title: Single Cell Transcriptomics of Refractory Epilepsy (RE) patients in Colombia.

city: Bogotá D.C

first: Jorge

last: Diaz-Riaño

address: Cra 1 Nº 18A - 12

country: Colombia

institute: Universidad de Los Andes

summary: The human neocortex is composed of dozens to hundreds of distinct cell types, whose gene expression patterns maintain the balanced electric signaling during all the life. Although the brain has shown a high adaptive capacity to tolerate disruptions, some alterations in these genetic programs can contribute to the pathogenesis of various neurological disorders, including epilepsy, autism spectrum disorder, Alzheimer’s disease, and Parkinson’s disease. Genetic factors are especially implicated in a specific form known as refractory or drug-resistant epilepsy (DRE), which is diagnosed when two or more antiepileptic treatment regimens fail to control seizures. In this study, we investigated the cellular and molecular landscape of DRE using brain tissue from five pediatric Colombian patients. Six samples collected during surgical resection were analyzed using single-cell RNA sequencing (scRNA-seq) and long-read genome sequencing (PacBio HiFi). We identified differentially expressed genes (DEGs) across distinct cell types, integrating transcriptomic data with single nucleotide polymorphisms (SNPs), insertions, deletions, and structural variants. Functional enrichment analysis revealed glial-driven dysregulation of synaptic signaling, impaired glial–neuronal communication, and altered expression of transporters and calcium signaling genes. Notably, aberrant activation of taste receptors in neurons was associated with neuroinflammatory processes. These findings suggest that DRE arises from complex, cell-type-specific disruptions that compromise network stability and seizure control.

overall_design: 6 brain tissue samples were collected from 5 patients diagnosed with refractory epilepsy, per ILAE criteria, who were selected for neurosurgery procedure were included. scRNA-Seq were employed to analyze the expression profile of cell types in samples.

last: Duitama


title: Cell-Selective Telomere Damage by Thiopurine-Based Oligonucleotide for Diffuse Large B-cell Lymphoma Immunotherapy

status: Public on Aug 04 2025

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 E Durate Rd

department: Shared Resources Department

country: USA

institute: City of Hope National Medical Center

type: Expression profiling by high throughput sequencing

summary: Telomerase (TERT) is an enzyme involved in maintaining telomere length in diffuse large B-cell lymphoma (DLBCL). Previous attempts to target TERT+ cancers faced challenges, including the delayed clinical responses and on-target/off-tumor toxicities. Here, we present a DLBCL-targeted oligonucleotide designed to deliver a synthetic TERT substrate, 6-thio-2’-deoxy-guanosine (6tdG), damaging telomeres and triggering apoptosis. In vitro, 6tdG-oligonucleotides (6tdGOs) were selectively cytotoxic to TERT + DLBCL cells without affecting activated T-cells or non-malignant TERT— cells. Repeated intravenous administration of 6tdGO, but not 6tdG nucleoside, had significant antitumor effects against xenotransplanted human DLBCL models and syngeneic E-myc/15A lymphoma in mice. In immunocompetent mice, treatment with 6tdGO induced systemic, lymphoma-specific and CD8 T-cell-mediated antitumor immune responses. The abscopal effects of 6tdGO were abolished in mice lacking expression of Sting1 or Ifnar1 but not Trl9. These findings suggest that 6tdGO-induced lymphoma cell death triggered STING-mediated type-I IFN signaling, thereby promoting recruitment/activation of CD8 T-cells. Importantly, the repeated 6tdGO treatments were well-tolerated in humanized hCD34/NOG mice. Except for the reduced percentage of human B-cells, 6tdGO did not decrease the numbers of hematopoietic stem cells, myeloid cells, or T-cells. Overall, 6tdGO offers an effective and safer strategy against aggressive TERT + DLBCL with potential to activate T-cell based antitumor immunity

overall_design: RNA was extracted using the Maxwell RSC simplyRNA tissue kit (Promega) from OCI-Ly18 cells treated for 2 days with PBS, 500nM CpG-ODN or 6tdGO-2 and 3μM 6tdG.

first: Chunsong

last: Yu

first: Elaine Y

last: Kang

first: Dongfang

last: Wang

first: Piotr

last: Swiderski

first: Ye

last: Feng

first: Timothy

last: Synold

first: Stephen

last: Forman

first: Larry

last: Kwark

first: Marcin

last: Kortylewski


title: Transcriptional regulation of postnatal aortic development

city: New Haven

first: Jay

last: Humphrey

state: CT

address: 55 Prospect St

department: Department of Biomedical Engineering

institute: Yale University

summary: The aorta exhibits tremendous changes in geometry, composition, and mechanical properties during postnatal development. These changes are necessarily driven by transcriptional changes, both genetically programmed and mechano-responsive, but there has not been a careful comparison of time-course changes in the transcriptional profile and biomechanical phenotype. Here, we show that the greatest period of differential gene expression in the normal postnatal mouse aorta occurs prior to weaning at three weeks of age though with important evolution of many transcripts thereafter. We identify six general temporal patterns, including transcripts that monotonically decrease to lower or increase to higher steady state values as well as those that either peak or dip prior to or near weaning. We show that diverse transcripts within individual groupings correlate well over time, and that sub-sets of these groups correlate well with the developmental progression of different biomechanical metrics that are expected to be involved in mechano-sensing. In particular, expression of genes for elastin and elastin-associated glycoproteins tend to correlate well with the ratio of systolic-to-diastolic stress whereas genes for collagen fibers correlate well with the daily rate of change of systolic stress and genes for mechano-sensing proteins tend to correlate well with the systolic stress itself. We conclude that different groupings of genes having different temporal expression patterns correlate well with different measures of the wall mechanics, hence emphasizing a need for age-dependent, gene-specific computational modeling of postnatal development.

overall_design: We compared biological processes using transcriptional analyses of aortic tissue harvested from wild-type mice at P2 (n=9), P10 (n=5), P21 (n=5), P42 (n=6), and P84 (n=6) to look at temporal changes.

first: Dar

last: Weiss

first: Nicola

last: Yeung

first: Abhay

last: Ramachandra


title: Identification of the Streptomyces WblA regulon reveals drastic effects on development and specialised metabolism

city: Norwich

first: Matt

last: Hutchings

state: Norfolk

address: Norwich Research Park, Colney Lane

country: United Kingdom

institute: John Innes Centre

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Specialised metabolites made by the genus Streptomyces form the basis of 55% of clinically used antibiotics as well as cancer therapeutics, immunosuppressants and other anti-infectives. Streptomyces venezuelae is a model for the genus because it is fast-growing, sporulates in liquid culture within 24 hours and coordinates production of the antibiotic chloramphenicol with sporulation. In this work we demonstrate that the conserved orphan response regulator OrrA directly controls the production of the conserved WhiB-like protein WblA which in turn binds to 90 target gene promoters, including genes required for aerial hyphae production and sporulation. We provide evidence that WblA directly controls the production of AdpA and BldN, key developmental regulators that are required for entry into sporulation and show that the cellular levels of the key developmental regulators AdpA, BldM, BldN, RsbN, WhiA, WhiB and WhiD are significantly altered in a ∆wblA mutant. Proteins encoded by 32 of the 33 predicted specialised metabolite biosynthetic gene clusters in S. venezuelae are also significantly affected by loss of WblA and we show that the ∆wblA mutant over produces the antibiotic chloramphenicol. This is the first time the WblA regulon has been defined in the genus Streptomyces and is consistent with previous reports that deletion of wblA has pleiotropic effects on antibiotic production and sporulation in diverse Streptomyces species.

overall_design: Chromatin immunoprecipitation sequencing (chip-seq) of Flag tagged MtrA. Samples were taken from liquid culture MYM+TE flasks after 12 hours and 16 hours of growth and compared to WT strains of the same background.

first: Kelly-Rose

last: Tulley

first: Neil

middle: A

last: Holmes

first: Ainsley

last: Beaton

first: Lucas

last: Balis

first: Edward

last: Hems

first: Gerhard

last: Saalbach

first: Rhea

last: Stringer

first: Govind

last: Chandra

last: Wolanski

first: Barrie

last: Wilkinson

first: Matthew

middle: I


title: Genomic Convergence in Hibernating Mammals Elucidates the Genetics of Metabolic Regulation in the Hypothalamus [snRNAseq]

city: Salt Lake City

first: Chris

last: Gregg

state: UT

address: 20 South 2030 East

department: Neurobiology and Anatomy

institute: University of Utah

summary:
Extreme metabolic adaptations can elucidate genetic programs governing mammalian metabolism. Here we used convergent evolutionary changes in hibernating lineages to define conserved cis-regulatory elements (CREs) and metabolic programs. We characterized mouse hypothalamus gene expression and chromatin dynamics across fed, fasted, and refed states, then used comparative genomics of hibernating versus non-hibernating lineages to identify cis-elements with convergent changes in hibernators. Multi-omics approaches pinpointed CREs, hub genes, regulatory programs, and cell types underlying lineage divergence. Hibernators accumulated loss-of-function effects for CREs regulating hypothalamic responses, and the refeeding period after fasting served as a key phase for molecular processes with convergent evolutionary changes. This work provides a genetic framework for harnessing hibernator adaptations to understand human metabolic control.
Convergent signals define cis-regulatory mechanisms behind food scarcity responses and hibernator-homeotherm divergence.

overall_design: Track gene expression in mouse hypothalamus through a series of diet conditions.

first: Elliott

last: Ferris

first: Christopher

first: Susan

last: Steinwand

first: Cornelia

middle: S

last: Hörndli

first: Pablo

middle: J

last: Maldonado-Catala

first: Josue

middle: D

last: Gonzalez Murcia

first: Riley

last: Spotswood

first: Adriana

middle: C

last: Rodriguez

first: Dimitri

last: Traenkner

first: Alun

last: Thomas

first: Crystal

last: Davey


title: Single cell RNA sequencing of post-radiation mouse jejunum with or without DIZE

city: Milwaukee

first: Joseph

last: Zenga

state: WI

address: 9200 W WISCONSIN AVE

institute: MEDICAL COLLEGE OF WISCONSIN

summary: In a radiation mass casualty event, exposed populations will suffer dose-dependent toxicity to multiple-organ systems.  Although several therapies are FDA-approved for treatment of the hematopoietic acute radiation syndrome (H-ARS), there are no FDA-approved medical countermeasures (MCM) for either acute gastrointestinal injury (GI) or late multi-organ toxicities known as the delayed effects of acute radiation exposure (DEARE).    Prior data suggest activation of the alternative renin angiotensin (RAS) enzyme angiotensin-converting enzyme 2 (ACE2) has therapeutic potential for mitigating multi-organ radiation injury, including GI acute radiation syndrome (GI-ARS).  Here, we evaluated whether pharmacologic activation of ACE2 mitigates GI-ARS in rodent models and protects against DEARE in GI-ARS survivors.

overall_design: 6 mice underwent radiation with sacrifice at post-radiation day 5. Single cell RNA seq was then performed from jejunum.

first: Zenga

last: Joseph

first: Himburg

last: Heather


title: Genomic Convergence in Hibernating Mammals Elucidates the Genetics of Metabolic Regulation in the Hypothalamus [bulk ATACseq]

summary: Extreme metabolic adaptations can elucidate genetic programs governing mammalian metabolism. Here we used convergent evolutionary changes in hibernating lineages to define conserved cis-regulatory elements (CREs) and metabolic programs. We characterized mouse hypothalamus gene expression and chromatin dynamics across fed, fasted, and refed states, then used comparative genomics of hibernating versus non-hibernating lineages to identify cis-elements with convergent changes in hibernators. Multi-omics approaches pinpointed CREs, hub genes, regulatory programs, and cell types underlying lineage divergence. Hibernators accumulated loss-of-function effects for CREs regulating hypothalamic responses, and the refeeding period after fasting served as a key phase for molecular processes with convergent evolutionary changes. This work provides a genetic framework for harnessing hibernator adaptations to understand human metabolic control.

