title: Saliva alleviates hypertension through enrichment of intestinal Bacteroides thetaiotaomicron

status: Public on Dec 31 2024

city: Shanghai

first: Shuo

last: Xu

address: Zhizaoju Road

country: China

institute: Shanghai ninth people's hospital

type: Expression profiling by high throughput sequencing

summary: Oral environment is closely linked to blood pressure regulation, yet the underlying mechanisms remain poorly understood. In this study, we demonstrated that saliva, abundantly secreted in the oral cavity, played a critical role in sustaining the abundance of Bacteroides thetaiotaomicron (Bt) in the gut microbiota, contributing to lowering blood pressure. Further investigation revealed that the mechanism driving this process originated from mucins and metal ions in saliva, which work synergistically to promote Bt growth. In turn, the significantly increased gut abundance of Bt contributed to blood pressure downregulation indirectly by synthesizing short-chain fatty acids and regulating sodium ion channels in the gut. Based on these findings, a unique saliva-driven surface-engineered probiotic strain was developed to advance clinical translational potential by boosting in vivo bioavailability, thus improving blood pressure management. This study not only revealed that saliva lowered blood pressure through gut microbiota but also proposes a novel perspective to hypertension management.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for colon of mice gavaged with PBS or Bacteroides thetaiotaomicron

first: Hui-Long

last: Luo

first: Jin-Yao

last: Liu

first: Sheng-Zhong

last: Duan


title: Effects and Mechanisms of ACSL4 Induces Immunosuppression in Colorectal Cancer

city: NanJing

first: Yiming

address: The Avenue of Sleeping Dradon

institute: China Pharmaceutical University

summary: Analysis of knockout ACSL4 gene in mouse colorectal cancer cell line. These results are for the role of the ACSL4 gene in colorectal cancer.

overall_design: mRNA profiles of ACSL4 knockout cells and ACSL4 control cells were generated by sequencing

first: Xinghua

last: Gao


title: Gene expression profile at single cell level of lungs of adult male and female C57BL/6 mice with andwithout high-fat diet-induced obesity

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

state: NY

address: Elm and Carlton Streets

department: Thoracic Surgery

country: USA

institute: Roswell Park Comprehensive Cancer Center

summary: Obesity is associated with various lung pathologies. We performed single nucleus RNA sequencing of formalin-fixed lungs of mice to obtain insights on this.

overall_design: Groups of male and female mice of about 6 months age had been kept on ad libitum for about 3 months on high-fat or control diet (Bioserv products S3282 and F4031, with 60% and 10% fat calories respectively), when they were sacrificed with carbon dioxide-based euthanasia. Lungs were immediately dissected, rinsed in PBS, and the left lower lung lobes flash-frozen in liquid nitrogen. Nuclei isolated from frozen tissues were used for sequencing.

first: Patnaik

last: Santosh Kumar


title: dinB_mSTM_ST34

city: Hangzhou

first: min

last: yue

address: No.1, Sub-Lane Xiangshan, Xihu District, Hangzhou, China

institute: Hangzhou Institute for Advanced Study, University of Chinese Academy of Science

summary: dinB, also known as dinP in certain bacterial species, was initially discovered in 1980. Wagner et al. found that dinB was a DNA polymerase belonging to the γ family and playing a crucial role in translesion DNA synthesis. This polymerase can insert deoxyribonucleoside triphosphates across replication-blocking lesions that could potentially be lethal. Previous studies have also indicated that dinB is conserved across various bacterial species. However, in the case of prokaryotes, the occurrence of natural dinB mutant in pathogenic bacteria and the impact of dinB loss on pathoadaptive evolution remains unaddressed. RNA-seq showed that frameshift dinB had cascading effects on the inner gene expression network. The downregulated genes were significantly enriched for several GO terms related to catalytic activity, cellular anatomical entity and metabolic process. As dinB has not been identified as a metabolic gene or a regulator, we reasoned that a frameshift mutation might disturb parts of the bacterial inner flow that were previously maintained by initially expressed dinB. This was particularly exemplified in flagella-associated genes. Unlike the WT strain, dinB frameshift down-regulated FljB and increased the expression level of FliC. Distinct properties of FliC and FljB flagella contribute to efficient motility towards and on host cell surfaces. A distinct expression pattern might result in the choice of host infection and the difference in immune response. In short, frameshift mutation and deletion of dinB altered the bacterial response to ciprofloxacin(CIP) and restructured the inner regulation network.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Single colonies were seeded into LB medium and cultured to ~0.1 of OD600. The bacterial solution containing 0.03125μg/ml CIP was subsequently incubated without shaking at room temperature for 10 min, and a liquid nitrogen flash freezer was used to stop the reaction.

first: Xiaolei

last: Wu

first: Min

last: Yue


title: Effect of rhpn2 knowout on gene expression of zebrafish embryos at 72 hpf (hours post fertilization) .

city: NANTONG

first: DAI

middle: YU

last: BEI

address: seyuan street num 9

institute: nantong university

summary: Hearing impairment due to hair cell damage has always been a problem for deaf patients，and there are many unknown genes for deafness.Presently, we have established a zebrafish model  that exhibits significant hearing loss induced by hair cell damged with rhpn2 was knockouted. Utilizing this model, we analyzed and compared the differentially expressed genes of wild type  and rhpn2 mutant embryos. The results revealed that 631 genes were down-regulated significantly in rhpn2 mutant embryos, respectively, compared with control.

overall_design: Wild type and rhpn2 mutants embryos were collected for transcriptome sequencing at 72 hpf .

first: Yubei

last: Dai

first: Jie

last: Gong

first: Dong


title: LPP_Plasma_UG3

city: Baltimore

first: Kenneth

middle: W

last: Witwer

state: Maryland

address: 733 N. Broadway

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University

type: Non-coding RNA profiling by high throughput sequencing

summary: Libraries of highly purified exRNA carriers from human blood plasma and process control samples

overall_design: 9 samples, 11 process controls, 2 library kits

first: Angela

middle: M

last: Zivkovic

first: Olesia

last: Gololobova

first: Yiyao

last: Huang

first: Andrey

last: Turchinovich


title: Genome-wide synthetic lethal Crispr screen identifies SRM as a target that enhances erdafitinib efficacy in FGFR-mutant bladder cancer

city: wuhan

first: 砚超

last: 余

state: 湖北

address: xinhua street

institute: huazhong university of science and technology

summary: Mutations of the fibroblast growth factor receptor (FGFR) family members are frequently observed in metastatic bladder cancer. The development of erdafitinib, a pan-FGFR inhibitor, provides a significant therapeutic advance in bladder cancer, but resistance still limits its efficacy. In this study, we perform an unbiased whole-genome CRISPR-Cas9 synthetic lethal screen on FGFR-mutant bladder cancer cell lines treated with erdafitinib-targeted therapy and identify SRM as a critical contributor to erdafitinib resistance. In polyamine metabolism, SRM catalyzes the production of spermidine, which subsequently promotes the hypusination of eukaryotic translation factor 5A (eIF5A). Moreover, we demonstrate that hypusinated eIF5A (eIF5AHyp) facilitates the efficient translation of HMGA2, which in turn promotes EGFR expression. Notably, pharmacologic inhibition of SRM using MCHA enhances the efficacy of erdafitinib both in vitro and in vivo. Together, these results offer evidence of the synthetic lethality between SRM inhibition and erdafitinib, suggesting that combination treatment is a promising therapeutic strategy to overcome erdafitinib resistance for FGFR-mutant bladder cancer.

overall_design: We perform RNA-seq on MGH-U3 cells to explore essential genes mediating erdafitinib resistance.


title: Cytotoxic T-cells drive out come in Inflammatory Dilated Cardiomyopathy

city: Maastricht

first: Maurits

last: Sikking

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

summary: Dilated cardiomyopathy (DCM) is often driven by myocarditis, however, the underlying immune mechanism remains unknown. We performed bulk-RNA sequencing of endomyocardial biopsies taken 9 months (interquartile range 4-26 months) from DCM diagnosis and we found that in patients with high cardiac inflammation (at least 7 CD3+ T-cells per mm2 or at least 14 CD45+ leukocyte per mm2 endomyocardial biopsy) Perforin-1, Granzyme-A, Granzyme-H, and Interleukin-17 receptor subunit C were more often expressed compared to patients with low cardiac inflammation (less than 3 CD3+ T-cells per mm2 and less than 5 CD45+ leukocytes per mm2 endomyocardial biopsy).

overall_design: Bulk RNA sequencing of endomyocardial biopsies of human subjects with heart failure due to non-ischemic dilated cardiomyopathy performed 9 months (interquartile range 4-26 months) after dilated cardiomyopathy diagnosis. Comparing RNA-seq profiles of patients with DCM and high cardiac inflammation compared to patients with DCM and low cardiac inflammation.


title: Manganese homeostasis modulates glucan and chitin unmasking in Candida albicans

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

country: Canada

institute: Universite de Montreal

summary: In our previous work, we generated a mutant of the Mn NRAMP transporter, smf12, to investigate the impact of Mn scarcity on the biology of C. albicans. We found that inactivation of SMF12 resulted in attenuated virulence, increased sensitivity to azoles, and activation of the unfolded protein response (UPR). To investigate further cellular processes affected in smf12, we carried out RNA-seq profiling under manganese (Mn) starvation. The transcriptional profile of smf12 growing in the Mn-free SC medium (SC-Mn) was compared to that of the WT strain growing under similar conditions. Upregulated transcripts in smf12 were mainly enriched in processes related to the synthesis and the processing of the three core polysaccharides of the fungal cell wall namely chitin (CHS2, 7, CDA2, CHT4), glucan (KRE1, 9, UTR2, PNG2) and phosphomannan (MNN1, 15, 41, 42, 43, 45, 47, BMT3, 4, 6, 7, KTR4, DFG5, FAV3). Transcripts related to cell wall signaling proteins and transcriptional control including the Cek1 MAP kinase, the histidine kinase Chk1 and the transcription factor Crz1 were also upregulated. This transcriptional signature is reminiscent of a situation in which the cell wall is undergoing remodeling in response to a specific perturbation.

overall_design: In this study, we identified transcripts that were modulated in the Candida albicans mutant of the manganese NRAMP transporter, smf12. The transcriptional profile of smf12 grown in Mn-free SC (SC-Mn) or Mn-supplemented medium (SC+Mn) was compared to that of the wild-type (WT) strain grown under similar conditions

first: Manon

last: Henry

first: Antony

middle: T

last: Vincent


title: Transcriptomic analysis reveals three important carbohydrate-active enzymes contributing to starch degradation of oleaginous yeast Lipomyces starkeyi

city: Tobuki-machi, Hachioji-shi

first: Kentaro

last: Mine

state: Tokyo

country: Japan

institute: Nissin Foods Holdings Co., Ltd.

summary: The oleaginous yeast Lipomyces starkeyi has a high capacity for starch assimilation, but the genes involved and specific mechanisms in starch degradation remain unclear. This study aimed to identify the critical carbohydrate-active enzyme (CAZyme) genes contributing to starch degradation in L. starkeyi. Comparative transcriptome analysis of cells cultured in glucose and soluble starch medium revealed that 55 CAZymes (including transcript IDs 3772, 1803, and 7314) were highly expressed in soluble starch medium. Protein domain structure and disruption mutant analyses revealed that 3772 encodes the sole secreted α-amylase (LsAmy1p), whereas 1803 and 7314 encode secreted α-glucosidase (LsAgd1p and LsAgd2p, respectively). Triple-gene disruption exhibited severely impaired growth in soluble starch, dextrin, and raw starch media, highlighting their critical role in degrading polysaccharides composed of glucose linked by α-1,4-glucosidic bonds. This study provided insights into the complex starch degradation mechanism in L. starkeyi.

