title: ACE2 Enhances Sensitivity to PD-L1 Blockade by Inhibiting Macrophage-Induced Immunosuppression and Angiogenesis [RNA-seq]

city: Shanghai

first: Peiyi

last: Xie

address: Fenglin Road No.180

institute: Zhongshan Hospital, Fudan University

summary: Anti-PD-L1-based combination immunotherapy has become the first-line treatment for unresectable hepatocellular carcinoma (HCC). However, the objective response rate is lower than 40%, highlighting the need to identify mechanisms of tolerance to immune checkpoint inhibitors and accurate biomarkers of response. Here, we employed next-generation sequencing to analyze HCC samples from 10 patients receiving anti-PD-L1 therapy. Activation of the renin-angiotensin system was elevated in nonresponders compared with responders, and ACE2 expression was significantly downregulated in nonresponders. ACE2 deficiency promoted HCC development and anti-PD-L1 resistance, whereas ACE2 overexpression inhibited HCC progression in immune competent mice. Mass cytometry by time of flight (CyTOF) revealed that ACE2 deficient murine orthotopic tumor tissues featured elevated M2-like tumor-associated macrophages (TAMs), displayed a CCR5+PD-L1+ immunosuppressive phenotype, and exhibited high VEGFα expression. ACE2 downregulated tumor intrinsic CCL5 expression by suppressing NF-κB signaling through the ACE2/angiotensin-(1–7)/Mas receptor axis. The lower CCL5 levels led to reduced activation of the JAK-STAT3 pathway and suppressed PD-L1 and VEGFα expression in macrophages, blocking macrophage infiltration and M2-like polarization. Pharmacological targeting of CCR5 using maraviroc enhanced the tumor suppressive effect of anti-PD-L1 therapy. Together, these findings suggest that activation of the ACE2 axis overcomes the immunosuppressive microenvironment of HCC and may serve as an immunotherapeutic target and predictive biomarker of response to PD-L1 blockade.

overall_design: HCC cells with ACE2 overexpression or control (5 × 105 /well) were seeded in the 6-well plate.  For Ang II treatment, 20 nM Ang II (HY-13948, MedChemExpress) was used to treat HCC cells for 24 h before experiments.


title: Total RNA Sequencing in Eyeballs isolated from Tetraselmis chuii treated Dry Eye Sydrome Mice

status: Public on Oct 15 2024

city: Gangneung-si, Gangwon-do

first: Sung-Chul

last: Hong

address: Saimdang-ro 679

department: Smart Farm Research Center

country: South Korea

institute: Korea Institute of Science and Technology

type: Expression profiling by high throughput sequencing

summary: The purpose of this study was to compare changes in gene expression in the eyeballs following ingestion of Tetraselmis chuii (T. chuii) in a BALB/C mouse model of dry eye syndrome (DES). The changes in gene expression before and after DES induction were compared preferentially, as were the changes in gene expression caused by T. chuii ingestion following DES induction

overall_design: We analyzed the gene expression patterns of eyeballs derived from WT, dry eye syndrome by inducing scoplamine, and T. chuii treated dry eye syndrome mice using RNAseq

first: Jin-Chul

last: Kim

first: Jaeyoung

last: Choi


title: Myc transcriptional bursts promote B cell positive selection by T cells in germinal centers

city: Rehovot

first: Sharon

last: Kagan Ben Tikva

state: Israel

address: 234 Herzl street

country: Israel

institute: Weizmann Institute

summary: Antibody affinity maturation occurs in secondary lymphoid organs within germinal centers (GCs) where B cells mutate their antibody-encoding genes in the dark zone (DZ) followed by a selection of the high-affinity variants in the light zone (LZ) by T cells. The amount of the T cell-derived selection signals is proportional to the BCR affinity and the magnitude of Myc expression. However, since the lifetimes of Myc mRNA and protein are extremely short, it is unclear how high levels of Myc are maintained in the GC B cell to allow positive selection. Here, by measuring Myc transcripts in situ at the single-cell level, we find that T cell help promotes the frequency of Myc transcriptional bursts. T cell help primarily increases the number of Myc-positive cells rather than the amount of Myc per cell. Measurement of Myc intronic and exonic transcripts in situ demonstrates that positive selection is mediated by Myc transcriptional bursts through a rapid increase in the active transcription sites rather than an elevation in transcription rate or gene accessibility. Thus, the amount of Myc transcriptional bursts over time in the LZ, rather than Myc abundance, dictates B cell selection in germinal centers.

overall_design: RNA-seq of DZ and LZ GC B cells, after  in vivo anti CD40 treatment or isotype control

first: SharonKagan

middle: B

last: Tikva

first: Hadas

last: Hezroni

first: Noa

last: Wigoda

first: Ziv

last: Shulman


title: CnbHLH130 positively regulates salt tolerance through CnCBL10-CnCIPK4 mediated SOS pathway in Campeiostachys nutans

status: Public on Oct 14 2024

city: Yangling

first: Juanjuan

last: Fu

state: Shaanxi

address: No.22 Xinong Road

country: China

institute: Northwest A&F University

summary: Campeiostachys nutans, a dominant perennial grass in the Qinghai-Tibet Plateau, exhibits high tolerance to salt stress. The Salt Overly Sensitive (SOS) pathway is key to plant salt stress tolerance. However, the pivotal role of the SOS pathway in response to salt stress in C. nutans remains unknown. Here, we identified CnbHLH130 as a novel transcriptional activator of CnCBL10, directly binds to the G-box motif in the promoter. CnbHLH130 responds to salt stress and positively regulate salt tolerance in rice and C. nutans. Interestingly, we found CnCBL10 and CnCIPK4 interact with CnbHLH130 by a Y2H screening assay. The interactions were confirmed by split-luciferase complementation (split-LUC), Pull-down, Co-immunoprecipitation (Co-IP) and bimolecular fluorescence complementation (BiFC) assays. Moreover, CnbHLH130 enhanced the interaction between CnCBL10 and CnCIPK4, which further phosphorylate and activate Na+/H+ antiporter CnSOS1 to exclude excess cytosolic Na+ from cells in the shoots. Genetic evidence showed that CnCBL10, CnCIPK4 and CnbHLH130 coordinately regulates salt tolerance in plants. In summary, this study demonstrated that CnbHLH130 acts as a novel core component and transcriptional activator regulating CnCBL10-CnCIPK4 mediated SOS pathway, thus conferring to the salt tolerance in C. nutans. This work advanced our understandings of how an alpine plant greatly survived in the Qinghai-Tibet Plateau by concise regulation of the SOS pathway in response to salt stress.

overall_design: 28-day-old C. nutans seedlings treated with or without 200 mM salt treatment for 5 d were used for RNA-seq analysis.


title: DNA Methylation of Cardiogenic Shock Patients under Extracorporeal Membrane Oxygenation

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

type: Methylation profiling by genome tiling array

summary:
Prognosis for cardiogenic shock patients under ECMO was our study goal. Success defined as survived more than 7 days after ECMO installation and failure died or had multiple organ failure in 7 days. Total 34 cases were enrolled, 17 success and 17 failure.
Peripheral blood mononuclear cells collected at ECMO installation 0, 2 hours and removal were analyzed.

overall_design: Analysis of the cardiogenic shock patients at extracorporeal membrane oxygenation treatment by methylation. DNA methylation between successful and failure groups were analyzed.

first: Tsai-Hsia

first: Yi-Jing

last: Hsiao

first: Yan-Ming

last: Chen

first: Hsuan-Yu

first: Sun-Liang


title: Comparative transcriptomics analysis of L-alanine-induced Bacillus subtilis S-2 and 312 strains

city: Wuhan

first: Shuang

last: Lu

address: East Lake Road 185

department: State Key Laboratory of Virology/Institute of Medical Virology/Department of Infectious Diseases

institute: School of Basic Medical Sciences/Renmin Hospital, Wuhan University

summary: Two wide type strains of Bacillus subtilis, S-2 and 312, were selected to study their genic differences treated by L-alanine through comparative transcriptomics analysis. The spores of B. subtilis S-2 were selected because of their high germination potential to L-alanine. The spores of B. subtilis 312 without a response to L-alanine were used as the control. The spores with or without L-alanine (100 mm) pretreatment were both cultured in the synthetic medium for 9 h, and then collected for sequencing.

overall_design: Bacillus subtilis S-2, 312, L-alanine-induced S-2 and L-alanine-induced 312 spores were generated by deep sequencing, in duplicate respectively

first: Xiaohua

last: Guo


title: Comparative genomics of Plasmodium yoelii nigeriensis N67 and N67C: Genome-wide polymorphisms, differential gene expression, and drug resistance

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

country: USA

institute: National Institutes of Health

summary: The study of rodent malaria parasites has significantly advanced our understanding of malaria parasite biology and host responses to parasite infections. There are four well-characterized rodent malaria parasite species (Plasmodium yoelii, P. chabaudi, P. berghei, and P. vinckei). Each species also has multiple strains that cause different disease phenotypes. P. yoelii nigeriensis N67C and N67, two isogenic parasites, are particularly intriguing as they differ in virulence and incite different immune responses in mice. The genome of the N67 parasite has been assembled recently, but not that of N67C. This study used PacBio HiFi sequencing data to assemble the N67C genome, compared the two genomes, and performed RNA sequencing to identify polymorphisms and differentially expressed genes (DEGs). Results:  The assembled N67C parasite genome consisted of 16 scaffolds and three contigs of approximately 22.5 Mb with 100% and 96.6% completeness based on well-characterized single-copy orthologs specific to the Apicomplexa phylum and the Plasmodium genus, respectively. A comparison between the annotated N67C and N67 genomes revealed 133 single nucleotide polymorphisms (SNPs) and 75 indels. Among the polymorphic sites, an S (N67) to N (N67C) amino acid substitution at position 114 (S114N) in the dihydrofolate reductase-thymidylate synthase (DHFR-TS) confers resistance to pyrimethamine in mice. Additionally, 302 differentially expressed genes (DEGs) were detected after comparing mRNA levels between the two parasites. Starting with the predicted and annotated 5,681 N67C and 5,749 N67 genes, we identified 4,641 orthogroups that included at least one gene from the four P. yoelii parasites (N67, N67C, 17X, and YM), whereas 758 orthogroups showed subspecies or strain-specific patterns. Conclusion: The identification of polymorphic sites between the N67 and N67C genomes, along with the detection of the DEGs, may provide crucial insights into the variations in parasite drug responses and disease severity between these two isogenic parasites. The functional characterization of these genetic differences and candidate genes will deepen our understanding of disease mechanisms and pave the way for developing more effective control measures against malaria.

overall_design: We compared the expression profiles of the mixed blood stages of N67 and N67C parasites with similar proportions of ring, trophozoite, and schizont stages using RNA-Seq data derived from five mice (for each parasite strain), each contributing to a distinct cDNA library (five replicates for each parasite).

