title: Mapping of Nab3 RNA-binding sites in Saccharomyces cerevisiae with abrogated binding of Nab3 to PIC2

summary: Using CRAC, we compared the transcriptomic occupancy of Nab3 in a Saccharomyces cerevisiae BY4741 parental strain (PIC2-GFP) and two derived mutants lacking Nab3 RNA-binding sites in PIC2. The purpose of the experiment was two-fold: on the one hand, we aimed to verify that the mutations inserted in the Nab3 binding sequences of PIC2 had indeed abrogated binding of Nab3 to the PIC2 transcript; on the other hand, we wanted to check whether differential binding of Nab3 to PIC2 would affect how the protein bound other targets in the genome. Sequencing outputs were processed using the pyCRAC pipeline and peak calling was performed with DBPeaks, our newly developed package for identification and comparison of binding sites defined by RNA-binding footprinting techniques (e.g., CRAC, iCLIP, PAR-CLIP, etc.).

overall_design: Two biological replicates of CRAC experiments performed in a parental Saccharomyces cerevisiae BY4741 strain (PIC2-GFP) and two derived mutants: mut-Nab3-BS and mut-NNS-BS. While mut-Nab3-BS lacks Nab3 RNA-binding sites in PIC2, the other strain has no Nab3 or Nrd1 RNA-binding sites in PIC2 (mut-NNS-BS). All strains encoded NAB3-HTF (HIS6-TEV-3xFLAG). When SC-Ura cultures containing 1% (w/v) raffinose reached an OD600 of 1, cells were UV cross-linked (254 nm; 500 mJ/cm2) in the Vari-X-linker (UVO3) and rapidly filtered on 0.8 μm membranes (Merck) using a filtration device connected to a vacuum pump. Membranes were collected in 50 mL tubes, flash frozen by submersion into liquid nitrogen and stored at -80ºC until the day of the experiment.   On the day of the experiment, pellets were resuspended in a volume of lysis buffer (150 mM NaCl, 50 mM Tris pH 7.8, 0.1% (v/v) Nonidet P-40, 1 EDTA-free protease inhibitor cocktail (Roche) per 50 mL and 5 mM β-mercaptoethanol) corresponding to twice their mass. Lysates were then transferred to a fresh 50 mL tubes, where they were mixed with 2 volumes of 0.5 mm zirconia beads (Thistle Scientific), and vortexed at maximum speed for five 1-minute intervals alternated with 1-minute incubations on ice. An additional volume of lysis buffer was pipetted into each sample before partitioning the cell debris by centrifugation at 4ºC (4000 rpm, 15 minutes) and spinning down lighter impurities in an additional centrifugation step (10000 rpm, 20 minutes) at 4ºC. Immunoprecipitation of the labelled protein from the supernatant was achieved during a two-hour incubation of the sample with 75 µL of anti-FLAG® M2 magnetic beads (Sigma-Aldrich, M8823-5ML) which had been previously washed three times with 1 mL TN150 buffer. Immobilised beads underwent three 5-minute washes with TN1000 buffer (50 mM Tris pH 7.8, 1 M NaCl, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol) and three additional 5-minute washes in 2 mL TN150 buffer (150 mM NaCl, 50 mM Tris pH 7.8, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol). Afterwards, beads were resuspended in 550 µL of TN150 and incubated with 1 µL of a 1:100 dilution of RNace-It™ for exactly 5 minutes at 37 °C. To prevent overdigestion of co-immunoprecipitated transcripts and elute the bait proteins from the anti-FLAG beads, the solution was mixed with 0.4 g of guanidium hydrochloride (Gu-HCl) and the necessary volume of NaCl and imidazole (pH 8.0) to reach a final concentration of 300 mM and 10 mM respectively. After removing the beads, samples were pipetted onto 50 µL of Ni-NTA agarose resin (Qiagen) equilibrated with wash buffer I (6 M Gu-HCl, 10 mM imidazole, 300 mM NaCl, 50 mM Tris-HCl pH 7.8, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol) and incubated at 4 °C overnight while rotating at 12 rpm.   Upon Ni-NTA binding, beads were transferred to Pierce columns (Thermo Fisher Scientific) and washed twice with 500 µL of wash buffer I before undergoing three additional washes of 500 µL with NP-PNK buffer (10 mM MgCl2, 50 mM Tris-HCl pH 7.8, 0.1% (v/v) Nonidet P-40, 5 mM β-mercaptoethanol). Alkaline phosphatase treatment was performed by resuspending immunoprecipitated RNA-protein conjugates in 80 µL of NP-PNK buffer containing 4 units of FastAP thermosensitive alkaline phosphatase (Thermo Fisher Scientific) and 80 units of RNasin® ribonuclease inhibitor (Promega) and incubating the samples at 37 °C for 1 hour. Dephosphorylation was stopped upon addition of 500 µL of wash buffer. Having equilibrated the Ni-NTA agarose with three washes of 500 µL with NP-PNK, we performed adapter ligation by resuspending the beads 80 µL of reaction mix containing 0.6 µM of the applicable App-PE 3′ adapter (5’App-NAGATCGGAAGAGCACACGTCTG-ddC 3’), 30 units of T4 RNA ligase 2 truncated K227Q (New England Biolabs), 60 units RNasin® (Promega) and 10% (w/v) polyethylene glycol 8000 (PEG 8000). The reaction took place at 25 °C for six hours.  After washing once with 500 µL of wash buffer I and three times with 500 µL of NP-PNK buffer, we 5’end radiolabelled co-immunoprecipitated RNAs by incubating the Ni-NTA resin with 60 µL of NP-PNK buffer containing 30 µCi 32P-γATP (PerkinElmer) and 30 units of T4 polynucleotide kinase (New England Biolabs). After a 40-minute incubation of the reaction at 37ºC, ATP (Roche) was supplemented to a final concentration of 1 mM and the reaction continued for another 20 minutes. The reaction was stopped by washing three times with 500 µL of wash buffer I and three 500 µL washes of NP-PNK buffer followed before the addition of the 5′ linker ligation mix. The reaction took place in a volume of 80 µL of NP-PNK buffer supplemented with 1.25 µM of the fitting adapter, 40 units of T4 RNA ligase 1 (New England Biolabs), 80 units of RNasin® and 10 mM ATP (Roche).  5’ adapter ligation was left to proceed overnight at 16 °C for all bait proteins. The adapter sequences were 5’-ACACGACGCTCTTCCGATCTNNNCGCTTAGCN-3’ and 5’-ACACGACGCTCTTCCGATCTNNNGACTTAGCN-3’ or 5’-ACACGACGCTCTTCCGATCTNNNTAAGCN-3’ for PIC2-GFP repeats 1 and 2 respectively; 5’-ACACGACGCTCTTCCGATCTNNNCACTAGCN-3’ and 5’-ACACGACGCTCTTCCGATCTNNNACTCAGCN-3’ for mut-Nab3-BS replicates 1 and 2 respectively;  and 5’-ACACGACGCTCTTCCGATCTNNNGTGACAN-3’ for both mut-NNS-BS libraries. After pooling suitable libraries together, the samples and its corresponding traces were submitted to Novogene, where paired-end sequencing of 150 bp-reads was performed in a NovaSeq 6000 system (Illumina).


title: A dual-mechanism antimicrobial peptide with antimutagenic activity targets the replisome and induces cell envelope stress

status: Public on Aug 25 2025

city: Trondheim

first: Amanda

middle: Holstad

last: Singleton

address: Erling Skjalgsons gate 1

department: Department of Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

type: Expression profiling by high throughput sequencing

summary: To combat the growing threat of multidrug-resistant bacteria, we need to develop novel antibiotics with unique modes of action. This study investigates the antibacterial properties of BTP-001 towards Escherichia coli. BTP-001 is a β-clamp targeting antimicrobial peptide containing an AlkB homologu 2 PCNA-interacting motif (APIM) linked to a cell penetrating peptide composed of 11 arginine residues (R11). Our data indicates that R11 mediates energy-dependent transport of BTP-001 across the cell membrane, possibly via iron transport systems such as the TonB-system. The full-length BTP-001 peptide rapidly affects the bacterial membrane, inducing increased expression and activation of the Cpx, E and Rcs cell envelope stress responses, which trigger the production of reaction oxygen species (ROS). This contributes to a rapid bactericidal effect as evidenced by increased short-term survival by addition of a ROS scavenger. Furthermore, we show that BTP-001 reduces the development of resistance to ciprofloxacin likely by binding to the β-clamp via APIM, thereby inhibiting translesion synthesis. In addition, our multi-omics data suggests that the -clamp is part of ribosomal complexes, and that regulation of translation is targeted by BTP-001.  In conclusion, BTP-001 exhibits a multifaceted mode of action which strengthens its potential as a novel therapeutic drug against antibiotic resistant bacteria

overall_design: To elucidate BTP-001’s mode of action, we conducted RNA-sequencing (RNA-seq) of E. coli MG1655 treated with 2 doses of the novel antibiotic peptide BTP-001 and 1 dose of the cell penetrating peptide R11. We chose a low dose of BTP-001 (1 µM) with no impact on growth and a high dose (3 µM; equivalent to the minimum inhibitory concentration [MIC]) that affected the growth but did not yield extensive lethality during batch cultivation in bioreactors. The R11 dose (1 µM) reflects the BTP-001 low dose. The high dose (3 µM) stalled growth for around 10 min before the culture recovered and eventually reached the same growth rate as the control. All experiments were conducted with continuous dissolved oxygen and off-gas analysis. All treatments were given at OD600 = 0.2 to ensure exponential growth during the entire sampling period. To investigate the temporal effects of BTP-001 on E. coli, the low dose of BTP-001 (1 µM) culture was sampled for transcriptomics  over a time course between 1 to 120 min after treatment.  The high dose of BTP-001 (3 µM) and R11 (1 µM) were sampled for transcriptomics 10 min after treatment.

last: Holstad Singleton

first: Olaug

middle: E

last: Torheim Bergum

first: Jana

last: Scheffold

first: Synnøve

last: Brandt Ræder

first: Lilja

last: Brekke Thorfinnsdottir

first: Lisa

middle: M

last: Røst

first: Caroline

last: Krogh Søgaard

first: Per

last: Bruheim

first: Marit

last: Otterlei


title: RNA sequencing analysis of ESRP1, 2 overepxressing PANC-1 and MIA-PaCa2

city: Seoul

first: Taehong

last: Min

address: 369, Sangdo-ro, Dongjak-gu, Seoul, Republic of Korea

department: School of Systems Biomedical Science

country: South Korea

institute: Soongsil University

summary: Epithelial splicing regulatory proteins (ESRPs) are splicing regulators known to play a critical role in epithelial-mesenchymal transition (EMT) and the progression of various cancers, including pancreatic ductal adenocarcinoma (PDAC). Numerous cancer-related genes, such as CD44, FGFR2, and CDNND1, are spliced by ESRP1 and 2 with differential expression of variants. Here, we analyzed ESRP1 and 2 overexpressing pancreatic cancer cells, PANC-1 and MIA-PaCa2, and discovered splicing targets of ESRPs.

overall_design:
To investigate the function of ESRP1 and ESRP2 in the progression of pancreatic cancer, we established the ESRP1 or ESRP2 overexpressing MIA-PaCa2 and PANC-1 cell lines.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different cells.