overall_design: To investigate the mechanism of starch degradation in oleaginous yeast Lipomyces starkeyi, we performed gene expression profiling analysis using data obtained from RNA-seq of WT cultured in 2 diffferent conditions at 3 time points (day2, 3, 4; n=3). Comparative gene expression profiling analysis was performed for RNA-seq data of WT cultured in glucose medium (Y1D5) and starch medium (Y1S5).

first: Hiroya

last: Taki

first: Juyoung

last: Kim

first: Jiro

last: Seto

first: Shinji

last: Matsuo

first: Rikako

last: Sato

first: Hiroaki

last: Takaku


title: The KU70-SAP domain has an overlapping function with DNA-PKcs in limiting the lateral movement of KU along DNA

city: New York

first: Shan

last: Zha

address: 1130 Saint Nicholas Ave.

institute: Columbia University

summary: The non-homologous end-joining (NHEJ) pathway is critical for DNA double-strand break repair and is essential for lymphocyte development and maturation. The Ku70/Ku80 heterodimer (KU) binds to DNA ends, initiating NHEJ and recruiting additional factors, including DNA-dependent protein kinase catalytic subunit (DNA-PKcs) that caps the ends and pushes KU inward. The C-terminus of Ku70 in higher eukaryotes includes a flexible linker and a SAP domain, whose physiological role remains poorly understood. To investigate this, we generated a mouse model with knock-in deletion of the SAP domain (Ku70DSAP/DSAP). Ku70DSAP supports KU stability and its recruitment to DNA damage sites in vivo. In contrast to the growth retardation and immunodeficiency seen in Ku70-/- mice, Ku70DSAP/DSAP mice show no defects in lymphocyte development and maturation. Structural modeling of KU on long dsDNA, but not dsRNA suggests that the SAP domain can bind to an adjacent major groove, where it can limit KU’s rotation and lateral movement along the dsDNA. Consistent with this model, in the absence of DNA-PKcs that caps the ends, Ku70DSAP fails to support stable DNA damage-induced KU foci. In DNA-PKcs-/- mice, Ku70DSAP abrogates the leaky T cell development and reduces both the qualitative and quantitative aspects of residual V(D)J recombination. Moreover, purified Ku70DSAP also has reduced affinity for DNA ends and dissociates more readily. These findings revealed a physiological role of the SAP domain in NHEJ by restricting KU rotation and lateral movement on DNA that is largely masked by DNA-PKcs.

overall_design: To elucidate the function of the KU70 SAP domain in vivo, we generated a mouse model with targeted deletion of the aa 558-608, encompassing the entire SAP domain of endogenous Ku70 while sparing the NLS. According to High Throughput Genomic Translocation (HTGT)-Seq, both V(D)J recombination and CSR, which entirely depend on KU and NHEJ, remain normal in Ku70DSAP/DSAP cells. Ku70DSAP reduced the residual SJs and leaking CJs in DNA-PKcs-/- lymphocytes and decreased the deletion size in V(D)J junctions recovered from DNA-PKcs-/- cells.

first: Yimeng

last: Zhu

first: Brian

middle: J

last: Lee


title: Natural product inhibition of SARS-CoV-2 guanine-N7 RNA cap methyltransferase shows potent cellular antiviral efficacy

first: Wei

last: Xie

address: No. 866 Yuhangtang Road, West Lake District

institute: Zhejiang University

summary: SARS-CoV-2 virus mimics host mRNA by capping its viral RNA to promote replication and evade host immune sensing. SARS-CoV-2 NSP14 is the N7-guanosine methyltransferase (N7-MTase) responsible for RNA cap-0 formation. Targeting NSP14 for antiviral drug development is an under-explored but promising strategy. Here we conducted a high-throughput screening on natural products library derived from Chinese herbal medicine to discover Emodin as a SARS-CoV-2 NSP14 inhibitor. Exploring Emodin derivatives, Questin was identified with potent cellular inhibitory activity (EC50=249 nM) against SARS-CoV-2, which inhibits NSP14 in an RNA cap competitive manner, making it one the most potent anti-coronaviral natural products. Mechanistically, besides catalyzing viral RNA capping, NSP14 by itself could remodel host transcriptome such as enriching CREBBP, a key host factor in cellular cyclic AMP response pathway, to promote viral infection. As a result, targeting NSP14 by Questin significantly impairs viral Replication & Translation step and reverses host transcriptome remodeled by NSP14. We next validated Questin as a promising lead with significantly improved toxicity upon acute exposure in zebrafish larvae. Taken together, our study not only demonstrates Questin as a potent drug lead for clinical antiviral application, but also highlights multiple antiviral potentials of NSP14 as therapeutic target.

overall_design: RNA-sequencing (RNA-seq) of cells expressing Nsp14 treated by Questin to reveal its molecular effects on host cells.

first: Mengxin

last: Luo


title: Effects of IWR-1 on the transcriptome of bovine embryonic stem cells and mouse embryonic fibroblasts

city: Jinan

first: YAO

last: XIAO

state: Shandong

address: 23788 Gong Ye Bei Road

department: Institute of Animal Science and Veterinary Medicine

institute: Shandong Academy of Agricultural Sciences

summary: The use of tankyrase inhibitors is essential for capturing livestock embryonic stem cells (ESC), yet their mechanisms of action remain largely uncharacterized. Previous studies indicate that their roles extend beyond the suppression of canonical WNT signaling. This study investigates the effects of the tankyrase inhibitor IWR-1 on the transcriptome of bovine embryonic stem cells (bESC) and mouse embryonic fibroblasts (MEF). We performed RNA-seq analysis on day 1 treated bESC and the co-cultured MEF. Comparing the transcriptomes of cells cultured in complete medium (IWR) and IWR-1-removed medium (IWRR), we identified small fractions of exclusively expressed genes in both bESC and MEF. Regulators of HIPPO pathways TEAD4, AMOTL2, and AJUBA and HIPPO targeted gene CYR61 were differentially expressed in bESC. We also found that IWR-1 altered expression of 8 genes in MEF associated with signaling pathways activated by TGF-β ligands, including Gdf6, Inhbb, Bmp4, Fst, Inhba, Thbs1, Tgfb1, and Bmp2.

sample_organism:
Bos taurus
Mus musculus

platform_organism:
Bos taurus
Mus musculus

overall_design: Five bESC, bESC1, bESC2,  bESC4,  bESC8,  and bESC11,  were derived from day 7.5 blastocysts and maintained on MEF. Cells were cultured with a medium supplemented with IWR-1. Each line of bESC were passaged into 2 wells in 6-well plates. On the day 0 of the experiment, culture medium was removed and rinsed with DPBS 3 times. Then, each line of bESC were treated with either the complete medium that supplemented with IWR-1 (IWR) or the IWR-1 removed medium (IWRR). The co-cultured bESC and MEF in each well were collected for RNA-seq on day 1.

first: Yao

last: Xiao

first: Yujiu

last: Wang

first: Minghan

last: Zhang

first: Yan

first: Zhihua

last: Ju

first: Jinpeng

first: Yaran

first: Chunhong

last: Yang

first: Xiuge

first: Jiang

last: Qiang

first: Yaping

last: Gao

first: Xiaochao

last: Wei

first: Wenhao

last: Liu

first: Yundong

first: Peng

last: Hu

first: Jinming

last: Huang


title: RNA-Seq of  nucleus pulposus cells with or without CircFUNDC1 overexpression

first: Tianyuan

last: Gu

state: Zhejiang

address: 3 Qingchun East Road, Shangcheng District, Hangzhou City, Zhejiang Province, China

department: Department of Orthopedic Surgery

institute: Zhejiang University School of Medicine Sir Run Run Shaw Hospital

summary: RNA-Seq was used to detect the dwonstream genes after CircFUNDC1 overexpression. Method: Three nucleus pulposus cell total RNA profiles of Ad-NC samples and Ad-CircFUNDC1 samples were analyzed.

overall_design: We collected three human nucleus pulposus samples and primary nucleus pulposus cells(NPCs) were cultured. Then, NPCs were transfected with CircFUNDC1 adenovirus (pAdeasy-EF1- hsa_circ_0007290-CMV-EGFP-N) or negetive adenovirus. After transfections, RNAs were collected and RNA-seq were performed

first: Ziang

first: Weiyu

last: Ni

first: Shasha

last: Yao


title: Gibberellin-deactivating GA2OX enzymes act as a hub for auxin-gibberellin crosstalk in Arabidopsis thaliana root growth regulation

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

summary: We combined transcriptomic profiling of auxin related mutants with genetic and biochemical approaches and live-cell imaging techniques of Arabidopsis roots to understand the role of auxin-driven gibberellin level changes during root development, particularly root cell elongation. We show that auxin negatively regulates the level of gibberellin in root elongation zone. Auxin signalling steers the expression of gibberellin deactivating enzymes - GIBBERELLIN 2-OXIDASES (GA2OX) exclusively in root elongation zone. Interestingly, GA2OX8 expression is high in tissues with elevated auxin levels, such as vasculature or stem cell niche, fitting with the observed effect of auxin on gibberellin level. Here we show that GA2OX enzymes are negative regulators of root cell elongation. Gibberellin decrease caused by GA2OX8 overexpression inhibits root cell elongation. In contrast, roots missing GA2OX genes elongate faster. These findings indicate that GA2OX8 enzymes represent an integration core of auxin and gibberellin signalling pathway in root elongation zone, vascular development and regulation of stem cell niche. Our results enhance understanding of complex mechanisms controlling root cell elongation.

overall_design: G1090::XVE>>AXR3-1(doi: 10.1038/nature13663), G1090::XVE>>ΔMP (doi: 10.3390/plants10112271) and Col-0 were grown on ½ MS plates for 5d and then whole plants were poured with 5ml of 2,5 μM estradiol-containing ½ MS liquid medium, making sure that all plants are treated. Additionally, all lines  were poured with dmso-containing ½ MS liquid medium. Leftover medium was removed, and plants grown vertically for 1.5h or 3h in cultivation room. After this, roots were harvested. To obtain transcriptomic data, RNA from 40-50 root tips (7-10 mm) of G1090::XVE>>AXR3-1, G1090::XVE>>ΔMP and Col-0 was extracted following the protocol (Plant Total RNA Mini Kit, Favorgen). cDNA library was prepared from polyA-enriched total RNA and sequenced by Illumina. The sequencing resulted in at least 20 million 150 bps long read pairs.

first: Monika

last: Kubalová

first: Matyáš

last: Fendrych

last: Müller


title: Transcriptomic analysis of liver lymphatic endothelial cell (LyEC) isolated from sham or bile duct ligation (BDL)-induced cholestasis mouse model

city: New Haven

first: Jain

last: Jeong

state: CONNECTICUT

address: 1 Gilbert St, TAC BUILDING, S220

institute: YALE UNIVERSITY

summary: This experiment aims to determine the  transcriptomic alteration in liver lympahtic endothelial cell (LyEC) in response to bile duct ligation (BDL)-induced cholestatic injury, which known to produce severe form of fibrosis and cirrhosis.   We uncover a transcriptomic changes in LyEC associated with early-stage fibrosis/cirrhosis and late-stage decompensated liver cirrhosis.  This work determines the functional change in lymphatic vessels and provides background necessary to discover  therapeutic targets for improving LyEC function in the progression of liver diseases.

