title: LncRNA GAS5 Regulates human Myometrial cells Contractions  In a m6A-Dependent Manner

first: Sun

last: Yue

address: jiangdong

summary: These findings highlighted the critical role of m6A modification in GAS5, providing a new method to explore RNA epigenetic regulatory patterns in human paturition.

overall_design: Comparative lncRNA expression analysis using data obtained from RNA-seq of 10 different tissues.

first: Yue

last: Sun

first: Shiyun

last: Huang

first: Ziyan

last: Jiang

first: Lizhou


title: RNA-seq analysis in roots of PuHox52 overexpression and wild type Populus ussuriensis under normal nitrogen and low nitrogen condition.

status: Public on Apr 02 2025

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

country: China

institute: Northeast Forestry University

type: Expression profiling by high throughput sequencing

summary: To gain insight into the molecular mechanism of PuHox52-mediated low-N adaption, we performed a transcriptome sequencing analysis (RNA-seq) using the PuHox52-OE lines and WT P. ussuriensis in roots under low-N for 3 wks, as well as roots under normal-N as controls.

overall_design: Selected top one internodes of in vitro propagated WT and PuHox52-OE plants, which were grown on WPM for 6 d to develop consistently, and then transferred to normal N or low-N medium for 3 wks. Roots were collected from three biological replicates respectively before total RNA extraction using the method of CTAB. Library construction and sequencing were performed by Biomarker Technologies (Beijing, China) and Bioacme Technologies (Wuhan, China).

first: Ming

last: Wei


title: RBPL-1, the C. elegans homolog of RBBP6, promotes meiotic homolog pairing through a conserved DWNN domain

status: Public on Apr 01 2025

city: Tsingtao

first: li

middle: pan

last: feng

state: shandong

address: Ao Shan Wei Street

department: College of Life Sciences

institute: shandong university

summary: Accurate chromosome segregation during meiosis depends on precise homolog pairing, a process driven by a series of specialized proteins that link chromosomes to cytoskeletal motors and coordinate chromosome movement for homolog recognition and alignment. Here, we demonstrate that RBPL-1, the C. elegans homolog of RBBP6, is necessary for normal meiotic progression, particularly for proper homolog pairing and associated nuclear reorganization. RBPL-1 is enriched on the autosomes in early and mid- pachytene nuclei. Depletion of RBPL-1 led to reduced levels of ZIM/HIM-8 family proteins and PLK-2 kinase, two critical mediators of homolog pairing. Notably, RBPL-1's role in homolog pairing is independent of the RING finger domain, which mediates ubiquitination, and its Zn knuckle domain, which is implicated in APA/mRNA processing. Instead, we reveal that the evolutionarily conserved yet functionally enigmatic DWNN domain is essential for RBPL-1's function. Our findings uncover a previously unrecognized regulatory mechanism governing homolog pairing during meiosis.

overall_design: To investigate whether RBPL-1 regulates homolog pairing at the transcriptional level or through APA, we conducted RNA seq and APA analysis on wild-type and auxin-induced degradation worms.

first: Ang


title: DUSP6 ablation restores CAR T fitness impaired by tumor CD58 loss through invigoration of AP-1 signaling

city: Beijing

first: Xinran

last: Ma

address: 28 Fuxing Road

institute: Chinese general PLA hospital

summary: Primary resistance to chimeric antigen receptor (CAR) T-cell therapies limited its widespread applications. Our prior genome-wide CRISPR/Cas9 screening revealed loss of CD58 as a crucial tumor intrinsic resistance factor by conferring insufficient immune synapse formation, impairing CAR-T activation and cytotoxicity. However, the specific signaling pathway and transcriptional changes that conveyed CAR T-cell dysfunction haven’t been addressed. Here we recognized an AP-1 dominated activation attenuation in CAR T cells impaired by tumor CD58 loss, driving synchronous mitochondrial biogenesis decrease, metabolic kinetics impairment, mitochondrial membrane potential loss and ROS accumulation. Moreover, this AP-1 attenuation triggered a death-receptor independent apoptosis through the intrinsic mitochondrial pathway. In seeking therapeutic strategies, we pharmacologically and genetically blocked three distinct inhibitory phosphatases positioned upstream of AP-1 signaling. Multi-faceted validation demonstrated dual specificity phosphatase 6 (DUSP6) blockade as an effective approach to supplement AP-1 signaling, notably decreased CAR T apoptosis, enhanced mitochondrial fitness, proliferation and long-term cytotoxicity. Transcriptomic profiles of DUSP6 ablated CAR T cells showed notably upregulated T-cell activation signatures and enriched metabolic pathways. Clinically, bulk and single-cell RNA-seq analysis revealed downregulated DUSP6 in patients responding to T cell-based immunotherapy, implying its relevance to outcome. Our findings repositioned CD58 not merely as an immune synapse component but as a metabolic checkpoint in CAR T biology, whose loss would trigger an AP-1-dependent mitochondrial derangement and created a permissive landscape for intrinsic apoptosis, ameliorable by ablation of inhibitory phosphatase DUSP6. Crucially, DUSP6 ablation presented a promising engineering target to potentiate CAR T-cell efficacy in broader applications.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Ctrl or DUSP6KO CAR T cells co-cultured with WT or CD58KO Nalm6 cells

first: Zhiqiang

last: Wu

first: Weidong

last: Han


title: Differential Expression and Correlation Analysis of Global Transcriptome for Obstructive Sleep Apnea Hypopnea Syndrome

city: Dali

first: Guangming

last: Wang

state: Yunnan Province

address: Center of Genetic Testing, The First Affiliated Hospital of Dali University

department: Center of Genetic Testing

summary: In order to investigate the gene expression patterns and molecular regulatory mechanisms of obstructive sleep apnea hypopnea syndrome (OSAHS), the global transcriptome expression profiles of OSAHS patients and healthy people were analyzed using transcriptome sequencing technology. Differential expression of circular RNA, microRNA, long noncoding RNA, and messenger RNA was investigated between the two groups.

overall_design: RNA sequencing was performed on OSAHS patients and healthy individuals (n=5 per group) to identify differentially expressed genes and related pathways.

first: Ziyi

last: Chen

first: Guihua

first: Lichen

last: Song

first: Yuanyuan

last: Zhang


title: Identification of Crohn’s disease subtypes in single cell RNA sequencing signatures of treatment naïve samples across the gastrointestinal tract

city: Atlanta

first: Greg

last: Gibson

state: GA

address: North Ave NW

country: USA

institute: Georgia Institute of Technology

summary: Crohn’s disease (CD) is characterized by chronic inflammation throughout the intestines. Previous single cell transcriptomic studies investigated the effect of CD post therapeutic intervention, however, the extent to which therapy modifies the intestinal inflammatory environment remains to be elucidated. To this end, a treatment naïve pediatric CD cohort was recruited to investigate initial disease onset across the intestines, highlighting shared and tissue-specific consequences of disease. Ileum, colon, and rectum biopsies were obtained, and single cell RNA-sequencing was performed. A clustering stability assessment workflow was developed to ensure clustering and downstream results were robust. Tensor decomposition was utilized to identify clinically meaningful groups within the intestines. Other bioinformatic tools were utilized to investigate differences across group status within each tissue. Expected cell types were identified after the clustering stability assessment was performed. Inflammation did not strongly influence cellular proportion profiles due to heterogeneity across donor and tissue. Tensor decomposition revealed distinct mesenchymal and cytotoxic T cell-mediated sources of disease pathology, corresponding to previously identified fibrotic and pro-inflammatory disease progression. Integrating transcriptomics and genome wide association summary statistics for CD suggested myeloid cells and T cells drive disease, highlighting potential cellular therapeutic targets. Tensor decomposition stratified donors into clinically meaningful groups based on their transcriptomic profile, suggesting these signatures can be utilized for personalized medicine.

overall_design: single cell RNA seq of intestinal biopsies from treatment naïve Crohn's disease individuals

first: Savannah

last: Washburn

first: Yeonjoo

last: Hwang

first: Sushma

last: Chowdary Maddipatla

first: Shanta

last: Murthy

first: Vasantha L.

last: Kolachala

first: Subra

last: Kugathasan

first: Peng

last: Qiu


title: Efficacy of IDOR-1117-2520, a novel, orally available CCR6 antagonist in a preclinical model of skin dermatitis

city: Allschwil

first: Pijus

last: Brazauskas

address: Hegenheimermattweg 91

country: Switzerland

institute: Idorsia Pharmaceuticals

summary: Background and Purpose:   The chemokine receptor CCR6 is important in guiding pathogenic T17 cells that are implicated in numerous autoimmune diseases including psoriasis to sites of inflammation via the chemokine CCL20. On this basis, pharmacological interventions that inhibit CCR6+ immune cell migration provide a novel therapeutic approach for such diseases. However, the translatability from pre-clinical models to human diseases of such an intervention has so far not been assessed in detail. Here, we evaluate the translatability of a preclinical model of Aldara induced skin inflammation to psoriasis with a particular focus on immune cell trafficking and assess the efficacy of the novel, orally available CCR6 antagonist IDOR-1117-2520 in this model.      Experimental Approach:   Here, we evaluated the in vivo therapeutic effects of IDOR-1117-2520, a novel, highly selective, potent, and orally available CCR6 small molecule inhibitor, in the Aldara mouse model of skin inflammation. To understand in detail CCR6 inhibition on the inflammatory response, flow cytometry, RNA sequencing, and transcriptome-based cell type deconvolution approaches were used to characterize immune cell migration patterns and to compare the results to publicly available human psoriasis transcriptomics data.      Key Results:   IDOR-1117-2520 dose dependently reduced infiltration of CCR6 + immune cells into inflamed skin and was equally efficacious as IL-17 and IL-23 inhibition in reducing inflammation in the skin. Pathway analysis highlighted the strong molecular similarities in immune response between human psoriasis and the Aldara mouse model. Genes associated with the IL-17/IL-23 pathway were prominently expressed in both human psoriasis and in the mouse model. CCR6 inhibition modulated multiple pathways associated with inflammation beyond the proximal IL-17/IL-23 pathway. A chemokine-chemokine receptor interaction map implicated the CCL20-CCR6 as the dominant axis in recruiting pathogenic T17 cells in this model system, as well as in human psoriasis.    Conclusion and Implications:   These results suggest that IDOR-1117-2520 could provide a promising novel targeted therapeutic approach to treating psoriasis and, potentially, other autoimmune diseases with an involvement of CCR6/CCL20 axis and the IL-17/IL-23 pathway. The data provide rationale for the further development of IDOR-1117-2520, which is currently being evaluated in a clinical phase 1 trial (ISRCTN28892128).

overall_design: We evaluated the in vivo therapeutic effects of IDOR-1117-2520, a novel, highly selective, potent, and orally available CCR6 small molecule inhibitor, in the Aldara mouse model of skin inflammation. RNAseq was used to understand in detail CCR6 inhibition on the inflammatory response. RNAseq was performed on the Aldara model ear punch on samples treated with IDOR-1117-2520 at selected timepoints.

first: Peter

last: Blanttmann

first: Bérengère

last: Renault

first: Mark

last: Murphy


title: LncRNA LUCAT1 and exosomal MIF induced by Helicobacter pylori promotes M2 macrophage polarization in gastric cancer

city: Seoul

first: Seo Yeon

last: Kim

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

country: South Korea

institute: Yonsei universtiy

summary: H. pylori infection induces upregulation of the long non-coding RNA LUCAT1 in gastric cancer cells, which facilitates the exosomal transfer of MIF (macrophage migration inhibitory factor) to the tumor microenvironment. This process shifts macrophages from the M0 to M2 phenotype, contributing to an aggressive gastric cancer progression by enhancing cell proliferation, migration, and invasion. The research suggests potential preventive and therapeutic strategies for gastric cancer by targeting LUCAT1 and MIF, highlighting the critical role of lncRNA-mediated mechanisms in H. pylori driven-cancer development.

overall_design:
RNA sequencing was performed on GC and normal cells exposed to H. pylori. LncRNA expression changes were analyzed, and key candidates were validated through functional assays.

