title: Novel resources to investigate leaf plasmodesmata formation in C3 and C4 monocots

city: Canberra

first: Florence

last: Danila

state: ACT

address: Building 134 Linneaus Way, Acton

country: Australia

institute: Australian National University

summary: Plasmodesmata (PD) are nanochannels that facilitate cell-to-cell transport in plants. More productive and photosynthetically efficient C4 plants form more PD at the mesophyll (M)-bundle sheath (BS) interface in their leaves than their less efficient C3 relatives. In C4 leaves, PD play an essential role in facilitating the rapid metabolite exchange between the M and BS cells to operate a biochemical CO2 concentrating mechanism, which increases the CO2 partial pressure at the site of Rubisco in the BS cells and hence photosynthetic efficiency. The genetic mechanism controlling PD formation in C3 and C4 leaves is largely unknown, especially in monocot crops, due to the technical challenge of quantifying these nanostructures with electron microscopy. To address this issue, we have generated stably transformed lines of Oryza sativa (rice, C3) and Setaria viridis (setaria, C4) with fluorescent protein-tagged PD to build the first spatiotemporal atlas of leaf pit field (cluster of PD) density in monocots without the need for electron microscopy. Across leaf development, setaria had consistently more PD connections at the M-BS wall interface than rice while the difference in M-M pit field density varied. While light was a critical trigger of PD formation, cell type and function determined leaf pit field density. Complementary temporal mRNA sequencing and gene co-expression network analysis revealed that the pattern of pit field density correlated with differentially expressed PD-associated genes and photosynthesis-related genes. PD-associated genes identified from our co-expression network analysis are related to cell wall expansion, translation and chloroplast signalling.

sample_organism:
Oryza sativa
Setaria viridis

platform_organism:
Oryza sativa
Setaria viridis

overall_design: Fluorescent protein-tagged plasmodesmata lines of rice and setaria were grown at different developmental stages then profiled for pit field density and RNA-seq.

first: HongTing

last: Tsang

first: Diep

last: Ganguly

first: Robert

last: Furbank

first: Susanne

last: von Caemmerer


title: Extensive functional divergence of the RosR transcription factor across haloarchaea [ChIP-Seq]

status: Public on Nov 20 2024

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

country: USA

institute: Duke University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: For microbial cells, an appropriate response to changing environmental conditions is critical for viability. Transcription regulatory proteins, or transcription factors (TFs) sense environmental signals to change gene expression. However, it remains unclear how TFs and their corresponding gene regulatory networks are selected for over evolutionary time scales. The function of TFs and how they evolve are particularly understudied in archaeal organisms. Here we identified, characterized, and compared the function of the RosR transcription factor across three related species of hypersaline adapted model archaea. RosR was previously characterized as a global regulator of gene expression during oxidative stress in the species Halobacterium salinarum (HsRosR). Here we use functional genomics and quantitative phenotyping to demonstrate that, despite strong conservation of HsRosR across species, its function diverges substantially. Surprisingly, RosR in Haloferax volcanii and Haloferax mediterranei regulates genes whose products function in motility and the outer membrane, leading to significant defects in motility when rosR is deleted. Given weak conservation and degeneration in the RosR cis-regulatory sequence across species, we hypothesize that the RosR regulatory network is easily rewired during evolution across related species of archaea.

sample_organism:
Haloferax volcanii DS2
Haloferax mediterranei ATCC 33500

overall_design: To determine the genome-wide location of binding of the RosR transcription factor, we conducted chromatin immunoprecipitation coupled to DNA sequencing (ChIP-seq) in rich medium, mid-exponential phase for each of the Hfx. volcanii and Hfx. mediterranei species of hypersaline archaeal cells.

first: Joey

last: Prinz

first: Mar

last: Martinez Pastor


title: Sphingosine kinase 2 (SphK2) knockout increases liver inflammation in an early MASH mouse model

city: Richmond

first: Kaitlyn

middle: G

last: Jackson

state: Virginia

address: 7414 Seminary Ave

department: Immunology

institute: VCU

summary:
To determine the effect of SphK2 KO on liver inflammation in an early MASH mouse model
To determine the effect of WDSW on liver inflammation in an early MASH mouse model

overall_design: Assessed two independent variables (diet, genotype) on on gene expression related to inflammation and the immune response in a MASH mouse model

first: Derrick

last: Zhao

first: Huiping

last: Zhou


title: Depletion of conventional CD4+ T cells is required for robust priming and dissemination of tumor antigen-specific CD8+ T cells in the setting of anti-CD4 therapy

city: Lebanon

first: Mary Jo

last: Turk

state: NH

address: 1 Medical Center Dr, Rubin FL7, Bench 33

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

type: Expression profiling by high throughput sequencing

summary: CD8 T cells are potent anti-tumor mediators. We analyzed CD8 T cells from B16 tumor-draining lymphnodes from mice receiving one of three different treatments.

overall_design: Mice were induced with 10,000 Pmel(thy1.1+) cells on D-1, and 200,000 B16 tumor cells intradermally on D0. Mice were then separated into 3 groups: 5 untreated, 5 anti-CD4 treated, and 5 ICB(anti-PD1 and anti-CTLA4) treated. Mice were sacrificed 12 days later and tumor-draining lymph nodes were harvested. Cells were stained with unique hashtag antibodies for (HTO).  We sorted CD62Llo, CD44hi CD8+ and CD44hi, Thy1.1+ Pmel cells from each pooled group by FACS.

first: Delaney

middle: E

last: Ramirez

first: Tyler

last: Searles


title: Clinical outcome is unlinked to injection of adipose-derived regenerative cells in the axilla of breast cancer-related lymphedema patients

city: Odense M

first: Charlotte Harken

middle: Harken

last: Jensen

address: Campusvej 55

department: Clinical Biochemistry/Clinical Research

country: Denmark

institute: Odense University Hospital/University of Southern Denmark

summary: Background: Injection of autologous adipose-derived regenerative cells (ADRCs) combined with lipotransfer has been suggested to alleviate symptoms in diseases including breast cancer-related lymphedema (BCRL). We recently performed a randomized controlled trial injecting lipoaspirate with ADRCs into the axilla of BCRL patients, and here we aimed in the intervention group to define in an unbiased fashion whether ADRC injection was linked to the clinical outcome. Results: Unbiased multifactorial analysis ranked and defined the clinical outcomes (Sf36 physical change, L-Dex Lymph Change, ICG mdanderson change) with the highest effect on BRCL patients. The 10 patients with the highest- and lowest effect (five responders and five non-responders) were included in the study. No difference between non-responders and responders were observed for injected ADRC number/size/viability (p>0.05). In scRNAseq, we did not find any major difference (p>0.05) between groups in ADRC composition regarding adipose derived stem cells, endothelial-, smooth muscle-, T-, B-, mast cells as well as macrophages, which was verified by flow cytometry. Differential subcluster gene expression between groups were for 92.5% of genes below the threshold of 1.5, and thus neglible. Together this suggested that the ADRC phenotype was indistinguishable between BRCL responders and non-responders to the intervention.

overall_design: 39 BCRL patients received lipotransfer assisted with autologous ADRCs (4.20x107 ± 1.75x107 cells) whereas 41 BCRL patients were included for placebo treatment. At 12 month follow-up, we assessed quality of life, lymphangiography, and bioimpedance enclosing 59 outcome parameters. Multifactorial analysis of clinical outcomes was used to define responders and non-responders to the intervention, and collected ADRCs from these patient groups were analyzed by single cell RNA sequencing (scRNAseq).

first: Ditte

middle: C

last: Andersen

first: Frederik

middle: A

last: Bjerre

first: Mads

last: Jørgensen

first: Jens

last: Sørensen

first: Charlotte

middle: H


title: ERCC6L2 suppresses chromosome translocation

city: Stanford

first: Jinglong

last: Wang

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford Medicine

summary: ERCC6L2  is a recently characterized component in DNA damage repair. To investigate its function in chromosome translocation, we conducted a study using K562 and HEK293T cell lines. We introduced twinned DNA double-strand breaks (DSBs) or genome-wide DSBs into these cell lines via nucleofection and transfection, respectively. Subsequently, we employed high-throughput genome translocation sequencing (HTGTS) to capture the translocation events (i.e., ligation between "prey(s)" and "bait") and the rejoining events (i.e., direct repair within the "bait" locus) under different conditions, including with or without ERCC6L2 deletion. We quantified the number of translocation events by normalizing them to the number of rejoining events, denoted as TL. Interestingly, ERCC6L2 deletion led to an increase in TL, indicating a higher frequency of translocations.

overall_design: We induced DNA double-strand breaks (DSBs) using CRISPR-Cas9 technology in various cell lines, including K562-derived cell lines (K562 and K562-ERCC6L2-/-) and the HEK293T-derived cell lines (HEK293T-iCas9 and HEK293T-iCas9-ERCC6L2-/-). To capture translocation events, we utilized one of the DSB sites, RAG1L as a bait, which allowed us to detect its ligation with the remaining DSB site(s) using high-throughput genome translocation sequencing (HTGTS).

first: Richard

middle: L

last: Frock


title: Nuclear compartmentalization of PD-L1 suppresses tumorigenesis and overcomes immunocheckpoint therapy resistance via histone macroH2A1 phosphorylation

city: Changsha

first: zhi

last: yang

address: No.87 Xiangya Road

country: China

institute: Xiangya Hospital Central South University

summary: Canonically PD-L1 functions as the inhibitory immune checkpoint on cell surface. Recent studies observed PD-L1 expression in the nucleus of cancer cells. But the biological function of nuclear PD-L1 (nPD-L1) in tumor growth and antitumor immunity is unclear. Here we enforced nPD-L1 expression and established stable cells. nPD-L1 suppressed tumorigenesis and aggressiveness in vitro and in vivo.  Compared with PD-L1 deletion, nPD-L1 expression repressed tumor growth and improved survival more significantly in immunocompetent mice. p-AMPKα facilitated nuclear PD-L1 compartmentalization and then cooperated with it to directly phosphorylate S146 of histone variant macroH2A1 (mH2A1) to epigenetically activate expression of genes of cellular senescence, JAK-STAT, and Hippo signaling pathways. Lipoic acid (LA) that induced nuclear PD-L1 translocation suppressed tumorigenesis and boosted antitumor immunity. Importantly, LA treatment synergized with PD-1 antibody and overcame immune checkpoint blockade (ICB) resistance, which may result from nPD-L1-increased MHC-I expression and sensitivity of tumor cells to IFN-γ. These findings offer a conceptual advance for PD-L1 function and suggest LA as a promising therapeutic option for overcoming ICB resistance.

overall_design: To explore the mechanisms by which nPD-L1 inhibits tumor growth and enhances antitumor immunity, we performed RNA-sequencing analysis to compare gene expression profiles between nPD-L1-overexpressed and vector groups in Hep3B cells with endogenous PD-L1 deletion.

first: Zhi

last: Yang

first: Yong

last: Liu

first: Junwei

last: Hou

first: Mien

last: Hung


title: Extensive functional divergence of the RosR transcription factor across haloarchaea

first: Amy

last: Schmid

platform_organism:
Haloferax volcanii DS2
Haloferax mediterranei ATCC 33500

overall_design: To determine the function of the RosR transcription factor across the species Haloferax volcanii (HVO), Haloferax mediterranei (HFX), we measured RNA expression by RNA-seq transcriptomics in rosR knockout strains of each species compared to its corresponding parent strain (ura3 , HBT; pyrE in HVO and HFX)

first: Joey

last: Prinz

first: Mar

last: Martinez Pastor


title: SPIN1 accelerates tumorigenesis and confers radioresistance of non-small cell lung cancer via orchestrating the FOXO3a/FOXM1 axis

