title: Cuscuta chinensis Lam. Flavonoids (CCLF) alleviate the symptoms of sepsis-associated encephalopathy via PI3K/AKT/Nrf2/HO-1 pathway

city: Jiangsu

first: Boxiang

last: Qi

address: 18 Sudi north road, Xuzhou, Jiangsu

institute: Xuzhou Children Hospital

summary: Sepsis-associated encephalopathy (SAE) affects up to 70% ofSepsis-associated encephalopathy (SAE) affects up to 70% of patients in intensive care units with severe systemic infection. However, the exact pathological mechanisms behind SAE remain unclear. In this study, we aimed to investigate the protective effects of flavonoid components extracted from CCL seeds on SAE animals and evaluate the transcriptomic alterations in the hippocampus using RNA sequencing. Our results showed that CCL seed extract improved learning and memory abilities and structural integrity of the blood-brain barrier in CLP-induced SAE animal models. RNA sequencing revealed that CCL treatment reversed SAE-induced transcriptomic alterations in the hippocampus. Additionally, CCL significantly reduced inflammation (TNF-α， IL-2, and IL-6) and oxidative stress (MDA and SOD activity), as well as inhibited neuron apoptosis in brain tissues. Furthermore, CCL restored the PI3K/AKT signaling pathway, leading to Nrf2 nuclear translocation and HO-1 expression both in vitro and in vivo. The PI3K inhibitor LY294002 blocked CCL's anti-apoptotic, anti-inflammatory, and anti-oxidative effects, demonstrating that CCL's bioactivities are dependent on the PI3K/AKT signaling pathway. In conclusion, CCL exhibits significant neuroprotective properties and may be a promising candidate for further clinical trials in SAE treatment.

overall_design: Nice healthy adult Specific Pathogen Free (SPF)-grade BALB/c mice were randomly divided in to three groups (n=9), of which 3 received sham operation (CTL group), 3 received Cecal ligation and puncture (CLP group) operation only, and 3 received both CLP and CCLF administration (200mg/kg, CCLF group).

first: Qi

last: Boxiang

first: Sheng

last: Liping

first: Qian

last: Tong


title: H2A monoubiquitination targeting by cohesi n subunits in Arabidopsis

status: Public on Jun 08 2024

city: shanghai

first: meng

last: liu

address: 1239,SiPing Road

country: China

institute: TongJi University

type: Expression profiling by high throughput sequencing

summary: Histone H2A monoubiquitination (H2Aub1) is a ubiquitous and conserved post-translational modification, playing a non-degradative role in multiple progresses including transcription regulation. In Arabidopsis thaliana, H2Aub1 is mediated by AtRING1s and AtBMI1s, catalytic subunits of Polycomb repressive complex 1 (PRC1). Despite PRC2-associated repressive role of H2Aub1, the mechanism regarding how H2Aub1 distributed on non-H3K27me3 region need to be explained. In this article, we show that the two cohesin subunits AtSCC3 and AtSYN4 directly interact with AtBMI1A/B/C, and theH2Aub1 levels are significantly reduced in atsyn4orAtSCC3RNAi plants. By ChIP-seq analysis, we found that AtSYN4 and AtSCC3 co-localize with H2Aub1 in genome, and are related to H3K27me3-independent transcription activation. Further, we provide evidences to show that AtSYN4 directly bind to G-box element and regulate H2Aub1 modification in G-box containing loci. These findings reveal that AtSCC3 and AtSYN4 are directly and functionally associated with AtBMI1s. Our study uncovers the mechanism of H2Aub1 targeting modification.

overall_design: The 7-day-old whole seedlings of wild type (WT) were sequenced.

first: Yu

last: Zhang


title: scRNA-Seq reveals anti-fibrotic mechanisms of TRPC6 inhibition [scRNA-seq]

city: Greifswald

first: Yao

last: Xu

state: State

address: Felix-Hausdorff-Straße 3

country: Germany

institute: University Medicine Greifswald

summary: Inhibition of transient receptor potential canonical 6 channels (TRPC6) alleviates tubular injury and renal fibrosis induced by unilateral ureteral obstruction (UUO).However, the exact renoprotective mechanisms are unknown. In this study, we utilized single-cell RNA sequencing (scRNA-Seq) to define the cellular and transcriptional landscape associated with renoprotection through in vivo TRPC6 inhibition, specifically using SH045 (larixyl N-methylcarbamate), in the UUO model.

overall_design: Six C57BL/6 mice underwent unilateral ureteral obstruction (UUO) surgery. Seven days post-surgery, the kidneys from Vehicle-treated (n=3) and SH045-treated (n=3) mice were harvested. The contralateral kidneys from Vehicle-treated mice (n=3) served as the control group (Ctrl group). A total of nine kidney samples were used for single-cell RNA sequencing (scRNA-seq). Additionally, two of these samples (one from the SH045 group and one from the Vehicle group) were simultaneously analyzed using spatial transcriptomics.


title: Graphene-polymer nanofibers enable optically induced electrical maturation in stem cell-derived cardiomyocytes and brain organoids

city: La Jolla

first: Adam

middle: Jeffrey

last: Engler

state: CA

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

country: USA

institute: UC San Diego

summary: Pluripotent stem cell (PSC)-derived electrically excitable cells provide a unique window into human disease and development, but they remain electrically immature compared to their in vivo counterparts, partially due to the lack of chronic stimulation. New classes of on-demand, electrically active biomaterials are being employed to enhance cell functions, and here, we fabricated biocompatible, electrospun polymer nanofibers containing light-reactive reduced graphene oxide (rGO). Fiber size, stiffness, and electrical conductivity scaled with rGO concentration which in turn produced conduction-dependent effects in PSC-derived cardiomyocytes and neurons; with acute light stimulation on scaffolds containing rGO, cardiomyocytes exhibited more calcium handling activity and were more synchronous, and neurons showed more peaks with higher frequency. Chronic repetitive, daily light stimulation of nanofibers integrated into mature brain organoids caused organoids to become increasingly more electrically responsive to stimulation over time, mature synapses of excitable neurons, and activate photoreceptor lineage pathways. This work outlines a tunable method where the electrical function of electrically excitable, PSC-derived cells can be titrated with rGO fibers and light stimulation, and it suggests that repetitive light stimulation may provide a novel method for retinal cell differentiation in organoids.

overall_design: To investigate the effects of light-training brain organoids with reduced grahene oxide (rGO)-polymer nanofibers, we cultured brain organoids with nanofibers containing various concentrations of rGO with daily light stimulation (light-trained) or no light stimulation (unstimulated) for 8 weeks prior to RNA-seq.

first: Erin

last: LaMontagne

first: Alexander

last: Savchenko

first: Gisselle

last: Gonzalez

first: Ritwik

last: Vatsyayan

first: Blanca

last: Martin-Burgos

first: Francesca

last: Puppo

first: Diogo

last: Biagi

first: Fabio

last: Papes

first: Shadi

middle: A

last: Dayeh

first: Alysson

middle: R

last: Muotri

middle: J


title: Novel O-GlcNAcylation on Thr71 of histone H4 preferentially localizes to active gene regions

status: Public on Jun 09 2024

city: Bunkyo-ku

first: Daisuke

last: Nara

state: Tokyo

address: 1-1-1 Yayoi

department: Dep. of Animal resource sciences

country: Japan

institute: The uniersity of Tokyo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report genome-wide distribution of newly discovered O-GlcNAcylated H4 at threonine 71 (H4T71Gc) in mouse embryonic stem cells (mESCs, J1 line) cultured in 25 mM glucose (mESCs-25mMG) or 1 mM glucose (mESCs-1mMG) condition, human embryonic stem cells (hESCs, H9) and human induced-pluripotent stem cells (hiPSCs, 201B7). We found that H4T71Gc preferentially localize to gene regions, especially those with relatively high expression levels. Interestingly, the localized gene region of H4T71Gc changes in response to changes in extracellular glucose concentration. This study using ChIP-seq analysis provides genomic distribution of novel histone O-GlcNAcylation in mouse and human pluripotent stem cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-seq analysis of H4T71Gc in mESCs, hESCs and hiPSCs.

first: D

first: S

last: Matsumoto

first: K

last: Hayakawa


title: Single-Cell Transcriptome Analysis Reveals Differential Signatures of Human Left-Sided and Right-Sided Colon

status: Public on Jun 10 2024

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

summary: In our study, we obtained paired normal left-sided and right-sided colon mucosa tissues by colonoscopy, and 9,642 individual cells were analyzed by single-cell RNA-seq, which aims to explore the differennces of cell component between the left and the right colon.

overall_design: This dataset consists of 4 10x Genomics libraries including paired Left colon and right colon tissues from two healthy patients. The first two libraries were obtained from a 48-year-old female by colonoscopy, and the second two libraries were obtained from a 46-year-old male.

first: Jingjing

last: Li

first: Lifenng

last: Sun

first: Xiaoxu

last: Ge

last: Wu

first: Jian

last: Wang


title: RNA-sequencing of orbitofrontal cortex following limited bedding and nesting stress model

city: Philadelphia

first: Mathieu

last: Wimmer

state: PA

address: 1701 N 13th Street

institute: Temple University

summary: RNA-sequencing of the orbitofrontal cortex was performed in male and female rats following exposure to the limited bedding and nesting model of early life adversity.

overall_design: 20 samples were anlayzed, including 5 male controls, 5 male experimental, 5 female controls, and 5 female experimental.

first: Samantha

last: Eck

first: Evie

last: Ordones Sanchez

first: Charlotte

last: Bavley

first: Reza

last: Karbalaei

first: Debra

last: Bangasser


title: Double-kill mechanism of artemisinin against Plasmodium

city: Shanghai

first: Jun

state: --- Select One ---

address: siping Rd.1239

institute: School of Medicine, Tongji University

summary: The mechanism by which artemisinin and its derivatives (ARTs) kill malaria parasites remains unclear. Haem or iron activates ARTs to produce free radicals that kill malaria parasites. However, adding iron or haem supply did not enhance, but instead attenuated, the antimalarial effect of ARTs, suggesting that the free-radical effect (FRE) is not the only antimalarial mechanism of ARTs. Here, through the single-cell RNA sequencing analysis of Plasmodium yoelii 17XNL and P. falciparum 3D7 in vivo and in vitro, we found that the sensitive stages to ARTs were associated with the expression of genes related to haem and iron (HI), DNA synthesis, antioxidation and the pentose-phosphate-pathway (PPP). Furthermore, the stages included an ART-sensitive cycle crucial for DNA synthesis that encompassed the release of iron through haem degradation to the activation of the PPP by iron. Additionally, the mechanism of haemozoin formation created a unique condition for interaction between ARTs and HI. In particular, HI can attenuate the antimalarial action of ARTs, strongly suggesting the existence of a HI-use-disturbance effect that combined with FRE to confer ARTs with a double-kill  antimalarial mechanism different from the effect of iron chelators.

sample_organism:
Plasmodium falciparum
Plasmodium yoelii

platform_organism:
Plasmodium falciparum
Plasmodium yoelii

overall_design: Single-cell RNA sequencing was used to analyze the expression of differentiated genes in P. yoelii yoelii 17XNL and P. falciparum 3D7 treated with artemether or dihydroartemisinin at different time points (0, 3, 9, and 24 hours).

