title: Loss of HLF enables metastasis via cell-collagen interaction in solid cancers

city: Chapel Hill

first: Austin

last: Hepperla

address: 7018B Mary Ellen Jones Building

institute: University of North Carolina at Chapel Hill

summary: Metastasis is the main cause of cancer-related deaths, yet the underlying mechanisms remain elusive. Using clear cell renal cell carcinoma (ccRCC), a tumor type with frequent lung metastases, we conducted an in vivo genome-wide CRISPR-Cas9 screen and identified HLF as a potent suppressor of lung metastasis. While HLF translocation is known as an oncogenic event in leukemia, its role in solid cancers remains unclear. Our study revealed that HLF depletion enhanced ccRCC migration and lung metastasis, whereas HLF overexpression abrogated these effects. This finding extended to multiple solid tumor types. In ccRCC patients, HLF expression was reduced at metastatic sites and associated with epigenetic silencing. HLF levels negatively correlated with migration potential in collagen. Mechanistically, HLF regulated leupaxin expression, affecting the integration of collagen stiffness and the actin cytoskeleton through paxillin, thereby repressing cancer cell migration and lung metastasis. These data indicate that HLF influences lung metastasis through cell-collagen interactions in solid tumors.

overall_design:
RNA-seq in ccRCC cell line 786-O in both knockout (CRISPR-Cas9 sgCtrl vs sgHLF) and overexpression (lentiviral empty vector vs HLF vector) of HLF. ATAC-seq in a ccRCC primary tumor cell line (786-O-P, from primary tumor) and a metastatic tumor cell line (786-O-LM, from lung metastasis) from 786-O cells following orthotopic injection into the kidney of mice.
ChIP-seq in ccRCC cell line 786-O for HA-tagged HLF and input under wild type conditions

first: Jin

last: Zhou

first: Jeremy

last: Simon

first: Kangsan

last: Kim

first: Qing

last: Hu

first: Lianxin

first: Cheng

last: Zhang

first: Chengheng

last: Liao

first: Alice

last: Fang

first: Yayoi

last: Adachi

first: Haoyong

last: Fu

first: Tao

last: Wang

first: Qian

last: Liang

first: Fangzhou

last: Zhao

first: Hongyi

last: Liu

first: Masashi

last: Takeda

first: Jun

first: Hongwei

last: Yao

first: Hua

last: Zhong

first: Peter

last: Ly

first: Lu

first: Payal

last: Kapur

first: Srinivas

last: Malladi

first: James

last: Brugarolas

first: M

first: Bo

last: Li


title: Esculetin modulates postprandial cholesterol metabolism involved in phagocytosis of adipose tissue macrophages (RNA-Seq)

status: Public on Apr 21 2025

city: Xiamen

first: Binbin

state: Fujian

address: Jinshan Road

department: Xiamen Cardiovascular Hospital

country: China

institute: Xiamen University

type: Expression profiling by high throughput sequencing

summary: Postprandial dyslipidemia is a significant risk factor for atherosclerotic cardiovascular diseases. High-density lipoprotein (HDL)-driven reverse cholesterol transport (RCT) plays a crucial role in clearing postprandial lipids. In this study, we aimed to investigate the role of esculetin, a hypolipidemic substance, in regulating postprandial cholesterol metabolism. We measured postprandial cholesterol levels and conducted metabolomics and transcriptomics studies to understand the effect and underlying mechanism of esculetin on postprandial cholesterol metabolism in mice fed a lipid-rich meal. We found that esculetin significantly elevated the postprandial HDL cholesterol levels and induced alterations in postprandial serum metabolomics and hepatic transcriptomics which involved in the key steps of HDL-driven RCT including lipid metabolism, ABC transporters and bile acid biosynthesis and secretion. Additionally, the ratio and the phagocytic activity of an adipose tissue macrophage subset highly expressing CD36 and Tim4 increased following esculetin administration in mice. CCAAT enhancer-binding protein beta (C/EBPβ), a key transcription factor, was involved in the effect of esculetin on macrophages phagocytosis in ox-LDL-stimulated macrophages cells. Therefore, esculetin appears to elevate postprandial HDL levels and regulate postprandial cholesterol metabolism which are associated with the increased phagocytosis of adipose tissue macrophages and C/EBPβ.

overall_design: To the transcriptomic alterations induced by esculetin in the liver, esculetin (0 or 180mg/kg/d) were daily administered to the mice by oral gavage for 7 days. In the first 4 days, the mice were fed with a control diet (CD) containing 10% kcal from fat. Then the mice were fed with a high- fat diet (HFD) containing 60% kcal from fat for additional 3 days to understand lipid-rich meals-induced postprandial lipid circulation.

first: Gang

first: Heng

last: Ye


title: Transcriptional complexity in the insect central complex: single nuclei RNA-sequencing of adult brain neurons derived from type 2 neuroblasts

status: Public on Apr 16 2025

city: Eugene

first: Chris

last: Doe

state: Oregon

address: 1585 E 13th Ave

country: USA

institute: University of Oregon

summary: In both invertebrates such as Drosophila and vertebrates such as mouse or human, the brain contains the most diverse population of cell types of any tissue. It is generally accepted that transcriptional diversity is an early step in generating neuronal and glial diversity, followed by the establishment of a unique gene expression profile that determines morphology, connectivity, and function. In Drosophila, there are two types of neural stem cells, called Type 1 (T1) and Type 2 (T2) neuroblasts. In contrast to T1 neuroblasts, T2 neuroblasts generate intermediate neural progenitors (INPs) that expand the number and diversity of cell types. The diversity of T2-derived neurons contributes a large portion of the central complex (CX), a conserved brain region that plays a role in sensorimotor integration. Recent work has revealed much of the connectome of the CX, but how this connectome is assembled remains unclear. Mapping the transcriptional diversity of neurons derived from T2 neuroblasts is a necessary step in linking transcriptional profile to the assembly of the adult brain. Here we perform single nuclei RNA sequencing of T2 neuroblast-derived adult neurons and glia. We identify clusters containing all known classes of glia, clusters that are male/female enriched, and 161 neuron-specific clusters. We map neurotransmitter and neuropeptide expression and identify unique transcription factor combinatorial codes for each cluster (presumptive neuron subtype). This is a necessary step that directs functional studies to determine whether each transcription factor combinatorial code specifies a distinct neuron type within the CX. We map several columnar neuron subtypes to distinct clusters and identify two neuronal classes (NPF+ and AstA+) that both map to two closely related clusters. Our data support the hypothesis that each transcriptional cluster represents one or a few closely related neuron subtypes.

overall_design: Post-mitotic neurons and glia derived from Type 2 neuroblasts were collected via FACS.

first: Derek

last: Epiney

first: Gonzalo

middle: N

last: Morales Chaya

first: Noah

middle: R

last: Dillon

first: Sen-Lin

last: Lai

middle: Q


title: Functional divergence of TBP homologs through distinct DNA binding dynamics

city: Vancouver

first: Sheila

last: Teves

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

country: Canada

institute: Life Science Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The TATA box-binding protein (TBP) is an evolutionarily conserved basal transcription factor common in the pre-initiation complex of all three eukaryotic RNA polymerases (RNA Pols). Despite their high conservation, homologous TBPs exhibit species- and tissue-specific functions that may contribute to the increasingly complex gene expression regulation across evolutionary time. To determine the molecular mechanisms of species- and tissue-specificity for homologous TBPs, we examined the ability of yeast TBP and murine TBP paralogs to replace the endogenous TBP in mouse embryonic stem cells. We show that, despite the high conservation in the DNA binding domain among the homologs, they cannot fully rescue the lethality of TBP depletion in mESCs, largely due to their inability to support RNA Pol III transcription. Furthermore, we show that the homologs differentially support stress-induced transcription reprogramming, with the divergent N-terminal domain playing a role in modulating changes in transcriptional response. Lastly, we show that the homologs have vastly different DNA binding dynamics, suggesting a potential mechanism for the distinct functional behavior observed among the homologs. Taken together, these data show a remarkable balance between flexibility and essentiality for the different functions of homologous TBP in eukaryotic transcription.

overall_design: Chromatin profiling was done for Pol II, Pol III, HA-tagged TBP homologs in mESCs for control, IAA, HS, HSIAA with 2 replicates for each condition.

first: Jieying

middle: H

last: Cui

middle: Z

last: Kwan

first: Armin

last: Faghihi

first: Thomas

middle: F

last: Nguyen

middle: S


title: Assessing the Evolution of Virulence in the Salmon Louse (Lepeophtheirus salmonis) in the Bay of Fundy

status: Public on Apr 18 2025

city: St. Andrews

first: Marc

last: Trudel

state: NB

address: 125 Marine Science Dr

institute: Department of Fisheries and Oceans Canada

summary: An unintended consequence of fish farming is the production of an environment which may be conducive for the evolution of virulence for pathogens interacting with the host in production. Rearing conditions used in salmon aquaculture such as high densities, compressed rearing cycles, limited genetic diversity of broodstock as well as practices applied to control infectious disease, may all lead to increased selection pressures for the evolution of virulence of pathogens. These selection pressures may also be occurring without the balancing of negative fitness costs of virulence due to a constant supply of naïve hosts entering the system every 18-24 months. Changes in virulence of Canadian Lepeophtheirus salmonis populations have not yet been assessed, despite having been identified as a crucial knowledge gap to understand the interactions between farmed and wild hosts as well as the impact of increased disease prevalence at sites which may harbour highly virulent strains. We developed a virulence challenge model by rearing lice originating from wild and farm sources for 6 generations and compared differences in virulence on their host, testing the hypothesis that lice originating from farms were more virulent than those from wild sources. RNA sequencing was completed for copepodid, chalimus II and adult stages of the louse as well as their respective attachment sites on the host to determine responses at the host-parasite interface. We describe the first instance of elevated lesion severity for host Atlantic salmon when infected with farm-sourced lice compared to their wild counterparts. However, this increase did not appear to translate to meaningful differences in host growth rates (e.g. change in lengths or weights). Approximately 900 transcripts had differential expression for at least one life stage between wild and farm sources of lice. Many of these transcripts had functions related to chitin- and heme-binding, serine-endopeptidase, metallo-endopeptidase, and trypsin-like activities.

sample_organism:
Salmo salar
Lepeophtheirus salmonis

platform_organism:
Salmo salar
Lepeophtheirus salmonis

overall_design: Investigations of virulence differences between wild- and farm-collected Lepeophtheirus salmonis on Atlantic salmon hosts. Wild- and farm-sources were collected and reared in laboratory conditions for multiple generations before Atlantic salmon were challenged with infections from each source of lice. Differential gene expression was measured between the two sources of L. salmonis and gene ontology, pathway enrichment and a pilot genome-wide association study were completed.