overall_design: Define bulk ATAC-seq peaks for Fed, Fasted, 12 hour refed, and 1 week refed mouse hypothalamus. 4 biological replicates for each feeding condition.


title: Immuno-laser capture microdissection of perfusion-fixed brain tissue coupled to RNA-seq

city: Farmington

first: Joel

middle: s

last: Pachter

address: 263 Farmington Ave

department: Immunology

institute: University of Connecticut Health

summary: Normal mouse brain was fixed by cardiac perfusion with 4% paraformaldehyde in PBS, then post-fixed by immersion in the same solution for 2hr at RT. Brain was embedded in cryomatrix and frozen sections were cut at 7 um on a cryostat.  Sections were immunostained with anti-CD31 antibody and anti-GFAP antibody to detect microvascular endothelial cells and surrounding astrocytes, respectively. Immediately after immunostaining, sections were subject to laser capture microdissection (LCM), using ultraviolet laser to ablate unwanted astrocytes and infrared laser to lift target endothelial tissue.  Total RNA was isolated from LCM-retrieved endothelial tissue and processed for RNA-seq.

overall_design: RNA-seq profiling of Immuno-laser capture microdissection of perfusion-fixed brain tissue

first: Shujun

last: Ge

first: Wenqi

last: Gan

first: Keaton

last: Karlinsey

first: Beiyan

last: Zhou


title: Genomic Convergence in Hibernating Mammals Elucidates the Genetics of Metabolic Regulation in the Hypothalamus [PLACseq_Fasted]

first: Chris

last: Gregg

overall_design: Track gene expression in C57BL6/J (B6) mouse hypothalamus through a series of diet conditions.

first: Elliott

last: Ferris

first: Christopher

first: Susan

last: Steinwand


title: Genomic Convergence in Hibernating Mammals Elucidates the Genetics of Metabolic Regulation in the Hypothalamus [PLACseq_Hybrid]

overall_design: Define chromatic contacts in CastEiJ (Cast) × C57BL6/J (B6) F1 hybrid mice. CastEiJ (Cast) × C57BL6/J (B6) F1 hybrid offspring derived from initial (F1cb (CB), Cast mother × B6 father) and reciprocal (F1bc (BC), Cast father × B6 mother) crosses.

first: Cornelia

last: Hörndli

first: Josue

last: Gonzalez Murcia


title: AT2-Derived GM-CSF Promotes CD301b⁺ cDC2 Generation and Type 2 Inflammation in the Lung

city: Zurich

first: Christoph

last: Schneider

address: Winterthurerstrasse 190

department: Physiology

country: Switzerland

institute: University of Zurich

summary: Pulmonary conventional dendritic cells (cDCs) are functionally and phenotypically heterogeneous antigen-presenting cells essential for orchestrating adaptive immune responses in the lung. Here, we define a critical role for granulocyte-macrophage colony-stimulating factor (GM-CSF) in generating a CD301b+ subset of terminally differentiated cDC2s. GM-CSF signaling is intrinsically required for their development, independent of GM-CSF-dependent alveolar macrophages. Absence of GM-CSF results in a defect similar to that seen in CD103+XCR1+ cDC1s. Unbiased single-cell transcriptomic profiling of CD11c+ cells identified both immature and differentiated cDC populations. GM-CSF deficiency disrupted anti-apoptotic Bcl2a1 upregulation and impaired progression to the CD301b+ transcriptional state. Despite their positioning in lymphoid cell-rich adventitial cuff areas, hematopoietic GM-CSF was dispensable. Instead, genetic GM-CSF gain- and loss-of-function studies showed that alveolar epithelial type 2 cell-derived GM-CSF is required for CD301b+ cDC2 formation and pulmonary type 2 immune responses, highlighting the central role of GM-CSF signaling in shaping the pulmonary myeloid landscape.

overall_design: The aim of this study was to delineate the role of GM-CSF in the differentiation and maturation of pulmonary conventional dendritic cells. We used genetic mouse models to verify the source of GM-CSF and single-cell transcriptomics to gain insight into immature and differentiated lung dendritic cell states. Using a neonatal alveolar macrophage transfer model into GM-CSF receptor deficient mice, we confirm the independence of DC development from alveolar macrophages and low-grade lung inflammation. Using bone marrow chimera and inducible GM-CSF overexpression in mice, we show that GM-CSF direct signaling is necessary for DC development and maturation and their function in type 2 immune responses in the airways, while also detailing the role of alveolar macrophages and GM-CSF signaling for eosinophil granulocytes.

first: Julia

last: Gschwend

first: Antonie

last: Lechner

first: Nikolaos D.

last: Sidiropoulos

first: Paul

last: Maier

first: Tilde

last: Andersson

first: Flurin

last: Sturzenegger

first: Basak

last: Corak

first: Nina

last: Brander

first: David A.

last: Bejarano

first: Elina

last: Wells

first: Sandra

last: Melo Carlos

first: Maximilian

last: Nitschké

first: Ari

last: Molofsky

first: Andreas

last: Schlitzer

first: Isabelle C.

last: Arnold

first: Sarah

last: Mundt

first: Burkhard

last: Becher

first: Manfred

last: Kopf

first: Hubert

last: Rehrauer


title: Identification of  ribosome-protected mRNA fragments (RPFs) associated with NAT10 in mouse hearts

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

country: China

institute: Harbin Institute of Technology

summary: The goal of this study is to identify ribosome-protected mRNA fragments (RPFs) to investigate gene expression dynamics at both transcriptional and translational levels associated with NAT10 in mouse hearts

overall_design: NAT10-FF mice and NAT10-CKO mice  were sacrificed at day 15 after birth,Ribosome Profiling Sequence (Ribo-seq) assay was performed to identify  ribosome-protected mRNA fragments (RPFs) associated with NAT10 in mouse hearts.

first: Lei

last: Shi


title: The effects of NAT10 on heart development in mice

summary: The goal of this study is to investigate how NAT10 regulates heart development in mice. mRNA profiles in hearts of Nat10flox/flox and cardiomyocyte-specific Nat10 knockout (Nat10-CKO) mice at 10 days old were generated by deep sequencing using Illumina  novaseq x plus (n=3 for each group).

overall_design: Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from hearts of Nat10flox/flox and Nat10-CKO mice at 10 days old. Three independent biological replicates for each group were used for RNA-seq. RNA-seq was performed by deep sequencing using an Illumina  novaseq x plus. Paired-end clean reads were aligned to the mouse reference genome(grcm39) with Hisat2 (2.2.1), and the aligned reads were used to quantify mRNA expression by using featureCounts (2.0.6).


title: Genomic Convergence in Hibernating Mammals Elucidates the Genetics of Metabolic Regulation in the Hypothalamus [ChIP-seq_mm]

first: Chris

last: Gregg

overall_design: Define H3K27ac peaks for mouse hypothalamus to compare with squirrel data.

first: Elliott

last: Ferris

first: Christopher

first: Susan

last: Steinwand

first: Dimitri

last: Traenkner


title: Genomic Convergence in Hibernating Mammals Elucidates the Genetics of Metabolic Regulation in the Hypothalamus [ChIP-seq_sq]

overall_design: Define H3K27ac peaks for ground squirrel hypothalamus to compare with mouse data.


title: Minimal impact of ivermectin on immune response and transcriptional profiles in naïve adults with mild COVID-19

city: Barcelona

first: Cèlia

last: Torres Vilanova

address: Roselló 132

department: Malaria Immunology

country: Spain

institute: ISGlobal

summary: Ivermectin (IVM), an antiparasitic, was tested in clinical trials as a potential treatment for COVID-19 due to its in vitro antiviral properties and hypothetical immunomodulatory effects. In this study, we explored the immunomodulatory effects of IVM in a clinical trial involving 24 mild COVID-19 patients who received IVM within 48 hours of symptom onset. The IVM group showed a trend towards lower viral loads post-treatment, and a significantly shorter duration of hyposmia/anosmia. We comprehensively analyzed immune responses by measuring antibody levels, cytokine profiles, immune cell subsets over 28 days and whole blood gene expression. The IVM group had increased levels of IgG against the SARS-CoV-2 nucleocapsid and IL-1RA, an anti-inflammatory cytokine. IVM did not affect the kinetics of SARS-CoV-2 T cells, despite a slight decrease in naive CD4+ T cells. Additionally, gene expression analysis showed a decrease in innate and antiviral responses and an increase of adaptive responses over time that were stronger in the placebo compared to the IVM group. In conclusion, despite some differences in IVM treated participants, our detailed analyses do not support significant immunomodulatory effects, reinforcing evidence that IVM is unlikely to be an effective treatment for COVID-19.

overall_design: Gene expression profile analysis of RNA-Seq data from 72 whole blood samples of 24 COVID-19 patients, collected at three timepoints: treatment day (D1), 4 days post-treatment (D4), and 7 days post-treatment (D7). Patients were randomly assigned (1:1) to receive a single oral dose of ivermectin (400 μg/kg) or placebo.

first: Marta

last: Ribes

last: Torres

first: Mar

last: Canyelles

first: Rocío

last: Rubio

last: Vidal

first: Luis

last: Izquierdo

first: Andres

last: Blanco-Di Matteo

first: Iñigo

last: Pineda

first: Alejandro

last: Fernandez-Montero

first: Carlota

last: Jordan-Iborra

first: Francisco

last: Carmona-Torre

first: Jose R

last: Yuste

first: Jose L

last: Del Pozo

first: Gabriel

last: Reina

first: Belen

last: Sadaba

first: Mirian

last: Fernández-Alonso

first: Pere

last: Santamaria

first: Carlo

last: Carolis

first: Ruth

last: Aguilar

first: Dídac

last: Macià

first: Carlos

last: Chaccour

last: Dobaño

first: Gemma

last: Moncunill


title: Rapid production of modified cattle and sheep from spermatid-like stem cells [scRNA-seq]

city: Hohhot

first: Lei

last: Yang

state: Inner Mongolia Autonomous Region

address: 24 Zhaojun Rd.

department: State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock

institute: Inner Mongolia University

summary: Haploid androgenetic stem cells (haSCs) are invaluable resources for studying animal traits and greatly impact livestock breeding, but livestock haSCs have yet to be obtained. Here, we report the derivation of cattle and sheep haSCs using the recombined FACE medium, and these cells harbor formative pluripotency features. Notably, knockout cattle and sheep can be obtained upon injection of the protaminized haSCs with targeted gene mutations into intact oocytes.

overall_design: Combination of F, A, C, and E small-molecule supports establishment of bovine haSCs (bE8 (scRNA), bE9 (scRNA), bE10 (scRNA), bE11 (scRNA), bE12 (scRNA), bE13 (scRNA), bE14 (scRNA), b-haSCs (scRNA), b-haSCs-PGC-D4-(scRNA)) at formative state of pluripotency.


