title: DNMT1 Facilitates the Progression of Metabolic Dysfunction-Associated Steatotic Liver Disease [snRNA-Seq]

city: Daejeon

first: Hanyong

last: Go

address: 125, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

country: South Korea

institute: KRIBB

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterized by notable epigenetic changes, such as alterations in DNA methylation. However, research on epigenetic modifications in human patient and animal models remains sparse. This study investigates the role of DNMT1 in MASLD progression. DNMT1 inhibition restores DNA methylation patterns and transcriptional activity, suggesting it as a potential therapeutic target for MASLD.

overall_design: Male C57BL/6N mice aged 8 weeks were divided into three groups (N = [insert number per group]). The control group was fed a standard diet (SD), while the MASLD group was fed a MASLD-inducing diet with a sucrose solution for 18 weeks. The third group received the same MASLD diet but was treated with oral Aza-TdC during the last 4 weeks. Liver samples were collected, and nuclei were isolated from frozen tissue, stained with DAPI, and subjected to fluorescence-activated cell sorting (FACS) to generate a single nuclei suspension. The suspension was then loaded onto the 10x Genomics Single Cell 3' V3 platform for sequencing.

first: Hyun Ahm

last: Sohn

first: Jun Min

last: Lee

first: Hee-Jin

last: Kim

first: Amal

last: Magdy

first: Hyo-Jung

last: Jung

first: Mirang


title: DNMT1 Facilitates the Progression of Metabolic Dysfunction-Associated Steatotic Liver Disease [ChIP-seq]

status: Public on Aug 12 2026

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Mouse liver samples were processed for ChIP sequencing on the Illumina NovaSeq Xsystem.


title: NNMT Loss Drives Prostate Cancer Progression through Epigenetic and Metabolic Reprogramming

city: Philadelphia

first: Erick

last: Mitchell-Velasquez

state: PA

address: 421 Curie Blvd

department: Cancer Biology

country: USA

institute: University of Pennsylvania

type: Expression profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: DNMT1 Facilitates the Progression of Metabolic Dysfunction-Associated Steatotic Liver Disease [RNA-seq]

overall_design: Mouse liver samples were processed for RNA sequencing on the Illumina HiSeq X system.


title: A spatiotemporal atlas of giant-cell formation during Meloidogyne incognita infection in tomato roots

city: Qingdao

first: Lijun

last: Jiang

state: Shandong

address: 11#, Keyuan Jing 4 Road

department: Chinese Academy of Agricultural Sciences

country: China

institute: Tobacco Research Institute

summary: Root-knot nematodes (RKNs; Meloidogyne spp.) are destructive agricultural parasites, but although giant cell formation is required for establishing parasitism, the mechanism of action has not been fully elucidated. Spatial transcriptomics enables precise spatiotemporal analyses of gene expression, facilitating studies of cell heterogeneity. We performed spatial transcriptomic sequencing on Moneymaker tomato root galls caused by M. incognita infection at 3, 5, and 7 days post-inoculation to investigate RKN-induced giant cell formation. Five major cell types were identified; of these, giant cell clusters were localized predominantly in the xylem, stele, and meristem. Four novel giant cell-specific marker genes were confirmed through RNA in situ hybridization. Pseudotime analysis revealed genes potentially associated with giant cell formation. Virus-induced gene silencing (VIGS) of four genes encoding a cyclin-dependent kinase, two cell division cycle-associated proteins, and a MYB3R-1-like transcription factor—hypothesized to maintain the cell cycle or gene expression during mitosis—resulted in significantly fewer galls and significantly smaller giant cells. This study established the first spatiotemporal atlas of RKN-infected tomato roots and identified genes associated with giant cell formation, laying a foundation for further research on the establishment of RKN feeding sites, providing novel insights into RKN pathogenic mechanisms, and potentially guiding novel control strategies.

overall_design: Meloidogyne incognita-infected Moneymaker tomato root gall sections of three time points (3d, 5d, 7d) were respectively analyzed using spatial transcriptomics.

first: Bingyan

last: Xie

first: Jinguang

last: Yang


title: Single cell sequencing of dura maters of dural metastasis models

city: Shanghai

first: Rui

last: Zeng

address: Dong An Road

institute: Fudan University

summary: Dural metastasis (DM) is a rarely researched disease with limited therapeutic options, largely due to our circumscribed understanding of dura mater.  However, recently emerging studies suggest the dura mater is an immune hub and implements immunosurveillance of the central nervous system. These evidences imply potential immunotherapies of DM. Here, we established a preclinical murine model of DM. We have employed a single cell sequencing approach using 10x Genomics scRNA-seq to study the tumor microenvironment of DM model. In comparison, the dura maters of nontumor mice and leptomeningeal metastasis (LM) mice were used as control groups. Briefly, the dorsal dura maters are isolated from the head of nontumor mice, 4T1-LM mice and 4T1-DM mice on day 12 since tumor cell inoculation, and are enzymatically digested to single cells with collagenase VIII and DNase I.

overall_design: 12 days after tumor cell inoculation,  the dorsal dura maters were isolated from the head of nontumor mice, 4T1-LM mice and 4T1-DM mice, and were enzymatically digested to single cells with collagenase VIII and DNase I. Mixtures of samples from 6 mice per group were subjected to subsequent droplet-based 10x Genomics single cell RNA sequencing. This study contains 3 replicates per group.

first: Jiaxu

last: Zhao

first: Yudan

last: Chi


title: DNMT1 Facilitates the Progression of Metabolic Dysfunction-Associated Steatotic Liver Disease

type: Methylation profiling by genome tiling array

summary: Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterized by notable epigenetic changes, such as alterations in DNA methylation. However, research on epigenetic modifications in human patient and animal models remains sparse.  This study investigates the role of DNMT1 in MASLD progression. DNMT1 inhibition restores DNA methylation patterns and transcriptional activity, suggesting it as a potential therapeutic target for MASLD.

overall_design: Mouse liver samples were processed using the Illumina Infinium Mouse Methylation BeadChip array to analyze DNA methylation profiles.

last: GO


title: RNA-seq of the cortex on C57BL/6 mice after high-methionine diet.

city: Taiyuan

first: Yuan

last: Fu

state: Shanxi

address: No. 56, Xinjian South Road, Yingze District

department: Department of Biochemistry and Molecular Biology, School of Basic Medicine

institute: Shanxi Medical University

summary: To investigate the genetic changes in the mouse cortex under high homocysteine conditions, we established normal and high methionine-fed mouse models.

overall_design: Male C57BL/6 mice were fed a high-methionine diet or a standard diet for more than 8 weeks. We then performed gene expression analysis on RNA-seq from two different groups.

first: Jianting

last: Li

first: Xiaolong

last: Gu


title: Comprehensive H3K27ac modification profiles of human induced pluripotent stem cells or human embryonic stem cells exposed to bisphenol A or thalidomide

city: Bunkyo-ku

first: Satoshi

last: Otsuka

state: Tokyo

address: 7-3-1 Hongo

country: Japan

institute: The University of Tokyo

summary: In this study, we examined the epigenetic toxicity of bisphenol A and thalidomide, focusing on their effects on cellular differentiation and gene expression. Thalidomide promoted ectodermal differentiation at the expense of other lineages, while bisphenol A had milder effects. Transcriptome analysis revealed distinct gene expression changes for each chemical, with thalidomide inducing more pronounced shifts. These changes correlated with increased H3K27ac modifications at enhancer regions of upregulated genes, linking gene expression alterations to epigenetic modifications. The findings emphasize the role of epigenetic mechanisms in developmental toxicity.

overall_design: Exposure to 0.1% DMSO, 10 (low) or 30 (high) nM bisphenol A, or 0.1 (low)or 1 (high) µM thalidomide for 48 hrs.

first: Xian-Yang

last: Qin

first: Tomohiro

last: Ito

first: Hiroko

last: Nansai

first: Mari

last: Katsura

first: Mika

last: Kobayashi

first: Akashi

last: Taguchi

first: Youichiro

last: Wada

first: Takahide

last: Kohro

first: Kuniya

last: Abe

first: Yoichi

last: Nakao

first: Hideko

last: Sone


title: ChIP-seq of H3K27ac and H3K27me3 in the hippocampus of C57BL/6 mice after high methionine feeding for more than 8 weeks.

summary: To explore whether high homocysteine status affects the enrichment of histone H3K27ac and H3K27me3 and thus affects the cognitive behavioral abilities of mice, we fed C57BL/6 mice with a high-methionine diet and a standard diet, then isolated the hippocampus for ChIP-seq studies of H3K27ac and H3K27me3. The sequencing data provided a new theoretical basis for the effects of high homocysteine on histone modification.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone variants H3K27ac and H3K27me3


title: RNA-seq of hippocampal tissues from high-methionine diet-induced hyperhomocysteinemia mice with or without betaine treatment

summary:
To investigate the genetic changes in the mouse hippocampus under high homocysteine conditions, we established normal and high methionine-fed mouse models.
Jianting, Li

overall_design:
High homocysteine levels represent an important risk factor for cognitive impairment. Although betaine is known to reduce Hcy levels, its effects on hyperhomocysteinemia (hHcy)-induced cognitive impairment and the underlying mechanisms remain unclear. To address this, mice were assigned to the control (Con) group, the high-methionine diet (HMD) group, and the betaine-treated HMD (Bet+HMD) group.
Male C57BL/6 mice were fed a high-methionine diet or a standard diet for more than 8 weeks. We then performed gene expression analysis on RNA-seq from two different groups.
We established an hHcy-induced cognitive impairment mouse model by feeding mice a high-methionine diet for 8 weeks, followed by betaine supplementation for 14 days. We then performed gene expression analysis on RNA-seq from three different groups.


title: Comprehensive transcriptomic profiles of human induced pluripotent stem cells or human embryonic stem cells exposed to bisphenol A or thalidomide


title: Role of MicroRNA155 in Hippocampal Neurogenesis and GABAergic Signaling in Alzheimer’s Disease [MIR155 Overexpression RNA Sequencing Data]

city: New York

first: Michelle E.

last: Ehrlich

state: NY

address: 1 Gustave L. Levy Pl, New York, NY 10029

department: Department of Psychiatry

institute: Icahn School of Medicine at Mount Sinai

summary: MicroRNA (miRNA) dysfunctions are implicated in neurodegenerative disorders, with microglial miR155 dysregulation extensively linked to neuroinflammation in Alzheimer's disease (AD). However, its role in other neural cell types remains unclear. Expanding on previous studies showing miR155 upregulation in hippocampal neurons of both AD model mice and AD patients, we found that in human induced pluripotent stem cell (hiPSC)-derived neural stem cells (NSCs), MIR155 regulates NSC proliferation, with MIR155 deletion increasing NSC numbers and overexpression downregulating NSC markers. In cortical neurons, MIR155 deletion is associated with increased neuronal outgrowth and GABAergic interneuron generation. In cortical organoids, MIR155 deletion promotes ventral patterning and increases GABAergic interneuron formation. Deleting miR155 in an AD mouse model induced the expansion of hippocampal NSCs in the sub-granular zone (SGZ) and the hilus, and promoted an increase in the number of hippocampal GABAergic interneurons, highlighting the novel role of miR155 in adult hippocampal neurogenesis and GABAergic interneuron signaling.

