title: Tumorigenicity of KRAS-ablated pancreatic cancer cells requires STAT3 function

city: Woodbury

first: Jonathan

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

summary: Oncogenic KRAS mutations underlie some of the deadliest human cancers. Genetic or pharmacological KRAS inactivation produces mixed outcomes, ranging from complete regression to frequent relapse. Mechanisms underpinning the resistance of cancer cells to KRAS inactivation remain to be understood. Here we investigate a conceptual framework of pancreatic ductal adenocarcinoma showing that CRISPR-mediated KRAS ablation impedes tumor growth contingent on the concomitant inactivation of the STAT3 transcription factor. Mechanistically, the incurred losses of KRAS and STAT3 disrupt a temporal balance between tumor cell differentiation, proliferation, and self-renewal. This in turn impairs tumor growth in mice and enhances their immune rejection, resulting in tumor clearance. Our findings identify a specific role for STAT3 in supporting cancer cell fitness with a particular focus on KRAS-inhibited tumors and provide a rationale for developing therapies targeting mutant KRAS and STAT3.

overall_design: Orthotopic injections into the pancreas of FVB male mice were performed with 104 iKRAS parental control (A9993) or iKRAS STAT3 KO cells in Matrigel diluted 1:10 with Opti-MEM using standard procedures (Kim et al 2009). For tumor formation, the drinking water was provided ad libitum and supplemented with 2% sucrose, doxycycline hyclate (0.5 mg/ml), neomycin (0.5 mg/mL) and ampicillin (1 mg/mL). The animals were observed for tumor development by palpation and orthotopic tumors were pooled from 2-3 individual mice at day 0 (~150-350mg) or following doxycycline removal for 4 days (day 4) (100-200mg).Single cell suspensions were prepared by treating tumor tissues with 1x collagenase/hyaluronidase (StemCell Technology), 0.5 mg/ml Liberase-DL (Roche), and 0.1 mg/ml DNase I (Sigma) for 45 minutes at 37C with continuous mixing. Single-cell RNA sequencing was performed by the Cold Spring Harbor Laboratory Single-Cell Biology Shared Resource, Genomics Technology Development.

first: Nancy

last: Reich


title: RPRD1B’s direct interaction with phosphorylated RNA Polymerase II regulates polyadenylation of cell cycle genes and drives cancer progression

status: Public on Feb 05 2025

city: Austin

first: Yan

middle: Jessie

last: Zhang

address: 100 E. 24th Street

country: USA

institute: University of Texas-Austin

type: Expression profiling by high throughput sequencing

summary: RNA Polymerase II (Pol II) regulates eukaryotic gene expression through dynamic phosphorylation of its C-terminal domain (CTD). Phosphorylation at Ser2 and Thr4 on the CTD is crucial for RNA 3’ end processing and facilitating the recruitment of cleavage and termination factors. However, the transcriptional roles of most CTD-binding proteins remain poorly understood. In this study, we focus on RPRD1B, a transcriptional regulator that interacts with the phosphorylated CTD and has been implicated in various cancers. We investigated its molecular mechanism during transcription and found that RPRD1B modulates alternative polyadenylation of cell growth transcripts by directly interacting with the CTD. RPRD1B is recruited to transcribing Pol II near the 3’ end of the transcript, specifically in response to Ser2 and Thr4 phosphorylation, but only after flanking Ser5 phosphorylation is removed. Transcriptomic analysis of RPRD1B knockdown cells revealed its role in cell proliferation via termination of the key cell growth genes at upstream polyadenylation sites, leading to the production of tumor suppressor transcripts that lack AU-rich elements (AREs) with increased mRNA stability. Overall, our study uncovers previously unrecognized connections between the Pol II CTD and CID, highlighting their influence on 3’ end processing and their contribution to abnormal cell growth in cancer.

overall_design: HEK293T cells were transduced with shRNA to knockdown RPRD1B via lentivirus transduction or shControl in HEK293T cells total RNA was collected. Total RNA was collected from cells and the library prep strategy  isolates polyA RNA for further analyis.

first: Rosamaria

middle: Y

last: Moreno

first: Svetlana

middle: B

last: Panina

middle: J


title: gene expression data of granulosa cells treated with DMSO or LY294002

city: Dummerstorf

first: Vijay simha

last: Baddela

address: Wilhelm-Stahl-Allee 2

department: Reproductive biology

country: Germany

institute: Leibniz institute for farm animal biology

summary: PI3K-AKT signaling is essential for various cellular processes, including cell viability, proliferation, and metabolism. Here, we investigated the genome-wide changes induced by PI3K-AKTsignaling in primary granulosa cell cultures treated with control (DMSO) and PI3K-AKT pathway inhibitor LY294002.

overall_design: RNA from DMSO treated granulosa cells  (3n) and LY294002 treated granulosa cells (3n) were processed for microarray analysis

first: Baddela

last: Vijay simha


title: Loss of DDX24 inhibits lung cancer progression by stimulating IKBKG splicing-mediated autophagy

city: Dalian

first: Wang

last: Yang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

country: China

institute: Dalian Medical University

summary: Lung cancer remains a major global health burden with limited therapeutic options. Alternative splicing, a critical post-transcriptional process, contributes to lung cancer progression through autophagy, although the underlying mechanisms remain largely unexplored. Here we reveal that loss of DDX24, an RNA-binding protein, suppresses lung cancer growth by promoting autophagy. Mechanistically, DDX24 regulates the alternative splicing of autophagy-related genes, including IKBKG. We demonstrate that DDX24 directly binds to IKBKG pre-mRNA, whereas DDX24 ablation promotes the generation of a pro-autophagic long splicing variant. Functional rescue experiments confirm that the long IKBKG isoform-mediated autophagy confers the anti-tumor effects of DDX24 depletion. These findings uncover a novel regulatory axis involving DDX24, IKBKG splicing, and autophagy in lung cancer and provide a potential therapeutic target for this devastating disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for A549 cells with DDX24 knockdown or not

first: Sun

last: Siwen

first: Jing

last: Xiaomeng

first: Lv

last: Yuesheng

first: Yang

last: Wang


title: Effect of Sorafenib on Myeloid-derived suppressor cells in HCC

city: Beijing

first: Chunxiao

last: Li

address: Huayuan Road

institute: Peking University Third Hospital

summary: Hepatocellular carcinoma (HCC) remains one of the leading causes of cancer-related deaths worldwide. Sorafenib, a multikinase inhibitor, is the first-line systemic therapy approved for advanced HCC, but its impact on the tumor microenvironment, particularly on myeloid-derived suppressor cells (MDSCs), is not fully understood.MDSCs are a heterogeneous population of immune cells that play a crucial role in promoting tumor growth and immune evasion by suppressing T cell function and facilitating an immunosuppressive microenvironment. This study investigates the effects of sorafenib on the function and phenotype of MDSCs in HCC.

overall_design: In this study, we first established a hepatocellular carcinoma (HCC) model in C57BL/6 mice using the murine HCC cell line Hepa1-6. Tumor cells were subcutaneously injected into the flanks of C57BL/6 mice to induce tumor formation. Once tumors reached a measurable size, mice were sacrificed, and peripheral blood was collected for further analysis.Myeloid-derived suppressor cells (MDSCs) were isolated from the peripheral blood using flow cytometry. The cells were characterized and sorted based on the surface markers CD45+7aad-CD11b+Gr-1+. The purity of the sorted MDSCs was verified through additional flow cytometric analysis.Isolated MDSCs were then subjected to in vitro treatment with sorafenib for 72 hours. The treatment concentration of sorafenib was optimized based on preliminary dose-response experiments to ensure effective modulation of MDSC function without inducing significant cytotoxicity.After the 72-hour treatment period, MDSCs were harvested and used for subsequent experiments


title: A Membrane Lipid Signature Unravels the Dynamic Landscape of Group 1 ILCs across the Health-Disease Continuum

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: In an era where the established lines between cell identities are blurred by intra-lineage plasticity, distinguishing between stable and transitional states becomes imperative. This challenge is particularly pronounced within the Group 1 ILC lineage, where the similarity and plasticity between NK cells and ILC1s obscure their classification and the assignment of their unique contributions to immune regulation. This study exploits the unique property of AsGM1—a membrane lipid associated with cytotoxic attributes absent in ILC1s—as a definitive criterion to distinguish between these cells. By prioritizing cytotoxic potential as the cardinal differentiator, the strategic use of this glycosphingolipid signature achieved precise delineation of the heterogenity of Group 1 ILCs across tissues. This capability extends beyond steady-state classifications, adeptly capturing the binary classification of NK cells and ILC1s during acute liver injury. By leveraging two established models of NK-to-ILC1 plasticity driven by TGFβ in endocrine tissues and Toxoplasma gondii infection, we demonstrate the stability of the AsGM1 signature during this reprogramming, which sharply contrasts with the loss of Eomes. The early detection of the AsGM1 signature at the immature NK (iNK) stage, preceding Eomes, and its stability, unaffected by transcriptional reprogramming that typically alters Eomes, position AsGM1 as a unique, site-agnostic marker for fate mapping NK-to-ILC1 plasticity. This provides a powerful tool to explore the expanding heterogeneity within the Group 1 ILC landscape, effectively transcending the ambiguity inherent to the NK-to-ILC1 continuum.

overall_design:
From the livers of RAG2 KO mice, group 1 ILCs (CD45+CD3-NK1.1+NCR1+) were sorted based on AsGM1 expression into AsGM1+ and AsGM1- samples. This was repeated to produce a total of 3 replicates.
AsGM1+ cells (which we define as NK cells) were sequenced and compared to sequenced AsGM1- cells (which we define as ILC1s).

first: Halle

middle: C

last: Frey

first: Xin

last: Sun

first: Fatima

last: Oudeif

first: Darleny

middle: L

last: Corona

first: Zijun

last: He

first: Taejoon

last: Won

first: Tracy

last: Schultz

first: Vern

last: Carruthers

first: Amale

last: Laouar

first: Yasmina


title: Ovariectomy Drives Increase an ECM Transcription Signature in the Posterior Eye and Retina

city: Atlanta

first: Andrew

last: Feola

address: 1365B Clifton Road NE

institute: Emory University

summary: The risk of developing glaucoma has recently been associated with the age of menopause. This study examines how age and surgical menopause via ovariectomy (OVX) impact gene expression in the posterior eye, including the sclera and optic nerve head. We examined how age and OVX impacted expression pathways linked to glaucoma, such as extracellular matrix (ECM) remodeling and TGF-β signaling. To compare these changes across different tissue regions, we also examined the retina. Using bulk RNA sequencing, we analyzed these changes in young (3-4 months) and middle-aged (9-10 months) Long-Evans rats. Our results demonstrate that both aging and OVX significantly alter gene expression in these ocular tissues. Specifically, OVX in young rats led to significant enrichment of ECM and TGF-β gene sets, while these effects were diminished in middle-aged rats, indicating an age-dependent influence. Early OVX triggered significantly enriched ECM remodeling and immune responses compared to later OVX. These findings underscore the critical role of menopause timing in modulating molecular pathways associated with glaucoma, suggesting that early menopause may heighten the risk of developing this condition. Notably, FOS was downregulated in the posterior eye and retina in aging and OVX animals. FOS is a major regulator of cell proliferation and survival, and its dysregulation may play an important role in aging and menopause for women. This study highlights the importance of considering women's health factors, such as menopause, in understanding and managing glaucoma risk.