first: Seong-Jin

last: Kim

first: Eunji

last: Hong

first: Hyeyeon

last: Park

first: Junil


title: PRDM16 restricts cellular senescence by upregulating GSTM1

city: Wuhan

first: Yuting

last: Zhu

state: Hubei

address: 1277 Jiefang Avenue

country: China

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Cellular senescence is a hallmark of aging, and the accumulation of senescent cells (SnCs) accelerates the aging process and contributes to aging-related organ disorders. The PRDMs exhibit robust transcriptional regulatory activity and govern a wide range of biological processes. However, the role of PRDMs in cellular senescence and aging remain unclear. Here, we have demonstrated that PRDM16, among PRDMs, is decreased significantly in multiple organs of aged mice compared to young mice. Global Prdm16 deletion contributes to cellular senescence in various organs, including the kidney, heart, lung, brain hippocampus, stomach, and gut; subsequently leading to accelerated aging-related organ injury. Furthermore, tubular specific Prdm16 deletion aggravates irradiation induced kidney aging, and aging-related kidney disease subjected to ischemia reperfusion surgery. Exogenous PRDM16 gene delivery by lentivirus effectively attenuates cellular senescence in vitro and in vivo. Mechanistically, PRDM16 improves glutathione metabolism and inhibits oxidative DNA damage, the driving force of senescence. Especially, PRDM16 increases glutathione-S-transferase activity by upregulating the transcription of GSTM1. Transfection of GSTM1 restored cellular senescence and kidney aging caused by PRDM16 deficiency. Taken together, we provide a potential target for investigating the anti-aging therapy.

overall_design: PRDM16 overexpressing and control HK-2 cell lines were constructed by lentivirus transfection. HK-2 cells were exposed to a single dose of 8 Gy X-ray irradiation and harvested at the 7th day post-irradiation. We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different cells at two groups.

first: Qian

last: Yuan


title: 3D genome architecture in MCF10A cells in repsonse to DNA damage and ER stress

city: Albany

first: Morgan

middle: A

last: Sammons

state: NY

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

country: USA

institute: University at Albany - SUNY

summary: The goal of this experiment was to assess changes in 3D chromatin structure in mammary gland epithelial cell line (MCF10A) response to chemical stimuli via etoposide (DNA damage) or tunicamycin (ER stress). Micro-C method with a comprehensive promoter capture panel was used to increase resolution using the proprietary approach of Cantata/Dovetail Genomics

overall_design: 3D genome architecture in MCF10A cells in repsonse to DNA damage (etoposide) and ER stress (tunicamycin), or control traetment (DMSO). Each experiment was done in biologgical duplicates.

first: Baniulyte

last: Gabriele

first: Sammons

last: Morgan


title: Suppressive effect of the anesthetic Propofol on the T cell function and T cell-dependent immune responses

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

country: Japan

institute: Ehime University

summary: General anesthesia is thought to suppress the immune system and negatively affect postoperative infection and the long-term prognosis of cancer. However, the mechanism underlying immunosuppression induced by general anesthetics remains unclear. In this study, we focused on propofol, which is widely used for sedation under general anesthesia and intensive care and examined its effects on the T cell function and T cell-dependent immune responses. We found that propofol suppressed T cell glycolytic metabolism, differentiation into effector T cells, and cytokine production by effector T cells. CD8 + T cells activated and differentiated into effector cells in the presence of propofol in vitro showed reduced antitumor activity. Furthermore, propofol treatment suppressed the increase in the number of antigen-specific CD8 + T cells during Listeria infection. In contrast, the administration of propofol improved inflammatory conditions in mouse models of inflammatory diseases, such as OVA-induced allergic airway inflammation, hapten-induced contact dermatitis, and experimental allergic encephalomyelitis. These results suggest that propofol may reduce tumor and infectious immunity by suppressing the T cell function and T cell-dependent immune responses while improving the pathogenesis and prognosis of chronic inflammatory diseases by suppressing inflammation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Control- and Propofol-treated CD8 T cells at five days after TCR stimulation.

first: Waichi

last: Yamamoto


title: ALDH1a3 inhibitor effects on Breast cancer Cells Transcriptome

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

summary: Aldehyde dehydrogenase (ALDH1) activity has long been established as a pro-tumorigenic feature of many cancers, yet the identification of specific isoforms that are enriched in cancer, the mechanism of action of this isoform(s), and viable therapeutic strategies to target this pathway have long remained absent. Whereas one of the well-established functions of the ALDH1a family is the conversion of retinaldehyde into retinoic acid to activate nuclear retinoid signaling, the retinoid pathway is paradoxically hypothesized as a cell-intrinsic tumor suppressor pathway. Here we resolve this long-standing conflict by showing that while ALDH1a3 is broadly overexpressed across diverse cancer types, ALDH1a3 expressing tumor cells often lose the sensitivity to retinoid signaling. Instead, all-trans retinoic acid produced by ALDH1a3 acts in a paracrine fashion to suppress anti-tumor immunity and promote tumor growth. We further used structure-based high throughput screening to develop a series of first-in-class, therapeutically viable antagonists of ALDH1a3 with potent anti-tumor immunotherapeutic activity, an excellent pharmacological profile and no evidence of toxicity. Findings of this study resolve prior contradictions in the retinoid pathway through the development of highly specific and potent ALDH1a3 inhibitors.

overall_design: To determine the effects of ALDH1a3 inhibitor MBE1.5 on gene expression regulation in breast cancer cells, 4 breast cancer cell lines including 3 ALDH1a3 positive cells and 1 ALDH1a3 negative cells are treated with MBE1.5 vs DMSO control for 9 hours. Total RNA were harvested from the cells and whole transcriptome expression were determined by RNAseq.

first: Mark

last: Espisito

first: Cao

last: Fang

first: Yibin

last: Kang


title: Differential N6-methyladenosine(m6A) modification in hypertrophic scar v.s. normal skin

city: Nanchang

first: dewu

last: liu

state: Jiangxi

address: 17 Yongwaizheng Street

institute: The First Affiliated Hospital of Nanchang University

summary: N6-methyladenosine (m6A) is the most prevalent internal modification in eukaryotes. Here, m6A-mRNA and lncRNA transcriptomes were profiled for HS and full-thickness normal skin (NS) tissues using human m6A-mRNA and lncRNA epitranscriptomic microarray. These data exhibited 5838 differentially m6A methylated transcripts (4706 mRNAs, 1132 lncRNAs) between HS and NS tissues. Of note, most of them (about 94%) were hypermethylated. And 3197 differentially expressed mRNAs (1466 upregulated and 1731 downregulated) were obtained by microarray. Conjoint analysis of differentially methylated and differentially expressed transcripts screened 815 transcripts (675 hyper-up, 140 hypo-down). Among them, IFNGR1 (ENST00000367739) and IL37 (ENST00000349806) are two of the most significant methylated transcripts in hyper-up and hypo-down groups. This study proposed a transcriptional regulatory network of m6A modifications on mRNA and lncRNA in human hypertrophic scar, which may bring a new clue into the development, pathogenesis, and treatment of abnormal scars.

overall_design:
4 samples(2 hypertrophic scars,2 normal skin);

Please note that experiments were carried out technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed as single channel. Thus each raw data file contains raw data for both IP and supernatant sample, and is linked to the corresponding IP sample records.

first: Xiaoxiao

last: Liu

first: Chunyan

last: Guo

first: Xiandong

last: Lu

first: Xiancai

last: Li

first: Shangfeng

last: Fu

first: Dewu


title: HeLa cell line exhibits single-clonal growth variation

city: Beijing

first: Xin

last: Zhang

state: Beijing

address: No.5 Yiheyuan Road

department: School of Life Sciences, BIOPIC

institute: Peking University

summary: The HeLa cell line is the first human-derived immortalized cell line， one of the most widely used cell lines in the world. While many researches had pointed out the heterogeneity of HeLa cells across laboratories and the low repeatability of experiments performed on HeLa cells, the reason how these heterogeneities generated is little known. We sorted cells into single cells, cultured them to single clones and performed multi-omics sequencing. The single cell-derived clones exhibited persistent growth variation both in vitro and in vivo. The corresponding WGS analysis revealed the single clones diverse in copy number even at the whole chromosome level. Our work explored the intrinsic mechanisms of the low repeatability of cell line experiments. We also provided a resource for single cell-derived clones.

overall_design: HeLa cell line 6 single clone bulk RNA-seq data and 3 single clones cell line-derived xenograft (CDX) RNA-seq data

first: Xiaodong

last: Su


title: Developmental toxicity of tire wear particle (TWP) leachates produced in the presence or absence of simulated natural light

city: East Lansing

first: Karilyn

last: Sant

state: MI

address: 1355 Bogue St., Life Science B440

department: Pharmacology & Toxicology

institute: Michigan State University

summary: Tire wear particles (TWP) are small micro- or nano-particles resulting from the friction of tire tread against roads. These microplastics have been found in waterways, usually through rain and wind, posing a potential risk to exposed aquatic life. The goal of this project was to assess the toxicity of chemical leachates from TWP and characterize how they may impact the health and development of aquatic life, like Danio rerio, zebrafish. Furthermore, we also determined if solar-simulated or dark conditions intensified the effects of TWP, considering processes like photodegradation and photochemical oxidation occur in sunlight. Zebrafish were exposed from 0-4 days post fertilization (dpf) to a filtered TWP solution at varying concentrations, and each concentration was leached in either solar-simulated or dark conditions. Mortality and hatching rates were quantified throughout the exposures, and physical anomalies were recorded at 4 dpf using microscopy. Ethyoxyresorufin-O-deethylase (EROD) activity, an indicator of Phase I biotransformation, was performed using fluorescent microscopt. RNA sequencing was performed for 4 dpf larvae. TWP exposures, regardless of leaching light status, increased mortality, yolk sac edema, pericardial edema, spinal curvature, and craniofacial malformations, while decreasing hatching and swim bladder inflation. Regardless of lighting during leaching, EROD activity increased in the liver and brain and decreased in the gut CYP1A. RNA sequencing revealed some conserved processes in response to TWP, regardless of light status during leaching, including those involved in neurobiological function. However, divergent responses were also observed for processes such as amino acid metabolism, steroid biosynthesis, and fatty acid metabolism. Overall, these results suggest a disruption of embryonic development in zebrafish when exposed to TWP, and that sunlight during chemical leaching can alter the molecular responses to TWP.

overall_design: All studies were performed using zebrafish. Zebrafish embryos were exposed to either control (egg water only) or TWP (10 g/L, leached for 1 or 6 days) from 0-4 dpf. For each exposure, leachates were proposed in the absence (dark) or presence (solar-simulated, to mimic southern California solar conditions) of light, to capture natural conditions. Samples were collected on 4 dpf. Four pooled samples (each containing 10 larvae at 4 dpf) were analyzed for each of the four exposure groups.

first: Jenielle

last: Domaoal

first: Christine

middle: S

last: Cho


title: Impaired social cognition caused by perinatal protein malnutrition evokes psychiatric-like disorders and is intergenerationally transmitted.

