title: Histone Methyltransferase ASH1L Primes Metastases and Metabolic Reprogramming of Macrophages in the Bone Niche (RNA-Seq)

first: Di

last: Zhao

state: Tx

address: Zayed Building Z7. 4018

summary: Bone metastasis is a major cause of cancer death; however, the epigenetic determinants driving this process remain elusive. Here, we uncover that histone methyltransferase ASH1L is genetically amplified in metastatic diseases and is required for cancer invasiveness and bone metastasis. In invading cancer cells, ASH1L rewires methylations at H3K4 and H3K36 and cooperates with transcriptional factor HIF-1α to induce pro-metastatic transcriptome. Leveraging our newly developed metastasis models and single-cell transcriptomic profiling, we demonstrate that ASH1L in invading cancer cells induces monocyte differentiation into lipid-associated macrophage (LA-TAM) and maintains their pro-tumoral and anti-inflammatory phenotype in the metastatic bone niche. Mechanistic studies reveal that IGF-2 is a direct target of ASH1L and mediates LA-TAMs’ differentiation and phenotypic changes by reprogramming oxidative phosphorylation. In patients with metastatic cancers, ASH1L overexpression is associated with enriched LA-TAMs. As a proof of concept, pharmacologic inhibition of the ASH1L-macrophages axis elicits robust anti-metastasis responses in preclinical models.

overall_design: To understand how ASH1L promotes metastasis, we performed transcriptome profiling, using RNA sequencing (RNA-seq) in control versus ASH1L-depleted PC-3M cells.

first: Yue

last: Lu

first: Chenling

last: Meng


title: RNA Transcripts Serve as a Template for Double-Strand Break Repair in Human Cells

status: Public on Mar 21 2025

city: New York

first: Simon

last: Powell

state: NY

address: 1250 1st Ave

country: USA

institute: Memorial Sloan Kettering Cancer Center

type: Expression profiling by high throughput sequencing

summary: Double-strand breaks (DSBs) are toxic lesions that lead to genome instability. While canonical DSB repair pathways typically operate independently of RNA, emerging evidence suggests that RNA:DNA hybrids and transcripts near damaged sites can influence repair outcomes. However, a direct role for transcript RNA as a template during DSB repair in human cells is yet to be established. In this study, we designed fluorescent- and sequencing-based assays, which demonstrated that RNA-containing oligonucleotides and messenger RNA serve as templates to promote DSB repair. We conducted a CRISPR/Cas9-based genetic screen to identify factors that promote RNA-templated DSB repair (RT-DSBR), and of the candidate polymerases, we identified DNA polymerase-zeta (Polζ) as the potential reverse transcriptase that facilitates RT-DSBR. Furthermore, by analyzing sequencing data from cancer genomes, we identified the presence of whole intron deletions, a unique genomic scar reflective of RT-DSBR activity generated when spliced mRNA serves as the repair template. These findings highlight RT-DSBR as an alternative pathway for repairing DSBs in transcribed genes, with potential mutagenic consequences.

overall_design: Gene expression profiling by RNA sequencing of human tumor samples containing whole intron deletions.


title: Histone Methyltransferase ASH1L Primes Metastases and Metabolic Reprogramming of Macrophages in the Bone Niche (CUT&RUN)

status: Public on Mar 20 2025

city: Houston

institute: MD Anderson Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: In metastatic PC-3M cells, we found that ASH1L depletion caused a global eduction in H3K36 and H3K4 methylations ; while overexpression of ASH1L increased these histone marks by Western blotting. To further dissect the impact of ASH1L on the landscape of histone methylations, we performed cleavage under targets and release using nuclease sequencing (CUT&RUN-seq)  to capture the genomic distribution of H3K4me3 and H3K36me3 in PC-3M cells with or without ASH1L depletion.


title: Single-cell RNA-Sequencing of Wild-type Perinatal Mice Thymi

status: Public on Mar 19 2025

city: Nashville

first: Bryan

middle: Robert

last: Helm

state: Tennessee

address: 2525 West End Avenue, Suite 1100

department: Center for Quantitative Science

institute: Vanderbilt University Medical Center

summary: We prepared enzymatically digested thymus single cell suspensions for scRNA-Seq. Cells were extracted from perinatal mice, and TEC cells were enriched via FACS using anti-EpCAM and Anti-CD45 to isolate EpCAM+ CD45- TECs.

overall_design: FACS purified TECs were obtained from P0, P3, P7, P10, P15 and P28 C57Bl6/J male and female thymuses. Supplicate experiments were performed for each time point except for P15.

first: Ellen

last: Richie

first: Anusha

last: Vasudev

first: Nandini

last: Singarapu

first: Qi

last: Liu

first: Ken

last: Lau


title: Next Generation Sequencing facilitates to identify the differential expression genes of  liver tissue from HBVN donors, HBVP donors, LF donors and  transplant donors.

city: Wuhan

first: xiufang

last: weng

address: 13# Hangkong Rd, Wuhan, Hubei

country: China

institute: Huazhong University of Science and Technology

summary: We obtained liver tissues from HBVN donors, HBVP donors, LF donors and  transplant donors  to rperforme next-generation sequencing (NGS).  Illumina mRNA-seq sample preparation kit was used to perform paired-end library sequencing with Illumina HiSeq 2000 and sequence analysis was determined using the Illumina data analysis pipeline. Based on the comparison results，we performed the GO and KEGG pathway enrichment analysis. That might suggest the different status of HBV-infected liver from liver surgery(AST<40) and liver transplantation(AST>40).

overall_design: Differential gene expression between liver tissue (HBVN,HBVP,LF,PL).

first: Xiufang

last: Weng


title: Insulin-like growth factor 2 (IGF2) as a Foxn1-independent driving force of exponential expansion in neonatal thymus

summary: Like all organs, the thymus grows in size and function rapidly during development, which comes to a halt after birth. However, the molecular mechanisms behind such a transition in the thymus remain obscure. Using single-cell RNA sequencing (scRNA-seq) of the murine thymic stroma, we identified that major transcriptomic changes occur in the endothelium and mesenchyme across the transition to homeostasis. Differentially expressed gene and intercellular network analyses of temporally resolved scRNA-seq data revealed fibroblast-derived insulin-like growth factor 2 (IGF2) as a candidate driving neonatal thymic expansion. We demonstrated IGF2 activity promotes a cortical TEC-specific proliferation and is tightly regulated at the thymic growth transition. Bulk RNA-seq of human thymi across the transition also revealed IGF2 to drive thymic expansion, suggesting an evolutionarily conserved role. Our study highlights the role of a fibroblast-derived IGF2 in promoting cTEC proliferation, resulting in early thymic expansion that is followed by down-regulation to establish homeostasis.

overall_design: Bulk RNA sequencing was performed on thymus tissues from human donors aged 3 days to 14 years.

first: Kang

last: Seung Woo

first: Helm

last: Bryan R.

first: Wang

last: Yu

first: Liu

last: Qi

first: Lau

last: Ken S.

first: Richie

last: Ellen R.

first: Hale

last: Laura P.

first: Manley

last: Nancy R.


title: An Lgr5-independent developmental lineage is involved in mouse intestinal regeneration (ATAC seq)

city: Brussels

first: Gilbert

last: Vassart

address: Route de Lennik 808

department: IRIBHM

country: Belgium

institute: ULB

summary: Collagenase/dispase treatment of intestinal tissue from adult mice generates cells growing in matrigel as immortal cystic spheroids in addition to differentiated organoids. Contrary to classical EDTA-derived organoids, these spheroids display poor intestinal differentiation and are independent of Rspondin/Noggin/EGF for growth. Their transcriptome resembles strikingly that of fetal intestinal spheroids, with downregulation of crypt base columnar cell (CBC) markers (Lgr5, Ascl2, Smoc2, Olfm4). In addition, they display upregulation of inflammatory and mesenchymal genetic programs, together with robust expression of YAP target genes. Lineage tracing, cell-sorting and single cell RNA sequencing experiments demonstrate that adult spheroid-generating cells belong to a hitherto undescribed developmental lineage, independent of Lgr5+ve CBCs, and are involved in regeneration of the epithelium following CBC ablation

overall_design: Comparing chromatin accessibility across the genome for Organoids vs Spheroids

first: Maryam

last: Marefati

first: Valeria

last: Fernandez-Vallone

first: Morgane

last: Leprovots

first: Gabriella

last: Vasile

first: Frédérick

last: Libert

first: Anne

last: Lefort

first: Gilles

last: Dinsart

first: Achim

last: Weber

first: Jasna

last: Jetzer

first: Marie-Isabelle

last: Garcia


title: An Lgr5-independent developmental lineage is involved in mouse intestinal regeneration

overall_design: Comparing trascriptome of Lgr5DTR HE versus WT


title: An Lgr5-independent developmental lineage is involved in mouse intestinal regeneration [Organoids vs Spheroids in sandwich protocol]

summary: Collagenase/dispase (CD fraction) treatment of intestinal tissue from adult mice generates cells growing in matrigel as immortal cystic spheroids in addition to differentiated organoids. Contrary to classical EDTA-derived organoids, these spheroids display poor intestinal differentiation and are independent of Rspondin/Noggin/EGF for growth. Their transcriptome resembles strikingly that of fetal intestinal spheroids, with downregulation of crypt base columnar cell (CBC) markers (Lgr5, Ascl2, Smoc2, Olfm4). In addition, they display upregulation of inflammatory and mesenchymal genetic programs, together with robust expression of YAP target genes. Lineage tracing, cell-sorting and single cell RNA sequencing experiments demonstrate that adult spheroid-generating cells belong to a hitherto undescribed developmental lineage, independent of Lgr5+ve CBCs, and are involved in regeneration of the epithelium following CBC ablation

overall_design: Comparing trascriptome of Organoids (EDTA fraction)  growing in medium containing ENR with transcriptome of adult spheroids (CD fraction) coming from sandwich protocol and growing in different condition medium


title: Novel brain-penetrant inhibitor of G9a methylase blocks Alzheimer’s disease proteopathology for precision medication

status: Public on Mar 18 2025

city: Chapel Hill

first: John

last: Wrobel

state: NC

address: 120 Mason Farm Rd

department: Department of Biochemistry and Biophysics

institute: University of North Carolina

type: Methylation profiling by high throughput sequencing

summary: Current amyloid beta-targeting approaches for Alzheimer’s disease (AD) therapeutics only slow cognitive decline for small numbers of patients. This limited efficacy exists because AD is a multifactorial disease whose pathological mechanism(s) and diagnostic biomarkers are largely unknown. Here we report a new mechanism of AD pathogenesis in which the histone methyltransferase G9a noncanonically regulates translation of a hippocampal proteome that defines the proteopathic nature of AD. Accordingly, we developed a novel brain-penetrant inhibitor of G9a, MS1262, across the blood-brain barrier to block this G9a-regulated, proteopathologic mechanism. Intermittent MS1262 treatment of multiple AD mouse models consistently restored both cognitive and noncognitive functions to healthy levels. Comparison of proteomic/phosphoproteomic analyses of MS1262-treated AD mice with human AD patient data identified multiple pathological brain pathways that elaborate amyloid beta and neurofibrillary tangles as well as blood coagulation, from which biomarkers of early stage of AD including SMOC1 were found to be affected by MS1262 treatment. Notably, these results indicated that MS1262 treatment may reduce or avoid the risk of blood clot burst for brain bleeding or a stroke. This mouse-to-human conservation of G9a-translated AD proteopathology suggests that the global, multifaceted effects of MS1262 in mice could extend to relieve all symptoms of AD patients with minimum side effect. In addition, our mechanistically derived biomarkers can be used for stage-specific AD diagnosis and companion diagnosis of individualized drug effects.

