title: Epigenetic silencing of JAM3 promoted progression in serous ovarian carcinoma through PI3K/AKT pathway

city: Guiyang City

first: Haiyan

last: Wang

state: Guizhou

address: No. 9, Beijing Road, Yunyan District,

institute: Guizhou Meidical University

summary: Junctional adhesion molecule 3 (JAM3) is frequently epigenetically silenced in cancers, but its functional role and regulatory mechanisms in serous ovarian carcinoma (SOC) remained poorly defined. This study integrated RNA sequencing (RNA-seq) with functional assays to delineate JAM3-driven pathways in SOC. RNA-seq analysis of JAM3-overexpressing SOC cells revealed significant downregulation of PI3K/AKT signaling components, a finding validated by Western blot. JAM3 promoter methylation, assessed via bisulfite sequencing and qMSP, was elevated in SOC tissues and inversely correlated with JAM3 expression. Functional studies demonstrated that JAM3 overexpression suppressed proliferation, migration, and invasion while inducing apoptosis, whereas JAM3 knockdown exacerbated aggressive phenotypes. Rescue experiments using the AKT inhibitor MK2206 confirmed PI3K/AKT pathway dependency in JAM3-mediated tumor suppression. Clinically, reduced JAM3 expression correlated with advanced tumor stage and poor prognosis. These results establish JAM3 as a tumor suppressor in SOC, acting through epigenetic modulation of PI3K/AKT signaling, and highlight its potential as a therapeutic target.

overall_design: The study includes two groups: the experimental group (A2780 ovarian cancer cells with stable JAM3 knockdown via siRNA) and the control group (A2780 cells transfected with empty vector). E Cells are cultured under standard conditions (37°C, 5% CO₂) to the logarithmic growth phase. JAM3 knockdown efficiency is validated using qRT-PCR and Western blot, ensuring a significant reduction in expression (>70%). Total RNA is extracted using TRIzol or commercial kits, followed by DNase treatment to eliminate genomic DNA contamination.

first: Chunlei

last: Wen

first: Jiling

last: Xie

first: Jiandong

first: Wenxiu

last: Yang


title: Salivary gland transcriptomic analysis in the IL-14α transgenic mouse model of Sjögren’s disease using Visium V1 3' spatial gene expression assay

status: Public on Jul 08 2025

city: Columbia

first: Gary

last: Weisman

state: MO

address: 547 Life Sciences Center, 1201 Rollins Rd

department: Biochemistry

country: USA

institute: University of Missouri

summary: Sjögren’s disease (SjD) is a systemic autoimmune disorder primarily affecting the exocrine glands and characterized by dry mouth and dry eye, the presence of anti-SSA and/or anti-SSB autoantibodies in blood serum, and chronic lymphocytic infiltration of salivary and lacrimal glands (i.e., sialadenitis and dacryoadenitis, respectively). The interleukin-14α transgenic (IL-14αTG) mouse model of SjD recapitulates many aspects of human SjD, including progressive sialadenitis, loss of salivary gland function, and development of B cell lymphoma. We performed Visium V1 3' spatial transcriptomic analysis of fresh frozen submandibular and sublingual glands from a 12-month-old IL-14αTG Sjögren’s-like mouse and age-matched C57BL/6 control mouse.

overall_design: One submandibular gland and one sublingual gland from 12-month-old female IL-14α transgenic or 12-month-old C57BL/6 control mouse was included in the Visium capture area for spatial transcriptomic analysis.

first: Lucas

middle: T

last: Woods

first: Kimberly

middle: J

last: Jasmer

first: Kevin

last: Munoz Forti

first: Alex

last: Kearns

middle: A


title: scComplete-Seq Reveals Comperehensive Picture of Transcriptome

city: Singapore

first: Shaun

last: Ngang

address: 14 Medical Drive, MD6 #14-01

department: iHealthtech

country: Singapore

institute: National University of Singapore

summary: Many of the underlying mechanisms of intercellular gene expression heterogeneity are still unknown despite the advancements in single-cell transcriptomics. One of the reasons is the partial detection of non-coding RNA types due to their small size and lack of polyadenylation. The ability to detect gene expression dynamics comprehensively would shed light on the regulation and disease-leading dysregulation in a cell-specific manner, and contribute to the discovery of biomarkers and novel therapeutics. We developed scComplete-seq, a single cell assay that enables concurrent profiling of total RNA. After successful integration of it on available high-throughput single-cell platforms, we validated it on cancer cell lines and applied it to peripheral blood mononuclear cells (PBMCs). This unveiled the distinct regulation of tRNAs, mtRNAs and enhancer RNA in monocytes, T and B cells upon Lipopolysaccharide (LPS) and PMA/Ionomycin stimulation compared to resting cells.

overall_design: For scComplete-seq, 10X Chromium platform was used with modified reagents and protocol. First, additonal E. Coli PolyA polymerase, ATP and modified TSO with LNA were added to the chromium v3.1 single index kit reagent (RT Reagent B, Reducing Agent B and RT Enzyme C). After the encapsulation, cells were incubated additional 37C for 25min before the reverse transcription and template switching. The assay is benchmarked using three different cells lines mixture consisting of K562, MCF7 and HEK29T. A total of 4800 cells loaded to Chromium device after hashing the samples with hashtags. scComplete-seq is further used to discover the rewiring of coding and non-coding transcriptome in unstimulated, LPS stimulated and PMA/Ionomycin stimulated PBMCs.

first: Fatma

middle: B

last: Dinçaslan

first: Lih

middle: F

last: Cheow


title: PLA2G4E Orchestrates optimal Synapse Development and Neuronal Maturation

city: Pamplona

first: Ana

last: Garcia Osta

state: Navarra

address: Juslarrocha 10, 3H

department: neuroscience

country: Spain

institute: Cima

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Myeloid TET2-IL-1 axis controls sympathetic-epithelial interaction to modulate intestinal inflammation

city: Chicago

first: Veronica

last: Locher

state: IL

institute: University of Chicago

summary: Inflammatory responses are mediated by complex multi-cellular interactions and understanding the identity and mechanism of these interactions is central to understanding the pathophysiology of immune-mediated diseases. In humans, somatic mutations in Tet methylcytosine dioxygenase 2 (TET2), a DNA demethylase, are commonly observed during ageing in myeloid cells1,2 and known to modulate inflammatory responses3. Using a mouse model that selectively lacks TET2 in myeloid cells, we show that myeloid cells and sympathetic neurons form a signaling nexus that controls the differentiation of enterochromaffin cells and serotonin production during colonic inflammation.  Specifically, we demonstrate that TET2 restricts IL-1 production by myeloid cells under physiological conditions that in turn controls the intestinal sympathetic activation.

overall_design: RNA was extracted from CD11b+ MACS-enriched single cell suspension from colons of Tet2f/f and Tet2DLysM mice

first: Deepika

last: Sharma


title: PLA2G4E Orchestrates optimal Synapse Development and Neuronal Maturation [KO_Pla2g4e]

summary: Constitutive Pla2g4e knockout mice exhibited significant behavioral alterations, particularly in memory function, different brain lipid composition, and decreased levels of cortical synaptic plasticity markers compared to wild-type counterparts.We performed gene expression profiling analysis animals lacking PLA2G4E to study the function of this enzyme in memory function.

overall_design: Comparative gene expression profiling analysis of RNA-seq data obtained from prefrontal cortex of wild type and PLA2G4E knock out mice.

last: García-Osta

first: Sara

last: Badesso

first: Mar

last: Cuadrado-Tejedor


title: Deep indel mutagenesis reveals the regulatory and modulatory architecture of alternative exon splicing

city: Heidelberg

first: Pablo

last: Baeza Centurion

address: Im Neuenheimer Feld 580

country: Germany

institute: DKFZ

summary: Altered splicing is a frequent mechanism by which genetic variants cause disease. However, the regulatory architecture of human exons remains poorly understood, making the therapeutic modulation of splicing in disease challenging. Here we show that deep indel mutagenesis (DIM) provides an efficient strategy to chart the regulatory landscape of human exons and to rapidly identify effective splice-modulating oligonucleotides. DIM defines a minimal exon length, uncovers a mechanism for the evolutionary birth of unusually short microexons and the repression of transmembrane domain-encoding exons, and reveals a checkerboard architecture of sequential enhancers and silencers in a model alternatively spliced exon. Accurate prediction of the effects of deletions using deep learning provides a resource, DANGO, that maps the splicing regulatory landscape of all human exons and predicts effective splice-altering antisense oligonucleotides genome-wide.

overall_design: Deep insertion-deletion mutagenesis of a model human alternatively-spliced exon (FAS exon 6).

last: Baeza-Centurion

first: Belén

last: Miñana

first: Andre

last: Faure

first: Mike

last: Thompson

first: Sophie

last: Bonnal

first: Ben

last: Lehner

first: Juan

last: Valcárcel


title: PLA2G4E Orchestrates optimal Synapse Development and Neuronal Maturation [shPLA2G4E]

summary: Constitutive Pla2g4e knockout mice exhibited significant behavioral alterations, particularly in memory function, different brain lipid composition, and decreased levels of cortical synaptic plasticity markers compared to wild-type counterparts.We performed gene expression profiling analysis os neurons  lacking PLA2G4E to study the function of this enzyme in synaptic transmission.

overall_design: Comparative gene expression profiling analysis of RNA-seq data obtained from neuronal cultures treated with lentiviral particles expressing shRNA agains Pla2g4e or scrambled


title: Differential gene expression analysis at different stages of neuronal development in mutant and wild type ATRX cells

city: Edinburgh

first: Graeme

last: Grimes

address: MRC Institute of Genetics & Molecular Medicine, Crewe Road,

country: United Kingdom

institute: University of Edinburgh

summary: Investigating transcription deregulation and interferon signaling activation in iPSC-derived neurons deficient for ATRX.

overall_design: Comparative gene expression profiling analysis of Quantseq 3' mRNA-seq data for induced pluripotent stem cells, neural progenitors and derived forebrain neurons mutant or wild type for ATRX.

first: Marie-Therese

last: El-Daher

middle: R

first: Yanick

last: Crow


title: Mutation of ATRX induces type I interferon signalling and defines a non-canonical role of nuclear cGAS in the regulation of chromatin state

type: Genome binding/occupancy profiling by high throughput sequencing


title: Severe Attenuation of Circadian Clock Output in the Heart following Sustained Augmentation of Cardiomyocyte Protein O-GlcNAcylation

status: Public on Jul 07 2025

city: Birmingham

first: Martin

last: Young

state: Alabama

address: 703 19th Street S

department: Medicine

institute: University of Alabama at Birmingham

summary: Background. Changes in circadian-related behaviors (e.g., the timing of food intake, sleep cycles) and the environment (e.g., light-dark cycles) increase the risk of numerous cardiometabolic diseases, including diabetes mellitus and cardiac disease. Recent studies indicate a close interrelationship between circadian clocks and the posttranslational modification, protein O-GlcNAcylation. The current study was designed to investigate whether a modest elevation of protein O-GlcNAcylation in the adult mouse heart, similar to levels observed during pathologic states, influenced circadian governance of the heart. Methods and Results. Cardiomyocyte-specific expression of a dominant negative O-GlcNAcase (dnOGAh) for a 2-week period resulted in an approximate 1.5-fold increase in cardiac protein O-GlcNAcylation, impacting 70% of core circadian clock components in the heart at the mRNA level. Further interrogation of cardiac mRNA species in dnOGAh hearts at candidate (RT-PCR) and unbiased (RNAseq) levels revealed a 95% loss of circadian governance of the cardiac transcriptome. This was despite persistent/augmented 24hr oscillations of the core circadian clock proteins BMAL1, REVERB, and PER2 in dnOGAh hearts. Direct comparison of dnOGAh hearts with cardiomyocyte-specific BMAL1 knockout (CBK) hearts underscored an apparent uncoupling of the core clock mechanism from clock control of downstream target genes in dnOGAh hearts, and highlighted that loss of circadian governance results in interstitial fibrosis. Conclusions. Sustained protein O-GlcNAcylation in the heart causes loss of circadian governance, likely downstream of the core circadian clock mechanism. Moreover, interstitial fibrosis appears to be a universal adverse outcome following impaired circadian governance.

