title: Loss of Alg13 Impairs Postnatal GABAergic Cortical Interneuron Development

city: Yinchuan

first: Xin

last: Qian

state: Ningxia

address: 804 Shengli Street

department: Department of Neurosurgery

institute: General Hospital of Ningxia Medical University

summary: Abnormal development of cortical neurons may be closely associated with the presence of neurological disorders, and deletion of the Alg13 gene was strongly associated with epilepsy susceptibility and seizure severity in mice. And the deletion of Alg13 gene is also found in some epileptic patients, which may prove that Alg13 gene plays a role in the development of cortical interneurons. Methods We used immunofluorescence to observe the effects of Alg13 deletion on the distribution and migration of interneurons in the cerebral cortex of postnatal mice, and applied transcriptome sequencing to identify neuronal developmental genes and verified the results using RT-qPCR. Results Alg13 deletion plays a key role in the spatiotemporal distribution of cortical interneurons in the mouse cerebral cortex by establishing an Alg13-deficient mouse model by immunofluorescence, and that the migratory ability of interneuron subtypes in mice was also significantly inhibited by Alg13 deletion, which may increase the susceptibility to epilepsy and the severity of seizures. By transcriptome sequencing as well as RT-qPCR we verified three genes associated with inhibitory interneuron development, Ndn, Dynlt1b, and C3. Conclusions  Abnormal development of interneurons may be regulated by Alg13, thus causing epilepsy-related disorders, which will help to further understand the pathogenesis and mechanisms of epilepsy, with a view to providing experimental basis and new therapeutic targets for the clinical application of controlling Alg13-associated refractory seizures, and enriching the understanding of the regulatory mechanisms of interneuron development.

overall_design: We compared the effects of Alg13 gene knockout on the distribution and migration of interneurons in the cerebral cortex of mice. KOP refers to the samples from Alg13 knockout mice at 1, 7, and 30 days, while WTP refers to the wild-type control mice at 1, 7, and 30 days.


title: Villification of the intestinal epithelium is driven by Foxl1

status: Public on Jan 05 2026

city: Philadelphia

first: Klaus

last: Kaestner

state: PA

address: 3400 Civic Center Blvd

department: Perelman School of Medicine

country: USA

institute: University of Pennsylvania

type: Expression profiling by high throughput sequencing

summary: The primitive gut tube of mammals initially forms as a simple cylinder consisting of the endoderm-derived, pseudostratified epithelium and the mesoderm-derived surrounding mesenchyme. During mid-gestation a dramatic transformation occurs in which the epithelium is both restructured into its final cuboidal form and simultaneously folded and refolded to create intestinal villi and intervillus regions, the incipient crypts. Here we show that the mesenchymal winged helix transcription factor Foxl1, itself induced by epithelial hedgehog signaling, controls villification by activating BMP and PDGFRa as well as planar cell polarity genes in epithelial-adjacent telocyte progenitors, both directly and in a feed- forward loop with Foxo3. In the absence of Foxl1-dependent mesenchymal signaling, villus formation is delayed, the separation of epithelial cells into mitotic intervillus and postmitotic villus cells impaired, and the differentiation of secretory progenitors blocked. Thus, Foxl1 orchestrates key events during the epithelial transition of the fetal mammalian gut.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed to investigate the role of the winged helix transcription factor Foxl1 in orchestrating villus formation during mouse fetal gut development. Proximal half of the small intestines were isolated from embryonic day 15.5 (E15.5) Foxl1-CreERT2-tdTomato mice, and single-cell suspensions were prepared using enzymatic digestion followed by FACS enrichment of live cells. Libraries were generated using the 10x Genomics Chromium Single Cell 3' v2 platform, with a target of ~5,000 cells per sample. The goal was to characterize Foxl1-dependent gene regulatory networks in mesenchymal telocyte progenitors and their impact on epithelial-mesenchymal cross talk and developmental signaling pathways. Comparative analyses were performed between control (heterozygous) and Foxl1-null (homozygous) embryos to define how loss of Foxl1 alters transcriptional programs essential for intestinal villification.

first: Guoli

last: Zhu

first: Jonathan

last: Schug

first: Deeksha

last: Lahori


title: Broad Profiling of Hepatic and Immunotoxic Effects of Per- and Polyfluoroalkyl Substances (PFASs) Across Sexes and Exposure Durations in C57/BL6 Mice

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

summary: Per and Poly-fluorinated alkyl substances (PFAS) are a class of chemicals commonly referred to as “forever chemicals”. Of this class, perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) are frequently found in the environment and blood of Canadians. Here, we sought to broadly characterize the effect of PFOS and PFOA on liver toxicity and immunotoxicity in both male and female mice. Experimental mice were exposed to PFOA or PFOS for 28 or 56 days, followed by a comprehensive evaluation that included 6 organ weights, 8 serum biomarkers of liver toxicity, and transcriptomic analysis across 15 treatment conditions. This revealed that both compounds caused hepatomegaly, increased serum liver enzymes, pancreatic atrophy, and reduced serum triglycerides (TGL) regardless of sex or duration of treatment. Transcriptomics identified enrichment of PPAR signaling, lipid metabolism dysfunction, and AGE-RAGE pathways across groups which supports a role for metabolic and oxidative stress in PFAS-induced hepatotoxicity. To characterize immunotoxicity 19 cytokine profiles, and 3 tissue types including the thymus, spleen, and blood were assessed for changes in population dynamics. Immune effects were distinctly sex specific. In males, PFOS led to broad cytokine suppression (IL-4, IL-17α, TNF-α, MCP-1) and a non-significant increase in peripheral T cells following PFOA exposure. In contrast, females exhibited minimal cytokine changes but showed significant alterations in thymocyte development. Together, these findings reveal three key outcomes: (1) both PFASs cause liver and pancreatic toxicity, (2) hepatic effects are largely sex-independent, and (3) immune perturbations are highly sex-dependent. These results underscore the importance of evaluating sex-specific effects in immunotoxicology studies of persistent environmental contaminants.

overall_design: Male and female C57BL/6-Elite mice (6–9 weeks old) were acclimated for two weeks, individually housed (males) or paired (females), with controlled diet and water. Starting at 8–11 weeks old, mice were orally dosed daily via gavage with either PFOA or PFOS at varying doses (0.166 to 1.5 mg/kg/day) for 28 or 56 days. Control groups included vehicle (0.5% Tween 20) and naïve (no gavage) mice. Body weight was recorded daily, and water consumption was measured weekly. After the dosing period, mice were euthanized 24 hours post-final dose for blood and organ collection (liver, pancreas, kidneys, GI tract), which were weighed for analysis.

first: Amelie

last: Blais

first: Allison

last: Loan

first: Eunnara

last: Cho

first: Asia

last: Woodtke

first: Houman

last: Moteshareie

first: Lauren

last: Bradford

first: Zhang

last: Gong

first: Martha

last: Navarro

first: Andy

last: Nong

first: Rocio

last: Aranda-Rodriguez

first: Kristin

last: Eccles

first: David

last: Prescott

first: Azam

last: Tayabali


title: INVESTIGATION OF DIPIRYDAMOLE-ELICITED SIGNALING IN THE BRAIN OF NIEMANN PICK TYPE C MICE: A MULTI-OMIC STUDY.

city: Rome

first: Sabrina

last: Tait

state: Italy

address: Viale Regina Elena 299

department: Dpt. Infectious Diseases

country: Italy

institute: Istituto Superiore di Sanità

summary: Niemann Pick type C1 (NPC1) is a rare, fatal disorder characterized by endosomal lipid accumulation that leads to damage of both peripheral organs and central nervous system (cerebellum and hippocampus are especially affected). Currently, miglustat is the only approved drug for NPC1, thus the identification of new treatments is mandatory. We have previously demonstrated that the drug dipyridamole (DIP), an approved medicine that is clinically employed as an antiplatelet agent, rescued recognition memory and increased hippocampal expression of calbindin. On the contrary, the drug was unable to improve cerebellar-dependent motor function. In order to understand the mechanism of action engaged by DIP to exert its protective action in the hippocampus, we performed a multi-omic analysis of gene and proteins modulated by the treatment in the hippocampus and cerebellum of a mouse model of NPC1 disease.

overall_design: In order to understand the effect of dipyridamole (DIP) onto the brain of NPC1 mice (BALB/cNctr-Npc1m1N/J strain) the following experimental groups were enrolled in the study:1) Npc1-/-DIP mice receiving DIP by intraperitoneal injection every day for 5 days/week at the dose of 30mg/kg in a sterile PBS:PEG400 solution starting from post-natal day 28 (PND28) until PND63-65. 2) Npc1-/-Veh mice receiving vehicle (PBS:PEG400); 3) healthy Npc1+/+Veh mice receiving vehicle (PBS:PEG400). At PND63–65 mice were sacrificed by cervical dislocation, hippocampus and cerebellum were immediately dissected and stored at -80°C until RNA extraction (N=4).

first: Federica

last: Fratini

first: Zaira

last: Boussadia

first: Lucia

last: Gaddini

first: Manuela

last: Marra

first: Loredana

last: Le Pera

first: Gloria

last: Venturini

first: Patrizia

last: Popoli

first: Antonella

last: Ferrante


title: The effect of pentafactor (M5) treatment on the transcriptome of keratinocyte cell line HaCaT

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

country: China

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

summary: HaCAT cells were treated with pentafactor (M5) to construct a psoriasis cell model, which was used to study the pathogenesis of psoriasis at the in vitro level. This study aimed to explore the genes activated by pentafactor (M5) treatment.

overall_design: Pentafactor (M5) consists of five cytokines: IL-1α (10 μg/L), IL-17 (10 μg/L), IL-22 (10 μg/L), TNF-α (10 μg/L), and Oncostatin M (10 μg/L). It can induce the proliferation and inflammation of keratinocytes. Its impact on the transcriptome of keratinocytes is mainly reflected in promoting the expression of inflammation-related genes, cell proliferation-related genes, and activating specific signaling pathways

first: Shanshan

last: Qin

first: Dandan

last: Li


title: MicroRNA-146a protects against Hepatocellular Carcinoma through suppression of CCL5

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah

summary: The microRNA miR-146a regulates several aspects of chronic inflammation, including the Hepatocellular Carcinoma (HCC) risk factor hepatosteatosis. Here, we find that loss of miR-146a leads to significantly increased tumor burden in a mouse model of HCC. Notably, this miR-146a-/- phenotype is most pronounced in females, who are typically not sensitive to this model. Mechanistically, we identified increases in dysfunctional CD8+ T-cells that express high levels of CCL5 and resemble Taa cells, as well as elevated levels of myeloid cells that resemble monocytic myeloid-derived suppressor cells (M-MDSCs), a class of myeloid cells that suppress tumor immunity. Deletion of Ccl5 from miR-146a-deficient mice returned tumor growth and the aberrant myeloid cell population to wild-type (WT) levels. Surprisingly, deletion of Ccl5 did not rescue the gross metabolic phenotype observed in miR-146a-/- mice subjected to HCC induction, indicating independent roles for miR-146a in its regulation of HCC and metabolic disease. Taken together, this work reveals a critical host protective role for miR-146a in HCC through suppression of CCL5, providing an impetus for targeting these pathways as a means to combat HCC. Further, the correlations with disease and Taa cells suggest that aging may increase HCC risk through the accumulation of Taa cells.