first: Jian

last: Wu

first: Cihan

last: Oguz

first: Awet

middle: A

last: Teklemichael

first: Fangzheng

last: Xu

first: Rachel

middle: V

last: Stadler

first: Amuza

last: Lucky

first: Shengfa

last: Liu

first: Osamu

last: Kaneko

first: Justin

last: Lack

first: Xin-zhuan

last: Su


title: Cyclin A2 endometrial deficiency and early pregnancy loss

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: Proper action of the female sex steroids, 17β-estradiol (E2) and progesterone (P4) on endometrium is essential for fertility.  Beyond its role in regulating the cell cycle, cyclin A2 (CCNA2) also mediates E2 and P4 signaling in vitro, but a potential role in modulating steroid action for proper endometrial tissue development and function is unknown.   To fill this gap in our knowledge, we examined human endometrial tissue from fertile and infertile women for CCNA2 expression and correlated this with pregnancy outcome.  Functional assessment of CCNA2 was validated in vivo using a conditional Ccna2 uterine deficient mouse model while in vitro function was assessed using human cell culture models.  We found that CCNA2 expression was significantly reduced in endometrial tissue, specifically the stromal cells, from women undergoing in vitro fertilization who failed to achieve pregnancy.  Conditional deletion of Ccna2 from mouse uterine tissue recapitulated the inability to achieve successful pregnancy which appears to be due to alterations in the process of decidualization, which was confirmed using in vitro models.  From these studies, we conclude that CCNA2 expression during the proliferative/regenerative stage of the menstrual cycle acts as a safeguard allowing for proper steroid responsiveness, decidualization and pregnancy.  When CCNA2 expression levels are insufficient there is impaired endometrial responsiveness, aberrant decidualization and loss of pregnancy.

overall_design: Total RNA (500ng) was isolated from dpc 0.5 uterine tissue from Ccan2 fl/fl and Ccna2 d/d mice (n = 4/genotype) and was used to initiate the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus (Illumina 20040525) library preparation protocol.  Stranded total RNA-sequencing was performed using the Illumina NovaSeq 6000 Sequencing System at the University of Kansas Medical Center – Genomics Core (Kansas City, KS).

first: Fatimah

last: Aljubran

first: Katelyn

last: Shumacher

first: Amanda

last: Graham

first: Courtney

last: Marsh

first: Michael

last: Lydic

first: Kristin

last: Holoch

first: Warren

last: Nothnick


title: Obesity facilitated colon cancer progression is mediated by increased diacylglycerol o-acyltransferases 1 and 2 (DGAT1/2) levels [RNA-seq]

city: NEW ORLEANS

first: Suzana

middle: D

last: Savkovic

state: LA

address: 1430 Tulane Ave JBJ 315

institute: Tulane University

summary: Background & Aims: The obesity epidemic is associated with increased colon cancer progression. As lipid droplets (LDs) fuel tumor growth, we aim to determine the significance of diacyltransferases, DGAT1/2, responsible for LDs biogenesis, in obesity-mediated colonic tumorigenesis. Methods: Human colon cancer samples, colon cancer cells, colonospheres, and ApcMin/+ colon cancer mouse model on a high-fat diet were employed. For DGAT1/2 inhibition, enzymatic inhibitors and siRNA were used. Expression, pathways, cell cycle, and growth were assessed. Bioinformatic analysis of CUT&RUN and RNAseq data was performed. Results: DGAT1/2 levels in human colon cancer tissue are significantly elevated with disease severity and obesity (vs normal). Their levels are increased in human colon cancer cells (vs non-transformed) and further enhanced by fatty acids prevalent in obesity; augmented DGAT2 expression is MYC-dependent. Inhibition of DGAT1/2 improves FOXO3 activity by attenuating PI3K, resulting in reduced MYC-dependent DGAT2 expression and LDs accumulation, suggesting feedback. This inhibition attenuated growth in colon cancer cells and colonospheres via FOXO3/p27kip1 cell cycle arrest and reduced colonic tumors in ApcMin/+ mice on a high-fat diet. Transcriptomic analysis revealed that DGAT1/2 inhibition targeted metabolic and tumorigenic pathways in human colon cancer and colon cancer crypts, stratifying human colon cancer samples from normal. Further analysis revealed that this inhibition is predictive of advanced disease-free state and survival in colon cancer patients. Conclusion: This is a novel mechanism of DGAT1/2-dependent metabolic and tumorigenic remodeling in obesity-facilitated colon cancer, which provides a platform for the future development of effective treatments for colon cancer patients.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-Seq of HT29 adherent and colonospheres treated with DGAT1/2 inhibitors. RNA-Seq of Apcmin/+ mice colon treated with DGAT1/2 Inhibitors and fed regular or high fat diet

first: Jenisha

last: Ghimire

first: Morgan

middle: E

last: Collins

first: Patricia

last: Snarski

first: Angelle

middle: N

last: King

first: Emmanuelle

last: Ruiz

first: Rida

last: Iftikhar

first: Harrison

middle: M

last: Penrose

first: Krzysztof

last: Moroz

first: Tyler

last: Rorison

first: Melody

last: Baddoo

first: Muhammad Anas

last: Naeem

first: Arnold

middle: H

last: Zea

first: Scott

middle: T

last: Magness

first: Erik

middle: F

last: Flemington

first: Susan

last: Crawford


title: Single-cell RNA-sequencing of the human esophagus to identify cell types

city: Philadelphia

first: Sydney

last: Shaffer

state: PA

address: BRB II/III, Room 445, 421 Curie Blvd

institute: University of Pennsylvania

summary: We performed single-cell RNA-sequencing on 6 samples form patients undergoing endoscopy.

overall_design: Pinch biopsies of normal squamous esophagus tissue were collected from Barrett's esophagus patients during routine surveillance endoscopy.

first: Raul

last: Reyes-Hueros

first: Rodrigo

last: Gier


title: Developmental exposure to perfluorooctanoic sulfonate（PFOS） impairs the endometrial receptivity

city: Lanzhou

first: Haofei

last: Shen

address: No.1 Donggang West Road, Chengguan District

institute: Lanzhou University

summary: Perfluorooctanoic sulfonate (PFOS) is difficult to degrade and tends to accumulate in the body, which causes widespread concern. The expression of genes related to endometrial receptivity and the differentiation of human endometrial stromal cells (hESCs) were assessed in this study concerning PFOS. In this study, we investigated the effect of PFOS exposure on endometrial tolerance by cell and animal experiments. The activity against endometrial mesenchymal cells was significantly reduced by PFOS intervention, and the apoptosis flow assay results showed that PFOS significantly promoted cell death in a concentration-dependent manner. Transmission electron microscopy results revealed mitochondrial damage in the PFOS-intervened group, and WB results showed that the expression levels of endometrial tolerance-related proteins Homeobox A10 (HOXA10) and integrin beta3 (ITGB3) were decreased, and the expression level of Forkhead box O1 (FOXO1) protein was increased. Animal studies have shown that PFOS can affect the locomotor cycle in mice, and significant damage to pinopodes morphology was observed after PFOS exposure administration. In the present study, we found that PFOS may synergistically affect the viability of endometrial mesenchymal stromal cells through accumulation in vivo, and that PFOS may contribute to the failure of embryo implantation by affecting mitochondrial function and consequently endometrial permissive sites.

overall_design: Few studies have evaluated the effect of PFOS on endometrial stromal cells in vitro, despite reports of its effects on the reproductive system. The process of PFOS interference with endometrial decidualization, which forms the substrate for embryo implantation, must be further investigated. Therefore, To enhance our understanding of the mechanisms of endometrial regulation after PFOS exposure, our study aimed to assess whether any associations exist between the following: (1) PFOS exposure and endometrial receptivity indexes; (2) PFOS concentrations and pinopodes morphology.

first: Ren

last: Rui

first: Zhou

last: Xinyue

first: Jia

last: Tianyu

first: Wang

last: Bin


title: Pre-existing cell states predict resistance to multiple treatments

first: Dylan

middle: L

last: Schaff

address: 421 Curie Blvd, BRB II/II rm 445

department: Bioengineering

summary: Pre-existing differences between individual cancer cells can predict which cells will become resistant upon the application of treatment. This understanding has been furthered by novel methods in DNA barcoding that allow tracking of clones and their cell states during treatment. However, previous studies using these techniques have been limited in their scope, focusing on how single cell-states lead to resistance to a single treatment. In this study, we performed multi-treatment, high-throughput clonal tracking and single-cell RNA-sequencing to trace rare clones through the development of resistance to many different treatments in parallel with the goal of identifying cell states associated with multi-treatment resistance. We found that clones that will go on to develop resistance to one treatment had an increased chance of separately developing resistance to other treatments with diverse mechanisms of action. Additionally, we identified high CD44 expression in treatment-naive cells as a predictor of future resistance to multiple different treatments. Furthermore, for cells within the same treatment condition, we found that differences in gene expression states prior to treatment can lead cells to follow divergent paths towards their ultimate resistance fate. This work provides a framework for extracting targetable gene expression states from complex resistance dynamics across multiple treatments to eliminate multi-treatment resistance.

overall_design: Trascribed clonal barcodes were introduced into melanoma cells and allowed to double so that there were multiple cells with each barcode. A subset of the population was then collected for scRNA-seq (called the untreated.naive sample). The remaining cells were then split six ways for treatment with four weeks of treatment with dabrafenib, trametinib, CoCl2, or acidic media or 2 weeks of treatment with cisplatin or doxorubicin followed by two weeks of treatment holiday. After four weeks, we performed scRNA-seq on the treated, now-resistant cells.

first: Phoebe

last: White

first: Christopher

last: Cote

first: Kevin

last: Lin

first: Aria

last: Fasse

first: Nancy

last: Zhang


title: Comprehensive identification of coronary artery disease-associated variants regulating vascular smooth muscle cell gene expression [CUT&RUN]

city: Charlottesville

first: Nicolas

last: Barbera

state: Virginia

address: 1335 Lee Street

department: Department of Genome Sciences

institute: University of Virginia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Coronary artery disease (CAD) is a complex disorder with genetic and environmental influences. Genome-wide association studies (GWAS) have identified over 300 genomic loci associated with disease risk. However, identifying the functional variants within these loci has been limited in large part due to linkage disequilibrium. This represents a critical step in understanding the molecular mechanisms underlying disease risk. To identify and prioritize candidate causal CAD-associated variants, we performed lentivirus-based massively parallel reporter assays (lentiMPRAs) in primary vascular smooth muscle cells (SMCs), which play significant roles in atherosclerosis, the underlying cause of CAD. We tested 25892 CAD-associated variants for their allele-specific enhancer activity in quiescent and proliferative SMCs, modeling healthy and disease conditions. We identified 122 candidate variants showing significant enhancer activity and differences in reporter gene expression between risk and non-risk alleles. We also identified 23 variants showing condition-biased allelic imbalance and 41 variants showing sex-biased allelic imbalance. We further functionally characterized 25892 variants by performing CUT&RUN assays to identify variants in enhancer and promoter regions of SMCs. By integrating the results of these experiments, we identified a credible set of 49 CAD-associated variants in functionally relevant regions. Furthermore, by comparing these identified variants with our previously obtained expression quantitative trait loci (eQTL) data, 27 of these 49 variants were associated with SMC gene expression levels. Finally, we performed CRISPRi experiments on 8 variants comprising 9 variant-gene pairs, rs35976034 (MAP1S), rs4888409 (CFDP1), rs73193808 (MAP3K7CL), rs67631072 (INPP5B/FHL3), rs1651285 (SNHG18), rs17293632 (SMAD3), rs2238792 (ARVCF), rs4627080 (NRIP3), to confirm their regulatory potential of nearby gene expression. Taken together, our results comprehensively fine-map the causal variants that confer increased risk of CAD through their effects on vascular smooth muscle cells.

