title: Resolving the design principles that control postnatal vascular growth and scaling

city: Chicago

first: Yogesh

last: Goyal

state: IL

address: 303 E Superior St

institute: Northwestern University

summary: After birth, tissues grow continuously until reaching adult size, with each organ exhibiting unique cellular dynamics, growth patterns, and (stem or non-stem) cell sources. Using a suite of experimental and computational multiscale approaches, we found that aortic expansion is guided by specific biological principles and scales with the vertebral column rather than animal body weight. Expansion proceeds via two distinct waves of arterial cell proliferation along blood flow that are spatially stochastic, yet temporally coordinated. Each wave exhibits unique cell cycle kinetics and properties, with the first wave exhibiting cell cycle durations as fast as 6 hours. Singlecell RNA sequencing showed changes in fatty acid metabolism concomitant with an increase in cell size. Mathematical modeling and experiments indicated endothelial cell extrusion is essential for homeostatic aortic growth and balancing excess proliferation. In a genetic model of achondroplasia, the aorta achieves proper scaling through enhanced cell extrusion while maintaining normal proliferation dynamics. Collectively, these results provide a blueprint of the principles that orchestrate aortic growth which depends entirely on differentiated cell proliferation rather than resident stem cells.

overall_design: Animals were sacrificed through CO2 inhalation before perfusion through the left ventricle with warm Versene solution (0.2g EDTA, 8g sodium chloride, 0.2g potassium chloride, 1.15g anhydrous sodium phosphate, 0.2g anhydrous potassium phosphate, dissolved in distilled water, pH 7.5) The aorta was dissected from the body and adventitia removed before being cut open to expose the endothelium. For the P5 and P10 timepoints, whole aortas were pooled into digestion solution (Liberase TH 70ug/mL, Sigma-Aldrich; DNase I, Qiagen; 10mM HEPES, Corning) and incubated at 37°C for 20 minutes while pipetting up and down every 2 minutes to generate a single-cell suspension. For P20 and P30 timepoints, aortas were cut open and pinned down with the endothelium facing up. After adding warm 1X trypsin (Gibco) for 5 minutes, a microfeather blade was used to gently scrape the endothelium of the aorta, as in previously established methods 17. The samples were incubated in 1X trypsin for an additional 5 minutes while pipetting up and down to generate a single-cell suspension. After neutralizing the digestion solution with DMEM containing 10% FBS, the cell suspension was filtered through a 20 uM cell strainer. Post-digestion cleanup was done prior to cell counting and viability assessment. Cell suspensions were loaded onto a Chromium Next GEM Chip G and run using the Chromium Controller iX (10X Genomics) to generate gel beads in emulsion (GEMs). Singlecell RNA sequencing libraries were constructed using the Chromium Next GEM Single Cell 3’ v3.1 (Dual Index). Sequencing was performed on a NextSeq2000 Sequencing System (Illumina). Gene expression matrices were generated by de-multiplexing, aligning, barcode processing, and UMI counting using CellRanger pipeline.

first: Danielle

last: Pi

first: Jonas

last: Braun

first: M. Luisa

last: Iruela-Arispe


title: Complement pathway activation mediates pancreatic cancer-induced muscle wasting and pathological remodeling [RNA-seq]

status: Public on May 11 2025

city: Gainesville

first: Andrew

middle: R

last: Judge

state: FL

address: 1275 Center Drive, Biomedical Sciences Building RM J303

country: USA

institute: University of Florida

type: Expression profiling by high throughput sequencing

summary: Cancer cachexia is a multifactorial condition characterized by skeletal muscle wasting that impairs quality of life and longevity for many cancer patients. A greater understanding of the molecular etiology of this condition is needed for effective therapies to be developed. We performed a quantitative proteomic analysis of skeletal muscle from cachectic pancreatic ductal adenocarcinoma (PDAC) patients and non-cancer controls, followed by immunohistochemical analyses of muscle cross-sections. These data provide evidence of a local inflammatory response in muscles of cachectic PDAC patients, including an accumulation of plasma proteins and recruitment of immune cells into muscle that may promote the pathological remodeling of muscle. Our data further support the complement system as a potential mediator of these processes, which we tested by injecting murine pancreatic cancer cells into wild type (WT) mice, or mice with genetic deletion of the central complement component 3 (C3-/- mice). Compared to WT mice, C3-/- mice showed attenuated tumor-induced muscle wasting and dysfunction and reduced immune cell recruitment and fibrotic remodeling of muscle. These studies demonstrate that complement activation is contributory to the skeletal muscle pathology and dysfunction in PDAC, suggesting that the complement system may possess therapeutic potential in preserving skeletal muscle mass and function.

overall_design: RNA-sequencing was performed on KPC pancreatic tumors (4 biological replicates per group) from C57BL/6J mice (WT; stock no: 000664) and complement C3 null mice (C3-/-; stock no: 029661) purchased from The Jackson Laboratory.

first: Sarah

middle: M

first: Jeremy

middle: B

last: Ducharme


title: Increased locomotor activity does not mitigate the effects of advanced maternal age in a mouse model

status: Public on May 10 2025

city: Burnaby

first: Julian

last: Christians

state: BC

address: 8888 University Drive

department: Biological Sciences

country: Canada

institute: Simon Fraser University

summary: Introduction: Advanced maternal age (AMA) increases the risk of pregnancy complications, in part due to impaired placentation. While exercise during pregnancy can improve outcomes, its potential to mitigate the effects of AMA has not been investigated. We evaluated the impact of exercise in a mouse model of AMA. Methods: Females were paired with males at 9 or 34 weeks of age, with one group of aged females having access to running wheels four weeks prior to and during pregnancy. Pregnant females (N = 19 per group) were collected at gestational day (GD) 11.5. Placentas were collected for RNA sequencing (N = 17-20 per group). Results: Aged females without access to running wheels had heavier fat depots, while those with access to running wheels did not differ from young females. The number of viable conceptuses and fetal size were lower in both groups of aged females. Hundreds of genes were differentially expressed between young females and each of the aged groups, but only one gene was affected by access to running wheels. The placental transcriptomes of both aged groups were more similar to that of young mice at GD 10.5 than to young mice at GD 11.5, suggesting delayed placental development. Conclusions: Our model reproduced previously-reported effects of age on fetal development and placental transcriptomics, but these were not mitigated by increased voluntary locomotor activity, despite a reduction in adiposity. Remarkably, increased voluntary locomotor activity had almost no effects on placental gene expression in aged mice.

overall_design: To investigate whether increased locomotor activity could mitigate adverse pregnancy outcomes in a mouse model of advanced maternal age, we mated 3 groups of mice: Young (age range 12-20 weeks), Aged (age range 37-45 weeks), and Aged/Exercised (same as Aged, but provided running wheels 4 weeks prior to mating and throughout pregnancy). We collected placentas at GD 11.5 and also collected placentas from some Young mice at GD 10.5. We performed gene expression profiling analysis using data from RNA-seq.

first: J

middle: K


title: Gene expression profile at single cell level of human laryngeal normal, preneoplastic and tumorigenic states

city: Hangzhou

first: Zi-Ming

last: Fu

state: Zhejiang

address: Qingchun Road 79

department: Department of Otolaryngology

country: China

institute: The First Affiliated Hospital, School of Medicine, Zhejiang University

summary: The mechanisms underlying the progression of vocal cord leukoplakia (VCL) to laryngeal squamous cell carcinoma (LSCC) remain unclear. We characterize the differences in the cellular microenvironment between VCL and LSCC at the single-cell resolution for the first time.

overall_design: In the study, we performed single-cell RNA sequencing on surgical tissues from 30 patients with vocal cord polyps (VCP), vocal cord leukoplakia (VCL) and laryngeal squamous cell carcinoma (LSCC).

first: Shui-Hong

last: Zhou


title: PABPC1 SUMOylation enhances cell survival by promoting mitophagy through stabilizing U-rich mRNAs within stress granules (RIP-Seq)

city: Shanghai

first: Jianxiu

last: Yu

address: Shanghai, China

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong universIty

summary: Stress granules (SGs) are cytoplasmic, membraneless organelles that modulate mRNA metabolism and cellular adaptation under stress, yet the mechanisms by which they regulate cancer cell survival remain unclear. Here, we identify Poly(A)-Binding Protein Cytoplasmic 1 (PABPC1), a core SG component, as stress-inducible SUMOylation target. Upon various stress conditions, SUMOylated PABPC1 promotes SG assembly and enhances cancer cell survival. Transcriptome-wide analysis reveals that SUMOylated PABPC1 selectively stabilizes mRNAs enriched in conserved U-rich elements. Mechanistically, SUMOylated PABPC1 interacts with RNA-binding protein TIA1 to form PABPC1-SUMO-TIA1 complex that recruits U-rich mRNAs into SGs, protecting them from degradation. This process facilitates the expression of U-rich genes, such as mitophagy-related genes FUNDC1, BNIP3L, thereby maintaining cellular homeostasis and promoting cell survival under adverse conditions. Our findings reveal that PABPC1 SUMOylation connects stress granule assembly with selective U-rich mRNA stabilization and mitophagy, promoting cancer cell stress adaptation.

