title: Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction [WGS]

city: Munich

first: Stephan

last: Hamperl

state: Bayern

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz-Zentrum Munich

summary: Transcription-replication conflicts (TRCs) can provoke genome instability. Progressing transcription and replication machineries profoundly impact their underlying chromatin template and thus, conflict sites are vulnerable to chromatin and epigenome alterations. Here, we engineered an inducible TRC reporter system using a genome-integrated R-loop-prone sequence. Using this system, we characterized the dynamic changes of the local chromatin structure inflicted by TRCs, leading to reduced nucleosome occupancy and replication fork blockage. Consequently, inducing a handful TRCs on the genome results in a measurable global replication stress response. We also find a TRC-specific increase in H3K79 methylation at the R-loop forming TRC-site. Accordingly, inhibition of the H3K79 methyltransferase DOT1L leads to increased cellular TRCs and exacerbated DNA damage response, suggesting that deposition of this mark is required for effective detection and resolution of TRCs. Thus, our work highlights the molecular dynamics and reveals specific epigenetic modifiers bookmarking TRC sites, relevant to cancer and other diseases.

overall_design: Whole Genome Sequencing of sonicated genomic DNA of a monoclonal cell line

first: Marcel

last: Werner

first: Manuel

last: Trauner

first: Tamas

last: Schauer


title: LncRNA H19 promoted alcohol-associated liver disease through dysregulation of alternative splicing and methionine metabolism

status: Public on May 01 2025

city: Indianapolis

first: Zhihong

last: Yang

country: USA

institute: Indiana University

type: Expression profiling by high throughput sequencing

summary: Long non-coding RNAs (lncRNAs) constitute a significant portion of the human genome. LncRNA H19 is among the first identified lncRNAs and is highly expressed during fetal development but decreases in the liver shortly after birth. H19 is reactivated during the development of various liver diseases; however, the role of H19 in the pathogenesis of alcohol-associated liver disease (ALD) remains elusive. Elevated levels of H19 were observed in human peripheral blood and livers of patients with alcohol-associated cirrhosis and alcohol-associated hepatitis. Similar observations were also seen in the livers of ethanol-fed mice. Hepatic overexpression of H19 promoted ethanol-induced liver steatosis and injury. Metabolomics analysis revealed a significant decrease in methionine levels in H19-overexpressed mouse livers. H19 was found to inhibit Betaine-homocysteine methyltransferase (BHMT), a key enzyme in methionine synthesis. H19 regulated the alternative splicing process of Bhmt through Polypyrimidine tract-binding protein 1 (PTBP1), resulting in a decrease in the Bhmt protein-coding variant. Maternally specific knockout of H19 (H19Mat+/-) or liver-specific knockout of the H19 differentially methylation domain (H19DMDHep-/-) in ethanol-fed mice led to an increase in BHMT expression and improvement in hepatic steatosis. Additionally, restoration of BHMT rescued H19 overexpression-mediated ethanol-induced fatty liver. In summary, we identified a novel mechanism of H19 regulating BHMT alternative splicing and methionine metabolism through PTBP1 in ALD. Targeting the H19-PTBP1-BHMT pathway could be a potential therapeutic intervention in patients with ALD.

overall_design: the RNA Sequencing analysis with the livers from ethanol-fed AAV-H19 injected and AAV-null injected mice


title: Effect of cigarette smoking on human tracheal epithelium

city: London

first: Ahmed

last: Alhendi

address: 5 University St

country: United Kingdom

institute: UCL

summary: We used single-cell RNA sequencing (scRNA-seq) to elucidate the effect of cigarette smoking on cell type populations in the human tracheal epithelium

overall_design: To investigate the effects of smoking on the human tracheal epithelium, we took tracheal brushings from three never-smoker patients and three current-smoker patients and performed scRNAseq.

first: Maral

middle: J

last: Rouhani

first: Imran

last: Uddin

first: Masahiro

last: Yoshida

first: Sandra

last: Gomez Lopez

first: Sam

last: Janes


title: A novel modeling of high-grade transformation in IDH mutant glioma

city: BETHESDA

first: Zachary

last: Sergi

address: 37 CONVENT DR

department: Neuro-Oncology Branch

institute: National Cancer Institute

summary:
Background. High-grade transformation (HT) is a key feature of IDH-mutant glioma, which is inevitable and unpredictable. Both genomic and metabolomic landscapes are going through dynamic processes during the transformation. Although HT phenomena have been observed clinically, the research of mechanisms underlying HT have been limited by the lack of in vitro models that can recapitulate the evolution of malignant transformation.
Methods. Here we established a unique pair of cell lines that was generated using tumor samples from the same patient at different stages of the disease. 403L cell line was obtained when patient’s tumor was astrocytoma, WHO grade 2 and 403H cell line was obtained when the tumor was transformed to astrocytoma, WHO grade 4. Using genomic, transcriptomic, and metabolomic analyses, the two cell models have been characterized extensively. The cell lines have been used to establish orthotopic xenograft models of the disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 403H & 403L cells. Each group was comprised of 3 biological replicates.

first: Zach


title: Super Pol II Domains enhance minor ZGA through 3D-interaction to ensure the integrity of major transcriptional waves in ZGA delayed mammals (porcine pol2)

city: Yangling

first: zhang

last: yong

state: Shanxi

address: No.3 Taicheng Road

country: China

institute: Northwest A&F University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Zygotic genome activation (ZGA) represents the inaugural post-fertilization transcription event. In mouse, RNA polymerase II (Pol II) initiates embryonic transcription through a step-wise transition, but the ZGA initiation process remains unclear in non-rodents. Here, Pol II profiling in bovine and porcine embryos, combined with multi-omics data across four mammalian species, revealed strong intergenic Pol II clusters, termed super Pol II domains (SPDs), that boost minor ZGA gene expression via chromatin interactions in bovine. Intriguingly, a similar strategy was found in human embryos, which also exhibit delayed ZGA followed by rapid up-regulation of minor ZGA genes. By contrast, these genes are precociously activated in porcine and mouse gametes before fertilization. Moreover, disruption of SPD structure, which decreases two minor ZGA genes KLF17 or DUXA expression, and knockdown them in bovine, leads to aberrant gene activation and impeded embryogenesis. Our findings highlight SPD enhancement as a species-specific evolutionary adaptation for initiating transcription in bovine and human embryos, thus illustrating previously underappreciated diversity in mammalian reproductive developmental strategies.

overall_design: The multiomics data (methylation, ChIP-seq,RNA-seq and Hi-C) on gametes and early embryos in bovine and porcine.

first: Jingcheng

last: Zhang

first: Hengkuan

last: Li

first: Linmi

first: Jie

last: Wu

first: Linjie

last: Song

first: Xin

last: Liu

first: Wenying

first: Zixiao

first: Mei

last: Jiao

first: Mingyang

last: Hu

first: Hexu

first: Zhangyuan

last: Pan

first: Binqiang

last: Shi

first: Yong

last: Wang

first: Debao

first: Yunxia

last: Zhao

first: Gang

last: Ren

first: Shuhong


title: Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction [ChIPseq]

first: Stephan

last: Hamperl

country: Germany

overall_design: Chromatin Immunoprecipitation-sequencing experiment  for RNA polymerase II Serine-2 phosphorylation and Histone H3 in synchronized U-2OS Clone#12 cells. Cells were synchronized by 2x thymidine block and release into S-phase for 4h. Cells were treated with  0 or 1 µg/mL Doxycycline. Immunprecipitations were conducted in biological triplicate.

first: Marcel

last: Werner

first: Manuel

last: Trauner

first: Tamas

last: Schauer


title: PPP2R1A mutations portend improved survival after cancer immunotherapy

city: Houston

first: Sanghoon

last: Lee

state: TX

address: 1881 East Road

institute: The University of Texas MD Anderson Cancer Center

summary: Immune checkpoint blockade (ICB) therapy is effective against many cancers, though resistance remains a major issue and novel strategies are needed to improve clinical outcomes. We studied ICB response in a cohort of patients with ovarian clear cell carcinoma (OCCC), a cancer type that poses significant clinical challenges and lacks effective therapies. Here we observed significantly prolonged overall and progression-free survival in patients with tumors harboring PPP2R1A inactivating mutations (PPP2R1Amut). Importantly, findings were validated in additional ICB-treated patient cohorts across multiple cancer types. Translational analyses from tumor biopsies demonstrated enhanced interferon-gamma signaling, and presence of tertiary lymphoid structures at baseline, as well as enhanced immune infiltration and expansion of CD45RO+ CD8+ T cells in the tumor neighborhood upon ICB treatment, in PPP2R1Amut tumors. Parallel pre-clinical investigations showed that targeting PPP2R1A (via pharmacologic inhibition or knockdown) in in vitro and in vivo models was associated with improved survival in the setting of treatment with several forms of immunotherapy, including chimeric antigen receptor-T cell therapy and ICB. Results from these studies suggest that therapeutic targeting of PPP2R1A may represent an effective strategy to improve patient outcomes following ICB or other forms of immunotherapy, though additional mechanistic and therapeutic insights are needed.

overall_design: To analyze the transcriptomic profiles of OCCC with different genetic backgrounds, we performed RNA-seq on clinical samples in the immunotherapy cohort, including samples from pre-treatment and on-treatment timepoints. After quality control, a total of 43 samples were used for analysis.

first: Yibo

last: Dai

first: Minghao

last: Dang

first: Linghua

first: Amir

last: Jazaeri


title: Super Pol II Domains enhance minor ZGA through 3D-interaction to ensure the integrity of major transcriptional waves in ZGA delayed mammals (porcine ATAC-Seq)

first: zhang

last: yong

summary: Zygotic genome activation (ZGA) represents the inaugural post-fertilization transcription event. In mouse, RNA polymerase II (Pol II) initiates embryonic transcription through a step-wise transition, but the ZGA initiation process remains unclear in non-rodents. Here, Pol II profiling in bovine and porcine embryos, combined with multi-omics data across four mammalian species, revealed strong intergenic Pol II clusters, termed super Pol II domains (SPDs), that boost minor ZGA gene expression via chromatin interactions in bovine. Intriguingly, a similar strategy was found in human embryos, which also exhibit delayed ZGA followed by rapid up-regulation of minor ZGA genes. By contrast, these genes are precociously activated in porcine and mouse gametes before fertilization. Moreover, disruption of SPD structure, which decreases two minor ZGA genesKLF17orDUXAexpression, and knockdown them in bovine, leads to aberrant gene activation and impeded embryogenesis. Our findings highlight SPD enhancement as a species-specific evolutionary adaptation for initiating transcription in bovine and human embryos, thus illustrating previously underappreciated diversity in mammalian reproductive developmental strategies.

first: Xin

first: Jingcheng

last: Zhang

first: Hengkuan

last: Li

first: Linmi

first: Jie

last: Wu

first: Linjie

last: Song

first: Wenying

first: Zixiao

first: Mei

first: Mingyang

first: Hexu


title: Super Pol II Domains enhance minor ZGA through 3D-interaction to ensure the integrity of major transcriptional waves in ZGA delayed mammals (HiC)

last: Liu

last: Jiao

last: Hu

first: Zhangyuan

last: Pan

first: Binqiang

last: Shi

first: Yong

first: Debao

first: Yunxia

first: Gang

first: Shuhong


title: Predisposition to hematopoietic malignancies by deleterious germline CHEK2 variants

city: Chicago

first: Lucy

last: Godley

state: Illinois

address: 303 E Superior Street

department: Medicine

institute: Northwestern University

summary: The role of germline CHEK2 variants in hematopoietic malignancies (HMs) is poorly understood. We examined pathogenic/likely pathogenic (P/LP) CHEK2 variants in a hereditary hematopoietic malignancy (HHM) and solid tumor risk cohorts, the UK Biobank, public acute myeloid leukemia (AML) datasets, and a knock-in mouse model. This submission is for the data from Chek2 p.161T mice,sorted CD34+ Bone Marrow cells,Bulk RNA Sequencing.