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first: Sang Kil

last: Lee

first: Da Hyun

last: Jung

first: Jung-Ho

last: Yoon

first: Ga Hee

first: Chul Hoon


title: Hypoxia-inducible factor 2α promotes protective Th2 cell responses during intestinal helminth infection

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Th2 cells must sense and adapt to the tissue milieu in order to provide protective host immunity and tissue repair. Here, we examined the mechanisms promoting Th2 cell differentiation and function within the small intestinal lamina propria. Single cell RNA-seq analyses of CD4+ T cells from the small intestinal lamina propria of helminth infected mice revealed high expression of the gene Epas1, encoding the transcription factor hypoxia-inducible factor 2a (HIF2α). In vitro, exposure to hypoxia or genetic HIF2α activation promoted Th2 cell differentiation, even under non-polarizing conditions. In mice, HIF2α activation in CD4+ T cells promoted intestinal Th2 cell accumulation in the absence of infection, and HIF2α-deficiency impaired CD4+ T cell-mediated host immunity to intestinal helminth infection. Our findings identified hypoxia, and the oxygen-regulated transcription factor Hypoxia-Inducible Factor 2α (HIF2α), as key regulators of Th2 cell differentiation and function within the small intestine.

overall_design: This submission contains 10x Gene Expression data from single CD4+ T cells sorted from the small intestine lamina propria of mice infected with the intestinal nematode parasite Heligmosomoides polygyrus or control uninfected mice. Samples were collected at 30 days post infection. Cells from multiple mice were pooled for each condition, and approximately 10,000 cells were captured from each pool.

first: Jasmine C.

last: Labuda

first: Tayla M.

last: Olsen

first: Sheenam

last: Verma

first: Samantha

last: Kimmel

first: Thomas H.

last: Edwards

first: Matthew J.

last: Dufort

first: Oliver J.

last: Harrison


title: RNA sequencing - E12 mouse embryonic cortices Emx1-Cre Zbtb7a-flox cHet vs cKO vs WT

city: Sioux Falls

first: Louis-Jan

last: Pilaz

state: SD

address: 2301 E 60th Street North

department: Pediatrics and Rare Disease

institute: Sanford Research

summary: This is RNA sequencing performed with embryonic day 12 (E12) microdissected mouse cortices with the following genotypes: Emx1 Cre/ +; Zbtb7a +/+ (WT), Emx1 Cre/+; Zbtb7a fl/+ (cHet) and Emx1 Cre/+; Zbtb7a fl/fl (cKO). The goal of this study was to understand the impact ot Zbtb7a knockout during cortical development.

overall_design: 3 cortices per condition coming from 2 separate litters

first: Neeraj

last: Tiwari

first: Pratiksha

last: KC


title: Hypoxia-inducible factor 2α promotes protective Th2 cell responses during intestinal helminth infection [RNA-seq]

overall_design: 3 technical replicates of 8 conditions, being Th0 normoxia ctrl, Th0 normoxia HIF2A-ON, Th0 hypoxia ctrl, Th0 hypoxia HIF2A-ON, Th2 normoxia ctrl, Th2 normoxia HIF2A-ON, Th2 hypoxia ctrl, Th2 hypoxia HIF2A-ON.


title: Bulk RNA sequencing data of femur bone marrow tissue derived from mice intramuscularly injected with a SARS-CoV2 mRNA vaccine

first: Jae-Hun

last: Ahn

address: Daehak-ro 101, Jongro-gu

department: Biomedical Research Institute

institute: Seoul National Universty Hospital

summary: SARS-CoV2 mRNA vaccine-induced side effects have been extensively reported in the clinical field. However, the potential toxicity of mRNA vaccines has not been fully identified. We aimed to clarify mRNA vaccine-induced bone marrow toxicity. Six-week-old CrlOri:CD1(ICR) female mice were used. A SARS-CoV2 S protein coding nucleoside-modified mRNA vaccine candidate or D-PBS (Negative control) was intramuscularly injected at left side femoral muscle twice at 2-week intervals (100 ug/head). Mice were sacrificed at 2 days post-secondary injection, and the bulk RNA sequencing for bone marrow of left side femur was performed. Notably, the mRNA vaccine induced significant decrease of erythroid cells in bone marrow. The bone marrow suppression was mediated by the complete mRNA vaccine, but not by mRNA only or LNP only. The RNA sequencing revealed that interferon-stimulated genes (ISGs), cell death-related genes and proteolysis-related genes were significantly upregulated, while erythrocyte development-related genes, hematopoietic cell differentiation-related genes and cytoskeleton-related genes were downregulated, in the bone marrow tissue of mRNA vaccine-injected mice compared to that of only LNP-injected mice. These findings indicate that the mRNA template is mainly involved in the mRNA vaccine-induced bone marrow suppression. We confirmed that the mRNA vaccine can cause pathological changes in bone marrow tissue. Although the underlying mechanism needs to be clarified, our findings suggest that mRNA vaccine-induced bone marrow suppression should be cautiously considered in the pre-clinical developmental process.

first: Jae-Hwan

last: Nam

first: Byeong-Cheol

last: Kang


title: scRNA-seq nased characrization of Cdh16-expression alveolar epithelial progenitor during mouse lung development

city: WenZhou

first: Jin

last: Wu

state: ZHejiang

address: Jingguan street 1#

institute: WenZhou Medical University

summary: We have employed a single cell sequencing approach using 10x Genomics scRNAseq to study Cdh16-expression alveolar epithelial progenitor during mouse lung development. Alveolar morphogenesis and regeneration rely on progenitors to replenish alveolar epithelia. Cdh16 positive cells constitute an epithelial progenitor pool capable of differentiating into both AT2 and AT1 cells.In this study, we present the first scRNA-seq analysis on of Cdh16 lineage traced cells during mouse lung alveologenesis, revealing their plasticity with a dynamic differentiation trajetory along with the embryonic stages as well as the postnatal days. Overall, our study elucidates the crucial role of the Cdh16 lineage as alveolar epithelial progenitors in lung development and regeneration.

overall_design: Cdh16CreERT2/wt;R26-tdTomatoflox/wt mice were used for in vivo lineage tracing experiments to label Cdh16Pos cells in embryonic lung tissues.Tamoxifen (Sigma-Aldrich) was administered to timed-pregnant females either via IP injection (0.1 mg/kg body weight) or through diet (0.4 g/kg food) since embryonic day 12.5 (E12.5), with embryonic lungs collected at E18.5 and postnatal day 10 (P10). TomatoPos cells were isolated by Fluorescence-activated cellsorting (FACS) and analyzed using scRNA-seq.

first: Jin-San

last: Zhang


title: Environmental aromatic amine induces pulmonary arterial hypertension associated with estrogen signaling and Serpine1

city: Baton Rouge

first: Tammy

middle: R

last: Dugas

state: LA

address: Skip Bertman Drive

department: Comparative Biomedical Sciences

institute: LSU School of Veterinary Medicine

summary: We examined the molecular pathways underlying the DAPM-induced pulmonary arterial hypertension in intact and ovariectomized female rats.

overall_design: 11-15 week old female (intact and ovariectomized) Sprague-Dawley rats were treated with vehicle (35% ethanol) and 25mg/kg DAPM orally once weekly for 12 weeks.

first: Ankit

last: Aryal

first: Ashlyn

middle: C

last: Harmon

first: Michelle

middle: A

last: Carroll-Turpin

first: Merilyn

middle: H

last: Jennings

first: Tomislav

last: Jelesijevic

first: Philip

last: Ebenezer

first: Qingzhao

last: Yu

first: Joseph

last: Francis


title: control versus allergic rhinitis basal cells in response to Der p1

city: Leuven

first: Emma

last: Ruysseveldt

address: UZ herestraat 49, box 811

department: Microbiology, immunology and transplantation

country: Belgium

institute: KU Leuven

summary: Basal cells are the epithelial progenitor cells of the airways and play a critical role in tissue homeostasis and repair. In a healthy upper airway epithelium, the basal cells are usually shielded from environmental triggers as they are positioned in close contact with the basement membrane. In allergic rhinitis, it is known that the epithelial barrier is dysfunctional and it is believed that in this situation basal cells become more accessible to airborne particles, however, it is not known whether basal cells can sense these triggers directly. In addition, previous research has shown that control basal cells phenotypically and functionally differ from allergic rhinitis (AR) basal cells. In this study, we aimed to further compare phenotypical differences between sorted primary control and house dust mite (HDM)-allergic AR basal cells, before and after culture, using bulk RNA sequencing. Moreover, we wanted to evaluate the basal cell transcriptional response to HDM-derived Der p1 to study their potential as an environmental sensor.

overall_design: Basal cell transcriptomics were analyzed from 6 control and 6 AR patients. For each patient sample, conditions included fresh basal cells (i.e., immediately after sorting), two weeks culture, and two weeks culture followed by 6 hours stimulation with 1 µg/mL Der p1 (22A02, Citeq Biologicals). Cultured cells were grown for one week in PneumaCult Ex Plus medium (05040, StemCell Technologies) followed by one week in BEGM (CC-3170, Lonza). Cells were lysed using RLT lysis buffer (79216, Qiagen) and RNA was extracted using the RNeasy Mini Kit (74104, Qiagen). Sample purity and RNA concentration was evaluated using a NanoDrop OneC UV-Vis Spectrophotometer (Thermo Fischer Scientific, Waltham, Massachusetts, USA), and quality control was performed using Bioanalyzer (Agilent). Library prep was done using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (196, Lexogen), followed by sequencing on the NextSeq 2000 device (Illumina, San Diego, California, USA). Quality control of the raw sequencing data was performed using FastQC. Within Galaxy, Cutadapt was used to remove the poly-A tail, mitochondrial RNA and ribosomal RNA. Trimmomatic was used to filter low quality read. Mapping to the hg38 human genome was performed using HISAT. Principal component analysis (PCA) was performed to visualize clustering between controls and AR samples under the respective conditions based on the transcriptome data. Differentially expressed genes (DEGs) were identified using the DESeq2 package in R. Multiple DEG comparisons were carried out, including 1) main effect control versus AR, and 2) control culture versus AR Der p1. DEGs were selected with adjusted p-value < 0.05 and |log2 fold change (log2 FC)| > 0.5. DEGs were visualized using volcano plot and heatmap created with the R packages ‘ggplot2’ and ‘ComplexHeatmap’, respectively. Gene set enrichment analysis (GSEA) of the DEGs was performed using the Molecular Signatures Database (MSigDB)27,28 and ‘ClusterProfiler’ package in R, evaluating overrepresentation of Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Hallmark, and cell type signature gene sets.

