title: Comprehensive analysis of differentially expressed lncRNA, and mRNA and their ceRNA networks in mice with the initial stage acute pancreatitis

city: Wenzhou

first: Chaohao

last: Huang

state: Zhejiang

address: Nanbaixiang Town, Ouhai District, Wenzhou City, Zhejiang Province, China 325000, China,

department: Department of Surgery

institute: First affiliated hospital of Wenzhou Medical University

summary: Acute pancreatitis (AP) is a prevalent digestive disorder with significant morbidity and mortality rates. This study, for the first time, employed high-throughput sequencing on pancreatic tissues from normal and AP mice to identify differentially expressed long noncoding RNAs (lncRNAs) and mRNAs, as well as related signaling pathways, in the early stage of AP. We found 261 lncRNAs and 1,522 mRNAs to be differentially expressed, with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealing gene functions enriched in cellular metabolism, intercellular structure, and positive regulation of inflammation. By constructing lncRNA-miRNA-mRNA networks, we explored underlying mechanisms and interactions in AP. Notably, knockout of Neat1 in mice inhibited pyroptosis in AP and severe acute pancreatitis (SAP) models, suggesting Neat1's pivotal role in AP pathogenesis. These findings highlight the importance of lncRNAs, particularly Neat1, in AP, offering new insights into SAP pathogenesis and potential therapeutic targets.

overall_design: To identify differentially expressed lncRNAs and mRNAs, as well as related signaling pathways, in the early stage of acute pancreatitis (AP), we established an AP mouse model by administering 200 μl of cerulein (200 μg/kg/h) 10 times and extracted pancreatic tissue RNA at the moment the modeling was completed.


title: Treatment and molecular analysis of bullous pemphigoid with tofacitinib: a case report and review of current literature

status: Public on Nov 13 2024

city: Chongqing

first: mingwang

last: zhang

address: No. 30 Gaotanyan Street, Shapingba District, Chongqing

department: Department of Dermatology

country: China

institute: Southwest Hospital, Army Medical University

type: Expression profiling by high throughput sequencing

summary: Bullous pemphigoid (BP) is a rare, life-threatening autoimmune blistering disease with pruritus and tension blisters/bullous as the main clinical manifestations. Glucocorticosteroids are the main therapeutic agents for it, but their efficacy is poor in some patients. Tofacitinib, a small molecule agent that inhibits JAK1/3, has shown incredible efficacy in a wide range of autoimmune diseases and maybe a new valuable treatment option for refractory BP. To report a case of refractory BP successfully treated with tofacitinib, then explore the underlying mechanism behind the treatment, and finally review similarities to other cases reported in the literature. Case report and literature review of published cases of successful BP treatment with JAK inhibitors. The case report describes a 73-year-old male with refractory BP that was successfully managed with the combination therapy of tofacitinib and low-dose glucocorticoids for 28 weeks. Immunohistochemistry and RNA sequencing were performed to analyze the underlying mechanism of tofacitinib therapy. A systematic literature search was conducted to identify other cases of treatment with JAK inhibitors. Throughout the 28-week treatment period, the patient experienced clinical, autoantibody and histologic resolution. Immunohistochemical analysis showed tofacitinib significantly decreased the pSTAT3 and pSTAT6 levels in the skin lesions of this patient. RNA sequencing and immunohistochemical testing of lesion samples from other BP patients identified activation of the JAK-STAT signaling pathway. Literature review revealed 17 previously reported cases of BP treated with four kinds of JAK inhibitors successfully, including tofacitinib (10), baricitinib (1), upadacitinib (3) and abrocitinib (3). Our findings support the potential of tofacitinib as a safe and effective treatment option for BP. Larger studies are underway to better understand this efficacy and safety.

overall_design: RNA sequencing was performed to identify whether the JAK- 300 STAT signaling was activated in BP skin lesions compared with 301 normal controls.

first: Mingwang

last: Zhang

first: Xiang

last: Li

first: Zhifang

last: Zhai


title: Role of growth differentiation factor 15 in mouse adipose tissue homeostasis

city: Nuthetal

first: Carla

last: Igual Gil

address: Arthur-Scheunert-Allee 114-116

country: Germany

institute: German Institute of Human Nutrition (DIfE)

summary: Recent research has identified growth differentiation factor 15 (GDF15) as a crucial factor in various physiological and pathological processes, particularly in energy balance regulation. We here investigated the role of GDF15 in adipose tissue physiology and metabolism by performing an RNA-Seq analysis of subcutaneous adipose tissue (sWAT) of 20 week old male and female Gdf15-KO mice compared to their WT littermates.  Our study revealed a broad downregulation of genes involved in lipid metabolism and furthermore, it uncovered sex-specific effects, with females being more affected by GDF15 loss than males. These insights enhance our understanding of GDF15's functions in adipose tissue physiology and underscore its potential as a therapeutic target for metabolic disorders.

overall_design: Subcutaneos adipose tissue of 20 week old, male and female wildtype (WT) and Gdf15 knockout (Gdf15-KO) mice fed ad libitum was dissected and RNA-Seq analyses were performed (n=6).

first: Susanne

last: Klaus

first: Markus

last: Jähnert


title: Effect of HES1 overexpression on gene expression of adipose stem cells [RNA-seq]

city: Wuhan

first: Chengcheng

state: hubei

address: Jiefang Road

department: Department of Hand Surgery, Union Hospital

institute: Huazhong University of Science and Technology

summary: In the current investigation, an RNA-seq analysis was conducted to examine the differentially expressed genes in old ADSCs (O-ADSCs) following the overexpression of HES1. The findings indicated that 448 genes exhibited increased levels, while 865 genes showed decreased levels in the oe-HES1 O-ADSCs compared to the oe-NC O-ADSCs. The GO analysis revealed that these genes are primarily localized in the nucleus and cytoplasm, and are involved in activities such as protein binding and DNA binding. Furthermore, they are associated with processes related to cell adhesion and the regulation of transcription by RNA polymerase II. The KEGG analysis indicated enrichment in pathways such as the NOD-like receptor signaling pathway, TNF signaling pathway, IL-17 signaling pathway, and PI3K-Akt signaling pathway.

overall_design: A comparative RNA-seq was conducted on a cohort comprising three  oe-HES1 O-ADSCs and three oe-NC O-ADSCs

first: Zhenbing

last: Chen

first: Sen

last: Ren


title: Redistribution of PU.1 partner transcription factor RUNX1 binding secures cell survival during leukemogenesis

status: Public on Nov 15 2024

city: Münster

first: Frank

last: Rosenbauer

address: Robert-Koch-Str. 43

department: Institut of Molecular Tumor Biology

institute: University Hospital Münster

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series

first: Alexander

last: Bender

first: Füsun

last: Boydere


title: Genome-wide DNA methylation profiling reveals a novel hypermethylated biomarker PRKCB in gastric cancer

city: Nanchang

first: Leyan

state: Jiangxi

address: Donghu District

institute: The First Affiliated Hospital of Nanchang University

type: Methylation profiling by high throughput sequencing

summary: Gastric cancer (GC) is one of the most common malignancies worldwide. Epigenetic changes, mainly the altered DNA methylation, have been implicated in many cancers. Here, we profile the DNA methylation pattern of GC and identify promising diagnostic epigenetic biomarkers.

overall_design: We investigated the genome-wide DNA methylation pattern in four pairs of GC and adjacent tissues using Illumina 935K BeadChip.

first: Yin

last: Zhu

first: Nianshuang


title: Decoding the DNA binding sites associated with HES1

summary: To investigate the DNA binding sites associated with HES1, a CUT & Tag assay was conducted utilizing an anti-flag antibody to isolate the DNA sequences that interact with HES1. Subsequently, these DNA sequences were subjected to analysis through DNA-seq. The results indicated that HES1 has the capability to bind to the promotor-transcription start sites of 1140 genes.

overall_design: A CUT & Tag assay was conducted utilizing an anti-flag antibody and an isotype control antibody to decode the DNA binding sites of HES1 in two adipose stem cells’ samples.


title: NOTCH dimerization contributes to maintenance of intestinal homeostasis

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

country: USA

institute: Cincinnati Children's Hospital Medical Center

summary: A tri-protein complex containing NICD, RBPj and MAMl1 binds DNA as monomer or, cooperatively, as dimers to regulate transcription. Mice expressing Notch dimerization-deficient (DD) alleles Notch1DD and Notch2DD (NDD) are sensitized to environmental insults but otherwise develop and age normally. Transcriptomic analysis of colonic spheroids uncovered no evidence of dimer-dependent target gene miss-regulation, confirmed impaired stem cell maintenance in-vitro, and discovered an elevated signature of epithelial innate immune response to symbionts, the likely underlying cause for heightened sensitivity in NDD mice. TurboID followed by quantitative nano-spray MS/MS mass-spectrometry analyses in a human colon carcinoma cell line expressing either Notch2DD or Notch2 revealed an unbalanced interactome, with reduced interaction of Notch2DD with the transcription machinery but relatively preserved interaction with the HDAC2 interactome suggesting it is dimer independent. To ask if elevated HDAC2 activity contributes to Notch loss of function phenotypes, we used the HDAC2 inhibitor Valproic acid (VPA) and discovered it could block the intestinal consequences of gamma secretase inhibitor (DBZ or DAPT) treatment in mice and spheroids, suggesting synergy between HDAC activity and pro-differentiation program in intestinal stem cells which may be exploitable therapeutically.

overall_design: Bulk RNA-sequencing on 2 mutant vs 3 wildtype colonic spheroids samples.

first: Preusse

last: Kristina

first: Dai

last: Quanhui

first: Kopan

last: Raphael


title: The gene expression of adipose stem cells obtained from donors of varying ages

summary: In the current investigation, a comprehensive analysis using high-throughput RNA sequencing (RNA-seq) was carried out on ADSCs obtained from donors of varying ages.  678 genes showed differential expression between ADSCs obtained from young and old donors  (Y-ADSCs and O-ADSCs), with 47 of these genes being TFs. The findings indicated that 316 genes exhibited decreased expression levels, while 362 genes displayed increased expression levels in O-ADSCs in comparison to Y-ADSCs. Subsequent analyses using GO and KEGG were performed to further elucidate the roles of the identified differentially expressed genes. The GO analysis revealed that these genes are predominantly localized in the plasma membrane and extracellular region, serving as constituents of the extracellular matrix and participating in protein binding. Additionally, they are implicated in processes related to cell adhesion and signal transduction pathways. KEGG analysis indicated enrichment in pathways such as neuroactive ligand-receptor interaction, calcium signaling, pathways in cancer, ErbB signaling, and cell adhesion molecules.

overall_design: A comparative RNA-seq was conducted on a larger cohort comprising five Y-ADSCs and six O-ADSCs


title: Effects of UBE2S knockout on Huh7 cells

city: xi'an

first: Renyu

state: Shaanxi

address: 169 Changle West Road

institute: Fourth Military Medical University

summary: As the main type of primary liver cancer, hepatocellular carcinoma (HCC) seriously endangers human health. UBE2S is upregulated in human HCC tissue and associated with poor prognosis. To explore the biological functions and molecular mechanisms of UBE2S in HCC cells, we explored the effects of UBE2S knockout on Huh7 cells using RNA-seq.

