title: Microglia-astrocyte interplay mitigates Aβ toxicity in a novel human 3D neurosphere model of Alzheimer’s Disease

city: Vancouver

first: Haakon

middle: B.

last: Nygaard

state: BC

address: 2215 Wesbrook Mall

department: Division of Neurology

country: Canada

institute: University of British Columbia

summary: Microgliosis and astrogliosis characteristically occur at Aβ plaques in the brains of Alzheimer’s disease (AD) patients although the impact of gliosis in AD is poorly understood. We studied the impact of Aβ-induced gliosis using human induced pluripotent stem cell (hiPSC)-derived 3D neurospheres (hiNS), containing only astrocytes and neurons versus hiNS with the addition of iPSC-derived microglia (hiMG). Applying Aβ to hiNS containing only astrocytes and neurons triggered pathological features of AD including plaque-like aggregates, reactive astrocytes, oxidative stress, neuronal dysfunction and cell death. In contrast, when hiMG were combined with hiNS, infiltrating hiMG effectively phagocytose Aβ and facilitate neuroprotection. Our findings further support a pivotal role for microglia in modulating astrocyte Aβ responses by inducing AD-associated gene expression in astrocytes, including the upregulation of APOE, crucial for Aβ clearance. This model, highlighting the neuroprotective potential of microglia-astrocyte interactions, offers a novel platform for exploring AD mechanisms and novel therapeutic strategies.

overall_design: High-throughput single nuclei transcriptomic profiles of human induced pluripotent stem cell (hiPSC)-derived 3D neurospheres (hiNS), generated by single nuclei RNA sequencing using the 10X Genomics platform.

first: Stefan

last: Wendt

first: Ada

last: Lin

first: Sarah

last: Ebert

first: Declan

last: Brennan

first: Wenji

last: Cai

first: Yanyang

last: Bai

first: Stefano

last: Sorrentino

last: Groten

last: Lee

last: Frew

first: Hyun

middle: B

last: Choi

first: Konstantina

last: Karamboulas

first: Mathias

last: Delhaye

first: David

last: Kaplan

first: Freda

last: Miller

first: Brian

last: MacVicar


title: H3K9me2 CUT&Tag analysis to examine the effect of Jmjd1a knockdown in 3T3-L1 pre-adipocyte cells

status: Public on Apr 29 2025

city: Maebashi

first: Tetsuro

last: Komatsu

address: 3-39-15 Showa-machi

country: Japan

institute: Gunma University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Adipocyte differentiation has been shown to require iron, but the underlying mechanism remains unclear. We have previously reported that iron supply through ferritinophagy is associated with demethylation of the repressive histone mark H3K9me2 in the differentiation-associated genes, which is mediated by the histone demethylase JMJD1A. To examine how JMJD1A regulates the gene expression program during adipocyte differentiation, in this study we peformed H3K9me2 CUT&Tag analysis using 3T3-L1 pre-adipocytes with Jmjd1a knockdown.

overall_design: 3T3-L1 cells were introduced with either control retroviral vector (shEmpty) or one expressing shRNA targeting Jmjd1a mRNA (shJmjd1a). For rescue experiments, either LacZ (as a control), wildtype (WT), or iron-binding deficient mutant JMJD1A (Mut) were expressed in shJmjd1a cells. These cells were then induced for adipocyte differentiation using the differentiation cocktail (insulin, DEX, and IBMX). On Day 2 of differentiaion, H3K9me2 CUT&Tag libraries were prepared as triplicate (n=3).

first: Takeshi

last: Inagaki


title: Mutant IDH1 cooperates with NPM1c or FLT3-ITD to drive distinct myeloid diseases and molecular outcomes

status: Public on Apr 30 2025

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

country: USA

institute: Weill Cornell Medical College

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RNA-seq analysis to examine the effect of Jmjd1a knockdown in 3T3-L1 pre-adipocyte cells

summary: Adipocyte differentiation has been shown to require iron, but the underlying mechanism remains unclear. We have previously reported that iron supply through ferritinophagy is associated with demethylation of repressive histone marks in the differentiation-associated genes, which is mediated by the histone demethylase JMJD1A. To examine how JMJD1A regulates the gene expression program during adipocyte differentiation, in this study we peformed RNA-seq analysis using 3T3-L1 pre-adipocytes with Jmjd1a knockdown.

overall_design: 3T3-L1 cells were introduced with either control retroviral vector (shEmpty) or one expressing shRNA targeting Jmjd1a mRNA (shJmjd1a). For rescue experiments, either LacZ (as a control), wildtype (WT), or iron-binding deficient mutant JMJD1A (Mut) were expressed in shJmjd1a cells. These cells were then induced for adipocyte differentiation using the differentiation cocktail (insulin, DEX, and IBMX). On Day 2 of differentiaion, RNA-seq libraries were prepared as triplicate (n=3).


title: Changes in nucleus accumbens core translatome accompanying incubation of cocaine craving

city: Portland

first: Alex

last: Kawa

state: OR

address: 3181 SW Sam Jackson Park Rd, L470

department: BEHN

institute: OHSU

summary: In the ‘incubation of cocaine craving’ model of relapse, rats self-administer cocaine and then experience a prolonged abstinence period. After this prolonged abstinence period, rats exhibit a progressive intensification (incubation) of cue-induced craving, and the expression of incubated craving depends on plasticity of excitatory synaptic transmission in nucleus accumbens (NAc) core medium spiny neurons (MSN). Previously, we found that the maintenance of this plasticity depends on ongoing protein translation, and that regulation of translation is altered after incubation of cocaine craving. Here we used male and female rats that express Cre recombinase in either dopamine D1 receptor- or adenosine 2a (A2a) receptor-expressing MSN to express a GFP-tagged ribosomal protein in a cell-type specific manner, enabling us to use Translating Ribosome Affinity Purification (TRAP) to isolate actively translating mRNAs from both MSN subtypes for analysis by RNA-Seq. We compared rats that self-administered saline or cocaine. Saline rats were assessed on abstinence day (AD) 1, while cocaine rats were assessed on AD1 or AD40-50. For both D1 and A2a MSN, there were few differentially translated (DT) genes between saline and cocaine AD1 groups. In contrast, a pronounced divergence was observed between cocaine rats on AD1 and AD40, and this was far more robust in D1 MSN. Finally, all comparisons revealed sex differences in translating mRNAs. This study, the first to combine TRAP-seq, transgenic rats, and a cocaine self-administration paradigm, identifies translating mRNAs specifically linked to incubation of cocaine craving in D1 and A2a MSN of the NAc core.

overall_design: Nucleus accumbens punches from adult male and female D1:Cre and A2a:Cre rats that self-administered cocaine or saline and were euthanized 1 or 40 days later. Translating RNA affinity purification (TRAP) was run on the tissue to collect TRAP RNA selectively from D1 or A2a (D2) expressing medium spiny neurons.

first: A

first: J

middle: G

last: Hashimoto

first: M

middle: M

last: Beutler

last: Guizzetti

middle: E

last: Wolf


title: A novel role for Neurog2 in MYCN driven neuroendocrine plasticity of prostate cancer

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

institute: University of Saskatchewan


title: A novel role for Neurog2 in MYCN driven neuroendocrine plasticity of prostate cancer (shRNA)

summary: Neuroendocrine prostate cancer (NEPC) presents a formidable clinical challenge owing to its aggressive progression and resistance to conventional therapies. A key driver of NEPC is the overexpression of MYCN, a well-established oncogene associated with neuroendocrine tumors. However, efforts to directly inhibit the N-Myc protein encoded by this gene have resulted in limited success, thereby hindering therapeutic advancements. To overcome this obstacle, we conducted unbiased genome-wide screening using isogenic prostate cancer cell lines to identify the synthetic vulnerabilities of MYCN. Among the identified candidates, NEUROG2 emerged as a significant candidate. Neurog2 is a proneural transcription factor (PTF) known for its role in developmental processes and trans-differentiation of adult cells. Our findings demonstrate that Neurog2 depletion does not affect non-malignant cells but significantly suppresses the growth of MYCN-overexpressing cells and tumors in orthotopic NEPC models. Furthermore, our observations indicate that Neurog2-driven modulation of PTFs potentially contribute to NEPC development. Thus, targeting Neurog2 holds promise as an effective therapeutic strategy for MYCN-overexpressing NEPC.

overall_design: Samples were collected at different time points after infection with the 90k shRNA libraries and probes were prepared to hybridize to microarray chips to identify SDL partners of MYCN gene.

first: Prachi

last: Walke

first: Jared

middle: W

last: Price

first: Frederick

middle: S

first: Andrew

last: Freywald

first: Anand

last: Krishnan


title: RNA-sequencing of whole lungs from mice with activating K-ras mutations and pharmacologic inhibition of STAT3

status: Public on Apr 28 2025

city: Houston

first: Michael

middle: Joseph

last: Clowers

state: Texas

address: 6565 MD Anderson Blvd

institute: MD Ancerson Cancer Center

summary: K-ras mutant lung adenocarcinoma (KM-LUAD) is a difficult-to-treat cancer subtype in which chronic inflammation pervades the tumor immune microenvironment (TIME). Pro-inflammatory pathways dampen the response to treatments, including immune checkpoint inhibitors, necessitating therapies that target this inflammatory signaling network in the TIME. One of the lynchpins of chronic inflammation in KM-LUAD is signal transducer and activator of transcription 3 (STAT3). Here, we tested the anti-tumor and early immunotherapeutic efficacy of TTI-101, a selective small-molecule inhibitor of canonical STAT3 signaling, in a K-rasG12D mutant lung cancer mouse model (CC-LR). Treatment of CC-LR mice with TTI-101 resulted in reduced tumor burden while increasing dendritic cell (DC) and T helper 1 (Th1) infiltration into the TIME. TTI-101 treatment decreased pY-STAT3 expression in tumors with accompanying increases in several NF-κB anti-tumor target genes including CXCL9, a chemokine for primed T cells. Transcriptional profiling of the TIME revealed improved immune activation and anti-tumor skewing, as well as B cell signaling enrichment. Analysis of human LUAD data demonstrated negative correlations between STAT3 and Th1/DC infiltration, with DC infiltration also conferring improved survival in LUAD patients with low STAT3. Our results highlight the importance of STAT3 in driving early tumorigenesis and offer a preventative treatment window for high-risk individuals and patients with early-stage KM-LUAD.

overall_design: RNA-seq profiling of whole-lung K-rasG12D tumors and their STAT3 inhibitor-treated conterparts (TTI-101) at age 14 weeks following 4 weeks of treatment.