first: Peter

middle: W

last: Hellings


title: A Pathway Analysis, Connectivity Mapping and Transcriptional Benchmark Dosing Based Exploration of Oxidative Stress Mediated Genetic Toxicology Modes of Actions

city: Mason

first: Bastian

middle: Gregory

last: Selman

state: Ohio

address: 8700 Mason Montgomery Rd

institute: Procter & Gamble

summary: While current genetic toxicology practices can detect downstream genotoxicity effects, such as gene mutation and double strand breaks, they are unable to detect the underlying Mode of Action (MoA) of a chemical or differentiate between direct and indirect acting genotoxicants without additional modification. The Adverse Outcome Pathway (AOP) framework is a useful tool to critically identify and evaluate MOAs and can enable subsequent quantitative dose response assessments of genotoxicity endpoints. The recently developed AOP, “Oxidative DNA damage leading to chromosomal aberrations and mutations” ( https://aopwiki.org/aops/296), pertains to one common genetic toxicology relevant MOA: oxidative stress. ROS are key to regulating many biological processes, however, when disrupted, an excess of ROS can eventually lead to DNA damage and double-strand breaks. Here, we look at 18 compounds with a complete or mixed oxidative stress MOA and use a combination of genomic tools such as Pathway analysis, Connectivity mapping and Transcriptional benchmark dose modeling to investigate the diversity of mechanisms that contribute to genotoxicity. TK6 cells were treated with the 18 compounds for 4 hours and the resulting genomic data was analyzed in correlation to the downstream genotoxic endpoint, micronucleus formation. We provide both a qualitative and quantitative analysis of the contribution of oxidative stress MoAs towards the overall genotoxicity outcome of each chemical. These methods have the potential to evolve into Next Generation Risk Assessment (NGRA) tools that can be used for determining the contribution of the oxidative stress MoA in a predictive toxicology setting.

overall_design: Human TK6 cells were treated with the 18 compounds for 4 hours in triplicate. The solvents (Water or DMSO) for each compound were also tested and used as controls.

first: Ashley

middle: J

last: Allemang

first: Nadira

last: De Abrew

middle: G

first: Mahmoud

last: Shobair

first: Xiaoling

first: Stefan

middle: S

last: Pfuhler


title: miRNA species as systemic mediators of environmentally persistent free radical-induced endothelial dysfunction [C57 mice]

first: Tammy

summary: Plasma miRNA data from particulate matter containing environmentally persistent free radical exposed mice

overall_design:
24 male C57BL/6J mice (n=8/group) were exposed to filtered air and environmentally persistent free radicals ( EPFR lo and EPFR) at the concentration of 250 µg/m3 for 4 hour/day for 5 days. Plasma were collected after the end of exposure on 5th day.
miRNA profiling was done in isolated exosomal RNA from plasma using NanoString nCounter MouseV1.5 miRNA expression assay kit.

first: Alexandra

last: Noel

first: Kurt

last: Varner


title: Turkey B-cell Transcriptome Profile During Turkey Hemorrhagic Enteritis Virus (THEV) Infection Highlights Upregulated Apoptosis and Breakdown Pathways That May Mediate Immunosuppression

city: Provo

first: Abraham

last: Quaye

state: UT

address: 4007 Life Sciences Building

department: Microbiology & Molecular Biology

institute: Brigham Young University

summary: Background: Infection with Turkey Hemorrhagic Enteritis Virus (THEV) can cause hemorrhagic enteritis, which affects turkey poults. This disease is characterized by immunosuppression (IMS) and bloody droppings. The clinical disease usually lasts only a few days but secondary opportunistic infections due to THEV-induced IMS extend the duration of illness and mortality, which exacerbates economic losses. Although an avirulent THEV strain with only subclinical disease is used as a vaccine, some immunosuppressive properties remain in this prophylactic strain. To elucidate the mechanisms mediating THEV-induced IMS, we performed the first transcriptomic analysis of a THEV infection using bulk RNA-sequencing.     Methods: After infecting a turkey B-cell line with the vaccine strain, samples in triplicates were collected at 4-, 12-, 24-, and 72-hours post-infection (hpi). Total RNA was extracted, and poly-Adenylated-tailed mRNAs were sequenced. Reads were mapped to the host turkey genome after trimming and gene expression was quantified with StringTie. Differential gene expression was performed with DESeq2 followed by functional enrichment analysis with gprofiler2 and DAVID from NCBI. RT-qPCR of select genes was performed to validate the RNA-sequencing data.   Results: A total of 2,343 and 3,295 differentially expressed genes (DEGs) were identified at 12 hpi and 24 hpi, respectively. At 12 hpi, 1,079 genes were upregulated and 1,264 genes downregulated, whereas 1,512 genes were upregulated and 1,783 genes downregulated at 24 hpi. The DEGs contributed to multiple biological processes including apoptosis, ER unfolded protein response, and cell maintenance. Multiple pro-apoptotic genes, including APAF1, BNIP3L, BMF, BAK1, RIPK1, and FAS were upregulated. Genes that play a role in ER stress-induced unfolded protein response including VCP, UFD1, EDEM1, EDEM3, and ATF4 were also upregulated and may contribute to apoptosis.    Conclusions: Our data suggest that several biological processes and pathways including apoptosis, immune response, ER response to stress, ubiquitin-dependent protein catabolic process, and repression of essential cellular maintenance are important aspects of the host cell response to THEV infection. It is possible that interplay between multiple processes may mediate apoptosis of infected B-cells, leading to IMS.

overall_design:
To understand the genetic basis by which THEV causes immunosuppression (IS) in infected turkeys, we performed an RNA-seq experiment to elucidate the transcriptomic profile of THEV-infected cells, highlighting key host genes, cellular/molecular processes and pathways affected during a THEV infection. We specifically focus on cellular processes that would help in elucidating THEV-induced IMS.
A THEV vaccine was used to infect a turkey cell line (MDTC-RP19) and harvested at 4-, 12-, 24-, and 72-hpi in triplicates. RNA-seq was done for polyA-tailed mRNA
Reads trimmed with Cutadapt were mapped to Meleagris gallopavo (turkey) genome obtained from NCBI using Hisat2. StringTie in estimation mode was used to generate normalized gene expression estimates from the BAM files for genes in the reference GTF file after which the prepDE.py3 script was used to extract read count information from the StringTie gene expression files, providing an expression-count matrix for downstream DEG analysis.
DEG analysis between mock- and THEV-infected samples was performed using the very popular DESeq2. Genes with P-adjusted value less than or equal to 0.05 were considered as differentially expressed and used as input for functional enrichment (Gene ontology [GO] and KEGG pathway) analyses.
GO and KEGG pathway analysis was performed using the R package gprofiler2 and DAVID (Database for Annotation, Visualization and Integrated Discovery; version 2021) online resource.

first: Brian

middle: D

last: Poole

first: Brett

last: Pickett

first: Joel

last: Griffitts

first: Bradford

middle: K

last: Berges


title: miRNA species as systemic mediators of environmentally persistent free radical-induced endothelial dysfunction [Transgenic mice]

last: Dugas

overall_design:
A cohort of 15 female 10 male mice deficient in AhR in AT-II cells and littermate control (n=5-7/group) were exposed to filtered air and environmentally persistent free radicals (EPFR) at the concentration of 250 µg/m3 for 4 hour/day for 5 days. Plasma were collected after the end of exposure on 5th day.
miRNA profiling was done in isolated exosomal RNA from plasma using NanoString nCounter MouseV1.5 miRNA expression assay kit.

first: Ankit

last: Aryal

first: Ashlyn

last: Harmon

first: Qingzhao


title: MMP19 in vascular smooth muscle cells protects against thoracic aortic aneurysm and dissection via the MMP19/Aggrecan/Wnt/β-Catenin axis

first: Baihui

last: Ma

address: 167 Beilishi Road

institute: Fuwai Hospital

summary: Background: Thoracic aortic aneurysm and dissection (TAAD) is a life-threatening cardiovascular event characterized by high mortality rates. Previous studies have shown that matrix metalloproteinases 19 (MMP19) was involved in TAAD formation, while the detailed role of MMP19 in TAAD pathogenesis and underlying mechanism remain unclear. Methods: To investigate the role of MMP19 in the progression of TAAD, we generated global Mmp19 knockout mice, as well as VSMCs (vascular smooth muscle cells)-specific Mmp19 knockdown mice, and established a BAPN-induced TAAD model. To elucidate the signaling pathways modulated by Aggrecan, we employed an adeno-associated virus serotype 9 (AAV9) vector encoding Acan short hairpin RNA (shRNA) for VSMC-specific knockdown of Acan. Ultimately, we injected an AAV vector encoding VSMC-specific Mmp19 into BAPN-induced TAAD mice to assess whether MMP19 can mitigate the development of TAAD. Results: Our findings revealed elevated mRNA and protein levels of MMP19 in the aortas of both TAAD mice and patients. The systemic ablation of Mmp19, as well as VSMC-specific Mmp19 knockdown, significantly exacerbated BAPN-induced progressive TAAD, and TAAD-related cardiovascular remodeling. Mmp19 deficiency resulted in the accumulation of Acan, but not Vcan, within the aorta, driving the phenotypic switch of VSMCs from contractile to synthetic state through activting Wnt/β-catenin signaling pathway. The selective inhibitor of Wnt/β-catenin signaling, MASB, was effective in reversing the dedifferentiation of VSMCs induced by aggrecan accumulation. Notably, the specific knockdown of Acan in VSMCs restored the contractile phenotype of VSMCs and inhibited Wnt/β-catenin signaling, thereby alleviating BAPN-induced TAAD in Mmp19-/- mice. Additionally, VSMC-specific complementation of MMP19 also alleviated the progressive TAAD phenotype in Mmp19-/- mice. Conclusions: The study underscores that MMP19 deficiency exacerbates TAAD by promoting Acan aggregation and destroying the homeostasis of VSMCs by activating Wnt/β-catenin signaling pathway. These results posit MMP19 as a promising novel therapeutic target for TAAD intervention.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  WT and  Mmp19-/- mice aorta tissues.

first: Qingyi

last: Zeng

first: Fangfang

last: Yang

first: Hang

first: Wenke

last: Li

first: Rui

last: Fu

first: Zeyu

last: Cai

first: Guoyan

last: Zhu

first: Chang

last: Shu

first: Mingya

last: Luo

first: Zhou

last: Zhou


title: Sex and genotype affect mouse hippocampal gene expression in response to blast-induced traumatic brain injury

city: East Orange

first: Bruce

middle: A.

last: Citron

state: NJ

address: 385 Tremont Ave.

