title: Establishment and Characterization of a Novel Murine Hepatoma Cell Line Allowing Concomitant Conditional Inactivation of Caspase-8 and IKKγ/NEMO

city: Aachen

first: Ralf

last: Weiskirchen

address: Pauwelsstr. 30

department: IFMPEGKC

institute: RWTH University Hospital Aachen

summary: Caspase-8 and the NF-kappa-B essential modulator (NEMO, also referred to as IKKγ) play critical roles in controlling TNF-α-induced cell death and survival in hepatocytes. The aim of this study was to generate a hepatocyte-derived cell line in which the Casp8 and Nemo genes can be conditionally inactivated simultaneously to investigate the significance of the corresponding signaling pathways. To this end, we induced hepatocellular carcinoma in Casp8f/fNemof/f mice using diethylnitrosamine (DEN) and established an immortalized hepatoma cell line from explanted liver tumors, which is subsequently referred to as ΔCN60. ΔCN60 cells still retain floxed Casp8 and Nemo alleles, allowing for efficient Cre-mediated deletion to generate Casp8ΔNemoΔ derivatives. Loss of both Caspase-8 and NEMO inhibits cell proliferation, increases expression of tumor and progenitor markers (AFP, CD133), reduces albumin expression, and blocks TNF-α-induced NF-κB p65 nuclear translocation. Casp8ΔNemoΔ ΔCN60 cells show increased RIP1 stability, altered RIP3 dynamics, and heightened sensitivity to prolonged TNF-α exposure, suggesting a shift towards necroptotic signaling. ΔCN60 serves as a versatile hepatoma model for investigating Caspase-8/NEMO/RIP1/RIP3-dependent pathways and TNF-α-induced liver damage, reducing the need for animal testing.

overall_design: mRNA bulk next-generation sequencing (NGS) was performed to demonstrate the translational potential of cell line termed ΔCN60


title: Non-canonical proteolytic activation of RNase L by SARS-CoV-2 3CLpro offsets inactivation of OAS1 antiviral signaling

status: Public on Apr 01 2026

city: Vancouver

first: Christopher

middle: M

last: Overall

state: BC

address: 2350 Health Sciences Mall

country: Canada

institute: UBC

type: Expression profiling by high throughput sequencing

summary: Upon sensing viral dsRNA, interferon-stimulated oligoadenylate synthetases (OAS) synthesize 2´-5´oligoadenylates that activate ribonuclease L (RNase L) to restrict viral replication. The predominant protective OAS during SARS-CoV-2 infection is the membrane-anchored OAS1 isoform p46. We show that SARS-CoV-2 3C-like main protease (3CL pro /M pro ) cleaves p46 at 381 STLQ 384 ↓A, removing the prenylated Cys 397 anchor, releasing p46 into the cytosol, and decreasing antiviral restriction. Unexpectedly, RNase L continues to restrict SARS-CoV-2 replication in p46-null cells. We identify RNase L as a second substrate within the OAS–RNase L pathway. Cleavage at 406 SCLQ 409 ↓S removes an inhibitory N-terminal domain, generating RNase L (410–741), a proteolytically activated product that restricts viral replication. A non-cleavable RNase L (Gln409Ala) mutant lacks antiviral activity in p46-null cells, confirming this non-canonical activation mechanism. RNA-seq revealed that the proteolytically activated RNase exhibits altered specificity toward cellular mRNA targets and that 3CL pro indirectly suppresses OAS3 transcripts without directly cleaving OAS3. We propose that the conserved 3CL pro -sensitive motif in RNase L functions as a failsafe tripwire that constrains complete loss of antiviral restriction despite simultaneous evasion of OAS1 p46. Thus, SARS-CoV-2 replication dynamics are intrinsically balanced by viral proteolysis within the OAS–RNase L axis, sufficient for polyprotein processing but countered by protease-triggered activation of RNase L and downstream antiviral restriction.

overall_design:
1) cell-free RNA integrity assay by RNAseq: transfection of HEK293 cells with plasmids encoding one of RNaseL, N-terminal fragment RNase L (1–409), or C-terminal fragment RNase L (410–741) then stimulated 24 h post-transfection with 50 ng/mL IFNa-2b. Cell lysates were incubated with 2.5 mg/mL p(I:C) for 4 h to stimulate 2-5A activation of RNase L, prior to RNA purification. (N = 2 per plasmid construct).
2) effect of SARS-CoV-2 3CLpro expression on transcriptome: HEK293 Flp-In T-REx cell lines with stably integrated SARS-CoV-2 3CL pro or 3CL pro (Cys145Ala) constructs were induced by the addition of 1 µg/mL doxycycline to the culture media (N =2 per condition). Cells were lysed 24 or 48 h post-induction and RNA was purified

last: Bell


title: Synovial Gene Expression Profiling Identifies Cardiovascular-Related Pathways Associated with Osteophyte Formation in Patients with Osteochondritis Dissecans of Humeral Capitellum After Osteochondral Autograft Transplantation

city: Kurume

first: Hiroki

last: Ohzono

state: Fukuoka

address: Asahimachi 67

department: Orthopedic surgery

country: Japan

institute: Kurume University

summary: This is the first genomic study of human OCD of the humeral capitellum demonstrating that the potential involvement of cardiovascular-related pathways, particularly ANGPTL-1, in postoperative osteophyte development after OAT surgery. These findings may contribute to elucidating the pathogenesis of OCD of humeral capitellum and to developing the future therapeutic interventions to prevent degenerative change of elbow in patients with OCD of humeral capitellum.

overall_design: Three samples from the normal group and three from the osteophyte group, collected from patients who underwent surgery for osteochondritis dissecans (OCD) of humeral capitellum, were subjected to DNA microarray analysis to compare gene expression profiles between the two groups.

first: Kozo

last: Furushima


title: Nuclei Isolation from Rat and Bovine White Adipose Tissue for Single-Nuclei RNA Sequencing

city: East Lansing

first: Leah

last: Terrian

state: MI

address: 775 Woodlot Dr.

country: USA

institute: Michigan State University

summary: Perivascular adipose tissue (PVAT) is a complex tissue that is increasingly recognized for its roles in vascular health and disease. The form and function of PVAT is different depending on species and anatomical location and understanding its cellular and molecular characteristics gives greater insights. We had previously successfully performed single nucleus RNA-sequencing (snRNAseq) on brown fat depots, the thoracic aortic PVAT (taPVAT) and subscapular brown adipose tissue (BAT), from Dahl SS rats.  However, application of the same nuclei isolation method to white adipose tissue (WAT) depots (perivascular and non-perivascular) from the same rat strain resulted in insufficient nuclei capture and low transcript numbers. These challenges were also encountered when processing WAT from cattle. While nuclei isolation methods have been developed and optimized for human and mouse WAT depots, they have not been evaluated across WAT depots from other species such as the cow and rat. Because these latter species are important models for cardiovascular and metabolic diseases, this study aimed to validate and optimize a nuclei isolation protocol for use with WAT from them. Protocols were evaluated based on (a) the quantity of nuclei isolated, (b) the quality of nuclei determined by microscopic visualization, and (c) the total number of detected transcripts and genes following snRNAseq. A modified protocol developed for human WAT, incorporating liquid nitrogen pulverization and Dounce homogenization of flash-frozen tissue was tested. This protocol, with key modifications for optimization, proved translatable to rat and cow WAT depots to improve nuclei yield (rat retroperitoneal fat: 3100 nuclei/mg tissue; rat mesenteric perivascular adipose tissue: 2200 nuclei/mg tissue; cow white fat 2050 nuclei/mg). Further analysis by snRNAseq, however, identified limitations. While cow WAT expressed nearly 1,720 median genes/cell, both rat white depots were significantly lower (mesPVAT: 189, RP fat: 294 median genes/cell), hindering downstream analyses in the rat tissue. These findings suggest that biological differences in adipose depots within and between species pose important challenges for the application of snRNAseq on rat WAT.

sample_organism:
Bos taurus
Rattus norvegicus

platform_organism:
Bos taurus
Rattus norvegicus

overall_design: Single-nucleus RNA-sequencing of adipose tissues from Dahl SS rat and Holstein dairy cow. Cow subcutaneuos white adipose tissue samples were taken from the right paralumbar fossa cranial to the tensor fascia latae muscle on the right flank. Rat adipose tissues were the thoracic aorta perivascular adipose tissue (PVAT), subscapular brown adipose tissue, mesenteric PVAT, and retroperitoneal adipose tissue. 5 samples were processed using Parse Biosciences WT Evercode v3 kit and 1 mesenteric PVAT sample was processed using 10x Genomics Chromium Next Gem 3' v3 kit. Sequencing was done by Novogene on an Illumina NovaSeq 6000.

first: Miguel

last: Chirivi

first: Janice

last: Thompson

first: Andres

last: Contreras

first: Stephanie

middle: W

last: Watts

first: Rance

last: Nault


title: Transcript landscape in the heart of inducible cardiomyocyte-specific Immt knockout mice at 10 weeks after tamoxifen injection

city: Cincinnati

first: Yasuhide

last: Kuwabara

state: Ohio

address: 240 Albert Sabin Way, Building S

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Immt gene encodes Mic60 protein which is a main component of the mitochondrial contact site and cristae organizing system (MICOS) protein complex. The MICOS complex plays pivotal roles for crisa juction formation and connection of inner mitochondrial membrane and outer mitocondrial membrane of mitochondria. Although it is well known that the cristae are crucial for energy production by OXPHOS, it is still precisely unknown how the Mic60 is important in the adult matured cardiomyocytes in vivo. To expand our knowledge about the Mic60 functions in the adult mouse heart, we utilized inducible cardiomyocyte-specific Immt gene knockout mice and conducted bulk RNA-seq with the hearts. This data highlights the early mitochondria stress response at transcript level in the hearts.

overall_design: To generate inducible cardiomyocytes-specific Immt gene knockout mice, we crossed Immt-loxP targeted mice with Myh6-MerCreMer transgenice mice and obtained Immtfl/fl-Myh6-MCM mice. Immt+/+-Myh6-Cre mice were used as a same age control. To knockout the Immt gene, we injected tamoxifen at 6 weeks of age tree times every other day. At 10 weeks after tamoxifen injection, we isolated total RNA from the hearts and carried out bulk RNA-seq.

first: Jeffery

last: D. Molkentin


title: Spatially-Resolved Multiomic Atlas of Leiomyosarcoma Identifies Two Clinically Relevant Epigenetically-Driven Cell States [scMultiomic]

city: Houston

first: Zhao

last: Zheng

state: TX

address: 1901 East Rd

department: Genomic Medicine

institute: md anderson cancer center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Leiomyosarcoma (LMS) is a malignant smooth muscle tumor characterized by substantial clinical and molecular heterogeneity. To investigate the cellular and regulatory landscape of LMS at single-cell resolution, we performed single-nucleus multiome sequencing to jointly profile gene expression (snRNA-seq) and chromatin accessibility (snATAC-seq) in 16 untreated primary leiomyosarcoma tumors arising from retroperitoneal, extremity, and uterine sites. After quality control, 94,439 nuclei were analyzed, revealing diverse tumor and microenvironmental cell populations including macrophages, T cells, and endothelial cells. Malignant cells segregated predominantly into two major transcriptional and epigenetic states: a dedifferentiated mesenchymal-like subtype (MES) and a differentiated smooth muscle cell–like subtype (SMC). Integration of transcriptomic and chromatin accessibility profiles identified distinct regulatory programs underlying these states, including enrichment of NFI transcription factor motifs in MES cells and AP-1 family motifs in SMC cells. These data provide a comprehensive multiomic resource for understanding tumor heterogeneity and regulatory mechanisms in leiomyosarcoma.