first: Fujiang

last: Guo

first: Chuang

last: Liu

first: Wenwen

last: Si

first: Bo

last: Chen

first: Wenyue

last: Xu

first: Jia

first: Xiling

last: Du

first: Chuantao

last: Fang


title: Elucidating the Mechanism of Radiation Therapy on Mesenchymal Cell Fate in Heterotopic Ossification

status: Public on Jun 07 2024

city: Dallas

first: Sneha

last: Korlakunta

state: TX

address: 6000 Harry Hines Blvd

department: Surgery

institute: UT Southwestern Medical Center

summary: Radiation therapy is a clinically proven, localized preventive measure for heterotopic ossification (HO). Despite its efficacy, there is a lack of standardization of radiation prescription dosing and fractionation, and the mechanism of the impact of radiation in HO prevention remains unknown. Here, using an established mouse model of traumatic HO induced by burn and tenotomy, we demonstrate that 7Gy in one fraction delivered to the injury site within 72 hours postoperatively significantly decreases HO formation and improves hindlimb range of motion. In-depth single-cell transcriptomic analyses, in combination with immunofluorescent staining, demonstrate decreased cellular numbers as well as aberrant endochondral differentiation and downregulation of associated upstream signaling pathways in irradiated mesenchymal progenitor cells. Our study provides the framework for future mechanistic and clinically relevant studies exploring radiation efficacy in preventing HO formation.

overall_design: To investigate the unknown mechanism of how postoperative radiotherapy prevents HO formation in a traumatic HO mouse model, cells from tenotomy inury site in control and post-radiation day 3 mice were isolated at 7 days post-injury for scRNA-seq.

first: Meng-Lun

last: Hsieh

first: Ji Hae

last: Choi

first: Yuanyuan

last: Zhang

first: Benjamin

last: Levi


title: Effect of oxygen and carbon dioxide on gene expression in Bordetella bronchiseptica strain RB50

city: Chapel Hill

first: Peggy

middle: A.

last: Cotter

state: North Carolina

address: 125 Mason Farm Rd, 6101 Marsico Hall Cb7290

department: Microbiology & Immunology

institute: UNC Chapel Hill

summary: The classical bordetellae (Bordetella pertussis, B. parapertussis, and B. bronchiseptica) are obligate aerobes that use only oxygen as their terminal electron acceptor for electron transport-coupled oxidative phosphorylation. Therefore, access to oxygen is critical for these bacteria to survive. To better understand how B. bronchiseptica changes its gene regulation when faced with different levels of oxygen, we grew liquid cultures of B. bronchiseptica RB50 in ambient air, 5% oxygen, and 2% oxygen. We also measured how the presence of 5% carbon dioxide affected gene expression in these bacteria, since they are respiratory pathogens and therefore get exposed to higher carbon dioxide levels during infection than are found in ambient air.

overall_design: We grew wild-type RB50 in shaking liquid cultures in either ambient air, 5% O2, 2% O2, or 5% CO2. We then assessed gene expression of bacteria in these conditions. Differential gene expression was determined between bacteria grown in ambient air and bacteria grown under conditions (i.e. air vs. 5% O2, air vs 2% O2, and air vs 5% CO2).

first: Liliana

last: McKay


title: Chemoradiotherapy-induced ACKR2+ tumor cells drive CD8+ T cell senescence and tumor recurrence

first: Yifei

last: Pei

address: Yueyang 320

department: Laboratory of Inflammation and Molecular Immunology

institute: Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences

summary: T cell senescence is a dysfunctional state distinct from exhaustion, yet the mechanism driving CD8+ T cell senescence directly in tumor microenvironment and its impact on cancer prognosis remain elusive. Here, by using single cell RNA sequencing of human cervical cancer tissues, we found that concurrent chemoradiotherapy (CCRT) specifically promoted CD8+ T cell senescence, which is driven by a subpopulation of ACKR2+ CCRT-resistance tumor cells. Mechanistically, in response to CCRT treatment, ACKR2 was directly induced and could also be upregulated through its ligands CC chemokines that produced by activated myeloid and T cells. Subsequently, these ACKR2+ tumor cell subpopulation also produced TGFβ to drive CD8+ T cell senescence, thereby compromising antitumor immunity. Moreover, retrospective analysis showed that ACKR2 level and CD8+ T cell senescence was greatly enhanced in cervical cancer patients who recurred after CCRT, thereby predicting poor prognosis in these patients. Overall, we identified a subpopulation of CCRT-resistant ACKR2+ tumor cells in driving CD8+ T cell senescence and thus tumor recurrence, which may represent a critical mechanism in mediating CCRT resistance, and highlighted the therapeutic potential of targeting ACKR2 or CD8+ T cell senescence in the treatment of CCRT-resistant cancer patients.

overall_design: To investigate whether and how chemoradiotherapy contributes to potential tumor recurrence, we established tumor samples from 3 cervical cancer patients before and after CCRT treatment. We performed single cell RNA-sequencing analysis by using 10x Genomics platform of all 6 samples.

first: Dongfang

last: Dai

first: Yichuan

last: Xiao


title: Transcriptomic changes assoicated with hepatic AHR or ARNT loss in female mice challenged with high-fat diet

city: Galveston

first: Cornelis

middle: Johan

last: Elferink

address: 301 University Boulevard

department: Pharmacology and Toxicology

institute: University of Texas Medical Branch

summary: The aryl hydrocarbon receptor (AHR) is an important hepatic transcription factor that appears to have a role in regulating endogenous liver metabolism. Canonical AHR-mediated regulation of transcription requires AHR binding to its DNA-binding partner, the AHR nuclear translocator (ARNT). We previously demonstrated that the AHR can regulate transcription independent of ARNT via “non-canonical” interactions with Kruppel-like factor 6, and that hepatic AHR loss can protect against high-fat diet (HFD) challenge. In this study, we examined the effects of hepatic AHR or ARNT loss in HFD-fed mice to determine whether AHR regulation of liver metabolism might partially occur independent of ARNT. The data show that similar to AHR loss, ARNT loss reduces HFD-driven hepatic lipid deposition, but does not recapitulate the diminished weight gain and adiposity observed in AHR KO animals. Utilizing transcriptomic sequencing analyses, we uncovered specific gene pathways that likely account for these phenotypic differences/similarities associated with AHR or ARNT loss. Together, these data highlight the physiological significance of ARNT-independent AHR activity, and identify discrete aspects of liver metabolism likely regulated via canonical AHR action.

overall_design: Next Generation Sequencing of adult female mice (6 months old, n=3 per genotype). All mice were maintained on a high-fat diet for 13 weeks. Genotypes: Ahr Flox, AHR KO, ARNT Flox, ARNT KO

first: Nathaniel

last: Girer

first: Jill

middle: K

last: Thompson

first: Steven

middle: G

last: Widen


title: Profile of N6-methyladenosine of Pb-exposed neurons presents epitranscriptomic alterations in Pi3K-AKT pathway-associated genes

city: Hefei

first: Danyang

last: Li

address: No. 193 Tunxi Road

institute: Hefei university of technology

summary: Lead (Pb) is a pervasive heavy metal with multi-organ toxicity. However, the molecular mechanisms of Pb-induced neurotoxicity are not fully understood. The dynamics of N6-methylademine (m6A) is an emerging regulatory mechanism for gene expression, which is closely related to nervous system diseases. To elucidate the association between m6A modification and Pb-mediated neurotoxicity, primary hippocampal neurons exposed to 5 μM Pb for 48 h were used as the paradigm neurotoxic model in this study. According to the results, Pb exposure reprogrammed the transcription spectrum. Simultaneously, Pb exposure remodeled the transcriptome-wide distribution of m6A while disrupting the overall level of m6A in cellular transcripts. United analysis of MeRIP-Seq and RNA-Seq was applied to further identify the core genes whose expression levels are regulated by m6A in the process of lead-induced nerve injury. GO and KEGG analysis unveiled that the modified transcripts were overrepresented by the PI3K-AKT pathway. Mechanically, we elucidated the regulatory role of the methyltransferase like3 (METTL3) in the process of lead-induced neurotoxicity and the downregulation of the PI3K-AKT pathway. In conclusion, our novel findings shed new light on the functional roles of m6A modification in the expressional alternations of downstream transcripts caused by lead, providing an innovative molecular basis to explain Pb neurotoxicity.

overall_design: P0 Sprague-Dawley (SD) rats were obtained from the Experimental Animal Center of Anhui Medical University (Auhui, China). Berif, the hippocampal tissue was detached stereoscopically from whole brain of P0 rats and digested by trypsinization (0.03%). The digested tissue were dissociated by trituration through sterile, fire-polished Pasteur pipettes. The dissociated neurons were plated in poly-L-lysine-precoated (0.5 mg/mL) dishes (100 cells per mm2) with serum-free neurobasal medium containing B27 and GlutaMAX. At DIV7, half the volume of media were removed and replaced with fresh neurobasal feeding media supplemented with Ara-C (2 μL/mL). Neurons were fed with PbAc (5 μM) at DIV12. The Pb dosage used in the cell experiment is chosen on the basis of its demonstration in the previous reports (Ding et al., 2018; Gu et al., 2019; Prins, Park, & Lurie, 2010) that it does not cause excessive neuronal death and leads to neuronal damage, as a way of establishing a replicable model for the study of lead-induced neurotoxicity (Data not shown). After culturing at 37 ℃ for 48 h in a 5% CO2 incubator, neurons were hrvested.

first: Shu

last: Ai

first: Hui-Li

last: Wang

first: Xiang-tao

last: Chen


title: Genome-wide chromatin localization profiling of transcription factor MML-1

city: London

first: Ruben

last: Esse

address: Guy's Hospital, Great Maze Pond

department: Department of Medical and Molecular Genetics

country: United Kingdom

institute: King’s College London

summary: MML-1 (Myc and Mondo-Like) encodes a Myc superfamily protein which, together with its partner MXL-2 (Max-like), regulates lifespan via distinct gene sets important for longevity. It is also required for normal migration of ray precursor cells in the male tail and for proper epidermal expression of extracellular matrix component genes. MML-1 binds to MXL-2, required for its protein stability. The MML-1/MXL-2 complex activate transcription mostly via E-box elements.

overall_design: Profiling of MML-1 chromatin localization in wild-type third larval (L3) stage Caenorhabditis elegans

first: Alla

last: Grishok


title: Understanding the biological processes of clear cell renal carcinoma carcinogenesis: an integrative multi-omics approach.

city: Lyon

first: James

last: Mckay

address: 25 Av. Tony Garnier

country: France

institute: IARC - International Agency for Research on Cancer

type: Methylation profiling by genome tiling array

summary: Multi-Omics analysis to gain novel insights into clear cell renal carcinoma aetiology and progression. The DNA methylation data of 121 clear clear renal carcinoma (ccRCC) were integrated with WGS and transcriptomic data using Multi-Omics Factor Analysis (MOFA) to detect the inter-patient variations related to aetiological and disease progression related factors.

overall_design: At the discovery phase, MOFA analysis integrated the DNA methylation (The Infinium MethylationEPIC BeadChip v1), transcriptomic, and WGS data of overlapping tumor samples to explore the major sources of ccRCC inter-patient variation captured by MOFA latent factors. At the validation phase, we used LASSO models to build signatures of MOFA factors in other datasets.

