title: N6-Methyladenosine Reader YTHDF3-Mediated CEBPA Translation Maintains Genomic Stability and Stem Cells Function to Prevent Liver Injury and Hepatocellular Carcinoma [m6a-seq]

status: Public on Feb 29 2024

city: Nanjing

first: Xiang

last: Zhong

state: Jiangsu

address: Tongwei Road

country: China

institute: Nanjing agricultural university

type: Methylation profiling by high throughput sequencing

summary: BACKGROUND & AIMS: Hepatocellular carcinoma (HCC) induced by chronic liver damage is a major cause of cancer mortality, but its precise epigenetic mechanisms are severely under studied. In addition, the role of N6-methyladenine (m6A) reader YTHDF3 in human diseases remains poorly understood. METHODS: Liver injury and hepatocarcinogenesis in mice were induced by chemical. CRISPR/Cas9 technology was used to construct Ythdf3 and Mettl14 knockout mice. Hepatic cell population characteristics was determined by means of 10X single-cell RNA-seq and flow cytometry. Cell proliferation and DNA damage were evaluated by immunofluorescence, immunohistochemistry, and western blot. Liver organoids were cultured to examine liver stem cells function. MeRIP-seq was used to reveal alterations in m6A methylation patterns impacted by chemical-induced liver injury. RIP-seq and Ribo-seq were applied to identify YTHDF3 targets and determine translation efficiency. Small interfering RNAs and dCas13b-FTO-sgRNA plasmids were used to evaluate the function of YTHDF3 and CEBPA in vitro. RESULTS: YTHDF3 depletion exacerbated chemical-induced liver injury with a reduction in functional hepatocytes and stem cells. Furthermore, METTL14 and YTHDF3-dependent RNA m6A dysregulation induced DNA damage and promoted development of HCC. Mechanistically, knockout of Ythdf3 impeded the translation of CCAAT/enhancer-binding protein-alpha (CEBPA), subsequently inhibited expression of PARP1 and PRDX2 to promote DNA damage and induce genomic instability, finally leading to liver injury and HCC. CONCLUSIONS: m6A/YTHDF3/CEBPA regulatory axis plays an essential role in governing cell fates and genomic stability, thereby preventing liver injury and HCC, and offers potential therapeutic avenue for targeting YTHDF3 and CEBPA in the treatment of HCC.

overall_design: M6A-seq was used to reveal alterations in m6A methylation patterns impacted by CCL4-induced liver injury.

first: Yaxu

last: Liang

first: Bin

last: Shen

first: Beicheng

last: Sun

first: Chuan

last: He


title: N6-Methyladenosine Reader YTHDF3-Mediated CEBPA Translation Maintains Genomic Stability and Stem Cells Function to Prevent Liver Injury and Hepatocellular Carcinoma [RIP-seq]

overall_design: RIP-seq  were applied to identify YTHDF3 targets in mouse with or without CCL4 administration


title: N6-Methyladenosine Reader YTHDF3-Mediated CEBPA Translation Maintains Genomic Stability and Stem Cells Function to Prevent Liver Injury and Hepatocellular Carcinoma [scRNA-seq]

type: Expression profiling by high throughput sequencing

overall_design: Hepatic cell population characteristics was determined by means of 10X single-cell RNA-seq in WT and Ythdf3 KO mice after CCL4 administration


title: Keloid Fibroblasts (KFs)  scRNA seq

city: Nantong

first: JingTing

last: Zhao

address: No. 99, Qingnian Middle Road, Chongchuan District

institute: Nantong Third People's Hospital

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of KFs in the intestine.

overall_design: KFs from the control group and those treated with HMME-SDT at 1.0 W/cm² and 1.5 W/cm² were harvested 24 hours post-treatment using TRIzol reagent. RNA sequencing was carried out by Singleron Biotechnologies.

first: Jingting

first: Zhiyi

last: Xu

first: Hui

last: Hua

first: Bingrong

last: Zhou


title: In situ tissue profile of rat trigeminal nerve in trigeminal neuralgia using spatial transcriptome sequencing

city: Shanghai

first: wenbin

last: wei

address: NO.639 Zhizaoju Road,Huangpu District

institute: Shanghai Ninth People 's Hospital, Shanghai Jiao Tong UniversitySchool of Medicine

summary: Investigation on the transcriptome and intercellular communication of different cells of trigeminal nerve in trigeminal neuralgia rat by spatial transcriptome sequencing

overall_design: Unilateral mechanical compression-induced TN rat model was prepared. The trigeminal root, semilunar ganglion and proximal branches from the diseased side of three individual were isolated and squeezed into the first three capture areas (trigeminal neuralgia, TN1, 2, 3), whereas the healthy side from two of three individual were put into the final capture area (healthy control, HC) of Visium Spatial Gene Expression Slide.

first: Wenbin

last: Wei

first: Yuemin

last: Liu


title: Phase separation mediated transcriptional activity of FOXK1 triggers glycolysis and facilitates renal fibrosis

city: Wuhan

first: Maoqing

last: Tian

address: 238 Jiefang Road, Wuchang District

institute: Renmin Hospital of Wuhan University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Tubular epithelial cells (TECs) undergo an energy metabolism shift from fatty acid oxidation (FAO) to glycolysis in renal fibrosis. The critical pathways leading to the halt of FAO in TECs have been well described, whereas the mechanism underlying the burst of glycolysis remains elusive. We herein reported a critical glycolysis regulator emerged in TECs amid the renal fibrosis, the transcriptional factor forkhead box protein K1 (FOXK1), which exhibited fibrogenic and metabolism-rewiring capacity. Genetic modification of FOXK1 in TECs altered the glycolytic metabolism and fibrotic lesion. The surge of a set of glycolysis-related genes following FOXK1 activation contributed to the energic shift. Nuclear-translocated FOXK1 formed condensates through liquid-liquid phase separation (LLPS) to drive the target genes transcription. The core intrinsically disordered regions (IDRs) within FOXK1 were further mapped and validated. Finally, we explored the therapeutic strategy targeting Foxk1 in the CKD mouse model by subcapsular injecting Foxk1-shRNA-carrying AAV9 vector.

overall_design: To explore the transcriptional regulatory mechanisms underlying the roles of FOXK1 in renal fibrosis, we performed chromatin immunoprecipitation-sequencing (ChIP-seq) to analyze the genome-wide distribution of FOXK1 in HK-2 cells. Cells were cultured in DMEM/F12 medium with 10% fetal bovine serum and 1% penicillin-streptomycin in a 37 °C incubator with 5% CO2. Cells were seeded on six-well culture plates for transfection and treatment with or without 10 ng/ml TGF-β1 for 24 hours.


title: Effect of PME-1 S156A mutant on gene expression of mouse brain

city: yamaguchi

first: Shunta

last: Ikeda

state: yamaguchi

department: Joint faculty of veterinary medicine

country: Japan

institute: Yamaguchi University

summary: Protein methylation is a reversible post-translational modification commonly occurring on carboxyl groups of leucine, glutamate, and isoprenylated cysteine, or the side-chain nitrogen atoms of arginine, lysine, and histidine residues. Histone methylation is well studied and shown to play a central role in the regulation of epigenetic gene expression. On the other hand, our knowledge of the importance of methylation in proteins other than histones is limited. Increased PME-1 expression and decreased LCMT-1 expression associated with decreased PP2Ac methylation levels were observed in the brain of AD patients. Therefore, it is crucial to understand the precise role of PP2A methylation in physiological and pathophysiological processes.To obtain a comprehensive view for the effect of loss of PME-1 methylesterase activity on brain development, we performed transcriptome analysis for E18.5 brain tissues.

overall_design: Whole brain of E18.5 mouse brain,PME-1 WT and PME-1 S156A, was collected  and then RNA was extracted with TRIzol Reagent for RNA seq.

first: Shinya

last: Ayabe

first: Saori

last: Mizuno

first: Atsushi

last: Yoshiki

first: Kenichi

last: Nakashima

first: Koichi

last: Sato

first: Takashi

last: Ohama


title: RARg bookmarking functions in prostate cancer (IMPACT-Seq)

city: WEST HOLLYWOOD

first: Moray

last: Campbell

state: CA

address: 8687 Melrose Avenue, Office B227.5G

country: USA

institute: Cedars-Sinai Medical Center

summary: To define the RARg complex in PCa cell models, including isogenic variants of 22Rv1, how this is targeted by miR-96, and regulates the AR cistrome, and how this is specifically enriched in G2/M cells and how these actions collectively shape the transcriptional programs associated with PCa outcomes.

overall_design: IMPACT-Seq was undertaken on HPr1AR or LNCaP cells transfected with 3' biotinylated miRIDIAN miR-96 mimic and scramble controls


title: RARg bookmarking functions in prostate cancer (RNA-Seq)

overall_design: RNA-SEQ in the presense of miR-96 mimic was undertaken on HPr1AR, LNCaP and 22Rv1 cells


title: N6-Methyladenosine Reader YTHDF3-Mediated CEBPA Translation Maintains Genomic Stability and Stem Cells Function to Prevent Liver Injury and Hepatocellular Carcinoma [Ribo-seq]

first: Xiang

last: Zhong

overall_design: Ribo-seq was applied to determine translation efficiency of YTHDF3 targets in mouse.

first: Yaxu

last: Liang

first: Bin

last: Shen

first: Beicheng

last: Sun

first: Chuan

last: He


title: Effect of BMS-582949 treatment on gene expression in osteoclasts

first: cheng

last: xu

state: Hubei

address: Sanjiaohu Road

institute: Jianghan University

summary: Controlling excessive osteoclastic activity is a promising strategy for many bone disease treatments. Here we report that 10 μM BMS-582949, a clinical p38α inhibitor,dromatically suppresses the osteoclast differentiation in vitro. Our results provide a evidence that BMS-582949 could be a candicdate drug for the therapy of osteolytic diseases.

overall_design: To investigate the function of BMS-582949 in osteoclastogenesis, mouse bone marrow cells from wild-type C57BL/6J mice were extracted and cultured for 3 days. The attached bone marrow-derived macrophages (BMMs) were then scraped, and reseeded in α-MEM medium with 10% FBS, 1% penicillin-streptomycin, 1% L-glutamine, and M-CSF overnight at 37 °C in a humidiﬁed atmosphere containing 5% CO2, and then stimulated by 40 ng/ml RNAKL and CM for 3 days in the presence or absence of 10 μM BMS-582949.The media was changed after 3 days. At day 4, total RNAs from matured osteoclasts were extracted using TRIzol reagents and performed subjected to RNA sequencing.