overall_design: Bulk RNA Sequencing of Chek2 p.161T C57BL/6 mice,sorted CD34+ Bone Marrow cells

first: Ryan

last: Stubbins

first: Stephen

last: Arnovitz


title: PPARɑ variant V227A reduces plasma triglycerides through enhanced lipoprotein lipolysis

city: Los Angeles

first: Alexander

last: Nguyen

state: CA

address: 675 Charles E Young Dr S

institute: University of California, Los Angeles

summary: Human single nucleotide variants in peroxisome proliferator-activated receptor-ɑ (PPARɑ) have been associated with beneficial metabolic phenotypes yet their physiologic impact is unclear. Here, we developed a mouse model of a human PPARɑ variant encoding a substitution of valine for alanine at position 227 (V227A) to explore the role of this variant on systemic metabolism. While the variant did not alter body mass or liver lipid accumulation, this variant reduced plasma triglycerides, consistent with human cohort observations. Gene expression analysis revealed that the variant enhances Ppara target gene expression in the liver in a manner consistent with PPARɑ synthetic agonist treatment. The variant increased hepatic transcript expression of Lpl, the predominant enzyme responsible for circulating triglyceride hydrolysis. Further characterization revealed that heart tissue from variant mice exhibited increased Lpl expression and triglyceride hydrolysis activity, indicating that the heart serves as a major mediator of circulating triglyceride clearance. These findings validate human observational studies and clarify the physiological impact of this variant on plasma triglycerides.

overall_design: RNA-seq profiling of wild-type (V227) and homozygous mutant (A227) liver tissue from adult male C57BL/6NHsd mice fasted for 6 hours (n=4)


title: Super Pol II Domains enhance minor ZGA through 3D-interaction to ensure the integrity of major transcriptional waves in ZGA delayed mammals (poricine H3K27ac)

first: zhang

first: Xin

first: Guowei

last: Bu

first: Yiliang

last: Miao


title: Endocrine cell ER stress conservation

status: Public on May 05 2025

first: Michael

middle: A

last: Kalwat

state: IN

address: 1210 Waterway Blvd Suite 2000

department: Lilly Diabetes Center of Excellence

institute: Indiana Biosciences Research Institute

summary: Endocrine cells are dedicated to the production and processing of hormones, from peptides to small molecules, to regulate key physiological processes including glucose homeostasis and metabolism. Because of this relatively high productivity, endocrine cells must handle a variety of stresses from oxidative stress to the unfolded protein response of the endoplasmic reticulum (UPRER). While much is known about the major pathways regulating the UPRER, the roles of endocrine cell type-specific, context-dependent, and time-dependent transcriptional changes are not well explored. To identify unique and shared responses to the UPRER across a subset of endocrine cell types, we tested representative lines for β-cells (insulin), α-cells (glucagon), δ-cells (somatostatin), X/A-cells (ghrelin), L-cells (glucagon-like peptide 1 (GLP1)), and thyrotropes (thyroid hormone and thyroglobulin). We exposed each cell type to the canonical ER stressor thapsigargin for 6 and 24 h, or vehicle (DMSO 0.1%) for 24 h and performed mRNA sequencing. Analysis of the data showed all lines responded to thapsigargin. Comparisons of up- and down-regulated genes between each line revealed both shared and unique transcriptional signatures. These data represent a valuable mineable set of candidate genes which may have cell type-specific functions during the UPRER, and have the potential to lead to new understanding about how different endocrine cells mitigate or succumb to ER stress.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: All cell lines were plated in 6 well tissue culture dishes until >75% confluent. Cells were treated with DMSO (0.1%) for 24 h or thapsigargin (100nM: MIN6, QGP-1, MGN3-1, GLUTag, PTH-C1; 500nM: αTC1-6 and PCCL3) for 6 and 24 h. RNA was isolated and 100ng of RNA used for RNAseq. MIN6 RNAseq data included in the processed data file is from GSE194200 for the DMSO 24 h and thapsigargin 6 h and 24 h.

first: Karina

last: Rodrigues-dos-Santos


title: Chromatin interaction maps of human arterioles reveal new mechanisms for the genetic regulation of blood pressure [RNA-seq]

status: Public on May 04 2025

city: Tucson

state: AZ

address: The University of Arizona

department: Physiology

institute: University of Arizona

summary: Arterioles are small blood vessels located just upstream of capillaries in nearly all tissues. The constriction and dilation of arterioles regulate tissue perfusion and are primary determinants of systemic blood pressure (BP). Abnormalities in arterioles are central to the development of major diseases such as hypertension, stroke, and microvascular complications of diabetes. Despite the broad and essential role of arterioles in physiology and disease, current knowledge of the functional genomics of arterioles is largely absent, partly because it is challenging to obtain and analyze human arteriole samples. Here, we report extensive maps of chromatin interactions, single-cell expression, and other molecular features in human arterioles and uncover new mechanisms linking human genetic variants to gene expression in vascular cells and the development of hypertension. Compared to large arteries, arterioles exhibited a higher proportion of pericytes which were strongly associated with BP traits. BP-associated single nucleotide polymorphisms (SNPs) were enriched in chromatin interaction regions in arterioles, particularly through enhancer SNP-promoter interactions, which were further linked to gene expression specificity across tissue components and cell types. Using genomic editing in animal models and human induced pluripotent stem cells, we discovered novel mechanisms linking BP-associated noncoding SNP rs1882961 to gene expression through long-range chromatin contacts and revealed remarkable effects of a 4-bp noncoding genomic segment on hypertension in vivo. We anticipate that our rich data and findings will advance the study of the numerous diseases involving arterioles. Moreover, our approach of integrating chromatin interaction mapping in trait-relevant tissues with SNP analysis and in vivo and in vitro genome editing can be applied broadly to bridge the critical gap between genetic discoveries and physiological understanding.

overall_design: Bulk mRNA_seq for human arterioles or tissue components of human arterioles.

first: Rajan

last: Pandey

first: Qiongzi

last: Qiu

first: Pengyuan

first: Hong

last: Xue

first: Jingli

last: Wang

first: Bhavika

last: Therani

first: Rong

last: Ying

first: Kristie

last: Usa

last: Grzybowski

first: Chun

last: Yang

first: Manoj

middle: K

last: Mishra

first: Andrew

middle: S

last: Greene

first: Allen

middle: W

last: Cowley Jr

first: Sridhar

last: Rao

first: Aron

middle: M

last: Geurts

middle: E

last: Widlansky

first: Mingyu

last: Liang


title: Super Pol II Domains enhance minor ZGA through 3D-interaction to ensure the integrity of major transcriptional waves in ZGA delayed mammals (H3K27ac)

first: zhang

last: yong

first: Jingcheng

last: Zhang

first: Hengkuan

last: Li

first: Linmi

first: Jie

last: Wu

first: Linjie

last: Song

first: Xin

last: Liu

first: Wenying

first: Zixiao

first: Mei

last: Jiao

first: Mingyang

last: Hu

first: Hexu

first: Zhangyuan

last: Pan

first: Binqiang

last: Shi

first: Yong

first: Debao

first: Yunxia

last: Zhao

first: Gang

last: Ren

first: Shuhong


title: Super Pol II Domains enhance minor ZGA through 3D-interaction to ensure the integrity of major transcriptional waves in ZGA delayed mammals (pol2 sperm)

first: zhang

first: Jingcheng

first: Hengkuan

last: Wang


title: A 3D Tumor Spheroid Model with Robust T Cell Infiltration for Evaluating Immune Cell Engagers

city: South San Francisco

first: Hin Ching

last: Lo

address: 1000 Gateway Blvd

institute: AbbVie Inc.

summary: A strong interest in drugs targeting the tumor microenvironment (TME) necessitates new experimental systems that incorporate key TME components. Compared to traditional 2D cell lines, 3D ex vivo spheroids from patient-derived xenograft (PDX) materials may better capture patient tumor characteristics. We developed and validated 3D tumor spheroid model from non-small cell lung cancer (NSCLC) PDXs to enable T cell infiltration. Histologic and transcriptomic analysis suggested that tumor spheroids closely recapitulate their source PDX tumor tissue. Consistent T cell infiltration into tumor spheroids was achieved using a well-established magnetic nanoparticle technology, which maintained T cell function and tumor-killing activity. Drug treatment studies with immunotherapy agents also demonstrated the potential scalability of 3D tumor-T cell spheroids in assessing drug activity, including tumor viability and cytokine secretion. This platform provides a useful tool for evaluating drug candidates that can be translated to patient tumor responses related to both tumor intrinsic and TME factors.

overall_design: To understand whether our PDX-derived spheroids recapitulate in vivo tumors in their gene expression profile, we performed RNA-seq on isolated human tumor cells from five PDX tumor models and their matched ex vivo spheroids. This included LU450, LU481, LU554, LU211, LU120. Samples were collected in triplicates. Principal component analysis (PCA) revealed that samples strongly cluster by patient of origin, regardless of whether samples came from freshly dissociated PDXs or PDX-derived spheroids. Some PDX models had RNA collected from multiple passages (LU450, LU481, LU554, LU211), where we saw that samples of different passages still clustered closely together by PDX lineage. In addition, we collected spheroid samples (LU120, LU481, LU554) without magnetic nanoparticles to perform comparisons with spheroids generated with magnetic nanoparticles, where we found no significant differences between the two conditions.

first: Hana

last: Choi

first: Kevin

last: Kolahi

first: Samantha

last: Rodriguez

first: Leiru

last: Gonzalez

first: Felix

last: Chu

first: Aditee

last: Shrotre

first: Xi

first: Aloma

last: D'Souza

first: Ron

last: Ferrando

first: Somdutta

last: Roy


title: Super Pol II Domains enhance minor ZGA through 3D-interaction to ensure the integrity of major transcriptional waves in ZGA delayed mammals (H3K4me3)

last: yong

sample_organism:
Bos taurus
Bos grunniens x Bos taurus

platform_organism:
Bos taurus
Bos grunniens x Bos taurus

last: Zhang

last: Li

first: Linmi

first: Jie

last: Wu

first: Linjie

last: Song

first: Xin

last: Liu

first: Wenying

first: Zixiao

first: Mei

last: Jiao

first: Mingyang

first: Hexu

first: Zhangyuan

first: Binqiang

first: Yong

first: Debao

first: Yunxia


title: Super Pol II Domains enhance minor ZGA through 3D-interaction to ensure the integrity of major transcriptional waves in ZGA delayed mammals (H3K27me3)

first: zhang

first: Jingcheng

first: Hengkuan

last: Hu

last: Pan

last: Shi

last: Wang

last: Zhao

first: Gang

last: Ren

first: Shuhong


title: Super Pol II Domains enhance minor ZGA through 3D-interaction to ensure the integrity of major transcriptional waves in ZGA delayed mammals (Bisulfite-Seq)

type: Methylation profiling by high throughput sequencing

sample_organism:
Bos taurus
Bos grunniens
Bos grunniens x Bos taurus

first: Linmi

first: Jie

first: Linjie


title: Super Pol II Domains enhance minor ZGA through 3D-interaction to ensure the integrity of major transcriptional waves in ZGA delayed mammals (ATAC-Seq)

platform_organism:
Bos taurus
Bos grunniens
Bos grunniens x Bos taurus

first: Xin

first: Wenying

first: Zixiao


title: Gene expression profile of embryonic and endometrial cells at postimplantation stage ex vivo to assess the effect of a selective COX-2 inhibitor celecoxib.