first: Ricardo

last: Cortez Cardoso Penha


title: KAS-seq profiling captures transcription dynamics during oocyte maturation

city: Nanjing

first: huiqing

last: an

address: 101 Longmian Rd, Nanjing, Jiangsu, China

institute: Nanjing Medical University

summary: In fully grown oocytes, the genome is considered to be globally transcriptionally silenced. However, this conclusion is primarily derived from the results obtained through immunofluorescence staining or inferred from the highly condensed state of chromosomes, lacking more direct evidence. Here, by using a kethoxal-assisted single-stranded DNA sequencing (KAS-seq) approach, we investigated the landscape of single-strand DNA (ssDNA) throughout the genome and provided a readout of the activity and dynamics of transcription during oocyte meiotic maturation. In non-surrounded nucleolus (NSN) oocytes, we observed a robust KAS-seq signal, indicating the high transcriptional activity. In surrounded nucleolus (SN) oocytes, the presence of ssDNA still persists although the KAS-seq signal was relatively weak, suggesting the presence of transcription. Accompanying with the meiotic resumption, the transcriptional activity gradually decreased, and global repression was detected in matured oocytes. Moreover, we preformed the integrative genomics analysis to dissect the transcriptional dynamics during mouse oocyte maturation. In sum, the present study delineates the detailed transcriptional activity during mammalian oocyte maturation.

overall_design: We utilized the KAS-seq technique to construct libraries for various developmental stages of mouse oocytes (GV, GVBD, MII) to investigate the dynamic changes of ssDNA during oocytes maturation.


title: Next Generation Sequencing (NGS) for quantitative transcriptomic analysis of colorectal tumor cell lines and their ENU mutants

city: Ube-shi

first: Kensuke

last: Shibata

state: Yamaguchi

address: 1-1 Minami-Kogushi 1-chome

institute: Yamaguchi univeristy

summary: Purpose: To understand differences of gene expression profiles between colorectal cell lines and their ENU mutants. Methods: RNA profiles were generated by deep sequencing using Illumina Next-seq. Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (GRCm38 release-95). Conclusions: Our study represents the detailed differential transcriptomic analysis using ENU mutants of colorectal tumors, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: mRNA profiles of tumors were generated by deep sequencing, in triplicate, using Illumina Next-seq.


title: Molecular changes implicate angiogenesis and arterial remodeling in systemic sclerosis-associated and idiopathic pulmonary hypertension

city: Pittsburgh

first: Yuechen

last: Zhou

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

summary: Pulmonary hypertension (PH) is a common complication of systemic sclerosis (SSc) and a leading cause of mortality among patients with this disease. PH can also occur as an idiopathic condition (idiopathic pulmonary arterial hypertension, iPAH). We sought to investigate the transcriptomic alterations in PH vascular populations to understand cellular mechanisms underlying pathobiology of systemic sclerosis associated and idiopathic pulmonary hypertension.

overall_design: We performed single-cell RNA sequencing on explanted lung tissue of patients with SSc-PH (n = 16), idiopathic pulmonary arterial hypertension (iPAH, n=3) and healthy controls (n=15).

first: Tracy

last: Tabib

first: Mengqi

last: Huang

first: Ke

last: Yuan

first: Yunhye

last: Kim

first: Christina

last: Morse

first: John

last: Sembrat

first: Eleanor

last: Valenzi

first: Robert

last: Lafyatis


title: TMEM232 is required for the formation of sperm flagellum and male fertility in mice

status: Public on Jun 06 2024

city: HeFei

first: hui

last: zhang

state: 请选择省份

address: No. 81 Meishan Road, Shushan District

department: college of life science

institute: anhui medical university

summary: Asthenoteratozoospermia is a major cause of male infertility. Thus far, the identified related genes can explain only a small share of asthenoteratozoospermia cases, suggesting the involvement of other genes. The transmembrane protein TMEM232 is highly expressed in mouse testes. In the present study, to determine its function of TMEM232 in testes, we constructed a Tmem232-null mouse model using CRISPR–Cas9 technology. Tmem232 knockout (KO) male mice was completely infertile, and their sperm were immotile, with morphological defects of the flagellum. Electron microscopy revealed an aberrant midpiece-principal junction and the loss of the fourth of nine doublet microtubules in the sperm of Tmem232-/-mice. Sperm cells presented an 8+2 conformation and an irregular arrangement of the mitochondrial sheath. Proteomic analysis indicated a downregulation in the expression of proteins associated with flagellar motility, sperm capacitation, and the integrity and stability of sperm structure, as well as an upregulation in the expression of multiple ribosome components in TMEM232-deficient spermatids. Additionally, TMEM232 was observed to be involved in ribophagy by interacting with autophagy-related proteins, such as ATG14 and ARMC3, to regulate ribosome homeostasis during spermiogenesis. These results suggest that TMEM232 is essential for normal sperm flagellum formation and plays an important role in the autophagic elimination of cytosolic ribosomes to provide energy for flagellar motility.

overall_design: To investigate the changes of gene expression in the mice testis after Tmem232 knockout, we collected testes from Tmem232-knockout and wild-type mice testis for transcriptome sequencing analysis

first: Hui

last: Zhang


title: Transcriptome sequencing of hippocampal tissue of APP/PS1 mice treated with rotating magnetic field for 12 months

first: Ruowen

last: Guo

state: Anhui

address: 350 Shushanhu Road

institute: Hefei institutes of physical science

summary: Amyloid beta (Aβ) monomers aggregate to form fibrils and amyloid plaques, which is one of the important mechanisms in the pathogenesis of Alzheimer's disease (AD). Since the Aβ1-42 aggregation has prominent role in plaque formation, which eventually lead to the patient's brain lesions and cognitive impairment, an increasing number of studies have been devoted to reduce Aβ aggregation process to slow down AD progression. Since the diphenylalanine (FF) sequence is critical for amyloid aggregation, and it has been shown that magnetic fields can affect the alignment of peptide assembly due to the diamagnetic anisotropy of aromatic rings, here we used a moderate-intensity rotating magnetic field (RMF) to explore its effect on Aβ aggregation and AD pathogenesis. Our data showed that RMF can directly inhibit Aβ amyloid fibril formation and reduce Aβ-induced cytotoxicity on neural cells in vitro. Using the AD mouse model APP/PS1, we found that the RMF can restore their motor ability to the healthy control level. Their cognitive impairments, including exploration ability, spatial and non-spatial memory abilities, were also significantly alleviated. Tissue examinations reveal that RMF has reduced amyloid plaque accumulation, attenuated microglial activation ,and reduced oxidative stress in the APP/PS1 mouse brain. Therefore, our data demonstrate the great potential of RMF to be developed as a non-invasive, high-penetration physical approach to be applied in the treatment of AD.

overall_design: APP/PS1 mice were divided into a sham magnetic exposure group and a rotating magnetic field group, and wild-type C57BL/6J mice of the same age were used as the control group. APP/PS1 mice were treated with a rotating magnetic field and sham magnetic exposure for 3 h to 6 h, 5 working days per week starting from 2 months of age (3 h/working days from 2 months to 11 months of age, 6 h/working days from 11 months to 14 months of age). After 12 months, total RNA was extracted from the hippocampal tissue of APP/PS1 mice, and transcriptome analysis was performed.


title: A new Nuclear-erythroid-2-Related Factor 2 activator for the treatment of human metabolic associated fatty liver disease

city: Clichy

first: Adel

last: Hammoutene

address: 100 Boulevard du Général Leclerc, Hôpital Beaujon, Secteur Jaune, Bât Abrami, Porte 4

department: Reasearch Center on Inflammation

institute: INSERM U1149

summary: Background and aims: Oxidative stress triggers nonalcoholic steatohepatitis (NASH) and fibrosis. Previous animal studies demonstrated that the transcription factor NRF2, the master regulator of antioxidant response, protects against NASH and fibrosis. S217879, a new generation NRF2 activator has been recently shown to trigger NASH resolution and to reduce established fibrosis in rodents. Our aim was to evaluate the therapeutic potential of S217879 in human metabolic associated fatty liver disease (MAFLD) and its underlying mechanisms using the relevant experimental 3D model of patient-derived precision cut liver slices (PCLS). Methods: We treated PCLS from 12 patients with MAFLD with S217879 or Elafibranor (PPARα/δ agonist used as a referent molecule) for two days. Safety and efficacy profiles, steatosis, liver injury, inflammation and fibrosis were assessed as well as mechanisms involved in NASH pathophysiology, namely antioxidant response, autophagy and ER-stress. Results: Neither Elafibranor nor S217879 had toxic effects at the tested concentrations on human PCLS with MAFLD. PPARα/δ and NRF2 target genes (PDK4, FGF21 and NQO1, HMOX1, respectively) were strongly upregulated in PCLS in response to Elafibranor and S217879, respectively. Compared to untreated PCLS, Elafibranor and S217879-treated slices displayed lower triglycerides and reduced inflammation (IL-1β, IL-6, CCL2). Additional inflammatory markers (CCL5, STING, ICAM-1, VCAM-1) were downregulated by S217879. S217879 but not Elafibranor lowered DNA damages (p-H2A.X, RAD51, XRCC1) and apoptosis (cleaved Caspase-3), and inhibited fibrogenesis markers expression (α-SMA, COL1A1, COL1A2). Such effects were mediated through an improvement of lipid metabolism, activated antioxidant response and enhanced autophagic flux, without effect on ER-stress. Conclusion: This study highlights the therapeutic potential of a new NRF2 activator for NASH using patient-derived PCLS supporting the evaluation of NRF2 activating strategies in clinical trials.

overall_design: We treated PCLS from 12 patients with MAFLD with S217879 or Elafibranor (PPARα/δ agonist used as a referent molecule) for two days. We then performed gene expression profiling analysis using data obtained from RNA-seq

first: Samira

last: Laouirem

first: Miguel

last: Albuquerque

first: Nathalie

last: Colnot

first: Angélique

last: Brzustowski

first: Dominique

last: Valla

first: Nicolas

last: Provost

first: Philippe

last: Delerive

first: Valérie

last: Paradis


title: Progressive meristem and single-cell transcriptomes reveal the regulatory mechanisms underlying maize inflorescence development and sex differentiation

city: Wuhan

first: liang

last: dong

address: No.1,Shizishan Street

institute: Huazhong Agricultural University

summary: Maize develops separate ear and tassel inflorescences with initially similar morphology but finally different architecture and sexuality. The detailed regulatory mechanisms underlying these changes still remain largely clear. In this study, through analyzing the time-course meristem transcriptomes and floret single-cell transcriptomes of ear and tassel we revealed the regulatory dynamics and pathways underlying inflorescence development and sex differentiation. Our study provides a deep understanding of the regulatory mechanisms underlying inflorescence development and sex differentiation in maize, laying the foundation to identify new regulators and pathways for maize hybrid breeding and improvement.

overall_design: To comprehensively reveal the regulatory dynamics underlying maize inflorescence differentiation and sex determination, we generated the time-course inflorescence meristems transcriptome by bulk RNA-seq and florets single-cell transcriptome by scRNA-seq.The meristem types include IM, SPM, SM, FM-stage1 (FM-S1), FM-S2 and FM-S3 in ear and tassel. FM-S2 and FM-S3 from ear and tassel were used for scRNA-seq. Next, to construct regulatory network of sex determination, we also generated the bulk RNA-seq data of ts1 and sk1 mutant and their WT using tassel or ear at early floret stage.

