title: Multi-Omics Analysis Reveals Nono-Kcnq2 Regulation of Neuronal Excitability in Neuropathic Pain

city: 贵阳

first: 鹏

last: 陈

state: 贵州

address: 贵州省贵阳市花溪区大学城栋青南路

institute: 贵州中医药大学

summary: Neuropathic pain imposes a profound, multidimensional burden on patients, largely due to limited therapeutic options stemming from inadequately understood pathomechanisms. In this study, we employed an integrated multi-omics approach to identify a novel Nono–KCNQ2 regulatory axis that underpins pain progression in chronic constriction injury (CCI) models. Proteomic analysis revealed a marked reduction in potassium ion channel protein expression accompanied by aberrant glutamatergic neuron activation during neuropathic pain progression. Additionally, phosphoproteomic profiling demonstrated that impaired phosphorylation of these channels—most notably KCNQ2—reduces ion permeability and promotes neuronal hyperexcitability. catTFRE analysis further indicated that diminished Nono transcription factor activity is associated with the downregulation of potassium ion channels in CCI rats. Moreover, single-cell RNA sequencing and spatial transcriptomics localized the co-expression of Nono and Kcnq2 to specific neuronal populations, namely Prph⁺ ventral horn and Nrxn3⁺ dorsal horn neurons, findings that were corroborated by immunofluorescence assays. Critically, CCI-induced Nono dysfunction within these subpopulations precipitates deficits in KCNQ2 signaling, ultimately leading to glutamatergic overactivation and enhanced pain sensitivity. Collectively, our findings underscore the pivotal role of ion channel transcriptional regulation in pain chronification and suggest that targeted modulation of Nono, coupled with pharmacological activation of KCNQ2, may represent a promising therapeutic strategy for neuropathic pain.

first: Peng

first: Zhibing

last: Wu

first: Shaoshuai

last: Tang

first: Qian

last: Gong

first: Chen

first: Wenjing

first: Ting

first: Ruixi

last: Luo

first: Zhaoyu

last: Qin

first: Long


title: FTO-Mediated m6A Demethylation Regulates PGC-1α-Dependent Mitochondrial Biogenesis to Attenuate Aluminum-Induced Neuronal Senescence [MeRIP-Seq]

status: Public on Jul 22 2026

city: Taiyuanshi

first: Zhaoya

last: Jin

address: Zhongdu Campus of Shanxi Medical University in Jinzhong City, Shanxi Province

country: China

institute: Shanxi Medical University

summary: This study employs integrated MeRIP-Seq and RNA-Seq to investigate how aluminum (Al) exposure drives neuronal senescence via m6A methylation dynamics. Triplicate samples of mouse hippocampal neuronal cells (HT22) were analyzed under control conditions and following treatment with aluminum maltolate (Al(mal)₃; 60, 120, 240 μM). Total RNA underwent fragmentation and m6A-specific immunoprecipitation (MeRIP) using m6A antibodies and Dynabeads. Libraries were prepared with the Illumina TruSeq Stranded mRNA Kit and sequenced on the HiSeq X10 platform (paired-end, 150 bp).  MeRIP-seq data (aligned to BosGru3.0via HISAT2) revealed Al-induced global hypermethylation (7,068 upregulated m6A peaks, MeTDiff, FDR < 0.05), enriched in coding sequences and annotated to senescence/neurodegeneration pathways (GO/KEGG). RNA-seq identified 6,369 differentially expressed genes (DESeq2, |log₂FC| > 1.5, p < 0.05). Integrative analysis demonstrated coordinated m6A hypermethylation and downregulation of PGC-1αmRNA, linking epitranscriptomic dysregulation to suppressed mitochondrial biogenesis.

overall_design: MeRIP-Seq and RNA-Seq were performed on mouse hippocampal neuronal cells (HT22) treated with aluminum maltolate (0–240 μM) to investigate epitranscriptomic regulation of neuronal senescence. Triplicate biological replicates per group (Control and Al-treated) were analyzed. RNA was fragmented and subjected to m6A immunoprecipitation using m6A-specific antibodies. Libraries were prepared with Illumina TruSeq kits and sequenced on HiSeq X10 (PE150). Data were aligned to the BosGru3.0genome using HISAT2. m6A peaks were called by MeTDiff (FDR < 0.05), and differentially expressed genes were identified by DESeq2 (|log₂FC| > 1.5, p < 0.05). Integrated analysis revealed m6A-mediated suppression of PGC-1α in mitochondrial dysfunction and senescence.

first: Shuai

last: Li

first: Jinzhu

last: Yin

first: Xiaoyu

last: He

first: Ru

last: Wang

first: Yang

last: Liu

first: Huifang

last: Zhang


title: Multi-Omics Analysis Reveals Nono-Kcnq2 Regulation of Neuronal Excitability in Neuropathic Pain [scRNA-Seq]

first: 鹏

address: 贵州省贵阳市花溪区大学城栋青南路

type: Expression profiling by high throughput sequencing

overall_design: In this study, we employed an integrated multi-omics approach to identify a novel Nono–KCNQ2 regulatory axis that underpins pain progression in chronic constriction injury (CCI) models. Proteomic analysis revealed a marked reduction in potassium ion channel protein expression accompanied by aberrant glutamatergic neuron activation during neuropathic pain progression. Additionally, phosphoproteomic profiling demonstrated that impaired phosphorylation of these channels—most notably KCNQ2—reduces ion permeability and promotes neuronal hyperexcitability. catTFRE analysis further indicated that diminished Nono transcription factor activity is associated with the downregulation of potassium ion channels in CCI rats. Moreover, single-cell RNA sequencing and spatial transcriptomics localized the co-expression of Nono and Kcnq2 to specific neuronal populations, namely Prph⁺ ventral horn and Nrxn3⁺ dorsal horn neurons, findings that were corroborated by immunofluorescence assays. Critically, CCI-induced Nono dysfunction within these subpopulations precipitates deficits in KCNQ2 signaling, ultimately leading to glutamatergic overactivation and enhanced pain sensitivity. Collectively, our findings underscore the pivotal role of ion channel transcriptional regulation in pain chronification and suggest that targeted modulation of Nono, coupled with pharmacological activation of KCNQ2, may represent a promising therapeutic strategy for neuropathic pain.

first: Peng

last: Chen


title: FTO-Mediated m6A Demethylation Regulates PGC-1α-Dependent Mitochondrial Biogenesis to Attenuate Aluminum-Induced Neuronal Senescence [RNA-Seq]


title: HuR coordinates systemic aging through platelet infiltration.

city: Beijing

first: liu

last: cihang

address: Xueyuan Road

institute: Peking University Health Science Center

summary: Aging involves morphological and functional changes across different organs, but how these changes are linked among the different organs remains to be elucidated. Here, we uncover a central role of platelets in systemic aging. In aged mice, the levels of platelet-secreted pro-inflammatory factors (PSPF) increased greatly in the serum and platelets, leading to a diffuse increase of platelet infiltration in brain, liver, lung, kidney, and aortic root. The RNA-binding protein HuR/ELAVL1, a major regulator of RNA metabolism, promoted the production of PSPF in platelets. Platelet-specific deletion of HuR reduced the expression of PSPF in platelets, alleviated platelet infiltration in brain, liver, lung, kidney, and aortic root, and delayed systemic aging. By using single-nucleus sequencing, platelet-specific HuR ablation was found to alleviate p53 and pro-inflammatory signaling pathways in liver, lung, and brain tissues in aged mice. Our findings highlight a role of platelets in coordinating aging traits across organs.

overall_design: To investigate the function of platelet HuR in systemic aging, we generated a conditional platelet-specific HuR knockout (cKO) mouse. RNA was extracted from  the platelets in male HuR cKO and their wild-type (WT) littermates at three month, as well as the platelets in Young (3 month-old) male mice and Old (24 month-old) male mice, respectively. Owing to the low RNA yield from platelets, platelets from 7 mice per group were pooled for RNA-seq analysis. We then performed gene expression profiling analysis using data obtained from RNA-seq of WT and cKO mice, as well as Young and Old mice. Comparative gene expression profiling analysis of RNA-seq data  for cKO mice and its WT littermates, as well as Young and Old.

first: Cihang

first: Ying

first: Tianjiao

last: Xia

first: Jing

last: Lin


title: eIF5A coordinates the transcription and translation of its target genes

city: Valencia

first: Jordi

last: Planells

state: Valencia

address: Doctor Moliner, 50 street

department: Biologia celular, biologia funcional y antropologia fisica

country: Spain

institute: Universitat de València

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Maintaining balanced cellular protein levels requires precise control of gene expression and effective coordination between the various stages of the process, from transcription to translation. In recent years, several components of the translation apparatus have been found in the nuclei of various eukaryotes, where they regulate transcription, mRNA processing or export, thereby integrating different stages of gene expression. eIF5A is an essential and evolutionarily conserved translation elongation factor, that is involved in viral infection and the development of diseases such as cancer and neurodevelopmental disorders. eIF5A promotes translation elongation by binding to ribosomes that stall at codons encoding problematic amino acids for peptide bond formation, such as consecutive prolines, also known as polyproline motifs. Although eIF5A shuttles between the nucleus and cytoplasm, its specific nuclear roles remain poorly defined. Here, we demonstrate that nuclear yeast eIF5A binds to chromatin and represses gene transcription by preventing the binding of RNA polymerase II. Chromatin binding and transcriptional repression by eIF5A has a major impact on genes encoding its own translational targets. The presence of polyproline motifs in genes imposes the translation and transcriptional control by eIF5A. Furthermore, eIF5A's active engagement in cytoplasmic translation is necessary for its repression of transcription. Our results suggest that eIF5A coordinates gene expression by promoting the cytoplasmic translation of specific genes while repressing their transcription in the nucleus, thus ensuring efficient final protein synthesis.

overall_design: ChIP-seq of eIF5 in WT BY4741 yeast cells

first: Barba-Aliga

last: Marina

first: Lianqi

last: Chi

first: Planells

last: Jordi

first: García-Martínez

last: José

first: Pérez-Ortín

last: José E.

first: Alepuz

last: Paula


title: Human induced pluripotent stem cell-derived skin organoids recapitulate donor-specific pigmentation diversity

city: Boston

first: Karl

middle: Russell

last: Koehler

state: MA

address: 3 Blackfan Circle

department: Otolaryngology-Head and Neck Surgery

country: USA

institute: Boston Children's Hospital-Harvard Medical School

summary: Skin and hair pigmentation vary widely across individuals, but the underlying mechanisms responsible for these differences remain poorly understood. To address this, we employ a recently developed skin organoid (SkO) culture system that bioengineers nearly complete skin, including hair follicles and pigmentation, from human pluripotent stem cells. In this study, we generate SkOs from a panel of iPSC lines derived from donors with varying skin tones – light- and dark-pigmented. By modulating TGFβ, BMP4, and FGF signaling pathways during early differentiation, followed by 4–5 months in floating culture, we generated SkOs. Through immunostaining and transmission electron microscopy, we observed distinct pigmentation patterns and differences in melanin production in both the skin and hair follicles of organoids derived from different donor lines. We further perform single-cell RNA sequencing to uncover gene expression profiles associated with these pigmentation differences. This work provides insights into the cellular and molecular bases of human pigment variation and highlights the SkO model as a powerful tool for studying individual differences in skin biology and development.

overall_design: Light- and dark-pigmented skin organoids (SkO) at day 130 for scRNA-seq using the Chromium Single Cell 3’ system (10x Genomics)

first: Karl R.