first: Dylan

last: Michaud

first: Mark

last: Fast

first: Brent

last: Wilson

first: Wenlong

last: Cai


title: Histone Chaperones Coupled to DNA Replication and Transcription Control Divergent Chromatin Elements to Safeguard Cell Identity [CUT&Run]

city: Riverside

first: Reuben

last: Franklin

state: CA

address: 3401 Watkins Drive

institute: University of California, Riverside

summary: The manipulation of DNA replication and transcription can be harnessed to control cell fate. Central to the regulation of these DNA templated processes are histone chaperones, which in turn are emerging as cell fate regulators. Histone chaperones are a group of proteins with diverse functions that are primarily involved in escorting histones to assemble nucleosomes and maintain the chromatin landscape. Whether distinct histone chaperone pathways control cell fate, and whether they function using related mechanisms, remains unclear. To address this, we performed a screen to assess the requirement of diverse histone chaperones in the self-renewal of hematopoietic stem and progenitor cells. Remarkably, all candidates were required to maintain cell fate to differing extents, with no clear correlation with their specific histone partners or DNA templated process. Among all the histone chaperones, the loss of the transcription-coupled histone chaperone SPT6 most strongly promoted differentiation, even more so than the major replication-coupled chromatin assembly factor complex CAF-1. To directly compare how DNA replication- and transcription-coupled histone chaperones maintain stem cell self-renewal, we generated an isogenic dual inducible system to perturb each pathway individually. We found that both SPT6 and CAF-1 perturbations required cell cycle progression to induce differentiation, with distinct effects on chromatin accessibility, transcription factor activity, and gene expression. Specifically, CAF-1 depletion increased accessibility at heterochromatic loci with a pronounced effect on H3K27me3 elements leading to aberrant multilineage gene expression. In contrast, SPT6 loss influenced promoter elements and triggered a more canonical differentiation state, that is in part dependent on the activity of AP-1 transcription factors. Thus, CAF-1 and SPT6 histone chaperones maintain cell fate through the control of distinct chromatin elements, providing a paradigm for how different histone chaperone pathways can be manipulated to alter cell fate.

overall_design: H3K4me1 and H3K9me3 CUT&RUN in iGMPs. Two experimental replicates.

first: Meijuan

last: Chen

first: Sihem

last: Cheloufi


title: Histone Chaperones Coupled to DNA Replication and Transcription Control Divergent Chromatin Elements to Safeguard Cell Identity [CUT&Tag]

overall_design: H3K27me3 CUT&Tag in iGMPs. Two experimental replicates.

first: Brian

last: Zhang


title: METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [MeRIP-Seq]

city: Ithaca

first: Weiyu

state: NY

address: 215 Tower Rd, Biotechnology Building

department: MBG

institute: Cornell University

summary: Using a METTL3 inducible knockout (iKO) system in human expanded potential stem cells (hEPSCs), we uncovered that unlike in mESCs, METTL3 was indispensable for hPSCs’ maintenance, and that loss of METTL3 caused significant upregulation of naïve pluripotency genes accompanied with impaired hEPSCs differentiation particularly towards to both trophoblastic and amnionic lineage. Mechanistically, METTL3 iKO in hPSCs substantially increased expression of two primate-specific transposable elements (TEs), SVA_D and HERVK/LTR5_Hs.

overall_design: To investigate the function of RNA m6A methylation in hPSCs, we attempted to knock out the main methyltransferase METTL3 in hEPSCs. We used a knockout and inducible transgenic expression (iKO) system to transgenically express a METTL3 cDNA and rescue the KO phenotype. We firstly introduced a doxycycline (DOX)-inducible METTL3 cDNA stably integrated into hEPSCs by piggyBac transposition followed by knocking out the endogenous METTL3 by the CRISPR/Cas9. In the presence of DOX, two independent iKO cell lines with different METTL3 mutations were selected for subsequent investigation. To ensure comparable METTL3 expression levels in METTL3 iKO hEPSCs as in normal cells, we titrated DOX concentration and selected 5.0 ng/ml. Upon DOX withdrawal, exogenous METTL3 protein became undetectable after 5 days of culturing over 2 passages

first: Haifeng

last: Fu


title: Histone Chaperones Coupled to DNA Replication and Transcription Control Divergent Chromatin Elements to Safeguard Cell Identity [ChIP-seq

overall_design: H3K27ac ChIP-seq in iGMPs. Two experimental replicates.


title: METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [CUT&Tag]


title: METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [ATAC-seq]


title: Histone Chaperones Coupled to DNA Replication and Transcription Control Divergent Chromatin Elements to Safeguard Cell Identity [ATACseq]

overall_design: Bulk ribo-depleted total RNA-seq and ATAC-seq in iGMPs. SPT6 KD (DOX), CAF-1 KD (IPTG), and neutrophil differentiated (NoE2) cells are compared to untreated iGMPs as control. Two clonal replicates for each experiment.


title: Ribociclib Derivative RB-BC Induces Apoptosis in Breast Cancer through p53 Pathway Activation

status: Public on Apr 15 2025

city: Lianyungang

first: Song

middle: meng

last: wei

address: China

institute: Jiangsu Ocean University

summary: Breast cancer persists as the most prevalent malignancy and principal contributor to cancer-associated mortality among women worldwide, exhibiting marked disease heterogeneity and therapeutic resistance. Consequently, the development of novel therapeutic agents remains imperative. Ribociclib, a cyclin-dependent kinase 4/6 (CDK4/6) inhibitor, has emerged as a focus in adjuvant breast cancer research due to its mechanism of cell cycle arrest induction.Building upon this rationale, we designed and synthesized a novel ribociclib derivative RB-BC, systematically investigating its anti-neoplastic efficacy and molecular mechanisms in breast cancer through integrated in vitro and in vivo experimental systems. The compound's anti-proliferative effects were quantitatively assessed via MTT assays , EdU incorporation assays , and colony formation assays .Functional characterization through cell adhesion assays, scratch wound healing assays, and Transwell invasion assays demonstrated RB-BC’s dose-dependent suppression of tumor migration and invasion. Mechanistic analyses via RNA sequencing and Western blotting revealed that its anti-tumor activity primarily stems from p53 pathway activation, inducing caspase-3-mediated apoptosis in breast cancer cells. Machine learning algorithms identified p53-associated genetic signatures, and subsequent bioinformatics analyses elucidated their significant correlation with immune cell infiltration dynamics in the tumor microenvironment (TME).Moreover, RB-BC effectively suppressed tumor growth in vivo and significantly disrupted angiogenesis in the chick chorioallantoic membrane (CAM) assay. In summary, the ribociclib-derived compound RB-BC demonstrates compelling potential as a candidate therapeutic agent for breast cancer.

overall_design: In order to investigate the role and mechanism of RB-BC in Breast Cancer, we treated MDA-MB-231 cells with RB-BC and without treatment. Then, we performed gene expression profiling analysis using RNA seq data from RB-BC and DMSO cells.

first: Boyu

first: Jing

last: JI


title: Spatial Visualization Provides Insight into Immune Modulation by an L-DBF Vaccine Formulation Against Shigella

status: Public on Apr 17 2025

city: Columbia

first: Ti

last: Lu

state: MO

address: 1201 Rollins St, 311 Bond Life Science Center

institute: University of Missouri-Columbi

summary: Shigellosis remains a global public health problem, especially in regions with poor sanitation measures. Our prior work has demonstrated the protective efficacy of a three-dose regimen of L-DBF, a recombinant fusion of IpaD and IpaB from Shigella flexneri with the LTA1 moiety of enterotoxigenic E. coli labile toxin. Here, we investigate how a two-dose regimen (one prime and one booster) of L-DBF, formulated in an oil-in-water emulsion called ME, modulates immune responses in the lung using a spatial transcriptomics approach. Our findings show significant changes in the lung immune landscape following the vaccination, including increased expression of B cell markers, antigen presentation genes, and T cell-associated markers. Our analysis also revealed significant reprogramming of fibroblasts and cardiomyocytes, showing that fibroblasts are shifted from extracellular matrix production to immune modulation, while cardiomyocytes enhanced the signaling for immune cell recruitment and vascular stability. The communication between alveolar type 2 (AT2) cells and cardiomyocytes also increased, reflecting coordinated support for immune readiness and maintaining tissue integrity. These findings underscore the potential of L-DBF/ME vaccination to enhance both humoral and cellular immunity, as well as to reshape lung immune architecture while enhancing immune readiness, thereby offering a promising approach for effective protection against Shigella infections.

first: Skyler

middle: T

last: Kramer

first: Mary

middle: A

last: York

first: Mst

last: Nusrat-Zahan

first: Debaki

last: Howlader

first: Zackary

middle: K

last: Dietz

first: Sean

last: Whittier

first: Nathan

middle: J

last: Bivens

first: Alexander

last: Jurkevich

first: Lyndon

middle: M

last: Coghill

first: William

middle: D

last: Picking

first: Wendy

middle: L


title: Incomplete paralog compensation generates selective dependency on TRA2A in cancer

city: Philadelphia

first: Peter

last: Choi

state: PA

address: 3501 Civic Center Blvd, CTRB 4400

department: Pathology and Laboratory Medicine

institute: The Children's Hospital of Philadelphia

summary: Paralogs often exhibit functional redundancy, allowing them to effectively compensate for each other's loss. However, this buffering mechanism is frequently disrupted in cancer, exposing unique paralog-specific vulnerabilities. Here, we identify a selective dependency on the splicing factor TRA2A. We find that TRA2A and its paralog TRA2B are synthetic lethal partners that function as widespread and largely redundant activators of both alternative and constitutive splicing. While loss of TRA2A alone is typically neutral due to compensation by TRA2B, we discover that a subset of cancer cell lines are highly TRA2A-dependent. Upon TRA2A depletion, these cell lines exhibit a lack of paralog buffering specifically on shared splicing targets, leading to defects in mitosis and cell death. Notably, TRA2B overexpression rescues both the aberrant splicing and lethality associated with TRA2A loss, indicating that paralog compensation is dosage-sensitive. Together, these findings reveal a complex dosage-dependent relationship between paralogous splicing factors, and highlight how dysfunctional paralog buffering can create a selective dependency in cancer.

overall_design: RNA-seq profiling of A549 and NCI-H23 cells upon CRISPRi single knockdown of TRA2A alone, TRA2B alone, or dual knockdown of TRA2A/TRA2B, with control knockdown for comparison. RNA-seq profiling of LN229 and LN319 cells overexpressing either Luciferase control or TRA2B cDNA, upon CRISPR knockout of either TRA2A or TRA2B, with control knockout for comparison.

first: Amanda

last: Lee


title: METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [ChIP-Seq]

first: Weiyu

last: Zhang

first: Haifeng


title: Fast pH-Driven Solubilization Method of Realgar (As4S4) to Reduce the Toxicity of Arsenic [As(III)] for Medical Purposes

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

summary: Acute promyelocytic leukemia (APL) is a fulminant form of hematological cancer, representing 5-15% of adult leukemias and also affecting children. It is characterized by the 15:17 chromosomal translocation, which produces the pathogenic retinoic acid receptor (RAR) alpha/promyelocytic leukemia protein (PML) fusion product. Remission of APL was recently achieved using the first chemotherapy-independent oral drug regimen in anticancer therapy, consisting of all-trans retinoic acid (targeting RARalpha) and the arsenic sulphide realgar (targeting PML). A broader use of realgar is, however, hampered by the poor solubility of this mineral. We here describe a scalable pH- and temperature-based solubilization process for realgar. The solution obtained displays higher therapeutic indices compared to other arseni-containing compounds, including opriment and arsenic trioxide (an intravenous chemotherapeutic counterpart), which is in line with the lower toxicity of realgar observed in clinical trials. Our data also show that solubilized realgar can disrupt HIV latency, the main barrier to an HIV/AIDS cure, in CD4 T cells of people living with HIV. This discovery may also open new avenues for designing therapies based on orally administrable arsenic-containing compounds.

