title: Human CD8+ T cell response in the lower airways during acute seasonal influenza infection

city: Saint Louis

first: Philip

last: Mudd

state: Missouri

address: 660 S. Euclid Ave.

department: Emergency Medicine

institute: Washington University in Saint Louis School of Medicine

summary: Lung tissue-resident CD8+ T cells facilitate viral clearance and protective immunity to influenza viruses in animal models. Their role during acute human infection is not clear. We use bronchoalveolar lavage samples collected from human subjects naturally infected with influenza B virus during the 2019-2020 influenza season to show that influenza-specific CD8+ T cells robustly expand in the lower airways during acute infection and target only a few epitopes from phylogenetically conserved internal influenza virus proteins. The expansion hierarchy of lower airway influenza-specific CD8+ T cells is not reflected in matched blood samples. Transcriptional analysis reveals a tissue-resident profile and less expression of cytotoxic effector molecules in lower airway influenza-specific CD8+ T cells. Collectively, we show that high-frequency, influenza-specific, mucosal tissue-resident CD8+ T cells recognizing a handful of conserved epitopes and exhibiting a unique functional phenotype expand in the lower airways during viral clearance, suggesting a role in controlling human infection.

overall_design: Examination of 8 single-cell RNA-seq samples with VDJ sequencing completed as biologic duplicates (samples A and B) from bronchoalveolar lavage cellular material obtained from 4 human subjects on a specific day post-onset of influenza-like illness symptoms. Matched examination of 4 single-cell RNA-seq samples with VDJ sequencing from FACS-sorted non-naive CD8+ T cells found in peripheral blood mononuclear cells  obtained from the same 4 human subjects who underwent phlebotomy at the time of bronchoscopy.


title: Monocytes acquire a tumor-associated IL1B program upon encountering patient-derived colon cancer organoids

status: Public on Feb 19 2026

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

type: Expression profiling by high throughput sequencing

summary: Tumor-associated monocytes and macrophages (TAM) accumulate in colorectal cancer (CRC) and play an active role in shaping the tumor microenvironment (TME). While they have been linked to both pro- and anti-tumor functions, understanding the cues that instruct the phenotype of individual subsets as well as their functional impact on the TME remains challenging. In this study, we established co-cultures comprising primary human monocytes and patient-derived organoids (PDOs) from CRC tumors to emulate myeloid cell/carcinoma interactions in vitro that drive tumor-associated monocyte  programming. Upon encountering PDOs, monocytes acquired a complex phenotype not reflected by classical TAM markers or polarization protocols. Single-cell RNA sequencing revealed that PDO-exposed monocyte transcriptionally resembled IL1B-programmed monocytes previously identified in CRC patients. This phenotype emerged independently of the tumors’ mutational profiles or CMS type. Mechanistically, soluble PDO-derived mediators induced the production of chemotactic CXCL2, CXCL5 and CXCL7, while phagocytic uptake of tumor debry limited the MHC class II-mediated antigen presentation capabilities of monocytes in co-culture. Additionally, our in vitro system allowed the functional assessment of PDO-exposed monocytes demonstrating a compromised capacity to mount an inflammatory response upon TLR stimulation. Together, our PDO–monocyte co-cultures offer a tractable, human-specific model system to study the interplay between epithelial cancer cells and monocytes, and advance our understanding of myeloid plasticity and function in cancer patients.

overall_design: Bulk RNA sequencing of EpCAM+ sorted PDOcells from patient 30 (PDO30) after four days of monoculture or co-culture with primary human monocytes

first: Bianca

last: Balzasch

first: Adelheid

last: Cerwenka


title: Phosphorylation of Runx protein controls thymocyte fate. [RNA-Seq]

city: Kanagawa

first: Kazuki

last: Okuyama

address: 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama

department: IMS

country: Japan

institute: RIKEN Yokohama

summary: To understand the impact of Runx3 WRPW variant on the gene expression profile, we performed RNA-seq using Runx3 +/+ and Runx3 +/WRPW mature CD8 SP thymocytes.

overall_design: Gene expression profiles in mature CD8 SP thymocytes from Runx3+/+ and Runx3+/WRPW mice were assessed by bulk RNA-seq analysis.

first: Chihiro

last: Ogawa

first: Satoshi

last: Kojo

first: Ichiro

last: Taniuchi


title: SRSF3 is a key regulator of epicardial formation

city: Oxford

first: Susann

last: Bruche

address: Institute of Developmental and Regenerative Medicine

department: Physiology, Anatomy & Genetics

country: United Kingdom

institute: University of Oxford

summary: The epicardium is a fundamental regulator of cardiac development and regeneration, functioning to secrete essential growth factors and to produce epicardium-derived cells (EPDCs) that contribute most coronary mural cells and cardiac fibroblasts. The molecular mechanisms controlling epicardial formation have not been fully elucidated. In this study, we found that the RNA-binding protein SRSF3 is highly expressed in the embryonic proepicardium and epicardial layer. Deletion of Srsf3 from the murine proepicardium led to proliferative arrest, which prevented proper epicardial formation. Induction of Srsf3 deletion after the proepicardial stage resulted in impaired epicardial proliferation and EPDC formation by E13.5. Single-cell RNA-sequencing showed SRSF3-depleted epicardial cells were eliminated, however, the surviving non-recombined cells became hyperproliferative and, remarkably, compensated for the early deficit, via a mechanism that involved Srsf3 up-regulation This unexpected finding attests the importance of SRSF3 in controlling epicardial proliferation, and highlights the significant confounding effect of mosaic recombination on embryonic phenotyping. Mapping the SRSF3–RNA interaction network by endogenous irCLIP identified binding to major cell cycle regulators, such as Ccnd1 and Map4k4, with both splicing and non-splicing roles. This research defines SRSF3 as a key regulator of epicardial cell proliferation.

overall_design: MEC-1 cells were seeded and transfected with 80pmol siRNA (control or two different oligos targeting Srsf3) using Lipfectamine RNAiMax 24h after seeding. Cells were harvested for RNA isolation 48h after transfection and RNA used to generate RNA-seq libraries to assess the impact of Srsf3 depletion on transcriptome and transcript processing.

first: Irina-Elena

last: Lupu

first: Anob

middle: M

last: Chakrabarti

first: Ian

middle: R

last: McCracken

first: Tamara

last: Carsana

first: Andia

middle: N

last: Redpath

first: Nicola

last: Smart


title: B Cell-Intrinsic Type I Interferon Signaling Contributes to Defective Vaccine [GEX]

city: Laval

first: Alain

last: Lamarre

state: Quebec

address: 531 Boul des Prairies,

department: Immunology virology

country: Canada

institute: Centre Armand-Frappier Santé Biotechnologie de l'INRS

summary: Affinity maturation and vaccine efficacy are compromised during chronic viral infections, yet the underlying mechanisms remain unclear. Using the LCMV Cl13 model, we show that IFN-I signaling in B cells plays a central role. IFN-I promotes early B cell activation but reduces clonal diversity and delays IgG1⁺ B cell entry into germinal centers, impairing high-affinity clone selection. Deletion of IFNAR1 in B cells partially restores NP-specific IGHV1-72 usage and GC access but fails to fully rescue affinity maturation, suggesting a contribution of extrinsic factors. Somatic hypermutation remains elevated in both genotypes, though slightly reduced in IFNAR1⁻/⁻ B cells. BASELINe analysis indicates weaker selection pressure in CDRs, potentially reflecting impaired affinity-based selection. This defect correlates with a reduced TFR/TFH ratio. Our results show that intrinsic and extrinsic IFN-I-dependent mechanisms synergize to disrupt B cell fate. These findings establish IFN-I as a key regulator of humoral immunity and highlight mechanisms underlying poor vaccine response.

overall_design: Three groups of mice were used: (1) LCMV-infected IFNAR1flox/flox mice or LCMV B IFNAR1+/+ (B cells with intact IFN-I signaling), including 2 females and 2 males; (2) LCMV-infected MB1cre IFNAR1flox/flox mice or LCMV B IFNAR1−/− (B cell-specific deletion of IFNAR1), including 1 female and 2 males; and (3) VSV-infected IFNAR1flox/flox mice (acute infection control), including 2 females and 1 male. Mice were infected with either LCMV Clone 13 or VSV and immunized with NP-CGG six hours later. Enriched splenic B lymphocytes were collected at day 14 post-infection.

first: Xavier

last: Laulhé

first: Yasmine

last: Adda-Bouchard

first: Guillaume

last: Lopez

first: Gabriel

last: Chamberlain

first: Anolie

last: Dubreuil

first: Tania

last: Charpentier


title: Integrated in vivo and multiparameter in vitro screen uncovers NFIL3 as driver of T cell dysfunction

city: New York

first: Sneha

last: Mitra

state: NY

address: 1275 York Avenue

country: USA

institute: Memorial Sloan Kettering Cancer Center

summary: CAR therapy has transformed the treatment landscape for hematological malignancies but its efficacy in solid tumors is limited, owing in part to insufficient functional persistence of the engineered T cells. To elucidate the basis for their functional decline, we conducted a multi- parameter in vivo discovery screen of 400 transcription factors, which revealed NFIL3 as a driver of CAR T cell dysfunction. Genetic disruption of NFIL3 in CAR T cells sustained their expansion, increased cytokine production, overall restraining terminal differentiation. Loss of NFIL3 enhances CAR T cell efficacy, improving tumor control and prolonging survival in xenograft and syngeneic mouse tumor models across different CAR designs. Under chronic stimulation, disruption of NFIL3 establishes a transcriptional state predictive of favorable clinical outcomes. Our findings underscore the power of comprehensive multi-parameter genetic screens conducted in vivo and reveal NFIL3 as a novel therapeutic target to enhance cancer immunotherapy.

overall_design: CAR T cells from two donors at the pre-stimulation, after two rounds and four rounds of tumor stimulation were counted and assessed for scRNA-seq analysis

first: Nayan

last: Jain

first: Yuzhe

last: Shi

first: Celina

last: May

first: Philip

last: Bucher

first: Anton

last: Dobrin

first: Zeguo

last: Zhao

first: Sophie

last: Hanina

first: Vinagolu

last: Rajasekhar

first: Christina

middle: S

last: Leslie

first: Franciso

middle: J

last: Sánchez-Rivera

first: Judith

last: Feucht

first: Michel

last: Sadelain


title: B Cell-Intrinsic Type I Interferon Signaling Contributes to Defective Vaccine [VDJ]

first: Alain

last: Lamarre

first: Xavier

last: Laulhé

first: Yasmine

last: Adda-Bouchard

first: Guillaume

last: Lopez


title: MondoA mediates transcriptional coordination between the MYC network and the integrated stress response in pancreatic ductal adenocarcinoma.