overall_design: Nuclei were isolated from fresh-frozen tumor tissues, and approximately 10,000 nuclei per sample were processed using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression platform according to the manufacturer’s protocol. Following nuclei transposition, GEM generation, barcoding, amplification, and separate ATAC and gene expression library construction, libraries were quality checked, quantified, and sequenced on an Illumina platform.

first: Denu

last: Ryan

first: Zheng

last: Zhao


title: Pan-Cancer Analysis Reveals Mutation-Driven TE Dysregulation as a Contributor to Immune Suppression [CUT&Tag]

city: hangzhou

first: HONGJIAN

last: QI

state: zhejiang

address: Dunyu road No.600

country: China

institute: westlake university

summary: Somatic mutations and transposable element (TE) dysregulation are hallmarks of cancer, yet how specific genetic alterations influence TE activity across tumor types remains unclear. Here, we mapped mutation–TE regulatory networks across 9,622 tumors representing 33 TCGA cancer types by integrating RNA-seq, whole-exome, and DNA methylation data. Comparative analysis of tumors with and without mutations identified 275 significant cancer–gene pairs associated with altered TE expression, many of which are transcription factors such as TP53, NSD1 and ARID1A. The changes in TE expression were also inversely correlated with DNA methylation changes in many cases. Unexpectedly, we observed that immune pathway activity is down-regulated when TE expression is induced, and up-regulated when TE is repressed. Functional validation in isogenic ARID1A- and CTNNB1-perturbed models recapitulated the changes in TE activity and immune responses observed in TCGA datasets. Together, these findings reveal mutation-driven TE activity reprogramming as a widespread feature and a potential source for immune modulation in human cancers.

overall_design: This study investigates the epigenomic and transcriptomic consequences of ARID1A loss in gastric cancer cells (NUGC4) and CTNNB1 overexpression in hepatocellular carcinoma cells (HepG2).For NUGC4 cells, we performed: (1) RNA-seq comparing wild-type (WT, n=4), ARID1A knockout (KO, n=2), and ARID1A CRISPRi knockdown (n=2 with vector controls, n=2); (2) ATAC-seq comparing WT (n=1) and ARID1A KO (n=2); (3) CUT&Tag for H3K27me3 comparing WT (n=1) and ARID1A KO (n=2); (4) WGBS comparing WT (n=2) and ARID1A KO (n=2).For HepG2 cells, we performed: (1) RNA-seq comparing vector control (n=2) and CTNNB1 overexpression (n=2); (2) WGBS comparing vector control (n=2) and CTNNB1 overexpression (n=2).All sequencing was performed on Illumina NovaSeq X Plus with paired-end reads.

first: Hongjian

last: Qi

first: Kai

last: Tian

first: Chicheng

last: Ma

first: Min

last: Huang

first: Yanxiao

last: Zhang


title: Pan-Cancer Analysis Reveals Mutation-Driven TE Dysregulation as a Contributor to Immune Suppression [ATAC-seq]


title: Pan-Cancer Analysis Reveals Mutation-Driven TE Dysregulation as a Contributor to Immune Suppression

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Oral Islatravir in Macaques Decreases Lymphocytes and Monocytes and is Associated with Immune Dysregulation

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Treatment and prevention of HIV with oral islatravir (ISL) in humans has been associated with decreases in total lymphocytes, CD4+ T-cells, and B-cells in a dose- dependent manner. We defined in macaques the effects of oral ISL on lymphocytes, monocytes, granulocytes, and gene expression in peripheral blood mononuclear cells (PBMCs). Female pigtailed macaques (n=5) received an HIV pre-exposure prophylaxis dose of oral ISL adjusted allometrically once a week for 12 weeks. Complete blood counts and B- and T-cells were monitored prior to, during, and after ISL treatment, and changes in counts were evaluated by using a repeated measures model. ISL treatment was associated with declines in lymphocytes (11.9%, p=0.0015) and monocytes (22.4%, p=0.0003) but not granulocytes (0.3%, p=0.9781). Total lymphocytes and monocytes returned to pre-treatment levels 6 weeks after treatment cessation (p=0.8244 and p=0.4620, respectively). Lymphocyte subpopulation analyses showed a significant decline in CD8+ (8.8%, p=0.0403) and CD20+ (73.4%; p<0.0001) cells but not CD4+ cells (0.1%; p=0.9989). Gene set enrichment analysis in PBMCs showed negative enrichment (padj<0.05) of gene pathways associated with immune regulation, cell proliferation, and inflammation. These results provide the first insights on the mechanisms of ISL-induced lymphopenia and highlight the value of the macaque model to study immune alterations at the preclinical stage.

overall_design: Five female Pig-tailed macaques (Macaca nemestrina) received oral ISL (30 mg/kg; WuXi AppTec, Shanghai, China) by gavage under anesthesia once a week for 12 consecutive weeks. Gene expression patterns were investigated in PBMCs collected immediately before ISL treatment (week 0), after 12 consecutive weeks of ISL treatment (week 12), and 6 weeks after treatment discontinuation (week 18).

first: Michele

middle: B

last: Dalya

first: Daniel

last: Kima

first: Seidu

last: Inusahb

first: Dawn

last: Littlea

first: Jiyoung

middle: S

first: Natalia

last: Makarovaa

first: Tiancheng

middle: E

last: Edwardsa

first: James

last: Mitchella

first: Walid

last: Heneinea

first: Yi

last: Panb

first: Charles

last: Dobarda

last: Garcia-Lerma

first: Derrik

last: Gratz


title: Transcriptome Analysis of Oral Submucous fibrosis and its Malignant Transformation

city: Bengaluru

first: Sukeerthi

last: Dasharathy

state: Karnataka

address: FMC building, Ramaiah University of Applied Sciences, New BEL Road

department: Biotechnology

country: India

institute: Ramaiah University of Applied Sciences

summary: Oral Submucous Fibrosis (OSMF) is a significant global oral health problem, particularly prevalent in India, with a high risk of progression to Oral Squamous Cell Carcinoma (OSCC). This study investigates the molecular mechanisms involved in the transformation of OSMF to OSCC using transcriptomic profiling. Methods: High-throughput RNA sequencing was performed on fresh de novo OSCC samples (n=8), OSMF transforming to OSCC, and normal oral mucosa (n=5 each) using Illumina-compatible NEXTflex Rapid Directional RNA-Sequencing. Results: Upregulated genes were associated with cytokine and immune responses (ABRA, TTTY14, EIF1AY), cellular proliferation and apoptosis (LINC00314, RPS4Y1, SERPINA5, TRIM63, FABP7), and energy metabolism, indicating metabolic adaptations during malignant progression. Pathway analysis showed increased expression of TNNT1, TNNI1, MYL4, and ACTN3, implicating muscle development and embryonic pathways in OSMF transformation. Conversely, genes related to epithelial differentiation and keratinization (FLG, FLG2, HRNR, TCHH, KRT73), immune regulation and tumor suppression (HLA-G, UNC5D), and metabolic signaling were downregulated, reflecting loss of tissue integrity and immune control. Conclusion: The observed gene dysregulation highlights impaired epithelial barrier function, altered immune responses, and enhanced metastatic potential, contributing to carcinogenesis and poor prognosis in OSMF-associated OSCC.

overall_design: RNA-seq profiling of Denovo Oral Squamous Cell Carcinoma (OSCC) and Oral Submucous Fibrosis (OSMF) to OSCC conditions to understand the molecular mechanisms behind the transition

first: Kavitha

last: Prasad

first: Sowmya

last: SV

first: Dominic

last: Augustine

first: Ananya

last: Anurag Anand

first: Prashanthi

last: Karyala

first: Roopa

last: Rao

first: Soma

last: Chaki


title: Weight loss at a cost: Semaglutide and PYY3-36 aggravate pre-existing metabolic osteoporosis in female rats

city: Wuerzburg

first: Simon

last: Kloock

address: Oberduerrbacherstr. 6

department: Endocrinology

country: Germany

institute: University Hospital Wuerzburg

summary: Incretin mimetics like semaglutide and peptide YY3-36 (PYY3-36) reduce appetite and body weight, however their individual and combined effects on bone health in the setting of metabolic disease and associated osteoporosis (MetOP) lack mechanistic insights. Here, a recently introduced MetOP rat model using Western diet and nitric oxide synthase inhibitor L-NAME is used to study effects of semaglutide, PYY3-36 and their combination on bone health. Semaglutide modestly imapired bone health by increased bone resorption, confirmed by microCT and histological analysis, RNA-Sequencing revealed a downregulation of cell cycle and osteoblast related genes. PYY3-36 treatment led to deteriorated bone markers and increased resorption, potentially limiting its clinical application, while angiogenesis and extracellular matrix-associated genes showed an upregulation in RNA-Seq based pathway analysis. Semaglutide and PYY3-36 in combination further aggravated bone loss in MetOP. These findings highlight the need to evaluate gut hormone–based weight loss strategies for long-term skeletal safety, especially in the vulnerable setting of pre-existing osteoporosis.

overall_design: RNA Sequencing profiling of rat femora treated with high fat diet and L-NAME, and additionally with semaglutide, PYY3-36 and a combination of both

first: Kloock

last: Simon

first: Dischinger

last: Ulrich


title: Pan-Cancer Analysis Reveals Mutation-Driven TE Dysregulation as a Contributor to Immune Suppression [WGBS]

first: HONGJIAN

last: QI

first: Hongjian

last: Qi

first: Kai

last: Tian

first: Chicheng

last: Ma

first: Min

last: Huang

first: Yanxiao

last: Zhang


title: Pan-Cancer Analysis Reveals Mutation-Driven TE Dysregulation as a Contributor to Immune Suppression [RNA-seq]


title: Prolactin receptor signaling mediates beta-cell epigenetic adaptations to promote OVOL2-binding

city: Baltimore

first: Nelmari

last: Ruiz Otero

email: nelmari634@gmail.com, nruizot1@jhu.edu

state: MD

address: 5501 Hopkins Bayview Circle Allergy & Immunology Center Bayview Campus Lab 2A10

institute: Johns Hopkins University

summary: Maternal pancreatic β-cells undergo functional and structural changes to adapt to increased metabolic demands during pregnancy. Lactogen signaling via the prolactin receptor (PRLR) contributes to these adaptations by increasing β-cell mass, insulin transcription and glucose-stimulated insulin secretion. Lactogen-responsive tissues such as the mammary glands and some hypothalamic nuclei display gestationally induced epigenetic changes, some of which persist long after birth. We have previously found that prolactin treatment in islets regulates the expression of epigenetic modifiers. However, whether lactogen signaling in β-cells mediates epigenetic changes to regulate chromatin accessibility has not been examined. Therefore, our objective was to determine whether PRLR signaling alters chromatin accessibility of β-cells to facilitate transcriptional regulation. We identified differentially accessible regions in wild type β-cells which had 718 overrepresented motifs following prolactin treatment of murine islets. Validating this approach, these included motifs bound by established PRLR signaling effectors such as the STAT family of transcription factors (TFs). Using RNA-sequencing we identified transcriptional changes in 41 TFs whose motifs were overrepresented in DARs. These TFs included several previously linked to PRLR signaling within β-cells, including Myc, Mafb and Esr1. Importantly, we also identified several TFs not previously associated with PRLR signaling, which included OVOL2 which is often associated with epigenetic regulation.  OVOL2 is a transcription factor involved in EMT inhibition and energy homeostasis with unknown roles in β-cell functions. Here, we establish that OVOL2 acts as a negative regulator of PRL-dependent effects on glucose stimulated insulin secretion and β-cell proliferation, establishing a novel regulatory pathway for PRLR signaling.

