title: CYP72A1182 is involved in metabolic resistance evolution to tembotrione in Palmer amaranth

city: Fort Collins

first: Todd

last: Gaines

state: CO

address: 1177 Campus Delivery

department: Agricultural Biology

institute: Colorado State University

summary: Evolution of metabolic herbicide resistance is a major issue for weed management. Few genes and regulatory mechanisms have been identified, particularly in dicotyledonous weed species. We identified putative causal genes and regulatory mechanism for tembotrione-resistance in Amaranthus palmeri. Cytochrome P450 candidate genes were identified through RNA-seq analysis. We validated their functions using heterologous expression in S. cerevisae. Promoters of the candidate P450 genes were analyzed. We performed QTL mapping to identify genomic regions associated with resistance. CYP72A1182 deactivated tembotrione. This gene had increased expression in other A. palmeri populations resistant to multiple herbicides, including-tembotrione. Resistant plants exhibited polymorphisms in the promoter of CYP72A1182. We identified QTLs linked to herbicide resistance, including one on chromosome 4 approximately 3 Mb away from CYP72A1182. CYP72A1182 is involved in tembotrione resistance in A. palmeri. Increased expression of this gene could be due to cis-regulation in the promoter, as well as trans-regulation from transcription factors; however further studies are in progress to test this hypothesis. The elucidation of regulatory genes is crucial for developing innovative weed management approaches and target-based novel molecules.

overall_design: Pseudo-F2 plants were generated by crossing HPPD-resistant population of Plamer amaranth (NER) and susceptible (NES). Six most susceptible and 6 most resistance were used for gene expression analysis. Time-points analyzed were 0, 6 and 12 h after tembotrione application. Plants from two crosses were used for analysis, cross 4 and cross 5. The total samples are 72.

first: Anita

last: Küpper

first: Patrick

last: Tranel

first: Carlos

last: Rigon

first: Franck

last: Dayan

first: Crystal

last: Sparks

first: Jacob

last: Montgomery

first: Roland

last: Beffa


title: Cancer-associated fibroblasts reveal aberrant DNA methylation across different types of cancer [RNA-seq]

status: Public on Feb 14 2025

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

type: Expression profiling by high throughput sequencing

summary: Cancer-associated fibroblasts (CAFs) are critical components of the tumor microenvironment. Several studies demonstrated molecular differences between CAFs and normal tissue-associated fibroblasts (NAFs). In this study, we isolated CAFs and NAFs from liver tumors and analyzed their DNA methylation profiles. A subset of the CAFs exhibited aberrant DNA methylation, which was also reflected on gene expression level. The DNA methylation at liver-CAF-specific CG dinucleotides (CpGs) was associated with survival in liver cancer data. An integrative analysis with public datasets of CAF versus NAF in different cancer types, including lung, prostate, esophagus, and gastric cancer, revealed overlapping epigenetic aberrations. CpGs with common aberrations in DNA methylation included cg09809672 (EDARADD), cg07134930 (HDAC4), and cg05935904 (intergenic). Aberrant DNA methylation at these sites was associated with prognosis in several cancer types. Thus, activation of CAFs by the tumor environment is associated with characteristic epigenetic modifications that could be used as biomarkers for disease stratification.

overall_design: Transcriptomic analysis of cancer associated fibroblasts (CAFs) and normal-tissue associated fibroblasts (NAFs) of human liver tumor samples. NAFs were isolated form neighboring tumor-free tissue.

first: Marco

last: Schmidt

first: Tiago

last: Maié

first: Thorsten

last: Cramer

first: Ivan

middle: G

last: Costa


title: Deciphering the Code of Resistance: A Genomic and Transcriptomic Exploration of the Cystoisospora suis Holland-I Strain

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

summary: Cystoisospora suis, a member of the apicomplexan order Coccidia and causative agent of neonatal porcine coccidiosis, poses a challenge to pig production due to the emergence of reduced efficacy of toltrazuril, the only EU-approved treatment. To address the critical gaps in understanding toltrazuril resistance and possibilities of early diagnostics, our study investigated the genetic basis of resistance through whole-genome DNA sequencing and transcriptome analysis of two C. suis strains, the toltrazuril-susceptible Wien-I and the resistant Holland-I. Additionally, we studied the mitochondrial genome and analysed mitochondrial gene expression in both strains. Our results show that genes encoding proteins involved in host-cell invasion displayed variable expression patterns and genetic mutations, suggesting adaptive changes in invasion mechanisms. Moreover, substantial fluctuations in the expression of genes linked to retrotransposons, accompanied by genetic alterations, were observed, highlighting their potential involvement in genomic rearrangements. Finally, our mitochondrial genome analyses revealed important insights into its genetic organization and conservation. Notably, the marked downregulation of CoI, CoIII and Cytb mRNA levels in the resistant strain Holland-I upon toltrazuril exposure highlights the dynamic response of mitochondrial genes to toltrazuril. These mitochondrial adaptations appear to be closely linked to the parasite drug resistance mechanism, potentially facilitating its survival under pharmacological stress. These findings enhance our knowledge of drug resistance mechanisms in Coccidia and highlight the need for novel management strategies, leading to the development of targeted treatments and controls.

overall_design: Transcriptomic analyses were carried out on the asexual merozoite stage of C. suis to assess transcript levels. The analysis was conducted on Holland-I strains with and without toltrazuril treatment, and on the Wien-I strain without treatment due to its sensitivity to the drug.

first: Teresa

last: Cruz-Bustos

first: Bärbel

last: Ruttkowski

first: Anja

last: Joachim


title: Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis

city: Nashville

first: Jonathan

middle: A

last: Kropski

state: TN

department: Medicine

country: USA

institute: Vanderbilt University Medical Center

summary: The pathophysiology of silicosis is poorly understood, limiting development of therapies for those who have been exposed to the respirable particle. We explored mechanisms of silica-induced pulmonary fibrosis in human lung samples collected from patients with occupational exposure to silica and in a longitudinal mouse model of silicosis using multiple modalities including whole-lung single-cell RNA sequencing and histological, biochemical, and physiologic assessments. In addition to pulmonary inflammation and fibrosis, intratracheal silica challenge induced osteoclast-like differentiation of alveolar macrophages and recruited monocytes, driven by induction of the osteoclastogenic cytokine, receptor activator of nuclear factor κΒ ligand (RANKL) in pulmonary lymphocytes, and alveolar type II cells. Anti-RANKL monoclonal antibody treatment suppressed silica-induced osteoclast-like differentiation in the lung and attenuated pulmonary fibrosis. We conclude that silica induces differentiation of pulmonary osteoclast-like cells leading to progressive lung injury, likely due to sustained elaboration of bone-resorbing proteases and hydrochloric acid. Interrupting osteoclast-like differentiation may therefore constitute a promising avenue for moderating lung damage in silicosis.

overall_design:
10X Genomics 5' scRNA-seq of lung explants from subjects with coal-workers pneumoconiosis. A subset of samples analyzed in this manuscript were previously released in GSE227136 and GSE135893.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Jennifer

last: Franks

first: Nicholas

last: Banovich

first: Ciara

last: Shaver

first: Francis

last: McCormack

first: Cole

last: Trapnell

first: Yoshihiro

last: Hasegawa


title: DNA demethylation in spermatogenesis presets the sites of  nucleosome retention in mouse sperm

city: Noda

first: So

last: Maezawa

state: Chiba

department: Applied Biological Science

country: Japan

institute: Tokyo University of Science

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is a heritable epigenetic mark from the parental germline to the embryo. In the male germline, it remains unknown how the site-specificity of DNA methylation conversely defines the sites of unmethylated DNA in mature sperm, which are tightly coupled to histone retention sites at gene regulatory elements implicated in paternal epigenetic inheritance. Here, we perform genome-wide profiling of DNA methylation during spermatogenesis based on the capture of methylated DNA by the methyl-DNA binding protein domain (MBD) and demonstrate that there is a site-specific change in DNA methylation during the mitosis-to-meiosis transition in spermatogenesis. Importantly, DNA demethylation sites during the mitosis-to-meiosis transition predetermine nucleosome retention sites in spermatozoa. These results suggest that site-specific DNA demethylation during the mitosis-to-meiosis transition of spermatogenesis prepares embryonic gene expression after fertilization. We propose that DNA demethylation in spermatogenesis is a novel phase of epigenetic reprogramming that contributes to embryonic gene regulation.

overall_design: MethylCap-seq for capturing MBD-bound DNA methylated regions in mouse male germ cells

first: Kai

last: Otsuka

first: Satoshi

last: Namekawa


title: The effects of miR-22-3p on differentiation of human dental pulp stem cells into neural progenitor-like cells

city: Sharjah

first: Muhammad

middle: Tehsil

last: Gul

address: University street

country: United Arab Emirates

institute: university of sharjah

summary: To investigate the role of miR22-3p mimic and inhibitor on the differentiation of HDPSC into NPCs, we transfected the cells with the treatment and induced the neural differentiation within 24 hours. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different treatments (mimic, inhibitor and control) at three time points (Days 1, 3, and 7).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HDPS cells and its transfected counterparts (miR22-3p mimic and inhibitor).

middle: T

first: Amir Ali

last: Khan

first: Rizwan

last: Qaisar

middle: N

last: Khattak

first: Manju

last: Jayakumar

middle: R

last: Samsudin


title: Gene expression profile at single cell level of cells isolated from the bone fracture gap and un-injured bone marrow in mouse osteotomy models

city: Dresden

first: Annemarie

last: Lang

address: Fetscherstrasse 74

institute: TU Dresden

summary: We investigated the cell composition in the bone fracture (osteotomy) gap under two different ambulatory loading conditions (stiif vs. compliant - external fixator). In addition, we applied an receptor inhibitor or respective isotype control to understand the role of a specific progenitor subpopulation during the onset of bone fracture repair.  Un-injured bone marrow was used as control. Some samples were combined prior to library prep as indicated in the sample titles

overall_design: Cells from the bone fracture (osteotomy) gap and contralateral bone marrow were isolated 3 days post-osteotomy. Erythrocyte lysis and live cells sorting was performed before scRNAseq. Female C57BL/6J mice (Jackson Laboratory) aged 14-16 weeks were used.

first: Joel

middle: D

last: Boerckel

first: Joseph

middle: M

last: Collins


title: Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus [Hi-C]

city: Paris

first: Romain

last: Koszul

address: 25 Rue du Dr Roux

department: Genetics and Genomics

country: France

institute: Institut Pasteur

summary: In eukaryotes, DNA-associated protein complexes co-evolve with genomic sequence to orchestrate chromatin folding into functional chromosomes. Here, we investigate the relationship between DNA sequence and the spontaneous loading and activity of chromatin components in the absence of co-evolutions. Using bacterial genomes integrated into S. cerevisiae, which diverged from yeast up to 1.5 billion years ago, we show that nucleosomes, cohesins and the transcriptional machinery can lead to the formation of two different chromatin archetypes, one being transcribed and the other silent. These two archetypes also form on eukaryotic exogenous sequences, and depend on sequence composition. They do not mix in the nucleus, leading to a bipartite nuclear compartmentalisation reminiscent of the organization of vertebrate nuclei. Our findings represent a significant advance in understanding the primary molecular mechanisms that govern the co-option or silencing of DNA sequences integrated into foreign genomes during natural horizontal gene transfers, or in synthetic genomics projects.

