title: Time courses analysis of the effect of latrunculin B-treatment on gene expression in in vitro differentiated pancreatic progenitor cells.

status: Public on Feb 19 2025

city: København N

first: Adam Kappel

last: Rump

address: Blegdamsvej 3

department: DanStem

country: Denmark

institute: University of Copenhagen

summary: The organization of the actin cytoskeleton is known to influence the endocrine versus ductal fate choice during pancreas development via YAP. However, the intermediate mechanism between changes to actin polymerization and changes in YAP activity during pancreas development has not been identified. Pharmacological inhibition of actin polymerization has also been shown to be a stronger inducer of endocrine fate choice than pharmacological inhibition of YAP activity, indicating that actin depolymerization may induce endocrine fate choice via additional pathways. To identify these mechanisms, we performed bulk RNA-sequencing of in vitro differentiated ESC-derived pancreatic progenitor cells treated with latrunculin B for 3, 6, 12, or 24 hours. This sequencing dataset revealed multiple promising candidates for actin depolymerization-induced YAP inactivators and YAP-independent endocrine induction, which have been validated by additional methods.

overall_design: To investigate the intermediate effects between actin depolymerization and endocrine specification, ESC-derived pancreatic progenitor cell were treated with the actin depolymerization agent latrunculin B for 3, 6, 12 or 24 hours. These samples were compared to samples harvested before treatment and samples harvested after 24 hours of DMSO treatment. Duplicates of 24hr untreated and 12hr LatB treated and triplicates of other samples were sequenced.

first: Adam

first: Anant

last: Mamidi

first: Henrik

last: Semb


title: The Histone Demethylase LSD1/ZNF217/CoREST Complex is a Major Restriction Factor of Epstein-Barr Virus Lytic Reactivation

city: Boston

first: Yifei

last: Liao

state: Massachusetts

address: 181 Longwood Ave, 8th Floor

country: USA

institute: Brigham and Women's hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Epstein-Barr virus (EBV) contributes to ~1.5% of human cancers, including lymphomas, gastric and nasopharyngeal carcinomas. In most of these, nearly 80 viral lytic genes are silenced by incompletely understood epigenetic mechanisms, precluding use of antiviral agents such as ganciclovir to treat the 200,000 EBV-associated cancers/year. To identify host factors critical for EBV latency, we performed a human genome-wide CRISPR-Cas9 screen in Burkitt B-cells. Top hits included the lysine-specific histone demethylase LSD1 and its co-repressors ZNF217 and CoREST. LSD1 removes histone 3 lysine 4 (H3K4) and histone 3 lysine 9 (H3K9) methylation marks to downmodulate chromatin activation. LSD1, ZNF217 or CoREST knockout triggered EBV reactivation, as did a LSD1 small molecule antagonist, whose effects were additive with histone deacetylase inhibition. LSD1 blockade reactivated EBV in Burkitt lymphoma, gastric carcinoma and nasopharyngeal carcinoma models, sensitized cells to ganciclovir cytotoxicity and induced EBV reactivation in murine xenografts. ZNF217 and LSD1 co-occupied the EBV immediate early gene BZLF1 promoter, which drives B-cell lytic cycle, as well as to the oriLyt enhancer regions recently implicated in EBV reactivation. LSD1 depletion increased levels of activating histone 3 lysine 4 (H3K4) methylation but not repressive histone lysine 9 methylation marks at BZLF1 and oriLyt and induced their interaction by long-range DNA looping. An orthogonal CRISPR screen highlighted a key H3K4 methyltransferase KMT2D role in driving EBV reactivation. Our results highlight H3K4 methylation as a major EBV lytic switch regulator and suggest novel therapeutic approaches.

overall_design: EBV+ Akata cells collected for chromatin immunoprecipitation, library preparation and sequencing.

first: Jinjie

last: Yan

first: Isabella

last: Kong

first: Zhixuan

last: Li

first: Weiyue

last: Ding

first: Sarah

last: Clark

first: Lisa

last: Giulino-Roth

first: Benjamin

last: Gewurz


title: Temporal constraints on enhancer usage and enhancer-promoter connectivity shape the regulation of limb gene transcription [CUT&Run]

status: Public on Feb 18 2025

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

summary: The repertoire of enhancers orchestrating gene expression during embryonic development shapes the forms and functions of organs. Within regulatory landscapes, enhancers control their target genes through spatially distinct or overlapping activities. However, the temporal specificity of enhancers repertoires—how their activities change over time to dynamically influence gene expression—is less well characterized. In this study, we introduce the regulatory trajectory framework to monitor how enhancer landscapes govern gene transcription in vivo across extensive developmental periods. This paradigm conceptually involves transcriptional initiation, marking the beginning of gene expression, followed by its maintenance over time, and ultimately decommissioning, leading to gene repression. To track and sort cells undergoing these distinct phases, we devised a transgenic recorder approach at the Shox2 model locus. Through this method, we discovered that cells maintaining Shox2 transcription in early and late limb development relies on distinct, temporally restricted enhancer repertoires. We demonstrate that eliminating early- or late-acting enhancers only transiently affects Shox2 expression indicating that these enhancer repertoires function independently. Additionally, we found that changes in the locus' 3D topology associate with enhancer activities and that a rapid loss of enhancer-promoter contacts occurs during decommissioning. Finally, we show that the decommissioning of the Shox2 locus can be actively driven by Hoxd13, a gene which expression is known to antagonize Shox2. Overall, our work uncovers the dependency of developmental genes on enhancers with temporally restricted activities to generate complex expression patterns over time and shed light on the dynamics of enhancer-promoter interactions.

overall_design: We devised a dual-reporter system to monitor Shox2 regulatory trajectories and sort cells undergoing these distinct phases. First, we inserted in mouse embryonic stem cells (mESCs), 1kb upstream of the Shox2 transcriptional start site, a regulatory sensor cassette constituted by a minimal β-globin promoter, a mCherry reporter gene followed by a destabilized PEST sequence, a P2A self-cleavage sequence and a CRE recombinase gene. These cells cells were then retargeted to integrate, at the Rosa26 locus, a cassette with a splice acceptor followed by a floxed 3x SV40pA STOP signal and the EYFP gene open reading frame. We studied the transcriptional identity of these cells by scRNA-seq. We the profile the identity of sorted cells by RNA-seq and their regulatory profile by CHiC and ChIP-seq

first: Raquel

last: Rouco


title: RNA splicing patterns contribute to burst size variation among HIV-1 infected Jurkat cell clones

status: Public on Feb 17 2025

city: Ann Arbor

first: Alice

last: Telesnitsky

state: MI

address: 1150 W. Medical Center Drive, 6714 MSII

department: Microbiology & Immunology

institute: University of Michigan

summary: Jurkat T cells were infected with barcoded HIV-1, and the resulting polyclonal pool was analyzed to identify factors contributing to burst size variation among HIV-1 infected cell clones.

overall_design: Amplicon-seq of barcoded HIV-1 present in cellular chromosomal DNA, cellular total and affinity capture RNA, and extracellular viral RNA.

first: Kamya

last: Gopal

first: Cleo

last: Burnett

first: Ann

last: Emery

first: Edmond

last: Atindaana

first: Ronald

last: Swanstrom

first: Jeffrey

last: Kidd


title: Unveiling the Cellular and Molecular Mechanisms of Diabetic Retinopathy with Human Retinal Organoids

status: Public on Feb 24 2025

city: Brno

first: Tomas

last: Barta

address: Kamenice 3

department: Faculty of Medicine

country: Czech Republic

institute: Masaryk University

type: Expression profiling by high throughput sequencing

summary: Diabetic retinopathy (DR) is a leading cause of vision impairment worldwide, driven by chronic hyperglycaemia and its complex metabolic consequences. While animal models have been widely used to study DR, they often fail to replicate human retinal physiology. To address this limitation, we utilized human retinal organoids as a model to investigate hyperglycaemia-induced changes, focusing on late-stage organoids (D150+28), where we performed next-generation sequencing (NGS). Transcriptomic analysis revealed significant disruptions in photoreceptor maturation, with a marked downregulation of genes associated with phototransduction and sensory perception. Oxidative stress-related pathways were upregulated, suggesting an enhanced reactive oxygen species (ROS) response. While photoreceptors were particularly vulnerable to hyperglycaemia, other retinal cell types, including bipolar cells, ganglion cells, and Müller glia, exhibited greater resilience. Additionally, glial activation, evidenced by increased expression of astrocyte markers (CD44, GFAP, TGFBR2), suggested a reactive gliosis response.

overall_design: Human-induced pluripotent stem cells (hiPSCs) were differentiated into retinal organoids following an established protocol. Retinal organoids were cultured for 150 days (D150) to achieve an advanced stage of differentiation. To investigate the effects of hyperglycaemia, organoids were exposed for 28 days to one of the following conditions: 1) Control: Standard maintenance medium containing 17.5 mM D-Glucose. 2) Hyperglycaemia (D-Glucose): Maintenance medium supplemented with additional 7.5 mM D-Glucose for a final concentration of 25 mM D-Glucose.

