title: Targeting Dual-specificity Phosphatase 23 to Overcome Chemoresistance and Stem Cell-like Behavior in Non-small Cell Lung Cancer Cells

status: Public on Jan 31 2025

city: Seoul

first: Sangmyung

last: Rhee

state: State...

address: 84, Heukseok-ro

country: South Korea

institute: Chung-ang university

type: Expression profiling by high throughput sequencing

summary: Chemoresistance poses a significant challenge in treating non-small cell lung cancer (NSCLC), often leading to poor outcomes. This resistance is closely linked to cancer stem cell (CSC)-like characteristics, including the ability to evade anoikis. In this study, we identified dual-specificity phosphatase 23 (DUSP23) as a key molecule involved in regulating CSC traits and chemoresistance. DUSP23 expression was significantly elevated in cell clusters grown under ultra-low adhesion (ULA) conditions that mimic CSC-promoting environments. Silencing DUSP23 reduced the formation of these clusters, suppressed the expression of the stemness markers SOX2, and enhanced anoikis sensitivity. Additionally, in cisplatin-resistant NSCLC cells, knockdown of DUSP23 decreased invasive behavior and induced apoptosis. These findings suggest that DUSP23 plays a pivotal role in maintaining CSC-like properties and chemoresistance by regulating SOX2. Targeting DUSP23 could offer a novel approach to overcome treatment resistance and improve outcomes for patients with NSCLC.

overall_design: We performed RNA sequencing analysis on A549 cell clusters with the knockdown of DUSP23, compared to control cell clusters.


title: Khdc3 Regulates Metabolism Across Generations in a DNA-Independent Manner [II]

city: New York

first: Matthew

last: Smith-Raska

state: NY

address: 1300 York Ave.

department: Pediatrics

country: USA

institute: Weill Cornell Medicine

summary: Genetic variants can alter the profile of heritable molecules such as small RNAs in sperm and oocytes, and in this manner ancestral genetic variants can have a significant effect on offspring phenotypes even if they are not themselves inherited.  Here we show that wild type female mice descended from ancestors with a mutation in the mammalian germ cell gene Khdc3 have hepatic metabolic defects that persist over multiple generations.  We find that genetically wild type females descended from Khdc3 mutants have transcriptional dysregulation of critical hepatic metabolic genes, which persist over multiple generations and pass through both female and male lineages.  This was associated with dysregulation of hepatically-metabolized molecules in the blood of these wild type mice with mutational ancestry.  The oocytes of Khdc3-null females, as well as their wild type descendants, had dysregulation of multiple small RNAs, suggesting that these epigenetic changes in the gametes transmit the phenotype between generations.  Our results demonstrate that ancestral mutation in Khdc3 can produce transgenerational inherited phenotypes, potentially indefinitely.

overall_design: Serum from wild type females descended from wild type ancestors (WT) or wild type females descended from Khdc3-null ancestors (WT*) was injected intraperitoneally into genetically wild type females (n=2). IP injections consisted of 200μl pooled serum that were injected every 12 hours for 3 doses (each mouse received a total of 600μl injected serum). The female WT mice were subsequently mated with a WT male 24 hours later. Livers from female mice of each offspring were dissected at 1 month of life. RNA was extracted and RNA sequencing was performed on the samples (n=4).

first: Liana

last: Senaldi


title: Assessment of the Anti-Tumor Effects of Poly(I:C) Combined with QS-21 on Melanoma Cells(B16F10)

city: nanjing

first: wenbo

last: zhang

state: jiangsu

address: jiangning longmiandadao 639

country: China

institute: China Pharmaceutical University

summary: This study explores the synergistic antitumor potential of Poly(I:C) and QS-21 in melanoma treatment. Through in vitro assays and animal models, we evaluated their combined impact on melanoma cell proliferation, apoptosis, and immune response. Our results indicate that Poly(I:C), an immunostimulant, activates the immune system to bolster antitumor activity. QS-21, an immunological adjuvant, enhances Poly(I:C)'s effects, together acting as an in situ vaccine to expose neoantigens and reignite the tumor-immune interaction. This research offers a promising immunotherapeutic approach for melanoma.

overall_design: The study involved the treatment of melanoma cells with four different conditions: vehicle (control), Poly(I:C), QS-21, and a combination of Poly(I:C) + QS-21. Each treatment was applied in vitro for a duration of 6 hours. Following the treatment, RNA was extracted from the cells for subsequent sequencing analysis. This design allows for the assessment of the individual effects of Poly(I:C) and QS-21, as well as their combined impact on the melanoma cells' gene expression profile.


title: Spinal neuronal ferroptosis aggravates peripheral nerve injury-induced neuropathic pain via modulating competing endogenous RNA axis - RNA-Seq

city: jining

first: gao

last: xu

state: Shandong

address: 89 Guhuai Road

institute: Affiliated Hospital of Jining Medical University

summary: Peripheral nerve injury-induced neuropathic pain presents a significant clinical challenge and the pathogenesis remains unclear. Recent findings have implicated spinal neuronal ferroptosis in the modulation of neuropathic pain progression, but the molecular mechanism is inadequately understood. This work constructed competitive endogenous RNA (ceRNA) regulatory network in neuronal ferroptosis model through total transcriptome sequencing. Bioinformatic analyses elucidated the biological roles and signaling pathways of differentially expressed genes associated with neuronal ferroptosis. In vitro experiments substantiated the involvement of two critical regulatory axes, namely lncRNA-Sh3bp5l/miR-92b-5p/Pgd and lncRNA-Scrn2/miR-133a-3p/Srxn1, in the regulation of neuronal ferroptosis. The knockdown of PGD and SRXN1 was observed to significantly inhibit the ferroptosis phenotype. Utilizing an in vivo chronic constriction injury (CCI) pain model, we demonstrated that the expression of ceRNA-mediated downstream targets, PGD and SRXN1, was localized within spinal neurons.  Furthermore, lncRNA-Sh3bp5l and lncRNA-Scrn2 were found to be upregulated in the ipsilateral spinal cord following CCI injury, accompanied by increased levels of PGD and SRXN1. In brief, this study explored the key ceRNA axis that regulates spinal neuronal ferroptosis, which might serve as the potential therapeutic targets for neuropathic pain.

overall_design: RNA sequencing of retinoic acid-induced N2a cells with or without RSL3 stimulation

first: Xu

last: Gao

first: Xiao

last: Liang

first: Longfei

first: Chunyang

last: Meng


title: Bulk RNA-seq profiling of human head and neck squamous cell carcinoma (HNSCC) with primary tumors and metastatic lymph nodes

city: Palo Alto

first: Andrew

last: Gentles

state: CA

address: 1265 Welch Rd

institute: Stanford University

summary: This bulk RNA-seq data serves as a testing dataset for a new computational framework MONTAGE that takes an input of integrated atlas of single-cell spatial proteomics and scRNA-seq to study spatial community composition changes along functional enrichment gradient in tissue. This bulk RNA-seq dataset was generated from proximal tissue sections used for profiling spatial proteomics and was used to test the robustness of spatial community identification against the paired spatial proteomics data.

overall_design: RNA-seq profiling of human head and neck squamous cell carcinoma (HNSCC) samples.

first: Serena

last: Chang

first: Weiruo

last: Zhang

first: Sylvia

last: Plevritis


title: The Role of Dock7 in Neuromuscular Health and Function

city: Birmingham

middle: S

last: Alexander

state: AL

address: 1900 University Blvd. THT 929 Box# 96

institute: University of Alabama at Birmingham

summary: Dedicator of cytokinesis (DOCK) proteins have critical roles in myoblast fusion, glucose metabolism, skeletal muscle regeneration, and neuronal polarity. Previously, we demonstrated that DOCK3 is a dosage-sensitive modifier of Duchenne muscular dystrophy (DMD) pathologies as DOCK3 expression was induced in response to dystrophic disease progression. Following a similar pattern, DOCK7 expression is upregulated in both human DMD muscle and multiple DMD mouse models. DOCK7 primarily activates a RAC1 signaling cascade that functions to modulate cytoskeletal actin-filament polymerization and organization. DOCK7 deficiency leads to hypotonia and ataxia. We hypothesized that DOCK7 plays an integral role in neuromuscular health and function through its activation of RAC1 signaling. The goal of this sequencing experiment is to determine whether Dock7 function is critical to skeletal muscle, motor neurons or both.

overall_design: We have generated Dock7 muscle KO (Dock7 mKO) and Dock7 motor neuron KO (Dock7 mnKO) mice by mating our Dock7 flox/flox conditional mice with our HSA-Cre (mKO; myofiber knockout) transgenic, and vChAT Cre (vKO; motor neuron knockout) drivers. Additionally, control Dock7 flox/flox mice were submittted. Dock7 null mice (Sox2-Cre; gKO) were provided by our collaborator, Katie Becker at University of New England.

first: Katherine

middle: G

last: English

first: David

middle: K

last: Crossman


title: Chlamydomonas reinhardtii (red) rich in protoporphyrin Ⅸ exerts anti-diabetic effects in liver tissue

city: Hangzhou, Zhejiang

first: xuefeng

last: Qu

address: Tianmushan Road 182th,

institute: Hangzhou Medical College

summary: The metabolites derived from microalgae have been attributed with various nutritional and medicinal properties. Therefore, our study aimed to investigate the potential beneficial effects of Chlamydomonas reinhardtii (red), a type of microalgae, in individuals with type 2 diabetes mellitus (T2DM). Mice were fed on high-fat diet and injected with a low dose of streptozotocin to induce T2DM. The diabetic mice were orally treated with either 1% sodium carboxymethylcellulose or Chlamydomonas reinhardtii (red) at doses of 1, 2, or 3 g/kg BW/day for a duration of 4 weeks. The liver sections were subjected to hematoxylin and eosin staining as well as oil red staining for the detection of pathological changes and lipid deposition, respectively. Inflammatory factors in serum were quantified using ELISA kits, while commercial kits were employed to assess oxidative stress-related indicators. Gene expression in liver was analysed by RNA-seq. The results revealed that Chlamydomonas reinhardtii (red) significantly ameliorated fasting blood glucose levels, body weight, triglyceride, and low density lipoprotein cholesterin, while also enhancing oral glucose tolerance and insulin sensitivity. In pathological analysis, Chlamydomonas reinhardtii (red) significantly improved lipid deposition and hepatic tissue damage. Furthermore, Chlamydomonas reinhardtii (red) could obviously decreased the protein expression of G-6-Pase and PEPCK, and regulated the SOCS2/JAK2/STAT5 signaling pathway. Transcriptomic analysis indicated that a total of 972 significantly differentially expressed genes in diabetic mice treated with Chlamydomonas reinhardtii (red). KEGG analyses revealed that lipid and atherosclerosis, MAPK signaling pathway, B cell receptor signaling pathway, TNF signaling pathway, NOD-like receptor signaling pathway, Toll-like receptor signaling pathway, PI3K-Akt signaling pathway were involved in Chlamydomonas reinhardtii (red) modulated process. Therefore, the continuous consumption of Chlamydomonas reinhardtii (red) may have anti-T2DM effects through the inhibition of gluconeogenesis, thus offering a promising alternative for T2DM patient.