city: Suita

first: Takehiro

last: Hiraoka

state: Osaka

address: 3-1 Yamadaoka

country: Japan

institute: Osaka University

summary: We have newly established a novel ex vivo implantation system. To verify the ex vivo embryonic and endometrial gene expression profile, we performed RNA-sequencing (RNA-seq).

overall_design: Embryos and endometria were co-cultured with or without celecoxib for 24h and the gene expression change was investigated. For embryos, solely cultured group was also included to examine the effect of implantation. For endometria, implantation sites (ISs) and inter-implantation sites (I-ISs) were included to assess the effect of embryonic attachment reaction.


title: Colonic transcriptomic data of interleukin-10-deficient mice

city: Chengdu

first: Lili

state: Sichuan

address: 2222 Xinchuan Road

institute: West China Hospital, Sichuan University

summary: Inflammatory bowel disease (IBD) is a chronic relapsing autoimmune disease of gastrointestinal tract (GI), involving in dysfunction of a variety of genes, such as Interleukin (IL)-10. Intense researches have demonstrated that IL10-deficient (IL10-/-) mice gradually exhibits features of spontaneous enterocolitis at 4-8 weeks of age and IL-10 is a significant immunomodulator in intestinal tract. Therefore, IL10-/- mice have become a classic model of enterocolitis to study the pathogenesis of IBD. To uncover the role of the underlying molecular mechanisms involved in IL10-/--associated chronic colitis, we constructed IL10-deficient mice and sequenced transcriptome of colon tissues from the mice with colitis in this study. Mechanically, we might find out new therapeutic targets for IBD according to the omics analysis.

overall_design: Colonic mRNA profiles of 56-day-old wild type (WT) and IL10-/- mice were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Kexin

last: Chen

first: Yongbin

last: Jia

first: Hao

last: Lin

first: Yushan

first: Hu


title: Super Pol II Domains enhance minor ZGA through 3D-interaction to ensure the integrity of major transcriptional waves in ZGA delayed mammals (pol2 normal)

first: zhang

last: yong

first: Jingcheng

first: Mei

first: Mingyang

first: Hexu

first: Zhangyuan

first: Binqiang

first: Yong

first: Debao

first: Yunxia


title: SMC1A, CTCF and MITF level on chromatin after knockdown of NIPBL in melanoma cell line

city: New York

first: Elissa

middle: WP

last: Wong

state: NY

address: 1275 York Avenue

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

summary: SMC1A, CTCF and MITF level on chromatin was studied after knockdown of NIPBL in 501mel

overall_design: SMC1A spike-in ChIP-seq was done using 501mel cells with shLuc or shNIPBL. CTCF and MITF ChIP-seq was done using 501mel cells with shLuc or shNIPBL.

first: Merve

last: Sahin

first: Rui

last: Yang

first: UkJin

last: Lee

first: Rohan

last: Misra

first: Effie

last: Apostolou

first: Deyou

last: Zheng

first: Yu

first: Christina

last: Leslie

first: Ping

last: Chi


title: Global DNA methylation analysis of NIPBL depletion in melanoma cell line

summary: DNA methylation was studied after knockdown of NIPBL in melanoma cell lines 501mel

overall_design: EM-seq was performed on shLuc, shNIPBL_#1, shNIPBL_#2 knockdown cells for 501mel

first: Yingqian

last: A-


title: Super Pol II Domains enhance minor ZGA through 3D-interaction to ensure the integrity of major transcriptional waves in ZGA delayed mammals (RNA-Seq)

first: zhang

first: Jingcheng

last: Zhang

first: Hengkuan

last: Li

first: Linmi

first: Jie

last: Wu

first: Linjie

last: Song

first: Xin

last: Liu

first: Wenying

first: Zixiao

first: Mei

last: Jiao

first: Mingyang

last: Hu

first: Hexu

last: Pan

last: Shi

last: Wang

last: Zhao

first: Gang

first: Shuhong


title: Gene expression analysis on melanoma cell lines and effects of NIPBL depletion

first: Elissa

last: Wong

summary: Gene expression was studied in melanoma cell lines with (SKMEL-23 and SKMEL-1128) or without (A375 and CLOL800) ALKATI expression. Effects on gene expression was also analyzed after knockdown of NIPBL in melanoma cell lines 501mel, COLO800 and A375

overall_design: RNA-seq was performed on SKMEL-23, SKMEL-1128, A375 and COLO800 without treatment. RNA-seq was performed on shLuc, shNIPBL_#1, shNIPBL_#2 knockdown cells for 501mel, COLO800 and A375

first: Merve

last: Sahin

first: Rui

last: Yang

first: UkJin

last: Lee

first: Rohan

last: Misra

first: Effie

first: Deyou

first: Yu

last: Chen

first: Christina


title: Transcriptomic analysis of RTT neurons expressing miR106a-specifc sponge

city: Davis

first: Rachisan Gabriel

middle: Djiake

last: Tihagam

address: 919 Drake Drive,, 113

department: BMG

institute: University of virginia

summary: The transcriptional silencing of a mammalian X chromosome is a complex but well-coordinated epigenetic process. The induction ofXistlong non-coding RNA and several protein-coding genes triggers reversible and dynamic epigenetic events to initiate, establish, and maintain X chromosome inactivation (XCI). However, small non-coding RNA function in XCI remains unidentified. Our genome-wide CRISPR/Cas9 screen in female fibroblasts examined the role of microRNA (miRNAs) in XCI. A striking finding was the identification of miR106a among the top genes from the screen. Through multiple approaches, we show that miR106a physically interacts with the conserved repeat A region in Xist. Surprisingly, this uncanonical miR106a-RepA pairing is required for the formation of N6-methyladenosine, an epigenetic RNA base modifier, which in turn stabilizes Xist.The XCI interference via miR106a inhibition has therapeutic implications for Rett syndrome (RTT) girls with a defectiveX-linked MECP2gene. Notably, the activation of silenced Mecp2 reverses the RTT-like phenotypes in adult mice1. Here, we discovered that the genetic inhibition of miR106a expressed Mecp2 from the inactive X chromosome in the brain of Tsix-Mecp2, a female symptomatic RTT murine model. We found that miR106a inhibition in Tsix-Mecp2 female mice significantly improved several facets of RTT pathology: the life span was increased, locomotor activity and exploratory behavior were improved, and apneas and breathing variabilities were diminished. Finally, miR106a-dependent MECP2 restoration in female human post-mitotic neurons normalizes morphological and functional deficits in RTT neurons. Together, our results implicate miR106a as a regulator in the transcriptional repression of the X chromosome and suggest that miR106a targeting might offer a feasible therapeutic strategy for RTT and other monogenic X-linked neurodevelopmental disorders.

overall_design: Human T158M neuron with Rett mutant is treated with miR inhibition, and the totally RNA was extracted from treated and control neurons. RNA libraries for RNA seq were prepared by Novogene. Sequence reads were trimmed for adaptor sequence/low quality sequence and the gene expression were then compared between the treated and control groups.

first: Sanchita

last: Bhatnagar

first: Song

last: Lou

first: Rachisan

last: Djiake Tihagam


title: Proteo-transcriptional architecture of human pressure overload: implications for heart failure

city: Nashville

first: Lindsey

middle: "Joey"

last: Stolze

state: TN

address: 1211 Medical Center Dr

institute: Vanderbilt University Medical Center

summary: Chronic pressure overload initiates a series of molecular alterations in the human heart that predate macroscopic organ-level remodeling and downstream heart failure (HF). We hypothesized that integrating easily accessible circulating mediators (proteome) with their expression in the heart (transcriptome) may prioritize targets for study in human pressure overload. Among individuals with severe aortic stenosis (AS)—a pressure overload state—we measured the circulating proteome (Olink) and examined associations with myocardial structure/function (N=519), cardiac MRI-based tissue fibrosis (N=145), and outcomes in AS (N=802). We constructed proteomic signatures of cardiac remodeling and tested their association with HF in the UK Biobank (N=36,668). For proteo-transcriptional integration, we examined a "remodeling proteome” prioritized by proteome-phenotype relations at the transcriptional level via single nuclear RNA-sequencing (snRNA-seq) in 20 human hearts (11 with AS at the time of surgical aortic valve replacement [AVR] and 9 donor hearts not used for transplantation). We identified three principal components of myocardial remodeling (across 12 echocardiographic measures in 503 patients with AS) loaded on cardiac morphology, systolic, and diastolic function traits. Proteins associated with these components (the “remodeling proteome”) specified both known and novel mediators of fibrosis, hypertrophy, and oxidative stress, several of which were associated with interstitial fibrosis by cardiac MRI. Proteomic signatures of remodeling were strongly linked to mortality (AS cohort and UK Biobank) and incident HF (UK Biobank). At a myocardial level, we observed broad differential expression of genes encoding the remodeling proteome between AS and donor hearts, featuring convergent fibrosis pathways (WNT9A, ITGA6, AGRN, CRIM1, SEMA4C, LAYN, PTX3, HMOX1) and metabolic-inflammatory signaling (ENPP2/ATX, TNF), among others. Differential expression of proteo-transcriptionally prioritized genes was prominent in fibroblasts, cardiomyocytes, and endothelial cells. Proteo-transcriptional prioritization in human pressure overload hearts identifies both known and novel targets that are mechanistically relevant to HF pathogenesis. Future integrative studies to index circulating biomarkers over time to myocardial tissue level is warranted to inform pathways of HF progression.

overall_design: Single-nuclear RNA-sequencing and ATAC sequencing (10X Multiome) of human heart tissue (left ventricle) from unused donor hearts and severe aortic stenosis.

first: Kaushik

last: Amancherla

first: Nathan

last: Tucker

first: Ravi

last: Shah

first: Sammy

last: Elmariah


title: Chromatin modification of melanoma cell line after knockdown of NIPBL

first: Elissa

summary: Chromatin modification was studied using various histone modification marks and CTCF after knockdown of NIPBL in 501mel

overall_design: CUT&RUN was performed using H3K4me1, H3K4me3, H3K27ac, H3K9me3, H3K27me3, H3K36me3 and CTCF antibodies using 501mel cells with shLuc or shNIPBL

first: Merve

last: Apostolou

last: Zheng

last: Leslie

first: Ping

last: Chi


title: Transcription start site analysis of NIPBL depletion in cancer cell line

last: Wong

summary: Transciption start site expression was studied after knockdown of NIPBL cancer cell lines (A549, H358, H2228, 22RV1, VCAP, C106, SW620, HCT116, CAMA-1)

overall_design: CAGE-seq was performed on shLuc and shNIPBL_#2 knockdown cells

last: Sahin

first: Rui

last: Yang

first: UkJin

first: Rohan


title: RNA expression in ex vivo ventilated human lungs

city: Oviedo

first: Guillermo

last: Albaiceta

address: Avenida de Roma s/n

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias

summary: Rationale: Overstretching of lung parenchyma may lead to tissue injury, especially during mechanical ventilation. There are no specific biomarkers of lung stretch.    Objectives: To identify transcriptomic signatures of micro-RNAs and genes specifically related to lung stretch and validate them in preclinical models.  Methods: Data on micro-RNA expression in response to stretch in experimental models were systematically pooled. Signatures were identified as those micro-RNAs or genes with differential expression in samples from stretched cells, and optimized using a greedy algorithm. Transcriptomic scores were calculated as the difference of geometric means in expression of up- and down-regulated features, and compared among different magnitudes of stretch. The accuracy of these scores was validated in animal models of lung injury, ex vivo mechanically ventilated human lungs and in bronchoalveolar lavage fluid (BALF) from patients under different ventilatory conditions.  Measurements and main results: Eight micro-RNAs were differentially expressed in stretched cell cultures (n=24). Amongst the genes regulated by these micro-RNAs, a 180-gene signature was identified in ex vivo models (n=106) and refined using data from animal models (n=143) to obtain a 4-gene signature. The corresponding scores were significantly higher in samples submitted to stretch or injurious mechanical ventilation. The microRNA signatures were validated in human tissue and BALF, with areas under the ROC curve between 0.89 and 1 respectively to identify lung overdistention.  Conclusions: Lung cell stretch induces the expression of specific micro-RNA and genes. These signatures may be used to obtain an index of lung overstretching that can be measured at the bedside.

