title: Epigenetic landscape of synthetic human centromeres: Euchromatic modifications coexist interdependently at CENP-A dense regions and prevent intrusion of other modifications [RNA-seq]

overall_design: RNA was extracted from each cell line carrying the human artificial chromosome, and cDNA was prepared by reverse transcription. Each position code was amplified from the cDNA sequence by a competitive PCR, and the ratio of each position code contained in the product was counted using a sequencer.


title: Effect of SIRT6 on renal tubular cells in diabetic kidney disease

status: Public on Jul 08 2026

city: Beijing

first: Qi

last: Jin

address: No.5, Beixiange, Xicheng District, Beijing

country: China

institute: Guang'anmen Hospital, China Academy of Chinese Medical Sciences

type: Expression profiling by high throughput sequencing

summary: To explore the role of SIRT6 in renal tubular epithelial cells in DKD mice, we extracted primary renal tubular epithelial cells from wild-type and tubular epithelial SIRT6-specific knockout DKD mice, respectively.

overall_design: We then performed gene expression profiling analysis of RNA-seq data of primary tubular cells from different groups.

first: Fang

last: Ma

first: Lanfang

last: Li

first: Peng

last: Qu

first: Yongli

last: Zhan

first: Liang

last: Peng


title: Deciphering resistance mechanisms to auxin-inducible protein degradation in mammalian cells [RNA-Seq]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hosipital

summary: Targeted protein degradation is a favorable strategy for studying the immediate downstream effects of protein loss-of-function, such as the auxin-inducible degron (AID) system. Although this system has been applied extensively to cell and animal models, degradation resistance to long-term auxin treatment has not been studied. With the advent of the new AID2 system, cellular toxicity caused by the high auxin concentrations required in the original AID1 system is no longer a concern, enabling the study of protein degradation over extended periods. In this study, we derived multiple miniAID-tagged knock-in human cell lines and a Ctcf-miniAID knock-in mouse strain to investigate mechanisms of degradation resistance. We revealed four independent resistance mechanisms, including a nonsense mutation in the CTCF coding sequence that removed the miniAID peptide, a missense point mutation in the miniAID coding region that disrupted ubiquitin complex targeting, and reduced expression of OsTIR1 adaptor protein. Resistance to auxin degradation was also observed in mouse primary CtcfminiAID/miniAID knock-in B-cell acute lymphoblastic leukemia cells through missense mutations of the OsTIR1(F74G) protein ex vivo and in vivo. By systematically characterizing degron resistance mechanisms in mammalian cells, we identified potential limitations of the AID system for long-term protein degradation studies.

overall_design: We used total RNA-seq to discovere the genetic mutation of CTCF and miniAID during long-term degradation induction in culture.

first: Wenjie

last: Qi

first: Judith

last: Hyle

first: Chunliang


title: Elimination of  aggressive cancers by a ferroptosis-inducing PROTAC

city: Haifa

first: Amir

last: Orian

address: Efron 1

country: Israel

institute: technion

summary: Aggressive and therapy-resistant cancers present a significant challenge to treatment, and are associated  with poor patients survival. Identifying molecular pathways and compounds that target these pathways is critical for improving patient outcomes. RNF4, an E3-ubiquitin ligase, is pivotal in oncoprotein stabilization and DNA repair, enhancing cancer cell survival driving tumorigenesis. Elevated RNF4 levels are associated with worse prognosis in cancer patients. Here, we describe the development of R4VPs, protein-targeted chimeras (PROTACs) that promote RNF4 degradation, and reduce the levels of its stabilized oncoproteins. Notably, R4VPs induce ferroptotic cell death selectively in cancer cells, sparing non-tumorigenic and primary cells. Surprisingly, R4VPs-induced ferroptosis is independent of RNF4 but preferentially targets tumor-driving mutations, particularly those in the EGFR pathway, while not affecting PI3K-transformed cells. R4VPs effectively induce cell death in therapy-resistant melanoma and sarcomas including patient-derived sarcoma tumor cells. Our findings highlight the potential of R4VPs as ferroptosis inducers as a  therapeutic strategy for therapy resistance, aggressive, and hard-to-treat cancers.

overall_design: RNA-seq profiling of A375R cells under three conditions: control (DMSO), 10 µM R4VPL3-1 (full PROTAC) treatment for 2 hours, and 10 µM VHL moiety-only treatment for 2 hours. Each treatment group includes 3 biological replicates. The aim was to identify differentially expressed genes (DEGs) between the treatment groups

first: Avital

last: Oknin-Vaisman

first: Deepanjan

last: Panda

first: Rostislav

last: Novak

first: Eliya

last: Bitman-Lotan

first: Nikolett

last: Pahor

first: Yamen

last: Abu-Ahmed

first: Guy

last: Kamnesky

first: Markus

last: Diefenbacher

first: Ashraf

last: Brik


title: Epigenetic landscape of synthetic human centromeres: Euchromatic modifications coexist interdependently at CENP-A dense regions and prevent intrusion of other modifications [DNA-seq]

city: Yonago

first: Junichiro

last: Ohzeki

address: 86 Nishi-cho

department: Chromosome Engineering Research Center

country: Japan

institute: Tottori University

summary: Centromere is specialized chromatin structure essential for equal chromosome segregation. Human centromere is organized on a portion of homogeneously repeated DNA sequence, and contains nucleosomes including centromere specific histone H3, CENP-A. Histone modifications around the CENP-A dense region are also thought to have important roles in centromere function. Here, we used human artificial chromosome (HAC) technology to create functional centromeric chromatin on a synthetic centromeric repeat DNA sequence that allowed for structural analysis at 2-kb resolution. Analysis using this HAC centromere showed that the CENP-A dense regions are approximately 18–50 kb in size and coexisted with euchromatic histone modifications in a mutually dependent manner. We also find that when DNA replication reduces CENP-A density, a heterochromatin modification H3K9me3 transiently intrudes CENP-A-dense regions, and that both the CENP-A deposition factor HJURP and the histone acetyltransferase KAT7 are important for pushing back this intrusion. The synthetic centromere DNA generated in this study is more effective at elucidating centromere chromatin structure than relying on naturally occurring DNA mutations, allowing for a more precise understanding and manipulation of centromere function.

sample_organism: Escherichia coli str. K-12 substr. DH10B

overall_design: Genomic DNA from each cell line carrying the human artificial chromosome or the input BAC plasmid was prepared. Each position code was amplified from the genome or BAC plasmid DNA sequence by a competitive PCR, and the ratio of each position code contained in the product was counted using a sequencer.

first: Kazuto

last: Kugou


title: Resolution of Inflammation Increases hematopoietic Stem Cell Number and Erythropoiesis

city: Jackson

first: Bioinformatics

last: Core

state: MISSISSIPPI

address: 2500 N state street

institute: Molecular and Genomics Core Facility

summary: Hematopoietic stem cells (HSC) are essential for blood production throughout our lives. To find new factors that control HSC formation, we screened for bioactive lipid mediators derived from n-3 polyunsaturated fatty acid (n-3 PUFA). n-3 PUFA-derived lipid mediators include compounds called specialized pro-resolving mediators (SPMs), which help resolve inflammation and fight infection. In this study, we investigated the pro-hematopoietic effects of n-3 PUFA-derived SPMs. We exposed zebrafish embryos to various SPMs and found one SPM compound derived from n-3 docosapentaenoic acid, 7(S),17(s)-dihydroxy docosapentaenoic acid (7,17-diHDPAn-3) that increases the expression of HSC markers like cmyb, scl/tal-1, and runx1. 7,17-diHDPAn-3 exposure also increases the expression of gata1, an erythroid progenitor marker, leading to a significant rise in erythrocyte numbers. We confirmed these effects on both primitive and definitive erythropoiesis in zebrafish. Importantly, the production of platelets, that share a common progenitor with erythrocytes, was unaffected. Further metabolomic and RNA-sequencing analysis revealed that 7,17-diHDPAn-3 exposure slightly altered the metabolic profile of RBCs and regulated the expression of the xpo1b and hsp90 genes involved in RBC maturation and heme synthesis, respectively. To understand the link between inflammation resolution and HSC formation, we exposed zebrafish to dexamethasone, which increases the expression of the HSC markers cmyb, and runx1. Co-treatment with 7,17-diHDPAn-3 and dexamethasone had a synergistic effect, demonstrating a novel role for inflammation resolution in stem cell formation. Our work identifies 7,17-diHDPAn-3 as a suitable natural compound to increase HSC number and erythropoiesis in vivo and might be considered for subsequent clinical analysis.

overall_design: All animal husbandry and experimental techniques were reviewed and approved by the UMMC Institutional Animal Care and Use Committee (IACUC #1161). The zebrafish were handled according to the guidelines specified by the IACUC. The AB wild-type strain was obtained from the Zebrafish International Resource Center (ZIRC), Tg(gata1: Dsred), and Tg(CD41:GFP).1,2 Zebrafish were raised in embryonic medium (E3) at 28.5°C under standard conditions with a 14 h light/10 h dark cycles.  Zebrafish embryos were randomly exposed to a variety of omega-3 metabolites at a concentration of 1.5 µM from 11-36 hours post fertilization (hpf) and assessed for HSC number. 7,17-diHDPAn-3 was dissolved in 100% ethanol. Zebrafish embryos were exposed to concentration ranging from 1 to 1.75 µM to find the optimal dose that increased hematopoietic stem cell and red blood cell numbers without causing abnormal phenotypes.

first: Kim

middle: C

last: Nguyen

first: Carol

middle: K

last: Cox

first: Daniel

last: Stephenson

first: Angelo

last: D’Alessandro

first: Luciano

middle: D

last: Mendoza

first: Erin

middle: B

last: Taylor

first: Jerry

last: Monroe

first: Yann

last: Gibert


title: m6A-eCLIP sequencing in mouse alpha cell line aTC1-6 cells with Scramble or Mettl14 KD

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: N6-methyladenosine (m6A) is a widespread RNA modification that plays a crucial role in regulating gene expression, affecting processes such as RNA stability, splicing, and translation. I Previous studies have shown that m6A is involved in fine-tuning β-cell function, but its impact on α-cells, which secrete glucagon in response to low glucose and amino acids, has not been fully investigated. Here, we show that METTL14, a key m6A writer, is essential for maintaining α-cell function and identity. Using a combination of in vitro and in vivo models, we demonstrate that metabolic stimuli such as low glucose and amino acids upregulate METTL14, enhancing glucagon secretion, while insulin downregulates it. Importantly, α-cell-specific knockout of Mettl14 in mice results in impaired glucagon secretion, increased insulin levels, and a surprising conversion of α-cells into β-cells. These findings reveal that m6A is a critical regulator of α-cell identity and function, expanding our understanding of RNA modifications in islet biology. By uncovering a role for METTL14 in maintaining α-cell integrity, our study opens new avenues for exploring RNA-based therapies in diabetes and other metabolic disorders.

overall_design: Immortalized mouse alpha cell line aTC1-6: 2 scramble siRNA controls (SCR) & 2 METTL14 siRNA KD (M14KD)

first: Dario

middle: F

last: De Jesus


title: Transcriptomic analysis of Bioprinted 3D Lung Spheroid Model Mimicking Tumor Microenvironment

city: Daejeon

first: In-Hwan

last: Jang

address: 125, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

department: Immunotherapy Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Conventional in vitro and in vivo models often fail to accurately predict clinical outcomes due to their inability to capture the full complexity of the tumor microenvironment (TME). Existing 3D models also face difficulties in reproducing TME complexity and encounter various engineering limitations. In this study, 3D embedded bioprinting was used to construct a heterogeneous lung spheroid (HLS) model that integrates key stromal factors to more closely simulate the TME. RNA sequencing–based transcriptomic profiling revealed gene signatures related to extracellular matrix remodeling, immune suppression, and tumor progression, which showed strong resemblance to patient-derived lung tumor samples and supported the model’s biological relevance. In summary, this model reproduces essential characteristics of the lung TME and holds promise as a tool for assessing advanced therapies targeting complex solid tumors.