overall_design: MeRIP-Seq/m6A-seq was performed using total RNA isolated from hippocampus tissue (5xFAD, wild-type) under different treatment conditions (MS1262, vehicle, none) to identify transcripts showing differential m6A modification.

middle: A

first: Adil

last: Muneer

first: Feng

last: Zhang

first: Xian

last: Chen


title: KRAS mutation-selective requirement for ACSS2 in colorectal adenoma formation.

city: 3601 Spruce Street

first: Yan

last: Zhou

state: PA

address: 333 Cottman Ave

department: Bioinformatics

institute: Fox Chase Cancer Center

summary: Oncogenic KRAS mutations are prevalent in colorectal cancer (CRC) and are associated with poor prognosis and resistance to therapy. There is a substantial diversity of KRAS mutant alleles observed in CRC. Emerging clinical and experimental analysis of common KRAS mutations suggest that each mutation differently influences the clinical properties of a disease and response to therapy. Although there is some evidence to suggest biological differences between mutant KRAS alleles, these are yet to be fully elucidated. One approach to study allelic variation involves the use of isogenic cell lines that express different endogenous Kras mutants. Here, we generated Kras isogenic Apc-/- mouse colon epithelial cell lines using CRISPR-driven genome editing by altering the original G12D Kras allele to G12V, G12R, or G13D. We utilized these cell lines to perform transcriptomic and proteomic analysis to compare different signaling properties between these mutants. Both screens indicate significant differences in pathways relating to cholesterol and lipid regulation that we validated with targeted metabolomic measurements and isotope tracing. We found that these processes are upregulated in G12V lines through increased expression of nuclear SREBP1 and higher activation of mTORC1. G12V cells showed higher expression of ACSS2 and ACSS2 inhibition sensitized G12V cells to MEK inhibition. Finally, we found that ACSS2 plays a crucial role early in the development of G12V mutant tumors, in contrast to G12D mutant tumors. These observations highlight differences between KRAS mutant cell lines in their signaling properties. Further exploration of these pathways may prove to be valuable for understanding how specific KRAS mutants function, and identification of novel therapeutic opportunities in CRC.

overall_design: 3 replicate samples from each genotype were used to compare gene expression difference between groups

first: Konstantin

last: Budagyan

first: Jonathan

last: Chernoff


title: Nuclear ACAT1 orchestrates natural killer cell dependent antitumor immunity in colorectal cancer

status: Public on Mar 17 2025

city: Guangzhou

first: Chen

last: Wei

state: Guangdong

address: Dongfengdong Road No.651

institute: Sun Yat-sen university Cancer center

summary: Natural killer (NK) cells play pivotal roles in antitumor immunity, yet their connection to tumor metabolism remains unclear. Our systematic analysis of multiomics data and survival data from colorectal cancer (CRC) patients uncovered a novel association between mitochondrial acetyl-CoA acetyltransferase 1 (ACAT1) and NK cell infiltration that influences disease progression. ACAT1, a metabolic enzyme involved in reversible conversion of acetoacetyl-CoA to two molecules of acetyl-CoA, exhibits nuclear protein acetylation activity through its translocation. Under immune stimulation, mitochondrial ACAT1 can be phosphorylated at serine 60 (S60) and enters the nucleus; however, this process is hindered in nutrient-poor tumor microenvironments. Nuclear ACAT1 directly acetylates lysine 146 of p50 (NFKB1), attenuating its DNA binding and transcriptional repression activity and thereby increasing the expression of immune-related factors, which in turn promotes NK cell recruitment and activation to suppress colorectal cancer growth. Furthermore, significant associations were found among low nuclear ACAT1 levels, decreased S60 phosphorylation, and reduced NK cell infiltration, as well as poor prognosis in CRC. Our findings reveal an unexpected function of ACAT1 as a nuclear acetyltransferase and elucidate its role in NK cell-dependent antitumor immunity through p50 acetylation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To isolate tumor-infiltrating NK cells from mice, tumors were dissected from ceca were cut into small pieces and subjected to enzymatic digestion. The digestion solution was filtered with 70 μm strainer and centrifuged at 500 g for 5 min. Cells were resuspended in MACS buffer and were Fc-blocked for 10 min. And then, cells were stained with Zombie UV™ Fixable Viability Kit following the manufacturer’s instruction and incubated with primary antibodies as follows: APC-CD45, FITC-CD3 with PE/Cyanine7-NKp46 for 30 min at 4°C. NK cells (CD3- NKp46+) were sorted by fluorescence-activated cell sorting (FACS) using MoFlo Astrios (BECKMAN). The purity (>98%) of sorted cells was checked on BECKMAN COULTER CytoFLEX LX cell analyzer.

first: Kun

last: Liao

first: Hao-Jie

first: Zi-Xuan

last: Zhao

first: Qi

last: Meng

first: Huai-Qiang

last: Ju

first: Rui-Hua

last: Xu


title: Blocking plasma cell fate enhances antigen-specific presentation by B cells to boost anti-tumor immunity

city: Professor

first: David

last: Nemazee

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: B cells engage in anti-tumor immunity but how they contribute to cancer suppression remains unclear. We found that inhibiting plasma cell differentiation either in IgMi mice lacking Igh elements needed for antibody secretion or in mice with B cell-specific knockout of Blimp-1 (Blimp-1 BcKO) promoted rather than inhibited antitumor immunity and increased numbers of activated B cells. Deficiency of Blimp-1 in tumor-infiltrating B cells generated a unique transcription profile associated with expansion of mutated clones targeting cognate tumor cells. Major histocompatibility complex class II (MHC II) was required for the anti-tumor efficacy. Blimp-1-deficient B cells had increased expression of CD80 and CD86 costimulatory molecules  that enhanced effector T cell function. The Blimp-1 inhibitor valproic acid suppressed tumor growth in a B cell-dependent manner. Thus, inhibition of plasma cell differentiation results in enhanced tumor-specific antigen presentation by B cells and thereby tumor repression, suggesting a potential avenue of immunotherapy against cancer.

overall_design: To explore the dynamics of tumor-infiltrating B cells, we generated single-cell RNA and B cell V(D)J libraries using a combination of sorted CD138+ and B220+ B cells from tumor-infiltrating lymphocytes (TILs) that were isolated from inoculated MC38 tumors on day 18 post-inoculation (DPI18).

first: Yunqiao

last: Li

first: Raag

last: Bhargava

first: Jenny

middle: T

last: Tran

first: Tanya

middle: R

last: Blane

first: Linghang

last: Peng

first: Fangkun

last: Luan

first: Zhe

last: Huang

first: Zefan

first: Yunfan

last: Sun

first: Changchun

last: Xiao


title: PRAME-mediated retinoid resistance in keratinocyte carcinomas is overcome by EZH2 inhibition

city: Montreal

first: Brandon

last: Ramchatesingh

state: Quebec

address: 1001 Decarie Boulevard

department: Experimental Medicine

country: Canada

institute: McGill University

summary: Preferentially Expressed Antigen of Melanoma (PRAME) is a cancer-testis antigen that is expressed in subsets of basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC), collectively termed keratinocyte carcinomas (KC). PRAME functions as a transcriptional co-repressor of retinoid signaling by guiding enhancer of zeste homologue 2 (EZH2), a repressive histone methyltransferase, to retinoic acid response elements (RARE) found in gene promoters. The functions and therapeutic relevance of PRAME expression in KC have not been investigated. In the present study, we evaluated the implications of PRAME expression upon KC development and response to retinoid-based therapeutics. High PRAME expression in tumors was negatively correlated with epidermal differentiation gene signatures.  Similarly, PRAME overexpression (OE) downregulated epidermal differentiation gene signatures, and impaired epidermal differentiation. PRAME OE also attenuated retinoid-induced RARE activation, growth suppression and differentiation responses. Conversely, low-PRAME tumors and PRAME-depleted KC cells possessed enrichment of epidermal differentiation gene signatures. PRAME depletion also restored retinoid-induced RARE activation, suppression of KC growth, keratinization suppression in SCC cells and cell death signaling in BCC cells. Furthermore, EZH2 inhibitors potentiated the retinoid-induced RARE activation and suppress the growth of PRAME-expressing BCC and cSCC cells. We demonstrate that PRAME confers retinoid resistance in KC, and we contend that PRAME-mediated retinoid resistance in KC may be overcome by targeting EZH2.

overall_design: To investigate the impacts of PRAME expression upon keratinocyte and keratinocyte carcinoma phenotypes, PRAME was overexpressed in Ker-CT keratinocyte and CAL-27 squamous cell carcinomas. PRAME was also knocked out in the basal cell carcinoma cell line UW-BCC1  using CRISPR-Cas9 gene editing. We further evaluated transcriptional response to all-trans retinoid acid (ATRA) compared to DMSO (vehicle) treatment.

first: Danny

last: Bergeron

first: Ivan

last: Litvinov


title: CD55 upregulation in T cells of COVID-19 patients suppresses type-I interferon responses [bulkRNA-seq]

status: Public on Apr 04 2025

city: Athens

first: Anastasia

last: Kotanidou

address: 45 Ipsilantou Str

department: 1st Department of Critical Care Medicine and Pulmonary Services

country: Greece

institute: Evangelismos Hospital, National and Kapodistrian University of Athens

summary: Complement overactivation, has been verified in COVID-19 patients. Complement regulatory proteins, including CD55, control complement overactivation thus eliminating complement deposition and cell lysis. We investigated complement regulatory protein expression in COVID-19 for potential deregulated expression patterns driving disease pathogenesis.  Single-cell RNA-seq revealed increased PBMCs CD55 expression in severely and critically ill patients. This increase was also detected upon integrated subclustering analysis of monocyte, T cell and B cell populations. FACS analysis confirmed the significant upregulation of CD55 expression in CD4+ and CD8+ T cell and monocyte populations of severely and critically ill COVID-19 patients. This upregulation was associated with decreased expression of type-I IFN-stimulated genes (ISGs) in patients with severe and critical COVID-19, indicating a suppressor effect of CD55. Silencing of CD55 in T cells from COVID-19 severely ill patients in-vitro and sensitization with SARS-CoV-2 peptides resulted in significantly augmented expression of ISGs and a reversal of their expression to levels similar to control or higher. The present study uncovers, to the best of our knowledge, a novel regulatory effect of CD55 on type-I IFN responses of severely ill COVID-19 patients, thus indicating its contribution to COVID-19 pathogenesis, and identifies a novel mechanistic pathway in the COVID-19 immune response.

overall_design: RNA sequencing of PBMCs from COVID-19 patients and healthy controls used for validation of gene expression data uncovered from scRNA-seq analysis.

first: Maria

middle: G

last: Detsika

last: Sakkou

first: Dimitris

last: Konstantopoulos


title: Dynamic regulation of somatic hypermutation in germinal centers enables rapid B cell clonal expansion without loss of affinity