overall_design: In the first sequencing experiment, Jurkat E6.1 cells and NB-4 cells were incubated for 48 hours with solvent (NaOH, pH 12.7), 0.5 μM realgar, or 0.5 μM arsenic trioxide. After 48 hours, total RNA was extracted and used for RNA-Seq, with each condition analyzed in triplicate. In the second sequencing experiment, Jurkat E6.1 cells and NB-4 cells were incubated for 48 hours with solvent (NaOH, pH 12.7) or 0.5 μM orpiment. After 48 hours, total RNA was extracted and used for RNA-Seq, with each condition analyzed in duplicate.

first: Iart Luca

last: Shytaj


title: Effect of siRNA-mediated GSK3 knock-down on the transcriptional signature of human GM-CSF-dependent monocyte-derived macrophages

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

institute: Hospital General Universitario Gregorio Marañón

summary: The functional versatility of macrophages is intrincately tied to factors such as their ontogeny and the specific tissue and extracellular environment. Monocyte-derived macrophages are oppositely instructed by M-CSF or GM-CSF. GM-CSF drives monocyte-derived macrophages towards heightened pro-inflammatory activity and the acquisition of the lung alveolar macrophage phenotype and gene profile whereas M-CSF gives rise to anti-inflammatory, pro-resolving, and immunosuppressive monocyte-derived macrophages. We explored the molecular impact of siRNA mediated knocking-down GSK3A, GSK3B or both (GSK3A/B) on the gene expression profile of GM-CSF-primed human monocyte derived macrophages. GSK3A/B knowdown skewed the transcriptional profile of GM-MØ towards an anti-inflammatory phenotype.

overall_design: mRNA profiles of human macrophages differentiated with GM-CSF (GM-MØ) and transfected with siRNA control (siCNT), siRNA for GSK3A (siGSK3A), siRNA for GSK3B (siGSK3B) or both (siGSK3A and siGSK3B) and analyzed 72 hours later.

first: Israel

last: Ríos

last: Puig-Kröger

first: Ángel

last: Corbí


title: Transcriptomic analysis of epidermal sheets 1 week after induced keratinocyte deletion of A20 (Tnfaip3) in adult mice

city: San Francisco

first: Sugandh

last: Kumar

state: California

address: N431, 2340 Sutter St

department: Computational Biology

institute: University of California San Francisco (UCSF)

summary: A20 (TNFAIP3) is genetically associated with both Psoriasis and Psoriatic Arthritis in humans. We find that induced deletion of A20 (Tnfaip3) in keratinocytes leads to fully penetrant psoriatic cutaneous inflammation and Psoriatic Arthritis-like joint disease in adult mice. To determine the early molecular pathways that trigger skin and joint inflammation, we performed transcriptomic profiling of epidermal gene expression 1 week following induced deletion of keratinocyte A20 in adult mice. Pathways analysis identified elevation of genes associated with MyD88-dependent and antiviral signaling following keratinocyte A20 deletion. Using compund mutants that prevent keratinocyte MyD88 signaling or antiviral signaling from Type I interferon receptors, we found that keratinocyte MyD88 signaling is required for development of psoriatic skin and joint inflammation following keratinocyte A20 deletion. These results identify unrestrained MyD88 signaling as a key mediator of psoriatic inflammation and psoriatic arthritis-like pathology caused by deletion of keratinocyte A20 in adult mice.

overall_design: RNASeq profiling of ear epidermal sheets derived from 8 week old A20F/F Krt5-CreERT2+ (A20KIKO) and A20F/F Krt5-CreERT2- (A20WT) mice (four distinct mice in each group) 1 week after first intraperitoneal tamoxifen injection.

first: Jared

last: Liu

first: Wilson

last: Liao

first: Barbara A

last: Malynn

first: Averil

last: Ma

first: Bahram

last: Razani


title: Histone Chaperones Coupled to DNA Replication and Transcription Control Divergent Chromatin Elements to Safeguard Cell Identity

first: Reuben

last: Franklin

summary: The manipulation of DNA replication and transcription can be harnessed to control cell fate. Central to the regulation of these DNA templated processes are histone chaperones, which in turn are emerging as cell fate regulators. Histone chaperones are a group of proteins with diverse functions that are primarily involved in escorting histones to assemble nucleosomes and maintain the chromatin landscape. Whether distinct histone chaperone pathways control cell fate, and whether they function using related mechanisms, remains unclear. To address this, we performed a screen to assess the requirement of diverse histone chaperones in the self-renewal of hematopoietic stem and progenitor cells. Remarkably, all candidates were required to maintain cell fate to differing extents, with no clear correlation with their specific histone partners or DNA templated process. Among all the histone chaperones, the loss of the transcription-coupled histone chaperone SPT6 most strongly promoted differentiation, even more so than the major replication-coupled chromatin assembly factor complex CAF-1. To directly compare how DNA replication- and transcription-coupled histone chaperones maintain stem cell self-renewal, we generated an isogenic dual inducible system to perturb each pathway individually. We found that SPT6 and CAF-1 perturbations required cell division to induce differentiation but had distinct effects on cell cycle progression, chromatin accessibility and lineage choice. CAF-1 depletion led to S-phase accumulation, increased heterochromatic accessibility, particularly at H3K27me3 sites, and aberrant multilineage gene expression. In contrast, SPT6 loss triggered cell cycle arrest, altered accessibility at promoter elements, and drove lineage-specific differentiation, that is in part influenced by AP-1 transcription factors. Thus, CAF-1 and SPT6 histone chaperones maintain cell fate through distinct mechanisms, highlighting how different chromatin assembly pathways can be leveraged to alter cell fate.

overall_design: Bulk RNA-seq, ATAC-seq, ChIP-seq, CUT&RUN, CUT&Tag, and scRNA-seq were performed on immortalized granulocyte-macrophage progenitors (iGMPs) to examine the role of histone chaperones SPT6 and CAF-1 in iGMP maintenance. Histone marks were profiled in untreated iGMPs while bulk RNA-seq, ATAC-seq, and scRNA-seq were performed in untreated, SPT6 KD, and CAF-1 KD iGMPs and in induced neutrophil differentiation (bulk RNA-seq and ATAC-seq only). Refer to individual sub-series for additional details

first: Meijuan

last: Chen

first: Brian

first: Sihem

last: Cheloufi


title: MUC1-C DEPENDENCY IN DRUG RESISTANT HR+/HER2- BREAST CANCER IDENTIFIES A NEW TARGET FOR TREATMENT WITH AN ANTIBODY-DRUG CONJUGATE

city: Brookline

first: Ayako

last: Nakashoji

state: Massachusetts

address: 450 Brookline Avenue,, Dana Building, room 830

institute: Dana Farber Cancer Institute

summary: MUC1-C is a common effector of treatment resistant HR+/HER2- BC cells and is a potential target for their treatment

overall_design: RNA Seq in HR+/HER2- Cell lines with doxicicline inducible MUC1-C shRNA silencing

first: Donald

last: Kufe


title: METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells

first: Weiyu

last: Zhang

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

overall_design: Refer to individual Series


title: Transcription Factors Form a Ternary Complex with NIPBL/MAU2 to Localize Cohesin at Enhancers

city: Bethesda

first: Gordon

last: Hager

state: MD

address: 41 Center Dr

department: NCI

institute: NIH

summary: The cohesin complex is a key player in dynamic genome architecture adjustments. The loading of the cohesin complex on chromatin is believed to be achieved by the cohesin-loader Nipped-B homolog (NIPBL). Recently, we and others proposed that direct interactions with transcriptions factors (TFs) would lead to accurate positioning of NIPBL on the DNA. In this study, we identified remarkable protein-protein interaction motifs (PPIMs) in the NIPBL sequence. Mutations of those motifs dramatically alters: (i) the global NIPBL chromatin binding, (ii) the NIPBL-dependent transcriptional program and (iii) the NIPBL proteome network including TFs. While we found that the MAU2/NIPBL interaction was relying on those PPIMs, we further discovered that MAU2 was directly interacting with dozens of TFs. Concomitantly, we found that numerous TFs were also able to interact with NIPBL through PPIMs. Finally, using nuclear receptors as models and then focusing on the Glucocorticoid Receptor (GR), we mechanistically dissect a trimeric complex formed by GR, NIPBL and MAU2 and investigate the importance of those interactions for GR transcriptional program.

overall_design: We developed a knock-down/rescue system in 3134 cells for NIPBL. We first generated an IPTG-inducible shNIPBL cell line by transduction. Then we re-introduced the indicated constructs thanks to a piggybag integration protocol. Biological replicates of 3134 shNIPBL cells expressing the different NIPBL constructs were then sub-cultured in charcoal-stripped serum for 3 days with 1mM of IPTG when indicated. 2 hours priors haversting, appropriate samples were treated with 100nM of Dexametasone, then the RNA were processed for extraction following the manufactor instruction


title: DNA binding and mitotic phosphorylation protect polyglutamine proteins from assembly formation

city: Stanford

first: Joanna

last: Wysocka

address: 265 Campus Dr.

institute: Stanford University

summary: Polyglutamine expansion is associated with pathogenic protein aggregation in neurodegenerative disorders. However, long polyglutamine tracts are also found in many transcription factors (TFs), such as FOXP2, a TF implicated in human speech. Here, we explore how FOXP2 and other glutamine-rich TFs avoid unscheduled assembly. Throughout interphase, DNA binding, irrespective of sequence specificity, has a solubilizing effect. During mitosis, multiple phosphorylation events promote FOXP2’s eviction from chromatin and supplant the solubilizing function of DNA. Further, human-specific amino-acid substitutions linked to the evolution of speech map to a mitotic phospho-patch, the ‘EVO patch’, and reduce the propensity of the human FOXP2 to assemble. Fusing the pathogenic form of Huntingtin to either a DNA binding domain, a phospho-mimetic variant of this ‘EVO patch’ or a negatively charged peptide is sufficient to diminish assembly formation, suggesting that hijacking mechanisms governing solubility of glutamine-rich TFs may offer new strategies for treatment of polyQ expansion diseases.

overall_design: ChIP-seq of FoxP2-EGFP and mutants in HEK293 cells.

first: Shady

last: Saad

first: Tomek

last: Swigut

first: Saman

last: Tabatabaee

first: Pranav

last: Lalgudi

first: Daniel

last: Jarosz


title: Role of mucin MUC5AC on tumor angiogenesis and lung adenocarcinoma development

city: Omaha

first: Imayavaramban

last: Lakshmanan

state: Nebraska

address: Durham Research Center I, Room 7005 Omaha,

department: Biochemistry and Molecular Biology

institute: University of Nebraska Medical Center

summary: MUC5AC is a secretory type of mucin, which is significantly overexpressed in lung adenocarcinoma and associated with poor survival outcomes. Expression of MUC5AC and its sialylation is required for alteration of tumor matrix remodeling through interacting with integrin β4 in lung adenocarcinoma. We have previously shown that sialylated MUC5AC is required for lung adenocarcinoma cell growth and metastasis. To understand the molecular mechanism of MUC5AC in lung adenocarcinoma development, we performed RNA sequence analysis using MUC5AC knockdown cells (A549-shMUC5AC) and scramble cells (A549-shRNA). We observed that several tumor matrix proteins including VCAN and integrin β4 were significantly downregulated and are associated with tumor angiogenesis. In this study, we reported that sialylated MUC5AC induces tumor angiogenesis by altering tumor matrix protein VCAN during lung adenocarcinoma development and metastasis.