city: Ciudad de Buenos Aires

first: Octavio

last: Gianatiempo

state: Buenos Aires

address: Ciudad Universitaria Pabellon II piso 4

department: Quimica Biológica

country: Argentina

institute: Universidad de Buenos Aires

summary: Maternal malnutrition remains one the major early-life adversities contributing poor health in one in five children worldwide. Clinical studies demonstrate that malnourished children are growth-impaired, exhibit behavioral changes and suffer from cognitive impairments. These health effects can persist even if nutrition becomes adequate later in life. Experimental studies on rodents have shown that maternal protein restriction is associated with the emergence of several adverse effects of offspring neurological development. In addition, reported effects of prenatal and/or postnatal protein malnutrition on the offspring include changes in exploratory behavior and anxiety, altered learning and memory abilities and a different response to aversive stimuli. These behavioral alterations characterize the symptoms of various psychiatric disorders that has been increasingly regarded as developmental disorders. Social behavioral deficits in psychiatric diseases have been hypothesized to arise form elevation in the cellular balance of excitation and inhibition within the cortex generally, and PFC specifically. Such imbalance may be caused either by increased activity in excitatory neurons or by reduction in inhibitory neuron function. Interestingly, decreases in inhibitory neurotransmission are a common finding in animal models of ASD. In addition, direct alterations of E/I balance within the PFC in adult mice have strong effect on social motivation. The critical question we have posed in this work is whether maternal protein malnutrition alters the offspring’s social cognition and if this were the case, if these behavioral deficits are transmitted to the following generation. We hypothesized that at the basis of such alterations in social cognition underlie changes in gene expression related to E/I signaling within the mPFC. Our results focus on damaging effects of maternal protein malnutrition even for generations that are not exposed to this environmental adversity.

overall_design: Brain mRNA profiles of 56-day old male and female mice subjected to perinatal low-protein or normal-protein diets

first: Estefanía

last: Fesser

first: Bruno

middle: G

last: Berardino

first: Nadina

last: Ferroni

first: Maite

last: Cambiasso

first: Germán

last: Falasco

first: Vanina

last: Fontana

first: Leandro

last: Urrutia

first: Silvina

middle: V

last: Sonzogni

first: Eduardo

middle: T

last: Cánepa


title: Bulk RNA-seq of rat sciatic nerve distal to crush after magnetic nanoparticle–mediated magnetic force stimulation

status: Public on Aug 24 2025

city: Jilin

first: wang

last: yang

address: Xin-Min Street NO. 1

institute: Orthopaedic Center, The First Hospital of Jilin University

summary: To explore the effect of magnetic mechanical force mediated by magnetic nanoparticles in a gradient magnetic field environment on the repair phenotype of Schwann cells in injured sciatic nerves, we established a rat sciatic nerve crush injury model and locally injected magnetic nanoparticles under the epineurium at the distal end of the crush site.

overall_design:
After modeling, the rats were exposed to a gradient magnetic field environment daily to subject the injured sciatic nerve to magnetic force stimulation. On the 7th day after magnetic force stimulation, the sciatic nerve tissue at the distal end of the crush site was collected for mRNA transcriptome sequencing to observe the effect of magnetic force stimulation mediated by magnetic nanoparticles on the gene expression profile in the sciatic nerve.
B7: magnetic force stimulation, C7: control, ND: sciatic nerve distal.


title: Bulk RNA-seq of RSC96 Schwann cells after magnetic nanoparticle uptake and magnetic force stimulation

summary: To explore the effect of magnetic mechanical forces mediated by magnetic nanoparticles on the repair phenotype of Schwann cells in a gradient magnetic field environment, we co-cultured magnetic nanoparticles with RSC96 cells.

overall_design: The magnetic nanoparticles were taken up by the cells, magnetizing the RSC96 cells, and the magnetized cells were exposed to a gradient magnetic field environment and subjected to magnetic force stimulation. Normal cultured control group cells and experimental group cells that received magnetic force stimulation were collected for mRNA transcriptome sequencing to observe the effect of magnetic nanoparticle-mediated magnetic force stimulation on the gene expression profile of Schwann cells.


title: A positive feedback loop between BACH1 and IL-1β promotes the progression of HPV-negative head and neck squamous cell carcinoma

city: beijing

middle: xi

last: lin

address: 10 You’anmen Outer West 1st Street

institute: capital medical univercity

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) is associated with a poorer prognosis compared to its HPV-positive counterpart; however, the underlying regulatory molecular mechanisms driving its progression remain poorly understood. In this study, we identify BTB Domain and CNC Homolog 1 (BACH1) as a critical oncogenic regulator that is upregulated in HPV-negative HNSCC. We demonstrate that BACH1 promotes tumor progression by enhancing the proliferation and inhibiting apoptosis of cancer cells. Mechanistically, BACH1 is associated with the SWI/SNF chromatin remodeling complex and transcriptionally activates downstream target genes, including IL1B, thereby inducing a transcriptional reprogramming that promotes proliferation and resists apoptosis. Notably, BACH1-driven upregulation of interleukin-1β (IL-1β) establishes a positive feedback loop that sustains oncogenic signaling. Pharmacological disruption of this axis using the IL-1 receptor antagonist Anakinra significantly attenuates tumor growth in vitro and in vivo. Clinically, co-upregulation of BACH1, BRG1, and IL-1β is correlated with reduced overall survival in patients with HPV-negative HNSCC. Collectively, our findings characterize the BACH1–IL-1β signaling axis as a prognostic biomarker and highlight IL-1R blockade as a promising therapeutic strategy for the treatment of HPV-negative HNSCC.

overall_design: Genome binding/occupancy profiling of BRG1 and BACH1 by high throughput sequencing.

first: Zishanbai

first: Miao

last: Wang

first: Wenjuan

first: Minghui

last: Zhao

first: Yiming

last: Ding

first: Tingyao

last: Ma

first: Zhaohan

first: Xilin

first: Yuchen

last: Xiang

first: Yaning

first: Wenying

last: Zhong

first: Zicheng

last: Wu

first: Xiaohong

last: Chen

first: Lin

last: Shan


title: CD248 enhances mechanotransduction in specific fibroblasts subset responsible for scar formation to aggravate fibrosis in kidney

city: Xi'an

first: Chao

last: Xu

address: 127 Changle West Road

institute: Air Force Medical University

summary: gene expression profiling of fibrotic kidney of unilateral ureteral obstruction (UUO) mice with or wothout CD248 knockout. The purose of this study was to confirm the gene expression changes of Cd248-/- fibrotic kidney compared with wild ype.

overall_design: Total RNA was extracted from fresh kidney tissue of UUO mice with or wothout CD248 knockout and analyzed by RNA-seq

first: Shaojie

last: Liu

first: Yike

last: Zhou


title: Transcriptome analysis to explore the shared and distinct immune signature between severe COVID-19 and bacterial sepsis

city: Chongqing

first: Huang

state: Chongqing

address: 10 Changjiang Access Road

department: Department of Blood Transfusion

institute: Daping Hospital, Army Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: To profile the landscape of circRNAs in neutrophils of COVID-19 and sepsis patients, we conducted comprehensive expression profiling analysis in a training cohort.

overall_design: Comparative circRNAs expression profiling analysis of RNA-seq data for neutrophils from four healthy donors,five critically ill patients with COVID-19 and ten bacterial sepsis patients.

first: Yao

last: Lu

first: Aiqing

last: Wen


title: Transcriptomic analysis of REVOLUTA and KANADI cell-types of Arabidopsis shoot apical meristem

city: Mohali

first: Hasthi

last: Ram

address: Sector 81

department: Agriculture biotechnology

country: India

institute: NABI (National Agri-Food Biotechnology Institute)

summary: Dorso-ventral (DV) patterning at the Shoot Apical meristem (SAM) is essential for organogenesis in Arabidopsis. Dorsal and ventral gene expressed domains are separated by boundaries from where the new organ initiation starts. Here by using cell-types specific transcriptomics approach, we have identified dorsal, ventral and boundary specific genes in SAM.

overall_design:
5 different cell-types, and 4 biological replicates for each cell-type were collcted through FACS, and used for RNA-Seq analysis:
BFP: Epidermal boundary
BFPGFP: Ventral Epidermal cell-types
BFPYFP:  Dorsal Epidermal cell-types
GFP:  Ventral Sub-epidermal cell-types
YFP: Dorsal Sub-epidermal cell-types

first: Marcus

last: Heisler


title: Potential mechanisms of zinc sulfate in inhibiting porcine reproductive and respiratory syndrome virus replication: attenuation of oxidative stress, inflammatory response, and apoptosis

status: Public on Aug 23 2025

city: taigu

first: Huizhen

last: Yang

address: Num 1 Ming Xian South Road

department: College of Veterinary Medicine

institute: Shanxi Agricultural University

summary: Zinc, the second most abundant essential trace element in living organisms, can effectively inhibit RNA viral infections. Porcine reproductive and respiratory syndrome virus (PRRSV) is a single-stranded RNA virus. It is still unknown whether zinc can suppress PRRSV replication and what its mechanism of action is.

overall_design: In this study, PRRSV-infected Marc-145 cell model was employed to systematically investigate zinc sulfate's anti-PRRSV mechanisms through integrated multi-omics approaches, including transcriptomics, real-time quantitative PCR, immunoblot, and flow cytometry.


title: A biomemetic senotherapy targeting MAT2A-mediated senescence-inflammation promotes wound regeneration through moonlighting reprogramming

city: Guangzhou

first: Dongming

last: Lv

state: None Selected

address: No.58 Zhongshan 2nd Road, Guangzhou, Guangdong Province, China,

institute: Sun Yat-sen University

summary: To evaluate the role of Mat2a in the wound healing, we generated the Mat2a KO mouse. We investigate the changes in wound healing process between the Mat2a KO mouse and WT mouse.

overall_design: Wound margin tissues of three Mat2a KO and WT mouse were collected, and diagested for single-cell sequencing analysis.

first: Lei

last: Ren

first: Zirui

first: Yanchao

last: Rong

first: Xiaoling

last: Cao

first: Bing

last: Tang


title: SIRT6 Is a Key Regulator of Pancreatic β-Cell Survival and Function During Aging

city: Indianapolis

first: Xiaocheng

middle: Charlie

last: Dong

state: IN

address: 635 Barnhill Dr, MS 1021D

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: SIRT6 has been implicated in anti-aging at the organismal level; however, its role in pancreatic beta cell aging is unclear. This study investigated the role of SIRT6 in pancreatic beta cell aging  using conditional SIRT6 transgenic overexpression mice at 10 and 16 months of age. Our data show that SIRT6 has a strong protective function against aging-associated oxidative stress, DNA damage, and multiple forms of cell death.

overall_design: Primary mouse pancreatic islets were isolated from control and SIRT6 transgenic mice at age of 10 and 16 months. Total RNAs were extracted from the mouse islets and subjected to RNA-seq analysis.

first: Jimin

last: Park

first: Sandali

middle: D

last: Lokuge

first: Menghao

last: Huang

first: Shen

last: Wang

first: Jingru

last: Liang

first: Ramkumar

last: Katturajan

first: Corinn

last: Marakovits

first: Jun

last: Wan

middle: C

first: Sheng

first: Zhihong


title: Metabolomic landscape of fetal organs development during late gestation in mice

city: Shanghai

first: Chanyi

last: Li

address: 168 Changhai Road

institute: The First Affiliated Hospital of Naval Military Medical University

summary: This experiment investigates the differential gene expression of the heart during different developmental stages of mouse embryonic development

overall_design: This experiment collected the hearts of ICR mice at embryonic stages 16.5 and 18.5, with three biological replicates per group for transcriptome sequencing.