overall_design: A combination of hiPSC technology, mouse models of AD pathology and transcriptomic profiling

first: Xiaodong

last: Zhu

first: Sam

last: Gandy

first: Michelle

last: E Ehrlich


title: Role of MicroRNA155 in Hippocampal Neurogenesis and GABAergic Signaling in Alzheimer’s Disease [MIR155 Knockout RNA Sequencing Data]


city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore ChIP-Seq results for H3K27ac in ut7 cell line.

first: Jian

last: Pan

first: Ailian

last: Guo

first: Zhiheng

last: Li


title: CUT-TAG for BRD4 in M07E cell line

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore CUT-TAG results for BRD4 in M07E cell line.

overall_design: CUT-TAG for BRD4 in M07E cell line


title: CCR1 deficiency promotes adipocyte browning via cAMP/PKA/CREB signaling to suppress obesity in mice

city: Wenzhou

first: Liang

last: Xu

state: Zhejiang

address: Chashan Higher Education Zone

department: School of Laboratory Medicine and Life Sciences

institute: Wenzhou Medical University

summary: Enhancing brown adipose tissue (BAT) activity and browning of white adipose tissue (WAT) are promising novel strategies for combating obesity and insulin resistance. Previously, we identified CCR1 as a key regulator of non-alcoholic steatosis. Here, we present evidence of the physiological role of CCR1 in obesity and energy homeostasis. Analysis of Ccr1-/- mice fed a high-fat diet (HFD) revealed inguinal WAT browning, increased BAT activation and brown-mediated genes expression, elevated whole-body energy expenditure, ameliorated macrophage homeostasis, decreased inflammation, and eventually attenuated insulin resistance and obesity. Moreover, Ccr1 deficiency increased adaptive thermogenesis under cold conditions. These phenotypes were also identified in HFD-fed mice treated with BX471, a CCR1 selective inhibitor. Mechanistically, Ccr1 knockout elevated WAT cyclic adenosine 3',5'-monophosphate (cAMP) levels, activating cAMP-dependent protein kinase (PKA) and its downstream transcription factor cAMP response element-binding protein, CREB. Overall, Ccr1 deficiency increases BAT activation and WAT browning through the cAMP-related PKA/CREB pathway, thereby preventing obesity and insulin resistance. In addition, CCR1 inhibition by BX471 protects against obesity. These findings shed light on novel strategies for the treatment of obesity and related diseases.

overall_design: To explore the role of CC chemokine receptor CCR1 in the progression of obesity, we fed the wild-type mice and CCR1-KO mice with a high-fat diet for 10 weeks. Total RNA was extracted from inguinal white adipose tissue for RNA sequencing.

first: Suili

last: Cai

first: Mengchen

last: Ma

first: Yanwen

last: Yu

first: Muling

last: Ye

first: Yuqin

first: Haoran

first: Yajiao

last: Wang


title: Defining Human Soft Tissue Heterogeneity In Response To  Peri-implantitis By Single-cell Sequencing

first: Yiling

last: Yang

address: Fenglin Road

institute: Zhongshan Hospital, Fudan University

summary: Peri-implantitis (PI) is a pathological condition occurring in tissues around dental implants, resulting in a high risk of treatment failure, which lack of efficacious treatment. The prevention and treatment of peri-implant mucositis is considered an effective and economical measure to prevent the occurrence of PI because oral mucosa provides the first line of defense against deleterious stimuli. Importantly, though there are similar morphological structure in the epithelium barrier between dental implant and natural teeth, the one around the implant having a lower capacity to seal tightly than it does around a natural tooth. Meanwhile, the immune system of peri-implant tissue is inferior in defense to periodontal tissue. Compared by natural teeth, the specific molecules and cell types involved in the pathogenesis of PI is still unclear. This study collected clinical patient gingival tissue samples and used single-cell RNA sequencing to analyze multiple aspects, discovering significant heterogeneity in the epithelial barriers and surrounding immune defenses of periodontitis and peri-implantitis, as well as related response molecules. It provided strong evidence for clinical strategies for the treatment of peri-implantitis.

overall_design: Human gingival tissue near with natural teeth samples (N, n=3) were collected from third molars during tooth extractions; these third molars were diagnosed as having no preservation value based on their history of infection, and were extracted after the inflammation had resolved, showing no bleeding on probing. Gingival tissue from Peri-implantitis patients (PI, n = 5) were defined as dental implant failures that require removal.

first: Yang

last: Sun


title: NNMT Loss Drives Prostate Cancer Progression through Epigenetic and Metabolic Reprogramming (RNA-Seq)

first: Erick

last: Mitchell-Velasquez

summary: Methionine metabolism plays a pivotal role in cancer, with methionine serving as the primary precursor for S-adenosylmethionine (SAM), a critical methyl donor in various methylation processes, including DNA and histone methylation. This study delves into the genetic deletion and silencing of Nicotinamide N-Methyltransferase (NNMT) in prostate cancer (PCa) and its impact on methionine metabolism and cancer progression. We identify significant loss of NNMT expression in PCa and metastatic castration-resistant prostate cancer (CRPC) compared to healthy prostate tissue. Functional experiments reveal a potential tumor-suppressive role of NNMT in PCa, supported by reduced cell proliferation, colony formation, and sphere formation upon NNMT overexpression. Moreover, we explore the sensitivity of NNMT-positive and NNMT-negative PCa to dietary methionine restriction (MR). NNMT-negative PCa exhibits resistance to MR, which is associated with increased mTORC1 activity. This resistance is characterized by elevated protein synthesis and reduced apoptosis, suggesting a complex interplay between dietary methionine and NNMT expression in cancer. In summary, this study sheds light on NNMT's multifaceted role in PCa progression, methionine metabolism, and epigenetic regulation. It also highlights potential therapeutic strategies for managing NNMT-negative tumors, offering new avenues for prostate cancer treatment.

overall_design: To investigate the effects of NNMT on transciprtion  in vivo and in vitro under physiologically relevant methionine levels

first: Qu

last: Deng

first: Mohammed

last: Alhusayan

first: Ramakrishman

last: Natesan

first: Sharan

last: Venkatesh

first: Priti

last: Lal

first: Rahul

last: Mannan

first: Irfan

middle: A

last: Asangani


title: NNMT Loss Drives Prostate Cancer Progression through Epigenetic and Metabolic Reprogramming (scRNA-seq)


title: NNMT Loss Drives Prostate Cancer Progression through Epigenetic and Metabolic Reprogramming (ChIP-Seq)

overall_design: To investigate the effects of NNMT on histone methylation in vitro under physiologically relevant methionine levels


title: DNA-replication stress induced transcriptome of Human Burkitt’s lymphoma cells identifies MBD1 as a novel suppressor of Germinal center derived B-lymphomagenesis

city: Kanazawa

first: Santosh

middle: Kumar

last: Gothwal

address: Kakumamachi

institute: Kanazawa University


title: DNA-replication stress induced transcriptome of Human Burkitt’s lymphoma cells identifies MBD1 as a novel suppressor of Germinal center derived B-lymphomagenesis [ChIP]

summary: Germinal center (GC) derived B-lymphomas (GCDBL) are concomitantly generated with high-affinity B cells during humoral immune response. Among GCDBLs are Burkitt’s lymphoma (BL), diffuse large B cell lymphoma (DLBCL), and Multiple myeloma (MM), which originate from distinct GC compartments. Whether specific transcription factors work in GCs to suppress the GCBLD is elusive.

overall_design: Raji cellls treated with DMSO, HU were processed for ChIP using histone H3K4me3 ab (CST) and library was prepared as per instruction (Thruplex DNA-seq kit, Takara  Japan).

last: Kumar Gothwal

first: Susumu

last: Kohno

first: Chiaki

last: Takahashi

first: Atsuyasu

last: Sato


title: DNA-replication stress induced transcriptome of Human Burkitt’s lymphoma cells identifies MBD1 as a novel suppressor of Germinal center derived B-lymphomagenesis [RNA]

overall_design: Three replicates from Raji cell line with hydroxyurea treatment and thymidine-Nocodazole treatment

middle: K


title: “Digital chromosome banding”: A scRNA-seq-based chromosome banding method distinguishes real and pseudo sex body

city: Urbana

first: Huanyu

last: Qiao

state: Illinois

address: 2001 South Lincoln Avenue

department: Comparative Biosciences

institute: University of Illinois Urbana-Champaign

summary: To investigate the hypothesis that silencing of meiotic silencing of unsynapsed chromatin (MSUC)-affected regions in defective germline cells could suppress essential genes and lead to cell apoptosis, we developed a new method "digital chromosome banding" to measure transcriptional levels within each 1 MB chromosomal region via single-cell RNA sequencing (scRNA-seq) datasets from wild type and spo11-/- spermatocytes. We successfully detected meiotic sex chromosome inactivation (MSCI) but no obvious MSUC at the pachytene stage. Furthermore, we revealed that pseudo sex bodies are unable efficiently silence chromosomes while gel-like structure of mature sex bodies potentially plays a key role in MSCI by blocking access to transcription factors and small molecules, indicating the crucial role of phase separation in meiotic silencing. This research has thus deepened the understanding of MSUC and MSCI mechanisms and introduced a novel approach for investigating chromosome-wise transcriptional regulation.

overall_design: We performed 10x scRNA-seq using testicular cells from WT and Spo11-/- testes.3976 and 3338 testicular cells were collected from WT and Spo11-/- respectively.

first: Yiheng

last: Peng

first: Shuangqi


title: Berberine Improved the Therapeutic Efficacy of UC-MSCs for Colitis via GLUT1-dependent Glycolysis

city: guangzhou

first: Wu

middle: Meng

last: ye

state: Guangdong

address: Guangzhou Yuexiu

department: The Biotherapy Center,

institute: the Third Affiliated Hospital, Sun Yat-Sen University

summary: In order to clarify the underlying mechanism of BBR improving the therapeutic effect of MSCs in DSS-induced colitis

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of MSCs treatment with the presence and obsence of berberine for 24h, and Comparative gene expression profiling analysis of RNA-seq data between them.

first: Yanwen

first: Mengye

last: Wu

first: Jianqi

last: Feng

first: Xiaolu

last: Guo


title: Triple-Negative Breast Cancer Cells Activate Sensory Neurons via TRPV1 to Drive Neurite Outgrowth and Tumor Progression

status: Public on Aug 11 2026

city: Medford

first: Madeleine

last: Oudin

address: 200 College Ave

institute: Tufts University

summary: The tumor microenvironment in triple-negative breast cancer (TNBC) is characterized by increased sensory nerve density, which contributes to cancer progression by promoting migration and metastasis. However, the origin of tumor-innervating nerves and the mechanisms driving sensory innervation into tumors remain poorly understood. Using in vivo retrograde labeling techniques, we show that mammary tumors are associated with an increase in nerves originating from the dorsal root ganglia. We find that the presence of breast tumor cells leads to significant changes in gene expression in vivo in dorsal root ganglia and in vitro in cultured sensory neurons, associated with growth, regeneration, excitability and injury. We find that TNBC cells trigger stress and activation markers and induce neuronal firing in a transient receptor potential vanilloid subtype 1 (TRPV1)-dependent manner. In both 2D and 3D cell culture models, TNBC cells promote outgrowth of sensory nerves that is abrogated with Trpv1 knockout. We identified c-Jun and IL-6 as an effector of neurite outgrowth that acts downstream of TRPV1 to promote outgrowth in vitro. Finally, in Trpv1 knockout mice, TNBC tumors exhibit delayed growth and reduced lung metastasis. These findings suggest a critical role for TRPV1 in tumor-nerve crosstalk, offering a potential target to reduce metastatic disease.