title: Rapid production of modified cattle and sheep from spermatid-like stem cells [RNA-seq]

sample_organism:
Bos taurus
Ovis aries

platform_organism:
Bos taurus
Ovis aries

overall_design: Combination of F, A, C, and E small-molecule supports establishment of bovine (b-haSCs (buRNA), b-haSCs-PGC-D1-(buRNA), b-haSCs-PGC-D4-(buRNA), b-IVF-fetus (E75), b-ProiCHI-fetus (E75)-normal, b-ProiCHI-fetus (E75)-retarded) and ovine (o-haSCs (buRNA), o-IVF-fetus (E65), o-ProiCHI-fetus (E65)-retarded) haSCs at formative state of pluripotency.


title: A Basophil-Fibroblast Pro-inflammatory Axis Fuels Type 2 Skin Inflammation

city: New York

first: Raman

last: Gill

state: NY

address: 1428 Madison Ave

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

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

overall_design: Refer to individual Series


title: A Basophil-Fibroblast Pro-inflammatory Axis Fuels Type 2 Skin Inflammation [RNA-Seq]

summary: To better understand the contribution of basophils and fibroblast IL-4 signaling on type 2 skin inflammation, we conducted bulk-RNA seq on from normal and MC903 treated Isotype Cntrl + Mar1 and Il4rafl/fl  + Il4raΔPdgfra models respectively.

overall_design: MC903 treated or vehicle control neck skin was harvested from WT Isotype control and MAR1 injected mice, Il4rafl/fl and, Il4raΔPdgfra mice (n=1 mice per sample). Briefly, skin samples were harvested, snap frozen, and cryosectioned. RNA was isolated and purified from each sample using the Quick-RNA Micro Prep Kit (Zymo Research). Libraries were prepared and sequenced by Novogene

first: Ichiro

last: Imanishi

first: Andrew

middle: L

last: Ji


title: Genomic Convergence in Hibernating Mammals Elucidates the Genetics of Metabolic Regulation in the Hypothalamus [snATACseq]

first: Chris

last: Gregg

overall_design: Define snATAC-seq peaks for Fed, Fasted, 12 hour refed mouse hypothalamus. 3 biological replicates for each feeding condition. (Refed mice are fasted for 72 hours and then fed regular chow for 12 hours)

first: Elliott

last: Ferris

first: Christopher

first: Susan

last: Steinwand

first: Dimitri

last: Traenkner


title: The effects of RNA binding activity and acetyltransferase enzyme activity of NAT10 on heart development

first: Zheng

last: Chen

summary: The goal of this study is to investigate whether RNA binding activity and acetyltransferase enzyme activity of NAT10 regulates heart development

overall_design:
At day 1 after birth, Nat10flox/flox mice were injected with AAV9-cTnT-GFP (1X 1011 VP/mouse) subcutaneously, and Nat10-CKO mice were injected with equal amount of AAV9-cTnT-GFP, AAV9-cTnT-NAT10, AAV9-cTnT-NAT10G641E, and AAV9-cTnT-NAT10K209A, respectively. Mice were sacrificed at day 12-14 after injection. Heart tissues were collected. mRNA profiles in these heart tissues were generated by deep sequencing using Illumina Novaseq 6000 platform (n=3 for each group).
Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from heart tissues. Three independent biological replicates for each group were used for RNA-seq. RNA-seq was performed by deep sequencing using an Illumina Novaseq 6000 platform. Paired-end clean reads were aligned to the mouse reference genome(GRCm38/mm10) with Hisat2 v2.0.5, and the aligned reads were used to quantify mRNA expression by using featureCounts v1.5.0-p3.
Our study represents the first detailed analysis of the effects on heart transcriptomes by the RNA binding activity and acetyltransferase enzyme activity of NAT10, generated by RNA-seq technology.

last: Shi

first: Xinzhi

last: Li


title: Targeting HASPIN kinase disrupts SR protein-mediated RNA splicing and synergizes with BCL-2 inhibitor venetoclax in AML

city: San Diego

first: Dong-Er

last: Zhang

state: California

address: 3855 Health Sciences Dr

department: Pathology

institute: UCSD

summary: Acute Myeloid Leukemia (AML) is a blood cancer complicated by acquired drug resistance, disease relapse, and low overall survival rates. Combination therapies using multiple targeted inhibitors can effectively treat AML patients. However, combination treatments are limited by the number of useable targets and our ability to create rational pairings using complimentary molecular mechanisms. Here, we used a human kinase domain-targeted CRISPR screen to identify histone H3 associated protein kinase (HASPIN) as a significant, understudied dependency in AML. HASPIN depletion significantly reduced growth rate, induced a cell cycle arrest, and dysregulated transcription in AML. A proteomics datamining study characterized splicing factors as major HASPIN kinase substrates and highlighted HASPIN’s role as a splicing regulatory kinase. Accordingly, HASPIN depletion strongly dysregulated splicing and inversed aberrant, pro-leukemic splicing programs in AML patients. HASPIN inhibitor CHR-6494 effectively reduced cell viability across AML subtypes while sparing healthy cells. Furthermore, a novel combination therapy consisting of CHR-6494 and BCL-2 inhibitor Venetoclax synergistically reduced AML cell viability and resensitized Venetoclax-resistant AMLs to treatment. Our study presents HASPIN kinase as a novel, therapeutic target for AML, underscores an underappreciated role in splicing regulation, and proposes a viable combination treatment for clinical use.

overall_design: RNA-sequencing of Kasumi-1 t(8;21) Human AML cell lines expressing either non-targeting control or HASPIN-targeting shRNAs. For analysis, 3 control samples were compared to 3 HASPIN knockdown samples.

first: Liu

last: Mengdan

first: Zhang

last: Dong-Er


title: Identification of mRNAs associated with NAT10 in mouse hearts

summary: The goal of this study is to identify mRNAs associated with NAT10 in mouse hearts.

overall_design:
At day 1 after birth, WT mice were injected with AAV9-cTnT-FLAG-NAT10 (3X 1011 VP/mouse) subcutaneously. Mice were sacrificed at day 20 after injection.  RNA immunoprecipitation sequence (RIP-seq) assay was performed to identify mRNAs associated with NAT10 in mouse hearts.
Then, immunoprecipitated RNA or Input was used for library construction with NEB NextR Ultra™ RNA Library Prep Kit (New England Biolabs). Library quality was assessed on the Agilent Bioanalyzer 2100 system. The libraries were sequenced on an Illumina Novaseq 6000 platform with a paired-end read length of 150 bp according to the standard protocols. Raw data (raw reads) of fastq format were firstly processed using fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low- quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Index of the reference genome ( grcm39-110) was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
mRNAs associated with NAT10 in mouse hearts were characterized.


title: A single-cell multiomics atlas of rice

city: Beijing

first: Xiaofeng

last: Gu

address: Zhongguancun south street

institute: Chinese Academy of Agricultrual Sciences

summary: Cell functions across eucaryotes are driven by specific gene expression programs that are dependent on chromatin structure. Here, we report a single-cell multiomics atlas of rice, one of the world’s major crop plants. By simultaneously profiling chromatin accessibility and RNA expression in 116,564 cells from eight organs we were able to identify cell-type specific gene regulatory networks and describe novel cell states, such as the “transition status” in floral meristems during panicle development. Based on our network analyses we uncovered the function of cell type-specific regulatory hubs RSR1, F3H and LTPL120 for rice development. Importantly, our analysis revealed a correlation between cell type and agronomic traits, and conserved and divergent cell type functions during evolution. In summary, this study not only offers a valuable single-cell multiomics resource for a major crop, but also enriches our understanding of the intricate roles and molecular underpinnings of individual cell types in rice.

overall_design: The experimental design involves single-cell RNA sequencing of root cells from Nip and osltpl120 mutant using the 10x Genomics Chromium Single Cell 3' Gene Expression technology. Cells were isolated and processed according to 10x Genomics protocols. Sequencing was performed on an Illumina NovaSeq 6000 platform. The dataset includes single-cell gene expression profiles with quality control steps to exclude low-quality cells and doublets, followed by normalization and batch effect correction.

first: Xiangyu

last: Wang

first: Huanwei

last: Huang

first: Sanjie

last: Jiang

first: Jingmin

last: Kang

first: Dongwei

first: Kailai

first: Shang

last: Xie

first: Chaofan

last: Liu

first: Guihua

last: Hu

first: Haoqian

first: Cheng

last: Tong

first: Cong

first: Liwen

first: Yike

last: Ding

first: Shangtong

first: Faming

first: Jan

middle: U

last: Lohmann

first: Zhe

last: Liang


title: An Anaerobic In Vitro Flow Model for Studying Interactions at the Gastrointestinal Host-Microbe Interface

city: Odense M

first: Jens

middle: Sivkær

last: Pettersen

state: Danmark

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

summary: This study characterizes the development of an anaerobic intestinal cell culture model based on a dual flow chamber system using Caco-2 cells. One goal of the study was to characterize the transcriptomic profile of Caco-2 cells grown in the anaerobic dual flow chamber system and characterizing the effect of oxygen- and flow conditions on the maturation of the cells.

overall_design: Caco-2 cells were cultured in the apical channel of a dual-flow chamber system, with or without deoxygenated medium (<1% O2 saturation), starting on day 7 post-seeding (DPS). These conditions were compared with Caco-2 cells cultured statically in Transwell inserts. RNA was harvested from the cells at 13 DPS.

first: Line

last: Bang

first: Thomas

middle: E

last: Andersen


title: Rapid generation of gene-edited cattle and sheep from spermatid-like formative haESCs [WGBS]

first: Lei

last: Yang

type: Methylation profiling by high throughput sequencing

summary: Haploid androgenetic embryonic stem cells (haESCs) can produce live mice, thus have potential for genetic manipulation. However, practical application is limited by self-diploidization, loss-of-imprint, low-birth-rate, and livestock haESCs have yet to be achieved. Here we show that combination of FACE medium supports establishment of durable haESCs from cattle and sheep that overcome above problems. Multi-omics and functional analysis of FACE-haESCs showed that at a naive-to-primed intermediate pre-gastrulation formative state of pluripotency. Moreover, transient protamine overexpression remodels ruminant haESCs nuclei into spermatid-like structures concomitant with removal of ICHI barrier, resulting blastocyst rate of Pro-ICHI similar to that of in vitro fertilization (IVF) embryos. As a proof-of-concept, we also developed a novel Pro-ICHI::ePE system to fast produce trait-improved cattle with exogene-free effects.

overall_design: Combination of F, A, C, and E small-molecule supports establishment of bovine and ovine haESCs at formative state of pluripotency.


title: mRNA-seq of individual genetically identical Caenorhabditis elegans adults

city: Eugene

first: Amy

middle: K

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

summary: Individual phenotypic differences persist even in genetically identical individuals, although separating genetic and environmental causation is difficult or impossible in most organisms. To understand the basis of individual differences in the absence of genetic differences, we measured two quantitative reproductive traits in genetically identical young adult Caenorhabditis elegans roundworms in a shared environment and performed single-individual mRNA-seq on each worm. We identified hundreds of genes for which expression variation was strongly associated with reproductive traits, some of which depended on prior environmental experience and some of which was random. Multiple small sets of genes together were highly predictive of reproductive traits across individuals.

overall_design: In the P0 generation, adult C. elegans hermaphrodites were allowed to lay progeny at day 1 or day 3 of adulthood. F1 progeny were then left at 20C throughout their life or shifted to 25C for 8 hours early in life. It was documented when each F1 worm reached egg-laying onset, and 24 hours after egg-laying onset, each F1 young adult worm was collected for individual worm mRNA-seq. The number of progeny laid in the first 24 hours was also measured for each worm.