first: Xu

last: Cheng

first: Hu

last: zhangfeng


title: Volatile compounds emitted by Plant Growth Promoting Fungi Tolypocladium inflatum GT22 alleviates copper and pathogen stress

city: Tainan City

first: Hao-Jen

last: Huang

address: No. 1., University Road

country: Taiwan

institute: National Cheng Kung University

summary: The intricate interactions between plants and microorganisms have garnered substantial scientific interest. While previous studies have highlighted the potential influence of various fungal volatile compounds(VCs) on plant growth and development, the precise mechanisms underlying this modulation still need to be discovered. In this study, we discovered that fungal volatile organic compounds from the soil-borne fungus Tolypocladium inflatum GT22 enhance the growth of Arabidopsis. Remarkably, following the priming of Arabidopsis with GT22 VC, it displayed an enhanced immune response, thereby mitigating the detrimental effects caused by both pathogenic infections and copper stress. Transcriptomic analyses of Arabidopsis seedlings treated with GT22 VCs revealed the differential expression of 90, 83, and 137 genes after 3, 24, and 48 hours of volatile exposure, respectively. These responsive genes are involved in growth, hormone regulation, defense mechanisms, and signaling pathways. Notably, the induction of genes related to innate immunity, hypoxia, salicylic acid (SA) biosynthesis and camalexin biosynthesis by GT22 VCs were reported. Among the VCs emitted by GT22, limonene is particularly noteworthy. Arabidopsis seedlings exposed to limonene exhibited not only growth promotion effects but also alleviation of copper stress, indicating that limonene may play a role in the interaction between GT22 and plants. Overall, the findings of this study provide evidence supporting that fungal VCs can promote plant growth and enhance both biotic and abiotic tolerance. Furthermore, our results suggest that seedlings exposed to T. inflatum GT22 VCs holds promising potential for harnessing beneficial effects to improve crop productivity.

overall_design: To investigate the molecular mechanisms triggered by T. inflatum GT22 VCs in Arabidopsis, the transcriptomic analysis was performed. RNA-seq data of 3, 24, 48 hr T. inflatum GT22 VCs treatment in Arabidopsis thaliana was analyzed.


title: Development of microRNA expression signatures for Buyang Huanwu decoction in treating intracerebral hemorrhage

city: Changsha

first: Zhe

last: Yu

address: Kaifu District, Xiangya Road, No.87

institute: Central South University

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify the potential miRNA asscociated with Buyang Huanwu decoction (BYHWD) in treating  intracerebral hemorrhage (ICH), we have employed miRNA expression profiling. 126 and 38 miRNAs were identified in the ICH vs sham group and the BYHWD vs ICH group, respectively. Specifically, 15 DEmiRNAs were intersected among the three groups. Expression of 14 miRNA (miR-7b-5p, miR-770-3p,miR-760-3p, miR-376c-5p, miR-1224-5p, miR-298-5p, miR-541-3p, miR-344d-3-5p, miR-653-5p, miR-7a-5p, miR-6540-5p,miR-146a-5p, miR-375-3p, and miR-3962) from this signature was quantified by RT-qPCR.

overall_design: Mice were randomly divided into 3 groups (n=5): the Sham, ICH, and BYHWD-H groups. The gavage administration started on the 1st day after the surgery for 14 consecutive days. Brain samples were dectected at 14 d after ICH.

first: Yang

last: Wang

first: Teng

last: Li


title: Selection of epigenetically privileged HIV-1 proviruses during treatment with panobinostat and interferon-α2a [RNA-seq]

city: Cambridge

first: Ce

last: Gao

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT and Harvard

summary: CD4 T cells with latent HIV-1 infection persist despite treatment with currently available antiretroviral agents and represent the main barrier to a cure of HIV-1 infection. Pharmacological disruption of viral latency may increase the immunological vulnerability of HIV-1-infected cells, but the clinical efficacy of latency-reversing agents for reducing HIV-1 persistence remains to be proven. Here, we show in a randomized, controlled human clinical trial that the histone deacetylase inhibitor panobinostat, when administered in combination with pegylated interferon-a2a, induces a structural transformation of the HIV-1 reservoir cell pool, characterized by a disproportionate overrepresentation of HIV-1 proviruses integrated in ZNF genes and in chromatin regions with reduced H3K27ac marks, the molecular target site for panobinostat. In contrast, proviruses near H3K27ac marks appeared to be actively selected against, likely due to increased susceptibility to panobinostat. These data suggest that latency-reversing treatment with panobinostat can accelerate immune selection of HIV-1 proviruses.

overall_design: We performed RNA-seq on isolated CD4T cells from PBMCs of 17 study participants in the ACTIVATE clinical trial to study the transcriptional profile in response to the different study medications.

first: Marie

last: Armani-Tourret

first: Ciputra

middle: A

last: Hartana

first: Isabelle

last: Roseto

first: Amy

last: Sbrolla

first: Katrina

last: Shea

first: Theresa

last: Flynn

first: Yelizaveta

last: Rassadkina

first: Liliana

last: Vela

first: Alexander

last: Hochroth

first: Carole

last: Lee

first: Francoise

last: Giguel

first: Rajeev

last: Malhotra

first: Frederic

middle: D

last: Bushman

first: Rajesh

middle: T

last: Gandhi

middle: G

first: Daniel

middle: R

last: Kuritzkes

first: Mathias

last: Lichterfeld


title: Astrocyte-derived thrombospondins 1 and 2 are required for cortical synapse development controlling goal-directed action performance.

city: Durham

first: Kristina

last: Sakers

state: NC

address: 307 Research Dr

institute: Duke University

summary: During development, controlled synaptogenesis is required to form functioning neural circuits that underlie cognition and behavior.  Astrocytes, a major glial-cell type in the central nervous system (CNS), promote synapse formation by secreting synaptogenic proteins. Thrombospondins 1 and 2 (TSP1/2), which act through their neuronal receptor α2δ-1, are required for proper intracortical excitatory synaptogenesis. In the adult brain, the loss of α2δ-1 impairs training-induced excitatory synaptogenesis in the anterior cingulate cortex (ACC), and this impairment leads to increased effort-exertion during high-effort tasks. Here, we tested whether TSP1 and TSP2 are required for controlling effort during operant conditioning by using a lever press for food reward training in mice. Surprisingly, we found that constitutive loss of TSP1/2 significantly reduced lever pressing performance when the effort required for a food reward was increased, a phenotype opposite of α2δ-1 loss. Loss of TSP1/2 reduced excitatory synapse number significantly in adult brains. However, in the ACC of TSP1/2 knockout mice, there was still training-induced excitatory synaptogenesis, likely through the upregulation of TSP4, a TSP isoform that is also synaptogenic. Unexpectedly, we also found a significant increase in inhibitory synapse number and function in the ACC of TSP1/2 knockout mice, which were eliminated after training. Finally, we found that astrocyte-specific ablation of TSP1/2 in developing but not adult astrocytes is sufficient to reduce performance during high-effort tasks. Taken together, our study highlights the importance of developmental astrocyte-derived synaptogenic cues TSP1 and 2 in establishing excitatory and inhibitory circuits that control effort during operant conditioning in adults.

overall_design: WT and Thbs1/2 KO mice were run through a behavioral goal-directed action paradigm to understand how Thbs1/2 play a role in effort exertion. RNA was collected from the anterior cingulate cortex (ACC) within 1 hour of the end of the behavioral experiment and sent for RNA-sequencing. The data represent bulk RNA from the entire ACC.

first: Oluwadamilola

middle: O

last: Lawal

first: Francesco

middle: P

last: Ulloa Severino

first: Shiyi

last: Wang

first: Dhanesh

last: Sivadasan Bindu

first: Sarah

last: Johnson

first: Henry

middle: H

last: Yin

first: Cagla

last: Eroglu


title: RARg bookmarking functions in prostate cancer (m6A-Seq)

first: Moray

last: Campbell

overall_design: m6A-Seq was undertaken on HPr1AR, LNCaP and 22Rv1 cells


title: Epigenetic disruption of the RARgamma complex impairs its function to bookmark AR enhancer interactions required for enzalutamide sensitivity in prostate cancer

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

overall_design: Refer to individual Series


title: SELENOK-Dependent CD36 Palmitoylation Regulates Microglial Functions and Aβ Phagocytosis

city: shenzhen

first: Zhonghao

last: Zhang

address: xueyuan

institute: shenzhen university

summary: Amyloid-beta (Aβ) is a key factor in the onset and progression of Alzheimer's disease (AD). Selenium (Se) compounds show promise in AD treatment. Here, we reveal that selenoprotein K (SELENOK), a selenoprotein involved in immune regulation and potentially related to AD pathology, plays a critical role in microglial immune response, migration, and phagocytosis. In vivo and in vitro studies corroborate that SELENOK deficiency inhibits microglial Aβ phagocytosis, exacerbating cognitive deficits in 5xFAD mice, which are reversed by SELENOK overexpression. Mechanistically, SELENOK is involved in CD36 palmitoylation through DHHC6, regulating CD36 localization to microglial plasma membranes and thus impacting Aβ phagocytosis. CD36 palmitoylation is reduced in the brains of AD patients and mice. Se supplementation promotes SELENOK expression and CD36 palmitoylation, enhancing microglial Aβ phagocytosis and mitigating AD progression. We have identified the regulatory mechanisms from Se-dependent selenoproteins to Aβ pathology, providing novel insights into potential therapeutic strategies involving Se and selenoproteins.

overall_design: Adult microglia mRNA profiles of 10-month-old wild type (WT) and Selk-/- mice

first: Pei

last: Ouyang

first: Zhiyu

last: Cai

first: Shujing

last: Lin

first: Jiaying

last: Peng


title: RARg bookmarking functions in prostate cancer (CUT&RUN)

overall_design: CUT&RUN was undertaken with antibodies to GFP (for RARgamma), AR, H3K27ac, H3S10P and IgG in 22Rv1 isogenic cell variants.  Specifically 22Rv1 cells stably transfected with an empty vector (22Rv1-mock) or a GFP-tagged RARgamma (22Rv1-RARgamma). 22Rv1-RARgamma-TACC1 cells were generated by transient transfection of TACC1 into 22Rv1-RARgamma cells; TACC1 protein expression was sustained for ~72h. Briefly, 0.5x106 cells were treated for DHT (10nM, 6h) or CD437 (400 nM, 6h).  To synchron


title: Comparative analysis of gene expression in tumors responding and non-responding to anti-CTLA-4 in a preclinical study of melanoma

city: Bethesda

first: Teresa

last: Przytycka

state: MD

address: 8600 Rockville Pike

department: NLM

institute: NIH

summary: To investigate the diverse responses of the M4 mouse melanoma to immune checkpoint inhibitors, the tumors responding (R) and nonresponding (NR) to anti-CTLA-4 from a preclinical study of M4 melanoma were subjected to mRNA sequencing. The differentially expressed genes were analyzed to identify the signaling pathways that asscoiated with the therapeutic responses of the tumors.

overall_design: 40 C57BL/6 mice were implanted with the M4 melanoma cell line (B2905). When the tumors reached to average size of 75 mm^3, they were randomized to three groups: (1) 5 mice left untreated; (2) 5 mice treated with isotype control IgG2b; (3) 30 mice treated with anti-CTLA-4. The antibodies were given twice a week for two weeks. 20 tumors of the group (3) and 5 tumors of the group (2) were harvested for RNA sequencing. In the 10-11 days after the last dose of treatment, tumors were identified as nonresponders, responders, and stable disease if their sizes continued to increase, decrease, and remain stable, respectively.