first: Yonghao

last: Sun

first: Liang

last: Dong

first: Lu

last: Kang

first: Fang

last: Yang


title: Transcriptomic analysis of subarachnoid cysts of Taenia solium reveals mechanisms for uncontrolled proliferation and adaptations to the microenvironment

city: Poznan

first: Michał

last: Szcześniak

address: Uniwersytetu Poznanskiego 6

department: Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

summary: Subarachnoid neurocysticercosis (SANCC) is caused by an abnormally transformed form of the metacestode or larval form of the tapewormTaenia solium. In contrast to vesicular parenchymal and ventricular located cysts that contain a viable scolex and are anlage of the adult tapeworm, the subarachnoid cyst proliferates to form aberrant membranous cystic masses within the subarachnoid spaces that cause mass effects and acute and chronic arachnoiditis. How subarachnoid cyst proliferates and interacts with the human host is poorly understood, but parasite stem cells (germinative cells) likely participate. RNA-seq analysis of the subarachnoid cyst bladder wall compared to the bladder wall and scolex of the vesicular cyst revealed that the subarachnoid form exhibits activation of signaling pathways that promote proliferation and increased lipid metabolism. These adaptions allow growth in a nutrient-limited cerebral spinal fluid. In addition, we identified therapeutic drug targets that would inhibit growth of the parasite, potentially increase effectiveness of treatment, and shorten its duration.

overall_design: Gene expression was calculated for three replicates of racemose cysts, vesicular cycts and scolex. This was followed by differential gene expression analysis.

last: Orrego

first: Michal

middle: W

last: Szczesniak

first: Carlos

middle: M

last: Vasquez

first: Manuela

last: Verastegui

first: Javier

last: Bustos

first: Hector

middle: H

last: García

first: Theodore

middle: E

last: Nash


title: Genome-wide mapping of H3K9me2 in DOT1L-deficient worms.

first: Ruben

last: Esse

summary: Histone modification marks such as H3K4me1 and H3K27ac have been used to map putative enhancers, but these marks represent only a fraction of the full repertoire of histone modifications decorating these regulatory regions. In mammals, methylation of histone H3 on lysine 79 (H3K79me), deposited by the methyltransferase DOT1L, is present at enhancers. In C. elegans, putative enhancers have been predicted based on chromatin modifications and regions of chromatin accessibility. Our own overlap analysis has revealed that both DOT-1.1, the C. elegans DOT1L homologue, and its major interacting partner, the chromatin-binding factor ZFP-1 (AF10 in mammals), are enriched at both distal and intragenic enhancers. Previous work has shown that Dot1 proteins prevent encroachment of heterochromatin to actively transcribed regions in yeast and in MLL-rearranged leukemias. Here we find that, in C. elegans, loss of DOT-1.1 is accompanied by ectopic H3K9me2, a hallmark of heterochromatin, at distal and intragenic enhancers. This observation suggests a new role for DOT1L in the control of heterochromatin formation at enhancers, which may partake on the control of developmentally regulated genes.

overall_design: Profiling of H3K9me2 in ced-3 and dot-1.1; ced-3 mutant third larval (L3) stage Caenorhabditis elegans.

first: Rube

first: Alla

last: Grishok


title: Epigenetic imprinting of H3K4me3 in adipose-derived stem cells by HFS diet consumption leads to a disturbed transcriptomic profile in adipocytes [ChIP-seq]

city: Mexico City

first: Armando

middle: Roberto

last: Tovar Palacio

state: México City

address: Belisario Dominguez 15

country: Mexico

institute: Instituto Nacional de Ciencias Médicas y Nutrición

summary: Adipose tissue metabolism is actively involved in the regulation of energy balance. Adipose-derived stem cells (ASCs) play a critical role in maintaining adipose tissue function through their differentiation into mature adipocytes. The aim of this study was to investigate the effect of an obesogenic environment on the epigenetic landscape of ASCs and its impact on adipocyte differentiation and its metabolic consequences. Our results showed that ASCs from mice fed a high-fat sucrose (HFS) diet exhibited reduced adipogenic capacity, increased fat accumulation, and formed larger adipocytes than those from the control group (C). The results showed that ASCs from mice fed the HFS diet had reduced adipogenic capacity. Mitochondrial analysis showed increased mitochondrial activity in undifferentiated ASC-HFS, but decreased respiratory and glycolytic capacity in mature adipocytes. The HFS diet significantly altered the H3K4me3 acetylation profile of ASCs in genes related to adipogenesis, mitochondrial function, inflammatory response and immunomodulation. After differentiation, adipocytes retained H3K4me3 alterations in genes related to inflammatory response and immunomodulation. RNA-seq confirmed the upregulation of genes associated with inflammatory and immunomodulatory pathways in adipocytes. This study demonstrates that HFS diet induces profound epigenetic and transcriptomic changes in ASCs, leading to impaired differentiation and dysfunctional adipocyte formation.

overall_design:
To investigate whether the development of obesity is associated with epigenetic modifications in adipocyte precursors, potentially leading to the generation of functionally altered adipocytes, we conducted a study in Wistar rats fed either a control (C) diet or a high-fat sucrose (HFS) diet for 6 months
Adipocyte precursors (ASCs) from both goups were isolated and differentiated into adipocytes (Ad). RNA-seq and ChIP-seq (H3K4me3) assays were conducted
Comparative gene expression profiling analysis of RNA-seq data for ASC-HFS vs ASC-C, and AD-HFS vs C group were performed

last: Tovar

first: Adriana

middle: B

last: Pérez-Jiménez

first: Iván

last: Torre-Villalvazo

first: Martí

last: Wilson-Verdugo

first: Dana

last: Lau-Corona

first: Erick

last: Muciño-Olmos

first: Diana

last: Coutiño-Hernández

first: Lilia

last: Noriega-López

first: Osbaldo

last: Resendiz-Antonio

first: Víctor

last: Valdés-Rodríguez

first: Nimbe

last: Torres


title: Deep Learning-based Pathway-Centric approach to characterize Recurrent Hepatocellular Carcinoma after Liver Transplantation

city: Toronto

first: Mamatha

last: Bhat

address: 101 college street

country: Canada

institute: University Health Network

summary: This study analyzed the clonal evolution at the transcriptomic level during the recurrence of hepatocellular carcinoma (HCC) after liver transplantation, utilizing a rare collection of primary and recurrent tumors.

overall_design: The study included patients who underwent liver transplantation for HCC, and paired tumor formalin-fixed paraffin-embedded (FFPE) samples were collected from the seven patients at both the initial resection and recurrence. Total RNA was extracted for gene expression analysis using the NanoString nCounter Tumor Signaling 360 Panel.

first: Jeffrey

last: To

first: Soumita

last: Ghosh

first: Xun

last: Zhao

first: Elisa

last: Pasini

first: Sandra

last: Fischer

first: Gonzalo

last: Sapisochin

first: Anand

last: Ghanekar

first: Elmar

last: Jaeckel


title: Effect of depletion of C10orf71 on gene expression in hearts from embryonic mice at E18.5 and adult mice

city: Beijing

first: Yang

last: Li

address: Anzhen Road, Chaoyang District

institute: Beijing Anzhen Hospital

summary: To explore the specific functional and cellular processes that affected by the mC10orf71 deletion, we compared total RNA expression in hearts from E18.5. Gene Ontology (GO) enrichment analysis showed that down-regulated genes were not significantly enriched in any biological process. The 327 genes up-regulated in KO mice were enriched for energy generation, electron transport chain and ATP synthesis, and many of them are encoded by mitochondrial DNA. These changes were likely to be a compensatory response to the impaired morphogenesis and dysfunction of the KO hearts. Then, we performed RNA-seq on hearts of adult WT and KO mice.  GO analysis of down-regulated genes identified two categories of biological processes: mRNA processing/splicing and muscle cell differentiation/contraction.

overall_design: We performed gene expression analysis using data obtained from RNA-seq of 4 WT mice and 4 KO mice at two time points

first: Yulin


title: A screening study identified decitabine as an inhibitor of Equid Herpesvirus 4 that enhances the innate antiviral response

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

summary: Equid herpesvirus 4 (EHV-4) is a frequent respiratory pathogen of the horse. EHV-4 sporadically induces abortion or neonatal death and although not clearly demonstrated its involvement in neurological forms is strongly suspected. Despite preventive treatments using vaccines against EHV-1/EHV-4, the resurgence of α-EHV infection still constitutes an important threat to the horse industry. Yet very few studies have been conducted on the search for antiviral molecules against EHV-4. A screening of 42 antiviral compounds was performed in vitro on E. Derm cells infected with EHV-4 405/76 reference strain (VR2230). Formation of cytopathic effects was monitored by Real-Time Cell Analysis (RTCA) and the viral load was quantified by qPCR. Aciclovir, the most widely used antiviral in vivo against alpha-herpesviruses, does not appear to be effective against EHV-4 in vitro. Potential antiviral activities were confirmed for 8 molecules (idoxuridine, vidarabine, pritelivir, cidofovir, valganciclovir, ganciclovir, aphidicolin, and decitabine). Decitabine is the most potent compound against EHV-4 in vitro.  A transcriptomic analysis revealed an increase of expression of different genes implicated in IFN response. Decitabine (DTB) seems to activate the immune antiviral pathway.

overall_design: Comparison of gene expression in dermal horse cells after 18 hours for cells infected or not with EHV-4 virus and/or treated with decitabine

first: Camille

last: Normand

first: Christine

last: Fortier

first: Côme

last: Thieulent

first: Gabrielle

last: Sutton

first: Catherine

last: Senamaud-Beaufort

first: Laurent

last: Jourdren

first: Corinne

last: Blugeon

first: Pierre-Olivier

last: Vidalain

first: Stéphane

last: Pronost

first: Erika

last: Hue


title: RNA transcriptome sequencing of human ear chondrocytes

city: Shanghai

first: xu

last: wu

address: 83 Fenyang Road

institute: EENT Hospital, Fudan University

summary: In order to elucidate the key genes influencing chondrocyte differentiation in monolayer culture, we conducted RNA sequencing on native chondrocytes, differentiated chondrocytes, and redifferentiated chondrocytes.

overall_design: 15 samples of human ear chondrocytes: 5 native groups,5 dedifferentiated groups and 5 re-differentiated groups

first: Xu

last: Wu

first: Aijuan

last: He

first: Tianyu

last: Zhang


title: Epigenetic imprinting of H3K4me3 in adipose-derived stem cells by HFS diet consumption leads to a disturbed transcriptomic profile in adipocytes [RNA-seq]

first: Armando

last: Tovar Palacio

last: Tovar

first: Adriana

last: Pérez-Jiménez

first: Iván

last: Torre-Villalvazo

first: Martí

last: Wilson-Verdugo

first: Dana

last: Lau-Corona

first: Erick

last: Muciño-Olmos

first: Diana

last: Coutiño-Hernández

first: Lilia

last: Noriega-López

first: Osbaldo

last: Resendiz-Antonio

first: Víctor

last: Valdés-Rodríguez

first: Nimbe

last: Torres


title: Splicing changes in gastrocnemius muscle from 3-month-old HSALR mice

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: The initial aim of the study was to determine the mechanisms underlying the positive effect of AICAR on the phenotype of HSALR mice, a well-known model for DM1. We have previously shown that treatment with AICAR reduces myotonia and mis-splicing in the HSALR mice. We here aimed to identify splicing and transcriptional changes in gastrocnemius muscle from HSALR mice treated or not with AICAR, as compared to FVB control mice. The data obtained from untreated mice were then used in the study focused on NMJ alterations and CaMKII deregulation in DM1.