city: Seattle

first: Brian

last: Freie

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Peripheral nerve-targeting and pain-promoting transcriptomic signatures in early Guillain-Barré syndrome [scRNA-seq]

city: Richardson

first: Jayden

last: O'Brien

state: TX

address: 800 W Campbell Rd

department: Neuroscience

institute: The University of Texas at Dallas

summary: Guillain-Barré syndrome (GBS) is an autoimmune disorder that causes sensory loss, motor deficits, autonomic dysfunction, and chronic neuropathic pain. The most common GBS variant, acute inflammatory demyelinating polyradiculoneuropathy (AIDP), primarily results from immune attack against myelin surrounding cranial and peripheral axons and associated Schwann cells. Pathogenic peripheral myelin-specific antibodies are hypothesized to contribute to pathogenesis; however, the specific immune mediators responsible for driving autoimmune injury in early disease stages remain incompletely understood. We performed bulk and single-cell RNA sequencing on peripheral blood mononuclear cells collected from early untreated AIDP-variant GBS patients and healthy controls to comprehensively deduce leukocyte transcript and signaling pathway alterations and predict interactions between pathogenic leukocytes and peripheral nervous system cells that could drive disease. Bulk transcriptomics showed a type I and II interferon- and JAK/STAT-driven proinflammatory signature in myeloid cells, while CD8+ T-cells were highly proliferative and expressed axon guidance genes. Single-cell transcriptomics revealed dysregulation of regulatory and CD4+ effector memory T-cells indicative of poorly controlled type 1 and type 17 immune response. A subset of intermediate CD14+CD16+ intermediate monocytes with a highly activated phenotype uniquely upregulated genes related to angiogenesis and the interleukin (IL)-6 family cytokine oncostatin M. Interactome analysis between GBS leukocytes, Schwann cells, and sensory neurons predicted increased engagement of ligand-receptor pairs with nerve integrity and pain functions. These included epiregulin, interferon-beta, adrenomedullin, clusterin, IL-6, and IL-15. Activated intermediate monocytes participated in a CCL4 to CCR1/CCR5 interaction toward both sensory neurons and Schwann cells. These results unearth specific molecular interactions by which specific leukocyte populations in AIDP-variant GBS may induce peripheral nerve injury and drive associated neuropathic pain.

overall_design: Peripheral blood mononuclear cells were isolated from early GBS patient and control blood and analyzed using scRNA-seq.

middle: A

first: Joseph

middle: B

last: Lesnak

first: Ishwarya

last: Sankaranarayanan

first: Asta

last: Arendt-Tranholm

first: Nikhil

last: Inturi

first: Spoorthi

last: Sadasivuni

first: Hemanth

last: Mydugolam

first: Katelyn

middle: E

last: Sadler

first: Theodore

last: Price

first: Eroboghene

last: Ubogu


title: Chemifortification of leaves through enhanced metabolic flux to tocopherol biosynthesis and plastoglobule proliferation.

city: Valencia

first: Javier

last: Forment

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (Universitat Politècnica de València-CSIC)

summary: Plant biofortification with phytonutrients typically relies on metabolic engineering strategies known as “push” (enhancing biosynthetic flux), “block” (inhibiting competing pathways), and “pull” (promoting metabolite storage). Here, we describe a novel chemifortification approach independent of genetic manipulation. A chemical screening identified X57, a synthetic compound that simultaneously activates all three mechanisms to enhance leaf tocopherol content. Besides their dietary value as vitamin E, tocopherols protect plants against oxidative stress and they are highly appreciated antioxidants in food and cosmetic formulations. X57 exerts a primary “push” effect by inducing tocopherol biosynthesis, in part by reactivating a direct pathway that reduces geranylgeranyl diphosphate (GGPP) to phytyl diphosphate, bypassing the need for chlorophyll-derived phytol. Accordingly, X57 promotes tocopherol accumulation in etiolated seedlings and restores tocopherol synthesis in mutants deficient in phytol phosphorylation. The “block” effect is mediated by downregulation of GGPP consumption for carotenoid synthesis. X57 also induces a “pull” effect via proliferation of plastoglobules (PG), plastidial lipoprotein bodies that synthesize and store tocopherols. X57-induced PG proliferation is driven by increased tocopherol levels and upregulation of genes for PG structural proteins such as fibrillins. X57 thus provides a powerful chemical tool for non-genetic vitamin E biofortification but also to better understand the coordination of plastidial isoprenoid metabolism and plastid differentiation.

overall_design: RNA-seq profiling of 5-day-old Arabidopsis thaliana seedlings treated with the chemical compound X57 or with mock conditions (0.05% DMSO) for 5 hours.

first: Pablo

last: Perez-Colao

first: Gaetan

last: Glauser

first: Jorge

last: Lozano-Juste

first: Manuel

last: Rodriguez-Concepcion


title: Interplay between CoREST, p300 and retinoic acid signaling in Acute myeloid leukemia [ATAC-seq]

status: Public on Feb 20 2026

city: Miami

first: Ramin

last: Shiekhattar

state: Florida

address: 1501 NW 10th Avenue

department: Department of Human Genetics

institute: University of Miami - Sylvester Comprehensive Cancer Center

summary: The histone demethylase KDM1A (LSD1), a component of the CoREST corepressor complex, is highly expressed in hematologic malignancies and regulates hematopoietic differentiation. Despite its essential developmental role, LSD1 inhibition has emerged as a promising strategy to enhance retinoic acid (RA)-responsive gene expression in subsets of acute myeloid leukemia (AML). Here, we show that LSD1 physically interacts with RAR/RXR heterodimers at specific genomic loci, restricting chromatin accessibility and transcriptional activation of differentiation programs. Single-agent inhibition of LSD1 or HDACs promotes only partial differentiation. In contrast, Corin, a dual LSD1/CoREST inhibitor, synergizes with all-trans retinoic acid (ATRA) to induce robust myeloid differentiation and apoptosis. Corin treatment increases H3K4me3 and H3K27ac at promoters of ATRA-responsive genes and disrupts CoREST–RAR/RXR complexes, enabling recruitment of the coactivator p300. This epigenetic switch facilitates transcriptional reprogramming essential for terminal differentiation. Our findings identify the functional antagonism between CoREST and p300 as a regulatory axis of RA signaling in AML. Targeting this mechanism with Corin and ATRA re-sensitizes non-APL AML cells to RA-induced differentiation, suggesting a broader therapeutic approach for overcoming resistance in ATRA-refractory leukemias.

overall_design: AML cell lines were treated with ATRA and Corin or DMSO (vehicle control), followed by ChIP-seq, ATAC-seq, RNA-seq, and CUT&RUN to assess transcriptional and epigenomic changes.

first: Mina

last: M. Tayari

first: Helena

last: Gomes Dos Santos

first: Sadat

last: Dokaneheifard

first: Monica

last: Valencia

first: Felipe

last: Beckedorff

first: Arigela

last: Harikumar

first: Justin

last: M. Watts

first: Philip

last: A. Cole


title: Novel Epigenetic Mechanisms of Endogenous CSE/H₂S in Smooth Muscle Cells for Abdominal Aortic Aneurysm [ChIP-Seq]

city: Beijing

first: ying

last: zhao

state: Beijing

address: 167, Beilishi Road, Xicheng District, Beijing

country: China

institute: Fuwai Hospital, Chinese Academy of Medical Sciences

summary: In this study, ChIP - seq was employed to investigate the impact of CSE on epigenetic modifications in vascular smooth muscle cells (VSMCs) and to uncover its influence on genome - wide DNA binding. We conducted ChIP - seq experiments on H3K9me3, H3K9ac, and H3K4me3 using primary smooth muscle cells from CSE knockout mice and wild - type (WT) mice after 24 - hour stimulation with Ang II. Our finding demonstrated that endogenous CSE/H₂S in smooth muscle regulates the expression of extracellular matrix through epigenetic modifications and participates in the occurrence and development of abdominal aortic aneurysm (AAA).

overall_design: Primary aortic smooth muscle cells isolated from C57BL/6N mice and global CSE - knockout mice were stimulated with angiotensin II for 24 hours. Subsequently, ChIP - Seq of H3K9me3,H3k9ac and H3k4me3 in primary vascular smooth muscle cells from CSE whole - body knockout mice and C57BL/6N mice.

first: Ying

last: Zhao

first: Changting

last: Cui

first: Huimin

last: Gao

first: Yaping

last: Niu

first: Ling

last: Cheng

first: Xiaodie

last: Shao

first: Haizeng

last: Zhang

first: Yuan

last: Wang

first: Zhenzhen

last: Chen

first: Liming

last: Yang

first: Bin

last: Geng


title: Gene expression profiles of CAR-T cells expressing constitutively active mutants of STAT3 and STAT5 [STAT3_3+5 _CART_rested]

city: Tokyo

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

institute: Keio University

summary: Augmenting cytokine signaling represents a pivotal strategy to enhance the therapeutic efficacy of chimeric antigen receptor (CAR) T cell therapy. However, the distinct roles of the downstream transcription factors STAT3 and STAT5 remain insufficiently defined. To elucidate their individual contributions, we engineered CAR-T cells to express constitutively active mutants of STAT3 (Y640F; caSTAT3) or STAT5 (N642H; caSTAT5). In vitro, caSTAT3 CAR-T cells demonstrated superior effector functions and a pronounced memory-associated phenotype, accompanied by broader transcriptomic alterations compared to their caSTAT5 counterparts. Despite impaired proliferative capacity in vitro, caSTAT3 CAR-T cells exhibited reduced systemic toxicity and sustained antitumor activity across multiple in vivo tumor models. In contrast, caSTAT5 CAR-T cells showed efficient intratumoral accumulation but also disseminated into non-malignant tissues, resulting in fatal toxicity. Notably, co-expression of caSTAT3 and caSTAT5 synergistically promoted both effector function and long-term persistence of CAR-T cells. Collectively, these findings provide mechanistic insights into the differential roles of STAT3 and STAT5 signaling in shaping the functional and safety profiles of CAR-T cell therapies.

overall_design: Human CD8+ T cells derived from three different healthy donors were retrovirally transduced with an anti-CD19 CAR gene (FMC63-28z), in combination with caSTAT3, or with both caSTAT3 and caSTAT5. The CAR-T cells were cultured overnight in cytokine-free medium, after which RNA was isolated and gene expression profiles were analyzed by RNA sequencing.

first: Haosong


title: Gene expression profiles of CAR-T cells expressing constitutively active mutants of STAT3 and STAT5 [STAT3_5_CART_rested]

first: Zhang

last: Haosong


title: Peripheral nerve-targeting and pain-promoting transcriptomic signatures in early Guillain-Barré syndrome [bulk RNA-seq]

first: Jayden

last: O'Brien

overall_design: Peripheral blood mononuclear cells were isolated from early GBS patient and control blood samples, underwent fluorescence-activated cell sorting (FACS) for CD11b+, CD4+, and CD8+ cells. Each underwent RNA extraction for bulk RNA sequencing.

first: Joseph

last: Lesnak

first: Ishwarya

last: Sankaranarayanan

first: Asta

last: Arendt-Tranholm

first: Nikhil

last: Inturi

first: Spoorthi

last: Sadasivuni

first: Hemanth

last: Mydugolam

first: Katelyn

last: Sadler

first: Theodore

last: Price

first: Eroboghene

last: Ubogu


title: Gene expression profile of control and NGB knockdown human cerebral organoids at day 65.

city: Nankang

first: Yuan-Hsuan

last: Liu

state: Taipei

address: 128, Section 2, Academia Road

department: Research Center for Applied Sciences

country: Taiwan

institute: Academia Sinica

summary: We use single cell RNA sequencing (scRNA-seq) to analyze the impact of NGB on early neural development based on cerebral organoids model.

overall_design: Three-dimensional cultured human cerebral organoids, derived from human induced pluripotent stem cells (hiPSCs), possess the remarkable capability to reconstitute in vivo three-dimensional cell arrangements. Moreover, they can faithfully recapitulate functional neural activity and gene expression profiles akin to those observed in the human brain. In this study, we employed lentiviral vectors to transduce short hairpin RNA (shRNA) targeting the NGB sequence, thereby generating an hiPSC line with NGB knockdown. Subsequently, this hiPSC line was utilized to generate cerebral organoids with NGB knockdown (shNGB) for future experimental analyses.

