title: Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland [scChIC]

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

summary: Single-cell multi-omics methods enable simultaneous mapping of chromatin states and transcriptomes, offering deep insights into gene regulation. Yet, the full potential of these approaches remains untapped for rare cell populations, as most methods require thousands of cells and are limited in their ability to capture multiple molecular layers comprehensively within the same cell.  Here, we introduce OneCell CUT&Tag a user-friendly method that provides matched high-resolution epigenome, full-transcriptome, and surface marker quantification from every cell, with input as low as one cell. Using this approach, we uncovered epigenomic priming of basal cells in the mammary gland and captured the dynamics of basal-to-luminal transdifferentiation. We identified a transitional cell population with intermediate epigenomic profiles—absent in reference populations—and demonstrated a continuous epigenomic progression from basal to luminal states, while transcriptomes exhibited a binary switch. Adaptable to diverse samples and tissues, this method also revealed the role of H3K27me3 in shaping zygotic expression programs. By matching multiple layers of molecular information at single-cell resolution, OneCell CUT&Tag dissects the complementary roles of each omics layer in shaping cellular identity and function, opening new avenues to study rare and complex biological systems.

overall_design: scChIC-seq (Zeller et al. 2023; PMID: 36539617) of H3K27me3 on MDA-MB-468 single-cells sorted in a 384-well plate

first: Eve

last: Moutaux

first: Anna

last: Schwager

first: Adeline

last: Durand

first: Mélanie

last: Miranda

first: Louisa

last: Hadj

first: Simon

last: Dumas

first: Mathias

last: Schwartz

first: Marthe

last: Laisné

first: Justine

last: Marsolier

first: Manuel

last: Guthmann

first: Délia

last: Dupré

first: Grégoire

last: Jouault

first: Mélissa

last: Saichi

first: Déborah

last: Bourc’his

first: Elisabetta

last: Marangoni

first: Nicolas

last: Servant

first: Leïla

last: Perié


title: Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland [zygotes_bulkCUT&RUN]

status: Public on Jul 03 2026

first: Céline

last: Vallot

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Bulk CUT&RUN on 50 murine zygotes obtained 23 hours post hCG treatment replicated on two mice.

first: Eve

last: Moutaux


title: Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland [zygotes_OneCell_multiome]

type: Expression profiling by high throughput sequencing

overall_design:
OneCell multiome (H3K27me3 / H3K4me1 + transcriptome) on single mouse zygotes

Zygotes were collected after hormonal induction with pregnant mare serum gonadotropin (5 IU) and human chorionic gonadotropin (hCG, 5 IU) 46–48-h later. Zygotes were collected at 23 post-hCG treatment in M2 medium. Cumulus cells were removed using M2 media containing hyaluronidase (Merck-Millipore, MR-051-F). The zona pellucida was removed with Pronase (Sigma-Aldrich, P8811), followed by two washes in M2 medium and one in culture media. Zygotes were then manually dispensed in 2 µl of M2 medium with 0.2µl Dynabeads Myone Carboxylic (Fisher, 10563775) and kept on ice. After a 5 min centrifugation at 800g at 4°C, the supernatant was removed using the magnetic plate and replaced by 2µl of OneCell lysis buffer. Plates were then frozen at -80°C and than processed according to multiomic OneCell CUT&Tag protocol with either H3K27me3 [CST, 9733] or H3K4me1 [CST, 5326] antibody.

Each zygote batch corresponds to zygotes obtained from one mouse.

first: Anna

last: Schwager

first: Adeline

last: Durand


title: Dysregulated thymus-ovary axis promotes virtual memory T cell polarization to aggravate PCOS pathology [scRNAseq-mouse]

city: Beijing

first: Chenlei

last: Xu

address: No. 38 Xueyuan Road, Haidian District

country: China

institute: Peking University

summary: Polycystic ovary syndrome (PCOS) is characterized by androgen excess, ovarian dysfunction and polycystic ovarian morphology and is classically considered as a disorder of the hypothalamic-pituitary-gonadal (HPG) axis. However, whether organs beyond the reproductive endocrine axis contribute to PCOS pathogenesis remains elusive. Herein, we identified a functional thymus-ovary axis involved in PCOS development.

overall_design: Using complementary mouse models, we demonstrated that thymic remodeling occurs early during disease development, preceding the onset of aberrant ovarian pathology. Disruption of thymic function or genetic ablation of adaptive immunity markedly attenuated PCOS-related lesions, indicating a central role for T cells. Mechanistically, CD8⁺ T cells acted as the dominant effector subset, with selective expansion of virtual memory CD8⁺ T (TVM) cells during PCOS progression. These cells preferentially accumulated in reproductive tissues, exacerbated ovarian inflammation and prolonged disease persistence following endocrine challenge. Functionally, adoptive transfer of TVM cells enhanced disease severity, whereas depletion of CD8⁺ T cells or selective restriction of TVM cell polarization by JAK inhibition alleviated PCOS phenotypes.

first: Yaruo

last: Qiu

first: Weixuan

last: Wang

first: Yao

last: Feng

first: Dan

last: Lv


title: Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series

first: Alexandra

last: Van Keymeulen

first: Amélie

last: Viaene

first: Mélanie

last: Miranda

first: Louisa

last: Hadj Abed

first: Simon

last: Besson-Girard

first: Marion

last: Lambault

first: Juliette

last: Bertorello

last: Dumas

first: Mathias

last: Schwartz

first: Marthe

last: Laisné

first: Justine

last: Marsolier

first: Manuel

last: Guthmann

first: Lorraine

last: Bonneville

first: Urvashi

last: Chitnavis

first: Cédric

last: Blanpain


title: Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland [frozen_pdx_OneCell_CUT&Tag]

first: Céline

last: Vallot

overall_design: OneCell CUT&Tag of H3K4me1 on human single-nuclei from frozen triple-negative breast tumors from patient-derived xenografts (HBCx-14 PDX model)

first: Eve

last: Moutaux

first: Anna

last: Schwager

first: Adeline

last: Durand

last: Hadj

first: Délia

last: Dupré

first: Grégoire

last: Jouault

first: Mélissa

last: Saichi

first: Déborah

last: Bourc’his

first: Elisabetta

last: Marangoni

first: Nicolas

last: Servant

first: Leïla

last: Perié


title: Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland [ChIP-seq]

overall_design: Single-cell ChIP-seq (Grosselin et al 2019; PMID: 31152164) of H3K27me3 on MDA-MB-468 single-cells.

first: Mélanie

last: Miranda

first: Louisa

first: Simon

last: Dumas

first: Mathias

last: Schwartz

first: Marthe

last: Laisné

last: Marsolier


title: Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland [scCUT&Tag]

last: Vallot

overall_design: 10x Genomics single-cell CUT&Tag of H3K27me3 on MDA-MB-468 single-cells

first: Justine

first: Manuel

last: Guthmann


title: The high expression of siglec10 in tumor macrophages may promote the progression of colorectal cancer

city: nantong

first: chuang

last: miao

state: jiangsu

address: No. 20 Xisi Road

department: Department of General Surgery

institute: Affiliated Hospital of Nantong University

summary: SIGLEC10, also known as sialic-binding immunoglobulin-like lectin 10, is a member of the SIGLEC family. SIGLEC10 is expressed on the surface of immune cells and is involved in the regulation of immune responses by recognizing microorganisms or cells with specific sialic acids. Among other cancer types, SIGLEC10 has been identified as a novel tumor-associated macrophage-associated immune checkpoint. This study suggests that siglec10 is an independent prognostic factor in patients with CRC and may be a promising immunotherapeutic target for CRC in the future.

overall_design: There were 6 samples, 3 positive groups and 3 negative groups

first: Chuang

last: Miao

first: Fei

last: Qian


title: Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland [transplantations_OneCell_multiome]

first: Céline

overall_design:
OneCell multiome (H3K4me1 + transcriptome) on control mouse mammary gland cells (d0) and basal cells grafted to the cleared fat pad at d4.5 post-engraftment.

Mammary glands from K14cre/RosaYFP34,35 adult female mice were dissected and the lymph nodes removed before processing. Tissues were washed in HBSS, and chopped into pieces of 1 mm3. The tissues were placed in HBSS plus 300 U/ml collagenase (Sigma) plus 300 mg/ml hyaluronidase (Sigma) and digested for 2 h at 37°C under shaking. EDTA at a final concentration of 5mM was added for 10 min to the resultant organoid suspension, followed by 0.25% Trypsin-EGTA for 2 min before filtration through a 40-mm mesh, two successive washes in 2% FBS/PBS and labelling. Unisuspension of cells were incubated in 250 ml (per 5 millions cells) of 2% FBS/PBS with primary antibodies for 30 min, with shaking every 10 min. Primary antibodies were washed with 2% FBS/PBS cells were resuspended in 2.5 mg/ml DAPI (Invitrogen) before analysis. Primary antibodies used were: APC-Cy7-conjugated anti-Epcam (1/100, clone G8.8, Biolegend), AF700-conjugated anti-CD29 (1/100, clone HMB1-1, Biolegend), APC-conjugated anti-CD45 (1/100, clone 30-F11, eBiosciences), APC-conjugated anti-CD31(1/100, clone 390, eBiosciences), APC-conjugated anti-CD140a (1/100, clone APA5, eBiosciences). Data analysis and cell sorting was performed on a FACSAria III sorter using the FACS DiVa software (BD Biosciences). Dead cells were excluded with DAPI; CD45+, CD31+ and CD140a+ cells were excluded (Lin-) before analysis of the YFP+ cells. Basal cells were defined as Lin-YFP+Epcam+CD29high population while luminal cells were defined as Lin-YFP+Epcam+CD29low. Sorted basal cells were collected in 300 ul DMEM 50%/FBS 50%.  Mammary fat-pad transplantation. 10.000 sorted basal YFP+ cells were resuspended in 10 ul DMEM 25%/FBS 25%/Matrigel 50% and injected into the number 4 glands of 4-week-old NOD/SCID female mice that had been cleared of endogenous epithelium, using a 26g Hamilton syringe. Transplanted glands were harvested 4.5 days after grafting and processed as described in the 2 previous sections for sorting of YFP+ cells.

