title: The mechanism of  Sinomenine (SIN) ameliorates the metabolic-associated steatohepatitis (MASH)

city: changzhou

first: gang

last: zhou

address: gehu middle road No.68

department: nanjing medical university

institute: nanjing medical university

summary: The alkaloid, sinomenine (SIN),7,8-didehydro-4-hydroxy-3,7-dimethoxy-17-methylmorphinan-6-one (C19H23NO4), was extracted from the rhizome of the Chinese medicinal plant, Sinomenium acutum (Thunb.) Rehd. et Wils. andS. acutum (Thunb.) Rehd. et Wils. Var. cinereum Rehd. et Wils.SIN has antiinflammatory, analgesic,immunosuppressive,antihypertensive, and antiarrhythmic effects. It has been used totreat rheumatoid diseases in humans.Our laboratory  has shown that SIN can attenuate the inflammation in dextran sulfate-induced colitis, but it is unclear in metabolic-associated steatohepatitis (MASH).

overall_design: Once the AML12 cells reached confluency , they were stimulated with FFAs for 24h, and then stimulated with FFAs and 200μM sinomenine for 48h


title: CD38+CD93+ microglia and macrophages drive neuroinflammation through glycolysis-histone lactylation axis in multiple sclerosis model mice

status: Public on Jan 01 2026

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

country: China

institute: Beijing Institute of Radiation Medicine

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Neuroinflammation is a pathological hallmark of several chronic neurological diseases, including multiple sclerosis (MS), and this process is driven by the sustained activation of myeloid cells. However, the pathogenic myeloid cells subset(s) and their regulation in MS remain unclear. Here, we identify a multiple sclerosis-associated microglia and macrophage (MSMM) subset defined as CD38+CD93+ that drives MS pathogenesis.  MSMM exhibits pro-inflammatory and neurotoxic characteristics accompanied by aberrant activation of glycolysis. Mechanistically, we found that aberrant activation of glycolysis results in excessive lactate production and elevation of histone lactylation in MSMM. Histone lactylation (H3K18la and H4K12la) in turn activates the transcriptional modules of genes governing neuroinflammation and glycolysis, thereby promotes the formation of MSMM. Blockade of MSMM with anti-CD38 plus anti-CD93 neutralizing antibodies ameliorates neuroinflammation and MS-like pathologies in an experimental autoimmune encephalomyelitis (EAE) mouse model of MS. Inhibition of glycolysis through Ldha knock out or LDHA inhibitor decreases the number of MSMM and attenuates EAE severity. Together, these findings reveal a MS-associated pathogenic cell subset and provide potential therapeutic approaches for MS.

overall_design: using single-cell RNA sequencing, spatial transcriptomics, and CUT&Tag to identify the pathogenic cell subset(s) involved in multiple sclerosispathogenesis

first: Rui-Yuan

last: Pan

first: Yuxiang

last: Wang


title: Genomic profiling of active vitamin D colonic responses in African- and European-Americans identifies an ancestry-related regulatory variant of POLB

city: Chicago

first: Sonia

middle: S

last: Kupfer

state: IL

department: Human Genetics

country: USA

institute: University of Chicago

summary: We measured genomic responses to active vitamin D, 1α,25-dihydroxyvitamin D (1,25D), in colonic organoids from individuals of African and European ancestry. Given protective effects of 1,25D for gastrointestinal conditions such as colorectal cancer, organoid cultures enabled evaluation of condition-specific responses in relevant target tissue. We found significant alterations in transcriptional and chromatin accessibility responses to 1,25D treatment, including some with ancestry-associated differences, and also elucidated the role of cis-genetic variance on treatment responses. Integration of genomic profiling with genetic mapping found an indel that explains ancestry-associated differences in the regulation of POLB response to 1,25D which showed signals of positive natural selection.

overall_design: Human colonic organoids derived from indivdiuals of African ancestry (AA) and European ancestry (EA) were cultured, differentiated,  and treated with either 100nm/L 1α,25-dihydroxyvitamin D (1,25D) or vehicle control (0.1% ethanol). RNA and DNA was extracted for RNA-seq and ATAC-seq. Treatment time was  4 hours for ATAC-seq and 6 hours for RNA-seq. After applying QC filters, paired treatment and control samples were available for  53 individuals (26 AA/27 EA) for RNA-seq analysis and 25 individuals (10 AA/15 EA) for ATAC-seq analysis. Differentially responsive genes and differential chromatin accessibility were analyzed in the set of all samples as well as by population. eQTL and aQTL mapping was also performed to identify genetic variants associated with condition-specific responses and chromatin accessibility.

first: David

last: Witonsky

first: Bharathi

last: Laxman

first: Hina

last: Usman

first: Margaret

middle: C

last: Bielski

first: Kristi

middle: M

last: Lawrence


title: Enhanced activities of OCT4 and SOX2 facilitates epigenetic reprogramming by modulating cell cycle [OSK CCC/FN RNA-seq]

city: Guangzhou

first: Hui

last: Zheng

state: Guangdong

address: No.190 Kaiyuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Fusing VP16  transcription activation domain with OCT4 and SOX2 (OvSvK) promoted the generation of induced pluripotency stem cells (iPSCs) by remodeling cell cycle and epigenetic modification. Multiomic analyses revealed that the other 80% upregulated genes experienced increase in H3K4me3 and decrease in H3K27me3 and were enriched with genes which undergo more intensive DNA demethylation during cell proliferation. Consistent results were obtained when siCcnd1, siCdkn2a and Ccne1 were screened out and used to mimic the cell cycle remodeling. In summary, these studies set up a correlation between epigenetic modification during cell cycle remodeling and cell fate conversion.

overall_design: For bulk RNA-seq, cells were infected with O, S, K, OS, OK and SK respectively and collected at  post-infected Day0. For single-cell RNA-Seq, reprogramming cells were collected at post-infected Day0, Day1, Day2, Day3 and Day4 using Fluidigm C1. For ATAC-seq, cells were infected with hCdt1 and hGeminin and also OSK or OvSvK. Cells at different cell cycle stage were isolated by fluorescence-activated cell sorting (FACS). For CUT&Tag, cells infected with OSK or OvSvK and collected at post-infected Day3 and Day2 respectively.

first: Lin

last: Guo


title: Per2 mediates neuroinflammation-driven depression after spinal cord injury and serves as a biomarker-target

city: Yinchuan City

first: guoyuan

last: he

address: 1160 Shengli Street, Xingqing District, Yinchuan City, Ningxia Autonomous Region

institute: Ningxia Medical University

summary: To identify differentially expressed genes in the hippocampal tissue associated with depressive-like behavior following spinal cord injury in mice, we conducted this sequencing analysis.

overall_design: comparative gene expression profilling analysis of RNA-seq data for hippocampus post-SCI and health control

first: Guo-yuan

last: He


title: Piezo1 dictates K⁺ homeostasis through coordinated regulation of the ubiquitin ligase Kelch-like 3 in RBCs and the kidney

city: Itabashi

first: Shigeru

last: Shibata

country: Japan

institute: Teikyo University

summary: The maintenance of potassium (K+) balance is a fundamental biological process involving multiple organs. However, mechanisms by which inter-organ communication regulates K+ homeostasis remain largely unexplored. By combining human genetics and mouse model generation using CRIPSR/Cas9, we demonstrate that the ubiquitin ligase Kelch-like 3 (KLHL3) orchestrates K⁺ transport across K⁺-storing erythrocytes and K⁺-excreting kidneys by interacting with the mechanosensitive Ca2+ channel Piezo1.

overall_design: We compared RNA profiles obtained from the spleen between wild-type and KLHL3 knock-in mice.

first: Kenichi

last: Ishizawa


title: Enhanced activities of OCT4 and SOX2 facilitates epigenetic reprogramming by modulating cell cycle [OSK/OvSvK CUT&TAG]


title: Transcriptome analysis of PDAC cells induced primary cilia and control

city: 上海

first: Xiaona

last: Zhang

address: No.197 Ruijin Er Road, Huangpu District, Shanghai 200025, China

institute: 上海交通大学医学院附属瑞金医院

summary: Primary cilia (PC) are non-motile cellular structure extending from the apical membrane of epithelial cells. They are central hubs for numerous signalling pathways implicated in various biological processes and are significantly decreased in various tumors, including pancreatic ductal adenocarcinoma. However, research on PC in oncology is limited, and the roles of their absence and presence in cancer cells are poorly understood. We analysed the effect of the induction of primary cilia in pancreatic ductal adenocarcinoma (PDAC) cells by RNA sequencing.Total RNA was extracted from control (n=6) and primary cilia induced (n=6) PDAC cells.A mechanistic study indicated that inversin, a protein located in PC, increased the expression and secretion of IL-1α by regulating the noncanonical Wnt/planar cell polarity pathway (Wnt/PCP). In conclusion, our study revealed the specific mechanism by which PC promote cell metastasis of tumor through IL-1α, highlighting the need for further investigation of PC as a potential therapeutic target for pancreatic ductal adenocarcinoma.

overall_design: We selected four PDAC cell lines derived from human pancreatic duct cells and induced them to grow primary cilia (PC) through serum starvation. These cilia were labeled red rods using acetylated α-tubulin antibody. Statistically, different cells were found to have varying degrees of PC increase after induction (48 h serum starvation). Under normal culture conditions, PC was present in 7%, 6.5%, 5%, and 11% of the CFPAC-1, CAPAN-1, BxPC-3, and PANC-1 cell lines, respectively. The frequency increased to 39%, 18%, 78%, and 64% after cilia induction. To explore the function of PC during tumorigenesis and development, we performed RNA-seq on CFPAC-1 and BxPC-3 cells induced PC.

first: Yang

last: Ma

first: Jia

last: Liu

first: Minmin

last: Shi

first: Baiyong

last: Shen


title: Potential Targets of Cholesterol Crystal Embolism

city: nantong

first: Zhaozhi

last: Wen

state: jiangsu

address: Seyuan Road 9

institute: Nantong University

summary: Cholesterol crystal (CC) embolism is a severe complication of atherosclerosis, associated with high morbidity and mortality due to its ability to cause acute kidney injury (AKI) and ischemic cortical necrosis. We have established a CC embolism mouse model induced by CC injection. Using this model, we observed significant transcriptomic changes across 17 cell types in the kidneys, with specific upregulation of genes like Cda in the proximal tubular cells, suggesting its potential as an AKI biomarker. Single-cell sequencing revealed the central role of CCL and MIF pathways in CC embolism and identified CCR5 and CD74 as potential therapeutic targets.

overall_design: Firstly, we established a cholesterol crystal embolism (CCE) mouse model induced by cholesterol crystal injection. Following the induction, kidneys from control and CCE mice were collected. Single-cell suspensions were prepared from the kidney tissues, and single-cell RNA sequencing (scRNA-seq) was performed using a large-scale platform (e.g., 10X Genomics) to analyze the transcriptomic changes across various cell types.

first: Chongxu

first: Bowen

last: Li

first: Huiping

last: Miao

first: Barbara

last: Klinkhammer

first: Peter

last: Boor

first: Hans

middle: J

last: Anders

first: Dong


title: Transcriptomic changes in Tatton-Brown-Rahman Syndrome models of neuronal development

city: Saint Louis

first: Kristen

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

summary: Human pluripotent stem cell (hPSC) models of Tatton-Brown-Rahman Syndrome (TBRS) were generated (R882H and P904L) and compared to isogenically paired controls (C-WT and WT, respectively). These models were used to specify cells as MGE-like ventral telencephalic neuronal progenitors (V-NPCs) and subsequently differentiate these into cortical GABAergic-like interneurons (V-INs) or to specify cells as dorsally patterned neuronal progenitors modelling the cortical ventricular zone (D-NPCs) and to subsequently differentiate these cells into cortical glutamatergic-like pyramidal neurons (D-INs). Finally, cells were directly reprogrammed from hPSCs to glutamatergic-like pyramidal neurons (iGluts) through overexpression of Neurogenin2.