first: Wuping

last: Liu

first: Xiaodong

first: Bo

first: Jiaying

last: Qin

first: Ning

last: Yi

first: Bianling

last: Xu

first: Jing

first: Zhigang

last: Xue

first: Hongli

last: Yan

first: Jinfeng


title: A Cell Type Enrichment Analysis Tool for Brain DNA  Methylation Data (CEAM) [BDR]

city: Maastricht

first: Ehsan

last: Pishva

state: Limburg

address: Universiteitssingel 40

department: Psychiatry and Neuropsychology

country: Netherlands

institute: Maastricht University

summary: DNA methylation signatures are highly cell type-specific, yet most epigenome-wide association studies (EWAS) are performed on bulk tissue, potentially obscuring critical cell type-specific patterns. Existing computational tools for detecting cell type-specific DNAm changes are often limited by the accuracy of cell type deconvolution algorithms. Here, we introduce CEAM (Cell-type Enrichment Analysis for Methylation), a robust and interpretable framework for cell type enrichment analysis in DNA methylation data. CEAM applies over-representation analysis with cell type-specific CpG panels from Illumina EPIC arrays derived from nuclei-sorted cortical post-mortem brains from neurologically healthy aged individuals. The constructed CpG panels were systematically evaluated using both simulated datasets and published EWAS results from Alzheimer’s disease, Lewy body disease, and multiple sclerosis. CEAM demonstrated resilience to shifts in cell type composition, a common confounder in EWAS, and remained accurate across a wide range of differentially methylated positions, underscoring its flexibility. Application to existing EWAS findings generated in neurodegenerative diseases revealed enrichment patterns concordant with established disease biology, confirming CEAM’s biological relevance. The workflow is publicly available as an interactive Shiny app (https://um-dementia-systems-biology.shinyapps.io/CEAM/) enabling rapid, interpretable analysis of cell type-specific DNAm changes from bulk EWAS.

overall_design: We aimed to profile DNA methylation of the four major cell types in the healthy human brain to define cell type-specific CpGs for our enrichment tool. Purified cell type fractions were obtained through performing FANS on post-mortem cortical brain samples of neurologically healthy individuals. Subsequently the purified cell nuclei were analyzed using the Infinium MethylationEPIC array in a cohort of 9 female and 10 male individuals resulting in 4(cell types)*20(individuals) = 80 samples.

first: Joshua

last: Müller

first: Valentin

last: Laroche

first: Jennifer

last: Imm

first: Luke

last: Weymouth

last: Harvey

first: Adam

middle: R

last: Smith

first: Daniel

last: van den Hove

first: Katie

last: Lunnon

first: Rachel

last: Cavill


title: A Cell Type Enrichment Analysis Tool for Brain DNA  Methylation Data (CEAM) [UKBBN2]

overall_design: We aimed to profile DNA methylation of four major cell types in the healthy human brain to define cell type-specific CpGs for our enrichment tool. Purified cell type fractions were obtained through performing FANS on post-mortem cortical brain samples of neurologically healthy individuals. Subsequently the purified cell nuclei were analyzed using the Infinium MethylationEPIC array in a cohort of 9 female and 10 male individuals resulting in 4(cell types)*19(individuals) = 76  samples. (one sample was deemed an outlier by the "outlyx" function leaving 75 samples for the analysis)


title: Molecular Signatures of Resilience to Alzheimer’s Disease in Neocortical Layer 4 Neurons

city: Stanford

first: Inma

last: Cobos

state: California

address: 300 Pasteur Drive, Lane Building, L235

institute: STANFORD UNIVERSITY MEDICAL SCHOOL

summary: Single-cell omics is advancing our understanding of selective neuronal vulnerability in Alzheimer’s disease (AD), revealing specific subtypes that are either susceptible or resilient to neurodegeneration. Using single-nucleus and spatial transcriptomics to compare neocortical regions affected early (prefrontal cortex and precuneus) or late (primary visual cortex) in AD, we identified a resilient excitatory population in layer 4 of the primary visual cortex expressing RORB, CUX2, and EYA4. Layer 4 neurons in association neocortex shared overlapping molecular signatures of resilience. Early in the disease, resilient neurons upregulated genes associated with synapse maintenance, synaptic plasticity, calcium homeostasis, and neuroprotective factors, including GRIN2A, RORA, NRXN1, NLGN1, NCAM2, FGF14, NRG3, NEGR1, and CSMD1. We also identified KCNIP4, which encodes a voltage-gated potassium (Kv) channel-interacting protein that interacts with Kv4.2 channels and presenilins, as a key factor linked to resilience. KCNIP4 was consistently upregulated in the early stages of pathology. Furthermore, AAV-mediated overexpression of Kcnip4 in a humanized AD mouse model reduced the expression of the activity-dependent genes Arc and c-Fos, suggesting compensatory mechanisms against neuronal hyperexcitability. Our dataset provides a valuable resource for investigating mechanisms underlying resilience to neurodegeneration.

overall_design: This single-nucleus RNAseq dataset was generated from postmortem fresh frozen human cerebral cortex from patients who died with Alzheimer’s disease (AD) and age-matched healthy controls. It contains ~ 500,000 nuclei, of which ~ 80% are neurons, from the prefrontal (BA9), precuneus (BA7) and primary visual (BA17) cortices from 46 donors, including 18 donors with no or low AD pathology (Braak 0-II), 10 with intermediate AD pathology (Braak IIII-IV), and 18 with high AD pathology (Braak V-VI). The samples were processed as described in our protocol at https://www.protocols.io/view/isolation-of-single-nuclei-from-postmortem-fresh-f-6tuhenw. Each sample was sorted by FANS (fluorescence-activated nucleus sorting) to collect two populations, one consisting of all nuclei and the other enriched for neurons (NeuN+). We annotated 18 excitatory and 19 inhibitory neuronal cell types, as well as glial and vascular cells.

first: S Akila Parvathy

last: Dharshini

first: Marcos

last: Otero-Garcia

first: Weijing

last: Tang


title: Synergistic Role of DGKalpha and zeta in Regulatory T cell function, stability, and pathogenecity

city: Durham

first: Xiaoping

last: Zhong

state: NC

address: Rm 133, 203 Research Drive, MSRB-1

department: Pediatrics

institute: Duke University Medical Center

summary: Regulatory T cells (Tregs) actively engage in immune suppression to prevent autoimmune diseases but also inhibit anti-tumor immunity. Although Tregs express a TCR repertoire with relatively high affinities to self, they are normally quite stable and their inflammatory programs are intrinsically suppressed. We report here that diacylglycerol kinases (DGK) alpha and zeta are crucial for homeostasis, suppression of proinflammatory programs, and stability of Tregs and for enforcing their dependence on CD28 costimulatory signal. Treg-specific deficiency of both DGKa and z derails signaling, metabolic, and transcriptional programs in Tregs to cause dysregulated phenotypic and functional properties and to unleash conversion to pathogenic exTregs, especially exTreg-T follicular helper (Tfh) 2 cells, leading to uncontrolled effector T cell differentiation, deregulated germinal center B cell responses and IgG1/IgE predominant antibodies/autoantibodies, and multiorgan autoimmune diseases. Our data not only illustrate the crucial roles of DGKs in Tregs to maintain self-tolerance but also unveil a Treg-to-self-reactive-pathogenic-exTreg-Tfh-cell program that is suppressed by DGKs and that could exert broad pathogenic roles in autoimmune diseases if unchecked.

overall_design: Splenocytes and lymph node cells from WT-Foxp3YFPiCre and DGKa-/-zf/f-Foxp3YFPiCre mice were enriched for CD4+ T cells using magnetic beads.  Enrichment of CD4+ T cells were sorted into CD4+CD8-Foxp3YFP+ regulatory T cells (Tregs) and CD4+CD8-Foxp3YFP- conventional T cells (Tcons). Total RNA from sorted Tregs and Tcons were purified and subjected to mRNAsequencing.

first: Lei

last: Li


title: Establishment of U2OS osteosarcoma cell line with GREM1 knockdown

first: hanyuchen

last: han

address: 27 Taiping Rd

institute: Beijing Institute of biotechnology

summary: To explore the downstream regulatory pathway of GREM1, we established a U2OS osteosarcoma cell line with GREM1 knockdown

overall_design: Comparative gene expression profiling analysis of RNA seq data between GREM1 knockdown U2OS cell lines and control U2OS cell lines

first: Yuchen

last: Han


title: Effect of depletion of Lrrk2 on mice acute kidney injury

first: Shun

last: Zhang

state: Shanghai

address: 1665, Kongjiang Road, Yangpu

department: Urology

institute: Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University

summary: To investigate the function of Lrrk2  in the regulation of actue kidney injury, we performed RNA-seq onLrrk2-/- mice (C57BL/6 N-Lrrk2tm1.Mjff/J).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mice with two genotypes(WT and Lrrk2-/-) and two groups (sham and I/R).

first: Haibo

last: Shen


title: Regulatory and antimicrobial dual functions of the pvf cluster in biocontrol strain Pseudomonas sp. MUP55

status: Public on Aug 22 2025

city: Perth

first: Hussain

last: Alattas

address: 90 South St

country: Australia

institute: Murdoch University

summary: Bacterial antimicrobial compounds and global regulatory networks are typically studied as separate systems, limiting our understanding of how these functions might be integrated. Here we reveal a dual-function system in the biocontrol strain Pseudomonas sp. MUP55, where the pvf cluster simultaneously functions as a global regulator of specialized metabolism and produces direct antimicrobial compounds. Metabolomic and transcriptomic analysis of a ∆pvfC mutant showed extensive global change of the regulation of metabolites and gene expression, with effects on specialized metabolites. Remarkably, pvfC differentially regulates dual siderophore systems and uncouples typically co-regulated small regulatory RNAs in the Gac/Rsm cascade. Heterologous expression confirmed the pvf cluster produces compounds with direct antimicrobial activity independent of its regulatory functions. Comparative genomic analysis revealed the MUP55 pvf cluster contains a rare additional pvfE gene found in only 3.4% of identified pvf clusters. This evolutionary integration of regulatory and defensive functions within a single genetic system provides an efficient strategy for bacterial competitive fitness and resource allocation, expanding our understanding of how beneficial microbes coordinate cellular processes while maintaining environmental competitiveness

overall_design: RNA-seq for the WT and the pvfC mutant.

first: Samuele

last: Sala

last: Murphy

first: Colin

last: Scott


title: Long noncoding RNA-dependent control of Myc transcriptional bursting [RNA-Seq]

city: New Haven

first: Nadya

last: Dimitrova

state: CT

address: 260 Whitney Ave YSB211

department: MCDB

institute: Yale University

summary: Genes are transcribed in short periods of activity, called bursts. Bursts are initiated by enhancer-promoter contacts and dynamically controlled by the levels of enhancer- and promoter-produced RNAs through a negative feedback mechanism. Here, by direct visualization of nascent transcripts, we show that chromatin-associated long noncoding RNAs (lncRNAs) contribute to the regulation of transcriptional bursting. We find that production of Pvt1 raises the baseline of RNA concentration in the locus of the Myc proto-oncogene and acts locally and in a dose-dependent manner to decrease the duration of Myc bursting. Premature termination of Pvt1 led to higher Myc expression and transcriptional activities, resulting in increased cellular proliferation and advanced tumor development in autochthonous models of lung cancer. These findings point to a critical lncRNA-mediated mechanism for Myc regulation and suggest a potentially widespread role for lncRNAs in fine-tuning gene expression through local control of transcriptional bursting.

overall_design: Primary Pvt1+/+ and Pvt1aP/P MEFs were isolated from littermate E13.5 MEFs and cultured in DMEM supplemented with 15% FBS, Pen/Strep, L-glutamine, NEAA, and b-ME. Samples were harvested in two biological replicates from two independent littermate pairs. For RNA-seq, total RNA was isolated using the Qiagen RNeasy Kit and submitted for library preparation and sequencing at the Yale Center for Genome Analysis (YCGA). For ATAC-seq and Hi-C, cryopreserved cells were submitted for library prepation and sequencing at YCGA.

