title: Effects of dietary postbiotic on growth performance hematological parameters and liver transcriptome of calves

city: Nakhon Ratchasima

first: Chao

last: Ban

address: 111 University Avenue Muang,

country: Thailand

institute: Suranaree University of Technology

summary: This study aimed to investigate the effect of postbiotic from dead cell Lactobacillus ingluviei CR37 on growth performance, antioxidant capacity, and liver transcriptional response of calves. Fourteen Holstein bull calves were assigned to 2 treatment groups: CON (n = 7) or DCLI (n = 7, fed 1 g/d of dead cell Lactobacillus ingluviei CR37 strain, containing 108 CFU/g). Calves received milk replacer (MR) at 1.75% of BW (based on air-dry weight) and the amount was adjusted weekly according to body weight, while fresh and clean water was provided ad libitum. All calves had free access to starter starting on day 33. On day 82, the MR solution was reduced to 50% of the previous week's allocation, and calves were completely weaned by day 89. Liver samples were collected after slaughter on day 90. Transcriptome analysis identified 33 DEGs, including 16 upregulated DEGs such as Endothelial lipase (LIPG), Peroxisomal Acyl-CoA oxidase 1 (ACOX1), Solute carrier family 27 member 6 (SLC27A6), and 17 downregulated DEGs such as Family with sequence similarity 107 member A (FAM107A), 4-Hydroxy-2-oxoglutarate aldolase 1 (HOGA1), Farnesyl diphosphate synthase (FDPS). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 11 significant pathways, including the PPAR signaling pathway and Pentose phosphate pathway. Taken together, postbiotic supplementation demonstrated potential benefits in improving lipid metabolism and mitigating oxidative stress in weaning calves.

first: Supreena

last: Srisaikham

first: Guilan

last: Wen

first: Xingzhou

last: Tian

first: Pipat

last: Lounglawan


title: Resilient CD133+CD24+ Kidney Progenitor Cells Drive Hypoxic Injury Recovery via HIF1A, EGFR, and EDN1 Expression

status: Public on Apr 03 2025

city: Grand Forks

first: Sonalika

last: Singhal

state: NS

address: 1301 N Columbia Rd

department: Pathology

country: USA

institute: University of North Dakota

type: Expression profiling by high throughput sequencing

summary: Kidney progenitor cells play a crucial role in the repair and regeneration of renal tubules following injury. This study investigates the differential responses of human renal tubular precursor TERT (HRTPT) CD133+CD24+ kidney progenitor cells and Human renal epithelial cell 24 TERT (HREC24T) CD133-CD24+ non-progenitor cells to hypoxic conditions, as well as their gene expression profiles. Whole transcriptome sequencing revealed distinct molecular characteristics, with HRTPT cells exhibiting enrichment in pathways associated with human and mouse embryonic stem cell pluripotency and hypoxia response. In vitro experiments demonstrated that HRTPT cells are more resistant to hypoxia, showing minimal cell death and a 100-fold increase in HIF1A protein levels. In contrast, HREC24T cells exhibited significant cell death and only a modest increase in HIF1A protein. Functional network analysis identified a central role for Endothelin-1 (EDN1) in the interaction between HIF1A and epidermal growth factor (EGF) signaling pathways. These results suggest that CD133+CD24+ kidney progenitor cells have enhanced survival mechanisms under hypoxic stress, enabling them to effectively proliferate and replace damaged tubular cells. This study provides novel insights into the protective role of kidney progenitor cells in renal injury and their potential therapeutic applications in kidney regeneration

overall_design: to investigate the differences between HRTPTprogrnitor  and HREC24T non-progenitor cells response to hypoxia

first: Sarmad

last: Al-Marsoummi

first: Donald

last: Sens

first: Seema

last: Somji

first: Scott

last: Garret

first: Sandeep


title: Heterogeneity in Somatic Cell Nuclear Transfer Embryo Reprogramming Across Mammalian Species

city: Urumchi

first: weijian

last: li

address: 311 East Nongda Road

country: China

institute: Xinjiang Agricultural University

summary: Somatic cell nuclear transfer (SCNT) enables the reprogramming of terminally differentiated somatic cells into a totipotent state, yet whether this process is governed by conserved mechanisms across mammalian species remains poorly understood. Here, we employed low input transcriptomics to profile global transcriptional dynamics during zygotic genome activation in SCNT embryos from five species: mouse, pig, cattle, goat, and sheep. Our analysis revealed distinct genome-wide expression patterns among these species, with 70.17% of differentially expressed genes (DEGs) being species-specific, while only 9.17% were shared DEGs. Functional annotation of the shared DEGs highlighted their enrichment in processes such as mRNA transcription, translation, and carbohydrate metabolism. Notably, we observed widespread pathway overactivation in SCNT embryos from cattle, mouse, and pig, whereas goat and sheep SCNT embryos exhibited broad suppression. Furthermore, weighted gene co-expression network analysis (WGCNA) demonstrated that species-specific effects exerted a far greater influence on reprogramming outcomes than the method of embryo generation (Fertilization or SCNT). Through systematic identification of key transcription factors, signaling pathways, epigenetic markers, and alternative splicing events, we uncovered species-specific regulatory patterns underlying reprogramming. Additionally, genome browser analysis revealed regional chromosomal expression anomalies in GDF9 and BMP15 during reprogramming across species. Collectively, our findings provide critical insights into the divergent mechanisms of reprogramming in mammalian species and establish a robust theoretical foundation for future studies in this field.

overall_design: Sheep IVF (three replicates) and SCNT 8-cell (four replicates) embryos were studied using RNA-seq.Data was sequenced using Illumina NovaSeq 6000

first: Weijian

last: Li

first: Xuguang

last: Wang


title: SARS-CoV-2 Infection Induces Pro-Fibrotic and Pro-Thrombotic Lipid-Laden Foam Cell Formation

city: Chapel Hill

first: Victor

last: Garcia

state: North Carolina

address: 120 Mason Farm Rd CB #7042

department: Division of Infectious Diseases

institute: University of North Carolina at Chapel Hill

summary: SARS-CoV-2 is the causative agent of COVID-19 and long COVID, two illnesses characterized by a dysregulated immune response. Macrophages have long been considered a key component of the dysregulated immune response occurring during severe cases of COVID-19 and long COVID. Using humanized mice implanted with human lung tissue, we demonstrate that macrophage replication is induced by SARS-CoV-2 infection which also promotes macrophage enlargement and the formation of lipid laden cells. Notably, we show that enlarged macrophages display a pro-fibrotic and pro-thrombotic phenotype. Even after immune-mediated clearance of replication competent virus, macrophage numbers remained elevated, and lung fibrosis and thrombi formation were still present. Importantly, we also showed that pre-exposure prophylaxis or early treatment with a SARS-CoV-2 antiviral, EIDD-2801, was able to reduce macrophage expansion and prevent COVID-19 mediated lung pathology such as fibrosis by reducing collagen deposition and decreasing smooth muscle actin, a biomarker of fibrosis. Elevated macrophage numbers were observed in a mouse-adapted SARS-CoV-2 model, and enlarged macrophage were elevated in a non-human primate model of SARS-CoV-2 infection, and in cadaveric human lung samples from SARS-CoV-2 infected individuals.  We postulate that SARS-CoV-2 infection induces the production of foam cells which in turn contribute to pathology associated with COVID-19 including thrombi formation.

overall_design: Mice with implanted human lung tissue (LOM) were used as an in vivo model to evaluate the infection of lung tissue with the  coronaviruses  SARS-CoV-2. Viruses were directly injected into the human lung tissue of LOM mice, and lung tissue was collected 2, 6 or 14days after exposure to determine virus titre and/or for analysis by histology, electron microscopy or transcriptome characterization use the GeoMx platform. GeoMX sequencing was completed only on day 0, 2, or 6.

first: Diana

middle: M

last: Battaglia

first: Ralph

middle: S

last: Baric

first: Corbin

middle: D

last: Jones

first: Angela

middle: R

last: Wahl

first: Edward

middle: P

last: Browne

first: J

middle: V


title: Mechanical Loading remodels transcriptional regulation in Osteocytes through Nucleus translocation of NRF2 [ChIP-seq]

city: Nanjing

first: Yue

last: Guo

address: No. 22, Hankou Road, Nanjing, China

institute: NanJing University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The mechano-responsiveness of osteocytes is critical for maintaining bone health, yet the molecular mechanisms underlying this process remain poorly understood. Here, we investigate the impact of mechanical loading on transcriptional and epigenetic remodeling in osteocytes. Using MLO-Y4 cells, we subjected osteocytes to mechanical loading and profiled their transcriptome and histone modifications. Our findings revealed significant transcriptional and epigenetic changes, with NRF2 emerging as a key regulator. We demonstrated that mechanical loading stabilizes NRF2 protein levels and promotes its nucleus translocation, leading to enhanced genomic binding of NRF2 and activation of its target genes. Further analysis confirmed cell type-specific functions of NRF2, with distinct binding profiles in osteocytes compared to astrocytes. These results highlight the pivotal role of NRF2 in the mechano-responsiveness of osteocytes. Unlike pharmacologic agents that stabilize NRF2, mechanical loading uniquely promoted NRF2 nucleus translocation and transcriptional activity. This underscores the irreplaceable role of mechanical stimuli, such as exercise, in promoting bone health. This study advances our understanding of osteocyte mechanotransduction and identifies potential therapeutic interventions for bone diseases.

overall_design: For the loaded group, MLO-Y4 cells were plated onto UniFlex™ Culture Plates coated with type I collagen (Flexcell International Corporation), which are 6-well plates with a soft silicone rubber membrane at the bottom of each well. When the cells reached 60% confluency, the plates were subjected to the Flexcell FX5000 Tension System and treated with equiaxial dynamic stretching at 0.5 Hz and 20% strain for 12 hours. For the unloaded group, , MLO-Y4 cells were plated onto 6-well cell culture plate (Corning). When the cell density reached 60% confluency, the plates were transferred to the cell incubator of the Flexcell FX5000 Tension System for 12 hours, serving as the control group. MLO-Y4 cells of each group were fixed by 1% formaldehyde solution (Sigma, F8775-25ML) and quenched with 1.25M glycine (Amresco, 200-272-2). Chromatin was collected and sheared using the Bioruptor Plus with 30 seconds on and 30 seconds off for 18 cycles. Immunoprecipitation was performed using 3–5 μg of H3K27ac (Abcam, ab4729); H3K4me3 (Abcam, ab8580) or NRF2 (Proteintech, 80593-1-RR) antibodies. DNA was purified using the DNA Clean & Concentrator-5 kit (Zymo, D4014). Libraries were then constructed from ChIP samples using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, E7370) and sequenced on a NovaSeq by Annoroad Gene Tech (Beijing) Co., Ltd. Two biological replicates were performed for each group.

first: Jing

last: Zhang

first: Zhaojun

last: Liu

first: Luyu

last: Gong

first: Qiaoqiao


title: Complement Activation Drives a Metastatic Phenotype of Ovarian Cancer Cells Co-Cultured with Adipocytes

