title: Spatially resolved m6A profiling using m6A-ARTR-DBiT

first: Chuan

last: He

state: Illinois

address: 929 E 57th St., GCIS E319

institute: The University of Chicago

summary: N6-methyladenosine (m6A) on RNA plays diverse regulatory roles, yet its spatial distribution within tissues remains largely unexplored. Here, we develop a spatial m6A profiling assay leveraging reverse transcription-based detection and deterministic barcoding in tissue (m6A-ARTR-DBiT), enabling spatially resolved sequencing of m6A within the native tissue context. Application of m6A-ARTR-DBiT to embryonic and adult mouse brain generated high-resolution whole transcriptome spatial m6A maps, offering insights into region-specific m6A modification.

overall_design: We developed an m6A profiling assay leveraging reverse transcription and deterministic barcoding in tissue (m6A-ARTR-DBiT) for spatial exploration of m6A modifications. We benchmarked this method on cell lines, demonstrating its capability to detect m6A modifications, and further applied m6A-ARTR-DBiT to mouse embryonic and brain tissues to generate high-resolution, whole-transcriptome spatial m6A maps.

first: Yu

last: Xiao

first: Zhiliang

last: Bai

first: Zhuoning

last: Zou

first: Rong

last: Fan


title: A conserved short 3 ́UTR short motif regulates gene expression in vertebrates

status: Public on Jan 14 2026

city: Porto

first: Bruno

last: Sousa

address: R. Alfredo Allen 208

country: Portugal

institute: Instituto de Investigaçã́o e Inovação em Saúde (i3S)

type: Expression profiling by high throughput sequencing

summary: The mRNA 3’ untranslated region contains important regulatory elements of gene expression, including upstream sequence elements (USEs), which modulate pre-mRNA 3’end processing and alternative polyadenylation. One of the best functionally characterized USE, located in the 3'UTR of the Drosophila polo gene, when disrupted, leads to downregulation of its expression and critical phenotypes in adult flies. Here, we found that the most conserved region of this USE (DplUSE) is also present in the 3'UTR of vertebrate genes, including zebrafish, mouse and human genes. Using reporter assays, we show that DplUSE increases gene expression in vitro in human cell lines and in vivo in zebrafish embryos. Importantly, in humans, DplUSE-containing genes are enriched in processes associated with serious diseases such as Congenital abnormalities. Concomitantly, we show that proper zebrafish development is disrupted when sequestering the molecular machinery that operates at the DplUSE, using a dominant negative strategy. As part of this molecular machinery, we found that the RNA binding protein PTBP1, PTBP1/hnRNPI, which has been previously shown to control USE-mediated gene expression in human cells,  is also required for the DplUSE function in human cells, as previously found for the fruit fly 31 orthologue Heph, suggesting an ultra-conserved mechanism present in distantly related bilateria. We also found that the SNP associated with malignant tumor of colon in the oncogene C11or53/POU2AF2,  is located within a DplUSE creating an ectopic consensus of DplUSE, which causes a gain of function in zebrafish gut. Moreover, in human cells, this SNP leads to an increase in mRNA and protein levels, indicating a possible mechanism of disease in colon cancer driven by disruption of the DplUSE. Taken together, these results show that a short 3’UTR motif in diverse bilaterian genes controls their mRNA expression levels via conserved RBP binding, with human disease implications.

overall_design: RNA-seq profiling of human HeLa cells with PTBP1 knockdown (siPTBP1) and a siRNA Non-target control (siNTC)

first: Ana

last: Eufrásio

first: Joana

last: Azevedo

last: Machado

first: Alexandre

last: Ferreira

last: Moutinho

first: Filipe

last: Henriques

last: Jesus

last: Tavares

first: Iris

middle: G

last: Kessler

first: Isabel

last: Pereira-Castro

last: Teixeira

first: Mafalda

last: Araújo

first: Pedro

middle: B

last: Pinto

first: José

last: Bessa

first: Alexandra

last: Moreira


title: Spatially resolved m6A profiling using m6A-ARTR-DBiT [spatial]

city: Chicago

last: He

country: USA

type: Methylation profiling by high throughput sequencing

last: Xiao

last: Bai

last: Fan


title: Testosterone treatment in transmen is associated with reduced hormone signaling in the mammary gland

city: San Francisco

first: Kiet

middle: Tuan

last: Phong

state: California

address: 600 16th Street

department: Department of Pharmaceutical Chemistry

institute: University of California, San Francisco

summary: Many transgender men receiving long-term testosterone replacement therapy (TRT) have high serum levels of testosterone, compared to the low levels seen in cisgender women. Compared to other sex hormones such as estrogen and progesterone, the effects of testosterone on the mammary gland have been relatively understudied. Comparison of mammary glands from transgender men on TRT and cisgender women can reveal the poorly understood consequences of testosterone expression on mammary gland biology and the long-term effects of TRT on patient health and disease outcomes. In this study, we performed single-cell RNA sequencing of breast tissues from cisgender women and transgender men on TRT. We identified that the donors on TRT had a decreased expression of genes downstream of estrogen signaling pathways in hormone receptor positive luminal epithelial, as well as a decrease in luteal phase gene activity in these donors. We confirmed this finding experimentally by showing reduced expression of progesterone receptor a/b, a prominent marker of estrogen signaling, in donors on TRT. Our results support the hypothesis that high levels of testosterone in transgender men on TRT suppresses hormone signaling in the breast through their impact on hormone receptor positive (HR+) mammary epithelial cells, with implications for TRT as an antagonist of estrogen receptor alpha (ER) signaling.

overall_design: To describe the effect of testosterone replacement therapy on the mammary gland in transgender men, we performed scRNAseq on healthy pre-menopausal and nulliparous breast tissues of 7 donors on testosterone and 7 not on testosterone, from either reduction mammoplasty or gender-affirming mastectomy surgeries. MULTI-seq barcoding and in silico SNP-based genotyping were used to multiplex samples in order to minimize batch effects. The pooled samples were selected for live (DAPI negative) and singlets by fluorescence activated cell sorting (FACS) prior to sequencing on a 10X Genomics platform.

first: Phong

last: Kiet

first: Song

last: Siyou

first: Kim

last: Esther

first: Conrad

last: Danny

first: Gartner

last: Zev


title: Transcriptional profiling of T cells of healthy individuals after treatment with supernatant of PBMCs of the same individuals treated overnight with sCD14 with isolated T cells cultured in TH17 polarizing condition and T cells treated with GABA overnight

city: Edmonton

first: Shima

last: Shahbaz

state: Alberta

address: 7-096 Katz Group Center for Pharmacy and Health Research

country: Canada

institute: University of Alberta

summary:
Comparison of transcriptional profiling of isolated T cells of healthy individuals after treatment with supernatant of peripheral blood mononuclear cells (PBMCs) of the same individuals treated overnight with soluble CD14 (sCD14) with isolated T cells cultured in TH17 polarizing condition and T cells treated with gamma-aminobutyric acid (GABA) overnight
In this study, we treated PBMCs of 7 healthy individuals with sCD14 overnight. The day after, the supernatant of treated PBMCs was collected and isolated T cells from the same individuals were stimulated with anti-CD3/CD28 and cultured with collected supernatant. We also cultured T cells from the same individuals with GABA overnight and stimulated them the day after with anti-CD3/CD28. Additionally, we cultured T cells from the same individuals in the presence of Th17 polarizing condition.

overall_design: RNA from T cells treated with different conditions was isolated and submitted for RNAseq analysis.

first: Shokrollah

last: Elahi

first: Amirhossein

last: Rahmati


title: Transcriptional profiling of isolated T cells of healthy individuals after treatment with supernatant of peripheral blood mononuclear cells (PBMCs) of the same individuals treated overnight with soluble CD14 (sCD14)

summary: In this study, we treated PBMCs of 6 healthy individuals with sCD14 overnight. The day after, the supernatant of treated PBMCs was collected and isolated T cells from the same individuals were stimulated with anti-CD3/CD28 and cultured with collected supernatant. RNA from T cells was isolated after 6 hours and submitted for RNAseq analysis.

overall_design: To investigate the differential gene expression pattern of T cells after treatment with the supernatant of PBMCs treated with sCD14


title: Disruption of jejunal and ileum homeostasis by malnutrition in systemic jejunal and ileum microbiota-host interactions in a pregnant sheep model

city: Hefei

first: Peng

last: Jiao

address: No. 130, Changjiang West Road, Hefei, Anhui Province, Anhui Agricultural University

country: China

institute: Anhui Agricultural University College of Animal Science and Technology

summary: In the current study, five late gestation multiparous ewes were restricted to a 30% feeding level to create a model of malnutrition, while five other ewes were fed normally as controls. All ewes were sacrificed and jejunal and ileal samples were collected for transcriptome sequencing to study metabolic changes.

overall_design: Compare the differences in transcriptome profiles between the jejunal and ileal sample from CON and TR ovis aries.

first: Weibin

last: Wu

first: Shengyong

last: Mao

first: Yanfeng

last: Xue


title: Schlafen 5 (SLFN5) is an Intracellular Immune Checkpoint and controls Interferon (IFN) Responses in Pancreatic Ductal Adenocarcinoma (PDAC)

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

summary: We provide evidence that human and murine SLFN5 proteins are modulators of Type I IFN responses and the immune response in pancreatic cancer.  Blocking expression of Slfn5 in PDAC enhances IFN-responses, suppresses tumor growth, and prolongs survival in immunocompetent mice. Notably, immunophenotypic analysis reveals a reduction in tumor-associated myeloid cells (TAMCs) alongside an increase in tumor infiltrating effector cells in tumors. These findings implicate SLFN5 acts as an intracellular immune checkpoint and identify it as a unique therapeutic target for the development of novel therapies for PDAC and possibly other malignancies

overall_design: RNA-Seq profiling of wildtype PANC-1 cells and SLFN5 knockout derivatives untreated or treated with interferon alpha (5,000 IU) for 6 hours

first: Leonidas

middle: C

last: Platanias

first: Frank

last: Eckerdt


title: DISTINCTIVE MOLECULAR SIGNATURE AND STRUCTURAL ALTERATIONS OF THE COLONIC BRUSH BORDER IN MICROSCOPIC COLITIS

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: BACKGROUND: Collagenous colitis (CC) and lymphocytic colitis (LC) are chronic inflammatory diseases of the colon of unknown etiology. We aimed to explore the underlying mechanisms of the colonic barrier dysfunction in MC by analysing the molecular pathways involved in the colonic epithelial brush border.  METHODS: We obtained colonic biopsies from CC and LC patients and from healthy controls (H) and irritable bowel syndrome with predominance of diarrhea (IBS-D) patients, as control groups. Transcriptomic and proteomic analysis by RNA-seq and liquid chromatography mass spectrometry, respectively, and an ultrastructural assessment or the epithelium by electron microscopy were performed. The impact of budesonide therapy on the epithelial structure was also evaluated in samples from CC patients Integrated clinical and biological data analysis was performed using R.  FINDINGS: A paired-omic analysis focused on the brush border identified a reduced expression of the inter-microvilli adhesion complex and the actin-bundling proteins in parallel to an increased expression of the actin-membrane connection of microvilli in MC patients compared to control groups. Moreover, colonic microvilli were shorter in length and reduced in number in CC and LC respect to controls. Treatment with oral budesonide partially recovered the ultrastructural alterations in parallel to clinical improvement. INTERPRETATION: Differentiated molecular and structural dysregulation of the colonic brush border features the colonic epithelium in MC. Given the fundamental role of the brush border in maintaining homeostasis, these previously undescribed findings open new perspectives to further define MC etiopathogenesis and the search of targeted therapies.