first: Qiao

first: Corinne

last: Dilsavor

first: Valid

last: Gahramanov

first: Erin

last: Floyd

first: Jane

last: Ding

first: Justin

last: Glynn

first: Ioannis

last: Chiotakakos

first: Christiane

last: Olivero

first: Jesse

last: Zamudio


title: Long noncoding RNA-dependent control of Myc transcriptional bursting [HiC]

last: Li


title: Long noncoding RNA-dependent control of Myc transcriptional bursting [ATAC-Seq]


title: WNT8B and WNT9B signaling promote the survival of dormant HGSOC cells through a non-canonical pathway that regulates cancer stem cell phenotypes.

city: London

first: Komila

last: Zakirova

state: ON

address: 790 Commissioners Road E

department: Pathology and Laboratory Medicine

country: Canada

institute: Western University

summary: Cancer cell dormancy and the resultant resistance to conventional therapies present significant challenges for the successful treatment of high-grade serous ovarian cancer (HGSOC). We used genome wide and specialized sgRNA libraries in CRISPR-based screens to identify critical features of dormancy and metastasis. Our findings demonstrate that Wnt ligands WNT8B and WNT9B are essential for sustaining cell survival during prolonged dormant spheroid culture conditions. Inhibition of Wnt signaling by WNT8B/9B knock out not only compromised spheroid cell viability, but also negatively affected spheroid formation. These Wnt ligands utilize a non-canonical signaling pathway to activate expression of stem cell genes during spheroid dormancy.

overall_design: We constructed a sgRNA library targeting a selected list of 2,740 genes and non-targeting controls. CRISPR screen was conducted in OVCAR8 cells. sgRNA identity and abundance were determined in three replicates for each condition: adherent (ADH), which involved initially infected cells expanded under adherent culture conditions, and spheroid (SPH) cells following 48 hours of suspension culture. Each condition contains data for cells expressing Cas9 (Cas9-positive) and those not expressing Cas9 (Cas9-negative). The sgRNA abundance for the initial plasmid library preparation are also provided in the readcounts table. The CRISPR screen was analyzed using the TRACS software package as described in GSE150246.

first: Fred

last: Dick


title: Fibroblast growth factors induce preadipocyte UCP1 expression and imprint on post-differentiation white and brown adipocyte function

city: Freising

first: Katharina

last: Küllmer

state: Bavaria

address: Gregor-Mendel Straße 2

country: Germany

institute: Technical University of Munich

summary: Objective: The presence of uncoupling protein 1 (Ucp1) is a hallmark of thermogenic adipocytes and enables heat production by dissipating energy from mitochondrial proton motive force as heat. The purpose of its recently discovered presence in preadipocytes in response to certain fibroblast growth factors (FGFs) remains elusive. Methods: In this study, we systematically investigated the potential of all paracrine FGFs to invoke Ucp1 expression in murine preadipocytes derived from interscapular brown and inguinal white adipose tissue. Results: The factors FGF2, FGF4, FGF8, and FGF9 induced Ucp1 expression in undifferentiated preadipocytes, with FGF2 acting most potently and rapidly. This premature Ucp1 induction did not translate into increased Ucp1 protein abundance or thermogenic activity after full adipogenic differentiation. Notably, preadipocyte treatment with FGFs and parallel Ucp1 expression led to a sustained suppression of interferon-stimulated genes after differentiation. Preadipocyte Ucp1 was required and sufficient for this lasting imprint. Conclusion: Thus, FGF-induced Ucp1 expression in preadipocytes programs a lasting post-differentiation anti-inflammatory status.

overall_design: Following primary preadipocyte isolation (stromal vascular fraction) from iBAT and iWAT (C57BL/6N, wild-type), cells were treated upon confluency with 5.5 nM FGF2 or let untreated for 48 hours.

last: Kuellmer

first: Tobias

last: Fromme


title: TTK defines a high-risk Oral Squamous Cell Carcinoma subtype through dual mTORC1/NF-κB activation

first: Tianjie

last: Liu

state: Shannxi

address: No.277, Yanta West Road

institute: The First Affiliated Hospital of Xi'an Jiaotong University

summary: Oral squamous cell carcinoma (OSCC) remains challenging to treat due to significant tumor heterogeneity, highlighting the need for identifying molecular subtypes with distinct therapeutic vulnerabilities. Here, we present a comprehensive molecular analysis of 709 OSCC cases, integrating single-cell RNA sequencing and bulk transcriptomic data. We identify a distinct molecular subtype of OSCC characterized by co-activation of the mTORC1 and NF-κB pathways, with TTK emerging as a central regulator of this co-activation. This subtype exhibits heightened genomic instability. Using protein mass spectrometry and immunoprecipitation, we demonstrate that TTK activates the NF-κB pathway through interaction with the TAK1-TAB protein complex. Functional in vitro and in vivo experiments further reveal that TTK inhibition significantly enhances cisplatin sensitivity in OSCC. These findings provide a basis for patient stratification and underscore the potential of targeting TTK in therapeutic strategies for this high-risk OSCC subtype.

overall_design: RNA-seq profiling of wildtype SCC-15 and CAL-27 cells and their knockdown derivatives (shTTK).

first: Huan

last: Jin

first: Yucheng

last: Guo

first: Wenqing

last: Bu

first: Fei

first: Yuxia

last: Hou


title: Positionally distinct interferon-stimulated dermal immune-acting fibroblasts promote neutrophil recruitment in Sweet's syndrome [RNA-seq]

city: San Diego

first: Kellen

last: Cavagnero

address: 9500 Gilman Dr

institute: Univeristy of California, San Diego

summary: Sweet’s syndrome is a poorly understood inflammatory skin disease. In this study, cellular and molecular landscape of skin from patients with SS, PG and healthy controls using  RNA sequencing have been defined.

overall_design: Human skin biopsies from affected individuals were collected and processed for library prep and next-generation sequencing at the Advanced Genomics Core at the University of Michigan.

first: Johann

last: Gudjonsson

first: Richard

last: Gallo

first: Lam

last: Tsoi


title: Positionally distinct interferon-stimulated dermal immune-acting fibroblasts promote neutrophil recruitment in Sweet's syndrome.

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

overall_design: Refer to individual Series


title: CDK1 regulation of P53 phosphorylation mediates cell cycle arrest and apoptosis of macrophages infected with clinical isolates of Mycobacterium tuberculosis from the Xinjiang region, China

city: Urumqi

first: Banghao

last: Sun

address: No. 8, Xinyi Road, Xinshi District

institute: Xinjiang Medical University School of Basic Medicine

summary: THP-1 Macrophages were infected with Mycobacterium tuberculosis clinical isolates from Xinjiang, China, and H37Rv for 24 hours, respectively, and their transcriptomes were sequenced to investigate the specific biological processes that occur after infection of macrophages with Mycobacterium tuberculosis clinical isolates from Xinjiang, China.

overall_design: L3-L6 are samples of macrophages infected with clinical isolates of Mycobacterium tuberculosis from Xinjiang, China;V1-V3 are samples of macrophages infected with H37Rv；C1-C3 are samples of macrophages not infected with any tuberculosis


title: Preadipocyte uncoupling protein 1 expression invoked by fibroblast growth factors imprints on post-differentiation white and brown adipocyte function

summary: The presence of uncoupling protein 1 (UCP1) is a hallmark of thermogenic adipocytes and enables heat production by dissipating energy from mitochondrial proton motive force as heat. The purpose of its recently discovered presence in preadipocytes in response to certain fibroblast growth factors (FGFs) remains elusive. In this study, we systematically investigated the potential of all paracrine FGFs to invoke Ucp1 expression in murine preadipocytes derived from interscapular brown and inguinal white adipose tissue. The factors FGF2, FGF4, FGF8, and FGF9 induced Ucp1 expression in undifferentiated preadipocytes, with FGF2 acting most potently and rapidly. This premature Ucp1 induction did not translate into increased Ucp1 thermogenic activity after full adipogenic differentiation. Notably, preadipocyte treatment with FGFs and parallel Ucp1 expression led to a sustained suppression of interferon-stimulated genes after differentiation. Preadipocyte Ucp1 was required and sufficient for this lasting imprint. Thus, FGF-induced Ucp1 expression in preadipocytes programs a lasting post-differentiation anti-inflammatory status.

overall_design: Primary white preadipocytes were isolated from murine Ucp1_KI (luciferase reporter, heterozygous) mice. Cells were treated with 5.5 nM FGF1, FGF2, FGF4, FGF8, or FGF9, or left untreated as control. Treatments were performed in triplicate for 48 hours in DMEM supplemented with 10% FBS, starting at ~80% confluency. RNA was directly isolated using the Promega kit and submitted for library preparation and sequencing (Novogene). Samples: Replicate 1: S1 (control), S2 (FGF1), S3 (FGF2), S4 (FGF4), S5 (FGF8), S6 (FGF9); Replicate 2: S7 (control), S8 (FGF1), S9 (FGF2), S10 (FGF4), S11 (FGF8), S12 (FGF9); Replicate 3: S13 (control), S14 (FGF1), S15 (FGF2), S16 (FGF4), S17 (FGF8), S18 (FGF9)


title: Dynamical network biomarker analysis using multi-organ RNA sequencing in metabolic syndrome model mice

city: Toyama

first: Makito

last: Oku

address: 2630 Sugitani

department: Research Center for Pre-Disease Science

institute: University of Toyama

summary: Dynamical network biomarker (DNB) theory has emerged as a powerful framework for detecting early warning signals of pre-disease states. Based on our previous work demonstrating its utility in adipose tissue of metabolic syndrome model mice, we conducted a comprehensive DNB analysis using RNA sequencing data across 13 organs and 14 to 16 time points in high-fat diet-fed mice. Our findings revealed organ-specific variation in the timing of early warning signals, suggesting heterogeneous inter-organ dynamics during the pre-disease state of metabolic syndrome. These results highlight the potential of DNB theory for elucidating systemic early-stage pathophysiology in complex metabolic disorders.

overall_design: Male C57BL/6J mice were fed high-fat diet (HFD) from eight weeks of age. From zero days (HFD onset) to 12 weeks, RNA-seq was conducted for 13 organs: epididymal white adipose tissue (eWAT), inguinal white adipose tissue (iWAT), interscapular brown adipose tissue (BAT), pancreas, liver, small intestine, soleus muscle, gastrocnemius muscle, hypothalamus, pituitary gland, neocortex, hippocampus, and olfactory bulb. At 16 and 20 weeks, RNA-seq was conducted only for eWAT. Six mice were measured per time point.

first: Akiko

last: Inujima

first: Keiichi

last: Koizumi

first: Kazutaka

last: Akagi

first: Shiho

last: Fujisaka

first: Tsutomu

last: Wada

first: Yasuhiro

last: Onogi

first: Toshiyasu

last: Sasaoka

first: Kazuyuki

last: Tobe

first: Makoto

last: Kadowaki

first: Xun

last: Shen

first: Jun-ichi

last: Imura

last: Aihara

first: Shigeru

last: Saito


title: Ontogeny of the spinal cord dorsal horn [Xenium]

city: Bethesda

first: Brian

last: Roome

state: MD

address: 35 Convent Drive

department: NINDS

institute: National Institutes of Health

summary: An exquisite example of form serving function is the dorsal horn of the spinal cord, the gateway  to the central nervous system for sensory information from the body. Each sensory input to the  dorsal horn targets a specific address within its laminated arrangement of diverse neuronal  populations. However, it is not known how this organization emerges during development from  an apparently homogenous pool of neural progenitors. Here, we found that both the excitatory  and inhibitory cell families of the mouse dorsal horn were born in successive waves as temporal  cohorts. The excitatory families then settled into a chronotopic map that transformed their birth  order into the dorsal laminae. Diversification of families into refined neuron types was mediated  by a dorsal-ventral progenitor gradient of Zic transcription factors. This work uncovered  fundamental temporal and spatial factors that establish the cell types and structure of the  spinal cord dorsal horn.