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

summary: Radioresistance is a predominant obstacle of effective treatments in non-small cell lung cancer (NSCLC), while the underlying mechanism remains incompletely elucidated. Spindlin 1(SPIN1) has been reported to participate in tumor initiation and progression, while its role in NSCLC tumorigenesis and radioresistance remains largely unknown. In this study, bioinformatics analysis, immunohistochemistry (IHC) and western blotting assays were performed to test SPIN1 expression in NSCLC samples and cell lines. The carcinogenic role of SPIN1 was evaluated by cell growth and proliferation, EdU staining, transwell and colony formation assays. Besides, the radiosensitivity of NSCLC cells was determined by clonogenic cell survival, neutral comet and γ-H2AX and Rad51 foci formation assays. Xenograft tumor model was constructed to access the effects of SPIN1 on tumorigenesis and radiosensitivity. Furthermore, RNA sequencing, quantitative real-time PCR, CHX and ubiquitination assays were applied to elucidate the correlation between SPIN1 and FOXO3a-FOXM1 axis. Therefore, our results suggest that the SPIN1-MDM2-FOXO3a/FOXM1 signaling axis is essential for NSCLC progression and radioresistance, and it could serve as therapeutic targets in irradiation-resistance NSCLC.

overall_design: The HCC827 cells transfected with SPIN1 siRNAs or negative control for 48h were used for RNA sequencing (RNA-seq).

first: Min

last: Zhong

last: Fang

first: Juntao

last: Zou

first: Xiao

first: Zezhi

last: Qiu

first: Ling

last: Zhou

first: Yi

last: Le

first: Zhen

first: Yanyu

last: Liao

first: Fengting

last: Nie

first: Xianpin

last: Wei

first: Jinbo

last: Zhan

first: Jianping

last: Xiong

first: Xiaojun

last: Xiang

first: Ziling


title: Viral and host M6A modification changes after infection of MARC145 cells by PRRSV SD16

city: ZHENG ZHOU

first: Yunyun

last: zhai

address: China Henan Zhengzhou Agricultural Road No. 63 (450002)

institute: Henan Agricultural University

summary: Viral infections can influence the dynamic changes of the epitranscriptome. However, due to the lack of understanding regarding the impact of PRRSV (Porcine reproductive and respiratory syndrome virus) on m6A modifications in host cells in vitro, we investigated the changes in viral and host mRNA N6-methyladenosine (m6A) modifications during the infection of MARC145 cells by the PRRSV SD16 strain. We found that the expression of major epitranscriptomic proteins changed before and after viral infection, reprogramming both the viral and host epitranscriptomes. Specifically, the expression of METTL3 increased after PRRSV infection. Overexpression of METTL3 promoted PRRSV gene expression and replication, while knockdown of METTL3 suppressed PRRSV gene expression and replication. These findings reveal the dynamic characteristics of the mRNA m6A modification program during PRRSV replication in vitro.

overall_design: We investigated the changes in viral and host mRNA N6-methyladenosine (m6A) modifications during the in vitro infection process with the PRRSV SD16 strain.

first: Guoqing

last: Zhuang

first: Aijun

last: Sun


title: Identification of reproduction-related genes in the hypothalamus of the sheep (Ovis aries) using the ONT full-length transcriptome sequencing technology

city: taian

first: zb

last: Ji

address: Daizong street NO.61,

institute: shandong agricultural university

summary: the hypothalamus tissues of high-reproduction small-tailed Han sheep and low-reproduction Wadi sheep were collected, and full-length transcriptome sequencing by Oxford Nanopore Technologies (ONT) was performed to explore the key functional genes associated with sheep fecundity. The differentially expressed genes (DEGs) were screened and enriched using DESeq2 software through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG).

overall_design: three healthy small-tailed Han sheep and three healthy Wadi sheep with similar body composition, were selected to form a high-reproduction group (HP group, small-tailed Han sheep) and a lowreproduction group (LP group, Wadi sheep). Oxford Nanopore Technologies (full-length transcriptome sequencing technology) was used for mRNA identification, screening, and functional analysis of the different groups.

first: Zhibin


title: EAF2 deficiency attenuates autoimmune disease in Faslpr mice by modulating B cell activation and apoptosis

city: Shanghai

first: Yingying

last: Luan

address: 130 Dong'an road

institute: Fudan University

summary: Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that presents significant challenges to human health. MRL/lpr mice, which develop SLE-like autoimmunity due to defective apoptosis in activated B and T cells, were used to study the role of apoptosis in autoimmunity. We generated Faslpr mice deficient in EAF2, a transcription elongation-associated factor known to promote apoptosis in germinal center (GC) B cells and crucial for preventing autoimmunity. Contrary to expectations, EAF2 deficiency significantly reduced lymphadenopathy and splenomegaly, extended lifespan, and alleviated nephritis by decreasing autoantibody production and reducing immune complex deposition in the kidneys. Additionally, EAF2 deficiency markedly reduced accumulation of activated B cells, GC B cells, and plasma cells in Faslpr mice. Moreover, the abnormal B220+CD3+ T cells typically observed in Faslpr mice were substantially reduced by EAF2 deficiency. Further analysis revealed that Eaf2-/-Faslpr B cells showed hyperactivation upon various stimulations, followed by increased death. RNA sequencing of the B220+CD3+ cells revealed a downregulation in survival-promoting genes such as Bcl-2 and Akt and an upregulation of proapoptotic genes. We conclude that the combined deficiency in FAS- and EAF2-mediated apoptotic pathways leads to B cell hyperactivation and subsequent death, thereby ameliorating systemic autoimmunity in this model.

overall_design: To delineate the signaling pathways involved in apoptosis, we sorted B220+CD3+ cells from Faslpr and Eaf2-/-Faslpr mice for RNA-Seq analysis

first: Ji-Yang

last: Wang


title: An E2 ubiquitin conjugating enzyme links diubiquitinated H2B to H3K27M oncohistone function

city: Oxford

first: Alan

last: Jiao

state: MA

address: Old Road Campus Research Building

country: United Kingdom

institute: Ludwig Institute for Cancer Research, Oxford University

summary: The H3K27M oncogenic histone (oncohistone) mutation drives ~80% of incurable childhood brain tumors known as diffuse midline gliomas (DMGs). The major molecular feature of H3K27M mutant DMGs is a global loss of H3K27 tri-methylation (H3K27me3), a phenotype conserved in Caenorhabditis elegans (C. elegans). Here we perform unbiased genome-wide suppressor screens in C. elegans expressing H3K27M, and isolate 20 suppressors, all of which at least partially restore H3K27me3. 19/20 suppressor mutations map to the same histone H3.3 gene in which the K27M mutation was originally introduced. Most of these create single amino acid substitutions between residues R26-Y54, which do not disrupt oncohistone expression. Rather, they are predicted to impair interactions with the Polycomb Repressive Complex 2 (PRC2) and are functionally conserved in human cells. Further, we mapped a single extragenic H3K27M suppressor to ubc-20, an E2 ubiquitin conjugating enzyme, whose loss rescued H3K27me3 to nearly 50% wild-type levels despite continued oncohistone expression and chromatin incorporation. We demonstrate that ubc-20 is the major enzyme responsible for generating di-ubiquitinated histone H2B. Our study provides in vivo support for existing models of PRC2 inhibition via direct oncohistone contact, and suggests that the effects of H3K27M may be modulated by H2B ubiquitination.

overall_design:
To investigate how ubc-20 mutants suppress K27M phenotypes, we performed CUT&RUN for H3K27me3 and H3K27M in wild-type (N2), K27M, and K27M; ubc-20(G155R) mutants.
Wild-type (N2), K27M, and K27M;ubc-20(G155R) C. elegans populations were grown to starvation on NA22-seeded agar plates at 20C, and L2 larvae starved for approximately 24h were collected for CUT&RUN.

first: Yang

last: Shi


title: Probiotic Bacteria-Released Extracellular Vesicles Enhance Macrophage Phagocytosis in Polymicrobial Sepsis Through Activating the FPR1/2 Pathway

city: Cincinnati

first: Guo-Chang

last: Fan

state: ohio

address: 231 Albert Sabin Way

department: Pharmacology & Systems Physiology

institute: University of Cincinnati

summary:
Background: Sepsis-induced organ failure and high mortality are largely ascribed to the failure of bacterial clearance from the infected tissues. Recently, probiotic bacteria-released extracellular vesicles (BEVs) have been implicated as critical mediators of intercellular communication which are widely involved in the regulation inflammatory response. However, their functional role in macrophage phagocytosis during sepsis has never been explored.
Methods: BEVs were collected from three different strains of probiotics including Lactobacillus plantarum WCFS1 (LP WCFS1), Lactobacillus rhamnosus Gorbach-Goldin (LGG), and Escherichia coli Nissle 1917 (EcN), or from LGG cultured under three pH conditions (pH5-acid, pH6.5-standard, pH8-akaline) through differential centrifugation, filtering, and ultracentrifugation of their culture supernatants. In vitro phagocytosis was measured in Raw264.7 and bone marrow-derived macrophages using pHrodo red E. coli BioParticles. The in vivo therapeutic effects of BEVs were tested using a feces-intraperitoneal-injection (FIP) model of polymicrobial sepsis.
Results: LGG-derived EVs (BEVLGG) were the best among these three probiotics BEVs in stimulating macrophages to take up bacteria. Furthermore, BEVLGG collected from pH8 culture condition (BEVpH8) exhibited the strongest capacity of phagocytosis, compared with BEVpH5 and BEVpH6.5. Treatment of septic mice with BEVpH8 significantly prolonged animal survival, increased bacterial clearance from the blood, peritoneal lavage, and multiple organs, decreased serum levels of pro-inflammatory cytokines, alanine aminotransferase (ALT, marker of liver injury) and creatinine (Cr, marker of kidney injury), in comparison with control-treated septic mice. Mechanistically, RNA-seq and bioinformatic analysis identified that the FPR1/2 signaling was remarkably activated, along with its downstream pathways (PI3K-Akt-MARCO and NADPH-ROS) in BEVpH8-treated macrophages, compared with control cells. Accordingly, pre-addition of Boc2, a specific antagonist of FPR1/FPR2, to macrophages significantly attenuated BEVpH8-mediated phagocytosis, compared to controls.
Conclusions: This study demonstrates that LGG-derived BEVs may have therapeutic effects against sepsis-induced organ injury and mortality through enhancing FPR1/2-mediated macrophage phagocytosis.

overall_design: To elucidate the potential mechanisms by which LGG-derived BEVs enhance macrophage phagocytosis of bacteria, we treated BMDMs with BEVpH5, BEVpH6.5, BEVpH8, or PBS as a control for 12 h, followed by isolating total RNAs for RNA-seq.