overall_design: young (3-4 months old, n=12) and middle-aged (9-10 months old, n=12) Long-Evans rats.  Each group was subdivided, with some animals undergoing surgical menopause via ovariectomy  (n=6) and the remaining animals undergoing a Sham surgery (n=6).


title: Modulation of biological activities in adipose derived stem cells by histone deacetylation

city: Linkoping

first: Sallam Hasan Saleem Abdallah

last: Abdallah

state: SWEDEN

address: Linköping

country: Sweden

institute: Linköping University

summary: Epigenetic mechanisms control stem cell homeostasis and differentiation as well as skin regeneration. In our study, we investigated the effects of Suberoylanilide hydroxamic acid (SAHA) on stem cells to understand the cellular and molecular impact. Adipose-derived stem cells received consecutive SAHA treatment for 72 hours. No change in the cell viability could be noticed at the studied concentrations. On the other hand, a decrease in the protein expression of histone deacetylases at 1000 nM was found. The cell proliferation marker (Ki-67) was increased after SAHA treatment compared to the vehicle as shown by immunofluorescence staining.  The expression of CCND1 gene expression was upregulated, while the protein expression of the proliferating cell nuclear antigen was downregulated. Alternatively, microarray analysis revealed 74 up regulated and 40 downregulated differentially expressed genes and revealed that CDKN1A and MDM2 were upregulated under the influence of SAHA. On the other hand, the proteomics analysis identified 631 upregulated proteins while 823 proteins were downregulated in comparison to the vehicle. The pathway enrichment analysis showed that cell cycle, ATP-dependent chromatin remodeling and DNA are among the regulated pathways. This study suggested that SAHA as pharmaco-epigenetic agent might alter ADSCs determination through coordinated biological processes

overall_design: The experment designed by runing three biological replicates for all the studied groups (control, EtOH and SAHA). One replicate of ETOH were excluded after quality check.

first: Sallam

first: Mouna

last: Tabebi

first: Sawsan

last: Qanadilo

first: Neserin

last: Ali

first: Wen

last: Zhong

first: Folke

last: Sjoberg

first: Moustafa

last: Elmasry

first: Ahmed

last: El-Serafi


title: Elucidating DNA-binding protein dynamics in Salmonella Typhimurium within macrophages using a breakthrough low-input ChIP-exo workflow [RNA-seq]

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

summary: We present genome-wide transcript expression profiles of Salmonella Typhimurium 14028s under both macrophage in vitro and in vivo conditions. These transcriptome data were integrated with ChIP-mini datasets to elucidate the transcriptional roles of H-NS and RpoD under macrophage in vivo conditions.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design:
[RNA-seq] Macrophage intracellular S. Typhimurium 14028s WT cells were used for the in vivo RNA-seq with a biological replicate.
[RNA-seq] Macrophage extracellular S. Typhimurium 14028s WT cells were used for the in vitro RNA-seq with a biological replicate.

first: Joon-Young

last: Park

first: Minchang

last: Jang


title: Neurotensin-Neurotensin Receptor 2 signaling in adipocytes regulates food intake through ceramide metabolism

city: Shanghai

first: Cenxi

last: Liu

address: Songhu Road 2005

institute: Fudan University

summary: Our previous study revealed that NTS suppressed the activity of brown adipose tissue via interactions with NTSR2. In the current study, we found that the depletion of Ntsr2 in the white adipocytes upregulated food intake, while the local treatment of NTS suppressed the food intake.

overall_design: To investigate the role of Ntsr2 in the regulation of food intake in the white adipocytes, we established the mice depleted Ntsr2 in the white adipocytes.

first: Wei

last: Fu


title: Male and female mouse heart miRNA sequencing

city: Chapel Hill

first: James

middle: Isaiah

last: Emerson

state: North Carolina

address: 132 Ridge Trail

department: Biochemsitry and Biophysics

institute: University of North Carolina- Chapel Hill

type: Non-coding RNA profiling by high throughput sequencing

summary: Purpose: The goal of this study is to identify the sex differential  miRNA tanscriptome  between male and female adult (4-6 wk. old) mouse hearts using small RNA-seq. Methods: miRNA profiles of male and female mouse hearts were generated by sequencing, n=4 for each sex, using Illumina HiSeq2500. The sequence reads were aligned to the mm10 reference genome using STAR via the bcbio-nextgen RNA-sequencing pipeline. Differential gene expression was determined by genwiz. Results: 11 miRNAs  were differentially expressed between male and female mice [ P value <0.05, |log2(Fold Change)| > 0.5], with 9 more highly expressed in female hearts and 2 more highly expressed in male hearts.

overall_design: Male and female adult hearts (4-6 wks), n=4 for each sex, were dissected in cold PBS and immediately homogenized in Trizol solution, and were kept in -20C until use. Small RNA from individual hearts was extracted using the miRVANA miRNA isolation kit (Thermo-Fisher AM1561). The concentration and quality of purified RNA were assessed by Tape Station (Agilent). Isolated small RNA samples were used for library prep and sequencing regardless of RIN score because small RNA bands were expected. The samples were enriched in RNAs <200nt.

first: Frank

last: Conlon

first: Kerry

last: Dorr


title: Spermine oxidase promotes Helicobacter pylori-mediated gastric carcinogenesis through acrolein production

city: Nashville

first: Keith

last: Wilson

state: Tennessee

address: 2215 Garland Ave

institute: Vanderbilt University

summary: Helicobacter pylori is the primary cause of gastric cancer and there is a need to discover new molecular targets for therapeutic intervention in H. pylori disease progression. We have previously shown that spermine oxidase (SMOX), the enzyme that catabolizes the back-conversion of the polyamine spermine to spermidine, is upregulated during infection and is associated with increased cancer risk in humans. We sought to determine the direct role of SMOX in gastric carcinogenesis during H. pylori infection. In this study, we demonstrate that transgenic FVB/N insulin-gastrin (INS-GAS) mice that develop gastric carcinoma with H. pylori infection were protected from cancer development with Smox deletion. RNA sequencing revealed that genes associated with the immune system and cancer were downregulated in the infected Smox–/– mice. Furthermore, there was a decrease in cell proliferation and DNA damage in infected Smox–/– animals. There was significant generation of adducts of the highly reactive electrophile acrolein, a byproduct of SMOX activity, in tissues from H. pylori-infected WT mice and humans. Genetic deletion of Smox or chemical inhibition of SMOX in murine organoids and human gastric epithelial cells and organoids, respectively, significantly reduced generation of acrolein induced by H. pylori. Furthermore, acrolein induced DNA damage in gastric epithelial cells, which was ablated with the electrophile scavenger 2-hydroxybenzylamine (2-HOBA). Infected 2-HOBA treated INS-GAS WT mice with reduced gastric carcinoma had attenuated gastric acrolein adduct formation.  These findings implicate SMOX and acrolein in H. pylori-induced carcinogenesis in gastric epithelial cells, thus indicating potential therapeutic targets.

overall_design:
RNA sequencing by Illumina NovaSeq6000 was performed on  gastric tissues of WT and Smox-/- mice infected or not with H. pylori PMSS1 for 8 weeks to determine the role of SMOX in H. pylori pathogenesis
RNA was extracted from the gastric tissue from 4-5 mice per genotype either uninfected or infected

first: Kara

middle: M

last: McNamara

first: Yvonne

last: Latour

first: Alain

middle: P

last: Gobert

middle: T


title: The small RNA sequencing for human serum of patients with endomeriosis

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

summary: Circulating miRNAs are potential non-invasive biomarkers, and some miRNAs were encapsulated by extracellular vesicles (EVs). In this study, we investigated EV miRNA profiles in the serum of patients with endometriosis.

overall_design: Small EVs (sEVs) in the serum were collected from 48 patients, and total RNAs were extracted. Then, small RNA sequencing was performed.

first: Ayako

last: Muraoka

first: Akira

last: Yokoi


title: The small RNA sequencing for endometrium and ovarian endometrial cysts of patients with endomeriosis

summary: miRNAs are associated with various diseases by regulating the expression of their target genes. In this study, we investigated EV miRNA profiles of endometriosis.

overall_design: Endometrium and ovarian endometrial cysts were collected from 5 patients with endometriosis. Moreover, normal endometrium was obtained from 5 patients without endometriosis. Total RNAs were extracted, and small RNA sequencing was performed.


title: A versatile in vivo platform for reversible control of transgene expression in adult tissues

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

summary: Temporal control of exogenous genes through artificial genetic circuits has advanced a range of biomedical interventions, including in vivo reprogramming. The doxycycline (Dox)-mediated Tet- ON system has been widely employed due to its highly reversible and tunable gene induction. Nonetheless, its effectiveness in vivo is limited by inherent resistance in some tissues. In the present study, mouse models were developed with the Tet-ON or complementary Tet-OFF system to thoroughly investigate the spatial and temporal control of transgene expression in adult tissues. The Tet-OFF system could induce gene expression in a broad spectrum of cell types, such as neuronal cells, cardiomyocytes, and skeletal muscle cells, in stark contrast with the Tet-ON system, which could only induce gene expression in particular tissues and cell types, mainly epithelial cells. Despite its broader reach, the Tet-OFF system exhibited slow inducibility and lacked tunability in the expression levels of transgenes. Capitalizing on the pharmacologic advantages of tetracycline (Tc), which has a shorter half-life in vivo and lower affinity for Tet repressor than Dox, we revisited its application. Remarkably, Tc enabled rapid, reversible, and graded control of transgene expression in the Tet-OFF system. Moreover, utilization of Tc mitigated the transcriptional perturbation associated with use of Dox. Our data suggest that the Tc-mediated Tet-OFF system not only enables more versatile control of transgene expression but may also offer a more biocompatible alternative, enhancing its suitability for applications such as tissue regeneration and organismal rejuvenation.

overall_design: Analyzing transcriptional profiles by RNA-seq in the livers of Tet-OFF mice treated with doxycycline (Dox) or tetracycline (Tc) for 7 days

first: Jumpei

last: Taguchi

first: Ohta

last: Sho

first: Fumie

last: Nakasuka

first: Takuya

last: Yamamoto


title: Structural and functional analyses of STM14_5441-STM14_5442: A potential mechanism for persister formation against aminoglycosides [resT RNA-seq]

status: Public on Feb 06 2025

city: Seoul

first: Seok-Won

last: Jang

address: 1, Gwanak-ro, Gwanak-gu,

institute: Seoul National University

summary: The ability to eliminate bacterial persister cells is still a medical challenge that has yet to be overcome. These cells represent a unique subpopulation within bacterial communities and are characterized by a reduced susceptibility to antibiotics with growth retardation. In this study, we investigated the molecular basis of persister formation in Salmonella Typhimurium 14028s under aminoglycoside stress.We analyzed the crystal structure of the STM14_5441–STM14_5442 complex, which belongs to the type II toxin-antitoxin system, and identified key ribosome binding residues in STM14_5441. Changes in the antibiotic susceptibility of Salmonella caused by the loss of the ribosome binding property of STM14_5441 were assessed. We conducted intracellular ATP assays under aminoglycoside stress and RNA-seq analysis following STM14_5441 induction.Our studies demonstrated the critical role of STM14_5441 in the formation of persister cells in Salmonella, particularly those under aminoglycoside stress. We observed that a loss of ribosome binding in STM14_5441 resulted in increased antibiotic susceptibility. Additionally, intracellular ATP assays revealed increased ATP levels in bacterial persister cells, and RNA-seq analysis identified several genes that play a role in the formation of these persister cells.The present data suggest that persister forms under aminoglycoside stress through the following mechanisms: i) inhibition of membrane hyperpolarization by impeding F1Fo ATP synthase activity and ii) enhanced poststress recovery by ATP storage and increased protein synthesis capacity. Based on this suggestion, we reannotated the STM14_5441-STM14_5442 TA pair as the ResTA (RNA cleavage-induced energy storage toxin-antitoxin) system. Furthermore, new insights into the function of TA systems may lay the groundwork for developing novel strategies to target bacterial persister cells, thereby preventing the accelerated emergence of antibiotic resistance in bacterial populations.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: To investigated the function of ResT, we established the strain harboring a plasmid with the STM14_5441 (resT) versus wild-type. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different strains induced after 15 min. Comparative gene expression profiling analysis of RNA-seq data for wild-type and pBAD33::resT inducted strain (wild-type and pBAD33::resT inducted strain)

first: Hyun-Jong

last: Eun

first: Bong-Jin

last: Lee


title: Steatohepatitis-induced vascular niche alterations promote melanoma metastasis III