overall_design: RNA expression was determinedby RNAseq in colonic biopsies in three types of colitis ( 12 CC ,12 LC and 13 IBS-D) and  11 Healthy subjects . We performed sequencing using Illumina NovaSeq 6000 system,  paired-end reads and 101 length.

first: Danila

last: Guagnozzi

first: Ana Maria

last: Gonzalez-Castro


title: Assessing mifepristone's effects on endometrial tissue in women with BRCA mutations: A randomised clinical trial

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

summary:
Background: The endometrium, regulated by steroid hormones, is particularly susceptible to disease under imbalanced hormonal conditions. Progesterone regulates cell growth differently across tissues, acting as a pro-tumorigenic agent in the breast while serving as a tumor suppressor in the endometrium by countering the effects of oestradiol. Progesterone receptor modulators like mifepristone may prevent breast cancer formation but raise concerns about unopposed oestradiol exposure in the endometrium. This study examines mifepristone’s impact on the endometrium, particularly its potential link to endometrial carcinogenesis in BRCA mutation carriers, who have DNA repair and replication vulnerabilities.
Methods: This study was part of a randomised, double-blind, placebo-controlled trial in which pre-menopausal women carrying BRCA1 or BRCA2 mutations were assigned to a three-month treatment with either mifepristone (50 mg) or a non-hormonal comparator (TrioB) every second day. Endometrial biopsies were collected pre- and post- treatment, processed, and analysed for changes in endometrial thickness, cellular composition, methylation patterns, and gene expression profiles. Compliance and safety monitoring were rigorously maintained.
Results: Mifepristone treatment led to amenorrhea in all treated participants, consistent with its inhibition of ovulation. Ultrasound showed a non-significant increase in endometrial thickness post-treatment. Cellular analysis indicated a shift in composition, with a reduction in epithelial cells and an increase in fibroblast levels, suggesting that endometrial thickening may primarily reflect stromal expansion rather than epithelial proliferation. This distinction is clinically important, as epithelial proliferation is more closely associated with carcinogenesis. DNA methylation analysis revealed no significant alterations in the TCGA-EC methylation index, and gene expression profiling showed no significant elevation in carcinogenesis-related genes.
Conclusions: Mifepristone treatment in BRCA mutation carriers does not significantly impact methylation or gene expression profiles associated with endometrial carcinogenesis. The findings support from the safety of short-term mifepristone use in this population, although long-time safety of mifepristone use in BRCA mutation carriers will be needed.

overall_design: Molecular analysis involved RNA and DNA extraction from 15 paired biopsies, RNA sequencing using the Smart-seq2 protocol, and methylation profiling with Illumina Human Methylation EPIC arrays. RNA-seq data were processed using Partek Flow, identifying genes of interest, while DNA methylation data supported the development of an endometrial cancer index. This index, trained on TCGA UCEC data, demonstrated robust accuracy and was applied to the study dataset to explore its diagnostic utility.


title: Jk DNA GAGA MOTIFS ARE REQUIRED FOR LOCAL NUCLEOSOME REMODELING AND Vk-Jk RECOMBINATION [ATAC-Seq]

first: Mark

last: Maienschein-Cline

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Immunoreceptor gene recombination requires complementary 12 bp and 23 bp recombination signal sequences (RSSs). In addition, the RSSs that assemble the RAG proteins, recombination centers, must be accessible yet flanked by a 5’ nucleosome decorated with H3K4me3. In Drosophila, DNA GAGA motifs play an important role in nucleosome positioning. Herein, we report that 5’ to each functional Jk RSS is a DNA GAGA motif conserved across mammalian species. In mice, the GAGA motif 5’ to Jk1 regulated local RSS accessibility and 5’ nucleosome placement. Furthermore, it was required for Vk-Jk1 recombination. Murine Jk3 is nonfunctional, having mutations in both RSS and GAGA motifs. Restoring both GAGA and RSS motifs rescued Vk-Jk3 recombination. In contrast, restoring the RSS alone did not. Genome-wide, strong cryptic 23 RSSs were preferentially bound to nucleosomes. Furthermore, evolutionary selection against cRSS only occurred in the A Compartment of B lymphocytes, not embryonic stem cells. These data indicate that in developing B cells, nucleosome positioning both enables and restricts recombination to Jk. Furthermore, our data suggest an expanded definition of recombination center-associated RSSs to include a 5’ GAGA sequence that dictates the local epigenetic state required for gene recombination.

overall_design: ATAC-seq of flow-sorted small pre-B cells from WT, Jk1-GAGAmut, Jk3-GAGA/RSS and Jk3-RSS mice.

first: Margaret

last: Veselits

first: Kaitlin

last: McLean

first: Nathaniel

middle: E

last: Wright

first: Michael

last: Okoreeh

first: Jacob

last: Maienshein-Cline

first: Malay

last: Mandal

first: Marcus

last: Clark


title: MYOD1L122R induces cancer stem cell pathways to impart chemotherapy and radiation-resistance in aggressive rhabdomyosarcoma [scATAC-seq]

city: Charlestown

first: Luis Antonio

last: Corchete

institute: Krantz Family Center for Cancer Research

summary: Rhabdomyosarcoma (RMS) is a common pediatric soft tissue sarcoma of skeletal muscle. Worse  outcomes are associated with specific subtypes of RMS, including the 10% of fusion-negative  tumors that harbor point mutations in the DNA binding domain of MYOD1 (myogenic  differentiation 1) transcription factor. Due to the rarity of these patient samples and dearth of cell  lines/animal models, the molecular function of MYOD1L122R remains unknown. Here, we create  the first animal model of this disease showing that MYOD1L122R is not oncogenic but collaborates  with RAS activation to create highly aggressive RMS in transgenic zebrafish, akin to what is  reported in human disease. Limiting dilution cell transplantation revealed that MYOD1L122R also  elevated the overall frequency of tumor propagating cells in the zebrafish model. We next  generated isogenic knock-in MYOD1L122R human cell line models and showed that these cells  were refractory to standard of care vincristine, actinomycin, and cyclophosphamide while also  elevating the overall frequency of tumor propagating cells. Indeed, single-cell RNA transcriptional  profiling and single-cell assay for transposase-accessible chromatin with sequencing (ATAC-Seq)  of patient and patient-derived xenografts confirmed the elevation of cancer stem cell programs  within MYOD1L122R tumors. Using unbiased whole-genome ChIP and RNA sequencing, we next  identified the shared and differential genomic binding regions by MYOD1L122R as compared to  wildtype MYOD1. Most notably, MYOD1L122R bound uniquely to and transcriptionally upregulated  mesenchymal pathway enriched genes that are known to correlate with RMS cancer stemness.  Finally, mechanistic studies uncovered that MYOD1L122R binds to the regulatory element of ROR2  (receptor tyrosine kinase like orphan receptor 2), upregulating its expression, which then turns on  a novel WNT11-ROR2-VANGL2 axis to induce non-canonical WNT signaling and elevate cancer  stemness.

overall_design: We performed single-cell ATAC sequencing of four mutant MYOD1L122R PDX samples, and combined with four previous scATCseq of PDX samples  that have wildtype MYOD1.

first: Yun

last: Wei

first: Luis

middle: A

last: Sanchez

first: Shuze

last: Wang

first: Esther

last: Rheinbay

first: David

middle: M

last: Langenau


title: MYOD1L122R induces cancer stem cell pathways to impart chemotherapy and radiation-resistance in aggressive rhabdomyosarcoma [RNA-seq_HDR]

overall_design: Paired-end RNA-seq of isogenic RD cell line models with genomic knock-in with CRISPR homology-directed-repair (RD HDR)


title: Metallothionein 1 Regulates Growth and Survival of DNMT3A;NPM1-Mutant Acute Myeloid Leukemia

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: Adult de novo acute myeloid leukemia (AML) is a hematologic malignancy with poor prognosis, commonly driven by mutations in genes including the DNA methyltransferase DNMT3A and nucleophosmin NPM1. We previously generated sequentially inducible mouse models of these mutations and observed transformation from clonal hematopoiesis (CH) to myeloproliferative disorder to AML. In transformed AML, leukemia-propagating cells have a myeloid-restricted progenitor cell phenotype (c-Kit+). Here, to identify mechanisms that sustain tumorigenesis, we performed single-cell RNA-seq of c-Kit+ cells from four primary Dnmt3a;Npm1-mutant AML samples. The most primitive subset of c-Kit+ cells, a multipotent progenitor population Multi-Lin-2, had increased expression of the antioxidant and heavy metal chelator metallothionein 1 (Mt1) in all AML samples. Cas9-mediated Mt1 knockout in primary Dnmt3a;Npm1-mutant AML resulted in reduced cell cycling and proliferation and increased pyroptosis in vitro and increased overall survival following transplant into congenic recipient mice. Examining the human DNMT3A;NPM1-mutant AML cell line, OCI-AML3, we found that the metallothionein isoform MT1G was increased in expression relative to normal CD34+ hematopoietic stem and progenitor cells. Cas9-mediated MT1G knockout in OCI-AML3 cells resulted in reduced proliferation and cell growth in vitro. Together, our study reports an essential role for metallothionein in growth and survival of DNMT3A;NPM1-mutant AML cells.

overall_design: To understand the molecular impact of malignant cell populations relative to their non-malignant analogues, we leveraged and recently produced healthy hematopoietic cell atlas of 87 cell states, spanning all major bone marrow lineages. This atlas includes rare and transitional cell states, with evidence deriving from cell surface protein or transcriptome evidence (CITE-Seq). As this atlas excludes predominant hematopoietic and stromal cell populations in the spleen, we combined identified distinct cell states from multiple integrated spleen scRNA-Seq for the annotation of our datasets (Methods). The subsequent malignant cell populations were compared to normal equivalents to derive gene expression impacts retained across distinct DNMT3A mouse models.

first: Patricia

last: Colom-Díaz

first: Jayna

middle: J

last: Mistry

first: Chih-Hsing

last: Chou

first: Mohammad

middle: D

last: Khan

last: Boyer

first: Ross

middle: L

last: Levine

first: H

last: Grimes

first: Jennifer

last: Trowbridge


title: MYOD1L122R induces cancer stem cell pathways to impart chemotherapy and radiation-resistance in aggressive rhabdomyosarcoma [RNAseq_Rdoe]

overall_design: We performed RNA-seq using doxycline inducible expression of Flag-tagged or 3xHA-tagged MYOD1 or Flag-tagged or 3xHA-tagged MYOD1L122R to identify gene expression differences in RD cell line.


title: MYOD1L122R induces cancer stem cell pathways to impart chemotherapy and radiation-resistance in aggressive rhabdomyosarcoma.