overall_design: Spinal cords taken from E16.5 mouse embryos were examined using the 10X Xenium v1 spatial transcriptomics platform, using the 247 gene mouse brain probe panel and with 100 additional custom gene probes.

first: R

middle: B

first: Ariel

middle: J

last: Levine


title: Decreased ALKBH5 in neutrophil correlates with disease activity in rheumatoid arthritis and ALKBH5 modulates neutrophil autophagy

city: nanchang

first: zhiwei

last: wu

address: No.17, Yongwai Street, Donghu District, Nanchang City, Jiangxi Province

institute: The First Affiliated Hospital of Nanchang University

summary: Neutrophils are key immune components in rheumatoid arthritis (RA), but the role of ALKBH5 in neutrophil function and RA progression remains unclear. METTL3, METTL14, WTAP, ALKBH5, FTO, YTHDF2, autophagy related gene were investigated by RT-qPCR. Autophagy, LC3B were respectively detected by flow cytometry analysis, Western blotting. Correlation analyses between ALKBH5 levels and RA disease activity, autophagy were performed, and receiver operating characteristic (ROC) curves were constructed to evaluate its predictive value. Univariate analysis and multivariate regression analysis were used to analyze the risk factors and construct predictive model. Sh-ALKBH5 lentiviral vectors was constructed and used to infect HL-60 cell line. The role of ALKBH5 in autophagy regulation was explored using RNA immunoprecipitation with next generation sequencing (RIP-Seq), m6A RNA Methylation Analysis, m6A immunocoprecipitation-quantitative polymerase chain reaction (MeRIP-qPCR) and Actinomycin D treatment. Results showed significantly reduced ALKBH5 levels in RA neutrophils compared to healthy controls (HC) and ankylosing spondylitis (AS) patients, correlating with RA disease activity. A novel predictive model incorporating ALKBH5, hemoglobin (HGB), and lymphocyte percentage (L%) exhibited enhanced efficacy in distinguishing RA patients from HC (AUC = 0.937) and AS patients (AUC = 0.943), and could reflect RA severity and activity. Additionally, autophagy levels in neutrophils were highest in RA synovial fluid, followed by RA peripheral blood, and lowest in HC peripheral blood, with ALKBH5 expression showing the opposite trend. Moreover, ALKBH5 negatively correlated with neutrophil autophagy and the silencing of ALKBH5 in HL-60 enhanced the autophagy. Silencing ALKBH5 increased m6A level of ATG7 mRNA and ATG7 mRNA stability. Mechanistically, ALKBH5 inhibited neutrophil autophagy through mediating m6A modification of the ATG7 mRNA. In conclusion, these findings demonstrate that ALKBH5 regulates neutrophil autophagy in RA, and the ALKBH5-HGB-L% model holds potential as a diagnostic and disease activity indicator for RA.

overall_design: Briefly, The HL-60 was treated with cell lysis buffer. Ten percent of the lysate was stored as "input," 80% was used for immunoprecipitation with anti-ALKBH5 antibody (Proteintech, Wuhan, China) ("IP"), and 10% was incubated with rabbit IgG (Cell Signaling Technology) as a negative control ("IgG").

first: Qing

last: Luo

first: Mengfan

last: Lan

first: Zhiwei

last: Wu

first: Shiqian

last: Wang

first: Peng

last: Fu

first: Qiuyun

last: Xiao

first: Biqi


title: Positionally distinct interferon-stimulated dermal immune-acting fibroblasts promote neutrophil recruitment in Sweet’s syndrome [snRNA-seq]

first: Kellen

last: Cavagnero

summary: Sweet’s syndrome (SS) is a poorly understood inflammatory skin disease. Using  RNA sequencing from patients with SS, Pyoderma_Gangrenosum (PG) and healthy controls, in the study, the gaps in the understanding of cellular and molecular landscape of SS and PG skin are addressed.

first: Johann

last: Gudjonsson

first: Richard

last: Gallo

first: Lam

last: Tsoi


title: ZNF512B associates with mitotic spindles, regulates metaphase exit and is crucial for stem cell differentiation

city: Giessen

first: Johannes

last: Groos

state: Hessen

address: Heinrich-Buff-Ring 58-62

department: Institute of Genetics

institute: Justus-Liebig-University Giessen

summary: Zinc finger proteins are a large family of DNA-binding factors that play key roles in diverse cellular processes including gene regulation, RNA metabolism and cell cycle control.  The zinc finger protein ZNF512B has recently been implicated in chromatin organization and transcriptional repression through its direct interaction with the nucleosome remodeling and deacetylase (NuRD) complex, its DNA-binding ability, and its association with the histone variant H2A.Z. Here, we uncover a previously unrecognized role for ZNF512B that is independent of both its zinc finger domains and NuRD association. We identify ZNF512B as a spindle-associated factor that regulates progression through mitosis, specifically controlling metaphase exit. ZNF512B’s N-terminal internal region, which contains 25 repeats of a six-residue motif predicted to form a β-helix structure, is required and sufficient for its spindle interaction. Elevated ZNF512B levels result in a profound metaphase arrest that is ultimately lethal, a phenotype arising from the combined activity of its spindle-binding and chromatin-tethering functions. Conversely, ZNF512B depletion accelerates stem cell proliferation, impairs differentiation, and upregulates genes linked to cell cycle progression.  Our findings position ZNF512B as a multifunctional protein that acts as a transcriptional repressor, a chromatin aggregator and a novel mitotic exit regulator through spindle fiber binding.

overall_design: Gene expression profiling analysis of RNA-seq data from V6.5 mESCs during differentiation toward cardiomyocytes (CM) and Neural progenitor cells (NPC). Samples were collected from naive (triplicate) , primed and fully differentiated CMs and NPCs in duplicates in wildtype and ZNF512B knockout.

first: Lena

middle: W

last: Paasche

first: Nadine

last: Daus

first: Felix

last: Diegmüller

first: Carlotta

last: Kreienbaum

first: Erekle

last: Kobakhidze

first: Jie

first: Stefanie

last: Wunderlich

first: Annette

last: Borchers

first: Joel

middle: P

last: Mackay

first: Tim

first: Sandra

last: Hake


title: Parental preconceptual α-cypermethrin exposure alters embryonic brain transcriptomics in mice: implications for autism spectrum disorder and stress vulnerability

city: Iowa City

first: Benjamin

last: Hing

state: IA

address: 51 Newton Road, BSB 6-509

institute: University of Iowa

summary: Pyrethroid insecticides are widely used in agriculture and households, and their exposure can affect neurodevelopment. Few studies have evaluated how preconception parental exposure could also affect this process. To address knowledge gap, adult C57Bl6/J mice were gavaged daily with -cypermethrin at a human relevant low  (0.3 mg/kg) or high (10 mg/kg) dose in corn oil for four weeks prior to conception. Offspring embryonic day 16 dorsal forebrain was extracted for transcriptomic analysis. In offspring forebrains of exposed compared to unexposed parents, there was increasing number of differentially expressed genes (DEGs) from paternal (least) to maternal to both parent  exposure (most).  A dose dependent effect was observed in offspring forebrain for paternal and maternal preconceptual exposures. Maternal and both parent exposures led to upregulated genes in offspring brain for biological processes involved in translation with predicted activation of EIF4E, a gene associated with autism. In contrast, paternal exposure upregulated cell cycle related DNA damage signaling processes. After any parent exposure, there was upregulation of biological processes involved in mitochondria function and oxidative stress and a downregulation of neuronal and synaptic processes with predicted inhibition of BDNF signaling. Weighted gene correlation network analysis identified modules associated with different parent treatment that were over-represented with DEGs with similar functional signatures as found in DEG-related pathways.  Importantly, DEGs in offspring forebrain after any parent exposure were over-represented with genes related to autism spectrum disorder (ASD) and stress vulnerability. The study highlights the potential contribution of preconception parental pyrethroid exposure to aberrant brain functioning.

overall_design: RNA-Seq of E16 dorsal forebrain of C57Bl/6J mice from different combination of parental exposured to α-cypermethrin.

first: Robert

last: Taylor

first: Samuel

last: Eliasen

first: Hanna

last: Stevens


title: Positionally distinct interferon-stimulated dermal immune-acting fibroblasts promote neutrophil recruitment in Sweet's syndrome [Nanostring CosMx SMI spatial transcriptomics]

first: Kellen

last: Cavagnero

summary: Sweet’s syndrome is a poorly understood inflammatory skin disease characterized by neutrophil infiltration to the dermis. Single-nucleus and bulk transcriptomics of archival clinical samples of Sweet’s syndrome revealed a prominent interferon signature in Sweet’s syndrome skin that was reduced in tissue from another neutrophilic dermatosis, pyoderma gangrenosum, as well as healthy controls. This signature was observed in different subsets of cells, including fibroblasts that expressed interferon-induced genes. Functionally, this response was supported by analysis of cultured primary human dermal fibroblasts that were observed to highly express neutrophil chemokines in response to activation by type I interferon. Furthermore, single-molecule resolution spatial transcriptomics of skin in Sweet’s syndrome identified positionally distinct immune-acting fibroblasts that included a CXCL1+ subset proximal to neutrophils and a CXCL12+ subset distal to the neutrophilic infiltrate. This study defines the cellular landscape of neutrophilic dermatoses and suggests dermal immune-acting fibroblasts play a role in the pathogenesis of Sweet’s syndrome through recognition of type I interferons.

overall_design: Nanostring CosMx SMI spatial transcriptomics 1000 gene panel applied to skin from patients with Sweet's syndrome (n=5) and healthy controls (n=2)


title: Gene expression profiling of triple-negative breast cancer cells and liver cancer cells perturbed by BET inhibitor JQ1

city: Chengdu

first: Yumei

last: Wang

address: 1166 LiuTai

institute: Chengdu University of TCM

summary: To obtain the gene expression profiles of triple-negative breast cancer MDA-MB-231 cells and liver cancer HepG2 cells perturbed by the BET inhibitor JQ1, we treated MDA-MB-231 and HepG2 cells with either DMSO (control) or 10 μM JQ1 for 24 hours. By comparing the expression profiles of DMSO-treated cells with those treated with JQ1, we can identify the genes affected by JQ1.

