title: Single Cell Map of RORgt Lineage APCs in Early Life

city: San Francisco

first: James

last: Gardner

address: 513 Parnassus Ave

institute: University of California, San Francisco

summary: A key feature of immune tolerance is the ability to distinguish pathogens from innocuous signals including dietary antigens, but the precise mechanisms of oral tolerance induction and the key cellular actors have remained unclear. Here we present a single cell map of RORγt-lineage antigen-presenting cells (APCs), specifically RORγt-lineage cells expressing the Autoimmune Regulator (Aire) gene – referred to as RORγt eTACs - that are present in early life. We have previously shown that these are a critical APC population required for oral tolerance induction in adult mice.

overall_design: We obtained mLN, spleen and other LNs (cervical, inguinal, axillary, brachial, and para-aortic) from two-week-old RORγt-lineage mice (RORγt-Cre×R26-lsl-tdTmt) and FACS-sorted tdTmt+ MHCII+ cells for subsequent scRNA-seq

first: Qualls

last: Anita

first: Yin

last: Han


title: Gene expression profiles of intratumoral asGM1- and asGM1+CD8+ T cells in response to PD-1 inhibition

status: Public on Mar 15 2025

city: Daejeon

first: Dongmin

last: Chun

address: 291, Daehak-ro, Yuseong-gu

department: Biological sciences

country: South Korea

institute: Korea Advanced Institute of Science & Technology (KAIST)

type: Expression profiling by high throughput sequencing

summary: In Panc02 tumor, PD-1 blockade promotes expansion of asGM1-expressing CD8+ T cells. Our RNA-sequencing analysis has revealed transcriptionally distinct populations of CD8+ T cells based on expression of asGM1.

overall_design: To elucidate biological significance of asGM1 expression by CD8+ T cells, we conducted bulk RNA-sequencing by sorting asGM1- or asGM1+CD8+ T cells from Panc02 tumor treated with isotype control or anti-PD-1 antibody.

first: Jiyeon

last: Park

first: Suk-Jo

last: Kang


title: Gene expression profiles of intratumoral asGM1- and asGM1+CD8+ T cells from mouse pancreatic tumor

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

overall_design: Refer to individual Series


title: Gene expression profiles of intratumoral asGM1- and asGM1+CD8+ T cells in response to in situ Flt3L expresson

summary: In Panc02 tumor, in situ Flt3L expression promotes expansion of asGM1-expressing CD8+ T cells. Our RNA-sequencing analysis has revealed transcriptionally distinct populations of CD8+ T cells based on expression of asGM1.

overall_design: To elucidate biological significance of asGM1 expression by CD8+ T cells, we conducted bulk RNA-sequencing by sorting asGM1- or asGM1+CD8+ T cells from Panc02 or Flt3L-expressing Panc02 tumor.


title: Spatial transcriptomic study of gene expression in lungs from alpha-1 antitrypsin deficient (A1ATD) patients homozygous for the SERPINA1 Z allele (ZZ).

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

country: USA

institute: Baylor College of Medicine

summary: Using Geomx's Digital Space Profiling method for WTA RNA transcriptomics in lung, we assessed paraffin-embedded lung sections from six A1AT deficient patients (ZZ).

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: After consenting, lung samples were collected from A1AT deficient patients from two Lung Biorepositories: uPenn and Baylor College of Medicine. Pathologist assessed lung samples were obtained from patients needing lung transplant. Lungs were fixed in formalin for 24 hours and subsequently embedded in paraffin. ROIs were collected from parenchyma, airway, vessel and lymphoid follicles.

first: Joselyn

middle: J

last: Rojas-Quintero

middle: A

first: Francesca

last: Polverino


title: imprinting disorders: Beckwith–Wiedemann, Silver–Russell, and Prader-Willi syndromes in Egyptian patients

city: Cairo

first: Amal

last: Mohamed

address: El-Bohooth

department: Human Cytogenetics

country: Egypt

institute: National Research Centre

summary: 19 patients with syndromic ImpDis were 8 clinically diagnosed with Silver-Russell syndrome (SRS), 7 with Prader-Willi syndrome (PWS), and 4 with Beckwith-Wiedemann syndrome (BWS).array chromosomal microarray (CMA) was performed for 12 patients

overall_design: The aim of this study is to achieve proper diagnosis of ImpDis in Egyptian patients through clinical evaluation and genetic testing


title: Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function [ATAC-Seq]

city: Stanford

first: Sai

last: Gourisankar

state: CA

address: 240 Pasteur Dr, Rm 4700

department: Chemical Systems Biology

institute: Stanford

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genes encoding subunits of the BAF (mammalian SWI/SNF) ATP-dependent chromatin remodeling complex are among the those most enriched for deleterious de novo mutations in intellectual disabilities and autism spectrum disorder, but the causative molecular pathways are not understood. Synaptic activity in neurons is critical for learning and memory and proper neural development. While BAF is required for activity-dependent developmental processes, such as dendritic outgrowth, the immediate molecular consequences of neuronal activity on BAF complexes are unknown. Here we report that neuronal activity induces dramatic remodeling of the subunit composition of BAF complexes within 15 minutes, concurrent with both phosphorylation and dephosphorylation of its subunits. These biochemical effects are a convergent phenomenon downstream of multiple calcium-activated signaling pathways in neurons and fibroblasts and correspond to changes in BAF-dependent chromatin accessibility. Our studies imply that BAF decodes signals at the membrane by altering the combinatorial composition of its subunits.

overall_design: ATAC-seq: to investigate the targets of the BAF complex in neurons, primary cortical neurons from E16.5 embryonic mice were cultured for 7 days in vitro and depolarized with 50 mM KCl for 10 minutes or 30 minutes to mimic neuronal activity, and/or treated with 0.1% DMSO or 100 nM FHT-1015 (an inhibitor of BAF ATPase activity). To investigate the effect of the PBAF complex, neurons were infected with Arid2KO (KO) or non-targeting (NT) CRISPR gRNAs, cultured for 7 days in vitro, and depolarized (30 mins) or left unstimulated. Also, to investigate the effects of Smarcc2 serine phosphorylations, gene knockout, vector (Vec), Smarcc2 wildtype (WT), Smarcc2 S586E, and Smarcc2 S586A were introduced into cortical neurons with non-targeting (NT) or Smarcc2KO (KO) CRISPR gRNAs, cultured for 18 days, and depolarized (30 mins) or left unstimulated. Unstimulated conditions in all cases included 1 uM TTX/100 uM D-AP5 overnight treatment to quiet spurious background activity.

first: Sabin

last: Nettles

first: Wendy

last: Wenderski

first: Joao

last: Paulo

first: Sam

middle: H

last: Kim

first: Kyra

last: Roepke

first: Claire

last: Ellis

first: Hind

last: Abuzaid

first: Steve

middle: P

last: Gygi

first: Gerald

middle: R

last: Crabtree


title: Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function


title: Stratification of renal cell carcinoma patients by abundance of sarcomatoid features reveals differences in survival and underlying pathobiology

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: Sarcomatoid renal cell carcinoma (sRCC) is histologically heterogenous, with variable sarcomatoid amounts intermixed within epithelial carcinoma, however current classification of this aggressive disease is homogenous and agnostic to sarcomatoid proportion. We investigated whether sRCC sub-classification could improve prognostic value and reveal biology underlying dedifferentiation and its clinical aggressiveness. Based on intratumoral abundance of sarcomatoid features, cases were classified as sarcomatoid-high (≥10% sarcomatoid features) or sarcomatoid-low (<10% sarcomatoid features) within a consecutive sRCC nephrectomy patient cohort at a single center (n=104). Compared to sarcomatoid-low patients (n=52), sarcomatoid-high patients (n=52) had significantly shorter overall survival (median 14.5 vs. 62.9 months, p<0.001) including in multivariable analysis, and significantly shorter metastasis-free survival among clinically localized patients (median 10.7 vs. 39.0 months, p=0.043). Transcriptomic analyses of n=45 sRCC tumors revealed significant upregulation of 10 Hallmark pathways relating to cell cycle/proliferation, epithelial-to-mesenchymal transition, reactive oxidative species, and interferon-alpha signaling in sarcomatoid-high (n=24) versus sarcomatoid-low (n=21) tumors. Categorization into transcriptomic clusters revealed predominance of proliferative, inflammatory, and immune effector phenotypes within sarcomatoid-high tumors versus hypoxia/angiogenesis in sarcomatoid-low tumors. Altogether, these findings indicate prognostic value for sRCC sub-classification into high versus low sarcomatoid groups and highlight key biology underlying differences in clinical outcome.

overall_design: To investigate the transcriptomic differences between sarcomatoid-high and sarcomatoid-low renal cell carcinoma patient samples

first: Eric

middle: C

last: Kauffman

first: Jason

middle: B

last: Muhitch

first: Nicholas

last: Salgia

first: Kevin

middle: E

last: Eng


title: Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function [RNA-Seq]

overall_design: RNA-seq: to investigate the targets of the BAF complex in neurons, primary cortical neurons from E16.5 embryonic mice were cultured for 7 days in vitro (DIV7) and depolarized with 50 mM KCl for 10 minutes or 30 minutes to mimic neuronal activity, and/or treated with 0.1% DMSO and left unstimulated. Also, to investigate the effects of Smarcc2 serine phosphorylations, gene knockout, vector (Vec), Smarcc2 wildtype (WT), Smarcc2 S586E, and Smarcc2 S586A were introduced into cortical neurons with non-targeting (NT) or Smarcc2KO (KO) CRISPR gRNAs, cultured for 18 days, and depolarized (30 mins) or left unstimulated. Unstimulated conditions in all cases included 1 uM TTX/100 uM D-AP5 overnight treatment to quiet spurious background activity.

first: S

first: W

first: J

first: K

first: C

first: H

first: G


title: A rapid and dynamic role for FMRP in the plasticity of adult neurons

city: New York

first: Daniel

last: Guzman Gundermann

address: 100 Washington Square E

institute: NYU

summary: Fragile X syndrome (FXS) is a neuro-developmental disorder caused by silencing Fmr1, which encodes the RNA-binding protein FMRP. Although Fmr1 is expressed in adult neurons, it has been challenging to separate acute from chronic effects of loss of Fmr1 in models of FXS. We have used the precision of Drosophila genetics to test if Fmr1 acutely affects adult neuronal plasticity in vivo, focusing on the s-LNv circadian pacemaker neurons that show 24-hour rhythms in structural plasticity. We found that over-expressing Fmr1 for only 4 hours blocks the activity-dependent expansion of s-LNv projections without altering the circadian clock or activity-regulated gene expression. Conversely, reducing Fmr1 expression prevented retraction of s-LNv projections. One FMRP target we identified in s-LNvs is sif, which encodes a Rac1 GEF. Our data indicate that FMRP normally reduces sif mRNA translation at dusk to lower Rac1 activity and acutely regulate neuronal plasticity.

overall_design: To identify the targets of Fmr1 in s-LNvs we expressed ADARcd and Fmr1-ADARcd in the s-LNvs of adult flies. We sorted their LNvs by using the Pdf-RFP transgene and then performed RNA-seq. Genomic DNA was isolated from flies which had the different transgenes to remove the posibility of SNPs being identified as targets.

