title: Cross-tissue reveals metabolic reprogramming of Tibetan tea in mice

city: Ya'an

first: Songqi

last: Duan

state: Sichuan

address: No.46, Xinkang Road, Yucheng District

department: College of Food Science

institute: Sichuan Agricultural University

summary: Metabolic diseases, such as obesity, diabetes, and cardiovascular diseases, pose significant health challenges in contemporary society. The development of these diseases is closely related to the balance of gut microbiota, the functionality of metabolic products, and metabolic dysregulation across various tissues and organs. Tibetan tea, a traditional post-fermented tea originating from Ya'an, Sichuan in Southwest China, is known for its unique fermentation process and flavor, as well as its multitude of health benefits, such as acting as a prebiotic, antioxidant, blood sugar reducer, antithrombotic, and obesity prevention agent. This has sparked widespread interest among scholars both domestically and internationally in its potential to address metabolic diseases such as obesity, diabetes, hyperlipidemia, and thrombosis formation. However, current research has mostly focused on the effects on single tissues, with less exploration into the role of Tibetan tea in multi-tissue responses. Therefore, this study employed large-scale sequencing technologies to deeply analyze the impact of Tibetan tea extract intervention on the gut microbiota and peripheral blood, as well as on the metabolism of 10 different tissues and organs, including the brain, brown fat, heart, liver, kidneys, pancreas, colon, white fat, skeletal muscle, and bone marrow in C57BL/6J mice under both normal and high-fat diet conditions. The aim was to reveal the holistic response and mechanism of host metabolism to Tibetan tea intervention, thereby providing new insights into nutritional intervention strategies for metabolic diseases.

overall_design: In this study, we investigated the effects of Tibetan tea consumption on mice subjected to either a standard chow diet or a high-fat diet. Mice were randomly divided into four groups, each comprising 5 animals. The groups were designated as follows: chow diet with water (CW), chow diet with Tibetan tea (CT), high-fat diet with water (HW), and high-fat diet with Tibetan tea (HT). The mice were accommodated under uniform conditions, which included a 12-hour light/dark cycle, and were given unrestricted access to food and water throughout the duration of the experiment, which lasted for 10 weeks. At the conclusion of the 10-week period, the mice were euthanized for the collection of various tissues, including brain, brown adipose tissue (BAT), heart, kidney, colon, pancreas, liver, bone marrow (BM), and skeletal muscle (SM). These tissues were subsequently subjected to transcriptome sequencing to elucidate the molecular effects of Tibetan tea consumption under different dietary conditions.

first: Ziqi

last: Wang


title: Effect of coixenolide on pancreatic tumor gene expression in HFD and CD groups

status: Public on Jul 17 2026

city: Hangzhou

first: Chen

last: Kaidi

address: Binwen Road, Hangzhou, Zhejiang

country: China

institute: Zhejiang Chinese Medical University

type: Expression profiling by high throughput sequencing

summary: To investigate the mechanism of coixenolide in obesity-associated PAAD, we established both CD and HFD murine models. Tumor tissues were collected post-coixenolide intervention. Our study revealed the immunomodulatory effects of coixenolide on obesity-linked pancreatic carcinogenesis

overall_design: scRNA-seg profling of CSO-treated and control groups in CD- and HFD-fed PAAD models


title: Impact of SPOP mutations on gene expression in prostate cancer

status: Public on Jul 16 2026

city: Houston

first: Di

last: Zhao

state: Tx

address: Zayed Building Z7. 4018

country: USA

institute: MD Anderson Cancer Center

summary: To determine SPOP mutations' effects on gene transcriptome in prostate cancer, we introduced wildtype versus F133V mutation of SPOP into DU145 cells, followed by RNA-sequencing

overall_design: DU145 Wildtype versus F133V

first: Yue

last: Lu


title: Transcriptome sequencing of wide type COS7 cell and ATL2/3 double knockout COS7 cells.

city: Beijing

first: Hanchi

last: Miao

state: Beijign

address: Datun Road No.15

institute: Institute of Biophysics，Chinese Academy of Sciences

summary: To investigate different gene expression in wide type COS7 cell and ATL2/3 double knockout COS7 cells, we carried out transcriptome sequencing and performed gene expression profiling analysis.

overall_design: Transcription profile of  wide type COS7 cell and ATL2/3 double knockout COS7 cells

first: Yuqi

last: Wasng

first: Yingying

last: Huang

first: Haoyang

last: Zhang

first: Lexin

last: Zheng

first: Xin

last: Zhou

first: Xiaoqun

first: Qing

last: Xie

first: Lei

last: Xue

first: Junjie

last: Hu


title: PRMT1-mediated arginine methylation redirects a metastasis-promoting transcriptional output of SMAD4 in pancreatic cancer

city: Wuhan

first: Yizhou

last: Liu

state: Hubei

address: 1277 Jiefang Ave

department: Department of Pancreatic Surgery

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology,

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by early metastatic dissemination and poor clinical outcomes. Although SMAD4 is frequently altered in PDAC, the majority of tumors retain wild-type SMAD4, which paradoxically acquires pro-metastatic functions during disease progression. How SMAD4 transcriptional output is reprogrammed to support metastasis in advanced PDAC remains poorly understood.Here, we identify protein arginine methyltransferase 1 (PRMT1) as a critical modifier that promotes a metastasis-promoting transcriptional state of SMAD4. PRMT1 catalyzes asymmetric dimethylation of SMAD4 at arginine 272 (R272), a modification that does not alter SMAD4 expression but stabilizes nuclear SMAD2/3-SMAD4 complexes and redirects SMAD4 chromatin engagement toward epithelial-mesenchymal transition (EMT) gene programs. Mechanistically, R272-methylated SMAD4 promotes the recruitment of a BRG1-CTCF transcriptional complex, enabling chromatin-dependent activation of pro-metastatic transcriptional outputs.Importantly, pharmacological inhibition of PRMT1, particularly in combination with BRG1 degradation, dismantles methylation-dependent SMAD4 transcriptional complexes, suppresses EMT programs, and markedly reduces liver metastasis in preclinical PDAC models.Together, these findings uncover a post-translational mechanism that governs SMAD4 transcriptional specificity and identify PRMT1-dependent methylation as a therapeutic vulnerability in SMAD4-wild-type pancreatic cancer.

overall_design: RNA sequencing for SMAD4 knock-out PANC-1 cells reconstituted with WT or R272K mutant SMAD4 on Day3.

first: Xueyi

last: Liang

first: Ruozheng

last: Wei

first: Yuhan

first: HeShui

last: Wu

first: Yingke


title: Transcriptomic Analysis Identifies Transient Mesendodermal State and Lineage Divergence in Human Pluripotent Stem Cell Differentiation

city: Lisboa

first: Alice

last: Borges

address: Av. Rovisco Pais

country: Portugal

institute: IBB

summary: Human pluripotent stem cells serve as a vital model for studying early human lineage specification, yet conventional assessments relying on canonical markers may overlook transient intermediate states and broader cellular programs. Here we combined directed differentiation of human induced pluripotent stem cells toward neuroectodermal, cardiac mesodermal, and hepatic endodermal lineages with comparative transcriptomic profiling across timepoints. Our analyses revealed a transient primitive streak-like mesendodermal state shared by mesodermal and endodermal trajectories, followed by lineage-specific divergence characterized by distinct transcriptional, metabolic, proliferative, and chromatin remodeling dynamics. Notably, endodermal differentiation exhibited rapid definitive endoderm commitment with enriched oxidative metabolism, whereas cardiac mesoderm differentiation showed progressive transcriptional remodeling and cardiac progenitor activation. These findings demonstrate that comparative transcriptomics can resolve developmental intermediates and cellular-state dynamics during human germ layer specification, providing a framework for evaluating lineage commitment beyond canonical marker expression.

overall_design: RNA-seq profiling of iPS-DF6-9-9T.B cells at Day0, Day1, Day3, Day6, Day9, Day12, Day16 of 2D neural ectoderm differentiation

middle: C

first: Mariana

middle: A

last: Branco

first: João

middle: P

last: Cotovio

first: Ana

middle: R

last: Gomes

first: Joana

middle: E

last: Saraiva

first: Leonilde

middle: M

last: Moreira

first: Joaquim

last: Cabral

first: Domingos

last: Henrique

first: Maria

last: Diogo

first: Tiago

middle: G

last: Fernandes


title: Effect of TGF-beta and K-975 in HOVX human vocal fold fibroblasts [RNA-seq]

city: New York

first: Ryosuke

last: Nakamura

state: NY

address: 435 E 30th Street

institute: New York University School of Medicine

summary: SMAD2/3 and YAP/TAZ are activated by TGF-beta signaling in human vocal fold fibroblasts. This study provides transcriptomic data regarding altered gene expression following TGF-beta treatment and YAP/TAZ inhibition.

overall_design: RNA-seq of HVOX human vocal fold fibroblats treated or untreated with TGF-beta1 and a YAP/TAZ inhibitor, K-975.


title: Effect of TGF-beta on SMAD2/3 and YAP/TAZ in HOVX human vocal fold fibroblasts {ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: SMAD2/3 and YAP/TAZ are activated by TGF-beta signaling in human vocal fold fibroblasts. This study provides ChIP-seq data regarding chromatin occupancy of SMAD2/3 and YAP/TAZ in these cells in response to TGF-beta treatment.

overall_design: ChIP-seq of HVOX human vocal fold fibroblats treated or untreated with TGF-beta1.


title: RNA-seq of cold stressed C. elegans

city: Freiburg

first: Gang

state: Freiburg

address: Schänzlestraße 1, 79104 Freiburg, Institute of biology III, 5th floor

department: Bio II/III

country: Germany

institute: University of Freiburg

type: Non-coding RNA profiling by high throughput sequencing

summary: Cold stressed and non-stressed wild type, sgk-1(ok538), pqm-1(ok485) and pqm-1(ok485); sgk-1(ok538) animals are collected for RNA-seq analysis, to reveal transcripteome changes. Cold stress triggers fat reallocation from intestine to oocytes, which is regulated by mTORC2/SGK-1 and PQM-1. To understand the underlying mechanism, animals are cold stressed at adult day 1 and collected for RNA-seq analysis.