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

overall_design: Refer to individual Series


title: Global landscape mapping of chromatin accessibility in therapy-induced senescent human stromal cells

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: We report the application of an improved assay for transposase-accessible chromatin with high-throughput sequencing in profiling changes of chromatin openning status in senescent human stromal cells. By obtaining over four billion bases of sequence from Tn5 transposase-processed chromosome DNAs, we generated genome-wide chromatin-state maps of human primary prostate stromal cells (with a starting cell number of 50,000). This study provides a framework for the application of ATAC-Seq technique towards spatiotemporal chromatin configuration of human stromal cells upon therapy-induced senescence, which is usually caused by typical DDR in damaged cells.

overall_design: Examination of three different cellular states in a primary normal human prosate stromal cell line, including proliferating cells, bleomycin-induced senescent cells and radiation-induced senescent cells.

first: Wei

last: Zhang


title: Deciphering the molecular mechanism of flight loss in mulberry silkworm through the integration of single-cell and spatial transcriptomics [B_scRNA-seq]

first: Qiancheng

last: Xiao

address: Building 25, No. 1188, LIANHANG Road, Pujiang Town, Minhang District, Shanghai

institute: Shanghai OE Biotech Co., Ltd

summary: Loss of flight is recurrently observed in flying species and markedly abates threats to human health and agricultural production posed by flying pests. However, our understanding of the flight organs involved remains limited. The silkworm Bombyx mori, a lepidopteran model insect, loses flight most recently, while the Bombyx mandarina capable of flight, therefore it is a good model for studying flight loss. Here, we represent the first description of the spatiotemporal architecture of Bombyx flight organs. We demonstrated that the weakened cellular function of NFDCs and FECs determining the flight energy and wing vein and flight muscle development largely result in flight loss in B. mori, and single-cell analyses of cotton bollworm flight organs and RNA interference (RNAi) of key genes validated these findings, and the cellular and molecular determinants of flight may be conserved across Lepidoptera. These findings will contribute to the understanding of flight loss encountered in flying species.

sample_organism:
Bombyx mori
Bombyx mandarina

platform_organism:
Bombyx mori
Bombyx mandarina

overall_design:
We used scRNA of to gain a global understanding of the cell types and expressed genes in wing discs of B. mori, B.mandarina and H. armigera
Please note that "FWD" represents 'Fore wing discs' and "HWD" represents 'Hind wing discs', which will develop into the fore-wings of moth and hind-wings of moth, respectively.

first: Rongpeng

last: Liu

first: Chen

last: Zhao

first: Jie

last: Hu

first: Yongbing

last: Ba

first: Yan

last: Ma

first: Yiting

last: Ran

first: Yuanyuan

last: Mu

first: Yinghao

last: Li

first: Xiaoqing

last: Xu

first: Yiyun

last: Tang

first: Qingjun

first: Yuqin

last: Chen

first: Zhiming

first: Kaiqi

last: Guo

first: Yuting

first: Zhiwei

first: Keshu

last: Dong

first: Xiao

last: Tan

first: Yumeng

last: Zhu

first: Zhonghuai

last: Xiang

first: Hanfu


title: Deciphering the molecular mechanism of flight loss in mulberry silkworm through the integration of single-cell and spatial transcriptomics [stRNA-seq]

first: Qiancheng

last: Xiao

overall_design:
We used spatial transcriptome RNA sequencing (stRNA-seq) to gain a spatial transcriptome atlas of spatiotemporal architecture in wing discs of B. mori and B.mandarina
Please note that "FWD" represents 'Fore wing discs' and "HWD" represents 'Hind wing discs', which will develop into the fore-wings of moth and hind-wings of moth, respectively.

first: Rongpeng

first: Chen

first: Jie

first: Yongbing

first: Yan

last: Zhang

last: Wang

first: Wei


title: MYOD1L122R induces cancer stem cell pathways to impart chemotherapy and radiation-resistance in aggressive rhabdomyosarcoma [RNAseq_Ruch2oe]

first: Luis Antonio

last: Corchete

overall_design: We performed RNA-seq using doxycline inducible expression of 3xHA-tagged MYOD1  or 3xHA-tagged MYOD1L122R to identify gene expression differences in Ruch2 cell line.

first: Yun

last: Wei

first: Luis

last: Sanchez

first: Shuze

first: Esther

last: Rheinbay

first: David

last: Langenau


title: Blood-Based microRNA Biomarker Signature of Early-Stage Pancreatic Ductal Adenocarcinoma with Lead-Time Trajectory in Pre-Diagnostic Samples

city: Houston

first: Warapen

last: Treekitkarnmongkol

state: TX

address: 2130 W. Holcombe Blvd.,  Unit 2951

department: Translational Molecular Pathology

institute: UT MD Anderson Cancer Center

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background & Aims: Early detection biomarkers for pancreatic ductal adenocarcinoma (PDAC) are needed since the clinically validated biomarker, CA19-9, has limited sensitivity and specificity for early-stage disease. Circulating miRNAs in plasma associated with cancer relevant pathways were developed as early detection biomarkers.
Methods: Whole transcriptome assay interrogated 2,083 miRNAs in 15 µl of plasma from multicenter diagnostic cohorts (N=203: controls, n=82; diagnosed PDAC cases: n=121) and a pre-diagnostic PLCO cohort (N=96; controls, n=48; pre-diagnosed cases, n=48). A three-miRNA biomarker signature was developed for early detection of PDAC.
Results: The three-miRNA signature detected PDAC from healthy controls independently (AUC = 0.974) and in combination with CA19-9 (AUC = 0.995). It also discriminated from pancreatitis (AUC = 0.931), improving performance of CA19-9 alone (AUC = 0.749) in combination (AUC = 0.954). Blinded validation in pre-diagnostic PLCO cohort revealed lead-time trajectory increase in AUC to 0.702 tat twelve-months before PDAC diagnosis.
Conclusions: Plasma miRNAs associated with oncogenic pathways may serve as PDAC early detection biomarkers, with model performance progressively increasing approximately twelve months before diagnosis.

overall_design: Whole transcriptome assay interrogated 2,083 miRNAs in 15 µl of plasma from multicenter age-matched cohorts (N=203: controls, n=82; diagnosed PDAC cases: n=121) and a pre-diagnostic PLCO age- and gender-matched cohort (N=96; controls, n=48; pre-diagnosed cases, n=48).

first: Subrata

last: Sen


title: MYOD1L122R induces cancer stem cell pathways to impart chemotherapy and radiation-resistance in aggressive rhabdomyosarcoma [ChIP-seq]

overall_design: We performed ChIP-seq using doxycline inducible expression of Flag-tagged MYOD1 or Flag-tagged MYOD1L122R, along with histone modification marks of H3K27ace, and H3K4me3 to identify global binding differences and histone modifications alterations introduced by these two proteins for RD and Ruch2 cell lines.


title: Genome-wide investigation of chromatin features in human senescent cells and characterization of genome-transcriptome interplays by CUT&Tag profiling

first: Yu

last: Sun

summary: Significant alterations in epigenetic landscapes can affect chromatin accessibility and genome-wide transcriptional expression. Cellular senescence, a stable state of growth arrest, is functionally engaged in numerous physiological and pathophysiological processes, and can promote organismal aging, restrain life quality and compromise healthspan. Mounting evidence suggests that senescent cells experience profound chromatin remodeling, but the underlying mechanisms linking epigenetic reorganization and gene expression profile remain less clear. In this study, we aimed to delineate the genome-wide redistribution of accessible chromatin regions leading to broad transcriptome expression changes during human diploid fibroblast (HDF) senescence, especially upon therapy-induced senescence (TIS). We report the distinct senescence-activated accessibility regions (SAARs) that tend to be distributed in H3K9me3-, H3K36me3- and H3K27ac-decorated enhancer regions, where the SAARs are responsible for increased SASP expression and multiple signaling events associated with SASP component secretion into the extracellular space. Mechanistically, a number of factors are involved in the activities of CCCTC-binding factor (CTCF), a master regulator of genome architecture facilitating establishment of  conserved chromatin loops by cooperating with cohesin and other partners. Taken together, results of this study help identify key transcription factors regulating the senescence-specific program with outputs from multi-omics analysis, and provide potential therapeutic targets for future pipelines of anti-aging industry.

overall_design: Primary human diploid fibroblasts (HDFs), namely PSC27, either proliferating (CTRL), exposed to ionizing radiation (RAD) or treated by the chemotherapeutic agent bleomycin (BLEO), were chemically dissociated, and fixed at room temperature. Cells were permeabilized and concentration was adjusted to 1x106 cells/ml. An fxCycle far red dye and RNase A were added and samples were incubated prior to resuspension at a concentration of 107 cells/ml and immediately processed for FACS. FACS was performed using BD FACSAria and appropriate gates were set based on the relative levels of fxCycle in order to isolate G0-G1 cells. After FACS sorting, cell were pelleted before frozen in liquid nitrogen and stored at −80°C. Hi-C library preparation was carried out using the in situ method described previously (Rao etal., 2014) with minor modifications.

first: Changxu

first: Xuefeng

last: Dou


title: MYOD1L122R induces cancer stem cell pathways to impart chemotherapy and radiation-resistance in aggressive rhabdomyosarcoma [scRNA-seq]

overall_design: We performed single-cell RNA sequencing of four mutant MYOD1L122R PDX samples (one already published with GSE195709), and combined with four previous scRNAseq of PDX samples  that have wildtype MYOD1 (GSE195709).


title: Effects of TMEM55B deficiency on hepatic gene expression of Western diet-fed male mice

city: Oakland

first: Marisa

last: Medina

state: CA

address: 5700 Martin Luther King Jr. Way

department: Pediatrics

institute: UCSF

summary: Transmembrane protein 55B (TMEM55B) is a lysosomal protein that modulates lysosome position and function. We examined the impact of TMEM55B deficiency on mitochondrial function and the development of Metabolic Dysfunction Associated with Steatohepatitis (MASH).  We found that several genes implicated in mitochondria function including mitophagy regulator Prkn (p=1.11e-10), and Immp2i (p=1.29e-22) and Sugct (p=8.82e-10) were downregulated in the livers of male mice treated with Tmem55b ASO compared to NTC ASO. In additon, the RNAseq analysis of 4-week Tmem55b vs. NTC ASO treatment demonstrated a functional enrichment of upregulated genes involved in cell adhesion (Flrt2, Egfl7, Col8a1, Pkp3, Pcdh17, Mcam) in the liver. Taken together, our data suggested that loss of TMEM55B accelerates diet-induced MASLD onset and progression in mice through impaired mitochondrial function.

overall_design: To investigate the role of TMEM55B in the onset and progress of MASLD, male 6-7 week-old C57BL/6J mice were treated with Tmem55b (N=4) or non-targeting control (N=4) ASOs at a dose of 25 mg/ kg body weight/wk and fed Western diet (43% fat, 0.2% cholesterol, Harlan Laboratories, Madison, WI) for 4 weeks. Total RNA was extracted from livers, checked for quality on a Bioanalyzer, and made into polyA-selected, strand-specific RNA-seq libraries for 150 bp paired-end sequencing on Illumina NovaSeq machines.

first: Yuanyuan

last: Qin

first: Elizabeth

last: Theusch

middle: W


title: Transcriptional profiling of skin cancer NK cells reveals the elevated glucocorticoid receptor activity alters their pro-inflammatory features.