overall_design: For the transcriptomic profile, liver lymphatic endothelial cells (LyECs) were isolated from LyEC-specific GFP reporter mice (IL7GFP/knock-in) liver at  2 weeks (n=3) and 4 weeks (n=3) after bile duct ligation (BDL) surgery or sham (n=3) mice.

first: Iwakiri

last: Yasuko


title: Comparative transcriptional analysis reveals gene expression changes in spore germination of opportunistic pathogenic fungi

city: East Lansing

first: Frances

last: Trail

state: MI

address: 612 Wilson Road, Room 342

department: Plant Biology

institute: Michigan State University

summary: In opportunistic human pathogenic fungi, changes in gene expression play a crucial role in the evolution of growth stages from early spore germination through host infection. Comparative transcriptomics from diverse fungal pathogens along closely related non-pathogenic model provided insights of regulatory mechanisms behind the initiation of infectious processes by different fungi. We examined the gene expression patterns of 3,845 single-copy orthologous genes (SCOGs) across five phylogenetically distinct species, including the opportunistic human pathogens Fusarium oxysporum, Aspergillus fumigatus, and A. nidulans, and nonpathogenic species Neurospora crassa and Trichoderma asperelloides, at four sequential stages spore germination.

sample_organism:
Fusarium oxysporum
Aspergillus nidulans
Aspergillus fumigatus

overall_design: The gene expression profile of conidial germination stages of Fusarium oxysporum NRRL32931, Aspergillus fumigatus AF293, and Aspergillus nidulans A4 on a standard medium (Bird medium) was generated. Four designated germination stages, including swelling conidia (stage 1), polar growth (stage 2), doubling of the long axis (stage 3), and first hyphal branching formation (stage 4), were examined to generate the gene expression profile.

first: Da-Woon

last: Kim

first: Malaika

middle: K

last: Ebert

first: Moonjely

last: Soumya


title: Effects and Mechanisms of ACSL4 Induces Immunosuppression in Colorectal Cancer [T84 cells]

first: Yiming

summary: Analysis of ACSL4 gene knockout in human colorectal cancer cell line. These results confirm the role of the ACSL4 gene in colorectal cancer.

first: Xinghua

last: Gao


title: Identification and characterization of human retinal stem cells capable of retinal regeneration

city: Wenzhou

first: Chenghao

last: Li

address: Wenzhou Medical University, Xueyuan Xi Road

institute: Wenzhou Medical University

summary: Human retinal stem cells hold great promise in regenerative medicine, yet their existence and characteristics remain elusive. Here, we preformed single-cell multi-omics and spatial transcriptomics of human fetal retinas and uncovered a novel cell subpopulation, human neural retinal stem-like cells (hNRSCs), distinct from RPE stem-like cell and traditional retinal progenitor cells. These hNRSCs reside in the peripheral retina within the ciliary marginal zone, exhibiting substantial self-renewal and differentiation potential. We conducted single-cell and spatial transcriptomic analysis of human retinal organoids (hROs), and revealed hROs have remarkable similar hNRSCs consistent with fetal retina, capable of regenerating all retinal cells. Furthermore, we identified crucial transcription factors, notably MECOM, governing hNRSC commitment to neural retinogenesis and regulating repair processes in hROs. Transplanting hRO-derived hNRSCs into the rd10 mouse of rapid retinal degeneration significantly repairs the degenerated retina and restores visual function. Together, our work identifies and characterizes a unique category of retinal stem cells from human retinas, underscoring their regenerative potential and promise for transplantation therapy.

overall_design: MECOM is involved in diverse differentiation scenarios across germ layers. To explore the functional roles of the MECOM gene in hNRSCs and their repair within hROs, we utilized a CRISPR/Cas9 strategy, incorporating a dual-infection technique to optimize the knockout efficiency of MECOM. Subsequent hRO repair experiments were conducted on the MECOM knockout hROs.We validated the MECOM knockout (KO) through RNA seq.

first: Hui

last: Liu

first: Yunlong

last: Ma

first: Yijun

last: Zhou


title: Transcriptome analysis of tendon in Mkx conditional knock out mice

city: Bunkyo-ku

first: Hiroshi

last: Asahara

address: 1-5-45 Yushima

department: Department of Systems BioMedicine

institute: Institute of Science Tokyo

summary: Tendons are crucial connective tissues that link muscle to bone. We have demonstrated that the transcription factor Mkx plays a pivotal role in tendon development and homeostasis by regulating collagen fibril organization through tendon cell fate determination from progenitor cells and promoting the expression of type I collagen and proteoglycans. However, the precise role of Mkx in tendon homeostasis after birth is not well understood. Therefore, we generated conditional Mkx knockout mice by crossing Mkx-CreER mice with Mkx floxed mice. Following tamoxifen administration, we performed transcriptome analysis of tendons from control mice (Mkx-CreER/+ and Mkx flox/+) and Mkx conditional knockout mice (Mkx-CreER/flox)

overall_design: Mkx-CreER/+, Mkx-flox, and Mkx-CreER/flox mice were administered tamoxifen at 6 weeks of age. After 4 weeks, the Achilles tendon was harvested, and total RNA was purified using the Direct-zol RNA MicroPrep Kit (Zymo Research). RNA-seq libraries were prepared using the GenNext RamDA-seq Single Cell Kit RMD-101 (TOYOBO), and the libraries were sequenced on a NovaSeq 6000 (Illumina).

first: Lin

first: Tomoki

last: Chiba


title: Neuronal Activity-Dependent Gene Dysregulation inC9orf72i3Neuronal Models of ALS/FTD Pathogenesis

city: Philadelphia

first: Aaron

last: Haeusler

address: 900 Walnut Street, JHN-Suite 410

department: Neuroscience

institute: Thomas Jefferson University

summary: The GGGGCC nucleotide repeat expansion (NRE) mutation in the C9orf72 (C9) gene is the most common cause of ALS and FTD. Neuronal activity plays an essential role in shaping biological processes within both healthy and neurodegenerative disease scenarios. Here, we show that at baseline conditions, C9-NRE iPSC-cortical neurons display aberrations in several pathways, including synaptic signaling and transcriptional machinery, potentially priming diseased neurons for an altered response to neuronal stimulation. Indeed, exposure to two pathophysiologically relevant stimulation modes, prolonged membrane depolarization, or a blockade of K+ channels, followed by RNA sequencing, induces a temporally divergent activity-dependent transcriptome of C9-NRE cortical neurons compared to healthy controls. These findings reveal the impact of neuronal activity on the ALS/FTD-associated transcriptome and may reveal pathways necessary for conferring neuronal resilience or degeneration.

overall_design: Comparative gene expression analysis of RNAseq data for human i3Neurons from the following conditions: Untreated (UT), TTX-silenced (for 16 hours or for 24 hours), potassium chloride, or tetraethylammonium. Two or three independent differentiations for 3 different i3Neurons lines were used for each condition.

first: Layla

last: Ghaffari

first: Emily

last: Welebob

first: Ashley

last: Boehringer

first: Kelly

last: Cyliax

first: Piera

last: Pasinelli

first: Davide

last: Trotti

middle: R


title: Wnt9b permits the androgen action in promoting Wolffian duct

city: Madison

first: Fei

last: Zhao

state: WI

address: 2015 Linden Drive

department: Comparative Biosciences

institute: University of Wisconsin-Madison

summary: The Wolffian or mesonephric duct is the embryonic primordium that gives rise to the epididymis, vas deferens and seminal vesicle. The androgen action in the Wolffian duct mesenchyme during fetal development is the predominant driver for Wolffian duct maintenance which is critical for male fertility. However, the androgen’s capability of promoting Wolffian duct maintenance was completely lost in the absence of Wnt9b in mice. In this study, we followed up with this interesting phenomenon and elucidated cellular and molecular mechanisms whereby Wnt9b facilitates Wolffian duct maintenance in male embryos. Wnt9b belongs to the WNT family of secreted proteins and is expressed in the Wolffian duct epithelium. We found that the Wolffian duct degeneration in Wnt9b-/- male embryos was accompanied with decreased cell proliferation in the epithelium but not in the mesenchyme during sexual differentiation. Wnt9b deletion did not impair testicular androgen synthesis but altered expression pattern of mesenchymal androgen receptor. The percentage of androgen receptor positive cells in the mesenchyme was significantly reduced, which can be the cause of decreased epithelial proliferation. Wnt9b actions can be transduced by both β-catenin-dependent and β-catenin-independent pathways in the context of target cells. Transcriptomic analysis of E12.5 Wnt9b+/+ and Wnt9b-/- mesonephroi revealed that expression of multiple WNT/β-catenin-target genes was reduced in the absence of Wnt9b. Deletion of mesenchymal β-catenin led to caudal Wolffian duct degeneration and cystic formation in the cranial region. Taken together, our study uncovers the important WNT9B-AR signaling axis mediating the epithelial-mesenchymal interaction in Wolffian duct development.

overall_design: To investigate the role of Wnt9b on Wolffian duct development and androgen action. In this model, we used a global knockout of Wnt9b. We prepared 3 Wnt9b+/+ and Wnt9b-/- male mesonephroi from mouse embryos at embryonic day E12.5.

first: McKenna

last: Crossen

first: Shuai

last: Jia

first: Joan

middle: S

last: Jorgensen

first: Andrew

last: Kelleher

first: Rulang

last: Jiang


title: Exploring Integrin α5β1 as a Potential Therapeutic Target for Pulmonary Arterial Hypertension: Insights from Comprehensive Multicenter Preclinical Studies

city: quebec

first: Sebastien

last: Bonnet

address: 2725 Ch Ste-Foy, Québec, QC G1V 4G5

institute: IUCPQ

summary: Pulmonary arterial hypertension (PAH) is characterized by obliterative vascular remodeling of the small pulmonary arteries (PA) and progressive increase in pulmonary vascular resistance (PVR) leading to right ventricular (RV) failure. Although several drugs are approved for the treatment of PAH, mortality remains high. Accumulating evidence supports a pathological function of integrins in vessel remodeling, which are gaining renewed interest as drug targets. However, their role in PAH remains largely unexplored. We found that the arginine-glycine-aspartate (RGD)-binding integrin a5b1 is upregulated in PA endothelial cells (PAEC) and PA smooth muscle cells (PASMC) from PAH patients and remodeled PAs from animal models. Blockade of the integrin a5b1 or depletion of the a5 subunit resulted in mitotic defects and inhibition of the pro-proliferative and apoptosis-resistant phenotype of PAH cells. Using a novel small molecule integrin inhibitor and neutralizing antibodies, we demonstrated that α5β1 integrin blockade attenuates pulmonary vascular remodeling and improves hemodynamics and RV function in multiple preclinical models. Our results provide converging evidence to consider α5β1 integrin inhibition as a promising therapy for pulmonary hypertension

overall_design: We found that the arginine-glycine-aspartate (RGD)-binding integrin a5b1 is upregulated in PA endothelial cells (PAEC) and PA smooth muscle cells (PASMC) from PAH patients and remodeled PAs from animal models. Blockade of the integrin a5b1 or depletion of the a5 subunit resulted in mitotic defects and inhibition of the pro-proliferative and apoptosis-resistant phenotype of PAH cells. Using a novel small molecule integrin inhibitor (MR5854) and neutralizing antibodies (M200), we demonstrated that α5β1 integrin blockade attenuates pulmonary vascular remodeling in vitro (RNAseq) and improves hemodynamics and RV function in vivo (preclinical models)

first: sebastien

last: bonnet


title: Phase separation of RXRγ drives tumor chemoresistance and represents a therapeutic target for small cell lung cancer

city: Guangzhou

first: Hong

last: Wang

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-sen University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Small cell lung cancer (SCLC) is the most lethal type of lung cancer, characterized by limited treatment options and rapid evolution from chemosensitivity to chemoresistance. However, the mechanisms underlying this evolution remain poorly understood. Identifying the druggable drivers and developing pharmacological strategies to overcome chemoresistance are imperative. Here, we show that Retinoid X receptor γ (RXRγ) is uniquely overexpressed in chemo-resistant SCLC tumors, and that RXRγ serves as an essential factor driving chemoresistance in SCLC. RXRγ forms phase-separated droplets with LSD1 in the nucleus, which enhances RXRγ-mediated gene transcription activity and reprograms gene expression, promoting tumor stemness and metastasis, and eventually driving SCLC chemoresistance. In turn, RXRγ antagonist disrupts RXRγ-LSD1 interaction, reducing their binding to the target gene locus, markedly suppressing the expression of the RXRγ target gene network. Finally, RXRγ antagonists strongly suppress tumor growth and metastasis and restore SCLC vulnerability to chemotherapy in multiple preclinical SCLC models, without overt toxicity, in mice. Thus, these results establish RXRγ as a key player in SCLC by phase separation and as a potential therapeutic target for this deadly disease.