first: John

middle: H

last: Willis

first: Erik

last: Johnson

first: Patrick

last: Phillips


title: Transcriptome analysis in HL-60 cells after combined treatment with ATRA and palbociclib

city: Kanazawa

first: Tomohisa

last: Baba

address: Kakuma-machi

country: Japan

institute: Kanazawa University

summary: It was reported that the CDK4/6 inhibitor, palbociclib,  can enhance ATRA-induced myeloid differentiation in HL-60 cells. Therefore, in this study, the changes in mRNA expression patterns were precisely and comprehensively analyzed

overall_design: Human acute promyelocytic leukemia HL-60 cells were treated with ATRA alone, palbociclib alone, or a combination of both for 48 hours. Changes in mRNA expression patterns were compared to those in untreated HL-60 cells. Triplicate samples were prepared for each condition

first: Soichiro

last: Kumamoto

first: Yoshikazu

last: Johmura


title: A Basophil-Fibroblast Pro-inflammatory Axis Fuels Type 2 Skin Inflammation [scRNA-Seq]

first: Raman

last: Gill

summary: To better understand cell-cell interactions driving type 2 skin inflammation, we conducted scRNA-seq on two murine models of type 2 skin inflamation, MC903 and Oxazolone (OXA), using the 10X genomics platform

overall_design: MC903/OXA treated or normal ear+neck skin were harvested and pooled for each sample (n=3 mice per condition). Briefly, skin samples were digested using the Miltenyi Multi-tissue dissociation kit. Dead cells were removed using the biolegend mojosort mouse dead cell removal kit. scRNA-seq libraries were generated and analyzed in-house using the 10X genomics platform

first: Ichiro

last: Imanishi

first: Alexis

last: Wilder

first: Andrew

last: Ji


title: Identifying Yen6, a LytTR DNA-binding transcription factor, as a temperature responsive regulator of virulence in Yersinia entomophaga MH96

city: Christchurch

first: Amber

middle: Rose

last: Paulson

address: Lincoln Research Centre, Cnr Springs Road And Gerald Street, Private Bag 4749

department: Forage Science

country: New Zealand

institute: AgResearch Litmited

summary: Yersinia entomophaga MH96 is a highly virulent entomopathogen that infects pest insects of economic importance. We discovered a new regulator, Yen6, which influences the virulence of MH96 in Galleria mellonella at 37 ˚C. Yen6 is directly upstream of the yen7 gene, which encodes for a RoeA-like PhoB-containing regulator and that is directly upstream of the Yen Toxin component (Yen-Tc) genes. We found that yen6 is the most temperature-responsive gene in MH96, producing both messenger RNA and non-coding RNA in its 3' untranslated region (UTR). Yen6 encodes a unique LytTR-containing transcription factor that targets sugar uptake genes and an RNA-binding protein. Of interest, the non-coding RNA from the yen6 3’ UTR overlaps with yen7 in the opposite orientation. Deleting yen6 did not significantly affect the transcriptional activity of yen7 or downstream Yen-Tc genes during infection at 37 ˚C. However, when we deleted the yen6 locus or induced yen6 plus a 478-bp region of its 3’ UTR at 25 ˚C, we observed a significant increase in the transcription/ translation rates of the Yen-Tc gene chi1 using a chi1:lacZ fusion. Our findings reveal a novel mode of virulence regulation in MH96, where the yen6 gene exerts control over multiple genes involved in G. mellonella infection and exhibits potential for dual functionality at both transcriptional and translational levels.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Yersinia entomophaga wild-type (MH96) and a mutant deficient for the yen6 gene (PL78_03730). This study also combines data from transcriptome series under GEO accession: GSE142509.

middle: R

first: Maureen

last: O'Callaghan

first: Xue-Xian

last: Zhang

first: Naran

last: Naren

first: Marion

last: Schoof

first: Mark R

last: Hurst


title: The effects of NAT10 on heart development

first: Zheng

last: Chen

summary: The goal of this study is to investigate how NAT10 regulates heart development

overall_design:
mRNA profiles in hearts of Nat10flox/flox and cardiomyocyte-specific Nat10 knockout (Nat10-CKO) mice were generated by deep sequencing using Illumina Novaseq 6000 platform (n=3 for each group).
Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from hearts of Nat10flox/flox and Nat10-CKO mice at 15 days old. Three independent biological replicates for each group were used for RNA-seq. RNA-seq was performed by deep sequencing using an Illumina Novaseq 6000 platform. Paired-end clean reads were aligned to the mouse reference genome(GRCm38/mm10) with Hisat2 v2.0.5, and the aligned reads were used to quantify mRNA expression by using featureCounts v1.5.0-p3.
Our study represents the first detailed analysis of heart transcriptomes from Nat10flox/flox and Nat10-CKO mice, generated by RNA-seq technology.

first: Lei

last: Shi

first: Xinzhi

last: Li


title: Using RNA sequencing to identify a putative miRNA network in placenta accreta spectrum

city: hangzhou

first: tian

last: dong

address: No.1, xueshi Road

institute: Women's Hospital, School of Medicine, Zhejiang University

type: Non-coding RNA profiling by high throughput sequencing

summary: A total of 185 miRNAs were differentially expressed between PAS and control groups. Integrated the lncRNA/miRNA interactions with the miRNA/mRNA interactions, a ceRNA network was constructed.

overall_design: we determined the differential lncRNA, miRNA and mRNA expression profiles between five placental implantation tissue and adjacent normal placental tissue by high-throughput RNA sequencing.

first: ying

last: jiang


title: Rapid generation of gene-edited cattle and sheep from spermatid-like formative haESCs [WGS]

last: Yang


title: Analysis of LDLR-/- Type and LDLRP2Y6R-/- Macrophage Transcriptomes after atherosclerosis

city: Nanjing

first: Yehogn

address: Jiangning

institute: China Pharmaceutical University

summary: The goals of this study are to investigate the effect of P2Y6R knockout in macrophage transcriptome profiling (RNA-seq) to understand how P2Y6R regulates macrophage during atherosclerosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 4 different bone marrow macrophages with ox-LDL at LDLR-/- and LDLR-/-P2Y6R-/- mice.

first: Q

last: Hu

first: Y

first: M

last: Zhou

first: C

last: Dai

first: H

last: Liu

first: X

last: Dong


title: Using RNA sequencing to identify a putative lncRNA-associated ceRNA network in placenta accreta spectrum

summary: A total of 760 lncRNAs, 185 miRNAs, and 265 mRNAs were differentially expressed between PAS and control groups. Integrated the lncRNA/miRNA interactions with the miRNA/mRNA interactions, a ceRNA network was constructed.


title: Using RNA sequencing to identify a putative network in placenta accreta spectrum


title: Rapid production of modified cattle and sheep from spermatid-like stem cells [CUT&Tag]

summary: Haploid androgenetic stem cells (haSCs) are invaluable resources for studying animal traits and greatly impact livestock breeding, but livestock haSCs have yet to be obtained. Here, we report the derivation of cattle and sheep haSCs using the recombined FACE medium, and these cells harbor formative pluripotency features. Notably, knockout cattle and sheep can be obtained upon injection of the protaminized haSCs with targeted gene mutations into intact oocytes.

overall_design: Combination of F, A, C, and E small-molecule supports establishment of bovine haSCs (input, H3K4me3, H3K27me3, PRM-0h, PRM-24h, PRM-48h, PRM-72h) at formative state of pluripotency.


title: Transcriptome Data from Root Tissues of the 'Sakonnakorn' Mulberry Cultivar

status: Public on Aug 03 2025

city: Bangkok

first: Apidet

last: Rakpenthai

state: Chatuchak

address: 50 Ngamwongwan Rd

country: Thailand

institute: Kasetsart University

summary: We employed RNA-seq to profile the transcriptome of Morus 'Sakonnakorn', a cultivar known for its rich secondary metabolite profile. This analysis aimed to elucidate the genetic regulation of the phenylpropanoid pathway and other related metabolic networks in response to specific elicitors.

overall_design: This study utilized 2.5-month-old stem cuttings of Morus ‘Sakonnakorn’, which were propagated aeroponically from a one-year-old parent plant. The experiment involved two treatment groups: one receiving medium molecular weight chitosan (CHI) and another grown in a nitrogen-deficient (-N) medium. A third, untreated group served as the control. For each condition, three biological replicates were maintained.

first: Mutsumi

last: Watanabe

first: Sutkhet

last: Nakasathien


title: Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels. [scATAC-Seq]

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

summary: Evolutionary adaptation to diurnal vision in ground squirrels has led to the development of a cone-dominant retina, in stark contrast to the rod-dominant retinas of most mammals. The molecular mechanisms driving this shift remain largely unexplored. Here, we perform single-cell RNA sequencing (scRNA-Seq) and chromatin accessibility profiling (scATAC-Seq) across developmental retinal neurogenesis in the 13-lined ground squirrel (13LGS) to uncover the regulatory basis of this adaptation. We find that 13LGS cone photoreceptors arise not only from early-stage neurogenic progenitors, as seen in rod-dominant species like mice, but also from late-stage neurogenic progenitors. This extended period of cone generation is driven by a heterochronic shift in transcription factor expression, with cone-promoting factors such as Onecut2, Pou2f1, and Zic3 remaining active in late-stage progenitors, while cone-differentiation factors Thrb, Rxrg, and Mef2c are expressed precociously in cone specification. Functional analyses reveal that Zic3 and Mef2c promote cone specification, acting through species-specific regulatory elements that drive their expression in late-stage progenitors. These results demonstrate that evolutionary modifications to gene regulatory networks underlie the development of cone-dominant retinas, providing insight into mechanisms of sensory adaptation and potential strategies for cone photoreceptor regeneration in vision disorders.

overall_design: In 13LGS, retinal neurogenesis begins around embryonic day 18 (E18), with birth occurring at E27 (blue-dotted line in Fig. 1A), and concludes by postnatal day 17 (P17)27. To comprehensively profile cellular-level changes in gene expression and chromatin accessibility, we conducted scRNA-Seq and scATAC-Seq analyses across ten developmental time points, spanning the full course of neurogenesis and the immediate post-neurogenesis period (E18–P21).

first: Kurt

last: Weir

first: Sangeetha

last: Kandoi

first: Roujin

last: An

first: Nicole

last: Pannullo

first: Isabella

last: Palazzo

first: Jared A.

last: Tangeman

first: Jun

first: Steven H.

last: DeVries

first: Dana K.

last: Merriman

first: Jiang

last: Qian

first: Seth

last: Blackshaw


title: ChIP-Seq analysis for histone H3.3 in HL-60 cells after combined treatment with ATRA and palbociclib

first: Tomohisa

last: Baba

summary: It was reported that the CDK4/6 inhibitor, palbociclib, can enhance ATRA-induced myeloid differentiation in HL-60 cells. Therefore, in this study, chromatin remodeling was precisely analyzed with a focus on histone H3.3 deposition.

overall_design: Human acute promyelocytic leukemia HL-60 cells were treated with ATRA alone, palbociclib alone, or a combination of both for 48 hours. Changes in the peaks of histone H3.3 deposition were compared each other. There is single sample for each condition.

