title: TRF2 downregulation acts as an upstream driver of heart failure

city: shanghai

first: Jing

last: Ye

address: Ruijin 2nd Road

institute: Shanghai Jiao Tong University Medical School Affiliated Ruijin Hospital: Shanghai, CN

summary: We have conducted  single‑nucleus RNA sequencing to investigate mouse cardiomyocytes with Terf2 cardiomyocyte-specific knockout. Cardiomyocytes play a crucial role in heart function. The down - regulation of TRF2 may affect cellular processes and gene expression patterns within cardiomyocytes. This study aims to reveal the changes in the nuclear transcriptome of these cells, providing insights into the molecular mechanisms underlying the impact of TRF2 down - regulation on cardiomyocyte function.

overall_design: The 10× Genomics platform (version 3.1) was used to load nuclei isolated from hearts of 3 cardiomyocyte-specific knockout Terf2 homozygous mice (Terf2(f,f) )  ,  3 heterozygous mice (Terf2(f,+))  and 3 control mice (Terf2(+,+)).

first: Eric

last: Gilson

first: Zimo

last: Sha

first: Peng

last: Chen

first: Yujie

last: Yang


title: Photorespiration is linked to DNA methylation by formate as a one-carbon source [BiSulfite-seq]

status: Public on Jan 04 2026

city: Neuherberg

first: Martin

last: Groth

address: Ingolstädter Landstr. 1

department: Institute of Functional Epigenetics

country: Germany

institute: Helmholtz Munich

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is a key epigenetic modification regulating genome organization, stability, and gene expression. Stable DNA methylation critically relies on methyl groups provided through folate-mediated one-carbon (C1) metabolism, yet the origin and regulation of C1 supply remain elusive. Here we demonstrate that photorespiration serves as a major C1 source for DNA methylation in Arabidopsis. We show that C1 from formate, a photorespiratory byproduct, is incorporated into 5-methyl-cytosine via the reductive cytosolic folate pathway. This occurs predominantly during the day, negatively regulating serine utilization as alternative C1 source. Consequently, suppression of photorespiration under elevated CO₂ levels alters the DNA methylation landscape, an effect exacerbated when regulation of C1 metabolism by the formate-dependent pathway is impaired. Thus, our findings link the fundamental metabolic process of photorespiration to epigenetic stability, highlighting how rising atmospheric CO₂ levels can induce DNA methylation changes.

overall_design: BS-seq analysis of Arabidopsis thaliana wild type compared to mthfd1 (m), thfs (t) single, and mt double mutants under long day (LD) conditions (8 samples in total); BS-seq analysis of mT-cr23 and mt-cr20 CRISPR-Cas9 lines (4 samples in total); BS-seq analysis of wild type and m under LD compared to short day (SD) conditions (8 samples in total); BS-seq analysis of wild type and m under high CO2 (3000 ppm) compared to control CO2 (410 ppm) conditions (8 samples in total); mRNA-seq analysis of wild type compared to mthfd1 (m), thfs (t) single, and mt double mutants under long day (LD) conditions (12 samples in total); and mRNA-seq analysis of wild type and m under high CO2 (3000 ppm) compared to control CO2 (410 ppm) conditions (12 samples in total).

first: Valentin

last: Hankofer


title: Photorespiration is linked to DNA methylation by formate as one-carbon source [RNA-seq]

type: Expression profiling by high throughput sequencing


title: An integrated clinical genomic and transcriptomic subgrouping of central chondrosarcoma

city: Leiden

first: Debora

last: Meijer

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

summary: Chondrosarcoma, a malignant cartilage-producing bone tumor, is the second most-common bone sarcoma. Chondrosarcomas are histologically graded, which is so far the best predictor of survival. Early mutations in isocitrate dehydrogenase (IDH)-1 and -2 genes are frequent, leading to the production of the oncometabolite D-2-hydroxyglutarate, which affects DNA methylation, resulting in a preferred chondrogenic differentiation over osteogenic differentiation of mesenchymal stem cells, which are currently considered the precursor cells of chondrosarcomas. DNA methylation profiling has previously revealed distinct profiles between IDH mutant and wild-type chondrosarcomas, but the presence of further DNA methylation subgroups indicates that classification based solely on IDH status is too simplistic. In this study, we aim to identify biological subgroups in chondrosarcomas by combining clinical data, IDH mutation status, gene expression and genome wide loss of heterozygosity (gwLOH).

overall_design: Tumors of 54 patients with chondrosarcoma (ACT, grade 2, grade 3 and dedifferentiatied chondrosarcoma)

middle: M

first: Judith

middle: V

last: Bovee


title: scRNA-seq analysis of aortic cells harvested from CNC-SMC-Cre;Smad4flox/flox;R26-tdT genotyped adult mice

city: Shanghai

first: Yi

last: Li

address: 320 Yueyang Road

country: China

institute: Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences

summary: The developmental heterogeneity of smooth muscle cells (SMCs) plays a crucial role in the prevalence of segment-specific aortic diseases. Traditional genetic tools, however, are insufficient for in vivo analysis of disease susceptibility associated with cellular origin. To overcome this challenge, we engineered a state-of-the-art dual recombinase-mediated intersectional genetic system, tailored to precisely target SMCs from distinct developmental origins. Employing this system, we selectively knocked out Tgfbr2 in the ascending aorta and Smad4 in the aortic arch. Our results distinctly demonstrate the indispensable roles these genes play in sustaining SMC integrity across different aortic segments. This advanced genetic system not only deepens our understanding of aortopathies but also significantly enhances the potential for modeling and elucidating the mechanisms driving segment-specific aortic diseases.

overall_design: Aortic cells were harvested from CNC-SMC-Cre;Smad4flox/flox;R26-tdT genotyped adult mice and analyzed using scRNA-seq .

first: Ximeng

last: Han

first: Enci

last: Wang

first: Huan

last: Zhu

first: Xiuzhen

last: Huang

first: Wenjuan

last: Pu

first: Mingjun

last: Zhang

first: Kuo

last: Liu

last: Zhao

first: Zixin

first: Ben

last: He

first: Bin

last: Zhou


title: Tumor Extracellular Vesicles lncOSLMT Drives Lung Inflammatory Premetastatic Niche Formation in Osteosarcoma via m6A-Dependent hnRNPA2B1/COX-2 Axis

city: Guangzhou

first: Zehao

last: Guo

state: Guangdong

address: zhongshan 2 road

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: Tumor-derived extracellular vesicles (EVs) play critical roles in premetastatic niche (PMN) formation. Here, we demonstrated that EVs from highly metastatic osteosarcoma cell lines preferentially localized to lung fibroblasts and induce inflammatory PMN formation. High-throughput profiling of EVs-derived long noncoding RNAs (lncRNAs) identified lncOSLMT as a candidate enriched in EVs and markedly upregulated in patient tumor and serum, with elevated levels correlating with poor prognosis. Mechanistically, in EVs, lncOSLMT directly bound the RNA-binding protein hnRNPA2B1. Following internalization by recipient lung fibroblasts, hnRNPA2B1 bound to N⁶-methyladenosine (m⁶A) -modified sites in the 3’UTR of PTGS2 mRNA, leading to transcript stabilization and increased COX-2 expression. For therapeutic intervention, we developed lactoferrin-resveratrol (LF-RES) nanoparticles, which loaded siRNA against lncOSLMT. Intravenous administration of LF-RES-siRNA in mice reduced EVs-induced lung inflammation and suppressed lung metastasis. Combination with EP2/EP4 antagonists produced enhanced anti-metastatic effects. These findings establish EVs-derived lncOSLMT as a key regulator of inflammatory PMN formation in the lung and highlight the potential of LF-RES-siRNA nanoparticles as a targeted anti-metastatic therapy in osteosarcoma.

overall_design: HFL-1 cells were treated with extracellular vesicles (EVs) derived from oelncOSLMT or vector control.

first: Xianbiao

last: Xie

first: Hongbo


title: RNA-seq of HFL-1 Cells Overexpressed GFP, GFP-ERG or GFP-ERG-ΔIDR13

city: Chengdu

first: Lu

state: Sichuan

address: #37 Guoxue Alley, Wuhou District

institute: west china hospital

summary: This dataset contains rawRNA-seq data from HFL-1 Cells  Overexpressed GFP, GFP-ERG or GFP-ERG-ΔIDR13. The experiment aims to explore the downstream genes of ERG and its phase separation-deficient mutant to uncover the role of ERG's LLPS activity in regulating gene expression in HFL-1 cells, providing insights into the regulatory networks controlled by ERG in cell senescence.

overall_design: RNA-seq of ERG, its LLPS-deficient mutant ΔIDR13 and GFP control in HFL-1 cells to understand the downstream genes and regulatory activity associated with ERG'S phase separation mechanism.


title: TDP-43 pathology triggers neuroinflammation and cognitive impairment by inducing microglial necroptosis

first: Shenrui

address: Kongjiang Road 1665, Yangpu District

institute: Xinhua Hospital, Shanghai Jiao Tong University School of Medicine

summary: Pathological TAR DNA-binding protein-43 (TDP-43) is a defining feature of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD) and Alzheimer’s disease (AD). However, the mechanism by which TDP-43 pathology disrupts microglial function and drives neuroinflammation remain unclear. In this study, we demonstrated that cytoplasmic mis-localized TDP-43 exacerbated neuroinflammation, induced cell death, and impaired phagocytic function in microglial cells, primarily through receptor interacting serine/threonine kinase 3 (RIPK3)-dependent necroptosis. Pharmacological inhibition of RIPK3 with GSK872 markedly attenuated these pathological effects in vitro. These findings were further corroborated in a murine model with cytoplasmic TDP-43 mis-localization, where GSK872 treatment remarkably alleviated neuroinflammation and restored cognitive deficits. Mechanistically, our findings indicate that the nuclear depletion of TDP-43, resulted from its cytoplasmic mis-localization, impairs its ability to transcriptionally repress the Ripk3 gene, subsequently leading to RIPK3 upregulation and activation of RIPK3-dependent necroptosis. Collectively, our findings establish RIPK3-dependent necroptosis as a critical driver of TDP-43 pathology-mediated neuroinflammation and identified necroptosis as a promising therapeutic target in TDP-43-associated neurodegenerative disorders.

overall_design: RNA-seq profiling of BV2 microglial cells with TDP-43 NLSmut expression and control BV2 cells.

first: Weiwei

last: Cheng


title: RNA-Seq analysis of roots of Stylosanthes guianensis in response to manganese toxicity

city: Haikou

first: Zhijian

last: Chen

email: jchen@scau.edu.cn, zjchen@catas.cn

address: Xueyuanlu 4

institute: Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences

summary: Stylo (Stylosanthes guianensis) is an important tropical legume with superior tolerance to manganese (Mn) toxicity, which severely constrains plant growth especially in tropical acid soils. However, the underlying mechanisms of Mn tolerance in stylo remain largely unknown. SgUBC2, an ubiquitin-conjugating enzyme, has been documented to involved in Mn tolerance in stylo. RNA-seq analysis showed that overexpression of SgUBC2 resulted in changes in a variety of Mn-responsive gene expressions, including genes associated with antioxidant defense response, ion transporter and organic acid metabolism.

overall_design: In this study, the transgenic composite stylo plants overexpressing SgUBC2 (OX-SgUBC2) were generated by Agrobacterium rhizogenes-mediated hairy root transformation metood. The composite stylo plants transformed with the pFGC5941 binary vector (EV) was used as control. After verification of SgUBC2 transcripts in the hairy roots via RT-qPCR analysis, roots of OX-SgUBC2 and EV lines were harvested for RNA-seq analysis.