overall_design: RNAseq was performed on RNA isolated from dnOGAh and littermate CON hearts collected at 4hr intervals over the 24hr day (2wks after doxycycline treatment initiation).

first: Gobinath

last: Shanmugam

first: Samuel

last: Chang

first: Helen

middle: E

last: Collins

first: Chae-Myeong

last: Ha

first: Selma

last: Kane

first: Luke

last: Potter

first: Lily

last: Xie

first: Luyun

last: Zou

first: Jianhua

last: Zhang

first: John

middle: C

last: Chatham

first: Adam

last: Wende


title: Deletion of AT1a (Angiotensin II Type 1a) Receptor or Inhibition of Angiotensinogen Synthesis Attenuates Thoracic Aortopathies in Fibrillin1C1041G/+ Mice

city: Lexington

first: Hisashi

last: Sawada

state: KY

address: 741 South Limestone BBSRB B251

institute: University of Kentucky

summary: Objective: A cardinal feature of Marfan syndrome is thoracic aortic aneurysm. The contribution of the renin-angiotensin system via AT1aR (Ang II [angiotensin II] receptor type 1a) to thoracic aortic aneurysm progression remains controversial because the beneficial effects of angiotensin receptor blockers have been ascribed to off-target effects. This study used genetic and pharmacological modes of attenuating angiotensin receptor and ligand, respectively, to determine their roles on thoracic aortic aneurysm in mice with fibrillin-1 haploinsufficiency (Fbn1C1041G/+). Approach and Results: Thoracic aortic aneurysm in Fbn1C1041G/+ mice was found to be strikingly sexual dimorphic. Males displayed aortic dilation over 12 months while aortic dilation in Fbn1C1041G/+ females did not differ significantly from wild-type mice. To determine the role of AT1aR, Fbn1C1041G/+ mice that were either +/+ or −/− for AT1aR were generated. AT1aR deletion reduced expansion of ascending aorta and aortic root diameter from 1 to 12 months of age in males. Medial thickening and elastin fragmentation were attenuated. An antisense oligonucleotide against angiotensinogen was administered to male Fbn1C1041G/+ mice to determine the effects of Ang II depletion. Antisense oligonucleotide against angiotensinogen administration attenuated dilation of the ascending aorta and aortic root and reduced extracellular remodeling. Aortic transcriptome analyses identified potential targets by which inhibition of the renin-angiotensin system reduced aortic dilation in Fbn1C1041G/+ mice. Conclusions: Deletion of AT1aR or inhibition of Ang II production exerted similar effects in attenuating pathologies in the proximal thoracic aorta of male Fbn1C1041G/+ mice. Inhibition of the renin-angiotensin system attenuated dysregulation of genes within the aorta related to pathology of Fbn1C1041G/+ mice.

overall_design: Comparative gene expression analysis of RNA-seq data for (1) ascending and descending aortas of Fbn1 C1041G/+ mice and wild type littermates and (2) the ascending aorta of control ASO vs AGT-ASO of Fbn1 C1041G/+ mice.


title: RBM4 modulate apoptosis and expression of inflammatory factors via alternative splicing in HeLa cells

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

summary: We overexpressed RBM4 in HeLa cells to study RBM4-regulated genes using RNA-seq technology, followed by bioinformatic analysis of target genes of RBM4-regulated transcriptional factors (TFs)

overall_design: transcrptional analysis of RBM4 overexpression and control in Hela cells

first: Wei-Yang

last: Wang


title: Transcriptomic stress responses in Vaccinium spp. F1 hybrids: Implications for temperature-resilient cranberry breeding using a crop wild relative

city: Encinitas

first: Audrey

last: Dickinson

state: California

address: 300 Quail Gardens Dr

department: Science and Conservation

institute: San Diego Botanic Garden

summary:
Cranberry (Vaccinium macrocarpon) is an important North American fruit crop with vulnerability to temperature extremes and a relatively recent domestication history. Hybridization with a cold-adapted crop wild relative (CWR), V. oxycoccos, offers a strategy for improving temperature stress tolerance.
We conducted RNA sequencing (RNA-seq) on V. macrocarpon and F1 hybrids between V. macrocarpon and V. oxycoccos subjected to acute heat and cold stress, capturing early transcriptional responses up to 30 minutes (heat) and 95 minutes (cold) after treatment onset. We then evaluated differences in responses across genotypes and stress conditions.
Differential expression analysis and functional profiling revealed cold-induced differences in pathways related to photosynthesis, ribosomes, defense, and hormone signaling. No subgenome-specific functional specialization was observed. Two F1 hybrids exhibited suggestive cold resilience, with expression changes elevated at 60 minutes but declining by 95 minutes. Hybrids also displayed substantial regulatory variation under stress and transgressive downregulation of photosynthesis genes under ambient conditions.
These findings suggest that V. oxycoccos introgression could be utilized in breeding cold-tolerant cranberry cultivars. Variation observed between F1 hybrids reflects the diversity introduced through CWR germplasm and provides opportunities for selection. Conservation of V. oxycoccos and other CWRs remains critical for future crop improvement.

sample_organism:
Vaccinium macrocarpon
Vaccinium oxycoccos

overall_design: RNA-seq profiling of V. macrocarpon and V. macrocarpon x oxycoccos hybrids under 15 and 30 minutes of heat treatments and 60 and 95 minutes of cold treatment. Additional RNA-seq of V. oxycoccos under ambient conditions.

first: Jackson

last: Kubal

first: Nicholas

last: Allsing

first: Emily

last: Murray

first: Todd

middle: P

last: Michael

first: James

last: Polashock


title: Regional differences in enterocyte function across development

city: Durham

first: Staci

last: Bilbo

state: North Carolina

address: 207 Research Dr, GSRB2

department: Psychology and Neuroscience

institute: Duke University

summary: The medial (jejunum) and distal (ileum) regions of the small intestine undergo dramatic functional changes after weaning. However, how these changes differ by region and developmental stage remains unclear. To address this, we performed bulk RNA sequencing on isolated epithelial cells from the jejunum and ileum of mice at postnatal day 6 (P6) and day 36 (P36) to analyze region- and age-dependent transcriptional changes

overall_design: A 2 cm segment of jejunum and ileum was isolated from the same mouse. The segments were incubated in EDTA to separate intestinal epthelial cells from the intestinal wall. 4 mice age were utlized including both male and female mice.

first: Block

last: Carina

first: Bagnat

last: Michel

first: Eroglu

last: Cagla

first: Sakers

last: Kristina


title: MAVS signaling of long-lived brain-resident myeloid cells is needed during viral encephalitis to adjust the transcriptome of CNS-infiltrating CD8+ T cells

city: Hannover

first: Ulrich

last: Kalinke

state: Lower Saxony

address: Feodor-Lynen-Str. 7

department: Institute for Experimental Infection Research

institute: Twincore, Centre for Experimental and Clinical Infection Research

summary: Neurotropic viruses like vesicular stomatitis virus (VSV) can infect the central nervous system (CNS) through the olfactory route. Following intranasal instillation, VSV moves along the axons of olfactory sensory neurons to the olfactory bulb. While within the olfactory bulb the spread of the virus is controlled by microglia activation and the recruitment of peripheral leukocytes, some of the underlying mechanisms remain unknown. To investigate these mechanisms, we used mice with conditional deletions of the mitochondrial antiviral-signaling protein (MAVS), an adaptor for RIG-I-like receptor (RLR)-signaling. By selectively deleting MAVS in neurons, astrocytes, or long-lived myeloid cells, we discovered that RLR-signaling specifically within brain-resident myeloid cells is crucial for protection against the virus. Mice with a MAVS deletion in these myeloid cells showed normal myeloid cell and leukocyte infiltration into the brain. However, the P2RY12+ microglia showed aberrant expression of genes involved in antigen cross-presentation.Furthermore, flow cytometry experiments revealed diminished MHC class I expression on MAVS deficient microglia. Moreover, CNS-infiltrating CD8+T cells had dysfunctional transcriptional profiles. Therefore, our findings indicate that during viral CNS infection, MAVS signaling in brain-resident myeloid cells, presumably microglia, is essential for antigen cross-presentation and the relicensing of protective, infiltrating CD8+ T cells.

overall_design: C57BL/6 (WT) and CX3CR1‑CreER±MAVSfl/fl mice were intranasally instilled with PBS or 10^3 PFU of VSV and on 6 days post treatment the olfactory bulb was prepared, immune cells were isolated and CD45+ CD11blow Ly6C− P2RY12+ microglia were directly sorted into 350 μl of β‑mercaptoethanol‑containing RA1 buffer for RNA extraction and subsequent bulk sequencing

first: Andreas

last: Pavlou

first: Felix

last: Mulenge


title: Effects of Ilex paraguariensis extracts on osteogenesis and bone microenvironment in mouse osteoblasts (MC3T3-E1)

city: Jinju-si

first: Se Hyo

last: Jeong

state: Gyeongsangnam-do

address: 501, Jinju-daero

country: South Korea

institute: Gyeongsang national unversity

summary: Osteoporosis is a metabolic disease characterized by the destruction of bone microarchitecture and bone loss, which increases the risk of fractures and reduces quality of life. Understanding the biological mechanisms that promote bone formation is therefore of great importance. In this study, we performed transcriptomic sequencing to molecularly elucidate the effects of Ilex paraguariensis extracts on bone formation and bone-related health. Thus, this study identifies the potential mechanisms by which Ilex paraguariensis and Ligularia fischeri extracts influence bone formation and the bone microenvironment and suggests potential targets and benchmarks for biological research.

overall_design: Ilex paraguariensis extracts were treated with MC3T3-E1 cells for 24 hours, and gene expression profiling analysis was performed on the RNA-seq data of the cells.

first: Hun-Hwan

last: Kim

first: Abuyaseer

last: Abusaliya

first: Se-Hyo

first: Bhosale Pritam

last: Bhagwan

first: Gon-Sup


title: Unanchored K63-linked polyubiquitin chains: a novel second messenger involved in G protein-coupled receptors early signaling events

city: Montreal

first: Marc

last: Servant

state: Quebec

address: P.O. Box 6128, Downtown Station

department: Faculty of Pharmacy

country: Canada

institute: Université de Montréal

summary: GPCR rapidly transduced extracellular cues via their ability to activate effector proteins leading to the production of a variety of well-characterized second messenger molecules. We describe here that the E3 ubiquitin ligase tumor necrosis factor receptor associated factor 6 (TRAF6) is required for the rapid and transient production of unanchored lysine (K)63-linked polyubiquitin chains in primary and transformed cells exposed to vasoactive agonists Angiotensin II (Ang II), Lysophosphatidic acid (LPA) and Thrombin (Thr). We further show that unanchored K63-linked polyubiquitin chains accumulate in Transforming Growth Factor beta-activated kinase 1 (TAK1) and IkappaB kinase beta (IKKbeta) immunocomplexes and are required for the T-loop phosphorylation of TAK1 leading to IKKbeta, c- Jun N-terminal kinases (JNK1/2) and p38 mitogen-activated protein kinases (p38) phosphorylation and the induction of transcriptional events. Our results support a novel paradigm in field of GPCR signal transduction, identifying unanchored K63-linked polyubiquitin chains as novel second messenger molecules.