Plates p1-p4, p9-p12 correspond to d0 control plates.
Plates p5, p7, p8, p13, p14 correspond to d4.5 plates.
Transplantations_rna sample corresponds to the transcriptomic part for all plates

first: Anna

last: Schwager

first: Eve

last: Moutaux

first: Adeline

last: Durand

last: Hadj

first: Délia

last: Dupré


title: Genome-wide maps of chromatin state in 142 cancer cell lines

city: Houston

first: Mahinur

last: Mattohti

state: TX

address: 6670 Bertner Ave

department: Surgery

country: USA

institute: Houston Methodist Research Institute


title: Growth of subcutaneous MC38 colorectal cancer triggers mild cachexia

city: Aurora

first: Andrea

last: Bonetto

state: Colorado

department: Pathology

institute: University of Colorado Anschutz Medical Campus

summary: Colorectal cancer (CRC) frequently manifests with cancer cachexia. To model CRC‑associated cachexia, we implanted MC38 murine CRC cells subcutaneously into mice and evaluated skeletal muscle responses. Tumor‑bearing mice showed mild but significant wasting of both the quadriceps and gastrocnemius muscles (p < 0.05). Quadriceps RNA was profiled using poly(A)‑selected, stranded RNA‑seq. Differential expression analysis (DESeq2) identified 616 significantly altered genes (|log2FC| ≥ 1, FDR < 0.05). Pathway enrichment revealed marked upregulation of neutrophil degranulation and inflammatory response programs, accompanied by downregulation of voltage‑gated potassium channel activity and potassium ion transport pathways. Together, these findings implicate heightened inflammatory/neutrophil‑associated signaling and reduced ion‑channel gene expression as key molecular features of skeletal muscle wasting in this CRC cachexia model. Raw FASTQ files and processed gene‑level counts are provided to support reuse and secondary analyses.

overall_design: Eight-week-old male C57BL/6 mice (The Jackson Laboratory, Bar Harbor, ME, USA) were group-housed and randomized into one of the following conditions: subcutaneous injection of 1.0 x 10^6 MC38 tumor cells in sterile saline (scMC38, n = 4) or an isovolumetric subcutaneous injection of sterile PBS (control, n = 4). The animals were weighed daily and then euthanized under light isoflurane anesthesia. Following euthanasia, the skeletal muscle was harvested and weighed. Quadriceps muscle tissue was used to extract RNA according to published protocols. Total RNA fromskeletalmuscle was extracted as described earlier.

first: Joshua

middle: R

last: Huot

first: Fabrizio

last: Pin

first: Caleb

middle: J

last: Gammon


title: Genome-wide maps of chromatin state in 142 cancer cell lines [patient]

summary: H3K27Ac enhancer mark ChIP-seq on 22 GBM patient samples.

overall_design: Examination of H3K27Ac histone modifications in GBM samples


title: ILC2 regulate a Pi16+ fibroblast progenitor niche in the pancreas (acute pancreatitis scRNA-seq)

city: Cambridge

first: Timotheus

last: Halim

address: University of Cambridge Li Ka Shing Centre, Robinson Way

department: CRUK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

summary: Local fibroblast development and densities underpin their role in regulating organ function and inflammation, although it remains unclear how tissue fibroblast topography is controlled in situ. Here we define group 2 innate lymphoid cells (ILC2) as key regulators of fibroblast homeostasis in the pancreas. We show that ILC2 co-localise with Pi16+Dpp4+Ly6c+Il33+ fibroblast progenitors in an interstitial niche of the exocrine pancreas, which demarcates and encapsulates the organ parenchyma. ILC2 specifically regulate the expansion of this progenitor population, while paradoxically also restraining differentiated intra-parenchymal Col15a1+ fibroblasts under inflammatory conditions. These homeostatic circuits reinforce fibroblast numbers after injury and set an inflammatory threshold at steady-state. Hence, ILC2-fibroblast dialogue represents a regulatory node that locally orchestrates tissue homeostasis and pathology.

overall_design: Mice were treated with PBS (n=3) or caerulein (hourly doses for 6 hours, 75ng/g) to induce acute pancreatitis, and sacrificed at day 1 (n=2), day 3 (n=3), or day 7 (n=2) following induction of acute pancreatitis. Pancreata were harvested and processed into single cell suspensions. Non-immune cells of the exocrine pancreas were sorted as live, nucleated, CD45- cells on a BD FACSAria sorter for scRNA sequencing.

first: Thomas

last: Yip

first: Julie

last: Stockis

first: Ashley

last: Sawle


title: ILC2 regulate a Pi16+ fibroblast progenitor niche in the pancreas


title: ILC2 regulate a Pi16+ fibroblast progenitor niche in the pancreas (naïve ILC2 scRNA-seq)

overall_design: The pancreas of a naive C57B6 mouse was harvested and processed into single cell suspensions. Live, CD45+, CD3-, B220-, Lineage (CD5, CD11b, CD11c, Gr-1, Ter119, CD19, F4/80, FcεR1α)-, CD127+, NK1.1- cells (ILCs) were sorted on a BD FACSAria sorter for scRNA sequencing.


title: ILC2 regulate a Pi16+ fibroblast progenitor niche in the pancreas (ILC2 bulk RNAseq)

overall_design: C57B6 mice were injected with PBS (n=5) or 200ng IL-33 (n=4) on days 0 and 1, and pancreata harvested on day 5 for processing into single cell suspensions. ILC2s were sorted as Live, CD45+, CD3-, B220-, Lineage-, KLRG1+ cells for RNA isolation and bulk RNA sequencing.


title: ILC2 regulate a Pi16+ fibroblast progenitor niche in the pancreas (coculture bulk RNA-seq)

overall_design: Live, CD45-, Epcam-, CD31-, Pdpn+, Pdgfra+ fibroblasts and CD45+, CD3-, B220-, Lineage- KLRG1+ ILC2s were sorted from mice using a BD FACSAria sorter and cocultured. Fibroblasts were isolated following coculture by sorting for Live, CD45+, Pdpn+, Pdgfra+ cells, and RNA obtained for bulk RNA-seq.


title: Shentong zhuyu decoction treatments regulate expression of inflammatory gene by potentially targeting transcription factors in dorsal root ganglia of rats with neuropathic pain

city: 武汉

first: Bang

last: Hu

address: 昙华林特1号

institute: 湖北中医药大学

summary: Shentong Zhuyu Decoction (STZYD) is a prescription of traditional Chinese medicine, which is widely used in many painful diseases including neuropathic pain (NPP). However, the potential pharmacological mechanism of STZYD is still unclear. The model of spinal nerve ligation (SNL) in rats was applied in this study. Then, RNA sequencing (RNA-seq) was used to screen differentially expressed genes (DEGs) between NPP model rats treated with STZYD and those without STZYD, and 301 DEGs and 14 transcription factors (TFs) were found. The differential expression of TFs is involved in the inflammatory reaction, apoptosis, nerve invasion and neurotoxicity of NPP. Then, the correlation between DEGs obtained in this project and these 14 TFs was analyzed. It was found that 14 TFs and 170 DEGs were co-expressed, with a total of 715 relationship pairs. Some DEGs are enriched into multiple inflammatory immune response biological processes. Therefore, we speculate that the differential expression of immune inflammation-related TFs may participate in the treatment of NPP by STZYD through transcriptional regulation of the differential expression of its target. The findings of this study provide a reference for further exploring the therapeutic targets of NPP.

overall_design:
In order to find out the mechanism of STZYD, we established a rat model of neuropathic pain. Subsequently, RNA-seq analysis was carried out on the dorsal root ganglion tissue of rats to obtain differentially expressed transcription factors and differentially expressed genes. Combined with the co-expression regulatory network, the regulatory mechanism of STZYD is expounded. This study provides a theoretical basis for the application of Shentong Zhuyu Decoction in the clinical treatment of neuropathic pain.
STZYD contains 12 kinds of herbs in total: Gentiana straminea Maxim. (Qinjiao, QJ), Ligusticum chuanxiong Hort. (Chuanxiong, CX), Prunus davidiana (Carr.) Franch. (Taoren, TR), Carthamus tinctorius L. (Honghua, HH), Glycyrrhiza uralensis Fisch. (Gancao, GC), Notopterygium inchum Ting ex H. T. Chang (Qianghuo, QH), Commiphora molmol Engl. (Moyao, MY), Angelica sinensis (Oliv.) Diels (Danggui, DG), Trogopterus xanthipes Milne-Edwards (Wulingzhi, WLZ), Cyperus rotundus L. (Xiangfu, XF), Achyranthes bidentata Bl. (Niuxi, NX), and Pheretima asperfillm (E. Perrier) (Dilong, DL).

first: Li

last: Li

first: Lin

first: Zhengchao

first: Fan

last: Dai

first: Guanjie

last: Zhong

first: Feng

first: Yi


title: Transcriptomic profiling of the biceps femoris long head 72 hours following a football match and associations with recovery biomarkers

status: Public on Jul 02 2026

city: Bethesda

first: Iago

last: Pinal-Fernandez

state: MARYLAND

address: 50 South Drive, Room 1142, Building 50, MSC 8024

department: NIAMS

institute: NIH

summary: This secondary integrative analysis of a previously published cohort investigated the molecular pathways underlying muscle recovery of the biceps femoris long head (BFLH) after a football match, by integrating newly generated transcriptomic data with clinical recovery markers over a 72-hour recovery period. BFLH muscle biopsies from 10 male, regional-first division football players were obtained seven days before a football match (MD-7) and three days post-match (MD+3). The final sample included 9 participants because 1 biopsy provided insufficient material for sequencing. Bulk RNA-sequencing was conducted to analyze differential gene expression considering Benjamini-Hochberg correction. Pathway enrichment analyses were conducted to identify biological processes altered between pre- and post-match conditions. Clinical markers, including creatine kinase (CK), hamstring rate of torque development (RTD), and sprint performance, were assessed before the match (MD) and at 24 (MD+1), 48 (MD+2), and 72 hours (MD+3) post-match. Correlations between transcriptomic and clinical variables were calculated using Spearman’s rank correlation. MYH1 was the most responsive gene, showing significant downregulation at MD+3 (log2FC = -1.116, q-value = 3.8 × 10-2). Pathway analyses identified 440 transcriptomic signatures at MD+3, reflecting stress response, immune and cytokine signaling, protein turnover, and structural remodeling. Changes in clinical variables during recovery were associated with coordinated expression shifts across genes related to different phases of the muscle damage-regeneration continuum, including muscle contraction, damage control, protein turnover, repair signaling, and myogenic regeneration. BFLH is not fully recovered three days after a football match, as evidenced by sustained downregulation of MYH1, pathway enrichment, and associations with clinical markers. Molecular recovery processes extend beyond 72 hours, suggesting this period is insufficient for complete BFLH recovery in football players.

overall_design: Bulk RNA sequencing (RNA-seq) was performed on frozen muscle biopsy specimens obtained from nine patients before and 72 hours after a football match.

first: Pedro

middle: L

last: Cosio

first: Lia

last: Moreno-Simonet

first: Joan

middle: A

last: Cadefau

first: Andrew

last: Mammen

first: Gil

last: Rodas

first: Jose

middle: C

last: Milisenda


title: Comparison of FOLR2-negative and FOLR2-positive human decidual macrophages at term

city: London

first: Victoria

last: Male

state: Not Applicable (Outside of US and Canada)

address: Metabolism, Digestion and Reproduction, Imperial College London, Chelsea and Westminster Hospital Campus, 369 Fulham Road

institute: Imperial College London

summary: The initiation of human labour is associated with inflammatory activation at the maternal-fetal interface; however, the cellular mechanisms driving this process remain incompletely understood. Decidual macrophages are abundant leukocytes within the decidua and are thought to play important roles in maintaining pregnancy and promoting labour-associated inflammation. Despite this, macrophage heterogeneity within the decidua remains poorly defined, with multiple classification systems proposed but no consensus regarding their biological relevance or application across gestation and labour. This thesis investigates decidual macrophage heterogeneity and function in decidua parietalis using flow cytometry, bulk RNA sequencing, RT-qPCR, ELISA, and functional tissue culture assays. Initial studies sought to validate a labour-associated macrophage population identified by single-cell RNA sequencing. Although a population with a similar phenotype was identified by flow cytometry, its extremely low abundance suggested it was unlikely to be a major driver of labour-associated immune adaptation. This prompted a broader investigation of decidual macrophage phenotyping strategies. Current and historical macrophage classification systems, including M1/M2 and several CD11c-based frameworks, failed to reliably distinguish macrophage subsets within this dataset. In contrast, a phenotyping strategy incorporating CD14, pan macrophage marker CD68, and tissue residency marker FOLR2 consistently identified monocytes, FOLR2- macrophages, and FOLR2+ macrophages across first trimester and term decidua, within both decidua parietalis and decidua basalis, and across term not in labour (TNL), term early labour (TeaL), and term in labour (TIL) samples. Bulk RNA sequencing validated FOLR2- and FOLR2+ macrophages as transcriptionally distinct populations. FOLR2- macrophages were enriched for pathways associated with neutrophil chemotaxis, antimicrobial responses, and inflammation, whereas FOLR2+ macrophages were enriched for antigen presentation, MHC class II assembly, and tissue-resident functions. Labour was associated with selective remodelling of the decidual myeloid compartment rather than global leukocyte infiltration. Monocyte abundance increased significantly during early labour, while the proportion of FOLR2- macrophages decreased before increasing again in established labour. Functional analyses demonstrated distinct cytokine profiles between macrophage subsets. FOLR2- macrophages preferentially expressed IL-8 and increased CCL5 expression during early labour, consistent with a chemotactic and inflammatory phenotype. In contrast, FOLR2+ macrophages exhibited high expression of IL-6, CCL2, MMP-9, and MMP-19, supporting roles in tissue homeostasis, leukocyte recruitment, and extracellular matrix remodelling. Furthermore, co-culture experiments demonstrated that FOLR2+ macrophages promoted degradation of chorionic collagen in vitro. Together, these findings support a model in which labour-associated immune adaptation is mediated by functionally specialised decidual macrophage populations rather than a single labour-specific macrophage subset. Functional analysis of FOLR2- macrophages suggests they contribute predominantly to inflammatory signalling and leukocyte recruitment, whereas FOLR2+ macrophages contribute to antigen presentation and tissue remodelling. This work establishes a simple and robust framework for decidual macrophage phenotyping that is applicable across gestation, decidual compartment, and labour status, providing a foundation for future studies investigating macrophage function at the maternal-fetal interface.

