title: Effect of depletion of SETD2 on gene expression in DSS-induced colitis

first: Jing

last: Feng

address: Zhizao ju road

department: Gastroenterology

institute: Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University

summary: We reported that the deletion of SETD2 in IECs leads to more serious colitis. We performed RNA sequencing to detect molecular differences in intestianl epithelial cells isolated from SETD2F/F and SETD2VIL-KO mice.

overall_design: RNA-sequencing of DSS-treated SETD2F/F and SETD2VIL-KO mouse IECs.

first: Xiangjun

last: Meng


title: A comparative multiomic atlas of human immunity to multiple COVID-19 vaccines

status: Public on Aug 12 2026

city: Stanford

first: Zhuoqing

last: Fang

state: California

address: 300 Pasteur Drive

country: USA

institute: Stanford

type: Expression profiling by high throughput sequencing

summary: The rapid development of multiple COVID-19 vaccines, based on mRNA, recombinant adenoviral vectors and adjuvanted proteins, was critical to curtailing the global pandemic, and created a unique opportunity to compare human immunity to distinct vaccine platforms encoding the same antigen. Here, we present a longitudinal comparative analysis of innate and adaptive immune responses to the Matrix-M-adjuvanted Novavax (NX) and chimpanzee adenovirus-based AstraZeneca (AZ) vaccines in 161 healthy South African volunteers across three doses over a 11-month period collected between 2021 and 2022. We  profiled 44 PBMC samples from 22 individuals receiving either AZ or NX, collected at baseline, and at 1 and 7 days after primary, secondary or booster doses. After pre-processing and quality control, which included removal of one sample (AZ, secondary day 1) due to low-quality cells, we obtained 162,037 high quality transcriptomes. No significant differences in frequency were observed after vaccination or between groups, but there were significant induction of interferon-stimulated gene expression early after vaccination. At baseline, myeloid cell clusters (CD14+ monocytes, CD16+ monocytes and cDC2) expressed these genes at higher magnitudes than other cell types. After primary NX vaccination, no cell type showed increased expression of these modules, consistent with bulk RNAseq, which revealed induction only at day 2. In contrast, primary AZ vaccination led to a striking upregulation of ISGs across all cell types at day 1. After NX boosting, CD16+ monocytes and several other cell types showed modest ISG induction, whereas secondary AZ vaccination elicited no induction of these responses.

overall_design:
Live frozen PBMCs were thawed, washed twice with RPMI supplemented with 10% FBS and 20 μg ml−1 DNase I (Sigma Aldrich), and resuspended in 1X-PBS. Cells were washed with PBS and stained with Zombie aqua fixable viability dye. Live cells were sorted into PBS supplemented with 5% FBS and stained with a cocktail of TotalSeq-A antibodies in PBS with 5% FBS, 2 mM EDTA and 5 mg/mL human IgG, washed twice with PBS plus 5% FBS, and resuspended in PBS supplemented with 1% BSA (Miltenyi), and 0.5 U μL RNase Inhibitor (Sigma Aldrich). About 9,000 cells were targeted for each experiment. Cells were mixed with the reverse transcription mix and subjected to partitioning along with the Chromium gel-beads using the 10X Chromium system to generate the gel-bead in emulsions (GEMs) using the 3′-V3 chemistry (10X Genomics).
no separate raw data files for GEX/ADT; all information have been provided in the processed file (mtx, features) files.


title: A CK2–β-TrCP kinase–E3 ubiquitin ligase cascade is a metabolic sensor regulating Tryptophan 2,3-dioxygenase stability

city: Martinsried

first: Brenda

middle: A

last: Schulman

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute of Biochemistry

summary: Small molecules toggling the ubiquitin-proteasome system (UPS) are powerful regulators of protein degradation, yet how endogenous ligands gate UPS decisions in human biology remains poorly understood. Here we define control of UPS access to Tryptophan-2,3-dioxygenase (TDO2), which converts the essential amino acid tryptophan (Trp) to N-formylkynurenine. When Trp concentrations are limiting, TDO2 is degraded to avert tryptophanemia. We discovered that a CK2–β-TrCP kinase-E3 ligase cascade generates and recognizes phosphodegrons in TDO2 unless shielded by Trp binding to an exosite. Effects of Trp analogs on CK2–β-TrCP-dependent ubiquitylation indicated the indole, amino, and carboxylate groups collectively protect TDO2. Cryo-EM reveals these moieties organize a Trp-ordered flap that covers the exosite and thereby restricts generation of adjacent phosphodegrons. In the absence of Trp, the flap is flexible, enabling phosphorylation-coupled ubiquitylation. Overall, our data uncovered an endogenous small molecule conformationally stabilizing its own metabolizing enzyme through protection from a phosphorylation-ubiquitylation cascade.

overall_design: genome-wide CRISPRi screen using the TOP5 CRISPRi library (Addgene Cat# 83969) with the fluorescent sfGFP-P2A-mCherry-tagged TDO2 reporter cell line in K562-dCas9-zim3 cells cultured in Trp starvation condition

first: Alina

middle: S

last: Thielen

first: Bastian

last: Bräuning


title: Modeling patient variants of Cnot1 and Cdc42bpb lead to distinct forms of congenital diaphragmatic hernia in mice

city: Bar Harbor

first: Stephen

last: Murray

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Congenital diaphragmatic hernia (CDH) is a common and severe congenital anomaly characterized by disruption of the diaphragm and impairment of lung development in utero. CDH presents as a spectrum of forms and severities, with diaphragm disruptions arising in the dorsal/posterior region correlating with more severe pulmonary disease and higher risk of mortality than those appearing in ventral/anterior regions, which can present asymptomatically. The genetic etiology underlying CDH is complex, with many genes implicated showing variable expressivity and incomplete penetrance in both human patients and mouse models. Here we present in vivo validation of two genes previously unassociated with CDH: the CDC42-interacting kinase CDC42BPB; and CNOT1, a scaffolding protein of the CCR4-NOT protein complex, critical for mRNA regulation through modifications such as deadenylation. Each gene was found to have a damaging, de novo missense variant in a recent large-scale CDH patient sequencing screen. Loss of Cdc42bpb leads to ventral diaphragmatic hernia, heart septal defects and minor lung epithelial differentiation defects in mouse embryos. Installation of the orthologous patient missense variant through CRISPR/Cas9 editing leads to less severe ventral diaphragm defects. Mouse embryos with either one or two copies of the orthologous Cnot1 variant, c.1867C>T (p.R623W), develop dorsal diaphragmatic hernias with low (<50%) penetrance, and mutants showed alterations in mRNA isoform expression consistent with the molecular role of Cnot1 in RNA splicing.  Taken together, these results underscore the power of in vivo functional modeling and reveal two previously unrecognized genetic drivers of diaphragm development and CDH pathogenesis.

overall_design: Developing diaphragms were dissected from embryonic day (E)13.5 and E14.5 mouse embryos heterozygous (Het), homozygous (Hom) or wiltype (WT) for the c.1876C>T,p.R623W missense variant. RNA was isolated and total RNA was pair-end sequenced with ribosomal RNA depletion. Reads were aligned to the mm10 reference genome, gene and transcript counts were quantified, and expression levels of genes and isoforms were compared across genotypes at both developmental stages.

first: Eric

middle: L

last: Bogenschutz


title: Bioprinted 3D vascularized human placenta models recapitulate early and late stages of pregnancy

city: Rockville

first: Marc

last: Ferrer

state: MD

address: 9800 Medical Center Dr.

department: NCATS (National Center for Advancing Translational Sciences)

institute: NIH (National Institutes of Health)

summary: The placenta is a highly dynamic organ that supports the growth and development of the fetus throughout the different stages of pregnancy. Malfunction of the placenta causes disorders of the pregnancy, including preeclampsia and pre-term birth. The study of the pathophysiology of the placenta at different stages of pregnancy has been hindered by limited access to the human placenta and lack of predictive cellular and animal models.  Here, we describe a 3D bioprinted vascularized human placenta barrier (hPB) tissue models using primary human trophoblasts and stroma cells that recapitulate the physiology of the human placenta at early and late stages of gestation. These bioprinted vascularized hPB tissue models mimic the architecture and function of late and early-stages human placenta, including barrier function, nutrient uptake, transporters activity and hormones secretion. These vascularized hPB models were assembled in a 96-well microplate format to enable robust ddrug screening for placenta diseases and safety.

overall_design: RNA-seq profiling of hPB models at early and late stages of gestation using primary or immortalized trophoblasts cells.

first: Cristina

last: Antich

first: Yu-Chi

last: Chen

first: Yanyan

last: Qu

first: Dingyin

last: Tao

first: Min Jae

last: Song

first: Ramkumar

last: Menon


title: Spatial mapping of Ethiopian cutaneous leishmaniasis lesions reveals patient-defined immune signatures

city: York

first: Paul

middle: M

last: Kaye

state: North Yorkshire

address: University of York, Heslington

country: United Kingdom

institute: Hull York Medical School, University of York

summary: Ethiopian cutaneous leishmaniasis (CL) shows remarkably heterogeneous clinical presentations, but the underlying immunopathological mechanisms driving this heterogeneity in disease presentation remains poorly understood. To characterise the local immune response in Ethiopian CL, we performed spatial transcriptomics (Visium, 10x Genomics) on paired (lesional and non lesional) skin punch biopsies from five Ethiopian CL patients. We used reference-free deconvolution, morphology-guided regional analyses, and immunohistochemistry to identify five5 dominant patient-defined immunopathological responses: i) epithelial hyperplasia with interferon-stimulated keratinocytes, ii) cytotoxicity with tertiary lymphoid structures, iii) granulomatous inflammation with proinflammatory response iv) granulomatous inflammation with M2-polarised myeloid cell responses , and v) fibrotic remodelling with active collagen synthesis. Future longitudinal studies are needed to distinguish whether these patterns represent discrete pathotypes or stages of disease progression. Improved understanding of disease pathotypes in Ethiopian CL directly supports the WHO 2030 roadmap for leishmaniasis control and informs future immune-based therapeutic strategies.