first: Meng-Ting

last: Chung

first: Yi-Chung

last: Tung


title: Butyrate extends health and lifespan in mice with mitochondrial dysfunction

city: Madrid

first: María

last: Mittelbrunn

state: Madrid

address: C/ Nicolás Cabrera, 1

institute: Centro de Biología Molecular Severo Ochoa

summary: Mitochondrial diseases progressively lead to multisystemic failure with treatment options remaining extremely limited. To investigate novel strategies that alleviate mitochondrial dysfunction, we have generated a tamoxifen-inducible, knockout mouse model of mitochondrial transcription factor A (TFAM), a nuclear-encoded protein involved in mitochondrial DNA (mtDNA) maintenance, under the control of the ubiquitin gene promoter — Tfamfl/flUbCre‑ERT2 (iTfamKO) mice. Systemic TFAM deficiency triggers mitochondrial decline in a myriad of tissues in adult mice. Consequently, iTfamKO mice manifest multiorgan dysfunction including lipodystrophy, sarcopenia, metabolic alterations, kidney failure, neurodegeneration, and locomotor dysregulation, which result in the premature death of these mice. Interestingly, iTfamKO mice display intestinal barrier disruption and gut dysbiosis, with diminished levels of microbiota-derived short-fatty acids (SCFAs), such as butyrate. Mice with a deficient proof-reading version of the mtDNA polymerase gamma (mtDNA-mutator mice) phenocopy the dysfunction of the intestinal barrier and bacterial dysbiosis with reduced levels of butyrate, suggesting that different mouse models of mitochondrial dysfunction share deficient generation of butyrate. Transfer of microbiota from healthy control mice or administration of tributyrin (TB), a butyrate precursor, delay multiple signs of multimorbidity extending lifespan in iTfamKO mice. Mechanistically, butyrate supplementation recovers epigenetic histone acylation marks that are lost in the intestine of Tfam deficient mice. Overall, our findings highlight the relevance of preserving host-microbiota symbiosis in disorders related to mitochondrial dysfunction.

overall_design: To investigate the theraputic potential of tributyrin (TB) in gut barrier integrity upon mitochondria dysfunction, we analysed ileum transcriptomics in Tfamfl/flUbCre‑ERT2 (iTfamKO) mice

first: Enrique

last: Gabandé Rodríguez

first: Manuel

last: Gómez de las Heras

first: Álvaro

last: Fernández Almeida


title: LMO2 regulates epithelial-mesenchymal plasticity of mammary epithelial cells

city: Santa Cruz

first: Paloma

last: Medina

state: CA

address: 1156 High St.

institute: University of California Santa Cruz

summary: Cellular plasticity in mammary epithelial cells enables dynamic cell state changes essential for normal developmental but can be hijacked by breast cancer cells to drive tumor progression. However, the molecular factors that maintain cellular plasticity through the regulation of a hybrid cell state (epithelial/mesenchymal) are not fully defined. As LMO2 has been previously shown to regulate metastasis, here we determined  the role of LMO2 in the normal mammary epithelial cells . Using lineage tracing and knockout mouse models we find that Lmo2 lineage-traced cells persist long-term in the mammary gland, both in the luminal and basal layer but have limited proliferative potential. Lmo2 loss does not impact mammary gland development, but acute deletion decreases in vivo reconstitution. Moreover, LMO2 knockdown in mouse and human mammary epithelial cells (MECs) reduces organoid formation. We find that LMO2 maintains a hybrid cell state and LMO2 knockdown promotes mesenchymal differentiation. Transcriptional profiling of LMO2 knockdown cells reveals significant enrichment in the epithelial-mesenchymal transition (EMT) pathway and upregulation of MCAM, a negative regulator of regenerative capacity in the mammary gland . Altogether, we show that LMO2 plays a role in maintaining cellular plasticity in normal mammary epithelial cells, adding insight into the normal differentiation programs hijacked by cancer cells to drive tumor progression.

overall_design: Bulk RNA sequencing was performed on MCF10A lines derived from human mammary epithelium

first: Shaheen

last: Sikandar

first: Veronica

last: Haro-Acosta


title: Gene expression profiles of CAR-T cells expressing constitutively active mutants of STAT3 and STAT5 [STAT3_5_CART_in_vivo]

first: Yuki

last: Kagoya

overall_design: Human CD8+ T cells were retrovirally transduced with an anti-mesothelin CAR construct (ss1-28z) alone, or in combination with either constitutively active STAT3 (caSTAT3) or STAT5 (caSTAT5). NSG mice inoculated with AsPC-1 cells were individually infused with the three types of CAR-T cells, and subcutaneous tumors were harvested 12 to 15 days post-infusion. In each experiment, CD8+ CAR-T cells were isolated from the tumors, total RNA was extracted, and gene expression profiles were analyzed by RNA sequencing.

first: Zhang

last: Haosong


title: Gene expression and V(D)J profiles of B-lineage cells from bone marrow samples of healthy adults (HA) and patients with multiple myeloma (MM)  and light-chain amyloidosis (AL).

city: Pamplona

first: Carmen

last: González

state: Navarra

address: Av. de Pío XII, 55

institute: University of Navarra

summary: We employed single-cell RNA sequencing combined with BCR sequencing (scRNA/BCR-seq) to identify transcriptional differences between clonal B cells and non-clonal B cells from MM and AL patients versus their healthy counterparts.

overall_design: Freshly collected bone marrow aspirate samples and extracted B-lineage cell by fluorescent-activated cell sorting (FACS)


title: Cell fate specification and conversion generate foveolar cone subtype patterning in human retinal organoids

city: Pittsburgh

first: Clayton

middle: Pio

last: Santiago

state: Pennsylvania

address: 1622 Locust St.

department: Ophthalmology

institute: University of Pittsburgh

summary: The mechanisms that generate patterns of cell types unique to humans are poorly understood. In the central region of the human retina, the high-acuity foveola is notable, in part, for its dense packing of green (M) and red (L) cones and absence of blue (S) cones. To identify mechanisms that promote M/L and suppress S cone patterning in the foveola, we examined human fetal retinas and differentiated human retinal organoids. During development, sparse S-opsin-expressing cones are initially observed in the foveola. Later in fetal development, the foveola contains a mix of cones that either co-express S- and M/L-opsins or exclusively express M/L-opsin. In adults, only M/L cones are present. Two signaling pathway regulators are highly and continuously expressed in the central retina: Cytochrome P450 26 subfamily A member 1 (CYP26A1), which degrades retinoic acid (RA) and Deiodinase 2 (DIO2), which promotes thyroid hormone (TH) signaling. Both CYP26A1 null mutant organoids and high RA conditions increased the number of S cones and reduced the number of M/L cones in human retinal organoids. In contrast, sustained TH signaling promoted the generation of M/L-opsin-expressing cones and induced M/L-opsin expression in S-opsin-expressing cones, showing that cone fate is plastic. Our data suggest that CYP26A1 degrades RA to specify M/L cones and limit S cones and that continuous DIO2 expression sustains high levels of TH to convert S cones into M/L cones, resulting in the foveola containing only M/L cones. Since the foveola is highly susceptible to impairment in diseases such as macular degeneration, a leading cause of vision loss, our findings inform organoid design for potential therapeutic applications.

overall_design: Control human retinal organoids or organoids cultured with T3 for 10 days or 200 days were dissociated into a single cell suspension and run on the 10x Genomics Chromium Single Cell System platform using the Chromium Single Cell 3' Reagent version 3 gene expression chemistry. Libraries were sequenced on Illumina NextSeq 500 and processed through the Cell Ranger pipeline using the GRCh38 reference genome.

first: Katarzyna

last: Hussey

first: Kiara

middle: C

last: Eldred

first: Brian

last: Guy

middle: P

first: Ian

last: Glass

first: Tom

last: Reh

first: Seth

last: Blackshaw

first: Loyal

last: Goff

first: Robert

last: Johnston Jr


title: Gene expression profiles of CAR-T cells expressing constitutively active mutants of STAT3 and STAT5 [STAT3_5_CART_activated]

overall_design: Human CD3+ T cells from three healthy donors were retrovirally transduced with an anti-CD19 CAR construct (FMC63-28z) alone, or in combination with either constitutively active STAT3 (caSTAT3) or STAT5 (caSTAT5). The CAR-T cells were stimulated with NALM-6 and cultured for an additional three days. CD8+ CAR-T cells were then isolated, followed by RNA extraction and RNA sequencing for gene expression profiling.


title: Mutual regulation of spermatogenesis-speciﬁc Argonaute proteins and Insulin/IGF-1 signaling in aging control [RNA-Seq]

city: Boston

first: Alla

last: Grishok

address: 72 E Concord

institute: Boston University

summary:
The potential role of small interfering RNAs (siRNAs) produced from double-stranded RNA in aging has not been fully addressed.
The networks of genes regulated by siRNAs and their partner Argonaute proteins are best understood in C. elegans, a pioneering
model of aging and small RNA studies. Here, we describe synergistic lifespan extension of insulin/IGF-1 signaling (IIS) mutant age-
1(hx546) by rde-4 or alg-3; alg-4 deﬁciencies. By analyzing gene expression and siRNA populations in these IIS and RNAi mutants,
we show here that redundant spermatogenesis-speciﬁc Argonautes ALG-3 and ALG-4 are capable of regulating IIS, potentially through direct control of the Major Sperm Protein (MSP) genes in the germline. MSPs and MSP domains of some mammalian proteins are secreted and directly inhibit the Eph receptor (EphR). In turn, EphR interacts with and destabilizes PTEN, a major negative regulator of IIS. We show that enhanced MSP expression correlates with EphR mislocalization and elevated PTEN levels in oocytes of alg-3/4(-) worms. At the same time, ALG-3/4 expression is regulated by IIS. Thus, we propose mutual regulation of IIS and ALG-3/4 through secreted ligands.

overall_design: Sequencing of mRNA and lncRNA in C. elegans N2 wild type, rde-4(ne301), age-1(hx546), and age-1(hx546); rde-4(ne301) mutant young adults

first: Thomas

last: Liontis

first: Valentina

middle: T

last: Pannarale

first: Andres

last: Mansisidor

first: Sasiru

middle: K

last: Pathiranage

first: Jeeya

middle: Y

last: Patel


title: Novel Epigenetic Mechanisms of Endogenous CSE/H₂S in Smooth Muscle Cells for Abdominal Aortic Aneurysm

first: ying

last: zhao

summary: Background: The incidence of abdominal aortic aneurysm is increasing year by year. Its rupture is associated with a high mortality rate, and recurrence is extremely likely even after treatment. The gasotransmitter hydrogen sulfide (H₂S) and its key generating enzyme, cystathionine -γ -lyase (CSE), possess anti -inflammatory, antioxidant, and anti -apoptotic properties, and have a cardiovascular protective effect. However, the role of CSE in AAA development and progression remains elusive. Methods: Using smooth muscle cell-specific CSE-knockout mice as models and angiotensin II, β-aminopropionitrile as inducers, it was found that CSE knockout in smooth muscle cells increased AAA incidence and mortality. Experimental results confirmed smooth muscle endogenous CSE/H₂S is involved in AAA development. However, its molecular mechanism remains a key scientific issue urgently needing solution. Thus, whole-genome RNA sequencing analysis was carried out on primary aortic smooth muscle cells isolated from Ang II-stimulated C57BL/6J mice (CSE WT)  and global CSE-knockout mice (CSE KO) to identify potential key downstream genes regulated by CSE. Results: The RNA - seq data highlighted the crucial role of CSE in the regulation of extracellular matrix and the PRC complex, which has implications for the development of AAA.