overall_design: The placenta and fetal membranes were collected from six donors giving birth by planned caesarian section at term. The decidua parietalis was scraped from the fetal membranes, mechanically disaggregated, enzymatically digested, and immune cells were isolated by density gradient centrifugation. FOLR2-negative (live CD45+ CD14+ CD71+ FOLR2-) and FOLR2-positive (live CD45+ CD14+ CD71+ FOLR2+) macrophages were sorted from each donor by flow cytometry. Cells were pelleted and RNA extracted using Qiagen RNEasy Micro Kits. 200 ng RNA was used to prepare cDNA libraries using an Illumina NEBNext Single Cell/Low Input RNA Library Prep Kit. Libraries were sequenced on a NextSeq2000.

first: Emilie

middle: O

last: Paterson

first: Katerina

last: Rekopoulou


title: Development of a Gene Editing Strategy to Enhance CAR-T Therapy Through Inducible IL-15 Expression at the PD-1 Locus

city: Granada

first: Karim

last: Benabdellah

state: Granada

address: Avenida de la Ilustración 114

country: Spain

institute: GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government PTS Granada

summary: Background: Adoptive cell therapy (ACT) with genetically engineered T cells expressing chimeric antigen receptors (CARs) has emerged as a promising treatment option for refractory leukaemia or lymphoma patients. Despite its success in type B malignancies, CAR-T cell therapy still faces challenges such as toxicity, inactivation by the tumour microenvironment (TME), and low cell persistence in patients. Results: In this study, we developed an AAV6/Cas9-based knock-in platform to repurpose the PD-1 locus for inducible IL-15 expression. We initially demonstrated that anti-CD19 CAR-T cells lacking PD-1 expression exhibited reduced expansion capacity and overall fitness compared to control CAR-T cells. However, as expected, they showed an improved ability to lyse PDL1+ target cells compared to CAR-T WT cells.  To enhance the fitness of PD-1 KO CAR-T cells, we generated PD-1KIL-15 CAR-T cells, which, in addition of been PD-1 KO, express IL-15 under the control of the PD-1 endogenous promoter. Compared to CAR T PD-1 KO cells, PD-1KIL-15 CAR-T cells I displayed improved phenotype, viability and metabolism... More importantly, they also demonstrated enhanced lytic capacity of PDL1+ CD19+ target cells, correlating with increased resistance to apoptosis and improved cell fitness. Conclusions: In summary, we present a new gene editing platform to generate 4th generation CAR-T cells (TRUCKs) that are PD-1 KO and express IL-15 upon T cell activation and/or exhaustion. This platform addresses the limitations associated with knocking-out PD-1 and those associated with sustained IL-15 cytokine expression. The same platform can be used to generate PD-1 KO TRUCKs targeting different antigens and expressing different cytokines under the control of the PD-1 gene promoter.

overall_design: This study employed a second-generation CD19-targeting CAR construct to generate engineered CAR-T cells with enhanced functionality through precise genome editing. Using CRISPR/Cas9 technology, the PDCD1 gene was disrupted to mitigate T cell exhaustion, and in a parallel knock-in strategy, an IL-15 transgene was inserted at the PDCD1 locus. Gene editing was performed via electroporation of RNP complexes, with AAV6 vectors used for homology-directed IL-15 integration. Editing efficiency and off-target activity were assessed by flow cytometry, Sanger sequencing, ICE, and CAST-Seq. Functional characterization included bulk RNA sequencing, metabolic profiling using SeaHorse technology, and cytotoxicity assays against CD19+ target cells.

first: M

last: Cortijo-Gutiérrez

first: PP

last: Jurado-Bascón

first: P

last: Carmona-Sáez

first: F

last: Martín

first: K


title: Transcriptome profiling of SCRMP knockout and control NCI-H69 small cell lung cancer cells

city: suzhou

first: Jiahao

last: Guo

address: Address: 16 Baita West Road, Gusu District, Suzhou

institute: SUZHOU MUNICIPAL HOSPITAL

summary: This series contains RNA-seq data from NCI-H69 small cell lung cancer cells with CRISPR/Cas9-mediated SCRMP knockout and corresponding negative control cells. SCRMP is a microprotein encoded by MIR7-3HG that promotes cisplatin resistance and DNA damage repair in SCLC. The experiment was designed to identify gene expression changes caused by SCRMP depletion and to explore pathways involved in DNA damage repair and homologous recombination.

overall_design: RNA-seq profiling of three biological replicates of SCRMP knockout NCI-H69 cells and three biological replicates of negative control NCI-H69 cells.

first: Yuli

last: Chen

first: Qinnan

first: Peng

last: Huang

first: Ming

last: Sun

first: Fengqi

last: Nie

first: Xianghua

last: Liu


title: ChIP-seq profiling of RBBP4 and P300 occupancy after CSNK2B knockdown in small cell lung cancer cells

summary: This ChIP-seq dataset profiles genome-wide occupancy of RBBP4 and P300 in NCI-H69 human small cell lung cancer cells after siRNA-mediated CSNK2B knockdown. The study was designed to investigate how the CSNK2B/RBBP4/P300 complex regulates chromatin occupancy and downstream transcriptional programs involved in DNA damage repair and cisplatin resistance.

overall_design: NCI-H69 cells were transfected with non-targeting control siRNA or siRNA targeting CSNK2B. Forty-eight hours after transfection, chromatin was immunoprecipitated with anti-RBBP4 (Abcam, ab79416; ChIP 1:100) or anti-P300 (Abcam, ab275378; ChIP 1:100) antibodies, with matched input DNA controls. ChIP and input DNA libraries were sequenced as paired-end 150 bp reads on the Illumina NovaSeq 6000 platform.

first: Ziwei

last: Li

first: Shaokun

last: Yu


title: Tbx3 controls retinal angiogenesis by driving retinogenesis

city: Syracuse

first: Andrea

middle: Sophia

last: Viczian

state: NY

address: 750 East Adams Street

department: Ophthalmology and Visual Sciences

institute: SUNY Upstate Medical University

summary: Retinal angiogenesis relies on a tightly coordinated sequence of retinogenesis, astrocyte migration, and vascular growth. Understanding this complex system requires dissecting apart its cellular and molecular drivers. To dissect the molecular links coupling retinogenesis to vascular development, we utilized conditional knockout mouse models to selectively delete the transcription factor T-box 3 (Tbx3) in 1) astrocytes, 2) postnatal retinal ganglion cells (RGCs), or 3) retinal progenitors. We demonstrate that the hypovascular phenotype observed in progenitor mutants most likely stems from a disruption in early retinogenesis. Embryonic analyses revealed that TBX3 is required during a critical retinogenic window coinciding with ATOH7 activity. While ATOH7+ progenitors are more abundant in Tbx3 mutants, the expression of key RGC and cone precursor factors (including TBX5, RXRɣ, ISL1/2, POU4F2, SHH, LHX4 and OTX2) is severely diminished, halting proper RGC and cone differentiation. Utilizing birth dating experiments and developmental immunostaining, we establish TBX3 as a novel upstream regulator of RGC and cone photoreceptor specification. Because the degeneration of RGCs is the definitive hallmark of diseases like glaucoma, identifying TBX3 as a master driver of early RGC formation positions it as a promising new candidate biomarker for early-stage glaucoma diagnosis and therapeutic targeting.

overall_design: RNAseq profile comparing the isolated retinas of wild-type (WT) and Tbx3 conditional knockout (Tbx3cKO) mice at embryonic day 13.5 (E13.5).

first: Joao-Carlos

last: Ribeiro-Silva

first: Nikita

last: Shah

first: Mark

last: Derbyshire

first: Sruti

last: Akula

first: Rachel

last: Burt

first: Zoe

last: Boyd

first: Carmen

last: Lee-Bennett

first: Anne

middle: S

last: Moon

first: Michael

middle: E

last: Zuber


title: A novel High-Throughput Ligase-Independent Mapping method to detect Viral Integration Sites

city: Scarborough

first: Guillaume

last: Filion

state: ON

address: 1265 Military Trail

country: Canada

institute: University of Toronto

summary: Integrated DNA elements are central to virology, functional genomics, and gene therapy, but current insertion-site mapping methods often rely on restriction digestion, ligation, or complex sequencing workflows that introduce bias and limit recovery. Here, we present Terminal Mapping, a high-throughput method that identifies host–insert junctions without restriction enzymes or DNA ligation. The workflow combines linear amplification from a known terminal sequence, enrichment of single-stranded products, terminal transferase-mediated poly-A tailing, and PCR amplification for high-throughput sequencing. Applied to Jurkat T cells transduced with HIV-1- and SIVmac251-derived vectors, Terminal Mapping recovered more HIV-1 insertion sites than inverse PCR, reproduced known integration biases, and showed improved robustness with long-read sequencing. It revealed shared but quantitatively distinct HIV-1 and SIVmac251 hotspots, as well as substantial differences between Jurkat cell sources. Comparison of 5′ and 3′ LTR-derived reads also provided an internal control for unintegrated viral DNA. Terminal Mapping therefore offers a rapid and flexible platform for profiling integrated genetic elements across vectors and cellular contexts.

overall_design: Jurkat T cells were transduced at multiplicity-of-infection 0.1 with HIV-1 or SIVmac251 constructs expressing GFP-Nef under the native viral promoter, positive cells were isolated by FACS at day 2 post transduction, and DNA was harvested at day 21 post transduction for analysis of insertion sites by Terminal Mapping.