overall_design: The RNA was isolated from Dorsal root ganglia of healthy versus tumor bearing mice. The FvB/NJ mice were used as control which do not have tumors. MMTV-PyMT mice which have spontaneous breast tumor development as they age were used as tumor bearing mice.

middle: J

first: Ankit

last: Pandey


title: IWC treatment remodulate the BALF cell component

city: Chengdu

first: Yun

last: Shi

address: No 37, Guoxuexiang

institute: West China Hospital, Sichuan University

summary: Inactivated whole cell(IWC) of bacteria can remodulate the alveolar macrophages(AMs) . We use single cell transcriptional analyses cell component of BALF after different IWC of bacteria.

overall_design: For sample 1- sample 6, C57Bl/6 mice (n-3 /group) were intranasal treated with different IWC.  At day7 and BALF cells were isolated from 3 mice/group and were pooled together as one sample for downstream process. For sample 7, and sample 8, alveolar macrophages (AM) were isolated from BALF and cultured in DMEM and sample 8 was stimulated with IWC(ab) for 7 days. Viability of the final cell suspension was calculated using a hemocytometer and Trypan blue (Corning) exclusion and was routinely > 85%.


title: Adenosine-to-Inosine Safeguards Early Human T-cell Lymphopoiesis by Suppressing MDA5-Mediated dsRNA Sensing

city: LA JOLLA

first: QINGFEI

last: JIANG

state: CA

address: 2880 TORREY PINES SCENIC DR

institute: UNIVERSITY OF CALIFORNIA SAN DIEGO

summary: Steady-state lymphopoiesis from hematopoietic stem and progenitor cells (HSPCs) is critical to maintaining immune competence throughout life. While epigenetic and transcriptional factors governing this process are well reported in both humans and mice, the epitranscriptomic regulation is largely unexplored. In this study, we investigated ADAR1-mediated adenosine-to-inosine (A-to-I) RNA editing during early human T-cell maturation using both human thymic tissues and an artificial thymic organoid (ATO) system. ADAR1 was highly expressed  in early T-cell progenitors, and its expression declines as T-cell progenitors progress to the CD4⁺CD8⁺ double-positive (DP) and single-positive (SP) stages. ShRNA-mediated ADAR1 depletion coupled with single-cell RNA sequencing (scRNA-seq) reveals that ADAR1 loss blocks the developmental transition from the Thy2 to Thy3 stage within the CD34⁺ progenitor compartment and leads to the emergence of distinct cell clusters encompassing mixed lineage cells with distinct gene expression patterns marked by global activation of interferon response pathways. Among the dsRNA sensors downstream of A-to-I RNA editing, MDA5 knockdown completely rescues the effects of ADAR1 loss and restores T-cell development. Together, these findings demonstrate dynamic stage-specific ADAR1 regulation and establish its essential role in driving early T-lymphocyte lineage specification through the ADAR1-MDA5 dsRNA-sensing axis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CB ATO following ADAR1 knockdown by shRNA.

first: Maria

last: Rivera

first: Isabella

last: Hoang

first: Sabina

last: Enlund

first: Thomas

last: Whisenant

first: Roman

last: Sasik

first: Frida

last: Holm

first: Dennis

last: Kuo

first: Qingfei

last: Jiang


title: Transcriptomic profiling of human keloid fibroblasts after mitochondria transplantation

city: Beijing

first: Wenjing

last: Wang

state: Beijing

address: No. 33 Ba-Da-Chu Road

department: Department of Plastic and Reconstructive Surgery

institute: Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: This study performed bulk RNA sequencing to characterize the transcriptomic changes induced by mitochondria transplantation in human keloid fibroblasts (KFs). Primary human keloid fibroblasts were treated with adipose-derived stem cell-derived mitochondria, and global gene expression profiles were compared between untreated and mitochondria-transplanted KFs

overall_design: Primary human keloid fibroblasts were divided into an untreated control group (KF) and an adipose‑derived stem cell‑derived mitochondria‑treated group (mitoKF). For the mitoKF group, cells were treated with adipose‑stem‑cell‑derived mitochondria at a dose of 25 μg mitochondrial protein per 1 × 10⁵ cells for 24 h. Total RNA was extracted from keloid fibroblasts with or without mitochondria treatment and subjected to bulk RNA sequencing. Differentially expressed genes and enriched biological pathways were analyzed to identify transcriptional changes induced by mitochondria treatment.


title: Transcriptomic profiling of MOC1 cells treated with fractionated irradiation to inform the application of COF-Tpy-Se-Cu

city: Zhengzhou

first: Yuantong

last: Liu

state: Henan

address: kexue road

institute: Zhengzhou University

summary: This study compared the transcriptomes of control MOC1 murine oral squamous cell carcinoma cells and MOC1 cells subjected to repeated fractionated irradiation. Three biologically independent samples from each group were analyzed by paired-end RNA sequencing. The study aimed to characterize transcriptional alterations and to provide a mechanistic basis for the subsequent evaluation of COF-Tpy-Se-Cu.

overall_design: MOC1 cells were compared with MOC1 cells subjected to repeated fractionated irradiation. Cells in the irradiation group received repeated irradiation at 2 Gy per fraction. Three biologically independent replicates were analyzed for each group. Each replicate was independently cultured, harvested, subjected to RNA extraction, and processed for library preparation. Paired-end RNA sequencing was performed on a DNBSEQ-T7 platform.


title: BET inhibition synergizes with Golcadomide by suppressing MYC and E2F pathways in diffuse large B-cell lymphoma [ChIP-Seq]

status: Public on Aug 13 2026

city: Summit

first: Junfei

last: Zhao

state: NJ

address: 556 Morris Ave

institute: Bristol Myers Squibb

summary: Golcadomide is a potential first-in-class Aiolos/Ikaros-degrading CRBN E3 ligase modulator (CELMoD) agent designed for the treatment of non-Hodgkin lymphoma (NHL) including diffuse large B-cell lymphoma (DLBCL). Aiolos and Ikaros are two critical lineage factors in lymphoid development that sustain lymphoma growth through recruitment of transcriptional complexes to enhancers and promotors of target genes. Through an epigenetic compound library screening, we found that BET inhibitors sensitize DLBCL cells to golcadomide. Using phenotypic assays and a multi-omics approach, we found that the combination treatment led to synergistic inhibition of MYC and E2F target genes, induction of p21, and subsequent cell cycle arrest. Genome-wide analysis revealed co-occupancy of Aiolos, Ikaros and BRD4 at the promoters of MYC and other genes involved in proliferation, as well as MYC-activating enhancers.

overall_design: ChIP-seq was conducted in SUDHL4 and WSUDLCL2 diffuse large B-cell lymphoma (DLBCL) cell lines to profile the genomic binding of Ikaros, Aiolos and BRD4 transcription factors, as well as histone modifications H3K27ac, H3K4me1, and H3K4me3. Cells were treated with DMSO (vehicle control), BMS-986158 (2.5 nM), CC-99282 (50 nM), or a combination of both compounds.

first: Hsu

last: Chih-Chao

first: Patrick

last: Hagner


title: Transcriptomic profiling of cancer cells treated with COF-Tpy-Se-Cu

summary: This study profiled the transcriptional response of murine oral squamous cell carcinoma MOC1-R cells to COF-Tpy-Se-Cu combined with ionizing radiation. MOC1-R cells were maintained under control conditions or treated with COF-Tpy-Se-Cu (30 μg mL−1) plus 4 Gy X-ray irradiation, with three biologically independent replicates per condition. Total RNA was collected 24 h after treatment and subjected to paired-end RNA sequencing. The dataset was generated to identify differentially expressed genes and biological processes.

overall_design: Six biologically independent MOC1-R cell samples were included in the study. Three independent cultures served as controls, and three independent cultures were treated with COF-Tpy-Se-Cu (30 μg mL−1) combined with 4 Gy X-ray irradiation. Total RNA was collected 24 h after treatment. RNA extraction, library preparation, and sequencing were performed independently for each biological replicate. Paired-end RNA sequencing was performed on a DNBSEQ-T7 platform. Gene-expression profiles were compared between the treated and control groups to identify treatment-associated transcriptional changes.


title: Bulk RNA sequencing of Hspa1a knockdown in GM-CSF-driven bone marrow-derived monocyte/dendritic cell cultures

city: Nanjing

first: Wang

last: Bo

address: 121 Jiangjiayuan, Nanjing City

institute: The Second Affiliated Hospital of Nanjing Medical University

summary: We performed bulk RNA sequencing of granulocyte-macrophage colony-stimulating factor (GM-CSF)-driven bone marrow-derived monocyte/dendritic cell cultures treated with Hspa1a-targeting shRNA or non-targeting control shRNA (sh-NC). The dataset was generated to identify Hspa1a-dependent transcriptional changes during monocyte-to-dendritic cell differentiation.

overall_design: Six biological samples were analyzed, comprising three independent sh-NC controls (G_1, G_2 and G_3) and three independent Hspa1a shRNA samples (CCCP_1, CCCP_2 and CCCP_3). Poly(A)-selected RNA libraries were sequenced using paired-end reads on an Illumina NovaSeq 6000.

first: Zeping

last: Gui

first: Neda

last: Feizi

first: Berkay

last: Demirors

first: Canxiang

last: Lin

first: Hehua

last: Dai

first: Mouhamad

last: Al Moussawy

first: Andrew

last: Friday

first: Steven

middle: M

last: Sanders

first: Latha

last: Halesha

first: Amanda

middle: L

last: Williams

first: Faruk

last: Sacirbegovic

first: Parmjeet

middle: S

last: Randhawa

first: Khodor

middle: I

last: Abou-Daya

first: Martin

middle: H

last: Oberbarnscheidt


title: Draft hybrid assembly and annotation of the Drosophila subpalustris genome

city: Houghton

first: Paul

middle: Donald

last: Goetsch

state: MI

address: 1400 Townsend Drive

department: Biological Sciences

institute: Michigan Technological University

summary: Species within the Drosophila quinaria group are models for ecological genetic studies on topics that include morphological diversity, color pattern development, and feeding behavior. Here, we performed bulk RNA-seq of mixed male and female adult flies to provide evidence for annotation of our hybrid assembly of the Drosophila subpalustris genome.

overall_design: We performed 2 biological replicates each of RNA samples isolated from 10-20 mixed male and female adult flies using a standard Trizol-chloroform phase searation followed by isopropanol precipitation. RNA sequencing reads were used as evidence for genome annotation using BRAKER v3.0.6.

first: William

last: Dion

first: Emily

last: Washeleski

first: Tessa E.

last: Steenwinkel

last: Taylor

first: Prajakta P.

last: Kokate

first: Aidan

last: VanDrie

first: Thomas

last: Werner

first: Paul D.


title: Draft hybrid assembly and annotation of the Drosophila palustris genome

summary: Species within the Drosophila quinaria group are models for ecological genetic studies on topics that include morphological diversity, color pattern development, and feeding behavior. Here, we performed bulk RNA-seq of mixed male and female adult flies to provide evidence for annotation of our hybrid assembly of the Drosophila palustris genome.