title: CAR-neutrophils produced in vivo to treat glioma

city: West Lafayette

first: Qing

last: Deng

state: IN

address: 915 Mitch Daniels Boulevard

department: Biological Science

country: USA

institute: Purdue University

summary: We used single-cell sequencing to compare gene expression and cell subset distribution of in vivo engineered CLTX- CAR- Neutrophils and conventional neutrophils in the tumors.

overall_design: Transcriptome profiles of Conventional neutrophil treated GBM mouse tumor tissue and In vivo Engineered CAR-neutrophil treated GBM mouse tumor tissue were generated by scRNA-seq technology using IIIumina NovaSeq6000

first: Chang

last: Yun

first: Xiaoping

last: Bao


title: Effect of Liver-specific SelO Knockout on the Liver Transcriptome of Mice on a Normal Diet

city: Tian Jin

first: Xiaofan

last: Jia

address: No.22, Qixiang Tai Road, Heping District, Tianjin

department: School of basic medical sciences

institute: Tianjin Medical University

summary: This study investigates the role of SelO in liver metabolism. RNA sequencing analysis of mouse liver tissues revealed significantly differentially expressed genes enriched in pathways related to fatty acid beta-oxidation and NAD-related metabolic processes. Our cell biology and biochemistry experiments suggest that SelO is involved in lipid metabolism. These findings indicate that the knockout of SelO leads to transcriptomic changes that align with increased lipid oxidation

overall_design: RNA-seq using total RNA. Three knockout samples, three control samples. Comparative gene expression profiling analysis of RNA-seq for liver tissues from control mice and knockout mice.

first: Yuan

last: Fu

first: Ting


title: Ultra high-throughput single-cell transcriptome and epitope profiling of healthy human PBMCs using SCITO-seq2

city: Seoul

first: Byungjin

last: Hwang

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

country: South Korea

institute: Yonsei University

summary: This study presents comprehensive single-cell transcriptome and surface protein profiling using SCITO-seq2, an enhanced platform that improves the recovery of unique transcripts while enabling simultaneous detection of surface proteins. The analysis was conducted in two phases: first, using healthy donor PBMCs to validate technical performance, and second, by comparing samples from healthy controls, patients with childhood systemic lupus erythematosus (cSLE), and patients with CTLA4 haploinsufficiency and autoimmune infiltration (CHAI). These results demonstrate the platform’s applicability to both normal and disease states.

overall_design:
The study consisted of two major experimental sets.
PBMC 1: Fresh PBMCs from a healthy donor were divided into four replicate pools, each labeled with pool-specific antibodies and RNA probes. After pooling, 200,000 cells were loaded onto a Chromium Next GEM Chip Q for GEM generation to assess data consistency across pools derived from the same sample.
PBMC 2: Fresh PBMCs were isolated from healthy donors (n=4), childhood systemic lupus erythematosus (cSLE) patients (n=4), and CTLA4 haploinsufficiency with autoimmune infiltration (CHAI) patients (n=2). For sample multiplexing, cells from healthy and cSLE groups were labeled with unique TotalSeq-B hashing antibodies and pooled within their respective groups, while CHAI samples were processed as individual pools.
All samples underwent fixation and RNA probe hybridization following the 10x Genomics protocol. For each experimental set, 200,000 cells were loaded onto a Chromium Next GEM Chip Q for GEM generation. Libraries were prepared using the 10x Genomics Fixed RNA Profiling protocol and sequenced on an Illumina NovaSeq 6000 platform with 2 × 150 bp paired-end reads.

first: Su-Hyeon

last: Lee

first: Bo-yeong

last: Jin

first: Murim

last: Choi


title: Mice with targeted deletion of the Vasoactive Intestinal Peptide (VIP) gene have spontaneous pulmonary arterial hypertension exaggerated with hypoxia

status: Public on Jan 03 2026

city: Hempstead

first: Anthony

last: Szema

state: New York

address: 500 Hofstra Blvd,

department: Department of Occupational Medicine, Epidemiology and Prevention,

institute: Donald and Barbara Zucker School of Medicine

summary: We earlier reported spontaneous moderate pulmonary arterial hypertension in Vasoactive Intestinal Peptide (VIP) gene knockout mice. In the current study, we show accelerated pulmonary artery pressure changes associated with vascular and cardiac remodeling changes in VIP KO mice subjected to hypoxia compared to control wild-type C57BL/6 mice in hypoxia chambers. There is differential whole-lung RNA sequencing expression between baseline normoxia wild-type and VIP KO mice groups. Under conditions of hypoxia vs. normoxia, we observe upregulation of spatial biology expression of CD45 in VIP KO mice with hypoxia, but not in wild-type mice with hypoxia. Moreover, wild-type hypoxia mice express alpha-actin and CD31, which is not seen in the VIP KO hypoxia cohort. Human lung tissue from pediatric patients with idiopathic pulmonary arterial hypertension (PAH) lacks immunohistochemical evidence of VIP, supporting the concepts that VIP plays a critical role in the immunopathogenesis of pulmonary hypertension and VIP or its analogues may potentially be used to treat PAH.

overall_design: Lung tissue RNA-seq profiling of C57BL/6 (wild-type mouse) vs.VIP knockout mouse in normoxia and 4 weeks of chronic Hypoxia (10% O2) exposure.

first: Akash

last: Gupta

first: Mohamed

last: Ahmed

middle: N


title: Integrated analysis of mRNA and miRNA expression profiling in double negative T cells converted from mouse CD4 T cells

city: Beijing

first: Dong

last: Zhang

address: #95 Yongan Street

institute: Beijing Friendship Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: To reveal the differential mechanism and the role of microRNA (miRNA) regulation in double negative T cell (DNT cell) conversion, we have analyzed the message RNA (mRNA) and miRNA expression profiles using high-throughput sequencing. Our results demonstrated that differentially expressed mRNAs and miRNAs represent extensively changes between naïve CD4 T cells, activated CD4 T cells and DNT cells.

overall_design: Examination of mRNA and miRNA expression in 3 cell types.

first: Dan

last: Tian


title: Cigarette smoke and biological age induce degenerative heterogeneity in retinal pigment epithelium [scRNA-seq]

city: Baltimore

first: Yang

state: MD

address: 620 Boulton St. Bel Air

institute: Johns Hopkins University

summary: Environmental exposure such as cigarette smoke induces epigenetic changes that can induce degenerative heterogeneity and accelerate aging. In early age-related macular degeneration (AMD), the leading worldwide cause of blindness among the elderly, retinal pigment epithelial (RPE) cell heterogeneity is a key change. Since smoking is the strongest environmental risk factor for AMD, we hypothesized that cigarette smoke induces degenerative RPE heterogeneity through epigenetic changes that are distinct from aging, and that with aging, the RPE becomes vulnerable to cigarette smoke insult. We administered cigarette smoke condensate (CSC) intravitreally to young and aged mice and performed snRNA-seq and snATAC-seq on the RPE/choroid. This analysis identified separate cell clusters corresponding to healthy and abnormal, dedifferentiated RPE in both aged vehicletreated and young CSC-treated mice. The dedifferentiated RPE were characterized by a global decrease in chromatin accessibility and decreased expression of genes in functional categories that were linked to hallmarks of aging. Notably, young, dedifferentiated RPE also exhibited a compensatory upregulation of hallmarks of aging-related genes, specifically those related to mitochondrial function and proteostasis. In contrast, aged dedifferentiated RPE did not express these compensatory changes, and did not survive CSC treatment, as experimentally verified with TUNEL labeling. These changes are relevant to early AMD because we identified through scRNA-seq, similar dedifferentiated and healthy macular RPE clusters in a donor who smoked and another with early AMD, but not from a nonsmoker. Degenerative cellular heterogeneity can include an abnormal cluster that jeopardizes cell survival and may represent an additional hallmark of ocular aging.

overall_design: The tenets of the Declaration for Helsinki for research involving human tissue were followed. Human eyes (n=3) were obtained from the Advancing Sight Network (Birmingham, AL). Preliminary experiments were conducted to determine the viability of RPE that was based on death to enucleation (D-E) time. Single cell RNA-seq on normal eyes from two different 86 yr old female donors with D-E of 3.3 and 6 hr with experimentation time of <24 hours and found that the 3.3 hr D-E interval globe exhibited superior viability (>70%), and nearly double the number of genes detected per cell (1301 vs 708 genes/cell). Therefore, globes with D-E times of < 6 hr and death to experimentation of <24 hr. Specifically, human globes from a 79 yr old female nonsmoker without AMD with a death to enucleation (D-E) time of 4.9 hr, a 67 yr old male smoker without AMD with a D-E of 3.8 hr, and a 67 yr old female smoker with early AMD (Minnesota Grade 2) with a D-E of 1.8 hr were immediately preserved on ice for overnight shipping to Hopkins, and dissected no later than 16 hr postmortem. After removing the anterior segment, the fundus was examined both with the retina and with the retina removed and classified using the Minnesota Grading Scale105. A 6 mm sample of the RPE/choroid in the macula was obtained using a 6 mm punch (Integra Lifesciences, Princeton, NJ) that was centered around the fovea. RPE/choroidal cells were dissociated using Papain Dissociation System (Worthington Biochemical, Lakewood, NJ) following the manufacturer’s instructions. Dissociated cells were resuspended in ice-cold PBS, 0.04% BSA and 0.5 U/μl of RNAse inhibitors. Cells were then filtered through a 50μm filter and processed for single-cell RNA-sequencing. Cell viability (>90%) was confirmed by negative staining with trypan blue.

first: Krishna

last: Singh

first: Jiang

last: Qian

first: James

middle: T

last: Handa


title: Impact of copper on the physiology and transcriptome of Methylosinus trichosporium OB3b grown on either methane or methanol

city: Ann Arbor

first: Peng

last: Peng

state: MI

address: 1351 Beal Avenue

institute: University of Michigan

summary: This study investigates the combined effects of copper availability and carbon source (methane versus methanol) on the physiology and transcriptome of Methylosinus trichosporium OB3b, a model Type II methanotroph. Methanotrophs oxidize methane to carbon dioxide through intermediates such as methanol, formaldehyde, and formate, using two forms of methane monooxygenase (MMO): the copper-dependent particulate MMO (pMMO) and the soluble MMO (sMMO). Although Msn. trichosporium OB3b can utilize both methane and methanol as sole carbon sources, growth on methanol is significantly affected by copper. In the presence of copper, methanol-grown cells exhibited impaired growth, formate accumulation, and decreased pH, while buffering with MOPS restored growth. NADH/NAD ratios increased nearly tenfold in methanol-grown cultures with copper, indicating redox imbalance. Transmission electron microscopy revealed disrupted intracytoplasmic membranes under these conditions. Transcriptomic analysis showed that genes involved in methanol oxidation were differentially expressed in response to copper and carbon source, and two siderophore biosynthetic gene clusters were repressed during methanol growth with copper. Overall, the findings suggest that Msn. trichosporium OB3b modulates metallophore expression and carbon metabolism to manage oxidative and redox stress under methanol growth conditions. Understanding these regulatory mechanisms is critical for optimizing methanotroph-based biotechnological applications, including methanol-driven biosynthesis of valuable compounds such as methanobactin.

overall_design: RNA-seq profiling of Methylosinus trichosporium OB3b grown on methane with and without copper, and grown on methanol without copper and with copper plus MOPS buffer.