overall_design: H128 cells were treated with HX531 (10 μM) for 48 h.

first: Jie

last: Huang

first: Zhenhua

last: Zhang

first: Yana

last: An


title: Sexually dimorphic effects of CYP2B6 in the development of fasting-mediated steatosis in mice: Effects are not mediated by the oxylipin products 9-HODE and 9-HOTrE

city: Clemson

first: Jazmine

last: Eccles

state: SC

address: 132 Long Hall

institute: Clemson University

summary: Cytochrome P450 2B6 (CYP2B6) is a sexually dimorphic, anti-obesity CYP enzyme responsible for the metabolism of xeno- and endobiotics, including the metabolism of polyunsaturated fatty acids (PUFAs) into 9-HODE and 9-HOTrE. However, hCYP2B6-Tg mice are sensitive to diet-induced hepatic steatosis despite their resistance to obesity. The purpose of this manuscript was determine if 9-HODE, 9-HOTrE, or other factors contribute to the sexually dimorphic steatosis observed in hCYP2B6-Tg mice. Cyp2b-null mice were injected with either 9-HODE or 9-HOTrE for 2 days then subjected to a fasting period of 20 hours to induce steatosis. Moderately increased serum lipids, especially in females, were observed after 9-HODE (TG, VLDL) and 9-HOTrE (HLD, LDL, cholesterol) treatment. No change in hepatic lipids and few changes in hepatic gene expression were observed in mice treated with either oxylipin, suggesting these oxylipins had little effect or their effects were extrahepatic. Therefore, to further investigate CYP2B6’s role in steatosis, hCYP2B6-Tg and Cyp2b-null mice were subjected to a 20-hour fast and compared. Both male and female hCYP2B6-Tg mice exhibited increased steatosis compared to Cyp2b-null mice. Serum cholesterol, triglycerides, HDL, and VLDL were increased in hCYP2B6-Tg males. Serum triglycerides and VLDL were decreased in hCYP2B6-Tg females, suggesting greater hepatic retention of lipids.  Hepatic oxylipin profiles revealed 8 perturbed oxylipins in hCYP2B6-Tg mice and only 1 in males when compared to Cyp2b-null mice. RNA-seq also demonstrated greater effects in females in terms of number of genes and GO terms perturbed. There were only a few overlapping GO terms and lipid metabolic processes was enriched in hCYP2B6-Tg male mice but repressed in hCYP2B6-Tg females compared to Cyp2b-nulls. In conclusion, hCYP2B6-Tg mice are sensitive to steatosis in males and females although the responses are different. In addition, the oxylipins 9-HODE and 9-HOTrE are unlikely to be a major cause of CYP2B6’s pro-steatotic effects.

overall_design: Male and female Cypb-null and hCYP2B6-Tg mice were fasted for 20 hours prior to necropsy. Cyp2b-null mice were treated with 9-HODE or 9-HOTrE for 2 days followed by a 20-hour fast. RNA-seq was performed on RNA extracts frim the liver.

middle: A

last: Eccles-Miller


title: Transcriptome comparison of tobacco cell cultures to address mechanism of auxin autonomous cell proliferation

first: Karel

last: Muller

summary: The response to auxin is regulated by spatiotemporally specific expression of the auxin signalling machinery and by precise regulation of auxin concentration through multiple biosynthetic and metabolite pathways supported by auxin transport involving influx, efflux, and intracellular transport. The rapid and steady proliferation of cells in plant cell cultures presents unique model for studying mechanisms involved in cell cycle regulation. Here we present transcriptome analyses in the habituated auxin-autonomous BY-2H and VBI-2 cell lines.

overall_design: To compare transcriptomic profiles of tobacco cell cultures, we isolated total RNA from cells harvested at the exponential (3 day old) and stationary (10 day old) stages of their growth cycle, three replicas for eas sample group.

last: Müller

first: Jan

last: Petrášek

first: Pavel

last: Jelínek


title: LIPOPROTEINS_Fractions_Healthy_Plasma_UG3

city: Baltimore

first: Kenneth

last: Witwer

address: 733 N. Broadway

institute: Johns Hopkins University

summary: Libraries of highly purified exRNA carriers from human blood plasma pool

overall_design: Plasma samples were from 12 healthy subjects, 10 male and 2 pregnant female subjects. 500 μL of plasma was adjusted to a density of 1.006 g/mL by underlaying it with a 1.0035 g/mL potassium bromide (KBr) solution in a 4.7 mL OptiSeal tube. The sample underwent ultracentrifugation at 110,000 RPM for 4 hours using a fixed-angle TLA-110 rotor. After the first ultracentrifugation, the top 4 mL (triglyceride-rich lipoprotein fraction) was collected. The remaining 700 μL was mixed with 1.1 mL of 1.34 g/mL KBr solution to reach a final density of 1.21 g/mL, resulting in a total volume of 1.8 mL. This mixture was underlaid with 2.9 mL of 1.21 g/mL KBr solution in a new OptiSeal tube and ultracentrifuged at 58,000 RPM for 12 hours. Post-centrifugation, the top 2 mL was collected, concentrated to 250 μL using a 50 kDa Amicon filter, and injected into a high-performance liquid chromatography (HPLC) system equipped with a size-exclusion column. This step separated intermediate-density lipoproteins (IDL), low-density lipoproteins (LDL), and various HDL subclasses. The bottom 2.7 mL from the second centrifugation was combined with 1.2 mL of 1.34 g/mL KBr solution to achieve a final density of 1.25 g/mL in a total volume of 3.9 mL. This solution was underlaid with 0.8 mL of 1.25 g/mL KBr solution in an OptiSeal tube and ultracentrifuged again at 110,000 RPM for 6 hours. The top 2 mL was then collected, concentrated to 250 μL, and subjected to further size-based separation using the same HPLC system. Fractions were collected using a temperature-controlled fraction collector, concentrated to 100 μL with a 50 kDa Amicon filter, and stored in 2% sucrose solution in -80C.RNA was extracted using Trisol LS and spin-column method. 8ul of isolated RNA were used to prepare libraries using BioliqX small RNA library kit. Libraries were sequinced using Illumina Nextseq 500 12 individual samples were sequenced in 4 lanes.

first: Angela

last: Zivkovic

first: Joanne

last: Agus

first: Olesia

last: Gololobova


title: Regional differences in gene expression and pathway activation in porcine intestinal organoids following PEDV infection.

city: Seoul

first: Jae Han

last: Park

address: 25, Nambusunhwan-ro 224-gil

country: South Korea

institute: Seoul national university

summary: Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic virus that causes severe gastrointestinal disease in neonatal piglets, often leading to high mortality. To advance the study of viral pathogenesis, it is essential to develop an in vitro model that accurately replicates swine enteric coronavirus infections. In this study, we designed a porcine intestinal apical-out organoid culture system that supports viral replication while allowing for long-term culture and experimental manipulation. Using apical-out organoids derived from the duodenum, jejunum, and ileum, we examined region-specific gene expression profiles in response to PEDV infection. Bulk RNA sequencing revealed distinct gene expression patterns, highlighting the regional differences in intestinal physiology during infection. Differential gene expression analysis indicated that each intestinal segment activates specific signaling pathways related to cell survival and antiviral responses following PEDV infection. Functional analyses identified key pathways involved in cell development, signaling, apoptosis, and survival. This study elucidates the mechanisms underlying the differential responses of specific intestinal regions to PEDV, which may inform the selection of optimal models for future PEDV research. In summary, our systematic investigation into the responses of various small intestine segments following PEDV infection provides deeper insights into viral pathogenesis.

overall_design: To investigate the effect of PEDV in apical-out organoids of duodenum, jejunum, and ileum of porcine, we conducted RNA sequencing of Mock or PEDV treated apical-out organoid of duodenum, jejunum, and ileum

first: Jiyoung

last: Heo


title: Functional characterization of PRP43a, a component for splicing disassembly in Arabidopsis

city: Chuncheon

first: Dong-Hoon

last: Jeong

state: Gangwon-do

address: Room #8306, Department of Life Science, 1 Hallymdaehak-gil

department: Dept. of Life Science

institute: Hallym University

summary: Pre-mRNA splicing is a crucial regulatory process in eukaryotes, ensuring accurate mRNA maturation and contributing to transcript diversity through alternative splicing (AS). This process is mediated by the spliceosome, a large molecular complex composed of small nuclear RNAs (snRNAs) and proteins. Structural and comparative analysis have showed that splicing factors are highly conserved across eukaryotes, though the extent of their functional conservation remains to be fully elucidated. In Arabidopsis, two homologous genes, PRP43a and PRP43b, encode components involved in spliceosome disassembly. To investigate the roles of these genes, we characterized T-DNA insertion mutants prp43a-1 and prp43b-1. While prp43b-1 homozygous mutants were embryonic lethal, prp43a-1 mutants displayed no significant developmental defects under normal conditions, nor did they exhibit impaired heat tolerance. However, RNA-seq analysis revealed transcriptional changes in prp43a-1 under normal conditions. Gene ontology (GO) analysis indicated and enrichment of stress-related processes among the differentially expressed genes (DEGs), suggesting a role for PRP43a in stress responses. Additionally, differential alternative splicing (DAS) analysis identified numerous PRP43a-dependent intron retention (IR) events, particularly under heat stress, indicating that PRP43a influences AS under environmental conditions. These findings suggest PRP43a as a modulator of splicing and gene expression, with potential roles in stress responses.

overall_design: Examinination of mRNA expression patterns in Arabidopsis prp43a-1 mutant

first: So Young

first: Hyun Suh

last: Chang

first: Se Hee

last: Lim

first: Yun Ju

last: Kim


title: Gene expression in F. tularensis subsp. tularensis SCHU P0, P5, and P9 strains.