overall_design: CD45 positive immune cells from C57BL/6 mice either WT or mutant for mir146 and/or Ccl5, and maintained under different diet and carcinogen conditions to young or aged timepoints, were purified from liver cell suspensions by FACS and processed for scRNAseq analysis using a 10x Genomics platform and a Novaseq 6000.

first: Morgan

middle: C

last: Nelson

first: Liam

last: O’Malley

first: Soh-Hyun

last: Lee

first: Kaylyn

middle: M

last: Bauer

first: Arevik

last: Ghazaryan

first: William

middle: W

last: Tang

first: Chad

last: VanSant-Webb

first: Van

last: Tran

first: Colton

last: Hernandez

first: Benjamin

last: Battistone

first: Amber

last: Thibeaux

first: June

middle: L

last: Round

first: Micah

middle: J

last: Drummond

first: H

middle: A

last: Ekiz

first: Kimberley

last: Evason

first: Warren

middle: P

last: Voth

last: O’Connell


title: Highly dynamic dural sinuses support meningeal immunity

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 35/GF-127, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: The central nervous system (CNS) is surrounded by three interconnected membranes referred to as the meninges, which host a diverse immune network1-3. Situated within the skull-interfacing dura mater are venous sinuses, which are large veins thought to serve predominantly as passive blood drains for the brain and skull4,5. However, these structures also represent an important neuroimmune interface6-8. Here, we sought mechanistic insights into this interface using intravital microscopy, revealing that the dural sinuses and associated endothelial cells are a highly dynamic surface that constantly restructures to modulate blood flow, fluid movement, and immune surveillance. Specifically, we demonstrate that sinuses are not passive drains but instead constrict and dilate under RAMP1-dependent smooth muscle control similar to arteries. In addition, the murine superior sagittal sinus is bifurcated into an upper and lower chamber, both comprised of specialized, highly fenestrated endothelial cells that allow the movement of fluids, macromolecules, and microbes between the sinus lumen and leukocyte-rich perisinus space. To protect this permeable interface, sinus endothelial cells (SECs) continually open and close their boundaries in a RAMP2-dependent manner. Transcranial RAMP2 antagonism impeded SEC boundary dynamics and immune cell movement along the sinus wall during steady state and after systemic viral infection. Interference with SEC dynamics during viral infection disrupted local antiviral immunity and facilitated pathogen entry into the meninges. These findings demonstrate that dural sinuses are dynamic venous drains with specialized SECs designed to control fluid movement and support both steady state immune surveillance and antiviral immunity.

overall_design: Pooled cells representing lower sagittal sinus ("SINUS") and rostral-rhinal hub ("HUB") in mouse were prepared for single cell RNA sequencing and sequenced to an average of 35,000 reads per cell.

first: Kelly

last: Monaghan

first: Nagela

middle: G

last: Zanluqui

first: Yijun

last: Su

first: Nicole

last: Peterkin

first: Jared

middle: S

last: Rosenblum

first: Jiamin

last: Liu

first: XiaoYang

last: Wang

first: Harshad

middle: D

last: Vishwasrao

first: Lawrence

last: Latour

first: Dorian

middle: B

last: McGavern


title: MECOM: A novel player in AR-driven Treatment Resistant Castration-Resistant Prostate Cancer

city: Buffalo

first: Remi

last: Adelaiye-Ogala

state: New York

address: 875 Ellicot Street

department: Department of Medicine

institute: University at Buffalo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Reprogramming of the androgen receptor (AR) cistrome is associated with disease progression, and advanced castrate-resistant prostate cancers (CRPC) tend to rely on a reprogrammed/non-canonical AR signaling that is addictive to AR signaling inhibitor (ARSI) resistance. We identified EVI1, an oncogenic nuclear transcription factor, EVI1 coded by MECOM, as a novel AR-recruited co-activator for non-canonical signaling. MECOM is exclusively overexpressed CRPC and enzalutamide-resistant CRPC and interacts with AR in the nucleus. MECOM knockdown cells exhibited decreased proliferation and critical cell survival transcriptional programs, suppressed super-enhancer (SE) activity, and affected non-canonical AR signature profiles. Intriguingly, MECOM overexpression is vulnerable to PARP inhibitors regardless of DDR or HRR gene mutation status. These insights uncover the mechanistic role of MECOM in AR reprogrammed cistrome and its vulnerability. More importantly, this study suggests that MECOM overexpression may be another biomarker that could significantly broaden the use of PARP inhibitors beyond those with HRR gene mutations.

overall_design:
RNA-Seq Profiling of wild type LREX, C42B-ER, CWR-R1 cells and their knockdown derivatives(ShMECOM).
CHIP-Seq Profiling on AR and H3K27ac pull downs on various cell lines LREX, C4-2BER and CWR-R1 wild type and ShMECOM knock down conditions.

last: Adelaiye Ogala

first: Surendra

last: Gulla

first: Tej

last: K Sharma

first: Ephraim

last: Gardner

first: Chennan

last: Li

first: Sean

last: Colligan

first: Cha

last: Xue

first: Shreya Shyam

last: Sundar

first: Brian

last: Capaldo

first: Jonathan

last: E. Bard

first: Tobi

last: Ogunbowale

first: Abbas

last: Jawadala

first: Min

last: Ma

first: Adam

last: Sowalsky

first: Kathleen

last: Kelly

first: Roberto

last: Pili

first: Jun

last: Qu

first: David

last: J VanderWeele


title: PSY Suppresses Colorectal Cancer Progression by Targeting Oncogenic Signaling and Metabolic Reprogramming

city: Seoul

first: Sanghee

last: Han

state: Dongdaemun-gu

address: 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, Republic of Korea

country: South Korea

institute: Kyunghee university

summary: Background: Colorectal cancer (CRC) is a leading cause of cancer-related mortality, driven by dysregulated oncogenic signaling and metabolic reprogramming. PSY, an herbal formula derived from Patriniae Radix, Coix Seed, and Mori Cortex Radicis, has shown potential anti-cancer effects, but its mechanisms in CRC remain unclear. Purpose: PSY’s multi-targeted effects on oncogenic signaling, metabolic pathways, and inflammation in CRC. Materials and Methods: Transcriptomic profiling (RNA sequencing), in vitro assays, and in vivo xenograft models were used to elucidate PSY’s mechanisms. Metabolic profiling via LC-MS/MS and serum lipid analysis were performed to assess its impact on lipid metabolism. Results: PSY activated the PERK/eIF2α/ATF4 stress pathway and suppressed PI3K/Akt/mTOR signaling, inducing apoptosis and inhibiting CRC cell proliferation. Xenograft models showed significant tumor growth suppression and reduced proliferation (Ki67) and inflammation markers (COX2, p-STAT3). Metabolic profiling revealed reduced cholesterol and fatty acid biosynthesis, including arachidonic acid, correlating with COX2 downregulation. Serum LDL and HDL levels decreased, with an increased LDL/HDL ratio. Conclusion: PSY demonstrates potential as a multi-targeted agent by disrupting oncogenic signaling, lipid metabolism, and inflammation in CRC. These findings support its further exploration for clinical applications.

overall_design: RNA-seq was conducted to identify transcriptomic changes in HCT116 colorectal cancer cells treated with PSY for 24 hours, compared to DMSO control.

first: Seok-Geun

last: Lee


title: Age-independent and targetable transcription factor networks regulate CD8+ T cell senescence in aging humans [RNA-seq_RNAi_TFs]

city: Piscataway

first: Ricardo

middle: Iván

last: Martínez Zamudio

state: New Jersey

address: 675 Hoes Lane West

department: Pharmacology

institute: Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School

summary: Aging impairs immunity in part through the accumulation of CD8+ T cells with senescence features, including a pro-inflammatory transcriptome and impaired proliferative capacity. Using senescent cell isolation coupled with multiomic profiling, we defined the epigenetic regulation of CD8+ T cell senescence in healthy younger and older humans. We discovered that the transition to senescence was controlled by chromatin state-specific transcription factor (TF) networks whose composition was largely insensitive to donor age. These TF networks mediated widespread enhancer remodeling, causing repression of genes essential for proliferation as well as upregulation of inflammatory and secretory pathways. Inhibition of AP1, KLF5, or RUNX2 modulated the transcriptional output and partially restored the blunted transcriptional response to stimulation of senescent CD8+ T cells. Our data also revealed CD8+ T cell senescence gene signatures predictive of response to CAR-T cell therapy in diffuse large B cell lymphomas. Overall, our study defines the gene regulatory mechanisms of senescence in human CD8+ T cells, provides a resource for the interrogation of CD8+ T cell senescence in disease, highlights TF network perturbation as a viable strategy to manipulate the senescence state of CD8+ T cells, and reveals senescent CD8+ T cell gene signatures as valuable prognostic tools for immunotherapy outcome.

overall_design: RNA-seq profiling of SA-ßGal-low and SA-ßGal-high CD8+ T cells isolated from the peripheral blood from 3 younger donors. The cells were electroporated with control and small interfering RNAs targeting JUN, KLF5 and RUNX (2  siRNAs per TF) and left either untreated or stimulated with anti-CD3/anti-CD28 antibodies for 16h prior to collection for RNA isolation.

first: Paolo S

last: Turano

first: Elizabeth

last: Akbulut

first: Hannah K

last: Dewald

first: Themistoklis

last: Vasilopoulos

first: Patricia

last: Fitzgerald-Bocarsly

first: Utz

last: Herbig

first: Ricardo Iván

last: Martínez-Zamudio


title: A novel stromal cell source of RANKL during sustained osteoclast activation in disuse osteoporosis

city: Tokorozawa

first: Masahiro

last: Shinohara

state: Saitama

address: 4-1 Namiki

country: Japan

institute: National Rehabilitation Center for Persons with Disabilities

summary: Disuse osteoporosis is a condition characterized by rapid bone loss induced by reduced mechanical loading on bones due to physical inactivity. An increase in osteoclast number is associated with bone loss in disuse osteoporosis. However, the mechanism of osteoclast induction in response to the lack of mechanical loading is not fully understood. To identify potential osteoclast-inducing cells under mechanical unloading conditions, we performed single-cell RNA sequencing (scRNA-seq) of bone and bone marrow cells from immobilized RANKL fate-mapping mice.

overall_design: 8-week-old RANKL-fate mapping mice (Tnfsf11tTA/+; LC1; Rosa26LSL-tdTomato), treated with doxycycline from E0 to birth to suppress labeling during the fetal period, were subjected to hindlimb immobilization for 2 weeks (Control: n=4, Immobilized: n=6). CD45.2-Ter119-tdTomato+ cells were isolated from bone and bone marrow and pooled according to sample group, and scRNA-seq was performed.