overall_design: RIP-Seq in H1299 stably expressing Myc-PABPC1-WT or K512R cells

first: Caihu

last: Huang

first: Jiayi

first: Runhui

last: Lu

first: Ari Jiazhuo

first: Arno Shengzhuo

first: Yingting

last: Cao

first: Lian

last: Li

first: Junya

first: Hongyan

first: Zihan

first: Yixin

last: Zhang

first: Anan

last: Xu

first: Ran

last: Chen

first: Yanli

last: Wang

first: Xian

last: Zhao

first: Jian

first: Yujie

first: Ming

first: Hailong


title: PABPC1 SUMOylation enhances cell survival by promoting mitophagy through stabilizing U-rich mRNAs within stress granules

first: Jianxiu

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series

first: Caihu

first: Jiayi

first: Runhui


title: An immunological mechanism of resistance to CDK4/6 inhibitors in breast cancer

status: Public on May 09 2025

city: West Hollywood

first: Simon

last: Knott

state: California

address: 8687 Melrose Ave

department: BFG

institute: Cedars Sinai

summary: Resistance to CDK4/6 inhibitors leads to treatment failure and disease progression in women with HR+HER2- breast cancer (BC). We delineated a hypoxia-sensitive, CCL2-dependent pathway recruiting IL17A-secreting γδ T cells to mouse HR+HER2- BCs upon CDK4/6 inhibition, resulting in repolarization of tumor-associated macrophages (TAMs) towards an immunosuppressive CX3CR1+ phenotype associated with resistance. Increased IL17A signaling and intratumoral γδ T cell abundance positively correlated with advanced grade and/or reduced survival in two cohorts of HR+HER2- BC patients. Circulating γδ T cells and plasma CCL2 levels negatively correlated with progression in an independent series of patients with HR+HER2- BC receiving CDK4/6 inhibitors. Intratumoral γδ T cells were increased in post- vs pre-treatment biopsies from HR+HER2- BC patients relapsing on CDK4/6 inhibitors. CX3CR1+ TAMs had negative prognostic impact in women with HR+HER2- BC receiving neoadjuvant PD-1 blockage and radiotherapy. Thus, γδ T cells and CX3XR1+ TAMs may favor resistance to CDK4/6 inhibitors in HR+HER2- BC patients.

overall_design:
scRNA sequencing of twelve ER+ adult female breast tumor samples at Baseline, 4 weeks after treatment initiation with PD1 and Radiation Therapy followed by PD1 along with surgical resection.

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

first: Giulia

last: Petroni

first: Claudia

last: Galasi

first: Kenneth

middle: H

last: Gouin 3rd

first: Aagam

last: Shah

first: Lorenzo

last: Galluzi


overall_design: Please read the detailed description in the manuscript in the Methods section.


title: Transcriptomic analyses reveal carbon dot-based seed priming in regulation of root growth in rice

city: Xuzhou

first: Cen

middle: Ai

state: Jiangsu

address: No.2 Kunpeng

institute: Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District

summary: Carbon dots (CDs) can affect plant growth and disease resistance and assist siRNA/DNA delivery. Salvia miltiorrhiza-Derived Carbon Dots were recently found to facilitate plants to adapt to environmental stresses through amplifying Ca2+ signaling and scavenging reactive oxygen species (ROS). More importantly, CDs can be degraded into CO2 and H2O within plant cells, thereby having fewer biosafety issues as compared to those undegradable ones and receiving more attentions in the plant community. However, the molecular mechanisms underlying effects of CD priming on plant growth and development have not been well characterized. In this study, we conducted transcriptomic assays and aim to reveal how CD priming affect root development through transcriptional reprogramming in rice.

overall_design: RNA-seq

first: Y

first: A

first: J

last: Jing

first: Z

last: Shi

last: Yang

first: W


title: NHR-66 Regulates Cuticular Collagen Expression and Modulates C. elegans Adhesion to Predatory Fungi

city: Nankang, Taipei

first: Hung-Che

last: Lin

address: 128 Academia Road, Section 2

country: Taiwan

institute: Academia sinica

summary: NHR-66, a nuclear hormone receptor in C. elegans, regulates cuticle collagen genes important for fungal adhesion. RNA-seq of wild-type and nhr-66 STOP-IN mutants exposed to Arthrobotrys oligospora revealed >1200 genes downregulated in mutants, including over 40% of the collagen gene family. GO analysis highlighted enrichment in cuticle structure terms.

overall_design: Late L4-stage wild-type and nhr-66 mutants were exposed to A. oligospora for 30 min. Total RNA was extracted, DNase-treated, and quality-checked (RIN ≥ 8.0). RNA-seq was performed, followed by PCA and differential gene expression analysis.

first: Yen-Ping

last: Hsueh

first: Han-Wen

last: Chang


title: NNMT inhibition in cancer-associated fibroblasts restores antitumor immunity.

first: CRI

last: Bioinformatics

address: 5801 S. Ellis Ave.

institute: University of Chicago

summary: Cancer-associated fibroblasts (CAFs) play a pivotal cancer-supportive role, yet CAF-targeted therapies remain elusive. Through spatial transcriptomics and single-cell RNA sequencing, we investigated the role of nicotinamide N-methyltransferase (NNMT) in high-grade serous ovarian cancer (HGSOC). Mechanistically, NNMT-induced H3K27me3 hypomethylation drives complement secretion from CAFs, attracting immunosuppressive myeloid-derived suppressor cells (MDSCs) to the tumor. NNMT knockout in immunocompetent mice impaired tumor growth in syngeneic ovarian, breast, and colon tumor models through enhanced CD8+ T cell activation. Using high-throughput screening, we developed a potent and specific NNMT inhibitor that reduces tumor burden and metastasis in multiple murine cancer models and restores immune checkpoint blockade efficacy by decreasing CAF-mediated MDSC recruitment and reinvigorating CD8⁺ T cell activation. Our findings establish NNMT as a central CAF regulator and promising therapeutic target to mitigate immunosuppression in the tumor microenvironment.

overall_design: We performed spatial transcriptomics on a tissue microarray including non-tumorous cancer-adjacent stroma (n = 10), ovarian tumours (n = 29), and omental metastases (n = 16), obtained from 30 patients with high-grade serous ovarian cancer. mRNA expression in formalin-fixed paraffin-embedded (FFPE) tissue was measured using the GeoMx Human Whole Transcriptome Atlas (NanoString, GMX-RNA-NGS HuWTA-4), which targets 18,000 protein-coding genes. Probe hybridisation and immunofluorescent staining were used to define the following areas of interest (AOIs): (1) pan-cytokeratin-positive (panCK⁺) cancer epithelium, (2) CD163-positive monocytes/macrophages, (3) CD45-positive CD163-negative immune cells, and (4) stroma (panCK⁻ CD163⁻ CD45⁻).

first: Janna

last: Heide

first: Agnes

middle: J

last: Bilecz

first: Samarjit

last: Patnaik

first: Maria

middle: F

last: Allega

first: Leonhard

last: Donle

first: Kaiting

first: Ethan

last: Teich

first: Yan

last: Li

first: Qiaoshan

first: Ke

last: Kong

first: Li

last: Liu

first: Tae

middle: G

first: Ken

middle: C

last: Cheng

first: Jonathan

last: Shrimp

first: Quinlin

last: Hanson

first: Min

last: Shen

first: Hongmao

last: Sun

first: Hardik

first: Lisa

last: Schweizer

first: Katarzyna

last: Zawieracz

first: Andrea

last: Olland

first: Andre

last: White

first: Robert

last: Suto

first: Razzaq

last: Alhunayan

first: Medine

last: Taşdemir

first: Noa

last: Longman

first: Hua

last: Liang

first: Matthias

last: Mann

first: Gordon

last: Stott

first: Matthew

middle: D

last: Hall

last: Schwörer

first: Ralph

last: Weichselbaum

first: András

last: Piffkó

first: Ernst

last: Lengyel


title: Derepressing nuclear pyruvate dehydrogenase induces therapeutic cancer cell reprogramming [ATAC-Seq]

city: Boston

first: Ting

last: Zhao

state: MA

address: 185 Cambridge st, Simches Building, CPZN4400

institute: MGH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Metabolites are essential substrates for epigenetic modifications. Although nuclear acetyl-CoA constitutes a small fraction of the whole cell pool, it regulates cell fate by locally providing histone acetylation substrate. Here, we report a nucleus-specific acetyl-CoA regulatory mechanism that can be modulated to achieve therapeutic cancer cell reprogramming. Combining phenotypic chemical screen, genome-wide CRISPR screen, and proteomics, we identified that the nucleus-localized pyruvate dehydrogenase complex (nPDC) is constitutively inhibited by the nuclear protein ELMSAN1 through direct interaction. Pharmacologic inhibition of the ELMSAN1-nPDC interaction derepressed nPDC activity, enhancing nuclear acetyl-CoA generation and reprograming cancer cells to a postmitotic state with diminished cell-of-origin signatures. Reprogramming was synergistically enhanced by histone deacetylase 1/2 inhibition, resulting in inhibited tumor growth, durably suppressed tumor-initiating ability, and improved survival in multiple cancer types in vivo, including therapy-resistant sarcoma patient-derived xenografts and carcinoma cell line xenografts. Our findings highlight the potential of targeting ELMSAN1-nPDC as epigenetic cancer therapy.

overall_design: For Fig. 5C and S5B: to study the relationship between chromatin accessibility and histone acetylation, we treated osteosarcoma cells with DMSO and ISX9 for 3 hours for ATAC-seq and CUT&Tag of H3K27ac.

first: Lai Ping

last: Wong

first: Ruslan

last: Sadreyev

first: David

last: Scadden


title: Derepressing nuclear pyruvate dehydrogenase induces therapeutic cancer cell reprogramming [CUT&Tag]

overall_design: For Fig. S5K: to study the effect of small molecules MGCD0103 and ISX9 on histone mark H3K27ac, we treated sarcoma cells with DMSO, MGCD0103, ISX9, and their combination M+I and performed CUT&Tag using H3K27ac antibody. For Fig. 5C and S5B: to study the relationship between chromatin accessibility and histone acetylation, we treated osteosarcoma cells with DMSO and ISX9 for 3 hours for CUT&Tag of H3K27ac and ATAC-seq.