first: Jeremy

middle: D

last: Semrau


title: The effect of culture medium from ferroptotic BMDMs on microglia

city: Nanjing, Jiangsu

first: xuan

last: zhao

address: 300 Guangzhou Road

department: Orthopedics

institute: The First Affiliated Hospital of Nanjing Medical University

summary: To investigate the altered gene expression levels in microglia treated with culture medium from ferroptotic BMDMs and normal BMDMs. Each group had a biological repeat (n=3). Results provide insight into the effect of culture medium from ferroptotic BMDMs on microglia.

overall_design: Three groups of microglia treated with ferroptotic BMDMs culture medium(FeM CM) versus three groups of microglia treated with normal BMDMs culture medium(C CM).

first: Shujie

last: Zhao

first: Guoyong

last: Yin

first: Xuan


title: CUT&Tag seq analysis of histone variant H2BE in stimulated neurons

status: Public on Jan 02 2026

city: Philadelphia

first: Emily

last: Feierman

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary: A cell’s ability to respond and adapt to environmental stimuli relies in part on transcriptional programs controlled by histone proteins. Histones affect transcription through numerous mechanisms including through replacement with variant forms that carry out specific functions. We recently identified the first widely expressed H2B histone variant, H2BE and found that it promotes transcription and is critical for neuronal function and long-term memory. However, how H2BE is regulated by extracellular stimuli and whether it controls activity-dependent transcription and cellular plasticity remain unknown. We used CUT&Tag and RNA-sequencing of primary neurons, single-nucleus sequencing of cortical tissue, and multielectrode array recordings to interrogate the expression of H2BE in response to stimuli and the role of H2BE in activity-dependent gene expression and plasticity. We find that unlike Further, we show that neurons lacking H2BE are unable to mount proper long-term activity-dependent transcriptional responses both in cultured neurons and in animal models. Lastly, we demonstrate that H2BE knockout neurons fail to undergo the electrophysiological changes associated with homeostatic plasticity in neurons after long-term stimulation. In summary, these data demonstrate that H2BE expression is inversely correlated to activity and necessary for long-term activity-dependent responses, revealing the first instance of a histone variant involved in the homeostatic plasticity response in neurons.

overall_design: Seizures were induced by IP injection of pentylenetetrazol. Cortices were microdissected and flash-frozen 2h after seizure. Nuclei were isolated using an iodixanol gradient and used as input for CUT&Tag.


title: Increased MALAT1 Levels in Thyroid Cancer are Linked to Metabolic Reprogramming and Lymphatic Infiltration in Chilean population

city: Santiago

first: Gino

last: Nardocci

address: Av. Mons. Álvaro del Portillo 12.455

country: Chile

institute: Universidad de los Andes

summary: Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a long non-coding RNA (lncRNA) implicated in cancer progression. In thyroid cancer, MALAT1 has been proposed as a potential biomarker, but its role in disease progression remains incompletely understood. Here, we analyzed MALAT1 RNA levels in tumoral and non-tumoral paired-thyroid samples from a cohort of Chilean thyroid cancer patients. We found a positive correlation with lymphatic infiltration. RNA-seq analysis revealed upregulation of genes associated with epithelial-to-mesenchymal transition and downregulation of cell-adhesion molecules. Metabolism-associated genes were also altered.

overall_design: RNA seq profiling of thyroid tissues obtained from papyllary thyroid cancer patients at the time of surgery. Samples come from tumor or adjacent (control) tissue

first: Michelle

last: Tobar-Lara

first: Andrea

last: Matamoros

first: Marcelo

last: Muñoz-González

first: Diego

last: Leiva

first: Gunther

last: Redenz

first: Patricio

last: Cabané

first: Alvaro

middle: A

last: Elorza

first: Rodrigo

last: Aguilar


title: RNA-seq analysis of neurons overexpressing histone variant H2BE and stimulated with BDNF

overall_design: WT neurons were isolated from E16 cortical tissue. Neurons were infected with control or H2BE expression lentiviruses. Neurons were then treated with BDNF or left unstimulated. 24h later neurons used for RNA-seq.


title: Cellular Mg2+ decrease causes a distinctive NF-κB-dependent form of cell death

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Mg2+ is an essential cofactor for numerous enzymes, supporting fundamental cellular processes. Phosphatase of regenerating liver (PRL) protein family, inhibits cyclin M (CNNM) Mg2+ efflux transporters. To elucidate the physiological role of PRL in Mg2+ homeostasis at the cellular level, we employed combined genetic knockout and knockdown approaches. Such PRL KO + KD led to marked reduction of intracellular Mg2+ levels and triggered extensive cell death. To investigate the mechanism underlying cell death induced by PRL KO + KD, we next performed transcriptomic analysis to profile the changes in global gene expression, which revealed activation of the NF-κB pathway, and accordingly, genetic deletion of NF-κB p65 subunit abrogated cell death. Similarly, CNNM overexpression triggered intracellular Mg2+ decrease, NF-κB activation and subsequent cell death. Notably, this form of cell death exhibited unique morphological features, including actin-driven fiber-like protrusions, distinguishing it from known cell death modalities. Our findings uncover a previously unrecognized mode of NF-κB-dependent cell death triggered by intracellular Mg2+ decrease.

overall_design: RNA-seq analysis of wild-type or PRL2-/-; PRL1+/- cells transfected with control or PRL1-siRNA

first: Koyuki

last: Kawamura

first: Yosuke

last: Funato

first: Hiroaki

last: Miki


title: Identification and profiling of microRNAs in the midgut of Laodelphax striatellus after rice black-streaked dwarf virus (RBSDV) infection

city: Jinan

first: jianhua

last: zhang

address: gongyebei street No. 23788

institute: Shandong Academy of Agricultural Sciences

summary: MicroRNAs (miRNAs) are endogenous small noncoding RNAs (18–25 nt) that are involved in many physiological processes including development, cancer, immunity, apoptosis and host-microbe interactions through posttranscriptional regulation of gene expression. In this study, we measured the profile of small RNAs in the midgut of Laodelphax striatellus after rice black-streaked dwarf virus (RBSDV) infection. We identified 19 insect miRNAs that were differentially expressed compared with the RBSDV-free (VF) control. Among them, seven were upregulated and 12 downregulated in the RB midgut. Four miRNAs exhibited high expression levels (>500 reads) in either the VF or RBSDV-infected (RB) midgut; among them, three were up-regulated. This study identified critical miRNAs involved in the RBSDV infection in the midgut of L. striatellus.

overall_design: The microRNAs expression profile during RBSDV infection in the midgut of L. striatellus.


title: CREB and H3K4 CUT&RUN seq of mouse fetal testis

city: Cincinnati

first: Shuyun

last: Li

state: NC

address: 3333 Burnet Ave

institute: CCHMC

summary: CUT&RUN analyses to examine CREB genomic binding sites in E13.5, E16.5, and E18.5 XY gonads, with H3K4me3 serving as a positive control indicative of active transcriptional regions.

overall_design: Male gonads were dissected and dissociated into individual cells by pipetting. The resulting cell suspension was filtered using a 70 µm filter, and 100,000 gonadal cells were used for CUT&RUN (Cleavage Under Targets & Release Using Nuclease) assays following an alternative protocol from Protocol.io (dx.doi.org/10.17504/protocols.io.zcpf2vn).

first: Shu-Yun

first: Satoko

last: Matsuyama

first: Sarah

last: Whiteside

first: Xiaowei

last: Gu

first: Jonah

last: Cool

first: Blanche

last: Capel

first: Tony

last: DeFalco


title: Circulating CD34+ Fibroblast Progenitors Participate in Heart Fibrosis of Allografts in Humans and Mice

city: Hangzhou

first: 小桐

last: 孙

address: 88 Jiefang Road

institute: The Second Affiliated Hospital, School of Medicine, Zhejiang University

summary: In this study, we employed single-cell RNA sequencing (scRNA-seq; 10X Genomics platform) combined with genetic lineage tracing in mouse models to comprehensively characterize the non-cardiomyocyte cellular composition of cardiac allografts. Fibrosis is one of the major causes of cardiac allograft malfunction, and is mainly driven by fibroblasts. In this study, we proposed that recipiene derived cells, expecailly CD34+ populations, are an important source of allograft fibroblasts, and play a crucial role in the fibrosis of transplanted hearts.

overall_design: Both control and transplanted hearts were enzymatically digested and processed by fluorescence-activated cell sorting (FACS) to isolate viable nucleated target cells. Then the cells were subjected to scRNA-seq analysis.

first: Xiaotong

last: Sun

first: Ting

last: Wang

first: Hui

last: Gong


title: The angiopoietin receptor Tie2 restricts proliferation and sprouting of cardiac endothelial cells

city: Helsinki

first: Madeleine

middle: Helena

last: Lackman

state: Uusimaa

address: Haartmaninkatu 8

department: Faculty of Medicine

country: Finland

institute: University of Helsinki

summary: Tie1 and Tie2 receptors are important in the maintenance of the vascular steady-state. We used scRNAseq to analyze how genetic deletion of Tie1 and Tie2 affects expression of proliferation-related genes in mouse endothelial cells.

overall_design: (1) Stromal-vascular fraction (SVF) of the mouse heart was prepared by enzymatic (mix of collagenases) digestion of the heart tissue. RBC were lyzed by RBC-lysis buffer. (2) EC-enriched fraction of the mouse heart was prepared by enzymatic digestion of the heart tissue. EC fraction was isolated using FACS and antibody staining of the EC markers. (3) EC-enriched fraction of the mouse kidney was prepared by enzymatic digestion of the kidney. EC fraction was isolated using FACS and antibody staining of the EC markers. (4) EC-enriched fraction of the mouse lung was prepared by enzymatic digestion of the lung. EC fraction was isolated using FACS and antibody staining of the EC markers.

first: Andrey

last: Anisimov

middle: H

first: Kari

last: Alitalo

first: Sinem

last: Karaman


title: Differential expression of mitomiRs in pancreatic islet cells associated with maternal protein restriction

city: Lausanne

first: Cecile

last: Jacovetti

address: Rue du Bugnon 9

department: Fundamental Neurosciences

country: Switzerland

institute: University of Lausanne

summary: In this study, we discovered cytosolic and mitochondrial small non-coding RNAs (tRNA-derived fragments, piRNAs and microRNAs) which may act as new regulators of cellular and metabolic functions. We analzyed the expression profile and function of tRNA-derived fragments in a previous study (https://doi.org/10.1016/j.molmet.2024.101955). In this current study, we focused our analysis on hundreds of microRNAs and piRNAs in the mitochondrial fractions versus whole cell lysates from pancreatic islets of progeny of rats exposed to a low-protein (LP) diet during in utero and lactation period and compared them to control rats. At 22 days of age, LP-exposed rats  exhibit a reduced body weight and a decreased beta-cell mass. These animals are more prone to develop diabetes and display a glucose intolerance at adulthood. In our analysis, we identified 6164 tRFs, 543 microRNAs, 118 piRNAs and 32 other types of small non-coding RNAs in the islets of  LP-exposed rats, among which 400 exhibited significant changes (total read counts ≥ 13 cutoff, p ≤ 0.05) compared to controls. Of these, 167 tRFs showed increased levels, while 233 small non-coding RNAs showed decreased levels in the LP-exposed rat islets. Analysis of mictochondrial content revealed the presence of 548 tRNA-derived fragments, 33 microRNAs, 18 piRNAs and 22 other types of small non-coding RNAs in the mitochondrial fractions of control rat islets while the mitochondrial fractions of LP-exposed rat islets contained 564 tRNA-derived fragments, 23 microRNAs, 9 piRNAs and 23 other types of small non-coding RNAs. Our analysis revaled 10 microRNAs that are concomitantly enriched in the mitochondria while being reduced in cytosol of LP-exposed islet cells. Our findings reveal a significant reshaping of mitochondrial small non-coding RNAs in pre-diabetic conditions, coinciding with a well-established mitochondrial metabolic defect under these conditions.