middle: G

last: Gundermann

first: Seana

last: Lymer

first: Justin

last: Blau


title: RNAseq in Acly wild-type or conditional KO mouse T-ALLs

city: New Brunswick

last: Herranz

state: New Jersey

address: 195 Little Albany Street

institute: Rutgers Cancer Institute of New Jersey

summary: C57BL6 mice harboring Acly conditional knockout NOTCH1-ΔE-induced leukemias were treated with vehicle (control) or tamoxifen to induce isogenic deletion of Acly. Here we report the gene expression profile of leukemic blasts obtained from the spleen from control- or tamoxifen-treated leukemic mice, either in an acute setting or in long-term survival setting

overall_design: RNAseq analysis of leukemic spleens in two genotypes and five samples per genotype.

first: Victoria

last: Silva

first: Amartya

last: Singh

first: Olga

last: Lancho

first: Patricia

last: Renck Nunes

first: Hossein

last: Khiabanian


title: Clostridium butyricum and its metabolite butyrate promote ferroptosis susceptibility in pancreatic ductal adenocarcinoma.

city: Shanghai

first: Xiaotong

last: Yang

address: 160 Pujian Rd, Shanghai

country: China

institute: Shanghai Jiaotong University

summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with limited therapeutic options. The diversity and composition of intra-tumoral microbiota are associated with PDAC outcomes, and modulating the tumor microbiota has the potential to influence tumor growth and host-immune response. Here, we explore whether intervention with butyrate-producing probiotic can limit PDAC progression. By analyzing TCGA (PAAD) dataset, we found that tumoral butyrate-producing microbiota links to better prognosis and less aggressive features of PDAC. Intervention with Clostridium butyricum or its metabolite butyrate triggered superoxidative stress and intracellular lipid accumulation, which enhanced ferroptosis susceptibility of PDAC. Our study reveals a novel antitumor mechanism of butyrate, and suggests the therapeutic potential of butyrate-producing probiotics in PDAC.

overall_design: For RNA preparation, KPC1199 cells were either untreated or treated with 1mM NaB for 24 hours, cells were used for RNA preparation. RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit (Illumina) using 5 μg of total RNA, according to manufacturer’s instructions.

first: Jing

last: Xue


title: Next Generation Sequencing Facilitates Quantitative Analysis of SLC7A5KO BM-B cell and  CTRL BM-B cell Transcriptomes

first: LU

last: MENG

address: No.320 Yue Yang Road

department: Immunology

institute: Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China

summary: The goals of this study are to compare transcriptome profiling (RNA-seq) of SLC7A5 deficeint BM-B cells to the control group. Bedises, we want to determine the cellular pathways which were regulated by SLC7A5 in BM-B cells.

overall_design: mRNA profiles of SLC7A5KO BM-B cells and  SLC7A5KO BM-B cells were generated by deep sequencing, in triplicate.

first: Junjie

last: Wen

first: Lu

last: Meng


title: Single-cell transcriptomic atlas of human cardiac arteries

city: Beijing

first: Song

last: Jiangping

address: 167A Beilishi Rd

department: Fuwai Hospital, National Center for Cardiovascular Diseases

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Although the cellular heterogeneity within arterial walls has been explored in mice and nonhuman primates, the cellular composition of human arterial walls remains unclear. We investigated the cellular composition of nondiseased cardiac arteries (3 aortas, 2 pulmonary arteries and 9 coronary arteries) from 3 heart transplantation patients by single-cell RNA sequencing. We created a cell atlas of human nondiseased cardiac arteries, and characterized the cellular compositions in different cardiac arteries. Our results could be used as a reference to identify vascular disease-associated cell populations and help investigate new therapeutic strategies for vascular diseases.

overall_design: Human heart samples were collected from 3 patients with end-stage heart failure undergoing cardiac transplantation. Aortas, pulmonary arteries, and coronary arteries, including right coronary artery, left anterior descending artery, and left circumflex branch, were obtained from 3 patients. Collected samples were sequenced using 10x Genomics 5' V2 single-cell RNA sequencing.

first: Jiangping

last: Song


title: MYB24 orchestrates terpene and flavonol metabolisms as light responses to anthocyanin depletion in grape variegated berries

first: Shao-shan

middle: Carol

last: Huang

address: 12 Waverly Pl

department: Biology

institute: New York University

summary: The presence of naturally-occurring color mutants in plants has permitted the identification of many regulatory genes implicated in the synthesis of discrete metabolic compounds, mostly anthocyanins and carotenoids. Conversely, transcription factors that coordinate more than one specialized metabolic pathway seem challenging to screen from a forward genetics’ perspective. We explored the relationship between different branches of the phenylpropanoid and isoprenoid pathways while examining an infrequent berry skin color variegation in grapevine. Red and white berry skin sections were compared at the genetic, transcriptomic and metabolomic levels showing that light-responsive flavonols and monoterpenes increased in anthocyanin-depleted areas. We disclosed an enrichment of the corresponding pathways among up-regulated genes from white-skin sections, accompanied by increased expressions of flavonol regulators and the still uncharacterized MYB24 gene. We used DAP-seq to examine the in vitro binding of affinity‐purified MYB24 protein to genomic DNA and demonstrated its binding in the promoter regions of 22 terpene synthase genes, in addition to 32 photosynthesis/light-related genes, including the flavonol-regulator HYH. We confirmed the activation of TPS35 and HYH promoter-luciferase reporters in the presence of MYB24 and the grape bHLH-MYC2. The integration of several datasets allowed to define a list of high confidence targets, suggesting MYB24 as a modulator of light responses including the synthesis of flavonols and terpenes. The correspondence between MYB24 and monoterpenes in all conditions surveyed implies that this regulatory network is broadly triggered towards berry ripening, and that the absence of anthocyanin sunscreens accelerates its activation most likely in a dose-dependent manner due to increased radiation exposure.

overall_design: MYB24 DAP-Seq. Comparison between MYB24 library (one replicate) against pHALO library (one replicate) as negative control.

first: José

middle: T

last: Matus

first: Dario

last: Cantu


title: Targeting AR in prostate cancer with siRNA

first: Nicholas

last: Mitsiades

address: One Baylor Plaza, Suite R407

department: Medicine and Molecular and Cellular Biology

summary: We investigated the role of AR in castration-resistant prostate cancer cells using AR siRNA.

overall_design: LNCaP MDV-3100/enzalutamide-resistant (MDV-R) cells were transfected with siRNA against AR or non-targeting control (siNT). RNA was extracted 72h post-transfection.

first: Salma

last: Kaochar

first: Cristian

last: Coarfa


title: Targeting GATA2 in prostate cancer with siRNA

summary: We investigated the role of GATA2 in castration-resistant prostate cancer cells using GATA2 siRNA.

overall_design: LNCaP-abl (Abl) cells and LNCaP MDV-3100/enzalutamide-resistant (MDV-R) cells were transfected with siRNA against GATA2 or non-targeting control (siNT). RNA was extracted 72h post-transfection.


title: A novel inducible cell lineage tracing system for simultaneous fluorescence cell labeling and single-cell clonal reconstruction

city: Chicago

first: Rui

last: Yi

state: IL

address: 303 E. Chicago Avenue

institute: Northwestern University

summary: In vivo clonal analysis utilizing recombinase-activated fluorescence cell labeling has become an essential method for visualizing stem cell activities and cell lineage formation. Recently, the simultaneous acquisition of cell lineage information and single-cell transcriptome data has further advanced our understanding of clonal cell evolution during development, tissue homeostasis, and disease progression. Here we present a novel inducible cell lineage tracing system, called TiTracer, which simultaneously activates fluorescence cell labeling and cellular barcode generation by transiently expressing template independent terminal transferase (TdT) and I-SceI homing endonuclease. We applied this system in HEK293T cells and primary mouse keratinocytes and performed single-cell RNA-seq for barcode recovery and clonal reconstruction.

overall_design: single cell RNA-seq of mouse keratinocytes

first: Haimin

last: Li

first: Dongmei

last: Wang

first: Yuheng

last: Fu


title: Targeting GATA2 in prostate cancer with dilazep (2)

summary: Using a bioinformatics algorithm, we screened in silico 2,650 clinically relevant drugs for a potential GATA2 inhibitor. We identified the vasodilator Dilazep as a potential GATA2 inhibitor. Dilazep exerted anticancer activity across a broad panel of PC cell lines. Global gene expression analysis revealed that dilazep suppressed the GATA2, AR, and cMyc transcriptional programs, including under CRPC conditions. We also documented suppression of cell cycle programs and decreased expression of oncogenic drivers, such as FOXM1, CENPF, EZH2, UBE2C, RRM2, as well as several mediators of metastasis, DNA damage repair and stemness. We provide, based on global gene expression analysis, proof-of-principle evidence that a small molecule can inhibit GATA2 in PC cells and can suppress its downstream AR, cMyc, and other cancer-driving effectors. We propose that GATA2 can be a therapeutic target in CRPC.

overall_design: LNCaP MDV-3100/enzalutamide-resistant (MDV-R) cells were treated with 50 µM dilazep or control for 48h.


title: Targeting GATA2 in prostate cancer with K11706 (2)

summary: We investigated the role of GATA2 in prostate cancer cells beyond the AR signaling axis, and characterized the pharmacological potency of the GATA2 small molecule inhibitor (SMI) K-11706 against prostate cancer cells. K-11706, which inhibited the proliferation and invasive behavior of PC cells, and dramatically reduced the genome-wide transcriptional activity of GATA2, AR, and cMyc, leading to downregulation of several prostate cancer drivers and AR/cMyc effector genes, notably FOXM1, EZH2, and CENPF. Transcriptional profiling and functional pathway analysis of the K-11706 transcriptomic footprint against curated databases delineated a biological network composed of genes involved in cell cycle/proliferation, stemness, metastasis and DNA repair.

overall_design: LNCaP MDV-3100/enzalutamide-resistant (MDV-R) cells were treated with 1 µM K-11706 or vehicle (DMSO) for 48h.


title: Regulation of uveal melanoma gene expression by retinoids

state: Texas

department: Medicine-Hematology & Oncology

summary: We examined the effects of all-trans-retinoic acid and 9-cis-retinoic acid on gene expression in Mel202 uveal melanoma cells

overall_design: Mel202 cells were treated with all-trans-retinoic acid (100 nM) or 9-cis-retinoic acid (100 nM) or EtOH control for 24 or 48 hrs in 6-well tissue culture plates.


title: Targeting p160 SRCs in prostate cancer with bufalin (2)

summary: The p160 Steroid Receptor Coactivators SRC-1, SRC-2, and SRC-3 are critical components of the AR transcriptional complex and are frequently upregulated in prostate cancer (PC). We showed that inhibition of the SRCs via a small molecule inhibitor significantly diminishes AR signaling output, expression of CRPC-associated transcripts and proliferation of CRPC cells both in vitro and in vivo.

overall_design: LNCaP MDV-3100/enzalutamide-resistant (MDV-R) cells were treated with 10 nM bufalin or control for 48h.


title: Targeting GATA2 in prostate cancer with dilazep (1)

overall_design: LNCaP cells and LNCaP-abl (Abl) cells were treated with 50 µM dilazep or control for 48h.


title: Targeting Wnt5A and SRC1 in prostate cancer with siRNA

summary: We investigated the role of Wnt5A and SRC1 in castration-resistant prostate cancer cells using corresponding siRNA.

overall_design: LNCaP-abl (Abl) cells were transfected with siRNA against Wnt5A or SRC1 or non-targeting control (siNT). RNA was extracted 72h post-transfection.