first: Lada

last: Polesovska


title: Mechanistic Insights into Targeting APLN/APJ for Ameliorating Testosterone and Reproductive Disorders in Type 2 Diabetes (CUT&Tag)

city: Guangzhou

first: Ke

last: Song

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

country: China

institute: Southern Medical University

summary: About 10% of couples of reproductive age worldwide suffer from infertility, with male factors accounting for about 50%, and testosterone is essential for male fertility, but the mechanisms behind the poor sperm quality and abnormally low blood testosterone levels in diabetic patients are unclear. In this study, we found that the peptide Apelin (APLN) significantly inhibited testosterone secretion from Leydig cells (LCs), which in turn led to decreased sperm quality. APLN was found to be localized to leydig cells in the testes of several diabetic mice, and its expression was significantly increased. The addition of APLN to mouse leydig cells decreased testosterone content and decreased the expression of genes related to testosterone synthesis, but the addition of ML221, an APLN receptor inhibitor, significantly increased the expression of testosterone synthesis genes. Injecting ML221 into diabetic mice significantly increased testosterone levels in the blood, increased sperm count as well as enhanced sperm motility and ultimately increased live birth rate of mice after in vitro fertilization. Proteomics revealed that ML221 significantly increased the expression of NR2F2 and further activated the transcription of testosterone synthesis genes. This study will further use mouse and cellular models to completely unravel the specific mechanisms by which APLN inhibits testosterone secretion and elucidate the causes of decreased sperm quality in diabetic patients. This study provides a new clinical target for the development of drugs to improve fertility in diabetic patients.

overall_design: In order to study the distribution of NR2F2 in LC cells, we performed CUT&Tag sequencing analysis on the high-glucose treatment group and the high-glucose + ML221 treatment group in mouse primary Leydig cells.

first: Xinyan

last: Yang


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

status: Public on Feb 13 2025

city: Beijing

first: Mingyang

last: Li

address: Yanyuan Subdistrict, Haidian District

institute: Peking University

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

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

first: Chuyun

last: Shao


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

sample_organism:
Homo sapiens
Cricetulus griseus

platform_organism:
Homo sapiens
Cricetulus griseus


title: A niche-dependent redox rheostat regulates epithelial stem cell fate in the distal colon

first: Jay

middle: R

last: Thiagarajah

state: MA

address: 300 Longwood Avenue

department: Division of Gastroenterology, Hepatology and Nutrition

institute: Boston Childrens Hospital

summary: The niche environment surrounding intestinal stem cells (ISCs) varies along the length of intestine and provides key cues that regulate stem cell fate. Here, we investigated the role of cellular redox balance in colonic ISC function. We show that hypoxia and Wnt signaling synergize to restrict the reactive oxygen species (ROS) generating enzyme NADPH oxidase 1 (NOX1) to the crypt base in the distal colon. NOX1 function maintains a more oxidative cell state that licenses cell cycle entry, altering the balance of asymmetric stem cell self-renewal and directing lineage commitment. Mechanistically, cell redox state directs a self-reinforcing circuit that connects hypoxia inducible factor 1 (HIF1a)-dependent signaling with regulation of the metabolic enzyme isocitrate dehydrogenase 1 (IDH1). Our studies show that cellular redox balance is a central and niche-dependent regulator of epithelial homeostasis and regeneration and provide a basis for understanding disease propensity in the distal large intestine.

overall_design: RNA seq of colonoids from WT and NOX1 KO mice.

first: Chen

last: Xi

first: Thiagarjah

last: Jay


title: Comparative Transcriptomic Analysis of Perfluoroalkyl Substances-Induced Responses of Exponential and Stationary Phase Escherichia coli

status: Public on Feb 14 2025

city: Gaithersburg

first: Molly

last: Wintenberg

state: MD

address: 100 Bureau Dr

department: Biosystems and Biomaterials Division

institute: National Institute of Standards and Technology

summary: Per- and polyfluoroalkyl substances (PFAS) are highly stable chemical contaminants of emerging concern for human and environmental health due to their non-natural chemistry, widespread use, and environmental persistence. Despite conventional metrology, mitigation strategies, and removal technologies, the complexity of this growing problem necessitates the need for alternative approaches to tackle the immense challenges associated with complex environmental PFAS contamination. Recently, biology has emerged as an alternative approach to detect and mitigate PFAS and understand the molecular-level responses of living organisms, including microorganisms, to these compounds. However, further study is needed to understand how microorganisms in different environments and growth phases respond to PFAS. In this study, we performed RNA sequencing at mid-exponential, early stationary phase, and late stationary phase of bacterial growth to determine the global transcriptional response of a model chassis, Escherichia coli MG1655, induced by two PFAS, perfluorooctanoic acid (PFOA) and perfluorododecanoic acid (PFDoA), and equivalent non-fluorinated carboxylic acids (NFCA), octanoic acid and dodecanoic acid. Differential gene expression analysis revealed PFOA and PFDoA induced distinct changes in gene expression throughout cultivation. Specifically, we identified significant changes in expression of the formate regulon and sulfate assimilation at mid-exponential phase and ferrous iron transport, central metabolism, the molecular chaperone network, and motility processes during stationary phase. Importantly, many of these changes are not induced by NFCAs. In summary, we found PFAS induced a system-level change in gene expression, and our results expand the understanding of bacterial-PFAS interactions that could enable the development of future real-time environmental monitoring and mitigation technologies.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Comparative gene expression analysis of RNA-Seq data for E. coli MG1655 treated with PFCAs or equivalent non-fluorinated carboxylic acids (NFCAs) to an untreated control group at three time points within the growth cycle was performed to investigate the transcriptional response of E. coli to PFAS.

middle: E

first: Olga

middle: B

last: Vasilyeva

first: Samuel

middle: W

last: Schaffter


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

city: Guiyang City

first: Youfu

last: He

state: Guizhou Province

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

institute: Guizhou Provincial People's Hospital

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

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

first: Y

first: Q

last: Wu

first: Z

last: Yu

first: J

last: Huang

first: L

last: Ai

first: X

last: Long


title: P0 kidney samples

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: The goal of our study is to analyze formation/development of nephron segments.

overall_design: Mouse kidneys at P0 were collected and subjected to scRNA-seq analysis.

first: Joo-seop

last: Park


title: Epigenetic priming promotes acquisition of TKI resistance and oncogene amplification in human lung cancer [CUT&RUN]

status: Public on Feb 26 2025

city: New Haven

first: Eric

last: Sun

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale University

summary: In mammalian cells, gene copy number is tightly controlled to maintain gene expression and genome stability. However, a near-universal molecular feature across cancer types is oncogene amplification, which promotes cancer progression by dramatically increasing the copy number and expression of tumor-promoting genes. For example, in tyrosine kinase inhibitor (TKI)-resistant lung adenocarcinoma (LUAD), oncogene amplification occurs in over 40% of patients’ tumors. Despite the prevalence of oncogene amplification in TKI-resistant tumors, the mechanisms facilitating oncogene amplification are not fully understood. Here, we find that LUAD tumors exhibit a unique chromatin signature demarcated by strong CTCF and cohesin deposition in drug-naïve tumors, which correlates with the boundaries of oncogene amplicons in TKI-resistant LUAD cells. Throughout the acquisition of TKI resistance, we identified a global chromatin priming effect, marked by a dynamic increase of H3K27Ac, cohesin loading, and inter-TAD interactions, which occurs before the onset of oncogene amplification. Furthermore, we have identified that the protein METTL7A, which was previously reported to localize to the ER and inner nuclear membrane, has a novel chromatin regulatory function in binding to amplified oncogenes and regulating cohesin recruitment and inter-TAD interactions. Surprisingly, we discovered that METTL7A remodels the chromatin landscape prior to any noticeable oncogene copy number gains. Furthermore, while METTL7A depletion has little effect on drug-naïve cells, METTL7A depletion prevents the formation of TKI resistant-clones, highlighting the specific role of METTL7A as cells are acquiring resistance. In summary, we discovered an unexpected mechanism required for the acquisition of TKI resistance regulated by a largely uncharacterized factor, METTL7A. This discovery sheds new light into maintenance of oncogene copy number and paves the way to the development of new therapeutics for preventing TKI resistance in LUAD.

overall_design: CUT&RUN: CUT&RUN was performed in PC9 wild-type, PC9 METTL7A KO (PC9_M7A_KO), and PC9 METTL7A Rescue (overexpression of METTL7A-MYC-tag_FLAG in METTL7A KO cells) against IgG, H2A, PDS5A, RAD21, and H3K27Ac.

first: Rebecca

middle: M

last: Starble

middle: G

first: Rana

last: Gybli

first: Jonathan

last: Radda

first: Jiuwei

last: Lu

first: Tyler

last: Jensen

first: Ning

first: Shuai

last: Zhao

first: Nitin

last: Roper

first: Gang

last: Wang

first: Jikui

last: Song

first: Katerina

last: Politi

first: Siyuan

first: Andrew

middle: Z

last: Xiao


title: A niche-dependent redox rheostat regulates epithelial stem cell fate in the distal colon II

first: Jay

last: Thiagarajah

first: Chen

last: Xi

first: Thiagarjah

last: Jay


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

status: Public on Feb 12 2025

city: San Francisco

middle: Michael

last: Budzik

state: CA

address: 513 Parnassus Ave.

department: Medicine

institute: UC San Francisco

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

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

first: Jeffrey

last: Chin


title: A Cryogel-Based Dendritic Cell Vaccine for Post-Surgical Breast Cancer Immunotherapy

city: Hsinchu City

first: ShengLiang

last: Cheng

address: No. 101, Sec. 2, Guangfu Rd., East Dist.