first: Seyed Javad

last: Moghaddam


title: Next Generation Sequencing analysis of OC43 and EV1 viral infection on macrophage-augmented intestinal organoids following treatment with nirmatrelvir and acetate

city: ROTTERDAM

first: guige

last: xu

address: Adrianastraat 203

country: Netherlands

institute: Erasmus medical center

summary:
The pathogenesis of enteric viral infections arises from dual mechanisms: intrinsic viral replication dynamics and dysregulated host immune-inflammatory cascades. To bridge this knowledge gap, we developed macrophage-augmented intestinal organoids (MaugOs), a physiologically relevant model engineered by co-culturing primary human intestinal organoids with autologous macrophages. Using this platform, we interrogated five enteric viruses with distinct intestinal tropisms: Echovirus 1, Echovirus 6, Rotavirus, seasonal coronavirus OC43, and *SARS-CoV-2*.
Key findings revealed that all tested viruses exhibited robust replication in MaugOs and activated canonical antiviral pathways (e.g., IFN-β/ISG15). Notably, Rotavirus, OC43, and *SARS-CoV-2* uniquely elicited inflammatory responses (IL-6/IL-8 upregulation), contrasting with the non-inflammatory phenotype of echoviruses. Mechanistically, acetate—a dominant gut microbial metabolite—dose-dependently attenuated virus-induced inflammation (NF-κB/STAT3 inhibition), while exhibiting cell-compartment-specific effects on viral replication: suppressing OC43 replication in macrophages but enhancing it in organoids.
Furthermore, we established a combinatorial therapeutic strategy in MaugOs by pairing the antiviral agent nirmatrelvir with either anti-inflammatory drugs or acetate, achieving dual suppression of viral load (↓90%) and cytokine storm (IL-6/IL-8 ↓70%). These results position MaugOs as a transformative platform for 1) dissecting spatial virus-immune-epithelial interactions and 2) accelerating drug discovery targeting both viral pathogenesis and immunopathology.

overall_design: mRNA profiles of  characterize OC43- and EV1-infected macrophage-augmented intestinal organoids following treatment with nirmatrelvir and acetate

first: Guige

last: Xu

first: Pengfei

last: LI


title: Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations

city: Urbana

first: Sihang

last: Zhou

state: IL

address: 601 S Goodwin Ave

institute: University of Illinois Urbana-Champaign

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA polymerase III (Pol III) transcription in cancer is linked with the emergence of snaR-A (small NF90-associated RNA isoform A), a hominid-specific ncRNA shown to enhance cell proliferation, migration, and invasion. Here, we investigate snaR-A-protein interactions to delineate its role as a putative driver of cancer progression. At the molecular level, we discover that snaR-A interacts with mRNA splicing factors, including SF3B2 - a core component of the U2 small nuclear ribonucleoprotein (snRNP) - and localizes to subnuclear foci enriched for splicing factors. Ectopic snaR-A overexpression leads to increased intron retention, a hallmark of inefficient splicing, whereas depletion of endogenous snaR-A reduces intron retention in mRNA subpopulations associated with 3’ intron-exon U2 snRNP residency and nuclear speckle proximity. We further show that high levels of snaR-A promotes cell migration in cells linked with increased intron retention, consistent with evidence supporting snaR-A as a negative prognostic factor in cancer. Taken together, these findings establish snaR-A as a molecular disruptor of splicing. We propose that snaR-A-related splicing disruption may phenocopy previously reported splicing defects and consequences attributed to mutations in U2 snRNP in cancer, eliciting an alternate, non-mutational pathway during tumorigenesis.

overall_design: To investigate the effect of SSB on snaR-A, we performed SSB knockdown in HEK293T and sequenced the samples. The experiment included three biological replicates for scramble and SSB knockdown. Raw mRNA signal counts were extracted.

first: Kevin

last: Van Bortle


title: Corticosterone with Normal vs High Protein Diet

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

summary: Discovery of how high protein diet influences gene expression in eWAT and liver from mice receiving corticosterone

overall_design: eWAT and liver from 10 week old male mice receiving Cort +/- Normal (20% kcal) or High (60% kcal) Protein Diet for 7 days

first: Jason

last: Collier

first: Susan

last: Burke


title: CLU alleviates Alzheimer’s disease-relevant processes by modulating astrocyte reactivity and microglia-dependent synaptic density [scRNA-seq]

city: Boston

first: Courtney

last: Benoit

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

summary: Genetic studies implicate Clusterin (CLU) in the pathogenesis of Alzheimer’s disease (AD), yet its precise molecular impact remains unclear. Through unbiased proteomic profiling and functional validation in CLU-deficient astrocytes, we identify increased NfkB-dependent signaling and complement C3 secretion. Reduction of astrocyte CLU induced microglia dependent modulation of extracellular APOE and phosphorylated tau, as well as increased microglial phagocytosis and reduced synapse numbers. By integrating mouse and human cellular models with comprehensive analyses of human plasma and brain tissue, we demonstrate that CLU AD risk alleles are associated with reduced CLU protein and heightened inflammatory profiles. These findings establish a mechanistic link between AD genetic risk factors, astrocyte reactivity, and microglia-mediated effects on synaptic integrity. Collectively, these results support a model in which CLU upregulation in response to neuropathology is associated with maintenance of cognitive function, while diminished astrocyte CLU levels heighten disease susceptibility.

overall_design: iNs and iAs (CLU WT or CLU KO) were differentiated to day 20 and iMGs were differentiated to day 40. On day 20, iAs were dissociated and replated on top of iN cultures. On day 21 (day 40 of iMG differentiation), iMGs were dissociated and replated on top of iN-iA co-cultures. All three cell types were then co-cultured together for an additional six days, after which they were dissociated and analyzed by single-cell RNA-sequencing.

first: Alex

last: Lish

first: Richard

last: Pearse

first: Tracy

last: Young-Pearse


title: Tissue RNAsSeq of germ-free IL10KO versus WT mice in the presence or absence of human gut microbes

city: Chicago

first: Michihiro

last: Takahama

state: Illinois

department: Pritzker School of Molecular Engineering

institute: University of Chicago

summary: IL10 plays a crucial role in regulating immune responses. Although IL10 deficiency induces spontaneous gut inflammation in a commensal-dependent manner, the importance of IL10 signaling in peripheral tissues other than gut remains poorly understood. To determine how peripheral tissues are transcriptionally responded to the commensal-induced IL10 signaling, we performed bulk RNA-seq on the gut, lungs, mesenteric lymph nodes, and kidneys of human fecal microbiota-transplanted (huFMT) IL10 KO, huFMT WT, untreated germ-free (GF) IL10 KO, and untreated GF WT mice.

overall_design: Bulk RNAseq of whole tissue obtained from gut (duodenum, Ileum and colon), lung, mLNs, kidney of GF WT, GF IL10KO, huFMT WT, and huFMT IL10KO mice.

first: Ki-Wook

last: Kim

first: Teruyuki

last: Sano

first: Nicolas

last: Chevrier

first: Madison

last: Plaster


title: Investigative needle core biopsies support multimodal deep-data generation in glioblastoma [Spatial Transcriptomics]

first: Natalie

middle: Y. R.

last: Agar

state: Massachusetts

address: Harvard Medical School

department: Neurosurgery

summary: Glioblastoma, IDH wild type (GBM) is a primary brain cancer with a poor prognosis and few effective therapies. The ability to investigate the tumor and its microenvironment during treatment would greatly enhance understanding of disease response, progression and impact of therapeutics. Stereotactic needle core biopsies are routine surgical procedures performed primarily for tumor diagnosis. Use of these biopsies for investigations into tumor and microenvironmental responses to treatment is rarely performed but holds great potential to support therapeutic monitoring and understanding of tumor evolution. However, it is unclear whether needle core biopsies are sufficient for multi-omics analysis and tumor models. Here we test the depth of data generation possible from stereotactic needle core biopsy tissue in two separate patients. In the first patient with recurrent GBM we performed highly resolved multi-omics analyses including single cell RNA sequencing, spatial-transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonotype analysis, and MHC Class I immunopeptidomics from biopsy tissue obtained from a single procedure. In a second patient we analyzed multi-regional core biopsies to decipher spatial and genomic variance and quantify intra and inter-sample heterogeneity. We also investigated the utility of stereotactic biopsies as a method for generating patient derived xenograft (PDX) models in a separate patient cohort. Dataset integration across modalities highlighted spatially mapped immune cell associated metabolic pathways, revealed poor correlation between RNA expression and the tumor MHC Class I immunopeptidome, and validated inferred cell-cell ligand receptor interactions. In conclusion, stereotactic needle biopsy cores are of sufficient quality to generate multi-omics data and PDX models, provide data rich insight into a patient’s disease process and tumor immune microenvironment and can be of value in evaluating treatment responses.

overall_design: This is a single subject experimental design where multi-modality measurements are taken from the tissue samples from the same subject. Sequential sections were used for GeoMx Protein and RNA profiling (samples with "protein" in title). CODEX and GeoMx -WTA platforms (samples with WTA in title) were used to compare immune cell distribution obtained from similar regions of interest (ROI) from non-adjacent sections of a single biopsy for quantitative comparison across spatial proteomics and transcriptomics data.

first: Kenny

last: Yu

first: Sreyashi

last: Basu

first: Gerard

last: Baquer

first: Ryuhjin

last: Ahn

first: Jennifer

last: Gantchev

first: Sonali

last: Jindal

first: Michael

last: Regan

first: Zaki

last: Abou-Mrad

middle: C

last: Prabhu

first: Marc

last: Williams

first: Alicia

middle: D

last: D’Souza

first: Seth

last: Malinowski

first: Kelsey

last: Hopland

first: Yuval

last: Elhanati

first: Sylwia

middle: A

last: Stopka

first: Alexei

last: Stortchevoi

first: Charles

last: Couturier

first: Zhong

last: He

first: Jingjing

last: Sun

first: Yulong

last: Chen

first: Alexsandra

last: Espejo

first: Kin Hoe

last: Chow

first: Smitha

last: Yerrum

first: Pei-Lun

last: Kao

first: Brittany

middle: P

last: Kerrigan

first: Lisa

last: Norberg

first: Douglas

last: Nielsen

first: Vinay

middle: K

last: Puduvalli

last: Huse

first: Rameen

last: Beroukhim

first: Yon Son

first: Sangeeta

last: Goswami

first: Adrienne

last: Boire

first: Sarah

last: Frisken

last: Cima

first: Matthias

last: Holdhoff

first: Calixto-Hope

last: Lucas

first: Chetan

last: Bettegowda

first: Stuart


title: A single-cell transcriptomic atlas of all cell types in the entire 5xFAD mouse brain in response to dietary inulin supplementation

city: Beijing

first: Xiaoyan

last: Wang

address: No.10, Xitoutiao, You 'an Gate

department: Department of Neurobiology

country: China

institute: School of Basic Medical Sciences, Capital Medical University

summary: Alzheimer’s disease (AD) is a progressive neurodegenerative disease that becomes a major threat to the aging population. Due to lack of effective therapy, preventive treatments are important strategies to limit AD onset and progression, of which dietary patterns have been implicated as a key influencer. Diet with high fiber content is known to have beneficial effects on cognitive decline in AD. However, a global survey on brain cell dynamics in response to high fiber intake at single-cell resolution is still missing. Here, we show that dietary inulin supplementation synergized with AD progression to specifically increase the abundance of Akkermansia muciniphila in gut microbiome of the 5x Familial AD (FAD) mice. By performing single-nucleus RNA sequencing on different regions of the whole brain with three independent biological replicates, we reveal region-specific changes in the proportion of neuron, astrocyte and granule cell subpopulations upon inulin supplementation in 5xFAD mice. Intriguingly, such dietary change only marginally alleviated astrogliosis and microgliosis, without affecting the amyloid-beta plaque burden. These results provide a comprehensive overview on the transcriptomic changes in individual cells of the entire mouse brain in response to high fiber intake, which provides a resourceful foundation for future mechanistic studies on related topics

overall_design: comparative gene expression profiling of snRNA-seq for Inulin-enriched diet and control diet in 5xFAD

first: Houyu

last: Zhang

first: Zhou

last: Wan

first: Xuetong

last: Li

first: Carlos

middle: F

last: Ibanez

first: Meng

last: Xie


title: Establishment of hematopoietic stem cell compartment after single cell transplantation tracked by FIT approach [scRNA-seq]

city: Tianjin

first: Caiying

last: Zhu

address: Heping District, Nanjing Road, 288

institute: Institute of Hematology and Blood Disease Hospital

summary: Tracing the hematopoietic regeneration of HSC clones by coupling single HSC transplantation and single-cell RNA sequencing (scRNA-seq) of  clone-derived cells from  1 to 12 months after transplantation.