city: Nanjing

first: Yuancheng

last: Li

state: JiangSu

address: No. 12 Jiangwangmiao Street

department: Institute of Dermatology

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

summary: The interplay between natural killer (NK) cells and tumor microenvironment (TME) is closely associated with tumor progression. We showed NK cells are common constituents in the tissue of skin cancers including basal cell carcinoma (BCC), cutaneous squamous cell carcinoma (cSCC), extramammary paget disease (EMPD) and acral melanoma (aMM). scRNA-Seq revealed an inter and intra-tumor transcriptional heterogeneity of NK cells in different skin TMEs. Unexpectedly, compared to peri-tumor, skin tumor NK cells down regulated the production of anti-tumor cytokines, IFN-γ and TNF-α, and up regulated the production of amphiregulin (AREG), a ligand of epidermal growth factor receptor (EGFR), which functions in promoting skin tumor growth and mediating immune tolerance.

overall_design: CD45+ cells from tumor and peri-tumor tissue were enriched and were subjected to scRNA-Seq, the NK cells sorted from PBMCs that were treated with glucocorticoid were subjected to bulk RNA-Seq

first: Yetao


title: Deciphering the molecular mechanism of flight loss in mulberry silkworm through the integration of single-cell and spatial transcriptomics [H_scRNA-seq]

first: Qiancheng

first: Rongpeng

last: Liu

first: Chen

last: Zhao

first: Jie

last: Hu

first: Yongbing

last: Ba

first: Yan

last: Ma

first: Yiting

last: Ran

last: Mu

first: Yinghao

first: Xiaoqing

last: Xu

first: Yiyun

last: Tang

first: Qingjun

first: Yuqin

last: Chen

first: Zhiming

first: Kaiqi

last: Guo

first: Yuting

first: Zhiwei

first: Keshu

last: Dong

first: Xiao

first: Wei

last: Tan

first: Yumeng

last: Zhu

first: Zhonghuai

last: Xiang

first: Hanfu


title: Post-lactational involution promotes recruitment of local CD8+ T cells with a resident-phenotype that controls breast cancer growth

city: Melbourne

first: Jianan

last: Wang

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: The mechanisms by which parity and breastfeeding mediate protection against breast cancer, particularly triple-negative breast cancer (TNBC), remain unclear. CD8+ T cells with a tissue-resident-like phenotype (TRM) are present in TNBCs and are associated with better clinical outcomes. In preclinical models of TNBC, CD8+ TRM-like cells can protect against BC recurrences. These cells are also present in healthy, non-cancer-affected breast tissue. We hypothesized that post-lactational involution could facilitate increased CD8+ T cell recruitment locally to the breast, improving immune surveillance against BC. Consistent with this, we observed significantly higher quantities of immune cells and CD103+CD8+ T cells in healthy breast tissue collected from parous vs. nulliparous women. In preclinical murine models, we observed that after a period of lactation and involution, CD8+ TRM-like cells increase in quantity the mammary gland. Using syngeneic models of TNBC, we show that these higher quantities of local CD8+ T cells in the mammary gland are associated with significantly decreased tumor growth, with higher intratumoral T cell content. We further find that parous women vs. nulliparous women who develop primary TNBC have significantly higher T cell infiltration in their tumors. Our data provide evidence that lactation and post-lactational involution result in quantitative and qualitative differences in local resident CD8+ T cells that can restrain mammary tumor outgrowth.

overall_design: Single cell suspensions of parous normal breast tissue were obtained by enzymatic dissociation as previously described on the day of surgery. Viable cells were FACS sorted by propidium iodide staining for CD45+CD3+CD45RO+CCR7- sub-population that were and further sorted CD8+CD69+CD103+ and CD8+CD69+CD103- T cell subsets

first: Balaji

last: Virassamy

first: Franco

last: Caramia

first: Peter

last: Savas

first: Michael

last: Harris

first: Sherene

last: Loi


title: RNA profiling in medial prefrontal cortex  of morphine addiction mice

city: Xi'an

first: Yuxiang

last: Zhang

state: Shaanxi

address: 76 Yanta West Road

department: College of Forensic Medicine

institute: Xi’an Jiaotong University

summary: total RNA-sequencing in mPFC from 3 saline control mice and 3 morphine addiction mice after morphine-induced conditioned place preference(CPP)

overall_design: Male C57BL/6J mice (8–10 weeks old) were treated with morphine (10 mg/kg, i.p.) and confined to the CPP apparatus for construction of morphine-induced conditioned place preference (CPP). After one-week of withdrawal in homecages, animals were sacrificed and the medial prefrontal cortex tissue was rapidly extracted for RNA-seq analysis.

first: Xixi

last: Yang

first: Chunxia

last: Yan

first: Dongyu

last: Yu


title: Aging-declined RNA Exportation Impairs Hematopoietic Stem Cells by Inducing R-Loop

city: Tianjin

first: Jianwei

address: 10 Yuexin Street, Binhai New Area

institute: HAIHE LABORATORY OF CELL ECOSYSTEM

summary: It is well acknowledged that aging-induced DNA damage accumulation impairs hematopoietic stem cell (HSC). While, how DNA damage is accumulated and how to eliminate it to rejuvenate aged HSCs are largely unknown. In this study, we observed that RNA exportation is compromised in aged HSCs due to aging-declined Alyref, the main component of TREX (transcription/export) complex. Targeted dysfunction of Alyref leads to RNA lingering in the nucleus and recapitulates the function of aged HSCs. Mechanistically, RNA accumulation in nucleus results in the formation of RNA:DNA hybrids, called R-loop structures, and subsequent induction of replication stress. Genome-wide profiling reveals significant increase of R-Loop in aged HSCs, which is significantly associated with resident RNA in the nucleus. Quantitative refill of Alyref in aged HSCs significantly restores RNA shuttling, dampens R-Loop and replication stress, and ultimately ameliorates the function of aged HSCs. In brief, our study for the first time demonstrates that aging-induced replication stress originates from the formation of aberrant RNA shuttling-driven R-loop structures and raises the possibility that quantitatively manipulating Alyref signaling can counter the physiologically deleterious effect of aging on HSCs.

overall_design: To  investigate the molecular differences among Alyref+/-, Alyref-/- and WT HSCs, freshly isolated HSCs from Alyref+/-, Alyref-/- and WT mice(C57BL6/N, 2-3 months) were subjected for RNA-seq; we then perform GSEA using data obtained from RNA-seq of Alyref+/-, Alyref-/- and WT HSCs.

first: Ruiqing

first: Qiongye

first: Qianwen

last: Sun


overall_design: To  evaluate the bulk poly(A)+RNA distribution between nucleus and cytoplasm of young and aged HSCs; freshly isolated HSCs (Lineage-ckit+Sca1+CD34-) were subjected for cytoplasmic and nuclear RNA fractionation;then the cytoplasmic and nuclear RNA were performed for RNA-seq;  cytoplasmin and nucler RNA  profiling analysis of  young and aged HSCs

last: Chen


title: Plastic state transitions and developmental potential predict response to Notch inhibition

city: Boston

first: Birgit

last: Knoechel

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

summary: The acquisition of immature cell states associated with an emergence of alternative cell fates may result in treatment resistance, yet the transcriptional and epigenetic processes dictating cellular plasticity in cancer remain elusive. To investigate how cell states drive transcriptional heterogeneity and impact developmental hierarchy, we performed single-cell transcriptomics on treated and untreated with NOTCH inhibitor T-cell acute lymphoid leukemia (T-ALL) patient-derived xenograft (PDX) models carrying activating NOTCH1 mutations. We identified cellular plasticity as an underlying mechanism of increased developmental potential which predicts response to Notch inhibition and determines the magnitude of NOTCH1-induced differentiation. Mapping 3D chromatin architecture revealed remodeling of the enhancer landscape by gain of short length enhancer-promoter interactions resulting in extensive transcriptional rewiring and state-specific dependencies in resistant cell states. Our study reveals the epigenetic and transcriptional changes responsible for treatment resistance and identifies drug vulnerabilities that may be exploited as therapeutic strategies for overcoming resistance.

overall_design:
Single cell expression profiles of 5 PDX models harbouring NOTCH1 activating mutations treated with the Notch1 inhibitor DBZ (Dipenzazepine)

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Submitter states that raw data can't be provided due to patient ethical issues
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first: Valeriya

last: Dimitrova

first: Julia

last: Frede

first: Anna

last: Montanaro

first: Noori

last: Sotoudeh Chafi

first: Hannah

last: Stuart

first: Huiyoung

last: Yun

first: Sayalee

last: Potdar

first: Alexandria

last: Van Scoyk

first: Shruti

last: Bhatt

first: Stephan

middle: R

last: Bohl

first: Praveen

last: Anand

first: Jake

last: Kloeber

first: Antonis

last: Kokkalis

first: Johannes

last: Waldschmidt

first: Anthony

last: Letai

first: David

last: Weinstock

first: Jon

last: Aster

first: Jens

last: Lohr


first: Jianwei

last: Wang

overall_design: To systemically examine the correlation of R-Loop with HSC aging, we profiled the R-Loop between young and aged HSCs; freshly isolated HSCs ( Lineage-ckit+Sca1+CD34-) were subjected for ssDRIP-seq;  profiling the genome-wide R-Loop at single-nucleotide resolution in young and aged HSCs to identify the exact region wherein R-Loop is strengthened upon aging

first: Ruiqing

last: Chen

first: Qiongye

last: Dong

first: Qianwen

last: Sun


title: Chemotherapy-induced extracellular matrix remodelling in HGSOC

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

summary: In this study we used two murine orthtotopic, transplantable synegeneic models, one that displays excellent response (60577) to carboplatin/paclitaxel and one that is highly chemoresistant (HGS2) and displays a weak response. We analysed the transcriptomes of these murine HGSOC tumours from both models across time in a therapeutic scheme that resembles the human condition.

overall_design: RNA sequencing on whole tumours from two murine orthtotopic, transplantable synegeneic HGSOC models (HGS2 timepoint-1 control, n = 3; HGS2 timepoint-1 treated, n = 3; HGS2 timepoint-2 control, n = 4; HGS2 timepoint-2 treated, n = 3; HGS2 timepoint-3 treated, n = 4; 60577 timepoint-1 control, n = 3; 60577 timepoint-1 treated, n = 3; 60577 timepoint-2 control, n = 3; 60577 timepoint-2 treated, n = 4; 60577 timepoint-3 treated, n = 4) . RNAseq was also performed on the 60577 and HGS2 cell lines grown in-vitro as monocultures (n = 2 perc cell line).

first: Panoraia

last: Kotantaki

first: Florian

last: Laforets

first: Frances

last: Balkwill


title: Spatial reorganization of chromosome architecture in human stromal cells upon therapy-induced senescence

first: Yu

summary: Cellular senescence is a basic biological process characterized by an essentially irreversible growth arrest. Senescent cells accumulate a variety of epigenetic alternations, but the three-dimensional (3D) organization of chromatin remains underexplored. We aim to characterize the 3D architecture of interphase chromosomes in proliferating, and therapy-induced senescent (TIS) cells of human stromal origin. Although the overall organization of chromatin into active (A) and repressive (B) compartments and topologically associated domains (TADs) is largely conserved between these conditions, a subset of TADs switches between compartments of proliferative versus TIS cells. On a global level, the Hi-C interaction matrices of senescent cells (TIS) are characterized by a relative gain of long-range, while a simultaneous loss of short-range interactions within chromosomes. Direct measurements of distances between genetic loci, chromosome volumes, and chromatin accessibility were performed. The structural model arising from this study provides a unique high-resolution view of the complex chromosomal architecture in human senescent cells.