overall_design: We explored the spatial folding of bacterial chromosomes integrated in a eukaryotic environment by performing Hi-C of yeast strains containing linearized and telomerized bacterial chromosomes.

first: Jacques

last: Serizay


title: Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus [Mnase-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: We explored whether nucleosomes were able to form on bacterial chromosomes integrated in a eukaryotic environment by performing MNase-seq analysis of yeast strains containing linearized and telomerized bacterial chromosomes.


title: Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus [ChIP-Seq]


title: Differential expression of lncRNAs enriched in coronary thrombus-derived exosomes from AMI patients relative to serum patients with AMI and their functional differences

city: Guiyang City

first: Youfu

last: He

state: Guizhou Province

address: No.83 Zhongshan East Road, Nanming District, Guiyang City, Guizhou Province, China

country: China

institute: Guizhou Provincial People's Hospital

summary: Purpose: to detect the expression differences of Long chain non coding RNA(Lnc RNA) in exosomes derived from Thrombus-derived exosomes in AMI patients, healthy human serum-source exosomes and AMI patients serum-source exosomes.  Methods: Total RNA containing Long chain non coding RNA was extracted from Thrombus-derived exosomes in AMI patients. Use Agilent lncRNA array for lncRNA analysis. Each lncRNA was repeatedly detected by the probe 30 times. The array also contains 2164 Agilent control probes. Agilent Feature Extraction (Agilent) was used to analyze the lncRNA array data for data aggregation, standardization and quality control. Perform the default 90th percentile normalization method for date preprocessing. To select differentially expressed genes, we used thresholds of ≥2 and ≤−2 fold change, and the Benjamini-Hochberg corrected p vlaue was 0.05.  Results: Compared with the Normal group, there were 2148 lncRNAs up-regulated and 2415 lncRNAs down-regulated in the serum group, and 2615 lncRNAs up-regulated and 452 lncRNAs down-regulated in the thrombus group. Compared with the serum group, there were 1374 lncRNAs up-regulated and 1218 lncRNAs down-regulated in the thrombus group.  Conclusion: The 2615 lncRNAs upregulated relative to the Noormal group are candidates for regulatory targets of thrombosis-related regulatory pathways.

overall_design: A total of 11 samples were taken. Among them, 3 were exosomes from healthy human serum, 4 were coronary thrombus-derived exosomes from AMI patients, and 4 were serum exosomes from AMI patients (from the same patient as the thrombus-derived exosomes were extracted).

first: Y

first: Q

last: Wu

first: Z

last: Yu

first: J

last: Huang

first: L

last: Ai

first: X

last: Long


title: Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus

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

overall_design: Refer to individual Series


title: Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus [RNA-Seq]

overall_design: We explored whether transcription occurs on bacterial chromosomes integrated in a eukaryotic environment by performing total, stranded RNA-seq analysis of yeast strains containing linearized and telomerized bacterial chromosomes.


title: The transcriptomic landscape of pediatrics with dengue virus infection reveals the severity-dependent immune response

city: Stanford

first: Zhiyuan

last: Yao

state: CA California

address: 1291 Welch Rd. Room S136

institute: Stanford University

summary: We performed virus inclusive single cell RNA sequencing of children with diverse DENV infection severity and profiled both cell type abundances and gene expression within each cell type.

overall_design: We collected PBMC samples of 20 DENV-infected children (ages: 2 to 16) and 4 healthy donors from a established cohort in Colombia.The 20 patients were classified into 3 clinical conditions: uncomplicated dengue without warning signs (D, n = 8), dengue with warning sign (DWS, n = 4), severe dengue (SD, n = 8) which were identified based on the discharge diagnoses using the WHO 2009 criteria. we adapted the commercial 5'-end droplet-based scRNA-seq (10X Genomics) by adding a capture oligonucleotide for the positive strand of DENV. each sample was first depleted of dead cells and subsequently split in two aliquots. The first aliquot was processed with the magnetic beads coated with CD3 antibody to remove T cells before remixing with the second, unprocessed one to decrease the T cell population to 30%-40%.

first: Fabio

last: Zanini

first: Yike

last: Xie


title: Tumor-reactive T cells in HNSCC patients are directed against cancer-associated fibroblasts

city: Heidelberg

first: Christel

last: Herold-Mende

department: Department of Neurosurgery

institute: University Hospital Heidelberg

summary: Endogenous T-cell (TC) responses against tumors determine patient prognosis and are the basis for successful immune checkpoint-blocking cancer immunotherapy. Yet, cell subsets and antigens they target in the tumor microenvironment remain largely unknown. In contrast to tumor cells, which are a clonally diverse and unstable cell population, non-malignant cells of the tumor stroma, particularly cancer-associated fibroblasts (CAFs) represent a large subset of genetically stable cells which nonetheless essentially contribute to tumor progression in many cancers. Here, we studied in a cohort of HNSCC patients to what degree tumor-reactive TCs may target CAFs and which CAF-associated antigens are recognized. Using autologous TCs, tumor cell, and CAF cultures from HNSCC patients, we show that tumor-reactive type 1 TC responses against CAFs commonly occur in HNSCC patients to a similar extent as TC responses against the tumor cells themselves. Due to simultaneous MHC-I and -II expression, CAFs were directly recognized by CD8+ cytotoxic and CD4+ helper TCs. Then, we performed automated 2D proteome fractionation of CAF lysates together with mass spectrometry-based proteome identification, differential transcriptome analyses of CAFs and laser-capture-microdissected tumor stroma and TC function assays. We identified several common antigens including TXNDC17, NANS, DNAJB11, and THBS2 being differentially expressed on CAFs and recognized by tumor-reactive TC repertoires of multiple patients. Taken together, CAFs are a major target cell type of tumor-reactive TC responses in HNSCC patients. Due to their MHC-II expression, differential expression of common CAF-selective immunogenic antigens and their essential role during tumor progression, they represent promising targets for anti-cancer immunotherapies.

overall_design: Comparative transcriptomic analysis of CAF, TUC, NF cells and dissected normal and tumor stroma

first: Rolf

last: Warta

first: Saskia

last: Roesch


title: Identification of differentially expressed genes by rapid induction of PML/RARa degradation using arsenic trioxide  in NB4 cells

city: Shanghai

first: Yun

last: Tan

state: Shanghai

address: Room 1109, Building 11, 197 Ruijin Er Rd

department: Shanghai Institute of Hematology

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

summary: Acute promyelocytic leukemia (APL) is characterized by the specific chromosome translocation t(15;17) that generates the promyelocytic leukemia/retinoic acid receptor-α (PML/RARα) fusion gene. Arsenic trioxide has been intensively reported to directly and rapidly degrade the PML/RARα fusion protein. Here, we treated NB4 cells (a widely used APL cell line) with arsenic trioxide and performed RNA-seq analysis to identify differentially expressed genes upon arsenic trioxide treatment.

overall_design: RNA-seq analysis of NB4 cells with or without arsenic trioxide treatment.

first: Kankan

last: Wang


title: ABL Kinase Inactivation Promotes Transcription-Replication Conflicts and Compromises Replication Forks Revealing a Therapeutic Vulnerability in Metastatic Small Cell Lung Cancer

status: Public on Feb 13 2025

city: Durham

first: Ann Marie

last: Pendergast

state: North Carolina

address: 308 Research Dr

department: Pharmacology and Cancer Biology

institute: Duke University

summary: Small cell lung cancer (SCLC) is a highly aggressive neuroendocrine cancer that is typically metastatic upon diagnosis, and has low overall survival. Despite being highly sensitive to first-line chemotherapy or radiotherapy, most patients with SCLC experience relapse and succumb from systemic metastasis. Here we report that inactivation of ABL tyrosine kinases markedly impaired outgrowth of metastatic SCLC tumors in mouse models, resulting in prolonged animal survival. Mechanistically, ABL inactivation in SCLC resulted in increased accumulation of transcription-replication conflicts, compromised replication fork progression, impaired expression and function of proteins implicated in transcription-coupled homologous recombination, and increased DNA damage. Because ABL inactivation increased DNA damage, we evaluated whether blocking the activity DNA damage-repair pathways in the presence of ABL inhibitors might synergize to promote SCLC cell death. We found that co-inactivation of ABL kinase and Ataxia telangiectasia and Rad3-related (ATR), the primary responder of replication stress, synergistically inhibited SCLC cell growth in vitro, and impaired metastatic dissemination and outgrowth compared to single agent treated mice. Thus, combined inactivation of ABL kinase and DNA damage-repair pathways might be exploited to block dissemination and outgrowth of SCLC metastases

overall_design: RNA-Seq profiling of SCLC H69 control cells and H69 treated with ABL kinase inhibitor, GNF5, for 48 hours.

first: Jing Jin

last: Gu

first: Jake

last: Hoj


title: High fluid shear stress induces Hippo/YAP pathway in articular cartilage superficial layer cells: a potential mechanistic link to 0steoarthritis

city: Guiyang

first: Haitao

last: Li

address: Affiliated Hospital of Guizhou Medical University,

institute: Guizhou Medical University

summary: Abnormal mechanical loading, which can lead to articular cartilage damage, is a significant contributor to the onset of osteoarthritis (OA). Articular cartilage superficial layer cells are among the first cells to respond to changes in the mechanical environment and are highly sensitive to mechanical stimuli. This study aimed to investigate the effects of high fluid shear stress on the articular cartilage superficial layer cells and the underlying mechanisms. We found that high fluid shear stress of 20 dyne/cm² induces inflammation and promotes catabolic processes in these cells. Short-term high fluid shear stress has a protective effect, but its efficacy varies with time. YAP plays a crucial role in mediating the effects of high fluid shear stress and may represent a potential therapeutic target for early-stage osteoarthritis. The study also established osteoarthritis models using anterior cruciate ligament transection (ACLT) or injection of sodium iodoacetate (MIA) to further confirm the findings.

overall_design: The Primary articular cartilage superficial layer cells were treated with or without 20 dyne/cm²  fluid shear stress

first: Hai

first: Yu

middle: X

last: Ou

first: Li

middle: F

last: Chen

first: Yong

first: Wei

first: Jian


title: Pt-seq unveils the genomic binding pattern of platinum-based drugs [Pt-seq]

city: Beijing

first: Mingyang

address: Yanyuan Subdistrict, Haidian District

institute: Peking University

summary: Platinum-based drugs (Pt drugs) are widely used in cancer chemotherapy, yet their genome-wide DNA binding patterns remain incompletely understood. Here, we present Pt-seq, an antibody-assisted, genome-wide method for mapping Pt-DNA adducts at single-base resolution. By employing exo- and endo- nucleases to remove background DNA, Pt-seq enables highly robust and sensitive profiling of binding sites for cisplatin, oxaliplatin, lobaplatin, and a Pt(IV) complex. Using Pt-seq, we identified hundreds to a few thousand binding clusters that are 10-20 kb in length and highly consistent among different Pt drugs. Notably, these binding clusters predominantly localize to centromeric and rDNA regions. In cisplatin-resistant cells, we found significantly reduced binding within these regions, suggesting a potential role in drug resistance. Moreover, we found that de novo mutations in cancer cells can create novel binding sites for Pt drugs. Based on this, we demonstrated that ICR-191, an acridine orange compound capable of inducing G insertions, enhances cisplatin-DNA crosslinking and sensitizes cells to Pt drugs. Collectively, Pt-seq sensitively profiles Pt drug-DNA interactions and deepens our understanding of the genome-wide effect of chemotherapeutic drugs.

sample_organism:
Homo sapiens
Cricetulus griseus

platform_organism:
Homo sapiens
Cricetulus griseus

overall_design: This dataset includes Pt-drugs treatment on HeLa cells, including cisplatin, oxaliplatin, lobaplatin and Pt-Bio-I, also includes cisplatin treatment on A549 wildtype and cisplatin-resistant cell lines (all Pt-seq libraries). Besides, this dataset includes Pt-seq of cisplatin treatment on CHO cell lines, with or without ICR-191 treatment as well. Target-seq libraries on HGPRT gene of CHO with or without ICR-191 treatment are also included.

first: Chuyun

last: Shao


title: Identification of hypoxia-induced metabolism-associated genes in canine tumors.