overall_design: Primary aortic smooth muscle cells isolated from C57BL/6J mice and global CSE - knockout mice were stimulated with angiotensin II for 24 hours. Subsequently, we performed RNA sequencing to explore the changes in the gene expression profile after the reduction of CSE levels. Our aim was to elucidate the downstream effects of CSE deficiency on the transcriptome of vascular smooth muscle cells, so as to gain in - depth insights into its regulatory mechanisms in abdominal aortic aneurysm (AAA).

first: Ying

last: Zhao

first: Changting

last: Cui

first: Huimin

last: Gao

first: Yaping

last: Niu

first: Ling

last: Cheng

first: Xiaodie

last: Shao

first: Haizeng

last: Zhang

first: Yuan

last: Wang

first: Zhenzhen

last: Chen

first: Liming

last: Yang

first: Bin

last: Geng


title: Mutations in the microexon splicing regulator srrm4 have minor phenotypic effects on zebrafish neural development

city: Bethesda

first: Tripti

last: Gupta

state: MD

address: 6 Center Drive

institute: NICHD

summary: Achieving a diversity of neuronal cell types and circuits during brain development requires alternative splicing of developmentally regulated mRNA transcripts. Microexons are a type of alternatively spliced exon that are 3–27 nucleotides in length and are predominantly expressed in neuronal tissues. A key regulator of microexon splicing is the RNA-binding protein Serine/arginine repetitive matrix 4 (Srrm4). Srrm4 is a highly conserved, vertebrate splicing factor that is part of an ancient family of splicing proteins. To better understand the function of Srrm4 during brain development, we examined neural expression of zebrafish srrm4 from days 1–5 of development using fluorescence in situ hybridization. We found that srrm4 has a dynamically changing expression pattern, with expression in diverse cell types and stages during development. We then used CRISPR-based mutagenesis to generate zebrafish srrm4 mutants. Unlike previously described morphant phenotypes, srrm4 mutants did not show overt morphological defects. Whole brain morphometric analysis revealed a reduction in optic tectum neuropil in G0 crispants that, unexpectedly, was also not replicated in stable mutants. Sequencing of wild-type and mutant transcriptomes revealed only minor changes in splicing and did not support a hypothesis of transcriptional adaptation, suggesting that another, as yet, unidentified mechanism of compensation is occurring. srrm4 thus appears to have a limited role in zebrafish neural development.

overall_design: RNA-Seq analysis of srrm4[y712] homozygous mutant and sibling wild-type head RNA at 3 days post fertilization.

first: Harold

last: Burgess

first: Gennady

last: Margolin


title: Single nucleus RNA-seq of  mouse kidney throughout postnatal development.

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

summary: We sought to characterize transcriptomic changes in cells of the Loop of Henle throughout posnatal developed.

overall_design: Nuclei were obtained from digestion of kidneys from which the cortex had been grossly removed and analyzed with snRNA-seq.

first: Jane N.

last: Warshaw

first: Denise K.

last: Marciano


title: The transcriptome of Ixodes scapularis salivary glands at single cell resolution

city: Hamilton

first: Lucas

last: Tirloni

state: MT

address: 903 S 4th Street

department: LB

institute: NIAID

summary: Applications of transcriptomics have significantly advanced the identification of numerous tick salivary molecules involved in feeding and the transmission of tick-borne pathogens. In this study, we analyze the salivary gland transcriptome of Ixodes scapularis, the main vector of Borrelia burgdorferi in the U.S., at single cell resolution.

overall_design: The Ixodes scapularis ticks used in this study were obtained from the tick-rearing facility at Oklahoma State University (Stillwater, OK, USA). Prior to infestation, unfed ticks were maintained at 21°C and 85% relative humidity. One day before feeding, female ticks were paired with males to allow mating. Adult ticks were placed on the outer ear of four naïve female New Zealand rabbits, restricted by orthopedic stockinets that were glued in place. A total of 20 female and 20 male ticks (40 ticks per ear, 80 ticks per rabbit) were allowed to attach. To classify ticks by blood-feeding index, partially fed ticks were collected from the host based on engorgement size, sorted by weight, and divided into biological triplicates: an unfed group (UF) (15 females per replicate, weighing 1.6 mg in average), group G2 (5 females per replicate, weighing 7.2 mg in average), and group G5 (4 females per replicate, weighting 41.5 mg in average). After removal from the host, ticks were rinsed sequentially with 1% bleach, nuclease-free water, 70% ethanol, and a final rinse with nuclease-free water. Ticks were dissected within two hours of removal. Salivary glands (SGs) were isolated and stored in fresh, ice-cold, nuclease-free HBSS buffer (Invitrogen, Carlsbad, CA, USA). To prepare a single-cell suspension, the salivary glands were dissociated following a mechanical and enzymatic protocol. The resulting cell suspension was filtered through a 40 µm Flowmi cell strainer and centrifuged at 600 rcf for five minutes to pellet the cells. The pellet was then resuspended in an appropriate volume of HBSS media to achieve the target cell concentration. Cell counting and viability were assessed using trypan blue staining and a Neubauer chamber for visualization. The single cell suspensions were loaded (7,000 cells) onto a Chromium Controller for GEM (Gel Bead-In-EMulsion) generation in triplicate for three groups and barcoding using the Chromium Single Cell 3’ Reagent Kits according to the manufacturer's protocol (10x Genomics). After cDNA synthesis, amplification, and library construction, the libraries were sequenced by the Illumina NovaSeq 6000 System. The raw sequencing data were demultiplexed and processed using the Cell Ranger Software Suite (10x Genomics). Cell Ranger was used to perform sample demultiplexing, barcode processing, and single-cell gene counting. The 'cellranger count' function was applied for alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting. The genome of I. scapularis published in 2021 (University of Maryland) was used as the reference genome for the alignment.  Following generation of gene-cell matrices from Cell Ranger, further analysis was performed using Seurat v3, an R package for analysis of single cell RNAseq data. Quality control was not applied to exclude cells with high mitochondrial gene content, because mitochondrial genes were expected to be upregulated in feeding groups.  The gene expression matrix was then normalized and scaled. Variable features were identified using the 'vst' method in the 'FindVariableFeatures' function. Dimensionality reduction was performed using principal component analysis (PCA). The most significant principal components were selected for downstream analyses. Based on these components, shared nearest neighbor (SNN) graph-based clustering was performed. Clusters were visualized using Uniform Manifold Approximation and Projection (UMAP). For each cluster, differential gene expression was performed to identify cluster-specific marker genes. These markers were used to annotate cell clusters based on known marker genes for cell types.


title: Post-replicative chromatin accessibility predicts cell fate change.

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

summary: It has long been hypothesized that DNA replication is important in reconfiguring the chromatin landscape during cell identity changes in development, disease, and reprogramming contexts. There is now a large body of work showing that DNA replication indeed alters chromatin structure and composition, but a function for these changes has remained elusive. Using replication-coupled ATAC-seq in differentiating embryonic stem cells and reprogramming mouse embryonic fibroblasts, we profiled replicated and unreplicated chromatin within the same cells and observed de novo chromatin opening specifically in the replicated fraction. These opening events created an accessibility landscape similar to that seen in the unreplicated fraction from later timepoints, especially in reprogramming. By parsing reprogramming fibroblasts based on proliferative history, we confirmed that reprogramming potential can be predicted by proliferation rate. This work bridges the gap between replication-induced structural chromatin changes and functional consequences by demonstrating that replication facilitates a “window of opportunity” that advances the chromatin landscape during cell identity change.

overall_design: repli-ATAC-seq time series in differentiating mouse embryonic stem cells and reprogramming mouse fibroblasts, and ATAC-seq in reprogramming mouse fibroblasts sorted based on CellViolet proliferation staining.

first: Teresa

last: Knudsen

first: Nazaret

last: Reveron-Gomez

first: Alva

last: Biran

first: Nicolas

last: Alcaraz

first: Sihem

last: Cheloufi

first: Konrad

last: Hochedlinger

first: Joshua

last: Brickman

first: Kathleen

last: Stewart-Morgan


title: Dynamic Reprogramming of Stromal Pdgfra-expressing cells during WNT-Mediated Transformation of the Intestinal Epithelium - Figure 3J

city: Piscataway

first: Michael

last: Verzi

state: NJ

address: 145 Bevier Road,

department: Department of Genetics

institute: Rutgers University

summary: Stromal fibroblasts of the mesenchyme regulate critical signaling gradients along the crypt-villus axis1 and provide a niche that supports intestinal stem cells in the intestine. Here we report that Pdgfra-expressing fibroblasts secrete ligands that promote a fetal-like state in the intestinal mucosa during early WNT-mediated tumorigenesis. Using a mouse model of WNT-driven oncogenesis and single-cell RNA sequencing (RNA-seq) of mesenchyme cell populations, we revealed a dynamic reprogramming of Pdgfra+ fibroblasts that facilitates WNT-mediated tissue transformation. Functional assays of potential mediators of cell-to-cell communication between these fibroblasts and the oncogenic epithelium revealed that TGFB signaling is notably induced in Pdgfra+ fibroblasts in the presence of oncogenic epithelium, and TGFB was essential to sustain fetal-like growth of organoids ex vivo. Genetic reduction of Cdx2 in the β-catenin mutant epithelium elevated the fetal-like transcriptome and accelerated WNT-dependent onset of oncogenic transformation of the tissue in vivo. These results demonstrate that Pdgfra+ fibroblasts are activated during WNT-driven oncogenesis to promote a fetal-like state in the epithelium that precedes and facilitates formation of tumors.

overall_design: RNAseq analysis from Pdgfra-lo CD81+ cells sorted from mice 4 or 6 days after Apc inactivation in epithelial cells using Apcflox/flox and the Villin-CreERT2 driver.

first: Oscar

last: Pellon-Cardenas

first: Prateeksha

last: Rout

first: S

last: Hassan

first: E

last: Fokas

first: Ping

last: He

first: I

last: Patel

first: J

first: O

last: Plotsker

first: A

last: Wu

first: R

last: Kumar

first: M

last: Akther

first: Alexandra

last: Logerfo

first: DE

last: Wagner

first: D

last: Boffelli

first: KD

last: Walton

last: Manieri

first: Kevin

last: Tong

first: Jason

last: Spence

first: NJ

last: Bessman

first: RA

last: Shivdasani


title: CD36/FABP5/PPARδ signaling axis defines spontaneously proliferating cardiomyocytes in neonatal stages

city: Houston

first: Tamer

last: Mohamed

address: 6770 Bertner Avenue

institute: Baylor College of Medicine

summary: Spontaneously cycling cardiomyocytes (CMs) represent a rare and unique population in the neonatal heart with the potential to drive cardiac regeneration in adulthood. While previous studies have observed their existence, the mechanisms regulating their cell cycle activity remain poorly understood. Here, we aim to identify the signaling axis that defines the spontaneously proliferating CMs in the neonatal stage.

overall_design: Using single-cell RNA sequencing of neonatal mice CMs at postnatal day 1 (NMCMs-P1) we identified CD36 as a marker of the spontaneously proliferating CMs and those who respond to the cell cycle induction. Both Cd36 global and CMs-specific knockout mice (CD36KO, CD36CKO) exhibited smaller hearts, fewer CMs, impaired CM proliferation, and limited regenerative capacity at P1 following apical resection. Bulk-RNAseq in CD36KO and CD36CKO showed downregulation of cell cycle genes, as well as Fabp5, Pparδ, and Rxrs. Spatial transcriptomics for P1 wild-type (WT) mice hearts identified and localized a subpopulation of CMs with high cell cycle activity and co-expression of Cd36, Fabp5, and Pparδ. To define the upstream modulator of this signaling pathway, we conducted spatial metabolomics which revealed a decrease in CD36KO and CD36CKO cardiac intracellular contents of retinyl ester which was further confirmed with quantitative internalization assays. At Nano molar concentrations, retinoic acid (RA) enhanced the cell cycle activity of WT-P1 NMCMs but not the CD36KO. Knockdown of Fabp5 abolished the RA effect on CM proliferation, while its overexpression enhanced the effect of RA. Crossbreeding CD36KO mice with Pparδ-cardiac specific overexpressing mice rescued the proliferative phenotype, restoring CM proliferation and regenerative capacity after apical resection in P1 to the WT levels. Furthermore, Pparδ overexpression in neonatal mice resulted in enhanced CM proliferation and improved regenerative capacity following apical resection.