first: Kei

last: Gochi

first: Eriko

last: Sumiya

first: Shinichiro

last: Sawa


title: Inherited resilience to clonal hematopoiesis by modifying stem cell RNA regulation [scRNA-seq]

city: Boston

first: Gaurav

last: Agarwal

state: MA

address: 1 Blackfan Circle

department: Division of Hematology/Oncology

institute: Boston Children's Hospital

summary: Somatic mutations that increase hematopoietic stem cell (HSC) fitness drive their expansion in clonal hematopoiesis (CH) and predispose to blood cancers. Although CH frequently occurs with aging, it rarely progresses to overt malignancy. Population variation in the growth rate and potential of mutant clones suggests the presence of genetic factors protecting against CH, but these remain largely undefined. Here, we identify a non-coding regulatory variant, rs17834140-T, that significantly protects against CH and myeloid malignancies by downregulating HSC-selective expression and function of the RNA-binding protein MSI2. By modeling variant effects and mapping MSI2 binding targets, we uncover an RNA network that maintains human HSCs and influences CH risk. Importantly, rs17834140-T is associated with slower CH expansion rates in humans, and stem cell MSI2 levels modify ASXL1-mutant HSC clonal dominance in experimental models. These findings leverage natural resilience to highlight a key role for post-transcriptional regulation in human HSCs, and offer genetic evidence supporting inhibition of MSI2 or its downstream targets as rational strategies for blood cancer prevention.

overall_design: Single-cell transcriptomic profiling by high throughput sequencing

first: Agarwal

last: Gaurav

first: Sankaran

last: Vijay


title: The G Protein-Coupled Receptor GPR31 Promotes Proinflammatory Responses in Pancreatic Islets and Macrophages

city: Chicago

first: Sarah

last: Tersey

state: IL

department: Medicine

institute: University of Chicago

summary: In type 1 diabetes (T1D), the innate and adaptive immune systems attack and eventually destroy the insulin-secreting islet β cells. During this process, β cells activate inflammatory signaling pathways that augment the dysfunction and destruction imposed by cellular autoimmunity. The 12-lipoxygenase (12-LOX) pathway produces the pro-inflammatory eicosanoid 12-HETE, which induces oxidative and endoplasmic reticulum stress and results in diminished insulin secretion and apoptosis. The G protein-coupled receptor 31 (GPR31) has been identified as a putative receptor for 12-HETE. In this study, we generated conventional GPR31 knockout mice. To interrogate the role of GPR31 in β cells, we treated islets from wildtype and Gpr31b-/- mice with proinflammatory cytokines and subjected the islets to RNA sequencing. Differentially expressed genes in Gpr31b-/- islets included those pertaining to receptor signaling, inflammation, oxidative stress, and macrophage migration — effects that are reminiscent of 12-LOX inhibition. Bone-marrow derived macrophages from Gpr31b-/- mice had reduced macrophage migration compared to wildtype macrophages. To mimic islet and macrophage inflammation as seen in T1D, wildtype and Gpr31b-/- mice were treated with the pro-diabetic toxin streptozotocin. Compared to wildtype, Gpr31b-/- mice had improved glucose tolerance and preserved β-cell mass. These results are consistent with previously published data using 12-LOX knockout mice and suggests that GPR31 mediates the proinflammatory responses of 12-HETE in the β cell.

overall_design: To investigate the knockout of Gpr31b in islets, primary islets were isolated from Gpr31b knockout and wildtype mice. Islets were treated with and without proinflammatory cytokines (TNF-α, IFN-γ, IL-1β) for 24 hours. RNA was isolated and processed for RNA-sequencing.

first: Raghavendra

last: Mirmira


title: Spatial single cell transcriptomic analysis of a lineage-traceable mouse model of DICER1 Syndrome informs tumor developmental hierarchy [scRNA-seq]

city: Vancouver

first: David

last: Huntsman

state: BC

address: 675 W 10th Ave

department: Molecular Oncology

institute: BC Cancer Research Centre

summary: DICER1 syndrome predisposes children and young adults to tumor development across various organs. Most of these cancers are sarcomas, which uniquely express the RNase IIIb domain-deficient form of DICER1 and exhibit histological and molecular similarities regardless of their anatomical origins. To uncover their cellular origin and developmental hierarchy, we established a lineage-traceable genetically engineered mouse model allowing for controlled activation of Dicer1 mutations in Hic1+ mesenchymal stromal cells. This resulted in the development of renal tumors closely mirroring human DICER1 sarcoma histologically and molecularly. Spatial single-cell transcriptomics analysis revealed that a Hic1+Pdgfra+Mfap4+ fibroblastic progenitor population, corresponding to perivascular universal fibroblasts of steady-state kidneys, exhibits the capability to undergo rhabdomyoblastic differentiation or transition into proliferative sarcomatous cells. Investigation of patient samples identified analogous cell states and developmental trajectories. This study uncovers a fibroblastic origin for DICER1 sarcoma and provides a faithful model for future mechanistic and translational investigation.

overall_design: Control mice and mice bearing a tamoxifen inducible compound heterozygous Dicer1 -/D1693N  genotype (HDT) were treated with tamoxifen; both express tdTomato in Hic1+ cells. Kidney cells and renal tumor cells were collected at various intervals (range 1-15 months), isolated with fluorescence activated cell-sorting (FACS) for a tdTomato reporter and antibody depletion of EpCAM, CD45, CD31, CD11b, and F4/80. Isolated cells were then analyzed with scRNA-seq.

first: Felix

middle: K

last: Kommoss

first: Joyce

last: Zhang

first: Branden

last: Lynch

first: Shary

last: Chen

first: Janine

last: Senz

first: Yana

last: Moscovitz

first: Lesley

last: Hill

first: Ross

last: Scott

first: Jonathan

last: Bush

first: Andrew

last: Roth

first: Kenneth

first: Gregg

last: Morin

first: Andreas

last: von Diemling

first: Tully

last: Underhill

first: William

last: Foulkes


title: Inherited resilience to clonal hematopoiesis by modifying stem cell RNA regulation [bulk RNA-seq]

first: Gaurav

last: Agarwal

overall_design: RNA-seq profiling of primary human CD34+CD45RA-CD90+ HSPCs, 7 days after CRISPR/Cas9 editing at dual loci to recapitulate germine-somatic interactions between inherited CHIP resilience and somatic ASXL1 mutations (AAVS1+AAVS1-guide2, AAVS1+ASXL1, ENH-1+ASXL1, MSI2-KO+ASXL1). Two independent replicates per condition.

first: Agarwal

last: Gaurav

first: Sankaran

last: Vijay


title: Single-cell transcriptome analysis reveals the association between ketone body synthesis and morphogenic profile of intestinal epithelia in neonatal mice

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

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

summary: The intestinal epithelium undergoes robust maturation postnatally, yet its early-life characteristics remain poorly understood. Using single-cell RNA sequencing, we analyzed intestinal epithelial cells from neonatal (10-day-old) and juvenile (21-day-old) mice reared under both specific pathogen-free and germ-free conditions. Among the various cell types comprising the intestinal epithelia, we found that enterocytes, in particular, exhibit markedly different features between these stages. Enterocytes of neonatal mice show reduced expression of secretory host defense-related genes independently of microbial colonization. These genes are upregulated in juvenile enterocytes in a microbiota-dependent manner. Conversely, neonatal enterocytes display upregulation of ketogenesis-related genes, which correlates with high expression of genes contributing to cell morphogenesis rather than serving primarily as an energy source. These findings provide novel insights into early-life maturation of intestinal epithelia offering implications for understanding neonatal intestinal pathologies.

overall_design: Small intestinal epithelial cells of neonatal and juvenile mice were isolated by flowcytometry and analyzed using single cell RNA-sequencing.

first: Kyoko

last: Mastuki

first: Taiki

last: Sakaguchi

first: Kiyoshi

last: Takeda


title: Miconazole attenuates  LPS-induced lung inflammation by modulating alveolar macrophage polarization  through the regulation of lipid metabolism

city: Hangzhou

first: Yicheng

last: Xie

address: 3333 Binsheng Rd

institute: Children’s Hospital Zhejiang University School of Medicine

summary: Miconazole (MCZ), an antifungal agent with anti-inflammatory potential, was evaluated in a lipopolysaccharide (LPS)-induced mouse model of lung inflammation.MCZ reduced inflammatory cell infiltration, suppressed the expression of inflammatory factors, and alleviated lung injury.Single-cell RNA sequencing revealed that MCZ decreased pro-inflammatory alveolar macrophages (AM1) and increased anti-inflammatory AM2 subsets, accompanied by a shift from lipid synthesis to lipid catabolism.MCZ also disrupted the interactions between inflammatory cells in vitro and regulated the polarization of macrophages by promoting the expression of CD206 and reducing the expression of CD86 and PLIN3.These findings highlight MCZ as a potential therapeutic agent for pulmonary inflammation via lipid metabolic reprogramming and immune modulation.

overall_design: Male ICR mice, aged 6-8 weeks, were purchased from Shanghai SLAC Laboratory Animal Co., Ltd. Lung tissue samples from all mice in the LPS group and the LPS + MCZ group   (LPS + 1 mg/kg MCZ) were collected and pooled for analysis. The left lower lobe of the lung was rapidly excised, placed in cold PBS, and cut into small fragments.

first: Jian

last: Shen


title: Antigen-selected gut IgA is generated from IgG1 germinal center B cells (BCR)

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

summary: Determine whether IgA B cells are derived from IgE B cells during allergy; understand whether IgE and IgA B cells induced during allergy share clonal relationships in the gut.

overall_design: C57Bl/6 WT or GC Fate Reporter (S1PR2CreERT2 Rosa-lsl-tdTomato) mice orally immunized with OVA+CT to generate OVA-specific IgA B cells. In one experiment, WT OVA-specific B cells from MLN, PP, and LP were sequenced for transcriptomes and BCRs. In another experiment OVA-specific B cells from GC Fate Reporter mice were separated based on tdTomato staining (tdTomato+=GC; tdTomato-=nonGC) and sequenced from MLN, PP, and LP.

first: Emily

last: Siniscalco

first: Gisela

last: Gabernet

first: Stephanie

last: Eisenbarth

first: Steven

last: Kleinstein


title: Control of Post-Meiotic Gene Expression by H2A.L.2

city: Grenoble

first: Florent

last: Chuffart

state: La Tronche

address: Site Santé - Allée des Alpes

country: France

institute: IAB - INSERM (U1209) - CNRS (UMR5309)

summary: H2A.L.2 is a specific variant of the H2A histone that accumulates late in the post-meiotic stages of mouse spermatogenesis, coinciding with the appearance of transition proteins (TPs). Since TP accumulation occurs during a period of general transcriptional shutdown, we hypothesized that the accumulation of TP and H2A.L.2 would not influence the transcriptome of condensing spermatids. To test this hypothesis, we isolated total RNA from fractionated mouse spermatogenic cells, including spermatocytes, round spermatids, and condensing spermatids. We then generated transcriptomes from both wild-type cells and cells deficient in H2A.L.2. Analysis of these transcriptomes confirmed our hypothesis, showing no significant differences in gene expression between cells with or without H2A.L.2. These findings suggest that H2A.L.2 plays a structural role in the nucleosome-to-protamine transition rather than a regulatory role in transcription.