overall_design: RNA-sequencing profile of primary islet cells cultured in the presence or absence (DMSO-controls) of recombinant prolactin (500ng/ml) for 24 hours.

last: Ruiz-Otero

first: Jin-Yong

last: Chung

first: Ronadip

middle: R

last: Banerjee


title: A complex mutational signature generated by cytarabine resistance

city: New haven

first: Dengchao

last: cao

state: CT

address: 300 george st, room6122

institute: Yale university

summary: T cell acute lymphoblastic leukemia (T-ALL) patients generally respond well to chemotherapy, but T-ALL cells at relapse are typically resistant to chemotherapy. The specific mechanisms leading to chemoresistance are incompletely understood. Here we use Mcm2 hypomorph (Mcm2hypo) T-ALL cell lines, which are prone to copy number variant mutations, to identify acquired mutations that underlie chemoresistance. We successfully generated 11 chemotherapy-resistant T-ALL cell lines, identifying excellent candidate genes responsible for resistance due to acquired mutations, including CNV, SNV, and small indels.These candidates included amplification of Abcb1a/b associated with vincristine resistance, amplification of Dhfr associated with methotrexate resistance, loss of Nr3c1 associated with prednisone resistance and loss of Dck associated with cytarabine resistance.

overall_design: RNA seq profiling of pareatal and chemotreapy resistatnt Mcm2 hypomorph T-ALL cell lines, icluding five drugs:cytarabine (ARAC), methotrexate (MTX), vincristine (VR), etoposide (EP), and prednisone (PD).

last: Cao


title: Prolactin receptor signaling mediates beta-cell epigenetic adaptations to promote OVOL2-binding [scATAC-seq]

summary: "Maternal pancreatic β-cells undergo functional and structural changes to adapt to increased metabolic demands during pregnancy. Lactogen signaling via the prolactin receptor (PRLR) contributes to these adaptations by increasing β-cell mass, insulin transcription and glucose-stimulated insulin secretion. Lactogen-responsive tissues such as the mammary glands and some hypothalamic nuclei display gestationally induced epigenetic changes, some of which persist long after birth. We have previously found that prolactin treatment in islets regulates the expression of epigenetic modifiers. However, whether lactogen signaling in β-cells mediates epigenetic changes to regulate chromatin accessibility has not been examined. Therefore, our objective was to determine whether PRLR signaling alters chromatin accessibility of β-cells to facilitate transcriptional regulation. We identified differentially accessible regions in wild type β-cells which had 718 overrepresented motifs following prolactin treatment of murine islets. Validating this approach, these included motifs bound by established PRLR signaling effectors such as the STAT family of transcription factors (TFs). Using RNA-sequencing we identified transcriptional changes in 41 TFs whose motifs were overrepresented in DARs. These TFs included several previously linked to PRLR signaling within β-cells, including Myc, Mafb and Esr1. Importantly, we also identified several TFs not previously associated with PRLR signaling, which included OVOL2 which is often associated with epigenetic regulation.  OVOL2 is a transcription factor involved in EMT inhibition and energy homeostasis with unknown roles in β-cell functions. Here, we establish that OVOL2 acts as a negative regulator of PRL-dependent effects on glucose stimulated insulin secretion and β-cell proliferation, establishing a novel regulatory pathway for PRLR signaling.

overall_design: scATAC-sequencing of wild type or beta-cell specific PRLR deleted murine islet cells cultured in the presence or absence (DMSO-controls) of recombinant prolactin (500ng/ml) for 24 hours.


title: New Biologic to Treat Heart Failure Modulates Immune and Stromal Networks for Endogenous Repair

city: Tucson

first: Jordan

last: Fink

state: AZ

address: 1501 N Campbell Ave

department: Sarver Heart Center

institute: University of Arizona

summary: Chronic heart failure remains a global epidemic without a cure. We report a first-in-class biologic that induces myocardial repair through multiple coordinated pathways including immune cell activation, anti-inflammation, and stromal cell recruitment to promote extracellular matrix (ECM) remodeling. Proteomics reveals a signature enriched in ECM reorganization and immune-modulatory pathways. The biologic acts in a site-specific, biphasic repair program: (1) an initial immune activation phase and (2) resolution characterized by the emergence of TREM2+ reparative macrophages and recruitment of stromal cells. These processes re-establish a regenerative milieu reminiscent of the neonatal heart. By integrating immune, stromal, and cardiomyocyte crosstalk, the biologic establishes a durable pro-reparative microenvironment that restores myocardial structure and function. This immune-guided strategy is a new paradigm for treating chronic ischemic heart failure.

overall_design:
Nanostring Digital Spatial Profiling was done to explore the transcriptomic changes that occur with treatment compared to non-treated hearts.
MI_alone with no treatment; treated with biologic

first: Adrian

last: Grijalva

first: Steven

last: Goldman


title: Hepatic transcriptonal responses in mice infected with Toxocara cati eggs embryonated at different temperatures

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: The influence of temperature on infectivity and pathogencity of T. cati eggs was studied.  Eggs were embryonated at different temperatures, inoculated into mice, and the hepatic transcritpomic response assesed by RNA-Seq.

overall_design: T. cati eggs were embryonated at either 22 degrees C for five weeks (control) or 37 degrees for two weeks (High Temp). 2500 eggs were inoculated into mice, which were then euthanized on day 21-22 post-infection.  Uninfected mice were also included.


title: Nuclear basket subunits Nup211 and Rsm1 influence RNA 3'-processing and  transcription termination in fission yeast

city: New York

first: Ana

last: Sanchez

state: NY

address: 430 E 67th Street, RRL-865

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: RNA-seq analysis compares gene expression of rsm1∆ and nup211-1435* mutants to the wild-type fission yeast (Schizosaccharomyces pombe)

overall_design: Two test samples and 1 control sample were processed (each sample has 3 replicate experiments).

first: Lauren

last: Bednor

first: Aleksei

last: Innokentev

first: Angela

last: Sem

first: Beate

last: Schwer

first: Stewart

last: Shuman


title: Acute combination of nitrogen and light induces the simulta-neous accumulation of astaxanthin and lutein in continuous cultures of the microalga Chromochloris zofingiensis

city: Sevilla

first: Marcos

last: Ramos-González

address: Calle Américo Vespucio 49

country: Spain

institute: Universidad de Sevilla

summary: Carotenoids are essential pigments in photosynthesis and other physiological processes, present in various organisms. Microalgae are considered an important natural source for the commercial production of some of these compounds. The accumulation of the carotenoids astaxanthin and lutein in response to nitrogen and light availability has been optimized in continuous photoautotrophic cultures of Chromochloris zofingiensis. Astaxanthin cellular content increased significantly as the nitrate concentration in the feed medium decreased, while that of lutein remained largely unchanged. The cellular levels of lutein and astaxanthin were inversely correlated with the nitrogen content of the biomass. Thus, for 4% N in the dry biomass, accumulation of astaxanthin was highest and that of lutein lowest. The opposite was recorded for 9% N. Average irradiance positively affected lutein accumulation at both high and low nitrate, whereas that of astaxanthin did only increase under nitrogen-limiting conditions. An integrated analysis of transcriptomics and carotenoid profiling data provides evidence that the response to nitrogen is more significant than that to light availability, and that a synergy exists between both factors, with enhancement of their individual effects. Regulation appears to be orchestrated at several levels: the expression pattern of cyclases suggests a redirection of lycopene to β-carotene, which is converted into astaxanthin through overexpression of BKT1. In turn, slightly higher lutein values are achieved by altering the α-carotene/lutein ratio, due to upregulation of CYP97A1 and CYP97C, especially under high irradiance conditions. The differential responses of astaxanthin and lutein to nitrogen and light availability could enable the programmed generation of C. zofingiensis biomass in continuous culture with a specific astaxanthin to lutein ratio, through careful adjustment of the nitrate concentration in the feed medium, using light irradiance as a modulator.

overall_design: RNA-seq profiling of the microalga Chromochloris zofingiensis CCAP 211/14 grown at a fixed dilution rate of 0.5 d-1, under two nitrate concentration in the feed medium (1 and 10 mM) and two maximum irradiance values on the reactor surface: 1000 µE m−2 s−1 for high light condition (HL) and 300 µE m−2 s−1 for low light condition (LL). Samples for analysis were collected for three consecutive days at 4 h after the start of the light cycle and analysed by triplicate.

first: María

last: Morales-Pineda

first: Mercedes

last: García-González

first: Elena

last: García-Gómez

first: Francisco

middle: J

last: Romero-Campero


title: Fruit and vegetable supplemented-diet ameliorates dextran sodium sulfate (DSS) -induced colitis by modulating host transcriptome and gut metagenome response

city: Beltsville

first: Gloria

last: Solano-Aguilar

address: 10300 Baltimore Ave

institute: USDA-ARS

summary: Dietary intake of fruits and vegetables (FV) has been inversely associated with lower risk of ulcerative colitis. A pig model was used to evaluate the impact of feeding FV on the host response to dextran sulfate sodium (DSS)-induced colitis. Methods: Six-week-old pigs were fed a grower diet alone or supplemented with lyophilized FV equivalent to the half (half-FV) or full (full-FV) daily levels recommended for humans by the Dietary Guidelines for Americans (DGA). Pigs were fed a 1) grower diet alone (negative control), 2) grower diet and orally treated with 4% DSS for 10 days to induce colitis (positive control), 3) half-FV diet treated with 4% DSS or 4) full-FV diet treated with 4% DSS. Pigs were monitored for the development of clinical signs of colitis. Proximal colon (PC) contents and mucosa (PCM) were collected for gut metagenome, tissue transcriptome and histopathological analysis. Results: Pigs fed the full-FV diet did not exhibit diarrhea, showed less fecal occult blood (FOB), PCM crypt hyperplasia but with no differential expressed genes (DEG) or changes in PC microbiome diversity (p < 0.05). Pigs within the half-FV group exhibited increased group FOB and DEG associated with tissue remodeling, crypt and goblet cell hyperplasia in the PCM and no changes in PC microbiome diversity and two pigs exhibiting diarrhea (p < 0.05).  Pigs within the DSS positive control group exhibited a reduced DEG involved with intestinal immune response and PC microbiome diversity with altered metagenome, increased group PCM erosion and FOB with persistent diarrhea in one pig (p < 0.05) Conclusions: Overall, our results showed that pigs fed a three-week full-FV supplemented diet, were resistant to DSS-induced colitis with a differential dose-dependent protective effect on host intestinal tissue and gut metagenome when exposed to an inflammatory challenge.