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

summary: Background: The preferred site of metastasis in ovarian cancer (OC) is the fat-rich omentum. The interaction between cancer cells and adipocytes induces transcriptomic changes driving an invasive and pro-metastatic phenotype. Here we studied the effects of the OC cell-adipocyte crosstalk by using direct co-culture with immortalized human visceral pre-adipocytes and OC cells. Methods:  OVCAR5 or OVCAR8 OC cells expressing either GFP or RFP were co-cultured with matured immortalized visceral pre-adipocyte (VNPAD). After direct co-culture, OC cells were FACS-sorted and cell proliferation, invasiveness, resistance to cisplatin were assessed. RNA-sequencing determined transcriptomic changes induced by co-culture.  Immunohistochemistry (IHC) and ELISA measured C3 expression in metastatic tumors and in malignant ascites.  Results: Direct co-culture with VNPAD led to increased proliferation, invasiveness and resistance to cisplatin of OC cells compared to  monoculture. RNA-sequencing revealed 205 differentially expressed genes (DEGs) common to both VNPAD co-cultured OVCAR5 and OVCAR8 cells and enriched pathways such as PI3K/AKT and complement activation. Co-culture induced lipid transfer into OC cells promoted upregulation of complement C3 and C5 units, as measured at mRNA and protein levels. C3 or C5 inhibition reverted the invasive phenotype of OC cells and C3 knockdown reduced tumor progression in a xenograft model. Increased C3 expression was detected in metastatic vs. primary ovarian tumors (p<0.0001)  and increased C3 secretion was observed in ascites from women with BMI > 25 (p = 0.01). C3 upregulation in OC cells was driven through activation of stress response pathway regulated by ATF4. Conclusions: Co-culture of adipocytes and cancer cells drives an invasive and chemo-resistant phenotype. These changes are induced by transfer of lipids from adipocytes to cancer cells causing activation of the complement proteins C3, C5, and  of the integrated stress response pathway.

overall_design: To study the interaction between adipocytes and ovarian cancer cells, we perform RNA-seq analysis of co-cultures. We co-cultured OC cells with adipocytes in proximity for 3 days. Cells were then separated using FACS sorting, and RNA was extracted for RNA-seq analysis. We compared OVCAR8 co-cultured vs OVCAR8 on monoculture (n=2). Later we compared OVAR5 co-cultured vs OVCAR5 on monoculture (n=2) to study the difference between cell lines when co-cultured with adipocytes.

first: Andres

last: Valdivia

first: Horacio

last: Cardenas

first: Ana

last: Isac

first: Guangyuan

last: Zhao

first: Yaqi

first: Hao

last: Huang

first: Jian-Jun

last: Wei

first: Mauricio

last: Cuello-Fredes

first: Sumie

last: Kato

first: Fernán

last: Gómez-Valenzuela

first: Aloysius

last: Klingelhutz


title: Early exercise disrupts a pro-repair extracellular matrix program during zebrafish fin regeneration

city: Eugene

first: Victor

last: Lewis

state: OR

address: 1229 University of Oregon 1318 Franklin Blvd.

department: Institute of Molecular Biology

institute: University of Oregon

summary: Understanding how mechanical stimulation affects cellular behaviors during tissue regeneration offers valuable insight into the mechanisms that regulate injury repair. We incorporated a swim tunnel exercise regimen during zebrafish caudal fin regeneration to explore exercise loading impacts on a robust model of tissue regeneration. Early exercise loading, initiated before or during blastema formation, resulted in reduced regenerative outcomes. Long-term tracking of fluorescently labeled cell lineages showed exercise loading disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated loading reduced an extracellular matrix (ECM) gene expression program, including for hyaluronic acid (HA) synthesis. Like exercise loading, HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury-upregulated HA establishes a pro-regenerative environment facilitating mechanotransduction.  HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes-associated protein (Yap). Further, exercise loading or HA depletion decreased nuclear Yap and Proliferative Cell Nuclear Antigen staining. We conclude early loading during fin regeneration disrupts expression of an HA-rich ECM supporting blastema expansion. Our study of mechanical loading during fin regeneration reveals a stage-dependent response similar to that seen in mammalian skeletal repair, where early exercise—applied during blastema establishment—impairs regeneration, while delayed loading during outgrowth does not, suggesting a conserved sensitivity to the timing and intensity of mechanical stimuli in regenerative processes.

overall_design: RNAseq profiling of 3 day post amputation fin regenerate blastema tissue following either swimming exercise (exp) or unexercised controls (control)

first: Kryn

last: Stankunas


title: Sitagliptin phosphate ameliorates chronic inflammation in diabetes mellitus via modulating macrophage polarization

city: Lanzhou

first: Xiaoxia

last: Hu

address: No. 222 South Tianshui Road, Lanzhou 730000, Gansu Province, P.R.China

institute: The Second Hospital & Clinical Medical School, Lanzhou University Lanzhou, China

summary: Aim: To investigate the effect and mechanism of Sitagliptin phosphate on inflammation and macrophage polarization in a mouse model of type 2 diabetes. Methods: In vitro, Raw264.7 cells were cultured with a high concentration of glucose (HG) and sitagliptin phosphate (SIG). The levels of inflammatory factors and the regulation of macrophage polarization were investigated, and the differentially expressed genes between HG and HG+SIG intervention were analyzed and enriched through transcriptomics. In vivo, C57BL/6J male mice were treated with HFD+STZ to establish a type 2 diabetes mouse model were investigated the effects of regulation of macrophage polarization in the pancreas and visceral adipose tissue. Results:In vitro cell experiments and transcriptomics showed that Sitagliptin phosphate decreased the secretion of inflammatory factors IL-6 and TNF-α induced by high-glucose, and increased secretion of anti-inflammatory factor IL-10 by enhancing macrophage polarization. In vivo, the body weight and abdominal visceral fat weight, the ratio of visceral fat weight to body weight and fasting blood glucose were significantly increased in the DM group compared with the Control (P<0.05), Sitagliptin phosphate treatments reversed the changes in the DM group. Moreover, histological analysis showed that compared with the Control group, the size of visceral adipocytes, hepatocyte lipid deposition and the ratio of M1/M2 macrophage were higher in the DM group, which were reversed by Sitagliptin phosphate treatments (P<0.05), insulin treatments did not have a significant effect(P＞0.05).Mechanistically, Western blot showed that compared with the normal group, HG upregulated the expression of mTORc1 protein, P-65 phosphorylation and P-65 protein expression in Raw264.7 cells (P<0.05), downregulated the expression of IKKβ (P<0.05) and PPAR-γ proteins (P<0.05), Sitagliptin phosphate and insulin treatments rescued these changes. Conclusion: These results indicated that Sitagliptin phosphate reduced high glucose-induced inflammation by improving the imbalance of macrophage polarization via modulating the mTORc1/ PPAR-γ/NF-κB in vitro and in vivo.

overall_design: The Raw264.7 cells were incubated with 35 mmol/l hyperglycemia (HG) and 35mmol/l hyperglycemia Sitagliptin phosphate (HG＋SIG) for 6 hours (with three replicates per group) and subjected to full transcriptional sequencing. Differentially expressed genes between the two groups were identified based on the (|log2 (fold change)|>1) criterion. All bulk RNA-seq data were transformed into TPM and log2, and differential gene analysis was performed using the limma R package v3.54.0 (cite: https://www.ncbi.nlm.nih.gov/ pmc/articles/PMC4402510/). Pathway gene set signature was derived from the Molecular Signatures Database (MSigDB) (https://www.gseamsigdb.org/gsea/msigdb) and the ssgsea function from the GSVA R package v1.46.0 as described previously (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-7) were utilized to determine the pathway score. The results were visualized using ggplot2 v3.5.0 (https://doi.org/10.32614/CRAN.package.ggplot2).


title: RTF1 mediates epigenetic control of Th17 cell differentiation via H2B monoubiquitination [RNA-seq]

city: South San Francisco,

first: Saiyu

last: Hang

state: CA

address: 1 DNA Way

institute: Genentech

summary: The transcription factor RTF1 has been identified as a gene associated with an increased risk of ulcerative colitis (UC) . In this study, we investigated its impact on modulating intestinal inflammation through the control of T cells expressing interleukin-17A (Th17) cells. Our results demonstrate that RTF1 deficiency disrupts the differentiation of Th17 cells, while leaving regulatory T cells (Treg) cells unaffected. Mechanistically, RTF1 facilitates Histone H2B monoubiquitination (H2Bub1), which requires its histone modification domain (HMD). Impaired Th17 differentiation was also observed in cells lacking the H2Bub1 E3 ligase subunit RNF40. This study underscores the essential role of RTF1 in H2Bub1-mediated epigenetic regulation of Th17 cell differentiation. Understanding this process provides valuable insight into addressing Th17-associated inflammatory disorders.

overall_design: RNA sequencing of control and RTF1-deficient  in-vitro-differentiated Th17 cells

first: Carolina

last: Galan

first: Guangqing

last: Lu

first: Richard

last: Gill

first: Dun

last: Li

first: Yifang

first: Jun

last: Huh


title: Mechanical Loading remodels transcriptional regulation in Osteocytes through Nucleus translocation of NRF2 [RNA-seq]

first: Yue

last: Guo

overall_design: We subjected  mouse long bone osteocyte-like cell line MLO-Y4 cells to mechanical loading for 12 h. Then we performed gene expression profiling analysis using data obtained from RNA-seq of MLO-Y4 cells under mechanical loading and unloaded MLO-Y4 cells. We also

first: Jing

last: Zhang

first: Zhaojun

last: Liu

first: Luyu

last: Gong

first: Qiaoqiao


title: Abnormal global longitudinal strain and reduced serum inflammatory markers in cardiac AL amyloidosis patients without significant amyloid fibril deposition

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

summary: Cardiac dysfunction in AL amyloidosis is thought to be partly related to the direct impact of AL LCs on cardiomyocyte function, with the degree of dysfunction at diagnosis as a major determinant of clinical outcomes. Nonetheless, mechanisms underlying LC-induced myocardial toxicity remain unclear. We identified gene expression changes correlating with human cardiac cell exposure to cardiomyopathy-associated AL LCs. We then confirmed these findings in a clinical dataset focusing on clinical parameters associated with pathways dysregulated at the gene expression level. Upon exposure to cardiomyopathy-associated AL LCs, cardiac cells exhibited gene expression changes related to myocardial contractile function and inflammation, leading us to hypothesize that there could be clinically detectable changes in global longitudinal strain (GLS) on echocardiogram and serum inflammatory markers in patients. Thus, we identified 29 patients with normal interventricular septum diameter (IVSd) but abnormal cardiac biomarkers, suggestive of LC-induced cardiac dysfunction. These patients display early cardiac biomarker staging, abnormal GLS, and significantly reduced serum inflammatory markers compared to patients with clinically evident amyloid fibril deposition. Collectively, our findings highlight early molecular and functional signatures of cardiac AL amyloidosis, with potential impact for developing improved patient biomarkers and novel therapeutics.

overall_design: RNA-seq profiling of induced pluripotent stem cell-derived cardiomyocytes at Day 15 of differentiation when undosed or dosed with amyloidogenic and non-amyloidogenic light chains.