first: Chi-Ping

last: Day

first: Eva

last: Guijarro

first: Glenn

last: Merlino


title: Selection of epigenetically privileged HIV-1 proviruses during treatment with panobinostat and interferon-α2a

first: Ce

last: Gao


title: Chromatin accessibility profiling by ATAC-seq in LNCaP-shNT and LNCaP-shTP53 cells

city: Chicago

first: Young

last: Yoo

address: 303 E. Superior

institute: Northwestern University

summary: The TP53 tumor suppressor is frequently altered in lethal, castration-resistant prostate cancer (CRPC). However, to date there are no effective treatments that specifically target TP53 alterations. Using transcriptomic and metabolomic analyses, we show here that TP53-altered prostate cancer (PCa) exhibits an increased dependency on asparagine and overexpresses asparagine synthetase (ASNS, the enzyme catalyzing the synthesis of asparagine). Mechanistically, loss/mutation of TP53 transcriptionally activate ASNS expression, directly as well as via ATF4, driving de novo asparagine biosynthesis to support CRPC growth. TP53-altered CRPC cells are sensitive to asparagine restriction by knockdown of ASNS and L-asparaginase treatment to deplete the intracellular and extracellular sources of asparagine respectively. This effect was rescued by asparagine addition. Notably, pharmacological inhibition of intracellular asparagine biosynthesis using a glutaminase (GLS) inhibitor and depletion of extracellular asparagine with L-asparaginase significantly reduced asparagine production and effectively impaired CRPC growth. This study highlights the significance of ASNS-mediated metabolic adaptation as a synthetic vulnerability in CRPC with TP53 alterations, providing a rationale for co-targeting intracellular and extracellular asparagine production to treat these lethal prostate cancers.

overall_design: We measured chromatin accessibility by ATAC-seq in isogenic LNCaP cells with or without TP53 KD by shRNA

first: Sarki

last: Abdulkadir


title: Neuroprotective potential of intranasally delivered L-myc immortalized human neural stem cells in female rats after a controlled cortical impact injury

city: Duarte

first: Margarita

last: Gutova

state: California

address: 1500 East Duarte Road

institute: City of Hope

summary:
Efficacious stem cell-based therapies for traumatic brain injury (TBI) depend on successful delivery, migration, and engraftment of stem cells to induce neuroprotection. L-myc expressing human neural stem cells (LMNSC008) demonstrate an inherent tropism to injury sites after intranasal (IN) administration. We hypothesize that IN delivered LMNSC008 cells migrate to primary and secondary injury sites and modulate biomarkers associated with neuroprotection and tissue regeneration. To test this, immunocompetent adult female rats received a controlled cortical impact injury (CCI) or sham surgery. LMNSC008 cells or a vehicle (VEH) were administered IN on postoperative days 7, 9, 11, 13, 15, and 17. The distribution and migration of eGFP-expressing LMNSC008 cells were quantified over 1 mm-thick optically cleared (CLARITY) coronal brain sections from TBI and SHAM controls. NSC migration was observed along white matter tracts projecting toward the hippocampus and regions of TBI. ELISA and Nanostring assays revealed a shift in tissue gene expression in LMNSC008 treated rats relative to controls. LMNSC008 treatment reduced expression of genes and pathways involved in inflammatory response, microglial function, and various cytokines and receptors. The data demonstrate a robust proof-of-concept for LMNSC008 therapy for TBI and provides a strong rationale for IN delivery for translation in TBI patients.
NanoString RNAseq sample preparation and data acquisition

overall_design: Brain tissue was dissected and RNA was isolated from snap frozen tissues according to a diagram in figure S6 and half was used for Nanostring analysis and half for protein ELISA assays. RNA expression in the ipsilateral and contralateral hemispheres of NSC and VEH-treated TBI brains was analyzed using the NanoString nCounter platform (NanoString Technologies) by digitally detecting and counting RNA expression in a single reaction without amplification. Each assay included six positive and eight negative RNA assay controls, plus ten mRNA housekeeping controls. RNA was hybridized with the Codeset from the gene panel at 65°C for 16 h. The post-hybridization probe-target mixture was quantified using the nCounter Digital Analyzer, and all data analyses were performed on nSolver (NanoString Technologies). All raw data were first normalized with internal positive and negative controls to eliminate variability unrelated to the samples, then normalized to the selected housekeeping genes using Geometric Means methods. Statistically significant (p<0.05) and < 2 fold up- or down- regulated genes were analyzed and clustered as described below.


title: Comprehensive transcriptional analysis of dorsal skin development in pigs

city: Ya'an

first: Xinyue

state: Sichuan

address: Xinkang street num 46

department: Department of Zoology,College of Life Science

institute: Sichuan Agricultural University

summary: The skin is the body's first line of defense and has multiple functions; its development is a complex, multifactorial regulatory process. Porcine skin is physiologically, anatomically and histologically more similar to human skin, and is often used as a model animal for human skin research. There are fewer studies on the transcriptome aspects of the skin during the porcine embryonic period, and the data obtained in this study may help to explain the age-related changes in transcriptional patterns during skin development and provide further reference for understanding human skin development at the molecular level. In this study, RNA sequencing was performed on the dorsal skin of Chenghua sows at embryonic day 56 (E56), embryonic day 76 (E76), embryonic day 105 (E105), and 3 days after birth (D3). Exploring RNA changes in porcine dorsal skin at four ages. Expression profiles of messenger RNAs, long-stranded noncoding RNAs, microRNAs, and cyclic RNAs were analyzed. The biological functions of their differential genes were investigated by gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. A number of skin-related differential genes were identified by intercomparison between RNAs at four time points, and KEGG functional analysis showed that these differential genes were mainly enriched in metabolic and developmental, immune, and disease pathways,and the pathways enriched in GO analysis were highly overlapping. Collagen is an important part of the skin, with type I collagen making up the largest portion. In this study, collagen, type I, alpha 1 (COL1A1) and collagen typeI alpha2 (COL1A2) was significantly upregulated at four time points. In addition, lncRNA-miRNA-mRNA and miRNA-circRNA co-expression networks were constructed.

overall_design: RNA sequencing was performed on the dorsal skin of Chenghua sows at embryonic day 56 (E56), embryonic day 76 (E76), embryonic day 105 (E105), and 3 days after birth (D3). Exploring RNA changes in porcine dorsal skin at four ages. Expression profiles of messenger RNAs, long-stranded noncoding RNAs, microRNAs, and circular RNAs were analyzed. The biological functions of their differential genes were investigated by gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis.

first: Mei

first: Yujing

last: Li

first: Yanzhi

last: Jiang


title: HER2 heterogeneity and treatment response-associated profiles in HER2-positive breast cancer in the NCT02326974 clinical trial

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: HER2-targeted therapies including antibody drug conjugates have shown great efficacy in HER2-positive breast cancer. However, resistance to treatment in part due to pre-existing HER2 heterogeneity (HET) is a significant clinical challenge and requires the use of rationally-designed combination therapies. Here we describe transcriptomic profiling of 287 biopsies from 129 patients in a phase II neoadjuvant clinical trial using a combination of T-DM1 and pertuzumab for early-stage HER2-positive breast cancer, we investigated the mechanisms driving T-DM1 resistance. In pre-treatment tumors from patients without a complete response (pCR), distinct molecular features were identified: HER2 HET tumors retained PI3K pathway activation and a basal-like phenotype, while HER2 Non-HET tumors exhibited lower PI3K pathway enrichment. T-DM1 treatment universally reduced HER2 protein expression and copy number heterogeneity while increasing PI3K pathway enrichment and luminal identity in residual tumors. Importantly, HER2 HET tumors showed minimal transcriptomic response compared to HER2 Non-HET tumors, in line with the lesser clinical response. The response to T-DM1 was not associated with hotspot PIK3CA/ERBB2 mutations but rather correlated with immune infiltration. HER2 Non-HET tumors exhibited less effective immune surveillance at baseline but became immune activated with T-DM1 treatment, while HER2 HET tumors exhibited a more immune suppressed microenvironment upon treatment. Our study highlights the multifaceted nature of T-DM1 resistance driven by HER2 heterogeneity and provides essential evidence for optimizing therapeutic strategies for these patients.

overall_design: RNA-seq ptofiling was conducted in 287 biopsied from 129 patients with early-stage HER2-positive breast cancer in a phase II neoadjuvant clinical trial of T-DM1 and pertuzumab combination

first: Zheqi

first: Otto

last: Metzger Filho


title: Identification of a SIRT3 activator that alleviates myocardial hypertrophy and fibrosis by regulating mitochondrial homeostasis

status: Public on Feb 28 2024

city: Chengdu

first: Wei

last: Liu

state: 四川省

address: 林荫街8号

institute: Sichuan University

summary: Sirtuin3 (SIRT3) is well known as a conserved nicotinamide adenine dinucleotide+ (NAD+)-dependent deacetylase located in the mitochondria that may regulate oxidative stress, catabolism and ATP production. Accumulating evidence has recently revealed that SIRT3 plays its critical roles in cardiac fibrosis, myocardial fibrosis and even heart failure (HF) , through its deacetylation modifications. Thus, discovery of SIRT3 activators and elucidating their underlying mechanisms of HF should be urgently needed. Herein, we identified a new small-molecule activator of SIRT3 (named 2-APQC) by the structure-based drug designing strategy. 2-APQC was shown to alleviate isoproterenol (ISO)-induced cardiac hypertrophy and myocardial fibrosis in vitro and in vivo rat models. Importantly, in SIRT3 knockout mice, 2-APQC could not relieve HF, suggesting that 2-APQC is dependent on SIRT3 for its protective role. Mechanically, 2-APQC inhibited the mammalian target of rapamycin-p70 ribosomal protein S6 kinase (p70S6K), c-jun N-terminal kinase (JNK) and transforming growth factor-β (TGF-β)/mothers against decapentaplegic homolog 3 (Smad3) pathways to improve ISO-induced cardiac hypertrophy and myocardial fibrosis. Based upon RNA-seq analyses, we demonstrated that SIRT3-pyrroline-5-carboxylate reductase 1 (PYCR1) axis was closely assoiated with HF. By activating PYCR1, 2-APQC could enhance mitochondrial proline metabolism, inhibited ROS-p38MAPK pathway and thereby protecting against ISO-induced oxidative damage. Moreover, activation of SIRT3 by 2-APQC could facilitate AMPK-Parkin axis to inhibit ISO-induced necrosis. Together, our results demonstrate that 2-APQC is a targeted SIRT3 activator that alleviates myocardial hypertrophy and fibrosis by regulating mitochondrial homeostasis, which may provide a new clue on exploiting a promising drug candidate for the future HF therapeutics.

overall_design: To further clarify the potential mechanism of 2-APQC in HF, we treated H9c2 cells with 2-APQC for 24 hours and ISO for 48 hours and then performed RNA-seq analysis to check the differential expression of genes

first: Ling

last: Zou

first: Jin

last: Zhang

first: Minru

last: Liao


title: Phase separation of N-myc differentially modulates the transcriptom

city: San Francisco

first: Xiaokun

last: Shu

address: 555 Mission Bay Boulevard South, CVRI,RM484

institute: University of California, San Francisco

summary: SPARK-ON tag does not perturb the core transcriptional function of n-Myc.~2260 DEGs with ≥ 1.5-fold change in transcript level, including ~1270~6900 DEGs with ≥ 1.5-fold change in transcript level, including ~3100 up-regulated. By compare n-Myc condensed phase and dilute phase, 99 DEGs that were differentially expressed with ≥ 1.5-fold change. in transcript levels, including 88 up-regulated genes and 11 down-regulated genes  and ~3800 down-regulated genes.

overall_design: analyze the transcriptome difference in single clone expressed n-Myc SPARK-ON under phase separation threshold.Use lenalidomide to induce n-Myc phase-separation without changing protein concentration. No SPARK-ON control is used to evaluate lenalidomide effect on transcriptome.