overall_design:
We enrolled six participants from the Spatial CL study investigating host-parasite interactions in Ethiopian CL at the Leishmaniasis Research and Treatment Centre (LRTC), University Hospital of Gondar (Gondar, Amhara Province, Ethiopia) between March-May 2022 with follow-up until November 2022. Participants were selected to represent diverse clinical presentations: localized cutaneous leishmaniasis (LCL, n=2), mucocutaneous leishmaniasis (MCL, n=2), and diffuse cutaneous leishmaniasis (DCL, n=2). Inclusion and exclusion criteria are available at Clinicaltrials.gov. Leishmania infection was verified by microscopy of Giemsa-stained skin slits and kDNA PCR of skin slit smears. Parasite genotyping by ITS-1 high-resolution melt PCR. After enrolment, 4mm and 2mm punch biopsies (KAI Medical, Solingen, Germany) were collected from lesional (index lesion) and non-lesional skin (upper thigh or shoulder), respectively, snap-frozen in liquid nitrogen within 15 minutes, and stored frozen until Visium processing (10X Genomics, CA, USA).Frozen tissue blocks were sectioned at 10 μm thickness and initial sections from each sample was assessed for RNA quality (RNA Integrity Number, RIN; 2.2-8.7).  Due to low RIN values, we adapted the 10x Genomics Visium FFPE protocol for frozen sections. SureSelect identified two L. aethiopica (P1, P2) and one L. tropica (P5) infection. Following clinical reassessment, one patient initially classified as DCL was diagnosed with leprosy and excluded; the remaining five patients (P1-P5) included two with mucosal involvement (P1, P3) and three with purely cutaneous lesions on the arm (P2), neck (P4), and leg (P5). Clinical data was collected and recorded in a REDCap database
contributor: SPATIAL CL, CONSORTIUM

first: Nidhi

last: Dey

first: Thao-Thy

last: Pham

first: Shoumit

first: Mekibib

last: Kassa

first: Tigist

last: Mekonnen

first: Helina

last: Fikre

first: Pieter

last: Monsieurs

first: Myrthe

last: Pareyn

first: Johan

last: Van Griensven

first: Malgorzata

last: Domagalska

first: Jean-Claude

last: Dujardin

first: Mezgebu

last: Asres

first: Mikias

last: Woldetensay

first: Wim

last: Adriaensen


title: GSDMD-dependent Stromal Pyroptosis Drives Maladaptive CD4⁺ T-cell Remodeling in Tet2-Deficient Hematopoiesis

city: Stony Brook

first: Kehan

last: Ren

state: NY

address: 101 Nicolls Road

department: Medicine

institute: Stony Brook University

summary: An inflammatory bone marrow microenvironment is increasingly recognized as critical in myeloid disease evolution, yet how stromal inflammation interfaces with adaptive immunity remains poorly defined. Here, we show that stromal pyroptosis drives mutation-specific myeloid expansion by coordinating monocytic remodeling and CD4⁺ T-cell activation. Genetic ablation of gasdermin D in the bone marrow stroma suppressed stromal pyroptosis and attenuated Tet2-deficient myeloid expansion. Tet2 deficiency skewed monocyte and macrophage differentiation toward an activated, antigen-presenting state that interacted with pyroptotic stromal cells to promote expansion of a distinct CD4⁺ T-cell population. These cells expressed canonical T follicular helper markers (Bcl6, Cxcr5, Il21, and Cd40l) together with interferon-responsive and tissue-interaction programs, consistent with an inflammation-adapted TFH-like (TFHL) state. CD40L produced by TFHL cells reinforced expansion of Tet2-deficient monocytes and macrophages, establishing a feed-forward stromal–immune circuit. Disruption of this axis through stromal gasdermin D deficiency or CD40L blockade attenuated myeloid expansion in vivo. Consistent with these findings, patients with isolated TET2 loss-of-function mutations exhibited CD4⁺ T-cell skewing and T-cell–rich tertiary lymphoid structures in the bone marrow. Together, these data identify a pyroptosis-dependent stromal–immune axis that links early myeloid inflammation to maladaptive adaptive immune remodeling and reveals a context-dependent therapeutic vulnerability in Tet2-deficient hematopoiesis.

overall_design: Multiple bone marrow transplantation models were used to dissect the cell-intrinsic and cell-extrinsic mechanisms that regulate innate and adaptive immune remodeling within the bone marrow microenvironment. Specifically, bone marrow cells from miR146a/mDia1 double-knockout (DKO) mice, miR146a/mDia1/Gsdmd triple-knockout (TKO) mice, or their wild-type littermate controls (TWT) were transplanted into wild-type recipient mice to determine the hematopoietic cell-intrinsic role of Gsdmd in reshaping the bone marrow microenvironment. This approach allowed us to assess how loss of Gsdmd in the context of miR146a/mDia1-deficient hematopoietic cells influences immune cell composition, inflammatory signaling, and niche remodeling after transplantation. To investigate the role of Gsdmd in non-hematopoietic compartments of the bone marrow microenvironment, Tet2-deficient bone marrow cells were transplanted into Gsdmd-/- recipients or wild-type recipients, with wild-type-to-wild-type transplantation serving as the baseline control. Lastly, to investigate the role of CD40L produced by Tfh-like CD4+ T cells, we administered a CD40L-blocking antibody in the Tet2-to-WT transplantation group and compared this group with Tet2-to-WT recipients treated with IgG isotype control antibody, Tet2-to-Gsdmd-/- recipients, and WT-to-WT recipients as the baseline control. This design allowed us to assess whether CD40L signaling mediates the effects of Tet2-deficient hematopoiesis on inflammatory remodeling of the bone marrow microenvironment.

first: Ermin

last: Li

first: Xu

last: Han

first: Honghao

last: Bi

first: Pan

last: Wang

first: Peng

last: Ji


title: OM-sqPCR enables one-Step multiplex quantification of circulating small-RNA subclasses for colorectal cancer classification

city: Nanjing

first: Ruixi

last: Ye

state: Jiangsu

address: 南京市栖霞区仙林大道163号

country: China

institute: Nanjing University

type: Non-coding RNA profiling by high throughput sequencing

summary: Accurate and multiplexed quantification of circulating small RNAs (sRNAs) remains technically challenging due to their structural diversity and low abundance. Here we present OM-sqPCR, an AI-assisted one-step multiplex quantitative PCR platform that enables simultaneous detection of microRNAs, transfer RNA–derived sRNAs (tsRNAs), and ribosomal RNA–derived sRNAs (rsRNAs) in a single closed-tube reaction. The system integrates optimized enzyme–buffer chemistry for short RNA templates with machine-learning–guided primer–probe design, enabling synchronized amplification across multiple optical channels. Applied to a multicentre clinical cohort (n = 651), OM-sqPCR identified a four-sRNA signature that discriminated colorectal cancer from controls with an area under the ROC curve (AUC) = 0.97, 85.9% sensitivity, and 93.1% specificity, outperforming serum carcinoembryonic antigen (CEA)  and maintaining high accuracy in early-stage disease (stage I–II, sensitivity: 84.6%). The workflow also validated biomarker panels for renal and thyroid cancers with comparable accuracy (AUC > 0.98). This generalizable, low-cost platform provides a scalable and automation-ready solution for unified small-RNA quantification across diverse clinical contexts.

overall_design: We applied OM-sqPCR to circulating biomarker discovery and validation in CRC and identified a 4-sRNA classifier with strong performance in blinded multicenter validation. We further evaluated the platform in proof-of-concept studies using previously reported circulating sRNA panels for renal cell carcinoma and thyroid carcinoma.


title: Immunomodulation of the prostate tumor microenvironment following inorganic Arsenic exposure

city: West Lafayette

first: Harish

last: Kothandaraman

state: IN

address: 201S South State St

department: Purdue Institute for Cancer Research

institute: Purdue University

summary: The tumor microenvironment shapes how prostate cancer (PCa) progresses through stromal-immune interactions. We investigated how adipose-derived mesenchymal/stromal cells (ASC) and chronic inorganic arsenic (iAs) exposure jointly influence PCa by using a Ras-driven murine model. ASC-conditioned media enhanced TC2Ras viability, while iAs reversed this effect. In vivo, ASC+iAs tumors showed increased weight, altered immune infiltration, and transcriptomic remodeling, including a sustained IFN-IRF1 axis and immune checkpoint upregulation. ASC-iAs crosstalk promotes immune tolerance, revealing mechanisms by which environmental toxicants modulate cancer immunity.

overall_design:
Tumors were generated by subcutaneous implantation of 125,000 TC2Ras prostate cancer cells, either alone or mixed with 1% ASC‑GFP cells, into both flanks of mice previously maintained for two weeks on low‑arsenic chow and Milli‑Q water. After implantation, mice were assigned to receive either 0 ppb or 300 ppb inorganic arsenic (iAs) in drinking water, generating four treatment groups. Tumors were collected at 21 days post‑implantation, with left and right flank tumors from each mouse combined, immediately preserved in RNAlater, and stored at −80°C. Total RNA was extracted from 15–18 mg tumor tissue using the Qiagen RNeasy Mini Kit, and samples with RIN >7.0 were used for library preparation with the Illumina TruSeq Stranded mRNA kit. Sequencing was performed on the Illumina NovaSeq 6000 platform with paired‑end reads, followed by adapter/quality trimming (Cutadapt), alignment to the Mus musculus genome (HISAT2), transcript assembly and quantification (StringTie/Ballgown), and differential expression analysis using DESeq2 and edgeR.

A300: Tumors generated by subcutaneous implantation of TC2Ras prostate cancer cells, treated with 300 ppb inorganic arsenic (iAs) in drinking water
ASC300: Tumors generated by subcutaneous implantation of TC2Ras prostate cancer cells mixed with 1% ASC-GFP cells, treated with 300 ppb inorganic arsenic (iAs) in drinking water
ASC: Tumors generated by subcutaneous implantation of TC2Ras prostate cancer cells mixed with 1% ASC-GFP cells only
Control: Tumors generated by subcutaneous implantation of TC2Ras prostate cancer cells only

first: Marxa

last: Figueiredo

first: Joseph

last: Shearer


title: The role of RNA-helicase MOV10 in the regulation of transcript levels during the development of mouse brain.

city: Urbana

first: Stephanie

last: Ceman

state: Illinois

address: 506 S Mathews Ave

department: Cell and Developmental Biology

institute: University of Illinois Urbana-Champaign

summary: It has previously been shown that MOV10 exhibits a distinct developmental expression pattern, with protein levels being very high in the brains of neonatal mice and almost completely absent in adult brains. To investigate the role of MOV10 in brain development, we generated a mouse model called Mov10 Deletion by crossing a Mov10 conditional knockout line with Emx1-Cre and a Mov10 heterozygous mutant. In this study, we performed bulk RNA sequencing on whole brain tissue collected from wild-type (WT) and Mov10 Deletion mice at postnatal days 0, 7, 14, and 23. The RNA extraction, library preparation, and sequencing was performed by Biostate.ai.

overall_design: RNA was collected from whole brains of WT C57BL/6J and Mov10 Deletion mice at postnatal days 0, 7, 14, and 23, with each sample containing RNA from three mice. Tissue was flash-frozen to preserve RNA integrity during shipment to Biostate.ai, where RNA extraction, library preparation, and RNA sequencing were performed.

first: Temirlan

last: Shilikbay

first: Rachan

last: Raj

first: David

last: Zhang


title: Unveiling a Novel Role for p19Arf in mESC Differentiation Toward the Pancreatic Lineage

city: Napoli

first: Dario

last: Antonini

address: Strada Vicinale Cupa Cintia, 21

country: Italy

institute: University of Naples "Federico II"

summary: The tumor suppressor ARF (p14 in human, p19 in mouse), has traditionally been characterized by its pivotal role in tumor surveillance. However, its involvement in an expanding range of cellular processes reveals that its functions are broader and more complex than initially appreciated. Here, we uncover a previously unrecognized role of p19ARF in endodermal differentiation, specifically in pancreatic lineage specification, using an in vitro differentiation model of mouse embryonic stem cells (mESCs). Using CRISPR/Cas9-mediated mutagenesis, we show that mESCs with mutations in p19Arf are unable to efficiently differentiate towards pancreatic progenitors. Transcriptomic profiling reveals substantial alterations in gene networks associated not only with lineage commitment but also with cytoskeletal organization and cell morphology. These changes correlate with a disruption in stem cell architecture and suggest the persistence of pluripotency feature in the absence of functional p19Arf. Taken together, our findings highlight a role for p19Arf in directing endodermal differentiation while maintaining the essential cellular properties of stem cells, thus expanding its relevance beyond tumor suppression.

overall_design: At Day 0 mESCs (Ctrlv2, Arf-B and Arf-C cells) were plated in 6-well dishes and treated for 4 days with Activin A (20 ng/mL) in the presence of Matrigel to induce them to differentiate towards the definitive endoderm. Next, cells were treated with Retinoic Acid (RA 5μM/ml) and Fibroblast Growth Factor (FGF10, 10 ng/ml) to induce differentiation towards PFE (Posterioe Foregut Endoderm). RNA was extracted at Day 0 and Day 8 from Ctrlv2, Arf-B and Arf-C cells, followed by sequencing.