title: Molecular Determinants of Functional Bacterial sRNA–mRNA Interactions Revealed by Integrating RNA Interactomes and Interpretable Machine Learning [Hfq-CLASH]

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary: Bacterial small RNAs (sRNAs) regulate gene expression by base pairing with target mRNAs, yet transcriptome-wide interactome mapping has shown that many sRNA–mRNA interactions detected in vivo have modest or not regulatory effects using orthogonal reporter assays. The molecular features that determine the functional outcome of sRNA-mRNA interactions remain poorly defined. Here, we integrated Hfq-CLASH interactome mapping with matched transcriptomic and proteomic profiling in Escherichia coli and developed an interpretable machine-learning framework to identify the molecular determinants that distinguish functional from non-functional interactions. Using sequence, structural, thermodynamic, duplex and protein-occupancy features, we found that transcriptomic and proteomic responses could be predicted with above-chance performance, achieving AUCs of 0.78 and 0.74, respectively. Feature attribution revealed that physical pairing alone is insufficient for regulation; instead, regulatory outcome is shaped by a coordinated interplay between RNA secondary structure, thermodynamic accessibility and local protein-binding context. Target-side Hfq occupancy emerged as a positive predictor of functional regulation, whereas AR2-domain occupancy on the sRNA was associated with non-responsive interactions, suggesting that distinct ribonucleoprotein states may separate productive regulation from non-productive binding. Together, these findings indicate that the regulatory fate of an sRNA–mRNA interaction is an emergent property of its biophysical context and protein-binding environment, rather than a direct consequence of physical pairing alone.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Hfq-CLASH was used to profile the RNA-RNA interactome of E. coli MG1655 using the protocol of Iosub et al eLife 2020 (PMID: 32356726) with some modifications specific for E. coli. MG1655 WT and Hfq-HTF (dual-affinity-tagged HTF strain) (PMID: 35732665). In brief, triplicate cultures of WT (untagged) and hfq-HTF (dual His-TEV-FLAG tagged Hfq) were grown to mid-exponentail phase and UV-croslinked. Libraries were prepared as previsouly described (PMID: 32356726, 35732665) and sequenced at Novogene using PE150 reads. Data were analysed using the Hyb-CRAC-R pipeline ( PMID: 35732665).

first: Daniel

last: Mediati

first: Fatemeh

last: Safari

last: Vafaee


title: Setd5 Coordinates Motor Neuron Development and Locomotor Function

city: hefei

first: wenxian

last: wang

address: No. 81, Meishan Road, Shushan District, Hefei City, Anhui Province

institute: Anhui Medical University

summary: Epigenetic regulation is essential for cell fate determination, yet its role in spinal motor neuron (MN) development remains poorly understood. SETD5, an epigenetic regulator, is mutated in SETD5 syndrome, which is characterized by intellectual disability and motor dysfunction. However, the mechanisms underlying these locomotor deficits remain elusive. Here, we integrated in ovo knockdown in chick embryos, conditional knockout strategies in mice and in vitro MN differentiation system to investigate Setd5 function during MN development. Setd5 ablation in MN progenitors (pMNs) with Olig2-Cre markedly reduced the Olig2+ progenitor pool by attenuating proliferation, as evidenced by diminished Ki67 and BrdU incorporation, while concurrently promoting premature differentiation, as shown by elevated Neurod1 expression and precocious generation of Mnx1+ newborn MNs.This imbalance disrupted MN subtype diversification, dysregulating key identity markers (Mnx1, Isl1, Lhx3, and Foxp1). Notably, late-stage Setd5 deletion with Isl1-Cre revealed a cell-context-specific requirement for Setd5 in maintaining Foxp1 expression selectively within thoracic preganglionic motor column neurons. These developmental defects resulted in aberrant axonogenesis, impaired neuromuscular junction formation, and severe locomotor phenotypes, including reduced spontaneous movement, poor motor coordination, and abnormal gait. Transcriptomic profiling of Setd5-deficient pMNs identified downregulation of cell-cycle genes and upregulation of neural differentiation programs, mechanistically linking Setd5 loss to the observed cellular phenotypes. Heterozygous animals displayed intermediate defects, confirming a dose-sensitive requirement. Collectively, our findings establish Setd5 as a critical epigenetic coordinator of MN proliferation and differentiation, and provide a mechanistic framework for understanding the motor abnormalities associated with SETD5 syndrome.

overall_design: RNA-seq profiling within in vitro differentiated motor neuron progenitors  from mouse embryonic stem cells.

first: Wenxian

last: Wang

first: Shuangling

last: Li

first: Qichen

last: Liu

first: Bing

last: Pan


title: Smart-seq profiling of border-associated alveolar macrophages in fibrotic mouse lungs

city: Shanghai

first: Jing

address: No. 227 South Chongqing Road, Shanghai

institute: Shanghai Jiao Tong University School of Medicine

summary: Fibrosis is commonly viewed as a pathological endpoint of persistent tissue injury and failed repair. Yet chronically injured tissues do not scar uniformly, indicating that local adaptive programs can buffer tissue stress and preserve structural integrity. Idiopathic pulmonary fibrosis (IPF) preferentially initiates within the subpleural region, but the cellular programs that bias subpleural remodeling toward fibrotic progression or preservation remain poorly understood. In this study, we identified a spatially restricted population of enlarged, lipid-laden alveolar macrophages located at the subpleural border, which we termed border-associated alveolar macrophages (BAAMs). Smart-seq profiling of sorted alveolar macrophage (AM) populations from fibrotic lungs identified a discrete set of functional genes defined as the BAAM transcriptional signature.

overall_design: BALF was collected from mice 14 days after bleomycin administration. BAAM-enriched and BAAM-poor fractions were separated by size-based filtration. Within these fractions, SSC^hi BODIPY^hi AMs were isolated by fluorescence-activated cell sorting (FACS) and compared with SSC^lo BODIPY^lo and SSC^int BODIPY^int AM populations. The sorted cell populations were subsequently subjected to Smart-seq analysis.

first: Jin

first: Wenying

last: Zhao

first: Yeke

last: Huang

first: Jiangxue


title: Chronic Reflux Stress Reshapes the EAC Transcriptional Landscape via APE1

city: Miami

first: Wael

last: El-Rifai

state: FL

address: Griffin Cancer Research Building,1425 NW 10th Ave

department: Department of Surgery and Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

summary: Gastroesophageal reflux disease (GERD) is the predominant risk factor for the development of Barrett’s esophagus and esophageal adenocarcinoma (EAC). However, the molecular mechanisms driving responses to chronic reflux conditions in EAC remain poorly defined. This study investigates the genome-wide transcriptional reprogramming and molecular stress responses mediated by apurinic/apyrimidinic endonuclease 1 (APE1) in EAC cells (OE33) surviving chronic, reflux-induced stress. By pairing a 15-day repeated acidified bile salt (rABS) exposure model with subsequent APE1 genetic silencing, this dataset defines the global differential gene expression profiles, altered signaling pathways, and transcriptional networks that depend on APE1 for acquired stress tolerance during sustained reflux insults.

overall_design: To evaluate the role of apurinic/apyrimidinic endonuclease 1 (APE1) in mediating adaptive transcriptional responses and genomic stability under chronic reflux conditions, human EAC cells (OE33) were exposed to an acidified bile salt cocktail (200 µM, pH 5.5) for 20 minutes daily over 15 days (rABS), while untreated parental cells served as baseline controls. Following the 15-day selection protocol, the surviving rABS-adapted OE33 cells were stably transduced with either a non-targeting control shRNA (shCtrl) or an APE1-targeted shRNA (shAPE1). Total RNA was isolated from three independent biological replicates for each experimental group.

first: Lei

last: Chen

first: Heng

last: Lu

first: Dunfa

last: Peng


title: Oral Delivery of R-spondin1-Loaded Small Extracellular Vesicles Activates WNT Signalling Pathway to Accelerate Intestinal Injury Repair and Reverse Ageing

city: Guangzhou

first: Shixiang

middle: Clover

address: Guanzhou street

institute: Guangzhou national labratory

summary: The intestine plays a crucial role in regulating metabolism and immunity, with functional decline occurring during injury and ageing. Stimulating the neogenesis of intestinal stem cells (ISCs) by activating the WNT/β-catenin signalling pathway represents a promising approach for intestinal tissue regeneration and injury repair. However, effective oral delivery of functional WNT signalling agonists to the gut remains challenging. Herein, we report a potent WNT/β-catenin signalling-inducing small extracellular vesicles (sEV) that can be administered orally and present remarkable therapeutic efficacy. We demonstrate that active R-spondin1 (RSPO1) protein can be loaded onto the surface of sEV via heparan sulfate proteoglycans. Notably, sEV-delivered RSPO1 (evRSPO1) effectively induces WNT/β-catenin signalling-inducing activity, enhances ISCs proliferation, and supports intestinal organoid growth in vitro. Importantly, oral administration of evRSPO1 activates the WNT/β-catenin signalling pathway in the cryptic stem cell niche, thereby accelerating tissue repair and regeneration in a radiation-induced intestinal injury model. Furthermore, evRSPO1 treatment induces ISCs proliferation and reverses the intestinal senescence phenotype in aged mice. Collectively, this study establishes evRSPO1 as a potential first-in-class, orally deliverable therapeutic that overcomes biological barriers to activate ISCs, enabling efficient intestinal tissue repair and rejuvenation.

overall_design: 18-month-old C57BL/6J mice were treated with ∼2 × 1010 particles sEV 200 µL, ∼1 × 1011 particles of sEV by oral administration twice a week for 2 weeks. Mice were euthanized after the last sEV administration for 24 h. The 2-month-old C57BL/6J mice were used as young controls.

first: Lingyan

last: Yang


title: Age-dependent alterations in the human striatum identify a PPP1R15B-miR-196a node as a modifier of Huntington’s disease phenotypes [miRNA array]

city: Saint Louis

first: Victoria

middle: A.

last: Church

state: MO

address: 660 Euclid

institute: Washington University School of Medicine

summary:
Polyglutamine expansion in Huntingtin (HTT) causes its aggregation and progressive loss of striatal neurons in Huntington’s disease (HD). HD is a mostly adult-onset neurodegenerative disorder with no disease-modifying therapies. Here we found that human striatal aging is associated with a global upregulation of genes involved in translation, including the translation and proteostasis regulator PPP1R15B (R15B). We used the R15B inhibitor Raphin1 to investigate if the age-associated changes could modify HD pathology. R15B inhibition rescued early learning and late motor deficits in HDYAC128 mice. In striatal medium spiny neurons directly reprogrammed from fibroblasts of symptomatic HD patients (HD-MSNs), Raphin1 reduced the formation of mutant HTT aggregates and neuronal death. Genetic knockdown of R15B also protected HD-MSNs from neurodegeneration whereas its overexpression exacerbated disease phenotypes. Moreover, both human striatum and reprogrammed MSNs exhibited age-dependent decline of miR-196a, a microRNA that directly targets non-conserved sites in human R15B 3’UTR and overexpressing miR-196a lowered mutant HTT aggregation. This work identifies age-dependent alterations in miR-196a and its target R15B and demonstrates the therapeutic potential of reversing these changes in diverse models and readouts of HD. We propose miR-196a and R15B as disease-modifying targets in HD.
We performed microRNA array on human cortex from young and old individuals to determine cortex gene-expression changes that occur during aging.