city: Shinjuku-ku

first: Akihiko

last: Uda

address: Toyama 1-23-1

department: Department of Veterinary Science

institute: National Institute of Infectious Diseases

summary: The microarray analysis of Francisella tularensis subsp. tularensis strains SCHU P9 (virulent) and SCHU P0/P5 (attenuated) revealed significant differences in gene expression. The results showed that 19 genes were upregulated in the virulent SCHU P9 strain, while two genes, including ftt_0965c, were significantly downregulated

overall_design: Francisella tularensis subsp. tularensis strains SCHU P9 (virulent) and SCHU P0/P5 (attenuated) were analyzed to screen for potential differences in gene expression. These strains were cultured on chocolate Eugon agar plates at 37°C for 2 days, with each strain being cultured in duplicate, providing two biological replicates per condition. After 48 hours of incubation, total RNA was extracted and quality-checked using a Bioanalyzer 2100. The microarray involved hybridizing the labeled RNA from these strains onto an Agilent microarray chip containing probes specific to the F. tularensis genome.

first: D

last: Tian

first: A

first: ES

last: Hotta

first: Y

last: Kuroda

first: M

last: Virhuez-Mendoza

first: T

last: Yamamoto

first: S

last: Morikawa

first: K

last: Maeda


title: Silver nanoparticles affect genes involved in ethylene signaling and stimulate root elongation of white mustard seedlings

first: Karel

last: Muller

summary: This work was focused on the germination of white mustard in the presence of high concentration of nitrate and silver nanoparticles (Ag NPs). High NO3- reduced primary root length while Ag NPs reversed the growth inhibition. Ag NPs increased root length also under normal conditions. RNA-seq of the seedling roots revealed that the presence of Ag NPs negatively affected the expression of genes involved in the ethylene signaling pathway. NO3- up-regulated auxin-responsive genes from SAUR family and down-regulated several auxin efflux carries, while Ag NPs down-regulated YUC9 associated with auxin biosynthesis and some SAUR genes. Comparison of transcriptional profiles of seedlings germinated on high NO3- with and without Ag NPs indicated that in the presence Ag NPs fewer genes involved in cell wall biogenesis and membrane functions and development were down-regulated and fewer genes involved in salicylic and jasmonic acid signaling were up-regulated. However, both Ag NPs and NO3- increased the expression of genes involved in response to various stresses (e.g. pathogens, hypoxia, oxidative stress) and suberin and cutin biosynthesis. We assume that the effect of Ag NPs was primarily related to the ethylene and auxin signaling pathways.

overall_design: Four treatments were used for RNA-seq: 1) water, 2) Ag NPs, 3) Ca(NO3)2 and 4) Ca(NO3)2 with Ag NPs

first: Přemysl

last: Landa

last: Müller

first: Sylva

last: Přerostová

first: Petr

last: Soudek


title: A Targeted Genome-wide Approach to Elucidate and Control Bacterial Adhesion to Physicochemically Diverse Biomaterials

city: Amherst

first: Lauren

last: Andrews

state: Massachusetts

address: 240 Thatcher Rd Life Sciences Laboratories N265

department: Chemical Engineering

institute: University of Massachusetts Amherst

summary: Escherichia coli is the leading cause of catheter-associated urinary tract infections, caused by biofilm formation on implanted biomaterial surfaces. Understanding the genes that cause cellular adhesion to diverse biomaterial surfaces may aid in the design of targeting anti-biofouling chemicals to prevent these biofilm infections, but our current knowledge on such surfaces is limited. Here, we incorporate a platform of six biomaterials of varying hydrophilicities and stiffnesses and a comprehensive genome-wide CRISPR interference (CRISPRi) library to elucidate genotype-phenotype relationships for cellular adhesion to physicochemically varied biomaterial surfaces in E. coli MG1655. After characterization of the biomaterials and CRISPRi tool, we designed a CRISPRi library of 34,315 unique designs targeting 99.0% of the genome in MG1655 (up to 8 designs per gene). We then performed pooled selections for adhesion to each biomaterial surface, elucidating over 400 novel gene hits to each biomaterial surface. Data analysis revealed greater correlations between biomaterials of the same hydrophilicity rather than stiffness, in addition to more gene hits associated with decreased adhesion across all six surfaces than increased adhesion. Monoclonal verification of select designs from the library exhibited strong correlations between results from the pooled selections and individual measurements for adhesion to each gel for most designs. The results from this study provide comprehensive gene sets for cellular adhesion to physicochemically diverse biomaterial surfaces that may be potential gene targets for the design of targeting anti-biofouling agents and offer insight that could be used for the design of “smart” biomaterials, both with potential to prevent biofilm infections.

overall_design: Competitive CRISPR interference (CRISPRi) selections for cellular adhesion of an E. coli MG1655 pooled cell library to a biomaterial surface were performed in duplicate for polydimethylsiloxane (PDMS) and polyethylene glycol (PEG) biomaterials of three different stiffness regimes each (Soft, Medium, or Stiff). Selections were also performed for planktonic growth in stationary media above each biomaterial chemistry. The CRISPRi library contained 34,315 unique gRNA designs targeting 99.0% of all annotated genes in the genome of MG1655, with both the Sp-dCas9 protein and gRNA expressed from a plasmid with a p15a replicon. The change in distribution of each gRNA design in the library before and after selection was used to determine gRNA fitness for cellular adhesion to these physicochemically diverse biomaterials

first: Stephen

last: Rondthaler

first: Brandon

last: Barajas

first: Dominic

last: Castaldi

first: Sarthak

last: Srivastava

first: Jessica

last: Schiffman

middle: B


title: HDAC7 is a potential therapeutic target in Acute Erythroid Leukemia [ChIP ERG]

city: Minato-ku

first: Wenyu

last: ZHANG

address: 4-6-1 Shirokanedai

department: Computational Biology and Medical Sciences

institute: The University of Tokyo

summary: Acute erythroleukemia (AEL) is a rare subtype of acute myeloid leukemia with a poor prognosis. In this study, we established a novel murine AEL model with Trp53 depletion and ERG overexpression. ERG overexpression in Trp53-deficient mouse bone marrow cells, but not in wild-type bone marrow cells, leads to AEL development within two months after transplantation with 100% penetrance. The established mouse AEL cells expressing Cas9 can be cultured in vitro, induce AEL in vivo even in unirradiated recipient mice, and enable to efficient gene ablation using the CRISPR/Cas9 system. We also confirmed the cooperation between ERG overexpression and TP53 inactivation in promoting the growth of immature erythroid cells in human cord blood cells. Mechanistically, ERG antagonizes KLF1 and inhibits erythroid maturation, meanwhile TP53 deficiency promotes proliferation of erythroid progenitors. Furthermore, we identified HDAC7 as a specific susceptibility in AEL by the DepMap-based two-group comparison analysis. HDAC7 promotes the growth of human and mouse AEL cells both in vitro and in vivo through its non-enzymatic functions. Our study provides experimental evidence that TP53 deficiency and ERG overexpression are necessary and sufficient for the development of AEL and highlights HDAC7 as a promising therapeutic target for this disease.

overall_design: To understand how ERG inhibits erythroid differentiation, F36P cells were transduced with MSCV-PIG and MSCV-PIG-AM-ERG plasmids and performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) after 1 µg/ml puromycin selection for 4 days.

last: Zhang

first: Susumu

last: Goyama


title: HDAC7 is a potential therapeutic target in Acute Erythroid Leukemia [RNA-seq F36P HDAC7KO]

overall_design: To understand how HDAC7 induces erythroid differentiation, we performed RNA-seq using F36P cells transduced with sgHDAC7 and sgNT. F36P cells were transduced with sgHDAC7 and sgNT (puromycin resistance) plasmids and performed bulk RNA-seq after 1 µg/ml puromycin selection for 4 days.


title: HDAC7 is a potential therapeutic target in Acute Erythroid Leukemia [RNA-seq F36P ERG]

overall_design: To understand how ERG inhibits erythroid differentiation, we performed RNA-seq using F36P cells with vector or ERG overexpression. F36P cells were transduced with MSCV-PIG and MSCV-PIG-AM-ERG plasmids and performed bulk RNA-seq after 1 µg/ml puromycin selection for 4 days.


title: HDAC7 is a potential therapeutic target in Acute Erythroid Leukemia [RNA-seq Mouse AEL]

overall_design: To assess the gene expression level changes of mouse AEL leukemic cells, we examined gene expression profiles of normal murine bone marrow erythroid precursor cell or AEL murine bone marrow leukemic cells by RNA-seq. Normal murine bone marrow cells were stained by using anti-CD71 and anti-Ter119 antibody, sorted cells and then extracted RNA. For AEL murine bone marrow cells, leukemic cells were transduced with ERG overexpression  (coexpress GFP) and sorted GFP+ cell then extracted RNA.


title: Multi-tissue single cell profiling of genetically diverse mouse models reveals mechanisms of resilience to obesity and diabetes [scRNA_seq_islet]

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

institute: The Jackson Laboratory

summary: Despite the importance of genetic factors to metabolic health, the cellular and molecular mechanisms mediating interindividual variation in progression along the continuum from health to type 2 diabetes mellitus (T2D) remain incompletely characterized. We studied three genetically diverse mouse strains with variable baseline metabolic physiology and distinct responses to a high fat high sugar diet. To understand genetically encoded differences in cell type-specific responses to diet, we profiled two key metabolic tissues, white adipose and pancreatic islets, using single cell gene expression and chromatin accessibility. In both tissues, strain background most strongly influenced both cell composition and cell type-specific gene expression, with substantial but smaller contributions of biological sex and diet. Transcriptomics and chromatin profiling revealed considerable differences between strains in immune infiltration in both tissues. Mechanisms of adipose expansion and energy utilization differed between strains, highlighting the importance of metabolite transport (Acly, Slc25a1), catecholamine signaling (Adrb3, Gpr143), preadipocyte cell fate (Cd81), and adipocyte subsets with thermogenic capabilities (Ckb, Ucp1, PGC-1ɑ). Gene expression patterns in pancreatic beta cells were unique in the most resilient mouse strain, pointing to the importance of beta cell maturation pathways (Mafa, Ucn3), glucose metabolism (Glp1r), the unfolded protein/endoplasmic reticulum stress response (Atf6, Wfs1), and oxidative stress (Atox1) in the face of increased demand for insulin and glucolipotoxicity. Transcription of the adipokine Adipsin (Cfd) demonstrated a cross-tissue link consistent with the preservation of beta cell health in CAST mice. Finally, linking obesity and T2D GWAS effector genes to chromatin and transcriptional signals in the mouse revealed plausible cell types and states where variants mediating human disease traits likely exert their effects. Overall, this single cell atlas of key metabolic tissues provides insights into inherited variability in metabolic susceptibility and resilience and serves as a framework for utilizing diverse mice to study the progression of complex disease in a controlled, reproducible system.

overall_design: Cells from mice of (up to) three different strains were pooled in each sample, and genetic demultiplexing was used to split cells by genetic background after data generation.

first: Daniel

last: Skelly

first: Candice

middle: N

last: Baker


title: Multi-tissue single cell profiling of genetically diverse mouse models reveals mechanisms of resilience to obesity and diabetes [scRNA_seq_adipose]


title: Different expressed genes beween osimertinib-treated and control group

city: hangzhou

first: Congying

last: Wang

address: Yuhangtang

institute: Zhejiang University

summary: Mice treated with osimertinib appeared skin problems. By comparing osimertinib group and control group, mechanisms were identified.

overall_design: To investigate the mechanisms on osimertinib-induced skin problems, mice models were established. After treating osimertinib for 42 days, skin tissues were collected to conduct RNA-seq.


title: Class A Scavenger receptors promote tumor progression and induce a unique macrophage phenotype in a mouse model of spontaneous breast cancer