title: NNMT inhibition in cancer-associated fibroblasts restores antitumor immunity

first: CRI

last: Bioinformatics

summary: Cancer-associated fibroblasts (CAFs) play a pivotal cancer-supportive role, yet CAF-targeted therapies remain elusive. Through spatial transcriptomics and single-cell RNA sequencing, we identified nicotinamide N-methyltransferase (NNMT) as a central CAF regulator in high-grade serous ovarian cancer (HGSOC) patients. Mechanistically, NNMT-induced H3K27me3 hypomethylation drives complement secretion from CAFs, attracting immunosuppressive myeloid-derived suppressor cells (MDSCs) to the tumor. Using high-throughput screening, we developed a potent, specific NNMT inhibitor that reduces tumor burden in multiple murine cancer models and restores immune checkpoint blockade efficacy by decreasing CAF-mediated MDSC recruitment and reinvigorating CD8⁺ T cell activation. Our findings establish NNMT as an essential CAF regulator and promising therapeutic target to mitigate immunosuppression in the tumor microenvironment.

overall_design: Single nuclei RNA-sequencing of omental metastases of seven chemotherapy-naïve high-grade serous ovarian cancer (HGSOC) patients.

first: Janna

last: Heide

first: Agnes

last: Bilecz

first: Samarjit

last: Patnaik

first: Maria

last: Allega

first: Leonhard

last: Donle

first: Kaiting

last: Yang

first: Ethan

last: Teich

first: Yan

last: Li

first: Qiaoshan

last: Lin

first: Ke

last: Kong

first: Li

last: Liu

first: Tae

first: Ken

last: Cheng

first: Jonathan

last: Shrimp

first: Quinlin

last: Hanson

first: Min

last: Shen

first: Hongmao

last: Sun

first: Hardik

last: Shah

first: Lisa

last: Schweizer

first: Katarzyna

last: Zawieracz

first: Andrea

last: Olland

last: White

first: Simon


title: PABPC1 SUMOylation enhances cell survival by promoting mitophagy through stabilizing U-rich mRNAs within stress granules (4sU-Seq)

first: Jianxiu

last: Yu

overall_design: mRNA stability profiles and lncRNA stability profiles in H1299 stably expressing Myc-PABPC1-WT or K512R cells

first: Caihu

last: Huang

first: Jiayi

first: Runhui

last: Lu

first: Ari Jiazhuo

first: Arno Shengzhuo

first: Yingting

last: Cao

first: Lian

first: Junya

first: Hongyan

first: Zihan

last: Zhou

first: Yixin

last: Zhang

first: Anan

last: Xu

first: Ran

last: Chen

first: Yanli

last: Wang

first: Xian

last: Zhao

first: Jian

first: Yujie

last: Fu

first: Ming

first: Hailong


title: Single cell gene expression of virus-specific WT amd KMT2D-deficient CD4+ T-cells

city: Chapel Hill

first: Matthew

last: Niederhuber

state: NC

address: 250 Bell Tower Dr.

institute: UNC-Chapel Hill

summary: To understand how KMT2D impacts anti-viral CD4 T-cell responses, we performed scRNA-seq on  WT and KMT2D-/- effector CD4 T-cells obtained from LCMV Armstrong infected mice

overall_design: WT and KMT2D-TCD mice were infected with LCMV Armstrong. 10 days later, I-Ab GP66-77 CD4+ cells from the spleen were isolated by FACS sorting, and gene expression was determined by scRNA-sequencing.

first: Jonathan Alexander

last: Cohen

first: Ashlyn A.

last: Buzzelli

first: Ichiro

last: Misumi

first: Lixin

last: Yang

first: Jason K.

last: Whitmire


title: Bulk RNA sequencing of skin biopsies from psoriasis patients treated with roflumilast or placebo

city: Aarhus

first: Hakim

last: Ben Abdallah

state: Denmark

address: Palle Juul-Jensens Boulevard 45

department: Dermatology and Venerology

country: Denmark

institute: Aarhus University Hospital

summary: This sub-study investigated the cellular and molecular effects of oral roflumilast treatment on psoriatic skin. Patients with moderate-to-severe psoriasis were allocated 1:1 to monotherapy with oral roflumilast 500 μg QD or placebo in a company-independent, randomized clinical trial (the PSORRO study, ClinicalTrials.gov NCT04549870).

overall_design: Skin punch biopsies from 24 patients were obtained at baseline, week 4 and week 12 for Bulk RNA-sequencing. Lesional skin were collected at each visit, whereas non-lesional skin were only collected at the baseline visit.


title: m6A is decoded by modified tRNAs to coordinate mRNA decay [Quant-seq]

city: Heidelberg

first: Bastian

last: Linder

address: Meyerhofstraße 1

department: Genome Biology Unit

country: Germany

institute: European Molecular Biology Laboratory (EMBL)

summary: Chemically modified mRNA nucleotides are emerging as key regulators of gene expression. Their effects are typically thought to be mediated through reader proteins that selectively bind to RNA molecules containing these modifications. Here, we present a new mechanism by which N6 methyladenosine (m6A) couples the translation of messenger RNA (mRNA) to its decay. m6A-modified codons are decoded inefficiently by the ribosome, rendering them “non-optimal”. At these codons, m6A slows down elongating ribosomes and thereby triggers translation-dependent decay of the mRNA. Inefficient decoding of m6A-modified codons is counteracted by the transfer RNA (tRNA) anticodon modification 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U). mcm5s2U increases the decoding efficiency of a subset of m6A codons and thereby alleviates m6A-mediated mRNA decay. This unanticipated link between the mRNA and tRNA epitranscriptomes controls the decay of mRNAs of important oncogenic signaling pathways. The biogenesis of m6A and mcm5s2U is coordinated in normal tissues but dysregulated in cancer, where a shift towards more mcm5s2U stabilizes these RNAs and is associated with higher tumor aggressiveness and poor prognosis. Thus, the balance between m6A and mcm5s2U acts as a pan-epitranscriptomic mechanism that regulates gene expression and curtails tumorigenesis.

overall_design: ActD and STM treatment followed by Quant-seq in U34 modification enzyme knockout.

first: Puneet

last: Sharma

first: Jie

last: Wu

first: Tosca

last: Birbaumer

first: Cristian

last: Eggers

first: Shino

last: Murakami

first: Roman

middle: E

last: Ott

first: Kai

last: Fenzl

first: Hannah

last: Vorgerd

first: Florian

last: Erhard

first: Samie

last: Jaffrey

first: Sebastian

middle: A

last: Leidel

first: Lars

last: Steinmetz


title: Single-cell long-read Hi-C, scNanoHi-C2, details 3D genome reorganization in embryonic-stage germ cells

city: Beijing

first: Jiansen

last: Lu

address: No. 5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

institute: Peking University

summary: During mouse development, embryonic stage germ cells (EGCs) make crucial fate decisions, with female ones embark on meiosis whereas male ones enter mitotic arrest until birth. Despite the mounting knowledge about their reprogramming of epigenetic modifications, the dynamics of 3D genome structures within individual EGCs remains elusive. Herein, we presented a single-cell-input long-read Hi-C method, scNanoHi-C2, and systematically dissected the reprogramming dynamics of EGC chromatin structures. We found that, despite the similar attenuation of A/B compartments and topologically associating domains (TADs), and the appearance of refined A/B compartments in autosomes comparable to spermatogenesis, the X chromosomes of female EGCs showed enhanced specific interactions between B compartments probably due to their incomplete reactivation. By reconstructing single-cell 3D genome models, we revealed the dynamic chromosome positioning during meiosis at single-cell level, showing that the neighborhood between non-homologous chromosomes of EGCs was relatively random. At the same time, the transposable elements (TEs) underwent dramatic chromatin reorganization, and a preferential asymmetric distribution of Alu/B2 elements around the meiotic TAD boundaries emerged, which reflected the formation of refined-compartments, maintaining the balances between global chromatin condensation and local meiotic-specific transcription. Notably, we demonstrated the specific chromatin loop extrusion around recombination hotspots during meiosis, which may provide a structural basis facilitating reliable homologous recombination. We also revealed an unexpected chromatin structure in mitotic arrested male EGCs distinct from the previously assumed G0 status, which may prime the unique genome structure for subsequent spermatogenesis. Altogether, our study revealed key features of the chromatin structure reprogramming in EGCs, emphasizing the potential roles of 3D genome structures for mammalian germ cell development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: we used a single-cell input Hi-C method, scNanoHi-C2, systematically dissected the reprogramming of chromatin architectures during the development of EGCs in E11.5-E18.5.

first: Wen

last: Li

first: Fuchou

last: Tang


title: EV-sorting small RNA in normal human plasma-EV compared with EV-depleted plasma

first: Zhi

middle: John

address: Shuangqing Road

department: School of Life Sciences

institute: Tsinghua University

summary: After mapping to transcriptome using bowtie2 and peak calling by RNA peak caller (cfPeak), count matrix was created by merge 3 pairs of samples. EV-sorting small RNA sites in normal human plasma total RNA-seq were annotated by comparing differentially expressed peaks (EV vs. EV-depleted Plasma).

