative genotoxicity assessment of chemicals I

first: Matthew

last: Meier

overall_design: A total of 90 samples were sequenced using a whole human transcriptome panel for this toxicogenomics study on a qualitative and quantitative genotoxicity assessment of chemicals, including technical controls (reference RNA; and cells with no treatment). The solvent controls were comprised of 0.5% DMSO in medium. 4 concentrations of each chemical were tested in triplicate, meaning in three different batches of HepaRGTM cells.

first: Anouck

last: Thienpont

first: Eunnara

last: Cho

first: Andrew

last: Williams

last: J Meier

first: Carole

last: L Yauk

first: Vera

last: Rogiers

first: Tamara

last: Vanhaecke

first: Birgit

last: Mertens


title: TET activity propagates transcriptional memory through embryonic dormancy [WGBS]

type: Methylation profiling by high throughput sequencing

summary: Dormancy is an essential biological process for the propagation of many life forms through generations and stressful conditions. Early embryos of many mammals are preservable for weeks to months within the uterus under dormancy, which can be induced in vitro through mTOR inhibition. Dormancy features silencing of the genome and abundant heterochromatin formation, which conflicts with the permissive and uncommitted genomic profile of pluripotent cells. Cellular strategies to maintain pluripotency in the fate of this conflict are not known.  Here we probed chromatin regulation during embryonic stem cells’ (ESC) entry into dormancy to identify mechanisms that ensure nsure faithful propagation of cellular identity through dormancy. We show a global increase in DNA methylation and loss of chromatin accessibility in dormant ESCs and find that TET DNA demethylases are essential to counteract this trend at key pluripotency regulatory elements. Perturbation of TET activity compromises transcriptional programs and embryo survival through dormancy; whereas its enhancement improves survival rates. We propose that key regulatory elements are bookmarked coordinately by TETs and transcription factors in dormancy for maintenance of cellular identity. Our results reveal the first essential chromatin regulator in establishing mammalian dormancy and paves the way to building its temporal regulatory code in embryonic and adult tissues.


title: TET activity propagates transcriptional memory through embryonic dormancy [FLASH - RNA-Seq]


title: TET activity propagates transcriptional memory through embryonic dormancy [ATAC-Seq]


title: Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis -  whole tissue scRNA-Seq

first: Alison

last: Simmons

overall_design: Cells from tissue (colon) and peripheral blood (PBMC), in patients with active ulcerative colitis (UC_I), paired non-inflamed areas at the same endoscopy (UC_NI), active immune checkpoint inhibitor-induced colitis (CC_I), patients given checkpoint inhibitors without colitis (CC_NI) all compared with healthy controls (HC). Patients with CC_I and CC_NI were either treated with anti-PD-1 immunotherapy (Monotherapy) or a combination of simultaneous anti-PD-1 and anti-CTLA4 immunotherapy (Dual therapy). Cell pools were either comprised of peripheral blood cells (PBMC) or enriched for Epithelium (Epi) or the remaining Stromal/Immune fraction (Stromal) - see methods for full details. Samples were subjected to 5' scRNA sequencing, yielding Gene expression (GEX), CITE-seq (ADT), T-cell receptor (TCR) and B-cell receptor (BCR) information.

first: Agne

last: Antanaviciute

first: Tarun

last: Gupta

first: Anna

last: Aulicino

first: Rosana

last: Babu

first: Chloe

last: Lee

first: Hashem

last: Koohy


title: CKD Rats

status: Public on Mar 14 2024

first: Jiawei

last: Song

address: 1 Xiannongtan Street

department: Institute of Materia Medica

institute: Peking Union Medical College

summary: Comparative gene expression profiling analysis of RNA-seq data for NC rats, adenine-induced CKD rats, and drug-treated CKD rats.