overall_design: RNA-Seq profiling was performed on proximal colon mucosa and comparisons were made between treatment groups DSS, Full FV DSS, Half FV DSS, and the control group. Tissue collection was performed after 3 weeks of  diet consumption followed by 10 days of oral DSS challenge.

first: Sukla

last: Lakshman

first: Celine

last: Chen

first: Ethiopia

last: Beshah

first: Aleksey

last: Molokin

first: Bryan

last: Vinyard

first: Harry

last: Dawson

first: Monica

last: Santin-Duran

first: Gonzalo

last: Bruna

first: Allen

last: Smith

first: Joseph

last: Urban


title: AXL is a novel ERK5/KLF4 target in MEKi-treated melanoma

first: Rupesh

last: Paudel

state: Bavaria

address: Josef-Schneider Straße 2

department: Department of Dermatology, Venerology und Allergology

summary: RAS/RAF/MEK/ERK1/2 MAPK pathway-based treatments, typically combination therapies with inhibitors for oncogenic BRAF V600 (BRAFi) and MEK1/2 (MEKi), are important treatment alternatives to immunotherapy in advanced BRAF-mutated melanoma. However, their benefit is limited by frequent therapy resistance, i.e. persistence and tumor progression/metastasis under sustained treatment. Furthermore, approximately 50% of the patients, including the NRAS-mutated subset, lack targetable BRAF oncogenes and profit poorly from MEKi. Recent preclinical studies suggest that co-inhibition of the MEK5/ERK5 MAPK pathway, which in different MAPK-activated tumors is compensatorily activated by MEKi, represents a promising strategy to overcome therapy resistance and trigger apoptosis and/or sustained cell cycle arrest. In NRAS-mutant melanoma compensatory ERK5 activation is accompanied by the induction of the two Krüppel-like factors KLF2 and KLF4 Their functional relevance in MEKi resistance, however,is unclear. Using siRNA and CRISPR/Cas9, we examined their contribution to MEKi resistance through functional assays and RNA sequencing. Surprisingly, KLF2 and KLF4 were dispensable for the proliferative and anti-apoptotic effects of compensatory ERK5 activation in MEKi-exposed melanoma. Instead, we identified AXL, a key receptor tyrosine kinase associated with metastasis and phenotypic switching, as critical ERK5/KLF4 target induced during MEKi resistance and demonstrate that KLF4 loss or AXL depletion results in reduced melanoma cell migration and invasion. Our study describes a novel ERK5/KLF4/AXL signaling axis that drives MEKi resistance and metastatic potential in NRAS-mutant melanoma. Targeting this pathway may enhance the efficacy of MAPK-directed therapies and potentially improve responses to immune therapy, where AXL expression similarly promotes tumor progression.

overall_design:
NRAS-mutant melanoma cell line FM79 were seeded in triplicate and transfected with either scrambled siRNA or siRNA against MEK5 or KLF2/KLF4. The following day, siRNA-transfected cells were either mock-treated or treated with 5 nM Trametinib for 48 hours prior to lysis and RNA extraction. Total RNA was used to perform RNA-seq experiment. The siScr+Trametinib samples (GSM9055470, GSM9055471 and GSM9055472) were part of previously published data series (GSE300191) and were used for reanalysis/comparision with siKLF2/KLF4 group.

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Simon

last: Goller

first: Stefanie

last: Schwarz

first: Katharina

last: Meder

first: Matthias

last: Goebeler

first: Marc

last: Schmidt


title: Electrically Preconditioned Neural Tissues Direct Circuit Reconstruction for Spinal Cord Repair

city: ChangChun

first: Xiyao

last: Yu

address: Xinmin Street

institute: Jilin University

summary: Spinal cord injury (SCI) creates a prohibitive microenvironment that limits the efficacy of neural stem cell (NSC) therapies. We developed electrically preconditioned engineered neural tissues (ENT) to address these limitations through: (1) pre-establishment of functional neural networks in vitro, and (2) enhanced host integration capacity. EGFP-expressing NSCs were differentiated in 3D Matrigel under 150 mV/mm physiological electric fields (EFs) and transplanted into T10 hemisection SCI mice. Outcomes were assessed through: Basso Mouse Scale (BMS) scoring, multiplex immunofluorescence (Nestin/MAP2/GFAP/MBP/Synaptophysin/ChAT), cortical somatosensory/motor evoked potentials (CSEP/CMEP), RNA sequencing and pathway analysis. At 28 days post transplantation, ENT transplanted animals showed significantly higher BMS scores and enhanced CSEP/CMEP amplitudes compared to the NSC suspension group. We conducted comprehensive evaluations of the histological structure and function of EF-preconditioned ENT and the mice that received ENT transplantation: (1) in vitro maturation of ENT: high neuronal differentiation, dense synaptic networks and myelinated axon; (2) in vivo integration: niche-directed migration (graft-derived cells showed central canal (Nestin+ cells) and grey matter (ChAT+ cells) homing), achieved functional synaptic integration and correlated with motor recovery. Mechanistic analysis revealed EF activation of pro-neuronal pathways and gliogenesis suppression. These results demonstrate that EF-preconditioned ENT contributes to structural neural network reconstruction, niche-directed homing, functional synaptic integration and significant motor recovery.

overall_design: RNA-seq profiling of electrically preconditioned engineered neural tissues (EF-preconditioned ENT) and control NSC suspensions, alongside functional and histological assessment of T10 hemisection spinal cord injury mice post transplantation; in vitro characterization of ENT maturation under 150 mV/mm physiological electric fields

first: Xiaoting

last: Meng


title: Ginkgolic Acid Targets HSPA8 to Trigger Ferroptosis in Hepatocellular Carcinoma via Chaperone-Mediated Autophagy-Dependent GPX4 Degradation

city: Chengdu City

first: Huizhen

last: Zou

address: No. 270, Tianhui Road, Rongdu Avenue, Jinniu District

institute: The General Hospital of Western Theater Command PLA

summary: Context: Ginkgolic acid (GAC), one of the major active constituents of Ginkgo biloba L. (Ginkgoaceae) extract, has been reported as a potential anticancer drugs. Objective: To investigate the effect of GAC on the viability of Human hepatocellular carcinoma (HCC) cells and its underlying mechanisms. Materials and methods: Human HCC cell lines and an orthotopic HCC mouse model were employed. RNA sequencing, drug affinity responsive target stability (DARTS) with LC-MS/MS, protein–protein interaction analysis, molecular docking, and cellular thermal shift assay (CETSA) were used to identify and validate GAC targets. Ferroptosis was evaluated by BODIPY probes, Annexin-V/PI staining, Western blotting, malondialdehyde (MDA), GSH/GSSG assays, and transmission electron microscopy (TEM). Cell viability was assessed by CCK-8 and colony formation assays. HSPA8 knockdown, mutant, and KFERQ-reporter cells were generated to investigate the role of HSPA8 and chaperone-mediated autophagy (CMA). Results: GAC effectively inhibits the viability of HCC by triggering ferroptosis. HSPA8 was identified as the directly target of GAC. The binding of GAC with HSPA8 enhancing its interaction with glutathione peroxidase 4 (GPX4), which leads to the degradation of GPX4 via CMA. This process depleted glutathione (GSH) and caused lipid peroxidation, finally inducing ferroptosis in HCC cells. Furthermore, GAC suppressed tumor growth in an orthotopic HCC model, increased lipid peroxidation and GPX4 degradation in tumor tissues. Discussion and conclusions: Our results revealed a novel mechanism by which GAC induces ferroptosis in HCC cells through direct targeting HSPA8 and promoting CMA-dependent GPX4 degradation. These findings demonstrate the potential of GAC as therapeutic approaches for HCC.

overall_design: RNA-seq profiling of HCCLM3 cell line treated with 10μM ginkglic acid or corresponding vehicle

first: Ruohong

last: Liu

first: Yufan

last: Zhang

first: Min

first: Zhiyuan

last: Yang

first: Kexi

last: Liao

first: Guoping

last: Wang

first: Beiyu

first: Lijun

last: Tang

first: Xia

last: Kang

first: Shuguo

last: Zheng


title: Promoter hypomethylation of cadherin-7: a novel epigenetic marker associated with cerebral small vessel disease

city: Cheonan

first: Keunsoo

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

summary: Introduction: Cerebral small vessel disease (SVD), manifesting as white matter hyperintensities (WMH), lacunar infarctions, and cerebral microbleeds on MRI, has been linked to epigenetic alterations. Methods: Genome-wide promoter methylation was profiled using the Infinium MethylationEPIC v2.0 array in peripheral inflammatory cells from 16 patients without SVD and 16 patients with all three imaging features. Results: EPIC profiling identified 17 promoter regions with significant differences between groups, and CDH7 hypomethylation emerged as an independent predictor of SVD imaging features. Conclusion: CDH7 hypomethylation was identified and validated as an epigenetic marker predictive of MRI-defined SVD imaging features.

overall_design: Peripheral blood inflammatory cells (buffy coat) from ischemic stroke patients were profiled on the Infinium MethylationEPIC v2.0 array. The EPICv2 cohort included 16 patients without SVD imaging features and 16 patients with all three SVD features (WMH, lacunes, microbleeds). Group comparisons were used to identify promoter methylation differences; selected markers were validated in a larger ischemic stroke cohort.

first: Jeeyeon

last: Kim

first: Jihye

last: Park

first: Young Ho

last: Lee

first: Byoung-Soo

last: Shin

first: Dae-Hyun

first: Dong-Ick

first: Seong Hwan

last: Ahn

first: Jae Guk

first: Hyun Goo

first: Hyeseon

last: Jeong

first: Kyu Sun

last: Yum

first: Hee-Yun

last: Chae

first: Do-Hyung

first: Jei


title: African Swine Fever Virus R238L and R298L Disrupt Lung Cell's Collagen Formation and Cell Adhesion Pathway by Tar-geting Transcription Factors Containing zf-C2H2 Domain