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

institute: Yamaguchi university

summary: The energy metabolism of tumors is biased toward glycolysis called as the Warburg effect. The tumor microenvironment is known to be hypoxic, which leads to activating hypoxia-inducible factor 1α (HIF1α) in tumor cells. The high expression of HIF1α plays a functional role in the enhancement of glycolysis and is correlated to poor outcomes in human cancers. However, in dogs, the molecular mechanisms involved in hypoxic tumor cells remain to be elucidated. In the present study, we investigated upregulated genes in hypoxia by RNA-seq analysis, the expression of proteins related to glycolysis in hypoxia by western blotting (WB), and the expression of the monocarboxylate transporter4 (MCT4) in a total of 96 canine tumor tissue by immunohistochemical (IHC) staining. The glycolysis and HIF-1 signaling pathways were upregulated in hypoxic melanoma cells by RNA-seq and WB. In addition, the experiment using HIF1α knockout melanoma cells showed a marker of glycolysis MCT4 was regulated by HIF1α activation. Hypoxia induced high lactate secretion due to the enhancement of glycolysis in canine melanoma cells. IHC analysis revealed membrane-localization of MCT4 protein was observed in urothelial carcinoma and lung adenocarcinoma tissues. We concluded canine MCT4 protein has a role in lactic acid efflux from glycolytic cells and might be a novel marker of hypoxia and glycolysis in canine tumors. This data may also be important in finding a new therapeutic target for MCT4 in the future.

overall_design: RNAseq analysis of canine malignant melanoma cells incubated under conditions of normoxia or hypoxia.

first: Taiki

last: Kato

first: Masashi

last: Sakurai

first: Kenji

last: Watanabe

first: Takayuki

last: Nakagawa

last: Baba

first: Takuya

last: Mizuno

first: Masaya

last: Igase


title: A Novel Rescue Strategy for Bone Marrow Hematopoietic Failure via Microenvironment Reconstruction with Reduced HSC Dependency [RNA-Seq]

city: chongqing

first: Debao

address: No. 13, Tianchi Avenue, Mudong Town, Banan District, Chongqing

institute: Chongqing International Institute for Immunology

summary: Hematopoietic stem cell transplantation (HSCT) represents the most effective therapeutic approach for hematopoietic malignancies, bone marrow (BM) failure syndromes, and primary immunodeficiency diseases. However, the clinical demand for HSCT is constrained by current limitations in HSC sources and expansion technologies. The BM niche is crucial providing a supportive microenvironment for the self-renewal and differentiation of HSCs, and its rejuvenation is essential for rapid and effective hematopoietic recovery. In this study, we demonstrate that costal-cartilage-derived stem cells (CDSCs) can achieve hematopoietic reconstruction comparable to HSCT, even with a significantly reduced number of hematopoietic stem and progenitor cells (HSPCs), while exhibiting low chimerism. We further show that transplanted CDSCs differentiate into various cell types, including bone marrow stromal cells (BMSCs), endothelial cells, and osteoblasts, and secrete pro-hematopoietic factors that restore the damaged BM niche. Moreover, in vitro-expanded CDSCs exhibit elevated expression of BMSC markers and enhance hematopoietic recovery in injury models. Notably, the combination of CDSCs with cyclosporine A is effective in treating aplastic anemia in mouse models. Collectively, these findings propose a novel strategy for treating BM hematopoietic failure through microenvironmental restoration and broaden the potential therapeutic scope of HSCT.

overall_design: This experiment was categorized into three groups, namely BM transplantation (BMT), novel transplantation involving CDSCs, and normal mice of the same age (Health). Cell samples were collected from the BM of these mice two weeks after transplantation and subjected to RNA-seq (Haplox, China).

first: Rui

last: Dong

first: Zhiguo

last: Ling


title: Transcriptome variation between 5 commonly used wild type laboratory yeast strains.

city: Saarbrüecken

first: Julia

last: Schulze-Hentrich

address: Campus A2.4

department: Genetics/Epigenetics

institute: Saarland University

summary: This dataset compares the transcriptome of five laboratory yeast strains (S. cerevisiae) cultured under standardized laboratory consitions (early exponential growth, cultured in synthetic complete glucose media at 30ºC).

overall_design: Gene expression changes were profiled in different yeast strains (BY4741, W303-1A, D273-10B, RM11-1a, CEN.PK2-1c) using 4 replicates each.

first: Mike

last: Renne

first: Robert

last: Ernst

first: Thomas

last: Hentrich


title: Ezh2 shapes T cell plasticity to drive atherosclerosis

city: Munich

first: Dorothee

last: Atzler

state: Bavaria

address: Pettenkoferstr. 9

department: IPEK

institute: LMU Munich

summary: The activation and polarization of T cells play a crucial role in atherosclerosis and dictate athero-inflammation. The epigenetic enzyme enhancer of zeste homolog 2 (EZH2) mediates the tri-methylation of lysine27 on histone3 (H3K27me3) and is pivotal in controlling T cell responses. To detail the role of T cell-EZH2 in atherosclerosis, we used human carotid endarterectomy specimens to reveal plaque expression and geography of EZH2. Atherosclerosis-prone Apoe-deficient mice with CD4+ and/or CD8+ T cell-specific Ezh2 deletion (Ezh2cd4-KO, Ezh2cd8-KO) were analyzed to unravel T cell-Ezh2’s role in atherosclerosis and T cell-associated immune status.EZH2 expression is elevated in advanced human atherosclerotic plaques and primarily expressed in the T cell nucleus, suggesting the importance of canonical EZH2 function in atherosclerosis. Ezh2cd4-KO, but not Ezh2cd8-KO mice showed reduced atherosclerosis with less advanced plaques, which contained less collagen and macrophages, indicating that Ezh2 in CD4+ T cells drives atherosclerosis. In-depth analysis of CD4+ T cells of Ezh2cd4-KO mice revealed that absence of Ezh2 results in a type II immune response with increased Il-4 gene and protein expression in the aorta and lymphoid organs. In vitro, Ezh2-deficient T cells polarized macrophages towards an anti-inflammatory phenotype. scRNAseq of splenic T cells revealed that Ezh2-deficiency reduced naive, Ccl5+ and regulatory T cell populations and increased the frequencies of memory T cells and invariant natural killer T (iNKT) cells. Flow cytometric analysis identified a shift towards T helper 2 (Th2) effector CD4+ T cells in Ezh2cd4-KO mice and confirmed a profound increase in splenic iNKT cells with high expression of Plzf, the characteristic marker of the iNKT2 subset. Likewise, Zbtb16 (Plzf-encoding gene) transcripts were elevated in the aorta of Ezh2cd4-KO mice, suggesting an accumulation of iNKT2 cells in the plaque. H3K27me3-chromatin immunoprecipitation followed by qPCR showed that T cell-Ezh2 regulates the transcription of the Il-4 and Zbtb16 genes. Our study uncovers the importance of T cell-EZH2 in human and mouse atherosclerosis. Inhibition of Ezh2 in CD4+ T cells drives type II immune responses, resulting in an accumulation of iNKT2 and Th2 cells, memory T cells and anti-inflammatory macrophages that limit the progression of atherosclerosis. We performed scRNAseq of splenic T cells isolated from Ezh2cd4-KO and respective controls fed with Western type diet, to study T cells during atherosclerosis progression.

overall_design: Following Western-type diet, spleens were isolated from Ezh2cd4-KO mice and controls after cervical dislocation. Living splenic CD45+CD3+ T cells (B220-Gr1-Ter119-) were sorted using a FACSAria III (BD Biosciences) and analyzed using scRNA-Seq.

first: Cecilia

last: Bonfiglio

first: Michael

last: Lacy

first: Vasiliki

last: Triantafyllidou

first: Donato

last: Santovito

first: Esther

last: Lutgens


title: Lactylation of LSD1 is an acquired epigenetic vulnerability of BRAFi/MEKi-resistant melanoma [RNA-seq]

city: Xiamen

first: aicun

last: li

address: South Xiang'an Road 4221-120, Xiang'an Campus, Xiamen University, Xiang'an District

institute: Xiamen University

summary: BRAFV600E mutant melanomas treated with BRAF inhibitor (Dabrafenib) and MEK inhibitor (Trametinib) almost invariably develop drug resistance (DTR). Restored glycolysis, frequently found in clinical targeted therapy-resistant melanoma biopsies, has been shown to elicit drug resistance. How resumed glycolysis controls the emergence of acquired resistance, especially via intrinsic mechanisms that circumvent the BRAF/MEK module, remains unknown. Here, we identify lactylation of LSD1, induced by re-accumulated lactate in DTR melanoma cells, selectively drives survival via epigenetic reprogramming. Mechanistically, lactylation of LSD1 promotes its interaction with FosL1, thereby preventing its ubiquitination and degradation by E3 ligase tripartite-motif-containing protein 21 (TRIM21). In DTR melanoma cells, chromatin binding capacity of FosL1 was significantly strengthened due to reduced acetylation, which in turn increases selective chromatin enrichment of LSD1. We further demonstrate that lactylated LSD1 co-orchestrates gene transcription with FosL1 to repress ferroptosis in DTR cells via interfering with transferrin receptor protein 1 (TFRC)-mediated iron uptake. LSD1 inhibitor (LSD1i) activates ferroptosis, resulting in drastic DTR melanoma regression in mice. Importantly, LSD1i-induced immunogenic ferroptosis synergizes with immune checkpoint blockade (ICB) in vivo. Together, our results highlight a crucial role of metabolic rewiring-induced epigenetic reprogramming as a bypass resistance mechanism in DTR melanoma, which provides a therapeutically actionable strategy to overcome acquired resistance to targeted therapy.