overall_design: The raw image data file acquired from high-throughput RNA sequencing is converted into the raw reads through base calling analysis following image processing. The assessment of the raw read quality was conducted using the FastQC program (version 0.11.8). The Trimmomatic program (version 0.36) was utilized to filter out bad quality data. RNA-seq reads were mapped to the mouse reference sequence GRCm38 through Hisat2 software (version 2.1.0). Calculate the read count for each gene using StringTie, subsequently normalize the reads using the TMM normalization method, and ultimately determine the FPKM values. Differentially expressed genes (DEGs) analysis was conducted using the R software. The P-values were corrected using multiple hypothesis testing. The threshold for the P-value was established by controlling the False Discovery Rate (FDR), with the adjusted P-value being referred to as the q-value. Additionally, the fold change in differential expression was calculated based on the FPKM values.ClusterProfiler was utilized for Gene Ontology (GO) analysis to elucidate the biological functions of DEGs with a fold change (FC) of at least 2 and a P-value less than 0.05, focusing on biological processes, molecular functions, and cellular components. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was performed using the DAVID database (https://davidbioinformatics.nih.gov/) to identify the critical pathways in which DEGs are involved. A P-value < 0.05 was considered statistically significant.

first: Zemi

last: Xie

first: Zhuoling

last: Chen

first: Siyuan

last: Wang

first: Yamin

first: Xue

first: Yuejin

last: Wu

first: Yangjunna

first: Dengfeng

last: Xu

first: Jingjin

last: Hu

first: Yin

first: Xuefeng


title: Effect of cyclic strain in neurons isolated from dorsal root ganglia

city: Pisa

first: Vittoria

last: Raffa

state: Please Select

address: S.S. 12 Abetone e Brennero, 4

department: Department of Biology

country: Italy

institute: Università di Pisa

summary: Organs and cells in our body are continuously exposed to mechanical forces. Neurons, in particular, encounter mechanical stimuli during neurodevelopment, aging, pathological conditions, and routine functions such as homeostatic processes and movement. How do cells, which endure mechanical stress on a daily basis, withstand these forces and remain functional throughout our long lifespans? To maintain their functionality, cells must have evolved self-repair mechanisms that allow them to tolerate stress and repair damage up to a manageable threshold.  This study aims to explore the relationship between damage and repair mechanisms that are crucial for preserving the structural and functional integrity of axons over time. Dorsal Root Ganglia neurons are used as a model system, as they are particularly relevant due to their exposure to daily mechanical movements. An experimental setup has been developed to apply repeated cycles of compression to neurons grown on an elastic substrate. Understanding how neurons respond to mechanical strain and sustain homeostasis will not only deepen our knowledge of the effects of mechanical stress on neurons but also provide valuable insights into restoring cellular functions.

overall_design: Three experimental groups were considered: - control group (CTRL), cells grown on the stimulation device but not subjected to compression cycles; - compressed sample (COMPRESSED), cells grown on the stimulation device, subjected to compression cycles (5% strain, 20 cycles), RNA extraction 6 h post-stimulation; - compressed sample (RECOVERY), cells grown on the stimulation device, subjected to compression cycles (5% strain, 20 cycles), RNA extraction 24 h post-stimulation; Six replicates per condition

first: Coppini

last: Allegra


title: Cancer-associated fibroblast-derived urea cycle metabolites promote colorectal cancer growth

city: Guangzhou

first: Zexiong

last: Cheng

address: No.601, West Huangpu Avenue

institute: Jinan University

summary: Urea cycle (UC) dysfunction is linked to both tumorigenesis and poor prognosis in multiple cancers. However, the role of UC metabolism in tumor-stroma crosstalk is unclear. Here, we show that colorectal cancer (CRC) cells induce reprogramming of UC metabolism in cancer-associated fibroblasts (CAFs), which is mediated by CRC-derived exosomes. Reprogrammed CAFs support CRC cell growth by providing UC metabolites, especially arginine (Arg). Consequently, Arg deprivation resulted in growth inhibition of CRC cells. Furthermore, we found that Arg deprivation increases CRC’s dependence on putrescine (Put) and upregulates the expression of the polyamine biosynthetic rate-limiting enzyme ornithine decarboxylase (ODC). Combined Arg deprivation and ODC inhibitor effectively restrains CRC cell growth. Our study illustrates the UC metabolic interaction between CAFs and CRC cells and demonstrates the potential therapeutic utility of Arg restriction and ODC blockade combination treatment for colorectal cancer.

overall_design: To explore the influence of CRC-derived exosomes on CAFs, we performed RNA sequencing (RNA-seq) in primary CAFs treated with HCT116-secreted exosomes (HCT116 Exo) or vehicle control.

first: Haipeng

first: Guopeng

last: Pan


title: Gene expression of maize-specific Exserohilum turcicum strain

city: Urbana

first: Mara

last: Krone

state: Illinois

address: 1102 S Goodwin Ave, Turner Hall

department: Crop Sciences

institute: University of Illinois

summary: Exserohilum turcicum is a fungal pathogen that causes northern corn leaf blight and sorghum leaf blight. However, strains are host-specific, meaning a strain typically only causes disease on either maize or sorghum. This pathosystem provides a unique opportunity to identify the mechanisms underlying host specificity through genomic and transcriptomic studies. To characterize host specificity, we (i) constructed de novo annotated assemblies of one sorghum- (15St008) and one maize-specific (Et52B) E. turcicum strain, ii) identified and characterized structural changes between the two genomes, and (iii) compared differential gene expression. This GEO project contains the gene expression of the maize-specific strain (Et52B) during in planta infection of maize and in axenic cultures.

overall_design: RNA-seq profiling of strain Et52B during in planta infection and in axenic cultures. In planta samples were collected 10 days after inoculations and mycelium from axenic liquid cultures were collected after 5 days of growth.

first: Pummi

last: Singh

first: Pragya

last: Adhikari

first: Tiffany

last: Jamann

first: Santiago

last: Mideros


title: Gene expression of sorghum-specific Exserohilum turcicum strain

summary: Exserohilum turcicum is a fungal pathogen that causes northern corn leaf blight and sorghum leaf blight. However, strains are host-specific, meaning a strain typically only causes disease on either maize or sorghum. This pathosystem provides a unique opportunity to identify the mechanisms underlying host specificity through genomic and transcriptomic studies. To characterize host specificity, we (i) constructed de novo annotated assemblies of one sorghum- (15St008) and one maize-specific (Et52B) E. turcicum strain, ii) identified and characterized structural changes between the two genomes, and (iii) compared differential gene expression. This GEO project contains the gene expression of the sorghum-specific strain (15St008) during in planta infection of sorghum and in axenic cultures.

overall_design: RNA-seq profiling of strain 15St008 during in planta infection and in axenic cultures. In planta samples were collected 10 days after inoculations and mycelium from axenic liquid cultures were collected after 5 days of growth.


title: ATR inhibition synergizes with alkylating PI polyamide targeting MYCN by suppressing DNA repair in MYCN-amplified neuroblastoma

city: Chiba

first: XIAOYI

last: LAI

state: 千葉県

address: 666-2 Nitona-cho Chuo-ku

country: Japan

institute: Chiba Cancer Center Research Institute

summary: Because a single treatment with CCC-002 downregulated the expression of DDR-related genes in CHP-134 cells, the expression profile of SK-N-BE(2) cells after co-treatment with CCC-002 and an ATR inhibitor was evaluated using a microarray assay

overall_design: SK-N-BE(2) cells were treated with CCC-002 alone or in combination with AZD6738 for 24 h. RNA was extracted for microarray. Samples (150 ng) were labeled with an RNA Spike-In Kit and analyzed on SurePrint G3 Human GE 8 × 60 K V2 microarrays following the recommendations of Agilent Technologies. Sample arrays were scanned using an Agilent SureScan microarray scanner. The sample replicates were as follows: CCC-002, 3 × 2; DMSO, 3 × 2; and combination, 3 × 2.

first: Xiaoyi

last: Lai

first: Atsushi

last: Takatori


title: High throughput CRISPRi screen identifies viability lncRNAs in human monocytes

city: Santa Cruz

first: Susan

last: Carpenter

address: Biomedical Sciences Building First Floor, Red Hill Road

department: MCD

institute: UC Santa Cruz

summary: Long noncoding RNAs are emerging as critical regulators of biological processes. While there are over 20,000 lncRNAs annotated in the human genome we do not know the function for the majority. Here we performed a high-throughput CRISPRi screen to identify those lncRNAs that are important in viability in human monocytes using the cell line THP1. We identified a total of 35 hits from the screen and validated and characterized two of the top intergenic hits. The first is a lncRNA neighboring the macrophage viability transcription factor IRF8 (RP11-542M13.2 hereafter referred to as long noncoding RNA regulator of monocyte proliferation, LNCRMP) and the second is a lncRNA celled OLMALINC (oligodendrocyte maturation-associated long intervening non-coding RNA) that was previously characterized to be important in oligodendrocyte maturation. Removal of LNCRMP and OLMALINC from monocytes severely limited their proliferation capabilities. RNA-seq analysis of knockdown lines showed that LNCRMP regulated proapoptotic pathways while knockdown of OLMALINC impacted genes associated with the cell cycle. This research highlights the importance of high-throughput screening as a powerful tool for quickly discovering functional long non-coding RNAs (lncRNAs) that play a vital role in regulating monocyte viability.

overall_design: THP1 CRISPRi expressing cells were infected with lentivirual containing single guide RNAs (sgRNAs) targeting  OLMALINC or LNCRMP. The infected cell were then selected with puromycin for 7 days. After 7 days of selection, total rna was collected and illumina based RNA sequencing was performed.

first: Cristina

last: Flores

first: Eric

last: Malekos


title: USP7 inhibitors disrupt EBNA1 interactome and EBV tumorigenesis

city: Philadelphia

first: Sarah

last: Alp

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

summary: Epstein-Barr virus (EBV) is a ubiquitous human ɣ-herpesvirus implicated in various malignancies, including Burkitt’s lymphoma and gastric carcinomas. In most EBV-associated cancers, the viral genome is maintained as an extrachromosomal episome by the EBV nuclear antigen-1 (EBNA1). EBNA1 is considered to be a highly stable protein that interacts with the ubiquitin-specific protease 7 (USP7), but the precise role of USP7 in controlling EBNA1 stability and function is not fully understood. Here, we show that pharmacological inhibitors and small interfering RNA (siRNA) targeting USP7 reduce EBNA1 protein levels. The USP7 inhibitor GNE6776 altered EBNA1 protein interactions, including disrupting its ability to bind to USP7. GNE6776 also inhibited EBNA1 binding to EBV oriP DNA and reduced viral episome copy number. GNE6776 selectively inhibited EBV+ gastric and lymphoid cell proliferation in cell culture and slowed EBV+ tumor growth in mouse xenograft models. Transcriptomic studies revealed that USP7 inhibition differentially affected EBV+ cancer cells compared to EBV- cells with a significant effect on chromosome segregation and mitotic cell division pathways. Our findings indicate that USP7 inhibition perturbs EBNA1 stability and function and can be exploited to target EBV+ cancer cells selectively.

overall_design: To invesitigate USP7 inhibitor, GNE6776, specific-effect on EBV+ positive cells, we treated EBV- and EBV+ gastric cancer cells with GNE6776.  We performed gene expression profiling using RNA-seq after treatment.