overall_design: RNASeq analysis conducted on HaCat cells stimulated with Lysophosphatidic acid (LPA). Production of stable HaCaT expressing FLAG 4x ZnF UBP : Platinum-A (Plat-A) retroviral packaging cell line (Cells BIOLABS) were transfected with the pMRX-ires-puro vector or with the pMRX-ires-puro Flag 4x ZnF UBP vector using Lipofectamine 3000 Transfection Reagent (Invitrogen) according to the manufacturer's instruction. The retroviral pseudoviruses were collected 48 hours after transfection and passed through a 0.45 µm filter. 1 600 000 HaCaT cells were infected with 2 ml of virus containing 10 mg/ml of polybrene for 48 hours and selected for 4 days with 1.5 µg/ml of puromycin, creating stable populations expressing either the pMRX-ires-puro vector or the pMRX-ires-puro Flag 4x ZnF UBP.  2) Stimulations: Serum-starved cells were stimulated with LPA (10 µM) for 15, 30 and 60 min or left untreated. RNA was extracted and submitted to RNASeq analysis

first: Priscilla

last: Doyon

first: Mohamad-Ali

last: El-Mortada

first: Jiunn

last: Roy

first: Firas

first: Simon-Pierre

last: Gravel


title: CD4 T cells

city: Salt Lake City

first: J. Scott

last: Hale

state: Utah

address: 15 N Medical Drive

department: Pathology

institute: University of Utah

type: Methylation profiling by high throughput sequencing


title: Sing cell RNA sequence analysis of control and P4HA1 KO mouse mammary gland

first: Jinpeng

last: Liu

state: Kentucky

address: 800 Rose St

institute: Markey Cancer Center

summary: In this study, we investigated the role of P4HA1 in mouse mammary glands by analyzing single cell gene expression profiles across two mouse groups: control (5Ht) and P4HA1-knockout (6Ho) mice.

overall_design: ScRNA-seq data were derived from two groups of mice: K14-cre; P4HA1 loxp/+ (control, 5Ht) mice and K14-cre; P4HA1 loxp/loxp (P4HA1-knockout, 6Ho) mice. For each group we used three pairs of 8-week-old mice, with each pair originating from the same breeding to minimize age and estrous cycle variations. P4HA1 expression was specifically silenced in the basal mammary epithelial cells in 6Ho mice.

first: Ren

last: Xu


title: PAMP signal elicited-stomatal condensation of SAIR1 fine-tunes translation for immunity

city: Beijing

first: Qiangsheng

last: Yu

address: Tsinghua university

department: School of life sciences

institute: Tsinghua university

summary: Plant guard cells perceive pathogens and close stomata to prevent invasion. Biomolecular condensates are central to life growth and stress adaptation, while their roles in regulating stomatal immunity remain unclear. Here, we identify a guard cell-preferential RRM-type RNA-binding protein (RBP) named SAIR1 (stomatal immune RBP 1). Upon pathogen infection and the pathogen-associated molecular pattern flg22 signaling, SAIR1 undergoes phase separation and forms condensates in guard cells to mediate stomatal immunity. Upon flg22 signals, the activated kinases MPK3/6 phosphorylate SAIR1 to initiate its condensation in guard cells. SAIR1 condensates associate with critical defense mRNAs, including those involved in salicylic acid (SA) signaling. SAIR1 interacts with pivotal immune translation regulators such as PABPs and eIFiso4G, and enhances translation of defense mRNAs, ultimately promoting stomatal closure. Our findings reveal that SAIR1 phosphorylation, condensation, and interactions with mRNAs and translation regulators link flg22-MPK3/6 signaling with SA pathways to mediate stomatal immunity.

overall_design: RNA-seq profiling of 3-week-old wild-type Col-0, sair1-1 and SAIR1-YFP-OX2 plants under mock or Pst DC3000 treatment for 24 h;RIP-seq of 3-week-old SAIR1-YFP-OX2 and 35S::GFP plants under flg22 treatment for 45 min; Ribo-seq profiling of 3-week-old wild-type Col-0, sair1-1 plants under mock or flg22 treatment for 45 min.

first: Jie

last: Wu

first: Yunfan

last: Jin

first: Zhi John

last: Lu

first: Susheng

last: Song

first: Tiancong

last: Qi


title: Human stem cell-derived GABAergic interneuron development reveals early emergence of subtype diversity followed by gradual electrochemical maturation [scRNA-seq]

city: South San Francisco

first: Robin

last: Zhou

address: 170 Harbor Way

institute: Neurona Therapeutics

summary: Medial ganglionic eminence-derived inhibitory GABAergic pallial interneurons (MGE-pINs) are essential for cortical development and function.  Dysfunction in MGE-pINs is associated with numerous neurological disorders. We developed a human MGE-pIN cell therapy candidate from pluripotent stem cells, which is undergoing clinical trial evaluation for drug-resistant epilepsy (NCT05135091). Here, we performed single nuclei RNA sequencing and analyzed the transcriptomes of xenografted hMGE-pINs over the lifespan of host mice. Comparative transcriptomic analyses with published human brain datasets revealed that over 97% of grafted human cells developed into pallial MGE-derived somatostatin (SST) and parvalbumin (PVALB) subtypes, including populations that exhibit selective vulnerability in Alzheimer’s disease. Transplanted hMGE-pINs progressed through distinct transcriptional states sequentially involving neuronal migration, synapse organization, and the maturation of electrophysiological properties, demonstrating a surprisingly rapid emergence of subclass-specific features within weeks after grafting. We present molecular, electrophysiological, and morphological data that collectively confirm the derivation of diverse bona-fide human SST and PVALB subtypes, providing a high-fidelity model to study human MGE-pIN development and functional maturation in both healthy and diseased states as well as a compositional atlas for regenerative cell therapy applications.

overall_design: Human ESCs were patterned into MGE projenitors and then differentiated into postmitotic pallial GABAergic interneurons. Cell identity and lot compostion at the end of process (EOP) was analyzed by using 10X Genomics scRNA-seq platform.

first: Marina

last: Bershteyn


title: Human stem cell-derived GABAergic interneuron development reveals early emergence of subtype diversity followed by gradual electrochemical maturation [snRNA-seq]

overall_design: Human ESC-derived MGE-type pallial postmitotic GABAergic interneurons were transplanted into mouse cortex and cortical tissue was dissected at various times 1-18 months post-transplant. Total nuclei from dissected mouse cortices were extracted and stained with an antibody against human-specific nuclear antigen to enrich human cells using fluorescence-activated nuclear sorting (FANS). Sorted nuclei were captured using the 10X Genomics snRNA-seq platform.


title: NAD+-dependent Sirt6 is a key regulator involved in telomere shortening of in vitro-cultured preimplantation embryos [Bisulfite-Seq]

city: shanghai

first: danjun

last: li

address: No. 639 Zhizaoju Road

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

summary: Telomere length (TL) is important for the maintaining the individual health of a species. However, recent studies have indicated that blastocyst culture may increase the risk of telomere shortening in the offspring of those undergoing in vitro fertilization (IVF) treatment, however, the underlying molecular mechanism remains unknown. Sirt6 is a NAD+-dependent epigenetic regulator that has recently been found to play an important role in maintaining telomere stability. Here, we report for the first time that NAD+ levels are significantly lower in blastocysts cultured in vitro than that in blastocysts developed in vivo, leading to impaired Sirt6 function, further triggering telomere shortening of the inner cell mass and possibly affecting newborn offspring. This phenotype could be effectively mitigated by supplementation with nicotinamide mononucleotide (NMN), a precursor of NAD+, during in vitro culture, while it could not be achieved in Sirt6 conditional knockout embryos. Furthermore, mtROS accumulation and epigenetic modifications may also play an important role in this process. Our results reveal the mechanism by which in vitro culture induces telomere shortening in preimplantation embryos, providing a potential target for improving in vitro culture conditions.

overall_design: In the in vivo group, pseudopregnant female ICR mice (10-12 weeks old) were mated with vasectomized males 2.5 days prior to embryo transfer. In the in vitro group, female ICR mice (10 -12 weeks old) were employed as pseudopregnant moms and mated with vasectomized ICR males 3.5 days before embryo transfer. Surrogated ICR mice were selected based on the presence of a vaginal plug and then anesthetized. The uterine horn was removed through the back. Thirty blastocysts from the in vivo or in vitro group were transferred to a single recipient, respectively. The surrogate mother mice were housed in a clean cage with sufficient water and high‐fat chow for 19-21 days before their F1 pups were born.  After birth, the tails of F1 pups were clipped at 1 week and 7 weeks of age respectively to extract genomic DNA for methylation sequencing (1W: In vivo: n=3, In vitro: n=3; 7W: In vivo: n=3, In vitro: n=3).


title: Transcriptional profile of sorted Th1 or Tfh from CD4 T cells with defieciency of Dnmt3a and/or Tet2 (set 1)

summary: DNA methylation programming is associated with enforcement of T cell dysfunction in the context of chronic viral infection. Loss of function in Tet2 and Dnmt3a is also associated with peripheral T cell lymphomas and human angioimmunoblastic T cell lymphoma. As such, we set to test how the loss of either Dnmt3a or Tet2 as well as the combined loss of Dnmt3a and Tet2 would fundamentally alter CD4 T cell functional and response during chronic viral infection.

overall_design: We utilized an adoptively-transfer model with SMARTA CD4 T cells (Cre+) with either Tet2 KO or Dnmt3a f/f or Tet2 KO; Dnmt3a f/f. Chronic viral infection was induced by infecting mice with LCMV-cl13. At day 7 post-infection, spleens were isolated and FACS sorting utilized to sort Th1 or Tfh SMARTA CD4 T cells. RNA was isolated by Tri-Reagent and purified by Direct-zol RNA-prep kit from Zymo.

first: Bryce

last: Fuchs

first: Brian

last: Dalley

first: Chris

last: Stubben


title: Culturing of primary mouse hepatocytes is associated with major changes to the proteome and transcriptome

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Primary hepatocytes are a commonly used in vitro model for studying liver metabolism, but prolonged culturing results in dedifferentiation. Here we characterized the transcriptome and proteome of whole liver and primary hepatocytes as either freshly isolated cells or after 24 hours of 2D-culturing. We found that after 24 hours of 2D-culturing, hepatocytes showed differential expression of over  10,000 genes and 3,000 proteins compared to freshly isolated cells. This was accompanied by a reduced transcriptional heterogeneity and a loss of zonal markers. Cultures contained ~10% non-hepatocytes, including stellate- and dedifferentiated endothelial cells. Culturing also increased abundance of proteins associated with oxidative stress and inflammation, and changed mitochondrial, extracellular, and ribosomal protein abundance.  The data generated are available in the shiny-app “Hepamorphosis, https://cbmr-rmpp.shinyapps.io/hepamorphosis/”. Our finding show that primary mouse hepatocytes undergo significant changes in culture, limiting their utility for studying physiological and molecular mechanisms related to the liver.