overall_design: In order to identify downstream factors regulated by UBE2S in hepatocellular carcinoma cells, we conducted RNA-seq analyses in Huh7 cells with UBE2S knockout.

first: Huijie

last: Bian


title: Spanish slug (Arion vulgaris) small RNA sequencing and annotation

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

type: Non-coding RNA profiling by high throughput sequencing

summary: Goal of the study is to characterize small RNAs in Spanish land slug, Arion vulgaris.

overall_design: Bulk small RNA-seq of 1 slug sample: - ovotestis, 1x WT

first: Petr

last: Svoboda

first: Valeria

last: Buccheri

first: Simin

last: Sakaki


title: TNF-α released by melanoma liver metastasis activates AKT and NFKβ1 pathways to promote collagen type I secretion by hepatocytes

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

summary: A total of four human melanoma liver metastasis (MLiM) formalin-fixed paraffin-embedded (FFPE) sections were analyzed using Nanostring GeoMx digital spatial profiling (NGDSP). The FFPE tissues were obtained from patients who underwent surgery and were pathological diagnosed with MLiM. Patients who had received any preoperative therapy were excluded. In each region of interest (ROI), two areas of interest (AOI)s were defined by HepPar1+ (hepatocytes); HMB45+ (melanoma cells) staining. A total of 43 AOIs were carefully reviewed for segments with sequencing saturation < 25%, nuclei fewer than 80, negative probe counts <3, or a surface area of <12,000 squared microns. Background correction and scaling were performed using geometric means and normalization was performed using Q3 averages of housekeeping genes. Genes with expression levels at or lower than limit of quantification (LOQ) in at least 5% of segments were filtered out. A total of 1,811 genes passed quality control and were analyzed. A total of seven ROIs with tumor margin (TM) and 13 ROIs with tumor center (TC) were selected, respectively. TM was defined as the areas on the border of malignant tumor cells close to normal tissue based on pathological features. TC was defined as central tumor tissue further inside from TM. In addition, 14 ROIs were selected at ANH. The ANH areas were defined as an area within 1,200 µm from the TM. Furthermore, nine ROIs were selected at the DNH areas. DNH was defined as an area at least 6 mm away from TM. Differential expressed genes (DEGs, Log2 fold-change >1.5, <-1.5, p < 0.05) were calculated on AOIs selected from MLiM comparing TC vs. TM; ANH vs. DNH; and ANH vs. Melanoma cells (TC+TM).

overall_design: Four FFPE tissue samples were analyzed by NanoString GeoMX Digital Spatial Profiling. The regions of interest (ROI) were collected in each tissue samples and segmented in areas of interest (AOI) based on the staining pattern of two fluorescently labeled cell type specific morphological markers: HepPar1+ and HMB45+.

first: Shodai

last: Mizuno

first: Matias

middle: A

last: Bustos

first: Kelly

middle: K

last: Chong

middle: S


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Toe1 konckout  Transcriptomes in differentiated C17.2 cells

city: shenzhen

first: TINGTING

last: DENG

address: 3002 Sungang West Road

institute: Shenzhen Second People's Hospital

summary: We extracted RNA from NC and KO-Toe1  differentiated C17.2 cells for high-throughput transcriptomic sequencing. In differentiated C17.2 cells, Toe1 primarily affected biological functions including peptidase activity, chemotactic factors, the ECM, and the TNF signaling pathway.

overall_design: mRNA profiles of  NC and KO-Toe1 were generated by deep sequencing using Illumina GAIIx.

first: Tingting

last: Deng


title: EV-derived miR-186-5p alleviates APAP-induced liver injury by the suppression of CXCL1

city: Guangzhou

first: Rukang

last: Liang

state: Guangdong

address: Shipai Street, Tianhe district

department: Biotherapy Center

institute: The Third Affiliated Hospital of Sun Yat-Sen University

summary: Acetaminophen (APAP) overdose is the major cause of drug-induced liver injury (DILI) and acute liver failure (ALF), and patients with advanced APAP toxicity rarely benefit from N-acetylcysteine (NAC), which is the first-line agent used in the clinic. Mesenchymal stromal cells (MSCs) and their extracellular vesicles (MSC-EVs) have shown promising effects in the treatment of DILI by decreasing neutrophil infiltration. However, the specific mechanism underlying the therapeutic effects of MSCs or MSC-EVs still needs to be elucidated. In this study, by using RNA-seq, we found that CXCL1, which is a chemoattractant for neutrophils, is a key molecule in MSC-mediated amelioration of DILI, and by luciferase reporter assay, we verified that MSC-EV-derived miR-186-5p binds to the 3’-UTR of CXCL1 to inhibit its expression in hepatocytes. Neutralizing CXCL1 reduces APAP-induced liver damage in vivo, and the agomir miR-186-5p shows excellent potential in the treatment of DILI. Overall, these findings suggest that the use of MSC-EVs may be a promising novel strategy for preventing DILI and that targeting the miR-186-5P/CXCL1 axis is a feasible approach for improving the efficacy of MSCs in the treatment of DILI.

overall_design: To investigate the potential target genes that whose expression is altered after MSC treatment, we performed RNA sequencing on liver tissues from the control (CTRL) group, the APAP+PBS (APAP_PBS) group, and the APAP +MSC (APAP_MSC) group 24h after APAP administration.

first: Erming

last: Zhao

first: Panlong

last: Li

first: Qi

last: Zhang

first: Qiuli

last: Liu

first: Yingcai


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Toe1 konckout  Transcriptomes in undifferentiated C17.2 cells

summary: We extracted RNA from KO-NC and KO-Toe1  undifferentiated C17.2 cells for high-throughput transcriptomic sequencing.In undifferentiated C17.2 cells, Toe1 primarily influenced key biological processes such as calcium ion binding, the extracellular matrix (ECM), and alpha-amino acid catabolism

overall_design: mRNA profiles of  KO-NC and KO-Toe1 were generated by deep sequencing using Illumina GAIIx.


title: Deletion of Ligand Dependent Corepressor-Like (LCoRL) Protects Against Diet-induced Obesity Deletion of Ligand Dependent Corepressor-Like (LCoRL) Protects Against Diet-induced Obesity

city: Dallas

first: Lara

last: Bideyan

state: TX

address: 5323 Harry Hines Blvd., MC: 9077 Y6.314

department: Internal Medicine

institute: UT Southwestern

summary:
ABSTRACT
OBJECTIVE: Genome Wide Association Studies (GWAS) in humans, dogs, and livestock have uncovered genes which may play a role in metabolism. However, functional analysis is required to link the metabolic phenotype with the associated gene. Here we identified the Ligand Dependent Corepressor-Like (LCoRL) as a potential metabolic regulator.
METHOD: We used CRISPR/Cas9 approaches in mice to generate a Lcorl null allele (Lcorl-/-). We characterized Lcorl-/- mice by assessing body weight, body composition, food intake, and glucose homeostasis as well as assessing transcriptional changes in Lcorl-/- livers by RNA-sequencing. Finally, we challenged mice with a 60% high fat diet (HFD) and a treadmill exercise stress test.
RESULTS: Mice homozygous for loss of Lcorl are viable and fertile. However, Lcorl-/- pups show stunted postnatal growth for the first few weeks of life. This is followed by a catchup growth, such that, Lcorl-/- mice are indistinguishable from wildtype littermates by 7-9 weeks of age. Three-week-old mice show reduced circulating insulin like growth factor-1 (IGF-1) levels without a change in pituitary Growth hormone (Gh) mRNA levels.  Interestingly, Lcorl-/- mice remain lean compared to wildtype littermates as they age. This is associated with a decrease in daily food intake.  Additionally, Lcorl-/- mice show no change in energy expenditure; however, Lcorl-/- mice show a greater amplitude of their respiratory exchange ratio (RER) compared to controls, suggesting differential usage of fat and carbohydrates across the light/dark cycle. This altered RER may result from the reduction in day-time food intake or disrupted mobilization of fat and carbohydrate stores. Consistent with enhanced metabolic health, Lcorl-/- mice also show improved glucose tolerance and insulin sensitivity. Finally, Lcorl-/- mice are protected against a 60% high fat diet challenge and show reduced exercise capacity in a stress test.
CONCLUSION: This phenotypic characterization of the Lcorl-/- mouse reveals that LCoRL is a causal gene resulting in the changes in metabolism seen in GWAS in humans and livestock and provides novel mechanistic insights of a gene important in human disease and economically valuable traits in livestock.

overall_design: To investigate the role of Lcorl, we created a Lcorl global knockout model. We harvested tissues from Lcorl KO and wildtype mice and conducted RNA-Seq on their livers. We performed differential gene expression analysis on Lcorl KO vs WT livers.

first: Steven

last: Wyler

first: Joel

last: Elmquist


title: Effect of Atractylodin on high fat diet-induced fatty liver disease

city: Chuncheon-si

first: Yoon Mee

last: Yang

state: Gangwon-do

address: 1 Kangwondaehak-gil

department: Pharmacy

country: South Korea

institute: Kangwon National University

summary: The escalating prevalence of metabolic diseases, driven by the rapid increase in obesity rates, necessitates effective therapeutic strategies. Insulin resistance and nonalcoholic fatty liver disease represent significant metabolic disorders. Atractylodin exhibits anti-inflammatory and antioxidant properties, suggesting potential hepatoprotective effects against acute liver damage. As therapeutic interventions for nonalcoholic steatohepatitis are lacking, this study aims to elucidate the pharmacological impact of Atractylodin on lipid and glucose metabolism.

overall_design: Eight-week-old male C57BL/6N mice were given a high-fat diet (HFD) ad libitum for 12 weeks. After 8 weeks of HFD feeding, mice were administered Atractylodin (10 mg/kg body weight) or a vehicle. Atractylodin was orally administered five days per week. After 4 weeks of drug administration, the mice were sacrificed.

first: Ga

middle: Y

last: Song

first: Yoon

middle: M


title: Multi-Modal Comparison of human Hepatic Stellate Cells identifies novel therapeutic targets for Metabolic Dysfunction-Associated Steatotic Liver Disease

city: La Jolla

first: David

last: Brenner

address: 10901 North Torrey Pines Road

institute: Sanford Burnham Prebys

summary: Background and aims: Metabolic dysfunction-associated steatotic liver disease (MASLD) progresses from steatosis (Metabolic dysfunction-associated steatotic liver, MASL) to Metabolic dysfunction-associated steatohepatitis (MASH) with fibrosis. Activation of Hepatic Stellate Cells (HSCs) into fibrogenic myofibroblasts plays a critical role in the pathogenesis of MASH liver fibrosis. Here we compared gene expression and chromatin accessibility profiles of human HSCs in NORMAL, MASL, and MASH livers at single cell resolution. Methods: 18 human livers were profiled using single-nucleus (sn) RNA-seq and snATAC-seq. High priority targets were identified and then tested in 2D human HSCs, 3D human liver spheroids, and HSC-specific gene knockout mice. Results: This study identified novel gene regulatory mechanisms underlying MASL- and MASH-associated HSC heterogeneity and outlined potential strategies for anti-fibrotic therapy. Specifically, MASH-enriched HSC-subcluster hA1, represented by highly fibrogenic population of myofibroblasts, served as a critical source of extracellular matrix protein (ECM) in MASH, and its activation was regulated via a cross-talk between lineage-specific (JUNB/AP1), cluster-specific (RUNX1/2) and signal-specific (FOXA1/2) transcription factors (TFs). Additionally, we identified a set of core genes (GAS7, SPON1, SERPINE1, LTBP2, KLF9, EFEMP1) that drive ECM production in hA1 HSCs. The pathological relevance of the selected hA1 targets, such as SERPINE1 and others, was demonstrated using siRNA-based HSC-specific gene knockdown or pharmacological inhibitor of SERPINE1 in 3D human MASH liver spheroids, and HSC-specific Serpine1 knockout mice with MASH. Conclusion: We identified potential targets for anti-fibrotic therapy of MASH in patients.