overall_design: A hydrogel was prepared using 1% collagen and dECM from the lung of a porcine. The prepared hydrogel and cell (A549, fibroblast) were mixed at a density of 1×10^7. The ratio of tumor cells to fibroblasts was 2:1. By using this hydrogel with cells, spheroid were made and cultured for 3 days.

first: Dahong

last: Kim

first: Seona

last: Jo

first: Junhyoung

last: Ahn

first: Hyungjun

last: Lim

first: Jae Jong

last: Lee

first: Yu-jin

first: Youngmee

last: Jung

first: Tae-Don

first: Su A

last: Park


title: IL-11 receptor is a novel target for drug development with pharmacological activity in fibro-inflammatory disease

city: San Diego

first: Yasmin

last: Vasquez

state: CA

address: 3612 Mount Ariane Dr

institute: Lassen Therapeutics

summary: IL-11, a novel target for drug development, has been associated with several fibroinflammatory diseases including thyroid eye disease (TED), where it plays an important role in signaling to stromal cells activating multiple intracellular pathways. In TED patient tissue, IL-11 is elevated and stimulates multiple effects important in disease progression, including the production of proinflammatory cytokines, hyaluronic acid (HA) and fibrotic markers. LASN01, a potent antibody to IL-11 receptor, inhibits these effects and is a potential therapeutic agent for TED. Teprotumumab, an antibody to IGF-1 receptor, inhibits HA production and adipogenesis and is effective in reduction of proptosis. Activation of the IGF-1 and IL-11 pathways in TED tissue induces the expression of fibroinflammatory genes regulated by LASN01 and lipid biosynthetic genes regulated by Teprotumumab. Clinical studies show that LASN01 is well tolerated and in a placebo-controlled phase II trial in TED, LASN01 resulted in a statistically significant resolution of clinical activity score (CAS) in 88% of treated patients (p=0.028), but had lesser effects on proptosis. The data supports the importance of IL-11 biology in fibroinflammatory disease and that IL-11 receptor is a pharmacologically active target for drug development.

overall_design: RNA-seq profiling of primary TED orbital fibroblasts isolated from 8 donors treated with LASN01 or teprotumumab and stimulated with IL-11 alone or IL-11 and IGF-1 for 6 or 48 hours.

first: David

last: King

first: Jamie

last: Swaney

first: Cadmus

last: Rich

last: Jun

first: Shira

last: Geller

first: Christine

last: Chidester

first: Merrick

last: Chai

first: Eric

last: Elliot

first: Deborah

last: Witherden

first: Hannah

last: Hershoff

first: Aarya

last: Kafi

first: Amy

last: Strauwald

first: Andrea

last: Kossler

first: Rona

last: Silkiss

first: Alan

last: Oester

first: Antonio M.

last: Garrido-Hermosilla

first: Mohsan

last: Malik

first: Don

middle: O

last: Kikkawa

first: Maria

last: Fardis


title: Developing a differentiation-inducing therapeutic strategy for sarcomatoid renal cell carcinoma

first: Jian

last: Liu

state: Beijing

address: hujialou

institute: Beijing Chaoyang Hospital

summary: Sarcomatoid renal cell carcinoma (sRCC) represents the least differentiated and most aggressive clinicopathological phenotype of RCC, with no established effective therapies and most patients surviving less than 1 year. Herein, based on the co-progenitor cell theory and the potential plasticity of sarcomatoid dedifferentiation, we developed a differentiation-inducing therapeutic strategy and identified PLOD2 as a potential intervention target by multi-omics screening. We demonstrated that PLOD2 is significantly upregulated in the sarcomatoid component of sRCC patients compared to the adjacent normal and neighboring epithelioid counterparts, functionally driving sarcomatoid dedifferentiation through concomitant activation of cancer stemness, dedifferentiation, and EMT, and correlating with higher tumor grade, metastasis, and poorer patient survival. Depletion of PLOD2 in sRCC cells resulted in efficient epithelioid differentiation, tumor suppression and sensitization to conventional RCC therapies of doxorubicin, gemcitabine, IFN-α and VEGFR-TKI. Further investigation revealed that, DCLK1, a recently identified cancer stem cell marker, was downstream of PLOD2 in mediating sarcomatoid dedifferentiation, and rescue of DCLK1 could partially restore the sarcomatoid appearance of PLOD2-ablated sRCC cells. Importantly, pharmacological targeting of PLOD2 by minoxidil, an FDA-approved drug for androgenetic alopecia, could induce sRCC differentiation and enhance the anti-tumor activity of conventional therapies. Overall, our study identifies a potential molecular biomarker and driver for sRCC, and offers a novel promising therapeutic strategy and intervention target for this intractable and devastating disease.

overall_design: PLOD2 was genetically ablated using CRISPR/Cas9 technology in 786-O cells, and the ablated and control cells were then subjected to RNA-seq profiling analysis.


title: γδ17T Cells Hinder Mandibular Bone Defect Healing

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

institute: HUJI

summary: Bone fracture healing requires coordinated interactions between immune cells and skeletal tissues, with flat bones exhibiting unique biomechanical and physiologic characteristics as compared with long bones. The mandible, the lower jawbone that supports the oral cavity, has distinct features due to 1) its proximity to the oral mucosa, which is enriched in immune cells and microbiota, and 2) [AQ: 7] its exposure to masticatory forces, making it a clinically relevant model for studying immune–skeletal interactions during fracture repair. Moreover, mandibular fractures are common maxillofacial injuries, posing challenges owing to functional and aesthetic considerations, as well as the risk of infection and impaired healing. Recent studies have highlighted conflicting roles for interleukin 17 (IL-17) and γδT cells in bone fracture or defect healing. As the primary source of IL-17 in the oral mucosa, γδT cells play a critical role in alveolar bone remodeling and respond to environmental factors such as the microbiota and age. We thus sought to investigate their role in the repair process of a mandibular defect. Here, we developed a murine model where a 1.5-mm drill hole defect spontaneously healed within 3 wk. Analysis revealed rapid leukocyte infiltration at the defect site by day 3, predominantly neutrophils and inflammatory monocytes, with γδT cells and adaptive leukocytes accumulating later at days 7 and 14. Depletion of γδT cells via Tcrd-GDL mice or genetic ablation of IL-17 in Il17af-/- mice accelerated the kinetics of mandibular healing. Bulk RNA sequencing and immunologic analysis revealed that while early recruitment of neutrophils and monocytes was unaffected in Il17af-/- mice, later inflammatory responses were diminished, resulting in accelerated repair. These findings suggest that IL-17–producing γδT cells (γδ17T cells) delay mandibular fracture repair by inhibiting inflammation resolution, thus prolonging the reparative phase. Targeting γδ17T cells or IL-17 may thus represent therapeutic strategies to enhance bone regeneration, particularly in challenging clinical settings involving mandibular fractures.

first: Reem

last: Naamnneh

last: Shoukair

first: Mai

last: Gara

first: Yasmin

last: Jaber

first: Shahd

last: Yacoub

last: Natanely

last: Saba


title: total RNA-seq from HG02679 (ENCSR270JED)

status: Public on Jul 24 2026

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Natural Killer Cell-Derived Extracellular Vesicles Reprogram Human Immunity to Enhance Tumour Cytotoxicity

city: Chalk River

first: Yi

last: Wang

state: Ontario

address: 286 Plant Road

department: Radiology and Health

country: Canada

institute: Canadian Nuclear Laboratories

summary: Despite evidence of natural killer cell–derived extracellular vesicles (NK-EVs) possessing intrinsic cytotoxicity, their broader immunomodulatory effects on human immune subsets remain poorly defined, representing a key knowledge gap that must be addressed to advance their clinical translation as cancer immunotherapeutics. In this study, the immunomodulatory effects of NK-EVs were evaluated on peripheral blood mononuclear cells (PBMCs), a mixed population of circulating immune cells, from healthy donors and patients with aggressive breast cancer. NK-EVs were produced through a clinically scalable production process and PBMCs exposed to NK-EVs were assessed using high-resolution single-cell transcriptomics and functional cytotoxicity assays. NK-EVs reprogrammed PBMC on a transcriptomic (gene regulation) and cellular level, resulting in functional improvement of the PBMCs' tumour cell killing capabilities. These effects were mediated through distinct PBMC subsets, including cytotoxic T cells, NK cells and myeloid cells. Interestingly, CD8+ T cells, CD56+ NK cells, and CD33+ myeloid cells appear to play a more prominent role in NK-EV-mediated immune reprogramming than CD4+ T cells, with genes involved in their activation being markedly affected upon EV stimulation. Notably, the responses were consistent across all biological PBMC donors (n=6), regardless of disease status. Collectively, these findings demonstrate that NK-EVs orchestrate coordinated immune activation, highlighting their promise as an immunotherapeutic for cancer and other immune-mediated diseases.

overall_design: Single-cell RNA sequencing of human PBMCs from healthy donors (n=3) and triple-negative breast cancer (TNBC) patients (n=3) treated with or without NK-cell derived extracellular vesicles (NK-EVs). PBMCs were cultured in ImmunoCult-XF T Cell Expansion Medium and treated with 5 x 10^11 EVs/mL NK-EVs for 72 hours. Four experimental groups were analyzed: (1) EV-treated healthy PBMCs (3 donors), (2) untreated healthy PBMCs (3 donors), (3) EV-treated diseased PBMCs (3 donors), and (4) untreated diseased PBMCs (3 donors). Single-cell libraries were prepared using 10x Genomics Chromium Next GEM Single Cell Fixed RNA Sample Prep Kit with V2 barcoding chemistry. Sequencing was performed on NovaSeq X platform targeting 10,000 cells per sample. Ethics approval was obtained from the Health Canada-Public Health Agency of Canada Research Ethics Board under protocol number REB#2022-028H.

first: Frederic

last: St-Denis-Bissonnette

first: Karan

last: Mediratta

first: Nicolas

middle: J

last: Ho

first: Melanie

last: Kirkby

first: Andrew

last: Stalker

first: Gauri

last: Muradia

first: Amit

last: Shrestha

first: Michele

last: Ardolino

first: Seung-Hwan

last: Lee

first: Dylan

last: Burger

first: Arvind

middle: S

last: Mer

first: Lisheng

first: Jessie

last: Lavoie


title: mRNA sequencing in mouse alpha aTC1-6 cells with Scramble, Mettl3 KD, or Mettl14 KD

first: Jonathan

last: Dreyfuss

summary: Immortalized mouse alpha cell line aTC6 cells were cultured in normal DMEM complete media with 25mM glucose and transfected with siRNA and lipofectamine RNAiMax.