first: Yuta

last: Moriguchi

first: Yoshikazu

last: Johmura


title: Real time PCR analysis during thermal manipulation in mule duck

city: Mont de Marsan

first: Marianne

last: Houssier

address: 371 rue du ruisseau

department: GB

country: France

institute: INRA NUMEA/IUT UPPA

summary:
This study proposes to describe impacts of an increase of temperature during embryogenesis by following hepatic metabolism at the level of mRNA in mule duck embryos
Two kinetic studies were designed to determine the level of expression of selected genes involved in liver metabolism throughout embryogenesis and at hatch

overall_design:
The livers of 8 mule duck embryos were collected every four days from the 12th day of embryogenesis (E12) until after hatching (Hatch/E30) for the daily kinetic and after the increase of temperature (30min, 1h, 2h, 3h, 4h, 5h and 7h), and gene expression analysis was performed. The expression levels of 95 mRNAs were quantified for these 13 sampling points and classified into major cellular pathways.
GA_RT-daily and hourly kinetics-mule duck-qPCR EvaGreen Biomark

first: Charlotte

last: Andrieux


title: Aging represses oncogenic KRAS-driven lung tumorigenesis and alters tumor suppression

city: Stanford

first: Emily

last: Shuldiner

address: 279 Campus Drive

department: Genetics

institute: Stanford University

summary: Most cancers are diagnosed in people over the age of sixty, but little is known about how age impacts tumorigenesis. While aging is accompanied by mutation accumulation — widely understood to contribute to cancer risk — it is also associated with numerous other cellular and molecular changes likely to impact tumorigenesis. Moreover, cancer incidence decreases in the oldest part of the population, suggesting that very old age may reduce carcinogenesis. Here we show that aging represses oncogenic KRAS-driven tumor initiation and growth in genetically engineered mouse models of human lung cancer. Moreover, aging dampens the impact of inactivating many, but not all, tumor suppressor genes with the impact of inactivating PTEN, a negative regulator of the PI3K/AKT pathway, weakened to a disproportionate extent. Single-cell transcriptomic analysis revealed that neoplastic cells from tumors in old mice retain many age-related transcriptomic changes, showing that age has an enduring impact that persists through oncogenic transformation. Furthermore, the consequences of PTEN inactivation were strikingly age-dependent, with PTEN deficiency reducing signatures of aging in cancer cells and the tumor microenvironment. Our findings suggest that the relationship between age and lung cancer incidence may reflect an integration of the competing effects of driver mutation accumulation and tumor suppressive effects of aging.

overall_design: Single-cell RNA sequencing of tumor-bearing lungs from young and old mice with KRAS-driven tumors with and without inactivation of the tumor suppressor PTEN. To enrich for cancer cells, whole-lung single-cell suspensions were divided into a cancer-cell fraction and a bulk fraction containing all other live cells by fluorescence-activated cell sorting.

middle: G

first: Saswati

last: Karmakar

first: Min

last: Tsai

first: Jess

last: Hebert

first: Yuning

last: Tang

first: Laura

last: Andrejka

first: Maggie

last: Robertson

first: Minwei

last: Wang

first: Colin

last: Detrick

first: Hongchen

last: Cai

first: Rui

first: Christian

last: Kunder

first: David

middle: M

last: Feldser

first: Dmitri

last: Petrov

first: Monte

last: Winslow


title: V. cholerae transcriptome of WT and rluB deletion mutant with sub-MIC tobramycin

city: paris

first: Zeynep

last: Baharoglu

address: 25 rue du dr roux

institute: Institut Pasteur

summary: We study gene expression levels of V. cholerae N16961 hapR+ corrected strain in exponential phase with tobramycin.

overall_design: Bacterial cells were grown to OD 0,25 and RNAseq was performed.

first: Leo

last: Hardy


title: Clinical evidence of Kelch13-dependent and -independent malaria treatment failure with Artemether-Lumefantrine

city: Brussels

first: Jacob

last: SOUOPGUI

address: Avenue Franklin Roosevelt 50

country: Belgium

institute: ULB

summary: Malaria remains a major public health threat, particularly in sub-Saharan Africa. In Rwanda, Artemether-Lumefantrine (AL; Coartem) has been the primary treatment for uncomplicated malaria, though its efficacy is increasingly in question. Using clinical data and Plasmodium biobanks from King Faisal Hospital Kigali, we analyzed 23 selected samples from patient with recurrent malaria. Genotyping confirmed recrudescence rather than reinfection. Following the initial AL treatment, 56.5% (microscopy) and 83.3% (qPCR) remained positive, with symptoms persisting. After a second treatment, positivity declined but was still notable. Sequencing analysis revealed widespread MDR1 Y184F mutations and cumulative Pfkelch13 mutations, including H384R in the BTB/POZ domain, associated with treatment failure. Four failing strains lacked kelch13 mutations, indicating alternative resistance mechanisms. These findings support the need for expanded genetic surveillance to preserve ACT efficacy.

overall_design: Amplicon sequencing:  gDNA from Plasmodium infected blood was extracted and specific plasmodium genes amplified and sequenced using MINION technology on R.10 flow cells.

first: Sandra

last: Fankem Noukimi

first: Jean-Bosco

last: Mbonimpa

first: Edgar

last: Mutebwa Kalimba

first: Yvan

last: Karuke

first: Mariama

last: Telly Diallo

last: Souopgui


title: Gpnmb is required for immune and fibrotic responses during zebrafish heart regeneration

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: Myocardial infarction occurs when coronary supply of oxygen and nutrients to a part of the heart is interrupted.  In contrast to adult humans, adult zebrafish have a unique ability to regenerate their heart after cardiac injury.  To identify potential regulators of the regenerative response, we performed transcriptomics profiling of regenerating coronary endothelial cells (cECs) at 7 days post cryoinjury, when revascularization is vigorous, and identified gpnmb to be upregulated.  Gpnmb (glycoprotein non-metastatic melanoma protein B) is a transmembrane glycoprotein implicated in inflammation resolution and tissue regeneration.  Expression analyses at earlier time points revealed gpnmb specific expression in infiltrating macrophages post cryoinjury in zebrafish ventricles.  Using newly generated gpnmb mutants, we analyze its role during heart regeneration and find that animals lacking gpnmb exhibit neutrophil retention and decreased macrophage recruitment as well as reduced myofibroblasts numbers.  Moreover, loss of gpnmb impairs coronary endothelial cell regeneration and cardiomyocyte dedifferentiation.  Transcriptomic analyses identified enhanced collagen production and extracellular matrix (ECM) related pathway activated in cryoinjured gpnmb mutant hearts.  Furthermore, gpnmb mutant hearts exhibit larger fibrotic scars revealing defects in cardiac regeneration.  Overall, these data suggest that gpnmb expressing macrophages modulate inflammation and ECM deposition after cardiac cryoinjury and highlight the importance of this subset of immune cells to support a regenerative response.

overall_design: To investigate the role of gpnmb during zebrafish heart regeneration, we generated gpnmb mutants and performed comparative RNAseq analysis on WT and MUT

first: Savita

last: Gupta

first: Didier

last: Stainier


title: Spatial transcriptomics of the normal and cytomegalovirus-infected guinea pig placenta

city: Minneapolis

first: Craig

middle: John

last: Bierle

state: Minnesota

address: 2001 6th Street SE

department: Pediatrics

institute: University of Minnesota

summary: Cytomegalovirus infection can disrupt placental development and function either by directly infecting placental cells or by eliciting a pathogenic immune response. Guinea pig cytomegalovirus (GPCMV) infection after mid-gestation causes transcriptional changes indicative of immune activation and focal infections at the base of the main placenta. In this study, we used spatial transcriptomics to quantify host and viral gene expression at the maternal-fetal interface at near single-cell resolution.

overall_design: Time-mated guinea pigs were GPCMV- or mock-infected at 35 days gestation and samples were collected at 21 days post-infection. The 10x Visium Spatial Gene Expression system was used to measure transcript-abunance at the maternal-fetal interface. Samples were trimmed so similar regions of interest were present on each of the 12 capture areas used in this study. 5 GPCMV-infected and 6 mock-infected placentas were analyzed in this study.

first: Zachary

middle: W

last: Berkebile

first: Colleen

last: Forster

first: Emma

last: Stanley

first: Fernanda

last: Rodriguez

first: Adam

last: Herman

first: Micah

last: Gearhart


title: IAA26: a key component in the regulation of age-related resistance in arabidopsis

city: College Park

first: Madhu

last: Kappagantu

state: MD

address: 4291 Fieldhouse drive

institute: University of Maryland

summary:
To investigate the association between IAA26 and age related resistance in arabidopsis
RNAseq analysis was used to differential gene expression in IAA26 mutants compared with wild type arabidopsis ecotype Shahdara

overall_design: iaa26-knockout and IAA26-stablilised lines were screened for their impact on plant development and defense in comparision with arabidopsis ecotype Shahdara (wild type)

first: Tamara

last: Collum

first: James

middle: N

last: Culver


title: The TBLR1/TBL1 co-factor complex acts as a transcriptional checkpoint in the brown adipose tissue response to prolonged cold exposure

status: Public on Aug 02 2025

city: Neuherberg

first: Peter

last: Weber

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

summary: Brown adipose tissue (BAT) is a key thermogenic organ, whose activation in response to cold environmental temperatures and β-adrenergic stimulation requires the proper function of the NCOR/HDAC3 corepressor complex in brown adipocytes. The NCOR/HDAC3 complex is large, and multi-component, including the transducin beta-like 1 (TBL1) and TBL1-related 1 (TBLR1) proteins. Loss of TBL1 in the hepatocytes and TBLR1 in the white adipocytes has been shown to impair fasting- and β-adrenergic-induced lipolysis. However, their roles in BAT thermogenesis remain unknown. Here, we report that deletion of TBLR1 alone in brown adipocytes does not impair the adaptive thermogenic response to prolonged cold exposure. In contrast, simultaneous deletion of TBL1 and TBLR1 dampens β-adrenergic-induced lipolysis and mitochondrial respiration in cultured mouse brown adipocytes. Transgenic mice with UCP1-Cre mediated double deletion of TBLR1 and TBL1 exhibit reduced whole-body energy expenditure during prolonged cold exposure, lower core body temperature, increased appearance of unilocular adipocytes in BAT, and suppressed expression of metabolic and myogenic PRDM16 target genes. Also, we found that TBLR1 and TBL1 interact with HDAC3 and PRDM16 in brown adipocytes, suggesting a direct involvement in PRDM16-controlled transcriptional program. These findings identify TBLR1/TBL1 complex as a critical regulator of BAT adaptation to prolonged cold and systemic energy homeostasis, shedding light on the context-dependent functions of corepressor complexes.

overall_design: RNA-seq profiling of brown fat from Ucp1CreERT2 positive TBLR1 fl/fl;TBL1 fl/fl and Ucp1CreERT2 negative TBLR1 fl/fl;TBL1 fl/fl control mice, housed at 30oC for 4 days and 8oC  for 6 days.

first: Sahika

last: Cingir Köker

first: Foivos-Filippos

last: Tsokanos

first: Rabih

last: El Merahbi

first: Ankush

last: Kumar Jha

first: Amit

last: Mhamane

first: Doris

last: Kaltenecker

first: Pauline

last: Morigny

first: Anne

last: Loft

first: Katarina

last: Klepac

first: Adriano

last: Maida

first: Claudia- Eveline

last: Molocea

first: Daniela

last: Hass

first: Elena Sophie

last: Vogl

first: Yongguo

last: Li

first: Mauricio

last: Berriel Diaz

first: Christian

last: Wolfrum

first: Alexander

last: Bartelt

first: Stephan

last: Herzig

first: Anastasia

last: Georgiadi


title: RNA sequencing of 4N intestinal and non-intestinal C. elegans cells in L1

city: Utrecht

first: Matilde

last: Galli

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Endomitosis is a non-canonical cell cycle in which cells undergo all four phases of a canonical cell cycle (G1, S, G2 and M), but do not initiate or complete cytokinesis during M phase. To identify the transcriptional differences between endomitosis and canonical cell cycles in C. elegans, we isolated cells from L1 larvae of a strain expressing intestinal-specific mCherry (elt-2p::mCherry-PH-P2A-H2B-mCherry) grown for 6 hours at 20ºC. We sorted intestinal and non-intestinal cells both with a 4N DNA content by FACS based on the mCherry expression and the Hoechst-34580 profile. We performed RNA-seq in intestinal (3 replicates) and non-intestinal cells (3 replicates) and differential gene expression analysis to identify the genes that are upregulated or downregulated in intestinal endomitosis compared to canonical cell cycles.