overall_design: 6 total samples were analyzed, these samples are the same individuals as used in the basal ganglia datasets also submitted with this manuscript.

first: VA

first: AS

last: Yoo


title: RNA sequencing upon CD146 knockdown/overexpression

city: Tianjin

first: Shuo

last: Qie

address: Huanhuxi Road, Tiyuanbei, Hexi District

department: Pathology

institute: Tianjin Medical University Cancer Institute & hospital

summary: RNA sequencing analysis was performed on liver cancer cells upon genetic manipulation of their CD146 levels. For these assays, total RNA samples were prepared using TRIzol reagent from Hep3B cells infected with lentiviruses expressing Tet-Control shRNA or Tet-CD146 shRNA, and HepG2 cells infected with lentiviruses expressing pLVX or CD146oe. The library and transcriptome sequencing were analyzed by AZENTA Life Sciences (Suzhou, China). Gene set enrichment analysis was applied to analyze the gene expression signatures using the Gene Ontology, Hallmark, and KEGG gene sets.

overall_design: Knockdown of CD146 was performed using Tet-on-induced Control shRNA or CD146 shRNA in Hep3B cells; while overexpression of CD146 was introduced into HepG2 cells via pLVX or CD146 vector.


title: Age-dependent alterations in the human striatum identify a PPP1R15B-miR-196a node as a modifier of Huntington’s disease phenotypes [RNA-Seq]

summary: Polyglutamine expansion in Huntingtin (HTT) causes its aggregation and progressive loss of striatal neurons in Huntington’s disease (HD). HD is a mostly adult-onset neurodegenerative disorder with no disease-modifying therapies. Here we found that human striatal aging is associated with a global upregulation of genes involved in translation, including the translation and proteostasis regulator PPP1R15B (R15B). We used the R15B inhibitor Raphin1 to investigate if the age-associated changes could modify HD pathology. R15B inhibition rescued early learning and late motor deficits in HDYAC128 mice. In striatal medium spiny neurons directly reprogrammed from fibroblasts of symptomatic HD patients (HD-MSNs), Raphin1 reduced the formation of mutant HTT aggregates and neuronal death. Genetic knockdown of R15B also protected HD-MSNs from neurodegeneration whereas its overexpression exacerbated disease phenotypes. Moreover, both human striatum and reprogrammed MSNs exhibited age-dependent decline of miR-196a, a microRNA that directly targets non-conserved sites in human R15B 3’UTR and overexpressing miR-196a lowered mutant HTT aggregation. This work identifies age-dependent alterations in miR-196a and its target R15B and demonstrates the therapeutic potential of reversing these changes in diverse models and readouts of HD. We propose miR-196a and R15B as disease-modifying targets in HD.

overall_design: We performed RNA-seq on human striatum from young and old individuals to determine striatal gene-expression changes that occur during aging.


title: Effects of Salmonella enterica serovar Enteritidis pathogenicity island ROD21 on the expression of virulence genes

city: Santiago

first: Susan

last: Bueno

state: Región Metropolitana

address: Avda. Libertador Bernardo O’Higgins #340

department: Departamento de Genetica Molecular y Microbiología

country: Chile

institute: Pontificia Universidad Católica de Chile

summary: Salmonella enterica serovar Enteritidis (SEn) is a pathogenic Gram-negative bacterium, which possesses several Pathogenicity islands (PAIs), including ROD21, an excisable PAI that has been linked to virulence in mice and poultry. Previous studies from our laboratory have shown that deletion of ROD21 can affect the virulence of SEn. We observed that both the deletion of ROD21 and the joined deletion of SEN1970 and SEN1998 have an impact on the transcriptional pattern of SEn in vitro. We observed changes in the transcription of genes located in SPI-2, which are required for intracellular survival and colonization. We also found that in both cases, genes related to the expression of flagellar machinery are downregulated, which could also be observed in the bacterial morphology in vitro. This observation was later backed up with in vivo experiments in mice, which showed a differential capacity of SEn ROD21 mutant strains to reach levels of colonization at later stages of infection, compared to the wild-type SEn strain. These results have led us to conclude that the deletion of ROD21 genes produces transcriptional changes relevant for the pathogenicity of SEn and its effective colonization in vivo, arguing for possible changes in the genome structure when these genes are deleted, which could affect transcription.

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: Salmonella ser. Enteritidis P125109 ΔROD21::frt and ΔintΔrdf::cat strains were cultured overnight at 37°C in LB broth with agitation, and diluted in LB to OD600 0.01. The cultures were incubated at 37°C with agitation until OD600=0.6, at which samples were centrifugated at 8,000g for 8 min, the supernatant was discarded, and RNA was isolated using TRizol. Samples were further purified from salts using drop dialysis in MF-Millipore™ membranes (0.025µm pore diameter) against nuclease-free water for 4 h on ice. RNA-seq was performed as follows: Libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Prep Kit and sequenced on an Illumina NovaSeq platform to a sequencing depth of at least 10 million read pairs (150 bp paired-end sequencing) per sample.

first: Isidora

middle: D

last: Suazo

first: Lucas

last: Vásquez-Herrera

first: Guillermo

last: Hoppe-Elsholz

first: Alexis

last: Kalergis


title: Metformin Modulates the Phenotypes of Tumor-associated Macrophages in Glioblastoma in a Context-Dependent Manner by Promoting the Homeostasis of Macrophages

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: Glioblastoma (GBM) remains the most aggressive primary adult brain cancer attributed to its immunosuppressive nature. Radiation therapy (RT) and concurrent temozolomide chemotherapy are the standard treatments for GBM. Emerging evidence indicates that metformin has potential as an anti-tumor agent that can reshape the immune landscape across various malignancies. We thus postulate that metformin may enhance the anti-tumor effect of RT by modulating the immunosuppressive milieu in GBM. We first explored multiple in vitro conditions, with or without pre-induction, and mimicked a tumor microenvironment to demonstrate a highly context-dependent effect of metformin on the polarization of bone marrow-derived macrophages (BMDMs). We then investigated the antitumor activity and immune-modulatory effects of metformin in combination with RT in GBM-bearing mice. The in vitro experiment showed that metformin inhibited the immunosuppressive effects of IL-4/IL-13 but also the immunostimulatory effects of Lipopolysaccharide (LPS) on BMDMs, demonstrating bidirectional immunomodulatory properties that depend on the baseline inflammatory stimulus. In a tumor cell co-culture environment, metformin exhibited context-dependent immunoregulatory effects, predominantly promoting M1-associated activation. Notably, concurrent metformin treatment counteracted M2 polarization typically induced by the tumor microenvironment. In a high m-MCSF inducted M2-dominated condition, metformin preferentially shifted the highly polarized M2 phenotype toward an M1-like state in a time- and dose-dependent manner but with limited promotion of M1 subtype maturation. RNAseq results on BMDM treated with metformin showed increased homeostasis. Metformin showed dose-dependent immunomodulatory effects when combined with RT in vitro.  In syngeneic GBM mouse models, concurrent metformin + RT significantly prolonged survival and reduced tumor burden by reprogramming tumor-associated macrophages (TAMs), elevating intratumoral CD8+ T-cell infiltration and the CD8+/Treg ratio, increasing circulating CD8+ T cells, reversing RT-induced expansion of monocytic myeloid-derived suppressor cells (mMDSCs), and expanding CD4+ and CD8+ effector memory populations in peripheral blood. Metformin demonstrates inhibitory effects on M2 phenotype of macrophages. However, it is not a simple M2 inhibitor; instead, it functions primarily as a neutralizer of highly polarized macrophage states by promoting transcriptomic homeostasis. This context-dependent activity enables metformin to relieve the profoundly immunosuppressive TME of GBM, potentiate the anti-tumor effects of RT, and enhance systemic immune memory.

overall_design: RNA-seq profilling of bone marrow-derived macrophages (BMDMs) without and with Metformin 0.1mM  and 2mM treatments for 24 hours.

first: Zhang

last: Chi

first: Mahfooz

last: Sadaf


title: RNA-sequencing of primary mouse lung fibroblasts treated with TGF-β1

first: Jing

last: Wang

summary: Fibroblast activation is accompanied by extensive transcriptional and metabolic remodeling that supports extracellular matrix production during pulmonary fibrosis. In this study, we investigated how palmitoleic acid, a lipid mediator generated by BAAMs through SCD1-dependent lipid remodeling, influences the transcriptional state of activated lung fibroblasts. Bulk RNA sequencing of primary mouse lung fibroblasts revealed coordinated upregulation of glycolytic pathways and suppression of oxidative phosphorylation and fatty-acid oxidation following fibroblast activation.

overall_design: Primary lung fibroblasts were isolated from mice and cultured in vitro. Cells were treated control with TGF-β1 (5ng/mL, 24h) or vehicle control. Following treatment, total RNA was collected from independent biological replicates and subjected to bulk RNA sequencing analysis.

first: Jin

first: Wenying

last: Zhao

first: Yeke

last: Huang

first: Jiangxue

last: Li


title: Transcriptomic profiling of diabetic wound tissues treated with multifunctional microneedles integrating spermidine- and TGF-β3-regulated dental pulp stem cell spheroids

city: Harbin

first: WenXuan

address: No. 300 Xuefu Road

institute: The Second Affiliated Hospital of Harbin Medical University

summary: Diabetic chronic wounds exhibit impaired tissue repair characterized by persistent inflammation, oxidative stress, defective extracellular matrix remodeling, and insufficient regeneration. In this study, RNA sequencing was performed to investigate transcriptomic changes in diabetic wound tissues following treatment with multifunctional microneedles (DST-MNs) integrating spermidine- and TGF-β3-regulated dental pulp stem cell spheroids. Full-thickness diabetic wounds were established in rats, and wound tissues from untreated diabetic wound animals and DST-MNs-treated animals were collected for transcriptome profiling. Differentially expressed genes and enriched biological pathways were analyzed to identify molecular mechanisms associated with DST-MNs-mediated wound repair. These data provide insights into transcriptional regulation involved in inflammatory modulation, extracellular matrix remodeling, angiogenesis, and diabetic wound regeneration.

overall_design: RNA sequencing was performed to characterize global gene expression changes in diabetic wound tissues after DST-MNs treatment. A diabetic full-thickness dorsal skin wound model was established in male Sprague–Dawley rats. Animals were randomly divided into untreated Control and DST-MNs-treated groups. Wound tissues were collected after treatment for transcriptomic analysis. Total RNA was extracted and subjected to high-throughput RNA sequencing using the DNBSEQ platform with paired-end sequencing. Three biological replicates were analyzed for each group (Control: C1, C2, and C3; DST-MNs treatment: ST1, ST2, and ST3). Differentially expressed genes between the two groups were identified, followed by functional enrichment analyses including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses to investigate biological processes associated with DST-MNs-mediated reconstruction of the diabetic wound microenvironment and tissue regeneration.

