title: Murine modeling of IDH-mutant 1p/19q-codeleted oligodendroglioma reveals genotype-specific phenotypes [sample_045-048]

city: Cincinnati

first: Timothy

last: Phoenix

state: OH

address: 231 Albert Sabin Way, MSB 3005M

department: Division of Pharmaceutical Sciences

institute: University of Cincinnati

summary: Oligodendroglioma is a primary central nervous system tumor classified by the presence of isocitrate dehydrogenase (IDH) mutations and codeletion of 1p/19q. Here we describe the generation of an IDH-mutant 1p/19q-codeleted oligodendroglioma mouse model using in utero electroporation. We identified IDH1R132H, PIK3CAE545K, CicKO, Fubp1KO and Cdkn2aKO as the optimal combination (termed OligoCdkn2a) to drive fully penetrant tumors that histologically resemble human grade II/III IDH-mutant, 1p/19q-codeleted oligodendroglioma. Replacing Cdkn2a with Trp53 loss in this mouse model shifted tumor histology towards high grade astrocytoma. OligoCdkn2a tumors displayed metabolic and transcriptional changes associated with IDH and CIC mutations, and single cell sequencing identified a bias towards oligodendrocyte differentiation compared to an IDH wild-type glioblastoma mouse model. OligoCdkn2a tumors represent the first mouse model system to recapitulate the genetic, histological and transcriptional features of human IDH-mutant 1p/19q-codeleted oligodendrogliomas, offering a platform to further dissect tumor biology and test new therapeutic strategies.

overall_design: Single-cell RNA-sequencing (scRNA-seq) was performed on tumor endpoint tissue from three genetically distinct brain tumor models. This dataset contains Oligo Cdkn2a (n=4).

middle: N

first: Ipsita

last: Kundu

first: Aaron

middle: Y

last: Mochizuki


title: Hierarchical, non-additive MARTX effector interplay rewires host transcription to drive Vibrio vulnificus invasion and lethal sepsis

status: Public on Apr 15 2026

city: Chicago

first: Francisco

last: Silva

state: Illinois

address: 420 E Superior street #9

department: Microbiology-Immunology

country: USA

institute: Northwestern University

type: Expression profiling by high throughput sequencing

summary: Multifunctional-autoprocessing repeats-in-toxin (MARTX) toxins deliver multiple effectors into host cells, yet how distinct effector combinations integrate to shape virulence remains poorly defined. Here, we systematically dissect effector interplay in the highly virulent pathogen Vibrio vulnificus. In the M-type MARTX toxin strain MO6-24/O, which delivers four effectors, we generated catalytically-inactivating point mutations in all combinations in situ. We found that effector composition influences virulence potential, revealing both virulence and anti-virulence factors. Integrated transcriptomics revealed that coordinated effector activity governs the magnitude and coherence of host response. Two functional effector modules define a regulatory–metabolic axis and a silencing–execution axis, each partially contributing to virulence. When combined into the holotoxin, these modules reprogram host transcription toward a highly activated state, supporting a model in which virulence emerges from non-additive effector crosstalk that rewires host transcriptional landscapes.

overall_design: RNA-seq profiling of host transcriptional responses to Vibrio vulnificus MARTX effector mutants representing single, double, and triple active configurations.

first: J.

last: Nguyen

last: Mills

last: Nieves-Rivera

first: S.

last: Dey


title: Surfaceome CRISPR activation screening uncovers ligands regulating tumor sensitivity to NK cell killing

city: Palo Alto

first: Ravi

last: Dinesh

state: CA

address: 265 Campus Drive

department: Pathology

institute: Stanford University

summary: Natural killer (NK) cell-based immunotherapies represent a promising avenue for cancer treatment due to their ability to eliminate cancer cells independently of antigen presentation and potential for “off-the-shelf” use. However, the molecular determinants governing tumor cell susceptibility to NK cell-mediated cytotoxicity remain incompletely understood. Here we employed CRISPR activation (CRISPRa) screening to systematically identify cancer cell surface regulators of NK cell killing across multiple cancer types. Using a comprehensive surfaceome-focused library, we screened human and murine cancer cell lines co-cultured with NK cells, identifying both known and novel ligands that modulate NK cell cytotoxicity. Our screens revealed established factors including CD43 (encoded by SPN), while uncovering previously uncharacterized regulators such as CD44, PDPN, and Siglec-1/CD169. Validation through complementary cDNA overexpression and genetic knockout approaches confirmed that disruption of CD43, CD44, PDPN, and Siglec-1 significantly altered cancer cell susceptibility to NK killing both in vitro and in humanized mouse models. Analysis of clinical datasets show that expression of identified factors correlates with patient survival outcomes in an NK-context dependent manner supporting their therapeutic relevance. Most notably, our mechanistic studies demonstrate that CD43-mediated NK cell resistance operates independently of its previously proposed interaction with Siglec-7 on NK cells. Furthermore, we find that targeting CD43 on either NK cells or engineered T cells substantially enhances their cytotoxic activity against leukemia cell lines. These results establish gain-of-function screening as a powerful approach for discovering immunoregulatory surface proteins and identify multiple promising targets for enhancing NK cell-based cancer immunotherapies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: K562, HGC-27, YAC-1, and B16F0 cells stably expressing CRISPRa SAM system components were infected with a custom sgRNA library targeting genes encoding the cancer cell surfaceome and carried forward at 1000X coverage per sgRNA. Library cells were co-cultured with or without primary NK cells for 24 hours, after which surviving cells were collected. Genomic DNA was extracted using the Zymo Quick-DNA Miniprep Kit. sgRNA sequences were amplified from genomic DNA and sequenced on an Illumina NextSeq 500 with 80bp single-end reads. Analysis was performed using the MAGeCK software pipeline under default conditions.

middle: K

first: Xiaotong

last: Wang

first: Imran

middle: A

last: Mohammad

first: Le

last: Cong

first: John

middle: B

last: Sunwoo


title: Transcriptomic signatures of Trichomonas vaginalis isolates that exhibit low, intermediate, and high resistance to metronidazole in vitro

city: Birmingham

first: Keonte

middle: Jamel

last: Graves

state: AL

address: 1900 University Blvd, THT 230

department: Medicine-Infectious Diseases

institute: The University of Alabama at Birmingham

summary: As part of efforts to identify genes associated with Trichomonas vaginalis resistance to 5-nitroimidazole drugs, thirty cryopreserved T. vaginalis isolates were revived and grown using Diamonds TYM medium. Minimum lethal concentrations (MLCs) for metronidazole (MTZ), tinidazole (TDZ), and secnidazole (SEC) were determined using a drug susceptibility assay. Transcriptome profiling was performed for 15 MTZ-sensitive (MTZ-S, MLC < 50µg/mL) and 15 MTZ-resistant (MTZ-R, MLC ≥ 50µg/mL) isolates using next generation RNA-sequencing. Bioinformatics analyses identified differentially expressed genes (DEGs). Among MTZ-R isolates, 6 exhibited MLCs of 50µg/mL, 5 had MLCs between 100-200 µg/mL, and 4 had MLCs ≥ 400 µg/mL. The low-, intermediate-, and high-level MLC resistant isolates were compared to the MTZ-S isolates and transcriptomic profiling identified 154, 425, and 175 DEGs respectively. MTZ-resistant T. vaginalis isolates exhibited altered expression of virulence factor genes compared to sensitive isolates, with variations in gene expression observed across different MLC levels.

overall_design: RNA sequencing, bioinformatics, and biostatistical analyses were performed to identify differentially expressed genes (DEGs) in the MTZ-resistant vs. sensitive T. vaginalis isolates.

middle: J

first: Colin

last: Reily

first: W

middle: E

last: Secor

first: Jan

last: Novak

first: Christina

last: Muzny


title: Murine modeling of IDH-mutant 1p/19q-codeleted oligodendroglioma reveals genotype-specific phenotypes

last: Phoenix

overall_design: Bulk RNA-sequencing was performed to analyze tumor endpoint tissue and primary murine cell lines across three distinct genetic models (Oligo Cdkn2a, Oligo Trp53, IDHWT GBM). For the tumor endpoint tissue cohort, 7 to 10 biological replicates per genetic condition were analyzed. For the primary cell lines, each genetic condition had one cell line with three technical replicates that was used for analysis.

middle: G

last: Kundu


title: An Isoform-resolved Single-cell Atlas of the Murine Placenta: Gestational Dynamics During Syngeneic and Semi-allogeneic Pregnancy

city: Yerevan

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Yerevan

address: Kogbatsi 1

department: Research and Development

country: Armenia

institute: PerikLab

summary: The maternal-fetal interface requires precise immune tolerance followed by coordinated inflammation at term. While single-cell studies defined placental cellular diversity, alternative splicing's contribution to immune regulation remains poorly understood. Here, we present an isoform-resolved single-cell transcriptomic resource of the murine placenta across mid- and late gestation in syngeneic and semi-allogeneic pregnancies. We identify global suppression of cytokine networks during mid-gestation semi-allogeneic pregnancies, accompanied by erythroid populations co-expressing immune programs. Isoform-level analysis reveals the coordinated generation of alternatively spliced cytokine receptor variants, including soluble decoys and intracellular traps, lacking necessary signaling domains. These variants co-express with canonical receptors, decoupling ligand binding from downstream signal transduction to fine-tune immune responses. At term, this landscape shifts to coordinated pro-inflammatory signaling. This interactive dataset provides a systems-level framework for understanding how post-transcriptional mechanisms shape immune adaptation during murine pregnancy.

overall_design: This study provides a high-resolution, isoform-level transcriptomic map of the murine placenta across two gestational milestones and two distinct immunological contexts. Semi-allogeneic pregnancies were established by mating CBA females with C57BL/6 males, while syngeneic controls utilized CBA pairings. Placentas were harvested at embryonic days 12.5 and 19.5, and tissues from biological replicates were pooled for each experimental condition to ensure robust cellular representation for single-cell RNA sequencing. By integrating these temporal and genetic variables, the experimental framework enables a precise characterization of how placental architecture and transcript isoforms shift in response to both developmental progression and maternal-fetal genetic disparity.

first: Olga

last: Perik-Zavodskaia

first: Saleh

last: Alrhmoun


title: Murine modeling of IDH-mutant 1p/19q-codeleted oligodendroglioma reveals genotype-specific phenotypes [sample_049-60]

first: Timothy

overall_design: Single-cell RNA-sequencing (scRNA-seq) was performed on tumor endpoint tissue from three genetically distinct brain tumor models: In this library there are: Oligo Cdkn2a (n=2), Oligo Trp53 (n=4), and IDHWT GBM (n=4). Two additional normal brain (cortex) samples not analyzed in the study are included in the dataset.

first: Ipsita

first: Aaron

last: Mochizuki


title: Macrophage signaling associates with fibrogenic program activation in periductal fibroblasts in pediatric primary sclerosing cholangitis.

first: Yunguan

state: oh

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: Two diagnostic liver biopsy specimens from pediatric patients with primary sclerosing cholangitis were profiled by single-cell spatial transcriptomics using the VizGen MERSCOPE platform with a custom 400-gene liver immunology panel. The material consisted of freshly cut, unstained sections from archived FFPE needle biopsies mounted on VizGen-provided slides for hybridization according to the manufacturer’s protocol. Both specimens contained focal periductal and bridging fibrosis.