first: Jin

last: Kim

first: Jiyoon

last: Lee


title: Discovery of Translation Regulatory Features and Cross-UTR Interactions through Precise Mapping of mRNA Ends and Machine Learning

city: Rehovot

first: Ariel

last: Ogran

address: 234 Herzl Street

department: Bimolecular Sciences

country: Israel

institute: Weizmann Institute of Science

summary: Cis-regulatory elements within 5′ and 3′ untranslated regions (UTRs) are critical for controlling mRNA translation efficiency (TE) and stability, but their coordinated functions remain poorly understood due to their complexity and variability. Here, we combined polysome profiling and mRNA decay measurements with TIF-seq2 to determine TE and half-lives of transcript isoforms (TIFs) with precisely defined 5′ and 3′ ends. We extracted regulatory features, positional k-mers, secondary structure characteristics, and TE measurements to build a multifaceted input for machine learning (ML) modeling. The resulting models demonstrated strong predictive power and revealed several unexpected findings. Specifically, 3′UTR regulatory features had a greater influence on TE than 5′UTRs, and negative regulatory features are more prevalent than positive ones for both translation and stability. We identified novel regulatory motifs in both UTRs, some with positional bias. Interestingly, AU-rich sequences in the 3’UTR, including the polyA signal, were identified and validated as translation enhancers. Finally, we found a crosstalk between 5’ and 3’ UTR through specific regulatory hubs. Together, these findings expand the understanding of translation regulation and suggest that UTR regulatory features evolve primarily to fine-tune inherently robust translation machinery for balanced protein expression.

overall_design: TIF-seq2 profiling was performed on primary mouse myoblasts cultured and differentiated into myotubes in vitro. Following differentiation, cells underwent polysome profiling and mRNA decay assays after treatment with actinomycin D for 0, 3, 6, and 12 hours.

first: Joseph

last: Green

first: Daniel

last: Hayat

first: Sansrity

last: Sinha

first: Ori

last: avinoam

first: Ido

last: Azuri

first: Rivka

last: Dikstein


title: Sleeping Beauty mutagenesis identifies BACH2 and other regulators promoting CD8+ T cell persistence and effector function under tumor-associated chronic antigen stimulation - esTAG

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

summary: ● Background: Genes that enhance T cell function could represent promising targets for improving engineered T cell therapies for cancer. While extensive CRISPR knockout screens have identified key genes that enhance T cell persistence, employing Sleeping Beauty (SB) insertional mutagenesis, which induces both gain- (GOF) and loss-of-function (LOF) mutations via the generation of fusion transcripts with endogenous genes, may uncover additional critical factors that previous approaches have overlooked. ● Methods: We developed transgenic mouse models carrying Doxycycline (Dox)-inducible SB engineered system (DiSBey) in primary T cells. Using DiSBey, we conducted screens to identify genes that enhance T cell persistence under chronic antigen exposure. Specifically, CD8⁺ T cells from Dox-fed DiSBey mice were subjected to repeated anti-CD3 stimulation over 18 days to mimic chronic antigenic stimulation. We then identified SB transposon genomic insertion sites and corresponding fusion transcripts from the persistent DiSBey CD8⁺ T cells using enhanced-specificity tagmentation sequencing (esTag-seq) and RNA-seq, respectively. ● Results: Under chronic stimulation, SB-mutagenized CD8⁺ T cells exhibited improved persistence and reduced terminal exhaustion phenotype. Across six independent screens, we identified 38 genes that were recurrently targeted by the SB transposon T2/Onc2 and differentially expressed under chronic anti-CD3 stimulation stress. Among these, T2/Onc2 insertions into Bach2 and Elmo1 were repeatedly found at the genomic level and were associated with altered nascent transcript expression. Bach2, previously recognized as a key regulator of T cell memory formation and resistance to chronic viral infection but less characterized in engineered T cells for cancer therapy, was found to enhance in vivo persistence in the B16-Ova tumor model. We further demonstrated that ectopic Bach2 expression levels influence engineered T cell differentiation lineage. A Bach2low signature allowed differentiation into both KLRG1⁺ and CD62L⁺ phenotypes, whereas Bach2high restricted differentiation predominantly to the CD62L⁺ subset. Finally, in human CART19-28ζ cells, BACH2 overexpression enhanced cytotoxicity and improved tumor control following chronic cancer stimulation in vivo. ● Conclusions: Controllable SB mutagenesis using DiSBey mice provides a novel platform for functional screening of genes that improve T cell therapeutic phenotypes. Our findings highlight a dose-dependent role of BACH2 in enhancing the function of engineered T cells under conditions of chronic antigenic stimulation.

overall_design: 2x2 Factorial Design using genotype and treatment. Genotype conditions: Wild type mouse T Cells and DiSBey T Cells undergoing T Cell mutagenesis Treatment conditions: Acute stimulation and Chronic stimulation (including 5 µg/ml anti-CD3ε). Input are samples before treatment was applied. Day: Samples were exposed to treatment and sampled at regular intervals.

first: Chang-Jung

first: Tyler

middle: A

last: Jubenville

first: David

last: Largaespada


title: Sleeping Beauty mutagenesis identifies BACH2 and other regulators promoting CD8+ T cell persistence and effector function under tumor-associated chronic antigen stimulation - RNAseq


title: Two evolutionarily conserved fatty acid desaturases control the production of omega-3 fatty acids and bioactive jasmonates in Marchantia polymorpha

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

institute: Centro Nacinal de Biotecnologia-CSIC

summary: In the model bryophyte Marchantia polymorpha, omega-3 (n3) polyunsaturated fatty acids (n3-PUFAs) and long-chain n3-PUFAs (n3-LCPUFAs) serve as precursors for bioactive jasmonates. However, how omega-3 fatty acid desaturases (n3-FADs) contribute to the production of n3-PUFAs and jasmonates remain unexplored. Here, we study the n3-FAD-dependent jasmonate signaling in the liverwort M. polymorpha. We found that MpFAD3, localized to the endoplasmic reticulum, prefers omega-6 (n6) arachidonic acid (ARA, 20:4n6) as the substrate thus controlling the biosynthesis of n3-LCPUFA derived jasmonates. Conversely, MpFAD7, found in the chloroplast, takes hexadecadienoic acid (HDA, 16:2n6) and linoleic acid (LA, 18:2n6) as substrates more efficiently and regulates the production of n3-PUFA derived jasmonates. Certain promiscuity was observed for these enzymes as evidenced by increased n6-(LC)PUFA levels in the doble Mpfad3fad7 mutant compared to single mutant lines individually. Mpfad7 and Mpfad3fad7 plants were more resistant to Fusarium oxysporum infection compared to wildtype control, suggesting a prominent role for n3-PUFA derived jasmonates in regulating defenses against necrotrophic pathogens. Remarkably, despite the lack of jasmonate-dependent anti-herbivore defenses in Mpfad3fad7 plants, Spodoptera exigua caterpillars performed equally badly on this double mutant and on wildtype plants, which states the dietary importance of essential n3-(LC)PUFAs for the caterpillar. Our results suggest that two conserved but specialized n3-FADs control n3-(LC)PUFA and jasmonate biosynthesis in Marchantia, and that food quality, namely the type and ratio of n3-(LC)PUFAs, contributes to insect performance in addition to jasmonate-dependent plant defenses.

overall_design: 3 replicates for mock and wound-treated samples, Tak-1 and Mpfad3fad7 double mutant

first: Guillermo

middle: H

last: Jimenez-Aleman

first: Santiago

last: Michavila

first: Gonzalo

last: Soriano

first: Sophie

last: Kneeshaw

first: Coral

last: Barbas

first: Maria

middle: F

last: Rey-Stolle

first: Angel

middle: M

last: Zamarreño

first: Jose

last: Garcıa-Mina

first: Selena

last: Gimenez-Ibañez

first: Francisco

last: Medina-Paz

first: Roberto

last: Solano


title: eIF5A depletion effect on synthesis and decay rates of yeast genes

city: Burjassot

middle: E.

last: Perez-Ortin

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary: Maintaining balanced protein levels requires precise control of gene expression and efficient coordination between the different stages of the process, from transcription to translation. In recent years, several components of the translational apparatus have been found in the nuclei of various eukaryotes, where they regulate transcription, processing or mRNA export, thus integrating different stages of gene expression. eIF5A is an essential and evolutionarily conserved translation elongation factor, which is involved in viral infection and in the development of diseases such as cancer and neurodevelopmental disorders. eIF5A promotes translation elongation by binding to ribosomes that stop at codons encoding amino acids problematic for peptide bond formation, such as consecutive prolines, also known as polyproline motifs. Although eIF5A shuttles between the nucleus and the cytoplasm, its specific nuclear functions remain poorly defined. In this work we demonstrate that nuclear eIF5A from the yeast Saccharomyces cerevisiae binds to chromatin and represses gene transcription by preventing the binding of RNA polymerase II. Chromatin binding and transcriptional repression by eIF5A have a major impact on genes encoding their own translational targets. Thus, the presence of polyproline motifs in the genes imposes translational and transcriptional control by eIF5A. In addition, the active engagement of eIF5A in cytoplasmic translation is required for its repression of transcription. Our results suggest that eIF5A coordinates gene expression by promoting cytoplasmic translation of specific genes while repressing their transcription in the nucleus, thus ensuring efficient final protein synthesis.

overall_design: We quantified the mRNA abundance (RA) and synthesis rate (SR) for all genes of the two yeast strains at log phase and at two different growth temperatures (25ºC/37ºC) using the GRO method (Garcia-Martinez Mol Cell 2004; Pérez-Ortín J Mol Biol 2013). Cells were grown at 37ºC for 4 hours and samples grown at 25ºC were used as control. The tif51A-1 mutant strain has a temperature sensitive eIF5A allele that is inactivated upon change to 37ºC. The wt strain (BY4741) was used as a control.

first: Marina

last: Barba-Aliaga

first: José

last: García-Martínez

middle: E

last: Pérez-Ortín

first: Paula

last: Alepuz


title: Sea nettle jellyfish venom targets proteoglycans to cause cell death and pain

city: Camperdown

first: G.

middle: Greg

last: Neely

state: NSW

address: Charles Perkins Centre, D17.

country: Australia

institute: University of Sydney

summary: Sea nettle jellyfish cause millions of painful stings annually with little known about how their venom works and no rational treatments available. Here we perform a systematic analysis of sea nettle venom / host interactions. The venom shows dose-dependent cytotoxic activity in human cells and this can be blocked by dual inhibition of apoptosis and necroptosis. Using whole-genome CRISPR screening we identified human genes and pathways that modify venom action. The top gene cluster identified regulates proteoglycan biosynthesis. We show exogenous heparin, a drug used clinically as an anticoagulant, blocks venom cytotoxicity at a physiologically relevant dose. This effect was therapeutic, inhibiting venom even one hour after exposure. Importantly, in vivo, heparin protected against acute spontaneous pain, thermal hyperalgesia, and mechanical allodynia induced by venom. This provides the exciting possibility of repurposing heparin, a safe, commercially available drug as a prophylactic or therapeutic to reduce the impact of sea nettle stings.

overall_design: Whole-genome pooled CRISPR knockout screen using Toronto KnockOut Library v3 (TKOv3) on HAP1 cells treated with venom from Chrysaora quinquecirrha (Atlantic sea nettle). Genomic DNA was extracted from cells from treated and control conditions, and the sgRNA-containing integrated sequences were amplified by PCR and sequenced by short-read Illumina sequencing.