overall_design: In order to characterize the expression profile of small non-coding RNAs in both compartments, mitochondria and cytosol, in a pre-diabetic context, we isolated total RNA from mitochondrial fractions and whole cell lysates from pancreatic islets of four LP-exposed rats and compared it to that of four controls (rats exposed to a control diet).

first: Romano

last: Regazzi


title: Cigarette smoke and biological age induce degenerative heterogeneity in retinal pigment epithelium

first: Yang

last: Jin

overall_design: C56BL/6J mice that were free of the Rd8 mutation (Jackson Labs, Bar Harbor, ME) were given water ad libitum and kept in a 12-hr light–12-hr dark cycle. For experiments, an equal number of male and female mice aged either 3- or 12-months old were given an IVT injection of 250 μg/ml CSC in 1 μl (Murty Pharmaceuticals, Inc. Lexington, KY) or an equal volume (1 μl) of vehicle (DMSO) in both eyes using a microinjection pump (Harvard Apparatus, Holliston, MA, USA) on day 1 and day 3.

first: Krishna

last: Singh

first: Jiang

last: Qian

first: James

last: Handa


title: Patient-derived liver organoids recapitulate epithelial heterogeneity and enable precision disease modelling of alcohol-associated liver disease

city: Barcelona

first: Pau

last: Sancho

address: C/ Rosselló, 149-153

country: Spain

institute: Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)

summary: Organoids are emerging as a powerful human-based in vitro tool in the biomedical field. However, patient-derived liver organoids fail to recapitulate the liver epithelial heterogeneity and its generation still requires liver  surgical resections, thus limiting personalized chronic liver diseases modeling. Here, we report the derivation of organoids from intact liver needle biopsies(b-Orgs) from alcohol-associated liver disease (ALD) patients for precision disease modeling and drug testing. B-Orgs were generated with an efficiency of 80% from patients with early and advanced stages of ALD. b-Orgs show an enriched hepatocyte phenotype as assessed by immunofluorescence, functional studies, and transcriptomics. Single cell RNA-sequencing revealed a heterogeneous epithelial composition comprising hepatocyte, biliary and progenitor hepatobiliary populations, mirroring the epithelial populations found in advanced ALD patients. Moreover, b-Orgs preserve disease-stage features, as b-Orgs from advanced ALD patients showed increased expression of genes related to epithelial-mesenchymal transition, angiogenesis and inflammation. Stimulation of b-Orgs with ethanol and pro-inflammatory mediators,promoted ALD features such asROS production, lipid accumulation, inflammation and decreased proliferation, which were mitigated in response to prednisolone. Overall, we provide a new methodology to obtain b-Orgs showing epithelial complexity and patient specific features, thus expanding organoid-based liver disease modelling for personalized medicine.

overall_design: single-cell RNA sequencing 3' (scRNA-seq)

first: Aina

last: Rill-Hinarejos

first: Silvia

last: Ariño

last: Sancho-Bru


title: Loss function of Fkbp5 leads to gene network alterations related to neuron development, mitochondria morphology, and calcium permissiveness at baseline and in alcohol stimulation conditions

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: RNA-seq was performed on the hippocampus of Fkbp5 KO and WT control mice with and without alcohol IP injection at 2g EtOH/Body weight dose

overall_design: Total RNA was isolated from hippocampus (hi) of both female (f) and male (m)  Fkbp5 KO and WT mice with (alc) or without (naive) alcohol injection. Gene expression was compared between Fkbp5 KO and WT in naïve and alcohol injection conditions. Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 2000 in triplicate.

first: Tiebing

last: Liang

first: Weidong

last: Yong

first: Zou

last: Yi

first: Lai

last: Zhao


title: Transcriptomics reveals the role of NHEJ in mycobacterial antiphage defense

status: Public on Jan 01 2026

city: Chongqing

first: Hongxiang

last: Xu

address: Tiansheng Road

institute: Southwest University

summary: In the ongoing arms race with phages, bacteria have evolved diverse defense systems, such as CRISPR-Cas and restriction-modification systems. The DNA double-strand break (DSB) repair system represents a core mechanism for maintaining genomic integrity and is vital for cell survival. However, it remains unknown whether and how these repair systems contribute to phage resistance. This study systematically investigates the role of the non-homologous end joining (NHEJ) during phage infection in Mycobacterium smegmatis. We found that NHEJ deficiency compromises host resistance to phage SWU1, as evidenced by increased plaque counts and reduced bacterial survival. Mechanistically, phages exploit host NHEJ for genomic repair; however, the error-prone nature of NHEJ leads to imperfect repair at phage cos sites, thereby blocking replication. The host modulates the balance between NHEJ and homologous recombination (HR) to control repair fidelity: NHEJ loss shifts the balance towards high-fidelity HR, which in turn promotes phage survival. Furthermore, NHEJ deficiency exacerbates infection-induced oxidative stress, leading to a compromise in bacterial viability. Our findings reveal the multifaceted functions of NHEJ in mycobacterium-phage interactions and provide new insights into how DNA repair systems shape antiphage defense and coevolution.

overall_design: M. smegmatis and its ΔkuΔligD were cultured in 7H9 medium to an OD600 of 2.0. Bacterial cells were collected by centrifugation and resuspended in fresh 7H9 medium to an OD600 of 1.0. The cultures were then infected with SWU1 phage at an MOI of 10, followed by a 30 minutes adsorption period at 37℃. Subsequent incubation was carried out at 37°C with shaking at 200 rpm for 30 and 180 minutes. At each time point, bacteria were harvested by centrifugation, and total RNA was extracted for RNA-seq analysis.


title: CUT&RUN analysis of transcription factor myc

first: Emily

last: Feierman

summary: Here we performed CUT&RUN, targeting FLAG-tagged WT and edited myc proteins in transfected HEK293T cells.

overall_design: We performed CUT&RUN against FLAG, myc, and a control IgG in HEK293T cells.


title: Alzheimer’s disease neuroinflammatory risk genes can be targeted with RNase-H active antisense oligonucleotides in human microglia

city: Beerse

first: An

last: De Bondt

address: Turnhoutseweg

country: Belgium

institute: Janssen Research & Development

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

overall_design: Refer to individual Series


title: Chrysin alleviates cardiomyocyte ferroptosis of diabetic cardiomyopathy by modulating SCD1

city: Nanjing

first: can

last: xiong

address: 101 Longmian Avenue, Jiangning District

department: Basic Medical Sciences

institute: Nanjing Medical University

summary: Our findings demonstrated that chrysin supplementation improved the impaired cardiac function in DCM mice and alleviated HG-induced damage in AC16 cells. Whole transcriptome sequencing analysis indicated that the cardioprotective effects of chrysin are closely associated with the inhibition of cardiomyocytes ferroptosis. Chrysin treatment attenuated elevated ferroptosis, as evidenced by reduced Fe2+ content and lipid peroxidation levels, enhanced antioxidant capacity and restored expression of SLC7A11 and GPX4.

overall_design: RNA-seq of AC16 cells treated with high glucose and chrysin

first: Fang

last: Chen


title: MED12 dictates epithelial ovarian cancer cell ferroptosis sensi- 2 tivity via YAP-TEAD1 signaling

city: Guangzhou

first: Xiaolin

last: Luo

address: Dongfeng Road No.651

institute: Sun Yat-sen University Cancer Center

summary: Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy, with 11 chemotherapy resistance representing a major therapeutic challenge. Emerging evidence 12 suggests that ferroptosis, an iron-dependent form of regulated cell death, may selectively 13 target chemoresistant cancer cells. Here, we identify MED12 as a critical regulator of fer- 14 roptosis sensitivity in EOC through modulation of the YAP-TEAD1 signaling pathway. 15 Using CRISPR/Cas9-mediated knockout and rescue experiments in EOC cell lines, we 16 demonstrate that MED12 deficiency significantly enhances sensitivity to ferroptosis in- 17 ducers (RSL3 and Erastin), as evidenced by reduced IC50 values. Transcriptomic and 18 chromatin accessibility analyses reveal that MED12 loss activates YAP signaling through 19 TEAD1 upregulation, increasing chromatin accessibility at YAP-TEAD1 target loci and 20 elevating expression of downstream effectors CYR61 and CTGF. Pharmacological inhibi- 21 tion of YAP with verteporfin or siRNA-mediated TEAD1 knockdown reverses ferroptosis 22 sensitivity in MED12-deficient cells, confirming pathway specificity. These findings es- 23 tablish MED12 as a modulator of the YAP-TEAD1-ferroptosis axis and suggest that tar- 24 geting this pathway could overcome chemoresistance in MED12-deficient EOC. Our work 25 provides a mechanistic foundation for exploiting ferroptosis induction as a therapeutic 26 strategy in ovarian cancer.

overall_design: RNAseq assay of HO8910 WT cells,  HO8910 MED12 KO1# cells and HO8910 MED12 KO2#


title: MED12 dictates epithelial ovarian cancer cell ferroptosis sensi-tivity via YAP-TEAD1 signaling

summary: Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy, with chem-otherapy resistance representing a major therapeutic challenge. Emerging evidence suggests that ferroptosis, an iron-dependent form of regulated cell death, may selectively target chemoresistant cancer cells. Here, we identify MED12 as a critical regulator of ferroptosis sensitivity in EOC through modulation of the YAP-TEAD1 signaling pathway. Using CRISPR/Cas9-mediated knockout and rescue experiments in EOC cell lines, we demonstrate that MED12 deficiency significantly enhances sensitivity to ferroptosis in-ducers (RSL3 and Erastin), as evidenced by reduced IC50 values. Transcriptomic and chromatin accessibility analyses reveal that MED12 loss activates YAP signaling through TEAD1 upregulation, increasing chromatin accessibility at YAP-TEAD1 target loci and elevating expression of downstream effectors CYR61 and CTGF. Pharmacological inhi-bition of YAP with verteporfin or siRNA-mediated TEAD1 knockdown reverses ferrop-tosis sensitivity in MED12-deficient cells, confirming pathway specificity. These findings establish MED12 as a modulator of the YAP-TEAD1-ferroptosis axis and suggest that targeting this pathway could overcome chemoresistance in MED12-deficient EOC. Our work provides a mechanistic foundation for exploiting ferroptosis induction as a thera-peutic strategy in ovarian cancer.

overall_design: 50,000 cells were processed using the ATAC protocol. Libraries were quantified with Bioptic Qsep100 Analyzer（Bioptic lnc.）and paired-end sequenced with read lengths of 150. The ENCODE ATAC-seq pipeline was used for quality control and statistical signal processing of short-read sequencing data, producing alignments and measures of en-richment. 150 bp paired-end reads were mapped to the reference genome build (human, hg38). Differentially sites were detected from ATAC-seq experiments using DiffBind R package.