overall_design: Single HSC from GFP mice accompanied with 5 × 10^5 BM cells (BMCs, competitor cells) from Ly5.2 mice were transplanted into lethally irradiated Ly5.2 mice (4.50 Gy, each of two doses, 3-hour apart) through tail vein injection. Cells were harvested  for scRNA-seq from selected repopulated primary recipients after transplanted for 1 month, 4 month  and 12 month.

first: Fang

last: Dong

first: Ping

first: Tao

last: Cheng


title: Investigative needle core biopsies support multimodal deep-data generation in glioblastoma [scRNA-seq]

first: Natalie

last: Agar

overall_design: This is a single subject experimental design where multi-modality measurements are taken from the tissue samples from the same subject. Multiple datasets with and without inhibitors (S1_L001, S1_L002) were combined, normalized, identified variable features, and applied principal component analysis (PCA).

first: Kenny

last: Yu

first: Sreyashi

last: Basu

first: Gerard

last: Baquer

first: Ryuhjin

last: Ahn

first: Jennifer

last: Gantchev

first: Sonali

last: Jindal

first: Michael

last: Regan

first: Zaki

last: Abou-Mrad

last: Prabhu

first: Marc

last: Williams

first: Alicia

last: D’Souza

first: Seth

last: Malinowski

first: Kelsey

last: Hopland

first: Yuval

last: Elhanati

first: Sylwia

last: Stopka

first: Alexei

last: Stortchevoi

first: Charles

last: Couturier

first: Zhong

last: He

first: Jingjing

last: Sun

first: Yulong

last: Chen

first: Alexsandra

last: Espejo

first: Kin Hoe

last: Chow

first: Smitha

last: Yerrum

first: Pei-Lun

last: Kao

first: Brittany

last: Kerrigan

first: Lisa

last: Norberg

first: Douglas

last: Nielsen

first: Vinay

last: Puduvalli

first: Jason

last: Huse

first: Rameen

last: Beroukhim

first: Yon Son

last: Kim

first: Sangeeta


title: Investigative needle core biopsies support multimodal deep-data generation in glioblastoma [BulkRNA-seq]

first: Natalie

last: Agar

overall_design: This is a single subject experimental design where multi-modality measurements are taken from the tissue samples from the same subject. Bulk RNAseq libraries were prepared from 10ng of RNA  (P1-1, P1-2, P1-3, P2-1, P2-2, P3-1, P3-2). Peripheral blood mononuclear cells (PBMCs) from the same patient were included as normal control.

first: Kenny

last: Yu

first: Sreyashi

last: Basu

first: Gerard

last: Baquer

first: Ryuhjin

last: Ahn

first: Jennifer

last: Gantchev

first: Sonali

last: Jindal

first: Michael

last: Regan

first: Zaki

last: Abou-Mrad

last: Prabhu

first: Marc

last: Williams

first: Alicia

last: D’Souza

first: Seth

last: Malinowski

first: Kelsey

last: Hopland

first: Yuval

last: Elhanati

first: Sylwia

last: Stopka

first: Alexei

last: Goswami

first: Adrienne

last: Boire

first: Sarah

last: Frisken

last: Cima

first: Matthias

last: Holdhoff

first: Calixto-Hope

last: Lucas

first: Chetan

last: Bettegowda

first: Stuart


title: Global modulation of gene expression and transcriptome size in aneuploid combinations of maize

status: Public on Apr 27 2025

city: Columbia

first: James

last: Birchler

state: MO

address: 310 Tucker Hall

institute: University of Missouri-Columbia

summary: Genomic imbalance refers to the more severe phenotypic consequences of changing a single chromosome compared to changing the whole genome set. Previous genome imbalance studies in maize have identified gene expression modulation in aneuploids of single chromosome arms. Here, the modulation of gene expression in more complex aneuploids, e.g. monosomy of one chromosome arm and trisomy of another. To determine the extent that combination aneuploids were additive, multiplicative, or rebalanced in terms of their effect on gene expression. A series of genetic crosses was performed to produce one, two, and three copies of one arm with independent one, two, and three copies of the other arm in each of the three genotypes for the opposite arm. In total, 31 combinations were analyzed. By examining RNA modulation, we discovered that cis genes on varied chromosome arms are generally more dosage-compensated in aneuploid combinations than in single aneuploidy even though some showed a clear dosage effect. For genes on the unvaried chromosomes (trans), there is greater modulation in most of the aneuploidy combinations. Finally, 22 of the 31 combinations were found to have an altered transcriptome size, suggesting that extensive stoichiometric changes of genomic regions upsets global mRNA transcription. Overall, these results have important implications for understanding the role of genomic stoichiometry for mechanisms of gene expression, the evolution of dosage-sensitive duplicated genes, the evolution of sex chromosomes, the rapid growth adaptation of aneuploid cancer cells, and the diploid of quantitative traits.

overall_design: Gene expression analysis of aneuploidy combinations and the diploid

first: Hua

last: Yang


title: UTD vs HER2.eSPR macrophage treatment in MC38.HER2 TIL

status: Public on Apr 26 2025

city: Duarte

first: Siqi

last: Chen

state: CA

address: E 1500 Duarte Rd.

department: Department of Immuno-Oncology

institute: City of Hope Beckman Research Institute

summary: Here, exploiting myeloid antibody-dependent cellular phagocytosis biology and phagocytosis checkpoint blockade, we report an enhanced synthetic phagocytosis receptor (eSPR) that integrates FcRγ-driven phagocytic chimeric antigen receptors (CARs) with built-in secreted CD47 blockers. To assess modulation of the tumor immune microenvironment by eSPR macrophages, untreated (UTD) and eSPR-macrophage-treated tumor tissues were extracted and processed. CD45⁺ tumor-infiltrating leukocytes were sorted and analyzed by single-cell RNA sequencing.

overall_design: Subcutaneous MC38.HER2 tumor models were generated via s.c. inoculation. Mice were randomized on day 7. UTD or HER2.eSPR macrophages (4×10^⁶ cells/mouse) were intratumorally injected on day 8. Mice were euthanized on day 11, and tumors were excised. Tumor tissue was weighed, chopped into ~1 mm pieces, and digested in RPMI supplemented with 2 mg/mL Collagenase I, 2 mg/mL Hyaluronidase, and 25 μg/mL DNase I (3 mL per 0.2 g tumor). Digestion was carried out at 37°C with vigorous shaking for 45 minutes. The reaction was quenched, passed through a 60-μm mesh, washed twice with PBS, stained with anti-CD45 antibody, and live CD45⁺ cells were sorted using a BD Aria III.

first: Mingye

last: Feng


title: Establishment of hematopoietic stem cell compartment after single cell transplantation tracked by FIT approach

first: Caiying

last: Zhu

overall_design: Refer to individual Series


title: Activation of the Imprinted Gene Network is a conserved signature of MASLD induced by the early life environment

status: Public on Apr 25 2025

city: Raleigh

first: Michael

last: Cowley

state: NC

address: 850 Main Campus Dr

department: Biological Sciences

institute: North Carolina State University

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) affects 30% of the world population. Its prevalence in the pediatric population is increasing, suggesting that the early life environment plays a role in the programming of MASLD. We previously proposed that imprinted genes, defined by their expression from a single parental allele, are strong candidates for driving MASLD in response to early life environmental exposures because of their susceptibility to environmental stress and their roles in liver metabolism. In support of this hypothesis, we previously showed that early life exposure to the toxic metal cadmium (Cd) or maternal metabolic syndrome (MetS) induce MASLD in juvenile mice and activate a transcriptional network in the liver enriched for imprinted genes termed the Imprinted Gene Network (IGN). Furthermore, artificial activation of the IGN in cultured hepatocytes or in vivo leads to MASLD-related phenotypes. Here, using publicly available bulk liver RNA-seq datasets, we tested whether early life exposure to other types of environmental stress that program juvenile MASLD also activate the IGN. We demonstrate that diverse types of stressors, including toxic metals, diet, and endocrine disruptors, activate the IGN in the liver. We also developed an in vitro model of toxicant exposure and show that the IGN is activated upon exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in a cell autonomous manner. Overall, our findings confirm the IGN as a conserved mechanism that could be targeted to mitigate the effects of multiple developmental stressors on liver disease.

overall_design:
Gene expression profiling analysis of RNA-seq data from HepG2 cells exposed to 75 µM BPA, 0.5 µM CdCl2, 10 µM PFOS, 0.1 µM TBTCl, or 100 nM TCDD for 24 hours. There are four experimental replicates for each exposure, including H2O control for CdCl2, and DMSO control for the remaining chemicals. DMSO content did not exceed 0.1% of the total cell culture media.

UPDATE: [May 28, 2025] The GSM8877036-GSM8877039 titles and treatments were changed from "PFOS" to "TCDD". The GSM8877040-GSM8877043 titles and treatments were changed from "TCDD" to "PFOS".

first: Vicmarie

last: Marrero-Colon

first: Sierra

last: Riegl

first: Makena

last: Neale


title: Upregulation of MMP3 promotes cisplatin resistance in ovarian cancer

status: Public on Apr 24 2025

city: San Juan

first: Mariela

last: Rivera-Serrano

state: PR

address: 601 Ave Universidad

institute: University of Puerto Rico Rio Piedras

summary: Seventy percent of women with ovarian cancer develop resistance to cisplatin, contributing to persistently high mortality rates. Understanding the mechanisms behind this resistance is crucial for developing improved therapies. Matrix metalloproteinase 3 (MMP3) is elevated in ovarian cancer patients, but its role in cisplatin resistance remains underexplored. We observed significantly higher MMP3 protein and mRNA levels in cisplatin-resistant high-grade serous ovarian cancer (HGSOC) cells compared to cisplatin-sensitive cells, with further increases following cisplatin treatment. Kaplan‒Meier analysis indicated that patients with lower MMP3 levels have better survival outcomes. MMP3 knockdown via siRNA reduced cell viability, proliferation, and invasion, effects enhanced by cisplatin; however, a chemical MMP3 inhibitor did not replicate these effects. To better understand MMP3’s role, we conducted RNA sequencing to analyze gene expression changes and used immunoprecipitation with mass spectrometry to identify MMP3-interacting proteins, making this the first study to explore this in cisplatin-resistant ovarian cancer. Surprisingly, multiple injections of liposomal MMP3-siRNA increased tumor size in a mouse model, while combining MMP3-siRNA with cisplatin reduced tumor growth. These findings highlight MMP3’s complex role in cisplatin resistance and raise concerns about its targeting in vivo.