first: Jia

first: Jun

last: Ye

first: Yan

last: Tang

first: Xinhua

last: Xiao

first: Yuling

last: Liu


title: TET activity propagates transcriptional memory through embryonic dormancy [CUT&Tag]

first: Maximilian

last: Stötzel

first: Aydan

last: Bulut-Karslioglu


title: On the way to elucidate the effects of cannabidiol (CBD) on living organisms - assessment of changes in the global transcription profile of liver in mouse model

status: Public on Mar 16 2024

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

country: Poland

institute: University of Agriculture in Krakow

summary: Cannabidiol (CBD) is a phytocannabinoid that has anti-inflammatory, immunomodulatory, antioxidant, anxiolytic, antipsychotic, and anticonvulsant effects. The metabolism of CBD occurs in the liver within a few hours after the dose is administered. This study aims to examine the effects of CBD on behavior, immune system activity, and stress levels, and to determine its impact on transcriptomic alterations in selected murine organs.

overall_design:
Male mice of the standard C57BL/6J strain were used. The animals were classified into two groups - (I) short-term CBD administration (2 days) and (II) long-term CBD administration (28 days). In each of the main groups, there were three subgroups receiving different doses of CBD - from low, commonly used in supplementation (0.2 mg/kg bw), through medium (10 mg/kg bw), to high, used in some clinical trials (20 mg/kg bw). Additionally, a control group (placebo/vehicle) was maintained in each of the main groups. Chemically pure Cannabidiol (CBD) was administered intraperitoneally (in the research group) to ensure that the substances reached the blood vessels of the digestive system. CBD was administered in a single daily dose. The mice were housed under standard conditions and with standard feeding and watering ad libitum. They were also tested daily (group I) or every third day (group II) to determine well-being and health. After the period of CBD administration, the mice were immediately euthanized and organs such as the brain, spleen and liver were collected. In this part of the experiment, liver samples were used to isolate total RNA. The recovered RNA was quality assessed and used to prepare directional libraries for high throughput transcriptome sequencing using CORALL mRNA-Seq V2 kit (Lexogen).  The libraries were sequenced commercially in a 2x150bp paired-end run. The obtained sequence data were used to analyze the differential expression between the different CBD dosages and the control group. Differentially expressed genes were classified into particular processes or functions and were subjected to statistical testing for overrepresentation. The synthesis of the obtained data will allow to propose potential mechanisms of CBD action and create an atlas of changes taking place in the transcriptome of the main target organs.

UPDATE: [11-04-2024] The Sample titles and treatments were corrected. The raw data and processed data associated with each GSMxxx accession number have not changed.

first: Jakub

last: Żurowski

first: Sebastian

last: Sawicki

first: Ewa

last: Ocłoń

first: Tomasz

last: Szmatoła

first: Igor

last: Jasielczuk

first: Karolina

last: Mizera-Szpilka


title: Single-cell RNA Sequencing of Murine Lungs to Compare Two Different Models of Alveolar Simplification

city: San Francisco

first: Vincent

last: Auyeung

state: CA

department: Medicine

institute: University of California, San Francisco

summary: Neonatal hyperoxia exposure causes alveolar simplification in mice and has been employed as a model to study bronchopulomonary dysplasia, or chronic lung disease of prematurity. Loss of epithelial TGF-beta signaling has also been shown to cause alveolar simplification in mouse models of lung development. We used single cell RNA sequencing (scRNA-seq) to analyze both of these models of lung injury to identify shared molecular and cellular mechanisms that contribute to pathogenic alveolar simplification.

overall_design: Neonatal mice on the C57BL/6 background were exposed to either hyperoxia (75% oxygen) or normoxia for 10 days begnning on day 0 and were recovered in normoxia until harvest at day 14. Tgfbr2 flox/flox (WT) mice were compared to Nkx2.1-cre;Tgfbr2 flox/flox (KO) littermates in either normoxic (RA) or hyperoxic (O2) conditions. Two mice of each genotype and of each exposure were harvested on day 7 and day 14 and lung tissues were digested to generate a single cell suspension and analyzed using scRNAseq.

first: Khan

last: Imran

first: Sheppard

last: Dean


title: Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis - CD3 scRNA-Seq

first: Alison

last: Simmons

overall_design: Flow-cytometry (FACS) sorted CD3 CD45 double positive T cells from paired tissue and blood, in patients with active ulcerative colitis (UC_I) or active immune checkpoint inhibitor-induced colitis (CC_I), compared with healthy controls (HC). Patients with CC_I were either treated with anti-PD-1 immunotherapy (Monotherapy) or a combination of simultaneous anti-PD-1 and anti-CTLA4 immunotherapy (Dual therapy).