title: Newly developed preclinical models reveal broad spectrum CDK inhibitors as potent drugs for CRPC exhibiting primary resistance to enzalutamide

city: Tokyo

first: Eijiro

last: Nakamura

state: Not in USA

address: Tukiji 5-1-1

department: Urology

institute: National Cancer Center Japan

summary: Androgen-deprivation therapy is a standard treatment for advanced prostate cancer. However, most patients eventually acquire resistance and progress to castration-resistant prostate cancer (CRPC). In this study, we established new CRPC cell lines, AILNCaP14 and AILNCaP15, from LNCaP cells under androgen-deprived conditions. Unlike most pre-existing CRPC cell lines, both cell lines expressed higher levels of androgen receptor (AR) and prostate-specific antigen (PSA) than parental LNCaP cells. Moreover, these cells exhibited primary resistance to enzalutamide. Since AR signaling plays a significant role in the development of CRPC, PSA promoter sequences fused with GFP were introduced into AILNCaP14 cells to conduct GFP fluorescence-based chemical screening. We identified flavopiridol, a broad spectrum CDK inhibitor, as a candidate drug that could repress AR transactivation of CRPC cells, presumably through the inhibition of phosphorylation of AR on the serine 81 residue (pARSer81). Importantly, this broad spectrum CDK inhibitor inhibited the proliferation of AILNCaP14 cells both in vitro and in vivo. Moreover, a newly developed liver metastatic model using AILNCaP15 cells revealed that the compound attenuated tumor growth of CRPC harboring highly metastatic properties. Finally, we developed a patient-derived xenograft (PDX) model of CRPC and DCaP CR from a patient presenting therapeutic resistance to enzalutamide, abiraterone, and docetaxel. Flavopiridol successfully suppressed the tumor growth of CRPC in this PDX model. Since ARSer81 was found to be phosphorylated in clinical CRPC samples, our data suggested that broad spectrum CDK inhibitors, might be a potent candidate drug for the treatment of CRPC, including those exhibiting primary resistance to enzalutamide.

overall_design: To investigate whether AILNCaP14 cells exhibit genes differentially regulated by AR compared to LNCaP cells, CAGE sequencing was used to analyze the differentially expressed genes (DEGs) between AILNCaP14 and LNCaP cells, with each experiment conducted in triplicate.

first: Takashi

last: Matsuoka

first: Aiko

last: Sugiyama

first: Takayuki

last: Sumiyoshi

first: Kei

last: Mizuno


title: Single cell RNA-seq comparison of cardiac fibroblasts from the left versus right ventricles [bulk RNA-seq]

city: Toronto

first: Michael

middle: Bradley

last: Dewar

state: Ontario

address: 661 University Avenue

department: Physiology

country: Canada

institute: University of Toronto

summary: Cardiac fibrosis is a key aspect of heart failure, leading to reduced ventricular compliance and impaired electrical conduction in the myocardium. Various pathophysiologic conditions can lead to fibrosis in the left ventricle (LV) and/or right ventricle (RV). Despite growing evidence to support the transcriptomic heterogeneity of cardiac fibroblasts (CFs) in healthy and diseased states, there have been no direct comparisons of CFs in the LV and RV. Given the distinct natures of the ventricles, we hypothesized that LV and RV-derived CFs would display baseline transcriptomic differences that influence their proliferation and differentiation following injury. Bulk RNA sequencing of CFs isolated from healthy left and right cardiac ventricles indicated that left ventricle-derived CFs may be further along the myofibroblast transdifferentiation trajectory than cells isolated from the right ventricle.  Single-cell RNA-sequencing (scRNA-seq) analysis of the two populations confirmed that Postn+ CFs are more enriched in the LV, whereas Igfbp3+ CFs were enriched in the RV at baseline. Notably, following pressure overload injury, the LV developed a larger subpopulation of pro-fibrotic Thbs4+/Cthrc1+ injury-induced CFs, while the RV showed unique expansion of two less-well characterized subpopulations of CFs (Igfbp3+ and Inmt+). These findings demonstrate that LV and RV-derived CFs display baseline subpopulation differences that may dictate their diverging responses to pressure overload injury. Further study of these subpopulations will elucidate their role in the development of fibrosis and inform whether LV and RV fibrosis require distinct treatments.

overall_design: Cardiac fibroblasts from the left and right ventricles (LV and RV) of Col1a1-GFP mice were isolated using Fluorescence-activated cell sorting (FACS) according to the presence or absence of GFP signal, and analyzed using bulk RNA-seq. Five LV replicates and four RV replicates were obtained,with each replicate made from the combined ventricular tissue of three to four mice. All samples were prepared from uninjured male mice.

middle: B

first: Fahad

last: Ehsan

first: Haisam

last: Shah

first: Dylan

last: Langburt

first: Alison

last: Hacker


title: Acute atopic dermatitis and urticaria imprints peripheral monocytes with proinflammatory-prone signature

city: Xiamen

first: dang

last: buyun

state: Fujian

address: Xiang 'an District Xiang Annan Road

institute: xiamen university

summary: Monocytes from patients with type 2 immune disorders exhibited an augmented inflammatory response upon LPS stimulation. RNA-seq analysis demonstrated significant upregulation of inflammatory cytokines, including IL-6, IL-12, and IL-1b. Moreover, there was a conspicuous enrichment of signaling pathways associated with inflammation. ATAC sequencing revealed heightened chromatin accessibility in patient monocytes, particularly in the promoter regions of inflammatory genes.

overall_design: Monocytes in  peripheral blood mononuclear cells (PBMCs) from patients diagnosed with atopic dermatitis and urticaria were collected for ATAC-seq

first: Buyun

last: Dang

first: Yinyin

last: Lv

first: Qingxiang

last: Gao

first: Shih-Chin

last: Cheng


title: Single cell RNA-seq comparison of cardiac fibroblasts from the left versus right ventricles

overall_design:
Cardiac fibroblasts from the left and right ventricles (LV and RV) of Col1a1-GFP mice were isolated using Fluorescence-activated cell sorting (FACS) according to the presence or absence of GFP signal, and analyzed using scRNA-seq.
Samples were prepared from uninjured mice, as well as from mice which underwent surgery to model pressure overload injury in either the LV or RV. LVs were isolated from mice with transverse aortic constriction (TAC) and TAC sham surgeries, while RVs were isolated from mice with pulmonary artery banding (PAB) and PAB sham surgeries.
All conditions were studied in both male and female mice. Male and female samples for surgery-operated mice were prepared independently of each other, while sample from the uninjured mice include both male and female tissue.

first: Dewar

last: Michael Bradley

first: Ehsan

last: Fahad

first: Shah

last: Haisam

first: Langburt

last: Dylan

first: Hacker

last: Alison


title: Dietary Succinate Supplementation Alleviates DSS-Induced Colitis via the IL-4Rα/Hif-1α Axis

summary: Succinate administration induced characteristic type 2 immunity via the tuft cell-ILC2 immune circuit, significantly ameliorating DSS-induced colonic inflammation by enhancing bactericidal capacity, reducing intestinal permeability, and modulating cytokine profiles in the colon. Succinate promoted expansion of myeloid cells in peripheral blood, mesenteric lymph nodes (MLN), and colonic lamina propria. The protective effect of succinate was abolished in Ccr2-/- mice but maintained in Rag1-/- mice. Adoptive transfer of monocytes from succinate-treated donors to naïve recipient mice mitigated intestinal inflammation. RNA-seq revealed increased expression of proinflammatory cytokines IL-1β, IL-6, and lactate upon lipopolysaccharide (LPS) stimulation in monocytes from succinate-treated mice. Moreover, the critical role of the IL-4Rα/Hif-1α axis in succinate-mediated protection was delineated.

overall_design: Mice were treated with or without 300 mM succinate for 7 days, and CD11b+Ly6Chi monocytes from bone marrow were sorted, then stimulated in presence or absence of LPS in vitro.And monocyte total RNA was extracted for RNA-seq

first: Laiying

last: Liang

first: Bayasi

last: Guleng


title: GacA reduces virulence and increases competitiveness in planta in the tumorigenic olive pathogen Pseudomonas savastanoi p. savastanoi

city: Malaga

first: Carla

middle: Ariadna

last: Lavado Benito

address: Boulevar Louis Pasteur

country: Spain

institute: University of Malaga

summary: GacS/GacA is a widely distributed two-component system playing an essential role as a key global regulator, although its characterization in phytopathogenic bacteria has been deeply biased, being intensively studied in pathogens of herbaceous plants but barely investigated in pathogens of woody hosts. P. savastanoi pv. savastanoi (Psv) is characterized by inducing tumours in the stem and branches of olive trees. In this work, the model strain Psv NCPPB 3335 and a mutant derivative with a complete deletion of gene gacA were subjected to RNA-Seq analyses in a minimum medium and a medium mimicking in planta conditions, accompanied by RT-qPCR analyses of selected genes and phenotypic assays. These experiments indicated that GacA participates in the regulation of at least 2152 genes in strain NCPPB 3335, representing 37.9 % of the annotated CDSs. GacA also controls the expression of diverse rsm genes, and modulates diverse phenotypes, including motility and resistance to oxidative stresses. As occurs with other P. syringae pathovars of herbaceous plants, GacA regulates the expression of the type III secretion system and cognate effectors. In addition, GacA also regulates the expression of WHOP genes, specifically encoded in P. syringe strains isolated from woody hosts, and genes for the biosynthesis of phytohormones. A gacA mutant of NCPPB 3335 showed increased virulence, producing large immature tumours with high bacterial populations, but showed a significantly reduced competitiveness in planta. Our results further extend the role of the global regulator GacA in the virulence and fitness of a P. syringae pathogen of woody hosts.

overall_design: the model strain Psv NCPPB 3335 and a mutant derivative with a complete deletion of gene gacA were subjected to RNA-Seq analyses in a minimum medium (SSM) and a medium mimicking in planta conditions (HIM)


title: Flexible and high-throughput simultaneous profiling of gene expression and chromatin accessibility in single cells

city: Leipzig

first: Volker

last: Soltys

address: Deutscher Platz 6

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

summary: Gene expression and chromatin accessibility are highly interconnected processes. Disentangling one without the other provides an incomplete picture of gene regulation. However, simultaneous measurements of RNA and accessible chromatin are technically challenging, especially when studying complex organs with rare cell-types. Here, we present easySHARE-seq, an elaboration of SHARE-seq, providing simultaneous measurements of ATAC- and RNA-seq within single cells, enabling identification of cell-type specific cis-regulatory elements (CREs). easySHARE-seq retains high scalability, improves RNA-seq data quality while also allowing for flexible study design. Using 19,664 joint profiles from murine liver nuclei, we linked CREs to their target genes and uncovered complex regulation of key genes such as Gata4. We further identify de-novo genes and cis-regulatory elements displaying zonation in Liver sinusoidal epithelial cells (LSECs), a challenging cell type with low mRNA levels, demonstrating the power of multimodal measurements. EasySHARE-seq therefore provides a flexible platform for investigating gene regulation across cell types and scale.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: easySHARE-seq to profile gene expression and chromatin accessibility in cell lines (HEK, OP-9) and murine liver nuclei

first: Yingguang

middle: F

last: Chan


title: Whole blood transcriptomics reveals G-CSF as a mediator of cardiopulmonary bypass- induced systemic inflammatory response syndrome

city: Parkville

first: Katherine

middle: R.

last: Martin

state: VIC

address: 1G Royal Parade!