overall_design: Peripheral whole blood samples were collected from individuals before therapy or surgery using EDTA-coated vacutainer tubes. Plasma was separated within 2 hr after collection by centrifuge at 1,900 g for 10 min at 4 ℃. All plasma samples were aliquoted and stored at -80°C. Plasma EV were purified by a membrane-affinity approach using exoRNeasy Midi Kit(Qiagen, 77144) following the manufacturer’s instructions. Plasma-nonEV (EV-depleted Plasma) component were collected from flow through part of MinElute spin column from kit. Both plasma EV RNA and Plasma nonEV RNA were extracted using QIAzol Lysis Reagent (QIAGEN, Beijing, China), and DNA contamination was removed by Recombinant DNase I (RNase-free) (TAKARA, Beijing, China). The total cfRNA libraries were prepared using our in-house protocol that improved from our previously published method, DETECTOR-seq. Library quantification was performed by Qubit dsDNA HS Kit and fragment size was checked by Agilent 2100 Bioanalyzer. Libraries were sequenced on DNBSEQ-T7 (MGI Tech.) with PE150.

first: Pengfei

last: Bao

first: Qing

last: Zhan

first: Shaozhen

last: Xing

first: Chun

last: Ning

first: Mengtao


title: Molecular recording of cellular protein kinase activity with chemical labeling

first: Erica

last: Valentini

address: Im Neuenheimer Feld 580

institute: DKFZ

summary: Protein kinases control most cellular processes and aberrant kinase activity is involved in numerous diseases. To investigate the link between specific kinase activities and cellular phenotypes in heterogeneous cell populations and in vivo, we introduce molecular recorders of kinase activities for later analysis. Based on split-HaloTag and a phosphorylation-dependent molecular switch, our recorders become rapidly labeled in the presence of a specific kinase activity and a fluorescent HaloTag substrate. The kinase activity in a given cell controls the degree of fluorescent labeling whereas the recording window is set by the presence of the fluorescent substrate. We have designed specific recorders for four protein kinases, including protein kinase A. We apply our protein kinase A recorder to sort heterogeneous cell populations for subsequent transcriptome analysis, in genome-wide CRISPR screens to discover regulators of PKA activity, and to track neuromodulation in freely moving mice.

overall_design: To investigate genetic changes crucial PKA activity regulation. A CRISPR mediated genetic screen was carried out on RKO colorectal cancer cell line using the Heidelberg CRISPR sgRNA library sub-library A. The pool of edited RKO-KinprolaPKA cells were expanded, labeled with CPY-CA dye and flourescently sorted according to the CPY-CA/EGFP signal ratio into 3 population. Important regulator of PKA identified from the sgRNA representation in each of the 3 samples.

first: De-en

last: Sun

first: Siu Wang

last: Ng

first: Yu

last: Zheng

first: Shu

last: Xie

first: Niklas

last: Schwan

first: Paula

last: Breuer

first: Dirk

last: Hoffmann

first: Julius

last: Michel

first: Daniel

last: Azorin

first: Kim

last: Boonekamp

first: Frank

last: Winkler

first: Wolfgang

last: Wick

first: Michael

last: Boutros

first: Yulong

last: Johnsson


first: Deen

address: Jahnstrasse 29

department: Chemical Biology

institute: Max Planck Institute for Medical Research

overall_design: Comparative gene expression profiling analysis of RNA-seq data for S24 cells stably transduced with either KinprolaPKA or Kinprolaon.

first: Siuwang

last: Li

first: Kai


title: m6A is decoded by modified tRNAs to coordinate mRNA decay [miCLIP]

first: Bastian

last: Linder

overall_design: To increase calling of m6A sites, additional miCLIP was performed on total RNA from HEK293T cells as previously described (see GSE63753)

first: Puneet

last: Sharma

first: Jie

last: Wu

first: Shino

last: Murakami

last: Fenzl

first: Hannah

last: Vorgerd

first: Florian

last: Erhard

first: Samie

last: Jaffrey

first: Sebastian

last: Leidel

first: Lars

last: Steinmetz


title: The nuclear cap-binding complex regulates subcellular RNA processing and surveillance of coding and non-coding RNAs

city: Philadelphia

first: Diep

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

summary: RNA cleavage is essential for processing and regulating all classes of RNA. Current methods to profile genome-wide RNA cleavage are biased towards cytoplasmic events and ignore compartmentalized differences. Here, we couple subcellular RNA fractionation with degradome profiling to detect genome-wide nucleoplasmic and cytoplasmic RNA cleavage in Arabidopsis thaliana. While mRNA cleavage dominated cytoplasmic fractions, we captured a diverse array of nucleoplasm-enriched RNA cleavage events. This included pre-mRNA cleavage and non-coding RNA processing, including microRNAs, ribosomal RNAs, small nucleolar RNAs, enhancer-associated RNAs, and retrotransposon-derived RNAs. Furthermore, we revealed that CAP-BINDING PROTEIN80/ABA HYPERSENSITIVE1 regulates RNA surveillance at the nuclear periphery during the pioneer round of translation. Our data also emphasized its role in stabilizing nucleoplasmic RNAs (e.g. mRNA-associated anti-sense RNAs) and affecting cytoplasmic mRNA cleavage. Overall, our results highlight the diversity of compartmentalized RNA cleavage and reveal that the nuclear cap-binding complex has numerous functions in subcellular RNA processing and surveillance.

overall_design: Subcellular RNA fractionation coupled with global mapping of uncapped and cleaved transcripts (subcellular GMUCT) to produce nucleoplasmic and cytoplasmic RNA-enriched degradomes was performed on early-stage flower buds of Arabidopsis WT and abh1 (abh1-8; Gregory et al 2008, Developmental Cell) plants in biological triplicate. In parallel, strand-specific mRNA sequencing was also performed on bulk RNA from WT and abh1 flower buds in biological triplicate.

first: Brian

last: Gregory


title: Sequencing de novo Mu transposon insertions across maize tissues

city: Athens

first: Brad

last: Nelms

state: Georgia

address: 120 East Green St

department: Genetics

institute: University of Georgia, Athens

summary: We sequenced insertion sites for the maize Mutator (Mu) transposon in leaf, root, endosperm, and pollen from Mu-active plants and Mu-inactive controls. Inherited insertions were identified using matched tissues, and then the abundance of de novo (post-zygotic) insertions was quantified and converted to variant allele frequencies (VAF). This dataset provides insight into the abundance of new transposon insertions within heterogeneous tissues and factors that shape mutation accumulation in multicellular organisms.

overall_design: Matched tissues were collected from Mu-active plants. Endosperm samples were first obtained by seed chipping; then the chipped seed was grown to collect V2 seedling leaves, primary root, and pollen at maturity (collected between 9 and 11 AM). Two genotypes were used for these experiments: (1) Mu-active plants, generated by crossing a mu-active male parent to a mu-inactive female parent, both of the W22 maize inbred background, and (2) Mu-inactive plants, which was the W22 mu-inactive female parent of #1.

first: Justin

last: Scherer


title: m6A is decoded by modified tRNAs to coordinate mRNA decay [SLAM-Seq]

overall_design: s4U labelling followed by GRAND-SLAM analysis of the wobble uridine (U34) modification enzymes knockouts


title: Derepressing nuclear pyruvate dehydrogenase induces therapeutic cancer cell reprogramming (RNA-seq_2)

first: Ting

last: Zhao

overall_design: To study the effect of ELMSAN1 overexpression and knockdown on transcriptomic changes

first: Shenglin

last: Mei

first: David

last: Sykes

last: Scadden


title: Derepressing nuclear pyruvate dehydrogenase induces therapeutic cancer cell reprogramming (RNA-seq_1)

overall_design: We used RNA-seq to study the effect of small molecule treatment on transcriptomic changes in sarcoma cells.

first: Lai Ping

last: Wong

first: Ruslan

last: Sadreyev


title: Derepressing nuclear pyruvate dehydrogenase induces therapeutic cancer cell reprogramming	 (H3K27ac Cut&Tag)

overall_design: We used CUT&Tag to study the effect of small molecule treatment on histone mark H3K27ac changes in sarcoma cells.

first: Lai

middle: P


title: Derepressing nuclear pyruvate dehydrogenase induces therapeutic cancer cell reprogramming (CRISPR)

overall_design: Genome-wide CRISPR activation (CRISPRa) screen was employed to identify genes whose overexpression blunted the treatment effect of ISX9 in 143B cells


title: Derepressing nuclear pyruvate dehydrogenase induces therapeutic cancer cell reprogramming	 (ATAC-seq)

overall_design: We used ATAC-seq to study the effect of small molecule treatment on chromatin accessibility changes in sarcoma cells.


title: OTUD3  prevents ulcerative colitis by modulating microbiota-mediated STING activation.