title: RNA-seq analysis of rat urethral tissue after tetrahedral DNA nanostructure (TDN) treatment

city: Guiyang

first: Jian

last: Li

address: No. 206, Sixian Street, Baiyun District

department: Department of Sports Medicine

institute: Beijing Jishuitan Hospital Guizhou Hospital

summary: Urethral injury often leads to excessive inflammation and fibrosis, which are major contributors to urethral stricture and impaired tissue repair. Tetrahedral DNA nanostructures (TDN) are emerging nucleic acid nanomaterials with favorable biocompatibility and immunomodulatory properties; however, their transcriptomic effects during urethral injury repair remain poorly understood.  In this study, a rat model of urethral injury was established using a mechanical method, and animals were treated with TDN or vehicle control. Urethral tissues were collected at defined time points after injury and treatment for RNA sequencing (RNA-seq) analysis. Transcriptomic profiling was performed to characterize global gene expression changes associated with urethral injury and to explore the molecular responses to TDN treatment.  This dataset provides a comprehensive resource for investigating gene expression programs involved in urethral injury, inflammation, and fibrosis, and may facilitate further studies on the molecular mechanisms underlying nucleic acid nanomaterial-based therapeutic strategies for urethral repair.

overall_design: Male rats were randomly assigned to different experimental groups, including a control group, a urethral injury model group, and a tetrahedral DNA nanostructure (TDN) treatment group. Urethral injury was induced using a mechanical method, followed by administration of TDN or vehicle control according to the experimental protocol.  Urethral tissues were harvested after treatment, and total RNA was extracted for transcriptome analysis. RNA sequencing (RNA-seq) was performed using an Illumina sequencing platform with paired-end reads. The resulting sequencing data were used to compare global gene expression profiles among experimental groups and to characterize transcriptional changes associated with urethral injury and TDN treatment.


title: Lactylation of HIF-1α at K172 drives HIF1 complex assemble to promote hypoxia-induced immune evasion in esophageal squamous cell carcinoma [CUT&Tag]

city: Beijing

first: Ji

last: Cong

address: No.17, Panjiayuan Nanli, South Huawei Road

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Hypoxia is a hallmark of the tumor microenvironment, but its role in immune evasion in esophageal squamous cell carcinoma (ESCC) remains to be fully elucidated. Here, we demonstrate hypoxia inversely correlated with anti-tumor immune signatures and CD8+ T cell infiltration in clinical samples and murine models. Functionally, reducing hypoxia with the agents TH-302 or PX-478 in the AKR model enhanced intratumoral CD8+ T cell infiltration and increased their expression of Granzyme B, IFNγ, and TNFα. Mechanistically, hypoxia-induced immune suppression was dependent on protein lactylation. Inhibiting lactylation reversed the hypoxic suppression of CD8+ T cell function and abrogated the hypoxia-driven transcriptional program, which involved pathways like glycolysis, TGFβ, and Notch signaling. This lactylation-dependent regulation operated by facilitating the formation of the HIF1 transcription complex. Specifically, mass spectrometry identified lactylation at the K172 site of HIF1α, which was crucial for its binding to HIF1β and subsequent target gene activation. Furthermore, in a preclinical ESCC model, pharmacological inhibition of HIF1α with PX-478 synergized with anti-PD-1 therapy, leading to superior tumor control and enhanced CD8+ T cell cytotoxicity.  Our study identifies HIF1α K172 lactylation as a pivotal mechanism of hypoxia-mediated immune escape in ESCC, suggesting a therapeutic strategy to improve immunotherapy.

overall_design: Genomic occupancy profiling of HIF1α for KYSE150 cells treated with as indicated.

first: Sujuan

last: Zheng


title: Vascular Smooth Muscle Cell-derived KIF13B Protects Against Atherosclerosis: Evidence from Humans and Mice

city: 海淀区

first: YiRan

last: Liu

state: 北京市

department: Department of Biomedical Informatics, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, Beijing, China

institute: PKU

summary: Atherosclerotic cardiovascular disease (ASCVD) remains a leading cause of death worldwide, with plaque instability being a major culprit. Phenotypic switching of vascular smooth muscle cells (VSMCs), the most abundant cell type in the vascular wall, is a central event in atherosclerosis, driving both plaque progression and stability, yet the underlying mechanisms are incompletely understood, limiting drug development targeting this process. Kinesin family member 13B (KIF13B) has been implicated in vascular biology, but its function in VSMCs is unknown. Here, we demonstrate that VSMC-specific deletion of Kif13b in mice overexpressed with proprotein convertase subtilisin/kexin type 9 exacerbated lesion development and impaired plaque stability, characterized by thinner fibrous caps and increased inflammation. Mechanistically, we identified that KIF13B facilitates the Potassium channel tetramerization domain containing 10 (KCTD10)-dependent ubiquitination and proteasomal degradation of Krüppel-like factor 4 (KLF4), a key driver of pathogenic VSMC transition. This KIF13B/KCTD10 axis constrains KLF4 protein levels, thereby inhibiting pro-inflammatory, fibroblast-like VSMC transition and preserving the contractile phenotype. Importantly, the adverse effects of Kif13b deficiency on atherogenesis were effectively rescued by the small-molecule KLF4 inhibitor Kenpaullone. Our results unveil a novel VSMC-specific atheroprotective role for KIF13B, define the KIF13B/KCTD10/KLF4 pathway as a key regulatory axis governing VSMC fate and plaque stability, and validate its therapeutic potential for treating advanced atherosclerosis.

overall_design: The aorta from Ldlr−/− and Ldlr−/−Kif13b−/− mice fed with WD for 20 weeks (mix n = 5 into 1 sample) were performed scRNA-Seq.

first: Guolin

last: Miao

first: Yiran


title: The effects of FTO inhibitors on MeRIP-seq profiles in small cell lung cancer cell line

city: Yiwu

first: Yixuan

last: Yu

address: 1575 Chouzhou North Road, Futian Street

institute: The Fourth Affiliated Hospital of School of Medicine, and International School of Medicine

summary: We reveal that pharmacological inhibition of fat mass and obesity-associated protein (FTO), a key m6A demethylase, exerts anti-tumor effects on the human small cell lung cancer (SCLC) cell line H69, with a close correlation to the remodeling of m6A modification landscape.  We observed that FTO inhibitor treatment significantly elevates global m6A levels in H69 cells, which is attributed to the suppressed demethylase activity of FTO. Meanwhile, the FTO inhibitor FB23-2 can inhibit the proliferation of SCLC.

overall_design: m6A-RIP seq profiling of human small cell lung cancer cell line NCI-H69 treated with DMSO or FTO inhibitor FB23-2


title: Differential Cellular Mechanisms Underlie Language and Executive Decline in Amyotrophic Lateral Sclerosis [RNA-seq]

city: New York

first: Christopher

last: Jackson

state: NY

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

summary: Half of all amyotrophic lateral sclerosis (ALS) patients demonstrate a spectrum of cognitive and behavioral changes over the course of the disease, but the mechanisms underlying this heterogeneity remain unclear. We assemble a high-resolution cellular map of prefrontal cortex regions of the ALS brain by integrating spatial and single-nucleus transcriptomic profiles of a cognitively stratified ALS patient cohort that includes non-neuropathological controls. We find cellular programs characteristic of ALS, including a frequent gliotic response. We also find that executive and language cognitive impairments differ from ALS without cognitive impairment, and from each other, in the extent and pattern of neuronal dysregulation and neuron-glial interactions across different brain regions. These findings reveal a relationship between cognitive phenotype and prefrontal cortex dysfunction in ALS.

overall_design: Bulk RNAseq libraries generated from 68 human donor prefrontal cortex samples (BA44/45 and BA46), across a range of non-neuropathological sudden-death controls, ALS patients, and ALS patients who exhibit cognitive impairment on a standardized screening exam

first: C

first: A

last: Daly

last: Roque

first: J

last: Petrescu

first: H

last: Phatnani


title: Large-scale transcriptomic analyses reveal downstream target genes of ZFY1 and ZFY2 transcription factors in male germ cells

city: Honolulu

first: Monika

last: Ward

state: Hawaii

address: 1960 East-West Rd

department: Institute for Biogenesis Research

institute: University of Hawaii

summary: The mouse zinc finger genes Zfy1 and Zfy2 are essential for male fertility. Recently, we produced Zfy1 knock-out (KO), Zfy2 KO, and Zfy1/2 double-knock-out (Zfy DKO) mice, and found that Zfy DKO males were infertile. The mechanism by which ZFY contributes to reproduction remains unknown but based on predicted protein sequence and in vitro assays we hypothesize that it controls expression of genes essential for spermatogenesis. To identify which genes ZFY regulates, we performed comparative transcriptome analysis of sorted male germ cells at three different spermatogenesis stages from three Zfy KO models and control wild-type males. Significantly altered germ cell transcriptomes were identified with Zfy2 KO and Zfy DKO. Analyses of differentially expressed genes supported that Zfy loss altered spermatogenesis, DNA packaging/chromatin organization, and apoptosis pathways. Alternative splicing was deregulated in Zfy KO models, affecting sperm function and chromatin regulation pathways. In support of in-silico findings, Zfy DKO males were shown to have impaired sperm chromatin organization, functional sperm deficiencies, and increased germ cell apoptosis. ZFY regulation of apoptotic pathways was demonstrated also in transfected human cells. We conclude that Zfy is a critical regulator of meiosis and spermiogenesis in addition to its previously described function as a cell-cycle regulator.

overall_design: We generated mice with knockout of Y chromosome genes Zfy1 (Zfy1, KO), Zfy2 (Zfy2 KO) and both Zfy1 and Zfy2 (Zfy DKO). As as control we used wild-type XY males (WT). All males were on C57BL/6 genetic background. We FACs-purified primary spermatocytes (SC1), secondary spermatocytes (SC2) and round spermatids (RS) from Zfy1 KO, Zfy2 KO, Zfy DKO and XY and performed RNA-seq.


title: Atypical NF-κB activation by endogenous DNA damage drives senescence and aging

city: Minneapolis

first: Paul

middle: D.

last: Robbins

state: Minnesota

address: 312 Church St. SE

department: Biochemistry, Molecular Biology and Biophysics

institute: UNIVERSITY OF MINNESOTA

summary: Chronic activation of NF-κB contributes to senescence and aging, but how endogenous DNA damage engages this pathway in vivo remains unclear. NF-κB can be activated by an atypical pathway in which genotoxic stress triggers ATM-dependent sumoylation of the regulatory subunit NEMO, yet the role of this axis in senescence and aging has not been tested. Here we introduced a knock-in NEMO double-lysine mutant (NEMO-DK) that prevents sumoylation at the conserved sites required for DNA damage-induced NF-κB activation, and examined its impact in Ercc1-/∆ mice, a model of accelerated, DNA damage-driven aging. We demonstrated that NEMO-DK markedly reduced senescence and SASP in primary fibroblasts and across multiple tissues, improved liver and skeletal muscle pathology, attenuated intervertebral disc degeneration, significantly delayed the onset and progression of aging symptoms and extended healthspan. These findings identify DNA damage-induced NEMO sumoylation as a key driver of NF-κB-mediated senescence in vivo and suggest that the atypical NF-κB pathway is a potential therapeutic target to mitigate aging-associated diseases.

overall_design: RNA was extracted from livers of female mice who were between 11-15 weeks old using Trizol reagent (Thermo Fisher, USA). Four independent biological replicates for WT, and two for NemoDK;Ercc1-/Δ and Ercc1-/Δ each were analyzed.