first: Alexander

last: Miethke


title: Loss of TET function in T regulatory cells yields ex-Treg cells biased toward T follicular helper cells, causing autoimmune diseases through autoantibody production - spleen and peripheral lymph nodes

city: La Jolla

first: Anjana

last: Rao

state: California

address: 9420 Athena Circle

department: Department of Signaling and Gene Expression

institute: La Jolla Institute for Immunology

summary: T regulatory cells (Treg cells) express the transcription factor FOXP3 and maintain immune homeostasis by attenuating effector responses. Treg cells are prone to lose FOXP3 and convert to pathological ‘ex-Treg’ cells under conditions of strong or chronic inflammation. One mechanism for loss of FOXP3 expression involves increased DNA methylation of intronic enhancers CNS1 and CNS2 in the Foxp3 locus; these enhancers are maintained in a demethylated state by TET enzymes, 5-methylcytosine (5mC) dioxygenases that generate 5-hydroxymethylcytosine (5hmC) and other oxidized methylcytosines that are essential intermediates in all pathways of DNA demethylation. We previously showed that FOXP3+ Treg cells from Tet2/3-deficient (Tet2/3 DKO) mice displayed increased methylation of CNS1 and CNS2 and converted to FOXP3-negative ex-Treg cells considerably more efficiently than WT Treg cells. Here we extend our previous analysis of Foxp3-Cre Tet2/3fl/fl mice. We classified the mice as DKO-moderate or DKO-severe based on the total number of leukocytes in the spleen and peripheral lymph nodes and investigated the phenotypic and molecular basis for the progressive inflammation occurring in these mice. RNA-seq as well as histological and immunocytochemical analyses showed a striking expansion of T follicular helper (Tfh) cells and plasma cells in Tet2/3 DKO-severe mice. And single-cell (sc) RNA-seq analyses suggested that this was due to skewed differentiation of both Tet2/3 DKO FOXP3+ Treg cells and Tet2/3 DKO FOXP3– ex-Treg cells into Tfh-like cells. Base-resolution “6-base” sequencing showed the expected loss of 5hmC and increased 5mC in Tfh cells purified from Tet2/3 DKO-severe mice, and suggested that the observed bias in gene expression patterns could arise either from a direct increase in methylation of essential enhancers due to TET deficiency, or from interference with binding of methylation-sensitive transcriptional repressors including CTCF.

overall_design: Naïve CD4+ T cells from Foxp3Cre WT mice (14-weeks-old) and Tfh cells from DKO-severe Foxp3-Cre Tet2/3fl/fl mice (14-weeks-old) were sorted and extracted genomic DNA using DNeasy Blood & Tissue Kit (Qiagen, #69504). The duet multiomics solution evoC method (6-base sequencing) was performed according to the manufacturer’s instructions (duet exoC User guide v.3), using 60-70 ng of sonicated genomic DNA as starting material (n=2). Data were processed as in the below reference and the mean coverage for the samples ranged from 10x to 20x. Libraries were sequenced at the UCSD Institute for Genomic Medicine Genomics Center using Illumina NovaSeq X Plus pair end 150 bp platform. Reference: Füllgrabe J et al. Simultaneous sequencing of genetic and epigenetic bases in DNA. Nat Biotechnol. 2023 Oct;41(10):1457–64.

first: Kazumasa

last: Suzuki

first: Leo

last: Arteaga-Vazquez

first: Bruno

last: Villalobos Reveles

first: Lot

last: Hernández-Espinosa

first: Isaac

middle: F

last: López-Moyado

first: Atsushi

last: Odonera

first: Daniela

last: Samaniego-Castruita

first: Ferhat

last: Ay

first: Arlet

last: Lara-Custodio

first: Patrick

last: Hogan

first: Hugo

last: Sepulveda


title: Scavenger Cells Failure to Maintain Systemic RNA Homeostasis Causes Epigenetically Inherited Germline Tumors

city: Tel Aviv

first: Hila

last: Gingold

address: 30 Haim Levanon Street

country: Israel

institute: Tel-Aviv University

type: Non-coding RNA profiling by high throughput sequencing

summary: Temporary disruptions to epigenetic mechanisms can misroute development and permanently alter cell fate. In particular, it was recently shown that transient loss of Polycomb silencing in flies irreversibly reprograms cells toward cancer (Parreno et al. 2024). Whether somatic dysfunction in parents can create multi-generational heritable susceptibility to tumorigenesis is unknown. In eutelic organisms like Caenorhabditis elegans, adult somatic cells no longer divide, precluding somatic cancer, yet tumors can still form in the continuously dividing germline. Here, we show that disruption of coelomocytes, somatic scavenger cells, just in C. elegans mothers, provokes transgenerationally heritable germline tumorigenesis that persists for multiple generations in genetically wild-type descendants. We found that when the coelomocyte’s phagocytic activity dysfunctions, it impairs clear out of RNA from body fluids, and thus disrupts systemic RNA homeostasis, allowing excess somatic RNAs to access the germline, and leading to widespread transcriptional and small RNA dysregulation and transgenerational loss of germline identity. Converging lines of evidence point towards small RNAs being the heritable agents carrying the pathological information. Together, these findings highlight mechanisms which maintain systemic RNA homeostasis as an important protective barrier against heritable tumorigenesis.

overall_design: RNA was extracted from gonads of  "day one" adult nematodes of different strains (N2 and RB950: cup-4(ok837)). The samples include 3 biological replicates. 6 samples are from small RNA sequencing and 5 samples are from total RNA sequencing, yielding a total of 11 samples.

first: Itai

last: Rieger

first: Yael

last: Mor

first: Itamar

last: Lev

first: Anat

last: Nitzan

first: Charlotte Beata

last: Kong

first: Sarit

last: Anava

first: Ronen

last: Zaidel-Bar

first: Oded

last: Rechavi


title: Loss of TET function in T regulatory cells yields ex-Treg cells biased toward T follicular helper cells, causing autoimmune diseases through autoantibody production [multiome]

first: Anjana

last: Rao

overall_design: TCRβ+ cells from pooled spleen and peripheral lymph nodes (cervical and inguinal) of Foxp3Cre WT and DKO-severe Foxp3-Cre Tet2/3fl/fl mice (14-weeks-old) were prepared, counted and loaded 10,000 single cells (n=1).

first: Kazumasa

last: Suzuki

first: Leo

last: Arteaga-Vazquez

first: Bruno

last: Villalobos Reveles

first: Lot

last: Hernández-Espinosa


title: TGF-beta promotes human T follicular helper cell stemness properties at the expense of effector function

city: Hengyang

first: Yixin

last: Yang

address: 湖南省衡阳市蒸湘区常胜西路28号

department: Hengyang Medical School

country: China

institute: University of South China

summary: Follicular helper T (TFH) cells are essential for germinal center reactions and the maintenance of long-lived humoral immunity. Transforming growth factor-β (TGF-β) is a multifunctional cytokine implicated in immune regulation, T-cell differentiation, and the maintenance of cellular stemness. Prior studies have shown that TGF-β promotes stemness across a wide range of cell types and facilitates the differentiation of naïve CD4⁺ T cells into various T helper cell subsets. However, its precise effects on TFH effector function and stem-like properties remain poorly understood. Here, the dual regulatory roles of TGF-β1 in modulating TFH effector functions and stem-like properties were investigated. We found that TGF-β1 treatment in vitro promoted human naïve CD4+ T cells differentiation into CXCR3⁺ TFH, but significantly attenuated their effector molecule expression and TFH-mediated memory B-cell differentiation and antibody production, whereas it enhanced the expression of stemness-associated molecules in TFH cells both differentiated in vitro from naïve CD4+ T cells and isolated from blood. Notably, TGF-β1 promoted proliferation and reduced apoptosis of naïve-derived TFH cells in vitro, but suppressed proliferation and increased early apoptosis in blood-derived mature TFH cells. Collectively, these findings indicate that TGF-β1 tunes the balance between TFH effector function and stem-like properties, and show differential regulations of the early phase of TFH differentiation and mature TFH cells, which may have implications for TFH-driven immune pathology and disease.

overall_design: Flow cytometry–sorted TFH cells derived from human naïve CD4+ T cells or circulating memory TFH cells stimulated with anti-CD3/CD28 beads and cultured in the absence or presence of TGF-β1. Bulk RNA sequencing was performed to assess transcriptional changes induced by TGF-β1 treatment.

first: Chanfeng

last: Wu

first: Xingyu

last: Zheng


title: Effect of ARNT on hypoxic response in Panc1 cells

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

summary: The hypoxic response is influence by both the tissue of origin and local environmental influences. The hypoxic response is mediated in large part by the hypoxia-inducible transcription factors HIF-1 and HIF-2, which share a common beta subunit (also called ARNT). We looked at Panc1 cells, a pancreatic adenocarcinoma cell line, and compared the response to hypoxia in both regular tissue culture media and in pancreatic TIFM (tumor interstitial fluid media), and assessed the degree to which ARNT knockout mediates the observed changes

overall_design: RNA-sequencing of Panc1 control cells and two independently derived clones of ARNT knockout cells, generated by CRISPR-Cas 9 technology. Samples are exposed to normoxia (20% O2)/regular media (DMEM + 10% FBS + 1% P/S), hypoxia (1% O2)/regular media, or hypoxia/pancreatic TIFM (described by Muir A et al., eLife 2023), for 48 hours.

first: Maimon

last: Hubbi

first: Chi

middle: V

last: Dang


title: Tex15 is required for vomeronasal sensory neuron diversity and enables male pheromone detection

city: Piscataway

first: Kevin

last: Monahan

state: NJ

address: 604 Allison Rd

department: Molecular Biology and Biochemistry

institute: Rutgers University

summary: The mouse vomeronasal organ (VNO) detects pheromones, which provide vital information needed to find a mate, detect predators, or alert to the presence of an intruder. Within the VNO, pheromones are sensed by two families of G-protein Coupled Receptors (GPCRs) the type 1 and type 2 vomeronasal receptors (V1Rs and V2Rs). However, little is known about the regulatory mechanisms that control the expression of V1R and V2R genes by vomeronasal sensory neurons (VSNs). Here we identify a transcriptional repressor, Testis-expressed gene 15 (Tex15), that regulates vomeronasal receptor gene choice and is required for the proper functioning of the vomeronasal system in regulating male behavior. We find that Tex15 is transiently expressed by VSN precursors prior to strong VR gene expression. The absence of Tex15 results in a pervasive change in the expression of V1R and V2R genes, which results in a less diverse repertoire of VR expressing cells and includes a dramatic reduction in the expression of specific receptors that have been tied to intermale aggression. Accordingly, Tex15 knockout mice exhibit lowered activation in the Accessory Olfactory Bulb (AOB) after exposure to male odorants, and a loss of stereotyped aggression between male mice. Taken together, these results show that Tex15 plays a critical role in pheromone sensing by ensuring that VSNs express a diverse set of receptor proteins.

overall_design: Bulk RNAseq profiling of the vomeronasal organ (VNO) from adult Tex15 knockout mice and Tex15 heterozygous controls

first: Nader

last: Boutros Ghali


title: Loss of TET function in T regulatory cells yields ex-Treg cells biased toward T follicular helper cells, causing autoimmune diseases through autoantibody production

overall_design: CD4+ YFP(FOXP3)- T cells were sorted from pooled spleen and peripheral lymph nodes (cervical and inguinal) from Foxp3Cre WT mice and Foxp3-Cre Tet2/3fl/fl mice (14-weeks-old) and RNA sequencing was performed (n=4)

first: Isaac

last: López-Moyado

first: Atsushi

last: Odonera

first: Daniela

last: Samaniego-Castruita

first: Ferhat

last: Ay

first: Arlet

last: Lara-Custodio

first: Patrick

last: Hogan

first: Hugo

last: Sepulveda


title: Effect of pancreatic tumor interstitial fluid media on transcriptional responses in PDAC cells

summary: Local metabolic signals can influence the transcriptional response. To better understand the effect of the microenvironment in pancreatic adenocarcinoma (PDAC), we compared pancreatic tumor interstitial fluid media (TIFM - described by Muir et al., eLife 2023) to regular media in two PDAC cell lines, MiaPaCa and Panc1, under two conditions, normoxia and hypoxia.