first: Christopher

last: Denes

first: Felicity

last: Chung

first: Graham

middle: G


title: Chromatin rewiring of β-globin and MYC enhancers by TGF-β1 drives defective erythropoiesis

city: Bronx

first: Kith

last: Pradhan

state: ny

address: 1300 Morris Park Ave

institute: Einstein College of Medicine

summary: Erythropoiesis is a tightly regulated process involving rapid cell proliferation with orderly differentiation to ensure production of millions of RBCs. TGF-β1 is a key regulator of erythropoiesis, however, the mechanisms via which it regulates erythropoiesis are not well elucidated. Using myelodysplastic syndromes patient samples, we show that elevated TGF-β1 and SMAD2 signaling correlates with the degree of anemia. Functional studies in primary human HSPCs demonstrate that TGF-β1 exerts a bifurcated effect — suppressing proliferation and inducing premature erythroid differentiation — both of which are rescued by clinical-stage TGFBR1 inhibitor. Through integrative RNA-seq, ChIP-seq, and Micro-C analyses, we found TGF-β1 activates the β-globin LCR, driving early differentiation, while concurrently disrupting the MYC enhancer–promoter interaction to block proliferation. We validated our erythropoiesis defect in vivo by performing single-cell RNA-seq in a TGF-β1 transgenic mouse. Our findings show that TGF-β1/SMAD2 signaling re-wire chromatin to regulate erythropoiesis by affecting β-LCR and MYC super enhancer regions.

overall_design: A total of 25 million cells were treated with TGF-β1. After a 2-hour treatment, the cells were pelleted at 350 x g for 15 minutes at 4°C. They were then washed once with ice-cold PBS. The following steps were followed using the Diagenode HighCell ChIP Kit (Cat# C01010060), according to the manufacturer's protocol.

first: Srinivas

last: Aluri

first: Amit

last: Verma


title: Lateral plate mesoderm directs human amnion and ventral skin organoid formation

first: Karl

last: Koehler

summary: Recently, we demonstrated that craniofacial skin, including dermis, epidermis, and hair, can be derived by manipulating signaling factors to co-induce epidermal-dermal progenitors. Here, we advance this approach by controlling the size and composition of cranial skin organoids (cSkOs) and incorporating lateral plate mesoderm (LPM) cells to create ventral skin organoids (vSkOs) and human amnion-like structures, termed Amnioids. Amnioids, resembling their extra-embryonic counterparts, are avascular and rapidly expand into large, hairless cysts, while vSkOs develop primitive vasculature and numerous hair follicles. Single-cell RNA sequencing identified distinct gene expression patterns and developmental trajectories, revealing the critical roles of Wnt and YAP/Hippo signaling in directing divergent fates. Functional experiments underscored the importance of mechanical forces and mesenchymal-epithelial interactions in shaping tissue growth and organization. This study presents a novel in vitro model to explore the interface of embryonic and extraembryonic tissues, with implications for understanding congenital disorders and advancing regenerative medicine.

overall_design: LPM, amnioid and cranial skin organoids (cSKO) at day 6, day 28, and day 104 as well as ventral skin organoids (vSKO) at day 128 using scRNA-seq

first: Koehler

last: Karl R.

first: Le

last: Anh Phuong


title: USAG-1 aggravates renal ischemia‒reperfusion injury via promoting GPX4 degradation‒induced ferroptosis

city: Zhengzhou

first: Xiaohu

last: Li

state: Henan

address: 1 Jianshe E Rd, Erqi District

department: Department of Kidney Transplantation

institute: The First Affiliated Hospital of Zhengzhou University

summary: We generated the HK2 celllines overexpressing USAG-1 (referred as to USAG-1_OE), and performed transcriptome sequencing to identify the differentially expressed genes compared to the control cell line (referred as to CON).

overall_design: Total RNA was extracted from HK2  cells with TRIzol reagent. The RNA purity and integrity were analyzed with the Agilent Bioanalyzer 2100 (Agilent). The mRNA was purified from total RNA after removal of rRNA and sequenced on an Illumina Hiseq2500 system


title: Single-cell gene expression profiles of cells from primary colorectal cancer and adjacent normal tissue [scRNA-Seq]

city: shanghai

first: He

last: Qian

address: No. 600 Yishan Road,  Shanghai, PRC, 200233.

institute: Shanghai Jiao Tong University

summary: Colorectal cancer (CRC) is the third malignancy worldwide. RAS mutant CRC has a worse prognosis and resistant to immune therapies. Current research on the tumor microenvironment of RAS-mutant CRC remains limited, with few studies systematically characterizing its cellular composition or functional dynamics. A total of 36 clinical surgical samples (tumors and paired adjacent normal tissues) from 18 patients with primary CRC were collected for single-cell transcriptome sequencing.At the same time, each patient underwent genome sequencing, and 18 patients were divided into RAS gene mutation group (n=10) and wild-type group (n=8). Therefore, revealing the functional cell types and mechanism of immune evasion in RAS mutant CRC by scRNA-seq may contribute to discover new therapeutic targets.

overall_design: 36 samples (tumor and adjacent normal tissue)  were subjected to 3' end single-cell RNA sequencing (scRNA-seq) using the 10× Genomics Chromium platform.

first: Qian

last: He

first: Zhigang

last: Wang


title: Charting Postnatal Heart Development Using In Vivo Single-Cell Functional Genomic [snRNA-Seq]

city: Chapel Hill

first: LI

last: QIAN

address: 111 Mason Farm Road, MBRB

department: Department of pathology

institute: UNC

summary: The transition at birth, marked by increased circulatory demands and rapid growth, necessitates extensive remodeling of the heart’s structure, function, and metabolism. This transformation requires precise spatial and temporal coordination among diverse cardiac cell types; central to this process is cardiomyocyte maturation, yet the regulatory mechanisms driving these changes remain poorly understood. Here, we present a temporal and spatial atlas of postnatal hearts by integrating single-nucleus transcriptomics with image-based spatial transcriptomics, which uncovers the dynamic regulatory networks of cardiomyocyte maturation. To functionally interrogate candidate regulators in vivo, we developed Probe-based Indel-detectable Perturb-seq, a high- throughput platform that uses probe-based chemistry to directly capture sgRNA expression, perturbation status, and transcriptomic profiles at single-nucleus resolution. Applying PIP-seq to postnatal cardiac development identified 21 novel regulators of cardiomyocyte maturation, highlighting critical nodal points in this process. Our study establishes a high-resolution framework for dissecting postnatal heart development, underscoring the integrative and highly ordered roles of microenvironment and intercellular communication in cardiomyocyte maturation. Importantly, PIP-seq enables systematic, high-throughput exploration of gene function and networks underlying complex biological processes in their native in vivo context.

overall_design: snRNA-seq:Nuclei from the postnatal hearts were harvested from mice at postnatal day 0 (p0, 2 replicates), day 7 (p7, 2 replicates), day 14 (p14, 2 replicates), and day 21 (p21, 2 replicates), respectively. 3'snRNA-seq library were prepared strictly following the manufacturer’s manual (Chromium Single Cell 3' Reagent Kits User Guide, CG000315).

first: Haofei

first: Yanhan

last: Dong

first: Marazzano

last: Colón

first: Gregory

last: Farber

first: Li

first: Jiandong

last: Liu


title: A transcriptomic atlas of immune cell populations in glaucomatous mouse retina and optic nerve

first: Milica

last: Margeta

address: 20 Staniford Street

department: Ophthalmology

institute: Mass Eye and Ear

summary: Immune cells play a critical role in pathogenesis of glaucoma. However, their ontogeny, gene expression profiles, spatial distribution, and functional changes in the retina and optic nerve in glaucoma remain poorly understood. We performed single-cell RNA sequencing to investigate the changes in immune cell populations in the microbead mouse model of glaucoma. 28,277 immune cells were successfully sequenced from microbead- and sham-injected retinas and optic nerves, identifying many different immune cell subsets.

overall_design: CD45+ immune cells isolated using flow cytometry and sequenced using 10X Genomics (n = 3-4 samples per group, each sample pooled from 8-10 eyes).

first: Zhuoran

last: Yin

first: James

last: Harris

first: Paul

last: Cullen

first: Dario

last: Tommasini

first: Ryan (Yixi)

last: Xue

first: Anthony

last: Mukwaya

first: George

last: Baldwin

first: Nasir

last: Uddin

first: Sandro

last: Da Mesquite

first: Karthik

last: Shekhar


title: Charting Postnatal Heart Development Using In Vivo Single-Cell Functional Genomic [PIP-Seq]

first: LI

overall_design: PIP-seq: AAV9 library carrying sgRNAs was injected into neonatal mice with Cas9 expression casette at a dosage of 4 x 1010 virus particles per pup at postnatal day 0. Hearts were harvested on postnatal day 14 and nuclei were extracted to generate library using 10X Chromium Fixed RNA Profiling Reagent Kits for Singleplexed Samples (CG000691).

first: Haofei

last: Wang

first: Yiran

last: Song

last: Qian


title: Spatial transcriptome profile of liver tissue from a patient with metabolic dysfunction-associated steatotic liver disease

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) causes progressive liver fibrosis and hepatocellular carcinoma (HCC). By using archived fixed surgical liver tissue affected with MASLD, we performed Visium Spatial Transcriptome profiling to study spatially-resolved moelcular dysregulatons associated with the clinical phenotypes of the disease and mechanisms of liver fibrogenesis and carcinogenesis.

overall_design: Surgically resected liver tissue from a patient with metabolic dysfunction-associated steatotic liver disease was used to prepare formalin-fixed paraffin-embedded tissue block and used for Visium spatial transcriptome profiling.

first: Hiroaki

last: Kanzaki

first: Soumith

last: Paritala

first: Naoto

last: Kubota

last: Fujiwara


title: miRNA expression profiling in SI epithelium-exosomes and serum-exosomes in young and aged mice

city: Nanjing

first: yunlu

last: Sheng

address: 300 Guangzhou Road

institute: the First Affiliated Hospital of Nanjing Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: To better understand the impact of aging on exosomal miRNAs of small intestinal epithelium and serum.

overall_design: SI epithelial and  circulating exosomes were both isolated from young and aged mice, then the exosome-containing miRNAs were extracted and analyzed synchronously by deep RNA sequencing.

first: Yunlu

first: Yijun

last: He

first: Guoxian

last: Ding


title: Premature senescence impairs hematopoietic stem cell function during sickle cell disease in mice and humans

city: Memphis

first: Shannon

last: McKinney-Freeman

state: TN

address: 262 Danny Thomas Pl

department: Experimental Hematology

institute: St. Jude Children's Research Hospital

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Premature senescence impairs hematopoietic stem cell function during sickle cell disease in mice and humans (Mouse Bulk RNA-Seq)

summary: Curative therapies using autologous genetically modified hematopoietic stem and progenitor cells (HSPCs) are now FDA-approved for sickle cell disease (SCD). However, there are concerns that the pathophysiology of SCD may degrade the quality of HSPCs required for these cellular therapies. We interrogated the phenotype and function of HSPCs in mice and individuals with SCD. We observed elevated cycling, DNA damage, reactive oxygen species, and hallmarks of senescence in bone marrow HSPCs from SCD mice, which correlated with a loss of long-term repopulating HSPCs. Bone marrow HSPCs from individuals with SCD also display hallmarks of senescence and diminished function. Transcriptomic profiling of mouse and human HSPCs revealed reduced expression of genes regulating cell cycle, DNA replication, and DNA repair, consistent with senescence. Treatment of SCD mice with the senolytic, ABT-263 (Navitoclax), increased HSPC frequency, restored HSPC transplantation activity, and decreased numbers of HSPCs with DNA damage. Thus, we demonstrate that stress-associated loss of function in the bone marrow of mice and individuals with SCD is reversible with senolytic therapy. Our work suggests a strategy for improving the function and fidelity of HSPCs collected for autologous gene therapy, which could further improve the efficacy and safety of these curative therapies.