first: Naghmeh

last: Hoghoughi

first: Sophie

last: Barral

first: Ekaterina

last: Bourova-Flin

first: Denis

last: Puthier

last: Rousseaux

first: Saadi

last: Khochbin


title: Symbiosis with Tuber indicum and T. panzhihuanense affected the leaf transcriptomic profiles of two tree species

city: Chengdu

first: Xiaoping

last: Zhang

state: Sichuan

address: Huimin Road, Chengdu, 611130, China

department: College of Resources

institute: Sichuan Agricultural University

summary: The understanding of host responses to Tuber colonization would facilitate the exploration of symbiotic interactions and contribute to truffle artificial cultivation. T. indicum and T. panzhihuanense were selected to colonize Pinus armandii and Carya illinoinensis for a two-and-a-half-year symbiosis experiment in this study. The molecular response of host leaf to Tuber symbiosis was analyzed using RNA-seq. T. indicum and T. panzhihuanense both triggered the defense-related regulation in host leaf, like secondary metabolism, cell wall biogenesis, plant hormone signal transduction and plant-pathogen interaction, with different patterns in P. armandii and C. illinoinensis.

sample_organism:
Carya illinoinensis
Pinus armandii

platform_organism:
Carya illinoinensis
Pinus armandii

overall_design: Host seedlings were treated with two truffle inocultaion. Seedlings without inoculation werer taken as control group. After 30 months, RNA-seq profiling of leaves of P. armandii and C. illinoinensis in different groups were conducted.

first: Chen

last: Li

first: Xiaolin

first: Aurélie

last: Deveau

first: Francis

last: Martin


title: Results of the window-of-opportunity PIONEER trial evaluating addition of the progesterone receptor (PR) agonist megestrol to letrozole for early-stage estrogen receptor (ER) positive breast cancer: exploiting ER-PR interaction

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

summary: The use of progestogens in breast cancer has been controversial. Recent preclinical studies have shown that progestogen-bound PR interacts directly with ER and reprograms ER transcriptional activity. Progestogen co-treatment also enhances the anti-tumor activity of anti-estrogen therapy in mouse xenografts. We report PIONEER (NCT03306472), a 198 patient, 3-arm, randomised phase IIb pre-operative window of opportunity study, which evaluated the anti-estrogen letrozole with or without megestrol at 40mg or 160mg daily. The trial met its primary endpoint, with a greater reduction in proliferation seen when megestrol was added to letrozole.  Mechanistically, this effect was accompanied by reduced ER genomic binding at canonical binding sites, indicating reduced ER transcriptional activity. These results support further evaluation of low dose megestrol, which has two parallel mechanisms for potentially improving breast cancer outcomes in combination with standard anti-estrogen therapy: alleviating. In addition to helping patients experiencing hot flashes as a side effect of treatmentand thereby helping with treatment adherence, megestrol has a and also a direct anti-proliferative effect. in breast cancer patients, when combined with standard anti-estrogen therapy.

overall_design: ChIPseq in core biopsies collected from breast cancer patients enrolled in the PIONEER trial before and after 15 days of treatment

first: Rebecca

last: Burrell

first: Sanjeev

last: Kumar

first: Danya

last: Cheeseman

first: Igor

last: Chernukhin

first: Richard

last: Baird


title: ATAD2 drives HIRA/histone H3.3-dependent chromatin dynamics

first: Florent

last: Chuffart

summary: ATAD2, expressed predominantly in embryonic stem cells as well as in spermatogenic cells emerges as a pivotal regulator of chromatin dynamics by mediating chromatin-bound histone chaperone turnover. Here, investigating the role of ATAD2 in spermatogenesis, we show that through its preponderant expression in haploid male germ cells, ATAD2 modulates the HIRA-dependent H3.3 genome localization and H3.3-dependent gene transcriptional regulation. Furthermore, by influencing histone eviction and the assembly of protamines, it ensures proper chromatin condensation and genome packaging in mature spermatozoa. The disruption of Atad2 results in aberrant mature spermatozoa genome organization, impacting male fertility. Collectively, these findings confirm the occurrence of an overlooked chromatin dynamic regulatory level controlling histone deposition-removal balance, depending on an ATAD2-controlled histone chaperone-chromatin interaction.

overall_design: Transcriptomic analysis was performed in mouse testes samples obtained from WT and Atad2 KO homozygote male pups (wt and ko), sacrificed at 20, 22, 24 and 26 days post-birth (d20, d22, d24 and d26).

first: Ariadni

last: Liakopoulou

first: Fayçal

last: Boussouar

first: Daniel

last: Perazza

first: Emeline

last: Lambert

first: Tao

last: Wang

first: Charlyne

last: Gard

first: Christophe

last: Arnoult

first: André

last: Verdel


title: Lysosomal sequestration of PARP inhibitors drives heterogeneous accumulation in ovarian cancer to increase efficacy [Spatial Transcriptomics]

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: PARP inhibitors have had a transformative impact in the treatment of high-grade serous ovarian cancer (HGSOC), but resistance remains a clinical hurdle. Increased expression of ABC drug efflux transporters has been identified as a resistance mechanism in patients but whether intracellular concentrations of these drugs is heterogeneous within tumours remains unclear. We developed a patient-derived explant multi-modal imaging pipeline which demonstrated significant cell-intrinsic heterogeneity of PARP inhibitor accumulation, both between patients and within tumours. Spatial transcriptomics revealed enrichment of apoptotic signatures in high-drug compared to low-drug regions, as well as metabolic and ECM-related differences. While some cases demonstrated a clear anticorrelation of PARP inhibitor levels with MDR1(ABCB1), this was not universal. Rucaparib, an intrinsically fluorescent PARP inhibitor accumulates heterogeneously at the single cell-level in established cell lines, and omics approaches revealed that this is driven by lysosomal sequestration, a pattern also observed in patient samples. Perturbation of lysosomal content altered intracellular levels of rucaparib and niraparib and impacted efficacy suggesting that lysosomes act as a drug reservoir to improve drug response.

overall_design: Spatial Transcriptomics analysis of high-grade serous ovarian cancer patient derived explants treated with niraparib and rucaparib

first: Carmen

last: Ramirez Moncayo

first: Restuadi

last: Restuadi

first: Louise

last: Fets


title: Lysosomal sequestration of PARP inhibitors drives heterogeneous accumulation in ovarian cancer to increase efficacy [RNA-seq]

overall_design: RNAseq of FACS-sorted cells with low and high Rucaparib levels at 2 and 24 hours.


title: Antigen-selected gut IgA is generated from IgG1 germinal center B cells (GEX)

first: Hailong

last: Meng

first: Emily

last: Siniscalco

first: Gisela

last: Gabernet

first: Stephanie

last: Eisenbarth

first: Steven

last: Kleinstein


title: Spatial single cell transcriptomic analysis of a lineage-traceable mouse model of DICER1 Syndrome informs tumor developmental hierarchy [Xenium]

first: David

last: Huntsman

overall_design: Control mice and mice bearing a tamoxifen inducible compound heterozygous Dicer1 -/D1693N genotype (HDT) were treated with tamoxifen; both express tdTomato in Hic1+ cells. Control and HDT kidney and renal tumor tissues, respectively, were formalin-fixed and paraffin-embedded (FFPE). For murine tissue microarray (TMA) construction, 1.0 mm cores of formalin-fixed, paraffin-  embedded (FFPE) tissue from control and HDT mice were used. For spatial transcriptomic analyses, 5 μm sections were obtained from FFPE cores of control and HDT mice and visualized via the 10X Genomics Xenium In Situ Gene Expression platform, using the Mouse Tissue Atlassing Panel, PN1000627.

first: Felix

last: Kommoss

first: Joyce

last: Zhang

first: Branden

last: Lynch

first: Shary

middle: Y

last: Chen

first: Janine

last: Senz

first: Yana

last: Moscovitz

first: Lesley

last: Hill

first: Wilder

last: Scott

first: Jonathan

last: Bush

first: Kenneth

first: Andrew

last: Roth

first: Andreas

last: von Diemling

first: William

last: Foulkes

first: Gregg

last: Morin

first: Tully

last: Underhill

first: Yemin


title: expression data from Arabidopsis Col-0 and avp1 mutants

first: Zhihang

last: Feng

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.388,Zhejiang Province,P.R.China

institute: Zhejiang University

summary:
Plant vacuolar mPPase AVP1 is essential for plant development and growth, genetic modification of AVP1 and its orthologs in crops have been shown to alter normal plant growth and responses to various abiotic stresses, such as drought and salinity stresses. Until now, the transcriptional reprograming in repsonse to the disruption of AVP1 remains elusive.
We used microarrays to detail the global programme of gene expression underlying the contribution of Arabidopsis AVP1 in repsonse to a continous low calcium treatment.

overall_design: Shoots from 14-day-old seedlings of Col-0 and one of the avp1 mutant (lcs7), grown on Yamagami agar plates supplied with either 2 mM Ca or 0.3 mM Ca, were used for RNA extraction and hybridization on Affymetrix microarrays. Three independent biological replicates were sampled for each genotype under the given conditions.

first: Takehiro

last: Kamiya

first: Baohai

last: Li


title: Antigen-selected gut IgA is generated from IgG1 germinal center B cells

first: Hailong

last: Meng

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

overall_design: Refer to individual Series


title: Caspofungin interferes with Candida albicans iron homeostasis

city: Oeiras

first: Catarina

last: Pimentel

state: Lisboa

address: Av. da República

department: MOSTMICRO

country: Portugal

institute: ITQB NOVA

summary: In this study we used a transcriptomic approach to determine whether caspofungin could impact iron homeostasis in Candida albicans, the most frequent cause of invasive candidiasis. Caspofungin affects iron homeostasis by inducing a high iron response. Caspofungin treatment leads to a downregulation of genes involved in iron uptake, while genes associated with iron storage and detoxification, as well as the transcription factor SFU1 that regulates the cell response to high iron, are upregulated.

overall_design: RNA-Seq of Candida albicans SC5314 cells exposed to FeSO4, caspofungin or both compounds was compared to untreated cells.

first: Andreia

last: Pedras


title: miRNA expression of upcyte human hepatocytes treated with valproate (VPA) 4mM, fatty acids (OP) 0,6 mM or vehicle (PBS)

city: Valencia

first: Ramiro

middle: Jover

last: Atienza

state: Valencia

address: Avenida Fernando Abril Martorell, 106.

department: Experimental Hepatology Unit

country: Spain

institute: IIS Hospital La Fe

summary:
Valproate (VPA) has been the first line, most-frequently prescribed anti-epileptic drug in children for the past 50 years. VPA causes, in some patients, idiosyncratic hepatotoxicity, which very often presents with hepatic steatosis. Experimental studies also support that VPA has a high potential to induce steatosis
The aims of this study are to demonstrate VPA-induced triglyceride (TG) accumulation in cultured human upcyte hepatocytes, to identify miRNAs that are deregulated by VPA and associated with TG levels in these cells, and to test these miRNAs, as potential non invasive biomarkers, in plasma of paediatric epileptic patients on VPA, to identify those with a potential risk of liver steatosis

overall_design: Human upcyte hepatocytes were exposed to subcytotoxic VPA concentrations. Hepatocytes increased intracellular TGs by 27% and 45% after 2 and 4 mM VPA for 24 h. The profiling of cellular miRNAs after 4 mM VPA by microarray analysis identified 43 deregulated human miRNAs

first: Jover Atienza

last: Ramiro

first: Soluyanova

last: Polina

first: Moro Castaño

last: Erika

first: Marco-Hernandez

last: Ana V.