first: Abou Bakr

last: Salama


title: Phosphorylation of Runx protein controls thymocyte fate.

city: Kanagawa

first: Kazuki

last: Okuyama

address: 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama

institute: RIKEN Yokohama

summary: To understand the impact of Runx3 WRPW variant on the histone marks, we performed ChIP-seq of H3K4me3 and H3K27me3 using Runx3 +/+ and Runx3 +/WRPW mature CD8 SP thymocytes.

overall_design: Investigation of alteration of H3K27me3 marks between Runx3 +/+ and Runx3 +/WRPW mature CD8 SP thymocytes.

first: Chihiro

last: Ogawa

first: Satoshi

last: Kojo

first: Ichiro

last: Taniuchi


title: YAP activation reverses aging-related visual dysfunction caused by impaired cell-matrix adhesion

city: Ulsan

first: Hyo Kyung

last: Lee

address: UNIST-gil 50

department: Biomedical engineering

country: South Korea

institute: UNIST

summary: Cellular senescence of retinal pigment epithelium (RPE) cells is a major contributor to age-related visual decline, particularly in the pathology of age-related macular degeneration (AMD). While genome-wide association studies (GWAS) have advanced our understanding of the genetic factors underlying AMD, the molecular mechanisms driving RPE senescence remain poorly understood. In this study, we performed single-cell RNA sequencing (scRNA-seq) on RPE cells from young and old mice, uncovering a close relationship between dysregulated genes involved in cell-matrix adhesion and RPE senescence. Using hydrogel systems to manipulate integrin-mediated cell-matrix adhesion, we demonstrated that impaired adhesion can induce cellular senescence in RPE cells. Mechanistically, we identified the mechanotransducer Yes-associated protein (YAP) as a key protector against RPE senescence. Notably, YAP activation alone was sufficient to trigger stem cell transcriptional programs and reverse aging phenotypes in senescent RPE cells. Furthermore, treatment with TRULI, a small-molecule YAP activator, significantly restored visual function in both an AMD mouse model and naturally aged mice. Our findings highlight the integrin-YAP mechanotransduction pathway as a fundamental mechanism preventing RPE senescence, positioning YAP activation as a promising strategy to reverse RPE aging and restore visual function.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
For scRNA-seq, young and old mice were sacrificed to dissociate cells from the RPE. Their eyes were immediately enucleated and the anterior eye cups were subsequently dissected. After carefully removing the retina, RPE cells were dissociated following the manufacturer’s instruction for the papain dissociation system (Worthington).
To analyze transcriptome profiles of three human ARPE19 cell line samples, ARPE19 cells expressing control vectors were cultured either on plastic or 1.5 kPa, and cells with overexpression of YAP-HA were cultured on 1.5 kPa.
For mouse samples, old mice treated either with or without TRULI were sacrificed for RNA extraction, and their eyes were immediately enucleated.

first: Gyuri

last: Kim

first: Chanok

last: Son

first: Yujeong

last: Oh

first: Jae-Byoung

last: Chae

first: Chul-Woo

last: Park

first: Chaekyu

first: Ja-Hyoung

last: Ryu

first: Semin

first: Jiwon

last: Jang

first: Hyewon

last: Chung


title: Mutual regulation of spermatogenesis-speciﬁc Argonaute proteins and Insulin/IGF-1 signaling in aging control [smallRNA-Seq]

first: Alla

last: Grishok

type: Non-coding RNA profiling by high throughput sequencing

summary: The potential role of small interfering RNAs (siRNAs) produced from double-stranded RNA in aging has not been fully addressed. The networks of genes regulated by siRNAs and their partner Argonaute proteins are best understood in C. elegans, a pioneering model of aging and small RNA studies. Here, we describe synergistic lifespan extension of insulin/IGF-1 signaling (IIS) mutant age-1(hx546) by rde-4 or alg-3; alg-4 deﬁciencies. By analyzing gene expression and siRNA populations in these IIS and RNAi mutants, we show here that redundant spermatogenesis-speciﬁc Argonautes ALG-3 and ALG-4 are capable of regulating IIS, potentially through direct control of the Major Sperm Protein (MSP) genes in the germline. MSPs and MSP domains of some mammalian proteins are secreted and directly inhibit the Eph receptor (EphR). In turn, EphR interacts with and destabilizes PTEN, a major negative regulator of IIS. We show that enhanced MSP expression correlates with EphR mislocalization and elevated PTEN levels in oocytes of alg-3/4(-) worms. At the same time, ALG-3/4 expression is regulated by IIS. Thus, we propose mutual regulation of IIS and ALG-3/4 through secreted ligands.

overall_design: Sequencing of small RNAs in C. elegans N2 wild type, rde-4(ne301), age-1(hx546), and age-1(hx546); rde-4(ne301) mutant young adults

first: Thomas

last: Liontis

first: Valentina

last: Pannarale

first: Andres

last: Mansisidor

first: Sasiru

last: Pathiranage

first: Jeeya

last: Patel


title: The sMAF transcription factor MAFG is a potent driver of melanoma

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

summary: While common mutations in potent proto-oncogenes and tumor suppressors induce melanoma formation, no recurrent mutations associated with the late stages of melanomagenesis have been identified. Instead, non-mutational mechanisms such as the deregulation of transcriptiona or epigenetic programs typically promote the malignang progression and metastasis of melanoma. We have previously identified the small MAFG transcription factor MAFG as a critical target of the melanoma suppressor miRNA miRN-29, prompting an in-depth evaluation of the role of MAFG in melanoma. MAFG expression is elevated in melanoma compared to melanocytes and increases with tumor stage. Ectopic expression of MAFG in human melanocytes and melanoma cells enhances proliferation in virto and promotes melanoma growth in vivo. Moreover, MAFG overexpression in BRAFV600E; PTEN+/- mice accelerated melanomagenesis, significantly shortening overall survival. Despite being a critical NRF2 dimerization partner, NRF2 was dispensable for the effects of MAFG. Moreover, MAFG overexpression in melanoma had no effect on the activity of NRF2 transcriptional reporters, nor did it induce transcriptional programs associated with NRF2. RNA sequencing and pathway analysis revealed MAFG-mediated effects on melanoma-associated processes such as pigmentation. Indeed, MAFG downregulated MITF and its target genes in the pigmentation pathway in melanoma cells. We next analyzed the connection between MAFG and MITF and found that MAFG binds to MITF to impede its binding to melanocytic differentiation genes, thus promoting a less differentiated and more aggressive phenotype. Our study establishes MAFG as a potent driver of melanoma development through the relocation of MITF.

overall_design: RNA was isolated from WM164, A375 and SKMEL28 cells overexpressing either GFP or MAFG using Qiagen miRNease kit

first: Olga

last: Vera

first: Xiaoqing

last: Yu

first: Florian

last: Karreth


title: Methylation profiling of BRAF-altered pediatric low-grade gliomas

city: Toronto

first: Cynthia

last: Hawkins

state: ON

address: 555 University Ave.

department: Pediatric Laboratory Medicine

institute: The Hospital for Sick Children

summary: Gliomas are a major cause of cancer-related death in adolescents and young adults (AYA, ages 15-39 years). Different molecular alterations drive gliomas in children and adults leading to distinct biology and clinical consequences. At the convergence of these age groups - the AYA population – little is known about the implications of pediatric vs adult-type alterations. To address this, we analyzed a population-based cohort of 1456 clinically and molecularly characterized gliomas  aged 0-39 years. Potentially targetable pediatric-type alterations were found in 31% of AYA gliomas and conferred superior outcomes compared to adult-type alterations (p<0.01). AYA low-grade gliomas with specific RAS/MAPK alterations exhibited senescent phenotype, tended to arise in different locations and were associated with superior outcome compared with children, suggesting different cellular origins. IDH mutations, BRAF p.V600E and FGFR alterations were associated with risk of malignant transformation for hemispheric tumors with worse outcome with increased age.  These observations have significant implications for understanding gliomagenesis. These insights may provide rationale for earlier intervention for certain tumors to disrupt the typical behavior, leading to improved outcome.

overall_design: We aimed to understand the methylation profiles of pediatric low-grade gliomas with BRAF alterations. Formalin-fixed paraffin embedded (FFPE) tissue from 87 surgical specimens (29 BRAF fusion, 58 BRAF V600E) were profiled using Illumina Infinium EPIC arrays.

first: Bennett

last: Julie

first: Levine

last: Adrian

first: Hawkins

last: Cynthia

first: Tabori

last: Uri


title: Loss of miR-29a/b1 cluster reprograms the tumor microenvironment and contributes to immunosuppression in lung cancer

first: Carl

last: Gay

address: 1515 Holcombe Blvd

department: Thoracic-Head & Neck Med Onc

institute: The University of Texas MD Anderson Cancer Center

summary: Immune checkpoint inhibitors (ICI), like those that block PD-1/PD-L1, have revolutionized oncological therapy for patients with non-small cell lung cancer (NSCLC). However, most patients demonstrate no clinical benefit or acquire resistance, even in PD-L1+ populations, highlighting the critical need to dissect tumor survival dependencies to overcome resistance. Using our unique Kras/p53-driven lung cancer models which demonstrate acquired or intrinsic resistance to ICI, we performed single cell RNA-sequencing and focused on predicted upstream regulators of differentially expressed genes (DEGs) in the malignant cell cluster of resistant tumors. We found that the micro-RNA, miR-29, was downregulated in tumors with anti-PD-1 resistance, leading to significant upregulation of a multitude of miR-29 targets. Interestingly, we found that the immunosuppressive molecule Enpp2/ATX was one of these genes modulated due to miR-29 loss, and re-expression of miR-29 in anti-PD-1 resistant models diminished ATX tumor expression, diminished the fibrotic microenvironment, and increased CD8 infiltration. Additionally, analysis of lung adenocarcinoma patients revealed miR-29-high patients had increased CD8A expression and enrichment in immunoregulatory pathways. Together, these data provide evidence that the miR-29 family broadly regulates the tumor microenvironment, including anti-tumor immune-related pathways in lung cancer, through control of ATX among many other target genes, with implications in ICI response.

overall_design: Kras/p53 mutant murine lung cancer cells were implanted in vivo. The 344SQ are the parental line and the 140P (PD1R1) samples were derived from the 344SQ cells after in vivo treatment and resistance to anti-PD-1 therapy. The 344SQ and PD1R1 tumors were collected after 4 and 6 weeks of in vivo growth (T1 and T2) and analyzed by scRNA-seq for differentially expressed genes between the two models specifically in the malignant compartment.