overall_design: Immortalized mouse alpha cell line: 3 scramble controls, 4 METTL3 KD and 4 METTL14 KD

first: Dario

last: De Jesus


title: Ezh2 and intracellular Ca2+ signals interdependently coordinate GVHD and CAR T cell responses [RNA-seq_2]

city: 3601 Spruce Street

first: Yan

last: Zhou

state: PA

address: 333 Cottman Ave

department: Bioinformatics

institute: Fox Chase Cancer Center

summary: During graft-versus-host disease (GVHD), Ca2+ signals are crucial for the establishment of T cell alloim-munity, however, excessive or prolonged Ca2+ signals lead to T cell death and dysfunction. How alloreac-tive T cells regulate a delicate regulate intracellular Ca2+ response to induce GVHD remains poorly defined. We demonstrate that Ezh2 acts as Ca2+ signaling brake to limit excessive intracellular Ca2+ responses in activated T cells, thereby promoting survival of alloreactive T cells that mediate GVHD. Ezh2 loss resulted in enhanced intracellular Ca2+ responses and upregulation of gene programs that promote effector differen-tiation in activated T cells. Conditional deletion of Stim1 (which mediates cytosolic Ca2+ entry) synthetical-ly rescued antigen-activated non-viable Ezh2-null T cells and their capacity to induce GVHD. Ezh2 re-pressed the expression of endoplasmic reticulum Ca2+ release channel inositol 1,4,5-trisphosphate (InsP3) receptor 2 (Itpr2) to modulate intracellular Ca2+ responses. Deleting Itpr2 in Ezh2-null T cells reduced cy-tosolic Ca2+ entry, improved their capacity to mediate GVHD and eliminate leukemia in mice. Our findings identify that Ezh2 is a master regulator of Ca2+ signals in antigen-driven T cells. Furthermore, selectively heightening intracellular Ca2+ signals in alloreactive T cells may lead to new strategies to control GVHD.

overall_design: RNAseq experiments for WT samples and Ezh2 and Stim1 double knockout samples were conducted and differentially expressed genes were identified.

first: Ying

first: Qing-Rong

last: Huang

last: zhou

last: Zhang


title: Ezh2 and intracellular Ca2+ signals interdependently coordinate GVHD and CAR T cell responses [RNA-seq_1]

overall_design: RNAseq experiments for WT samples, Ezh2 knockout samples and Stim1 knockout samples were conducted and differentially expressed genes were identified.

last: Wang

first: Yi


title: Tune p53 transactivation and tumor suppression activity by modulating its liquid-liquid phase separation propensity

city: Hangzhou

first: Guozhen

state: Zhejiang Province

address: No.866 Yuhangtang Road

institute: Zhejiang University

summary: p53, essential in cancer defence, is involved in transcriptional and DNA repair condensates. However, whether condensation can be driven by endogenous p53 and the functional significance of condensates in p53’s working and regulatory mechanisms were unknown. We show that endogenous p53 forms nanoscale condensates, co-localizing with different co-factors, enabling distinct functions within segregated compartments in cells. Antagonists disperse these condensates, whereas activators enhance coalescence and alter p53 dynamics within these structures. Notably, we reveal a dual role for p53: it maintains tumor suppression and, paradoxically, boosts expression of neuron-related genes, which in certain contexts, can promote cancer cell growth. We developed liquid-liquid phase separation- enhanced p53 variants that amplify selected target gene transactivation and suppress oncogenic gene upregulation, curtailing proliferation of cancer cells resistant to wild-type p53. These findings reveal a critical role of liquid-liquid phase separation in p53 functional regulation, offering subtle control over its transcriptional landscape, particularly with respect to specific genes intersecting neuronal signalling and cancer pathways..

overall_design: To investigate genes regulated by p53, we overexpressed control vector or wild-type p53(WT) in H1299 cells; To investigate effect of LLPSEp53s, we overexpressed p53, LLPSEp53_1 and LLPSEp53_2 in H1299 cells. We then performed gene expression profiling analysis using data obtained from RNA-seq of different samples.


title: Enhanced liver regeneration via targeted mRNA delivery for partial in vivo reprogramming

city: Seoul

first: Seunghee

last: Hong

address: 50 Yonsei-ro, Seodaemun-gu

department: Biochemistry

institute: Yonsei university

summary: Recent studies suggest that injury-induced dedifferentiation, which leads to the formation of ‘injury-responsive cells’, contributes significantly to tissue repair across various organs, including the liver. Utilizing Yamanaka factors (Oct4, Sox2, Klf4, and c-Myc: OSKM) for in vivo partial reprogramming generates ‘injury-responsive cells’ in the intestine, mirroring those derived from injury-induced dedifferentiation. Thus, the transgene induction of OSKM or viral delivery of Oct4, Sox2, and Klf4 shows promise in facilitating tissue regeneration in the intestine, liver, skeletal muscle, and retina. Herein, we demonstrated that transient OSKM induction produces two distinct liver progenitor-like cell populations. One of these populations resembles liver progenitor-like cells (LPLCs) generated by acute acetaminophen (APAP) injury without triggering immune responses. To explore in vivo reprogramming as a viable strategy for tissue regeneration, we employed lipid nanoparticles (LNP) carrying OSKM mRNA (OSKM-mRNA-LNP) to stimulate LPLCs formation. Notably, the production of Sox9+ LPLCs, and OSKM-induced dedifferentiation, was closely correlated with successful tissue regeneration in the liver post APAP injury. Thus, the OSKM-mRNA-LNP approach represents a promising therapeutic intervention for the repair of acute liver injuries.

overall_design: We used whole liver samples for single nucleus RNA sequencing. There were control, APAP and OSKM groups (n=2 per group). APAP livers were sampled 48 h after 300 mg/kg APAP I.P. injection. OSKM livers were sampled 72 h after 0. 15 mg/kg doxycycline administration. Whole samples were prepared using reprogrammable mice to minimize the genetic background effect.

first: Beom-Ki

last: Jo

first: Young Seok

last: Song

first: Woohyun

first: Hee-Ji

last: Eom

first: Yon Jae

first: Jumee

last: Kim

first: Seung-Woo

last: Cho

first: Hyuk-Jin

last: Cha


title: Effects of dexamethasone and desisobutyryl ciclesonide on gene expression

city: Pittsburgh

first: Uma

last: Chandran

address: 5607 Baum Blvd

institute: University of Pittsburgh

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Dipyridamole, a compound that increases extracellular adenosine levels, as a preventive treatment for rheumatoid cachexia

city: Madrid

first: Aranzazu

last: Mediero

state: Madrid

address: Avda. Reyes Catolicos 2

department: Rheumatology

country: Spain

institute: Fundacion Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz

summary: Muscle decline due to chronic inflammation is a common condition in RA patients called rheumatoid cachexia (RC). Adenosine and ATP levels are essential in the control of myogenesis, anabolism/catabolism and senescence of muscle cells. Dipyridamole, an antiplatelet drug, is able to modulate adenosine levels in muscle cells and is an interesting therapeutic agent for RC. K/BxN mice model was treated with dipyridamole daily and sacrificed at the highest point of pawn inflammation. Cytokines arrays were performed in serum and muscle. Histology of TA and ankle was analyzed. Protein expression of myogenesis, purinergic system and senescence key markers were studied. Nucleotide content of GA was analyzed via HPLC. 2D and 3D culture models with C2C12 cells were performed to confirm the results obtained in mice model. RA mice developed weight loss, muscle size and activity decline and increment of senescence and atrophy. All this is dependent on the low adenosine levels and decreased expression of adenosine A2A/A2BR in RA muscle. Dipyridamole was able to prevent inflammation and muscle pathologies in RA mice due to adenosine and A2A/A2BR maintenance also cAMP/AMPK activation. This finding suggests dipyridamole is an interesting preventive drug to RA patients for counteracts RC development.

overall_design: Arthritic K/BxN mice were generated by crossing KRN mice with NOD/Lt mice. Adult arthritic K/BxN mice were bled and the serum were pooled and acquired from Charles River. Age-matched, male recipient, 12-wk-old C57BL/6J mice were purchased from Charles River Laboratories (Barcelona, Spain) and divided in two groups: 1.- arthritic mice (RA)  received serum transfer, 100 μL intraperitoneal (IP) at day 0 and 2 (n=4), and 2.- RA+Dipy mice, that received serum transfer 100 μL IP at day 0 and 2, and were treated with dipyridamole 25mg/kg/day administered daily starting day 0 (n=4). All motor activity tests were performed prior to serum inoculation and at the highest point of inflammation. Mice were euthanized on day 16 and gastronemius (GA) was collected. RNA-seq analysis RNA was isolated from GA (20µg) of RA and RA+Dipy mice (n=4 each) following the RNeasy Fibrous Tissue Mini Kit. Libraries preparation and sequencing were carried out in Fundación ParqueCientífico de Madrid. Total RNA quality and concentration was assessed on 4200 TAPEStation(Agilent), using a RNA ScreenTape. Then, 500ng of total RNA from each sample were used as input for library preparation with "NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®" (New England BioLabs) following manufacturer recommendations for Poly(A) mRNA protocol. Libraries were validated and quantified by TapeStation and an equimolecular pool was made, purified using AMPure XP beads (Beckman Coulter) and titrated by PicoGreen. Library pool was sequenced on a NovaSeq6000 (Illumina) where clusters were formed and sequenced in a 1x100single-read sequencing run. FastQ files were preprocessed with fastp (version 0.20.0) with default parameters. Preprocessed fastq files were aligned to the GRCm38.p6/mm10 mouse genome using STAR (version 2.7.3a).  Read counts were extracted using htseq-count in non-stranded mode. Two conditions differential expression analysis was performed using DESeq2 (version 1.44.0) (ref1) including DESeq normalization (80). Genes with adjusted p-value < 0.05 were taken as significant (80). Gene set enrichment analysis (GSEA) (ref2) was applied using GSEA (version 4.3.3) to the normalized genes' read counts obtained from DESeq2 (80, 81). We used Gene Ontology (biological processes) Reactome pathways as gene sets. Gene sets with a FDR < 0.05 was taken as significant.

last: Muñoz

first: Miguel

last: Bonilla

first: Maria

last: Castaño


title: Fibrillarin-dependent 2′-O-methylation modulates RPS28 ribosome incorporation and oncogenic translation

city: Uppsala

first: Rubin

last: Dasgupta

address: Husargatan 3, BMC 582, D9:3

country: Sweden

institute: Uppsala University

summary: Fibrillarin (FBL), a core component of the C/D box small nucleolar ribonucleoprotein (snoRNP) complex, catalyzes the 2'-O-methylation (Nm) of the ribose 2'-hydroxyl moiety in ribosomal RNA (rRNA). Distinct Nm patterns contribute to ribosome heterogeneity, which is linked to selective translation of oncogenes. FBL dysregulation generates an aberrant Nm signature in triple-negative breast cancer (TNBC), the most aggressive breast cancer subtype. This study investigated the role of FBL in TNBC via translation-driven mechanisms. Our findings show that FBL knockdown impairs tumorigenic traits, triggers metabolic stress, and reduces the translation efficiency of oncogenes, such as metastasis-associated protein 1 (MTA1), interleukin-1 receptor-associated kinase 1 (IRAK1), and thymosin beta 10 (TMSB10). RiboMethSeq confirmed that the rRNA Nm sites exhibited differential sensitivity to FBL depletion. Additionally, FBL knockdown leads to alterations in 18S ribosome structure and specifically reduced  RPS28 incorporation into ribosomes. Notably, silencing RPS28 also disrupted both the oncogenic phenotype and downregulated MTA1, IRAK1, and TMSB10 expression. These findings reveal a complex interplay between FBL, rRNA Nm modifications, and RPS28 in shaping oncogenic protein pools and ribosomal composition in TNBC, offering promising insights into therapeutic approaches targeting this aggressive cancer subtype.