overall_design: Single nuclei sequencing from liver biopsies (L), freshly isolated liver cells in suspension (CS), and primary hepatocytes following 24 hours of culture on collagen (PH)

first: Morten

last: Dall

first: Ben

last: Stocks

first: Daniel

last: Cervone

first: Atul

middle: S

last: Deshmukh

first: Jonas

last: Treebak


title: NAD+-dependent Sirt6 is a key regulator involved in telomere shortening of in vitro-cultured preimplantation embryos

summary: Telomere length is important for the maintaining the individual health of a species. However, recent studies have indicated that the telomere length of somatic cells can be drastically decreased in the offspring receiving in vitro fertilization (IVF) therapy, however, the underlying molecular mechanism remains unknown. Sirt6 is a NAD+-dependent epigenetic regulator that has recently been found to play an important role in maintaining telomere stability. Here, we report for the first time that NAD+ levels are significantly lower in blastocysts cultured in vitro than that in blastocysts developed in vivo, leading to impaired Sirt6 function, further triggering telomere shortening of the inner cell mass and possibly affecting newborn offspring. This phenotype could be effectively mitigated by supplementation with NMN, a precursor of NAD+, during in vitro culture.While it could not be achieved in Sirt6 conditional knockout embryos. Our results reveal the mechanism by which in vitro culture induces telomere shortening in preimplantation embryos, providing a potential target for improving in vitro culture conditions.

overall_design: Females were superovulated by an intraperitoneal injection of 10 IU pregnant mare serum gonadotrophin (PMSG), followed 48 h later by an intraperitoneal injection of 10 IU human chorionic gonadotrophin (hCG). Females were naturally mated with males after the hCG injection. All superovulated female mice were plugged vaginally after mating and randomly divided into the two groups (in vivo or in vitro). After in vivo development, D3.5 blastocysts (in vivo group) were collected by flushing each uterus of the plugged females with modified human tubal fluid media supplemented with 10% serum substitute supplement (mHTF-SSS). For the in vitro group, at 19-21 h post-hCG treatment, in vivo fertilized zygotes were collected from oviducts and cumulus cells were removed via digestion with hyaluronidase for 3-5 min. The zygotes were rinsed with mHTF-SSS, and placed in 20 ul drops of synthetic oviductal medium enriched with potassium (KSOM) covered with paraffin oil, and then equilibrated overnight in an incubator at 37℃ and 5% CO2. The zygotes were grown to the blastocyst stage at 37℃with 5% CO2 atmosphere in vitro. The blastocysts in both groups were chosen on the basis of their developmental status and morphology and quickly frozen in liquid nitrogen and stored at -80°C. RNA sequencing was performed on total RNA extracted from collected blastocysts in vivo and in vitro to identify genes that cause telomere shortening in vitro culture (In vivo: n=3; In vitro: n=3).


title: Unveiling Tissue-Specific Transcriptional Adaptations in iPSC-Derived Fibroblasts via Co-Culture Systems

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

summary: Induced pluripotent stem cell-derived fibroblasts (iFBs) are promising tools for autologous disease modelling, but their ability to replicate tissue-specific fibroblast characteristics remains unclear. Fibroblasts are highly heterogeneous, with distinct subtypes playing critical roles in tissue function and organ integrity. This study investigates whether iFBs can acquire tissue-specific transcriptional profiles through co-culture with cells found in the skin (keratinocytes), heart (cardiomyocytes), gut (intestinal) and lung (bronchial epithelial Transcriptomic analyses revealed that iFBs exhibit transcriptional plasticity, adopting molecular phenotypes aligned with their co-culture environment across all three germ layers.Additionally, paracrine signalling induced tissue-specific changes in indirectly co-cultured iFBs, though these adaptations were transient without sustained interaction.These findings demonstrate the potential of iFBs to mimic native fibroblast behaviour but also highlight the need for validation in complex tissue models to account for variability in iPSC differentiation and functional stability. By providing evidence of tissue-specific plasticity, this study supports the utility of iFBs in developing physiologically relevant in vitro systems.

overall_design: iFBs derived from three different human induced pluripotent stem cell lines (healthy donors) were co-cultured with four distinct cell types mentioned in the abstract. RNA was then extracted from the co-cultured iFBs and compared to iFBs cultured without co-culture. Additionally, separate iFBs, cultured in different mediums but without co-culture, were also collected for further analysis.

first: Amar J

last: Azad

last: Weiner 3rd

first: Sarah

last: Hedtrich


title: Comprehensive profiling of RNAs enriched in small extracellular vesicles of colorectal cancer patients

city: Brno

last: Jugas

address: Kamenice 5

country: Czech Republic

institute: CEITEC MU

summary:
The main objective of this project was to determine RNA expression profiles in small extracellular vesicles isolated from low volumes of blood serum of colorectal cancer (CRC) patients and to compare the data with those of healthy controls (HC) in order to identify molecules (mainly lncRNAs and protein-coding genes) that could serve as novel non-invasive biomarkers for early diagnosis of CRC.
In total, we have identified 4,014 transcripts to be differentially expressed between two studied groups (adjusted P < 0.05). From those, 1,469 were assigned to lncRNAs (36.6%), while protein-coding genes represented the second most common gene biotype (1,166 transcripts; 29%). The hierarchical clustering proved that it is possible to distinguish CRC samples from HC based on the expression of all significantly deregulated genes as well as protein coding genes and lncRNAs, separately or in combination. As this study was primarily focused on lncRNAs, more stringent criteria concerning several different parameters were set to identify lncRNAs with the highest potential to discriminate the two groups of samples. In total, we got 21 molecules, which met our requirements and thus were chosen for further evaluation in the training phase of the study by RT-qPCR.

overall_design: In total, 150 samples were involved in the study including 100 serum samples of CRC patients and 50 serum samples of HC. No replicates were involved.

first: Petra

last: Vychytilova-Faltejskova

first: Lucie

last: Pifkova

first: Tina

last: Catela Ivkovic

first: Milana

last: Sachlova

first: Ondrej

last: Slaby


title: Nur77 induces GSDMC-mediated pyroptosis

city: xiamen

first: feng

last: deyi

state: xiamen

address: Xiamen University

institute: xiamen university

summary: Pyroptosis is a type of lytic cell death executed by members of the gasdermin family. It has been demonstrated that induction of pyroptosis can effectively inhibit tumor growth, which implicates a new strategy for clinical tumor therapy, especially for those tumors (such as melanoma) that are insensitive or resistant to the induction of apoptosis.By means of a chemical compound DBIC, designed and identified by our group recently, to induce GSDMC-mediated pyroptosis in melanoma cells.

overall_design: To investigate the mechanism of pyroptosis induced by DBIC based on the fact that hemin inhibted DBIC-induced pyroptosis. We then performed gene expression profiling analysis data obtained from RNA-seq of four groups.Comparative gene expression profiling analysis of RNA-seq data for Ctrl, DBIC, Hemin and DBIC+Hemin.

first: Liu-zheng

last: Wu

first: Ya-ying

last: Huang

first: Hai-jing

last: Hu


title: Methylome description of CD4 T cells during chronic viral infection with either deletion of Dnmt3a, Tet2 or both Dnmt3a and Tet2.

first: J. Scott

last: Hale

summary: The purose of this experiment was to determine how the loss of Tet2 and Dnmt3a altered the methylation program of CD4 Th1 and Tfh cells during chronic viral infection.

overall_design: Utilizing a SMARTA-Tg CD4 T cell adoptive-transfer model followed by LCMV-cl13 to induce chronic viral infection, spleens were collected at day 7 post-infection. After enrichment, SMARTA-Tg CD4 Th1 or Tfh cells were FACS Sorted into FACS Buffer. DNA was extracted using the Quick-DNA Micro-prep Kit (Zymo), and library construction with the NEBNext Enzymatic Methyl-seq kit was conducted. Samples were then sequenced.

first: Brian

last: Dalley

first: Chris

last: Stubben

first: Timothy

last: Parnell

first: Bryce

last: Fuchs


title: Exploring the Factors regulating RNA Enrichment in EVs

city: Newark

first: Mona

last: Batish

state: Delaware

address: 15 Innovation Way

institute: University of Delaware

summary: Extracellular vesicles (EVs) are small particles that are released by cells and mediate cell-cell communication by transferring bioactive molecules such as RNA. RNA cargo of EVs, including coding and non-coding RNAs, can change the behavior of recipient cells, affecting processes including gene expression, proliferation, and apoptosis. CircRNAs are stable and resistant to degradation and have been shown to be enriched in EVs. They play key roles in gene regulation and are also emerging as promising biomarkers for disease diagnosis due to their stability and disease-specific expression. While microRNAs (miRNAs) are the most well studied RNA cargo of EVs, very little is known about the mechanisms of enrichment of circular RNAs (circRNAs) as well as long linear RNAs. Here, we take a comprehensive genome-wide approach to investigate the role of structuredness and shape along with GC%, size, exon count, and coding potential, in the sorting and enrichment of circular and long linear RNAs into EVs. We developed a model using these parameters to predict the likelihood of EV packaging of RNA and it was validated by using single molecule RNA imaging of EV bound RNAs. Furthermore, we found that structuredness could explain the relative enrichment of circRNAs over their linear counterparts. These results were validated on existing public databases of circular and linear RNAs in EVs. By identifying and analyzing these factors, we aim to better understand the complex mechanisms behind EV-mediated RNA transfer and its impact on cell communication in both health and disease. This mechanistic understanding of RNA enrichment in EVs is crucial for engineering EVs with selective RNA cargo.

overall_design: To explore the factors involved in sorting and enrichment of RNAs into EVs, we seqeunced linear and circular RNAs from cell and EVs fractions.

first: Ahmed

last: Abdelgawad

first: Yiyao

first: Kenneth

middle: W

last: Witwer


title: Next Generation Sequencing Facilitates Quantitative Analysis of the Role of Dhx16 in hematopoietic stem cells [RNA-seq]

city: Chongqing

first: Zhigang

last: Li

state: China

address: NO.30 GaotanYan  Street, Shapingba District

institute: Southwest Hospital, Army Medical University

summary: To identify genes and the molecular pathways involved in the Dhx16 regulating hematopoietic stem cells (HSC) in mice, we performed RNA-Sequence of HSC freshly sorted from mice. mRNA profiles of HSC in Dhx16fl/fl (floxp) and Dhx16-CKO(cKO) were generated by deep sequencing,  using Illumina HiSeq 2000.Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the mouse genome (build mm10). Our results represent the first detailed analysis of HSC transcriptomes in Dhx16-knockout mice and found that Dhx16 regulated multiple mRNA pathways in HSC.

overall_design: The mRNA profiles of HSC in Control and Dhx16-knockout mice were generated by deep sequencing,  using Illumina HiSeq 2000.

first: Yu

last: Hou


title: Adipocytes induced distinct gene expression profiling of triple negative breast cancer cells

city: Hefei, Anhui

first: dou

last: yin

address: 81 Meishan Road

department: Department of Pathophysiology School of Basic Medical Sciences

institute: Anhui Medical University

summary: We investigated how adiposity reprograms the metabolism and progression of triple-negative breast cancer (TNBC) cells compared to non-TNBC cells. MDA-MB-468 (TNBC) and BT474 (non-TNBC) cells were co-cultured with mature adipocytes, followed by RNA-seq analysis to assess the metabolic impact of adipocyte on TNBC cells.

overall_design: MDA-MB-468 and BT-474 cells were cultured with DMEM/F12 complete medium containing 10%FBS. The medium used for human adipocytes was a high-glucose DMEM medium containing 10% FBS.using 10% FBS, 0.5 mM IBMX, 1 µM dexamethasone, and 10 µg/mL insulin for 3 days. Differentiation was further promoted with DMEM containing 10% FBS and 10 µg/mL insulin for 3 days, followed by maintenance in DMEM with 10% FBS for an additional 4 days until mature adipocytes, rich in lipid droplets, were fully formed. Subsenquently, breast cancer cells were cocultured with mature adipocytes  via transwell coculture system for 72 hours. Total RNA of breast cancer cells with the presence or absence of adipocytes  were conducted for RNA sequencing (RNA-seq) .