first: Lei

middle: J

last: Zhang

first: Carolina

last: Soto-Palma

first: Brian

last: Hughes

first: Aiping

last: Lu

first: Nam

last: Vo

first: Laura

last: Niedernhofer


title: Lactylation of HIF-1α at K172 drives HIF1 complex assemble to promote hypoxia-induced immune evasion in esophageal squamous cell carcinoma [ATAC-seq]

first: Ji

last: Cong

overall_design: Comparative chromatin accessibility profiling analysis of bulk ATAC-seq data from KYSE30 cells treated with as indicated.

first: Sujuan

last: Zheng


title: Functionally heterogeneous intratumoral CD4+CD8+ double positive T cells can give rise to single positive T cells [scRNA-seq + scTCR-seq]

city: Seattle

first: Lawrence

last: Fong

state: Washington

address: 1100 Fairview Ave. N.

department: Immunotherapy Integrated Research Center

institute: Fred Hutchinson Cancer Center

summary: Conventional single positive (SP) CD4+ and CD8+ T cells recognize tumor antigens and help mediate clinical responses with cancer immunotherapy. Double positive CD4+CD8+ (DP) T cells have also been described in human cancers, but their role in the tumor microenvironment (TME) remains unclear. By generating a multi-omic single cell atlas of DP and SP T cells, we find that DP T cells possess phenotypic heterogeneity similar to SP T cells that includes multiple clonally expanded populations of cytotoxic DP T cells in human renal cell carcinoma (RCC). These intratumoral DP T cells can mediate by both MHC class I- and class II-dependent killing of autologous tumor cells. In addition, transcriptional profiling of DP TCR-bearing T cells revealed a gene signature enriched for clinical responders to PD-1 blockade in advanced RCC. We confirm prior observations of SP T cells transitioning into DP T cells and more notably, demonstrate that intratumoral T cells are capable of bidirectional differentiation in which DP T cells serve as precursors to SP T cells in vivo.  In the latter scenario, intratumoral DP T cells are shown to express Rag2, suggesting that the tumor may act as an extrathymic site of T cell development. These findings reveal the multiple roles that DP T cells can possess in anti-tumor immunity.

overall_design: To characterize T-cell heterogeneity in renal cell carcinoma (RCC), we performed single-cell RNA sequencing (scRNA-seq) and single-cell TCR sequencing (scTCR-seq) using the 10x Genomics platform. Samples were collected from each patient’s tumor tissue, adjacent normal tissue, and peripheral blood mononuclear cells (PBMCs), along with PBMCs from healthy donors. To assign cells to their respective individuals following sequencing, we applied demuxlet, which leverages donor-specific genetic variants derived from bulk RNA-seq to enable genotype-based sample demultiplexing.

first: Tony

last: Li

first: Arielle

last: Illano

first: Marcel

last: Arias-Badia


title: Characterization of PAXIP1 in alternative lengthening of telomeres

city: New york

first: Jihye

last: Paik

address: 1300 York Ave.

institute: Weill Cornell Medical College

summary: Telomere length maintenance is essential for cellular immortalization and tumorigenesis. About 10% − 15% of human cancers rely on the recombination-based alternative lengthening of telomeres (ALT) to sustain their replicative immortality, yet the underlying molecular mechanism remains incompletely understood. Here we found the chromatin binding protein PAXIP1 as a novel ALT regulator and identified PAGR1 as its main functional protein partner. Mechanistically, we show that PAXIP1/PAGR1 complex complements with the PML nuclear body scaffold protein to promote ALT-directed telomere maintenance, independently from its MLL3/MLL4 complex-associated transcriptional function. We propose PAXIP1/PAGR1 complex as a functional component of break-induced telomere repair.

overall_design: SAOS2 cells were lentivirally infected to express Cas9. Specific guide RNAs targeting PAXIP1 and/or PML were stably expressed in these cells.

first: Hwang

last: Soo Yeon

first: Yang

last: Sieun

first: Paik

last: Jihye

first: Zheng

last: Hongwu


title: Lactylation of HIF-1α at K172 drives HIF1 complex assemble to promote hypoxia-induced immune evasion in esophageal squamous cell carcinoma [RNA-Seq]

overall_design: Comparative gene expression profiling of RNA-seq data of KYSE150 cells treated with as indicated.


title: ATAC-seq for PHF8-knockout CT26 cell and parental cell.

city: Shang Hai

first: zhengke

last: lian

address: 500 Dongchuan Rd

institute: East China Normal University

summary: CT26 cells with or without PHF8 knockout were processed using the High-Sensitivity Open Chromatin Profile Kit according to the manufacturer’s instructions.DNA was extracted using Tagment DNA Extract Beads, purified with NovoNGS DNA Clean Beads, and amplified by PCR. Libraries that passed quality control were sequenced on an Illumina NovaSeq X Plus platform.

overall_design: We compared the chromatin open profile of control and PHF8 knockout CT26 cells. Two biological replicates are set for each group.


title: Alzheimer’s disease neuroinflammatory risk genes can be targeted with RNase-H active antisense oligonucleotides in human microglia (APOE subset_GEO)

first: An

last: De Bondt

summary: Microglia play important roles in maintaining brain homeostasis. The discovery of genetic variants in the genes encoding Apolipoprotein E (APOE) and triggering receptor expressed on myeloid cells 2 (TREM2) as the strongest risk factors for Alzheimer’s disease (AD) highlights the importance of microglial biology in the brain. The sequence, structure and function of microglial proteins are poorly conserved across species, and this hampered the development of APOE and TREM2 targeting therapeutic strategies. One way to target APOE and TREM2 is to modulate their expression using antisense oligonucleotides (ASOs). In this study, we identified ASOs that selectively and potently reduce human APOE and TREM2 levels in human myeloid cells including iPSC-derived microglia. We demonstrated that a single bolus delivery of the ASOs in the mouse cerebrospinal fluid is sufficient for the ASO to be pharmacologically active and modify the phenotype of xenografted human microglia throughout the rodent brain for at least 4 weeks. This study is the first proof-of-concept that the expression of microglial genes can be modulated using ASOs in a dose-dependent manner in order to manipulate human microglia phenotypes in vivo, and demonstrates the utility of these ASOs both as research and therapeutic tools to modulate neuroinflammation.

overall_design: ASO-mediated RNAse-H reduction of APOE expression in human microglia in vitro (cultured human microglia).

first: Lina

last: Vandermeulen

first: Ivana

last: Geric

first: Mohamed

last: Kreir

first: Ashley

first: Annelies

last: Nonneman

first: Leen

last: Wolfs

first: Rafaela

last: Policarpo

first: Nicola

last: Fattorelli

first: Ilse

last: Van Den Wyngaert

first: Mark

last: Fiers

first: Bart

last: De Strooper

first: Constantin

last: d’Ydewalle

first: Renzo

last: Mancuso


title: Cut&tag of H4K20me1 for PHF8-knockout CT26 cell and parental cell.

summary: CT26 cells with or without PHF8 knockout were processed using the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit according to the manufacturer’s instructions.DNA was extracted using Tagment DNA Extract Beads, purified with NovoNGS DNA Clean Beads, and amplified by PCR. Libraries that passed quality control were sequenced on an Illumina NovaSeq X Plus platform.

overall_design: We compared the H4K20me1 of control and PHF8 knockout CT26 cells. Two biological replicates are set for each group.


title: RUNX1 is Expressed in a Subpopulation of Dermal Fibroblasts and is Associated with Disease Severity of Systemic Sclerosis [scRNA-seq]

city: Lebanon

first: Rezvan

last: Parvizi

state: NH

address: 1 Medical Center Drive

department: Biomedical Data Science

institute: Dartmouth College

summary: The activation of Runt-related transcription factor 1 (RUNX1) in fibroblasts has been implicated in wound healing and fibrosis; however, the role of RUNX1 in the fibrotic progression of the autoimmune disease systemic sclerosis (SSc) is not known. Leveraging gene expression, genome-wide DNA methylation, and single-cell resolution data of SSc skin and fibroblast, we analyzed the impact of RUNX1 dysregulation in SSc dermal fibrosis. RUNX1 function was subsequently assessed using siRNA, pharmacologic inhibition, and CRISPR knockout in 2D and 3D fibroblasts cultures. Analysis of gene expression in multiple cohorts demonstrated an association between the severity of dermal fibrosis and the expression levels of RUNX1 in the skin of patients with SSc. Epigenomic analyses of methylation identified hypomethylated CpG sites proximal to the RUNX1 gene, implicating their potential role in the increased expression of RUNX1. Analysis of single-cell RNA-seq data from skin biopsies of individuals with SSc revealed that RUNX1 is higher in subpopulations of fibroblasts enriched in SSc, which are believed to contribute to fibrosis. RUNX1 CRISPR KO resulted in reduced alpha smooth muscle actin (α-SMA) expression. Inhibition of RUNX1 activity caused a reduction in fibroblast activation, contraction, extracellular matrix components, and proliferation rates including a reduction in SFRP4, LUM and COL1A1. This study is the first to demonstrate a potential role for RUNX1 in the pathogenesis of systemic sclerosis dermal fibrosis. RUNX1 is associated with more severe SSc fibrosis and is associated with a subpopulation of dermal fibroblasts implicated in fibrosis.

overall_design: Skin fibroblasts isolated from SSc patients (n=2) were treated for 72 hours with either RUNX1 siRNA (Dharmacon, catalog ID E-003926-00-0010) or non-targeting control pool siRNA (NC, Dharmacon, D-001910-10-05). Single cell suspensions were then processed for scRNA-seq.

first: Parvizi

last: Rezvan

first: Gudjonsson

middle: E

last: Johann

first: Whitfield

middle: L

last: Michael


title: Alzheimer’s disease neuroinflammatory risk genes can be targeted with RNase-H active antisense oligonucleotides in human microglia (TREM2 subset_GEO)

first: An

last: De Bondt

overall_design: ASO-mediated RNAse-H reduction of TREM2 expression in human microglia in vitro (cultured human microglia).

first: Lina

last: Lu


title: Effect of I-125 Seed Implantation on Gene Expression in the Facial Nerve of Rabbits with Facial Nerve Injury

city: Kunming

first: Yu

last: Liu

address: No.295 Xichang Rd

institute: Affiliated Stomatology Hospital of Kunming Medical University

summary: Oral and maxillofacial tumors, particularly malignant ones, account for approximately 20% of head and neck malignancies. This anatomical region is characterized by complex structures and dense neurovascular networks. Tumor progression or surgical procedures can readily cause facial nerve injury, subsequently leading to impairments in patient communication, emotional expression, and social functioning. Brachytherapy using Iodine-125 (I-125) seeds has been widely employed in the treatment of various solid tumors due to its advantages, such as straightforward application and continuous low-dose radiation delivery to the tumor target area. However, recent studies have indicated that I-125 seed implantation may exert damaging effects on surrounding tissues, muscles, and nerves. Nevertheless, its specific mechanism of action in the context of facial nerve injury remains unclear. In this study, a rabbit model of facial nerve transection injury was established. I-125 seeds were implanted into the injury site, and facial nerve tissues from both the injury model and the I-125 implanted injury model were collected for transcriptome sequencing. The aim was to further untangle the molecular mechanism of I-125 radiation in facial nerve injury.

overall_design: To investigate the effect of I-125 seed implantation on facial nerve gene expression, a rabbit model of facial nerve injury was established via transection injury, and I-125 seeds were implanted into the injured area. On day 14 after modeling, injured facial nerve tissues were collected from the model group and the I-125 implantation group for RNA-seq analysis.