overall_design: Four strains of different genetic backgrounds are used. Wild type, sgk-1(ok538), pqm-1(ok485), and pqm-1(ok485); sgk-1(ok538) double mutants. Two treatment conditions, cold stress and non-stressed were used for all strains. Two replicates were collected for each condition, per strain. In total sixteen sampels were collected and used for RNA-seq analysis. The file names "PS_ctrl" and "PS_CS" indicate pqm-1(ok485); sgk-1(ok538) double mutant in non-stressed (ctrl) or cold stressed (CS) conditions

first: Piyush

last: Gupta


title: KRAS-Mutation Driven RASA2 Promotes Pancreatic Cancer Metastasis via TGFB2-Dependent Non-Canonical Hedgehog/GLI1 Activation

city: Shanghai

first: taochen

last: he

address: 180 Fenglin Road, Shanghai, China

institute: Zhongshan Hospital Fudan University

summary: KRAS mutations are a major driver of pancreatic ductal adenocarcinoma (PDAC), promoting tumor initiation, progression, and metastasis. RASA2, a Ras GTPase-activating protein, modulates KRAS protein levels in wild-type contexts, yet its role in KRAS-mutant PDAC remains unclear. Here, we systematically investigated the biological function and molecular mechanisms of RASA2 in KRAS-mutant PDAC. Integrative analyses of multiple datasets and patient-derived samples demonstrated that RASA2 is consistently upregulated in KRAS-mutant PDAC and significantly associated with poor prognosis and metastatic progression. Gain- and loss-of-function studies revealed that RASA2 markedly enhances PDAC cell migration and invasion in both KRAS-mutant and KRAS-wild-type models, indicating that its pro-metastatic activity is largely independent of KRAS mutational status. Transcriptomic profiling and mechanistic interrogation uncovered that RASA2 activates GLI1 through a TGFB2-dependent, Sonic Hedgehog–independent non-canonical Hedgehog signaling pathway. Mechanistically, RASA2 directly interacts with the transcriptional regulator RTF1, facilitating H2BK120 ubiquitination at the TGFB2 promoter and thereby augmenting TGFB2 transcription. This epigenetic activation of TGFB2 subsequently drives non-canonical Hedgehog/GLI1 signaling to confer pro-metastatic traits. Pharmacologic inhibition of TGFB2 signaling or genetic silencing of GLI1 effectively abrogated RASA2-driven migratory, invasive, and metastatic phenotypes both in vitro and in vivo. Collectively, our findings identify RASA2 as a critical mediator of PDAC metastasis downstream of oncogenic KRAS and uncover a previously unrecognized RASA2–RTF1–H2BK120ub1–TGFB2–GLI1 signaling axis. KRAS mutation drives RASA2 upregulation, while the pro-metastatic activity of RASA2 is largely independent of KRAS mutational status. These findings reveal a previously unrecognized mechanism by which oncogenic KRAS promotes metastatic progression through RASA2-dependent epigenetic and transcriptional reprogramming and nominate the RASA2–TGFB2–GLI1 axis as a potential therapeutic target in PDAC

overall_design: Total RNA was isolated from BxPC-3 cells stably overexpressing RASA2 and vector control cells. Three independent biological replicates were collected for each group. RNA libraries were prepared and sequenced on an Illumina NovaSeq 6000 platform using paired-end 150 bp sequencing

first: Taochen

last: He

first: Qiangda

last: Chen

first: Yanfei

last: An

first: Zhihang

last: Xu

first: Zhenlai

last: Jiang

first: Jiande

last: Han

first: Yuqi

last: Xie


title: Transglutaminase 2 Deletion Enhances Astrocyte-to-Neuron Metabolic Support and Attenuates Subacute Pathology Following Repetitive Mild Traumatic Brain Injury

first: Benjamin

last: Weekley

address: 310 E 92nd St

department: Neuroscience

institute: Mount Sinai

summary: Mild traumatic brain injury (mTBI) is the most common form of central nervous system (CNS) injury and is often characterized by persistent neuroinflammation, metabolic dysregulation, and oxidative stress. Repetitive injuries compound these pathologies and lead to multifocal axonal injuries and long-term functional deficits. Despite the prevalence of mTBIs, the cellular mechanisms that facilitate or prevent recovery following injury remain poorly defined. Here, we extend our previous work on the role of the protein transglutaminase 2 (TG2) in CNS injury and we hypothesize that transcriptional regulation by TG2 restricts metabolic versatility in astrocytes following TBI, thereby impairing neuronal energetic support and worsening pathological outcomes. We utilized an established weight-drop model of repetitive mTBI followed by multi-parametric analysis of TBI pathology in complete TG2 knockout and wild type mice. At 28 days post-injury, TG2-/- mice showed marked attenuation of TBI pathology, compared to wild type mice, in vulnerable white matter and default mode network (DMN) brain regions, as assessed by functional MRI, diffusion MRI, and immunohistochemistry. Integrated epigenomic, proteomic, and metabolomic profiling of cortical astrocytes isolated 28 days after injury revealed a pronounced metabolic restriction in wild type astrocytes which was attenuated in the TG2-/- mice. This rescue was associated with a de-repression of gene networks involved in lipid metabolism and metabolic homeostasis. Together, these studies provide mechanistic insights on the metabolic dysregulation that characterizes persistent TBI pathology and they establish a foundation for evaluating TG2 as a therapeutic target for TBI.

overall_design: CUT&RUN-seq from whole brain mouse astrocytes performed 28 days post TBI or SHAM treatment. This was performed in both wild-type and TG2-/- mice.

first: T

last: Delgado

last: Arefin

first: J

last: Rodwell-Bullock

first: M

last: Chowdhury

first: A

middle: B

last: Crum

first: B

first: I

last: Maze

first: P

middle: S

last: Brookes

last: Meeks

first: G

last: Johnson


title: Endotome as an Unrecognized Source of Human Peri-Aortic Brown Adipocytes

city: Hong Kong

first: Tianming

last: Wu

state: Hong Kong

address: LKS Int Biomed Sci Bldg

department: School of Biomedical Sciences

institute: Chinese University of Hong Kong

summary: Brown adipose tissue (BAT) uncouples nutrient catabolism from ATP synthesis to dissipate energy as heat, making it a promising regenerative medicine approach for metabolic disorders. In mice and humans, classical BAT is thought to arise developmentally from a PAX3+/MYF5+ dermomyotome precursors, yet lineage tracing studies reveal that the majority of cervical and all peri-aortic brown adipocytes derive from PAX3+/MYF5− somitic origins, suggesting an alternative, poorly understood developmental trajectory.  Recent single-cell RNA sequencing (scRNA-seq) of mouse organogenesis and human trunk embryoid models identified a previously unrecognized somite compartment, the endotome, as a precursor pool for vascular endothelium and smooth muscle cells. Here, by interrogating scRNA-seq datasets from mouse somite development alongside our in-house human trunk embryoid model (hTEM), we characterize the EBF2+ endotome as an MYF5-independent source of UCP1+ brown adipocytes in a spatiotemporal manner. Mechanistically, we show that TGF-β-induced epithelial-to-mesenchymal transition (EMT) is required for endotome commitment, and that sequential BMP inhibition followed by WNT activation, rather than the BMP activation and WNT inhibition used for dermomyotome-derived BAs, fully potentiates a BA fate. Consequently, endotome-derived BAs resemble in vivo peri-aortic BAT. The developmental authenticity of these endotome precursors is further validated by differentiation into smooth muscle and vascular endothelial cells in response to HGF and VEGFA, respectively. Collectively, we demonstrate that recapitulating the developmental sequence of signaling cues governing endotome plasticity enables efficient brown adipocyte production from human pluripotent stem cells. Our work identifies a novel source of BAT and establishes a streamlined, rapid, and cost-efficient method to generate metabolic active brown adipocytes, with broad implications for regenerative medicine.

overall_design: hESC-derived somite were differentiated into the reported endotome fate for brown adipocyte genesis in this study. To profile molecular identity of endotome, CUT&Tag (cst, 77552S) was performed in day-6 somite and day-8 endotome cells using anti-EBF2 (R&D, AF7006) and anti-H3K27ac (active motif, 39133) antibodies. Single cell RNA squencing (scRNA-seq) was performed on endotome lineage derived peri-aortic-like BA cultures (day 6, 8, 12, 16, 20 and 24). As developmental references, scRNA-seq analysis of MSC-derived beige adipocytes and  dermomyotome-derived interscapular BA cultures (day 6, 8, 13, 20, 26, 36, 46) were performed. To validate the multi-lineage potency of endotome cells, vascular smooth muscle cells (vSMC) (day 13, 20) were induced from endotome and subjected to scRNA-seq analysis.

first: Hao

last: Yu

first: Stephen

last: Dalton


title: Effect of NAT10 knockdown on gene expression in human valve interstitial cells

first: Dong

address: 28 Fuxing street

institute: Chinese PLA general hospital

summary: Calcific aortic valve disease is characterized by osteogenic differentiation and calcification of human valve interstitial cells. We found that NAT10 expression was increased in calcified human aortic valves and that NAT10 positively regulates the calcification of valve interstitial cells. To investigate the downstream regulatory molecules of NAT10 in human valve interstitial cells, RNA-seq was performed in cells with NAT10 knockdown and matched negative controls. Transcriptomic comparison between shNAT10 and shNC groups was used to identify NAT10-regulated genes and pathways potentially involved in valve interstitial cell calcification. These data provide a molecular resource for understanding the role of NAT10 in the regulation of human valve interstitial cell function and calcific aortic valve disease.

overall_design: RNA-seq profiling of human valve interstitial cells transfected with shNAT10 or negative control shRNA. Differential gene expression analysis was performed by comparing shNAT10-treated cells with shNC-treated cells to identify downstream targets regulated by NAT10.


title: Mouse kidney-specific Glut2 knockout

city: Lexington

first: Kavaljit

middle: H

last: Chhabra

state: KY

address: 760 Press Avenue

institute: University of Kentucky

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RXRα Suppression Drives Hepatic Metabolic and Immune Dysfunction in Sepsis: Differential gene expression in septic and non-septic dogs

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: Sepsis is a life-threatening condition where a dysregulated host response to infection causes organ dysfunction and the collapse of metabolic and immune functions. Here, we identify hepatocyte Retinoid X Receptor α (RXRα) as a central integrator of host resilience during polymicrobial sepsis. We show that hepatic Rxra expression is transcriptionally dependent on the upstream regulator Hepatocyte Nuclear Factor 4 α (HNF4α), and that sepsis rapidly suppresses RXRα abundance at both the mRNA and protein levels. Transcriptomic profiling further reveals that the septic liver develops partial resistance to pharmacological RXR activation by its agonist Bexarotene (Bex). Despite this, prophylactic treatment with Bex preserves metabolic stability, enhances bacterial clearance, and improves survival. Using hepatocyte-specific inducible RXRα-deficient mice (RXRαiAlbKO), we demonstrate that this protective effect is strictly dependent on hepatocyte RXRα. Mechanistically, the loss of RXRα in hepatocytes leads to a profound reduction in the liver-resident macrophage, Kupffer cells (KC), resulting in uncontrolled bacterial dissemination and increased mortality. This defect is phenocopied by selective KC depletion. These findings establish that hepatocyte RXRα is essential for maintaining the hepatic macrophage niche, thereby linking hepatocellular transcriptional competence to systemic antibacterial defense.

overall_design: RNA-seq profiling of a liver biopsy of septic and non-septic dogs requiring abdominal surgery (13 sepsis, 9 non-sepsis).

first: Matyas

last: Jelinek

first: Jolien

last: Vandewalle

first: Marah

last: Heyerick

first: Tineke

last: Vanderhaeghen

first: Céline

last: Van Dender

first: Madeleine

last: Hellemans

first: Daria

last: Fijalkowska

first: Martin

last: Guilliams

first: Karolien

last: De Bosscher

first: Claude

last: Libert


title: Reduced-representation bisulfite sequencing (RRBS) of mouse kidney in kidney-specific Glut2 knockout (rGlut2 KO)

summary: Glycosuria, whether genetically induced or triggered by SGLT2 inhibitors, activates compensatory glucose-producing pathways that limit glucose lowering in type 2 diabetes. To define these pathways, we studied renal Glut2 knockout mice, which progressively lose Slc5a2 (encoding SGLT2) expression yet maintain normoglycemia despite marked urinary glucose loss. To characterize DNA methylation changes associated with chronic glycosuria, reduced-representation bisulfite sequencing (RRBS), in which genomic DNA was digested with MspI to enrich for CpG-rich regions, was performed on kidney tissue from 12-week-old male rGlut2 KO and wild-type control mice (3 biological replicates per group). Libraries were prepared and sequenced by ZymoResearch (project ID: zr24946). Reads were quality-trimmed using Trim Galore and aligned to the mouse reference genome (mm10) using Bismark, and CpG methylation was called using MethylDackel.

overall_design: Reduced-representation bisulfite sequencing was performed on kidney tissue from 12-week-old male kidney-specific Glut2 knockout (rGlut2 KO) and wild-type control mice. Three biological replicates per group were sequenced independently to identify differentially methylated CpG sites associated with chronic glycosuria.