overall_design: 2-aminopyridine-3-carboxylic acid imidazolide (2A3) was used as a general probe for the interrogation of RNA structures in cells. MDA-MB-231 cells, containing SCR, KD1 and KD2, were counted and viability was assessed 48 h prior to the experiment using a Cell Counter (Invitrogen™ Countess™ II Automated Cell Counter). Cells were seeded in duplicates at 0.5 × 10^6 cells per well in 6-well plates. Immediately before probing, the culture medium was replaced with 900uL of fresh, prewarmed medium. Either 100uL of 2A3 SHAPE reagent or 100uL of DMSO, background, was added per well, followed by gentle mixing the plate. Cells were incubated at 37C for 15 min with moderate shaking. Reactions were quenched by addition of 1mL 1M DTT. Cells were transferred into tubes and pelleted by centrifugation at 900 rpm for 5 min, supernatants were discarded, and pellets were snap-frozen on dry ice. Pellets were stored at –80C for 12 h prior to RNA extraction. RNA was purified using the GeneJET RNA Purification Kit (Thermo Scientific, cat. K0732) according to the manufacturer’s instructions. RNA concentrations were determined with a NanoPhotometer® NP80 (Implen GmbH) (Table S9). Residual genomic DNA was removed by treatment with TURBO DNase (Invitrogen™, cat. AM1907) at 37C for 30 min, followed by ethanol precipitation. Final RNA concentrations were determined with a NanoPhotometer® NP80 (Implen GmbH). Reverse transcription reactions with specific primers were performed as previously described by Smola et al.  After inactivation of SuperScript™ II Reverse Transcriptase (Invitrogen™, cat. 18064014) at 72C for 15, 1uL of RNase H and 0.25uL of 250mM Mg(oAc)2 were added and incubated at 37C for 20 min, followed by adding 1uL of Proteinase K (Roche, cat. 3115828001) and incubation at 37C for 15 min. cDNA samples were purified using the GeneJET Gel Extraction Kit (Thermo Scientific, cat. K0692). Libraries were prepared using specific primers and Platinum SuperFi II PCR Master Mix (Invitrogen™, cat. 12368010), and dsDNA was purified using the GeneJET Gel Extraction Kit (Thermo Scientific, cat. K0692) (Table S11, Figure S11). Ligation of amplicons was performed according to the manufacturer’s instructions (Oxford Nanopore Technologies, Native Barcoding Kit 24 V14, SQK-NBD114.24).


title: GABA promotes resistance to immunotherapy of patients with TLS-positive tumors [Spatial Transcriptomics]

city: PARIS

first: Isaias

last: Hernandez-Verdin

state: Ile-de-France

address: GH PITIE SALPETRIERE ICM IHU A, 47 Boulevard DE L'HOPITAL

department: Genetics and Development of Nervous System Tumors

country: France

institute: Institut du cerveau

summary: Tertiary lymphoid structures (TLS) correlate with favorable responses to immune checkpoint inhibitors (ICI) in various cancers, yet many patients with TLS-positive tumors are resistant to treatment. Multi-omic profiling of clear cell renal cell carcinoma (ccRCC) and soft tissue sarcoma tumors (STS) reveals an upregulation of gamma-aminobutyric acid (GABA)-related signatures in non-responders to ICI. In ccRCC, TLS from non-responders located near GABA-producing tumor cells, exhibit impaired B cell maturation, reduced IgG production, higher GABA receptor expression and tricarboxylic acid cycle activation. In vitro, exposure of human B cells to GABA reduces HLA-DR expression, proliferation and immunoglobulin secretion by receptor independent and dependent mechanisms. Pharmacological inhibition of GABA-synthesis increases ICI response and immune infiltration, particularly by B cells, in a TLS-positive STS mouse model. Our findings unravel GABA as an immunoregulatory metabolite and provide a rationale for its therapeutic targeting to overcome ICI resistance in patients with TLS-positive tumors.

overall_design: Spatial transcriptomics (n=19, all TLS-positive) of ccRCC tumors from the BIONIKK cohort (NCT02960906)

first: Anne

last: Calvez

first: Cheng-Ming

last: Sun

first: Antoine

last: Bougoüin

first: Pierre

last: Hirt

first: Eric

last: Pinaud

first: Matthew

last: Smith

first: Craig

middle: E

last: Wheelock

first: Virginie

last: Verkarre

first: Yann-Alexandre

last: Vano

first: Lucie

last: Garnier

first: Théo

last: Bouloudani

first: Guilhem

last: Pupier

first: Dahbia

last: Djaroun

first: Christian

last: Wu

first: Asmat

last: Ullah

first: Lucile

last: Vanhersecke

first: Alban

last: Bessede

first: Jean-Philippe

last: Guegan

first: Laurence

last: Albiges

first: Sylvère

last: Durand

first: Guido

last: Kroemer

first: Agusti

last: Alentorn

last: Italiano

first: Stéphane

last: Oudard

first: Catherine

last: Sautès-Fridman

first: Wolf

middle: H

last: Fridman


title: Fibrillarin regulates oncogenic protein pools and ribosome protein composition in triple-negative breast cancer

city: Mannheim

first: Francesca

last: Tuorto

address: Ludolf-Krehl-Str. 13-17

department: Division of Biochemistry  Mannheim Institute for Innate Immunoscience (MI3)

country: Germany

institute: Deutsches Krebsforschungszentrum

summary: Cancer cells hijack various gene expression regulation programs to support their increased metabolic demands, including translation. Emerging data suggests that specific aspects of translation, such as initiation, fidelity and efficiency, can be regulated by alterations in any of the ribosome components, being ribosomal proteins or RNA (rRNA). rRNA is highly decorated with chemical modifications that can influence its stability, folding, and interaction with other molecules. Thus, we hypothesised that chemical modifications may play an essential role in controlling the pool of oncogenic proteins in triple-negative breast cancer (TNBC). As a result, this study focuses on studying the role of fibrillarin, the catalytic enzyme responsible for the deposition of 2'-O-methylation, the most abundant rRNA modification, in the context of TNBC’s aetiology and tumour progression. Using Ribosome profiling (Ribo-seq), we identified proto-oncogenes, e.g., MTA1, IRAK1 and TMSB10, whose translation efficiency is downregulated upon fibrillarin depletion. Understanding the dynamics between 2'-O-methylation and translational control of gene expression of these proto-oncogenes will facilitate the development of effective cures against TNBC.

overall_design: Ribo-seq and RNA-seq analysis for MDA-MB-231 cell line and a loss-of-function approach using two distinct shRNAs, KD1 and KD2, to target fibrillarin mRNA.

first: Paula

last: Groza

first: Johanna

last: Schott

last: Aguilo


title: GABA promotes resistance to immunotherapy of patients with TLS-positive tumors [RNA-seq]

first: Isaias

last: Hernandez-Verdin

overall_design: Bulk RNA-seq (n=92, 82% TLS-positive) of ccRCC tumors from the BIONIKK cohort (NCT02960906)

first: Anne

last: Calvez

first: Cheng-Ming

last: Sun

first: Antoine

last: Bougoüin

first: Pierre

last: Hirt

first: Eric

last: Pinaud

first: Matthew

last: Smith

first: Craig

last: Wheelock

first: Virginie

last: Verkarre

first: Yann-Alexandre

last: Vano

first: Lucie

last: Garnier

first: Théo

last: Bouloudani

first: Guilhem

last: Pupier

last: Djaroun

last: Wu


title: Investigating the role of INTS12 on transcriptional elongation dynamics

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

overall_design: DRB TTchem-seq (Gregersen et al., 2020) comparing transcript elongation dynamics in wild-type and INTS12 knock-out HEK293 FlpIn TREx cells. Cells were treated with 100uM DRB for 2hrs in order to inhibit progression of RNA polymerase II past the early elongation checkpoint. DRB was then washed out and samples were collected for TTchem-seq analysis at 15', 30' and 45' timepoints following DRB wash-out. Samples were also collected without addition of DRB to investigate the effects of INTS12 KO on steady-state transcription dynamics.

first: Daniel

last: Blears

first: Riyaz

last: Sahah

first: David

last: Lopez Martinez

first: Nova

last: Fong

first: Ryan

last: Sheridan

last: Bentley

first: Jesper

last: Svejstrup


title: Expression data from primary mouse fibroblasts from E18.5 embryos treated with vehicle, Dexamethasone, Ciclesonide, Des-Isobutrylciclesonide

first: Uma

last: Chandran

summary:
Comparative analysis of synthetic glucocorticoids in the embryonic lung fibroblasts
Affymetrix whole genome expression studies were performed using microchips

overall_design: Primary fetal mouse lung fibroblasts were prepared from E18.5 fetal mice, plated in 10cm culture plates and maintained in Waymouth media supplemented with 10% fetal bovine serum. Prepared primary fetal mouse lung fibroblasts were cultured in 6 well plates and treated for 6 hours with 10-6M DES-Cic, dexamethasone and control media.

first: Paula

last: Monaghan Nichols

first: Timothy

last: Cole


title: Mov10 suppresses excessive inflammation by regulating the TNFα–NF-KB pathway

city: Chongqing

first: Chang

middle: Lin

last: Zhen

address: Baianba

institute: Chongqing Three Gorges Medical College

summary: We next sought to explore the underlying mechanism by which Mov10 regulates HSC function.We isolated Lin-c-kit+ cell from mice 12 days after 4.5 Gy IR and performed RNA immunoprecipi-tation sequencing (RIP-seq). Bioinformatics analysis identified Mov10-bound transcripts as po-tential Mov10 targets, with GO pathway enrichment analysis highlighting pathways related to production of molecular mediator of immune response and response to tumor necrosis factor (TNF)

overall_design: Mov10-binding transcripts from RIP-seq in mouse HSCs at 12 days post-4.5 Gy IR


title: PRDM16 Modulates Aspects of Cell-Cycle Dynamics and Maturation in Human iPSC-Derived Cardiomyocytes

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

summary: Understanding the molecular mechanisms that mediate entry into quiescent states of cardiac tissues, along with their associated metabolic rewiring, is crucial for comprehending the postnatal changes driving physiological hypertrophy and functional maturation. PRDM16 has been identified as a critical regulator of both proliferation and maturation in fetal-like human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Our study demonstrates that PRDM16 orchestrates the proliferative axis of hiPSC-CMs by modulating CDK1 and phospho-AKT levels, two key drivers of cardiac proliferation. Reduced PRDM16 expression significantly impairs the metabolic and structural maturation of hiPSC-CMs, leading to dysregulated sarcomeric protein expression ratios and compromised engineered heart tissue (EHT) function. Conversely, mild PRDM16 overexpression promotes metabolic shifts and structural protein changes toward maturation. These findings provide new insights into the molecular mechanisms governing cardiomyocyte development and highlight PRDM16 as a potential therapeutic target for enhancing cardiac regeneration and repair, since transient PRDM16 downregulation creates a roadblock to maturation in favor of proliferation. Overall, this work underscores the central role of PRDM16 in controlling the proliferation-maturation axis of cardiomyocyte biology.

overall_design: Cardiomyocytes derived from human induced pluripotent stem cells (hiPSCs) from line 201B7-FUCCI, transfected with scramble or siPRDM16, and subjected to lentiviral transduction of GFP or PRDM16.