department: Pharmacology, Physiology, & Neuroscience, Rutgers- NJMS

institute: VA New Jersey Health Care System

summary: Blast-induced traumatic brain injury (bTBI) has been identified as an increasingly prevalent cause of morbidity and mortality in both military and civilian populations over the past few decades. Functional outcomes following bTBI vary widely among individuals, and chronic neurodegenerative effects including cognitive impairments can develop without effective diagnosis and treatment. Genetic predispositions and sex differences may affect gene expression changes in response to bTBI and influence an individual’s probability of sustaining long-term damage or exhibiting resilience and tissue repair. Male and female mice from eight genetically diverse and distinct strains (129S1/SvImJ, A/J, C57BL/6J, CAST/EiJ, NOD/ShiLtJ, NZO/HlLtJ, PWK/PhJ, WSB/EiJ) which encompassed 90% of the genetic variability in commercially available laboratory mice were exposed to a single bTBI (180 kPa) using a well-established shock tube system. Subacute changes in hippocampal gene expression due to blast exposure were assessed using RNA-seq at 1-month post-injury. We identified patterns of dysregulation in gene ontology terms and canonical pathways related to mitochondrial function, ribosomal structure, synaptic plasticity, protein degradation, and intracellular signaling that varied by sex and/or strain, including significant changes in genes encoding respiratory complex I of the electron transport chain in male WSB/EiJ mice and the glutamatergic synapse across more than half of our groups. This study represents a multi-level examination of how genetic variability may influence response to bTBI and provides a foundation for the identification of potential therapeutic targets that could be modulated to improve the health of Veterans and others with histories of blast exposures.

overall_design: We compared mRNA levels by RNA-seq of total RNA from mouse hippocampal samples for the matrix of sham vs. blast TBI, male vs. female, 8 different strains, n=3/group, 32 total groups, 96 total animals

first: Kathleen

middle: E

last: Murray


title: Mitochondrial unfolding protein CLPX is required for oocyte competence during ovarian aging

city: Shenzhen

first: Renwu

last: Hua

address: Haiyuan 1st Road

institute: HKU-SZH

summary: Ovarian aging has reproductive and overall health implications with increased infertility, miscarriage rates, and adverse outcomes associated with menopause. Mitochondrial dysfunction is one of the main mechanisms of female reproductive aging. Mitochondrial protein homeostasis maintains mitochondrial function and globally dysregulated unfolded mitochondrial protein response accelerates reproductive aging. However, the role of oocyte mitochondrial proteostasis in determining oocyte quality is unknown. ClpX (Caseinolytic Protease X) is a mitochondrial protein unfoldase that maintains mitochondrial protein homeostasis. In this study, we uncovered that Clpx deficiency, either through genetic ablation or natural decline with aging in mice, leads to the disrupted mitochondrial proteostasis in oocytes. Oocyte-specific knockout of Clpx impaired oocyte quality and developmental competence, thereby leading to female subfertility. Transcriptomic and micro-proteomic analyses of Clpx null oocytes revealed dysregulated mitochondrial function, protein processing and meiosis. Notably, Clpx deficiency promoted PGD2 synthesis and DP1/PKA/cAMP and DP2/AKT/mTOR signaling pathways by upregulating Ptgds. The PGD2 synthesis inhibitor AT-56 restored the developmental competence of Clpx knockout and aged oocytes. Our findings indicate the pivotal role of oocyte mitochondrial proteostasis in the regulation of oocyte quality with aging and pave the way for future investigations assessing the potential therapeutic value of these pathways to improve infertility treatment outcomes.

overall_design: RNA-seq profiling of oocyte-specific knockout of GV (germinal vesicle) and ovulated oocytes in mice

first: Tianren

last: Wang


title: Brain region-specific and systemic transcriptomic dysregulation in a human alpha-synuclein overexpressing rat model

city: Saarbrüecken

first: Julia

last: Schulze-Hentrich

address: Campus A2.4

department: Genetics/Epigenetics

country: Germany

institute: Saarland University

summary: Synucleinopathies are age-dependent neurodegenerative diseases characterized by alpha-synuclein accumulation with distinct vulnerabilities across brain regions. Understanding early disease stages is essential to uncover initial molecular changes that might enable earlier diagnosis and causal therapy. Here, we profiled longitudinal and brain region-resolved gene expression changes in a rat model of synucleinopathies overexpressing human SNCA. Transcriptomic analyses on gene and transcript level of striatal, frontocortical, and cerebellar tissue in 5- and 12-month-old transgenic (BAC SNCA) and wild type rats revealed that SNCA overexpression leads to age-dependent transcriptomic changes that largely occur region-specific. In frontal cortex, dysregulation of myelination-associated genes agreed with Parkinson patient data as shown before. In addition, BAC SNCA rats displayed more gene expression changes at younger age, with a common and distinctive dysregulation pattern across all three examined brain regions. We also identified a cross-regional set of differential genes with similar perturbation patterns that were affected by SNCA overload. This set was also partially reflected in the gut transcriptome of the same rat model, suggesting a systemic impact of SNCA overload. Taken together, our findings highlight both brain region-specific vulnerabilities and global molecular perturbations associated with alpha-synuclein biology and provide insights into early transcriptomic changes in synucleinopathies.

overall_design: Gene expression changes were profiled in striatal, frontocortical and, cerebellar tissue of 5- and 12-months-old rats. For each time point, 5 wild-type and 5 transgenic rats, overexpressing human SNCA were analyzed.

first: Vivien

last: Hoof

first: Thomas

last: Hentrich


title: PTEN mutations impair CSF dynamics and cortical networks by dysregulating periventricular neural progenitors

city: New Haven

first: Kristopher

last: Kahle

state: Connecticut

address: 333 Cedar St

institute: Yale University Department of Neurosurgery

summary: Enlargement of the cerebrospinal fluid (CSF)-filled brain ventricles (ventriculomegaly) is a defining feature of congenital hydrocephalus (CH) and an underrecognized concomitant of autism. Here, we show that de novo mutations in the autism risk gene, PTEN, are among the most frequent monogenic causes of CH and primary ventriculomegaly. Mouse Pten-mutant ventriculomegaly results from aqueductal stenosis due to hyperproliferation of periventricular Nkx2.1+ neuroprogenitor cells (NPCs) and increased CSF production from hyperplastic choroid plexus. Pten-mutant ventriculomegalic cortices exhibit network dysfunction from increased activity of Nkx2.1+ NPC-derived inhibitory interneurons. Raptor deletion or post-natal everolimus treatment corrects ventriculomegaly, rescues cortical deficits, and increases survival by antagonizing mTORC1-dependent Nkx2.1+ NPC pathology. Thus, PTEN mutations concurrently alter CSF dynamics and cortical networks by dysregulating Nkx2.1+ NPCs. These results implicate a non-surgical treatment for CH, demonstrate a genetic association of ventriculomegaly and ASD, and help explain neurodevelopmental phenotypes refractory to CSF shunting in select CH patients.

overall_design: Examine the knockout effect of PTEN on choroid plexus, subventricular zone and cortex

middle: T

first: Emre

last: Kiziltug

first: Tyrone

last: DeSpanza Jr.


title: Redox disruption using electroactive liposome coated gold nanoparticles for cancer therapy

city: Tainan

first: Li-Chan

last: Chang

address: 7F., No. 35, Xiaodong Rd., North Dist., Tainan City 704017, Taiwan (R.O.C.)

department: Institute of Clinical Medicine

country: Taiwan

institute: National Cheng Kung University

summary: Cancer remains a global health challenge necessitating innovative therapies. We introduce a strategy to disrupt cancer cell redox balance using gold nanoparticles (Au NPs) as electron sinks combined with electroactive membranes. Utilizing Shewanella oneidensis MR-1 membrane proteins, we develop liposomes enriched with c-type cytochromes. These, coupled with Au NPs, facilitate autonomous electron transfer from cancer cells, disrupting redox processes and inducing cell death. Effective across various cancer types, larger Au NPs show enhanced efficacy, especially under hypoxic conditions. Oxidative stress from Au@MIL (MIL: membrane-integrated liposome) treatments, including mitochondrial and endoplasmic reticulum lipid oxidation and mitochondrial membrane potential changes, triggers apoptosis, bypassing ironmediated pathways. Surface plasmon band and X-ray absorption near-edge structure (XANES) analyses confirm electron transfer. A SiO2 insulator coating on Au NPs blocks this transfer, suppressing cancer cell damage. This approach highlights the potential of modulated electron transfer pathways in targeted cancer therapy, offering refined and effective treatments.

overall_design: Human Hep G2 hepatocellular carcinoma cells (H) and human MDA-MB-231 triple-negative breast cancer cells (M) were treated with 300 ppm Au@MIL nanoparticles (MIL: Shewanella oneidensis MR-1 membrane-integrated liposome) for 24 hours. The treated groups were labeled as H_N and M_N, while untreated control groups were labeled as H_C and M_C. Total RNA was extracted from experimental cells using Trizol Reagent (#15596026, Thermo Fisher Scientific). For RNA library preparation, the refined RNA was processed with the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's guidelines.

first: Ying-Chi

last: Chen

first: Wen-Pin

last: Su

first: Chen-Sheng

last: Yeh


title: Erbin knockout leads to differential gene expression in the rat proximal tubular epithelial cell line NRK-52E

city: Nanjing

first: Yuhui

last: Zang

address: 163 Xianlin Road

institute: Nanjing University

summary: We generated the Erbin-deficient NRK-52E sublines (referred as to KO) using CRISPR/Cas9 approach, and performed transcriptome sequencing to identify the differentially expressed genes compared to the control (referred as to NC).

overall_design: Total RNA was extracted from NRK-52E subline cells with TRIzol reagent. The RNA purity and integrity were analyzed with the Agilent Bioanalyzer 2100 (Agilent). The mRNA was purified from total RNA after removal of rRNA and sequenced on an Illumina Hiseq2500 system.

first: Shao

last: Fang

first: Zhang

last: Junfeng

first: Zang

last: Yuhui


title: Single-cell RNA-seq reveals TCF7 as a novel regulator of human induced pluripotent stem cells differentiation to definitive endoderm

city: Shanghai

first: Yuan

last: Min

address: 1239 Siping Road

institute: Tongji university

summary: Endodermal cells differentiated from human induced pluripotent stem cells can produce multiple functional epithelial cells of vital organs and tissues that can be used for disease modeling as well as cell therapy. However, the detailed molecular mechanism of how hiPSCs differentiate towards definitive endoderm is not fully understood. By analyzing single-cell RNA sequencing data of  definitive endoderm differentiation from human embryonic stem cells, transcription factor 7 (TCF7) was identified as a gene that transiently increases then decreases during differentiation of  definitive endoderm.

overall_design: Endodermal cells differentiated from human induced pluripotent stem cells were transfected with si-TCF7 ,si-TBXT and si-NC and analyzed using scRNA seq.

first: Ke

last: Wei

first: Min

last: Yuan

first: Hongjie

last: Zhang

first: Xiaodong

last: Zhao


title: CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response.

city: Singapore

first: Ajay

last: Mathuru

state: Singapore

address: 28 Medical Drive, #5-COR

department: Physiology

country: Singapore

institute: NUS

summary: CCSER1, a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways, including calcium signaling and neuroactive ligand-receptor interaction, in CCSER1-deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior, as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases, such as addiction and neurodevelopmental disorders.

overall_design:
We generated CRISPR/Cas-9 mutants in the gene CCSER1 - CCSER1_P471 or CCSER1_M, and CCSER1_S48Y* or CCSER1_S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains, homozygous mutants were raised to adulthood. WT controls were siblings from the heterozygous incross.
RNA-seq analysis performed on whole brains and of whole body without the brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired-end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument.