first: Camille

last: Edwards

last: Singh Bawa

first: George

middle: J

last: Murphy


title: SARS-CoV-2 Infection Induces Pro-Fibrotic and Pro-Thrombotic Lipid-Laden Macrophage Expansion in Lungs

first: Victor

last: Garcia

overall_design: BLT-L were used as an in vivo model to evaluate the infection of lung tissue with the recombinant coronaviruses SARS-CoV, MERS-CoV and SARS-CoV-2, as well as the full-length bat coronaviruses WIV1-CoV and SHC014-CoV12,13,44,45. Viruses were directly injected into the human lung tissue of BLT-L, and lung tissue was collected 2, 6 or 14days after exposure to determine virus titre and/or for analysis by histology, electron microscopy or RNA sequencing.

first: D

last: Battaglia

first: R

last: Baric

first: C

last: Jones

first: A

last: Wahl

first: E

last: Browne

first: J


title: Rorγt-positive dendritic cells are required for the induction of peripheral regulatory T cells in response to oral antigens

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University School of Medicine in St. Louis

summary: The intestinal immune system maintains tolerance to harmless food proteins and gut microbiota through peripherally-derived RORγt+Tregs (pTregs), which prevent food intolerance and inflammatory bowel disease. Recent studies suggested that RORγt+ antigen-presenting cells (APCs), which encompass rare dendritic cell (DC) subsets and type 3 innate lymphoid cells (ILC3s), are key to pTregs induction. Here, we developed a mouse with reduced RORγt+APCs by deleting a specific cis-regulatory element of Rorc encoding RORγt. Single-cell RNA-sequencing and flow cytometry analyses confirmed the depletion of a RORγt+DC subset and ILC3s. These mice showed a secondary reduction in pTregs, impaired tolerance to oral antigens and increase in Th2 cells. Conversely, newly and previously generated ILC3-deficient mice showed no pTregs or Th2 cells abnormalities. Lineage tracing revealed that RORγt+DCs share a lymphoid origin with ILC3s, consistent with their similar phenotypic traits. These findings highlight a unique role of lymphoid RORγt+DCs in maintaining intestinal immune balance and preventing conditions like food allergies.

overall_design: We performed single-cell RNA sequencing on sort purified CD3-B220-CD11c+MHC-II+ tdTomato+ hCD2– and hCD2+ DCs extracted from mLNs of 15days old Gm38411-iCre-hCD2 R26tdTomato reporter mice. 12 mice were used, with each biological replicate being labelled with a unique Hashtag antibody.

first: Patrick

last: Fernandes Rodrigues


title: RNA-seq  for orthotopic lung tumor treated with taurine and proline

city: Guangzhou

first: Tuliang

last: Liang

state: Guangdong

address: Office 213, Guangdong Provincial Academy of Chinese Medical Sciences

institute: The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hos

summary: This study aimed to clarify their role in lung cancer progression, offering insights into potential therapeutic targets. This is the first study to reveal the promoting effects of taurine and proline in lung cancer, suggesting a link to poorer prognosis.

overall_design: Taurine and proline were found to promote lung tumor progression in established lung cancer mouse models, and then orthotopic lung tumor treated with taurine and proline were analyzed by RNA-seq.  Normal lung (control) also included.


title: Downstream targets of Isl1 in the hindlimb field and genital tubercle

status: Public on Apr 04 2025

city: Athens

first: Douglas

last: Menke

state: GA

address: 500 DW Brooks Drive

department: Genetics

institute: University of Georgia

summary: Despite the incredible morphological diversity found within vertebrates, embryonic  development is often regulated by shared foundational mechanism maintained from a common  ancestor. For instance, the tetrapod limb displays tremendous variation in size and shape but  largely develops according to conserved gene regulatory networks, including signaling pathways,  transcription factors, and enhancers. The phallus of amniotes is also thought to share a basic  homology originating from their last common ancestor over 300 million years ago. The genital  tubercle (GT) of mammals – the embryonic precursor to the penis and clitoris – shows  similarities with the external genitalia of other amniotes prior to sexual differentiation. Many  genes and enhancers show a common role in both the limbs and the external genitalia, and  disruption of these loci can cause aberrant phenotypes in both structures. Among these shared  limb-genital genes is Isl1. The Isl1 gene encodes a homeodomain transcription factor that is  required for initiation of the hindlimb bud and for normal GT development. This study uses a  combination of RNA-seq, ChIP-seq, and comparative genomics to identify potential targets of  ISL1 during both hindlimb initiation and GT outgrowth. ChIP-seq data from mouse, chick, and  other species reveals targets that are likely conserved from the last common ancestor of   amniotes. A subset of ISL1 targets are shared between the hindlimb and the external genitalia,  supporting the hypothesis that aspects of phallus development were coopted from the limb gene  regulatory network. This systematic investigation of ISL1 transcriptional targets expands our  knowledge of Isl1’s role in appendage development and generates further testable hypotheses  concerning the establishment of these structures.

sample_organism:
Alligator mississippiensis
Gallus gallus
Mus musculus
Trachemys scripta
Anolis sagrei

overall_design: RNA-seq was used in Isl1 cKO and control mice to find differentially expressed genes downstream of Isl1 in the hindlimb field and the genitalia. ChIP-seq was used to identify ISL1 binding loci genome-wide in multiple species of amniotes.

first: Sergio

middle: G

last: Minchey

first: Sungdae

last: Park

first: Brooke

middle: A

last: Armfield

first: Rajee

last: Rajakumar

first: Darius

last: Ramkhalawan

first: Martin

last: Cohn

middle: B

first: Benjamin

last: Parrot


title: Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [miRNA sclera]

city: New York

first: Andrei

middle: V.

last: Tkatchenko

state: NY

department: Edward S. Harkness Eye Institute

institute: Columbia University

type: Non-coding RNA profiling by high throughput sequencing

summary: During postnatal development, the optical geometry of the eye is refined through a process called emmetropization. During eye emmetropization, optical defocus triggers a signaling cascade that originates in the retina, propagates across other ocular tissues and results in scleral wall remodeling. This signaling is associated with large-scale changes in gene expression, which was extensively studied at the mRNA level. Although several studies investigated the role of non-coding RNAs in eye emmetropization, the role of microRNAs (miRNAs) and other non-coding RNAs remains poorly understood. We performed a genome-wide analysis of the miRNA-mRNA gene regulatory networks underlying optical-defocus-induced myopia using massive parallel RNA sequencing (RNA-seq). Our analysis revealed a widespread involvement of miRNAs in optical defocus perception and visually guided eye emmetropization underlying myopia development. We found that a relatively small number of miRNAs (39 miRNAs total) regulate expression of over 450 mRNAs, or 59% of all mRNAs differentially expressed in the eyes of mice with optical-defocus-induced myopia.  MiRNAs were also found to be involved in the regulation of the absolute majority of the biological processes and signaling pathways underlying visually guided eye emmetropization and myopia.

overall_design: Analysis of microRNA expression in the RPE/choroid/sclera of C57BL/6J mice in which myopia was induced with -20D lenses for 10 days

first: Tatiana


title: Ageing signatures in NSG mice

city: Bergen

first: Simona

last: Chera

address: Haukelandsbakken 15

country: Norway

institute: University of Bergen

summary:
Purpose: Understanding the role of an active immunesystem in ageing.
Methods: Male NSG (NOD scid gamma) immunodeficient mice were maintained in normal housing condition. Islet cells were isolated  at different age points  and mRNA were extracted before shipping to Qiagen for analysis.
Results: In NSG mice multiple of the metabolic pathways that are observed to be deregulated in ageing immunocompotent mice are infered to be sustained.

overall_design: mRNA from pancreatic islets from NSG mice at 6, 12, 24, and 40 weeks of age

first: Legøy

last: Thomas A.

first: Mathisen

last: Andreas F.

first: Ghila

last: Luiza

first: Chera

last: Simona


title: Primary infection enhances neutrophil-mediated host defense by educating HSPCs

city: tianjin

first: wu

last: peng

address: 288 Nanjing Road

institute: Peking Union Medical College,

summary: Hematopoietic stem and progenitor cells (HSPCs) can give rise to all kinds of immune cells including neutrophils. Neutrophils are the first line of defense in the innate immune system with a short lifespan, due to which it is well-accepted that neutrophils have no immune memory. However, recent reports showed that the changes in HSPCs induced by primary stimulation could last a long time, which contributes to enhancing response to subsequent infection by generating more monocytes or macrophages equipped with stronger anti-bacterial function. Here, we used the reinfection mice model to reveal that primary infection could improve neutrophil-mediated host defense by training neutrophil progenitors in mammals, providing a new idea to enhance neutrophil number and improve neutrophil functions, which is pretty pivotal for patients with compromised or disordered immunity.

overall_design: There are 2 single-cell mouse samples consist of  bone marrow (BM): enrich by cKit+ from untreated mice, treated with HIEC.

first: Peng

last: Wu

first: Rongxia

last: Guo


title: RTF1 mediates epigenetic control of Th17 cell differentiation via H2B monoubiquitination [CUT&RUN]

first: Saiyu

last: Hang

overall_design: Cleavage Under Targets and Release Using Nuclease (CUT&RUN) profiling of RTF1 and H2Bub1 in in-vitro-differentiated Th17 cells

first: Carolina

last: Galan

first: Guangqing

last: Lu

first: Richard

last: Gill

first: Dun

last: Li

first: Yifang

last: Liu

first: Jun

last: Huh


title: Phosphodiesterase 12 facilitates the growth and metastatic capabilities of gastric cancer cells by activating the TCAF2/JAK2/STAT3 axis

status: Public on Apr 02 2025

city: beijing

first: Li-Na

last: Zhang

address: College of Chemistry and Life Science

institute: Beijing University of Technology

summary: Phosphodiesterase 12 (PDE12), also known as 2-PDE, is a key molecule in the 2-5A antiviral system and a member of the endonuclease-exonuclease-phosphatase (EEP) superfamily of deadenylases. Current research on PDE12 mainly focuses on mitochondrial mRNA degradation, mitochondrial protein translation, and the related human diseases caused by mitochondrial oxidative phosphorylation disruption. However, the biological role and molecular mechanisms of PDE12 in human cancers remains unclear.

overall_design: In the present study, we found that PDE12 was highly expressed in gastric cancer tissues and cell lines. Gain- and loss-of-function experiments confirmed that PDE12 promoted the proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) of gastric cancer cells. PDE12 knockdown also caused gastric cancer cell cycle arrest in G0/G1 phase by regulating the expression of G1 phase-specific Cyclins and CDKs. Our further studies indicated that PDE12 positively regulated the expression of TRPM8 channel-associated factor 2 (TCAF2), which functioned as an oncogene in gastric cancer. TCAF2 knockdown significantly suppressed gastric cancer cell proliferation, migration and invasion, and also reversed the promoting effect of PDE12 overexpression on the growth and metastasis of gastric cancer cells. Furthermore, our findings revealed a novel mechanism by which PDE12/TCAF2 axis promoted gastric cancer progression by activating the JAK2/STAT3 signaling pathway. Taken together, our data strongly indicate that PDE12 exerts an oncogenic function in gastric cancer progression at least partly via activating the TCAF2/JAK2/STAT3 signaling axis. These observations provide new insights into the tumorigenesis and metastasis of gastric cancer, and suggest that PDE12 may serve as a novel therapeutic target for gastric cancer.