first: Kanae

last: Tani

first: Yasuko

last: Matsumura

first: Megumi

last: Narita

first: Antonio

last: Lucena-Cacace


title: Effect of DSX knock down by RNA intereference on sex-bias gene expression at different larval stages and adul parts in the parasitoid wasp Nasonia vitripennis

city: Wageningen

first: Julien

last: Rougeot

address: Droevendaalsesteeg 1

department: Plant Science Group

country: Netherlands

institute: Wageningen University and Research (Netherlands)

summary: All animals exhibit sexual dimorphism, from the molecular to the behavioral level. Sexual dimorphism is particularly well-known in insects, where differences in colors, shape, behavior, neurophysiology, and much more have been studied. However, little is known about the genetic and molecular mechanisms leading to these differences, and most of our knowledge relies on the Drosophila melanogaster model. The current model presents the transcription factor Doublesex (DSX) as the main switch to control male and female-specific gene expression across development. In this study, we uncover sex-biased gene expression in Nasonia vitripennis with a unique level of detail by comparing male and female transcriptomes at different developmental stages, from 1-day-old embryos to adults separated into head, thorax, and abdomen. Additionally, we knocked down dsx by RNA interference and analyzed its effects on gene expression in males and females at different developmental stages and adult body parts, revealing hundreds of genes under the control of DSX.

overall_design: Target gene knock-down in male and female was achieved by RNA interference (RNAi) in N. vitripennis larvae and pupae at different developmental times (4, 6, and 8 days after egg laying) by injecting a double-strand RNA targeting dsx mRNA or a non-specific gene as a control (GFP). Larval and pupal samples were collected 3 days later, as well as dissected adult parts (head, thorax, abdomen) after emergence, and 1-day-old embryos laid by injected mothers (parental RNAi). Total RNA was extracted and sequenced. Gene expression was compared between male and female, and dsx-RNAi and control for every time point.

first: Filippo

last: Guerra

first: Eveline

last: Verhulst


title: Investigating microenvironment in CMML

city: Taipei

first: Yu-Hung

last: Wang

address: N0 7, Chung-Shan South Rd

country: Taiwan

institute: National Taiwan University Hospital

summary: Inflammatory microenvironment in chronic myelomonocytis leukemia

overall_design: mRNA profiles of 90 CMML patients using RNA-seq

first: Hwei-Fang

last: Tien

first: Wen-Chien

last: Chou

first: Chien-Chin

last: Lin


title: Investigating microenvironment in MDS II

summary: A perturbed microenvironment is associated with inferior prognosis in myelodysplastic syndromes

overall_design: mRNA profiles of MDS patients and healthy donors using RNA-seq


title: Transcriptomic Signatures Reveal Overlapping Shared and DistinctYet State-Specific Preoptic Neuronal Ensembles Activated by Anesthesia and Sleep

status: Public on Jul 07 2026

city: Philadelphia

first: Allan

middle: I

last: Pack

address: 125 South 31st St

institute: University of Pennsylvania

summary: General anesthesia and non-rapid-eye-movement (NREM) sleep share overlapping neuronal circuitry within the preoptic area (POA), yet they are fundamentally distinct states. We performed single nucleus RNA sequencing (snRNA-seq) on the POA from adult C57BL/6J mice after 30-minutes of breathing either 1.2% isoflurane in oxygen or an oxygen control. Cell clusters were identified by projecting to the existing cellular taxonomy established in our previously published POA snRNA-seq dataset of recovery sleep (GEO: GSE243489) and transcriptional changes in rapid primary response genes (rPRGs) was used to define isoflurane-activated or isoflurane-inhibited clusters. Finally, multiplex fluorescence in situ hybridization was performed to independently corroborate the snRNA-seq results.

overall_design: Methods:   Male and female C57BL/6J mice aged 3-4 months were used for this study (Stock 000664, Jackson Laboratories, ME). Mice were housed on a 12 h:12 h light–dark cycle (lights on at 6:00pm) with ad libitum access to food and water for a minimum of 3 weeks. Prior to isoflurane exposure, mice were habituated to gas-tight, temperature-controlled, 200 mL cylindrical chambers with 100% oxygen flowing at 200 mL/min for 2 h per day for 4 days, as previously described.19 On the experimental day, mice were exposed to either 1.2% isoflurane in 98.8% oxygen (Iso, n=5/sex) or 100% oxygen (Oxy, n=5/sex) for 30 minutes between Zeitgeber time (ZT) 13-15, a window optimized to capture changes in acute rapid primary response genes while minimizing transcriptional changes from secondary physiological effects associated with anesthetic exposure. During the exposure, mice were kept normothermic by placing all righting reflex cylinders in a 37 °C water bath.19 Concentrations of isoflurane were monitored and titrated within ±0.02% using a Riken FI-21 refractometer (AM Bickford).

first: Xiaofeng

last: Guo

first: Toshihiro

last: Imamura

first: Andrzej

middle: Z

last: Wasilczuk

first: Xiaoyan

last: Zhang

first: Brendan

middle: T

last: Keenan

first: Miyoko

first: Shimizu

last: Naoki

first: Max

last: Kelz


title: RNA-Seq Analysis of Transcriptome profile in IEC 4.1 cells treated with Interferon Gamma

city: Chicago

first: Aiyu

last: Gong

state: IL

address: 1735 W. Harrison St

department: MPI

institute: Rush University

summary: This study aims to measure the impact of interferon-gamma on the transcriptome profile in cultured IEC 4.1 cells. Cells were treated with interferon-gamma for 6hr. Cells not treated with interferon-gamma were used as a control. Total RNA was collected for the genome-wide analysis and sequencing using DNBSEQ platform.

overall_design: IEC 4.1 murine intestinal epithelial cells were grown to 80% confluence for two groups: the control (Group A, cells not treated with interferon-gamma) and the treated (Group B, cells treated with interferon gamma 10ng/ml for 6 hours). Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.

first: Xian-Ming

last: Chen


title: Nonsense mediated decay degrades nonproductive RNAs produced by alternative RNA splicing in response to heat stress in Arabidopsis

city: Qingdao

first: zhaoxia

last: Li

state: Shandong

address: 700, Changcheng Road, Changyang

department: Agronomy College

institute: Qingdao Agricultural University

summary: Elevated temperature enhances the frequency of alternative RNA splicing (AS) in plants producing RNA isoforms, some of which are productive, likely expanding the repertoire of stress responses, while other isoforms are nonproductive or possibly toxic. This raises the question whether plants can recognize and degrade nonproductive RNA isoforms by nonsense-mediated decay (NMD). In this study Arabidopsis seedlings were subjected to heat stress and RNA isoforms were identified that were upregulated by heat treatment but spared degradation in NMD mutants or in seedlings in which translation was blocked by cycloheximide. The differentially expressed isoforms (DEIs) produced in response to heat stress and that might be relevant to NMD were grouped according to expression patterns. Group 1 DEIs were rapidly heat-induced, then declined during futher heat treatment, but the transcripts were spared from degradation when NMD was compromised. Group 2 DEIs were not upregulated in response to heat; however, their transcript levels declined during heat treatment, but were spared when NMD was blocked. Group 3 DEIs were constitutively expressed although at higher levels when NMD was blocked. While the common targets of NMD are RNA transcripts with premature termination codons (PTCs), other seemingly normal transcripts, such as those with long 3’-untranslated regions (3’-UTRs) are probablistics NMD targets.  Long 3’-UTRs from some Arabidopsisi genes such as WRKY70, ACS11, YUCC5, OSM, and SARD1, were confirmed to be NMD targets using a modified Dual-Luciferase (LUC) 3’-UTR test system in protoplasts. Following heat stress, upstream frameshift (upf) mutants tended to spare from degradation NMD targets, such as transcripts with PTCs.  Despite their penchant for sparing transcripts from degradation, upf mutants were more sensitive to stress, which demonstrates the importance of NMD to resist abiotic stresses, such as heat stress.

overall_design: Each sample was collected in 3 biological replicates, and each replicate from mutiple plants under the same condition.

first: Zhaoxia

first: Renu

last: Srivastava

first: Sivanandan

last: Chudalayandi

first: Andrew

last: Severin

first: Stephen

last: Howell


title: Fecal and epithelial microbiota in Apc(Min/+) and wild-type littermates

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

institute: National Taiwan University

summary: Accumulating evidence suggests a strong link between intestinal microbiota and colorectal cancer initiation, beyond genetic factors. The origins of dysbiosis (altered microbiota composition) remain poorly understood, especially in genetically susceptible hosts. Our previous study has demonstrated that the presence of intraepithelial bacteria as a consequence of intestinal barrier dysfunction shaped dysbiotic microbiota that contributed to colitis development. Here, we evaluated the fecal and epithelial microbiota in age-matched Apc(Min/+) and wild-type littermates. The fecal samples and purified epithelial cells from intestinal segments (ileum and colon) were collected at various time points for analysis of microbiota composition by PacBio full-length 16S rRNA gene sequencing.

overall_design: The gut microbiota in intestinal epithlial cell and fecal samples was analyzed at various time points in ApcMin mice and wildtype littermate mice

first: YiHsuan

first: YuChen

last: Pai


title: RNAseq from MDA-MB-231 shYB-1 and sh control

city: vancouver

first: Gregg

last: Morin

address: 675 West 10th Ave

institute: Canada's Michael Smith Genome Sciences Centre

summary: Elevated YB-1 expression correlates with poor patient survival and drug resistance in diverse tumor types, notably in metastatic tumors. In this report, we characterized the role of YB-1 in breast tumor initiation and progression, in primary cells or cell lines. Notably, YB-1 blockade in MDA-MB-231 cells shown that YB-1 has a major role in tumor progression and dissemination, but not in in vitro settings. Our data suggests induction of YB-1 expression is associated with the activation of a HIF1α program.

overall_design: 8 samples in total were analyzed. Four from stably shScr transduced MDA-MB-231 cells and four from shYB-1- transduced MDA-MB-231 cells. For each category, three samples from MDA-MB-231 derived tumors and one from MDA-MB-231 in vitro culture.

first: Sylvain

last: Lefort

first: Amal

last: El-Naggar

first: Susanna

last: Tan

first: Shane

last: Colborne

first: Gian

middle: L

last: Negri

first: Martin

last: Hirst

first: Barry

last: Gusterson

first: Poul

last: Sorensen

first: Connie

last: Eaves


title: Single-Cell Transcriptomic Analysis of Kaposi Sarcoma

city: St. Louis

first: Lee

last: Ratner

state: Missouri

address: 4451 Clayton Ave, St. Louis

department: Department of Medicine

institute: Washington University in St. Louis

summary: Kaposi Sarcoma (KS) is a complex tumor caused by KS-associated herpesvirus 8 (KSHV). Histological analysis reveals a mixture of “spindle cells”, vascular-like spaces, extravasated erythrocytes, and immune cells. In order to elucidate the infected and uninfected cell types in KS tumors, we examined twenty-five skin and blood samples from sixteen subjects by single cell RNA sequence analyses. Two populations of KSHV-infected cells were identified, one of which represented a CD34-negative proliferative fraction of endothelial cells, and the second representing CD34-positive cells expressing endothelial genes found in a variety of cell types including high endothelial venules, fenestrated capillaries, and endothelial tip cells. Although both infected clusters contained cells expressing lytic and latent KSHV genes, the CD34+ cells expressed more K5 and less K12. Novel cellular biomarkers were identified in the KSHV infected cells, including the sodium channel SCN9A. The number of KSHV positive cells was found to be less than 10% of total tumor cells in all samples and correlated inversely with tumor-infiltrating immune cells. T-cell receptor clones were expanded in KS tumors and blood, although in differing magnitudes. Changes in cellular composition in KS tumors after treatment with antiretroviral therapy alone, or immunotherapy were noted. These studies demonstrate the feasibility of single cell analyses to identify prognostic and predictive biomarkers.