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Despite recent advancements in melanoma therapy, hepatic metastasis in malignant melanoma patients remains associated with significantly reduced overall survival rates. Given the rising prevalence of metabolic liver diseases such as nonalcoholic fatty liver disease and nonalcoholic steatohepatitis (NAFLD/NASH), we investigated whether metabolic changes influence hepatic melanoma metastasis. Our study found that induction of advanced NASH in C57BL/6N mice through a choline-deficient L-amino acid (CDAA)-defined diet for ten weeks significantly increased hepatic metastasis, as demonstrated by injecting B16F10Luc2 and Wt31 melanoma cells. B16F10Luc2 cells showed heightened metastatic potential even with shorter periods of CDAA feeding before liver fibrosis developed. Conversely, hepatic steatosis induced by a high-fat diet alone did not promote increased melanoma metastasis. Early pre-fibrotic changes in the hepatic vascular niche, particularly in liver sinusoidal endothelial cells (LSECs), appeared to be responsible for the enhanced metastasis, characterized by continuous endothelial dedifferentiation and upregulation of adhesion molecules VCAM1, ICAM1, and E-selectin. Functionally, B16F10Luc2 cell retention in the hepatic vascular niche was significantly increased early after CDAA feeding, with ICAM1 inhibition leading to a notable reduction in cell retention. In summary, our findings highlight the hepatic vascular niche's sensitivity to metabolic alterations, suggesting potential avenues for preventing hepatic melanoma metastasis through angiotargeted therapies.

overall_design: 5 CDAA vs. 5 Chow were compared, with each n consisting of 3 pooled animals to obtain enough cells. Samples were pooled after organ harvesting and then LSEC isolation was performed. After isolation, RNA was extracted and sequenced and gene expression was analysed.

first: Victor

last: Olsavszky

first: Johannes

last: Hoffmann


title: RNAseq of peripheral blood mononucleated cells exposed to platelet-rich fibrin and enamel matrix derivatives.

city: Vienna

first: Hannes

last: Kühtreiber

state: Vienna

address: Lazarettgasse 14

department: Department of Dermatology

country: Austria

institute: Medical University Vienna

summary: Platelet-rich fibrin (PRF) and Enamel Matrix Derivatives (EMD) can support the local regenerative events in periodontal defects. There is reason to suggest that PRF and EMD exert part of their activity by targeting the blood-derived cells accumulating in the early wound healing blastema. However, the impact of PRF and EMD on blood cell response remains to be discovered. To this aim, we have exposed human peripheral blood mononucleated cells (PBMCs) to PRF lysates and EMD, followed by bulk RNA sequencing. A total of 111 and 8 genes are up- and down-regulated by PRF under the premise of an at least log2 two-fold change and a minus log10 significance level of two, respectively. Representative is a characteristic IFN response indicated by various human leukocyte antigens (HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQA2, HLA-DRA, HLA-DRB1, HLA-DRB5), gamma Fc receptors (FCGR1A, FCGR1B, FCGR3B), chemokines (CXCL9-11), and calprotectin (S100A8/9 and S100A12), complement (C1QA/B, C2) and interferon-induced guanylate-binding proteins (GBP1, GBP5). With EMD, 67 and 29 genes are up- and down-regulated, respectively. Characteristics of the upregulated genes are tensins (TNS1 and TNS3). Among the genes downregulated by EMD were epsilon Fc receptors (FCER1A; FCER2) and Fc receptor-like proteins (FCRL1, FCRL3) and CX3CR1. Genes commonly upregulated by PRF and EMD were most noticeably NXPH4 and MN1, but also FN1, MMP14, MERTK, and AXL. Our findings suggest that PRF provokes an inflammatory response, while EMD dampens IgE signaling in peripheral mononucleated blood cells.

overall_design: Preparation and stimulation of PBMCs: This isolation of PBMCs was approved by the ethics committee of the Medical University of Vienna  and conducted according to the principles of the Helsinki Declaration and Good Clinical Practice. Written informed consent was obtained from all donors. Human peripheral blood mononuclear cells (PBMCs) were obtained from three healthy male volunteers by venous blood draw. Cells were separated by Ficoll-Paque (G.E. Healthcare Bio-Sciences AB, Sweden) density gradient centrifugation. Heparinized anticoagulated blood specimens were processed immediately after venipuncture, diluted 1:2 in Hanks balanced salt solution (HBBS, Lonza, Basel, Switzerland), and transferred carefully to 50 ml tubes containing Ficoll‒Paque solution (G.E. Healthcare Bio-Sciences AB, Sweden). The tubes were centrifuged for 15 minutes at 800 g at room temperature without braking, and buffy coats with mononuclear cells were obtained. Cells were washed in HBSS and resuspended in a CellGro serum-free medium (CellGenix, Freiburg, Germany; 25 × 106 cells/ml). Cell concentrations were determined on a Sysmex automated cell counter (Sysmex Inc., USA). For each experiment, PBMCs from the three donors were incubated for 20 hours without or with 300 µg/mL of enamel derivative matrix (EMD; Straumann AG, Basel, Switzerland) or a 30% solution of a PRF lysate.

first: Layla

last: Panahipour

first: Reinhard

last: Gruber


title: Steatohepatitis-induced vascular niche alterations promote melanoma metastasis II

overall_design: 4 CDAA vs. 4 Chow were compared. RNA was extracted from cryo-tissue, sequenced and gene expression was analysed.


title: Steatohepatitis-induced vascular niche alterations promote melanoma metastasis I


title: Specific modulation of 28S_Um2402 rRNA 2'-O-ribose methylation as a novel epitranscriptomic marker of ZEB1-induced epithelial-mesenchymal transition in different mammary cell contexts.

city: Lyon

first: Hermes

last: Paraqindes

address: 28 rue Laennec

country: France

institute: CRCL

type: Methylation profiling by high throughput sequencing

summary: The epithelial–mesenchymal transition (EMT) is a dynamic transdifferentiation of epithelial cells into mesenchymal cells. EMT programs exhibit great diversity, based primarily on the distinct impact of molecular activities of the EMT transcription factors. Using a panel of cancer cell lines and a series of 71 triple-negative primary breast tumors, we report that the EMT transcription factor ZEB1 modulates site-specific chemical modifications of ribosomal RNA (rRNA). Overexpression of ZEB1 and ZEB2, but not TWIST1, decreased the level of 2′-O-ribose methylation (2′Ome) of 28S rRNA at position Um2402. ZEB1 overexpression specifically reduced the expression of the corresponding C/D box small nucleolar RNAs (snoRNAs) SNORD143/144, which guide the rRNA 2′Ome complex at the 28S_Um2402 site. During ZEB1-induced EMT induction/reversion, the levels of both 2′Ome at 28S_Um2402 and SNORD143/144 were dynamically comodulated. Taken together, these data demonstrate that 2′Ome rRNA epitranscriptomics is a novel marker of ZEB1-induced EMT.

overall_design: ribosomal RNA 2'-O-ribose methylation profile in EMT using RiboMethSeq technology

first: Virginie

last: Marcel

first: Chloé

last: Morin


title: Extracellular vesicles contribute to the beneficial metabolic effects of voluntary exercise training in a mouse model of Alzheimer's disease

city: Brisbane

first: Michael

last: Pearen

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

summary: Alzheimer's disease (AD) is a neurodegenerative disorder characterized by cognitive decline and memory loss. It has been suggested that alterations in energy metabolism, specifically an increase in resting energy expenditure (REE), may be a key factor in the development and progression of AD. Regular physical activity may improve cognitive function in patients with AD, and although the mechanisms are unclear, organ-to-organ communication may play a role. We hypothesize that changes to extracellular vesicles (EVs) in response to regular physical activity might be involved in organ-to-organ communication mediating the improvement to cognitive function caused by regular physical activity in patients with AD. In this experiment, we profiled the microRNA composition of extracellular vesicles (EVs) purified from the blood of sedentary (sedEV) and/or acutely exercised (exEV) mice as part of understanding this hypothesis.

overall_design:
Wild type mice were placed into two groups: exercise and sedentary. After three days of acclimation, exercise mice underwent 60-minutes of treadmill exercise to exhaustion. After exercise, blood was collected for plasma extraction from exercise mice with blood also being collected from control sedentary mice.
Extracellular vesicles (EVs) were isolated from pooled plasma (from 20 mice in each group). RNA was extracted for EV-rich fractions and small RNA-seq was performed.

first: Oliver

middle: K

last: Fuller

first: Emma

middle: D

last: McLennan

first: Casey

last: Egan

first: Jae

last: Pyun

first: Mariana

last: de Mendonca

first: Nimna

last: Perera

first: Guilherme

last: Defante Telles

first: Benoit

last: Smeuninx

last: Burrows

first: Ghizal

last: Siddiqui

first: Darren

last: Creek

first: John

middle: W

last: Scott

middle: A

first: Pamali

last: Fonseka

first: Joseph

last: Nicolazzo

first: Suresh

last: Mathivanan

first: Grant

last: Ramm

first: Martin

last: Whitham

first: Mark

last: Febbraio


title: The impact of inhibiting Dgat2 and Pnpla2 functional enhancers on the transcriptome of 3T3-L1 adipocytes.

city: Sichuan

first: Sha

last: Zeng

address: 211 Huimin Road

institute: Sichuan Agricultural University

summary: In order to explore the impact of enhancer inhibition on adipocyte differentiation and triglyceride deposition at the transcriptome level, we infected cells with lentiviral vectors containing dCas9-KRAB-sgRNAs (experimental group) or dCas9-KRAB-Control (control group) at a multiplicity of infection (MOI) of 100 for 12 hours in 1 mL culture medium. Transcriptome analysis via RNA sequencing (RNA-seq) was conducted on dCas9-KRAB-Dgat2-En4, dCas9-KRAB-Pnpla2-En5, and dCas9-KRAB-Control cells at day 7 of differentiation.

overall_design: Gene expression profiling analysis of mRNA-seq data from dCas9-KRAB-Dgat2-En4, dCas9-KRAB-Pnpla2-En5, and dCas9-KRAB-Control cells on the 7th day of differentiation.