overall_design: Cleavage-under-targets-&-release-using-nuclease (CUT&RUN) for histone modifications H3K4me3, H3K27ac, and H2BK20ac in primary vascular smooth muscle cells in standard and serum-free media

first: Alexia

last: Wallace

first: Noah

middle: R

last: Perry

first: Lily

last: Lei

first: Hester

last: den Ruijter

first: Mete

last: Civelek


title: A Humanized Monoclonal Antibody Targeting an Ectonucleotidase Rescues Heart Function after Myocardial Infarction

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: We have recently demonstrated that the ectonucleotidase ENPP1 (ectonucleotide pyrophosphatase/phosphodiesterase 1) is upregulated in the heart after myocardial infarction (MI) and initiates an aberrant metabolic cascade that worsens cell death and heart repair. Genetic loss of function approaches demonstrated that animals deficient in ENPP1 exhibited enhanced heart repair and had significantly superior post MI heart function. Whether human ENPP1 protein can be therapeutically targeted after heart injury remains unknown. Here, we engineer a humanized monoclonal antibody targeting human ENPP1 (hENPP1mAb) and demonstrate high affinity and specificity of binding to the catalytic domain of human ENPP1. In mice, genetically engineered, to express the human ENPP1 ortholog instead of murine ENPP1 (humanized ENPP1 mice), we demonstrate that administration of hENPP1mAb significantly rescued post MI heart function compared to IgG injected animals. Using metabolomics, single nuclear transcriptomics, and cellular respiration assays, we demonstrate that administration of the hENPP1mAb induces organ wide metabolic and transcriptional reprogramming of the heart that enhances myocyte cellular respiration and decreases cell death and fibrosis in the infarcted heart. Biodistribution and safety studies with radiolabeled hENPP1mAb showed specific organ wide distribution without any organ toxicity. Finally, in humanized ENPP1 animals that have also been genetically engineered to exhibit antibody clearance kinetics similar to humans, we demonstrate that a single "shot" of the hENPP1mAb after MI is sufficient to rescue post infarct cardiac dysfunction. Taken together our observations provide proof of concept on how the human ectonucleotidase ENPP1 can be therapeutically targeted to prevent heart failure after MI.

overall_design: Single nuclei were isolated from IgG and hENPP1mAb treated mice injured heart tissue after MI and analyzed using snRNAseq.

first: Shen

last: Li

first: Arjun

last: Deb


title: Transfer learning associates CAFs with EMT and inflammation in tumor cells in human tumors and organoid co-culture in pancreatic ductal adenocarcinoma

city: Baltimore

first: Jacquelyn

middle: W

last: Zimmerman

state: Maryland

address: 1650 Orleans St, Room 186

institute: Johns Hopkins Sidney Kimmel Comp. Cancer Center

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

overall_design: Refer to individual Series


title: Human IL-6 fosters long-term engraftment of human patient derived myeloma cells in immunodeficient mice

first: Zainul

last: Hasanali

address: 3620 Hamilton Walk, 230 John Morgan Building

summary: Multiple myeloma is a largely incurable and life-threatening malignancy of antibody-secreting plasma cells. An effective and widely available animal model that recapitulates human myeloma and related plasma cell disorders is lacking. We show that busulfan-conditioned hIL-6 transgenic NSG mice (NSG+hIL6) reliably support the engraftment of malignant and pre-malignant human plasma cells including from patients diagnosed with pre- and post-relapse myeloma, plasma cell leukemia, and AL amyloidosis. Consistent with human disease, NSG+hIL6 mice engrafted with patient-derived myeloma cells developed blood M spikes, and a majority developed anemia, hypercalcemia, and/or bone lesions. Singe cell RNAseq analyses showed non-malignant and malignant cell engraftment, the latter expressing a wide array of mRNAs associated with myeloma cell survival and proliferation. Myeloma-engrafted mice given CAR T-cells targeting plasma cells or bortezomib experienced reduced tumor burden. Our results establish that NSG+hIL6 mice provide an effective patient derived xenograft model for study and preclinincal drug development for myeloma and related plasma cell disorders.

overall_design: NSG+hIL6 mice were engrafted with primary bone marrow mononuclear cells from a patient with relapsed t(4;14) (MMSET-FGFR3 fusion) IgG lambda multiple myeloma through intraosseous injection of cells into the left femur after prior busulfan conditioning. After 52 weeks, bone marrow was harvested from both femurs and processed through the Parse Biosciences Evercode Fixation and Whole Transcriptome mini kits for library preparation and then submitted to Azenta LifeSciences for paired end illumina sequencing. Two libraries were prepared, one with 10,000 cell input and a second with 5,000 cell input. They were sequenced at equimolar concentrations to allow for deeper sequencing of the 5,000 cell fraction. Raw data was processed through the Parse Biosciences Pipeline using Python R.

first: David

last: Allman


title: ACE2 Enhances Sensitivity to PD-L1 Blockade by Inhibiting Macrophage-Induced Immunosuppression and Angiogenesis

first: Peiyi

last: Xie

overall_design: For ChIP analysis, MHCC97H cells were fixed employing 1% formaldehyde for 30 min, followed by adding 1.25 mol/L glycine for 5 minutes to end the reaction. DNA samples were sonicated in a Biorupter Pico (Diagenode) to acquire nearly 300 bp fragments. Next, the MicroPlex Library Preparation Kit (Diagenode) was employed for library preparation, followed by sequencing through the HiSeq 2000 Illumina platform of the NIG. The quality of the ChIP-seq raw data files were evaluated through FASTQ quality check (FASTQC). FastQ files were evaluated in the public server usegalaxy.org where the sequence reads were aligned to the mouse reference genome (mm9) using Bowtie2 (version 0.4) with default parameters.


title: Transfer learning associates CAFs with EMT and inflammation in tumor cells in human tumors and organoid co-culture in pancreatic ductal adenocarcinoma [Bulk RNA-seq]

summary: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy characterized by an immunosuppressive tumor microenvironment enriched with cancer associated fibroblasts (CAFs). This study provides a convergence approach to identify tumor cell and CAF interactions through the integration of single-cell data from human tumors with human organoid co-culture. Analysis of a comprehensive atlas of PDAC single-cell RNA sequencing (scRNA-seq) data associates CAF density with increased inflammation and epithelial-mesenchymal transition (EMT) in epithelial cells. Transfer learning to transcriptional data from patient-derived organoid and CAF co-cultures provides in silico validation of CAF induction of inflammatory and EMT epithelial cell states. Further experimental validation in co-cultures demonstrates integrin beta 1 (ITGB1) and vascular endothelial factor A (VEGF-A) interactions with Neuropilin-1 (NRP1) mediating CAF and epithelial crosstalk. This study introduces transfer learning from human single-cell data to organoid co-culture for experimental validation of discoveries of cell-cell crosstalk, and identifies fibroblast-mediated regulation of EMT and inflammation.

overall_design:
Patient matched organoids and cancer associated fibroblasts were generated from PDAC surgical speciments gathered at JHU. Samples were cultured in either monoculture or coculture conditions using a matrigel substrate. For bulk-RNA sequencing, samples were FACS sorted based on EPCAM (for organoids) and FAP (for CAFs) expression prior to RNA isolation.
**Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns***

first: Zimmerman

last: Jacquelyn

first: Fertig

last: Elana

first: Tandurella

last: Joseph

first: Guinn

last: Samantha


title: Urinary concentrations of phthalate and phthalate alternative metabolites and sperm DNA methylation: A multi-cohort and meta-analysis of men in preconception studies

city: Detroit

last: Pilsner

state: MI

address: 275 E Hancock St

department: Department of Obstetrics and Gynecology

institute: Wayne State University

summary: Phthalates are ubiquitous pollutants in the environment; however, the mechanisms of phthalate-associated reproductive disorders in men are not fully understood. The aim of this study is to investigate associations between urinary phthalate metabolite concentrations and sperm DNA methylation. The study was conducted on 697 men from three prospective pregnancy cohorts: Longitudinal Investigation of Fertility and the Environment (LIFE) Study, Sperm Environmental Epigenetics and Development Study (SEEDS), and Environment and Reproductive Health (EARTH) Study.

overall_design: Eighteen phthalate and two phthalate alternative metabolites were quantified by mass spectrometry in preconception urinary samples and sperm DNA methylation was measured via Illumina EPIC Array (v1). Regional methylation analyses were conducted to identify cohort-specific loci associated with urinary phthalate metabolites.

first: Karolina

last: Nowak

first: J


title: The miRNA/mRNA regulation by Translin associated factor X (TRAX) in WT and R6/2 HD mice

first: Yijuang

last: Chern

address: 128 Sec. 2, Academia Rd.

department: Institute of Biomedical Sciences

institute: Academia Sinica

type: Non-coding RNA profiling by high throughput sequencing


title: SOD2 promotes gastric tumorigenesis mediated by Helicobacter pylori and enhances resistance to 5-fluorouracil in gastric cancer

first: Yantao

last: Duan

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

summary: Helicobacter pylori (H. pylori) infection is the most common risk factor for gastric cancer (GC). The effect of the antioxidase manganese superoxide dismutase (SOD2) in gastric tumorigenesis remains unclear. We explored the molecular and mechanical links between H. pylori, inflammation, and SOD2 in GC. We found SOD2 was upregulated in GC. GC patients with high SOD2 expression showed worse overall survival. H. pylori infection promoted SOD2 expression by transcriptionally activating the NF-κB signaling pathway. Knockdown of SOD2 led to increased levels of reactive oxygen species and oxidative stress in response to H. pylori infection. Our research demonstrated that SOD2 can serve as an inhibitor of ferroptosis by activating AKT, stabilizing GPX4 protein, which subsequently induces 5-fluorouracil resistance. These findings reveal a mechanism whereby H. pylori can promote gastric carcinogenesis by activating the NF-κB/SOD2/AKT/GPX4 pathway, leading to the inhibition of ferroptosis. This may provide a promising therapeutic target for GC.

overall_design: MGC803 gastric cancer cells co-cultured with or without H. pylori for 6 h (n=3)


title: Non-overlap of tumor acidosis and hypoxia: new rationale to target fatty acid desaturase activity in cancer.