overall_design: To identify the downstream MMP3 effectors that contribute to cisplatin resistance in ovarian cancer cells we carried out a transcriptome-wide analysis via RNA sequencing (RNA-seq) after siRNA-mediated MMP3 knockdown with and without cisplatin in OVCAR3CIS cells.

first: Marienid

last: Flores

first: Fatma

last: Valiyeva

first: Pablo

last: Vivas


title: An integrated transcriptomic cell atlas of human endoderm-derived organoids

city: Basel

first: Gray

last: Camp

address: Grenzacherstraße 183

department: Institute of Human Biology

country: Germany

institute: Roche Pharma Research and Early Development

summary: Human pluripotent stem cells and tissue-resident fetal and adult stem cells can generate epithelial tissues of endodermal origin in vitro that recapitulate aspects of developing and adult human physiology. Here, we integrate single-cell transcriptomes from 218 samples covering organoids and other models of diverse endoderm-derived tissues to establish an initial version of a human endoderm-derived organoid cell atlas (HEOCA). The integration includes nearly one million cells across diverse conditions, data sources and protocols. We compare cell types and states between organoid models, and harmonize cell annotations through mapping to primary tissue counterparts. Focusing on the intestine and lung, we provide examples of mapping data from new protocols, and show how the atlas can be used as a diverse cohort to assess perturbations and disease models. The HEOCA makes diverse datasets centrally available, and will be valuable to assess fidelity, characterize perturbed and diseased states, and streamline protocol development.

overall_design:
Ileal organoids derived from human tissue samples were subjected to either control conditions or different growth factors (TNFα + RANKL for increased microfold cells or IL-4 + IL-13 for increased tuft cells), viral response cytokines (IFNα + IFNγ and IFNβ) and inflammatory agents (TNFα + IL-6 + IL-17A + IFNγ + IL-18 + OSM + SCF). scRNAseq experiments were performed to study the differentiation and cellular profile under these different conditions.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Xu

last: Quan

first: Halle

last: Lennard

first: Hediyeh-zadeh

last: Soroor

first: Kuijs

last: Merel

first: Riedweg

last: Rya

first: Kilik

last: Umut

first: Recaldin

last: Timothy

first: Yu

last: Qianhui

first: Rall

last: Isabell

first: Frum

last: Tristan

first: Adam

last: Lukas

first: Parikh

last: Shrey

first: Kfuri-Rubens

last: Raphael

first: Gander

last: Manuel

first: Klein

last: Dominik

first: Curion

last: Fabiola

first: He

last: Zhisong

first: Fleck

last: Jonas Simon

first: Oost

last: Koen

first: Kahnwald

last: Maurice

first: Barbiero

last: Silvia

first: Mitrofanova

last: Olga

first: Maciag

last: Grzegorz Jerzy

first: Jensen

last: Kim B.

first: Lutolf

last: Matthias

first: Liberali

last: Prisca

first: Spence

last: Jason R.

first: Gjorevski

last: Nikolche

first: Beumer

last: Joep

first: Treutlein

last: Barbara

first: Theis

last: Fabian

first: Camp

last: Gray


title: DNGR-1 regulates proliferation and migration of bone marrow dendritic cell progenitors

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: Conventional dendritic cells (cDCs) are sentinel cells that play a crucial role in both innate and adaptive immune responses. cDCs originate from a common progenitor (pre-cDC) in the bone marrow (BM) that travels via the blood to seed peripheral tissues before locally differentiating into functional cDC1 and cDC2 cells, a process known as cDCpoiesis. We show that DNGR-1, an innate immune receptor expressed by cDC progenitors and type 1 cDCs, functionally regulates cDCpoiesis in mice. In a competitive chimera setting, cDC progenitors lacking DNGR-1 exhibit increased proliferation and tissue migratory potential. Compared to their wildtype counterparts, DNGR-1-deficient cDC progenitor cells display superior colonization of peripheral tissues but an altered distribution. These findings suggest that cDCpoiesis can be regulated in part by cell-intrinsic processes driven by signals from innate immune receptors such as DNGR-1 that may respond to alterations in the BM milieu

overall_design: Transcriptome analysis was performed in bone marrow and spleen pre-cDCs population from DNGR1 KO CD42.2 and BL/6 CD45.1 mice (bone marrow chimeras)

first: Ana

last: Cardoso

first: Caetano

last: Reis-e-Sousa


title: A novel role for Neurog2 in MYCN driven neuroendocrine plasticity of prostate cancer (CRISPR)

first: Franco

last: Vizeacoumar

overall_design: genome-wide CRISPR knock-out screen for synthetic dosage lethal interactions of MYCN overexpressing cells. There are two model cells used and for each model there are 5 samples done in duplicates. Total of 10 samples

first: Prachi

last: Walke

first: Jared

last: Price

first: Frederick

first: Andrew

last: Freywald

first: Anand

last: Krishnan


title: RNA Sequencing Gene Expression Profiles in Wild-Type and MLK2 and MLK3 double knockout (MLK2-/-MLK3-/-) Mouse Lung Endothelial Cells Under Normoxic and Hypoxic Conditions

status: Public on Apr 23 2025

first: Shashi

last: Kant

address: 4 Blackfan Circle, Room 614

department: Cardiovascular Medicine

institute: Brigham Women's Hospital

summary: MLK2 and MLK3 are key regulators of angiogenesis, particularly under hypoxic conditions. To investigate the underlying mechanisms, we performed unbiased RNA sequencing on primary lung endothelial cells isolated from wild-type and MLK2 and MLK3 double knockout (MLK2-/-MLK3-/-) mice exposed to normoxia or hypoxia. Transcriptomic analysis revealed significant enrichment of the “Pathways in cancer” and “HIF1α signaling pathway,” which regulate proangiogenic genes. Our RNA Seq data suggest that, mechanistically, MLKs act through the long noncoding RNA H19 to regulate angiogenic gene expression. These findings identify the MLK-H19 axis as a critical regulator of endothelial function and a key driver of tumor-associated angiogenesis

overall_design: In order to identify downstream pathways of MLK family, RNA was extracted from C57BL/6J and MLK2-/-MLK3-/- MLECs grown under hypoxia (1% oxygen for 90 minutes) or normoxia (21% oxygen) and RNA seq analysis was performed.

first: Amada

last: Caliz

first: Hyung-Jin

last: Yoo

first: Gaganpreet

last: Kaur

first: Heather

last: Learnard

first: John

last: Keaney Jr


title: High resolution transcriptome analysis on a mouse model of hypoxic ischemic encephalopathy using single-nucleus RNA-seq

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

institute: Osaka university

summary: Hypoxic-ischemic encephalopathy (HIE) encompasses brain injuries resulting from reduced or interrupted oxygen or blood flow to the brain before, during, or immediately after birth. During the acute phase, neuronal damage is driven by excitotoxicity, with permanent injury manifesting over the subsequent hours. Current treatment options have limited efficacy, underscoring the need for deeper insights into HIE pathogenesis and the development of novel therapeutic strategies. Recent advances in single-cell RNA sequencing (snRNA-seq) have enabled molecular investigations of diverse diseases. However, the large size of neurons has posed challenges in studying conditions where neuronal damage is central. To address this, we employed snRNA-seq to evaluate region-specific neuronal damage in a mouse model of HIE. Our HIE model was established in postnatal day-7 mice, with cortical and hippocampal tissues harvested from the ipsilesional side one week post-injury. Analysis revealed pronounced changes in the hippocampus, especially in the CA1 region, with a significant reduction in neuronal populations in the affected hemisphere. These alterations were specific to combined hypoxic-ischemic conditions and were not observed with hypoxia or ischemia alone. In contrast, changes in the cerebral cortex were less prominent. Transcriptomic analysis showed similar gene expression patterns in the cortex and hippocampus of the HIE group, including the identification of genes related to viral response pathways, suggesting a potential link to interferon activation. These findings provide valuable insights into the molecular and anatomical impact of HIE and highlight the hippocampus as a critical focus for understanding disease mechanisms and therapeutic development.

overall_design: HIE group (hypoxia exposure added to unilateral common carotid ligation), Hypoxia group, CL group (unilateral common carotid ligation), and Sham group(only sham surgery performed) mice were created on postnatal day7, and the cortex and hippocampus of the ipsilesional side were harvested for single-nucleus RNA sequencing one week later, respectively.A total of 4 mice, 2 males and 2 females per group, were included.


title: Single-cell analysis reveals human spermatogenesis and germ cell-sertoli cell interaction

city: Shenzhen

first: Shimin

last: Wang

address: 3025# Shennan Road

institute: The Eighth Affiliated Hospital, Sun Yat-sen University

summary: Non-obstructive azoospermia (NOA) is a highly heterogeneous and complex disease. However, there is lack of the research on latent biological mechanisms. Here, we performed single-cell RNA sequencing (scRNA-seq) and Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) on patients with obstructive azoospermia and NOA. Our study identified 12 germ cell subtypes and 8 sertoli cell subtypes. Further analysis identified several stage-specific marker genes of germ cells, such as ID4, TEX19, SCML1, and DMC1 and identified several stage-specific marker genes of sertoli cells, such as SOX2, BEND2, MLC1, PGAM2, and CFH. Furthermore, Notch1/2/3 signaling and integrin were involved in the interaction between germ cells and sertoli cells. Overall, we mapped the scRNA-seq and scATAC-seq of human spermatogenesis, and analyzed germ cell and somatic cell types and their key molecular markers. It gives us a comprehensive insight in spermatogenesis and provide a fresh perspective on diagnosis and treatment for NOA.

overall_design: There were five samples from testicular tissues of two OA patients and three NOA patients.

first: Hongxiang

first: Bicheng

last: Jin

first: Dong

last: Zhao


title: CLU alleviates Alzheimer’s disease-relevant processes by modulating astrocyte reactivity and microglia-dependent synaptic density [RNA-Seq]

first: Courtney

last: Benoit

overall_design: Mice of all control and experimental genotypes (5xFAD and 5xFAD/CLU-2kb-KI) and both sexes (n=4-5 per sex) were used for bulk RNA sequencing. Mice were anesthetized at 4 months of age using CO₂ inhalation. Following transcardial perfusion with 1X phosphate-buffered saline (PBS), brains were extracted, and hemispheres were separated along the midline. The left hippocampus was dissected and flash-frozen on dry ice. Samples were pulverized using a Bessman Tissue Pulverizer. Half of pulverized hippocampus was used for bulk RNA sequencing.