first: Ziqi

last: Li

first: Qinjiao

last: Du


title: Elucidating transcription factor binding dynamics in Salmonella Typhimurium under macrophages in vivo conditions using a low-Input ChIP-exo approach [ChIP-mini]

first: Donghyuk

last: Kim

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We present the low-input ChIP-exo minimization (ChIP-mini) method, which is suitable for processing small bacterial cell numbers, as few as 4.8x10⁶ (bacterial culture volume: 10 µl). This method faithfully maintains the relevant binding profiles of Escherichia coli K-12 MG1655 RpoD, as generated by the traditional ChIP-exo method (bacterial culture volume: 50 ml). Additionally, ChIP-mini was applied in the conventional infection process of mouse macrophages-like cells (J774A.1, RAW264.7) and human epithelial cells (HeLa, INT407) with Salmonella Typhimurium 14028s to directly capture both host extracellular and intracellular bacteria (extracellular and intracellular ChIP-mini). These applications of ChIP-mini in infectious S. Typhimurium provided near-base pair resolution to measure the impact of environmental changes on the binding profiles of H-NS and RpoD.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design:
[Intracellular ChIP-mini] Mouse macrophage-like cells (J774A.1, RAW 264.7) and human epithelial cells (HeLa, INT407) intracellular S. Typhimurium 14028s WT and hns-8myc tagged cells were co-crosslinked for the intracellular ChIP-mini with a biological replicate.
[IMS intracellular ChIP-mini] Mouse macrophage-like cells (J774A.1) intracellular S. Typhimuirum 14028s hns-8myc tagged cells were isolated by immunomagnetic separtion (IMS) from co-crosslinked infected J774A.1 samples for the intracellular ChIP-mini with a biological replicate.
[Extracellular ChIP-mini] Mouse macrophage-like cells (J774A.1, RAW 264.7) and human epithelial cells (HeLa, INT407) extracellular S. Typhimurium 14028s WT and hns-8myc tagged cells in DMEM media were crosslinked for the extracellular  ChIP-mini with a biological replicate.
[ChIP-exo] E. coli K-12 MG1655 WT and rpoH-8myc tagged cells were grown to mid-log phage, cultured in M9 minimal 0.2% glucose with a biological replicate. For ChIP-exo of mid-log cells, 50 ml of culture media was used to make crosslinking cells (number of cells: 2.4x1010). S. Typhimurium 14028s WT and hns-8myc tagged cells were grown for overnight, cultured in LB media with a biological replicate. For ChIP-exo of overnight-grown cells, about 2.4X1010 cells was used to make crosslinking cells (media volume: 5ml, OD600 : ~6).
[ChIP-mini] E. coli K-12 MG1655 WT and rpoH-8myc tagged cells were grown to mid-log phage, cultured in M9 minimal 0.2% glucose with a biological replicate. For ChIP-exo, 6.25 ml (3.0x109), 1.6 ml (7.68x108), 200 ?l (9.6x107), 25 ?l (1.2x107), 10 ?l (4.8x106), and 5 ?l (2.4x106) of culture media was used to make crosslinking cells.

first: Joon Young

last: Park

first: Minchang

last: Jang


title: Characterizing spatial and global host innate immune responses against SARS-CoV-1 and -2 infection in pathologically relevant human lung epithelial cells

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

summary: Severe acute respiratory syndrome coronavirus-1 (SARS-CoV-1) and -2 (SARS-CoV-2) are beta-coronaviruses (β-CoVs) that have caused significant morbidity and mortality worldwide. Therefore, a better understanding of host responses to β-CoVs would provide insights into the pathogenesis of these viruses to identify potential targets for medical countermeasures. Our objective is to use a systems biology approach to explore the magnitude and scope of innate immune responses triggered by SARS-CoV-1 and -2 infection over time in pathologically relevant human lung epithelial cells (Calu-3/2B4 cells). Total RNA extracted at 12, 24, and 48 hours after β-CoVs infection of Calu-3/2B4 cells were subjected to RNA sequencing, bioinformatics, and functional enrichment analysis to select genes whose expressions were significantly modulated upon infection over time. The results of our study demonstrate that SARS-CoV-1 and -2 stimulate similar yet distinct innate antiviral signaling pathways in pathologically relevant human lung epithelial cells. Upregulated genes found at multiple time points regulated the viral life cycle, interferons, and interferon-stimulated genes (ISGs). Based on their profound modulation upon infection, we selected four ISGs, i.e., bone marrow stromal cell antigen 2 (BST2), Z-DNA Binding Protein 1 (ZBP1), C-X-C Motif Chemokine Ligand 11 (CXCL11), and Interferon Induced Transmembrane Protein 1 (IFITM1) for characterization as potential drug targets against β-CoVs.

overall_design: Calu-3/2B4 cells were subjected to SARS-CoV-1 or SARS-CoV-2 infection at a multiplicity of infection (MOI) of 1.0. Our controls were uninfected (mock infected) Calu-3/2B4 cells. At three different time points (12-, 24-, and 48-hours post-infection), we collected total RNA. Afterwards, gene expression profiling analysis of RNA-seq data was performed comparing SARS-CoV-1- and SARS-CoV-2-infected to mock-infected cells and SARS-CoV-1- to SARS-CoV-2-infected cells.

first: Vivian

last: Tat

first: Aleksandra

last: Drelich

first: Kamil

last: Khanipov

first: Pinghan

last: Huang

first: Jason

last: Hsu

first: Kempaiah

middle: R

last: Kempaiah

first: Chien-Te

last: Tseng

first: George

last: Golovko


title: Genetic disruption of class I HLA in cutaneous T-cell lymphoma

city: Palo Alto

first: Michael

last: Khodadoust

state: CA

address: 1701 Page Mill Rd

department: Medicine (Oncology)

institute: Stanford University School of Medicine

summary: Genetic disruption of class I HLA is a common mechanism of immune evasion and immunotherapy resistance in many other cancers but has not yet been characterized in cutaneous T-cell lymphoma (CTCL). We performed single-cell RNA sequencing (scRNA-seq) on tumor samples from patients with CTCL to demonstrate the tumor-specificity and intratumoral heterogeneity of such abnormalities.

overall_design: Peripheral blood mononuclear cells were isolated from whole blood using Ficoll-Paque centrifugation. Skin biopsies were dissociated into single cell suspensions using either the Tumor Dissociation Reagent (BD Biosciences) or gentleMACS Tumor Dissociation Kit (Miltenyi Biotec). After dead cell removal and CD45+ enrichment (the latter only in the case of skin biopsies), cells were analyzed using droplet-based scRNA-seq (10x Genomics).

first: Alexa

last: Kwang


title: Tofogliflozin Attenuates Renal Lipid Deposition and Inflammation via PPARα restoration in Diet-induced Steatohepatitic mice

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

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

overall_design: Refer to individual Series


title: Tofogliflozin Attenuates Renal Lipid Deposition and Inflammation via PPARα restoration in Diet-induced Steatohepatitic mice. (microRNA-Seq)

summary: Aims: We have previously demonstrated hepatic, cardiac, and skin inflammation in high-fat diet-induced steatotic liver disease model. However, the molecular mechanism in the kidney in this model is still not clear. It has been recently reported that SGLT2 inhibitors improved chronic kidney disease (CKD). Therefore, we evaluated the effect of tofogliflozin on renal lipid metabolism and inflammation in this model. Methods: Male 8-10-week-old C57Bl/6 mice were fed high-fat/high-cholesterol/high-sucrose/bile acid (HF/HC/HS/BA) diet with 0.015% tofogliflozin (Tofo group) or HF/HC/HS/BA diet alone (Cont group). After eight weeks, serum lipid profiles and histology, lipid content, mRNA/microRNA and protein expression levels in the kidney were examined.  Results: The Tofo group showed significant reduction in body weight (26.9±0.9 vs 24.5±1.0 g; p<0.001) and kidney weight compared to the Cont group. Renal cholesterol (9.1±1.6 vs 7.5±0.7 mg/g; p<0.05) and non-esterified fatty acid (NEFA) (12.0±3.0 vs 8.4±1.5 µEq/g; p<0.01) were significantly decreased in the Tofo group. Transmission electron microscopy revealed a decreasedd number of lipid droplets. mRNA sequencing analysis revealed that fatty acid metabolism-related genes were upregulated and NFκB signaling pathway-related genes were downregulated in the Tofo group. microRNA sequencing analysis indicated that miR-21a was downregulated and miR-204 was upregulated in the Tofo group. Interestingly, the expression of PPARα, which has been known to be negatively regulated by miR-21, was significantly increased, leading to enhancing β-oxidation genes, Acox1 and CPT1 in the Tofo group. Conclusions: Tofogliflozin decreased renal cholesterol and NEFA content and improved inflammation through the regulation of PPARα and miR-21a.

overall_design: Kidney of C57BL/6 mice fed a high-fat, high-cholesterol, bile-salt diet (HF/HC/HS/BA diet) containing tofogliflozin for eight weeks (n=3). As a control, kidney of C57BL/6 mice fed a HF/HC/HS/BA diet without tofogliflozin for eight weeks (n=3).

first: Sae

last: Nishihara

first: Masahiro

last: Koseki

first: Katsunao

last: Tanaka

first: Takashi

last: Omatsu

first: Ayami

last: Saga

first: Hiroshi

last: Sawabe

first: Hiroyasu

last: Inui

first: Takeshi

last: Okada

first: Tohru

last: Ohama

last: Okuzaki

first: Yoshihiro

last: Kamada

first: Masafumi

last: Ono

first: Makoto

last: Nishida

first: Mikio

last: Watanabe

first: Yasushi

last: Sakata


title: Tofogliflozin Attenuates Renal Lipid Deposition and Inflammation via PPARα restoration in Diet-induced Steatohepatitic mice. (RNA-Seq)


title: Whole transcriptome sequencing and circ_hsa_0001847 on proliferation and invasion of oral squamous cell carcinoma

city: Wuhu City

first: wenjie

last: wen

address: No.22 Wenchang West Road

institute: wannan medical college

summary: Oral squamous cell carcinoma (OSCC) accounts for approximately 90% of malignant epithelial tumors in the oral and maxillofacial region, which is characterized by a high metastatic potential and an unfavorable prognosis. The specific process of oral mucosal carcinogenesis and progression is very complicated. We screened 2310 mRNAs differentially expressed in cancer and paraneoplastic tissues, of which 1019 were upregulated and 1291 were downregulated; 14216 differentially expressed lncRNAs, of which 8829 were upregulated and 5387 were downregulated; and 167 differentially expressed circRNAs, of which 18 were upregulated and 149 were downregulated. Oral squamous cell carcinoma cells had a higher level of hsa_circ_0001847 expression than hok cells (P<0.05). Reduced hsa_circ_0001847 expression inhibited oral squamous cell carcinoma cell proliferation, migration, and invasiveness (P<0.05). Oral tissues contain differentially expressed mRNAs, lncRNAs, and circRNAs, and these differentially expressed mRNAs, lncRNAs, and circRNAs may be involved in the development of OSCC.