overall_design: Bulk RNA-Seq of long-Term HSCs (LT-HSCs) sorted from mouse bone marrow from animals with or without sickle-cell disease in the Townes model mouse at 6 months of age.

first: Aditya

last: Barve

first: Adam

middle: B

last: Cornwell

first: Preeti

last: Dabas

first: Pramika

last: Sriram

first: Emilia

last: Kooienga

first: Zakiya

last: Kelley

first: Alex

last: Kopyov

first: James

last: Johnson

first: Jacquelyn

last: Myers

first: Esther

last: Obeng

first: Guolian

last: Kang

first: Yunus

last: Olufadi

first: Terri

last: Cain

first: Lindsay

last: Talbot

first: David

last: Spence

first: Mauricio

last: Cortez

first: Sam

last: Miller

first: Akshay

last: Sharma


title: Regulation of intracellular heme by FLVCR2 modulates retinal angiogenesis

city: Rancagua

first: Nicolas

last: Santander

address: Libertador Bernardo O'Higgins 611

country: Chile

institute: Universidad de O´Higgins

summary: Fowler syndrome is an embryonic lethal disease with proliferative vasculopathy and hydranencephaly-hydrocephaly of the central nervous system due to mutations in Feline Leukemia Virus Subgroup C Receptor-Related Protein 2 (FLVCR2) characterized by large regions of hypovascularization along with glomeruloid formation of poorly organized vascular endothelial cell mass. Recent animal models have characterized reduced vascularization in brain in gene deletion models of Flvcr2. Here, we use conditional knockout of Flvcr2 in mice and knockdown in cell culture to explore retinal development and further understand the mechanism of angiogenic regulation by Flvcr2. Gene deletion of Flvcr2 or chemical inhibition of heme synthesis led to reduced retinal vascular expansion and reduced formation of deep capillary plexus with a partial penetrance of a severe phenotype with dramatic reduction in vascular expansion and glomeruloid and endothelial mass formation. Cell culture studies reveal reduced heme content in cells with Flvcr2 knockdown associated with increased stalk cell specification and hyperproliferation that could be reversed with addition of heme precursor. These effects could be recapitulated with chemical inhibition of heme synthesis and reversed with soluble hemin addition. Overexpression of Flvcr2 or addition of soluble hemin prevented VEGF induced proliferation without affecting receptor activation. Collectively, the data indicate a newly identified role for heme in the regulation of tip/stalk specification and vascular angiogenesis.

overall_design: We obtained total RNA from bovine retinal endothelial cells treated with succinylacetone or an siRNA against FLVCR2, with their respective controls. We sequenced poliA+ RNA.

first: Andreia

last: Goncalves

last: Antonetti

first: Thomas

last: Arnold


title: Mindbomb1 is a Novel Negative Regulator of BMP Signaling

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.


title: Premature senescence impairs hematopoietic stem cell function during sickle cell disease in mice and humans (Human Bulk RNA-Seq)

first: Shannon

last: McKinney-Freeman

overall_design: Human bone marrow HSPCs (CD45+Lineage-CD34+CD38-) were sorted by FACS from cryopreserved SCD and non-SCD patient bone marrow samples and prepared for bulk RNA-Sequencing.

first: Aditya

last: Barve

first: Adam

last: Cornwell

first: Preeti

last: Dabas

first: Pramika

last: Sriram

first: Emilia

last: Kooienga

first: Zakiya

last: Kelley

last: Kopyov


title: Premature senescence impairs hematopoietic stem cell function during sickle cell disease in mice and humans (Mouse CITE-Seq)

overall_design: SCD and non-SCD mouse bone marrow samples from 2- and 6-month old animals (n = 4 biological replicates per condition) were enriched for c-Kit+ cells (i.e. total HSPCs) via magnetic enrichment using anti-CD117 microbeads. c-Kit-enriched samples were prepared for CITE-seq with a panel of seven Totalseq-A antibodies. Single-cell capture was performed with the 10x Genomics 3’ v3 platform and sequenced on an Illumina Novaseq 6000. CITE-Seq staining and 10x cell capture were performed for all 2-month animals in one batch, and all 6-month animals in another. Sequencing for each library type was performed with all samples together.

first: Alex

first: James

last: Johnson

first: Jacquelyn

last: Myers

first: Esther

last: Obeng

first: Guolian

last: Kang

first: Yunus

last: Olufadi

first: Terri

last: Cain

last: Talbot

last: Spence


title: Mindbomb1 is a Novel Negative Regulator of BMP Signaling (H838: MIB1 iKO, +BMP4, -/+ BMP inhibitor)

last: Piskol

summary: The effects of MIB1 loss or BMP4 exposure are all negated by LDN193189, an inhibitor of type 1 BMP receptors, which suggests MIB1 functions as a novel negative regulator of the BMP pathway

overall_design: The BMP pathway was inhibited with LDN193189 (LDN) in the presence or absence of MIB1 and then reactivated by washing out the inhibitor for a period of time after which RNA was collected.

first: Charisa

middle: L

last: Cottonham

first: Gloria

last: Hernandez

first: Christian

middle: W

last: Siebel


title: NeuroD1-based in situ neural regeneration for the treatment of radiation-induced brain injury

city: Guangzhou

first: Yamei

last: Tang

state: Guangdong

address: 107 Yan Jiang West Road

department: Department of Neurology

institute: Sun Yat-Sen Memorial Hospital

summary: We aimed to study the therapeutic effects of in situ neural regeneration technology in radiation-induced brain injury (RIBI). We overexpressed the neural transcription factor NeuroD1 in the astrocytes of the injured area using an adeno-associated virus (AAV) in a RIBI mouse model. The therapeutic effects were compared with a RIBI mouse model treated with a control virus. Subsequently, we explored the therapeutic effect in transcriptome through a bulk RNA sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RC: Radiation+Control (RA+Ctrl), RN: Radiation+NeuroD1 (RA+ND1)

first: Xudong

last: Yan

first: Ke

last: Zhong

first: Yajie

last: Sun

first: Meijuan

last: Zhou

first: Gong

last: Chen

first: Yongteng

last: Xu


title: Expansion of cytotoxic CD4 T-cell clusters in lymph nodes of patients with Common Variable Immunodeficiency

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

summary:
Background:
Patients with common variable immunodeficiency (CVID) suffer from hypogammaglobulinemia due to an inadequate differentiation of long-lived humoral immunity in germinal centers (GC).
Objective:
To further characterize the transcriptome and phenotype of T follicular helper (TFH) cells as key players in the GC reaction of CVID patients.
Methods:
Sorted TFH cells from CVID lymph nodes and healthy control tonsils were analyzed by bulk-RNA-sequencing. Altered protein expression was verified by flow cytometry and CyTOF analysis. Tissue localization of cells was determined by multi-fluorescence imaging.
Results:
Transcriptome analysis of sorted TFH cells revealed an enrichment of cytotoxicity-associated gene sets in CVID patients. Extended immune phenotyping identified different cytotoxic CD4 memory populations expressing T-bet, EOMES, CRTAM, Perforin, and Granzyme A and B. Two clusters co- expressing markers of TFH differentiation such as CXCR5, ICOS, and PD1 were expanded in CVID lymph nodes. One of them additionally expressed high levels of FoxP3. Histological sections confirmed the increase in Granzyme-B+EOMES+ CD4 cells in GCs of patients’ lymph nodes. Only few of these cells circulate in peripheral blood.
Discussion:
Our study reports for the first time that the previously reported type 1 polarization in lymph nodes of CVID patients is associated with an expansion of two distinct cytotoxic CD4 TFH cell clusters within GCs which were very rare in peripheral blood. Further investigations directly in secondary tissues are required to explore their role in the GC failure in CVID.

first: Melanie

last: Boerries

first: Kathryn

middle: J

last: Payne

first: David

last: Friedmann

first: Klaus

last: Warnatz


title: Transcription profiles of tomato+ and tomato- platelets

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

summary: Tomato+ and tomato- platelets in the transgenic mouse strain were generated by ML-HSC and P-HSC through distinct pathways. To determine if these two subsets of platelets present different molecular profiles, we examined the transriptomes of tomato+ and tomato- peripheral platelets from adult (10 weeks old) mouse

overall_design: Tomato+ and tomato- platelet subsets from adult mouse peripheral blood were FACS sorted. Total RNA was isolated to construct libraries for bulk RNA-seq. Differentially expressed gene analysis was performed to compare tomato+ and tomato- platelet subsets.

first: Yiran

last: Meng


title: SUMO E3 Ligase SIZ1-mediated SUMOylation of LBD29 positively regulates lateral root formation in Arabidopsis thaliana

city: Qingdao

first: Qianlan

last: Yin

state: Shandong

address: 72 Coastal Highway

department: College of Life Science

institute: Shandong University

summary: Roots are very important at different stages of plant growth, and the formation of lateral roots is essential for strengthening the roots and absorbing nutrients from the soil. Therefore, it is of great significance to uncover the molecular mechanism of lateral root development in plants for understanding plant life process and improving plant adaptation to environment. As an important post-translational modification of small protein types, small ubiquitin-like modifier is involved in many biological processes such as transcriptional regulation, cell cycle regulation, and immune response. SUMO E3 ligase plays a key role in the SUMO process and plays an important role in plant growth and development. In Arabidopsis thaliana, SIZ1 encodes a SUMO E3 ligase, which plays an important role in plant life, especially in stress response. We analyzed the expression sites of SIZ1 and found that it was obviously expressed in lateral roots, especially in the nucleus of lateral roots. Previous studies on SIZ1 mainly focused on biological stress and abiotic stress, but the molecular mechanism of SIZ1 regulating lateral roots has not been studied. We propose a mechanism by which hemicylation of LBD29 mediated by SIZ1 regulates the occurrence of lateral roots in Arabidopsis Thaliana, which provides a new idea and direction for subsequent research on lateral root development.

overall_design: In order to study whether SIZ1 participated in auxin signaling pathway, exogenous IAA was used to treat Col-0 and siz1. By analyzing the results of RNA-seq before and after treatment, SIZ1 was determined to be involved in the auxin signaling pathway

first: Jiaxuan

last: Sui

first: Yiying

first: Xiuyuan

last: Yu


title: Altered expression of reticulon-like 16 (RTNLB16) disrupt growth, fertility and decrease sensitivity to ABA and senescence in Arabidopsis thaliana