first: Jessica

last: Konen

first: Yanhua

last: Tian

first: Yuanxin

last: Xi


title: Sex-specific KDM6A-HNF4A-CREBH network controls lipoprotein cholesterol metabolism and atherosclerosis via epigenetic reprograming of hepatocytes

city: HUDDINGE

first: Lin

last: Chen

address: Blickagången 16, Flemingsberg,Neo

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

summary: The liver is a central organ controlling lipid and cholesterol metabolism and plays a key role in regulating lipoprotein profiles and cardiovascular disease risk. Males and females show clear differences in cholesterol handling and susceptibility to atherosclerosis, but the molecular basis for these sex-specific effects remains incompletely understood. Here we show that the X-linked histone demethylase 6A (KDM6A) is essential for maintaining healthy cholesterol metabolism in the liver. Reducing KDM6A levels in human liver cells disrupts gene programs involved in lipoprotein regulation linked to cardiovascular disorders. Consistently, female mice lacking KDM6A specifically in hepatocytes develops pro-atherogenic blood lipoprotein profiles and increased atherosclerosis under genetic and dietary stress, whereas males are largely unaffected. Mechanistically, KDM6A cooperates with Hepatocyte Nuclear Factor 4 Alpha (HNF4A) to promote chromatin activation and enable CREBH (encoded by CREB3L3)-dependent transcription of lipid metabolic genes. These findings identify KDM6A as a sex-linked regulator of hepatic cholesterol metabolism.

overall_design: ChIP-seq of histone modification H3K4me1, H3K4me2, H3K27ac, H3K27me3 in HROHep03 cells, Huh1 cells(siLuc, siKDM6A and siHNF4A groups) and mice(WT and KO groups). ChIP-seq of CREBH in PCSK9+WD mice(WT and LKO groups). ChIP-seq of CREBH in HRO cells (siLuc and siKDM6A groups).

first: Rongrong

last: Fan


title: Sex-specific KDM6A-HNF4A-CREBH network controls lipoprotein cholesterol metabolism and atherosclerosis via epigenetic reprograming of hepatocytes [CUT&Tag]

overall_design: CUT&TAG of KDM6A in HROhep03, Huh7 and Huh1 cells(siLuc and siHNF4A group).


title: Microtranscriptome of canine tubulopapillary mammary tumors

city: Araçatuba

first: Flavia

middle: Lombardi

last: Lopes

state: São Paulo

address: Rua Clovis Pestana, 793

department: DAPSA

country: Brazil

institute: FMVA-UNESP

summary: We aimed to describe miRNA expression in tubulopapillary canine mammary tumors.

overall_design: Four female dogs, aged between 2 and 4 years, were presented at Luiz Quintiliano de Almeida Veterinary Hospital at the School of Veterinary Medicine, São Paulo State University (Unesp) for mastectomy. Immediately after resection, samples (n = 12, 3 per animal) were collected under ethical approval #2008-007478. Subsequently, part of each tissue sample underwent histopathological analysis and immunophenotyping, while the remainder was preserved in RNAlater (Thermo Fisher Scientific®) at 4ºC overnight and then stored at -80ºC. Control samples (n = 4) were harvested from the mammary tissue of female dogs that were ethically euthanized from non-infectious unrelated conditions. These samples were kept in RNAlater (Thermo Fisher Scientific®) at 4ºC overnight and then stored at -80ºC. RNA extraction was performed using the mirVana™ miRNA Isolation Kit (Thermo Fisher Scientific®), according to manufacturer’s instructions.

first: Nayra-Cristina

middle: H

last: Valle

first: Matheus

middle: F

last: Soares

first: Natália

last: Scaramele

first: Amanda

middle: O

last: Furlan

first: Maria-Fernanda

first: Juliana

last: Felix

first: Fernando

middle: V

last: Fernandes

first: Vinicius

last: Zamboni

first: Igor-Luiz

last: Senhorello

first: Alexandre

middle: L

last: Andrade


title: Sex-specific KDM6A-HNF4A-CREBH network controls lipoprotein cholesterol metabolism and atherosclerosis via epigenetic reprograming of hepatocytes [RNA-seq]

overall_design:
RNA-seq profilling of wildtype Huh7 and HROhep03 cells and their knockdown derivatives (siKDM6A, siHNF4A).  RNA-seq profilling of wildtype mice livers and KDM6A-LKO mice livers(both female and male).
RNA-seq profilling of wildtype Huh1 cells and their knockdown derivatives (siKDM6A, siHNF4A).  RNA-seq profilling of PCSK9+WD mice livers and KDM6A-LKO mice livers(female).


title: SHANK3 deficiency alters early progenitor dynamics and reveals shared pathways with neurodegeneration

city: São Paulo

first: Victor

middle: Hugo

last: Calegari de Toledo

state: SP

address: R. do Matão, 303 - Butantã

department: Genética

institute: Universidade de São Paulo

summary: Phelan-McDermid Syndrome (PMS), primarily linked to SHANK3 haploinsufficiency, presents with complex neurodevelopmental features, including developmental regression, whose underlying mechanisms are poorly understood. This study investigated the impact of SHANK3 disruption across multiple levels, from gene expression in patient-derived iPSC neurons to in vivo brain network activity. RNA-sequencing of iPSC-derived neurons from PMS patients with SHANK3 disruption only (n = 9) and controls (n = 7) revealed dysregulation in differential gene expression and co-expression modules linked to cell cycle, RNA metabolism, and metabolic pathways in SHANK3-mutated neurons. All modules were correlated with PMS regression and enriched for genes implicated in neurodevelopmental or neurodegenerative disorders, such as autism, ADHD, and Alzheimer’s disease. At the cellular level, SHANK3-mutated cultures exhibited increased proliferation of neural progenitors and intermediate progenitor markers. Differentiated neurons showed reduced morphological complexity, specific changes in postsynaptic marker density and puncta size, and electrophysiological characteristics suggestive of neuronal hyperexcitability. Electroencephalography (EEG) in a PMS patient cohort (n = 20) compared to controls (n = 30) demonstrated hyperconnectivity and excessive high-frequency oscillations, suggesting altered neural network dynamics. In summary, the use of different analytical approaches suggested that SHANK3 haploinsufficiency disrupts neurodevelopmental trajectories and revealed that regression in PMS may share common genes and pathways with neurodegeneration. We also characterized molecular and neurophysiological markers that can be useful in therapeutic protocols for PMS.

overall_design: In order to investigate the effect of SHANK3 haploinsufficiency, isolation and reprogramming of peripheral blood cells was conducted to differentiate into neurons. Total RNA was extracted from the cultured neurons and sequenced, and quantification data of transcripts was used for differential expression analysis and weighted gene correlation network analysis. The neuron cell cultures were also characterized through a variety of functional assays.

first: Elisa

last: Varella Branco

first: Elizabeth

last: Shephard

first: Igor

last: Cabreira Ramos

first: Ellen

last: Mirando Lacerda

first: Laura

last: Machado Lara Carvalho

first: Marcella

last: Almeida Fiuza

first: Mayara

last: Paschalidis

first: Claudia

last: Ismania Samogy Costa

first: Ana

last: Sanctis Girardi

last: Victorino Krepischi

first: Erasmo

last: Barbante Casella

first: Guilherme

last: Polanczyk

first: Karina

last: Griesi-Oliveira

first: Fabio

last: Papes

first: Lucas

last: Alvizi

first: Gerson

last: Shigeru Kobayashi

first: Maria

middle: R

last: Passos-Bueno


title: In vitro modeling of nutritional and mitochondrial-targeted therapies for osteosarcoma

city: Philadelphia

first: Marni

middle: J

last: Falk

state: PA

address: 3401 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: To investigate the effects of mitochondrial perturbation in osteosarcomas, we cultured cells in 10 mM galactose media which forces mitochondria to use oxidative phosphorylation to compare with standard culture in glucose media accompanied in some cell lines by additional drug treatments that further modulate mitochondrial function (cycloheximide, metformin) or are chemotherapies known to involve the mitochondria (ONC201, ONC206 Clp proteases.

overall_design: To asses the effect of galactose media and/or drug treatment, we performed RNA-seq on osteosarcoma cell lines.

first: Min

last: Peng

first: Heeyong

last: Yoon

first: Kelsey

last: Keith


title: AtDEK2, a dual histone mark reader regulates plant immunity

city: Gif Sur Yvette

first: Xiaoning

last: HE

address: 630,Rue Noetzlin

country: France

institute: universite-paris-saclay

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

overall_design: Refer to individual Series


title: RNA sequencing of WM164 cells overexpressing  tethered MafG-MITF (T-MGM)

first: jiqiang

last: yao

summary: To elucidate the functional role of MafG and MITF dimer, we constructed a tethered heterodiimer of MafG and MITF linked with a flexible linker and overexpress in WM164 cells to evaluate the effect in gene expression profile.

overall_design: RNA was isolated from WM164 cells  overexpressing GFP or  MafG-MITF thethered dimer (T-MGM) using Qiagen miRNease kit

first: Zulaida

last: Soto-Vargas

first: Xiaoqing

last: Yu

first: Florian

middle: A

last: Karreth


title: Defining molecular signatures of the solid/pseudopapillary and pseudoglandular patterns in so-called "solid-tubulocystic intrahepatic cholangiocarcinoma vs. NIPBL::NACC1 fusion hepatic carcinoma"

status: Public on Feb 18 2026

city: Birmingham

first: Amr

last: Elkholy

state: AL

address: 1824 6th Ave S, WTI 330A B

institute: University of Alabama at Birmingham

summary: Solid-tubulocystic variant of intrahepatic cholangiocarcinoma (ST-iCCA) is newly described entity characterized by two distinct histologic growth patterns: (1) solid sheets of tumor cells with focal necrosis giving pseudopapillary appearance and (2) tubular or pseudoglandular structures containing pink, colloid-like material. Tumor cells are inhibin-positive and harbor NIPBL::NACC1 fusion gene. To date, only 28 cases of ST-iCCA have been documented. While prior molecular studies provided insights into ST-iCCA, genetic profiles of individual histologic components have not been explored. This study presents first transcriptomic analysis comparing the solid/pseudopapillary and pseudoglandular components of ST-iCCA. Two cases of histologically confirmed ST-iCCA were identified for RNA sequencing which was performed on solid/pseudopapillary component, pseudoglandular component, and normal tissue. Analysis revealed distinct gene expression profiles for each pattern. Solid/pseudopapillary component uniquely overexpressed DMRTA1, NEXMIF, PRDM6, SORCS3, and NALF, while pseudoglandular component exhibited unique overexpression of HRG, ITIH3, TAT, APOA2, CP, ALDOB, CPS1, F2, KHG1, SERPINC1, HPX, C9, ADGRF1, MUC21, SAA2, SPRR2A, SAA1, FGL1, CFHR1, and LBP. These findings establish unique gene signatures for these variants of ST-iCCA, providing potential biomarkers for differential diagnosis, prognosis and targeted therapy. The distinct genetic profiles may also uncover novel therapeutic targets to address the aggressive nature of ST-iCCA.

overall_design: In this study, we aimed to investigate the gene expression of two histologically and molecularly confirmed cases of solid-tubulocystic variant of intrahepatic cholangiocarcinoma (ST-iCCA), focusing on differential gene expression patterns between the two concordant growth patterns: pseudoglandular (PG) and the solid/pseudopapillary (PP).

first: Prachi

last: Bajpai

first: Fatme

last: Ghandour

first: Ekta

last: Jain

first: Raima

last: Memon

first: Chirag

last: R Patel

first: Santhosh

last: Kumar Karthikeyan

first: Sankarasubramanian

last: Jagadesan

first: Babu

last: Guda

first: Farrukh

last: Afaq

first: Sooryanarayana

last: Varambally

first: Upender

last: Manne

first: Sameer

last: Al Diffalha


title: Transcriptome of canine tubulopapillary mammary tumors

first: Flavia

last: Lopes

summary: We aimed to describe mRNA expression in tubulopapillary canine mammary tumors.

