title: Identifying differentially expressed genes (DEGs) between shNC and shGm26917 female germline stem cells (FGSCs) [RNA-Seq]

summary: Integrated analysis of RNA-seq and Ribosome profiling and sequencing (Ribo-seq) data was performed to identify translation efficiency altered upon Gm26917 knockdown.

overall_design: FGSCs were infected with lentivirus to knockdown Gm26917 and detected TE by RNA-seq


title: Dysregulated differentiation kinetics underlie essential role of DNA damage repair in cloned placentas [scMutiomics]

status: Public on Jun 18 2026

city: Shanghai

first: Shanshan

last: Yi

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: College of Life Science and Technology

country: China

institute: Tongji University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: To investigate the mechanisms underlying cloned placenta hyperplasia, we employed single-nuclei RNA and ATAC-seq multi-omics at the critical window of placental overgrowth. Our work offers the first comprehensive and novel single-nuclei–level dissection of developmental barriers in SCNT placentas, demonstrating that genomic instability constitutes the principal determinant of SCNT placental dysfunction, and outlines a feasible approach to improve reproductive cloning outcomes.

overall_design: We conducted 10X multiome snRNA- and snATAC sequencing experiments comparing naturally fertilized (NF) and somatic cell nuclear transfer (SCNT) placentas at embryonic days (E) 12.5, 14.5, and 18.5.  SCNT placentas rescued by samll molecule Farrerol were futher collected at E12.5 for sing cell multiome sequencing to assess transcriptional and chromatin accessibility changes.

first: Guang

last: Yang

first: Mingzhu

last: Wang

first: Rui

last: Gao


title: A transfer RNA modification drives genome-wide synonymous recoding across human commensal bacterial families

city: Chicago

first: Hoang Anh

middle: V

last: Tran

state: IL

address: 5801 S Ellis Ave

country: USA

institute: University of Chicago

summary: Inosine modification on tRNA anticodon (I34) is universally conserved in three kingdoms of life and critical to tRNA decoding capabilities. We found that tRNALeu(IAG) in commensal human bacterial families in Lactobaccilales is concurrent with genome-wide synonymous leucine codon reprogramming. Pathway analysis reveals drastic synonymous Leu codon shifts in metabolism proteins, where many genome-wide dominant UUA in families without tRNALeu(IAG) is reprogrammed to CUU, CUC and UUG in families with tRNALeu(IAG). We provide biochemical and phenotypic results to support mechanisms that enable synonymous Leu codon substitutions to confer greater translation equivalency and growth fitness. The appearance of a single tRNA modification can propel the genome-wide evolution of synonymous codons.

sample_organism:
Streptococcus mutans
Homo sapiens

platform_organism:
Streptococcus mutans
Homo sapiens

overall_design: RNA-seq profiling of (i) tongue dorsum scrapings collected from 1 female and 3 male volunteers on two consecutive days, and (ii) wild-type UA159 Streptococcus mutans and its isogenic tRNA mutant JCC341, innoculated with or without 0.15% glucose, and harvested at 1 h and at early stationary phase.

first: Christopher

middle: D

last: Katanski

first: Chathuri

last: Pathirage

first: Jenny

last: Chang

first: Iva

last: Veseli

first: Tyler

last: Smith

first: Marcus

last: Foo

first: Yuan

last: Wu

first: Yichen

last: Hou

first: Dominika

last: Rudzka

first: Mohammad Amin

last: Bayat Tork

first: Karen

last: Lolans

first: Amy

last: Willis

first: Weixin

last: Tang

first: A

last: Murat Eren

first: Michael

last: Federle

first: Kristin

last: Koutmou

first: Tao

last: Pan


title: Photochemical modification of two fluorene-based molecules yields structurally distinct DNA intercalators with potent anti-MRSA activity

city: London

first: David

last: Heinrichs

state: ON

address: Microbiology and Immunology, 3014 Dental Sciences Building, 1151 Richmond Street

country: Canada

institute: University of Western Ontario

summary: Photoconvertible fluorene-containing compound targets S. aureus by DNA intercalation and damage

sample_organism: Staphylococcus aureus subsp. aureus USA300_FPR3757

overall_design: A total of 9 samples were analyzed. Samples were acquired from 3 independent experiments. 3 samples were WT S. aureus treated with a vehicle control, 3 samples were WT S. aureus treated with DB10-R and 3 samples were WT S. aureus treated with DB10-Y

first: Avery

last: Gaudreau

first: Matthew

last: Beckner


title: Metabolic reprogramming drives pancreatic β cell neogenesis from α cells [RNA-Seq 2]

first: Guangxing

last: Lu

address: 上海市淞沪路2005号

institute: Fudan University

summary: Loss of functional β cells is a hallmark of diabetes, and restoring β cell mass remains a critical goal in the quest for a specific therapy. One potential strategy is to convert non-β cells in the islet, such as α cells, into insulin-producing cells. Although several compounds have been identified to induce β cell-like features in α cells, none have yet been successfully translated into clinical applications. In this study, we identify PRC2 inhibitors as potent inducers of β cell-enriched gene expression in α cells, acting through modulation of the AR-ETV1 complex. AR inhibition suppresses glycogen synthesis and enhances the pentose phosphate pathway (PPP). Direct metabolic reprogramming with methyl esterified 6-phosphogluconate (ME-6-PG), an intermediate metabolite of the PPP, induces β cell-like features in α cells, stimulate β cell regeneration and ameliorates diabetes. Our findings demonstrate that metabolic reprogramming can drive β cell regeneration and highlight a promising therapeutic strategy for diabetes.

overall_design: To investigate the effect of enzalutamide on αTC1 cells, we extracted total RNA from αTC1 cells treated with enzalutamide, and then performed RNA-seq.

first: Yufeng

last: Zhang


title: Metabolic reprogramming drives pancreatic β cell neogenesis from α cells [ATAC-seq 2]

overall_design: To investigate the changes of chromatin landscape in αTC1 cells with EPZ011989 treatment, we performed ATAC-seq.


title: Transcriptional profiling of AGPS knockout breast cancer cells treated with TGF-B

city: Cambridge

first: Whitney

last: Henry

state: MA

address: 500 Main St

department: Biology

institute: MIT

summary: This study investigates the transcriptional changes associated with depleting ether lipids via AGPS (alkylglycerone phosphate synthase) knockout in epithelial PyMT-1099 murine breast cancer cells. RNA-Seq was performed to compare the gene expression profiles between AGPS knockout and control cells, both in the presence and absence of TGF-B treatment. The data provide insights into how ether lipid metabolism intersects with TGF-B-mediated signaling pathways and epithelial-to-mesenchymal transition (EMT) in breast cancer.

overall_design: Transcriptional profiling of TGF-treated WT and AGPS KO PyMT-1099 breast cancer cells

first: Henry

last: Whitney


title: Metabolic reprogramming drives pancreatic β cell neogenesis from α cells [RNA-Seq]

overall_design: To investigate the effect of EPZ011989 on αTC1 cells, we extracted total RNA from αTC1 cells treated with EPZ011989, and then performed RNA-seq.


title: Lineage Plasticity Driven by GATA6 Loss Fuels Colorectal Cancer Metastasis

status: Public on Jun 22 2026

city: New York

first: Norihiro

last: Goto

state: NY

address: 413 East 69th Street

department: Department of Medicine

institute: Weill Cornell Medicine

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

overall_design: Refer to individual Series


title: Synchronised regeneration of osteochondral defects via spatially patterned implants of stable and hypertrophic cartilage organoids

city: Leuven

first: Liuqi

last: Peng

state: BELGIUM

address: Janseniusstraat 45, B0204

country: Belgium

institute: KU Leuven

summary: Repairing deep osteochondral defects remains clinically challenging due to the intrinsic inability of articular cartilage to self-repair and the need for integrated yet distinct regeneration of articular cartilage and subchondral bone. Here, we present a scaffold-free, modular strategy that spatially bioassembles iPSC-derived chondrocytes (iChon) organoids with human periosteum-derived cell (hPDC) organoids to engineer zonated osteochondral assembloids. The resulting iChon+hPDC assembloids exhibit intrinsic spatial organization, forming chondral- and osteo-like zones with an intermediate interface without exogenous scaffolds. In vitro characterization confirmed layered glycosaminoglycan-rich cartilage and collagen I-rich bone-like domains, with an intermediate interface emerging through self-directed matrix organization. Upon implantation into full-thickness osteochondral defects, iChon+hPDC assembloids promoted robust hyaline cartilage restoration, subchondral bone reconstruction, and partial restoration of collagen fiber anisotropy. Transcriptomic profiling revealed complementary biological programs, with iChon exhibited extracellular matrix remodeling and early developmental plasticity and hPDC in endochondral ossification pathways. This work provides a robust, scaffold-free platform for osteochondral regeneration that can be adapted toward patient-specific repair through integration of iPSC-derived cell sources and precise spatial assembly of zonated organoids.

overall_design: RNA-seq was performed on four groups of organoid or cartilage-like samples derived from different human cell sources and protocols. Group 1: Organoids derived from human articular chondrocytes (hACs) after 21 days of chondrogenic differentiation; Group 2: Organoids formed by re-seeding dissociated iChonMass nodules and culturing for 21 days; Group 3: iPSC-derived cartilage nodules (iChonMass) after 8 weeks of chondrogenic differentiation; Group 4: Organoids derived from human periosteum-derived cells (hPDCs) after 21 days of chondrogenic differentiation. All samples were sequenced using the Illumina HiSeq4000 platform platform, with single-end 75 bp reads.

last: peng

first: Isaak

last: Decoene

first: Hanna

last: Svitina

first: Ioannis

last: Papantoniou


title: Metabolic reprogramming drives pancreatic β cell neogenesis from α cells [ATAC-seq]

overall_design: To investigate the changes of chromatin landscape in αTC1 cells with Enzalutamide treatment, we performed ATAC-seq.


title: Loss of Gak leads to lysosome dysfunction and immune modulation in podocytes

city: New Haven

first: Patricia

last: Bunda

state: CT

address: 300 Cedar St S370

institute: Yale School of Medicine

summary: Lysosome impairment causes cellular and organ dysfunction, highlighting its crucial role in homeostasis. In this study, we uncovered the indispensable role of cyclin G-associated kinase (GAK) in maintaining podocyte lysosome integrity. We previously showed that podocyte-specific loss of Gak (Gak-KO) leads to severe proteinuria, podocyte injury, and kidney failure. To identify which GAK domains are necessary for its function, we used a transgenic mouse expressing a truncated 62-kDa C-terminal GAK protein (GAK C62). Our findings showed significant accumulation of autophagic vesicles in Gak-KO podocytes, attributed to impaired lysosomal degradation secondary to lysosomal hydrolase mistrafficking. Notably, GAK C62 expression completely rescued these phenotypes at both cellular and organismal levels. Moreover, in vivo RNA-seq and cytokine profiling demonstrated enrichment of immune-related pathways and IL-11 production in Gak-KO podocytes. Overall, this study underscores the importance of lysosome integrity and suggests how its dysfunction may lead podocytes to adopt immune-like properties, with potential autocrine and paracrine effects within the kidney.