overall_design: For each cell type and cell line, 3-4 biological replicates were generated from independent differentiations of hPSCs and used to compare differences between each TBRS model and the paired isogenic control (R882H vs C-WT and P904L vs WT).

first: Chapman

last: Gareth

first: Determan

last: Julianna

first: Kroll

last: Kristen


title: Ultra-processed foods sourced 7-ketositosterol aggravates colitis through gut dysbiosis induced-PDLIM3 activation

city: Tianjin

first: Jing

last: Yan

address: 154 Anshan Road in Heping District

institute: Tianjin Medical University General Hospital

summary: Excessive ultra-processed foods (UPFs) consumption has been reported to increase the risk of inflammatory bowel disease (IBD). However, the specific mechanisms remain unclarified. As an important ingredient of UPFs, 7-ketositosterol (KS) is mainly synthesized from high-temperature heating oils. We find that KS intake is higher in IBD patients and related to disease activity. KS exacerbats colitis in a gut microbiota-dependent manner in mice, altering the gut microbiota composition, increasing the abundance of potential pathogenic bacteria, especially Staphylococcus_lentus (SL). Morevoer, SL aggravates DSS-induced colitis. Mechanically, KS up-regulates the expression of PDZ and LIM Domain 3 (PDLIM3). SL-derived lysin motif peptidoglycan-binding domain-containing protein (LPDP) interacts with PDLIM3, and activates p38MAPK/NF-κB signaling pathway. Furthermore, tubuloside B, selected by high-throughput screening, blocks the interaction of PDLIM3 and LPDP, and ameliorates SL-aggravated colitis. Our study reveals that KS exposure promotes colitis via gut microbiota and PDLIM3 interaction, providing evidence of IBD pathogenesis and potential therapeutic strategy for IBD treatment.

overall_design: In KS aggravated DSS-induced colitis model, colonic tissue from mice in DSS group and DSS+KS group was collected, extracted and purified for RNA sequencing, and feces from mice in control group, KS group, DSS group and DSS+KS group was collected for 16s rRNA sequencing.

first: Xiaoqi

last: Pang

first: Qi

last: Chen

first: Jingjing

last: Wang

first: Zimin

first: Ge

last: Jin

first: Hailong

last: Cao


title: DNA methylation changes in Tatton-Brown-Rahman Syndrome models of neuronal development

type: Methylation profiling by high throughput sequencing

summary: Human pluripotent stem cell (hPSC) models of Tatton-Brown-Rahman Syndrome (TBRS) were generated (R882H and P904L) and compared to isogenically paired controls (C-WT and WT, respectively). These models were used to specify cells to MGE-like ventral telencephalic neuronal progenitors (V-NPCs) and subsequently differentiate into cortical GABAergic-like interneurons (V-INs) or to differentiate cells into cortical glutamatergic-like pyramidal neurons (D-INs). Finally, cells were directly reprogrammed from hPSCs to glutamatergic-like pyramidal neurons (iGluts) through overexpression of Neurogenin2.


title: Enhanced activities of OCT4 and SOX2 facilitates epigenetic reprogramming by modulating cell cycle [CCB/FNB ATAC-seq]

first: Hui

last: Zheng

first: Lin

last: Guo


title: The possible mechanism of boronized Ti6Al4V/HA promoting osteogenic differentiation of osteoblasts

city: changsha

first: hong

middle: yi

last: chen

state: HuNan provience

address: 72 Xiangya Road

institute: Xiangya Stomatological HospitalCentral South University

summary: In our previous work, we successfully fabricated a boronized Ti6Al4V/HA composite implant by mixing Ti6Al4V, nano-HA, and TiB₂ powders followed by microwave sintering. Both in vitro cellular assays and in vivo animal experiments confirmed the material’s excellent bioactivity and osseointegration potential, demonstrating its promise for clinical applications (5,6). However, the detailed mechanisms by which the material’s physical structures (e.g., increased surface roughness and micro/nanostructured topography) and chemical components (bioactive boron and HA) promote osteogenic differentiation and enhance osseointegration remain unclear and warrant further investigation.To address this limitation, we employed RNA sequencing (RNA-seq) to perform genome-wide transcriptomic profiling of osteoblasts cultured on boronized Ti6Al4V/HA composite surfaces, with the aim of identifying key osteogenesis-related genes and elucidating the mechanisms by which this composite material promotes osteogenic differentiation. This study provides a theoretical basis for the rational design of boronized titanium-based composite implants by adjusting particle size or the relative content of boron and HA, and contributes to a deeper understanding of how material properties regulate osteogenic responses and improve osseointegration.

overall_design: Genes related to osteogenic differentiation were screened out through RNA-seq and analysis, and verification and functional experiments were carried out.

first: Yihong

first: Xiaojie

first: Lei

last: Li


title: Changes in H3K27me3 in Tatton-Brown-Rahman Syndrome Neuronal Progenitor Cells

first: Kristen

summary: Human pluripotent stem cell (hPSC) models of Tatton-Brown-Rahman Syndrome (TBRS) were generated (R882H and P904L), and compared to isogenically paired controls (C-WT and WT, respectively). These models were used to generate MGE-like ventral telencephalic neuronal progenitors (V-NPCs) and dorsally patterned neuronal progenitors modelling the cortical ventricular zone (D-NPCs). Cut and Tag for the tri-methylation of histone H3 at the lysine 27 residue (H3K27me3) was performed, to assess how loss of DNMT3A function due to TBRS-associated mutations affects deposition of H3K27me3

overall_design: For each cell type and cell line, 4 biological replicates were generated from independent differentiations of hPSCs and used to compare differences between each TBRS model and the paired isogenic control (R882H vs C-WT and P904L vs WT).

first: Gareth

last: Chapman

first: Julianna

last: Determan


title: PT109B Rapidly Converts Astrocytes to Dopaminergic Neurons and Alleviates Parkinson's Disease in Mice.

city: Guangdong

first: Shisong

state: Shenzhen

address: No. 66, Gongchang Road, Guangming District

department: School of Medicine

institute: Sun Yat-Sen university

summary: Reprogramming astrocytes into neurons using chemical small molecules has emerged as a promising therapeutic strategy for Parkinson's disease (PD). Here, we have identified PT109B, a novel multi-kinase inhibitor, as a potent agent that induces the direct reprogramming of astrocytes into functional induced dopaminergic neurons (iDANs) beginning with a remarkably short 6-hour window. Within just half a month, PT109B facilitated the maturation of iDANs, characterized by synaptic structures, electrophysiological properties, sustained dopamine release, and long-term viability (for over 3 months). Mechanistically, PT109B drove this conversion through cell cycle arrest, astrocytic activation, and upregulation of key basic Helix-Loop-Helix (b-HLH) transcription factors, including NeuroD1, Nurr1, Ngn2, and Ascl1. Importantly, oral administration of PT109B in a 6-OHDA-induced PD mouse model exhibited significant therapeutic efficacy by reprogramming astrocytes to functional neurons in the striatum, leading to improved motor functions. These findings suggest PT109B as a promising therapeutic candidate for PD.

overall_design: RNA-seq of primary rat midbrain astrocytes at 1.5, 3, and 6 hours post-PT109B treatment

first: Cailv

last: Wei

first: Yang

last: Yang

first: Tsz Hei

last: Fong

first: Yuan

last: Liu

first: Chao

last: Ding

first: Zeyu

last: Zhu

first: Jianwen

last: Zhou

first: Kang

last: Jia

first: Zhixian

last: Zhang

first: Qianhui

last: Shen

first: Yu

last: Ren

first: Zhi

last: Liang

first: Yanping

first: Yalin

last: Tu

first: Cheng

last: Long

first: Wenbin

last: Deng

first: Qiang

first: Karl Wah-Keung

last: Tsim

first: Rongbiao

last: Pi


title: Innate Lymphoid Cells Integrate Sensing and Plasticity to Control Fungal Infections [ILC Sequencing]

city: Vienna

first: Philipp

last: Penninger

address: Dr. Bohr-Gasse 9

country: Austria

institute: Medical University of Vienna

summary: Innate lymphoid cells (ILCs) are crucial regulators of tissue immunity, yet their role in antifungal defense remains incompletely understood. Through our findings, we demonstrate that pulmonary ILCs can sense fungal pathogens by recognizing fungal cell wall components via pattern recognition receptors, leading to the activation and type-1 polarization in vitro. Mechanistically, we identify Syk/Akt-dependent signaling as one of the key drivers of ILC activation upon fungal encounters. Aspergillus fumigatus infection reshapes this response in vivo, where elevated TGF-β and IL-1β levels facilitate a shift from type-1 ILC activity to IL-17A release. Ultimately, IL-17-producing ILCs are crucial in resolving the infection and restoring normal tissue homeostasis. Moreover, adoptive transfer models in lymphocyte-deficient Rag2-/-γc-/- mice reveal that ILCs restrain excessive inflammation while hindering fungal clearance, highlighting their dual role in regulating antifungal immunity. Remarkably, ILCs lacking the non-receptor tyrosine kinase Tec disrupts caspase-8 activation, leading to enhanced proliferation of type-1 ILCs. Consequently, improved fungal clearance enhances host survival by strengthening antifungal immunity. Our findings uncover hitherto unrecognized roles of ILCs as fungal sensors and early modulators of antifungal immunity. Therefore, targeting Tec kinase signaling in ILCs holds great promise as a therapeutic option to enhance antifungal immunity, especially in patients at risk for invasive A. fumigatus infections.

overall_design: Smart-Seq2 (bulk RNAseq) analysis of sorted CD90+lin- pulmonary ILC subsets derived from Aspergillus fumigatus (ATCC204305) infected mice (3*10^7 spores/mouse) or corresponding controls. ILCs of isolated mice were compared to control mice (mock infected, saline). Each sample corresponds to pooled biological replicates (n=3-4/sample); Cells were then stained for CD45 expression, lineage markers to exclude T cells, B cells, myeloid cells, erythroid cells and conventional NK cells (anti-CD49b [DX5], -CD5, -CD3ε, -TCRβ, -CD45R [B220], -CD19, -CD11b, -CD11c, -Gr-1 [Ly-6G/C], -7-4, -Ter-119; all from Miltenyi Biotech), CD90/Thy1 (anti-CD90) and viability (Zombie Dye Violet, Biolegend)

first: Irina

last: Tsymala

first: Karl

last: Kuchler


title: Innate Lymphoid Cells Integrate Sensing and Plasticity to Control Fungal Infections [whole lung tissue after ILC transfer_Afu infected]

overall_design: Bulk RNAseq of whole lung tissue samples from infected Rag2-/-Il2rg-/- mice to investigate the impact of transferred ILCs on Aspergillosis outcome. Outcome of Aspergillus infection was compared between wild type ILC-receiving mice (+wt ILCs), Tec-kinase deficient ILC receiving mice (+Tec-/- -ILCs) and mice not receiving transfer (no transfer controls). Pulmonary ILC subsets were MACS-enriched (lineage cell depletion) and expanded in vitro for 14 days. Mice received sorted pulmonary ILC subsets at 14 days and 3 days before infection. Mice were intranasally infected with 3*10^7 Aspergillus fumigatus spores (ATCC204305). Lung tissue samples were extracted after 17 hours and stored in RNA-later at -80°C. Each sample represents biological replicates


title: Targeting microglial PPARα ameliorates the outcome of ischaemic stroke by enhancing interaction with infiltrating peripheral monocytes/macrophages

city: Xiamen

first: Xilin

last: Jiang

address: No. 4221 Xiang'an South Road

institute: Xiamen University

summary: Microglial PPARα downregulation enhances inflammation and worsens ischemic brain injury by promoting Mo/MΦ infiltration, shifting them to a proinflammatory state, and disrupting the BBB. Restoring PPARα expression via AAV transfection reverses these effects, exerting neuroprotection by enhancing microglia–macrophage crosstalk through IL-4 signaling. Targeting microglial PPARα may offer a therapeutic strategy for mitigating acute ischemic stroke.