first: Lina


title: HDAC inhibitors sensitize colorectal cancer to ferroptosis via m6A modification of FSP1

first: Mengying

last: Xing

address: 163 Xianlin Avenue

department: The State Key Laboratory of Pharmaceutical Biotechnology

institute: Nanjing University

summary: Ferroptosis therapy has been well-established in various cancers; however, colorectal cancer (CRC) is highly resistant to ferroptosis, which hinders the use of ferroptosis therapy in CRC. Through drug screening, we found histone deacetylase inhibitor (HDACi) significantly sensitized ferroptosis. Mechanically, HDACi reduced FSP1 by promoting its mRNA degradation, a known ferroptosis defense molecular. In further research, we confirmed that HDACi specifically targeted HDAC1 and suppressed the H3K27ac modification of FTO and ALKBH5. The activation of FTO and ALKBH5 resulted in a reduction of N6-methyladenosine (m6A) modification on FSP1 mRNA, leading to its degradation and ultimately sensitizing CRC to ferroptosis. The combination of HDACi and ferroptosis inducers synergically reduced CRC both in vivo and in vitro. In conclusion, our research reveals how HDACi sensitized ferroptosis and prompts the combination of HDACi/ferroptosis inducers as a promising therapeutic strategy for solid tumors.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 treated with SAHA and TSA.

first: Zhou

last: Yang

first: Bing

last: Yao


title: MEK-dependent bioenergetic demand drives terminal CD8+ T cell exhaustion

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

summary: Loss of mitochondrial function contributes to CD8+ T cell dysfunction during persistent antigen encounter. How chronic antigen leads to this metabolic dysfunction remains unclear. Here, we show that TCR-dependent mitochondrial NADH accumulation drives production of ROS, ultimately leading to mitochondrial dysfunction. Among TCR-dependent proximal signaling components, MEKi uniquely reduced nutrient uptake and mitochondrial NADH accumulation while increasing proliferation. As a result, MEKi during chronic TCR stimulation reduced terminal T cell exhaustion. Mechanistically, we found that chronic MEK activation in T cells drove ATP demand by increasing global protein synthesis rates in vitro and in vivo. MEKi reversed chronic TCR stimulation-driven increases in RNA polymerase II CTD phosphorylation, reducing transcription rates at effector- and terminal-exhaustion associated genes while maintaining transcription of memory-associated genes. These findings establish MEK-dependent metabolic demand as a driver of T cell exhaustion and elucidate the role of MEKi in enhancing immunotherapy efficacy.

overall_design: Nascent RNA-seq was performed on mouse CD8+ T cells under chronic (with and without MEK inhibition) or acute stimulation to examine nascent transcriptional changes linked to T cell exhaustion.

first: Tanmana

last: Mitra

first: Madeline

last: Hwee

first: Ruben

last: Jose Jesus Faustino Ramos

first: Hui

first: Travis

last: Hartman

first: Justin

last: Cross

first: Miguel

last: de Jesus

first: Morgan

last: Huse

first: Valerie

last: Longo

first: Pat

last: Zanzonico

first: Santosha

last: Vardhana


title: C1Q + TPP1 + macrophages promote colon cancer progression through SETD8-driven p53 methylation.

city: Palermo

first: Veronica

last: Veschi

address: Via del Vespro, 131

country: Italy

institute: University of Palermo

summary: In many tumors, the tumor suppressor TP53 (p53) is not mutated, but experiences functional inactivation. Notwithstanding, restoring p53 function emerges as an appealing therapeutic approach for tumors exhibiting wild-type p53 (p53WT). However, the mechanisms underlying the functional inactivation of p53 in these tumors remain poorly understood. Previously, we identified SETD8 as a critical suppressor of p53 activity in neuroblastomas. SETD8 is the sole known enzyme that mono-methylates p53 on lysine 382 (p53K382me1), resulting in the inhibition of its pro-apoptotic and growth-arresting functions. In this study, we observed high expression levels of SETD8 and p53K382me1 in 185 colorectal cancer (CRC) tissue samples, being negatively associated with patient survival probability. Significantly, the expression of p53K382me1 resulted confined to colorectal cancer stem cells and tumor-associated macrophages (TAM) in tissues obtained from CRC patients. Within CRC patient cohorts, high expression of p53K382me1 levels in both stem and immune cells predict decreased survival probability. The SETD8-mediated inactivation of p53 through p53K382me1 may serve as an early requirement for tumor initiation, particularly in inflammation-induced cancers, and as a functional biomarker and therapeutic target in advanced CRCs

overall_design:
To investigate the cross-talk between colorectal cancer stem cells (CR-CSC) and tumor-associated macrophages (TAM) we performed in vitro co-culture experiments and we collected the resulting conditioned media (CM3 or C3). To evaluate changes in transcriptomic profile of CR-CSCs after their cross-talk with TAMs we treated CR-CSCs with conditioned media 3,  and then we performed RNA-seq analysis.
We then performed gene expression profiling analysis using data obtained from RNA-seq of CR-CSCs untreated or treated with CM3 (C3).
Comparative gene expression profiling analysis of RNA-seq data for CR-CSCs untreated vs treated with CM3.

first: Sebastiano

last: Di Bella


title: Large-scale characterisation of cell line xenografts identifies SMAD4 as key regulator of breast cancer morphology and aggressiveness

city: Utrecht

first: Stefan

last: Prekovic

address: Universiteitsweg 100

department: CMM

country: Netherlands

institute: UMC Utrecht

summary: Breast cancer (BC) is a complex and heterogeneous disease with diverse molecular subtypes, tumour growth dynamics, varying morphologies and high metastatic potential. Many advances have progressed our understanding of the disease, yet fundamental understanding of what makes breast cancer an aggressive entity is lacking. While the majority of available studies rely on a limited set of models, failing to recapitulate the full spectrum of breast cancer, an extensive resource of well characterized xenograft models may aid in gaining solid and reproducible insights into BC biology. In this study, we generated mouse models from 26 different human BC cell lines, each with unique characteristics, using mammary intraductal (MIND) and fat pad transplantation (FPT) methodologies. Our models faithfully recapitulate human disease and cover the full spectrum of disease progression, from in situ disease to metastatic growth, while retaining distinct growth characteristics and molecular subtype. Comprehensive pathological analysis revealed two distinct tumour growth morphologies: indolent vs aggressive. Transcriptomics analysis identified the TGF-beta pathway as a potential regulator of these two phenotypes. Strikingly, we were able to completely reverse aggressive nodular-growing tumours to a more indolent disease by knockout of SMAD4. This research provides a valuable resource of fully characterized in vivo cell line xenograft models and reveals novel insights into the factors driving BC tumour growth behaviour and aggressiveness. It therefore serves as a basis for understanding the underlying mechanisms of tumour development and progression and enables accurate choice of model for future studies.

overall_design: To characterize what drives breast cancer invasiveness we established human breast cell line xenograft mouse models and chacaterized both the originating cell line as well as the emerged tumours. We generated RNA-sequencing data from the 10 parental cell lines, 10 outgrown tumours from the different cell lines when these were transplanted into the fat pad (FP) of recipient mice and 10 transpanted tumours when the cells were xenografted via the MIND (mouse intraductal) methodology. We extended the latter panel by an additional 9 MIND-xenografted tumours.

first: Catrin

last: Lutz

first: Jos

last: Jonkers


title: HyDrop v2: Scalable atlas construction for training sequence-to-function models

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

summary: Deciphering cis-regulatory logic underlying cell type identity is a fundamental question in biology. Single-cell chromatin accessibility (scATAC-seq) data has enabled training of sequence-to-function deep learning models allowing decoding of enhancer logic and design of synthetic enhancers. Training such models requires large amounts of high-quality training data across species, organs, development, aging, and disease. To facilitate the cost-effective generation of large scATAC-seq atlases for model training, we developed a new version of the open-source microfluidic system HyDrop with increased sensitivity and scale: HyDrop v2. We generated HyDrop-v2 atlases for the mouse cortex and Drosophila embryo development and compared them to atlases generated on commercial platforms. HyDrop-v2 data integrates seamlessly with commercially available chromatin accessibility methods (10x Genomics). Differentially accessible regions and motif enrichment across cell types are equivalent between HyDrop-v2 and 10x atlases. Sequence-to-function models trained on either atlas are comparable as well in terms of enhancer predictions, sequence explainability, and transcription factor footprinting. By offering accessible data generation, enhancer models trained on HyDrop-v2 and mixed atlases can contribute to unraveling cell-type specific regulatory elements in health and disease.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design:
singe-nucleus ATAC profiling of frozen mouse cortex tissue from adult BL/6Jax. The nuclei were dissociated and barcoded with different single-cell platforms and chemistries: 10x v1, 10x v2, HyDrop v1 and HyDrop v2.
single-nucleus ATAC profiling of whole Drosohila melaogaster embryo of developmental stage 17. The embryos were collected at age 16 to 20h old, dechorionated and the nuclei lysed to be processed with different single-cell plattforms: 10x v2 and HyDrop v2.
single-nucleus ATAC profiling of mixed samples (which ones) of cell lines as barnyard. The cells where lysed and barcoding was performed with single-cell platform HyDrop v2.

first: Hannah

last: Dickmänken

first: Marta

last: Wojno

first: Koen

last: Theunis

last: Christiaens

first: Florian

last: De Rop

first: Natalie

last: to be determined

first: Katina

middle: I

last: Spanier

first: Roel

last: Vandepoel

first: Suresh

last: Poovathingal

first: Stein

last: Aerts


title: Effect of BAY2402234 treatment on gene expression in nasopharyngeal carcinoma C666-1 cells

city: Huai'an

first: Xingchen

last: Dong

state: Jiangsu Province

address: No.1 Huanghe West Road

department: Department of Otorhinolaryngology

institute: Huai'an No.1 People's Hospital

summary: The DHODH inhibitor BAY2402234 has shown promising anti-tumor effects in various cancer types, but its molecular mechanisms in nasopharyngeal carcinoma remain unclear. This study investigates the transcriptomic changes induced by BAY2402234 in C666-1 nasopharyngeal carcinoma cells. We performed RNA-seq analysis of C666-1 cells treated with 2nM BAY2402234 for 48 hours compared to untreated control cells. Differential gene expression analysis revealed significant alterations in multiple pathways, including p53 signaling, cell cycle regulation, apoptosis, and ribosome biogenesis. Our findings provide insights into the molecular mechanisms underlying BAY2402234's anti-tumor effects in nasopharyngeal carcinoma, highlighting its potential as a therapeutic agent through modulation of critical cellular pathways involved in cancer progression.

overall_design: RNA-seq profiling of C666-1 nasopharyngeal carcinoma cells treated with 2nM BAY2402234 for 48 hours compared to untreated control cells.


title: Transcription Activator FgDDT Interacts with FgISW1 to Regulates Hyphal Development and Virulence in Fusarium graminearum

city: Hefei

first: zhao

middle: xiao

last: zhen

address: Anhui Agricultural University, 130 Changjiangxilu, Shushan District, Hefei, Anhui Province, China

institute: Anhui Agricultural University

summary: The Imitation Switch (ISWI) chromatin remodeling factors are known to form stable remodeling complexes with members from a family of proteins, termed DDT-domain proteins. ISWIs have been reported to be involved in various biological processes in many eukaryotic species. However, the regulatory mechanisms of DDT-domain proteins in ISWI complexes remain unclear. In this study, using ChIP-seq assays, we found that FgDDT binds to the promoter of MAPK and growth-related gene, activating its expression. Moreover, we identified and characterized two additional ISWI genes, FgISW1 and FgISW2, indicating that the ISWI components FgISW1 and FgDDT, rather than FgISW2, are essential for fungal development and virulence. Subsequently, we illustrated that FgDDT binds to FgISW1 to form an ISWI complex that activates the expression of functional genes in Fusarium graminearum, contributing to the virulence and development of F. graminearum. We also we observed that FgDDT is highly conserved in Fusarium species, but exhibits low similarity in Homo sapiens and Arabidopsis thaliana. These findings provide a basis for further studies on the molecular mechanisms by which ISWI complexes function in fungi.