first: Nayra-Cristina

last: Valle

first: Matheus

last: Soares

first: Natália

last: Scaramele

first: Amanda

last: Furlan

first: Maria-Fernanda

middle: S

first: Juliana

last: Felix

first: Fernando

last: Fernandes

first: Vinicius

last: Zamboni

first: Igor-Luiz

last: Senhorello

first: Alexandre

last: Andrade


title: Agonistic GITR therapy in combination with chemotherapy to promote tumor immunity in pancreatic ductal adenocarcinoma

city: Bern

first: Hanne

last: Hillen

address: Murtenstrasse 31

department: IGMP

country: Switzerland

institute: University Bern

summary: Despite advances immunotherapy has shown limited efficacy in pancreatic ductal adenocarcinoma (PDAC). The tumor microenvironment (TME) of PDAC is profoundly immunosuppressive, creating a barrier to effective antitumor immune responses. This work highlights the emerging role of co-stimulatory molecules, particularly the type I transmembrane protein glucocorticoid-induced TNFR-related protein (GITR), in modulating the immunosuppressive TME of PDAC. By enhancing T cell activation and effector functions, GITR holds promise as a target for novel immunotherapeutic strategies in PDAC.Here, we show that GITR is highly expressed and further increased by neoadjuvant chemotherapy in human PDAC and a murine PDAC model. GITR activation reduced the number of regulatory T cells and increased the number of activated cytotoxic effector lymphocytes in the TME, thereby reducing tumor growth and prolonging survival. Moreover, spatial transcriptomic analysis showed GITR expression primarily in lymphocytes in proximity to tumor cells in human PDAC. Altogether, our data present GITR as a potential novel target for neoadjuvant treatment that could be combined with standard chemotherapy.

overall_design: We used murine tumors grown from Pan02 cancer cells injected subcutaneously and harvested 14 day after injection. Three tumors for each condition were pooled before sequencing. One sample contains data from tumors grown in mice which received intraperitoneal injections of PBS on days 7 and 11 post cancer cell injection, and the other sample contains data from tumors grown in mice which received intraperitoneal injections of agonistic anti-GITR monoclonal antibody (DTA-1) on days 7 and 11 post tumor cell injection as well.

first: Steve

last: Robatel

first: Ivanina

last: Mutisheva

first: Joshua

last: Müller

first: Martin

last: Wartenberg

first: Feiyang

last: Ma

first: Lukas

last: Bäriswyl

first: Delphine

last: Lee

first: Robert

last: Modlin

first: Ulf

last: Kessler

first: Max

last: Nobis

first: Kaspar

last: Z'graggen

first: Mirjam

last: Schenk


title: Age-associated chromatin reorganization drives overexpression of a novel Btaf1 variant regulating HSC self-renewal and MkP differentiation in male mice

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

summary: Age-associated hematopoietic stem cell (HSC) dysfunction is accompanied by dramatic transcription changes, but it remains unclear whether specific transcripts could orchestrate these HSC aging phenotypes. Here, we performed epigenetic profiling in male mice to investigate the regulatory mechanisms underlying the HSC aging transcriptome and screen for potential aging driver genes. We show dysregulated 3D chromatin organization, altered histone modifications and changed chromatin accessibility shape the HSC aging transcriptome. From the compilation of these data, we identified a new looping structure formed between part of the Btaf1 gene and the whole Ide gene in old HSCs (OHSCs) which is accompanied by overexpression of a novel, shorter variant of Btaf1 (nBtaf1). Mechanistically, elevated expression of nBtaf1 drives the aging-associated overexpression of HSC- and megakaryocyte progenitor (MkP)-related genes by regulating TBP binding at their promoters which contributes to HSC expansion and elevated MkP production in aged mice. ShRNA mediated knockdown of nBtaf1 restores a younger HSC transcriptome and specifically represses aging-associated HSC expansion and elevated MkP production. In summary, our data provide high resolution analysis of a dysregulated HSC aging epigenome and reveal a novel Btaf1 variant that drives HSC aging phenotypes in mice.

overall_design: ChIP-sequencing, RNA-sequencing, and Hi-C were performed to compare the transcriptome between Young and Old mice samples.

first: Le

last: Zong

first: Yaqiang

last: Cao

first: Fei

first: Ferda

last: Tekin-Turhan

first: Wakako

last: Kuribayashi

first: Keji

last: Zhao

first: Isabel

last: Beerman


title: A novel potent and selective GCN2 inhibitor, APL-4098, has anti-leukemic activity through dysregulation of mitochondrial function

city: London

first: Kevin

last: Blighe

address: 207 Regent Street

institute: Clinical Bioinformatics Research Ltd.

summary: Purpose: GCN2, one of the four kinases that activate the Integrated Stress Response to maintain proteostasis, has been shown to support cancer cell growth and survival in multiple preclinical cancer models. Acute myeloid leukemia (AML) is an aggressive hematological malignancy with dismal prognosis and high relapse rates that is marked by a dependency on finely tuned proteostasis. Here, we investigate the anti-leukemic potential of a new small-molecule GCN2 inhibitor, APL-4098.  Experimental design: selectivity and potency of APL-4098 were assessed using biochemical and cell-based assays. Anti-leukemic effects were evaluated ex vivo in primary patient-derived AML and in vivo using cell line-derived (CDX) and patient-derived (PDX) xenograft models. Synergy of APL-4098 and venetoclax was examined in the PDX. RNA sequencing and metabolic assays were used to explore APL-4098 mechanism of action.  Results: APL-4098 exhibited nanomolar-range potency against and high selectivity for GCN2. APL-4098 showed strong anti-proliferative activity ex vivo across two independent cohorts of primary AML patient cells, including cytotoxic effects on the leukemia stem cells (LSCs) and in vivo, achieving 98% tumor growth inhibition in an AML CDX. In a PDX, APL-4098 preferentially depleted the LSC-enriched compartment and, in combination with venetoclax, reduced leukemia burden by over 98%. Transcriptomic and metabolic analyses revealed APL-4098 compromises mitochondrial function and elicits the mitochondrial unfolded protein response.  Conclusions: APL-4098 is a novel, potent and selective GCN2 inhibitor with strong preclinical efficacy against AML cells, including LSCs. Our findings support APL-4098 as a promising candidate for AML treatment.

overall_design:
Experimental design: selectivity and potency of APL-4098 were assessed using biochemical and cell-based assays. Anti-leukemic effects were evaluated ex vivo in primary patient-derived AML and in vivo using cell line-derived (CDX) and patient-derived (PDX) xenograft models. Synergy of APL-4098 and venetoclax was examined in the PDX. RNA sequencing and metabolic assays were used to explore APL-4098 mechanism of action.

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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: Monica

last: Roman-Trufero

first: Gavin

last: Whitlock

first: Claire

last: Seydoux

first: Bianca

last: Perfler

first: Armin

last: Zebisch

first: Richard

last: Butt

first: Matthew

last: Fuchter

first: Holger

last: Auner

first: Nadine

last: Clemo


title: Patient-derived cell lines unveil COL1A2 as a predictor of docetaxel resistance in breast cancer

city: Guiyang

first: jianjun

last: huang

state: Guizhou

address: 9, Beijing Road

department: School of Clinical Medicine

institute: Guizhou Medical University

summary: Breast cancer is the most common type of malignant tumour among women globally, with a major cause of cancer-related mortality worldwide. Chemoresistance presents a significant challenge in breast cancer therapy and serves as the primary factor contributing to tumour recurrence and metastasis. At present, there is a paucity of effective predictive strategies in this field. In this study, we successfully established patient-derived primary cancer cell lines (PCCL) from four patients with HR+/HER2- breast cancer (Luminal B, HER2 non-amplified) using primary cell culture technology. The retention of the original tumour's pathological characteristics and drug response heterogeneity was confirmed. The aim was to delve into the mechanisms and predictive models underlying chemotherapy resistance in HR+/HER2- breast cancer. Our investigation revealed varying sensitivities of PCCL to taxanes, including docetaxel. Through RNA sequencing and protein-protein interaction (PPI) network analysis, we discovered that the COL1A2 gene is significantly overexpressed in HR+/HER2- breast cancer patients exhibiting docetaxel resistance. Notably, this overexpression shows a negative correlation with the patients' pathological complete response rate (pCR) and recurrence-free survival (RFS). In functional assays, higher COL1A2 expression correlated with diminished docetaxel sensitivity in HR+/HER2-negative breast cancer cells. These findings are consistent with the imaging assessments and postoperative pathological outcomes of patients who underwent neoadjuvant therapy (AC-T regimen). These findings suggest that COL1A2 is associated with reduced chemotherapy sensitivity in HR+/HER2- breast cancer and may serve as a candidate biomarker to guide neoadjuvant taxane selection. Overall, this study provides a novel theoretical foundation for selecting neoadjuvant chemotherapy drugs for advanced breast cancer patients.

overall_design: RNA-seq of human Breast cancer: docetaxel-resistant group and docetaxel-sensitive group


title: Differential gene expression in thalamic postmortem tissue of subjects with obsessive compulsive disorder

city: Pittsburgh

first: Susanne

last: Ahmari

address: 450 Technology Dr Suite 223

department: Psychiatry

institute: University of Pittsburgh

summary: Obsessive-compulsive disorder (OCD) is a severe psychiatric illness associated with hyperactivity and hyperconnectivity in corticostriatalthalamocortical circuits of the prefrontal cortex. We previously identified dysregulated mRNA expression in the medial orbitofrontal cortex and striatum of subjects with OCD, affecting a wide range of processes and cell types. The purpose of this study was to examine OCD-related differential expression in the thalamus, using a postmortem cohort of 10 subjects with OCD and 11 unaffected comparison subjects. Tissue was collected from four higher-order thalamic nuclei: the mediodorsal magnocellular (MDmc), mediodorsal parvocellular (MDpc), ventral anterior (VA), and ventrolateral posterior (VLp) nuclei.

overall_design:
Frozen postmortem tissue was collected from 10 postmortem subjects with obsessive compulsive disorder (OCD) and 11 matched subjects with no psychiatric illnesses (CON). Tissue was collected from the mediodorsal magnocellular (MDmc), mediodorsal parvocellular (MDpc), ventral anterior (VA) and ventrolateral posterior (VLP) nuclei of the thalamus.
Data obtained from total RNA sequencing was used to assess OCD-related differential expression of mRNA and lncRNA genes

first: Shale

last: Springer

middle: E


title: The BOD1L subunit of the SETD1A complex sustains the expression of DNA damage repair genes despite restraining H3K4 trimethylation [single_end_RNAseq]

city: Dresden

first: Anna

last: Poetsch

address: Tatzberg 47/49

institute: TU Dresden

summary: Background  SETD1A is the histone 3 lysine 4 (H3K4) methyltransferase central to the mammalian version of the highly conserved eight subunit Set1 complex (Set1C) that apparently conveys H3K4 trimethylation (H3K4me3) onto all active Pol II promoters. Accordingly, the Setd1a mouse knock-out dies in early embryogenesis at the epiblast stage and mouse embryonic stem cells (ESCs) die when SETD1A is removed. Results We report that ESC death is accompanied by loss of expression of DNA repair genes and accumulating DNA damage. BOD1L and BOD1 are homologs of the yeast Set1C subunit, Shg1, and subunits of the mammalian SETD1A and B complexes. We show that the Shg1 homology region binds to a highly conserved central a-helix in SETD1A and B. Like mutagenesis of Shg1 in yeast, conditional mutagenesis of Bod1l in ESCs promoted increased H3K4 di- and tri-methylation but also, like loss of SETD1A, loss of expression of DNA repair genes, increased DNA damage and cell death. Conclusions In contrast to similar losses of DNA repair gene expression, the converse changes in H3K4 methylation after loss of SETD1A or BOD1L implies that H3K4 methylation is not essential for expression of the DNA repair network genes. Because BOD1L becomes highly phosphorylated after DNA damage and acts to protect damaged replication forks, the SETD1A complex, and BOD1L in particular, are key nodes for the DNA damage repair network.