overall_design: Primary microglia were isolated from CD45.2 WT and KO mice and subjected to OGD followed by reoxygenation. During reoxygenation, peritoneal macrophages from CD45.1 mice were introduced for co-culture. After a defined period, CD45.1⁺ microglia were sorted and subjected to RNA-seq.


title: Profiling local translatomes and RNA binding proteins of somatosensory neurons reveals specializations of individual axons [RIP-seq]

city: Boston

first: Rosalind

middle: A

last: Segal

state: MA

address: 360 Longwood Ave, LC6301

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: Individual neurons have one or more axons that often extend long distances and traverse multiple microenvironments, yet it is not known how the composition of individual axons is established or locally modulated to enable neuronal plasticity. Here, we use spatial translatomics to identify local axonal translatomes in anatomically and functionally specialized neurons in the dorsal root ganglia (DRG). DRG neurons extend long central and peripheral axons in separate directions and through distinct microenvironments to enable somatosensation. Using Translating Ribosome Affinity Purification and RNA sequencing, we generated a comprehensive resource of mRNAs preferentially translated within each axon. Locally translated proteins include pain receptors, ion channels, and translational machinery, which establish distinct electrophysiologic properties and regenerative capacities for each axon. Furthermore, we identify RNA-binding proteins associated with sorting and transporting functionally related mRNAs. These findings provide resources for addressing how axonal translation shapes the spatial organization of neurons and enables subcellular neuroplasticity.

overall_design: RNA Immunoprecipitation (RIP) sequencing of mRNAs bound to SFPQ and SRSF10 proteins in primary rat dorsal root ganglia (DRG) neurons.

first: Elizabeth

last: Silagi

first: Ezechukwu

last: Nduka

first: Maria

middle: F

last: Pazyra-Murphy

first: Jesus

last: Zuniga Paiz


title: Targeting Notch Signaling to Restore Neural Development and Behavior in Autism

city: Isehara

first: Takatoshi

last: Iijima

state: Kanagawa

address: 143 Shimokasuya

institute: Tokai University

summary: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social deficits and repetitive behaviors, influenced by both genetic and environmental factors. However, the molecular mechanisms underlying this heterogeneity remain unclear. This study highlights dysregulation of the Notch signaling pathway as a shared molecular mechanism in inherited and non-hereditary ASD models in mice and humans. Aberrant HDAC3-mediated epigenetic activation of Notch signaling during embryonic forebrain development disrupts the specification of caudal ganglionic eminence (CGE) precursors into VIP+ GABAergic interneuron subtypes (VIP-INs). CGE-specific ablation of Notch1/2 genes in ASD models rescues the VIP-IN loss, E/I balance, and selectively improves social behaviors. Remarkably, a single antenatal dose of a γ-secretase inhibitor, previously used in the clinical trials for cancer treatment, effectively ameliorates multiple ASD-associated neuronal, behavioral, and transcriptomic levels in adult models. Thus, the study confers a critical convergence of ASD risk factors on Notch signaling dysregulation and establishes this pathway as a promising therapeutic target for developmental and behavioral deficits in ASD.

overall_design: Pregnant mice received intraperitoneal (i.p.) injections of VPA at E13, E15, or E18. To assess rescue effects, Ro4929097 was administered at E17. Offspring were analyzed at P2.

last: Iijima (corresponding)

first: Yoko

last: Hanno (first)(corresponding)

first: Hiroyuki

last: Hosokawa

first: Moe

last: Nakanishi

first: Akinori

last: Takase

first: Jun

last: Nomura

first: Masami

last: Tanaka

first: Masayuki

first: Masatoshi

last: Ito

first: Katsunaka

last: Mikami

first: Katsuto

last: Hozumi

first: Goichi

last: Miyoshi

first: Toru

last: Takumi


title: CLL stimulation with agonist mix that mimic the microenvironment

city: Avaino

first: Riccardo

last: Bomben

address: Via Franco Gallini 2

department: DRDAT

country: Italy

institute: Centro di Riferimento Oncologico Aviano IRCCS

summary: To identify miRNAs modulated by microenvironment stimulation in presence or absence of Ibrutinib

overall_design: The experimental conditions were assessed at 24 h. CLL cells were stimulated with agonist mix in presence of anti-IgM and Ibrutinib 1 uM (Condition D) or with DMSO and control beads (Condition C) vs CLL cells treated only with anti-IgM and Ibrutinib 1 uM (Condition B) or with DMSO and control beads (Condition A). Condition A: DMSO+control beads; Condition B: Anti-IgM beads+Ibrutinib 1uM; Condition C: DMSO+control beads+agonist mix (IL-10; CpG; CD40L); Condition D: Anti-IgM beads+Ibrutinib 1uM+agonist mix (IL-10; CpG; CD40L)

first: T

last: Bittolo

first: R

first: L

middle: I

last: Hernández


title: Profiling local translatomes and RNA binding proteins of somatosensory neurons reveals specializations of individual axons [TRAP-seq]

first: Rosalind

last: Segal

overall_design: Translating Ribosome Affinity Purification (TRAP) paired with RNA-seq profiling of central axons, peripheral axons, and cell somas of Nav1.8-positive dorsal root ganglia (DRG) sensory neurons. Central axons were collected from lumbar 1-6 dorsal roots and spinal cord, peripheral axons were collected from sciatic nerves, and cell somas were collected from lumbar 1-6 dorsal root ganglia.

first: Elizabeth

last: Silagi

first: Ezechukwu

last: Nduka

first: Maria

last: Pazyra-Murphy

first: Jesus

last: Zuniga Paiz


title: Targeting YAP-Hhip mediated osteogenesis in Gli1+ osteogenic progenitors suppresses aberrant subchondral bone remodeling in osteoarthritis

first: Yang

last: Xiao

address: 22  Zhongguancun South Avenue, Haidian District

institute: Peking University School and Hospital of Stomatology

summary: Our findings demonstrated that YAP plays a critical role in subchondral bone remodeling. Furthermore, targeting the YAP-Hhip axis through regulation of Hh-Gli1 signaling in Gli1+ osteogenic progenitors could inhibit OA progression. This may offer new therapeutic insights for treating OA.

overall_design: We generated Gli1-CreERT2;Yapfl/fl mice, in which deletion of Yap blocked the YAP signaling in the Gli1+ cell lineage. A mouse model with osteoarthritis-like changes in the temporomandibular joint (TMJ) was induced by partial discectomy (PD). Smoothened agonist administration was also used intraperitoneally after PD. Micro-CT, histological analysis, immunofluorescence staining, and RNA-seq were conducted for analyses.


title: Systematic characterization of LUHMES cell-based Parkinson’s disease models reveals potential novel  drug targets.

city: Gebze

first: Tunahan

last: Cakir

state: Kocaeli

address: Gebze, Kocaeli, Turkey

department: Department of Bioengineering

country: Turkey

institute: Gebze Technical University

summary: Parkinson's disease (PD) encompasses incurable and progressive loss of dopaminergic neurons in patients and the research for effective disease-modifying treatments are still ongoing.  In this study, using a systems biology-based approach we show that 6-OHDA treatment of alpha-synuclein-overexpressing LUHMES cells can be used as a physiologically relevant model of PD. RNAseq analysis in these LUHMES-based disease models validate genes including HMOX1 and IGF2R in common with previously identified PD genes. We further confirm that quercetin and rutin can partially alleviate cell death in this model and show that the expression of genes related to PD as well as those related to mitochondria and energy metabolism are back to basal levels in control cells upon quercetin or rutin pre-treatment.  When RNAseq analysis was performed on drug-pretreated LUHMES PD models, protein folding, misfolded protein binding and unfolded protein response pathways were found to be affected. We believe these findings offer new avenues of innovative therapeutic strategies for PD.

overall_design: Differentiated wildtype LUHMES cells or cells overexpressing alpha-synuclein were treated with 6-OHDA to generate the in vitro PD models.  RNA-seq analysis was performed for four samples in each group. Quercetin (CEBPB) or rutin (AKR13C) were applied to 6-OHDA treated alpha-synuclein overexpressing LUHMES cells to test their neuroprotective effect.

first: Esra

middle: N

last: Yigit

first: Ekin

last: Sonmez

first: Regan

last: Odongo

first: Ozgenur

last: Akdas

first: Seyma

last: Cimen

first: Gurkan

last: Ozturk

first: Isil

last: Aksan Kurnaz


title: Research on Peripheral Nerve Aging and Degeneration: Cellular Changes and Mechanism Exploration from the Perspective of Single-Cell Sequencing

city: XuZhou

first: Bin

last: Pan

state: JiangSu

address: 99 Huaihai West Road,Quanshan District

institute: The Affiliated Hospital of Xuzhou Medical University

summary: As age increases, there are structural and functional alterations in the Peripheral Nervous System (PNS),significantly affecting movement, sensation, and autonomic function. Understanding the characteristics and mechanisms of PNS aging is crucial for preventing and treating related diseases. This study employed single-cell sequencing technology to analyze the dorsal root ganglia (DRG) and sciatic nerve (SN) of aging rats, in comparison to adult rats. The research investigated the mechanisms underlying peripheral nervous system (PNS) aging and degeneration, revealing the transcriptional profiles of various cell types.Significant differences were observed in the proportion of Schwann cells between the DRG and SN of adult and aged rats. The Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Gene Set Enrichment Analysis (GSEA) revealed that pathways related to neurodegeneration were upregulated in Schwann cells. Additionally, lipid metabolism pathways were upregulated in the  SN of aged rats, suggesting that certain lipid signaling molecules may influence cell proliferation. Through further re-clustering of myelinating Schwann cells, six distinct subtypes were identified. The anti-aging protein protocadherin 9 (PCDH9) was preliminarily screened and found to be significantly downregulated with age. In vitro experiments confirmed that PCDH9 expression is associated with Schwann cell proliferation and differentiation. By using gene expression analysis and cell type across several age groups, this study offers important insights into the mechanisms of PNS aging and degeneration.

overall_design: Single-cell sequencing analysis of dorsal root ganglion samples and sciatic nerve samples in adult rats (3 months old) and elderly rats (20 months old)

first: Yuyang

last: Zhuo

first: Yingcai

last: Xu


title: Antigen specificity of clonally-enriched CD8+ T cells in multiple sclerosis

city: San Francisco

first: Joseph

last: Sabatino

state: CA

address: 1651 4th St, Room 421A

institute: UCSF

summary: CD8+ T cells are the dominant lymphocyte population in multiple sclerosis (MS) lesions where they are highly clonally expanded.  The clonal identity, function, and antigen specificity of CD8+ T cells in MS are not well understood.  Here we report a comprehensive single-cell RNA-seq and T cell receptor (TCR)-seq analysis of the cerebrospinal fluid (CSF) and blood from a cohort of treatment-naïve MS patients and control participants.  A small subset of highly expanded and activated CD8+ T cells were enriched in the CSF in MS that displayed high activation, cytotoxicity and tissue-homing transcriptional profiles.  Using a combination of unbiased and targeted antigen discovery approaches, MS-derived CD8+ T cell clonotypes recognizing Epstein-Barr virus (EBV) antigens and multiple novel mimotopes were identified.  No CD8+ T cell cross-reactivity was found between the EBV epitopes and self-antigens, but EBV DNA was detected in CSF, including in the same individuals with highly expanded CD8+ T cells.   These findings shed vital insight into the role of CD8+ T cells in MS and lend further support an important role of EBV in MS immunopathology.