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

institute: Bar-Ilan University

summary: Reticulon family proteins are membrane-spanning proteins localized in the endoplasmic reticulum (ER) and are present in all eukaryotes. In animal cells, these proteins, known as reticulons, have a wide range of functions. These functions encompass involvement in vesicle formation, ER membrane morphogenesis, and the inhibition of nerve regeneration. Conversely, in plants, our understanding of the function of reticulon-like family proteins (RTNLBs) remains limited.         In the plant Arabidopsis, the RTBLB gene family comprises twenty-one members, with RTNLB16 being the most intricate. The AtRTNLB16 gene consists of seven splice variants, each encoding seven distinct protein isoforms. An Arabidopsis T-DNA mutant (Salk_122275/rtnlb16-1), which is a knockout for the upper coding frame isoform 7 while concurrently overexpressing the other isoforms through the CaMV 35S promoter at the left border of the T-DNA insertion, exhibits growth retardation, reduced chlorophyll levels, and insensitivity to abscisic acid or senescence stimuli.             Under a diurnal regime of 16 hours of light followed by 8 hours of darkness, which activates the 35S promoter, the expression of RTNLB16 transcripts in the rtnlb16-1 mutant intensifies, resulting in profound growth inhibition. Conversely, growing under a continuous low-light (CLL) condition curbs the overexpression and mitigates this phenotype.      Under a diurnal regime of 16 hours of light followed by 8 hours of darkness, which activates the 35S promoter, the expression of RTNLB16 transcripts in the rtnlb16-1 mutant intensifies, resulting in profound growth inhibition. Conversely, growing under a continuous low-light (CLL) condition curbs the overexpression and mitigates this phenotype.           We utilized the altered expression of the RTLB16 gene in this mutant line due to its dependence on the light regime. Our aim was to uncover the biological processes in which it participates. To achieve this, we conducted RNA sequencing on leaves from four-week-old wild-type (Col-0) and rtnlb16-1 plants grown under CLL or 16:8 light regimes.

overall_design: Col-0 and rtnlb16-1 plants where grown under CLL conditions (light intensity ~50 µmol/sec/m2) or under 16:8 dark:light conditions ((light intensity ~80 µmol/sec/m2) for four weeks. Leaf samples for RNA extraction where collected from four weeks old plants in three biological replicates. Each replicate consisted of mature leaves pooled from at least tree different plants.


title: Loss of ATP-dependent citrate lyase Drives Left Ventricular Dysfunction by Metabolic Remodeling

city: Los Angeles

first: Anja

last: Karlstaedt

state: California

address: 127 San Vincente Blvd

department: Cardiology

institute: Cedars Sinai Medical Center

summary:
Background: Metabolic remodeling is a hallmark of the failing heart. Oncometabolic stress during cancer increases the activity and abundance of the ATP-dependent citrate lyase (ACL, Acly), which promotes histone acetylation and cardiac adaptation. ACL is critical for the de novo synthesis of lipids, but how these metabolic alterations contribute to cardiac structural and functional changes remains unclear.
Methods: We utilized human heart tissue samples from healthy donor hearts and patients with non-ischemic cardiomyopathy. Further, we used CRISPR/Cas9 gene editing to inactivate Acly in cardiomyocytes of MyH6-Cas9 mice. In vivo, positron emission tomography and ex vivo stable isotope tracer labeling were used to quantify metabolic flux changes in response to the loss of ACL. We conducted a multi-omics analysis using RNA-sequencing and mass spectrometry-based metabolomics and proteomics. Experimental data were integrated into computational modeling using the metabolic network CardioNet to identify significantly dysregulated metabolic processes at a systems level.
Results: Here, we show that ACL expression is reduced in patients with reduced ejection fraction undergoing heart transplantation compared to healthy donors. In mice, loss of ACL increases glucose oxidation while reducing fatty acid oxidation to sustain contractile function. Ex vivo isotope tracing experiments revealed a reduced efflux of glucose-derived citrate from the mitochondria into the cytosol, confirming that citrate is required for reductive metabolism in the heart. We demonstrate that increased cytosolic citrate availability increases IDH1 protein abundance and flux. These compensatory metabolic alterations reduce histone 3 pan-acetylation and increase histone 3 lysine 4 methylation. Analysis of transcriptomic and protein data from heart tissue samples revealed downregulation of YAP and its target genes. Computational flux analysis and genome-scale metabolic modeling identified IDH1 as a therapeutic target to overcome the reduction of ACL.
Conclusions: This study mechanistically delineates how cardiac metabolism compensates for suppressed citrate metabolism in response to ACL loss and uncovers metabolic vulnerabilities in the heart.

overall_design: To establish the role of ACL in the heart, we knockdown (KD) Acly using MyH6-Cas9 mice. Cardiomyocytes were isolated using ex vivo heart perfusions. RNA-Sequencing was conducted to quantify gene expression changes between control and Acyl-KD mice.


title: Mindbomb1 is a Novel Negative Regulator of BMP Signaling (H838: MIB1 iKO)

first: Robert

last: Piskol

summary: Sequencing data in NCIH838 lung adenocarcinoma cells show that MIB1 loss leads to the upregulation of BMP target genes.

overall_design: To explore the functional relationship between MIB1 and TGF-beta, we analyzed the transcriptomes of NCI-H838 cells with MIB1 expression and those with MIB1 loss (MIB1-iKO)

first: Charisa

last: Cottonham

first: Gloria

last: Hernandez

first: Christian

last: Siebel


title: AtYchF1 modulates selective translation

city: Hong Kong

first: Hon-Ming

last: LAM

address: Room EG02, East Block, Science Centre,The Chinese University of Hong Kong,Shatin, N.T. Hong Kong.

department: School of Life Sciences

institute: The Chinese University of Hong Kong

summary: To study the translational regulation of AtYchF1

overall_design: RNA-seq analysis using RNA isolated from different fractions in polsyome profiling of 4 different arabidopsis lines at mock treatment

first: Sau-Shan

last: Cheng

first: Jacky

middle: C

last: Ngo

first: Yee-Shan

last: Ku

first: Zhixia

last: Xiao

first: Ming-Yan

last: Cheung

last: Lam


title: Functional heterogeneity of dentate gyrus mossy cells along the longitudinal axis of the hippocampus

city: Daegu

first: Yong-Seok

last: Oh

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Brain Sciences

country: South Korea

institute: Daegu-Gyeongbuk Institute of Science and Technology (DGIST)

summary: Glutamatergic mossy cells (MCs) display unique connectivity by projecting their axons bilaterally along the longitudinal axis of the dentate gyrus (DG). However, it is unclear whether MCs are heterogeneous in their neuronal properties and functions. Here, we demonstrated within-cell-type heterogeneity of MC subpopulations depending on their dorsoventral location.  Gene expression profiles of dMCs and vMCs were associated with different neurobiological processes including axon guidance, synaptic transmission, and neurometabolism. Despite common activation by external stimuli, dMCs, but not vMCs, provide net inhibitory control of granule cell excitability across the longitudinal axis of the DG. Intrinsic heterogeneity within MCs provides substantial mechanisms underlying functional differentiation as well as association across the longitudinal extent of the hippocampus.

overall_design: Translating RNA profiles of Dorsal and Ventral mossy cells in Drd2-TRAP mice

first: Jin-Hyeok

last: Jang

first: Minseok

last: Jeong


title: The evolution of the p53 transcriptional response across primates [ATAC-seq]

city: Boulder

first: Robin

middle: D.

last: Dowell

state: CO

address: 596 UCB

department: Molecular, Cellular and Developmental Biology

institute: University of Colorado Boulder

summary: p53 is a transcription factor that acts as a central signaling node in cells. It is activated by DNA damage, senescence, amino acid starvation, among other stressors; and in turn controls diverse cellular responses including apoptosis, cell cycle arrest, metabolic changes, etc. It is not clear the extent with which the transcriptional response by such an important regulator has evolved across animals. We generated nascent transcription (PRO-seq), chromatin accessibility (ATAC-seq), and steady-state mRNA expression (RNA-seq) datasets from 10 primates, 1 ungulate, and 1 bird; to investigate the initial transcriptional response upon p53 activation with Nutlin-3a.

sample_organism:
Pan paniscus
Homo sapiens

platform_organism:
Pan paniscus
Homo sapiens

overall_design: We used lymphoblastoid cell lines derived from 1 individual each from 12 animal species: Human (Homo sapiens), Chimp (Pan troglodytes), Bonobo (Pan paniscus), Gorilla (Gorilla gorilla), Orangutan (Pongo pygmaeus), Gibbon, (Nomascus leucogenys), Rhesus macaque (Macaca mulatta), Baboon (Papio anubis), Squirrel monkey (Saimiri boliviensis), Owl monkey (Aotus nancymaae), Cow (Bos taurus), and Chicken (Gallus gallus). PRO-seq datasets were treated for 1 hour with either DMSO (negative control), or 20 μM of Nutlin-3a. ATAC-seq datasets were treated for 1 hour with either DMSO (negative control), or 20 μM of Nutlin-3a. RNA-seq datasets were treated for 6 hours with either DMSO (negative control), or 20 μM of Nutlin-3a.

first: Daniel

last: Ramirez

middle: D


title: Transcriptomic analysis of PM2.5 and/or fucoidan-treated ARPE-19 retinal pigment epithelial cells

status: Public on Jul 21 2026

city: Taipei

first: ZHI-HU

last: LIN

address: No. 145, Zhengzhou Rd

department: Department of Ophthalmology

country: Taiwan

institute: Taipei City Hospital

summary: This study investigated the transcriptomic effects of PM2.5 in human ARPE-19 retinal pigment epithelial cells and evaluated the transcriptional responses associated with fucoidan treatment. ARPE-19 cells were assigned to four conditions: vehicle control, fucoidan (400 μg/mL), PM2.5 (200 μg/mL), and combined fucoidan plus PM2.5 treatment. Cells were treated for 24 hours before total RNA collection. RNA sequencing was performed to characterize PM2.5-induced gene expression changes and to determine how fucoidan modulates these transcriptional responses.

overall_design: ARPE-19 cells were divided into four experimental groups: CTL (equivalent volume of PBS), F400 (fucoidan, 400 micrograms/mL), P200 (diesel particulate matter SRM 1650b, 200 micrograms/mL), and PF (fucoidan, 400 micrograms/mL, plus PM2.5, 200 micrograms/mL, added simultaneously). Treatments were initiated at approximately 80% confluence and continued for 24 hours. Two independent biological replicates were analyzed per condition, resulting in eight RNA-seq libraries.

first: Tsai

last: Ching-Yao

first: Chen

last: Chueh-Tan

first: Lin

last: Zhi-Hu

last: Tung-Yi


title: Transcriptomic analysis of Dunaliella salina cultivated in Sistan deep water

city: zabol

first: yasoub

last: shiri

department: agricultur

country: Iran

institute: Rizabol

summary: RNA sequencing was performed to investigate the transcriptomic response of Dunaliella salina cultivated in Sistan deep water. Four RNA-seq libraries representing two biological replicates for the control and two biological replicates for the deep water treatment were generated using the Illumina NovaSeq 6000 platform. Raw sequencing data are available in SRA under BioProject PRJNA1267574. Processed gene count data are provided.

overall_design: Two biological replicates of control cultures and two biological replicates of deep water-treated cultures were analyzed by RNA sequencing.

first: Najmeh

last: Rameshieh

first: Abbasali

last: Emamjomeh

first: Ahmad

last: Gharaei

first: Leila

last: Mehravaran

first: Yasub

last: Shiri


title: Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain [RNA-Seq]

city: Evanston

first: Yue

last: Yang

state: IL

address: 2200 Campus Dr

department: Neurobiology

institute: Northwestern University

summary: Exceptionally long genes and cis-regulatory enhancers are selectively activated in mammalian brain neurons, and these loci are mutation hotspots in neurological disorders. However, the organization of these large genomic elements at the level of chromosome folding, beyond local enhancer-promoter interactions, remains poorly understood. Here, we report the discovery of a genomic subcompartment in the mouse cerebellum formed by near-megabase long enhancers and their associated long genes encoding synaptic or signaling proteins. Genomic regions within this subcompartment are enriched in the outer-half of the nucleus, while other transcriptionally active structures are enriched in the nuclear interior. Using an in vivo CRISPR genetic mini-screen, we uncover a specific role for the transcription factor Etv1 in coupling the compartmentalization of neuronal long genes with their expression. Together, our study defines mechanisms that organize transcriptionally active genes across chromosomes in the mammalian brain.