first: Manisha

last: Kabi


title: ID2 secures cDC1 specification by antagonizing E proteins at a pleiotropic Zeb2 enhancer [scRNA-seq]

city: St. Louis

first: Feiya

last: Ou

state: MO

address: 4939 Children's Place

department: Pathology & Immunology

institute: Washington University in St. Louis

summary: The transcriptional regulator ID2 is required for type 1 classical dendritic cell (cDC1) specification, yet the mechanism has remained obscure. We previously identified the Zeb2 -165-kb enhancer as key to normal hematopoiesis, controlled by competing CEBP and NFIL3 inputs during myeloid dendritic cell divergence. Here, we uncover an unprecedented role for E proteins in myelopoiesis and demonstrate that ID2 promotes cDC1 development by antagonizing E protein activity at E-boxes within the Zeb2 enhancer. Deleting these E-boxes abolishes lymphoid B cell and plasmacytoid dendritic cell (pDC) development while skewing myelopoiesis toward cDC1s. Remarkably, E-box deletion rescues cDC1 development in Id2-deficient mice. These findings support a two-step model in which NFIL3 transiently represses Zeb2, followed by ID2-mediated inhibition of E proteins to stabilize cDC1 fate specification. Further, this work defines a paradigm of “site-specific pleiotropy,” wherein distinct transcription factor motifs–E-boxes and CEBP sites–within a single enhancer direct diverse cell fates.

overall_design: Bone marrow cells from Zeb2 -165-kb enhancer variants (WT, DC, and DE) were hashtagged with TotalSeq B antibodies (BioLegend). Lin- KIThi-int cells were sorted and subjected to scRNA-seq.

first: Kenneth

middle: M

last: Murphy


title: Androgen Receptor-Driven RASSF3 Upregulation Promotes CKD Progression by Inhibiting Gαs/Gq Activity to Mediate Metabolic Reprogramming [DT]

city: Shenzhen

first: Shu

last: Yang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

institute: shenzhen people's hospital

summary: Male sex is a risk factor for Chronic Kidney Disease (CKD), but the underlying mechanism is not yet clear. Given the well-established central role of TGF-β in CKD, we hypothesize it reprograms AR’s transcriptional network, shifting AR’s kidney function from healthy to pathogenic. Transcriptomic profiling identified RASSF3 as a critical downstream target of DHT and TGF-β1, upregulated in kidneys from male CKD patients and mice but not females. Tubule-specific Rassf3 knockout in mice prolonged survival and protected against CKD models, whereas its overexpression exerted opposite effects. Mechanistically, RASSF3 binds Gα subunits Gq and Gαs, accelerating their GTP-to-GDP transition (active to inactive) to suppress their activity—an interaction that drives kidney tubule metabolic reprogramming and exacerbates kidney injury and CKD progression. GTPase-deficient Gq/Gαs mutants or Gq/Gαs knockout abolished RASSF3-mediated metabolic reprogramming, confirming dependence on Gq/Gαs GTPase activity. AR transcriptionally upregulates RASSF3 via interaction with SP1 (a TGF-β downstream target). Importantly, δ-tocopherol binds RASSF3’s Ras-associating domain, inhibiting its activity and alleviating CKD. Our study uncovers the molecular basis of AR-driven CKD sexual dimorphism, elucidates mechanisms linking AR to kidney metabolic dysregulation, and identifies RASSF3 as a novel CKD therapeutic target.

overall_design: For co-stimulation treatment, human tubular epithelial cells (hTECs) were simultaneously incubated with dihydrotestosterone (DHT) and transforming growth factor-β1 (TGF-β1) at indicated concentrations for the designed time course.


title: Androgen Receptor-Driven RASSF3 Upregulation Promotes CKD Progression by Inhibiting Gαs/Gq Activity to Mediate Metabolic Reprogramming [R3]


title: Topical Vascular Organoid Therapy Promotes Microvascular Regeneration and Functional Recovery in Porcine Ischemic Cardiomyopathy

city: Palo Alto

first: Yujiro

last: Kawai

state: CA

address: 870 Quarry Road

department: Department of Cardiothoracic Surgery

institute: Stanford University

summary: Background: Ischemic heart disease (IHD) remains a leading cause of morbidity and mortality worldwide, with microvascular dysfunction playing a key role in the progression to ischemic heart failure.　Current revascularization strategies restore epicardial blood flow but fail to address impaired microcirculation. To overcome this limitation, we developed a scaffold-free vascular organoid therapy.Methods: An IHD pig model was created by occluding the left anterior descending artery. Bilayer vascular organoids (VOs) composed of human endothelial progenitor cells and mesenchymal stem cell–derived smooth muscle cells were transplanted onto the left ventricular 14 days after infarction. Animals were followed for four weeks with cardiac MRI and histological analyses.Results: VO transplantation preserved left ventricular ejection fraction, modestly improved regional function, and enhanced microvascular density and maturation. Transplanted cells migrated into host myocardium, and angiogenesis-related genes were upregulated.Conclusions: Topically transplanted VOs promote microvascular regeneration and help preserve cardiac function after ischemic injury.

overall_design: The objective of this study was to evaluate the therapeutic efficacy and underlying molecular mechanisms of topically transplanted vascular organoids (composed of human smooth muscle cells [SMCs] and human endothelial progenitor cells [EPCs]) in a porcine model of ischemic heart disease. To induce ischemia-reperfusion injury (IRI), Yorkshire pigs underwent left anterior descending (LAD) balloon occlusion for 60 minutes. On post-IRI day 14, animals were randomly assigned to either the experimental group (topical implantation of scaffold-free EPC-SMC vascular organoids or the control group (fibrin glue only). To identify the specific genes and transcriptional programs regulated by the vascular organoid therapy within the ischemic border zone, RNA-seq was performed using tissue samples harvested from the mid-border zone of both groups. Differentially expressed genes (DEGs) and gene-set enrichment analysis (GSEA) were subsequently analyzed to explore pathways related to angiogenesis, hypoxia, and tissue remodeling.

first: John

last: Farag

first: Koji

last: Kawago

first: Eric

last: Pfrender

first: Umayr

last: Syed

first: Yasuhiro

last: Shudo


title: Expression data of hippocampal neural stem cells from rat

city: Fuchinobe

first: EIji

last: Munetsuna

country: Japan

institute: Azabu University

summary:
Neural stem cells (NSCs) are essential for brain development and adult hippocampal neurogenesis, yet early-life environmental stress may induce persistent dysfunction through epigenetic mechanisms. In this study, we investigated the long-term effects of maternal high-fructose corn syrup (HFCS) intake on NSCs using a rat DOHaD model. Maternal HFCS exposure induced persistent impairments in NSC proliferation and differentiation, accompanied by hippocampus-dependent cognitive dysfunction in offspring. Mechanistically, transient downregulation of Dnmt3a in fetal NSCs was associated with sustained repression of Spp1, encoding intracellular osteopontin (iOPN), a regulator of NSC function.
We performed Affymetrix Clariom S microarray analyses of hippocampal NSCs isolated from offspring of control and maternal HFCS-fed rats and identified transcriptomic alterations associated with maternal HFCS exposure.

overall_design: Hippocampal NSCs isolated from male offspring of control and maternal high-fructose corn syrup (HFCS)-fed rats at embryonic day 20.5 (E20.5) were cultured under undifferentiated conditions for 7 days. Total RNA was extracted using the RNeasy Kit and subjected to Affymetrix Clariom S Rat Array analyses to investigate transcriptomic alterations induced by maternal HFCS exposure.

first: Itsuki

last: Kageyama

first: Hiroya

last: Yamada

first: Mirai

last: Yamazaki

first: Takuya

last: Wakasugi

first: Yuri

last: Kamiya

first: Masaki

last: Ohshiro

first: Manaka

last: Ito

first: Yoshiki

last: Tsuboi

first: Takashi

last: Watanabe

first: Genki

last: Mizuno

first: Yoshitaka

last: Ando

first: Hiroaki

last: Ishikawa

last: Suzuki

last: Ohashi

first: Eiji


title: Ninjurins 1 Regulate Hematopoietic Stem Cell Amplification Through Canonical WNT Signaling Independently of Plasma Membrane Rupture Activity

city: Murcia

first: Lola

last: Rodríguez Ruiz

address: C/Campus universitario, 5

institute: University of Murcia

summary: Ninjurin-1 (NINJ1), a protein recently linked to plasma membrane rupture (PMR) during inflammasome activation, plays a well-established role in cell death. However, its function in hematopoiesis has remained unexplored. In this study, we identify a novel, PMR-independent role for Ninj1 in regulating hematopoiesis using zebrafish models. Ninj1 deficiency resulted in significantly reduced neutrophil, erythrocyte, and hematopoietic stem/progenitor cell (HSPC) numbers, independently of its plasma membrane rupture (PMR) activity. Surprisingly, Ninj1 deficiency also alleviated neutrophilia and keratinocyte hyperproliferation in a chronic inflammation model, revealing a role beyond inflammasome-mediated cell death. To further investigate thisnoncanonical function, we identified PMR-deficient Ninj1 mutants (A56P and D50A).  Expression of the A56P mutant rescued hematopoietic defects in Ninj1-deficient larvae, while the dominant-negative D50A mutant recapitulated the phenotypes of Ninj1 deficiency, confirming that Ninj1 regulates hematopoiesis independently of PMR. Furthermore, Ninj1 deficiency increased susceptibility to intracellular bacterial infection due to impaired neutrophil and macrophage recruitment, while overexpression of the A56P mutant enhanced immune cell recruitment and resistance to infection. Finally, we discovered that Ninj1 and Ninj2 cooperatively regulate the amplification of nascent hematopoietic stem cells (HSCs) from the hemogenic endothelium via canonical Wnt signaling. Importantly, this regulatory mechanism is conserved in human HSPCs, underscoring its evolutionary significance and translational potential. These findings position Ninjurins as critical regulators of HSC development and immune responses, with promising implications for enhancing HSC production in regenerative medicine and developing therapies for hematological and infectious diseases.

overall_design: Human cord blood CD34+ HSPCs were edited with CRISPr-Cas9 (NINJ1 and NINJ2, AAVS1 as a control) and expanded for 5 days in StemSpan SFEM II and StemSpan CD34+ Expansion Supplement. 4 differents donnors at day 3 and 5.


title: Single-cell spatial transcriptomics analysis of murine normal pancreas (N), pancreatitis (P), and PDAC formalin-fixed paraffin-embedded (FFPE) samples using Visium HD.

city: CAMBRIDGE

first: Giulia

last: Biffi

state: Cambridgeshire

address: Cancer Research UK, Robinson Way

summary: We investigated the single-cell spatial transcriptomics of murine normal pancreas (N), pancreatitis (P) and PDAC formalin-fixed paraffin-embedded (FFPE) samples using Visium HD.

overall_design: 10 samples, including 3 normal pancreas (N), 4 pancreatitis (P), and 3 PDAC samples

first: Wenlong

last: Li

first: Muntadher

last: Jihad

first: Alwin

last: Koonan-Lonappan


title: Epigenetic repression of IL-1β by C1QBP restricts Dectin-1-mediated host defense against invasive candidiasis

city: shang hai

first: Hui

last: Wang

address: shang hai

institute: Tongji University

summary: Invasive candidiasis, predominantly caused by Candida albicans, threatens immunocompromised individuals with high mortality. Dendritic cell-derived interleukin-1β, orchestrated via Dectin-1-mediated β-glucan recognition, is central to antifungal defense. While the Dectin-1/Syk/CARD9 axis governing Il1b transcription is defined, the epigenetic regulatory mechanisms remain elusive. Here we identify Complement C1q binding protein (C1QBP) as a critical negative regulator of Dectin-1-mediated interleukin-1β production. C1QBP sequesters phosphorylated protein kinase C δ in the cytoplasm, preventing its nuclear transport. Nuclear phosphorylated-PKCδ activates the RNF20/RNF40 ubiquitin ligase complex, which recruits the methyltransferase DOT1L to catalyze histone H3 lysine 79 trimethylation at the Il1b locus to promote its transcription. DC-specific C1QBP depletion enhances interleukin-1β secretion, amplifies protective T helper 17 cell responses, and improves host resistance to systemic C. albicans infection in mice. Collectively, our findings establish C1QBP as a key checkpoint in a PKCδ-dependent epigenetic pathway that constrains antifungal immunity, highlighting its therapeutic potential for invasive fungal diseases.