overall_design: Sample details: MUC5AC knockdown lung adenocarcinoma cells-A549-shMUC5AC (N=3) Scramble lung adenocarcinoma cells-A549-shRNA (N=3)

first: Zahraa

middle: W

last: Alsafwani

first: Surinder

last: Batra

first: Apar

last: Ganti


title: METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [4C]

first: Haifeng

last: Fu


title: Transcriptomic analysis of WT and Polg D257A/D257A bone marrow derived macrophages (BMDMs) challenged with Pseudomonas aeruginosa

status: Public on Apr 14 2025

city: Bar Harbor

first: Phillip

last: West

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: Mitochondrial diseases (MtD) represent a significant public health challenge due to their heterogenous clinical presentation, often severe and progressive symptoms, and lack of effective therapies. Environmental exposures, such bacterial and viral infection, can further compromise mitochondrial function and exacerbate the progression of MtD. Infections in MtD patients more frequently progress to sepsis, pneumonia, and other detrimental inflammatory endpoints. However, the underlying immune alterations that enhance immunopathology in MtD remain unclear, constituting a key gap in knowledge that complicates treatment and increases mortality in this vulnerable population. This dataset reports transcriptomic changes in bone marrow derived macrophages isolated from wild type (WT) C57BL/6J mice and a mouse model of polymerase gamma (Polg)-related MtD (Polg D257A/D257A), both at rest and six hours after infection with Pseudomonas aeruginosa strain PAO1. These data reveal a hyperinflammatory innate immune status in Polg D257A macrophages characterized by elevated expression of genes involved in interferon and inflammatory cell death pathways.  This work sheds new light on innate immune dysregulation in a model of mitochondrial dysfunction and reveals potential targets for limiting infection- and inflammation-related complications in Polg-related MtD.

overall_design: After 7 days of differentiation of mouse bone marrow progenitor cells into bone marrow-derived macrophages (BMDMs), macrophages were plated and challenged with GFP-expressing Pseudomonas aeruginosa strain O1 (PAO1) for six hours. Total cellular RNA from WT and Polg D257A/D257A BMDMs was prepared using the Quick-RNA microprep kit (Zymo Research) and subjected to Illumina Stranded mRNA library preparation and RNA sequencing at the Experimental Genomics Core of the Texas A&M Institute for Genome Sciences and Society. FASTQ files were normalized, processed, and analyzed using BaseSpace Sequence Hub (Illumina). In brief, the STAR algorithm of RNAseq Alignment V2.0.0 software was utilized to align the results to the Mus musculus/mm10 (RefSeq) reference genome, then RNA-seq Differential Expression V1.0.0 software was used to obtain differential gene expression values and determine statistically significant changes in Polg D257A/D257A BMDMs relative to WT.

first: Jordyn

last: VanPortfliet


title: Role of ST6GalNAc-I in immunosuppression and lung adenocarcinoma development

summary: Tumors are prone to immune escape by developing strategies to evade immunity. ST6GalNAc-I is an O-glycosyltransferase, which catalyzes the addition of sialic acid onto the first sugar GalNAc (Tn) and results in the formation of Neu5Acα2, 6GalNAc (STn) carbohydrate antigen. SialylTn plays an important role in tumor progression, angiogenesis, and metastasis. RNA sequence analysis was performed using genetically engineered LUAD mouse model tumors (KrasG12D/+; Trp53R172H/+; Ad-Cre (KPA) and KrasG12D/+; Ad-Cre (KA)). We have performed RNA sequence analysis using KPA tumors (N=3), KA tumors (N=3), and littermate control lung tissues (N=3).  In comparison to normal lung tissues, several genes were significantly overexpressed in KPA and KA-derived LUAD tumors, including Meg3, Slc7a5, Cxcr1, Awat1, Kng2, Gjb3, Mfi2, and Dlk1. More specifically, St6galnac-I was significantly overexpressed in aggressive-type KPA tumor tissues compared to KA and normal lung tissues. Expression of ST6GalNAc-I is associated with tumor progression and angiogenesis by immunosuppression. Mechanistically, ST6GalNAc-I promotes tumor cell sialylation that impacts tumor angiogenesis by altering mucin MUC5AC. Similarly, ST6GalNAc-I regulates Nectin2 sialylation which leads to immunosuppression and tumor progression. Overall, our study defined that ST6GalNAc-I is a critical molecule for tumor cell sialylation for disease aggressiveness.

overall_design: Sample details: Normal lung tissues (N) (N=3),  KrasG12D/+; Ad-Cre (KA) (N=3), (KrasG12D/+; Trp53R172H/+; Ad-Cre (KPA) N=3)


title: CXCL12-CXCR4 signaling mediates the formation of a macrophageal niche for mammary gland development and tumorigenesis

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University


title: Transcriptomic analysis of WT and Polg D257A/D257A lungs six hours after intratrachael instillation of Pseudomonas aeruginosa

summary: Mitochondrial diseases (MtD) represent a significant public health challenge due to their heterogenous clinical presentation, often severe and progressive symptoms, and lack of effective therapies. Environmental exposures, such bacterial and viral infection, can further compromise mitochondrial function and exacerbate the progression of MtD. Infections in MtD patients more frequently progress to sepsis, pneumonia, and other detrimental inflammatory endpoints. However, the underlying immune alterations that enhance immunopathology in MtD remain unclear, constituting a key gap in knowledge that complicates treatment and increases mortality in this vulnerable population. This dataset reports transcriptomic changes in lungs from wild-type mice and a mouse model of polymerase gamma (Polg)-related MtD (Polg D257A/D257A) six hours post intratrachael instillation of Pseudomonas aeruginosa strain PAO1. These data reveal a hyperinflammatory innate immune status in Polg D257A lungs characterized by elevated expression of genes involved in interferon and inflammatory cell death pathways.  This work sheds new light on innate immune dysregulation in a model of mitochondrial dysfunction and reveals potential targets for limiting infection- and inflammation-related complications in Polg-related MtD.

overall_design: WT and Polg D257A/D257A mice (4 females per genotype, 12 months old) on a C57BL/6J background were challenged with 1x10^5 GFP-tagged Pseudomonas aeruginosa strain PAO1 by intratrachael instillation under anesthesia. 6 hours post instillation, mice were sacraficed and lungs were isolated and snap frozen in liquid nitrogen. Frozen lung tissue was crushed into powder in liquid nitrogen, then total RNA was extracted using a Direct-Zol RNA miniprep kit (Zymo Research). Stranded libraries were constructed by the Genome Technologies Scientific Service at The Jackson Laboratory using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science according to the manufacturer’s protocol. Libraries were then sequenced 150bp paired-end on an Illumina NovaSeq X Plus using the 10B Reagent kit.  FASTQ files were imported into Partek Flow software (build 12.5.0, Illumina), reads were aligned with STAR Aligner 2.7.8a, then filtered and normalized into the assembeled count file.


title: Transcriptomic analysis of WT and Polg R292C/R292C lungs six hours after intratrachael instillation of Pseudomonas aeruginosa

summary: Mitochondrial diseases (MtD) represent a significant public health challenge due to their heterogenous clinical presentation, often severe and progressive symptoms, and lack of effective therapies. Environmental exposures, such bacterial and viral infection, can further compromise mitochondrial function and exacerbate the progression of MtD. Infections in MtD patients more frequently progress to sepsis, pneumonia, and other detrimental inflammatory endpoints. However, the underlying immune alterations that enhance immunopathology in MtD remain unclear, constituting a key gap in knowledge that complicates treatment and increases mortality in this vulnerable population. This dataset reports transcriptomic changes in lungs from wild-type mice and a mouse model of polymerase gamma (Polg)-related MtD (Polg R292C/R292C) six hours post intratrachael instillation of Pseudomonas aeruginosa strain PAO1. These data reveal a hyperinflammatory innate immune status in Polg R292C lungs characterized by elevated expression of genes involved in interferon and inflammatory cell death pathways.  This work sheds new light on innate immune dysregulation in a model of mitochondrial dysfunction and reveals potential targets for limiting infection- and inflammation-related complications in Polg-related MtD.

overall_design: WT and Polg R292C/R292C mice (3 males per genotype, 3 months old) on a C57BL/6N background were challenged with 1x10^6 GFP-tagged Pseudomonas aeruginosa strain PAO1 by intratrachael instillation under anesthesia. 6 hours post instillation, mice were sacraficed and lungs were isolated and snap frozen in liquid nitrogen. Frozen lung tissue was crushed into powder in liquid nitrogen, then total RNA was extracted using a Direct-Zol RNA miniprep kit (Zymo Research). Stranded libraries were constructed by the Genome Technologies Scientific Service at The Jackson Laboratory using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science according to the manufacturer’s protocol. Libraries were then sequenced 150bp paired-end on an Illumina NovaSeq X Plus using the 10B Reagent kit.  FASTQ files were imported into Partek Flow software (build 12.5.0, Illumina), reads were aligned with STAR Aligner 2.7.8a, then filtered and normalized into the assembeled count file.


title: TGFB1/CXCL5 Axis Regulation by LCN2 Overexpression: A Promising Strategy to Inhibit Colorectal Cancer Metastasis and Enhance Prognosis

city: Xi'an

first: Xiaotian

last: Song

address: Changle west road

institute: xijing hospital

summary: Background: Distant metastasis remains a major reason for the high recurrence and mortality of colorectal cancer (CRC). However, the underlying molecular mechanisms driving metastasis in CRC remain poorly understood. In this study, we investigated the mechanisms underlying the inhibitory effects of lipocalin-2 (LCN2) on CRC metastasis. Methods: We assessed the expression and clinical significance of LCN2 in human CRC specimens and CRC cell lines using, immunohistochemistry, and western blot analyses. We evaluated the migratory and invasive capabilities of CRC cells influenced by LCN2 using in vitro transwell assays and in vivo lung metastatic models. RNA sequencing and proteome analysis were employed to identify potential downstream targets of LCN2. Rescue experiments were conducted to further elucidate the potential mechanisms of LCN2 and its downstream effectors in CRC. Results: LCN2 exhibited high expression levels in human CRC tissues and an inverse correlation with N classification, advanced AJCC stages, and shorter overall survival. LCN2 expression independently predicted a more favorable outcome for CRC patients. Upregulation of LCN2 effectively suppressed CRC cell metastasis both in vitro and in vivo. Mechanistically, Transforming growth factor beta 1 (TGFB1) and C-X-C motif chemokine ligand 5 (CXCL5) were identified as downstream effectors of LCN2, with LCN2 inhibiting CRC metastasis through repression of the TGFB1/CXCL5 axis. Furthermore, either TGF-βR1 inhibitor SB431542 or CXCR2 antagonist SB225002 treatment moderately decreased the migratory and invasive capabilities of DLD-1-LV-shLCN2 cells, whereas the combination treatment of the two agents dramatically decreased the migratory and invasive capabilities of DLD-1-LV-shLCN2 cells. Conclusions: This study underscores LCN2 as an independent protective factor and prognostic biomarker for CRC patients. Combined treatment with the SB431542 and the SB225002 significantly attenuated LCN2-related CRC metastasis. Targeting the LCN2/TGFB1/CXCL5 axis emerges as a promising therapeutic strategy for managing LCN2-related metastatic CRC.