overall_design: It was proved by ChIP-seq data and RNA-seq assays that FgDDT binds to the promoter of MAPK and growth-related gene, activating its expression.

first: Xiaozhen

last: Zhao


title: CITED4 is Required for Exercise-induced Cardiac Growth and Cardiomyogenesis in Mice

first: Haobo

last: Li

state: MA

address: MEDR410 / Lunder Bldg Dock, 255 Charles St

department: Department of Anesthesia, Critical Care, and Pain Medicine

institute: Massachusetts General Hospital and Harvard Medical School

summary:
To investigate the role of CITED4 in heart in exercise, we generated cardiomyocyte-specific CITED4 knockout (KO) by crossing CITED4 flox/flox (Flox) mice with aMHC-Cre mice and subjected them to either sedentary or exercise for eight weeks.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Flox and KO mice subjected to sedentary or exercise.

first: Anthony

last: Rosenzweig


title: Compartment size and proliferation shape the murine T cell receptor repertoire in splenic T- and B cell zones during an immune response

city: Nijmegen

first: Franka

last: Buytenhuijs

state: Please select your county

address: Toernooiveld 200

institute: Radboud University

summary: The adaptive immune system recognizes billions of unique antigens using highly variable T cell receptors (TCRs). To what extent TCR features shape the spatial distribution of the TCR repertoire (TCR-R) within lymphoid organs remains unclear.  Here, we compared the TCR-R composition in T cell zones (TCZ), B cell zones (BCZ), and germinal centers (GC) of the spleen by analyzing the complementarity-determining region 3 of the beta chain (CDR3β) in microdissected splenic compartments from na\"ive and immunized mice.  While we found substantial differences in TCR-R composition between these compartments, these differences largely disappeared once the effects of compartment size and proliferation were accounted for: During steady state, the few T~cells found in BCZs strongly resemble random subsets of those found in TCZs. After immunization, expanded clones started appearing in the TCZ at day 3 and later shifted to the BCZ. GCs harbored even further expanded clones that were grouped into clusters with high sequence similarity. TCR-R differences during the immune response were well explained by a Galton-Watson model of T~cell proliferation, suggesting that this could be the central factor shaping the observed TCR-R differences. Similarly, while TCR length and closeness to germline appeared to differ between the compartments, our models of random distribution and proliferation explained these differences almost entirely.  Hence, our findings suggest that splenic TCR-Rs are shaped predominantly by compartment size and proliferation rates rather than TCR sequence features. This would imply that quantitative assessment of TCR-R dynamics across heterogeneous spatial compartments during an immune response is only possible when these effects are explicitly accounted for.

overall_design: TCRbeta sequencing data of mouse spleen. Eight- to twelve-week-old C57BL/6J mice were either immunized by injecting 200 μl phosphate-buffered saline (PBS) containing 10^9 SRBC into the tail vein or 200 μl PBS as control. Animals were assigned randomly to the experimental groups. Control mice were sacrificed 3 days post-immunization (3d p.i.), and immunized mice were sacrificed 3d, 4d, and 7d p.i., respectively, resulting in four groups: `PBS’ (n=8), `SRBC 3d’ (n=8),`SRBC 4d’ (n=8), and `SRBC 7d’ (n=6).

first: Cornelia

last: Tune

first: Andrea

last: Schampel

first: Lisa-Kristin

last: Schierloh

first: René

last: Pagel

first: Jürgen

last: Westermann

first: Johannes

last: Textor


title: Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [mRNA sclera]

first: Andrei

last: Tkatchenko

overall_design: Analysis of mRNA expression in the RPE/choroid/sclera of C57BL/6J mice in which myopia was induced with -20D lenses for 10 days

first: Tatiana


title: Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [mRNA retina]

overall_design: Analysis of mRNA expression in the retina of C57BL/6J mice in which myopia was induced with -20D lenses for 10 days


title: Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia

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

overall_design: Refer to individual Series


title: Neuronal ABCA7 deficiency aggravates mitochondrial dysfunction and neurodegeneration in Alzheimer’s disease [II]

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: Loss-of-function variants of the ABCA7 gene are associated with the increased risk of Alzheimer's disease (AD). How neuronal ABCA7 contributes to AD pathogenesis is unknown. Using neuron-specific Abca7 knockout mice (nAbca7−/−) with or without 5×FAD amyloid model background and postmortem AD brains, we investigated AD-related phenotypes through comprehensive approaches including transcriptomics and lipidomics. Lipidomics analysis detected altered lipid profiles in the brains and synaptosomes of 5×FAD; nAbca7−/− mice compared to controls. Transcriptomics profiling revealed that neuronal ABCA7 deficiency altered the expression of genes and pathways related to mitochondrial homeostasis and apoptosis, particularly in excitatory neurons. Consistently, synaptosomes isolated from 5×FAD; nAbca7−/− mice showed diminished mitochondria respiration and reduced synaptic protein levels, which are further supported by results from human AD brains. Our findings reveal that neuronal ABCA7 plays a critical role in mitochondrial homeostasis important for neuronal function and survival in the presence of AD pathology.

first: Ni

last: Wang

first: Takahisa

last: Kanekiyo


title: Aberrant circTMEM45A Facilitates ESCC Inflammatory Progression by upregulating the NLRP3/Caspase1/IL-1β pathway through m5C-mediated NLRP3 Activation

city: Shijiazhuang

first: Jia'xiang

last: Wu

address: Shijiazhuang 050011,China

institute: The Fourth Hospital of Hebei Medical University

summary: Esophageal squamous cell carcinoma (ESCC) is a highly invasive, metastatic upper gastrointestinal malignancy. With the continuous deepening of personalized precision medicine, targeted therapy and immunotherapy have greatly improved the current treatment dilemma of esophageal cancer, but not all patients can benefit from them, and the overall efficacy is still poor. Circular RNA (circRNA) has become a key regulator of cancer development and progression and is expected to become a biomarker for the diagnosis and prediction of various cancers. Our goal is to find effective early diagnostic markers and therapeutic intervention targets by identifying the circRNA expression pattern of ESCC.

overall_design: To identify the circRNA expression pattern of ESCC, we sequenced ribosomal RNA-depleted total RNA extracted from three pairs of ESCC tissues and corresponding adjacent tissues to determine the differential circRNA expression profiles in ESCC.


title: The self-renewal function of Oct-4 can be replaced by the EWS-OCT-4 fusion protein in embryonic stem cells

city: SEOUL

first: EUN JOO

last: LEE

state: MAPOGU

address: SOGANG R 1206

department: LIFE SCIENCE

country: South Korea

institute: SOGANG UNIVERSITY

summary: EWS-Oct-4 can effectively replace Oct-4, which has significant implications for advancements in stem cell research and regenerative medicine

overall_design: we used J1 ESC cell line as control group, and EWS-OCT4, OCT4 stable cell line as an experimental group.  All experiments are triplicated.

first: Eun Joo

last: Lee

first: Ruijing

last: Sun

first: Jung Ho

last: Kim


title: Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [miRNA retina]

summary: During postnatal development, the optical geometry of the eye is refined through a process called emmetropization. During eye emmetropization, optical defocus triggers a signaling cascade that originates in the retina, propagates across other ocular tissues and results in scleral wall remodeling. This signaling is associated with large-scale changes in gene expression, which was extensively studied at the mRNA level. Although several studies investigated the role of non-coding RNAs in eye emmetropization, the role of microRNAs (miRNAs) and other non-coding RNAs remains poorly understood. We performed a genome-wide analysis of the miRNA-mRNA gene regulatory networks underlying optical-defocus-induced myopia using massive parallel RNA sequencing (RNA-seq). Our analysis revealed a widespread involvement of miRNAs in optical defocus perception and visually guided eye emmetropization underlying myopia development. We found that a relatively small number of miRNAs (39 miRNAs total) regulate expression of over 450 mRNAs, or 59% of all mRNAs differentially expressed in the eyes of mice with optical-defocus-induced myopia.  MiRNAs were also found to be involved in the regulation of the absolute majority of the biological processes and signaling pathways underlying visually guided eye emmetropization and myopia.

overall_design: Analysis of microRNA expression in the retina of C57BL/6J mice in which myopia was induced with -20D lenses for 10 days


title: Neuronal ABCA7 deficiency aggravates mitochondrial dysfunction and neurodegeneration in Alzheimer’s disease

overall_design: Using neuron-specific Abca7 knockout mice (nAbca7−/−) with or without 5×FAD amyloid model background and postmortem AD brains, we investigated AD-related phenotypes through comprehensive approaches including transcriptomics and lipidomics.


title: Neuronal ABCA7 deficiency aggravates mitochondrial dysfunction and neurodegeneration in Alzheimer’s disease [5xFAD_snRNAseq]


title: NOXA dependent induction of apoptosis in pancreatic cancer cells

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

country: Germany

institute: Christian-Albrechts-University Kiel

summary: Investigation of NOXA dependent apoptosis in pancreatic cancer cell lines with CRISPR/Cas9 mediated knockouts for NOXA and RUNX1 including parental cell lines.

overall_design: Cells have been treated for 6h with 3µM of AI-10-49 and corresponding vehicle controls

first: Maria

last: Doffo

first: Apoorva

last: Baluapuri

first: Ulrich

last: Keller

first: Mathias

last: Wirth


title: Electrostatic properties of disordered regions control transcription factor search and pioneer activity [ChIP-Seq]

city: Lausanne

first: Sim

last: Sakong

state: Vaud

address: AI 1133, Station 19

department: SV-IBI

country: Switzerland

institute: EPFL

summary: Transcription factors (TFs) recognize specific target sites within cis-regulatory regions to control gene expression. Prokaryotic TFs combine 1D and 3D diffusion mechanisms to efficiently locate their binding sites. In contrast, the determinants of target search efficiency of eukaryotic TFs within the chromatinized genome are poorly characterized. Here we combine in vivo and in vitro single molecule imaging to dissect the role of charged disordered regions of the mammalian Sox2 and Sox17 TFs in their ability to search for their binding sites. We demonstrate that the DBD flanking region of Sox2 (DFRSox2) dramatically enhances Sox2 search efficiency as compared to the negatively-charged DFRSox17 through distinct mechanisms on naked versus nucleosomal DNA. Enhanced search on naked DNA is primarily mediated by an increase in target recognition rate during 1D sliding. In contrast, target site recognition within nucleosomal DNA is mainly enhanced by increased nonspecific interactions with nucleosomes, facilitating binding to closed chromatin and reinforcing pioneering activity. These findings provide critical insights into the biophysical mechanisms governing TF target search beyond the DBD, and demonstrate how charged disordered regions modulate TF target search on the chromatinized genome.