overall_design: Cross-sectional single-cell sequencing analysis of blood and CSF from a cohort of MS patients and control subjects

first: Kristen

last: Mittl

first: Fumie

last: Hayashi

first: Ravi

last: Dandekar

first: Ryan

last: Schubert

first: Ebtesam

last: Hassan

first: Josiah

last: Gerdts

first: Lindsay

last: Oshiro

first: Rita

last: Loudermilk

first: Ariele

last: Greenfield

first: Danillo

last: Augusto

first: Akshaya

last: Ramesh

first: Edwina

last: Tran

first: Kanishka

last: Koshal

first: Kerry

last: Kizer

first: Joanna

last: Dreux

first: Alaina

last: Cagalingan

first: Florian

last: Schustek

first: Lena

last: Flood

first: Tamson

last: Moore

first: Lisa

last: Kirkemo

first: Tiffany

last: Cooper

first: Meagan

last: Harms

first: Refujia

last: Gomez

first: Leah

last: Sibener

first: Bruce

last: Cree

first: Stephen

last: Hauser

first: Jill

last: Hollenbach

first: Marvin

last: Gee

first: Michael

last: Wilson

first: Scott

last: Zamvil


title: Targeting Tumor-associated CCR2+ Macrophages with Proteolipid Nanovesicles to Inhibit Pancreatic Cancer Recurrence Following Irreversible Electroporation

city: Shanghai

first: Weichen

last: Xu

state: Shanghai

address: No. 301, Middle Yanchang Road, Shanghai, 200072

department: Medical ultrasound

institute: Shanghai Tenth People’s Hospital, School of Medicine, Tongji University

summary: Irreversible electroporation (IRE) has emerged as a promising radical ablative therapy for PDAC; however, its clinical efficacy is hindered by the high recurrence rate. Herein, using a preclinical orthotopic PDAC tumor model, we comprehensively characterized the tumor immune microenvironment following IRE treatment through scRNA-seq. Our findings provide direct evidence that IRE treatment induces a CCR2+ tumor-associated macrophages (CCR2+ TAMs)-mediated immunosuppressive microenvironment in the residual tumor, ultimately accelerating tumor recurrence. Targeting CCR2+ TAMs enhances antitumor immunity and improves the chemotherapeutic response in PDAC.

overall_design: Following the establishment of orthotopic pancreatic tumors in mice, tumors were treated with irreversible electroporation (IRE) or subjected to sham surgery once they reached a certain size. Three days post-treatment, tumor samples were collected and analyzed using 10x Genomics scRNA-seq analysis.

first: Liping

last: Sun


title: CRISPLD2 regulates adipocyte function

city: OKC

first: David

last: Sparling

state: OK

address: 1200 Children’s Avenue, Suite 4D

department: Section of Pediatric Diabetes and Endocrinology

institute: Oklahoma Children’s Hospital OU Health

summary: Obesity with accompanying adipose fibrosis is associated with worsening insulin resistance. Weight loss and adipose tissue turnover are conversly associated with improved insulin signaling and overall health. We previously found the secreted protein CRISPLD2 up-regulated in adipocytes during weight loss; CRISPLD has been suggested regulate inflammation and tissue turnover. As loss of CRISPLD2 is embryonic lethal, we developed mice with adipocyte-specific inducible CRISPLD2 overexpression to explore its function. Single-cell RNAseq analysis of the stromal vascular fraction (SVF) during long-term adipocyte CRISPLD2 overexpression demonstrated broad down-regulation of collagen transcription across multiple cell types; we found similar down-regulation of fibrosis via picosirius red staining of adipose tissue overexpressing CRISPLD2, along with a decrease in adipocyte cell size in chow-fed animals.

overall_design: scRNAseq of Mouse stromal vascular fraction from control and CRISPLD2 overexpression mice. This was performed on 2 males of each genotype, Tg and Double Tg. A double transgenic mouse was developed by crossing mice carrying a the inducible crispld2 plasmid with C57BL/6-Tg(Adipoq-rtTA)2Zvw/J mice from Jackson lab (RRID:IMSR_JAX:033448) (CLD2AD).  Single transgenic mice carrying only the TRE-mCLD2 served as the control group. These mice were fed Teklad Rodent Diet plus doxycycline to induce the crispld2 transgene. Single Cell experiment was done on the stromal vascular fraction of these mice following isolation. Cell ranger and Parktek Software was used to visualize the data,, quality control was performed then cell types were identified and additioanl analsis of gene expression in those populations was analyzed.

first: Beth A

last: Griesel

first: Kylie

last: Williams

first: Nagib

last: Ahsan

first: Philipp E

last: Scherer

first: Ann Louise

last: Olson

first: David P


title: Gastric Cancer AVIL overexpression and pharmacologic inhibition in GES1 and AGS cell lines.

city: Charlottesville

first: Robert

last: Cornelison

state: VA

address: 345 Crispell Drive Carter-Harrison Research Building MR6 B710 Carter-Harrison Research Building MR6 B710

department: pathology

institute: UVA School of Medicine

summary: AVIL is an oncogenic driver of gastric cancer.  To test the oncogenic ability of AVIL, we established stable AVIL overexpression in normal human gastric epithelial cell line GES1 and performed RNA-sequence. We also use AVIL inhibitor compound A to treat gastric cancer cell line AGS and do transcriptome analysis.

overall_design: control plasmid vs AVIL overexpression in GES1|small molecule inhibition of AVIL in gastric cancer AGS cell line DMSO vs CompoundA


title: Effect of aging on gene expression in the skeletal muscle

city: Saint louis

first: Kentaro

last: Mori

state: Missouri

address: 660 S. Euclid Avenue

summary: To identify the anti-aging myokine, we looked for genes whose expressions are lower in aged skeletal muscle compared with young skeletal muscle

overall_design: Comparative gene expression profiling analysis of RNA-seq data for skeletal muscle from young and aged mice

first: Shin-ichiro

last: Imai


title: Tryptophan-rich diet improves high-fat diet-induced cognitive dysfunction and blood-brain barrier disruption through FFAR3 activation

city: Nanjing

first: Xiaoliang

last: Wang

address: Department of Anesthesiology

institute: Nanjing First Hospital

summary: Increasing evidence indicates that high-fat diets (HFDs) are strongly associated with cognitive deficits. Tryptophan (Trp), an essential amino acid, has been implicated in regulating metabolic and neurological pathways, but its direct role in mitigating HFD-induced cognitive dysfunction has been insufficiently explored. We hypothesized that enhancing Trp availability could protect the brain from HFD-induced impairments by preserving blood-brain barrier (BBB) integrity and neuronal function. Mice fed HFD alone exhibited deficits in Morris Water Maze, Fear Conditioning, and Novel Object Recognition tests, accompanied by decreased expression of tight junction proteins claudin-1 and occludin. Trp supplementation restored these behavioral and molecular indices to levels comparable to the normal diet mice. Notably, we identified indole-3-propionic acid (IPA), a metabolite of Trp, as a key mediator underlying these protective effects. Administration of IPA replicated the cognitive improvements and BBB preservation seen with Trp supplementation. Transcriptomic analyses further revealed that both IPA and Trp supplementation converge on pathways regulating neuronal health and BBB function, including PPAR signaling, extracellular matrix organization, and adherens junction regulation. Mechanistically, IPA activates free fatty acid receptor 3 (FFAR3) in brain microvascular endothelial cells, thereby reducing paracellular permeability and restoring tight junction protein expression. Collectively, these results highlight the therapeutic promise of a Trp-rich diet in countering HFD-induced cognitive decline, with IPA-mediated FFAR3 activation as a pivotal mechanism underlying BBB preservation and neuronal protection. Our findings pave the way for novel, diet-based strategies to mitigate the growing burden of obesity-related neurocognitive disorders.

overall_design: Animals were fed their respective diets for 12 weeks, and body weight and food intake were measured weekly. All diets were obtained from Beijing HFK Bioscience Co., Ltd. (catalog number: H10045), with tryptophan supplemented at 0.5% by weight to the base H10045 formulation. Mice in the HFD + IPA group received daily oral gavage of IPA (100 mg/kg body weight) prepared in sterile saline. The intervention lasted for 12 weeks. 3 mice in each group.

first: Cailong

last: Pan


title: Tissue-specific long read RNA sequencing of Lumbricus rubellus.

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

country: United Kingdom

institute: King's College London

summary: Cwmystwyth is an abandoned lead mine site. The soil of this metalliferous mine site is inhabited by lead hyper-resistant Lumbricus rubellus earthworms. The nature of their resistance to heavy metal lead has not been elucidated in fine detail, especially within a tissue-specific context. Moreover, earthworms have yet to be studied using long read transcriptomic technologies. Hence, various tissues of a Cwmystwyth earthworm were dissected and long read RNA sequenced using the PacBio Sequel Ile system.

overall_design: Various tissues of a clade “B” Lumbricus rubellus earthworm were RNA extracted and long read RNA determined using PacBio HiFi sequencing.

first: Maxim

last: Karpov

last: Short

first: Peter

last: Kille

last: Spurgeon

middle: R


title: Discovery and characterization of zoonotic viruses with multi-species, multi-organ bat organoids (bulkRNA-seq)

city: Daejeon

first: Dongbin

last: Park

address: 55, Expo-ro

country: South Korea

institute: Institute for Basic Science

sample_organism:
Rhinolophus ferrumequinum
Cnephaeus serotinus

overall_design: To explore host-pathogen interactions and assess spillover risks, we developed a panel of bat organoid models including five species and four organ types. Based on these multi-species and multi organd bat organoids, species- and tissue-specific replication patterns of various zoonitic viruses were examined and novel bat-borne viruses were characterized.

first: Young Ki

last: Choi


title: Discovery and characterization of zoonotic viruses with multi-species, multi-organ bat organoids

summary: This longitudinal scRNA-seq analysis examines age-related differences, focusing particularly on the B cell response, between young-adult and aged ferrets during SFTSV infection.


title: Brown adipocyte-derived exosomes in type 2 diabetes mellitus impair endothelial function via elevated intracellular calcium load

city: Yinchuan

first: Xiaojie

last: Ruan

state: Ningxia

address: No.489, Helan West Street, Xixia District, Yinchuan City, Ningxia

institute: Ningxia University

summary: Atherosclerosis is a leading cause of macrovascular complications in type 2 diabetes mellitus (T2DM). Lipid metabolism disorders in T2DM alter exosomal cargos, affecting vascular endothelial cells and impairing vascular endothelium-dependent relaxation.  This study investigates the link between T2DM and atherosclerosis, focuing on adipose tissue-derived exosomes (AT-Exosomes) as key pathogenic factors in T2DM.

overall_design: AT-exosomes derived from diabetic (C57BLKS-Leprdb/db) and non-diabetic (C57BLKS-Leprdb/+) mice were co-cultured with vascular aorta to evaluate pathogenicity. RNA screening in mouse aortic endothelial cells (MAECs) identified differential genes impacted by T2DM BAT-derived versus healthy BAT-derived exosomes.