department: John T. Reid Trusts Laboratory

country: Australia

institute: WEHI

summary: Objectives: Systemic inflammatory response syndrome (SIRS) is a frequent complication of cardiopulmonary bypass (CPB). SIRS is associated with significant morbidity and mortality, but its pathogenesis remains incompletely understood, and as a result biomarkers are lacking, and treatment remains expectant and supportive. This study aimed to understand the pathophysiological mechanisms driving SIRS induced by CPB and identify novel therapeutic targets that might reduce systemic inflammation and improve patient outcomes. Methods: 21 patients undergoing cardiac surgery and CPB were recruited, and blood was sampled before, during and after surgery. SIRS was defined using the American College of Chest Physicians/Society of Critical Care Medicine criteria. We performed immune cell profiling, whole blood transcriptomics and measured individual mediators in plasma/serum to characterise SIRS induced by CPB. Results: Nineteen patients fulfilled criteria for SIRS, with a mean duration of 2.7 days. Neutrophil numbers rose rapidly with CPB and remained elevated for at least 48 hours afterwards. Transcriptional signatures associated with neutrophil activation and degranulation were enriched during CPB. We identified a network of cytokines governing these transcriptional changes, including granulocyte colony stimulating factor (G-CSF), a regulator of neutrophil production and function. Conclusions: We identified neutrophils and G-CSF as major regulators of CPB induced systemic inflammation. Short-term targeting of G-CSF could provide a novel therapeutic strategy to limit neutrophil mediated inflammation and tissue damage in SIRS induced by CPB.

overall_design:
Venous blood was sampled pre and postoperatively and venous and arterial blood was collected after 60 mins on CPB. Blood was collected into PAXgene Blood RNA collection tubes (PreAnalytiX GmbH, Hombrechtikon, Switzerland), which were stored at −20°C until RNA was extracted
Groups: PRE, Day_1, 60A (arterial line), 60V (venous line).

first: Cristina

last: Gamell

first: Roberto

last: Bonelli

first: Tsin

middle: Y

last: Tai

first: Jacinta

last: Hansen

first: James

last: Tatoulis

first: Monther

last: Alhamdoosh

first: Nicholas

last: Wilson

first: Ian

last: Wicks


title: Bidirectional crosstalk between cancer cells and cancer-associated fibroblasts in mixed organoid system elicits transcriptomic characteristics of pancreatic cancer with potential therapeutic vulnerabilities

city: Suwon

first: Jae-Il

last: Choi

address: 164, World cup-ro, Yeongtong-gu

department: Pathology

country: South Korea

institute: Ajou University School of Medicine

overall_design: Refer to individual Series


title: Bidirectional crosstalk between cancer cells and cancer-associated fibroblasts in mixed organoid system elicits transcriptomic characteristics of pancreatic cancer with potential therapeutic vulnerabilities [RNA-seq]

summary: Pancreatic cancer's aggressiveness and poor response to conventional treatment have long necessitated a personalized medicine platform. Patient-derived pancreatic cancer organoids (PCOs) with matching genetic mutations have emerged as valuable tools for drug screening. However, PCOs, composed solely of cancer cells, may exhibit different characteristics from the original tumors due to the absence of the tumor microenvironment (TME). To address these issues, we extensively characterized the transcriptomic features of matched patient-derived mixed PCO-CAF systems, combining pancreatic cancer cells and cancer-associated fibroblasts (CAFs), compared to PCOs and the original tumors. The mixed PCO-CAF model closely resembled the patient tissue's transcriptomic traits, indicating its potential in reflecting the TME. Single-cell RNA sequencing revealed different cell populations in the mixed PCO-CAF system, including myofibroblast-like CAFs and inflammatory CAFs, influencing the essential features of cancer cells in the TME. Several growth factors and cytokines were identified in both the patient tissue and mixed PCO-CAFs, suggesting the importance of intercellular signaling communication. Importantly, disrupting these interactions could lead to antitumor responses. Given the cumulative implications of our dataset, the mixed PCO-CAF emerges as a clinically applicable paradigm for personalized therapeutics.

overall_design: Total RNAs from five corresponding sets of patient tumor tissue, patient-derived PCO, and mixed PCO-CAF were isolated.

first: Min

middle: J

last: Yang

first: Kyoung-Jin

last: Woo

first: So

last: Park

first: Dakeun

last: Lee

first: Seokhwi

last: Kim


title: Impact of DFMO and AMXT 1501 on Gene Expression and Capsule Regulation in Streptococcus pneumoniae

city: Starkville

first: Bindu

last: Nanduri

state: MS

address: 240 Wise Center Dr.

institute: Mississippi State University

summary: Streptococcus pneumoniae (Spn), a Gram-positive bacterium, poses a significant threat to human health, causing mild respiratory infections to severe invasive conditions. Despite availability of vaccines, challenges persist due to serotype replacement and antibiotic resistance, emphasizing the need for alternative therapeutic strategies. This study explores the intriguing role of polyamines, ubiquitous, small organic cations, in modulating virulence factors, especially the capsule, a crucial determinant of Spn's pathogenicity. Utilizing chemical inhibitors, difluoromethylornithine (DFMO) and AMXT 1501, this research unveils distinct regulatory effects on the gene expression of Spn D39 serotype in response to altered polyamine homeostasis. DFMO inhibits polyamine biosynthesis, disrupting pathways associated with glucose import and interconversion of sugars. In contrast, AMXT 1501, targeting polyamine transport, enhances the expression of polyamine and glucose biosynthesis genes, presenting a novel avenue for regulating the capsule independent of glucose availability. Despite ample glucose availability, AMXT 1501 treatment downregulates glycolytic pathway, fatty acid synthesis and ATP synthase, crucial for energy production while upregulating two-component systems responsible for stress management. This suggests a potential shutdown of energy production and capsule biosynthesis, redirecting resources towards stress management. Following DFMO and AMXT 1501 treatments, countermeasures such as upregulation of stress response genes and ribosomal protein were observed but appear to be insufficient to overcome the deleterious effects on capsule production. This study highlights the complexity of polyamine-mediated regulation in S. pneumoniae, particularly, capsule biosynthesis. Our findings offer valuable insights into potential therapeutic targets for modulation of capsule in a polyamine dependent manner, a promising avenue for intervention against S. pneumoniae infections.

overall_design: To comprehensively examine the influence of the polyamine synthesis inhibitor (DFMO) and the transport inhibitor (AMXT 1501) on the gene expression of Streptococcus pneumoniae D39, our study aims to elucidate the intricate mechanisms underlying capsule regulation by polyamines.

first: Moses

last: Ayoola

first: Leslie

last: Shack

first: Otto

last: Phanstiel IV


title: Pleiotropic effects of PhaR regulator in Bradyrhizobium diazoefficiens microaerobic metabolism

city: Granada

first: Socorro

last: Mesa

address: C/Profesor Albareda 1

department: Soil and Plant Microbiology

institute: CSIC

summary: Genome-wide transcription profiling of B. diazoefficiens (formerly B. japonicum) and a phaR mutant, both cultured under microoxic conditions (0.5% O2) in Götz minimal medium supplemented with mannitol. Keywords: microoxia, polyhydroxybutyrate, protein-DNA interaction, proteomics, Rhizobia, transcriptomics

overall_design: Comparative transcriptional profiling of a phaR mutant strain with wild type, both grown microoxically in minimal medium supplemented with mannitol

first: J

middle: I

last: Quelas

last: Cabrera

first: R

last: Díaz-Peña

first: L

last: Sánchez-Schneider

first: A

last: Jiménez-Leiva

first: G

last: Tortosa

first: M

last: Delgado

last: Pettinari

last: Lodeiro

first: C

last: Del Val

first: S


title: ceRNA-microarray reveals abnormal RNA of tuberculosis in PBMC

city: Beijing

first: Jing

last: Dong

address: Beiguan Street

institute: Beijing Chest Hospital, Capital Medical University

summary: RNAs can provide abundant pathological information regarding etiology and could include candidate biomarkers for diagnosis of tuberculosis.Our study focused on RNA expression profiles. The purpose of our study is characterized the RNA profiles of tuberculosis patients and identified significant lncRNAs, circRNA and mRNA associated with tuberculosis as diagnostic biomarkers and treatment target.

overall_design: PBMC from a total of 8 tuberculosis patients and 9 age- and gender-matched Health controls were included high-throughput ceRNA microarray analysis. Tuberculosis patients were diagnosed based on positive Mycobacterium tuberculosis culture, positive Xpert MTB/RIF, positive microscopy, or positive histology. All enrolled HCs were confirmed as not infected with Mycobacterium tuberculosis. All subjects had no other immune system diseases.

first: Ruixue

last: Song

first: Xuetian

last: Shang

first: Yingchao

last: Wang

first: Qiuyue

last: Liu

first: Zhiguo

last: Zhang

first: Hongyan

last: Jia

first: Mailing

last: Huang

first: Chuanzhi

last: Zhu

first: Qi

last: Sun

first: Boping

last: Du

first: Aiying

last: Xing

first: Zihui

last: Li

first: Lanyue

first: Liping

last: Pan

first: Zongde


title: The role of Rv1476 in regulating stress response and intracellu-lar survival of Mycobacterium tuberculosis

city: Alar

first: Aikebaier

last: Reheman

address: Tarim Avenue, Alar City

institute: Tarim University

summary: The virulence of Mycobacterium tuberculosis (M.tb) is related to many factors, including intra-cellular survival, cell wall permeability, and cell envelope proteins. However, the biological function of M.tb membrane protein Rv1476 remains unclear. To investigate the potential role played by Rv1476, we constructed an Rv1476 overexpression strain and found overexpression of Rv1476 enhanced the intracellular survival of M.tb, while having no impact on the growth rate in vitro. Stress experiments demonstrated that the Rv1476 overexpression strain displayed increased susceptibility to different stresses compared to the wild type strain. Transcriptome analysis showed that Rv1476 overexpression causes changes in the transcriptome of THP-1 cells, and differential genes are mainly enriched in cell proliferation, fatty acid degradation, cyto-kine-cytokine receptor interaction, and immune response pathways. Rv1476 overexpression in-hibited the expression of some anti-tuberculosis-related genes, such as CCL1, IL15, IL16, ISG15, GBP5, IL23, ATG2A, IFNβ, and CSF3. Altogether, we concluded that Rv1476 plays an important role in M.tb survival in macrophages.

overall_design: Construct an overexpression strain of Mycobacterium tuberculosis Rv1476 and analyze the effect of the overexpression strain of Mycobacterium tuberculosis Rv1476 on the transcriptome of THP-1 cells.

first: Rehanguli

last: Wuxiuer

first: Yifan

first: Huaiyuan

last: Cai

first: Pingyang

last: Wei

first: Gang

last: Cao

first: Xi

last: Chen


title: Bidirectional crosstalk between cancer cells and cancer-associated fibroblasts in mixed organoid system elicits transcriptomic characteristics of pancreatic cancer with potential therapeutic vulnerabilities [scRNA-seq]

first: Jae-Il

last: Choi

overall_design: Tumor biopsy sample were collected from endoscopic ultrasound-guided fine needle biopsy (EUS-FNB) samples, and matched patient-derived PCO, and mixed PCO-CAF were cultured for scRNA-seq.