first: Elena

last: De Marino

first: Giuliana

last: Napolitano

first: Giuseppina

last: Roscigno

first: Valeria

last: Lucci

first: Geppino

last: Falco

first: Viola

last: Calabrò

first: Maria

last: Vivo

first: Tiziana

last: Angrisano

first: Alessandra

last: Pollice


title: Effects of 3xFlag-MORC1 WT and dIDR-bpNLS expression on TRIM28 chromatin occupancy in doxycycline-inducible NIH3T3 cells

city: Tokyo

first: Yosuke

last: Isota

address: Faculty of Science Bldg.3, Rm126, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, JAPAN

department: Graduate school of science

country: Japan

institute: The University of Tokyo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Doxycycline-inducible NIH3T3 cells expressing 3xFlag-mCherry (control), 3xFlag-MORC1 WT, or 3xFlag-MORC1 dIDR-bpNLS were used to assess MORC1-dependent changes in TRIM28 genomic localization. Cells were harvested 24 h after doxycycline induction.

overall_design: TRIM28 ChIP-seq analysis of doxycycline-induced NIH3T3 cells expressing 3xFlag-mCherry (control), 3xFlag-MORC1 WT, or 3xFlag-MORC1 dIDR-bpNLS.

first: Hiyu

last: Chiwata

first: Peilin

last: Li


title: Gene expression changes induced by doxycycline-inducible 3xFlag-MORC1 WT and 3xFlag-MORC1 dIDR-bpNLS expression in NIH3T3 cells

summary: Doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-mCherry (control), 3xFlag-MORC1 WT, or 3xFlag-MORC1 dIDR-bpNLS were used to evaluate transcriptional changes caused by MORC1 WT or MORC1 dIDR-bpNLS expression. Cells were harvested 48 h after doxycycline induction, and transcriptome-wide gene expression profiles were obtained.

overall_design: RNA-seq analysis of doxycycline-induced NIH3T3 cells expressing 3xFlag-mCherry (control), 3xFlag-MORC1 WT, or 3xFlag-MORC1 dIDR-bpNLS.


title: Chromatin accessibility changes induced by 3xFlag-MORC1 WT and dIDR-bpNLS expression in doxycycline-inducible NIH3T3 cells

summary: Doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-mCherry (control), 3xFlag-MORC1 WT, or 3xFlag-MORC1 dIDR-bpNLS were used to examine MORC1-dependent changes in chromatin accessibility. Cells were harvested 48 h after doxycycline induction.

overall_design: ATAC-seq analysis of doxycycline-induced NIH3T3 cells expressing 3xFlag-mCherry (control), 3xFlag-MORC1 WT, or 3xFlag-MORC1 dIDR-bpNLS.


title: Gene expression profiling of wild‑type NIH3T3 cells

summary: Gene expression profiling was performed on wild‑type NIH3T3 cells to measure transcriptome‑wide gene expression levels.

overall_design: RNA-seq of wild-type NIH3T3 cells.


title: Genome-wide binding profiles of 3xFlag-MORC1 WT and dIDR-bpNLS in doxycycline-inducible NIH3T3 cells

summary: Doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 WT or 3xFlag-MORC1 dIDR-bpNLS were used to determine MORC1 genomic localization patterns. Cells were harvested 24 h after doxycycline induction.

overall_design: Flag ChIP-seq analysis of doxycycline-induced NIH3T3 cells expressing 3xFlag-MORC1 WT or 3xFlag-MORC1 dIDR-bpNLS.


title: Loss of BCAP31 or POLR1E Accelerates Aging in C. elegans and Is Linked to Senescence in Vascular Endothelium

city: Zhengzhou City

first: li

last: Mengyu

address: No. 100 Lianhua Street, Fengyang Street, Zhongyuan District

institute: Bioengineering College

summary: Aging involves the progressive decline of cellular function, yet the key molecular regulators that determine aging require further identification. Building on our previous finding that the intracellular domain of CD44 (CD44ICD) is a critical aging regulator, we performed an interactome screen to identify its functional partners. This approach revealed BCAP31 and POLR1E as two previously unrecognized modulators of senescence. Depletion of their respective orthologs in Caenorhabditis elegans (C. elegans) shortened lifespan and accelerated age-related functional decline. In human vascular endothelial cells, knockdown of BCAP31 or POLR1E induced premature cellular senescence, whereas their overexpression countered it. Importantly, the protein levels of both BCAP31 and POLR1E decreased during physiological aging across species, including in senescent endothelial cells, aged nematodes, and tissues from old mice, with BCAP31 reduction being particularly pronounced in the cardiovascular system. Our findings establish BCAP31 and POLR1E as evolutionarily conserved components of a CD44-associated network that protects against cellular senescence and organismal aging, highlighting new potential targets for mitigating age-related vascular decline.

overall_design: The influence of BCAP31 and POLR1E on nematode ageing was investigated by silencing their homologues y54g2a.18 or rpoa-49 in Caenorhabditis elegans via RNAi. Transcriptome sequencing was employed to identify differentially expressed genes between RNAi y54g2a.18 or RNAi rpoa-49 and the RNAi control.


title: Pharmacological inhibition of METTL1 as a therapy against solid and haematological cancers [RNA-Seq]

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

institute: Storm Therapeutics

summary: The N7-methylguanosine (m7G) modification is one of the most prevalent modifications on tRNA, mainly catalysed by the METTL1-WDR4 protein complex. The m7G methyltranferase METTL1 has been connected to oncogenic transformation and maintenance of several aggressive malignancies but the impact of a therapeutic targeting a tRNA-modifying enzyme is yet to be determined. Here, we present the development and characterisation of STM9005, a highly selective and potent first-in-class tRNA methyltransferase inhibitor of METTL1. Treatment of numerous tumour models with STM9005 reduces cancer growth, causes cellular changes and dysregulates cell cycle progression. These cellular effects were accompanied by a selective decrease of m7G on a subset of tRNAs and a reduction in their expression levels, which led to an impact on oncogenic mRNA translation. We illustrate that pharmacological inhibition of METTL1 in vivo impairs tumour growth and leads to a significant prolongation of survival in various mouse cancer models of different tissue origin. Collectively, our results provide strong proof-of-concept that targeting of tRNA methylation is a novel avenue of anti-cancer therapy, and illustrate that catalytic inhibition of METTL1 represents a novel therapeutic strategy against a number of aggressive malignancies.

overall_design: RNA-seq profiling of OE21 cells treated with DMSO or STM9005 for 1 or 3 days


title: Spatiotemporal development of deep excitatory neuronal types within the mouse neocortex

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

summary: Here, we investigate the developmental spatiotemporal properties of distinct cortical cell types, specifically the subplate and claustrum using single-cell spatial transcriptomics.

overall_design: We performed single-cell spatial transcriptomics on the brains of male and female mice across four critical developmental timepoints: E12.5, E15.5, E18.5 and P1.

first: Shalini

last: Iyer


title: Impact of viral dsRNA on endometrial decidualization

city: Coventry

first: Jan

middle: Joris

last: Brosens

state: Warwickshire

address: Warwick Medical School

institute: University of Warwick

summary: Viral infections are associated with early pregnancy loss as well as later gestational complications including preeclampsia and fetal growth restriction. While viral components, including viral double-stranded RNA (dsRNA), have been shown to affect placental trophoblast function; how these components may affect maternal endometrial function is less understood. Endometrial stromal cells make up the bulk of the human endometrium and they undergo a specialized hormone-driven differentiation process termed decidualization monthly in preparation for pregnancy. We have previously shown that these stromal cells exhibit robust inflammatory responses to bacterial LPS and viral dsRNA. The goals of this study are to determine the effects of prior viral dsRNA exposure on endometrial decidualization and whether this affects subsequent placentation and pregnancy outcomes. Using a combination of 2D endometrial stromal cell cultures, 3D human endometrial assembloids, as well as mouse models of decidualization and pregnancy, we demonstrate that exposure to viral dsRNA [Poly(I:C)] 48 hours prior to hormonal stimulation impaired decidualization in vitro and in vivo. Similarly, preimplantation exposure to Poly(I:C) on GD0.5 in timed-mated dams inhibited decidualization as well as reduced implantation success and induced fetal growth restriction. This was associated with altered placentation, in particular, formation of the Syn-TII cells in the labyrinth zone, and dysregulated expression of glucose and amino acid transporters in the placenta. This work emphasizes the importance of preconception endometrial health for successful pregnancy and identifies a novel mechanism by which prior viral infection can lead to implantation failure as well as later pregnancy complications.

overall_design: Human endometrial assembloid cultures, comprising epithelial organoids in a stromal cell matrix, were pre-treated with 1ug/ml viral dsDNA [Poly(I:C)] for 48hr before induction of decidualization using MPA and 8-bromo-cAMP. Control cultures (without Poly(I:C), with or without decidualisation) were processed in parallel. RNA was harvested on Day 4 of decidualization and subjected to RNA sequencing using Illumina protocols.

first: Emma

last: Lucas

first: Thomas

last: Rawlings

first: Laiba

last: Jamshed

first: Mancy

last: Tong

middle: J


title: The Natural Product Corramycin Acts as a DNA Gyrase Poison and Overcomes Fluoroquinolone Resistance in Mycobacterium tuberculosis

city: Saarbrücken

first: Franziska

last: Fries

state: Saarland

address: Campus E8 1

department: Microbial Natural Products

institute: Helmholtz Institute for Pharmaceutical Research Saarland

summary: Despite significant advancements in drug development and discovery, tuberculosis remains one of the world’s deadliest infectious diseases. The rise and global spread of multidrug-resistant strains underscore a critical need for new antibiotics with distinct mechanisms of action. Screening of a myxobacterial extract library uncovered the previously unrecognized antitubercular activity of corramycin, a natural product with potent bactericidal activity against both drug-sensitive and -resistant Mycobacterium tuberculosis. Corramycin enters the bacterial cell by exploiting multiple transport systems, and induces DNA double-strand breaks through a novel form of DNA gyrase poisoning. The cryo-electron microscopy structure of M. tuberculosis gyrase in complex with corramycin reveals that the natural product targets a site overlapping with the binding site of synthetic fluoroquinolones, thereby locking the gyrase in an inactive conformation and preventing re-ligation of DNA. Importantly, its unique mode of binding allows corramycin to overcome fluoroquinolone resistance, highlighting its promise as a novel antibiotic scaffold to address the antimicrobial resistance crisis.