first: Wei

last: Zhao


title: Transcriptional programs of in vitro-expanded HSPCs with acute disruption of Lmo2 before and after co-culture with OP9-DLL1

city: Pasadena

first: Samantha

last: Chang

address: 1200 E California Blvd

department: Biology and Biological Engineering

institute: California Institute of Technology

summary: Though Lmo2 is a well-established member of the hematopoietic stem/progenitor program, its function in normal T cell development has remained unclear and difficult to study. Lmo2’s quick downregulation in thymic-seeding progenitor cells makes it particularly challenging to precisely perturb for mechanistic analyses; however, a recent in vitro HSPC expansion method provides a platform for probing a greater number of progenitor cells during an extended window of time through the T cell DN stages. Consequently, we performed loss-of-function experiments in expanded HSPCs and analyzed subsequent gene expression with bulk RNA-seq and single cell RNA-seq to reveal Lmo2’s previously unknown role in early T cell development.  Remarkably, premature loss of Lmo2 in expanded HSPCs results in the specific upregulation of the T cell program. Bulk RNA-seq at day 5 of OP9-Dll1 co-culture reveals that the DN1 (CD44+CD25-) population derived from expanded HSPCs with the Lmo2 knockout (KO) have higher expression of T cell-related genes, such as the TCR signaling genes Lat, Itk, Lck, Zap70, Cd3e, and Cd3g, and higher transcriptional activation of the T cell receptor (TCR)-C beta locus when compared to DN1 controls. These findings are supported by single cell RNA-seq (scRNA-seq), where Lmo2-KO cells have higher expression of T cell program members like Tcf7 and higher transcriptional activation of the (TCR)-C gamma locus by the day 3 timepoint. Interestingly, before entering a Notch environment, there is minimal difference between Lmo2 KO and their control counterparts by scRNA-seq. Furthermore, the d3 and d5 datasets do not strongly indicate that Lmo2 KO causes a downregulation of the stem/progenitor program.  The scRNA-seq dataset also introduces the impact of Flt3L pre-treatment for 4 days of expansion (Flt3L-priming) before seeding onto OP9-DLL1 co-cultures. Differences due to Flt3L-priming can only be seen in a subpopulation of samples before entering a Notch signaling environment; by the day 3 timepoint, cells are virtually indistinguishable by priming, suggesting that developmental acceleration caused by Flt3L-priming is distinct from Lmo2-related mechanisms.  Taken together, these datasets provide gene expression profiles of control-derived and Lmo2 KO-derived DN populations to present Lmo2 as an important controller of early T cell developmental kinetics.

overall_design: In vitro HSPC expansion, retroviral infection and early T cell development: Lineage negative (lin-) bone marrow from 8-10 weeks old Cas9 x Bcl2 mice was harvested and obtained via lineage depletion with biotinylated antibodies (TCRb, TCRgd, CD19, NK1.1, CD49b, CD11b, CD11c, Ly6G/C), streptavidin microbeads (Miltenyi Biotec) and MACS LS columns (Miltenyi Biotec). These lin- cells were expanded in HSPC expansion medium (F12 DMEM, 1 mg/mL of PVA, 1× Insulin–transferrin–selenium–ethanolamine, 10 mM HEPES (pH 7.3-7.5) , 1× Penicillin–streptomycin–glutamine) supplemented with 100 ng/mL of mouse thrombopoietin (TPO) and 10 ng/mL of mouse stem cell factor (SCF) for 10-14 days. Expanded HSPCs were enriched for the LSK population by Sca1-positive selection using PE-conjugated anti-Sca1 and anti-PE microbeads (Miltenyi Biotec) (bulk RNA-seq), or else sorted for ELSK phenotype (scRNA-seq). 3 different sgRNA expressing vectors against Lmo2 were created by inserting a 19-mer sgRNA, designed using the CHOPCHOP web tool, into the empty E42 control vector with an mTurqoise2 reporter (Addgene #189799). These 3 sgRNA expressing vectors were pooled for packaging in Phoenix-Eco cells using Fugene 6 Transfection Reagent (Promega). Retroviral supernatant was then harvested and added to a non-tissue culture plate coated with 50 μg/mL RetroNectin (Takara bio) (1×PBS at 4°C overnight and then removed of unbound RetroNectin). After centrifuge at 2000xg at 32°C for 2 hours, thawed expanded HSPCs were incubated in HSPC expansion medium on the retroviral vector-bound plate at 37°C overnight in a 5% CO2 environment. Infection with Lmo2 KO vectors was compared to infection with control vectors to ensure the appropriate baseline was used for analysis. Infected cells were harvested after overnight incubation and seeded onto OP9-Dll1 stromal cells in OP9 medium (alphaMEM, 20% FBS, 1×PSQ, and 50 microM beta-mercaptoethanol) supplemented with 10 ng/mL human Flt3L and 10 ng/mL human IL-7.  Bulk RNA-seq: Expanded HSPCs after Sca1-positive selection were frozen in Bam Banker solution (FUJIFILM) and later thawed in the same HSPC expansion media conditions for 4-5 days before retroviral infection with control or Lmo2 KO vectors.  At day 5 of co-culture, cells were harvested and FACS sorted for Live Lin- CD45+ infection+ (mTurqoise2+) DN populations: DN1 (CD25-) and DN2 (CD25-Thy1+). Total RNA was isolated from 80,000 – 300,000 cells and processed for bulk RNA-sequencing. Two independent experiments were conducted (Exp1 and Exp2).  Single Cell RNA-seq: After 10-14 days of expansion, HSPCs were ELSK-sorted and then placed in "unpriming" or "Flt3L-priming" conditions for 4 days total, where at day 2 of priming they underwent retroviral infection with control or Lmo2 KO vectors. Two timepoints were collected: before seeding cells onto OP9-DLL1 (preNotch: LiveLin-infection+) and after 3 days of co-culture on OP9-DLL1 (d3: LiveLin-CD45+infection+), making 8 conditions total. Cell from each of the 8 conditions were stained with unique hashtag oligos (HTOs) and harvested on the same day, where approximately 20,000 cells total (2,500 cells per condition) were loaded onto the same 10x Genomics Chromium Controller.

first: Boyoung

last: Shin

first: Ellen

middle: V

last: Rothenberg


title: Hand and Arm Dysfunction is Prevalent Following Hemodialysis Access Placement and Associated with Higher Rate of Access Failure

city: Gainesville

first: Terence

last: Ryan

address: 1864 Stadium Rd

institute: University of Florida

summary: This project aimed to map transcriptome changes in the forearm skeletal muscle of patients with chronic kidney disease undergoing hemodialysis access placement surgery. Muscle biopsies were obtained from the brachioradialis muscle pre- and at several timepoints post-operatively.

overall_design: bulk RNA sequencing was performed on brachioradialis muscle specimens obtained from CKD patients undergoing hemodialysis access placement surgery

first: Kim

last: Kyoungrae

first: Ryan

last: Terence E.

first: Scali

last: Salvatore T.


title: Effects of UTX Knockout on Gene Expression in an Ischemia-Reperfusion-Induced Acute Kidney Injury Model

city: wu han

first: chentai

last: peng

state: State/Province

address: 湖北省武汉市华中科技大学同济医学院药学院

institute: 华中科技大学

summary: Wild-type mice and Utx Pax2-cre mice were subjected to sham operation or ischemia-reperfusion (I/R) treatment, respectively. After the designated treatment periods, the mice were euthanized, and kidney tissues were collected. RNA from the kidney tissues was extracted using the Trizol reagent.

overall_design: RNA-seq analysis of transcriptomic profiles in wild-type and Utx Pax2-Cre mice subjected to ischemia-reperfusion (I/R) treatment.

first: Hong

last: Chen

first: Kun

last: Huang

first: Ling

last: Zheng

first: Chentai

last: Peng

first: Yancai

last: Wu


title: NSD2 aggravates metabolic dysfunction-associated steatotic liver disease progression by suppressing TFEB-mediated autophagy-lysosomal pathway

city: Beijing

first: Yuan

last: Qiao

address: Beijing

institute: China-Japan friendship hospital

summary: Extensive research has demonstrated that impaired autophagy contributes to the development of metabolic dysfunction-associated steatotic liver disease (MASLD). Qiao et al. identified NSD2 in the liver as a novel and essential regulator of MASLD. NSD2 epigenetically represses TFEB transcription through trimethylation of histone H4 at lysine 20 (H4K20me3), thereby impairing autophagic flux to exacerbate hepatic steatosis. In conclusion, NSD2 functions as a crucial epigenetic regulator of impaired autophagic flux in the liver, offering a novel therapeutic target for MASLD management.

overall_design: We conducted CUT&Tag analysis using anti-H4K20me3 antibody in control and shNsd2 human HepG2 cells.

first: Liang


title: Lineage plasticity of the integrated stress response is a hallmark of lung cancer evolution.

city: Montréal

first: Antonis

last: Koromilas

state: QC

address: 3755 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: Lady Davis Institute - McGill University

summary: Lung adenocarcinoma (LUAD) progresses from a single alveolar type 2 (AT2) cell to a complex, malignant tissue through a multi-step process involving acquisition of high plasticity and stem cell-like traits in a subset of cancer cells. Oncogenic transformation and signals from the tumor microenvironment (TME) activate the integrated stress response (ISR), a key survival mechanism that allows tumor cells to adapt and thrive under stress. Using single-cell transcriptomics, we identified high stemness and plasticity cell clusters in mouse LUAD tumors expressing mutant KRAS and lacking TP53 (KP model), which displayed elevated ISR program expression. Disrupting ISR via the genetic loss of phosphorylated eIF2a (p-eIF2a) or the transcription factor ATF4 hindered LUAD growth and the emergence of high-plasticity, stemness-associated lineages, resulting in the formation of a distinct cell state characterized by mitochondrial dysfunction. Additionally, treatment with ISRIB - a small-molecule ISR inhibitor with low toxicity and cognitive benefits - led to an accumulation of AT2-like LUAD cells, blocking developmental progression and tumorigenesis. In human LUAD, the ISR program is similarly elevated in KRAS-mutant tumors with high plasticity and stemness features and correlates with poor patient outcomes. These findings suggest that ISR is a key driver of LUAD progression and targeting ISR could provide a promising approach to slow LUAD progression and improve lung cancer treatment outcomes.

overall_design: To investigate the role of integrated stress response, specifically p-eIF2, in LUAD evolution, we conducted scRNA-seq on GFP+/CD45- lung tumor cells isolated by Fluorescence-Activated Cell Sorting (FACS).

first: Shiqi

last: Diao

first: Jia Yi

last: Zou


title: Affymetrix SNP array data for 14q12 deletion

city: Lianyungang

first: Fang

last: Zhang

state: Jiangsu

address: Qindongmen Street No.669

institute: Lianyungang Maternal and Child Health Hospital

summary: Copy number analysis of Affymetrix 750K SNP arrays was performed for one amniotic fluid sample.

overall_design: 14q12 deletion


title: Gene expression profile at single cell level of genetically defined organoid models in neoplastic evolution of head and heck squamous cell carcinoma

city: Los Angeles

first: De-Chen

last: Lin

address: CSA 210, 2250 Alcazar Street

department: Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center

institute: University of Southern California

summary: To investigate the molecular mechanisms driving neoplastic evolution in head and neck squamous cell carcinoma, we established genetically defined mouse tongue organoid models harboring key driver mutations: control (Ctrl), Trp53/Cdkn2a dual-knockout with a control vector (DKOC), and Trp53/Cdkn2a dual-knockout with the PIK3CA E545K mutation (DKOP), and performed single-cell RNA sequencing (scRNA-seq) using the 10x Genomics platform on these organoid lines.