overall_design: Human lungs not suitable for transplantation were exvivo perfused and maintained on continous positive airway pressure (CPAP, n=3) of 10 cmH2O or ventilated with a tidal volume of 12 ml/Kg of predicted body weight and zero end-expiratory pressure to induce ventilator-induced lung injury (VILI, n=3). After 4 hours of CPAP/ventilation, lungs were deflated and a portion of tissue homogenized in trizol.

first: Inés

last: López-Alonso

first: Cecilia

last: López-Martínez


title: Enhancer connectome of melanoma cell lines

summary: Enhancer connectome was studied in melanoma cell lines that express ALK ATI

overall_design: H3K27ac HiChIP was performed using SKMEL-23 and SKMEL1128 cells

last: Lee

last: Misra

first: Effie

first: Deyou

first: Yu

last: Chen

first: Christina


title: Chromatin conformation of melanoma cell line after knockdown of NIPBL

summary: Chromatin conformation was studied after knockdown of NIPBL in 501mel

overall_design: HiC was performed using 501mel cells with shLuc or shNIPBL


title: Inorganic carbon levels regulate growth via SigC signaling cascade in cyanobacteria

city: Freiburg

first: Wolfgang

middle: R.

last: Hess

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

summary:
Gene expression changes were followed in cultures of the cyanobacterium Synechocystis sp. PCC 6803 substrain GT-T cultivated at ambient air or supplemented with 3% CO2. The acclimation to different CO2 concentrations is crucial for photoautotrophic organisms living in aquatic environments such as cyanobacteria. Samples were taken before and 1 h and 24 h after transfer to the3 % CO2 environment. The analyzed strains were wild type, a deletion mutant of gene ssl2982/rpoZ (ΔrpoZ) and two suppressor strains (R1, ΔrpoZ-S1 and R2, ΔrpoZ-S2).
In cyanobacteria, elevated CO2 is known to down-regulate carbon concentrating mechanisms and accelerate photosynthesis and growth, but mechanism(s) of carbon signalling remains only poorly understood. Here we reveal a novel signalling cascade connecting the amount of CO2 and growth in the model cyanobacterium Synechocystis sp. PCC 6803. Deletion of the small ω subunit of the RNA polymerase (RNAP) in the ΔrpoZ strain prevents normal high-CO2-induced up-regulation of numerous photosynthetic genes, and low expression of peptidoglycan synthesis genes induced lysis of dividing ΔrpoZ cells in high CO2.  Spontaneously raised secondary mutations in the ssr1600 gene rescued the high-CO2-sensitive phenotype of the ΔrpoZ strain. Biochemical analyses showed that the ssr1600 gene encodes an anti-σ factor antagonist of group 2 σ factor SigC, and 3D structural modelling suggest that Slr1861 functions as an anti-SigC factor. In ΔrpoZ, excess formation of RNAP-SigC lead to high CO2 sensitive phenotype, whereas the drastically reduced Ssr1600 content in the suppressor mutants reduce the formation of the RNAP-SigC holoenzyme to the similar level as in the control strain, allowing almost normal transcriptome and growth of suppressor lines in high CO2. We propose that the SigC σ factor, the anti-SigC factor Slr1861 and the anti-SigC antagonist Ssr1600 forms a growth regulating signalling cascade in cyanobacteria.

overall_design: Total RNA was prepared from cells of Synechocystis sp. PCC 6803 wild type strain GT-T, the ΔrpoZ mutant lacking the RNA polymerase ω subunit and of two suppressor mutants. Samples were taken in biological replicates. Total RNA was DNase-treated using TURBO DNase (Thermo Fisher Scientific). 2 µg DNase-treated RNA were labeled with Cy3 using the ULS Fluorescent Labeling Kit for Agilent arrays (Kreatech). A high-resolution microarray manufactured by Agilent (Design ID 075764, format 8 × 60 K, slide Layout = IS-62976-8-V2) was used. 600 ng labeled RNA were used for hybridization for 17 h at 65 °C, per array.

first: Juha

last: Kurkela

first: Linda

last: Vuorijoki

first: Serhii

last: Vakal

first: Otso

last: Turunen

first: Satu

last: Koskinen

first: Viktoria

last: Reimann

first: Mithila

last: Ray

middle: R

first: Tiina

last: Salminen

first: Taina

last: Tyystjärvi


title: 4C-seq analysis of NIPBL depletion in melanoma cell line

first: Elissa

last: Wong

summary: Genomic interactions of ALK ATI or ULK4 intron 31 viewpoint was studied after knockdown of NIPBL in melanoma cell lines 501mel

overall_design: 4C-seq was performed from ALK ATI or ULK4 intron 31 viewpoint on shLuc or shNIPBL_#2 knockdown cells for 501mel

first: Merve

last: Sahin

first: Rui

last: Yang

first: UkJin

first: Rohan

last: Apostolou

last: Zheng

last: Leslie

first: Ping

last: Chi


title: Histone modification of melanoma cell lines and cohesin level after knockdown of NIPBL

summary: Histone mark for active enhancer H3K27ac was studied using various melanoma cell lines. SMC1A level on chromatin was studied after knockdown of NIPBL in 501mel

overall_design: ChIP-seq was performed using H3K27ac antibody on SKMEL-23, SKMEL-1128, 501mel, COLO800 and A375. SMC1A ChIP-seq was done using 501mel cells with shLuc or shNIPBL

last: Lee

last: Misra

first: Effie

first: Deyou

first: Yu

last: Chen

first: Christina


title: Distinct transcriptional profile in CD4+ T-lymphocytes among obese children with asthma

city: Baltimore

first: Rulin

last: Wang

state: Maryland

address: 1650 Orleans Street

institute: Johns Hopkins University

summary: Obesity is a risk factor for asthma severity and morbidity, displaying a distinct clinical phenotype that is less responsive to inhaled corticosteroids. CD4+ T-cells are central to the immunologic pathways of asthma and may contribute to the unique obese asthma phenotype. We sought to characterize the single cell CD4+ transcriptional profile among obese children with asthma compared to matched normal weight children with asthma.

overall_design: From the AIRWEIGHS study cohort of 160 participants, we selected 8 normal weight and 8 obese participants after excluding those taking systemic steroids in the last 30 days or on biologics. Of the 8 participants from each weight category, 4 were poorly controlled (defined as Asthma Therapy Assessment Questionnaire [ATAQ] score≥3) and 4 were well controlled (ATAQ score<3). Normal weight was defined as BMI percentile between 5th and 85th percentile and obese as BMI≥ 95th percentile.

first: Vickram

last: Tejwani

first: Srinivasan

last: Yegnasubramanian

first: Meredith

middle: C

last: McCormack

first: Franco

last: D’Alessio


title: The role of serum miRs in IgA nephropathy

city: Leicester

first: Izabella

middle: Zofia Anna

last: Pawluczyk

address: University Road

department: Cardiovascular Sciences

institute: University of Leicester

type: Non-coding RNA profiling by high throughput sequencing

summary: To ascetain whether a serum miR signature can distinguish patients with progressive IgAN from the stable form and to determine the signature specificity for IgAN by comparing serum miR profiles with  subjects with membranous nephropathy and healthy subjects.

overall_design:
Serum from 10 patient with either progressive IgAN, Stable IgAN, membranous nephropathy and healthy subjects which were age and sex-matched and sent to Exiqon/Qiagen for next generation sequencing (NGS)
h= healthy subject
m= membranous nephropathy
np= IgAN non-progressor
n= IgAN progressor

middle: Z

first: Jasraj

last: Bhachu

first: Jonathan

last: Barratt


title: Transcription start site analysis of NIPBL depletion in melanoma cell line

first: Elissa

last: Wong

summary: Transciption start site expression was studied after knockdown of NIPBL in melanoma cell lines 501mel

overall_design: CAGE-seq was performed on shLuc, shNIPBL_#1, shNIPBL_#2 knockdown cells for 501mel

first: Merve

last: Sahin


title: TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer

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

overall_design: Refer to individual Series


title: Identification of a micro-RNA signature of lung stretch

first: Guillermo

last: Albaiceta


title: Affymetrix SNP array data for diversity analysis in deepwater rice

city: New Delhi

first: Tapan

last: Mondal

state: DELHI

address: LBS Centre, Pusa

country: India

institute: ICAR-National Institute for Plant Biotechnology

summary: In the present investigation, the genetic diversity architecture of 96 deep-water rice genotypes of Assam and association mapping strategy was, for the first time, applied to determine the significant SNPsand genes for deep-water rice. These genotypes are known for their unique elongation ability under deep-water condition.The internode elongation under water related genes will be identified here can provide affluent resources for rice breeding especially in flood-prone areas. We investigated the genome-wide association studies (GWAS) using 50 K rice genic SNPchip across 96 deep-water rice genotypes collected from different flood-prone districts/villages of Assam.

overall_design: Genome‑wide association studies using 50 K rice genic SNP chip unveilgenetic architecture for anaerobic germination of deep‑water ricepopulation of Assam, India

first: Megha

last: Rohilla


title: microRNA expression in ex vivo ventilated human lungs

summary:
Rationale: Overstretching of lung parenchyma may lead to tissue injury, especially during mechanical ventilation. There are no specific biomarkers of lung stretch.
Objectives: To identify transcriptomic signatures of micro-RNAs and genes specifically related to lung stretch and validate them in preclinical models.
Methods: Data on micro-RNA expression in response to stretch in experimental models were systematically pooled. Signatures were identified as those micro-RNAs or genes with differential expression in samples from stretched cells, and optimized using a greedy algorithm. Transcriptomic scores were calculated as the difference of geometric means in expression of up- and down-regulated features, and compared among different magnitudes of stretch. The accuracy of these scores was validated in animal models of lung injury, ex vivo mechanically ventilated human lungs and in bronchoalveolar lavage fluid (BALF) from patients under different ventilatory conditions.
Measurements and main results: Eight micro-RNAs were differentially expressed in stretched cell cultures (n=24). Amongst the genes regulated by these micro-RNAs, a 180-gene signature was identified in ex vivo models (n=106) and refined using data from animal models (n=143) to obtain a 4-gene signature. The corresponding scores were significantly higher in samples submitted to stretch or injurious mechanical ventilation. The microRNA signatures were validated in human tissue and BALF, with areas under the ROC curve between 0.89 and 1 respectively to identify lung overdistention.
Conclusions: Lung cell stretch induces the expression of specific micro-RNA and genes. These signatures may be used to obtain an index of lung overstretching that can be measured at the bedside.