overall_design: RNA-seq was perform to obtain LSD1-/FosL1-dependent transcriptomic signatures

first: Han

last: You

first: Aicun

last: Li

first: Zhicheng

last: Gong


title: Co-translational regulation of Mmf1 expression depends upon its mitochondrial targeting, ubiquitination of Egd1 by Not4, Caf130 and NGD: MitoENCay

city: Geneve

first: George

last: Allen

state: Geneve

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

summary: The Ccr4-Not complex is a conserved multi protein complex with diverse roles in the mRNA life cycle. Recently we determined that the Not1 and Not4 subunits of Ccr4-Not inversely regulate mRNA solubility and thereby impact dynamics of co-translation events. One mRNA whose solubility is most extremely inversely regulated by Not1 and Not4 is MMF1 encoding a mitochondrial protein that is translated with apparent ribosome pausing. In this work we uncover a mechanism that limits MMF1 overexpression in fermenting yeast and does not require MMF1 5’ or 3’ untranslated sequences but is mediated solely by the MMF1 coding sequence. This mechanism depends upon co-translational targeting of the MMF1 mRNA to the mitochondria, promoted by its mitochondrial targeting sequence, the Egd1 subunit of the NAC complex, the Om14 outer membrane protein and components of the mitochondrial import machinery as well as by Not4. Thereby, levels and translation of the MMF1 mRNA are limited by a mechanism that we have named Mito-ENCay involving ubiquitination of Egd1 by Not4, the Caf130 subunit of the Ccr4-Not complex and RQC. Our results indicate that this mechanism is used for highly expressed mRNAs that depend upon co-translational interactions for appropriate folding, such as ribosomal protein mRNAs in fermenting yeast.

overall_design: One part of the project involved comparing ribosome profiling in WT cells and Caf130 deletion. This was done for two duplicates each.

first: Siyu

last: Chen

first: Olesya

middle: O

last: Panasenko

first: Martine

last: Collart


title: Ezh2 shapes T cell plasticity to drive atherosclerosis II

summary: The activation and polarization of T cells play a crucial role in atherosclerosis and dictate athero-inflammation. The epigenetic enzyme enhancer of zeste homolog 2 (EZH2) mediates the tri-methylation of lysine27 on histone3 (H3K27me3) and is pivotal in controlling T cell responses. To detail the role of T cell-EZH2 in atherosclerosis, we used human carotid endarterectomy specimens to reveal plaque expression and geography of EZH2. Atherosclerosis-prone Apoe-deficient mice with CD4+ and/or CD8+ T cell-specific Ezh2 deletion (Ezh2cd4-KO, Ezh2cd8-KO) were analyzed to unravel T cell-Ezh2’s role in atherosclerosis and T cell-associated immune status.EZH2 expression is elevated in advanced human atherosclerotic plaques and primarily expressed in the T cell nucleus, suggesting the importance of canonical EZH2 function in atherosclerosis. Ezh2cd4-KO, but not Ezh2cd8-KO mice showed reduced atherosclerosis with less advanced plaques, which contained less collagen and macrophages, indicating that Ezh2 in CD4+ T cells drives atherosclerosis. In-depth analysis of CD4+ T cells of Ezh2cd4-KO mice revealed that absence of Ezh2 results in a type II immune response with increased Il-4 gene and protein expression in the aorta and lymphoid organs. In vitro, Ezh2-deficient T cells polarized macrophages towards an anti-inflammatory phenotype. scRNAseq of splenic T cells revealed that Ezh2-deficiency reduced naive, Ccl5+ and regulatory T cell populations and increased the frequencies of memory T cells and invariant natural killer T (iNKT) cells. Flow cytometric analysis identified a shift towards T helper 2 (Th2) effector CD4+ T cells in Ezh2cd4-KO mice and confirmed a profound increase in splenic iNKT cells with high expression of Plzf, the characteristic marker of the iNKT2 subset. Likewise, Zbtb16 (Plzf-encoding gene) transcripts were elevated in the aorta of Ezh2cd4-KO mice, suggesting an accumulation of iNKT2 cells in the plaque. H3K27me3-chromatin immunoprecipitation followed by qPCR showed that T cell-Ezh2 regulates the transcription of the Il-4 and Zbtb16 genes. Our study uncovers the importance of T cell-EZH2 in human and mouse atherosclerosis. Inhibition of Ezh2 in CD4+ T cells drives type II immune responses, resulting in an accumulation of iNKT2 and Th2 cells, memory T cells and anti-inflammatory macrophages that limit the progression of atherosclerosis. We performed RNAseq on splenic CD4+ T cells isolated from Ezh2cd4-KO mice and Ezh2cd4-WT controls using an efficient sequencing method (Prime-seq).

overall_design: RNA sequencing of CD4+ T cells from EZH2cd4-WT and -KO mice.

first: Aleksandar

last: Janjic


title: LPC-promoted Th1 differentiation

city: Changsha

first: Panpan

last: Liu

state: China

address: Xiangya road

institute: Xiangya hospital

summary: To evaluate the gene expression profile via RNA-seq after treatment with LPC under Th1 polarizing conditions.

overall_design: Mouse naïve CD4+ T cells were activated in vitro for 3 days with CD3/CD28 antibodies under Th1-polarizing conditions in the presence of vehicle control or LPC (20 μM).

first: Xiang

first: Cong

last: Peng


title: CRISPR screening identifies regulators of enhancer mediated androgen receptor transcription in advanced prostate cancer

city: Bethesda

first: David

last: Takeda

state: MD

address: 37 Convent Drive

department: National Cancer Institute

institute: National Institutes of Health

middle: Y

first: Rachel

last: Xiang

first: Shin-Ai

last: Lee

first: Caroline

last: Tyndall

first: Anusha

last: Bhatia

first: JuanJuan

last: Yin

first: Cassandra

last: Singler

first: Benjamin

middle: J

last: Hauk

first: Matthew

middle: P

last: Kipp


title: A Multipotent PROX1+ Tumor Cell Population Emerges During Intestinal Tumorigenesis and Mediates Radioresistance in Colorectal Cancer

city: Helsinki

first: Pauliina

last: Kallio

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

summary: Colorectal carcinoma (CRC) progression is associated with an increase in PROX1+ tumor cells, which exhibit features of CRC stem cells and contribute to metastasis. Here, we aimed to provide a better understanding to the function of PROX1+ cells in CRC, investigating their progeny and their role in therapy resistance. PROX1+ cells in intestinal adenomas of ApcMin/+ mice expressed intestinal epithelial and CRC stem cell markers, and cells with high PROX1 expression could both self-renew tumor stem/progenitor cells and contribute to differentiated tumor cells. Most PROX1-lineage traced tumor cells were stem/progenitor cells, which can supply cells to multiple intestinal tumor cell lineages, whereas most lineage-traced LGR5+ tumor cells were enterocytes, indicating that PROX1+ and LGR5+ tumor stem cells have distinct differentiation programs. Although the PROX1+ tumor cells proliferated slower than PROX1- cells, irradiation increased the proportion of PROX1+ cells in human CRC cell lines, patient-derived organoids, and tumor xenografts. Furthermore, transcripts related to DNA damage repair (DDR) were enriched in PROX1+ vs. PROX1- cells in adenomas and in CRC tumor cells from patients. Experiments with PROX1 silencing and overexpression indicated that PROX1 expression enhances CRC cell colony formation following irradiation. PROX1 interacted with DDR proteins, including components of non-homologous end-joining (NHEJ) and base excision repair, and inhibition of NHEJ repair led to a decreased proportion of PROX1+ cells following irradiation. In conclusion, PROX1+ cells are irradiation-resistant tumor stem/progenitor cells capable of self-renewal and differentiation. DDR inhibitors could represent a strategy to target the treatment-resistant PROX1+ tumor stem cells.

overall_design:
Tumors from the small intestines of ApcMin mice were dissociated into single-cells and subjected to scRNA-seq.
Tumors from the small intestines of ApcMin mice treated with i) +/- 2 Gy irradiation ii) tamoxifen to induce lineage tracing of PROX1+ cells, were dissociated into single-cells and subjected to scRNA-seq.

first: Cinzia

last: Bessone

first: Fatemeh

last: Seyednasrollah

first: Jefim

last: Brodkin

first: Marika

last: Lassila

first: Jenny

last: Högström

first: Alejandra

last: González-Loyola

first: Tatiana

middle: V

last: Petrova

first: Caj

last: Haglund

first: Kari

last: Alitalo


title: Lactylation of LSD1 is an acquired epigenetic vulnerability of BRAFi/MEKi-resistant melanoma [ChIP-seq]

first: aicun

last: li

overall_design: ChIP-seq performed in this study was designed to uncover the role of LSD1-/FosL1-mediated regulation of gene transcription.

first: Han

last: You

first: Aicun

last: Li

first: Zhicheng

last: Gong


title: Targeting MAPK14 by lobeline upregulates Slurp1-mediated inhibition of alternative activation of TAM and retards colorectal cancer growth

city: Nanjing

first: yang

last: sun

state: Jiangsu

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

institute: Nanjing University

summary: Colorectal cancer often produces an immunosuppressive microenvironment, which prevents them from responding to immunotherapy. Effective treatment options have not been found yet. Here, based on the observation that Lobeline, an alkaloid from the herbal medicine Lobelia Chinensis, inhibited tumor in MC38 colon cancer xenograft mouse model. We performed single-cell transcriptome sequencing analysis of Lobeline and PBS-treated tumors in mice, and found that Lobeline promoted TAM polarization towards M1-like while inhibited its polarization towards M2-like. In addition, Lobeline upregulated the mRNA level of secreted Ly-6/UPAR-related protein 1 (Slurp1) in cancer cells. The inhibitory effect of Lobeline on tumor load and regulation of TAM polarization disappeard in Slurp1-/- mice or WT mice injected with Slurp1 knockdown adenovirus, suggesting that Slurp1 mediates the process of Lobeline regulates TAM polarization and inhibits tumor progression. Through target responsive accessibility profiling (TRAP), isothermal titration calorimetry (ITC) and microcalorimetric mobility shift assay (MST), we demonstrated that MAPK14 was the target protein of Lobeline. At the mechanistic level, upon binding to MAPK14 in colon cancer cells, Lobeline prevented the nuclear translocation of MAPK14, which decreases the level of phosphorylated p53. Subsequently, the negative transcriptional regulation of Slurp1 by p53 was inhibited, that facilitated the transcription and secretion of Slurp1. Furthermore, the combination of Lobeline and PD-1 antibody showed stronger anti-tumor effect. Thus, these findings suggested that the Lobeline-mediated anti-tumor immune activation might be a promising therapeutic strategy for colorectal cancer.

overall_design: scRNA-seq profiling of total tumor cells in MC38 mouse transplanted tumor.