overall_design: Wild-type mouse tongue organoids were first generated from wild-type C57BL/6 mice and subsequently genetically engineered into three lines: Ctrl, DKOC, DKOP. ScRNA-seq was performed to assess the impact of the dual-knockout of Trp53/Cdkn2a and the additional PIK3CA E545K mutation on gene expression profiles and cellular states within these organoid models.

first: Hua

last: Zhao

first: Young-Min

last: Park

first: Yueyuan

first: Qiong

last: Mao

first: Casey

last: Collet

first: Boyan

last: Hu

first: Tianming

last: Zhou

first: Luda

first: Stephanie

last: Wong

first: Yuhao

last: Pan

first: Anette

last: Monreal

first: Uttam

middle: K

last: Sinha

first: Parish

last: Sedghizadeh

first: Alice

last: Soragni


title: Impact of 3D-printed perfusable synthetic vasculature on stem-cell based early-stage cerebral organoids

city: Cambrigde

first: Jose

last: Vargas Asencio

address: 400 Main st

department: PILM

institute: MIT

summary: Stem-cell based cerebral organoids were integrated with 3D-printed perfusable synthetic vasculature. The impact of perfusion was evaluated on month-old cerebral organoids was analyzed by comparing the molecular-level changes in perfused and not-perfused vascularized cerebral organoids

overall_design: The cerebral organoids were grown on the custom-made synthetic perfusion platform for around a month in two different conditions- with or without continuous  media perfusion. For sequencing, the vascularized cerebral organoids were dissociated using the neural tissue dissociation kit (manufacturer: Miltenyi). The plastic debris from the synthetic vasculature were removed using a bead column before sending the single cells for sequencing.

first: Srinivasa

last: Pujari

first: Jisoo

last: Kim

last: Vargas-Asencio

first: Justin

last: Swaney

first: Kwanghun

last: Chung


title: METTL3-dependent m6A RNA Modifications Orchestrate the HNF1B-associated Redox and the Metabolic Vulnerability in Cancer [MeRIP-seq]

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

institute: Yonsei University

summary: Internal RNA modifications, such as N6-methyladenosine (m6A), are widespread in mammalian cells but their importance in cancer metabolism remains poorly understood. Here, we demonstrate that the m6A methyltransferase complex, composed of METTL3 and METTL14, is a critical regulator of the metabolic dependencies in human cancers. Inhibiting METTL3-mediated m6A modifications, both genetically and chemically, significantly impairs the antioxidant capacity of pancreatic cancer cells, sensitizing them to the oxidative stress. We found that m6A modifications at the 3'-untranslated regions (3'-UTRs) of the HNF1B mRNA enhances its stability and expression levels. Furthermore, the loss of HNF1B triggers oxidative stress-induced cell death across multiple cancer types, recapitulating the metabolic dysfunction caused by m6A depletion and revealing HNF1B as a key mediator of the glutathione metabolic program. By establishing a link between m6A modifications and cellular antioxidant responses via HNF1B, our findings suggest that METTL3 is a metabolic vulnerability in cancer and highlight its potential as a therapeutic target for m6A-directed therapies in cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: m6A MeRIP-seq profilings of various pancreatic cancer cell lines with indicated perturbations.

first: Jae-Seok

first: Hwa-Ryeon

first: Minji

last: Park


title: METTL3-dependent m6A RNA Modifications Orchestrate the HNF1B-associated Redox and the Metabolic Vulnerability in Cancer [ChIP-seq]

overall_design: H3K4me3, H3K4me1, and H3K27ac ChIP-seq profilings of various pancreatic cancer cell lines with indicated perturbations.


title: Gat1 mediated Schwann cell proliferation after nerve decompression in peripheral constriction injury of rat sciatic nerve

city: Tainan

first: Chunwei

last: Lin

address: No. 1, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

summary: Peripheral compressive neuropathy results in significant neuropathic pain, muscle weakness, and prolonged neuroinflammation. Surgical decompression remains the gold standard for treatment; however, the outcomes are often suboptimal, and patients have a high recurrence rate. In this study, we employed a reproducible and controllable chronic constriction injury (CCI) rat model to simulate early nerve decompression. The rat sciatic nerve was constricted for a short duration, followed by release, which induced reversible sensorimotor dysfunction. We further explored the genes involved in nerve regeneration via NanoString analysis. Compared with the control nerves, the differentially expressed genes (DEGs) Mmp12, Il1rn, Fcgr3, Hmox1, Lst1, Ccl2, Nlrp3, Il2rg, and Sell were downregulated in the constricted nerves at days 7 and 14 after release. Other significant DEGs, such as Gsn, Ugt8a, Snca, Slc6a1, Pmp22, Kdm5d, Mal, Plp1, Slc2a1, Gjb1, Cyp27a1, and Plekhb1, were upregulated on days 7 and 14. When the correlations between these upregulated DEGs and nerve regeneration were investigated, we found that Slc6a1, also known as GABA transporter 1 (Gat1), was associated with nerve regeneration. To further understand its role, we overexpressed Gat1 in a rat neuronal Schwann cell line, RT4-D6P2T. This led to increased viability of the Gat1-overexpressing cells. Additionally, neuronal markers including Nefh, S100b, and Ngfr, along with cell proliferation signaling molecules, such as p-Akt and p-Mapk, were elevated in these cells. The increase in viability and neuronal marker expression was inhibited by the Gat1 inhibitor tiagabine in Gat1-overexpressing cells. To simulate neuronal damage and recovery, we treated the cells with H2O2 for 2 hours and then allowed them to recover in growth medium for 1 and 7 days. The data indicated that the mRNA and protein levels of Gat1 were reduced on day 1 but upregulated by day 7. Consistently, the decrease in the expression of neuronal markers observed on day 1 was reversed by day 7. Taken together, our findings demonstrate that Gat1 plays a significant role in neuronal regeneration in both a cell model and an animal model of CCI.

overall_design: The L4-5 DRGs from the nerve injured site were harvested and the RNA expression level was further analyzed with NanoString’s nCounter technology on Day -7 (no nerve injury as Naïve group), Day 0 (nerve injury as control), including  Day 1 and Day 5 after UHF stimulation.

first: Yuan-Shuo

last: Hsueh

first: Szu-Han

last: Chen

first: Wan-Ling

last: Tseng

first: Hui-Hua

last: Chang

first: Yuan-Yu


title: METTL3-dependent m6A RNA Modifications Orchestrate the HNF1B-associated Redox and the Metabolic Vulnerability in Cancer [RNA-seq]


title: Comparision of PBMC from PTEN loss and WT glioblastoma patients

city: Boston

first: David

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: Glioblastoma (GBM) is a lethal type of brain tumor that is resistant to immunotherapy. Genetic profiling studies have indicated that the tumorigenesis of GBM is linked to somatic genomic alterations in key driver genes, such as TP53, PTEN, CDKN2A, RB1, EGFR, and NF1. These genes regulate critical pathways related to cell growth and resistance to immunotherapy, including the use of immune checkpoint inhibitors (ICIs). One reason for resistance to ICI therapy may be the presence of immunosuppressive myeloid cells, including macrophages and myeloid-derived suppressor cells (MDSCs). We conducted an unbiased analysis to identify specific genetic alterations in GBM cells that may influence MDSC biology and contribute to resistance against immunotherapy.

overall_design: PBMCs were collected from patients with PTEN wild-type (WT) and PTEN loss GBM. The EasySep™ Dead Cell Removal (Annexin V) Kit (STEMCELL, # 7899) was used to eliminate dead cells from each PBMC sample. A total of 9 PBMC samples from PTEN WT and PTEN loss GBM patients were analyzed. Barcoding, library preparation, and sequencing were performed and analyzed by the NUSeq Core at Northwestern University.

first: Lizhi

last: Pang

first: Peiwen


title: The Role of the Thymus in ALS development in a SOD1 ALS model

city: Paris

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

country: France

institute: Sorbonne Universite

summary: Study looking at the role of thymus biology in SOD1 ALS

overall_design: Whole thymus and ingunial lymph node samples were collected at D120 in SOD and WT mice and processed for whole RNA-sequencing. For sorted cell populations, cells were sorted and then were subjected to RNA-sequencing. Finally, the same set of Tregulatory cells were placed in vitro and activated for a variety of lengths of time.

first: Julia

last: Lemos

first: Piera

last: Smeriglio


title: Systematic Comparison of 10X Genomics and Parse Single Cell RNA Technologies across PBMC and CD8+ TEMRA Cells

first: Alejandro

last: Espinoza

address: 610 Charles E Young Dr S. 5000C

institute: University of California, Los Angeles

summary: Single-cell RNA sequencing technologies provide insights into gene expression at the cellular level, enabling detailed analysis of cellular heterogeneity. In this study, we systematically compared two scRNA-seq platforms—10X Genomics and Parse Biosciences—using human peripheral blood mononuclear cells (PBMCs) and terminally differentiated effector memory CD8+ T cells (TEMRAs). We identified significant differences in gene expression variability and platform-specific biases, such as ribosomal and mitochondrial gene capture. 10X has a bias for shorter genes, while Parse exhibited enhanced detection of longer transcripts. In CD8+ TEMRAs, the expression of key genes related to immune responses were underrepresented in Parse cells compared to 10X cells (e.g. GNLY, PRF1 and GZMB). These findings underscore the need for careful selection of scRNA-seq platforms based on specific research objectives, as platform-specific biases can influence cell type identification and as well as mechanistic insights from derived from gene expression data. Our results provide critical insights for selection of scRNA-seq experimental platform in immunological studies.

overall_design: Human PBMC samples  were collected and sequenced from three healthy donors. Terminally differentiated effector memory CD8+ T cells re-expressing CD45RA were purified using fluorescence-activated cell sorting. For PBMCs we performed both Chromium Next GEM Single Cell 3′ Gel Bead Kit v3.1 and the Evercode Whole Transcriptome kit v2 . TEMRA cells were sequences using Chromium Next GEM Single Cell 3′ Gel Bead Kit v3.1 and Evercode WT Mini kit v2.

first: Bruno

last: Silva de Andrade

first: Robert

middle: L

last: Modlin

first: Matteo

last: Pellegrini


title: Ceramides drive colorectal cancer metastasis through a revival stemness program [BulkRNAseq_InVitro]

city: CAMBRIDGE

first: Qiming

last: Zhang

address: 88 Ames Street

institute: Koch institute

summary: We demonstrate that tumor-intrinsic ceramide metabolism is crucial in initiating colorectal cancer (CRC) metastasis, a process further enhanced by dietary fat intake

overall_design: In vitro AKP organoids were treated with palmitic acid or carmofur, a ceramidase inhibitor, to test the effect of fatty acid and ceramide levels on the transcriptional changes of AKP organoids

first: Swagata

last: Goswami

first: Omer

middle: H

last: Yilmaz


title: c-MET inhibition is synthetic lethal with ARID1A loss via targeting GPX4 and promoting ferroptosis

city: Guangzhou

first: Changjie

last: Wu

state: Guangdong

address: 1838 Guangzhou Avenue North, 510515 Guangzhou, Guangdong, China

institute: Southern Medical University

summary: ARID1A, a subunit of the SWI/SNF chromatin-remodeling complex, functions as a tumor suppressor in various cancer types. Owing to its high frequency of inactivating mutations, ARID1A has emerged as a promising target for the development of anticancer drugs. In this study, we report that ARID1A-deficient colorectal cancer (CRC) cells induce synthetic lethality when treated with inhibitors of c-MET receptor tyrosine kinase. c-MET specific inhibitor PHA-665752 as well as two other FDA-approved drugs, crizotinib and cabozantinib, selectively inhibited the growth of ARID1A-deficient CRC cells in vitro and in xenograft tumor models. Mechanistically, we identified triple genetic interactions between ARID1A, c-MET, and GPX4 in CRC cells, where GPX4, a key regulator of ferroptosis, is a common transcription target of ARID1A and c-MET signaling. ARID1A inactivation significantly downregulated both c-MET and GPX4 levels, and the c-MET inhibitor further diminished GPX4 levels in ARID1A-deficient CRC cells, leading to increased lipid peroxidation and glutathione depletion, ultimately inducing ferroptosis. This study reveals a novel synthetic lethal relationship between ARID1A and c-MET signaling in promoting ferroptosis and proposes c-MET inhibitors as a potential therapeutic strategy for ARID1A-deficient CRC.