overall_design: RNA-seq libraries were prepared from the cerebellum of postnatal day 10 or 14 mice. Additional RNA-seq libraries were prepared from from electroporated granule neurons in postnatal day 10 or 14 mice that were enriched with FANS using the mCherry and NeuN antibodies or enriched from ribosomes using monoclonal GFP antibodies. Libraries were sequenced on the Illumina NextSeq 550 platform to obtain 37 bp paired-end reads. Two to eleven biological replicates were performed for all conditions.

first: Ziyu

last: Zhao

first: Omar

last: Payán Parra

first: Shin-ichiro

last: Fujita

first: Francesco

last: Musella

first: Nicolas

last: Scrutton Alvarado

first: Frank

last: Alber

first: Tomoko

last: Yamada


title: Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain [SPRITE]

overall_design: SPRITE libraries were prepared from the cerebellum of P22 mice. Libraries were sequenced on the Illumina HiSeq X or NovaSeq platform (Admera Health) to obtain 150bp paired-end reads. Two biological replicates were performed.


title: Hepatic tissue-derived extracellular vesicles miRNA regulates hypoxia tolerance in Pelteobagrus vachellii by reprogramming metabolism to maintain liver homeostasis

city: heze

first: guosong

last: zhang

state: shandong

address: No. 1, University Road, Heze City

institute: Heze University

summary: Hypoxia is a critical environmental stressor that affects fish survival and physiological metabolism. Extracellular vesicles (EVs) mediate intercellular signal communication and perform vital functions in the stress response of aquatic organisms; however, the functional regulatory mechanisms of EVs under hypoxia in fish remain unelucidated. In this study, we optimized enzymatic digestion and combined with ultracentrifugation and high-precision iodixanol density gradient centrifugation, high-purity hepatic EVs were efficiently isolated from Pelteobagrus vachelli, which were internalized by primary hepatocytes successfully. Integrative analyses of the EVs miRNAome and hepatic transcriptome were performed to construct a miRNA-mRNA negative regulatory network, identifying metabolic reprogramming, HIF-1 signaling, cellular homeostasis and stress response as core pathways in hypoxic adaptation. In vivo functional validation revealed that hypoxia-induced EVs (Hypo-EVs) reduced the critical asphyxiation point, enhanced blood oxygen-carrying capacity, and alleviated hypoxia-induced hepatic oxidative damage in a dose-dependent manner, thereby significantly improving the hypoxia tolerance of P. vachelli. Mechanistic studies revealed that miR-135a is the core functional molecule within Hypo-EVs, and its expression was significantly downregulated under hypoxia. Overexpression of miR-135a reversed the hypoxic protective capacity of Hypo-EVs, whereas inhibition of miR-135a significantly enhanced hypoxia tolerance. Dual-luciferase and in vivo validation confirmed that miR-135a directly targets the 3'-UTRs of the glycolysis/gluconeogenesis key genes hk1 and pck2, negatively regulates glucose metabolism at the post-transcriptional level and mediates hypoxia adaptation through metabolic reprogramming. Collectively, this study clarifies the molecular mechanism by which the Hypo-EVs/miR-135a/hk1/pck2 signaling axis regulates hypoxia tolerance in P. vachellii. These findings provide theoretical references for research on fish hypoxic response mechanisms and stress-resilient aquaculture regulation.

overall_design: Experimental materials and hypoxic stress treatment The experimental procedures were approved by the Ethics Review Committee for Animal Experimentation of Heze University. Experimental fish were purchased from Sichuan Rongsen Fishery Co., Ltd. Healthy P. vachellii of uniform specifications (body length 11.5 ± 1.5 cm, body weight 15 ± 0.94 g) were selected. Fish were acclimated for two weeks and fasted for 48 h before the experiment. Based on previous experience, 1 mg/L was selected as the hypoxic stress threshold. To establish hypoxic conditions, aeration and water circulation were turned off, and the water body was sealed. Pure nitrogen was bubbled to reduce DO from 6.8 mg/L to 1.0 mg/L, which was maintained constantly at 1.0±0.1 mg/L. Fish were anesthetized at designated time points for hepatic tissue collection. Nitrogen bubbling was terminated, and reoxygenation (6.8 mg/L) was performed at the corresponding time points for sampling. Liver tissues were snap frozen in liquid nitrogen and stored at −80°C.

first: Xia

last: Liang

first: Guosong

last: Zhang

first: Shaowu

last: Yin

first: Fenfei


title: Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain

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

overall_design: Refer to individual Series


title: Computational modeling and preclinical evaluation support targeting somatic instability for Huntington’s disease treatment.

city: Philadelphia

first: Paul

middle: T

last: Ranum

state: PA

address: Latus Bio, 2929 Arch Street CIRA Center, 8th Floor - Suite 2

department: Research

institute: Latus Bio

summary: Huntington’s disease (HD) is caused by an expanded CAG trinucleotide repeat within the huntingtin (HTT) gene. Genetic modifiers of disease onset and progression in HD implicate somatic instability (SI) of the expanded CAG repeat as a key pathogenic driver, with MSH3 emerging as a leading therapeutic target. To inform development of an SI-targeting therapy, we generated a computational model that uses HD patient data to infer therapeutic effects of reducing SI. To target SI experimentally, we designed an artificial microRNA to lower MSH3 mRNA (miMSH3) after delivery with AAV-DB-3, a previously described medium spiny neuron (MSN)-targeting AAV capsid variant. AAV-DB-3.miMSH3 achieved 48–94% MSH3 mRNA reduction in MSNs of nonhuman primates (NHPs). Predictive modeling indicates this level of knockdown would delay motor symptom onset by more than 5 years in most HD gene-positive individuals, with many predicted to experience delays exceeding 50 years. Applied to a representative patient, the model predicts 50–120 % slowing of HD progression as measured by change from baseline in the composite Unified Huntington Disease Rating Scale (cUHDRS). Finally, AAV-DB-3.miMSH3 reduced Msh3 mRNA and protein by up to 27% and 40%, respectively, and SI by up to 46% in HdhQ111 mice. Cumulatively, the preclinical experimental data and the computational model support the translational potential of AAV-DB-3.miMSH3 as a disease-modifying therapy for HD.

overall_design: Two types of RNAseq samples are included in this submission; The first type is huntington's disease patient derived IPSc neurons RNAseq.  These cells have a HTT exon 1 CAG repeat length of 49 CAGs. Cells were then treated with vehicle, AAV-DB-3.mTFP1 expressing mTFP1 fluorescent reporter or AAV-DB-3.miMSH3. Bulk RNA seq analysis was conducted across three multiplicity of infection (MOI) doses of 1×104, 1×105, and 1×106 vector genome (vg)/cell, and three independent experiments.  The second type of RNAseq that was performed in this study was on human HEK-293 cells which were transfected with plasmid driving expression of CMV promoter driven miMSH3-11, miMSH3-06, miHDS1, or CMV promoter expressing GFP. Both these RNAseq efforts were done to evaluate off target effects of miRNA knockdown using the evaluated miRNA constructs.

first: Bryan

middle: P

last: Simpson


title: Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain [ChIP-Seq]

overall_design: ChIP-seq libraries using the H3K27ac antibody were prepared from electroporated granule neurons in postnatal day 10, 14, or 20 mice that were enriched with FANS using the mCherry and NeuN antibodies. ChIP-seq libraries using the Brd4 antibody were prepared from postnatal day 22 mice. Libraries were sequenced on the Illumina NextSeq 550 platform to obtain 37 bp paired-end reads. Two to four biological replicates were performed for all conditions.

middle: A


title: Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain [Hi-C]

overall_design: Hi-C libraries were prepared using the cerebellum from postnatal day 6 or 22 mice or cerebellar vermis from mice at day 1 to 28 after electroporation. Libraries were sequenced on the Illumina NextSeq 500 or 550 platform to obtain 36-37 bp paired-end reads or on a NovaSeq X Plus (Admera Health) to obtain 150bp paired-end reads. Two to six biological replicates were performed for all conditions.


title: RBMS1 Suppresses Ovarian Cancer Malignant Progression Through Post-transcriptional regulation expression of NEDD4

city: Harbin

first: Jing

last: Tang

state: Heilongjiang

address: No. 157 Baojian Road, Nangang District

institute: Harbin medical university

summary: Ovarian cancer (OC) is the deadliest gynecologic malignancy of the female reproductive system, with the molecular mechanisms driving its malignant progression not fully understood. This study aimed to identify tumor-suppressive RNA-binding proteins (RBPs) and characterize their post-transcriptional regulatory roles in OC. We screened for progression-associated RBPs through integrative analysis of multi-omics datasets from TCGA, GTEx, CPTAC, and TNMplot, and validated RBMS1 expression in clinical OC tissues via immunohistochemistry. The functional effects of RBMS1 on OC cell proliferation, migration, and invasion were assessed via in vitro and in vivo gain- and loss-of-function assays. Downstream targets of RBMS1 were identified by LC-MS/MS and RIP-seq, with regulatory relationships confirmed by rescue experiments. The deposited RIP-seq data provide genome-wide RBMS1-bound RNA profiles in OC cells. Our results show that RBMS1 is downregulated in OC and exerts tumor-suppressive effects through a novel RBMS1–NEDD4 regulatory axis.

overall_design: RIP-seq assay was conducted with anti-RBMS1 antibody and normal IgG control. Enriched RNA from immunoprecipitated complexes in cells was purified and subjected to high-throughput sequencing.

first: Yuguang

last: Ye

first: Qingyu

last: Guo

first: Shuoshuo

last: Wang


title: Transcriptomic profiling of gastrocnemius muscle in dysferlin-deficient B6.A-Dysfprmd/GeneJ mice

city: Moscow

first: Nikita

middle: Sergeevich

last: Gladyshev

address: Tsyurupy 3

country: Russia

institute: Petrovsky National Research Centre of Surgery

summary: This study investigated transcriptomic alterations in gastrocnemius muscle associated with dysferlin deficiency. Bulk RNA sequencing was performed on gastrocnemius muscle from 3-month-old homozygous B6.A-Dysfprmd/GeneJ mice and age-matched C57BL/6 control mice. Gene-level expression profiles were used to characterize molecular changes associated with the early manifestation of dysferlinopathy.

overall_design: Six independent gastrocnemius muscle samples were analyzed: three homozygous B6.A-Dysfprmd/GeneJ mice and three age-matched C57BL/6 control mice. Each animal represented an independent biological replicate. Poly(A)-selected directional RNA-seq libraries were sequenced on an Illumina NovaSeq 6000 using paired-end 2 x 61 bp reads.

first: Limaev

last: Igor S.

first: Gladyshev

last: Nikita S.

first: Yakovlev

last: Ivan A.

first: Shigapova

last: Leila Kh.

first: Shagimardanova

last: Elena I.

first: Chekmareva

last: Irina A.

first: Kopylov

last: Evgeniy D.

first: Gusev

last: Oleg A.

first: Deev

last: Roman V.