sample_organism:
Escherichia coli
Mycobacterium tuberculosis

overall_design: Transcriptomic analyses of E. coli and M. tuberculosis treated with various concentrations of corramycin

first: Jennifer

last: Herrmann

first: Rolf

last: Müller


title: Ice-free vitrification of embryos and its impact on post-warming outcomes

city: Ithaca

first: Ellie

last: Duan

state: New York

address: 507 Tower Rd., Ithaca, NY 14853, Ithaca, NY 1485

department: Animal Science

institute: Cornell University

summary: Vitrification protocols are widely used for mammalian embryo cryopreservation. Post-warming outcomes are impaired by cryodamage from crystalline intracellular ice, whose formation depends on both the cooling and warming rates. Here, time-resolved X-ray diffraction measurements on bovine embryos indicated that current standard tools and protocols achieved ice-free cooling, but that intracellular ice always formed during warming. Increasing cooling rates by a factor of ~30 over current standard rates allowed ice-free cooling and warming, even when cryoprotectant concentrations were reduced by 30%. Embryos cooled at ultrafast rates exhibited survival and developmental competence rates close to those of unvitrified controls and significantly better than those cooled at standard rates. Increased global H3K9me3 intensity was found with both standard and ultrafast cooling relative to controls, while DNA methylation (5mC and 5hmC) was comparable for all groups.  Transcriptomic analysis indicated adhesion and cell-junction assembly genes were downregulated while DNA damage repair pathway genes were upregulated with standard cooling relative to controls, and cell-development and differentiation pathway genes were downregulated with standard cooling relative to ultrafast cooling.  Embryos vitrified with the ultrafast cool protocol retain full developmental potential and can establish successful pregnancies. Overall, increased cooling rates improved post-cryopreservation outcomes in part by minimizing ice formation, minimizing DNA damage, and preserving gene expression related to embryonic developmental functions.

overall_design: From 3 replicates for each of the three embryo groups studied (Control, Standard cool and Ultrafast cool), pools of 5-10 embryos that hatched during the first 24 hours post thaw were collected

first: Abdallah

last: Abdelhady

first: Jingzhi

last: Zhang

first: Chia-Kuan

last: Wu

first: Yoke Lee

last: Lee

first: Meihong

last: Shi

first: Patrick

last: Crane

first: Mariana Diel de

last: Amorim

first: Ian

middle: R

last: Porter

first: Qiudi

last: Zheng

first: Robert

middle: E

last: Thorne

first: Jingyue (Ellie)

first: Soon Hon

last: Cheong


title: Transcriptomic analysis of acute and carrier GAS samples from oropharyngeal throat swabs.

city: Chicago

first: Jason

last: Wood

state: IL

address: 900 S Ashland Ave rm 1057

department: Research Informatics Core

institute: University of Illinois at Chicago

summary: The carrier state of Streptococcus pyogenes (Group A Strep, GAS), is defined by the presence of the organism without symptoms or an immune response. Carriage poses challenges for clinical management and contributes to transmission in the community. Comprehensive genomic and transcriptomic analyses of naturally acquired human GAS carriage have been lacking. In this study, we collected longitudinal samples from individuals before and after antibiotic treatment for acute pharyngitis, performing whole genome sequencing and RNA-seq on selected isolates. This is the first report of transcriptional profiling of GAS directly from human derived oropharyngeal swabs. Transcriptional profiling from oropharyngeal swabs identified distinct gene expression patterns between the acute infection and post-treatment carriage phases, although early acute expression profiles did not predict treatment failure.

overall_design: Children were recruited from four pediatric clinics in Madison, WI, USA and eligible for this study if they were between 5 and 15 years of age, had been diagnosed with acute pharyngitis, and had not been treated with antibiotics in the previous 30 days. Children were excluded from this study if they had an allergy to β-lactam antimicrobials or were treated with an antibiotic other than a β-lactam. Two swabs were obtained from the posterior pharynx. A rapid antigen detection test (RADT) was used for initial diagnosis. If the RADT was positive, the child and family were informed by the research staff that the child was eligible for the study. At that point, the second swab of the original pair was sent to the laboratory to be cultured for GAS using standard methods. The cultured isolate was preserved. Treatment was undertaken with an appropriate dose of either amoxicillin or penicillin V for 10 days. The patient then returned for follow-up 13-14 days after initiation of treatment. If the child was asymptomatic and lacked apparent inflammation of the pharynx or tonsils, a double swab was used to sample the posterior pharynx. If the follow-up swab was negative for GAS on culture, the patient was deemed to have presented with an acute infection. If the follow-up swab was positive, the second swab was assigned as probably carrier. An additional set of swabs was then obtained 1 week later, i.e around 14 days after completing antibiotics. If the swab was still positive, the subject was deemed a confirmed-carrier and the swab and cultured isolates were stored at -80°C. Cultured isolates and swab samples were processed for RNA-seq.

first: Laura

middle: C

last: Cook

first: Mark

last: Mainschein-Cline

first: Michael

last: Federle

first: Ellen

last: Wald

first: Gregory

middle: P

last: DeMuri

first: Kevin

last: Quirk

first: May

last: Xu


title: TNFR1 expression on cancer cell is critical for immunoescape, shaping an immunosuppressive tumor microenvironment [EO771]

city: Pamplona

first: David

last: Ruiz Guillamón

state: Navarra

address: Av. de Pío XII, 55

department: Programa de Inmunología e Inmunoterapia

country: Spain

institute: Centro de Investigación de Medicina Aplicada (CIMA) - Clínica Universidad de Navarra

summary: TNFα reportedly mediates multiple protumor and immunosuppressive functions acting on stromal cells in cancer-bearing hosts as a result of enhancing activation immune cell death of T lymphocytes, causing dysfunction of dendritic cells and/or eliciting chemokines which attract myeloid-derived suppressor cells. Experiments performed in transplantable tumors in which we silenced TNFR1 with CRISPR/Cas9 showed the inability of the TNFR1 KO variants to engraft in immunocompetent hosts, whilst engraftment in immunodeficient or CD8 T lymphocyte-depleted mice was preserved. The mechanism was related to secondary inflammatory mediators elicited by TNFα in malignant cells themselves, including CXCR1/2 chemokines and interestingly TNFα itself. As a result, TNFR1 KO variants recruited drastically fewer myeloid-derived suppressor cells into the tumor microenvironment, thus explaining the immune escape of the WT variants. Interestingly, TNFR1-sufficient tumor cells, when co-engrafted with the TNFR1 KO variants, rescued tumorigenicity of the same tumor lesion but not of a distantly implanted TNFR1 KO tumor. Secondary mediators chiefly include CXCR1/2-acting chemokines and prostaglandin E2 synthetase. Similar effects were observed upon knocking-down TNFR1 in a human tumor cell line. Moreover, human TNFR1 KO HT29 variants, when xenografted in immunodeficient mice, released lower levels of CXCL8 (IL-8) and recruited fewer murine myeloid cells into the tumor microenvironment. Analyses of scRNAseq data sets from human solid tumors corroborate the role of TNFR1 on tumor cells to induce secondary proinflammatory mediators. All together, we provide evidence for an essential role of TNFR1 expressed on the surface of tumor cells in immunoscape and further support TNF neutralization in the clinic to improve the efficacy and safety of approved immunotherapy approaches.

overall_design: Bulk RNA-seq profiling on WT EO771 cells and TNFR1 KO variants, untreated and treated with TNFa at 6h and 24h.

first: Elixabet

last: Bolaños

first: Lorena

last: Cañas-Zabala

first: Irene

last: Olivera

last: Ruiz-Guillamón

first: Ignacio

last: Melero


title: Transcriptomes of different glioblastoma cell lines

city: Frankfurt

first: Tobias

last: Schmid

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry I

institute: Goethe University Frankfurt

summary: Glioblastoma (GB) is the most aggressive type of brain cancer with a devastating prognosis. Myeloid cells, especially monocytes and macrophages, comprise the majority of immune cells within the GB tumor microenvironment (TME), where they contribute to the development of an immunosuppressive milieu hindering potential anti-tumor immune responses. Type I interferons (IFN) usually facilitate a pro-inflammatory shift in monocytes and macrophages and allow for anti-tumor functions. Using RNA-sequencing, we observed that type I IFN-stimulated genes (ISGs) are globally downregulated in primary human monocytes co-cultured with GB cells both upon direct cell-cell contact and upon the exchange of soluble factors. Surprisingly, the reduction of type I IFN responses did not result from changes in interferon-α/β-receptor (IFNAR) availability and activation. Instead, we identified GM-CSF as a critical, GB cell-derived factor, which decreased ISG expression in monocytes at extremely low concentrations (< 10 pg/mL) via induction of the TGF-β signaling pathway. Importantly, type I IFN response gene expression and GM-CSF activity in human GB biopsies appeared to be mutually exclusive. In detail, active GM-CSF signaling inhibited ISG expression in the same cell as well as in neighboring monocyte-derived macrophages. In conclusion, our data provide evidence for a so far unknown GM-CSF- and TGF-β-dependent type I IFN inhibitory mechanism in GB with potential implications for future therapeutic approaches.

overall_design: RNA-seq profiling of the transcriptomes of 4 different GBM cells lines (LN229, T98G, U87, U251) after 48 hours of untreated culture

first: Sofie

last: Meyer

first: Rebekka

last: Bauer

first: Bernhard

last: Brüne


title: Transcriptome changes in primary human monocytes in response to type I IFN or co-culture with glioblastoma cells

overall_design: RNA-seq profiling of primary human monocytes after 48 hours of co-culture with human LN229 glioblastoma cells or after 6 hours of treatment with 1 ng/mL IFN-β


title: Genome-wide identification of NAC transcription factors in Elymus sibiricus and functional characterization of EsANAC029 in light response

city: MianYang

first: Chanjuan

last: Wu

state: Si Chuan

address: No. 59, Middle Section of Qinglong Avenue, Fucheng District

institute: Southwest University of Science and Technology

summary: Elymus sibiricus L. is a perennial grass of high pastoral and ecological value, playing a critial role in to livestock production and ecological restoration on the Qinghai-Tibet Plateau. NAC transcription factors are crucial regulators of plant development and abiotic stress responses, yet they remain uncharacterized in E. sibiricus. Here, we report the first genome-wide analysis of the NAC family in this allohexaploid species, and identified 290 EsNAC genes. These genes are classified into 14 subfamilies, 11 of which have undergone significant expansion mainly through segmental duplication events, suggesting a potential genetic basis for adaptation to plateau environments. We revealed a pronounced enrichment of light-responsive cis-elements in the promoters of these genes. Further analysis in Arabidopsis showed significant overlap between AtNAC and a set of light-repressed genes, strongly implicating the NAC family in light inhibition pathways. Notably, heterologous overexpression of EsANAC029 (an ortholog of Arabidopsis AtANAC029) in Arabidopsis recapitulated a clear light-inhibition phenotype, including chlorosis and dwarfism. Transcriptomic profiling indicated that EsANAC029 represses the expression of chlorophyll biosynthesis and photosynthesis-related genes, thereby reducing chlorophyll accumulation, impairing photosynthetic capacity, and ultimately leading to growth retardation. In addition, EsANAC029 upregulates genes associated with defense-related pathways, linking light perception with stress adaptation. This work identifies EsANAC029 as a key negative regulator of photosynthesis, likely serving as an integrative node that connects light perception with stress adaptation.

overall_design: Examination of the mRNA expression of 25-day-old wild type and EsANAC029-OE Arabidopsis


title: TNFR1 expression on cancer cell is critical for immunoescape, shaping an immunosuppressive tumor microenvironment.

overall_design: Bulk RNA-seq profiling of WT HT29 cells untreated and treated with TNF at 6h and 24h.


title: Transcriptomes of primary human monocytes in co-culture with glioblastoma cell lines upon modulation of GMCSF levels

overall_design: RNA-seq profiling of primary human monocytes after 24 hours of indirect co-culture with human LN229 or U251 glioblastoma cells, or treated with human recombinant GM-CSF, or after neutralization of GM-CSF


title: CpG Hypermethylation and WNT/AP-1 cooperativity Define the Epigenetic Landscape and a Clinical Subgroup of High-Risk Pediatric Adrenocortical Carcinoma [methylation array]