first: Dou

last: Yin

first: Fang

last: Ma

first: Nana

last: Fang

first: Xiaohui

last: Wei


title: Dhx16 regulates alternative splicing of pre-mRNA in hematopoietic stem cells [ISO-Seq]

summary: To investigate whether Dhx16 knockout affects alternative splicing of pre-mRNA in HSCs, we sorted Dhx16-deficient and control HSCs and performed ISO-Seq for full-length transcriptome sequencing.

overall_design: The full-length transcriptome sequencing of HSC in Control and Dhx16-knockout mice based on the PacBio third-generation sequencing platform


title: Analysis of tumor infiltrating lymphocytes from murine PAN02 subcutaneos tumors under SMAC mimetic and BET inhibitor treatment

city: Vienna

first: Martin

last: Aichinger

address: Dr. Boehringer-Gasse 5-11

country: Austria

institute: Boehringer-Ingelheim

summary: A multi-omic analysis of CITE-seq and advanced flow cytometry of a syngeneic model of PDAC unveils distinct phenotypic correlations of augmented anti-tumor immunity and a substantially reduced immunosuppressive tumor microenvironment (TME). This study presents BETi and SMACm as a promising drug combination for cancer patients with a multi-layered impact on both tumor cell intrinsic, as well as TME-dependent mechanisms.

overall_design: In vivo treatment of mice harboring subcutaneous PAN02 PDAC tumors, analysis of the tumor microenvironment using CITEseq.

first: Florian

last: Ebner

first: Artem

middle: V

last: Artemov

first: Jesse

last: Lipp


title: Neutrophil modulation by IL-1β-induced fibroblasts

city: nanjing

first: xiaoyun

last: chen

state: nanjing

address: nanjing

institute: xiangya

summary: Neutrophils are key contributors to the pathogenesis of SLE. Using single-cell sequencing data from SLE skin lesions, we identified a subcluster of CXCL1+ fibroblasts primarily induced by IL-1β. To better understand the effects of CXCL1+ fibroblasts on neutrophils, we established a conditional culture model using culture supernatants from control and IL-1β-stimulated fibroblasts. Neutrophils were collected after 21 hours of conditional culture and subjected to RNA-seq. Our findings revealed that neutrophils exhibited a distinct pro-inflammatory phenotype, expressing higher levels of pro-inflammatory cytokines such as IL1B, TNFA, IL8, and OSM.

overall_design: Fibroblasts were treated with either control or IL-1β(10 ng/mL) and cultured for 48 hours. The fibroblast culture supernatants were collected and used for conditional culturing with neutrophils. Neutrophils were then collected, and RNA was extracted using Trizol and assessed for concentration and quality with a Nanodrop 2000 spectrophotometer. DESeq2 analysis was performed to identify significantly differentially expressed genes (DEGs) using Q value < 0.05 and fold change > 2 as thresholds.

first: Ming

last: Zhao

first: Qianjin

last: Lu

first: Sujie

last: Jia


title: Effect of IL-1β on gene expression of human dermal fibroblasts

summary: Fibroblasts display significant heterogeneity and exhibit distinct gene expression profiles under different cytokine stimulations. We utilized RNA-seq to analyze the expression profile differences between control and IL-1β stimulated fibroblasts（ n=3）. Our analysis revealed 1756 differentially expressed genes between WT and Smyd1-KO hearts [adjusted P-value <0.05, |log2(fold change)| > 0.5]. Among these, 755 genes were upregulated, and 843 genes were downregulated in IL-1β stimulated human dermal fibroblasts. Notably, IL-1β stimulation can induce fibroblast differentiation into pro-inflammatory fibroblasts, characterized by the expression of neutrophil-related chemokines (CXCL1, CXCL2, CXCL3), ferroptosis-related genes (PTGS2, TNFAIP6), and pro-inflammatory cytokines (IL6). Our findings lay the groundwork for understanding the IL-1β-induced fibroblast expression of specific gene profiles.

overall_design: Fibroblasts were treated with control or IL-1β (10 ng/mL) for 24 hours in 6-well plates. After discarding the supernatant and washing with PBS, RNA was extracted using Trizol and assessed for concentration and quality with a Nanodrop 2000 spectrophotometer. DESeq2 analysis identified significantly differentially expressed genes (DEGs) using Q value < 0.05 and fold change > 2 as thresholds.

first: Xiaoyun

last: Chen


title: Xist upstream deletion impairs topological contacts of Xist locus and affects Xist coating/expression and autosomal gene expression [4C]

city: Bangalore

first: SRIMONTA

last: GAYEN

state: Karnataka

address: GE14, new biological science building, Indian institute of Science

department: Department of Developmental biology and Genetics

country: India

institute: Indian Institute of Science, Bangalore, India

summary: In this study, we have investigated the role of Xist upstream region located near the Xist-TAD boundary in maintenance of imprinted X-chromosome inactivation in extraembryonic endoderm stem cells (XEN). We found that deletion of Xist upstream region(~6Kb) leads to the alterations of Xist intra-TAD contacts and upregulate Xist expression. Moreover, it impaired the interactions of the Xist locus across X-chromosomes and autosomes. Moreover, Xist upstream deletion resulted dispersal of Xist coating and loss of accumulation of diffrent repressive chromatin marks on the inactive-X. Surprisingly there was no effect on inactive-X gene silencing, however, it affeted the autosomal gene expression.

overall_design: We performed RNA-seq in  WT XEN clones  and Xist upstream deleted XEN cell clones (two biological replicates for each deletion) to investigated the effect of Xist upstream deletion in XEN cells.  We also performed ChIP-seq and 4C experiments in WT XEN and Xist deleted XEN cells.

first: Sudeshna

last: Majumdar

first: Lakshmi

last: Bammidi

first: Hemant

last: Naik

first: Avinchal

last: Manhas

first: Akash

last: Kalita

first: Nidarshan

last: Sundarraj

first: Girija

last: Bariha

first: Dimple

last: Notani

first: Srimonta

last: Gayen


title: Fibroblast growth factor receptor signaling modulates cholesterol storage in a SOAT1-dependent manner to promote mammary tumor cell invasion

city: Minneapolis

first: Kaylee

last: Schwertfeger

state: MN

address: 420 Delaware St. SE MMC 609

department: Lab Medicine and Pathology

institute: University of Minnesota

summary: Signaling by fibroblast growth factor receptors (FGFRs) is active in up to 85% of breast cancers and results in enhanced proliferation, migration, and invasion of tumor cells. Here, we show that FGFR signaling regulates cholesterol metabolism in breast cancer. Specifically, we demonstrate that FGFR signaling promotes cellular cholesterol storage by upregulating expression of the enzyme sterol O-acyltransferase 1 (SOAT1). Moreover, we demonstrate that inhibition of SOAT1 attenuates FGFR-driven colony formation and invasion in tumor cells. Finally, we identify a relationship between SOAT1 inhibition and decreased integrin expression and fibronectin binding by tumor cells. Taken together, these findings suggest a previously undiscovered metabolic role for FGFR signaling in breast cancer and present a therapeutic vulnerability that could be targeted in FGFR-driven breast cancer.

overall_design: Mouse mammary epithelial cells (HC-11) expressing a chemically inducible FGFR1 were treated with B/B homodimerizer for 2 hours prior to RNA extraction. Control samples were treated with a solvent control for the same amount of time.

first: Kathryn

middle: L

first: Ying

last: Wang

first: Christine

middle: H

last: O'Connor


title: Single-cell transcriptome analysis reveals atypical monocytes circulating ahead of acute graft-versus-host disease clinical onset

city: Lausanne

first: Evarist

last: Planet

address: Route Cantonale 15

country: Switzerland

institute: EPFL

summary: Acute graft-versus-host disease (aGVHD) represents the rejection of the skin, gut and liver tissues of the recipient of an allogenic hematopoietic stem cell transplantation (HSCT) by the donor T-cells. The onset of aGVHD is often rapid and its evolution unpredictable. We undertook the single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) collected before aGVHD clinical onset in three patients and at aGVHD diagnosis in one, using four HSCT recipients who remained free of aGVHD as controls. This analysis unveiled the presence in the circulation of particular subpopulations of monocytes and cytotoxic T cells (CTLs) in pre-aGVHD samples up to 18 days before clinical disease. These pre-aGVHD monocytes were characterized by an upregulation of the M2 polarity marker CD163, and the transmembrane protein SIGLEC1/CD169, while their CTL counterparts stood out for the upregulation of the CXCL10 receptor CXCR3 and the antigenic stimulation marker CD70. The occurrence of CD163/CD169-co-expressing monocytes upstream of aGVHD onset was validated using RNAseq data from an independent cohort and by flow cytometry of blood samples. These findings point to potential early diagnostic tools and preventive therapeutic strategies for aGVHD.

overall_design: Single-cell RNA-Seq of PBMCs from 8 post allo-HSCT recipients

first: Filipe

last: Martins


title: Xist upstream deletion impairs topological contacts of Xist locus and affects Xist coating/expression and autosomal gene expression [RNA-Seq]


title: RNAseq of motor neurons with differential vulnerability to ALS isolated from the SOD1G93A mouse model of ALS

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

summary: ALS is characterised by thedegeneration of somaticmotor neurons (MNs), that control voluntary muscle, while visceral motor neurons remain preserved. Some somatic motor neurons are also relatively resilient to degeneration, including oculomotor and trochlear motor neurons that regulate eye movement.In this study we aim to investigate the longitudinal transcriptional dynamics of resistant and vulnerable MN populations in response to the SOD1G93A ALS-causative mutation.  We have conducted bulk RNA sequencing of MNs isolated from the SOD1G93A mouse at presymptomatic (p56) and symptomatic (p112) stages using laser capture microdissection followed by Smart-seq2 RNA sequencing. Oculomotor and trochlear (CN3/4) MN, and visceral MNs from the vagus nucleus (CN10) represent resilient neuron groups that were analysed. MNs from the lumbar spinal cord (SC) and hypoglossal (CN12) nucleus were utilised as two vulnerable populations.

overall_design: We used laser capture microdissection to isolate discrete neurons from transgenic SOD1G93A mice and wildtype littermates  (Jax Stock No 00435).  We analyzed a total of 54 samples with 3-5 biological replicates per condition. We included four neuronal groups with differential vulnerability in ALS and investigated two time points troughout  disease progression including pre-symptomatic stage and symptomatic stage (P56,P112)

first: Irene

last: Mei

first: Susanne

last: Nichterwitz


title: Single cell Transcriptome characterization of the effects of exosomes from different sources on testicular tissue of male mice

city: Changchun

first: Tong

last: Chen

state: Jilin

address: No. 5333, Xi'an Road, Lvyuan District

institute: Jilin University

summary: Collect the blood circulation exosomes from antibiotic treated or wild type mice, and then inject them into the recipient mice through tail vein, collect the testicular tissue of the recipient mice, conduct transcriptome sequencing, and analyze and compare gene expression differences

overall_design: Inject PBS (BP), blood exosomes from wild-type mice (BE), and intestinal microbiota imbalance mice (BdE) into the mouse model of azoospermia induced by Baixiaoan.