overall_design: Human stromal cells, either proliferating (CTRL), treated by the chemotherapeutic agent bleomycin (BLEO) or damaged by ionizing radiation (RAD), were chemically dissociated, and fixed at room temperature. Cells were permeabilized and concentration was adjusted to 1x106 cells / ml. An fxCycle far red dye and RNase A were added and samples were incubated prior to resuspension at a concentration of 107 cells/ml and immediately processed for FACS. FACS was performed using BD FACSAria and appropriate gates were set based on the relative levels of fxCycle in order to isolate G0-G1 cells. After FACS sorting, cell were pelleted before frozen in liquid nitrogen and stored at −80°C. Hi-C library preparation was carried out using the in situ method described previously (Rao et al., 2014) with minor modifications.

first: Changxu


title: Transcriptomic signatures of immune suppression and cellular dysfunction distinguish latent from transcriptionally active HIV-1 infection in dendritic cells

status: Public on Jan 13 2026

city: Amsterdam

first: Neeltje

last: Kootstra

address: Meibergdreef 9

country: Netherlands

institute: AmsterdamUMC

summary: Dendritic cells (DCs) are essential for antiviral immunity but are also susceptible to HIV-1 infection. Although sensing and restriction pathways in DCs are well described, the mechanisms underlying latent infection and its functional consequences remain unclear. Here, we performed transcriptomic profiling of monocyte-derived DCs harboring transcriptionally active (Active-HIV) or latent HIV-1 (Latent-HIV) proviruses using a dual-reporter virus. Gene set enrichment analysis revealed suppression of metabolic and stress-modulatory programs in Active-HIV compared to unexposed DCs. In contrast, Latent-HIV showed broad downregulation of pathways, including interferon and innate responses and metabolic programs, indicating a hyporesponsive and dampened antiviral state despite the absence of differentially expressed genes (DEGs). DEG analysis of Active-HIV versus Latent-HIV showed that active transcription associates with cellular stress, cytoskeletal remodeling, and RNA-processing. Functional analyses further demonstrated activation of RNA processes, suppression of antigen-presentation pathways, and altered membrane and cytoskeletal signaling in Active-HIV. These pathways suggest that transcriptionally active HIV-1 leverages cellular machinery to support replication, creating a metabolically strained yet immunologically engaged state that disrupts antigen presentation. Conversely, latently infected DCs display a hyporesponsive state consistent with proviral silencing. This dichotomy reveals distinct mechanisms of DC dysfunction that may facilitate HIV-1 persistence and immune evasion.

overall_design: Primary monocyte-derived dendritic cells were infected with a VSV-G pseudotyped dual-reporter HIV-1 for five days. Transcriptionally active HIV-1-infected cells (MKO2+GFP+) and latently infected cells (MKO2+GFP-) were isolated by FACS. HIV-1-uninfected and -unexposed cells were included as controls.

first: Shirley

last: Man

first: Jade

last: Jansen

first: Neeltje A.

first: Teunis B.H.

last: Geijtenbeek


title: Calhm6: A Gatekeeper of Macrophage Plasticity and Immune Response [BMDM]

first: Jing

last: Geng

address: No.30 Huangcheng West Road, Xiwu Av (Administration, Teaching, Residential area

department: The Second Affiliated Hospital

summary: The dysregulation of macrophage differentiation is a significant contributing factor to the development of infection, inflammation, and even tumors. However, there are still numerous uncertainties surrounding the mechanism by which macrophage plasticity is controlled. Here, we report that Calhm6 regulates macrophage plasticity in a bidirectional negative feedback way to maintain host defense and tissue homeostasis. Specifically, the deficiency of Calhm6 greatly enhances the expression of pro-inflammatory mediators, bactericidal activity, and the M1-like differentiation of macrophages. Mechanistically, the accumulation of Calhm6 and intracellular calcium was increased by LPS-IFNγ through Irf1, which made M1-like signal turn off and weakened bactericidal activity.  Instead, the IL-4 signal inhibits the transcription of Calhm6 via Stat6, preventing macrophages from over-differentiating into M2-like cells. Additionally, we have identified a distinct isoform of Calhm6, which exhibits contrasting functionality compared to the full-length of Calhm6. Furthermore, both full-length or isoform of Calhm6 can be released into the extracellular or serum through ectosomes, thereby exerting a systemic influence on the differentiation and plasticity of macrophages in host. Overall, our work reveals the mechanism of calcium-driven Calhm6 in regulating the host defense and tissue homeostasis of macrophages, and provides ectosomes wrapped with Calhm6 as a therapeutic agent to improve anti-infection and tissue repair.

overall_design: To find the plasticity switch in macrophage, we treated BMDM with pathogens including E.coli, S.aureus, C.albicans, and LPS, then performed RNA sequencing.

first: Yanlong

last: Xin


title: Calhm6: A Gatekeeper of Macrophage Plasticity and Immune Response [Raw264.7-OE]

overall_design: To investigate the function of CALHM6 in macrophage, we established OE-Calhm6fl/OE-Calhm6iso cell lines which overexpress of Calhm6 or isoform of CALHM6, then examine these cell lines' gene profile by RNAseq


title: M-cadherin regulates the formation of adherens junctions and secondary myofibers during fetal myogenesis to determine adult myofiber number and muscle mass

city: Tarrytown

first: Michael

last: Stec

state: NY

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

summary: Cadherin-mediated adhesion of skeletal muscle stem cells within their niche is necessary for normal adult muscle maintenance and regeneration; however, the role of cadherins in regulating muscle development and growth has not yet been elucidated. Here, we show that M-cadherin protein is localized to adherens junctions in developing muscle, and that deletion of CDH15, the gene encoding M-cadherin, results in the loss of adherens junctions in fetal mouse muscle. This loss of adherens junctions is associated with reduced secondary myofiber formation, ultimately resulting in reduced adult myofiber number and muscle mass. Concordantly, via large-scale exome sequencing, we found that humans with predicted loss-of-function variants in the CDH15 gene had significantly reduced lean mass, indicating that M-cadherin functions to regulate muscle mass in both mice and humans. Overall, these data highlight a previously unrecognized role of M-cadherin in controlling fetal myofiber formation and establishment of adult muscle mass.

overall_design: Bulk RNASeq sequencing of WT and Cdh15 KO mice from multiple tissues

first: David

last: R. Golann

first: Patrick

last: J. Ferrara

first: Naveen

last: P. Khan

first: Margaret

last: Hung

first: Virgiinia

last: Hughes

first: Samer

last: Nuwayhid

first: Jonas

last: Bovijn

first: Peter

last: Dornbos

first: Luca

last: Lotta

first: Peisheng

last: Shi

first: Qi

last: Su

first: Yajun

last: Tang

first: Mark

last: W. Sleenman

last: J. Stec


title: As2S2 restores erythroid maturation in sf3b1-deficient zebrafish by upregulating smad7

first: Fan

last: Wu

address: DongFang road 1881

institute: Shanghai Municipal Hospital of Traditional Chinese Medicine

summary: SF3B1 is among the most frequently mutated genes in myelodysplastic syndromes (MDS) and is closely associated with aberrant erythropoiesis, yet strategies to restore terminal erythroid maturation in SF3B1-linked disease are limited. Using a zebrafish sf3b1 knockdown model, we demonstrate that arsenic disulfide (As2S2) reinstates erythroid reporter expression and hemoglobinization in morphants and yields partial persistence of rescue at later stages. Integrated transcriptomic analyses show that As2S2 remodels metabolic and translational programs and attenuates TGF-β pathway activity, notably inducing the inhibitory mediator smad7. Combining smad7 overexpression with pharmacologic TGF-β inhibition enhances recovery, consistent with a Smad7-dependent mechanism. These results identify As2S2 as an in vivo chemical probe that counteracts sf3b1-dependent erythroid failure via upregulation of Smad7 and highlight Smad7 as a candidate for therapeutic modulation in SF3B1- associated ineffective erythropoiesis.

overall_design: mRNA profiling by high throughput sequencing to dissect the molecular mechanism by which As₂S₂ rescues erythroid maturation defects via regulating Smad7/TGF-β axis in SF3B1 knockout zebrafish model


title: Calhm6: A Gatekeeper of Macrophage Plasticity and Immune Response

first: Jing

last: Geng

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

overall_design: Refer to individual Series


title: Hawaiian bobtail squid symbiont, Leisingera sp. ANG-M7, uses a “combined arms” strategy to overcome competitor resistance

city: Delaware

first: Andrea

middle: Maria

last: Suria

address: 61 S Sandusky Street

department: Biological Sciences

institute: Ohio Wesleyan University

summary: Competition between bacteria can impact the ability to colonize a host. In the accessory nidamental gland (ANG) reproductive symbiosis of the Hawaiian bobtail squid, Euprymna scolopes, symbionts colonize various epithelium lined tubules of adult females. We hypothesize that symbionts may use competitive mechanisms to  determine ANG tubule colonization outcomes. One ANG strain, Leisingera sp. ANG-M7, was found  to inhibit another ANG symbiont, Leisingera sp. ANG-DT, in vitro. Transposon mutagenesis was used to determine the genes required for this antimicrobial activity. Seven ANG-M7 transposon mutants were found with significantly decreased ability to inhibit ANG-DT compared to WT ANG-M7. Of these mutants, three strains (P08F1, P24E3, P40B12) were selected for transcriptome sequencing to look for shared pathways that were significantly different from WT.

overall_design: RNA-seq profiling of Leisingera sp. ANG-M7 WT and transposon mutants (P08F01, P24E03, P40B12) grown in SWT broth, 29°C, 200 rpm, for 8 hours.

first: Alecia

middle: N

last: Septer


title: Loss of Mtarc1 Protects Against Steatotic Liver Disease in Mice

city: Cambridge

last: Chaffin

address: 75 Ames Street

department: Cardiovascular Disease Initiative

institute: Broad Institute of MIT and Harvard

summary: Background & Aims: Metabolic dysfunction-associated steatotic liver disease (MASLD) spans from simple steatosis to metabolic dysfunction-associated steatohepatitis (MASH) and can progress to cirrhosis or hepatocellular carcinoma. Despite its prevalence, effective therapies are lacking. Recent genome-wide association studies identified a common missense variant (rs2642438) in the Mitochondrial Amidoxime Reducing Component 1 (MTARC1) gene that protects against liver cirrhosis without increasing cardiovascular disease risk. Biochemical and disease risk signatures associated with carriers of this missense variant also aligned with those of a known loss-of-function MTARC1 variant, suggesting mARC1 inhibition as a potential MASLD treatment.  Methods: To validate mARC1 loss-of-function as protective against MASLD, we generated Mtarc1 knockout (KO) mice and placed them on a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD). Effects of Mtarc1 KO on obesity and type 2 diabetes were explored using a high-fat diet. Hepatocytes from Mtarc1 KO mice were isolated to explore the molecular mechanisms by which Mtarc1 KO impacts lipid metabolism.  Results:  Mtarc1 KO mice exhibited no vital growth or development defects. With a high-fat diet-induced obesity model, obese Mtarc1 KO mice exhibited reduced liver mass and lower cholesterol levels, with no effect on glucose homeostasis. In a CDAHFD-induced MASLD model, mARC1 deficiency significantly reduced liver steatosis, profibrosis, and inflammation. Untargeted metabolomics profiling further showed hepatic enrichment of phospholipids in Mtarc1 KO mice. Primary hepatocytes isolated from Mtarc1 KO mice exhibited reduced lipid droplet accumulation, decreased fatty acid uptake, and increased lipid secretion.  Conclusions: These findings support mARC1 inhibition as a promising therapeutic strategy for MASLD/MASH.