overall_design: In this study, we provided six samples before and after systemic Candida albicans infection, namely WT Naive; WT Day 2; WT Day 6. One sample was from three murine kidney tissues.

first: Xinming

last: Jia


title: Genome-wide maps of chromatin state in 142 cancer cell lines [cell line]

city: Houston

first: Mahinur

last: Mattohti

summary: Epigenetic aberrations are a hallmark of cancer; however, we have limited information on chromatin aberrations present in cancer cells. Here we provide genome-wide maps for histone modification binding for 6 reference histone markers in 145 cancer cell lines belonging to 9 cancer types generating 680 chromatin maps. NMF clustering for H3K27ac-defined enhancers classified cancer cells into 5 distinct subtypes. These subtypes were either correlated with the developmental trajectory of original tissue or cell phenotype such as mesenchymal features. We identify a cluster consisting of different tumor types but with a unique enhancer profile and its dependency on key oncogenes. Detailed characterization of bivalent state switches between cancer cells and their normal counterparts identified epithelial-to-mesenchymal driver transcription factors to be activated via this mechanism in breast, GBM and melanomas. Finally, we identify cancer-specific lengthening of H3K4me3 domains on oncogenes and their shortening on specific tumor-suppressors, respectively. Overall, our study provides epigenome reference maps for widely-used cancer cell lines which will be useful for discovery of important principles about chromatin mediated cancer gene regulation.

overall_design: Examination of 6 different histone modifications in 142 cell types

first: Kunal

last: Rai


title: Single-nuclei RNA-sequencing (snRNA-seq) of murine pancreatic tumors derived from the orthotopic transplantation of Smad4 WT or Smad4 KO pancreatic ductal adenocarcinoma (PDAC) KPC (i.e. KrasG12D; p53 mutant) organoids in C57BL/6J mice.

summary: We investigated the impact of SMAD4 loss in PDAC tumors from orthotopically grafted organoid-derived mouse models using snRNA-sequencing.

overall_design: 6 samples in total - 3 PDAC samples with Smad4 WT (KP); 3 PDAC samples with Smad4 KO (KPS)


title: Tissue-specific consequences of impaired RNA surveillance converge on mitochondrial homeostasis

city: Los Angeles

first: Lauryn

last: Higginson

address: 1050 Childs Way

department: Biological Sciences

institute: University of Southern California

summary: RNA surveillance pathways maintain transcriptome integrity by eliminating aberrant, excess, and non-functional RNAs, yet it remains unclear whether distinct tissues exhibit equivalent requirements for RNA quality control. Here, we investigated the tissue-specific consequences of impaired RNA surveillance using a Drosophila allelic series of the RNA exosome subunit Rrp40. Comparative transcriptomic analyses revealed that neuronal-enriched head tissue and muscle-enriched thorax tissue exhibit largely distinct molecular programs following reduced RNA exosome activity despite disruption of the same RNA surveillance machinery. Antisense RNAs emerged as particularly sensitive targets of RNA exosome dysfunction and accumulated preferentially in neuronal tissue, indicating enhanced requirements for RNA-level quality control within the nervous system. Although tissue-specific transcriptomic alterations diverged substantially, multiple analyses converged on mitochondrial homeostasis pathways as a common vulnerability. Reduced RNA exosome activity was associated with widespread dysregulation of nuclear-encoded mitochondrial genes, mitochondrial dynamic pathways, and mitochondrial RNA regulatory programs, accompanied by progressive defects in mitochondrial organization, membrane potential, and ATP production. Mitochondrial dysfunction was further associated with activation of proteostatic stress pathways, including p62 accumulation and increased ubiquitination. Together, these findings demonstrate that tissue context shapes the molecular consequences of impaired RNA surveillance while revealing mitochondrial homeostasis as a convergent vulnerability to transcriptome instability. More broadly, our results suggest that distinct tissue-specific defects in RNA regulation can converge on common cellular pathways that ultimately determine tissue homeostasis.

overall_design: RNA seq profiling of RNA exosome subunit Rrp40 mutants (Rrp40-G11A and Rrp40-G146C) and Rrp40 WT controls from Day 1 fly head or thorax tissue.

first: Xingjun

first: Derrick

last: Morton


title: Low physiological pH drives P300-mediated acetylation of PARP1 and promotes PARP inhibitor resistance

status: Public on Jul 05 2026

first: Yuan

last: Qi

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

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

overall_design: Refer to individual Series


title: A global regulatory atlas of Streptomyces reveals conserved and diversified transcriptional networks across actinomycetes

city: Ledien

first: Gilles

middle: P.

last: van Wezel

address: Sylviusweg 72

department: Institute of Biology Leiden

country: Netherlands

institute: Leiden University

summary: Here, we apply DNA affinity purification sequencing (DAP-seq) to 789 31 predicted TFs of Streptomyces coelicolor, generating genome-wide binding maps for 393 32 regulators and expanding the experimentally supported regulome from ~8% to ~50%. 33 Integration with ChIP-seq reveals pleiotropic regulators and hierarchical network architecture 34 linking primary metabolism, development and biosynthetic gene clusters (BGCs). This GEO data set include 11 ChIP-seq results discussed in our manuscript

overall_design: Target TFs are taged with 3xFLAG tag on a integrated plasmid and transferred into the wild type strain.

first: Hannah

last: Augustijn

first: Hiroshi

last: Otani

first: Augustin

last: Rigolet

first: Rachel

last: Stuij

first: Vina My

last: Pham

first: Leo

last: Baumgart

first: Le

last: Zhang

first: Yu

first: Chao

last: Du

first: Simona

last: Cernat

first: Sébastien

last: Rigali

first: Ronan

last: O’Malley

first: Marnix

middle: H

last: Medema

first: Nigel

last: Mouncey

middle: P


title: Bulk RNA-sequencing analyses of multi-stroma flow-sorted from cocultures with murine pancreatitis (P)-derived organoids, PDAC organoids, or PDAC organoids following initial coculture with P organoids (ie P-to-PDAC or sequential).

first: Giulia

last: Biffi

institute: University of Cambridge

summary: We investigated the transcriptomic differences of multi-stroma flow-sorted from cocultures with murine pancreatitis (P)-derived organoids, PDAC organoids, or PDAC organoids following initial coculture with P organoids (ie P-to-PDAC or sequential).

overall_design: 12 samples: 4 multi-stroma from P organoid coculture, 4 from PDAC organoid coculture, 4 from P-to-PDAC organoid coculture (i.e sequential)

first: Wenlong

last: Li

first: Muntadher

last: Jihad


title: Comparative RNA-seq analysis of PM2.5 responses in wildtype and malignantly transformed mouse mammary epithelial cells cultured as spheroids

status: Public on Jul 04 2026

city: Linz

first: Tamara

last: Lang

address: Krankenhausstraße 5

department: Pathophysiology

country: Austria

institute: Johannes Kepler Universität

summary: Exposure to fine particulate matter (PM2.5) has been implicated in cancer initiation and progression, yet its effects on normal versus transformed epithelial cells in a three-dimensional context remain incompletely understood. In this study, we performed bulk RNA sequencing of spheroid cultures of wildtype EpH4 mouse mammary epithelial cells and their malignantly transformed counterpart, EpH4-AS. Both cell types were analyzed under untreated conditions and following PM2.5 exposure. This dataset enables comparative analysis of differential transcriptomic responses of malignant transformation and healthy WT cells after exposure to PM2.5 in a 3D culture system.

overall_design: Bulk RNA sequencing was conducted on spheroid (3D) cultures of wildtype EpH4 and malignantly transformed EpH4-AS mouse mammary epithelial cells. For each cell type, samples were either left untreated or exposed to PM2.5, resulting in four experimental groups, each in duplicates. RNA-seq was used to characterize genome-wide gene expression differences related to malignant transformation, PM2.5 exposure, and their interaction.

first: Wechselberger

last: Christian

first: David

last: Demmel

first: Johannes

last: Pröll


title: Epstein-Barr Virus Induced B cell Methionine Dependency is a Targetable Metabolic Vulnerability

city: BOSTON

first: Shaowen

last: White

state: MA

address: 181 Longwood Ave, Channing Labs Room 861

department: Medicine

institute: Brigham and Women's Hospital

summary: EBV uses latency III oncoproteins to drive abnormal B cell proliferation to establish lifelong latency, and oncoprotein+ B cells correlate to pathology in autoimmune diseases such as systemic lupus erythematosus and multi-sclerosis. EBV-driven B cell outgrowth shows unique features that are different from both cancerous and cytokine-activated B cells, especially in their metabolism. Building on our previous observation that EBV+ tumors depend on methionine for viral epigenetic regulation, we tested whether EBV latency III program B cells share a similar phenotype. Surprisingly, the effect of methionine restriction on latency III cells is distinct and far more drastic—reducing RPMI media methionine level to 10% completely blocked B cell transformation, and to 1% resulted in rapid death of LCL and latency III Burkitt cells. Transcriptomic and liquid chromatography mass spectrometry-based metabolomic analyses revealed that methionine restriction downregulated genes related to the pentose phosphate pathway which supports cystine reduction, and upregulated genes related to ferroptosis, a lipid peroxidation (LPO)-mediated cell death. Isotope-labeled amino acid tracing indicated that methionine was shunt to cysteine biosynthesis pathway. Methionine restriction can be rescued by a combination of quenching LPO (Fer-1 and DFO) and removing toxic cystine buildup (NAC and penicillamine). In mice models, either dietary methionine restriction or injection of engineered methioninase abolished lymphoblastoid cell line tumor growth without having effects on body weight, and refractory tumor cells upregulated pathways against LPO, and downregulated cystine intake, highlighting methionine’s multiple roles in antagonizing LPO and redox pressure via modulating cysteine metabolism. In tonsil organoid model, moderate methionine restriction blocks EBV+ cell outgrowth but did not affect T cell activation and normal germinal center development, implying therapeutic potential. In a B cell transformation assay with a panel of loss-of-function BAC viruses, we identify EBNA2, EBNA-LP, and LMP2A deletion provided protection.

overall_design: RNA-seq profiling of EBV+ lymphoblastoid cell GM12878. For in vitro methionine restriction, GM12878 cells were cultured in media with 100 μM or 1 μM methionine media for 24 hr. For in vivo methionine restriction, GM12878 cell tumor xenograft were implanted for 1 week in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) immunocompromised strain #005557 mice, and then mice were on control or methionine-free diet for 4 more weeks. Three biological replicates were included for each media condition.

first: Rui

last: Guo

first: Bidisha

last: Mitra

first: Hanqi

first: Rishi

last: Puri

first: John

last: Asara

first: Benjamin

last: Gewurz


title: IL-2/CD25 Fusion Protein Enhances Expansion of Antigen-Specific CD8⁺ T Cells to Suppress Hepatocellular Carcinoma

city: Hang Zhou

last: Xu

address: Huansha Roud

institute: Zhejiang University

summary: To investigated how IL-2/CD25 change the Immune microenvironment of hepatocelluar carcinoma

overall_design: Hydrodynamic tail vein injection was employed to deliver plasmids encoding Nras and C-myc into mice to establish an in situ hepatocellular carcinoma model. In parallel, mice were co-injected with an IL-2/CD25 expression plasmid, while control groups did not receive this plasmid. Two weeks post-injection, liver tissues were harvested, dissociated into single-cell suspensions, and subjected to single-cell RNA sequencing to comprehensively characterize the immune landscape and functional states within the tumor microenvironment under different treatment conditions.