first: Chhabra

last: Kavaljit H


title: Single-nucleus multiome RNA and ATAC sequencing of mouse kidney in kidney-specific Glut2 knockout (rGlut2 KO)

summary: Glycosuria, whether genetically induced or triggered by SGLT2 inhibitors, activates compensatory glucose-producing pathways that limit glucose lowering in type 2 diabetes. To define these pathways, we studied renal Glut2 knockout mice, which progressively lose Slc5a2 (encoding SGLT2) expression yet maintain normoglycemia despite marked urinary glucose loss. Nuclei were isolated from three pooled flash-frozen kidney samples per group (12-week-old male rGlut2 KO and wild-type control mice) and single-nucleus gene expression and ATAC libraries were constructed using the 10x Chromium Multiome kit (Singulomics Corporation). Libraries were sequenced with ~200 million paired-end reads (PE150) on the Illumina NovaSeq. Reads were aligned to mm10 (2020-A) using Cell Ranger ARC 2.0.2. Downstream analysis used Seurat v5.1.0 and Signac v1.13.0.

overall_design: Single-nucleus RNA-seq and ATAC-seq were performed simultaneously on pooled kidney nuclei from rGlut2 KO and wild-type control mice using the 10x Genomics Chromium Multiome platform. Nuclei from three 12-week-old male mice per group were pooled prior to library preparation, generating one library per group.


title: Zanubrutinib monotherapy for IgG4-related head and neck disease

city: Palo Alto

first: Saurabh

last: Gawde

state: CA

address: 269 Campus Drive, CCSR 2220

institute: Stanford University

summary: IgG4-related disease (IgG4-RD) is commonly treated withglucocorticoids and B cell depletion, but cumulative toxicity and relapse underscore the need for alternative approaches. In this phase 2 open-label proof-of-concept trial, ten participants with lacrimal and submandibular gland IgG4-RD received zanubrutinib 80 mg twice daily without glucocorticoid induction or background immunosuppression. The primary endpoint was change in lacrimal and submandibular gland volume at week 24, assessed by blinded FDG–PET/MRI (evaluable n=8). Mean percent change from baseline was −46.7% for lacrimal and −29.9% for submandibular gland volume (both P=0.008), with concordant reductions in total lesion glycolysis (−91.6 g) and serum IgG4 (−417.0 mg/dL). We also  Single-cell immune profiling demonstrated reversal of disease-associated B cell transcriptional programs, selective suppression of IgG4-skewed plasmablasts, and attenuation of cytotoxic CD4⁺ T cells. Adverse events were mild; one serious event occurred (COVID-19). These findings support BTK inhibition as a steroid-sparing, non-B-cell-depleting therapeutic strategy in IgG4-RD. ClinicalTrials.gov identifier: NCT04602598.

overall_design: Peripheral blood mononuclear cells (PBMCs) from patients 3, 4, 5, 7, 8, 9, and 10 were collected at baseline, week 12, and week 24 (patient 8 baseline and week 12 only). n=7 age-, sex-, and race/ethnicity-matched healthy control PBMCs were obtained from the Stanford Rheumatology Biorepository (IRB-61344). B cells were enriched for each sample using the EasySep Human Pan-B Cell Enrichment Kit (StemCell Technologies). PBMCs and B cells from each sample were captured using the BD Rhapsody microwell system and scRNA-seq was performed. Libraries for whole transcriptome (WTA), TCR and BCR were generated and sequenced using paired end sequencing.

first: Matthew C.

last: Baker

first: Tobias

middle: V

last: Lanz

first: Audra

last: Horomanski

first: Robert

last: Fairchild

first: Yuhan

last: Liu

first: Maria

last: Vitale

first: Evan

last: Maestri

first: Friederike

last: Held

first: Mariani

last: Deluna

first: Walter

last: Park

first: Haziq

last: Siddiqi

first: Lauren

last: Taylor

first: Sachi

last: Bopardikar

first: Mehdi

last: Khalighi

first: Benjamin

middle: L

last: Franc

first: Mrudula

last: Penta

first: Scott

middle: D

last: Boyd

first: Purvesh

last: Khatri

first: Han

last: Zhu

first: Nancy

last: Pham

first: Kip

last: Guja


title: Cohesin haploinsufficiency and inv(16) cooperate to reinforce Fli1 gene transcriptional programs during acute myeloid leukemia initiation and maintenance

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8797 Watertown Plank Rd

department: Stem Cell Transriptional Regulation

institute: Versiti Blood Research Institte

summary: Core binding factor (CBF) acute myeloid leukemias most commonly harbor the translocations t(8;21) or inv(16). Cohesin mutations are less commonly observed in inv(16) than in t(8;21), suggesting that they may negatively impact leukemic initiation or maintenance in this setting. We used a mouse model of inv(16) with haploinsufficiency of the cohesin subunit Smc3 and paradoxically found that inv(16);Smc3D/+ mice have a reduced leukemic latency compared to inv(16);Smc3+/+ mice, suggesting a role for cohesin loss in leukemic initiation or maintenance. Given the known role of cohesin haploinsufficiency in altering chromatin accessibility, we demonstrated an increase in chromatin accessibility in inv(16);Smc3 D/+ HSPCs prior to leukemia development, with an enrichment for Fli1 DNA binding motifs. We also observe an increase in Fli1 expression and enhanced Fli1 target expression in the most primitive hematopoietic stem cells using scRNA-seq, linking enhanced Fli1 activity in the inv(16);Smc3D/+ setting to leukemic initiation consistent with elevated RAS activity, which is common in inv(16) AML. We further show that Fli1 is essential for the maintenance stage of inv(16);Smc3D/+ AML. Our data demonstrate that cohesin loss drives both leukemic initiation and maintenance in inv(16) AML, identifying Fli1 as a previously unrecognized therapeutic vulnerability.

overall_design: bulk ATAC sequencing of lineage depleted murine bone marrow

first: Alison

last: Meyer

first: Katelyn

last: Heimbuch

first: Kirthi

last: Pulakanti

first: Cary

last: Stelloh

first: Cruz-Rodriguez

last: Nataly

first: Josiah

last: Murray

first: Dandan

last: Wang

first: Lisa

last: Latzko

first: Sebastian

last: Vosberg

first: Philipp

last: Greif

first: Lucio

last: Castilla

first: John

last: Pulikkan

first: Subramaniam

last: Malarkannan


title: Thymosin β4 alleviates sepsis-associated acute kidney injury by suppressing MAPK signaling pathway

city: Guangzhou

first: Xiaojun

last: Ouyang

address: No. 58 Zhongshan Er Road

institute: the First Affiliated Hospital of Sun Yat-sen University

summary: Sepsis-associated acute kidney injury (SA-AKI) is a common complication in septic patients and is associated with high mortality and progression to chronic kidney disease (CKD). Previous studies have demonstrated that thymosin β4 (Tβ4) attenuates lipopolysaccharide (LPS)-induced liver injury and ischemic AKI via inhibiting inflammatory response. Here, we aimed to investigate the effects of Tβ4 on SA-AKI and elucidate its underlying mechanisms. In vivo and in vitro models of SA-AKI were established using LPS. Tβ4 was administered 30 min after LPS exposure. Transcriptome sequencing was performed to explore the underlying molecular mechanisms, which were further validated by western blotting in vitro. In SA-AKI mice, serum Tβ4 levels were markedly decreased. Administering Tβ4 significantly ameliorated the renal dysfunction and morphological injury in LPS-treated mice. Consistently, Tβ4 reduced renal inflammation and apoptosis in SA-AKI mice. Transcriptome-sequencing analysis indicated that MAPK signaling pathway was involved in both SA-AKI pathogenesis and the protective effect of Tβ4. Western blotting of the renal tissues confirmed that LPS markedly increased the phosphorylation of JNK1/2, p38 MAPK and ERK1/2, whereas Tβ4 significantly suppressed their activation. Furthermore, pharmacological activation of MAPK pathway with anisomycin abrogated the inhibitory effects of Tβ4 on MAPK signaling in in vitro SA-AKI models. In conclusion, Tβ4 alleviates renal inflammation and apoptosis in SA-AKI by suppressing MAPK signaling pathway. Tβ4 may represent a potential therapeutic strategy for early intervention in SA-AKI.

overall_design: RNA-seq profiling of fresh kidney tissues from 3 mice per group (CTL, LPS, LPS+Tβ4).

first: Zhiyuan

last: Long

first: Xiaodan

last: Xu

first: Bei

last: Jin

first: Cheng

last: Cheng

first: Yifang

last: Gao

first: Xiaoyun

last: Jiang


title: Dendritic cell-mediated antigen presentation regulates tertiary lymphoid structure development in cancer [MERFISH]

first: Laszlo

last: Halasz

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

summary: Tertiary lymphoid structures (TLS) correlate with favorable responses to immunotherapy, yet the mechanisms governing their formation and maintenance in tumors remain poorly defined. Through high-resolution spatial mapping across human tumors, we identified a consistent accumulation of CCR7⁺ mature dendritic cells (DC) within TLS. To dissect their function, we developed a non-small cell lung cancer (NSCLC) model that recapitulates mature TLS formation. Using this model, we demonstrate that TLS induction requires IFNγ-driven maturation of type 1 conventional dendritic cells (cDC1), their migration to tumor-draining lymph nodes (tdLN), and the subsequent recruitment of tdLN-primed T cells into the tumor microenvironment. As tumors progress, TLS persist even in the absence of tdLN T cell egress, coinciding with impaired cDC1 migration to tdLN and their retention within intratumoral stromal hubs enriched in CCR7 ligands. Timed depletion of cDC1 or blockade of their localization to these hubs disrupts TLS maintenance. Strikingly, concomitant genetic ablation of both MHC class I and II on cDC1 abolishes the maintenance of TLS, T follicular helper (TFH) cells, germinal center formation, tumor-specific IgG production, and the differentiation of progenitor exhausted CD8⁺ T cells. These findings establish that local cDC1-mediated antigen presentation to CD8⁺ and CD4⁺ T cells is a central orchestrator of anti-tumor TLS programs and compelling targets for therapeutic intervention.

overall_design: Vizgen MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization) of human liver cancer (HCC; n = 8) and lung cancer. (NSCLC; n = 7)

first: Raphael

last: Mattiuz

first: Brian

last: Soong

first: Miriam

last: Merad


title: Systematic Benchmarking of CUT&Tag Improves the Reliability and Reproducibility of Chromatin Analysis II

first: Sridhar

last: Rao

summary: Cleavage under target and tagementation (CUT&Tag) is a widely used assay for analyzing epigenomic localization of proteins and histone PTMs. This study is focused on increasing the reproducibility of CUT&Tag through standardization of both wet bench and downstream data analysis. We find that 10K cells is the minimum input requirement for robust genome-wide profiling of H3K27ac, H3K9me3, H3K4me3, and H3K36me3 in mESCs cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Cell number standardizations for CUT&Tag were performed using murine ESC's. Standardized targets were H3K27ac, H3K9me3, H3K4me3, and H3K36me3 for mESCs. Cell numbers used for standardization were 10K, or 100K cells. There are at least two replicates for all these conditions. This study also contains bulk CUT&Tag data for RAD21 in OCI-AML3 leukemia cell line which was used to determine how deduplication strategies affect peak calling.

first: Josiah

last: Murray

first: Atrayee

last: Ray

first: Khanmi

last: Kasomva

first: Erica

last: Steen

first: Cary

last: Stelloh

first: Kirthi

last: Pulakanti

first: Phillip

last: Doerfler

first: Navonil

last: De Sarkar

first: Qiongzi

last: Qiu

first: Yong

last: Liu

first: Alison

last: Meyer

first: Aron

last: Geurts

first: Allen

middle: W

last: Cowley Jr.

first: Mingyu

last: Liang


title: Dendritic cell-mediated antigen presentation regulates tertiary lymphoid structure development in cancer.