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

overall_design: Refer to individual Series


title: Peak analysis of small cell-free RNA in oral cancer plasma finds recurrently protected narrow regions with clinical potential

first: Zhi

last: Lu

summary: Oral cancer is characterized by poor prognosis and low survival rate despite sophisticated surgical and radiotherapeutic modalities. Lymphatic metastasis of oral cancer is a complex process involving multiple post-transcriptional biological processes. Thus, feasible detection of cancer metastasis in plasma could be challenging and beneficial. We recruited patients with oral squamous cell carcinoma (OSCC), one of the common oral cancer types, and checked the lymphatic metastatic status and profiled small RNA in plasma samples.

overall_design: Peripheral whole blood samples were collected from individuals before therapy or surgery using EDTA-coated vacutainer tubes. Plasma was separated within 2 hr after collection. All plasma samples were aliquoted and stored at -80°C. CfRNAs were extracted using miRNeasy serum/plasma miRNA isolation kit (QIAGEN, Shanghai, China), and DNA contamination was removed by Recombinant DNase I (RNase-free) (TAKARA, Beijing, China). Small libraries were prepared according to the manual of QIAseq miRNA library kit (QIAGEN, Shanghai, China). Library quantification was performed by Qubit dsDNA HS Kit. Library fragment size and quality were checked using Agilent 2100 Bioanalyzer. Libraries were sequenced on Illumina HiSeq X-ten with PE150.

first: Pengfei

last: Bao

first: Shaozhen

last: Xing

first: Qing

last: Zhan


title: Fibroblast-restricted inflammasome activation promotes atrial fibrillation and heart failure with diastolic dysfunction

city: Houston

last: Li

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Background: Atrial fibrillation (AF) is commonly associated with diastolic dysfunction. Both conditions involve overactivation of inflammatory signaling and cardiac fibroblasts (FBs). While the activation of the NLRP3-inflammasome in cardiomyocytes is known to cause atrial electrical remodeling and arrhythmogenicity, the role of FB NLRP3-inflammasome in heart disease is unknown. Objectives: We aimed to elucidate the contribution of FB-specific NLRP3-inflammasome activation to cardiac function and arrhythmogenesis. Methods: Human atrial FBs were isolated from atrial biopsies of AF and sinus rhythm patients. We established an FB-specific knockin (FB-KI) mouse model with FB-restricted expression of constitutively active NLRP3. Cardiac function and AF susceptibility were assessed through echocardiography, tissue Doppler, programmed electrical stimulation, and optical mapping. Results: NLRP3 and IL1B were upregulated in atrial FBs of patients with persistent AF. FB-KI mice exhibited enlarged left atria, enhanced AF-susceptibility, and heart failure with diastolic dysfunction. FBs from FB-KI mice were more transdifferentiated, migratory, and proliferative than those from control. FB-KI mice showed increased fibrous content in both atria and ventricles, atrial gap junction remodeling, and reduced atrial conduction velocity. Single-nuclei RNA-seq analysis revealed prominent transcript remodeling of metabolic pathways across multiple cell types, enhanced extracellular matrix signaling, and altered intercellular communications. Knockdown of Nlrp3 in FBs via adeno-associated virus type-dj/8 mediated transfer of shRNA reduced AF-susceptibility and prevented cardiomyopathy in FB-KI mice. Conclusions: FB-restricted activation of the NLRP3-inflammasome promotes cardiac fibrosis and AF-susceptibility. This study identifies the FB NLRP3-inflammasome activation as a key mechanism governing the concomitant AF and heart failure with diastolic dysfunction.

overall_design:
Single replicates from either control or CF-KI (constitutive activation of NLRP3 in fibroblasts ) heart nuclei were used for single-nuclei RNA-Seq.
Note: The Nlrp3 allele was silenced in non-Cre-expressing cells in this model.

first: Luge

first: Cristian

last: Coarfa

first: Yue

last: Yuan

first: Issam

last: Abu-Taha

first: Jia

last: Song

first: Xiaolei

last: Wang

first: Xiaohui

last: Chen

first: Lisa

last: Mullany

first: Michelle

last: Tallquist

first: Stanley

last: Nattel

first: Dobromir

last: Dobrev


title: Single-cell transcriptomics reveals that human milk feeding shapes neonatal immune cell interleukin signaling pathways in a non-randomized clinical trial

status: Public on May 08 2025

city: College Station

first: Destiny

last: Mullens

state: Texas

address: 2253 TAMU

department: Nutrition

institute: Texas A&M University

summary: Objective: The study aimed to characterize circulating immune cell subpopulation gene expression in human milk-fed (HMF) compared to cow's milk formula-fed (FF) infants using single-cell transcriptomics.  Methods: Peripheral blood mononuclear cells (PBMCs) were isolated from healthy HMF (n=6), and FF (n=3) infants who were 3 to 3.5 months old and enrolled in a non-randomized clinical trial. Single-cell RNA sequencing (scRNA-seq) was used to generate a PBMC atlas and evaluate gene expression in immune cell subsets. Differential expression analysis was performed on each cell type independently after clustering the cells by similar marker gene expression using the scGEAToolbox. Differentially expressed genes (DEGs) were subjected to pathway analyses using an online functional enrichment analysis program.  Results: The relative abundance (%) of T and B lymphocytes, natural killer (NK) cells, and plasmacytoid dendritic cells were similar, while monocytes were higher in FF infants than in HMF infants (22.6 ± 10.7 vs 8.3 ± 5.6; P = 0.0314). In addition, innate and adaptive immune cells from FF infants exhibited a higher activation state compared to HMF infants. We identified 16 distinct cell subsets from the major immune cell types: three monocyte subsets, four NK subsets, two B cell subsets, and seven T cell subsets. Transcriptional profiles of each peripheral innate and adaptive immune cell subtype varied between HMF and FF infants. Pathway enrichment analysis of cell-specific transcriptional changes within subsets of major cell types revealed that the interleukin (IL)-4/IL-13 signaling pathways were upregulated in FF infants relative to HMF infants.  Conclusion: These findings suggest that human milk downregulates peripheral immune cell cytokine transcriptional signatures linked to allergic inflammation and infection relative to formula feeding.

overall_design: Peripheral blood mononuclear cells isolated from human milk-fed or formula-fed infants.

first: Michael

middle: L

last: Salinas

first: Bharath

last: Mulakala

first: Laurie

last: Davidson

first: James

last: Cai

first: Sharon

last: Donovan

first: Robert

middle: S

last: Chapkin

first: Laxmi

last: Yeruva


title: m6A is decoded by modified tRNAs to coordinate mRNA decay [ribosome profiling]

first: Bastian

last: Linder

summary: In eukaryotes, the genetic code is transcribed into messenger RNA (mRNA) in the nucleus and decoded by transfer RNA (tRNA) in the cytosol.  Nuclear mRNA processing events that do not affect the nucleotide sequence of an mRNA are thought to be invisible to tRNAs during protein translation in the cytosol.  Here, we report a mechanism by which the modified mRNA nucleotide N6‑methyladenosine (m6A) connects nuclear mRNA processing to tRNA decoding. m6A is deposited in the protein coding sequence (CDS) of mRNAs with long exons, where it slows the decoding of a subset of m6A-modified codons in vivo.  Translation of codons with m6A at the wobble position is facilitated by 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), a modified nucleotide of the tRNA anticodon loop that juxtaposes the wobble-m6A.  This unanticipated link between the mRNA and tRNA epitranscriptomes controls mRNA half-life in a translation-dependent manner and connects the exon-intron architecture of mRNAs to their turnover.  The pathways for m6A and mcm5s2U biogenesis are tightly co-regulated in human tissues but deregulated in cancer cells. In breast cancer, a shift towards more mcm5s2U is associated with tumor aggressiveness and poor prognosis.  Thus, the m6A/mcm5s2U-balance has evolved as a pan-epitranscriptomic mechanism that coordinates gene expression changes and curtails tumorigenesis.

overall_design: Ribosome profiling analysis of the wobble uridine (U34) modification enzymes knockouts

first: Puneet

last: Sharma

first: Jie

last: Wu

first: Sebastian

last: Leidel

first: Samie

middle: R

last: Jaffrey

first: Lars

last: Steinmetz


title: Modeling diabetic alpha cell dysfunction using stem cell-derived alpha cells [Bulk RNA-seq]

city: Rochester

first: Quinn

last: Peterson

state: MN

address: 150 3rd St SW

institute: Mayo Clinic

summary: Dysfunction of pancreatic alpha cells contributes to the pathophysiology of diabetes. Features of diabetic alpha cell dysfunction include glucagon hypersecretion, defects in proglucagon processing, and altered transcriptomic profile. The lack of an in vitro human alpha cell model has prevented the investigation, and potential correction, of these dysfunctional phenotypes. Here, we show that induction of endoplasmic reticulum stress in stem cell-derived alpha (SC-α) cells induces hypersecretion of glucagon. ER stress also increases the secretion of glicentin and expression of GLP-1, peptides produced by alternate cleavage of proglucagon by the prohormone convertase 1 (PC1/3) enzyme. Additionally, ER stress establishes a diabetic transcriptional state in SC-α cells characterized by downregulation of MAFB, as well as glycolysis and oxidative phosphorylation pathways. We show that sunitinib, a tyrosine kinase inhibitor, protects SC-α cells against the ER stress-induced glucagon hypersecretion phenotype. Thus, SC-α cell model can advance our knowledge of islets in health and diabetes.

overall_design: Human pluripotent stem cells were differentiated into stem cell-derived alpha cells. Stem cell-derived alpha cells underwent a 48-hour drug treatment in 30 mL bioreactors at 40 rpm with either DMSO vehicle or tunicamycin drug to induce ER-stress. Samples from the vehcile and experimental groups were analyzed using bulk RNA-seq. Samples were sequenced in two batches.

first: Swikriti

last: Shrestha

first: Lauren

last: Jennings

first: Kyle

last: Knofczynski

first: Sharath

last: Shivakumar


title: Modeling diabetic alpha cell dysfunction using stem cell-derived alpha cells

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


title: Modeling diabetic alpha cell dysfunction using stem cell-derived alpha cells [scRNA-seq]

overall_design: Human pluripotent stem cells were differentiated into stem cell-derived alpha cells and analyzed using scRNA-seq.


title: Coordinated Expression of Retained Introns and Poison Exons in Renal Cell Carcinoma

first: Gilbert

last: Giri

address: 120 Mason Farm Road

institute: University of North Carolina at Chapel Hill

summary: Coordinated intron retention and poison exon inclusion define a subset of kidney tumors by introducing premature stop codons that typically trigger nonsense-mediated decay (NMD). In this study we investigate how mTOR activity modulates these NMD targets, revealing that mTOR inhibition increases the expression of transcripts bearing retained introns and poison exons in certain patient-derived tumors. Our findings show that tumors with low NMD and mTOR activities are more aggressive and have worse outcomes yet display pronounced immune infiltration, highlighting a potential role for these RNA isoforms in shaping tumor progression and immune responses.