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary: In the course of antibody affinity maturation, germinal center (GC) B cells mutate their immunoglobulin (Ig) heavy and light chain genes in a process known as somatic hypermutation (SHM). Panels of mutant B cells with different binding affinities for antigen are then selected in Darwinian fashion, leading to a progressive increase in affinity among the population. As with any Darwinian process, rare gain-of-fitness mutations must be identified while common loss-of-fitness mutations are avoided. Progressive acquisition of mutations therefore poses a risk during large proliferative bursts, when GC B cells go through several cell cycles in the absence of affinity-based selection. Using a combination of in vivo mouse experiments and mathematical modeling, we show that GCs achieve this balance by strongly suppressing SHM during clonal burst-type expansion, so that a large fraction of the progeny generated during such bursts do not deviate from their ancestral genotype. Intravital imaging and image-based cell sorting of a new CyclinE(A)/cyclin-dependent kinase 2 (CDK2) reporter mouse strain showed that B cells actively undergoing proliferative bursts lack the transient CDK2low “G0-like” phase of the cell cycle in which SHM takes place. We propose a model in which inertially cycling B cells largely delay SHM until the G0-like phase that follows their final round of division in the DZ, thus maintaining affinity as they clonally expand in the absence of selection.

overall_design: Single

first: Juhee

last: Pae

first: Niklas

last: Schwan

first: Bertrand

last: Ottino-Loffler

first: William

middle: S

last: DeWitt

first: Amar

last: Garg

first: Juliana

last: Bortolatto

first: Ashni

last: Vora

first: Jin-Jie

last: Shen

first: Alvaro

last: Hobbs

first: Luka

last: Mesin

first: Frederick

last: Matsen IV

first: Michael

last: Meyer-Hermann

first: Gabriel

middle: D

last: Victora


title: APOE determines cell type-specific pathological landscape of Alzheimer's disease

city: Jacksonville

first: Zonghua

last: Li

state: FL

address: 4500 San Pablo Rd S

department: Neuroscience

institute: Mayo Clinic

summary: The apolipoprotein E (APOE) gene is the strongest genetic risk modifier for Alzheimer's disease (AD), with the APOE4 allele increasing risk and APOE2 decreasing it compared to the common APOE3 allele. Using single-nuclei RNA sequencing of the temporal cortex from APOE2 carriers, APOE3 homozygotes, and APOE4 carriers, we found that AD-associated transcriptomic changes were highly APOE genotype-dependent. Comparing AD with controls, APOE2 carriers showed upregulated synaptic and myelination-related pathways, preserving synapses and myelination at the protein level. Conversely, these pathways were downregulated in APOE3 homozygotes, resulting in reduced synaptic and myelination proteins. In APOE4 carriers, excitatory neurons displayed reduced synaptic pathways similar to APOE3, but oligodendrocytes showed upregulated myelination pathways like APOE2. However, their synaptic and myelination protein levels remained unchanged or increased. APOE4 carriers also showed increased pro-inflammatory signatures in microglia but reduced responses to amyloid-β pathology. These findings reveal APOE genotype-specific molecular alterations in AD across cell types.

overall_design: Single-nucleus RNA sequencing (snRNA-seq) was performed on temporal cortex samples from 60 cases. After quality control, 56 cases were retained for analysis, including 29 pathologically confirmed Alzheimer's disease (AD) cases and 27 controls. Within the AD group, 8 individuals were APOE2 carriers (E2/3), 10 were APOE3/3 homozygotes, and 11 were APOE4 carriers (E3/4 or E4/4). Among controls, 9 subjects were APOE2 carriers, 10 were APOE3/3 homozygotes, and 8 were APOE4 carriers

first: Yuka

last: Martens

first: Yingxue

last: Ren

first: Yunjung

last: Jin

first: Hiroaki

last: Sekiya

first: Sydney

middle: V

last: Doss

first: Naomi

last: Kouri

first: Monica

last: Castanedes-Casey

first: Trace

last: Christensen

first: Kai

last: Chen

first: Chia-Chen

last: Liu

first: Yixing

first: Alexandra

last: Soto-Beasley

first: Baayla

last: Boon

last: A

first: Tadafumi

middle: C

last: Ikezu

first: David

last: Bennett

first: Ross

last: Reichard

first: Ronald

last: Petersen

first: Takahisa

last: Kanekiyo

first: Owen

last: Ross

first: Melissa

middle: E

last: Murray

first: Dennis

middle: W

last: Dickson

first: Guojun

last: Bu

last: Zhao


title: Predictive Biophysical Neural Network Modeling of a Compendium of in vivo Transcription Factor DNA Binding Profiles for Escherichia coli

city: Boston

first: James

last: Galagan

state: Massachusetts

address: 36 Cummington Mall

department: Biomedical Engineering

institute: Boston University

summary: The DNA binding of most Escherichia coli Transcription Factors (TFs) has not been comprehensively mapped, and few have models that can quantitatively predict binding affinity. We report the global mapping of in vivo DNA binding for 139 E. coli TFs using ChIP-Seq. We used these data to train BoltzNet, a novel neural network that predicts TF binding energy from DNA sequence. BoltzNet mirrors a quantitative biophysical model and provides directly interpretable predictions genome-wide at nucleotide resolution. We used BoltzNet to quantitatively design novel binding sites, which we validated with biophysical experiments on purified protein. We have generated models for 125 TFs that provide insight into global features of TF binding, including clustering of sites, the role of accessory bases, the relevance of weak sites, and the background affinity of the genome. Our paper provides new paradigms for studying TF-DNA binding and for the development of biophysically motivated neural networks.

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

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-Seq) of 139 TFs from Escherichia coli K-12 MG1655 under native and inducible expression modes, plus in vitro ChIP-Seq of one TF, and Library-ChIP of 3 TFs.

first: Patrick

last: Lally

first: Laura

last: Gómez-Romero

first: Víctor

middle: H

last: Tierrafría

first: Patricia

last: Aquino

first: Claire

last: Rioualen

first: Xiaoman

last: Zhang

first: Sunyoung

last: Kim

first: Gabriele

last: Baniulyte

first: Jonathan

last: Plitnick

first: Carol

last: Smith

first: Mohan

last: Babu

first: Julio

last: Collado-Vides

first: Joseph

last: Wade


title: An Lgr5-independent developmental lineage is involved in mouse intestinal regeneration [scRNA-Seq]

first: Gilbert

last: Vassart

overall_design: Unrecombined cells are rare in crypts of VilCre/Rosa26Tomato double heterozygotes. "PlusMinus" cells, Epcam+ve/Rosa26Tomato-negative alongside "PlusPlus" cells, Epcam-positive/Rosa26Tomato-positive cells from the same fraction were isolated via FACS from the fraction generating adult spheroids. This fraction, remaining after EDTA extraction of crypts from the intestine. These two population of cells underwent single-cell RNA sequencing.

first: Maryam

last: Marefati

first: Valeria

last: Fernandez-Vallone

first: Morgane

last: Leprovots

first: Gabriella

last: Vasile

first: Frédérick

last: Libert

first: Anne

last: Lefort

first: Gilles

last: Dinsart

first: Achim

last: Weber

first: Jasna

last: Jetzer

first: Marie-Isabelle

last: Garcia


title: Targeting Setdb1 in T Cells Induces Transplant Tolerance without Compromising Antitumor Immunity

city: NEW BRUNSWICK

first: Xiaosheng

last: Tan

state: NJ

address: 89 French St

institute: RUTGERS

summary: Suppressing immune responses promotes allograft survival but also favors tumor progression and recurrence. How to selectively suppress allograft rejection while maintaining or even enhancing antitumor immunity is challenging. Here, we found mice deficient in Setdb1, an H3K9 methyltransferase, retained allograft-related rejection but exhibited retentive antitumor immunity. RNA-Seq showed that Setdb1 deficiency did not affect T-cell activation or cytokine production, but it induced an increase in regulatory T (Treg) cell-associated gene expression. Treg cell depletion impaired graft acceptance in Setdb1-deficient mice, indicating that the Treg cells promoted allograft survival. Surprisingly, Treg cell-specific Setdb1 deficiency did not prolong allograft survival, suggesting that Setdb1 may function prior to Foxp3 induction. Using single-cell RNA sequencing, we found that Setdb1 deficiency induced a new Treg population in the thymus. This subset of Treg cells expressed less IL-1R2 and IL-18R1. Mechanistically, during Treg cell induction, Setdb1 was recruited by transcription factor ATF and modified histone methylation. Our data define Setdb1 in T cells as a target for suppressing allograft rejection while maintaining antitumor immunity.

overall_design: CUT&Tag was performed using the Hyperactive Universal CUT&Tag Assay Kit. The sequencing process was outsourced to Novogene Co., Ltd. Briefly, after harvesting, CD25+ enriched T cells were counted and divided into groups of 200,000 cells each. The cells were centrifuged at 600 g for 5 minutes at room temperature. Each sample was resuspended in 100 μl of pre-cooled NE Buffer, mixed gently, and incubated on ice. Following incubation, the cells were centrifuged again at 600 g for 5 minutes at room temperature, and the pellets were resuspended in 100 μl of wash buffer. Next, 10 μl of Concanavalin A-coated magnetic beads, pre-activated at room temperature, were added to each sample and incubated for 10 minutes. The unbound supernatant was removed, followed by an overnight reaction between the H3K9me3 group sample and anti-H3K9me3 antibodies (1:50, Proteintech), as well as between the SETDB1 group sample and anti-SETDB1 antibodies (2 μg, Proteintech) in Antibody Buffer at 4°C. After washing, the bound antibodies were reacted with secondary antibodies and then incubated with pA/G-Tnp Pro (0.04 μM). Next, the samples were fragmented with TTBL, followed by the addition of 10% SDS and DNA spike-in to each sample. To extract the genomic DNA, DNA Extract Beads Pro were activated and added to each sample. The extracted DNA fragments were amplified by PCR with indexing primers (Vazyme, TD202), and the library was purified using VAHTS DNA Clean Beads (Vazyme, N411). The specific gene sequences were analyzed by DNA sequencing on an Illumina PE150 platform (Illumina) by Vazyme. Adapter sequences and low-quality reads in the raw CUT&Tag data were filtered using BBDuk (version 38.44). The filtered reads were then aligned to the mouse mm10 reference genome using Bowtie2 (version 2.4.2) with the parameters “--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.” Duplicate reads were removed with the MarkDuplicates function in GATK (version 4.2.0). Coverage (bigWig) files were generated from the resulting BAM files using the bamCoverage tool in deepTools. Peak calling was performed using MACS2 (version 2.2.7.1) with the parameters “--keep-dup all --broad --broad-cutoff 0.05.” Finally, quantitative differences in binding and corresponding p-values were determined using MAnorm (version 1.3.0).

first: Zunsong

last: Hu

first: Peixiang

last: Lan


title: Microbial Bile Acid Metabolites regulate Central Nervous System autoimmunity

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

summary: the commensal gut microbiota modulates multiple sclerosis with unknown mechanisms. Commensal bacteria producing bile acid-deconjugating enzymes are fundamental to generate secondary bile acid metabolites (BAM) with immunoregulatory function. We show that immune regulatory BAM prevent autoimmunity in the central nervous system by inducing immune tolerance at the intestinal level and peripherally limiting effector function and aggressiveness of myelin-reactive T cells. We validated the key role of microbiota-induced BAM in humans by showing that relapsing-remitting multiple sclerosis patients have significantly reduced level of an important immune regulatory BAM (deoxycholic acid) and lower abundance of BAM-producing bacteria that correlate with increased percentages of peripheral effector Th17 cells. Our data indicate that the immune regulatory biliary network is crucial for the prevention of central nervous system autoimmunity.