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

summary: A population of cancer cells located in the acidic tumor compartment were shown to exhibit an aggressive phenotype making it very attractive to target them. In this study, an unbiased strategy was used to isolate acidic, non-hypoxic cancer cells from hypoxic (acidic) and non-acidic (non-hypoxic) ones. We used a combination of carbonic anhydrase CA9 antibodies as a marker of acidosis regardless of the pO2 environment and HRE-GFP reporter as a hypoxia marker to isolate distinct cell populations from 3D tumor spheroids. Transcriptomic analysis of sorted CA9-positive but hypoxia-negative cancer cells led us to identify fatty acid (FA) desaturase activity as an enriched pathway in these cells.

overall_design: In this study, an unbiased strategy was used to isolate acidic, non-hypoxic cancer cells from hypoxic (acidic) and non-acidic (non-hypoxic) ones. We used a combination of carbonic anhydrase CA9 antibodies as a marker of acidosis regardless of the pO2 environment and HRE-GFP reporter as a hypoxia marker to isolate (by FACS) distinct cell populations from 3D tumor spheroids.

first: Katarzyna

last: Glowacka

first: Olivier

last: Feron


title: miRNA-seq for WT and R6/2 (HD) mice with Translin-associated protein X (TRAX) knockdown

summary: For the bilateral intrastriatal delivery of AAV expressing control or TRAX shRNA, mice were anesthetized with ketamine/xylazine HCl (87.56 and 7.5 ug/kg, respectively, via an intraperitoneal injection) and injected with the indicated AAV (2 µl per injection spot, 2.5*10^9 vector genome/µl) with a 10 ml syringe (Hamilton, Reno, NV, USA) at a rate of 0.5 ul/min. The AAV was injected at the desired position: AP+0.5, L±2, DV-2.5 and -3.5 mm relative to bregma and the dura surface. Then the mouse brains were removed from the mice directly for dissection of striatum. RNA was extracted by TRIzol reagent or miRNeasy mini kit (Qiagen). DNase digestion was performed by the DNA-free™ Kit (Life Technologies, Carlsbad, CA, USA) or the RNase-free DNase set (Qiagen) following the manufacturer’s instructions. The concentration and purity of RNA were measured at 260, 280 and 230 nm by a NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA). Sample libraries were prepared using the QIAseq miRNA Library Kit (QIAGEN) according to the manufacturer's protocols. Adaptors are ligated sequentially to the 3' and 5' ends of miRNAs. Subsequently, universal cDNA synthesis with UMI assignment, cDNA cleanup, library amplification and library cleanup are performed. Libraries were sequenced on an Illumina instrument (75-cycle single-end read, 75SE). Sequencing data was processed using the Illumina software BCL2FASTQ v2.20. Initially, the sequences generated went through a filtering process to obtain qualified reads. Trimmomatic (1) was implemented to clip the 3′ adaptor sequence, trim or remove the reads according to the quality score and discard trimmed reads shorter than 18 nucleotides. Qualified reads after filtering low-quality data were analyzed using miRDeep2 (2) for aligning reads to the reference genome downloaded from UCSC. Only reads that mapped perfectly to the genome five or less times were used for miRNA detection, since miRNAs usually map to few genomic locations. MiRDeep2 estimates expression levels of known miRNAs, and also identifies novel miRNAs. The small RNA library construction, NGS deep sequencing and bioinformatic analysis were accomplished by Welgene Biotech. Co., Ltd. (Taipei, ROC).

overall_design: Striatal miRNA profiles of 10.5-weeks-old wild type (WT) and R6/2 (HD) mice injected with AAV harboring control (WT-C and R6/2-C) or shTRAX (WT-T and R6/2-T) as indicated into the striatum at 5 weeks of age.

first: Yu

last: Weng


title: Obesity facilitated colon cancer progression is mediated by increased diacylglycerol o-acyltransferases 1 and 2 (DGAT1/2) levels

first: Suzana

last: Savkovic

overall_design: CUT&RUN: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for binding sites of Myc in human HT29 colon cancer cells stimulated by Oleic Acid

first: Jenisha

last: Ghimire

first: Morgan

last: Collins

first: Patricia

last: Snarski

first: Angelle

last: King

first: Emmanuelle

last: Ruiz

first: Rida

last: Iftikhar

first: Harrison

last: Penrose

first: Krzysztof

last: Moroz

first: Tyler

last: Rorison

first: Melody

last: Baddoo

first: Muhammad Anas

last: Naeem

first: Arnold

last: Zea

first: Scott

last: Magness

first: Erik

last: Flemington

first: Susan

last: Crawford


title: RNA sequencing of distinct histologic regions of primary human hepatoblastomas by Smart-3SEQ

status: Public on Oct 13 2024

city: Cincinnati

first: Peng

middle: Vijaykumar

last: Wu

state: OH

address: 3333 Burnet Ave., MLC7013

institute: Cincinnati Children's Hospital Medical Center

summary: To characterize histology-based transcriptional heterogeneity of human hepatoblastoma, Smart-3SEQ was used to perform RNA sequencing of distinct histologic regions isolated by laser capture microdissection from formalin-fixed paraffin-embedded primary human hepatoblastoma specimens.

overall_design: RNA sequencing was performed on 74 distinct histologic regions isolated by laser capture microdissection from 17 FFPE primary human hepatoblastoma specimens

first: Chunfang

last: Zhu

first: Sujay

last: Vennam

first: Robert

last: West

first: Roel

last: Nusse


title: Transfer learning associates CAFs with EMT and inflammation in tumor cells in human tumors and organoid co-culture in pancreatic ductal adenocarcinoma [MULTIseq]

first: Jacquelyn

last: Zimmerman

overall_design:
Patient matched organoids and cancer associated fibroblasts were generated from PDAC surgical speciments gathered at JHU. Samples were cultured in either monoculture or coculture conditions using a matrigel substrate. For single cell sequencing, samples were underwent the MULTIseq pipeline to multiplex barcodes. Deposited are samples cocultured for 12HR.

***************************************************************
Submitter states that missing raw data are being made available for controlled access in dbGaP.
***************************************************************

first: Elana

last: Fertig

first: Joseph

last: Tandurella

first: Samantha

last: Guinn


title: Roles of H2A.Z histone variant isoforms during enterocyte-like differentiation process

city: TOULOUSE

first: Didier

last: Trouche

address: Université Toulouse III Paul Sabatier - Bât 4R4, 118 route de Narbonne

country: France

institute: Centre for Integrative Biology (CBI) of Toulouse MCD

summary:
The histone variant H2A.Z plays important functions in the regulation of gene expression. In mammals,
it is encoded by two genes, giving rise to two highly related isoforms named H2A.Z.1 and H2A.Z.2,
which can have similar or antagonistic functions depending on the promoter. Knowledge of the physiopathological
consequences of such functions emerges, but how the balance between these isoforms
regulates tissue homeostasis is not fully understood. Here, we investigated the relative role of H2A.Z
isoforms in intestinal epithelial homeostasis. Through genome-wide analysis of H2A.Z genomic localization
in differentiating Caco-2 cells, we uncovered an enrichment of H2A.Z isoforms on the bodies of
genes which are induced during enterocyte differentiation, stressing the potential importance of H2A.Z
isoforms dynamics in this process. Through a combination of in vitro and in vivo experiments, we further
demonstrated the two isoforms cooperate for stem and progenitor cells proliferation, as well as
for secretory lineage differentiation. However, we found that they antagonistically regulate enterocyte
differentiation, with H2A.Z.1 preventing terminal differentiation and H2A.Z.2 favoring it. Altogether,
these data indicate that H2A.Z isoforms are critical regulators of intestine homeostasis and may provide
a paradigm of how the balance between two isoforms of the same chromatin structural protein can
control physiopathological processes.

overall_design:
ChIP-seq : Samples were prepared in duplicates from subconfluent (Sc) or 7 days post-confluent (Pc) populations of Caco-2/15 cells expressing flagged version of H2A.Z.1 or H2A.Z.2 isoform.
ChIP-seq reads were aligned to hg38 human genome using BWA and processed (sorting, PCR duplicates, minimum quality of 25 and indexing). BigWig were obtained using Deeptools with exactScaling parameters and CPM normalization. Peaks were called uing MACS with the significance cut-off q-value <=0.001

RNA-seq : Samples were prepared in duplicates from subconfluent (Sc) or 7 days post-confluent (Pc) populations of Caco-2/15 cells expressing flagged version of H2A.Z.1 or H2A.Z.2 isoform. The quality of each raw sequencing file (fastq) was checked with FastQC. Stranded paired-end reads were mapped to human rDNA genome and unmapped reads were aligned on hg38 using STAR (v2.5.2b) and processed using samtools keeping only primary alignement. Raw reads count were obtained using HT-seq.

first: Jérémie

last: RISPAL

first: Virginie

last: JOUFFRET

first: Fabrice

last: ESCAFFIT

last: TROUCHE


title: RNA-seq for WT and R6/2 (HD) mice with Translin-associated protein X (TRAX) knockdown

first: Yijuang

last: Chern

summary: For the bilateral intrastriatal delivery of AAV expressing control or TRAX shRNA, mice were anesthetized with ketamine/xylazine HCl (87.56 and 7.5 ug/kg, respectively, via an intraperitoneal injection) and injected with the indicated AAV (2 µl per injection spot, 2.5*10^9 vector genome/µl) with a 10 ml syringe (Hamilton, Reno, NV, USA) at a rate of 0.5 ul/min. The AAV was injected at the desired position: AP+0.5, L±2, DV-2.5 and -3.5 mm relative to bregma and the dura surface. Then the mouse brains were removed from the mice directly for dissection of striatum. RNA was extracted by TRIzol reagent or miRNeasy mini kit (Qiagen). DNase digestion was performed by the DNA-free™ Kit (Life Technologies, Carlsbad, CA, USA) or the RNase-free DNase set (Qiagen) following the manufacturer’s instructions. The concentration and purity of RNA were measured at 260, 280 and 230 nm by a NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA). RNA was qualified by a Bioanalyzer 2100 (Agilent Technology, Santa Clara, CA, USA) with an RNA 6000 LabChip kit (Agilent Technology). For mRNA, the RNA was prepared based on Illumina’s official protocol. Library construction was carried out by TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, San Diego, CA, USA) followed by AMPure XP beads (Beckman Coulter, Brea, CA, USA) size selection. Libraries were sequenced using sequencing-by-synthesis (SBS) technology (Illumina). Sequencing data and FASTQ reads were generated using an inhouse Welgene ’Biotech pipeline according to Illumina’s base calling program bcl2fastq v2.20.

overall_design: Striatal mRNA profiles of 10.5-weeks-old wild type (WT) and R6/2 (HD) mice injected with AAV harboring control (WT-C and R6/2-C) or shTRAX (WT-T and R6/2-T) as indicated into the striatum at 5 weeks of age.

first: Yu

last: Weng


title: CRISPR screens unveil nutrient-dependent lysosomal and mitochondrial nodes impacting intestinal tissue-resident memory CD8+ T cell formation

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital


title: The diagnostic and prognostic value of pulmonary virome and its host response for ARDS

city: Guangzhou

first: Bingxue

last: Hu

state: China Mainland (PRC)

address: Guangzhou 510700

institute: Vision MedicalsCo., Ltd.

summary: This study aims to explore the relationship between the respiratory virome, specifically bacteriophages, HERV and the host response in ARDS and to assess their value in predicting the prognosis of ARDS.

overall_design: To discover the role of the respiratory virome in ARDS diagnosis and prognosis prediction, identifying the associated host response pathways.

first: Zhenju

last: Song

first: Yi

last: han

first: Bin

last: Yang


title: Transcriptomic profiling of LLC LeptoM vector control, Nr1h2/3 DKO and RXRa/b/g TKO upon stimulation with 1μM 9 cis-retinoic acid (RA) in vitro

city: New York

first: Xinran

last: Tong

state: NY

address: 417 E 68th St

department: HOPP

institute: MSKCC

summary: To understand transcriptional regulation of nuclear receptors, LXRs and RXRs, in leptomeningeal metastatic cancer cells, we use CRISPR-Cas9 to knockout Nr1h2/3 genes (encoding LXRβ/α) or RXRa/b/g genes (encoding RXRα/β/γ) in LLC LeptoM cell lines, with small guide RNA targeting lacZ as vector control. We then subjected these cell lines for bulk RNA sequencing with or without stimulation of 1μM 9 cis-RA. Pathway analysis of the differentially expressed genes between LLC LeptoM vector control with RA stimulation to DMSO treatment revealed upregulation of developmental related pathways and lipid metabolism pathways. Meanwhile, loss of function in LXR or RXR both resulted in dysregulation of multiple lipid metabolism pathways, in which RXR made a broader impact.