first: Lieberman

last: Paul

first: Chen

last: Christopher

first: Preston-Alp

last: Sarah


title: Epidermal stem cell-derived EVs induced myofibroblasts mesenchymal-epidermal transition alleviate scarring via the miR-200s/ZEBs axis

first: Miao

last: Zhen

address: No.58 Zhongshan Er Road

institute: The First Affiliated Hospital of Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary: Hypertrophic scar (HS) is a prevalent yet unresolved wound healing complication characterized by persistent hyperactive and proliferative fibroblasts, leading to excessive extracellular matrix (ECM) synthesis and collagen contraction. Our previous studies have identified epidermal stem cells (ESCs) as critical for wound healing and HS remodeling, with its extracellular vesicles (EVs) playing a vital role. However, the specific mechanisms remain unclear. In this study, we first discovered that ESC-EVs could effectively induce the mesenchymal-epidermal transition (MET) of HS fibroblasts (HSFs) and inhibit their biological activity. Furthermore, by next-generation sequencing and multiplexed CRISPR/Cas9 system, we elucidated that this therapeutic effect is mediated by the miR-200 family (miR-200s) encapsulated in ESC-EVs, which targeted and inhibited ZEB1 and ZEB2 in HSFs. This vital role and mechanism have been thoroughly validated in both in vitro cell experiments and in vivo rat tail HS (RHS) models. These findings not only shed light on a previously unidentified mechanism of ESC-EVs for HS, but also provide potential novel targets and strategies for its precise treatment.

overall_design: The miRNAs high-throughput sequencing of extracellular vesicles derived from epidermal stem cells and human skin fibroblasts.

first: Peng

last: Wang


title: Metabolic reprogramming of macrophages via engineered nanoparticles after volumetric muscle loss

city: Ann Arbor

middle: V

last: Brooks

state: Michigan

address: 109 Zina Pitcher Pl

department: Molecular and Integrative Physiology

institute: University of Michigan

summary: Volumetric muscle loss (VML) injuries are characterized by an exacerbated and chronic inflammatory state that inhibits muscle stem-cell mediated repair, leading to fibrosis and attenuation of neuromuscular strength. The excessive infiltration of myeloid cells in VML injuries leads to the depletion of nutrients needed by myogenic progenitors for tissue repair. Mitigating the inflammatory response and fibrosis are potential approaches to enhance therapies for VML. The adenosine monophosphate-activated protein kinase (AMPK) pathway plays a critical role in myeloid responses to injury by regulating cellular metabolism, suppressing glycolysis, and attenuating fibrosis-inducing pathways such as transforming growth factor-beta (TGFβ). AMPK Activation reduces fibrosis and promotes muscle stem cell differentiation, however, a limiting factor of AMPK agonists such as AICAR (5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside) is that these therapies display low bioavailability. As such, there remains an unmet need for strategies to target AMPK in skeletal muscle to enhance therapeutic efficacy and prevent muscle degeneration. To address this need, we used synthetic protein nanoparticles (SPNPs) to encapsulate AICAR. SPNPs can have high drug loading (>10wt%), allow for a sustained release of the packaged drug (72 hours), and have a demonstrated targeting capacity. Increasing the bioavailability of AICAR through packaging into SPNPs would be enabling for improving metabolism after trauma and extensible to other AMPK agonists and small molecules, which in turn can further augment existing regenerative therapies to promote healing

overall_design: Quadriceps muscles from mice were given a VML injury and treated with either AICAR and Vehicle loaded SPNPs (x1011 particles) at 1,4,7 days post-injury (dpi). Muscles were collected at 8 dpi, digested into single cell suspensions, FACS sorted to obtain live cells and processed for single cell sequencing.

first: Jesus

middle: A

last: Castor-Macias

first: Celeste

last: Piotto

first: Albert

last: Cheng

first: Steve

last: Guzman

first: Jacqueline

last: Larouche

first: Joerg

last: Lahann

first: Carlos

last: Aguilar


title: Integration of network pharmacology, transcriptomics, and experimental verification to investigate the mechanism of action of cepharanthine hydrochloride against prostate cancer

city: Chongqing

first: Jingzhen

last: Zhu

address: Xinqiaozhengjie

department: Department of Urology, Urologic Surgery Center

institute: Xinqiao Hospital, Third Military Medical University (Army Medical University)

summary: Transcriptomic sequencing and differential expression analysis were used to identify the key target protein of CH and the key signaling pathways involved in its therapeutic effects against PCa.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PC-3 cells(Cepharanthine hydrochloride 5μM) and control cell

first: Zongming

last: Dong


title: cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [snRNA-seq]

city: Pittsburgh

first: Michael

last: Tsang

address: 3501 Fifth Ave. BST3-5062

department: Cell Biology

institute: University of Pittsburgh

summary: Cardiac regeneration involves interplay of complex interactions between many different cell types, including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress-response, myofibril assembly, proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this, we determined that cited4a, a p300/CBP transcriptional co-activator, is induced after injury in mature cardiomyocyte population. Moreover, loss-of-cited4a mutants showed increased dedifferentiation, proliferation and accelerated heart regeneration. Thus, suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration.

overall_design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 days post amputation (dpa) and uninjured controls (UI). Extracted hearts were frozen in liquid Nitrogen and nuclei were isolated as described in methods section.

first: Rachel

last: Forman-Rubinsky

first: Brent

middle: T

last: Schlegel

first: Dhivyaa

last: Rajasundaram


title: High throughput CRISPRi screen identifies viability lncRNAs in human monocytes [II]

first: Susan

last: Carpenter

overall_design: Library infected and selected THP1-CRISPRi-sgRNA cells were expanded to 2000X coverage. Cells were selected with puromycin for 7 days. Cells were grown until day 21 and genomic DNA was removed and PCR amplification of genomic sgRNA sequences were conducted as previously described in detail in https://doi.org/10.1016/j.celrep.2020.108541.

first: Cristina

last: Flores

first: E

last: Malekos


title: Mutant EZH2 alters the epigenetic network and increases epigenetic heterogeneity in B cell lymphoma (CUT&Run)

city: Rehovot

first: Ofir

last: Griess

address: Hetzel

country: Israel

institute: Weizmann Institute of Science

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Diffuse large B cell lymphomas and follicular lymphomas show recurrent mutations in epigenetic regulators; among these are loss-of-function mutations in KMT2D and gain-of-function mutations in EZH2. To systematically explore the effects of these mutations, alone or in combination, on the epigenetic landscape, we applied a single cell approach, based on Cytometry by Time of Flight (CyTOF), to probe a wide array of histone modifications. We show that mutant-EZH2 elicits extensive effects on the epigenome of lymphomas, beyond alterations to H3K27 methylations, and is dominant over KMT2D mutations. Utilizing the single-cell data, we present computational methods to measure epigenetic heterogeneity. We identify an unexpected characteristic of mutant-EZH2, but not KMT2D, in increasing heterogeneity, shedding light on a novel oncogenic mechanism mediated by this mutation. Finally, we present analysis to reveal potential cross talk between various modifications in the epigenetic network, validated by functional perturbations. Our work highlights novel roles for mutant-EZH2 in lymphomagenesis and establishes new concepts for measuring epigenetic heterogeneity and intra-chromatin connectivity in cancer cells

overall_design: 0.2m of cells were incubated with primary antibody, then pAG-MNase enzyme  was added to each sample followed by incubation step of 1 h at 4°C. Targeted digestion was done by 15 min incubation on ice block (0°C) under low salt conditions. DNA purification was done using Nucleospin gel and PCR clean-up kit (Machery-Nagel, 740609 ). Sequencing was done on a Next-Seq 500 instrument (Illumina) using a V2 150 cycles mid output kit, allocating 10M reads per sample (paired end sequencing).

first: Noa

last: Furth

first: Nofar

last: Harpaz

first: Nicoletta

last: Di Bernardo

first: Tomer

middle: M

last: Salame

first: Bareket

last: Dasa

first: Ioannis

last: Karagiannidis

first: Yusuke

last: Isshiki

first: Menachem

last: Gross

first: Ari

last: Melnick

first: Wendy

last: Beguelin

first: Guy

last: Ron

first: Efrat

last: Shema


title: Circle-seq revealing eccDNA profiling of human bone marrow mesenchymal stem cells

city: Chengdu

first: Yuxi

last: Gu

address: No.17, Section 3, Renmin South Road, Wuhou District, Chengdu

institute: West China hospital of stomatology, Sichuan University

summary: Extrachromosomal circular DNAs (eccDNAs) have been discovered in various species and play a significant role in cancer development However, our understanding of eccDNAs in normal cells is limited. Here, we conducted eccDNA sequencing by Circle-seq in undifferentiated human bone marrow mesenchymal stem cells (uhBMSCs) and their differentiation into osteoblasts (OBs), chondrocytes (CCs), and adipocytes (ACs) to gain knowledge about eccDNAs in cell differentiation,

overall_design: Circle-seq for uhBMSCs, Obs, CCs and Acs

first: Yidan

last: Song

first: Shuhua

last: Wang

first: Jun

last: Liu


title: Effectiveness of low-intensity exercise in mitigating active arthritis exacerbation in a mouse rheumatoid-arthritis model

city: Tsukuba

first: Takehito

last: Sugasawa

state: Select State

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary:
Objective
To investigate the effects of low-intensity exercise on active arthritis in a SKG mouse model of human rheumatoid arthritis (RA) pathology.
Methods
Twenty-four female SKG mice were divided into three groups: sedentary (control), AR (induced arthritis), and AREx (induced arthritis plus low-intensity exercise). Arthritis was induced via intraperitoneal administration of mannan. After a 2-week inflammation period, low-intensity treadmill exercise was performed only in the AREx group. Arthritis was assessed weekly during the rearing period. After 4 weeks of exercise, histological and bone morphometric analyses of the right ankle joint were performed. A histological analysis of the gastrocnemius muscle was also performed. Bulk mRNA sequencing was conducted on the left synovial membrane-fat pad (SM-FP) complex.
Results
The synovitis score showed no change; however, the arthritis score was significantly lower in the AREx group than in the AR group (p<0.05), indicating that low-intensity exercise suppressed arthritis exacerbation. The calcaneal and talar bone volumes decreased in the AR group, whereas the AREx group showed no significant change. In the SM-FP complex tissue, the gene expression of inflammatory cytokines decreased in the AREx group compared with the AR group, particularly the suppression of IL6/Jak/Stat3. Immunohistochemical analysis revealed significantly decreased expression of pro-inflammatory cytokines and increased expression of anti-inflammatory cytokines in the synovium of the AREx group compared with the AR group (p<0.05).
Conclusion
Low-intensity exercise therapy for active RA showed anti-inflammatory and suppressive effects on arthritis exacerbation in SKG mice, a mouse model of human RA pathology.

overall_design: Low-intensity treadmill exercise was performed after inducing arthritis in SKG/Jcl model mice. The results were compared between the sedentary group (PBS administration), the arthritis group (Mannan 20 mg), and the arthritis + exercise group (Mannan 20 mg + Treadmill), and showed that low-intensity treadmill exercise had an inhibitory effect on arthritis exacerbation.

first: Kaichi

last: Ozone

first: Tatsunori

last: Kumagai

first: Kouhei

last: Arakawa

first: Wenchao

first: Sora

last: Kawabata

first: Naoki

last: Shimada

first: Haruna

last: Takahashi

first: Moe

last: Yoneno

first: Yuki

last: Minegishi

first: Kei

last: Takahata

first: Michiaki

last: Sato

first: Yuichiro

last: Oka

first: Naohiko

last: Kanemura


title: EWSR1/FLI1 Expression in Human Mesenchymal Stem Cells derived from Experimental Teratomas Leads to Ewing´s Sarcoma Tumorigenesis [RNA-seq]