overall_design: Five OSCC patients' cancer tissues and paracancerous tissues were collected for whole transcriptome sequencing analysis to screen differentially expressed mRNA, long-stranded noncoding RNA (lncRNA), and circular RNA (circRNA) and bioinformatics [gene ontology (GO) enrichment analysis with genomic database (KEGG) pathway analysis and transcript enrichment analysis, etc.]. Target molecules closely associated with oral squamous cell carcinogenesis, migration, and invasion were identified using a miRNA-circRNA association network.

first: Deng

last: Chao


title: Recirculating regulatory T cells mediate thymic regeneration

city: Duarte

first: Anastasia

middle: I

last: Kousa

address: 1500 E Duarte Rd

department: Hematology / HCT

institute: City of Hope


title: Effect of  verapamil treatment on gene expression of osteoclast differentiated from mouse bone marrow-derived macrophages

first: Xiankun

last: Cao

address: Zhizaoju load No.639

department: orthopedic

institute: Shanghai Ninth People's Hospital affiliated to Shanghai Jiao tong University School of Medicine

summary:
To investigate the changed genes after verapamil treatment, we extracted primary BMMs from wild-type and then induced them to differentiate into osteoclasts with or without verapamil treatment for 5 days
We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different cells (3 pairs repeat) at the same time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control osteoclasts and the verapamil treatment osteoclasts (3 pairs repeat).

first: An

last: Qin

first: Jie

last: Zhao


title: Recirculating regulatory T cells mediate thymic regeneration [visium]

overall_design: Spatial transcriptomic profiles of thymic tissue from 2-month-old and 18-month-old mice after injury

first: Andri

last: Lemarquis

first: Kimon

middle: V

last: Argyropoulos

first: Lorenz

last: Jahn

first: Brianna

last: Gipson

first: Lucia

last: Serrano-Marin

first: Kristen

last: Victor

first: Yuzuka

last: Kanno

first: Narina

middle: N

last: Girotra

first: Hana

last: Andrlova

first: Jennifer

last: Tsai

first: Enrico

last: Velardi

first: Roshan

last: Sharma

first: Chenyi

last: Mao

first: Olov

last: Ekwall

first: Andrew

last: Goldstone

first: Jarrod

last: Dudakov

first: Susan

last: DeWolf

first: Marcel

last: van den Brink


title: Effect of  verapamil treatment on gene expression of osteoblast differentiated from mouse bone marrow-derived mesenchymal stem cells

first: Xiankun

last: Cao

summary:
To investigate the changed genes after verapamil treatment, we extracted primary BMSCs from wild-type and then induced them to differentiate into osteoblasts with or without verapamil treatment for 7 days
We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different cells (3 pairs repeat) at the same time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control osteoblasts and the verapamil treatment osteoblasts (3 pairs repeat).

first: An

last: Qin

first: Jie

last: Zhao


title: Recirculating regulatory T cells mediate thymic regeneration [single cell]

first: Anastasia

last: Kousa

overall_design: Single cell RNA-seq profiles of CD45+ RAG2GFP- thymic cells from 2-month-old and 18-month-old mice at steady state and at days 1, 4 and 7 after sublethal total body irradiation (SL-TBI).

first: Andri

last: Lemarquis

first: Kimon

last: Argyropoulos

first: Lorenz

last: Jahn

first: Brianna

last: Gipson

first: Lucia

last: Serrano-Marin


title: Morusinol efficiently inhibits M2-like polarization of macrophages in vitro

city: soochow

first: Hao

last: Xu

state: State...

address: No. 1, Shizi street, Suzhou

institute: Soochow University

summary: The emergence of natural products and their derivatives has notably influenced cancer treatment, making morusinol, an herbal medicine-derived monomer, a promising candidate. To comprehensively assess the impact of morusinol on immune function, we conducted whole transcriptome analysis (RNA sequencing, RNAseq) on macrophages treated with either vehicle or morusinol.

overall_design: The macrophages were treated with either vehicle or morusinol for 12 h, followed by RNA sequencing analysis.

first: Bingzong

last: Li

first: Wenzhuo

last: Zhuang


title: Morusinol is a Potent Therapeutic Agent Against DLBCL II

summary: The emergence of natural products and their derivatives has notably influenced cancer treatment, making morusinol, an herbal medicine-derived monomer, a promising candidate. To comprehensively assess the impact of morusinol on DLBCL cells, we conducted whole transcriptome analysis (RNA sequencing, RNAseq) on  SU-DHL-8 and Farage cell lines treated with either vehicle or morusinol.

overall_design: SU-DHL-8 and Farage cells were treated with either vehicle or morusinol for 12 h, followed by RNA sequencing analysis.


title: IL6/JAK/STAT3-mediated crosstalk between cancer associated fibroblasts and epithelial cells promotes lineage plasticity and prostate cancer progression [scRNA-seq]

first: Gilles

last: Laverny

address: 1 rue Laurent fries

institute: IGBMC

summary: Prostate cancer is a heterogeneous disease with a slow progression and a highly variable clinical outcome. The tumor suppressor gene TP53 is frequently mutated in prostate cancer and predictive of an early metastatic dissemination and unfavorable patient outcome. The progression of solid tumors to metastatic cancer is often associated with increased cell plasticity, but the mechanism underlying TP53-loss induced disease aggressiveness is unknown. Here we show that Trp53 deficiency in Pten-null prostatic epithelial cells does not impact the early proliferation of Pten-null epithelial cells and prostatic intraepithelial neoplasia formation, nor growth arrest and senescence entry at later time. Moreover, we demonstrate that it induces epithelial cell plasticity by stimulating IL6 production in cancer-associated fibroblasts, that in turn enhances Jak/Stat signaling in epithelial cells and promotes metastatic dissemination. Thus, TP53 restrains prostate cancer progression by preventing a pro-tumorigenic crosstalk between PTEN-deficient prostatic epithelial cells and the tumor microenvironment.

overall_design: We performed single-cell RNA sequencing of cells isolated from 3 dissociated sarcomatoid-free prostates of Pten/Trp53(i)pe-/- mice 5 months after gene inactivation.

first: Darya

last: Yanushko

first: Beatriz

last: German Falcon

first: Rana

last: El Bizri

first: Despoina

last: Pervizou

first: Céline

last: Keime

first: Tao

last: Ye

first: Christelle

last: Thibault-Carpentier

first: Sandrine

last: Henri

first: Daniel

last: Metzger


title: Combined analysis of metabolomics, proteomics, and transcriptomics to identify biomarkers for resistant hypertension

city: Jinan

first: Wenqing

last: Yang

address: No. 4655, University Road, University Science and Technology Park

institute: Shandong University of Traditional Chinese Medicine

summary: Resistant hypertension (RH) has emerged as a formidable challenge in the realm of hypertension prevention and treatment, owing to its potential for causing severe target organ damage. The identification of biomarkers assumes paramount significance in unraveling the pathogenesis of RH and facilitating early diagnosis and treatment. Despite the conduct of several single omics studies on RH, the intricate pathogenesis of this condition remains only partially understood. In this study, we comprehensively analyzed metabolomics, proteomics, and transcriptomics on healthy individuals, hypertensive patients, and those with RH. A variety of substances were screened, as potential diagnostic markers for RH. The hypoxia-inducible factor-1 (HIF-1) signaling pathway was identified as the pathogenic signaling pathway for RH. In conclusion, this study provides multi-omics analysis information to enhance our understanding of the pathogenesis of RH and to explore potential diagnostic markers, providing new insights for the search for effective therapeutic targets.

overall_design: To screen for biomarkers of resistant hypertension, we performed transcriptomic analyses in patients with resistant hypertension (RH group), hypertensive patients (EH group), and healthy individuals (N group). We performed gene expression profiling analysis using data obtained from RNA-seq of three groups. Comparative gene expression profiling analysis of RNA-seq data between RH and EH, RH and N.


title: IL6/JAK/STAT3-mediated crosstalk between cancer associated fibroblasts and epithelial cells promotes lineage plasticity and prostate cancer progression.


title: IL6/JAK/STAT3-mediated crosstalk between cancer associated fibroblasts and epithelial cells promotes lineage plasticity and prostate cancer progression [scATAC-seq]

overall_design: NOT PROVIDED; REQUESTED


title: Class switch recombination regulation by extracellular vesicles mediated intercellular epigenomic signaling

city: Zurich

first: Richard

last: Chahwan

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

summary: B cell maturation is crucial for effective adaptive immunity and requires a complex signaling network to control gene expression and protein function to mediate antibody diversification. B cells also rely on extracellular signaling queues from other cells within the germinal center. Recently, a novel class of intercellular signaling mediated by extracellular vesicles (EVs) has emerged. Studies have shown B cell EVs mediated signaling is involved in immune response regulation, infection control, and tumorigenesis. However, the mechanistic role of B cell EVs in B cell maturation is not yet established. We herein study the biological properties and physiological function of B cell EVs in the context of B cell maturation. We use novel technologies to characterize B cell EVs surface marker signatures, molecular cargo and physiological roles in B cell maturation. A new specialized nanoparticle analyzer was used to profile B cell EVs at the single particle level and characterize their surface markers and sub-populations at various maturation stages. EV ncRNA cargo was characterized by RNA-seq and bioinformatic analyses identified an EVs mediated regulatory network for B cell maturation. A previously uncharacterized micro-RNA (miR-5099) in combination with a set of long non-coding RNA carried within B cell EVs is shown to be important for antibody diversification signaling. The physiological role of EVs in B cell maturation is investigated using EV blockade assays and complementation studies using diverse EV sources further confirmed the physiological role and mode of action of EVs in B cell maturation.

overall_design: To investigate how EV-RNA regulate CSR, we profiled RNA from unstimulated and stimulated primary B cells and CH12F3 and paired EVs. Differential RNA expression between cells and secreted EVs; unstimulated and stimulated were analyzed to identify responsible RNA

first: Kevin

last: Yim

first: Ala'a

last: Al Hrout


title: Dendrophenol inhibits vascular calcification by activating IL13RA2-dependent inhibition of STAT3 and attenuating WNT3/b-catenin signaling pathway

city: Hefei

first: Yuanli

last: Chen

address: School of Food and Biological Engineering, Hefei University of Technology, Hefei, China

institute: Hefei University of Technology

summary: In this experiment,we used HASMCs cells to explore the mechanisms by which Dendrophenol affects smooth muscle cell osteogenic differentiation and related mechanisms. We found that IL13RA2 expression was significantly reduced during the induction of osteogenic differentiation in HASMCs, and normal levels were restored after Dendrophenol treatment, thus Dendrophenol may treat vascular calcification through IL13RA2. Further, we found that IL13RA2 interacts with the transcription factor STAT3, suggesting that the therapeutic effect of Dendrophenol may be mediated through STAT3. In addition, we further investigated the link between IL13RA2/STAT3 and the classical WNT/b-catenin pathway and found that WNT3 plays an important role in this process. The mechanism of action of Dendrophenol was further clarified.

overall_design: To investigate the mechanism of action of Dendrophenol treatment for osteogenic differentiation of HASMCs, we cultured HASMCs under phosphate conditions and detected the differential genes by RNA-seq with or without Dendrophenol conditions.

first: Tingting

last: Zhang

first: Mengmeng

last: Zhu

first: Jialing

last: Ma

first: Zhenghong

last: Liu


title: Morusinol is a Potent Therapeutic Agent Against DLBCL

first: Hao

last: Xu

summary: The emergence of natural products and their derivatives has notably influenced cancer treatment, making morusinol, an herbal medicine-derived monomer, a promising candidate. To comprehensively assess the impact of morusinol on DLBCL cell, we conducted whole transcriptome analysis (RNA sequencing, RNAseq) on the SU-DHL-2 cell line treated with either vehicle or morusinol.