title: Targeting GATA2 in prostate cancer with K11706 (1)

overall_design: LNCaP cells and LNCaP-abl (Abl) cells were treated with 1 µM K-11706 or vehicle (DMSO) or H2O for 48h.


title: Effect of naphthalene on gene expression of C57BL/6J mouse lung cells

status: Public on Mar 14 2025

city: Seoul

first: Bogun

last: Kim

address: 145, Anam-ro

department: Department of Biotechnology

institute: Korea University

summary: Transcriptomic analysis on naphthalene exposed mouse lung cells was performed to discover molecular biomarkers for environmental toxin responses in respiratory orgnas. DEG analysis revelaed 293 genes with significant expression changes in naphthalene treated samples. GO enrichment analysis result showed GO terms related to cillum, axoneme and dynein complex were enriched in down-regulated genes and stress response terms in up-regulated genes. These results indicate when exposed to naphthalene, genes with increased expression levels are associated with chemical response and inflammation, while genes with decreased expression levels are associated with pseudostratified epithelical cells in respiratory organ.

overall_design: RNA-seq profiling of wildtype C57BL/6J male mouse lung cells after treated with naphthalene. 4 control samples and 4 naphthalene-treated samples was analyzed.

first: Hye-Jeong

last: Han

first: Amartuvshin

last: Baasankhuu

first: Angela

last: Prameswari

first: Karina

last: Kalani

first: Sangwoo

last: Lee

first: Woo-Keun

first: In-Geol

last: Choi

first: Cheol-Hee

first: Hyun-Taek


title: Targeting p160 SRCs in prostate cancer with bufalin (1)

first: Nicholas

overall_design: LNCaP cells and LNCaP-abl (Abl) cells were treated with 10 nM bufalin or control for 48h.


title: IQGAP3 bridges matrix stiffness with cancer stem cell maintenance and radioresistance by stabilizing SOX2 II

city: Pittsburgh

first: Po

last: Zhang

state: Pennsylvania

address: 5115 Centre Ave

institute: University of Pittsburgh,

summary: Drivers of therapeutic resistance in cancer include evolution of tumor cell heterogeneity and the tumor microenvironment (TME). Here, we found that increased matrix stiffness promotes radioresistance in glioblastoma (GBM) and maintains the tumor cell hierarchy. Differential gene expression revealed that stiff matrices induced expression of IQGAP3 (IQ Motif Containing GTPase Activating Protein 3) specifically in GBM stem cells (GSCs). IQGAP3 promoted GSC self-renewal and survival upon radiation treatment through binding and stabilization of the core stem cell transcription factor, SOX2. Targeting IQGAP3 reduced SOX2 protein levels in vitro and in vivo, increasing GSC radiosensitivity and inhibiting tumor growth. Structure-function drug screening of FDA-approved agents blocking IQGAP3 binding to SOX2 identified Trimetrexate as a brain penetrant pharmacologic disruptor of IQGAP3 function in radioresistance, sensitizing GSCs to radiotherapy. Our results identify molecular underpinnings for biomechanical promotion of cancer stem cell maintenance and therapeutic resistance, informing a therapeutic strategy to augment efficacy of radiotherapy.

overall_design: RNA-seq data analysis of GSCMES20 cultured on substrates with different stiffnesses, with or without radiotherapy, and with or without IQGAP3 knockdown.

first: Xujia

last: Wu

first: Donghai

first: Jeremy

last: Rich


title: GRHL and PGR control WNT4 expression in the mammary gland via 3D looping of conserved and species-specific enhancers [4C-Seq]

city: Amsterdam

first: Renee

last: van Amerongen

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

summary: This dataset belongs to a study in which we functionally dissect the cis-acting enhancer network and spatiotemporal transcriptional mechanisms that regulate WNT4 expression in the mouse mammary gland and the human breast. As part of these efforts, we performed 4C chromatin conformation capture in BC44 and HC11 (two mouse mammary epithelial cell lines) using the Wnt4 promoter as a viewpoint.

overall_design: 1x10e6 BC44 or HC11 cells were crosslinked with 2% (v/v) formaldehyde in PBS/10% FBS for 10min at RT in 15cm cell culture dishes while shaking. Cells were isolated by using a cell scraper, lysed for 10min in lysis buffer and homogenized with a dounce-homogenizer. Nuclei were digested with 200U DpnII (NEB) in DpnII buffer (NEB) complemented with 0.3% SDS and 2% Triton X-100 for 4hr, an additional 200U DpnII O/N and another 200U DpnII for 4 hr the following day at 37C while shaking. The first ligation was performed with 100U T4 DNA ligase O/N at 16C in a total volume of 15ml. Following decrosslinking and phenol/chloroform extraction, the DNA was digested with NlaIII in Cutsmart buffer (NEB) O/N at 37C while shaking. After digestion a second ligation was carried out with T4 DNA ligase (Thermo Scientific) in a total volume of 15ml O/N at 16C. DNA was isolated via phenol/chloroform extraction and purified with the ChIP DNA Clean & Concentrator Kit (Zymo Research). 50-100ng DNA template per reaction and 1ug in total was used to amplify PCR-specific libraries for the Wnt4 promoter viewpoint with the Expand Long Template PCR system (Sigma) using specific primers. Successful reactions were pooled and purified with the High-pure PCR Product Purification Kit (Sigma). Equal amounts of libraries were combined, and all library preparation and sequencing steps were performed by MAD: Dutch Genomics Service & Support Provider, Swammerdam Institute for Life Sciences, University of Amsterdam. Paired-end sequencing (for cost-effectiveness, only single reads needed for analysis) was performed on a NextSeq550. For processing raw 4C-seq data, the publicly available 4C mapping pipeline for mapping (mm9) and filtering 4C data was used (https://github.com/deWitLab/4C_mapping) using default settings. The R package PeakC was used to analyze processed triplicates of 4C-seq data and identify significantly interacting regions within a window size of 400kb (https://github.com/deWitLab/peakC).

first: Yorick

last: van de Grift

first: Renée


title: A TFEB-TGFβ axis systemically regulates diapause, stem cell resilience and protects against senescence.

city: Köln

first: Adam

last: Antebi

address: Joseph Stelzmann Strasse 9b

country: Germany

institute: Max Planck Institute for Biology of Aging

summary: Diapause is a long-lived state of resilience that allows organisms to outlast adversity. C. elegans can endure months in a fasting-induced adult reproductive diapause (ARD) and, upon refeeding, regenerate and reproduce. Here, we find that mutants of ARD master regulator hlh-30/TFEB arrest in a novel senescence-like state during ARD and refeeding, in which germline stem cells are characterized by DNA damage, nucleolar expansion, cell cycle arrest, and mitochondrial dysfunction, alongside dysregulated immune and growth metabolic signatures, elevated senescence-associated β-galactosidase and premature aging at the organismal level. Forward genetic screens reveal a TFEB-TGFβ signaling axis that systemically controls diapause, stem cell longevity, and senescence, aligning nutrient supply to proper metabolism and growth signaling. hlh-30 mutation misaligns nutrient cues and growth signaling, triggering senescence and abrogating stem cell and organismal longevity, which can be restored by downregulating TGFβ signaling. Notably, TFEB’s vital role is conserved in mouse embryonic and human cancer diapause. Thus, ARD offers a powerful model to rapidly characterize diapause-related regulatory pathways and study stem cell longevity and senescence in vivo, directly relevant to mammals.

overall_design: RNA-seq profiling of wildtype C. elegans, hlh-30(tm1978), hlh-30(tm1978) daf-1(m40), daf-1(m40), at 48 hours ARD and at 12 hours refeeding after 48 hours of ARD

first: Jennifer

last: Mak


title: GRHL and PGR control WNT4 expression in the mammary gland via 3D looping of conserved and species-specific enhancers [ATAC-Seq]

summary: This dataset belongs to a study in which we functionally dissect the cis-acting enhancer network and spatiotemporal transcriptional mechanisms that regulate WNT4 expression in the mouse mammary gland and the human breast. As part of these efforts, we characterized the chromatin accessibility landscape in the pubertal mouse mammary gland. For this, we FACS sorted basal, luminal and stromal cell populations and performed bulk ATAC-seq analysis

overall_design: The 3rd and 4th mammary gland fat pads from 6 puberty (p35) FVB/N mice were dissected, chopped to small pieces and incubated for 2h at 37°C in an orbital shaker in a digestion mix composed of DMEM/F12, 5 % FBS, 1% Penicillin / Streptomycin, 25mM HEPES and 300 U/ml Collagenase IV. Red blood cells were lysed with ACK Lysing Buffer and single cell suspensions were generated by consecutive digestion steps with Trypsin-EDTA and DNAseI. Cells were stained in HBSS containing 10% FBS with the following antibodies (eBioscience): anti-Mouse CD45-Biotin (clone 30-F11), anti-Mouse CD31-Biotin (clone 390), anti-Mouse TER-119-Biotin (clone Ter-119), anti-Mouse CD326-PE (clone G8.8), anti-Mouse CD49f-FITC (clone GoH3) and Streptavidin-APC. DAPI was used for live/dead cell discrimination. 55.000 luminal, basal and stromal cells were sorted into ice-cold 10mM HEPES containing 10% FBS using a BD FACSAria III equipped with a 100 um nozzle at 20psi. ATAC-seq samples were prepared according to the protocol from Buenrostro et al. (2013, 2015). Briefly, freshly sorted cells were washed once in 50ul ice-cold PBS and gently resuspended in 50ul cold lysis buffer (10mM Tris-HCl, pH 7,4; 10mM NaCl; 3mM MgCl2 and 0.1% NP-40) to isolate nuclei. The transposase reaction (Illumina Nextera DNA Library Preparation Kit, FC-121-1030) was performed for 30 min at 30°C and DNA was purified using MinElute PCR purification columns (Qiagen, #28004). DNA fragments were amplified using custom primers (Buenrostro et al., see table below) and NEBNext Ultra II Q5 Master Mix (#M05445). The following PCR conditions were used: 72 °C for 5 min; 98°C for 30 sec, 8 cycles of 98°C for 10 sec, 63°C for 30 sec and 72 °C for 1 min. Libraries were purified with the MinElute PCR purification kit. An additional, single left-sided purification with AMPure XP beads (Beckman Coulter #A63880) was performed to remove primer dimers. Libraries were quantified with qPCR before paired-end sequencing on an Illumina NextSeq 550 system (2 x 75 bp, performed by MAD: Dutch Genomics Service & Support Provider, Swammerdam Institute for Life Sciences, University of Amsterdam). Sequencing data were processed using the ATAC-Seq pipeline of the Kundaje lab (https://github.com/kundajelab/atac_dnase_pipelines) with default parameters and mouse genome version mm9.

first: Katrin

last: Wiese

first: Nika

last: Heijmans


title: PHF19 drives PRC2 sub-nuclear compartmentalization to promote motility in TNBC cells [RNA-seq]

city: Stuttgart

first: Cristiana

last: Lungu

state: BW

address: Allmandring 31

department: Institute of Cell Biology and Immunology

institute: University of Stuttgart

summary: Polycomb Repressive Complex 2 (PRC2), a master regulator of gene expression and chromatin organization, is frequently hijacked in aggressive malignancies such as triple-negative breast cancer (TNBC). Here, we identify a distinct spatial organization of PRC2 in TNBC cells, where the complex assembles into micron-sized nuclear bodies. Using high-resolution spatial proteomics on these endogenous compartments, we identify PHD Finger Protein 19 (PHF19) as the central driver of these structures. We further demonstrate that an intrinsically disordered region (IDR) within PHF19 promotes its clustering into nuclear bodies and link this spatial organization to enhanced cell motility. These findings shed light on a previously unrecognized layer of PRC2 regulation in TNBC cells, demonstrating how its subnuclear compartmentalization, shaped by accessory subunits, orchestrates functional outcomes critical for cancer progression.