overall_design: RNA-sequencing of Panc1 or MiaPaCa lines, after exposure to either normoxia (21% O2) or hypoxia (1% O2) in either regular media (DMEM + 10% FBS + 1% P/S) or pancreatic TIFM for 48 hours.


title: Analysis of gene expression in primary human foreskin keratinocytes (HFK) +/- HPV16 or HPV6 E7

city: Boston

first: Elizabeth

last: White

state: MA

address: 150 Harrison Ave, Jaharis 909

department: Developmental, Molecular, and Chemical Biology

institute: Tufts University School of Medicine

summary: This RNA-seq study in primary human forekin keratinocytes was to define genes that are differentially expressed in the presence or absence of HPV16 E7 and HPV6 E7 proteins, in each case identifying gene regulation that depends on the RB1 binding motif in E7.

overall_design: mRNA profiles in primary HFK were generated for the following samples (# of replicates): GFP (3), HPV16 E7 (3), HPV16 E7 ∆DLYC (3), HPV6 E7 (3), HPV6 E7 ∆GLHC.


title: Placental gene signatures associated with high neonatal adiposity: role for immune cell activation

first: Perrie

last: O'Tierney-Ginn

address: 800 Washington St

institute: Tufts Medical Center

summary: Fetal fat accumulation is an important indicator of the nutritional environment in pregnancy and placental function. Excessive fat accretion leading to high adiposity at birth, however, can increase a child’s long-term risk for obesity and metabolic disease. While maternal body mass index is associated with neonatal adiposity, there is a wide variation in body composition among babies born to both women with and without obesity. The placenta orchestrates a complex exchange of nutrients and signals between the mother and baby. To better understand the molecular mechanisms that govern fetal fat accumulation, we profiled the transcriptomics of 79 placentas collected from mothers with and without obesity. We identified a set of 18 neonatal adiposity-associated genes, common to pregnancies with and without obesity. A co-expressed cluster of these genes are involved in innate immune responses, particularly neutrophil activation. We also identified neonatal adiposity-associated genes unique to mothers with or without obesity, suggesting different biological pathways support high newborn adiposity, and/or are responsive to a common initial immune signal. These findings suggest that placental inflammation may influence fetal fat accumulation. Understanding these pathways may help identify novel ways to support healthy fetal growth and reduce the risk of long-term disease.

overall_design: Placental samples (n=79) were selected from four groups based on maternal pre-pregnancy BMI (Lean: 18-24.9 kg/m^2; Obese: 30-40 kg/m^2) and neonatal adiposity tertiles (low/high % body fat): LELA (n=20), LEHA (n=19), OBLA (n=20), OBHA (n=20). Differentially expressed genes were assessed between high and low adiposity neonates within maternal adiposity status.

first: Jason

last: Laird

first: Deepak

last: Venkataraman

first: Hannah

last: Yen

first: Chelsea

last: Liu

last: Catalano

first: Ruggero

last: Spadafora

first: Nanguneri

last: Nirmala

last: O’Tierney-Ginn


title: CENPF overexpression facilitates the G1/S cell cycle transition of hepatocellular carcinoma cells via MYC pathway

city: Beijing

first: Saiping

last: Qi

address: 95 Yong-an Road, Xi-Cheng District

institute: Beijing Friendship Hospital, Capital Medical University

summary: Centromere protein F (CENPF), a mitosis-related protein, is overexpressed in hepatocellular carcinoma (HCC) and has emerged as a promising biomarker for early HCC. However, with ultra-large molecular weight of 358kDa of CENPF, no study has directly explored its carcinogenicity with an overexpression model. In the present study, a CRISPR/dCas9 system was applied to construct the CENPF overexpression model. CENPF was upregulated and downregulated to analyze its functions in vitro. CENPF knockdown cell models showed inhibition of HCC proliferation. Notably, as a cell cycle protein with high constitutive expression in G2/M phase, CENPF overexpression cell models also showed inhibitory effects, probably due to the toxic effect of excessive CENPF expression on G2/M transition. However, in both CENPF downregulation and overexpression models, cell cycle assays showed CENPF promoted G1/S transition in HCC cells. RNA-seq showed that CENPF overexpression activated the MYC pathway, thereby promoting G1/S transition. The rescue experiment indicated that the MYC pathway inhibitor 10058-F4 counteracted the G1/S transition induced by CENPF overexpression in HCCLM3 cells. CENPF overexpression might facilitate HCC cells G1/S cell cycle transition via the MYC pathway.

overall_design: RNA-seg profiling of the CENPF knockdown Huh-7 cells and the CENPF-overexpressing HCCLM3 and Huh-7 cells

first: Donghu

last: Zhou

first: Sisi

last: Chen

first: Liying

last: Sun

first: Jian

last: Huang


title: Shared anti-biofilm targets of biofilm regulators Wor3 and Bcr1 in Candida albicans RPMI

city: Athens

first: Katharina

last: Goerlich

state: GA

address: 120E Green St

department: Microbiology

institute: University of Georgia

summary:
Candida albicans is an opportunistic fungal pathogen and a natural component of the
human microbial flora. One central C. albicans virulence trait is the ability to produce a
biofilm, which is regulated by several transcription factors. Mutations of some biofilm
transcriptional regulators cause the same severe biofilm-defective phenotype in multiple
clinical isolates. Mutations of others, such as Wor3, Bcr1, Ndt80, and Ume6, have mild
or variable phenotypes among clinical isolates. We hypothesized that Wor3 may have a
shared function with one of the other variable-phenotype biofilm regulators. This
hypothesis predicts that a double mutant lacking Wor3 and the shared-function
regulator will have a severe biofilm defect in all clinical isolates. We observed that a
wor3Δ/Δ bcr1Δ/Δ has a severe biofilm defect in vitro in 5 strain backgrounds tested. It
also has a severe oral biofilm defect in a mouse oropharyngeal candidiasis model in the
SC5314 reference strain background. RNA-seq data indicate that 5 genes encoding
cell surface/secreted proteins are upregulated in wor3Δ/Δ, bcr1Δ/Δ, and wor3Δ/Δ
bcr1Δ/Δ strains: CWH8, DAG7, JEN2, PGA6, and YWP1. Deletion mutations of CWH8,
DAG7, PGA6, or YWP1 enables biofilm formation in vitro in an SC5314-derived
wor3Δ/Δ bcr1Δ/Δ strain, and deletion of YWP1 enables biofilm formation in vitro in
wor3Δ/Δ bcr1Δ/Δ strains from 4 other genetic backgrounds. YWP1 has been shown to
have anti-biofilm activity previously, but CWH8, DAG7, and PGA6 are newly described
anti-biofilm genes. Our study illustrates the value of strain variation considerations for
gene function analysis and the importance of repression targets of biofilm regulators. In
addition, our results expand the number of anti-biofilm genes.

overall_design: RNA-seq profiling of WT (SC5314 A22) C. albicans cells and their mutant derivatives (wor2△/△, bcr1△/△, wor2△/△bcr1△/△, wor3△/△, andwor3△/△bcr1△/△). Cells were grown for 4h at 37C in RPMI.

first: Aaron

middle: P

last: Mitchell


title: ATP synthasome contributes to efficient energy flux in malignant breast cancer

city: Kaohsiung

first: Chia-Jung

last: Li

state: Kaohsiung

address: No.386, Dazhong 1st Rd., Zuoying Dist., No.386, Dazhong 1st Rd., Zuoying Dist.

country: Taiwan

institute: Kaohsiung Veterans General Hospital

summary: Background: This study investigates the metabolic alterations associated with breast cancer progression and elucidates the underlying mechanisms. Adenine nucleotide translocase 2 (ANT2), a mitochondrial protein essential for cellular energy metabolism, facilitates the exchange of ADP and ATP across the inner mitochondrial membrane. The role of ANT2, particularly its interaction with the ATP synthasome, in breast cancer metastasis remains poorly understood. Methods: We analyzed ANT2 in breast cancer using genetic and clinical methods, validating its expression in human tissues. Gene enrichment studies and functional assays assessed ANT2's role in mitochondrial function and cancer metabolism. Knockdown experiments and pharmacogenomic screening evaluated ANT2's impact on metastasis and identified potential inhibitors in 3D cultures and orthotopic mouse models. Results: ANT2 was significantly overexpressed in metastatic breast cancer, correlating with reduced survival. Knockdown of ANT2 impaired cell migration and invasion, reduced ATP production, and diminished oxidative phosphorylation (OXPHOS) activity in MCF7-F4 cells. In vivo, siRNA-mediated ANT2 silencing in JC-M3 cells decreased tumor growth and lung metastases in mice. Pharmacogenomic analysis identified cymarin as an ANT2 inhibitor, reducing spheroid formation in 3D cultures and tumor burden in vivo, alongside downregulation of epithelial-to-mesenchymal transition (EMT) and OXPHOS markers. ANT2 colocalized with ATP5B, forming an ATP synthasome that enhanced energy flux in hyperinvasive cells. Conclusions: ANT2 drives breast cancer metastasis by enhancing mitochondrial energy production via the ATP synthasome. Its inhibition, particularly with cymarin, disrupts tumor bioenergetics and metastatic potential, positioning ANT2 as a promising therapeutic target.

overall_design: To recapitulate the in vivo evolution of metastatic potential, a stepwise in vivo selection system was established using JC mouse mammary carcinoma cells. Parental JC cells (JC-P) were isolated from orthotopic tumors 14 days after transplantation. Metastatic subpopulations were subsequently enriched through serial intravenous injection of JC-P–derived cells followed by isolation of lung metastatic lesions 28 days post-injection. This in vivo selection cycle was repeated for three consecutive rounds, yielding a highly metastatic derivative cell line, designated JC-M3. Transcriptomic differences among JC-WT, JC-P, and JC-M3 cells were then profiled by RNA sequencing.

first: Yen-Dun Tony

last: Tzeng

first: Yu-Ting

last: Kang

first: Tzu-Hung

last: Hsiao

first: Pei-Yi

last: Chu

first: Su-Boon

last: Yong

first: Shih-Chieh

last: Lin

first: Meng-Yu

last: Wu

first: Ling-Ming

last: Tseng

first: Ming-Feng

last: Hou

first: Zhi-Hong

last: Wen

first: Tzu-Sheng

last: Hsu

first: Chih-Chiang

last: Hung

first: An-Jen

last: Chiang

first: Kuan-Hao

last: Tsui


title: Integrin β3 Deficiency Unleashes Spontaneous Pulmonary Inflammation by Promoting B Cell Hyperactivation via the CD40-CD40L Axis

city: Shanghai

first: Shuang

last: Liu

address: 197 ruijin 2nd road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Background: Pulmonary immune homeostasis relies on stringent control of adaptive immunity. Integrin β3 is a critical mediator of cellular adhesion and platelet function. However, its specific role in modulating adaptive immunity, particularly B cell immune response, remains poorly understood.Results: We identified that β3⁻/⁻ mice showed a spontaneous pulmonary inflammation characterized by B cell activation and in situ immune complex deposition in alveoli. Multi-omics integration identified that the CD40-CD40 Ligand (CD40L) axis was strongly implicated in this pathology process. Mechanistically, the absence of β3 potentiates CD40L-CD40 engagement on B cells, leading to hyperactivation of the NF-κB pathway. Notably, reduced ITGB3 expression in patients with autoimmune disease correlated significantly with enhanced transcriptional signatures of B cell activation and inflammation.Methods: Histopathology characterized the pulmonary phenotype of constitutive β3-deficient (β3⁻/⁻) mice. Integrated transcriptomic and proteomic profiling of lung tissue was then performed to map the molecular landscape of spontaneous pulmonary inflammation. Related mechanisms were investigated by histopathology and functional assays, and established clinical relevance by analyzing transcriptomic datasets from patients with autoimmune diseases.Conclusions: Our findings redefine integrin β3 as a threshold regulator of the B cell activation. Consequently, the β3-CD40L-CD40 axis represents a promising therapeutic target for managing B cell-related autoimmune diseases.