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

institute: Yangtze University

summary: Collagen formation pathways influence the primary structure of the extracellular ma-trix, while cell adhesion participates in the regulation of cell-cell interaction process. The collagen synthesis and degradation or cell adhesion procedure can be disrupted by viral infections, thereby playing a crucial role in virus-host interactions. The regulatory mechanisms of these two pathways during African Swine Fever Virus (ASFV) infection remain unclear. This study identified key host genes involved in the transcriptional regulation of lung tissue from ASFV-restored individuals through weighted Kendall correlation analysis of transcription factor binding sites (TFBSs) to differentially ex-pressed genes (DEGs). Among these, SP2 and KLF6 emerged as important candidate transcription factors (TFs). AFSV-host interaction prediction based on the Do-main—Domain method indicated that the R238L and R298L proteins of ASFV can target host's TFs, SP2 and KLF6. Förster resonance energy transfer assay demonstrated that ASFV’s R238L and R298L proteins can competitively bind to SP2 and KLF6’s zf-C2H2 domains. Real-time PCR demonstrated that R238L and R298L protein over-expression downregulated the SP2 and KLF6’s target genes in both HeLa and 3D4/21 cell models. During ASFV infection, SP2 regulates the collagen formation signaling pathway genes, while KLF6 modulates the expression of cell adhesion genes. Collagen matrix formation and cell adhesion profoundly influence viral infectivity, transmis-sion, and immune evasion, while also significantly impacting host immune recognition and response. The ASFV's R238L and R298L proteins, along with their target TFs SP2 and KLF6, provided clues in elucidating the pathogenesis mechanisms of ASFV infec-tion and identifying its therapeutic targets.

overall_design: The samples for RNA-seq experiment were collected from three groups of animals with different antibody levels, the negative, low, and high.

first: Min

last: Yao


title: Identification of conserved mecciRNAs

city: Hefei,

first: Xu

last: Liu

state: Anhui Province

address: School of Basic Medical Sciences University of Science and Technology of China 443 Huangshan Road

summary: To identify conserved mecciRNAs in mammals, we isolated mitochondrial RNA from PLC and 3T3 cells and performed RNA-seq, which was subsequently used for mecciRNA identification.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Mitochondria were isolated from PLC and 3T3 cells, and mitochondrial RNA was extracted and subjected to RNA-seq to identify mecciRNAs. Bioinformatic analyses were performed to identify a conserved pair of mecciRNAs between human and mouse, followed by functional characterization.


title: 8-week-old mouse mandible scRNA-seq reveals bone marrow microenvironment

city: Chengdu

first: Yi

last: Fan

state: Sichuan

address: No.14, 3Rd Section of Ren Min Nan Rd.

institute: West China Hospital of Stomatology, Sichuan University

summary: We explored the cellular composition of the bone marrow stroma by scRNA-seq profiling from mice mandible of 8-week-old. After viability assessment, 3,568 high-quality cells were captured using the 10x Genomics Chromium Single Cell platform, with rigorous quality control thresholds: >500 UMIs/cell, < 25% mitochondrial reads.

overall_design: We filtered the non-hematopoietic cell containing Cd45-/Ter119- population via magnetic-activated cell sorting (MACS).  The transcriptomes of individual cells were analyzed, and dimensionality reduction was performed via t-distributed stochastic neighbor embedding (t-SNE) implemented in Seurat v4.1.0. Unsupervised clustering identified 13 transcriptionally distinct populations.


title: Single-cell RNA sequencing reveals M2-like macrophage signatures associated with mesenchymal stem cell treatment in a murine sepsis model

city: Chiba

first: Takahisa

last: HISHIYA

state: Chiba

address: 1-8-1,inohana, chuo-ku

institute: Chiba university

summary: Mesenchymal stem cells (MSCs) have shown therapeutic potential in preclinical sepsis models, but the mechanisms remain unclear. Using a murine cecal ligation and puncture model, we performed single-cell RNA sequencing of CD45+ immune cells 6 hours after MSC administration. MSC treatment improved survival and induced transcriptional reprogramming of macrophages toward an M2-like phenotype, accompanied by reduced inflammatory signatures. These findings provide mechanistic insight into MSC-mediated immune modulation in sepsis.

overall_design: In vivo murine sepsis model induced by cecal ligation and puncture (CLP). Human adipose-derived MSCs were administered intravenously. Peripheral blood CD45+ immune cells were collected 6 hours post-CLP and analyzed using single-cell RNA sequencing to evaluate immune cell composition and transcriptional changes.

first: Takehiko

last: Oami

last: Hishiya

first: Seiji

last: Miyauchi

first: Chiaki

last: Iwamura

first: Kiyoshi

last: Hirahara

first: Taka-aki

last: Nakada


title: Anti-SLC7A11 monoclonal antibody Inhibits Tumor Progression through a Janus-faced Effect on CD4+ and CD8+ T Cells in Colorectal Cancer [RNA-seq]

city: Beijing

first: Jichang

last: Li

address: No. 8, Xishiku Street, Xicheng District

institute: Peking University First Hospital

summary: SLC7A11 is aberrantly overexpressed in numerous solid tumors, including colorectal cancer (CRC), where it serves as a key regulator of cystine import and ferroptosis. However, its therapeutic potential and feasible targeting strategies remain less well understood. Our findings reveal that elevated SLC7A11 expression is critical for the activation of regulatory T cells and is associated with advanced tumor grade, lymphatic metastasis, and poor prognosis in CRC patients. A monoclonal antibody  that blocks the transporter function of SLC7A11 induces apoptosis across multiple cancer cell types and demonstrates significant therapeutic efficacy in preclinical mouse models of colon cancer. Additionally, inhibition of SLC7A11 reprograms the tumor immune microenvironment, transforming it from a 'cold' to a more immunogenic state by suppressing regulatory T cell activation. These results highlight the dual role of SLC7A11 in modulating CD4+ and CD8+ T cell responses, positioning SLC7A11 as a crucial orchestrator of tumor immune evasion and a promising therapeutic target.

overall_design: To investigate the effects of the SLC7A11 monoclonal antibody  on different T cell populations, we isolated CD4+T cells and CD8+ T cells from human peripheral blood using magnetic beads. Subsequently, we treated these cells withSLC7A11 monoclonal antibody  (100 µg/ml) for 24h and assessed the changes in the activity and proliferation of CD4+ T cells and CD8+ T cells.

first: Yuhang

last: Yin

first: Haopeng

last: Hong

first: Xiaoxue

last: Pan

first: Chang

middle: A

last: Meng

first: Jing

last: Zhu

first: Xin

last: Wang

first: Yucun

first: Pengyuan

first: Shanwen

last: Chen


title: Unveiling Ribosomal Dysfunction and Impaired Signaling Pathways in the Cortical Region of FAD5x Mice

city: Baton Rouge

first: Manas

middle: Ranjan

last: Gartia

state: LA

address: 3261 Patrick F Taylor Hall

department: Mechanical and Industrial Engineering

institute: Louisiana State University

summary: Alzheimer's Disease represents the most significant form of neurodegenerative disease worldwide with progressive dementia and synaptic dysfunction. Though the accumulation of β-amyloid and hyperphosphorylated tau protein is the most observed pathological feature of AD, the emergence of ribosomal dysfunction and oxidative stress has recently gained interest. In this study, we conducted a comprehensive multi-omics investigation, which included transcriptomic, proteomic, and lipidomic analyses, on cortical region from FAD5x mice, a transgenic model of AD. Gene and protein expression analysis demonstrated ribosomal pathways were largely affected in the cortex. Histological and immunohistochemistry imaging showed increased amyloid-β and tau pathology leading to extensive cortical neurodegeneration. RNAseq analysis revealed increased oxidative RNA damage, indicating a potential mechanism of ribosomal stress. Elevated expression of RPL11, RPL6, and other large ribosomal subunit proteins was observed, consistent with impaired protein synthesis. This dysregulation may contribute to neurodegenerative processes in AD. Among the large subunit ribosomal proteins, RPL29 were downregulated at the gene expression level in AD, although its protein expression revealed a statistically insignificant rise. Comparison between the transcriptome and proteome demonstrated evidence of impaired translation, suggesting failed translational control. Lipidomic analyses revealed alterations in the levels of phospholipids, sphingolipids and lipid mediators in AD that is closely linked to the alterations in the neuroinflammatory pathways at the transcriptomic and proteomics levels. Multi-omics integration demonstrates that ribosomal dysregulation, oxidative stress, and protein homeostasis are affected, leading to neuronal damage in AD. According to this study, ribosomal malfunction plays a significant role in the pathophysiology of AD and serve as a potential target for therapeutic interventions.

overall_design: RNA-seq profiling of wildtype B6 mice (control) and FAD5x mice( Alzheimer's model )

first: Kirti

last: Agrawal

first: Sujoy

last: Ghosh


title: How interdiction of inositol pyrophosphate catabolism perturbs the fission yeast response to phosphate starvation

first: Ana

last: Sanchez

summary: RNA-seq analysis compares gene expression in the fission yeast Schizosaccharomyces pombe wild-type and HASX mutant at various times after phosphate starvation (1, 2, and 4 h) with that of wild-type cells grown in phosphate-replete conditions (0 h, prior to phosphate starvation).

overall_design: 6 test samples and 1 control sample were processed (each sample has 3 replicate experiments).

first: Jill

last: Babor

first: Isabel

last: Prucker

first: Henning

last: Jessen

first: Beate

last: Schwer

first: Stewart

last: Shuman


title: Anti-SLC7A11 monoclonal antibody Inhibits Tumor Progression through a Janus-faced Effect on CD4+ and CD8+ T Cells in Colorectal Cancer [scRNA-seq]

first: Jichang

last: Li

overall_design: CT26 colorectal cancer cells were injected at the cecal junction of mice to establish a mouse model of orthotopic colon cancer. When tumors reached 50 to 100 mm³, the mice were randomly assigned to a control group or treatment group. Mice were treated every two days with anti-IgG (10 mg/kg body weight) or SLC7A11-Ab (10 mg/kg body weight). Tumor length and width were measured using digital calipers, and subcutaneous tumor growth was assessed every three days.

first: Yuhang

first: Haopeng

last: Liu


title: LncRNAs coordinate doxycycline-induced gene expression response in human iPSCs (RNA-seq)

city: Boulder

first: Mingfeng

state: CO

address: 709 Mohawk Dr

institute: University of Colorado

summary: Long non-coding RNAs are known to regulate gene expression. However, less is understood about the temporal dynamics of lncRNA regulation, particularly how they influence early, middle, and late gene expression. To investigate this, we generated 17 genetically defined, Doxycycline-inducible lncRNA transgene hiPSC lines and performed high-density time-course RNA-seq and ATAC-seq. We observed that most lncRNA transgenes showed expected induction and subsequent changes in gene expression. However, the putative target genes of the different lncRNAs had substantial overlap, and control cell lines showed a similar set of induced genes, leading us to conclude that the substantial effect of doxycycline prevented identification of lncRNA-specific effects. Although doxycycline-induced gene expression changes have been reported previously, the large size of the current study allowed us to identify a highly reproducible doxycycline response gene signature (DRGS). We further observe that the DRGS occurs in most human cell lines tested with Dox exposure. Notably, the DRGS includes 18 endogenous lncRNAs that exhibit highly reproducible temporal regulation by Dox itself. Our results suggest these lncRNAs act synergistically as "co-response amplifiers" associated with the stress response; some are linked to different cell fates, such as epithelial-mesenchymal transition or nervous system development.

overall_design: The genomic integration strategy utilized the H11 safe harbor locus on chromosome 22. The Tet-On inducible expression cassette containing the target lncRNA was integrated through Cre-LoxP recombination (Lox2272/Lox511), followed by puromycin selection. Using this platform, we generated 17 lncRNA-expressing cell lines and one control cell line expressing mRNA for Green Fluorescent Protein (GFP). Next, we performed RNA-seq (0, 2, 4, 8, 16, 24, 48, and 96 hours, 3 replicates) and ATAC-seq (every 30 minutes from 0 to 2.5 hours, 3 replicates) after doxycycline induction.