overall_design: Single-cell transcriptomic profiles were generated from 25 Kaposi sarcoma skin lesions and peripheral blood samples obtained from 16 subjects. Samples were analyzed to identify KSHV-infected and uninfected cell populations, characterize cellular heterogeneity and viral gene expression patterns, assess immune cell composition and T-cell receptor clonality, and evaluate changes in cellular composition associated with antiretroviral therapy and/or immunotherapy

first: Daniel

middle: A

last: Rauch

first: Paula

last: Valiño Ramos

first: Mariam

last: Khanfar

first: John

last: Harding

first: Ancy

last: Joseph

first: Anam

last: Fahad

first: Paul

last: Simonson

first: Isabel

last: Risch

first: Obi

last: Griffith

first: Malachi


title: Methylomic Analysis of Nasal Brushings Poorly Discriminates Subgroups in Pediatric Acute Respiratory Distress Syndrome

city: Little Rock

first: James

middle: Garrett

last: Williams

state: AR

address: 13 Children's Way

department: Pediatrics

institute: University of Arkansas for Medical Sciences

type: Methylation profiling by genome tiling array

summary: Pediatric acute respiratory distress syndrome (PARDS) is biologically heterogeneous. To determine whether the nasal epithelial methylome identifies subgroups of PARDS, we profiled genome-wide DNA methylation in nasal brushings from 21 children with PARDS and 3 pediatric ICU controls using the Infinium MethylationEPIC v2.0 array. After estimating and adjusting for cell-type composition, we performed unsupervised clustering and cell-type-specific differential methylation analysis. Cellular composition explained the majority of variation in the unadjusted methylome, and composition-adjusted clustering yielded only weak subgroup structure. These data indicate that, at this sample size, the nasal methylome poorly discriminates PARDS subgroups.

overall_design: Nasal epithelial brushings were collected within 24 hours of PARDS diagnosis (or of PICU admission for controls). Genomic DNA from 24 samples (21 PARDS, 3 controls) was bisulfite-converted and profiled on the Illumina Infinium MethylationEPIC v2.0 BeadChip. Ten samples were residual DNA re-analyzed from a prior enzymatic methyl-seq study and 14 were newly collected (see Supplemental Table 1). No case/control array pairing or block randomization was applied.

middle: G

first: Nirmeen

last: Elmadany

first: Rashika

last: Joshi

first: Rhonda

last: Jones

first: Nathan

last: Gregor

first: Patrick

last: Lahni

first: Steven

middle: W

last: Standage

first: Brian

last: Varisco


title: Peptide E from Bifidobacterium adolescentis LA20-k9 fermentation inhibits feline renal cellular senescence via the SMAD7/p-SMAD3/IL6-CXCL8 axis

city: Wuhu

first: Yu

last: Du

address: No. 8, Yinhe Avenue, Fanchang Economic Development Zone, Fanchang District

institute: Nourse Centre for Pet Nutrition

summary: Aging is an inevitable biological phenomenon that drives progressive functional decline at cellular and tissue levels, with chronic kidney disease (CKD) affecting up to 80% of cats over 15 years of age. Probiotic-derived metabolites hold anti-aging promise, but their renal protective mechanisms remain largely undefined. In this study, we investigated the anti-senescence effects of fermented brown algae extracts from Bifidobacterium adolescentis LA20-K9 (LA20FM) on feline kidney cells. Both the LA20FM<3 kDa and LA20FM>30 kDa molecular weight fractions mitigated doxorubicin-induced senescence, as evidenced by reduced SA-β-gal activity and decreased CDKN1A/CDKN2A expression. Peptide E, which was isolated from the LA20FM<3 kDa fraction, was identified as the principal bioactive component. RNA-sequencing revealed that peptide E downregulated senescence-associated genes, including IL6, CXCL8, GDF15, and KRT15, while upregulating the anti-senescence gene SMAD7. Mechanistically, peptide E enhanced SMAD7 expression, which in turn suppressed SMAD3 phosphorylation and consequently reduced IL6 and CXCL8 transcription. Crucially, SMAD7 knockdown completely abrogated these protective effects. Collectively, our findings identify peptide E as a novel bioactive peptide that antagonizes renal cellular senescence via the SMAD7/p-SMAD3/IL6-CXCL8 axis, offering a potential therapeutic candidate for age-related kidney dysfunction in felines.

overall_design: To investigate the mechanism by which peptide E inhibits senescence in feline kidney cells, RNA-sequencing was performed on DOX-induced senescent feline kidney cells (PETCC 2610) with or without peptide E treatment using the Illumina NovaSeq 6000 platform (paired-end 150 bp), with three biological replicates per condition. Differential gene expression analysis was conducted to identify key senescence-associated and senescence-inhibitory genes regulated by peptide E.

first: Yanping

last: Xu


title: Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [ChIP-Seq]

city: Boston

first: Evgeny

last: Deforzh

address: 60 Fenwood Rd, Brigham and Women's Hospital Neurology Department, 9th Floor

department: Neurology

institute: Brigham and Women's Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The human genome is pervasively transcribed into protein-coding and regulatory non-coding RNAs whose functions are coordinated within higher-order nuclear architectures. However, direct mapping of RNA–RNA and DNA–DNA interaction networks in complex human tissues at single-cell resolution has remained a major challenge. Here, we present SCIENCE-seq, a multimodal single-cell interactomics platform enabling simultaneous detection of RNA–RNA interactions and chromatin DNA–DNA contacts within individual cells. Applied to primary glioma specimens, SCIENCE-seq reveals cancer-specific interactions organized by lncRNAs and centered on key oncogenic drivers, including EGFR, hTERT, SOX2, CDK6, CDC42, CD47, and HOX loci. These datasets uncover previously unrecognized molecular relationships between premature lncRNAs and pre-mRNAs that regulate transcription, alternative splicing, and polyadenylation. Notably, we identify a glioma-specific trans-chromosomal HOX hub driven by five interacting lncRNAs. Targeting these RNA and DNA interactions with steric antisense oligonucleotides (ASOs) or CRISPRi enables selective inhibition of oncogenic programs in malignant cells while sparing normal tissue, establishing chromatin interactomes as actionable therapeutic targets.

overall_design: Bulk H3K27Ac or H3K27Me3 ChIP-Seqs were performed to access the chromatin status (active or silent) of cis-regulatory elements in GBM8 and NHA. Additionally, PPARD binding profile was measured by bulk ChIP-Seq in NHA after all-trans-retinoic acid treatment.


title: XCR1+ and CD11b+ migratory dendritic cells cooperate for the crosspriming of intratumoral CD8+ T cells with a tissue-resident memory phenotype

city: Paris

last: Vaudiau

address: 25 rue du Docteur Roux

department: Immunology

institute: Institut Pasteur

summary: The composition and diversity of tumor-infiltrating CD8+ T cell populations have important consequences on the development of anti-tumor immunity. In a murine model of lung cancer, we have addressed the role of dendritic cell subsets on the generation of various types of tumor-infiltrating CD8+ T cells. We show that CD44+PD1- effector and PD1+TIM3+ exhausted, tumor-infiltrating CD8+ T cells require XCR1+ DC1s but not IRF4-dependent CD11b+ DC2s. By contrast, CD103+CD69+ TRM-like, tumor-infiltrating CD8+ T cells require both DC1s and DC2s. The same requirement is found in tumor-draining lymph nodes where we identify CD103+ TRM-like precursors that are dependent on both XCR1+ DC1s and CD11b+, migratory DC2s. Mechanistically, we evidence that both types of migratory DCs cooperate. Mild TCR triggering by low MHCI-peptide density at the surface of cross-presenting migratory DC2s and low IL-12 support TGFb-dependent TRM specification in lymph nodes. High TCR triggering and high MHCI-peptide density at the surface of cross-presenting migratory DC1s and high IL-12 support proliferative expansion and CXCR6 acquisition. Altogether, these findings highlight the induction of intratumoral TRM-like cells under the collective aegis of multiple DCs subsets within tumor-draining lymph nodes reconciliating TRM phenotype instruction with proliferative expansion.

overall_design:
In this project, we have worked in the KP (KRASG12D; p53-/-) model of murine lung cancer. 14 days after intravenous injection of the KP cell line, CD8+ T cells or CD11c+MHCII+ cells were stained with CITE-Seq antibodies then sorted by flow cytometry from pooled lungs or lymph nodes of 3 C57BL/6J mice before scRNA-seq analysis.Single cells were isolated using a 10X Chromium droplet-based approach and sequenced. 5 different samples are provided:
Lung_CD8_KP_WT : Lung CD8+ T cells of WT (C57BL6/J) mice with KP tumors
LN_CD8_KP_WT : Lymph nodes CD8+ T cells of WT (C57BL6/J) mice with KP tumors
LN_CD8_KP_CD11c_IRF4 : Lymph nodes CD8+ T cells of Cd11ccrexIrf4fl/fl mice with KP tumors
LN_DC_KP_WT : Lymph nodes CD11c+MHCII+ T cells of WT (C57BL6/J) mice with KP tumors
LN_DC_KP_CD11c_IRF4 : Lymph nodes CD11c+MHCII+ T cells of Cd11ccrexIrf4fl/fl mice with KP tumors

first: Pierre

last: Bourdely

first: Maria

last: Semitekolou

first: Agathe

last: Ok

first: Louise

last: Gorline

first: Aboubacar

last: Coulibaly

first: Matthieu

last: Rastello

first: Aurélie

last: Semervil

first: Roberto

last: Savoldelli

first: Yohan

last: Gerber-Ferder

first: Fillipe

last: Rosa do Carmo

first: Mathias

last: Vétillard

first: Audrey

last: Rood

first: Jérémie

last: Bornères

first: Abdenour

last: Abbas

first: Marie

last: Guillin

first: Judith

last: Weber

first: Syrine

last: Bouallègue

first: Konstantina

last: Pamboukas

first: Zacarias

last: Garcia

first: Florent

last: Ginhoux

first: Camille

last: Bleriot

first: Philippe

last: Bousso

first: Yosuke

last: Kumamoto

first: Guillaume

last: Darasse-Jèze

first: Emmanuel

last: Gautier

first: Marc

last: Dalod

first: Eric

last: Tartour

first: Tessa

last: Bergsbaken

first: Klaas

middle: P

last: Van Gisbergen

first: Kairbaan

middle: M

last: Hodivala-Dilke

first: Massimiliano

last: Mazzone

first: Loredana

last: Saveanu

first: Julie

last: Helft

first: Federica

last: Benvenuti

last: Guermonprez


title: Integrated multi-omics reveals the cellular and molecular interactions governing the invasive niche in skin cancer II

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: To progress, tumors need to invade the surrounding tissues. However, the heterogeneity of cell types at the tumor-stroma interface and the complexity of their potential interactions hampered mechanistic insights for efficient therapeutic targeting. Here, combining single-cell and spatial transcriptomics on human basal cell carcinomas (BCCs), we define the cellular contributors of the invasive front. In the invasive niche, tumor cells harbor a collective migration phenotype, supported by the expression of cell-cell junction complexes. In physical proximity, we identify cancer-associated fibroblasts (CAFs) with extracellular matrix-remodeling features, as required to support collective migration. Moreover, while tumor cells specifically express Activin A, we find Activin A-induced gene signature enrichment in adjacent CAFs subpopulations, further supporting their biological crosstalk. Altogether, our data identify the subpopulations and their transcriptional reprogramming contributing to the spatial organization of the BCC invasive niche. They also bring the proof-of-concept for integrated spatial and single-cell multi-omics to decipher cancer-specific invasive properties and develop therapeutic targeting.