overall_design: mRNA profiles of intestinal (3 biological replicates) and non-intestinal cells (3 biological replicates) generated from pools of 500 cells with an adapted CEL-seq protocol and paired-end sequencingon an Illumina NextSeq500 platform.

first: Ramon

last: Barrull-Mascaró

first: Sonia

last: Veltkamp

first: Samia

last: Boutaibi

first: Lotte

last: van Rijnberk

first: Rebecca

last: Lippmann


title: ARD1 facilitates ferroptosis evasion via the induction of glutathione synthesis through catalysis of PABPC1 acetylation in HCC [CRISPR screen]

city: Wuhan

first: Minghe

last: Zhang

state: Hubei

address: Donghu Road

institute: WuHan University

summary: Aberrant upregulation of intracellular antioxidant glutathione (GSH) is implicated in promoting tumor proliferation, inducing drug resistance, and inhibiting ferroptosis across various malignancies, including hepatocellular carcinoma (HCC). However, the mechanism underlying the GSH metabolism reprogramming in HCC remains poorly understood. In this study, we employed a genome-wide CRISPR‒Cas9 screen and RNA-seq to identify ARD1 as a pivotal facilitator of de novo GSH synthesis in HCC. Notably, ARD1 upregulation is positively correlated with elevated GSH levels and a poor prognosis in HCC patients. In vivo and in vitro functional assays revealed that ARD1 promotes HCC cell proliferation and inhibits ferroptosis in a GSH-dependent manner. LC‒MS/MS-based stable isotope labeling revealed that ARD1 increases GSH levels by stabilizing the γ-glutamylcysteine ligase catalytic subunit (GCLC) transcript.  Overall, this research underscores the crucial role of ARD1 in GSH metabolic reprogramming and ferroptosis regulation in HCC and reveals a novel strategy for ferroptosis-based targeted therapy for HCC.

overall_design: The CRISPER-PoolTM KOUT human library containing 123,441 sgRNAs targeting 19,050 genes and 1,864 miRNAs was purchased from Genechem Co., Ltd. (Shanghai, China). After Huh-7 cells were transduced with various concentrations of the lentiviral library (2.5%-60%) for 72 hours, 2.5 μg/ml puromycin (Biosharp, China) was added to the medium, and the functional multiplicities of infection (MOIs) were assessed via a CCK-8 assay. A total of 2 × 108 Huh-7 cells were transduced with the corresponding amounts of lentiviral particles at functional MOIs to ensure 500-fold coverage and subjected to selection for cells stably infected for 72 hours with 2.5 μg/ml puromycin. The transduced cells were then divided into two groups and treated with or without the glutathione synthesis inhibitor buthionine sulfoximine (BSO; MCE, USA) at the IC20. Following 24 days of selection, at least 5 × 107 cells were collected and subjecred to  DNA extraction, PCR amplification and sgRNA sequencing.

first: Yingyi

last: Liu

first: MInghe

first: Yufeng

last: Yuan


title: Transcriptional profiling of brown preadipocytes with Low or High adipogenic potential

city: Québec

first: Mathieu

last: Laplante

state: Qc

address: 2725 Chemin Sainte-Foy

department: Medicine

country: Canada

institute: Université Laval

summary:
Brown adipose tissue (BAT) serves as a key heat-producing organ required to maintain body temperature and homeothermy in mammals. BAT recruitment and activation deeply impacts metabolic homeostasis in both mice and humans. Despite recent advances, the nature of the factors that functionally characterize brown adipose precursors is still incompletely characterized. Here, we provide a comprehensive transcriptomic analysis of brown preadipocyte cell lines with low or high adipogenic potential.
Here, we we used microarrays to define the transcriptional profile of brown preadipocytes with either low or high adipogenic potential. This analysis provides information about the processes that characterize the adipogenic commitment of brown preadipocytes.

overall_design: We performed limiting dilutions of an immortalized brown preadipocyte culture and successfully derived new clonal sub-lines that showed either a low, mid, or high capacity for lipid accumulation when stimulated with an established adipogenic cocktail.To define the transcriptional signature defining the adipogenic potential of brown adipocytes, we have run microarray analyses on low and high adipogenic lines prior to their differentiation, at sub-confluence.

first: Charles

last: Colas

first: Blandine

last: Secco

first: Mathilde

last: Mouchiroud

first: Romain

last: Villot

first: Laurence

last: Belley

first: Alona

last: Kolnohuz

first: Bochra

last: Chadel

first: Yves

last: Gélinas

last: Morissette

first: Nolwenn

last: Samson

first: Audrey

last: Poirier

first: Laura

last: Tribouillard

first: Alyson

last: Dufour

first: Manal

last: Al Dow


title: Interleukin 11 drives dermal fibroblast activation in mechanical stretch-mediated skin expansion

city: Shanghai

first: Yunhan

last: Liu

state: Shanghai

address: 639 Zhizaoju Road,

department: Department of Plastic and Reconstructive Surgery

institute: Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine

summary: In plastic and reconstructive surgery, mechanical stretch (MS) forces are frequently used to stimulate skin regeneration in order to produce additional skin for repairing tissue defects. Fibroblast activation in response to MS is crucial for skin growth during skin expansion. While its function in skin expansion is unknown, interleukin 11 (IL11) has been described as a cytokine that is increased in response to mechanical stimuli. In this study, we demonstrated that the expression of IL11 and IL11 receptor alpha subunit (IL11RA) was significantly increased in dermal fibroblasts (DFs) of the well-regenerated expanded skins (ESs) in human and mouse samples. However, IL11 was relatively lacking in the poorly-regenerated human ESs. Through the inhibition of IL11 signaling, MS-induced fibroblast proliferation, extracellular matrix (ECM) production, and myofibroblast activation were all inhibited in vitro. Consistently, depletion of IL11 signaling in vivo reduced skin regeneration during skin expansion, as evidenced by decreased dermal thickness and inhibited fibroblast function. Notably, transcriptomic analysis revealed that MS stimulation induced the upregulation of pathways associated with cell proliferation, collagen synthesis, stress response, and cell activation, whereas these pathways were downregulated in the IL11RA knockdown group. Mechanistically, we discovered that WNT5B acts as a downstream regulator of IL11-mediated cell activation in the presence of MS. Finally, the administration of recombinant IL11 via intradermal injection into mice significantly promoted fibroblast activation and halted the reduction in dermal thickness that occurred during skin expansion. In summary, our study demonstrated that IL11 signaling plays a crucial role in the activation of fibroblasts induced by MS, making it a promising target for clinical application in enhancing skin regeneration during skin expansion.

overall_design: To investigate the function of IL11 signaling in the regulation of MS-induced fibroblast activation, we established CCD-1064sk cell lines in which IL11RA gene has been knocked down by shRNA (NC，SH2, and SH3 ), and subjected them to control culture (Ctrl) or continuous static MS (MS) for 48h. We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different cells. Comparative gene expression profiling analysis of RNA-seq data for CCD-1064sk cells subjected with MS and IL11RA-ShRNA.

first: Tao

last: Zan


title: ChICseq analysis of active and repressive histone modifications in intestinal and non-intestinal C. elegans cells [ChIC-seq]

first: Matilde

last: Galli

summary: Endomitosis is a non-canonical cell cycle in which cells undergo all four phases of a canonical cell cycle (G1, S, G2 and M), but do not initiate or complete cytokinesis during M phase. We found that cytokinesis genes, as well as many cell-cycle genes, are transcriptionally downregulated during endomitosis of the C. elegans intestine. To understand the mechanisms underlying cell-cycle gene repression, we isolated cells from L1 larvae of a strain expressing intestinal-specific mCherry (elt-2p::mCherry-PH-P2A-H2B-mCherry) grown for one hour at 20ºC. We sorted intestinal and non-intestinal cells by FACS based on the mCherry expression. We performed ChIC-seq (or CUT&RUN) to map the H3K4me3, H3K9me3, H3K27me3 and H3K36me3 histone modifications and analyze whether promoter regions of cell-cycle genes are more enriched with active or repressive marks in intestinal cells undergoing endomitosis.

overall_design: ChIC-seq of H3K4me3 (3 biological replicates), H3K9me3 (2 biological replicates), H3K27me3 (3 biological replicates) and H3K36me3 (3 biological replicates) in intestinal and non-intestinal cells generated from pools of 1000 cells. A negative control where no antibodies were added (NoAb control) was performed in non-intestinal cell samples (2 biological replicates).

first: Ramon

last: Barrull-Mascaró

first: Sonia

last: Veltkamp

first: Samia

last: Boutaibi

first: Lotte

last: van Rijnberk

first: Rebecca

last: Lippmann


title: ARD1 facilitates ferroptosis evasion via the induction of glutathione synthesis through catalysis of PABPC1 acetylation in HCC

first: Minghe

last: Zhang

overall_design: PLC/PRF/5 cells were transfected with ARD1 overexpressing plasmids or control vector. After validation of transfection efficiency, cells were collected and utilized for RNA sequencing transcriptome analysis.

first: Yingyi

first: MInghe

first: Yufeng

last: Yuan


title: Disruption of the Placenta-Brain Axis in Transgenic Mice Lacking Serotonin Transporter (SERT) in Trophoblast Cell

city: Columbia

first: Trupti

last: Joshi

state: Missouri

address: 103 Math Science Building

department: Department of Biomedical Informatics, Biostatistics and Medical Epidemiology (BBME)

institute: University of Missouri-Columbia

summary: Selective serotonin reuptake inhibitors (SSRIs) are commonly prescribed drugs to pregnant women experiencing depression. While such drugs might be beneficial in combating depression by competitively binding to serotonin transporter (SERT), they can adversely affect the placenta and fetal brain development. Parietal trophoblast giant cells (pTGCs) in the mouse placenta are postulated to internalize maternal serotonin (5-HT) via transport through SERT, encoded by Slc6a4. The placenta provides the initial source of 5-HT to the emerging brain via the placental-brain axis. Disruption of 5-HT acquisition by pTGCs due to genetic deletion of Slc6a4 is hypothesized to impact placental and fetal brain development. A transgenic mouse line with the SERT transporter selectively deleted was created by pairing mice with Cre-recombinase linked to proliferin (Prl2c2) with LoxP sites flanking the Slc6a4 gene. Proliferin is solely expressed by pTGCs and other giant cells of the placenta. To compare placental and fetal brain development in selective Sl6a4 KO and WT mice, 5-HT content in the placenta and fetal brains of the mice was measured. No significant differences in 5-HT content were evident between knockout (KO) and wild-type (WT) placenta and fetal brain. However, there was significantly lower average number of pTGCs in KO placentas compared to WT (p ≤ 0.05). Sexually dimorphic differences in gene expression were evident in the placenta and fetal brain between KO and WT counterparts with female conceptuses showing the most dramatic responses. Findings suggest that ablation of SERT in pTGC disrupts the placenta-brain axis in a sex-dependent manner. These results might have important clinical ramifications for pregnant women being treated with SSRIs.