overall_design: MDA-MB-231 and HepG2 cells were treated with 0.1% DMSO or 10 μM JQ1 for 24 hours followed by RNA isolation

first: Lei

last: Xiang

first: Yu

last: Gui

first: Dong


title: CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts [RNA-Seq rescue]

city: Kansas City

first: Ariel

middle: Alejandro

last: Bazzini

state: Missouri

institute: Stowers Institute for Medical Research

summary: The Maternal-to-Zygotic transition (MZT) is a reprograming process encompassing zygotic genome activation (ZGA) and the clearance of maternally-provided mRNAs. While some factors regulating MZT have been identified, there are thousands of maternal RNAs whose function has not been ascribed yet. Here, we have performed a proof-of-principle CRISPR-RfxCas13d maternal screening targeting mRNAs encoding protein kinases and phosphatases in zebrafish and identified Bckdk as a novel post-translational regulator of MZT. Bckdk mRNA knockdown caused epiboly defects, ZGA deregulation, H3K27ac reduction and a partial impairment of miR-430 processing. Phospho-proteomic analysis revealed that Phf10 (Baf45a), a chromatin remodeling factor, is less phosphorylated upon Bckdk depletion. Further, phf10 mRNA knockdown also altered ZGA and Phf10 constitutively phosphorylated rescued the developmental defects after bckdk mRNA depletion. Altogether, our results demonstrate the competence of CRISPR-RfxCas13d screenings to uncover new regulators of early vertebrate development and shed light on the post-translational control of MZT mediated by protein phosphorylation.

overall_design: Transcriptomic analysis of the mRNA knockdown conditions in the maternal screening at 4 or 6hpf using RfxCRISPR-Cas13d system

first: Luis

last: Hernández-Huertas

first: Miguel A.

last: Moreno-Mateos


title: CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts [CUT&Run]

overall_design: Cut&Run of H3k27ac in zebrafish embryos injected only with RfxCas13d protein and embryos injected with RfxCas13d protein and a mix of 2 gRNAs targeting bckdk mRNA (Bckdk KD)

first: Jose M.

last: Santos-Pereira

first: Ariel A.


title: Ontogeny of the spinal cord dorsal horn

first: Brian

last: Roome


title: Gene expression changes related to immunosuppression in patients with traumatic brain injury (Part 1)

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

summary:
Background : Traumatic brain injury (TBI) can alter various immune functions, including immunosuppression and constitutes a risk factor for nosocomial infections and organ dysfunction. Although TBI can induce a decline in immune cell function, the detailed mechanisms remain unclarified. This study aimed to clarify the mechanism of immunosuppression caused by TBI using a comprehensive transcriptome analysis of immune cells.
Methods : Six patients with traumatic brain injury and acute subdural hematoma were admitted to our hospital. We focused on three major subsets of immune cells responsible for the immune response: CD4+ T cells, CD8+ T cells, and monocytes. We evaluated the changes in immune function after injury using comprehensive transcriptome analysis. Blood samples were collected immediately after admission and one week later, and the data were compared with those of healthy volunteers.
Results : CD4+ T cells and CD8+ T cells decreased over seven days following injury, and a decrease in cell adhesion and endoplasmic reticulum function was observed. It was suggested that the process of protein synthesis from RNA was impaired and that overall cell function was reduced. Monocytes also show a decrease in endoplasmic reticulum function, but classical and nonclassical monocyte subsets show an increase in functions related to platelet activation and tissue repair.
Conclusions : Comprehensive transcriptome analysis confirmed a decrease in endoplasmic reticulum function in CD4+ T cells, CD8+ T cells, and monocytes. This study facilitates further elucidation of the mechanisms of immunosuppression due to trauma and the development of new therapeutic strategies to suppress secondary infections.

overall_design: We performed a retrospective, observational, case-control, single-center study.  Samples from the patients were collected at two timepoints: within 24 h of admission and on the 7th or 8th day of admission. PBMCs were isolated from fresh whole blood. Two panels were used to identify subsets of CD4+ T cells, CD8+ T cells, and monocytes from PBMCs. Total RNA was extracted from the sorted cells. Whole-transcriptome sequencing was performed on an Illumina NovaSeq 6000 platform using a 151-base pair-end sequencing strategy.

first: Hiroshi

last: Ito

first: Masakazu

last: Ishikawa

first: Hisatake

last: Matsumoto

last: Ogura

last: Okuzaki

first: Jun

last: Oda


title: Ontogeny of the spinal cord dorsal horn [scRNA-seq]

summary: An exquisite example of form serving function is the dorsal horn of the spinal cord, the gateway to the central nervous system for sensory information from the body. Each sensory input to the dorsal horn targets a specific address within its laminated arrangement of diverse neuronal populations. However, it is not known how this organization emerges during development from an apparently homogenous pool of neural progenitors. Here, we found that both the excitatory and inhibitory cell families of the mouse dorsal horn were born in successive waves as temporal cohorts. The excitatory families then settled into a chronotopic map that transformed their birth order into the dorsal laminae. Diversification of families into refined neuron types was mediated by a dorsal-ventral progenitor gradient of Zic transcription factors. This work uncovered fundamental temporal and spatial factors that establish the cell types and structure of the spinal cord dorsal horn.

overall_design: Spinal cords taken from E14.5 and E16.5 mouse embryos at three axial levels were run on the 10X Chromium 3' gene expression assay. All spinal cord cells were indiscriminately collected, and neurons were selected post-sequencing for further analysis. The goals of this work were to identify hierarchical organization of dorsal horn neurons, and to use described axes of variation to uncover basic ontogenic principles.

first: Robert

first: Archana

last: Yadav

first: Lydia

last: Flores

first: Amrit

last: Puarr

first: Diana

last: Nardini

first: Alexander

last: Richardson

first: Ronald

last: Waclaw

first: Ruth

last: Arkell

first: Vilas

last: Menon

first: Jane

middle: E

last: Johnson

last: Levine


title: Zeaxanthin augments CD8+ effector T cell function by enhancing TCR stimulation

city: Chicago

first: Jiacheng

last: Li

state: IL

address: 900 E 57th Street,

department: Medicine

institute: University of Chicago

summary: The detailed mechanisms underlying regulatory significance of dietary components in modulating anti-tumor immunity remain largely unknown. Here, we applied a co-culture screen approach using a blood nutrient compound library to identify zeaxanthin, a dietary carotenoid pigment found in many fruits and vegetables that is important for eye health, as an immunomodulator that enhances cytotoxicity of CD8+ T cells towards tumor cells. Oral zeaxanthin, but not lutein, a carotenoid with similar structure, enhances anti-tumor immunity in vivo. Integrated multi-omics mechanistic studies reveal that zeaxanthin directly promotes T-cell receptor (TCR) stimulation on CD8+ T cell surface, leading to improved intracellular TCR signaling for effector T cell function. Hence, zeaxanthin treatment augments effectiveness of immune checkpoint inhibitor in vivo and human TCR-engineered CD8+ T cells to induce cell death in co-cultured tumor cells. Our findings uncover a previously unknown immunoregulatory function of zeaxanthin, which has translational potential as a dietary element in immunotherapy.

overall_design: RNA seq profiling of mouse primary CD8+ T cells treated with Zeaxanthin, Lutein, and DMSO. (n=3)

first: Freya

last: Zhang

first: Rukang

first: Jiayi

last: Tu

first: Zhicheng

last: Xie

first: Takemasa

last: Tsuji

first: Hardik

last: Shah

first: Matthew

last: Ross

first: Ruitu

last: Lyu

first: Junko

last: Matsuzaki

first: Kelly

last: Xue

first: Fatima

last: Choudhry

first: Chunzhao

last: Yin

first: Hamed

last: Youshanlouei

first: Michael

last: Drazer

first: Yu-Ying

last: He

first: Marc

last: Bissonnette

first: Yuancheng

first: Hui

last: Mao

last: Huang

first: Lei

last: Dong

first: Rui

last: Su

first: Chuan

first: Kunle

last: Odunsi

first: Syed

first: Hao

last: Fan

first: Jing

last: Chen


title: Exploring the anti-breast cancer effects of Thai traditional formulary medicine (TTFM) extracts using gut microbiota and gene expression profiles in CLDX mouse models

city: Bangkok

first: Ariya

last: Kkamwut

country: Thailand

institute: Chulalongkorn University

summary: Identification of the effects of Thai traditional formulary medicine (TTFM) on the tumor gene expression profiles in breast cancer mouse models.

overall_design: This research aimed to study the gene expression profiles of tumor samples from CLDX mouse models treated with or without Thai traditional formulary medicine (TTFM) extracts. Mice were injected with 3x105 4T1 cells into the left mammary fat pad via subcutaneous injection under aseptic conditions. Two weeks post-transplantation, mice were treated with or without TTFM. At the end of the experiment, the mice were euthanized via CO2 inhalation. Tumor tissues were collected, rinsed with PBS, stored in DNA/RNA Shield™, snap-frozen in liquid nitrogen, and kept at -80ºC until further use.

last: Khamwut


title: RNA seq for HLECs transfected with siID3

first: Han

last: Peng

address: 303 E Chicago Ave, Ward 9-120

institute: Feinberg School of Medicine, Northwestern University

summary: To understand the role of ID3 in human limbal epithelial cells (HLECs), HLECs were transfected with siID3 or sicontrol . RNAs isolated from these cells were subjected to RNA seq analysis

overall_design: HLECs from 3 donors were transfected with a 20 nM siRNA pool against ID3 (Invitrogen, Carlsbad, CA, USA) or nontarget control (Invitrogen, Carlsbad, CA, USA) as previously described for 3 days. Then, cells were processed for total RNA isolation using miRNeasy kit (Qiagen, Hilden, Germany). Expression profiling was conducted using a Next-Generation Sequencing platform at Northwestern University Center for Genetic Medicine core. Gene differential expression profiles obtained from RNA-seq analysis were subjected to gene ontology analysis using DAVID.

first: Elwin

last: Clutter

first: Robert

middle: M

last: Lavker


title: Innate immune signaling by ZBP1-RIPK1 axis drives neuroinflammation in Alzheimer's disease

city: Shanghai

first: Ziwen

last: Song

address: No. 100, Haike Road, Pudong New Area, Shanghai

institute: Chinese Academy of Sciences

summary: Z-DNA is a non-canonical structure capable of activating innate immune signaling through Z-DNA-binding protein 1 (ZBP1). However, the functional significance of ZBP1-mediated detection of Z-DNA in Alzheimer's disease (AD) remains poorly defined. Here, we found that ZBP1 is amplified in AD microglia, triggering innate immune response and neuroinflammation through sensing Z-form mitochondrial DNA (mtDNA). We show that fragmented oxidized mtDNA (Ox-mtDNA), produced during oxidative stress, cleaved by mitochondria nucleases, and released via the mPTP-VDAC channel, serves as the source of Z-form mtDNA. We demonstrated that Z-DNA-activated ZBP1 engages RIPK1, promoting RIPK1 kinase activation and RIPK1-kinase dependent transcription of pro-inflammatory molecules and intracellular inflammatory signaling mediators for various inflammatory pathways. Deletion of ZBP1 or genetic inhibition of RIPK1 kinase limits the innate immune response, neuroinflammation, Aβ pathology, and behavioral deficits in an AD mouse model. Our findings demonstrate that innate immune signaling by Z-form mtDNA-ZBP1-RIPK1 axis drives microglia-mediated neuroinflammation in AD, providing new insights into the immune mechanisms underlying AD pathogenesis and revealing a potential therapeutic avenue for AD.

overall_design: mRNA profiles of hippocampus derived from paired WT, 5×FAD, Ripk1D138N/D138N, Zbp1-/-, and Zbp1-/-;5×FAD mice aged 9 months. ZBP1-binding RNA profiles of hippocampus derived from paired WT and 5×FAD.