department: Institute of Biomedical Engineering

country: Taiwan

institute: National Tsing Hua University

summary: Triple-negative breast cancer (TNBC) is an aggressive malignancy with high mortality and limited treatment options. While surgical resection removes the primary tumor, it often fails to prevent recurrence or metastasis, and despite the promise of immunotherapy, the response to immune checkpoint blockade remains poor. Here, we develop a cryogel-based dendritic cell (DC) vaccine that integrates gold nanodot-lipopolysaccharide (AuLPS)-loaded DCs, doxorubicin (Dox), and a PD-1 immune checkpoint blockade, effectively enhancing anti-tumor immunity in the post-surgical setting. The AuLPS nanoparticles (NPs) stabilize LPS assembly, optimizing Th1 adjuvant activity, thereby improving DC vaccine efficacy while minimizing adverse effects. The cryogel enables the sustained localized release of therapeutic agents at the surgical site, preserving DC viability, migration, and functionality within the tumor microenvironment. This strategy enhances DC activation and potentiates robust T-cell activation in both tumor-draining lymph nodes and tumor beds, leading to durable anti-tumor immunity. When administered at the post-surgical site in an orthotopic TNBC model, the aPD-1+Dox+AuLPS@DC cryogel vaccine significantly delays tumor recurrence, reduces distant metastases, and prolongs survival. These findings highlight cryogel-based DC vaccines as a promising post-surgical immunotherapy to overcome the limited response to immune checkpoint blockade and improve TNBC outcomes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine TNBC tumors with or without treatment of DOX and AuNP treated BMDC co-loaded cryogel

first: Yunching

last: Chen

first: Shu-Yi

last: Lin

first: Jane


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

city: La Jolla

first: Stacey

middle: Marie

last: Glasgow

state: California

address: 9500 Gilman Dr, 3216 Pacific Hall

institute: University of California San Diego

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

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

first: Hanhee

last: Jo

first: Aneesh

last: Dalvi

first: Wenqi

last: Yang

first: Elizabeth

last: Morozova

first: Sarah

last: Munoz


title: Gene expression profile at single level of embryonic kidney cells 16 weeks post-transplantation

city: Tokyo

first: Satoshi

last: Hatsuse

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

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

summary: Embryonic kidney (metanephros) is known to mature after in vivo transplantation. We used scRNA-seq to analyze the maturity of embryonic kidney cells after transplantation.

overall_design: Embryonic kidneys transplanted in 8-week-old syngeneic rat were urinary-reconstructed 3 weeks post-transplantation, collected 16 weeks post-transplantation, and  analyzed using scRNA-seq.


title: SMARCA4 Inhibits Breast Tumor progression through Transcriptional Activation of GTPase Activating Factor ARHGAP29 and RHOA Suppression [ATAC]

city: Plainsboro

first: Yong

last: Wei

state: NJ

address: LTL227 Wathington Road

department: Molecular Biology

institute: Princeton University

summary: The chromatin-remodeling SWI/SNF complex emerged as a potent suppressor of tumor spheroid growth. SMARCA4 was identified as a top candidate to suppress TNBC growth in 3D tumor spheroid model using genome-wide CRISPR screen. Specifically, the loss of the SWI/SNF ATPase subunit SMARCA4 promotes tumor spheroid growth with reduced compactness, and enhanced the growth in breast primary tumors and metastasis across multiple breast cancer models. Further investigations revealed its function in inhibiting the RHOA pathway. SMARCA4 is required for the transcription of Rho GTPase activating factor ARHGAP29, achieved through direct binding to its promoter to provide DNA accessibility. The loss of SMARCA4 resulted in reduced ARHGAP29 levels and hyperactive RHOA signaling. This subsequently disrupted cell adhesion, facilitated a loose spheroid structure and promoted spheroid growth.

overall_design: Whole genome chromatin accessibility profiles for SMARCA4 manipulated derivatives of TNBC SUM159 cells were determined using ATACseq. The panel of 4 derivative samples include NTC (non-targeting control), KD1 (SMARCA4 knockdown), KD1+SMARCA4 (rescue) and KD1+Vec (rescue control)

first: Zheng

last: Sun

first: Yibin

last: Kang


title: Integrative Gene and Isoform Co-expression Networks Reveal Regulatory Rewiring in Stress-related Psychiatric Disorders [PBMC]

status: Public on Feb 10 2025

city: Munich

first: Janine

last: Knauer-Arloth

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

summary: Isoform-specific expression patterns have been implicated in stress-related psychiatric disorders like major  depressive disorder (MDD), yet the extent of their involvement and their interrelationships remain unclear. We constructed co-expression networks for individuals affected (n=210, 81% with depressive symptoms) and unaffected (n=95) by stress-related psychiatric disorders. We incorporated total gene expression (TE) and isoform ratio (IR) data and validated the inferred networks using advanced graph generation techniques. Our analysis revealed distinct network topology and structure between the two groups. Investigation of the 127 shared hubs (degree >= 10) found that these hubs exhibit co-regulatory patterns unique to each network. The affected individuals’ network also contained 61 hub nodes with a minimum absolute fold increase of two in connectivity compared to the unaffected individuals’ network. Notably, 49% of these hubs showed evidence for association with psychiatric disorders. Gene Ontology enrichment analysis revealed distinct biological processes associated with hubs, such as mRNA processing for affected and immune response and cell adhesion for unaffected individuals. Enrichment analysis of GWAS loci further supported these findings. Analysis of the isoform-specific nodes showed distinct protein-protein interactions compared to gene-level analysis.

overall_design: The total RNA-seq of PBMCs from 229 participants with stress-related mental disorders and 70 healthy controls was determined.

first: Ghalia

last: Rehawi

first: Elisabeth

last: Binder


title: Impact of human anti-O-specific polysaccharide (OSP) antibody on Vibrio cholerae O1 in complex media containing mucin

first: Smriti

last: Verma

address: 55 Fruit Street

department: Department of Infectious Diseases

institute: Massachusetts General Hospital

summary: Antibodies targeting the O-specific polysaccharide (OSP) of Vibrio cholerae O1 are a main determinant of protection against cholera. These antibodies can agglutinate bacteria, and can also directly inhibit V. cholerae motility, including at sub-agglutinating conditions. In order to evaluate for possible additional impacts of OSP-specific antibody on V. cholerae, we assessed the transcriptional profile of V. cholerae exposed to an anti-OSP human monoclonal antibody (G1), including in the presence of mucin, the principal component of intestinal mucous. We identified a subset of genes whose expression was significantly altered in the presence of anti-OSP antibody and mucin, including those involved in V. cholerae metabolism, transport, stress response, biofilm formation, motility, and secondary messenger signaling. Our results suggest a broad impact of anti-OSP antibodies on V. cholerae in the presence of mucin and identify several possible mechanisms by which anti-OSP antibodies might protect against cholera.

overall_design: Vibrio cholerae C6706 bacteria cultured under toxin-inducing conditions were diluted to a subagglutinating optical density (600 nm) of ≤0.1 and exposed to two concentrations (0.0125 µM and 0.125 µM) of human monoclonal immunoglobulin (Ig) G1 targeting V. cholerae O-specific polysaccharide component of LPS (clone G1 - CF21.2.G01) or anti-flagellin antibody as a control (clone B12 -AT11.1.B12) in either Luria Bertani (LB) broth or LB containing 1% w/v porcine stomach mucin (LBM).

first: Edward

middle: T

last: Ryan


title: Integrative Gene and Isoform Co-expression Networks Reveal Regulatory Rewiring in Stress-related Psychiatric Disorders [whole blood]

overall_design: The total RNA-seq of whole blood from 37 participants with no stress-related mental disorders (controls) was determined.


title: The landscape of enhancer transcription in prostate cancer [ATAC-Seq]

status: Public on Feb 09 2025

city: Wuhan

first: Zezhong

last: Xiong

address: 1095 Jiefang Ave. Wuhan, P.R.China

institute: Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary:
Current genome-wide detection of chromatin accessibility uses the assay for transposase-accessible chromatin (ATAC-seq). To a provide panoramic view of the chromatin accessibility landscape in prostate cancer and normal  prostate, we performed ATAC-seq in 20 pairs of prostate cancer tissues and matched adjacent tissues.
Assay of transposase accessible chromatin with high-throughput sequencing (ATAC-seq) for 20 pairs of prostate cancer tissues and matched adjacent tissues.

overall_design: Comparative analysis of ATAC-seq data for prostate cancer tissues and matched adjacent tissues

first: Yue

last: Ge


title: Effect of external cues on clock-driven time-of-day specific protection from Influenza A infection

status: Public on Feb 08 2025

city: Philadelphia

first: Thomas

last: Brooks

address: 3400 Civic Center Blvd

department: ITMAT

institute: University of Pennsylvania

summary: Influenza and other respiratory viral pathogens are leading causes of mortality and morbidity. We have previously shown that circadian rhythms confer temporal protection from influenza infection. Here, we investigate whether the endogenous circadian clocks need optimal cycling of entraining cues to mediate this protection. We used two key entraining factors-- light-dark cycling and meal timing-- to determine their relative importance in allowing the host to benefit from its endogenous circadian rhythms. First, we demonstrate that disrupting environmental lighting cues, within a critical window of vulnerability, abrogated the time-of-day specific protection; this poor outcome is mediated by a dysregulated immune response evidenced by the accumulation of inflammatory monocytes and CD8+ cells in the lungs and transcriptomic profile with an exaggerated immune response. Importantly, rhythmic meal timing mitigated the adverse effects of disrupted light cycles. Our findings highlight the crucial interplay between peripheral and central clocks in shaping influenza outcomes, offering significant translational potential for improving the care of critically ill patients with respiratory viral infections.