overall_design: LLC LeptoM vector control, Nr1h2/3 DKO and RXRa/b/g TKO were seeded into 6 well plates and added either DMSO or 1μM 9 cis-RA one day after seeding. After treatment for 48hrs, cells were harvested with RNA lysis buffer and further processing for sequencing. This experiment has two to three biological replicates different rounds of collection.

first: Adrienne

last: Boire


title: Chromatin accessibility profiling of freshly isolated mouse lung cancer LLC- and breast cancer 4T1- derived leptomeningeal metastatic cancer cells from different anatomical locations [ATAC-Seq]

summary: Cancer cells metastatic to the leptomeninges encounter a metabolically-challenging extreme microenvironment. To understand adaptations to this space, we subjected leptomeningeal-metastatic (LeptoM) mouse breast and lung cancers isolated from either the leptomeninges or orthotopic primary sites to ATAC- and RNA-sequencing. When inhabiting the leptomeninges, the LeptoM cells demonstrated transcription downstream of retinoid-X-receptors (RXRs). We found evidence of local retinoic acid (RA) generation in both human leptomeningeal metastasis and mouse models in the form of elevated spinal fluid retinol and expression of RA-generating dehydrogenases within the leptomeningeal microenvironment. Stimulating LeptoM cells with 9-cis RA induced expression of transcripts encoding de novo fatty acid synthesis pathway enzymes in vitro. In vivo, whereas knockout of Stra6 did not alter cancer cell leptomeningeal growth, knockout of Rxra/b/g interrupted cancer cell lipid biosynthesis and arrested cancer growth. These observations illustrate a mechanism whereby locally-generated developmental cues metabolically reprogram metastatic cancer cells and suggest novel therapeutic approaches.

overall_design: We harvested LLC and 4T1 LeptoM cells from mouse leptomeningeal space, separating the CSF free-floating (floating) and pia mater-attached (adherent), or from orthotopic mouse lung (lung) or mammary fat pad (mfp). All cells were treated with the same enzymatic cocktail and prepared for flow cytometry-based sorting with fluorescent marker. Chromatin accessibilities were profiled by ATAC-sequencing.

first: Richard

last: Koche

first: Pierre-Jacques

last: Hamard


title: Transcriptomic profiling of freshly isolated mouse lung cancer LLC- and mouse breast cancer 4T1- derived leptomeningeal metastatic cancer cells from different anatomical locations [RNA-Seq]

overall_design: We harvested LLC and 4T1 LeptoM cells from mouse leptomeningeal space, separating the CSF free-floating (floating) and pia mater-attached (adherent), or from orthotopic mouse lung (lung) or mammary fat pad (mfp). All cells were treated with the same enzymatic cocktail and prepared for flow cytometry-based sorting with fluorescent marker. Differential gene expressions were calculated for each two groups, with a focus on the commonly changed genes from the cells residing in the leptomeningeal space to the orthotopic site.


title: Cavefish

city: Tallahassee

first: Evan

last: Lloyd

state: FL

address: 107 Chieftain Way

institute: Florida State University

overall_design: Refer to individual Series


title: Genome-wide Identification of Lipoxygenases in Luffa aegyptiaca and Functional Characterization in Response to Abiotic Stress

city: Hangzhou

first: lianyu

last: lin

state: Zhejiang

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.866

institute: Zhejiang University

summary: RNA-seq of four Luffa aegyptiaca samples in response to heat stress

overall_design: Total RNA was extracted from selected tissues using a plant-specific RNA extraction kit, ensuring minimal degradation and contamination.

first: Huang

last: Hao

first: Haisheng

last: Zhu

first: Lianyu

last: Lin


title: Profiling of freshly isolated mouse lung cancer LLC- and mouse breast cancer 4T1- derived leptomeningeal metastatic cancer cells from different anatomical locations


title: Aging is associated with a modality-specific decline in taste

summary: Deficits in chemosensory processing are associated with healthy aging, as well as numerous neurodegenerative disorders, including Alzheimer’s Disease (AD). In many cases, chemosensory deficits are harbingers of neurodegenerative disease, and understanding the mechanistic basis for these changes may provide insight into the fundamental dysfunction associated with aging and neurodegeneration. The fruit fly, Drosophila melanogaster, is a powerful model for studying chemosensation, aging, and aging-related pathologies, yet the effects of aging and neurodegeneration on chemosensation remain largely unexplored in this model, particularly with respect to taste. To determine whether the effects of aging on taste are conserved in flies, we compared the response of flies to different appetitive tastants. Aging impaired response to sugars, but not medium-chain fatty acids that are sensed by a shared population of neurons, revealing modality-specific deficits in taste. Selective expression of the human amyloid beta (Ab) 1-42 peptide bearing the Arctic mutation (E693E) associated with early onset AD in the neurons that sense sugars and fatty acids phenocopies the effects of aging, suggesting that the age-related decline in response is localized to gustatory neurons. Functional imaging of gustatory axon terminals revealed reduced response to sugar, but not fatty acids. Axonal innervation of the fly taste center was largely intact in aged flies, suggesting that reduced sucrose response does not derive from neurodegeneration. Conversely, expression of the amyloid peptide in sweet-sensing taste neurons resulted in reduced innervation of the primary fly taste center. A comparison of transcript expression within the sugar-sensing taste neurons revealed age-related changes in 66 genes, including a reduction in odorant-binding protein class genes that are also expressed in taste sensilla. Together, these findings suggest that deficits in taste detection may result from signaling pathway-specific changes, while different mechanisms underly taste deficits in aged and AD model flies. Overall, this work provides a model to examine cellular deficits in neural function associated with aging and AD.

overall_design: Labella of female drosophila were pooled in groups of xx and analyzed by scRNASeq

first: Alex

middle: C

last: Keene

first: Elizabeth

last: Brown


title: Transcriptomic profiling of the oocyte-cumulus-granulosa cell complex from estrogen receptor beta knockout mice

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

summary: Objective: To study the role of estrogen receptor beta in follicle development and maturation and in the response to gonadotropin stimulation aiming at superovulation.  Animals: Healthy wild-type and estrogen receptor beta (ERβ) knockout female mice aged 4 weeks, 7 weeks, and 6 months. analysis. Main Outcomes: Oocyte yield after superovulation, transcriptomic profiling of cumulus cells and oocytes and immunohistochemical analyses. Results: Superovulation of ERβ knockout (Esr2-KO) mice results in reduced oocyte yield at 6-months of age compared to wild-type (WT) mice. RNA-seq analysis of cumulus cells from superovulated WT and Esr2-KO mice identified genes and pathways associated with among others adhesion, proliferation, Wnt-signaling, and placed ERβ in bipotential granulosa cell cluster. Loss of ERβ increased expression of the other estrogen receptors Esr1 and Gper1. Conclusion: Our results show that ERβ has an important role in regulating ovulation in response to exogenous gonadotropins in 6-month-old mice, but not in younger mice. Our transcriptomic and immunohistochemical observations suggest a dysregulation of the granulosa cell communication and lack of tight coordination between granulosa cell replication and antrum expansion. A significant upregulation of other estrogen receptors supports a compensatory mechanism sustaining fertility during younger age in Esr2-KO mice.

overall_design: Experimental study and transcriptomics analyses

first: Nageswara


title: The effects of CD4 T cell Nr4a family on NASH progression (RNA-Seq)

city: Shinjuku

first: Daisuke

last: Aki

state: Tokyo

department: School of Medicine

country: Japan

institute: Keio University

summary: NASH is characterized by hepatic steatosis, inflammation, fibrosis and liver damage, which eventually results in liver dysfunction due to cirrhosis or hepatocellular carcinoma. However, the cellular and molecular mechanisms underlying NASH progression remain largely unknown. In this study, we aimed to elucidate the impact of  Nr4a family in CD4 T cells in NASH development.

overall_design: Total RNA was extracted from sorted hepatic CD4 T cells of WT or T cell specifc Nr4a1/2 deficient mice fed a choline deficient, high-fat diet consisting of 60 kcal% fat and 0.1% methionine diet. We performed gene expression profiling analysis using data obtained from the cells (n=3 per group).

first: Akihiko

last: Yoshimura


title: The role of EPSCs and nPSCs heterogeniety and transcriptomic composition in Blastoid formation.

city: Thuwal

first: Ali

last: Balubaid

address: Technology drive

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: human naïve pluripotent stem cells and extended potential stem cells were both used to form blastoid models. We used scRNAseq to investigate the biases founding cell lines have on the formed models.

overall_design: iPSCs cultured two different media conditiones (PXGL, EPS) were sequenced.

first: Samhan

last: Alsolami


title: The effects of CD4 T cell Nr4a family on NASH progression

overall_design: Hepatic CD4 T cells from WT or T cell specifc Nr4a1/2 deficient mice fed a choline deficient, high-fat diet consisting of 60 kcal% fat and 0.1% methionine diet were sorted. We performed gene expression profiling analysis using data obtained from the pooled cells (n=2 per group).

first: Taeko

last: Hayakawa


title: Effects of aging on gene expression in multiple tissues in surface and cave Astyanax mexicanus

summary: Dysregulation of sleep has widespread health consequences and represents an enormous health burden. Short-sleeping individuals are predisposed to the effects of neurodegeneration, suggesting a critical role for sleep in the maintenance of neuronal health. While the effects of sleep on cellular function are not completely understood, growing evidence has identified an association between sleep loss and DNA damage, raising the possibility that sleep facilitates efficient DNA repair. The Mexican tetra fish, Astyanax mexicanus provides a model to investigate the evolutionary basis for changes in sleep and the consequences of sleep loss. Multiple cave-adapted populations of these fish have evolved to sleep for substantially less time compared to surface populations of the same species without identifiable impacts on healthspan or longevity. To investigate whether the evolved sleep loss is associated with DNA damage and aging, we compared the transcriptional response to aging between surface and cave morphs of A. mexicanus

overall_design: To investigate differences in the transcriptional response to aging, we dissected the whole brain, liver, heart, gut, and a portion of muscle, from young (~1 year) and aged (7-8 year) surface and cave fish, extracted the RNA from each sample, and performed gene expression analysis.

first: Lloyd

last: Evan

first: Xia

last: Fanning

first: Moore

last: Kinsley

first: Zertuche

last: Carolina

first: Rastogi

last: Aakriti

first: Kozol

last: Rob

first: Kenzior

last: Olga

first: Warren

last: Wesley

first: Appelbaum

last: Lior

first: Moran

last: Rachel L.

first: Zhao

last: Chongbei

first: Duboue

last: Erik

first: Rohner

last: Nicholas

first: Keene

last: Alex C.