first: Chunjin

last: Li

first: Xu

last: Zhou


title: Cardiomyocyte glucocorticoid receptor and transcriptional rhythms in the heart

city: Durham

first: John

last: Cidlowski

state: NC

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: Ventricular arrhythmias demonstrate a prominent diurnal rhythm, commonly presenting in the morning on waking. Transcriptional rhythms in cardiac ion channels contribute to this phenomenon but the underlying mechanisms are incompletely understood. We have evidence in mice suggesting the glucocorticoid receptor (GR), the transcriptional effector of glucocorticoids, regulates ion channels previously implicated in the diurnal rhythm in cardiomyocyte excitability and ventricular arrhythmia susceptibility. To determine if the GR is a direct regulator of the transcriptional rhythms in the heart, RNA-seq was performed on RNA isolated from the left ventricular (LV) free wall of cardiomyocyte-specific GR knockout mice (cardioGRKO) and their littermate control mice (GRflox) at ZT0 (start of lights on) and ZT12 (start of lights off) time points.

overall_design: Mice with conditional knockout of GR in cardiomyocytes (cardioGRKO) have been previously described (Sci Signal. 2019 Apr 16;12(577):eaau9685. doi: 10.1126/scisignal.aau9685). Hearts were removed from adult male cardioGRKO mice and their littermate control mice (GRflox) at ZT0 (start of lights on) and ZT12 (start of lights off) time points. The left ventricular (LV) free wall was dissected from the heart. Total RNA was isolated from the LV free wall using Qiagen RNeasy Mini kit. A TruSeq RNA kit (Illumina, San Diego, CA) was utilized to prepare the poly(A)-enriched RNA-seq libraries that were sequenced on the Illumina NovaSeq 6000 in a 75-base paired-end mode according to the manufacturer’s protocol.

first: Robert

last: Oakley

first: Jianying

first: Alicia

last: D'Souza


title: Single cell gene expression profile of irradiated small intestinal crypt cells of WT and CREPT KO mice

city: Beijing

first: Tingwei

last: Lan

address: Tsinghua University, Haidian District

department: School of Medicine

institute: Tsinghua University

summary: To investigate the role of CREPT in intestinal regeneration, we performed single cell RNA sequencing (scRNA-seq) analyses on irradiated small intestinal crypt cells of WT and CREPT KO mice to figure out the change of different types of intestinal epithelial cells.

overall_design: CREPT was specifically deleted in intestinal epithelial cells with Villin-cre. Small intestinal crypts were isolated from irradiated WT and CREPT KO mice at 3 and 5 days post irradiation (dpi). Viable single cells were sorted by fluorescence-activated cell sorting (FACS) and subjected to scRNA-seq.


title: Transcriptomic Profiling of SARS-CoV-2 Spike Protein S1 Subunit Mediated Changes in Human Vascular -Pericytes, -Endothelial cells (ECs), -Smooth Muscle Cells and Lymphatic ECs: Evidence for Differential Gene Regulation

city: Schlieren

first: Giovanna

last: Azzarito

address: Wagistrasse 14

department: Reproductive endocrinology

institute: University Hospital Zurich

summary: SARS-CoV-2 S1 spike protein (S1-SP) plays a critical role by actively facilitating host and virus interaction via ACE2 to mediate the deleterious effects of COVID19. Evidence suggests that SP devoid of virus is not latent and modulate proinflammatory actions. Circulating SP levels increase in subjects recieving mRNA vaccines and those who develop post-vaccination myocarditis. However the mechanism(s) involved remain unclear. Since interaction between circulating factors and vascular cells play a key role in the pathophysiology of cardiovascular complication, using microarrays we assessed the modulatory effects of S1-SP on genes of key vascular cells (human vascular and lymphatic endothelial cells (VECs; LECs), -pericytes (PCs), and –smooth muscle cells (SMCs). Transcriptomic profiling of genes from microarray studies revealed that treatment of PCs, VECs, LECs and SMCs with 10ng/ml S1-SP for 36 hours upregulated 3935, 2512, 1422, 19  genes, respectively; and downregulated 3935, 3223, 1170, 37 genes, respectively. S1-SP significantly modulated genes in PCs, LECs and VECs, but not in SMCs. Pathway enrichment analysis of modulated genes showed significant regulation of several pathways, including TGF-β regulation of extracellular matrix, focal adhesion, pathways in cancer in PCS, VECs and LECs; whereas  coronavirus disease, ribosome, cytoplasmic ribosomal protein, translation, protein metabolism, influenza infection, disease pathways were regulated in PCs and VECs, but not in LECs. Moreover, interleukin-2 and cellular senescence pathways were significantly regulated in both LECs and  VECs. In LECs, significant modulation in  IL-4 regulation of apoptosis, Oncostatin M, T cell receptor regulation of apoptosis, TNF-α effects on cytokine activity/cell motility & apoptosis, p53 signaling and fluid shear stress and atherosclerosis was also observed. Transcriptomic analysis showed induction of key COVID associated pro-inflammatory, coagulatory and matrix/adhesion molecules in PCs (PECAM1, CDH5, S1PR1, VWF, ESM1, EDN1, EFEMP1, ERG, ICAM2), but downregulation in VECs. Interestingly top genes that were downregulated in PCs (MYCT1, MMRN1, SEMA5A, GREM1, CEMIP, THBS2, BICC1, MYOCD, COL3A1, COL1A1, IGFBP3, PLPPR4, ITGA11, ADAMTS12, COL11A1, POSTN) were upregulated in VECs. Of the top 20 genes up or down -regulated in LECs 7 were similar to PCs and 4 to VECs, suggesting that S1-SP induces differential actions in vascular cells. Of all the genes regulated by S1-SP in PCs, VECs and LECs only two  (FAP and P3H2) and eight (TMEM200A,MMP1, PLPP4, RGS5, TENM3, SULF1, COL12A1, SPOCK1) were up- and down regulated, respectively. DRG analysis highlighted contrasting modulation of genes associated with: myocarditis, metabolism (Glycolysis, one crbon metabolism, urea cycle and oxidative phosphorylation) and inflammation in PCs and VECs. No modulation of DRGs was observd  in SMCs whereas mixed regulation compared to PCs was observd in LECs. Taken together our findings provide first evidence that S1-SP differentially modulates genes in PCs, LECs, VECs. Importantly it modulates key genes and associated with the pathophysiology of myocarditis, mitochondrial metabolism, inflammation and Covid associated genes. The comparative transcriptomic profiling of S1-SP induced changes in vascular PCs, VECs, LECs and SMCs, provides important insights to elucidate the mechansims mediating the deleterious CV actions of circulating S1-SP associated with COVID-19 and /or mRNA vaccine.

overall_design: Raghvendra,K,Dubey

first: Raghvendra

middle: K

last: Dubey

first: Marinella

last: Rosselli


title: Transcriptome characterization of the effects of exosomes from different sources on testicular tissue of male mice

overall_design: Inject PBS (BP), blood exosomes from wild-type mice (BE), and intestinal microbiota imbalance mice (BdE) into the mouse model of germ cell depletion induced by busulfan.


title: Xist upstream deletion impairs topological contacts of Xist locus and affects Xist coating/expression and autosomal gene expression [ChIP-Seq]

first: SRIMONTA

last: GAYEN

overall_design: We performed RNA-seq in WT XEN clones and Xist upstream deleted XEN cell clones (two biological replicates for each deletion) to investigated the effect of Xist upstream deletion in XEN cells. We also performed ChIP-seq and 4C experiments in WT XEN and Xist deleted XEN cells.

first: Sudeshna

last: Majumdar

first: Lakshmi

last: Bammidi

first: Hemant

last: Naik

first: Avinchal

last: Manhas

first: Akash

last: Kalita

first: Nidarshan

last: Sundarraj

first: Girija

last: Bariha

first: Dimple

last: Notani

first: Srimonta

last: Gayen


title: Mesenchymal Stem Cell Transplantation Attenuates Venous Stenosis of Hemodialysis Vascular Access Arteriovenous Fistula [Mouse MSC]

city: Rochester

first: Sanjay

last: Misra

address: 200 First Street SW

department: Radiology

institute: Mayo Clinic

summary: Arteriovenous fistula (AVF) is the preferred vascular access for patients undergoing hemodialysis and the majority of AVFs fail because of venous intimal hyperplasia (VNH). Results from our lab have shown that adipose tissue-derived mesenchymal stem cell (MSC) transplantation to the adventitia of the outflow vein of AVF attenuates VNH in an immunodeficient mice. in the present study efficacy of AMSCs transplantation in treating AVF failure was tested in a chronic kidney disease (CKD) followed by an AVF created in C57BL/6 mice and porcine models as described in methods. Moreover, a phase 1 trial was performed in small group of endstage renal disease (ESRD) patients who are in hemodialysis. To explore the molecular mechanisms involved in MSCs transplantation improving AVF durability, we performed RNA-seq transcriptome analysis of the outflow veins of AVFs excised from mice and Pigs the after adventitial transplantation of MSCs from the donor inbred C57BL/6 mice or pigs respectively. RNA-seq on AMSCs isolated from donor mice, pigs and from patients of Phase 1 study  was performed and CD markers of MSCs were compared to assess the homogenicity of isolated AMSCs with in the species.

overall_design: RNA-seq of MSCs isolated from adult mouse fat pads

first: Sreenivasulu

last: Kilari

first: Edwin

last: Takahashi


title: Mesenchymal Stem Cell Transplantation Attenuates Venous Stenosis of Hemodialysis Vascular Access Arteriovenous Fistula [Mouse GV_MSCvsNT]

summary: Arteriovenous fistula (AVF) is the preferred vascular access for patients undergoing hemodialysis and the majority of AVFs fail because of venous intimal hyperplasia (VNH). Results from our lab have shown that adipose tissue-derived mesenchymal stem cell (MSC) transplantation to the adventitia of the outflow vein of AVF attenuates VNH in an immunodeficient mice. in the present study efficacy of AMSCs transplantation in treating AVF failure was tested in a chronic kidney disease (CKD) followed by an AVF created in C57BL/6 mice and porcine models as described in methods. Moreover, a phase 1 trial was performed in small group of endstage renal disease (ESRD) patients who are in hemodialysis. To explore the molecular mechanisms involved in MSCs transplantation improving AVF durability, we performed RNA-seq transcriptome analysis of the outflow veins of AVFs excised from mice and Pigs the after adventitial transplantation of MSCs from the donor inbred C57BL/6 mice or pigs respectively. RNA-seq on AMSCs isolated from donor mice, pigs and from patients of Phase 1 study  was performed and CD markers of MSCs were compared to assess the homogenicity of isolated AMSCs with in the species.Mesenchymal Stem Cell Transplantation Attenuates Venous Stenosis of Hemodialysis Vascular Access Arteriovenous Fistula

overall_design: Chronic Kidney disease created to a C57BL6J mouse as described in methods. 28days later an arteriovenous fistula was clreated by ligation of carotid artery and jugular vein. immidiatly after AVF creation, 250000 MSCs from C57 donor mouse of same gender were layred on the adventitia of the AVF outflow veins. 3 days after AVF creation, animals were euthanized and the outflow veins of AVFs were harvested.


title: Mesenchymal Stem Cell Transplantation Attenuates Venous Stenosis of Hemodialysis Vascular Access Arteriovenous Fistula [Human MSC]

overall_design:
RNA-seq of Adipose derived mesenchymal stem cells (MSC)
Sanjay, Misra


title: RNA expression NKp44- ILC3s and  NKp44+ ILC3s in lung cancer

first: Hang

last: Cheng

address: Xin Min Street

summary:
Purpose: To detect RNA-seq of NKp44- ILC3s and  NKp44+ ILC3s in lung cancer and find the differences between these tow group.
Results:Compared with those of NKp44+ILC3s, NKp44-ILC3s had 12,965 DEGs, with 6161 up-regulated genes and 6804 down-regulated genes,most DEGs related to the functions of cellular process, biological regulation, cell component, and molecular binding.