overall_design: Gastrocnemius muscle from 3-month-old mice. HSALR mice (n= 5 per group); FVB control mice (n=3 per group). Treatment = vehicle or AICAR

first: Jochen

last: Kinter

first: Perrine

last: Castets

first: Robert

last: Ivanek

first: Michael

last: Sinnreich


title: A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis

first: Shuchang

last: Liu

address: 203 Lothrop Street

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

overall_design: Refer to individual Series


title: Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells

status: Public on Jun 05 2024

city: Stanford

middle: Charles

last: Lanz

address: 327 Campus Dr.

department: Biology

institute: Stanford University

summary: Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how cell size influences physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be compositionally different. Here, we utilize the natural heterogeneity of hepatocyte ploidy and yeast genetics to establish that ploidy-to-cell size ratio is a highly conserved determinant of proteome composition. In both mammalian and yeast cells, genome dilution by cell growth elicits a starvation-like phenotype, suggesting that growth in large cells is restricted by genome concentration in manner that mimics a limiting nutrient. Moreover, genome dilution explains some proteomic changes ascribed to yeast aging. Overall, our data indicate that genome concentration drives changes in cell composition independently of external environmental cues.

overall_design: 6 samples submitted. mRNA sequencing files for yeast populations of three different mean sizes (in duplicate)


title: Shared and unique transcriptomic signatures of antidepressant and probiotics action in the mammalian brain

city: Singapore

first: Nirmala

last: Arul Rayan

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary: To comprehensively characterize the intrinsic molecular effects of ADs independently of the specifics of particular disease models, we generated 300 transcriptomic profiles from 10 brain regions in naïve rats. Three classical tricyclic antidepressants as Bupropion, desipramine, fluoxetine and a probiotic formulation (Lacidofil®) massively altered gene expression in most regions [>1,500 differentially expressed genes (DEGs)], suggesting that traditional single-gene or single-pathway analyses may under-represent the complexity of molecular responses.

overall_design: To complement our multi-regional epigenome and transcriptome map of chronic fluoxetine action (Rayan et al. Mol Psychiatry (2022). https://doi.org/10.1038/s41380-022-01725-1), we used bulk RNA-seq to profile the Bupropion-, Desipramine-, Fluoxetine-, Maltodextrin- and Probiotic-  induced genome-wide transcriptome changes (post 3 week treatment) in 10 brain regions. Here we deposit these RNA-seq profiles (10 regions, 6 treatment groups, 5 replicates; 10*6*5= 300 profiles). To reduce the effects of inter-animal biological variation, each RNA-seq sample was pooled from 2 animals (60 animals in total).

last: Rayan

first: Michelle

last: Lim

first: Jonathan

last: Aow

first: Shyam

last: Prabhakar

last: Meaney


title: scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular players in heart rhythm regulation

city: Warsaw

first: Karim

last: Abu Nahia

address: Księcia Trojdena 4

institute: IIMCB Warsaw

summary: We utilized scRNA-seq to delineate the diversity of cell types in the zebrafish heart. Transcriptome profiling of over 50,000 cells at 48 and 72 hpf defined at least 18 discrete cell lineages of the developing heart. Utilizing well-established gene signatures, we identified a population of cells likely to be the primary pacemaker and characterized the transcriptome profile defining this critical cell type. Two previously uncharacterized genes, atp1b3b and colec10, were found to be enriched in the sinoatrial cardiomyocytes. CRISPR/Cas9-mediated knockout of these two genes significantly reduced heart rate, implicating their role in cardiac development and conduction. Additionally, we describe other cardiac cell lineages, including the endothelial and neural cells, providing their expression profiles as a resource. Our results established a detailed atlas of the developing heart, providing valuable insights into cellular and molecular mechanisms, and pinpointed potential new players in heart rhythm regulation.

overall_design: Whole hearts were extracted from double transgenic individuals [sqet31Et x Tg(myl7:mRFP) and sqet33mi59BEt x Tg(myl7:mRFP)]. The term “pseudo-replicates” was used to denote samples of two different genotypic backgrounds (sqet31Et and sqet33mi59BEt) at the same developmental stage (in total 4 samples, 2 per each developmental stage). Embryos were anesthetized with Tricaine (0.16 mg/ml in egg water) and large-scale extraction was performed according to a previously published protocol, with minor adjustments. Hearts were manually separated from the remaining tissue under a fluorescence stereomicroscope and collected into 0,5 ml of EDM (L-15/10% FBS). Single-cell heart suspension was obtained according to Bresciani et al. Ultimately, cells were resuspended by gentle pipetting, loaded on the cell counting chamber, visually inspected under the microscope (Zeiss Apotome), and quantified by Countess automated cell counter (Invitrogen). After viability and quantity check, dissociated cells derived from embryonic zebrafish hearts at 48 hpf and 72 hpf were loaded on 10x Chromium Controller Chip G (10x Genomics) and processed according to the Chromium Next GEM Single Cell 3’ Reagent Kits v.3.1. Final libraries were sequenced (read 1 - 28 cycles, i7 index - 8 cycles, i5 index - 0 cycles,  read 2 - 91 cycles) on Nextseq 500 (Illumina).

first: Cecilia

middle: L

last: Winata


title: AGO2 silences mobile transposons in the nucleus of quiescent cells [RIP-seq]

city: Bethesda

first: Joana

last: Vidigal

state: MD

address: 37 Convent Dr, Room 6056

department: LBMB

institute: NIH/NCI

summary: Argonaute 2 (AGO2) is a cytoplasmic component of the miRNA pathway with essential roles in development and disease. Yet, little is known about its regulation in vivo. Here, we show that in mouse quiescent cells, AGO2 localizes almost exclusively to the nucleus. In quiescent splenocytes, AGO2’s subcellular localization is modulated by the Pi3K-AKT-mTOR pathway, a well-established regulator of quiescence. Signaling through this pathway in proliferating cells promotes AGO2 cytoplasmic accumulation at least in part by stimulating the expression of TNRC6, an AGO2 binding partner in the miRNA pathway. In contrast, low signaling in quiescent cells enables AGO2 to accumulate in the nucleus where it binds to young mobile transposons co-transcriptionally. Loss of AGO2 in quiescent cells results in upregulation of transposon transcripts suggesting it performs functions analogous to those of PIWI in the germline. Our results point to an essential but previously unrecognized nuclear role for AGO2 during mammalian quiescence as part of a genome-defense system against transposable elements.

overall_design: small RNA sequencing following immunopercipitation of AGO2 using an antibody against the HA epitope in Ago2HA/HA mice.

first: Manish

last: Kumar


title: A vagal-brainstem interoceptive circuit for cough-like defensive behaviors in mice

city: Ann Arbor

first: YING

last: CAO

state: Michigan

address: 615 N Main St

institute: university of michigan

summary: Respiratory defensive behaviors, like coughing, play a crucial role in protecting the respiratory system, ensuring its integrity and optimal function. How these critical behaviors are regulated by sensory stimuli within the body remains largely unknown. Here, we show that the nucleus of the solitary tract (NTS) in mice, a key hub in the brain for processing internal sensory signals and mediating interoceptive processes, contains heterogenous neuronal populations that differentially control breathing. Within these subtypes, activation of tachykinin 1 (Tac1) neurons triggers a specific respiratory behavior. Our detailed characterization of respiratory defensive behaviors reveals that these responses are cough-like behaviors. Chemogenetic silencing or genetic ablation of Tac1 neurons significantly reduces cough-like behaviors induced by tussive challenges. These Tac1 neurons receive synaptic inputs from the bronchopulmonary chemosensory and mechanosensory neurons in the vagal ganglion, and directly integrate the medullary regions to control sequential phases of cough-like defensive behaviors. We propose that these Tac1 neurons are a key component of the airway-vagal-brain neural circuit that controls cough-like defensive behaviors in mice, and they coordinate the downstream modular circuits to elicit the sequential motor pattern of forceful expiratory responses.

overall_design: Five mice at postnatal day 5 were euthanized by isoflurane inhalation followed by  decapitation. The brain was isolated and embedded in 4% agarose II in artificial cerebrospinal  fluid (ACSF) and sectioned at 200um thickness on a VT 1000S vibratome (Leica). The caudal  NTS tissue and adjacent regions in the dorsal vagal complex were manually dissected based on  the morphology (the relative position to area postrema, 4th ventricle, and central canal), and  referred as the NTS. Tissue was pulled together in hibernate A solution (Gibco), followed by  digestion with 20 u/ml papain (Worthington Biochemical Corporation) and serial trituration by  Pasteur pipets to generate single cell suspension. The cells were stained with 0.2% DyeCycle  Ruby (Invitrogen) at 37 degree for 15 minutes before passing through a 70um cell strainer  (Falcon). The live cell suspensions were sorted and collected by a BD FACSAria III Cell Sorter  (BD Biosciences) with a nozzle diameter of 100 um. The FACS sample was loaded to the 10X  Chromium platform for capturing. The following cDNA synthesis with PCR and library  preparation were done according to the manufacturer’s protocol. Sequencing was performed on a NovaSeq sequencer (Illumina)

first: Noam

last: Gannot

first: Xingyu

last: Li

first: Chrystian

middle: D

last: Phillips

first: Ayse

last: Ozel

first: Karin

last: Koecklin

first: John

middle: P

last: Lloyd

first: Lusi

last: Zhang

first: Katie

last: Emery

first: Tomer

last: Stern

first: Jun

middle: Z

first: Peng


first: Nirmala

last: Arul Rayan

summary: To comprehensively characterize the intrinsic molecular effects of ADs independently of the specifics of particular disease models, we generated 300 transcriptomic profiles from 10 brain regions in naive rats. Three classical tricyclic antidepressants, Bupropion, desipramine, fluoxetine, and a probiotic formulation (Lacidofil®) can massively alter gene expression in most regions [>1,500 differentially expressed genes (DEGs)], suggesting that traditional single-gene or single-pathway analyses may under-represent the complexity of molecular responses. Using spatial transcriptomics in the prefrontal cortex from an independent set of animals, we further delineated DEGs and molecular pathways that exhibited layer-specific differential regulation by probiotics and fluoxetine.

overall_design: To complement our multi-regional epigenome and transcriptome map of chronic fluoxetine action (Rayan et al. Mol Psychiatry (2022). https://doi.org/10.1038/s41380-022-01725-1), we used bulk RNA-seq to profile the Bupropion-, Desipramine-, Fluoxetine-, Maltodextrin- and Probiotic-  induced genome-wide transcriptome changes (post 3 week treatment) in 10 brain regions. Here we deposit these RNA-seq profiles (10 regions, 6 treatment groups, 5 replicates; 10*6*5= 300 profiles, GSE222756). To reduce the effects of inter-animal biological variation, each RNA-seq sample was pooled from 2 animals (60 animals in total). We complemented the bulk RNA-seq with 10x Visium spatial omics assay, focusing on the ILC and PLC. Although these two adjacent brain regions are often studied as a whole, they showed distinct treatment responses in our analyses. We treated an independent cohort of rats with FT (n=4) vs Sham (n=4), Pro (n=4) vs Mal (n=2). We then extracted cortical slices and generated 10x Genomics Visium spatial transcriptomics profiles comprising ~33,000 spatially localized spots, with a median of 2,100 detected genes per spot.