first: Inés

last: López-Alonso

first: Cecilia

last: López-Martínez


title: Transcriptomics of Pseudomonas aeruginosa PA14 upon deletion of the sigma factor RpoS

status: Public on Apr 30 2025

city: Monterrey

first: Luis

middle: Mauricio

last: Salazar-García

address: Av. Eugenio Garza Sada 2501 Sur

country: Mexico

institute: Tecnológico de Monterrey

summary: We report RNA-seq data of Pseudomonas aeruginosa PA14 (UCBPP-PA14) and an isogenic rpoS-STOP mutant generated using CRISPR/Cas9 base editing. Transcriptomic profiling during exponential growth in rich medium highlights the regulatory influence of RpoS. These data enable exploration of RpoS-dependent responses in the virulent PA14 strain.

overall_design: RNA-seq profiling of P. aeruginosa PA14 and its rpoS-STOP mutant at mid-log phase cells (8h).

first: Luis Mauricio

last: Salazar-Garcia

first: Jose Manuel

last: Villalobos-Escobedo


title: microRNA expression in bronchoalveolar lavage fluid from mechanically ventilated patients with cardiogenic shock

overall_design: A bronchoalveolar lavage was performed in 7 patients included in a clinical trial testing tidal volume of 6 and 3 ml/Kg predicted body weight (PBW) during venoarterial ECMO for cardiogenic shock (Amado-Rodríguez et al., Ann Intensive Care 2021, PMID 34453620), Lung strain was calculated for each tidal volume as the ratio between tidal and end-expiratory lung volumes. MicroRNAs were measured in these samples.

first: Laura

last: Amado-Rodríguez


title: RNA seq on murine basal keratinocytes and murine Lrig1 positive sorted keratinocytes

city: Nice

first: Chloe

last: Feral

address: 28 avenue de valombrose

department: Ircan

country: France

institute: Inserm

summary: Unbiased approach to identify Epidermal Niche signals responsible for Hair follicle stem cells activation. We have analysed specifically Lrig1 positive cells using a genetically modified mouse where GFP is expressed under Lrig1 promoter at D28. We sorted cells and analyse Sorted GFP+ cells versus the basal cells from the same mouse.

overall_design: RNA seq profiling of basal keratinocytes at D28 and Lrig1 positive GFP+ sorted cells.

first: Soline

last: Estrach

first: Chloé


title: Transcriptome alterlation by ZIC5 knockdown in pancreatic cancer cell line, PANC-1.

city: Hachioji-city

first: Reiko

last: Satow

state: Tokyo

address: 1432-1 Horinouchi

department: Life Sciences

institute: Tokyo University of Pharmacy and Life Sciences

summary: To examine the transcriptome alterlation caused by ZIC5 knockdown in pancreatic cancer, we performed RNA-Seq analysis.

overall_design: Human pancreatic cancer cell line, PANC-1, was transfected with siRNA for ZIC5 or negative control siRNA. After 48h,  total RNA was extracted and RNA-Seq analysis was performed.


title: ISDH-seq: a robust methodology for profiling and characterization of open chromatin

city: Nanjing

first: Zhaoguo

last: Li

state: Jiangsu

address: No.1 Weigang

institute: Nanjing Agricultural University

summary: We present in situ DNase I hypersensitivity sequencing (ISDH-seq), a novel methodology for genome-wide open chromatin characterization in plants, which can be applicable to 100-200K nuclei. Compared to conventional DNase-seq and ATAC-seq applied to the same rice tissues, ISDH-seq detects 72% and 120% more open chromatin sites (OCSs), respectively. ISDH-specific OCSs exhibit unique epigenetic signatures: hypomethylation, co-enrichment with H3K27me3, and strong spatial chromatin interaction associations.ISDH-seq overcomes method-specific biases in OCS detection, expands the plant regulatory genome atlas, and offers cross-species applicability. This technology provides critical insights into noncoding regulatory mechanisms and their biological implications in plant genomes.

overall_design: This study profiles open chromatin landscapes in Oryza sativa (rice) using two-week-old seedlings under untreated conditions. We developed ISDH-seq (in situ DNase I hypersensitivity sequencing) and compared its performance with DNase-seq and ATAC-seq on the same batch of seedling tissues (Biological replicates n=2).

first: Wenli

last: Zhang


title: foxl2l regulates female meiotic entry during juvenile gonadal development in zebrafish

city: Taipei

first: Bon-chu

last: Chung

address: No. 128, Sec. 2 Academia Rd., Nangang Dist.

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: Sex determination is distinct from development of other organs for its diversity among species. In zebrafish, the sex determination in juvenile stage could be hermaphroditic or gonochoristic. However, the detail mechanism is still unclear. Here in this study, we found that the transcription factor that belongs to forkhead box family, Foxl2l, is required for determination of female fate in zebrafish. Foxl2l was expressed from larva stage and became female bias in juvenile stage. The expression was restricted in pre-meiotic germ cells. Disruption of Foxl2l function by CRISPR/Cas9 system resulted in all-male phenotype in the mutant. Germ cells in foxl2l mutant were arrested in pre-meiotic stage at 21 dpf, the critical period for female meiotic entry. To further verify the downstream mechanism of Foxl2l on female sex determination, wildtype or foxl2l mutant germ cells labeled by foxl2l:egfp at 21 days post fertilization (dpf) and germ cells labeled by ziwi:egfp at 26 dpf were analyzed by RNA-seq and single-cell RNA-seq respectively

overall_design: Trunks of foxl2l:egfp;foxl2l-/- or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART-Seq HT kit seq (Takara Bio), cDNA library was constructed by Nextera XT DNA Library Prep Kit (Illumina Inc.) and RNA-sequencing was performed by Illumina NextSeq 500. Each genotype contained triple samples.

first: Ching-hsin

last: Yang


title: Cytosolic DNA sensing instructs resident cell population vitality and organismal longevity

city: Boston

first: Katherine

last: Sulka

state: MA

address: 136 Harrison Avenue

department: Immunology

institute: Tufts Medical School- Graduate School of Biomedical Sciences

summary: Single cell RNA sequencing of  FACS purified 3-mo and 12-mo WT and STING-KO mouse brains and single cell RNA sequencing of single cell suspensions from 2-mo and 24-mo WT and STING-KO mouse brains.

overall_design: Expression profiling of young (n=2 grouped/genotype) and aged (n=2 grouped/genotype) mouse tissue by scRNA-seq high throughput sequencing.

first: Kimberly

last: Carroll

first: Jacob

last: Hopkins

first: Machlan

last: Sawden

first: Albert

last: Tai

first: Shruti

last: Sharma


title: Modulation of Glucocorticoid Receptor Function under Iron Overload

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: Acute iron overload leads to ferroptosis, in a mouse model of FeSO4 challenge causing lethal shock, associated with inflammation and multiple organ failure (MOF). We investigated molecular aspects causing this phenomenon upon FeSO4 overload, with a focus on the glucocorticoid receptor (GR), an important anti-inflammatory transcription factor. We report that Fe overload activates the HPA axis, leading to corticosterone increases in the blood, acutely causing upregulation of GR-dependent genes in liver. Since a GR blocker, mutant GR mice and removal of adrenals sensitize mice for Fe-induced toxicity, GR appears essential to resist ferroptosis, and stimulation appears an interesting option to deal with ferroptosis. However, DEX treatment is unable to protect mice against FeSO4- induced death and MOF. This dilemma is shown, by RNA-seq, to be the result of a quick and complete inactivation of GR biological function by Fe2+, shortly after the initial activation. This inactivity of GR seems to be the result of a complete lack of GR to bind ligand. We discuss the possible mechanism and complications for ferroptosis progression during diseases

overall_design: RNA-seq profiling of mouse livers after a total of 8 hours: 6 hours iron treatment (FeSO4) + 2 hours of DEX and respective controls, for a total of 4 groups with 3 biological replicates per group

first: Wanting

last: Zhu

first: Tineke

last: Vanderhaeghen

first: Jolien

last: Vandewalle

first: Melanie

last: Eggermont

first: Nicky

last: Verhoog

first: Claude

last: Libert


title: Direct microglia replacement reveals pathologic and therapeutic contributions of brain macrophages to a monogenic neurological disease [RNA-seq]

city: Philadelphia

first: F. Chris

last: Bennett

address: 3150 Civic center blvd

institute: UPenn

summary: Krabbe disease, also named Globoid Cell Leukodystrophy (GLD) for its distinct lipid- laden macrophages, is a severe leukodystrophy caused by galactosylceramidase (GALC) mutations. Hematopoietic stem cell transplant (HSCT) ameliorates disease and is associated with central nervous system (CNS) engraftment of GALC+ donor macrophages. Yet, the role of macrophages in GLD pathophysiology and HSCT remains unclear. Using single-cell sequencing we revealed early interferon response signatures which precede progressively severe macrophage dyshomeostasis, and identified a molecular signature of globoid cells, which we validated in human brain specimens. Genetic depletion and direct microglia replacement by CNS monocyte injection rapidly replaced >80% of endogenous microglia with healthy monocytes in the twitcher (GalcW355*) mouse, a faithful model of GLD. Perinatal microglia replacement completely normalized transcriptional signatures, rescued histopathology, and doubled average survival. Overall, we uncovered distinct forms of microglia dysfunction, and evidence that direct, CNS-limited microglia replacement improves a monogenic neurodegenerative disease, a promising therapeutic target.

overall_design: Myeloid cells were isolated from Twitcher and WT mouse brains, FACS sorted for CD45, CD11b posititivy, and sequenced using 10x chromium controller system. Samples include WT and twitcher animals transplated with WT monocytes, and unamanipulated WT and Twi animals.

first: William

middle: H

last: Aisenberg

first: Frederick


title: Exon Level Expression Profiling: a Novel Unbiased Transcriptome

city: Monroe

first: Yong-Yu

last: Liu

state: LA

address: 1800 Bienville Dr Rm368, 1800 Bienville Dr

institute: University of Louisiana at Monroe

summary:
Transcriptome analysis of mRNA samples from NCI/ADR-RES ovarian cancer cells treted with actinomycin D
Emergent cancer drug resistance and further metastasis mainly attribute to altered expression levels and functional activities of multiple genes of cancer cells under chemotherapy. In response to challenge with anticancer drugs, enhanced ceramide glycosylation catalyzed by glucosylceramide synthase (GCS) confers drug resistance and enrichment with cancer stem cells. p53 mutations, which gain function in tumor progression, are prevalently extant in ovarian cancers. Via integrated gene expression assessments, we characterized GCS-responsive genes in ovarian cancer cells treated with dactinomycin. NCI/ADR-RES cells dominantly expressed a p53 mutant (7 aa de-leted in exon-5) and displayed anti-apoptosis; however, silencing GCS expression ren-dered these cells sensitive to dactinomycin-induced apoptosis. Microarray analyses of NCI/ADR-RES and its GCS transfected sublines found that elevated GCS expression or ceramide glycosylation associated to altered expression of 41 genes, notably coding for ABCB1, FGF2, ALDH1A3, apolipoprotein E, laminin 2, chemokine ligands, and IL6, with cellular resistance to induced apoptosis and enrichment with cancer stem cells, promoting cancer progression. These findings were further corroborated through in-tegrated genomic analyses of ovarian cancer from The Cancer Genome Atlas (TCGA) and cancer resistance to platinum-based chemotherapy. Altogether, our present study indicates that altered ceramide glycosylation can modulate expression of these GCS-responsive genes and alter cancer cell attributes under chemotherapy.