first: Isabela

last: Pereira

first: Sajad

last: Sofi


title: Integrative MeRIP-seq and RNA-seq Analysis Reveals m⁶A-Mediated Epigenetic Regulation of Host-Virus Interactions during HSV-2 Infection

city: kun ming

first: Li ji xiong

institute: Institute of Medical Biology, Chinese Academy of Medicine

summary: Herpes simplex virus type 2 (HSV-2) is a highly prevalent pathogen responsible for genital herpes and is characterized by neurotropism and the ability to establish lifelong latent infection. N6-methyladenosine (m⁶A) is a widespread epitranscriptomic modification that plays a critical role in regulating RNA metabolism and gene expression. Although m⁶A modification has been shown to play a role in the life cycles of various viruses, its involvement in HSV-2 infection has not yet been investigated. In this study, we employed methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) to profile m⁶A modifications and transcriptomic changes in human foreskin fibroblasts (HFF-1) infected with HSV-2. We identified 9,477 common m⁶A peaks and 15,842 differentially methylated peaks, with a predominant localization within coding sequences (CDS). Functional enrichment analysis revealed that differentially m⁶A-modified genes are involved in key biological processes, including gene expression, neural signaling, and immune responses. Pathway analysis highlighted significant enrichment in the NOD-like receptor signaling pathway, Rap1 signaling, endocytosis, and adherens junction pathways. RNA-seq analysis identified 6,172 differentially expressed genes, of which 3,181 were upregulated and 2,991 downregulated. Integrative analysis of the two datasets revealed that genes exhibiting both altered m⁶A methylation and differential expression were significantly enriched in pathways including TNF signaling and the NOD-like receptor pathway. This study provides the first comprehensive landscape of m⁶A epitranscriptomic modifications and their association with transcriptomic reprogramming during HSV-2 infection, offering new insights into the epigenetic mechanisms of virus–host interactions

overall_design: High-throughput sequencing of HFF-1 cells and uninfected cell samples infected with HSV-2 for 24 hours was carried out by MeRIP-seq and RNA-seq sequencing, and the changes of m6A modification and gene expression differences between infected and uninfected groups were further analyzed through sequencing results, so as to explore the interaction between m6A modification between viruses and hosts in HSV-2 infection

first: Jixiong

first: Jiandon

last: Shi

first: Yunzhang

last: Hu


title: Heterogeneity in Inflammatory Responses to Endotoxin at the Feto-Maternal Interface

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

summary: The feto-maternal interface (FMi), comprising fetal chorionic trophoblast cells (CTCs) and maternal decidual stromal cells (DECs), plays a critical role in providing immune tolerance during pregnancy. Intrauterine inflammation is a major trigger of adverse outcomes such as preterm birth, yet the cell-specific inflammatory responses at the FMi leading to immune intolerance show heterogeneity; however, the inflammatory characteristics remain poorly defined. To investigate the differential inflammatory responses of fetal and maternal cell populations at the FMi upon exposure to endotoxin (lipopolysaccharide, LPS), and to delineate molecular pathways underlying the heterogeneity in the inflammatory signature. Primary CTCs and DECs were isolated from human term fetal membrane tissues. Cells were treated with LPS (100 ng/mL) for 48 hours. Transcriptomic profiling was performed to assess differentially expressed genes and pathway enrichment. Inflammatory cytokines were quantified using multiplex immunoassays. Protein-level responses were validated using western blotting. Regulatory network analysis identified upstream drivers of cell-specific responses. LPS induced a robust and uniform inflammatory response in DECs, marked by high expression of pro-inflammatory chemokines, and prostaglandin biosynthesis enzymes associated with adverse pregnancy outcomes. In contrast, CTCs showed an attenuated response, characterized by selective induction of stress-associated genes with minimal activation of classical inflammatory pathways. Transcriptomic network analysis revealed distinct cell-type-specific regulatory hubs, including STAT1 and IRF7 in DECs and RELA and MYD88 in CTCs. Notably, DECs also activated anti-inflammatory signaling and pyroptosis-related pathways, which were largely absent in CTCs, indicating compartmentalized immune regulation at the feto-maternal interface. Our findings reveal a fundamental heterogeneity in inflammatory responses at the FMi, with maternal cells exhibiting greater sensitivity to endotoxin-induced activation compared to fetal chorion trophoblast cells. These differential reactivity responses may be an evolved mechanism to shield the fetus from excessive inflammation or to impede the inflammatory onslaught from reaching the fetus. Understanding cell-specific responses provides a foundation for understanding tolerance and mediators of intolerance at the FMi and identifying potential targets for therapeutic strategies in inflammation-associated pregnancy complications.

overall_design: DEC: LPS vs PBS Decidual cells (DEC) were cultured under standard conditions and exposed to lipopolysaccharide (LPS) to model an inflammatory environment, with PBS-treated cells serving as controls. Cell lysates were collected and subjected to quantitative transcriptomic profiling to identify inflammation-induced alterations in protein expression and signaling pathways.  CTC: LPS vs PBS Chorion trophoblast cells (CTC) were treated with LPS to induce innate immune activation, while parallel PBS-treated cultures served as baseline controls. Proteomic analysis was then performed to characterize LPS-driven shifts in cellular pathways and stress-response networks in trophoblasts.

first: Vineet

last: Mahajan

first: Madhuri

last: Tatiparthy

first: Ananth

last: Kammala


title: Monocyte Subset Predicts Clinical Outcomes in Fibrotic Hypersensitivity Pneumonitis

city: Denver

first: Evans

last: Fernandez

address: 1400 Jackson St.

institute: National Jewish

summary: This study aimed to identify circulating immune cell populations associated with disease severity and progression in fibrotic hypersensitivity pneumonitis (fHP). Using single-cell RNA sequencing of peripheral blood mononuclear cells from 33 fHP patients (NCT02958917) and 36 sex-matched healthy controls (GSE196735, pools 1-3), we identified significant shifts in immune cell composition. Compared to controls, fHP patients exhibited a marked increase in classical monocytes (CD14⁺), non-classical monocytes (CD16⁺), and myeloid-derived dendritic cells. Classical monocytes, in particular, were strongly correlated with baseline lung fibrosis severity—quantified by data-driven texture analysis of high-resolution computed tomography—and with reduced progression-free survival. Pathway analysis revealed that monocytes from patients with severe disease were enriched for inflammatory and metabolic processes, whereas those from patients with poor outcomes showed upregulation of interferon and NF-κB signaling. These findings highlight peripheral monocytes as promising prognostic biomarkers in fHP and suggest their role in driving fibrotic progression through dysregulated immune responses.

overall_design:
Human PBMC mRNA profiles at single-cell resolution

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

first: Brian

last: Vestal

first: Sonia

last: Leach

first: Beth

last: Canono


title: Transcriptional and proteome profiling of human bronchial epithelial cell BEAS-2B exposed to e-cigarette aerosol condensate

city: Belgrade

first: Mila

last: Ljujic

address: Vojvode Stepe 444a

department: Human Molecular Genetics and Genomics

country: Serbia

institute: IMGGE

summary: We performed RNA-sequencing to evaluate the effect of acute exposure to e-cigarette aerosol condensate on lung bronchial epithelial cells by comparing the effects of carrier liquid consisting solely of propylene glycol and vegetable glycerine with e-cigarette containing nicotine and flavor.  Overall design BEAS-2B cells were exposed to e-cigarette aerosol condensate generated from carrier liquid (propylene glycol and vegetable glycerine) and from e-cigarette containing 18mg/ml nicotine and Virginia tobacco flavor for 24h. Untreated cells were used as control.

overall_design: RNA-seq profiling of BEAS-2B cells untreated or exposed for 24h to 2% electronic cigarette vapour condensate or propylene glycol/vegetable glycerine solution as a  control treatment

first: Sara

last: Trifunovic

first: Jelena

last: Kusic-Tisma

first: Katarina

last: Smiljanic

first: Aleksandra

last: Divac Rankov

last: Dinic


title: FLARE: a Long-Read Nanopore Fragmentomics Pipeline Integrating Copy Number, Methylation, and End-Motif Analysis for Liquid Biopsy

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Cell-free DNA (cfDNA) fragmentation patterns encode biologically and clinically relevant information beyond fragment length, reflecting nuclease activity, chromatin organization, and tissue of origin. Fragmentomics has therefore emerged as a promising strategy to enhance circulating tumor DNA (ctDNA) detection, particularly in cancers with low tumor fractions. However, most existing approaches are optimized for short-read sequencing, limiting their applicability to third-generation platforms. Here, we present FLARE (Fragmentation and Long-read Analysis of Regulatory Epigenetics), an integrated and scalable fragmentomics pipeline specifically optimized for Oxford Nanopore long-read sequencing. FLARE preserves native cfDNA fragment ends and enables the simultaneous analysis of copy number alterations, tumor fraction estimation, methylation-derived signals, fragment length distributions, and 5′ end-motif profiles.

overall_design: Plasma cfDNA was collected longitudinally from six patients with recurrent or metastatic head and neck squamous cell carcinoma at baseline (C1D1) and during immunotherapy (C5D1). cfDNA libraries were prepared without PCR amplification and sequenced using Oxford Nanopore Technologies to preserve native fragment structure and methylation signals. Sequencing data were processed through the FLARE pipeline, integrating read alignment, fragment size stratification, genome-wide copy number profiling, and tumor fraction estimation using both CNV-based (ichorCNA) and methylation-based models. Fragmentomic features were further characterized through 5′ end-motif analysis and unsupervised pattern discovery using non-negative matrix factorization. Longitudinal comparisons were performed to evaluate changes in tumor fraction, fragment size distribution, and fragmentation signatures over time.


title: Glioblastoma cells imitate neuronal excitability in humans

city: Copenhagen

first: Joachim

last: Weischenfeldt

address: Ole Maaløes Vej 5

department: BRIC

institute: University of Copenhagen

summary: Background: Glioblastomas are renowned for their pronounced intratumoral heterogeneity, characterized by a diverse array of plastic cell types. However, the physiological and transcriptomic features of the cells residing in the invasive leading edge (LE), including both neurons and glioblastoma cells (GBCs), remain unclear, challenging our comprehension of the glioblastoma pathophysiology. Methods: To elucidate molecular and morphophysiological features of LE cells, we established an experimental workflow enabling the investigation of GBCs and neurons within cancer-infiltrated organotypic tissue specimens from the same patients. With this approach, we characterized the electrophysiological properties of cells in the neocortical tumor LE (LE cells). We further performed single-cell Patch-seq experiments, enabling transcriptomic analysis of electrophysiologically recorded LE cells. Results: Upon depolarization, 58% of LE cells exhibited aberrant action potentials (aAPs). Electrophysiological assessment showed that a subset of GBCs generated aAPs, with no significant differences in aAP propertiescompared to LE neurons. Transcriptomic analysis of 144 LE cells revealed four transcriptomic clusters, including two GBC populations and two neuronal populations. LE GBCs exhibited diverse cellular states, including mesenchymal-like, astrocyte-like, neural progenitor-like, and oligodendrocyte-precursor cell-like phenotypes.  Notably, LE GBCs exhibiting aAPs displayed reduced mitotic pathway activity and developmental regulatory ionchannel CaV1.2. Cell-cell interaction analysis illustrates a higher signaling interaction between aAP LE cells compared to no-aAP LE cells. Conclusion: In summary, we find comparable electrical properties between neurons and a subset of GBCs in the leading edge, suggesting an active electrophysiological role of GBCs in the tumor's pathophysiology.

overall_design:
Acute and cultured slices of human glioblastoma tumors were prepared, and whole-cell patch-clamp recordings were performed, followed by nucleus extraction for transcriptomic analysis. RNA was reverse-transcribed, amplified, and sequenced using the SMART-seq v2 protocol.