first: Laszlo

last: Halasz

overall_design: Visium spatial transcriptomics of human colorectal cancer (CRC; n = 4), liver cancer (HCC; n = 1) and lung cancer (NSCLC; n =2)

first: Raphael

last: Mattiuz


title: RNA-seq analysis of dorsal root ganglia (DRG) from MIA-induced osteoarthritis mice with acupuncture or no treatment: Focus on neuro-immune crosstalk genes

first: Tang

last: Tianran

address: Chinese PLA General Hospital, No. 28, Fu Xing Road, Haidian District, Beijing 100853, China

institute: Chinese PLA General Hospital

summary: Osteoarthritis (OA) is a chronic musculoskeletal disorder characterized by mechanical allodynia and dorsal root ganglion (DRG) neuroinflammation. Acupuncture at ST36 alleviates OA pain, but its effect on DRG transcriptional profiles remains unclear. This study aimed to identify key genes/pathways involved in acupuncture-mediated DRG neuro-immune remodeling using RNA sequencing.

overall_design: L3-L5 DRG tissues were isolated from 3 groups of C57BL/6 mice (n=3 per group) MIA group (OA induced by intra-articular injection of monosodium iodoacetate); MIA+Acupuncture group (OA mice treated with daily manual acupuncture at ST36 for 7 days).

first: Tianran

last: Tang

first: Tianyu

last: Jiang


title: Restored clearance of senescent neutrophils by tissue-resident macrophages limits organ aging

city: Stanford

first: Katrin

middle: I

last: Andreasson

address: 1201 Welch Road

department: Neurology and Neurological Sciences

summary: Single-cell RNA sequencing of sorted mouse liver cells from young (6-8 month) and aged (23-25 month) Cx3cr1CreER;EP2wt/wt (WT) and Cx3cr1CreER;EP2lox/lox (EP2 cKO) male mice. Liver cells were enzymatically dissociated and live CD45+, CD1d+, or CD31+ cells were FACS-sorted in a 1:1:1 ratio, then processed using the 10x Genomics Chromium X platform (Next GEM Single Cell 3' Gene Expression). This dataset supports the finding that tissue-resident macrophage (TRM)-selective EP2 (PTGER2) deletion restores efferocytic clearance of senescent neutrophils and reverses age-associated transcriptional programs in Kupffer cells, preventing multi-organ aging phenotypes.

overall_design: Eight biological samples (n=2 mice per group) representing four experimental conditions: EP2 WT Young (6-8 mo), EP2 WT Aged (23-25 mo), EP2 cKO Young (6-8 mo), and EP2 cKO Aged (23-25 mo). Each sample is from an individual male C57BL/6J mouse liver. Tamoxifen was administered to both genotypes at 4-6 months of age.

first: Yuting

middle: J

last: Tan

first: Travis

last: Conley

first: Fuwen

last: Yao

first: Fernando

last: Garcia-Marques

first: Damilola

last: Akinyemi

first: Van

last: Dinh

first: Qian

last: Wang

first: Abel

last: Bermudez

first: Jieun

last: Kim

first: Julia

last: Belk

first: Oliver

last: Soehnlein

first: Sharon

last: Pitteri


title: RNAseq of human neutrophil small non-coding RNAs from adults with SLE and age-matched healthy controls

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

summary: We report small non-coding RNA expression in blood neutrophils from (1) healthy adults (2) adults with systemic lupus erythematosus (SLE).

overall_design: Neutrophils (purity >99%) were isolated from whole blood using HetaSep followed by negative selection with the Stem Cell human neutrophil isolation kit. RNA was isolated from 0h neutrophil cell pellets using Trizol:chloroform, cleaned up by Qiagen miRNeasy kit including on-column DNase digest and sequenced on the Illumina NovaSeq X Plus platform.

first: Grace

last: Filbertine

first: Xuan

last: Liu


title: Single-cell RNA-sequencing of myeloid cells in E0771 breast tumours from CD1d-KO and WT mice

city: London

first: Patricia

last: Barral

address: Great Maze Pond

department: CIBCI

institute: King's College London

summary: Myeloid cells play crucial roles in cancer progression, influencing tumour growth, metastasis, and response to immunotherapy. Tumour-infiltrating myeloid cells are highly heterogeneous, with functions ranging from anti-tumour to tumour-promoting. The mechanisms shaping these populations remain poorly understood and may offer therapeutic opportunities. Here, we identified the lipid-presenting molecule CD1d as a regulator of tumour progression and myeloid heterogeneity in the tumour microenvironment. CD1d-deficient mice exhibit reduced tumour growth and altered immune-infiltrates in breast cancer models. Similarly, targeting CD1d with an antibody, suppresses tumour growth, reshapes the myeloid landscape, and improves anti-PD-1 immunotherapy efficacy. The CD1d-dependent control of myeloid cell functional differentiation is cell-intrinsic and conserved in human and mouse. Single-cell RNA-sequencing revealed an enhanced proinflammatory program and accumulation of inflammatory monocytes in tumours from CD1d-KO animals. Subsequently, we generated a CD1d-KO-associated gene signature that predicts clinical outcomes and response to immunotherapy in breast cancer patients. Thus, CD1d could be targeted to alter tumour-infiltrating myeloid populations and enhance immunotherapy responses.

overall_design: Six samples: three biological replicates from WT C57BL/6 mice and three from CD1d-KO mice bearing E0771 orthotopic breast tumours. Tumours were harvested at day 15 post-injection, and CD45+ CD11b+ and/or CD11c+ myeloid cells were isolated by FACS and analysed by 10x Genomics single-cell RNA-sequencing

first: María

last: Conde Poole


title: High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation with CsdA or PNPase in E.coli

city: Taipei

first: Sue

last: Lin-Chao

address: 128 Academia Road, Section 2, Nankang,

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: Our results show the RNA transcripts in complex with the helicase CsdA or the exoribonuclease PNPase. We used CsdA or a catalytically inactive variant of PNPase (PNPase D492G) as bait to capture enriched substrates bound by the enzymes. Sequencing of RNA isolated by crosslinking immunoprecipitation with these enzymes identified numerous transcripts bound to CsdA or PNPase.

overall_design: We ectopically expressed FLAG-tagged variants of CsdA or PNPase D492G in E. coli strain lacking PNPase and several RNA helicases. The strain also carried a deletion in the region encoding amino acids 500-1,061 of RNase E to prevent assembly of the RNA degradosome. After inducing the expression of the FLAG-tagged proteins, cultures were treated with formaldehyde to crosslink protein-RNA complexes. FLAG-tagged proteins, crosslinked to RNA, were immunoprecipitated using Anti-FLAG M2 Magnetic Beads, followed by de-crosslinking and RNA isolation. RNA sequencing and peak calling analysis with PEAKachu allowed identification of RNA transcripts crosslinked to CsdA or PNPase.

first: Pankaj

last: Leonard Tirkey

first: Ander

last: Hernandez Plagaro

first: Shu-Yun

last: Tung

first: Chang-I

last: Yu

first: Yueh-Yu

last: Chien

first: Chen-Hsin


title: Comparison of global mRNA decay at single-gene resolution in E. coli Δrnb Δrnr versus E. coli Δrnb Δrnr Δfbp

summary: We determined whether deletion of the glycolysis gene fbp broadly modulates transcript stability in a strain where PNPase is the sole exoribonuclease. We analyzed global RNA degradation at single-gene resolution after rifampicin treatment of E. coli Δrnb Δrnr Δfbp versus the isogenic parental strain, E. coli Δrnb Δrnr, using RNA sequencing. ERCC spike-in standards were incorporated before cDNA library preparation and used for normalization of read-counts-per-gene. We found 1321 transcripts with significantly different degradation patterns between the strains.

overall_design: To demonstrate the glycolytic metabolite-dependent modulation of PNPase activity in vivo, we constructed an E. coli mutant lacking RNase II and RNase R. In this mutant (E. coli Δrnb Δrnr), PNPase is the only exoribonuclease. Using this parental strain, we additionally deleted fbp to generate E. coli Δrnb Δrnr Δfbp. This single mutation interrupts glycolytic flux without requiring changes to culture medium or the addition of glucose analogs. We treated exponentially growing cultures of E. coli Δrnb Δrnr and E. coli Δrnb Δrnr Δfbp with rifampicin to halt RNA synthesis. RNA samples were isolated at multiple time points and used for RNA-seq. To enable a quantitative comparison of RNA levels, we added ERCC spike-in standards to the RNA samples before sequencing.

last: Hernández Plágaro

first: Oleg

last: N Murashko

first: Kun-Hai

last: Yeh


title: MAPK- driven glioma progression and  reprogramming of the tumor-associated immune response

city: San Francisco

first: Joanna

last: Phillips

address: 1450 Third Street, Room HD492B

institute: University of California San Francisco

summary: Glioma evolution is associated with disease progression and therapeutic resistance. We recently identified a group of MAPK-driven glioma with CDKN2A homozygous deletion that are low-grade and immune enriched. However, Over time, these tumors can progress to aggressive, higher-grade tumors. While low-grade tumors may be amenable to immunotherapeutic strategies, it is unknown how the tumor and its microenvironment evolve.

overall_design: To investigate this, we tested PXA tumor sampels before and after progression (G2= before progression, G3= after progression) and across patients using transcriptomic inclusing snRNA sequencing and proteomic approaches to elucidating the factors involve in the progression of tumor.

first: Elaheh

last: Hashemi


title: Systematic Benchmarking of CUT&Tag Improves the Reliability and Reproducibility of Chromatin Analysis [Crosslinking]

first: Sridhar

last: Rao

summary: Cleavage under target and tagementation (CUT&Tag) is a widely used assay for analyzing epigenomic localization of proteins and histone PTMs. This study is focused on increasing the reproducibility of CUT&Tag through standardization of both wet bench and downstream data analysis. We find that 10K cells is the minimum input requirement for robust genome-wide profiling of H3K7me3 in mESCs and rat C6 cells. For CTCF 50K cells are needed. EGS crosslinking and de-duplication strategies were also explored.

overall_design: Cell number standardizations for CUT&Tag were performed using murine ESC's and rat C6's. Standardized targets were H3K27me3 and CTCF. Cell numbers used for standardization were 1K, 10K, 50K, or 100K cells. There are at least two replicates for all these conditions. This study also contains single cell CUT&Tag data for RAD21 in OCI-AML3 leukemia cell line which was used to estimate biological duplication in CUT&Tag. There are 1,493 single cell samples (one sample per single cell). Different crosslinking conditions were tested for CTCF in OCI-AML3 cells: Uncrosslinked (0mM EGS), 0.2mM EGS, 0.1% Formaldehyde, and dual crosslinking (either 0.2mM EGS + 0.1% Formaldehyde or 0.5mM EGS + 0.1% Formaldehyde) were used.

first: Josiah

last: Murray

first: Atrayee

last: Ray

first: Khanmi

last: Kasomva

first: Erica

last: Steen

first: Cary

last: Stelloh

first: Kirthi

last: Pulakanti

first: Navonil

last: De Sarkar

first: Yong

first: Alison

last: Meyer

first: Aron

last: Geurts

first: Allen

last: Cowley Jr.

first: Mingyu

last: Liang


title: RNAseq analysis of human neutrophil mRNA from adults with SLE and age-matched healthy controls

first: Helen

last: Wright

summary: We report gene expression profiles of blood neutrophils from (1) healthy adults (2) adults with systemic lupus erythematosus (SLE).

overall_design: Neutrophils (purity >99%) were isolated from whole blood using HetaSep followed by negative selection with the Stem Cell human neutrophil isolation kit. RNA was isolated from 0h neutrophil cell pellets using Trizol:chloroform, cleaned up by Qiagen RNeasy kit including on-column DNase digest and sequenced on the Illumina NovaSeq X Plus platform.

first: Grace

last: Filbertine


title: PAN2 Maintains mRNA Poly(A) Tail Homeostasis and Regulates RNA Degradation During Early Embryonic Development in Mice [PAIso-seq]