overall_design: A498 and A704 cells were treated with either DMSO, mTORi, SMG1i, or PladB, for 24 hours

first: Dominguez

last: Daniel

first: Kim

last: William


title: Functions of histone crotonylation in early mouse embryos by RNA-seq

city: Wuhan

first: Li-quan

last: Zhou

state: Hubei

address: 13 Hangkong road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

summary: Echs1 plays important roles in histone lysine crotonylation. Although it has been studied in many systems, its functions in early embryos remain unclear. In this study, we knocked down Echs1 in mouse oocytes and examined its impact on transcriptome in early mouse embryos.

overall_design: Mouse zygotes were treated with sodium acetate or sodium crotonate, and early 2-cell embryos were collected for RNA-seq analysis.

first: Yin

last: Ying

first: Zhou

last: Liquan


title: Impact of Echs1 on DNA methylome in early mouse embryos

type: Methylation profiling by high throughput sequencing

summary: Echs1 plays important roles in histone lysine crotonylation. Although it has been studied in many systems, its functions in early embryos remain unclear. In this study, we knocked down Echs1 in mouse oocytes and examined its impact on epigenome in early mouse embryos including DNA methylome.

overall_design: Generally, siRNA against Echs1 was injected into mouse oocytes, and fertilized oocytes were cultured to early 2-cell stage for DNA methylome analysis by WGBS.


title: Functions of histone crotonylation in early mouse embryos by ChIP-seq

overall_design: Generally, siRNA against Echs1 was injected into mouse oocytes, and fertilized oocytes were cultured to early 2-cell stage for epigenome analysis by ChIP-seq.


title: Epigenome and transcriptome profiling of urine progenitor renal cells

city: Badalona

first: IJC

last: Bioinformatics

state: Catalonia

address: Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

summary: We characterized the transcriptome and methylome of renal progenitor cells in the urine of a cohort of stable kidney transplant recipients to elucidate whether the origin of the donor (living or deceased donor) was associated with a specific molecular reprogramming.

overall_design: Total RNA from 37 human urine progenitor renal cells (dead and alive donors) plus 10 progenitor renal cells from nephrectomy analysed by RNAseq.

first: Maria

last: Berdasco

first: Josep

middle: M

last: Cruzado


title: Cardiac macrophage CD163 protects pressure overload-induced heart failure via interleukin-10

city: Xiamen

first: Binbin

last: Liu

address: Jinshan Road

institute: Xiamen University

summary: Cardiac macrophages (cMacs) elimination exacerbates pressure overload-induced heart failure. However, the role of functionally distinct subsets of cMacs in heart failure remains largely unknown. CD163, a macrophage-specific scavenger receptor expressed in a subset of cMacs, has been associated with cardiovascular events through its circulating soluble form. This study aimed to elucidate the functional role of the CD163+ cMacs subset in pressure overload-induced heart failure. Transverse aortic constriction (TAC) was used to induce pressure overload. TAC-induced left ventricular systolic dysfunction, characterized by reduced ejection fraction and fractional shortening, was significantly aggravated in Cd163−/− mice post-surgery. Genes differentially expressed due to CD163 deficiency were enriched in pathways related to mitochondrial bioenergetics and homeostasis. Transmission electron microscopy revealed an increase in dysfunctional mitochondria in cardiomyocytes of Cd163−/− mice post-TAC. Additionally, decreased serum interleukin (IL)-10 levels and reduced IL-10 expression in cMacs were observed in Cd163−/− mice post-TAC. IL-10 supplementation significantly reversed TAC-induced reductions in left ventricular systolic function in Cd163−/− mice and improved mitochondrial functions in cardiomyocytes. Furthermore, decreased IL-10 levels and increased soluble CD163 were identified as risk factors for heart failure in hypertensive patients. Thus, CD163 in cMacs attenuates pressure overload-induced left ventricular systolic dysfunction through IL-10.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT-TAC AND WT-SHAM  AND CD163-/- TAC AND CD163-/- SHAM

first: Wei

last: Ni

first: Cuilian

last: Dai


title: DNA methylation of Human Urine Renal Progenitors after kidney transplantation

type: Methylation profiling by genome tiling array

summary: The Illumina Infinium MethylationEPIC Beadchip was used to obtain genomewide methylation profiles from Human Urine Renal Progenitors obtained after kidney transplantation from lived donors or dead donors

overall_design: Bisulphite converted DNA from 35 human urine progenitor renal cells plus 6 progenitor renal cells from nephrectomy were hybridised to the Illumina Infinium MethylationEPIC Beadchip.


title: Intestinal inflammation promotes gut commensal-specific CD4 T cell to initiate molecular mimicry-mediated neuroinflammation

status: Public on May 07 2025

city: Chicago

first: Margarette

middle: Helen

last: Clevenger

state: IL

address: 900 E 57th St

department: Pritzker School of Molecular Engineering

institute: University of Chicago

summary: The microbiota has been recognized as a critical contributor to various diseases, with multiple reports of changes in the composition of the gut microbiome in the context of not only inflammatory bowel disease (IBD), but also neurodegenerative diseases. These microbial shifts can exert systemic effects by altering the release of specific metabolites into the bloodstream, and the gastrointestinal microbiota has further been reported to exhibit immunomodulatory activity through the activation of innate and adaptive immunity. However, it remains unclear how the intestinal microbiota contributes to inflammation in the central nervous system (CNS), where these microorganisms are typically absent. Here, we report that ileum- and cecum-colonizing segmented filamentous bacteria (SFB)-specific T cells can induce inflammation in both the intestines and the CNS. Commensal-specific CD4 T cells that are dysregulated in the inflamed gut can become licensed to infiltrate into the CNS irrespective of their antigen specificity and have the potential to be re-stimulated by host protein-derived antigens in the CNS via molecular mimicry, whereupon they produce high levels of GM-CSF, TNFa, IFNg, and IL-17A, triggering neurological damage. We find that these infiltrated commensal-specific CD4 T cells initiate CNS inflammation by activating microglia through their IL-23R dependent encephalitogenic program and their IL-23R-independent GM-CSF production. Together, our findings reveal a potential mechanism whereby perturbation of commensal-specific T cells can contribute to extraintestinal inflammation.

overall_design: To ascertain the contribution of microglia in the TCR7B8-mediated CNS inflammation, we depleted microglia and macrophages by supplementing CSF1R inhibitor (PLX5622) into the normal mouse food. The sorted 1.0 x 105 cells of CD4-TdTomato+ Csf-2- (GM-CSF)-sufficient or -deficient TCR7B8 naïve CD4 T cells were retro-orbitally injected into adult SFB-colonizing Rag2-/- (6 weeks-old) mice. Four days following the naïve CD4 T cell transfer, PLX5622-formulated AIN-67A or AIN-67A as a control were provided. Fresh diets were provided every week for 6 weeks. At 6 weeks following the naïve T cell transfer, the brainstem, thalamus, and hypothalamus—regions characterized by robust CD4⁺ T cell infiltration and activated microglia—were dissected and cells in the indicated tissues were collected for single cell transcriptomic analysis.

first: Zachary

last: White

first: Teruyuki

last: Sano

first: Nicolas

last: Chevrier


title: Method for deletion of variant surface antigen genes at subtelomeric region of Plasmodium falciparum.

first: Shiroh

last: Iwanaga

address: 3-1 Yamadaoka

department: Molecular protozoology

institute: RIMD, Osaka University

summary: Plasmodium falciparum expresses variant surface antigens (VSAs), including PfEMP1, RIFIN, and STEVOR, on the surface of infected red blood cells. These antigens interact with host receptors on vascular endothelial and immune cells, contributing to both parasite pathogenicity and immune evasion. VSAs are encoded by large multigene families, comprising dozens to hundreds of genes located primarily in heterochromatic regions such as subtelomeric domains, which are notoriously refractory to genetic manipulation. In addition, because P. falciparum parasites undergo antigenic variation by randomly switching VSA expression, it is challenging to use parasites that stably express target VSAs for experimental purposes. As a result, functional characterization of these VSAs has been limited, despite their well-established clinical significance. Here, we present a novel method for targeted deletion of subtelomeric regions in P. falciparum chromosomes by combining the heterochromatin-accessible AsCas12a-UL nuclease with telomere healing. Using this approach, we successfully deleted both subtelomeric regions of chromosome 2. Furthermore, we achieved simultaneous removal of up to seven subtelomeric regions using tandemly arrayed crRNAs, with an efficiency exceeding 85%. This method provides a powerful tool for generating VSA-null parasites, facilitating precise genetic dissection of individual VSA gene families and their roles in host–parasite interactions.

overall_design: Long-read sequencing was performed to determine the sequence at the ends of the deleted subtelomeric regions in Plasmodium falciparum.

first: Farahana

last: Dewayanti


title: A gut sense for a microbial pattern regulates feeding

city: DURHAM

first: Diego

middle: V.

last: Bohórquez

state: North Carolina

address: 203 RESEARCH DR, Room 221

department: Medicine

institute: Duke University

summary: To coexist with its resident microorganisms, the host must have a sense to adjust its behaviour in response to them. In the intestine, a sense for nutrients transduced to the brain through neuroepithelial circuits guides appetitive choices. However, a sense that allows the host to respond in real time to stimuli arising from resident gut microorganisms remains to be uncovered. Here we show that in the mouse colon, the ubiquitous microbial pattern flagellin—a unifying feature across phyla—stimulates Toll-like receptor 5 (TLR5) in peptide YY (PYY)-labelled colonic neuropod cells. This stimulation leads to PYY release onto NPY2R vagal nodose neurons to regulate feeding. Mice lacking TLR5 in these cells eat more and gain more weight than controls. We found that flagellin does not act on the nerve directly. Instead, flagellin stimulates neuropod cells from the colonic lumen to reduce feeding through a gut–brain sensory neural circuit. Moreover, flagellin reduces feeding independent of immune responses, metabolic changes or the presence of gut microbiota. This sense enables the host to adjust its behaviour in response to a molecular pattern from its resident microorganisms. We call this sense at the interface of the biota and the brain the neurobiotic sense.