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

last: Tong

first: Josephine

middle: D

last: Hendriksen

first: Kirstine

last: Elbæk

first: Attila

last: Ozsvar

first: Jens

middle: T

last: Eschen

first: Francisco

middle: G

last: Rodríguez-González

first: Ilayda

last: Pusat

first: Emilie

last: Littau Christensen

first: Mads

last: Rahbæk

first: Kathrine

last: Pii Frederiksen

first: Søren

middle: O

last: Cortnum

first: Ann

last: Sindby

first: Kaare

last: Meier

first: Nikola

last: Mikic

middle: C

last: Sørensen

first: Jonathan

last: Ting

first: Marco

last: Capogna

first: Bjarne

last: Kristensen

first: Wen-Hsien

last: Hou

first: Anders

last: Korshøj


title: Differential T cell clonal dynamics underlie outcomes to frontline chemoimmunotherapy in advanced gastric cancer [paired scRNA/TCR-seq]

city: Cambridge

first: Samuel

last: Wright

state: MA

address: 415 Main St.

institute: Broad Institute of MIT and Harvard

summary: The addition of aPD1 to 5-FU/platinum in advanced gastric cancer (GC) yields variable responses. To understand cooperativity between chemotherapy and immunotherapy, we previously reported a phase II trial sequentially adding pembrolizumab to 5-FU/platinum. In this study, we use single-cell RNA- and TCR-sequencing to analyze 66,813 T cells from primary tumor biopsies pre-treatment, post-chemotherapy, and post-immunotherapy in 33 patients. We observed greater abundance, persistence, and recruitment of T cells with predicted tumor-reactivity in patients with prolonged progression-free survival (slow progressors). Increased B cell abundance and predicted B cell to T cell interactions supported T cell memory and co-stimulation, providing a mechanism for increased abundance and persistence of progenitor-exhausted and tumor-reactive T cells in slow progressors. T cell clones emerging in the tumor after immunotherapy were in the blood before treatment only in slow progressors. Our study thus highlights pre-treatment and early chemotherapy-induced T cell dynamics and B cell to T cell interactions that may drive durable response to chemoimmunotherapy in GC.

overall_design:
Tumor samples were collected from gastric patients and analyzed using paired scRNA/TCR-seq.
Paired scRNA:TCR-seq Data

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

first: A

last: Mehta

last: Klempner

first: R

last: Park


title: The phytosterol 24 (S)-saringosterol alters lipid homeostasis and inflammatory pathways in a cell-specific manner.

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: Liver X receptors (LXR alpha/beta) are nuclear receptors that play a crucial role in regulating various biological processes, including lipid metabolism and inflammation. Activation of these receptors using synthetic pan LXR agonists, such as T0901713 and GW3965 has demonstrated neuroprotective effects, making them promising therapeutic targets for neurodegenerative disorders like Alzheimer’s Disease (AD). However, the clinical applications of synthetic pan-LXR agonists are limited by adverse hepatic effects including hypertriglyceridemia and steatosis. Thus, dissociating the beneficial effects of LXR agonism from the deleterious side effects in the liver will be required for the development of LXR agonists as better potential therapeutics. In this study, we investigated 24(S)-saringosterol, a phytosterol derived from the seaweed Sargassum fusiforme, which has previously been reported to exhibit LXR agonist activity without inducing hepatic steatosis. To elucidate its effects on lipid metabolism and inflammatory pathways, we used two distinct cell lineages-myeloid and hepatic cells. Our results demonstrate that 24(S)-saringosterol exhibits a stronger activation of LXR regulated gene expressions leading to dose-dependent upregulation of the cholesterol efflux transporter ABCA1 in both cell types. In myeloid cells, including microglia and bone marrow-derived macrophages, like GW3965, 24(S)-saringosterol exhibited anti-inflammatory effects by downregulating genes involved in interferon- pathways and promoted cholesterol efflux by upregulating ABCA1 via LXR activation. In myeloid as well as hepatic cells, 24(S)-saringosterol reduced the expression of cholesterol biosynthesis genes as well as LDLR via SREBP2, in contrast to GW3965, which upregulated expression of lipid synthesis genes via SREBP1. These findings highlight the therapeutic potential of 24(S)-saringosterol as a dissociated LXR agonist that effectively mitigates the adverse effects associated with synthetic LXR agonists. This compound represents a promising candidate for further investigation in the context of AD and other metabolic and inflammatory disorders.

overall_design: Primary mouse microglia, bone derived macrophages, and hepatocytes were cultured and treated with either Vehicle (Etoh), 1 micromolar of GW3964 or 10 micromolar of 24(S)-saringosterol . Post 24 hr treatment, cells were washed and RNA was extracted using Zymo Research Quick RNA Miniprep Plus kit (cat#R1058). The extracted RNA was submitted for bulk RNA sequencing.

first: Manmeet

last: Singh

first: Monique

last: Mulder

first: Anil

last: Cashikar

first: Steven

last: Paul


title: Nuclear FGF2, Androgen Receptor and Wnt Pathway Activation Define a Targetable Subset of Antiprogestin-Resistant Luminal Breast Cancer

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: We used PR+ T47D and T47D‑YA cell lines engineered to overexpress FGF2 to investigate FGF2‑driven antiprogestin resistance. Transcriptome profiling, qRT-PCR, immunohistochemistry, and in vivo assays were performed to assess hormone receptor expression, pathway alterations, and therapeutic response. We evaluated nuclear androgen receptor (AR) and FGF2 in luminal breast cancer specimens. RNA-seq showed that FGF2 overexpression dysregulated Wnt signaling, downregulated estrogen receptor (ER) and PR, and upregulated AR expression. PR isoform B (PRB) predominated over isoform A, consistent with an antiprogestin-resistant phenotype. FGF2-overexpressing xenografts showed antiprogestin resistance, increased proliferation, and lung metastasis. AR and Wnt pathway blockade impaired tumor growth, and combined treatment further reduced tumor and metastatic burden. In clinical samples, nuclear FGF2 correlated with elevated AR levels in ER+PR− and PRB-high tumors.

overall_design: Total RNA was isolated from T47D-YA cells overexpressing the 18 or 22.5 kDa FGF2 isoforms, and from empty vector controls (MOCK) for further RNA-sequencing.

first: Caroline

last: Lamb

first: Claudia

last: Lanari


title: Machine Learning Analysis of the Human Initiator Region Reveals Key Features of Different Types of Core Promoters

city: La Jolla

first: James

middle: T.

last: Kadonaga

state: California

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: The initiator (Inr) is the starting point for the transcription of many genes. Here, we generated highly predictive machine learning models of the human Inr region, and determined that the Inr is present in about 60% of focused human promoters, identified a novel TATA-specific Inr, and detected the overlapping but functionally distinct TCT motif. Quantitative genome-wide analyses revealed a strict and synergistic interaction between the Inr and DPR, an inverse relationship between the TATA and DPR, a flexible and sometimes independent function of the TATA box in relation to the Inr, and different properties of the TCT motif in humans versus Drosophila.

overall_design: HARPE (high-throughput analysis of randomized promoter elements) and SVR (support vector regression) analyses of the human initiator (Inr) region. HARPE was performed in vitro and in human (HeLa) cells.

first: Torrey

last: Rhyne-Carrigg

first: Long

last: Vo ngoc

last: Medrano

first: Kassidy

last: Gillespie


title: Differential T cell clonal dynamics underlie outcomes to frontline chemoimmunotherapy in advanced gastric cancer [TCR-seq]

last: Wright

overall_design:
PBMC samples were collected from gastric patients and analyzed using bulk TCR-seq.

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Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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title: Single-nucleus RNA sequencing and functional studies of acute methamphetamine-induced cognitive impairment

city: Nanjing

first: fang

last: lu

address: 300 Guangzhou Road

department: Department of Nephrology

institute: the First Affiliated Hospital of Nanjing Medical University

summary: Cognitive impairment is a hallmark phenotype of methamphetamine (Meth) abuse, yet the cellular mechanisms driving these deficits remain poorly understood. This study aims to investigate the cellular composition, gene expression profiles, key signaling pathways, intercellular communication networks, and transcription factor activity in hippocampal tissues from control mice and those acutely exposed to Meth, thereby elucidating the mechanistic underpinnings of Meth-induced neurotoxicity. Single-nucleus RNA sequencing (snRNA-seq) was employed to investigate the transcriptomes of nuclei isolated from the hippocampus of acute Meth-treated and control mice. Our study provides a systemic understanding of the transcriptome alterations induced by Meth exposure in mouse hippocampus, which may offer clues for therapeutic strategies against acute Meth exposure.

overall_design: Single-nucleus RNA sequencing (snRNA-seq) was applied to hippocampus of acute Meth-treated and control mice to define the transcriptomic andscape at the single-celresolution.

first: Di

last: An

first: Fang

last: Lu

first: Yifei

last: Wang

first: Zhongman

last: Zhang

first: Peipei

last: Huang

first: Jun

first: Xufeng

last: Chen


title: Single Cell RNA Seq of Mouse Retina from AAV-overexpressed IFN-beta and Control

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

summary: Type-I IFNs have been implicated in the development and progression of retinal disease, however the concequence of long term ocular exposure to Type-I IFN and the cell types that are impacted has not been characterized.  This study uses AAV2 to overexpress IFN-beta to achieve prolonged retinal exposure with a single intravitreal injection.  We have then employed a single cell RNA sequencing approach using 10x Genomics scRNAseq examine the retinal cell types responsive to Type-I IFN.

overall_design: C57BL/6J mice were administered either AAV2-CAG-IFNbeta or AAV2-CAG-Null (control).  After 10 weeks of exposure, the retinas were collected and analyzed via scRNAseq.

first: Chao

last: Ebeling

first: Fabian

last: Koechl

first: Debasish

last: Sinha

first: Derrick

last: Feenstra


title: Effects of diet and Pseudocapillaria tomentosa (Pt) infection on the gut transcriptome in zebrafish

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

summary: Diet strongly shapes the host’s transcriptional response to P. tomentosa exposure, suggesting that nutritional status influences both parasite burden and the host’s capacity to mount an effective molecular response.