overall_design: Fresh basal cell carcinoma tumors of two patients were minced and enzymatically dissociated to single cell suspension. All single living cells were FACS-sorted and processed with the Chromium Next GEM single cell 3' reagent v3.1 kit (10x Genomics) to perform single cell RNA sequencing. Sequencing was performed on an Illumina HiSeq 4000 device. The sequence reads that passed quality filters were analyzed with Seurat R package (v.4.0.1).

first: Laura

last: Yerly

first: François

last: Kuonen


title: XCR1+ and CD11b+ migratory dendritic cells cooperate for the crosspriming of intratumoral CD8+ T cells with a tissue-resident memory phenotype [RNA-Seq]

first: Nathan

last: Vaudiau

overall_design:
In this project, we have worked in the KP (KRASG12D; p53-/-) model of murine lung cancer. Briefly, the KP cell line was injected intravenously in C57BL/6J mice and CD8+ T cell and dendritic cell populations were assessed at day 14 post-injection. Two bulk RNA-Seq datasets were generated:
- CD8+ T cells populations from individual lungs or lymph nodes of 3-4 KP tumor-bearing mice were FACS-sorted and bulk-RNA sequencing was performed.
- CTV-loaded naïve OT-I cells cultured for 2 days with flow cytometry-sorted migratory DC1 or migratory DC2 from tumor-draining lymph node of mice bearing KP-OVA tumors. CD103+ and CD103- divided OT1 activated by DC1 or DC2 were FACS-sorted and bulk-RNA sequencing was performed.

first: Pierre

last: Bourdely

first: Maria

last: Semitekolou

first: Agathe

last: Ok

first: Louise

last: Gorline

first: Aboubacar

last: Coulibaly

first: Matthieu

last: Rastello

first: Aurélie

last: Semervil

first: Roberto

last: Savoldelli

first: Yohan

last: Gerber-Ferder

first: Fillipe

last: Rosa do Carmo

first: Mathias

last: Vétillard

first: Audrey

last: Rood

first: Jérémie

last: Bornères

first: Abdenour

last: Abbas

first: Marie

last: Guillin

first: Judith

last: Weber

first: Syrine

last: Bouallègue

first: Konstantina

last: Pamboukas

first: Zacarias

last: Garcia

first: Florent

last: Ginhoux

first: Camille

last: Bleriot

last: Bousso


title: USP22 is a novel vulnerability regulating MEIS1 protein abundance and gene transcription in KMT2Ar acute leukemia

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

institute: Hannover Medical School

summary: Patients with acute leukemias harboring translocations involving gene lysine methyltransferase 2A (KMT2A) have a poor prognosis due to chemotherapy resistance with rapid relapse following standard treatments. The resulting KMT2A fusion proteins dysregulate gene expression, leading to an upregulation of leukemogenic transcription factors such as HOXA9 and MEIS1, which drives leukemic transformation. Although Menin inhibitors are proving to be promising new therapeutics for patients with KMT2A-rearranged (KMT2Ar) acute leukemia, resistance mechanisms have already been described and new therapeutic approaches for this patient subgroup must be identified. Here, a genome-wide CRISPR/Cas9 screen in a KMT2Ar B-cell acute lymphoblastic leukemia (ALL) cell line identified the deubiquitinase USP22 as a novel regulator of MEIS1 protein stability. USP22 is a member of the Spt-Ada-Gcn5 acetyltransferase (SAGA) multiprotein complex, which has crucial functions in shaping the chromatin landscape and modulating transcription. Genetic depletion of USP22 impaired cellular growth and proliferation in KMT2Ar acute leukemia models. Chromatin immunoprecipitation revealed cooperative binding between USP22 and MEIS1 at critical oncogenic target genes suggesting that USP22 safeguards leukemogenic transcription by protecting MEIS1 from proteasomal degradation. Genetic or chemical inhibition of USP22 led to polyubiquitination of MEIS1 resulting in proteasomal degradation and downregulation of the expression of target genes. Our study identifies USP22 as a novel regulator of MEIS1 protein stability, that could potentially be exploited as a therapeutic target in the future in KMT2Ar leukemias.

overall_design: ChIP sequencing of MEIS1 and USP22 in MV411 and SEM cell lines


title: Chlamydia serovars in uterus- scRNA-seq, CITE-seq and TCRab

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: This study is part of the immgenT Open Source Project, specifically from IGT33, which focuses on characterizing T cell populations in the uterus during Chlamydia trachomatis D and L2 infections. Mice received 1% transgenic NR23.4 (CD8) and NR1 (CD4) T cells intravenously 24 hours before infection to track antigen-specific CD8 and CD4 T cell responses. Mice were infected transcervically with C. trachomatis serovars D (UW-3/Cx) and L2 (434/Bu) (5x10E6 IFU) at day 0 and rechallenged at day 28 post-infection (5x10E6 IFU). T cells were isolated from the uterus of C57BL/6J mice at multiple time points: 5 and 15 days post-primary infection and 3 and 5 days post-secondary challenge. All animals were pre-treated with medroxyprogesterone acetate to synchronize estrous cycles.

overall_design: Single-cell suspensions from the uterus were prepared using collagenase XI and DNase I. TCRβ/γδ+ T cells were profiled using single-cell RNA sequencing (10x Genomics), combined with CITE-seq (TotalSeq C) and paired TCR α/β sequencing. Samples were pooled using hashtags.

first: Andrea

last: Lebron Figueroa

first: David

last: Zemmour

first: Christophe

last: Benoist


title: RNA exosome-dependent transcriptional adaptation masks gene essentiality

city: Bad Nauheim

first: Jan

last: Detleffsen

state: Hessen

address: Ludwigstraße 43

institute: Max Planck Institute for Heart and Lung Research

summary: CRISPR-based gene knockouts assume that phenotypes directly reflect gene function. Here, we show that RNA exosome-dependent buffering frequently masks knockout phenotypes. Using combinatorial CRISPR screens, we identify RNA exosome-dependent genes whose loss-of-function phenotypes are revealed only when RNA surveillance is impaired. We find that the RNA exosome is required for both the initiation and maintenance of transcriptional adaptation, in which disruption of a trigger gene induces the compensatory upregulation of a buffering gene. Mechanistically, intronic Alu elements provide sequence homology between trigger-buffer gene pairs and regulate the formation of circular RNAs that suppress compensatory transcription. Disrupting splicing, deleting intronic Alu elements, or targeting the resulting circular RNAs reduces circular RNA abundance and enables transcriptional adaptation. Our results uncover a sequence-encoded mechanism in which intronic Alu-derived circular RNAs gate RNA exosome-dependent transcriptional adaptation to mask gene phenotypes, and suggest that gene essentiality is actively regulated by RNA exosome-mediated buffering, with broad implications for the interpretation of context-specific gene dependencies.

overall_design: RNA-seq analysis of the RNA exosome components EXOSC4 and DIS3 in hTERT-RPE1 cells. RNA was extracted from wild-type (WT) cells and cells depleted of EXOSC4 or DIS3. Depletion was achieved with siRNAs.

first: Sebastian

last: Süsser

first: Ronay

last: Cetin

first: Antonella

last: Vera-Guapi

first: Cosmin

last: Tudose

first: Chiara

last: Becht

first: Thomas

last: Rohde

first: Martin

last: Wegner

last: Heigwer

first: Gabriel

last: M. C. Longo

first: Alessandro

last: Vinceti

first: Sweta

last: Taylan

first: Siu

last: Wang Ng

first: Anjan

last: Venkatesh

first: Yves

last: Matthess

first: Tabea

last: Hoffmann

first: Simone

last: Schaubeck

first: Koraljka

last: Husnjak

first: Jannik

last: Lübke

first: Colm

last: Ryan

first: Francesco

last: Iorio

first: Vassilis

last: Roukos

first: Michael

last: Boutros

first: Mario

last: Looso

first: Maximilian

last: Billmann

first: Manuel

last: Kaulich


title: Tumor-selective protein translation of mRNA drugs for targeted tumor therapy

city: Beijing

first: Xiangdong

last: Zhang

address: Tsinghua University

institute: Tsinghua Univercity

summary: mRNA-based therapies necessitate precise, specific, and patient-friendly control of therapeutic protein translation to ensure treatment safety and efficacy. However, achieving tumor-specific mRNA translation regulation remains a significant challenge. Herein, we developed an mRNA 2’-OH cloaking reagent, CR-3, enabling tumor-specific regulation of mRNA translation. CR-3 can efficiently and effectively block the translational capacity of mRNA. Within tumor cells exhibiting high expression of NAD(P)H quinone dehydrogenase 1 (NQO1), the translational ability of this mRNA can be almost fully restored. The translational efficiency of cloaked mRNA in tumor cells is more than 100-fold greater than that in normal cells. Additionally, 2’-OH cloaking enhances the stability and half-life of mRNA, resulting in a 49% increase in target protein production. The cloaked apoptogenic protein BAX mRNA achieved tumor cell-specific clearance, and mitigated systemic toxicity in both subcutaneous xenograft mouse model and chemically induced mouse model of hepatocellular carcinoma, in contrast to conventional non-cloaked BAX mRNA. This approach may pave the way for the development of safe, convenient, and responsive tumor-targeted mRNA therapeutics.

overall_design: RNA-seq profiling of HepG2 cells under five conditions (n=3 biological replicates per group): untransfected control (UT), non-cloaked eGFP mRNA (O), weak-cloaked eGFP mRNA (W, 0.1 M CR-3, 0.5 h, 25C), medium-cloaked eGFP mRNA (M, 0.5 M CR-3, 1 h, 30C), and strong-cloaked eGFP mRNA (S, 1 M CR-3, 2 h, 37C). Cells were harvested at 48 h post-transfection for transcriptome analysis to evaluate the effect of mRNA cloaking on global gene expression.

first: Xucong

last: Teng

first: Jinghong

last: Li


title: 16S rRNA gene amplicon sequencing of gut microbiota from APAP-induced acute liver injury mice treated with Polygonatum odoratum extract

city: Guilin

first: lanyu

last: li

address: No. 1 Zhiyuan Road, Lingui District

institute: Guilin Medical University

summary: 16S rRNA V3-V4 amplicon sequencing was performed on fecal samples from 12 male C57BL/6J mice across three groups (4 replicates each): Control (distilled water, 3 days), Model (distilled water, 3 days + APAP 300 mg/kg i.p.), and PoH (PO extract 3 g/kg p.o. daily for 3 days + APAP 300 mg/kg i.p.). Sequencing was performed on an Illumina NovaSeq 6000 platform using paired-end 250bp reads.

overall_design: Three-group comparison: Control vs. APAP-induced acute liver injury (Model) vs. APAP + Polygonatum odoratum extract treatment (PoH). Fecal samples were collected from male C57BL/6J mice for 16S rRNA V3-V4 amplicon sequencing, with 4 biological replicates per group.