first: Ming-Xia

last: Zhao

first: Li-Sha

last: Zhou

first: Mei-Jing

last: Wang

first: Yang

last: Sun


title: Transcription factor ELF-1 protects against colitis by maintaining intestinal epithelium homeostasis

status: Public on Feb 12 2025

city: Zhengzhou

first: Peng

address: Science Avenue

institute: Zhengzhou University

summary: Inflammatory bowel disease (IBD) is a chronic, relapsing, and remitting disease characterized by chronic inflammation in the gastrointestinal tract. The exact etiology and pathogenesis of IBD remain elusive. Although ELF-1 has been known to be highly expressed in epithelial cells for past twenty years, little is known about its function in epithelial cells and epithelial-related IBD. Here, we demonstrated that ELF-1 deficiency in mouse lead to exacerbated DSS-induced colitis, marked by inflammation dominated by neutrophil infiltration and activation of IL-17 signaling pathways in various immune cells, including Th17, ILC3, γδT and NKT cells. Bone marrow transfer experiments confirmed ELF-1 deficiency in non-hematopoietic cells intrinsically worsened DSS-induced colitis. On one hand, ELF-1 deficiency enhanced the production of pro-inflammatory chemokines in colonic epithelial cells, leading to extensive infiltration of neutrophils and other immune cells into the colonic mucosal tissue. On the other hand, ELF-1 directly regulated the expression of the Rack1 gene in colonic epithelial tissue, which has been proved to play critical roles in maintaining intestinal homeostasis. Altogether, ELF-1 plays a protective role in colitis by maintaining intestinal epithelium homeostasis.

overall_design:
Two colon tissues from DSS-treated WT mice were obtained to perform ChIP-seq assay.
China, Zhengzhou university


title: LPC-treated mouse skin

first: Panpan

last: Liu

summary: To further understand the molecular mechanism of LPC

overall_design: Transcriptome profiling in the LPC-treated skin lesions. Intradermal administration of 10 μl LPC (10mM) or 10 μl normal saline (Vehicle) once per day for 6 consecutive days during the application of IMQ in mice (BALB/c) ear. Four mice in each group were sacrificed on Day4 and Day7, and skin lesions were used for whole-genome transcriptome analysis.

first: Xiang

last: Chen

first: Cong

last: Peng


title: Dual Role of IL-6 in Maintaining the resistance of Gastrointestinal stromal tumor and tumor angiogenesis

city: Yancheng

first: XINYI

last: ZHANG

address: Renmin Road No.66

institute: Yancheng First People's Hospital

summary: Resistance is a major obstacle to the effective treatment of many tumor types, including Gastrointestinal stromal tumor (GIST). Although Imatinib (IM) is considered the gold standard for targeted therapy in GIST, resistance to IM ultimately occurs in many patients, leading to disease progression. The precise mechanisms underlying this resistance remain poorly understood. Our study reveals that high expression of Interleukin-6 (IL-6) is closely associated with poor survival outcomes in patients with GIST. Elevated levels of IL-6 not only sustain the viability of GIST cells but also promote tumoral angiogenesis within the tumor microenvironment (TME) via paracrine mechanisms. Notably, the combination of the IL-6 receptor inhibitor Tocilizumab (TCZ) with IM significantly inhibited tumor growth in a GIST xenograft mouse model. Mechanistic investigations indicate that IL-6, through its interaction with IL-6R, reactivates the PI3K/Akt/mTOR signaling pathway, which is suppressed by IM. Additionally, as a secreted protein, IL-6 regulates the secretion of vascular endothelial growth factors controlled by the JAK2/STAT3 signaling pathway in endothelial cells via paracrine action. Thus, IL-6 may serve as a critical biomarker for predicting the prognosis of GIST, and the combined treatment strategy of IM with TCZ shows promising potential in overcoming resistance in GIST.

overall_design: RNA seq of  Human 882R and T1R  in control and experiment IL-6 knock down group


title: Multilevel Plasticity and Altered Glycosylation Drive Aggressiveness in Hypoxic and Glucose-Deprived Bladder Cancer Cells

city: Porto

first: Andreia

middle: Ferreira

last: Peixoto

address: Rua Dr. António Bernardino de Almeida

country: Portugal

institute: Portuguese Oncology Institute of Porto (IPO Porto)

summary: Bladder tumours with aggressive characteristics often present microenvironmental niches marked by low oxygen levels (hypoxia) and limited glucose supply due to inadequate vascularization. The molecular mechanisms facilitating cellular adaptation to these stimuli remain largely elusive. Employing a multi-omics approach, we discovered that hypoxic and glucose-deprived cancer cells enter a quiescent state supported by mitophagy, fatty acid β-oxidation, and amino acid catabolism, concurrently enhancing their invasive capabilities. Reoxygenation and glucose restoration efficiently reversed cell quiescence without affecting cellular viability, highlighting significant molecular plasticity in adapting to microenvironmental challenges. Furthermore, cancer cells exhibited substantial perturbation of protein O-glycosylation, leading to simplified glycophenotypes with shorter glycosidic chains. Exploiting glycoengineered cell models, we established that immature glycosylation contributes to reduced cell proliferation and increased invasion. Our findings collectively indicate that hypoxia and glucose deprivation trigger cancer aggressiveness, reflecting an adaptive escape mechanism underpinned by altered metabolism and protein glycosylation, providing grounds for clinical intervention.

overall_design: RNAseq profiling of T24 and 5637 cell lines exposed to normoxia or hypoxia plus glucose restriction for 24h.

first: Dylan

last: Ferreira

last: Miranda

first: Marta

last: Relvas-Santos

first: Rui

last: Freitas

first: Tim

last: S. Veth

last: Brandão

first: Eduardo

first: Paula

last: Paulo

last: Cardoso

first: Cristiana

last: Gaiteiro

first: Sofia

last: Cotton

first: Janine

last: Soares

first: Luís

last: Lima

first: Filipe

last: Teixeira

first: Rita

first: Carlos

last: Palmeira

first: Albert

last: J. R. Heck

first: Maria

last: Oliveira

first: André

last: M. N. Silva

first: Lúcio

last: Santos

first: Alexandre


title: Molecular basis for condensin enrichment at pericentromeres [Brn1 ChIP-seq Lrs4-Ycg1 2]

city: Edinburgh

first: Daniel

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

country: United Kingdom

institute: University of Edinburgh

summary: Faithful chromosome segregation requires packaging of the genome on both global and local scales. Condensin plays a crucial role at pericentromeres to resist spindle forces and ensure the oriented attachment of kinetochores to microtubules at mitosis. Here we demonstrate that budding yeast condensin is recruited to pericentromeres through a direct interaction between its Ycg1 subunit and the pericentromeric adaptor protein, shugoshin (Sgo1). We identify a Short Linear Motif (SLiM), termed CR1, within the C-terminal region of Sgo1 which inserts into a conserved pocket on Ycg1. Disruption of this interface abolishes the Sgo1-condensin interaction, prevents condensin recruitment to pericentromeres and results in defective sister kinetochore biorientation in mitosis. Similar motifs to CR1 are found in known and potential condensin binding partners and the Ycg1 binding pocket is broadly conserved, including in mammalian CAP-G proteins. Overall, we uncover the molecular mechanism that targets condensin to define a specialized chromosomal domain.

overall_design: To determine whether direct Lrs4-Ycg1 binding is responsible for condensin (Brn1) recruitment to rDNA regions

first: Menglu

last: Wang

first: Adele

last: Marston


title: A hypoxia-responsive tRNA-derived small RNA confers renal protection via RNA autophagy

city: Santa Cruz

first: Todd

last: Lowe

state: CA

address: 1156 High St

department: Biomolecular Engineering

institute: UC Santa Cruz

type: Non-coding RNA profiling by high throughput sequencing

summary: Emerging studies have revealed diverse cellular functions of tRNA-derived small RNAs (tsRNAs, or tDRs). Here, we show that a hypoxia-induced tDR, derived from the 3’ end of tRNA-Asp-GTC (tRNA-Asp-GTC-3’tDR), activates, while its inhibition blocks autophagic flux in kidney cells. Functional gain/loss-of-function studies in murine kidney disease models demonstrate a significant reno-protective function of tRNA-Asp-GTC-3’tDR. Mechanistically, tRNA-Asp-GTC-3’tDR assembles stable G-quadruplex structures and sequesters pseudouridine synthase PUS7, preventing catalytic pseudouridylation of histone mRNAs. The resulting pseudouridylation deficiency directs histone mRNAs to the autophagosome-lysosome pathway, triggering RNA autophagy. We confirm this tDR-induced RNA autophagy pathway in murine and human kidney diseases. Together, our findings identify a novel role for tRNA-Asp-GTC-3’tDR in regulating RNA autophagy in kidney cells to maintain homeostasis and protect against kidney injury.

overall_design: Small RNA-seq profiling HEK cells transfected with a 3' tRNA-Asp tDR or scrambled control.

first: Guoping

last: Li

first: Lingfei

last: Sun

first: Cuiyan

last: Xin

first: Tian

last: Hao

first: Prakash

last: Kharel

first: Aidan

middle: C

last: Manning

first: Christopher

middle: L

last: O'connor

first: Henry

last: Moore

first: Shuwen

last: Lei

first: Priyanka

last: Gokulnath

first: Xinu

last: Yang

first: Ritin

last: Sharma

first: Krystine

last: Garcia-Mansfield

first: Priyadarshini

last: Pantham

first: Chunyang

last: Xiao

first: Hanna

first: Emeli

last: Chatterjee

first: Seungbin

last: Yim

first: Leo

middle: B

last: Ren

first: Michail

last: Spanos

first: Hua

last: Zhu

first: Haobo

first: Ji

first: James

last: Markmann

first: Louise

last: Laurent

first: John

last: Rossi

first: Oluwaseun

last: Johnson-Akeju

first: Quanhu

last: Shen

first: Ravi

last: Shah

first: William

last: Goddard III

first: Pavel

last: Ivanov

first: Patrick

last: Pirrotte

first: Markus

last: Bitzer

first: Joseph

last: Bonventre

first: Saumya

last: Das


title: Infiltration-RNAseq reveals enhanced defense responses in Nicothiana benthamiana leaves overexpressing the banana MaWRKY45 gene

city: Mérida

first: Sergio

last: García

state: Yucatán

department: Biotechnology

country: Mexico

institute: Centro de Investigación Científica de Yucatán A. C.

summary: Members of the WRKY transcription factor (TF) family play a crucial role in regulating plant defense responses to biotic stress.  Here, we report that the constitutive overexpression of the banana MaWRKY45 gene in the leaves of the model plant Nicotiana benthamiana enhances the transcript levels of immune response genes. Among the genes that were up-regulated, we identified those involved in PAMP-triggered immunity, effector-trigger immunity and systemic acquired resistance, among others. These results provide insights into the molecular mechanisms triggered downstream of a single TF such as the banana MaWRKY45. Our findings suggest that MaWRKY45 is a promising candidate for banana breeding programs focused on enhancing disease resistance.