title: Gene expression data from white adipose tissue (WAT) treated with Vigna Umbellata extract (VE)

city: TSUKUBA

first: ELDA NURAFNIE

last: IBNU RASID

state: IBARAKI

address: 1-1-1 TENNODAI

institute: UNIVERSITY OF TSUKUBA

summary:
Gene expression profiling reveals DEGs in WAT
We evaluated the effects of Vigna Umbellata on WAT of ob/ob mice through an untargeted whole-genome transcriptome analysis

overall_design: The microarray analysis was conducted on control ob/ob mice group and VE treated group using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) and GeneChip™ Hybridization, Wash and Stain Kit (ThermoFisher Scientific) following the manufacturer’s instructions. Firstly, about 100 ng of RNA from each sample was obtained to synthesize complementary DNA (cDNA) for complementary RNA (cRNA) synthesis. cRNA was purified and reverse transcribed for single-stranded cDNA (ss-cDNA) synthesis, purification, fragmentation and labelling. ClariomTM S Array (Mouse; ThermoFisher Scientific) were hybridized with samples extracted from WAT. Tissue samples were prepared from control groups, including ob/ob mice (n = 3) and, when applicable, wild-type mice (n = 3), as well as from VE-treated groups receiving 50 mg/kg BW (n = 3) and 100 mg/kg BW (n = 3). All of the samples were hybridized for 16 hours in a 45 degree celcius incubator, washed and stained on the GeneChip™ Fluidics Station (ThermoFisher Scientific). The scanning was performed using GeneChip Scanner (ThermoFisher Scientific). The raw image data was obtained using the Transcriptome Analysis Console (TAC) software (ver. 4.0.2, ThermoFisher Scientific) and raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above back-ground (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7. Finally, genes that passed the filter criteria of p value <0.05 (one-way between-subjects ANOVA) and fold change >1.1 (in linear space) were considered as differentially expressed genes (DEGs).

first: Elda Nurafnie

last: Ibnu Rasid


title: Gene expression data from liver treated with Vigna Umbellata extract (VE)

summary:
Gene expression profiling reveals DEGs in liver.
We evaluated the effects of Vigna Umbellata on liver of ob/ob mice through an untargeted whole-genome transcriptome analysis.

overall_design: The microarray analysis was conducted on control ob/ob mice group and VE-treated group using the GeneChip WT PLUS Reagent Kit (ThermoFisher Scientific) and GeneChip™ Hybridization, Wash and Stain Kit (ThermoFisher Scientific) following the manufacturer’s instructions. Firstly, about 100 ng of RNA from each sample was obtained to synthesize complementary DNA (cDNA) for complementary RNA (cRNA) synthesis. cRNA was purified and reverse transcribed for single-stranded cDNA (ss-cDNA) synthesis, purification, fragmentation and labelling. ClariomTM S Array (Mouse; ThermoFisher Scientific) were hybridized with samples extracted from liver. Tissue samples were prepared from control groups, including ob/ob mice (n = 3) and, when applicable, wild-type mice (n = 3), as well as from VE-treated groups receiving 50 mg/kg BW (n = 3) and 100 mg/kg BW (n = 3). All of the samples were hybridized for 16 hours in a 45 degree celcius incubator, washed and stained on the GeneChip™ Fluidics Station (ThermoFisher Scientific). The scanning was performed using GeneChip Scanner (ThermoFisher Scientific). The raw image data was obtained using the Transcriptome Analysis Console (TAC) software (ver. 4.0.2, ThermoFisher Scientific) and raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above back-ground (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7. Finally, genes that passed the filter criteria of p value <0.05 (one-way between-subjects ANOVA) and fold change >1.1 (in linear space) were considered as differentially expressed genes (DEGs).


title: Single-cell RNA-seq analysis of the adult rat anterior pituitary

city: Yokohama

first: Ken

last: Fujiwara

state: Kanagawa

department: Faculty of Science

institute: Kanagawa University

summary: Single-cell RNA sequencing was performed to characterize gene expression profiles in the anterior pituitary of adult male Wistar rats. The dataset was used to examine the expression of BMP receptors in gonadotrope populations based on marker gene expression.

overall_design: Single-cell suspensions were prepared from the anterior pituitary of an adult male Wistar rat. Cells were processed using the 10x Genomics Chromium platform, and libraries were sequenced on an Illumina NovaSeq 6000. Data were processed using Cell Ranger and used for downstream expression analysis without formal cell type annotation.


title: RNA sequencing of Kv8.2 knockout mouse retina

city: Iowa City

first: Sheila

last: Baker

state: IA

address: 51 Newton Rd

department: Biochemistry and Molecular Biology

institute: University of Iowa

summary: Photoreceptors rely on potassium homeostasis for normal function. To investigate transcriptional changes associated with loss of Kv8.2, RNA sequencing was performed on retinas from Kv8.2 knockout (KO) and wild-type (WT) mice at 1 month of age.

overall_design: Retinas from 3 wild-type (WT) and 5 Kv8.2 knockout (KO) mice were collected at 1 month of age, with two retinas pooled per sample. RNA sequencing was performed to compare WT and KO retinas. Two KO samples were excluded based on exploratory analysis, and differential expression analysis was conducted on 3 WT and 3 KO samples.

first: Miles

last: Pufall


title: Bulk RNA-seq analysis of Delta-like 4 (Dll4) knockdown in LPS- or TNF-α-stimulated THP-1 cells

city: Rochester

first: Shumin

last: Wang

state: New York

address: 601 Elmwood Avenue, Box CVRI

department: CVRI

institute: University of Rochester medical center

summary: Monocyte-mediated inflammation, rather than T cell activation, is a major cause of chronic inflammation. Here, we investigated the contribution of delta-like 4 (Dll4)-Notch signaling in monocyte-mediated inflammation. To investigate the biological functions and molecular mechanisms of monocyte Dll4, bulk RNA sequencing (RNA-seq) was performed in THP-1 cells transfected with Dll4 siRNA or control siRNA for 24 hours in the presence of LPS or TNF-α stimulation. Four experimental groups were analyzed: control siRNA + LPS, Dll4 siRNA + LPS, control siRNA + TNF-α, and Dll4 siRNA + TNF-α. Each group included five biological replicates (n=5 per group). The RNA-seq analysis was designed as a discovery experiment powered to detect moderate-to-large expression differences.

overall_design: RNA-seq profiling of THP-1 cells treated with Dll4 siRNA or control siRNA for 24 hours under inflammatory stimulation with either LPS or TNF-α. Total RNA was extracted after 24 hours and sequenced for bulk transcriptomic analysis.

first: Jinjiang

last: Pang


title: An adaptive cellular source of IL-17A and IL-17F is critical for the induction of experimental autoimmune encephalomyelitis II

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

address: 60 Fenwood Road,

summary: T helper 17 (TH17) cells have been suggested to play an important role in the pathogenesis of many autoimmune disorders, including multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE). However, recent studies suggest that interleukin (IL)-17 may be dispensable for the induction of EAE. Here, we use an adoptive transfer model of EAE to demonstrate that an adaptive cellular source of IL-17 is absolutely required for the induction of EAE disease. We further show that B cells can regulate the transfer of EAE disease in this context. Transcriptional profiling of TH17 cells in our model suggest that loss of IL-17A/F in T cells results in a lack of an IL-23 receptor (IL23R)–driven signaling signature. Our data demonstrates the critical importance of an adaptive immune cellular source of IL-17A and IL-17F to mediate EAE, and that IL-17 signaling is required for IL-23-mediated TH17 cell pathogenicity.

overall_design: Bulk RNA-seq of the transferred 2D2-IL-17A/F-DKO CXCR6+ TH17 cells, 2D2-IL-17A/F-DKO SLAMF6+ TH17 cells, 2D2-WT CXCR6+ TH17 cells, and 2D2-WT SLAMF6+ TH17 cells isolated from the CNS of the RAG2-/- hosts at the peak of disease.

first: Allen

middle: W

last: Ho

first: Linglin

last: Huang

first: Sumiti

last: Sandhu

first: Sheng

last: Xiao

first: Melissa

last: Sgodzai

first: Ella

last: Ullerich

first: Rajesh

middle: K

last: Krishnan

first: Alexandra

last: Schnell

first: Vijay

last: Kuchroo


title: An adaptive cellular source of IL-17A and IL-17F is critical for the induction of experimental autoimmune encephalomyelitis I


title: Analysis of Host and Microbiome Responses to Antibiotics Reveals Microbiota-Independent Effects on Gut Immune Response [NeuronRNASeq]

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St

country: Israel

institute: Bar-Ilan University

summary: Antibiotics are thought to affect host physiology by altering the gut microbiota. But which effects of antibiotics are microbiota-dependent or -independent is not clear. Here, we present a resource encompassing host and microbiota response to antibiotic treatment and computational tools to analyze them. We show how antibiotic administration routes affect host and microbiota responses and how combining antibiotics alters their individual activity. We developed CompoRes, a tool to determine whether perturbation affects the host directly or via the microbiota, and discovered microbiota-independent effects of antibiotic treatment. We found that circadian expression of MHC class II in the colon is functional in germ-free mice and is controlled by feeding via glucose. This expression pattern was lost during vancomycin treatment as the antibiotic altered feeding behaviour in a microbiota-independent manner. Together, our study provides tools for analysis of host response to different microbiota compositions which can also identify microbiota-independent effects of perturbations.

overall_design: PC12 cells were seeded in 6- or 12-well plates and maintained in RPMI 1640 medium supplemented with 2% FBS, 1% L-glutamine, and 1% penicillin/streptomycin. To induce neuronal differentiation, 50 ng/mL Nerve Growth Factor (NGF) was added every 48 hours for seven days. Following differentiation, cells were treated with 500 µg/mL vancomycin for 24 hours for RNA extraction.

first: Amir

last: Erez


title: TLR9-Mediated Macrophage-ILC Activation Induces Antigen-Independent Antiviral Immune Memory in the Lung

city: Tokyo

first: Asuka

middle: Joy

last: Tobuse

state: Tokyo

address: 4 - 6 - 1 Shirokanedai Minato-ku

department: Microbiology and Immunology

institute: University of Tokyo, Institute of Medical Science

summary: Our study investigates the innate stimulatory properties of CpG-𝛽-glucan complexed adjuvant in local tissue. We report the single-cell transcriptomes from whole lungs of adult mice following intranasal administration of adjuvant to identify adjuvant-mediated changes to immune cell composition in local tissue.

overall_design: From C57BL/6J wild-type, 6-wk, female mice, whole lungs were isolated at 1- and 3-days after intranasal administration of CpG-𝛽-glucan complexed adjuvant. Single-cell RNASeq was performed after dead cell removal, via the 10X Chromium  platform.

first: Kouji

last: Kobiyama

first: Ken

last: Ishii


title: Transcriptional signatures of dermal papilla cells during cashmere growth [RNA-Seq]

city: Shenyang

first: Huiling

last: Xue

address: 120 Dongling Road,110866 Shenyang,China

institute: Shenyang Agricultural University

summary: This study investigates regulatory molecules and machanisms of cashmere growth by profiling dermal papilla cells (DPCs) from secondary (SHF) and primary hair follicles (PHF) during the early anagen and anagen phases in both male and female cashmere goats. A comprehensive genome-wide transcriptomic analysis was then performed to characterize the differentially expressed molecular signatures associated with follicle types (SHF vs. PHF), developmental phases, and sex.

overall_design: RNA-seq was performed on dermal papilla cells from secondary and primary hair follicles of male and female cashmere goats during early anagen (June) and anagen (October).