overall_design: Mononuclear cells were isolated from lung cancer tissue. NKp44- ILC3s and  NKp44+ ILC3s were sorted by cytometry. mRNA profiles of NKp44- ILC3s and  NKp44+ ILC3s were detected by RNA seq technigue

first: Jingtao

last: Chen


title: Mesenchymal Stem Cell Transplantation Attenuates Venous Stenosis of Hemodialysis Vascular Access Arteriovenous Fistula.

summary: Arteriovenous fistula (AVF) is the preferred vascular access for patients undergoing hemodialysis and the majority of AVFs fail because of venous intimal hyperplasia (VNH). Results from our lab have shown that adipose tissue-derived mesenchymal stem cell (MSC) transplantation to the adventitia of the outflow vein of AVF attenuates VNH in an immunodeficient mice. In the present study efficacy of Human AMSCs transplantation in treating AVF failure was tested in FoxN1 Nude mice with surgically created AVF. To explore the molecular mechanisms involved in MSCs transplantation improving AVF durability, we performed RNA-seq transcriptome analysis of the outflow veins of AVFs excised from mice 3 days after adventitial transplantation of MSCs.

overall_design: An AVF created in 9 week old mice and immidietly after AVF creation 250000 human adipose-derived stem cells in 10 ul of serum-free media were planted to the outer surface of the outflow vein (MSC) or untreated. AVF outflow veins were harvested 3 days after AVF creation for RNA seq.


title: The effect of antibiotic induced imbalance of gut microbiota on the expression profile of miRNA in circulating extracellular vesicles

first: Tong

type: Non-coding RNA profiling by high throughput sequencing

summary: By measuring the miRNA expression profile in the blood circulating extracellular vesicles of mice with antibiotic induced intestinal microbiota imbalance through miRNA seq, it was determined that intestinal microbiota imbalance leads to significant changes in the miRNA expression profile in the blood circulating extracellular vesicles

overall_design: Mice were given a mixture of antibiotics (Vancomycin 0.5 mg/ml, Neomycin 1 mg/ml, Ampicillin 1 mg/ml, Metronidazole 1 mg/ml; Shanghai yuanye Bio-Technology Co., Ltd) in drinking water for four weeks according to established protocols，isolate the serum exosomes by differential centrifugation.

first: Chunjin

last: Li

first: Xu

last: Zhou


title: Regional differences in neonatal enterocytes

status: Public on Jul 06 2025

first: Staci

last: Bilbo

address: 207 Research Dr, GSRB2

institute: Duke University

summary: We report bulk scRNAseq data obtained from 2 P6 mice. Input was isolated epithelium cells of the small intestine in a 2cm segment of  the jejunum and 2 cm segment in the ileum of the same mouse, 1 male and 1 female were included in the analysis.

overall_design: A 2 cm segment of jejunum and ileum was isolated from the same mouse. The segments were incubated in EDTA to separate intestinal epthelial cells from the intestinal wall and then incubated in dispase to generate a single cell suspension. Cells were barcoded using PIP-Seq technology.

first: Carina

last: Block

first: Michel

last: Bagnat

first: Cagla

last: Eroglu

first: Kristina

last: Sakers


title: Epigenomic profiling of circulating chromatin to detect and monitor squamous transformation in prostate cancer

city: Boston

first: Karl

last: Semaan

state: MA

address: Brookline Ave 450

institute: Dana-Farber Cancer Institute

summary: Transformation to squamous cell carcinoma is a rare resistance mechanism in patients with advanced prostate cancer that impacts both prognosis and treatment. Herein, we profile circulating chromatin in serial plasma samples collected from a patient with metastatic prostate cancer that experienced squamous transformation. We detect dynamic changes in gene regulation from circulating chromatin reflecting the emergence of squamous differentiation, enabling non-invasive diagnosis and monitoring of this resistance phenotype.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K27ac and H3K4me3, and low pass whole genome sequencing on cell-free DNA.

first: John

last: Cannifff

first: Hunter

last: Savignano

first: Sylvan

last: Baca

first: Jacob

last: Berchuck


title: Mesenchymal Stem Cell Transplantation Attenuates Venous Stenosis of Hemodialysis Vascular Access Arteriovenous Fistula

first: Sanjay

last: Misra

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

sample_organism:
Homo sapiens
Sus scrofa
Mus musculus

platform_organism:
Homo sapiens
Sus scrofa
Mus musculus

overall_design: Refer to individual Series


title: Phenotypic screen in vivo identifies sclerostin as a regulator for the development of nonalcoholic steatohepatitis in mice

city: Shanghai

first: Guangxing

last: Lu

address: 上海市淞沪路2005号

institute: Fudan University

summary: Employing the piggyBac (PB) transposon insertion as a tool, we established a collection of >5000 mouse strains for phenotypic screen in vivo. A pipeline was established in order to identify mutations which contribute to the development of lipid metabolism disorder and liver diseases with the serum level of triglyceride (TG) as readout. Among 9 mouse strains, one strain of mouse was selected with elevated TG, which contained with an insertion to the 3’ UTR of Sost gene (SostPB/- mice) and this insertion induced the overexpression of Sost mRNA and SOST protein in multiple tissues. When fed on a MCD diet, SostPB/- mice showed higher level of lipid content,  fibrosis and inflammationin the liver, which indicated that the WNT signaling inhibitor SOST aggravates the liver damages in the mice with NASH. To investigate the related mechanism, RNA-seq and targeted metabolomics were employed. SostPB/- mice showed upregulation of oxygen radical-related genes and decrease of vitamin C. Dietary supplement of vitamin C via drinking water normalized the changes of liver lipid content, fibrosis and inflammationin of SostPB/- mice.These results indicated the vitamin C is the key metabolite mediating the effects of SOST on the development of NASH.

overall_design: To investigate the effect of Sost overexpression in mice's NASH development, we extracted total RNA from livers of Sost-/- and SostPB/- mice fed on a MCD diet, and then performed RNA-seq.


title: Mesenchymal Stem Cell Transplantation Attenuates Venous Stenosis of Hemodialysis Vascular Access Arteriovenous Fistula [P33_MSC]

overall_design: RNA-seq of pig MSC

first: Sreenivasulu

last: Kilari

first: Edwin

last: Takahashi


title: Fibroblast-derived CSF1 is essential for intestinal macrophage maintenance

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

summary: Tissue-resident macrophages are considered to be maintained through the interaction with the local microenvironment. However, precise mechansims which regulate the gut macrophage population remains elusive. We performed single cell RNA sequencing (scRNA-seq) of gut fibroblasts to characterize the cells which may potentially contribute to the local maintenance of macrophages in the gut.

overall_design: PDPN-positive fibroblasts isolated from the small intestine of 4-week-old C57BL/6 mice (n=2) or from the colon of 9-week-old C57BL/6 mice (n=3) were subjected to scRNA-seq analysis, respectively.

first: Daichi

last: Nonaka

first: Soichiro

last: Yoshida

first: Miyuki

last: Watanabe

first: Eriko

last: Sumiya


title: Splicing transcriptome analysis reveals retained introns in retinal genes of the 5xFAD mouse, suggesting early diagnosis of Alzheimer’s disease through vision impairment

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

institute: Chung-Ang University

summary: Alzheimer’s disease (AD) is an age-related neurodegenerative disorder in which neuronal and synaptic loss of the brain leads to cognitive impairment and dementia. Therefore, the early diagnosis of AD with various biomarkers is important for the prevention and treatment. Although retina pathology is emerging biomarker that associated with AD, detailed molecular mechanisms of retinal impairments remain unclear. Here, we identify the genome-wide dysfunction of alternative splicing in the early stage of 5xFAD transgenic mouse retina by the RNA-seq analysis. Especially, retained intron (RI) highly enriched in phototransduction and retinal genes of 1.5-month-old 5xFAD mouse retina that significantly associated with retinal physiological impairment of rod photoreceptors by electroretinogram (ERG) analysis. These results indicate that the abnormal scotopic ERG associated with global splicing impairment may be useful early detection biomarker for AD.

overall_design: We compared transcript and retained intron expression profiles between mouse retina of wild type and 5xFAD. RNA-seq for 1-month and 6-month were performed in mouse retina between wild type and 5xFAD.


title: Identification of fibroblast-derived sFRP2 as a new therapeutic target and engineering of siRNA therapies for uterine scarring

city: Chongqing

first: Siqi

last: Zhang

address: No. 1, Youyi Road

department: Department of Pharmaceutics

institute: Third Military Medical University

summary: Uterine scarring (US) is a common complication following uterine injury, characterized by abnormal wound healing in the endometrial or myometrial tissue. However, the underlying mechanisms contributing to scar formation remain unclear, impeding the development of effective drugs for US. Here, we identified that secreted frizzled-related protein 2 (sFRP2) is highly expressed in human and mouse uterine tissues with US, particularly in uterine fibroblasts (UFIBs). Using mouse models, we demonstrated that sFRP2 overexpression in the healthy uterus induced US features and exacerbated surgery-induced scarring, while sFRP2 knockout inhibited US development and scarring-transformation in UFIBs, highlighting the critical role of sFRP2 in mediating US. Mechanistically, sFRP2 promotes uterine scar formation by activating the non-canonical Wnt signaling pathway and calcium influx in UFIBs. Additionally, therapeutic potential of targeting sFRP2 was demonstrated by developing siRNA against sFRP2 and engineering delivery systems of lipid nanoparticles and injectable hydrogel. These siRNA therapies effectively inhibited sFRP2 expression, alleviated uterine scar formation, and improved pregnancy outcomes in mice, underscoring the great potential of sFRP2 as a promising therapeutic target for US.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA seq of  Human uterine myometrial tissue and Mouse uterine tissue in control and Scar uterus disease group


title: The kinase PLK1 promote melanoma progression in the BRAFV600E/PTEN-deficient mouse

city: Lexington

first: Xiaoqi

last: Liu

state: KY

address: 760 Press Avenue, Research Building 2, Room 330

institute: University of Kentucky

summary: To investigate the role of PLK1 in melanoma progression, we introduced the overexpression of PLK1 to the BRAFV600E/PTEN-deficeint melanoma mouse model. After tumor induction, we harvested the tumors and performed the RNA-seq to analyze the expression profile of tumors from either cohort respectively.

overall_design: RNA-seq profilling of tumors from BrafCA/+ / Ptenloxp/loxp and BrafCA/+ / Ptenloxp/loxp / Plk1  mouse

first: Mao

last: Fengyi

first: Liu

last: Xiaoqi


title: Chemoproteomic profiling by a bioorthogonal probe reveals cell growth inhibition by histone H4 dopaminylation

first: Yang

last: Yaqi

address: No.1678 Dongfang Road, Pudong, Shanghai, China

institute: Shanghai Children Medical Centre

summary: Dopaminylation, the covalent attachment of dopamine to the side chain of glutamine (Gln, Q) in proteins, has been identified as a class of posttranslational modification. Due to the limited number of substrates, the functions and underlying molecular mechanisms of dopaminylation are not fully characterized. Utilizing an alkyne-functionalized dopamine probe, we have developed a method to selectively enrich dopaminylated proteins in the whole-cell context. We identified 4133 proteins potentially modified with dopamine and validated the modification of histone H4 glutamine 27 by dopamine (H4Q27dop). H4Q27dop can inhibit cell proliferation through downregulating cyclin D1 gene CCND1 transcription, a classical well-known proliferation promoter. Our study provides a valuable resource of putative substrate proteins modified with dopamine and reveals a novel mechanism of dopamine regulating cell growth in a neuroblastoma cancer model.