overall_design: The SU-DHL-2 cell was treated with either vehicle or morusinol for 12 h, followed by RNA sequencing analysis.

first: Bingzong

last: Li

first: Wenzhuo

last: Zhuang


title: Swift Induction of Human Spinal Lower Motor Neurons and Robust ALS Cell Screening via Single-Cell Imaging

city: Bunkyo-ku

first: Selena

last: Setsu

state: Tokyo

department: Institute for Quantitative Bioscience

institute: University of Tokyo

summary: This study presents a newly developed method to rapidly and efficiently induce human spinal lower motor neurons (LMNs) from induced pluripotent stem cells (iPSCs) for elucidation of pathomechanism or drug screening in amyotrophic lateral sclerosis (ALS). Previous methods had several limitations, such as poor efficiency and low purity of LMN induction and the labor-intensiveness of the induction and evaluation procedures. Our new protocol achieved nearly 80% induction efficiency in just a few weeks by combining a small molecule-based approach and transduction of transcription factors. To overcome cellular heterogeneity, we analyzed morphology and viability of iPSC-derived LMNs on a cell-by-cell basis using time-lapse microscopy and machine learning, establishing a highly accurate pathophysiological evaluation system. Our rapid, efficient, and simplified protocol and our single-cell based evaluation method provides a way to conduct large-scale analysis and drug screening using motor neurons derived from iPSCs.

overall_design: Motor neurons were differenciated from iPS cells derived from ALS patients and healthy controls and performed total RNA-sequencing.

first: Satoru

last: Morimoto

first: Shiho

last: Nakamura

first: Fumiko

last: Ozawa

first: Yukihide

last: Tomari

first: Hideyuki

last: Okano


title: GPR34 senses demyelination to promote neuroinflammation and cognition impairment in Alzheimer's disease

first: XiqQiong

last: Wang

state: Anhui

address: School of Life Sciences, No. 443 Huangshan Road

institute: University Of Science And Technology Of China

summary: Sterile neuroinflammation initiated by damage-associated molecular patterns (DAMPs) has been regarded as an important driver in Alzheimer's disease (AD) and can occur prior or independently of the deposition of extracellular amyloid-β (Aβ) plaques and intracellular tau neurofibrillary tangles (NFTs). Genetic ablation or pharmacological inhibition of GPR34 reduced microglia activation, Aβ deposition and cognition impairment. Moreover, GPR34 inhibition prevented aging associated neuroinflammation and cognition impairment without the presence of Aβ plaques.

overall_design: Examination of GPR34 effection on microglia in 5XFAD mice.

first: Rongbin

last: Zhou

first: Zonghui

last: Huang

first: Xiaqiong

first: Yubo

first: Bolong

last: Lin


title: Exploring  Genetic Differences of Angelicae pubescentis roots from Different Regions Based on transcriptome

status: Public on Feb 04 2025

city: Lanzhou

first: Chaogui

last: Hu

state: Anning

address: Gansu Agricultural University, Lanzhou 730070, China

institute: Gansu Agricultural University

summary: Analysis of gene expression of medicinal plants from different habitats is essential for quality control. This analysis completed the transcriptome sequencing of 12 samples of Angelicae Pubescentis Radix from four different habitats, and a total of 81.24 G CleanData was obtained. The effective data volume of each sample was distributed in 5.97 ~ 7.01 G, the Q30 base distribution was 93.81 ~ 94.67 %, and the average GC content was 42.5 %. A total of 67438 Unigenes were spliced, with a total length of 84034485 bp and an average length of 1246.1 bp.

overall_design: This study mainly investigated the gene expression differences of Angelicae Pubescentis Radix from four different producing areas. Each producing area had 3 replicates. The variables of the experiment are different ecological environments.

first: Qian


title: Role of Kindlin-2 in  breast cancer immune evasion

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: Kindlin-2 (K2) plays a major role in driving TNBC tumors progression and metastasis through the regulation of several hallmarks of cancer. We have employed a single cell RNA sequencing approach using 10x Genomics scRNAseq to study the role of Kindlin-2 in immune evasion of TNBC tumors. Tumors derived from control 4T1 cells or their K2-KO derivatives grown in syngeneic immune competent BALB/c mine werw subjected to scRNAseq to indentify the efect of loss of K2 on the tumor immune environment.

overall_design: Control or K2-KO 4T1 cells were injected in the mammry fat pads of female BLB/c mice.tumors reach 150 mm3, tumors wer excised, followed by disociation into sigle cell supspension then analyzed using scRNAseq.

first: Khalid

last: Sossey-Alaoui

first: E


title: Neurobehavioral phenotypes in the pan-neuronal GAL4 zebrafish line Tg(elavl3:KalTA4)

city: Worcester

first: Summer

last: Thyme

state: MA

address: 55 N Lake Ave

institute: UMass Chan

summary: The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish, the Tg(elavl3:KalTA4) (HuC) line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tg(elavl3:KalTA4) zebrafish larvae compared to wildtype siblings, which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tg(elavl3:KalTA4) larvae showed alterations in brain activity, brain morphology, and behavior, including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA-seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis, we used economical low-pass whole genome sequencing to map the Tol2-mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga, a known cell cycle regulator, is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan-neuronal lines include the length of the elavl3 (HuC) promoter (9 kb) and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines, we cloned five neuronal promoters (atp6v0cb, elavl3, rtn1a, sncb, and stmn1b) ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase-based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines.

overall_design: Tg(elavl3:KalTA4) zebrafish were crossed with Tg(4xUAS-hmgn6) zebrafish to produce wildtype, elavl3:KalTA4, 4xUAS-hmgn6, and elavl3:KalTA4; 4xUAS-hmgn6 offspring. At 6 dpf, heads were collected for sci-RNA-seq.

first: Anna

last: Moyer


title: Hepatocyte Rho-Associated Kinase Signaling is Required to Survive Liver Injury

city: San Francisco

first: Jessica

last: Herrera

address: 513 Parnassus Ave, HSE 590

department: Surgery

institute: UCSF

summary: Rho-associated kinases 1 and 2 (ROCK1 and ROCK2) are downstream effectors of RhoA and regulate various critical cell functions such as actomyosin contractility, apoptosis, proliferation, and cell migration. Some studies utilizing inhibitors suggested that ROCK inhibition could serve as a treatment for liver fibrosis. However, more investigation is needed to understand the role of ROCK signaling in hepatocytes with injury in vivo. Rock1fl/fl, Rock2fl/fl, and Rock1fl/fl;Rock2fl/fl mice were injected with adeno-associated virus serotype 8 (AAV8)-thyroid hormone-binding globulin (TBG)-Cre for targeted gene deletion in hepatocytes, or injected with AAV8-TBG-Null to generate littermate controls (WT). Mice were then given a 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet to induce cholestatic liver injury. Serum liver function tests, liver histology, and RNAseq analyses were performed. Mice deficient in both ROCK1 and ROCK2 (DKO) showed early mortality, decreased hepatic synthetic function, and increased hepatocellular injury compared to WT. Mice deficient in ROCK1 only (R1KO) or ROCK2 only (R2KO) demonstrated minimal differences compared to WT, indicating that the two ROCK isoforms had redundant roles in this disease model. Compared to WT, histologic analysis showed that DKO mice had significantly greater loss of liver parenchyma.  RNAseq analysis indicated upregulation of apoptotic and inflammatory genes in DKO compared to WT liver. Immunostaining showed an increase in p21 and cleaved caspase 3 in DKO mice compared to WT, indicating that deletion of ROCK potentially leads to p21 overexpression and cell death. These results demonstrate that hepatocyte ROCK signaling is essential in promoting cell survival in the setting of liver cholestatic injury.

overall_design: We examined the role of liver epithelial ROCK by deleting the isoforms Rock1 and Rock2 separately or simultaneously in male mice using an inducible Cre/loxP-mediated gene knockout. Weinduced fibrotic liver disease using the 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) injury model to investigate the role of ROCK in the hepatocyte response to injury. Differential gene expression profiling analysis of RNA-seq data was conducted for WT vs R1KO and R2KO, and for WT vs DKO given DDC diet. Single KO WT samples, R1WT and R2WT, were combined into one WT group for analysis. DKO mice were separated into 2 week or 4 week collection due to the mice being in moribound state; however, all mice were combined into two groups, WT and DKO, for analysis.

first: Yun

last: Weng

first: Tyler

last: Lieberthal

first: Marcus

last: Paoletti

first: Tammy

last: Chang


title: B2M knockout for hypo-immunity alters the global profiles of membrane-proteins and cytokines and impairs therapeutic efficacy of human stem cells

city: Guangzhou

first: Haibo

last: Peng

address: Jinwan Road 368

institute: Zunyi Medical University

summary: β2-microglobulin (B2M) is the light chain subunit of type I human leukocyte antigen complexes that play a key role in the immune system. Genetic knockout (KO) of B2M in human pluripotent stem cells (hPSCs) has been used as a major approach together with many other strategies to generate hypo-immunogenic, universal stem cells for allogeneic cell transplantation without triggering immune rejection. However, this approach assumes that B2M is dispensable for stem cell differentiation and therapy, although it lacks evidence from thorough evaluation. Here, we conducted genome-wide analyses of isogenic pairs of wild-type (WT) and B2M-KO hESCs and their derived mesenchymal stem cells (E-MSCs), which revealed proteomic and transcriptomic alternations due to the KO. Over 200 proteins were mistargeted  from the plasma membranes of B2M-KO hESCs and E-MSCs, suggesting that B2M is crucial for protein trafficking in the subcellular organelles. The expression of osteo-chondrogenic determinants and inflammation-related cytokines differed dramatically in B2M-KO E-MSCs from WT E-MSCs, consistent with the impaired osteogenic differentiation and wound-healing efficacy of B2M-KO E-MSCs. This study reveals previously unrecognized functions of B2M, which alerts cautions be used when applying B2M-KO cells to therapy.

overall_design: RNA seq of  human pluripotent stem cells (hPSCs)  in control and experiment B2M group


title: RNA-seq analysis of E11.5 and E12.5 Mboat7 KO cortices

city: Tokyo

first: Nozomu

last: Kono

address: Hongo 7-3-1, Bunkyo-ku

institute: Universtiy of Tokyo

summary: To investigate whether Mboat7 KO mice showed any abnormality before E11.5, we evaluated the global gene expression patterns in the cortices of Mboat7 heterozygous mice and KO mice at E11.5 using RNA-sequencing. No significant differences in gene expression were observed, suggesting that Mboat7 KO mice develop normally until E11.5.  Even at E12.5 when the phenotype starts to become apparent, little difference in gene expression were observed in Mboat7 KO mice.

overall_design: RNA-seq profiling of E11.5 and E12.5 cortices obtained from Mboat7+/- and Mboat7-/- mice.