overall_design: podocyte-specific TRAP-seq profiling in wildtype (WT), Gak-KO, and C62 Gak-KO mice at 3-4 weeks of age

first: Shuta

last: Ishibe


title: Liver Single-Cell Atlas of MASH and Fibrosis Models in Mice

city: Wenzhou

first: Weiwei

last: Zhu

address: Wenzhou Medical University, University Town, Chashan

institute: Wenzhou Medical University

summary: Metabolic dysfunction-associated steatohepatitis (MASH) and liver fibrosis represent distinct yet interconnected pathological processes underlying chronic liver disease progression. While high-fat diet (HFD)-induced MASH models recapitulate metabolic inflammation, carbon tetrachloride (CCl₄)-induced models capture toxicant-driven fibrogenesis.  Here, we performed single-cell RNA sequencing (scRNA-seq) on liver tissues from HFD-induced MASH and CCl₄-induced fibrosis mouse models to construct a high-resolution atlas of liver cellular heterogeneity. This work establishes a valuable resource for dissecting liver disease mechanisms, enabling targeted therapeutic discovery and offering a framework for integrating diverse preclinical models of chronic liver injury.

overall_design: Eight-week-old male C57BL/6 mice were randomly divided into three groups (n = 2 per group). The control (CON) group received no treatment and was maintained under standard laboratory conditions. The MASH group was fed a high-fat diet (HFD; 60% kcal from fat) for four months to induce metabolic dysfunction-associated steatohepatitis. The CCl₄ group was fed a normal chow diet for three months, followed by intraperitoneal injections of 10% CCl₄ solution (0.1 mL per injection, twice per week) for four weeks to induce hepatic fibrosis.  At the end of the treatment period, all mice were sacrificed, and hepatocytes and non-parenchymal liver cells were isolated using collagenase perfusion digestion. Cells from mice in the same group were pooled. After counting, hepatocytes and non-parenchymal cells were mixed at a 1:1 ratio. The resulting cell suspension was used for library preparation and single-cell RNA sequencing.

first: Guang

last: Liang


title: Transcriptome profiling of parental and lenvatinib-resistant TPC-1 thyroid cancer cells

first: jun

middle: Yun

last: Wang

address: Fudan University Shanghai Cancer Center, 270 Dong'an Road, Xuhui District, Shanghai, China

department: Head and Neck Surgery

institute: Fudan University Shanghai Cancer Center

summary: To uncover transcriptional alterations associated with lenvatinib resistance in papillary thyroid carcinoma, we performed paired-end RNA-Seq (2 × 150 bp, NovaSeq 6000) on parental TPC-1 cells and an in-house generated lenvatinib-resistant sub-line (TPC-1-Len). Total RNA from three biological replicates per group was extracted with TRIzol, libraries were prepared with poly(A) selection, and sequencing was carried out at OE Biotech (Shanghai, China). Differential gene expression was analysed using DESeq2 (Q < 0.05)

overall_design: 2 × 2 design: parental vs lenvatinib-resistant TPC-1 cell lines; three independent cultures per condition; no drug treatment at RNA harvest.


title: Decoding the response to a PP2A inhibitor in pancreatic cancer

city: Göttingen

first: Nignjun

last: Duan

address: Robert-Koch-Straße 40

country: Germany

institute: Universitätsmedizin Göttingen

summary: The high failure rate of a cancer drug from target definition to clinical implementation highlights the need to prioritize context-specific targets. Here, we identify PP2A as an important target in pancreatic ductal adenocarcinoma (PDAC) by cancer-dependency scores. We characterized how inhibition of PP2A with the clinical grade inhibitor LB100 affects PDAC cells. Mesenchymal PDAC cells are highly susceptible to LB100-induced death. CRISPR-Cas9 drop-out screens revealed the contribution of the transcription cycle, splicing, or translation to the LB100 response. Mechanistically, PP2A inhibition disables the RNA polymerase II pause checkpoint, leading to CDK9-mediated transcriptional elongation linked to a ER stress response correlated with the formation of stress granules, autophagy, and cell death. We provide evidence for a PP2A inhibitor-sensitive subtype of PDAC and offer detailed insights into the cellular response induced by PP2A inhibitors.

overall_design: To investigate how PP2A inhibitor LB100 affects gene transcriptions, we checked the genomic distributions of total RNA polymerase II.


title: Circadian Disruption Triggers Trophoblast Differentiation Failure via CLOCK-Dependent Chromatin Instability

city: Shenzhen

first: Qixin

last: Xu

state: Guangdong

address: No. 4009, Xinzhou Road, Futian District, Shenzhen, Guangdong Province

institute: Women and Children's Medical Center

summary: Preeclampsia (PE), a life-threatening hypertensive disorder of pregnancy, lacks effective therapies due to poorly understood pathogenesis. While maternal sleep disturbances are epidemiologically linked to PE, the molecular mechanisms remain elusive. Here, we identify the circadian regulator CLOCK as a master epigenetic stabilizer critical for placental development, whose dysfunction drives PE pathogenesis. Through multi-omics analyses of human PE placentae and mechanistic studies in murine models, we demonstrate that maternal sleep deprivation downregulates placental CLOCK, recapitulating PE phenotypes, and CLOCK deficiency triggers global chromatin decompression, suppresses WNT/β-catenin signaling, and arrests trophoblast differentiation. Mechanistically, CLOCK interacts with heterochromatin proteins HP1α and H1.0 to maintain nucleosome stability, while its loss increases chromatin accessibility and suppresses WNT/β-catenin signaling. Single-cell RNA-seq reveals CLOCK’s selective expression at the onset of differentiation, where its absence locks cells in a stem-like state. Crucially, WNT activation, stabilization of chromatin and melatonin rescues growth defects in CLOCK-deficient trophoblasts, highlighting actionable therapeutic strategies. Our findings establish a unifying mechanism for PE, linking maternal sleep disturbances, placental epigenetic instability, and impaired differentiation. These findings not only advance PE management but also illuminate a universal mechanism by which circadian regulators safeguard chromatin stability across developmental and disease contexts.

overall_design: RNA-seq analysis of HTR8 cells with knockdown of the CLOCK gene

first: Xiaotian

last: Li

first: Huanqiang

last: Zhao


title: Transcriptome analysis of KRT15 knockdown in lenvatinib-resistant papillary thyroid carcinoma cells

summary: Lenvatinib resistance is a major clinical obstacle in the treatment of radioiodine-refractory papillary thyroid cancer (PTC), and clarifying its molecular mechanisms is crucial for developing effective therapeutic strategies. In this study, we identify Keratin 15 (KRT15) as a key driver of this resistance. We found that KRT15 overexpression is associated with an unfavorable clinical prognosis in PTC patients. Mechanistically, KRT15 interacts with Keratin 81 (KRT81) to form a regulatory complex that upregulates Diacylglycerol Kinase B (DGKB). This KRT15-KRT81-DGKB axis drives metabolic reprogramming by increasing the expression of key fatty acid oxidation (FAO) enzymes, such as CPT1A and ACOX1, which enhances cellular energetics and promotes survival under therapeutic stress. Consequently, inhibition of this pathway successfully resensitizes resistant cells to lenvatinib. Taken together, our study reveals a novel mechanism where cytoskeletal proteins mediate metabolic adaptation in drug-resistant PTC cells, identifying the KRT15-KRT81-DGKB pathway as a promising therapeutic target to overcome lenvatinib resistance in refractory PTC patients.

overall_design: To identify genes regulated by KRT15 that contribute to lenvatinib resistance in papillary thyroid carcinoma (PTC), we performed transcriptome sequencing on lenvatinib-resistant TPC-1 cells (TPC-1-Len). These resistant cells were transfected with either a small hairpin RNA targeting KRT15 (sh-KRT15) to induce knockdown, or a non-targeting negative control shRNA (sh-NC). Gene expression profiles of the sh-KRT15 TPC-1-Len cells were compared to those of the sh-NC TPC-1-Len control cells to identify differentially expressed genes. The experiment was performed with three biological replicates for each condition.


title: RNA Sequencing of nmr-2(ok3324) and  wild type (WT) N2 C. elegans

city: Houston

first: Benson

last: Otarigho

state: Texas

address: 6767 Bertner Avenue

department: Department of Genetics

institute: The University of Texas MD Anderson Cancer Center

summary: Although extensive knowledge exists regarding the mechanism through which neurotransmitter signaling regulates immunity, there remains a limited understanding of how glutamatergic signaling modulates molecular immunity. In this study, we explore dysregulated genes and pathways in nmr-2(ok3324) compared to WT animals.

overall_design: RNA was extracted from synchronized L4 stage nmr-2(ok3324) and WT animals grown at 20 C using Qiagen extraction kits and following standard methods

first: Alejandro

last: Aballay


title: Exogenous Photoreceptor-Specific N-Glycosylated PROM1 Rescues Retinal Degeneration in Patient and Animal Models

city: Guangzhou

first: Xiufeng

last: Zhong

address: 54 xianlie Rd

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: PROM1 (CD133/AC133) is widely expressed across various tissues, yet paradoxically, its mutations are exclusively associated with retinal degeneration. The mechanisms underlying this retina-specific vulnerability remain poorly understood, and no effective treatment currently exists for PROM1-associated inherited retinal dystrophies (IRDs). To address these gaps, we employed retinal organoids (ROs) to delineate the spatiotemporal expression patterns of PROM1, identifying its co-localization with the ciliary marker ARL13B and the outer segment (OS) marker PRPH2 during photoreceptor differentiation. Furthermore, using hiPSCs, hiPSC-RPE cells, and ROs, we discovered photoreceptor-specific mRNA alternative splicing isoforms and distinct protein N-glycosylation patterns of PROM1. To investigate disease mechanisms and therapeutic potential, personalized hiPSCs and ROs were derived from an individual with a PROM1 c.619G>T (p.E207X) homozygous mutation and his unaffected heterozygous mother. The mutation induced pronounced nonsense-mediated decay (NMD) and nonsense-associated altered splicing (NAS), resulting in complete loss of PROM1 protein and severe disruption of OS-like structure in patient-derived ROs (Hom-ROs). To rescue these defects, a photoreceptor-specific AAV7m8-CRXp-hPROM1 vector was engineered, which successfully restored PROM1 expression and OS-like structure in Hom-ROs. Therapeutic efficacy was further validated in vivo using Prom1-/-  mice, where subretinal delivery of AAV8-CRXp-hPROM1 achieved robust, photoreceptor-specific expression of human PROM1, significantly preserving OS structure and visual function. Our study establishes a mechanistic link between PROM1 deficiency and photoreceptor pathology and provide the first preclinical evidence supporting gene augmentation therapy for PROM1-IRD, highlighting its translational potential.

overall_design: To investigate the pathogenic mechanism of PROM1-associated IRD, we generated personalized retinal organoids (ROs) from three sources: an IRD patient with a homozygous PROM1 c.619G>T (p.E207X) nonsense mutation (Hom-RO), his unaffected heterozygous mother (Het-RO), and a healthy control individual (C1-RO). On day 150 of differentiation, six ROs per sample were collected with three biological replicates per group. Under phase-contrast microscopy, each RO was mechanically dissected using tungsten needles to remove the central dark core while retaining the outer transparent photoreceptor layer.

first: Ping

first: Fuying

last: Guo

first: Yuan

first: Guifu

last: Chen

first: Xiaojing

last: Song

first: Dandan

last: Zheng

first: Guanjie

last: Gao

first: Wenjing

last: Yin

first: Suai

last: Zhang


title: USP43 promotes gemcitabine resistance by regulating cholesterol homeostasis through E2F1 stabilization in bladder cancer