overall_design: RNAseq profiling of Slc6a4 WT and Slc64a4/SERT KO fetal brain and placenta mouse samples that were extracted at E12.5.

first: David

middle: T

last: Ellenberger

first: Zhen

last: Lyu

first: Rosalind

last: Herrington

first: Jessica

middle: A

last: Kinkade

first: Gustavo

last: Leone

first: Ji Ying

last: Sze

first: Nathan

middle: J

last: Bivens

first: Robert

middle: F

last: Baker

first: Michael

last: Roberts

first: Cheryl

middle: S

last: Rosenfeld


title: Staphylococcus aureus delays wound repair by harnessing the agr quorum sensing system to target keratinocyte lipid metabolism [scRNA-seq]

city: La Jolla

first: Michelle

middle: D

last: Bagood

email: mbagood@ucsd.edu, mdbagood@gmail.com

state: CA

address: 9452 Medical Center Dr.

institute: UCSD

summary: We used single cell sequencing to examine the response of murine dorsal skin and periwound tissue to vehicle, wild type S. aureus, or S. aureus agr mutant.

overall_design: Dorsal skin of C57 BL/6 mice was wounded or not and wounds or intact skin were inoculated with vehicle, S. aureus, or S. aureus agr mutant. 24 hours after wounding and inoculation, 2mm of intact or periwound tissue was collected and analyzed with scRNAseq.


title: Staphylococcus aureus delays wound repair by harnessing the agr quorum sensing system to target keratinocyte lipid metabolism [Spatial Transcriptomics]

summary: We performed spatial transcriptomics to characterize wound tissue response to commensal and pathogenic staphylococcus strains. Our analysis has revealed unique epithelial responses to each strain.

overall_design: Murine intact dorsal skin and dorsal skin wounds that were treated with different staph strains were embedded in the same FFPE block and then analyzed using spatial transcriptomics.


title: UCHL5 promotes Tumorigenesis of Bladder Cancer by Activating AKT/mTOR signaling pathway and targeting c-myc, SLC25A19, and ICAM5.

first: Yuanfei

last: Cao

state: hubei province

address: 169 Donghu Road

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

summary:
Purpose: To investigate the tumor-promoting role of UCHL5 in bladder cancer.
Method: We established the UCHL5 knockdown cell line in which the target gene was knocked down by shRNA. RNA was extracted from cells using trizol reagent(Invitrogen)
Result: Through RNA-sequencing analysis of wild-type and UCHL5 deficient T24 cell lines, the downstream signaling pathways that UCHL5 may be involved in were determined. We found that the AKT/mTOR signaling pathway and c-Myc,SLC25A19, and ICAM5 were significantly inactivated when UCHL5 was knocked down in bladder cancer.
Conclusion: UCHL5 enhances the AKT/mTOR pathway, which consequently upgraded the expression of c-myc,SLC25A19, and ICAM5, ultimately promoting the occurrence and progression of bladder cancer. UCHL5 may suggest potential utility for bladder cancer therapy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for T24 cells and its KD derivatives (shUCHL5).

first: Hua

last: Yu

first: Tao

last: Liu

first: Tongzu

last: LIIu


title: Transcriptomic Evidence of Acquired Cannabis Hypersensitivity in Cannabinoid Hyperemesis Syndrome

status: Public on Aug 01 2025

city: Washington, DC

first: Timothy

last: McCaffrey

state: District of Columbia

address: 2300 I Street, NW, Ross Hall #203

institute: The George Washington University Medical Center

summary: Cannabinoid hyperemesis syndrome (CHS) is a paradoxical and increasingly prevalent disorder characterized by recurrent vomiting in people with chronic cannabis use. Despite its growing clinical impact, the underlying mechanisms remain poorly understood. Contrary to prevailing hypotheses implicating the endogenous cannabinoid system (ECS), we found no significant changes in ECS-related transcripts. Instead, CHS was associated with marked activation of the adaptive immune system, including upregulation of B-cell related immunoglobin transcripts and altered expression of T cell, monocyte, and neutrophil-related transcripts. DEGs also suggested increased matrix degradation, and reduced adhesion and protease inhibitor transcripts, consistent with impaired gut barrier function. Digital HLA isotyping revealed increased MHC Class I expression, Class II allele restriction, and down-regulation of IgE receptor transcripts, a known response to elevated IgE levels in allergic hypersensitivity. Together, these findings suggest that CHS may represent an acquired, gut-restricted, immune-mediated hypersensitivity response to cannabis. This transcriptomic analysis provides new mechanistic insights into CHS and lays groundwork for future studies to identify biomarkers, clarify immune triggers, and develop targeted therapies.

overall_design:
A genome-wide RNA sequencing was used to characterize transcriptomic differences and identify potential pathways involved in CHS pathogenesis. In this pilot study, whole blood RNA sequencing was performed on 7 patients with CHS and 7 matched controls. Differentially expressed genes (DEGs) were identified, annotated and analyzed by automated and manual analysis. RNA sequences were further analyzed by digital isotyping for HLA Class I and II allele usage.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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first: Andrew

last: Meltzer

first: Ziva

last: Cooper

first: Ryan

last: Heidish

first: Aditya

last: Loganathan

first: Tarun

first: Taylor

last: Bolden

first: Isabella

last: Lagunazad

first: John

last: Perkins

first: Kevin

last: Jaatinen

first: Jacob

last: Adelman

first: Joseph

last: Miller

first: Stephanie

last: Eucker

first: Eileen

last: Phillips


title: NagA deletion of Mycobacterium tuberculosis leads to a defective cell wall integrity and invokes unique host signatures rendering the pathogen attenuated in guinea pigs.

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

summary: Mtb N-acetylglucosamine-6-phosphate deacetylase (NagA, Rv3332) belonging to the amido-hydrolase superfamily catalyzes a reaction which generates vital amino-sugars required as precursors for Mtb cell wall biosynthesis or glycolysis. In this study, a nagA gene deletion mutant of Mtb was generated, which showed an altered cellular morphology and cell wall structure. In vitro experiments revealed the importance of NagA under lysosomal, hypoxic and antibiotic stress and in biofilm formation. MtbΔnagA mutant showed reduced bacillary count inside macrophages in comparison to the parental strain. Deletion of nagA rendered the pathogen attenuated in guinea pigs exhibiting significantly lower bacillary counts as well as much reduced pathological damage in infected tissues in comparison to the wild type strain. Moreover, guinea pigs infected with MtbΔnagA mutant showed cent percent survival rate. Further, RNA sequencing analysis of the lung tissues from infected guinea pigs revealed that MtbΔnagA infection led to significantly lesser changes in gene expression in the host compared to the uninfected control while inducing a stronger immune response.  In contrast, the virulent Mtb strain drastically altered the host transcriptome favouring its survival. To conclude, our study demonstrated the importance of NagA in M. tuberculosis pathogenicity establishing it as a potential anti-tubercular target. Further, we consider MtbΔnagA to have potential to be explored as a TB vaccine candidate.

overall_design: To investigate the role of NagA in the growth and pathogenesis of M.tuberculosis, we knocked out nagA by homologous recombination technique. We infected guinea pigs with wild type (Rv), nagA mutant (NK) and complemented strain of Mtb, aerogenically and then performed host RNA-Sequencing analysis. Type of sample: RNA isolated from infected/uninfected lung tissue of guinea pigs Experimental conditions: 10 weeks post infection Sample groups: RNA samples from guinea pigs infected with M.tuberculosis wild type strain (Rv), MtbΔnagA mutant strain (NK) or uninfected animals (UN) Replicates: Three replicates for each group Controls/References: RNA samples isolated from Mtb wild type strain infected (Rv) and uninfected guinea pigs (UN)

first: Neha

middle: L

last: Nagpal

first: Prachi

last: Nangpal

first: Madavan

last: Vasudevan

first: Garima

last: Khare


title: Long-chain fatty acid β-oxidation regulates embryonic development by H3K18 acetylation in mice [RNA-seq]

city: 温州

first: kefan

last: zheng

address: 瓯海区茶山街道温州医科大学

institute: wenzhou medical university

summary: Fatty acids are not only important as energy sources, but also playing crucial roles in maintaining cellular homeostasis.Inhibition of long-chain fatty acid β-oxidation (LCFAO) results in preimplantation developmental arrest, downregulated expressions of S phase-related genes, and loss of H3K18ac modification. By profiling the landscape of H3K18ac, we show that H3K18ac is enriched on the promoter regions of S phase-related genes and correlates with their expression. Taken together, we demonstrate that LCFAO could regulate mouse preimplantation development by H3K18ac, providing new evidence for metabolic-epigenetic crosstalk in regulating embryonic development.

overall_design: RNA-seq analysis of mouse 8-cell and morula embryos in both control and TMZ inhibitor-treated groups.

first: Qingran

last: Kong

first: Hao

last: Li

first: Qi

last: Zhao

first: Kefan

last: Zheng

first: Hongdi

last: Cui

first: Entong

last: Song


title: Impact of Mare Milk-Derived Small Extracellular Vesicles on Proliferation, Phagocytosis, and Migration in RAW264.7 Macrophage

city: Hohhot

first: Qin

last: Si

address: Hohhot, Inner Mongolia, China

institute: Inner Mongolia International Hospital

summary:
Mare milk is rich in nutrients and bioactive compounds, suggesting that its exosomes may possess immunomodulatory properties.
We used microarray technology to profile the global gene expression of mare milk-derived small extracellular vesicles (MM-sEVs) and identified distinct classes of differentially expressed miRNAs targeting pathways and associated with diseases.

overall_design: Mare milk-derived small extracellular vesicles (MM-sEVs) were isolated from three individual horses (T1, T2, T3) for RNA extraction and hybridization on microarrays. The study aimed to profile miRNA expression and identify targeted pathways and disease associations. Samples were collected to assess biological variability among different equine sources

first: Shuang

last: Wang

first: Qingkai

last: Lan


title: Selective inhibition of BRAF and CRAF sensitizes NF1-deficient malignant peripheral nerve sheath tumors to MEK inhibitors

city: Select

first: Angelina

middle: V.

last: Vaseva

address: Pediatrics

institute: Oregon Health Science University

summary: Background: Treatment for patients with malignant peripheral nerve sheath tumors (MPNST) is an unmet clinical need. Loss of NF1 in MPNST leads to hyperactivation of RAS oncoproteins, however little is known about relevant downstream oncogenic signaling and effective targeted therapies in MPNST are still lacking. Methods: Conditional gene expression, CRISPR-CAS9, and shRNA-mediated knockdown were used to perform gain/loss-of-function experiments to explore the effect of reconstituting the GTPase-activating protein-related domain of NF1 or knockdown of A/B/CRAF kinases on ERK signaling output and MPNST cell growth. Colony formation, cell proliferation and live cells imaging assays were performed to assess cell growth in response to genetic manipulations or drug treatments. Pathway enrichment analysis on RNA sequencing following drug perturbation, efficacy studies in cell-line-derived and patient-derived xenograft models, and immunoblotting/immunohistochemistry were conducted to assess tumor growth and ERK pathway activity in cells or in pharmacodynamic analyses of tumor xenografts. Results: NF1 loss activates RAS/ERK signaling through B/CRAF, and cell growth and ERK signaling of NF1-MPNST are dependent on B/CRAF, but not ARAF. Genetic or pharmacological inhibition of B/CRAF using paralog-selective RAF inhibitor (RAFi) significantly potentiates MEK inhibitor (MEKi) treatment through more effective suppression of ERK signaling and proliferation. This is shown in multiple traditional and patient-derived cell line and xenograft models, including those with acquired resistance to MEKi.