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

summary: RNA homeostasis regulators and surveillance factors function in the global transcriptome of oocytes and early embryos. Among them, the CNOT6L and CNOT7 proteins of the BTG4, PABPN1L, and CCR4-NOT subunits, as well as TUTs, are involved in the degradation of maternal mRNA, and are crucial for oocyte maturation and early embryonic development. However, the physiological functions of the PAN2-PAN3 complex, which is upstream of CCR4-NOT, in female reproductive cells have not yet been clarified. In this study, we have found that the absence of maternal Pan2 leads to embryonic developmental disorders and a significant decline in female reproductive capacity. By applying PAIso-seq2 and mass spectrometry analysis, we investigated the distribution and dynamics of mRNA poly(A) tails during early embryonic development. We found that the absence of Pan2 in early embryos perturbed the global balance of poly(A) tails, which in turn disrupted the transcriptome, affected mRNA degradation, and led to the accumulation of aberrant proteins. Furthermore, the maternal mRNA degradation mediated by PAN2 is crucial for the normal initiation of ZGA, and it can also regulate the expression of factors that determine cell fate in early mouse embryos. These findings highlight the crucial physiological role of PAN2 in early embryos and expand our understanding of the relationship between RNA homeostasis and the poly(A) tail.

overall_design: In brief, total RNA was extracted with TRIzol Reagent and Direct-zol RNA MicroPrep (Zymo Research, Cat. no. R2060), and the barcode containing adapter were ligated to the 3’-end of mRNA. After being purified by the RNA Clean & Concentrator-5 kit (Zymo Research, Cat. no. R1016), the RNA were RT into cDNA by the UMI containing template-switching oligo (TSO) primer and the first PCR amplification were proceeded. Then the cDNA from rRNA will be removed by the CRISPR-Cas9 system and the second PCR amplification will be performed to get enough cDNA. Then the cDNA from each sample will be concatenated into long molecules by following the MAS-ISO-seq procedure. Finally, all the samples were mixed up according to the molar ratios of cDNA, and at least 500ng of cDNA was sent for SMRTbell library preparation and sequenced on PacBio Revio platform.

first: Yuke

last: Wu

first: Xuan


title: Systematic Benchmarking of CUT&Tag Improves the Reliability and Reproducibility of Chromatin Analysis [Cell number]

first: Sridhar

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

first: Josiah

last: Liu


title: In vitro HFpEF human engineered heart tissues (hEHTs)

city: Tokyo

first: hidenori

last: tani

address: 1-1-4, Hanedakuko, Ota-ku, Haneda Innovation City Zone A

country: Japan

institute: Fujita Medical Innovation Center Tokyo, Fujita Health University

summary: We induced HFpEF in hEHTs via culture medium loading and conducted a comprehensive analysis of the pathophysiology and therapeutic effects of SGLT2 inhibitors

overall_design: hEHTs composed of hiPS-CM, hiPS-Epi, and HUVEC were subjected to two weeks of media loading. Three samples of each were analyzed in four groups: 1. Ctrl, 2. Fibro, 3. HFpEF, and 4. HFpEF + SGLT2i.

first: Hidenori

last: Tani

first: Shugo

last: Tohyama


title: Sequencing of polyA+ RNA from shCtrl and shMETTL8 HeLa for m3C site identification

city: Chicago

first: Caraline

last: Sepich

state: Illinois

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

summary: N3-methylcytidine (m3C), an RNA modification involving methylation of cytidine at the Watson-Crick face, has been identified in human tRNA, mitochondrial tRNA (mt-tRNA), and mRNA. In tRNA, it has been shown to play important roles in tRNA structure and translation. m3C remains understudied in mRNA due to its markedly lower levels, the lack of high-resolution techniques to reproducibly map its location, and under-characterization of its effector proteins on this RNA type. Additionally, METTL8 has been identified as a writer of m3C on mt-tRNA, but has also been shown to have isoforms with nuclear localization. Here, we apply a new approach which utilizes the high readthrough and mutation rates of Protoscript II (PSII) at m3C sites in combination with AlkB demethylation to map m3C at single-base resolution in polyA-purified RNA from HeLa cells either with METTL8-targeting shRNA or control shRNA to assess how the method works on mRNA and to investigate which, if any, of the sites change with METTL8 knockdown.

overall_design: We established stable cell lines with either METTL8 or control shRNA. From each cell line, we purified polyA-enriched RNA (from total RNA). We split the sample into three parts after fragmentation, 3’-repair, and 3’-adaptor ligation. Two of the three parts were used as technical replicates for sequencing, while the third part underwent AlkB treatment to demethylate m3C. All 3 parts underwent reverse transcription with Protoscript II for library preparation. Libraries were sequenced on a NovaSeq6000 SP flow cell twice, once with 100bp single end reads and again with 50bp paired end reads (due to an initial technical processing error). To utilize data from both sequencing runs, Read1 files from both were merged and analysis was performed by modifying the framework used by Zhou et al 2019 (PMID: 31548705) to count mutation rates at each base that is a C in the reference genome.

last: Sepich-Poore

first: Kinga

last: Pajdzik

first: Hui-Lung

last: Sun

first: Li-Sheng

last: Zhang

first: Qing

last: Dai

first: Chuan

last: He


title: MiR-342 suppression of an E2F signaling network limits metastatic outgrowth of triple negative breast cancer [RNA-Seq]

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

summary: Metastasis occurs with high frequency in patients with triple negative breast cancer (TNBC) and its aetiology remains poorly understood. Through integrated analysis of metastatic TNBC mouse models and patient datasets, we identified miR-342 as a clinically relevant suppressor of TNBC metastasis. Ectopic expression of miR-342 was sufficient to repress TNBC metastasis in immune competent and xenograft mouse models, specifically limiting the outgrowth of disseminated tumour cells. Using a multi-omics approach, including Argonaute-HITS-CLIP, we identified the global complement of miR-342 targets in TNBC. Through targeting of E2F1 and many downstream E2F target genes, miR-342 orchestrates both transcriptional and post-transcriptional regulatory networks that converge to suppress E2F signalling in TNBC. Consistent with this, inhibition of the E2F pathway with the CDK4/6 inhibitor palbociclib reduces metastatic outgrowth of TNBC. These findings demonstrate the existence of a pro-metastatic E2F pathway that is downregulated by miR-342 and implicate the clinical utility of CDK4/6 inhibitors to limit TNBC metastasis in patients where the tumour expresses low levels of miR-342.

overall_design: RNA-seq profiling of MDA-MB-231HM cells after addition of 20nM of miR-342-3p, miR-342-5p or negative control miRvana mimics for 72hrs

first: Philip

last: Gregory

first: John

last: Toubia

first: Kate

last: Dredge

first: Andrew

last: Bert


title: MiR-342 suppression of an E2F signaling network limits metastatic outgrowth of triple negative breast cancer

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

overall_design: Refer to individual Series


title: MiR-342 suppression of an E2F signaling network limits metastatic outgrowth of triple negative breast cancer [HITSCLIP]

overall_design: HITS-CLIP of AGO in MDA-MB-231HM cells after treatment with 20nM of miR-342-3p, miR-342-5p or negative control miRvana mimics

middle: A


title: Differential Transcriptomic Responses to MRQ 74 and MRQ 76 Rice Extracts in HT-29 Cells; Implications for Apoptosis and Cell Cycle Regulation

city: Kuala Terengganu

first: Norhaslinda

last: Ridzwan

state: Terengganu

address: No 50C, Kampung Pantai Ali

country: Malaysia

institute: Universiti Sultan Zainal Abidin

summary: Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, and resistance to conventional chemotherapy necessitates exploration of alternative bioactive compounds. Malaysian fragrant rice varieties MRQ 74 and MRQ 76 have demonstrated cytotoxic and pro-apoptotic effects in HT-29 colorectal adenocarcinoma cells; however, their global molecular mechanisms remain unclear. Transcriptomic profiling was performed using RNA sequencing (RNA-seq) to characterize gene expression changes in HT-29 cells treated with MRQ 74 3UP, MRQ 76 3P, and 5-fluorouracil (5-FU) for 24-h and 48-h. Differentially expressed genes (DEGs) were identified using |log₂FC| ≥ 1 and adjusted p-value ≤ 0.05. Functional enrichment analyses were conducted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Selected apoptosis- and cell cycle-related genes were validated by qRT-PCR. High-quality sequencing data (>97% clean reads; >94% Q30; >96% mapping rate) confirmed robust transcriptomic profiling. At 24-h, MRQ 74 predominantly activated immune-related pathways, including antigen processing and cytokine signalling, whereas MRQ 76 induced modest replication-associated responses. By 48-h, MRQ 76 demonstrated marked suppression of DNA replication and cell cycle regulatory genes, with significant enrichment of DNA replication and cytokine–cytokine receptor interaction pathways. In contrast, MRQ 74 maintained sustained immunomodulatory and cell adhesion pathway enrichment. 5-FU induced extensive and progressive transcriptional disruption, reflecting broad cytotoxic stress. qRT-PCR validation confirmed concordant expression trends for key apoptotic regulators. Hence, MRQ 74 and MRQ 76 exert distinct, time-dependent molecular effects in HT-29 cells, with MRQ 74 primarily modulating immune-associated pathways and MRQ 76 targeting proliferative machinery. These findings provide transcriptomic evidence supporting the potential of rice-derived bioactive as complementary anticancer agents in CRC.

overall_design: Bioinformatics analysis of RNA-seq data was conducted through a professional analytical service provided by Apical Scientific Sdn. Bhd. using RNA samples generated in this study. Library preparation and high-throughput sequencing were performed on an Illumina platform.

first: Mohd Adzim Khalili

last: Rohin

first: Norhayati

last: Abd Hadi

first: Mohd Fadzelly

last: Abu Bakar

first: Norazlina

last: Saad

first: Ruziana

last: Ishak


title: Patient-derived cornea organoids as drug repurposing models for aniridia-associated keratopathy

city: Izmir

first: Burak

last: Kahveci

address: Izmir

country: Turkey

institute: Izmir Biomedicine and Genome Center

summary: Background and aim: Aniridia-associated keratopathy (AAK) is a serious ocular surface disease resulting from PAX6 haploinsufficiency due to mutations in the PAX6 gene. This study aims to investigate the efficacy of drug repurposing using a corneal organoid model developed from patient-derived iPSCs and to elucidate the pathophysiology of AAK. Methods: A 90-day stepwise differentiation protocol was used to generate corneal organoids from iPSC cell lines developed from aniridia patients and a healthy control. The produced corneal organoids were characterized using histology, immunofluorescence, qPCR, western blot, and transcriptomics. Two known agents, Duloxetine and Ataluren, were tested for corneal organoids for the restoring PAX6 protein expression. Results: Histological analyses showed that the corneal organoids had a similar architecture to the native corneal tissue. Corneal epithelial, stromal, and endothelial cell biomarker staining showed positive expressions. AAK corneal organoids exhibited features that indicate the AAK disease phenotype, such as thickening of the epithelial cell layers and decrease in expressions of PAX6, ΔNP63, and keratocan genes. An increase in PAX6 protein was observed in organoids produced from AAK1 after duloxetine treatment and in organoids produced from AAK2 following ataluren treatment. AAK3 did not respond to either agent, indicating that there was no mutation-specific drug activity. Transcriptomic analyses showed clear corneal differentiation and absence of retina or lens profile in organoids. Conclusion: This study presents patient-specific organoid models for AAK using iPSCs and offers insight into mutation effects and PAX6 restoration following drug repurposing. The findings form the basis of personalized treatments for congenital aniridia.

overall_design: RNA-seq profiling was performed from undifferentiated human induced pluripotent stem cells and human induced pluripotent stem cell-derived organoids at Day 30 and Day 90.