overall_design: RNA-seq technology was used to detect differentially expressed genes in DLD-1-LV-shLCN2 cells and DLD-1-LV-shNC cells

first: Shuai

last: Xu

first: Dan

first: Qingchuan

last: Zhao

first: Pengfei

last: Yu


title: Disruption of the Novel Nested Gene Aff3ir Mediates Disturbed Flow-Induced Atherosclerosis in Mice

city: Tianjin

first: Shuo

last: He

address: 22 Weather Station Road

institute: Tianjin Medical University

summary: Disturbed shear stress-induced endothelial atherogenic responses are pivotal in the initiation  and progression of atherosclerosis, contributing to the uneven distribution of atherosclerotic  lesions. This study investigates the role of Aff3ir-ORF2, a novel nested gene variant, in disturbed flow-induced endothelial cell activation and atherosclerosis.

overall_design: MEFs were isolated from WT and AFFEir-ORF2-/- mice.Then we performed whole transcriptome analysis using RNA-sequencing.

first: Yi

last: Zhu

first: Jinlong


title: Transcriptomic profiling of the preterm,hyperoxia exposed, rabbit's lung

city: PARMA

first: Barbara

last: Montanini

state: PR

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

institute: University of Parma

summary: Bronchopulmonary dysplasia (BPD) is a multifactorial chronic lung disease of premature neonates. The development of BPD depends on several prenatal and postnatal factors that induce inflammation, altering alveolar growth and pulmonary vascular development. Animal models are essential to investigating the precise molecular pathways leading to BPD. The preterm rabbit combines many advantages of both small (e.g., rodents) and large BPD models (i.e., preterm lambs and baboons). For instance, preterm rabbits display mild-to-moderate respiratory distress at delivery, which, along with ongoing exposure to high oxygen concentration (95% O2), leads to functional and morphological lung changes that resemble the phenotype of human BPD. Nevertheless, the molecular pathways leading to the development of the BPD-like phenotype in this model remain largely ununderstood. We, therefore, aimed to characterize the longitudinal gene expression in the lungs of preterm rabbits continuously exposed to 95% O2 on postnatal days 3, 5, and 7. The longitudinal transcriptomic analysis revealed different expression patterns for several genes and pathways. Over time, extracellular matrix organization and angiogenesis were increasingly downregulated, while apoptosis, RNA processing, and inflammation showed the opposite trend.

overall_design: On the 28th day of gestation (term 31 days), does (3.8±0.3 kg of body weight) were initially sedated with intramuscular (i.m.) medetomidine 2 mg/kg (Domitor®, Orion Pharma, Finland). Ten minutes later, the animals received 25 mg/kg of ketamine (Imalgene®, Merial, France) and 5 mg/kg of xylazine (Rompun®, Bayer, Germany) i.m. When adequate sedation was reached, does were placed in the supine position, shaved on the abdomen, and euthanized with an overdose of 100 mg/kg of pentothal sodium (50 mg/kg MSD Animal Health, USA). Pups were then extracted through hysterectomy. After one hour, surviving pups were weighed and placed into incubators (Okolab, Naples, Italy) under normoxia (21% O2) or hyperoxia (95 % or 70 % O2) conditions for up to 7 days. Before lung harvesting, pups were euthanized with a pentothal sodium overdose.

first: Nicola

last: Casiraghi

first: Ilaria

last: Minato

first: Carlotta

last: Boggi

first: Francesca

last: Ricci

first: Matteo

last: Storti


title: Autophagy disruption and mitochondrial stress precede photoreceptor necroptosis in multiple mouse models of inherited retinal disorders

city: Edinburgh

first: Roly

last: Megaw

address: Crewe Road

country: United Kingdom

institute: University of Edinburgh

summary: Inherited retinal diseases (IRDs) are a leading cause of blindness worldwide. One of the greatest barriers to developing treatments for IRDs is the heterogeneity of these disorders, with causative mutations identified in over 280 genes. It is therefore a priority to find therapies applicable to a broad range of genetic causes. To do so requires a greater understanding of the common or overlapping molecular pathways that lead to photoreceptor death in IRDs and the molecular processes through which they converge. Here, we characterise the contribution of different cell death mechanisms to photoreceptor degeneration and loss throughout disease progression in humanised mouse models of IRDs. Using single-cell transcriptomics, we identify common transcriptional signatures in degenerating photoreceptors. Further, we show that in genetically and functionally distinct IRD models, common early defects in autophagy and mitochondrial damage exist, triggering photoreceptor cell death by necroptosis in later disease stages. These results suggest that, regardless of the underlying genetic cause, these pathways likely contribute to cell death in IRDs. These insights provide potential therapeutic targets for novel, gene-agnostic treatments for IRDs applicable to the majority of patients.

overall_design: One mutant sample was compared to one wild type control sample in each experiment. Control samples are from age-matched littermates.

first: Fay

last: Newton

first: Mihail

last: Halachev

first: Linda

last: Nguyen

first: Lisa

last: McKie

first: Pleasantine

last: Mill


title: METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [RNA-Seq]

city: Ithaca

first: Weiyu

last: Zhang

address: 215 Tower Rd, Biotechnology Building

institute: Cornell University

summary: Using a METTL3 inducible knockout (iKO) system in human expanded potential stem cells (hEPSCs), we uncovered that unlike in mESCs, METTL3 was indispensable for hPSCs’ maintenance, and that loss of METTL3 caused significant upregulation of naïve pluripotency genes accompanied with impaired hEPSCs differentiation particularly towards to both trophoblastic and amnionic lineage. Mechanistically, METTL3 iKO in hPSCs substantially increased expression of two primate-specific transposable elements (TEs), SVA_D and HERVK/LTR5_Hs.

overall_design: To investigate the function of RNA m6A methylation in hPSCs, we attempted to knock out the main methyltransferase METTL3 in hEPSCs. We used a knockout and inducible transgenic expression (iKO) system to transgenically express a METTL3 cDNA and rescue the KO phenotype. We firstly introduced a doxycycline (DOX)-inducible METTL3 cDNA stably integrated into hEPSCs by piggyBac transposition followed by knocking out the endogenous METTL3 by the CRISPR/Cas9. In the presence of DOX, two independent iKO cell lines with different METTL3 mutations were selected for subsequent investigation. To ensure comparable METTL3 expression levels in METTL3 iKO hEPSCs as in normal cells, we titrated DOX concentration and selected 5.0 ng/ml. Upon DOX withdrawal, exogenous METTL3 protein became undetectable after 5 days of culturing over 2 passages

first: Haifeng

last: Fu


title: Effect of GSK3 inhibition on the transcriptional signature of human alveolar macrophages

first: Amaya

last: Puig Kröger

summary: The remarkable plasticity of macrophages is tied to extracelular cues and their subsequently signaling pathways. The transcriptional factor MAFB is critical to prompt the aquisition of an anti-inflammatory phenotype in macrophages. As MAFB activity and stability is highly regulated by GSK3,  we explored the molecular impact of blocking GSK3 on the gene expression profile of human alveolar macrophages (AMØ), whose development and gene expression profile is GM-CSF-dependent. GSK3 inhibition skewed the transcriptional profile of AMØ towards an anti-inflammatory phenotype.

overall_design: mRNA profiles of human alveolar macrophages (AMØ) purifed from bronchoalveolar lavage fluid in presence or absence of 10 micromolar of GSK3 a/β inhibitor (CHIR99021) for 24 hours.

first: Israel

last: Ríos

first: Rafael

last: Delgado

last: Puig-Kröger

first: Ángel

last: Corbí


title: Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA

city: Wageningen

first: Daan

middle: C.

last: Swarts

address: Stippeneng 4

department: Laboratory of Biochemistry

country: Netherlands

institute: Wageningen University

summary: Thhe dataset contains small interfering DNAs (siDNAs) that associated with MaAgo during heterologous expression in E. coli in absence or presence of MaACE1. The goal of the study was to 1) determine what type of siDNAs associate with MaAgo 2) from what sequences these siDNAs are derived and 3) whether MaACE1 influences the length or type of the siDNAs associated with MaAgo.

overall_design: His-MBP-tagged-MaAgo was heterologously expressed in E. coli in presence or absence of MaACE1. His-MBP-tagged-MaAgo was purified using niNTA purification and subsequent Amylose purifcation. Nucleic acids were extracted from MaAgo, and a small DNA library was constructed as previoiusly described by Olovnikov et al. (https://pubmed.ncbi.nlm.nih.gov/24034694/). Detailed method are given in the associated publication.

first: Bobadilla

middle: U

last: Pilar

first: Koopal

last: Balwina

first: Swarts

middle: C

last: Daan


title: A spatio-temporal brain miRNA expression atlas identifies sex-independent age-related microglial driven miR-155-5p increase [microglia]

status: Public on Apr 13 2025

city: Saarbrücken

first: Annika

last: Engel

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

type: Non-coding RNA profiling by high throughput sequencing

summary: An in-depth understanding of the molecular processes composing aging is crucial to develop therapeutic approaches that decrease aging as a key risk factor for cognitive decline. Herein, we present a spatio-temporal brain atlas (15 different regions) of microRNA expression across the mouse lifespan (7 time points) and two aging interventions. MicroRNAs are promising therapeutic targets, as they silence genes by complementary base-pair binding of messenger RNAs and mediate aging speed. We first established sex- and brain-region-specific microRNA expression patterns in young adult samples. Then we focused on sex-dependent and independent brain-region-specific microRNA expression changes during aging. We identified three sex-independent brain aging microRNAs (miR-146a-5p, miR-155-5p and miR-5100). For miR-155-5p, we showed that these expression changes are driven by aging microglia and target mTOR signaling pathway components and other cellular communication pathways. In this work, we identify strong sex-brain-region-specific aging microRNAs and microglial miR-155-5p as a promising therapeutic target.

overall_design: Microglia from four young (3 months) and four aged (21 months) male mice (C57BL/6) were sampled.

first: Viktoria

last: Wagner

first: Oliver

last: Hahn

first: Aulden

middle: G

last: Foltz

first: Micaiah

last: Atkins

first: Amila

last: Beganovic

first: Ian

middle: H

last: Guldner

first: Nannan

last: Lu

first: Aryaman

last: Saksena

first: Ulrike

last: Fischer

first: Nicole

last: Ludwig

first: Eckart

last: Meese

first: Tony

last: Wyss-Coray

first: Andreas

last: Keller


title: Multiple anti-tumor programs are activated by blocking BAD phosphorylation: RNA-seq of Bad+/+ or Bad3SA MMTV-PyMT breast tumors

city: Edmonton

first: John Maringa

last: Githaka

state: AB

address: 5-73 Medical Sciences Building, University of Alberta

institute: University of Alberta

summary:
Purpose: The goals of this study are to compare transcriptome (RNA-seq) differences between wild type and mutant Bad using MMTV-PyMT mouse breast cancer model.
Methods: MMTV-PyMT breast cancer model tumors samples (6 independent mice for each genotype) were RNA-sequenced. Reads quality control and alignment to reference genome was done using fastp and STAR aligner respectively. Differentially expressed genes (DEGs) were computed using DESeq2.