first: Huanghui

last: Qin

first: Runxiao

last: Chen

first: Ying

last: Shi

first: Caibin

first: Yiming

last: Bin

first: Zhaoming

last: Zeng

first: Bin

last: Deng

first: Lanyu


title: Circadian Clock Gene Modulation and Selective Reprogramming in Response to Copy-back Viral Genomes During Infection

city: St Louis

first: Carolina

middle: B

last: Lopez

state: MO

address: 425 S Euclid Ave

summary: The circadian clock regulates fundamental cellular processes that include the host response to infection. However, its intersection with the mechanisms driving antiviral immunity remains poorly explored. Copy-back viral genomes (cbVGs) generated during virus replication strongly stimulate immunity during infection with negative-sense RNA viruses. Here, we demonstrate that the model lung epithelial cells A549 are circadian-competent, and by tracking the circadian clock at single-cell resolution across an active infection timeline, we show that infection with Sendai virus progressively disrupts the molecular clock architecture, driven primarily by cbVGs. Furthermore, we show that MAVS signaling is essential for the induction of the circadian clock activating component ARNTL2, while PKR signaling is required for the cbVG-specific induction of the repressive components NR1D1, NR1D2, and PER1. A similar cbVG-specific signature was observed in cells infected with a cbVG-high respiratory syncytial virus stock, demonstrating that cbVG-driven clock reprogramming extends to phylogenetically distinct negative-sense RNA viruses. In addition, we established through gain- and loss-of-function experiments that ARNTL2 is functionally required for amplifying the transcriptional response to infection, with selective effects on the expression of specific antiviral genes including CCL5. Together, these findings demonstrate that the host clock is actively disrupted by a subset of viral genomes produced during virus replication and specific clock genes are repurposed to enhance the host response to infection.

overall_design: Control or BMAL2-expressing A549 lung epithelial cells were infected with Sendai Virus at an MOI of 1.5. RNA was collected from mock-infected and Sendai virus-infected cells at 24 hours post infection and RNA-sequencing was performed.

first: Nicole

last: Rivera

first: Emna

last: Achouri

first: Matthew

last: Hackbart

first: Maria

middle: F

last: Gonzalez Aponte

first: Yanling

last: Yang

first: Erik

last: Herzog

last: B. López


title: Genomic and spatial transcriptomics identify fibroblast-associated microenvironment in early mycosis fungoides progression

city: Seoul

first: Myoung Eun

last: Choi

address: Song-pa gu

institute: Asan medical center

summary: Mycosis fungoides (MF) is the most common cutaneous T-cell lymphoma. To characterize the tumor microenvironment at single-cell spatial resolution, we applied NanoString CosMx Spatial Molecular Imaging (SMI) with a 1000-plex panel to formalin-fixed paraffin-embedded (FFPE) skin biopsies from MF patients. This dataset includes patch-stage and plaque-stage MF lesions from 16 patients, comprising 65,717 cells profiled across multiple fields of view per patient.

overall_design: Skin punch biopsies were obtained from 16 patients with mycosis fungoides (8 patch-stage, 8 plaque-stage). FFPE sections were processed for CosMx SMI profiling using the 980-plex RNA panel. Each patient sample constitutes one GEO Sample. Cell segmentation, transcript detection, and expression quantification were performed using NanoString AtoMx software. Downstream analysis was performed in R using Seurat v5.

first: Myoung

first: Ji

first: Hwa-Jeong

last: Shin

first: Chong

last: Won

first: Sung

last: Chang

first: Mi

last: Lee

first: Woo

middle: J


title: Single-cell transcriptomic profiling of pituitary adenoma from patient with Cushing's disease

city: Shanghai

first: Cui

last: Zhang

address: 197, Ruijin 2nd Road

institute: Ruijin Hospital

summary: We performed single-cell transcriptomic profiling of a pituitary adenoma from a patient with a rare subtype of Cushing's disease using the 10x Genomics platform. The analysis revealed the cellular landscape of the tumor, identifying distinct cell populations, their transcriptional signatures, and the degree of intratumoral heterogeneity. These findings provide insights into the cellular architecture of this uncommon ACTH-secreting pituitary adenoma variant.

overall_design: SnRNA-seq was performed on a cryopreserved CCS pituitary tumor sample from a patient with Cushing's disease. Nuclei were isolated by mortar-based homogenization and purified by iodixanol density gradient centrifugation, with quality assessed by AOPI staining and trypan blue. Libraries were prepared using the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics), targeting 10,000 nuclei, and sequenced on an Illumina NovaSeq X Plus platform (PE150, ~100 Gb). Raw data were processed with Cell Ranger (v5.0.1) aligned to GRCh38-2020-A, followed by quality filtering. Publicly available scRNA-seq datasets were integrated with the snRNA-seq data using Seurat (v5.3.0) with CCA-based batch correction, followed by dimensionality reduction, clustering, and UMAP visualization.


title: snATAC-seq from HCT116 (ENCSR270OJH)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Transcriptomic profiling of Rb1-treated DC2.4 dendritic cells

first: Yuxiang

last: Lu

address: 1200 Cailun Road

institute: shanghai university of traditional chinese medicine

summary: Ginsenoside Rb1 was investigated for its effects on dendritic cell function and antitumor immunity. Bulk RNA-seq was performed on murine DC2.4 dendritic cells treated with vehicle or Rb1 to identify transcriptional changes associated with impaired antigen presentation, LGALS2-related signaling, and suppression of the JAK-STAT pathway.

overall_design: DC2.4 murine dendritic cells were treated with vehicle or Rb1 (10 uM) for 24 h. Two biological replicates were included for each condition. Gene-level raw count and FPKM matrices were generated and used to compare Rb1-treated cells with vehicle-treated controls.

first: Li

last: Yuan

first: Lu

last: Yuxiang

first: Zhou

last: Shiling

last: Jiaxing

first: Feng

last: Yuanlong

first: Ma

last: Fen

first: Zhang

last: Jiwei


title: Transcriptomic profiling of lung tissue from wild-type and TMPRSS2-knockout rats

city: Berlin

first: Yue

last: Qiu

address: Robert-Rössle-Straße 10

institute: Max Delbrück Center - Berlin

summary: This RNA-seq dataset profiles lung tissues from wild-type Sprague-Dawley rats and crTMPRSS2 (TMPRSS2-knockout) rats. The experiment was used to assess transcriptional changes associated with loss of TMPRSS2, including altered expression of inflammatory, innate immune, and adaptive immune response-related genes.

overall_design: Total RNA from lung tissues of WT and crTMPRSS2 rats was analyzed by mRNA-seq. The design includes two genotypes (WT and crTMPRSS2 knockout) with three biological replicates per genotype. Differential expression was analyzed as KO vs WT.

first: Qiu

last: Yue

first: Popova

last: Elena

first: Bader

last: Michael


title: Transcriptomic analysis of bone-marrow-derived macrophages treated with extracellular vesicles (EVs) from Aspergillus flavus

city: Guiyang

first: Yinhui

last: Jiang

address: No. 6, Ankang Avenue, GUI 'an New Area, Guizhou Province

institute: Guizhou Medical University

summary: We performed transcriptomic analysis of bone-marrow-derived macrophages (BMDMs, C57BL/6 mice) treated with extracellular vesicles (EVs) from A. flavus strain LD-F1 or LD-F1-b, with PBS-treated (phosphate buffer saline) cells as control.

overall_design: We incubated BMDMs (2 × 106 cells/mL; 105 cells per well in 24-well plates) with EVs (20 µg per well) or PBS for 6 h. We collected the treated cells and extracted total RNAfor sequencing on the Illumina NovaSeq platform, with two biological replicates per condition.


title: Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation

city: Tokyo

first: Shoin

last: Tei

address: 1-1-1 Yayoi, Bunkyo-ku

department: Institute for Quantitative Biosciences

institute: The University of Tokyo

summary: Cohesin organizes 3D chromatin architecture, including promoter–enhancer loops, yet its loss has surprisingly modest effects on steady-state gene expression. We address this paradox by demonstrating that cohesin acts at different stages of transcription. First, it promotes Pol II promoter recruitment by facilitating enhancer–promoter communication that maintains active promoter chromatin states. Second, it delays pause release by transiently associating with the transcriptional machinery during the pause–release transition. Kinetic modelling suggests that reduced Pol II recruitment and enhanced pause release have compensatory effects, contributing to minimal changes in steady-state gene expression across genes upon cohesin loss. In contrast, cohesin depletion impairs robust transcriptional induction in response to external stimuli. Moreover, cohesin ensures sufficient pausing duration as a quality-control-like step to promote elongation complex assembly and transcription processivity. Here, we show that cohesin regulates multiple steps of transcription, offering mechanistic insight into cohesin-related diseases, including cancers and cohesinopathies.

overall_design: CUT&Tag in HCT-116 cell line

first: Toyonori

last: Sakata

first: Atsunori

last: Yoshimura

first: Toyoaki

last: Natsume

first: Masato

last: Kanemaki

first: Takashi

last: Sutani

first: Masashige

last: Bando

first: Katsuhiko

last: Shirahige


title: Gene expression changes in ventricular tissues were identified through RNA sequencing analysis of a mouse model of cardiac hypertrophic remodeling induced by angiotensin II (Ang II)

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary: Forsythoside I (FI), a representative caffeoyl phenylethanoid glycoside isolated from Forsythia suspensa, has been previously validated to exert anti-inflammatory and anticancer effects. Nevertheless, research regarding its potential role in cardiovascular diseases, particularly pathological cardiac hypertrophy, and the underlying molecular mechanisms remains largely unknown.

overall_design: The mice were randomly divided into three experimental groups: saline + vehicle, angiotensin II (Ang II) + vehicle, and Ang II + Forsythoside I (FI). Cardiac hypertrophic remodeling was induced on day 0 by subcutaneous implantation of an Ang II-containing osmotic minipump in the dorsal neck region. FI (50 mg/kg) was administered intraperitoneally every other day from one day prior to Ang II infusion through day 14.Total RNA was extracted from ventricular tissues (n=4 per group) at the endpoint using TRIzol reagent (Invitrogen) according to the manufacturer's protocol.

first: Shu-Jing

last: Liu

first: Wei-Jia

last: Yu

first: Qing-Song

last: Li

first: Shi-Nong

first: Zhi-Chao

last: Dong

first: Hui-Hua

first: Qiu-Yue

last: Lin


title: Transcriptomic profiling of Peniophora incarnata T-7 during lignocellulose degradation under different substrate conditions

city: Changsha

first: Jiangshan

last: Ma

state: Hunan

address: No. 498 Shaoshan South Road, Tianxin District

institute: Central South University of Forestry and Technology

summary: Peniophora incarnata T-7 is a white-rot fungus with a pronounced capacity for preferential lignin degradation. To investigate the molecular responses of this strain during lignocellulose degradation, P. incarnata T-7 was cultured on different lignocellulosic substrates, including poplar wood, Chinese fir wood, and rice straw, with PDA medium as the control. RNA-seq was performed to characterize substrate-induced gene expression profiles and to identify genes potentially involved in lignin, cellulose, and hemicellulose degradation. This dataset provides transcriptomic resources for understanding the lignocellulose-degrading mechanism and substrate-adaptive responses of P. incarnata T-7.

overall_design: Peniophora incarnata T-7 was cultured under four conditions with a cultivation period of 30 days: poplar wood (PW), Chinese fir wood (FW), rice straw (RS), and PDA medium as the control. Three biological replicates were prepared for each condition. Total RNA was extracted from mycelial samples, and RNA-seq libraries were constructed for transcriptome sequencing. Differential gene expression analysis was performed to compare substrate-induced transcriptional responses among the lignocellulosic substrates and the control condition, with particular attention to lignocellulose-degrading enzymes, transcription factors, and genes derived from different duplication modes.

first: Gao-Qiang

first: Yujiang

last: Qin

first: Haoling

last: Hu

first: Bingqian

last: Xie