overall_design: Specific pathogen-free 8-12 week-old C57bl/6J mice  were placed in circadian cabinets on reverse light-dark cycles. After 4-6 weeks of acclimatization in these cabinets, mice were anesthetized lightly with isoflurane prior to being infected intranasally (i.n.) with mouse-adapted influenza virus (PR8 ). Given the use of circadian cabinets, mice were simultaneously infected at either ZT23 or ZT11 and maintained in 12 hr light-dark cycle. The dose chosen was likely to cause >50% mortality when mice were infected at ZT11. On day four p.i. a subset of ZT23-LD mice were moved to constant light until the end of the study. Lungs were collected at day 8 p.i., at the same ZT as the initial infection, and RNA was extracted.

first: Oindrila

last: Paul

first: Gregory

last: Grant

first: Shaon

last: Sengupta


title: Paraventricular nucleus CRH neurons regulate acute lung injury via sympathetic nerve–neutrophil axis [neutrophil]

status: Public on Feb 07 2025

city: Changsha

first: Dai

last: Ruping

state: Hunan

address: Ren-Min Central Road

department: Anesthesiology

institute: The Second Xiangya Hospital of Central South University

summary: Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) are severe conditions with high morbidity and mortality, and effective treatments are limited. Neuroimmune interactions play a critical role in lung homeostasis, but it remains unclear if specific brain regions regulate lung inflammation. Here, we unveil the critical role of neuroimmune signaling in ALI, focusing on the regulatory function of corticotropin-releasing hormone (CRH) neurons in the paraventricular nucleus (PVN) of the hypothalamus. Using viral tracing, chemogenetic modulation, and pharmacological interventions in mouse models of ALI induced by intranasal lipopolysaccharide and cecal ligation and puncture (CLP), we found that lung injury activated CRHPVN neurons that projected to the lung. Activation of these neurons protected mice from ALI and death, reducing neutrophil infiltration and effector functions in the lung. In contrast, inhibiting CRHPVN neurons exacerbated ALI. Notably, the beneficial impact of CRHPVN neuron activation is compromised by the pulmonary chemical sympathectomy or inhibition of the β2-adrenergic receptor. These protective effects were dependent on sympathetic nerves, with norepinephrine released locally to modulate neutrophil functions via β2-AR–β-arrestin2 signaling, inhibiting the NF-κB pathway. Our findings reveal a brain-lung axis that regulates immune responses in ALI, suggesting novel therapeutic targets for ALI and ARDS.

overall_design: CRH-IRES-Cre mice were injected with AAV2/9-Ef1α-DIO-mCherry (control group) or AAV2/9-Ef1α-DIO-hM3Dq-mCherry (experimental group) into the paraventricular nucleus (PVN). After viral expression, CNO was intraperitoneally injected, and 1 hour later, LPS (20 mg/kg) was administered intranasally to induce acute lung injury (ALI). Neutrophils in the lung were isolated using magnetic beads after 24 h of modeling for neutrophil bulk RNA-seq.

first: Ruping

last: Dai

first: Hui

last: Li


title: Decoding functional haematopoietic progenitor cells in the adult human lung

first: Mark

middle: Roberts

last: Looney

address: 513 Parnassus

institute: UCSF

summary: Comparative transcriptomic profiling of pulmonary and medullary CD34+ haematopoietic progenitor was performed to reveal shared and organ-specific gene signatures.

overall_design: Lin-CD34+ HSPCs were sorted from matched human lung and bone marrow and subjected to single-cell RNA sequencing.

first: Catharina

last: Conrad

first: Mélia

last: Magnen

first: Jessica

last: Tsui

first: Harrison

last: Wismer

first: Mohammad

last: Naser

first: Urmila

last: Venkataramani

first: Bushra

last: Samad

first: Simon

middle: J

last: Cleary

first: Longhui

last: Qiu

first: Marco

last: De Giovanni

first: Nicole

last: Mende

first: Emmanuelle

last: Passegué

first: Elisa

last: Laurenti

first: Alexis

last: Combes


title: EGFR-induced lncRNA TRIDENT promotes drug resistance in non–small cell lung cancer via phospho-TRIM28-mediated DNA damage repair

status: Public on Feb 06 2025

city: Boston

first: Jonathan

middle: David

last: Lee

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

summary: Long noncoding RNAs (lncRNAs) play numerous roles in cellular biology and alterations in lncRNA expression profiles have been implicated in a variety of cancers. Here, we identify and characterize a n lncRNA, TRIM28 Interacting DNA damage repair Enhancing Noncoding Transcript (TRIDENT), whose expression is induced upon epithelial growth factor receptor (EGFR) activation, and which exerts pro-oncogenic functions in EGFR-driven non–small cell lung cancer. Knocking down TRIDENT leads to decreased tumor-cell proliferation in both in vitro and in vivo model systems and induces sensitization to chemotherapeutic drugs. Using ChIRP-MS analysis we identified TRIM28 as a protein interactor of TRIDENT. TRIDENT promotes phosphorylation of TRIM28 and knocking down TRIDENT leads to accumulation of DNA damage in cancer cells via decreased TRIM28 phosphorylation. Altogether, our results reveal a molecular pathway in which TRIDENT regulates TRIM28 phosphorylation to promote tumor cell growth and drug resistance. Our findings suggest that TRIDENT can be developed as a biomarker or therapeutic target for EGFR mutant non–small cell lung cancer.

overall_design: RNAseq profiling of H1975-TRE-dCas9-KRAB cells with NT control gRNA, TRIDENT gRNA1 AND TRIDENT gRNA2 after treating with 4ug/ml of doxycycline for 72 hours

first: Tanvi

last: Saxena

first: Anan

last: Quan

first: Erica

last: Chan

first: Nina

last: Kozlova

first: Latika

last: Matai

middle: D

first: Rajesha

last: Rupaimoole

first: Francisco

last: Beca

first: Taru

last: Muranen

first: Frank

last: Slack


title: Paraventricular nucleus CRH neurons regulate acute lung injury via sympathetic nerve–neutrophil axis

first: Dai

last: Ruping

overall_design: CRH-IRES-Cre mice were injected with AAV2/9-Ef1α-DIO-mCherry (control group) or AAV2/9-Ef1α-DIO-hM3Dq-mCherry (experimental group) into the paraventricular nucleus (PVN). After viral expression, CNO was intraperitoneally injected, and 1 hour later, LPS (20 mg/kg) was administered intranasally to induce acute lung injury (ALI). Lung tissues were collected 8 hours post-LPS for RNA sequencing.

first: Ruping

last: Dai

first: Hui

last: Li


title: SMARCA4 Inhibits Breast Tumor progression through Transcriptional Activation of GTPase Activating Factor ARHGAP29 and RHOA Suppression [RNA]

first: Yong

last: Wei

overall_design: Total RNA samples were collected from non-targeting shRNA control (NTC) and SMARCA4 knockdown derivatives (KD1 and KD2) of human triple negative breast cancer (TNBC) cell SUM159 cultured in both  2D and 3D spherioid culture system. The whole transcriptome profiling were determined using RNAseq. Three repeats of each 3D samples were profiled while single sample pair for 2D culture is used.

first: Zheng

last: Sun

first: Yibin

last: Kang


title: Tumorigenicity of KRAS-ablated pancreatic cancer cells requires STAT3 function

status: Public on Feb 05 2025

city: Woodbury

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

summary: Oncogenic KRAS mutations underlie some of the deadliest human cancers. Genetic or pharmacological KRAS inactivation produces mixed outcomes, ranging from complete regression to frequent relapse. Mechanisms underpinning the resistance of cancer cells to KRAS inactivation remain to be understood. Here we investigate a conceptual framework of pancreatic ductal adenocarcinoma showing that CRISPR-mediated KRAS ablation impedes tumor growth contingent on the concomitant inactivation of the STAT3 transcription factor. Mechanistically, the incurred losses of KRAS and STAT3 disrupt a temporal balance between tumor cell differentiation, proliferation, and self-renewal. This in turn impairs tumor growth in mice and enhances their immune rejection, resulting in tumor clearance. Our findings identify a specific role for STAT3 in supporting cancer cell fitness with a particular focus on KRAS-inhibited tumors and provide a rationale for developing therapies targeting mutant KRAS and STAT3.

overall_design: Orthotopic injections into the pancreas of FVB male mice were performed with 104 iKRAS parental control (A9993) or iKRAS STAT3 KO cells in Matrigel diluted 1:10 with Opti-MEM using standard procedures (Kim et al 2009). For tumor formation, the drinking water was provided ad libitum and supplemented with 2% sucrose, doxycycline hyclate (0.5 mg/ml), neomycin (0.5 mg/mL) and ampicillin (1 mg/mL). The animals were observed for tumor development by palpation and orthotopic tumors were pooled from 2-3 individual mice at day 0 (~150-350mg) or following doxycycline removal for 4 days (day 4) (100-200mg).Single cell suspensions were prepared by treating tumor tissues with 1x collagenase/hyaluronidase (StemCell Technology), 0.5 mg/ml Liberase-DL (Roche), and 0.1 mg/ml DNase I (Sigma) for 45 minutes at 37C with continuous mixing. Single-cell RNA sequencing was performed by the Cold Spring Harbor Laboratory Single-Cell Biology Shared Resource, Genomics Technology Development.

first: Nancy

last: Reich


title: CHD3 regulates BMP signalling response during cranial neural crest cell specification