first: Alex

last: Lish

first: Richard

last: Pearse

first: Tracy

last: Young-Pearse


title: Mitochondrial membrane hyperpolarization modulates nuclear DNA methylation and gene expression through phospholipid remodeling [RNA-Seq]

status: Public on Apr 22 2025

city: Research Triangle Park

first: Elizabeta

last: Gjoneska

state: North Carolina

address: 111 TW Alexander Dr., David P Rall Building A030

department: Neurobiology Laboratory

institute: National Institute of Environmental Health Sciences (NIEHS/NIH)

summary: Maintenance of the mitochondrial inner membrane potential (ΔΨm) is critical for many aspects of mitochondrial function. While ΔΨm loss and its consequences are well studied, little is known about the effects of mitochondrial hyperpolarization. In this study, we used cells deleted of ATP5IF1 (IF1), a natural inhibitor of the hydrolytic activity of the ATP synthase, as a genetic model of increased resting ΔΨm. We found that the nuclear DNA hypermethylates when the ΔΨm is chronically high, regulating the transcription of mitochondrial, carbohydrate and lipid genes. These effects can be reversed by decreasing the ΔΨm and recapitulated in wild-type (WT) cells exposed to environmental chemicals that cause hyperpolarization. Surprisingly, phospholipid changes, but not redox or metabolic alterations, linked the ΔΨm to the epigenome. Sorted hyperpolarized WT and ovarian cancer cells naturally depleted of IF1 also showed phospholipid remodeling, indicating this as an adaptation to mitochondrial hyperpolarization. These data provide a new framework for how mitochondria can impact epigenetics and cellular biology to influence health outcomes, including through chemical exposures and in disease states.

overall_design: We aimed to investigate the transcriptome of a genetic model of mitochondrial membrane potential hyperpolarization (increased Δψm). RNA from the following treatment groups were isolated from n=3 biologically independent replicates: 1) HEK293T cells containing a doxycycline-inducible dominant negative DNA polymerase gamma (WT); 2) the isogenic cell line knockout for the gene ATP5IF1 (IF1-KO_NOV0082); 3) IF1-KO expressing GFP (ATP_EVgfp), 4) the IF1-KO isogenic cell line overexpressing ectopic IF1 with GFP (ATP_cDNAgfp); 5) IF1-KO cells transfected with pcDNA3.1_empty vector (IF1-KO); 6) IF1_KO cells transfected with pcDNA3.1-UCP4(SLC25A27)-NE vector overexpressing UCP4 (IF1_KO_UCP4). RNA was quantified using Nanodropand, and for quality control, samples were re-assessed using Qubit 3.0. RNA integrity was confirmed using Agilent RNA 6000 Nano Kit in 2100 Bioanalyzer (Agilent).

first: Mateus

last: Mori

first: Oswaldo

last: Lozoya

first: Ashley

last: Brooks

first: Carl

last: Bortner

first: Cristina

last: A. Nadalutti

first: Birgitta

last: Ryback

first: Brittany

last: Rickard

first: Marta

last: Overchuk

first: Imran

last: Rizvi

first: Tatiana

last: Rogasevskaia

first: Kai

middle: T

last: Huang

first: Prottoy

last: Hasan

first: György

last: Hajnóczky

first: Janine

middle: H

last: Santos


title: Role of TET3 in mouse embryonic and adult hematopoiesis [EM-Seq]

city: New York

first: Meelad

last: Dawlaty

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

summary: In this study: we mapped genome-wide DNA methylation levels in Tet3F/F (control) and cKO Tie2+/cre; Tet3F/F (cKO) Lin– bone marrow cells by enzymatic methyl-sequencing (EM-seq).

overall_design: We investigated the roles of TET3 in gene regulation in Lin– bone marrow cells. Analysis and integration of EM-seq, E5hmC-seq, and RNAseq revealed novel functions of TET3 in hematopoietic cells. For EMseq, Lin– cells were isolated from 2-month old bone marrow of either Tet3F/F and Tie2+/cre; Tet3F/F mice. DNA was extracted from Lin– cells isolated from 2 mice per genotype (Quick-DNA miniprep kit - Zymo, D3024). 200ng of DNA was used per sample per experiement. Libraries were prepared following NEBNext EM-seq kit  following manufacturer instructions and subjected to 300-bp paired-end sequencing at Novogene using their NovaSeq X Plus (PE150-25B) platform. Spike-in lambda (negative control), and pUC19 (5mC positive control) DNA were used as controls. Details of EM-seq procedure and data analyses are described in detail in the methods section of the manuscript.

first: Harmony

last: Ketchum


title: Peroxidasin is associated with a mesenchymal-like transcriptional phenotype and promotes invasion in cutaneous metastatic melanoma

city: Christchurch

first: Carlos

middle: Christopher

last: Smith-Diaz

state: Canterbury

address: 2 Riccarton Avenue, Christchurch Central City

department: Pathology and Biomedical Science

country: New Zealand

institute: University of Otago

summary: Cutaneous melanoma is a highly invasive, heterogeneous and treatment resistant cancer. It’s ability to dynamically shift between transcriptional states or phenotypes results in an adaptive cell plasticity that may drive cancer cell invasion or the development of therapy resistance. The expression of peroxidasin (PXDN), an extracellular matrix peroxidase, has been proposed to be associated with the invasive metastatic melanoma phenotype. We have confirmed this association by analysing the transcriptomes of 70 metastatic melanoma cell lines with variable levels of PXDN expression. This analysis highlighted a strong association between high PXDN expression and the undifferentiated invasive melanoma phenotype. To assess the functional role of PXDN in melanoma invasion, we performed a knockout of PXDN in a highly invasive cell line (NZM40). PXDN knockout decreased the invasive potential by ~50 % and decreased the expression of epithelial-mesenchymal transition and invasive marker genes as determined by RNAseq and substantiated by proteomics analysis. Bioinformatics analysis of differentially expressed genes following PXDN knockout highlighted decreases in genes linked to extracellular matrix formation, organization and degradation as well as signalling pathways such as the WNT pathway. This study provides compelling evidence that PXDN plays a functional role in melanoma invasion by promoting an invasive, mesenchymal-like transcriptional phenotype.

overall_design: NZM40 WT and PXDN KO cells (generated by CRISPR-Cas9 KO) were seeded at 700,000 cells in 10 mL of MEM-alpha medium with reduced FBS (0.75%) in a 10 cm cell culture dish for 48 h. After 48h, the cells were replenished with fresh 0.75% FBS medium for 5 hours before the medium was fully removed and replaced with 6 mL medium containing 0% FBS. After 22 h, the cells were washed twice with PBS, the buffer was removed thoroughly and the cells were harvested by scraping in residual PBS. The cells were snap frozen on dry ice and stored at -80 degrees until RNA extraction. Five biological replicates of each cell line were analysed, with cell pellets being harvested on different days.

last: Smith-Díaz

first: Abhishek

last: Kumar

first: Andrew

last: Das

first: Kenny

last: Chitcholtan

first: Paul

last: Pace

first: Nicholas

last: Magon

first: Sultana

last: Hossain

first: Michael

middle: R

last: Eccles

first: Christine

last: Winterbourn

first: Martina

last: Paumann-Page


title: Role of TET3 in mouse embryonic and adult hematopoiesis [E5hmC-seq]

middle: M

summary: In this study: we mapped genome-wide DNA hydroxymethylation levels in Tet3F/F (control) and cKO Tie2+/cre; Tet3F/F (cKO) Lin– bone marrow cells by enzymatic 5-hydroxymethylation sequencing (E5hmC-seq).

overall_design: We investigated the roles of TET3 in gene regulation in Lin– bone marrow cells. Analysis and integration of EM-seq, E5hmC-seq, and RNAseq revealed novel functions of TET3 in hematopoietic cells. For E5hmC-seq, Lin– cells were isolated from 2-month old bone marrow of either Tet3F/F and Tie2+/cre; Tet3F/F mice. DNA was extracted from Lin– cells isolated from 2 mice per genotype (Quick-DNA miniprep kit - Zymo, D3024). 200ng of DNA was used per sample per experiement. Libraries were prepared following NEBNext E5hmC-seq kit  using manufacturer instructions and subjected to 300-bp paired-end sequencing at Novogene using their NovaSeq X Plus (PE150-25B) platform. Spike-in lambda (negative control) and T4 (5hmC positive control) DNA were used as controls. Details of E5hmCseq procedure and data analyses are described in detail in the methods section of the manuscript.


title: Role of TET3 in mouse embryonic and adult hematopoiesis

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


title: Monocytes can efficiently replace all brain macrophages and instruct different microglial identities depending on their origin

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

summary: Microglia and border-associated macrophages (BAMs) are critical for brain health and their dysfunction is closely linked to disease. Replacing brain macrophages holds significant therapeutic promise, but remains challenging. Here, we demonstrate that monocytes can efficienty replace all brain macrophages. Monocytes readily replaced embryonal BAMs upon their depletion and engrafted as monocyte-derived microglia (Mo-Microglia) upon more sustained niche availability. Mo-Microglia expanded comparably to their embryonic counterparts and showed similar longevity. However, monocytes were unable to replicate the unique identity of embryonically-derived BAMs and microglia. Using humanized models, we found that human monocytes exhibited similar behavior, enabling us to identify putative Mo-Microglia in Alzheimer’s disease patients. In mice and humans, the ontogeny of monocytes shaped their identity as brain macrophages. Importantly, mouse fetal liver monocytes exhibited a distinct epigenetic landscape and could develop a bonafide microglial identity. Our results illuminate brain macrophage development and highlight the potential of monocytes as an abundant progenitor source for brain macrophage replacement therapies.

overall_design:
CITE-seq and scRNA-seq.: CD45+ CD11b+ CX3CR1mid CLEC12- high brain or leptomeningeal cells from Flt3-Cre R26-YFP mice, which received control chow or 2 weeks PLX3397 chow followed by 7 weeks of repopulation on control chow; CD45+ brain cells from adult and neonate C57BL/6 mice, following an adoptive transfer of Cx3cr1 GFP/+ bone marrow derived monocytes; CD45+ CD11b+ brain cells from  Cx3cr1CreER:Csf1rfl/fl neonate mice,  intracerebrally injected with Cx3cr1 GFP/+  E14 fetal liver monocytes; CD45+ CD11b+ GFP+  brain cells from Cx3cr1CreER:Csf1rfl/fl mice, intracerebrally injected with CD319+ (MDP-Mo) or CD177+ (GMP-Mo) bone marrow monocytes from Cx3cr1Cre-GFP/+ mice; C57BL/6 E14 fetal liver monocytes and adult bone marrow monocytes; CD45+ cells from brains of naive hCSF1:Rag2-/-:γc-/-  mouse neonates, intracerebrally injected at PD4 with either human cord or adult blood-derived MACS-sorted monocytes. SnATACseq:  C57BL/6 E14 fetal liver monocytes and adult bone marrow monocytes.
For the raw sequencing reads of the scRNA-seq samples from human monocytes injected in mouse brains, sensitive genetic information was eliminated by masking the donor-specific single nucleotide variants using BAMboozle v0.5.0

first: Kiavash

last: Movahedi


title: A high-quality transcriptomic map of Salix brachista

city: Kunming

first: Jindan

last: Wang

state: Yunnan

address: Lanhei road

institute: Kunming Institute of Botany, Chinese Academy of Sciences

summary: Transcriptomic sequencing of Salix brachista to make a high-quality transcriptomic map.Utilizing Illumina and ONT data, we conducted transcript assembly, expression quantification, differential gene analysis, and alternative splicing to construct a comprehensive transcriptome map. This work lays a robust foundation for understanding the gene expression patterns of Salix brachista.

overall_design: A transcriptomic map was generated using RNA-seq analysis of seven different organs: roots, stems, young leaves, mature leaves, monoecious flowers, female flowers, and male flowers. This analysis involved three biological replicates to ensure accuracy and thoroughness.