first: Ruiyao

last: Zhu


title: Homeostatic signals induce the development of peripheral helper T cells promoted in the pathogenesis of rheumatoid arthritis

city: Fukuoka

first: Ryosuke

last: Tsurui

address: 3-1-1 Maidashi Higashi-ku

department: Department of Orthopaedic Surgery

country: Japan

institute: Graduate School of Medical Sciences, Kyushu University

summary: Dysregulated T cell homeostasis has been implicated in the pathogenesis of rheumatoid arthritis (RA), in the joint of which peripheral helper T (Tph) cells accumulate and form ectopic lymphoid organs. We examined whether homeostatic signals are involved in the development of Tph cells. Human peripheral blood mononuclear cells(PBMCs) were cultured with IL-7, resulting in the development of PD-1highCXCR5+ Tph-like cells from human peripheral blood CD4 T cells after culture. These IL-7-induced Tph-like (IL-7-Tph) cells produced CXCL13 and IL-21 and helped B cells produce IgG.  Comprehensive gene expression analysis further supported their similarity with Tph cells in RA joint, and synovial fluid from RA patients (RASF) greatly promoted the IL-7-induced development of Tph-like cells. Our results demonstrate an antigen-nonspecific developmental pathway of Tph cells triggered by homeostatic signals and promoted by the local joint environment, which accounts for the accumulation of Tph cells in RA joints.

overall_design: Development of Tph-like cells was assessed by flow cytometry, gene expression, and functional analysis. To further verify the similarity between IL-7-Tph and RA-Tph cells, transcriptome analysis by bulk RNAseq was performed.


title: Specific tRNAs promote mRNA decay by recruiting the CCR4-NOT complex to translating ribosomes (Ribo-seq)

status: Public on Nov 21 2024

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: The CCR4-NOT complex is a major regulator of eukaryotic messenger RNA (mRNA) stability. Slow decoding during translation promotes association of CCR4-NOT with ribosomes, accelerating mRNA degradation. We applied selective ribosome profiling to further investigate the determinants of CCR4-NOT recruitment to ribosomes in mammalian cells. This revealed that specific arginine codons in the P-site are strong signals for ribosomal recruitment of human CNOT3, a CCR4-NOT subunit. Cryo–electron microscopy and transfer RNA (tRNA) mutagenesis demonstrated that the D-arms of select arginine tRNAs interact with CNOT3 and promote its recruitment whereas other tRNA D-arms sterically clash with CNOT3. These effects link codon content to mRNA stability. Thus, in addition to their canonical decoding function, tRNAs directly engage regulatory complexes during translation, a mechanism we term P-site tRNA-mediated mRNA decay.

overall_design: We performed CNOT3-selective ribosome profiling to identify the features of mRNAs that were associated with co-translational recruitment of CNOT3 to ribosomes. CNOT3-bound and total ribosomal footprints were isolated and sequenced.

first: Xiaoqiang

first: Victor

last: Cruz

first: He

last: Zhang

first: Jan

middle: P

last: Erzberger

middle: T


title: PROSER1 Modulates DNA Demethylation through Dual Mechanisms to Prevent Syndromic Developmental Malformations

city: Dundee

first: Kasper

middle: Dindler

last: Rasmussen

address: Dow Street

department: Division of Molecular, Cellular, and Developmental Biology (MCDB)

institute: School of Life Sciences, University of Dundee

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: PROSER1 Modulates DNA Demethylation through Dual Mechanisms to Prevent Syndromic Developmental Malformations [ChIP-seq]

summary: The link between DNA methylation and neurodevelopmental disorders is well established. However, how DNA methylation is fine-tuned – ensuring precise gene expression and developmental fidelity – remains poorly understood. PROSER1, a known TET2 interactor, was recently linked to a severe neurodevelopmental disorder. Here, we demonstrate that PROSER1 interacts with all TET enzymes and stabilizes chromatin-bound TET-OGT-PROSER1-DBHS (TOPD) complexes, which regulate DNA demethylation and developmental gene expression. Surprisingly, we find that PROSER1 also sequesters TET enzymes, preventing widespread demethylation and transposable element de-repression. Our findings identify PROSER1 as a key factor which both positively and negatively regulates DNA demethylation essential for mammalian neurodevelopment.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for endogenous PROSER1 in mESCs using PROSER1 KO as background control, and endogenous TET2 in wildtype and PROSER1 KO mESCs. ChIP-seq in wildtype and PROSER1 KO mESCs for the following histone modifications: H3K27ac, H3K4me1. Enzymatic methyl-seq (EM-seq) in wildtype, PROSER1 KO and PROSER1 KO+Rescue mESCs. RNA sequencing (RNA-seq) in wildtype, PROSER1 KO and PROSER1 KO+Rescue mESCs and wildtype, PROSER1 KO and PROSER1 KO+Rescue mESCs after 2 days differentiation in N2B27 medium ("day2" samples).

first: Anna

last: Fleming

first: Elena

middle: V

last: Knatko

first: Xiang

last: Li

first: Ansgar

last: Zoch

first: Zoe

last: Heckhausen

first: Stephanie

last: Stransky

first: Alejandro

middle: J

last: Brenes

first: Simone

last: Sidoli

first: Petra

last: Hajkova

first: Dónal

last: O'Carroll

middle: D


title: PROSER1 Modulates DNA Demethylation through Dual Mechanisms to Prevent Syndromic Developmental Malformations [EM-seq]


title: Effect of feeding on gene expression in WT, raga-1, and rsks-1 mutant animals

city: Higashihiroshima

first: Takafumi

last: Ogawa

state: Hiroshima

address: 1-3-1 Kagamiyama

institute: Hiroshima University

summary: After subjecting WT, raga-1, and rsks-1 (S6K) animals to this growth arrest, we compared them by RNA sequencing (RNA-seq) to a group that was released from arrest by feeding for four hours

overall_design: To investigate the nutrient response on gene expression, we treated WT, raga-1, and rsks-1 animals with 4 hours of feeding at the L1 larval stage.

first: Ziyun

last: Wu

first: Meltem

last: Isik

first: T

last: Blackwell


title: Identification of apelin/APJ signaling dysregulation in a human iPSC-derived granulosa cell model of Turner syndrome

city: Nankang

first: Jean

last: Lu

state: Taipei

address: 128 Academia Road, Section 2, IBMS, N401F

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary: The interaction between germ cells and somatic cells in the ovaries plays a crucial role in establishing the follicle reserve in mammals. Turner syndrome (TS) predominantly occurs in females who have either a partial or complete loss of one of their X chromosomes. Our understanding of the role granulosa cells (GCs) play in TS disease progression and pathogenesis remains limited. Here, we elevated GC differentiation efficiency up to the level of 80% differentiated cells from iPSCs. In our attempt to replicate the differentiation process of embryonic granulosa cells, we observed that specific genes—GATA4, FOXL2, AMHR2, CYP19A1, and FSH—were downregulated in Turner syndrome-derived granulosa cells (TS-GCs). Additionally, dysregulation of the cell cycle was observed in TS-GCs. To reveal the endogenous defects in the TS-GCs, we conducted a comparison of the global transcriptome patterns between differentiated granulosa cells derived from iPSCs in both healthy and Turner syndrome groups. The apelin/APJ pathway displayed a differential between the healthy and TS groups. Supplementation of apelin ligands and activation of apelin/APJ downstream signals via Akt/PKB restored the cell cycle progression and marker gene expression. We hypothesize that during early embryonic development failures in apelin/APJ signaling in GCs in Turner syndrome patients leads to abnormalities in ovarian development and consequently to early loss of oocytes and infertility.

overall_design: We developed and employed an optimized granulosa cell differentiation protocol to exam the granulosa cells’ function as a ‘disease in a dish’’ model using iPSCs. We differentiated iPSCs reprogrammed from TS probands and unaffected individual fibroblasts into ovarian granulosa cells.The generated hiPSC lines corresponding to each original fibroblast source are listed as follows: Control group includes GRC-WT2-10 (AG02102) and GRC-WT4-4 (AG08470); Disease group includes GRC-TS1-1 (GM01176), GRC-TS1-2 (GM01176), GRC-TS2-4 (GM06563) and GRC-TS2-6 (GM06563); Normal group includes four luteinized adult granulosa cells (cumulus GC).

first: Wei-Ju

last: Chen


title: Transcriptional analysis of ocular tissue from MCMV infected neonatal mice treated with CXCR3 blocking antibody

city: Philadelphia

first: Jessica

last: McCord

state: PA

institute: Thomas Jefferson University

summary: Congenital CMV is the leading cause of congenital infections leading to several different neurological complications including ocular pathology. MCMV infeciton of newborn BALB/c mice is a known mouse model to study human infection. Here we evaluated transcriptional changes in the eye caused by blocking CXCR3 during MCMV infection.

overall_design: Balb/c mice were infected with MCMV or injected with PBS (controls) less than 24hrs after birth. Mice infected with MCMV were treated with anti CXCR3 blocking antibody or an irrelavant control antiboy at post natal day 0, 5 and 10.  Whole eyes were collected from 5 mice per group at post natal day 15 . The retina and RPE/choroid were seperated from the rest of the ocular tissue for RNA extraction.

first: Christopher

last: Snyder


title: microRNA-637/661 ameliorate hypoxic induced pulmonary arterial hypertension by targeting TRIM29 signaling pathway

city: Suzhou

first: Jie

last: Zhou

state: Jiangsu

address: NO.242, Guangji Road

institute: Suzhou Municipal Hospital

summary: To investigate the synergistic effect of miR637/miR661 in PAH regulation, we overexpressed these two microRNAs in HPASMC cells cultured in a low oxygen environment.We then performed the RNA-seq assay to analysis gene expression profiles.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for overexpressing miR637 and miR637 in HPASMC cultured in low oxygen environment.

first: Liyang

last: Jiang


title: Effect of feeding on gene expression in HEK-293E cells either treated with Torin1 or not.

summary: We examined how mTORC1 influences mRNA expression and alternative splicing during a growth response in human embryonic kidney (HEK) 293E cells, in which mTORC1 is not hyperactive.  We released a starvation-induced growth arrest by refeeding, then analyzed mRNA levels and alternative splicing events one and four hours later under either control or Torin1 treatment conditions.

overall_design: To investigate the nutrient response on gene expression, we treated HEK-293E cells with either 1 or 4 hours of feeding, with or without Torin1 treatment.


title: Gonadotropin-releasing hormone 3 and gonadotropes relationships in female zebrafish pituitary revealed by single-cell transcriptomics

first: Sakura

last: Tanaka

state: CA

address: 1201 Welch Road

institute: Stanford University

summary: Gonadotropin-releasing hormone (GnRH) governs reproduction in vertebrates by regulating pituitary gonadotropins. Zebrafish, however, is an exception as gnrh3–/– fish, which lack the hypophysiotropic GnRH3, are fertile, suggesting that zebrafish utilizes a Gnrh-independent mechanism to regulate reproduction. To elucidate the role of Gnrh3 and the Gnrh-independent mechanisms that regulate the pituitary gonadotropes, we profiled the gene expression in individual pituitary cells of wild-type and gnrh–/– adult female zebrafish and identified transcriptionally defined cell types. The classical Lh and Fsh gonadotropes expressed both gonadotropin beta subunits with a ratio of 13:1 (lhb:fshb) and 40:1 (fshb:lhb), respectively. We discovered that Lh gonadotropes predominantly express genes encoding receptors for Gnrh (gnrhr2), thyroid hormone, estrogen, dopamine, and steroidogenic factor 1 (SF1). No Gnrh receptor expression was enriched in Fsh gonadotropes, instead, the expression of cholecystokinin receptor (cckrb) and galanin receptor (gal1rb) were enriched in these cells. The hereditary loss of Gnrh3 gene resulted in downregulation of fshb in Lh gonadotropes. Likewise, targeted chemogenetic ablation of Gnrh3 neurons led to a decrease in the number of fshb+/lhb+ cells. Our studies suggest that Gnrh3 directly acts on Lh gonadotropes through Gnrhr2, but the outcome of this interaction is still unknown. Gnrh3 also regulates fshb expression, probably via a non-Gnrh receptor route. Altogether, while Lh secretion and synthesis are likely regulated by multiple factors in a Gnrh-independent manner, Gnrh3 seems to play a role in the cellular organization of the pituitary in zebrafish.