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

summary: Ewing sarcoma is an aggressive bone and soft tissue neoplasm, unique to humans, characterised by EWSR1/ETS rearrangements and whose cellular origin remains unknown. We report that human embryonic stem cells expressing EWSR1/FLI1 can form experimental teratomas. Mesenchymal stem-like cells (hMSLCs) isolated from these teratomas lack tumourigenic capacity despite retaining low levels of EWSR1/FLI1 expression. Subsequent transduction of hMSLCs with EWSR1/FLI1 results in the expression of endothelial and neural genes, the acquisition of an Ewing sarcoma transcriptional signature and the formation of tumours in the spine and in soft tissues. These lesions are frequently haemorrhagic and composed of small round cells expressing discriminating markers of Ewing sarcoma. In summary, EWSR1/FLI1 enforces an aberrant endothelial-neural hybrid transcriptome and endows in vivo transforming capacity when expressed in a highly undifferentiated mesenchymal stem cell. This new experimental approach provides a test bench to elucidate the biology of translocation-dependent prenatal tumours, ranging from leukaemia to a variety of sarcomas.

overall_design: Human pediatric mesenchymal stem cells (hpMSC) mRNA and teratoma-derived human mesenchymal stem cells (hMSLC) mRNA, each sample in duplicate;  mRNA of three human Mesenchymal Stem Like Cells (hMSLCs) lines infected with EWS-FLI1 or with control lentivirus, each sample in duplicate

first: Hernández-Muñoz

last: Inmaculada


title: Non-CG DNA methylation and MeCP2 stabilize repeated tuning of long genes that distinguish closely related neuron types [WGBS]

city: St. Louis

first: Mati

middle: Tesfaye

last: Nemera

state: Missouri

address: 660 S Euclid Ave

department: Neuroscience

institute: Washington University in St. Louis School of Medicine

type: Methylation profiling by high throughput sequencing

summary: The extraordinary diversity of neuron types in the mammalian brain is delineated at the highest resolution by subtle gene expression differences that may require specialized molecular mechanisms to be maintained. Neurons uniquely express the longest genes in the genome and utilize neuron-enriched non-CG DNA methylation (mCA) together with the Rett syndrome protein, MeCP2, to control gene expression, but the function of these unique gene structures and machinery in regulating finely resolved neuron type-specific gene programs has not been explored. Here, we employ epigenomic and spatial transcriptomic analyses to discover a major role for mCA and MeCP2 in maintaining neuron type-specific gene programs that define high resolution cell types. We uncover differential susceptibility to MeCP2 loss in neuronal populations depending on global mCA levels and dissect methylation patterns and intragenic enhancer repression that drive overlapping and distinct gene regulation between neuron types. Strikingly, we show that mCA and MeCP2 regulate genes that are repeatedly tuned to differentiate neuron types at high cellular resolution, including spatially resolved, vision-dependent gene programs in the visual cortex. These repeatedly tuned genes display genomic characteristics, including long length, numerous intragenic enhancers, and enrichment for mCA, that predispose them to regulation by MeCP2. Thus, long gene regulation by the MeCP2 pathway maintains differential gene expression between closely-related neurons to facilitate the exceptional cellular diversity in the brain.

overall_design: Cerebellum, striatum, and hypothalamus tissues and INTACT-isolated subclasses of neurons from the cortex were profiled by whole-genome bisulfite-seq.

first: James

middle: R

last: Moore

first: Rinaldo

middle: D

last: D'Souza

first: Nicole

last: Hamagami

first: Adam

middle: W

last: Clemens

first: Diana

middle: C

last: Beard

first: Alaina

last: Urman

first: Victoria

last: Mendoza

first: Yasmin

last: Razia

first: Travis

last: Law

first: John

last: Edwards

first: Harrison

last: Gabel


title: Bacterial Peptidoglycan Serves as a Critical Modulator of the Gut-Immune-Brain Axis in Drosophila.

city: Marseille

first: Olivier

last: Zugasti

state: Provence-Alpes-Cote d'Azur

address: 163 Avenue de Luminy

country: France

institute: Institut de Biologie du Développement de Marseille

summary: Metabolites released by gut-associated bacteria can modulate many physiological processes in the host, including its behavior. By employing a model of oral bacterial infection, we recently uncovered that bacterial peptidoglycan (PGN) influences fly female egg-laying behavior by activating the NF-kB cascade in a subset of brain neurons. While shedding light on PGN as a potential mediator of communication between the microbiota and the brain in Drosophila, these findings prompt us to study the impact that PGN can exert on all brain cells. Using high-resolution mass spectrometry, we demonstrate that the PGN released by gut-associated bacteria can rapidly be detected in the central nervous system (CNS), hence demonstrating that following translocation from the gut to the hemolymph, the insect blood, it can be directly perceived by brain cells. By combining whole-genome transcriptome analyses, comprehensive genetic assays and reporter gene systems, we show that bacterial infection primarily elicits a PGN dose-dependent NF-kB immune response in glial cells forming the outer cell layer of the blood-brain barrier. Overall, our findings establish that gut-derived PGN is a critical mediator of the gut-brain axis in Drosophila. In addition to triggering behavioral changes, sensing of circulating PGN by the CNS also induces a local immune response of the BBB.

overall_design: We have gathered evidence indicating that peptidoglycan (PGN) originating from the microbiota can access the Drosophila brain, thereby influencing the transcription of specific genes. To investigate this phenomenon, we subjected adult female Drosophila to a 24-hour diet comprising either bacteria or sucrose (as a control condition). Subsequently, we dissected the brains to compare the gene expression profiles under both dietary conditions. This experimental protocol was conducted on both wild-type animals and a mutant strain known as PGRP-LB, which encodes a PGN-degrading enzyme. In the PGRP-LB mutant, the levels of microbiota-derived PGN are elevated in the fly body cavity. Each biological condition will be replicated three times to ensure robustness and reliability of the results

first: Julien

last: Royet

first: Ivo

last: Gomperts Boneca


title: Cardiomyocyte-specific LARP6 overexpression prevents Angiotensin II-induced myocardial dysfunction and interstitial fibrosis

city: Columbia

first: Jacob

middle: Jeffrey

last: Russell

state: MO

address: 1401 Ashland Rd, Apartment E

department: Biomedical Sciences

institute: University of Missouri

summary: La ribonucleoprotein 6, Translational Regulator (LARP6), a multifunctional mRNA binding protein with well-described pro-fibrotic effects, increases type I collagen mRNA half-life, translation, and deposition in non-cardiac tissues. In the heart LARP6 is expressed in cardiomyocytes, not primarily involved in fibrosis, where its role is unknown. To investigate the role of cardiomyocyte-derived LARP6 on cardiac function and remodeling, we generated a cardiomyocyte-specific LARP6 overexpressing transgenic mouse model (LARP6-Tg). Baseline longitudinal studies up to 10 months of age revealed that constitutive overexpression of LARP6 had no significant effect on cardiac function or morphology despite inducing mild interstitial fibrosis versus wild-type littermates (WT). Subsequently, we hypothesized that cardiomyocyte-specific LARP6-Tg mice would exhibit exacerbated cardiac remodeling and dysfunction in response to hypertensive stress via angiotensin II (Ang II) infusion. Ang II (1000 ng/kg/min for 21 days) induced hypertension and cardiac hypertrophy in WT and LARP6-Tg mice of both sexes. Unexpectedly, Ang II-induced cardiac dysfunction was prevented in LARP6-Tg mice. Cardiac gene expression profiling predicted increased fibrosis and cardiomyocyte death in Ang II-treated WT mice and inhibition of cardiomyocyte death in Ang II-treated LARP6-Tg mice, versus saline-treated controls. Surprisingly, Ang II-induced interstitial fibrosis was reduced in LARP6-Tg mice and associated with attenuation of cardiomyocyte cell death and reduced myofibroblast activation. These data support a mild pro-fibrotic action of cardiomyocyte LARP6 in unstressed mice and, paradoxically, that LARP6 overexpression is sufficient to prevent Ang II-induced cardiac interstitial fibrosis and dysfunction. Sustained induction of LARP6 has therapeutic potential in hypertensive heart disease.

overall_design: 40 week old LARP6 transgenic or WT littermate mice on a C57BL6J background were infused with either sterile saline or Ang II (1000 ng/kg body weight/min). Mice were echoed before pump implant and after 21 days, and cardiac tissue collected for sequencing and immnohistochemistry.

middle: J

first: Tadashi

last: Yoshida

first: Li

last: Lee

first: Lixin

last: Ma

first: Daniel

last: Davis

first: Laurel

last: Grisanti

first: Margot

last: Ruff

first: Chastidy

last: Bailey

first: Shawn

middle: B

last: Bender

first: Chandrasekar

last: Bysani


title: IRF4-regulated transcriptional heterogeneity of lung resident CD11b+ cDC2 subsets during influenza virus infection

city: OKLAHOMA CITY

first: Susan

middle: E

last: Kovats

state: OK

address: 825 NE 13TH ST.

institute: OKLAHOMA MEDICAL RESEARCH FOUNDATION

summary: Lung-resident conventional dendritic cells (cDCs) coordinate immune responses to respiratory viruses in the respiratory tract or after migration to mediastinal lymph nodes (mLN). Migratory DCs include cDC1s (CD103+XCR1+CD24hi) expressing IRF8 or cDC2s (CD11b+SIRPa+CD24+) expressing IRF4. IRF4+ cDC2s are divided into a CD24hi subset that requires IRF4 for differentiation and a CD24int subset that is present in the absence of IRF4. During influenza A virus (IAV) infection of mice, we characterized the kinetics of cDC2 subset accumulation in the lung and mLN and their differences in IRF4-dependent gene expression and function.  We found that the two IRF4-expressing cDC2 subsets upregulated CD86 to high levels, produced IL-12p40 and the chemokines CCL17 and CCL2, and were capable of acquiring antigen in vivo and activating antigen-specific CD8+ T cells. Notably, the CD11b+CD24int cDC2 subset expressed canonical cDC markers and transcription factors and expanded to high numbers in the lung and mLN by day 6 post-infection. Transcriptome analyses on day 5 post-infection revealed that the CD11b+CD24int cDC2 subset expressed both IRF4 and IRF8 and harbored an elevated interferon response signature compared to the CD11b+CD24hi subset. Analyses of mice lacking Irf4 in CD11c+ cells showed that IRF4 promoted the function of CD11b+CD24int cDC2s, including the capacity to migrate to mLN and to produce CCL17 and CCL22, consistent with their altered gene expression profile in the absence of IRF4. In sum, our data show that the two lung-resident CD11b+ cDC2 subsets present in naïve mice elaborated distinct and common functional responses regulated by IRF4 during IAV infection.

overall_design: We used flow cytometry to sort cDC subsets from the lungs of WT and IRF4-deficient (KO) mice on day 5 post influenza virus infection. We then performed Lexogen Quant-seq RNA sequencing and DESeq analyses. 4 biological replicates (separate mouse) each DC subset.