overall_design: 18 single nucleus ATACseq samples, 18 single nucleus RNAseq samples from human MASH, MASL, NORMAL livers.

first: Sara

middle: B

last: Rosenthal

first: Hyun

last: Kim

first: Xiao

first: Charlene

last: Miciano

first: Xiaomeng

last: Hou

first: Michael

last: Miller

first: Justin

last: Buchanan

first: Olivier

last: Poiron

first: Daisy

last: Chilin-Fuentes

first: Cuijuan

last: Han

first: Mojgan

last: Hosseini

first: Raquel

last: Carvalho Gontijo Weber

first: Sadatsugu

last: Sakane

first: Huayi

first: Karin

last: Diggle

first: Sebastian

last: Preissl

first: Christopher

last: Glass

first: Bing

last: Ren

first: Allen

last: Wang

first: Tatiana

last: Kisseleva


title: Single cell RNA seq reveals cellular and transcriptional heterogeneity in the splenic CD11b+Ly6Chigh monocyte population expanded in sepsis-surviving mice

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

summary: Patients surviving a septic episode exhibit persistent immune impairment and increased mortality due to enhanced infection vulnerability. In the present study, using the cecal ligation and puncture (CLP) model of polymicrobial sepsis, we addressed the hypothesis that functional, metabolic, and phenotypic alterations in splenic CD11b+Ly6Chigh myeloid cells contribute to the immune impairment in sepsis-surviving mice. Herein, we showed the cellular and transcriptional heterogeneity of the expanded splenic CD11b+Ly6Chigh population in CLP-survivors. We also showed that CD11b+Ly6Chigh cells presented phenotypic and functional disparity between C57BL6/J and BALB/c strains.

overall_design: Six-Nine weeks of age Male C57BL/6 and Balb/c got surgeries and survivors after 4 weeks were euthanized.  Splenic monocytes from CLP or sham-operated mice were isolated by negative selection, and CD11b+ Ly6C high populations were purified by Fluorescence-activated cell sorting, and analyzed by scRNA-seq. Two sham and three CLP mice in each strain were distinguished by cell hashing antibodies (Biolegend).

first: Myoungsun

last: Son

first: Haruki

last: Watanabe


title: Divergent transcriptomic profiles in depressed individuals with hyper- and hypophagia implicating inflammatory status

city: Belmont

first: Shu

last: Dan

state: MA

address: 115 Mill St

department: Basic Neuroscience

institute: McLean Hospital, Harvard Medical School

summary: We used bulk RNAseq to examine differences in blood transcriptomic profiles between depressed individuals with hyperphagia (MDD-hyper) compared to depressed individuals with hypophagia (MDD-hypo) at rest before and after the stress task, controlling for repeated measures.

overall_design: A total of 78 samples from 20 individuals are included in the study. Each participants participate in 2 visits, one with a MAST task and one without. The blood samples for  bulkRNAseq was taken before and after the task.

first: Julia

last: Hall

first: Laura

last: Holsen

first: Torsten

last: Klengel


title: SntB triggers the antioxidant pathways to regulate development and aflatoxin biosynthesis in Aspergillus flavus

city: Fuzhou

first: Chi

last: Yang

address: No.15 Shangxiadian Road, Cangshan District

institute: Fujian Agriculture and Forestry University

summary: In this study, sntB gene deletion (ΔsntB), complementary (Com-sntB), and HA tag fused to snt2 strain (snt2-HA) strains were constructed by using the homologous recombination method, respectively. It was found in this study that SNTB plays a key role in development, secondary metabolism and pathogenicity of A. flavus. The mechanism was explored by Chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq).

overall_design: To reveal the potential complex regulatory network of the sntB, RNA-seq analysis was carried out on the WT and ΔsntB strains. ChIP-seq analysis was carried out on the WT and sntB-HA strains.

first: Zhenhong

last: Zhuang


title: Dysregulated ac4C modification of mRNA in a mouse model of early stage Alzheimer's disease [acRIP-seq]

status: Public on Nov 12 2024

city: shanghai

first: danhong

last: wu

address: 3rd Floor, Building 2, 801 Heqing Road, Shanghai

department: Department of Neurology

institute: Shanghai Fifth People’s Hospital, Fudan University

summary: In this study, ac4C modifications in mRNA were investigated using three-month-old 5×FAD transgenic mice, a widely recognized model of Alzheimer's disease, along with age- and sex-matched wild-type (WT) controls. To elucidate the role of ac4C-modified mRNA in AD, we employed three analytical techniques: acetylated RNA immunoprecipitation sequencing (ac4C-RIP-seq), RNA sequencing (RNA-seq), and proteomic analysis. The first two were used to identify mRNAs carrying ac4C modifications and to quantify mRNA abundance, respectively.

overall_design: acetylated RNA immunoprecipitation -sequancing (acRIP-seq) was used to determine the acetylation modification of mRNA in the hippocampus from 3 month mice (3 5xFAD mice and 3 WT mice). Then IgG- sequancing was used to correct the result of acRIP-seq.

first: Haonan

last: Ji

first: Haiqian

last: Zhou

first: Jingbo

last: Qie

first: Wenmei

last: Lu

first: Haitao

last: Gao

first: Danhong

last: Wu


title: Effect of HES6 knockdown on gene expression in vitro differentiated megakaryocytes, erythroblasts and precursor cells, cultured from CB CD34+ HSPCs.

city: Ghent

first: Tom

last: Taghon

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

summary: Cord blood CD34+ hematopoietic precursors (3 donors) were control or HES6 shRNA (HES6 knockdown) transduced and cultured for four days in media containing SCF, TPO and EPO to drive differentiation towards megakaryocytes and erythroid cells. After four days four subpopulations were sorted for RNA isolation to research the effect of HES6 knockdown on gene expression. We sorted megakaryocytes (CD41+) and early (CD71+ CD235-) and late (CD71+ CD235+) erythroblasts (CD41-) and CD34- precursor cells (CD41- CD71- CD235- CD34-).

overall_design: Gene expression profiling by high throughput sequencing of 4 different cell types (megakaryocytes, CD34- precursors, early and late erythroblasts) for 3 replicates with control or HES6 knockdown (2 conditions: shRNA1 and shRNA2, both targeting human HES6).

first: Tamara

last: De Vos

last: Putteman


title: Setd2 reprograns lipid metabolism for the resolution of inflammation via H3K36me3 modification

first: kun

last: chen

address: No.800 Xiangyin Road, Yangpu District

institute: Zhejiang University

summary: Purpose: The goal of this study is to identify differential Setd2-mediated H3K36me3 modificaion in the resolution phase of inflammation induced by  LPS  Methods: We profiled chip-seq with H3K36me3 antibody in bone marrow-derived macrophages stimulated with LPS for 0h, 4h, 16h.  Results: We find different H3K36me3 enrichment peaks under LPS stimulation at different time.

overall_design: BMDMs were stimulated with LPS for 0h, 4h, 16h, and then subjected to ChIP-seq.

first: Xuetao

last: Cao

first: Kun

last: Chen


title: Dysregulated ac4C modification of mRNA in a mouse model of early stage Alzheimer's disease [mRNA-seq]

overall_design: mRNA-seq was used to determine the abundance of mRNA in the hippocampus from 3 month mice (3 5xFAD mice and 3 WT mice).


title: Bulk RNA sequencing of primary mouse microglia

city: Cambridge

first: Timothy

middle: R

last: Hammond

address: 350 Water Street

institute: Sanofi

summary: We used primary mouse microglia to determine whether Bruton's tyrosine kinase (BTK) inhibition could attenuate differential gene expression induced by Fc receptor stimulation.

overall_design: Bulk RNA sequencing was performed with primary mouse microglia, treated with an IgG stimulus and/or an inhibitor of Bruton’s tyrosine kinase (BTK).


title: Integrated multi-modal analysis reveals tumor and immune characteristics that distinguish Epstein-Barr virus-positive and -negative B cell post-transplant lymphoproliferative disorders [scRNA-seq]

city: Stanford

first: Jiaying

last: Toh

state: California

address: 1201 Welch Road

institute: Stanford University

summary: The highly prevalent oncogenic Epstein-Barr virus (EBV) can drive tumorigenesis with disrupted host immunity, causing malignancies including post-transplant lymphoproliferative disorders (PTLD). PTLD can also arise in the absence of EBV but the biological differences underlying EBV(+) and EBV(-) B cell PTLD and the associated host-EBV-tumor interactions remain poorly understood. Here, we reveal the core differences between EBV(+) and EBV(-) PTLD, characterized by increased expression of genes related to immune processes or DNA interactions respectively, and the augmented ability of EBV(+) PTLD B cells to modulate the tumor microenvironment through elaboration of monocyte-attracting cytokines/chemokines. We create a reference resource of proteins distinguishing EBV(+) B lymphoma cells from EBV(-) B lymphoma including the immunomodulatory molecules CD300a and CD24, respectively. Moreover, we show that CD300a is essential for maximal survival of EBV(+) PTLD B lymphoma cells. Our comprehensive multi-modal analyses uncover the biological underpinnings of PTLD and offer opportunities for precision therapies.

overall_design: CD300A knockout (KO) cell lines were generated from three EBV(+) B PTLD patient-derived spontaneous lymphoblastoid cell lines (AB5, JB7, VB5) via CRISPR/Cas9 gene editing, using nucleofection to introduce ribonucleoprotein complexes composed of Cas9-2NLS and CD300A sgRNA. Corresponding mock controls for each cell line were also generated via nucleofection with Cas9-2NLS in the absence of sgRNA. No single-cell cloning was performed for CD300A KO cell lines. The resulting bulk cell populations were analysed using scRNAseq.


title: Integrated multi-modal analysis reveals tumor and immune characteristics that distinguish Epstein-Barr virus-positive and -negative B cell post-transplant lymphoproliferative disorders

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

overall_design: Refer to individual Series


title: Transcriptome analysis of human embryonic stem cell-derived cartilage pellets at three stages of differentiation

city: Irvine

first: Maksim

middle: V

last: Plikus

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: RNA-sequencing data was obtained from cultured cartilage pellets differentiated from human embryonic stem cells via neural crest intermediate  at three consecutive stages of differentiation. The transcriptome of each stage was analyzed and compared against other stages, creating a "timeline" of cartilage differentiation.

overall_design: RNA-sequencing was performed on whole tissue of cartilage pellets, cultured in chondrogenic media. Pellets were analyzed on days 21, 30 and 45 of culture in differentiation supporting media. Four-to-five replicates were analyzed per time point.