first: Wenxuan

first: Zansheng

first: Xinrui

last: Luan

first: Ying

first: Xiaojun

last: Han

first: Han

last: Jin


title: Transcriptomic profiling of two-dimensional cultured cells and three-dimensional dental pulp stem cell spheroids regulated by spermidine and TGF-β3

summary: Dental pulp stem cells (DPSCs) exhibit distinct biological behaviors under conventional two-dimensional (2D) culture and three-dimensional (3D) spheroid conditions. To investigate the transcriptional regulation associated with spheroid formation and biomimetic factor-mediated functional modulation, RNA sequencing was performed on human DPSCs cultured under 2D and 3D conditions with or without spermidine (SPD) and transforming growth factor-β3 (TGF-β3) treatment. Four experimental groups, including 2D cultured DPSCs (DPSC_2D), ST-GH-treated 2D cultured DPSCs (DPSC_2ST), 3D DPSC spheroids (DPSC_3D), and ST-GH-treated 3D DPSC spheroids (DPSC_3ST), were analyzed. Transcriptomic profiling identified differentially expressed genes associated with extracellular matrix (ECM) organization, cell adhesion, angiogenesis, inflammatory regulation, and tissue regeneration. Comparative analyses revealed that 3D spheroid formation enhanced regenerative-associated transcriptional signatures, while SPD/TGF-β3 treatment further promoted ECM remodeling, angiogenic signaling, and suppression of inflammation-related pathways. These findings provide molecular insights into the regulatory effects of 3D spheroid architecture and endogenous biomimetic cues on DPSC regenerative functionality.

overall_design: RNA sequencing was performed to characterize transcriptomic differences between human DPSCs cultured under two-dimensional (2D) and three-dimensional (3D) spheroid conditions and to investigate the effects of spermidine (SPD) and transforming growth factor-β3 (TGF-β3) supplementation. Four experimental groups were included: DPSC_2D (2D-cultured DPSCs without treatment), DPSC_2ST (2D-cultured DPSCs treated with ST-GH containing SPD and TGF-β3), DPSC_3D (3D DPSC spheroids without treatment), and DPSC_3ST (3D DPSC spheroids treated with ST-GH). Each group contained three biological replicates. Total RNA was extracted and subjected to high-throughput RNA sequencing. Differential expression analysis, Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and Gene Set Enrichment Analysis (GSEA) were performed to identify biological pathways associated with spheroid formation and SPD/TGF-β3-mediated functional regulation.


title: SETDB2 inhibits thyroid cancer progression by regulating the expression of the splicing factor U2AF1

city: Dalian

first: yuesheng

last: lv

address: Lianhe Road

department: Τhe First Affiliated Hospital of Dalian Medical University

institute: Department of General Surgery

summary: Objective: This study aimed to investigate SETDB2 expression, clinical significance, and molecular mechanism in thyroid cancer progression. Methods: SETDB2 expression and prognosis were analyzed using TCGA and CPTAC databases, and validated by immunohistochemistry in 90 clinical samples (primary, recurrent, metastatic papillary, and anaplastic carcinoma). Overexpression and knockdown models were established in BCPAP and BHT101 cells. Proliferation was assessed by CCK‑8, colony formation, and EdU assays. RNA‑seq and qPCR identified downstream targets, with rescue experiments via U2AF1 overexpression. Results: SETDB2 was significantly downregulated in recurrent and metastatic papillary and anaplastic thyroid carcinoma, and low expression correlated with poor prognosis. SETDB2 overexpression suppressed proliferation and colony formation in anaplastic BHT101 cells, whereas knockdown promoted growth in papillary BCPAP cells. U2AF1 was identified as a key downstream target, and its overexpression partially reversed the inhibitory effects of SETDB2 on proliferation. Conclusion: SETDB2 acts as a tumor suppressor in thyroid cancer; its loss promotes progression, likely through regulating U2AF1. The SETDB2‑U2AF1 axis represents a potential therapeutic target.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BHT101 cells with SETDB2 overexpression or not

first: Yao

last: Chen

first: Xiaomeng

last: Jing

first: Qi

last: Jiang

first: Keer

first: Jiangning

last: Gu

first: Yuesheng

last: Lv

first: Dan


title: Endothelial VEGFR2 insufficiency promotes the transition of lymphatic to hematopoietic transcriptional programs [Vegfr2_siRNA_mLEC]

city: Suzhou

first: Yulong

last: He

address: 199 Ren-Ai Road

institute: Soochow University

summary: Vascular endothelial growth factor receptor-2 (VEGFR2) is a key target for regulating the endothelial cell lineage and angiogenesis. It is also expressed by lymphatic endothelial cells (LECs) while its participation in lymphangiogenesis remains inadequately characterized. We demonstrate in this study that VEGFR2 is highly expressed in dermal initial lymphatic vessels and valves. The induced deletion of pan-endothelial Vegfr2 at the neonatal stage produced a potent suppression of dermal lymphatic growth, characterized by a thinner lymphatic diameter, a decreased number of LECs and lymphatic valves. Mechanistically, VEGFR2 insufficiency led to a dramatic decrease in lymphatic VEGFR3, a key regulator mediating signals for lymphatic growth and remodeling. RNA sequencing analysis revealed that GO terms enriched for downregulated genes included biological processes related to EC development while pathways related to hematopoiesis and immune responses were upregulated in the skin of Vegfr2 mutants compared with littermate controls. This was further confirmed by RNA-seq analysis of dermal tissues 48 hours after endothelial Vegfr2 deletion. Consistently, targeting Vegfr2 in PROX1+ cells produced an inhibitory effect on dermal lymphatic growth and recapitulated a similar altered transcriptomic signature. The alteration of lymphatic gene expression was further validated by siRNA-mediated Vegfr2 knockdown in primary LECs, showing a transcriptional trend toward a hematopoietic fate. Findings from this study imply that VEGFR2 is required for the maintenance of endothelial identity, and its insufficiency triggers a transcriptional reprogramming that diminishes VEGFR3-mediated lymphangiogenesis.

overall_design: For the induction of gene deletion, new-born pups were treated by two-five daily intragastrical or intraperitoneal injections of tamoxifen (Sigma-Aldrich, T5648-5G) from the postnatal day 1 (P1-2, 60 μg/day) or the postnatal day 10 (P10-12 or 14, 200 μg/day). Skin tissues were collected from the endothelial or lymphatic specific knockout and littermate control mice for RNA-seq profiling at P3 (Kdr-ecko) or P21  (Kdr-ecko, (Kdr-lecko). For the knockdown experiment, LECs were transfected with siRNA duplex oligoribonucleotides (50 nM) targeting mouse Vegfr2 using CALNP™ RNAi in vitro transfection reagent (D-Nano Therapeutics, DN001-10). RNA from the transfected and control cells was extracted for  RNA-seq analysis 48 h later.

first: Taotao

first: Xudong

last: Cao

first: Fei

last: Zhou

first: Xiujuan


title: α-Ketoglutarate improves the development of vitrified-warmed bovine embryos by alleviating oxidative stress

city: Hefei

first: Wenjie

last: Yu

address: No.130 West Changjiang Road

institute: Anhui Agricultural University

summary: The inherently low reproductive efficiency of cattle is a major constraint on the development of the cattle industry. Embryo vitrification and warming are of great significance for the utilization of embryo resources and the improvement of the reproductive efficiency of cattle, thereby supporting the propagation of elite breeds and biological breeding. Oxidative stress is a major factor reducing the survival rate and developmental competence of vitrified-warmed embryos. In a previous study in cattle, the antioxidant α-ketoglutarate (AKG) was found to promote oocyte maturation and early embryonic development in vitro by alleviating oxidative stress. However, whether AKG can effectively alleviate cryoinjury by reducing oxidative stress, therefore improving quality and development of vitrified-warmed blastocysts, remains unclear. In the current study, in vitro produced bovine embryos were produced and AKG was supplemented to vitrification-warming solutions to explore its effects on the quality and developmental efficiency of vitrified-warmed blastocysts. The results revealed that vitrification and thawing markedly increased oxidative stress and apoptosis levels, while decreasing the survival rate, hatching rate, mitochondrial activity, and the ratio of ICM/TE cells in blastocysts. Supplementation with 25 μM AKG effectively alleviated oxidative stress, apoptosis, and increased the survival rate, hatching rate, mitochondrial activity as well as the ratio of ICM/TE. Single-cell RNA sequencing also showed that AKG treatment induced significant alterations in pathways associated with oxidative stress, apoptosis, mitochondrial function, and lipid metabolism in vitrified-warmed blastocysts. Collectively, these findings demonstrate that AKG improves the quality and developmental competence of vitrified-thawed bovine blastocysts by regulating oxidative stress. This study provides a theoretical basis for optimizing embryo vitrification-warming protocols, enhancing the utilization efficiency of vitrified embryos, and improving cattle reproductive performance.

overall_design: Utilizing single-cell RNA sequencing technology, we conducted an in-depth investigation into  the molecular mechanisms underlying the effects of vitrification-warming on bovine blastocysts and the protective effects of AKG on vitrified-warmed blastocysts

first: Yingying

last: Yue

first: Xunuo

last: Shao

first: Weipeng

last: Zhang

first: Wenzhuo

first: Xinqi

last: Gan

first: Zhiyuan

last: Yang

first: Jason G

last: Knott

first: Yunhai

first: Zubing


title: Multi-tissue transcriptomic landscape reveals synergistic mechanisms of exercise and GLP-1 agonist in ameliorating diabetic phenotypes in db/db mice [Muscle]

city: Wuhan

first: Zhenghong

last: Kang

state: Hubei

address: 461 Luoyu Road, Hongshan District, Wuhan City, Hubei Province

department: School of Sports Medicine

institute: Wuhan Sports University

summary: Type 2 diabetes mellitus (T2DM) involves coordinated multi-organ metabolic dysfunction, yet the systems-level effects of combined pharmacological and exercise interventions remain unclear. Male db/db mice received semaglutide, high-intensity interval training (HIIT), or both for eight weeks. Multi-organ bulk RNA-seq with qPCR validation and CellChat analysis was performed in heart, kidney, liver, hippocampus, and skeletal muscle. Combined treatment produced the greatest reductions in food intake, body weight, and fasting glucose. Transcriptomic responses were organ-dependent, most pronounced in skeletal muscle and liver. Under combination therapy, DEGs in hippocampus and liver no longer reached thresholds relative to single interventions, consistent with unchanged hippocampal Glp1r and hepatic Plpp7 by qPCR, whereas heart, kidney, and skeletal muscle retained concordant regulation with further reductions in cardiac Cyp2ab1 and renal/muscle Apoa1. Cross-organ analysis identified coordinated modulation of the PPARα–Plin4 axis and suppression of lipid metabolic pathways, confirmed by qPCR. Inter-organ network analysis revealed increased communication numbers but reduced interaction strength under combination therapy. These findings demonstrate organ-specific transcriptional adaptation to combined HIIT and semaglutide.

overall_design: In this study, db/db mice underwent an 8-week intervention of HIIT, semaglutide administration, or their combination. Phenotypic assessments included food intake, body weight, and fasting blood glucose. Multi-organ transcriptomic profiling (heart, liver, kidney, hippocampus, skeletal muscle) was performed, followed by differential expression analysis, integrative intersection analysis, and GO/KEGG pathway enrichment to identify intervention-specific and shared molecular signatures.