overall_design: mRNA-Seq of TNBC cell lines BoM-1833 and MDA-MB-436 following 72 hours siRNA-mediated knockdown of PHF19.

first: Zeynab

last: Najafova


title: PHF19 drives PRC2 sub-nuclear compartmentalization to promote motility in TNBC cells [ChIP-seq]

overall_design: ChIP-Seq of H3K27me3 was performed in  TNBC cell lines BoM-1833 and MDA-MB-436 following 72 hours siRNA-mediated knockdown of PHF19.


title: The genetic basis for synchronised time perception in populations of plants

city: York

first: Daphne

last: Ezer

address: Wentworth Way

country: United Kingdom

institute: University of York

summary: In order to efficiently breed plants for climate change, it is critical to identify traits in seedlings that are effective predictors of agronomically important traits at maturity that could be used to screen lines.  Our work shows that the response of circadian clock to changes in photoperiod in seedling Arabidopsis is predictive of bolting time and bolting-associated traits, including the degree of synchronization in bolting.  Using the first ever Recombinant Inbred Lines (RILs) between African and European Arabidopsis lineages, we find distinct Quantitative Trait Loci (QTLs) associated both with the synchronicity of circadian responses to photoperiodic changes and with bolting-related traits. Two QTLs contain K-Homology Domain RNA binding proteins (KH17 and KH29) associated with splicing variants in the MADS AFFECTING FLOWERING2 and 3 (MAF2, MAF3) genes, including generating chimeric transcripts between these two adjacent genes containing the MADS-box of MAF2 and the K-box dimerisation domain of MAF3.  Many of the variants in KH17 in Arabidopsis ecotypes are found within its prion-like domain and are associated with de-coupling the mean and synchronicity of flowering time.  Therefore, we have identified novel potential mechanisms that link synchronised responses on a diurnal scale and a developmental scale.

overall_design: RNA-seq of Tnz-1 and Ws-2 parental ecotypes and Recombinant Inbred Lines of these lines in 12-day old seedlings that were entrained in Short day (8hrs light/16hrs dark) at ZT10, either in the dark or after 2 hours of extended light.

first: Sarah

last: Lock

first: Kayla

last: McCarthy

first: James

last: Ronald

first: Muhammad

middle: U

last: Anwer

first: Amanda

middle: M

last: Davis

first: Marc

last: Hallstein

first: Ethan

last: Redmond

first: Marina

last: Knight

first: Seth


title: Brain Sensing of Metabolic State Regulates Circulating Monocytes

city: Manchester

first: Giuseppe

last: D’Agostino

address: Rumford Street off Dover Street

department: Division of Diabetes, Endocrinology & Gastroenterology

institute: The University of Manchester

summary: Changes in energy availability alter the dynamics of circulating immune cells. The existing view is that these effects are due to altered nutrient levels affecting peripheral tissue metabolism. Here, using mice, we show that the brain's perception of hunger and satiety alone is sufficient to drive these immune changes. Hunger-promoting AgRP neurons in the hypothalamus are both sufficient and necessary for the reduction in circulating Ly6CHi classical monocytes observed during fasting. Mechanistically, these neurons suppress hepatic mTOR signaling via sympathetic regulation, decreasing circulating CCL2 and monocyte numbers. AgRP neuron-induced corticosterone release plays a permissive role in this process. These changes in monocyte dynamics can occur independently of actual nutrient levels, revealing an unexpected brain-mediated control of peripheral immunity in response to perceived variation in energy state.

overall_design: The aim of this study was to determine whether the immunoregulatory effects of fasting are solely dependent on altered nutrient availability or if brain-initiated responses also play a role. To this end, we used genetic tools such as chemo- and optogenetics to manipulate the activity of key hypothalamic neurons encoding hunger and satiety, creating synthetic representations of these states on demand. This approach allowed us to isolate and assess the direct effects of neural activation on circulating leukocyte dynamics independently of the actual nutritional state. Male and female mice were grouped post-weaning, with transgenic and littermate control animals co-housed and receiving identical treatments to ensure a level of randomization. Experimenters were blinded to genotype, and no further blinding was necessary due to the use of objective readouts. In pharmacological experiments using only wild-type mice, experimenters were not blinded to treatments. Sample sizes were determined based on previous experiments and the availability of genetically modified animals. No outliers were excluded, and the number of replicates and individual experiments are specified in each figure legend.

first: Joao Paulo

last: Cavalcanti de Albuquerque

first: Jenna

last: Hunter

first: Rita

last: Domingues

first: Erika

last: Harno

first: Amy

last: Worth

first: Fabrizio Maria

last: Liguori

first: Aurora

last: D’Alessio

first: Gabriella

last: Aviello

first: David

last: Bechtold

first: Anne

last: White

first: Simon

last: Luckman

first: Matthew

last: Hepworth


title: STAT6 mutations compensate for CREBBP mutations and hyperactivate IL4/STAT6/RRAGD/mTOR signaling in Follicular Lymphoma

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

summary: Activating mutations in STAT6 are common in Follicular Lymphoma (FL) and transformed FL and various other B cell lymphomas. Here, we report RNA-seq based gene expression data on normal human lymph node derived B lymphocytes (NBC; N = 6), and primary human FL WT (N = 11) or mutant (N = 4) for STAT6 before and after ex vivo stimulation with IL4. We found that STAT6 mutants result in broad based augmentation of IL4-induced gene expression. Unexpectedly, in FL with WT STAT6 we measured reduced baseline and IL4-induced gene expression levels when compared with NBC lymphocytes or FL with STAT6 mutations. We tracked the attenuated IL4/JAK/STAT6 response to co-existing CREBBP mutations and experimentally verified that intact CREBBP is required for the induction of many IL4-induced genes. One of the IL4-induced genes here identified is RRAGD, a small G-protein involved in lysosomal mTOR activation. We show that IL4 treatment induced RRAGD expression, that RRAGD is required for mTOR activation in lymphoma cells and that IL4-enhanced BCR signaling induced mTOR activation. The IL4 and BCR-induced mTOR activation was reduced by CREBBP mutants and augmented by mutant STAT6, establishing a link between STAT6 mutations and mTOR regulated pro-growth pathways in lymphoma.

overall_design: The targeting of CREBBP, RRAGD or AAVS in lymphoma cell lines was done using the pLENTI-CRISPRv.2 lentiviral vector and four guides each selected from the Brunello library.  The B lymphocytes were cultured for 4 h in the presence or absence of 10 ng/ml of IL4.  Total RNA was purified using the Trizol reagent followed by RNAeasy column purification (Qiagen).  RNA was assessed using the Bioanalyzer (Agilent #5067-1513) and a Qubit RNA High Sensitivity assay (Thermofisher # Q32855).

first: Qiangqiang

last: Shao

first: Sami

middle: N

last: Malek


title: Nanostring gene expression analysis of Tregs islated from Kdr KO versus transgene control SB1 tumors

city: Bethesda

first: Mohamed-Reda

last: Benmebarek

state: MD

address: 10 Center Drive

department: Thoracic and GI Malignancies Branch

institute: NIH

summary:
Tumor-infiltrating Tregs were FACS sorted using their YFP signal from processed SB1 tumors implanted in Kdr(fl/fl)xFoxp3(yfp-cre) or Kdr(+/+)xFoxp3(yfp-cre) mice, fro which RNA was isolated for Nanostring analysis usig the Murine Cancer Immune Profiling Panel
Anti-VEGF treatment has shown clinical activity in combination with checkpoint inhibitor  therapy, but the exact mechanism is not known. We show that adding VEGF blockade to  the ICB combination of anti-CTLA4 + anti-PD-L1 in cholangiocarcinoma unleashed a  therapeutic efficacy driven through a novel multimodal mechanism dependent on BAFF  production by T and myeloid cells, leading to a BAFF-dependent proinflammatory B cell  response characterized by Germinal center B cell and plasma cell expansion, as well as  IL-12 production. The mechanism culminates in a BAFF and IL-12-dependent expansion  and rewiring of Tregs towards an anti-tumor Th-1-like fragile state. We translated this  approach to the clinic with encouraging outcomes following an interim analysis of the first  six CCA patients. Using paired PBMC, serum and tumor biopsy samples from patients  treated with anti-CTLA4, anti-PD-L1 and anti-VEGF, we again observed treatmentassociated  immunological changes characterized by Treg expansion and rewiring  towards fragile and unstable states and a proinflammatory cytokine profile including  elevated BAFF and IL-12 levels. Correlating immune changes with overall survival  identified BAFF and IL-12 as potential biomarkers of treatment response. Finally, we  explored the direct effect of VEGFR2 signaling on Treg transcriptional programming.  Fragile and unstable Tregs showed diminished VEGF/VEGFR2 signaling. A mouse model  genetically ablating VEGFR2 expression on Tregs led to diminished suppressive function  and delayed tumor growth, an effect that was further enhanced by ICB therapy.

overall_design: 6 samples were analysed including 3 biological replicates fro 2 groups (KO versus control)

first: Tim

last: Greten


title: Genome-wide binding of wild-type p53 and R248Q missense mutant variants in isogenic human acute myeloid leukemia (AML) cell lines

city: Zurich

first: Steffen

last: Böttcher

address: Rämistrasse 100

department: Medical Oncology and Hematology

country: Switzerland

institute: University of Zurich, University Hospital Zurich

summary: TP53, encoding for the tumor suppressor p53, is the most frequently mutated gene in human cancer. The selective pressures shaping its mutational spectrum, dominated by missense mutations, have remained enigmatic, and neomorphic gain-of-function (GOF) activities have been implicated. We generated isogenic human leukemia cell lines of the most common TP53 missense mutations using CRISPR/Cas9. Functional, DNA binding, and transcriptional analyses revealed loss-of-function (LOF) without GOF effects of missense mutations. Comprehensive mutational scanning of p53 single amino acid variants demonstrated that DNA-binding domain missense variants exert dominant-negative effects (DNE).  The precise functional and molecular mechanisms of the DNE have remained elusive. Using a variety of novel model systems including CRISPR-edited human isogenic cell lines, transcriptional reporter cell lines, and targeted protein degradation assays combined with functional and molecular analyses we functionally characterize the DNE and demonstrate that formation of heterotetramers between R248Q and WT p53 impairs proper WT p53 functionality by preventing DNA binding and subsequent target gene transactivation.