first: Rekha

last: Jakhar

first: Karen

last: Crasta


title: BCAT1-Mediated N-Myc Stabilization Contributes to Tumorigenesis of MYCN-Amplified Neuroblastoma

city: Suzhou

first: Zimu

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: Neuroblastoma (NB) is a common neuroendocrine tumor in early childhood, and the poor prognosis of high-risk NB is due to its poorly differentiated characteristics and immunosuppressive microenvironment. Around 25% of high-risk NB in children is caused by MYCN gene amplification. In this study, we found that Branched-chain amino acid transaminase 1 (BCAT1) is overexpressed in NB, especially those with MYCN amplification, and is a positively correlated with MYCN expression. Moreover, BCAT1 may be a risk factor for NB, significantly affecting proliferation of NB cells. Besides, we revealed that MYCN directly regulated BCAT1 transcription through binding to BCAT1 promoter, thus enhancing BCAT1-MYCN cooperativity. The highly disordered loop region of the MYCN protein makes it readily degraded under natural conditions, making it difficult to obtain the real structure of MYCN through experiments. We performed GROMACs optimization on the MYCN structure obtained from Alphafold, which increased the reliability of the MYCN structure and met the requirements of subsequent protein docking experiments. In this study, we found that after BCAT1 binds to the disordered regions of MYCN, it can improve the overall stability of MYCN. Therefore, we hypothesized that BCAT1 can enhance the stability of MYCN, suggesting that BCAT1 may be a potential therapeutic target for MYCN-amplified NB. In summary, these findings establish BCAT1 is a critical oncogenic factor in NB and provide a new potential target for treatment of NB with MYCN amplification.

overall_design: mRNA profiles of SK-N-BE(2) cells transfected with control shRNA-Control (shControl) or shRNA-BCAT1 (shBCAT1) were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Hongli

last: Yin


title: TFAP2C and HNRNPK control cellular bioenergetic metabolism and prion propagation [CRISPR screen]

city: Zurich

first: Davide

last: Caredio

state: Switzerland

department: Institute of Neuropathology

institute: University Hospital of Zurich

summary: Heterogenous Nuclear Ribonucleoprotein K (HNRNPK) is a limiting factor for prion propagation. However, little is known about the function of hnRNP_K other that it is essential to cell survival. Here, we performed a synthetic-viability CRISPR ablation screen to identify functional epistatic interactors of HNRNPK. We found that deletion of Transcription Factor AP-2γ (TFAP2C) mitigated the survival of hnRNP_K-depleted LN-229 and U-251MG cells, whereas its overexpression hypersensitized cells to the loss of hnRNP_K. HNRNPK ablation induced downregulation of genes related to lipid and glucose metabolism, decreased cellular ATP and enhanced catabolism through modulation of the mTOR and AMPK pathways. Conversely, TFAP2C overexpression promoted mTOR anabolic activity, and its deletion countered the energetic crisis resulting from HNRNPK ablation. We then found that TFAP2C overexpression reduced prion propagation in wild-type cells and neutralized prion accumulation in HNRNPK-suppressed cells. We conclude that TFAP2C and HNRNPK are genetic interactors controlling cell metabolism, bioenergy and prion propagation.

overall_design: We conducted a genome-wide CRISPR ablation screen for synthetic lethal/viable interactions of HNRNPK in LN-229 cells. Cells were transduced with a lentivirus-packaged Brunello library using an MOI of 0.3, maintaining a coverage of approximately 1000 cells/sgRNA throughout the screen. After 24 hours (Day 1), 280 million cells were collected as a baseline reference to assess library distribution. The remaining cells were selected for 7 days. On Day 7, cells were further transduced with CRISPR knockout guides targeting HNRNPK or with non-targeting (NT) control guides. After 7 additional days under selection, cells were harvested on Day 14 for genomic DNA extraction and sequencing. The screen was repeated in two biological replicates. Differential gene enrichment analysis was performed using EdgeR, identifying significant sgRNAs (log2 fold change ≤ -1 or ≥ 1, FDR < 0.01).

first: Stefano

last: Sellitto


title: A functional connection between the Microprocessor and a variant NEXT complex

city: Aarhus C

first: Katsutoshi

last: Imamura

address: Bissensgade 16, 4. tv

country: Denmark

institute: Aarhus University

type: Non-coding RNA profiling by high throughput sequencing

summary: In mammalian cells, primary miRNAs are cleaved at their hairpin structures by the Microprocessor complex, whose core is composed of DROSHA and DGCR8. Here, we show that 5’flanking regions, resulting from Microprocessor cleavage, are targeted by the RNA exosome in mouse embryonic stem cells (mESCs). This is facilitated by a physical link between DGCR8 and the nuclear exosome targeting (NEXT) component ZCCHC8. Surprisingly, however, both biochemical and mutagenesis studies demonstrate that a variant NEXT complex, containing the RNA helicase MTR4 but devoid of the RNA-binding protein RBM7, is the active entity. This Microprocessor-NEXT variant also targets stem-loop containing RNAs expressed from other genomic regions, such as enhancers. In contrast, Microprocessor does not contribute to the turnover of less structured NEXT substrates. Our results therefore demonstrate that MTR4-ZCCHC8 can link to either RBM7 or DGCR8/DROSHA to target different RNA substrates depending on their structural context.

overall_design: Mouse ES cells were produced by knocking out ZCCHC8 using CRISPR/Cas9. 15-30nt was extracted from the total RNA of WT and ZCCHC8 KO mESC. Three  biological replicates were generated for  small RNA-seq.

first: William

last: Garland

first: Manfred

last: Schmid

first: Lis

last: Jakobsen

first: Kengo

last: Sato

first: Jérôme

middle: O

last: Rouvière

first: Kristoffer

last: Pors Jakobsen

first: Elena

last: Burlacu

first: Marta

last: Loureiro Lopez

first: Søren

last: Lykke-Andersen

first: Jens

last: Andersen

first: Torben

last: Heick Jensen


title: TFAP2C and HNRNPK control cellular bioenergetic metabolism and prion propagation [RNA-seq]

overall_design: To investigate the molecular basis of the genetic epistatic interaction between HNRNPK and TFAP2C, we performed RNA-seq analysis on LN-229 cells depleted of hnRNP K, Tfap2c, or both proteins. Non-targeting controls (NT and NT3) were used in combination with HNRNPK- and TFAP2C-targeting CRISPR knockout guides. Three biological replicates were run for each condition, but replicate 2 for the NT3/NT, NT/HNRNPK, and TFAP2C/NT conditions was excluded from the analysis due to low RNA quality

first: Matteo

last: Bimbati


title: Effect of  genetic deletion of Gsdmd on mice fed an oxalate rich-diet

city: München

first: Yoshihiro

last: Kusunoki

address: Ziemssenstr. 5

institute: LMU Klinikum

summary: The role of pyroptosis, an inflammatory form of cell death involving the formation of Gasdermin-D (GSDMD) pores, in chronic oxalate nephropathy remains unknown. We report genetic deletion of Gsdmd exacerbated oxalate nephropathy in mice in association with accelerated necroptosis.Our transcriptional analysis using kidneys from mice fed an oxalate-rich diet or control diet revealed significant changes in the gene sets related to leukocyte migration, chemokine pathways, mitochondrial dysfunction, and complement pathways between Gsdmd KO and WT mice. These differences may be attributed to variations in the substances released during cell death.

overall_design:
To investigate potential therapeutic targets in chronic oxalate nephropathy, we fed WT mice an oxalate-rich, calcium-depleted diet to induce progressive oxalate nephropathy, or control diet, and sacrificed them on day 20.
We then performed gene expression profiling analysis using data obtained from  RNA-seq of kidneys from mice fed an oxalate rich-diet or fed a control food.
Furthermore, to investigate the effect of genetic Gsdmd deletion on chronic oxalate nephropathy, we fed Gsdmd kcockout mice an oxalate rich-diet and conducted gene expression profiling analysis using data obtained from  RNA-seq of kidneys from these mice.

first: Li

last: Chenyu

first: Hans Joachim

last: Anders


title: S. cerevisiae Mub1, a substrate adaptor of E3 ubiquitin ligase,  modulates sensitivity to cell wall stressors through multiple transcription factors

city: Zagreb

first: Bojan

last: Zunar

address: Pierottijeva 6

country: Croatia

institute: University of Zagreb Faculty of Food Technology and Biotechnology

summary: Yeasts evolved a complex regulatory program to build and maintain their cell wall, the primary structure through which they interact with their environment. However, how this program ties to essential cellular processes mostly remains unclear. Here, we focus on Saccharomyces cerevisiae Mub1, an adaptor protein of E3 ubiquitin ligase Ubr2, previously associated with regulating proteasome genes through transcription factor Rpn4. We show that S. cerevisiae cells lacking Mub1 become hyper-tolerant to standard cell wall stressors, outperforming wild-type cells. This protective mub1Δ phenotype stems from the activity of several transcription factors, leading to the inhibition of cell wall remodelling, a typically protective process that becomes maladaptive during chronic cell wall stress in laboratory conditions. Based on these results, we suggest Mub1 regulates not only Rpn4 but a much broader range of transcription factors and thus serves as an in-so-far unrecognised regulatory hub directly linking cell wall robustness with the ubiquitin-proteasome system.

overall_design: To investigate the source of the mub1Δ phenotype, we grew exponential phase S. cerevisiae wild type (BMA41) and its mub1Δ derivative for 5 hours, either in standard chemically defined yeast medium or standard chemically defined yeast medium supplemented with 20 µg/ml Calcofluor white. We then performed gene expression profilling analysis using RNA-seq data for all four conditions, in duplicates. RNA-seq reads were mapped with HISAT2 2.2.1, using default parameters, and count matrices produced with featureCounts 2.0.3.

last: Žunar

first: Ana

last: Novačić

first: Nada

last: Šupljika

first: Igor

last: Stuparević


title: A bruton’s tyrosine kinase inhibitor reduces stemness and invasiveness of patient-derived glioblastoma tumorspheres

city: Seoul

first: Kibyeong

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

institute: Yonsei University

summary: Glioblastoma (GBM), the most prevalent primary brain tumor, remains incurable due to the presence of cancer stem cells (CSC), which can be isolated as tumorspheres (TS) that exhibits classical characteristics of CSCs including stemness and invasiveness. The significantly elevated expression of Bruton’s tyrosine kinase (BTK) in GBM tissues identifies BTK as a potential therapeutic target in GBM. Consequently, ibrutinib, an FDA-approved BTK inhibitor for hematological malignancies, has been repurposed as a candidate for GBM treatment, demonstrating inhibitory effects on proliferation, stemness, and invasiveness of GBM cell lines and TSs. However, its broad-spectrum activity targeting other Tec family kinases and members of the epidermal growth factor receptor (EGFR) family, poses potential life-threatening risks, necessitating the development of more selective alternatives. To address this, BTK selective analogs (SPA1758, SPA1763, SPA8004, SPA8007, SPA8009) were synthesized with the aim of targeting two key characteristics of GBM TSs: stemness and invasiveness. WST and ATP assays identified SPA8007 and SPA8009 as the most effective candidates with superior cytotoxic effects in TSs. Additionally, both SPA8007 and SPA8009 significantly inhibited neurosphere formation and reduced invasiveness in GBM TSs. Furthermore, SPA8007 demonstrated improved survival rates in a GBM xenograft mouse model and reduced the expression of invasiveness markers significantly, as observed in immunohistochemistry (IHC) analysis. These findings highlight SPA8007 as potential novel chemotherapeutic agents with high specificity and efficacy to enhance GBM therapy.

overall_design: RNA-seq of patient-derived GBM TS, treated with BTK inhibitors for 72 hours.