overall_design: Pituitaries of WT and Gnrh3 knockout female zebrafish were dissociated and analyzed using single cell RNA sequencing

first: Tanaka

last: Sakura

first: Yu

last: Yang

first: Levavi-Sivan

last: Berta

first: Zmora

last: Nilli

first: Zohar

last: Yonathan


title: Heart failure with preserved ejection fraction in pigs causes shifts in post transcriptional regulation of matrix associated pathways

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

summary: Background: Left ventricular pressure overload (LVPO) can lead to heart failure with a preserved ejection fraction (HFpEF), whereby increased LV chamber stiffness (LV Kc) is a hallmark. However, how post-transcriptional pathways, specifically microRNAs (miRs) may contribute to increased LV Kc and HFpEF progression remains unclear. This project tested the central hypothesis that the development of HFpEF secondary to a prolonged LVPO stimulus, will result in a shift in miRs that will be related to LV Kc. Methods: LVPO was induced in pigs (n=9) by sequential occlusion of an ascending aortic cuff and studies performed at 5 weeks of LVPO. Age and weight matched pigs (n=6) served as referent controls. LV function and left atrial area (LA) were measured by echocardiography and LV Kc by speckle tracking. LV myocardial miRs were quantified using an 84 miR array (rt-PCR). Results: LA area, LV mass, and Kc- increased with LVPO consistent with the HFpEF phenotype. A total of 36 (43%) miRs shifted of which 18 miRs correlated to LV Kc. An additional 29 miRs correlated to LA dilation. These miRs mapped to functional domains relevant to Kc such as fibrosis and calcium handling. Conclusion: These unique findings identified a specific set of miRs that change with the development of HFpEF and related to LV stiffness properties and thus may hold relevance in terms of prognosis and therapeutic targets.

first: Stephanie

last: Samani

first: Francis

last: Spinale

first: Hao

last: Ji

first: Michael

last: Shtutman


title: Transcriptional profiling of eyes from MCMV infected neonatal mice during retinal development

summary: Congenital CMV is the leading cause of congenital infections leading to several different neurological complications including ocular pathology. MCMV infeciton of newborn BALB/c mice is a known mouse model to study human infection. Here we evaluated transcriptional changes caused by the infection in the eye over the course of development from post natal day 5 to 28.

overall_design: Balb/c mice were infected with MCMV or injected with PBS (controls) less than 24hrs after birth and whole eyes were collected for RNA extraction on post natal day 5, 10, 15 and 28. 6 eyes from 6 mice were used for each time point. Each sample contains 2 eyes combined.


title: Effect of the reduced mTORC1 activity on gene expression in LAM cells

first: Takafumi

last: Ogawa

summary: mTORC1 is inhibited by rapamycin or Torin1 in lymphangioleiomyomatosis (LAM) 621-101 (TSC2-deficient) cells, in which mTORC1 activity is elevated, and we compared these effects to inhibition of S6K and its target SRPK2.

overall_design: To investigate the effect of mTORC1 inhibition on gene expression, we assessed the gene expression affected by Rapamycin, Torin1, an S6K inhibitor PF4708671(PF), an SRPK1 inhibitor SRPIN340 (SRPIN), or SRPK2 knockout(SRPK2KO) in LAM cells.

first: Ziyun

last: Wu

first: Meltem

last: Isik

first: T

last: Blackwell


title: Key Codonopsis pilosula Seedlings Drought-Responsive Genes and Pathways Revealed by Comparative Transcriptome

city: lanzhou

first: hongyan

last: Wang

state: gansu

address: No. 1 yingmen village, Anning district

department: College of Agronomy

institute: Gansu Agricultural University

summary: To unravel the molecular mechanisms underpinning Codonopsis pilosula drought stress tolerance, we conducted comprehensive comparative transcriptome and physiological analyses of two C. pilosula cultivars that had been exposed to drought treatment for four days.

overall_design: The test cultivars of C. pilosula were Weidang No. 1 (Q2/W1), a variety promoted in Dingxi, Gansu Province (the seed was obtained from the Dry Farming Research and Promotion Center of Dingxi, Gansu Province), and Gandang No. 1 (Q4/G1), a cultivar selected by the group of Yuan Chen and Feng-xia Guo of Gansu Agricultural University. All were naturally shade-dried seeds harvested in the same year.

first: Hongyan

first: Yuan

last: Chen

first: Lanlan

last: Liu

first: Fengxia

last: Guo


title: The Similarity and Difference: Response and Molecular Characteristics of Peripheral Sensory Neurons Associated to Pain and Itch

first: Li

state: Please select...

address: Shanghai Pudong New Area Renji Hospital

institute: shanghai jiaotong university

summary: The dorsal root ganglion (DRG) neurons take in charge of primary detection and transmission of peripheral pain and itch stimuli, however, as two distinct noxious sensation, it is still attractive for this field that how the DRG neurons differentially response and code pain and itch. Here, we investigate the response and activation spectrum of DRG neurons under peripheral pain and itch stimuli using in vivo two-photon calcium imaging, and find differences in the responsive intensity to pain and itch between multisensory neurons (both pain and itch) and single-sensory neurons (either pain or itch). Besides, single-cell RNA sequencing (scRNA-seq) is used to reveal the heterogeneity of distinct subpopulations based on their expression of pain- or itch-related marker genes and indicates the similarity and difference of their transcriptomic changes under chronic pain and itch. Our results will provide fundamental insights to the peripheral pain and itch differential coding mechanism, moreover, benefit the development of pain and itch therapies.

overall_design: High-throughput analyses the lumbar4-5 dorsal root ganglia(DRG)  from acetone-ether-water (AEW) mice to descibe transcriptomic profiles under itch state. There are  2 samples from the AEW group.

first: Jiemin

last: Yin

first: Youqiang

last: Meng

first: Congrui

last: Ye

first: Junhui

first: Sa

first: Wen

first: Po

last: Gao

first: Yingfu

last: Jiao

first: Weifeng

last: Yu

first: Yinghui

last: Fan


title: Transcriptome profiles characteristics of peripheral immune in Severe Fever with Thrombocytopenia Syndrome patients

city: Jinan

first: yuwei

last: Zhang

state: Shandong

address: No.16992 Jingshi Road

department: Pathogenobiology

institute: SDCDC

summary: To investigate the response mechanisms of Severe fever with thrombocytopenia syndrome (SFTS) patients, we conducted transcriptomic analysis of peripheral immunity in 14 SFTS patients, ranging from modal infection to severe and fatal disease. Our results observed the potential mechanism for the heterogeneity of clinical symptoms, which can further elucidate the interaction between viruses and hosts and contribute to clinical treatment.

overall_design: we conducted transcriptomic analysis of peripheral immunity in 6 healthy individuals and 14 SFTS patients, ranging from modal infection to severe and fatal disease.

first: Xiaolin

last: Jiang

first: Yuwei

first: Xiangjuan

first: Qing

last: Duan


title: Single-cell sequencing of the PBMC of dialysis patients

status: Public on Nov 22 2024

city: New York

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

summary: By using 10X Genomics technology, single-cell RNA sequencing (scRNAseq) of the PBMCs from two dialysis patients with high and low risk of development of early acute rejection (EAR) post transplant to identify immune cell subpopulations and their transcriptomic signatures associated with the risk of EAR. Analysis of the transcriptomic profiles of a total number of 11,966 cells determined NK and T cell subsets association with the EAR risk, especially decreased CD56Dim and increased CD4 CTL populations in high risk patients.

overall_design: Single-cell profiling of PBMC identified immune cell modulation associated with the risk of early acute rejection.

first: Jia

last: Fu


title: Arginine methylationof the p30 C/EBPα oncoprotein regulates progenitor proliferationand myeloid differentiation

city: Berlin

first: Achim

last: Leutz

address: Robert-Rössle-Straße 10

country: Germany

institute: Max Delbrück Center

summary: The transcription factor CCAAT enhancer binding protein alpha (C/EBPα) is a master regulator of myelopoiesis. CEBPA encodes a long (p42) and a truncated (p30) protein isoform from a single mRNA. Mutations that abnormally enhance expression of p30 are associated with acute myelogenous leukemia (AML). We show by mutational analysis that three highly conserved arginine residues (R140,147,154) located at the p30 C/EBPα N-terminus, previously found to be methylated, are involved in myeloid lineage commitment, progenitor proliferation, and differentiation. The conservative amino acid substitution with lysine that retains the amino acid side chain charge enhanced progenitor proliferation, while a non-conservative substitution with uncharged side chains (alanine or leucine) impaired proliferation and enhanced granulopoietic differentiation. Analysis of protein-protein interactions (PPI) suggested that arginine methylation of p30 C/EBPα differentially determines its capacity to interact with SWI/SNF and MLL complexes. Pharmacological targeting of p30 C/EBPα arginine methylation may have clinical relevance in myeloproliferative and inflammatory diseases, in neutropenia, and in leukemic stem cells.

overall_design: To investigate the role of arginine methylation in celll differentiation and proliferation, the three arginine residues of-interest were replaced by alanine (A), leucine (L) or lysine (K). Mouse CebpaΔ/ΔCebpbΔ/Δ v-Abl transformed pre-B cells ( termed dKO-B cells) were retrovirally infected with virus carrying pMSCV-IRES-EGFP-based p30 constructs (including WT or A, L, K mutated constructs). After virus infection, EGFP+ cells were sorted at day 4 p.i. and subjected to bulk RNA-sequencing. Quadruplicate samples harvested in different batches were processed altogether (RNA extraction, library preparation and sequencing).

first: Linh

last: Nguyen

first: Karin

last: Zimmermann

first: Elisabeth

last: Kowenz-Leutz

first: Dorothea

last: Dörr

first: Anja

last: Schütz

first: Jörg

last: Schönheit

first: Alexander

last: Mildner


title: The potential global neutralizing effects of AB-free kava against cigarette smoke exposure in mice

city: Gainesville

first: Chengguo

last: Xing

state: FL

address: 1345 Center Drive

institute: University of Florida

summary: RNA seq was applied to the lung and liver tissues from mice with different treatment regimen to evaluate the potential effects on global transcription.

overall_design: There are four groups: control, tobacco, kava, and tobacco + kava

first: Tengfei

last: Bian

first: Allison

last: Lynch

first: Zhiguang

last: Huo

first: Haocheng

last: Ding

first: Zhixin

last: Tang


title: RADIP technology comprehensively identifies H3K27me3-associated RNA–chromatin interactions

city: Yokohama

first: XUFENG

last: SHU

state: Kanagawa

address: 1 Chome-7-22 Suehirocho, Tsurumi Ward

department: IMS

institute: RIKEN

summary: Many RNAs associate with chromatin, either directly or indirectly. To investigate the function of these RNAs, many technologies for mapping regions where RNAs interact across the genome have been developed. Adding information on the proteins involved in these RNA–chromatin interactions is critical for further analysis. Here, we developed RADIP (RNA and DNA interacting complexes ligated and sequenced (RADICL-seq) with immunoprecipitation), a novel technology that combines RADICL-seq technology with chromatin immunoprecipitation to characterize RNA–chromatin interactions mediated by individual proteins. We applied an anti-H3K27me3 antibody to the RADIP technology and generated libraries from mouse embryonic stem cells. We identified various RNAs, including protein-coding RNAs and non-coding RNAs, that were associated with chromatin via H3K27me3 mediation and that may facilitate the spread of Polycomb repressive complexes over broad regions of the mammalian genome.