first: Ramos

last: Raul

first: Plikus

last: Maksim


title: ESR1 Y537S and D538G mutations drive resistance to CDK4/6 inhibitors in estrogen receptor-positive breast cancer

first: Chang-Ching

last: Lin

address: 4554 Glenwick Ln, Apt 2203

department: Harold C. Simmons Comprehensive Cancer Center

institute: UT Southwestern Medical Center

summary: Purpose: Breast cancers with ESR1 mutations are resistant to antiestrogen therapy. We aimed to investigate the association of ESR1 mutations with resistance to CDK4/6 inhibitors (CDK4/6i) using real-world data analysis and experimental validation. Patients and Methods: A total of 3,958 patients with estrogen receptor-positive (ER+) metastatic breast cancer with DNA sequencing data were analyzed. Breast tumor DNA and circulating tumor (ct) DNA were sequenced using the Tempus xT tumor assay and Tempus xF liquid biopsy, respectively. Patients were stratified into either treated with CDK4/6i (breast tumors: 1,070; ctDNA: 1,885) or CDK4/6i naïve (breast tumors: 750; ctDNA: 253). Engineered MCF7 cells carrying ESR1 Y537S or D538G knock-in mutations were used to study antitumor efficacy of the CDK4/6i, palbociclib in vitro and in vivo.  Results: In both xF and xT assays, ESR1 mutations were the only somatic alterations significantly more frequent in those who received CDK4/6i than those who did not. Knock-in of ESR1 Y537S or ESR1 D538G in MCF7 cells resulted in upregulation of cell cycle-related gene signatures upon treatment with CDK4/6i ± antiestrogen compared to cells with non-mutant ESR1. MCF7 xenografts harboring ESR1 Y537S and D538G mutations established in nude mice were resistant to palbociclib. Conclusions: We report herein real-world and preclinical evidence that ESR1 mutations, particularly Y537S and D538G, can drive resistance to CDK4/6 inhibitors.

overall_design: To investigate the effects of ESR1 Y537S and D538G mutations on sensitivity to CDK4/6 inhibitors, we treated MCF7 cells harboring ESR1 wild-type, Y537S, or D538G mutations with palbociclib alone or in combination with estrogen-deprived media or fulvestrant.

first: Lin

last: Chang-Ching

first: Guo

last: Lei


title: Integrated multi-modal analysis reveals tumor and immune characteristics that distinguish Epstein-Barr virus-positive and -negative B cell post-transplant lymphoproliferative disorders [Affymetrix]

overall_design: Microarrays were used to elucidate the B cell intrinsic differences between B cells transformed with EBV and B cells transformed in the absence of EBV. Specifically, we profiled the transcriptome of five EBV(+) B cell lymphoma lines derived from patients with EBV(+) PTLD with morphology corresponding to diffuse large B cell lymphoma (DLBCL) (AB5, JB7, JC62, MF4, VB5), and two EBV(-) DLBCL cell lines (Pfeiffer, Toledo).


title: Cell therapy with human IL-10-producing ILC2s limits xenogeneic Graft-versus-Host Disease by inhibiting pathogenic T cell responses

city: Toronto

first: Sarah

last: Crome

state: ON

address: 101 College Street

country: Canada

institute: University Health Network

summary: IL-10-producing group 2 innate lymphoid cells (ILC210) have important functions in regulating immune responses, yet their therapeutic potential remains largely unexplored. Here, we demonstrate that cell therapy with  human ILC210 inhibits pathogenic T cell responses in humanized mouse models of Graft-versus-Host Disease (GVHD). Both prophylactic or post-onset adoptive transfer of human ILC210 significantly reduced GVHD severity and improved survival in NOD-scid IL2Rγnull (NSG) mice. Notably, ILC210 provided comparable protection to regulatory T cells (Tregs) without impairing T cell engraftment, instead decreasing intestinal T cell infiltration and suppressing CD4+Th1 and CD8+Tc1.  Additionally, ILC210 conferred superior protection from GVHD than conventional IL-10-/lowILC2s, and blocking IL-10 and IL-4 abrogated the protective effects of ILC210 cell therapy. In GVHD-protected HSCT recipients, ILC2s with an ILC210 phenotype were present at normal levels and inversely correlated with Th1 cells, consistent with findings in humanized mouse models. Critically, ILC210 did not impair T cell-mediated graft-versus-leukemia effects in a humanized model. CITE-seq analysis identified CD49d and CD86 as novel markers that allow for enrichment of ILC210 from conventional ILC2s, and to track ILC210 in patient studies. These results establish a platform for >2000-fold expansion of human ILC210 with a stable phenotype and underscore ILC210 potential in cell therapies for GVHD and other immune-mediated diseases.

overall_design:
ILC2s, ILC3, CD56bright and CD56dim NK cells were all stained and FACS sorted from a healthy donor. Cells were expanded for 28 days in distinct growth media for each cell type. Cells were stained with TotalSeqC antibodies including hashtags and then analyzed using CITE-seq. Stained ILC2s were mixed 1:1 with CD56dim NK cells and ILC3s mixed 1:1 with CD56dim NK cells. Each mixed sample was run on separate lanes and identified using hashtag antibodies. ILC2s and CD56dim NK cells were stained with Hashtag1, CD56bright NK cells with Hashtag2 and ILC3s with Hashtag3.

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Kyle

middle: T

last: Reid

middle: Q


title: Protective mechanisms of Qingda granule in hypertensive kidney injury: Focus on ERK/RSK1-mediated mitochondrial protection

first: Daxin

address: Qiuyang Rd, MinhouShangjie, Fuzhou, Fujian 350122, China.

institute: fujian univerity of TCM

summary: The objective of this study was to compare blank control mice (WT) with AngII-induced hypertensive mice (M).  Angii-induced hypertensive mice (M) and QDG intervention group (QDG);    Different genes expressed in renal tissue and identify new targets for reversing hypertension-induced renal damage.

overall_design: RNA sequencing was performed on the renal tissues of WT, Model and QDG groups (n = 3 in each group) at 6 weeks of age to identify different expression genes and related pathways.

first: Shan

first: Meiling

last: Wang

first: Enqi

last: Su

last: Yao

first: Qihang

last: Ding

first: Jiankang

last: Zhang

first: Peizhi

last: Jia

first: Dawei

last: Lian

first: Ling

first: Qiaoyan

last: Cai

first: Chunyu

last: Zhao

first: Yaoyao

last: Xu

first: Jianfeng

last: Chu

first: Jun

last: Peng


title: Comparative characterization of human accelerated regions in neurons [PIPseq]

city: SAN FRANCISCO

first: Yin

last: Shen

state: CALIFORNIA

address: 513 Parnassus Ave

institute: UCSF

summary: Human accelerated regions (HARs) are conserved genomic loci that have experienced rapid nucleotide substitutions following the divergence from chimpanzees. HARs are enriched in candidate regulatory regions near neurodevelopmental genes, suggesting their roles in gene regulation. However, their target genes and functional contributions to human brain development remain largely uncharacterized. Here, we elucidate the cis-regulatory functions of HARs in human and chimpanzee induced pluripotent stem cell (iPSC)-induced excitatory neurons. Using genomic and chromatin looping information, we prioritized 20 HARs and their chimpanzee orthologs for functional characterization via single-cell CRISPRi, and demonstrated their species-specific gene regulatory functions. Our findings reveal diverse functional outcomes of HAR-mediated cis-regulation in human neurons, including attenuated NPAS3 expression by altering the binding affinities of multiple transcription factors in HAR202 and maintaining iPSC pluripotency and neuronal differentiation capacities through the upregulation of PUM2 by 2xHAR.319. Finally, we use prime editing to demonstrate differential enhancer activity caused by several HAR26;2xHAR.178 variants. In particular, we link one variant in HAR26;2xHAR.178 to elevated SOCS2 expression and increased neurite outgrowth in human neurons. Thus, our study sheds new light on the endogenous gene regulatory functions of HARs and their potential contribution to human brain evolution.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: Single cell RNA-seq data for 2-week excitatory neurons derived from human and chimpanzee iPSCs.

first: Xiekui

last: Cui

first: Han

last: Yang


title: Human Hypertrophic Cardiomyopathy mRNA Profiling.

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

summary: Cardiac biopsies were obtained from hypertrophic cardiomyopathy (HCM) patients and controls and subjected to mRNA profiling.

overall_design: A total of 23 controls and 97 HCM cases were studied.

first: Michael

last: Ackerman

first: Ramin

last: Garmany


title: DICER is downregulated in mouse adipose tissue during high-fat diet feeding

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: The adipose tissue plays an important role in controlling whole-body energy balance, and proper regulation of adipose tissue function is essential for metabolic health. In response to energy surplus, the adipose tissue needs to expand, which may lead to local areas of hypoxia within the tissue. This is thought to promote whole-body insulin resistance. Here we report that DICER, a key enzyme in the maturation of miRNAs and a potential marker of adipocyte health, is profoundly downregulated in mouse adipose tissue within the first week of high-fat diet (HFD) feeding, and this effect is sustained in response to long-term HFD feeding. The downregulation of DICER protein occurs in both mature adipocytes and in the stromal vascular cells. Mechanistically, we provide evidence that hypoxia and hypoxia-inducible factor 1-α (HIF1α) facilitate ubiquitination of DICER to target it for autophagy-mediated degradation, and we show that DICER and HIF1α interact in adipose tissue after HFD feeding, which may signal for DICER degradation. Finally, despite reductions in DICER protein, we were not able to detect any differences in global miRNA levels in subcutaneous adipose tissue of mice after one or three weeks of HFD-feeding. In conclusion, the nutritional challenge of HFD feeding in mice leads to a large reduction in adipose tissue DICER protein, which is induced by hypoxia during tissue expansion and mediated through an interaction with HIF1α.

overall_design: miRNA sequencing of subcutaneous adipose tissue from mice having been on either a control diet or a high-fat diet for 1 day, 1 week or 3 weeks.

first: Søren

last: Madsen

first: A

last: Peluso

first: Morten

last: Dall

first: Patricia

last: Petersen

first: Kaja

last: Plucinska

first: Marta

last: Pradas-Juni

first: Jan-Wilhelm

last: Kornfeld

first: Brice

last: Emauelli

first: Sara

middle: G

last: Vienberg

first: Jonas

last: Treebak


title: Lipid-orchestrated paracrine circuit coordinates mast cell maturation through functional interaction with fibroblasts [fibroblast]

city: Tokyo

first: Yoshitaka

last: Taketomi

address: 7-3-1 Hongo, Bunkyo-ku,

department: CDBIM, Graduate School of Medicine,

country: Japan

institute: The University of Tokyo

summary: Interaction of mast cells (MCs) with fibroblasts is essential for MC maturation within tissue microenvironments, although the underlying mechanism is incompletely understood. Through a phenotypic screening of >30 mouse lines deficient in lipid-related genes, we found that deletion of the lysophosphatidic acid (LPA) receptor LPA1, like that of the phospholipase PLA2G3, the prostaglandin D2 (PGD2) synthase L-PGDS, or the PGD2 receptor DP1, impairs MC maturation and thereby anaphylaxis. Mechanistically, MC-secreted PLA2G3 acts on extracellular vesicles (EVs) to supply lysophospholipids, which are converted by fibroblast-derived autotaxin (ATX) to LPA. Fibroblast LPA1 then integrates multiple pathways required for MC maturation by facilitating integrin-mediated MC-fibroblast adhesion, IL-33-ST2 signaling, L-PGDS-driven PGD2 generation, and feedforward ATX-LPA1 amplification. Defective MC maturation resulting from PLA2G3 deficiency is restored by supplementation with LPA1 agonists or PLA2G3-modified EVs. Thus, the lipid-orchestrated paracrine circuit involving PLA2G3-driven lysophospholipid, eicosanoid, integrin, and cytokine signaling fine-tunes MC-fibroblast communication, ensuring MC maturation.