first: Hua

last: Liu

first: Shijie

last: Lai

first: Jianting

last: Sun

first: Zhiyu

last: Wang

first: Yanzhi

last: Xu


title: Endothelial VEGFR2 insufficiency promotes the transition of lymphatic to hematopoietic transcriptional programs [Vegfr2_lecko_P21skin]

first: Yulong

first: Taotao

last: Li

first: Xudong

first: Fei

first: Xiujuan


title: Endothelial VEGFR2 insufficiency promotes the transition of lymphatic to hematopoietic transcriptional programs [Vegfr2_ecko_48h_skin]

last: He


title: Endothelial VEGFR2 insufficiency promotes the transition of lymphatic to hematopoietic transcriptional programs [Vegfr2_ecko_P21skin]

last: Cao


title: Molecular Determinants of Functional Bacterial sRNA–mRNA Interactions Revealed by Integrating RNA Interactomes and Interpretable Machine Learning

first: Jai

last: Tree

summary: Bacterial small RNAs (sRNAs) regulate gene expression by base pairing with target mRNAs, yet transcriptome-wide interactome mapping has shown that many sRNA–mRNA interactions detected in vivo have modest or not regulatory effects using orthogonal reporter assays. The molecular features that determine the functional outcome of sRNA-mRNA interactions remain poorly defined. Here, we integrated Hfq-CLASH interactome mapping with matched transcriptomic and proteomic profiling in Escherichia coli and developed an interpretable machine-learning framework to identify the molecular determinants that distinguish functional from non-functional interactions. Using sequence, structural, thermodynamic, duplex and protein-occupancy features, we found that transcriptomic and proteomic responses could be predicted with above-chance performance, achieving AUCs of 0.78 and 0.74, respectively. Feature attribution revealed that physical pairing alone is insufficient for regulation; instead, regulatory outcome is shaped by a coordinated interplay between RNA secondary structure, thermodynamic accessibility and local protein-binding context. Target-side Hfq occupancy emerged as a positive predictor of functional regulation, whereas AR2-domain occupancy on the sRNA was associated with non-responsive interactions, suggesting that distinct ribonucleoprotein states may separate productive regulation from non-productive binding. Together, these findings indicate that the regulatory fate of an sRNA–mRNA interaction is an emergent property of its biophysical context and protein-binding environment, rather than a direct consequence of physical pairing alone.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: E. coli MG1655 strains carrying individual deletions of chiX, gadY, ryhB, sdsR, or spf were transformed with either an empty pBAD+1 or the corresponding sRNA complementation plasmid. Strains were cultured in LB medium supplemented with ampicillin 100 µg.mL-1 at 37˚C with shaking at 220 RPM.  Three independent biological replicates were prepped for each strain. Cultures were grown to mid-exponential phase (OD600 = 0.6), and sRNA expression was induced with 0.2% (w/v) L-arabinose for 30 min. Following induction, cultures were immediately treated with 95:5 (v/v) ethanol:phenol stop solution. Cells were harvested and mechanically lysed with zirconia beads using a FastPrep-24 5G bead-beating system. Total RNA was then isolated using GTC-phenol extraction. Residual genomic DNA was removed by treatment with RQ1-RNase-free DNase (Promega). RNA concentration was determined using a Qubit fluorometer, and RNA integrity was assessed using a TapeStation (Agilent). RNA samples were submitted to Novogene for directional prokaryotic RNA-sequencing library preparation, including depletion of bacterial rRNA. Libraries were sequenced using a 150-bp paired-end strategy on an Illumina NovaSeq platform.

first: Daniel

last: Mediati

first: Monika

last: Vesse

first: Fatemeh

last: Safari

first: Saleh

last: Alquethamy

last: Vafaee


title: Inflammasome Hyperactivation Disrupts  Construction of the Gas Exchange Surface through the NLRP3-IL-18-TNFa Axis [scRNA-seq]

city: La Jolla

first: Rongbo

address: 9500 Gilman Drive

department: Pediatrics

institute: UC San DIego

summary: Inflammation is a prominent feature of tissue injury, and a driver of chronic disease. However, the precise molecular mechanisms underlying the impact of inflammation remains unclear in many injury settings including in alveolar development to build the gas exchange surface in lung. Here we show that in mice, overexpression of patient-derived activated variants of Nlrp3 (Nlrp3act), a central sensor within the inflammasome, resulted in severe simplification of alveoli. Such histology is accompanied by a striking decrease of cell proliferation and marker expression of secondary crest myofibroblasts (SCMFs) whose contractility is essential for septa formation. Such a drastic effect on lung structure was only observed when the variants were overexpressed in the first two weeks after birth, but not later. While both downstream proinflammatory cytokines IL-1β and IL-18 are upregulated, inactivation of Il18, but not Il1b in the Nlrp3act background reversed simplification. Also unlikely in other tissue settings where Mmp9 is a critical mediator downstream of the inflammasome, inactivation of Mmp9 also did not reverse Nlrp3act phenotypes, suggesting context-dependent mechanisms. scRNAseq followed by validation revealed IL-18-dependent increase of Tnfα in myeloid cells, capable of signaling through its widely-expressed receptors to all structural cells including SCMFs. Addition of recombinant TNFα to mesenchymal cells enriched for SCMFs led to reduced contractile gene expression. Finally, inactivation of Tnfα in the Nlrp3act background led to a robust reversal of simplification. These findings together demonstrate an inflammasome-IL-18-TNFα axis that dictate lung mesenchymal cell states, thereby control the building of the gas exchange surface.

overall_design: single-cell RNA-seq (scRNAseq) was performed on all 4 compartments of the lung, sorted and reproportioned to ensure balanced representation of CD45+ immune cells, EpCAM+ epithelial cells, CD31+ endothelial cells, and CD45-EpCAM-CD31- mesenchymal cells isolated from the lungs of LysMcre;Nlrp3A350V mutant and control mice at P8

first: Xin


title: NET1 mRNA localization to the midbody is required for ARP2/3-dependent initiation of mitotic abscission

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

summary: The recruitment and activation of abscission machinery following mitosis is tightly regulated in time and space, yet the mechanisms controlling this process are poorly understood. We find that RNA localization and local translation at the midbody regulates when and where abscission-regulating proteins are expressed. The 3′UTR of NET1 mRNA contains an element that is necessary and sufficient for RNA targeting to the midbody. Mislocalization of NET1 mRNA results in a loss of NET1 protein, a Rho family GEF, throughout the intercellular bridge as well as slower cell proliferation and delayed abscission. This coincides with a loss of Arp2/3 at the abscission site and is dependent upon NET1 binding to Rho family GTPases. These findings establish midbody RNA localization and local translation as a key layer of regulation over abscission timing and identify a role for NET1 as a regulator of Arp2/3-mediated branched actin accumulation at the abscission site.

overall_design: RNAseq-centered MPRA testing the ability of endogenous sequences to drive a reporter RNA to the midbody of dividing cells


title: Phosphorylation Protects Oncogenic RAS from LZTR1-Mediated

city: Bethesda

first: Ryan

last: Young

state: MD

address: 9000 Rockvill Pike, Bld. 10, rm. 6N105

department: LYMB

institute: NIH/NCI

summary: Oncogenic KRAS and NRAS mutations are common in hematologic malignancies, but how they signal in that context is less well characterized than in carcinomas. To uncover novel RAS biology and potential therapeutic vulnerabilities, we employed a multi-omics screening approach in multiple myeloma to identify regulators of RAS activity.  We report that the phosphatase PP1C dephosphorylates the conserved T148 residue on RAS, which in turn permits LZTR1-dependent proteasomal degradation.  Notably, LZTR1 is ineffective against KRAS A146 gain-of-function mutations, which are adjacent to T148 and prevalent in hematologic cancers, such as diffuse large B cell lymphoma and acute myeloid leukemia.   Remarkably, we find that KRAS protein is four-fold less stable in hematologic versus carcinoma cells, offering a unique therapeutic opportunity targeting RAS protein stability mechanisms.  The kinases PAK1 and PAK2 were shown to shield RAS  from LZTR1-dependent degradation by phosphorylating T148, and targeting PAK1/2 activity improved RAS-directed therapy.  Collectively, our findings reveal a regulatory circuit  governing RAS stability that is preferentially active in blood cancers and potentially druggable.

overall_design: CRISPR screening data using the Brunello whole genome library in human multiple myeloma lines (XG7 and RPMI-8226) ectopically expressing GFP-KRASG12D.

first: Zhang

last: Lin

first: Young

last: Ryan M.


title: Trans-regulatory gene mapping prioritizes disease drivers in asthma

city: Chicago

first: Isabella

middle: M.

last: Salamone

state: IL

address: 920 E 58TH ST

department: Human Genetics

institute: University of Chicago

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

overall_design: Refer to individual Series


title: Genetic and chemical interrogation of methionyl-tRNA synthetase reveals a shared vulnerability across diverse mycobacteria

first: Dan

last: Luo

state: Shanghai

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

summary: This dataset contains host–pathogen dual RNA-seq profiles from RAW264.7 macrophages infected with Mycobacterium abscessus MetRS_KD or PLJR962 vector control strains. The experiment was designed to analyze host and bacterial transcriptional changes after ATC induction of metS knockdown during macrophage infection. Mixed host–pathogen total RNA was subjected to both eukaryotic and prokaryotic rRNA depletion, followed by strand-specific paired-end RNA-seq.

overall_design: RAW264.7 macrophages were seeded in 6-well plates at 1 × 10^6 cells per well and infected with M. abscessus MetRS_KD or PLJR962. After extracellular bacteria were removed, ATC was added to induce metS knockdown, and infected cells were incubated for an additional 24 h. For each biological replicate, cells from two wells were pooled. Three biological replicates were prepared for each group, giving six paired-end dual RNA-seq libraries.

first: Weile

last: Xie

first: Longlong

first: Jijie

last: Jiang

first: Guocheng

last: Zhao

first: Mengke

last: Hou

first: Keyu

last: Xiao

first: Lan

last: Qian

first: Jianming

last: Zhang

first: Guanghui

last: Dang

first: Siguo

last: Liu

first: Zhe


title: Gene Expression Changes Induced by FBXW5 overexpression in triple-negative breast cancer cells

city: Jinan

first: Tong

last: Chen

address: No.107 Wenhua Xi Road

institute: Qilu Hospital of Shandong University

summary: To investigate the role of FBXW5 as a tumor-intrinsic immunosuppressive regulator in triple-negative breast cancer (TNBC), we established FBXW5 overexpression models in TNBC cell lines 4T1 (mouse) and MDA-MB-468 (human). Total RNA was extracted and subjected to transcriptome sequencing using next-generation sequencing technology to identify downstream pathways.

overall_design: We randomly divided 4T1 and MDA-MB-468 cells into two groups, each comprising two replicate samples. One group was transfected with FBXW5 overexpression construct, while the other received vector control. Following successful overexpression, total RNA was extracted using TRIzol reagent. After RNA quality control, transcriptome sequencing was performed on theIllumina NovaSeq X plus platform.


title: A Rare Nestin-Expressing Granule Cell Precursor Subpopulation Underlie Shh-Medulloblastoma Formation

city: Long Island City

first: Salsabiel

last: El Nagar

state: NY

address: 45-18 Ct Square W

institute: Mangrove Neuro

summary: We identify a rare Nestin-expressing granule cell precursor (GCP) subpopulation in the normal early postnatal cerebellum and show that it is spatially restricted, molecularly distinct and highly competent to form SHH-MB. Single cell RNA sequencing revealed Nestin-expressing GCPs have a transcriptome indicating reduced neuronal differentiation and enrichment for stem cell genes compared to bulk GCPs and more closely align with SHH MB cells.