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

summary: Tumor-associated macrophages (TAMs) are a critical component of the immune response to cancer, and their role in modulating cancer progression is well-recognized. Macrophages express pattern-recognition receptors, including Class A Scavenger Receptors (SR-A), that are pivotal in regulating macrophage activation and polarization to different phenotypes. While evidence links an increased prevalence of SR-A-expressing TAMs to worse patient outcomes in certain cancers, a definitive role for SR-A in cancer remains to be fully established. Using mouse models of spontaneous breast cancer, we found that the absence of SR-A expression significantly delayed the development of palpable tumors and decreased the number of lung metastases in tumor-bearing mice. Next, we utilized a soluble SR-A protein to demonstrate that SR-A binds specifically to glycans on the surface of breast cancer cells. We used single-cell RNA sequencing of isolated TAMs to understand how SR-A promotes breast cancer progression. We identified a distinct SR-A-dependent TAM subpopulation characterized by high arginase (Arg1) gene expression and low expression of MHCII and other immune response-related genes. The gene-expression profile and signaling-pathway activity of TAMs in this subpopulation indicate that SR-A induces a tumor-supportive TAM phenotype in the tumor microenvironment. Together, our findings demonstrate a specific role for SR-A in binding to glycans on breast cancer cells, inducing a tumor-supportive TAM phenotype, and promoting breast cancer progression. These results shed light on the complex interplay between TAMs and cancer cells, and provide new insights into potential targets for therapeutic intervention in breast cancer.

overall_design: To determine if SR-A is involved in the progression of breast cancer, we compared tumor growth and metastasis in PyMT-SR-A-/- mice with their wild-type control counterparts (PyMT-SR-A+/+)

first: Behjatolah

last: Monzavi-Karbassi

first: Thomas

last: Kelly

first: Fariba

last: Jousheghany

last: Webber

first: Asangi

last: Kumarapeli

first: Christy

last: Simecka

first: Duah

last: Alkam

first: Stephanie

middle: D

last: Byrum

first: Eric

last: Siegel

first: Steven

last: Post


title: Supra-epigenomic impact of the human JC polyomavirus

city: New York

first: Ziyu

last: Lu

address: 1230 York Avenue

institute: The Rockefeller University

summary: Human and animal viruses possess remarkable capabilities in hijacking host processes to facilitate viral infection. Viruses use various strategies to target antiviral response mechanisms while promoting cellular phenotypic states that benefit viral replication. Viruses that replicate and assemble in the nucleus, including human pathogenic DNA viruses, need to balance maximal use of the host DNA replication machinery while at the same time avoid damage to the nucleus before generating a large number of viruses that will support the spread of infection. We have identified a novel mechanism of virus interference with the cell nucleus that involves virus-mediated modulation of nuclear mechanical properties. One of the most widespread human viruses, the JC polyomavirus, interferes with nuclear architecture to form virus-occupied space and substantially reduces the rigidity of the infected human cell nucleus. The JC virus's impact on nuclear rigidity is mediated by the viral nonstructural protein, Agnoprotein (Agno). The Agno interference with nuclear mechanics is governed by structurally diverse mimics of host proteins that support chromatin interaction with the key chromatin regulator, heterochromatin protein 1 alpha (HP1α), and is critical for JC virus infection in vitro. The ability to control chromatin organization and thus nuclear mechanics reveals a previously unknown virus strategy of hijacking the mechanism controlling nuclear physical properties to maximize virus production within the nucleus.

overall_design: In vitro cultured primary human astrocytes (Creative Biolabs; NCC20-9PZ01; Lot NR34) at passage number 3 cultured in 6-wells were infected with JC virus (NHA_JCV-WT) or Agno-deficient JC virus (NHA_JCV-deltaAgno) by incubation with the virus for 12h or were left uninfected (NHA_uninfected). 10 days after infection, cells were collected and directly used for single cell RNA-Seq library generation followed by paired-end sequencing on the Illumina NovaSeq 6000 platform. After alignment and quality control of the data, the sequencing data were used to address the degree of virus infection and for differential gene expression analysis to address the impact of JC virus infection of primary human astrocyres on host gene expression by comparing the gene expression data from JCV infected cells with the gene expression data from uninfected cells. The contribution of Agnoprotein to the virus induced gene expression changes were addressed by comparing the gene expression data from JCV infected cells with the gene expression data from Agno-deficient JCV infected cells. One biological replicate per condition was used for the analysis.

first: Uwe

last: Schaefer

first: Yekaterina

last: Miroshnikova

first: Wei

last: Xie

first: Adam

middle: G

last: Larson

first: Shoudeng

last: Chen

first: Martina

last: Bradic

first: Yehuda

last: Goldgur

first: Ved

middle: P

last: Sharma

first: Junyue

last: Cao

first: Dinshaw

last: Patel

first: Geeta

last: Narlikar

first: Sara

last: Wickström

first: Alexander

last: Tarakhovsky


title: Investigation of Upstream-Binding Protein (UBP1) on breast cancer progression

first: Nagendra

last: Kaushik

state: Nowon-Gu

address: 20 Kwangwoongil, Wolgye Dong 447-1

department: Biophysics

institute: Kwangwoon University

summary: To investigate the UBP1 function in the regulation of breast cancer stem cell maintenance and metastasis

overall_design: Comparative RNA expression profiling analysis of QuantSeq 3’ mRNA-Seq data for MCF7 cells following UBP1 overexpression (control, UBP1-overexpressed cells).

first: Neha

first: Apurva

last: Jaiswal

first: Eun

middle: H

last: Choi


title: HDAC7 is a potential therapeutic target in Acute Erythroid Leukemia [ChIP-seq H3K27ac]

first: Wenyu

last: ZHANG

overall_design: To understand how ERG inhibits erythroid differentiation,F36P cells  were transduced with MSCV-PIG and MSCV-PIG-AM-ERG plasmids and performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) after 1 µg/ml puromycin selection for 4 days.

last: Zhang

first: Susumu

last: Goyama


title: Multi-tissue single cell profiling of genetically diverse mouse models reveals mechanisms of resilience to obesity and diabetes [snATAC_seq_adipose]

first: Gary

last: Churchill

first: Daniel

last: Skelly

first: Candice

last: Baker

first: Olivier

last: Poirion


title: Transcriptome analyses of GPR39-overexpressed and GPR39-activated HEK293 cells

city: Pyeongchang-gun

first: Minsoo

last: Kang

address: 1447, Pyeongchang-daero, Daehwa-myeon

department: graduate school of international agricultural technology

institute: Seoul National University, Republic of Korea

summary:
To get insight of molecular mechanism of GPR39, we investigated transcriptomic response in GPR39 overexpressed HEK293 cells after TC-G-1008 stimulation
We identified 814 differentially expressed genes (DEGs) fold change cutoff = 1.5 in the GPR39 overexpressed HEK293 and GPR39 overexpressed HEK293 cells with TC-G-1008 treatment, those including 364 up-regulated and 450 down-regulated genes
These findings suggest that MAPK/Erk, PI3K/Akt and Glycerolipid metabolism signaling pathways would be putative signaling pathways dominantly altered by GPR39 activation.

overall_design: HEK293 cell line was treated in DMEM with 10% FBS (Gibco) with Cumate 0.03mg/mL or TC-G-1008 (1uM)

first: Joonghoon

last: Park

first: Jongsoo

last: Mok


title: Intraesophageally challenge of OVA to epicutaneously sensitized mice with loss of epithelial Ikkβ results in experimental EoE that is faithful to human EoE esophageal mucosal pathology. [I]

city: Chicago

first: Marie-Pier

last: Tetreault

state: IL

address: 300 East Superior Street

department: Medicine/GI&Hep division

institute: Northwestern University

summary: We report a novel mouse model that can faithfully mimic human EoE

overall_design: EoE: Three to four month old Cre+; IKKBL/L mice and littermate controls (IkkβL/L) were treated topically on the ears for 14 days with 2nmol of MC903 (Tocris Bioscience) and 100 μg of OVA , once daily. On day 15 and 17, mice were challenged intraesophageally (IE) with 50 mg OVA. Sensitization: Cre+;IkkβL/L mice and littermate (IkkβL/L) genetic controls were treated on the ears with a combination of MC903 and OVA and gavaged with water. Vehicle: Cre+;IkkβL/L mice and littermate genetic controls were treated on the ears with a combination of ethanol and PBS and gavaged with water.

first: Margarette

last: Clevenger

first: Cenfu

last: Wei


title: Comparative Analysis of In vivo Endothelial Cell Translatomes Across Central Nervous System Vascular Beds (Tie2)

city: Oklahoma City

first: Willard

last: Freeman

address: 825 NE 13th St

institute: Oklahoma Medical Research Foundation

summary: Endothelial cells (ECs) display organ- and tissue-specific heterogeneity. In the eye, the retinal and choroidal vascular beds are distinct networks with different morphological and functional features with the former representing a tight barrier and the latter, a permeable fenestrated vasculature. Given that retinal health critically relies on the function of these vascular beds and that their dysfunction is implicated in a variety of retinal diseases, a molecular understanding of both physiological and pathophysiological characteristics of these distinct vasculatures is critical. Given their interspersed anatomic distribution among parenchymal cells, the study of EC gene expression, in vivo, has been hampered by the challenge of isolating pure populations of ocular ECs in sufficient quantities for large-scale transcriptomics. To address this challenge, we present a methodological and analytical workflow to facilitate inter-tissue comparisons of the in vivo EC translatome isolated from choroid, retina, and brain using the Cre-inducible NuTRAP flox construct and two widely-used endothelial cre mouse lines, constitutive Tie2-Cre and Tamoxifen-inducible Cdh5-CreERT2, which express EGFP and mCherry tags for cell-specific isolation of nuclei and ribosomes. Within each model, inter-tissue comparison of TRAP-RNAseq enrichment (TRAP translatome vs input transcriptome) showed tissue-specific gene enrichments with differential pathway representation. For each mouse model, inter-tissue comparison of the EC translatome (choroid vs brain, choroid vs retina, and brain vs retina) showed over 50% overlap of differentially expressed genes (DEGs) between the three paired comparisons, with differential pathway representation for each tissue. Pathway analysis of DEGs in the Cdh5-NT vs Tie2-NT comparison for retina, choroid, and brain predicted inhibition of processes related to myeloid cell function and activation, consistent with more specific targeting of ECs in the Cdh5-NT than in the Tie2-NT model. While TRAP enriches for EC transcripts in both models, it also captures myeloid transcripts in the Tie2-NT model. We confirmed these observations with a cell sorting approach. We suggest experimental/analytical considerations should be taken when selecting cre-lines to target ECs.

overall_design: Tie2-cre+; NuTRAP+ RNA isolated via TRAP method - Input and Positive Fractions; 3 tissues with 3 biological replicates

first: Ana

last: Chucair-Elliott

first: Kevin

last: Pham

first: Audrey

last: Cleuren

first: Christopher

last: Schafer

first: Courtney

last: Griffin

first: Sarah

last: Ocanas

first: Michael

last: Elliott


title: Methylation and Transcriptomic Profiling Reveals Short Term and Long Term Regulatory Responses in Polarized Macrophages