title: Identification of exosome-like nanovesicle (ENV) associated miRNAs in edible plants

city: Mysore

first: Gopinath

last: Meenakshisundaram

state: Karnataka

address: Cheluvamba Mansion

department: Molecular Nutrition

country: India

institute: Central Food Technological Research Institute

summary: MicroRNAs (miRNAs) are small non-coding RNAs between 18-23nts in size which regulate the translation and stability of target mRNAs. miRNAs are present in dietary plants and are conventionally thought to be degraded during the gastrointestinal digestion process. Recent reports suggest that a few dietary microRNAs may exhibit resistance to this process, enter systemic circulation and exert biological effects on animal physiology, currently known as cross-kingdom regulation. However, such horizontal transfer of miRNAs via different kingdoms is highly likely for miRNAs that are present intrinsic extracellular vesicles which increases their bioavailability. These vesicular structures from plants are known as Exosome-like nanovesicles (ENV). ENVs have been isolated from several edible plants. ENV-derived miRNAs are probably more bioavailable and are spontaneously absorbed in intestinal epithelium to suppress target transcripts in human/microbial/viral kingdoms. Such cross-kingdom regulation exhibited by ENV-miRNAs, if properly investigated and validated, may aid in the development of non-toxic and cost-effective therapeutics to treat human diseases. In this line, we purified ENVs from four edible plants (Soy bean, ginger, amla and turmeric). Small RNA population from these ENVs were isolated and profiled through small RNA sequencing to identify ENV-associated miRNAs enriched in each species.

sample_organism:
Glycine max
Allium sativum
Curcuma longa
Emblica officinalis

overall_design: To identify the miRNAs enriched in edible plant ENVs from Soybean, ginger, amla and turmeric, plant samples were procured from local markets. Each plant material was procured from two different sources and used as biological replicates. ENVs were purified under identical conditions from these plants by differential centrifugation followed by poly ethylene glycol precipitation. After isolation of total RNA from the ENVs, microRNAs were identified by small RNA sequencing.

first: Sreeram

middle: P

last: Kalarikkal

first: Meghana

last: Kumar


title: Effects of UV-B radiation on whole-body gene expression of surface and cave Astyanax mexicanus

first: Evan

last: Lloyd

summary: Dysregulation of sleep has widespread health consequences and represents an enormous health burden. Short-sleeping individuals are predisposed to the effects of neurodegeneration, suggesting a critical role for sleep in the maintenance of neuronal health. While the effects of sleep on cellular function are not completely understood, growing evidence has identified an association between sleep loss and DNA damage, raising the possibility that sleep facilitates efficient DNA repair. The Mexican tetra fish, Astyanax mexicanus provides a model to investigate the evolutionary basis for changes in sleep and the consequences of sleep loss. Multiple cave-adapted populations of these fish have evolved to sleep for substantially less time compared to surface populations of the same species without identifiable impacts on healthspan or longevity. To investigate whether the evolved sleep loss is associated with DNA damage and cellular stress, we compared the DNA Damage Response (DDR) between A. mexicanus populations.

overall_design: To investigate differences in the DNA damage response, we subjected surface and cave larvae, at 6 days post-fertilization, to 60 seconds of UV-B radiation, or 60 seconds of white light as control. We then pooled individuals in groups of 4, extracted the RNA from each pooled sample, and performed gene expression analysis.

first: Fanning

last: Xia

first: Kinsley

last: Moore

first: Carolina

last: Zertuche

first: Aakriti

last: Rastogi

first: Rob

last: Kozol

first: Olga

last: Kenzior

first: Wesley

last: Warren

first: Lior

last: Appelbaum

first: Rachel

last: Moran

first: Chongbei

last: Zhao

first: Erik

last: Duboue

first: Rhoner

first: Alex

last: Keene


title: The inhibitory effect of ZSCAN18 on proliferation in gastric cancer cells

city: tianjin

first: ren

middle: bao

last: qing

state: hexi

address: huanhu west road

institute: Cancer Hospital affiliated to Tianjin Medical University

summary:
Background: Zinc finger and scan domain containing 18 (ZSCAN18) belongs to zinc finger transcription factor superfamily, which consists of the hundreds of members that play critical roles in all steps of tumorigenesis. Although hypermethylation of ZSCAN18 promoter and its consequent deficiency in a variety of malignancies has been reported recently, its functions and mechanisms in the initiation and progression of gastric cancer (GC) are not clear. This study aims to investigate the roles of ZSCAN18 in gastric carcinogenesis.
Methods: Methylation of ZSCAN18 promoter in GC cell lines were analyzed via MassARRAY and treatment of 5-Aza-2'-deoxycytidine. Bioinformatics analysis, qRT-PCR, western blot, immunohistochemistry, CCK-8, colony formation, and in vivo xenograft tumor model were used to examine the expression and function of ZSCAN18. Survival analysis was performed to determine the correlation between ZSCAN18 expression and prognosis of patients with GC. Genes modulated by ZSCAN18 in NCI-N87 cells were identified through RNA next generation sequence screening and further verified by qRT-PCR in AGS and NCI-N87 cells.
Results: ZSCAN18 expression was markedly reduced in GC tissues as compared with that in adjacent normal tissues due to hypermethylation in GC. Likewise, ZSCAN18 expression was also significantly reduced in a panel of GC cell lines as the result of densely methylated ZSCAN18 promoter. Forced expression of ZSCAN18 inhibited proliferation in AGS and NCI-N87 cells in vitro. Additionally, ZSCAN18 impaired growth of NCI-N87 cells in immunodeficient mice. Survival analysis showed that ZSCAN18 expression was positively associated with favorable outcome in patients with GC. RNA next generation sequence screening showed three representative genes (FGF20, CEACAM5 and TP53INP2) involved in downstream signaling pathways modulated by ZSCAN18.
Conclusions: Collectively, this study unveils the anti-cancer role of ZSCAN18 in GC, providing a promising diagnostic and therapeutic target.

overall_design: The mRNA levels of NCI-N87 cells overexpressing ZSCAN18 and empty vector were analyzed by RNA sequencing

first: Ren

middle: b

first: Li

last: Bin

first: Deng

middle: j

last: yu

first: Ma

last: gang


title: Honokiol attenuates oxidative stress and vascular calcification in chronic kidney disease via the upregulation of heme oxygenase-1

status: Public on Oct 12 2024

first: Xuemin

last: Xian

address: 253 Industrial Avenue

institute: Zhujiang Hospital, Southern Medical University

summary: In this study, we repoort the protective effect of ursolic HONOKIOL (HKL) on vascular calcification in chronic kidney disease. To elucidate the molecular mechanism underlying the anti-vascular calcification effect of HKL, we performed RNA-seq to identify the gene expresion under HKL treatmment.

overall_design: Human vasculr smooth muscle cells were cultured in calcifying medium in the presence or absence of HKL for 48 hours. RNA-seq was performed to determine the downstream target of HKL. The gene expression level was calculated using the Fragment Per Kilobase of Million mapped reads (FPKM) methods. Differential expression was assessed using the DEGseq packages.

first: Xiuli

last: Zhang


title: Autoimmune CD4 T cells maintain function and survive in chronic autoimmunity by restricting terminal differentiation (NOD)

city: Salt Lake City

first: Maria

last: Bettini

state: Utah

address: University of Utah

department: Pathology

institute: University of Utah

summary: The mechanisms behind survival of autoimmune CD4 T cells during chronic stimulation are unclear. Examining early time-points during T cell priming showed that activation of autoimmune CD4 T cells in the absence of infectious signals allowed maintenance of TCF1 expression, albeit at reduced levels. Tcf7 locus was epigenetically modified in circulating autoimmune CD4 T cells, suggesting a pre-programmed de novo methylation of the locus in early stages of autoimmune CD4 T cell differentiation which mirrored the epigenetic profile of recently recruited CD4 CD62L+ T cells in the tissue.  Collectively, the data presented here show that the unique environment during autoimmune CD4 T cell priming allows T cells to finetune TCF1 expression to maintain long-term survival and function.

overall_design: Single cell ATACseq/RNAseq analysis was performed using 10X Multiome kit. TCR+ cells were sorted from non-draining lymph nodes and pancreatic islets of two 10-week-old NOD female mice

first: Nouf

last: Aljobaily

first: Denise

last: Allard

first: Bryant

last: Perkins

first: Arielle

last: Raugh

first: Tessa

last: Galland

first: Yi

last: Jing

first: W. Zac

last: Stephens

first: Matthew

first: J. Scott

last: Hale


title: Autoimmune CD4 T cells maintain function and survive in chronic autoimmunity by restricting terminal differentiation

overall_design: pancreatic islets, spleen+non-draining lymph nodes were harvested from BDC2.5 transferred cells into congenically labelled NOD mice. BDC2.5 CD4+Vb4 cells were sorted and subjected to 10X multiome scATAC/Gene expression sequncing


title: COM33 reverses the expression of carboplatin-induced EMT and ERK signaling in SKOV3 cells

city: Wenzhou

first: Jie-Xue

last: Pan

address: Nanbaixiang Street, Ouhai District

department: Reproductive Medicine Center

institute: The First Affiliated Hospital of Wenzhou Medical University

summary: The SKOV3 cells were treated with carboplatin or a combination of carboplatin and COM33 for 48h. The cells were lysed by TRIzol and total RNA was used for library construction. After cluster generation, the library preparations were sequenced on an Illumina HiSeq 4000 platform by Shanghai Life Genes Biotech Co. Ltd (Shanghai, China), and 150 bp paired-end reads were generated. After processing, filtering and checking quality, differentially expressed genes (DEGs) were screened using the following criteria: P < 0.05 and absolute log2 (fold change) > 1.0.

overall_design: To elucidate the underlying mechanisms of COM33 in increasing carboplatin sensitivity, we performed RNA-seq analysis using SKOV3 cells.

first: Jiexue

first: Zhiyang

last: Zhou


title: RNA Infrastructure Profiling Illuminates Transcriptome Structure in Crowded Spaces

city: Stanford

first: Lu

last: Xiao

state: California

address: 369 N-S Axis, Stauffer I, 109

institute: Stanford University

summary: The cellular function of RNA is intimately linked to its structure. The 3D structure of RNA is intricate and compact, and is often complexed with other macromolecules for regulatory interaction. These interactions frequently lead to occluded environments that block structure probing by current reagents. Our RNA infrastructure profiling method (RISP) quantitatively compares standard acylation probes to new small-sized probes, and reveals ca. 80% more structural data for intracellular RNAs underlying protein contacts. Comparative analysis also reveals information about close contacts in ribonucleoprotein complexes such as small nuclear RNAs in the spliceosome. In addition, RISP analysis with small agent AcIm reveals pronounced signals for m6A methylation sites of RNAs in their native cellular setting, even in crowded environments.

overall_design: The sequencing experiments were performed in two biological replicates. Comparative analysis of deep sequencing data using our RBRP popeline with certain adjustment identifies structure information in crowded space.

first: Eric

last: Kool


title: Effect of metronidazole on microglial gene expression and gut microbiome composition in the 5XFAD mice model of Alzheimer's disease

city: Boston

first: Caroline

last: Wasen

state: MA

address: 60 Fenwood rd

institute: Harvard Medical School

summary: The gut microbiota and innate immune system play critical roles in Alzheimer’s disease (AD). Bacteroides is elevated in AD patients and correlates with cerebrospinal fluid levels of Aβ and tau. We found that increased amyloid-β (Aβ) plaques in Bacteroides fragilis treated APP/PS1-21 mice were associated with altered cortical expression Aβ processing genes. B. fragilis suppressed peripheral CD4+ T cell production of GM-CSF and IL-4 and transcriptional changes in microglia related to GM-CSF and IL-4 signaling, phagocytosis, and protein degradation. Furthermore, B. fragilis impaired the microglial uptake of intracranially injected Aβ42, whereas Erysipelotrichaceae strains increased uptake. Depleting murine Bacteroidetes with metronidazole decreased amyloid load in aged 5xFAD mice, increased CD4+ T cell GM-CSF production, and activated microglial pathways related to cytokine signaling, phagocytosis and lysosomal degradation. These data suggest that the gut microbiome may contribute to AD pathogenesis by suppressing peripheral cytokines and microglia phagocytic function, leading to impaired immune-mediated Aβ clearance.