overall_design: n=20 RRMS patient stools, n=20 Healthy control stools

first: Martina

last: Cencicchio

first: Marika

last: Falcone

first: Federica

last: Ungaro


title: An Lgr5-independent developmental lineage is involved in mouse intestinal regeneration II

first: Gilbert

last: Vassart

overall_design: Examination of the transcriptome of adult intestinal spheroids cultivated in ENR medium upon cells seeding directly in Matrigel.These two sample were compared with small intestinal organoids and fetal small intestinal spheroids presented in an already existed project from our own lab available at GEO under accession number GSE65395. The isolation and the culture conditions remained the same in both studies.

first: Maryam

last: Marefati


title: SORBS2 regulates integrin-cytoskeleton interactions and extracellular matrix composition in heart failure

city: Utrecht

first: Louk

last: Timmer

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Heart failure is associated with high mortality rates and reduced quality of life. Because of the tight connection between Nppa expression and cardiomyocyte stress, we first determined NPPA correlated genes during heart failure. In this study, we identify SORBS2 as conserved NPPA correlated gene and detail its molecular function and association with heart failure. We used RNA-sequencing on murine whole heart tissue to study the effect of cardiomyocyte-specific genetic loss of Sorbs2 in adult mice in a healthy situation and heart failure model.

overall_design: RNA-sequencing was performed on whole ventricular heart tissue in a 2x2 experimental set-up (genotype x condition). (1): Hearts were collected 16 weeks after transverse aortic banding or sham surgery. (2) Both conditions included mice with inducible cardiomyocyte specific knock-out of Sorbs2 at moment of surgery or control mice.

first: Elvira

last: den Hertog

first: Danielle

last: Versteeg

first: Harm

last: Post

first: Job

last: Verdonschot

first: Jantine

last: Monshouwer-Kloots

first: Eirini

last: Kyriakopoulou

first: Ilaria

last: Perini

first: Petra

last: van der Kraak

first: Aryan

last: Vink

first: Lorena

last: Zentilin

first: Mauro

last: Giacca

first: Albert

last: Heck

first: Eva

last: van Rooij


title: scRNA-seq for thymocyte subsets from WT or SETDBf/fCD4-Cre mice

first: Xiaosheng

last: Tan

summary: Suppressing immune response promotes allograft survival, but also favors tumor progression and recurrence. How to selectively suppress allograft rejection while maintaining or even enhancing antitumor immunity is challenging. Here, we found mice deficient in Setdb1, an H3K9 methyltransferase, retained allograft but enhanced antitumor immunity. To explore the underlying mechanism, RNA-Seq was applied to compare the transcriptome between CD4+ T cells from wildtype mice and Setdb1-deficient mice. The data show that Setdb1 deficiency did not affect T cell activation or cytokine production, but induced more regulatory T (Treg) cell-associated gene expression. Treg cell depletion impaired the graft acceptance in Setdb1-deficient mice, indicating that the Treg cell promoted allograft survival. Surprisingly, Treg cell-specific Setdb1 deficiency could not prolong allograft survival, suggesting Setdb1 might function before Foxp3 induction. By using single cell RNA sequencing, we found that Setdb1 deficiency induced a new Treg population in thymus. This subset of Treg cells expressed less IL-1R2 and IL-18R1. Mechanistically, during Treg cell induction, Setdb1 was recruited by transcription factor ATF and modified histone methylation. Our data define Setdb1 in T cells as a target to suppress allograft rejection but maintain the antitumor immunity.

overall_design: Thymocytes from WT or SETDBf/fCD4-Cre mice were enriched by anti-CD25 beads

first: Peixiang

last: Lan


title: Let-7 restrains an oncogenic epigenetic circuit in AT2 cells to prevent ectopic formation of fibrogenic cell intermediates and pulmonary fibrosis [eCLIP-seq]

status: Public on Mar 16 2025

first: Maria

middle: Elisa

last: Ruiz Echartea

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Analysis of lung alveolar type 2 (AT2) progenitor stem cells has highlighted fundamental mechanisms that direct their differentiation into alveolar type 1 cells (AT1s) in lung repair and disease. However, microRNA (miRNA) mediated post-transcriptional mechanisms which govern this nexus remain understudied. We show here that the let-7 miRNA family serves a homeostatic role in governance of AT2 quiescence, specifically by preventing the uncontrolled accumulation of AT2 transitional cells and by promoting AT1 differentiation to safeguard the lung from spontaneous alveolar destruction and fibrosis. Using mice and organoid models with genetic ablation of let-7a1/let-7f1/let-7d cluster (let-7afd) in AT2 cells, we demonstrate prevents AT1 differentiation and results in aberrant accumulation of AT2 transitional cells in progressive pulmonary fibrosis. Integration of enhanced AGO2 UV-crosslinking and immunoprecipitation sequencing (AGO2-eCLIP) with RNA-sequencing from AT2 cells uncovered the induction of direct targets of let-7 in an oncogene feed-forward regulatory network including BACH1/EZH2/MYC which drives an aberrant fibrotic cascade. Additional analyses using CUT&RUN-sequencing revealed an important epigenetic role of let-7 in promotion of histone acetylation and methylation, thereby reprogramming AT2 cells into fibrogenic ADIs.

overall_design: Enhanced AGO2 UV-crosslinking and immunoprecipitation sequencing (AGO2-eCLIP+let7) of chimeric miRNA-mRNA complexes from lungs of wild-type mice following 6-days of bleomycin treatment.

first: Antony

last: Rodriguez

first: Cristian

last: Coarfa


title: Let-7 restrains an oncogenic epigenetic circuit in AT2 cells to prevent ectopic formation of fibrogenic cell intermediates and pulmonary fibrosis

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

overall_design: Refer to individual Series


title: Let-7 restrains an oncogenic epigenetic circuit in AT2 cells to prevent ectopic formation of fibrogenic cell intermediates and pulmonary fibrosis [CUT&RUN]

overall_design:
CUT&RUN-seq of H3k27ac modification from purified AT2 cells from let-7afd knockout and control groups of mice. The AT2 cells were pooled from two mice per group following 6-days of tamoxifen.
CUT&RUN-seq of H3k27ac modification from purified AT2 cells from let-7afd knockout and control groups of mice. The AT2 cells were pooled from two mice per group following 6-days of tamoxifen.


title: Dietary oleic acid drives obesogenic adipogenesis via modulation of LXRasignaling

city: New Haven

first: Matthew

last: Rodeheffer

state: Connecticut

address: 316 Cedar St.

department: Comparative Medicine

institute: Yale University

summary: Dietary fat composition has changed substantially as the obesity epidemic has spread. Adipocyte hyperplasia is a major mechanism of fat mass expansion in obesity, but how dietary fats contribute to obesogenic adipocyte hyperplasia is unknown. Here we employed various dietary strategies, including an unbiased dietary screen, to determine the effect of dietary fat composition on adipocyte hyperplasia in mice. We identified oleic acid (OA) as the only dietary fatty acid that induces adipogenesis and obesogenic hyperplasia at physiologic levels. OA induced differentiation via AKT2 signaling, a hallmark of obesogenic hyperplasia. We also demonstrate that reduction of LXR signaling in APCs is necessary for OA-stimulated adipogenesis. Furthermore, blocking LXRaphosphorylation at S196 results in APC hyperproliferation upon HFD feeding, suggesting that LXRaphosphorylation inhibits HFD-stimulated proliferation. As OA is associated with numerous health effects, our findings that OA is a unique physiologic metabolic regulator underscores the importance of understanding the mechanisms by which OA effects metabolic health.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from adipocyte precursor cells (APCs) from male mice fed a control (SD) and high-fat diet (HFD) for 3 days.

first: Allison

last: Wing

first: Elise

last: Jeffery

first: Chris

last: Church

first: Jennifer

last: Goodell

first: Rocío

last: del M Saavedra-Peña

first: Brandon

last: Holtrup

first: Maud

last: Voisin

first: Zenan

last: Wang

first: Michael

middle: J

last: Garabedian

first: Rohan

last: Varshney

last: Rudolph

first: Moumita

last: Saha

first: Nora

last: Alavi

first: Mariana

last: Floody

first: Thomas

last: Zapadka


title: NF-kB signaling driven by oncogenic Ras contributes to tumorigenesis in a Drosophila carcinoma model

city: Oslo

first: Tor Erik

last: Rusten

address: Ullernschaussen 70

department: Molecular Cell Biology

country: Norway

institute: University of Oslo

summary: Cancer-driving mutations synergize with inflammatory stress signaling pathways during carcinogenesis. Drosophila melanogaster tumour models are increasingly recognized as models to inform conserved molecular mechanisms of tumorigenesis with both local and systemic effects of cancer. Although initial discoveries of the Toll-NFkB signaling pathway in development and immunity was pioneered in Drosophila, limited information is available for its role in cancer progression. Using a well-studied cooperative RasV12 -driven epithelial-derived tumour model, we here describe functions of Toll- NF-kB signaling in malignant RasV12, scrib- tumors. The extracellular Toll pathway components ModSP and PGRP-SA and intracellular signaling Kinase, Pelle/IRAK, are rate-limiting for tumor growth. The Toll pathway NFkB protein Dorsal, as well as cactus/IkB show elevated expression in tumors with highest expression in invasive cell populations. Oncogenic RasV12, and not loss of scribble, confers increased expression and heterogenous distribution of two Dorsal isoforms, DorsalA and DorsalB in different tumour cell populations. Mechanistic analyses demonstrates that Dorsal, in concert with the BTB-transcription factor Chinmo, drives growth and malignancy by suppressing differentiation, counteracting apoptosis and promoting invasion of RasV12, scrib- tumors.

overall_design: RNASeq profiling of FACS sorted cells from day 6 eye-antennal discs with Gmr-GFP (control) GFP+ (RasV12, scrib-/-) tumor cells and GFP- tumor microenvironment cells  from tumor carrying discs.

first: Caroline

last: Dillard

first: Jose

last: Teles Reis

first: Ashish

last: Jain

first: Antunes

last: Goncalves Antunes

first: Yanyan

last: Qi

first: Roland

last: Le Borgne

first: Paula

last: Ruiz Duran

first: Heinrich

last: Jasper


title: Snord67 promotes breast cancer metastasis by guiding U6 modification and modulating the splicing landscape

status: Public on Mar 15 2025

city: Durham

first: Katherine

middle: Ismei

last: Zhou

address: 2301 Erwin Rd

institute: Duke University

summary: Previously considered “housekeeping” genes, small nucleolar RNAs (snoRNAs) are increasingly understood to have wide-ranging functions in cancer, yet their role in metastasis remains unknown. Here, we identify the snoRNA Snord67 as a regulator of lymph node (LN) metastasis in female breast cancer. Snord67 expression is enriched in LN metastases in an immune-competent mouse model of breast cancer. In an orthotopic breast cancer model, loss of Snord67 decreases LN metastasis. In a model of lymphatic metastasis, Snord67 loss decreases LN tumor growth and distant metastases. In breast cancer cell lines, Snord67 knockout results in loss of targeted 2′-O-methylation on U6 small nuclear RNA, as well as widespread changes in splicing. Together, these results demonstrate that Snord67 regulates splicing and promotes the growth of LN metastases and subsequent spread to distant metastases. SnoRNA-guided modifications of the spliceosome and regulation of splicing may represent a previously unappreciated, potentially targetable pathway in cancer.