overall_design: Examination of wild-type p53 and R248Q missense mutant DNA-binding in isogenic MOLM13 human AML cell lines under steady-state conditions (DMSO) or after induction of DNA damage (Daunorubicin)

first: Benjamin

last: Ebert


title: Subgrouping Germinal Center-Derived B-Cell Lymphomas based on Machine Learning-deduced DNA Methylation Modules

city: Ulm

first: Selina

last: Glaser

address: Albert-Einstein-Allee 11

institute: Ulm University and Ulm University Medical Center

type: Methylation profiling by genome tiling array

summary: Despite all being derived from germinal center B-cells, follicular and diffuse large B-cell lymphomas are biologically and clinically heterogeneous. DNA methylation has emerged as a robust biomarker for classification of solid tumors, but its application to subtype mature B-cell lymphomas is still in its beginning. Therefore, we conducted array-based DNA methylation analyses on 177 molecularly well-characterized mature B-cell lymphomas from the ICGC MMML-Seq project. The Phenotype-Genotype Many-to-Many Relations Analysis machine learning method was applied to identify significant biclusters of CpGs and samples. The analysis revealed 300 CpGs forming four modules, which ordered the lymphomas into seven methylation patterns (MP1-7). These MP1-7 showed significant associations with biological features of the lymphomas. For example, MP1 and MP2 both predominately comprised follicular lymphomas but significantly differed in age at diagnosis and proliferation history. MP4-MP7 consisted mainly of diffuse large B-cell lymphomas but showed differences regarding their cell-of-origin signatures. MP6 showed enrichment of cases with an MCD/C5-like mutational signature with MYD88 alterations as hallmark. The 300 CpGs also segregated apart Burkitt lymphoma and non-malignant B-cell populations.  The identified CpG modules and methylation profiles, thus, reflect properties of mature B-cell lymphomas across different biologic layers from age at diagnosis to mutational signatures.

overall_design: We collected 177 samples (cryo-preserved) from patients with follicular lymphoma (FL), diffuse large B cell lymphoma (DLBCL) and follicular lymphoma with diffuse large B cell lymphoma (FL-DLBCL) (cryo-preserved material) from the ICGC MMML-Seq consortium. The samples were analyzed using the Infinium HumanMethylation450 BeadChip array.

first: Ole

last: Ammerpohl

first: Reiner

last: Siebert


title: The histone methyltransferases EHMT1 and EHMT2 repress the expression of genes related to excitability and cell death in oligodendrocyte progenitors [RNA-seq]

first: Patrizia

last: Casaccia

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

summary: Oligodendrocyte progenitor cells (OPCs) represent a population of electrically active and dividing cells, which are capable of responding to neuronal activity, by proliferating and differentiating. Here we report that the repressive euchromatic H3K9me2 histone mark, deposited by the histone mehyltransferases EHMT1 and EHMT2 enzymes, increases in proliferating OPCs in mice following optogenetic stimulation of neuronal activity. Using primary cultured OPCs with genetic deletion of Ehmt1 and Ehmt2, and pharmacological inhibition of EHMT enzymatic activity, we reveal the importance of these enzymes in repressing the expression of genes regulating cell death and electrical properties in proliferating OPCs. Consistent with these findings, we detect higher levels of cholinergic muscarinic receptors, fewer numbers of oligodendrocyte lineage cells and lower levels of the myelin basic protein (MBP) in mice with lineage specific ablation of Ehmt1 and Ehmt2. Together these data suggest that the repressive H3K9me2 histone mark, whose levels increase in proliferating OPCs after neuronal stimulation, is an important modulator of cell death and proteins regulating the electrical properties of OPCs.

overall_design: To investigate the role of EHMT1/EHMT2 in oligodendrocytes, we performed RNA-sequencing on mouse primary oligodendrocyte progenitors comparing Ehmt1/Ehmt2 knocked down samples to control. Knocked down of Ehmt1 and Ehmt2 was performed in vitro by infecting cells with an Adenovirus expressing Cre recombinase and a RFP protein (knockdown samples), or RFP only (control samples).

first: Mathilde

last: Pruvost

first: Hye-Jin

last: Park

first: Meng

last: Li

first: Jia

last: Liu


title: Overlapping and distinctfunctions of SPT6, PNUTS and PCF11 in regulating transcription termination [ChIP-Seq]

city: Paris

first: Fabienne

last: Bejjani

address: 27 Rue Fg St Jacques

country: France

institute: Institut Cochin

summary: The histone chaperone and transcription elongation factor SPT6, integral to RNA Polymerase II (RNAPII) activity, also plays a crucial role in regulating transcription termination. In an attempt to identify the pathways employed by SPT6 in this regulation, we found that while SPT6 and its closest partner IWS1 interact and co-localize with RNAPII, their functions diverge significantly at gene termination sites. Our data revealed that SPT6 depletion, unlike IWS1, results in extensive readthrough transcription, indicating that SPT6 independently regulates transcription termination. Further analysis identified that the cleavage and polyadenylation factor PCF11 and the phosphatase regulatory protein PNUTS collaborate with SPT6 in this process. These findings suggest that SPT6 may facilitate transcription termination by recruiting PNUTS and PCF11 to RNAPII. Additionally, SPT6 and PNUTS jointly restrict promoter upstream transcripts (PROMPTs), whereas PCF11 presence is essential for their activation in the absence of SPT6. This study elucidates the distinct and overlapping functions of SPT6, PCF11, and PNUTS in transcription termination, highlighting the pivotal role of SPT6 in ensuring proper transcription termination at the 5’ and 3’ ends of genes.

overall_design: Chromatin Immunoprecipitation sequencing (ChIP-seq) for SPT6, IWS1, PNUTS and RNAPII (siCT versus siPNUTS conditions) in HeLa cells

first: Stéphane

last: Emiliani


title: Disease-associated astrocyte epigenetic memory promotes CNS pathology [For 3 times stimulation and Germ Free Mice]

city: Boston

first: Zhaorong

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

overall_design: In this study we generated ATAC-Seq data from TNF-Alpha and PBS stimulated astrocytes from Germ Free Mice and Normal Mice. Normal mice the mouse are stimulated 3 times. Germ Free Mice are stimulated 2 times and 3 times (one dataset each condition).

first: Hong-Gyun

last: Lee

first: Francisco

last: Quintana


title: Biosynthesis of oxyresveratrol in mulberry (Morus alba L.) is mediated by a group of p-coumaroyl-CoA 2'-hydroxylases acting upstream of stilbene synthases

city: Valencia

first: Tomás

last: Matus

state: Valencia

address: Carrer del Catedràtic Agustín Escardino Benlloch

country: Spain

summary: Mulberry (Morus alba L.) is considered a millenary medicinal plant and a food source for silkworms. Different M. alba extracts offer a variety of biological and pharmacological properties that are largely attributed to stilbenoids, a small group of phenylpropanoids, including resveratrol and oxyresveratrol. These are naturally present in non-renewable parts of mulberry trees, impeding their efficient extraction. As a way to bypass this spatiotemporal restriction, we generated cell suspensions from mulberry leaf petioles and demonstrated that the combined use of methyl jasmonate and two different types of cyclodextrins were able to elicit a high production of resveratrol and oxyresveratrol. As oxyresveratrol-producing enzymes are still unknown, we improved the structural and functional annotation of the mulberry genome by integrating short and long-read sequencing data and combined it with time series transcriptome, metabolite and proteome data in response to cell elicitation to identify a complete set of phenylpropanoid and stilbenoid related genes. These included 23 stilbene synthase (STS) genes and a group of six p-coumaroyl-CoA 2'-hydroxylases (C2’Hs), all being highly co-expressed with resveratrol and oxyresveratrol production. We transiently transformed grapevine (Vitis vinifera L.) calli and Nicotiana benthamiana plants to functionally validate the role of C2’Hs in the first committed step of oxyresveratrol synthesis, which provides an alternative substrate for STSs by hydroxylating p-coumaroyl-coA into 2’4’-dihydroxycinnamoyl-CoA. Finally, we offer tools for genomic and transcriptomic exploration also in the context of jasmonate elicitation aiding in the characterization of novel stilbenoid-modifying and regulatory genes in the Morus genus.

overall_design: To investigate the effect at different times of elicitation with methyl jasmonate and cyclodextrin in cell cultures obtained from Morus alba stems.

first: Antonio

last: Santiago


title: PRMT5 inhibition by SCR-6920 leads to downregulation of HIF-1α and exhibits synergistic antitumor activity with bevacizumab in ovarian cancer

city: Shanghai

first: Weijie

last: Chen

address: Furonghua Road 118

institute: Simcere Zaiming Pharmaceutical Co.

summary: Protein arginine methyltransferase 5 (PRMT5) is a desirable anticancer target due to its extensive involvement in cellular processes associated with tumor initiation and progression. This study describes an oral PRMT5 selective inhibitor, SCR-6920, with potent inhibitory activity against multiple tumor types. Cryo-EM structure shows that SCR-6920 binds to PRMT5:MEP50 in a substrate-competitive mode with high binding affinity. Notably, RNAseq analysis links vascular endothelial growth factor (VEGF) to PRMT5 and further studies show that SCR-6920 downregulates hypoxia-inducible factor-1α (HIF-1α) expression through the ubiquitin-proteasome degradation pathway, thereby reducing downstream VEGF secretion. Further in vivo efficacy study demonstrates a synergistic effect for SCR-6920 combined with bevacizumab against ovarian cancer. Additionally, SCR-6920 improves the efficacy of clinical first-line ovarian cancer therapies (paclitaxel, docetaxel, doxorubicin, and olaparib). SCR-6920 has progressed into phase 1 clinical trials for solid tumors, and this study paves the way for its future clinical combination exploration in ovarian cancer.

overall_design: To determine the oncogenic properties of PRMT5, we performed RNA sequence analysis on A2780 cells that were treated with either DMSO or SCR-6920 for 48 hours.

first: Guimei

last: Yang

first: Huixia

last: Dou

first: Feng

last: Zhou


title: Overlapping and distinctfunctions of SPT6, PNUTS and PCF11 in regulating transcription termination [RNA-Seq]

overall_design: Identification of the transcriptomes regulated by SPT6, IWS1, PNUTS, PCF11 and by the double depletion of SPT6+PNUTS and SPT6+PCF11 in HeLa cells


title: Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes

city: Warsaw

first: Dariusz

last: Plewczynski

state: mazovia

address: Banacha 2c

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

summary: Chromosome Conformation Capture (3 C) methods, including Hi-C (a high-throughput variation of 3 C), detect pairwise interactions between DNA regions, enabling the reconstruction of chromatin architecture in the nucleus. HiChIP is a modification of the Hi-C experiment that includes a chromatin immunoprecipitation (ChIP) step, allowing genome-wide identification of chromatin contacts mediated by a protein of interest. In mammalian cells, cohesin protein complex is one of the major players in the establishment of chromatin loops. We present an improved cohesin HiChIP experimental protocol. Using comprehensive bioinformatic analysis, we show that a dual chromatin fixation method compared to the standard formaldehyde-only method, results in a substantially better signal-to-noise ratio, increased ChIP efficiency and improved detection of chromatin loops and architectural stripes. Additionally, we propose an automated pipeline called nf-HiChIP (https://github.com/SFGLab/hichip-nf-pipeline) for processing HiChIP samples starting from raw sequencing reads data and ending with a set of significant chromatin interactions (loops), which allows efficient and timely analysis of multiple samples in parallel, without requiring additional ChIP-seq experiments. Finally, using advanced approaches for biophysical modelling and stripe calling we generate accurate loop extrusion polymer models for a region of interest and provide a detailed picture of architectural stripes, respectively.

overall_design: FA-EGS-HiChIP for SMC1 and standard FA-HiChIP for CTCF performed in the HG00731 lymphoblastoid cell line from the 1000 Genome Project.