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

summary: Gemcitabine (GEM) serves as a foundational therapy for bladder cancer (BLCA), but chemoresistance significantly limits its therapeutic efficacy. Elucidating the molecular mechanisms underlying this resistance is crucial for reversing GEM resistance. In this study, we revealed that the classical oncogene E2F1 is highly expressed in GEM-resistant cells and promotes chemoresistance. We further demonstrated that E2F1 induces GEM resistance by transcriptionally activating NSDHL, a key enzyme in cholesterol biosynthesis, thereby increasing cholesterol production. Additionally, we characterized USP43 as the deubiquitinase responsible for stabilizing E2F1, which plays an essential role in the GEM-induced upregulation of E2F1 expression. Collectively, our findings highlight the critical role of the USP43/E2F1/NSDHL axis in cholesterol-mediated GEM resistance in BLCA, providing novel insights and therapeutic targets for overcoming chemoresistance.

overall_design: To uncover the underlying mechanism by which USP43 modulates lipid metabolism in BLCA, RNA-seq analysis was performed on T24 cells transfected with siNC or siUSP43.

first: Mingxing

first: Tianyun

last: Liu

first: Xinghuan


title: DNA methylation profiles of hospitalized COVID-19 patients

city: Los Angeles

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

type: Methylation profiling by high throughput sequencing

summary: DNA methylation plays a role in the pathogenesis of viral infections and disease progression.  We aimed to explore its connection to the trajectories of COVID-19 disease.  To achieve this, we examined samples from the IMPACC cohort, which includes hospitalized COVID-19 patients categorized into five disease trajectory groups (TGs) based on the dynamics and severity of respiratory symptoms during the acute phase of SARS-CoV-2 infection (the first 28 days).

overall_design: We profiled the longitudinal changes of peripheral blood mononuclear cell (PBMC) DNA methylation patterns with targeted bisulfite sequencing (TBS-seq) in a subset of 75 IMPACC patients recruited at the Ronald Reagan UCLA Medical Center.

first: Harry

last: Pickering

first: Elaine

middle: F

last: Reed

first: Matteo

last: Pellegrini


title: Identifying differentially acetylated mRNA between female germline stem cells (FGSCs) and differentiated FGCs (Dif-FGCs)

first: Ji

last: Wu

address: No.800, Dongchuan Road

institute: Shanghai Jiao Tong University

summary: By combining RNA-seq analysis of differentiation-induced transcriptional changes with genome-wide ac4C profiling (acRIP-seq), we systematically investigated how N4-acetylcytidine modification regulates gene expression programs driving cellular differentiation. Key differentiation regulators showing both ac4C modification and expression changes were prioritized for functional validation.

overall_design: acRIP-seq  profilling of FGSCs and Dif-FGCs (DAY3) was performed to  analyze mRNA ac4C modification


title: A genome-wide functional analysis of conserved intronic regions reveals essential roles for speckle-associated detained introns [RNAseq_candidates.HAP1]

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

summary: Thousands of human introns harbour extended regions of high evolutionarily conservation that have not been previously characterized. A survey of these sequences reveals that they are associated with intron retention and enriched in genes that function in RNA processing, chromatin remodelling and neuronal biology. Using a dual CRISPR-Cas editing approach, we targeted 2,600 of these regions for deletion and observe that a subset of these perturbations affectaffects cell growth. Many of these ‘fitness’ sequences affect intron retention and or expression levels of their host genes. Deletions in nuclear speckle-associated retained introns in the FNBP4 and DDX5 genes are further linked to downstream effects on cell growth-related genes and intron retention, respectively. The DDX5 deletion additionally results in the accumulation of R-loops overlapping first introns in speckle-proximal genes. Overall, the results highlight multifactetedmultifaceted, critical roles of highly conserved intronic sequences in the control of gene regulation, R-loop resolution and cell growth.

overall_design: RNA-Seq of HAP1 cells in which intronic deletions or CRISPR gene knockouts have been created, or cells with deletions in intergenic regions as control. For three of the genes, siRNA-mediated knockdowns were performed in addition, along with control non-targeting knockdown. Every treatment was done in biological duplicate.

first: Shaghayegh

last: Farhangmehr

first: Mingkun

first: Syed

last: Nabeel-Shah

first: Kevin

last: Brown

first: Jason

last: Moffat

first: Benjamin

middle: J

last: Blencowe


title: Identifying differentially expressed genes (DEGs，including lncRNA and mRNA) between shNC and shNAT10 female germline stem cells (FGSCs)

summary: Integrated analysis of long RNA-seq and RNA in situ conformation sequencing (RIC-seq) data was performed to identify genes and RNA-RNA interaction pairs altered upon Nat10 knockdown.

overall_design: Long RNA-seq  profilling of shNC and shNAT10 FGSCs was performed to Integrate analysis with RIC-seq


title: A genome-wide functional analysis of conserved intronic regions reveals essential roles for speckle-associated detained introns [RNAseq_candidates.RPE1]

overall_design: RNA-Seq of RPE-1 cells in which intronic deletions or CRISPR gene knockouts have been created, or cells with deletions in intergenic regions as control. Every treatment was done in biological duplicate.


title: Fatty Acid Esters of Hydroxy Fatty Acids (FAHFA) Derivatives as Dual Modulators of Lipid Metabolism and Gut Microbiome in Obesity

city: Singapore

first: Hong Sheng

last: Cheng

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine,

country: Singapore

institute: Nanyang Technological University

summary: Fatty Acid Esters of Hydroxy Fatty Acids (FAHFAs), endogenous lipids with anti-inflammatory and metabolic benefits, face challenges in clinical translation due to instability and high synthesis costs. This study introduces a scalable synthetic platform to engineer novel FAHFA derivatives with enhanced stability through bioisosteric modifications (e.g., amide, triazole bonds). Screening identified 12-TAASA and 12-HDTZSA as lead compounds, demonstrating potent inhibition of lipid uptake in hepatic cells without compromising glucose absorption. In a diet-induced obesity mouse model, oral administration of these derivatives reduced weight gain, improved glucose tolerance, and attenuated ectopic lipid deposition, rivaling the efficacy of semaglutide. Mechanistically, 12-TAASA and 12-HDTZSA remodeled the gut microbiome by enriching SCFA producing taxa. 12-TAASA also suppressed intestinal lipid absorption via transcriptomic regulation of key genes. These findings position synthetic FAHFAs as dual-action therapeutics, targeting both host lipid metabolism and gut microbiota dysbiosis, offering a promising strategy for obesity and metabolic disorders.

overall_design: Male C57BL/6J mice (8–10 weeks old) were maintained under thermoneutral conditions (30 ± 2°C) on a 12-hour dark/light cycle with free access to LIDPAD for four weeks to induce obesity and metabolic syndrome. Control mice received a matched control diet. Treatment groups received either semaglutide subcutaneously (100 μg/kg; twice weekly) or FAHFAs (12-SAHSA, 12-TAHSA, 12-SAASA, 12-TAASA, or 12-HDTZSA; 100 mg/kg; daily via oral gavage) concurrent with the LIDPAD diet. After four weeks of treatment, animals were euthanized using an overdose of xylazine/ketamine prior to tissue collection. Collected tissues were fixed with 4% PFA or snap frozen with liquid nitrogen for subsequent analyses. Intestinal mucosa of mice treated with different FAHFAs were harvested by scraping the luminal surface of the small intestine. Total RNA was extracted using the Pure-NA Fastspin Total RNA Extraction Kit (Everlife, Singapore). RNA sequencing libraries were prepared and sequenced on a DNBSEQ-T7 (BGI, China) with 150 bp paired-end reads. Reads were aligned to the Mus musculus reference genome (GRCm39) using HISAT2. Gene counting was performed using FeatureCounts.

first: Hao

last: Xie

first: Choon-Hong

last: Tan

first: Nguan Soon


title: A genome-wide functional analysis of conserved intronic regions reveals essential roles for speckle-associated detained introns [RNAseq_CHX]

overall_design: RNA-Seq of HAP1 and RPE-1 cells after treatment with the translation inhibitor cycloheximide (CHX), or DMSO vehhicle control, each in biological triplicate


title: RNAseq analysis in undifferntiated and differnciated CT27 human trophobast stem cells

city: Kansas City

first: Soumen

last: Paul

state: KS

address: Hemenway Building 3901 Rainbow Boulevard

department: Department of Pathology & Laboratory Medicine

institute: University of Kansas Medical Center

summary: In this study CT27 human TSC were cultured in stem state culture condition and also differentiated to Extravillous trophblast lineage and global RNAseq was performed to capture gene expression pattern.

overall_design: CT27 human TSCs were cultured in stem state culture condition and were also differentiated to Extravillous trophblast lineage, then Total RNA was isolated and global gene expression analyses were done via RNA-sequencing.

first: Ananya

last: Ghosh

first: Rajnish

last: Kumar


title: Multiomic single nuclei profiling of a mouse model of Alzheimer’s disease reveals that ACSS2 confers neuronal resilience to tauopathy [ChIP-seq]

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: Loss of cell identity and global epigenomic dysregulation are emerging as key contributors to Alzheimer’s disease (AD). The mechanisms by which protective or risk-conferring epigenetic marks are established and maintained are under intense investigation. ACSS2 (Acetyl-CoA Synthetase 2) is a key metabolic enzyme that is nuclear-localized in neurons. In healthy brains, ACSS2 fuels histone acetylation and drives expression of neuronal genes that regulate learning and memory. Here, we examine how loss of ACSS2 contributes to AD-associated cellular, genomic and behavioral outcomes, focusing on long-term steady state changes. Using a mouse model of human pathological AD-Tau injection, we show that loss of ACSS2 exacerbates Tau-related memory impairments, while dietary supplementation of acetate rescues learning in an ACSS2-dependent manner. Combining state-of-the-art proteomic and genomic approaches, we demonstrate that this effect is accompanied by ACSS2-dependent incorporation of acetate into hippocampal histone acetylation, which facilitates gene expression programs related to learning. We identify the most severely affected hippocampal neuronal populations, including pyramidal cells of the perforant pathway and Cajal-Retzius cells. Overall, these results reveal ACSS2 as a neuroprotective metabolic enzyme in key hippocampal neuronal populations, and dysregulation of which may play an important role in the etiology of AD. These findings may guide development of future therapies for AD, other tauopathies and related dementia.

overall_design: Contains H3K27ac ChIP-seq data (with matching input samples) obtained from male mice (dissected dorsal hippocampus) treated intracranially with either PBS or purified tau protein from human AD patient brains. Mice have either WT or ACSS2KO genetic background. The purpose of the study is to examine the interaction between the ACSS2 absence and the presence of pathological Tau, with a focus on memory. Four study groups are provided: PBS-WT, PBS-KO, Tau-WT, Tau-KO, with two biological replicates each for PBS-WT and PBS-KO and three biological replicates each for Tau-WT and Tau-KO.

first: Gabor

last: Egervari

first: Desi

last: Alexander

first: Hua

last: Huang

first: Greg

first: Connor

last: Hogan

first: Mariel

last: Mendoza

first: Hong

last: Xu

first: Virginia

last: Lee

first: Ben

middle: A

last: Garcia

first: Nancy

middle: M

last: Bonini

first: Shelley

middle: L

last: Berger


title: The single-cell transcriptome data of in vitro cultured cells isolated from porcine skeletal muscle.