first: Michelle

last: Lim

first: Jonathan

last: Aow

first: Shyam

first: Michael


title: PanethcellTNF-signalinginducesbacterialsepsis: transcriptome of intestinal epithelial cells 8h after TNF

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: Paneth Cells (PCs) are secretory cells located in the crypts of Lieberkühn of the small intestine. They produce antimicrobial peptides (AMPs) and are thought to keep the microbiome under control. The cytokine TNF, which functions mainly via its TNF receptor 1 (TNFR1 or P55), is a driving force in many inflammatory bowel disease (IBD) patients, but its impact on PCs is poorly known. We have generated PC-specific P55 knockout mice (P55Paneth KO) and found that these mice are protected against lethal TNF-induced systemic inflammatory response syndrome (SIRS). The impact of TNF on PCs is characterized by morphological changes and by intestinal bacterial translocation into organs, such as liver, in which these bacteria induce expression of numerous genes, associated with typical sepsis signatures. The presence of these bacteria cause lethality of the mice. Based on bulk RNA-SEQ on pure PCs, P55 signaling stimulated mainly a type-I IFN response in the PCs, which drives the bacterial translocation and lethality via IFNAR1. Interestingly, based on ER stress reporter mice, PCs constitutively have high amounts of spliced XBP1 (XBP1s) protein, presumably to support their secretion of AMPs, and TNF eradicates this XBP1s production, leading to failure of the unfolded protein response (UPR). This causes reduced antimicrobial activity in PCs, in a P55 and IFNAR1-dependent way. Our data suggest a novel axis induced by TNF in PCs, leading to interferon-induced UPR failure causing lethal bacterial translocation to the liver (and other organs)

overall_design: To investigate the effect of TNF on the intestinal epithelial cells (IEC) transcriptome, cells  were isolated 8h after TNF or PBS (control) injection in mice that were given normal dinking water of water with 25mM ZnSO4. 2 PBS and 4 TNF samples were taken for RNA isolation and sequencing from each of the water and zinc groups.

first: Charlotte

last: Wallaeys

first: Natalia

last: Garcia-Gonzalez

first: Jolien

last: Vandewalle

first: Tineke

last: Vanderhaeghen

first: Hester

last: Dufoor

first: Melanie

last: Eggermont

first: Riet

last: De Rycke

first: Serge

last: Verbanck

first: George

last: Kollias

last: Souffriau

first: Richard

middle: S

last: Blumberg

first: Takao

last: Iwawaki

first: Claude

last: Libert


title: Single-cell Transcriptomes and Follicular Fluid Proteomics of Ovine Atretic Follicles Reveal the Underlying Mechanisms of Oocyte Degeneration

city: Hohhot

first: Song

last: Yukun

state: Inner Mongolia

address: Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction

institute: Inner Mongolia Agricultural University

summary: Background: In mammals, female fertility is determined by the outcome of follicular development (ovulation or atresia). Follicular atresia is a complex physiological process that results in the degeneration of oocytes from the ovary. However, the molecular mechanisms of oocyte degeneration and key protein markers of follicular atresia remain unclear. In this study, we explored the complex transcriptional regulatory mechanisms and protein profiles in oocytes and follicular fluid in atretic follicle stages using single-cell RNA sequencing and tandem mass tag proteomics.  Results: First, through paired analysis of different follicle development stages, we identified 175 atresia-specific genes and eight candidate oocyte-secreted factors, including PKG1, YTHDF2, and MYC. Meanwhile, we also characterized unique features of the oocyte transcriptional landscape in the atretic follicle stage that displayed cell death-related transcriptional changes and mechanisms, such as autophagy (TBK1 and IRS4), necroptosis (PKR), and apoptosis (MARCKS). Moreover, we identified atresia-specific genes, namely FTH1, TF, and ACSL4, which may participate in regulation of oocyte ferroptosis in atretic follicles through a series of mechanisms including ferritinophagy, ferritin transport, and lipid metabolism. Additionally, we uncovered 333 differentially expressed proteins that may coordinate follicular atresia and revealed key pathways, such as negative regulation of angiogenesis, metabolic pathways, and transcription and mRNA splicing, that lead to oocyte degeneration. Finally, by combining transcriptome and proteomics analyses, we identified two oocyte-secreted biomarkers, PGK1 and ANGPT2, that may be associated with follicular atresia.  Conclusions: In conclusion, our work provides a comprehensive characterization of oocyte degeneration in ovine atretic follicles, which provides a basis for establishing an oocyte quality evaluation system and understanding the mechanism of follicular atresia in sheep, as well as an important reference for in vitro production of embryos.

overall_design: Understanding the degradation process that occurs in oocytes in atretic follicles is not only an important biological topic but also crucial from an assisted reproductive technology perspective. In this study, we integrated a Smart-seq2 survey of oocytes within atretic follicles and their FF proteomic profiles to generate a multi-omics atlas of atresia-related oocyte alterations and molecular mechanisms at the ovine antral follicular stage, focusing on identifying candidate biomarkers associated with follicular atresia.


title: Chromatin structure and gene expression signatures in FUS low and high expressed hematopoietic stem cells

city: Tianjin

first: Jianwei

last: Wang

address: 10 Yuexin Street, Binhai New Area

institute: HAIHE LABORATORY OF CELL ECOSYSTEM

summary: Aged hematopoietic stem cells (HSCs) exhibit compromised reconstitution capacity. In this study, we observed that the expression of FUS is increased in aged HSCs. We aimed to analysis the changes of chromatin structure  and  gene expression signatures in FUS low and FUS high  expressed hematopoietic stem cell (lineage-, c-kit+ Sca-1+ CD34-) using tagHi-C and RNA-seq .We also conducted  CTCF CUT&RUN experiment in Young(2 months) and Aged(30 months) hematopoietic stem cell (lineage-, c-kit+ Sca-1+ CD34-)  to analysis  CTCF signal changes. These hematopoietic stem cell (HSC) were purified from the bone marrow of mice with fus-gtp or different ages. Results provide insight how aberrant FUS mobility effects chromatin structure and promotes HSC aging .

overall_design: We compare chromatin structure  and gene expression signatures using Hi-C, RNA-seq, CTCF CUT&RUN in Fus low, Fus high, Aged, Young HSCs from the bone marrow of mice.


title: SNP arrays in colorectal adenocarcinoma cell lines

city: Catania

first: Daniele

middle: F

last: Condorelli

state: Italy

address: Via S. Sofia 64

department: Biomedical and Biotechnological Sciences

country: Italy

institute: University of Catania

overall_design: We analyzed, by last-generation high-resolution SNP-array, Caco2, HCT-116 and HT-29 colorectal adenocarcinoma cell lines in order  to determine the number of copy number abnormalities (CNAs) and copy neutral-loss of heterozygosity (CN-LOH) regions. CACO-2 and HT-29 cell lines showed a strong aneuploid karyotype; HCT-116 cell line is characterized by a near diploid karyotype.

first: Barresi

last: Vincenza


title: Single-cell analyses offer insights into the different remodeling programs of arteries and veins (scRNA-Seq)

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: We compared 3 non-diseased human arteries (brachial) and 3 veins (2 basilic, 1 cephalic) by single cell RNA sequencing and histology.

overall_design: Vessels were collected in cold cell culture media and enzymatically digested to generate single-cell suspensions. Samples were run using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10X Genomics) with a target capture of 10,000 cells or as indicated otherwise. Libraries were sequenced on the Illumina NovaSeq 6000. FASTQ files were generated with Cell Ranger's mkfastq pipeline (version 6.0.2). The Cell Ranger's count pipeline (version 6.0.2) was used to generate raw gene-barcode matrices from alignment to the 10X Genomics pre-built Cell Ranger human reference package (version 2020-A), from GRCh38 Ensembl build 98/GENCODE v32 gene annotations.

first: Laisel

last: Martinez

first: Roberto

middle: I

last: Vazquez-Padron

middle: J


title: Single-cell analyses offer insights into the different remodeling programs of arteries and veins


title: Spatiotemporal Control of InflammatoryLytic Cell Death Through Optogenetic Induction of RIPK3 Oligomerization

city: Urbana

first: Kai

last: Zhang

state: IL

address: 600 South Mathews Avenue

department: Biochemistry

institute: University of Illinois at Urbana-Champaign

summary: Necroptosis is a programmed lytic cell death involving active cytokine production and plasma membrane rupture through distinct signaling cascades. However, it remains challenging to delineate this inflammatory cell death pathway at specific signaling nodes with spatiotemporal accuracy. To address this challenge, we developed an optogenetic system, termed Light-activatable Receptor-Interacting Protein Kinase 3 or La-RIPK3, to enable ligand-free, optical induction of RIPK3 oligomerization. La-RIPK3 activation dissects RIPK3-centric lytic cell death through the induction of RIPK3-containing necrosome, which mediates cytokine production and plasma membrane rupture. Bulk RNA-Seq analysis reveals that RIPK3 oligomerization results in partially overlapped gene expression compared to pharmacological induction of necroptosis. However, La-RIPK3 activates a group of genes likely regulated by RIPK3 kinase-independent processes. Using patterned light stimulation delivered by a spatial light modulator, we demonstrate precise spatiotemporal control of necroptosis in La-RIPK3-transduced HT-29 cells. Optogenetic control of proinflammatory lytic cell death could lead to the development of innovative experimental strategies to finetune the immune landscape for disease intervention.

overall_design: To gain insights into RIPK3 mediated gene expression, we performed a transcriptomic analysis to identify differentially expressed genes (DEGs) in HT-29 cells. Cells were freshly transduced with the corresponding lentivirus before sample preparation for RNA-seq. DEG analysis focus on the following comparisions: La-RIPK3 light vs. La-RIPK3 dark; La-RIPK light vs. La-RIPK3 light+RIPK3 kinase inhibitor. Controls including non-transduced HT29 cells under light and dark treatment.

first: Teak-Jung

last: Oh


title: Granulocyte dynamics: A key player in the immune priming effects of crickets

city: Chuncheon-si

first: Saeyoull

last: Cho

address: 1, Kangwondaehak-gil

country: South Korea

institute: Kangwon Univ.