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Macrophage plasticity allows the adoption of distinct functional states in response to environmental   cues. While unique transcriptomic profiles define these states, focusing solely on transcription neglects   potential long-term effects. The investigation of epigenetic changes can be used to understand how   temporary stimuli can result in lasting effects. Moreover, epigenetic alterations play an important role   in the pathophysiology of macrophages, including phenomena related to the trained innate immunity,   which allow faster and more efficient inflammatory responses upon subsequent encounters with the   same pathogen. In this study, we used a multi-omics approach to elucidate the interplay between gene   expression and DNA-methylation, unravelling the long-term effects of diverse polarizing environments   on macrophage activity. We identified a common core set of genes that are differentially methylated   regardless of exposure suggesting a potential mechanism for rapid adaptation to various stimuli. These   conserved epigenetic modifications might represent a fundamental state that allows for flexible   responses to various environmental cues. Functional analysis revealed that processes requiring rapid   responses displayed transcriptomic regulation, whereas functions critical for long-term adaptations   exhibited co-regulation at both transcriptomic and epigenetic levels. Our study unveils a novel set of   genes critically linked to the long-term effects of macrophage polarization. This discovery underscores   the potential of epigenetics in elucidating how macrophages establish long-term memory and influence   health outcomes.

overall_design: We studied how the macrophage polarization leads to long-term reprogramming. We did this by first turning monocytes into macrophages using a chemical trigger (phorbol 12-myristate 13-acetate), and then exposing them to various signaling molecules (LPS, INFgamma, IL13, IL14) at different time points.

first: Giorgia

last: Migliaccio

first: Jack

last: Morikka

first: Giusy

last: Del Giudice

first: Maaret

last: Vaani

first: Lena

last: Mobus

first: Angela

last: Serra

first: Antonio

last: Federico


title: Comparative Analysis of In vivo Endothelial Cell Translatomes Across Central Nervous System Vascular Beds

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

overall_design: Refer to individual Series


title: Comparative Analysis of In vivo Endothelial Cell Translatomes Across Central Nervous System Vascular Beds (EC sorted)

overall_design: Tie2-cre+; NuTRAP+ RNA from FACS sorted cells - Input and Positive Fractions; 3 biological replicates


title: Next generation sequencing analysis of the single-cell transcriptomes of the T cell eclited by fecal phageome

city: Hangzhou

first: Aikun

last: Fu

address: No. 866 Yuhangtang Road

summary: By performing single-cell RNA sequencing (scRNA-seq) analysis on the T cells which stimulated by phageome from normal or severe acute pancreatitis mice, we seek to understand which T cells contribute to the inflammation in pancreatitis. t-distributed stochastic neighbor embedding (tSNE) identified 5 distinct T cell cluster, including effector CD8, naïve CD8, CD4, proliferating CD8 and stem like CD8. Stimulation by different phages did not change the T cell heterogeneity. Comparison of genes revealed a significant enrichment in the cell proliferation after SAP derived phages treatment. Differential gene expression analysis confirmed that SAP derived phages treatment skewed the cell pattern toward more IL-7r expression, while control derived phages treatment induce the IL-22 expression.

overall_design: In order to precisely isolate T cells that respond to viral stimulation, an in vitro proximity labeling system FucoID was employed in which DCs were pre-treated with phages isolated from healthy or SAP mice, followed by co-cultured with T cells isolated from the gut of GF mice. Through this interaction-dependent labeling approach, DCs antigen presented T cells can be separated from bystander T cells based on their cell-surface enzymatic fucosyl-biotinylation and next analyzed by single-cell RNA sequencing.

first: Fengqing

last: Lin

first: Lianglan

last: Li

first: Weiqin


title: Multi-tissue single cell profiling of genetically diverse mouse models reveals mechanisms of resilience to obesity and diabetes [scATAC-seq_islet]

first: Gary

last: Churchill

first: Daniel

last: Skelly

first: Candice

last: Baker

first: Olivier

last: Poirion


title: Comparative Analysis of In vivo Endothelial Cell Translatomes Across Central Nervous System Vascular Beds (Cdh5)

first: Willard

last: Freeman

overall_design: Cdh5(PAC)-cre/ERT2+; NuTRAP+ RNA isolated via TRAP method - Input and Positive Fractions; 3 tissues with 3 biological replicates

first: Ana

last: Chucair-Elliott

first: Kevin

last: Pham

first: Audrey

last: Cleuren

first: Christopher

last: Schafer

first: Courtney

last: Griffin

first: Sarah

last: Ocanas

first: Michael


title: Natural killer cells cooperate with neutrophils to suppress pathological angiogenesis in neovascular age-related macular degeneration [scRNA-seq]

city: Tianjin

first: Xue

last: Dong

state: TIANJIN

address: Qixiangtai Road

department: Department of Pharmacology

institute: Tianjin Medical University

summary: Neovascular age-related macular degeneration (nvAMD) is the leading cause of blindness in the elderly population associated with focal inflammation, however, understanding of the precise immune components governing this process is still limited. Here, we identified natural killer (NK) cells as a prominent lymphocyte population infiltrating the perivascular space of choroidal neovascularization (CNV) lesions. O-link analysis and single-cell RNA sequencing approaches identified CCR5-expressing NK cells is essential for further NK cell recruitment and extravasation in CNV site. NK cells suppress pathological angiogenesis via through  clearance of senescent vasculatures, a process that requires neutrophil extracellular traps (NETs). Mechanistically, the release of NETs results  from NKG2D-dependent NK cell activation and production of IFN-γ at CNV lesions. Notably , age is the strongest risk factor for AMD to an aged immune system; our human and mouse data showed that aged NK cells exhibited compromised protective effects. Additionally, expansion of NK cells by IL-2 complex improved CNV formation. Collectively, our results revealed a previously unrecognized role of NK cells in suppressing nvAMD progression, suggesting these cells as a potential target for future immune therapies for patients  with nvAMD.

overall_design: To gain insight into the infiltration of different immune cells, features of NK cells and cell-cell interaction between NK cells and neutrophils, we included adult mice and aged mice 3 days after laser burn or without CNV modeling for single-cell RNA sequencing.

first: Yinting

last: Song


title: Obesity regulates the fate of peripheral blood mononuclear cells through FoxM1

city: Jeongeup-si

first: Hanna

last: Suh

address: 30, Baekhak 1-gil, Jeongeup-si, Jeollabuk-do, Republic of Korea

institute: Korea institute of toxicology

summary: Obesity is associated with various diseases such as metabolic disorders, joint problems, and inflammations. Over 50% of pets, including dogs and cats, are obese, making a comparative study necessary at gene level. Since circulating peripheral blood mononuclear cells (PBMCs) reflect the organs related to obesity, we compared the mRNA expression in normal and obese PBMCs of dogs. Our findings show that there are 425 differentially expressed genes (DEGs) (p < 0.05, |log2 fold| ≥ 1) that exhibit distinct gene expression between normal and obese PBMCs. In Kyoto encyclopedia of genes and genomes (KEGG) and Ingenuity Pathway Analysis (IPA) indicate that obesity affect the PBMC cell cycle through FoxM1. These results suggest that obesity causes functional change of PBMCs through cell cycle regulation. In conclusion, obesity suppresses the PBMCs-mediated immune response through FoxM1.

overall_design: To compare DEG profiles of PBMCs between normal dogs and obese dogs

first: Ju

middle: Y

last: Lee

first: Hong-Geun

last: Oh

first: Han

first: Jeong

last: Hwang


title: RNA-seq analysis of bead-purified B cells of wild-type BALB/c mice stimulated in vitro with TLR9 agonists (CpG ODN 1826, Hokkaido System Science) or left unstimulated.

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

summary: The goal of this study was to develop a B-cell specific gene signature to catalog induced genes after short term in vitro TLR9 stimulation of wild-type BALB/c B cells. B cells were bead purified from splenocytes (two spleens combined for one replicate) of 7-11-week-old wild-type BALB/c mice. The bead purified B cells (10 million (M) per replicate) were stimulated for 4 hours at 10M/ml with TLR9 agonist CpG (CpG ODN 1826, Hokkaido System Science) at 10µg/ml or left unstimulated. RNA was isolated using the RNeasy Plus Mini Kit (QIAGEN). Samples were sequenced on an NextSeq500 (Illumina, Inc) with 2 x 75 bp paired-end reads (20 million reads per sample).  B-cell specific gene signature of induced genes after short term in vitro TLR9 stimulation was cataloged.

overall_design: mRNA profiles of  B cells of wild-type BALB/c mice stimulated in vitro with TLR9 agonists (CpG ODN 1826, Hokkaido System Science) or unstimulated, were generated in three replicates, by sequencing on an Illumina NextSeq500 using PE 150 Cycles High Output flowcell.

first: Claire

last: Leibler

first: Shuchi

last: Smita


summary:
RNA-seq analysis of bead-purified B cells of (i) 5-7-week-old Tlr779 or Tlr7WT (all Tlr9-/-) MRL/lpr mice,stimulated or not with TLR7 agonists (CL097, invivogen) and of (ii) 5-7-week-old Tlr997 or Tlr9+/- (all Tlr7-/-) MRL/lpr mice, stimulated or not with CpG (ODN 1826, Hokkaido System Science) .
The goal of this study was to evaluate if CL097 or CpG induced qualitatively different responses in Tlr7WT or Tlr779 (all Tlr9-/-) B cells and in Tlr9+/- or Tlr997 (all Tlr7-/-) B cells, respectively.

overall_design: mRNA profiles of (i) Tlr779 or Tlr7WT (all Tlr9-/-) B cells stimulated  with CL097 or unstimulated  and of (ii)  Tlr997 or Tlr9+/- (all Tlr7-/-) B cells stimulated with CpG or unstimulated,  were generated in three replicates, by sequencing on an Illumina NextSeq500 using PE 150 Cycles High Output flowcell.


title: Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs

city: Ann Arbor

first: Lydia

last: Freddolino

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

summary: Recent research has indicated the presence of heterochromatin-like regions of extended protein occupancy and transcriptional silencing of bacterial genomes. We utilized an integrative approach to track chromatin structure and transcription in E. coli K-12 across a wide range of nutrient conditions. In the process, we identified multiple loci which act similarly to facultative heterochromatin in eukaryotes, normally silenced but permitting expression of genes under specific conditions. We also found a strong enrichment of small regulatory RNAs (sRNAs) among the set of differentially expressed transcripts during nutrient stress. Using a newly developed bioinformatic pipeline, the transcription factors regulating sRNA expression were bioinformatically predicted, with experimental follow-up revealing novel relationships for 36 sRNA-transcription factors candidates. Direct regulation of sRNA expression was confirmed by mutational analysis for five sRNAs of metabolic interest: IsrB, CsrB and CsrC, GcvB, and GadY. Our integrative analysis thus reveals additional layers of complexity in the nutrient stress response in E. coli and provides a framework for revealing similar poorly understood regulatory logic in other organisms.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: In order to provide an unbiased identification of the regulatory logic underlying transcriptional responses to nutrient starvation, we grew E. coli K12 cells through exponential and stationary stages of growth in two media types: minimal media with either glucose or casamino acids as the sole carbon sources. We harvested samples from several timepoints in each case and performed RNA-seq, RNA polymerase ChIP-seq, and in vivo protein occupancy display (IPOD) experiments.