city: Hwaseong

first: Kwang-Hwan

last: Choi

address: 10, Dongtan-daero 21-gil

department: R&D center

country: South Korea

institute: Space F corporation

summary: Porcine muscle-derived stem cells hold significant potential as a resource for both cellular agriculture and regenerative medicine. In this study, stem cells were isolated from porcine skeletal muscle tissue and cultured in vitro to investigate their transcriptional profiles using single-cell RNA sequencing (scRNA-seq). This high-resolution analysis revealed distinct subpopulations within the cultured cells and provided insights into the molecular dynamics of myogenic differentiation. The results highlight the heterogeneity of muscle stem cells during in vitro culture and identify key regulatory genes associated with various stages of myogenic commitment. These findings contribute to a deeper understanding of stem cell behavior under culture conditions and offer valuable data for optimizing expansion and differentiation protocols.

overall_design: The single-cell transcriptome profiling of in vitro cultured cells isolated from porcine skeletal muscle.

first: Ji Won

last: Yoon

first: Min-Jeong

last: An

first: Hojun

first: Byoung-Hoon

last: Kim


title: FMRP Regulates Neuronal RNA Granules Containing Stalled Ribosomes, Not Where Ribosomes Stall

city: Montreal

first: Senthilkumar

last: Kailasam

state: Quebec

address: 740 Dr. Penfield Avenue, #4200

department: Human Genetics

institute: McGill University

summary: Local protein synthesis is a crucial process that maintains synaptic proteostasis. Ribosomes stalled at elongation make up a sizable percentage of mRNAs translated in developing neurons. The protein lost in Fragile X syndrome (FMRP) is highly enriched in RNA granules containing stalled ribosomes, both of which play crucial roles in regulating forms of synaptic plasticity such as metabotropic glutamate receptor-dependent long-term depression (mGLUR-LTD). Previous examination of ribosome protected fragments (RPFs) from neuronal stalled ribosomes have identified motifs matching those found in mRNAs associated with FMRP, as recognized by FMRP cross-linking immunoprecipitation (CLIP) (Anadolu et al., 2023, Journal of Neuroscience doi: 10.1523/JNEUROSCI.1002-22.2023). To investigate if FMRP recognition of these sequences is important for determining where mRNAs are stalled, we examined stalled ribosomes RPFs isolated from P5 mice lacking the FMRP protein. We found that the loss of FMRP had no effect on the proteins associated with RNA granules, structure of the ribosomes and stalling sites, or where accumulations of RPFs occurred. However, there was a significant decrease in the amount of stalling on mRNAs previously shown to be associated with FMRP by cross-linking immunoprecipitation (CLIP). In addition, there was a decrease in the number of RNA granules containing stalled polysomes as assayed by ribopuromycylation in distal neurites and, unlike RNA granules in WT neurons, the remaining distal RNA granules were resistant to reactivation by stimuli that induce mGLuR-LTD. These results show important roles for FMRP in regulating RNA granules containing stalled ribosomes, but not in determining where ribosomes are stalled.

overall_design: Ribosome profiling of ribosomes from RNA Granules extracted through sucrose gradient sedimentation and RNA-seq samples of C57BL/6 and FMR1-KO mouse strains. Treatment condition: high Mg2+ (10mM) and high nuclease treatment (M-protocol ) vs. cellular level Mg2+ (2.5 mM) and normal level nuclease treatment.

first: Jewel

last: Li

first: Mehdi

last: Amiri

first: Jingyu

last: Sun

first: Nahum

last: Sonenberg

first: Joaquin

last: Ortega

first: Wayne

middle: S

last: Sossin


title: RNA-seq profiling of radioiodine-treated differentiated thyroid cancer cells reveals DDR pathway regulation during iodine tolerance

city: Shanghai

first: Xiaotong

last: Qiu

address: 301 yanchang road

institute: Tongji University school of medicine

summary: Aim: To investigate the role of ataxia-telangiectasia mutated (ATM) in thyroid cancer (TC) progression and radioactive iodine (RAI) resistance, exploring its potential as a therapeutic target. Methods: Single-cell RNA sequencing of 28 TC tumors / normal tissues traced ATM dynamics during dedifferentiation. Clinical validation used tissue microarrays (TMAs) on 89 RAI resistance (RAIR) and RAI-avid differentiated thyroid cancer (DTC) specimens. Preclinical models evaluated the synergy between the ATM inhibitor AZD1390 and RAI. Mechanistic studies employed RNA-seq, comet assays, cell cycle analysis, and AP site quantification. Results: scRNA-seq revealed progressive ATM upregulation during malignant progression, correlating with cell cycle dysregulation. TMAs confirmed elevated ATM expression in anaplastic thyroid cancer (ATC) vs. papillary thyroid cancer, PTC and RAIR tumors. In vivo, AZD1390 + 131I synergistically suppressed tumor growth and enhanced apoptosis. RAI predominantly induced apurinic/apyrimidinic (AP) sites rather than double-strand breaks (DSBs). ATM inhibition disrupted base excision repair (BER) coordination and G2/M checkpoint control, forcing cells with unresolved AP sites into mitotic catastrophe. Conclusion: ATM mediates RAIR in thyroid cancer by promoting AP site repair and inducing cell cycle arrest. Inhibiting ATM converts repairable damage into lethal DNA lesions, restoring RAI sensitivity, suggesting ATM as a therapeutic target for RAI-refractory thyroid cancer.

overall_design: RNA-seq profiling of differentiated thyroid cancer cells after radioiodine irradiation.

first: Yongji

last: Jiang

first: Simin

last: Liu

first: Li

last: Zhao

first: Chuanzi

last: Zuo

first: Yanlei

last: Huo

first: Chao

last: Ma


title: Multiomic single nuclei profiling of a mouse model of Alzheimer’s disease reveals that ACSS2 confers neuronal resilience to tauopathy [RNA-seq Acetate]

first: Gregory

last: Donahue

overall_design: Contains RNA-seq data obtained from male mice (dissected dorsal hippocampus) treated intracranially with either PBS or purified tau protein from human AD patient brains. Mice have been fed either a high acetate or control diet. The purpose of the study is to examine the interaction between elevated acetate and the presence of pathological Tau, with a focus on memory. Four study groups are provided: PBS-control, PBS-acetate, Tau-control, and Tau-acetate, with three biological replicates each. All samples were harvested on the same day and processed together.

first: Gabor

last: Egervari

first: Desi

last: Alexander

first: Hua

last: Huang

first: Greg

first: Connor

last: Hogan

first: Mariel

last: Mendoza

first: Hong

last: Xu

first: Virginia

last: Lee

first: Ben

last: Garcia

first: Nancy

last: Bonini

first: Shelley

last: Berger


title: The transcriptome data of in vitro cultured cells isolated from porcine skeletal muscle

first: Kwang-Hwan

last: Choi

summary: Porcine muscle-derived stem cells hold significant potential as a resource for both cellular agriculture and regenerative medicine. In this study, stem cells were isolated from porcine skeletal muscle tissue and cultured in vitro to investigate their transcriptional profiles using bulk RNA sequencing. This transcriptomic analysis provided an overview of gene expression changes during myogenic differentiation under culture conditions. The results revealed dynamic shifts in gene expression patterns over time and identified key regulatory genes associated with various stages of myogenic commitment. These findings contribute to a deeper understanding of stem cell behavior in vitro and offer valuable data for optimizing expansion and differentiation protocols.

overall_design: The transcriptome profiling of in vitro cultured cells isolated from porcine skeletal muscle.

first: Ji Won

last: Yoon

first: Min-Jeong

last: An

first: Dong-Kyung

first: Byoung-Hoon

last: Kim


title: Developmental Dynamics of Skeletal Muscle Can Be Recapitulated In Vitro from Pig Embryonic Stem Cells

city: Seoul

first: Jinsol

last: Jeong

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: Understanding skeletal muscle development in pigs is required for fundamental developmental biology and its application in biomedical and agricultural industries. Here, we employed a directed myogenic differentiation approach to guide pig embryonic stem cells (ESCs) through presomitic mesoderm (PSM) and somite (SM) stages, ultimately generating myogenic progenitors (MPs) and mature muscle cells. The core signaling pathways, including WNT/β-catenin and BMP, along with several growth factors, were involved in sequential myogenic lineage induction in pigs. During differentiation, single-cell RNA sequencing revealed stage-specific transcriptional dynamics with three distinct ‘Myogenic states’, reflecting the in vivo developmental trajectory: PSM progenitors commitment into posterior PSM, posterior PSM transitioning into anterior PSM, and anterior PSM/SM giving rise to dermomyotome/muscle cells. These findings provide a comprehensive in vitro roadmap of pig skeletal muscle development, advancing developmental biology and biotechnology in livestock.

overall_design: The single cell transcriptomic profiling of undifferentiated pig embryonic stem cells and pig embryonic stem cell-derived cells at days 8, 12, 20, and 25 of directed myogenic differentiation was constructed using single cell RNA sequencing.

first: Chang-Kyu


title: The cistrome response to hypoxia in human umbilical vein endothelial cells

city: Tallahassee

first: Ayush

last: Singh

state: Florida

address: 319 Stadium Dr,

department: Department of Biological Science

institute: Flordia State University

summary: The primary goal of this study was to achieve a comprehensive, high-resolution understanding of how human umbilical vein endothelial cells (HUVECs) remodel their chromatin landscape in response to hypoxic stress. While it is well established that hypoxia-inducible factors (HIFs) play a pivotal role in activating hypoxia-responsive genes, the discovery that only a small fraction of known hypoxia response elements (HREs) is bound by HIFs under low-oxygen conditions suggests the involvement of additional, complementary regulatory factors. To investigate these putative co-regulatory elements, we adapted and applied a recently developed technique, MOA-seq (MNase-defined cistrome-Occupancy Analysis), which excels at identifying genome-wide, protein-occupied loci (MOA footprints) with approximately 30-bp resolution. By profiling small MNase-sensitive footprints, MOA-seq offers an orthogonal and more precise view of transcription factor (TF) occupancy compared to traditional methods like ChIP-seq or ATAC-seq. Through a time-course analysis (1, 3, and 24 hours of hypoxia), we generated a "cistrome atlas" of MOA footprints for more than 5,000 candidate regulatory regions undergoing hypoxia-induced changes. Our approach not only recapitulated canonical hypoxia-regulated pathways but also uncovered novel sites and TF motifs that do not co-localize with HIF-binding motifs. These high-resolution footprints revealed new potential avenues for understanding how endothelial cells respond to low-oxygen environments, beyond the classic HIF-centric paradigm. Critically, such a broad scope of regulation underscores the complexity of vascular remodeling, oxidative stress responses, and angiogenic signaling processes vital to both normal physiological adaptation and the development of pathologies such as cancer, atherosclerosis, and other hypoxia-linked conditions. By integrating MOA-seq TF occupancy profiling with differential gene expression analyses, we are expanding the toolkit for dissecting gene regulatory networks over time. This insight has far-reaching implications: the newly uncovered regulatory elements may serve as potential therapeutic targets or biomarkers for diseases where hypoxia is a key driver. Moreover, the single-assay simplicity of MOA-seq provides a scalable strategy for profiling diverse cellular contexts, adding value to fundamental research and translational applications.

overall_design: MOA-seq profiling of human umbilical vein endothelial cells (HUVECs) after 0, 1, 3, and 24 hours of hypoxia exposure.