first: Euna

last: Jo

first: Yoojung

last: Oh

first: Seok-Gu

last: Kang


title: Identification of HELLS as a Novel DNA G-quadruplex Helicase [ChIP-Seq]

city: Riverside

first: Yinsheng

last: Wang

state: California

address: 501 Big Springs Road

institute: UC-Riverside

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Guanine quadruplexes (G4s) are unique secondary structures of nucleic acids with functions in many biological processes. Understanding the biological functions of DNA G4s requires the knowledge about their recognitions by cellular proteins. Affinity pull-down coupled with LC-MS/MS analysis was previously employed to identify G4-binding proteins (G4BPs); the approach, however, has limitations in capturing weak and transient interactions, potentially leading to false-positives. Here, we developed a photoclick chemistry-based method, in combination with LC-MS/MS, for uncovering G4BPs. By incorporating a photoactivatable ortho-nitrobenzylamine (o-NBA) moiety into G4 DNA probes and employing UVA irradiation along with stringent washing, we identified 99 proteins enriched with G4 structures derived from the human telomere. We further validated the abilities of one of these proteins, HELLS, in binding and resolving G4 structures both in vitro and in chromatin. Together, we developed a photoclick chemistry-based approach for identifying novel G4BPs. Our work led to the discovery of new G4BPs, and uncovered novel functions of HELLS in recognizing and unwinding G4 structures in vitro and in cells.

overall_design: Genome-wide profiling analysis of G4 structures in shCtrl and shHELLS U2OS cells

first: Zi

last: Gao

first: Xiaomei

last: He


title: The E3 ubiquitin ligase RNF112 inhibits bladder cancer progression by attenuating lipid synthesis through the degradation of c-Myc

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

summary: The E3 ubiquitin ligase RNF112 exhibits significant downregulation in bladder cancer, correlating with disease progression and unfavorable prognosis. Experimental evidence from in vitro and in vivo studies indicates that RNF112 suppresses bladder cancer proliferation, migration, and lipid synthesis. Mechanistically, RNF112 interacts directly with the MBII domain of MYC through its N-terminal zinc finger motif. The catalytic site C97 of RNF112 facilitates K48-linked polyubiquitination of the K389 residue on the c-Myc protein, accelerating its degradation. The restoration of c-Myc expression has been shown to mitigate the inhibitory impacts of RNF112 on the growth, migration, and lipid synthesis of bladder cancer cells. Additionally, our research validates the interaction of c-Myc with the ACLY promoter, leading to an enhancement of its transcriptional activity. RNF112 exerts its inhibitory effects on lipid synthesis in bladder cancer through the regulation of c-Myc. In conclusion, RNF112 suppresses the proliferation, migration, and lipid synthesis of bladder cancer cells by facilitating the ubiquitin-mediated degradation of c-Myc.

overall_design: To study the downstream mechanisms by which RNF112 controls the development of bladder cancer, we performed RNA sequencing on the T24 bladder cancer cell line. The experiment included three replicates for the control group and three replicates for the RNF112 overexpression group.

first: Kangping

last: Xiong

first: Huimin

last: Xu

first: Xinghuan


title: Fermented sunflower meal in diets for Atlantic salmon

city: Ås

first: Linn

middle: Haug

last: Eide

address: Oluf Thesens vei 6

country: Norway

institute: Norwegian University of Life Sciences

summary: The increasing aquaculture production volumes have caused an escalating demand for alternative protein feed ingredients. Agro-industrial by-products such as sunflower meal are relatively abundant and cheap, but the inclusion levels are limited due to the presence of antinutritional factors and fiber. Solid state fermentation is a processing method with the aim of reducing the content of fiber and antinutritional factors and improving nutritional value in plant protein raw materials. In this study, Atlantic salmon (Salmo salar) at two commercial-like fish farms were fed diets containing 5% non-fermented sunflower meal (as a control diet) and two experimental diets with 5% or 10% fermented sunflower meal.  The field trial lasted for eight and 11 months in a coastal and fjord location, respectively with the aim of comparing the effect of fermented diets on growth performance, gut microbiota, distal intestine histology and gene expression of Atlantic salmon under different environmental conditions. The findings revealed that diets with fermented sunflower meal sustained growth performance, improved intestinal health by reducing the prevalence of prominent inflammation and ectopic goblet cells and promoted gut lactic acid bacteria Lactiplantibacillus and Lactobaccilaceae after long-term feeding. Our results suggest that fermented sunflower meal is suitable as a protein source for Atlantic salmon when included at a level of up to 10% in the diet.

overall_design: To investigate if increasing inclusion of fermented sunflower meal (0 %, 5 % and 10 %) in the diets for farmed Atlantic salmon has an impact on gene expression in the distal intestine. We performed gene expression profiling analysis using data obtained from 10 fish per dietary group on two different locations.

first: Byron

last: Morales-Lange


title: Transcriptional Dysregulation in the Hippocampus of a Mouse Model for Parkinson's - Linked Cognitive Decline is Driven by Sex, Age, and Alpha-synuclein overexpression

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

summary: Cognitive decline is the most common and detrimental non-motor symptom of Parkinson’s disease (PD), and is an understudied disease entity. Pathologically, cognitive decline in PD is associated with alpha-synuclein (aSyn) misfolding and synapse loss in hippocampus and prefrontal cortex, leading to cognitive impairment and, ultimately, dementia. The mechanisms of cognitive decline and the factors driving them in PD are unknown. In the present study, we have used longitudinal gene expression profiling to characterise hippocampal molecular events in a transgenic mouse overexpressing E46K mutated aSyn, a model of early PD. Uncovering early events leading to disease is an essential step toward prognostic biomarker identification and early interventions. Transgenic aSyn induced synaptophysin loss in hippocampus and cortex of these mice. Comparing 4 different ages of mice from both sexes uncovered that hippocampal gene expression changes are sexually dimorphic and strongly modulated by the age, and by aSyn overexpression. Pathways that emerged across different comparisons were connected to a variety of neuronal functions, collagen synthesis/remodeling, cellular stress, and inflammatory responses. The findings indicate that sex and age are essential factors to consider when studying PD-associated cognitive decline. This may have important implications for prognostic biomarker identification and monitoring, and for timing of therapeutic approaches.

overall_design: To investigate effects of overexpression of E46K human alpha-synuclein on the murine hippocampal transcriptome, we analyzed differential gene expression by RNA-seq at (i) four different time points, (ii) in male and female, and (iii) in transgenic as well as wilde type animals. All on a C57Bl6/J x DBA/2J hybrid background.

first: Manuel

last: Buttini

first: Alessia

last: Sciortino

first: Thomas

last: Hentrich

middle: M


title: Parkinson's disease (PD) genetic asymmetry in neuronal nuclei from paired hemisphere samples of prefrontal cortex (ATAC-Seq)

city: Grand Rapids

first: Gerry

last: Coetzee

state: MI

address: 333 Bostwick Ave NE

department: CNS

institute: Van Andel Research Institute

summary: We measured chromatin accessibility in neuronal nuclei from cortex derived from PD (18 male, 10 female) and healthy control (2 male, 2 female) brains.  Each brain sample consisted of cortex from both right and left hemispheres. Th side of PD onset, age, duration of disease, as well as technical variables were used to define linear models related to DiffBind scores. Significant differences  due to age, disease, sex, hemisphere, side of PD onset, or combinations were determined

overall_design: Frozen prefrontal cortex was prepared and sorted to isolate neuronal nuclei. DNA was preparred for bulk ATAC-sequencing. Peaks were called with MACS2 and compared using DiffBind for differences.

first: Gerhard

first: Steven

last: Pierce

first: JC

last: vanderSchans

first: Elizabeth

last: Ensink


title: Regulation of fetoplacental metabolism in pig

city: Columbia

first: SUSANTA

last: BEHURA

state: MO

address: 920 East Campus Dr

institute: University of Missouri

summary: RNA sequencing was performed to profile gene expression in the placentae of male and female fetusues (day 45) of pig. Genes showing sex-bias expression were identfieid.

overall_design: In this study, the Large White x Landrace gilts from the University of Missouri Swine Research Farm were used. The gilts were bred by artificial insemination (AI). The day of AI was considered as gestation day (GD) 1. On GD 45, pregnant pigs (n=6) were euthanized. The uterine horns were opened on the antimesometrial side and all the fetuses and corresponding placentae were removed. Total RNA from the male and female placentae (in triplicates) were used for RNA-seq analysis.

first: Shankar

middle: P

last: Poude

first: Maliha

last: Islam

first: Timothy

last: Safranski

first: Susanta

last: Behura


title: Disrupted minor intron splicing activates reductive  carboxylation-mediated lipogenesis to drive  metabolic dysfunction–associated steatotic   liver disease progression

first: Yinkun

last: Fu

address: chongqing Rd

department: school of medicine

institute: shanghai jiaotong university

summary: Aberrant RNA splicing is tightly linked to diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD). Here, we revealed that minor intron splicing, a unique and conserved RNA processing event, is largely disrupted upon the progression of metabolic dysfunction-associated steatohepatitis (MASH) in mice and humans. We demonstrated deficiency of minor intron splicing in the liver induces MASH transition upon obesity-induced insulin resistance and LXR activation. Mechanistically, inactivation of minor intron splicing leads to minor intron retention of Insig1 and Insig2, resulting in premature termination of translation, which drives proteolytic activation of SREBP1c. This mechanism is conserved in human patients with MASH. Notably, disrupted minor intron splicing activates glutamine reductive metabolism for de novo lipogenesis through the induction of Idh1, which causes the accumulation of ammonia in the liver, thereby initiating hepatic fibrosis upon LXR activation. Ammonia clearance or IDH1 inhibition blocks hepatic fibrogenesis and mitigates MASH progression. More importantly, the overexpression of Zrsr1 restored minor intron retention and ameliorated the development of MASH, indicating that dysfunctional minor intron splicing is an emerging pathogenic mechanism that drives MASH progression. Additionally, reductive carboxylation flux triggered by minor intron retention in hepatocytes serves as a crucial checkpoint and potential target for MASH therapy.

overall_design: To investigate the gene expression in mouse liver fed NASH diet, we established mice fed with chow diet or CDA-HFD for 6 months.we performed gene expression profile using data obtained from RNA-seq of liver from control and CDA-HFD mice.

first: Xuyun

last: Zhao

first: Xin

last: Peng

first: Hongyong

last: Song


title: Toll-like receptor 2 deficiency exacerbates dextran sulfate sodium (DSS)-induced intestinal injury by Marinifilaceae dependent attenuating cell cycle signaling

first: yunjie

last: shi

address: No 800，Xiangyin Road

institute: Naval Medical University

summary: Ulcerative colitis (UC) is an intestinal pathology characterized by chronic recurrent inflammation, which requires in-depth exploration of its mechanisms. To investigate the biological effects of TLR2 on DSS-induced intestinal inflammation in mice, we constructed the WT and TLR2-KO colitis mice model. We found TLR2-KO mice were severely susceptible to DSS-induced colitis. To determine how TLR2 exerted a protective effect in DSS-induced colitis, we compared the global gene expression profiles in the gut between WT and TLR2-KO mice by RNA-Seq. Results suggested that cell cycle pathway-related genes were significantly downregulated in gut of TLR2-KO colitis mice. 16S rRNA gene sequencing demonstrated remarkable variation in the composition of gut microbiota between WT and TLR2-KO colitis mice. Compared with WT colitis mice, the relative abundance of Marinifilaceae, Rikenellaceae, Desulfovibrionaceae, Tannerellaceae, Ruminococcaceae, Clostridia, Mycoplasmataceae were significantly higher in the gut of TLR2-KO colitis mice at family level. Moreover, we found that the relative abundance of Marinifilaceae was negatively correlated with the expression of cell cycle signaling related genes by microbiome diversity-transcriptome collaboration analysis. We came to this conclusion: TLR 2-KO exacerbated DSS-induced intestinal injury by Marinifilaceae dependent attenuating cell cycle signaling.