overall_design: Transcriptomic profiling of lung and spleen tissue from β3-/- and WT mice.


title: Telomere interacting proteins Tert and Terb1 regulate meiotic progression in zebrafish

first: Kavita

last: Venkataramani

address: 100 Morrissey Blvd

department: Biology

institute: University of Massachusetts

summary: Telomeres have a prominent role in meiosis – telomere tethering to nuclear envelope proteins is essential for successful meiosis and fertility. This is accomplished through meiosis-specific telomere adaptor complexes that interacts with protein complexes spanning the nuclear envelop to connect with motor proteins. Connecting telomeres to motor proteins through this protein chain drives rapid prophase I movements (RPM) of chromosomes, which results in clustering of telomeres at one side of the nucleus to form the meiotic bouquet. Telomere attachment to the nuclear envelop proteins and RPMs are essential for homologue chromosome pairing, synapsis, and meiotic recombination. Mutations disrupting telomerase reverse transcriptase (tert) result in multiple pathologies including impaired fertility. Here, we investigate effects of loss of tert function on meiosis in zebrafish. We demonstrate that tert mutant meiotic germ cells have shortened telomeres and display defects in meiotic progression with eventual loss of meiotic cells with age, followed by loss of mitotic germ cells several months later. These data indicate that meiotic cells are more sensitive to shortened telomeres than mitotic germ cells. Furthermore, we found that orthologues to the mouse meiotic telomere adaptor complex genes, terb1, terb2, and majin, are expressed primarily in meiotic germ cells in zebrafish. Through mutant analysis we show that zebrafish terb1 is necessary for formation of the meiotic bouquet and completion of meiosis, suggesting that zebrafish Terb1 functions as a meiotic telomere adaptor protein, similar to mouse Terb1. These data point to the importance of telomere maintenance and telomere associated proteins in meiotic prophase I during spermatogenesis.

overall_design: Total RNAseq from testes of 3 mpf and 5.5 mpf tert +/+ and tert -/- samples

first: Kellee

last: Renee Siegfried

first: Jessica

last: Nicole Perriello

first: Gaea

last: Dominguez

first: Sophia

last: Coraline Chaviar

first: Cheyenne

last: Louise Petrino

first: Julia

last: Felicia Micozzi

first: Amelia

last: Babb


title: U2AF regulates the translation and localization of nuclear-encoded mitochondrial mRNAs

city: Bethesda

first: Gloria

last: R Garcia

email: gloria.garcia@nih.gov, garciagr@vt.edu

address: Bldg 41, rm B303

institute: NIH

summary: The mechanisms underlying molecular targeting to mitochondria remain enigmatic, yet this process is crucial for normal cellular function. The RNA binding proteins U2AF1/2 form a heterodimer (U2AF) that shuttles between the nucleus and cytoplasm, regulating splicing in the nucleus and translation in the cytoplasm. Our study identifies an unexpected role for U2AF in mitochondrial function. We demonstrate that U2AF interacts with nuclear-encoded mitochondrial mRNAs and proteins, inhibits translation, localizes to the mitochondria, and regulates mRNA localization to mitochondria. Moreover, an oncogenic point-mutation in U2AF1(S34F) disrupts this regulation, leading to altered mitochondrial structure, increased translation, large changes in the mitochondria proteome, and OXPHOS-dependent metabolic rewiring, recapitulating changes observed in bone marrow progenitors from patients with myelodysplastic syndromes. These findings reveal a non-canonical role for U2AF, where it modulates multiple aspects of mitochondrial function by regulating the translation and mitochondrial localization of nuclear-encoded mRNAs.

overall_design: Ribosome profiling (Ribo-seq) was performed in human bronchial epithelial cells (HBECs) expressing either U2AF1wt/wt or U2AF1wt/S34F alleles to assess ribosome occupancy, with sequencing of monosome and disome ribosome-protected fragments from three biological replicates per genotype.

middle: R

last: Garcia

first: Murali

last: Palangat

first: David

last: Sturgill

first: Daniel

last: Larson


title: Real-time quantitative PCR analysis of human prostate adenocarcinoma cells (LNCaP)

city: Davie

first: Appu

last: Rathinavelu

state: FL

department: Rumbaugh Goodwin Institute for Cancer Research

institute: Barry and Judy Silverman College of Pharmacy, Nova Southeastern University

summary: LNCaP (Human prostate adenocarcinoma) cells were cultured in in-vitro conditions and treated with C-phycocyanin (C-PC) (500 µg/mL) for 24 hours. Gene expression profiling was conducted using the RT² ProfilerTM PCR Array Human Apoptosis (Cat. No. PAHS-012Z, Qiagen, SABiosciences, Valencia, CA, USA) panel compared to the control.

overall_design: qPCR gene expression profiling.  LNCaP cells were used and treated with C-PC (500 µg/mL) for 24 hours. Equal amount total RNA from each sample was used prior to gene expression analysis. Each sample was run in triplicates treated sample were compared with control samples.

first: Shyam

last: Sundar Jaganathan

first: Umamaheswari

last: Natarajan

first: Thiagarajan

last: Venkatesan


title: Conserved metanephric kidney development and genome methylation in the red-eared slider turtle (Trachemys scripta elegans)

city: Memphis

first: Troy

last: Camarata

state: TN

address: 1003 Monroe Avenue

department: Biomedical Sciences

institute: Baptist University College of Osteopathic Medicine

type: Methylation profiling by high throughput sequencing

summary: Mammals and reptiles possess a metanephric kidney as the terminal renal organ for homeostasis of solutes and waste products. The development of the metanephric kidney has primarily been studied in mammalian model systems. Little is known about the conservation of metanephric kidney formation in non-mammalian species such as reptiles. Uniquely, reptiles maintain kidney progenitor cell populations throughout life and continually develop new nephrons, the functional unit of the kidney. The red-eared slider turtle, Trachemys scripta elegans, was utilized to investigate the conservation of reptilian metanephric kidney development. The nephron progenitor cell (NPC) marker, Six2, was detected in whole-mount turtle kidneys in a similar pattern to mammals. However, there were differences in progenitor cell niche morphology where turtle NPC populations formed distinct elongated rows instead of the rosette-like morphology found in the mouse. The pattern of NPC populations in the embryonic turtle kidney was maintained in the adult turtle. Whole-genome bisulfite sequencing was performed on cortical tissue containing the NPC populations from adult turtle kidneys and compared to those of adult mice. Significant conservation of gene methylation was detected in adult cortical tissue between the two species, although unique signatures were detected in turtle samples related to DNA repair and β-catenin signaling. This suggests a high level of conservation of metanephric kidney development at the genetic level.

sample_organism:
Mus musculus
Trachemys scripta elegans

platform_organism:
Mus musculus
Trachemys scripta elegans

overall_design: Whole genome bisulfite sequencing of adult renal cortical tissue isolated from Trachemys scripta elegans (red-eared slider turlte) and Mus musculus.


title: Primary Cilia Mediate Stress Vulnerability and Exercise Antidepressant Adaptation: Evidence for Ventral Hippocampal Astrocytic Ciliary Remodeling by Exercise

city: Seoul

first: Dong-Joo

last: Hwang

address: 1239, Yangjae-daero, Songpa-gu

department: Institute of Sport Science

country: South Korea

institute: Korea National Sport University

summary: Chronic stress engenders marked inter-individual heterogeneity in vulnerability to depression and anxiety, indicating that distinct neurobiological processes shape susceptibility and resilience. To identify the mechanisms underlying this divergence, mice subjected to chronic restraint stress (CRST) were stratified into stress-susceptible or resilient phenotypes using multidimensional behavioral clustering. To examine how exercise modifies these stress-defined endophenotypes, we used a graded treadmill paradigm in which low-, moderate-, and high-intensity exercises were parametrically defined relative to the ventilatory threshold (VT). Only low-intensity exercise performed below VT produced robust antidepressant and anxiolytic effects in susceptible mice. Whole-brain c-Fos mapping revealed the selective recruitment of the ventral hippocampus (vHPC) during low-intensity exercise. Chemogenetic silencing of vHPC neurons abolished these behavioral benefits, indicating that vHPC engagement is essential for exercise-induced resilience. Transcriptomic profiling of vHPC showed that this adaptive state was associated with the coordinated modulation of primary cilium-associated gene networks. Morphometric analyses confirmed that chronic stress-induced pronounced elongation of primary cilia, particularly in astrocytes, whereas low-intensity exercise restored both ciliary length and the proportion of ciliated astrocytes. These structural recalibrations coincided with reduced expression of proinflammatory cytokines, including IL-1α and fractalkine, suggesting that astrocytic cilia act as a key interface linking stress signaling to neuroimmune regulation. Collectively, these findings outline a mechanistic cascade in which exercise below the VT engages vHPC circuits, reorganizes cilia-related transcriptional programs, and restores astrocyte and inflammatory homeostasis, converting stress-susceptible states into resilient phenotypes.

overall_design: RNA-seq profiling of sedentary controls (SED), stress-susceptible animals (SUS), and stress-susceptible animals subjected to low-intensity exercise (SUS+LE)

first: Joon-Yong

last: Cho


title: Identification of aging and senescence markers of male African turquoise killifish livers

city: Bunkyo-ku

first: Satoshi

last: Kofuji

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Institute of Science Tokyo

summary: Vertebrates grow and mature with age after birth (aging change), deteriorate (senescence), and eventually die. However, many aspects remain unclear regarding the distinction between aging change and senescence at the body, organ and cell levels. In this study, we aimed to isolate molecular markers distinguishing aging change from senescence in the short-lived vertebrate African Turquoise killifish (N. furzeri). First, the lifespan of N. furzeri was divided into growth (young), mature (adult), and senescent (old) stages. Changes between young and adult were defined as “aging change”, while changes between adult and old were defined as “senescence”. Metabolome and gene expression analyses of the liver identified several metabolites and genes as aging and senescence markers. These results indicate that molecular markers reflecting aging change and senescence at the organ levels can be isolated using N. furzeri.

overall_design: RNA-seq data for the livers of Nothobranchiu furzeri (GRZ strain) at young, adult, and old stages.

first: Hiroshi

last: Nishina


title: Attenuation of oxygen-induced neovascularization and inflammation by neutralizing antibody to VEGFA and/or ANG-2

city: Yokohama

first: Hiroto

last: Abe

state: Kanagawa

address: 216 Totsuka-cho, Totsuka-ku

institute: Chugai Pharmaceutical. Co. Ltd.