first: Yuki

last: Ishino


title: GCN5a is a telomeric lysine acetyltransferase whose loss primes Toxoplasma gondii for latency (RNAseq)

city: Indianapolis

first: Michael

middle: James

last: Holmes

state: IN

address: 635 Barnhill Drive

department: Pharmacology & Toxicology

institute: Indiana University School of Medicine

summary: Toxoplasma gondii is a protozoan parasite that causes persistent infection in warm-blooded vertebrates by undergoing differentiation from a replicative stage (tachyzoites) to a latent encysted stage (bradyzoites). Stage differentiation is critical for transmission and pathogenesis and relies on gene regulation driven by a network of transcription and epigenetic factors. We previously found in non-cystogenic type I RH strain parasites that the lysine acetyltransferase (KAT), GCN5a, is dispensable in tachyzoites but required to upregulate stress-response genes, suggesting a link with bradyzoite conversion. To address this possibility, we generated endogenously tagged GCN5a parasites and a genetic knockout in cystogenic type II Pru strain. We show that GCN5a protein, but not mRNA, increases during differentiation and complexes with unique protein partners, most of which contain AP2 domains. Pru strain tachyzoites lacking GCN5a augment bradyzoite-specific gene expression in the absence of stress. Loss of GCN5a slowed tachyzoite replication and heightened sensitivity to bradyzoite conversion but resulted in smaller cyst sizes compared to wildtype. Using CUT&Tag, we delineated the chromosomal occupancy of GCN5a relative to the essential KAT, GCN5b. While GCN5b localizes to coding regions, GCN5a surprisingly localizes exclusively to telomeres. These findings suggest that the loss of GCN5a leads to telomere dysfunction, which slows replication and promotes the transition to latency.

overall_design: RNAseq of GCN5A-3xHA (tagged) and GCN5A-knockout Toxoplasma gondii parasites grown under tachyzoite and bradyzoite culture conditions for 48hrs


title: GCN5a is a telomeric lysine acetyltransferase whose loss primes Toxoplasma gondii for latency (CUT&Tag)

overall_design: GCN5A and GCN5B (both endogenously tagged with 3xHA at C-terminus) were profiled for genome occupancy by CUT&Tag after 48hrs of tachyzoite and bradyzoite-inducing conditions. Untagged parental PruΔKu80ΔHX included in singlet as controls


title: Single-cell RNA and TCR sequencing reveals distinct systematic immune response induced by SABR with or without prior anti-PD-1 therapy

first: Yanjuan

last: Chen

state: Guangdong

address: Guangzhou

department: Department of Geriatrics and Division of Rheumatology and Research

institute: The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital)

summary: Previous studies have demonstrated that stereotactic body radiation therapy (SBRT) could activate systemic immune response, however, these researches showed limitations in comprehensively characterizing changes of T cell profile and T cell receptor (TCR). In the present study, we applied scRNA-seq and scTCR-seq to observe the dynamics of T cell and TCR repertoire from peripheral blood mononuclear cells (PBMCs) in early stage non-small-cell lung cancer (NSCLC) patients receiving SBRT with or without prior anti-PD-1 therapy, demonstrating the distinct systemic immune response between SBRT and ISBRT group. An enrichment of CD8-TE, CD8-EM, and CD4-TE clusters with increased cytotoxic and exhausted score were observed after treatment in SBRT group, while a decrease of those were presented in ISBRT group. Moreover, gene expression analysis revealed T cell mediated cytotoxicity signaling and T cell proliferation signaling were enriched in SBRT group while decreased in SBRT group. Analysis of TCR repertoire indicated a substantial alteration of TCR repertoire after treatment. The proportions of the large clone of TCR were increased after treatment in SBRT group while an opposite alteration existed in ISBRT group. After treatment, both SBRT and ISBRT group generated numerous new TCR clones which were mainly enriched in CD8 TE. Single clones and large clones were the mainly types of new TCRs in SBRT group, whereas in ISBRT group single clones accounted for the majority of new TCRs. These findings suggested that systemic immunity was activated in distinct pattern between the SBRT and ISBRT group, and provide evidence for future development of new treatment regimen.

overall_design: Single cell RNA-seq and T-cell receptor repertoire sequencing with 43,051 T cells sorted from the peripheral blood of patients with metastatic non-small cell lung cancer (NSCLC) were performed on the 10x Genomics platform. Sampling grouping included pre- and post-therapy of stereotactic ablative radiation therapy (SABR) with or without prior anti-PD-1 therapy.

first: Chao

last: Liu

first: Jinming

last: Yu

first: Zongcheng

last: Li

first: Bing

last: Sun


title: Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats

city: Solna

first: Hong

last: Yang

state: Stockholm

address: Tomtebodavägen 23A

department: Systems Biology

institute: KTH Royal Institute of Technology/Science For Life Laboratory

summary: Excessive consumption of sucrose, in the form of sugar-sweetened beverages, has been implicated in the pathogenesis of metabolic dysfunction‐associated fatty liver disease (MAFLD) and other related metabolic syndromes. The c-Jun N-terminal kinase (JNK) pathway plays a crucial role in response to dietary stressors, and it was demonstrated that the inhibition of the JNK pathway could potentially be used in the treatment of MAFLD. However, the intricate mechanisms underlying these interventions remain incompletely understood given their multifaceted effects across multiple tissues. In this study, we challenged rats with sucrose-sweetened water and investigated the potential effects of JNK inhibition by employing network analysis based on the transcriptome profiling obtained from hepatic and extrahepatic tissues, including visceral white adipose tissue, skeletal muscle, and brain. Our data demonstrate that JNK inhibition by JNK-IN-5A effectively reduces the circulating triglyceride accumulation and inflammation in rats subjected to sucrose consumption. Coexpression analysis and genome-scale metabolic modelling reveal that sucrose overconsumption primarily induces transcriptional dysfunction related to fatty acid and oxidative metabolism in the liver and adipose tissues, which are largely rectified after JNK inhibition at a clinically relevant dose. Skeletal muscle exhibited minimal transcriptional changes to sucrose overconsumption but underwent substantial metabolic adaptation following the JNK inhibition. Overall, our data provides novel insights into the molecular basis by which JNK inhibition exerts its metabolic effect in the metabolically active tissues. Furthermore, our findings underpin the critical role of extrahepatic metabolism in the development of diet-induced steatosis, offering valuable guidance for future studies focused on JNK-targeting for effective treatment of MAFLD.

overall_design: 160 snap-frozen rat tissues (liver, vWAT, SkM, and brain) were processed for RNA sequencing on the Illumina NovaSeq6000 system.

first: Hasan

last: Turkez

first: Cemil

last: Bayram

first: Ismail

last: Bolat

first: Adil

last: Mardinoglu


title: Impact of Early Bisphenol A Exposure on Transcriptome and Chromatin Accessibility in Brain Oligodendrocytes of Juvenile Mice

city: Paris

first: Anne-Laure

last: Schang

state: Select Option

address: 4, Avenue de l'Observatoire

department: Faculté de Pharmacie

institute: Université Paris Cité

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

overall_design: Refer to individual Series


title: Impact of Early Bisphenol A Exposure on Transcriptome and Chromatin Accessibility in Brain Oligodendrocytes of Juvenile Mice [RNA-seq]

summary: This study evaluates the neurodevelopmental effects of bisphenol A (BPA) on oligodendrocytes, the neural cells responsible for myelination in the central nervous system. The primary aim was to investigate the changes in transcriptome and chromatin compaction induced by early BPA exposure in oligodendrocytes isolated from 2-week-old juvenile mice.

overall_design: OF-1 mice were exposed to BPA in utero starting from gestational day 7 and continued during lactation. BPA was administered at a concentration of 250 µg/mL in the mothers' drinking water, leading to an estimated exposure of 40 µg/kg/day. On post-natal day 16, brains were collected from 9 control mice (5 males, 4 females) and 10 BPA-exposed mice (5 males, 5 females). Brain cells were dissociated, and oligodendrocytes were isolated using magnetic cell sorting with anti-O4 antibodies.  Chromatin from 50,000 cells of each sample (total = 19) was Tn5-tagmented, and DNA was extracted for sequencing (ATAC-seq). Additionally, RNA was extracted from the remaining cells of 4 samples per group (total = 16) for transcriptome analysis using RNA-seq.

first: Vanessa

last: NAFFAA

first: Celine

last: KEIME

first: Juliette

last: VAN STEENWINCKEL

first: Pierre

last: GRESSENS

first: Nicolas

last: AUZEIL

last: SCHANG


title: Impact of Early Bisphenol A Exposure on Transcriptome and Chromatin Accessibility in Brain Oligodendrocytes of Juvenile Mice [ATAC-seq]


title: Singel cell RNA sequencing of an F1 cross of Marek’s disease resistant and susceptible chickens

city: Athens

first: Deborah

last: Velez-Irizarry

state: GA

address: 934 College Station Road

department: US National Poultry Research Center

institute: USDA, Agricultural Research Service

summary: Marek's disease virus (MDV) is a highly contagious alphaherpesvirus with widespread incidence in the poultry industry. The double stranded DNA virus infects chickens and turkeys causing a lymphoproliferative disease known as Marek's disease (MD). Infected and susceptible birds develop T cell lymphomas that cause peripheral nerve degeneration, partial or complete paralysis and immunosuppression. Previously, our lab performed scRNA seq of splenic-derived cells from MD resistant Line 6 (L6) and MD susceptible Line 7 (L7) during MDV infection to identify major immune cell subsets. In this study we extend this previous analysis by adding scRNA seq of a first-generation (F1) L6 x L7 population to characterize allele specific expression in individual immune cell types. The joint analysis of scRNA seq of the L6, L7 and F1 cross provide a deeper understanding of how genetic variation impacts gene expression variation in immune cell types and identify regulatory mechanism playing a key role in MD resistance.

overall_design: The experimental design consisted of 20 L6 x L7 F1 chickens randomly allocated to either an MDV-challenge or control (unchallenged) group, i.e., 10 chicks per condition. The challenged group receive an intra-abdominal injection at two weeks of age with 2,000 pfu JM/102W strain MDV. Birds were housed 6 days post-infection in HB units and humanly euthanized. Splenic derived lymphocytes were collected from each bird for sequencing. Three birds per condition were selected for 10X Genomics scRNA seq.

first: Hans

last: Cheng

first: Cari

last: Hearn


title: Various forms of calorie restriction, but not a nonrestricted low-fat diet, reverse obesity-associated tumor growth and lung metastasis in a mouse model of triple-negative breast cancer (microarray)