overall_design: To evaluate alternative splicing patterns, we performed RNA sequencing of 24 matched pairs of primary breast tumors and lymph node metastases from human patients with breast cancer.

first: Yvonne

middle: L

last: Chao

middle: I

first: Kwame

middle: K

last: Forbes

first: Alessandro

last: Porrello

first: Gabrielle

middle: M

last: Gentile

first: Yinzhou

last: Zhu

first: Aaron

last: Chack

first: Dixcy

last: John Mary

first: Haizhou

last: Liu

first: Eric

last: Cockman

first: Lincy

last: Edatt

first: Grant

last: Goda

first: Justin

last: Zhao

first: Hala

last: Abou Assi

first: Hannah

last: Wiedner

first: Yi-Hsuan

last: Tsai

first: Lily

last: Wilkinson

first: Amanda

last: Van Swearingen

first: Lisa

last: Carey

first: Jimena

last: Giudice

first: Daniel

last: Dominguez

first: Christopher

last: Holley

first: Chad

last: Pecot


first: Katherine

last: Zhou

overall_design: To investigate changes in gene expression and alternative splicing upon Snord67 knockout in the murine triple-negative breast cancer cell lines 4T1 and MDA-MB-231-D3H2LN-luc (D3H2) cells, we performed RNA sequencing of polyA-selected RNA from triplicates of 4T1 wild-type cells, two 4T1 Snord67 knockout clones, D3H2 wild-type cells, and one D3H2 Snord67 knockout clone.

first: Yvonne

last: Chao

first: Kwame

last: Forbes

first: Alessandro

last: Porrello

first: Gabrielle

last: Gentile

first: Yinzhou

last: Zhu

first: Aaron

last: Chack

middle: A


title: MAX inactivation deregulates the MYC network and induces neuroendocrine neoplasia in multiple tissues [ChIP-seq]

city: Seattle

first: Brian

last: Freie

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: The MYC transcription factor requires MAX for DNA binding and widespread activation of gene expression in both normal and neoplastic cells. Surprisingly, inactivating mutations in MAX are associated with a subset of neuroendocrine cancers including pheochromocytoma, pituitary adenoma and small cell lung cancer. Neither the extent nor the mechanisms of MAX tumor suppression are well understood. Deleting Max across multiple mouse neuroendocrine tissues, we find Max inactivation alone produces pituitary adenomas while Max inactivation loss cooperates with Rb1/Trp53 loss to accelerate medullary thyroid C-cell and pituitary adenoma development. In the thyroid tumor cell lines, MAX loss triggers a striking shift in genomic occupancy by other members of the MYC network (MNT, MLX, MondoA) supporting metabolism, survival and proliferation of neoplastic neuroendocrine cells. Our work reveals MAX as a broad suppressor of neuroendocrine tumorigenesis through its ability to maintain a balance of genomic occupancies among the diverse transcription factors in the MYC network.

overall_design: Mice were generated with conditional mutations in Rb/p53, and Max/Rb/p53 in neuroendocrine cells by crossing into a tamoxifen inducible Ascl-CRE background. Thyroid and pituitary tumors were observed in these mice, and this was accelerated by Max deficiency. Tumors and cell lines from these mice were then profiled by RNA-Seq. We also performed ChIP-Seq for MAX and members of the extended MYC/MAX network (MNT, MLX, MLXIP) to determine how MAX loss changes occupation of the extended MYC network, and how these changes are associated with altered transcription in cancers that develop as a consequence of Max mutation. RP cells are Rb/p53 deficient, and RPMax are Rb/p53/Max deficient

first: Ali

last: Ibrahim

first: Bob

last: Eisenman

first: David

last: McPherson


title: Let-7 restrains an oncogenic epigenetic circuit in AT2 cells to prevent ectopic formation of fibrogenic cell intermediates and pulmonary fibrosis [RNA-seq]

city: Houston

first: Maria

last: Ruiz Echartea

overall_design:
Fresh flow sorted let-7afd knockout and control lung murine AT2 cells obtained from conditional AT2 knockout mice were examined by RNA-seq. The AT2 cells were collected from pools of three mice per group (n=3) following 6-days of tamoxifen administration.
Whole lungs were examined by RNA-seq from conditional AT2 specific let-7afd knockout and control mice following 6-days of tamoxifen. The whole lungs were collected from three mice of each genotype.
Whole lungs were examined by RNA-seq from conditional AT2 specific let-7afd knockout and control mice following 6-months of booster tamoxifen. The whole lungs were collected from four mice of each genotype.
Let-7afd knockout and control lung murine AT2 cell 3D organoids cultures were grown in AMM media for 14-days and then examined by RNA-seq. The organoids were collected from two mice of each genotype following 6-days of tamoxifen.

first: Antony

last: Rodriguez

first: Cristian

last: Coarfa


title: MAX inactivation deregulates the MYC network and induces neuroendocrine neoplasia in multiple tissues [RNA-seq]


overall_design: To investigate transcriptome-wide 2′-O-methylation in 4T1 wild-type cells and two 4T1 Snord67 knockout clones (Snord67KO-1 and Snord67KO-2), we isolated polyA mRNA and performed ribose oxidation sequencing (RibOxi-seq). For each of the three cell lines, control and oxidized RNA samples were prepared and used to determine 2′-O-methylation at each nucleotide position.

first: Dixcy

last: John Mary

first: Haizhou

last: Liu

first: Eric

last: Cockman

first: Lincy

last: Edatt

first: Grant

last: Goda

first: Justin

last: Zhao

first: Hala

last: Abou Assi

first: Hannah

last: Wiedner

first: Yi-Hsuan

last: Tsai

first: Lily

last: Wilkinson

first: Amanda

last: Van Swearingen

first: Lisa

last: Carey

first: Jimena

last: Giudice

first: Daniel

last: Dominguez


title: The Solanum lycopersicum PIF8a predominantly regulate the low R/FR response in tomato

city: Rishon LeZion,

first: Yogev

last: Burko

address: 68 HaMaccabim Rd.,

department: Plant Biology

country: Israel

institute: Volcani Institute

summary: PHYTOCHROME-INTERACTING FACTORs (PIFs) regulate growth-related gene expression in response to environmental conditions. Among their diverse functions in regulating signal responses, PIFs play an important role in thermomorphogenesis (the response to increased ambient temperature) and in the shade-avoidance response. While numerous studies have examined the varied roles of PIFs in Arabidopsis (Arabidopsis Thaliana), their roles in crop plants remain poorly investigated. This study delves into the conservation of PIFs activity among species by examining their functions in tomato (Solanum lycopersicum) and comparing them to known PIF functions in Arabidopsis using single and higher-order mutants of tomato PIF genes (SlPIFs). We demonstrate that, in contrast to Arabidopsis, PIFs are not required for thermomorphogenesis-induced stem elongation in tomato. In addition, whereas Arabidopsis PIF8 has a minor effect on plant growth, tomato SlPIF8a plays a key role in the low red/far-red (R/FR) response. In contrast, SlPIF4 and SlPIF7s play minor roles in this process. We also investigated the tissue-specific low R/FR response in tomato seedlings and demonstrate that the aboveground organs exhibit a conserved response to low R/FR, which is regulated by SlPIFs. Our findings provide insights into PIF-mediated responses in crop plants, which may guide future breeding strategies to enhance yield under high planting densities.

overall_design: Three biological replicates of wild-type, slpif8a, and slpifq (slpif47a7b8a) mutant plants grown in a long day (LD) at constant 24°C white light (24WL, ~200 µmol m−2 s−1) or white light supplemented with far-red light (24FR, ~200 µmol m−2 s−1, R/FR= 0.6).


title: Systemic Inflammation Impairs Human Myelopoiesis [scRNA-Seq]

city: Nijmegen

first: Hendrik

last: Stunnenberg

state: Gelderland

address: Geert Grooteplein 28

department: Molecular Biology

institute: Radboud University

summary: Systemic inflammation (SI) is a prevalent condition with a high mortality rate1. Survivors of hyperinflammatory state of SI frequently enter a long-lasting immunosuppressive state2 deteriorating their life quality3,4. Due to the extensive heterogeneity in SI etiology, the underlying mechanisms are not well understood. Here, we characterized the short and long-term effects of lipopolysaccharide (LPS)-induced SI (LPS-SI, also called endotoxemia5) on blood monocytes and bone marrow (BM) cells. Similar to clinical features of SI, we observed a profound but transient acute LPS response, followed by a long-term immunosuppressed state. Single-cell transcriptomic analysis of LPS-SI acute phase unveiled the loss of BM monocytes and the appearance of an inflammatory monocyte-like (i-Mono’s) population, expressing gene programs similar to a cell state identified in early-stage sepsis patients6. We observed impairment of myelopoiesis one week after LPS-SI manifested by a significant loss of intermediate and non-classical monocytes which is associated with reduced expression of interferon type I (IFN-I) genes. We confirm that this compromised myelopoiesis also happens in late-stage sepsis patients. Importantly, IFNb treatment reverted the LPS-induced immunosuppression in monocytes. Our results deepened the knowledge about SI and its long-lasting effects on myelopoiesis, substantiating the importance of IFN-I in the pathophysiology of SI-induced immunosuppression.

overall_design:
Characterization of short and long-term effect of LPS induced systemic inflammation on human hematopoiesis, with especiall focus on myelopoiesis, using bulk and single-cell RNA-seq
NOTE FROM SUBMITTER: Not Allowed to Deposit Raw File Due to Donor Consent

first: Farid

last: Keramati


title: Systemic Inflammation Impairs Human Myelopoiesis


title: Systemic Inflammation Impairs Human Myelopoiesis [bulkRNA-Seq]


title: Dietary oleic acid drives obesogenic adipogenesis via modulation of LXR⍺ signaling

status: Public on Mar 14 2025

first: Matthew

last: Rodeheffer

summary: Dietary fat composition has changed substantially as the obesity epidemic has spread. Adipocyte hyperplasia is a major mechanism of fat mass expansion in obesity, but how dietary fats contribute to obesogenic adipocyte hyperplasia is unknown. Here we employed various dietary strategies, including an unbiased dietary screen, to determine the effect of dietary fat composition on adipocyte hyperplasia in mice. We identified oleic acid (OA) as the only dietary fatty acid that induces adipogenesis and obesogenic hyperplasia at physiologic levels.  OA induced differentiation via AKT2 signaling, a hallmark of obesogenic hyperplasia. We also demonstrate that reduction of LXR signaling in APCs is necessary for OA-stimulated adipogenesis. Furthermore, blocking LXRa phosphorylation at S196 results in APC hyperproliferation upon HFD feeding, suggesting that LXRa phosphorylation inhibits HFD-stimulated proliferation. As OA is associated with numerous health effects, our findings that OA is a unique physiologic metabolic regulator underscores the importance of understanding the mechanisms by which OA effects metabolic health.

overall_design: Identification of differentially expressed genes from RNA-seq data of 3T3-L1 (adipocyte precursor cell line) cells differentiated for 24h. Cells were treated with vehicle, oleic acid, or oleic acid and LXR agonist T0901317.