first: Karolina

last: Buka

first: Zofia

last: Parteka-Tojek

first: Abhishek

last: Agarwal

first: Michał

last: Denkiewicz

first: Sevastianos

last: Korsak

first: Mateusz

last: Chiliński

first: Krzysztof

last: Banecki

last: Plewczyński


title: Transcriptional profiling of Caenorhabditis elegans nematodes bearing overexpression of NPP-16/CeNUP50 variants.

first: Fasih

middle: Mubtasim

last: Ahsan

state: MA

address: 185 Cambridge Street, CPZN 6500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Deregulated nutrient sensing and metabolism are hallmarks of aging, whereas hormetic nutrient stress extends the lifespan and health span across species. As the only gateway governing nucleocytoplasmic trafficking, the nuclear pore complex (NPC) is critical for most fundamental cellular processes and becomes dysfunctional with age. However, the complexity of NPC composition and structure makes granular determination of the age-related role of specific nucleoporins challenging. Here we demonstrated that NUP50, a nuclear basket protein induced by AMP-activated protein kinase (AMPK) in a post-transcriptional and evolutionarily conserved way, is required for the metabolic rewiring and longevity of hormetic nutrient stress in Caenorhabditis elegans. Of interest, NUP50 sufficiently promotes transcriptomic alteration for lipid catabolism activation, extending lifespan independent of nuclear transport, but through its intrinsically disordered region (IDR) that binds to the promoter of catabolic genes. Our findings uncover a conserved nucleoporin as a metabolic switch bridging energy sensing, metabolic adaptation, and aging regulation by mediating transcription directly.

overall_design: Wild-type (N2) animals and animals bearing integrated transgenic overexpression of full length NPP-16/CeNUP50 (MGH558) or NPP-16/CeNUP50 IDR deletion (MGH721)  were bleach synchronized, plated on OP50-1 NGM agar plates, and collected at adult day 1 for total RNA extraction in biologically independent quadruplicates (12 total samples).

first: Yifei

first: Alexander

last: Soukas


title: Anti-VEGF treatment enhances antitumor responses by targeting regulatory T cells

first: Mohamed-Reda

last: Benmebarek

summary: Cholangiocarcinoma (CCA) shows limited response to systemic treatments including immunotherapy. We initiated an open-label phase II clinical trial testing bevacizumab (anti-VEGF-A) plus tremelimumab (anti-CTLA-4) and durvalumab (anti-PD-L1) in patients with primary liver cancer. Exceptional responses were observed in patients with CCA that were accompanied with moderate to severe, yet manageable immune-related events in the majority of patients. Correlative studies using paired PBMC and serum samples demonstrated a proinflammatory cytokine profile, reinvigoration of precursor exhausted CD8+ T cells, and expansion of regulatory T cell and non-classical monocyte subsets. We utilized subcutaneous, orthotopic as well as plasmid-induced murine CCA models to better understand how anti-VEGF-A enhances anti-tumor immunity induced by anti-CTLA4 plus anti-PD-L1. We describe a novel multi-modal mechanism of how anti-VEGF-A therapy enhances immune checkpoint inhibitor-induced immune responses. The treatment effect was dependent on an increase in tumor infiltrating B cells and IL-12 causing Treg rewiring towards fragile and unstable states. Using a mouse model that genetically ablates VEGFR2 expression on Tregs, we show that the VEGF /VEGFR2 axis on Tregs contributes to the pro-tumoral function of Tregs and supports tumor progression in a syngeneic CCA model. This study provides clinical evidence that simultaneously targeting three immunosuppressive axes, namely VEGF-A, CTLA-4 and PD-L1, can elicit strong anti-tumor immunity to potentiate CCA regression and merits broader evaluation in other cancers.

overall_design: In-depth immune transcriptome profiling at single cell level was performed by applying 5’ scRNA-sequencing (10X Genomics) to 14 paired PBMC samples from the triple treated cohort obtained at baseline (prior to treatment initiation) and 22 days post triple therapy.

first: Cihan

last: Oguz

first: Justin

last: Lack

first: Tim

last: Greten


title: LILRB3 agonism and antagonism using monocolonal antibodies

city: Houston

first: Shu-Hsia

last: Chen

address: 6670 Bertner Avenue

institute: Houston Methodist

summary: To explore the downstream signaling of the LILRB3 receptor, agonist and antagonist antibodies were used. As the LILRB3 ligand remains unknown, antibody mediated signalling is our best means of further ellucidating the mechanisms of LILRB3. This study explores LILRB3 in the context of AML, using the u937 cell line as a model.

overall_design: U937 cells were treated with IFNy to stimulate LILRB3 expression. Subsequently U937 cells were treated with antagonist or agonist antibodies and transcriptional profile was compared to U937 cells treated with nonspecific IgG control. Each group contains 3 replicates

first: Sunny

last: Mai

first: Alan

last: Hodges

first: Ping-Ying

last: Pan


title: Investigation of the RNMT/RAM RNA interactome in mouse embryonic stem cells [Brain_seCLIP]

city: Dundee

first: Fiona

last: Haward

address: Life Sciences, Dow St

institute: University of Dundee

summary: Pilot investigation to determine the endogenouse RNA-binding targets of the cap methlytransferase complex RNMT/RAM in mouse ES cells

overall_design: RNMT seCLIP (a single-end adaptation of the eCLIP method) was perfomed in undifferentiated mouse ES cells following the protocol from Van Nostrand et al (2017). After lysis, RNA was digested with an optimised concentration of RnaseI and immunprecipitation carried out using either an antibody for RNMT or an isotype control. A size-matched input control was prepared from each sample.

first: Victoria

last: Cowling


title: bovine muscle transcriptome

city: Hohhot

first: lin

last: zhu

state: Antioxidants

address: The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock Co-built by the School of Life Sciences of Inner Mongolia University and the Ministry of Agriculture

institute: Inner Mongolia University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

overall_design: Muscle mRNA profiles of 24-month-old wild-type (WT) and MSTN+/- cattle

first: Lin

last: Zhu


title: Macrophage OPA1 maintains anti-inflammatory state and metabolic homeostasis by regulating metabolic reprogramming and mtDNA-cGAS-STING pathway

status: Public on Mar 13 2025

first: Hong

last: Zhang

address: 600 Yishan Road

department: Shanghai Diabetes Institute

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Adipose tissue macrophages (ATMs) play an important role in regulating adipose tissue inflammation and metabolic homeostasis. Mitochondria are pivotal hubs for macrophage-mediated inflammation. Here, we observed a negative correlation between macrophage optic atrophy type 1 (OPA1) and obesity in both humans and mice. Myeloid OPA1-deficient mice were susceptible to obesity and related systemic insulin resistance, glucose dysregulation, and hepatic steatosis upon high-fat diet (HFD). This is due to the impairment of M2-like macrophage features and the promotion of pro-inflammatory phenotypes. Mechanically, OPA1 loss resulted in metabolic reprogramming, as evidenced by reduced mitochondrial respiration, increased glycolysis, and elevated mtDNA release. This activated the cGAS-STING-IRF7 pathway in M2 macrophages, inducing anti-inflammatory conversion to a pro-inflammatory state. In contrast, myeloid OPA1 transgenic mice exhibited reduced inflammation and obesity. Collectively, we identified macrophage OPA1 as a novel regulator of immune metabolism. Targeting OPA1 may represent an effective therapeutic strategy against obesity and metabolic disorders.

overall_design: To investigate the influence of changes in transcriptional patterns that modulate macrophage function via OPA1 signaling, we performed RNA-sequencing (RNA-seq) on BMDMs isolated from OPA1f/f versus OPA1f/f; Lyz2-Cre mice after IL-4 stimulation for 24 h.

first: Daixi

last: Wang

first: Cheng

last: Hu


title: Structural Insights into DNMT3A-3L-Mediated de novo DNA Methylation on Chromatin

city: Grand Rapids

first: Peter

last: Jones

address: 333 Bostwick Ave NE

department: Center of Epigenetics

institute: Van Andel Research Institute

summary: DNA methylation is one of the critical epigenetic mechanisms, yet its establishment and regulation during mammalian embryonic development remain poorly understood. DNA methyltransferases DNMT3A and DNMT3B require catalytically inactive variants such as DNMT3L or DNMT3B3 to function effectively during gametogenesis and early embryogenesis. Abnormal DNA methylation can lead to genomic instability and oncogenesis, underscoring the importance of deciphering its molecular mechanisms, especially during embryonic development, where DNMT3L is primarily expressed. Here, we present a high-resolution cryo-EM structure of the nucleosome-bound full-length DNMT3A2-3L and oligomeric structures of the DNMT3A2-3L complex in its nucleosome-free state. Notably, in the nucleosome-bound complex, we observed a 180° rotational difference in the C-terminal “Switching Helix” of DNMT3L compared to its counterpart in DNMT3B3 within the DNMT3A2-3B3-NCP complex, eliminating the direct interactions with the nucleosome acidic patch. Instead, we identify a previously unrecognized mechanism in which the DNMT3L ADD domain significantly contributes to nucleosome engagement, while the DNMT3A PWWP domain inhibits nucleosome binding, suggesting an additional layer of regulatory complexity. Furthermore, our first-ever discovery of the novel oligomeric arrangement of DNMT3A2-3L in its nucleosome-free state highlights its dynamic assembly and indicates potential allosteric regulation. Based on the structures and supporting biophysical data, we propose that the DNMT3A-3L complex senses histone tail modifications and dynamically searches for and engages with linker DNA by selecting or reorganizing the complex to a more stable and active heterotetrameric state, shedding light on its role in co-regulating DNA methylation on chromatin.

overall_design: To assess the role of DNMT3L C-terminal “Switching Helix” and ADD domain in restoring DNA methylation in cells, we analyzed DNA methylation in DKO8 cells expressing either wild-type or mutant DNMT3L 56 days post-infection using the Infinium MethylationEPIC BeadChip array.

first: Minmin

last: Liu


title: Single cell RNA sequencing of human normal and failing heart

city: Wuhan

first: Si

state: Hubei

address: Jiefang Avenue

institute: Huazhong University of Science and Technology

summary: we performed single cell RNA sequencing (scRNA-seq) in human normal and failing hearts. Heart tissues from 3 ICM and 2 DCM patients, as well as heart tissues from 3 donors were used for scRNA/TCR-seq.

overall_design: Establishing a comprehensive cell atlas of immune cells in human heart failure at single cell level.

first: Ting-Ting

last: Tang

first: Xiang

last: Cheng

first: Nian-Guo

last: Dong


title: Genome-wide maps of nuclear lamina interactions in AML12 cells upon MATR3 KD  [DamID-Seq]

first: Xuan

last: Cao

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health,  Chinese Academy of Sciences

summary: We performed DamID-seq assay in WT and MATR3-depleted AML12 cells to investigate the Lamina-associated-domains (LADs) affected by loss of MATR3.

overall_design: Two replicates for each sample.

first: Bo

last: Wen

first: Yuwen


title: Neuronal chromatin remodeling factors in the mammalian nervous system [RNA-seq]

city: Mississauga

first: Ho Sung

last: Rhee

state: ON

address: 3359 Mississauga Rd

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

summary: Chromatin remodeling factors play important roles in accessibility formation of regulatory DNA. The mechanism by which chromatin remodeling factors regulate regulatory DNA regions that activate expression of cell type-specific genes during the nervous system development remains unknown. Chromatin remodeling complexes have neuron-specific factors, which are often mutated in patients with neurological disease. Here we demonstrate that neuronal chromatin remodeling factors activate neuronal gene expression during the nervous system development.