overall_design: Breast tumors for six independent mice for each genotype (PyMT-Bad+/+ and PyMT-Bad3SA end-point age matched mice), were harvested and snap-frozen in RNAlater® solution (Sigma Aldrich cat#R0901). To extract RNA, samples were thawed on ice and tissue retrieved with sterile forceps. Excess RNAlater® Solution was blotted away with an absorbent lab wipe. Tissue was then promptly lysed with a hand homogenizer (VWR Cat# 47747-370) and RNA extraction was carried out following the manufacturers protocol (QIAGEN’s RNAeasy plus mini kit cat#74134). Elution was done using RNase free water. Nanodrop (NanoDrop™ 2000/2000c model) was used to measure the RNA samples concentration. 100ng/μl RNA samples were made by diluting 2000ng of RNA to a final volume of 20μl RNase free water. RNA samples were submitted to Génome Québec for sequencing using the Illumina NovaSeq 6000 sequencer in 100bp paired-end.

first: John

first: Ing

last: Goping


title: Navigating the Cold: Integrative Transcriptome Sequencing Approach Reveals Ionoregulatory and Whole-Body Responses to Cold Acclimation in Drosophila ananassae

city: Planegg-Martinsried

first: Vera

middle: Miyase

last: Yilmaz Bachmaier

state: Bavaria

address: Grosshaderner St. 2

department: Evolutionary Biology

institute: LMU Munich

summary: Understanding how species adapt to changing environments is a major goal in evolutionary biology and can elucidate the impact of climate change. Climate imposes inevitable effects on the geographical distribution of insects as their body temperature primarily depends on the environment. The vinegar fly Drosophila ananassae expanded from its tropical ancestral range to more temperate regions, which requires adaptation to colder temperatures. Transcriptome and genome-wide association studies focusing on the ancestral-range population identified the targets of selection related to ionoregulatory tissues. However, how cosmopolitan D. ananassae adapted to colder environments, where low temperatures last longer, is still unknown. Here, we present a study on the effect of long-term cold exposure on D. ananassae, examining the gene expression variation in the whole body and the ionoregulatory tissues, namely the hindgut and the Malpighian tubule. To elucidate molecular mechanisms of cold adaptation during species expansion, we included cold-tolerant and cold-sensitive strains from the ancestral species range and cold-tolerant strains from the derived species range. We show that cold acclimation improves cold tolerance and results in differential expression of more than half of the transcriptome in the ionoregulatory tissues and the whole body. Notably, we provide complementary insight into molecular processes at four levels: strains, populations, phenotypes, and tissues. By determining the biochemical pathways of phenotypic plasticity underlying cold tolerance, our results enhance our understanding of how environmental changes affect thermal adaptation in natural populations.

overall_design: To investigate the cold acclimation response of different Drosophila ananssae populations (of ancestral origin or derived) having different cold toleance phenotypes (tolerant or sensitive) in the whole body and in the ionoregulatory tissues -hindgut and Malpighian tubules-, we exposed the flies to mild cold condition (10˚C) for 4 days. Differential expression analysis was performed to compare populations and phenotypes.

last: Yilmaz

first: Zhihui

last: Bao

first: Sonja

last: Grath


title: Oral ENPP1 inhibitor designed using generative AI as next generation STING modulator for solid tumors

city: Shanghai

first: Hui

last: Cui

address: JinKe road

institute: Insilico Medicine

summary: NCOMMS-24-54326: Despite the STING-type-I interferon pathway playing a key role in effective anti-tumor immunity, the therapeutic benefit of direct STING agonists appears limited. In this study, we used several artificial intelligence techniques and patient-based multi-omic data to show that Ectonucleotide Pyrophosphatase/Phosphodiesterase 1 (ENPP1), which hydrolyzes STING-activating cyclic GMP-AMP (cGAMP), is a safer and more effective STING-modulating target than direct STING agonism in multiple solid tumors. We then leveraged our generative chemistry artificial intelligence-based drug design platform to facilitate the design of ISM5939, an orally bioavailable ENPP1-selective inhibitor capable of stabilizing extracellular cGAMP and activating bystander antigen-presenting cells without inducing either toxic inflammatory cytokine release or tumor-infiltrating T-cell death. In murine syngeneic models across cancer types, ISM5939 synergizes with targeting the PD-1/PD-L1 axis and genotoxic chemotherapy in suppressing tumor growth with good tolerance. Our findings provide new evidence supporting ENPP1 as a novel innate immune checkpoint across solid tumors and reports the first AI design-aided ENPP1 inhibitor, ISM5939, as a cutting-edge STING modulator for cancer therapy, paving a new path for immunotherapy advancements.

overall_design: To further investigate how the tumor immune microenvironment was remodeled, tumor tissues from all groups（Vehicle, Cisplation,ISM033-154,ISM033-154-BID+Cis） were subjected to bulk RNA sequencing

first: Congying

last: Pu

first: Xin

last: Cheng

first: Man

last: Zhang

first: Luoheng

last: Qin

first: Zhilin

last: Ning

first: Wen

first: Shan

last: Chen

first: Yuhang

last: Qian

first: Feng

last: Wang

first: Ling

first: Xiaoxia

last: Lin

first: David

last: Gennert

first: Frank

last: Pun

last: Ren

first: Alex

last: Zhavoronkov


title: Novel Ribociclib Derivative RB-1 Exhibits Anti-breast Cancer Actions by Regulating p53 and Cell Cycle Pathways

status: Public on Apr 12 2025

city: Lianyungang

first: Sen

address: No. 59 Cangwu Road, Haizhou District, Lianyungang City, Jiangsu Province

institute: Jiangsu Ocean University

summary: Breast cancer remains the most prevalent malignancy among women globally, with its incidence continuing to rise and ranking as the leading cause of cancer-related mortality in females. Ribociclib, a cyclin-dependent kinases 4 and 6 (CDK4/6) inhibitor, suppresses tumor cell proliferation by blocking the transition from the G1 to S phase. This study investigates the molecular mechanisms and therapeutic efficacy of RB-1 (7-cyclopentyl-N-ethyl-N-methyl-2-((3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)amino)-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide), a novel Ribociclib derivative, in inhibiting breast cancer progression. The effects of RB-1 on breast cancer cell viability were evaluated via MTT assay. In vitro and in vivo experiments demonstrated that RB-1 significantly inhibited cell proliferation, colony formation, and the proportion of EdU-positive cells in multiple breast cancer cell lines (e.g., MDA-MB-231 and SKBR3). The chicken chorioallantoic membrane (CAM) assay revealed that RB-1 treatment markedly suppressed tumor angiogenesis, outperforming Ribociclib. Mechanistic studies indicated that RB-1 regulates the p53 signaling pathway and cell cycle-related targets (e.g., E2F targets, mitotic spindle assembly), specifically inhibiting CDK4/6-mediated cell cycle progression. Furthermore, machine learning analysis identified Hyaluronan-Mediated Motility Receptor (HMMR) as a diagnostic and prognostic biomarker for breast cancer, with its expression significantly correlating with tumor-infiltrating immune cells. This study highlights the anti-cancer potential of RB-1 and elucidates its molecular mechanisms, offering a promising therapeutic candidate and novel targets for breast cancer treatment.

overall_design: In order to investigate the role and mechanism of RB-1 in Breast Cancer, we treated MDA-MB-231 cells with RB-1 and without treatment. Then, we performed gene expression profiling analysis using RNA seq data from RB-1 and DMSO cells.

first: Jing

last: JI


title: New strategy for breast cancer treatment: Neoribocic inhibits tumor proliferation through cell cycle blockade

status: Public on Apr 11 2025

first: Song

last: wei

address: China

summary: As one of the most common malignant tumors in the world, breast cancer is still a major challenge to human health despite the continuous improvement of treatment methods. Therefore, it is of great clinical significance to develop new anti-breast cancer drugs to improve the therapeutic effect. As a CDK4/6 inhibitor, Ribociclib has shown potential in breast cancer treatment. Based on this, we designed and synthesized a new type of ribocyclib derivative Neoribocic, and deeply studied its role mechanism in breast cancer.  Research results show that Neoribocic can significantly inhibit the proliferation, migration and invasion ability of breast cancer cells in in vitro experiments, and show excellent anti-tumor activity. By analyzing MDA-MB-231 cells treated with Neoribocic through RNA sequencing (RNA-Seq), we found that Neoribocic may block the progression of breast cancer cells in the G2/M stage by activating the p53 signaling pathway, thus exerting their anti-tumor effect. . In addition, in vivo experiments further confirm that Neoribocic can not only effectively inhibit tumor growth, but also significantly inhibit the angiogenesis in the chicken embryonic cyst membrane, suggesting that it may have an anti-angiogenesis effect.

overall_design: In order to investigate the role and mechanism of Neoribocic in Breast Cancer, we treated MDA-MB-231 cells with Neoribocic and without treatment. Then, we performed gene expression profiling analysis using RNA seq data from Neoribocic and DMSO cells.

first: Kadirya

last: Asan


title: Bulk RNA seq of in vitro co- culture of distinct subtypes of oral cancer associated primary fibroblasts and oral cancer cell line

city: Kalyani

first: Sandeep

last: Singh

state: West Bengal

address: NSS TB Hospital, Block A

department: Biomedical Genomics

country: India

institute: BRIC-National Institute of Biomedical Genomics

summary: Heterogeneity in oral cancer associated fibroblasts (CAFs)in tumor microenvironment modulate plasticity of malignant epithelial cells to drive tumorigenesis, ultimately leading to poorer clinical outcome. Myofibroblastically differentiated CAFs induce stochastic plasticity in oral cancer cells. We co-cultured non-myofibroblasts and myofibroblasts with oral cancer cell lines to understand distinct CAF driven cancer cell transcriptional reprogramming.

overall_design: Gene expression profiling analysis of RNA seq data from in-vitro 48 hrs co-culture of untreated(C1 CAF) and TGFb treated primary CAFs (myofibroblasts/C2 CAF) with oral cancer cell line SCC070. CAFs and SCC070 cells were sorted  by flow cytometry using CD90 marker before library preparation.

first: Paromita

last: Mitra

first: Nidhan

last: Biswas

first: Ankit

last: Patel


title: A spatio-temporal brain miRNA expression atlas identifies sex-independent age-related microglial driven miR-155-5p increase [brain regions]

first: Annika

last: Engel

overall_design: From 75 C57BL/6JN mice (male and female), we obtain samples from fifteen different brain regions (three cortical regions (motor cortex, visual cortex and entorhinal cortex), anterior (dorsal) and posterior (ventral) hippocampus, hypothalamus, thalamus, caudate putamen (part of the striatum), pons, medulla, cerebellum and the olfactory bulb, corpus callosum, choroid plexus and the subventricular zone) and seven differnt age stages (3 month to 28 months). Analysing was done using the miRNA sequencing data.