first: Ibrahim

last: Hatipoglu

first: Sean

last: Turner


title: RNA sequencig of glioblastoma stem cells after induction of ferroptosis

city: Warsaw

first: Barbara

last: Olejniczak

address: Pawinskiego 5

department: Department of Neurooncology

country: Poland

institute: Mossakowski Medical Research Institute, Polish Academy of Sciences

summary: To investigate the effect of hypoxia on ferroptosis induction in glioblastoma stem like cells (GSCs).

overall_design: Glioblastoma stem like cells derived from patients (GSCs, n=8) treated with DMSO (0.1% final concentration), and ferroptosis inducer at 3 uM (RSL3 in DMSO). Subsequently cells were cultured for 24h in either Normoxia (21% oxygen and 5% CO2) or Hypoxia (1% oxygen, 5% CO2). Cells were centrifuged (500xg, 5 min), medium decanted and pellets snap frozen for RNA after isolation with phenol-chloroform method combined with isopropanol precipitation at -80C overnight.

first: Kamil

last: Krawczyński

first: Agnieszka

last: Bronisz

first: Jakub

last: Godlewski

first: Jeffrey

last: Palatini

first: Krzysztof

last: Goryca


title: RNA-seq circadian winter 2020

city: Houston

first: exRNA

last: BRL

state: TX

address: One Baylor Plaza

department: Molecular & Human Genetics - Milosavljevic

institute: Baylor College of Medicine

summary: Changes in concetration and type of circulating RNA species during diurnal cycle

overall_design: 29 samples, 3 donors, collection 3 times a day, one lost sample. T1=8:30 am, T2, 2:00 PM, T3, 7:00 PM

first: Ionita

last: Ghiran


title: The impact of maternal diet on endocrine islet progenitor cells in mice

city: Nashville

first: Guoqiang

last: Gu

state: TN

address: 2213 Garland Avenue, MRB4, Rm 9415

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: The goal of this study is to examine how altering maternal diet, including poor- or over-nutrition, impacts the gene expression levels in islet progenitors, including those cells that have not been committed to the endocrine fate and those having committed to it. At present, we will determine the gene expression changes in these progenitors.

overall_design: Ngn3-eGFP mice was used to purifiy progenitor cells. These mice have eGFP cDNA replacing the coding regions of Ngn3. In Ngn3eGFP/eGFP embryos, the eGFP+ cells represent progenitors that are ready to become islet progenitors but have not done so. In Ngn3eGFP/+ embryos, the eGFP+ cells are committed endocrine cells. For purifying  these cells, 6-weeks old Ngn3eGFP/+ female mice was fed with control nornal dient (ND), figh-fat diet (HFD), or low protein diet (LPD) for two weeks. They were then crossed with Ngn3eGFP/+ males that have been fed with control diet. After mating, females were kept on the same diet until embryo collection at E15.5. The Ngn3eGFP/eGFP and Ngn3eGFP/+ embryos were identified via genotyping and used for panceatic tissue collection, dissociation, and FACS-sorting. eGFP+ cells were used for RNA preparation, which were subject to RNAseg using the Illumina platforms (NovaSeq 6000) in the Vanderbilt Technologies for Advanced Genomics (VANTAGE), who also provides quality control data and primary data processing for alignment and feature (gene) identification. Note that two samples were prepared in a similar fashion, except the cells were sorted from the hypothalamus of E15.5 mice.

first: Simone

last: Nevills

first: Yanwen

last: Xu

first: Ruiying

last: Hu


title: Single-nucleus transcriptional profiling of the placenta reveals the syncytiotrophoblast stress response to COVID-19

first: Rachel

last: Keuls

email: Rachel.Keuls@bcm.edu, rkeuls@gmail.com

department: MCB

summary: It is poorly understood how maternal covid-19 results in severe placental disorders. Single nuclei sequencing (sci-rna-seq3) was used to profle transcriptomic changes in the human placenta in response to maternal COVID-19.

overall_design: sci-rna-seq3 was performed on 4 placentas from healthy control patients, and 4 placentas from patients with symtpomatic COVID-19 during the third trimester, and 1 placenta from a patient with symptomatic COVID-19 in the second trimester that was harvested at term post recovery


title: Plasma Cell Type Isolated EVs

city: Boston

middle: Calin

state: MA

address: 3 Blackfan Circle

department: Medicine

institute: Beth Israel Deaconess Medical Center

summary: To characterize the EVs produced by blood based cell types

overall_design: 4 donors, plasma used to isolate EVs of red blood cells, neutrophils, and platelets

first: Jennifer

last: Jones

first: Getulio

last: Pereira

first: Robert

last: Fullem


title: RNA sequencing of dorsal root ganglia tissues from mice with paclitaxel induced neuropathy

city: Madison

first: Zachary

last: Campbell

state: WI

address: 1111 Highland Avenue

department: Anesthesiology

institute: University of Wisconsin - Madison

summary: Paclitaxel causes profound neuropathic pain. To explore how it alters nascent translation, we conducted ribosome profiling and RNA-seq in mouse DRG tissues

overall_design: Comparative gene expression analysis of RNA-seq and ribosome profiling data on mouse DRG tissues.

first: June

last: de La Peña

first: Rebecca

last: Chase


title: RNA sequencing of murine dorsal root ganglia tissues

summary: To survey translational efficiency in DRG tissues, we examined translation using ribosome profiling and RNA abundance using RNA-seq. This dataset provides a baseline measurment for protein synthesis rates in murine DRG tissues.


title: Non-CG DNA methylation and MeCP2 stabilize repeated tuning of long genes that distinguish closely related neuron types [RNA-seq]

first: Mati

last: Nemera

overall_design: To examine the impact of genome topology on CA methylation in a specific cell type, we conducted Hi-C analysis on PV nuclei isolated from the mouse cortex through the INTACT method.

first: James

last: Moore

first: Rinaldo

last: D'Souza

first: Nicole

last: Hamagami

first: Adam

last: Clemens

first: Diana

last: Beard

first: Alaina

last: Urman

first: Victoria

last: Mendoza

first: Yasmin

last: Razia

first: Travis

last: Law

first: John

last: Edwards

first: Harrison

last: Gabel


title: Post stimulation immune response in suspected ZC3H12A deficiency

city: Doha

first: nico

last: marr

email: nico_marr@outlook.com, tkhan@sidra.org

address: AL RAYYAN

department: Research

country: Qatar

institute: Sidra Medicine

summary: ZC3H12A deficiency has not been reported in humans yet but mechanistic in vitro as well as mouse study data show strong evidence that ZC3H12A acts as a negative immune regu;ator  This series contains RNA sequencing data from primary fibroblasts obtained from patients with DBR1 deficiency, including mock-treated vs virus-infected cells. Cells from healthy unrelated controls and patients with STAT1 or TLR3 deficiency were analyzed for comparison.

overall_design: Stimulation of PBMCs  from two patients (brothers), two unaffected siblings  and 4 unrelated, healthy controls for two hours with LPS/R848/IL1B or TNFa or left untreated.

first: Salim

last: Bougarn

first: Taushif

last: Khan

first: Manar

last: Ata

first: Fatima

last: Al-Ali

first: Mohammed

last: Toufiq

first: Evonne

last: Chin-Smith

first: Mehdi

last: Adeli

first: Nico

last: Marr

first: Andrea

last: Guennoun


title: MicroRNA-409-3p/BTG2 Signaling Axis Improves Impaired Angiogenesis and Wound Healing in Obese Mice

city: BOSTON

first: BASAK

last: ICLI

address: 800 Washington St Box 80

department: MOLECULAR CARDIOLOGY RESEARCH INSTITUTE

institute: TUFTS MEDICAL SCHOOL

summary: Wound healing is facilitated by neoangiogenesis, a complex process that is essential to tissue repair in response to injury. MicroRNAs are small, non-coding RNAs that can regulate the wound healing process including stimulation of impaired angiogenesis that is associated with Type-2 diabetes (T2D). Expression of miR-409-3p was significantly increased in the non-healing skin wounds of patients with T2D compared to the non-wounded normal skin, and in the skin of a murine model with T2D. In response to high glucose, neutralization of miR-409-3p markedly improved EC growth and migration in human umbilical vein endothelial cells (HUVECs), promoted wound closure and angiogenesis as measured by increased CD31 in human skin organoids, while overexpression attenuated EC angiogenic responses. Bulk mRNA-Seq transcriptomic profiling revealed BTG2 as a target of miR-409-3p, where overexpression of miR-409-3p significantly decreased BTG2 mRNA and protein expression. A 3′ untranslated region (3′-UTR) luciferase assay of BTG2 revealed decreased luciferase activity with overexpression of miR-409-3p, while inhibition had opposite effects. Mechanistically, in response to high glucose, miR-409-3p deficiency in ECs resulted in increased mTOR phosphorylation meanwhile BTG2 silencing significantly decreased mTOR phosphorylation. Endothelial specific and tamoxifen-inducible miR-409-3p knock out mice (MiR-409IndECKO) with hyperglycemia that underwent dorsal skin wounding showed significant improvement of wound closure, increased blood flow, granulation tissue thickness (GTT), and CD31 that correlated with increased BTG2 expression. Taken together, our results show that miR-409-3p is a critical mediator of impaired angiogenesis in diabetic skin wound healing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HUVECs which are transfected with miR-409-3p or Non-specific control. 4 technical replicates are pooled for each total-RNA samples.

first: Basak

last: Icli

first: Furkan

last: Bestepe


title: Modulation of RUNX1-BRD4 cooperation by post-translational modification of a histone-like motif in the Runt domain

city: Singapore

first: Yoshiaki

last: Ito

address: 14 Medical Drive

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

summary: The RUNX1 transcription factor is strongly influenced by post-translational modifications. Here, we investigate a post-translational modification hotspot within a short peptide region in the evolutionarily conserved DNA-binding Runt domain. Cancer-specific mutations have been found clustered in this region, which also partially resembled the N-terminal tail of histone H4. We found that lysine acetylation of this histone-like motif promoted RUNX1 interaction with the BET-domain transcription co-activator BRD4,resulting in enhanced RUNX1 phosphorylation and transcriptional activity. Flanking post-translational modifications, such as arginine methylation and threonine phosphorylation, strongly inhibited the RUNX1-BRD4 complex formation. RNA sequencing revealed that knockdown of RUNX1 and BRD4 resulted in downregulation of genes associated with cell proliferation, suggesting that RUNX1 and BRD4 cooperated in driving cell cycle progression in gastric cancer. We identified AMIGO2 – known for its roles in invasion, proliferation and survival in cancer – as a common transcriptional target of RUNX1 and BRD4. Depletion of RUNX1 and BRD4 impaired cell proliferation and invasion in gastric cancer cells. Our work therefore indicates an oncogenic function for RUNX1-BRD4 interaction. Post-translational modification is reversible and can be pharmacologically targeted. We provide a basis for future design of drugs to specifically target the RUNX1-BRD4 interaction.

overall_design: Analysing transcriptome changes after RUNX1 or BRD4 depletion. AGS gastric adenocarcinoma cells were treated with control siRNA, siRNA targeting RUNX1 or BRD4 for 48 h. RNA samples were subjected to transcriptome sequencing. RNA libraries were prepared and sequenced by the MGISEQ-2000 (DNBSEQ) platform - Paired-end 100bp Sequencing / 40M Paired-end reads or 8Gb clean data per sample.