overall_design: Examination of RNA-seq profiles of mouse ES cell-derived neurons by deep sequencing

first: Kaitlin

last: Montanera

first: Alyssa

last: Ialongo

first: Ssu-Yu

last: Yeh


title: Expansion of endogenous T cells in CSF of pediatric and young adult CNS tumor patients undergoing locoregional delivery of IL13R⍺2-targeting CAR T cells: an interim analysis

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

summary: Outcomes for pediatric brain tumor patients remain poor, yet there is optimism that chimeric antigen receptor (CAR) T cell therapy can improve prognosis. Here, we present interim results from the first six patients treated on an ongoing phase I clinical trial (NCT04510051) of IL13BBζ-CAR T cells delivered weekly into the lateral cerebral ventricles. Our preliminary clinical findings suggest CAR T cell therapy is safe and well tolerated in both lymphodepleted and nonlymphodepleted patients, and may offer modest clinical benefit. In addition to our clinical findings, we carried out a series of correlative analyses leveraging single cell genomics and orthogonal methods to profile PBMCs, mononuclear cells in the cerebrospinal fluid (CSF) and post-treatment tumors. leveraging both single cell genomics and more traditional approaches. These studies identified important interactions between CAR T infusions and the endogenous immune system. Notably, we identified and characterized a population of expanding CAR- CD8+ T cells identified in the CSF. Furthermore, we found these and other immune changes observed in the CSF were not well captured by PBMCs. Conversely, we provide evidence of clonally expanded TCRs shared between CSF and post-treatment tumor. While these data are limited, our findings suggest T cell dynamics observed in the CSF are reflected in the tumor, but not in PBMCs. Taken together, these initial findings provide support for continued investigation into locoregionally-delivered IL13BBζ-CAR T cells for children and young adults with brain tumors, and provide important insights into endogenous immune response during therapy.

overall_design: This study included scRNA- and scTCR-seq from cerebrospinal fluid (CSF), peripheral blood mononuclear cells (PBMCs), engineered CAR T products, and tumors from 5 pediatric patients with brain tumors as part of an ongoing phase I clinical trial with IL13BBζ-CAR T cells. Patient's CSF and PBMCs were sequenced at multiple time points during the course of CAR T treatment. Tumor samples included both pre- and post-CAR T treatment samples. Some patients received lymphodepletion and others did not. Comparisons of scRNA- and scTCR-seq were performed between windows of radiographic response and non-response, among different time points of the CAR T treatment, and between patients that did not receive lymphodepletion and did receive lymphodepletion.

first: Leo

middle: D

first: Angela

last: Taravella Oill

first: Suzette

last: Blanchard

first: Melody

last: Wu

first: Jonathan

last: Hibbard

first: Colt

last: Egelston

first: Sean

last: Sepulveda

first: Lance

last: Peter

first: Julie

last: Kilpatrick

first: Margarita

last: Muñoz

first: Tracey

last: Stiller

first: Noah

last: Shulkin

first: Jamie

last: Wagner

first: Ally

last: Dolatabadi

first: Monica

last: Nisis

first: Jennifer

middle: K

last: Shepphird

first: Gabriela

last: Sanchez

first: Chetan

last: Lingaraju

first: Mishika

last: Manchanda

first: Heini

last: Natri

first: Léonce

last: Kouakanou

first: Grace

last: Sun

first: Cheryl

last: Oliver-Cervantes

first: Joseph

last: Georges

first: Shilpa

last: Shahani

first: Maryam

last: Aftabizadeh

first: Stephen

last: Forman

first: Saul

last: Priceman

last: Ressler

first: Leonidas

last: Arvanitis

last: Cotter

first: Massimo

last: D’Apuzzo

first: Benita

last: Tamrazi

first: Behnam

last: Badie

first: Tom

last: Davidson

first: Christine

last: Brown


title: Neuronal chromatin remodeling factors in the mammalian nervous system [ATAC-seq]

first: Ho Sung

last: Rhee

overall_design: Examination of ATAC-seq profiles of mouse ES cell-derived neurons by deep sequencing

first: Montanera

last: Kaitlin

first: Ialongo

last: Alyssa

first: Yeh

last: Ssu-Yu

first: Rhee

last: Ho Sung


title: CEPD proteins activate N starvation response genes by interfering with the repressive activity of transcription factors TGA1 and TGA4 [II]

city: Göttingen

first: Christiane

last: Gatz

state: Lower Saxony

address: Julia-Lermontowa-Weg 3

department: Plant Molecular Biology and Physiology

institute: Georg-August-University Göttingen

summary: Plants have developed a variety of adaptive responses to variable nitrogen (N) conditions in the soil. N starvation leads to profound alterations in the transcriptome, allowing improved N acquisition, allocation and remobilization. In Arabidopsis thaliana, N starvation-induced CEPD (C-TERMINALLY ENCODED PEPTIDE DOWNSTREAM) proteins have been shown to be required for transcriptional activation of genes involved in high affinity nitrate transport. CEPDs belong to a plant-specific class of glutaredoxin-like proteins (called ROXYs in A. thaliana) that interact with TGACG-binding transcription factors (TGAs). Here show that TGA1 and TGA4 act as molecular links between CEPDs (ROXYs 6-9) and target promoters. CEPDs permit activation of gene expression by binding to TGA1/4 at target promoters, thereby interfering with a strong repression mechanism that is recruited by TGA1/4. Although CEPDs resemble glutaredoxins with glutathione-dependent oxidoreductase activity, a ROXY9 variant with a cysteine to serine exchange at the putative catalytic cysteine can confer low nitrogen-induced target gene expression. This finding excludes that ROXY9 functions by altering the redox state of target proteins. Still, changing the conserved binding site from CCLC to CPYC abrogated ROXY9 activity suggesting that the PY sequence may interfere with ROXY9-protein interactions that are required to render the TGA1/4-mediated repressive mechanism dysfunctional.

overall_design: RNA was prepared from roots of Col-0 wild-type, tga1 tga4 double mutant, roxy6 roxy7 roxy8 roxy9 quadruple mutant (cepd), and cepd tga1 tga4 hexuple mutant plants cultivated under FN/FN and FN/LN conditions. Samples are from one experiment with four independent biological replicates. For each biological replicate, roots were harvested from 10 plantlets grown together on one plate.

first: Corinna

last: Thurow

first: Anja

last: Pelizaeus

first: Pascal

last: Mrozek

first: Ben

last: Hoßbach

first: Jelena

last: Budimir

first: Kerstin

last: Schmitt

first: Oliver

last: Valerius

first: Gerhard

last: Braus


title: CEPD proteins activate N starvation response genes by interfering with the repressive activity of transcription factors TGA1 and TGA4

overall_design: RNA was prepared from roots of Col-0 wild-type and roxy6,7,8,9 quadruple mutant (cepd) plants subjected to LN conditions. Samples from four independent experiments with each sample containing roots from 50 plantlets grown on five separate plates were analyzed. For Col-0, we had to exclude one data set since the corresponding sample had been contaminated with leaf material.


title: An atypical atherogenic chemokine that promotes advanced atherosclerosis and hepatic lipogenesis

city: Munich

first: Omar

last: El Bounkari

address: Feodor-Lynen-Straße 17

department: Institute for Stroke and Dementia Research (ISD)

institute: LMU Klinikum

summary: Atherosclerosis is the underlying cause of myocardial infarction and ischemic stroke. It is a lipid-triggered inflammatory condition of arterial vessels driven by cytokines and chemokines. Chemokines that affect both vascular and metabolic pathologies are rare. Here we show that D-dopachrome tautomerase (D-DT)/macrophage migration inhibitory factor-2 (MIF-2), a paralog of the atherogenic cytokine MIF, is a novel atypical chemokine promoting athero-sclerotic plaque formation and hepatic lipid accumulation. Mif-2 deficiency and its pharma-cological blockade in hyperlipidemic atherogenic Apoe–/– mice protected against lesion formation and vascular inflammation in early and advanced atherogenesis. MIF-2 promoted monocyte migration and arrest on aortic endothelial monolayers, promoted B-cell recruitment, and increased foam cell formation. Employing biochemical and cellular assays, we identified CXCR4 as a novel receptor for MIF-2. Notably, Mif-2–/–Apoe–/– mice exhibited decreased plasma lipid levels, smaller livers, and reduced hepatic lipid accumulation compared to Apoe–/– mice. Comparison of the hepatic transcriptome and lipidome between Apoe–/– and Mif-2–/–Apoe–/– mice revealed a notable enrichment of lipogenesis-related pathways, triacylglycerides, diacylglycerides, and cholesterol esters in Mif-2-proficient mice. Mechanistic experiments in hepatocytes suggested that MIF-2 regulates activation of SREBP transcription factors to induce down¬stream lipogenic genes, while upstream, this pathway was mediated by the receptors CD74 and CXCR4, and PI3K/AKT but not AMPK signaling. Proximity ligation and FLIM-FRET multiphoton-microscopy indicated that CXCR4 and CD74 form a MIF-2-inducible heteromeric complex. Lastly, MIF-2 was found upregulated in unstable human carotid plaques from atherosclerotic patients undergoing carotid endarterectomy (CEA), suggesting a role for MIF-2 in advanced stages of athero¬sclerosis. Moreover, plasma concentrations of MIF-2 were increased in patients with coronary artery disease (CAD) and correlated with disease severity. Together, these data identify MIF-2 as a novel atherogenic chemokine and CXCR4 ligand associated with CAD that not only promotes lesion formation and vascular inflammation, but also affects hepatic lipogenesis in a CD74/CXCR4/SREBP-mediated manner. MIF-2 may thus be a novel player in atherosclerotic and metabolic disease.

overall_design: To understand the dual role of MIF-2 in advanced atherosclerosis and lipid metabolism, we compared the effects of Mif-2 deficiency in Apoe–/– mice (DKO) on differential gene expression in the liver compared to Apoe–/– (WT) control mice after 12 weeks of HFD.

first: Ji

last: Hao

first: Bishan

last: Yang


title: POT1 mutations identify inferior outcomes in chronic lymphocytic leukemia and disrupted telomere biology function

city: 江苏 / 南京市 / 鼓楼区

first: Jiazhu

last: Xu

address: 广州路300号

institute: the First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital

summary: Telomere protection 1 (POT1) is an important subunit in the shelterin complex, considered the telomere protector. POT1 dysfunction may lead to telomere length dysregulation and genomic instability. Both germline and somatic POT1 mutations have been identified in CLL patients, suggesting the development of the disease. This study aimedto evaluate the occurrence of POT1 mutations throughout CLL's progression and determine their prognostic significance.

overall_design: Our study included four hundred and forty-six patients with CLL from our center, including 390 TN (treatment-naive) patients and 56 R/R (relapse/refractory) patients. All patients were diagnosed from January 2017 to December 2022 based on International Workshop on CLL guidelines. Essential clinical characteristics and biological parameters were obtained from medical records. The next-generation sequencing panel included 126 common driver genes in lymphoid malignancies. To gain insight into the potential pathogenic mechanism of POT1 mutations in CLL, we performed RNA sequencing (RNA-seq) in three POT1 mutant and matched three wild-type CLL patients. All the differentially expressed genes (DEGs) were used to perform functional enrichment analysis to identify potential biological functions.