overall_design: To Identify genome-wide H3K27me3-mediated RNA-chromatin interactions in mouse ESC.

first: Xufeng

last: Shu

first: Masaki

last: Kato

first: Piero

last: Carninci


title: Golgi-ER Axis Regulates Anti-Tumor T Cell Immunotherapeutic Response

city: Charleston

first: Stefano

last: Berto

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

summary: The cumulative role of cellular organelle’s in shaping the life and function of a cell has been long acknowledged. While each organelle plays a specific role in the growth and development of T cells, numerous studies have thus far focused on targeting mitochondria, endoplasmic reticulum, or lysosome related pathways to improve anti-tumor T cell immune response. Here we highlight the tumor microenvironment (TME) mediated disruption of Golgi architecture and function, termed Golgi stress, contributes to altered redox signaling and affects cell survival. Importantly, the decreased expression if GM130, a marker of Golgi stress and indicating the disruption of Golgi architecture, was reverted upon treatment with hydrogen sulphide (H2S) donor GYY4137, or over expressing cystathionine β-synthase (Cbs), an enzyme involved in biosynthesis of endogenous H2S. Activation and expansion of tumor reactive TCR or chimeric antigen receptor bearing T cells expanded with exogenous H2S promoted stemness, antioxidant capacity and exhibited an increase effector cytokine secretion that correlated to increased protein translation. In in vivo models of melanoma and lymphoma, anti-tumor T cells conditioned ex vivo with exogenous H2S or overexpressing Cbs demonstrated superior tumor control upon ACT. Further, sorting anti- tumor T cells based on Golgi structure and abundance resulted in identification of a Golgihi subset of T cells with a unique metabolic signature, superior fitness, and enhanced anti-tumor capacity. These data suggest that H2S can be used an immunomodulatory agent to enhance the efficacy of ACT, and that the structure and function of the Golgi apparatus is an important feature of T cells that determines their anti-tumor capacity.

overall_design: Splenocytes isolated from the spleens of Pmel-1 mice were activated with gp100 peptide in the presence or absence of H2S (GYY4137 0.5mM) treatment for 3 days and expanded for 3 more days. Control and H2S-treated T cells were then isolated for mRNA isolation.

first: Nathaniel

last: Oberholtzer

first: Shikhar

last: Mehrotra


title: Investigating the Etiology of Craniofacial and Cardiac Malformations in a Mouse Model of SF3B4-Related Syndromes

city: Montreal

first: Loydie

last: Jerome-Majewska

state: QC

address: 1001 Decarie Blvd EM0.2210

department: Pediatrics

country: Canada

institute: McGill University Health Centre Glen Site

summary: Pathogenic variants in SF3B4 are responsible for the acrofacial disorders Nager and Rodriguez Syndrome, also known as SF3B4-related Syndromes, associated with malformations in the head, face, limbs, vertebrae as well as the heart. To uncover the etiology of craniofacial malformations found in SF3B4-related syndromes, mutant mouse lines with homozygous deletion of Sf3b4 in neural crest cells (NCC) were generated. Like in human patients, these embryos had craniofacial and cardiac malformations with variable expressivity and penetrance. The severity and survival of Sf3b4 NCC mutants was modified by the level of Sf3b4 in neighbouring non NCC. RNA sequencing analysis of heads of embryos prior to morphological abnormalities showed significant changes in expression of genes forming the NCC regulatory network, as well an increase in exon skipping. We identified several key transcription factors and histone modifiers involved in craniofacial and cardiac development with increased exon skipping. Increased exon skipping was also associated with use of a more proximal branch point, as well as an enrichment in thymidine bases in the 50bp around the branch points. We propose that decrease in Sf3b4 causes changes in the expression and splicing of transcripts required for proper craniofacial and cardiac development, leading to abnormalities.

overall_design: To investigate the role of Sf3b4 in craniofacial development we generated mouse embryos with deletion of Sf3b4 in neural crest cells. Heads of 3 embryos prior to morphological abnormalities were pooled. 3 such pools were generated and analysed from Sf3b4 wild type and Sf3b4 neural crest cell mutant embryos.

first: Shruti

last: Kumar

first: Eric

last: Bareke

first: Jacek

last: Majewski


title: Epigenetic Regulation of Non-canonical Menin Targets Modulates Menin Inhibitor Response in Acute Myeloid Leukemia

city: Birmingham

first: xinyue

last: zhou

state: Alabama

address: WTI 510G 1824 6th Ave S

department: hematology and oncology

institute: university of alabama at birmingham

summary: Menin inhibitors that disrupt Menin-MLL interaction hold promise for treating specific acute myeloid leukemia subtypes, including KMT2A rearrangements (KMT2A-r), yet resistance remains a challenge. Here, through systematic chromatin-focused CRISPR screens, along with genetic, epigenetic, and pharmacologic studies in a variety of human and mouse KMT2A-r AML models, we uncover a potential resistance mechanism independent of canonical Menin-MLL targets. We show that a group of non-canonical Menin targets, which are bivalently co-occupied by active Menin and repressive H2AK119ub marks, are typically downregulated following Menin inhibition. The loss of Polycomb Repressive Complex 1.1 (PRC1.1) subunits, such as PCGF1 or BCOR, leads to Menin inhibitor resistance by epigenetic reactivation of these non-canonical targets, including MYC. Genetic and pharmacological inhibition of MYC can resensitize PRC1.1-deficent leukemia cells to Menin inhibition. Moreover, we demonstrate that leukemia cells with the loss of PRC1.1 subunits exhibit reduced monocytic gene signatures and are susceptible to the BCL2 inhibition, and combinational treatment of venetoclax overcomes the resistance to Menin inhibition in PRC1.1-deficient leukemia cells. These findings highlight the important roles of PRC1.1 and its regulated non-canonical Menin targets in modulating Menin inhibitor response and provide potential strategies to treat leukemias with compromised PRC1.1 function.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PRC1.1 complex components knockout in MLL-r AML cells treated with DMSO or VTP50469.

first: Xinyue

last: Zhou

first: Rui

last: Lu


title: Progranulin enhances the engraftment of transplanted human iPS cell-derived cerebral neurons

city: Fukuoka

first: Keitaro

last: Yamagami

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

institute: Kyushu University

summary: Cerebral organoids (COs) in cell replacement therapy offer a viable approach to reconstructing neural circuits for individuals suffering from stroke or traumatic brain injuries. Successful transplantation relies on effective engraftment and neurite extension from the grafts. Earlier research has validated the effectiveness of delaying the transplantation procedure by one week. Here, we hypothesized that brain tissues one week following a traumatic brain injury possess a more favorable environment for cell transplantation when compared to immediately after injury. We performed a transcriptomic comparison to differentiate gene expression between these two temporal states. In controlled in vitro conditions, recombinant human progranulin (rhPGRN) bolstered the survival rate of dissociated neurons sourced from human-induced pluripotent stem cell-derived cerebral organoids (hiPSC-COs) under conditions of enhanced oxidative stress. This increase in viability was attributable to a reduction in apoptosis via Akt phosphorylation. In addition, rhPGRN pretreatment before in vivo transplantation experiments augmented the engraftment efficiency of hiPSC-COs considerably and facilitated neurite elongation along the host brain’s corticospinal tracts. Subsequent histological assessments at three months post-transplantation revealed an elevated presence of graft-derived subcerebral projection neurons—crucial elements for reconstituting neural circuits—in the rhPGRN-treated group. These outcomes highlight the potential of PGRN as a neurotrophic factor suitable for incorporation into hiPSC-CO-based cell therapies.

overall_design: Examination of gene expression level in 2 kinds of mouse brain tissues (immediately after brain injury and 1-week after brain injury). The number of samples including each group is 4.

first: Jun

last: Takahashi


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

overall_design: Refer to individual Series


title: DNA methylation classifier to diagnose pancreatic ductal adenocarcinoma metastases from different anatomical sites

first: Mihnea

middle: P.

last: Dragomir

state: Berlin

address: 1 Charitéplatz

department: Pathology

institute: Charité - Universitätsmedizin

summary:
Background
We have recently constructed a DNA methylation classifier that can discriminate between pancreatic ductal adenocarcinoma (PAAD) liver metastasis and intrahepatic cholangiocarcinoma (iCCA) with high accuracy (PAAD-iCCA-Classifier). PAAD is one of the leading causes of cancer of unknown primary and diagnosis is based on exclusion of other malignancies. Therefore, our focus was to investigate whether the PAAD-iCCA-Classifier can be used to diagnose PAAD metastases from other sites.

Methods
For this scope, the anomaly detection filter of the initial classifier was expanded by 8 additional mimicker carcinomas, amounting to a total of 10 carcinomas in the negative class. We validated the updated version of the classifier on a validation set, which consisted of a biological cohort (n = 3579) and a technical one (n = 15). We then assessed the performance of the classifier on a test set, which included a positive control cohort of 16 PAAD metastases from various sites and a cohort of 124 negative control samples consisting of 96 breast cancer metastases from 18 anatomical sites and 28 carcinoma metastases to the brain.

Results
The updated PAAD-iCCA-Classifier achieved 98.21% accuracy on the biological validation samples, and on the technical validation ones it reached 100%. The classifier also correctly identified 15/16 (93.75%) metastases of the positive control as PAAD, and on the negative control, it correctly classified 122/124 samples (98.39%) for a 97.85% overall accuracy on the test set. We used this DNA methylation dataset to explore the organotropism of PAAD metastases and observed that PAAD liver metastases are distinct from PAAD peritoneal carcinomatosis and primary PAAD, and are characterized by specific copy number alterations and hypomethylation of enhancers involved in epithelial-mesenchymal-transition.