overall_design: To investigate transcriptome differences of Nes expressing GCPs and with other GCPs, we performed scRNA-seq analysis of P1 cerebellum. 4 samples (1 posterior cerebellum each) corespond to Nes-Cfp mice at p1 and 5th sample correspond to Nes-Cfp; Atoh1-Gfp mice. In this case, 3 samples were pouled and the double positive  Cfp - Gfp population was purified using fluorescent activated cell sorting (FACS).

first: Salsabiel El

last: Nagar

first: Yinwen

last: Liang

first: Alexandra

last: Joyner


title: KMT5A Maintains Muscle Stem Cell Quiescence Through Epigenetic Regulation of Notch Signaling

city: Madison

first: Jeonghye

middle: Hannah

last: Hwang

state: Wisconsin

address: 1111 Highland ave.

department: Department of Cell and Regenerative Biology

institute: University of Wisconsin-Madison

summary: Quiescence preserves muscle stem cell (MuSC) identity and regenerative capacity, but the epigenetic mechanisms that support this state remain incompletely understood. Here, we show that the H4K20 monomethyltransferase KMT5A sustains canonical Notch signaling in quiescent MuSCs through catalytic deposition of H4K20me1. Loss of Kmt5a led to delayed reduction of Rbpj and other canonical Notch pathway genes, whereas acute catalytic inhibition of KMT5A was sufficient to suppress their expression, indicating that H4K20me1 supports transcriptional competence at Notch loci. Genetic restoration of Notch signaling rescued quiescence-associated features in Kmt5a-deficient MuSCs but did not restore post-activation survival or regenerative output. During physiological activation after injury, H4K20me1 at Notch loci remained largely preserved while H4K20me3 accumulated. Together, these findings identify KMT5A-dependent H4K20me1 as a chromatin mechanism that maintains the Notch- dependent quiescence program and distinguish homeostatic Kmt5a loss from physiological MuSC activation.

overall_design: CUT&Tag was performed to profile the genome-wide distribution of H4K20me1 and H4K20me3 in mouse muscle stem cells (MuSCs). MuSCs were isolated from adult C57BL/6 mice and MuSC-specific Kmt5a KO mice. Freshly isolated MuSCs from non-injured muscle were considered quiescent, whereas MuSCs collected 2 days after BaCl2-induced injury (2 dpi) were defined as activated. CUT&Tag was performed using antibodies against H4K20me1 and H4K20me3.

first: Adam

middle: Y

last: Chu

first: Roméo

last: Blanc


title: Cryo-EM structure, enzymatic activity and genome targeting of canonical PRC1

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz

country: Germany

institute: Max Planck Institute of Biochemistry

summary: Canonical Polycomb Repressive Complex 1 (cPRC1) preserves cell fate decisions by repressing inappropriate transcription of developmental regulator genes. We report the cryo–electron microscopy structure of tetrameric human cPRC1 bound to a nucleosome in complex with the ubiquitin-conjugating enzyme UBCH5C. cPRC1 adopts a compact, highly integrated architecture in which the subunits RING1B, BMI1, and PHC2 form an extended interface that positions UBCH5C on the nucleosome to enable efficient monoubiquitination of histone H2A at lysine 119. This organization is conserved in Drosophila, where mutational analyses identify the PHC2 ortholog Polyhomeotic (Ph) as a central scaffold and targeting factor. The Ph HD domain is required for complex assembly, whereas the Ph SAM domain is dispensable for assembly but essential for cPRC1 recruitment to Polycomb target genes and productive H2A monoubiquitination at these loci.

overall_design: Analyses of ChIP-seq profiles generated from wild-type and mutant Drosophila embryos.

first: Martina

last: Cafiso

first: Jacques

last: Bonnet


title: An engineered oncolytic parapoxvirus induces immunogenic tumor cell death and displays antitumor efficacy by enhancing T cell responses

city: changchun

first: Qi

last: Li

address: No. 5333 Xi'an Avenue, Changchun City, Jilin Province

institute: Institute of Zoonosis, and College of Veterinary Medicine, Jilin University

summary: By harnessing B16-derived immunologically ‘cold’ tumor models, we assessed therapeutic effects of ORFV recombinants .

overall_design: Comparative gene expression profiling analysis of RNA-seq data from mouse B16 tumors treated with IL15 or PBS.

first: Jing

last: Lin

first: Fei

last: Gao

first: Xinyue

last: Wang

first: Ying

last: Ma

first: Chengyi

first: Haizhu

last: Wu

first: Fanglin

last: Zhao

first: Yinghao

last: Song

first: Mengshi

last: Xu

first: Wenqi

last: He

first: Kui

first: Guowen

first: Jiyu

last: Guan


title: Integrated Chemokine and Cytokine Signaling Shapes Context-Dependent T Cell Transcriptional Programs

city: Sao Paulo

first: Patricia

last: Severino

state: Sao Paulo

address: Rua Comendador Elias Jafet, 755

department: Albert Einstein Research and Education Institute

country: Brazil

institute: Hospital Israelita Albert Einstein

summary: Tissue cells continuously secrete chemokines to convey their spatial position and  physiological state, thereby coordinating immune cell localization and maintaining tissue  homeostasis. Although chemokine receptor engagement is classically mediated by G  protein–coupled receptors, the extent to which cytokines modulate chemokine receptor  signaling and transcriptional outcomes remains poorly defined. Here, we investigated how  the cytokines IL-15 and IL-32α influence T-cell responses to the chemokines CXCL8 and  CCL20.  Our transcriptomic analyses revealed that these cytokines and chemokines combinations  generate context-dependent transcriptional programs. IL-15 and CXCL8 interactions  produced dominant IL-15 like transcriptional signatures, suggesting hierarchical signaling  integration. In contrast, IL-32α combined with CXCL8 elicited a distinct cooperative  transcriptional profile enriched for genes related to vesicular remodeling, mTOR-associated  metabolic activity, and cytoskeletal organization. These non-additive and synergistic effects  highlight how chemokines and cytokines networks can either reinforce shared pathways or  reprogram specific modules that control T cell activation, migration, and persistence.  Together, our findings provide new insights into the integrated nature of cytokine and  chemokine signaling, emphasizing their capacity to dynamically shape T cell functional  plasticity under complex inflammatory and tumor-associated microenvironments..

overall_design: In this study, we evaluated the effects of IL-15 and IL-32α on the signaling of the  chemokines CXCL8 and CCL20 and their respective receptors. Both IL-15 and IL-32α have  been proposed to enhance chemokine secretion and receptor expression, thereby modulating  the effector functions of T cells and dendritic cells. The chemokines  CXCL8 and CCL20 are critical mediators of immune-cell migration, yet the mechanisms  governing their regulation remain complex and incompletely understood.

first: Messias

last: de Oliveira Pacheco

first: Larissa

last: Figueiredo Diniz

first: Gabriela

last: Alves Theodoro

first: Sabrina

last: do Nascimento

first: Matheus

last: Farinaro Vesco

first: Helder

last: Nakaya

first: Luiz

last: Vicente Rizzo

first: Fernanda

last: Agostini da Rocha

first: Patrícia

first: Luciana

last: Cavalheiro Marti


title: The intrinsically disordered AR2 microdomain of RNase E binds mRNA translation initiation regions

city: Sydney

first: Jai

last: Tree

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

institute: University of New South Wales

summary: RNA decay is central to gene regulation and ensures that once genes are expressed, they have a finite lifespan. In Escherichia coli, bulk degradation is carried out by the RNA degradosome, a multi-protein complex that is scaffolded by the endoribonuclease RNase E. RNase E recognises RNA substrates through at least four RNA-binding sites that feed RNA to the catalytic centre. The ribonuclease consists of a structured N-terminal domain that contains the catalytic site, and an intrinsically disordered C-terminal domain that contains two unstructured RNA-binding sites termed RBD and AR2. The intrinsically disordered domain provides a major pathway for RNA recruitment to the catalytic centre, including mRNAs targeted by regulatory small RNAs (sRNAs). To understand how sRNA-mRNA pairs are recognised by the intrinsically disordered C-terminal domain we have engineered protease cleavage sites that separate the AR2 microdomain from RNase E and performed UV-crosslinking and sequencing (termed split-CRAC). We find that the AR2 binding site recognises AUAA motifs within mRNA translation initiation regions (RBS and start codons) and is depleted of sRNA interactions. We demonstrate that the AUAA motif is required for sRNA regulation of the highly abundant murein lipoprotein, Lpp, and that mRNAs with an AR2 motif tend to be more stable and more highly expressed.

overall_design: Protease-cleavable CRAC was used to map RNA interactions with AR2 microdomain of the endoribonucelase RNase E. In short, TEV protease cleavage sites were engineered into the chromosomal copy of rne in E. coli str. MG1655 that allow release of the AR2 microdomain after protease digestion. Full length RNase E, the protease cleavable AR2 mutant, and an untagged negative cotnrol were UV-crosslinked in biological triplicate and CRAC was performed to recover RNAs crosslinked to RNase E and the AR2 subdomain. The protocol for preparation of CRAC librarises is based on PMID: 27836995 with updates to the protcol described in PMID: 37925184.

first: Mediati

last: Daniel

first: Tree

last: Jai


title: Comprehensive single-nucleus molecular and cell profiling features for cardiac tissues across platforms

city: South San Francisco

first: Chi-Ming

last: Li

state: CA

address: 750 Gateway Blvd

department: Target Discovery & Biology

institute: Amgen

summary: Single-nucleus RNA sequencing (snRNA-Seq) enables high-resolution transcriptomic profiling of complex tissues such as the heart, where dissociation into intact single cells is challenging. Among the commercially available snRNA-Seq platforms, 10X Genomics Chromium and Takara Bio’s ICELL8 cx represent technically distinct approaches. However, a systematic comparison of their performance in cardiac tissue remains limited. Here, we benchmarked the 3’-Chromium, 5’-Chromium, and ICELL8 cx platforms using nuclei isolated from both mouse and human heart tissues, including healthy donor samples and those from patients with non-ischemic cardiomyopathy. We evaluated key metrics including nuclei capture efficiency, library complexity, transcript detection sensitivity, RNA biotype coverage, ambient RNA contamination, and cell type resolution. Our results show that the Chromium platforms yield higher nuclear throughput with robust capture efficiency and low contamination, whereas ICELL8 cx provides deeper transcriptomic coverage per nucleus, detecting a broader diversity of RNA biotypes, including low-abundance non-coding RNAs, albeit with lower total nuclei captured. Both platforms resolved major cardiac cell populations with consistent cell-type proportions and marker gene expression. These findings provide a practical guide for selecting snRNA-Seq workflows optimized for cardiac tissue research, balancing trade-offs between cell throughput and transcriptome depth.

overall_design: Whole heart tissue from wildtype male mice was digested and single nuclei were isolated based on DRAQ5 staining using flow cytometry. snRNA-seq libraries were prepared following 10X Genomics and Takara ICELL8 cx protocols and analyzed.

first: Haewon

last: Shin

first: Urvi Nikhil

last: Shroff

first: Xianglong

last: Zhang

first: Tracy

last: Yamawaki

first: Daniel R.

last: Lu

first: Junedh M.

last: Amrute

first: Andrea

last: Bredemeyer

first: Amrita

last: Das

first: Brandon

last: Ason

first: Simon

last: Jackson

first: Kory J.

last: Lavine