overall_design: Transcriptomes (SCRB-Seq) of Cck-labeled small intestinal epithelial cells, Pyy-labeled colonic epithelial cells, other small intestinal and colonic enterocytes, vagal nodose neurons, and dorsal root ganglia neurons

first: W

middle: W

first: N

last: Reicher

first: E

last: Alway

first: M

last: Kaelberer

first: D

middle: V


first: Linghan

last: Mei

address: 900 East 57th Street

overall_design: Four IL10KO mice were gavaged with human stool from a healthy donor. At 16 weeks post-gavage, the brain, ileum and colon were collected and processed into single cell suspensions. From there, effector CD4 T cells were isolated by FACS. Bulk TCR-seq were performed on these cells to assess their TCR repertoires.


title: RG motifs promote piRNA-mediated gene silencing

city: Los Angeles

first: Carolyn

middle: Marie

last: Phillips

state: CA

address: 1050 Childs Way, RRI 201

institute: University of Southern California

summary: Argonaute proteins are essential players in RNA silencing pathways, and their N-terminal extensions, particularly in the PIWI clade, often harbor conserved sequences like RG motifs. Despite their prevalence in Argonaute proteins, the role of these motifs remains poorly understood. In this study, we focus on the RG motifs within the N-terminal region of Caenorhabditis elegans PRG-1, a PIWI clade Argonaute. Using sequence alignment across Caenorhabditis species, we identify three conserved RG motifs that are methylated, as confirmed by mass spectrometry. The region surrounding these motifs is intrinsically disordered, as predicted by disorder algorithms and structural modeling. While the RG motifs are critical for fertility, germline morphology, and piRNA silencing, they are not required for PRG-1 expression, localization, or piRNA loading. Notably, mutation of the RG motifs results in defects in downstream small RNA production, specifically the depletion of mutator class siRNAs, without affecting piRNA biogenesis. These findings suggest that the RG motifs of PRG-1 play a crucial role in linking piRNA-mediated silencing to siRNA production, and that their function is critical for fertility and germline maintenance in C. elegans. Despite these defects, the phenotypic severity in the RG mutant is milder than in a PRG-1 null mutant, highlighting the complexity of PRG-1 function and its post-translational modifications.

overall_design: Total small RNA sequencing of N2, prg-1(null), and prg-1(3xAG). mKate::PRG-1/mKatePRG-1(3xAG) immunoprecipitation from whole worm extract followed by small RNA purification, library preparation, and sequencing

first: Dylan

last: Wallis


title: Gene expression profiling of WT and Aldh1a1 KO mouse lung tissues (Part 2)

status: Public on May 06 2025

first: Daisuke

last: Motooka

summary: To explore potential impact of Aldh1a1 deficiency in the retinoic acid signaling in the lung, gene expression levels were compared between wildtype and Aldh1a1 deficient lung tissues. The expression levels of retinoic acid responsive genes were very similar between wildtype and Aldh1a1 deficient lungs, suggesting that Aldh1a1 deficiency has minimal impact on retinoic acid signaling.

overall_design: Lung tissues were isolated from two mice per group (Aldh1a1+/+ and Aldh1a1-/-) and enzymatically digested. Extracted and purified total RNA samples were used for RNA-seq analysis.

first: Yasutaka

last: Okabe

first: Noriko

last: Shinjyo


title: Derepressing nuclear pyruvate dehydrogenase induces therapeutic cancer cell reprogramming

city: Boston

first: Ting

last: Zhao

address: 185 Cambridge st, Simches Building, CPZN4400

institute: MGH

summary: Metabolites are essential substrates for epigenetic modifications. Although nuclear acetyl-CoA constitutes a small fraction of the whole cell pool, it regulates cell fate by locally providing histone acetylation substrate. Here, we report a nucleus-specific acetyl-CoA regulatory mechanism that can be modulated to achieve therapeutic cancer cell reprogramming. Combining phenotypic chemical screen, genome-wide CRISPR screen, and proteomics, we identified that the nucleus-localized pyruvate dehydrogenase complex (nPDC) is constitutively inhibited by the nuclear protein ELMSAN1 through direct interaction. Pharmacologic inhibition of the ELMSAN1-nPDC interaction derepressed nPDC activity, enhancing nuclear acetyl-CoA generation and reprograming cancer cells to a postmitotic state with diminished cell-of-origin signatures. Reprogramming was synergistically enhanced by histone deacetylase 1/2 inhibition, resulting in inhibited tumor growth, durably suppressed tumor-initiating ability, and improved survival in multiple cancer types in vivo, including therapy-resistant sarcoma patient-derived xenografts and carcinoma cell line xenografts. Our findings highlight the potential of targeting ELMSAN1-nPDC as epigenetic cancer therapy.

overall_design: Refer to individual Series


title: Identification of the transcriptomic signature of engrafted CTC derived subpopulations isolated after orthotopic tumor resection as compared to parental cells

city: Pamplona

first: Elizabeth

last: Guruceaga

address: Pio XII 55

institute: CIMA

summary: Identification of the transcriptomic signature of engrafted CTC derived subpopulations as compared to parental cell lines after orthotopic inoculation of tumor cells and surgical tumor resection. Circulating tumor cells (CTC) engrafting in the post-resection tumor bed derived from a orthotopic injection of murine 4T1 or ANV5 cells were isolated in different mice. Engrafted CTC derived from ANV5 were called CTC700, CTC803. Engrafted CTC derived from 4T1 were called CTC1589 and CTC1592.

overall_design: Triplicates of each different cell line or derivatives were used.

first: Fernando

last: Lecanda

first: Borja

last: Ruiz-Fernandez de Córdoba


title: Heterozygosity for Crohn’s Disease Risk Allele of ATG16L1 Protects against Bacterial Infection

first: Ken

last: Cadwell

address: 421 Curie Blvd

institute: Perelman School of Medicine University of Pennsylvania

summary: The T300A substitution in ATG16L1 associated with Crohn’s Disease impairs autophagy, yet up to 50% of humans are heterozygous for this allele. Here we demonstrate that heterozygosity for the analogous substitution in mice (Atg16L1T316A), but not homozygosity, protects against lethal Salmonella enterica Typhimurium infection. One copy of Atg16L1T316A was sufficient to enhance cytokine production through inflammasome activation, which was necessary for protection. In contrast, two copies of Atg16L1T316A inhibited the autophagy-related process of LC3-associated phagocytosis (LAP) and increased susceptibility. Macrophages from human donors heterozygous for ATG16L1T300A displayed elevated inflammasome activation while homozygosity impaired LAP similar to mice. These results clarify how the T300A substitution impacts ATG16L1 function and suggest it can be beneficial to heterozygous carriers, providing an explanation for its prevalence.

overall_design: we performed RNA-seq analysis of BMDMs from wild-type (Atg16L1T/T), Atg16L1T/A or Atg16L1A/A mice two hours post-inoculation with Salmonella （MOI=100) or mock treatment

first: Xiaomin

last: Yao

first: Eugene

last: Rudensky


title: In vivo CRISPR activation screen identifies a lipid metabolism regulator as a driver of bone metastasis

first: Li

last: Ma

address: MD Anderson Cancer Center, Zayed Building, Z7.2036, 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

summary: The role of lipid metabolism in bone metastasis has not been documented. Here, by using an in vivo CRISPR activation screening system coupled with positive selection, we identify acyl-CoA binding protein (ACBP) as a previously undescribed bone metastasis driver. In non-metastatic cancer cells, overexpression of wild-type ACBP, but not the acyl-CoA binding deficient mutant, stimulates fatty acid oxidation (FAO) and bone metastasis. Conversely, knockout of ACBP in highly bone-metastatic cells abrogates metastatic bone colonization. Mechanistically, ACBP-mediated FAO boosts ATP and NADPH production, reduces reactive oxygen species, and inhibits lipid peroxidation and ferroptosis. ACBP expression correlates with metabolic signaling, bone-metastatic ability, and poor clinical outcomes. Notably, FAO blockade or treatment with a ferroptosis inducer inhibits bone metastasis. Altogether, our findings reveal the role of lipid metabolism in tumor cell adaptation and thriving in the bone, and suggests that agents that target FAO or induce ferroptosis hold potential as bone metastasis drugs.

overall_design: RNA sequencing (RNA-seq) of control and ACBP-knockout BoM-1833 cells cultured in the presence of oleic acid, an 18-carbon monounsaturated fatty acid, to gain insights into ACBP-regulated genes and pathways.

first: Zheng

last: Caishang

first: Teng

last: Hongqi


title: Glycosaminoglycan-driven lipoprotein uptake protects tumours from ferroptosis

city: Dallas

first: Javier

last: Garcia Bermudez

address: 6000 Harry Hines Blvd

department: CRI

institute: UT Southwestern Medical Center

summary: Lipids are essential components of cancer cells due to their structural and signaling roles. To meet metabolic demands, many cancers take up extracellular lipids; however, how these lipids contribute to cancer growth and progression remains poorly understood. Here, using functional genetic screens, we identify lipoprotein uptake—the primary mechanism for lipid transport in circulation—as a key determinant of ferroptosis sensitivity in cancer. Lipoprotein supplementation robustly inhibits ferroptosis across diverse cancer types, primarily through the delivery of α-tocopherol (α-toc), the most abundant form of vitamin E in human lipoproteins. Mechanistically, cancer cells take up lipoproteins through a pathway dependent on sulfated glycosaminoglycans (GAGs) linked to cell-surface proteoglycans. Disrupting GAG biosynthesis or acutely degrading surface GAGs reduces lipoprotein uptake, sensitizes cancer cells to ferroptosis, and impairs tumour growth in mice. Notably, human clear cell renal cell carcinomas, a lipid-rich malignancy, exhibit elevated levels of chondroitin sulfate and increased lipoprotein-derived α-toc compared to normal kidney tissue. Altogether, our work establishes lipoprotein uptake as a critical anti-ferroptotic mechanism in cancer and implicates GAG biosynthesis as a therapeutic target.