overall_design: RNA-seq

first: Joongsup

last: Shim

first: Xu

first: Yijiang

last: Song


title: Ceramides drive colorectal cancer metastasis through a revival stemness program [BulkRNAseq_GFP]

overall_design: Alive cells were isolated from normal colons or primary colon tumors of high fat diet-fed samples and the matched control samples by fluorescence-activated cell sorting (FACS) and then scRNAseq experiments and analyses were performed.


title: Ceramides drive colorectal cancer metastasis through a revival stemness program [BulkRNAseq_HFD]

overall_design: Basp1-eGFP-DTR; AKP-tdT organoids were generated and then injected orthotopically into mouse colon. The primary tumors were collected and digested and GFP-positive and GFP-negative populations were sorted by FACS.


title: Ceramides drive colorectal cancer metastasis through a revival stemness program [scRNA-seq]


title: AP2XI-3-dependent gene regulation in Toxoplasma gondii tachyzoites [RNA-seq]

city: Wuhan

first: Fan

last: Fuqiang

address: 1 Shizishan St

institute: Huazhong Agricultural University

summary: Toxoplasma proliferation is governed by its flexible but tightly regulated cell division cycle, that remarkably depends on appropriate and temporal transcriptional waves throughout the division cycle although the underlying regulation network is still unclear. Here we reported the transcriptional factor, AP2XI-3, as an essential cell cycle related gene regulator in G1 progression. After AP2XI-3 depletion, tachyzoites growth was obviously arrested in G1 phage and daughter budding progression was also destroyed. Intriguingly, the growth arrest of mutant parasites was also observed in vitro. Combining analysis of RNA sequencing and Cut & TAG revealed the key regulatory role of AP2XI-3 in G1 phage related biomass accumulation and cellular competent. AP2XI-3 controlled and targeted a set of RNA transcription, metabolism or protein biosynthesis related genes, whose dysregulation functionally disrupted cell homeostasis and parasite division. Altogether, our finding demonstrated the functional role of AP2XI-3 in transcriptional controlling of G1 progression and revealed its potential ability as a drug design target.

overall_design: Toxoplasma gondii with AP2XI-3 tagged with (mAID-3HA) and its parental strain were treated with IAA and processed polyA-enriched RNAseq in tachyzoites

first: Xiaoyan

last: Yin

first: Fuqiang

last: Fan

first: Bang

last: Shen


title: Ceramides drive colorectal cancer metastasis through a revival stemness program [ATAC-seq]

overall_design: Organoids treated with HFD, CD, Control, PA and then ATACseq experiments and analyses were performed.


title: Mesenchymal stem cell-derived extracellular vesicles regulate M1 and M2 macrophages

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

summary: Mesenchymal stem cells (MSCs) can respond to micrenvironmental cues to exert immune suppression or stimulation. Both MSCs and macrophages (MΦs) are part of the bone marrow microenvironment. Separately, both cell types can influence the behavior of breast cancer cells towards dormancy and reverse dormancy. This study assessed the MΦ−ΜSC axis, specifically determined how activated MSCs could influence the type of MΦ. The toll like receptor 4 (TLR4) on MSCs was activated with LPS and then used to assess how this influence the type of MΦ. We demonstrated that activated MSCs can convert M2 MΦs to M1 type and vice versa. Interestingly, the transition is not stable showing re-transition to the original type. This suggested the ability of activated and inactivated MSCs to maintain homeostasis by dictating the MΦ type. We quantitated cytokine levels in the media from activated and inactivated MSCs without evidence of significant changes. Using siRNA and pharmacological inhibitors, the results supported a role for MSC derived extracellular vesicles (EVs) as mediators of MΦ transition. We assessed our published miRNA arrays from cancer activated MSCs and identified one of four potential miRNAs that has been reported to regulate myeloid cells. We further investigated molecular changes with RNA-Seq using extracts from activated and inactivated MSCs, and EVs from M1 and M2 MΦs

overall_design: Macrophages were grown in indirect co-culture with MSCs that had been activated using LPS. The transwell containing MSCs was removed, and the media replaced with 2% exosome free serum. RNA was then collected from the  macrophages, as well as from the M1- and M2-released EVs. These data correlate with GEO Series GSE239547.

first: Nykia

last: Walker

first: Yahaira

last: Naaldijk

first: Yannick

last: Kenfack

first: Lauren

last: Sherman

first: Preanela


title: Wnt/β-catenin/ATF3 signaling promotes AKI to CKD progression by regulating mitophagy in mice [mouse]

city: Xiamen

first: Liangxiang

last: Xiao

address: No. 201-209, Hubin South Road

institute: Zhongshan Hospital of Xiamen University

summary: Sustained activation of Wnt/β-catenin signaling has been shown to promote AKI to CKD progression. However, its underlying mechanisms remain largely unclear. In this study, we investigated this issue via unilateral ischemia/reperfusion injury in mice and hypoxia/reoxygenation (H/R) in HKC-8 cells. Both in vitro and in vivo, overexpression of Wnt1 promoted mitochondrial dynamics and mitophagy damage. Furthermore, we revealed that ATF3 not only is a transcriptional target of canonical Wnt/β-catenin signaling but is also an important pathogenic mediator of kidney disease. ATF3 was expressed in various CKD animal models, including UUO, UIRI, ADR and 5/6NX. In vitro, exogenous ATF3 induced mitochondrial dynamics and mitophagy, and silenced ATF3 expression protected mitochondrial function. Finally, compared with normal individuals, patients with various kidney diseases presented markedly elevated levels of ATF3. In addition, ATF3 levels are closely correlated with renal injury markers and renal fibrosis area in patients. Thus, these results suggest that Wnt/β-catenin/ATF3 signaling activation promotes AKI to CKD progression by regulating mitochondrial dynamics and mitophagy. ATF3 can serve as a promising potential biomarker for AKI to CKD progression.

overall_design: Mice transfected with either p-Wnt-1 or pcDNA3 were sequenced.

first: Gewenhan

last: Chen

first: Yanni

last: Zhou

first: Mengjiao

last: Lin

first: Anting

last: Li

first: Shijie

last: Lu

first: Xue

last: Hong


title: Ceramides drive colorectal cancer metastasis through a revival stemness program [BulkRNAseq_CRISPR]

first: Qiming

last: Zhang

overall_design: The ibonucleoprotein CRISPR protoco was used to generate Degs1 knockout organoids. shYAP1 was used to generate YAP knockdown organoids. RNA was extracted on to check the expression changes after Degs1-KO and YAP1-KD.

first: Swagata

last: Goswami

first: Omer

last: Yilmaz


title: Cellular stress, inflammation and barrier damage in gut epithelial cells caused by aspartame

city: Davos Wolfgang

first: Cezmi

middle: A.

last: Akdis

state: Grisons

address: Herman-Burchard-Strasse 9

department: SIAF

country: Switzerland

institute: University of Zurich

summary: Aspartame has been widely used as a sweetener in foods and beverages since the 1980s. In this study, we aimed to assess the effect of aspartame on gut epithelial cell biology, inflammation, and the epithelial barrier. Aspartame shows cytotoxic effects and epithelial barrier damage as well as proinflammatory cytokine release in gastrointestinal epithelial cells, organoids and organ-on-a-chips at concentrations corresponding to daily used doses in food products. Cellular cytotoxicity was observed in as low as 1.25 mg/ml doses. RNA sequencing analysis revealed that aspartame significantly altered the transcriptome in gut-on-a-chip models, showing upregulation of pathways such as unfolded protein response, activated pro-apoptotic and inflammatory, and downregulation of DNA repair and replication mechanisms pathways. Aspartame exposure upregulated proinflammatory genes, particularly in the TNF signalling pathway, and induced multiple chemokine responses. It activated the NF-κB pathway via oxidative stress, promoting inflammation on NF-κB reporter monocyte cells and causing gut epithelial cell death. Aspartame affected genes involved in tight and adherens junctions, disrupting gut epithelial barrier integrity in a dose-dependent manner in gut-on-a-chip models. Additionally, aspartame suppressed key DNA repair and replication genes involved in double-strand break repair, mismatch repair, and DNA replication. Overall, our findings indicate that at commonly consumed levels, aspartame induces cellular stress, inflammation, and epithelial barrier damage in gastrointestinal epithelial cells. These findings underscore the biological relevance of our results and raise concerns that daily dietary intake of aspartame may pose previously underappreciated risks to gut health.

overall_design: A gut-on-a-chip system was used to assess the effect of aspartame on colon epithelial cells. Gut-on-a-chip cultures were established with OrganoPlate® 3-lane 64 plates  (Mimetas BV, Leiden, The Netherlands) following the manufacturer's protocols.On day 8 of gut-on-a-chip culture, the chips were exposed to 10mg/ml and 2.5mg/ml aspartame dissolved in culture media for 24 hours.  RNA from the gut-on-a-chip culture were harvested at 24 hours of the aspartame exposure.

first: Yagiz

last: Pat

first: Duygu

last: Yazici

first: Can

last: Zeyneloglu

first: Huseyn

last: Babayev

first: Sena

last: Ardicli

first: Asuncion

last: Garci-Sanchez

first: Xiangting

last: Bu

first: Anja

last: Heider

first: Oliva

last: Giannelli Viscardi

first: Lihong

last: Chang

first: Sheri

last: Simmons

first: Anthony

last: Almada

first: Christine

last: Avena

first: Tye

last: Jensen

first: Raja

last: Dhir

first: Ismail

last: Ogulur

last: A. Akdis


title: Expanding the Coding Potential of the Mitochondrial Genome with MitoRiboSeq

city: Amsterdam

first: Joana

last: Silva

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: The Netherlands Cancer Institute

summary: The mitochondrial genome encodes 13 well-characterized mRNAs but, similar to the nuclear genome, it has the potential to encode many additional proteins through previously unannotated open reading frames. Using MitoRiboSeq, we detected dozens of new mitochondrial-derived microproteins in both cell lines and liver tissues. We demonstrate that MOTS-c, a previously described microprotein, shows a significant decrease during senescence induction, and its supplementation is sufficient to prevent key cellular dysfunctions associated with this process. This work significantly deepens our understanding of the mitochondrial genome and underscores its relevance for functional and therapeutic discoveries.