summary: Neovascularization is a major cause of blindness in various retinal diseases, and inflammation aggravates the pathological and clinical conditions of these diseases. VEGFA or ANG-2 neutralizing antibodies have been used to block pathological neovascularization. In this work, the effects of intraocular administration of neutralizing antibodies against VEGFA, ANG-2, or bispecific to these two factors on pathological findings were examined in the oxygen-induced retinopathy (OIR) mouse model. At both postnatal day (P)17 and P19, anti-VEGFA and -ANG-2 administration suppressed neovascularization, and the bispecific antibody attenuated neovascularization more efficiently. However, oxygen-induced vaso-obliteration was not modified by these antibodies. Numbers of photoreceptor, amacrine, and bipolar cells were reduced in the OIR retina, and the antibodies reversed these changes. Microglia-specific gene expression increased in the OIR retina, and administration of the antibodies reduced the IBA1-positive area in the OIR retina, although these antibodies did not affect marker gene expression. Labeled VEGFA and ANG-2 were found to be co-localized with microglia, suggesting that VEGFA and ANG-2 affect microglia activation directly. Taken together, neutralizing antibody to VEGFA or ANG-2 attenuated oxygen-induced neovascularization and inflammation, and the bispecific antibody more efficiently suppressed some features than the single antibody to VEGFA or ANG-2.

overall_design: RNA-seq profiling of retina from C57BL/6J mice at P17 and P19 which were exposed to 75% O2 from P7 to P12, returned to room air, and intravitreally injected 1 µl of control IgG (0.4 µg/µl), anti-VEGFA (B20.4.1., 0.2 µg/µl), ANG-2 (LC10, 0.2 µg/µl), or VEGFA/ANG-2 bispecific antibody (B20.4.1_LC10, 0.4 µg/µl) at P14.

first: Hirokazu

last: Oohashi

first: Toshiro

last: Iwagawa

first: Chihiro

last: Kawaji

first: Yuta

last: Inokuchi

first: Tetsuhiro

last: Soeda

first: Kosuke

last: Saita

first: Makoto

last: Aihara

first: Sumiko

last: Watanabe


title: Prognostic accuracy of a peripheral blood transcriptome signature in chronic hypersensitivity pneumonitis

city: Denver

first: Evans

last: Fernandez

state: CO

address: 1400 Jackson St.

institute: National Jewish

summary: The prognostic value of peripheral blood mononuclear cell (PBMC) expression profiles, when used in patients with chronic hypersensitivity pneumonitis (CHP), as an adjunct to traditional clinical assessment is unknown. RNA-seq analysis on PBMC from 37 patients with CHP at initial presentation determined that (1) 74 differentially expressed transcripts at a 10% false discovery rate distinguished those with (n=10) and without (n=27) disease progression, defined as absolute FVC and/or diffusing capacity of the lungs for carbon monoxide (DLCO) decline of ≥10% and increased fibrosis on chest CT images within 24 months, and (2) classification models based on gene expression and clinical factors strongly outperform models based solely on clinical factors (baseline FVC%, DLCO% and chest CT fibrosis).

overall_design: RNA-seq analysis of PMBCs from adults with chronic hypersensitivity pneumonitis stratified by disease severity based on FVC and CT findings.

last: Fernández Pérez

first: Laura

middle: D

last: Harmacek

first: Brian

last: O’Connor

first: Thomas

last: Danhorn

last: Vestal

first: Lisa

last: Maier

first: Tilman

middle: L

last: Koelsch

first: Sonia

last: Leach


title: STAG2 loss amplifies EWS-FLI1-driven microsatellite enhancer activity promoting Ewing's sarcoma aggressiveness [ChIP-Seq]

city: Ann Arbor

first: Abhijit

last: Parolia

state: MI

address: 1500 E Medical Center Dr

institute: Michigan Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Ewing sarcomas are driven by chromosomal translocations that fuse a FET RNA‑binding protein to an ETS transcription factor, most commonly generating the EWS-FLI1 fusion oncoprotein. EWS-FLI1 engages GGAA microsatellite repeats to create de novo enhancers and activate oncogenic transcriptional programs—a neomorphic gain-of-function essential for Ewing sarcoma pathogenesis. In addition to the truncal fusion, recurrent loss‑of‑function alterations in the cohesin subunit STAG2 occur in approximately 10–15% of Ewing sarcomas and are associated with adverse clinical outcomes. Yet, how STAG2-cohesin deficiency remodels EWS-FLI1 chromatin occupancy and gene regulatory network remains incompletely understood. Here, using genetic STAG2 loss‑of‑function models combined with functional multi-omic profiling, we show that STAG2-cohesin loss in Ewing sarcoma cells reprograms the EWS-FLI1 cistrome by shifting its binding preference at GGAA microsatellite repeats. Despite increased EWS–FLI1 protein abundance, disruption of STAG2 eliminates more than 40% of EWS-FLI1 binding sites. The lost sites are enriched for elements harboring 1–4 GGAA repeat motifs, with a simultaneous gain in EWS-FLI1 binding at multimeric enhancers containing ≥5 GGAA repeat sequences. Notably, reprogrammed EWS-FLI1 sites show concomitant changes in chromatin accessibility and H3K27ac abundance, which preferentially amplify EWS-FLI1 activity at multimeric enhancers and drive marked up‑regulation of canonical microsatellite‑regulated target genes in STAG2‑null cells. By integrating Hi‑C–derived chromatin interaction maps with altered EWS-FLI1 occupancy, we derive distinct monomeric (1xGGAA) and multimeric (≥10xGGAA) EWS-FLI1 transcriptional signatures and show that STAG2 inactivation selectively augments the multimeric signature while attenuating monomeric activity. We further define a prognostic signature of GGAA-repeat enhancers that is significantly upregulated in patient tumors with aggressive clinical features and deleterious STAG2 alterations. Together, these findings reveal that loss of STAG2–cohesin does not simply attenuate EWS-FLI1 function but reprograms its cistrome toward microsatellite multimeric GGAA neo‑enhancers, thereby amplifying a high‑risk EWS–FLI1 transcriptional state in Ewing sarcoma.

overall_design: Comparative DNA binding profiles of noted proteins in Ewing Sarcoma cells with loss of STAG2.

first: Alec

last: Chu

first: Eleanor

last: Young

first: Sanjana

last: Eyunni


title: STAG2 loss amplifies EWS-FLI1-driven microsatellite enhancer activity promoting Ewing's sarcoma aggressiveness [ATAC-seq]

overall_design: Comparing chromatin accessibility using ATAC-seq in A673 cell lines treated with control or STAG2-targeting shRNA.


title: Tweaking lentiviral vector design balances efficacy and safety in liver-directed gene therapy for familial hypercholesterolemia

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

summary: Elevated low-density lipoprotein (LDL) cholesterol is the hallmark of familial hypercholesterolemia (FH), an inherited disease mostly due to mutations in the LDL receptor (LDLR)-encoding gene. Here we enforced overexpression of LDLR in hepatocytes by in vivo lentiviral vector (LV) gene therapy and normalized circulating LDL cholesterol in a mouse model of FH. One year after gene therapy we detected a high incidence of hepatic tumors in treated mice. Analysis of LV genomic integration sites in the liver tumors revealed expanded clones bearing LV insertions within the Fyn-related kinase (Frk) gene, a known hepatic oncogene, inducing the formation of aberrant LDLR-FRK transcripts. When we purposely overexpressed LDLR-FRK by LV gene transfer, we observed hepatocellular hyperplasia and hypertrophy, supporting a role of this chimeric protein in oncogenesis. Since high expression of this chimeric oncogene and the LDLR likely cooperated to cause liver toxicity, we reduced the strength of LDLR expression within LV. We achieved normalization of circulating LDL cholesterol in two FH mouse models and prevention of atherosclerosis, even under high-fat diet challenge, without any long-term liver tumorigenicity. Overall, our in-depth assessment of the efficacy and safety of in vivo gene therapy for FH provides new insights into mechanisms of action and potential vulnerabilities, with implications for future developments of lipid-lowering gene therapies.

overall_design: To analyze the global gene expression profile of the livers of treated mice and of liver tumors, we performed transcriptomic analysis of histologically normal liver samples from LV-treated or untreated Ldlr-/- mice and of six of the liver tumors found in LV-treated mice

first: Cesare

last: Canepari

first: Michela

last: Milani

first: Marco

last: Monti

first: Ivan

last: Merelli

first: Alessio

last: Cantore


title: Aplysia Pleural Ganglia 7 Days After Long-Term Sensitization Training.

city: River Forest

first: Robert

last: Calin-Jageman

state: IL

address: 7900 West Division

department: Psychology

institute: Dominican University

summary: We used a custom-designed microarray to characterize the transcriptional response that persists 5 days after long-term sensitization training in the marine mollusk Aplysia californica, a time-point at which recall has partially decayed but there is still clear sensitization memory expressed in most animals.  Aplysia were exposed to a 1-day unilateral LTS training protocol (4 rounds of noxious shock at 30 min intervals, each shock 10s of 1/2s off 1/2on 90mA 60-hz biphasic square-wave shock). Duration of the tail-elicited siphon withdrawal reflex was measured before training, 1 day after training, and 5 days after training.  From the 1-day post-tests we selected 32 animals showing strong sensitization responses (at least 30% increase in reflex duration on the side of training).  At the 5-day post-test we observed substantial but not complete decay of the expresison of sensitizaiton.  Plueral ganglia were harvested immediately after the 5-day post tests for microarray analysis; these ganglia contain the VC nociceptors known to help encode sensitization memory.  Samples from a left-trained and right-trained animal were combined to smooth out lateralized gene expression (32 animals produced 16 microarray samples, each having a set of trained plueral ganglia and a set of untrained plueral ganglia).  In addition, within each batch of animals collected we matched the highest-forgetting left-trained animal with the highest-forgetting right-trained animal, and so on, producing samples consistent in levels of forgetting and considerable diversity in forgetting across samples.

overall_design: Within-subjects comparison. Each array is a two-color approach hybridized to a matched trained and untrained set of samples (with each sample containing tissue from a left- and right-trained animal). Conducted with 16 biological replicates, meaning 16 arrays, each comparing paired trained and untrained samples.

first: Irina


title: Cardiomyocyte-Derived TGFB3 Attenuates Cardiac Fibrosis and Preserves Cardiac Function in Heart Failure

first: Jieyuan

last: Xue

address: 280 South Chongqing Road

institute: Shanghai Jiao Tong University

summary: Heart failure (HF), the common end-stage of cardiovascular diseases, features cardiac fibrosis. Transforming growth factor-β3 (TGFB3), a key TGFB/SMAD ligand, is upregulated in cardiac disorders, but its cellular source and precise role are debated. This study examined TGFB3 in human and mouse heart failure tissues. Histological and molecular analyses showed its increase mainly from cardiomyocytes, induced by angiotensin II. Circulating TGFB3 in patients positively correlated with plasma proBNP, a heart failure severity marker. A cardiomyocyte-specific TGFB3 knockout mouse model showed its absence worsens cardiac dysfunction and fibrosis under pressure overload. Mechanically, TGFB3 competes with TGFB1 for receptors, reducing Smad3 phosphorylation and profibrotic gene activation. Loss of TGFB3 in cardiomyocytes increased expression of profibrotic mediators such as CTGF and SERPINE1, ultimately accelerating fibrotic remodeling during HF progression. These findings identify cardiomyocyte-derived TGFB3 as a crucial endogenous modulator that protects against pathological cardiac fibrosis and highlight its therapeutic potential in HF.

overall_design: To investigate the gene expression change in  heart of TGFB3 cardiomyocyte conditional KO mice with TAC operation. We performed gene expression profile using data obtained from RNA-seq of heart from wild type and KO mice.