overall_design: to investigate the role of dopamine in regulating SK-N-SH cell proliferation, we treated SH-SY5Y cells with dopamine.

first: Yinfeng

first: Yaqi

last: Yang

first: Wenyan

last: Wu

first: Wenting

last: Song


title: Mesenchymal Stem Cell Transplantation Attenuates Venous Stenosis of Hemodialysis Vascular Access Arteriovenous Fistula [P33 GV RAW]

first: Sanjay

last: Misra

overall_design: RNA-seq

first: Sreenivasulu


title: Loss of NR2F6 reduces tissue-resident macrophages and protects from Salmonella typhimurium infection

city: Innsbruck

first: Johannes

last: Woelk

address: Peter-Mayr-Str. 1a

department: Cell Genetics

institute: Medical University of Innsbruck

summary: Nuclear receptors regulate key functions of mononuclear phagocytes and are critical components of the innate immune system, acting as regulators of organ health and disease. In healthy mice, NR2F6 deficiency alters tissue-resident macrophage populations in the liver, lung, and spleen. In response to Salmonella Typhimurium infection, mice deficient in the nuclear receptor NR2F6 exhibit improved clinical outcomes, characterized by reduced weight loss, bacterial loads in the spleen and liver, and decreased plasma pro-inflammatory cytokines. Despite unchanged basal iron metabolism in the spleen and liver, iron regulatory proteins and the IL-6-hepcidin axis are altered in Nr2f6-deficient mice during Salmonella infection, reducing hypoferremia. Transcriptomic analysis of splenic red pulp macrophages reveals significant alterations of phagocytosis-related genes, including upregulation of Sirpa. In vitro, phagocytosis of red blood cells, regulated by the inhibitory CD47-Sirp axis, and Salmonella Typhimurium phagocytosis is significantly impaired in Nr2f6-deficient splenic macrophages. Blocking Sirp in vitro restores the phagocytic activity of Nr2f6-deficient macrophages to wild-type levels. In vivo, Salmonella Typhimurium loads are partially increased post-infection in anti-Sirp treated Nr2f6-deficient mice. These findings uncover a previously unrecognized role of NR2F6 in host-pathogen interactions, positioning it as a potential therapeutic target for infectious diseases.

overall_design: RPMs were sorted from the spleen of wild-type C57BL/6 mice or Nr2f6-deficient mice. RPM were identified as live/CD45+/Lin-CD11bmid/F4/80+/CD64-/CD169-/CD106+ on a FACS Aria III. We sequenced RNA from RPM lysates of 3 wild-type and 2 Nr2f6-deficient mice.

first: Woelk

last: Johannes

first: Pfeifhofer-Obermair

last: Christa

first: Benz

last: Julia

first: Brigo

last: Natascha

first: Bamberger

last: Milena

first: Kleiter

last: Alexeja

first: Hermann

last: Martin

first: Weiss

last: Günther

first: Hermann-Kleiter


title: Transcriptional differences in jejunum and ileum of a conditional knockout of Dab2 in the intestine

status: Public on Jul 05 2025

first: Staci

last: Bilbo

department: Psychology and Neuroscience

summary: We report bulk RNAseq data obtained from P6 mice. Input was isolated epithelium cells of the small intestine in a 2cm segment of  the jejunum and 2 cm segment in the ileum of P6 Dab2 cWT and Dab2 cKO mice. Conditional deletion of Dab2 wa

overall_design: A 2 cm segment of jejunum and ileum was isolated from the same mouse. The segments were incubated in EDTA to separate intestinal epthelial cells from the intestinal wall. 4 mice age were utlized including both male and female mice.

first: Block

last: Carina L

first: Bagnat

last: Michel

first: Eroglu

last: Cagla

first: Sakers

last: Kristina


title: Reactivation of mammalian regeneration by turning on an evolutionarily disabled genetic switch [scRNA-seq]

first: Weifeng

last: Lin

state: Beijing

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences

summary: Mammals display prominent diversity in the ability to regenerate damaged ear pinna, but the genetic changes underlying the failure of regeneration remain elusive. We performed comparative single-cell and spatial transcriptomic analyses of rabbits and mice recovering from pinna damage. Insufficient retinoic acid (RA) production, caused by the deficiency of rate-limiting enzyme Aldh1a2 and boosted RA degradation, was responsible for the failure of mouse pinna regeneration. Switching on Aldh1a2 or RA supplementation reactivated regeneration. Evolutionary inactivation of multiple Aldh1a2-linked regulatory elements accounted for the deficient Aldh1a2 expression upon injury in mice and rats. Furthermore, the activation of Aldh1a2 by a single rabbit enhancer was sufficient to improve ear pinna regeneration in transgenic mice. Our study identified a genetic switch involved in the evolution of regeneration.

sample_organism:
Oryctolagus cuniculus
Mus musculus

platform_organism:
Oryctolagus cuniculus
Mus musculus

overall_design: Mice and rabbits injuried ear-pinna tissues were collected for scRNA-seq with 10X platform

first: Xiaohui

last: Jia

first: Wei

last: Wang


title: Multimodal antigenic escape to GPRC5D-targeted T-cell engagers in multiple myeloma [scATAC-seq]

city: Calgary

first: nizar jacques

last: Bahlis

state: AB

address: 3330 Hospital Dr NW HMRB328

department: Medicine

institute: University of Calgary

summary: Tumor intrinsic adaptations with emerging resistant clones following T cell targeted immunotherapies pose a major barrier to durable remissions in multiple myeloma (MM). Through integrated genomic, transcriptomic, and epigenomic interrogation of clonal plasma cells, we observed antigenic drift in 68.4% of relapsed cases following anti-GPRC5D T cell engager (TCE) therapy. These escape events were driven by three distinct mutational mechanisms involving i) focal to large biallelic deletions at the GPRC5D gene locus, ii) monoallelic deletion coupled with GPRC5D single nucleotide variants (SNVs) or insertions/deletions (indels) on the remaining allele, as well as iii) epigenetic GPRC5D promoter/enhancer silencing. Beyond biallelic deletions resulting in complete antigenic loss, we demonstrate that GPRC5D SNVs and indels mutate anti-GPRC5D TCE binding epitopes or more commonly affect G-protein couple receptor family conserved motifs critical for protein membrane trafficking resulting in endoplasmic reticulum (ER) GPRC5D trapping. Multiple subclones bearing distinct genomic alterations at GPRC5D locus co-emerged within individual cases, depicting their convergent evolutionary trajectories. Importantly, anti-GPRC5D TCEs with varying epitope specificity, affinity, and valency differentially targeted mutant subclones, underscoring their non-redundant functional roles in overcoming resistance

overall_design: Experiments were conducted on primary patient bone marrow samples, after informed consent, in accordance with the Declaration of Helsinki and following the approval by the Medical Center Institutional Review Board. Sorted CD138+ cells were collected from patients’ bone marrow aspirates pre-and post-treatment with anti-GPRC5D T cell engagers, counted and viably frozen. Frozen cells were then thawed at 37°C, resuspended in RPMI 1640 medium (Gibco) and washed twice by centrifugation at 2000 rpm for 5 min. The desired number of nuclei [2000-8000] was targeted and processed according to the Nuclei Isolation for Single Cell ATAC sequencing (CG000169, 10x Genomics, Pleasanton, CA, USA). Nuclei isolation was performed as indicated in the nuclei isolation protocol for Single Cell ATAC Sequencing (10x Genomics). Based on the starting number of cells and desired final nuclei concentration, primary MM cells were lysed and resuspended in an appropriate volume of chilled Diluted Nuclei Buffer. The resulting nuclei were immediately used to generate scATAC-seq libraries using the Chromium Single Cell ATAC reagent kit (CG000168, 10x Genomics) according to the manufacturer’s protocol.

first: Holly

last: Lee

first: Noémie

last: Leblay

first: Sungwoo

last: Ahn

first: Sacha

last: Benaoudia

first: Elham

last: Hasheminasabgorji

first: Mansour

last: Poorebrahim

first: David

last: Jung

first: Paola

last: Neri

first: Nizar


title: Multimodal antigenic escape to GPRC5D-targeted T-cell engagers in multiple myeloma [scRNA-seq]

overall_design: Experiments were conducted on primary patient bone marrow samples, after informed consent, in accordance with the Declaration of Helsinki and following the approval by the Medical Center Institutional Review Board. Unbiased mRNA profiling were conducted by using scRNA-seq from the GemCode system (10x Genomics) accordingly to the manufacturer’s protocols. Single cell library preparation of CD138+  were carried out on the Chromium platform (10x Genomics) using the Single Cell 3ʹ reagent kits v3 according to the manufacturer’s protocol. Samples were processed with CellRanger suite v7.1.0 against the human reference genome GRCh38 with default parameters


title: Single-cell level gene expression profiles of adult Drosophila midguts with lineage tracing targeting enteroendocrine cells

city: Tsukuba

first: Ryusuke

last: Niwa

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

summary: Differentiated cells exhibit cellular plasticity,where they dedifferentiate into stem cells. We studied cellular plasticity of secretory enternendocrine cells (EEs) in the fruit fly Drosophila melanogaster. We used flies that had EEs lineage-traced and resolved single-cell transcriptomics of all cell types in their midguts. Our scRNA-seq data have characterized cell-type-gene expression profiles, with a specific focus on EE lineages.

overall_design: Flies had EEs lineage traced from adulthood to 7 days of age. Cells from their guts were collected and proceeded to 10X Genomics scRNA-seq.

first: Qingyin

last: Qian

first: Yuya

last: Sanaki


title: Serum microRNA Profiling at an Early and Late Stages of Rotenone-Induced Parkinson’s Disease in Rats

city: Hyderabad

first: Pankaj

middle: Singh

last: Dholaniya

state: Telangana

address: S46 School of Life Sciences

department: Biotechnology and Bioinformatics

institute: University of Hyderabad

summary: This study investigates alterations in serum microRNA (miRNA) expression during the early (10-day) and late (terminal) stages of Parkinson’s disease (PD) in a rotenone-induced rat model. Rotenone, a mitochondrial complex I inhibitor, was administered to induce PD-like pathology by impairing ATP production. Blood serum samples were collected from control, early-stage PD (EPD), and late-stage PD (LPD) groups following treatment. Serum was processed for small RNA extraction and subjected to high-throughput sequencing using the Illumina platform with a single-end read length of 50 bp. Differential miRNA expression across stages was profiled to identify potential circulating biomarkers and gain insight into disease progression.

overall_design: To investigate circulating miRNA expression changes during the progression of Parkinson’s disease, we utilised a rotenone-induced rat model representing early and late stages of the disease. Adult male rats were randomly assigned to three groups: Control, Early Parkinson’s Disease (EPD, 10 days of rotenone treatment), and Late Parkinson’s Disease (LPD, terminal stage more than 40 days of prolonged rotenone exposure). Rotenone (2.0 mg/kg/day) was administered daily via intraperitoneal injection in male Wistar rats to induce dopaminergic neurodegeneration. Following the completion of treatment and behavioural validation of the disease model, blood samples were collected from all animals at their designated endpoints. Blood was allowed to clot at room temperature and then centrifuged to isolate serum.  Serum samples from all groups were submitted to a commercial sequencing facility for small RNA sequencing. Library preparation was performed according to standard protocols for small RNA analysis. Sequencing was conducted using the Illumina platform, generating approximately 20 million raw reads per sample with a single-end read length of 50 base pairs.

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