first: Min

last: Yang

first: Kyoung-Jin

last: Woo

first: So

last: Park

first: Dakeun

last: Lee

first: Seokhwi

last: Kim


title: Dynamic and distinct histone modifications facilitate human trophoblast lineage specification

city: Rensselaer

first: Bum-Kyu

state: New York

address: One Discovery Drive, Cancer Research Center, RM332

institute: University of Albany-SUNY

summary: The placenta serves as an essential organ for nurturing fetal growth throughout pregnancy. Histone modification is a crucial regulatory mechanism involved in numerous biological processes and development. Nevertheless, there remains a significant gap in our understanding regarding the precise mechanisms and extent to which various histone modifications influence the critical process of trophoblast lineage differentiation, which is fundamental to placental development. Here, we conducted a comprehensive mapping of H3K4me3, H3K27me3, H3K9me3, and H3K27ac loci during trophoblast stem cells (TSC) differentiation into syncytiotrophoblasts (ST) and extravillous trophoblasts (EVT) to investigate the regulatory roles and dynamic changes in histone modifications in trophoblast lineage specification.

overall_design: ChIP-seq were performed for various histone modfication (H3K4me3, H3K27me3, and H3K9me3, and H3K27ac) in human trophoblast stem (TS) cells, cyncytiotrophoblat, Extravillous trophoblast. Input was sequenced for a control.


title: Gene expression profile at single cell level of Anaplastic ependymoma (EPN) and H3K27M-mutant diffuse midline glioma (BG)

city: Shenzhen

first: Qian

address: 7019 Yitian Road

institute: Shenzhen Children's Hospital

summary: Anaplastic ependymoma and H3K27M-mutant diffuse midline glioma were analyzed and compared by scRNA-seq.

overall_design: Tumor samples were collected from patients with clinical anaplastic ependymoma (EPN) and one H3K27M mutant diffuse midline glioma (BG). Samples were prepared as single cell suspensions and analyzed using scRNA-seq.


title: Distinct Intestinal Microbial Signatures Linked to Accelerated Biological Aging in People with HIV

city: New York

first: Michael

last: Corley

state: NY

address: 413 East 69th Street

department: Medicine, Division of Infectious Diseases

institute: Weill Cornell Medicine

summary:
Genome-wide DNA methylation profiling of  colon and ileal biopsies, blood samples from people living with HIV on ART and their matched HIV-negative counterparts.
Despite having similar chronological ages, PWH on ART exhibit accelerated biological aging in the colon, ileum, and blood, as measured by various epigenetic aging clocks, compared to HIV-negative controls. Investigating the relationship between microbial translocation and biological aging, PWH on ART had decreased levels of tight junction proteins in the colon and ileum, along with increased microbial translocation.

overall_design: Bisulfite converted DNA from PBMC, Colon, and Illeum tissue were hybridized to the Illumina MethylationEPIC Beadchip


title: Host transcriptome response to heat stress and Eimeria maxima infection in meat-type chickens

city: Athens

first: Samuel

middle: E

last: Aggrey

state: GA

address: 110 Cedar Street

department: Poultry Science

institute: University of Georgia

summary: Eimeria (E.) maxima parasite infects the midgut disrupting the jejunal and ileal mucosal lining causing high morbidity and mortality in chickens. Heat stress (HS) is a seasonal stressor that affects biological functions leading to poor performance. Our objective was to elucidate how HS, E. maxima infection, and their combination affect the ileum transcriptome. Two-hundred and forty 2-week-old males Ross708 chickens were randomly allocated into four treatment groups: thermoneutral control (TNc), thermoneutral infected (TNi), heat stress control (HSc), and heat stress infected (HSi), with 6 replicates each of 10 birds. Infected groups received 200x103 sporulated E. maxima oocysts/bird, and heat treatment groups were raised at 35oC. At 6-day post-treatment, five chickens per group were randomly sampled, and ileum tissues were collected for RNA extraction and sequencing using NGS Illumina sequencing platforms. A total of 413, 3377, 1908, and 2304 DEGs were identified when applying the comparisons: TNc vs HSc, TNc vs TNi, HSi vs HSc, and TNi vs HSi, respectively, at cutoff ≥1.2-fold change (FDR: q<0.05). HSc vs TNc showed upregulation of lipid metabolic pathways and degradation and metabolism of multiple amino acids, and downregulation of most immune-related and protein synthesis pathways. TNc vs TNi displayed upregulation of most of the immune-associated pathways and eukaryotic mRNA maturation pathways, and downregulation of fatty acid metabolism and multiple amino acid metabolism pathways including tryptophan. Comparing HSi versus HSc and TNi revealed that combining the two stressors restored some normal cellular functions, e.g., oxidative phosphorylation and protein synthesis, and reduced the intensity of immune response associated with E. maxima infection. Tryptophan metabolism was upregulated, including genes that contribute to catabolizing tryptophan through serotonin and indole pathways; which might result in reducing the cytoplasmic pool of nutrients and calcium available for the parasite to scavenge and consequently might affect the parasite’s reproductive ability.

overall_design: Two hundred and forty 14-day-old Ross 708 male broilers (Gallus gallus) were randomly allocated into four treatment groups: Thermoneutral control (TNc), thermoneutral infected (TNi), heat stress control (HSc), and heat stress infected (HSi). The thermoneutral and HS groups were raised at 20℃ and 35℃, respectively. The infected groups received via oral gavage 2x105 E. maxima sporulated oocysts/bird, while the control groups were mock-infected with water. E. maxima infective doses were acquired from a single oocyst cloning. All the chickens were housed in wired-floor cages and ad libitum supplied with water and a non-medicated standard grower diet. Five chickens were randomly selected from each treatment group at 6 day-post-infection (dpi) to sample ~1 cm of ileum tissue from Meckel's diverticulum. Ileum samples were snap-frozen in liquid nitrogen and then, stored at -80oC for later RNA extraction and cDNA library construction. The prepared cDNA libraries were sequenced by 150 bp paired-end read chemistry using the Illumina HiSeq 2000 system.


title: LATS1/2 Loss Promote Tumor Immune Evasion in Endometrial Cancer through Downregulating MHC-I Expression

city: 上海

middle: lan

state: 上海

address: 上海市浦东新区芳芯路210弄

institute: Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji

summary: LATS1/2 is frequently mutated and down-regulated in endometrial cancer (EC), but the contribution of LATS1/2 to endometrial tumor progression remains unclear. Here, we discovered an unexpected role of LATS1/2 in regulating MHC class I expression in EC. We demonstrate that the knockout of LATS1/2 in EC cells resulted in significant down-regulation of multiple genes of MHC/HLA Class I family and leaded to insensitivity to tumor immunotherapy. Furthermore, we found that the regulation of LATS1/2 on MHC/HLA expression does not depend on the classical Hippo pathway but on their direct interaction with STAT1 to phosphorylate STAT1 to promote STAT1 accumulating and moving into the nucleus to enhance the transcriptional activation of IRF1/NLRC5 on MHC-I. The kinase-dead mutant LATS1/2 attenuates STAT1 phosphorylation at Ser727. The expressions of LATS1/2, MHC-I, CD8A and p-STAT1（S727）are positive correlation in tissues of EC confirming our findings furtherly. Furthermore, LATS1/2 expression was negatively correlated with tumor stage in EC tissues. These findings reveal novel molecular mechanisms underlying tumor immunogenicity deficiency and elucidate the potential immunotherapy biomarker targeting LATS1/2 in EC.

overall_design: To study the biological function of LATS1/2 in EC, we generated LATS1/2 double knockout (dKO) cell lines using CRISPR/Cas9 methods. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells. Comparative gene expression profiling analysis of RNA-seq data for KLE cells and its LATS1/2-dKO derivatives.


title: Transciptomic signature of chronic antibody-mediated kidney rejection traited by extracorporeal photopheresis

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary:
Background: The benefit of extracorporeal photopheresis on the course of kidney transplant rejection is unknown. The aim of our study was to investigate the variations in transcriptomics on graft biopsies when extracorporeal photopheresis was used to treat chronic humoral rejection after kidney transplantation.
Methods: we retrospectively analyzed the mRNA expression of 770 genes of interest in graft biopsies performed before and after treatment. Eight patients received an average of 23 extracorporeal photopheresis sessions over 4 months between the two biopsies.
Results: Transcriptomic analysis of the graft biopsies identified a significant (adjusted p-value< 0.05) increase in CAV1 mRNA in all patients and a significant decrease in CD19, IL21, PAX5, and SFTPA2 mRNAs in 7 of 8 patients.
Conclusions: In patients treated with extracorporeal photopheresis for chronic humoral rejection after renal transplantation, omic analysis of repeated biopsies shows a reduction in fibrotic and inflammatory transcriptomic signatures.

overall_design:
It is a retrospective single-center, pilot, case series of 8 kidney transplant recipients with biopsy-proven cABMR according to Banff classification and treated by ECP therapy between 2016 and 2020 at Lille University Hospital, France.
Half of the patients met the criteria for active cABMR and the other half for inactive cABMR, but all them had a microvascular inflammation score (g+ptc) greater than or equal to 2. ECP procedure was based on an induction phase with 2 ECP sessions per week during the first 6 weeks, then one session weekly from week 6 to 12 and a maintenance phase with two ECP sessions monthly until repeated biopsy. Each patient had biopsy-proven cABMR and systematic biopsy after three months of ECP treatment. Ten-µm-thick sections were obtained from frozen or alcohol-formalin-acetic acid (AFA) fixed-paraffin embedded tissue-block to collect the 300 ng of RNA required for analyses. RNA was isolated and extracted using the tissue RNA Isolation Kit (Roche Diagnostics GmbH, Mannheim, Germany), and then concentration was assessed with the NanoDrop spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA). 300ng of total RNA from each sample was then hybridized to the nCounter® Human Organ Transplant Panel (NanoString Technologies, Seattle, WA, USA). This panel evaluates the expression of 758 target genes and 12 internal reference genes for data normalization. Expression data were normalized and analyzed with the nSolver Analysis Software (version 4.0.70).
Arnaud Lionet and Marine Van triempon participated in pateint care; Martin Figeac and Céline Villenet performed the transcriptomic analysis, jean baptiste Gibier performed the histologic analysis.


title: Interleukin-23 receptor signaling in regulatory T cells in a mouse model of inflammation-associated cancer.

city: Nashville

first: Justin

last: Jacobse

state: Tennessee

address: 2215 Garland Avenue

institute: Vanderbilt University Medical Center

summary: The pro-inflammatory cytokine interleukin-23 (IL-23) has been implicated in colorectal carcinogenesis (CRC). Yet, the cell-specific contributions of IL-23 receptor (IL-23R) signaling in CRC remain unknown. One of the cell types that highly expresses IL-23R are colonic regulatory T cells (Treg cells). The aim of this study was to define the contribution of Treg cell-specific IL-23R signaling in sporadic and inflammation-associated CRC. In mice, the role of IL-23R in Treg cells in colitis-associated cancer (CAC) was investigated using azoxymethane/dextran sodium sulphate in wild-type Treg cell reporter mice (WT, Foxp3YFP-Cre), and mice harboring a Treg cell-specific deletion of IL-23 (Il23rΔTreg). Il23rΔTreg mice had increased dysplasia compared to WT mice associated with decreased tumor-infiltrating macrophages. The role of Treg cell IL-23R in sporadic CRC was examined via orthotopic injection of the syngeneic colon cancer cell line MC-38 submucosally into the colon/rectum of mice. In the sporadic cancer model, Il23rΔTreg mice had increased survival and decreased tumor size compared to WT mice. Additionally, MC-38 tumors of Il23rΔTreg mice had a higher frequency of pro-inflammatory macrophages and IL-17 producing CD4+ T cells. This data suggests that loss of IL-23R signaling in Treg cells permits IL-17 production by CD4+ T cells that in turn promotes pro-inflammatory macrophages to clear tumors. These findings further support and highlight the importance of selecting a physiologically relevant model based on the type of cancer in which to evaluate the role of specific genes in late tumorigenesis. Finally, single-cell RNA-seq analysis of a previously published dataset in human sporadic cancer, revealed that IL23R was highly expressed in CRC compared to other cancers and specifically in tumor-associated Treg cells.