first: Freddolino

last: Lydia

first: Kribelbauer

last: Judith

first: Tavazoie

last: Saeed


title: Phase separation of RXRγ drives tumor chemoresistance and represents a therapeutic target for small cell lung cancer

city: Guangzhou

first: Hong

last: Wang

address: 132, Waihuandonglu, Daxue Cheng

institute: Sun Yat-sen University

summary: Small cell lung cancer (SCLC) is the most lethal type of lung cancer, characterized by limited treatment options and rapid evolution from chemosensitivity to chemoresistance. However, the mechanisms underlying this evolution remain poorly understood. Identifying the druggable drivers and developing pharmacological strategies to overcome chemoresistance are imperative. Here, we show that Retinoid X receptor γ (RXRγ) is uniquely overexpressed in chemo-resistant SCLC tumors, and that RXRγ serves as an essential factor driving chemoresistance in SCLC. RXRγ forms phase-separated droplets with LSD1 in the nucleus, which enhances RXRγ-mediated gene transcription activity and reprograms gene expression, promoting tumor stemness and metastasis, and eventually driving SCLC chemoresistance. In turn, RXRγ antagonist disrupts RXRγ-LSD1 interaction, reducing their binding to the target gene locus, markedly suppressing the expression of the RXRγ target gene network. Finally, RXRγ antagonists strongly suppress tumor growth and metastasis and restore SCLC vulnerability to chemotherapy in multiple preclinical SCLC models, without overt toxicity, in mice. Thus, these results establish RXRγ as a key player in SCLC by phase separation and as a potential therapeutic target for this deadly disease.

overall_design: H128 cells were treated with HX531 for 48 h. (Control group, we named Con-2; treated group, we named H10-2)

first: Jie

last: Huang

first: Zhenhua

last: Zhang

first: Yana

last: An


title: Human astrocyte encapsulation for delivery of cytokines to modulate neuroinflammation

city: Houston

first: Robert

last: Krencik

state: TX

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

summary: RNAsequencing for comparison of human pluripotent stem cell-derived astrocyte response to inflammatory cytokine treatment (Interleukin 1 alpha, TNFalpha, and Complement C1q; aka ITC) while encapsulated within alginate capsules (aka AstroCapsules).

overall_design: Three separate batches of AstroCapsules were generated and subdivided into two group. One group received treatment with vehicle-only (AstroCapsules) while the other group received treatment with a combination of inflammatory cytokines (AstroCapsuleITC). RNAsequencing was performed with samples 48 hours after treatment.

first: Samira

last: Aghlara-Fotovat


title: Phase separation of RXRγ drives tumor chemoresistance and represents a therapeutic target for small cell lung cancer [ChIP-Seq]

overall_design: ChIP-Seq


title: Characterizing EMT-Linked Heterogeneity in Breast Cancer Circulating Tumor Cells at the Single-Cell Level

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

summary: In this study, we evaluate gene expression patterns in single circulating tumour cells discovered in liquid biopsies from breast cancer patients. The experiment included cells collected from early, metastatic and relapsed breast cancer patients.

overall_design: The cells were isolated using density gradient centrifugation and CD45-based immunomagnetic depletion.  Immunofluorescently-stained cells were picked using micromanipulation (Eppendorf TransferMan 4r). Finally RNA was prepared for NGS using Smart-seq2 method and Nextera XT library protocol.

first: Justyna

last: Topa

first: Aleksandra

last: Markiewicz

first: Anna

last: Zaczek

first: Alicja

last: Stasczak


title: Phase separation of RXRγ drives tumor chemoresistance and represents a therapeutic target for small cell lung cancer [RNA-Seq]

overall_design: RNA-Seq


title: Effects of NCL Knockdown on Fibroblast-Like Synoviocytes

city: Hong Kong

first: chunhao

last: cao

address: Hong Kong

department: School of Chinese Medicine

country: Hong Kong

institute: Hong Kong Baptist University

summary: Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by systemic inflammation, synovial hyperplasia, and the destruction of bone and cartilage. Despite the use of various immunosuppressive disease-modifying antirheumatic drugs (DMARDs), a considerable proportion of RA patients remain symptomatic. As RA progresses, fibroblast-like synoviocytes (FLSs) undergo a phenotypic transition to an aggressive state, making them attractive non-immune cellular targets for RA treatment. However, there are currently no clinically available therapies that selectively ablate RA-FLSs due to the lack of specific molecular targets.  Our research focuses on the knockdown of the nucleolin (NCL) gene in RA-FLSs. NCL is expressed in the cell  of RA-FLSs and plays a crucial role in their aggressive transition. By specifically knocking down NCL, we observed significant inhibition of the harmful phenotypes exhibited by RA-FLSs.

overall_design: To investigate whether NCL plays a critical role in the tumor-like transformation and overactivation of RA-FLSs, we established an RA-FLSs line in which the  target gene was silenced  down by shRNA


title: Metabolic engineering of yeast for de novo production of kratom monoterpene indole alkaloids

city: Leiden

first: Ron

last: Dirks

address: Sylviusweg 74

institute: Future Genomics Technologies BV

summary: Monoterpene indole alkaloids (MIAs) from Mitragyna speciosa (“kratom”), such as mitragynine and speciogynine, are promising novel scaffolds for opioid receptor ligands for treatment of pain, addiction, and depression. While kratom leaves have been used for centuries in South-East Asia as stimulant and pain management substance, the biosynthetic pathway of these psychoactives have only recently been partially elucidated. Here, we demonstrate the de novo production of mitragynine and speciogynine in Saccharomyces cerevisiae through the reconstruction of a five-step synthetic pathway from common MIA precursor strictosidine comprising fungal tryptamine 4-monooxygenase to bypass an unknown kratom hydroxylase. Upon optimizing cultivation conditions, a titer of ~290 µg/L kratom MIAs from glucose was achieved. Untargeted metabolomics analysis of lead production strains led to the identification of numerous shunt products derived from the activity of strictosidine synthase (STR) and dihydrocorynantheine synthase (DCS), highlighting them as candidates for enzyme engineering to further improve kratom MIAs production in yeast. Finally, by feeding fluorinated tryptamine and expressing a human tailoring enzyme, we further demonstrate production of fluorinated and hydroxylated mitragynine derivatives with potential applications in drug discovery campaigns. Altogether, this study introduces a yeast cell factory platform for the biomanufacturing of complex natural and new-to-nature kratom MIAs derivatives with therapeutic potential.

overall_design: RNA-seq study of red- and green-veined Mitragyna speciosa leaves at three different developmental stages.

first: Michael

last: Jensen

first: Juraithip

last: Wungsintaweekul


title: CCDC12 regulates selective shear of RBM47 to promote breast cancer progression

city: Shanghai

first: Xinrui

address: 197 Ruijin Rd II

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

summary: Purpose: TThe Coiled coil domain containing (CCDC) protein is an egg that is closely related to malignant tumors. Methods:Breast cancer cells MDA-MB-231(NC), MDA-MB-231(shCCDC12)were deeply sequenced by Illumina sequencing platform (HISEQ2500) in triplices. Genes with adjusted p values < 0.05 and |foldChange| > 2 were defined as differential expression Genes (DEGs) and enriched with GO and KEGG. Several essential genes were validated by qRT-PCR using QuantStudio 5 (Thermo Fisher) and SYBR Green assays. The White Family. Studies have shown that CCDC protein is abnormally expressed in malignant tumors and changes cell proliferation cycle by regulating cell transcription factors Stage, promote the invasion and metastasis of malignant tumor cells. How does CCDC12 as a shear gene affect the biology of breast cancer Scientific activity remains to be further studied. Results: To verify the biological properties of CCDC12 in breast cancer, we studied breast cancer  MDA-MB-231 knocked down the expression of CCDC12 in the cell line, and previous studies showed that TCGA and CPTAC database scores The mRNA and protein expression levels of CCDC12 gene were significantly up-regulated in normal breast cancer tissues compared with tumor tissues. Knocking down the expression level of CCDC12 in MDA-MB-231 cells can significantly inhibit cell growth, proliferation and migration. In tumor formation experiments in nude mice, low expression of CCDC12 can inhibit tumor growth. Knock down CCDC12 on MDA-MB-231 Splicing event analysis was performed by cell transcriptome sequencing, and differential analysis found that CCDC12 expression was differentially induced in breast cancer cells The RNA binding motif protein 47 (RBM47) Skipped exon, causing RMB47 to open The structure of the reading frame changes, altering gene function. Conclusions:This study confirmed that CCDC12 regulates the invasion and metastasis of breast cancer cells by regulating the variable shear of RBM47, inducing cell cycle arrest and promoting cell apoptosis. The results of RNA-Seq were consistent with our in vitro and in vivo experiments.

overall_design: mRNA expression profiles of CCDC12 knock-down and Control groups.

first: Liping

last: Zhu

first: Zhoujie

last: Ye


title: Comparative gene expression in healthy African American and White Non-Hispanic skin

first: Irina

last: Budunova

state: Illinois

address: 303 E Chicago Ave, Ward Bldg, #9-132

department: Dermatology

summary: The risk of atopic dermatitis, hidradenitis suppurativa, lupus erythematosus is significantly higher in African Americans (AA), while White Non-Hispanic (WNH) subjects have a greater risk of psoriasis. The mechanisms underlying disparity in inflammatory skin diseases risks are poorly understood, and the molecular landscape of skin of color  including  transcriptome and proteome are not well known.  To assess whether and how  gene expression pattern in normal skin may affect predisposition to specific skin inflammatory diseases, we performed analkysis of gene expression in full thickness skin biopsies obtained from  healthy African American and White Non-Hispanic volunteers (all females, aged 22-46).

overall_design: The study included  healthy female volunteers without history of skin and systemic inflammatory diseases, aged 22-46 years with darkly pigmented skin (Fitzpatrick score V-VI, self-identified as AA) and lightly pigmented skin (Fitzpatrick score I-II, self-identified as WNH).  4 mm full thickness skin biopsies werte collected from the inner upper arm area (relatively sun-protected area).

first: Dmitry

last: Trubetskoy


title: Aging attenuates the infrapatellar fat pad’s paracrine capacity to promote extracellular matrix    production in aged chondrocytes

city: Boston

first: Gabrielle

last: Gilmer

state: MA

address: 149 13th Street

department: Pathology

summary: Objective: To elucidate the age and sex-specific impact of the IFP secretome on aged chondrocytes, and uncover the exact mechanism driving these effects.  To explore mediators of the IFP on chondrocytes, we performed mass-spectrometry proteomics of CM from young versus aged male IFP and mass spectrometry on aged male chondrocytes treated with CM of the same experimental groups. Network analysis interrogated age-dependent changes in communication between IFP-derived secreted proteins and chondrocytes.  Results: Col2 and aggrecan expression were significantly increased in chondrocytes co-cultured with young IFP tissue compared to aged IFP tissue, and young CM compared to aged CM. There was no significant increase in SOX9 under any of the different conditions. Similar trends were seen in female experiments. Multi-omics results combined with network analysis suggested IFPs secrete succinate co-A ligase related factors that regulate Hox-dependent spliceosome gene expression in chondrocytes in an age-dependent manner.  Conclusions: This study suggests that a young IFP secretome enhances ECM production by aged chondrocytes, in part through enhanced mitochondrial activity. However, this beneficial effect decreases with age.

overall_design: Design: Using male C57BL6 mice, aged chondrocytes were co-cultured with young (n=5) or aged (n=5) IFPs in a transwell system for 72 hours. To establish the direct effects of the IFP secretome on chondrocyte integrity, we incubated aged chondrocytes with untreated control media, conditioned media (CM) from young IFP (n=5), or CM from aged IFP (n=5) for the same duration. Outcomes for both experiments included SOX9, type II collagen (Col2), and aggrecan. Experiments were repeated with female models.

first: Ella

last: D'Amico

first: Fabrisia

last: Ambrosio