first: Viktoria

last: Wagner

first: Oliver

last: Hahn

first: Aulden

last: Foltz

first: Micaiah

last: Atkins

first: Amila

last: Beganovic

first: Ian

last: Guldner

first: Nannan

last: Lu

first: Aryaman

last: Saksena

first: Ulrike

last: Fischer

first: Nicole

last: Ludwig

first: Eckart

last: Meese

first: Tony

last: Wyss-Coray

first: Andreas

last: Keller


title: Hepatic iNKT cells facilitate colorectal cancer metastasis by inducing a fibrotic niche in the liver

city: Zurich

first: Maries

last: van den Broek

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

summary: To better understand how disseminated cancer cells activate hepatic iNKT cells, we performed single-cell RNA sequencing of NKT cells sorted from livers 24 hours after intrasplenic injection of PBS or APTKA organoids

overall_design: Hepatic NKT cells (single, live, CD45+, CD115-, F4/80-, CD19-, Ly6G-, CXCR6+, CD8-, NK1.1+, NKp46- cells) were isolated by fluorescence-activated cell sorting (FACS) 24 hours after intrasplenic injection of PBS or APTKA organoids. 5 mice per conditions were used. Cells from each sample were labeled using the BD Single-Cell Multiplexing Kit and pooled according to their respective conditions.

first: Marc

last: Nater


title: The immune NIK1/RPL10/LIMYB signaling module regulates photosynthesis and translation under biotic and abiotic stresses

status: Public on Apr 10 2025

city: Vicosa

first: Elizabeth

middle: Pacheco

last: Fontes

state: Minas Gerais

address: Av. PH Rolfs, S/N

country: Brazil

institute: Universidade Federal de Vicosa

summary: Photosynthesis and translation are targets of metabolic control and development in plants, yet how stress signals coordinately regulate these opposing energy-producing and consuming processes remains enigmatic. Here, we unravel a growth control circuit that ties photosynthesis to translational control in response to biotic and abiotic signals. Our findings reveal that the L10-INTERACTING MYB DOMAIN-CONTAINING PROTEIN (LIMYB), a key player of the NUCLEAR SHUTTLE PROTEIN-INTERACTING KINASE 1 (NIK1)/ RIBOSOMAL PROTEIN L10 (RPL10) antiviral signaling pathway, not only downregulates translation genes, but also represses photosynthesis-related genes and photosynthesis itself. LIMYB repressor activity regulated by phosphorylation is crucial for the decline in photosynthesis under stress. NIK1 activation by PAMPs or the phosphomimetic NIK1-T474D represses photosynthesis-related genes and photosynthesis in control but not in lymyb lines. Furthermore, heat and osmotic stress also activate the NIK1/RPL10/LIMYB signaling circuit in wild type. These stresses induce NIK1 phosphorylation, but not marker gene repression, in limyb, indicating that LIMYB connects NIK1 activation to stress-mediated downregulation of translation- and photosynthesis-related genes. This coordinated repression via the NIK1/RPL10/LIMYB module may help plants adapt to changing environments.

overall_design: Were used three biological replicates of a pool of 12-day-old Col-0, LIMYB-32-L1, and LIMYB-32-L3 seedlings and examined differences between Col-0 and LIMYB lines using the Deseq2 differential gene expression method39,40. RNA sequencing was obtained using the Illumina Hi-seq 2500 platform. Libraries for RNA-seq were prepared with the TrueSeq-RNA Sample Prep Illumina kit (Illumina, cat # 20020595). The paired-end 100-bp

first: Marco Aurélio

last: Ferreira

first: Ruan

last: Teixeira

first: Otávio

last: Brustolini

first: Thainá

last: Saia

first: James

last: Jean-Baptiste

first: Nathalia

last: Ribeiro

first: Sâmera

last: Breves

first: Fellipe

last: Sampaio

first: Eulálio

last: Santos

first: Borys

last: Leon

first: Celio

last: Oliveira

first: Christiane

last: Duarte

first: Lucas

last: Lima

first: Leandro

first: Humberto

last: Ramos

first: Pedro

last: Reis


title: RNA polymerase I transcription is essential for establishing the chromatin architecture in mouse but not in human embryos [ChIP-seq]

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: The distinctions in 3D genome between humans and mice, as well as the mechanisms underlying de novo organization, remain unexplored. Our study revealed an extensive reorganization of the 3D genome from human oogenesis to early embryogenesis, displaying significant differences to the mouse, notably dramatically attenuated TADs at GV stage in human. The 3D genome reconstruction timing also differs between species, which it initiates at the 4-cell stage in human, while in mouse, it commences at the 2-cell stage in mouse. We discovered that RNA polymerase I (Pol I) is crucial for establishing the chromatin structures during mouse embryogenesis, but not in human embryos. Intriguingly, the absence of Pol I transcription weakens TAD structure in mouse female germline stem cells, whereas it fortifies it in human counterparts. Our findings provide valuable insights into chromatin organization during germ cell and embryonic development and have implications for fertility preservation and birth defect prevention.

overall_design: Examination of the chromatin architecture in human and mouse gametes development and early embryonic development.

first: Changliang

last: Hou


title: RNA polymerase I transcription is essential for establishing the chromatin architecture in mouse but not in human embryos [RNA-seq]


title: Dynamics of bacterial operons during genome-wide stresses is influenced by premature terminations and internal promoters

city: Tampere

first: Rahul

last: Jagadeesan

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

summary: Bacterial gene networks have many operons, each coordinating the kinetics of a few genes in time and strength. In E. coli, nearly half of these operons also have internal promoters, which allow regulating the downstream genes, independently from upstream genes. We studied their role during genome-wide stresses targeting a few key elements of the transcription machinery, namely, RNAP and Gyrase. We show that absolute differences in response strength between genes in the same operon follow a sinusoidal function of the distance between them. This results from the combined effect of elongation fall-offs and internal promoters. The frequency of this function is regulated by the positioning of internal promoters, while its amplitude differs with the perturbation strength. Moreover, we find that positive supercoiling buildup partially explains the RNAP fall-off rates. Finally, we report similar sinusoidal patterns in Escherichia coli cells subject to other stresses, as well as in Bacillus subtilis, Corynebacterium glutamicum, and Helicobacter pylori. Overall, our results suggest that the strength, number, and positioning of internal promoters in operons are influenced by a genome-wide need to compensate for RNAP fall-offs and provide distal genes in the operon with similar response strength as genes proximal to the primary promoter.

overall_design:
Examination of genome-wide responses under Antibiotics (Novobiocin and Rifampicin)
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GENEWIZ, Inc. (Leipzig, Germany)

first: Suchintak

last: Dash

first: Cristina

last: Palma

first: Ines

last: Baptista

first: Vatsala

last: Chauhan

first: Jarno

last: Mäkela

first: Andre

middle: S


title: Platelet-Rich Fibrin Potentiates Dental Pulp Stem Cell Angiogenesis through Mitochondrial Transfer-Meditated Metabolic-Signaling Integration

city: Changchun

first: Siyu

last: Chen

address: Qinghua Road

institute: Jilin University

summary: Therapeutic angiogenesis in inflammatory microenvironments is constrained by mitochondrial dysfunction in mesenchymal stem cells (MSCs). This study demonstrates that platelet-rich fibrin (PRF) serves as a mitochondrial reservoir that transfers functional mitochondria to dental pulp stem cells (DPSCs) via extracellular vesicle-dependent mechanisms. Multi-omics analyses revealed that PRF-derived mitochondria activated the tricarboxylic acid (TCA) cycle in DPSCs, driving concurrent fatty acid biosynthesis and JAK2/STAT4-mTOR pathway activation. This metabolic-signaling integration enhanced VEGF secretion and cell migration under inflammatory conditions. PRF’s fibrin matrix further sustained mitochondrial release while providing topological guidance for DPSC recruitment. In vivo, PRF-DPSC composites significantly accelerated wound closure and neovascularization compared to controls, supported by histomorphometric and molecular analyses. Beyond cytokine delivery, this work establishes PRF as a mitochondrial-augmented biomaterial to reverse MSC metabolic insufficiency, offering a translatable strategy for vascular regeneration in hostile microenvironments.

overall_design: Siyu, Chen

first: Jing

last: Zhou

first: Yihan

last: Wang

first: Xiuyu

last: Liu

first: Huixin

last: Lv

first: Yanmin


title: Lack of a role of NHE4 in renal ammonia metabolism

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

institute: University of Alabama at Birmingham

summary: Kidneys from a male and female mouse were used for single nucleus isolation and transcriptome analyses using the 10X Genomics platform.

overall_design: Frozen kidney from  mice were on the C57/Bl6 background strain and were homozygous for the floxed AR allele (AN Harris, RA Castro, HW Lee, JW Verlander, and ID Weiner. Role of the Renal Androgen Receptor in Sex Differences in Ammonia Metabolism.  Am J Physiol Renal 321: F629-F44, 2021).  The WT mice used for this paper were Cre-negative mice.  Samples were homogenized with Nuclei lysis buffer plus RNAse inhibitors to generate single nucleus suspensions. Nuclei were loaded into Chromium Next GEM Chip G Single Cell Kit and libraries made with the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1.  Sequencing was performed with a targeted depth of 20K reads per nucleus on the NovaSeq 6000 with the UAB Genomics Core (Director Dr. Michael Crowley). Fastq files were mapped using mm10 genome, and fragments were counted with the 10X Genomics CellRanger pipeline (7.1.0).

first: Autumn

middle: N

last: Harris

first: Hyun-Wook

last: Lee

first: I

last: Weiner


title: A novel Ribociclib derivative, YW-LF, exerts anti-breast cancer effects by activating the p53 pathway.

first: Song

middle: meng

last: wei

summary: Breast cancer remains the most prevalent malignancy among women worldwide. Although ribociclib, a cyclin-dependent kinase 4/6 (CDK4/6) inhibitor, has demonstrated significant antitumor activity in breast cancer therapy, its clinical application is limited by hematological toxicity, cardiotoxicity, and patient tolerance. In this study, we synthesized a novel ribociclib derivative, YW-LF, and systematically evaluated its antitumor activity and underlying mechanisms. Through a series of in vitro assays—including MTT, colony formation, EdU incorporation, transwell migration, and invasion experiments—as well as in vivo evaluation using a chick chorioallantoic membrane (CAM) model, we demonstrated that YW-LF significantly inhibited breast cancer cell proliferation, migration, and invasion, while effectively suppressing tumor growth and angiogenesis. Compared to the positive control ribociclib, YW-LF exhibited superior antitumor efficacy. Transcriptomic profiling revealed that YW-LF suppressed tumor progression by activating the p53 signaling pathway and apoptosis-related pathways. Western blot analysis further validated the dysregulation of key proteins, providing protein-level evidence for its mechanism of action. Additionally, machine learning-based bioinformatics analysis identified three core genes (ADRB1, ATOH8, and CCNE2) with potential clinical significance in breast cancer diagnosis and treatment. Immune infiltration analysis highlighted the strong correlation of these genes with specific immune cell subsets within the tumor microenvironment, underscoring their critical roles in modulating breast cancer immunobiology. Collectively, this study elucidates the therapeutic potential of YW-LF, a ribociclib derivative, in breast cancer treatment and delineates its multifaceted mechanisms, offering a promising strategy to overcome the limitations of current CDK4/6 inhibitors.