first: Jizhong

last: Xuan


title: Gene expression analysis using RNAseq upon SBNO1 knockdown in the HCC cell line Hep3B

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: Aberrant Notch signaling has been identified as a possible catalyst for hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA) development. Genetic studies in Drosophila observed that the knockout of strawberry notch (sno) mimics loss of notch. Here, we elucidated the role of the mammalian Strawberry Notch 1 (SBNO1) in HCC and CCA development.

overall_design: Hep3B cells were transfected with NTC, siSBNO1#1 or siSBNO1#2 using Lipofectamine RNAiMAX Transfection Reagent. Total RNA was extracted using the Macherey-Nagel RNA Extraction Kit (Macherey-Nagel, Düren, Germany).

first: Stephanie

last: Roessler


title: Epigenetic remodeling in sarcoma promotes T cell infiltration via modulation of the Hippo pathway (human)

city: Stockholm

first: Mireia

last: Cruz De los Santos

address: Karolinska NKS J6:20

department: Oncology Pathology

country: Sweden

institute: Karolinska Institutet

summary: Immunotherapy in osteosarcoma remains limited by insufficient T cell infiltration. Considering the importance of epigenetics in sarcomagenesis, the impact of histone modifications in shaping the immune microenvironment was investigated. Using patient-derived ex vivo spheroids and in vivo metastatic osteosarcoma models, we found that pharmacological elevation of H3K27ac by the histone deacetylase 1/3 inhibitor entinostat promotes CD8⁺ T-cell activation, cytotoxicity, and the recruitment of CD8+CD103⁺ tissue-resident memory (TRM) T cells. Mechanistically, these immune-boosting effects are triggered by a Hippo pathway switch, in which Yes-associated protein 1 (YAP1) is suppressed and vestigial-like family member 3 (VGLL3) is induced, thereby rewiring transcription. Furthermore, we identified that VGLL3/CD103 signatures predict a response to anti-PD-1 treatment in sarcoma patients, and that combining H3K27ac induction with anti-PD-1 further augments T cell-mediated killing in ex vivo autologous patient-derived spheroid models. Our findings reveal an epigenetic-Hippo-immunomodulatory axis in osteosarcoma that also extends to other sarcomas, providing a rationale for incorporating epigenetic preconditioning with immunotherapy to improve patient outcomes and pointing towards novel biomarkers for treatment guidance.

overall_design: Sarcoma patient-derived ex vivo spheroid cultures from Chondroblastic Osteosarcoma (CBOS1) and a Myxofibrosarcoma patient (MFS1) treated with Entinostat (1µM) or vehicle (DMSO) during 24 hours.   Stable knock-downs were also performed in MSF1 patient ex vivo spheroids for VGLL3 (shVGLL3), YAP1 (shYAP1), and scramble control (shSCR) to study the impact of the Hippo Pathway.

first: Lundqvist

last: Andreas

first: Cruz De los Santos

last: Mireia


title: IGF2BP3 promotes progression of head and neck cancers through the circHECTD2/hsa_miR_4310/7157-5p/Smad2 signaling axis in an m6A modification–dependent manner

city: Jinan City

first: kainan

last: wu

state: Shandong

address: No. 107, Wenhua West Road, Lixia District, Jinan City, Shandong Province, China

institute: DeparQilu Hospital of Shandong University

summary: Accumulating evidence indicates that N6-methyladenosine (m6A) modification of circular RNAs (circRNAs) plays a pivotal role in regulating cancer progression. However, in head and neck squamous cell carcinoma (HNSCC), the biological functions and underlying mechanisms of m6A modification in circRNAs remain insufficiently elucidated. In this study, we demonstrated that IGF2BP3, an upstream m6A reader, is associated with poor clinical outcomes. IGF2BP3 stabilizes circHECTD2 through binding, and m6A modification enhances this interaction. Mechanistic investigations revealed that IGF2BP3 binds to and stabilizes circHECTD2, which functions as a sponge for hsa-miR-4310 and hsa-miR-7157-5p, thereby preventing the degradation of SMAD2 mRNA and promoting tumor proliferation, invasion, and metastasis in HNSCC. Collectively, these findings suggest that IGF2BP3 and circHECTD2 may serve as promising prognostic biomarkers and therapeutic targets for HNSCC.

overall_design: To identify downstream circRNAs regulated by IGF2BP3, we intersected the circRNA-seq and MeRIP-circRNA-seq datasets, which yielded three candidate circRNAs

first: Kainan

last: Wu

first: Dapeng

last: Lei


title: Chromatin Immunoprecipitation sequencing (ChIP-seq) for SBNO1 and TAF4

summary: Chromatin Immunoprecipitation sequencing (ChIP-seq) using antibodies specifc for SBNO1 and TAF4 or IgG control were performed using HuCCT1 cells.

overall_design: ChIP was performed using the SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads, Cell Signaling #9003). Sequencing was carried out by BGI Hongkong Tech Solution using the DNBseq™ platform.


title: Temporal regulation of human reactive astrocytes reveals their capacity for antigen presentation

city: Atlanta

first: Emily

middle: Jane

last: Hill

state: Georgia

address: 615 Michael Street

department: School of Medicine

institute: Emory University

summary: Astrocytes adapt to injury and disease by entering reactive states with altered gene expression, morphology, and function, but we still do not know how these states evolve over time in human cells or whether they acquire immune effector properties. Using human cortical organoids (hCOs) and primary fetal cortical tissue, we mapped the temporal dynamics and plasticity of inflammatory human astrocytes. Brief and prolonged exposure to inflammatory cytokines elicited robust, time-dependent changes in astrocyte transcriptomes and chromatin accessibility, and these exposures produced distinct acute and chronic reactive signatures. Despite these widespread genomic alterations, astrocytes that experienced either acute or chronic cytokine exposure reverted to a quiescent gene expression and chromatin state within days of cytokine withdrawal, which demonstrates a high degree of plasticity. Chronic inflammatory settings, but not acute ones, revealed a second layer of reactivity in which astrocytes induced major histocompatibility complex class II (MHCII) genes and surface MHCII protein. We validated MHCII expression and surface localization in primary human fetal astrocytes, in organotypic fetal cortical slices that include microglia, and in human brain tissue from patients with chronic inflammatory lesions. We propose that delayed MHCII emergence reflects progressive activation of interferon linked signaling in astrocytes, including low level interferon gamma production. Through co-immunoprecipitation and mass spectrometry of MHCII complexes from TIC-treated fetal astrocytes we identified candidate MHCII-presented peptides and confirmed that astrocytes can process and display exogenous peptides derived from human fetal neurons.

overall_design:
Human cortical organoids were exposed to TNF-a, IL-1a, and C1q to form reactive astrocytes. Astrocytes were isolated from organoids after various durations of exposure (1, 7, 31, or 84 days), as well as from age-matched controls. Paird ATAC and RNA libraries were created and sequenced to assess chromatin accessibility differences in astrocytes after neuroinflammatory exposure.

***************************************************************
GSM9374750: raw data files were permanently lost
***************************************************************

first: Caitlin

last: Sojka

first: Maureen

middle: M

last: Sampson

first: Hsiao-Lin

last: Wang

first: Shainoor

last: Showrin

first: Alexia

middle: T

last: King

first: Anson

last: Sing

first: Jianjun

last: Chang

first: Victor

last: Faundez

first: Timothy

first: Sriram

last: Venneti

first: Steven

last: Sloan


title: MIZ-1 (c-Myc-interacting Zinc Finger Protein-1, ZBTB17) is required for  efficient B cell receptor signaling [RNA-seq]

city: Montréal

first: Tarik

last: Moroy

address: 110 Pine Ave W, Montreal

country: Canada

institute: IRCM

summary: B cell receptor (BCR) signaling is required for the regulation of normal B lymphocyte development. We found that mice expressing a POZ domain-deficient MIZ-1 (MIZ-1ΔPOZ) exhibit impaired BCR signaling. Transcriptomic and ChIP-seq analyses reveal that, in addition to autophagy related genes, MIZ-1 directly regulates genes involved in BCR signaling and actin cytoskeleton dynamics.

overall_design: For RNA isolation, B220+ splenocytes were lysed in TRI Reagent (Sigma) and isolated RNA was cleaned using the RNeasy Mini Kit (Qiagen). For RNA sequencing (RNA-seq), a biological duplicate of sequencing libraries was prepared from RNA extracts. Ribosomal RNA were depleted (Ribo-Zero™ Magnetic Gold Kit, Epicentre) and library was prepared using KAPA Stranded RNA-Seq Kit with RiboErase. NGS sequencing (pair-end 50 cycles) was done on HiSeq 2000/2500 System (Illumina).

first: Julie

last: Ross

first: Eva-Maria

last: Piskor

first: Charles

last: Joly-Beauparlant

first: Lucia Paola

last: Gabrielli Tabarez

first: Elie

last: El-Ghorayeb

first: Arnaud

last: Droit

first: Christian

last: Kosan


title: Fecal Metagenomic Signatures of Lifespan Variation in Dogs: Findings from the Dog Aging Project

city: Tempe

first: Noah

last: Snyder-Mackler

state: AZ

address: 427 East Tyler Mall

institute: Arizona State University

summary: Dog Aging Project fecal metagenomic data from the Precision Cohort

overall_design: Dog Aging Project Dogs  sampled to define aging in the gut microbiome.

first: Daniel

last: Promislow

first: Elhanan

last: Borenstein


title: Distinct nociceptor roles in inflammation and itch revealed by subset-specific transcriptomic adaptation

city: Toulouse

first: Lilian

last: Basso

address: INSERM UMR1291 – CNRS UMR5051 - University Toulouse III CHU Purpan – BP 3028

country: France

institute: INFINITY INSERM U1291

summary: This study identifies two distinct subsets of sensory neurons that separately regulate itch and inflammation in allergic contact dermatitis. MrgprD⁺ nonpeptidergic neurons adopt a transient regenerative program during inflammation and are essential for itch behavior, while Trpv1⁺ peptidergic neurons limit inflammation by restraining neutrophil infiltration. These findings uncover parallel, nonredundant neuronal circuits that independently control inflammatory and pruritic responses in the skin.

overall_design: We induced a mouse model contact dermatitis in GINIP-DTR mice where GINIP+ neurons were depleted.

first: Tiphaine

last: Voisin

first: Nadine

last: Gheziel


title: Neurogenin-2 Reprograms Human Microglial Lineage Cells into Neurons In Vitro and in Chimeric Brains

city: Piscataway

first: Ziyuan

last: Ma

address: 604 Allison Rd

department: Cell Biology and Neuroscience

institute: Rutgers University

summary: Progressive neuronal loss is a hallmark of many neurological disorders, yet the adult human brain has a limited capacity for endogenous neuronal replacement. Direct neuronal reprogramming represents an alternative strategy for generating new neurons. Microglia, the brain’s resident immune cells, are uniquely positioned as candidate cellular substrates due to their abundance, self-renewal capacity, high motility, and rapid recruitment to sites of injury. Here, using live-cell imaging and electrophysiological recordings, we show that human pluripotent stem cell (hPSC)–derived primitive macrophage progenitors (PMPs) and their microglial derivatives exhibit robust neuronal reprogramming competence. Inducible expression of NEUROG2 in hPSC-derived PMPs drives acquisition of neuronal morphology, sequential expression of early and mature neuronal markers, organization of synaptic proteins, and functional excitability characterized by action potential firing. Singlenucleus RNA sequencing reveals a continuous, directionally ordered reprogramming trajectory marked by suppression of myeloid transcriptional programs, progression through intermediate remodeling states, and progressive activation of neuronal gene regulatory networks, consistent with a regulated lineage conversion rather than partial identity switching. Using a xenotransplantation-based human microglia chimeric brain model, we further demonstrate that inducible NEUROG2 expression reprograms donor-derived human microglia toward a neuronal identity in vivo, with stable neuronal marker expression maintained for up to eight months. Together, these findings establish human microglial lineage cells as a previously unexplored substrate for neuronal reprogramming, providing a conceptual framework for microglia-based strategies aimed at neuronal replacement and neural repair.