overall_design: Cells; Swiss 3T3 fibroblasts cocultured with or without bone marrow-derived mast cells; Fibroblast genotype, Lpar1+/+ and Lpar1-/-; Mast cell genotype, WT; Condiotion, coculture for 24 h; RNA, total RNA samples pooled from three samples

first: Yasumasa

last: Nishito

first: Makoto

last: Murakami


title: Microglia-RPE Cell Communication via the SPP1-ITGAV Axis Drives EMT and Retinal Degeneration in Dry AMD

city: shenzhen

first: bing

last: zeng

address: huaqiang road

institute: Shenzhen Aier Eye Hospital

summary: Age-related macular degeneration (AMD) is a leading cause of vision loss, with its dry form characterized by retinal pigment epithelium (RPE) degeneration and photoreceptor loss. However, the underlying mechanisms driving these pathological changes remain poorly understood. Here, we identify a critical role for microglia-RPE cell interactions mediated by the SPP1-ITGAV signaling axis in dry AMD pathogenesis.

overall_design: The experiment was set up with three groups of control cells and three groups of cells overexpressing CD51-ICD.


title: Lipid-orchestrated paracrine circuit coordinates mast cell maturation through functional interaction with fibroblasts [mast cell]

overall_design: Cells; bone marrow-derived mast cells cocultured with or without Swiss 3T3 fibroblasts; Mast cell genotype, Pla2g3+/+ and Pla2g3-/-, Fibroblast genotype, Lpar1+/+ and Lpar1-/-; Condition, coculture for 4 days; RNA, total RNA samples pooled from three samples


title: Histone H3K4ac, as a marker of active transcription start sites and enhancers, plays roles in histone eviction and RNA transcription

city: Busan

first: Jin

last: Kang

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

department: Department of Molecular Biology

institute: Pusan National University

summary: We propose that H3K4ac acts as marker of active TSSs and enhancers and plays roles in histone eviction and RNA transcription.

overall_design: H3K4ac, H3K4me1, H3K4me2, H3K4me3 and histone H3 ChIP-seq was performed in control, Δp300, and ΔMLL3/4 K562 cells.

first: AeRi

last: Kim


title: Comparative characterization of human accelerated regions in neurons [HyPR-seq]

first: Yin

last: Shen

overall_design: Characterization of the function of HARs in 2-week-old excitatory neurons derived from human and chimpanzee iPSCs.

first: Xiekui

last: Cui

first: Charles

last: Cai

first: Ian

last: Jones


title: Comparative characterization of human accelerated regions in neurons [PLAC-Seq]

summary: Human accelerated regions (HARs) are conserved genomic loci that have experienced rapid nucleotide substitutions following the divergence from chimpanzees1,2. HARs are enriched in candidate regulatory regions near neurodevelopmental genes, suggesting their roles in gene regulation3. However, their target genes and functional contributions to human brain development remain largely uncharacterized. Here, we elucidate the cis-regulatory functions of HARs in human and chimpanzee induced pluripotent stem cell (iPSC)-induced excitatory neurons. Using genomic4 and chromatin looping information, we prioritized 20 HARs and their chimpanzee orthologs for functional characterization via single-cell CRISPRi, and demonstrated their species-specific gene regulatory functions. Our findings reveal diverse functional outcomes of HAR-mediated cis-regulation in human neurons, including attenuated NPAS3 expression by altering the binding affinities of multiple transcription factors in HAR202 and maintaining iPSC pluripotency and neuronal differentiation capacities through the upregulation of PUM2 by 2xHAR.319. Finally, we use prime editing to demonstrate differential enhancer activity caused by several HAR26;2xHAR.178 variants. In particular, we link one variant in HAR26;2xHAR.178 to elevated SOCS2 expression and increased neurite outgrowth in human neurons. Thus, our study sheds new light on the endogenous gene regulatory functions of HARs and their potential contribution to human brain evolution.

overall_design: Comparative genome interactions for 2-week excitatory neurons derived from human and chimpanzee iPSCs.

first: Han

last: Yang


title: Comparative characterization of human accelerated regions in neurons [ATAC-seq]

overall_design: Comparative chromatin accessibility for 2-week excitatory neurons derived from human and chimpanzee iPSCs.


title: Comparative characterization of human accelerated regions in neurons [RNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 2-week excitatory neurons derived from human and chimpanzee iPSCs.


title: Targeted partial reprogramming of age-associated cell states improves markers of health in mouse models of aging

city: San Diego

first: sanjeeb

middle: k

last: sahu

address: Lajolla

institute: AltosLabs

summary: The study aims to explore the effects of CDKN2A-OSK expression across various tissues and human primary cells using next-generation sequencing. Mouse tissues and human cultured cells were collected at specific time points, followed by RNA extraction and next-generation sequencing. The sequencing data for mouse RNA were aligned to the mm9 genome, while the human RNA data were aligned to the Hg38 genome using standard RNA alignment and analysis protocols.

overall_design: LAKI mice were transduced with AAV carrying Cdkn2a-OSK (also referred as p16-OSK) on day 60, and tissues were harvested on day 135 for downstream RNA processing. IMR90 cells were serially passaged to different culture ages, representing various stages of senescence. IMR90 cells undergoing stress-induced aging were generated by treatment with various stressors, including DNA-damaging agents like etoposide and bleomycin, and oncogenic RAS. AAV-DJ was added at the specified culture ages, with media replenished every other day. Cells were analyzed 12 days post-AAV treatment. Day 20 cells represent healthy cells, day 125 cells represent late senescence, and days 50 and 85 represent intermediate stages.

first: Sanjeeb

last: Sahu

first: Pradeep

last: Reddy

first: Jinlong

last: Lu

first: Juan Carlos

middle: I

last: Belmonte


title: Loss of self-tolerance leads to altered gene expression and IMD pathway activation in Drosophila melanogaster

city: Normal

first: Nathan

last: Mortimer

state: IL

address: Campus Box 4120

department: School of Biological Sciences

institute: Illinois State University

summary: Immune self-tolerance is the ability of a host’s immune system to recognize and avoid triggering immune responses against self-tissue. This allows the host to avoid self-directed immune damage, while still responding appropriately to pathogen infection. A breakdown of self-tolerance can lead to an autoimmune state in which immune cells target healthy self-tissue, leading to inflammation and tissue damage. In order to better understand the basic biology of autoimmunity and the role of the innate immune system in maintaining self-tolerance, we have recently characterized the Drosophila melanogaster tuSz autoimmune mutant. This mutant strain can serve as a model of innate immune mediated self-tolerance, and here we identify transcripts that are deregulated in flies experiencing a loss of self-tolerance. We found that these changes include the ectopic activation of pro-inflammatory signaling through the Relish/NFκB transcription factor, alterations in transcripts encoding proteins predicted to mediate organismal metabolism, and a downregulation of transcripts linked to developmental processes. This study can provide insight into the transcriptional and physiological changes underlying self-tolerance and autoimmunity.

overall_design: Differential gene expression in whole Drosophila melanogaster larvae from three genotypes, with 3 replicates per genotype

first: Pooja

last: Kr


title: Single cell sequencing of sheep testis

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: We report the side-effects of ZEA on the testis,

overall_design: Single cell sequencing revealed ZEA damage to testis

first: Shen

last: Li

first: Lingjiang

last: Min


title: Gene expression profile at single cell level of gingiva and alveolar bone tissues of canines with peri-implantitis and healthy conditions

status: Public on Nov 11 2024

city: Guangzhou

first: Ming

last: Wang

summary: Peri-implantitis is a common complication characterized by chronic inflammation of the periodontal tissue. This disease is marked by irreversible and progressive degradation of the gingiva and alveolar bone, ultimately leading to tooth loss.Most current research has focused on the entire periodontal tissue, which restricts a comprehensive understanding of the heterogeneity between gingiva and bone tissues, and hinders the development of targeted host therapies for peri-implantitis. To uncover the pathogenic mechanisms of peri-implantitis, our study employed a tissue-specific approach to investigate the interactions between stromal and immune cells in gingiva and bone tissues separately, using single-cell sequencing techniques. This strategy aims to develop the insights of the pathogenesis of peri-implantitis, providing a scientific basis for the treatment of peri-implantitis.

overall_design: The bilateral mandibular second, third and fourth premolars of one Beagle dog were extracted simultaneously for the further implant. The left mandibular teeth were used for the conduction of peri-implantitis model, while the right teeth were used for the healthy control. Gingva and bones tissues were obtianed for single-cell sequencing after an 8-week observation.

first: Ningbo

last: Geng

first: Yixin

last: Xia


title: Genetic Basis, Quantitative Nature, and Functional Relevance of Evolutionarily Conserved DNA Methylation [CareGiver cohort]

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

summary: DNA methylation (DNAm) is a key epigenetic mark that modulates regulatory elements and gene expression, playing a crucial role in mammalian development and physiological function. Despite extensive characterization of DNAm profiles across species, little is known about its evolutionary conservation. Here, we conducted a comparative epigenome-wide analysis of great apes to identify and characterize sequence- and methylation-conserved CpGs (MCCs). Using 202 DNAm arrays, alongside 6 matched genotype and 13 matched transcriptomic datasets, we identified 11,500 MCCs for which methylation was evolutionarily related to sequences of CpGs and methylation quantitative trait loci. MCCs were the most stable across healthy human tissues and exhibited weaker genetic associations than other CpGs. Moreover, MCCs showed minimal associations with demographic, environmental factors, and noncancer diseases, yet demonstrated stronger associations with certain cancers than other CpGs, particularly gastrointestinal cancers. Functional enrichment analysis revealed that genes associated with MCC methylation in cancer were enriched for cancer driver genes and canonical cancer pathways, highlighting a significant regulatory role for MCCs in tumorigenesis. Collectively, our findings reveal the extent of DNAm conservation in great ape evolution, its association with genetic conservation, and its relevance to human diseases. These integrative analyses offer evolutionary insights into epigenetic variation and its functional implications in human populations.

overall_design: 88 healthy participants from CareGiver cohort were used

first: Gregory

middle: E

last: Miller


title: Spatially organized inflammatory myeloid-CD8+ T cell aggregates linked to Merkel-cell Polyomavirus driven Reorganization of the Tumor Microenvironment

first: Magdalena

last: Matusiak

address: 300 Pasteur Dr

department: Pathology

summary: Merkel cell carcinoma (MCC) is an aggressive skin cancer with high propensity for metastasis, caused by Merkel cell polyomavirus (MCPyV), or chronic UV-light-exposure. How MCPyV modulates immune responses within the tumor microenvironment and how such are linked to patient outcomes remain unknown partly due to technical barriers to understanding the spatial organization of the tumor microenvironment at single-cell resolution. We interrogated the cellular and transcriptional landscapes of 60 MCC-patients using Co-detection-by-indexing (CODEX) and targeted bulk RNA sequencing. Notably, we identified an enrichment of dysfunctional T cells spatially associating with CXCL9+ myeloid cells at the tumor invasive front as key feature of virus-positive MCC. While MCPyV-positivity and CD8+ T cell infiltration correlated with metastasis-free-survival, responses to immune checkpoint blockade were high regardless of virus-status. Instead, we found an enrichment of central memory T cells within tertiary-lymphoid-structures that associated with response to immune-checkpoint blockade. These findings highlight fundamental differences in the organization of the native tumor microenvironment of virus-positive MCC, that are linked to differential survival outcomes and could be used for personalized treatment strategies.