summary: This study investigates immune priming effects associated with granulocytes in crickets through a comprehensive analysis. Kaplan-Meier survival analysis reveals a significant contrast in survival rates, with the heat-killed Bacillus thuringiensis (Bt)-primed group (B-1) exhibiting an impressive ~80% survival rate compared to the PBS buffer-primed group (A-1) with only ~10% survival 60 hours post live Bt infection. Hemocyte analysis underscores elevated hemocyte counts, particularly in granulocytes of the B-1 group, suggesting a correlation between heat-killed Bt priming and heightened immune activation. Microscopy techniques further explore granulocyte morphology, unveiling distinctive immune responses in the B-1 group characterized by prolonged immune activation, heightened granulocyte activity, phagocytosis, and extracellular trap formation, contributing to enhanced survival rates. In particular, after 24 hours of injecting live Bt, most granulocytes in the A-1 group exhibited ETosis (death with release of extracellular traps), while in the B-1 group, the majority of granulocytes were observed to maintain highly activated extracellular traps, sustaining the immune response. Gene expression analysis supports these findings, revealing differential regulation of immune-related genes such as antibacterial humoral response, detection of bacterial lipopeptides, and cellular response to bacteria lipopeptides. Additionally, groups A (preinjected with heat-killed Bt), B (preinjected with heat-killed E. coli), and C (preinjected with PBS) were re- injected with live Bt and evaluated for survival rates over two- and nine-day intervals. Two days later, only group C displayed low survival rates. After injecting live Bt 9 days later, group B surprisingly showed a similarly low survival rate, while group A exhibited a high survival rate of ~60% after 60 hours, with actively moving and healthy crickets. In conclusion, this research provides valuable insights into both short-term and long-term immune priming effects in crickets, contributing to our understanding of invertebrate immunity with potential applications in public health.

overall_design: We divided 1,800 crickets into 8 groups and conducted the experiments with 75 crickets per group, 3 repetitions (8ⅹ75ⅹ3=1,800 crickets). In this study, immune priming was induced using two groups, A and B. PBS buffer and heat-killed Bacillus thuringiensis (Bt) were utilized for this purpose, resulting in the induction of immune priming. Two days later, live Bt was injected again to create groups A-1 and B-1. Subsequently, the immune priming effect was assessed by examining survival rates, the immune activation of granulocytes, and conducting RNA-Seq analysis for both the A-1 and B-1 groups. Next, group C, D, and E was the first injection of PBS (control), heat-killed E. coli, and heat-killed Bt. After 2 days, live Bt was injected into all groups and they were named group C-1, D-1, and E-1. 9 days after the first injection, we injected live Bt into group C, D, and E (called C-2, D-2, and E-2).

first: Youngwoo


title: Neurocellular Endoplasmic Reticulum Stress Response in Alzheimer's Disease and Related Dementias (ADRD) Risk

city: McAllen

first: Satish

last: Kumar

state: Texas

address: 5300 North L Street (MBMRF-2.219)

department: Division of Human Genetics & South Texas Diabetes and Obesity Institute, UTRGV School of Medicine

institute: University of Texas Rio Grande Valley

summary: Currently, more than 55 million people around the world suffer from dementia, and Alzheimer's disease-related dementia (ADRD) accounts for nearly 60-70% of all those cases. The spread of AD pathology and progressive neurodegeneration in the hippocampus and cerebral cortex is strongly correlated with cognitive decline in AD patients; however, the molecular underpinning of the ADRD causality is still unclear. Studies of postmortem AD brains and animal models of AD suggest that elevated endoplasmic reticulum (ER) stress may have a role in ADRD pathology through altered neurocellular homeostasis in brain regions associated with learning and memory. To study the ER stress-associated neurocellular response and its effects on neurocellular homeostasis and neurogenesis, we modeled an ER stress challenge using Thapsigargin (TG), a specific inhibitor of sarco/endoplasmic reticulum Ca2+ ATPase (SERCA), in induced pluripotent stem cell (iPSC)-derived neural stem cells (NSCs) of two individuals from our Mexican American Family Study (MAFS). High-content screening and transcriptomic analysis of the control and ER stress-challenged NSCs showed that NSC’s ER stress response resulted in a significant decline in NSC self-renewal and an increase in apoptosis and cellular oxidative stress. A total of 2300 genes were significantly (moderated t statistics FDR corrected p-value ≤ 0.05 and Fold Change absolute ≥ 2.0) differentially expressed (DE). Pathway enrichment and gene network analysis of DE genes suggests that all three unfolded protein response (UPR) pathways (PERK, IRE1, and ATF6) were significantly activated and cooperatively regulated the NSC’s transcriptional response to ER stress. Our results show that IRE1/XBP1 mediated transcriptional regulation of E2F1 and its downstream targets have a dominant role in inducing G1/S-phase cell cycle arrest in the ER stress-challenged NSCs. The ER stress-challenged NSCs also showed activation of CHOP-mediated apoptosis and dysregulation of synaptic plasticity and neurotransmitter homeostasis-associated genes. Overall, our results suggest that ER stress-associated attenuation of NSC self-renewal, increased apoptosis, and dysregulated synaptic plasticity and neurotransmitter homeostasis plausibly play a role in the causation of ADRD.

overall_design: Well-characterized NSC lines generated from validated iPSCs of 2 different individuals were ER stress-challenged using Thapsigargin (TG) for 24 hours. TG is a specific inhibitor of sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) and is a classical tool commonly used to study ER stress and UPR biology in mammalian cells. Both, vehicle-treated controls and ER stress-challenged NSCs were then quantitatively measured for cell proliferation, apoptotic cell death, protein aggregation, oxidative stress, mitochondrial function cellular phenotypes by high content screening (HCS) analysis and for genome-wide gene expression using deep mRNA sequencing.

first: Joanne

last: Curran

first: John

last: Blangero


title: Spatial Transcriptomics Unravels Palmitoylation and Zonation-Dependent Gene Regulation by AEG-1 in Mouse Liver

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

summary: Obesity-induced metabolic dysfunction-associated steatohepatitis (MASH) leads to hepatocellular carcinoma (HCC). Astrocyte-elevated gene-1/Metadherin (AEG-1/MTDH) plays a key role in promoting MASH and HCC. AEG-1 is palmitoylated at residue cysteine 75 (Cys75) and a knock-in mouse representing mutated Cys75 to serine (AEG-1-C75S) showed activation of MASH- and HCC-promoting gene signature when compared to wild-type littermates (AEG-1-WT). The liver consists of 3 zones, periportal, midlobular and pericentral, and zone-specific dysregulated gene expression impairs metabolic homeostasis in the liver, contributing to MASH and HCC. Here, to elucidate how palmitoylation influences AEG-1-mediated gene regulation in regards to hepatic zonation, we performed spatial transcriptomics (ST) in the livers of AEG-1-WT and AEG-1-C75S littermates.

overall_design: Liver sections of female AEG-1-WT and AEG-1-C75S littermates were subjected to spatial transcriptomics.

first: Alissa

last: Saverino

first: Xufeng

last: Qu

first: Rachel

last: Mendoza

first: Suchismita

last: Raha

first: Debashri

last: Manna

first: Ali

last: Ermi

first: Mark

middle: A

last: Subler

first: Jolene

last: Windle

first: Jinze

last: Liu

first: Devanand

last: Sarkar


title: Ketogenic diet modifies ribosomal protein dysregulation in KMT2D Kabuki Syndrome

city: Westmead

first: Brian

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

summary: Background Kabuki syndrome (KS) is a genetic disorder caused by DNA mutations in KMT2D, a lysine methyltransferase that methylates histones and other proteins, and therefore modifies chromatin structure and subsequent gene expression. Ketones, derived from the ketogenic diet, are histone deacetylase inhibitors that can ‘open’ chromatin and encourage gene expression. Preclinical studies have shown that the ketogenic diet rescues hippocampal memory neurogenesis in mice with KS via the epigenetic effects of ketones.  Methods Single-cell RNA sequencing and mass spectrometry-based proteomics were used to explore molecular mechanisms of disease in individuals with KS (n=4) versus controls (n=4).  Findings Pathway enrichment analysis indicated that loss of function mutations in KMT2D are associated with ribosomal protein dysregulation at an RNA and protein level in individuals with KS (FDR <0.05). Cellular proteomics also identified immune dysregulation and increased abundance of other lysine modification and histone binding proteins, representing a potential compensatory mechanism. A 12-year-old boy with KS, suffering from recurrent episodes of cognitive decline, exhibited improved cognitive function and neuropsychological assessment performance after 12 months on the ketogenic diet, with concomitant improvement in transcriptomic ribosomal protein dysregulation.

overall_design: In this study, we utilised high-throughput single-cell RNA sequencing to characterise the transcriptomic profiles of children with KS compared to controls.

first: Erica

last: Tsang

first: Velda

middle: X

last: Han

first: Shrujna

last: Patel

first: Russell

middle: C

last: Dale


title: Knock down of APE1 suppressed gastric cancer metastasis via improving immune disorders caused by myeloid-derived suppressor cells

city: Lianyungang

first: Baoming

last: Zhang

address: No. 6 Zhenhua East Road

institute: The First Peoples Hospital of Lianyungang

summary: Gastric cancer is a highly immunogenic malignancy. Immune tolerance facilitated by myeloid-derived suppressor cells (MDSCs) has been implicated in gastric cancer resistance mechanisms. The potential role of APE1 in regulating gastric cancer metastasis by targeting MDSCs remains uncertain. In this study, the plasmid Plxpsp-mGM-CSF was used to induce high expression of granulocyte-macrophage colony-stimulating factor (GM-CSF) in GES-1 cells. For tumor transplantation experiments, AGS, AGS+GM-CSF and AGS+GM-CSF-siAPE1 cell lines were established by transfection, followed by subcutaneous implantation of tumor cells. MDSCs, Treg cells, IgG, CD3 and CD8 levels were assessed. Transfection with siAPE1 significantly inhibited tumor growth compared to the AGS+GM-CSF group. APE1 gene knockdown modulated the immune system in gastric cancer mice, characterized by a decrease in MDSCs and an increase in Treg cells, IgG, CD3 and CD8. In addition, APE1 gene knockdown resulted in decreased levels of pro-MDSC cytokines (HGF, CCL5, IL-6, CCL12). Furthermore, APE1 gene knockdown inhibited proliferation, migration and invasion of AGS and MKN45 cells. AGS-GM-CSF cell transplantation increased MDSC levels and accelerated tumor growth, whereas APE1 knockdown reduced MDSC levels, inhibited tumor growth and attenuated inflammatory infiltration in gastric cancer tissues.

overall_design: To investigate the influence of APE1 on regulation of gastric cancer, and si-APE1 using AGS cell line.


title: Single-cell transcriptomic analysis of mouse lung cDC2s at various times post allergic sensitization

city: Research Triangle Park

first: Hideki

last: Nakano

state: NC

address: 111 TW Alexander Drive

department: Immunity, Inflammation and Disease Laboratory

institute: NIEHS

summary: Conventionaldendritic cells (cDCs) in the lung that drive effector T cell differentiation, and initiate allergic responses upon inhalation of allergens. CD11b+type 2 cDCs (cDC2s) are heterogeneous, but the relationship among  subpopulations has been elusive. To analyze their developmental pathways of cDC2 subpopulations, we performed single cell RNA-sequencing (scRNAS-Seq) of total lung cDC2s at various times following inhalation of house dust extracts, and detected multiple clusters based on their differential transcriptomes. The data of cDC2 transcriptome at steady state, early and later stages after activation will be applicable for the maturation pathway analysis of cDC2s.