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

institute: Childens Cancer Center - University hospital Augsburg

summary: Our integrative epigenomic analysis identified four molecularly distinct subgroups based on DNA methylation profiles, each marked by unique transcriptional programs, cellular compositions, and tissue architectures. These molecular subtypes outperformed traditional histopathological classifications in predicting clinical outcomes and addressed the longstanding lack of robust risk markers in pACT.

overall_design: DNA methylation anaylsis (EPIC/EPICv2 Illumina) of 109 pACT samples together with data sets from Clay et al. and Bueno et al. to establish DNA methylation-based subgroups with Consensus Clustering.

first: Mauice

last: Loßner

first: Marina

last: Kunstreich

first: Nic

middle: G

last: Reitsam

first: Irmengard

last: Sax

first: Marlena

last: Mucha

first: Felix

last: Dorn

first: Lorenz

last: Helmschrott

first: Maria

middle: D

last: Hernandez Ramirez

first: Sebastian

last: Dintner

first: Konstantin

last: Okonechnikov

first: Martin

last: Sill

first: Ina

last: Oehme

first: Heike

last: Peterziel

first: Enrique

last: Blanco-Carmona

first: Eva

last: Sipos

first: Stefan

last: Wudy

first: Christoph

last: Slavetinsky

first: Jörg

last: Fuchs

first: Bruno

last: Märkl

last: Jüttner

first: Christian

last: Vokuhl

last: Frühwald

first: Antje

last: Redlich

last: Pfister

first: Matthias

last: Schlesner

first: Rainer

last: Claus

first: Michaela

last: Kuhlen

first: Pascal

last: Johann


title: PAN2 Maintains mRNA Poly(A) Tail Homeostasis and Regulates RNA Degradation During Early Embryonic Development in Mice

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

summary: RNA homeostasis regulators and surveillance factors function in the global transcriptome of oocytes and early embryos. Among them, the CNOT6L and CNOT7 proteins of the BTG4, PABPN1L, and CCR4-NOT subunits, as well as TUTs, are involved in the degradation of maternal mRNA, and are crucial for oocyte maturation and early embryonic development. However, the physiological functions of the PAN2-PAN3 complex, which is upstream of CCR4-NOT, in female reproductive cells have not yet been clarified. In this study, we have found that the absence of maternal Pan2 leads to embryonic developmental disorders and a significant decline in female reproductive capacity. By applying PAIso-seq2 and mass spectrometry analysis, we investigated the distribution and dynamics of mRNA poly(A) tails during early embryonic development. We found that the absence of Pan2 in early embryos perturbed the global balance of poly(A) tails, which in turn disrupted the transcriptome, affected mRNA degradation, and led to the accumulation of aberrant proteins. Furthermore, the maternal mRNA degradation mediated by PAN2 is crucial for the normal initiation of ZGA, and it can also regulate the expression of factors that determine cell fate in early mouse embryos. These findings highlight the crucial physiological role of PAN2 in early embryos and expand our understanding of the relationship between RNA homeostasis and the poly(A) tail.

overall_design: Maternal Pan2-deletion zygotes and 2-cells were subjected to RNA-seq using the Smart-seq2 method with minor modifications.


title: Integrated single-cell and spatial transcriptomics of ovarian immune landscape reveal role of distinct macrophages in classic galactosemia associated with premature ovarian insufficiency

city: BETHESDA

first: Veronica

last: Gomez-Lobo

address: 10 Central Dr. Bldg10, Rm 8N248

institute: NIH

summary: Premature ovarian insufficiency (POI) is a complication that affects 80% of females with classic galactosemia (CG), caused by mutations in the GALT gene. Immune system regulates normal physiological processes and pathological aspects of the ovarian function. While previous animal studies have shown that accumulation of toxic galactose metabolites trigger cellular stress pathways, contribute to the disease's complications, it remains unclear how these influence the immune landscape in CG patients. Here, we investigated the molecular and cellular changes in the ovarian immune environment that may impact the ovarian function contributing to early onset of POI in prepubteral girls with CG. We noticed a marked increase in both monocyte and tissue derived macrophages, and expression of pro-inflammatory cytokines in the CG ovary. Furthermore, we noticed oxidative stress induced activation of NLRP3 inflammasome, which contributed to recruitment of macrophages, induction of pyroptotic cell-death, and overall exacerbation of the inflammatory response.

overall_design: CG and control ovarian FFPE sections were processed for Visium spatial transcriptomic protocol (10x Genomics).

first: Raghuveer

last: Kavarthapu

first: Son

last: Vo

first: Natalie

last: Hanby

first: Thang

last: Pham

first: Christophe

last: Vanpouille

first: Margaret

last: Brunette

first: Hong

last: Lou

first: Maria

last: Sierra

first: Jacqueline

last: Yano


title: PAN2 Maintains mRNA Poly(A) Tail Homeostasis and Regulates RNA Degradation During Early Embryonic Development in Mice [RNA-seq2]


title: UBA1 knockdown impairs muscle function in Drosophila and mice and dysregulates the levels of UBA1-sensitive proteins.

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

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

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: Refer to individual Series


title: UBA1 knockdown impairs muscle function in Drosophila and mice and dysregulates the levels of UBA1-sensitive proteins [mouse]

summary: Gene expression changes induced by knockdown of UBA1 in the skeletal muscle of Drosophila and mice

overall_design: RNA-sequencing data from mouse tibialis anterior skeletal muscles electroporated with non-targeting (NT) control siRNAs or with siRNAs targeting UBA1. For each condition, 4 biological replicates were analyzed.

first: Michelle

last: Curley

first: Fabio

last: Demontis


title: USP7 sequencing in non-treated  MDA-MB-231 cells

city: Chongqing

first: Tianshu

last: Yang

state: --- Select One ---

address: No. 83, Xinqiao Zhengjie, Shapingba District, Chongqing City

institute: Xinqiao Hospital

summary: Here, we examined the interactions between PRMT6 and USP7 complex, to form a transcription-repressive complex that co-occupies TAZ  promoter.

overall_design: Examination of usp7 target genes in MDA-MB-231 cell line.

first: Weidong

last: Xiao


title: UBA1 knockdown impairs muscle function in Drosophila and mice and dysregulates the levels of UBA1-sensitive proteins [Drosophila]

overall_design: RNA-sequencing data from Drosophila skeletal muscles that express a control RNAi (mcherry RNAi) or UBA1 RNAi #1 and #2 (BL#76066 and BL#25957). For each condition, 3 biological replicates were analyzed.


title: DNA origami vaccines program antigen-focused germinal centers

first: Darrell

middle: J.

last: Irvine

state: MA

address: 77 Massachusetts Ave

institute: Massachusetts Institute of Technology

summary: Priming rare subdominant precursor B cells in germinal centers (GCs) is a central goal of vaccination to generate broadly neutralizing antibodies (bnAbs) against HIV. Multivalent immunogen display on protein nanoparticles is a well-established method to promote such responses. However, these nanoparticles generate scaffold-specific B cells that could theoretically limit bnAb precursor expansion in GCs. We rationally designed DNA origami-based virus-like particles (VLPs) displaying a germline-targeting HIV Env immunogen, which elicited no scaffold-specific antibody responses and increased the expansion of epitope-specific GC B cells relative to off-target B cells >10-fold compared with a state-of-the-art clinical protein nanoparticle, which failed to expand bnAb precursors in these conditions. Our results demonstrate that minimizing off-target responses enhances bnAb priming and support DNA-VLPs as a potent vaccine platform.

overall_design: CD4bs-specific GC B cells were FACS-sorted from inguinal lymph nodes harvested from VH1-2 mice immunized subcutaneously with 5 μg p60mer or d30-60mer-PADRE. LNs were mechanically dissociated, filtered, and stained first with NIR live dead stain, followed by a cocktail of primary antibodies and fluorescenlty labeled eOD-60mer probes.Cells were also stained with Totalseq C anti-mouse hashing antibodies (BioLegend, 1:100) before FACS CD4bs-specific GC B cells  gated on live B220+/CD38loGL7hi/IgG+/eOD++KO- populations.  Cells were subsequently processed according to the 10x Genomics 5' Immune Profiling v3 protocol.

first: Anna

last: Romanov

first: Yiming J

last: Zhang

first: Lauren

last: Duhamel

first: Mark

last: Bathe


title: HDAC Inhibition Reprograms Stem Cell Fate to Suppress Infantile Hemangioma Vasculogenesis

city: Shanghai

first: Qian

last: Bian

address: Jinzun Road No.115

department: Shanghai Institute of Precision Medicine, Ninth People’s Hospital

institute: Shanghai Jiao Tong University School of Medicine

summary: Infantile hemangioma (IH), the most common vascular tumor of infancy, relies on hemangioma stem cells (HemSCs) to drive pathological vasculogenesis during the proliferating phase. While beta-blockers are currently first-line treatment for IH, resistance and rebound growth necessitates novel strategies. Here, we identify histone deacetylase inhibitors (HDACi) as a potential epigenetic drug for IH. The pan-HDAC inhibitor SAHA significantly suppresses in vivo vasculogenesis in a murine IH model. Mechanistically, SAHA selectively blocks the differentiation of HemSCs into pericytes by destabilizing NOTCH3 protein through acetylation-primed ubiquitination and proteasomal degradation, thus disrupting perivascular support which is indispensable for IH vasculogenesis. Furthermore, the blockade of pericyte differentiation by SAHA synergizes with propranolol, which inhibits endothelial differentiation of HemSCs, in a complementary manner. Additionally, SAHA promotes adipogenic differentiation of HemSCs and accelerates IH involution. Collectively, our work highlights the clinical significance of cell fate determination during IH progression, and establishes HDAC inhibition as a novel therapeutic option for IH through targeting pericyte differentiation of HemSCs, which provides a promising enhancement to current treatment strategies of refractory IH.

overall_design: RNA-seq and H3K27Ac CUT&Tag libraries were constructed in HemSCs treated with 1 μM SAHA or Vehicle control (0.1% DMSO) for 16 hr. For RNA-seq, total RNA was extracted with FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme, Cat #RC112-01). After passing quality controls for RNA integrity and confirming the absence of RNA degradation and contaminations, RNA-seq libraries were generated by Annoroad (Beijing, China) with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, Cat #NR604-01/02) following the manufacturer’s protocols. RNA-seq libraries from three biological replicates of each group were sequenced on an Illumina NovaSeq 6000 platform at PE150 mode.  CUT&Tag was performed as previously described using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, Cat #TD903) with spike-in modifications. In brief, 50,000 cells were harvested, washed with PBS and incubated with activated Concanavalin A-coated beads at room temperature for 10 min, followed by overnight incubation with primary antibody (H3K27Ac, Abcam, Cat #ab4729, 1:50 dilution) at 4°C. Samples were then incubated with the secondary antibody for 1 hr at room temperature, washed twice with Dig-wash buffer, and incubated with pA/G Tn5 at a final concentration of 0.04 μM for 1 hr at room temperature. Tagmentation was then performed at 37°C for 1 hr. For spike-in calibration, control DNA template (Hyperactive DNA Spike-in Control for CUT&Tag, Vazyme, Cat #NS101-01) was added during DNA extraction of each sample at the concentration of 0.5 pg/50,000 cells. PCR amplification and purification was performed for sequencing on Illumina platform.