first: Kaiyun

last: Chen

first: Rengang

last: Zhang

first: Yuan

last: Huang

first: Jiahui


title: Inhibition of PRC1.1 augments Wnt signaling to promote bone remodeling

first: Liangyu

last: Xing

address: 22nd Qixiangtai Road

institute: Tianjin Medical University

summary: The Wnt/β-catenin signaling play critical roles in bone formation and homeostasis. However, chromatin regulatory mechanisms governing transcriptional response to the signaling are poorly understood. Polycomb group proteins are conserved epigenetic repressors safeguarding cell identity and functions, through forming multi-subunit complexes (PRCs). Their activities on histone modifications relies on interaction with the core enzyme, providing basis for therapeutic intervention. Here in aging osteoblasts, we observed a selective gain of PRC1.1 function, with KDM2B serving as a chromatin binding factor while BCOR and PCGF1 as key catalytically accessory proteins for histone H2A monoubiquitylation (H2AK119ub1). Using genetic models, we found that osteoblast-specific KDM2B inactivation significantly improves bone structure and density under steady-state conditions or scenarios of bone loss, such as aging, estrogen deficiency (following ovariectomy), or acute trauma. This improvement is attributed to the activation Wnt signaling. Transcriptomic and epigenomic analyses in purified osteoblasts demonstrate that KDM2B inactivation results in decreased H2AK119ub1 levels at the promoters of Wnt/β-catenin target genes, leading to their derepression. Through virtual screening and experimental validation, we identified a small molecule termed iBP, that specifically inhibits the interaction between BCOR and PCGF1, thereby suppressing PRC1.1 activity. Importantly, this inhibitor enhances bone formation in mouse models with bone loss. Therefore, our findings suggest that targeting PRC1.1 strengthens cellular response to Wnt signaling and may offer a promising strategy to combat bone deterioration.

overall_design:
In Aging CUT&Tag, used osteoblasts from femur of young(3M) and old(18M) mice to detect H2AK119ub1 modification level. In CKO CUT&Tag, used Kdm2b deleted osteoblasts and control to detect H2AK119ub1 modification level.

In Aging RNA-Seq, examination of gene expression changes in osteoblasts between young(3M) and old(18M) mice. In  CKO RNA-Seq, examination of gene expression changes in  Kdm2b deleted osteoblasts and control.

first: Xudong

last: Wu


title: Time course analysis of gene expression in the liver of the 70% partial hepatectomy mouse model.

city: Fujisawa

first: Yoshinao

last: Oki

state: Kanagawa

address: 1866 Kameino

department: Department of Applied Biological Science

institute: Nihon University College of Bioresource Sciences

summary:
The liver has a remarkable regenerative capacity, allowing it to regain mass through compensatory hypertrophy of the remaining tissue after the surgical removal of 70% of its mass. During this regenerative process, lipid accumulation and proliferation of liver parenchymal cells have been observed; however, the full extent of the underlying regenerative mechanisms remains unclear.
Our study performed a comprehensive gene expression analysis using microarrays on liver samples collected at 0, 1, 2, 3, 4, 7, and 14 days following 70% partial hepatectomy in mice.

overall_design: Total RNA was extracted from livers collected from mice at 0, 1, 2, 3, 4, 7, and 14 days after 70% partial hepatectomy. Each sample was processed in triplicate as biological replicates. Gene expression profiles were analyzed using microarray experiments with the Affymetrix mouse genome array.

first: Koichiro

last: Kano


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

status: Public on Apr 21 2025

city: Kalyani

first: Sandeep

last: Singh

state: West Bengal

address: NSS TB Hospital, Block A

department: Biomedical Genomics

country: India

institute: BRIC-National Institute of Biomedical Genomics

summary: Heterogeneity in oral cancer associated fibroblasts (CAFs)in tumor microenvironment modulate plasticity of malignant epithelial cells to drive tumorigenesis, ultimately leading to poorer clinical outcome. We identified a receptor tyrosin kinase 'TEK' or Tie2 involved in myofibroblastic differentiation of CAFs. Differentiated CAFs induce stochastic plasticity in oral cancer cells both in stemness and EMT axes. Inhibiting Tie2 in myofibroblastically differentiated CAFs purturbed their cancer cell remodelling ability. Here in this study we performed scRNA seq analysis to understand distinct CAF driven transcriptionl states of cancer cells to undertsand CAF driven cancer cells reprogramming in a higher resolution.

overall_design: Oral cancer tumor derived Primary fibroblasts were cultured. Undifferentiated CAFs (C1 CAFs) were treated with TGFβ  for 48 hours to induce myofibroblastic differentiation. After myofibroblastic differentiation the CAFs were treated with Tie2 inhibitor. Following that, oral cancer cells were co-cultured for 96 hours with 3 different CAF phenotypes; nonmyofibroblasts (C1 CAFs), myofibroblasts (C2 CAFs), Tie2 inhibited myofibroblasts (Tie2i C2 CAFs) respectively and later harvested and scRNA-seq was performed using 10x Genomics Chromium platform

first: Paromita

last: Mitra

first: Arindam

last: Maitra


title: Mitochondrial membrane hyperpolarization modulates nuclear DNA methylation and gene expression through phospholipid remodeling [EPIC1]

first: Elizabeta

last: Gjoneska

type: Methylation profiling by genome tiling array

overall_design: We aimed to investigate the DNA methylome of a genetic model of mitochondrial membrane potential hyperpolarization (increased Δψm). DNA from the following treatment groups were isolated from n=4 biologically independent replicates: 1) HEK293T cells containing a doxycycline-inducible dominant negative DNA polymerase gamma (DN-POLG) (WT); 2) the isogenic HEK293T DN-POLG cell line knockout for the gene ATP5IF1 (IF1_KO); 3) the IF1-KO isogenic cell line overexpressing ectopic IF1 (IF1_OE); 4) IF1_KO cells treated with DMSO 1:1000 (IF1_KO_DMSO); 5)  IF1_KO cells treated with G6PDi 50 μM, a glucose-6-phosphate dehydrogenase inhibitor (IF1_KO_G6PDi), 6) IF1_KO cells treated with DNP (2,4-dinitrophenol) 25 μM, a mild AAC-dependent uncoupler (IF1_KO_DNP); 7) IF1_KO cells transfected with pcDNA3.1_empty vector (IF1_KO_empty); 8) IF1_KO cells transfected with pcDNA3.1-UCP4(SLC25A27)-NE vector overexpressing UCP4 (IF1_KO_UCP4). DNA was quantified using Nanodrop, and for quality control, samples were re-assessed using Qubit 3.0. DNA methylation was assessed by Infinium Methylation EPIC v1.0.

first: Mateus

last: Mori

first: Oswaldo

last: Lozoya

first: Ashley

last: Brooks

first: Carl

last: Bortner

first: Cristina

last: A Nadalutti

first: Birgitta

last: Ryback

first: Brittany

last: Rickard

first: Marta

last: Overchuk

first: Imran

last: Rizvi

first: Tatiana

last: Rogasevskaia

first: Kai

first: Prottoy

last: Hasan

first: György

last: Hajnóczky

first: Janine

last: Santos


title: Transcriptomic profiling in canine B-cell lymphoma supports a synergistic effect of BTK and PI3K inhibitors

city: Rostock

first: Hugo

middle: Murua

last: Escobar

address: Schillingallee 35

department: Clinic for Hematology, Oncology and Palliative Care

institute: Rostock University Medical Center

summary: B-cell receptor (BCR) signaling has revealed itself as a critical pathway in the pathogenesis of B-cell lymphoma. Within this pathway, the inhibition of Bruton’s tyrosine kinase (BTK) or Phosphoinositide 3-kinases (PI3Ks) alone presents encouraging efficacy in the treatment of certain both canine and human hematological malignancies. Here we characterized the effects of the BTK inhibitor Ibrutinib and the PI3K inhibitor AS-605240 as single and combined agents in the canine pre-clinical diffuse large B cell lymphoma (DLBCL) model CLBL-1 by assaying cell proliferation and metabolic activity, and performing RNA-seq to measure gene expression changes. We found 2,336 differentially expressed genes (DEGs) across all treatment types and time points relative to the control. The largest number of DEGs were induced by the combination of Ibrutinib and AS-605240. These genes were involved in adaptive immune response, leukotriene D4 metabolic and terms related to regulation of GTP and GTPase mediated signal transduction. Weighted gene co-expression network analysis (WGCNA) detected nine gene modules, five of which were associated with treatment response. Eighteen-percent of genes within these modules were also differentially expressed. Notably, we observed one module that was exclusively associated with the combined treatment whose gene members were related to cellular metabolism, homeostasis signaling, and protein synthesis and regulation. Narrowing in on highly connected genes of modules associated with treatment response with large fold changes across treatments which play roles in the main targeted pathways identified PAG1, PRKAR2A, ACACA, FOS, and PRKCA as potential primary candidates of the synergistic treatment effect.

overall_design: RNA-Seq profiling of CLBL-1, a canine B-cell line derived from a DLCL, treated with  dimethyl sulfoxide (DMSO), AS-605240 (AS), Ibrutinib (Ibr), or the combination of the two (Ibr+AS) for 24, 48 or 72 hours.


title: Gene-expression analysis after intratumoral treatment with Shingle VZV vaccine and HPV16 L1-derived peptides

city: Bethesda

first: Nicolas

last: Cuburu

state: MD

address: 37 convent drive

department: CCR

institute: NIH/NCI

summary:
Analysis of whole tumor mRNA with nanostring immune exhaustion platforrm
Analyzed the expression of  785 genes from the total tumor RNA extracted from 16 solid murine tumors

overall_design: 16 samples, 4 groups, 4 replicates per group, tumor samples were harvested 48hr after the last of 4 consecutive intratumoral injections

first: John

last: Schiller

first: Claire

middle: E

last: Bradley


title: Long circulating RNAs identified as biomarker candidates for risk stratification in childhood acute lymphoblastic leukemia

city: Montreal

first: Sinnett

last: Daniel

address: 3175 Chem. de la Cote-Sainte-Catherine

institute: CHU Ste-Justine Research Center

summary: Analysis of tumoral RNA is essential for childhood acute lymphoblastic leukemia (ALL) diagnosis and prognosis to detect mutations, cryptic fusions and gene expression patterns. Small vesicles circulating in the blood, such as exosomes carry nucleic acids that might be involved in cancer formation and progression, thus presenting a potential for discovery of non-invasive biomarker for diagnosis and monitoring. Here we report the identification of 47 circulating exosome-encapsulated RNA transcripts (30 mRNAs, 5 lncRNAs, 9 circRNAs and 3 pseudogenes) constituting putative biomarker in 2 molecular subgroups of childhood ALL patients. Exosomes were purified from peripheral blood collected at diagnosis from 10 patients positive for the ETV6-RUNX1 and TCF3-PBX1 fusions as well as from conditioned culture medium (CCM) of their representative cell models. Long transcriptome profiling via total RNA sequencing, supported by the implementation of a novel data analysis pipeline confirmed the presence of mRNAs, fusion transcripts, long non-coding and circular RNAs in exosomes. Differential expression analysis comparing tumoral and exosomal RNA revealed 2 transcripts enriched in both leukemic subtypes while 38 were exclusively enriched in ETV6-RUNX1+ patients and 7 were exclusively enriched in TCF3-PBX1+ patients. These are the first results highlighting specific enrichment of long RNA transcripts in exosomes among two distinct ALL subtypes, suggesting the need for investigation of larger cohorts to identify and validate novel circulating biomarkers.