overall_design: Expression profiling by high throughput sequencing

first: Ferhat

last: Alkan


title: Ecologically designed three-member microbial consortia promote growth in Brassicaceae members by modulating growth-defense tradeoff

city: singapore

first: Hitesh

last: Tikariha

address: 5A Engineering Drive 1, #02-03 T-Lab Building

country: Singapore

institute: National university of singapore

summary: Both microbiological and genomics approaches demonstrated the significant PGP potential and stability of bacterial consortia SAB, which outperformed its members. Phenotypic data indicated that SAB treatment positively impacted shoot and root biomass growth. Furthermore, greenhouse experiments confirmed the consistent and significant performance of SAB treatment on choy sum plants in various soil conditions. Transcriptomics data of boht root and shoot at two different time point revealed that SAB triggered a parallel activation of growth and defense response in shoot that by pass the growth defense tread-off through microbiome mediated signaling and beneficial services.

overall_design: A three-membered bacterial consortium (SAB) was formulated by considering the natural interactions among its members through genome-scale metabolic modeling along with the PGPR properties. The consortium was found to promote growth in several leafy vegetables like Choy-sum and Kai-lan in both laboratory and greenhouse conditions. Transcriptome analysis was carried out from the leaves and root system of the consortium-treated Choy-sum plants at 8 and 18 days of their growth in pots with peat-moss soil, with their respective untreated control.  The seeds were treated with SAB consortium and sowed in peat-moss soil.  Plants were grown in a controlled environment with a 16/8-hour light and dark cycle at 22 degrees Celsius temperature.

first: Mrinmoy

last: Mazumdar

first: Mayalagu

last: Sevugan

first: Shruti

last: Pavagadhi

first: Sanjay

last: Swarup


title: The Transcription Factor T-bet Plays a Crucial Role in Regulating the Immune Regulatory Function of Double-Negative T Cells

city: Beijing

first: Xiaotong

last: Han

address: No,8,South Road of The Worker's Stadium,Chaoyang Dist. Beijing

institute: Beijing Chao-Yang Hospital

summary: This study found that, compared to conventional CD4+ / CD8+ T cells, double-negative T (DNT) cells express high levels of IFN-γ, and IFN-γ can dose-dependently enhance the in vitro conversion efficiency of DNT cells, suggesting that DNT cells tend to adopt a Th1 phenotype. Single-cell sequencing revealed that DNT cells exhibit high expression of the transcription factor T-bet. Knockout of T-bet significantly downregulated IFN-γ expression in DNT cells and reduced their suppressive capacity on macrophages in vitro. Transcriptome sequencing further elucidated the specific mechanism by which T-bet regulates the immune regulatory function of DNT cells.

overall_design: RNA-seq profiling of wild-type cDNT cells and Tbx21-knockdown cDNT cells.


title: Maintenance of β-cell identity through the transcription co-factors TBL1X and TBL1XR1

city: Neuherberg

first: Alina

middle: Agnes

last: Walth-Hummel

address: Ingolstädter Landstrasse 1

country: Germany

institute: Helmholtz Munich

summary: Loss of β-cell identity is a main mechanism of β-cell dysfunction in diabetes, controlled by transcription factors that induce β-cell identity gene expression and “disallowed” gene repression. How transcription factors facilitate simultaneous expression and repression is not fully understood, representing a serious knowledge gap in diabetes research. We identified the transcriptional co-factors transducin β-like 1 x-linked (TBL1X) and its homolog TBL1X-related (TBL1XR1) (short: TBL/R1) as crucial regulators of β-cell identity and function, as β-cell specific knockout in mice leads to progressive hypoinsulinemia and hyperglycemia. Single-cell RNA sequencing revealed loss of β-cells, the emergence of polyhormonal cells, and reduced β-cell maturity upon TBL/R1 knockout, indicating dedifferentiation. Interactome screens and chromatin immunoprecipitation showed TBL/R1 directly regulate insulin gene expression by forming a gene regulatory network with PAX6 and HDAC3, which was also evident in human models. Our study uncovers a new regulatory layer maintaining β-cell identity, crucial for diabetes development and progression.

overall_design: To investigate the transcriptomic changes in pancreatic beta-cells upon TBL1X and TBL1XR1, pancreatic islets from mice with a beta-cell specific TBL1X and TBL1XR1 kockout (n=4) and control littermates (n=4) were isolated and subjected to RNA-Seq

first: Maria

last: Rohm


title: Core protein synthesis adaptations drive biological novelty in octopus

city: Cambridge

first: Rishav

last: Mitra

state: Massachusetts

address: 16 Divinity Avenue

institute: Harvard University

summary: Much of biology focuses on how differences in the genetic code give rise to new functions, but far less attention is given to adaptations in other components of the central dogma. Octopuses exhibit complex nervous systems and sophisticated behaviors that rival vertebrates, but via an entirely distinct evolutionary history. How did octopuses distinctly evolve such novel traits? Here, we serendipitously discover that octopus ribosomes contain a structural adaptation in the catalytic ribosomal RNA (rRNA) domain, a conserved center for protein synthesis across all life1. This rRNA modification is unique among all animals and mediates enhanced accuracy of protein synthesis, decreases protein misfolding and aggregation, and supports translation during adaptive RNA editing when occupying new environments. Thus, the octopus uses modifications in the core protein synthesis machinery to drive biological novelty, a strategy which could support the evolution of unique organismal traits across life.

sample_organism:
Octopus bimaculoides
Euprymna berryi

platform_organism:
Octopus bimaculoides
Euprymna berryi

overall_design: To characterise gene expression differences in cephalopods, we performed RNA-Seq on arm and brain tissues derived from Octopus bimaculoides and Euprymna berryi. Additionally, to quantify RNA editing, we performed RNA seq from octopus and squid tissues that were subjected to a cold acclimation protocol (6 degrees C decline in ambient temperature over 2 weeks).

first: Amy

last: Lee

first: Nicholas

last: Bellono


title: RNA-seq of  colon

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

summary:
Objective: Inflammatory bowel disease (IBD), encompassing ulcerative colitis (UC) and Crohn’s disease (CD), represents a challenging group of chronic gastrointestinal inflammatory disorders. While trained immunity, a form of innate immune memory, has shown promise in combating infection and cancer, its role in chronic inflammatory diseases, particularly inflammatory bowel disease (IBD), remains relatively underexplored. This study aims to investigate the potential of trained immunity to ameliorate IBD.
Results: BG induced trained immunity significantly ameliorates DSS-induced colitis. Mechanistically, β-glucan primed the hematopoietic compartment, leading to a profound shift in monocyte fuction. Both bone marrow transplantation from trained donors to naïve recipients and adoptive transfer of trained peripheral monocytes provided protection against DSS colitis. Notably, trained mice displayed enhanced bactericidal activity against intestinal bacterial infections. Furthermore, single-cell RNA sequencing revealed that β-glucan-induced trained immunity resulted in an expansion of reparative Cx3cr1 intestinal macrophages originating from Ly6Chi monocytes, facilitating faster recovery of the colon epithelium.
Conclusion: Our findings demonstrate that β-glucan effectively induces trained immunity, leading to a multifaceted protective response against experimental colitis. These findings provide compelling evidence for the therapeutic potential of harnessing trained immunity to treat IBD and offer a novel approach to modulating intestinal inflammation and restoring gut homeostasis.

overall_design: RNA sequencing on colonic samples collected at multiple time points following DSS administration.

first: Yinyin

last: Lv

first: Qiongyun

last: Chen


title: Suppression of mitochondrial energy production by peptide from photosynthetic bacterial protein inhibits tumor growth

city: Chicago

first: DUY BINH

last: TRAN

state: IL

address: 840 S. Wood St

department: Surgery

institute: University of Illinois Chicago

summary: Accumulating evidence suggests that bacteria play significant roles in cancer homeostasis. While tumor microbiome has been reevaluated recently, the impact of these bacterial products on tumors has not been widely explored. We previously showed that crosstalk between cancer and P.aeruginosa mediates tumor suppression through bacterial cupredoxin azurin and we designed an azurin-derived peptide. In this study, we identified photosynthetic bacteria/cyanobacteria, such as Chloroflexia, in tumor specimens. Given that Chloroflexus aurantiacus contains at least two cupredoxin genes, we focused on designing novel cell-penetrating peptides derived from the photosynthetic bacterial electron transfer protein auracyanin. Chloroplasts in plants are believed to originate from a cyanobacterial endosymbiont, and some protein characteristics of chloroplasts and mitochondria share commonalities in ATP-dependent energy production. This suggests that such bacterial proteins can alter mitochondrial functions. Consistent with this model, we demonstrated that aurB, a peptide from auracyanin B, localized at mitochondria, blocked their energy production by targeting the gamma subunit of ATP synthase, thereby significantly inhibiting xenografted PC3 tumor growth. More strikingly, aurB in combination with radiation significantly inhibited DU145 tumor volume by 99% at week 5 (vs PBS control, P<0.001) in the tibial bone metastatic model. Reflecting on the anti-tumor effects, the number of metastatic lesions in the lung was significantly reduced (91% reduction vs PBS, P<0.001). A multiplex RNA expression profiling showed that inhibition of ATP production by aurB enhanced the efficacy of radiation by the modulations of multiple pathways through HIF-1α. Collectively, our findings indicate that such electron transfer proteins could represent a significant source of promising novel peptide-based agents for targeting the mitochondrial energy production system that is aberrantly activated in cancers.

overall_design: This stydy analyzed tumor tissues from 12 samples, including 3 samples from PBS (control group), 3 samples from aurB treatment (10 mg/kg), 3 samples from irradiation group (IR, 2.0 Gy), and 3 samples from combination group [aurB (10 mg/kg) and IR (2.0 Gy)].Total mRNA expression was measured on a nCounter SPRINT Profiler (NanoString Inc, Seattle, WA, USA) using the nCounter Human Metabolic Pathways Panel (#XT-CSO-HMP1-12, NanoString), covering 768 human mRNAs associated with metabolic processes.

first: Duy Binh

last: Tran


title: Bulk muscle RNA-sequencing of mice co-exposed to simvastatin and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)

city: East Lansing

first: Tim

last: Zacharewski

state: Michigan

address: 1129 Farm Ln

department: Biochemistry and Molecular Biology, Integrative Toxicological Sciences

institute: Michigan State University

summary: Bulk RNA-sequencing of 60 muscle samples from C57Bl/6NCrl males gavaged every 4 days for 84 days with 0.1 to 10 µg/kg TCDD or sesame oil vehicle, half of whom were exposed to ~70 mg/kg/day of simvastatin (n=5 per dose). Gavaging and tissue collection occurred between ZT0-3.

overall_design: Beginning on post-natal day (PND) 30, male C57BL/6 mice were repeatedly gavaged every 4 days for 84 days with 2,3,7,8-tetrachlorodibenzo-p-dioxin (0.1, 0.3, 1, 3, or 10 µg/kg TCDD) or sesame oil vehicle, half of whom were exposed to ~70 mg/kg/day of simvastatin supplemented in their chow (n = 5 per dose). Mice were sacrificed on PND 114 with CO2. Gavaging and tissue collection occurred between ZT0 and ZT3. Tissues were flash frozen in liquid nitrogen and stored at -80°C. For total RNA extraction using trizol, 100 mg was used per muscle sample. Only samples which passed Nanodrop and RIN quality control were used. 150 bp paired-end RNA reads were sequenced using a Novaseq 6000.

first: Warren

last: Sink

first: Jesmin

last: Ara

first: Rance

last: Nault

first: John

last: Lapres


title: AP2XI-3 binding sites in Toxoplasma gondii [CUT&Tag]

first: Fan

last: Fuqiang

overall_design: Toxoplasma gondii with AP2XI-3 tagged with (mAID-3HA) were collected and processed by CUT&Tag protocol to determine AP2XI-3 binding sites genome-wide in tachyzoites

first: Fuqiang

last: Fan

first: Xiaoyan

last: Yin

first: Bang

last: Shen