first: Qiming

last: Chen

first: Hao

last: Rong

first: Jiang

last: Li

first: Jiawei

last: Zheng


title: TDP2-mediated DNA repair regulates the dynamics of neuronal early response gene transcription and cortical neuron connectivity

city: Dallas

first: Ram

last: Madabhushi

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Neuronal activity induces topoisomerase IIb (TOP2B) to form DNA double strand breaks (DSBs) within the promoters of specific early response genes (ERGs), such as Fos, FosB, and Npas4, and these DSBs facilitate rapid ERG transcription. Yet how activity-induced DSBs are repaired and the significance of such mechanisms for neuronal function remain unclear. Here we show that the proteasome and the enzyme, tyrosyl-DNA phosphodiesterase 2 (TDP2), catalyze the initial processing of TOP2B-mediated DSBs in neurons. Knockdown of Tdp2 delayed the repair of neuronal activity-induced DSBs and prolonged the expression of ERGs in primary mouse cortical neurons, indicating that TDP2-mediated DNA repair is essential for the temporal control of ERG transcription. Deletion of Tdp2 in excitatory forebrain neurons caused DSB accrual and ERG overexpression, and these changes were associated with increased excitatory synaptic transmission and cortical circuit dysfunction. Mutations in TDP2 cause the disease, SCAR23 (spinocerebellar ataxia, autosomal recessive 23), which manifests predominantly with neurological abnormalities. We show that whereas proliferating cells possess redundant pathways to process TOP2B-mediated DSBs, these pathways are relatively inactive in postmitotic neurons. Together, these results underscore the neuroprotective roles of TDP2 and suggest that activity-induced DSBs could be relevant sources of DNA lesions for neurodegeneration.

overall_design: RNAseq profiling of cortical tissue extracted from 6 month old wild-type (WT; Tdp2fl/fl, CAMKII:Cre negative) and Tdp2 conditional knockout mice (cKO; Tdp2fl/fl, CAMKII:Cre positive)

first: Morgan

last: Crewe

first: Alexander

last: Pope

first: Sandra

last: Fajardo Briseno

first: Ryan

last: Stott

first: Ilse

last: Delint-Ramirez

first: Li-Huei

last: Tsai

first: Kimberly

last: Huber


title: Transcriptome analysis of cisplatin-treated KGN human ovarian granulosa cells

city: Jinzhou

first: Chao

last: Liu

state: Liaoning

address: Jinzhou Medical University, No. 40, Section 3, Songpo Road, Linghe District, Jinzhou City, Liaoning Province

institute: Jinzhou Medical University

summary: Cisplatin is a major chemotherapeutic agent in cancer treatment. However, studies have shown that chemotherapy can induce aging in the body, leading to an increased risk of Premature Ovarian Insufficiency in women. Therefore, this study conducted transcriptome sequencing analysis on KGN cells after cisplatin treatment.

overall_design: KGN cells treated with 10μM cisplatin for 48 hours and KGN cells cultured normally for 48 hours

first: Runzhi

last: Wang

first: Xinnong


title: Apoptosis of Mdm2-deficient osteocytes enhances osteogenesis through TRPM8-enriched apoptotic vesicles

city: Wuhan

first: Xin

address: Luojia Hill, Wuchang District

institute: Wuhan University

summary: During homeostasis, osteocyte apoptosis is typically associated with bone loss through enhanced osteoclast recruitment and bone resorption. However, whether apoptotic osteocytes also regulate bone formation remains elusive. Here we report that conditional deletion of Mdm2, an E3 ubiquitin ligase regulating cell survival, causes osteocyte apoptosis but paradoxically results in a marked increase in bone mass attributed to up-regulated osteogenic activity. Single-cell RNA sequencing reveals enhanced osteoblastic differentiation of bone marrow mesenchymal stem cells (BMSCs) in conditional knockout mice, with enrichment of cellular calcium related pathways. Mechanistically, apoptotic vesicles (apovs) from Mdm2-deleted osteocytes are engulfed by BMSCs. TRPM8, a calcium channel protein, is enriched in osteocyte-derived apovs and transported into BMSCs, thereby promoting osteoblastic differentiation. Additionally, pharmacological inhibition of TRPM8 attenuates the high bone mass phenotype in conditional knockout mice. Therefore, Mdm2 deletion in osteocytes leads to osteocyte apoptosis, which enhances bone formation through communicating with BMSCs via TRPM8-enriched apovs. Our findings underscore the pivotal role of osteocytes in bone homeostasis and unveil a previously unrecognized mechanism whereby osteocyte apoptosis stimulates osteogenesis through affecting the fate of BMSCs in a TRPM8-mediated paracrine mechanism.

overall_design: Cells extracted from bone marrow and bone pieces were collected after lineage depletion using Lineage depletion kit and Fluorescence-activated cell sorting (FACS). Cells were analyzed using scRNA-seq. Each sample contained cells from five Dmp1-Cre; Mdm2flox/flox (Mdm2cKO) mice as well as their control littermates. Primary osteocytes were isolated from femurs of Mdm2cKO mice and processed for bulk RNA sequencing.

first: Huiwen

first: Zhi

first: Yiping

first: Guobin

last: Yang

first: Guohua

last: Yuan


title: A transcriptional atlas of gyrification reveals dynamic spatio-temporal gene expression in the developing ferret cortex

city: Bundoora

first: Mary

last: Tolcos

state: VIC

address: 225-245 Plenty Rd

country: Australia

institute: RMIT University

summary: The correct folding of the cerebral cortex is essential for healthy brain development, and disruptions to this process can result in serious structural and functional abnormalities. While basal radial glia cells (bRGCs) in the expanded outer subventricular zone (oSVZ) are known to contribute to gyrification, the gene regulatory mechanisms driving regional cortical folding remain poorly defined. This study examined differential gene expression within the oSVZ of the developing ferret cortex, focussing on regions prospective of the coronal gyrus (CG) and suprasylvian sulcus (SSS) at the onset (postnatal day 5, n = 5) and middle (postnatal day 15, n = 5) of gyrification. We performed high-throughput, paired-end RNA sequencing on discrete laser capture microdissected oSVZ regions from 50 consecutive brain sections, followed by differential expression analysis, gene ontology, and pathway enrichment using EdgeR and SRplot. The data revealed distinct regional transcriptional signatures enriched for genes involved in progenitor cell proliferation, self-renewal, and neurogenesis, as well as temporal enrichment for axonogenesis and the extracellular matrix (ECM). RT-qPCR validation supported several spatial and temporal differences, confirming consistent expression trends for key candidates (e.g., PI4KB, FOXC1, PRUNE1, and FOXM1) and revealing region- and age-specific dynamics. These data suggest the presence of differential transcriptional profiles within the oSVZ that may guide the formation of gyri and sulci though localised regulation of progenitor behaviour. By identifying and validating molecular candidates involved in early cortical folding, this study enhances our understanding of the mechanisms driving gyrification and provides a framework for investigating the genetic basis of cortical malformations.

overall_design: Tissue was collected by laser capture microdissection of the outer subventricular zone (oSVZ) from the ferret brain. oSVZ tissue was collected from beneath the coronal gyrus, and the suprasylvian sulcus in 5 biological replicates at 2 ages (5 days old; P5, and 15 days old; P15). The total sample size was n = 5 at P5, and n = 5 at P15. RNA was processed using RNeasy Micro Kit (QIAGEN) and paired-end SPIA RNA sequencing performed on an Illumina Next2000 sequencer by Monash Health Translation Precinct Medical Genomics Facility (Clayton, VIC, Australia).

first: Mikaela

last: Barresi

first: Alice

last: Johnstone

first: Sebastian

last: Quezada

first: Anita

last: Quigley


title: Targeting S100A9 to inhibit the malignant progression of acute myeloid leukemia

city: guiyang

first: 李

middle: 瑞

last: 引

address: Guiyang City, Guizhou Province

institute: 贵州医科大学

summary: This study aims to identify potential small molecule inhibitors targeting S100A9 using CADD (Computer-Aided Drug Design) virtual screening, and to investigate their effects on Acute Myeloid Leukemia (AML) cell lines. S100A9 is a key regulator in the pathogenesis and progression of AML, and targeting it may provide a promising therapeutic approach to mitigate the malignant advancement of AML. Through virtual screening, we selected B2, a small molecule compound, as a promising candidate for further experimental validation. The study focuses on the interaction between B2 and S100A9 and evaluates the compound’s ability to inhibit AML cell proliferation and survival. The effects of B2 on gene expression and cellular processes in AML cell lines were analyzed to better understand its potential as a therapeutic agent. This research provides new insights into the molecular targeting of S100A9 in AML treatment, with the aim of developing more effective and targeted therapeutic strategies.

overall_design: This study investigates the effect of B2 treatment on U937 cells. The experimental group consists of cells treated with 1 µM B2 for 36 hours, while the control group is treated with an equal concentration of DMSO for 36 hours. The study includes both experimental and control groups to assess the impact of B2 on U937 cell behavior, with a focus on gene expression changes following treatment.

first: Dan

last: Ma

first: Junzhao

last: Wan

first: Ruiyin

last: LI


title: Pharmacological inhibition of METTL1 as a therapy against solid and haematological cancers

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

institute: Storm Therapeutics

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Pharmacological inhibition of METTL1 as a therapy against solid and haematological cancers [mim-tRNA-Seq]

summary: The N7-methylguanosine (m7G) modification is one of the most prevalent modifications on tRNA, mainly catalysed by the METTL1-WDR4 protein complex. The m7G methyltranferase METTL1 has been connected to oncogenic transformation and maintenance of several aggressive malignancies but the impact of a therapeutic targeting a tRNA-modifying enzyme is yet to be determined. Here, we present the development and characterisation of STM9005, a highly selective and potent first-in-class tRNA methyltransferase inhibitor of METTL1. Treatment of numerous tumour models with STM9005 reduces cancer growth, causes cellular changes and dysregulates cell cycle progression. These cellular effects were accompanied by a selective decrease of m7G on a subset of tRNAs and a reduction in their expression levels, which led to an impact on oncogenic mRNA translation. We illustrate that pharmacological inhibition of METTL1 in vivo impairs tumour growth and leads to a significant prolongation of survival in various mouse cancer models of different tissue origin. Collectively, our results provide strong proof-of-concept that targeting of tRNA methylation is a novel avenue of anti-cancer therapy, and illustrate that catalytic inhibition of METTL1 represents a novel therapeutic strategy against a number of aggressive malignancies.

overall_design: Adapted modification-induced mismatch tRNA-seq (mim-tRNA-seq) profiling of B16F10 and MLL-AF9/Flt3ITD/+ cells treated with DMSO or STM9005 for 3 days


title: An Antioxidant Adhesive Hydrogel Informed by Single-Cell RNA Sequencing for Scarless and Functional Vocal Fold Repair

city: Chengdu

first: Hui

state: sichuan proviince

address: No. 37 Guoxue Xiang, Chengdu, 610041, P.R. China

institute: West Chian Hospital, Sichuan university

summary: This RNA-sequencing experiment aimed to investigate the transcriptional changes in vocal fold tissues following hydrogel treatment. Specifically, the study sought to determine whether the application of the SIS-OHA-TA (SOT) hydrogel modulates gene expression profiles associated with oxidative stress, apoptosis, and tissue repair, thereby contributing to scar-free healing.

overall_design: Experimental Design Rabbit vocal fold injury models were established and divided into three groups: untreated injury (Control), SOT hydrogel treatment (SOT), and normal vocal folds without injury (Normal). Tissue samples were harvested 1 week post-injury for transcriptomic analysis. Total RNA was extracted from each group and subjected to high-throughput RNA sequencing. Quality control, library preparation, and sequencing were performed by [insert sequencing service provider/lab].