Conclusions
The updated PAAD-iCCA-Classifier (available at https://classifier.tgc-research.de/) can accurately classify PAAD samples from various metastatic sites and it can serve as a diagnostic aid.

overall_design:
Internal testing of a classifer using 16 FFPE samples after Infinium HD FFPE DNA Restore Kit and analyed using Illumina Infinium MethylationEPIC BeadChip.
Internal testing of a classifer using 25 FFPE samples after Infinium HD FFPE DNA Restore Kit and analyzed using Illumina Infinium MethylationEPIC BeadChip v1/v2
The updated PAAD-iCCA-Classifier (available at https://classifier.tgc-research.de/) can accurately classify PAAD samples from various metastatic sites and it can serve as a diagnostic aid.

first: Teodor

last: Calina


title: PARN is essential to GSIS in beta cells

city: BEIJING

address: Malianwa street

institute: China Agriculture University

summary: To investigated the function of PARN in beta cells, we generated the specific deletion of Parn in beta cells.

overall_design: Explore RNA directly bound by PARN

first: Xiaomei

last: Xie


title: The micro RNA expression of 5 nomal breast tissues and 15 breast cancer tissues

city: Gunma

first: Sasagu

last: Kurozumi

address: 3-39-22, Showa, Maebashi

department: General Surgical Science

institute: Gunma University

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are short non-coding RNAs that regulate the function of target genes at the post-transcriptional phase. MiRNAs are considered to play roles in the development, progression and metastasis of cancer. Recent studies have indicated that particular miRNA signatures are correlated with tumor aggressiveness, response to drug therapy, and patient outcome in breast cancer. In the present research, we would like to evaluate the morphological and biological characters of breast cancer stratified by miRNAs signature.

overall_design: The frozen tissue samples from 5 normal breast tissue and 15 invasive breast cancer diagnosed at Gunma University were initially retrieved, and the statuses of ER and HER2 were assessed and the intrinsic subtypes of these breast cancers decided (ER-positive/HER2-negative: 5 cases; HER2-positive/ER-negative: 5 cases; triple negative: 5 cases).

first: Naohiko

last: Seki


title: Immunosuppressive inflammation driven by LPS/TLR4 signalling in hepatocellular carcinoma with low immune cell infiltration

city: Villejuif

first: Sylvie

last: JOB

address: UMR-S 1193 INSERM/Université Paris Saclay Hôpital Paul Brousse

country: France

institute: INSERM

type: Expression profiling by genome tiling array

summary: Non-inflamed liver tumors (i.e. immunologically silent and desert phenotype) account for two-thirds of hepatocellular carcinomas (HCC) and represent a major challenge for immune-based cancer therapies. Elucidating the factors behind the lack of T cell response would enable us to define an appropriate therapy to induce antitumor immunity based on tumor immunobiology. We applied unsupervised machine learning to the transcriptome of a rigorously selected set of non- or poorly infiltrated HCC, identified independent modular components and explored their characteristics through gene enrichment analysis and integration of molecular, cytometric, immunohistochemical and clinicopathological data. Here we demonstrate that non-/poorly infiltrated HCC (referred to as cold HCC) exhibits intricate, multi-layered mechanisms by which tumors evade the immune response. These include the recruitment of immunosuppres-sive myeloid cells into the tumor microenvironment (TME) in relation to tumor richness in Gram-negative bacterial lipopolysaccharide (LPS) and activation of the LPS/TLR4 signaling pathway. LPS-containing cold HCCs undergo immunosuppressive inflammation, likely via activation of the EGFR, LPS/TLR4 and NFKB signaling pathways. This is associated with increased expression of the checkpoint inhibitor TIM3 and its ligand, galectin 9 (Gal9). All the immune evasion factors detected in cold HCC are also at play in infiltrated HCC, suggesting in the latter the presence of TME regulatory signals opposing them. This study highlights mechanisms of immune tolerance in non-infiltrated HCC and supports the role of tumor ex-trinsic mechanisms in regulating tumor immunity in HCC.

overall_design: 67 HCC tumors and 15 non-tumors were selected  for RNA extraction and hybridization on Affymetrix microarrays.

first: L

last: Al Asadi

first: S

last: Job

first: H

last: Halse

first: A

last: Dos Santos

last: Laurent-Bellue

first: N

last: Moniaux

last: Deshayes

last: Bigorgne

first: M

last: Bonvalet

first: R

last: Adam

first: D

last: Azoulay

last: Castaing

last: Cherqui

last: Sa Cuhna

first: O

last: Rosmorduc

first: C

last: Guettier

first: E

last: Vibert

last: Marabelle

first: J

last: Faivre


first: xinyue

last: zhou

overall_design: ChIP-seq data for PRC1.1 complex components knockout in MLL-r AML cells treated with DMSO or VTP50469.

first: Xinyue

last: Zhou

first: Rui

last: Lu


title: Comprehensive transcriptome profiling and functional analysis of the meagre (Argyrosomus regius) immune system

city: Valdeolmos

first: Pedro

last: Perdiguero

state: Madrid

address: Ctra. de Algete a El Casar Km 8.1

department: Animal Health Research Centre

country: Spain

institute: CISA-INIA

summary: Meagre (Argyrosomus regius) belongs to the family Sciaenidae and is a promising candidate for Mediterranean aquaculture diversifcation. As a relatively recent species in aquaculture, the physiological consequences of the immune system activation in meagre are understudied. Spleen, as a primary lymphoid organ has an essential role in meagre immune and inﬂammatory responses. In this study, we have evaluated the in vivo effects of lipopolysaccharide (LPS) on the spleen transcriptome of meagre by RNA-seq analysis at 4 and 24 h after injection. The assembled transcripts were assigned to immunological processes. At 24 h, the number and type of differential immune-related genes regulated by LPS was higher than at 4 h. However, at 4 h the upregulation of immune-related genes was greater. Several genes related to the innate immune response were upregulated including tolllike receptor 5, and multiple interferons and interferon-related proteins. In the present work, it was shown that several chemokines and chemokine ligands (e.g. cxcl10, ccl21) as well as cytokines (e.g. il1b, il12, il27) were overexpressed as a result of LPS injection, supporting their role as mediators of the innate and adaptive immune response. KEGG analysis found that LPS-stimulated immune responses mainly involve cytokine and protein-protein interactions involved in pathogen response. Specifcally, genes involved in the MHCI and MHCII pathways were induced as early as 4 h post LPS injection. These results will help to understand the pathogenesis and host defense system in meagre.

overall_design: Individual juvenile fish (22 g) of meagre (Argyrosomus regius) were divided into two groups and injected intraperitoneally with 10 μg/g fsh of lipopolysaccharides (LPS) extracted from Photobacterium damselae subsp. piscicida Lg41/01 or phosphate buffer saline (PBS).  The spleen was removed from 12 fish pooled into 3 groups of 4 fish for each sampling point (4 and 24 h), both from PBS treated fish (control samples) and LPS treated fsh (experimental samples) at 4 h and 24 h after treatment [n = 3 (pools, 4 fish/pool)/treatment/sampling point)]

first: P

last: Monteiro

last: Díaz-Rosales


title: Sodium oligomannate disrupts the adherence of Ribhigh bacteria to gut epithelia to block SAA-triggered Th1 inflammation in 5XFAD transgenic mouse

city: SAN DIEGO

first: Xinyi

state: California

address: 9500 Gilman Dr, La Jolla

institute: University of California, San Diego

summary: Sodium oligomannate (GV-971), an oligosaccharide drug approved in China for treating mild-to-moderate Alzheimer's disease (AD), was previously found to recondition the gut microbiota and limit altered peripheral Th1 immunity in AD transgenic mice. As a follow-up study, we here provide advances by pinpointing a Lactobacillus murinus strain that highly expressed a gene encoding a putative adhesin containing Rib repeats (Ribhigh-L.m.) that was particularly enriched in 5XFAD transgenic mice. Mechanistically, Ribhigh-L.m. adherence to the gut epithelia upregulated fecal metabolites, among which lactate ranked as the top candidate. Lactate stimulated the epithelial production of serum amyloid A (SAA) in gut via GPR81-NFκB axis, contributing to peripheral Th1 activation. Moreover, GV-971 disrupted the adherence of Ribhigh-L.m. to gut epithelia via directly binding to Rib, leading to the reduced SAA and alleviated Th1-skewed inflammation. These findings were replicated in early-staged AD patients. Together, we gained further insights between gut bacteria and AD progression and the mechanism of GV-971 in treating AD.

overall_design: Intrabacterial whole RNA sequencing from each purified lactobacillus murinus bacteria strains isolated from the fecal samples of 41-week-age WT and Tg mice in 5XFAD Alzheimer's disease models

last: Wang

first: Zuoquan

last: Xie

first: Jie

last: Yuan

first: Enjing

last: Jin

first: Wen

last: Lian

first: Shuaishuai

last: Chang

first: Guangqiang

last: Sun

first: Zhengnan

last: Feng

first: Hui

last: Xu

first: Chen

last: Du

first: Xinying

last: Yang

first: Aihua

last: Xia

first: Ji

last: Qiu

first: Qingli

last: Zhang

first: Feifei

last: Lin

first: Jia

last: Liu

first: Liang

last: Li

first: Xiaoguang

first: Zhongping

last: Xiao

first: Zhou

last: Yi

first: Zhiyu

last: Luo

first: Changrong

last: Ge

first: Mingyue

last: Zheng

first: Yi

last: Jiang

first: Tao

first: Jing

first: Qihao

last: Guo

first: Meiyu

last: Geng


title: KCNB1-Leptin receptor complexes couple electric and endocrine function in the melanocortin neurons of the hypothalamus

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary: The neurons of the melanocortin system regulate feeding and energy homeostasis through a combination of electrical and endocrine mechanisms. However, the molecular basis for this functional heterogeneity are poorly understood. Here, a voltage-gated potassium (K+) channel named KCNB1 (alias Kv2.1), formed stable complexes with the leptin receptor (LepR) in proopiomelanocortin (POMC) expressing neurons of the Arcuate nucleus of the hypothalamus (ARCPOMC). Mice lacking functional KCNB1 channels (NULL mice), exhibited constitutive depolarization of ARCPOMC neurons along with aberrant POMC production. In NULL neurons, canonical LepR-STAT3 signaling--which underlies POMC production--was impaired, whereas non-canonical insulin receptor substrate PI3K/Akt/FOXO1 and ERK signaling were significantly upregulated. Accordingly, the NULL animals were insensitive to anorexic stimuli induced by leptin administration and produced less adipose tissue and circulating leptin than WT animals. Taken together, these findings unveil an exquisite mechanism of metabolic regulation whereby synergistic control of neuronal excitability and endocrine function is achieved through the partnership between a K+ channel and a hormone receptor. As aberrant KCNB1 channels cause developmental and epileptic encephalopathies, these results further establish a K+ channel as a causative link between epileptic and metabolic disorders.

overall_design: The goal was to use transcriptome analysis to determine differences in mRNA levels in the hypothalami of C57BL6/J mice (wild type, WT) and homozygous Kcnb1NULL KI mice (C57BL/6J-Kcnb1em2Sesf/J) here called NULL. The Kcnb1NULL allele bears a nonsense (stop) mutation in the exon coding for the S4 transmembrane domain of the KCNB1 protein. This results in a truncated protein (37 kDa vs  110 kDa of the WT protein) that is not trafficked to the plasma membrane and is quickly degraded. Results from preclinical models of obesity have not underscored a clear sex-dependence. Therefore age-matched animals of either sexes were used. Specifically we used one WT and one NULL six month-old and two WT and two NULL one month-old animals (total 6 mice).

first: Elena

last: Forzisi-Kathera-Ibarra

first: Leonard

last: Castillo

first: Christian

last: Roser

first: Anika

last: Gaur

first: Prachi

last: Lad

first: Stefania

last: Dutto

first: Pinguye

last: Pan

first: Federico

last: Sesti


title: Analysis of Molecular Mechanism of Singapore grouper iridovirus (SGIV) Infection by single cell RNA sequencing (scRNA-seq)

city: Guangzhou

first: Huang

last: Youhua

address: Wushan Street five road No. 483

institute: South China Agricultural University

summary: The spleen of grouper is the target organ of SGIV attack.We used single cell RNA sequencing (scRNA-seq) to analyze the effect of SGIV infection on spleen cells of Epinephelus Lanceolatus.

overall_design: The changes of spleen of Epinephelus Lanceolatus before and after SGIV infection were detected by single cell RNA sequencing.