overall_design: RNA-seq profiling of mouse embryonic stem cells

first: Giovanni

last: Ciotta

first: Sukhdeep

last: Singh

first: Andrea

last: Kranz

first: Ashish

last: Gupta

first: Davi

last: Coe Torres

first: Jun

last: Fu

first: Rupam

last: Choudhury

first: Nico

last: Liske

first: Wai

last: Kit Chu

first: Dmitrii

last: Severinov

first: Chuna

last: Choudhary

first: Lenka

last: Gahurova

first: Ali

last: Al-Fatlawi

first: Michael

last: Schroeder

first: Rein

last: Aasland

first: Konstantinos

last: Anastassiadis

first: Francis

last: Stewart


title: A novel Adnp frameshift variant disrupts Wnt signaling leading to chromatocytoskeletal defects and autism-related behavior in mice

city: Edegem

first: Dale

middle: John

last: Annear

state: Antwerpen

address: Prins Boudewijnlaan 43/6

department: Center of Medical Genetics

country: Belgium

institute: University of Antwerp

summary: Background: Heterozygous de novo variants in the transcription factor Activity-Dependent Neuroprotective Protein (ADNP) cause a severe neurodevelopmental disorder, termed the Helsmoortel-Van der Aa syndrome (HVDAS), that is characterized by autism, intellectual delay, and malfunctions in several other organ systems. The ADNP gene is essential for embryonic development and interacts with components of several chromatin remodeling complexes, though the exact pathophysiological mechanisms remain hidden.  Methods: We used CRISPR/Cas9 genome editing to create a 14-base pair deletion in the murine Adnp gene to study the effects of the variant in a heterozygous disease-relevant mouse model.  Results: Heterozygous mice carrying the c.2463_2476del (p.Leu822Hisfs*6) deletion are viable and fertile. Introduction of the 14-base pair deletion reduced cellular Adnp levels in the brain as well as its associations to chromatin, paralleled by a genome-wide increase in chromatin accessibility. Morphology analysis showed mild neuroanatomical changes in brain regions related to cognition, memory and learning, and motor skills. Behavioral testing in heterozygous Adnp mice confirmed cognitive defects in the Morris water maze test, increased anxiety in the elevated plus maze test, repetitive behavior after marble burying, and impaired social interactions. Transcriptome sequencing of the frontal cortex, an essential region involved in executive functions, cognition, and motor control, showed predominant downregulation of the Wnt signaling pathway. Cytoskeletal abnormalities were further coupled to synaptic plasticity deficits with dysregulated transcription factors implicated in lineage specification, as well as alterations in neuronal cell numbers. Adnp can also directly regulated mechanisms of synaptic plasticity by interacting with Camk2a and Dbn1. The frameshift variant interfered with these complexes and caused aberrant Camk2a phosphorylation at synapses. Mass spectrometry of the frontal cortex of heterozygous Adnp mice identified changes of multiple chromatin interacting proteins and cytoskeletal components, confirming chromatocytoskeletal dysregulations detected in the bulk transcriptome. Ultimately, Hi-C analysis detected fine-scale, locus-specific differences in 3D genome architecture in the heterozygous Adnp 14-base pair deletion mice, which are associated with transcriptional changes.  Conclusions: We generated a disease-relevant heterozygous Adnp mouse model that parallels many of the molecular and behavioral aspects observed in Helsmoortel-Van der Aa patients. We demonstrate that Adnp has a primary nuclear role involving Wnt signaling coupled with cytoskeletal deficits. Our novel mouse model is thus a valuable model to study the human disorder and may be used for preclinical studies.

overall_design: RNAseq of the frontal cortex in adolescent WT and HET littermates. Differential gene expression seven WT and seven HET mice was analyzed 13,383 expressed genes.

first: Claudio Peter

last: D’Incal

first: Elisa

last: Cappuyns

first: Flora

last: Paldi

first: Mathijs

middle: B

last: van der Lei

first: Dale John

first: Clara

last: Milián Alastruey

first: Frank

last: Kooy


title: Delta-8-Tetrahydrocannabinol Mitigates Murine Autoimmune Hepatitis through Epigenetic Regulation of Immune Dynamics

city: COLUMBIA

first: Hamida

last: Hamida

state: SC

address: 6311 Garners Ferry Road

department: Pathology, Microbiology & Immunology

institute: University of South Carolina School of Medicine

summary: Autoimmune hepatitis (AIH) is an immune-mediated liver disease characterized by an imbalance between effector and regulatory immune responses. Epigenetic regulation, particularly via microRNAs (miRNAs), is emerging as a critical modulator of the immune system during inflammatory diseases. Cannabinoids are increasingly recognized for their immunosuppressive and anti-inflammatory properties; however, the impact of delta-8-tetrahydrocannabinol (Δ⁸-THC), a novel minor compound found in Cannabis plant with less psychoactive property than Δ⁹-THC, remains entirely unexplored in combating autoimmune hepatitis. To address this gap, we investigated the immunoregulatory and hepatoprotective effects of Δ⁸-THC in Concanavalin A (ConA)-induced murine model of AIH. We found that Δ⁸-THC effectively ameliorated ConA-induced liver injury by restoring intrahepatic innate and adaptive immune homeostasis through the preservation of tolerogenic Kupffer cells, suppression of inflammatory monocytes, neutrophils, and natural killer cells. Moreover, Δ⁸-THC reversed the inflammatory lymphoid microenvironment in the liver caused by ConA by decreasing inflammatory CD4+ T cells and promoting expansion of regulatory T cells. These effects were correlated with the preservation of hepatoprotective miR-199a-3p and miR-100-5p expression in hepatic immune cells that were markedly downregulated in ConA-treated mice. Ingenuity Pathway Analysis identified mTOR, a key immune regulator of T cell differentiation, as a target of these miRNAs. Consistently, Δ⁸-THC treatment reduced hepatic mTOR expression in vivo and in vitro. Functional assays using miRNA mimics and inhibitors confirmed direct regulation of mTOR by these miRNAs, where miRNA-mediated mTOR suppression promoted regulatory T cells differentiation and inhibited Th1 and Th17 responses. Together, these findings identify Δ⁸-THC is as a novel anti-inflammatory and hepatoprotective compound that attenuates autoimmune liver injury through epigenetic regulation of the miRNA-mTOR signaling axis, revealing its potential immunomodulatory effects in autoimmune and inflammatory diseases.

overall_design:
Total RNA, including miRNA, was extracted from liver immune cells using the miRNeasy Mini Kit (QIAGEN, Cat# 217004). RNA quantity was determined with the Qubit High Sensitivity RNA Assay Kit (ThermoFisher, Waltham, MA). miRNA libraries were generated using the QIAseq miRNA Library Kit (QIAGEN) and sequenced on an Illumina NextSeq 550 plateform. The resulting FASTQ files were processed using the GeneGlobe RNA-seq Analysis Portal (QIAGEN) to perform sequence alignment and generate raw read counts.

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

last: Kakar

first: Manikandan

last: Palrasu

first: Amarnath

last: Marudamuthu

first: Xiaoming

last: Yang

first: Kiesha

last: Wilson

first: Prakash

last: Nagarkatti

first: Mitzi


title: The BOD1L subunit of the SETD1A complex sustains the expression of DNA damage repair genes despite restraining H3K4 trimethylation [paired_end_RNAseq]

first: Anna

last: Poetsch

first: Giovanni

last: Ciotta

first: Sukhdeep

last: Singh

first: Andrea

last: Kranz

first: Ashish

last: Gupta

first: Davi

last: Coe Torres

first: Jun

last: Fu

first: Rupam

last: Choudhury

first: Nico

last: Liske

first: Wai

last: Kit Chu

first: Dmitrii

last: Severinov

first: Chuna

last: Choudhary

first: Lenka

last: Gahurova

first: Ali

last: Al-Fatlawi

first: Michael

last: Schroeder

first: Rein

last: Aasland

first: Konstantinos

first: Francis


title: Asymmetry and redundancy of STAT5 paralogs across CD8+ T cell differentiation states

city: Maimi

first: Alejandro

last: Villarino

state: Florida

address: 1600 NW 10th Ave, Rosenstiel Medical Science Building (RMSB), Room 3152A

institute: University of Miami

summary: Fostering STAT5 signaling is key to immunotherapies that leverage CD8+ T cell biology. Using mouse models, we demonstrate that the two mammalian STAT5 paralogs, STAT5A and STAT5B, are at once redundant and functionally distinct in CD8+ T cells. Thus, they are asymmetric paralogs, exhibiting both widespread homology at molecular level and functional asymmetry at cellular level, with STAT5B emerging as dominant. For mechanisms, we determined that STAT5B is twice as abundant, accounting for two-thirds of the total STAT5 pool, and present evidence that it also has distinct, paralog-specific properties. We also defined cytokine- and cell state-restricted STAT5B functions and devised a core signature that spotlights key downstream properties and serves as bioinformatic probe. Together, these studies affirm the centrality of STAT5 in CD8+ T cells, reveal common and circumscribed activities for STAT5A and STAT5B, and present a unifying model that foregrounds both redundancy and asymmetry.

overall_design:
mRNA-seq analysis of cytokine treated CD4+ and CD8+ T cells from mice lacking Stat5a or Stat5b, along with WT controls

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

last: Ristin

first: Molly

last: Dalzell

first: Christopher

last: Armstrong

first: Nisa

last: Ilsin

first: Antonio

middle: M

last: Fontanella

first: Luis

last: Nivelo

first: Lothar

last: Hennighausen

first: John

last: O’Shea


title: Logistic regression for estimating functional effects with spatial transcriptomics

city: St. Louis

first: Hysell

middle: V.

last: Oviedo

state: Missouri

address: 4370 Duncan Ave

department: Neuroscience

institute: Washington University in St. Louis School of Medicine

summary: Spatial transcriptomics (ST) unlocks new potential for studying gene functions in biological processes which depend on the orchestration of transcription across space. However, despite their growing number, analysis tools for ST remain largely aimed at data exploration, with few resources for theory-driven hypothesis testing. What's missing is a way to test whether a factor of interest affects functionally relevant parameters of a gene's spatial distribution. We present a tool to fill this gap, which we call a warped sigmoidal Poisson-process mixed-effects (WSP, pronounced "wisp") model. WSP models are the first ST tool allowing researchers to test biologically critical questions without bespoke preprocessing pipelines for identifying key spatial parameters. By aligning coordinates to an axis of interest and letting a likelihood-based regression find between-group effects on expression rates and boundaries, WSP models replace error-prone manual preprocessing with minimally biased hypothesis testing. WSP models are implemented by wispack ("wisp package"), an R package written in Rcpp. After introducing WSP models, we demonstrate the statistical validity of wispack using semi-synthetic simulated data and demonstrate its ability to test for effects by applying it to MERFISH data from mouse somatosensory cortex and bulk sequencing data from mouse liver lobules with extrapolated spatial coordinates.

overall_design: Spatial transcriptomes of 721 selected genes in developing mouse brains were collected using the Vizgen MERSCOPE platform. At postnatal days 12 and 18, two horizontal brain sections from two individual mice were collected and imaged. Processed data were then aligned to the Common Coordinates Framework v3, and cells within the primary somatosensory cortex were used for analysis.

last: Barkasi

first: Cody

middle: N

last: Pham

first: Demetrios

last: Neophytou