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

summary: lean control, obese, and formerly obese C57BL6N mice which underwent weight loss via low-fat diet or various forms of calory restriction were injected with E0771 cells and tumor growth was monitored

overall_design: RNA was isolated from tumors and subject to microarray analysis

first: Michael

middle: F

last: Coleman

first: Stephen

last: Hursting


title: Age and obesity associated immune dysfunction mammary tumor growth

summary: lean control, obese (DIO), aged 6 (young) or 18months (Aged)  C57BL6N mice which underwent weight loss via intermittent calory restriction (ICR) or not (ad lib) were injected with E0771 cells and tumor growth was monitored

overall_design: RNA was isolated from tumors and subject to mircoarray analysis


title: Effect of High Glucose on the Gene Expression Profiling in Cardiac Fibroblasts from Rats at Different Ages

first: Quqian

last: Mo

state: Guangdong Province

address: No.280, Outer Ring East Road, University Town

department: Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine

institute: Guangdong Pharmaceutical University

summary:
Background: Cardiac fibroblasts (CFs) play a vital role in the physiological and pathological processes of the heart. Previous studies have demonstrated that high glucose stimulation induces the transformation of CFs into myofibroblasts, contributing to cardiac fibrogenesis. However, in vivo experiments have predominantly utilized adult animals, whereas most in vitro studies have focused on CFs derived from neonatal animals. The responses of CFs from different age groups to high glucose levels remain unclear. This study aimed to investigate transcriptional alterations in CFs at distinct developmental stages in response to high glucose exposure.
Methods: CFs were isolated from neonatal (S1, 0–3 days), juvenile (S2, 3–4 weeks), adult (S3, 10–13 weeks), and aged (S4, 20 months) rats. CFs were exposed to normal (5.5 mM, NG) or high glucose (33 mM, HG). The cellular RNA was extracted for sequencing and analysis. Differentially expressed genes (DEGs) were validated by quantitative real-time PCR. Results: After NG treatment, fibrosis and inflammation-related gene expression in CFs (e.g., Col8a1, Col8a2, IL-6, Ccl2, Ccl20, Mmp2 and Mmp9) increased with age, while proliferation-related genes (MCM family, Sox10, Sox11) decreased. HG treatment most affected S3-CFs, showing 228 DEGs; it suppressed growth-related genes (Adra1d, Htr2b) and enhanced inflammatory genes (IL-6, Olr1). In S1-CFs, 197 inflammation-rich genes were upregulated under HG. S4-CFs displayed 166 DEGs, mostly metabolic downregulation (G6pc). S2-CFs had the fewest DEGs (112), focusing on cell metabolism. Conclusions: Fibrosis- and inflammation-associated gene expression in CFs showed an age-dependent stepwise elevation. CFs from distinct developmental stages responded differently to HG stimulation, with S3-CFs exhibiting the most pronounced response. These findings highlight the developmental characteristics of CFs and provide implications for the selection of appropriate CFs to investigate diabetes-associated cardiac fibrosis.

overall_design: To investigate the difference of gene expression profile of rat cardiac fibroblasts at different ages under normal glucose and high glucose conditions, we extracted primary rat cardiac fibroblasts at four different age groups and cultured them in DMEM containing 5.5mM or 33mM glucose.

first: Angyu

last: Zhan

first: Ruining

last: Bai

first: Shaoling

last: Lin

first: Jiaojiao

last: Feng

first: Tongjun

last: Li

first: Zijian

last: Lao

first: Xiao

last: Yang

first: Keke

last: Wang

first: Xianglu

last: Rong

first: Lexun


title: TF ChIP-seq Caenorhabditis elegans (supplemental II)

city: Seattle

first: Louis

last: Gevirtzman

state: WA

address: 3720 15th Ave NE

department: Genome Science

institute: University of Washington

summary: A catalog of transcription factor (TF) binding sites in the genome is critical for  deciphering regulatory relationships.  Here we present the culmination of the efforts of the  modENCODE (Model Organism ENCyclopedia Of DNA Elements) and modERN (model  organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding  events in vivo in two major model organisms, Drosophila melanogaster (fly)  and Caenorhabditis elegans (worm).  These datasets comprise 605 TFs identifying 3.6M sites in  the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the  regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters  termed “metapeaks”, that larger metapeaks have characteristics of high occupancy target (HOT)  regions, and that the importance of consensus sequence motifs bound by TFs depends on  metapeak size and complexity.  Combining ChIP-seq data with single cell RNA-seq data in a  machine learning model identifies particular TFs with a prominent role in promoting target gene  expression in specific cell types, even differentiating between parent-daughter cells during  embryogenesis.  These data are a rich resource for the community that should fuel and guide  future investigations into TF function.  To facilitate data accessibility and utility, all strains  expressing GFP-tagged TFs are available at the stock centers for each organism.  The chromatin  immunoprecipitation sequencing data are available through the ENCODE Data Coordinating  Center, GEO, and through a direct interface (http://epic.gs.washington.edu/modERN/) that  provides rapid access to processed data sets and summary analyses, as well as widgets to probe  the cell type-specific TF-target relationships.

overall_design: Reanalysis of raw data files in BioProject PRJNA63463  using ENCODE TF/Histone ChIP-Seq pipeline version 1.3.6  https://github.com/ENCODE-DCC/chip-seq-pipeline2

first: Michelle

last: Kudron

first: Alec

last: Victorsen

first: Bridget

middle: C

last: Lear

first: Jiahao

last: Gao

first: Jinrui

last: Xu

first: Swapna

last: Samanta

first: Emily

last: Frink

first: Adri

last: Tran-Pearson

first: Chau

last: Huynh

first: Dionne

last: Vafeados

first: Ann

last: Hammonds

first: William

last: Fisher

first: Martha

last: Wall

first: Greg

last: Wesseling

first: Vanessa

last: Hernandez

first: Zhichun

first: Mary

last: Kasparian

first: Kevin

last: White

first: Ravi

last: Allada

first: Mark

last: Gerstein

first: LaDeana

last: Hillier

first: Susan

middle: E

last: Celniker

first: Valerie

last: Reinke

first: Robert

middle: H

last: Waterston


title: TF ChIP-seq Drosophila melanogaster  (supplemental II)

first: Louis

last: Gevirtzman

overall_design: Reanalysis of raw data files in BioProject PRJNA63463 using ENCODE TF/Histone ChIP-Seq pipeline version 1.3.6  https://github.com/ENCODE-DCC/chip-seq-pipeline2

first: Michelle

last: Kudron

first: Alec

last: Victorsen

first: Bridget

last: Lear

first: Jiahao

last: Gao

first: Jinrui

last: Xu

first: Swapna

last: Samanta

first: Emily

last: Frink

first: Adri

last: Lin


title: RNA-sequencing of sorted epidermal cells from murine dorsal skin

city: Göttingen

first: Anja

last: Uhmann

address: Heinrich-Düker-Weg 12

department: Institute of Human Genetics

institute: University of Göttingen

summary: Comparative transcriptome analyses confirmed the HF-SC identity of tdT+/tdTneg CD49fhigh CD34+ Sca-1neg cells and suggests and IFE identity of the tdT+/tdTneg CD49fhigh CD34+ Sca-1+ population

overall_design: mRNA profiles of sorted dorsal skin cells from adult CD4Cre R26-tdT lineage tracing mice were generated by RNA-sequencing


title: Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome III

city: Boulder

first: Meaghan

last: Courvan

state: CO

address: 596 UCB

department: Biofrontiers

institute: University of Colorado, Boulder

summary: Individuals with Down syndrome have a increased likelihood of suffering from inflammatory and autoimmune conditions, due to the presence of four interferon receptors on chromosome 21. Transcription of genes plays a key role in the interferon response, and the Mediator kinases, CDK8 and CDK19, are essential in potentiating this transcription. Given the role CDK8/19 play in the interferon response, and the fact that selective inhibitors of these kinases exist (such as Cortistatin A), it is possible that targetting Mediator kinase activity may alleviate symptoms of chronic inflammation in Down syndrome.

overall_design: Examination of effects of Mediator kinase inhibition (through treatment with selective inhibitor Cortistatin A) on transcription (through RNA-seq) in two T21 lymphoblastoid cell lines, one collected at 24 hours from a sibling to a D21 cell line previously analyzed by the lab, and one collected at 4.5 hours in a non-sibling T21 cell line.

first: Kira

last: Cozzolino

first: Dylan

last: Taatjes


title: Heparan sulfate regulates myofibroblast heterogeneity and function to mediate niche homeostasis during alveolar morphogenesis

city: Chengdu

first: Hua

last: He

state: Sichuan

address: 2222 Xinchuan Rd

institute: West China Second University Hospital Sichuan University


title: Dysregulation of gene expression during gastrulation results in impaired primitive erythropoiesis and vascular development in Trim71-KO embryos

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: During embryonic development in mice, global deficiency of Trim71 (Trim71-KO) leads to defects in vascular development of the yolk sac and impaired primitive erythropoiesis. These phenotypes start to become apparent at E9.5. We analyzed changes in gene expression by single-cell RNA-sequencing (scRNA-seq) in whole Trim71-KO embryos compared to wildtype embryos at an early developmental stage (E7.5, late gastrulation) to investigate the onset of these phenotypes. Furthermore, we analyzed Trim71-KO and wildtype yolk sacs at E9.5 by scRNA-seq to gain insight into the changes in gene expression at the developmental stage when vascular defects have become apparent.

overall_design: Timed mating of heterozygous Trim71+/- mice was performed and embryos were isolated at E7.5 or E9.5. Genotyping of embryos for the Trim71 locus was performed using the ectoplacental cone from E7.5 embryos or the embryo tail of E9.5 embryos. Whole E7.5 Trim71+/+ and Trim71-/- embryos, or E9.5 Trim71+/+ and Trim71-/- yolk sacs were used for cell isolation and subsequent scRNA-seq.

first: Tobias

last: Beckröge

first: Bettina

last: Jux

first: Hannah

last: Seifert

last: Theobald

first: Elena

last: De Domenico

first: Stefan

last: Paulusch

first: Marc

last: Beyer

first: Andreas

last: Schlitzer

first: Elvira

last: Mass

first: Waldemar

last: Kolanus


title: Novel Placental Biomarker Shows Predictive Potential for Spontaneous Preterm Labor

city: Baltimore

first: Bingbing

last: Wang

state: MD

address: 655 W. Baltimore St

department: Ob/Gyn

institute: University of Maryland School of Medicine

summary:
Objective: Human parturition involves many events among mother, fetus, and placenta, and the initiation of these events is the consequence of activation of a series of endocrine and immune responses. Multiple underlying pathways account for the cascade of events that culminate in spontaneous preterm labor. In this study, we aimed to characterize these signaling pathways of placental origin at molecular levels.

Study design: We used single-cell RNA-sequencing (sc-RNA-seq) analysis to probe transcriptional heterogeneity in human placenta delivered at preterm or term and then used RNA in situ hybridization (RNA-ISH) assay on formalin-fixed paraffin-embedded (FFPE) placental tissues to validate these results.

Results: By using sc-RNA-seq on villous cytotrophoblast (CTB) isolated from a preterm placenta, we found that signaling pathways implicated in the initiation of term or preterm labor including ferroptosis, kisspeptin (KISS1), and senescence were constitutively activated in distinct cellular clusters of these trophoblastic stem cells. RNA-ISH-based spatial gene expression profiling in FFPE tissues revealed that pregnancy-specific beta-1-glycoprotein 4 (PSG4), a potent molecular driver for cellular aging, was significantly increased in preterm placentas (N = 30) compared to their full-term counterparts (N = 9). Furthermore, PSG4 mRNA signals were predominantly detected in the villous syncytiotrophoblast and the discontinuous monolayer of CTB as well as the intervillous space where maternal blood circulates.

Conclusion: Our study provides strong support for PSG4 overexpression serving as a biomarker for pregnant women at risk for preterm delivery, which can allow for the development of timely and clinical preventive strategies.

overall_design: Cytotrophoblast from preterm placenta (35 weeks of gestational age were subjected to sc-RNA-seqeuancing with a term placenta (38 weeks of gestational age) as the control.

first: Karl

last: Seif

first: Jun

last: Lei

first: Mary

last: Mangione

first: Sifa

last: Turan

first: Irina

last: Burd

first: Peixin

last: Yang