overall_design: 5xFAD and wildtype mice received either normal drinking water (H2O) or drinking water supplemented with metronidazole (MTZ) starting at 9 months of age. The first 7 days, the mice received 200 mg/mL metronidazole in their drinking water followed by a dose of 40 mg/mL for an additional 9 weeks.

last: Wasén

first: Julia

last: Vincentini

first: Christian

last: Gauthier

first: Juliana

last: Lopes

first: Oleg

last: Butowsky

first: Laura

last: Cox

first: Howard

last: Weiner


title: Autoimmune CD4 T cells maintain function and survive in chronic autoimmunity by restricting terminal differentiation (whole genome enzymatic methylation sequencing)

first: Maria

last: Bettini

type: Methylation profiling by high throughput sequencing

overall_design: ndLN and pancreatic islets were subjected to whole genome enzymatic methylation sequencing

first: Nouf

last: Aljobaily

first: Denise

last: Allard

first: Bryant

last: Perkins

first: Arielle

last: Raugh

first: Tessa


title: Elevated DNA Damage without signs of aging in the short-sleeping Mexican Cavefish

first: Evan

last: Lloyd

summary: Dysregulation of sleep has widespread health consequences and represents an enormous health burden. Short-sleeping individuals are predisposed to the effects of neurodegeneration, suggesting a critical role for sleep in the maintenance of neuronal health. While the effects of sleep on cellular function are not completely understood, growing evidence has identified an association between sleep loss and DNA damage, raising the possibility that sleep facilitates efficient DNA repair. The Mexican tetra fish,Astyanax mexicanusprovides a model to investigate the evolutionary basis for changes in sleep and the consequences of sleep loss. Multiple cave-adapted populations of these fish have evolved to sleep for substantially less time compared to surface populations of the same species without identifiable impacts on healthspan or longevity. To investigate whether the evolved sleep loss is associated with DNA damage and cellular stress, we compared the DNA Damage Response (DDR) and oxidative stress levels betweenA. mexicanuspopulations. We measured markers of chronic sleep loss and discovered elevated levels of the DNA damage marker γH2AX in the brain, and increased oxidative stress in the gut of cavefish, consistent with chronic sleep deprivation. Notably, we found that acute UV-induced DNA damage elicited an increase in sleep in surface fish but not in cavefish. On a transcriptional level, only the surface fish activated the photoreactivation repair pathway following UV damage. These findings suggest a reduction of the DDR in cavefish compared to surface fish that coincides with elevated DNA damage in cavefish. To examine DDR pathways at a cellular level, we created an embryonic fibroblast cell line from the two populations ofA. mexicanus. We observed that both the DDR and DNA repair were diminished in the cavefish cells, corroborating thein vivofindings and suggesting that the acute response to DNA damage is lost in cavefish. To investigate the long-term impact of these changes, we compared the transcriptome in the brain and gut of aged surface fish and cavefish. Strikingly, many genes that are differentially expressed between young and old surface fish do not transcriptionally vary by age in cavefish. Taken together, these findings suggest that have developed resilience to sleep loss, despite possessing cellular hallmarks of chronic sleep deprivation.

overall_design: To characterize the transcriptomic profiles of surface fish embryonic fibroblast cells (SEF) and Pachón embryonic fibroblast cells (PEF), we generated bulk RNA sequencing data from 3 replicates from similar cell passage numbers.

first: Fanning

last: Xia

first: Kinsley

last: Moore

first: Carolina

last: Zertuche

first: Aakriti

last: Rastogi

first: Rob

last: Kozol

first: Olga

last: Kenzior

first: Wesley

last: Warren

first: Lior

last: Appelbaum

first: Rachel

last: L Moran

first: Chongbei

last: Zhao

first: Erik

last: Duboue

first: Nicolas

last: Rohner

first: Alex

last: C Keene


title: Effect of EphrinB2 on gene expression in cultured lymphatic endothelial cells (LECs) under hypoxia

status: Public on Oct 11 2024

city: Shanghai

first: Liming

last: Chen

state: Shanghai

address: 180 Fenglin Road, Xuhui District

institute: Zhongshan Hospital, Fudan University

summary: EphrinB2 (erythropoietin-producing hepatoma interactor B2) is a key member of the Eph/ephrin family, promoting angiogenesis, vasculogenesis, and lymphangiogenesis during embryonic development. However, the role of EphrinB2 in cardiac lymphangiogenesis following myocardial infarction (MI) and the potential molecular mechanism remains to be demonstrated.

overall_design:
To investigate the effect of EphrinB2 on LECs under hypoxia, we overexpressed EphrinB2 in vitro by adenoviral vectors

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first: Yingnan

last: Bai

first: Fanghao

last: Guo

first: Shijun

last: Wang

first: Yunzeng

last: Zou

first: Junbo

last: Ge


title: Trans-generational adaptation to maternal climate through hormone transport in plants [bulk RNA-seq]

city: Norwich

first: William

last: Bezodis

address: Norwich Research Park, Colney Lane

department: Crop Genetics

country: United Kingdom

institute: John Innes Centre

summary: Whether and how organisms can inherit environmental information from their parents is a major question in evolutionary theory. Plants have evolved to link reproductive development to seasonal environmental cues and seed dormancy is highly contingent on the environmental temperature during seed set, although the mechanism by which seeds acquire seasonal timing information is unclear. Here we show that loss of maternal like heterochromatin protein 1 (LHP1) causes an inability of progeny seeds to sense temperature and that this is linked mechanistically to reduced ABA levels in seeds and hyperaccumulation of free nitrate. Remarkably, single cell transcriptomics reveals that in both maternal fruit and seed tissues, the effect of small changes in temperature closely phenocopies the lhp1 mutant phenotype and ABA biosensor imaging reveal large fluxes of maternal ABA into seeds is modulated by temperature cues. We show that temperature activates ABA production in leaves and that maternal ABA is necessary and sufficient for progeny seeds to acquire seed dormancy. Thus, we reveal that the climate experience of mother plants causes adaptation of progeny behaviour via hormone transport during seed set.

overall_design: siliques were dissected to separate fruit tissue and seed tissue which were sequenced seperately. Lhp1-6 and WT Col-0 were grown at 16°CD/14°CN.

first: Xiaochao

first: Steven

last: Penfield


title: RNA half-life regulation reveals countercyclical regulation of buffered RNAs and RNAs undergoing changes in abundance [trim-Qfilt]

first: Leslie

middle: Ellen

last: Sieburth

state: UT

address: 257 South 1400 East

department: Biology

summary: mRNA abundances are regulated by the opposing forces of transcription and decay, and yet how decay contributes to mRNA abundance regulation is largely unexplored. We addressed this question using genome-wide data on mRNA rates of abundance change, half-lives, and transcription rates of leaf cells responding to a transdifferentiation stimulusulus.  Half-life regulation was common (22% of mRNAs underwent changes in half-life), but RNA abundance regulation by decay alone or by decay that supported transcriptional regulation was rare. Instead, most altered RNA half-lives opposed changes in transcription. Oppositionally regulated mRNAs were characterized by large changes in transcription and decay rates yet changes in mRNA abundances were either modest or undetectable, suggestive of RNA buffering.  Oppositionally-regulated and buffered RNAs showed very similar dynamics, suggesting use of a common mechanism. The strongest contributions of RNA decay to RNA abundance regulation was in synergistically regulated transcripts, where rate changes in decay and transcription rates worked together to change RNA abundances.

overall_design:
To investigate rates of RNA abundance change for comparison with RNA decay rates following a stimulusulus response, we preformed a time course experiment of mock and stimulusulus.
Detached leaves of 10 d old Arabidopsis thaliana seedlings were treated with mock conditions or with a transdifferentiation treatment for 5, 6, 7, 8, 9, or 10 h. Tissue was collected for RNA extraction and RNA seq analysis.

first: Reed

last: Sorenson


title: Cancer-associated fibroblast driven paracrine IL-6/STAT3 signalling promotes migration and dissemination in invasive lobular carcinoma

city: Edinburgh

first: Esme

last: Bullock

address: Edinburgh Cancer Research Centre, IGC, Western General Hospital, Crewe Road

institute: University of Edinburgh

summary: Invasive Lobular Carcinoma (ILC) is an under-studied yet common subtype of breast cancer. A key feature of ILC tumours, due to their single-file invasive growth pattern, is a high stromal content and in particular, an abundance of cancer-associated fibroblasts (CAFs). We identified that IL-6 secreted from primary ILC patient-derived CAFs drives STAT3 activation in ILC cell lines and found that IL6, STAT3, pSTAT3 and subsequent downstream gene expression induced by IL-6 within CAF conditioned media is upregulated in ILC tumours compared to Invasive Ductal Carcinoma tumours, the most common subtype of breast cancer. This dataset contains 3`-mRNAseq data from ILC cell lines (SUM44PE and MDA-MB-134VI) and patient-derived organoids (HCI-013 and HCI-018) stimulated with either recombinant human IL-6 (10 ng/ml) for 24 hours or 1 week or SUM44PE cells stimulated with CAF conditioned media (CAF CM)collected from ED26 primary ILC CAFs (characterised here: doi.org/10.3390/cancers14040904) +/- an IL-6 neutralising antibody. RNA was extracted using Qiagen RNeasy mini-kit and libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen Inc, #015).

overall_design: Invasive Lobular Carcinoma cell lines (SUM44PE and MDA-MB-134VI) or patient-derived organoids (HCI-013 and HCI-018) stimulated with primary ILC CAF conditioned media for 24 hours +/- anti-IL-6 neutralising antibody (SUM+CM experiments) or + 10 ng/ml recombinant human IL-6 for 24 hours (+ IL-6 experiments) or 1 week.

first: Valerie

middle: G

last: Brunton

first: Sana

last: Shabbir


title: RNA half-life regulation reveals countercyclical regulation of buffered RNAs and RNAs undergoing changes in abundance

overall_design:
To investigate RNA decay rates following a stimulusulus response, we analyzed RNA abundance after 8 h stimulus and calcualted the decay rates from RNA abundances after 15, 60, and 240 min transcription inhibition by 1 mM cordycepin.
Detached leaves of 10 d old Arabidopsis thaliana seedlings were treated with mock conditions or with a transdifferentiation treatment for 5, 6, 7, 8, 9, or 10 h. Tissue was collected for RNA extraction and RNA seq analysis.


title: Catalytic-independent functions of INTAC confer sensitivity to BET inhibition [CUT&Tag]

first: runyuan

last: mao

address: 131 Dongan Road, Xuhui District, Shanghai

institute: Fudan University

summary: Chromatin and transcription regulators are critical to defining cell identity through shaping epigenetic and transcriptional landscapes, with their misregulation being closely linked to oncogenesis. Pharmacologically targeting these regulators, particularly the transcription activating BET proteins, has emerged as a promising approach in cancer therapy, yet intrinsic or acquired resistance frequently occurs with poorly understood mechanisms. Using genome-wide CRISPR screens, we find that BET inhibitor efficacy in mediating transcriptional silencing and growth inhibition depends on the auxiliary module of the INTAC complex, a global regulator of polymerase pause-release dynamics. This process bypasses a requirement for INTAC's catalytic activities and instead leverages direct engagement of the auxiliary module with the RACK7/ZMYND8–KDM5C complex to remove histone H3K4 methylation. Targeted degradation of the COMPASS subunit WDR5 to attenuate H3K4 methylation restores sensitivity to BET inhibitors, highlighting how simultaneously targeting coordinated chromatin and transcription regulators can circumvent drug-resistant tumors.