first: Viktor

last: Pastukh

first: Justin

last: Roberts

first: Zachary

last: Turpin

first: Zehta

last: Glover

first: Grant

middle: T

last: Daly

first: Jane

last: Benoit

first: Mark

middle: N

last: Gillespie

first: Hank

middle: W

last: Bass


title: GH-resistant (Laron) mice: gene therapy with a liver-specific GH receptor causes unbalanced upregulation of female-biased and growth-related genes

first: Kian Chuan

last: Sia

address: MD11, Basement 1, 10 Medical Drive, Singapore 117597

institute: Department of Surgery, National University of Singapore

summary: Growth hormone (GH) receptor (GHR) mutations give rise to GH-resistance (Laron syndrome). We previously treated GH-resistant Ghr-/- mice (Laron mice) with adeno-associated virus (AAV) delivering mouse (m)Ghr controlled by a constitutively active liver-specific promoter (HLP). A single injection of AAV-HLP-mGHR resulted in a significant but limited increase in body length and weight, consistent with studies of IGF-1 treatment in humans and mice. Here, we performed RNA-seq on male and female mouse livers comprising the following groups: GHR+/+ (wild-type), GHR-/- (Laron), AAV-HLP-mGHR-treated GHR-/- (treatment group), and AAV-HLP-Luc (Luciferase)-treated GHR-/- (control group). Only four genes showed significant differential expression in GHR -/- mouse liver following Luciferase vector treatment, indicating minimal effect of the AAV-HLP vector. AAV-HLP-mGHR stimulated significant expression changes in 448 genes compared to AAV-HLP-Luc control, substantially fewer than the 2781 genes whose expression was altered in GHR-/- compared to GHR+/+. AAV-HLP-mGHR treatment induced the GH-responsive IGF signaling genes Igf1 and Igfals ~16-fold compared to AAV-HLP-Luc control, but only to 40–45% of GHR+/+ liver levels. The treatment also upregulated a small subset of genes beyond GHR+/+ expression levels (p-adj < 0.05), including the proto-oncogenes Ascl1, Tmprss4, and others. Finally, genes dysregulated upon GHR loss and upregulated in livers of AAV-HLP-mGHR-treated mice were significantly enriched for sex-biased genes, consistent with the major role of GH and GHR in regulating liver sex differences. While gene replacement therapy is a potential therapy for Laron syndrome, an unregulated constitutively active promoter may drive unexpected and unbalanced changes in liver gene expression that will require monitoring.

overall_design: RNA-seq profiling of liver tissues from untreated GHR+/+ (wild-type) mice and GHR−/− (Laron) mice, as well as GHR−/− mice treated with AAV-HLP-mGHR (mouse growth hormone receptor) and control GHR−/− mice treated with AAV-HLP-Luciferase (AAV-HLP-Luc). See Sia et al., 2022 (PMID: 35105948) for further details.

first: Joshua

middle: K

last: Tay

first: Kian

middle: C

first: Siti Humairah

last: Mohd Rodhi

first: Shu

middle: U

last: Gan

first: Zhen

middle: Y

last: Fu

first: Maxim

last: Pyatkov

first: John

last: Kopchick

first: Michael

last: Waters

first: David

last: Waxman

first: Kok

middle: O

last: Lee


title: JAB1/CRL4B Complex Represses PPARG/ACSL5 Expression to Promote Breast Tumorigenesis

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

summary: Fatty acid metabolism is critical for tumor progression, supplying bioenergetic and biosynthetic substrates to rapidly proliferating cancer cells. However, the precise mechanisms by which fatty acid metabolism influences breast cancer progression remain unclear. In this study, we aimed to explore the molecular mechanism by which JAB1 promotes breast cancer progression through regulating fatty acid metabolism. Our results shows that C-Jun activation domain-binding protein-1 (JAB1) is identified as an oncogene in breast cancer. JAB1 stabilizes CUL4B expression via deubiquitination, thereby promoting cell proliferation, invasion, and stemness. Mechanistically, JAB1 forms a transcriptional repressor complex with the Cullin 4B-Ring E3 ligase (CRL4B) complex, and co-occupy on the promoters of key fatty acid metabolism genes, PPARG and ACSL5, thus leading to their transcriptional repression. This disrupts fatty acid metabolism, increases mitochondrial oxygen consumption, and provide the energetic demands  to breast cancer cells. Notably, JAB1 inhibition reverses chemotherapy resistance associated with CUL4B overexpression. These findings underscore the pivotal role of JAB1 in regulating breast cancer progression and indicate that JAB1 inhibitors could serve as promising therapeutics for patients with the elevated CUL4B expression.

overall_design: RNA-seq analysis of MDA-MB-231 cells transfected with siNC and siJAB1.

first: Ting

last: Hu

first: Yan

last: Wang


title: Effect of RS2Z35 and RS2Z36 single and double knockout on gene expression and splicing during control and heat stress conditions in tomato (Solanum Lycopersicum) leaf tissue [ovaries]

city: Frankfurt am Main

first: Remus

middle: Richard Elrik

last: Rosenkranz

address: Max-von-Laue-Str. 9

institute: Goethe University Frankfurt

summary:
To investigate the role of Serine/Arginine-rich protein RS2Z36 in tomato fruit development, we established a single knockout in tomato and performed RNA-Seq on ovaries (2 days post-anthesis)
We then performed gene expression analysis using data obtained from RNA-seq.

overall_design: Differential gene expression analysis of RNA-seq data conducted in ovaries of RS2Z36 protein knockout plants compared to WT (Solanum lycopersicum). Ovaries were 2 days post-anthesis, 3 replicates per line consisting of 10-15 ovaries each

middle: R

first: Sotirios

last: Fragkostefanakis


title: Exploring the role of macrophage marker CD68 in pediatric acute myeloid leukemia

city: Gent

first: Laurens

last: Van Camp

address: C. Heymanslaan 10

institute: Ghent University

summary: Pediatric acute myeloid leukemia (pedAML) is a childhood malignancy with relapse rates of approximately 30%. CD68, a macrophage marker involved in phagocytosis and macrophage recruitment, may contribute to AML biology. We analyzed CD68 expression using the TARGET database and performed survival analyses, mRNA/protein profiling, and functional assays in AML cell lines, pedAML samples, and cord blood samples. High CD68 transcript levels correlated with KMT2A-rearrangements and inversion 16. Survival analysis showed that high CD68 predicted worse event-free survival, though not independently in a multivariate analysis. Flow cytometry confirmed higher CD68 expression in 7/8 pedAML samples compared to cord blood samples. Functionally, CD68 knockdown reduced proliferation and increased drug sensitivity, while overexpression promoted growth and resistance. Gene set enrichment analysis (GSEA) indicated enrichment of MAPK signaling, AP-1-mediated stress response, and epithelial-mesenchymal transition (EMT)/migration-associated pathways in CD68-high models. Together, these findings suggest that CD68 contributes to a pro-tumorigenic and stress-adaptive phenotype in pedAML and may represent a biologically relevant therapeutic target.

overall_design: Knockdown and overexpression of CD68 in THP-1 and MOLM-13, and in HL-60 and KASUMI-1 cell lines, respectively.

first: Jolien

last: Vanhooren

first: Barbara

last: Depreter

first: Mattias

last: Hofmans

first: Inge

last: D'Hont

first: Christophe

last: Chantrain

first: Laurence

last: Dedeken

first: An

last: Van Damme

first: Anne

last: Uyttebroeck

first: Tim

last: Lammens

last: De Moerloose


title: Astrocyte molecular changes during basolateral amygdala-related emotional behaviors [set4]

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: Astrocytes tile the central nervous system (CNS) and have fundamental roles in physiology and disease, yet there remain open questions about their contributions to physiological and pathological processes in the CNS. The basolateral amygdala (BLA) integrates rewarding and aversive stimuli and is integral to mood regulation and emotional behaviors. As many past studies have focused on neurons in the BLA, the contribution of BLA astrocytes to emotional behaviors is largely unknown. A major bottleneck has been the paucity of reliable tools to explore astrocyte functions and molecular mechanisms in vivo. This shortfall has been addressed by recent developments in the field reporting approaches to systematically explore the role of astrocytes with improved tools. Here, we used several such tools to elucidate BLA astrocytic changes during emotional behavioral responses. Applying several mouse models of stress (negative emotional triggers) and astrocyte-specific adenoassociated viruses (AAVs), [Ca2+] imaging, RNA sequencing, and proteomics, we explored the role of astrocytes at the molecular and cellular level in the BLA. We analyzed the data to evaluate how astrocytes might be exploited in vivo to improve behavioral outcomes in emotion-related disorders such as anxiety and depression.

overall_design: Tissue from the mouse basolateral amygdala (BLA) was dissected from 16 adult male and female Aldh1l1-Cre/ERT2 x Ribotag mice (4 mice were pooled by sample). Samples from the hippocampus, striatum and somatosensory ortex were also collected to integrate  the amygdala data into the prious 13 CNS regions dataset (GSE198024) via batch-correction. After homogenization, RNA was purified from cleared lysate as the input and control, and astrocyte-specific ribosome-associated RNA was precipitated via a hemagglutinin (HA) tag. t

first: Sara

middle: G

last: Pelaz

first: Katsu

last: Mitsui

first: Fuying

last: Gao

first: Bal

last: Khakh


title: Astrocyte molecular changes during basolateral amygdala-related emotional behaviors [set2]


title: Astrocyte molecular changes during basolateral amygdala-related emotional behaviors [set3]


title: Astrocyte molecular changes during basolateral amygdala-related emotional behaviors [set1]


title: Astrocyte molecular changes during basolateral amygdala-related emotional behaviors

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

overall_design: Refer to individual Series


title: Developmental functions of rapgef1b in neural crest specification and presomitic mesoderm patterning

city: Hyderabad

first: Megha

last: Kumar

address: F202, Zebrafish facility, CSIR CCMB , HABSIGUDA

country: India

institute: CSIR-CCMB

summary: Rapgef1, a cell fate determinant and effector of multiple signaling events is essential for mammalian embryonic development. Here, we investigated the developmental role of rapgef1 using zebrafish as a model. We show that rapgef1 is maternally expressed and alternately spliced isoforms of its two paralogs, rapgef1a and rapgef1b show development and tissue-specific expression. CRISPR-Cas9 and morpholino-based targeting of rapgef1b resulted in developmental defects in the embryonic brain and somites. The rapgef1b morphants showed altered expression of lineage determinants of the cranial neural crest. Comparative transcriptome and altered expression analysis of morphants revealed fresh insights into the developmental functions of rapgef1b in presomitic mesoderm, and somitogenesis. During early embryonic mitoses, the morphants showed mitotic defects such as diffused spindle poles and chromosome mis-congression. Our results demonstrate that rapgef1b is required for normal embryonic mitoses, cranial neural crest specification, somitogenesis, and myogenesis during embryonic development.

overall_design: RNA seq gene expression profiles of 1dpf control (WT) and rapgef1b KD zebrafish embryos. Three replicates of control and rapgef1b KD samples.

first: Tuhina

last: Prasad

first: Sharada

last: Iyer

first: Sian

last: D'Silva

first: Reuben

last: Mathew

first: Divya

last: Sowpati

first: Vegesna

last: Radha


title: Distinct differentiation trajectories leave lasting impacts on gene regulation and function of V2a neurons [Bulk RNA-seq]

city: San Francisco

first: Faranak

last: Fattahi

department: Cellular and Molecular Pharmacology

institute: University of California San Francisco

summary: In development, early regionalization steps segregate populations of cells and direct them to specific cell fates. In some instances, this process separates populations of progenitors which eventually become analogous cell types. V2a neurons are a population of excitatory interneurons which are found throughout the hindbrain and spinal cord, two regions of the CNS that arise from different progenitors in development. Plasticity in the V2a population after spinal cord injury has increased interest in this population as a therapeutic target. We therefore set out to examine how progenitor lineage influences V2a gene regulation and ultimately function. To do so, we differentiated V2a neurons from human stem cells via two distinct progenitor populations. Single nucleus multiomic analysis showed that different V2a lineages were enriched for different transcription factor motifs and differentially expressed hundreds of genes relevant to neuron function, such as axon growth and calcium handling. Attempting to ‘skip’ developmental patterning by induced transcription factor expression yielded a population unlike either developmentally relevant population, highlighting the importance of following developmental steps in establishing cell identities in vitro. Lastly, we employed the CellOracle tool and lentiviral knockdown to perturb lineage-specific gene regulatory networks and identify CREB5 and TCF7L2 as regulators unique to a spinal-like lineage. Overall, this work highlights how small differences in differentiation protocols can influence mature cell fate and uncovers new regulators of neural diversity along the anterior-posterior axis of the central nervous system.