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

summary: CHD3 is a component of the NuRD chromatin remodeller. Mutations in CHD3 cause Snijders Blok-Campeau Syndrome, a neurodevelopmental disorder marked by intellectual disability and craniofacial abnormalities. To unveil the role of CHD3 in craniofacial development, we differentiated CHD3-null induced pluripotent stem cells (iPSCs) into cranial neural crest cells (CNCC). We found that CHD3 expression is low in iPSCs and neuroectoderm, but it is upregulated during CNCC specification, where CHD3-containing NuRD opens the chromatin at BMP-responsive enhancers, to allow binding of DLX5 and other factors. CHD3 loss leads to repression of BMP target genes and imbalance between BMP and Wnt signalling, which ultimately results in aberrant mesodermal fate. Consequently, cranial neural crest specification fails, replaced by mesodermal identity, which can be partially rescued by titrating Wnt levels. Our findings highlight a novel role for CHD3 as pivotal regulator of BMP signalling, essential for proper neural crest specification and craniofacial development.

overall_design:
RNA-seq of CHD3-WT, CHD3-HET-KO and CHD3-KO iPSC lines  (3 replicates per line)
RNA-seq of CHD3-WT and CHD3-KO cell lines at day 18 of in vitro cranial neural crest cell specification in late maintenance media (at least 2 replicates per line)
RNA-seq of CHD3-WT and CHD3-HET-KO cell lines at day 18 of in vitro cranial neural crest cell specification in early maintenance media (3 replicates per line)
RNA-seq of CHD3-WT and CHD3-KO cell lines at day 14 of in vitro cranial neural crest cell specification in early maintenance media (at least 2 replicates per line)
ChIP-seq of CHD3 in two CHD3-WT cell lines at day 14 of in vitro cranial neural crest cell specification
ChIP-seq of CHD3 in CHD3-WT cell line at day 18 of in vitro cranial neural crest cell specification
ChIP-seq of DLX5 in one CHD3-WT cell line and two CHD3-KO cell lines at day 14 of in vitro cranial neural crest cell specification
ATAC-seq of CHD3-WT and CHD3-KO cell lines at day 18 of in vitro cranial neural crest cell specification (2 replicates per line)
ATAC-seq of CHD3-WT and CHD3-KO cell lines at day 14 of in vitro cranial neural crest cell specification (2 replicates per line)
ATAC-seq of CHD3-WT and CHD3-KO iPSC lines (2 replicates per line)
ATAC-seq of CHD3-WT and CHD3-KO cell lines at day 4 of in vitro cranial neural crest cell specification (2 replicates per line)
ATAC-seq of CHD3-WT and CHD3-KO cell lines at day 10 of in vitro cranial neural crest cell specification (2 replicates per line)
ChIP-seq of MBD3 in two CHD3-WT cell lines at day 14 of in vitro cranial neural crest cell specification

first: Zoe

middle: H

last: Mitchell

first: Joery

last: den Hoed

first: Willemijn

last: Claassen

first: Martina

last: Demurtas

first: Laura

middle: L

last: Deelen

first: Philippe

last: Campeau

first: Karen

last: Liu

first: Simon

last: Fisher


title: CAV2-expressing Nerves induce Metabolic Switch toward Mitochondrial Oxidative Phosphorylation to Promote Cancer Stemness

status: Public on Feb 04 2025

city: tianjin

first: Zhang

last: ze

address: Huanhu Xi Road, Tiyuan Bei, Hexi District, Tianjin

institute: Tianjin Medical University Cancer Institute and Hospital

summary: Cancer cells and the nervous system engage in a dynamic interplay, significantly influencing initiation and progression in head and neck squamous cell carcinoma (HNSCC). Our findings highlight that cancer cells drive an increase in caveolin-2 (Cav2) expression within trigeminal ganglia and associated neural fibers in the tumor milieu, fostering a reciprocal attractant relationship between tumor cells and nerves. Notably, the knockout of Cav2, either globally or specifically in sensory neurons or glial cells, markedly attenuates the growth of orthotopically implanted tongue tumors. Moreover, Cav2-expressing nerves are implicated in shifting cancer cell metabolism towards mitochondrial oxidative phosphorylation, a process involved in maintenance of cancer stem cells (CSCs). Our results also demonstrate that Cav2-expressing nerves confer stemness properties to cancer cells. Disruption of Cav2 expression, both globally and in specific neural cell types, impedes tumorigenesis and progression in a 4-NQO- induced HNSCC mouse model.This interplay observed between cancer cells, neurons, and glial cells suggests a potential mechanism through which tumor-associated nerves might influence cancer stemness via metabolic reprogramming. This highlights a possible new direction for anticancer therapy that warrants further investigation.

overall_design:
After 72 hours of co-culture with wild TG or Cav2 -/- TG, total RNA of SCC15 cells was extracted using TRIzol reagent, and RNA quality was assayed by Nanodrop and Bioanalyzer. Three biological replicates with good quality RNA were used to make cDNA libraries.

Please note that the records have been updated with raw data files on Apr 21, 2025.

first: Ruoyan

first: Zhonghao

first: Chunli

last: Wang


title: The landscape of enhancer transcription in prostate cancer [RNA-Seq]

first: Zezhong

last: Xiong

summary:
To construct the enhancer transcription expression profile, we performed RNA-seq in 20 pairs of prostate cancer tissues and matched adjacent tissues.
We then performed enhancer transcription expression profiling analysis using data obtained from RNA-seq of 20 pairs of samples.

overall_design: Comparative transcripts expression profiling analysis of RNA-seq data for prostate cancer tissues and matched adjacent tissues

first: Yue

last: Ge


title: Dynamic investigation of hypoxia-induced L-lactylation

city: Shenzhen

first: Rui

last: Li

address: Lishui street

institute: Peking university

summary: The recently identified histone modification lysine lactylation can be stimulated by L-lactate and glycolysis. Although the chemical group added upon lysine lactylation was originally proposed to be the L-enantiomer of lactate (KL-la), two isomeric modifications, lysine D-lactylation (KD-la), and N-ε-(carboxyethyl) lysine (Kce), also exist in cells, with their precursors being metabolites of glycolysis. The dynamic regulation and differences among these three modifications in response to hypoxia have not been investigated previously. In this study, we demonstrate that intracellular KL-la, but not KD-la or Kce, is upregulated in response to hypoxia. Depletion of glyoxalase enzymes, GLO1 and GLO2, had minimal impact on KD_x001E_la, Kce, or hypoxia-induced KL-la. Conversely, blocking glycolytic flux to L-lactate under hypoxic conditions by knocking out LDHA/B completely abolished the induction of KL-la, but increased KD-la and Kce. We further observed a correlation between the level of KL-la and HIF-1α expression under hypoxic conditions and when small molecules were used to stabilize HIF-1α in the normoxia condition. Our result demonstrated that there is a strong correlation between HIF-1α and KL-la in lung cancer tissues, and that patient samples with higher grade tend to have higher KL-la levels. Using a proteomics approach, we quantified 66 KL-la sites that were upregulated by hypoxia and demonstrated that p300/CBP contributes to hypoxia-induced KL-la. Collectively, our study demonstrates that KL-la, rather than KD-la or Kce, is the prevailing lysine lactylation in response to hypoxia. Our results therefore demonstrate a link between KL-la and the hypoxia-induced adaptation of tumor cells.

overall_design: ChIP-seq of the histone modification H3K18L-la in normoxia and hypoxic MCF-7 cells.

first: Jinjun

last: Gao

first: Ruilong

first: Kevin

last: Huang

first: Ziyuan

first: Xinlei

last: Sheng

first: Kasturi

last: Chakraborty

first: Chang

last: Han

first: Di

last: Zhang

first: Lev

last: Becker

first: Yingming

last: Zhao


title: RNA-seq analysis of E11.5 and E12.5 Mboat7 KO cortices

first: Nozomu

last: Kono

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

institute: Universtiy of Tokyo

summary: To investigate whether Mboat7 KO mice showed any abnormality before E11.5, we evaluated the global gene expression patterns in the cortices of Mboat7 heterozygous mice and KO mice at E11.5 using RNA-sequencing. No significant differences in gene expression were observed, suggesting that Mboat7 KO mice develop normally until E11.5.  Even at E12.5 when the phenotype starts to become apparent, little difference in gene expression were observed in Mboat7 KO mice.

overall_design: RNA-seq profiling of E11.5 and E12.5 cortices obtained from Mboat7+/- and Mboat7-/- mice.

first: Yuki

last: Ishino


title: Long-read sequencing disentangles isoform complexity at allele-specific loci

status: Public on Feb 03 2025

first: Daniel

last: Andergassen

address: Biedersteiner Straße 29

department: Institute of Pharmacology and Toxicology

institute: Technical University of Munich

summary: In recent years, long-read sequencing technologies have detected transcript isoforms with unprecedented accuracy and resolution. However, it remains unclear whether long-read sequencing can effectively disentangle the isoform landscape of complex allele-specific loci that arise from genetic or epigenetic differences between alleles. Here, we combine the PacBio Iso-Seq workflow with the established phasing approach WhatsHap to assign long reads to the corresponding allele in polymorphic F1 mouse hybrids. Upon comparing the long-read sequencing results with matched short reads, we observed general consistency in the allele-specific information and were able to confirm the imprinting status of known imprinted genes. We then explored the complex imprinted Gnas locus known for allele-specific non-coding and coding isoforms and were able to benchmark historical observations. This approach also allowed us to detect isoforms  from both the active and inactive X chromosomes of genes that escape X chromosome inactivation. The described workflow offers a promising framework and demonstrates the power of long-read transcriptomic data to provide mechanistic insight into complex allele-specific loci.

overall_design:
To capture the allele-specific expression landscape through long-read sequencing, we bred C57BL/6J (BL6) females carrying a heterozygous deletion of the proximal A-repeat (Xist −/+) with a CAST/EiJ (CAST) male. We then collected RNA from a whole brain sample from a resultant F1 female (BL6ΔXist × CAST) and performed long-read sequencing.
The allele-specific analysis was conducted by counting the reads from each allele and calculating a ratio. This analysis was compared to short-read sequencing allele-specific analysis and does not include replicates.