overall_design: C57BL/6 Foxp3YFP-Cre (The Jackson Laboratory, Bar Harbor, ME, stock #016959, designated WT) and ll23rΔTreg (designated KO), lacking IL-23R in FOXP3+ Treg cells, were used. Inflammation-associated carcinogenesis: 7-8-week-old mice were co-housed, bedding was mixed 14 days prior to the start of the protocol, and 3 days prior to start of the protocol mice were placed on deprivation caps to acclimate mice to drinking from water bottles exclusively. Mice were intraperitoneally injected with 10 mgkg-1 azoxymethane (Sigma-Aldrich) and exposed to three 5-day cycles of 3.5% dextran sodium sulphate (TdB consultancy, Uppsala, Sweden). Each DSS cycle was followed by a 16-day recovery period of regular autoclaved water. At the experimental endpoint, tumor and adjacent normal (full thickness colon) was collected for RNA-sequencing.

first: Jeremy

middle: A

last: Goettel


title: Selection of Ethanol Tolerant Strains ofCandida albicansby Repeated Ethanol Exposure Results in Strains with Reduced Susceptibility to Fluconazole

city: Boston

first: Andrew

last: Day

address: 136 Harrison Ave

department: Molecular Microbiology

institute: Tufts University

summary: Candida albicansis a commensal yeast that has important impacts on host metabolism and immune function, and can establish life-threatening infections in immunocompromised individuals. Previously,C. albicanscolonization has been shown to contribute to the progression and severity of alcoholic liver disease. However, relatively little is known about howC. albicansresponds to changing environmental conditions in the GI tract of individuals with alcohol use disorder, namely repeated exposure to ethanol. In this study, we repeatedly exposedC. albicansto high concentrations (10% vol/vol) of ethanol—a concentration that can be observed in the upper GI tract of humans following consumption of alcohol. Following this repeated exposure protocol, ethanol small colony (Esc) variants ofC. albicansisolated from these populations exhibited increased ethanol tolerance, altered transcriptional responses to ethanol, and cross-resistance/tolerance to the frontline antifungal fluconazole. These Esc strains exhibited chromosomal copy number variations and carried polymorphisms in genes previously associated with the acquisition of fluconazole resistance during human infection. This study identifies a selective pressure that can result in evolution of fluconazole tolerance and resistance without previous exposure to the drug.

overall_design:
Cultures of SC5314 or Esc strains (small colony strains isolated from populations repeatedly exposed to ethanol) were grown to post-exponential phase and 10^8 cells for each were seeded into 1 mL cultures of DMEM with 10% H2O or EtOH and incubated for 4 hours at 37⁰C with 5% CO2. Immediately following the incubation, cells were centrifuged at 6000 rpm for 1 min and supernatant was removed. Cells were then resuspended in 1 mL of RNA-later and immediately frozen at −80⁰C until they were ready for extraction. Cells were then thawed on ice. Cells were lysed and RNA was extracted by bead-beating. RNA was isolated using the Invitrogen Purelink RNA mini kit with the on-column DNase treatment. RNA was eluted in 40uL of ultrapure H2O and RNA yield and purity were assessed on a Nanodrop. Three biological replicates of SC5314, Esc6, Esc7, or Esc8 following exposure to medium A with 10% water or 10% EtOH were sent for sequencing. All samples sequenced had RNA integrity scores of 9.2 or greater. cDNA libraries were made by Genewiz and RNA-seq was performed by Genewiz using a HiSeq platform: gene expression was considered significant only if adjusted-P-value (calculated by Benjamini-Hochberg test) was less than 0.05 and log2-fold change was greater than the absolute value of 0.5. RNA-sequencing was aligned to Candida albicans SC5314 (assembly ASM18296v3) as the reference genome. Raw counts were determined using DESeq.

Submitter states that missing raw files are due to file loss.

first: Carol

last: Kumamoto


title: Stranded bulk Illumina RNASeq of human mammary tumors before and after neoadjuvant chemotherapy treatment

city: Liège

first: Claire

last: Josse

state: Liège

address: rue de l'hopital, 1

country: Belgium

institute: CHU Liege

summary: This study is designed to find a reliable marker enabling to predict the response to treatment in patients with early breast cancers treated by neoadjuvant chemotherapy. This marker would allow on one hand to select more homogeneous patient cohorts requiring treatment escalation strategies, and on the other hand reduce the burden of toxicity (both treatment-related and financial) for the patients that will already derive high benefit from the conventional treatments. In this study, gene expression profiles were measured and correlated with the clinical response to neoadjuvant chemotherapy and other features like the epithelial to mesenchymal transition and the tumor immune cell infiltration.

overall_design: The gene expression of 95 tumors samples of primary breast cancer patients were analyzed pre-neoadjuvant chemotherapy by bulk stranded RNA sequencing. Among those 95 patients, 29 did not respond completely to the neoadjuvant chemotherapy, and the residual tumor after treatment were sequenced by the same technique.

first: Françoise

last: Derouane

first: Jérôme

last: Ambroise

first: Cedric

last: van Marcke

first: Martine

last: Berlière

first: Mieke

last: Van Bockstal

first: Christine

last: Galant

first: Hélène

last: Dano

first: Guy

last: Jerusalem

first: Vincent

last: Bours

last: Thiry

first: Aurélie

last: Daumerie

first: Caroline

last: Bouzin

first: Cyril

last: Corbet

first: François

last: Duhoux


title: Role of NR4A1 and non-classical monocytes in a mouse model of neovascular age-related macular degeneration

city: Chicago

first: Jeremy

middle: Arin

last: Lavine

state: Illinois

address: McGaw M343

department: Ophthalmology

institute: Northwestern University

summary: Neovascular AMD (nAMD) causes vision loss from destructive angiogenesis, termed choroidal neovascularization (CNV). Cx3cr1-/- mice display non-classical monocyte and microglia alterations, and increased CNV size, suggesting that non-classical monocytes may inhibit CNV formation. While Nr4a1-/- mice are deficient in non-classical monocytes, results are confounded by macrophage hyper-activation. Nr4a1se2/se2 mice lack a transcriptional activator, resulting in non-classical monocyte loss, without macrophage hyper-activation. We subjected Nr4a1-/- and Nr4a1se2/se2 mice to the laser-induced CNV model and performed multi-parameter flow cytometry. We found that both models lack non-classical monocytes, but only Nr4a1-/- mice displayed increased CNV area. Additionally, CD11c+ macrophages were increased in Nr4a1-/- mice. Single-cell transcriptomic analysis uncovered that CD11c+ macrophages were enriched from Nr4a1-/- mice and expressed a pro-angiogenic transcriptomic profile that was disparate from prior reports of macrophage hyper-activation. These results suggest that non-classical monocytes are dispensable during laser-induced CNV, and NR4A1 deficiency shifts the transcriptional profile toward a pro-angiogenic phenotype.

overall_design: Ocular CD45+ immune cells were isolated by FACS and scRNA-seq was performed on sham and laser-treated wildtype and Nr4a1-/- eyes.

first: Steven

last: Droho

last: Voigt

first: Jacob

middle: K

last: Sterling

first: Amrita

last: Rajesh

first: Kyle

middle: S

last: Chan

first: Carla

middle: M

last: Cuda

first: Harris

last: Perlman


title: small-RNA sequencing after 2 days forced abstinence from heroin or sucrose self-administration in male rats

city: Philadelphia

first: Stephanie

last: Daws

state: PA

address: 3500 N Broad St

institute: Temple University

summary: We report the miRNAs differentially expressed in the orbitofrontal cortex of adult male rats that self-administered heroin after 2 days of forced abstinence.

overall_design: miRNA profiles in orbitofrontal cortex of heroin exposed animals versus naïve animals.

last: Sillivan


title: Single cell analysis of MYD88 L265P and MYD88 WT Waldenström macroglobulinemia (WM) patients

first: Tina

last: Bagratuni

address: Lourou 4-2

department: Department of Therapeutics

country: Greece

institute: NKUA

summary: To elucidate the differences occurring in the B cell composition between WM patients, we performed single cell RNA sequencing on CD19 + sorted cells from patients with MYD88 L265P versus MYD88 WT phenotype and compared them with two healthy controls.

overall_design: Single cell RNA sequencing of CD19+ bone marrow sorted cells of WM patients and two healthy donors was performed on the 10x Genomics Chromium Illumina NovaSeq6000 platform according to standard procedures.

first: Foteini

last: Aktypi

first: Ourania

last: Theologi

first: Efstathios

last: Kastritis

first: Meletios-Athanasios

last: Dimopoulos


title: Tumor-specific activation of folate receptor beta and its use in reprogramming the tumor microenvironment

city: West Lafayette

first: Philip

middle: S.

last: Low

state: IN

address: 720 Clinic Drive

department: Chemistry

institute: Purdue University

summary: Folate-TLR7 agnost was designed to reprogram the FRβ-expressing TAMs/MDSCs in the tumor microenvironemt. We used single cell RNAseq to demonstrate that this selective repolarization of myeloid cells in solid tumors not only changes their properties towards a less immunosuppressive phenotype, but also induces a general proinflammatory transition throughout the entire tumor mass.

overall_design: Tumors from either FA-TLR7 agonist or vehicle treated mice were isolated, digested for single cell RNAseq. The changes of targeted myeloid cells and other cells that impacted indirectly (T cell/ NK cells, fibrobalsts, etc) were analyzed.

first: Fenghua

last: Zhang

first: Bo

last: Huang

first: Sagar

last: Utturkar

first: Weichuan

last: Luo

first: Gregory

last: Cresswell

first: Boning

first: Muyi

last: Liu

first: Nadia

last: Lanman


title: Epigenomic Analyses Identify FOXM1 As a Key Regulator of Anti-Tumor Immune Response in Esophageal Adenocarcinoma

city: Los Angeles

first: Qian

last: Yang

state: CA

address: 8700 Beverly Blvd

department: Department of Surgery

institute: CEDARS SINAI MEDICAL CENTER

summary: We identified FOXM1 as an EAC-specific candidate transcription factor using GSEA analysis. Functionality of FOXM1 was evaluated in both EAC patient derived organoids and EAC cell lines by measuring cell proliferation, colony formation, and xenograft growth. A FOXM1 signature through the overlap of ESO26, SKGT4, and OE33 intersected ChIP-seq peaks and ESO26 siFOXM1 RNA-seq downregulated genes. Upstream transcriptional regulation of FOXM1 was evaluated with this FOXM1 gene signature and validated using pharmacological inhibition. GSEA analysis determined that immune related pathways were upregulated in ESO26 cell lines treated with siFOXM1 or in TCGA EAC patients with low FOXM1 expression. Syngeneic xenografts found increases in CD8+ T cell infiltration in FOXM1 knockdown tumors. Loss of FOXM1 led to increased secretion of CD8+ T cell Th1 chemokines which play a role in the migration of CD8+ T cells upon loss of FOXM1. Finally, the loss of FOXM1 also increased Ex-vivo cytotoxic killing of murine cancer cells.