first: Jin

last: Zhu

first: Xin

last: Ouyang

first: Lifu

last: Yu

first: YeMei

last: Qian

first: JinYi

last: Li

first: Xun

last: Sheng

first: FengFeng

last: Jia


title: Effects of dietary inulin and Ichthyophthirius multifiliis  (Ich) infection on the gill transcriptome in zebrafish

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: Infection was the dominant driver of host transcriptional responses in the gills, inducing widespread differential gene expression associated with innate immunity, epithelial barrier function, ribosome biogenesis, proteasome activity, and cellular stress responses, while suppressing pathways linked to growth, signalling, and tissue homeostasis. Inulin had comparatively (and expectedly)  modest transcriptomic effects, yet diet-associated gene regulation was evident, and infected inulin-fed fish displayed strong up-regulation of immune and barrier-associated genes

overall_design: To examine whether diet-induced changes in the zebrafish gut microbiome influenced zebrafish susceptibility to I. multifiliis and subsequent host-parasite interactions, we utilised 4 groups of 30 adult AB wildtype zebrafish (Fig. 1). Two of the groups (n = 60) were given a control diet whilst the two other groups (n = 60) were given the same diet supplemented with 20% inulin. One group from each diet (n = 2 × 30) was infected with 4000 I. multifiliis per fish after 35 days of diet intervention. The other group from each diet (n = 2 × 30) was a non-infected control. The fish were euthanised after 5 days of infection, and a subset of samples (37) were used for RNA-Seq.

middle: R


title: Diurnally-regulated corticosterone and melatonin inversely control endotoxin-induced acute immune responses

city: Rehovot

first: Montaser

last: Haddad

address: Herzl St 234

department: Department of Immunology & Regenerative Biology

country: Israel

institute: Weizmann Institute of Science

summary: The timing of endotoxin administration in mice matters and is associated with diurnal variation in survival; however, underlying mechanisms remain poorly understood. Here, we report that afternoon LPS challenges in mice induce a robust inflammatory response involving increased neutrophil activation and release of cytotoxic mediators, causing higher mortality compared to challenges at midnight. Mechanistically, the cyclic patterns of corticosterone and melatonin hormones differentially modulate neutrophil responses. The afternoon corticosterone peak was associated with heightened incidence and severity of LPS-induced hyperinflammation. Conversely, higher melatonin levels at midnight conferred protection to challenged mice by restraining the magnitude of inflammation. High cortisol and low melatonin profiles detected in septic patients mirror those observed in mice and suggest a novel prognostic marker for sepsis.  Our study unveils a regulatory network that links light/dark signals and circadian-regulated hormones to the intensity of the host’s inflammatory response to infection.

overall_design: To investigate how endotoxin challenges affect neutrophil gene expression, we sorted neutrophils from BM and blood of WT mice 4 hr following LPS administration at ZT10 or ZT18 and subjected them to bulk RNA sequencing

first: Noa

last: Wigoda

first: Steffen

last: Jung

first: Orit

last: Kollet


title: MIC-Drop-seq: Scalable single-cell phenotyping of mutant vertebrate embryos

city: SALT LAKE CITY

first: Clayton

last: Carey

state: UT

address: 1390 President's Circle

department: Biology

institute: University of Utah

summary: Pooled perturbation screens can reveal cellular regulatory networks, yet scaling these techniques for large-scale screens in animals remains challenging. To address this, we developed MIC-Drop-seq, which combines high-throughput CRISPR gene disruption in zebrafish embryos with phenotyping by multiplexed single-cell RNAseq. In one MIC-Drop-seq experiment, we simultaneously identified changes in gene expression and cell abundance across 74 cell types resulting from loss of function of 50 transcription factors. These observations recapitulated many known phenotypes, while also uncovering novel functions in brain and mesoderm development. A key advantage of whole-animal screens is that they reveal how changes in one cell type affect the development of other cell types. Surprisingly, such cell-extrinsic phenotypes were abundant, indicating that transcription factors frequently exert effects beyond the cells where they are expressed to adjacent cells. We propose that MIC-Drop-seq will facilitate efforts to dissect the complete gene regulatory networks that guide animal development.

overall_design:
This submission includes single-cell RNA sequencing data from pooled CRISPR-perturbed zebrafish embryos and amplicon sequencing for CRISPR validation.
Dataset 1 contains 1 scRNA-seq sample from 40 pooled embryos at 24 hpf, each injected with MIC-Drop droplets targeting one of 8 genes (tbx16, tbxta, cdx4, foxa2, hoxb1b, rx3, hand2, tyr). Genotypes are multiplexed via gRNA capture using 10X feature barcoding.
Dataset 2 contains amplicon sequencing of genomic DNA from MIC-Drop injected embryos and wild-type controls to validate CRISPR editing efficiency at target loci.
Dataset 3 contains 16 scRNA-seq samples (4 biological replicates × 4 technical pools) from a screen of 50 transcription factors. Each pool contains ~250 embryos at 24 hpf, with each embryo injected with droplets targeting one of 50 genes.

first: Saba

last: Parvez

first: Zachary

last: Brandt

first: Brent

last: Bisgrove

first: Christopher

last: Yates

first: Randall

last: Peterson

first: James

last: Gagnon


title: Role of m⁶A-Modified GAS6 in Rheumatoid Arthritis: Insights from Multi-Omics Analysis

city: Hefei

first: Shu

state: Anhui

address: No. 117, Meishan Road, Shushan District

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

summary: Synovial tissue samples were collected from RA and HC were used for m⁶A seq and RNA seq analysis. Peripheral blood mononuclear cells (PBMCs) were isolated from RA and HC. The mRNA expression of GAS6 and MERTK was quantified by qRT-PCR, and inflammatory cytokine (IL-1β, IL-6, IL-10, and TGF-β1) were detected by ELISA. GAS6, MERTK were knocked down in RA-FLS using siRNA interference. CCK-8 were used to assess cell viability, Flow cytometry to assess apoptosis , and Cell scratch assay to evaluate cell migration rate. Immunofluorescence and Western blott was used to determine protein localization and expression.

overall_design: Synovial tissue samples were collected from RA and HC were used for RNA seq analysis.

first: Feng

first: Lei

last: Wan

first: MengYuan

last: Xu

last: Cheng


title: HNRNPH2 variant linked to intellectual disability disrupts myelination by impairing oligodendrocyte differentiation

city: Zhuhai

first: Bin

last: Wang

state: Zhuhai

address: Room 2007, Building 6, North HuanDao  Road 2515,

institute: Guangdong institute of intelligence and science technoloty

summary: Mutations in heterogeneous nuclear ribonucleoprotein H2 (HNRNPH2) lead to an X-linked neurodevelopmental disorders (NDDs) characterized by abnormal brain development and cognitive impairments. However, the underlying cellular and molecular mechanisms remain poorly understood. Here, we report that mice carrying the homologous P213L point mutation exhibit cognitive deficits and behavioral abnormalities resembling intellectual disability (ID). Notably, Hnrnph2P213L mice exhibit significant myelination defects, primarily due to impaired differentiation of oligodendrocyte progenitor cells. Mechanistically, the P213L mutation downregulates myelination-related genes by disrupting the interaction between hnRNPH2 and its target transcripts. Moreover, the myelin-enhancing drug benztropine rescues myelination, restores myelin-related gene expression and ameliorates cognitive deficits, highlighting the role of hnRNPH2 P213L-induced myelin abnormalities in the pathogenesis of ID. This study uncovers a crucial mechanistic link between myelin dysfunction and ID, providing potentially therapeutic ways for X-linked NDDs.

overall_design: RNA-seg profiling of cerebral cortex in wildtype and Hnrnph2P213L mice at postnatal day 7

first: Yang

last: Jiao

first: Qiu

first: Xinyu

last: Hu

first: Xiaoyi

last: Liao


title: RUNX1 is Expressed in a Subpopulation of Dermal Fibroblasts and is Associated with Disease Severity of Systemic Sclerosis

first: Rezvan

last: Parvizi

type: Methylation profiling by genome tiling array

overall_design: A total of 16 samples [eight samples from 2D monolayer cultures of fibroblasts isolated from two patients with Systemic Sclerosis (SSc) or one healthy control donor, and eight samples from 3D cultures (2 replicates from each biological sample)] were selected for DNA extraction. Genomic DNA was extracted using the Qiagen QIAcube by QIAamp DNA Mini Kit. To ensure that all samples met DNA quality control criterion, we used Agilent 4200 TapeStation (Genomic DNA ScreenTape, Agilent technologies, Santa Clara, CA). Between 500 ng and 1 µg of DNA from these 2D and 3D samples were bisulfite converted and processed according to the Illumina Infinium MethylationEPIC array protocols at the University of Southern California’s Molecular Genomics Core Laboratory (Los Angeles, CA).

first: Toledo

last: Diana

first: Michael

last: Whitfield


title: Functionally heterogeneous intratumoral CD4+CD8+ double positive T cells can give rise to single positive T cells [bulkRNA-seq]

first: Lawrence

last: Fong

first: Tony

last: Li

first: Arielle

last: Illano

first: Marcel

last: Arias-Badia


title: Cellular senescence in human liver under normal aging and cancer

city: St Louis

first: Alla

last: Karpova

state: MO

address: 700 Rosedale avenue Campus Box 1000

institute: Washington University St Louis

summary: Cellular senescence, a stress-induced program causing stable cell-cycle arrest, is a hallmark of liver aging, fibrosis, and cancer. However, the cell-type-specific mechanisms, spatial organization, and cancer-associated alterations in the liver remain unclear. We profiled 43 normal human livers spanning ages and fibrosis stages using single-cell multiome, Xenium spatial transcriptomics, and CODEX, complemented by fibrotic mouse models and 24 colorectal cancer liver metastases. We found CDKN1A+ senescent hepatocytes, fibroblasts, cholangiocytes, and endothelial cells associated with age, liver disease, or cancer. Senescence differed between aged and fibrotic livers, with similar mouse patterns. Spatially, CDKN1A+ hepatocytes localized periportally, while SERPINE1+ aging-associated hepatocytes formed spatial clusters potentially mediated by Claudins and THBS1. Fibrotic regions contained CXCL12+ senescent fibroblasts interacting with CXCR4+ immune cells. Chemotherapy intensified senescence in hepatocytes by five-fold relative to aging, and led to unique CDKN2A+ populations. Across conditions, senescent cells shared AP-1 activation, pro-inflammatory cytokines, and apoptosis resistance, suggesting therapeutic opportunities.

overall_design: Briefly, 8-week-old male C57BL/6J mice received sham or 75% proximal small bowel (sbr) resection. Mice were randomized into 2-, 10-, 26-, and 52-week cohorts. Each mouse liver was collected at the assigned time point, inspected for tumors and sectioned for H&E and SR staining highlighting fibrotic tissue. Selected mouse liver samples were further subjected to snRNA-Seq.