first: Castell

last: Jose V.


first: Florent

last: Chuffart

first: Ariadni

last: Liakopoulou

first: Fayçal

last: Boussouar

first: Daniel

last: Perazza

first: Sophie

last: Barral

first: Emeline

last: Lambert

first: Tao

last: Wang

first: Ekaterina

last: Bourova-Flin

first: Charlyne

last: Gard

first: Denis

last: Puthier

last: Rousseaux

first: Christophe

last: Arnoult

first: André

last: Verdel

first: Saadi

last: Khochbin


title: Gene regulatory network determinants of rapid recall in human memory T cells [WGS]

city: Cincinnati

first: Artem

last: Barski

state: OH

address: 3333 Burnet Av

department: Allergy

institute: Cincinnati Children's Hospital

summary: We applied sc-multiome-seq technology (tandem transcriptome and chromatin accessibility) to a TCR activation time course of naive and memory human CD4+ T cells, to elucidate the molecular drivers of rapid recall at genome scale. WGS data were used to deconvolute donors within the same scMultiome library.

overall_design: Whole genome sequencing and variant calling: DNA was isolated using a PureLink Genomic DNA Kit (Thermo Fisher). Whole-genome sequencing was performed at Novogene.

first: Alex

last: Katko

first: Svetlana

last: Korinfskaya

first: Michael

last: Kotliar

first: Leah

last: Kottyan

first: Emily

last: Miraldi

first: Sarah

last: Potter


title: Resetting proteostasis with calumenin prevents the aggregation of misfolded vimentin during organ fibrosis

city: JiNan

first: Kaige

last: Lyu

state: ShanDong

address: SCHOOL OF PHARMACY ROOM 612, NEW SCIENTIFIC RESEARCH BUILDING OF PHARMACY  NO.44 WENHUA XI ROAD JINAN SHANDONG 250012 CHINA

institute: ShanDong University

summary: Calumenin maintain vimentin proteostasis to prevent organ fibrosis

overall_design: Cells were lysed in TRIzol reagent, and total RNA was extracted by using a Rapid RNA Extraction Kit per the manufacturer’s protocol. The integrity of the RNA was verified via agarose gel electrophoresis, and the RNA concentrations were quantified with a NanoDrop spectrophotometer. RNA-Seq libraries were prepared and sequenced on an Illumina NovaSeq 6000. The index of the reference genome was built by using HISAT2 (v2.0.5), and paired-end clean reads were aligned to the reference genome.

first: Ting

last: Dong

first: Xue

last: Jiao

first: Huirui

first: Yinghui

last: Gao


title: Gene regulatory network determinants of rapid recall in human memory T cells

summary: Rapid recall is the hallmark of memory T cells. While naïve T cells require days to mount an effector response to a new threat, antigen-experienced memory T cells can produce cytokines within hours of the repeatencounter. The establishment of memory and control of rapid recall across lifespan is poorly understood, yet the mechanisms are fundamental to pathogen defense and immunological diseases. Epigenetic poising is a likely mechanism. Indeed, compared to naïve, memory cells exhibit enhanced chromatin accessibility proximal to rapid recall genes, but the transcription factors (TFs) that establish, maintain and utilize these putative regulatory elements are unknown. Here, we leverage single-nuclei (sn)multiome-seq (simultaneous snRNA-seq and snATAC-seq) to (1) characterize the dynamic activation responses of naïve and memory CD4+ T cell subsets and (2) reconstruct the underlying gene regulatory networks, at genome scale.  Our analysis uncovered thousands of genes and putative regulatory elements with rapid-recall dynamics, shared and unique across the several memory populations. A core of memory-associated TFs (MAF, PRDM1, RUNX2, SMAD3 and KLF6) was predicted to orchestrate rapid recall and maintain accessible chromatin at rapid-recall gene enhancers in resting memory cells.  KLF6 binding to its predicted target genes was confirmed by ChIP-seq, while the memory-associated activities of all five factors replicated in independent scRNA-seq studies. Using GWAS to link our T cell populations and their dynamic chromatin landscapes to human phenotypes, we nominate CD4+ T cell populations, rapid recall responses and gene regulatory mechanisms that might mediate genetic risk to autoimmune and inflammatory diseases.

overall_design:
We applied sc-multiome-seq technology (tandem transcriptome and chromatin accessibility) to a TCR activation time course of naïve and memory human CD4+ T cells, to elucidate the molecular drivers of rapid recall at genome scale. WGS was used to deconvolute donors. ChIP-sequencing of a CD4T cells stimulated for 5 hours was performed with two separate KLF6 antibodies to confirm the GRN-predicted role of KLF6.
Suspensions of primary hCD4 T cells from healthy donors were partially depleted of CD27+ cells (TCM and naive populations) to improve resolution of TEM populations. TCR stimulation time course includes four time points: resting, 2.5h (early activation), 5h (peak activation for memory cells), and 15h (late activation), for a total of 16 scMultiome-Seq experiments (4 time points x 4 donors; each sample includes fifth spike-in resting control donor cells).

first: Sarah J


title: Effect of gastodin (GAS) on gene expression of CAR 11-3 T cells

city: Beijing

first: Shuai

last: Huang

address: yangfangdianxi 1

institute: beijingshijiytan hospital

summary: To investigate the mechanism of how GAS promotes CAR11-3 migration on transcriptional level.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of CAR11-3 T cells treated by GAS at two time points.Comparative gene expression profiling analysis of RNA-seq data forCAR11-3 T cells treated with GAS or not.


title: Global RNA stability profiling upon silencing of CPSF6 in HepG2 cells

city: Guangzhou

first: Keren

last: Zhou

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

summary: RNA binding proteins often paticipate in the regulation of RNA deday. Here, we present the global RNA statility profiling upon silencing of CPSF6 in HepG2 cells by  Actinomycin D treatment.

overall_design: RNA stability assay were carried out according to the previous methods with some modifications. HepG2 cells were transfected with CPSF6 siRNAs which were purchased from RiboBio (China) into 12 well plates and cultured for 48h to get 80% confluence. Then cells were treated with 5ug/ml Actinomycin D (Selleck, America) and harvested at 0h, 3h and 6h with Trizol. Total RNA were finally analyzed using qRT-PCR and RNA sequencing (RNA-seq). According to the ratio provided in the instruction, ERCC spike-in RNA (Thermo Fisher) were added into 5μg total RNA following with construction for mRNA sequencing libraries with NEBNext Ultra Directional RNA library Prep Kit. RNA stability profiling was generated from two biological replicates.

first: Shurong

last: Liu

first: Jianjun

last: Chen

first: Jianhua

last: Yang

first: Bin

last: Li

first: Lianghu

last: Qu


title: Effect of Ttc22 exon2-3 deficiency on gene expression in colon tissues of C57BL mouse

first: Wei

last: Tian

state: Beijing

address: Fu-Cheng-Lu #52, Haidian District

institute: Peking University Beijing cancer hospital

summary: To inspect the funtion of Ttc22 gene in colon of Ttc22 knockout mice, high-throughput mRNA sequencing of colon from Ttc22+/+/Ttc22+/-/Ttc22-/- mice (male, 58 weeks old) was carried out.   RNA-sequencing unveils that the differentially expressed genes in colon tissues from Ttc22-/- mice were mainly enriched within pathogen infection- and immuno-related system.

overall_design: Total RNA was isolated from the colon tissues of Ttc22+/+/Ttc22+/-/Ttc22-/- mice (n=3) using an RNA Extraction Kit. RNA high throughput sequencing was performed by Cloud-Seq Biotech (Shanghai, China). Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina NovaSeq 6000 instrument with 150bp paired end reads. Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA.

first: Gu

last: Liankun

first: You

last: Abin

first: Deng

last: Dajun


title: Zmiz1-dependent Native Stem Cell Transcriptional Circuits in Normal and Malignant Immature T cells [RNA-seq]

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary:
The discovery of early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) was based on expression of stem cell genes that are characteristic of mouse ETP cells, the most primitive multipotent cells in the thymus. Using complementary mouse and human genetic models and genome-wide expression and chromatin profiling integrated with 3D chromatin mapping, we show that the PIAS-like coactivator ZMIZ1 promotes immature T-ALL proliferation by recruiting the transcription factor MYB in feedforward circuits to cooperatively induce MYCN, MEF2C, and BCL2, which were recently associated with the high-risk bone marrow progenitor (BMP-like) subset.
In the first experiment (Batch RS6)  short hairpin RNAs shZMIZ1-13 (L13) and shZMIZ1-15 (L15) target the gene ZMIZ1
In the second experiment (Batch RS7)  the gene MYB is knocked down.

overall_design: RNA-Seq analysis of LOUCY cells, a human immature T-ALL cell line, that was transduced with shControl, shZMIZ1-13, shZMIZ1-15, and shMYB . Four biological replicates were performed for each shRNA.

first: Mark

last: Chiang


title: Genetic rescue of mitochondrial complex I reverses metabolic defects in circadian mutant mice

first: Joseph

last: Bass

address: 303 E Superior St, Lurie 7-220

institute: Northwestern University

summary:
We used single nuclei RNA-seq to compare gene expression from adipocyte circadian mutant mice +/- expression of the yeast NADH dehydrogenase (NDI1).

We used RNA-sequencing of fractionated adipocytes from the visceral white adipose tissue of control mice, mice lacking the circadian clock activator Bmal1, and mice lacking the mitochondrial complex I subunit Ndufs2.

overall_design:
Visceral white adipose tissue (WAT) was isolated from 3-month old male mice and was homogenized, followed by filtering and centrifugation to isolate nuclei. Nuclei were then analyzed for single nuclei RNA-sequencing with 10X genomics.