first: Lison

last: Lemoine

first: Sarah

last: Hoelzl

first: Tim

middle: P

last: Hasenbein

first: Elisabeth

last: Graf


title: The landscape of enhancer transcription in prostate cancer

first: Zezhong

last: Xiong

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

overall_design: Refer to individual Series


title: Akkermansia muciniphila outer membrane protein Amuc_0904  promotes goblet cell differentiation

city: 天津市

first: Liu

last: yang

state: 天津市

address: qixiangtai Road

institute: Tianjin medical university

summary: Akkermansia muciniphila is recognized as a promising probiotic that improves the symptoms of a variety of diseases. However, the role and mechanism of A. muciniphila in regulating intestinal homeostasis remain to be explored. Here, we discovered that A. muciniphila was dramatically increased during colitis recovery, and its colonization greatly increased goblet cells to protect the intestinal barrier in mice. Amuc_0904, a previously uncharacterized A. muciniphila outer membrane protein, was identified to induce goblet cell differentiation.

overall_design: Total RNA was extracted from HT-29 cells using TRIzol Reagent according the manufacturer’s instructions. The RNA quality was determined using a 2100 Bioanalyser (Agilent), and the RNA concentration was quantified using the ND-2000 (NanoDrop Technologies). RNAseq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA). Paired-end RNAseq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2×150 bp read length) according to the standard protocols by Majorbio Bio-Pharm Technology Co. Ltd. The raw paired-end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://ccb.jhu.edu/software/hisat2/index.shtml). The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) in a reference-based approach.


title: KMT2C/KMT2D-dependent H3K4me1 mediates DNA replication timing and origin firing

city: New York

first: Tony

state: NY

address: 450 East 29th St, Rm 807

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

summary: Mammalian genomes are replicated in a precise, cell-type-specific order during the S phase, a process that correlates with local transcriptional activity, chromatin modifications, and chromatin architecture. However, the causal relationships between these features and DNA replication timing (RT), particularly during cell fate transitions, remain largely unknown. Here, we employed machine learning to quantify chromatin features — including epigenetic marks, histone variants, and chromatin architectural factors — that best predict local RT under steady-state conditions and RT changes during early embryonic stem (ES) cell differentiation. We found that approximately one-third of the genome exhibits RT changes during differentiation. Chromatin features collectively predicted steady-state RT and RT changes with high accuracy. Notably, histone H3 lysine 4 monomethylation (H3K4me1), catalyzed by KMT2C/D, emerged as a top predictor. Genetic deletion of Kmt2c/d (but not Kmt2c alone) or their enzymatic activities erased genome-wide RT dynamics during cell differentiation. Sites that typically gain H3K4me1 in a KMT2C/D-dependent manner during differentiation failed to transition towards earlier RT, often without affecting transcriptional activation. Further analysis at KMT2C/D binding sites revealed a local requirement for KMT2C/D in promoting DNA replication origin firing. Our findings identify KMT2C/D-dependent H3K4me1 as a functional regulator of RT and origin firing, highlighting a causal relationship between the epigenome and DNA replication that is largely independent of transcription. These insights should be relevant to various diseases associated with KMT2C/D mutations. Mammalian genomes are replicated in a precise, cell-type-specific order during the S phase, a process that correlates with local transcriptional activity, chromatin modifications, and chromatin architecture. However, the causal relationships between these features and DNA replication timing (RT), particularly during cell fate transitions, remain largely unknown. Here, we employed machine learning to quantify chromatin features — including epigenetic marks, histone variants, and chromatin architectural factors — that best predict local RT under steady-state conditions and RT changes during early embryonic stem (ES) cell differentiation. We found that approximately one-third of the genome exhibits RT changes during differentiation. Chromatin features collectively predicted steady-state RT and RT changes with high accuracy. Notably, histone H3 lysine 4 monomethylation (H3K4me1), catalyzed by KMT2C/D, emerged as a top predictor. Genetic deletion of Kmt2c/d (but not Kmt2c alone) or their enzymatic activities erased genome-wide RT dynamics during cell differentiation. Sites that typically gain H3K4me1 in a KMT2C/D-dependent manner during differentiation failed to transition towards earlier RT, often without affecting transcriptional activation. Further analysis at KMT2C/D binding sites revealed a local requirement for KMT2C/D in promoting DNA replication origin firing. Our findings identify KMT2C/D-dependent H3K4me1 as a functional regulator of RT and origin firing, highlighting a causal relationship between the epigenome and DNA replication that is largely independent of transcription. These insights should be relevant to various diseases associated with KMT2C/D mutations.

overall_design: Okazaki-fragment (Ok-seq) sequencing was performed on naïve (N) and transformed epi-blast-like (formative, F) mouse embryonic stem cells. Three experimental conditions were analyzed for each naive and formative ES cell conditions: control cell lines with loss of KMT2C (CKO), loss of both KMT2C and KMT2D (DKO), and double catalytic mutant KMT2C and KMT2D cells. Two biological replicates of Ok-seq were performed per condition.

first: Liana

last: Goehring

first: Deniz

last: Gökbuget

first: Robert

last: Blelloch


title: Profiling replication timing in WT, MLL3KO and MLL3/4dKO cells during naive to formative ESC differentiation [Bio-Repli-seq]

address: 35 Medical Center Way

department: Urology

summary: We performed BioRepli-seq for WT, MLL3KO and MLL3/4dKO ESCs the naive to formative ESC differentiation.

overall_design: Three replicates derived from independent cultures were collected per genotype and cell state (naive and formative)

last: Goekbuget


title: Combined loss of obscurin and obscurin-like 1 in murine hearts results in diastolic dysfunction, altered metabolism and deregulated mitophagy.

status: Public on Feb 01 2025

first: Stephan

last: Lange

address: 9500 Gilman Dr

institute: UC San Diego

summary: RNAseq raw data generated from total cardiac RNA of cardiac specific Obscurin x Obsl1 knockout mice

overall_design: Three biological replicates were analyzed for four genotypes (control [CTL], obscurin knockout [Obsc], Obsl1 knockout [OL1], obscurin x Obsl1 double knockout [dKO])

first: Matúš

last: Soták

first: Emma

last: Börgeson


title: Predictive modeling of chromatin features underlying replication timing

first: Ryan

last: Boileau

last: Huang


title: Profiling of chromatin features during naive to formative ESC differentiation [CUT&Tag]

summary: We performed CUT&Tag for various chromatin features during the naive to formative ESC differentiation.

overall_design:
Two replicates derived from independent cultures were collected per chromatin feature and cellular state (naive and formative)
Please note that *merged.cpm.bw was generated from both rep1 and rep2 samples, and is linked to the corresponding rep1 sample records.


title: identify the secreted gene in Casp8-silenced mouse hepatocyte cell line

first: Xiaobo

last: Wang

address: 630 W 168tth street

institute: Columbia University

summary: Hepatocyte caspase-8 is elevated in MASH and promotes fibrosis independently of apoptosis changes. To investigate how hepatocyte caspase-8 might drive liver fibrosis progression in MASH, we focused on activated hepatic stellate cells (HSCs), which are the primary source of collagen-producing myofibroblasts and central players in MASH fibrosis. To assess a potential link between hepatocyte caspase-8 and HSC activation, we used an ex vivo model where primary murine HSCs were cultured with conditioned media from siCasp8-treated or control primary hepatocytes. Supporting our hypothesis, HSC activation markers were reduced in HSCs exposed to conditioned media from Casp8-silenced AML12 hepatocytes compared to controls. To pinpoint caspase-8-dependent secretory proteins that could activate HSCs, we conducted RNAseq on these cells, identifying secretory genes reduced in Casp8-silenced AML12 hepatocytes.

overall_design: Scrambled control siRNA and Casp8 siRNAs were transfected into AML12 cells using Lipofectamine RNAiMAX (Life Technologies) at a final concentration of 40 nM siRNA in 24-well plates, following the manufacturer’s instructions. After 48 hours, the cells were collected for RNA sequencing. Gene expression profiling was performed using RNA-seq data from four biological replicates. Comparative analysis of gene expression focused on differences between scrambled (scr) control and siCasp8-treated AML12 hepatocyte cells.

first: Ira

last: Tabas


title: RNA m1A methyltransferase TRMT61A induces MAPK/ERK signaling and is a therapeutic target in colorectal cancer [Ribo-Seq]

city: hong kong

first: xiaoting

last: zhang

address: Rm 708, 7/F., Li Ka Shing Medical Science Building , Prince of Wales Hospital, Shatin, N.T., Hong Kong

institute: The Chinese University of Hong Kong

summary: The role of N1-methyladenosine (m1A) in cancer remains poorly understood. Here we investigate the functional importance of RNA m1A methyltransferase TRMT61A in colorectal cancer (CRC) and assess its potential as a therapeutic target. Our findings demonstrate consistent elevation of TRMT61A expression and RNA m1A levels in primary CRC tissues, which correlate significantly with poor patient survival. Through CRISPR/Cas9 screenings, TRMT61A is the most essential gene among m1A regulators. We further elucidate that TRMT61A facilitates CRC tumorigenesis and progression by enhancing the stability of mRNA of crucial targets, including ONECUT2, thereby activating the MAPK/ERK signaling pathway in an m1A-dependent manner. Of note, we show promising anti-CRC effects by inhibiting TRMT61A using nanoparticleencapsulated siTRMT61A or our identified small molecule compound, PGG. Collectively, our study uncovers the essential role of TRMT61A-m1A in CRC by activating the ONECUT2-MAPK/ERK pathway. Targeting TRMT61A holds promise as a therapeutic approach for treating CRC.