overall_design:
We assembled a cohort of 24 B-ALL patients equally distributed into cases carrying the ETV6-RUNX1 or the TCF3-PBX1 fusion genes. From this cohort, a subset of 10 patients (5 ETV6-RUNX1+ and 5 TCF3-PBX1+) had both total tumoral RNA and total PB exosomal RNA sequenced.
As controls for tumoral samples we included 3 B-cell samples CD10+/CD19+ blood cord cells.
As controls for exosomes samples we included previously published blood exosome RNAseq datasets of 32 healthy controls (GSE100206). Raw counts and TPM values are available in the processed data under column names Exos_PB_CTRL_SRR5712482 to Exos_PB_CTRL_SRR5712513
For comparison purposes we included previously published blood exosome RNAseq datasets of 12 colorectal carcinoma (CRC) patients (GSE100063), 21 hepatocellular carcinoma patients (HCC) (GSE100207) and 14 pancreatic carcinoma (PAAD) patients (GSE100232). Raw counts and TPM values are available in the processed data under column names Exos_PB_CRC_SRR5687235 to Exos_PB_CRC_SRR5687246, Exos_PB_HCC_SRR5712516 to Exos_PB_HCC_SRR5712536 and Exos_PB_PAAD_SRR5714908 to Exos_PB_PAAD_SRR5714921
Cellular models of ETV6-RUNX1+ B-ALL (REH) and TCF3-PBX1+ B-ALL (697) were also used for protocol optimization and transcriptome analysis. For both cell lines, we sequenced total RNA from whole cell extracts (Cells), microvesicles (MVs), small extracellular vesicles (Sevs) and immuno-affinity purified (CD9/CD63/CD81) exosomes (Exos).

first: Lucas

last: Poncelet

first: Daniel

last: Sinnett


title: Mitochondrial membrane hyperpolarization modulates nuclear DNA methylation and gene expression through phospholipid remodeling [EPICv2]

first: Elizabeta

last: Gjoneska

overall_design: We aimed to investigate the DNA methylome of a chemical exposure model of mitochondrial membrane potential hyperpolarization (increased Δψm). DNA from the following treatment groups were isolated from n=3 biologically independent replicates for chemical exposures, and n=4 to investigate the role of PEMT in DNA methylation in IF1-KO cells: 1) HEK293T cells containing a doxycycline-inducible dominant negative DNA polymerase gamma (DN-POLG) treated with DMSO (1:1000 v/v) for 10 days (WT); 2) WT cells treated with telmisartan 2 μM for 10 days (TMS); 3) WT cells treated with annatto 10 μM for 10 days (ANTO); 4) the isogenic HEK293T DN-POLG cell line knockout for the gene ATP5IF1 (IF1_KO); 5) IF1_KO cells transfected with pcDNA3.1-PEMT-flag (IF1_KO_PEMT_OE). DNA was quantified using Nanodrop, and for quality control, samples were re-assessed using Qubit 3.0. DNA methylation was assessed by Infinium Methylation EPIC v2.0.

first: Mateus

last: Mori

first: Oswaldo

last: Lozoya

first: Ashley

last: Brooks

first: Carl

last: Bortner

first: Cristina

last: Huang


title: Macrophage PKM2 depletion ameliorates hepatic inflammation and acute liver injury in mice

status: Public on Apr 19 2025

city: Guangzhou

first: Liu

last: Junli

state: Guangdong

address: Guangzhou, Jinan university

country: Singapore

institute: jinan university

summary: Pyruvate kinase M2 (PKM2), the rate-limiting enzyme of glycolysis, plays a critical role in macrophage activation and a broad spectrum of chronic liver diseases. However, whether PKM2 contributes to the pathogenesis of acute liver injury (ALI) remains largely unexplored. By bioinformatic screening and analysis of ALI liver, we found that PKM2 was significantly upregulated in the liver tissues of ALI patients and mice. Immunofluorescence staining further demonstrated that PKM2 was markedly upregulated in macrophages during ALI progression. Notably, macrophage PKM2 depletion effectively alleviated acetaminophen (APAP)- and lipopolysaccharide/D-galactosamine (LPS/D-GalN)-induced ALI, as demonstrated by ameliorated immune cells infiltration, pro-inflammatory mediators, and hepatocellular cell death. PKM2-deficient macrophages showed M2 anti-inflammatory polarization in vivo and in vitro. Furthermore, PKM2 deletion limited HIF-1α signaling and aerobic glycolysis of macrophages, which thereby attenuated macrophage pro-inflammatory activation and hepatocyte injury. Pharmacological PKM2 antagonist efficiently ameliorated liver injury and prolonged the survival of mice in APAP-induced ALI model. Our study highlights the pivotal role of macrophage PKM2 in advancing ALI, and therapeutic targeting of PKM2 may serve as a novel strategy to combat ALI.

overall_design: LPS/IFN-γ-primed BMDMs from PKM2ΔMAC and PKM2FL/FL mice were subjected to RNA sequencing analysis (n = 3 per group).

first: Ziwei

last: Kang

first: Ruoyan

last: Xie

first: Yiming

last: Cui

first: Zhiwei

last: Chen

first: Jincheng

last: Li

first: Jinyu

last: Lv

first: Weijia

last: Ye


title: Role of TET3 in mouse embryonic and adult hematopoiesis [RNA-Seq]

first: Meelad

last: Dawlaty

state: New York

summary: In this study: We identified TET3 target genes by transcriptomic profiling of Tet3F/F and Tie2+/cre; Tet3F/F Lin– bone marrow cells by RNA-sequencing.

overall_design: We investigated the roles of TET3 in gene regulation in Lin– bone marrow cells. Analysis and integration of EM-seq, E5hmC-seq, and RNAseq revealed novel functions of TET3 in hematopoietic cells. Lin– cells were isolated from 2-month old bone marrow of either Tet3F/F and Tie2+/cre; Tet3F/F mice. RNA was extracted from Lin– cells isolated from 2 mice per genotype (RNeasy micro kit). Library preparation and RNAseq were performed by Novogene (https://en.novogene.com/) on an NovaSeq X Plus Series (PE150) platform and 20-30 million reads were generated per sample. Details of RNAseq procedure and data analyses are described in detail in the methods section of the manuscript.

first: Harmony

last: Ketchum


title: The design, pharmacology, and toxicology exploring of a novel chemically modified siRNA targeting hepatic angiotensinogen with potential application for hypertension treatment

city: Beijing

first: Gengshen

last: Song

state: Beijing

address: No. 6, Hongda ZhongLu, Beijing Economic-Technological Development Area

institute: Beijing Youcare Kechuang Pharmaceutical Technology Co., Ltd.

summary: Angiotensinogen is the precursor of angiotensin II, a potent vasopressor in the renin-angiotensin-aldosterone system. Small interfering RNAs targeting hepatic angiotensinogen have been proven to be effective on blood pressure lowering in hypertension patients through reducing AGT levels in blood, and such effect could last over 6 months. Existing siRNA molecules has been high effective. However, it may be possible to develop novel siRNA molecules with improved inhibitory activity and longer duration period. In this study, we demonstrated an entire development process for a novel siRNA targeting hepatic angiotensinogen. Through proper combination of bioinformatics on-target/off-target screening on sequences, chemical modification patterns and liver-targeting delivery ligands, we have developed siRNA molecules with equivalent or better inhibitory activity, duration of effect and safety profile compared with siRNA molecules discovered previously. Furthermore, our analysis also revealed the correlation between efficacy and free energy of siRNAs. At present, no model can accurately predict the activity and off-target risk of fully modified siRNA molecules, thus efficient screening procedures are essential during the development of siRNA candidates. This study has provided a detailed and useful reference for the development of potent and safe siRNAs, which could also guide the future development of siRNAs on other targets.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: RNAseq of primary rat or human hepatocytes treated with 1 nM, 10 nM or 100 nM of different siRNAs


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

status: Public on Apr 18 2025

city: Riverside

first: Reuben

last: Franklin

address: 3401 Watkins Drive

institute: University of California, Riverside

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

overall_design: 10X Genomics 3' V4 scRNA-seq in iGMPs, 48 hSPT6 KD (DOX) and 48 h CAF-1 KD (IPTG).

first: Brian

last: Zhang

first: Sihem

last: Cheloufi


title: Esculetin modulates postprandial cholesterol metabolism involved in phagocytosis of adipose tissue macrophages

city: Xiamen

first: Binbin

last: Liu

state: Fujian

address: Jinshan Road

department: Xiamen Cardiovascular Hospital

institute: Xiamen University

summary: Postprandial dyslipidemia is a recognized risk factor for atherosclerosis. High-density lipoprotein (HDL)-mediated reverse cholesterol transport plays a crucial role in mitigating this risk by clearing postprandial lipids. This study aimed to investigate the impact of esculetin, a 4-Hydroxycoumarin, on postprandial cholesterol metabolism and excretion after a high-fat meal. Esculetin significantly elevated postprandial HDL cholesterol levels in serum and postprandial bile acid levels in bile, and altered serum metabolomics in mice fed a high-fat meal, indicating esculetin promotes HDL-driven cholesterol excretion after a high-fat meal. Furthermore, esculetin administration in mice led to an increase in the ratio and phagocytic activity of a subset of adipose tissue macrophages (ATMs) expressing high levels of CD36 and Tim4. Inhibition of CD36 by Sulfo-N-succinimidyl oleate (SSO) blocked esculetin-induced elevation of postprandial serum HDL and bile acid levels in bile. Additionally, esculetin demonstrated the ability to increase the uptake of oxidized LDL (ox-LDL) via CD36 in a macrophage cell line, which might involve alteration of the epigenetic landscape controlled by CCAAT enhancer-binding protein beta (C/EBPβ). Esculetin-induced increased uptake of ox-LDL and elevation of CD36 was inhibited in C/EBPβ-deficient cells. A relatively higher expression of C/EBPβ was observed in CD36+ ATMs, and esculetin increased the ratio of C/EBPβ+ CD36+ ATMs in mice fed a lipid-rich meal. Overall, these findings suggest esculetin promotes HDL-mediated postprandial cholesterol excretion by directly binding to C/EBPβ and enhancing CD36-dependent phagocytosis in ATMs.

overall_design: Esculetin-induced chromatin accessibility profiling via the assay for transposase-accessible chromatin using sequencing (ATAC-seq) in ox-LDL-treated RAW264.7 cells.  RAW264. 7 cells were treated with 25 ug/mL DIL-oxLDL and esculetin (0 or 40 ug/mL) for 24 hr.