Bulk RNA-seq: Visceral white adipose tissue (WAT) was isolated from 3-month old male mice and was digested with collagenase followed by differential centrifugation to float the adipocytes. The adipocyte fraction was then homogenized followed by RNA isolation, library preparation, and sequencing.

first: Chelsea

last: Hepler

first: Nathan

last: Waldeck

first: Joe


title: Spatial Transcriptomics in the Human Left Atrial Appendage and Pulmonary Vein Sleeve

city: Cleveland

first: Han

last: Sun

address: 9500 Euclid Ave

department: QHS

institute: Cleveland Clinic

summary: Human left atrial appendage (LAA) and pulmonary vein (PV) tissues were obtained from unused lung or heart transplant donors.  Paired LAA and PV sleeve tissues were obtained from two subjects, and an additional 6 PV samples were obtained from other donors.  After tissue sectioning and staining, spatial RNAseq was performed.  mRNAs from~1000 to 2500 genes were sequenced  in each spatial area.  Seurat clustering yielded 15 different clusters. These grossly split into two segregating populations, the left and right sides, with one connecting population.  Multiple cells and cell types may reside in each 55 µm diameter spatial area. A clear asymmetry of clusters was observed in the PV sections, with less asymmetry in the LAA sections. Cell-type marker genes derived from human LAA single nuclei RNAseq were used to determine the dominant cell types in the 15 different clusters.  The left side segregating clusters were enriched in cardiomyocytes, while the right side segregating clusters were enriched for other cell types including fibroblasts, vascular smooth muscle cells, endothelial cells, and adipocytes.  Spatial transcriptomics clearly resolved the venous, cardiomyocyte, and epicardial regions of the PV tissues, as well as fibrotic regions in LAAs and PVs.  Spatial expression of the AF-associated genes PITX2, SHOX2, and HCN4 was also mapped, confirming higher expression of the cardiac master transcription factor SHOX2 in the PV vs. LAA tissues.  Expression of the hyperpolarization-activated ion channel HCN4 was sporadic in both PV and LAA specimens.

overall_design: Human frozen tissues were sectioned, placed on 10X Genomics Visium sldies and processed for RNAseq by spatial region.

first: Juying

last: Han

first: Christine

last: Moravec

first: Toshihiro

last: Okamoto

first: Kenneth

last: McCurry

first: A

last: Gillinov

first: Mina

last: Chung

first: Davd

last: Van Wagoner

first: John

last: Barnard

first: Jonathan

last: Smith


title: Suppression of Notch during efferocytosis prevents macrophages inflammatory polarization [RNA-seq.HumanMouse]

status: Public on Jan 08 2026

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: We investigated the mechanism of suppression of Notch during efferocytosis. Genetically activation of Notch or ablation of Rubicon in marophages induced pro-inflammatory polarization and enhance anti-tumor effect.

overall_design: We performed RNA seq and slam-seq in the presence or abscence of apoptotic Jurkat cells to study how genes expression is regulated during efferocytosis in different genotypes.

first: Zhenrui

last: Li

first: Douglas

last: Green


title: Cardiac Thoracic DRG Poly RNAseq Data in rats post MI

status: Public on Jan 04 2026

city: Omaha

first: Hanjun

last: Wang

state: Nebraska

address: 984455 University of Nebraska Medical Center 985850 University of Nebraska Medic

department: Anesthesiology

institute: University of Nebraska Medical Center

summary: The overall goal is to detect any signficant changes in the rat thoracic DRG mRNA expressions post myocardial infarction.

overall_design: Thoracic DRGs were collected 8 weeks after MI or sham surgery (MI, n = 5; sham, n = 4). mRNA libraries were prepared on an Illumina NextSeq, generating 75bp reads. Demultiplexing used bcl2fastq v2.16.0.10. Adapters and low-quality bases were trimmed with cutadapt. Reads were aligned to the Rattus norvegicus rn6 reference with STAR v2.3.0. Gene-level counts were summarized against Partek v6.6 annotations (Partek Inc., St. Louis, MO, USA). Library sizes were normalized with the trimmed mean of M-values (TMM) method. Differential expression for MI versus SHAM was modeled in edgeR using a generalized linear model with likelihood-ratio tests and Benjamini-Hochberg FDR control.

first: Samuel

last: Gillman


title: RNA-seq analysis of QRICH1 knockdown in Huh7 cells

city: Seoul

first: Su-Yeon

last: Park

state: National Research Foundation of Korea

address: Cancer Molecular Targeted Herbal Research Center, College of Korean Medicine, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 02447, South Korea

institute: Kyung Hee University

summary: This study investigates the transcriptomic changes following QRICH1 knockdown in Huh7 hepatocellular carcinoma cells using RNA sequencing.

overall_design: This study includes RNA-seq profiling of Huh7 hepatocellular carcinoma cells under two experimental conditions: siControl and siQRICH1 knockdown. Biological replicates were generated for each condition, and differential gene expression analysis was performed to investigate transcriptional changes associated with QRICH1 depletion.


title: Regulation of gene expression by clay minerals

city: Vernon Hills

first: DONGPING

last: WANG

address: 777 Forest Edge Dr

department: Amlan

institute: OilDri Corporation of America

summary: Transcriptome analysis reveals over 50 gene transcripts showed significant changes due to sorbent mineral treatment. Mineral treatment results in a transcriptome profiling skewed towards inhibition of P. aeruginosa’s virulence network. The sorbent mineral interferes with several bacterial activities, including quorum sensing, iron scavenging, cytotoxicity, biofilm formation and immune evasion.

overall_design: Pseudomonas aeruginosa cultures treated by clay minerals are compared to cultures without clay treatment

first: Dongping


title: Plasminogen lipid cargo drives macrophage TLR2 activation independent of protease activity

city: Nashville

first: Danielle

last: Michell

state: TN

address: 2220 Pierece Ave

institute: Vanderbilt Univ. Medical Center

summary: Plasminogen (Plg) is a highly abundant, liver-secreted plasma protein and zymogen precursor of plasmin, a key serine-protease in fibrinolysis. Zymogen Plg (Glu-Plg) has been reported to transport extracellular RNA, cholesterol, and oxidized phospholipids (oxPL) cargo which likely defines the biological functions of non-enzymatic Plg particles, including immunogenicity towards innate immune cells. Here, we demonstrate that native Plg dose-dependently activates NF-kB transactivity, pro-inflammatory gene expression and cytokine secretion in primary macrophages through toll-like receptors, i.e., toll-like receptor 2 (TLR2), as identified through a TLR screen. Plg stimulation of macrophages and NF-kB transactivity reporter cells were sensitive to small molecule inhibitors of TLR2, and Tlr2 and Myd88 genetic-deficiency. Plg treatments were found to stimulate both mouse and human primary macrophages but failed to activate microglial cells and vascular smooth muscle cells. Both C29, and its derivative ortho-vanillin, were found to inhibit macrophage TLR2 signaling and cytokine secretion in vitro, as profiled by proximity extension assays (PEA). Plg activation of TLR2 was observed to be independent of Plg’s conversion to plasmin or down-stream plasmin protease activity, as Plg stimulation of TLR2 were not affected by active-site mutagenesis, lysine analogues ε-aminocaproic acid and tranexamic acid, VPLCK peptide inhibitor, α2-anti-plasmin, α2-macroglobin, or urokinase plasminogen activator (uPA, Plau-/-) and tissue plasminogen activator (tPA, Plat-/-) macrophage deficiency. Mass spectrometry-based untargeted lipidomics demonstrated the full profile of bioactive lipids covalently bound or loosely associated with human Plg particles. Plg’s immunogenicity towards macrophages was found to be dependent, in part, through lipid cargo, as lipid removal with lipases and organic lipid extractions were found to reduce Plg’s capacity to activate macrophages. Plg-deficiency in hypercholesterolemic mice were observed to be associated with reduced atherosclerosis and intravenous injections of ortho-vanillin were found to significantly reduce lesion area and alter macrophage sub-phenotypes in mouse lesions, as per single cell RNA sequencing. Results from these studies support that Glu-Plg’s lipid cargo and TLR2 may be viable drug targets to reduce chronic inflammation without compromising fibrinolysis.

overall_design: Total RNA sequencing of bone marrow-derived macrophages treated with and without human plasminogen for 24h

first: Danielle L.

first: Kasey C.

last: Vickers


title: Effect of SOD1K123R mutation on gene expression in nucleus pulposus cells treated with lactate.

city: Chongqing

first: Yuyao

last: Zhang

address: No.83, Xinqiao Zhengjie, Shapingba District

institute: Xiqiao hospital

summary: Among musculoskeletal disorders, intervertebral disc degeneration (IVDD) is the primary cause of discogenic pain and associated disability and productivity loss in the workforce worldwide.Oxidative stress is an important inducing and aggravating factor of intervertebral disc degeneration. We found that lactate could induce the lactylation of SOD1 lysine 123 in nucleus pulposus cells, which impaired the antioxidant ability of the enzyme. Therefore, we mutated lysine (Lys) to arginine (Arg) at residue 123 of SOD1 in nucleus pulposus cells to eliminate the lactylation at residue 132 and investigated the underlying mechanism by RNA sequencing.

overall_design: After knocking down SOD1 in nucleus pulposus cells, RNA-seq was performed after transfection of wild-type SOD1 and K123R mutant SOD1 with 10 mM lactate for 7 days

first: Yu

last: Zhai

first: Lin

last: Chen

first: Minghan

last: Liu

first: Changqing


title: SOX11 Downregulation and IL-7/IL22RA2 Upregulation Might be a Potential Mechanism of Exosome in Promoting Schwann Cell Proliferation

city: Yinchuan

first: He

last: ZhongYi

address: No. 1160, Shengli Street, Xingqing District

institute: Ningxia Medical University

summary: The characterization process was performed by transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA), and Western blot. SCs were co-cultured with menstrual blood-derived MenSCs-Exos to assess their proliferation through CCK-8 assay and flow cytometry. RNA-Seq was utilized to identify differentially expressed genes (DEGs) linked to SC proliferation. DEGs were subjected to GSEA and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Several DEGs were validated by qRT-PCR and Western blot. Results: MenSCs exhibited osteogenic and adipogenic differentiation potential, and MenSCs-Exos demonstrated typical exosomal characteristics. These exosomes were efficiently internalized by SCs, promoting their proliferation and cell cycle progression. RNA-Seq identified 113 DEGs (60 upregulated and 53 downregulated genes) in the MenSCs-Exos-treated SCs. Compared to the MenSCs-conditioned medium group, 18 specific DEGs were further identified and found to be enriched in pathways related to cytokine signaling, mitochondrial function, and autophagy. qRT-PCR and Western blot showed notably upregulated IL22RA2 and IL-7 expression and a reduction in SOX11 level.

overall_design: SCs were co-cultured with menstrual blood-derived MenSCs-Exos，plated and treated with either MenSCs-CM (referred as M-SCs group) or MenSCs-Exos (referred as E-SCs group). Employing Trizol reagent (Invitrogen, USA), total RNA was isolated from three groups, namely, control SCs (SCs group), SCs treated with MenSCs-CM (M-SCs group), and SCs treated with MenSCs-Exos (E-SCs group).RNA-Seq was utilized to identify differentially expressed genes (DEGs) linked to SC proliferation.


title: Mouse myocardial infarction

city: Harbin

first: Feiyong

state: Heilongjiang Province

address: 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province

department: College of Pharmacy

institute: Harbin Medical University

summary: Cardiac ischemia-reperfusion (I/R) injury is a leading cause of disability and mortality worldwide, but the underlying mechanism remains largely unknown. Despite the emerging recognition of circular RNAs (circRNAs) as pivotal regulators in cardiac development and disease, their roles in cardiac I/R injury have yet to be thoroughly investigated. In this study, we identified a circRNA, named circArhgap26, which was regulated by m6A-modification.

overall_design: All mice were treated with sham operation and myocardial infarction for 1 Day (n=3 per group).  Arraystar arrays were performed according to the manufacturer's directions on RNA extracted from cardiac tissue. Total RNA was extracted from each sample using TRizol Reagent according to the protocol from manufacturer. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Arraystar Mouse mRNA and ncRNA Microarray V3.0 is applied for the global profiling of mouse lncRNAs and protein-coding transcripts. About 35,923 lncRNAs and 24,881 coding transcripts can be detected by our third-generation mRNA and lncRNA microarray.

first: Mingyu


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

first: Zehao

last: Guo

address: zhongshan 2 road

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

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Extracellular vesicles (EVs) isolated from different cell lines were subjected to lncRNA sequencing.