overall_design: Human pluripotent stem cells were transfected with lentiviral shRNA constructs and purified before before being differentiated  to V2a neurons to examine the effect of target gene knockdown on mature neuron transcriptional regulation. We compared differentiation conditions through either neuroectodermal progenitors (NEP) or neuromesodermal progenitors (NMP) before identically differentiating to mature neurons. Cultures underwent a second round of selection between days 7 and 9 to ensure the shRNA construct had not been silenced. At day 19, whole RNA samples were collected using QIAspin RNeasy Plus Miniprep Kit and sampled using a Mercurius High Sensitivity BRBseq Kit.

first: Fattahi

last: Faranak

first: Elder

last: Nicholas


title: Distinct differentiation trajectories leave lasting impacts on gene regulation and function of V2a neurons [multiome_scATAC-seq]

overall_design: Human pluripotent stem cells were differentiated to V2a neurons to examine the effect of early progenitor lineage on mature neuron regulation. We compared differentiation conditions that included transit through neuroectodermal progenitors (NEP), neuromesodermal progenitors (NMP), or via direct induction of transcription factors NGN2 and LHX3 (IND).  NEP and NMP neurons were collected at day 19, while IND neurons were collected at day 4 and 10 post induction. All samples were cryopreserved prior to nuclei extraction for 10X Genomics Multiome.

first: Nicholas

last: Elder


title: Effect of miR-4800-3p overexpression on gene expression related to metastasis in pancreatic cancer cell lines (MIA PaCa-2 and PSN-1)

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

summary: Understanding the molecular characteristics of pancreatic cancer liver metastases is essential for advancing individualized treatment strategies. This study identifies miR-4800-3p as a potential contributor to liver metastasis. miR-4800-3p appears to promote liver metastasis by directly targeting PLAA, inhibiting ubiquitination, and stabilizing METTL3 protein. This process enhances the expression of the oncogene GPRC5A, potentially driving metastatic progression.

overall_design: To identify the target mRNA of miR-4800-3p, MIA PaCa-2 and PSN-1 cell lines were established and transfected with either miR-4800-3p mimics or negative control (scramble) oligonucleotides. Gene expression profiling was performed using RNA-seq data obtained from these two cell lines. A comparative analysis of the RNA-seq data was conducted to evaluate gene expression profiles between miR-4800-3p-transfected cells and scramble controls.

first: Satoru

last: Miyahara

first: Yoshito

last: Tomimaru

first: Hidenori

last: Takahashi

first: Hidetoshi

last: Eguchi


title: Distinct differentiation trajectories leave lasting impacts on gene regulation and function of V2a neurons


title: Distinct differentiation trajectories leave lasting impacts on gene regulation and function of V2a neurons [snRNA-seq]


title: Transcriptome analysis of cell line/patient-derived xenograft (PDX) samples of myeloid leukemia associated with Down syndrome (ML-DS)

city: Wilmington

first: Anilkumar

last: Gopalakrishnapillai

state: DE

address: 200 Powder Mill road

institute: Nemours Children's Health

summary: Myeloid leukemia associated with Down syndrome (ML-DS) is a rare pediatric cancer in which 10-20% patients who are relapsed/refractory have very limited treatment options. Novel treatment options may be identified via transcriptome profiling.

overall_design: Transcriptome profiles in ML-DS cell line/PDX models in comparison with human bone marrow-derived CD34+ cells

first: Sonali

middle: P

last: Barwe

first: Meredith

last: Tavenner

first: Aimy

last: Sebastian

first: E

last: Kolb

first: Yana

last: Pikman

first: Johann

last: Hitzler


title: Changes in gene expression between larvae and adult mosquitoes collected from different locations in Eastern India

city: Columbia

first: SUSANTA

last: BEHURA

state: MO

address: 920 East Campus Dr

institute: University of Missouri

summary: In this study, gene expression and splice variants were analyzed in Aedes aegypti larvae and adults collected at differen locations in Eastern India.

overall_design: Aedes aegypti larvae and adults were collected from three locations. Total RNA were extracted from pooled mosquitoes (n=10) from each locations, so total 6 samples (3 locations x 2 developmental stages) were generated. They were used for RNA sequencing.

first: Biswadeep

last: Dash

first: Susanta

last: Behura


title: Dual Roles of Melatonin in Rescuing Inflammation-caused Cell Mitochondrial Dysfunction and Cementoblastic Differentiation

city: Xi'an

first: Xuan

last: Li

address: 145, Changlexi Road

institute: School of Stomatology, Fourth Military Medical University

summary: Inflammation-induced mitochondrial dysfunction functionally impairs periodontal ligament stem cells (PDLSCs) and hinders their therapeutic efficacy for periodontal regeneration. Melatonin, a mitochondrion-targeted molecule, is considered a promising  anti-inflammatory agent in therapeutics, but whether melatonin protects PDLSC cementoblastic differentiation against inflammation-induced damage and the underlying molecular mechanisms remain unclear. In this study, we confirmed that melatonin rescued PDLSC cementoblastic dysfunction across an inflammatory environment, and the melatonin-induced recovery was linked to the ameliorated mitochondrial function of the treated PDLSCs. Next, an interaction between LINC01444 and HSPD1 was identified as a mechanism mediating such melatonin-caused mitochondrial changes in terms of lncRNA microarray analysis, mass spectrometry and functional studies. In this context, suppressing LINC01444 was found to increase the total and cytoplasmic expression of HSPD1 protein, and in turn, the cell mitochondria function was ameliorated. We further revealed another route where melatonin was able to inhibit m6A modification of LINC01444 (mediated by METTL3 and IGF2BP2), thereby the stability and expression of LINC01444 were largely decreased. Our data indicate that LINC01444 is a key target involved in melatonin-rescued cell mitochondrial function and cementoblastic differentiation, wherein melatonin not only prevents LINC01444 from interacting with HSPD1 to exert its damage to PDLSCs, but also inhibits LINC01444 from modifying by m6A to maintain its stability and expression.

overall_design: PDLSCs were Cultured in Cementoblastic Medium with Inflammatory Cytokines (Infla), or Cementoblastic Medium with Inflammatory Cytokines Plus Melatonin (Infla + Mel).

first: Bei-Min

last: Tian

first: Yuan

last: Yin

first: Xiao-Tao

last: He

first: Fa-Ming

last: Chen


title: Total RNA expression in mouse heart tissues after injections of VEGFA-containing extracellular vessicle, lipidnanoparticles and naked-VEGFA mRNA

city: Skövde

first: Jane

last: Synnergren

address: Högskolevägen 1

country: Sweden

institute: University of Skövde

summary: The study used the next-generation sequencing to compare mRNA content of mouse heart tissue after direct injection of different VEGFA-containining extracellular vesicles (EVs), lipidnanoparticles (LNPs) or naked VEGFA-mRNA to untreated control. The EVs used were originated from human  lung epithelial (HTB), umbilical vein endothelial (HUVEC), or cardiac progenitor cells (CPCs) in which the cells were treated with LNPs containing VEGFA prior to the collection of EVs, fractions of the VEGFA-mRNA ended up in the EVs. Our goal is to carry out functional and pathway analysis of the differentially expressed genes. The RNA profiles of EV content from heart tissues were generated by RNA-Seq using Illumina NovaSeq6000. Differentially expressed genes were identified using the DESeq2 package. We found that the VEGFA mRNA was among the most upregulated genes in the injected hearts.  We also identified multiple genes and pathways that are significantly associated with angiogenesis and cardiac conditions. Inflamatory response genes and pathways were upregulated by the LNPs and naked-mRNA injection to a greater extend compared to EV injection. The result suggested that the injection of EVs caused less transcriptional changes in the heart tissue.

overall_design: mRNA profiles of heart tissues from mice after being injected with HTB-EVs (n = 3), HUVEC EVs (n =3), CPC-EVs (n = 3), VEGFA-LNPs (n = 3). Untreated mice (n = 3) were used as control

first: Muhammad

last: Nawaz

first: Sepideh

last: Heydarkhan-Hagvall

first: Benyapa

last: Tangruksa

first: Franziska

last: Kohl

first: Hernán

last: González-King Garibotti

first: Yujia

last: Jing

first: Abdel

last: Bidar

first: Karin

last: Jennbacken

first: John

last: Wisemen

first: Leif

last: Hultin

first: Lennart

last: Lindfors

first: Hadi

last: Valadi


title: chromatin landscape and transciptome regulated by RBBP4/p300 complex in glioblastoma

city: Austin

first: Gaspar

last: Kitange

address: 16th Avenue NE

institute: University of Minnesota


title: ZNF512B Safeguards Genome Integrity at Regulatory Regions to Repress SASP and Inflammation

city: Odense M

first: Sanjeeb

middle: Kumar

last: Sahu

address: CAMPUSVEJ 55

department: Department of Molecular Medicine

country: Denmark

institute: University of Southern Denmark

summary: Cellular senescence drives aging and disease largely through the senescence-associated secretory phenotype (SASP), yet its regulatory mechanisms remain unclear. Using a SASP reporter combined with a CRISPR-Cas9 screen targeting active regulatory elements, we identify the zinc finger protein ZNF512B as a key suppressor of SASP. ZNF512B loss induces DNA damage, activates cGAS-STING signaling, and triggers inflammatory transcriptional reprogramming. In contrast, ZNF512B promotes preferential DNA repair at regulatory genomic regions, limiting SASP induction. Mechanistically, ZNF512B is rapidly recruited to DNA damage sites via distinct zinc finger domains and facilitates NuRD complex targeting to damaged chromatin, enabling precise repair. In human neuromuscular organoids, ZNF512B deficiency induces inflammation, lineage imbalance, and cytokine secretion resembling ALS-associated pathology. In vivo, ZNF512B overexpression reduces DNA damage and inflammation following acute liver injury. Together, these findings support a mechanism of preferential DNA repair that contributes to maintaining genome integrity to suppress SASP and inflammation.


title: Defining transcripts regulated by RBBP4/p300 complex in glioblastoma [RNA-seq]

summary: Purpose: Next-generation sequencing (NGS) has revolutionized the ability to conduct genome wide transcriptional regulation. The goals of this study was to identify potential genes regulated by RBBP4/p300 complex by comparing transcriptome profiling (RNA-seq) generated in GBM43 expressing control non-targeting shRNA with cells expressing shRNA targeting RBBP4 or p300. Commonly downregulated and upregulated genes by both shRBBP4 and shp300 were considered to potentially be regulated by RBBP4/p300 complex.