first: Ali

middle: C

last: Koc

first: Gamze

last: Kocak

first: Adil

last: Mardinoglu

first: Gokhan

last: Karakulah

first: Canan

last: Utine

first: Sinan

last: Guven


title: Lineage Tracing Reveals a Common Ancestor of Supraclavicular Brown and Inguinal Beige Adipocytes

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

summary: Like human scBAT, supraclavicular brown adipose tissue (scBAT) consists of loosely connected thin strips of brown adipocyte islands and is located in the mouse neck. We traced the origin of scBAT to Mef2c-anterior heart field (AHF)-marked (Mef2c-AHF⁺) cells. To investigate the differentiation potential of these cells, we isolated and immortalized Mef2c-AHF⁺ cells (named Mef2c-AHF-P5 cells) from mouse scBAT. Using this cell line, we performed RNA sequencing to profile gene expression induced by either standard adipogenic induction medium (IM) or a combination of Bmp7 and Rosiglitazone. Our results indicate that IM and the Bmp7-Rosiglitazone (BR) combination induce distinct gene expression profiles during the early differentiation of Mef2c-AHF⁺ cells.

overall_design: Two biological replicates of Mef2c-AHF+ cells differentiated for 2 days (2D) using either standard brown adipogenic induction medium (IM) containing IBMX, dexamethasone, insulin, and T3, or a combination of Bmp7 and Rosiglitazone (BR) were profiled by RNA seq.

first: Qianxing

last: Mo

first: Miao-Hsueh

last: Chen


title: SIX1 is required for adult cochlear sensory epithelium homeostasis and auditory function

city: New York

first: Xiaohui

last: Ma

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: The mammalian auditory sensory epithelium consists of luminal hair cells (HCs), whose stereociliary bundles convert sound vibrations into electrical signals, and basal supporting cells (SCs), which provide mechanical stability and homeostasis. During development, the transcription factor SIX1 specifies otic epithelial cells into neurosensory progenitors and commits progenitors to the HC lineage, but its contribution after birth has remained elusive. Here we show that SIX1 is essential for maintaining the structure and function of the sensory epithelium in the adult cochlea. Conditional deletion of Six1 in SCs, inner HCs, or outer HCs of 5–6-week-old mice results in profound deafness. SC-specific deletion causes rapid SC loss followed by secondary HC degeneration, whereas Six1 loss in inner or outer HCs disrupts stereociliary-bundle architecture and leads to progressive HC death. To uncover the underlying regulatory circuitry, we mapped genome-wide SIX1 occupancy in the mature cochlea. SIX1 binds DNA elements/enhancers near genes involved in cell adhesion, junctional integrity, actin dynamics, hair-bundle assembly, ion-channel, mechanotransduction, and cell survival, many of which are frequently mutated in hereditary deafness. Motif analysis showed that these SIX1-bound sites retain the core co-motifs found in SIX1 peaks in embryonic cochlea, suggesting reuse of embryonic cofactors. Notably, SIX1 occupies an intronic enhancer of Srf and physically interacts with SRF protein, positioning SIX1 atop an SRF-centered actin-cytoskeletal circuit crucial for bundle stability. Together, our findings redefine SIX1 as a lifelong regulator of cochlear homeostasis and reveal its downstream networks that maintain the adult auditory sensory epithelium.

overall_design:
Cochleae were dissected from 4-5-week-old wild-type mice and used for CHIP-seq experiment.

snRNA-seq: Cochlear tissues were collected from control and Six1^cKO^ littermate mice 2 weeks following tamoxifen administration and immediately dissected on ice.

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
***************************************************************

first: Asamiya

last: Ian

first: Louie

last: Elizabeth

first: Chen

last: Ying

first: Pin-Xian

last: Xu


title: Effect of SOX11 knock-out and rescue on the gene expression profile of Z138 cells

city: Barcelona

first: Virginia

middle: Amador

last: Espinosa

state: Barcelona

address: Carrer del Rosselló, 149

country: Spain

institute: FCRB - IDIBAPS

summary: Fastq transcriptomic sequencing files from Z138 MCL cell line with differential SOX11 expression. Samples include SOX11 wild-type (WT), SOX11 knockout (KO), and SOX11 re-expression (resc) in the KO background. The dataset includes 3 biological replicates per condition.

overall_design: Transcriptomic profiling of Z138 cell line, SOX11 knockout and SOX11 rescue by RNA-seq

last: Amador

first: Anna

last: de Bolòs


title: CUT&RUN profiling of SOX11 and SMARCA4 in mantle cell lymphoma

summary: CUT&RUN experiments were performed in mantle cell lymphoma (MCL) cell lines (Z138, Granta-519, and JVM2) under different genetic and treatment conditions. In Z138 cells (wild-type and SOX11 knockout), samples were either untreated or treated with the PROTAC degrader AU-15530 0.5 µM for 24 hours. In JVM2 cells, three conditions were tested: parental JVM2, JVM2TRE-SOX11:HA, and JVM2TRE-SOX11:HA treated with AU-15530 0.5 µM for 24 hours. Antibodies against SOX11, SMARCA4, and IgG (as negative control) were used. Peaks were called and visualized using BigWig signal tracks, which are provided as supplementary processed data.

overall_design: CUT&RUN experiments were performed to profile SOX11 and SMARCA4 binding in MCL cell lines under various genetic and treatment conditions. The cell lines included Z138 wild-type (WT), Z138 SOX11 knockout (SOX11KO), Granta-519, and JVM2 with inducible SOX11 expression (JVM2TRE and JVM2TRESOX11HA). Treatments included the PROTAC degrader AU-15330 or vehicle (DMSO). Negative control IgG samples were included for each cell line and condition. The Z138 samples included three biological replicates.

last: De Bolòs


title: Systematic Benchmarking of CUT&Tag Improves the Reliability and Reproducibility of Chromatin Analysis

first: Sridhar

last: Rao

address: 8797 Watertown Plank Rd

institute: Versiti Blood Research Institte

overall_design: This study contains single cell CUT&Tag data for RAD21 in OCI-AML3 leukemia cell line which was used to estimate biological duplication in CUT&Tag. There are 1,493 single cells included. Since this is paired end data, there are two fastq files. The fastq reads contain the sample barcode at the end of their read name (read-name:[i7]_[i5]). Note that the barcode in the read flag (NNNNNN+NNNNNNN) is the experimental index sequence detected by the illumina sequencer. This is typically the same as the sample barcode sequence, but can differ by one nucleotide. Thus, users should use the sample barcode that is at the end of the read name, and not the sequence present in the read flag (which is also in the read header, but seperated from the read name by a " "). An example read is as follows: @lh00134:328:22H7WJLT3:4:1101:33315:1176:GAAATGCC_ACCGCCCA 1:N:0:GAAATGCC+ACCGCCCA CTATTGCGCCAGGTTTCAATTTCTATCGCCTATACTTTATTTGGGTAAAT + 9I9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

first: Josiah

last: Murray

first: Atrayee

last: Ray

first: Khanmi

last: Kasomva

first: Erica

last: Steen

first: Cary

last: Stelloh

first: Kirthi

last: Pulakanti

first: Navonil

last: De Sarkar

first: Yong

last: Liu

first: Alison

last: Meyer

first: Aron

last: Geurts

first: Allen

last: Cowley Jr.

first: Mingyu

last: Liang


title: Effect of AU-15330 treatment on Z138 gene expression profile

last: Espinosa

summary: AU-15330 treatment RNA-seq dataset: Fastq transcriptomic sequencing files from Z138 mantle cell lymphoma (MCL) cell line treated with the SMARCA4 degrader AU-15530. Cells were treated for 8 or 24 hours with 0.5 μM AU-15530 or control (DMSO). The dataset includes 3 biological replicates per condition (AU-15530 8h, AU-15530 24h, DMSO 8h, DMSO 24h).

overall_design: RNA-seq profiling Z138 and their AU-15330 derivative treated cells for 8 or 24 hours


title: Spatial profiling reveals TREM2+ macrophages as central to Mycobacterium tuberculosis pathogenesis in human pulmonary tuberculosis

first: Parambir

last: Dulai

state: IL

address: 259 E Erie St Ste 1600

institute: Northwestern University

summary: Tuberculosis (TB) remains a major global health challenge, with disease progression typically beginning as pneumonia before the development of granulomas. While organized granulomas have long been the focus of TB pathogenesis research, the early development of TB pneumonia has been underexplored. Using spatial transcriptomics, high-resolution proteomics, and scRNA-seq on human pulmonary TB lesions, we reveal a striking compartmentalization of immune responses between early pneumonia and mature granulomas. The immunologic composition of granulomas was distinct from the pneumonia; granulomas are enriched for antimicrobial gene expression in both macrophages and T cells and show reduced bacterial antigen burden. In contrast, TREM2-expressing foamy macrophages are the predominant cell type occupying alveolar spaces in TB pneumonia with T cells infrequent. These TREM2⁺ macrophages exhibit a lipid-associated gene program, accumulate lipid droplets, and harbor Mycobacterium tuberculosis antigens and mRNA—corresponding to increased bacterial viability in vitro. We further show that the M. tuberculosis virulence lipids, PDIM and mycolic acids, potently induce and activate TREM2 signaling in TREM2-expressing macrophages, promoting an intracellular niche permissive for bacterial growth. These findings establish TREM2⁺ macrophages as an early niche for M. tuberculosis survival and implicate TB pneumonia as a critical stage in disease transmission. Targeting this foamy macrophage population may offer opportunities to interrupt early TB progression and transmission.

overall_design: 5 TB patient samples were obtained from the department of pathology at the Charles Nicole Hospital in Tunis. These cases may correspond to tuberculosis with an atypical clinical presentation with acid fast bacilli negative and pseudo-tumor appearance. Patients were taken at the time of diagnosis, before initiating treatment.

first: Rosane

last: Teles

first: Chaouki

last: Benabdessalem

first: Jonathan

last: Perrie

first: Cenfu

last: Wei

first: Julie

last: West

first: Bruno

last: Silva

first: Priscila

middle: R

last: Andrade

first: Lilah

last: Mansky

first: Prajan

last: Divakar

first: Linda

last: Fischbacher

first: Karen

last: Lamb

first: Feiyang

last: Ma

first: Kimia

last: Rategh

first: Aparna

last: Pillai

first: Samuel

last: French

first: Emna

last: Romdhane

first: Mohamed-Ridha

last: Barbouche

first: Eynav

last: Klechevsky

first: Marco

last: Colonna

first: Adrie

last: Steyn

first: Soumaya

last: Rammeh

first: Steven

last: Bensinger

first: Daniel

last: Barber

first: Bryan

last: Bryson

first: Matteo

last: Pellegrini

first: John

middle: T

last: Belisle

first: Barry

last: Bloom

first: Robert

last: Modlin


title: Pax8 regulates proximal-tubule-specific identity via distal enhancer elements

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

summary: Pax8 can reversibly modulate proximal-tubule-specific gene expression and epithelial morphology in cultured proximal tubule cells. Pax8 loss dynamically alters activity of distal enhancer elements but not promoters. These observations strongly suggest that Pax8 regulates proximal tubule phenotype via distal enhancer elements

overall_design: A line of proximal tubule epithelial cells with conditional Pax8 and a constitutive driver of tamoxifen-dependent Cre was derived from adult transgenic mice. Pax8 was depleted from these cells by addition of 4-OH tamoxifen to the culture medium.