first: Xingxing

last: Xie

first: Yulu

first: Daichao

last: Xu


title: Behavioral and Neurochemical Changes in Mice Induced by Low-level Lead Exposure: Implications for ADHD and Conduct Disorders

city: Seoul

first: Yeonghoon

last: Son

address: 75, Nowon-ro

institute: Korea Institute of Radiological & Medical Sciences (KIRAMS)

summary: By using RNA sequencing (RNA-seq), we analyzed gene expression profiles in the striatum to demonstrate the molecular mechanisms of lead exposure at adolescent in mice model

overall_design: Comparative gene expression profiling analysis of RNA-seq data in striatum of mice brain following lead exposure

first: Ye Ji

last: Jeong

first: Hyun-Yong

last: Kim

first: Soo-Ho

last: Lee

first: Yoonsoo

last: Choi

first: Hyung-Do

first: Hae-June


title: AMIGO2 overexpression effect on colon cancer cell line

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary:
Analysis of SW480 colon cancer cells overexpressing AMIGO2. Result provide insight into the role of AMIGO2 in colon cancer.
Amphoterin-inducible genes and open reading frame 2 (AMIGO2) have been reported to play a role in promoting malignant transformation in several cancer types, including human colon cancer. However, the exact role of AMIGO2 in human colorectal cancer invasiveness remains unclear. We established an AMIGO2 overexpression line (SW480_A9) and a vector control line (SW480_E11) using a human colon cancer cell line (SW480) and analyzed differential expression of AMIGO2 on a microarray (Toray 3D-Gene).

overall_design: Microarray analysis was performed on two groups of SW480 cells, i.e., AMIGO2-overexpression (SW480_A9) and vector control (SW480_E11).

first: Runa

last: Izutsu

first: Mitsuhiko

last: Osaki


title: CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts [RNA maternal screening]

first: Ariel

last: Bazzini

overall_design: Transcriptomic analysis of the mRNA knockdown conditions in the maternal screening at 4 hpf using RfxCRISPR-Cas13d system


title: Differential gene expression in bone marrow derived macrophages during Candida albicans infection

city: Ann Arbor

first: Michael

last: McFadden

state: Michigan

address: 6751 Medical Science II, 1137 Catherine Street

department: Microbiology & Immunology

institute: University of Michigan

summary: Here, we measure early changes in gene expression in macrophages after Candida albicans infection for 4 hours.

overall_design: WT immortalized bone marrow-derived macrophages were seeded in 6-well plates overnight, then infected with C. albicans (MOI=1) for 4 hours, then RNA was extracted and sequenced to measure differential gene expression

first: Teresa

last: O'Meara

first: Mary

last: O'Riordan


title: Shikonin inhibits the malignant progression of triple-negative breast cancer

city: Xi'an

first: wen

last: liu

address: New temple Road num 1

institute: Tangdu Hospital of Air Force Medical University

summary: To investigate the underlying mechanism of shikonin in TNBC, we performed high-throughput sequencing to screen differentially expressed genes 24 hours after shikonin treatment

overall_design: Target genes and related regulatory pathways were identified by RNA-seq and KEGG enrichment analysis

first: Wenna

last: Liu

first: Ying

last: Liang


title: Upregulation of adenosine A2A receptor by astrocytes is sufficient to trigger hippocampal multicellular dysfunctions and memory deficits

city: Lille cedex

first: David

last: Blum

address: 1, Place de Verdun

country: France

institute: Inserm UMR-S1172

summary: Adenosine is an ubiquitous neuromodulator that ensures cerebral homeostasis. It exerts numerous functions through the activation of G-protein-coupled adenosine receptors (ARs), in particular A1 (A1R) and A2A (A2AR) receptors. Interestingly, A2AR levels are upregulated in cortical and hippocampal regions in several pathological conditions such as Alzheimer's disease, tauopathies or epilepsia. Such abnormal upregulations have been particularly reported in astrocytes, glial cells that play a key role in regulating synaptic plasticity. However, the overall impact and the underlying mechanisms associated with increased A2AR in astrocytes remain poorly understood. In the present study, we induced the upregulation of A2AR in hippocampal astrocytes using dedicated AAVs and comprehensively evaluated the functional consequences in 4 months-old C57Bl6/J mice. Our results show that A2AR upregulation primarily promotes alterations of astrocyte reactivity, morphology and transcriptome, with a link to aging-like phenotype as well as secondary impairments of neuronal excitability and microglial phenotype. These changes driven by a restricted A2AR upregulation in hippocampal astrocytes were sufficient to induce impairments of short-term spatial memory and spatial learning. This study highlights the impact of astrocytic A2AR upregulation, as seen in various neurological conditions, on the development of a detrimental multicellular response associated with memory alterations and provides an additional proof-of-concept for the value of targeting this receptor in different neurodegenerative conditions.

overall_design: To determine the impact of astrocytic A2AR upregulation in the mouse hippocampus, we bilaterally injected dedicated adeno-associated viral (AAV) vectors allowing the selective expression of A2AR (AAV-A2A) or GFP (AAV-GFP), taken as a control, in the CA1 astrocytes of 2 months old C57Bl6/J mice. We then performed a RNA sequencing analysis from hippocampal astrocytes of AAV-A2A and AAV-GFP-injected mice after cell sorting. For that, we used magnetic cell sorting thanks to ACSA-2 (Astrocyte Cell Surface Antigen 2) magnetic microbeads in order to isolate astrocytes from freshly dissected hippocampi.

first: Agathe

last: Launay

first: Emilie

last: Faivre


title: Effect of BRAF and MEK inhibition in KRAS mutant NSCLC cell line NCI-H358

city: Berkeley

first: Paul

last: Severson

state: CA

address: 91 Bolivar Dr.

institute: Plexxikon Inc

summary: Paradoxical RAF activation by chemical RAF inhibitors (RAFi) is a well-understood ‘on-target’ biological and clinical phenomenon.  In this experiment, we profile the time-dependent gene expression changes that are specific to dabrafenib, selumetinib and the combination of dabrafenib plus selumetinib.

overall_design: NCI-H358 cells were treated with DMSO, 1uM dabrafenib, 30 nM selumetinib, or 1uM dabrafenib plus 30 nM selumetinib for 4 hours or 24 hours. Four independent biological replicates were prepared making a total of 32 samples.

first: Andrew

last: Kidger

first: Simon

last: Cook


title: Curcumol Protects Against Myocardial Infarction by targeting STING to Suppress Type I Interferon Response in Macrophage

first: YU

last: GUANYE

address: Yanchang Road No. 301

department: Cardiovascular Department

institute: Shanghai Tenth People's Hospital

summary: Macrophages play a crucial role in the pathological process after myocardial infarction (MI). Curcumol (Cur), a natural compound extracted from the Curcumae Rhizoma (CR), has demonstrated both anti-tumor and anti-inflammatory activities. We had found that Cur had cardio-protective effect in MI and the effect was reduced thanks to macrophage depletion. To elucidate the mechanism of Cur on macrophage in MI, we performed RNA-seq on macrophages in MI heart treated with Cur or not.

overall_design: MI model were performed on C57BL/6JGpt male mice. In curcumol treatement group, mice were treated with 30 mg/kg curcumol was administered via oral gavage once daily for 7 days. CD45+CD64+ macrophages were isolated by FACS from hearts of mice treated with or without curcumol on day 7 after MI. RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara). Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, USA) according to the manufacturer’s instructions.

first: Yang


title: CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts [RNA 6hpf]


title: Gene expression changes related to immunosuppression in patients with traumatic brain injury (Part 2)

first: Daisuke

last: Motooka

first: Hiroshi

last: Ito

first: Masakazu

last: Ishikawa

first: Hisatake

last: Matsumoto

last: Ogura

last: Okuzaki

first: Jun

last: Oda


title: Loss of Nuclear Receptor Nr4a3 Alleviates Cellular Senescence to Promote Adult Direct Cardiac Reprogramming (RNA-Seq)

city: wuhan

first: ZHANGYI

middle: ZHANGYI

last: YU

state: hubei

address: donghu street

department: Frontier Science Center for Immunology and Metabolism

institute: wuhan university

summary: Direct cardiac reprogramming of fibroblast to cardiomyocytes represents a potential means of restoring cardiac function following injury.   However, aged and adult fibroblast are less efficient for reprogramming compared with neonatal fibroblast. In this study, through the joint analysis of RNAseq and ATACseq, we found that compared with Neo-iCM, cardiac related features were down-regulated with aging, while fibrosis and SASP related genes were significantly up-regulated with aging. Single-cell transcriptomics reveals a bifurcated trajectory of aged iCM reprogramming. Then, we screened 51 transcriptomic and epigenomic regulators of the barriers to aged-iCM reprogramming and found that Nuclear receptor subfamily 4 group A member 3 (Nr4a3), an pro-inflammatory transcription factor, induced cellular senescence to inhibit direct reprogramming during aging. Mechanistically, knockdown of Nr4a3 enhanced direct cardiac reprogramming by promoting cardiac gene programs and inhibiting fibrosis pathway and secretes SASP. In addition, knockdown of Nr4a3 promoted human reprogramming in primary ventricular human cardiac fibroblasts (HCFs) and improved heart function after MI.

overall_design:
To comprehensively decipher why iCM reprogramming is dramatically hindered in adult and aged CFs, we investigated the global transcriptomic changes of CFs from neonatal to advanced age.
To comprehensively decipher why iCM reprogramming is dramatically hindered in adult and aged CFs, we investigated the global transcriptomic changes of iCMs from neonatal to advanced age.
To determine the molecular basis by which overexpression of Nr4a3 inhibits iCM reprogramming, we conducted RNA-seq using OENr4a3-CFs and OECtrl-CFs collected at reprogramming day 7.
To determine the molecular basis by which knockdown Nr4a3 enhances iCM reprogramming, we conducted RNA-seq using shNr4a3-iCMs and shNT-iCMs collected at reprogramming day 7.

first: Li

last: Wang

first: Mengxin

first: Zhangyi

last: Yu


title: Loss of Nuclear Receptor Nr4a3 Alleviates Cellular Senescence to Promote Adult Direct Cardiac Reprogramming (CUT&Tag)

summary: Direct cardiac reprogramming of fibroblast to cardiomyocytes represents a potential means of restoring cardiac function following injury. However, aged and adult fibroblast are less efficient for reprogramming compared with neonatal fibroblast. In this study, through the joint analysis of RNAseq and ATACseq, we found that compared with Neo-iCM, cardiac related features were down-regulated with aging, while fibrosis and SASP related genes were significantly up-regulated with aging. Single-cell transcriptomics reveals a bifurcated trajectory of aged iCM reprogramming. Then, we screened 51 transcriptomic and epigenomic regulators of the barriers to aged-iCM reprogramming and found that Nuclear receptor subfamily 4 group A member 3 (Nr4a3), an pro-inflammatory transcription factor, induced cellular senescence to inhibit direct reprogramming during aging. Mechanistically, knockdown of Nr4a3 enhanced direct cardiac reprogramming by promoting cardiac gene programs and inhibiting fibrosis pathway and secretes SASP. In addition, knockdown of Nr4a3 promoted human reprogramming in primary ventricular human cardiac fibroblasts (HCFs) and improved heart function after MI.

overall_design: To determine the molecular basis by which knockdown Nr4a3 enhances iCM reprogramming, we conducted CUT&Tag profiling of two histone modifications including histone H3 acetylation on lysine 27 (H3K27ac, a mark for active enhancers and promoters) and histone H3 trimethylation on lysine 27 (H3K27me3, a repressive epigenetic mark) using shNr4a3-iCMs and shNT-iCMs collected at reprogramming day 7

last: Liu


title: CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts [Slam-seq]

first: Ariel

last: Bazzini