overall_design: We performed RNA-seq, or CUT&Tag to investigate the role of INTAC auxiliary module in mediating BETi sesitivity. In this study, samples for each condition were collected in biological duplicates. Eμ-Myc cells were treated with DMSO, JQ1, or MS67 combined with JQ1 for 48 hours.

first: Pengyu

last: Fan

first: Xue-Ying

last: Shang

first: Aixia

last: Song

first: Run-Yuan

last: Mao

first: Fei

middle: X


title: Catalytic-independent functions of INTAC confer sensitivity to BET inhibition

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

overall_design: Refer to individual Series


title: Catalytic-independent functions of INTAC confer sensitivity to BET inhibition [RNA-seq]

overall_design: We performed RNA-seq or CUT&Tag to investigate the role of INTAC auxiliary module in mediating BETi sensitivity. In this study, samples for each condition were collected in biological duplicates. Eμ-Myc cells were treated with DMSO, JQ1, or MS67 combined with JQ1 for 48 hours.

last: Chen


title: Targeted Ubiquitination and Degradation of GOLM1 by CC-885 Suppresses Hepatocellular Carcinoma Growth and Metastasis

city: lianyungang

first: He

last: Jingliang

address: tongguan

institute: Jiangsu Ocean University

summary: Hepatocellular carcinoma (HCC) is a leading cause of cancer mortality, necessitating innovative therapeutic approaches. This study demonstrates that the compound CC-885 exerts potent anti-tumor effects in HCC both in vitro and in vivo. CC-885 significantly inhibited proliferation, migration, and invasion of HCC cells. In vivo, CC-885 markedly reduced tumor growth and angiogenesis in chick embryo and mouse xenograft models. Mechanistically, CC-885 selectively reduced GOLM1 protein levels via ubiquitin-mediated proteasomal degradation, without affecting its mRNA levels. GOLM1 knockdown mimicked the anti-proliferative effects of CC-885, while overexpression of GOLM1 conferred resistance to CC-885-induced apoptosis and growth inhibition. CC-885 facilitated the interaction between GOLM1 and the E3 ubiquitin ligase CRBN, promoting GOLM1 ubiquitination and degradation. Transcriptomic analyses revealed that CC-885 and GOLM1 knockdown modulated key pathways involved in apoptosis, NF-κB signaling, and cell proliferation. These findings highlight CC-885 as a promising therapeutic agent for HCC, primarily by facilitating the CRBN-dependent degradation of GOLM1, underscoring its potential for clinical application.

overall_design: To investigate the role of CC_885 in hepatocellular carcinoma and its mechanism, we performed HCCLM3 cells with and without CC_885 treatment. Then, we performed gene expression profiling using RNA-seq data of HCCLM3_CC-885 and HCCLM3_DMSO cells.

first: Jingliang

last: He

first: Bin

last: Liu


title: Effect of knockdown of lncRNA MRF on gene expression during osteogenic induction of human BMSCs

city: Guangzhou , Guangdong

first: ning

last: qing

address: Sun Yat sen University Sun Yat sen Memorial Hospital, No. 107 Yanjiang West Road, Yuexiu District

institute: Sun Yat-sen Memorial Hospital

summary: Mesenchymal stem cells (MSCs), known for their ability to differentiate into osteoblasts, play a pivotal role in bone metabolism. Prior to this study, we identified a novel lncRNA called MCP1 regulatory factor (MRF), which exhibits significant involvement in immune regulation of BMSCs. Moreover, we observed noticeable expression changes of MRF during the osteogenic differentiation of BMSCs. However, the exact role and underlying mechanism of MRF in the osteogenic differentiation of BMSCs remain elusive. QRT-PCR analysis was used to assess the expression of MRF. RNA interference and overexpression plasmids were employed to modulate MRF expression and observe changes in the osteogenic differentiation capacity of BMSCs. Downstream pathways involved in MRF-mediated regulation of BMSCs' osteogenic differentiation were predicted using transcriptome sequencing. The functionality of MRF in vivo was validated through a mouse tibial drilling defect model. In patients with osteoporosis, there is a conspicuous escalation in the expression of MRF within BMSCs. During the bone differentiation process of BMSCs, the MRF gradually diminishes over time. The knockdown of MRF amplifies the osteogenic differentiation of BMSCs, promoting an increased expression of bone-related proteins such as RUNX2, ALP, and COL1A1. Transcriptome sequencing and western blot indicated that cAMP/PKA/CREB signaling pathway was significantly activated after lncRNA-MRF knockdown. The mouse tibial drilling defect model demonstrates that the knockdown of MRF conspicuously advances ossification in vivo. MRF modulates the cAMP/PKA/CREB signaling axis through FSHR, thereby adjusting the ossification differentiation of BMSCs. Our research suggests that MRF may a potential target for bone related disorders.

overall_design: To investigate the regulatory role of lncRNA MRF in the osteogenic differentiation of BMSCs, we collected BMSCs from three different patient sources and used third-generation BMSCs for experiments. Each group of BMSCs was divided into two groups, which were subjected to lncRNA MRF knockdown sirna treatment and negative control sirna treatment were performed, followed by osteogenic induction for three days. TRIzol was used to extract the total RNA from each group of samples.

first: Qing

last: Ning

first: Ming

last: Li

first: Jun

last: Tang


title: Genome-wide screens identify FBOX11-CCNC axis as a suppressor of CD155 mediated cancer immune evasion

first: Shiyu

address: 301 Middle Yan Chang Road, Shanghai

institute: Shanghai Tenth People's Hospital of Tongji University; School of Medicine; Tongji University

summary: The CD155/TIGIT axis plays a crucial role in the suppression of anti-tumor responses. The clinical benefit for patients with diverse types of advanced cancers that has been observed upon blockade of the interaction between CD155 and TIGIT has highlighted the need to study the mechanisms by which CD155 is regulated. Here we identify Cyclin C (CCNC) as a novel modulator of CD155 by using a genome-wide CRISPR-Cas9 screen. Notably, CCNC depletion increases the CD155 expression at the transcriptional level in a broad range of cancer cells. We further found that CCNC suppresses the CD155 expression by inhibiting the transcriptional activity of FOSL2. We further found that the stability of CCNC is negatively regulated by the E3 ubiquitin ligase complex component FBXO11. Functionally, CCNC depletion significantly suppresses the anti-tumor activity of natural killer (NK) and T cells both in vitro and in vivo. Clinically, the expression level of CCNC is negatively correlated with CD155 in cancer patient tissues. Together, our findings provide insights into the biology of CD155 regulation, identify a previously unrecognized master regulator of this critical immune checkpoint and highlight a combination immunotherapy (TIGIT/PD-1 co-blockade) as a promising anti-cancer therapeutic strategy to overcome immune evasion by CCNC-deficient tumor cells.

overall_design: We generated CCNC knockout T24 cells and performed total mRNA sequencing to determine how the gene expression is altered in both parental and CCNC-KO cells.

first: Yadong

last: Guo

first: Xudong

last: Yao

first: Ping

last: Wang


title: Klf5 OE ES

city: Otsu

first: Masatsugu

last: Ema

state: Shiga

address: Seta, Tsukinowa-cho

department: Research Center for Animal Life Science

institute: Shiga University of Medical Science

summary: Krüppel-like factors (Klfs) are DNA-binding transcriptional factors that regulate multiple physiological features, including the cell cycle, cell differentiation and tissue organization. Klf2, Klf4 and Klf5 are crucial for maintenance of pluripotent and somatic stem cells. We show that Klf2, Klf4 and Klf5 genes are required for normal neural development in a redundant manner and depletion of all three genes in neural precursor cells results in impaired activation of Notch signaling and early lethality. Klf5 plays a dominant role in maintenance of neural precursor cell populations by suppressing their differentiation and radial migration in developing mammalian brain. Klf4 and Klf5 also regulate proliferation of neural precursor cells in an opposing fashion. Klf4 promotes generation of quiescent neural stem cells, whereas Klf5 supports vigorously dividing intermediate progenitor cells. Our findings provide insight into mechanisms by which neural precursor cells provide large numbers of differentiating cells and a few quiescent neural stem cells.

overall_design: Klf5 OE (clone 1 and 2) ES cells were maintained in ES medium + 15%FBS + LIF. Total RNAs from those ES cells were prepared using the RNeasy Kit. WT (clone1 and 2) ES cells were already deposited as a GSE9244. Downregulated and upregulated genes were extracted for comparison between WT (clones 1 and 2) and Klf OE (clones 1 and 2) using Transcriptome Analysis Console Software (Thermo Fisher Scientific).

first: Kazuhiko

last: Uchida

first: Seji

last: Hitoshi


title: Effects of ketogenic diet and caloric restriction on ischemic tolerance

city: Moscow

first: Anastasiya

last: Zharikova

address: Leninskie gory 1/73

country: Russia

institute: MSU

summary: The ketogenic diet (KD) is used to treat a number of brain pathologies. In this study, we undertook detailed transcriptomic profiling of rat brain after KD and ischemic stroke to uncover effects of KD and its specific mechanisms. We evaluated how a 2-month KD affected gene expression in intact brain tissue and after middle cerebral artery occlusion (MCAO). We found transcriptional reprogramming in the brain after stroke and KD treatment. KD altered the expression of genes involved in the regulation of glucose and fatty acid metabolism, mitochondrial function, immune response, Wnt-associated signaling, stem cell development, and neurotransmission in both intact rats and after MCAO.

overall_design: The experiments were performed on young (3 months, 320–350 g) male Wistar rats. The rats were divided into 2 experimental groups: rats fed a standard diet (3227 kcal/kg, of which fats 367 kcal/kg (11%), proteins 768 kcal/kg (24%), carbohydrates 2091 kcal/kg (65%); N1324 Altromin, Germany) and rats fed ketognic diet with a high fat and low carbohydrate content (6431 kcal/kg, of which fats 5405 kcal/kg (84%), proteins 680 kcal/kg (11%), carbohydrates 346 kcal/kg (5%); C 1084, Altromin, Germany). The rats were fed the selected diet for 2 months. Thereafter, the group of rats was subjected to middle cerebral artery occlusion (MCAO), and all rats were then fed the same diet for further 2 weeks.

first: Anastasia

middle: A

first: Nadezda

middle: V

last: Andrianova

first: Denis

middle: N

last: Silachev

first: Vladimir

middle: O

last: Nebogatikov

first: Irina

middle: B

last: Pevzner

first: Ciara

middle: I

last: Makievskaya

first: Ljubava

middle: D

last: Zorova

first: Grigoriy

last: Maleev

first: Galina

last: V Baydakova

first: Dmitry

last: Chistyakov

first: Sergey

last: Goriainov

first: Marina

last: Sergeeva

first: Inna

middle: Y

last: Burakova

first: Artem

last: Gureev

first: Vasily

last: Popkov

first: Aleksey

last: Ustyugov

first: Egor

last: Plotnikov