first: Allison

last: Wing

first: Elise

last: Jeffery

first: Chris

last: Church

first: Jennifer

last: Goodell

first: Rocio

last: Saavedra-Peña

first: Brandon

last: Holtrup

first: Maud

last: Voisin

first: Zenan

last: Wang

first: Thomas

last: Zapadka

first: Michael

last: Garabedian

first: Rohan

last: Varshney

last: Rudolph


title: Metastatic medulloblastoma remodels the local leptomeningeal microenvironment to promote further metastatic colonization and growth

city: Toronto

last: Taylor

state: ON

address: 686 Bay St.

institute: Hospital for Sick Children

summary: Medulloblastoma metastasis often occurs in the leptomeningeal spaces; however, the biology of the metastatic tumour cells and the local leptomeningeal niche are poorly characterized. We performed single-cell RNA sequencing to analyze the leptomeningeal metastatic niche in a medulloblastoma mouse model.

overall_design: Mouse SHH primary tumours and matched spinal leptomeninges with metastasis (4 mice) and normal spinal leptomeninges (3 control mice) were processed for single-cell RNA sequencing.


title: Inhibition of MBTPS1 reprograms cold into inflamed tumors and potentiates anti-PD-1 immunotherapy

city: Guangzhou

first: ZHE

last: Fu

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

summary: Despite notable advancements in cancer immunotherapy, the overall response rate among cancer patients remains low. Therefore, exploring strategies combining immunotherapy with adjuvant approaches to augment adaptive immune responses, such as by boosting the infiltration of T lymphocytes, is an attractive strategy. To pinpoint key regulators of tumor immunity, we developed a focused single guide RNA (sgRNA) library targeting membrane and secreted protein genes. Utilizing this library, we conducted an in vivo clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 screen in colorectal cancer mice model. We revealed that the loss of MBTPS1 in tumor cells enhanced anti-tumor immunity and synergized with anti-PD-1 therapy. Mechanistic studies uncovered that tumor cell-intrinsic MBTPS1 could compete with USP13 for binding with STAT1, thereby disrupting the USP13-dependent deubiquitination and stabilization of STAT1. MBTPS1 deficiency induced CXCR3+ CD8+ T cells infiltration in the tumor microenvironment by upregulating mRNA levels of Cxcl9, Cxcl10 and Cxcl11 transcribed by STAT1. Our study revealed that targeting MBTPS1 in cancer cells could turn cold tumors into inflamed ones, thereby enhancing the efficacy of anti-PD-1 blockade.

overall_design: To investigate the function of MBTPS1 in cancer immunotherapy regulation, we conducted gene expression profiling analyses utilizing Mbtps1 knockout and control MC38 cells, with each group comprising 3 replicates. Furthermore, we performed sequencing on C57BL/6 wild-type mice implanted with either MBTPS1 knockdown or control MC38 cells, with each group consisting of 5 replicates.

first: Yi-Yu

first: Zhe

first: Jin-Fei

last: Lin


title: Gene expression profile of adult ventricular myocytes (AVM) from mouse model B3AR-Tg and WT littermates 9 weeks post TAC surgery

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

institute: Université catholique de Louvain

summary: Cardiac β3-adrenergic receptors (β3AR) are upregulated in diseased hearts and mediate antithetic effects to those of β1AR and β2AR. β3AR agonists were recently shown to protect from myocardial remodeling in preclinical studies and to improve systolic function in patients with severe heart failure. The mechanisms involved, however, remain elusive. Here we used a transgenic mouse model with moderate, cardiac-specific expression of the human β3AR (β3AR-Tg) (with levels similiar to those observed in human cardiac bisopsies) to dissect downstream effects after transaortic constriction (TAC)

overall_design: Comparative gene expression profiling between  adult ventricular myocytes (AVM) of B3AR-Tg and WT littermates 9 weeks post TAC surgery

first: Jean-Luc

last: Balligand

first: Lauriane

last: Michel


title: Mouse hippocampi transcriptomics of Daam1 microexon KO (RNA-seq)

city: BARCELONA

first: Patryk

last: Polinski

state: BARCELONA

address: C/ del Dr. Aiguader, 88

country: Spain

institute: EMBL Barcelona

summary: To investigate the impact of Daam1 microexon removal on hippocampal function, we have generated RNA-seq data from adult male mice. Actin cytoskeleton dynamics is crucial for neurogenesis and neuronal function. Precise quantitative and qualitative regulation of actin polymerization is achieved by multiple actin-binding proteins, among which formins are particularly versatile. Here, we investigate how neuronal-specific splicing expands formin's functional diversity in the brain. We uncovered a highly conserved microexon in DAAM1 that extends the linker region of its FH2 domain, leading to remarkable changes in actin polymerization rates and structure. Microexon deletion causes neuritogenesis defects and increased calcium influx in in vitro differentiated mouse neurons, and mice carrying this deletion exhibit deficient long-term memory formation. These memory defects were associated with higher activity of DAAM1's interactor RhoA, increased ARC protein levels, postsynaptic deficiencies, fewer dendritic spines and impaired long-term potentiation. In summary, precise post-transcriptional regulation of DAAM1's FH2 domain is a novel mechanism for modulating actin polymerization in neural spinesneurons and is essential for proper brain function.

overall_design: We dissected hippocampus from WT and Daam1-MIC_KO adult mice and perform RNA-seq

first: P

first: M

last: Dierssen

last: Irimia


title: Inhibition of MBTPS1 reprograms cold into inflamed tumors and potentiates anti-PD-1 immunotherapy [scRNA-seq]

overall_design: To delineate the effects of MBTPS1 loss on the tumor microenvironment, we conducted single-cell RNA sequencing on murine MC38 tumors from both the Mbtps1 knockout (SHM) and control groups.

first: Yan

last: Hu


title: Transcriptomic Analysis of CAD Cell Differentiation

status: Public on Mar 12 2025

city: University of Richmond

first: Omar

middle: A.

last: Quintero-Carmona

state: VA

address: 138 UR Drive

department: Biology

institute: University of Richmond

summary: CAD cells were derived from Cath.a cells, a mouse central nervous system catecholaminergic cell line.  Serum-starved CAD cells undergo morphological changes and resemble isolated neurons when observed by microscopy.  We carried out an RNAseq transcriptomic analysis to examine differentiated CAD cells for expression signatures related to neuronal functions, identifying ~1900 transcripts whose expression changed with differentiation.  Pathview analysis identified ~80 KEGG pathway gene sets that were differentially expressed, including upregulation of at least 13 neuron-related pathways.  This dataset can be explored more deeply, allowing further investigation into expression changes relevant to studying neuronal functions in this easy-to-culture model system.

overall_design: RNAseq profiling of CAD cells differentiated for 5 days compared to undifferentiated CAD cells

first: Dora

last: Posfai

first: Carlos

last: Cevallos

first: Anna

last: White

first: Brooke

last: Fazio

first: Lillian

last: Wendt

first: Jasmine

last: Feng

first: April

last: Horton

first: John

last: Warrick


title: Direct targets of the transcription factor Six1 identify novel candidate deafness genes

status: Public on Mar 13 2025

city: London

first: Andrea

last: Streit

address: Great Maze Pond

department: CCRB

country: United Kingdom

institute: King's college London

summary: Branchio-otic (BOS) and Branchio-oto-renal (BOR) syndromes are autosomal dominant disorders featuring multiple birth defects including ear, renal and branchial malformations. Mutations in the homeodomain transcription factor SIX1 and its co-factor EYA1 have been identified in about 50% of BOS/BOR patients, while causative mutations are unknown in the other half. We hypothesise that SIX1 target genes represent new BOS/BOR candidates. Using published transcriptomic and epigenomic data from chick ear progenitors, we first identify putative Six1 targets. Next, we provide evidence that Six1 directly regulates these targets: Six1 binds to their enhancers and functional experiments in Xenopus and chick confirm that Six1 controls their expression. Finally, we show that most chick Six1 targets are also expressed in the human developing ear and are associated with known deafness loci. Together, our results not only characterise the molecular mechanisms that mediate Six1 function in the developing ear, but also provide new candidates for human congenital deafness.

overall_design: Molecular characterisation of developing otic vesicle (OV) in humans is currently limited. We present the first transcriptome analysis of human embryonic OV from Carnegie stage (CS) 13 and CS14. OV (right and left), dorsal hind brain (DHB) and ventral hind brain (VHB)  fresh tissues was dissected from a single embryo per replicate to perform bulk RNA seq. In total two bilogical replicated for each tissue was collected for both the stages respectively. To identify genes enriched in the OV at each of the developmnetal time points (CS13 &CS14) differential gene expression analysis using DESeq2 was performed comparing the bulk RNA seq data obtained from OV and DHB tissues from respective stages.

first: Ramya

last: Ranganathan

first: Fereshteh

last: Sari

first: Scarlet

last: Wang

first: Alexandre

last: Thiery

first: Ailin

last: Buzzi

first: Sally

last: Moody


title: Single cell atlas of the Drosophila embryonic salivary gland reveals key morphogenetic control steps

city: Cambridge

first: Katja

last: Röper

state: Cambridgeshire

address: Cambridge Biomedical Campus,, Francis Crick Ave

department: Cell Biology Division

institute: MRC LMB

summary: In order to investiage the morphogenetic control of early tube development in the Drosophila melanogaster embryo we performed single-cell-RNAseq-analysis of FACS-isolated early salivary gland placodal cells (stage 10-12), making up less than 0.4% of cells within the embryo to look for early tubulogeneic signatures. In order to identify salivary gland specific signals from epidermal signatures we also performed single-cell-RNAseq-analysis on FACS-isolated epidermal cells in stage 10-12 Drosophila melanogaster embryos for the purpose of differential expression anaylsis.

overall_design: Two batches of salivary gland (SrcGFP) and one batch of epidermal tagged cells (ArmYFP) were obtained and isolated by flow cytometry from Drosophila embryos stage 10-12, and analysed by single cell sequencing.

first: Annabel

last: May


title: Effect of RPD3 phosphorylation on gene expression in glucose and sucrose

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

institute: Hubei university

overall_design: Total RNA was isolated from exponential growing yeast cells by standard phenol-chloroform extraction procedures and the quality of RNA was examined using Agilent Bioanalyzer according to the manufacturer’s instructions. Library construction, sequencing and bioinformatics analysis were performed . There are three biological replicates for WT  and Rpd3-2SA mutants in glucose and sucrose treatment conditions. Differential expression levels of aligned sequences were calculated using significant thresholds set at fold change over 1.5 and adjusted P-value < 0.05

first: Dai

last: Jing


title: Next Generation Sequencing Facilitates Quantitative Analysis of wild typeHDAC1 and HDAC1_S434A  Transcriptomes with or without PKA inhibitor H89 treatment

summary: Cells need to reprogram their metabolism to adapt to extracellular nutrient changes. The histone acetyltransferase SAGA (Spt-Ada-Gcn5-acetyltransferase) complex has been reported to acetylate its subunit Ada3 and form homo-dimers to enhance its ability to acetylate nucleosomes and facilitate metabolic gene transcription. How cells transduce extracellular nutrient changes to SAGA structure and function changes remains unclear. Here, we found that SAGA is deacetylated by Rpd3L complex and uncovered how its deacetylase activity is repressed by nutrient sensor protein kinase A (PKA). When sucrose is used as the sole carbon source, PKA catalytic subunit Tpk2 is activated, which phosphorylates Rpd3L catalytic subunit Rpd3 at serine 50 and serine 354 to inhibit its ability to deacetylate Ada3. Moreover, Tpk2 phosphorylates Rpd3L subunit Ash1 at serine 149 and serine 388, which specifically reduces the interaction between Rpd3L and SAGA. By phosphorylating both Rpd3 and Ash1, Tpk2 inhibits Rpd3L-mediated Ada3 deacetylation, which promotes SAGA dimerization, nucleosome acetylation and transcription of genes involved in sucrose utilization and tricarboxylate (TCA) cycle, resulting in metabolic shift from glycolysis to TCA cycle. Most importantly, PKA phosphorylates HDAC1, the Rpd3 homolog in mammals to repress its deacetylase activity and promote TCA cycle gene transcription. Blocking PKA-catalyzed HDAC1 phosphorylation reduced TCA cycle and impaired cell growth. Our work hence reveals a conserved role of PKA in regulating Rpd3/HDAC1 and metabolism adaptation and provides a potential target for future cancer treatment.