overall_design:
1.      To investigate the mechanism triggered downstream of the banana MaWRKY45 transcription factor, we overexpressed the cDNA coding secuence of the gene in leaves of Nicothiana benthamiana via agroinfiltration and then performed RNAseq.
2.      We then performed gene expression analysis using data obtained from the mock treatment samples and the overexpression of MaWRKY45 samples after three days of agroinfintration.
3.      Comparative gene expression analysis of RNAseq data from mock and MaWRKY45 overexpression samples.

last: García-Laynes

first: Carlos

last: Calderón-Vázquez

last: Puch-Hau

first: Virginia

middle: A

last: Herrera-Valencia

first: Santy

last: Peraza-Echeverria


title: A fetal oncogene NUAK2 is an emerging target in glioblastoma

city: La Jolla

first: Stacey

middle: Marie

last: Glasgow

state: California

address: 9500 Gilman Dr, 3216 Pacific Hall

institute: University of California San Diego

summary: Glioblastoma Multiforme (GBM) is the most prevalent and highly malignant form of adult brain cancer characterized by poor overall survival rates. Effective therapeutic modalities remain limited, necessitating the need for novel treatments. Neurodevelopmental pathways have been implicated in glioma formation, with key neurodevelopmental regulators being re-expressed or co-opted during glioma tumorigenesis. Here we identified a serine/threonine kinase, NUAK family kinase 2 (NUAK2), as a fetal oncogene in mouse and human brains. We found robust expression of NUAK2 in the embryonic brain that decreases throughout postnatal stages and then is re-expressed in malignant gliomas. However, the role of NUAK2  in GBM tumorigenesis remains unclear. Here, we demonstrate that CRIPSR-Cas9 mediated NUAK2 deletion in GBM cells results in suppression of proliferation and migration, while overexpression leads to enhanced proliferation and migration in both in vitro and in vivo models. Further investigation of the downstream biological processes dysregulated in the absence of NUAK2 reveals that NUAK2 modulates extracellular matrix (ECM) components to facilitate migratory behavior. Lastly, we determined that pharmaceutical inhibition of NUAK2 is sufficient to impede the proliferation and migration of malignant glioma cells. Our results suggest that  NUAK2 is an actionable therapeutic target for GBM treatment.

overall_design: Bulk RNA-sequencing of NUAK2-WT and NUAK2-CR U251 cell lines.

first: Hanhee

last: Jo

first: Aneesh

last: Dalvi

first: Wenqi

last: Yang

first: Elizabeth

last: Morozova

first: Sarah

last: Munoz


title: Somatic mutations distinguish melanocyte subpopulations in human skin

city: San Francisco

first: Alan

middle: Hunter

last: Shain

address: 2340 Sutter St. N326

department: Dermatology

institute: University of California, San Francisco

summary: To better understand the homeostatic mechanisms governing melanocytes, we performed deep phenotyping of single-cell expansions of melanocytes from human skin. In total, we interrogated the mutational landscapes, gene expression profiles, and morphological features of 297 melanocytes from 31 donors. To our surprise, a population of melanocytes with low mutation burden was maintained in sun damaged skin. These melanocytes were more stem-like, smaller, and less dendritic than their counterparts with high mutation burdens. We used single-cell spatial transcriptomics (10X Xenium) to reveal the spatial distribution of melanocytes inferred to have low and high mutation burdens (LowMut and HighMut cells), based on their gene expression profiles. LowMut melanocytes were found in hair follicles as well as in the interfollicular epidermis, whereas HighMut melanocytes resided almost exclusively in the interfollicular epidermis. We propose that melanocytes in the hair follicle occupy a privileged niche, protected from UV radiation, but periodically migrate out of the hair follicle to replenish the interfollicular epidermis after waves of photodamage. More broadly, our study illustrates the advantages of a cell atlas that includes mutational information, as cells can change their cellular states and positional coordinates over time, but mutations are like scars, providing a historical record of the homeostatic processes that were operative on each cell.

overall_design: We used the Xenium analyzer (10X Genomics) to interrogate the localization of melanocytes with high and low mutation burdens in human skin. The Xenium platform measures spatial expression patterns across hundreds of transcripts at subcellular resolution over a large field of view (up to 1x2cm). When choosing probes, we started with a generic skin panel, designed to mark common cell lineages in the skin, and supplemented it with custom targets, which included all genes upregulated in melanocytes with high and low mutation burdens (a total of 360 genes in the panel). We chose a formalin-fixed paraffin-embedded (FFPE) sample of normal skin from the back of a 63 year old male who had been diagnosed with melanoma. The skin came from the non-lesional portion (i.e. the normal, adjacent skin) of a wide excision biopsy of the patient’s melanoma.

first: Bishal

last: Tandukar

first: Delahny

last: Deivendran

middle: H


title: Molecular basis for condensin enrichment at pericentromeres [Brn1 ChIP-seq Lrs4-Ycg1]

first: Daniel

last: Robertson

first: Menglu

last: Wang

first: Adele

last: Marston


title: Immunostimulatory effects of Streptococcus sanguinis extracellular membrane vesicles protect oral gingival epithelial cells from periodontal pathobiont damage

city: Portland

first: Emily

last: Helliwell

state: Oregon

address: 3181 SW Sam Jackson Park Rd, MRB433

institute: Oregon Health and Science University

summary: Gingival epithelial cells internalize Streptococcus sanguinis EMVs within 24 hours of inoculation, resulting in an immune response that does not cause cell death.  To look at the global transcriptomic response to S. sanguinis EMVs, we performed an RNA sequencing experiment comparing SK36 EMV and PBS-inoculated TIGK cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Homo sapiens gingival epithelial cells (TIGK CRL3397) 24 hours after inoculation with either S. sanguinis SK36 EMVs (1011 per sample) or an equal volume of PBS

first: Jens

last: Kreth


title: NGLY1 mutations cause protein aggregation in human neurons

city: San Diego

first: April

middle: Elizabeth

last: Williams

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Biallelic mutations in the gene that encodes the enzyme N-glycanase 1 (NGLY1) cause a rare disease with multi-symptomatic features including developmental delay, intellectual disability, neuropathy and seizures. NGLY1’s activity in human neural cells is currently not well understood. To understand how NGLY1 gene loss leads to the specific phenotypes of NGLY1 deficiency, we employed direct conversion of NGLY1 patient-derived induced pluripotent stem cells (iPSCs) to functional cortical neurons. Transcriptomic, proteomic, and functional studies of iPSC-derived neurons lacking NGLY1 function revealed several major cellular processes that were altered, including protein aggregate-clearing functionality, mitochondrial homeostasis, and synaptic dysfunctions. These phenotypes were rescued by introduction of a functional NGLY1 gene and were observed in iPSC-derived mature neurons, but not astrocytes. Finally, laser capture microscopy followed by mass spectrometry provided detailed characterization of the composition of protein aggregates specific to NGLY1-deficient neurons. Future studies will harness this knowledge for therapeutic development.

overall_design: Examination of RNA of NGLY1 patients and control ngn2-derived neurons.

first: Andreea

last: Manole

first: Fred

last: Gage

first: Maria

last: Marchetto

middle: E


title: Effects of CREB5 overexpression on gene expression in Hepatocellular Carcinoma HepG2 cells

city: Hefei

first: anqi

last: wang

address: 218 Jixi Road

institute: The First Affiliated Hospital of Anhui Medical University

summary: In order to investigate the role of CREB5 in HCC cells and find its downstream targets, we overexpressed CREB5 by lentiviral technique and established a stable overexpressed CREB5 hepG2 cell line. Then, two groups of cells (n=3), the control group and the overexpressed group, were used for gene expression profiling.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 cells  (Vecctor, CREB5).

first: Anqi

first: Sitong

last: Yan

first: Guoping

last: Sun


title: WNT signaling contributes to the extrahepatic bile duct proliferative response to obstruction in mice

city: Ann Arbor

first: Ashley

last: Calder

state: Michigan

address: 109 Zina Pitcher Place

department: Internal Medicine

institute: University of Michigan

summary: Biliary obstruction and cholangiocyte hyperproliferation are important features of cholangiopathies affecting the large extrahepatic bile ducts (EHBD). The mechanisms underlying obstruction-induced cholangiocyte proliferation in the EHBD remain poorly understood. Developmental pathways, such as WNT signaling, have been implicated in regulating injury responses in many tissues, including the liver and bile ducts. To investigate the contribution of WNT signaling to the EHBD cholangiocyte proliferative response to obstructive injury, we conducted a comprehensive study using complementary in vivo and in vitro models with pharmacologic interventions and computational approaches. To model obstruction, we used bile duct ligation (BDL) in mice. Human and mouse biliary organoids and mouse biliary explants were used to investigate the effects of WNT activation and inhibition in vitro. We observed a rapid upregulation of WNT ligand expression associated with increased biliary proliferation following obstruction. Cholangiocytes were identified as both WNT ligand-expressing cells and WNT responsive cells. Inhibition of WNT signaling decreased cholangiocyte proliferation in vivo and in vitro, while activation increased proliferation. WNT proliferative effects on cholangiocytes were β-catenin-dependent. Our studies suggest that cholangiocyte-derived WNT ligands can activate canonical WNT signaling to induce proliferation after obstructive injury. These findings implicate the WNT pathway in injury-induced cholangiocyte proliferation within the EHBD.

overall_design: Bulk RNA-seq of extrahepatic bile duct's isolated from C57BL/6 mice 48-hours after sham or bile duct ligation surgeries.

first: Ashley N.

first: Mirabelle Q.

last: Peter

first: Theresa M.

last: Keeley

first: Nureen H.

last: Mohamad Zaki

first: John W.

last: Tobias

first: Linda C.

last: Samuelson

first: Timothy L.

last: Frankel

first: Nataliya

last: Razumilava


title: CTCF distribution around AsisI sites in IDHwt and IDHR132H DIvA cells

first: Fengchao

last: Lang

address: Convent Dr, Room 1142, Building 37

institute: NCI

summary: IDH1 mutation impacts CTCF binding and function through methylating cytosine in the CTCF binding motif. We hypothesize that the impairment of CTCF-associated DNA repair process may be relevant to the loss of CTCF chromatin association and shifts in chromatin conformation. Chromatin immunoprecipitation-sequencing confirmed the loss of CTCF coverage in the proximity sites of AsisI sites in IDH1 mutant cells.

overall_design: ChIP-seq for CTCF was performed in IDH1 wild-type and mutant DIvA cells with or without 4OHT treatment. 4C-seq with two DSB sites was performed in IDH1 wild-type and mutant DIvA cells with or without 4OHT treatment.