first: Agne

last: Antanaviciute

first: Tarun

last: Gupta

first: Anna

last: Aulicino

first: Rosana

last: Babu

first: Chloe

last: Lee

first: Hashem

last: Koohy


title: A critical role for Hepatocyte Nuclear Factor 4 alpha in polymicrobial sepsis-associated metabolic reprogramming and death: effect of CLP/SHAM in Hnf4a WT and KO mice

status: Public on Mar 12 2024

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: In sepsis, limited food intake and increased energy expenditure induce a starvation response, which is compromised by a quick decline in expression of hepatic PPARα, a transcription factor essential in intracellular catabolism of free fatty acids. The mechanism upstream of this PPARα downregulation is unknown. We found that sepsis causes a progressive hepatic loss-of-function of HNF4α, which has strong impact on the expression of several important nuclear receptors, including PPARα. HNF4α depletion in hepatocytes dramatically increases sepsis lethality, steatosis and organ damage and prevents an adequate response towards IL6, which is critical for liver regeneration and survival. An HNF4α agonist protects against sepsis at all possible levels, irrespectively of bacterial loads, suggesting HNF4α is crucial in disease tolerance to sepsis. In conclusion, hepatic HNF4α fails in sepsis, causing PPARα downregulation and metabolic problems and a disturbed IL6-mediated acute phase response. The data open new insights and therapeutic options in sepsis.

overall_design: RNA-seq in WT mice and Hnf4a KO (inducible: induced by tamoxifen) mice sebjected to SHAM or CLP surgery, livers were isolated for transcripome profiling, using 4 biological replicates

first: Céline

last: Van Dender

first: Ville

last: Paakinaho

first: Tineke

last: Vanderhaeghen

first: Jolien

last: Vandewalle

first: Maarten

last: Claes

first: Bart

last: Roman

first: Jan

last: De Waele

first: Siska

last: Croubels

first: Karolien

last: De Bosscher

first: Jorma

last: Palvimo

first: Claude

last: Libert


title: A critical role for Hepatocyte Nuclear Factor 4 alpha in polymicrobial sepsis-associated metabolic reprogramming and death: H3K27ac and H3K4me3 after CLP sepsis model

summary: Sepsis is a maladaptive host response towards an infection leading to tissue damage, organ failure, and ultimately death. In sepsis, limited food intake and increased energy expenditure induce a starvation response, which is hindered by hepatic disappearance of the key transcription factor PPARα. Since PPARα acts as a central player in intracellular catabolism of fatty acids (FAs), sepsis results in excess free FAs, which cause lipotoxicity. The mechanism upstream of the PPARα downregulation in sepsis is unknown. A potential mechanism resides in HNF4α, which regulates liver lipid metabolism directly by activating Ppara gene expression and indirectly by interacting with PPARα itself. A proper functioning of HNF4α is essential for maintaining liver identity. We here show that sepsis causes a progressive HNF4α loss-of-function in the liver, which impacts expression of several nuclear receptors, among which PPARα, and is characterized by a reduced HNF4α DNA binding. Specific HNF4α depletion in the liver dramatically worsens sepsis lethality, associated with increased steatosis and hepatocyte damage. HNF4α dysfunction also prevents an adequate response towards IL6, controlled by CEBPβ and STAT3, which is critical for a proper liver regeneration and survival. In addition, the HNF4α agonist NCT partially protects against sepsis by limiting hepatic steatosis and liver dysfunction. In conclusion, hepatic HNF4α fails in sepsis, causing PPARα downregulation and consequent metabolic problems on the one hand, and a disturbed IL6-mediated acute phase response and regeneration on the other hand. The data open new insights and therapeutic options in sepsis

overall_design: Chip-seq for histone modifications H3K27ac and H3K4me3 after in Sham and CLP conditions using 4biological replicates per group.