overall_design: We laser capture microdissected circular tissue regions of 0.5 mm in diameter of FFPE merkel cell carcinoma samples and performed sequencing

first: Maximilian

last: Haist

first: Sujey

last: Vennam

first: ChunFang

last: Zhu


title: Transcriptome analysis of ear cartilage lipochondrocytes at multiple stages of differentiation.

first: Maksim

last: Plikus

summary: RNA-seq data was obtained from mouse ear cartilage lipochondrocytes at varying postnatal stages. The transcriptome of each stage was analyzed and compared against other stages, creating a "timeline" of cellular events. Adult transcriptome data was analyzed and compared against adult white adipose tissue adipocyte transcriptome.

overall_design: Transcriptome profiling of mouse ear cartilage lipochondrocytes at five postnatal stages. Samples were compared against each other or to inguinal adipocyte controls. Three replicates per sample.

first: Raul

last: Ramos

first: Tao

last: Peng


title: Genetic Basis, Quantitative Nature, and Functional Relevance of Evolutionarily Conserved DNA Methylation [EVOIMMUNOPOP project]

overall_design: 171 individuals living in Belgium, from the EVOIMMUNOPOP project

first: Lluis

last: Quintana-Murci

first: Etienne

last: Patin


title: Differential KEAP1/NRF2-mediated signaling widens the therapeutic window of redox-targeting drugs in SCLC therapy [array]

city: Heidelberg

first: Nikolas

last: Gunkel

state: *Not Applicable

address: Im Neuenheimer Feld 280

department: Research Group Cancer Drug Development

institute: German Cancer Research Center (DKFZ)

summary: Small cell lung cancer (SCLC) patients experience rapid disease progression despite frequently achieving a complete response to first-line therapy. Maintenance treatments, aiming at controlling residual tumor cells, generally fail due to cross-resistance, inability to target tumor vulnerabilities, or dose-limiting side effects.  Here, we show that SCLC cells, like their cell-of-origin, pulmonary neuroendocrine cells (PNECs), exhibit notably low activity in pathways protecting against reactive oxygen species (ROS). When exposed to a novel thioredoxin reductase 1 (TXNRD1) inhibitor, these cells quickly exhaust their ROS-scavenging capacity, independent of their molecular subtype and the resistance status against first-line therapy. Importantly, SCLC cells, in contrast to non-cancerous cells, cannot adapt to drug-induced ROS stress because they repress ROS defense enzymes through multiple layers of epigenetic and transcriptional mechanisms. By exploiting this differential ability to manage oxidative stress, we demonstrate that the therapeutic dose of TXNRD1 inhibitors can be safely increased in vivo through pharmacological activation of the NRF2 stress response pathway using Bardoxolon-Methyl (CDDO-Me), leading to improved tumor control without added toxicity to healthy tissues.  These findings underscore the therapeutic potential of TXNRD1 inhibitors in cancers like SCLC, which are marked by reduced ROS-scavenging capacity and strong suppression of adaptive resistance mechanisms.

overall_design: To investigate the effect of the NRF2 inducer CDDO-me on small cell lung cancer (SCLC) and healthy tissue, we treated cell lines representing SCLC (HCI-H69, HCI-H82, HCI-H526) and normal tissues (Beas-2b, HaCaT) with CDDO-me or vehicle (DMSO), extracted RNA and perfomed expression profiling on biological triplicates.

first: Johanna

last: Hummel-Eisenbeis

first: Jana

last: Samarin


title: ADAR1 Deficiency Relies upon NOCT to Activate Endothelial Innate Immunity and Apoptosis.

city: Pittsburgh

first: Shu-Ting

last: Cho

state: PA

address: 450 Technology Drive

department: Computational and Systems Biology

institute: University of Pittsburgh

summary: NOCT contributes to endothelial pathophenotypes driven by ADAR1 deficiency.

overall_design: Gene expression profile on ADAR1 or combined ADAR1 and NOCT deficient human PAECs

first: Chen-Shan

last: Woodcock


title: Differential KEAP1/NRF2-mediated signaling widens the therapeutic window of redox-targeting drugs in SCLC therapy

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

overall_design: Refer to individual Series


title: Metastasis of colon cancer requires Dickkopf-2 to generate cancer cells with Paneth cell properties

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

institute: Seoul National University

summary: Metastasis is the leading cause of cancer-related mortality. Paneth cells provide stem cell niche factors in the homeostatic condition, but the underlying mechanisms of cancer stem cell niche development are unclear. Here we report that Dickkopf-2 (DKK2) is essential for Paneth-like cell generation during the metastasis of colon cancer. Splenic injection of DKK2-knockout (KO) cancer organoids into C57BL/6 mice resulted in a significant reduction of liver metastases compared to the control cancer organoids in spite of the presence of carcinogenic mutations in Apc, Kras and Tp53 genes. RNA-seq analysis of DKK2 KO organoids showed reduction of Paneth cell marker genes such as Lysozymes and Defensins. Ingenuity pathway analysis (IPA) of the RNA-seq data and assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) suggested HNF4A as a downstream target of DKK2. Chromatin immunoprecipitation followed by sequencing (Chip-seq) analysis showed that HNF4A binds to the open chromatin regions of Sox9, a well-known transcription factor for Paneth cell differentiation. Reduction of Paneth-like cells in the absence of DKK2 has been confirmed in the murine metastatic model of colon cancer using flow cytometry, immunohistochemistry and single cell RNA-seq. These data suggest the necessity of DKK2 in Paneth-like cell generation. Thus, DKK2 contributes to stem cell niche development during the metastatic progression of colon cancer.

overall_design: Dickkopf-2 knockout colon cancer organoids carrying mutations in Apc, Kras and Tp53 genes were applied for ChIP-sequencing using recombinant Anti-HNF4-alpha antibody, ChIP Grade (ab181604) and rabbit IgG isotype antibody.

first: Jae Hun

last: Shin

first: Alfred

last: Bothwell


title: DNA aptamers that modulate biological activity of model neurons

first: Brandon

last: Wilbanks

state: Minnesota

address: 222 3rd Ave SW

summary: There is an urgent need for agents that promote health and regeneration of cells and tissues, specifically to treat diseases of the aging nervous system. Age-associated nervous system degeneration and various diseases are driven by many different biochemical stresses, often making it difficult to target any one disease cause. Our laboratory has previously identified DNA aptamers with apparent regenerative properties in murine models of multiple sclerosis by selecting aptamers that bind oligodendrocyte membrane preparations. Here, we selected from vast libraries of molecules (~1014 unique DNAs) those with the ability to bind cultured human SH-SY5Y neuroblastoma cells as a neuronal model, followed by screening for aptamers capable of eliciting biological responses, with validation of binding in differentiated SH-SY5Y, human iPSC-derived sensory neurons, and hESC derived cortical neurons. This demonstrates a proof-of-concept workflow to identify biologically active aptamers by cycles of cell selection.

overall_design: RNA seq profiling of apatmer-treated SHSY5Y cells

first: Wilbanks

last: Brandon


title: Mechanism of OGT-mediated FASN glycosylation regulating JNK/ICAM1 pathway in Liver cancer stem cell metastasis

first: changgui

last: zhong

address: Guangzhou University Town, Panyu District, Guangzhou

institute: South China University of Technology

summary: We performed transcriptome sequencing analysis on LCSCs with different metastatic abilities. KEGG enrichment showed that genes upregulated during LCSC3 metastasis were related to cell membrane pathways. qPCR and flow cytometry confirmed that FASN expression was significantly upregulated during LCSCs metastasis. ICAM1 affects EMT, invadopodia formation, migration and invasion ability of LCSCs. ICAM1 plays a key role in the process of liver metastasis and the development of hepatocellular carcinoma in mice. FASN is also highly expressed during LCSC metastasis. Silencing FASN reduces the expression level of stemness genes, migration and invasion ability, and self-renewal ability of LCSCs. GSEA analysis indicated that transcriptome sequencing results after FASN knockdown were mainly enriched in the EMT process. FASN affects the expression of ICAM1 through the JNK/c-Jun axis in the MAPK pathway, and OGT is involved in the glycosylation process of ICAM1 regulating FASN, thereby affecting the migration ability of LCSCs.

overall_design: Liver cancer stem cells were isolated from clinical tissues and stably subcultured in mouse embryonic fibroblasts. After 2-5 generations, the liver cancer stem cells were knocked down with siFASN for 48 hours and then collected 48 hours after the treatment.

first: Changgui

last: Zhong


title: Transcriptional reprogramming primes CD8+ T cells towards exhaustion in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome [ATAC-seq]

city: Ithaca

first: David

last: Iu

state: NY

address: 427 Biotechnology Building

department: Molecular Biology and Genetics

institute: Cornell University

summary: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME) is a severe, debilitating disease, with mounting evidence pointing to immune dysregulation as a key contributor to pathophysiology. To characterize the gene regulatory state underlying dysregulation of T cells in ME, we performed multiomic analysis of distinct subsets by integrating single-cell RNA-seq, RNA-seq and ATAC-seq, and further analyzed CD8+ T cell subpopulations following symptom provocation. Certain subsets of CD8+ T cells, as well as certain innate lineages of T cells, displayed the most pronounced dysregulation in ME. We observed upregulation of key transcription factors associated with T cell exhaustion in CD8+ T cell effector memory subsets, as well as an altered chromatin landscape and metabolic reprogramming consistent with an exhausted immune cell state. To validate these observations, we analyzed expression of exhaustion markers using flow cytometry, detecting a higher frequency of exhaustion-associated transcription factors, and supporting a novel state of immune dysregulation in ME, which may ultimately provide a basis for future therapies.

overall_design: RNA-seq and ATAC-seq were performed on FACS purified naive (CD45RA+CCR7+) and antigen-experienced (CD45RA-CCR7+/-) CD8+ T cells from 7 ME patients and 7 healthy sedentary controls.

first: Jessica

last: Maya

first: Luyen

last: Vu

first: Elizabeth

last: Fogarty

first: Adrian

middle: J

last: McNairn

first: Faraz

last: Ahmed

first: Paul

last: Munn

first: Jennifer

last: Grenier

first: Maureen

last: Hanson

first: Andrew

last: Grimson


title: Mechanism of OGT-mediated FASN glycosylation regulating JNK/ICAM1 pathway in Liver cancer stem cell metastasis [Transwell]

state: Guangdong

summary: We performed transcriptome sequencing analysis on LCSCs with different metastatic abilities.  KEGG enrichment showed that genes upregulated during LCSC3 metastasis were related to cell membrane pathways. qPCR and flow cytometry confirmed that FASN expression was significantly upregulated during LCSCs metastasis. ICAM1 affects EMT, invadopodia formation, migration and invasion ability of LCSCs. ICAM1 plays a key role in the process of liver metastasis and the development of hepatocellular carcinoma in mice. FASN is also highly expressed during LCSC metastasis. Silencing FASN reduces the expression level of stemness genes, migration and invasion ability, and self-renewal ability of LCSCs. GSEA analysis indicated that transcriptome sequencing results after FASN knockdown were mainly enriched in the EMT process. FASN affects the expression of ICAM1 through the JNK/c-Jun axis in the MAPK pathway, and OGT is involved in the glycosylation process of ICAM1 regulating FASN, thereby affecting the migration ability of LCSCs.