first: Karambir

last: Kaur

first: Haiqing

last: Fu

first: Javeria

last: Zaheer

first: Diego

last: Ribeiro

first: Mirit

middle: I

last: Aladjem

first: Chunzhang

last: Yang


title: EDF1 accelerates ganglioside GD3 accumulation to boost CD52-mediated CD8+ T cell dysfunction in neuroblastoma

city: Guangzhou

first: lei

last: Miao

address: 9#, Jinsui Road,Tianhe District

institute: Guangzhou women and children's medical center

summary: Background Heterogeneous clinical features and prognosis in neuroblastoma (NB) children are frequently dominated by immune elements. Dysfunction and apoptosis in immune cells result from the exposure to continuous tumor-related antigen stimulation and coinhibitory signals. To date, key factors pointing to the restriction of NB-specific CD8+T cells remain elusive. Methods We performed bulk-RNA sequencing and lipidomic analyses of children with mediastinal neuroblastoma. Bioinformatics analysis and validation of molecular biology assays were applied to uncover the underlying mechanism. Results Three subtypes were identified using nonnegative matrix factorization (NMF), we highlighted an apoptotic status of infiltrated CD8+T cells, along with the highest CD52 expression in Cluster3 (C3) subtypes, and verified high EDF1 expression in NB cells led to Lactosylceramide (LacCer) and downstream ganglioside-GD3 accumulation, which subsequently increased chemotaxis, CD52 and immune checkpoint expression, and apoptosis-related events in activated CD8+T cells. Mechanistically, EDF1 was recruited as a coactivator to form the NF-κB/RelA/EDF1 complex, which prevented the methylation of targeted site after binding to the promoter of GD3 synthase ST8SIA1, resulting in elevated ST8SIA1 transcription. Conclusion These findings characterizes the content of GD3 in NB cells, which is regulated by the EDF1/RelA/ST8SIA1 axis, is responsible for CD8+T cell dysfunction and inducing immune escape of NB cells. Inhibiting EDF1 may decreases suppressive factors and resolve apoptotic CD8+T cells. Controlling NB-associated GD3 levels through metabolic intervention is beneficial for tuning the depth and duration of response to current NB therapies.The integration of transcriptomic and lipidomic data provided a better understanding of the interaction between LacCer metabolites and the immune status in NB.

overall_design: RNA-seq profiling of  89 surgically resected MNB tumors. Total RNA from MNB samples were extracted for cDNA library construction and sequencing using an Illumina NovaSeq 6000 platform.

first: Di

last: Li

first: Meng

first: Zhenjian

last: Zhuo

first: Jue

last: Tang

first: Jing

last: He

first: Lei


title: WNT signaling contributes to the extrahepatic bile duct proliferative response to obstruction in mice [scRNA-seq]

first: Ashley

last: Calder

summary: Biliary obstruction and cholangiocyte hyperproliferation are important features of cholangiopathies affecting the large extrahepatic bile duct (EHBD). The mechanisms underlying obstruction-induced cholangiocyte proliferation in the EHBD remain poorly understood. Developmental pathways, such as WNT signaling, have been implicated in regulating injury responses in many tissues, including the liver and bile ducts. To investigate the contribution of WNT signaling to the EHBD cholangiocyte proliferative response to obstructive injury, we conducted a comprehensive study using complementary in vivo and in vitro models with pharmacologic interventions and computational approaches. To model obstruction, we used bile duct ligation (BDL) in mice. Human and mouse biliary organoids and mouse biliary explants were used to investigate the effects of WNT activation and inhibition in vitro. We observed a rapid upregulation of WNT ligand expression associated with increased biliary proliferation following obstruction. Cholangiocytes were identified as both WNT ligand-expressing cells and WNT responsive cells. Inhibition of WNT signaling decreased cholangiocyte proliferation in vivo and in vitro, while activation increased proliferation. WNT proliferative effects on cholangiocytes were β-catenin-dependent. Our studies suggest that cholangiocyte-derived WNT ligands can activate canonical WNT signaling to induce proliferation after obstructive injury. These findings implicate the WNT pathway in injury-induced cholangiocyte proliferation within the EHBD.

overall_design: Single-cell RNA-seq of extrahepatic bile ducts in sham and bile duct ligated mice 24-hours post-surgery.

first: Ashley N.

first: Mirabelle Q.

last: Peter

first: Theresa M.

last: Keeley

first: Nureen H.

last: Mohamad Zaki

first: John W.

first: Linda C.


title: Skatole attenuates osteoarthritis by protecting chondrocytes and mediating macrophage repolarization through regulating the NFκB/MAPK signaling pathway and metabolic reprogramming II

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

institute: Zhejiang University

summary: Osteoarthritis (OA) is the most common joint disease, but there are currently no disease-modifying OA drugs (DMOADs) yet approved by the regulatory agencies. Regulating macrophage polarization can alleviate synovial inflammation and then repair articular cartilage damage, providing a new target for OA treatment. Here, we found that Skatole can modulate macrophage polarization and attenuate OA. Skatole hindered M1 macrophage polarization while promoting M2 macrophage polarization. Mechanistically, Skatole activated Stat6, suppressed the phosphorylation of IKK, IκBα, and p65 in NFκB signaling pathway, and inhibited MAPK signaling activation. RNA-seq analysis revealed that Skatole downregulated the expression of inflammation-related genes, while upregulating genes involved in glutathione metabolism and oxidative phosphorylation, thereby reducing ROS levels and inhibiting M1 macrophage polarization. Moreover, conditional medium (CM) from M1 macrophages treated with Skatole balanced anabolism and catabolism in mouse chondrocytes while inhibiting cell apoptosis. Intriguingly, in IL1β-treated chondrocytes, Skatole directly suppressed inflammation and catabolism, without significantly affecting cell apoptosis or anabolism; In vivo experiments showed that Skatole increased M2 polarization and decreased M1 polarization of synovial macrophages, alleviated synovitis, and lessend articular cartilage damage in destabilization of medial meniscus (DMM)-induced OA mice. Our finding suggest that Skatole has the potential to function as a DMOAD.

overall_design: Expression profiling by high throughput sequencing

first: Weiyun

last: Wang


title: WNT signaling contributes to the extrahepatic bile duct proliferative response to obstruction in mice [24hr. Bulk]

overall_design: Bulk RNA-seq of whole extrahepatic bile ducts in sham and bile duct ligated mice 24-hours post-surgery.

middle: N

first: Mirabelle

middle: Q

first: Theresa

middle: M

first: Nureen

first: John

middle: W

last: Tobias

first: Linda

last: Samuelson

first: Timothy

last: Frankel

first: Nataliya

last: Razumilava


title: Tax1bp1 promotes inflammatory signaling and necrosis during Mycobacterium tuberculosis infection of alveolar macrophages

first: Jonathan

middle: Michael

last: Budzik

address: 513 Parnassus Ave.

department: Medicine

institute: UC San Francisco

summary: Crosstalk between autophagy, host cell death, and inflammatory host responses to bacterial pathogens enables effective innate immune responses that limit bacterial growth while reducing coincidental host damage. Mycobacterium tuberculosis thwarts innate immune defense mechanisms in alveolar macrophages (AMs) during the initial stages of infection and in recruited bone marrow-derived cells during later stages of infection. How protective inflammatory responses are achieved during Mycobacterium tuberculosis (Mtb) infection and the differences in these responses in macrophage subtypes are obscure. Here, we discovered that the autophagy receptor Tax1bp1 plays a critical role in enhancing inflammatory cytokine production and promoting the susceptibility of mice to infection with Mtb. These results were surprising because Tax1bp1 instead restricts Mtb growth during infection of bone marrow-derived macrophages (BMDMs), as we previously showed (Budzik et al. 2020), and terminates cytokine production in response to cytokine stimulation or viral infection. Tax1bp1 also leads to increases in bacterial growth and inflammatory responses during infection of mice with Listeria monocytogenes, an intracellular pathogen that is not effectively targeted to canonical autophagy. In contrast to its role in restricting Mtb growth in BMDMs, Tax1bp1 promotes Mtb growth in AMs, neutrophils, and recruited monocyte-derived cells from the bone marrow. In Mtb-infected AMs, Tax1bp1 enhances necrosis and inflammatory cytokine synthesis while restraining apoptosis, changing the mode of host cell death to favor Mtb replication. Similar to Tax1bp1-deficiency in AMs, the expression of phosphosite-deficient Tax1bp1 restricts Mtb growth. Together, these results show that Tax1bp1 plays a crucial role in linking the regulation of autophagy, cell death, and pro-inflammatory host responses to augment susceptibility to bacterial infection.

overall_design:
Primary murine alveolar macrophages from wild-type and Tax1bp1-deficient C57Bl/6 mice were infected ex vivo with M. tuberculosis at a multiplicity of infection of 2.
36 hours post-infection, samples were lysed in Trizol reagent for subsequent RNA purification.
Three independent biological replicate infections were performed.

first: Jeffrey

last: Chin


title: Chromatin bound transcriptome of hESCs

city: Toronto

first: Kirti

last: Mittal

state: Ontario

address: Santos Lab, 25 Orde Street, Room 6-1001 MRS

country: Canada

institute: Lunenfeld-Tanenbaum Research Instit

summary: In this study, we performed RNA-seq to compare chromatin transcriptomes in primed and naive hES cells.

overall_design: RNA-seq in chromatin fractions of RSeT and primed hESCs were done

first: Miguel

last: Ramalho-Santos


title: Gene expression analysis of T-cell leukemia/lymphoma associated mutations of PLCG1 in Hut78 cells

city: New Haven

first: Longhui

last: Zeng

state: CT

address: Yale University, 333 Cedar Street, SHM-C-434 Su lab

department: Cell biology

institute: Yale University

summary: The most frequently mutated gene PLCG1 was identified in Adlut T-cell leukemia/lymphoma patients. Here, we employed bulk RNA-seq analysis to clariy regulated genes and signaling pathways of PLCG1 mutations in Hut78 cells. We further defined unique genes and pathways for PLCG1 mutation by comparing to T cell receptor stimulation group.

overall_design: PLCG1-GFP wild type (WT), R48W, S345F, and D1165H mutations were respectally introduced into human T-cell lymphoma Hut78 cell line by lentivirus.  Flow cytometry was used to sort satble expression cell lines using GFP channel. T cell receptor stimulation group: PLCG1 wild type Hut78 cells were activated by anti-CD3/CD28 antibodies for 3 days.

first: Xiaolei

last: Su


title: Epitope tagging with genome editing in mice reveals that the proton channel OTOP1 is apically localized and not restricted to Type III “sour” taste receptor cells

city: Los Angeles

first: Wenlei

last: Ye

address: HNB 301, 3641 Watt Way

institute: University of Southern California

summary: The gustatory system allows animals to assess the nutritive value and safety of foods prior to ingestion. The first step in gustation is the interaction of taste stimuli with one or more specific sensory receptors, that are generally believed to be present on the apical surface of the taste receptor cells. However, this assertion is rarely tested. We recently identified OTOP1 as a proton channel and showed that it is required for taste response to acids (sour) and ammonium. Here we examined the cellular and subcellular localization of OTOP1 by tagging the endogenous OTOP1 protein with an N-terminal HA epitope (HA-OTOP1).  Using the HA-OTOP1 mouse and high-resolution imaging, we show that OTOP1 is strictly localized to the apical tips of taste cells throughout the tongue and oral cavity. Interestingly, immunoreactivity is observed in the actin-rich taste pore above the tight junctions defined by Zonula Occludens-1 (ZO-1) and also immediately below these junctions. Surprisingly, OTOP1 immunoreactivity is not restricted to Type III taste receptor cells (TRCs) that mediate sour taste but is also observed in glia-like Type I TRCs proposed to perform housekeeping functions, a result that is corroborated by scRNA-seq data.  The apical localization of OTOP1 supports the contention that OTOP1 functions as a taste receptor and suggests that OTOP1 may be accessible to orally available compounds that could act as taste modifiers.