overall_design: ChIP-seq experiments, utilizing a Halo-tag antibody, were conducted in CGR8-derived mouse embryonic stem cells expressing Halo-Sox2, Halo-Sox2a, Halo-Sox17, or Halo-Sox17b upon doxycycline addition. Two biological replicates of the ChIP procedure were carried out in the cells expressing Halo-Sox2 or Halo-Sox2a.

first: Beat

last: Fierz

first: David

last: Suter


title: Electrostatic properties of disordered regions control transcription factor search and pioneer activity [ATAC-Seq]

overall_design: ATAC-seq experiments were performed on CGR8-derived mouse embryonic stem cells induced with doxycycline to express Halo-Sox2, Halo-Sox2a, as well as on CGR8-derived cells lacking doxycycline-inducible transgenes (Ctrl).


title: DNA methylation associated with future risky ethanol use.

city: Winston-Salem

first: Kip

last: Zimmerman

state: NC

address: Medical Center Blvd

institute: Wake Forest School of Medicine

type: Methylation profiling by high throughput sequencing

summary: Alcohol use disorder (AUD) is a highly prevalent, complex, multifactorial and heterogeneous disorder, with 11% and 30% of adults meeting criteria for past-year and lifetime AUD, respectively. Identification of the molecular mechanisms underlying risk for AUD would facilitate effective deployment of personalized interventions. Studies using rhesus monkeys and rats, have demonstrated that individuals with low cognitive flexibility and a predisposition towards habitual behaviors show an increased risk for future heavy drinking. Further, low cognitive flexibility is associated with reduced dorsolateral prefrontal cortex (dlPFC) function in rhesus monkeys. To explore the underlying unique molecular signatures that increase risk for chronic heavy drinking, a genome-wide DNA methylation (DNAm) analysis of the alcohol-naïve dlPFC-A46 biopsy prior to chronic alcohol self-administration was conducted. The DNAm profile provides a molecular snapshot of the alcohol-naïve dlPFC, with mapped genes and associated signaling pathways that vary across individuals. The analysis identified 1,463 differentially methylated regions (DMRs) related to unique genes that were strongly associated with average ethanol intake consumed over 6 months of voluntary self-administration. These findings translate behavioral phenotypes into neural markers of risk for AUD, and hold promise for parallel discoveries in risk for other disorders involving impaired cognitive flexibility.

overall_design: Genome-wide DNA methylation (DNAm) analysis of the alcohol-naïve dlPFC-A46 biopsy prior to chronic alcohol self-administration was conducted. The DNAm profile provides a molecular snapshot of the alcohol-naïve dlPFC, with mapped genes and associated signaling pathways that vary across individuals

first: Rita

last: Cervera-Juanes

first: Larry

last: Wilhelm

first: Clara

middle: C

last: Lowe

first: Steve

middle: W

last: Gonzales

first: Tim

last: Carlson

first: Robert

last: Hitzemann

first: Betsy

last: Ferguson

first: Kathleen

last: Grant


title: Size-Modulated Mesoderm-Endoderm Divergence and Myocardial Cavitation in Micropatterned Cardioids

middle: William

last: McKellar

address: 101 6th Ave

institute: New York Genome Center

summary: The human heart, originating from the splanchnic mesoderm, is the first functional organ to develop, co-evolving with the foregut endoderm through reciprocal signaling. Previously, cardioid models offered new insights on cardiovascular cell lineages and tissue morphogenesis during heart development, while mesoderm-endoderm crosstalk remain incompletely understood. Here, we integrated micropatterned cardioids, CRISPR-engineered reporter hiPSCs, deep-tissue imaging, and single-cell RNA sequencing (scRNA-seq) to explore synergistic mesoderm-endoderm co-development. scRNA-seq with PHATE trajectory mapping reconstructed lineage bifurcations of mesoderm-heart and endoderm-foregut lineages, identifying key cell types in cardiac and hepatic development. Ligand-receptor interaction analysis highlighted mesodermal cells enriched in non-canonical WNT, NRG, and TGF-β signaling, while endodermal cells exhibited VEGF and Hedgehog activity. We found that micropattern sizes influenced cellular composition, cardioid cavitation, contractile functions, and mesoderm-endoderm signaling crosstalk. The cardioids generated from 600 µm diameter circle patterns showed larger cavity formation resembling early heart chamber formation. Our findings establish micropatterned cardioids as a model for mesoderm-endoderm co-development, enhancing our understanding of heart-foregut synergy during early embryogenesis.

overall_design: GCaMP6f reporter hiPSC cell lines were differentiated into cardiac organoids and cultured upon a micropatterned surface allowing for geometric control of multiple sizes. After successful differentiation into cardioids functioning organoids were imaged with samples collected at multiple time points for scRNA-Seq analysis.

first: Plansky

last: Hoang

first: Andrew

last: Kowalczewski

first: Nhu

middle: Y

last: Mai

first: Meng

last: Chai

first: Lance

middle: X

last: Lian

first: Yi

last: Zheng

first: Iwijn

last: De Vlaminck

first: Huaxiao

last: Yang

first: Benjamin

last: Cosgrove

first: Zhen

last: Ma


title: PPARa regulates ER-lipid droplet protein Calsyntenin-3b to promote ketogenesis in hepatocytes

city: Los Angeles

first: Yajing

last: Gao

address: 675 Charles E Young Dr S

department: Pathology and Laboratory Medicine

institute: University of California, Los Angeles

summary: Ketogenesis requires fatty acid flux from intrahepatic (lipid droplets) and extrahepatic (adipose tissue) lipid stores to hepatocyte mitochondria.  However, whether inter-organelle contact sites regulate this process is unknown.  Recent studies have revealed a role for Calsyntenin-3b (CLSTN3b), an endoplasmic reticulum-lipid droplet contact site protein, in the control of lipid utilization in adipose tissue.  Here, we show that Clstn3b expression is induced in the liver by the nuclear receptor PPARa in settings of high lipid utilization, including fasting and ketogenic diet feeding.  Hepatocyte-specific loss of CLSTN3b in mice impairs ketogenesis independent of changes in PPARa activation.  Conversely, hepatic overexpression of CLSTN3b promotes ketogenesis in mice.  Mechanistically, CLSTN3b affects LD-mitochondria crosstalk, as evidenced by changes in fatty acid oxidation, lipolysis-dependent mitochondrial respiration, and the mitochondrial integrated stress response.  These findings define a function for CLSTN3b-dependent membrane contacts in hepatic lipid utilization and ketogenesis.

overall_design: RNA-Sequencing of Liver from 14 week old littermate control and Alb Cre+ Clstn3 F/F male mice on ketogenic diet for 4 weeks and euthanized after 6 hour fast

first: Lauren

middle: F

last: Uchiyama

first: Alexander

last: Nguyen

first: Peter

last: Tontonoz


title: Examining how TNRC6 binding to its targets changes with the T6B peptide using RIPseq

city: San Diego

first: Norjin

last: Zolboot

address: 10550 North Torrey Pines Rd, DNC-222

department: Neuroscience

institute: The Scripps Research Institute

summary: Prior studies have demonstrated that the T6B peptide can selectively de-repress miRNA targets in non-neuronal cells. However, since neurons may have a different expression profile of miRNA pathway genes as well as other binding partners of TNRC6, we sought to validate the intended function of T6B in neurons. We performed RNA immunoprecipitation of TNRC6 followed by sequencing (TNRC6 RIPseq) in cultured cortical pyramidal neurons transduced with mutant T6B (control) or T6B. We reasoned that TNRC6 would indirectly pull down miRNA targets through its high-affinity binding with AGO in control neurons, but not in the presence of T6B, which outcompetes TNRC6 binding to AGO.

overall_design: We cultured cortical pyramidal neurons from E18-18.5 mouse embryos, transduced them with AAV expressing mutant T6B (control) or T6B at day in vitro (DIV) 10 and collected them at DIV14.

first: Yao

last: Xiao

first: Ian

last: MacRae

first: Giordano

last: Lippi


title: Targeting SCD triggers lipotoxicity of cancer cells and enhances anti-tumor immunity in breast cancer brain metastasis mouse models

city: Boston

first: Alessandro

last: Sammarco

institute: Massachusetts General Hospital

summary: Breast cancer brain metastases (BCBM) are incurable, and new therapies are urgently needed. BCBM upregulate Stearoyl-CoA Desaturase (SCD), an enzyme that catalyzes the synthesis of monounsaturated fatty acids, suggesting a potential metabolic vulnerability. Here, we test the effect of a brain-penetrant, clinical-stage SCD inhibitor (SCDi) on breast cancer cells and mouse models of BCBM. We show that SCDi markedly reshapes the lipidome of breast cancer cells, resulting in endoplasmic reticulum stress, DNA damage, impaired DNA damage repair, and cytotoxicity. Importantly, SCDi alone or combined with a PARP inhibitor prolongs the survival of BCBM-bearing mice. Furthermore, pharmacological inhibition of SCD enhances antigen presentation by dendritic cells, increases interferon signaling, promotes the infiltration of cytotoxic T cells, and decreases the proportion of exhausted T cells and regulatory T cells in the tumor microenvironment (TME) in a syngeneic mouse model of BCBM. Additionally, SCDi reduces the engagement of immunosuppressive pathways, including the PD-1:PD-L1/PD-L2 and PVR/TIGIT axes in the TME. These findings suggest that SCD inhibition could be an effective strategy to both intrinsically reduce tumor growth and reprogram anti-tumor immunity in the brain microenvironment to treat BCBM.

overall_design: Immunocompetent C57BL/6 female mice were intracranially implanted with GFP-expressing EO771 cells. Mice were then treated either with vehicle (Control) or SCDi for 14 days. After brain tissue dissociation, tumor cells (DAPI-/CD45-/GFP+) and immune cells (DAPI-/CD45+/GFP-) were isolated by FACS-sorting and analyzed by 10x scRNA-seq.

first: Giorgia

last: Guerra

first: Katharina

last: Eyme

first: Kelly

last: Kennewick

first: Yu

last: Qiao

first: Joelle

last: El Hokayem

first: Kevin

last: Williams

first: Baolong

last: Su

first: Cagri

last: Cakici

first: Hayk

last: Mnatsakanyan

first: Valentina

last: Zappulli

first: Steven

last: Bensinger

first: Christian

last: Badr


title: Mapping microRNA-target interactions in abundant cell types with Spy3-AGO2 Pull-down [CLIP-seq]

first: Norjin

last: Zolboot

summary: Studies have demonstrated that T6B can selectively de-repress miRNA targets in non-neuronal cells. However, since neurons may have a different expression profile of miRNA pathway genes as well as other binding partners of TNRC6, we sought to validate the intended function of in neurons. The first step was to identify bona fide miRNA targets in PNs, we performed AGO2 crosslinking and immunoprecipitation followed by sequencing (CLIPseq).

overall_design: To identify the miRNA-target interactions occuring in cultured cortical pyramidal neurons (PNs),we dissected and dissociated cortices from E18-18.5 embryos. After 14 days in culture, we collected the cells for AGO2 CLIPseq. CLIPseq studies were performed by Eclipse Bioinnovations Inc (San Diego, www.eclipsebio.com) according to the published single-end seCLIP protocol (Van Nostrand et al., 2017).