first: Youhua

last: Huang

first: Weihua

last: Xu

first: Xiaohong

first: Qiwei

last: Qin


title: Robust bisulfite free SMRT Sequencing of mdC based on a novel hpTet3-enzyme

city: Munich

first: Raheleh

last: Salehi

state: Bavaria

address: Würmtalstraße 201

department: Chemisty

institute: LMU

summary: Genomic DNA contains next to the four canonical nucleosides dA, dC, dG and T the additional base 5-methyldeoxycytidine (mdC). The presence of this methylated cytidine nucleoside in promoter regions or gene bodies has an instrumental effect on the transcriptional activity of the corresponding gene. The methylation patterns of genes are therefore responsible for either silencing or activation of genes. Sequencing of mdC positions in the genome is consequently of paramount importance for early cancer diagnostics in order to determine incorrect expression of genes. Today, the bisulfite method is the gold standard for mdC-sequencing, which has however the caveat that the majority of the input DNA is degraded during the bisulfite treatment. In addition, bisulfite sequencing is rather error prone. Here we report a benign, bisulfite free mdC sequencing method based on 3rd generation single molecule SMRT sequencing. The fundament of the technology is a new Tet3 enzyme that oxidizes mdCs with high efficiency to 5-carboxycytidine (cadC). caC in turn provides and excellent read out by SMRT sequencing using specially trained AI-based algorithms.

overall_design:
We developed a novel TET3 enzyme that oxidizes mdCs with high efficiency to 5-carboxycytidine (cadC) for biochemical and molecular biological application.
We created three different synthetic model genomes from whole-genome amplified (WGA) lambda genomes: (1) unmodifed DNA obtained from WGA, (2) M.SssI methylated DNA containing 5mC in CpG context, (3) hpTet3 oxidized M.SssI-DNA containing only 5caC in a CpG context.
Each DNA was subjected to UHPLC-QQQ-MS for qc of the individual enzymatic steps. Subsequently, each DNA was sequenced on a Sequel IIe system.
We evaluated and compared the kinetic porfiles from the Sequel IIe in the close proximity of a CpG site. In addition we used the individual data sets to train deep-learning algorithms for 5mC and 5caC and compared there performance with respect to recalling of CpG sites, accuracy and percision.

first: Hanife

last: Sahin

first: Shariful

last: Islam

first: Markus

last: Müller

first: Pascall

last: Giehr

first: Thomas

last: Carell


title: Effect of MIDKINE on in vitro culture of FLT3LG-bone marrow derived dendritic cells

city: Madrid

first: Xavier

last: Catena

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

institute: CNIO

summary: Gene expression analysis of the effect of MIDKINE (MDK) on bone marrow derived dendritic cells (BMDCs) cultured with Fms Related Receptor Tyrosine Kinase 3 Ligand (FLT3LG).

overall_design: Bone marrow cells from C57BL/6J mice were flushed and cultured with Fms Related Receptor Tyrosine Kinase 3 Ligand (FLT3LG) (50 ng/ml). On the 7th day FLT3LG) (50 ng/ml) was renewed with or without recombinant human MIDKINE (10 ng/ml) for 2 days. 500ng of total RNA samples were used. Each condition was analyzed in triplicates.

first: X

first: O

last: Graña-Castro

first: M

middle: S

last: Soengas


title: Expression Profile of  Whole Transcriptome Sequencing Analysis in Non-Small Cell Lung Cancer

city: Zhengzhou

first: Liping

last: Dai

state: Henan

address: 40 Daxue Road

institute: Zhengzhou University

summary: To characterize the differentially expressed circRNAs and lncRNAs between NSCLC tissues and paired adjacent noncancerous tissues

overall_design: Five NSCLC tissues and paired adjacent noncancerous tissues was performed by whole transcriptome sequencing analysis to demonstrate the expression profile of ncRNAs in NSCLC

first: Ting

last: Yang

first: Longtao

last: Ji


title: Single-cell transcriptomics of non-functioning and functioning PitNET subtypes reveals differences in the tumor microenvironment and tumor-specific gene expression signatures that correlate with aggressive tumor growth

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

summary: Pituitary neuroendocrine tumors (PitNET) are among the most common intracranial tumors. Despite a frequently benign course, aggressive behavior occurs for unexplained reasons, especially in functional PitNET. Tumor behavior is known to be under the influence of the tumor microenvironment (TME). However, the relationship between TME cells and aggressive tumor behavior has not been adequately explored in PitNET. We used single-cell RNA sequencing and other analyses to comparatively characterize the transcriptome of seven gonadotroph and three lactotroph PitNET and correlate it with clinical behavioral patterns. In our lactotroph PitNET samples, we detect a highly proliferative gene profile with significantly increased expression levels in tumors with aggressive behavioral patterns within a bulk RNA-seq cohort of 134 PitNET samples. We also report high intratumoral heterogeneity in both gonadotroph and lactotroph PitNET and detect gene expression programs belonging to epithelial, endocrine and immunological functional networks in both subtypes. Direct comparison of the lymphoid compartment of both subtypes reveals increased CD4+ T cell abundances in gonadotroph and increased CD4-/CD8- double negative T cell and natural killer T cell abundances in lactotroph PitNET. Also notable is the presence of proliferative lymphocytes, whose occurrence in the bulk RNA-seq cohort positively correlates with more aggressive tumor behavior. Increased CD8+ T cell and natural killer (NK) cell abundancies, however, correlate significantly with reduced aggressiveness indicating anti-tumoral effects. Our study expands the knowledge of the differences in cellular composition of functional and non-functional PitNET subtypes and lays the foundation for further studies on the influence of lymphoid cells on the variable aggressive behavior of PitNET. Regarding the treatment of drug-resistant lactotroph PitNET, proliferative lymphocytes, CD8+ T and NK cells could represent potentially valuable targets for the development of new cancer immunotherapies in the future.

overall_design: Comparative gene expression profiling of seven gonadotroph and three lactotroph human PiNET by scRNAseq (10x Genomics)

first: T

last: Potthoff

first: Daniela

last: Jeising

first: Daniel

last: Münter

first: Eric

last: Suero-Molina

first: Walter

last: Stummer

first: Wolfgang

last: Hartmann

first: Matthias

last: Dottermusch

first: Lea

last: Altendorf

first: Ulrich

last: Schüller

first: Sophia

last: Scheuermann

first: Christian

last: Seitz

last: Albert

first: Kornelius

last: Kerl


title: Lymphatic-derived 25-hydroxycholesterol promotes immunity in melanoma by inhibiting PPAR-γ in tumor associated macrophages and monocytes

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

summary: In melanoma, lymphangiogenesis correlates with metastasis and poor prognosis and promotes immunosuppression. However, it also potentiates immunotherapy by supporting trafficking of immune cells. Lymphatic endothelial cells (LECs) are highly plastic cells that shape their phenotype according to distinct microenvironments, which likely define their functional properties, such as immunomodulation. Here, we show in a lymphangiogenic murine melanoma model that LECs upregulate the enzyme Ch25h, which catalyzes the formation of 25-hydroxycholesterol (25-HC) from cholesterol and plays important roles in regulating lipid metabolism, gene expression, and immune activation. LECs represent the main source of extracellular 25-HC in tumors, leading to the inhibition of PPAR- in intra-tumoral macrophages and monocytes. This prevents their immunosuppressive phenotype and instead promotes their conversion into proinflammatory myeloid cells that support effector T cell functions. We identify here in mechanistic detail a novel LEC function that supports anti-tumor immunity, which can be therapeutically exploited in combination with immunotherapy.

overall_design: mRNA profiles of lymphatic endothelial cells derived from tumors,  tumor draining lymph nodes and non draining lymph nodes in mice transplanted with lymphangiogenic mouse melanoma cell line

first: Juan

last: Dubrot

first: Dale

last: Brighouse

last: Lemeille

first: Stéphanie

last: Hugues


title: Sphingosine kinase 2 (SphK2) knockout alters metabolic gene expression in an early MASH mouse model

city: Richmond

first: Kaitlyn

last: Jackson

state: Virginia

address: 7414 Seminary Ave

department: Immunology

institute: VCU

summary:
To determine the effect of SphK2 KO on liver metabolic-associated gene expression in an early MASH mouse model
To determine the effect of WDSW on liver metabolic-associated gene expression in an early MASH mouse model

overall_design: Assessed two independent variables (diet, genotype) on on gene expression related to inflammation and the immune response in a MASH mouse model

first: Derrick

last: Zhao

first: Huiping

last: Zhou


title: Dcp1a, a novel Mek substrate, regulates the self-renewal and differentiation of mouse embryonic stem cells [RNA-seq]

status: Public on Nov 19 2024

city: Tianjing

first: Jiayu

last: Yu

address: Weijin street

institute: Nankai university

summary: Mek inhibitor is widely applied to maintain pluripotency, while prolonged Mek inhibition compromises the developmental potential of mouse embryonic stem cells (ESCs). To better understand the mechanism of Mek in pluripotency maintenance, we first demonstrated that Mek regulates gene expression at post-transcriptional steps. Consistently, many of the 66 Mek substrates identified by quantitative phosphoproteomic analysis are involved in RNA processing. We further confirmed that S563 of Dcp1a, a mRNA decapping cofactor and P-body component, is phosphorylated by Mek1. Dcp1a, as well as two other P-body components Edc4 and Dcp2, are required for the proper self-renewal and differentiation of ESCs, indicating the role of P-bodies in ESCs. Dephosphorylation of Dcp1a S563 facilitates both self-renewal and differentiation of ESCs, through promoting P-body formation and RNA storage. In summary, our study identified 66 Mek substrates supporting the Erk-independent function of Mek, and revealed that Dcp1a, phosphorylated by Mek, regulates ESC self-renewal and differentiation, through modulating P-body formation.

overall_design: We compared RNA-seq analysis of cytoplasmic and nuclear RNA from DMSO or 1 μM PD treated ESCs. ESCs were cultured with DMSO or 1 μM PD  for 3 passages, and then ESCs were treated with 5 μg/ml Actinomycin D for 0 or 8 hours, and   subjected to RNA-seq. Furthermore, to investigate the role of Dcp1a in ESCs,  we compared  gene expressing profiling of RNA-seq data for WT, Dcp1a KO ESCs, and WT,Dcp1a KO  EBs.

first: Nannan

first: Changzhen

last: Guo

last: Ding

first: Zichan

last: He

first: Qingye

last: Zhang

first: Jingai

first: Yuying

last: Wang


title: PARN is essential to GSIS in beta cell

overall_design: To compare the gene expression between Ctrl and cKO

first: Xiaomei

last: Xie


title: D53 is a dual-function transcription repressor of strigolactone signaling in cotton.

city: Xi`an

first: Chen

middle: Hao

last: Ren

state: Shannxi

address: No. 620, West Chang'an Street, Chang'an District, Xi'an City

department: College of Life Sciences

institute: Shannxi Normal University

summary: Strigolactones (SLs), a class of phytohormones, play a pivotal role in governing critical aspects of plant development, including shoot branching and root development. DWARF53 (D53) is a key repressor in the SL signaling. Nevertheless, its involvement and regulatory mechanisms in cotton fiber development—a representative single-cell model, has remained elusive. In this study, we unveil GhD53 represses the transcription of SL-inducible genes GhFAD3-2 and GhFAD3-4, which are involved in linolenic acid biosynthesis—a stimulant of cell elongation, thus inhibiting cotton fiber elongation. We demonstrate that GhD53's inhibitory influence on cotton fiber elongation is relieved in the presence of SLs, as GhD53 undergoes degradation. This alleviation of GhD53 repression triggers the activation of GhFAD3 expression, promoting fiber cell elongation. Remarkably, GhD53 serves as a dual-function transcription repressor, impeding SLs’ role in fiber elongation. Firstly, as a transcription factor, GhD53 directly binds to GhFAD3 promoters, suppressing their transcription. Secondly, GhD53 physically interacts with GhSLRF, a bHLH-type transcription factor, preventing it from binding to GhFAD3 promoters and repressing its transcription activation activity. GhD53 emerges as a pivotal component in the regulatory network governing SL signaling transduction. Overall, our findings provide novel insights into D53’s role in SL signaling and delineate a comprehensive framework for transmitting SL signals to modulate plant cell elongation behavior.