first: Yanlei

last: Liu

first: Minglin

last: Wang

first: Xinyue

last: Liang


title: IL-17–Driven Tumor Cell–Intrinsic Inflammatory Programming Creates an Immunotherapy-Permissive Microenvironment

city: Sakai

first: Kosuke

last: Murakami

state: Osaka

address: 1-14-1, Miharadai, Minami-ku

institute: Kindai University

summary: Ovarian clear cell carcinoma (OCCC) is a chemoresistant subtype of ovarian cancer with limited effective therapeutic options. Although immune checkpoint inhibitors (ICIs) have shown little benefit in unselected ovarian cancer populations, clinical activity observed in a subset of OCCC patients suggests the presence of a histotype-specific immune vulnerability that remains poorly defined. To elucidate this biology, we integrated transcriptomic analyses from multiple independent human OCCC cohorts with immunohistochemical profiling and mechanistic studies using an immunocompetent syngeneic OCCC mouse model. Tumor cell–intrinsic and microenvironmental responses to IL-17 were investigated through in vitro stimulation assays, in vivo IL-17 administration, single-cell RNA sequencing of tumor-infiltrating T cells, and immune checkpoint blockade in a Th17-biased partial chimera model. OCCC was characterized as an IL-6–high tumor entity with a globally immune-sparse but CD4⁺ T-cell–skewed tumor immune microenvironment. Transcriptomic analyses identified a Th17-associated program marked by elevated RORC expression in a subset of tumors. Across large clinical cohorts, an IL17A^high subset demonstrated a T cell–inflamed gene expression profile independent of microsatellite instability and tumor mutational burden; however, this phenotype was not associated with survival in untreated disease. Mechanistically, IL-17 directly activated NF-κB–dependent inflammatory programs in OCCC tumor cells, inducing cytokines involved in T-cell recruitment and activation. In vivo, IL-17 remodeled the immune microenvironment, increasing infiltration and activation of both CD4⁺ and CD8⁺ T cells. Single-cell profiling further revealed expansion of Th17/Tfh-like CD4⁺ T cells and cytotoxic, non-terminally exhausted CD8⁺ T cells. Consistent with these findings, anti–PD-L1 therapy significantly improved survival exclusively in Th17-biased partial chimera mice. Collectively, these results demonstrate that a Th17-biased, IL-17–responsive immune contexture in OCCC engages tumor cell–intrinsic NF-κB inflammatory signaling to prime antitumor T-cell states and enable checkpoint blockade efficacy. This immune biology is predictive rather than prognostic, supporting a biomarker-driven immunotherapy strategy for OCCC within otherwise ICI-refractory ovarian cancer.

overall_design: Bulk RNA-seq was performed to define the NF-κB–dependent transcriptional program induced by IL-17 stimulation in murine ovarian clear cell carcinoma (OCCC) tumor cells. Cells were transfected with either a non-targeting control siRNA (siNC) or 2 kinds of siRNAs targeting Nfkb, followed by stimulation with recombinant IL-17 (or vehicle control as indicated). Total RNA was extracted from biological triplicates per condition and subjected to Illumina-based RNA sequencing. Differential expression analyses were conducted to (i) identify IL-17–responsive genes under control siRNA conditions and (ii) determine the extent to which IL-17–induced transcriptional changes require canonical or non-canonical NF-κB signaling.

first: Shiki

last: Takamura

first: Chiho

last: Miyagawa

first: Kazuhiro

last: Kakimi

first: Noriomi

last: Matsumura


title: Chromatin ends and promoter loops organize chromosome-sized domains in Tetrahymena

city: Hefei

first: Zhengyu

last: Luo

address: huanshang

institute: USTC

summary: Three-dimensional genome architecture shapes how regulatory elements controls gene expression, yet how compact unicellular genomes are folded is poorly understood. Ciliates such as Tetrahymena thermophila carry a fragmented, gene-dense somatic macronucleus (MAC) and a silent germline micronucleus (MIC), imposing distinct constraints on chromosome folding. Here we combine nucleosome-resolution Micro-C, ATAC-seq and RNA-seq to map 3D chromatin organization across Tetrahymena life cycle stages and in the related ciliate Tetrahymena pyriformis. We find that MAC chromosomes lack strong mammalian-style compartments and TADs but behave as short interaction units whose telomere-capped ends form accessible, strongly interacting hubs. Within these units, chromatin loops concentrate at promoter-proximal open chromatin and are closely associated with transcription level. During conjugation, long-range internal loops and promoter–promoter contacts are transiently weakened and then rebuilt, while end–end interactions persist. Similar promoter- and end-anchored folding in T. pyriformis points to a conserved ciliate strategy for organizing gene-rich genomes in three dimensions.

sample_organism:
Tetrahymena pyriformis
Tetrahymena thermophila

overall_design: Micro-C of T. thermophila cells at different life cycle stages: vegetative growth, starvation, conjugation 1.5hpm, 3hpm, 8hpm, 12hpm, 24hpm, and Refeeding 24 hours.                                                                       Hi-C of T. thermophila cells at vegetative growth stage with FA or FA + DSG crosslinking.                              Micro-C, ATAC-seq and RNA-seq with vegetative growth T. pyriformis cells.

first: Tengfei

last: Hu

first: Xiaoyuan

last: Song


title: Analysis of pancreatitis-derived organoids and PDAC organoids cocultured with multi-stroma

city: CAMBRIDGE

first: Giulia

last: Biffi

address: Cancer Research UK, Robinson Way

summary: We investigated the crosstalk between cocultures of pancreatitis (P)-derived organoids (P1 or P5) or PDAC organoids (T6-LOH or T13-LOH) and multi-stroma (pancreatic stellate cells PSC5, pancreatic fibroblasts FIBRO27 and mesothelial cells M-G1).

overall_design: 4 samples pooled in 1 OCM file - 2 coculture samples of P organoids and multi-stroma; 2 coculture samples of PDAC organoids and multi-stroma.

first: Wenlong

last: Li

first: Muntadher

last: Jihad


title: An endogenous auxin network shapes virulence and plant adaptation in Dickeya dadantii

city: Madrid

first: Zulema

last: Udaondo

address: Darwin 3

department: Microbial Biotechnology

institute: CNB-CSIC

summary: Indole-3-acetic acid (IAA) is a central phytohormone regulating plant growth and development and is increasingly recognized as an intra- and inter-kingdom signaling molecule that modulates diverse bacterial processes relevant during plant–microbe interactions. While IAA biosynthesis is widespread among plant-associated bacteria, the mechanisms through which this auxin regulates bacterial physiology and virulence, as well as those controlling its production, remain poorly understood. Here, we show that IAA synthesis deficiency in the globally relevant phytopathogen Dickeya dadantii triggers global transcriptional reprogramming and results in reduced virulence and fitness during plant infection. IAA was found to regulate the expression of the AaeXAB efflux pump, which mediates endogenous IAA secretion and confers resistance to plant defense–related phytohormones, including auxin and salicylic acid. This efflux system also contributes to successful plant infection and colonization in D. dadantii. Phylogenetic analyses revealed that the AaeXAB pump is commonly present among Pseudomonadota isolated from plant-associated environments. Moreover, IAA deficiency altered the expression of an indole-responsive regulator, suggesting cross-talk between IAA- and indole-mediated signaling networks. Our data also uncover a complex regulatory circuit coordination IAA production in D. dadantii, involving the ExpIR and Vfm quorum-sensing systems and the transcriptional regulators TyrR, TrpR, and LrhA. Collectively, our findings provide new insights into the role of IAA as a bacterial signal promoting plant adaptation and virulence. Targeting IAA biosynthesis and efflux pump activity may offer promising avenues for microbiome engineering and the development of anti-virulence strategies in phytopathogenesis.

overall_design: RNA sequencing was performed at Novogene Company Limited (United Kingdom) using samples from the wild-type D. dadantii 3937 and the ∆iaaM-km3 mutant grown in minimal medium supplemented with 0.25 mg/mL L-tryptophan (IAA precursor) and harvested at the early stationary phase of growth. Before sequencing, RNA integrity and quantification were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). One microgram of total RNA per sample (three biological replicates per strain) was used to construct the sequencing libraries. These libraries were generated by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs; #E7530), following the manufacturer's recommendations. Prior to library construction, ribosomal RNA was depleted with Illumina Ribo-Zero Plus rRNA Depletion Kit (Illumina; Ref. 20037135), according to the manufacturer's instructions. The resulting libraries were quantified by quantitative PCR and the inserts were measured using a LabChip GX instrument, using the LabChip NGS 3K reagent kit (PerkinElmer; CLS960013). Libraries were sequenced using the NovaSeq 6000 Illumina platform and paired-end reads were generated.

first: Amalia

last: Roca

first: Saray

last: Santamaria-Hernando

first: Juan

last: Cabrera

first: Ana

last: Nogueira

first: Emilia

last: Lopez-Solanilla

first: Miguel

last: Matilla


title: T follicular helper 1 cells in blood potentially mirror salivary gland-infiltrating T cells in Sjögren’s disease

city: Tsukuba

first: Saori

last: Abe

address: Tennodai 1-1-1

institute: University of Tsukuba

summary: Understanding the intricate relationship between peripheral blood immune profiles and the inflammatory environment within affected tissues is pivotal for uncovering mechanisms driving autoimmune diseases. This study aimed to characterize CD4+ T cell subsets in peripheral blood that mirror the inflammatory milieu of labial salivary glands (LSG) in primary Sjögren’s disease (pSjD). Using multicolor flow cytometry and T cell receptor (TCR) sequencing, we identified CXCR3+CXCR5+ T follicular helper 1 (Tfh1) cells as significantly elevated in the circulation of pSjD patients and even more prominently increased in the LSG, with blood PD-1+ICOS+ Tfh1 cells positively correlating with titers of antinuclear, anti-SS-A, and anti-SS-B antibodies. In contrast, CXCR3+CXCR5− Th1 cells were enriched in LSG but reduced in circulation. TCR analysis demonstrated that circulating Tfh1 cells shared extensive clonal similarity with LSG T cells. In the LSG, cytokines such as IL-6, IL-12, IL-21, and TGF-β were upregulated, with TGF-β and TCR recognition promoting Tfh1 differentiation. This microenvironment led to increased production of IL-2, TNF-α, and IL-21, promoting the expansion of CD19+CD38+ B cells. These findings underscore circulating Tfh1 cells as reflections of glandular inflammation and highlight TGF-β as a key driver of Tfh1 differentiation, presenting a potential therapeutic target.

overall_design: TCR seq from sorted T cell subset of blood, and paired minor salivary gland biospsy.

first: Hiroto

last: Tsuboi

first: Hiroyasu

last: Aoki


title: TGF-alpha/EGFR signalling mediates retinoic acid-induced lung repair

city: London

first: Charlotte

last: Dean

address: Imperial College London Hammersmith Campus, Level 5 Dr Victor Phillip Dahdaleh (VPD) Building, Du Cane Rd

institute: Imperial College London

summary: Retinoic acid (RA) signalling is an important regulator of lung development and repair. To investigate the molecular mechanisms underlying RA-mediated responses in lung endothelial cells, we profiled the gene expression of human pulmonary microvascular endothelial cells (HPMECs) treated with RA or ethanol (EtOH) vehicle control. Whole-genome expression analysis using Affymetrix Human U133 Plus 2.0 GeneChips identified transcriptional changes associated with angiogenesis, wound healing, and signalling pathways relevant to alveolar repair.