overall_design: Malignant Peripheral Nerve Sheath Tumor (MPNST) cell lines were treated with MEK inhibitor trametinib, BRAF/CRAF inhibitor LXH254, or the combination of both for 48hours. RNA sequencing was then performed and gene expression analysis was done from 3 cell lines.

first: Siyuan

first: Funan

last: He


title: Hells protects mitochondrial integrity via Nr2f2 suppression during osteoclast differentiation

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

summary: Osteoclasts are bone-resorbing cells essential for skeletal remodeling. The chromatin remodeler Hells has been implicated in epigenetic regulation during cellular differentiation, but its role in osteoclastogenesis remains unclear. To investigate the function of Hells in osteoclast differentiation, we performed RNA sequencing of bone marrow-derived macrophages (BMMs) treated with RANKL, with or without siRNA-mediated knockdown of Hells. This dataset provides transcriptomic profiles of Hells-deficient and control osteoclast precursors, offering insight into the epigenetic control of osteoclastogenesis.

overall_design: RNA-seq profiling of bone marrow-derived macrophages (BMMs) with or without HELLS knockdown at Day 2 of RANKL-induced osteoclast differentiation.

first: Myoung Jun

last: Kim


title: CUT&Tag profiling of H3K18LA modification in rat pancreas with acute pancreatitis

city: 安徽省合肥市新站区

first: 诗亚

last: 马

address: 安徽省合肥市瑶海区银领时代

institute: Anhui Medical University

summary: This study explores histone modification dynamics in acute pancreatitis. Sprague-Dawley rats were intraperitoneally injected twice with L-arginine (2.5 g/kg, 1-hour interval) to induce acute pancreatitis. Pancreatic tissues were harvested after 48 hours. CUT&Tag was performed using anti-H3K18LA antibody (IP) and corresponding input control to assess promoter-associated chromatin changes in the inflamed pancreas.

overall_design: Acute pancreatitis was induced in Sprague-Dawley rats by two intraperitoneal injections of L-arginine (2.5 g/kg) with a 1-hour interval. After 48 hours, pancreatic tissue was collected. CUT&Tag was performed using anti-H3K18LA antibody to identify histone modification patterns related to promoter activity. Input DNA from the same samples was used as control. The goal was to evaluate H3K18LA enrichment in the inflamed pancreas.

first: Xueying

last: Ma

first: Zhiyu

last: Han

first: Shiya

first: Zhaojian

last: Shen

first: Weili

last: Yu


title: Exploring the biological basis for the identification of different syndromes in ischemic heart failure based on joint multi-omics analysis

city: Zhengzhou

first: Yilin

last: Zhang

address: Zhengdong New District

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

summary: IHF is a major chronic disease that seriously threatens human health. Qi deficiency and blood stasis syndrome (QDBS), Yang deficiency with blood stasis syndrome (YDBS) and Yang deficiency and blood stasis with fluid retention syndrome (YDBSFR) are the basic syndromes of IHF in Chinese medicine. This study aims to explore the biological basis of the three IHF syndromes through integrated multi-omics research. We analyzed and integrated transcriptomic, proteomic, and targeted metabolomic data from IHF patients and healthy persons to obtain the key biomarkers and enriched pathways of QDBS, YDBS and YDBSFR(Registration No.: ChiCTR2200058314). These biomarkers were combined with clinical indicators to construct the "Disease-Syndromes-Clinical phenotypes-Biomarkers-Pathways" network, and the obtained differential genes and proteins were externally validated. The potential biomarkers for QDBS included SDHD, IL10, ACTG1, VWF, MDH2, COX5A, Valeric acid, Succinic Acid and L-Histidine, which were predominantly enriched in TCA cycle, oxidative phosphorylation, platelet activation, and neutrophil extracellular trap formation pathways, demonstrating associations with energy metabolism, coagulation system, and immune-inflammatory responses.YDBS potential biomarkers included TSHR, PRKG1, ATP1A2, GNAI2, APOA2, PLTP, 3-Hydroxybutyrate, Hexadecanoic acid and Palmitelaidic acid, and the combined pathways were mainly enriched in thyroid hormone synthesis, regulation of lipolysis in adipocytes, cholesterol metabolism and PPAR signaling pathways, correlating with hormonal regulation and lipid metabolism. The potential biomarkers of YDBSFR were CNGB1, KCNMA1, PIK3R2, HSPA8, C3, FH, Oxamic acid, N-Acetyl-L-alanine, 4-Hydroxyhippuric acid, and the combined pathways were mainly enriched in aldosterone-regulated sodium reabsorption, cGMP-PKG signaling pathway, neutrophil extracellular trap formation and TCA cycle signaling pathways, which are related to hormone regulation, signal transduction, immune-inflammatory response and energy metabolism. Platelet activation was involved in the whole process of IHF. External validation demonstrated the above core targets. This study investigated the biological basis of QDBS, YDBS and YDBSFR in IHF from a modern biomedical perspective, providing references for the objective research of TCM syndrome differentiation.

overall_design: RNA sequencing analysis of blood samples from QDBS, YSBS,YDBSFR patients with IHF.

first: Jingjing

last: Wei

first: Lijie

last: Qiao

first: Rui

first: Hongjie

last: Ren

first: Anshe

first: Yang

last: Sun

first: Aolong

first: Bin

last: Li

first: Xinlu

first: Mingjun

last: Zhu


title: RNA-seq profiling of Pleurotus ostreatus exposed to BBP with or without cytochrome P450 inhibition

city: Changsha

last: Zhuo

state: Hunan

address: Tianma 2nd Street , Yuelu District, Changsha, Hunan 410082, P.R.China

institute: GEMB

summary: This study provides transcriptomic insights into the degradation of butyl benzyl phthalate (BBP) by the white-rot fungus Pleurotus ostreatus. RNA-seq was conducted for samples treated with BBP alone or in combination with the cytochrome P450 inhibitor piperonyl butoxide (PB). The aim was to investigate the role of fungal enzymes in BBP metabolism. Differentially expressed genes related to xenobiotic degradation, oxidative stress, and P450 activity were identified and analyzed.

overall_design: Pleurotus ostreatus GEMB-PO1 was cultured under three conditions: control (CK), BBP treatment (50 mg/L), and BBP plus piperonyl butoxide (BBP+PB, 50 mg/L BBP with 1 mM PB). Fungal mycelia were harvested after 3 days for RNA extraction and sequencing. Three biological replicates were included for each group.

first: Yu

last: Xun

first: Ling

last: Feng

first: Nasi


title: PFOS perturbs mitochondrial metabolism in skeletal muscle in vivo

city: Clemson

first: William

last: Baldwin

state: SC

address: 132 Long Hall

institute: Clemson University

summary: The purpose of this project was to investigate the effects of PFOS on skeletal muscle in vivo. To perform this work, Cyp2b-null and hCYP2B6-Tg mice were treated with 0, 1, or 10 mg/kg/day PFOS for 21 days. Gastrocnemius muscle was collected during necropsy and various assays were performed. RNA seq was performed to determine what gene expression changes occured due to PFOS treatment and the difference between genotypes.

overall_design: Male and female Cyp2b-null and hCYP2B6-Tg mice (n = 3-5) were treated with 0, 1, or 10 mg/kg/day PFOS via oral gavage for 21 days. Mice were euthanized via carbon dioxide asphyxiation followed by heart puncture. Gastrocnemius muscle was collected and snap frozen in liquid nitrogen.

first: Jazmine

last: Eccles-Miller

first: Lanie

last: Williams


title: Immunostimulatory CELMoD combination overcomes resistance to T cell engagers caused by high multiple myeloma burden

city: Broomfield

first: Caleb

middle: Karl

last: Stein

state: CO

address: 12735 Yates Street

institute: Mayo Clinic

summary: Bispecific T cell engagers (TCE) targeting BCMA and CD3 induce deep hematologic responses in approximately 60% of heavily pre-treated multiple myeloma (MM) patients. Pre-treatment with iberdomide and dexamethasone reshaped the bone marrow T cell compartment, promoted infiltration of naïve T cells, and generated 100% response rates and the longest survival in subjects with high tumor burden. This was accompanied by more favorable T cell profiling, with limited expansion of regulatory T cells and exhaustion. In total, administering TCE following dexamethasone and iberdomide treatments provided deeper and more durable responses with reduced risk of CRS. Whole Bone Marrow single cell profiling of immune phenotype of untreated and treated de novo Vk murine model.

overall_design: Age matched de novo Vk*MYChCRBN mice with MM received vehicle, dexamethasone at 10 mg/kg, IBER at 10 mg/kg or combination. 23 hours later, mice were euthanized and BM cells collected. After ACK lysis, 8,000 mononuclear cells/sample were processed using the 10XGenomicsChromium single cell 3’V2 kit. For a subsequent repeat, we performed ACK lysis of samples from one mouse per treatment to obtain 5,000 mononuclear cells which were processed using the 10XGenomicsChromium automated single cell 5’v2 kit. Illumina libraries were sequenced on a partial Novaseq S4 lane to obtain 50,000 reads/cell. Gene counting was performed using Cell Ranger version 7.1.0 or higher.

first: Erin

last: Meermeier

first: Marta

last: Chesi


title: The Acetyltransferase ARD1 Induces Glutathione Synthesis to Facilitate Ferroptosis Evasion in Hepatocellular Carcinoma

first: Minghe

institute: WuHan University

summary: Aberrant upregulation of the intracellular antioxidant glutathione (GSH) is implicated in promoting tumor proliferation, inducing drug resistance, and inhibiting ferroptosis across various malignancies, including hepatocellular carcinoma (HCC). Targeting the mechanism underlying GSH upregulation in HCC could represent a therapeutic strategy to improve patient outcomes. In this study, we employed a genome-wide CRISPR‒Cas9 screen and targeted metabolomics to identify the acetyltransferase ARD1 as a pivotal facilitator of de novo GSH synthesis in HCC. Notably, ARD1 upregulation was positively correlated with elevated GSH levels and poor prognosis in HCC patients. In vivo and in vitro functional assays revealed that ARD1 promoted HCC cell proliferation and inhibited ferroptosis in a GSH-dependent manner. LC‒MS/MS-based stable isotope labeling revealed that ARD1 increased GSH levels by stabilizing γ-glutamylcysteine ligase catalytic subunit (GCLC) mRNA, which was mediated by the RNA-binding protein PABPC1. Mechanistically, ARD1 acetylated PABPC1 at K167, augmenting its cytoplasmic retention by disrupting PABPC1-importin α7 complex formation. Cytoplasmic PABPC1 then interacted with eIF4G to collaboratively stabilize GCLC mRNA, preventing its degradation, increasing GSH synthesis, and ultimately conferring ferroptosis resistance in HCC cells. Furthermore, oxidative stress induced by hydrogen peroxide suppressed ARD1 ubiquitination and degradation, thereby promoting PABPC1 cytoplasmic translocation and inducing GCLC expression. ARD1 suppression promoted sorafenib-mediated ferroptosis in HCC patient-derived xenograft tumors with high ARD1 and GCLC expression. Overall, this research uncovers an oxidative stress–ARD1–PABPC1–GCLC axis with a crucial role in GSH metabolic reprogramming and ferroptosis regulation in HCC and reveals a strategy for ferroptosis-based targeted therapy for HCC.

overall_design: Huh-7 and Hep-3B cells were transfected with siRNA targeting ARD1 or negative control.After validation of transfection efficiency, cells were collected and utilized for RNA sequencing transcriptome analysis.

first: Yingyi

last: Liu

first: Yufeng

last: Yuan