title: Structural assembly of the glycan-rich, chitin-reinforced adhesive of Hydra is coordinated by a lectin-like protein, HvAb1

city: Innsbruck

first: Birgit

last: Lengerer

address: Technikerstr. 25

country: Austria

institute: University of Innsbruck

summary: Aquatic animals deploy adhesives, in numerous essential functions, and reversibility is a key adaptation. The molecular mechanisms of reversible wet adhesion remain poorly understood. Using a model organism, the freshwater cnidarian Hydra vulgaris, we dissect the mechanism of molecular assembly in a secreted adhesive and uncover a glycan and protein-based architecture organized by a lectin-like protein, Hydra vulgaris adhesive protein 1 (HvAb1). We identify HvAb1 as a nonredundant organizer of the adhesive matrix, being basal-disc specific and secreted. Knockdown of HvAb1 severely impaired attachment and disrupted footprint architecture in a mosaic pattern, with only HvAb1-positive regions of the adhesive footprint retaining their normal structure. The adhesive is wheat germ agglutinin (WGA)-reactive and contains a fibrillar chitin-based sub-network, synthesized by a basal-disc-specific chitin synthase. Applying exogeneous chitinase abolished both WGA staining and Hydra attachment, indicating that WGA-positive components perform essential roles in adhesion. Our results therefore describe a glycan-dominated matrix, organized via a lectin-like protein (HvAb1), which is reinforced by chitin and enables reversible adhesion underwater. This establishes Hydra as a tractable model to better understand the principles of reversible adhesion underwater and, potentially, inform future bioinspired, sustainable adhesives.

overall_design: Budless Hydra vulgaris (AEP) were electroporated 3 times  with gene-specific siRNA and then the basal disc was amputated and allowed to fully regenerate. RNA was isolated from a cohort of 10 whole animals and sequenced to compare gene expression levels.

first: Mario

last: Kanetscheider


title: Transcriptomic profiling of chronic rhinosinusitis with nasal polyps

city: Shanghai

first: Hai

last: Lin

state: Shanghai

address: No. 600, Yishan Road, Xuhui District

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

summary: Chronic rhinosinusitis with nasal polyps (CRSwNP) is a heterogeneous inflammatory disease characterized by diverse immune responses and molecular endotypes. This study performed bulk RNA sequencing of nasal mucosal tissues from 22 subjects, including 8 healthy controls, 9 eosinophilic CRSwNP (eCRSwNP), and 5 non-eosinophilic CRSwNP (neCRSwNP) patients. Transcriptomic analysis was conducted to characterize inflammatory signatures. This dataset provides transcriptomic resources for investigating inflammatory heterogeneity in CRSwNP.

overall_design: Bulk RNA sequencing was performed on nasal mucosal tissues collected from three groups: healthy controls, eosinophilic chronic rhinosinusitis with nasal polyps (eCRSwNP), and non-eosinophilic chronic rhinosinusitis with nasal polyps (neCRSwNP). Transcriptomic profiles were compared among groups to identify differentially expressed genes.

first: Yuelong

last: Gu

first: Weitian

last: Zhang


title: Gene expression data from liver treated with Vigna Umbellata extract (VE).

city: TSUKUBA

first: ELDA NURAFNIE

last: IBNU RASID

state: IBARAKI

address: 1-1-1 TENNODAI

country: Japan

institute: UNIVERSITY OF TSUKUBA

summary:
Gene expression profiling reveals DEGs in liver.
We evaluated the effects of Vigna Umbellata on liver of ob/ob mice through an untargeted whole-genome transcriptome analysis.

overall_design: The microarray analysis was conducted on control ob/ob mice group and VE-treated group with comparison to wild type (WT) group using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) and GeneChip™ Hybridization, Wash and Stain Kit (ThermoFisher Scientific) following the manufacturer’s instructions. Firstly, about 100 ng of RNA from each sample was obtained to synthesize complementary DNA (cDNA) for complementary RNA (cRNA) synthesis. cRNA was purified and reverse transcribed for single-stranded cDNA (ss-cDNA) synthesis, purification, fragmentation and labelling. ClariomTM S Array (Mouse; ThermoFisher Scientific) were hybridized with samples extracted from liver. Tissue samples were prepared from control groups, including ob/ob mice (n = 3) and, when applicable, wild-type mice (n = 3), as well as from VE-treated groups receiving 100 mg/kg BW (n = 3). All of the samples were hybridized for 16 hours in a 45 degree celcius incubator, washed and stained on the GeneChip™ Fluidics Station (ThermoFisher Scientific). The scanning was performed using GeneChip Scanner (ThermoFisher Scientific). The raw image data was obtained using the Transcriptome Analysis Console (TAC) software (ver. 4.0.2, ThermoFisher Scientific) and raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above back-ground (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7. Finally, genes that passed the filter criteria of p value <0.05 (one-way between-subjects ANOVA) and fold change >1.1 (in linear space) were considered as differentially expressed genes (DEGs).

first: Elda Nurafnie

last: Ibnu Rasid


title: Gene expression data from brain treated with Vigna Umbellata extract (VE)

summary:
Gene expression profiling reveals DEGs in brain (hypothalmus)
We evaluated the effects of VE on brain of ob/ob mice through an untargeted whole-genome transcriptome analysis

overall_design: The microarray analysis was conducted on control ob/ob mice group and VE treated group with comparison to wild type (WT) group using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) and GeneChip™ Hybridization, Wash and Stain Kit (ThermoFisher Scientific) following the manufacturer’s instructions. Firstly, about 100 ng of RNA from each sample was obtained to synthesize complementary DNA (cDNA) for complementary RNA (cRNA) synthesis. cRNA was purified and reverse transcribed for single-stranded cDNA (ss-cDNA) synthesis, purification, fragmentation and labelling. ClariomTM S Array (Mouse; ThermoFisher Scientific) were hybridized with samples extracted from WAT. Tissue samples were prepared from control groups, including ob/ob mice (n = 3) and, when applicable, wild-type mice (n = 3), as well as from VE-treated groups receiving 50 mg/kg BW (n = 3) and 100 mg/kg BW (n = 3). All of the samples were hybridized for 16 hours in a 45 degree celcius incubator, washed and stained on the GeneChip™ Fluidics Station (ThermoFisher Scientific). The scanning was performed using GeneChip Scanner (ThermoFisher Scientific). The raw image data was obtained using the Transcriptome Analysis Console (TAC) software (ver. 4.0.2, ThermoFisher Scientific) and raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above back-ground (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7. Finally, genes that passed the filter criteria of p value <0.05 (one-way between-subjects ANOVA) and fold change >1.1 (in linear space) were considered as differentially expressed genes (DEGs).

first: Sharmin

last: Aktar


title: Prenatal inflammation primes pulmonary immune cells to postnatal hyperoxia induced lung injury

city: Wilmington

first: Deepthi

last: Alapati

state: DE

address: 1600 Rockland Road

department: Pediatrics

institute: Nemours Children's health

summary: Bronchopulmonary dysplasia (BPD) arises from a combination of prenatal and postnatal environmental factors, but the impact of prenatal inflammation on subsequent postnatal lung injury remains unclear. We aimed to investigate how prenatal lipopolysaccharide (LPS)-induced chorioamnionitis alters the composition of resident pulmonary immune cells and modifies the response to hyperoxia-induced lung injury in neonatal rats. Pregnant Sprague-Dawley rats received intra-amniotic injections of LPS or normal saline (NS) at embryonic day 20. Pups were euthanized on postnatal day 1 (P1) or exposed to 85% oxygen (O₂) or room air (RA) for 14 days and euthanized on postnatal day 14 (P14) for analysis. Resident pulmonary immune cells were quantified by flow cytometry. Mann–Whitney and ANOVA tests were used for group comparisons (p<0.05). mRNA from pulmonary immune cells collected on P1 was subjected to RNA sequencing and differential gene expression analysis. On P1, prenatal LPS exposure did not change the overall percentage of CD45⁺ pulmonary immune cells but decreased the percentages of CD3⁺CD4⁺ T cells, CD3⁺CD8⁺ T cells, and CD45R⁺ B cells compared with the NS+RA group. In contrast, CD161⁺ NK cells and CD43⁺ monocytes were significantly increased. Upregulated genes were enriched in inflammatory biological processes. By P14, cell composition in the LPS+RA group normalized. However, a second insult with postnatal hyperoxia resulted in an increased proportion of CD161⁺ NK cells in the LPS+O₂ group only and an increased proportion of CD43⁺ monocytes in the NS+O₂ group only, with a relative reduction in monocytes in the LPS+O₂ group at P14. In this rat model of BPD, LPS-mediated in-utero inflammation primes neonatal lung immune cells for a dysregulated response to postnatal hyperoxia. Dual prenatal and postnatal injuries result in persistent elevation of NK cells and reduction of monocytes, while other immune subsets respond differentially, suggesting that prenatal events condition the neonatal lung immune system in ways that may influence BPD pathogenesis.

overall_design: Pregnant Sprague-Dawley rats received intra-amniotic injections of LPS or normal saline (NS) at embryonic day 20. Pups were euthanized on postnatal day 1 (P1) . mRNA from pulmonary immune cells collected on P1 was subjected to RNA sequencing and differential gene expression analysis.

first: Anabalagan

last: Saminathan

first: Papah

last: Michael B

first: Glazewski

last: Lisa

first: Hesek

last: Anne

first: Karl

last: Franke

first: Erin

last: Crowgey

first: Alapati

last: Deepthi


title: The H3K36M oncohistone inhibits NSD2 to activate a SETD2-dependent antiviral-like immune response in KRAS-driven lung cancer

first: Carson

last: Poltorack

address: 421 Curie Blvd, Rm 445

department: Pathology

institute: University of Pennsylvania Perelman School of Medicine

summary: Mutations in histone 3 at or near lysine 36 (H3K36) have dominantly acting oncogenic effects in multiple tumor types by limiting H3K36-directed methyltransferases. Paradoxically, we find that expression of the H3K36M oncohistone unexpectedly inhibits tumor formation in KRAS-driven lung adenocarcinoma by inducing a potent immune-mediated tumor clearance. Mechanistically, oncohistone expression derepresses endogenous retroviral element transcription, results in the accumulation of double-stranded RNA (dsRNA), and activates an innate antiviral-like immune response that eradicates tumor growth. Surprisingly, while inactivation of the H3K36 di-methyltransferase NSD2 replicated all effects of oncohistone expression, inactivation of the H3K36 tri-methyltransferase SETD2 abolished element derepression and all associated downstream anti-cancer effects that are induced by oncohistone expression. These observations restructure our understanding of the roles of H3K36 methylation, the consequences of its deregulation in cancer, and shape our expectations for therapeutic interventions targeting H3K36 methyltransferases.

overall_design: Four mouse lung tumor samples profiled with 10x Genomics Xenium in situ spatial transcriptomics using a 5006-gene mouse panel. One sample per genotype: Kras-Ctrl, Kras-H3K36M, Kras-Setd2KO, Kras-H3K36M-Setd2KO.

first: Amy

last: Gladstein

first: Akino Mercy Charles

last: Solomon

first: Sharan

last: Venkatesh

first: Keren

last: Adler

first: Maggie

middle: R

last: Robertson

first: Stephanie

last: Stransky

first: Valerie

last: Irizarry-Negron

first: Dain

last: Ruiz

first: Dingwen

last: Tao

first: Nelson

middle: F

last: Freeburg

first: Simone

last: Sidoli

first: Irfan

last: Asangani

first: Sydney

last: Shaffer

first: David

last: Feldser


title: Knockdown and overexpression of injury-responsive transcription factors in cultures of adult mouse dorsal root ganglia

city: San Francisco

first: Trent

middle: A.