overall_design: Primary HPMECs were cultured on Matrigel and treated with either RA or EtOH vehicle control. Total RNA was extracted at three time-points: before treatment (t = 0 h), initiation of tube-like structures (t = 40 min), and formation of tube networks ( t= 4 h). Four RNA samples were prepared per treatment group from independent experiments (n = 4 per condition), with each RNA sample pooled from three technical replicates. Labelled cDNA was hybridised to Affymetrix Human U133 Plus 2.0 arrays.

first: Sek-Shir

last: Cheong

first: David

last: Chambers


title: Curative treatment of advanced, poorly immunogenic metastatic murine cancer models using an in situ vaccine, low-dose radiopharmaceutical, and immune checkpoint inhibition

city: MADISON

first: Rene

last: Welch

state: WI

address: 1111 Highland Avenue,

department: Department of Biostatistics and Medical Informatics

institute: University Wisconsin - Madison

summary: Background Focal tumor radiation may prime adaptive anti-tumor immunity and this can be augmented by combination with intratumoral delivery of immune adjuvants. However, the abscopal propagation of anti-tumor immune response from such in situ vaccine (ISV) approaches is not consistently achieved in metastatic disease. Targeted radionuclide therapy (TRT) can deliver radiation to all tumor site in metastatic settings and low dose TRT can promote the clonal expansion and propagation of T cell-mediated anti-tumor immune response. We hypothesized that combining ISV to prime and low-dose TRT to propagate anti-tumor immunity could promote response to dual immune checkpoint blockade (DCP; anti-PD-L1 and anti-CTLA-4) in murine models of poorly immunogenic metastatic disease. Methods: C57BL/6 mice were engrafted with a primary tumor (right flank), a secondary tumor (left flank), and intravenously injected tumor cells to model advanced metastatic disease using the syngeneic MOC2 head and neck squamous cell carcinoma model or the B78 melanoma model. Mice were randomized to receive monotherapy or double or triple combinations of low-dose TRT, ISV targeting the primary tumor, and DCP. Tumor growth and survival were measured and mice rendered tumor-free mice were re-challenged with tumor engraftment to assess immune memory. Immune response was assessed by immunohistochemistry, flow cytometry, and quantitative PCR. Results: In two poorly immunogenic, syngeneic murine tumor models of advanced metastatic cancer, when compared to dual combinations or monotherapies, a triple combination of TRT+DCP+ISV enabled eradication of bulky well-established tumors, prevented development of lung metastases from circulating tumor cells (4 of 7 mice with circulating B16 melanoma and 14 of 15 mice with circulating MOC2 HNSCC developed no lung metastases), and extended survival (p < 0.01). This combination conferred T cell-dependent, tumor-specific immune memory,  enabling uniform rejection of tumor re-engraftment (0% vs 100% for both B78 melanoma and MOC2 re-engraftment in disease-free triple-therapy treated mice vs age matched control mice). TRT+DCP+ISV activated both innate and adaptive immune response pathways in the primary and secondary tumors. Conclusions: Combining ISV and low-dose TRT is a promising approach to prime and propagate anti-tumor immunity and to promote response to checkpoint inhibition in settings of poorly immunogenic metastatic cancers.

overall_design: For MOC2 model, C57BL/6 mice were divided into 5 groups such as PBS, in situ vaccine (ISV)+ dual immune checkpoint blockade (DCP; anti-PD-L1 and anti-CTLA-4), Targeted radionuclide therapy (TRT)+ISV, TRT+DCP and TRT+ISV+DCP tratments groups. 2 million huEGFR-expressing MOC2 cells (M2h) were engrafted subcutaneously into the right flank for the primary tumors, and 4 days later 1 million MOC2WT cells were engrafted into the left flank for the secondary tumor. 1 million

first: Trishna

last: Debnath

first: Won Jong

last: Jin

first: Ravi

last: Patel

first: Peter

last: Carlson

first: Mahfuzur

last: Rahman

first: Tracy

last: Berg

first: Caroline

last: Kerr

last: Welch Schwartz

first: Yujuan

last: Wang

first: Meredith

last: Hyun

first: Jamey

last: Weichert

first: Reinier

last: Hernandez

first: Paul

last: Sondel

first: Zachary

last: Morris


title: HT-29 cells exposed to lead ion by transcriptome

first: hailiang

last: hu

address: jixi road

institute: First Affiliated Hospital of Anhui Medical University

summary: The study involved dividing cells into two distinct groups: a treatment group (T) exposed to 8 mM lead acetate, based on previous literature, and a control group (C) treated with a solution that did not contain lead acetate. Transcriptome analysis was leveraged to detect changes in gene expression in HT-29 cell lines before and after exposure to lead acetate

first: Suwei

last: Jiang

first: Hailiang

last: Hu


title: ScRNA-Seq analysis of spontaneous regeneration of inner ear hair cells in a novel injury model revealed the key role of dlx5a

city: 南通市

first: Guiyi

last: Zhang

state: 江苏

address: 江苏省南通市崇川区

institute: Nantong University

summary: We established a hair cell injury model in the zebrafish inner ear by injecting neomycin at 5 dpf. To capture the key time points of hair cell damage and regeneration, we performed single-cell RNA sequencing on inner ear samples collected at selected intervals following injury.

overall_design: To elucidate the transcriptional landscape and cellular composition underlying crista HC regeneration, we dissected the otic vesicles containing crista and macula HCs from Tg(agr2:kaede; pou4f3:mGFP) zebrafish embryos at 6, 24, and 48h post-neomycin injection, as well as from control embryos at 6, 24, and 48h post-PBS injection. Single-cell RNA sequencing was performed using the singleron platform.

first: Jie

last: Gong

first: Chao

last: Yang

last: Guo

first: Xun

first: Ying

last: Xu

first: Fuping

last: Qian

first: Xin

first: Dong

last: Liu


title: Identification of PEG10 as a biomarker for DICER1-related tumor predisposition syndrome

city: Los Angeles

first: Mona

last: Wu

state: California

address: 4650 Sunset Boulevard

institute: CHLA

type: Non-coding RNA profiling by high throughput sequencing

summary: Background:  MicroRNAs (miRNAs) are short non-coding RNA molecules that downregulate messenger RNA (mRNA) expression. Mature miRNAs (designated -5p or -3p) are produced by the endonuclease DICER1. Mature miRNAs are loaded into the AGO2-containing RNA-Induced Silencing Complex where they target mRNAs via a seed sequence in the mRNA’s 3’ untranslated region (3’ UTR). Children with pathogenic variants of DICER1 have a highly elevated risk of cancers in many different organs– recognized as DICER1-related tumour predisposition (DRTP). These tumours/lesions have one inactivated copy and one “hotspot” mutated copy of DICER1.  All “hotspot” DICER1 mutations impair 5p miRNA production.  DICER1 DNA sequencing has become the diagnostic standard but an immunohistochemical (IHC) diagnostic method may improve patient care via faster return of results. Methods:  Using AGO2 miR-eCLIP and RNAseq data of a mouse cell model of DRTP (E1705K) I identified paternally expressed gene 10 (Peg10) as a diagnostic candidate.  Validation of cell overexpression (mRNA and protein) and de-repression of Peg10 3’ UTR was assessed.  Dependence on Peg10 for cell viability was measured (post 72-hour siRNA-mediated knockdown). IHC staining of two tumour microarrays (TMAs) was performed and scored (H-score) to evaluate its use in the clinic (Area Under Curve, AUC).   Results:  In E1705K, Peg10 displayed elevated RNA and protein levels as well as de-repression of its 3’ UTR.  Peg10 knockdown does not impact cell viability. TMA1 (41 female samples) had an AUC of 0.80 (considered of good clinical utility) while TMA2 (95 male and female samples) had an AUC was 0.71 (fair clinical utility).  Conclusion:  E1705K identified Peg10 as a biomarker that is elevated in DRTP tumours from both sexes bearing a variety of DICER1 hotspot variants. Elevated Peg10 mRNA levels are in part due to lack of 5p-mediated interactions with its 3’ UTR.

overall_design: RNAseq of dicer1-/- mouse mesenchymal stromal cells rescued with human DICER1WT, DICER1E1705K, DICER1D1320A, and empty vector


title: Reduced dosage of Kmt2d modifies the transcriptional landscape of Tbx1 haploinsufficiency towards phenotypes of 22q11.2DS

city: Bronx

first: Bernice

last: Morrow

address: 1301 Morris Park Ave, Price Center, Room 469

department: Genetics

institute: Albert Einstein College of Medicine

summary: Haploinsufficiency of TBX1, which occurs in 22q11.2 deletion syndrome (22q11.2DS), leads to a heterogeneous spectrum of clinical manifestations, including craniofacial anomalies, immunodeficiency, and congenital heart defects. The variability in syndromic presentation between patients may be partially explained by variants in chromatin regulatory genes that act to further modify TBX1 function. To investigate this relationship, we selected KMT2D as a candidate gene due to its role in the etiology of Kabuki syndrome which shares overlapping features with 22q11.2DS. We demonstrate that conditional inactivation of Kmt2d in the Tbx1 lineage in Tbx1 heterozygous mice leads to fully penetrant perinatal lethality and increased incidence of craniofacial dysmorphism, thymus and parathyroid gland hypoplasia, and aortic arch anomalies. At early stages, mutant embryos were found to have defects of the caudal pharyngeal apparatus, including abnormal patterning of the 3rd pouch endoderm, hypoplastic 4th arches, and defective 4th arch arteries. Finally, analysis of single cell RNA-sequencing revealed dysregulation, and largely downregulation, of genes involved in basic cellular functions, suggesting that Tbx1 and Kmt2d developmentally converge upon essential biological processes. Overall, these results indicate that reduced dosage of Kmt2d perturbs the developmental landscape of the Tbx1 heterozygote, eliciting phenotypes that are shared between 22q11.2DS and Kabuki syndrome.

overall_design: Experimental crosses were set between Tbx1Cre/+;Kmt2df/+ males and Kmt2df/f;Gfpf/f females. Dissections for E9.5 embryos were performed on the same day and embryos were microdissected and genotyped before being pooled into either cHet or cKO tubes for FACS sorting followed by preparation for scRNAseq.

first: Miller

last: Daniella

first: Jackson

last: Kevyn

first: Cox

last: Timothy

first: Morrow

last: Bernice


title: Identification of PEG10 as a biomarker for DICER1-related tumor predisposition syndrome [RNA-Seq]


title: Analysis of Host and Microbiome Responses to Antibiotics Reveals Microbiota-Independent Effects on Gut Immune Response [16S rRNA seq]

first: Shai

last: Bel

overall_design: Mice were randomly divided into either control or antibiotic treatment groups. Mice were treated twice a day for 3 days, and once more on the 4th day, via either oral gavage, intraperitoneal or intravenous injection. Mice received 2.5mg of either ampicillin, metronidazole, neomycin, vancomycin or a mix of all four antibiotics, in 100µl of PBS. Control mice received 100µl of PBS. Four hours after the last treatment mice were euthanized and tissues extracted.

first: Amir

last: Erez


title: Analysis of Host and Microbiome Responses to Antibiotics Reveals Microbiota-Independent Effects on Gut Immune Response.

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

overall_design: Refer to individual Series


title: Analysis of Host and Microbiome Responses to Antibiotics Reveals Microbiota-Independent Effects on Gut Immune Response

overall_design: Mice were randomly divided into either control or antibiotic treatment groups. Mice were treated twice a day for 3 days, and once more on the 4th day, via intraperitoneal injection. Mice received 2.5mg vancomycin in 100µl of PBS. Control mice received 100µl of PBS. For treatment of germ-free mice, mice were removed from sterile isolators into Tecniplast ISOchages, where they were maintained for the duration of the treatment.