first: Jeffery

last: Beamish

first: Jason

last: Watts

first: Ma

last: Wan

first: Don

last: Delker


title: Regulation of neurogenesis and neuronal migration by Rrm2 and Timp3 following seizures

city: San Antonio

first: Jenny

last: Hsieh

state: Texas

address: 1 UTSA Circle, SEB 4.166

department: Neuroscience, Developmental and Regenerative Biology

institute: University of Texas at San Antonio

summary: Temporal lobe epilepsy is associated with aberrant neurogenesis and ectopic migration of adult-born granule cells (abGCs), yet the molecular mechanisms driving these changes remain poorly defined. Using a pilocarpine-induced mouse model of temporal lobe epilepsy and chemogenetic silencing of abGCs via Designer Receptors Exclusively Activated by Designer Drugs (DREADDs), we previously demonstrated that abGC inhibition reduces both ectopic migration and seizure susceptibility. To identify underlying molecular regulators, we performed RNA sequencing of FACS-isolated abGCs and identified Rrm2 and Timp3 as top candidate genes modulated by seizure activity and neuronal silencing. To assess their functional roles, we pharmacologically inhibited Rrm2 with Triapine (3-AP) and Timp3 with the LXR agonist T0901317 (T09). Inhibition of Rrm2 significantly reduced seizure frequency, decreased hilar abGC migration, and altered neuronal differentiation. While T09 treatment did not significantly alter Timp3 transcript levels, it increased the number of DCX+ neurons in the hilus, suggesting an effect on neuronal migration independent of robust knockdown. These findings highlight distinct roles of Rrm2 and Timp3 in hippocampal plasticity following seizures. Together, these data identify new molecular targets for modulating aberrant neurogenesis in epilepsy.

overall_design: RNA-seq profiling of C57BL/6 wildtype mice with different treatment conditions (CAG-GFP Pilo + CNO, Seizures; CAG-GFP Sham + CNO, WT (No Seizure); DREADD Sham + CNO, No Seizures; DREADD Pilo + CNO, Seizures and Silenced) at Day14 for differentially expressed genes.

first: Adebayo

middle: O

last: Adeyeye

first: Parul

last: Varma

first: Nico

last: Enerlan

first: Marissa

last: Coppin


title: Time-restricted feeding blocks kidney fibrosis and damage through diminished CD8+ T cell infiltration in obese mice

city: Birmingham

first: Kelly

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

institute: University of Alabama at Birmingham

summary: Obesity is a major risk factor for chronic kidney disease. Our lab previously showed that a short-term (2 week) time restricted feeding (TRF) intervention in an established model of diet induced obesity (DIO) reduced kidney interstitial fibrosis, increased tubular brush border integrity, and decreased CD3+ T cell numbers. There is very little known about kidney damage and T cell inflammation in obesity. Single cell RNA sequencing was used to determine transcriptomes of CD45+ cells isolated from kidneys.

overall_design: Male C57Bl6/J mice were on 20 weeks of high fat diet (diet induced obesity) or normal diet (ND) with either 2 weeks of continued ad libitum feeding or time restricted feeding to the active period of the mouse. Kidneys were collected at ZT13-15 (beginning of dark phase) and CD45+ (immune) cells were multiplexed with BioLegend totalsefq B Hashing antibodies, FACS sorrted, and sequenced using the 10X Genomics platform. An additional set of DIO, TRF and normal diet (ND) samples were not multiplexed but were also run on the 10X Genomics platform.

first: Claudia J

last: Edell

first: Kyle

last: Moore

first: Keri

last: Kemp

first: Kelly A

first: Jennifer S

last: Pollock


title: Inflammatory microglia with lysosomal and lipid dysfunction drive chronic progressive demyelination

city: Bonn

first: Ozgun

last: Gokce

address: Venusberg Campus 1

institute: Uniklinikum Bonn

summary: Dysfunctional immune responses impair tissue repair and contribute to neurodegeneration. We examined whether chronic demyelination could drive inflammation towards a pathological, tissue-destructive state. Comparative analysis of genetic and toxic models of acute and chronic demyelination identified a disease-promoting microglial state, characterized by sustained pro-inflammatory activation and enhanced myelin-destructive activity in chronic demyelination. Mechanistically, they exhibited lysosomal cholesterol sequestration with reduced lipid droplet formation. Lipidomic profiling showed defective cholesterol esterification, while transcriptomics uncovered a dysregulated metabolic program marked by upregulated cholesterol synthesis and diminished sterol efflux. Restoring cholesterol homeostasis with a brain-penetrant desmosterol mimetic normalized microglial function, reduced pro-inflammatory activation (e.g. C-C Motif Chemokine Ligand 4 expression), mitigated myelin damage, and improved motor performance in a mouse model of leukodystrophy. Our findings uncover a previously unrecognized pro-inflammatory microglial state characterized by lysosomal dysfunction and increased myelin reactivity, highlighting a novel therapeutic target for demyelinating disorders.

overall_design: Brain cells from C57BL/6J, Tg(Plp)72Kan and Cuprizone treated C57BL/6J (6 weeks / 12 weeks) mice wer dissociated into single cell suspension and analysed using scRNAseq. Brain cells from 4 month or 8 month old C57BL/6J and Tg(Plp)72Kan mice were isolated by Fluorescent-activated cell sorting (FACS) and analysed using scRNAseq.

first: Stefan

last: Berghoff

first: Lena

last: Spieth

first: Simona

last: Vitale

first: Lennart

last: Schlaphoff

first: Martin

last: Zirngibl

first: Lu

last: Liu

first: Alkmini

last: Damkou

last: Roth

first: Charlene-Annett

last: Hurler

first: Leon

last: Hosang

first: Katrin

last: Perez Anderson

first: Simon

last: Besson-Girard

first: Marvin

last: Reich

first: Astrid

last: Feiten

first: Ludwig

last: Huber

first: Christoph

last: Müller

first: Georg

last: Kislinger

first: Lina

last: Dinkel

first: Janos

last: Groh

first: Anna

last: Williams

first: Arthur

last: Liesz

first: Martina

last: Schifferer

first: Klaus-Armin

last: Nave

first: Sarah

last: Jäkel

first: Sabina

last: Tahirovic

last: Giera

first: Mikael

last: Simons


title: Lsp2 links mTORC1 to TOP mRNA translation and lifespan in Drosophila

city: changsha

first: Jun

last: Wang

state: HuNan

address: Lushan

department: College of Life Science

institute: Hunan Normal University

summary: Mechanistic target of rapamycin complex 1 (mTORC1) senses nutrient availability to orchestrate metabolic processes critical for physiological homeostasis and organismal aging 1. While mTORC1 preferentially regulates the translation of 5′-terminal oligopyrimidine (TOP) motif-containing mRNAs that predominantly encode ribosomal proteins (RPs) via the translational repressor 4E-BP 2, this mTORC1 function is resistant to rapamycin inhibition 3. TOP mRNAs are exceptionally abundant, thus imposing a major translational burden on cells; yet how their translation is physiologically tuned and linked to longevity remain unexplored. Here we identify Lsp2, originally known as a storage protein 4, as an adipose effector and feedback activator of mTORC1 that modulates lifespan in Drosophila. Lsp2 expression is induced by essential amino acids (EAAs) via mTORC1 and gated by additional signals of nutrient sufficiency. Genetic ablation of Lsp2 robustly extends lifespan without impairing key life-history traits such as reproduction. Translatomic profiling shows that loss of Lsp2 selectively reduces global TOP mRNA translation in a 4E-BP–dependent manner, thereby extending lifespan via a mechanism distinct from rapamycin. Evolutionarily, TOP motifs co-emerged with 4E-BP and are present in nearly all Drosophila RP mRNAs. Moreover, we demonstrate that their role in translational control extends to Drosophila. Collectively, our findings reveal a nutrient-induced physiological factor that amplifies mTORC1 output in TOP mRNA translation and regulates organismal longevity.

overall_design: (i) Diet group: 7-days-old w1118 iso (iso31) females raised on CD followed by 2 days with either a control diet (2% sucrose, with the title D2S1-D2S3) or a protein-rich diet (2% sucrose + 3.3% yeast extract, with the title DYE2S1-DYE2S3) at 25ºC; (ii) Age group: 3-day-old (as Young, with the title OR_3A-OR_3C) and 50-day-old (as Old, with the title OR_50A-OR_50C) Oregon-R flies raised on CD at 25°C; (iii) Lsp2 and Rheb overexpression: flies with fat body specific overexpression of Lsp2 (control w1118 with the title ctrl1-ctrl3, Lsp2 with the title lsp21-lsp23) or Rheb (control w1118(CJ1) with the title ctrl4-ctrl6, Rheb with the title rheb1-rheb3)  by LppTS and respective control raised on CD for 3 days prior to a sugar-only diet (5% sucrose) for 2 days at 29°C.

first: Yirong

first: Zongzhao

last: Zhai

first: Zixin

last: Cai


title: PAN2 Maintains mRNA PolyA Tail Homeostasis and Regulates Translation during Spermiogenesis in Mouse [PAIso-seq]

first: Heng-yu

last: Fan

summary: Elongation and shortening of the polyA tail are the most common type of post-transcriptional mRNA regulation in eukaryotic cells. Two protein complexes, PAN2-PAN3 and CCR4-NOT, are major cytoplasmic deadenylases that trim the mRNA polyA tails. While PAN2-PAN3 removes the distal portion of the long polyA tails, CCR4-NOT removes adenosine closer to the 3'-UTR. Some subunits in the CCR4-NOT complex have been shown to play synergistic biochemical functions during mouse germ cell development. However, the in vivo functions of the upstream deadenylase PAN2-PAN3 remain unclear, particularly in mammals. In this study, we found that germline-specific deletion of Pan2 leads to male infertility. Pan2 knockout did not affect the prophase of meiosis I, but led to abnormal spermiogenesis and apoptosis of male germ-cells. By Palso-seq and Ribo-lite, we found that the deletion of Pan2 increased the number of long-tail mRNAs in spermiogenesis and disrupted the translation efficiency of genes that should be highly translated at this stage. These findings highlight the crucial physiological functions of PAN2 in gametogenesis and expand our understanding of the posttranscriptional regulation of mRNAs in specific physiological processes.

overall_design: In brief, total RNA was extracted with TRIzol Reagent and Direct-zol RNA MicroPrep (Zymo Research, Cat. no. R2060), and the barcode containing adapter were ligated to the 3’-end of mRNA. After being purified by the RNA Clean & Concentrator-5 kit (Zymo Research, Cat. no. R1016), the RNA were RT into cDNA by the UMI containing template-switching oligo (TSO) primer and the first PCR amplification were proceeded. Then the cDNA from rRNA will be removed by the CRISPR-Cas9 system and the second PCR amplification will be performed to get enough cDNA. Then the cDNA from each sample will be concatenated into long molecules by following the MAS-ISO-seq procedure. Finally, all the samples were mixed up according to the molar ratios of cDNA, and at least 500ng of cDNA was sent for SMRTbell library preparation and sequenced on PacBio Revio platform.

first: Yuke

last: Wu

first: Xuan


title: Hepatocytes spatial transcriptomics analysis of healthy and MASH patients

city: Osong-eup, Heungdeok-gu

first: WANG

last: FENG

state: Cheongju-si, Chungcheongbuk-do

address: Osongsaengmyeong ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, Republic of Korea

country: South Korea

institute: chungbun national university

summary: Spatial transcriptomics of hepatocytes was employed to identify differentially expressed genes between healthy tissues and those from MASH patients.

overall_design: Hepatocytes transcriptome DSP-RNA profiling of 4 healthy and 11 MASH patients was conducted using NanoString GeoMx.Hepatocytes (CK8/18+) areas of interest (AOIs) were annotated. Unique molecular identifier (UMI) encoded gene expression count data was generated by Illumina sequencing. The processed count data was then analyzed using R/Bioconductor.

first: FENG

last: WANG

first: Ekihiro

last: Seki

first: Yoon Seok

last: Roh


title: Cohesin haploinsufficiency and inv(16) cooperate to reinforce Fli1 gene transcriptional programs during acute myeloid leukemia initiation and maintenance.

city: Milwaukee

first: Sridhar

last: Rao

overall_design: Refer to individual Series


title: Spatial transcriptomics analysis of hepatocytes from liver tissues of 24-week-old mice on NCD and FFD diets.