overall_design: We analyzed mRAN from 6 treatment conditions using the Affymetrix Human Genome U133 Plus 2.0 platform. Array data was processed by Transcriptome Analysis Console (TAC). No techinical replicates were performed.

first: Liu

last: Yong-Yu

first: Kang

last: Lin

first: Zhao

last: Yunfeng

first: Mostaq

last: Saqline


title: Whole genome bisulfite sequencing of nicotine-exposed sperm reveals differences in global DNA methylation levels, which would partially reverse following cessation

city: Shanghai

first: Jiajun

last: Cui

address: No.131, Dong'an Road, Xuhui District, Shanghai, China

institute: Obstetrics and Gynecology Hospital of Fudan University

summary: DNA methylation, a pivotal epigenetic modification, regulates the expression of numerous genes during spermatogenesis and influences health outcomes in offspring. We have conducted whole genome bisulfite sequencing (WGBS) to explore the effects of nicotine exposure on global sperm DNA methylation patterns. Previous studies have shown that nicotine exposure increased DNA methylation status in sperm, whereas the detailed mapping of global DNA methylation patterns remains elusive. In addition, whether the DNA methylation changes induced by nicotine may be reversible upon cessation is still unclear. Here, we demonstrated the effects of nicotine exposure on global sperm DNA methylation patterns and verified the reversibility of this phenomenon, providing new insights into the mechanisms by which smoking affects male fertility and the long-term health of offspring.

overall_design: Three-week-old C57BL/6J male mice were divided into three groups: (1) Control group (C), which received normal drinking water; (2) Nicotine-exposed group (N), which received drinking water with 200 μg/mL nicotine for 8 weeks; and (3) Nicotine withdrawal group (NW), which received normal drinking water for an additional 5 weeks following 8 weeks of nicotine exposure. Followed by treatment, sperm was extracted, and WGBS was performed on total sperm DNA.

first: Yu

last: Zhang

first: Guolian

last: Ding


title: Direct microglia replacement reveals pathologic and therapeutic contributions of brain macrophages to a monogenic neurological disease

overall_design: Myeloid cells were isolated from Twitcher and WT mouse brains, FACS sorted for CD45, CD11b positivity, and sequenced using 10x chromium controller system. Samples include WT and twitcher animals transplanted with WT monocytes, and unmanipulated WT and Twi animals.

first: Yuanchao

first: Mariko

middle: L


title: Revealing the impact of Pseudomonas aeruginosa quorum sensing molecule 2’-aminoacetophenone on human bronchial-airway epithelium and pulmonary endothelium using a human-airway-on-a-chip

first: Laurence G

last: Rahme

state: Massachusetts

address: 340 Thier Research Building

institute: Massachusetts General Hospital, Harvard Medical School

summary: Pseudomonas aeruginosa (PA) causes severe respiratory infections utilizing multiple virulence functions. Our previous findings on PA quorum sensing (QS)-regulated small molecule, 2’-aminoacetophenone (2-AA), secreted in host infected tissues, revealed its effect on immune and metabolic functions favoring a long-term presence of PA in host tissues. However, studies on 2-AA’s effect on bronchial-airway epithelium and pulmonary endothelium remain elusive. To evaluate 2AA’s spatiotemporal changes in the human airway, considering endothelial cells as the first point of contact when the route of lung infection is through the bloodstream, we utilized the microfluidic bronchial-airway-on-a-chip lined by polarized human bronchial-airway epithelium and pulmonary endothelium. Using this platform, we performed RNA-sequencing to analyse responses of 2-AA treated primary human pulmonary microvascular endothelium (HPMEC) and adjacent primary normal human bronchial epithelial (NHBE) cells from healthy female donors and potential cross-talk between these cells. Analyses unveiled specific signaling and biosynthetic pathways to be differentially regulated by 2-AA in epithelial cells, including HIF-1 and pyrimidine signaling, glycosaminoglycan, and glycosphingolipid biosynthesis, while in endothelial cells were fatty acid metabolism, phosphatidylinositol and estrogen receptor signaling, and the proinflammatory signaling pathways.  As part of the significant overlap in gene regulation and signaling pathways in both cell types impacted by 2-AA were genes implicated in immune response and cellular functionality. Moreover, we found cellular responses differentially regulated in each cell type, affecting barrier permeability, cholesterol metabolism, and oxidative phosphorylation.  These 2-AA-mediated distinct responses may result from the cross-talk between these cells. Murine in-vivo and additional in vitro cell culture studies confirmed cholesterol accumulation and its effect on lung physiology by 2-AA. Results also revealed specific biomarkers associated with cystic fibrosis and idiopathic pulmonary fibrosis to be modulated by 2-AA in both cell types, with the cystic fibrosis transmembrane regulator expression to be affected only in endothelial cells. The 2-AA-mediated effects on epithelial and endothelial cells within a microphysiological dynamic environment that mimics the human lung airway enhance our understanding of the influence of this QS signaling molecule in HPMEC  and NHBE cells. This study provides novel insights into their functions and potential interactions, paving the way for innovative therapeutic strategies to combat PA lung infections.

overall_design: Using the microfluidic human airway-on-a-chip, RNA seq profiling was performed of untreated and 2-AA (20 μM) treated HPMEC (human pulmonary microvascular endothelial cells) and NHBE (normal human bronchial epithelial) cells with continuous flow of

first: Shifu

last: Aggarwal

first: Arijit

last: Chakraborty

first: Kelsey

last: Wheeler

first: Roberto

last: Plebani

first: Stephen

last: Lory

first: Katia

last: Karalis


title: Intramuscular adipose tissue physically restricts functional muscle recovery

city: GAINESVILLE

first: Daniel

last: Kopinke

state: FL

address: 1200 Newell Dr.,

institute: University of Florida

summary: With age and disease, skeletal muscle is progressively lost and replaced by fibrotic scar and intramuscular adipose tissue (IMAT). While strongly correlated, it remains unclear whether IMAT has a functional impact on muscle. In the present study, we evaluated the effects of IMAT during muscle injury by creating a mouse model where the cellular origin of IMAT, fibro/adipogenic progenitors (FAPs), are prevented from differentiating into adipocytes (FATBLOCK model). We found that blocking IMAT after an adipogenic injury allowed muscle to regenerate more efficiently, resulting in enhanced function. Our data explain why acute muscle injuries featuring IMAT infiltration, such as rotator cuff tears and acute denervation injuries, exhibit poor regeneration and lead to a loss in muscle function. It also demonstrates the therapeutic importance of preventing IMAT formation in acute injuries in order to maximize regeneration and minimize loss in muscle mass and function.

overall_design: Transcriptomic profiling using RNAseq was performed on RNA derived from whole muscle lysate from tibialis anterior muscle 5 days post glycerol injury. Two groups of whole muscle were sequenced, one from wild type muscle, and another from FAPs in which ppary was conditionally deleted. A total of 6 control and 6 FAP-no ppary samples were used.

first: Alessandra

last: Norris

first: Victoria

last: Palzkill

first: Ambili

middle: B

last: Appu

first: Kiara

last: Fierman

first: Christian

middle: D

last: Noble

first: Terence

last: Ryan


title: PCBP1 regulates transcription by binding ssDNA at promoters

city: Charleston

first: Philip

last: Howe

state: SC

address: 173 Ashley Avenue

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary:
To investigate the role of PCBP1 in transcription through its ability to bind DNA, we performed a CRISPR knockout of PCBP1 in A549 lung adenocarcinoma cells and generated a genome wide map of PCBP1's DNA binding using CUT&RUN.
We used RNA-seq of A549 WT cells and two A549 PCBP1 KO cell lines we generated to quantify gene expression changes. We used PCBP1 CUT&RUN to generate a map of PCBP1's DNA binding sites.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for A549 cells and PCBP1 KO derivatives. Analysis of PCBP1 DNA binding using Cleavage Under Targets & Release Under Nuclease (CUT&RUN). Two biological replicates for PCBP1, IGG, and H3K4me3 (positive control) antibodies.

first: Joseph

middle: A

last: Karam


title: NRF2 supports non-small cell lung cancer growth independent of CBP/p300-enhanced glutathione synthesis [shNRF2_RNAseq]

city: South San Francisco

first: Scott

last: Foster

address: Genentech

institute: Genentech

summary: Nuclear factor erythroid 2-related factor 2 (NRF2) is a stress responsive transcription factor that is mutationally activated in a subset (~25%) of clinically-aggressive non-small cell lung cancers (NSCLC). Mechanistic insight into drivers of the NRF2 dependency remains poorly understood. Here, we defined a novel NRF2 target gene set linked to NRF2-dependency in cancer cell lines, and observed that a significant portion of these genes is devoid of promoter-proximal NRF2. Using integrated genomic analyses, we characterized extensive NRF2-dependent enhancer RNA (eRNA) synthesis and NRF2-mediated H3K27ac deposition at proximal and distal enhancer regions regulating these genes. While CBP/p300 is a well-validated direct interaction partner of NRF2 with prominent functions at enhancers, we report that this interaction is not required for NRF2-dependent NSCLC cell growth, indicating that NRF2 can sustain sufficient transcriptional activity in the absence of CBP/p300 coactivation. Broad metabolic profiling established a primary role for CBP/p300 in NRF2-dependent accumulation of glutathione and glutathione-related metabolites. While redox homeostasis via enhanced glutathione production is commonly associated with the normal physiological role of NRF2, collectively our results suggest that NRF2-dependent cancer cell growth does not require this enhanced glutathione production.

overall_design: RNAseq of knockdown of NRF2 by shRNA across two cell lines, A549 and NCI-H460, at 0, 3, 6 and 24 hours

first: Ryan

middle: J

last: Conrad

first: James

last: Mondo

first: Timothy

last: Sterne-Weiler


title: NRF2 supports non-small cell lung cancer growth independent of CBP/p300-enhanced glutathione synthesis

overall_design: RNA-seq results in A549 cells that express both shNRF2 in addition to either: Wildtype NRF2, Neh4/5 mut NRF2, DeltaNeh1 NRF2, or Luciferase. Time points of 0 and 24 hours.


title: NRF2 supports non-small cell lung cancer growth independent of CBP/p300-enhanced glutathione synthesis [shNRF2_PROseq]

overall_design: PROseq of knockdown of NRF2 by shRNA across two cell lines, A549 and NCI-H460, at 0, 3, and 6 hours


title: Single-cell RNA sequencing of nicotine-exposed testes reveals differences in cell proportion and transcription

first: Jiajun

last: Cui

summary: We have conducted single-cell RNA sequencing using 10x Genomics scRNAseq to explore the biological effects of nicotine exposure on mice testes. Previous studies have shown that nicotine exposure can alter male fertility, whereas the molecular changes in testicular tissue remain elusive. Here, we demonstrated the effects of nicotine exposure on cell proportion and transcription in testes, providing new insights into the mechanisms by which smoking affects male fertility.

overall_design: Three-week-old C57BL/6J male mice were divided into two groups: (1) Control group, which received normal drinking water; (2) Nicotine-exposed group, which received drinking water with 200 μg/mL nicotine for 8 weeks. Followed by treatment, single-cell RNA sequencing was performed on fresh, intact testes.