overall_design: Total RNA was isolated from HepG2 cells by standard phenol-chloroform extraction procedures and the quality of RNA was examined using Agilent Bioanalyzer according to the manufacturer’s instructions. Library construction, sequencing and bioinformatics analysis were performed . There are three biological replicates for WT  and HDAC1_S434A mutant in the presence or absence of PKA inhibitor H89. Differential expression levels of aligned sequences were calculated using significant thresholds set at fold change over 2 and adjusted P-value < 0.05

last: Wenjing

first: Ma

last: Rui


title: Light augments antidepressant response via astroglial modulation of lateral habenula

city: San Diego

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Successful antidepressant treatments are still difficult to achieve. Recently, bright light stimulation (BLS) was shown effective in non-seasonal depression but its mode of action remains elusive. We demonstrate, using a new mouse model of depression resistant to antidepressants including ketamine, that both chemogenetic activation of lateral habenula (LHb) astroglia and serotonin (5-HT) depletion prevented the potentiating effect of BLS on the antidepressant response. These results show that improved behavioral outcome produced by BLS requires habenular astroglia and 5-HT tone as crucial buffer systems.

overall_design: PFC mRNA profiles of 10-weeks-old  naïve, stressed, and Ketamine + Scopolamine + light treated wild type mice were generated by deep sequencing, in duplicate, using Illumina.

first: Sarah

last: Delcourte

first: Renaud

last: Rovera

first: Howard

last: Cooper

first: Hiep

last: Le

first: Satchidananda

last: Panda

first: Rihab

last: Azmani

first: Olivier

last: Raineteau

first: Christine

last: Coutanson

first: Ouria

last: Dkhissi-Benyahya

first: Nasser

last: Haddjeri


title: Profiling the cell-specific small non-coding RNA transcriptome of the human placenta

status: Public on Mar 11 2025

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

institute: University of British Columbia

type: Non-coding RNA profiling by high throughput sequencing

summary: The human placenta is the composite of multiple cell types, each which contributes uniquely to placental function. Small non-coding RNAs (sncRNAs) are regulators of gene expression and can be cell-specific. The sncRNA transcriptome of individual placental cell types has not yet been investigated due to difficulties in their procurement and isolation. Using a custom sequencing method, we explored the expression of seven sncRNA species (miRNA, piRNA, rRNA, scaRNA, snRNA, snoRNA, tRNA) from whole chorionic villi and four major sample-matched FACS-sorted cell type (cytotrophoblast, stromal, endothelial, Hofbauer) samples from 9 first trimester and 17 term placentas. After normalization for technical variables, samples clustered primarily by cell type lineage. No sncRNAs were uniquely expressed by cell type, however, mean expression differed by cell type for 115 sncRNAs. Known placentally-expressed sncRNAs showed differing expression by cell type and trimester. Expression of few sncRNAs varied by sex. Lastly, sample-matched sncRNA expression and DNA methylation correlation was not significant, although high correlation (>R2±0.6) was observed for some sncRNA-CpG pairs. This study represents the first exploration of the sncRNA transcriptome of bulk placental villi and placental cell types, informing about the expression and regulatory patterns underlying human placental development.

overall_design: Small RNA-seq profiling of human placental cell types and their matched bulk chorionic villi samples in first trimester and term cases

first: Nikita

last: Telkar

first: Desmond

last: Hui

first: Maria

middle: S

last: Peñaherrera

first: Victor

last: Yuan

last: Martinez

first: Greg

last: Stewart

first: Alexander

middle: G

last: Beristain

first: Wan

last: Lam

middle: P


title: Dual DNA demethylation mechanisms implement epigenetic memory driven by the pioneer factor PAX7 [ChIP-bis]

city: Montréal

first: Juliette

middle: Emilie

last: Harris

state: Québec

address: 110 avenue des Pins O

institute: IRCM

summary: Pioneer transcription factors have the unique ability to open chromatin at enhancers to implement new cell fates. They also provide epigenetic memory through demethylation of enhancer DNA but the underlying mechanisms remain unclear. We now show that the pioneer PAX7 triggers DNA demethylation using two replication-dependent mechanisms, including direct PAX7 interaction with the UHRF1-DNMT1 complex that is responsible for DNA methylation maintenance. PAX7 binds to UHRF1 and prevents its interaction with DNMT1, thus blocking activation of its enzyme activity. The TET DNA demethylases also contribute to the replication-dependent loss of DNA methylation. Thus, PAX7 hijacks UHRF1 to block activation of DNMT1 after replication leading to loss of DNA methylation by dilution and the process is accelerated by the action of TET demethylases.

overall_design: ChIP-bisulfite sequencing (ChIP-bis-seq) in mouse corticotrope AtT-20 cells with ER-Pax7 ectopic expression. Treated with tamoxifen (tam, ER-Pax7 activation) or mimosine (mim, cell cycle arrest).

first: Alexandre

last: Mayran

first: Arthur

last: Gouhier

first: Yves

last: Gauthier

first: Nawal

last: Hajj Sleiman

first: Samir

last: Merabet

first: Micheal

last: Dukatz

first: Pavel

last: Bashtrykov

first: Albert

last: Jeltsch

first: Haig

last: Djambazian

first: Shu-Huang

last: Chen

first: Aurelio

last: Balsalobre

first: Jacques

last: Drouin


title: Dual DNA demethylation mechanisms implement epigenetic memory driven by the pioneer factor PAX7 [RNA-seq]

overall_design: RNA-seq in mouse corticotrope AtT-20 cells with ER-Pax7 ectopic expression. Treated with tamoxifen (tam, ER-Pax7 activation).


title: The Dominant Role of Polyadenylation in Regulating Maternal mRNA Dynamics in Dormant Oocytes and the Function of ZAR1 in this Process_PAIso-seq2

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

summary: During the meiosis, the oocytes will keep dormant for a long time that the transcription will not be activated until zygotic genome activation (ZGA), thus the dynamic and homeostasis of maternal transcriptome deserved to be explored. In the previous researches, the maternal transcripts were reported to be drastically down-regulated by using Smart-seq2. However, we found out that the detection of Smart-seq2 can be biased by the polyA tail length of mRNAs due to the oligo-d(T) primer. In contrast, the down-regulation of maternal transcripts detected by total RNA-seq was relatively small, and the dynamic of polyA tail length were much acuter. ZAR1 is an RBP that had been reported to be important to stablize maternal mRNA. However, the differential expression of maternal transcripts in Zar1/2-/- oocytes were also different when detected by total RNA-seq and Smart-seq2, which hinted an interruption of polyadenylation. By combining total RNA-seq, LACE-seq, PAIso-seq2 and IP-MS and found out that ZAR1 may target the CDS of maternal transcripts and regulate its stability in GV stage oocytes and by interacting with other proteins to regulate the polyadenylation of mRNAs. In this research, by jointly analyzing multi-omics data, we discussed the limitation of Smart-seq2 on oocytes, reexplored the dynamic of maternal transcriptome and reported the new roles of ZAR1 on regulating maternal transriptome.

overall_design: In brief, total RNA was extracted with TRIzol Reagent and Direct-zol RNA MicroPrep (Zymo Research, Cat. no. R2060), and the barcode containing adapter were ligated to the 3’-end of mRNA. After being purified by the RNA Clean & Concentrator-5 kit (Zymo Research, Cat. no. R1016), the RNA were RT into cDNA by the UMI containing template-switching oligo (TSO) primer and the first PCR amplification were proceeded. Then the cDNA from rRNA will be removed by the CRISPR-Cas9 system and the second PCR amplification will be performed to get enough cDNA. Then the cDNA from each sample will be concatenated into long molecules by following the MAS-ISO-seq procedure. Finally, all the samples were mixed up according to the molar ratios of cDNA, and at least 500ng of cDNA was sent for SMRTbell library preparation and sequenced on PacBio Revio platform.

first: Yuke

last: Wu

first: Jingwen

last: Liu

first: Falong

last: Lu

first: Hengyu


title: Psychological Stress-Induced Systemic Corticosterone Directly Sabotages Intestinal Stem Cells Activity

first: zhengrong

last: yao

address: Zijinhua road

institute: zhejiang university

summary: Stress exerts profound impacts on the gastrointestinal tract, yet its effects on intestinal stem cells (ISCs) have not been fully explored. Here, we unveiled a notable reduction in both the quantity and proliferative capacity of ISCs under chronic stress condition, which was mediated by elevated corticosterone levels resulting from the activation of the hypothalamic-pituitary-adrenal (HPA) axis. Mechanistically, corticosterone directly impairs ISCs by interacting with its receptor, nuclear receptor subfamily 3 group c member 1 (NR3C1), which promoted FKBP prolyl isomerase 5 (FKBP5) expression to negatively regulate the AKT activation by mediating the dephosphorylation at the Ser473, thus enhancing the nuclear translocation of the forkhead box O (FoxO) to inhibit the proliferative activity. Collectively, these findings provide a novel mechanistic insight into the deleterious effects of psychological stress on gut, and underscore corticosterone as a key mediator linking stress to ISCs dysfunction.

overall_design: To deeply deciphered the molecular mechanisms that drives the deleterious effect of stress on ISCs via corticosterone, we conducted RNA-seq on Lgr5-GFPhi ISCs purified by fluorescence-activated cell sorting (FACS) from mice subjected to once exposure to either restraint stress or corticosterone injection. We then performed gene expression profiling analysis using data obtained from RNA-seq of 12 different ISCs. Comparative gene expression profiling analysis of RNA-seq data for Ctrl versus CRS ISCs, and Vehicle versus CORT ISCs.

first: Xiaole

last: Sheng

first: Lanfei

last: Jin

first: Zhengrong

last: Yao

first: Longtao

last: Zhu

first: Jiaji

last: Gu

first: Junxuan

last: Peng

first: Xin

last: Xu

first: Xiaolong

last: Ge

first: Wei

last: Zhou

first: Jinghao

first: Zhengping

first: Rongpan

last: Bai


title: The Dominant Role of Polyadenylation in Regulating Maternal mRNA Dynamics in Dormant Oocytes and the Function of ZAR1 in this Process_total RNA-seq

first: Heng-yu

overall_design: 30 GV or MII stage oocytes were harvested from WT and Zar1/2-/- female mice as described for one group and three groups per sample were collected for replication. RNA of oocytes were extracted by TRIzol, and ERCC were added as spike-in. Extracted RNA were used for total RNA-seq library construction by rRNA deletion (rRNA Depletion Module (H/M/R), ABclonal, Cat. no. RK20348) and library construction (Fast RNA-seq Lib Prep Kit V2, ABclonal, Cat# RK20306).