overall_design: In vitro-cultured primitive macrophage progenitor (PMP)  cells derived from human embryonic stem cells (hESCs) with doxycycline-inducible hNEUROG2 expression were used for the reprogramming study. Single nuclei were collected at 5 and 12 days after doxycycline induction, as well as from no-doxycycline controls, and subjected to single-nucleus RNA sequencing (snRNA-seq).

first: Jin

last: Mengmeng

first: Ma

last: Ziyuan

first: Jiang

last: Peng


title: MIZ-1 (c-Myc-interacting Zinc Finger Protein-1, ZBTB17) is required for  efficient B cell receptor signaling [ChIP-seq]

first: Tarik

last: Moroy

overall_design: Chromatin immunoprecipitation was carried out on B220+ splenocytes from Miz-1WT or MIZ-1DPOZ (MB1-cre X Miz-1floxedPOZ) mice using Miz-1 antibody (H-190, Santa Cruz). Briefly, 10 million cells were fixed with 1% Formaldehyde for 10 minutes with agitation at room temperature. Fixation was blocked by the addition of 125 mM glycine for 5 minutes with agitation at room temperature. Cells were pelleted by centrifugation at 4°C and snap freeze until utilisation. Fixed cells were lysed subsequently with cell lysis buffer and nuclei lysis buffer for 30 minutes on ice each. Samples were sonicated with Covaris and  precleared with dynabeads (protein A dynabeads + protein G) for 2h with agitation at 4°C. Unbound material was then incubated with Miz-1 antibody (Santa Cruz) for 2h with agitation at 4°C. Protein-chromatin complexes were collected using dynabeads overnight with agitation at 4°C. Complexes bound beads were then washed and eluted from beads for 4h at 65°C. RNAse and proteinase K were added to the mix for 1h at 42°C. DNA was extracted using QIAquick kit (Qiagen). DNA was then used to prepare librairies (KAPA Hyper Kit) for NGS sequencing (pair-end, 50 cycles) on HiSeq 2000/2500 System (Illumina).

first: Julie

last: Ross


title: STAG2 loss amplifies EWS-FLI1-driven microsatellite enhancer activity promoting Ewing's sarcoma aggressiveness [RNA-Seq]

first: Abhijit

last: Parolia

overall_design: Comparative transcriptomic (RNA-seq) profiling of Ewing sarcoma cell lines across treatment conditions using shRNA or siRNA against FLI1 and STAG2.

first: Alec

last: Chu

first: Eleanor

last: Young

first: Sanjana

last: Eyunni


title: Dynamics of Natural Killer Cell Function upon Recurrent Stimulation

city: Minneapolis

first: Samira

last: Azarin

state: Minnesota

address: 421 Washington Avenue Southeast, 151, Amundson Hall

department: Chemical Engineering and Materials Science

institute: University of Minnesota

summary: Natural killer (NK) cells have shown potential for allogeneic cell-based cancer immunotherapies. For development of economical off-the-shelf allogeneic therapies, maximal expansion of the NK cells from each donor must be achieved while maintaining efficacy and uniformity of the cell product. The most robust expansion method utilizes weekly stimulation with engineered feeder cells derived from the K562 cell line. However, the effects of repeated stimulation on NK cell growth, metabolism, and function are not well understood. In this study, we demonstrated a distinct shift in growth kinetics and metabolism around week 3-4 of repeated K562 feeder cell stimulation, followed by a change in cytokine secretion and killing ability. While Seahorse metabolic flux assays and transcriptomics suggested a transition from glycolytic metabolism to oxidative metabolism after the first week of stimulation, the shift in growth kinetics generally correlated to reduced metabolic activity. Collectively, these results indicate that serial stimulation sustains large-fold NK cell expansion that can be exploited for NK cell therapy; however, this expansion has important impacts on NK cell growth, metabolism, and function. Careful characterization is critical when developing large-scale biomanufacturing processes that ensure clinical efficacy of the final cellular product.

overall_design:
Bulk RNAseq of peripheral blood-derived NK cells (PBNK) at day 0, 7, and 35 from 4 separate healthy donors (Donor 5, 6, 7, and 8, labeled biol rep 1, 2, 3, and 4) after restimulation every 7 days with irradiated K562 cells engineered to express membrane-bound 41BBL and IL21 (feeder-expanded). Day 0 cells were collected after enrichment of NK cells from leukocyte reduction chambers. GSM8289866 and GSM8289870 were reused from GSE268341 as part of this analysis, which are day 7 samples from two separate donors. These samples were similarly processed to the other samples new to this analysis. Processed data (TPM) is provided for the new samples here as well as reused samples together in the referenced spreadsheet.

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

first: Jennifer

last: One

first: Janani

last: Narayan

first: Frank

last: Cichocki

first: Wei-Shou

last: Hu


title: Mapping self-associating chromatin hubs identifies Id proteins as key determinants of exhausted T cell fate

city: Nutley

first: Haihui

last: Xue

address: 123 Metro Boulevard, Bldg. 123, Rm. 5527

department: Center for Discovery and Innovation

institute: Hackensack University Medial Center

summary: The goal of this study is to determine how transcription cofactors, Id2 and Id3, mediate differential regulation  of exhausted CD8 T cell fate decision and differentiation at the early stage of responses to chronic viral infection.

overall_design: Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) was performed on sort-purified antigen-specific CD8+ T cells on day 8 post-infection with LCMV clone 13.

first: Hu

last: Wei

last: Sheng'en

first: Zang

last: Chongzhi

first: Xue

last: Hai-Hui


title: Gene expression in glycerol-grown Yarrowia lipolytica Hyb6 (EPA- and DPA-producing strain) across different growth phases and under two amino acid supplementation conditions

city: Saarbruecken

first: Michael

last: Kohlstedt

address: Campus A1.5

institute: Saarland University

summary: mRNA was sampled during exponential growth phase (10 h), early stationary/production phase (48 h), and late production phase (96 h)  strains: Y. lipolytica Hyb6 (EPA- and DPA-producing strain)  (Gemperlein et al., 2019)

overall_design: Three different setups were analyzed: condition 1 (Reference), condition 2 (15 mM L-lysine addition), and condition 3 (15 mM ketogenic amino acids mixture addition), with samples collected at 10, 48, and 96 h

first: Hang

last: Qi

first: Christoph

last: Wittmann


title: Age- and Sex- Driven Transcriptional and Metabolic Diversity in Myeloid-Derived Suppressor Cells After Mouse Sepsis

city: Gainesville

first: Jaimar

last: Rincon

address: 1600 SW Archer Road

department: Departament of Surgery

institute: University of Florida

summary: Sepsis induces profound immune dysregulation, often resulting in chronic critical illness characterized by persistent immunosuppression and poor outcomes. Myeloid-derived suppressor cells (MDSCs) are central mediators of this immunosuppressive phenotype, yet the influence of age and sex on their transcriptional and metabolic states remain poorly understood. Here, we employed single-cell RNA sequencing of splenic leukocytes from young (3-4 months) and older (18-24 months) adult male and female mice subjected to a clinically relevant murine sepsis model to define age- and sex-specific MDSC phenotypes. We identified significant differences regarding age and sex in MDSC expansion, transcriptome, canonical pathway activation, RNA velocity, mitochondrial metabolism, and predicted cell-cell communication after sepsis. Using drug2cell analysis of total leukocytes we also identified cohort-specific drug target profiles. These findings underscore the importance of age and sex in shaping sepsis-induced MDSC biology and suggest that personalized immunomodulatory strategies targeting MDSCs could improve sepsis outcomes.

overall_design: scRNA sequencing was performed on young and older, male and female B6 mice after sepsis (CLP+daily chronic stress for 7 days) as well as in age and sex matched naïve mice.

first: Christine

last: Rodhouse

first: Dayuan

last: Wang

first: Hongru

last: Tang

first: Valerie

last: Polcz

first: Miguel

last: Hernández-Ríos

first: Xuanxuan

last: Yu

first: Leandro

last: Balzano-Nogueira

middle: C

first: Angel

last: Charles

first: Seiichiro

last: Fujishima

first: Quan

last: Vo

first: Marvin

last: Dirain

first: Ricardo

last: Ungaro

first: Dina

last: Nacionales

first: Leilani

last: Zeumer-Spataro

first: Larissa

last: Langhi Prata

first: Shawn

last: Larson

first: Gemma

last: Casadesus

first: Feifei

last: Xiao

first: Shannon

last: Wallet

first: Maigan

last: Brusko

first: Tyler

last: Loftus

first: Letitia

last: Bible

first: Alicia

last: Mohr

first: Paramita

last: Chakrabarty

last: Kladde

first: Clayton

last: Mathews

first: Lyle

last: Moldawer

first: Robert

last: Maile

first: Guoshuai

last: Cai

first: Philip

last: Efron


title: TREATING HIPPOCAMPAL NEURAL STEM CELLS WITH NANO-PULSED LASER THERAPY GENERATES NEURONS RESILIENT AGAINST Aβ OLIGOMER TOXICITY

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

summary: Alzheimer’s disease (AD) is the leading cause of dementia worldwide, and despite the passage of over a century since its discovery, we have yet to discover a cure. Hippocampal synaptic dysfunction driven by toxic amyloid-β oligomers (AβO) is an early event in the progression of neurodegeneration and cognitive decline in AD. Non-invasive therapies such as photobiomodulation (PBM) are receiving increased attention in AD research due to the accessibility and relative safety compared to novel drug trials, and have been shown to induce synaptic resilience in animal models of AD. Nano-pulsed laser therapy (NPLT) is a type of PBM therapy using pulsed 808nm near-infrared laser light and optoacoustically generated ultrasound waves to stimulate deeper brain structures than would be accessible by traditional PBM therapy. Here we use NPLT to stimulate adult hippocampal neural stem cells (NSC) and differentiate them in vitro to assess resilience of the mature neurons against AβO toxicity. We found that neurons differentiated from NPLT-treated NSC are resilient against AβO binding and mitochondrial toxicity, and show increased expression of genes associated with autophagy and proteostasis.