overall_design: To examine the function of TLR2 signaling in intestinal injury repair, researchers developed Dextran Sulfate Sodium Salt (DSS)-induced colitis and injury models in both wild-type (WT) mice and TLR2 knockout (TLR2-KO) mice. To assess changes in the gut microbiota, 16S rRNA sequencing was conducted on fecal samples from both the TLR2-KO and WT enteritis mouse models.

first: Yunjie

last: Shi

first: Kaiwen

last: Sheng

first: Cong

last: Liu

first: Hao

last: Wang


title: Generation of human spermatogonia from pluripotent stem cells

city: Philadelphia

first: Eoin

middle: Christopher

last: Whelan

state: PA

address: 3800 Spruce St

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

type: Methylation profiling by high throughput sequencing

summary: Failures in germline development are a major cause of male infertility. However, the search for novel treatments is hampered by the lack of experimental systems that faithfully recapitulate human spermatogenesis. Here, we have developed a system to differentiate human induced pluripotent stem cells (iPSCs) into primordial germ cell-like cells that self-organize within xenogeneic reconstituted testes (xrTestes) generated from mouse fetal testicular cells. Subsequent transplant of xrTestes into immunodeficient mice resulted in efficient generation of undifferentiated and differentiated spermatogonia as well as preleptotene spermatocytes with striking similarities to their in vivo counterparts. As the fertilization competency of human iPSC-generated germ cells cannot be evaluated due to ethical constraints, we utilized a similar strategy to differentiate rhesus iPSCs through all fetal germ cell stages into spermatogonia-like cells. Together, these newly identified models of human gametogenesis will allow further mechanistic assessment of both germ cell development and genetic causes of infertility.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: iPSCs derived from humans and macaques were used to generate first PGCLCs and, following transplantation into a recipient mouse along with mouse fetal somatic cells, generate differentiating germ cell types. Single-cell analysis of such xrTestes are represented by these datasets. Additionally, knockout datafrom DND1-KO and NANOS3-KO iPS-derived germ cells is provided along with whole genome bisulfite sequencing.

middle: C

first: Young

last: Hwang

first: Ryo

last: Yokomizo

first: Yasunari

last: Seita

first: N

middle: A

last: Leu

first: Keren

last: Cheng

first: Jill

last: Ginsberg

first: Rebecca

middle: L

last: Linn

first: Sandra

last: Ryeom

first: Kotaro

last: Sasaki


title: MATR3 Promotes Liver Cancer Progression by Suppressing DHX58–Mediated Type I Interferon Response

city: Hangzhou

first: Zhaofeng

last: Xiao

address: No.261, Wunsa Road, Shangcheng District, Hangzhou, Zhejiang, China

institute: Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province

summary: To investigate the mechanism of Matr3 in liver cancer, we stably knocked out Matr3 in Hepa1-6 cells and performed RNA sequencing with wild-type Hepa1-6 cells

overall_design: Comparative gene expression profiling analvsis of RNA-seq data for Hepa 1-6 cells and its Matr3 KO derivatives

first: Huan

last: Chen

last: Xu

first: Yiyuan


title: Identification of HELLS as a Novel DNA G-quadruplex Helicase

first: Yinsheng

first: Zi

last: Gao

first: Xiaomei

last: He


title: Chloride Nucleotide-Sensitive Channel 1A (CLNS1A) Regulates Genome Stability and Cell Cycle Progression to Control Pathogenic T Helper 17 Cell Function and Autoimmunity

city: New York

first: Maxwell

last: McDermott

state: NY

address: 550 1st Ave

department: Pathology

institute: NYU Langone Health

summary: RNA-sequencing of myelin-specific 2D2 CD4+ T cells isolated from the spinal cord and spleen of mice with EAE.

overall_design: CD4+ T cells isolated from the spleen of 2D2 mice were activated by stimulation with aCD3 (1ug/ml) and aCD28 (1ug/ml) in the presence of IL1b (20ng/ml), IL6 (20ng/ml) and IL23 (20ng/ml), aIL4 (5mg/ml) for 96 hours to induce pth17 cell differentiation. Samples of naive and pTh17 were collected. pTh17 cells were transferred into Rag1-/- hosts.  Donor 2D2 CD4+ T cells were isolated from the spleen and spinal cord of the Rag1-/- host mice at day 14 after EAE induction, and enriched by FACS.

first: Liwei

first: Stefan

last: Feske


title: Effect of depletion of LEMD3 on chromatin accessibility of A7r5 vascular smooth muscle cells [ATAC-seq]

city: Beijing

first: Yunxi

last: Liao

state: Beijing

address: 38 Xueyuan Rd, Haidian District

institute: School of Basic Medical Sciences, Peking University

summary: The contractile phenotype of vascular smooth muscle cells is essential for maintaining vascular homeostasis.In this study, we found that LEMD3, a nuclear membrane protein, may be involved in maintaining the contractile phenotype of vascular smooth muscle cells through a genome-scale CRISPR screen. Mechanistically, we combined RNA-seq with ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) to find out differentially expressed genes and altered chromatin accessibility. By overlapping down-regulated genes and genes located in less accessible chromatin regions, we identified 143 genes including VSMCs contractile genes such as Acta2, Cnn1, Tagln, and key transcription factor Srf, suggesting that LEMD3 maintains VSMCs contractile phenotype by regulating chromatin accessibility.

overall_design: A7r5 cells were transfected with scrambled siRNA or siRNA targeting Lemd3.

first: Wenqiang

last: Li


title: Effect of depletion of LEMD3 on chromatin accessibility of A7r5 vascular smooth muscle cells [Hi-C]


title: HIV-1 integration sites in the cells depleted for host facors SON, SRRM2; HIV-1 integration sites infected wild type HEK293T cells and HEK293T cells lacking CPSF6 but complemented for CPSF6 mutants. [CPSF6]

city: Boston

first: Parmit

middle: Kumar

last: Singh

state: MA

address: 450 Brookline Avenue

department: Department of Cancer Immunology and Virology

institute: Dana-Farber Cancer Institute

summary: SON and SRRM2 were depleted in U2OS and HeLa cells and infected with HIV-1. Similarly HEK293T cells were infected with HIV-1 virus.

overall_design: DNA from infected cells were used to make integration libraries by ligation-mediated PCR. PCR products were sequenced by Illumina. Integration sites were determined against hg19. Random integration control or RIC were generated against hg19 as a control.

first: Alan

last: Engelman


title: Pioneer factor ETV2 safeguards endothelial cell specification

first: Danyang

state: Massachusetts

address: 300 longwood ave

department: Cardiology

institute: Boston Children's Hospital

summary: Mechanisms of cell fate specification are central to developmental biology and regenerative medicine. ETV2 is a master regulator for the endothelial cell lineage specification. Here, we study mechanisms by which ETV2 overexpression in human iPSC-derived mesodermal progenitors efficiently specifies ECs.

overall_design: Chromatin accessibility, gene expression profiling, and TF chromatin occupancy was assessed using high-throughput sequencing.


title: Chloride Nucleotide-Sensitive Channel 1A (CLNS1A) Regulates Genome Stability and Cell Cycle Progression to Control Pathogenic T Helper 17 Cell Function and Autoimmunity [RNA-seq]

summary: RNA-sequencing of in vitro differentiated shRenilla (control) and shClns1a transduced pTh17 cells.

overall_design: CD4+ T cells isolated from the spleen of 2D2 mice were activated by plate-bound aCD3 (1 ug/ml) and aCD28 (1 ug/ml) in the presence of IL1b (20ng/ml), IL6 (20ng/ml) and IL23 (20ng/ml), aIL4 (5mg/ml). 24 hours post activation, cells were transduced with shRenilla (control) or shClns1a.  48 hours post activation, cell were detached and cultured in the presence of IL1b (20ng/ml), IL6 (20ng/ml), IL23(20ng/ml), and aIL4 (5mg/ml)  for an additional 72 hours. Cells were restimulated with aCD3 (1 ug/ml) and aCD28 (1 ug/ml) for an additional 0, 6 or 24 hours. Transduced cells were enriched by FACS.

last: Wang


title: Chloride Nucleotide-Sensitive Channel 1A (CLNS1A) Regulates Genome Stability and Cell Cycle Progression to Control Pathogenic T Helper 17 Cell Function and Autoimmunity [CUT&RUN]

summary: CUT&RUN sequencing of CLNS1A and PRMT5 in in vitro differentiated pTh17 cells.

overall_design: CD4+ T cells isolated from the spleen of WT mice were activated by plate-bound aCD3 (1 ug/ml) and aCD28 (1 ug/ml) in the presence of IL1b (20ng/ml), IL6 (20ng/ml) and IL23 (20ng/ml), aIL4 (5mg/ml) for 3 days.


title: HIV-1 integration sites in the cells depleted for host facors SON, SRRM2; HIV-1 integration sites infected wild type HEK293T cells and HEK293T cells lacking CPSF6 but complemented for CPSF6 mutants.[SON_SRRM2]


title: Sox9 marks limbal stem cells and is required for asymmetric cell fate switch in the corneal epithelium

first: Panteleimon

last: Rompolas

address: 421 Curie Blvd., BRB II/III Room 1014

department: Dermatology

institute: University of Pennsylvania

summary: Adult tissues with high cellular turnover require a balance between stem cell renewal and differentiation, yet the mechanisms underlying this equilibrium are unclear. The cornea exhibits a polarized lateral flow of progenitors from the peripheral stem cell niche to the center; attributed to differences in cellular fate. To identify genes that are critical for regulating the asymmetric fates of limbal stem cells and their transient amplified progeny in the central cornea, we utilized an in vivo cell cycle reporter to isolate proliferating basal cells across the anterior ocular surface epithelium and perform single-cell transcriptional analysis. This strategy greatly increased the resolution and revealed distinct basal cell identities with unique expression of structural genes and transcription factors. We focused on Sox9; a transcription factor implicated in stem cell regulation across various organs. Sox9 was found to be differentially expressed between limbal stem cells and their central corneal progeny. Lineage tracing analysis confirmed that Sox9 marks long-lived limbal stem cells, which generate progeny that expands centripetally to replenish the cornea. Conditional deletion of Sox9 led to abnormal differentiation and squamous metaplasia in the central cornea, suggesting that it is required for braking cell division symmetry. By inhibiting terminal differentiation of transient amplified progenitors, forcing them into perpetual symmetric divisions, we replicated the Sox9 loss-of-function phenotype. Our findings reveal an essential role for Sox9 in the spatial regulation of asymmetric fate in the corneal epithelium that sustains tissue homeostasis.

overall_design: To investigate the mechanism of stem cell fate regulation in the ocular epithelium we used a reporter mouse model (Cyclin B1-GFP) that marks actively cycling cells in vivo. By fluorescently activated cell sorting we purified GFP-positive cells from freshly excised mouse corneas and performed single-cell RNA sequencing analysis.