first: Yuke


title: Transcriptome Analyses Reveal Molecular Responses of Three Potato (Solanum tuberosum L.) Cultivars to Cold Stress

city: Xining

first: xiang

last: Li

state: Qinghai

address: No. 251 Ningda Road, Chengbei District

institute: Qinghai University

summary: Potato (Solanum tuberosum L.), as an important food crop on the Qinghai-Tibet Plateau, is prone to low temperature and frost damage during the seedling stage, causing economic losses for farmers. In this study, transcriptome analyses were conducted on the leaves of Atlantic, KY130 and KY140 potato varieties following exposure to cold stress (CS). The genes StPAL(Soltu.Atl.09_2G005110) and StGAD(Soltu.Atl.11_3G000340), suggesting their involvement in the regulation of cold resistance in potato. “Flavonoid-related metabolism,” “lipid metabolism,” “amino acid metabolism,” “carbohydrate metabolism,” “nucleotide metabolism,” and “energy metabolism” might play an important role in the cold resistance of potato. Our results provided novel insights into the molecular mechanisms underlying cold resistance in potato.

overall_design:
Transcriptome analyses were conducted on the leaves of Atlantic, KY130 and KY140 potato varieties following exposure to cold stress (CS). CK(25℃, 12h) and CS( -4℃, 12h ) rep3

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Submitter states that missing raw files are due to file loss.
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first: Xiang

first: Zhenzhen

last: Zheng

first: Yun

first: Shenglong

last: Yang

first: Wang

last: Su

first: Heng

last: Guo

first: Guangji

last: Ye

first: Jiang

last: Wang


title: An in vivo screening platform using PDX models reveals KEAP1, USP22 and other drivers of chemoresistance in small cell lung cancer

city: Seattle

first: David

last: MacPherson

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: Small cell lung cancer (SCLC) is characterized by exquisite chemosensitivity followed by rapid emergence of chemoresistance. To identify genetic events that drive resistance to cisplatin-etoposide chemotherapy, we conducted cDNA overexpression and CRISPR knockout screens in an in vivo platform centered on chemosensitive patient derived xenograft (PDX) models of SCLC. cDNA overexpression screens revealed MYC, MYCN and MYCL as drivers of tumor cell growth through chemotherapy. CRISPR knockout screens identified the KEAP1/NRF2 pathway and members of the SAGA (Spt-Ada-Gcn5 acetyltransferase) complex, including the deubiquitylase USP22. We demonstrated that knockout of either KEAP1 or USP22 switches chemosensitive PDX models to become chemoresistant, with our data supporting distinct molecular consequences of each, including suppression of DNA damage signaling upon USP22 deletion. Data from the IMpower133 clinical trial revealed that a substantial proportion of SCLC patients exhibit KEAP1/NFE2L2 genetic alterations, with activation of an NRF2 transcriptional signature associated with reduced SCLC patient survival with chemotherapy.

overall_design:
We generated isogenic USP22, KEAP1, and control knockout models in SCLC PDX models FHSC14 and NCI109B.
Isogenic PDX tumors were collected after 48-hour in-vivo treatment with cisplatin+etoposide or saline.
Gene expression profiling of FHSC14 and NCI109B sgCtrl, sgUSP22, and sgKEAP1 treated with cisplatin+etoposide or saline was performed by RNAseq.

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Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
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first: Best

last: Scott

first: Brumage

last: Lauren


title: The Dominant Role of Polyadenylation in Regulating Maternal mRNA Dynamics in Dormant Oocytes and the Function of ZAR1 in this Process_LACE-seq

last: Fan

overall_design: The LACE-seq method can be found in the work by Su Ruibao et.al. Briefly, 2 μg per sample ZAR1 antibody was coupled to the activated protein A/G magnetic beads. Then 30 GV stage oocytes were harvested from WT and Zar1/2-/- female mice as described and were irradiated twice with UV-C light on ice at 400 mJ for RBP-RNA crosslinking. Afterwards, the cells were lysed on ice, and the antibody-coupled beads were added to the lysate, and the ZAR1 target RNA was then immunoprecipitated by beads and fragmented by MNase. Then the RNA dephosphorylation and the first-strand synthesis of RT were both performed on beads, and the 3’ linker and biotin-carried T7-RT primer w be added to the RNA at this step. Then the first-strand cDNA was released and captured by streptavidin beads, and the followed polyA tailing and pre-amplification were both performed on beads, and the products were purified for further in vitro transcription (IVT). After IVT amplificating, the DNA template would be removed, and the remaining RNA was purified for further RT and PCR barcoding. The barcoded libraries were sequenced on the Illumina HiSeq 2500 at Novogene.

last: Wu

first: Ruibao

first: Changchang

last: Cao

first: Yuanchao

last: Xue

first: Hengyu


title: hnRNPA2B1 promotes osteogenesis differentiation of human adipose-derived stem cells through PHC2/GATA6/BMP axis [CUT&RUN]

status: Public on Mar 10 2025

city: Chengdu

first: Hongyu

last: Gao

state: Sichuan

address: hengdu City, Sichuan Province, Wuhou District people's South Road, three 14

institute: Sichuan University

summary: m6A modification is prevalent on messenger RNA and plays a crucial role in various eukaryotic biological processes, including growth, development, disease, and aging. hnRNPA2B1, a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family, has been identified as an m6A reader. In this study, hnRNPA2B1 was shown to promote osteogenesis differentiation of human adipose-derived stem cells (hASCs) in vitro. Furthermore, the overexpression of hnRNPA2B1 facilitated bone defect healing in in vivo models of bone defects. hnRNPA2B1 RIP-seq, mRNA-seq, and MERIP-seq were used to identify PHC2 as the target gene of hnRNPA2B1. hnRNPA2B1 enhances the stability of PHC2 mRNA through m6A regulation. PHC2 binds to the promoter region of GATA6 and represses GATA6 expression by increasing H3K27me3 levels. GATA6, in turn, inhibits BMP signaling pathways and the osteogenesis differentiation of hASCs. hnRNPA2B1-PHC2-GATA6-BMP axis offers a promising perspective for the development of stem cell based bone tissue engineering.

overall_design: CUT&RUN-seq was designed to identify the gene regions directly interact withPHC2. PHC2 IP gourp and IgG group were set to avoid non-specific binding.

first: Yidan

last: Song

first: Yuxi

last: Gu

first: Liangyu

last: Luo

first: Jun

last: Liu


title: CUT&Tag analysis of HDAC1 binding profile with or without PKA inhibitor H89 treatment

first: Yu

last: Qi

overall_design: Cut tag  analysis of HDAC1 binding profile with or without PKA inhibitor H89 treatment , sample we collected  from HepG2 cells

first: Wenjing

last: Dai

first: Qi

last: Yu

first: Rui

last: Ma


title: Dual DNA demethylation mechanisms implement epigenetic memory driven by the pioneer factor PAX7 [ChIP-seq]

first: Juliette

last: Harris

overall_design: ChIP-seq in mouse corticotrope AtT-20 cells with ER-Pax7 ectopic expression. Treated with tamoxifen (tam, ER-Pax7 activation) or mimosine (mim, cell cycle arrest).

first: Alexandre

last: Mayran

first: Arthur

last: Gouhier

first: Yves

last: Gauthier

first: Nawal

last: Hajj Sleiman

first: Samir

last: Merabet

first: Micheal

last: Dukatz

first: Pavel

last: Bashtrykov

first: Albert

last: Jeltsch

first: Haig

last: Djambazian

first: Shu-Huang

last: Chen

first: Aurelio

last: Balsalobre

first: Jacques

last: Drouin


title: Transcripts identified by microarray analysis that were deregulated in P0+8d cultures of murine ureters of Pax2cre/+; Pparg fl/fl (Pparg-cKO) or controls upon treatment with purmorphamine.

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

summary: Evaluation of the transcriptional changes in murine Pparg-cKO and control P0+8d ureters upon treatment with purmorphamine.

overall_design: Ureters of newborn (P0) Pax2-cre/+; Pparg (fl/fl) (Pparg-cKO) or control pubs were dissected and cultured for 8 d in medium containing 2 µM purmorphamine or in medium without purmorphamine. Total RNA from these ureters was analyzed by microarray analysis.

first: Andreas

last: Kispert

first: Carsten

last: Rudat


title: G1 length dictates heterochromatin landscape [ChIP-seq]

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: Stem cells have lower facultative heterochromatin as defined by trimethylation of histone H3 lysine 27 (H3K27me3) compared to differentiated cells. However, the mechanisms underlying these differential H3K27me3 levels remain elusive. Because H3K27me3 levels are diluted two-fold in every round of replication and then restored through the rest of the cell cycle, we reasoned that the cell cycle length could be a key regulator of total H3K27me3 levels. Here, we demonstrate that a fast cell cycle sets low levels of H3K27me3 in serum-grown murine embryonic stem cells (mESCs). Extending the G1 phase leads to an increase in global H3K27me3 in mESCs due to the formation of de novo Polycomb domains, and the length of the G1/S block correlates with the extent of gain in H3K27me3, arguing that levels of the modification depend on the time available between successive rounds of replication. Similarly, accelerating the G1 phase in HEK293 cells decreases H3K27me3 levels. Finally, we applied this principle in tumor cells harboring a dominant negative H3K27M allele that reduces H3K27me3 levels. In these cells, extending G1 increases H3K27me3 levels, pointing to an unexpected means to rescue the effect of oncohistones. Our results suggest cell cycle length as a universal mechanism to modulate heterochromatin formation and, thus, cellular identity.

overall_design: Chromatin Immunoprecipitation and sequencing (ChIP-seq) for H3K27 trimethylation (H3K27me3) and H3K27 acetylation (H3K27ac) for mouse embryonic stem cells (mESCs) grown in serum/LIF or 2i media.

first: Abby

last: Trouth

first: Kamesh

last: Ravichandran

first: Philip

middle: R

last: Gafken

first: Sara

last: Martire

first: Gabriel

middle: E

last: Boyle

first: Giovana

last: Veronezi

first: Van

last: La

first: Stephanie

last: Namciu

first: Laura

last: Banaszynski

first: Jay

middle: F

last: Sarthy


title: Dual DNA demethylation mechanisms implement epigenetic memory driven by the pioneer factor PAX7

first: Juliette

last: Harris

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

overall_design: Refer to individual Series


title: G1 length dictates heterochromatin landscape [CUT&Tag]

overall_design: Cleavage Under Target and Tagmentation (CUT&Tag) for H3K27 trimethylation (H3K27me3)


title: Chromatin loops are an ancestral hallmark of the animal regulatory genome.

city: Barcelona

first: Arnau

last: Sebé-Pedrós

address: C/ Dr. Aiguader, 88

department: Systems and Synthetic Biology

institute: Centre for Genomic Regulation (CRG)

sample_organism:
Ephydatia muelleri
Trichoplax adhaerens
Mnemiopsis leidyi
Nematostella vectensis
Sphaeroforma arctica
Capsaspora owczarzaki
Salpingoeca rosetta
Hormiphora californensis
Cladtertia collaboinventa


title: Transcripts identified by microarray analysis that were deregulated in E18.5 Pax2-cre/+;Parg(fl/fl) (Pparg-cKO) ureters.

summary: Evaluation of the transcriptional changes in E18.5 ureters upon loss of Pparg in the ureteric epithelium.

overall_design: Total RNA from dissected ureters of E18.5 Pparg-cKO and control embryos was analyzed by microarray analysis.