title: Mapping microRNA-target interactions in abundant cell types with Spy3-AGO2 Pull-down [SAP-seq]

summary: To illuminate the molecular mechanisms driving neuronal differentiation we generated a mouse line amenable to mapping miRNA-target interactions in rare cell types. Biochemical approaches to purify AGO2-miRNA-target complexes have successfully mapped MTIs in abundant populations of neurons. However, due to their technical complexity and high background, these approaches are not suitable for mapping interactions in rare cell populations such the many neuronal subtypes that compose the mammalian brain. We therefore generated a mouse line with a conditional SpyTag3, which is small and offers near-infinite affinity for pull-downs, in the endogenous Ago2 gene. We then developed a method Spy3-AGO2 pull-down and sequencing (SAPseq), which we first benchmarked for in vivo use using cortical pyramidal neurons, an abundant population.

overall_design: To identify the miRNA-target interactions occuring in developing pyramidal neurons (PNs), we crossed VGLUT2-Cre mice to conditional Spy3-AGO2 mice to generate VGLUT2-Cre;Spy3-AGO2 mice. We then isolated their cortices at P14. We then performed AGO2 pull-down using a SpyCatcher3 resin followed by RNA sequencing to generate miRNA libraries and target libraries

first: Yao

last: Xiao


title: Mapping microRNA-target interactions in cell lines with Spy3-AGO2 Pull-down [mESC SAP-seq]

summary: Mapping of microRNA (miRNA) targets using AGO2 CLIPseq and HEAPseq has provided major insight into the function of miRNAs in various systems. HEAPseq is a powerful method because it allows for cell type-specific mapping of miRNA targets and relies on a mouse line harboring a conditional HaloTag in the endogeous Ago2 locus. However, the homozygous mice are not viable, suggesting that the insertion of the large (>1 kb) HaloTag conditional cassette in the Ago2 gene promoter region, or appending the HaloTag domain to the AGO2 protein, is deleterious to some aspects of AGO2 function. To overcome this limitation, we created tagged AGO2 mouse and mESC lines designed for minimal perturbation of miRISC function. We used a cleavable SpyTag3, which rapidly forms a covalent bond with its ligand SpyCatcher3 and is ten times smaller than HaloTag (3 vs 33 kDa)36. To minimize any perturbation on AGO2 expression and protein structure, constitutive Spy3-AGO2 mice and mESC lines were created by inserting the SpyTag3 coding sequence into exon 2 of the Ago2 gene, which is separated from the promoter region by a 38 kb intron and encodes a small unstructured region of AGO2 – the only part of the protein sequence that is not perfectly conserved between mice and humans. We then developed a method SAPseq, based on HEAPseq and benchmarked it first using mESCs.

overall_design: We cultured mESCs and performed AGO2 pull-down using a SpyCatcher3 resin followed by RNA sequencing to generate miRNA libraries and target libraries

first: Ian

last: MacRae


title: Neurocellular stress response to Mojave Type A Rattlesnake venom: A study of molecular mechanisms using a human iPSC-derived neural stem cell model

city: McAllen

first: Satish

last: Kumar

state: Texas

address: 5300 North L Street (MBMRF-2.219)

department: Division of Human Genetics & South Texas Diabetes and Obesity Institute, UTRGV School of Medicine

institute: University of Texas Rio Grande Valley

summary: The Mojave rattlesnake (Crotalus scutulatus scutulatus) is classified as the “highest medically important” snake in the risk categories in the United States. Although responsible for fewer snakebite envenomations and deaths compared to other species, Mojave rattlesnake venom is poorly characterized and shows significant geographical variability. The venom of Type A animals primarily contains the β-neurotoxin referred to as Mojave Toxin (MTX), which is responsible for the neurotoxic effects that make bites from this snake particularly feared. Previous studies have shown that β-neurotoxin from different snake species produced similar but complex effects by mechanisms that are not fully understood. We performed a genome-wide transcriptomic analysis of the neurocellular response to Mojave Type A rattlesnake venom using induced pluripotent stem cell (iPSC) -derived human neural stem cells (NSCs) to unveil the molecular mechanisms underlying the damage caused by this snake’s envenomation. Our results suggest that snake venom metalloproteases (svMPs), although have a limited repertoire in type A animal venom, facilitate venom spread by digesting tissue's extracellular matrix. The MTX, which is composed of heterodimers of basic and acidic phospholipase A2 (PLA2) and is the dominant constituent of this venom, co-opts the host arachidonic acid and Ca2+ second messenger mechanisms in a dose- and time-dependent escalating venom damage. The release of arachidonic acid and the rapid increase in intracellular Ca2+ caused by the PLA2 activity of MTX triggers multiple signaling cascades. The activation of MAPKs and NF-κB regulated proinflammatory cascades were the top enriched pathways in the shorter 4-hour NSC response to venom challenge and suggest a significant role of PKC-δ in the activation of MAPKs. The rapid increase in intercellular Ca2+ and resulting cellular depolarization plausibly have a role in neurotransmitter overload in the cholinergic and glutamatergic excitatory synapses and MTX-induced presynaptic blockade of nerve signals. The expression of the acetylcholinesterase gene (ACHE), which degrades acetylcholine, and the downregulation of GRIK1 and GRIK3 genes, which encode KA-iGluRs proteins suggest a cellular response to neurotransmitter overload in the excitatory synapses. Our results also show that the MTX/svPLA2 mediated dysregulation of Ca2+ homeostasis, particularly depletion from the endoplasmic reticulum (ER), causes ER stress and upregulation of unfolded protein response (UPR). The UPR and the oxidative stress caused by ROS generated in CYP1A1-mediated hydroxylation of arachidonic acid, contribute to mitochondrial membrane permeabilization. The activation of UPR, mitochondrial toxicity, and oxidative stress, constitute the degenerative phase of the venom challenge in NSCs and synergistically contribute to apoptotic and ferroptotic programmed cell death.

overall_design: Well-characterized, low-passage human NSCs generated from validated iPSCs of four different individuals were challenged with vehicle control, and 10 µg/mL and 30 µg/mL Mojave Type A rattlesnake venom and then analyzed at 4- and 24-hour by deep mRNA sequencing.

first: Joanne E

last: Curran

first: John

last: Blangero


title: Pharmacologic degradation of WDR5 suppresses oncogenic activities of SS18-SSX and provides a therapeutic of synovial sarcoma [CUT&RUN]

city: Durham

last: Yu

state: North Carolina

address: Medical Science Res Bldg III, 3 Genome Court

institute: Duke University

summary: Disease-causing aberrations of childhood cancers recurrently target the chromatin pathway genes leading to epigenetic dysregulation. For example, almost 100% of patients with synovial sarcoma (SS) carry an abnormal gene fusion termed SS18-SSX, which produces a disease-specific oncofusion protein that is incorporated into the SWI/SNF chromatin-remodeling complex and profoundly alters its functionalities. Thus, targeting epigenetic dependencies in childhood cancer holds great promise for improving current treatment of the affected patients. Leveraging on the cancer cell dependency dataset, medicinal chemistry tool compounds and genomic profiling approaches, we here show WDR5, a chromatin factor involved in the deposition of histone H3 lysine 4 (H3K4) methylation, to be an unexplored vulnerability of SS. Mechanistically, WDR5 and SS18-SSX associate with one another and colocalize significantly at the target oncogenes where WDR5 is essential for optimal chromatin binding of the SS18-SSX-containing chromatin modelers. Using the WDR5-targeted Proteolysis Targeting Chimera (PROTAC) compound, we further show that pharmacologic degradation of WDR5 in SS cells not only suppressed the SS18-SSX-related oncogenic gene-expression programs but additionally led to p53 activation and tumor cell senescence through downregulation of ribosomal proteins (RPs) and activation of nucleolar stress response. Importantly, the WDR5-targeted PROTAC significantly suppressed malignant growth of SS in vitro and in vivo. Taken together, we report WDR5 as a SS dependency and demonstrate the WDR5 PROTAC degrader to be a promising strategy for the treatment of SS.

overall_design: We used CUT&RUN to assess the genome-wide binding of SS18-SSX and WDR5 in the HSSY II human SS cells, either mock- or compound-treated

first: Greg

last: Wang

first: Bo

last: Pan


title: CREB3 gain of functions variants protect against ALS

city: Strasbourg

first: Salim

last: Megat

state: Alsace

address: 1 rue Eugène Boeckel

country: France

institute: Center for Research in Biomedicine of Strasbourg (CRBS)

summary: Amyotrophic lateral sclerosis (ALS) is a fatal and rapidly evolving neurodegenerative disease arising from the loss of glutamatergic corticospinal neurons (CSN) and cholinergic motoneurons (MN). Here, we performed comparative cross-species transcriptomics of CSN using published snRNA-seq data from the motor cortex of ALS and control postmortem tissues, and performed longitudinal single cell RNA-seq data on male Sod1G86R mice. We report that CSN undergo ER stress and altered mRNA translation, and identify the transcription factor CREB3 and its regulatory network as a resilience marker of ALS, not only amongst vulnerable neuronal populations, but across all neuronal populations as well as other cell types. Using genetic and epidemiologic analyses we further identify the rare variant CREB3R119G (rs11538707) as a positive disease modifier in ALS. Through gain of function, CREB3R119G decreases the risk of developing ALS and the motor progression rate of ALS patients.

overall_design: Full length cDNA was obtained using the SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Clontech, CA) according to the manufacturer’s instructions. 11 cycles of cDNA amplification were performed using the Seq-Amp polymerase. 600ng of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT kit (Illumina) followed by 12 cycles of library amplification. Following purification using Agencourt AMPure XP beads (Beckman Coulter), the size and concentration of the libraries were assessed on an Agilent 2100 Bioanalyzer. The libraries were then loaded in the flow cell at a concentration of 3nM, clusters were generated by using the Cbot and sequenced on the Illumina HiSeq 4000 system as paired-end 2x50-base reads, following Illumina's instructions. Raw reads were mapped to the mouse reference genome GRCm38 with STAR version 2.7.0 61 and default parameters using Ensembl gene annotations (version 87). Gene-level abundance estimates were estimated using the option–quantMode geneCount in STAR.

first: Caroine

last: Rouaux


title: IDH status dictates oHSV mediated metabolic reprogramming affecting anti-tumor immunity

city: Augusta

first: Balveen

last: Kaur

address: CN-3205, 1410 Laney-Walker Blvd

department: Pathology

institute: Augusta University

summary: Identification of IDH mutations has uncovered the crucial role played by metabolism in glioma-genesis. Oncolytic herpes virus (oHSV) therapy initiates direct tumor debulking by tumor lysis and also activates antitumor immunity however little is known about the role of glioma metabolism in determining oHSV efficacy. Here we identified that oHSV therapy rewired central carbon metabolism with increased glucose utilization towards oxidative phosphorylation and shuttled glutamine towards reductive carboxylation in IDH wildtype (wt) glioma. The switch in metabolism resulted in increased lipid synthesis, and cellular ROS. PKC induced ACSL4 in oHSV treated cells led to lipid peroxidation and ferroptosis. Ferroptosis was critical to launch an antitumor immune response important for efficacy. Mutant IDH (IDHR132H) gliomas are incapable of reductive carboxylation and hence ferroptosis. Pharmacological blockade of IDHR132H induced ferroptosis and antitumor immunity. This study provides a rationale to treat high grade IDHR132H glioma patients under oHSV treatment with IDHR132H inhibitor.

overall_design: CD45+ immune cells isolated from 005 GSC tumor bearing hemisphere of C57BL/6 mice 5 days post oHSV treatment with or without Ferrostatin-1 and analyzed using sc-seq.