last: Wu

first: Bihui

last: Pan

first: Jiale

last: Zhang

first: Zhangdi


title: Insulin promotes LTP in mice by switching the energy substrate preference of astrocytes to fatty acids [Rattus]

city: Baltimore

first: Norman

last: Haughey

address: 2912 Saint Paul St

institute: Johns Hopkins School of Medicine

summary: A total of 37,185 transcripts were detected from RNA extracts from primary cultured astrocytes, and neurons isolated from Rattus hippocampus. After exposing astrocytes to insulin (200 nM) for 6h, 883 transcripts were upregulated 2SD or greater and 852 transcripts were downregulated 2SD or greater compared with vehicle treated control astrocyte cultures. This general pattern of gene expression was maintained for at least 12h in astrocytes where the expression of 811 genes were increased and 849 genes decreased compared with vehicle treated astrocytes. Informatic interrogation of genes with expression greater or less than 2 SD at the 6h and 12h time points in astrocytes identified signaling pathways associated with fatty acid activation, fatty acid β-oxidation, cAMP, gap junction, dendritic cell maturation ceramide degradation, triacylglycerol degradation and phospholipase activation. The functional association of gene changes in astrocytes after treatment with insulin for 6 and 12 h were almost exclusively related to the synthesis and storage of diacylglycerides, sterols, and other lipids. After exposing primary cultured Rattus hippocampal neurons to insulin (200 nM) for 6h, 753 genes were upregulated and 660 genes downregulated. This general pattern of gene expression was maintained for at least 12h when 768 genes were upregulated versus 736 genes downregulated in insulin treated neurons. Changes in gene expression profiles of neurons exposed to insulin for 6h, and 12h identified signaling pathways associated with actin-based motility, tight junctions, dendritic cell maturation, serotonin receptor, CREB (cAMP-response element binding protein), and axonal guidance. The functional association of gene changes in neurons after treatment with insulin for 6h, and 12h were largely related to neuroprotective/neurotrophic effects including tyrosine kinase tec-1 activation, synaptogenesis activation, and regulation of actin based cytoskeleton activation by the Rho family GTPases.  These data suggest that insulin regulates neurotrophic signaling/functions in neurons and primary regulates lipid metabolism associated with fatty acid oxidation in astrocytes.

overall_design: Effect of Insulin exposure in the regulation of lipid metabolism in the brain.  There are two cell  types, astrocytes and neurons.  For each cell type one sample was treated with insulin for either 6hours, or 12hours and compared to a control of 0minutes treatment, for a total of six samples.

middle: J

first: Saja

middle: S

last: Khuder

first: Bouchra

last: Taib

first: Pragney

last: Deme


title: Insulin promotes LTP in mice by switching the energy substrate preference of astrocytes to fatty acids [Mus]

summary: A total of 46,202 transcripts were detected from RNA extracts from Mus musculus hippocampus. Genes were filtered by setting the minimum FPKM value to log2, followed by a parametric statistical test to identify differentially expressed genes. Within 15 min of insulin administration, 181 transcripts were upregulated and 55 were downregulated. At this early time-point, genes with altered expression were almost exclusively related to neuronal functions. Within 1h following insulin treatment, a similar number of transcripts (173) were upregulated and the expression of three-fold more genes (140) were downregulated. At this time-point, 12 genes associated with the release of lipids and fatty acids were increased. Within 6h following intranasal insulin administration, the number of transcripts with elevated expression remained similar (164), but the number of genes with reduced expression declined to 77. At this time point the genes with elevated expression were largely relate to lipid metabolism. These data demonstrate that insulin delivered directly to the brain produces a rapid, robust, and time-dependent modification in gene expression related to lipid metabolism.

overall_design: Effect of Insulin exposure in the regulation of lipid metabolism in the brain


title: Loss of PRICKLE1 in the myometrium leads to reduced fertility, abnormal myometrial architecture, and aberrant extracellular matrix deposition in mice.

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: Uterine leiomyomas (UL) are the most prevalent benign tumors of the female reproductive tract, originating from the myometrium and affecting up to 75% of reproductive-age women. Symptoms of UL include pelvic pain, pressure, dysmenorrhea, menorrhagia, anemia, and reproductive dysfunction. Currently, there is no effective long-term pharmacotherapy for UL, making them the leading cause of hysterectomies in the United States. The lack of treatment options is attributed to the absence of accurate animal models and a limited understanding of UL pathogenesis. Previous research has shown the ablation of Rest within the myometrium results in a UL phenotype in mice. PRICKLE1, also known as Rest-interacting LIM-domain Protein (RILP), plays a significant role in the nuclear localization of REST and Wnt/planar cell polarity (PCP) signaling, making it a critical target for UL studies. In the context of PCP, UL structural proteins show abnormal organization, structure, and expression levels, potentially influenced by PRICKLE1 loss. The exact role of PRICKLE1 in UL pathogenesis remains unclear but may be crucial for developing long-term pharmacotherapies. To explore PRICKLE1's role in UL, we developed a myometrial conditional knockout (cKO) of Prickle1 using our myometrial-specific icre. Our findings demonstrate that PRICKLE1 loss in the myometrium results in a UL phenotype characterized by fibrotic structures, excessive extracellular matrix (ECM) production, altered ECM and smooth muscle cell organization, increased Esr1 and Pgr expression, and dysregulated Wnt/PCP signaling. This novel mouse model serves as a valuable preclinical tool for understanding UL pathogenesis and developing future pharmacotherapies.

overall_design: Whole uteri of Prickle1 f/f MiC cKO and control mice aged 6 months were isolated. Control samples (n=3) were pooled and cKO samples (n=3) were pooled.

first: Roberts

last: Emily

first: Bhurke

last: Aishwarya

first: Ganeshkumar

last: Sornakala

first: Gunewardena

last: Sumedha

first: Arora

last: Ripla

first: Chennathukuzhi

last: Vargheese


title: Primary Trophoblasts treated with Corticotropin Releasing Hormone (CRH)

city: Seattle

first: Alison

last: Paquette

state: WA

address: 1900 Ninth Avenue

department: Center for Developmental Biology and Regenerative Medicine

institute: Seattle Children's Research Institute

summary: Primary trophoblast cells were treated with corticotropin releasing hormone (CRH) and then subjected to RNA extraction and sequencing.

overall_design: Primary trophoblast cells were treated with 0, 10, or 100nM corticotropin releasing hormone (CRH) for 24 or 72 hrs.


title: ATAC-seq of small cell lung cancer cell lines

city: Hamamatsu

first: HIROFUMI

last: WATANABE

state: Select State

country: Japan

institute: Hamamatsu University of Medicine

summary: Assessment of the chromatin accessibility landscape by bulk ATAC-seq comparing Lu139-NEUROD1 with Lu139-EGFP control and H524-ASCL1 with H524-EGFP control

overall_design: Lu139-NEUROD1 cells, Lu139-EGFP cells, H524-ASCL1 cells, and H524-EGFP cells were treated with doxycycline for 72 hours and were collected at 2.0 × 105 cells/tube in duplicate at 4°C. ATAC-seq was performed

first: Hirofumi

last: Watanabe

first: Yusuke

last: Inoue


title: Erlotinib Suppresses Tumorigenesis in a Mouse Model of Colitis-Associated Cancer

city: Galveston

first: Haiping

last: Hao

address: 301 University Blvd

institute: UTMB NGS Core

summary: Colitis-associated cancer (CAC) in inflammatory bowel diseases exhibits more aggressive behavior than sporadic colorectal cancer; however, the molecular mechanisms remain unclear. No definitive preventative agent against CAC is currently established in the clinical setting. We investigated the molecular mechanisms of CAC in the azoxymethane/dextran sulfate sodium (AOM/DSS) mouse model and assessed the antitumor efficacy of erlotinib, a small molecule inhibitor of the epidermal growth factor receptor (EGFR). Erlotinib premixed with AIN-93G diet at 70 or 140 parts per million (ppm) inhibited tumor multiplicity significantly by 96%, with ~60% of the treated mice exhibiting zero polyps at 12 weeks. Bulk RNA-sequencing revealed more than a thousand significant gene alterations in the colons of AOM/DSS-treated mice, with KEGG enrichment analysis highlighting 46 signaling pathways in CAC development. Erlotinib altered several signaling pathways and rescued 40 key genes dysregulated in CAC, including those involved in the Hippo and Wnt signaling. These findings suggest that the clinically-used antitumor agent erlotinib might be repurposed for suppression of CAC, and that further studies are warranted on the crosstalk between dysregulated Wnt and EGFR signaling in the corresponding patient population.

overall_design: To investigate the genetic, epigenetic, and signaling pathway mechanisms by which CAC manifests and is therapeutically affected by erlotinib, differential gene expression profile analysis was performed using RNA sequencing of total RNAs isolated from the colons of C57BL/6J mice. The comparative groups consisted of (1) vehicle control, (2) CAC, and (3) CAC+Erlotinib treatment. Gene ontology and KEGG pathway enrichment was performed on the gene lists.

first: Max

last: Liu

first: Xiaoying

last: Zhong

first: Srikruthi

last: Krishnachaitanya

first: Rongliwen

last: Ou

first: Roderick

middle: H

last: Dashwood

first: Don

middle: W

last: Powell

first: Qingjie

last: Li


title: Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

summary: Purpose: To investigate the mechanism of how Notch-Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods:  Approximately 1000 hearts dissected from 96 hpf Tg(myl7:mCherry) embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K-AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2-PI3K signaling pathway.

overall_design: 96 hpf Tg(myl7:mCherry) zebrafish embryos treated with DMSO or DAPT 100 μM were collected for RNA-seq.

first: Jin-xiu

last: Liang

last: Cheng

first: Pei-dong

last: Han


title: Changes in the primary cilia in Alzheimer’s disease early development is associated with alterations in the axon initial segment.

city: beijing

first: HAN

last: WANG

state: beijing

address: peking university

institute: peking university

summary: Many pathological alterations happen decades before cognitive decline in Alzheimer’s disease (AD) patients. Identifying the earliest changes in AD neurons is crucial for AD diagnosis and therapy development targeting upstream events in AD pathogenesis. Here, we demonstrated the early common alterations in the hippocampal neurons from 3 familial AD mouse lines (APP/PS1, 5FAD, 3*Tg) are associated with the primary cilium morphology and ciliary GPCRs. The primary cilia interact with the axon initial segment (AIS) through ciliary GPCR signaling and transcriptional regulation of AIS mater organizer protein AnkG. Our results provide new insights for AD pathogenesis especially during early stage, and a novel mechanism by which ciliary signaling may modulate neuronal activity through regulating the structure and plasticity of the AIS. Understanding AD development at early stage could help identifying new potential targets for AD prevention and therapy.

overall_design: To investigate the specific function of SSTR3 in early AD, we used wild-type mice and SSTR3-knocked out mice. Then we conducted RNA sequencing analysis using the hippocampal tissues from  the two types of mice to compare gene expression.

last: Wang

first: Zhehui

last: Sun


title: LARP6 promotes carcinogenic features of triple negative breast cancer cell line by directly modulating alternative splicing of associated genes

city: YinChuan

first: Li

last: Guo

address: Victory Street

institute: Ningxia Medical University

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

overall_design: Refer to individual Series