first: Ming

last: Xiong


title: Pharmacological inhibition of METTL1 as a therapy against solid and haematological cancers [Ribo-Seq]

overall_design: Ribo-seq profiling of OE21 cells treated with DMSO or STM9005 for 1 or 3 days


title: Napabucasin eliminates multiple myeloma through STAT3 inhibition-mediated stemness ablation and ER stress-induced immunogenic cell death

city: 徐州市

first: Tengyuan

state: 江苏省

address: 云龙区骆驼山

institute: xuzhou medical university

summary: Signal transducer and activator of transcription 3 (STAT3) is a pivotal oncogenic driver in multiple myeloma (MM), where its constitutive activation promotes malignant plasma cell proliferation, survival, and drug resistance in the bone marrow microenvironment. Despite therapeutic advances, MM remains incurable due to persistent STAT3-driven tumorigenesis and the resilience of MM stem cells. Here, we investigated the therapeutic potential of Napabucasin (BBI608), a novel STAT3 inhibitor, in MM. Our data demonstrate that BBI608 potently suppresses MM cell proliferation in vitro and in vivo, while significantly impairing clonogenic potential and inducing robust apoptosis. Mechanistically, BBI608 exhibits dual efficacy by not only targeting bulk tumor cells but also eradicating the stem-like compartment of MM cells, addressing a critical therapeutic challenge. Moreover, we reveal that BBI608 triggers immunogenic cell death (ICD) via activation of endoplasmic reticulum (ER) stress and the unfolded protein response (UPR), which subsequently enhances T-cell-mediated anti-tumor immunity. Our findings underscore STAT3 inhibition as a promising strategy to simultaneously eradicate MM cells, target stem cell reservoirs, and harness anti-tumor immunity, providing a robust rationale for clinical translation of BBI608 in MM therapy.

overall_design: RNA-seq profiling of RPMI8226 and KMS11 cells treated with BBI608 or DMSO control for 48 hours, in three biological replicates.

first: Yuqian

last: Sha

first: Peiyu

first: Wenyu

last: Li

first: Yan

last: Zhang

first: Mei

first: Wenya

first: Jianquan

last: Gu

first: Hai

last: Cheng

first: Mingshan

last: Niu

first: Kailin

last: Xu

first: Yao

last: Yao


title: piRNA direct the chromatin reader to its genomic targets

city: Ithaca

first: Yicheng

last: Luo

state: NY

address: 215 Tower Rd

department: Molecular Biology and Genetics

institute: Cornell University

summary: The chromatin reader Rhino (Rhi) is an HP1-paralog and master regulator of piRNA biogenesis in Drosophila that drives the transcription of piRNA precursors. While Rhi binds the heterochromatic mark H3K9me3, this interaction is insufficient to explain its specific occupancy, as Rhi is excluded from the majority of H3K9me3-enriched loci. Instead, we find that Rhi recruitment is orchestrated by several competing pathways, including the piRNA-guided protein Panoramix (Panx) and the DNA-binding protein Kipferl (Kipf). We demonstrate that Panx functions as a piRNA-guided modular scaffold that directs Rhi to its targets through a dual-mode mechanism: its N-terminus recruits the H3K9 methyltransferase machinery, while its C-terminus directly binds the Rhi chromodomain. While H3K9me3 deposition provides a necessary foundation, it acts in synergy with the direct Panx-Rhi physical bridge to drive robust Rhi occupancy. Furthermore, Rhi recruitment is amplified by the cytoplasmic inheritance of maternal piRNAs, forming a transgenerational feed-forward loop. Our results reveal that the piRNA pathway imparts sequence-specificity to the H3K9me3 code, utilizing a direct physical bridge to program the genomic distribution of the chromatin reader Rhi.

overall_design: piRNA production by high throughput sequencing

first: Wenjiang

last: Zhou

first: Zhaohui

last: Jin

first: Baira

last: Godneeva

first: Xiawei

last: Huang

first: Haoqing

last: Wang

first: Peng

last: He

first: Ying

first: Alexei

last: Aravin


title: Lung environment in healthy old age shapes the phenotype and CCR2-mediated recruitment of a subset of apoptotic, high-turnover alveolar macrophages

city: San Antonio

first: Larry

last: Schlesinger

state: Texas

address: 8715, W Military Drive, Larry Schlesinger Laboratory, Texas Biomedical Research Institute

department: Host Pathogen Interactions program

institute: Texas Biomedical Research Institute

summary: Immune system changes with age lead to chronic systemic inflammation termed "inflammaging", contributing to age-related pathologies. Alveolar macrophages (AMs) maintain lung homeostasis and health. The impact of inflammaging on resident and recruited AM populations requires further definition. Herein, we examined the effect of age on the phenotype and ontogeny of AMs from humans, non-human primates and mice. We identify 3 AM subpopulations in old age, two of which are increased more than 10-fold with age. RNA-seq analysis identifies unique transcriptional profiles of the 3 AM subpopulations. Adoptive transfer experiments in mice reveal the importance of the alveolar environment in AM recruitment and phenotypic change in old age. Monocyte-derived AM recruitment in old age requires CCR2 and leads to relatively short-lived AMs with high turnover due to Fas-mediated apoptosis. These studies provide new insight on the impact of the alveolar environment in healthy old age on AM phenotype and function.

overall_design: Alveolar macrophages (AMs) were isolated from both 10 young and 10 old mice. Cells were then stained and sorted by sorted into CD11c+ CD11b- populations from young and old mice, and CD11c- CD11b+ and CD11c+ CD11b+ populations from old mice using the BD FACSAria II flow cytometer flow cytometry using BV421 anti-CD11b (clone M1/70) and PE anti-CD11c (clone N418) antibodies. The post-sorted cells were then verified based on the gating strategy, and the purity of the populations was confirmed through gating. mRNAseq performed.

first: Susanta

last: Pahari

first: Miranda

last: Lumbreras

first: Arkajyoti

last: Paul

first: Abul

last: Azad

first: Hao

first: Hong

last: Cai

first: Zhao

last: Lai

first: Diego

last: Maselli

first: Jay

last: Peters

first: Jordi

middle: B

last: Torrelles

first: Joanne

last: Turner

first: Florent

last: Ginhoux

first: William

last: Lafuse

first: Yufeng

first: Eusondia

last: Arnett


title: Paternal methamphetamine exposure enhances methamphetamine susceptibility in male rat offspring

city: Pittsburgh

first: BaDoi

middle: Nguyen

last: Phan

state: PA

address: 5000 Forbes Ave

department: Anesthesiology

institute: Stanford University

summary: We previously demonstrated that male progeny of cocaine-experienced sires resisted cocaine, expressed as delayed acquisition of cocaine self-administration. Here, we sought to determine whether this phenotype extended to another psychostimulant, methamphetamine. Surprisingly, relative to saline-sired rats, male, but not female, methamphetamine-sired offspring demonstrated increased susceptibility to methamphetamine taking. Single nuclei RNA- and ATAC-sequencing of the nucleus accumbens was used to identify molecular drivers of phenotypes in cocaine- and methamphetamine-sired offspring. Sequencing results revealed unique profiles of gene expression and open chromatin in offspring nucleus accumbens. Differential gene expression in cocaine-resistant, cocaine-sired offspring and methamphetamine-susceptible, methamphetamine-sired offspring illuminates potential novel treatment targets for psychostimulant use disorders.

overall_design: We extracted nuclei from fresh frozen nucleus accumbens of experimentally naïve methamphetamine-sired, cocaine-sired, and saline-sired male offspring (n=4/group) for same cell RNA-seq and ATAC-seq using the 10X Genomics Multiomics Assay

first: Chris

last: Pierce

first: Sarah

last: Swinford-Jackson


title: Distinct epigenetic alterations and accelerated mitotic aging define second primary breast cancers

city: Santa Monica

first: Melanie

last: Goldfarb

state: California

address: 2200 Santa Monica blvd

department: Surgical Oncology

institute: Saint Johns Cancer Institute

type: Methylation profiling by genome tiling array

summary: Second primary breast cancers (SPBCs) are becoming increasingly common among cancer survivors and are linked to poorer clinical outcomes compared to first primary breast cancers (FPBCs). While the molecular features of FPBCs are well characterized, the biological underpinnings of SPBCs remain largely unexplored. SPBC tumors exhibited 11,321 differentially methylated CpG sites compared to FPBCs, with hypermethylation enriched at gene promoters involved in morphogenesis, hormone signaling, and cell adhesion. Transcriptomic analysis revealed coordinated downregulation of hormone signaling pathways, including estradiol, progesterone, and androgen receptors, independent of somatic mutations. SPBC tumors also showed altered methylation at aging- and cancer-associated TF binding sites and significantly elevated mitotic age, indicative of epigenetic aging and increased proliferative history. SPBC tumors represent a distinct molecular subtype of breast cancer, defined by suppressed endocrine signaling and accelerated mitotic aging. These epigenetic hallmarks may reflect the cumulative effects of prior malignancy and treatment, potentially contributing to more aggressive disease behavior. Our findings provide a foundation for developing personalized risk stratification and therapeutic approaches for survivors at risk of SPBC

overall_design: We performed genome-wide DNA methylation profiling on ER-positive, HER2-negative breast tumors from patients with SPBC (n = 13) and FPBC (n = 29) treated at Providence Saint John's Health Center. DNA methylation profiles were generated using the Infinium MethylationEPIC 850K BeadChip (Illumina, Inc.) according to the manufacturer’s protocol

last: Marzese

first: Andrés

middle: F

last: López

first: Javier

middle: I

last: Orozco


title: RNA-seq data for NCI-H23 in response to KRAS inhibitor

first: Shaofei

last: Wang

state: Shanghai

address: 131 Dongan Road, Xuhui District, Shanghai 200032, P.R. China

institute: Fudan University

summary: We determined the gene expression profile of KRAS-mutant NCI-H23 NSCLC cells in the presence or absence of KRASG12C inhibitor, either sotorasib (AMG-510) or asagrasib (MRTX849), by high throughput RNA-sequencing.

overall_design: Gene expression profiling analysis of RNA-seq data from NCI-H23 NSCLC cells after treatment by vehicle (DMSO),  sotorasib (AMG-510, 1 μM) or asagrasib (MRTX849, 100 nM) for 24h. Three biological replicates were prepared for each condition.

first: Deyu

first: Xiting

last: Huang

first: Man

last: Xiao

first: Peng

last: Yang

first: Kaicheng

last: Zhou

first: Runze

last: Miao

first: Xuyao

last: Zhang

first: Jiajun

last: Fan


title: Neural Circuit Dysfunction in SAH Mice: Targeting PSAP for Therapeutic Intervention in Consciousness Disorders

city: Suzhou

first: Haiying

last: Li

state: Jiangsu

address: 188 Shizi Street

department: Department of Neurosurgery

institute: The First Affiliated Hospital of Soo-chow University

summary: We have employed a single-nucleus RNA sequencing approach to investigate the neural circuit mechanisms of consciousness disorders after subarachnoid hemorrhage (SAH), focusing on the regulatory role of the Psap/Gpr axis in oligodendrocytes on CL-mPFC circuit conduction and white matter integrity, and validate potential therapeutic intervention.

overall_design: 12 hours after inducing subarachnoid hemorrhage in mice via the filament perforation method, single-nucleus transcriptome sequencing was performed on mouse brain tissue within the range from the mPFC origin (Bregma 2.34 mm) to the CL termination (Bregma -2.18 mm).