overall_design: RNA-seq profiling of  liver tissue from wildtype, Mtarc1 heterozygous knockout, and Mtarc1 homozygous knockout  mice on a choline-deficient, L-amino acid-defined, high-fat diet. Wildtype mice on normal chow diet were also included.

first: Xiaofei

last: Yin

last: Ellinor


title: Lack of synergy between AR targeted therapies and PARP inhibition in homologous recombination- proficient prostate cancer

first: Nicole

last: Traphagen

institute: Dana-Farber Cancer Institute

summary: Recent clinical trials have explored the combination of androgen receptor (AR) pathway inhibitors and poly (ADP-ribose) polymerase (PARP) inhibitors as a potential treatment for castration-resistant prostate cancer. This combination treatment is based on the premise that AR directly regulates expression of DNA repair genes, leading to synergy between PARP and AR inhibition. Despite some promising preclinical evidence, this combination therapy has shown limited efficacy in patients with homologous recombination (HR)-proficient tumors. To investigate this discrepancy between preclinical and clinical results, we profiled the effects of PARP inhibition in prostate cancer models in the presence or absence of AR inhibition. Surprisingly, AR inhibition impaired response to PARP inhibitors in castration-sensitive cells and had no effect on response in castration-resistant cells. AR inhibition also did not regulate DNA repair in either the castration-resistant or castration-sensitive setting. Instead, we find that cell cycle progression is required for response to PARP inhibition in homologous-recombination proficient prostate cancer.

overall_design: RNA-seq profiling of LNCaP and 22RV1 cells treated with PARP inhibitors and AR inhibition

first: Myles

last: Brown


title: Systematic characterization of brain cellular crosstalk reveals a novel role for SEMA6D in TREM2-associated microglial function in Alzheimer’s disease

city: St Louis

first: Ricardo

last: D'Oliveira Albanus

state: MO

address: 4370 Duncan Avenue, Suite 6306D, Jeffrey T. Fort Neuroscience Bdg.

department: Neurology

institute: Washington University School of Medicine

summary: In this study we characterized the transcriptional effects of SEMA6D treatment in WT and TREM2 KO human induced pluripotent stem cell-derived microglia (iMGL) using RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and TREM2 KO iMGL under SEMA6D treatment or no treatment.

first: Tae-Wan

last: Kim

first: Gina

last: Finan


title: Lack of synergy between AR targeted therapies and PARP inhibition in homologous recombination- proficient prostate cancer [ATAC-seq]

overall_design: ATAC-seq profiling of LNCaP and 22RV1 cells treated with PARP inhibitors and AR inhibition


title: Targeting the Alk4 pathway protects against age-related bone loss.

city: Augusta

first: David

last: Maridas

state: GA

address: 1460 Laney Walker Blvd., CB2917

institute: Augusta University

summary: Osteoporosis is a chronic age-related condition where imbalanced activities between bone-forming osteoblasts and bone-resorbing osteoclasts result in the progressive loss of bone volume and reduced bone quality. While drugs that target osteoclast activity have been developed, there remains a lack of efficient therapies that increase osteoblast function in aging bones. Here, we showed that in mouse femurs, levels of Activin signaling progressively increased with age and strongly correlated with the loss of trabecular bone. When we removed Alk4, the type I receptor for Activin in osteoblast progenitors, Alk4 cKO mice had increased numbers of osteoblasts, an increased rate of bone formation, and increased trabecular bone acquisition. These results indicate that Activin through Alk4 signaling inhibits bone formation and osteoblast activity and is likely associated with osteoporosis. Furthermore, when we injected 2-year-old male mice with Alk4-Fc to capture circulating Activin, aged mice were protected against loss of trabecular bone in both femurs and L5 vertebrae. Remarkably, Alk4-Fc also prevented the age-related decrease in muscle mass that normally accompanies age-related bone loss, indicating that circulating Activins also play a role in sarcopenia. In summary, our preclinical mouse models reveal that circulating Activins play a primary role in age-related bone and muscle loss and can be efficiently targeted to alleviate osteoporosis and sarcopenia in aging mice.

overall_design: RNA seq of W20 cells treated with vehicle, BMP2 (100ng/mL), Activin A (100ng/mL) or BMP2 (100ng/mL)+Activin A (100ng/mL)


title: Single-cell Profiling Reveals Diverse γδ T Cell Subsets in Ulcerative Colitis

city: Freiburg

first: Jakob

last: Arnold

address: Breisacher Str. 66

country: Germany

institute: Uniklinik Freiburg

summary: γδ T cells maintain intestinal immune homeostasis, but their contributions to human ulcerative colitis (UC) are poorly understood. We characterized γδ T cells in intestinal biopsies obtained from patients  with UC and healthy donors using single-cell RNA sequencing, T cell receptor profiling, and mass cytometry. UC reduced CD103+Vγ4Vδ1+  intraepithelial γδ lymphocytes (γδ IELs) and increased γδ T cell subsets with stem-like phenotypes expressing T cell factor-1 (TCF-1) and programmed cell death receptor 1 (PD-1), or effector-like phenotypes expressing granzyme B, perforin, and T-box expressed in T cells (T-bet). γδ T cell composition changes in UC correlated with decreased expression of epithelial BTNL3 and BTNL8   and increased BTN3A1 and BTN3A3  , suggesting altered recruitment and activation  . Clinical improvement recovered γδ IELs and reduced inflammation-associated subsets. Inflammation-associated changes were observed in peripheral blood γδ T cells. Thus, distinct γδ T cell subsets in different niches exert protective or pathogenic functions in UC.

overall_design:
scRNA-seq, CITE-seq, TCR-seq

GSM9444084: Colonic gdT cells (batch #1); samples of HD and UC donors are multiplexed (table matching each barcode to a specific donor is provided with FLASHseq_R1_meta.tsv)
GSM9444085: Colonic gdT cells (batch #2); samples of HD and UC donors are multiplexed (table matching each barcode to a specific donor is provided with FLASHseq_R2_meta.tsv)
GSM9444086: PBMC derived TCRgd Vd1 cells (batch #1, GEX); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2, Hu.Hashtag_3; UC donors: Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444087: PBMC derived TCRgd Vd1 cells (batch #1, HTO); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2, Hu.Hashtag_3; UC donors: Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444088: PBMC derived TCRgd Vd1 cells (batch #1, TCR); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2, Hu.Hashtag_3; UC donors: Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444089: PBMC derived TCRgd Vd1 cells (batch #2, GEX); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2; UC donors: Hu.Hashtag_3, Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444090: PBMC derived TCRgd Vd1 cells (batch #2, HTO); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2; UC donors: Hu.Hashtag_3, Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444091: PBMC derived TCRgd Vd1 cells (batch #2, TCR); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2; UC donors: Hu.Hashtag_3, Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444092: PBMC derived TCRgd Vd2 cells (batch #1, GEX); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2, Hu.Hashtag_3; UC donors: Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444093: PBMC derived TCRgd Vd2 cells (batch #1, HTO); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2, Hu.Hashtag_3; UC donors: Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444094: PBMC derived TCRgd Vd2 cells (batch #1, TCR); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2, Hu.Hashtag_3; UC donors: Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444095: PBMC derived TCRgd Vd2 cells (batch #2, GEX); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2; UC donors: Hu.Hashtag_3, Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444096: PBMC derived TCRgd Vd2 cells (batch #2, HTO); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2; UC donors: Hu.Hashtag_3, Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6
GSM9444097: PBMC derived TCRgd Vd2 cells (batch #2, TCR); samples of HD and UC donors are multiplexed by cell hashing (HTO); HD donors: Hu.Hashtag_1, Hu.Hashtag_2; UC donors: Hu.Hashtag_3, Hu.Hashtag_4, Hu.Hashtag_5, Hu.Hashtag_6

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


title: Knockdown of Histone H1.5 leads to a loss in centromeric transcription

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary: Mammalian linker histone proteins (Histone H1) comprise a group of 11 non-allelic variants which have key roles in modulating chromatin organization. Subtype specific genomic distribution can contribute to a fine- tuned regulation of gene expression and chromatin architecture. In this study, we report that the variant histone H1.5 localizes to human centromeres and has a functional role in regulation of centromeric noncoding transcription. We used immunofluorescence to visualize the localization of the H1.5 to the centromere in astrocytes and performed chromatin immunoprecipitation which revealed an interaction of H1.5 with centromeric-protein A (CENP-A) nucleosomes in vivo in human cells. In vitro reconstitution of chromatin demonstrates that H1.5 can robustly bind to both CENP-A mono-nucleosomes and arrays of nucleosomes. Functionally, depletion of H1.5 from cells results in the loss of centromeric satellite transcription and leads to accumulation of mitotic defects. These data point to a hitherto unreported role for H1.5 in regulation of mitotic integrity in human cells.

overall_design: SVGp12 cells were subjected to histone H1 subtype knockdown using siH1.5/siH1.0/siScramble smartpool  oligos. After 72hours , cells were harvested for total RNA- extraction.

first: Ankita

last: Saha

first: Minh

last: Bui

first: Daniël

middle: P

last: Melters

first: Ganesan

last: Arunkumar

first: Reda

last: Bentahar

first: Yamini

last: Dalal


title: Chromatin-mediated anticipatory control of type I interferon production in plasmacytoid dendritic cells (Combined snRNA-seq and snATAC-seq of ΔTB pDC activation)

city: New York City

first: Eduardo

last: Esteva

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: Type I interferons (IFN-I) including IFN-β and multiple IFN-α subtypes are key antiviral proteins encoded within a single locus. The antiviral response of most cell types involves primarily IFN-β, whereas professional IFN-I-producing plasmacytoid dendritic cells (pDCs) secrete all IFN-I subtypes. We report that the IFN-I locus in quiescent pDCs showed multiple distinct features, including i) localization in the active intranuclear chromosomal compartment; ii) distinct three-dimensional chromatin organization, and iii) poised promoters at multiple Ifna genes. Accordingly, IFN-I production specifically by pDCs was dependent on the chromatin-organizing cohesin complex. The intranuclear translocation and promoter poising were mediated by the pDC-enriched transcription factor IRF8. Finally, we identified several IRF8- and/or cohesin-binding regulatory regions across the IFN-I locus. One of these enhanced IFN-β induction in all cells, whereas two others enhanced pDC-specific induction of adjacent Ifna genes. Thus, the unique IFN-I-producing capacity of pDCs is facilitated by the anticipatory chromatin organization imparted by IRF8 and cohesin.

overall_design: Combined snRNA-seq and snATAC-seq was performed on pDCs from unstimulated or CpG-stimulated FL-BMDC cultures derived from mice expressing green fluorescent protein (GFP) transgene driven by the CAGGS promoter (control) and IfnΔTB2/TB3/TB4 (ΔTB) mice.