first: Linda

middle: S

last: Chuang

first: Nur

last: Mawan

first: Vincent

last: Oei

first: Khine

last: Myint

first: Yu

middle: X

last: Teh

first: Omer

last: An

first: Paul

last: Liu


title: Gene expressions in HUVECs treated with exosomes released from PK-45H cells

status: Public on Jan 30 2025

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

institute: Hirosaki University

summary: In the present study, we examined gene expression of human umbilical vein endothelial cells (HUVECs) treated with exosomes released from human pancreatic cancer PK-45H cells using Agilent microarray.

overall_design: Gene expressions in HUVECs treated or not with 10 ng/µL of exosomes released from PK-45H cells for 24 h or 48 h were examined by Agilent SurePrint G3 Human GE microarray 8×60K.


title: RAD51 family factors remodel the NHEJ system to modulate stress-induced biosynthesis of diterpenoid phytoalexins in rice.

city: Yangzhou

first: Mingnan

last: Qu

state: Jiangsu

address: Pazhou Dadao Rd, 17-19

institute: Yangzhou Univerisity

summary: Double-strand break (DSB) damage are primarily repaired via homologous recombination (HR) and non-homologous end joining (NHEJ) in Eukaryotes. We reveals that HR subcomplex RAD51A1-RAD51C in rice (Oryza sativa L.) inhibits classic NHEJ pathway while acts as a transcriptional mediator underlying alternative NHEJ signaling. RAD51C hijacks the KU70 at DSBs, facilitated by its partner RAD51A1 or TOP6B responding environmental cues (pathogens and 4℃). Consequently, the enhanced alternative NHEJ signaling generates the phosphorylated SOG1, which activates the regulatory network in diterpenoid phytoalexin biosynthesis and a group of enzyme genes in phenylpropanoid pathway. Intriguingly, SOG1-BRCA1-RAD51 associates with RAD51C-RAD51D-XRCC3 to form a transcription pre-initiation complex in this process. Phenotypically, chemical disease resistance and 4℃-conditioned stomatal closure are compromised in single mutants (atm-3, sog1, and rad51c-1), double mutants (rad51a1 rad51a2 and rad51d xrcc3). In summary, HR pathway integrates classic and alternative NHEJ pathways to orchestrate stress-activated specific metabolism in rice. Hierarchical collaboration of global DSB-repair machinerys enable plant adaptability to DSB-related environmental stresses.

overall_design: RNA-seq assay in the leaves of sog1 mutant, rad51c xrcc3 double mutant and their WT ZH11 under normal condition or at 20 h after γ-irradiation treatment of 40 Gy.

first: Zhan

last: Xu

first: Jemaa

last: Essemine


title: Acute Myeloid Leukemia Induces Natural Killer Cell Exhaustion via Inhibition of the PI3K-AKT Pathway

city: beijing

first: Juan

last: Xie

address: No.11 Xizhimen South Street, Xicheng District, Beijing, P.R.China

department: hematology

institute: peking university people's hospital

summary: Acute myeloid leukemia (AML) relapse is associated with a poor prognosis. Natural killer (NK) cells therapy induce leukemia remission; however, NK cells were susceptible to be exhausted post infusion. Determination of the mechanism of NK cell exhaustion in AML patients may provide insights for enhancing AML therapy. Here, we investigated NK cell exhaustion in relapsed AML patients post allo-HSCT based on phenotypic, functional, and RNA sequencing analyses. Compared with those from the complete remission and healthy control groups, NK cells from the relapsed group exhibited less maturity, higher inhibitory receptor expression and poorer cytotoxicity. AML cells could induce NK cell exhaustion through inhibition of PI3K-AKT pathway. Activation of PI3K-AKT was effective to increase NK cell cytotoxicity in exhausted NK cells. Excessive activation of the NKG2A/HLA-E axis is responsible for the inhibition of the PI3K-AKT pathway. Anti-HLA-E restored NK cell cytotoxicity against AML by increasing the phosphorylation of AKT in exhausted NK cells and knockout of the klrc1 in NK92 cells increased the phosphorylation of AKT and cytotoxicity against THP-1 cells. Moreover, blocking NKG2A was effective in controlling NK cell exhaustion and promoting cytotoxicity in AML mice. In summary, AML cells induced NK cell exhaustion via excessive activation of NKG2A/HLA-E axis and inhibition on PI3K-AKT pathway. Blocking the NKG2A axis is an effective way to reverse the inhibition of PI3K-AKT signaling on exhausted NK cells.

overall_design: To idetify the NK cells transcription profile among complete remession and relapsed patient post allogeneic hematopoietic stem cell transplantation ,we sorted bone marrow derived NK cells from 2 relapsed patients, 2 complete remession patients and 2 healthy donors and performed RNA seqencing analysis.

first: XueFei


title: Epigenetic vulnerabilities of leukemia harboring inactivating EZH2 mutations

city: Toronto

first: Sehyun

last: Cheon

state: Ontario

address: 101 College St., Suite 700

country: Canada

institute: Structural Genomics Consortium

summary: We investigated the epigenetic vulnerabilities of acute myeloid leukemia (AML) and myelodysplastic/myeloproliferative disorders (MDS/MPN) by performing a chemical probe screen in patient cells. Paradoxically, we observed increased sensitivity to EZH2 and EED inhibitors in AML and MDS/MPN patient cells harboring EZH2 mutations. Expression analysis indicated that EZH2 inhibition elicited upregulation of pathways responsible for cell death and growth arrest, specifically in patient cells with mutant EZH2. The identified EZH2 mutations had drastically reduced catalytic activity, resulting in lower cellular H3K27me3 levels and were associated with decreased EZH2 and PRC2 component EED protein levels. Overall, this study provides an important understanding of the role of EZH2 dysregulation in blood cancers and may indicate disease etiology for these poor prognosis AML and MDS/MPN cases

overall_design:
RNA-Seq transcriptome analysis of AML patient cells, DMSO control and EZH2i EPZ6438 inhibitor treated with three biological replicates.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Victoria

last: Vu

first: Dalia

last: Barsyte-Lovejoy


title: The SLC1A1/EAAT3 Dicarboxylic Amino Acid Transporter is an Epigenetically Dysregulated Nutrient Carrier that Sustains Oncogenic Metabolic Programs

city: Cleveland

first: Abhishek

last: Chakraborty

state: OH

address: 9620 Carnegie Ave NB4-120

department: Cancer Biology

institute: Cleveland Clinic

summary: Inactivation of pVHL tumor suppressor in clear cell Renal Cell Carcinoma (ccRCC) increases the abundance of Histone H3 lysine 27 acetylation (H3K27ac). We hypothesized that H3K27ac, a marker of transcriptional activation, drives the expression of critical oncogenes in ccRCC. Using H3K27ac ChIP-Seq; RNA-Seq; an in vivo positive selection screen; cell-based functional studies; and clinical validations; here, we report the identification of the SLC1A1/EAAT3 aspartate (Asp) and glutamate (Glu) transporter as a ccRCC oncogene. pVHL loss promotes SLC1A1 expression in a HIF-independent manner. SLC1A1 inactivation impedes ccRCC growth both in vitro and in vivo via depletion of Asp/Glu-derived metabolites, and sensitizes ccRCCs to metabolic therapeutics (e.g., glutaminase blockers). In human ccRCC biospecimens, higher SLC1A1 expression is associated with metastatic disease and clusters with elevated expression of other solute careers, but not HIF/Hypoxia pathways. Altogether, our studies identify a HIF-independent metabolic hub in ccRCC and credential SLC1A1 as an actionable ccRCC oncogene.

overall_design: RNA-Seq and H3K27ac ChIP-Seq of UM-RC-2 and 786-O cells expressing VEC or VHL.

first: David

last: Orlando

first: Matthew

middle: G

last: Guenther

first: Treg

last: Grubb


title: Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects-in-common on the lysosome, oxidative phosphorylation and the ribosome

city: Adelaide

first: Karissa

last: Barthelson

state: South Australia

address: North Terrace Campus

country: Australia

institute: The University of Adelaide

summary: Here, we use intra-family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96_K97del) and our model of Sanfilippo syndrome (MPS IIIB, nagluA603fs ) in young adult brains (6 months of age). We identified distinct changes to gene expression in each model at both ages. However, important commonalities were also observed, pointing to fundamental, underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases.

overall_design: We crossed a psen1Q96_K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish, to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 months of age in shared environments (4 tanks side-by-side in the same recirculating water system). Then, the entire was euthanised by cold water shock. Each fish was genotyped, then n = 8 fish per wild type, EOfAD-like (psen1 Q96_K97del heterozygous) and MPS IIIB (naglu A603fs homozygous) genotype were selected for RNAseq of their brain RNA

first: Barthelson

last: Karissa

first: Lardelli

last: Michael


title: Old World alphaviruses use distinct mechanisms to infect brain microvascular endothelial cells for neuroinvasion

city: Los Angeles

first: Pablo

middle: Aldair

last: Alvarez

state: CA

address: 615 Charles E Young Dr S

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California, Los Angeles

summary: Several alphaviruses bypass the blood-brain barrier (BBB), causing debilitating or fatal encephalitis. Sindbis virus (SINV) has been extensively studied in vivo to understand alphavirus neuropathogenesis; yet the molecular details of neuroinvasion at the BBB remain poorly understood. We investigated alphavirus-BBB interactions by pairing a physiologically-relevant, human pluripotent stem cell-derived model of brain microvascular endothelial cells (BMECs) with our model neuroinvasive SINV strains. Our system demonstrates that SINV neuroinvasion correlates with robust infection of the BBB. Specifically, SINV genetic determinants of neuroinvasion enhance viral entry into BMECs. We also identify solute carrier family 2 member 3 (SLC2A3, also named GLUT3) as a potential BMEC-specific entry factor exploited for neuroinvasion. Strikingly, efficient BBB infection is a conserved phenotype that correlates with the neuroinvasive capacity of several Old World alphaviruses, including chikungunya virus. Here, we reveal BBB infection as a shared pathway for alphavirus neuroinvasion that can be targeted for preventing alphavirus-induced encephalitis.

overall_design: RNA sequencing profiling of human pluripotent stem cell-derived brain microvascular endothelial-like cells (hPSC-BMELCs) and primary human umbilical vein endothelial cells (HUVECs) under basal conditions.

first: Angelica

last: Medina

first: Hengli

last: Tang

first: Melody

last: Li


title: Host senescence determines the success of hepatocyte transplantation in a mouse model of liver injury

city: Edinburgh

first: Stuart

last: Forbes

address: 5 Little France Drive

department: Centre for Regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

summary: Hepatocyte transplantation has shown promise for genetic diseases but has mixed efficacy for acute and severe liver injury. Limited cell engraftment and poor function of donor hepatocytes in recipient liver are significant hurdles for clinical efficacy. Hepatocyte senescence is a key feature of many liver diseases. Senescence-driven liver injury could be induced in Ahcre+Mdm2fl/fl mice in controlled and predictable levels through excision of hepatocyte Mdm2. Host senescence and injury was a requirement for initial donor hepatocyte engraftment and repopulation, but too much was inhibitory to this. Long-term expansion of transplanted hepatocytes improved histological features of injury and liver function. However graft function could spontaneously decline due to transmission of senescence from host to donor cells. Modification of the host niche prior to transplantation with senotherapeutic drug ABT737 improved donor cell proliferative capacity. Targeting paracrine senescence may be a way to improve donor hepatocyte function, optimise therapy and guide translation into the clinics.