overall_design: To identify the functional downstream effectors of TRMT61A, we performed meRIP-seq in HCT116 cells with or without TRMT61A knockout


title: RNA m1A methyltransferase TRMT61A induces MAPK/ERK signaling and is a therapeutic target in colorectal cancer [MeRIP-Seq]


title: Gene expression profile at single cell level of OVA+ cells elicited by LTA1/OVA vaccine at different time points and CD4+T cells from naïve spleen as control

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

institute: Tulane University

summary: Our previous work showed that vaccine elicited Klebsiella pneumoniae specific CD4+ tissue resident memory (TRM) cells in the lung provide serotype independent immunity against K. pneumoniae for up to 6 months.  However, vaccine efficacy wanes in proportion to lung CD4+ TRM cell number.  To study what controls TRM maintenance, apart from antigen, we developed an LTA/1Ovalbumin (OVA) model and tetramer pulldown method to enrich OVA+ lung CD4+ TRM cells over time. We applied single-cell RNA-sequencing (scRNA-seq) of these cells, collected on days 30, 90 and 184 after prime immunization with OVA and our prior Th17 adjuvant, E. coli heat labile toxin A1 (LTA1). As control, we used splenic CD4+ T cells from naive mice

overall_design: OVA+ cells from different time points were enriched by OVA-tetramer pulldown and analyzed by scRNAseq.

first: Kejing

last: Song

first: Haoran

last: Yang

middle: K


title: RNA m1A methyltransferase TRMT61A induces MAPK/ERK signaling and is a therapeutic target in colorectal cancer II

overall_design: To identify the functional downstream effectors of TRMT61A, we performed RNA-seq in HCT116 cells with or without TRMT61A knockout

first: XIAOTING

last: ZHANG

last: QIN

first: FENFEN

last: JI


title: RNA m1A methyltransferase TRMT61A induces MAPK/ERK signaling and is a therapeutic target in colorectal cancer I


title: Expression data of small and large intestinal epitheliall cells from Nfat5fl/fl  and Nfat5IEC-KO mice

city: Seoul

first: Bong-Ki

last: Hong

address: 222 Banpo-daero, Seocho-gu

department: School of Medicine

country: South Korea

institute: Catholic University of Korea

summary:
Gene expression profile data of small and large intestinal epitheliall cells from Nfat5fl/fl  and Nfat5IEC-KO mice
We used microarrays to detail the global programme of gene expression of small and large intestinal epitheliall cells from Nfat5fl/fl  and Nfat5IEC-KO mice and identified differential genes.

overall_design: Small and lage intestinal cells were isolated for RNA extraction and hybridization on the Affymetrix GeneChip Mouse Gene 2.0 ST array. We sought to obtain up- or down-regulated gene expression of small and large intestinal epithelial cells from Nfat5fl/fl  and Nfat5IEC-KO mice. To that end, we hand-selected most down-regulated genes of small and large intestinal epitheliall cells from Nfat5fl/fl  and Nfat5IEC-KO mice

first: Wan-Uk

last: Kim

first: Se-Hyeon

last: Park


title: Resolution of SARS-CoV-2 infection in human lung tissues is driven by CD163+ inflammatory monocytes (RNA-Seq)

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

summary: The lung-resident immune mechanisms driving resolution of SARS-CoV-2 infection in humans remain elusive due to limitations associated with human studies. Using mice co-engrafted with a human immune system and fetal lung xenograft (fLX), we mapped the immunological events defining resolution of SARS-CoV-2 infection in human lung tissues. Viral particles and RNA are rapidly cleared from fLX following a peak of viral replication. Clearance is associated with the emergence of a short-lived inflammatory monocyte (iMO) and a macrophage-like T-cell subset enriched in viral RNA. iMO exhibit an exclusive antiviral response, and the upregulation of monocyte chemoattractive signals by infected fLX underscores a link between circulating CD4+ monocyte recruitment and iMO differentiation. Consistently, mice systemically depleted for human CD4+ cells but not for CD3+ T-cells fail to robustly clear infection and display signatures of chronic infection. Our findings uncover iMO differentiation as a critical hallmark of successful resolution of SARS-CoV-2 infection in human lung tissues, and open avenues to understand the drivers of persistently active SARS-CoV-2 infection.

overall_design: Bulk RNA-seq from fetal lung xenografts in BLT-L mice infected with SARS-CoV-2. Samples taken 2 and 12 days postinfection (dpi) were compared to naïve.

first: Devin

last: Kenney


title: Resolution of SARS-CoV-2 infection in human lung tissues is driven by CD163+ inflammatory monocytes


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

status: Public on Jan 31 2025

city: Columbia

first: Jacob

middle: Jeffrey

last: Russell

state: MO

address: 1401 Ashland Rd, Apartment E

department: Biomedical Sciences

institute: University of Missouri

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

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

first: Tadashi

last: Yoshida

first: Li

last: Lee

first: Lixin

last: Ma

first: Daniel

last: Davis

first: Laurel

middle: A

last: Grisanti

first: Margot

last: Ruff

first: Chastidy

last: Bailey

first: Shawn

last: Bender

first: Chandrasekar

last: Bysani


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

city: Guangzhou

first: Miao

last: Zhen

address: No.58 Zhongshan Er Road

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

type: Non-coding RNA profiling by high throughput sequencing

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

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

first: Peng

last: Wang


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Control and FTO Inhibitor-treated Uterine Leiomyosarcoma Cell Transcriptome

city: Chicago

first: Qiwei

last: Yang

address: 5841 S. Maryland Avenue

department: Obstetrics and Gynecology

institute: University of Chicago

summary: We report that FTO inhibition alters multiple biological pathways in uterine leiomyosarcoma cells

overall_design: Examine the transcriptome alteration in uterine leiomyosarcoma cells with or without FTO inhibitor

first: Ayman

last: Al-Hendy


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

status: Public on Jan 30 2025

city: Los Angeles

first: Pablo

middle: Aldair

last: Alvarez

address: 615 Charles E Young Dr S

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California, Los Angeles

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

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

first: Angelica

last: Medina

first: Hengli

last: Tang

first: Melody

last: Li


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

city: Cleveland

first: Jessica

last: Williams

state: OH

address: 9620 Carnegie Ave N Bldg

department: Neurosciences

institute: Cleveland Clinic

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

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

first: Rachel

last: Tinkey

first: Brandon

middle: C

last: Smith

first: Maria

last: Habean


title: The CGG triplet repeat binding protein 1 counteracts DNA secondary structure formation to prevent transcription-replication stress

city: Munich

first: Stephan

last: Hamperl

state: Bayern

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz-Zentrum Munich

summary: CGGBP1 has been implicated in transcription regulation. We tried to investigate the molecular mechanism of how transcription is regulated by depletion of CGGBP1 protein.

overall_design: siRNA for CGGBP1 or its control was transfected into U-2OS Tet-ON cells and cultured for 72h followed by SLAM-Seq analysis.

first: Henning

last: Ummethum

first: Florian

last: Erhard


title: Single-cell and spatial transcriptomics of vulvar lichen sclerosus reveal multi-compartmental alterations in gene expression and signaling cross-talk

status: Public on Jan 27 2025

city: Irvine

first: Xing

last: Dai

address: 825 Health Sciences Road

department: Biological Chemistry

institute: UC Irvine

summary: Vulvar diseases are a critical but often overlooked issue in women's health, impacting many women and frequently causing long-term physical and emotional challenges. Lichen sclerosus (LS) is a chronic inflammatory skin disease that causes scarring of the vulva and is associated with an increased risk of malignancy. The molecular pathogenesis of vulvar LS (VLS) is not well understood, preventing development of any FDA-approved therapies. Here, we utilize single-cell and spatial transcriptomics to analyze lesional and non-lesional skin from VLS patients, as well as healthy control vulvar skin. Our studies, which reveal histologic, cellular, and molecular heterogeneities within VLS, also identify unifying molecular changes across fibroblasts, immune cells, keratinocytes, and melanocytes in lesional skin. The findings depict a scenario of cellular stress and damage affecting both fibroblasts and keratinocytes, along with a complex immune landscape indicating enhanced CD8+ T cell cytotoxicity but also signs of exhaustion. They further suggest aberrant cell-cell signaling across, and increased activation of IFN, JAK/STAT and p53 pathways in, specific cell types. Using monolayer and organotypic culture models, we demonstrate that the depletion of select genes, which are downregulated in VLS lesional skin keratinocytes, partially recapitulates VLS-like stress-associated changes. Collectively, these data provide novel insights into the pathogenesis of VLS, identifying potential biomarkers and therapeutic targets for future research.

overall_design: We performed siRNA knockdown of ATF3, APOE, and CXCL14 in N/TERT-2G keratinocytes and bulk RNA-seq analysis.