first: Yuxuan

last: Zheng

first: Guolian

last: Ding


title: Rigor and Reproducibility of GeoMx Digital Spatial mRNA Profiling performed on Human Kidney Tissues

city: Seattle

first: Shreeram

last: Akilesh

state: WA

address: 1959 NE Pacific St, Box 356100

department: Laboratory Medicine and Pathology

institute: University of Washington

summary: Spatial transcriptomic profiling enables precise quantification of gene expression with simultaneous localization of expression profiles onto tissue structures. This new technology promises to improve our understanding of the disease mechanisms. Therefore, there is intense interest in applying these methods in clinical trials or as laboratory developed tests to aid in diagnosis of disease. Before these applications can been more broadly deployed in clinical research and diagnostics, it is necessary  to thoroughly understand the technology’s performance in real world conditions. In this study, we vet technical reproducibility, data normalization methods and assay sensitivity of digital spatial profiling, one widely used spatial transcriptomic methodology. Using clinically sourced human tissue specimens, we find that digital spatial profiling exhibits high rigor and reproducibility. Our approach lays the foundation for incorporation of digital spatial profiling methods into clinical workflows.

sample_organism:
Homo sapiens
blank sample

platform_organism:
Homo sapiens
blank sample

overall_design: Human nephrectomy tissues were fixed in formalin and paraffin embedded (FFPE) and multiple tissue chunks were embedded into one block (multi-tissue block). Four consecutive 5µm thick sections from the kidney multi-tissue block were applied to charged slides and baked at 60°C for 1 hour. After deparaffinization and rehydration, sections were subjected to heat induced antigen retrieval with Tris EDTA, pH 9 for 15 minutes followed by 1µg/ml proteinase K digestion for 15 minutes at 37°C. All 4 slides were hybridized overnight at 37°C with the Cancer Transcriptome Atlas (CTA) probe mix encompassing 1,825 genes. Per Nanostring’s protocol, sections are usually incubated with 250µl of probe mix and coverslipped using a 40x22 mm RNase-free HybriSlip coverslip (ThermoFisher). However, in order to extend the use of the probes, which are the most expensive component of the digital spatial profiling workflow, we utilized 100µl of probe mix per slide and coverslipped sections using a 22x22mm HybriSlip. The following day, all 4 slides were subjected to stringency washes and counterstained with fluorescently labeled antibodies recognizing pan-cytokeratin (Cy3 channel), CD10 (Cy5 channel) as well as DNA (Syto13, FITC channel). One slide was then loaded into the instrument while the others were stored in 2x SSC in the dark at 4°C for staggered collections. On 3 subsequent days, one of the remaining labeled slides was restained with Syto13 for 10 minutes before loading onto the instrument. After loading onto the instrument and scanning, ROI selection was performed, and UV-released barcode probes were collected in staggered fashion into a 96-well collection plate (24 ROI/day). After 4 consecutive days of ROI selection, libraries were generated using a SeqCode construction kit from Nanostring. The libraries were sequenced using a NextSeq 2000 P2 flowcell (100 cycle kit). Sequenced barcodes were mapped to genes and ROIs using the Nanostring GeoMx NGS Pipeline, version 2.0.21.


title: Comparison of CosMx and GeoMx profiling performed on the same human kidney tissues [CosMx]

overall_design: Tissues were collected in deidentified fashion with approval of the University of Washington’s IRB Study 1297.  Fresh human kidney tissues were sourced from patient’s undergoing nephrectomy for removal of kidney tumors. Samples of uninvolved kidney (4 donors), and a portion of the kidney tumor (renal cell carcinoma, RCC; 1 donor) were fixed in 10% neutral buffered formalin for 24-48 hours and then transferred to 70% ethanol for another 24 hours. Samples from all 4 donors (5 pieces of tissue) were paraffin embedded into a single multi-tissue block prior to sectioning. We profiled this tissue block for both digital spatial profiling (GeoMx DSP) and single molecular imaging (CosMx SMI). We aimed to test the rigor and reproducibility of GeoMx DSP and compare its performance against CosMx SMI.


title: Bulk White Blood Cells in MAFLD/MASH

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

institute: Boehringer Ingelheim Pharma GmbH & Co KG

summary: Background & Aims: Metabolic dysfunction associated steatotic liver disease (MAFLD) progresses to steatohepatitis (MASH) and is a major cause of liver cirrhosis. In the early disease stage, liver inflammation is absent. However, the early involvement of the peripheral immune cell compartments in disease progression is poorly understood and single cell profiles of peripheral immune cells in MAFLD/MASH are not known. Methods: MAFLD/MASH patients and healthy volunteers have been prospectively enrolled into a cross-sectional study characterized by White Blood bulk RNA-Seq.

overall_design: Bulk RNA-seq samples were collected from white blood cells from healthy controls and MAFLD/MASH patients

first: Agnes

last: Steixner-Kumar

first: Diana

last: Santacruz

first: Tobias

last: Geiger

first: Werner

last: Rust

first: Dennis

last: Böttner

first: Oliver

last: Krenkel

first: Ehsan

last: Bahrami

first: George

last: Okafo

first: Thomas

middle: F

last: Barth

first: Mark

last: Haenle

first: Wolfgang

last: Kratzer

first: Patrycja

last: Schlingeloff

first: Julian

last: Schmidberger

first: Heike

last: Neubauer

first: Alec

last: Dick

first: Markus

last: Werner


title: Digital Spatial Profiling of Human Kidney Biopsies from Patients with Minimal Change Disease

first: Shreeram

last: Akilesh

overall_design: We applied whole transcriptome atlas (WTA) digital spatial profiling (>18,000 genes) to understand the gene expression profiles of glomeruli from n=10 patients with MCD and n=4 controls. We had previously generated cancer transcriptome atlas (CTA, 1,825 genes) measurements from n=12 glomeruli of 3 individuals with histologically normal kidney biopsies. In this study, we performed WTA measurements on n=20 glomeruli from those same 3 individuals. After performing QC and Q3 normalization, we identified a subset of 451 genes that were measured above the limit of quantification (LOQ) in the glomeruli hybridized with CTA probes. We then compared the average counts of these genes (across the 3 donors) against the average Q3 normalized counts generated using the WTA probe mix on the same 3 donors’ kidney biopsy tissues.


title: Co-culture CRISPR screens reveal ATG9A as a regulator to macrophage-mediated cytotoxicity in cancer

city: San Francisco

first: Meng

last: Zhang

address: 1450 3rd Street

institute: University of California, San Francisco

summary: This study investigates the role of cancer cell surface proteins in modulating the response of cancer cells to macrophage-induced cytotoxicity. Utilizing two targeted CRISPR screens using OVCAR-8 cell line and a targeted CRISPR library for cancer cell surface proteins, ATG9A was identified as a key regulator. ATG9A KO increased the sensitivity of cancer cells to macrophage-induced cytotoxicity. Subsequent RNA sequencing and other analysis elucidated the underlying mechanisms; ATG9A KO in cancer cells not only enhances inflammatory cytokines production but also plays a crucial role in the plasma membrane repair following macrophage co-culture. These findings reveal novel targets for enhancing macrophage-mediated cytotoxicity in cancer, offering additional avenues for therapeutic intervention.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: mRNA-seq was performed in control sgGAL4 and sgATG9A OVCAR-8 ovarian cancer cells. In this study, two million sgGAL4 or sgATG9A SKOV3 cells were subcutaneously injected into the flanks of NSG mice. Tumor growth was monitored bi-weekly and calculated using the formula: (length ×h²Once tumors reached approximately 50 mm³e were randomized into treatment groups and received intraperitoneal injections of Trastuzumab (10 mg/kg) or human IgG isotype control every 2-3 weeks. Additionally, mice were fed a diet containing the CSF1R inhibitor PLX5622 at 1200 ppm. After 6-7 weeks of treatment, mice were euthanized, and tumors were harvested for downstream analyses.

first: Tianyi

last: Liu

first: Felix

last: Feng


title: Combined inhibition of KAT6A/B and Menin reverses estrogen receptor-driven gene expression programs in breast cancer (CRISPR-Seq)

first: Scott

last: Armstrong

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

summary: KAT6A is a histone acetyltransferase that is emerging as a therapeutic target in cancer, including estrogen receptor positive (ER+) breast cancer. We performed CRISPR screens to identify the chromatin adaptor Menin as a regulator of KAT6A inhibitor response. Co-treatment with KAT6A/B and Menin inhibitors had synergistic anti-proliferative effects in ER+, but not ER-, breast cancer lines. Our data revealed that KAT6A and Menin cooperatively regulate ER-driven gene expression and chromatin accessibility via direct effects on ESR1 expression and at ER target genes. KAT6A and Menin co-localize at promoters of ESR1 and ER-driven genes and combined KAT6A/B and Menin inhibition selectively displaced RNA Pol II from chromatin at these loci. Combined KAT6A/B and Menin inhibition was effective in ER+ patient-derived organoids and in models of endocrine resistance. KAT6A/B and Menin inhibitors are currently in clinical trials and have shown manageable toxicity profiles, underscoring the potential therapeutic relevance for ER+ breast cancer.

overall_design: We performed a CRISPR–Cas9-based screen to identify regulators of response to KAT6A/B inhibition (PF-9363) in MCF7 breast cancer cell lines. MCF7 Cas9 expressing cells were infected with an epigentic-focused CRISPR guide library at an MOI of approximately 0.3. Cells were selected in puromycin and were cultured in triplicate in DMSO or 50nM PF-9363 for 30 days.

first: Sarah

middle: N

last: Olsen

first: Charlie

last: Hatton

first: Yanhe

last: Wen


title: Combined inhibition of KAT6A/B and Menin reverses estrogen receptor-driven gene expression programs in breast cancer (ATAC-Seq)

overall_design: Using ATAC-seq we examined changes in chromatin accessibility following 48 hours of Menin and/or KAT6A/B inhibition in MCF7 breast cancer cell lines.


title: Single-cell landscape of peripheral immune cells in MAFLD/MASH

first: Eric

last: Simon

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

overall_design: Refer to individual Series


title: CEPs suppress auxin signaling but promote cytokinin signaling to inhibit root growth in Arabidopsis

first: Yuwen

address: No. 1, Weigang, Xiaolingwei Street

institute: Nanjing agricultural university

summary: C-terminally encoded peptides (CEPs) are peptide hormones that function as mobile signals coordinating crucial developmental programs in plants. Previous studies have revealed that CEPs exert negative regulation on root development through interaction with CEP receptors (CEPRs), CEPR DOWNSTREAMs (CEPDs), the cytokinin receptor ARABIDOPSIS HISTIDINE KINASE (AHKs) and the transcriptional repressor Auxin/Indole-3-Acetic Acid (AUX/IAA). However, the precise molecular mechanisms underlying CEPs-mediated regulation of root development via auxin and cytokinin signaling pathways still necessitate further detailed investigation. In this study, we examined prior research and elucidated the underlying molecular mechanisms. The results showed that both synthetic AtCEPs and overexpression of AtCEP5 markedly supressed primary root elongation and lateral root (LR) formation in Arabidopsis. Molecular biology and genetics elucidated how CEPs inhibit root growth by suppressing auxin signaling while promoting cytokinin signaling. In summary, this study elucidated the inhibitory effects of AtCEPs on Arabidopsis root growth and provided insights into their potential molecular mechanisms, thus enhancing our comprehension of CEP-mediated regulation of plant growth and development.

overall_design: There were two treatments, mock and AtCEP5, and three time points were taken at 6h, 12h and 24h for each treatment, and samples were taken before treatment, i.e. at 0h.