summary: Spatial transcriptomics analysis of hepatocytes was performed to identify differentially expressed genes in liver tissues of 24-week-old mice maintained on NCD and FFD diets.

overall_design: Transcriptomic profiling of hepatocytes from liver tissues of 3 NCD and 3 FFD mice was conducted using NanoString GeoMx DSP-RNA technology. Hepatocyte-specific areas of interest (AOIs) were annotated based on Albumin expression. Unique molecular identifier (UMI)-encoded gene expression count data was generated through Illumina sequencing. The processed count data was subsequently analyzed using R/Bioconductor.


title: Cohesin haploinsufficiency and inv(16) cooperate to reinforce Fli1 gene transcriptional programs during acute myeloid leukemia initiation and maintenance [scRNA-seq]

summary: Core binding factor (CBF) acute myeloid leukemias most commonly harbor the translocations t(8;21) or inv(16). Cohesin mutations are less commonly observed in inv(16) than in t(8;21), suggesting that they may negatively impact leukemic initiation or maintenance in this setting. We used a mouse model of inv(16) with haploinsufficiency of the cohesin subunit Smc3 and paradoxically found that inv(16);Smc3D/+ mice have a reduced leukemic latency compared to inv(16);Smc3+/+ mice, suggesting a role for cohesin loss in leukemic initiation or maintenance. Given the known role of cohesin haploinsufficiency in altering chromatin accessibility, we demonstrated an increase in chromatin accessibility in inv(16);Smc3 D/+ HSPCs prior to leukemia development, with an enrichment for Fli1 DNA binding motifs. We also observe an increase in Fli1 expression and enhanced Fli1 target expression in the most primitive hematopoietic stem cells using scRNA-seq, linking enhanced Fli1 activity in the inv(16);Smc3D/+ setting to leukemic initiation consistent with elevated RAS activity, which is common in inv(16) AML. We further show that Fli1 is essential for the maintenance stage of inv(16);Smc3D/+ AML. Our data demonstrate that cohesin loss drives both leukemic initiation and maintenance in inv(16) AML, identifying Fli1 as a previously unrecognized therapeutic vulnerability.

overall_design: 10x genomics v.3.1

first: Alison

middle: E

last: Meyer

first: Katelyn

last: Heimbuch

first: Kirthi

last: Pulakanti

first: Cary

last: Stelloh

first: Nataly

last: Cruz-Rodriguez

first: Josiah

last: Murray

first: Dandan

first: Lisa

last: Latzko

first: Sebastian

last: Vosberg

first: Philipp

last: Greif

first: Lucio

last: Castilla

first: John

last: Pulikkan

first: Subramaniam

last: Malarkannan


title: Elongating heart organoids recapitulate early heart morphogenesis and model congenital heart disease

city: Suwon-si

first: Jinwoo

last: Lee

state: Gyeonggi-do

address: 2066, Seobu-ro, Jangan-gu

institute: Sungkyunkwan university

summary: Early heart development involves heart tube elongation, looping, and axial patterning, yet these processes remain difficult to study experimentally. While pluripotent stem cell-derived heart organoids model cardiomyocyte differentiation, they do not recapitulate early morphogenetic events. Here, we generate elongating heart organoids (EHOs) from human induced pluripotent stem cells that undergo coordinated elongation and looping-like curvature, resembling early cardiac morphogenesis. EHOs establish a venous-to-arterial axis with spatially organized sinus venosus-like, atrial, and ventricular cardiomyocytes, and exhibit sequential propagation of contractile activity along this axis. Single-cell transcriptomics and trajectory analyses, together with pulse-labeling, support a model in which progressive incorporation of cardiac cells from proliferative splanchnic mesodermal cells at the venous pole drives elongation of the cardiac structure. Consistent with in vivo phenotypes, TBX5 deletion results in shortened EHOs with reduced looping-like curvature and irregular contractions. Together, EHOs provide a human in vitro system that enables investigation of early cardiac morphogenesis.

overall_design: scRNA-seq of hiPSC-derived elongating heart organoids at day 5 and day 13 of differentiation.

first: Ahri

last: Kim

first: Yideul

last: Jeong

first: Gyu-Un

last: Bae

first: Jong-Sun

last: Kang


title: Cohesin haploinsufficiency and inv(16) cooperate to reinforce Fli1 gene transcriptional programs during acute myeloid leukemia initiation and maintenance [ATAC-seq]

first: Sridhar

last: Rao

overall_design: bulk ATAC sequencing of lineage depleted murine bone marrow

first: Alison

last: Meyer

first: Katelyn

last: Wang


title: Kv1.3 inhibition alleviates neuropathology via neuroinflammatory and resilience pathways in a mouse model of Aβ pathology

status: Public on Jul 15 2026

city: NEW HAVEN

first: UPASNA

last: SRIVASTAVA

state: CT

address: 300 George Street , Department of Neurology, Yale School of medicine

department: Neurology

institute: YALE University

summary:
Abstract
Inhibition of voltage-gated potassium channel Kv1.3 is a therapeutic strategy to curb microglia-mediated neuroinflammation in neurodegeneration, although the cellular and signaling mechanisms of disease-modification by Kv1.3 blockers are unclear. In this study, we delineate protective mechanisms of Kv1.3 blockade in a mouse model of Alzheimer's disease (AD) pathology using comprehensive transcriptomics and proteomics profiling of brain, corresponding with neuropathological effects of two translationally relevant Kv1.3 blockers, namely small molecule PAP-1 and peptide ShK-223. Following 3 months of treatment, both molecules reduced Ab plaque burden. Single nuclear RNA seq (snRNA seq) of brain nuclei showed that PAP-1 disproportionately impacted oligodendrocytes and microglia and increased crosstalk between neurons and astrocytes with endothelial cells. In contrast, ShK-223 had pronounced effects on glutamatergic neurons and astrocytes. Both blockers increased expression of myelination genes in oligodendrocytes and synaptic genes in neurons. Neuroprotective effects of PAP-1 were further confirmed by bulk brain transcriptomics and proteomics whereby PAP-1 increased levels of synaptic, cognitive resilience and mitochondrial proteins, while decreasing glial and immune pathways including STAT1/3 phosphorylation. Using proximity labeling and co-immunoprecipitation, we found that Kv1.3 interacts with STAT1/3 in microglia. Using microglial cell lines and primary microglia, we discovered a preferential functional coupling between Kv1.3 and type 2 but not type 1 IFN signaling. Brain-level disease modification by Kv1.3 blockade was reflected in the cerebrospinal fluid (CSF) via reduced levels of neurofilament-light (NEFL) and resilience protein RPH3A, both of which are increased in human AD CSF. Together, this study demonstrates functional links between Kv1.3 channels and type 2 IFN signaling and reveals distinct cellular effects of Kv1.3 blockers in AD pathology that correspond with reduced neuropathology and neuroinflammation, augmentation of resilience and neuro-vascular pathways, along with biomarkers of therapeutic effect.

overall_design: Whole-brain RNA from 12 samples, 5xFAD mice representing Control, PBS, ShK-223 and PAP-1 treatment groups was sequenced using paired-end RNA-seq. Reads were aligned to the Mus musculus reference genome (GRCm38/mm10) using STAR v2.7.11a and analyzed with DESeq2 v1.40.2.

first: Upasna

last: Srivastava

first: Srikant

last: Rangaraju


title: Overexpression of Drosophila TET Causes Eye Development Abnormalities, Affecting Retinal Determination and Pathway Regulation

city: Beirut

first: Margret

last: Shirinian

address: Bliss street

country: Lebanon

institute: American University of Beirut

summary: The discovery of somatic recurrent driver mutations in Histone H3.3 has profoundly revolutionized our understanding of high-grade gliomas (HGG) in children. Mutations in H3.3K27M and H3.3K36M disrupt normal gene regulation associated with eye development, piRNA biogenesis primarily through transposable element derepression. The regulation of transposable elements (TEs) is intricately linked to DNA methylation, particularly in mammalian models. This regulatory process is orchestrated through the interplay of key molecular players, namely the ten-eleven translocation (TET) proteins and DNA methyltransferases. We aim in this study to elucidate the interplay between mammalian TET2 and endogenous Drosophila Tet (dTet) concerning the H3.3K27M -induced eye phenotypes. Our findings demonstrate that the co-expression of the mTET2 R43G (non-catalytic) mutant with H3.3K27M amplifies the eye overgrowth phenotypes. Furthermore, the overexpression of dTet exacerbates the eye phenotype irrespective of H3.3K27M expression. Interestingly, overexpression of dTet upregulates wingless (wg); a key regulator in the Wnt signaling pathway and eye development, potentially repressing essential transcription factors required for eye specification resulting in the complete loss of eyes. Our results identify a novel role of dTet in the early stages of eye development, elucidating its impact on both retinal determination and wingless signaling pathways, which collectively regulate eye growth and differentiation.

overall_design: We performed genetic crosses to see the effect of overexpressing histone mutants together with Drosophila dTet in adult compound eyes using eye-Gal4 driver. Since the overexpression of dTet exacerbated the eye phenotype irrespective of H3.3K27M expression we focused the study on overexpression of dTet. We then performed bulk-RNA sequencing on eye imaginal discs of flies overexpressing dTet in the compoud eyes driven by ey-Gal4.We have then compared the gene expression profile of dTet with Histone H3.3K27M and H3.3K36M perviously published

first: Malak

last: Kleit

first: Jawdat

last: Sandakly

first: Abdullah

last: El-Kurdi

first: Abdulmajid

last: Shehab

first: Jad

last: Madi

first: Sarah

last: Mantash

first: Nada

last: Jabado


title: Rapid and functional intestinal regeneration after full-organ transection in zebrafish larvae is regulated by opposing effects of IL-22 and IL-26 [scRNA-seq]

city: Paris

first: Pedro Pablo

last: HERNANDEZ CERDA

address: 11-13 rue Pierre et Marie Curie, BDD building

country: France

institute: Institut Curie

summary: The intestinal epithelium is among the most regenerative tissues, continuously renewing and repairing after damage. Severe injuries that disrupt all tissue layers, however, pose a distinct challenge, requiring restoration of the epithelium together with its surrounding tissues. Whether and how a vertebrate intestine can restore architecture and function after complete loss of gut continuity remains unknown. Here, we establish a larval zebrafish model of severe intestinal injury, in which full-organ transection disrupts all gut tissue layers. Following injury, the intestine rapidly reattaches, restores lumen continuity, and resumes food transit. This repair process is accompanied by mesenchymal remodeling and restoration of muscle continuity, and is promoted by transient epithelial proliferation. Injury induces a sox17-expressing epithelial progenitor-like state, with localized re-expression of this embryonic gut marker at the wound site. Injury also triggers transient neutrophil and macrophage recruitment to the wound site and broadens the range of epithelial cell types that express il22. STAT3 signaling is required for timely epithelial reattachment and injury-induced proliferation. Loss of IL-22 blunts early repair-associated responses, impairs reattachment, reduces proliferation, and limits lumen restoration. In contrast, loss of IL-26 enhances early epithelial repair programs, accelerates gap closure, and elevates proliferation in a mitosis-dependent manner. Together, these findings establish zebrafish larvae as a tractable vertebrate model for full-organ intestinal regeneration and identify IL-22 and IL-26 as opposing regulators of STAT3-associated repair

overall_design: Single-cell RNA-seq was performed on dissociated cells from dissected guts of 5-day post-fertilization wild-type zebrafish larvae under uninjured conditions or at 24 hours after full-organ intestinal transection. Dissected guts were pooled to generate one 10x Genomics single-cell library for each condition. The study was designed to characterize intestinal cell populations and identify cell-type-specific transcriptional responses to severe intestinal injury.

first: Ignacio

last: Medina-Yáñez

first: Pedro

last: Hernandez