overall_design: Liver cancer stem cells were seeded on Transwell, and 48 hours after seeding, the cells in the upper and lower chambers were collected for transcriptome sequencing.


title: Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors

first: Timothy

last: Hughes

state: Ontario

address: 160 College Street, Room 1350

department: Terrence Donnelly Centre for Cellular and Biomolecular Research

institute: University of Toronto

summary: We describe an effort (“Codebook”) to determine the sequence specificity of 332 putative and largely uncharacterized human transcription factors (TFs), as well as 61 control TFs. Nearly 5,000 independent experiments, including in vitro and in vivo assays, produced motifs for most of the uncharacterized TFs analyzed (180, or 53%), the vast majority of which are unique to a single TF. The data highlight the extensive contribution of transposable elements to TF evolution, both in cis and trans, and identify tens of thousands of conserved, base-level binding sites in the human genome. The use of multiple platforms provides an unprecedented opportunity to benchmark and analyze TF sequence specificity, function, and evolution, as further explored in accompanying manuscripts. Over 1,421 human TFs are now associated with a DNA binding motif. Extrapolation from the Codebook benchmarking suggests that many of the binding motifs for well-studied TFs may inaccurately describe the TF’s true sequence preferences.

overall_design: Protein binding microarray (PBM) experiments were performed for 173 diverse human DNA-binding proteins (462 experiments). Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006.

first: Arttu

last: Jolma

first: Kaitlin

middle: U

last: Laverty

first: Ali

last: Fathi

first: Ally

middle: W

last: Yang

first: Isaac

last: Yellan

first: Ilya

last: Vorontsov

first: Sachi

last: Inukai

first: Judith

last: Kribelbauer

first: Antoni

last: Gralak

first: Rozita

last: Razavi

first: Mihai

last: Albu

first: Alexander

last: Brechalov

first: Zain

last: Patel

first: Vladimir

last: Nozdrin

first: Georgy

last: Meshcheryakov

first: Ivan

last: Kozin

first: Sergey

last: Abramov

last: Boytsov

first: Oriol

last: Fornes

first: Vsevolod

last: Makeev

first: Jan

last: Grau

first: Ivo

last: Grosse

first: Philipp

last: Bucher

first: Bart

last: Deplancke

last: Kulakovskiy


title: Differential contributions of fetal mononuclear phagocytes to Zika neuroinvasion versus neuroprotection during congenital infection

city: Singapore

first: Ashley

last: St John

address: 8 College Rd

country: Singapore

institute: Duke-NUS

summary: Fetal microglia had a protective role once differentiated in the brain, as their absence increased infection burden and neuronal death. Conversely, monocyte depletion reduced non-productive neuroinflammation. We used Single-cell RNA sequencing (scRNA-seq) to identify transcriptional profiles linked to the protective versus detrimental contributions of mononuclear phagocyte subsets during ZIKV infection in the fetal brain.

overall_design: To investigate the role of mononuclear phagocytes during ZIKV infection in the fetal brain in a pregnant mouse model.

middle: L

last: St. John

first: Florent

last: Ginhoux

first: Zhong

last: Chengwei

first: Tatsuya

last: Kozaki

first: Jinmiao

last: Chen

first: Wilfried

middle: A

last: Saron


title: Cytosolic N6AMT1-dependent translation supports mitochondrial RNA processing [RNA-Seq]

city: Epalinges

first: Alexis

last: Jourdain

address: Boveresses 155, CP51

department: Immunobiology

country: Switzerland

institute: University of Lausanne

summary: Mitochondrial biogenesis relies on both the nuclear and mitochondrial genomes, and imbalance in their expression can lead to inborn errors of metabolism, inflammation, and aging. Here, we investigate N6AMT1, a nucleo-cytosolic methyltransferase that exhibits genetic codependency with mitochondria. We determine transcriptional and translational profiles of N6AMT1 and report that it is required for the cytosolic translation of TRMT10C (MRPP1) and PRORP (MRPP3), two subunits of the mitochondrial RNAse P enzyme. In the absence of N6AMT1, or when its catalytic activity is abolished, RNA processing within mitochondria is impaired, leading to the accumulation of unprocessed and double-stranded RNA, thus preventing mitochondrial protein synthesis and oxidative phosphorylation, and leading to an immune response. Our work sheds light on the function of N6AMT1 in protein synthesis and highlights a cytosolic program required for proper mitochondrial biogenesis.

overall_design: Established N6AMT1-depleted and control human chronic myelogenous K562 cell lines using lentiviral transduction of CRISPR/Cas9 sgRNA.

first: Mads

middle: M

last: Foged

first: Emeline

last: Recazens

first: Sylvain

last: Chollet

first: Miriam

last: Lisci

first: George

last: Allen

first: Boris

last: Zinshteyn

first: Doha

last: Boutguetait

first: Christian

last: Münch

first: Vamsi

middle: K

last: Mootha


title: Comparative Effects of Arecoline, Caffeine, and Nicotine on Transcription Level in the NAc of Mice

city: Haikou

first: Feifan

last: Zhou

address: 58 Renmin Avenue

institute: Hainan University

summary: Though widely consumed, current research on the neural mechanisms of arecoline, caffeine, and nicotine remains limited, and the similarities and differences of these three substances on the nervous system are still not clear. This study used RNA-seq to analyze the gene expression in the nucleus accumbens (NAc) of mice, and further compared the behavioral changes through open field and conditioned place preference (CPP), exploring the effects of different psychoactive substances at the transcriptional and behavioral levels. Gene Ontology enrichment analysis revealed that nicotine and caffeine significantly alter biological processes related to synaptic function, and KEGG pathway analysis showed that  the differentially expressed genes in the nicotine-treated group were significantly more enriched in pathways related to substance dependence compared to the other two treatment groups, with arecoline showing the least enrichment. Furthermore, only acute caffeine treatment significantly increased mouse activity, and only nicotine induced CPP. These results provided a scientific basis for evaluating the effects of arecoline, caffeine, and nicotine on the nervous system.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for nucleus accumbens (NAc) of C57BL/6 male mice receiving 4-day exposure to saline, arecoline,caffeine and nicotine.

first: Shaofang

last: Huang

first: Xinran

last: Wang


title: Transcriptional reprogramming primes CD8+ T cells towards exhaustion in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome [RNA-seq]

first: David

middle: S

last: Iu

first: Jessica

last: Maya

first: Luyen

last: Vu

first: Elizabeth

last: Fogarty

first: Adrian

last: McNairn

first: Faraz

last: Ahmed

first: Paul

middle: R

last: Munn

first: Jennifer

last: Grenier

first: Maureen

last: Hanson

first: Andrew

last: Grimson


title: Cytosolic N6AMT1-dependent translation supports mitochondrial RNA processing [Ribo-seq]

first: Alexis

last: Jourdain

first: Mads

last: Foged

first: Emeline

last: Recazens

first: Sylvain

last: Chollet

first: Miriam

last: Lisci

first: George

last: Allen

first: Boris

last: Zinshteyn


title: Differential KEAP1/NRF2-mediated signaling widens the therapeutic window of redox-targeting drugs in SCLC therapy [seq]

first: Nikolas

last: Gunkel

summary: Small cell lung cancer (SCLC) patients experience rapid disease progression despite frequently achieving a complete response to first-line therapy. Maintenance treatments, aiming at controlling residual tumor cells, generally fail due to cross-resistance, inability to target tumor vulnerabilities, or dose-limiting side effects. Here, we show that SCLC cells, like their cell-of-origin, pulmonary neuroendocrine cells (PNECs), exhibit notably low activity in pathways protecting against reactive oxygen species (ROS). When exposed to a novel thioredoxin reductase 1 (TXNRD1) inhibitor, these cells quickly exhaust their ROS-scavenging capacity, independent of their molecular subtype and the resistance status against first-line therapy. Importantly, SCLC cells, in contrast to non-cancerous cells, cannot adapt to drug-induced ROS stress because they repress ROS defense enzymes through multiple layers of epigenetic and transcriptional mechanisms. By exploiting this differential ability to manage oxidative stress, we demonstrate that the therapeutic dose of TXNRD1 inhibitors can be safely increased in vivo through pharmacological activation of the NRF2 stress response pathway using Bardoxolon-Methyl (CDDO-Me), leading to improved tumor control without added toxicity to healthy tissues. These findings underscore the therapeutic potential of TXNRD1 inhibitors in cancers like SCLC, which are marked by reduced ROS-scavenging capacity and strong suppression of adaptive resistance mechanisms.

overall_design: To investigate the effect of the NRF2 inducer CDDO-me on SCLC-derived tumors and healthy tissue, we generated a xenograft model by subcutaneous injection of human NCI-H526 cells into NSG mice. Tumor-bearing mice were injected intraperitoneally for 4 consecutive days with 3 mg/kg of CDDO-me or vehicle as a control (5 mice per group). Afterwards, we harvested the tumor, heart, kidney, liver, and lung tissues and performed RNA sequencing (RNAseq) and differential expression analysis on each tissue.

first: Hana

last: Nuskova

first: Hamed

last: Alborzinia


title: Liver in humanized-liver mice: Control vs 4,4'-Methylenebis(2-chlorobenzenamine) treatment

city: Osaka

first: Shugo

last: Suzuki

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

institute: Osaka Metropolitan University Graduate School of Medicine

summary: The gene expression profiling between Control and 4,4'-Methylenebis(2-chlorobenzenamine) exposure for 4 weeks in liver of F1-TKm30 female mice transplanted with commercially available human hepatocytes.

overall_design: Female 8-week-old NOG mice expressing HSVtk mutant clone 30 cDNA under the control of mouse transthyretin gene enhancer/promoter (F1-TKm30 mice) were transplanted with commercially available human hepatocytes. After 9 or 13 weeks (17- or 21-week-old), mice were treated with 0 or 0.05% 4,4'-Methylenebis(2-chlorobenzenamine) (MOCA)  for 4 weeks. After treatment, mice were sacrificed, and removed livers. Control and MOCA treatment: 4 control female mice, 5 MOCA-treated female mice, respectively.


title: Daphnia magna Single Cell Atlas

city: Boston

first: Kseniia

last: Petrova

address: 200 Longwood

department: System's biology

institute: HMS

summary: This is the first view of Daphnia single-cell transcriptomics-based cell atlas. Daphnia is a freshwater plankton crustacean which is both a classic and emerging new model for eco-physiology, toxicology, and evolutionary genomics. We were able to identify over 30 distinct cell types about half of which could be functionally annotated.

overall_design: Several Daphnia magna samples were prepared by cell dissociation and barcoding for single-cell transcriptomics using inDrops technology. The samples were prepared and indexed in a way that allowed male/female, young/old, and body/head comparisons.