overall_design: In order to investigate the role and mechanism of YW-LF in Breast Cancer, we treated MDA-MB-231 cells with YW-LF and without treatment. Then, we performed gene expression profiling analysis using RNA seq data from YW-LF and DMSO cells.

first: Ying

last: JI


title: Splicing factor U2AF2 promotes inclusion of exons with poor nucleosome phasing

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Spliceosome recognition of pre-mRNA junctions requires binding of splicing factors to the 3' splice site. Most splicing occurs co-transcriptionally, but how splicing factors bind expressed gene is not understood. We show that the SF3B1, U2AF1, and U2AF2 splicing factors bind active promoters of both intron-containing and intronless genes. RNase A treatment reduces binding at promoters, implicating general interactions with nascent transcripts in promoter localization. Strikingly, U2AF2 also accumulates on the bodies of some genes and is not eliminated by RNase treatment. Neither RNA polymerase II nor the active gene body chromatin mark H3K36me3 is required to maintain U2AF2 on chromatin. We found that most exons in U2AF2-bound have phased nucleosomes at their exon-intron boundaries. However, some exons are poorly phased, and these require U2AF2 for inclusion in mature mRNA. We propose that nucleosome phasing and U2AF2 binding ensure exon inclusion.

overall_design: We used Cleavage under targets and Release using nuclease (Cut-and-Run), a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing

first: Weifang

middle: F

last: Wu

first: Kami

last: Ahmad

first: Steven


title: The inflammatory micro-environment induced by targeted CNS radiotherapy is underpined by disruption of DNA methylation [Array]

city: London

first: Silvia

last: Marino

address: 4 Newark Street

department: Blizard Institute

institute: Queen Mary University of London

type: Methylation profiling by genome tiling array

summary: Although targeted radiotherapy (RT) is integral to the increasing survival of cancer patients, it has significant side-effects, the cellular and molecular mechanisms of which are not fully understood. During RT epigenetic changes occur in neoplastic tissue, but few studies have assessed these in non-neoplastic tissue and results are highly variable. Using bulk DNA methylation and RNA sequencing as well as spatial transcriptomics (ST) in a unique cohort of patient tissue samples, we show distinct differences in DNA methylation patterns in irradiated brain tissue, whilst ST characterisation identifies specific micro-environmental niches present after irradiation and highlights neuropeptides that could be propagating neuroinflammation. We also show that in a cerebral organoid (CO) model of early changes in neurons after irradiation there are similar DNA methylation alterations and disruption of the DNA methylation machinery, suggesting that early but persistent epigenetic dysregulation plays a role in neurotoxicity. We provide a link between radiotherapy induced neuroinflammation and disruption of DNA methylation for the first time and suggest possible driving mechanisms for this chronic neuroinflammation.

overall_design:
DNA methylation was performed on brain tissue from surplus FFPE surgical materials of patients who received radiotherapy for the treatment of cerebral lesions. The experimental samples comprised cases where neurosurgical removal of a brain lesion occurred following radiotherapy, and the control samples included peri-lesional CNS tissue that had not received radiotherapy. H&E and subsequent unstained sections were obtained from the representative FFPE blocks and non-lesional brain tissue was morphologically identified and marked. Extraction of nucleic acids was performed from the delineated healthy tissue. DNA methylation profiles were compared between the irradiated and non-irradiated cases.
For the DNA methylation analysis of COs, organoids were treated with 24 Gy dose at day 48 and collected at 4 weeks post-irradiation and the unirradiated organoids served as controls. Subsequent extraction of nucleic acids were performed from each CO.

first: Thomas

middle: O

last: Millner

first: Yunchen

last: Xiao


title: Liver Portal Fibroblasts Induce the Functions of Primary Human Hepatocytes In Vitro

city: Chicago

first: Salman

last: Khetani

address: 851 S Morgan Street

department: Biomedical Engineering

institute: University of Illinois at Chicago

summary: In vitro human liver models are critical to mitigate the species-specific differences observed for toxicology, disease modeling, and regenerative medicine. Interactions with mesenchyme (i.e., fibroblasts), as in liver development, can promote the survival and phenotypic functions of primary human hepatocytes (PHHs) in culture; however, the use of liver-derived fibroblasts in such co-cultures remains elusive. Portal fibroblasts (PFs) in and around the portal liver triad influence bile duct formation during liver development, but their role in regulating homeostatic hepatic functions is unknown. Here, we show that human liver PFs, but not hepatic stellate cells, induced long-term and high levels of phenotypic functions in PHHs within industry-standard micropatterned co-cultures and spheroids. While PF-conditioned media induced some hepatic functions, partly via insulin-like growth factor binding protein-5 signaling, direct contact co-culture was necessary to induce optimal functional levels. Inhibiting Notch signaling reduced progenitor-like characteristics of PHHs and further enhanced their functions in co-cultures. Lastly, inhibiting transforming growth factor-β signaling suppressed the overgrowth and inflammation in higher passage PFs while enabling similar inductive effects on PHH functions as with the lower passage PFs. Overall, this work demonstrates a unique role for PFs in modulating hepatic functions and provides all-human and all-liver co-culture strategies for applications.

overall_design: Portal Fibroblasts and Hepatic Stellate Cells from two donors were compared with bulk RNA sequencing analysis

first: Brown

last: Grace

first: Bodke

last: Vedant

first: Ware

last: Brenton

first: Khetani

last: Salman


title: Dicer deficient adult microglia negatively impacts the process of demyelination and remyelination

city: Cleveland

first: Nagendra

middle: Kumar

last: Rai

state: Ohio

address: 9620 Carnegie Ave N Bldg, Cleveland, OH 44106

department: Neuroscience

institute: Cleveland Clinic Lerner College of Medicine

summary: Microglia, the resident immune cells of the central nervous system (CNS), are important regulators of normal brain activities. In CNS demyelinating diseases like multiple sclerosis (MS), the functions of these cells are of particular interest. Based on the observation of diminished Dicer positive microglia/macrophages number in demyelinating white matter lesions (WMLs) of human MS brains, here we probed the impact of impaired microRNA (miRNA)-mediated post-transcriptional gene regulation in a mouse model lacking microglia/macrophage-specific Dicer1 expression during demyelination and remyelination. Conditional Dicer1 ablation and loss of miRNAs expression in adult microglia led to extensive demyelination and impaired myelin processing. Interestingly, demyelination was accompanied by increased apoptosis of mature oligodendrocytes (OLs) and arresting oligodendrocyte progenitor cells (OPCs) in the precursor stage. At the transcriptional level, Dicer1-deficient microglia led to downregulation of microglial homeostatic genes, increased cell proliferation, and a shift towards a disease-associated phenotype. Loss of remyelination efficiency in these mice was accompanied by stalling of OPCs in the precursor stage. Collectively, finding from this study highlight a new role of microglial miRNAs in promoting a pro-regenerative phenotype in addition to promoting OPC maturation and differentiation during demyelination and remyelination.

overall_design: To evaluate the effects of miRNA loss on microglial gene expression in tamoxifen -induced Dicer1 KO animals, adult Cx3cr1creERT2 mouse brain microglia (CD45int/Cd11b+) were flow-sorted and processed for RNA sequencing (RNA-seq). Three biological replicates of WT and KO mice microglia were analyzed for 4 conditions. 1-Naïve_only tamoxifen injected (3 Cre- and 3 Cre+), 2-Demyelination _tamoxifen injection at 4-5 weeks (CUP- 6w) (3 Cre- and 3 Cre+), 3-Remyelination_ tamoxifen injection at 4-5 weeks (CUP-6w+6w normal diet) (3Cre- and 3 Cre+), 4-Remyelination_Tamoxifen injected at 5w of CUP feeding (CUP-6w+6w normal diet) (3Cre- and 3 Cre+)

first: Ranjan

last: Dutta

first: Ajai

last: Tripathi

middle: K

first: Aaron

last: Perles

first: Haley

last: Courtney

first: Claire

last: Jones

first: Adya

last: Sapra

first: Jason

last: Plemel


title: Gfi1 controls the formation of effector CD8+ T cells during chronic infection and cancer

first: Oluwagbemiga

last: Ojo

state: Alabama

department: Radiation Oncology

institute: University of Alabama, at Birmingham

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

overall_design: Refer to individual Series


title: Gfi1 controls the formation of effector CD8+ T cells during chronic infection and cancer [RNA]

summary: During chronic infection and tumor progression, CD8+ T cells gradually lose their cytotoxic effector function and become “exhausted”. These “exhausted” CD8+ T cells are highly heterogenous and comprised of various subsets, including a self-renewing progenitor subset that gives rise to Ly108-CX3CR1+ effector cells with some cytotoxic capabilities. Generation of these effectors is essential for the control (although limited) of chronic infection and tumor. However, the precise cues and mechanisms directing their formation and maintenance remains incompletely understood. In this study, using genetic mouse models challenged with the LCMV clone 13 infection and syngeneic MB49 urothelial adenocarcinoma, we show that the expression of a transcriptional repressor, growth factor independent 1 (Gfi1) is dynamically regulated in “exhausted” CD8+ T cells. By controlling chromatin accessibility and transcriptomic programs, Gfi1 governs the generation of the effector cells. Deletion of Gfi1 in T cells arrests the progenies from progenitors in a Ly108+CX3CR1+ Transitional state, without further differentiation into effector cells. Given the programmable chromatin profile of these transitional cells, we reason that they are a better target than the highly irreprogrammable terminally differentiated cells for therapeutic interventions to combat chronic infection and cancer. Our results show that Gfi1 is a novel epigenetic and transcriptional regulator of CD8+ T cell exhaustion.

overall_design: Gfi1fl/fl CD4cre-/- (Wildtype) or Gfi1fl/fl CD4cre-/- (Gfi1cKO) mice were infected with LCMV clone 13. GP33+ antigen specific CD8+ T cell subsets from wildtype (Progenitor, Effector, Transitional, and Terminally Exhausted) and Gfi1cKO (Progenitor and Transitional) mice were FACS sorted 30 days post infection. Bulk RNA sequencing was used to investigate gene expression in sorted cells. Samples are pooled biological replicates. Naive CD8+ T cells isolated from uninfected wildtype and Gfi1cKO mice were included as controls.

middle: A

first: Hongxing

last: Shen

first: Jennifer

middle: T

last: Ingram

first: Robert

last: Welner

first: Georges

last: Lacaud

first: Allan

middle: J

last: Zajac

first: Lewis

middle: Z

last: Shi


title: High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development

status: Public on Apr 09 2025

city: Los Angeles

first: Jifan

last: Feng

state: CA

address: 2250 Alcarza Street CSA 103

institute: University of Southern California

summary: The differentiation of post-migratory cranial neural crest cells (CNCCs) into distinct mesenchymal lineages is crucial for craniofacial development. Here we report a high-resolution spatiotemporal transcriptomic and cell-type atlas of CNCC-derived mesenchymal lineage diversification associated with mouse palatogenesis. We systematically defined each mesenchymal cell type by mapping their transcriptomic profiles to spatial identities.

overall_design: To systematically evaluate the dynamic cell fates of all the cell populations associated with palate development, we performed scRNA-seq analysis of the tissues in the palatal region across all key stages of palatogenesis (E12.5, E13.5, E14.5, E15.5, and E18.5).

first: Yang

last: Chai