first: N

last: Adams

first: E

first: B

last: Reizis


title: Macrophage Immune-Competent Colon Assembloids for Functional Interrogation of Neuroinflammation-Induced Colonic Dysmotility

city: College Station

first: Shreya

last: Raghavan

state: Texas

address: Texas A&M University, Emerging Technologies Building 3120, 101 Bizzell St

department: Department of Biomedical Engineering

institute: Texas A&M University

summary: Functional gastrointestinal disorders (FGIDs) affect ∼40% of the global population and are frequently characterized by colonic dysmotility. Symptomatic manifestations of colonic dysmotility significantly reduce quality of life in inflammatory bowel disease (IBD), diabetes, and Gulf War Illness (GWI). Current in vitro models lack the integration of functional physiology with immune and neuronal complexity required to establish causal links between neuroinflammation and dysmotility. Here, an immune-competent bioengineered colon assembloid is introduced that integrates multiple cell types of the external colonic wall, along with functional readouts of motility. Within bioengineered colon assembloids, various inflammatory insults resulted in enteric neuroinflammation, cascading to changes in colonic motility. Key mechanisms of dysmotility following inflammatory insult within the bioengineered colon assembloids included impaired neuronal regeneration, and aberrant smooth muscle remodeling. The bioengineered colon assembloid model mimicked diverse aspects of enteric neuroinflammation. Ultimately, the platform offers a physiologically relevant avenue to interrogate neuroimmune crosstalk and dissect mechanisms of colonic dysmotility, paving the way to new therapeutic strategies to improve colonic motility.

overall_design: RNA-Seq profiling of Bioengineered Colon Assembloids exposed to inflammatory insult using Pyridostigmine Bromide (PB) and Tumor Necrosis Factor- alpha (TNF-α) under Acute (Day 4) and Chronic (Day 7) conditions.

first: Claudia

last: Collier

first: Karla

last: Ortega Sandoval

first: Aelita

last: Salikhova

first: Shrinarayanee

last: Rengarajan

first: Anvitha

last: Tharakesh

first: Alana

last: Aristimuno Millan

first: Shanthi

last: Srinivasan


title: Aging-declined RNA Exportation Impairs Hematopoietic Stem Cells by Inducing R-Loop

first: Jianwei

last: Wang


title: Boehmeria nivea (L.) Gaud. Ameliorates Oxidative stress-mediated Inflammatory Responses and Apoptosis in LPS/CSC-induced Chronic Obstructive Pulmonary Disease Mouse Model

city: Jeongeup-si

first: Ba-Wool

last: Lee

state: Jeollabuk-do

address: Korea Research Institute of Bioscience and Biotechnology, center 2

country: South Korea

summary: Introduction: Boehmeria nivea (L.) Gaud. has traditionally been regarded as a functional food with applications in various inflammatory disorders. However, its role in chronic obstructive pulmonary disease (COPD) has not yet been clarified. Methods: In this study, the preventive efficacy of the ethyl acetate fraction of B. nivea (L.) Gaud. leaves (EA-BN) was evaluated in a COPD model established by intranasal instillation of lipopolysaccharide (LPS; 0.5 mg/kg body weight) and cigarette smoke condensate (CSC; 12.5 mg/kg body weight) in male C57BL/6N mice. The experimental groups received dexamethasone (3 mg/kg) as a positive control or EA-BN at doses of 200 mg/kg. Results: EA-BN administration significantly reduced T helper 1 cytokine levels and decreased macrophage and neutrophil counts in bronchoalveolar lavage fluid. Histological analyses revealed that EA-BN mitigated alveolar destruction and inflammatory infiltration, whereas pulmonary function tests demonstrated improvements in the FEV0.1/FVC ratio and lung elastance in the LPS/CSC-induced COPD. Additionally, EA-BN alleviated oxidative stress by promoting the nuclear translocation of Nrf2 and enhancing the expression of its downstream targets, HO-1 and NQO1, leading to a reduction in reactive oxygen species and nitric oxide production. EA-BN downregulated thioredoxin-interacting protein and NLRP3 inflammasome activation, thereby suppressing caspase-1 and IL-1β expression, and also attenuated apoptosis by modulating the Bax/Bcl-2/caspase-3 pathway. Discussion: Collectively, these findings suggest that EA-BN possesses antioxidant, anti-inflammatory, and anti-apoptotic properties, supporting its potential as a preventive agent against COPD.

overall_design: This study investigated transcriptomic changes in lung tissue using an LPS/CSC-induced COPD mouse model and evaluated the effect of EA-BN treatment. Male C57BL/6N mice were assigned to three groups for RNA-seq analysis: Normal control (NC; PBS intranasal instillation with vehicle), COPD (LPS/CSC intranasal instillation with vehicle), and EA-BN-H (LPS/CSC intranasal instillation with EA-BN 200 mg/kg). LPS (0.5 mg/kg) and CSC (12.5 mg/kg) were intranasally instilled under light anesthesia on days 1, 6, and 13. EA-BN (200 mg/kg; in 2% DMSO) or vehicle was administered orally once daily from days 1 to 14. Lung tissues were collected on day 15, and total RNA was extracted using TRIzol reagent. RNA quality was assessed prior to library preparation, and RNA-seq was performed to compare gene expression profiles among NC, COPD, and EA-BN-H groups.

first: Ji-Hye

last: Ha

first: Da-Hye

last: Yi

first: Ju-Hong

last: Kim

first: Seong-Hun

last: Jeong

first: Ju Hwan

first: Kyungsook

last: Jung

first: Hyung Jae

first: Ji-Young

last: Park

first: Woo Sik

first: Young-Bae

last: Ryu

first: Hyung-Jun

last: Kwon

first: Jong-Choon

first: In-Sik

last: Shin

first: In-Chul


title: Expression data from mice spleens

city: SEOUL

first: SOYOUN

last: WOO

address: 25, Magokdong-ro 2-gil, Gangseo-gu

institute: Ewha Womans University, College of Medicine

summary:
Female C57BL/6J mice, 8 weeks old, were DNCB-induced dermatitis on skin. For the effect of tonsil-derived mesenchymal stem cells (T-MSCs)treatment, cells were added to dermatitis model.
After 10 days, spleen cells were isolated for RNA expression analysis.

overall_design:
Vehicle control, Vehicle + T-MSCs, DNCB (138630; Sigma-Aldrich), and DNCB + T-MSCs
contributor: Macrogen

first: Hyun

first: Kyung-Ah

last: Cho

first: So-Youn

last: Woo


title: Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs at the Mest-Copg2 locus [Capture Hi-C]

first: Bongmin

last: Bae

address: 16 Divinity Ave

institute: Harvard University

summary: Genomic imprinting is an epigenetic phenomenon in which genes exhibit restricted or biased expression from one allele according to parental origin. Imprinted gene expression plays a crucial role in the development, including the brain. Higher-order chromatin structure has long been associated with gene regulation, particularly in the context of spatial enhancer-promoter interactions. Given the characteristic parental allele-biased expression pattern of imprinted genes, a compelling question is whether the three-dimensional organization of parental genomes plays a role in imprinted gene regulation. Using a capture Hi-C approach, we identifiedparental allele-specific higher-order chromatin structures across multiple imprinted domains in the mouse brain. These allele-specific structural features largely stem from annotated imprinting control regions (ICRs), concomitant with allele-specific binding of CTCF. Detailed analysis suggests that transcriptional start sites (TSS) of active and inactive alleles of imprinted genes form distinct chromatin interactions, differing in degree and/or type. CRISPRi screeningrevealed a distal cis-regulatory element that modulates imprinted expression of the Mest-Copg2locus in neurons, and its regulatory mechanism is tightly associated with allele-specific chromatin interactions. Further investigation revealed that both a cis-acting long non-coding RNA and allele-specific enhancer-promoter architecture modulates Mest-Copg2 imprinted expression. Together, this study highlights the interplay between chromatin structure and regulatory landscapes that modulate allele-specific expression of imprinted genes.

overall_design: Region capture Hi-C datasets from 8-weeks-old mouse cortices, including forward (BxC) and reverse (CxB) crosses. / Region capture Hi-C datasets from hybrid mESC treated with DMSO or DNMTi (GSK-3484862). / Region capture Hi-C datasets from primary cortical neurons isolated from F1 E16 embryos (BxC crosses).

first: Amanda

last: Whipple


title: Robust effector memory features of human T-bet-hi B cells  induced by repeated mRNA vaccination

city: Daejeon

first: Jeongsoo

address: 291 Daehak-ro, Yuseong-gu

institute: KAIST

summary: The heterogeneity of memory B cells in response to repetitive cognate antigen challenges remains to be fully elucidated. Here we identified a transcriptionally distinct cluster of T-bethi B cells, among SARS-CoV-2 RBD-specific B cells in PBMCs from healthy individuals vaccinated with the BNT162b2 SARS-CoV-2 mRNA vaccine. Our findings indicate that T-bethi B cells can be defined by a combination of CD11c and FcRL5 receptors, and are distinguished by distinct gene regulatory networks associated with effector functions. Notably, these T-bethi B cells were affinity-matured and exhibited rapid differentiation into antibody-secreting cells (ASCs) producing neutralizing antibodies comparable to classical memory B cells, underscoring their role in early recall responses. Taken together, these findings illuminate the potent effector memory roles of T-bethi B cells in adaptive immunity following vaccinations.

overall_design: The stained B cells were sorted into tetramer+ cells and tetramer− cells and cells from 4 individuals were pooled, stained with CITE-seq antibodies to be included in a single gem (tube) , 2 gems per a single timepoint. Timepoints are as follows: T1 (D0), T2 (D7 after 1st dose), T3 (D14 after 1st dose), T4 (D14 after 2nd dose), T5 (D180 after 2nd dose), T6 (D14 after 3rd dose) and T7 (D90 after 3rd dose)


title: Rainbow trout adipose tissue depots (VAT, SAT, IMAT) - miRNAs

city: Barcelona

first: Enrique

last: Rosell-Moll

address: Av Diagonal, 643 4º floor

institute: University of Barcelona

summary: The aim of this study was to characterize different adipose tissue depots in rainbow trout (Oncorhynchus mykiss) through the analysis of mRNA and miRNA expression profiles. Mature adipocytes were isolated from visceral (VAT), subcutaneous (SAT), and intramuscular (IMAT) adipose tissues, and RNA sequencing (RNA-seq) was performed. Data were curated, quality-checked, and filtered prior to downstream analyses. This dataset contains the FASTQ files generated in the study. The results will contribute to a better understanding of the molecular differences and similarities among adipose depots in fish reared under standard aquaculture conditions, providing a foundation for improving adiposity control, animal health, fillet yield, and overall product quality.

overall_design: Cell type comparison design. Three adipose tissue depots (VAT, SAT and IMAT) in rainbow trout under standard aquaculture conditions.