last: Watkins

address: 675 Nelson Rising Lane, Rm 214A

institute: University of California at San Francisco

summary: The Activating Transcription Factor-4 (ATF4) contributes to pro-regenerative transcriptional responses following optic axon damage. Here we use an in vitro model of axon regeneration to investigate the contributions of ATF4 to the transcriptional injury response of adult mouse sensory neurons of the dorsal root ganglion (DRG). We find that, in contrast to optic axon injury, the upregulation of the pro-regenerative transcription factor ATF3 is not ATF4-dependent, and without that contribution, ATF4 instead limits adult DRG axon regrowth in collaboration with C/EBPgamma. Knockdown of ATF4 enhances axon regeneration in this model while regulating a collection of genes largely non-overlapping with those regulated by injury-activated pro-regenerative transcription factors, including ATF3 and c-Jun. We find that overexpression of ATF4 suppresses axon regeneration in a C/EBPgamma-dependent manner. This effect, however, is not a simple reciprocal of ATF4 knockdown, as it is also correlated with suppression of ATF3- and c-Jun-dependent transcription. Together these findings suggest that axon injury induces an ATF4-dependent transcriptional program that limits regeneration in parallel with pro-regenerative responses.

overall_design: RNA-seq profiling of neuron-enriched cultures of adult wildtype mouse dorsal root ganglion (DRG) 42 h after cell isolation and immediate transfection with ON-TARGETplus siRNA targeting axon injury-responsive transcription factors Atf3, Atf4, Jun, Rest, Alyref, Stat3, or Klf6, or transfection with mRNA for overexpression of Atf4 or Cebpg.


title: A Single-Cell Atlas of Transcriptional and Immunoglobulin Repertoire Evolution in Early B Cell Development

city: La Jolla

first: Bryan

last: Briney

address: 10550 N Torrey Pines Rd

department: Immunology and Microbiology

institute: Scripps Research

summary: The development of human B cells in the bone marrow can be separated into functionally and transcriptionally distinct subsets, which while canonically described have yet to be profiled deeply and individually and with NGS and bioinformatic techniques. In this study, single-cell RNA sequencing was performed on 65,110 B cells from six healthy donors to observe the foundation of the diversity observed in mature immune repertoires. Following the established narrative of development, committed B cells undergo heavy and light chain recombination, which together form the functional BCR. However, a granular per-subset phenotypic analysis reveals proliferative bursts following each recombination event, an aspect of BCR recombination previously undescribed in the pro-B phase of development. Heavy and light chain pairing becomes more similar to that of mature, circulating B cells with progress through lymphopoiesis, deleting features associated with autoreactivity. Prominent among these repertoire alterations is a substantial shortening of heavy chain CDR3s, and changes in V, D, and J gene usage. This study provides a detailed snapshot of the transcriptomic and repertoire genetics landscape of developing B cells, providing a deeper understanding of the repertoire-shaping influence of early selection processes, and introducing new avenues for repertoire development research.

overall_design: Bone marrow samples from six healthy donors were enriched for CD34⁺ cells and B cells using magnetic bead separation. Cells from each donor were labeled with BioLegend Cell Hashing antibodies and multiplexed prior to single-cell sequencing. Separate High-throughput 10x Genomics Chromium reactions were performed for each cell subset, with each reaction containing the corresponding enriched population from all six donors (i.e., whole bone marrow, CD34⁺-enriched, or B cell-enriched samples).

first: Charlotte

last: DiBiase

first: Jonathan

last: Hurtado


title: Matched single-cell and Visium HD spatial transcriptomics of a chronic antibody-mediated rejection kidney graft

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

summary: Chronic antibody-mediated rejection (CAMR) is a leading cause of late kidney allograft failure and shares features of chronic immune activation with systemic autoimmune diseases, but how circulating immune states connect to spatially organized graft injury and whether related immune features recur in autoimmune inflammation remain unclear. Here, we integrated single-cell profiles from peripheral blood and kidney graft samples from patients with CAMR or stable allograft function and healthy controls with independent transplant cohorts, bulk transcriptomic datasets, spectral flow cytometry, multiplex immunofluorescence, high-resolution spatial transcriptomics, and a large blood immune reference spanning autoimmune and inflammatory diseases. CAMR was associated with reproducible myeloid expansion and enrichment of SLC8A1+ monocytes/macrophages, ANK3+CD4+ memory T cells, ZEB2hi T cells, and CD16+ NK cells. These subsets exhibited migratory and tissue-interacting programs characterized by the recurrent expression of CXCR4 and ZEB2. In graft tissue, CXCL12-expressing fibroblasts and CXCR4-expressing immune cells were increased in CAMR. High-resolution spatial transcriptomics localized this fibroblast–immune architecture to perivascular regions marked by endothelial activation and stromal remodeling, and placed CAMR-associated immune states within adjacent immune-rich neighborhoods, supporting a CXCL12-CXCR4 axis that may be associated with local immune accumulation. Comparisons with large-scale blood immune reference data and spatial transcriptomic datasets from rheumatoid arthritis and systemic lupus erythematosus suggested partial recurrence of related immune states and fibroblast–immune organization. Together, this study links circulating CAMR immune remodeling to a spatially organized CXCL12-CXCR4 fibroblast-immune niche, and suggests that elements of this niche recur across alloimmune and autoimmune inflammation.

overall_design: Renal biopsy tissue from the same patient with chronic antibody-mediated rejection (CAMR) was profiled using both single-cell RNA sequencing and 10x Genomics Visium HD spatial transcriptomics. The matched single-cell dataset was used as a reference for cell-type deconvolution of the spatial transcriptomic data using RCTD.

first: Xuyang

last: Xia

first: Yangjuan

last: Bai

first: Binqi

last: Yang

first: Wei

last: Mao

first: Hongyu

first: Yamei

last: Li

first: Yajiao

last: He

first: Jing

last: Wu

first: Bei

last: Cai

first: Yu

last: Fan

first: Haotian

last: Yu

first: Yang

last: Guo

first: Yanmei

last: Liu

first: Xi

last: Tang

first: Huayun

last: Yan

first: Tao

last: Zhou

first: Yiqi

last: Deng

first: Wanchun

first: Minyuan

last: Cao

last: Shu

first: Yun-Ying

last: Shi

first: Lanlan

last: Wang


title: Peripheral blood bulk RNA-seq validation cohort for chronic antibody-mediated rejection

first: Heng

last: Xu

overall_design: Peripheral blood samples from 12 individuals, including 4 patients with chronic antibody-mediated rejection (CAMR), 4 kidney transplant recipients with stable allograft function (SAF), and 4 healthy controls (HC), were subjected to bulk RNA sequencing. The resulting transcriptomic data were used to validate cell-type composition differences through computational deconvolution analysis.

first: Xuyang

last: Xia

first: Yangjuan

last: Bai

first: Binqi

last: Yang

first: Wei

last: Mao

first: Hongyu


title: Single-cell RNA-seq atlas of peripheral blood and kidney graft immune cells in chronic antibody-mediated rejection

overall_design: Peripheral blood samples from 29 individuals, including 18 patients with chronic antibody-mediated rejection (CAMR), 6 kidney transplant recipients with stable allograft function (SAF), and 5 healthy controls (HC), were profiled by single-cell RNA sequencing as the discovery cohort. Matched renal biopsy tissues from 7 of the CAMR patients were also subjected to single-cell RNA sequencing as a tissue validation cohort. In addition, peripheral blood samples from an independent cohort comprising 4 patients with CAMR, 4 recipients with SAF, and 4 HCs were profiled by single-cell RNA sequencing for independent validation.

first: Yamei

last: Li

first: Yajiao

last: He

first: Jing

last: Wu

first: Bei

last: Cai

first: Yu

last: Fan

first: Haotian


title: Tumor NLRP3 Amplification Promotes Immunotherapy Resistance by Inhibiting STAT1 Signaling and Suppressing MHC Class I Expression

city: Chapel hill

first: Brent

last: Hanks

state: North Carolina

address: 450 West Dr

department: Medicine

institute: UNC at Chapel Hill

summary: Immunotherapy resistance remains a significant challenge in immuno-oncology and predictive biomarkers are needed to guide combination immunotherapy selection for the individual patient.  Using transcriptional signature analysis as well as accessible tissue and plasma-based assays, we show that elevated tumor-intrinsic NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3) signaling activity correlates with checkpoint inhibitor resistance in several independent cohorts of stage III/IV melanoma and gastroesophageal (GE) adenocarcinoma patients.  In situ hybridization studies demonstrate that tumor NLRP3 copy-number gain is observed in immunotherapy resistant melanomas and GE adenocarcinomas harboring enhanced NLRP3 signaling activity.  Spatial transcriptomic analysis of GE adenocarcinomas reveals that NLRP3 signaling activity inversely correlates with NOD-, LRR-, and CARD-containing 5 (NLRC5) and major histocompatibility (MHC) class I-associated gene expression. Indeed, pre-clinical models of melanoma and GE adenocarcinoma demonstrate that Nlrp3 amplification suppresses NLRC5-mediated MHC class I upregulation, while pharmacologic NLRP3 inhibition augments tumor MHC class I surface levels. Upon activation, mechanistic studies reveal that NLRP3 binds to and inhibits STAT1 dimerization, nuclear translocation, and NLRC5 transcription.  Consistent with these findings, inhibiting the NLRP3 inflammasome augments tumor STAT1-NLRC5 signaling, MHC class I surface expression, and overcomes anti-PD-1 resistance in an orthotopic model of microsatellite stable chromosomal instability (CIN) gastric adenocarcinoma.  This work reveals a fundamental link between cellular stress and tumor-mediated immune evasion.  In addition, these findings indicate that the tumor NLRP3 inflammasome signaling pathway merits further clinical study as a therapeutic target and a source of companion biomarkers for overcoming checkpoint inhibitor resistance in cancer patients.

overall_design: RNA seq analysis of the whole tumor and sorted cells  from control CRISPR, NLRP3A tumor of syngenic mice and RNA seq analysis of whole tumor of WT and NLRP3 knock out melanoma specific transgenic mice.

first: Balamayooran

last: Theivanthiran

first: Nagendra

last: Yarla

first: Kaylee

last: Villareal


title: ERG function in prostate cells is regulated by distinct positive feedback loops depending on AKT signaling status

city: Bloomington

first: Peter

last: Hollenhorst

state: IN

address: 1001 E Third St, Biology 200

institute: Indiana University

summary: A chromosomal rearrangement that causes aberrant expression of the ERG transcription factor is the most common genomic alteration in prostate cancer. Expression of ERG in prostate cells can promote either luminal epithelial or mesenchymal cell fates depending on the status of the PI3K/AKT signaling pathway. Phosphorylation of ERG by ERK is important for oncogenic activity and can be regulated by the TLR4 signaling pathway. Here we found that the TLR4 pathway regulated ERG phosphorylation when AKT signaling was low, but the VEGF pathway promoted ERG phosphorylation when AKT signaling was high. Inhibition of the PI3K/AKT pathway in ERG-positive prostate cells resulted in loss of androgen receptor expression, gain of mesenchymal markers and loss of sensitivity to androgen receptor inhibition.

overall_design: This is a single-cell RNA seq comparison of the immortalized normal prostate epithelial cell line RWPE1 with the same line expressing exogenous ERG and myristoyated AKT

first: Saranya

last: Rajendran

first: Sean

last: McCabe