first: Gang

last: Wang

first: Heng


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

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


title: Gene expression profile at single cell level of retinal cells of mitochondrial ND6 13997 G>A mutant mouse

city: Hangzhou

first: Cheng

last: Ai

state: Zhejiang

address: 866 Yuhangtang Road

institute: Institute of Genetics, Zhejiang University School of Medicine

summary: LHON is a paraLeber hereditary optic neuropathy (LHON) is a paradigm for mitochondrial retinopathy due to mitochondrial DNA (mtDNA) mutations. However, the mechanism underlying retinal cell-specific effects of LHON-linked mtDNA mutations remains poorly understood and there has been no effective treatment or cure for this disorder. We use scRNA-seq to study the retinal cell-specific deficiencies caused by LHON-linked ND6P25L mutation.

overall_design: Retinas from Wildtype and ND6 mutant mice of 7 month old was dissected and analyzed by scRNA-seq

first: Chunyan

first: Junbin

last: Qian

first: Yimin

last: Zhu

first: Minxin

last: Guan


title: RNA-seq Analysis of the Longissimus Muscle of Laiwu and Yorkshire Pigs

city: Yangling, CN

first: Wen Chuan

last: Peng

address: No.22, Xinong Road, Yangling District, Xianyang City, Shaanxi Province

institute: Northwest A&F University

summary: Intramuscular fat (IMF) content is the determining factor for meat taste.  To reveal the genetic basis of IMF content, genetic studies have made some progress in lean-type pig breeds, but fewer studies have been conducted in Chinese fat-type pigs.   We selected Laiwu and Yorkshire pigs as models, and transcriptomic analysis was conducted on the longissimus dorsi muscle to investigate the gene expression patterns linked to high and low intramuscular fat (IMF) content. The purpose of the study was to determine the differences in intramuscular fat between the two breeds and identify the reasons for the differences. To further systematically investigate the potential biologic significance of phenotype divergence, the identified DEGs were annotated into multiple pathways based on KEGG bioinformatic databases (P < 0.05).   According to the identified DEGs, the results revealed a number of enriched pathways in AMPK signaling pathway, cAMP signaling pathway, PPAR signaling pathway, and so on. Functional enrichment analysis showed that PPARγ, ADIPOQ, LEP, LIPE, SCD, FABP4 and PLIN1 were represented.

overall_design: RNAseq was performed on longissimus dorsi muscle of Laiwu and Yorkshire pigs of the same weight.Library construction and RNA-seq were performed by Illumina Novaseq™6000 (LC-Bio Technology CO, Ltd, Hangzhou, China). The raw data were filtered using the Fast QC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/,0.11.9). Then the clean reads were aligned against the pig reference genome Sus scrofa 11.1 (http://www.ensembl.org/info/data/ftp/index.html) using HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1).

first: Wen

first: Jiang

middle: W

last: Wu


title: A small molecule esculetin accelerates postprandial lipid circulation by activating C/EBPb and augmenting CD36-mediated phagocytosis in adipose tissue macrophages

summary: Rationale: Exogenous lipid metabolism, influenced by dietary intake, contributes to postprandial dyslipidemia. Adipose tissue macrophages (ATMs) mediate the phagocytosis of postprandial lipids from the exogenous diet, generating high-density lipoprotein (HDL) particles that facilitate lipid circulation and excretion. However, the underlying mechanisms remain poorly understood. This study investigates the effects of esculetin, a coumarin compound, on postprandial cholesterol circulation and excretion following a high-fat meal. Methods: Mice were fed a lipid-rich meal for three days to assess the effects of esculetin on postprandial lipid circulation, using serum lipid profiling and metabolomics analysis. Epididymal white adipose tissue (eWAT) removal and flow cytometry were performed to analyze ATMs and confirm their role in mediating esculetin’s effects on postprandial lipemia. Epigenetic profiling, transcriptome analysis, chromatin immunoprecipitation, and Terahertz chemical microscopy were employed to elucidate the molecular targets and mechanisms of esculetin. Results: Esculetin significantly elevates postprandial HDL cholesterol levels to values comparable to pitavastatin and modifies serum metabolites involved in bile-mediated cholesterol excretion, leading to increased bile acid concentrations in the bile. This effect is mediated by an increased ratio and phagocytic activity of a subset of ATMs expressing the scavenger receptor CD36, as eWAT removal and CD36 blockade inhibit this response. Furthermore, esculetin enhances the uptake of oxidized LDL via CD36, as demonstrated in cultured macrophages, and induces epigenetic changes controlled by the key transcription factor C/EBPβ, accompanied by increased C/EBPβ binding to the Cd36 promoter. A direct interaction between esculetin and C/EBPβ was observed using Terahertz chemical microscopy. Additionally, the activation of C/EBPβ by esculetin in ATMs was confirmed in vivo. Conclusion: Esculetin accelerates postprandial lipid circulation by binding to C/EBPβ and enhancing CD36-dependent phagocytosis in ATMs.

overall_design: RAW 264.6 cells were transfected with the LentiCRISPR v2 plasmid containing gRNA against Cebpb or empty vector using the Gene Pulser Xcell Eukaryotic System (165-2661, Bio-Rad, CA, USA). Cells were stimulated with 25 µg/mL DIL-oxLDL and either 0 or 40 µg/mL esculetin for 24 hr


title: Rare Subset of T Cells Form Integrin-dependent Clustering with Circulating Tumor Cells to Foster Metastasis in Breast Cancer

city: Chicago

first: Huiping

state: IL

address: 303 E Superior St, Room 5-250B

institute: Northwestern University

summary: The immune ecosystem, particularly T cells, is central to maintaining effective anti-tumor responses. However, how immune cells in the periphery blood interact with circulating tumor cells (CTCs) - critical mediators of metastatic spread 1-8 – remains largely unexplored. Here, our analysis of the blood specimens from patients with advanced breast cancer (N=1,529) revealed that over 75% of the CTC-positive blood specimens contained heterotypic CTC clusters with CD45+ white blood cells (WBCs). These CTC-WBC clusters correlate with breast cancer subtypes (triple negative and luminal B), racial groups (Black), and unfavorable clinical outcomes. Using flow cytometry and ImageStream, we characterized the diverse WBC composition in these heterotypic clusters, such as overrepresented T cells and underrepresented neutrophils. Most strikingly, a rare subset of CD4 and CD8 double positive T (DPT) cells showed an up to 140-fold enrichment in the CTC clusters (~14.2%) versus its frequency in WBCs (0.1%). DPT cells shared part of profiles with CD4+ T cells and others with CD8+ T cells but exhibited unique features of T cell exhaustion and immune suppression (TIM-3 and PD-1). Single-cell RNA sequencing further identified distinct cell adhesion profiles of DPT cells and CTCs. CRISPR/Cas9-mediated gene depletion pinpointed the integrin VLA4 (β1/α4) in DPT and its ligand VCAM1 in tumor cells as essential mediators of heterotypic CTC clusters. Anti-α4 (VLA4) neutralizing antibodies markedly reduced CTC–DPT cell clustering and blocked metastatic lesion formation in murine models in vivo. These findings uncover a pivotal role for a rare T cell subset in fostering cancer dissemination through heterotypic CTC cluster interactions. It lays a foundation for innovative therapeutic strategies aimed at preventing and targeting metastasis of breast cancer, thus benefiting Black and non-Black patients.

overall_design: CD45+ white blood cells from breast cancer patient and healthy control liquid biopsy blood samples were sorted using fluorescence activated cell sorting (FACS) and analyzed by scRNA-seq

first: David

last: Scholten

first: Andrew D

last: Hoffmann

first: Matthew

last: Schipma

first: Priyam

last: Patel

first: Ching Man

last: Wai


title: Circadian Regulation of Murine Inguinal Adipocytes

city: Hanover

first: Jay

last: Dunlap

state: NH

address: 702 Remsen

department: Molecular and Systems Biology

institute: Geisel School of Medicine at Dartmouth

summary:
The focus of this research is in the area of biological clocks. Importance: Metabolic dysregulation is the major preventable risk factor for leading causes of chronic disease-related deaths. More specifically, chronic obesity is correlated with adipocyte hypertrophy and hyperplasia, both of which may be circadianly regulated. All circadian clocks are cell-intrinsic, and circadian oscillators that are tissue-specific control metabolic homeostasis by fine-tuning nutrient utilization; adipose tissue responds to microenvironmental changes in a clock-dependent manner. The objective of this work is to understand how circadian rhythms affect adipocyte biology. To delineate the relationship between the cellular circadian system and adipocyte biology in the absence of organismal cues, circadian output was  characterized by transcriptionally profiling in vitro differentiated adipocytes from inguinal adipose tissue over 3 circadian days with a 2-hour resolution via RNAseq. Goal: Determine what aspects of adipocyte biology and environmental stimuli can be influenced by time-of-day. Impact: Findings from this study will increase our understanding of clock-controlled energy metabolism and adipocyte dysfunction, advancing our understanding of the non-linear association between weight, energy expenditure and risk in chronic disease.
Purpose: The goals of this study are to understand the molecular basis of the biological clock in mammals and the means through which it controls metabolism. PER2::LUC transgenic mice were used as a source of adipocyte stem cells for studies on the role of the clock in adipocyte biology.
Methods: There are two biological replicates. 4 male mice aged 8-12 weeks under 12:12 light-dark cycle and standard chow were used per replicate. The inguinal stromal vascular fraction (SVF) was isolated post-mortem at ZT10*lights on, resting phase, 10am*. Isofluorine anesthesia and cervical dislocation were the method of sacrifice.  Pre-adipocytes were isolated as in (Oeckl 2020, DOI: 10.1016/ j.xpro.2020.100118) with modifications and seeded onto three 35mM plastic bottom tissue culture plates (MatTek) in "base media" (DMEM F/12 + GlutaMAX (Gibco xxxx-018) with penicillin/streptomycin and 10% fetal bovine serum (Gibco: Ref#10437-028). Cells were passaged every 48 hours for a total of 3 passages with a split ratio of 1:2.8. In final passage, cells were seeded into 35mM plastic dishes (MatTek). After confluence, differentiation was induced with  dexamethasone, rosiglitazone and IBMX, biotin, insulin, pantothenate ( "differentiation media"). After 4 days of differentiation, dex, rosi and IBMX were removed from the media ( "maintenance media"). After 4  days in culture, cells were synchronized with 50% FBS, 50% "base media" and 10uM forskolin for 2-2.5hours. Media was switched to "maintenance media" containing 0.01% bright d-luciferin (GoldBio #LUCK-100) in batches of 4 dishes, topped with glass microscopy slides and sealed with vacuum grease before loading into a Lumicycle housed in a 37C, 0%CO2 incubator. Circadian parameters including amplitude were determined using LumiCycle Analysis software (Actimetrics, v.2.44).

overall_design:
In total, 62 samples were analyzed. Two age-matched biological replicates are included. Each time series includes 12 through 72 hours post-synchronization with a 2-hour resolution. Replicate 2 is missing 60h timepoint. Before sequencing, circadian period length was confirmed manually in Excel (mean, +/- SD) as calculated by the Per2::Luc bioluminescence traces using all samples with at least two peaks.

UPDATE [May-02-2025] The Rep1 Samples were removed, the Rep2 Samples were renamed to Rep1, and the Rep3 Samples were renamed to Rep2. The associated data files did not change.

first: Jennifer

last: Worthen

first: Armina-Lyn

last: Frederick

middle: J

last: Loros

first: Phillip

last: Dumesic