first: Gabriela

last: Rice

first: Olivia

last: Farrelly

first: Sixia

last: Huang

first: Ning

first: Christopher

last: Lengner


title: Inner Nuclear Membrane Protein LEMD3 Stabilizes 3D Chromatin Architecture and Maintains Vascular Smooth Muscle Cell Identity

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

overall_design: Refer to individual Series


title: Chloride Nucleotide-Sensitive Channel 1A (CLNS1A) Regulates Genome Stability and Cell Cycle Progression to Control Pathogenic T Helper 17 Cell Function and Autoimmunity [ATAC-seq]

summary: Assay for transposase-accessible chromatin with sequencing (ATAC-seq) for shRenilla (control) or shClns1a transduced pTh17 cells restimulated with aCD3/CD28 for 24h.

overall_design: CD4+ T cells isolated from the spleen of WT mice were activated by plate-bound aCD3 (1 ug/ml) and aCD28 (1 ug/ml) in the presence of IL1b (20ng/ml), IL6 (20ng/ml) and IL23 (20ng/ml), aIL4 (5mg/ml). After 24 hours of activation  Cells were transduced with shRenilla or shClns1a, then co cultured for another 24 hours to induce knockdown.  Cells where then deattached, the media was changed, and samples were further cultured in the presence of IL1b (20ng/ml), IL6 (20ng/ml), IL23(20ng/ml), and aIL4 (5mg/ml) for an additional 96 hours.


title: Effect of depletion of LEMD3 on gene expression of A7r5 vascular smooth muscle cells [RNA-seq]


title: Impact of overexpression of DRBD18 and its methyl mutants on the gene expression pattern of T. brucei: A transcriptomic approach

city: Buffalo

first: Laurie

last: Read

address: 955 Main Street

department: Department of Microbiology and Immunology

institute: University at Buffalo

summary: Arginine methylation of RNA-binding proteins (RBPs) plays a crucial role in the post-transcriptional regulation of gene expression in Trypanosoma brucei, the causative agent of African trypanosomiasis. This protozoan has evolved intricate mechanisms to regulate gene expression at the mRNA level, allowing it to adapt to diverse environmental conditions encountered during its complex life cycle. The process of arginine methylation involves the addition of methyl groups to specific arginine residues within RNA-binding domains of proteins. This modification can profoundly impact the binding affinity of RBPs to their target mRNAs, thereby influencing mRNA stability, localization, and translation efficiency. DRBD18 is one of the RNA-binding proteins (RBPs) in T. brucei that undergoes arginine methylation and has been involved in various aspects of mRNA metabolism and post-transcriptional gene regulation. Studies have shown that arginine methylation of DRBD18 can modulate its interaction with target mRNAs, leading to differential regulation of gene expression. Here, we have done a comprehensive transcriptomic analysis of T. brucei overexpressing DRBD18 and its methyl mutants R->F (methylmimic) and R->K (hypomethylated), aiming to elucidate the regulatory mechanisms orchestrated by DRBD18 and its potential impact on the parasite's gene expression landscape. We identified specific mRNA targets exhibiting differential expression patterns in response to DRBD18, R->F and R->K overexpression, providing insights into the regulatory pathways modulated by this RBP.

overall_design: To find out the impact of overexpression of DRBD18 and its methyl mutants (R->F and R->K), we generated two methyl mutants. The first one is DRBD18(R->F), here we mutated the three identified methyl arginines to phenylalanine, creating a methyl mimic DRBD18. In the second methyl mutant, DRBD18(R->K), we replaced the methyl arginine with lysine. We used a doxycycline-inducible system to overexpress these N-terminal MYC tagged DRBD18, R->F and R->K. Three biological replicates of each cell line in the presence and absence of doxycycline, grown for 36 hr. have been used to isolate RNA for RNA sequencing.

first: Parul

last: Pandey

first: Brianna

last: Tylec

first: Alexandra

last: Glathar


title: Identification of target RNAs associated with DRBD18 and its methyl mutants

summary: Arginine methylation of RNA-binding proteins (RBPs) plays a crucial role in the post-transcriptional regulation of gene expression in Trypanosoma brucei, the causative agent of African trypanosomiasis. This protozoan has evolved intricate mechanisms to regulate gene expression at the mRNA level, allowing it to adapt to diverse environmental conditions encountered during its complex life cycle. The process of arginine methylation involves the addition of methyl groups to specific arginine residues within RNA-binding domains of proteins. This modification can profoundly impact the binding affinity of RBPs to their target mRNAs, thereby influencing mRNA stability, localization, and translation efficiency. DRBD18 is one of the RNA-binding proteins (RBPs) in T. brucei that undergoes arginine methylation and has been involved in various aspects of mRNA metabolism and post-transcriptional gene regulation. T. brucei PRMT1 (TbPRMT1), a major type I protein arginine methyltransferase, modulate the function of DRBD18 by arginine methylation. Studies have shown that arginine methylation of DRBD18 can modulate its interaction with target mRNAs, leading to differential regulation of gene expression. This study aims to identify the in vivo transcriptome-wide binding of DRBD18 in TBPRMT1 knockdown cells, which leads to decipher the specific mRNA targets, providing insights into the regulatory pathways modulated by this RBP.

overall_design: To find out the direct targets of DRBD18 and its methyl mutants (R→F and R→K) as well as hypomethylated DRDB18 in TbPMT1 RNAi cell lines, we used a doxycycline-inducible system to overexpress these N-terminal MYC tagged DRBD18, R→F and R→K in DRBD18 RNAi cell line. Three biological replicates of each cell line in induced condition were grown for 36 hr (DRBD18 constructs) and 48 hours (TBPRMT1 knockdown). RNA immunoprecipitation was done using an anti-MYC antibody for the DRBD18 WT and methyl mutants and an anti-DRBD18 antibody for the PRMT1 experiments and RNA was isolated from Input and RIP samples and sent for sequencing.


title: The effect of IL-17 signaling inhibition on radiation dermatitis (RD) using a mouse model

city: Bronx

first: Shaun

last: Wu

state: New York

address: 1301 Morris Park Avenue, Room 355

institute: Shinoda Lab

summary: It has been previously shown that there is involvement of IL-17 signaling in the development of severe radiation dermatitis from RNA-sequenicng of human RD skin samples. In this project, we tested the hypothesis using a mouse model of RD previously developed by Liao et al. (PMID: 28406748)

overall_design: The skin on the left flank of C57BL/6J wild-type mice was exposed to a single X-ray dose of 25 Gy to induce radiation dermatitis. One group received IL-17 neutralizing antibody once prior to irradiation and once a week afterward up to three weeks to test its preventative effect.

first: Kosaku

last: Shinoda


title: Effect of depletion of LEMD3 on histone modification H3K27ac of A7r5 vascular smooth muscle cells [ChIP-seq]

first: Yunxi

summary: The contractile phenotype of vascular smooth muscle cells is essential for maintaining vascular homeostasis.In this study, we found that LEMD3, a nuclear membrane protein, may be involved in maintaining the contractile phenotype of vascular smooth muscle cells through a genome-scale CRISPR screen. To further explore the impact of Lemd3 knockdown on global landscape of H3K27ac and H3K9me3, we performed ChIP-sequencing of scrambled siRNA-transfected and Lemd3 siRNA-transfected rat VSMCs.

first: Sudun

last: Guan


title: Reprogramming chromosome ends by functional histone acetylation

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

summary: Cancers harness embryonic programs to evade aging and promote survival. Normally, sequences at chromosome ends called telomeres, shorten with cell division, and function as a countdown clock to limits cell replication. Therefore, a crucial aspect of cancerous transformation is avoiding replicative aging, by activation of telomere repair programs. In mouse embryonic stem cells (mESCs), the transient expression of the gene Zscan4, correlates with chromatin de-condensation and telomere extension. Head and neck cancers reactivate ZSCAN4, which in turn regulates the cancer stem cell (CSCs) phenotype. Our new study reveals a novel role for human ZSCAN4 in facilitating functional histone H3 acetylation at the telomere chromatin. Next-generation sequencing reveals ZSCAN4 enrichment at chromosome ends and its pivotal role in facilitating histone H3 acetylation at telomeres. These epigenetic changes correlate with ZSCAN4-induced telomere elongation, while CRISPR/Cas9 knockout of ZSCAN4 leads to telomere shortening in cancer cells. Our study elucidates the intricate involvement of ZSCAN4 in modulating telomere histone acetylation, and its interaction with telomeric proteins. These findings suggest ZSCAN4 induction as a novel link between cancer stemness and telomere maintenance. Future strategies aimed at blocking ZSCAN4 may provide new therapeutic approaches to effectively target cancer stem cells and limit their replicative lifespan.

overall_design: tet-FLAG-ZSCAN4-Tu167 cells were grown to 50% confluency and incubated for 48 hours with or without 1 µg/ml doxycycline. ChIP was done using the Pierce Magnetic ChIP Kit (Thermo Scientific) according to the manufacturer’s instructions. Antibodies used for ChIP: Anti-ZSCAN4 (10 µg) (Origene); anti-H3K14ac and H3K18ac (4 µg); Cell signaling), and the provided anti-RNA Polymerase II (1µg) and a Rabbit IgG (10 µg) were used as additional controls.

first: W

last: Meltzer

first: Aditi

last: Gupta

first: Phyo

middle: N

last: Lin

first: Robert

last: Brown

first: Michal

last: Zalzman


title: Joint transcriptional disruption of Ret and Ednrb drives cell fate reversal in the Enteric Nervous System in Hirschsprung disease

first: Ryan

last: Fine

address: 435 E 30th Street

department: Center for Human Genetics and Genomics

institute: NYU Langone


title: Overexpression of DEPDC1B contributes to malignant progression and immune infiltration in lung adenocarcinoma

city: 重庆市

first: 东宇

last: 王

address: 重庆市渝中区重庆医科大学

institute: 重庆医科大学

summary: Dysregulated expression of DEPDC1B (DEP domain-containing protein 1B) has been reported to be implicated in various types of malignancies. However, its functional implication as well as the underlying molecular mechanism in lung adenocarcinoma (LUAD) remains elusive. In this study, the role and clinical significance of DEPDC1B in LUAD has been systematically investigated. Our results first showed that DEPDC1B is significantly upregulated in various types of cancers including LUAD, and high DEPDC1B expression is remarkably associated with poor survival in LUAD patients. Functional study demonstrated that DEPDC1B knockdown inhibited cell growth, cell cycle progression, colony formation, cell migration and motility. Furthermore, xenograft nude mouse model experiments showed that DEPDC1B silencing resulted in significant inhibition of tumor growth in vivo. Detailed mechanistic experiments revealed that DEPDC1B knockdown caused down-regulation of various downstream genes including NID1, FN1 and EGFR, and inactivation of multiple critical pathways including ERK and PI3K-AKT pathways.

overall_design: To explore the  function of DEPDC1B in LUAD, we established A549 cell lines in which DEPDC1B gene has been knocked down by shRNA. And then total RNA were harvested, followed by cDNA library construction, and subjected to RNA-seq analysis.

first: Xiaofeng

last: Zuo

first: Dongyu

last: Wang

first: Chuntao

last: Tao

first: Xuanqi

last: Dou