overall_design: RNASeq profiling of adult rat hippocampal neural stem cells treated with NPLT at 24 hours and 5 days post-differentiation

first: Kevin

last: Johnson

first: Auston

last: Grant

first: Shrinath

last: Kadamangudi

first: Armando

last: Arizpe

first: Kathia

first: Rinat

last: Esenaliev

first: Giulio

last: Taglialatela

first: Maria-Adelaide

last: Micci


title: TFR cells regulate the specificity of anti-commensal IgA in the gut and repress global IgA responses via IL-10

city: Indianapolis

first: Prasida

last: Holla

state: IN

address: 1044 W walnut St

department: Pediatric Infectious Diseases

institute: Indiana University School of Medicine

summary: Immunoglobulin A (IgA) most predominant antibody isotype at mucosal surfaces and is regulated by both T cell-dependent (TD) and independent (TI) mechanisms. In the TD pathway, T follicular helper (TFH) cells provide help to B cells to generate high-affinity antibodies. T follicular regulatory (TFR) cells fine-tune antibody responses, but precisely how these cellsregulate microbiota-directed IgA at mucosal sites has been unclear. Here, we used a TFR-deficient mouse model (Foxp3Cre Bcl6fl/fl; Bcl6FC) in which the gut microbiota develops in the absence of TFR cells, while the broader regulatory T cell compartment remains intact. While Bcl6FC mice showed similar levels of IgA-coated commensal bacteria to wild-type mice in the naïve state, following oral immunization, Bcl6FC mice exhibited a durable increase in IgA-coated commensal bacteria in feces and small intestine, without changes in overall community composition or epithelial barrier permeability. IgA-seq analysis of Bcl6FC mice revealed an increased diversity of IgA-coated taxa, both in naïve and orally immunized mice. IgA coating index analysis, a measure of IgA affinity, identified higher IgA binding to multiple taxa in Bcl6C mice compared to control mice. Consistent with these findings, sera from immunized Bcl6FC mice showed increased IgA binding to Alloprevotella and Klebsiella species but not to E. coli or Group A/B Streptococcus compared to control mice. B cell receptor repertoire sequencing demonstrated divergent patterns of somatic hypermutation (SMH) for IgA and IgG, where TFR cells repressed IgA SMH but enhanced IgG somatic hypermutation. Mechanistically, suppression of commensal-directed IgA required TFR-derived IL-10 but was independent of CTLA-4. IL-10 directly inhibited TGF-β-driven IgA class switching of B cells in vitro. Together, our data identify TFR cells as critical gatekeepers of mucosal IgA responses, constraining commensal-specific IgA responses through a novel IL-10-dependent pathway. Our findings haveimportant implications for regulation of the microbiome by TFR cells and IgA.

overall_design: RNA-seq of B cell receptors (BCRs) from sorted germinal center B cells were sequenced

first: Abdul

last: Abdi

first: Hong

last: Liu

first: Adepeju

last: Oshodi

first: Kristin

last: Hollister

first: Qiang

last: Chen

first: Alexander

last: Dent


title: Biomimetic microfibers for myelin-enhancer screening and neural regeneration

city: Kodaira

first: Lili

last: Quan

address: 4-1-1 Ogawa-Higashi

department: National Institute of Neuroscience

institute: National Center of Neurology and Psychiatry

summary: Remyelination is crucial for the functional restoration of neural circuits, with oligodendrocyte wrapping of axons being the final and essential step. However, its regulatory mechanisms remain unclear, partly due to the lack of effective evaluation systems of oligodendrocyte wrapping. Here, we developed a novel culture platform with aligned microfibers that mimic axonal structure and chemistry to quantify oligodendrocyte wrapping. Compound screening with this system identified that dimemorfan, a sigma-1 receptor agonist, enhances oligodendrocyte wrapping and transcriptomic profiles detected by RNA-seq. In addition, dimemorfan promoted wrapping in human iPSC-derived oligodendrocytes. Our findings provide a new platform for drug discovery for brain regeneration and advance the understanding of remyelination mechanisms.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: O4+ rat primary oligodendrocytes were cultured on laminin fragment iMatrix-511 (0.1 µg /µL, 892012, Nippi)-coated control microfiber platforms or on oxygen plasma etched microfiber platforms in myelin medium supplemented with PDGF-AA (10 ng/mL) for 2 days, followed by myelin medium for an additional 5 days before RNA isolation. iPSC-derived oligodendrocytes were plated on iMatrix-511-coated etched microfiber platforms and cultured in PDGF medium for 3 days, then changed to glial medium with or without 2 µM dimemorfan before RNA isolation.

first: Rieko

last: Muramatsu


title: DKC1: a robust prognostic factor and potential therapeutic target in Multiple Myeloma

city: jinan

first: chenxi

last: sun

address: 247th of Beiyuan Road

institute: The Second Qilu Hospital of Shandong University

summary: Multiple Myeloma (MM) is an incurable plasma cell malignancy. Dyskerin pseudouridine synthase 1 (DKC1), a nucleolar protein, is essential for RNA modification and cellular homeostasis, yet its role in MM remains unclear. Here, we report that elevated DKC1 expression independently predicted poor outcomes in MM and further refined prognostic stratification beyond the ISS system. Functional assays showed that DKC1 promoted MM cell proliferation, survival, and colony formation, whereas DKC1 knockdown or pharmacological inhibition of DKC1 by pyrazofurin inhibited proliferation and colonies, induced apoptosis, and suppressed tumor growth in xenografts. Mechanistically, DKC1 promotes tumor progression by stabilizing ATF5 mRNA through pseudouridylation, a direct post-transcriptional mechanism evidenced by site-specific pseudouridine mapping. Together, these findings highlight DKC1 as both a critical prognostic biomarker and a promising therapeutic target.

overall_design: RNA-seq profiling of wildtype RPMI8226 cells and their knockdown derivatives (shDKC1).

first: Chengyun

last: Zheng

first: Yang

last: Jiang

first: Chenxi

last: Sun


title: Isolation protocol of viable human central nervous system T cells

city: Amsterdam

first: Jeen

last: Engelenburg

address: Meibergdreef 47

country: Netherlands

institute: Netherlands Institute for Neuroscience

summary: Brain tissue-resident memory T(RM) cells are sentinels who survey the human brain and contribute to homeostasis in the central nervous system. Here, we present a protocol for the isolation of T cells from post mortem human brain material. We describe the procedures to isolate viable cells from blood, choroid plexus, leptomeninges, cerebrospinal fluid (CSF), and white matter. The potential application of this protocol allows users to isolate primary brain T cells and phenotype them using flow cytometry or sequencing approaches.

overall_design: RNAseq profiling of human brain T cell and microglia isolations with different enzymatic digestions and/or the addition of transcription/translation inhibitors


title: Tumor-like proliferation of CCM3 knockout endothelial cells: Insights from semaxinib treatment and transcriptome profiling of co-cultures

city: Greifswald

first: Robin

middle: A.

last: Pilz

address: Fleischmannstr. 43

department: Institute for Human Genetics

institute: University Medicine Greifswald

summary: We used RNA-seq to study the effect of semaxinib treatment on induced pluripotent stem cell (iPSC)-derived wild-type (WT) and CCM3 knockout (KO) endothelial cells (iEC) in co-culture.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and CCM3 KO iECs in co-culture under DMSO or semaxinib treatment with 3 biological replicates each

first: Valeriia

last: Saenko

first: Dariush

last: Skowronek

first: Ute

last: Felbor

first: Matthias

last: Rath

middle: A


title: The transcriptomic profile of the naïve or CpG-stimulated Rfx7-deficient mouse Follicular B cells and RFX7-transfected lymphoma human cell line U-2932

city: Bellinzona

first: Greta

last: Guarda

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine (IRB)

summary: PART 1) Alterations of the transcription factor RFX7 have been reported in different B-cell malignancies. We therefore set out to study the role of RFX7 in B cell activation. So we performed bulk RNA-seq on sorted wild-type or Rfx7-deficient follicular B cells, either naive or activated with CpG. PART 2) RFX7 frameshift and non-sense mutations have been reported in different B-cell malignancies. We therefore set out to study the role of selected truncations in a human lymphoma cell line. We performed bulk RNA-seq on sorted U-2932 cells transfected with different RFX7 encoding constructs.

overall_design: PART 1) FO B cells were FACS-sorted as B220+/CD19+/CD23+ and either directly processed or activated with CpG (2 μg/ml) for 18h in vitro. PART 2) U-2932 cells were transfected with different eGFP- or mCherry-RFX7 encoding plasmids for 24h and sorted for eGFP and/or mCherry positivity.


title: Brimonidine protects IHC ribbon synapses and SGNs from noise-induced hearing loss

city: Jinan

first: Jing

last: Cai

address: 4 Duanxing West Road

department: Shandong Provincial ENT Hospital

institute: Shandong University

summary: Exposure to excessive noise levels can result in hearing impairment. Currently, there are no effective pharmacological interventions available for the prevention of noise-induced hearing loss. This study was designed to investigate the protective effects of brimonidine, an α2-adrenergic receptor agonist, against noise-induced inner ear damage in mice, as well as to explore the underlying mechanisms. Eight-week-old male C57BL/6 mice were randomly assigned to one of three experimental groups: a control group, a noise exposure (NE) group (exposed to broadband noise, 8–16 kHz, at 100 dB SPL for 2 hours), and a brimonidine-treated group (which received intraperitoneal injections of 1 mg/kg brimonidine prior to noise exposure). Our findings demonstrate that brimonidine significantly attenuates noise-induced hearing loss in young adult mice. Furthermore, brimonidine markedly reduces glutamate (Glu) accumulation in the inner ear. RNA sequencing analysis suggests that brimonidine exerts its protective effects, in part, through the downregulation of inflammatory cytokines and immunoglobulin-related pathways. These results indicate that brimonidine is a promising pharmacological agent for the prevention of noise-induced hearing loss.

overall_design: By comparing the results of three groups of sequencing, the mechanism of noise exposure-induced damage and the protective mechanism of bromomonidine were determined.

first: Lei

last: Xu

first: Yongdong

last: Song

last: Zhang

first: Yu

last: Jin

first: Ligang

last: Kong

first: Haibo

last: Wang


title: BOLL-containing Aggregate Mediates Translational Regulation During Human Oogenesis

city: Fuzhou

first: Ying

last: Li

state: Fujian

address: No. 2, Xueyuan Road, University Town

institute: Fuzhou University

summary: Human oocyte meiosis utilizes a specialized translational control strategy to coordinate meiotic progression, mediated through dynamic regulation of mRNA stores. While germ cell-specific RNA-binding proteins (RBPs) are known to orchestrate this post-transcriptional program, the mechanistic basis of RBP-mediated cell fate specification remains elusive. Here, we demonstrate that BOLL, a Deleted in Azoospermia (DAZ) family protein, forms protein aggregates during meiotic prophase to drive translational reprogramming in human oogenesis. We determined that BOLL enhance translation efficiency of cell cycle regulators, as demonstrated by integrative translatome-transcriptome analysis combined with RNA immunoprecipitation sequencing. We also revealed the functional interaction network of BOLL with core translation machinery components through its conserved DAZ containing domain. Crucially, we identified the SDS-resistant protein aggregates as BOLL structural signature in human oocyte-like cells, demonstrated by semi-denaturing electrophoretic analysis. These finding delineate a protein aggregate-mediated regulatory paradigm where BOLL aggregates exert spatiotemporal control over cell cycle related genes during the meiotic prophase of human oogenesis.

overall_design: To investigate the role of BOLL protein aggregates in translational regulation during human oocyte development, we utilized an in vitro human stem cell-derived oocyte-like cell (OLC) model. This model mimic key meiotic stages by combining BMP4-induced differentiation with BOLL overexpression. Base on this system, we employed integrated multi-omics profiling (RIP-seq combined with transcriptome-translatome sequencing) to comprehensively identify BOLL-bound mRNA targets and quantify their translation efficiency. Furthermore, co-immunoprecipitation coupled with mass spectrometry was used to define the network of proteins interacting with BOLL. To specifically characterize the functional significance of BOLL to form aggregates, we generated truncation mutants disrupting its aggregation-prone domains. These mutants were then rigorously compared to full-length BOLL using biochemical assays to confirm loss of aggregation, co-immunoprecipitation to assess disrupted protein interactions, and functional reporter assays to measure impaired translational activation of target genes.

first: Lingya

last: Mao

first: Boyuan

last: Liang

first: Kehkooi

last: Kee