first: Gang

last: Chen

first: Lu

last: Peng


title: CCL20 Released by Drug-Tolerant Persisters Impairs Immunotherapy in EGFR-Mutated Lung Adenocarcinoma

city: Hong Kong

first: Hoi-Hin

last: Kwok

address: Sassoon Road

institute: The University of Hong Kong

summary: EGFR-mutated lung adenocarcinoma (LUAD) often shows suboptimal response to immune checkpoint inhibitors (ICIs), attributed to an immunosuppressive tumor immune microenvironment (TIME). Drug-tolerant persisters (DTPs), a subpopulation of cancer cells that can survive initial therapy, contribute to this resistance by releasing CCL20, a chemokine that fosters tumor immune privilege. This preclinical study aims to explore the role of CCL20 in modulating TIME and its impact on ICI efficacy in EGFR-mutated LUAD. We utilized a humanized mouse model engrafted with EGFR-mutated NCI-H1975 LUAD cells and human peripheral blood mononuclear cells (PBMCs) to mimic a human immune system. Mice were treated with anti-PD-1, anti-CCL20, or a combination of both. Xenograft growth was monitored, and resected xenograft were analyzed using single-cell RNA sequencing (scRNA-seq) and multiplex immunofluorescence microscopy to assess changes in tumor cell transcriptional profiles and immune cell infiltration including. Results demonstrated that anti-PD-1 or anti-CCL20 monotherapy showed minimal effects on tumor growth, their combination significantly suppressed tumor progression and CCL20 expression in DTP subpopulations and altered the transcriptional profile of tumor cells. Combined treatment also reduced hypoxia-related genes and appeared to enhance stress response pathways. In addition, the combined treatment enhanced infiltration of immune cells, shifting the TIME toward an immunogenic state. In conclusion, co-inhibition of CCL20 and PD-1 remodels the TIME, overcoming ICI resistance in EGFR-mutated LUAD. These findings suggest that targeting CCL20 alongside PD-1 blockade could enhance immunotherapy efficacy, offering a novel therapeutic strategy for this patient population.

overall_design: Mice were treated with anti-PD-1, anti-CCL20, or a combination of both. Xenograft growth was monitored, and resected xenograft were analyzed using single-cell RNA sequencing.

first: Jiashuang

first: Nerissa Chui-Mei

last: Lee

first: Junyang

last: Deng

first: David Chi-Leung

last: Lam


title: Phytosulfokine peptide regulates the growth-immunity trade-off through CAMTA3-mediated transcriptional signaling in Arabidopsis

city: zhejiang jinhua

first: zhang

middle: peng

last: hong

address: xinshijiedao 688

institute: zhejiang normal university

summary: Phytosulfokine (PSK) peptide hormone promotes plant growth while suppressing endogenous immunity. However, the underlying mechanism remains poorly understood. Here we show that PSK regulates the trade-off between growth and immunity by mediating stabilization and cytosol-nucleus translocation of Calmodulin-binding Transcription Activator 3 (CAMTA3). By genetic screening of an Arabidopsis thaliana mutant library, we identified a mutant named growth retardation and autoimmunity 1 (gra1). Map-based cloning and bulk population sequencing disclosed that GRA1 encodes TYROSYLPROTEIN SULFOTRANSFERASE (TPST) for the biosynthesis of sulfated peptides. Treatment with PSK can restore the reduced callus proliferation of gra1 mutants and overexpression of PSK can promote plant growth but reduce immune responses. RNA-seq and genetic studies show that PSK regulates plant growth and immunity through salicylic acid pathway. Further, we revealed that PSK stabilizes CAMTA3 and enables its translocation from cytosol to nucleus by facilitating its binding to calmodulin 6 (CaM6) and CaM7, and CAMTA3 inhibits the expression of SYSTEMIC ACQUIRED RESISTANCE DEFICIENT 1 (SARD1) and CALMODULIN-BINDING PROTEIN 60g (CBP60g) to inhibit salicylic acid biosynthesis and plant immunity. Collectively, we disclose a signaling pathway PSK-PSKR-CaM6/7-CAMTA3-SARD1/CBP60G that regulates the trade-off between plant growth and immunity.

overall_design: All rosette leaves of 18-day-old wild type, gra1-1, and pskr1 pskr2 mutants were individually harvested and flash-frozen in liquid nitrogen.Three biological replicates were taken for each sample.

first: Penghong

first: Yujia

first: Fang

last: Yu

first: Qi

last: Tan

first: Pingfei

last: Han

first: Jiangzhe

last: Zhao

first: Wei

first: Xiaoxian

last: Zhu

first: Yanjun

first: Kewei


title: CEBPG induces epithelial-mesenchymal transition and facilitates DNA double-strand break repair in lung adenocarcinoma cells

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

summary: Epithelial-mesenchymal transition (EMT) is crucial in cancer progression and is driven by EMT–inducing transcription factors (EMT-TFs). Although core EMT-TFs are well characterized, much remains unknown of context-dependent EMT-TFs restricted to specific tissues or cell types. Here, we identified CEBPG as a novel inducer of EMT in lung adenocarcinoma cells by examining regions of extensive histone H3 lysine 4 trimethylation occupancy that are often a hallmark of cellular identity. Transiently induced during TGF--driven EMT, ectopic CEBPG induced mesenchymal-like morphologies and gene expression, while its RNAi knockdown attenuated EMT. Domain mapping analysis of CEBPG demonstrated the indispensability of the leucine zipper domain, rather than the DNA binding domain, suggesting the involvement of protein partners. Co-immunoprecipitation and mass spectrometry identified interactions of CEBPG with non-homologous end joining (NHEJ) factors and CEBPB. Importantly, CEBPG silenced the transcriptional activities of CEBPB, thereby nullifying its effects that restrict EMT. Alternatively, CEBPG enhanced NHEJ activity and repair of etoposide-induced DNA double-strand breaks, promoting cellular survival under anticancer DNA damage stress. Together, our study reveals that CEBPG serves a dual role as an EMT regulator and a DNA repair facilitator, contributing to enhanced malignant traits in lung adenocarcinoma cells.

overall_design: Comaprison between A549 control cells and A549 cells overexpressing CEBPG.

first: Minoru

last: Terashima

first: Ryusuke

last: Suzuki

first: Kusuma

last: Suphakhong

first: Tatsunori

last: Nishimura

first: Takahisa

last: Takino

first: Shin-Ichi

first: Takumi

last: Nishiuchi

first: Shoichiro

last: Tange

first: Akihiko

last: Ishimura

first: Dominic

last: Voon

first: Goro

last: Sashida

first: Takeshi


title: Local brain reprogramming mitigates Alzheimer's disease and associated bone loss

city: Changsha

first: Meidan

last: Wan

address: Xiangya street

institute: Central South University

type: Methylation profiling by high throughput sequencing

summary: Alzheimer's disease (AD) is a debilitating neurodegenerative disorder marked by glia cell inflammation, neuron loss, cognitive impairment, and systemic dysfunctions, including bone loss. The progression of AD is accompanied by aging and epigenetic alterations that disrupt cellular homeostasis. Here, we demonstrate that a coexpression vector (AAV-OSK) containing Oct4, Sox2, and Klf4 preserves microglial and neuronal cells identities, while reducing neuroinflammation and neuronal apoptosis. Localized brain treatment with AAV-OSK enhances cognitive function, neuronal health, Aβ plaque clearance, microglial activity, and myelin integrity in early- and late-stage AD mouse models. Reduced representation bisulfite sequencing (RRBS) analysis indicated that these therapeutic benefits require DNA demethylation during reprogramming. Furthermore, this brain reprogramming approach also improves osteogenesis in AD-affected bone tissue. These findings suggest that reprogramming brain tissue can unlock youthful epigenetic information through DNA demethylation offering a novel strategy to improve both brain and extracerebral organ health in AD individuals.

overall_design: Methylation differences analysis of RRBS sequencing data for the brain of WT mice ,  APP/PS1 mice, and OSK-treatment APP/PS1 mice.

first: Zhenxing

last: Wang

first: Lu

last: Shen

first: Hui

last: Xie


title: Spatial transcriptomics of Slc16a1-Col2a1CreERT2 mouse spinal motion segments reveals compartment-distinct differences in the intervertebral disc

city: Philadelphia

first: Makarand

last: Risbud

address: 1015 Walnut Street

institute: Thomas Jefferson University

summary: The intervertebral disc is a compartmentalized structure, with an inner nucleus pulposus (NP) surrounding by annulus fibrosus (AF), and bordered superiorly and inferiorly by cartilaginous endplates. Glucose is known to be the primary energy source for the disc -- in which gets metabolized into lactate. While lactate efflux out of the NP is critical, the fate of lactate is undetermined. Thus, we've generated Slc16a1-Col2a1CreERT2 mice which inhibit lactate transport into the AF and EP compartments of the disc. We took into an exploratory approach and employed spatial transcriptomics which allowed us to capture positional gene information, including crosstalk between disc compartments, in which otherwise would be lost without spatial sequencing. Our analysis revealed the consequences of long-term MCT1 inhibition in the AF- and endplates on gene expression.

overall_design: Spinal motion segments were dissected from 6-month-old Mct1 mice, including the intervertebral disc and adjacent vertebra, and one FFPE block was made for each genotype. Each block contained four discs, with one disc per mouse (n = 4 discs/genotype).  One section from each block was assigned to each capure area (Mct1cKO, Mct1CTR) in which were used for analysis.

first: Maria

last: Tsingas

middle: V


title: IWC immunization induces reprogramming of AMs via chromatin remodeling

first: Yun

last: Shi

address: No 37, Guoxuexiang

institute: West China Hospital, Sichuan University

summary: We found the IWC of Acinetobacter baumannii intranasal immunization could induce alveolar macrophases training to exert the protection for bacterial infection. To characterize the epigenetic landscape of IWC treated TR-AMs and CD13+ cell derived AMs, we performed bulk ATAC-seq from these cells to see the epigenetic programming.

overall_design: . We i.n. immunized CD45.2+ mice with IWC and isolated CD45.2+ CD11C+ AMs and CD45.2+ CD13+ AMs from BALF and transferred them to CD45.1 mice separately and sorted these cells back at day 24 after transfer and did ATAC-seq of these cells. The unimmunized CD45.2+ AMs were used as control cells.


title: Effect of lactate supplementation on gene expression of rat endplate cells

summary: Lactate, which was once considered a waste product, is being reconsidered as the fulcrum of metabolism. Beyond its role as a metabolic fuel, lactate has emerged as a signaling molecule including its role in lactyation which influences gene expression. In the intervertebral disc, cells are highly glycolytic and under the Warburg effect, are known to produce substantial amounts of lactate. Here, we investigate lactate's role as a signaling molecule in the context of endplate cells within the intervertebral disc. In vivo deletion of lactate importer, MCT1, in the annulus fibrosus (AF) and EP, yields a degenerative disc phenotype with an immature bony endplate characterized by cartilaginous remnants and lack of vascularization. In vitro metabolomics with lactate supplementation suggested that EP cells do not prefer lactate as a metabolic fuel. However, lactate supplementation was shown to significantly increase lactylation. Thus, herein we assessed the downstream effects on gene expression and its influence on major cellular processes. This study provides new insights into the significance of lactate in disc biology.

overall_design: To investigate the effects of lactate supplementation on endplate (EP) cells of the intervertebral disc, primary EP cells were treated with 20mM lactate or 20mM NaCl (controls for osmolarity) for 24 hours in hypoxia. RNA-sequencing was then conducted on RNA isolated from EP cells from control and lactate-treated groups. Each group contains five biological replicates.