first: Xianbiao

last: Xie

first: Hongbo


title: Alkaloids from Evodia rutaecarpa Inhibit the Occurrence and Development of Gallbladder Cancer In Vivo and In Vitro

city: Shanghai

first: Yijie

address: No. 160 Lanxi Road, Putuo District

department: Putuo Hospital

institute: Shanghai University of Traditional Chinese Medicine

summary: Gallbladder cancer (GBC) poses a significant health burden with dismal prognosis due to frequent metastasis and recurrence. Although evodiamine has demonstrated potent inhibitory effects on proliferation and metastasis in various cancers, its role in GBC remains unexplored, and the underlying mechanisms are yet to be elucidated.

overall_design: :The inhibitory effects of evodiamine on GBC cells were evaluated in vitro using a cell viability assay. Cell migration capacity was assessed via wound healing and Transwell assays. Apoptosis and cell cycle distribution were analyzed by flow cytometry and Western blotting (WB). The molecular mechanisms were investigated using Quantitative polymerase chain reaction (qPCR) and WB to quantify ZEB1 gene expression. In vivo, the anti-tumor activity of evodiamine was verified in a nude mouse model.


title: Effect of HIF-1alpha knockout in gene expression profile of osteosarcoma cells in vivo.

city: Tokyo

first: Takatsune

last: Shimizu

address: 2-4-41, Ebara, Shinagawa-ku

department: Pathophysiology

institute: Hoshi University

summary: To explore in vivo changes in gene expression of osteosarcoma cells upon depletion of HIF-1alpha we performed RNAseq analysis using Mock control AXT cells and HIF-1alpha KO AXT cells. HIF1alpha was knocked out using CRISPR-Cas9 with two different target sequences. KO1-1 and KO1-2 cells are derived from target sequence#1:5’- AGATGTGAGCTCACATTGTGGGG -3’ (exon3) and KO2 cells are from  #2:5’-GCTAACAGATGACGGCGACATGG-3’ (exon5). AXT cells were established from BMSCs of Ink4a/Arf null mouse by overexpressing human c-MYC (Shimizu T, et al. Oncogene, 2010).

overall_design: 2x10^6 Mock control cells and HIF-1alpha KO cells emmbedded in matrigel were inoculated into C57BL/6scid mice and harvested tumors next day. Tumors were disrupted using a BioMasher (Nippi, Tokyo, Japan) and total RNA was extracted.


title: 35 somites tail single cell RNAseq in control and homocysteine treated chicken embryo

city: Clermont-Ferrand

first: Felipe

last: Maurelia

address: 28, place Henri Dunant - BP 38

institute: iGRED

overall_design: LMO multiplexing of single cells prior to BD Rhapsody single cell encapsulation

first: Stephanie

last: Maupetit-Mehouas

first: Nicolas

last: Allègre

first: Yoan

last: Renaud

first: Pouria

last: Hosseinna

first: Jonas

last: Cruzel

first: Claire

last: Chazaud

first: Charlène

last: Guillot


title: Multi-tissue transcriptomic aging atlas reveals predictive aging biomarkers in the killifish

city: Stanford

first: Jingxun

state: CA

address: 290 Jane Stanford Way, Room E365

department: Genetics

institute: Stanford University - Stanford, CA

summary: Aging is associated with progressive tissue dysfunction, leading to frailty and mortality. Characterizing aging features, such as changes in gene expression and dynamics, shared across tissues or specific to each tissue, is crucial for understanding systemic and local factors contributing to the aging process. We performed RNA-sequencing on 13 tissues at 6 different ages in the African turquoise killifish, the shortest-lived vertebrate that can be raised in captivity. This comprehensive, sex-balanced 'atlas' dataset reveals the varying strength of sex-age interactions across killifish tissues and identifies age-altered biological pathways that are evolutionarily conserved. Demonstrating the utility of this resource, we discovered that the killifish head kidney exhibits a myeloid bias during aging, a phenomenon more pronounced in females than in males. In addition, we developed tissue-specific 'transcriptomic clocks' and identified biomarkers predictive of chronological age. We show the importance of sex-specific clocks for selected tissues and use the tissue clocks to evaluate a dietary intervention in the killifish. Our work provides a comprehensive resource for studying aging dynamics across tissues in the killifish, a powerful vertebrate aging model.

overall_design: These samples are to be added to GSE308970. This dataset includes gene expression profiling analysis (by RNA-seq) for FACS-sorted cells from head kidney of male killifish. The protocol included in this metadata file only applies to these five samples below, but not any other sample in the submission.

first: Emma K

last: Costa

first: Ian H

last: Guldner

first: Man-Ru

last: Wu

first: Param P

last: Singh

first: Anne

last: Brunet

first: Tony

last: Wyss-Coray


title: RNA-seq analysis of lung tissue in young mice versus old mice

city: Jinan

first: Huirui

last: Wang

state: -- None selected --

address: 44 Wenhuaxi Road

institute: Shandong University

overall_design: Lung tissues were collected from young mice (3-month-old) and old mice (18-month-old), washed with PBS, cut into appropriate sizes, and total RNA was extracted for RNA-seq sequencing.

first: Ting

last: Dong

first: Yinghui

last: Gao


title: Clariom D Pico gene array of primary GBM cells grown as 3D (LD⁺) spheroid cultures or 2D (LD⁻) cultures

city: Lund

first: Mattias

last: Belting

address: Barngatan 4

department: Department of Clinical Sciences, Division of Oncology

country: Sweden

institute: Lund University

summary:
In this study, we aimed to elucidate the molecular underpinnings of metabolic adaptation in the stressed TME. LD accumulation has been well documented in glioblastoma (GBM), a prototypical high-grade brain malignancy characterized by severe acidosis, hypoxia, and metabolic heterogeneity. Unexpectedly, we observed a prominent enrichment of pathways related to glycocalyx remodeling in the LD-rich niche of patient tumors, particularly those involving CS biosynthesis and PG regulation. These findings prompted us to explore how glycan remodeling intersects with lipid metabolism in GBM and whether this interaction contributes to tumor stress adaptation. Our results highlight an acidosis-induced glycan program with potential as a metabolic vulnerability, offering new therapeutic avenues for targeting the lipid-stressed niche in aggressive tumors.
We used microarrays to evaluate transcriptional signature realted to 3D (LD⁺) cultures compared to 2D (LD⁻) cultures from primary glioblastoma (GBM) cell line.

overall_design: Primary cell cultures derived from three independent GBM patients were grown in 3D (LD⁺) and 2D (LD⁻) cultures. In total 18 samples (6 types of samples in three biological replicates) underwent RNA extraction with AllPrep DNA/RNA Micro Kit for RNA, and hybridization on Affymetrix Clariom Human D Pico microarray cartrige. Gene expression profiles obtained from  3D (LD⁺) cultures were compared to the profile  2D (LD⁻) cultures for each primary cell line.

first: Anna

last: Bång-Rudenstam

first: Myriam

last: Cerezo-Magaña

first: Marton

last: Horvath

first: Hugo

last: Talbot

first: Emma

last: Gustafsson

first: Stevanus

last: Jonathan

first: Chaitali

last: Chakraborty

first: Itzel

last: Nissen

first: Kelin

last: Gonçalves de Oliveira

first: Axel

last: Boukredine

first: Sarah

last: Beyer

first: Julio

last: Enriquez Perez

first: Maria

last: C Johansson

first: Lena

last: Kjellén

first: Emil

last: Tykesson

first: Anders

last: Malmström

first: Toin

last: H van Kuppevelt

first: Karin

last: Forsberg-Nilsson

first: Jeffrey

last: Esko

first: Silvia

last: Remeseiro

first: Johan

last: Bengzon

first: Valeria

last: Governa


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

city: Guangzhou

first: Zehao

last: Guo

overall_design: Nude mice were injected with 143B-derived EVs or MNNG/HOS-derived EVs via the tail vein, followed by RNA sequencing of lung tissues.

first: Xianbiao

last: Xie

first: Hongbo

last: Li


title: Clariom D Pico gene array of acidosis adapted and control PANC1 pancreatic cancer cells

first: Mattias

last: Belting

summary:
In this study, we aimed to elucidate the molecular underpinnings of metabolic adaptation in the stressed TME. LD accumulation has been well documented in glioblastoma (GBM), a prototypical high-grade brain malignancy characterized by severe acidosis, hypoxia, and metabolic heterogeneity. Unexpectedly, we observed a prominent enrichment of pathways related to glycocalyx remodeling in the LD-rich niche of patient tumors, particularly those involving CS biosynthesis and PG regulation. These findings prompted us to explore how glycan remodeling intersects with lipid metabolism in GBM and whether this interaction contributes to tumor stress adaptation. Our results highlight an acidosis-induced glycan program with potential as a metabolic vulnerability, offering new therapeutic avenues for targeting the lipid-stressed niche in aggressive tumors.
We used microarrays to evaluate transcriptional signature of adaptation to acidosis (pH 6.4) in PANC1 pancreatic cancer cells.

overall_design: PANC1 pancreatic cancer cells were adated to acidic condition (pH 6.4) or not (non-adapted= control) during 10 weeks. In total 6 samples (2 types of samples in three biological replicates) underwent RNA extraction with RNAeasy mini kit, and hybridization on Affymetrix Clariom Human D Pico microarray cartrige. Gene expression profile obtained from acidosis-adapted PANC1 pancreatic cancer cells was compared to the profile of non-adapted control cells.

first: Anna

last: Bång-Rudenstam

first: Myriam

last: Cerezo-Magaña

first: Marton

last: Horvath

first: Hugo

last: Talbot

first: Emma

last: Gustafsson

first: Stevanus

last: Jonathan

first: Chaitali

last: Chakraborty

first: Itzel

last: Nissen

first: Kelin

last: Gonçalves de Oliveira


title: Iron deficiency protects against Plasmodium infection and drives parasite molecular reprofiling.

city: Parkville

first: Peter

last: Hickey

address: 1G Royal Parade

country: Australia

institute: WEHI

summary: Background: Iron deficiency, anaemia and Plasmodium infection represent significant global health challenges with overlapping geographical distributions, particularly affecting pregnant women in Africa. Previous evidence suggests complex interactions between iron status and malaria susceptibility. However, the mechanisms and clinical implications of this relationship remain poorly understood. Methods: We employed a multi-layered approach to clarify the association between iron deficiency and malaria infection risk. First, we analysed clinical data from Malawian pregnant women (n=711) participating in the REVAMP clinical trial—an RCT of intravenous iron versus oral iron—to assess associations between iron status and P. falciparum parasitaemia detected by ultra-sensitive qPCR. All eligible women received intermittent preventive anti-malaria treatment. Then, we utilised a genetic mouse model (Tmprss6-knockout) to isolate the effect of iron deficiency on P. berghei infection and progression to clinical disease. Finally, we explored direct effects of iron chelation on cultured P. falciparum parasites through transcriptomic and proteomic analyses. Results: In REVAMP, iron deficiency was associated with a 50% reduced probability of P. falciparum qPCR positivity at baseline (95% CI [30%-64%], p<0·0001). Iron intervention given at baseline did not significantly modify the probability of subsequent parasitaemia across the pregnancy. In the murine model, iron-deficient Tmprss6-knockout mice exhibited significantly improved survival compared to controls (median survival 15·5 vs 7·0 days) and protection from cerebral malaria (survival 83% vs 17%). Iron chelation in P. falciparum cultures induced substantial transcriptomic (1,397 differentially expressed genes) and proteomic changes (121 differentially expressed proteins; 46 matched differentially expressed gene/protein pairs), primarily affecting processes involved in host cell invasion, protein export, and nutrient acquisition. Conclusion: Our findings consistently demonstrate that iron deficiency protects against Plasmodium infection across clinical, pre-clinical, and in vitro models. Importantly, in the presence of adequate malaria prevention intravenous iron supplementation did not significantly increase subsequent parasitemia prevalence. These results provide mechanistic insights into iron and malaria interactions and support current WHO recommendations for iron supplementation in pregnant women in malaria-endemic regions when coupled with adequate malaria prevention strategies.