overall_design: RNAseq was conducted using RNA extracted from GBM43shNT, GBM43shRBBP4 and GBM43shp300

middle: J

first: Jann

last: Sarkaria


title: Mapping chromatin landscape regulated by RBBP4/p300 complex in glioblastoma  [ChIP-seq]

summary: We report the application of ChIPseq to map the chromatin landscape associated with RBBP4/p300 complex in glioblastoma. For this, we performed RBBP4 and p300 specific ChIP followed by sequencing in GBM44 and 154 and identified regions co-occupied by  RBBP4 and p300. We also used H3K9ac and H3K27Ac to map the potential promoters and/or enhancers controlled by histone acetylation mediated through RBBP4/p300 comolex.

overall_design: ChIPseq was conducted using antibodies against RBBP4 and p300 (GBM44 and GBM154); H3K9Ac and H3K27Ac in GBM43 expressing control shRNA and cells expressing shRBBP4 or shp300.


title: A Pseudomonas aeruginosa LysR-type transcriptional regulator, PA3321, essential for productive biofilm and influences virulence and pathogenesis [ChIP-seq]

status: Public on Jun 17 2026

city: Honolulu

first: Hung

last: Vo

state: Hawaii

address: 1800 East-West Road Life Sciences Building, Rm 318

department: Microbiology

institute: University of Hawaii at Manoa

summary: The transposon insertion mutation of regulator PA3321 (PA3321∷Tn) significantly reduced biofilm formation, while enhancing virulence in Drosophila melanogaster fruit fly and BALB/C mouse infection models. This regulator influenced bacterial motility, c-di-GMP signaling, and the RhlI-RhlR and Pseudomonas quinolone signal (PQS) quorum-sensing (QS) systems. We used  RNA-seq assays to identify the regulatory mechanisms of PA3321. We observed that 391 genes were up-regulated and 114 genes were down-regulated in the absence of PA3321, many of which are involved in rhamnolipid synthesis, type II, type III, and type VI secretion systems, and QS systems.

overall_design: The ChIP-seq assays were performed as previously described. Briefly, the regulator mutant strain PA3321∷Tn containing IPlac-3xTY1-PA3321 was grown and induced by isopropyl β-D-1-thiogalactopyranoside (IPTG) (0.25 mM) in LB at 30 °C for 48h without shaking. After induction, bacterial cells were cross-linked with paraformaldehyde, harvested, and lysed by freezing and thawing. Supernatants containing the DNA-regulator complexes were sheared to an average size of 100–500 bp in a Roche® nebulizer. The TY1-tagged PA3321 regulator bound to its regulated DNA region/fragment was enriched and captured using TY1 mouse monoclonal antibody and DiaMag® anti-mouse IgG-coated magnetic beads (Diagenode®), respectively. Captured DNA-regulator complexes were reversed cross-linked and purified using the QIAquick PCR Purification Kit (QIAGEN). Purified DNA fragments were used as a template for library construction according to the Illumina ChIP-seq sample preparation protocol and sequenced at TUCF Genomics, where DNA libraries were prepped and 50 bp single-end reads were sequenced with the Illumina HiSeq 2,500. ChIP-seq data were aligned to the Pa wt PA01 genome with Bowtie2, peaks called with MACS2, and consensus binding regions determined with MEME.

first: Yun

last: Heacock-Kang

first: Jan

last: Zarzycki-Siek

first: Ian

last: A. McMillan

first: Tung

last: Hoang


title: High-resolution transcriptome analysis reveals a multilayered and dynamic transcriptional architecture in the archaeal virus SSV1

city: Brussels

first: Wouter

last: Magnus

address: Pleinlaan 2

institute: Vrije Universiteit Brussel

summary: Fuselloviridae infecting thermoacidophilic Sulfolobales are among the best-studied archaeal viruses, with the Saccharolobus Spindle Shaped Virus 1 (SSV1)-Saccharolobus solfataricus interaction serving as a model system. After infection, SSV1 establishes a chronic infection with new virions continuously budding from the infected cell. UV irradiation triggers virus replication, increased virion production and a tightly orchestrated temporal transcription cycle. However, gene regulatory mechanisms post-UV-induction remain elusive. In this study, we investigated the SSV1 transcriptomic landscape post-UV-induction using high-resolution, long-read ONT-cappable-RNA-sequencing. Through end-to-end sequencing of primary transcripts, we generated a comprehensive transcript map of SSV1, identifying 21 transcription start sites (TSSs), including 12 newly described sites, and 19 termination sites (TTSs), of which 9 are novel. This enabled refinement of transcription units and operon structures across the genome. Five new antisense RNAs were discovered, including one encoded antisense to the open reading frame of a putative viral toxin gene a291, which we hypothesize to be a cis-encoded regulatory RNA. In addition, spontaneous recombination between two direct repeats in the SSV1 structural genes vp1 and vp3 was confirmed. To our knowledge, this is the first implementation of cappable-seq for an archaeal virus, and the first base-resolution analysis of the SSV1 transcriptome. It reveals a previously unappreciated level of transcriptional complexity, illustrating how high-resolution transcriptomics can deepen understanding of viral transcriptome architecture and regulatory networks.

sample_organism:
Saccharolobus solfataricus
Sulfolobus spindle-shaped virus 1

overall_design: ONT-cappable-sequencing of SSV1-infected S. solfataricus S441 in both non-induced carrier state and at various time points post-UV-induction

first: Maarten

last: Boon

first: Jorien

last: Poppeliers

first: Jonathan

last: Abshier

first: Kenneth

last: Stedman

first: Rob

last: Lavigne

first: Eveline

last: Peeters


title: RNA sequencing of vtRNA-knockout HEK293T cell lines

city: Boulder

first: Wayne

last: Hemphill

state: Colorado

address: 3415 Colorado Ave

department: Biochemistry

institute: University of Colorado Boulder

summary: HEK293T cell lines lacking one or more of the human VTRNA1 paralogs, alongside wild-type parental cells, had their RNA sequenced by Plasmidsaurus (poly-A enrichment) and/or Genewiz (rRNA depletion). Differential expression was performed to determine transcriptomic effects of vtRNA knockout, as well as to compare the two sequencing approaches.

overall_design: Wild-type (WT), genetically edited control (CTRL), or vtRNA knockout (KO) HEK293T cells were grown under standard conditions, their total RNA isolated, then their RNA samples submitted to Plasmidsaurus and/or Genewiz for poly-A enrichment and rRNA depletion RNA sequencing, respectively.

first: Thomas

last: Cech


title: Continuous evolution of gene libraries towards arbitrary functions reveals the versatility of biomolecular evolution in vivo

city: Irvine

first: Alireza

last: Tanoori

address: 419 South Circle View Dr.

institute: University of California, Irvine

summary: Life relies on constant biomolecular innovation, but the slowness of natural evolution limits our ability to witness new gene functions emerging in real-time. Consequently, much remains unknown about how – and how easily – functional biomolecules originate and evolve. To address this gap, we encoded diverse gene libraries (e.g., open reading frames from Saccharomyces cerevisiae and Escherichia coli) onto an orthogonal DNA replication (OrthoRep) system and exposed the resulting continuously hypermutating genetic repertoires to a multitude of complex selection pressures in vivo. This experimental template mimics the “multi-gene, multi-objective” possibility landscape of natural evolution, but at drastically accelerated evolutionary speed. In only ~100 generations (~1 month), populations evolved an abundance of novel gene functions when challenged with diverse pressures including vitamin deficiency, metal toxicity, promoter inactivity, and protein degradation. Notably, several evolved outcomes originated from sequences with no initial effect on fitness, demonstrating both emergence and evolution of biomolecular function. Evolved outcomes proved highly potent, typically increasing fitness by several-fold under selection. Evolved genes spanned a range of molecular functions including de novo metal binding, transcription factor activity, and modulation of protein degradation, as supported by biochemical and RNA-seq experiments. Overall, our findings show that novel gene functions can originate with surprising ease in cellular contexts and motivate further continuous evolution experiments that agnostically explore the fertility of sequence space in vivo.

overall_design: RNA-seq data of yeast cells overexpressing various evolved transgenes or a nonsense control in non-selective (adenine-rich) and selective (low adenine) media

first: Alexander

last: Pisera

first: Chang

last: Liu


title: Alternative splicing generates a constitutively active Fn14 isoform that signals independently of TWEAK

city: Perth

first: Nathan

middle: Michael

last: Main

state: WA

address: 305, Bentley WA 6102

country: Australia

institute: Curtin Medical Research Institute

summary: Fibroblast growth factor-inducible 14 (Fn14) is a tumour necrosis factor (TNF) receptor family member and therapeutic target in cancer and inflammatory disease. However, clinical strategies aimed at blocking its activation by preventing engagement with its ligand TNF-like weak inducer of apoptosis (TWEAK) have demonstrated limited efficacy, suggesting alternative mechanisms of Fn14 activation. Here, we identified Fn14β, a novel Fn14 isoform, encoded by the alternatively spliced transcript TNFRSF12A-202. Transcriptomic analyses showed that TNFRSF12A-202 is expressed across human tissues and liver disease contexts, localises to fibrotic regions in vivo, and is associated with reduced overall survival in hepatocellular carcinoma. Structural modelling predicted that Fn14β lacks the extracellular TWEAK-binding domain while retaining the intracellular TRAF-binding signalling domain. CRISPR/Cas9-mediated selective ablation of the canonical Fn14 isoform demonstrated that endogenous Fn14β is expressed and sufficient to drive downstream transcriptional programmes shared with canonical Fn14a. Functional analyses further showed that Fn14β activates NF-κB signalling and promotes proliferation independently of TWEAK. Together, these findings identified Fn14β as a novel constitutively active, TWEAK-independent Fn14 isoform and provided a mechanistic basis for ligand-independent Fn14 signalling, with implications for therapeutic strategies targeting the TWEAK/Fn14 pathway.

overall_design: RNA-seq was performed to compare gene expression profiles in wild-type LX-2 cells, recombinant human TWEAK-treated wild-type LX-2 cells, CRISPR/Cas9-derived Fn14α knockout LX-2 cells, and CRISPR/Cas9-derived total Fn14 knockout LX-2 cells, with four biological replicates per group.

middle: M

first: Melissa

last: Eccles

first: Rodrigo

last: Carlessi

first: Sara

last: Pasic

first: Giuseppe

last: Verdile

first: Grant

middle: A

last: Ramm

first: John

last: Olynyk

first: Benjamin

last: Dwyer

first: Pieter

last: Eichhorn

first: Janina

middle: E

last: Tirnitz-Parker


title: Targeting the translation complex eIF4F disrupts BCR::ABL1 tranlstion and overcomes drug resistance in CML

city: Vancouver

first: Xiaoyan

last: Jiang

state: BC

address: 675 w10th Ave

department: TFL

institute: BC Cancer Research Center

summary: Chronic myeloid leukemia (CML) is driven by the constitutively active BCR::ABL1 kinase, which promotes uncontrolled cell proliferation. While tyrosine kinase inhibitors (TKIs) such as imatinib (IM) have revolutionized CML treatment, resistance, particularly in leukemia stem cells (LSCs), remains a significant barrier to curative therapy. Using a high-content antibody microarray and bioinformatics analyses, we investigated differences in the proteome and phosphorylation landscape of IM-resistant cells and identified highly activated members of the eukaryotic translation initiation complex (eIF4F), particularly eIF4G1, a core component of the eIF4F complex. Notably, these eIF4F complex members are highly expressed and activated in CD34+ CML stem/progenitor cells and in IM-resistant cells. Genetic inhibition of eIF4G1 or pharmacological targeting with the small-molecule inhibitor SBI-756 diminished eIF4F complex assembly, induced an overall reduction in translation initiation of drug-resistant cells, reduced BCR::ABL1 expression, impaired the survival of nonresponder patient stem/progenitor cells, and sensitized them to TKIs, with strong synergistic effects both in vitro and in a PDX model. Molecular and functional validation studies implicated an important role for eIF4G1 in mediating BCR::ABL1 translation initiation and in key downstream targets, including cyclin D3, c-MYC, MCL1, and MDM2, thereby further disrupting the malignant phenotype. These effects were also seen in BCR::ABL1+ acute lymphoblastic leukemia (ALL) cells. These findings underscore the potential of eIF4F complex inhibition, particularly targeting eIF4G1, as a new therapeutic strategy to overcome TKI resistance in CML and other BCR::ABL1+ malignancies.