title: Combined inhibition of KAT6A/B and Menin reverses estrogen receptor-driven gene expression programs in breast cancer (ChIP-Seq)

overall_design: Using ChIP-seq we examined  chromatin occypancy of BRPF1, KAT6A, Menin, KMT2A, H3K9ac, and H3K4me3 in breast cancer cell lines


title: Endogenous Glucocorticoid Receptor Activation Modulates Early-Stage Cell Differentiation in Pancreatic Progenitors of Mice and Humans

city: Autonomous CIty of Buenos Aires

first: Santiago

middle: Andres

last: Rodriguez Segui

address: Intendente Guiraldes s/n

country: Argentina

institute: IFIBYNE-UBA-CONICET

summary: Understanding pancreatic development is instrumental to diabetes research and β-cell replacement therapies. Here, we investigate glucocorticoid receptor (GR) signaling during early pancreas development in mice and humans. Previous reports suggest that glucocorticoids do not play a significant role in mouse pancreas development before the second transition. In this study, we demonstrate that, under physiological conditions, the GR is selectively active in mouse pro-acinar and early endocrine cells from embryonic day 11.5, silenced in bipotent progenitors, and reactivated during endocrine commitment. In mouse pancreatic explants, ectopic GR activation globally promotes acinar fate. Surprisingly, GR activation in human in vitro-derived multipotent pancreatic progenitors steers lineage commitment toward a bipotent/endocrine trajectory and upregulates genes for which expression profiles resemble those of SOX9 and HES1 during human embryonic pancreatic bipotential and endocrine progenitor fate choice. Our combined epigenomic and single-cell transcriptomic analyses suggest that these newly identified marker genes may play important roles in human pancreas development. Taken together, our findings position the GR pathway as an endogenous developmental modulator of early-stage pancreatic progenitor cell differentiation and provide insights into the underlying transcriptional mechanisms involved.

overall_design: Pancreatic differentiation was induced in FSPS13.B human induced pluiripotent stem cells. To generate the treatments on Day 13 (multipotent pancreatic progenitor stage) and Day 16 (bipotent/endocrine progenitor stage) cells, dexamethasone (Dex, 100nM) or the EtOH vehicle (Ctrl) were added to the corresponding culture medium composition 24 h before cell collection. Thus, to generate Day 13 treated and untreated cells, Dex or EtOH was added on day 12 to the days 9-13 media composition. To generate Day 16 treated and untreated cells, Dex or EtOH was added on day 15 to the days 14-16 media composition.

first: Silvio

last: Traba

first: Lucas

last: Bacigalupo

first: Daniella

last: Fradin

first: Irene

last: Talon

first: Ana

last: Heidenreich

first: Daniele

last: Muraro

first: Jose

last: Garcia-Bernardo

first: Christopher

last: Gribben

first: Fatima

last: Lugtu

first: Juan

middle: I

last: Burgos

first: Agustin

last: Romero

first: Mariya

last: Chhatriwala

first: Adali

last: Pecci

first: Ludovic

last: Vallier

last: Rodríguez-Seguí


title: Gene profiling of the antitumor effects of Cxcl13-positive pancreatic stellate cells in an allogeneic subcutaneous transplantation model.

city: Hirosaki

first: Shuji

last: Shimoyama

state: Aomori

address: 5 Zaifu-cho

department: Department of Neurophysiology

institute: Hirosaki University Graduate School of Medicine

summary:
Pancreatic stellate cells are a kind of fibroblasts present in the pancreas and are the cells of origin of cancer-associated fibroblasts. In our previous study, we demonstrated the presence of Cxcl13-positive pancreatic stellate cells as a subpopulation of pancreatic stellate cells. In their genetic profiling, they were predicted to have anti-tumor effects, but their behavior in pancreatic cancer tissue in vivo is unknown.
Whole transcriptome analysis was performed to identify genes altered in tumors in which Cxcl13-positive pancreatic stellate cells were allogeneically subcutaneously transplanted with a pancreatic cancer cell line. In addition to the Cxcl13-positive pancreatic stellate cells,  tumors transplanted with myofibroblastic pancreatic stellate cells were also subjected to whole transcriptome analysis.

overall_design: Novel pancreatic fibroblast (nPaf) cells or myofibroblastic pancreatic fibroblast (myPaf) and pancreatic cancer cell lines (generated from KPCY mice) were mixed in Matrigel and injected into the right flank of 10-week-old C57BL6 female mice (n=3, respectively). Four weeks after, they were sacrificed by cervical dislocation and subcutaneous tumors were removed. The samples were subjected to whole transcriptome analysis or qRT-PCR.

first: Yutaro

last: Hara

first: Hiroki

last: Mizukami


title: Effect of overexpress of circPPARG1 on gene expression during adipogenic differentiation of Intramuscular adipocytes

city: Nanning

first: Huang

last: JiePing

address: Xixiangtang District

institute: Guangxi University

summary: To investigate the function circPPARG1 in the regulation of adipogenic differentiation, we overexpressed circPPARG1 in Intramuscular adipocytes

overall_design: First, Intramuscular adipocytes were planted in six-well plates in triplicate. When the cells reach 80% confluence, transduction was performed. Adenovirus were added to cells at the indicated MOI. Then, The culture medium was exchanged three hours later. Next, When transduction was performed for 48 hours, cells were treated with an inducing medium. Finally, Cells were collected for RNA sequencing after 48 hours of induction.

first: Jieping

last: Huang


title: Cardiac Piezo1 Exacerbates Lethal Ventricular Arrhythmogenesis by Linking Mechanical Stress with Ca2+ Handling After Myocardial Infarction

city: Hangzhou

first: Sheng-an

last: Su

state: Zhejiang

address: No. 88 Jiefang Road

institute: Zhejiang University

summary: Ventricular arrhythmogenesis is a key cause of sudden cardiac death following myocardial infarction (MI). Accumulating data show that ischemia, sympathetic activation, and inflammation contribute to arrhythmogenesis. However, the role and mechanisms of abnormal mechanical stress in ventricular arrhythmia following MI remain undefined. We aimed to examine the impact of increased mechanical stress and identify the role of the key sensor Piezo1 in ventricular arrhythmogenesis in MI. Concomitant with increased ventricular pressure, Piezo1, as a newly recognized mechano-sensitive cation channel, was the most up-regulated mechanosensor in the myocardium of patients with advanced heart failure. Piezo1 was mainly located at the intercalated discs and T-tubules of cardiomyocytes, which are responsible for intracellular calcium homeostasis and intercellular communication. Cardiomyocyte-conditional Piezo1 knockout mice (Piezo1Cko) exhibited preserved cardiac function after MI. Piezo1Cko mice also displayed a dramatically decreased mortality in response to the programmed electrical stimulation after MI with a markedly reduced incidence of ventricular tachycardia. In contrast, activation of Piezo1 in mouse myocardium increased the electrical instability as indicated by prolonged QT interval and sagging ST segment. Mechanistically, Piezo1 impaired intracellular calcium cycling dynamics by mediating the intracellular Ca2+overload and increasing the activation of Ca2+-modulated signaling, CaMKII, and calpain, which led to the enhancement of phosphorylation of RyR2 and further increment of Ca2+leaking, finally provoking cardiac arrhythmias. Furthermore, in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), Piezo1 activation remarkably triggered cellular arrhythmogenic remodeling by significantly shortening the duration of the action potential, inducing early afterdepolarization, and enhancing triggered activity.This study uncovered a proarrhythmic role of Piezo1 during cardiac remodeling, which is achieved by regulating Ca2+handling, implying a promising therapeutic target in sudden cardiac death and heart failure.

overall_design: RNA-seq was applied to profile the transcriptomes of myocardium from Piezo1fl/fl and Piezo1Cko mice at the 6th-week post-MI.

first: Yuhao

last: Zhang

first: Wudi

last: Li

first: Yutao

last: Xi

first: Yunrui

last: Lu

first: Jian

last: Shen

first: Yuankun

last: Ma

first: Yaping

last: Wang

first: Yimin

first: Lan

last: Xie

first: Hong

first: Yao

first: Meixiang

last: Xiang


title: Universal fibroblasts across tissues can differentiate into niche cells for hematopoietic stem cells

city: Suita

first: Kei

last: Higaki

state: Osaka

address: Nanobiotechnology building 3F, 1-3 Yamadaoka

department: Graduate School of Frontier Biosciences, Graduate School of Medicine, Immunology Frontier Research Center, World Premier International Research Center (WPI)

institute: Osaka University

summary: A single cell transcriptional profile of fibroblasts in the lung, ectopic bones and fetal limbs

overall_design: Fibroblasts were FACS-isolated from the lung, fetal limbs and ectopic bones formed in recipient mice transplanted with lung universal fibroblasts of Ubc-GFP mise. 5000-10000 cells were loaded onto 10X Genomic Chromium Single Cell Expression Solution version 3. platform. cDNA was sequenced by Illumina NovaSeq 6000.

first: Shota

last: Aiba

first: Takashi

first: Yoshiki

last: Omatsu

last: Nagasawa


title: Pexophagy-driven redox imbalance promotes virus-induced ferroptosis

status: Public on Apr 29 2025

first: Yingjie

last: Sun

address: 518 Ziyue Road

institute: Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science

summary: Peroxisomes are critical organelles that maintain cellular redox homeostasis. Many viruses induce oxidative stress and degrade peroxisomes, but the mechanisms and consequences remain unclear. In this study, we systematically investigate how virus-induced pexophagy regulates peroxisome homeostasis. Using Newcastle disease virus (NDV) as a model, we demonstrate that NDV infection triggers excessive ROS production, activating the phosphorylation and peroxisomal localization of Ataxia-telangiectasia mutated (ATM). Activated ATM promotes the interaction between the peroxisomal receptor PEX5 and the autophagy receptor p62, driving pexophagy. Pexophagy-mediated peroxisome degradation leads to excess active iron and ROS accumulation, contributing to NDV-induced ferroptosis. Notably, this mechanism is shared by other viruses, such as vesicular stomatitis virus (VSV) and H9N2 avian influenza virus (IAV). Our study provides new insights into how virus-induced pexophagy disrupts redox homeostasis to promote ferroptosis, highlighting a novel link between viral infection, peroxisome degradation, and programmed cell death.

overall_design: RNA-seq was conducted to compare gene expression profiles at multiple NDV infection time points (6, 12, 18, 24 hpi.) against the time-matched uninfected controls at each time point. Each group of samples included three replicates. Total RNA was extracted using TRIzol® Reagent following the manufacturer’s protocol. RNA quality was assessed via 5300 Bioanalyser and NanoDrop ND-2000, with only high-quality RNA (OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) used for sequencing library construction. RNA-seq libraries were prepared at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. using the Illumina® Stranded mRNA Prep, Ligation protocol. PolyA-selected mRNA was fragmented, reverse-transcribed into cDNA, end-repaired, and adapter-ligated, followed by PCR amplification and size selection (300 bp). Libraries were sequenced on the NovaSeq X Plus platform. Raw reads were quality-controlled by fastp and aligned to the reference genome via HISAT2. Mapped reads were assembled using StringTie. Differentially expressed genes (DEGs) were identified using DESeq2 or DEGseq, with thresholds of |log2FC|≥1 and FDR<0.05 (DESeq2) or FDR<0.001 (DEGseq). Functional enrichment analysis was also performed to interpret biological significance.

first: Yang

last: Qu

first: Chan

last: Ding