first: E

last: Capilla

first: I

last: Navarro

first: D

last: Garcia de la serrana


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (CITE-Seq of SMC3 KO splenic cDCs +/- activation)

first: Eduardo

last: Esteva

summary: The cohesin protein complex extrudes chromatin loops between CTCF-bound sites to organize chromosomes into topologically associated domains, yet biological implications of this process remain obscure. We show that cohesin is required for the post-mitotic differentiation and function of antigen-presenting dendritic cells (DCs), particularly for antigen cross-presentation and IL-12 secretion by type 1 conventional DCs (cDC1s) in vivo. The chromatin organization of DCs was shaped by cohesin and the DC-specifying transcription factor IRF8, which controlled chromatin looping and chromosome compartmentalization, respectively. Notably, optimal expression of IRF8 itself required CTCF/cohesin-binding sites demarcating the Irf8 gene. During DC activation, cohesin was required for the induction of a subset of genes with distal enhancers. Accordingly, the deletion of CTCF sites flanking the Il12b gene reduced IL-12 production by cDC1s. Our data reveal an essential role of cohesin-mediated chromatin regulation in cell differentiation and function in vivo, and its bi-directional crosstalk with lineage-specifying transcription factors.

overall_design: scRNA-seq with "hashtagging" according to the CITE-seq protocol was performed on cDCs from the spleen of CD11c-Cre/+ (Control) or CD11c-Cre/+ Smc3fl/fl (Smc3ΔDC) mice, either in the presence or absence of in vivo treatment with LPS and profilin

first: N

last: Adams

first: A

last: Ra

first: B

last: Reizis


title: Optimizing intestinal glucotonic effect via atypical protein kinase C

city: Seoul

first: Hyeonuk

last: Jeon

address: 50-1, Yonsei-ro, Seodaemun-gu

department: College of Medicine

institute: Yonsei University

summary: Intestinal glucotonic transformation, defined as increased intestinal serum glucose uptake and secretion into the lumen, influences bariatric surgery-associated glycermic control. This study aims to identify downstream molecules that mediate the function of the identified target as an effective intestinjal glucotonic activator. Altered transcriptomes were evaluated in variable intestinal glucotonic models and big data-based drug discovery systems. Protein kinase C (PKC) activation mimicked transcriptome alterations observed during intestinal glucotonic transformation. Among the PKC subfamilies, atypical PKC (aPKC) promoted glucose transporter 1 (GLUT1)-mediated intestinal glucotonic transformation without inducing oncogenic proliferation. Intestinal aPKC activation via a transposon expression vector induced serum glucose uptake into intestinal tissues and excretion into the lumen. Prostratin, a non-tumorigenic phorbol ester, activated aPKC and induced a similar glucotonic effect. Collectively, we identified the prostratin and aPKC/GLUT1 signaling pathways as effective targets for treating diabetes, providing insights into the future development of antidiabetic and weight loss drugs.

overall_design: Following RYGB surgery, intestinal tissues from rats were isolated and analyzed using scRNA-seq to investigate the molecular mechanism of aPKC/GLUT1-mediated glucotonic transformation.

first: Chan Woo

last: Kang

first: Zhen-Yu

last: Hong

first: Sungsoon

last: Fang

first: Insuk

last: Sohn

first: Cheol Ryong

last: Ku


title: Liver-specific delivery of MDM2 antisense oligonucleotides counteracts diet-induced metabolic dysfunction-associated steatotic liver diseases

city: Hung Hom

first: Kenneth King Yip

last: Cheng

state: Kowloon

address: Y948, Lee Shau Kee Building, The Hong Kong Polytechnic University

department: Department of Health Technology and Informatics

country: Hong Kong

institute: The Hong Kong Polytechnic University

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) encompasses a spectrum of pathogenic conditions ranging from steatosis, inflammation and fibrosis with limited treatment options. We previously demonstrated an upregulation of hepatic murine double minute 2 (MDM2) in human subjects with MASLD. Genetic deletion of hepatic MDM2 and pharmacological inhibition of systemic MDM2 improves steatosis and fibrosis in mouse models. In this study, we further developed and investigated the therapeutic potential of a hepatocyte-specific triantennary N-acetylgalactosamine (GalNAc)-conjugated antisense oligonucleotide targeting MDM2 (GalNAc-Mdm2ASO) in two distinct dietary-induced mouse models of MASLD: a high-fat-high-cholesterol (HFHC) diet and a choline-deficient L-amino acid-defined high-fat diet (CDAHFD). In the HFHC-induced MASLD model, GalNAc‐Mdm2ASO not only alleviated liver injury, steatosis, and fibrosis but also improved obesity-related insulin resistance and hyperlipidaemia. The hepatoprotective effects of GalNAc-Mdm2ASO treatment were associated with a reduced accumulation of hepatic cholesterol and ceramide, both of which are known to trigger MASLD. In CDAHFD-induced MASLD mouse model, GalNAc‐Mdm2ASO significantly mitigated hepatic inflammation, cholesterol accumulation, and fibrosis but not triglyceride accumulation. Overall, we prove hepatic inhibition of MDM2 using GalNAc-Mdm2ASO as a promising therapeutic agent for MASLD in two rodent models with distinct pathogenesis.

overall_design: RNA-seq profiling of liver samples of GalNAc-conASO and GalNAc-Mdm2ASO groups (n = 4-5) fed the HFHC/CDAHFD diet.

first: Md Moinul

last: Hoque

first: Mengjie

last: Kong

first: Yuan

last: XinYi

first: Zhou

last: Xiangyu

first: Steve

last: Ting-Yuan Yeh

first: Kekao

last: Long

first: Huige

last: Lin

first: Kenneth

last: King Yip Cheng


title: DAXX Directs H3.4-to-H3.3 Histone Replacement During Spermatogenesis

city: Davis

first: Satoshi

last: Namekawa

address: One Shields Avenue

institute: University of California, Davis

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

overall_design: Refer to individual Series


title: Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells (H3K27me3 CUT&RUN of SMC3KO FL-BMDCs +/- activation)

first: Eduardo

last: Esteva

overall_design: CUT&RUN for H3K27me3 was performed on cDCs purified from 4-OHT-treated FL-BMDC cultures from Rosa26CreER/+ or Rosa26CreER/+ Smc3fl/fl mice, after cultures were either unstimulated or stimulated with CpG-B for 6 hours (2 replicates per genotype/stimulation condition).

first: N

last: Adams

first: D

last: Martinez-Krams

first: E

first: A

last: Galitsyna

first: B

last: Reizis


title: Improvement of Enfumafungin Production by Hormonema carpetanum via Mutagenesis and Process Optimization: Mutant Generation and Preliminary Transcriptomic Analysis

city: Shanghai

first: Haodong

last: Chen

address: Gebaini Road 285#

institute: China State Institute of Pharmaceutical Industry

summary: Enfumafungin, a triterpenoid antifungal compound, serves as the key starting material for the synthesis of ibrexafungerp and SCY-247. However, its low fermentation yield and high production cost constrain its supply, limiting drug accessibility and the ability to meet clinical demand. Consequently, enhancing enfumafungin biosynthesis is crucial for achieving large-scale production. In this study, physical and chemical mutagenesis treatments were adopted for Hormonema carpetanum ATCC 74360, and a genetically stable high-producing mutant, H. carpetanum ENF-5-29, was generated. This mutant produced 817 mg/L enfumafungin in flasks, a 30-fold increase over that of wild-type ATCC 74360. Comparative transcriptome analysis revealed that the proposed biosynthetic pathway from glucose to enfumafungin presented the most significant upregulation in the mutant. The fermentation medium and conditions were subsequently optimized to further enhance enfumafungin production. Transcriptome analysis revealed improved yields under low-temperature culture, likely due to the upregulated expression of key genes in the mevalonate pathway and the enfumafungin biosynthetic gene cluster (BGC). Together, these transcriptome findings provide molecular insight into enhanced enfumafungin production. Furthermore, batch fermentation of ENF-5-29 in a 5 L bioreactor achieved a yield of 1,621 mg/L, the highest yield reported to date. Our results demonstrate the efficacy of mutagenesis for H. carpetanum improvement and pinpoint key targets for future genetic engineering aimed at enhancing enfumafungin biosynthesis.

overall_design: RNA-seq profiling of wildtype ATCC 74360 and mutant ENF-5-29 at stationary phase of fermentation.

first: Junyi

last: Wang

first: Haolong

last: Huang

first: Jiali

last: Gui

first: Songbai

last: Yang

first: Wen

last: Tang

first: Jiawei

first: Shaoxin


title: Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs at the Mest-Copg2 locus [ATAC-seq]

first: Bongmin

last: Bae

overall_design: ATAC-seq datasets from 8-weeks-old mouse cortices, including forward (BxC) and reverse (CxB) crosses.

first: Daniel

last: Loftus

first: Amanda

last: Whipple


title: Transcription analysis of CBX3::ALK Fusion and EML4-ALK Fusion that drives ALK Activation

city: Taipei City

first: han-ying

last: cheng

address: No. 155, Sec. 2, Linong St., Beitou Dist.

department: Institute of clincal medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Kinase gene fusions are critical oncogenic drivers and key targets in precision oncology. Here, we report a previously undescribed out-of-frame CBX3::ALK fusion identified in metastatic melanoma. Remarkably, this fusion generates a biologically active ALK protein. In this study, we performed RNA-seq to compare the transcriptional profile of CBX3::ALK with the well-characterized EML4-ALK fusion. Our goal is to evaluate the similarities between these fusions and investigate potential therapeutic targets for CBX3::ALK.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Comparative transcriptomic analysis of NIH/3T3 and MeWo cell lines expressing CBX3-ALK or EML4-ALK fusion genes versus control vectors.

first: Jen-Fan

last: Hang

first: Han-Ying

last: Cheng

first: Yu-Shuen

last: Tsai

first: Muh-Hwa


title: Allelic chromatin structure is a pervasive feature of imprinted domains and functions cooperatively with cis-acting long non-coding RNAs at the Mest-Copg2 locus [RNA-seq]

overall_design: Total RNA-seq from hybrid BxC and CxB primary cortical neurons. / Total RNA-seq from hybrid KRABxCast NPC-derived neurons treated with scramble (LV-Scrb) or enhancer-targeting (LV-E105) gRNAs.  /  mRNA-seq from hybrid mESC treated with DMSO or DNMTi (GSK-3484862).

first: Katherine

last: Gu


title: Myelin antigen capture in the CNS by B cells expressing EBV latent membrane protein 1 leads to demyelinating lesion formation [BRB-seq]

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: The efficacy of B cell depletion therapies, and association with the B lymphotropic Epstein- Barr virus (EBV) implicate B cells in the demyelinating autoimmune disease multiple sclerosis. After observing myelin-reactive B cells in the naïve human repertoire, we studied how such cells behave in the central nervous system. In mice, viral infections induce infiltration of B cells independent of phenotype and specificity into the otherwise lymphocyte-poor brain, and myelin-reactive B cells then capture antigen directly from parenchyma. Trafficking of these antigen-loaded B cells to draining lymph nodes was not observed, and without T cell help, antigen-capturing B cells die rapidly. CD40L signaling or EBV latent membrane protein 1 (LMP1) can override this checkpoint, leading to in situ plasma cell differentiation and antibody-mediated, demyelinating lesion formation. These observations explain the dependency of disease incidence on prior EBV infection, and the increased risk associated with brain infections, and suggest possible treatment strategies.

overall_design: B cells were sorted from mouse brain and lymph node samples and put in culture with human fibroblasts expressing or not their antigen.

first: Julien

last: Roux

first: Nicholas

last: Sanderson

first: Mika

last: Schneider

first: Hyein

last: Kim

first: Tobias

last: Derfuss