overall_design: BCR::ABL1+ cell line were treated wiith or without IM and then were harvested for antibody array. Three BCR::ABL1+ cell  lines were used in the analysis. Two replicates for ID (BCR-ABL) cell line, and four replicates for IDA (BCRABL+AHI-1) cell line, and three replicates for IDSH3(BCR-ABL+AHI-1 SH3 Del) cell line.

first: Ryan

last: Yen

first: Lambert

last: Yue

first: Steven

last: Pelech


title: Glial cell states bias the regeneration of neuron types across the newt life cycle

city: New York

first: Maria

middle: Antonietta

last: Tosches

state: NY

address: 1212 Amsterdam Ave

department: Biological Sciences

institute: Columbia University

summary: Salamanders have outstanding regenerative abilities, which tend to decline in post-metamorphic life stages. Among various tissues, these amphibians can regenerate the brain from ependymoglia cells, an adult neural stem cell population. Ependymoglia cells are heterogeneous; yet, whether ependymoglia cell diversity underlies variation of regenerative capacity across brain regions and life cycle stages remains poorly studied. Here we present a cell type comparison of regeneration in the pallium (dorsal telencephalon) of pre- and post-metamorphic newts. We found that ependymoglia cells exist in a continuum of cell states ranging from active proliferation to quiescence across life cycle stages, with a deep quiescence state featuring expression of mammalian astrocyte genes. Ependymoglia cell state changes are associated with a slower onset of proliferation and neurogenesis in post-metamorphic animals. Comparisons with developmental and adult neurogenesis reveal that pallial ependymoglia cells retain regional restrictions but can override temporal fate restrictions in response to an injury, producing neurons that are normally born only in early development. We thus find that brain regeneration in newts is not a simple amplification of adult neurogenesis, but a distinct process where the initial molecular state of ependymoglia cells biases the relative proportions of regenerated neuron types. Our findings establish post-metamorphic newts as a system to study how astrocyte-like glial cells can activate a neurogenic program in response to brain injury.

overall_design: scRNAseq of adult salamander (Pleurodeles waltl) telencephalon. Whole Cells were dissociated using papain. All dissociated cells were multiplexed using distinct Cell Multiplexing Oligos (10x Genomics 3’ CellPlex Multiplexing kit) per stage, prior to GEM formation.

first: Alonso

last: Ortega Gurrola

first: Mayra

last: Kalaora

first: Dreyton

last: Amador

first: Jamie

last: Woych

first: Maria Antonietta


title: P-SSP7 infection of Prochlorococcus MED4 under standard light, high light, and darkness

city: Richland

first: Lindsey

last: Anderson

address: 902 Battelle Boulevard

institute: Pacific Northwest National Laboratory

summary: Cyanophage infection outcomes depend strongly on host physiological state, yet the transcriptional dynamics of the P-SSP7–Prochlorococcus MED4 interaction under different light regimes remain poorly understood. This dataset captures the time-resolved transcriptional response of Prochlorococcus MED4 following infection with cyanophage P-SSP7 under three light conditions: standard light, high light, and darkness.

sample_organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

overall_design: This study used a time-series RNA-seq design to characterize transcriptional responses of Prochlorococcus marinus MED4 to cyanophage P-SSP7 infection across three light regimes: standard light, high light, and darkness. Infection was initiated at an MOI of 10, and infected cultures were sampled in biological triplicate at 0, 0.5, 1, 2, 4, 8, and 24 h post-infection. For the dark treatment, additional samples were collected at 26 and 32 h to capture transcriptional responses following return to standard light. Parallel uninfected controls were included for the standard light and high light conditions.

first: Pavlo

last: Bohutskyi

first: Zachary

last: Johnson

middle: N

first: Margaret

last: Cheung


title: Bulk RNA-seq of male mouse endothelial cells after vehicle or LPS stimulation

city: Cleveland

first: Iuliia

last: Molokotina

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

summary: This study profiles transcriptional responses of male wild-type mouse endothelial cells following inflammatory stimulation with LPS relative to vehicle controls. Three independent male endothelial cell isolations were used as biological replicates. Cells were treated for 8 h with vehicle/starvation media or 500 ng/mL LPS, then lysed for RNA isolation and RNA-seq. media or 500 ng/mL LPS, then lysed for RNA isolation and RNA-seq.

overall_design: Bulk RNA-seq comparing male vehicle/control endothelial cells versus male endothelial cells stimulated with 500 ng/mL LPS for 8 h. Biological replicates are M1, M2, and M3.

first: Molokotina

last: Iuliia

first: Ford

last: Josh

first: Byzova

last: Tatiana


title: Microbiome-Derived RNA Promotes Heritable Defense Against Intracellular Pathogens in Caenorhabditis elegans

city: Washington

first: Jordan

middle: D

last: West

state: District of Columbia

institute: The George Washington

summary: Intestinal microbiota shape host immunity, but whether they can pre-activate defense against intracellular pathogens remains unclear. Here, we identify a natural microbiome member, Stenotrophomonas indicatrix JUb19, as the first example of a bacterium that partially induces the Intracellular Pathogen Response in Caenorhabditis elegans in the absence of infection. This response is coupled to broader metabolic remodeling, suggesting that combined immune and metabolic changes contribute to defense. We show that bacterial single-stranded RNA contributes to this effect, identifying a novel microbiome-derived signal that links microbial exposure to host defense. JUb19 exposure reduces susceptibility to both viral and microsporidian pathogens and confers inherited protection to unexposed progeny, but at a cost to parental fitness. These findings reveal a mechanism by which microbiome-derived RNA programs immunity against intracellular pathogens across generations.

overall_design: RNA seq profiling of wild-type C. elegans fed JUb19 and OP50 at 50 and 48 h respectively.

first: Samuel

last: Schwartz

last: Li

first: Peri

last: Roper

first: Vladimir

last: Lažetić


title: Hemin Impairs Interferon Signaling in Periodontal Cells

city: Vienna

first: Reinhard

last: Gruber

address: Sensengasse 2a

country: Austria

institute: Medical University Vienna

summary: Hemin has been shown to exert potent immunomodulatory effects in the oral microenvironment, yet its global transcriptional targets remain elusive. In this study, we performed high-throughput Bulk RNA-sequencing to investigate the transcriptomic reprogramming induced by Hemin in human oral epithelial cells (HSC-2) under inflammatory conditions. Our transcriptomic analysis revealed that Hemin effectively reversed the inflammatory signature induced by IL-1β and TNF-α. Specifically, Hemin treatment profoundly and selectively paralyzed the interferon (IFN)-stimulated gene axis (e.g., CXCL10, CXCL11), alongside triggering compensatory NRF2-driven redox stress defenses (e.g., HMOX1). These RNA-seq data provide a comprehensive landscape demonstrating Hemin's role as a targeted repressor that fundamentally uncouples JAK-STAT interferon responses.

overall_design: Human oral epithelial cells (HSC-2) were divided into four groups (n=3 biological replicates per group): untreated control, IL-1β/TNF-α, hemin alone (10 μM), and IL-1β/TNF-α + hemin. Total RNA was extracted following 9 hours of treatment. Sequencing libraries were prepared utilizing the QuantSeq 3’ FWD protocol and subsequently sequenced on an Illumina NextSeq2000 instrument in single-end mode.

first: Xiaoyu

last: Huang

first: Panahipour

last: Layla


title: Empowering macrophage to bridge innate and adaptive antitumor immunity through dual targeting of PCSK9 and innate immune checkpoint

city: Shanghai

first: Kaicheng

last: Zhou

address: No.826 Zhangheng Road

institute: Fudan University School of Pharmacy

summary: Macrophage-directed immunotherapy has emerged as a promising strategy to eliminate tumors by unleashing phagocytosis, exemplified by blockade of the CD47-SIRPα “don’t eat me” axis. However, despite robust enhancement of phagocytosis, such approaches often fail to generate durable antitumor immunity in solid tumors, highlighting a critical disconnect between innate immune activation and effective T cell responses. Here, we identify PCSK9 as an adaptive resistance factor induced by macrophage immune checkpoint blockade. Tumor-derived PCSK9 promotes lysosomal degradation of MHC-I in macrophages, thereby impairing antigen cross-presentation and limiting CD8⁺ T cell priming. This previously unrecognized mechanism reveals how phagocytosis-targeted therapies can paradoxically suppress adaptive immunity. To overcome this resistance, we engineered bispecific fusion proteins that concurrently target the CD47-SIRPα phagocytosis checkpoint and the PCSK9–MHC-I antigen presentation axis, among which SIRPαD1-αPCSK9 emerged as the optimal format. Dual targeting synergistically enhances macrophage phagocytosis, preserves antigen cross-presentation capacity, and reprograms the tumor microenvironment toward an immunostimulatory state. Consequently, SIRPαD1-αPCSK9 elicits robust activation of both innate and adaptive antitumor immunity, leading to potent tumor control with improved safety. These findings uncover a novel mechanism of resistance to macrophage-centered immunotherapy and establish a rational dual-targeting strategy that bridges phagocytosis and T cell activation, offering a new paradigm for macrophage-driven cancer immunotherapy.

overall_design: C57BL/6 mice were subcutaneously inoculated with 5×10^6 MC38 cells per mouse to establish MC38 tumor-bearing mouse models. Three days after tumor cell inoculation, the mice were initiated with drug treatment for 14 days before tumor collection. All therapeutic agents were administered via intraperitoneal injection twice a week with equimolar doses among different experimental groups, and the specific dosage of each group was as follows: isotype control group (equimolar control dose), αPCSK9 monotherapy group (7.2 mg/kg), mSIRPαD1-Fc monotherapy group (4 mg/kg), combination group (4 mg/kg mSIRPαD1-Fc plus 7.2 mg/kg αPCSK9), and bispecific fusion protein mSIRPαD1-αPCSK9 monotherapy group (11.0 mg/kg). Mice were euthanized 14 days after the first treatment for tumor tissue collection. Due to the limited size of individual tumors, three tumors per group were pooled to obtain sufficient viable cells for downstream single-cell RNA sequencing. To retain both immune and tumor cell populations, tumors were enzymatically dissociated into single-cell suspensions and subsequently sorted by flow cytometry into CD45⁺ (immune) and CD45⁻ (non-immune) fractions. CD45+ cells were recombined with unsorted cells in a 2:1 ratio. The resulting cell mixtures were subjected to scRNA-seq using the 10x Genomics Single Cell 3’ Protocol.

first: Caili

last: Xu

first: Xiaozhi

last: Hu

first: Yanyang

first: Yun

last: Sun

first: Zihan

last: Dou

first: Rui

first: Wenjing

last: Xue

first: Qinchao

first: Xiting

first: Xianxin

last: Hua

first: Dianwen

last: Ju

first: Xuyao

last: Zhang