overall_design: Eukaryotic genomic DNA exists in the form of chromatin. Research on the interaction between proteins and DNA in the chromatin environment. Interaction is a basic approach to elucidate the regulatory mechanism of gene expression in eukaryotic organisms. Chromatin immunoprecipitation (ChIP) technology.ChIP (Chromatin immunoprecipitation assay) is a method for studying DNA-protein interactions in vivo.

first: Wang

last: Huiqin


title: Targeting glioblastoma with a brain penetrant drug that impairs brain tumour stem cells via NLE1-Notch1 complex

city: Ottawa

first: Arezu

last: Jahani-Asl

state: Ontario

address: 451 Smyth Road

department: Department of Cellular and Molecular Medicine

institute: University of Ottawa

summary: Brain tumour stem cells (BTSCs) are a population of self-renewing malignant stem cells that play an important role in glioblastoma tumour hierarchy and contribute to tumour growth, therapeutic resistance, and tumour relapse. Thus, targeting of BTSCs within the bulk of tumours represents a crucial therapeutic strategy. Here, we report that Edaravone is a potent drug that impairs BTSCs and impedes glioblastoma tumorigenesis. We show that Edaravone inhibits the self-renewal and growth of BTSCs harbouring a diverse range of oncogenic mutations without affecting non-oncogenic neural stem cells. Global gene expression profiling revealed that Edaravone significantly alters BTSC transcriptome and attenuates the expression of a large panel of genes involved in cell cycle progression, stemness, and DNA repair mechanisms. Mechanistically, we discovered that Edaravone directly targets Notchless homolog 1 (NLE1) and impairs Notch signalling pathway, alters the expression of stem cell markers, and sensitizes BTSC response to ionizing radiation (IR)-induced cell death. Importantly, we show that Edaravone treatment in preclinical models delays glioblastoma tumourigenesis, sensitizes their response to IR and prolongs the lifespan of animals. Our data suggest that repurposing of Edaravone is a promising therapeutic strategy for glioblastoma patients.

overall_design: To investigate the effect in vitro of Edaravone treatment on brain tumor stem cells. Three biological replicates by condition (vehicle control and Edaravone) were obtained.

first: Audrey

last: Burban

first: Ahmad

last: Sharanek

first: Aldo

last: Hernandez-Corchado

first: Hamed

last: Najafabadi

first: Vahab

last: Soleimani


title: Investigating the Mechanism of Chinese Medicine Formula AACO Against Chronic Heart Failure by Network Pharmacology Analysis and Experimental Validation

city: Shanghai

first: cheng

last: lu

state: Shanghai

address: Pudong New Area

institute: Shanghai University of Traditional Chinese Medicine

summary:
A traditional Chinese medicine (TCM) formula, containing Astragalus membranaceus (Fisch.) Bunge, Aconitum wilsonii Stapf ex Veitch, Curcuma longa L., and Radix ophiopogonis (AACO), has clinically proven therapeutic value for the treatment of chronic heart failure (CHF).
In this study, we explored the potential pharmacological mechanism underlying the activity of the AACO formula against CHF.

overall_design: All TAC mice were administered AACO solution at 0.386 µg/g (TCM group),  or an equivalent amount of double-distilled water (control group), once daily for 8 weeks.Independent experiments were performed  using different donors for each experiment.

first: Cheng

last: Lu

first: Yongming

last: Liu


title: Effects of the  C5aR1 blockade, Poly I:C and anti/PD1 combined  treatment in the gene expression  in LLC tumors

city: Pamplona

first: Daniel

last: Ajona

state: Navarra

address: Adva Pio XII 55

institute: Cima-University of Navarra

summary: In syngeneic solid tumor models, C5aR1 inhibition significantly enhanced the effectiveness of poly I:C, a toll-like receptor 3 (TLR3) agonist, combined with Programmed cell death protein 1 (PD-1)/Programmed cell death ligand-1 (PD-L1) blockade. In this experiment we aim to determine the effects of C5aR1 inhibition in the genes expression of Lewis Lung Cancer (LLC) tumors treated with poly I:C and PD-1 blockade combined treatment.

overall_design: To analyze distinct transcriptomic profile of tumors treated with vehicle, the poly I:C and PD-1 blockade or the poly I:C, PD-1 blockade and C5aR1 blockade.

first: Yaiza

last: Senent

first: Ruben

last: Pio


title: Effect of MIDKINE on in vitro culture of FLT3LG-bone marrow cells

first: Xavier

last: Catena

summary: Gene expression analysis of the effect of MIDKINE (MDK) on bone marrow cells cultured with Fms Related Receptor Tyrosine Kinase 3 Ligand (FLT3LG).

overall_design: Bone marrow cells from C57BL/6J mice were flushed and cultured with Fms Related Receptor Tyrosine Kinase 3 Ligand (FLT3LG) (50 ng/ml) and with or without recombinant human MIDKINE (10 ng/ml) for 3 days. 500ng of total RNA samples were used. Each condition was analyzed in triplicates.

first: X

first: O

last: Graña-Castro

first: M

last: Soengas


title: Transcriptome analysis of AVEN wildtype(WT) and overexpression (OE) in colorectal cancer

city: Nanjing

first: liu

last: xin

address: Xianlin Road

institute: Nanjing University of Chinese Medicine

summary: Transcriptome sequencing was used to analyze changes in related signaling pathways and gene expression in colon cancer cells when AVEN was overexpressed .

overall_design: Examination of  AVEN wildtype(WT) and overexpression (OE) in colorectal cancer cell lines RKO and HCT116

first: Rongfang

last: Wei

first: Mengjie

last: Guo


title: A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease

city: Oxford

first: Tom

last: Thomas

address: Old Road Campus, Roosevelt Dr, Headington

institute: University of Oxford

summary: Precision medicine in immune-mediated inflammatory diseases (IMIDs) requires a cellular understanding of treatment response. We describe a therapeutic atlas for Crohn’s disease (CD) and ulcerative colitis (UC) following adalimumab, an anti-tumour necrosis factor (anti-TNF) treatment. We generated ~1 million single-cell transcriptomes, organised into 109 cell states, from 216 gut biopsies (41 subjects), revealing disease-specific differences. A systems biology-spatial analysis identified granuloma signatures in CD and interferon (IFN)-response signatures localising to T cell aggregates and epithelial damage in CD and UC. Pretreatment differences in epithelial and myeloid compartments were associated with remission outcomes in both diseases. Longitudinal comparisons demonstrated disease progression in nonremission: myeloid and T cell perturbations in CD and increased multi-cellular IFN signalling in UC. IFN signalling was also observed in rheumatoid arthritis (RA) synovium with a lymphoid pathotype. Our therapeutic atlas represents the largest cellular census of perturbation with the most common biologic treatment, anti-TNF, across multiple inflammatory diseases.

overall_design:
Longitudinal sampling of gut regions from patients with CD, UC undergoing adalimumab treatment (PMID: 39438660)
Please note that processed data tar archives contain the *h5 files (including the directories/path).

first: Devika

last: Agarwal

first: Holm

last: Uhlig

first: Simon

last: Travis

first: Calliope

last: Dendrou

first: Christopher

last: Buckley


title: Epithelial deletion of CUL4B increased myeloid-derived suppressor cells-mediated immunosuppression to promote ApcMin/+ tumor formation

city: Jinan

first: bei

middle: Bei

address: Wenhua XiRoad No.44

institute: Shandong University

summary: Cullin 4B (CUL4B) is a scaffold protein of E3 ubiquitin ligase complex and has been found frequently overexpressed in various types of cancer. By repressing tumor suppressors, CUL4B is indicated as pro-oncogenic gene in oncogenesis. Reversely, recent studies reveal that deletion of CUL4B in hematopoietic system exerts tumor suppressive effect in tumor bearing hosts. However, the role of CUL4B in tumor initiation remains unknown. Here we report that CUL4B deficiency in the intestinal epithelium accelerates ApcMin/+ tumor formation. CUL4B in cancer cells restricts the accumulation of tumor-infiltrating CD11b+Gr-1+ MDSCs to prohibit the adenoma permissive microenvironment and thus increases the number of antitumor CD8+ T cells. Addition of MDSCs to ex vivo cultured ApcMin/+; Cul4bΔIEC tumor organoids rescues their phenotypic alteration in stemness, suggesting a reciprocally strengthened immunosuppressive effect between CUL4B deficient tumor cells and MDSCs. Mechanistically, inhibiting CUL4B epigenetically activates the expression of secreted chemokines and proteins including G-CSF to enroll MDSCs. Our findings suggest that epithelial deletion of CUL4B creates a tumor-prone microenvironment during ApcMin/+ tumor formation and provide a potential strategy to overcome colon cancer initiation and progress in the Wnt-disturbed context.

overall_design: mRNA profile of colon adenoma and adjacent normal tissue from 3-month, 4-month and 5-month ApcMin/+; Cul4bWT and ApcMin/+; Cul4bΔIEC mice


title: Dcp1a, a novel Mek substrate, regulates the self-renewal and differentiation of mouse embryonic stem cells [Ribo-seq]

first: Jiayu

last: Yu

overall_design: To demonstrate the role of Mek in post-transcriptional regulation of gene expression,  ESCs were cultured with DMSO or 1 μM PD  for 3 passages.  Ribosome profiling was performed to validate DMSO or PD treated transripts translation rates.

first: Nannan

last: Zhao

first: Changzhen

last: Ding

first: Zichan

last: He

first: Qingye

last: Zhang

first: Jingai

first: Yuying

last: Wang


title: Single-nucleus RNA-sequencing of orbitofrontal cortex in rat model of Methamphetamine-induced sensitization

city: Ningbo

first: Qiong

last: Li

state: Zhejiang

address: Kongpu

institute: Ningbo University

summary: Due to the complexity and diversity of the cellular changes, our understanding of the exact molecular and cellular mechanisms underpinning behavioral sensitization remains incomplete. Therefore, the present study explored the single-cell transcriptional changes in the orbitofrontal cortex (OFC) — a region implicated in decision-making and reward-related behaviors15,16— in a rodent model of methamphetamine-induced sensitization. Our study provides insights into the molecular mechanisms cells associated with the development of drug addiction.

overall_design: Animals included in current study were all 8-week-old male Sprague-Dawley rats. Rats were treated with 1 mg/kg METH or saline (intraperitoneal) for 7 days in the METH and saline groups, respectively. Then all rats were deeply anesthetized with pentobarbital (60 mg/kg, i.p.) and sacrificed, and the OFCs of four per group were rapidly removed and prepared for single nucleus isolation on ice. The nucleus-barcoded 3’ gene expression libraries were sequenced on an Illumina NovaSeq6000 system.


title: Transcriptome data derived from muscle and brain in CT-26-induced mouse cancer cachexia models

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

summary: Identification of a Cancer Cachexia Signature through Transcriptomic Analysis of Muscle and Hypothalamic Tissues from CT-26-Induced Cachectic and Control Mice.

overall_design: mRNA profiles were obtained from the gastrocnemius and hypothalamus of mice with CT-26-induced cachexia and control mice, with each sample analyzed in triplicate.

first: Aeyung

last: Kim

first: NoSoo