title: A-T to G-C base editing efficiency at targeted gene sites in HEK293T cell line

status: Public on Mar 11 2024

city: Guangzhou

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

institute: Southern Medical University

summary: A-T to G-C base editing efficiency at targeted gene sites in HEK293T cells using the dCas12f-ABE design or the Cas12f-ABE design. Found that the total A-T to G-C conversion efficiency of Circular gRNAs exhibited about two-fold increase compared with U6 gRNAs. We further analyzed the pattern for A-T to G-C conversion on the target site, and observed that the most efficient base editing occurred in a narrow window A3 (3bp downstream of the PAM) similar to U6 gRNAs. In summary, Circular gRNAs with dCas12f-ABE design could enhance A-T to G-C base editing efficiency in a narrow window.

overall_design: To test whether Cas12f/cgRNA system could improve the efficiency of cas12f mediated base editing, we transiently transfected different plasmids encoding gRNAs and dCas12f-ABE or the Cas12f-ABE. We constructed the library with two rounds of PCR using indexed and universal primers to amplify on-target sites. The library was performed Deep-sequencing, and then our sequenced reads were trimmed and aligned to the reference.

first: Xin

last: zhang

first: Ying

last: Lin

first: Zhili

last: Rong


title: Transcriptional regulation by the Velvet complex during sexual development in Neurospora crassa

status: Public on Mar 01 2024

city: Sevilla

first: Gabriel

last: Gutierrez

address: PO BOX 1095

department: Genetics

institute: University of Seville

summary: Comparative transcriptomic analysis of genes regulated during sexual development in dark and light in the wild type and the ∆ve-1 mutant.

overall_design: In this study we perfom a RNAseq analysis to examine the regulatory role of VE-1 in gene expression in different times before and after fertilization in dark and light conditions

first: Sara

last: Cea-Sánchez

last: Martín-Villanueva

last: Gutiérrez

first: David

last: Cánovas

first: Luis

last: Corrochano


title: TET activity propagates transcriptional memory through embryonic dormancy [RNA-seq]

first: Maximilian

last: Stötzel

first: Aydan

last: Bulut-Karslioglu


title: Nuclear Receptor Corepressors Non-Canonically Drive Glucocorticoid Receptor-Dependent Activation of Hepatic Gluconeogenesis [ATAC-Seq]

status: Public on Feb 22 2024

city: Philadelphia

first: Mitchell

last: Lazar

address: 3400 Civic Center Blvd

department: Perelman School of Medicine

institute: University of Pennsylvania

summary: Nuclear receptor corepressors (NCORs) function in multiprotein complexes containing histone deacetylase 3 (HDAC3). In the liver, loss of HDAC3 causes a marked hepatosteatosis largely due to derepression of genes involved in lipid metabolism. Here we show that adult loss of both NCOR1 and 2 (dKO) in hepatocytes phenocopies the hepatomegalic fatty liver phenotype. In addition, dKO livers exhibited a dramatic reduction in glycogen storage and gluconeogenic gene expression that was not observed with hepatic KO of individual NCORs nor HDAC3, resulting in profound fasting hypoglycemia. This surprising HDAC3-independent activation function of NCOR1/2 was due to an unexpected loss of chromatin accessibility upon deletion of NCORs that prevented glucocorticoid receptor binding and stimulatory effect on gluconeogenic genes. These studies reveal an unanticipated, non-canonical activation function of NCORs that is required for metabolic health.

overall_design: Analysis of chromatin accessibility in HNF4a+ hepatocytes isolated from control and NCOR1/2 dKO livers.

first: Amy

middle: K

last: Hauck

first: Rashid

last: Mehmood


title: Nuclear Receptor Corepressors Non-Canonically Drive Glucocorticoid Receptor-Dependent Activation of Hepatic Gluconeogenesis

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

overall_design: Refer to individual Series


title: Nuclear Receptor Corepressors Non-Canonically Drive Glucocorticoid Receptor-Dependent Activation of Hepatic Gluconeogenesis [ChIP-Seq]

overall_design: Analysis of GR and NCOR1 binding in the liver. Control and NCOR1/2 dKO mice were IP injected with saline or 1 mg/kg Dexamethasone and then euthanized 2 hours later.