overall_design: To investigate how diet-induced changes in the zebrafish gut  transcriptome influence zebrafish susceptibility to P. tomentosa and subsequent host-parasite interactions, we utilised six groups of 18 adult AB wildtype zebrafish. Two of the groups (n = 36) were given a control diet while , two other groups (n = 36) were given the control diet supplemented with 20% inulin, and the last group was given received a high-fat diet consisting of egg yolk powder (n = 36). One group from each diet (n = 3 × 18) was exposed to P. tomentosa by adding infective eggs to the tank water after 14 days of diet intervention. The remaining groups from the respective diets (n = 3 × 18) were non-infected controls. The fish were euthanised after 29 or 30 days of the first exposure to P. tomentosa. A subset of Intestine samples (n=43) were stored in RNAlater.


title: Multimodal profiling reveals a Notch-responsive regenerative subpopulation of cochlear supporting cells [2]

city: Omaha

first: Litao

last: Tao

state: NE

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University

summary: Regeneration enables organisms to repair damaged tissues, yet this capacity is strikingly limited in the cochlear sensory epithelium, essential for sound detection. A major cause of hearing loss arises from the irreversible loss of sensory hair cells (HCs) in the cochlea. While supporting cells (SCs) have a latent ability to trans-differentiate into HCs, this regenerative potential is rapidly lost after development. Using live imaging and single-cell multiomics of cochlear explants, we uncovered the cellular and molecular heterogeneity underlying the limited regenerative capacity of the neonatal mouse cochlea. Notch repression broadly silenced key SC genes, yet only a rare subpopulation of Deiters cells (DC), termed responsive DCs, initiated the trans-differentiation into HC fate. These cells underwent coordinated transcriptional and enhancer remodeling, linking epigenetic priming with morphological plasticity, while other SCs remained refractory despite robust Notch targets downregulation. Our study provides a molecular definition of a fate-primed SC state, revealing Notch inhibition as a selective trigger that unmasks rare regenerative competence.

overall_design: RNA-seq profiling of supporting cells (SC) isolated from murine cochlear explants after 24h of Notch inhibition treatment, and corresponding control samples. Two developmental time points, P0 and P6. Four replicates per treatment/control at P0 and three replicates at P6.

first: Lama

last: Khalaily

first: Shahar

last: Kasirer

first: Katherine

last: Domb

first: Mi

last: Zhou

first: Buwei

last: Shao

last: Taiber

first: Ran

last: Elkon

first: David

last: Sprinzak

first: Karen

last: Avraham


title: Targeting LPAR4 overcomes stress adaptation to CDK4/6 inhibition in soft tissue sarcoma [RNAseq]

city: Houston

first: Jlenia

last: Guarnerio

state: TX

address: 6767 Bertner Ave

institute: MD Anderson Cancer Center

summary: CDK4/6 inhibitors are under active clinical evaluation in sarcoma, yet the mechanisms governing sensitivity and resistance remain unclear. We show that the CDK4/6 inhibitor abemaciclib not only suppresses tumor cell proliferation but also induces robust type I interferon signaling driven by dsRNA accumulation, which is essential for its anti-tumor activity. Abemaciclib reshapes the sarcoma immune microenvironment by increasing T cell infiltration and enhancing intratumoral interferon-producing monocytes. Integrated transcriptomic and proteomic analyses identified Lysophosphatidic Acid Receptor 4 (LPAR4) as an adaptive stress-response factor upregulated in tumor cells upon treatment and associated with poor patient prognosis. Functionally, LPAR4 mitigates interferon-induced mitochondrial stress, limiting reactive oxygen species accumulation and apoptosis, while its silencing exacerbates mitochondrial dysfunction and promotes tumor cell death. In vivo, LPAR4 loss synergizes with abemaciclib to inhibit tumor growth and prolong survival. These findings establish LPAR4 as a key regulator of stress adaptation and a promising target to potentiate CDK4/6-based therapies.

overall_design: Transcriptomic profiling of mouse undifferentiated sarcoma cells (p53 k.o. Ccne1 o.e.) with or without treatment with the CDK4/6 inhibitor abemaciclib, and with or without knock-down of Lpar4.

first: Jin-Fen

last: Xiao

first: Emily

middle: Y

last: Ko


title: Targeting LPAR4 overcomes stress adaptation to CDK4/6 inhibition in soft tissue sarcoma [CITEseq]

overall_design: Mice bearing undifferentiated pleiomorphic sarcoma (UPS) tumors were treated with vehicle or with the CDK4/6 inhibitor abemaciclib (n=4 mice per group, 8 mice total). Live cells were isolated from tumors for single-cell RNA-sequencing.


title: Cancer associated fibroblasts promote epithelial to mesenchymal transition and classical to basal change in pancreatic cancer cells in association with loss of IL-8 expression

city: Baltimore

first: Jacquelyn

last: Zimmerman

state: MD

address: 1650 Orleans St

institute: Johns Hopkins

summary: Pancreatic ductal adenocarcinoma (PDAC) carries an extremely poor prognosis, in part resulting from cellular heterogeneity that supports overall tumorigenicity. Cancer associated fibroblasts (CAF) are key determinants of PDAC biology and response to systemic therapy. While CAF subtypes have been defined, the effects of patient-specific CAF heterogeneity and plasticity on tumor cell behavior remain unclear. Here, multi-omics was used to characterize the tumor microenvironment (TME) in tumors from patients undergoing curative-intent surgery for PDAC. In these same patients, matched tumor organoid and CAF lines were established to functionally validate the impact of CAFs on the tumor cells. CAFs were found to drive epithelial-mesenchymal transition (EMT) and a switch in tumor cell classification from classical to basal subtype. Furthermore, we identified CAF-specific interleukin 8 (IL-8) as a contributing modulator of tumor cell subtype. Finally, we defined neighborhood relationships between tumor cell and T cell subsets.

overall_design:
Patient matched organoids and cancer associated fibroblasts were generated from PDAC surgical speciments gathered at JHU. Samples were cultured in either monoculture or coculture conditions using a matrigel substrate. For bulk-RNA sequencing, samples were FACS sorted based on EPCAM (for organoids) and FAP (for CAFs) expression prior to RNA isolation.

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Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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title: Transcript landscape in the heart of inducible cardiomyocyte-specific Immt knockout mice

city: Cincinnati

first: Yasuhide

last: Kuwabara

state: Ohio

address: 240 Albert Sabin Way, Building S

institute: Cincinnati Children's Hospital Medical Center

summary: Immt gene encodes Mic60 protein which is a main component of the mitochondrial contact site and cristae organizing system (MICOS) protein complex. The MICOS complex plays pivotal roles for crisa juction formation and connection of inner mitochondrial membrane and outer mitocondrial membrane of mitochondria. Although it is well known that the ristae are crucial for energy production by OXPHOS, it is still precisely unknown how the Mic60 is important in the adult matured cardiomyocytes in vivo. To expand our knowledge about the Mic60 functions in the adult mouse heart, we utilized inducible cardiomyocyte-specific Immt gene knockout mice and conducted bulk RNA-seq with the hearts. Our data highlights the mitochondria stress response at transcript level in the hearts.

overall_design: To generate inducible cardiomyocytes-specific Immt gene knockout mice, we crossed Immt-loxP targeted mice with Myh6-MerCreMer transgenice mice and obtained Immtfl/fl-Myh6-MCM mice. Immt+/+-Myh6-MCM mice were used as a control. To knockout the Immt gene, we injected tamoxifen at 6 weeks of age tree times every other day. At 20 weeks after tamoxifen injection, we isolated total RNA from the hearts and carried out bulk RNA-seq.

first: Jeffery

last: D. Molkentin


title: Bulk RNA Seq of Mouse RPE/Choroid from AAV-overexpressed IFN-beta and Control

first: Roland

last: Schmucki

summary: Type-I IFNs have been implicated in the development and progression of retinal disease, however the concequence of long term ocular exposure to Type-I IFN and the cell types that are impacted has not been characterized.  This study uses AAV2 to overexpress IFN-beta to achieve prolonged retinal exposure with a single intravitreal injection.  We have then employed a bulk RNA to examine the response of the RPE and choroidal cells to prolonged Type-I IFN exposure.

first: Chao

last: Huang

first: Martin

last: Ebeling

first: Debasish

last: Sinha

first: Derrick

last: Feenstra


title: The deubiquitinase USP1 promotes the progression of AML by stabilizing ID1 [ID1 CUT&Tag in AML]

city: suzhou

first: yang

last: yang

address: zhongnan road

institute: soochow university

summary: Acute myeloid leukemia (AML) represents a clonal malignant disorder affecting the hematopoietic system, predominantly featuring abnormal clonal proliferation of myeloid precursor cells and linked to unfavorable prognosis. This investigation seeks to improve clinical outcomes through examing the mechanistic role ubiquitin-specific protease 1 (USP1) in AML. Data analysis from The Cancer Genome Atlas (TCGA) and TARGET databases demonstrated that USP1 exhibits high expression in AML, where increased show positive correlation with poor prognostic outcomes. In vitro studies using short hairpin RNA (shRNA) for USP1 knockdown showed significant suppression of AML cell proliferation and enhanced apoptosis. Additionally, in vivo investigations indicated that USP1 knockdown inhibited tumor growth and enhanced survival rates. The USP1 inhibitor SJB3-019A displayed similar effects on AML cells. Co-immunoprecipitation (CO-IP) coupled with mass spectrometry analysis indicated that USP1 associates with ID1, mediating its function via deubiquitination mechanisms. CUT&Tag findings additionally demonstrated that ID1 modulates target genes involved in AML. This investigation confirms that USP1 serves a critical role in facilitating the proliferation and survival of AML cells through ID1 stabilization. The findings suggest that the USP1 inhibitor SJB3-019A represents a promising new therapeutic approach for treating AML.

overall_design: CUT&Tag profiles of ID1 in CMK and MEG01 cells were generated by CUT&Tag sequencing, in double, using Illumina NovaSeq X plus.

first: Yang

last: Yang


title: Enhanced woody biomass production in hybrid aspen through xylem-specific overexpression of Arabidopsis thaliana LBD genes

city: Helsinki

first: Leo

middle: Matti Iivari

last: Vainio

state: Uusimaa

address: Viikinkaari 1

department: OEB

country: Finland

institute: University of Helsinki

summary: Woody biomass is a critical renewable resource for sustainable energy and material production, yet strategies to increase its yield while simultaneously improving quality remain limited. Here, we demonstrate that xylem-specific overexpression of Arabidopsis thaliana LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors markedly enhances stem secondary growth and alters wood composition in hybrid aspen (Populus tremula × Populus tremuloides Michx., clone T89). Using the LMX5 promoter to drive targeted expression of A. thaliana LBD4 and LBD11 in the developing xylem, we observed substantial stimulation of secondary xylem formation. Histological analyses revealed distinct roles for each gene: LBD4 primarily promoted xylem development through increased cell expansion, whereas LBD11 enhanced both cell proliferation and expansion. This dataset was used to analyze the LBD overexpression lines

overall_design: For gene expression analysis, three-week-old stem internodes from the WT and transgenic LBD4-OE and LBD11-OE trees were used.

first: Melis

last: Kucukoglu Topcu

first: George

last: Woodward