first: Indira

last: Krishnan

first: Lev

last: Yamplosky

first: Leon

last: Peshkin

first: Kseniya


title: The Role of Fibroblasts in Diabetic Ulcer Healing and the Therapeutic Potential of Platelet-Rich Plasma (PRP): Insights from Single-Cell Sequencing and Animal Models

city: Zhongshan

first: Chenyan

last: Long

address: Sunwen East Road, Zhongshan City, Guangdong Province

institute: ZhongshanCity People’s Hospital

summary: Objective: This study aims to investigate the diversity of fibroblasts present in diabetic ulcers and their impact on the wound healing process, as well as to evaluate the effectiveness of Platelet-Rich Plasma (PRP) therapy in the management of diabetic ulcers. Methodology: The single-cell dataset GSE165816 from the GEO database was utilized to analyze DFU-healer and DFU-nonhealer samples in order to evaluate variations in fibroblasts. Functional characteristics of fibroblasts were investigated through analyses of cell communication, transcription factors, and pseudotime analysis. Additionally, a diabetic ulcer rat model was established to compare the therapeutic effects of PRP, followed by histological and transcriptomic sequencing analyses. Result: Single-cell sequencing analysis identified a greater abundance of fibroblasts in the group of diabetic foot ulcer (DFU) patients who exhibited healing. The findings from biological informatics analysis emphasized the critical role of fibroblasts in the wound healing process. Treatment with PRP notably enhanced wound healing in diabetic ulcers in rats, and transcriptomic analysis indicated that gene expression levels post-PRP treatment resembled those of the non-diabetic ulcer group, with a strong association to fibroblasts. Conclusion: Fibroblasts are essential in the process of healing diabetic ulcers, as certain transcription factors have the potential to facilitate wound closure. PRP therapy has been shown to enhance the healing process in diabetic ulcer rat models, possibly through the modulation of gene expression and the promotion of extracellular matrix arrangement. This research offers novel insights and potential therapeutic approaches for managing diabetic ulcers.

overall_design: The rats were categorized into three distinct groups for the experiment: the non-diabetic ulcer group (sham group), the diabetic ulcer group (control group), and the diabetic ulcer + PRP treatment group (PRP group). After successfully inducing diabetic ulcers in the rats, the PRP group received 0.5 ml of PRP injected into the wound site on days 1, 7, 14, and 21, while the other groups received an equal volume of saline injections.. Subsequently, the wounds were dressed with Vaseline gauze, clean dressings, and secured with adhesive tape.

first: Zhenghao

last: He

first: Ju

last: Tian


title: Liver in F1-TKm30 mice: Control vs 4,4'-Methylenebis(2-chlorobenzenamine) treatment

summary: The gene expression profling between Control and 4,4'-Methylenebis(2-chlorobenzenamine) exposure for 4 weeks in liver of F1-TKm30 female mice.

overall_design: Female 17- or 21-week-old NOG mice expressing HSVtk mutant clone 30 cDNA under the control of mouse transthyretin gene enhancer/promoter (F1-TKm30 mice) were treated with 0 or 0.05% 4,4'-Methylenebis(2-chlorobenzenamine) (MOCA) for 4 weeks. After treatment, mice were sacrificed, and removed livers. Control and MOCA treatment: 4 control female mice, 4 MOCA-treated female mice, respectively.


title: An in vivo repertoire of zebrafish cardiomyocyte-specific cis-regulatory elements [RNA-Seq]

city: Clayton

first: Hieu

middle: Tri

last: Nim

state: VIC

address: Monash University Clayton Campus, Wellington Rd

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

summary: cis-Regulatory elements (cREs) are essential for the spatio-temporal control of gene expression during development and disease. However, cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell-types, predominantly cardiomyocytes. Therefore, cardiomyocytes-specific modelling is required to understand the cis-regulation of the developing heart. Zebrafish are an ideal model to study heart development, as they share a number of physiological features with the human heart during development. Therefore, we present a comprehensive cardiomyocyte-specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling, providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes, validating these genomic regions as cardiac regulatory elements. We share this comprehensive, reproducible cardiomyocyte-specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects.

overall_design: Cardiomyocytes were isolated from the Tg(myl7::GFP) zebrafish transgenic line. Larvae were collected 72 hpf (hours post fertilization). GFP-positive (30,000 cells, n=3 biological replicates) and GFP-negative cells (500,000 cells, n=3 biological replicates) were collected, and RNA-sequencing was performed on these samples.

first: Marcus

last: Tondl

first: Gulrez

last: Chahal

first: Monika

last: Mohenska

middle: T

first: Mirana

last: Ramialison


title: An in vivo repertoire of zebrafish cardiomyocyte-specific cis-regulatory elements


title: High efficacy of combined MEK Inhibitor Trametinib and RTK Inhibitor Anlotinib Therapy in KRAS-Mutant Lung Cancer

city: Shanghai

first: Baohui

last: Han

address: 227 South Chongqing Road

department: Department of Respiratory and Critical Care Medicine

institute: Shanghai Chest Hospital

summary: Oncogenic KRAS mutations frequently detected in non-small cell lung cancer (NSCLC)1,2, have been considered undruggable until recent development of inhibitors, e.g., sortorasib, adagrasib or divarasib, specifically targeting KRASG12C 3-6. However, it still remains as a big challenge to target all the KRAS mutants besides KRASG12C 2,7,8. We here found that MEK inhibitor trametinib treatment results in the feedback activation of multiple receptor tyrosine kinases (RTKs) in NSCLC, and combined treatments with trametinib and anlotinib, a pan-RTK inhibitor, effectively inhibited KRAS-mutant lung cancer progression.

overall_design: KRAS-mutant NSCLC cells were treated with trametinib (10nM) for 2, 5, and 10 days in 6-well plates. 4 KRAS-mutant NSCLC cell lines (A549, Calu-1, H460 and H23) were used in trametinib adaptive resistance analysis. 3 samples for each timepoint were collected for sequencing and bioinformatic analysis. For the combinational analysis, A549 cells were treated with trametinib (10nM) or anlotinib (1μM) or combination treatments for 24 hours in 6-well plates. 3 samples for each treatment were collected for sequencing and bioinformatic analysis.

first: Yikai

last: Zhao

first: Xinlei

last: Cai


title: High-throughout sequencing of colorectal cancer and non-small cell lung cancer cells treated actived compound YHM18

city: wenzhou

first: sunhui

last: xing

address: Ouhai district Chashan Street higher education park

institute: wenzhou medical university

summary: The high-throughput sequencing technology was performed after the treatment of human colorectal cancer cells HCT116 and non-small cell lung cancer cells A549 with the active compound YHM18 designed and synthesized by ourselves, to explore the expression of genes related to cell proliferation, adhesion, migration and invasion of human colorectal cancer cells HCT116 and non-small cell lung cancer cells A549 after the treatment of the active compound and to find an interesting target gene, GTSE1.

overall_design: Human colorectal cancer cells HCT116 and non-small cell lung cancer cells A549 were treated with active compound YHM18 at the concentration of 2 µM for 48 hours.

first: Sunhui

last: Xing

first: Xiaohui

last: Zheng


title: Redox sensor KEAP1 promotes stemness and prevents reductive stress in exhausted CD8+ T cells via inhibiting NRF2

city: Dallas

first: Chen

last: Yao

state: Texas

address: 5901 FOREST PARK RD, NS6 218

institute: UT Southwestern Medical Center

summary: Persistent antigen stimulation exposes CD8+ T cells to various metabolic stresses and induces a dysfunctional state termed T-cell exhaustion. Exhausted CD8+ T cells are continuously replenished by a recently discovered self-renewing stem-like CD8+ T-cell subset, which maintains long-term immunity and provides proliferative burst in response to immunotherapies. Although the redox system plays an important role in regulating T-cell activation, how cellular redox affects the differentiation of stem-like and exhausted CD8+ T cells is incompletely understood. Here, we showed that both antigen stimulation and terminal differentiation reduced mitochondrial oxidation and reactive oxygen species (ROS) in exhausted CD8+ T cells, which displayed a chromatin state primed for regulation by the redox sensing KEAP1-NRF2 pathway. During chronic viral infection, KEAP1 promoted expansion of antiviral CD8+ T cells and facilitated their differentiation into the stem-like subset in a cell autonomous manner. In addition, KEAP1 was required for establishing proper transcriptional programs of stem-like and exhausted CD8+ T cells. Mechanistically, KEAP1 maintained oxidation by upregulating genes involved in mitochondrial oxidation and repressing NRF2-driven transcription of antioxidant pathways. Deleting KEAP1 binding domain in NRF2 released NRF2 from regulation by KEAP1, impaired expansion and stemness of CD8+ T cells, and dysregulated multiple metabolic pathways including redox pathways. Thus, our study revealed a novel role of the redox pathway in regulating the molecular program and differentiation of stem-like and exhausted CD8+ T cells during chronic antigen stimulation.

overall_design: Control and  Keap1KO P14 cells isolated from spleens  were sorted for scRNA-Seq. Termianlly exhausted control and  Keap1KO P14 cells isolated from spleens  were sorted for ATAC-Seq anallysis. Control and  CA-NRF2 OE P14 cells isolated from spleens  were sorted for scRNA-Seq or multiome analysis. Sorted CA-NRF2 expression CD8 T cells were used for ChIP-Seq experiment.

first: Tuoqi

last: Wu

first: Ziang

last: Zhu


title: The type 1 diabetes-associated lncRNA ARGI participates in virus-induced pancreatic β cell inflammation.

city: Donostia - San Sebastian

first: Koldo

last: Garcia

address: Paseo Beguiristain S/N

country: Spain

institute: Biodonostia HRI

summary: We performed the functional characterization of a virus-induced T1D-associated lncRNA named ARGI (Antiviral Response Gene Regulator). ARGI overexpression in pancreatic beta cells leads to the transcriptional activation of several antiviral genes, including genes of the T1D-associated IRF7-driven inflammatory gene network (IDIN). Upon a viral insult, ARGI is upregulated in the nuclei of pancreatic beta cells and binds to the transcription factor CTCF to interact with the regulatory regions of IFN and interferon-stimulated genes (ISGs), promoting their transcriptional activation in an allele-specific manner.  The presence of the T1D risk allele in ARGI induces a hyperactivation of the antiviral and type I IFN response genes in beta cells, an expression signature that is typically overserved in the pancreas of T1D patients.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for EndoC-βH1 human pancreatic beta cell line, between control condition and ARGI overexpression

first: Izortze

last: Santin

first: Itziar

last: González-Moro


title: DNA methylation insulates exons from CTCF loops with nuclear speckles (CUT&TAG)

city: Cambridge

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

institute: Harvard University

summary: CTCF is necessary for the formation and maintenance of many DNA loops and Topologically Associating Domains, but the genomic features that influence CTCF looping are incompletely understood. We characterized the downstream effects of treating cells with a DNMT1 inhibitor and acute depletion of nuclear speckles to study the factors that influence CTCF looping.

overall_design: SON Cut&Tag for K562 and HCT116 cells treated with a DNA methylation inhibitor (DNMT1i) and DMSO control.

middle: B

first: Shelby

last: Roseman

first: Allison

middle: P

last: Siegenfeld

first: Ceejay

last: Lee

first: Nicholas

middle: Z

last: Lue


title: DNA methylation insulates exons from CTCF loops with nuclear speckles

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

overall_design: Refer to individual Series