overall_design: CD11b+cDC2s (CD45+ CD11c+ I-A+ Siglec-F– CD88– F4/80– CD103– Live/Dead–) from naive C57BL/6 mice, and mice 6 and 18 hours after inhalation house dust extract together with ovalbumin werepurified by flow cytometry sorting, and labeled with barcoded antibodies then loaded into the Single Cell Chip followed by forming single cell. The Gene Expression library and the ADT Library were prepared using the Chromium single cell 3′ v3 library and gel bead kit (10x Genomics) and additional reagents recommended in the protocol of Total A-seq (Biolegend). The two libraries were mixed at 10:1 molar ratio (Gene Expression library to ADT library) andsequenced by the NIEHS Epigenomics and DNA Sequencing Core Laboratory on NovaSeq 6000 (Illumina) with paired-end sequencing (Read 1: 28; Read 2: 90).

first: Donald

middle: N

last: Cook


title: Trastuzumab-associated cardiotoxicity in Patient Specific iPSC-derived cardiomyocytes from HER2+ breast cancer patients

city: New York

first: Jens

last: Hansen

state: NY

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Trastuzumab is a monoclonal targeted therapy widely used to treat human epidermal growth factor receptor 2 (HER2+) over expressed breast cancer which confers an aggressive cancer type and comprises ~25% of breast cancer. Trastuzumab yields improved breast cancer related outcomes, but survival benefits are in part offset by cardiotoxicity - as evidenced by 10-15% of patients develop cardiomyopathy and 2-4% develop congestive heart failure. Approximately 20-30% of patients have either temporary or permanent discontinuation of trastuzumab therapy due to its cardiotoxicity, raising concern for inadequate cancer treatment and recurrence. Current screening strategies for trastuzumab-induced cardiotoxicity rely on non-invasive imaging such as echocardiography, but conventional imaging techniques provide limited a priori risk stratification for cardiotoxicity. We have utilized patient-specific iPSC-CMs derived from HER2+ breast cancer patients with and without evidence of TIC as a model to better elucidate the mechanisms of Trastuzumab-indued cardiotoxicity.

overall_design:
We have recruited HER2+ breast cancer patients with evidence of cardiotoxicity from Trastuzumab (TX) and control HER2+ breast cancer patients without cardiotoxicity (NT).
Induced pluripotent stem cells were reprogrammed from the patient’s peripheral blood mononuclear cells and then differentiated into iPSC-derived cardiomyocytes (iPSCM-CMs) which were treated with Trastuzumab and performed bulk RNA sequencing.

first: Angel

last: Chan

first: Yuguang

last: Xiong

first: Eric

last: Sobie

first: Ravi

last: Iyengar


title: Cytokine stimulated keratinocytes (TCF4 KD)

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

summary: In order to study the molecular mechanisms involving TCF4 in keratinocytes under different inflammatory responses, control and TCF4 knock down keratinocytes were stimulated with inflammatory cytokines and conducted RNA-seq to profile the gene expression.

overall_design: Control and TCF4 knock down keratinocytes are stimulated with cytokines such as IL17A, IL17C or a combination of IL17A/TNFa

first: Johann

last: Gudjonsson

first: Lam

last: Tsoi


title: Lupus neutrophils transcriptome

city: Seattle

first: Rayan

last: Najjar

address: 750 Republican Street

department: Medicine/Rheumatology

institute: University of Washington

summary: Neutrophils are understudied in lupus. We performed RNA-sequencing of neutrophils from patients with lupus and healthy controls.

overall_design: Bulk RNA-seq data of freshly isolated neutrophils from patients with systemic lupus erythematosus and healthy controls.

first: Mustelin

last: Tomas

first: Najjar

last: Rayan


title: Deletion of miR-204 and miR-211 in murine retinal pigment epithelium results in slow retinal degeneration

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

institute: International Centre for Translational Eye Research

summary: To determine the gene expression changes in the retina of miR-204/miR-211 RPE conditional knockout (dKO) mice, we collected retina samples from dKO and controls animals at 6 months of degeneration, generated single-cell suspensions, and created scRNA-seq libraries (Parse Biosciences), and sequened the libraries.

overall_design: Two retinas from each mouse (4 control, 5 dKO) were independently processed; the resulting single-cell suspensions were fixed and frozen using the Parse Biosciences WT V2 chemistry fixation kit instructions. The library was constructed with all samples simultaneously, with a target of 4000 cells per animal according to the manufacturer instructions, and 8 sub-libraries were generated.

first: Samuel

middle: W

last: Du

first: Damian

last: Panas

first: Krzysztof

last: Palczewski


title: Nr4a1 regulates cell-specific transcriptional programs in inhibitory GABAergic interneurons

city: La Jolla

first: Anton

last: Maximov

state: CA

address: 10550 North Torrey OPines Rd

department: Neuroscince

institute: Scripps Research

summary: The patterns of synaptic connectivity and physiological properties of diverse neuron types are shaped by distinct gene sets. Our study demonstrates that, in the mouse forebrain, the transcriptional profiles of inhibitory GABAergic interneurons are regulated by Nr4a1, an orphan nuclear receptor whose expression is transiently induced by sensory experiences and is required for normal learning. Nr4a1 exerts contrasting effects on the local axonal wiring of Parvalbumin- and Somatostatin-positive interneurons, which innervate different subcellular domains of their postsynaptic partners. The loss of Nr4a1 activity in these interneurons results in bidirectional, cell-type-specific transcriptional switches across multiple gene families, including those involved in surface adhesion and repulsion. Our findings reveal that combinatorial synaptic organizing codes are surprisingly flexible and highlight a mechanism by which inducible transcription factors can influence neural circuit structure and function.

overall_design: The first goal of this study was to identify genes whose expression levels are altered in cortical Parvalbumin (PV)- or Somatostatin (Sst)-positive GABAergic interneurons (INs) during associative learning.  This was achieved using RiboTag, a technique for immuno-isolation of translating mRNAs in complexes with ribosomes containing a genetically targeted HA epitope-tagged protein, Rpl22. We introduced RiboTag into each IN population by crossing the Cre recombinase-dependent Rpl22-HA mouse allele with well characterized PvalbCre and SstCre drivers, extracted cell-specific pools of mRNAs from the cortices and hippocampi of young adults at postnatal day (p) 60, and analyzed these mRNAs by deep sequencing (RNA-seq).  We surveyed acute changes in IN transcriptomes that were elicited by contextual fear conditioning (CFC), a neurobehavioral paradigm for the acquisition of stable associative memory from an adverse environment where animals received series of foot shocks. In parallel experiments, PvalbCre/RiboTag and SstCre/RiboTag mice received single doses of the GABA receptor antagonist, pentylenetetrazol (PTZ), to identify genes whose mRNA levels were altered by artificial widespread network excitation as a frame of reference. We also used RiboTag to survey transcriptional profiles of Nr4a1-deficient PV and Sst cells in Nr4a1 conditional knockpoiut mice.

first: Min

last: Huang


title: Enhancing the anti-tumor efficacy of Bispecific T cell engagers via cell surface glycocalyx editing

city: San Diego

first: Jaroslav

last: Zak

address: 10550 North Torrey Rd

department: Immunology and Microbial Sciences

institute: The Scripps Research Institute

summary: Bispecific T-cell engager (BiTE)-based cancer therapies that activate the cytotoxic T cells of a patient’s own immune system have gained momentum with the recent FDA approval of Blinatumomab for treating B cell malignancies. However, this approach has had limited success in targeting solid tumors. We have reported the development of BiTE-sialidase fusion proteins that enhance tumor cell susceptibility to BiTE-mediated cytolysis by T cells via targeted desialylation at the BiTE-induced T cell-tumor cell interface. Targeted desialylation results in better immunological synapse formation, T-cell activation and effector function. As a result, BiTE-sialidase fusion proteins show remarkably increased efficacy in inducing T-cell-dependent tumor cell cytolysis in response to target antigens compared to the parent BiTE molecules alone. This enhanced function is seen both in vitro and in in vivo xenograft and syngeneic solid tumor mouse models. Our findings highlight BiTE-sialidase fusion proteins as promising candidates for the development of next-generation bispecific T-cell engaging molecules for cancer immunotherapy. This transcriptomic dataset documents the effect of BiTE-sialidase vs uncojugated BiTE on T cells including the upregulation of effector associated genes.

overall_design: 1.2 million hPBMCs and 0.1 million MDA-MB-231 cells were incubated together under the treatment of either 4 nM 4D5 BiTE or 4 nM 4D5 BiTE-sialidase (three biological replicates for each condition). After 48 hours of incubation, the mixture was stained with DAPI and anti-CD3 antibody to sort CD3+ T cells by flow cytometry and subjected to RNA isolation and library preparation for bulk RNA-sequencing.

first: Peng

last: Wu

first: Zhuo

last: Yang

first: Yingqin

last: Hou


title: BIOLOGICAL EFFECTS OF CORTICOSTEROIDS ON PNEUMOCOCCAL PNEUMONIA IN MICE AND HUMANS

city: San Francisco

first: Aartik

last: Sarma

address: 513 Parnassus Ave

institute: University of California, San Francisco

summary:
Rationale: Streptococcus pneumoniae is the most common bacterial cause of community acquired pneumonia. Some clinical trials have demonstrated a beneficial effect of corticosteroid therapy in community acquired pneumonia, but the mechanisms of this benefit remain unclear.
Objectives: To investigate the biologic effects of corticosteroids in pneumococcal pneumonia in mice and in patients
Methods: We studied lower respiratory tract transcriptomes from an observational cohort of mechanically ventilated patients and from a pneumonia model in mice. We also carried out comprehensive physiologic, biochemical, and histological analyses in mice to identify mechanisms of lung injury in S. pneumoniae with and without adjunctive steroid therapy.
Measurement and Main Results: Transcriptomic analysis identified pleiotropic effects of steroid therapy on the lower respiratory tract in critically ill patients with pneumococcal pneumonia, findings that were reproducible in mice. In mice with pneumonia, dexamethasone in combination with ceftriaxone reduced (1) pulmonary edema formation, (2) alveolar protein permeability, (3) proinflammatory cytokine release, (4) histopathology lung injury score, and (5) hypoxemia, but did not increase bacterial burden.
Conclusions: In combination with appropriate antibiotics in mice, treatment of pneumococcal pneumonia with steroid therapy reduces hypoxemia, pulmonary edema, lung permeability, and histologic criteria of lung injury, and also altered inflammatory responses at the protein and gene expression level. The concordance of transcriptional data in the mouse model and in patients with pneumococcal pneumonia supports the translational relevance of this work.

overall_design:
Humans: Tracheal aspirate samples were collected from an observational cohort of mechanically ventilated patients. 10 patients had S. pneuomoniae pneumonia and were treated with antibiotics prior to specimen collection. Of these 10 subjects, five were treated with corticosteroids. Tracheal aspirate samples were also available from five control subjects intubtaed neurological injury who had normal chest radiographs and were not immunosuppressed. Mice: Mice were assigned to one of six experimental groups: 1) Control, 2) Dexamethasone, 3) SP, 4) SP + Dexamethasone, 5) SP + Ceftriaxone, 6) SP + Ceftriaxone + Dexamethasone
*** The records will be updated with the mouse data in a few weeks***
***Please note that the UCSF IRB has restricted sharing the raw data because some of the samples were collected under a waiver of consent and could in theory be identifiable. Therefore, raw data is not provided***

first: Hiro

last: Taenaka

first: Katherine

last: Wick

first: Michael

last: Matthay