first: Upasana

last: Sahu


title: Genetic and anatomical determinants of olfaction in dogs and wild canids

first: Alice

last: Mouton

state: CA

address: 610 Charles E. Young Dr. East

department: Ecology and Evolutionary Biology

institute: UCLA

summary: Understanding the anatomical and genetic basis of complex phenotypic traits has long been a challenge for biological research. Domestic dogs offer a compelling model as they demonstrate more phenotypic variation than any other vertebrate species. Dogs have been intensely selected for specific traits and abilities, directly or indirectly, over the past 15,000 years since their initial domestication from the gray wolf. Because olfaction plays a central role in critical tasks, such as the detection of drugs, diseases, and explosives, as well as human rescue, we compared relative olfactory capacity across dog breeds and assessed changes to the canine olfactory system to their direct ancestors, wolves, and coyotes. We conducted a cross-disciplinary survey of olfactory anatomy, olfactory receptor (OR) gene variation, and OR gene expression in domestic dogs. Through comparisons to their closest wild canid relatives, the gray wolf and coyote, we show that domestic dogs might have lost functional OR genes commensurate with a documented reduction in nasal morphology as an outcome ofthe domestication process priorto breed formation.Critically, within domestic dogs alone, we found no genetic or morphological profile shared among functional or genealogical breed groupings, such as scent hounds, that might indicate evidence of any human-directed selection for enhanced olfaction. Instead, our results suggest that superior scent detection dogs likely owe their success to advantageous behavioral traits and training rather than an “olfactory edge” provided by morphology or genes.

overall_design: RNAseq data from 17 dog's olfactory epithelium tissue extracted using the Invitrogen TRIzol® Plus RNA Purification Kit.

first: Marco

last: Morselli

first: Matteo

last: Pellegrini

first: William

last: Murphy


title: Genomewide profiling of differentially H3K4me3 marked genes in colon cancer cells versus normal colon epithelial cells.

city: Calgary

first: Ravinder

last: Bahia

state: Alberta

address: 3330 Hospital drive NW

department: Cell Biology and Anatomy

country: Canada

institute: University of Calgary

summary: To identify differentially marked genes with a narrow or broad H3K4me3 pattern, we performed ChIP-seq using formaldehyde crosslinked chromatin from three colorectal cancer cell lines and normal colonic epithelial cell line and was digested with micrococcal nuclease to the extent that 70% of the chromatin was cleaved to mononucleosomes.

overall_design: To explore the differentially marked genes with a narrow or broad H3K4me3 pattern, we performed ChIP-seq using formaldehyde crosslinked three colorectal cancer cell lines and normal colonic epithelial cells.

middle: K

first: Camila

last: Lopez

first: Gino

last: Nardocci

first: James

middle: R

last: Davie


title: Expression data from Msh2KO mouse endometrial carcinogenesis

city: Chapel Hill

first: Melinda

middle: S

last: Yates

address: 160 Medical Drive

institute: University of North Carolina at Chapel Hill

summary:
Lynch syndrome (LS), caused by inherited mutations in DNA mismatch repair genes including MSH2, carries a 60% lifetime risk of endometrial cancer (EC). Beyond hypermutability, mechanisms driving LS-associated EC remain unclear. We investigated MSH2 loss in EC pathogenesis using a mouse model (PR-Cre Msh2(LoxP/LoxP), abbreviated Msh2KO), primary cell lines, human tissues, and human EC cells with isogenic MSH2 knockdown. By eight months, 58% of Msh2KO mice developed endometrial atypical hyperplasia (AH), a precancerous lesion. At 12-16 months, 47% exhibited either AH or ECs with histologic similarities to human LS-ECs. Transcriptomic profiling of EC from Msh2KO mice revealed a signature of mitochondrial dysfunction. Subsequent studies in vitro and in vivo revealed mitochondrial dysfunction based upon two mechanisms: reduced mitochondrial content and structural disruptions in retained mitochondria. Human LS-ECs also exhibited reduced mitochondrial content compared to non-LS-ECs. Functional studies demonstrated metabolic reprogramming of MSH2-deficient EC cells, including decreased oxidative phosphorylation and heightened susceptibility to glycolysis suppression. These findings identified mitochondrial dysfunction and metabolic disruption as consequences of MSH2 deficiency in EC. Mitochondrial and metabolic aberrations should be evaluated as biomarkers for endometrial carcinogenesis or risk stratification and represent potential targets for cancer interception in women with LS.
To achieve Msh2 loss in the endometrium, we bred progesterone receptor Cre knock-in (PR-Cre) mice to Msh2(LoxP/LoxP) mice to produce PR-Cre+Msh2(LoxP/LoxP) mice with targeted loss of MSH2 expression in tissues that express PR, including the uterus (hereafter abbreviated Msh2KO). Control mice contain Msh2(LoxP/LoxP) without PR-Cre. We profiled Msh2KO endometrial tumors, Msh2KO benign endometrium, and control mouse benign endometrium using transcriptomic profiling of microdissected glands via microarray analysis (ClariomD, Affymetrix).

overall_design: We compared expression profiles from Msh2KO tumors (N=7), Msh2KO mice with benign endometrium (N=6), and age-matched control mice (N=4). All mice were 12-16 months of age at time of sacrifice and tissue harvest.

first: Mikayla

last: Bowen


title: Enhancing TREM2 expression activates microglia and modestly mitigates Tau pathology and neurodegeneration

city: Rochester

first: Shuwen

last: Zhang

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: TREM2, a microglia-specific receptor, is strongly associated with Alzheimer’s disease (AD) risk and modulates microglial responses critical to AD pathogenesis. However, its role in tauopathy and neurodegeneration remains unclear. Here, by using a PS19 tauopathy mouse model with inducible overexpression of human wild-type TREM2 (TREM2-WT) or the R47H variant (TREM2-R47H), we show that TREM2-WT overexpression modestly reduces soluble phosphorylated tau (p-tau) levels and mildly preserves neuronal integrity, whereas TREM2-R47H fails to impact p-tau levels or neurodegeneration. Single-cell RNA sequencing revealed that TREM2-WT enhances disease-associated microglia (DAM) signatures, while TREM2-R47H drives the MHCII+ microglial phenotypes. These findings demonstrate that TREM2-WT confers modest benefits in tauopathy models, whereas TREM2-R47H exhibits reduced functionality. Our study underscores the therapeutic potential of enhancing TREM2 activity to modulate microglial responses and mitigate neurodegeneration in AD.

overall_design: Single-cell RNA sequencing from the cortex of 24 mice. 12 were TREM2-WT and 12 were TEM2-R47H. Among the TREM2-WT group, 6 were control and 6 were tamoxifen-induced. Among the TREM2-R47H group, 6 were control and 6 were tamoxifen-induced.

first: Kai

last: Chen

first: Fuyao

last: Li

first: Tadafumi

first: Yuka

last: Martens

last: zhao


title: Effects of SOX9 Downregulation on the Transcriptomic Landscape of Pancreatic Ductal Adenocarcinoma Cells

city: Moscow

first: Liya

last: Kondratyeva

address: Ulitsa Miklukho Maklaya, 16/10

country: Russia

institute: Institute of bioorganic chemistry of the Russian Academy of Sciences

summary: SOX9 is recognized as a crucial master regulator of gene transcription, playing a significant role in the developmental and differentiation processes of tissue and organ formation, particularly in the pancreas. Its overexpression has been associated with various tumors, including pancreatic cancer, and is often discussed as a potential prognostic marker. In this study, we conducted SOX9 knockdown in Colo375 and PANC-1 cell lines using RNA interference, followed by comprehensive transcriptome analysis of the transfected cells. We performed gene annotation and pathway analysis, as well as examined gene signatures related to survival and chemoresistance in pancreatic cancer within the transcriptomes of siSOX9 transfected cells. Notable differences were observed between the transcriptomes of SOX9 knockdown and control cells, including the activation of signaling pathways, differentiation processes, transcription, and methylation, alongside a reduction in the expression of genes associated with the cell cycle and apoptosis. The analysis revealed alterations in transcription factors, differentially expressed genes, oncogenes, tumor suppressor genes, genes related to epithelial-mesenchymal transition, drug resistance, and those included in prognostic signatures for pancreatic cancer in the SOX9 knockdown cells. The findings suggest that SOX9 may not serve as a reliable prognostic marker in pancreatic cancer.

overall_design: RNA-seq profiling was performed on pancreatic cancer cell lines (PANC-1 and Colo357) and their SOX9 knockdown derivatives 72 hours after siRNA transfection.

first: Kirill

last: Kashkin

first: Eugene

last: Kopantzev

first: Igor

last: Chernov


title: Identification of  miRNAs as promising biomarkers for diagnosis with combined analysis of mRNA transcriptome using next-generation sequencing in glioblastoma patients

city: Debrecen

first: Zsuzsanna

last: Birkó

address: Egyetem tér 1.

department: Humangenetics

country: Hungary

institute: University of Debrecen

summary: Applying Next Generation Sequencing technique we compared the mRNA expression pattern of tumor tissue sample of 5 GPs and peritumoral region of 5 lower grade (I-II) Glioma patients, serving as control group. To determine the difference on mRNA expresion level between GBM and control cases, we performed cluster analysis on the NGS dataset of 6 replicates for each of the two goups of samples with iDEP 96 software. In order to characterize the extent of up- or downregulation, log2FC values were calculated using the iDEP.96 web tool applying the DESeq2 algorithm. On the base of that 6125 known mRNAs were identified to be differentially expressed using a threshold of false discovery rate (FDR) <0.05 and fold-change> 2 during the analysis. Among them, 2253 mRNAs were upregulated (log2FC > 2) and 3872 mRNAs were downregulated (log2FC < -2) with biological revelance in tissue samples comparing with the control samples. To validate our results obtained by NGS, seven upregulated mRNAs: E2F2, HOXD13, VEGFA, CDC45, AURKB, HOXC10, MYBL2  and seven downregulated mRNAs:FABP6, PRLHR, NEUROD6, CBLN1, HRH3, HCN1, RELN  were chosen for RT-qPCR analysis. As the result of that   E2F2, HOXD13, VEGFA, CDC45, AURKB, HOXC10, MYBL2 was significantly upregulated while FABP6, PRLHR, NEUROD6, CBLN1, HRH3, HCN1, RELN was significantly downregulated, compared with those in the control samples.

overall_design: Tissue samples were gathered from peritumoral region of 5 individuals diagnosed with lower grade (Grade I-II.) glioma, serving as control group, and from 5 patients with GBM. All samples in both group were confirmed histopathologically. These intraoperative quick-frozen tissue samples were stored at -80⁰C until further processing. Total RNA was isolated from  the tissue samples of GBM and control group as well. Global transcriptomic profile was studied by RNA-sequencing applying the Illumina NextSeq500 platform including mRNA sequencing. In the case of all samples 3 replicates were included. In order to identify up-, or down-regulated miRNAs the GBM samples were compared to the  control samples.

first: Dóra

last: Géczi

first: Álmos

last: Klekner

first: István

last: Balogh

first: András

last: Penyige

last: Szilágyi

first: József

last: Virga

first: Andrea

last: Bakó

first: Bálint

last: Nagy

first: Bernadett

last: Torner