overall_design: Esophageal Cancer cell lines ESO26 and SKGT4 were harvested, and ChIPseq was performed using a FOXM1 antibody. ESO26 cells knock down of FOXM1 with siRNA and control were generated by deep sequencing, in duplicate, using Illumina GAIIx.

first: Benjamin

last: Ziman

first: Yueyuan

last: Zheng

first: Megha

last: Sheth

first: Chehyun

last: Nam

first: Hua

last: Zhao

first: Uttam

last: Sinha

first: De-Chen

last: Lin


title: Expression Data from ATDC5 cells treated with Yoda1

city: Hamburg

first: Thorsten

last: Schinke

address: Martinistr. 52

department: Department of Osteology and Biomechanics

institute: University Medical Center Hamburg-Eppendorf

summary:
Chondrocytes can potentially perceive mechanical stimuli via Piezo channels. We investigated the effect of the Piezo1 agonist Yoda1 on chondrocyte-like ATDC5 cells.  Chondrocytes can potentially perceive mechanical stimuli via Piezo channels. We investigated the effect of the Piezo1 agonist Yoda1 on chondrocyte-like ATDC5 cells.  Chondrocytes can potentially perceive mechanical stimuli via Piezo channels. We investigated the effect of the Piezo1 agonist Yoda1 on chondrocyte-like ATDC5 cells.  Chondrocytes can potentially perceive mechanical stimuli via Piezo channels. We investigated the effect of the Piezo1 agonist Yoda1 on chondrocyte-like ATDC5 cells.
We used microarray analysis to detail the global gene expression of ATDC5 cells in response to 6 hours of treatment with 5µM Yoda1.

overall_design: 2 sample sets with 3 independent repetitions for each sample set were compared. 1st sample set: ATDC5 cells treated with DMSO for 6h; 2nd sample set:  ATDC5 cells treated with 5 µM Yoda1 for 6h

first: Timur

last: Yorgan

first: Laura

last: Brylka


title: Transcriptomic Profiling for Prognostic Biomarkers in Early-stage Squamous Cell Lung Cancer (SqCLC)

city: Zagreb

first: Maja

last: Šutić

address: Bijenicka street 54

department: Division of Molecular Medicine

country: Croatia

institute: Ruder Boskovic Institute

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

overall_design: Refer to individual Series


title: Multipotent bone marrow cell-seeded polymeric composites drive long-term, definitive urinary bladder tissue regeneration

city: MAYWOOD

first: SEBY

last: EDASSERY

state: IL

address: CTRE121,2160 S FIRST AVE

institute: Loyola University

summary: To date, there are no efficacious translational solutions for end-stage urinary bladder dysfunction. Current surgical strategies including urinary diversion and bladder augmentation enterocystoplasty (BAE) utilize autologous intestinal segments (e.g. ileum) to increase bladder capacity to protect renal function. Considered the standard of care, BAE is fraught with numerous short- and long-term clinical complications. Previous clinical trials employing tissue engineering approaches for bladder tissue regeneration have also been unable to translate bench-top findings into clinical practice. Major obstacles still persist which need to be overcome in order to advance tissue engineered products into the clinical arena. These include scaffold/bladder incongruencies, the acquisition and utlity of appropriate cells for anatomic and physiologic tissue recapitulation, and the choice of appropriate animal model for testing. Here we demonstrate that the elastomeric, bladder biomechanocompatible poly(1,8-octamethylene-citrate-co-octanol) (PRS; synthetic) scaffold co-seeded with autologous bone marrow-derived mesenchymal stem cells (MSCs) and CD34+ hematopoietic stem/progenitor cells (HSPCs) supports robust long-term, functional bladder tissue regeneration within the context of a clinically relevant baboon bladder augmentation model simulating bladder trauma. Partially cystectomized baboons were independently augmented with either autologous ileum or stem cell-seeded small intestinal submucosa (SIS; a commercially available biological scaffold) or PRS grafts. Stem cell synergism promoted functional tri-layer bladder tissue regeneration including whole graft neurovascularization in both cell-seeded grafts. However, PRS-augmented animals demonstrated fewer clinical complications and more advantageous tissue characterization metrics compared to ileum and SIS-augmented animals. Two-year study data demonstrate that PRS/stem cell-seeded grafts drive bladder tissue regeneration and are a suitable alternative to BAE.

overall_design: Investigate the gene expression profile of urinary bladder tissue that has undergone tissue regeneration in either stem cell seeded/scaffold composites or traditional bladder enterocystoplasty.

first: Seby

last: Edassery

first: Arun

last: Sharma


summary: Squamous cell lung cancer (LUSC) is a frequently diagnosed histological subtype of lung malignancy associated with high mortality due to limited number of treatment options. Identification of potential targets suitable for drug development using high-throughput methods is still lacking. Therefore, the purpose of this research is to analyze expression profiles of mRNA and miRNA in LUSC, aiming to identify the key molecules associated with tumorigenesis and prognosis (overall survival; OS). We performed differential gene expression analysis, pathway enrichment analysis and gene ontology analysis on RNA-seq data obtained from 23 FFPE tumor samples and 3 FFPE healthy individuals. TCGA LUSC and GTEx healthy donors’ cohorts were used for validation. We identified 1133 up-regulated and 644 down-regulated genes, common for both cohorts. The most significant up-regulated genes were involved in cell-cycle regulation pathways, while down-regulated genes predominately belonged to immune-related pathways. Survival analysis performed on selected genes, commonly dysregulated in both cohorts and performed only on non-metastatic patients, identified novel prognostic biomarkers associated with OS in early-stage LUSC patients (HOXC4-worse OS, p=0.0001; LILRA5-better OS, p=0.0086). In total, 50 differentially expressed genes are correlated with patients’ OS. Aiming to get better insight into the profile of the tumor microenvironment, we estimated levels of immune-cells infiltration in LUSC and identified 4 subtypes based on immune-cell infiltration levels. Protein-protein interaction (PPI) network was built based on differentially expressed genes, and PPI modules and hub-genes were identified. Weighted gene co-expression network analysis was conducted to identify significant modules and hub-genes in correlation to clinical traits. Differential analysis on miRNA-Seq data, obtained from 16 tumor and 4 healthy tissue samples, was conducted as well. 75 up-regulated and 47 down-regulated miRNAs were identified. Further, targets of differentially expressed miRNA were identified, following gene ontology analysis and miRNA-mRNA networks construction.

overall_design: Gene expression profiling of RNA-Seq data from 23 patients diagnosed with squamous cell lung cancer (LUSC), and 3 healthy controls. Profiling was done on FFPE tissue samples, for both LUSC and control samples.

first: Jelena

last: Knežević


title: A progesterone derivative linked to a stable phospholipid activates breast cancer cell response without leaving the cell membrane

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

summary: This work show that hormone action, which is assumed to act via binding to intracellular nuclear receptors, can also trigger a global cellular response acting on membrane bound receptors. We designed a progestrone-like compound attached to a phospholipid that cannot cross the cellular membrane, acting on membrane-attached progesterone receptors. Its signalling activates the MAP kinase pathway and reaches the nuclei, where its response is comparable to the natural hormonal response at the level of transcription, chromatin binding and cellular proliferation. These results are of widespread importance, not only for what it implies for the action of nuclear hormone receptors, but also because it identifies possible targets for clinical treatment of breast cancer patients at the cell membrane level.

overall_design: Examination of progesterone target genes activation via interaction of membrane-bound progesterone

first: Jofre

last: Font-Mateu

first: Pol

last: Sanllehí

first: Jesus

last: Sot

first: Beatriz

last: Abad

first: Nicolas

last: Mateos

first: Juan

last: Torreno-Pina

first: Roni

middle: H

last: Wright

first: Maria

last: Garcia-Parajo

last: Joglar

first: Felix

last: Goñi

first: Miguel

last: Beato


title: UMSBP2 is chromatin remodeler that functions in regulation of gene expression and suppression of antigenic variation in trypanosomes [ATAC-seq]

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of trypanosomatids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and play an essential role in chromosome ends protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its, previously described, DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression that plays a role in the control of antigenic variation in T. brucei.

overall_design: To determine the comparative differences between the accessible region of chromatin in the UMSBP2 knockdown Trypanosoma brucei brucei compared to the wild type ( 3 replicates for each of the 2 conditions)

first: Awakash

last: Soni

first: Olga

last: Klebanov-Akopyan

first: Esteban

last: Erben

first: Amnon

last: Harel

first: Katreena

last: Yamin

first: Itay

last: Onn

first: Joseph

last: Shlomai


title: Mosaic deletion of claudin-5 reveals rapid non-cell-autonomous consequences of blood-brain barrier leakage

city: Stockholm

first: Michael

last: Vanlandewijck

address: Blickagången 6

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

summary: Claudin-5 (CLDN5) is an endothelial tight junction protein essential for blood-brain barrier (BBB) formation. Abnormal CLDN5 expression is common in brain disease, and knockdown of Cldn5 at the BBB has been proposed to facilitate drug delivery to the brain. To study the consequences of CLDN5 loss in the mature brain, we induced mosaic endothelial-specific Cldn5 gene ablation in adult mice (Cldn5iECKO). These mice displayed increased BBB permeability to tracers up to 10 kDa in size from 7 days post induction (dpi) and ensuing lethality from 11 dpi. Single-cell RNA sequencing at 12 dpi revealed profound transcriptomic differences in brain endothelial cells regardless of their Cldn5 status in mosaic mice, suggesting major non-cell-autonomous responses. Reactive microglia and astrocytes suggested rapid cellular responses to BBB leakage. Our study demonstrates a critical role for CLDN5 in the adult BBB and provides molecular insight into the consequences and risks associated with CLDN5 inhibition.

overall_design: The samples are mouse brain vasculature, freshly isolated and digested into single cell suspensions. These were subjected to the 10x Genomics Gene expression v3.1 chemistry and sequenced on a NextSeq platform as per manufacturers' recommendations.

first: Elisa

last: Vázquez-Liébanas

first: Giuseppe

last: Mocci

first: Weihan

last: Li

first: Bàrbara

last: Laviña

first: Avril

last: Reddy

first: Claire

last: O’Connor

first: Natalie

last: Hudson

first: Zaher

last: Elbeck

first: Ioannis

last: Nikoloudis

first: Konstantin

last: Gaengel

first: Matthew

last: Campbell

first: Christer

last: Betsholtz

first: Maarja

last: Mäe


title: RNAseq of jejunal scrapings of pigs fed  or fasted four- and six-week-old piglets

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: Gene expression profiles from pig jejunum scrapings either fed or fasted at four and six weeks of age (n=16 per group). Result indicate that the fasting intervention was more severe in the four-week-old piglets, but also induced changes functinal changes in especially metabolic function and cell proliferation in the six-week-old piglets.

overall_design: interventional study

first: Anna

last: Bekebrede

first: Jaap

last: Keijer

first: Vincent

last: de Boer


title: Trypanosoma cruzi conserved proteome microarray

city: New Orleans

first: Eric

last: Dumonteil

state: LA

address: 1440 Canal st.

department: Tropical Medicine

institute: Tulane University

summary: Antibody recognition of Trypanosoma cruzi conserved proteins was assessed by evaluating pools of patient IgG samples on microarrays of 400,000 peptides covering these proteins as 15-mers with an overlap of 13 amino acids.

overall_design: Trypanosoma cruzi conserved proteome

first: Alicia

last: Majeau

first: Claudia

last: Herrera