overall_design: RNA seq profiling of 3D7 Plasmodium falciparum ring-stage synchronised parasite cultures exposed to concentrations of 0 and 12.5µM of DFO for 30 hours.

first: Danielle

last: Clucas

middle: F

first: Ricardo

last: Ataíde

first: Bennet

last: Cavan

first: Pasricha

last: Sant-Rayn


title: Calumenin prevents fibroblasts senescence and lung aging by promoting vimentin proteostasis

first: Huirui

last: Wang

summary: Progressive lung fibrosis is linked to aging-related dysfunction in fibroblasts, which remains poorly understood. We aimed to assess the impact of calumenin deficiency on fibroblast senescence and lung fibrosis.

overall_design: In the present work, we knocked out or knocked down calumenin in fibroblasts and conducted RNAseq analysis to investigate the effects of calumenin on senescence and fibrosis signaling pathways in fibroblasts. By integrating proteomics data results, we aimed to provide a more precise analysis.

first: Ting

last: Dong

first: Yinghui

last: Gao


title: A cell-type-resolved human brain atlas of microRNAs and tRNA fragments.

city: JERUSALEM

first: Serafima

last: Dubnov

address: The Edmond J. Safra Campus, Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

summary: Small non-coding RNAs (sncRNAs), including microRNAs (miRs) and tRNA fragments (tRFs), regulate diverse brain molecular pathways involved in development, inflammation and neurodegeneration, and dynamically respond to stress insults in various neurological contexts. Nevertheless, the cell-type-specificity of brain miRs and tRFs remains poorly characterized, limiting the interpretation of their function. To address this issue, we generated a comprehensive, cell-type-resolved atlas of human brain small non-coding RNAs from live brain tissue. Specifically, we isolated neurons, astrocytes, microglia and oligodendrocytes from neurosurgery-obtained fresh human brain specimens and profiled their small RNA repertoires using small RNA-sequencing. Our atlas revealed multiple cell-type differences in miR and tRF expression and identified small RNA cell type biomarkers. Furthermore, we demonstrated that miR cell-type-specificity may be regulated by specific quantitative trait loci located in cell-type-associated enhancer regions. We identified higher levels of 5’-tRNA-halves in neurons, compared to glia, including a particular neuronal enrichment of 5’-tRNA-halves derived from Glycine, Leucine and Lysine-linked tRNAs. Intriguingly, these neuronal tRF families were significantly upregulated in Alzheimer’s disease postmortem brain samples, compared to age-matched controls, possibly reflecting a neuronal response to disease. Our atlas and an accompanying statistical tool for miR cell-type-enrichment analysis together provide a novel publicly available resource for dissecting small RNA cell type origin and function in the fresh human brain.

overall_design: Small RNA-seq profiling of lightly formalin fixed, neurosurgery-obtained fresh brain specimens, FACS-sorted to distinct cell-type-specific populations, representing neurons, astrocytes, microglia and oligodendrocytes.

first: Lihen

last: Laski

first: Ido

last: Zchut

first: Ofek

last: Avidan

first: Estelle

last: Bennet

first: David

last: Greenberg

first: Adi

last: Tujerman

first: Mor

last: Nitzan

first: Iddo

last: Paldor

first: Hermona

last: Soreq


title: Clariom D Pico gene array of microdissected lipid droplet (LD)+ and LD- human GBM areas.

first: Mattias

last: Belting

summary:
In this study, we aimed to elucidate the molecular underpinnings of metabolic adaptation in the stressed TME. LD accumulation has been well documented in glioblastoma (GBM), a prototypical high-grade brain malignancy characterized by severe acidosis, hypoxia, and metabolic heterogeneity. Unexpectedly, we observed a prominent enrichment of pathways related to glycocalyx remodeling in the LD-rich niche of patient tumors, particularly those involving CS biosynthesis and PG regulation. These findings prompted us to explore how glycan remodeling intersects with lipid metabolism in GBM and whether this interaction contributes to tumor stress adaptation. Our results highlight an acidosis-induced glycan program with potential as a metabolic vulnerability, offering new therapeutic avenues for targeting the lipid-stressed niche in aggressive tumors.
We used microarrays to evaluate transcriptional signature realted lipid droplet (LD)+ and LD- regions of patient glioblastoma (GBM) sections.

overall_design: Lipid droplet (LD)+ and LD- human GBM tumor areas were captured by laser capture microdissection (LCM), excluding vasculature and CD68⁺ immune cells. The samples were microdissected, underwent RNA extraction with AllPrep DNA/RNA Micro Kit for RNA, and hybridization on Affymetrix Clariom Human D Pico microarray cartrige.  2 samples in total  pooled from 5 patients: 1 for LD+/CD68- (LD+ cancer cell) and 1 for LD-/CD68- (LD- cancer cell) areas respectively. Gene expression profiles of LD+ GBM cancer cell areas were compared to the profile of LD- GBM cancer cell areas.

first: Anna

last: Bång-Rudenstam

first: Myriam

last: Cerezo-Magaña

first: Marton

last: Horvath

first: Hugo

last: Talbot

first: Emma

last: Gustafsson

first: Stevanus

last: Jonathan

first: Chaitali

last: Chakraborty

first: Itzel

last: Nissen

first: Kelin

last: Gonçalves de Oliveira

first: Axel

last: Boukredine

first: Sarah

last: Beyer

first: Julio

last: Enriquez Perez

first: Maria

last: C Johansson

first: Lena

last: Kjellén

first: Emil

last: Tykesson

first: Anders

last: Malmström

first: Toin

last: H van Kuppevelt

first: Karin

last: Forsberg-Nilsson

first: Jeffrey

last: Esko

first: Silvia

last: Remeseiro

first: Johan

last: Bengzon

first: Valeria

last: Governa


title: Basal IFNλ2/3, but not IFNλ1, signaling is sufficient to control virus infection in intestinal epithelial cells

city: Gainesville

first: Yagmur

last: Keser

state: Florida

address: 1200 Newell Dr.

department: Molecular Genetics and Microbiology (MGM)

institute: University of Florida

summary: Interferon-lambdas (IFNλs) serve as critical mediators of antiviral defense at mucosal surfaces. Beyond their established role in regulating innate immune responses during infection, recent evidence demonstrates that IFNλs are constitutively expressed in pathogen-free environments, termed "basal" IFN expression. While intestinal epithelial cells constitutively express all basal IFNλ subtypes (IFNλ1, IFNλ2, and IFNλ3), their individual contributions to antiviral immunity remain poorly defined. Here, we systematically investigate the distinct roles of IFNλ1 and IFNλ2/3 in regulating intrinsic antiviral immunity using human intestinal epithelial T84 cells. Through genetic depletion of IFNλ1 or IFNλ2/3, we show that basal IFNλ2/3, but not IFNλ1, is essential for restricting replication and spread of diverse viruses, including vesicular stomatitis virus (VSV), mammalian orthoreovirus (MRV), rotavirus (RV), and vaccinia virus (VV). Transcriptomic profiling revealed that IFNλ2/3 selectively controls the basal expression of interferon-stimulated genes (ISGs), including key antiviral effectors and components of the IFN signaling machinery (e.g., STAT1, STAT2, IRF9). Loss of IFNλ2/3 reduced total STAT1 protein levels and blunted responsiveness to exogenous IFNλ, indicating compromised interferon signaling capacity. Furthermore, basal IFNλ2/3 was required for activating paracrine JAK/STAT signaling and ISG induction in neighboring bystander cells, thereby amplifying antiviral protection across the epithelial layer. These findings reveal a functional hierarchy among IFNλ subtypes and establish IFNλ2/3 as the dominant, non-redundant regulators of epithelial immune readiness. Our study provides the first comprehensive analysis of basal IFNλ subtype functions in the gut epithelium and underscores the central role of basal IFNλ2/3 in maintaining mucosal antiviral defense.

overall_design: To define the distinct roles of IFNλ subtypes in maintaining immune homeostasis and antiviral defense at basal levels in human intestinal epithelial cell, we generated T84 IFNλ1 KO, IFNλ2/3 KO and IFNLR KO cells. T84 WT and KO cells were seeded and harvested at two days post-seeding, and sent for RNA sequencing.

first: Sena

last: Bumin

first: Sorin O.

last: Jacobs

first: Steeve

last: Boulant

first: Megan

last: Stanifer

first: Amelia

last: Perez Valiente


title: Acidosis and hypoxia responsive gene expression profiles of U87MG glioblastoma cells

first: Mattias

last: Belting

summary:
In this study, we aimed to elucidate the molecular underpinnings of metabolic adaptation in the stressed TME. LD accumulation has been well documented in glioblastoma (GBM), a prototypical high-grade brain malignancy characterized by severe acidosis, hypoxia, and metabolic heterogeneity. Unexpectedly, we observed a prominent enrichment of pathways related to glycocalyx remodeling in the LD-rich niche of patient tumors, particularly those involving CS biosynthesis and PG regulation. These findings prompted us to explore how glycan remodeling intersects with lipid metabolism in GBM and whether this interaction contributes to tumor stress adaptation. Our results highlight an acidosis-induced glycan program with potential as a metabolic vulnerability, offering new therapeutic avenues for targeting the lipid-stressed niche in aggressive tumors.
We used microarrays to evaluate transcriptional signature of acidosis adaptation, short-term acidosis (pH 6.4) or short-term hypoxia in U87MG GBM cells.

overall_design: U87MG GBM cancer cells were adapted to acidic condition (acidosis-adapted, pH 6.4) or not (non-adapted= control) during 10 weeks. Alternatively U87MG GBM cells were treated in short-term acidosis at pH 6.4 or 7.4 (pH control) or in short-term hypoxia, grown at normoxic (21% oxygen) or hypoxic (1% oxygen) conditions for 48 h. In total 18 samples (6 types of samples in three biological replicates) underwent RNA extraction with RNAeasy mini kit and was subjected to genome-wide transcriptional analysis with Illumina HumanHT-12 V3.0 expression beadchip. Gene expression profile obtained from acidosis-adapted U87MG GBM cells was compared to the profile of non-adapted control cells and gene expression profiles obtained from short-term acidic (pH 6.4) or hypoxic U87MG cells was compared their respective control samples.

first: Anna

last: Bång-Rudenstam

first: Myriam

last: Cerezo-Magaña

first: Marton

last: Horvath

first: Hugo

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