overall_design: Differential expression between hepatocytes isolated from induced AhCre+Mdm2fl/fl (senescent) [n=3] and healthy control (AhCre-) mice [n=3]

middle: L

last: Gadd

first: Sofia

last: Ferreira-Gonzalez

first: Tak

middle: Y

last: Man

first: Alastair

last: Kilpatrick

first: Ian

middle: P

last: Smith

first: Rhona

last: Aird

first: Daniel

last: Rodrigo-Torres

first: John

middle: A

last: Hallett

first: Candice

last: Ashmore-Harris

first: Hannah

last: Esser

first: Marisa

last: Ferreira

first: Mark

last: Macmillan

first: Wei-Yu

last: Lu


title: Ribosome profiling of dorsal root ganglia tissues from mice with paclitaxel induced neuropathy

first: Zachary

middle: T

last: Campbell

first: June

last: de La Peña

first: Rebecca

last: Chase


title: Ribosome profiling of murine dorsal root ganglia tissues


title: PBMC immune transcriptome analysis in kids fed on doe's milk(Control) versus kids fed on replacer milk (Test)

city: Patna

first: Rajni

last: Kumari

state: Bihar

address: ICAR Research Complex For Eastern Region, ICAR Parisar, P. O. Bihar

country: India

institute: ICAR-RCER

summary: To study differential expression of genes in kids fed on does milk(Control) versus  kids fed on replacer milk (Test)

overall_design: To study differential expression of genes in kids fed on does milk (Control) versus kids fed on replacer milk (Test)

first: Ratna

last: Prabha

first: S

last: Ahlawat

first: A

last: Dey

last: Dayal

first: P

last: Chandran

middle: K

last: Ray

first: J

last: Kumar


title: PBMC immune transcriptome analysis in kids fed on doe's milk(Control) versus  kids fed on replacer milk (Test) post-PPR vaccination

summary: To study differential expression of genes in kids fed on doe's milk(Control) versus  kids fed on replacer milk (Test) post  PPR Vaccination

overall_design: To study differential expression of genes in kids fed on doe's milk (Control) versus kids fed on replacer milk (Test) post PPR Vaccination


title: Ribosomal RNA biosynthesis functionally programs tumor-associated macrophages in breast cancer

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

institute: Univ of Alabama at Birmingham

summary: Macrophages are among the important cellular components of the innate immune system, serving as the first line of immune defense. They are also among the first immune cells to be reprogrammed by the evolving tumor milieu into tumor-supportive macrophages that support tumor progression and promote therapeutic evasion. Unexpectedly, we uncovered that macrophages from preneoplastic breast lesions were enriched for ribosome biosynthesis genes evidencing that this is an early event that is maintained in the tumor tissue. Furthermore, following treatment with irradiation or chemotherapy, breast tumors demonstrated an abundance of tumor-supporting macrophages that displayed an enrichment of signatures of ribosomal RNA expression and ribosome biosynthesis. In alignment with this, rRNA synthesis was increased in tumor-supportive macrophages. In preclinical models of mammary cancer, a low dose of the RNA biogenesis inhibitor BMH-21 pivoted pro-tumor macrophages to macrophages with antitumor potential and supported an inflammatory tumor microenvironment. This pivot was accomplished by p53-NF-κB-orchestrated impaired ribosome biogenesis checkpoint signaling that activated an inflammatory program in macrophages. Finally, inhibiting ribosome biogenesis augmented the effectiveness of neoadjuvant therapy underscoring unexpected and unprecedented evidence that ribosome biogenesis is a targetable dependability to reprogram the tumor immune microenvironment.

overall_design: To investigate the affect of BMH-21 on the translatome of M2 polarized macrophages. RAW 264.7 cells were polarized then treated with 500nM BMH-21 or DMSO control. RNA was isolated from the polysome fractions and gene expression analysis was performed by RNA-seq. Comparaitve analysis of RNA-seq data was done with BMH-21 treated cells versus DMSO controls.

first: Brandon

last: Metge

first: Li'an

last: Williams

first: Courtney

last: Swain

first: Dominique

last: Hinshaw

first: Amr

last: Elhamamsy

first: Rajeev

last: Samant

first: Lalita

last: Shevde


title: Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer

city: Seodaemun-gu

first: Insuk

last: Lee

state: Seoul

address: 50 Yonsei-ro

department: Biotechnology

institute: Yonsei University

summary: Anaplastic lymphoma kinase (ALK) rearrangement is a major oncogenic driver in non-small cell lung cancer (NSCLC). While ALK tyrosine kinase inhibitors have shown promising therapeutic effects, overcoming resistance with immunotherapy becomes necessary when resistance develops. However, various clinical trials have revealed that their efficacies remain limited. To investigate the tumor microenvironment (TME) factors contributing to poor immune checkpoint blockade responses in ALK-positive patients, we performed single-cell RNA and ATAC sequencing on lung adenocarcinoma (LUAD) tumors with and without ALK rearrangements. Integrative analysis with additional public LUAD cohorts revealed distinct immune landscapes in ALK-positive tumors, marked by enriched innate immunity and depleted adaptive immunity. ALK-positive malignant cells exhibit higher stemness and aggressive phenotype. Tumor-associated macrophages (TAMs) in these tumors predominantly maintain pro-tumoral M2-like states, reinforcing immune suppression. B cells show reduced immune reactivity and impaired tertiary lymphoid structure formation, while CD8+ T cells display bystander-like signatures and reduced tumor reactivity. Single-cell chromatin accessibility profiles combined with regulatory network analysis suggest that differences in transcription factor activities, rather than chromatin accessibility, may underlie T cell dysfunction. These findings provide insights into the immunosuppressive TME of ALK-positive LUAD, potentially explaining the failure of recent immunotherapy trials and highlighting targets for improving efficacy.

overall_design: Single-cell RNA and TCR libraries were generated using the Chromium controller in accordance with the 10x Chromium Next GEM Single Cell 5-v2_CellSurfaceProtein_UserGuide (CG000330). Cell suspensions were initially diluted with nuclease-free water to a target concentration of 10,000 cells. These suspensions were then combined with the master mix, Single Cell 5′ Gel Beads, and Partitioning Oil, and loaded into a Next GEM Chip K. Within the droplets, RNA transcripts from individual cells were barcoded and reverse-transcribed. The resulting cDNA was pooled and subjected to PCR enrichment. Following amplification, the cDNA was size-selected to generate three distinct library types: 5ʹ Gene Expression, V(D)J Enriched, and Cell Surface Protein. For the Cell Surface Protein Library, the cDNA pool underwent further enrichment using index PCR. The V(D)J Enriched Library required two rounds of amplification with specific primers. The 5’ Gene Expression Library was processed through end repair, addition of a single ‘A’ base, adapter ligation, and subsequent purification and PCR enrichment. Quantification of the purified libraries was performed using qPCR as outlined in the qPCR Quantification Protocol Guide (KAPA), and quality assessment was conducted using the Agilent Technologies 4200 TapeStation. Finally, sequencing was carried out on the HiSeq platform (Illumina) according to the read length specifications provided in the user guide. Single-cell ATAC Libraries were generated using the Chromium controller in accordance with the 10x Single Cell ATAC protocol (CG000168). Initially, nuclei were isolated and incubated with Transposase in a Transposition Mix. These transposed nuclei were then combined with master mix, Single Cell ATAC gel beads, and Partitioning Oil in a Chip E, where DNA fragments are barcoded in droplets during thermal incubation. The resulting barcoded DNA fragments were pooled and underwent sample index PCR. Quantification of the purified libraries was performed using qPCR as described in the qPCR Quantification Protocol Guide (KAPA), and quality assessment was conducted with the Agilent Technologies 4200 TapeStation. Finally, sequencing was carried out on the HiSeq platform (Illumina) following the read length specifications provided in the user guide.

first: Seungbyn

last: Baek

first: Euijeong

last: Sung

first: Gamin

last: Kim

first: Min

middle: H

last: Hong

first: Chang

first: Hyo

last: Shim

first: Seong

last: Park

first: Hye

middle: R


title: Novel Transcripts of EMT Driving the Malignant Transformation of Oral Submucous Fibrosis [Whole transcriptome]

city: Manipal

first: Raghu

last: Radhakrishnan

state: Karnataka

address: Madava Nagar, Manipal

department: Oral and Maxillofacial Pathology and Microbiology

institute: Manipal College of Dental Sciences, Manipal

summary: OSF is a chronic, progressive, fibrotic condition of the oral mucosa that carries an elevated risk of undergoing malignant transformation. We aimed to identify and validate novel genes associated with the regulation of epithelial to mesenchymal transition (EMT) in Oral submucous fibrosis (OSF). Genes regulating EMT were identified through differential gene expression analysis, with a LogFC threshold of -1 and +1, and padj value < 0.05, utilizing data retrieved from GEO datasets, TCGA-HNSC dataset and whole transcriptome data generated from tissue samples of OSF, OSFSCC (OSF associated with OSCC) and OSCC (Oral squamous cell carcinoma). The curated EMT genes were correlated with functional states of cancer, subjected to clustering to identify the candidate genes. The EMT genes, namely MMP9, SPARC and ITGA5 were identified to be the novel candidate genes. Comprehensive pathway analysis and immunohistochemical analysis confirmed their role in regulating EMT in OSF, OSCC, and OSFSCC. Integration of bioinformatics and proteomics led to the discovery of novel candidate genes regulating EMT. The significant role of candidate genes MMP9, SPARC, and ITGA5 observed in fibrosis and malignancy indicates a novel mechanism of transition from fibrosis associated type 2 EMT to type 3 EMT, driving OSF to malignancy.

overall_design: Whole transcriptome sequencing was performed for normal(NOM) (n=2), oral submucous fibrosis (OSF)(n=2) and oral squamous cell carcinoma(OSCC) (n=2) with the parameters of 2x150bp, 60M reads/sample on HiSeq X Ten/Novaseq.


title: Mitochondrial reverse electron transport in myeloid cells   perpetuates neuroinflammation

city: Cambridge

first: Regan

last: Hamel

address: Cambridge Biosciences Campus, Hills Rd

department: Clinical Neurosciences

institute: University of Cambridge

summary: Sustained smouldering, or low grade, activation of myeloid cells is a common hallmark of several chronic neurological diseases, including multiple sclerosis. Distinct metabolic and mitochondrial features of myeloid cells guide diverse functional states. How these features act to perpetuate neuroinflammation is currently unknown. Using a multiomics approach, we identify a new molecular signature that perpetuates the activation of microglia by the reverse electron transport through complex I and the subsequent production of reactive oxygen species. Blocking reverse electron transport in pro-inflammatory myeloid cells protects against neurotoxic damage and improves functional outcomes in animal disease models in vivo. Our data show that reverse electron transport in myeloid cells is a potential new therapeutic target to foster neuroprotection in smouldering inflammatory central nervous system diseases.

overall_design: Resident microglia and infiltrating myeloid cells were isolated via FACS from a Cx3cr1-fate mapping mouse line at the peak or chronic phase of EAE, as well as healthy controls. Cells were then analysed via scRNAseq.


title: A serotonergic mechanism is involved in the procognitive effect of CB1R peripheral inhibition in a mouse model of fragile X syndrome

city: Barcelona

first: Andrés

last: Ozaita

address: Dr Aiguader, 88

department: Department of Medicine and Life Sciences

institute: Universitat Pompeu Fabra

summary: Using RNA sequencing, we perform gene expression profile of five Fmr1 KO mice treated with vehicle and four Fmr1 KO mice sub-chronically treated with AM6545 at a dose of 1 mg/kg. To evaluate hippocampal modifications promoted by peripheral CB1R modulation, we analyze gene expression and describe the upregulation of serotonin receptor 4 as the main gene modified after sub-chronic AM6545 treatment in fragile X syndrome.