first: Jiahui

last: Xu

last: Sun


title: Dietary restriction promotes anti-tumor immunity via T cell mediated ketone body metabolism

status: Public on Jan 28 2025

city: Grand Rapids

last: Oswald

state: MI

address: 333 Bostwick Ave NE

department: Metabolism

institute: Van Andel Institute

summary: Diet can shape immune function in vivo, but the molecular mechanism remains poorly defined. In this study, we investigated how a reduction in food intake (hereafter referred to as dietary restriction or DR) affects CD8+ T cell function in multiple models. We found that DR reduced tumor burden in mice in a CD8+ T cell-dependent manner, indicating that the anti-tumor effects of DR are mediated by the immune system. Consistent with this observation, DR increased CD8+ T cell effector function, including production of interferon-γ and granzyme B. Moreover, analysis of tumor infiltrating CD8+ T cells showed DR led to a decrease in markers of T cell exhaustion (PD1, TIM3, TOX) and an increase in markers of cell stemness (LY108, TCF1). In a model of Listeria infection, we further showed that DR enhances CD8+ T cell mitochondrial fitness and bioenergetic capacity, indicating that DR impacts both CD8+ T cell metabolism and effector function. Using stable isotope tracing, we identified that CD8+ T cells from mice on DR preferentially consumed the ketone body β-hydroxybutyrate (βOHB), which is elevated 3-fold in serum of in mice on DR relative to ad libitum-fed mice. Notably, the effects of DR on anti-tumor immunity were attenuated in conditional knockout mice in which T cells are unable to catabolize βOHB, supporting that DR enhances anti-tumor immunity, in part, through increasing βOHB availability and metabolism by T cells. Current and future studies are exploring the effects of DR on different immune cell populations within tumors to further delineate the mechanism(s) by which DR enhances the immune response in cancer.

overall_design: B16-OVA cells were injected into B6 mice for tumor establisment. Mice were on either dietary restriction (DR) or ad-libitium (AL) diets n =4. 12 days post tumor injection, tumors were harvested and live CD45+ cells were isolated and stained with antibodies (HTO/ADT). Cells were then preped for CITE-Seq.

first: Michael

last: Dahabieh

first: Lisa

last: DeCamp

first: Nicholas

last: Bunda

first: Joesph

last: Longo

first: Russell

last: Jones


title: Single-oocyte mRNA sequencing reveals that AMH-overexpression alters oocyte gene expression

status: Public on Jan 26 2025

city: Dunedin

last: Pankhurst

state: Otago

address: 270 Great King St

department: Department of Anatomy

country: New Zealand

institute: University of Otago

summary: Research Question: Does over-expression of AMH lead to changes in oocyte gene expression in mice? Design: Naturally ovulated oocytes were dissected from the oviduct of wild-type, and AMH-overexpressing (Thy1.2-AMHTg/0) mice and single oocytes underwent transcriptome sequencing (n=11 and n=10, respectively). Results: Oocytes from Thy1.2-AMHTg/0 females displayed 39 significantly expressed differentially expressed genes (DEGs) compared to wild-type mouse oocytes. The most prominent gene expression changes were a 70-fold increase in Rpsa3a, a 22-fold increase in Hormad1 and a 5.6-fold increases in Fnip2 in the oocytes from Thy1.2-AMHTg/0 mice. Gene ontology analysis indicated that among the DEGs, the most enriched pathways were mitochondrial genes and DNA repair genes. Conclusions: These data show that overexpression of AMH, through its actions on granulosa cells, can lead to changes in the expression of specific genes in mouse oocytes.

overall_design: RNA-seq profiling of individual, naturally ovulated oocytes obtained from either wild-type or Thy1.2-AMHTg/0 (AMH-overexpressing) female mice.

first: Timothy

last: Hore

middle: W


title: Post-transcriptional monoadenylation by TENT2 terminates human RNA polymerase III transcript 3' end processing and promotes 7SL RNA biogenesis [global_RNAseq]

city: La Jolla

first: Cody

last: Ocheltree

address: 9500 Gilman Drive

institute: UCSD

summary: Small non-coding RNAs (sncRNAs) are subject to a variety of 3' end trimming and tailing activities during biogenesis, which dictate whether they undergo maturation or are instead subjected to degradation. To investigate the dynamics of human sncRNA 3' end processing at a global level we performed genome-wide 3' end sequencing of nascently-transcribed and steady state sncRNAs. This revealed widespread post-transcriptional adenylation of nascent sncRNAs, which came in two distinct varieties. One is characterized by oligoadenylation, which is transient, promoted by TENT4A/4B polymerases, and observed primarily on unstable sno- and scaRNAs that are not fully processed at their 3' ends. The other is characterized by monoadenylation, which is broadly catalyzed by TENT2 and stably accumulates at the 3’-end  of many RNA Polymerase-III-transcribed (Pol-III) RNAs as well as a subset of small nuclear RNAs. This monoadenylation event terminates 3' end uridylation/deuridylation dynamics characteristic of nascent Pol-III RNAs and, in the case of 7SL RNAs, prevents their accumulation with nuclear La protein and promotes their biogenesis towards assembly into cytoplasmic signal recognition particles.

overall_design: Total small RNA (100-500 bp) and small RNAs nascently-labeled with EU for 2 hours were extracted and libraries were prepared in biological triplicate for 3'-end global sequencing of small RNAs.

first: Tim

last: Nicholson-Shaw

first: Jens

last: Lykke-Andersen


title: Single-cell and spatial transcriptomics of vulvar lichen sclerosus reveal multi- compartmental alterations in gene expression and signaling cross-talk

first: Christina

last: Kraus

address: 118 Medical Surge 1

department: Dermatology

institute: University of California, Irvine

summary: Vulvar diseases are a critical but often overlooked issue in women's health, impacting many women and frequently causing long-term physical and emotional challenges. Lichen sclerosus (LS) is a chronic inflammatory skin disease that causes scarring of the vulva and is associated with an increased risk of malignancy. The molecular pathogenesis of vulvar LS (VLS) is not well understood, preventing development of any FDA-approved therapies. Here, we utilize single-cell and spatial transcriptomics to analyze lesional and non-lesional skin from VLS patients, as well as healthy control vulvar skin. Our studies, which reveal histologic, cellular, and molecular heterogeneities within VLS, also identify unifying molecular changes across fibroblasts, immune cells, keratinocytes, and melanocytes in lesional skin. The findings depict a scenario of cellular stress and damage affecting both fibroblasts and keratinocytes, along with a complex immune landscape indicating enhanced CD8+ T cell cytotoxicity but also signs of exhaustion. They further suggest aberrant cell-cell signaling across, and increased activation of IFN, JAK/STAT, and p53 pathways in specific cell types. Using monolayer and organotypic culture models, we demonstrate that the depletion of select genes, which are downregulated in VLS lesional skin keratinocytes, partially recapitulates VLS-like stress-associated changes. Collectively, these data provide novel insights into the pathogenesis of VLS, identifying potential biomarkers and therapeutic targets for future research.

overall_design: We performed scRNA-seq on patient-matched LE and NL vulvar skin samples collected from punch biopsies of patients with biopsy-proven VLS, using the 10x Genomics Chromium platform.

first: Peng

first: Wei

last: Zhao

first: Quy

last: Nguyen

first: Arjun

last: Nair

first: Melanie

last: Oakes

first: Qing

last: Nie


title: Heritable non-genetic phenotypes are enriched for stress responses as a form of bet hedging

city: Newark

first: Mark

last: Blenner

state: Delaware

department: Department of Chemical and Biomolecular Engineering

institute: University of Delaware

summary: To produce humanized therapeutics, Chinese hamster ovary (CHO) cells have become the preferred host organism. During manufacturing batches, these cells encounter critical levels of environmental stressors such as ammonia, lactate, and osmolality accumulation that can significantly reduce cell health and productivity. It is therefore crucial that stress adaptation and resistance be factored into cell line development (CLD) considerations. An alternative to screening stress sensitivity during CLD, where the scaled-down micro-environment makes it difficult, is selecting for or engineering cell lines with a stress resistant phenotype. In this study, we employee population-based transcriptomic analysis and differential gene expression analysis on stress-induced CHO cells to identify biomarkers for engineering stress resistance. These biomarkers are identified as genes displaying heritable properties while being differentially expressed in the presence of manufacturing relevant stress levels. Using this workflow, 199 genes displayed transcriptional variability characteristic of a bistable system that formed six network communities of co-fluctuating genes. These communities were enriched in genes related to response to stimuli, regulation of apoptotic processes, and regulation of gene expression or metabolic pathways. Significant overlap with differentially expressed genes in stress-induced production fed-batch flasks reinforce the relevancy of these heritable genes states for stress adaptation. Assessing the overlap and the biological function, six genes were identified as promising biomarkers for engineering a stress-resistant phenotype. Cell line engineering methods may be employed in the future to bias clonal populations for higher stress tolerance and adaptability to manufacturing stress, therefore increasing cell health and productivity in at-scale bioreactors.

overall_design:
Population-based transcriptomic analysis, known as MemorySeq, in which single-cell derived mini-pools (40 samples) of CHOZN® GS -/- ZFN Clone 23 gene expression is measured in an attempt to correlate highly variable genes with those displaying heritable patterns. Samples compared to bulk RNA-Seq as a noise control to monitor innate biological variability. Collection of genes demonstrating heritable expression patterns compared to differentially expressed genes from day 5 of stress-induced production fed-batch flasks to identify heritable genes critical to stress recognition and adaptation
Please note that only R1 raw data fastq file is provided for the 'MemorySeq_Sample26_Single-Cell-26' sample (as R2 file is corrupted).

first: Grissom

last: Spencer

first: Dixon

last: Zachary

first: Singh

last: Abhyudai

first: Blenner

last: Mark


title: Resolution of SARS-CoV-2 infection in human lung tissues is driven by CD163+ inflammatory monocytes (scRNA-Seq)

first: Jacquelyn

last: Turcinovic

overall_design: Single-cell RNA-seq from fetal lung xenografts in BLT-L mice infected with SARS-CoV-2. Samples taken 2 and 12 days postinfection (dpi) were compared to naïve.

first: Devin

last: Kenney

first: Christelle

last: Harly