overall_design: Taste cells from the circumvallate papillae (CV) of mice were isolated by removing the epithelial cell layer from the tongue and trimmed to remove excess epithelial cells. Single cells were isolated via enzymation, trituration and used for scRNA sequencing.

first: Joshua

middle: P

last: Kaplan

first: Heather

last: Kileen

first: Ziyu

last: Liang

first: Anne

last: Tran

first: Jingyi

last: Chi

first: Chinwen

last: Yang

first: Paul

last: Cohen

first: Emily

middle: R

last: Liman


title: Detecting gene copy number alterations by comprehensive genomic profiling: a comparative study in a real-world series of FFPE tumor samples

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: Copy number alterations (CNAs) play a fundamental role in cancer development and constitute a potential tool for tailored treatments. The CNAs recognition in formalin fixed paraffin embedded (FFPE) material, to date, relies on fluorescence in situ hybridization, but the introduction of large-scale next-generation sequencing (NGS) has dramatically improved their discovery at genome-wide level. The detection of CNAs by NGS in FFPE material is, nonetheless, a complex issue, which still requires validation studies. Herein, the CNAs detection by a widely used NGS assay (Oncomine Comprehensive Assay plus®, OCA+) were evaluated in 14 FFPE samples mirroring diagnostic daily practice and compared to a whole-genome assay. OCA+, a targeted DNA panel, showed lower CNAs detection sensitivity and equal specificity for gains and losses. According to proprietary software pipeline, OCA+ accurately identify gains characterized by CN ≥5,2. A much less robust threshold (CN ≤1.18) was identified that maximized the difference between true and false positive losses. Orthogonal FISH tests validated seven CNAs characterized by CN gain ≥6 or complete loss.  Considering the CNAs growing significance in precision medicine, our findings further prompt towards a robust validation of NGS detection in FFPE materials.

overall_design: The current molecular diagnostic procedure in our laboratories relies on the amplicon-based Oncomine Comprehensive Assay plus® (OCA+) targeted gene panel (Thermofisher), which beyond the identification of SNVs, tumor mutational burden and microsatellite instability also allows the detection of genes with gain, loss and loss of heterozygosity (LOH) in shorter time than other commercially available target gene panels, compliant with the turn-around-time and the costs for NGS analyses required by the National and Regional healthcare systems. Considering the potential use of NGS as a method for CNAs discovery, the assessment of its accuracy in FFPE material obtained in daily practice conditions must be considered a milestone. To this end, OCA+ performance was investigated in 14 samples from diagnostic routine and results were compared to those obtained using the Whole Genome Array (WGA) OncoScan® (OCS) [8], which has been already successfully validated for CNAs detection in FFPE samples [9, 10]. Potentially “druggable” alterations were investigated by fluorescence in situ hybridization (FISH).

first: Fabio

last: Bozzi

first: Elena

last: Conca

first: Marco

last: Silvestri

first: Gianpaolo

last: Dagrada

first: Alice

last: Ardore

first: Donata

last: Penso

first: Daniele

last: Lorenzini

first: Chiara

middle: C

last: Volpi

first: Desiré

middle: V

last: Trupia

first: Adele

last: Busico

first: Iolanda

last: Capone

first: Federica

last: Perrone

last: Tamborini

first: Andrea

last: Vingiani

first: Giancarlo

last: Pruneri


title: Oxidation of thymine by TET2 dioxygenase carrying leukemia-derived neomorphic mutations

city: Shanghai

first: Dan

last: Zhou

address: 131 Dong 'an Road, Xuhui District

institute: Fudan University

summary: TET enzymes oxidize 5-methylcytosine (mC) in DNA, contributing to the regulation of gene transcription and genome functions. Deficiency of TET2 promotes the development of clonal hematopoiesis and various blood cancers, yet the mechanism by which TET2 mutations facilitate tumorigenesis remains to be explored. Here, we report that a subset of TET2 mutations identified in leukemia patients alter the substrate specificity of TET2 from acting on mC to thymine. This neomorphic activity results from substitutions at key residues involved in the interactions with the mC base, including Asn1387 and His1904. Recombinant human TET2 proteins harboring the mutation of these residues can catalyze the oxidation of thymine to 5-hydroxymethyluracil (hmU) and 5-formyluracil (fU). Exogenous expression of the TET2 Asn1387Thr (N1387T) mutant in transfected cells leads to hmU accumulation, with the highest level in cells lacking SMUG1-initiated base excision repair pathway. Endogenous knock-in of N1300T, the murine equivalent of N1387T, in mouse embryonic stem cells induces hmU production, causing DNA lesions and transcriptional activation of DNA damage response genes. These findings suggest that certain patient-derived TET2 mutations acquire unexpected gain-of-functions beyond an impairment in mC oxidation, and thymine oxidation by the neomorphic mutants may impose risks to genome stability, presumably contributing to malignant transformation.

overall_design: To further characterize the consequences of N1300T mutant expression, we performed RNA sequencing for Tet2 WT, N1300T, and KO ES cells. Principal Component Analysis (PCA) showed that the mRNA expression profile in N1300T cells was significantly different than that of WT and KO cells

first: Guangbo

last: Jin

first: ShaoQin

last: Rong

first: YuShuang

last: Wu

first: DongRui

last: Yin

first: Xiao

last: Ding

first: ZhouHao

last: Deng

first: MengYao

last: Sheng

first: Hai

last: Gao

first: GuoLiang

last: Xu


title: Obesity and adverse SDoH impact NK cell function

city: Bethesda

first: Neelam

last: Redekar

address: 9000 rockville pike

department: NIAID

institute: NIH

summary: African American (AA) women are disproportionally affected by obesity, particularly in the setting of adverse social determinants of health (aSDoH), which contribute to cardiovascular disease (CVD) and cancer disparities. Obesity and aSDoH appear to impair Natural Killer cells (NKs), which are critical in the innate immune response; however, the underlying mechanisms are largely unknown. We sought to investigate signaling pathways involved in NK dysfunction related to obesity in AA women from under-resourced neighborhoods disproportionately exposed to aSDoH. We determined in freshly isolated NK cells that obesity and higher social isolation, as well as higher depression and lower socioeconomic status, are associated with a shift in NK cell subsets away from CD56dim/CD16+ cytotoxic NK cells. Using ex vivo data, we identified LDL as a serum marker related to NK cell function in an AA population from under-resourced neighborhoods.  Additionally, NK cells from AA women with obesity and LDL-treated NK cells displayed a loss in NK cell function. Comparative unbiased RNA sequencing analysis revealed DUSP1-dependent signaling as a common factor. Subsequent experiments involving chemical inhibition of DUSP1 signaling and DUSP1 overexpression in NK cells highlighted the significance of DUSP1 in lysosome biogenesis and, ultimately, NK cell function. Our data demonstrate a pathway by which obesity in the setting of aSDoH may relate to NK dysfunction, making DUSP1 an important target for further investigation of CVD and cancer disparities.

overall_design: The NK cells from the indicated age-matched AA women with and without obesity, and after overnight exposure to either LDL or empty vector were used for gene expression profiling. Dusp1 overexpressing NK92 cells were examined against the NK92 control cell line to study Dusp1 regulation.

first: Yvonne

last: Baumer

first: Tiffany

last: Powell-Wiley


title: Transcriptome analysis in the olfactory bulb of high-fat diet-fed mice

city: Hwasun, Jeollanam-do

first: Young-Kook

last: Kim

address: 264, Seoyang-ro

department: Department of Biochemistry

country: South Korea

institute: Chonnam National University Medical School

summary: Metabolic imbalance contributes to cognitive impairment, anxiety, depressive behavior, and impaired olfactory perception. As the synaptic signal from the olfactory bulb is directly transmitted to memory consolidation-related brain regions, recent studies have focused on the study of olfactory dysfunction in patients with obesity and diabetes accompanied by cognitive dysfunction. In this study, we investigated the transcriptomic change of olfactory bulb in high-fat diet-fed mice compared to that of normal diet-fed mice. We sampled olfactory bulbs from high fat diet mice, performed RNA sequencing, and measured protein and mRNA levels in olfactory bulb tissue. Also, we tested cytokine secretion in blood plasma of high fat diet mice. We found differences in the expression of protein-coding mRNAs and non-coding RNAs involved in insulin, lipid metabolism, neurogenesis, serotonin, dopamine, and gamma-aminobutyric acid-related signaling in the olfactory bulb of high-fat diet-fed mice compared to control mice. Our analyses suggest diverse targets for the treatment of olfactory dysfunction related to various neuropathologies in patients with metabolic syndrome.

overall_design: We sampled olfactory bulbs from normal fat diet (NFD) or high fat diet (HFD)-fed mice, performed RNA sequencing, and measured protein and mRNA levels in olfactory bulb tissue.

first: Danbi

last: Jo

first: Seoyoon

last: Choi

first: Juhyun

last: Song


title: Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization [RNA-seq]

city: Hong Kong

first: QIANG

last: SUN

address: Ngan Shing Street

department: Department of Orthopaedics and Traumatology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Mammalian genome is hierarchically organized by CTCF and cohesin through loop extrusion mechanism to facilitate the organization of topologically associating domains (TADs). Mounting evidence suggests additional factors/mechanisms exist to orchestrate TAD formation and maintenance. In this study, we investigate the potential role of RNA binding proteins (RBPs) in TAD organization. By integrated analyses of global RBP binding and 3D genome mapping profiles from both K562 and HepG2 cells, our study unveils the prevalent enrichment of RBPs on TAD boundaries and define boundary associated RBPs (baRBPs). We found that baRBP binding is correlated with enhanced TAD insulation strength and in a CTCF independent manner. Moreover, baRBP binding is associated with nascent promoter transcription. Additional experimental testing was performed using RBFox2 as a paradigm. Knockdown of RBFox2 in K562 cells causes moderate TAD reorganization. Moreover, RBFox2 enrichment on TAD boundaries is a conserved phenomenon in C2C12 myoblast (MB) cells. RBFox2 is down-regulated and its bound boundaries are remodeled during MB differentiation into myotubes (MTs). Finally, transcriptional inhibition indeed decreases RBFox2 binding and disrupts TAD boundary insulation. Altogether, our findings demonstrate that RBPs can play active role in modulating TAD organization through co-transcriptional association and synergistic action with nascent promoter transcripts.

overall_design: RNA-seq: K562 scNC vs siRBFox2

first: Huating

last: Wang

first: Qiang

last: Sun

first: Qin

last: Zhou