overall_design: mRNA profiles of hippocampal synaptoneurosomes from Fmr1 KO mice after sub-chronic AM6545 or vehicle administration.

first: Lucía

last: de los Reyes-Ramírez

first: Araceli

last: Bergadà-Martínez


title: RNA-seq in human immortalized keratinocytes for understanding effects of low-dose ALA-PDT (0.5mmol/L 635±5nm, 3J/cm2).

city: Nantong

first: Zhinan

last: Shi

address: Chongchuan district

institute: Nantong university

summary: The aim of this study is identifying potential signaling pathways involve with low-dose ALA-PDT induced effect, using transcriptomic analysis.

overall_design: Light treatment with low-dose ALA-PDT (0.5mmol/L 635±5nm, 3J/cm2) in human immortalized keratinocytes. There are two of experimental tries with differentiated post incubation time after low-dose ALA-PDT treatment. (n=3): Control, Low-dose ALA-PDT (treatment and post incubation for 12h), Low-dose ALA-PDT (treatment and post incubation for 48h).

first: Hui

last: Hua

first: Bingrong

last: Zhou

first: Li

last: Gu

first: Jing

last: Wang


title: Chemical perturbations impacting histone acetylation regulate colorectal cancer differentiation

city: Boston

first: Zhixin

last: Li

state: Massachusetts

address: 450 Brookline Avenue, D742

institute: Dana-Farber cancer institute

summary: Histone acetylation governs broad gene expression programs in normal tissue and disease states. By applying a small chemical compound library targeting epigenetic regulators to a dual endogenous reporter system, we found that inhibiting histone deacetylase (HDAC) 1/2 initiates colorectal cancer (CRC) differentiation. Inhibiting the enzymatic pocket of HDAC1/2 induced differentiation and reduced proliferation across in vitro and in vivo models. On-target HDAC1/2 inhibition was validated using biochemical, chemical, and genetic approaches. A survey of histone posttranslational modifications from HDAC1/2 selective inhibition nominated acetylation of specific H3 and H4 lysine (K) residues as potential regulators of differentiation. Genome-wide profiles of these histone acetylation marks indicated that gains in histone 3 lysine 27 acetylation (H3K27ac) most strongly correlated to opening of chromatin and upregulation of genes associated with differentiation upon HDAC1/2 inhibition. Blocking acetylation of H3K27 by degrading its writer EP300 rescued the differentiation phenotype induced by HDAC1/2 inhibition in a patient-derived CRC model by single cell RNA-sequencing among other readouts. These results highlight the importance of specific chemically targetable histone modifications in governing cancer cell states and implicate precision targeting of H3K27ac as a potential therapeutic approach for CRC.

overall_design: To define the mechanism(s) by which MRK60 promotes CRC differentiation, we started with the analysis of gene expression profiles from CRC cells treated with MRK60.

first: Pornlada

last: Likasitwatanakul

first: Paul

last: Doan

first: Nilay

last: Sethi


title: Estrogen-induced NETs promote aseptic inflammation via NKCC1

city: Nanjing

first: Dijun

last: Chen

address: Xianlin

department: Life Sciences

institute: Nanjing University

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

sample_organism:
Macaca fascicularis
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Using VBIM technique to discover ARMC4/ODAD2 as a novel negative regulator of NF-κB  and a new tumor suppressor in colorectal cancer

city: INDIANAPOLIS

first: Matthew

last: Martin

state: IN

address: 635 BARNHILL DR

institute: Indiana University School of Medicine

summary: Since nuclear factor (NF) κB plays pivotal roles in inﬂammation and cancer, understanding its regulation holds great promise for disease therapy. Using the powerful validation-based inser-tional mutagenesis (VBIM) technique established by us previously, we discovered armadillo re-peat containing protein 4 (ARMC4), a rarely studied protein known to date, as a novel negative regulator of NF-κB in colorectal cancer (CRC). High expression of ARMC4 downregulated the expression of NF-κB-dependent genes. We report the expression differences of NF-kB target genes in a novel inhibitor of NF-kB activity.  Through RNA-seq we identified a group of NF-kB target genes specifically regulated by ARMC4.  This study provides a framework for identifying genes downregulated and upregulated by a novel inhibitor of NF-kB activity.

overall_design: Examination of NF-kB target gene differences in samples with and without Il-1B

first: Tao

last: Lu


title: Immunomodulatory properties of slowly cycling and mesenchymal-like castration-resistant prostate cancer stem cells

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: PA

address: 5117 Centre Ave

institute: University of Pittsburgh

summary: Tumors are constituted by different subpopulations of cells; this heterogeneity has multiple dimensions -genetic, epigenetic, and level of differentiation- with several clinical implications. On this work we outline the hierarchical organization of the normal epithelial of the prostate gland, and we observe that this organization is co-opted by tumors arising from this tissue. We uncovered two subsets of normal and cancer stem cells in different mouse models of prostate cancer; one population is largely quiescent with an EMT phenotype, and the other more committed toward epithelial differentiation and poised for activation in response to androgen stimuli. Whole exome sequencing revealed common pathways to these cells; exposing the prominence of integrin signaling and focal adhesion kinase (FAK) on the stem/progenitor cells behavior. Also we start to unveil a previously unnoticed property of cancer stem cells, the ability to modulate the tumor immune microenvironment and we link this function to downstream FAK signaling.

overall_design: To examine the characteristics and relationships of the prospectively identified subpopulations of prostate cells, the five subpopulations of cells defined by b4, Sca-1, and EpCAM expression, were sorted to purity by FACS and were used for RNAseq. These populations are defined as follows: DPE- (Lin-, ItgB4 hi, Sca1 hi, EpCAM low); DPE+ (Lin-, ItgB4 hi, Sca1 hi, EpCAM hi), BS (Lin-, ItgB4 hi, Sca1 low, EpCAM hi), SS (Lin-, ItgB4 low, Sca1 hi), DNE- (Lin-, ItgB4 low, Sca1 low, EpCAM low); DPE+ (Lin-, ItgB4 low, Sca1 low, EpCAM hi). This was done with both, normal gland (C57BL/6J mice) and prostate tumors of transgenic mouse models (PB-Tag, Hi-Myc (ARR2-Pb-cMyc), Ptenpc/pc (Pb-Cre4; Ptenfl/fl), and PB-ERG Pten-/- (Pb-Cre4; Ptenflox/flox; Rosa26ERG/ERG)). Finally to explore the role of integrin signaling on cancer stem cells, PB-TAg mice bearing tumor were treated with a FAK inhibitor or with vehicle as control, and then subject to the same analysis as above.

first: Javier

last: Otero

first: Filippo

last: Giancotti


title: Batf2 is a regulator of interferon gamma signaling in astrocytes during neuroinflammation

first: Jessica

last: Williams

address: 9620 Carnegie Ave N Bldg

department: Neurosciences

summary: Astrocytic interferon (IFN)g signaling is associated with reduced neuroinflammation; however, downstream effectors responsible for regulating this protection are unknown. Here we identify an interferon-specific transcription factor, basic leucine zipper ATF-like transcription factor (BATF)2, that plays a key role in modulating the consequences of IFNg signaling in astrocytes. Chromatin immunoprecipitation (ChIP) sequencing revealed that BATF2 binds and prevents the overexpression of interferon regulatory factor (IRF)1 and IRF1 targets such as Caspase-1. We also show that Batf2-/- mice exhibit exacerbated clinical disease severity in a murine model of CNS autoimmunity, and express increased astrocyte-specific IRF1 and Caspase-1, suggesting an amplified interferon response in vivo. Additionally, we demonstrate that BATF2 is expressed primarily in astrocytes within multiple sclerosis lesions and that this expression is co-localized with IRF1. Collectively, our results further support evidence of protective functions for IFNg and implicate BATF2 as a key suppressor of overactive immune signaling in astrocytes during neuroinflammation.

overall_design: ChIP sequencing of BATF2 in primary human spinal cord astrocytes stimulated with interferon (IFN)g or media as a control. Spinal cord astrocytes were obtained commercially from ScienCell.

first: Rachel

last: Tinkey

first: Brandon

middle: C

last: Smith

first: Maria

last: Habean


title: Endothelial cell-secreted bone targeting exosomes promote angiogenesis coupling with osteogenesis via the PERK-ATF4-CRELD2 pathway

city: Guangzhou

first: Zhilong

last: Pi

address: 111 Liuhua Road

institute: General Hospital of Southern Theater Command of PLA

summary: The role of endoplasmic reticulum (ER) stress in bone metabolism and the management of associated diseases has garnered significant interest. However, its role in regulating bone homeostasis and skeletal development remains largely unclear. Osteoblast development and bone formation are enhanced by a particular subtype of CD31hi endomucinhi (CD31hiEMCNhi) endothelium. However, it is still unclear how endothelial exosomes contribute to the production of CD31hiEMCNhi endothelium and bone formation. This research revealed that human umbilical vein endothelial cells (HUVECs)-exosomes (Exos) enhanced the formation of osteoblast and angiogenic effects in vitro. Furthermore, in mice treated with HUVECs-Exos, osteoblast production, and CD31hiEmcnhi vessels were significantly increased. The mechanism by which HUVECs-Exos CRELD2 improved angiogenesis coupling with osteogenesis involved triggering the PERK-ATF4-CRELD2 pathway's ER stress. As a result, HUVECs-Exos CRELD2 may be used as a potential bone metabolic disease nanodrug.

overall_design: MC3T3 cells were treated with HUVEC-derived exosomes  for 48 hours. The control group was untreated. Three replicates per group.


title: Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA-seq]

city: Berkeley

first: Megan

last: Martik

state: California

address: 163 Weill Hall

department: Molecular and Cell Biology

institute: University of California Berkeley

summary: During vertebrate development, the heart primarily arises from mesoderm, with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here, by integrating bulk and single cell RNAseq with ATAC-seq, we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1, sox9a, tfap2a and ets1. Notably, we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore, expression of all transcription factors from the migratory cardiac crest gene subcircuit are reactivated after injury at the wound edge. Together, our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination, with key factors re-activated during regeneration.

overall_design: Migratory cardiac neural crest cells (mcherry +) and non-neural crest cells from the same tissue (mcherry -) were FAC-sorted from 16 somite-stage Tg(-4.9sox10:GAL4-UAS-cre;UAS:NfsB-mCherry;myl7:nucGFP) embryos. Migratory trunk neural crest cells (GFP +) were FAC-sorted from 24hpf Tg(-4.9sox10:eGFP) embryos.

first: Marianne

last: Bronner

first: Rekha

last: Dhillon-Richardson

first: Alexandra

last: Haugan

first: Luke

last: Lyons

first: McKenna

last: Joseph


title: Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk ATAC-seq]

overall_design: Migratory cardiac neural crest cells (mcherry +) and non-neural crest cells from the same tissue (mcherry -) were  FAC-sorted from 16 somite-stage Tg(-4.9sox10:GAL4-UAS-cre;UAS:NfsB-mCherry;myl7:nucGFP) and analyzed using bulk ATAC sequencing.

first: Joseph

last: McKenna