first: Li

last: Ding

first: Daniel

last: Alligood


title: PTEN variant and genetic backgrounds combine to modify cerebellar neuronal differentiation in autism spectrum disorder

city: Cleveland

first: Ya

last: Chen

state: OH

address: 2109 Adelbert Road, Room 747A

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Mutations in the PTEN gene have been implicated in autism spectrum disorders (ASD), particularly among individuals with comorbid macrocephaly. In our previous study, we demonstrated that the PTEN p.Ile135Leu variant, in an ASD-related genetic background dependent fashion, disrupts both cortical neurogenesis and gliogenesis. While abnormal cerebellar development is a recognized feature of ASD, the specific cellular targets and timing of disruptions during cerebellar differentiation and development remain poorly understood. To investigate these aspects, we applied our previously established cerebellar organoid protocol and used isogenic human iPSC lines harboring this PTEN-variant. We examined the expression of Purkinje cells, granule cells, interneurons, and glial cells prior to 22 weeks of differentiation, assessed genes expression at 8 weeks, and evaluated spontaneous spikes activity in Purkinje cells after 11 weeks. We observed that cell-type-specific expression patterns differed between the PTEN p.Ile135Leu variant in control versus ASD-genetic backgrounds. However, these background differences were diminished in PTEN knockout lines across both backgrounds. Our single-cell RNA sequencing (scRNA-seq) dataset revealed that the PTEN p.Ile135Leu variant increased the number of interneuron progenitor cells, whereas PTEN knockout led to an expansion of meningeal-like cells in both genetic contexts. Moreover, both the PTEN p.Ile135Leu variant and PTEN knockout abolished spontaneous simple spikes activity in Purkinje cells across both backgrounds, including PTEN-corrected patient-derived lines. Together, these findings provide direct evidence linking PTEN dysfunction and genetic background to altered cerebellar differentiation and neuronal network activity in human cerebellar organoids.

overall_design: For 10X scRNA-seq, we used the Chromium Nest GEM Single Cell 3’ Kit v3.1 (10x Genomics, 1000268) for all scRNA-seq library preparations. Single-cell suspensions from Chap WT/WT, Chap WT/I135L, Chap KO/KO, Apex WT/WT. Apex WT/I135L and Apex KO/KO were loaded onto the chromium Next Chip G Single Cell Kit (10x Genomics, 1000120) and processed with Chromium Controller 10v Genomics (10x Genomics) to generate single-cell gel beads in emulsion. The libraries were sequenced on the NovaSeqX platform using paired-end sequencing, with the first read having a length of 28 bases and the second read having a length of 90 bases.  Raw fastq files were uploaded into the 10x Genomics cloud and reads were aligned to Human (GRCh38) with Cell Ranger. The generated filtered raw matrix including barcodes, features and matrix were uploaded into Seurat v5.

first: Anthony

last: Wynshaw-Boris


title: Single cell sequencing of Stellate Ganglion of mice retrolabeled from interscapular brown adipose tissue and forelimb

first: Daniele

last: Neri

address: 630 West 168th Street

institute: Columbia University Irving Medical Center

summary: To identify the molecular signature of the sympathetic neurons innervating interscapular brown adipose tissue (iBAT) in mice, we isolated, sorted, and sequenced single cells from the stellate ganglia (SG) of mice three days after injections of CTB-555 in iBAT and CTB-488 in forelimb. Each cell was analyzed for their emission after excitation at 488 and 555nm, and was assigned to either 488-positive, 555-positive, or none.

overall_design: Six C57BL/6J male mice between six and eight weeks of age were injected with CTB-488 in their forelimb and with CTB-555 in their iBAT. Three days later, SGs were harvested, dissociated, and single cells were sorted in 96-well plates. Two mice were used for each set, for a total of three sets. Ganglia were pooled within sets. Four plates per set were collected, except for the third set, where only three plates were collected, for a total of 1039 cells across 11 plates. Finally, plate-based single cell sequencing was performed.

first: Seoeun

last: Lee

first: Lori

last: Zeltser


title: Cellular senescence in human liver under normal aging and cancer [Xenium]

overall_design: This dataset includes Xenium 5K data for 12 liver samples from SBR and Sham cohort mice. Briefly, 8-week-old male C57BL/6J mice received sham or 75% proximal small bowel (sbr) resection. Mice were randomized into 2-, 10-, 26-, and 52-week cohorts. Each mouse liver was collected at the assigned time point, inspected for tumors and sectioned for H&E and SR staining highlighting fibrotic tissue. Selected mouse liver samples were further subjected to Xenium 5K.


title: Three methylthio-alkane reductase homologs in Rhodopseudomonas palustris have distinct substrate specificities

city: St. Paul

first: Nicole

last: Marquez Reyes

address: 1445 Gortner Ave

department: Plant and Microbial Biology

institute: University of Minnesota - Twin Cities

summary: Bacteria play a critical role in the global sulfur cycle by using enzymes capable of cleaving strong bonds such as C-S. Most described enzymes require oxygen for their activity, but recent work has uncovered anaerobic alternatives. Among these are the methylthio alkane reductases (Mar), a group of nitrogenase-like enzymes that reduce volatile organic sulfur compounds (VOSCs) in the absence of oxygen. The purple non-sulfur bacterium Rhodopseudomonas palustris encodes three Mar homologs, providing a unique system to study their distinct functions. Here, we characterize the activity of these enzymes using genomic (RB-TnSeq) and transcriptomic (RNA-Seq) approaches to assess the essentiality and expression patterns of the different Mar enzymes under sulfate limitation. Growth assays with knockout strains supplied with different VOSCs, combined with measuring the specific reaction by-product, revealed that Mar1 preferentially acts on shorter-chain substrates. Our findings highlight the functional diversification of Mar enzymes and expand our understanding of their role in anaerobic sulfur metabolism.

overall_design: RNA profilling of WT Rhodopseudomonas palustris CGA009 cells grown in the presence and absence of sulfate (absence in this case being < 200µM of sulfate) and 1mM MT-EtOH (a volatile organic sulfur compound)

first: Kathryn

last: Fixen


title: Resolving the 4D chromatin dynamics during early random X chromosome inactivation II

city: Beijing

first: Hao

last: Xie

address: No.5 Yiheyuan Road

institute: Peking University

summary: X chromosome inactivation is a process that compensates X-linked gene dosage in mammalian female cells. The silencing of a randomly selected chromosome is accompanied by dramatic three-dimensional reorganization across the entire chromosome. To investigate the four-dimensional chromatin dynamics during early inactivation stages, we applied the multi-omics sequencing technique HiRES, which simultaneously detects three-dimensional genome and transcriptome in single cells, in a mouse embryonic stem cell line with induced random inactivation. The three-dimensional genome and transcriptome dual-omics data allowed us to identify random inactivation trajectories at single-cell resolution. We characterized multiple layers of X-chromosome reorganization and discovered a transient structural state shared by both X chromosomes, associated with biallelic Xist expression. By constructing single-cell inactivation trajectories, we found that most chromatin remodeling either accompanied or followed gene silencing. Further analysis of interaction decay kinetics revealed that TAD attenuation began from loss of interactions on TAD anchors. This study thus provides a detailed depiction of fine-scale chromatin reorganization during the initiation of random X chromosome inactivation.

overall_design: To initiate random X-chromosome inactivation (rXCI), we induced the differentiation of female hybrid mouse embryonic stem cells (mESCs) obtained from a cross between the C57B6/J and CAST/EiJ mouse strains by removing 2i/Lif. Subsequently, we harvested cells at multiple time points during the differentiation process, spanning from day 0 to day 4. We then utilized HiRES technology to simultaneously obtain 3D genome and transcriptome data at the single-cell level.

first: Xiaowen

last: Liu

first: Zhiyuan


title: MFAP2 promotes xenograft HNSCC growth and progression in mice through the β-catenin signaling pathway

city: Hohhot

first: Xiaobo

last: Cui

address: No. 1, Tongdao North Street

department: Department of Otolaryngology

institute: the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia

summary: The aim of this work is to explore the role of MFAP2 on HNSCC development

overall_design: Then RNA-sequencing analysis were performed and signaling pathway were identified.

first: Haixia

last: Xu

first: Lin

last: Ren

first: Xiaoqing


title: Chemogenetic activation of iBAT-projecting sympathetic neurons

city: New York

summary: To investigate the activation of sympathetic nerves projecting to brown fat, we injected a neuron-specific, retrograde, AAV in the interscapular brown adipose tissue (iBAT) of Th-Cre mice expressing the excitatory designed receptor exclusively activated by a designer drug (DREADD) hM3Dq under Cre control. Over three weeks later, we anesthetized these mice, stimulated them with DCZ or Saline, and collected their iBAT 30 minutes later to profile their gene expression. In parallel, we performed a similar study on separate set of wild type (WT) mice without virus injection.

overall_design: RNA-Seq profiling of iBAT collected from Th-Cre and WT mice, 30 minutes after being stimulated with either DCZ or Saline

first: Dominique

last: Bozec

first: Lucas

last: Castro e Souza

first: Alexis

last: Fohn

first: Natalie

last: Lopatinski


title: Precision CRISPR annotation of the functional enhancer landscape in primary human T cells

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary: Precise modulation of T cell function through engineering the non-coding genome holds great promise for advancing next-generation immunotherapies. However, robust high-throughput approaches to annotate functional cis-regulatory elements (CRE) in human T cells remain limited. Here, we developed a simple and highly efficient CRISPR interference (CRISPRi) perturbation platform to systematically annotate CREs in human primary T cells. Using this platform, we identified novel CREs controlling PDCD1, HAVCR2, and TBX21 expression. Combinatorial CRE perturbations revealed synergistic CRE pairs that fine-tune PDCD1 and HAVCR2 expression, while Cas9-indel-based mutagenesis pinpointed the critical nucleotides within each enhancer that are essential for their activity. Functional experiments demonstrated that CRE-edited HAVCR2 outperformed conventional total gene knockout in enhancing CAR T cells anti-tumor efficacy. Moreover, CRE editing of PDCD1 and HAVCR2 repressed PD-1 and TIM-3 expression in human tumor-infiltrating lymphocyte CD8 T cells, highlighting their regulatory role in disease relevant exhausted T cells. Together, this approach offers a compact CRISPRi platform that enables high-throughput dissection of functionally relevant genomic regions in T cells, providing insights for mechanistic studies and precision genome engineering for advanced cellular therapies.

overall_design: ATAC-seq was used to characterize chromatin landscape of T cell subsets from PBMCs healthy donors and to guide CRISPRi screens

first: Ping

last: Wang

first: Josephine

last: Giles

first: Hua

last: Huang

first: Sasikanth

last: Manne

first: John

last: Wherry


title: Transcriptomic analysis of the sprout-suppressive effects of rosemary essential oil on potato tubers

city: Shenyang

first: Baodong

last: Wei

state: Liaoning

address: Dongling Street

institute: Shenyang Agricultural University

summary: Postharvest sprouting of potato tubers compromises food safety and causes economic losses. This study employed RNA-seq to investigate the molecular mechanisms by which rosemary essential oil (REO) suppresses postharvest sprouting in potato tubers (cultivar 'Keshan'). Tubers were divided into two groups at the onset of storage: a control group and a group treated with REO fumigation. Transcriptomic profiles were analyzed at two time points: at day 0 (baseline) and after 40 days of storage. This design allowed for the identification of differentially expressed genes in response to both storage time and REO treatment, with a specific focus on pathways related to plant hormone signaling and carbohydrate metabolism.

overall_design:
RNA-seq profiling of control and rosemary essential oil (REO) fumigated potato tubers at day 0 and day 40 of storage. The experiment included 3 biological replicates per condition (9 samples total), allowing for the comparison of gene expression changes over time and in response to REO treatment.

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Submitter states that missing raw files are due to file loss.
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first: Shutong

last: Wu

first: Xiangbin

first: Di

first: Peng

last: Zhang

first: Guozheng

last: Qin

first: Jiangkuo

last: Li