overall_design: RNA Sequencing of kidney cancer patient tissue samples. Patient samples are de-identified and are either from the adjacent kidney or a paired clear cell renal cell carcinoma (ccRCC)  primary tumor.

first: Divya

last: Bezwada


title: Physiological Roles of an Acinetobacter-specific σ Factor

city: Madison

first: Kevin

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

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


title: Profiling epigenetic aging at cell-type resolution through long-read sequencing

first: Alec

last: Eames

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital, Harvard Medical School

summary: DNA methylation can give rise to robust biomarkers of aging, yet most studies profile it at the bulk tissue level, which masks cell type-specific alterations that may follow distinct aging trajectories. Long-read sequencing technology enables methylation profiling of extended DNA fragments, enabling mapping to their cell type of origin. In this study, we introduce a framework for evaluating cell type-specific aging using long-read sequencing data, without the need for cell sorting. Leveraging cell type-specific methylation patterns, we map long-read fragments to individual cell types and generate cell type-specific methylation profiles, which are used as input to a newly developed probabilistic aging model, LongReadAge, capable of predicting epigenetic age at the cell-type level. We use LongReadAge to track aging of myeloid cells and lymphocytes from bulk leukocyte data as well as circulating cell-free DNA, demonstrating robust performance in predicting age despite limited shared features across samples. This approach provides a novel method for profiling the dynamics of epigenetic aging at cell-type resolution.

overall_design:
Long-read SMRT sequencing of plasma cell-free DNA from 5 generally-healthy individuals of diverse ages to understand and profile aging dynamics of DNA methylation.

***************************************************************
Raw files for human/patient samples are being made available in dbGaP (https://www.ncbi.nlm.nih.gov/gap/) for controlled access to the personally identifiable sequence data.
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first: Mahdi

last: Moqri

first: Jesse

last: Poganik

first: Vadim

middle: N

last: Gladyshev


title: Physiological Roles of an Acinetobacter-specific σ Factor [ChIP-seq]

summary: The Gram-negative pathogen Acinetobacter baumannii is considered an "urgent threat" to human health due to its propensity to become antibiotic resistant. Understanding the distinct regulatory paradigms used by A. baumannii to mitigate cellular stresses may uncover new therapeutic targets. Many γ-proteobacteria use the extracytoplasmic function (ECF) σ factor, RpoE, to invoke envelope homeostasis networks in response to stress. Acinetobacter species contain the poorly characterized ECF "SigAb;" however, it is unclear if SigAb has the same physiological role as RpoE. Here, we show that SigAb is a metal stress-responsive ECF that appears unique to Acinetobacter species and distinct from RpoE. We combine promoter mutagenesis, motif scanning, and ChIP-seq to define the direct SigAb regulon, which consists of sigAb itself, the stringent response mediator, relA, and the uncharacterized small RNA, "sabS." However, RNA-seq of strains overexpressing SigAb revealed a large, indirect regulon containing hundreds of genes. Metal resistance genes are key elements of the indirect regulon, as CRISPRi knockdown of sigAb or sabS resulted in increased copper sensitivity and excess copper induced SigAb-dependent transcription. Further, we found that two uncharacterized genes in the sigAb operon, "aabA" and "aabB", have anti-SigAb activity. Finally, employing a targeted Tn-seq approach that uses CRISPR-associated transposons, we show that sigAb, aabA, and aabB are important for fitness even during optimal growth conditions. Our work reveals new physiological roles for SigAb and SabS, provides a novel approach for assessing gene fitness, and highlights the distinct regulatory architecture of A. baumannii.

overall_design: ChIP-seq of HaloTagged SigAb protein in Acinetobacter baumannii ATCC 17978 grown in rich defined medium. Experiment performed in triplicate.

first: Emily

last: Bacon

first: Rubén

last: Iruegas-López

first: Amy

middle: B

last: Banta

first: Michael

last: Place

first: Ingo

last: Ebersberger

first: Jason

last: Peters


title: Physiological Roles of an Acinetobacter-specific σ Factor [RNA-seq]

overall_design: RNA-seq in Acinetobacter baumannii ATCC 17978 of sigAb and relA overexpression strains (plasmid based OE) and their empty vector counterparts for comparison. RNA-seq performed as a timecourse after induction of OE (0-60 min for sigAb, 0-10 min for relA)


title: Loss of the predicted cell adhesion molecule MPZL3 promotes EMT and chemoresistance in ovarian cancer

city: Pittsburgh

first: Nadine

last: Hempel

address: 5051 Centre Ave

department: UPMC Hillman Cancer Center

institute: University of Pittsburgh

summary: Myelin protein zero-like 3 (MPZL3) is an Immunoglobulin-containing transmembrane protein with predicted cell adhesion molecule function. Loss of 11q23, where the MPZL3 gene resides, is frequently observed in cancer. Yet the role and consequences of altered MPZL3 expression have not been explored in tumor development and progression. We addressed this in ovarian cancer, where both MPZL3 amplification and deletions are observed in respective subsets of high-grade serous specimens. While high and low MPZL3 expressing populations are similarly observed in primary ovarian tumors from an independent patient cohort, metastatic omental tumors largely display decreased MPZL3 expression, suggesting that MPZL3 loss is associated with metastatic progression. MPZL3 knock-down leads to an increase in EMT gene expression in OVCAR4 and OVCA433 cell lines, a transcript signature that is associated with poor patient outcomes. MPZL3 promotes homotypic cancer cell adhesion in some cell lines, and decreasing MPZL3 expression enhances invasion and clearance of mesothelial cell monolayers. Conversely, MPZL3 loss abrogates cell cycle progression and proliferation. This was associated with increased resistance to cisplatin and olaparib and reduced DNA damage and apoptosis in response to these agents in OVCAR4 cells. Enhanced cisplatin resistance was further validated in vivo. These data demonstrate for the first time that loss of the predicted adhesion molecule MPZL3 results in EMT and decreased proliferation in ovarian cancer. Our study suggests that decreased MPZL3 expression is a phenotype of ovarian cancer tumor progression and metastasis and may contribute to treatment failure in advanced-stage patients.

overall_design: To investigate the role of MPZL3 in ovarian cancer cell line OVCA433, MPZL3 expression was knocked down using two indepdent shRNA hairpins (shRNA#1 - TRCN0000137304, shRNA#3 - TRCN0000137252) and RNA sequencing carried out.

first: Hempel

last: Nadine

first: Worley

last: Beth


title: Loss of the predicted cell adhesion molecule MPZL3 promotes EMT in OVCAR4 cells

overall_design: To investigate the role of MPZL3 in ovarian cancer cell line OVCAR4, MPZL3 expression was knocked down using two indepdent shRNA hairpins (shRNA#1 - TRCN0000137304, shRNA#2 - TRCN0000413087) and RNA sequencing carried out.

first: Cheng

last: Ya-Yun


title: Heterogeneity of thymic output in the elderly and its association with sex and smoking

city: London

first: Paula

last: Longhi

address: Charterhouse Square

department: William Harvey Research Institute

country: United Kingdom

institute: Queen Mary University of London

summary: Thymic involution is an age-related process that results in reduced T cell production and impaired adaptive immunity. However, it remains uncertain the extent of thymic activity later in life and how this contributes to immunological ageing. Here, we identified thymic tissue within mediastinal adipose locations in aged individuals and confirmed its functional capacity through multi-omics analysis. Percentage of CD31+ CD4+ T cells correlated positively with thymic tissue presence. Thymic output in elderly showed a high degree of heterogeneity was modulated by gender and smoking history. Thymus activity was associated with a diverse TCR repertoire, unique transcriptomic profile, and distinct epigenetic signature. Adipose tissue inflammation was found to be independent of thymic activity but associated with the presence of circulating T cells with an immunosenescent phenotype. Further analysis revealed functional and phenotypic heterogeneity within distinct naïve CD4 T cell subsets, which are influenced by thymic activity.

overall_design: To investigate if natural involution of the thymus in old age associates with increased risk of mortality, we investigated whole blood derived DNA methylation (DNAm) for a correlation between DNAm GrimAge clock age acceleration and recent thymic emigrants (RTEs). Blood derived DNAm changes previously associated with smoking were also specifically analaysed to explore any association between smoking and thymic output.

first: C

middle: G

last: Bell


title: Exploring the Role of DNMT1 in RNA m⁵C Methylation (RNA-BS-SEQ NSUN2 Knock down)

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

summary: DNA methyltransferase 1 (DNMT1) is an enzyme known for DNA methylation maintenance. However, point mutations in its RFTS domain lead to late-onset neurodegeneration such as the autosomal dominant cerebellar ataxia-deafness and narcolepsy (ADCA-DN) disorder. Here we demonstrated that wild-type DNMT1 also has the capability to bind to mRNA transcripts and facilitate 5-methylcytosine (m5C) RNA methylation by recruiting NOP2/Sun RNA methyltransferase 2 (NSUN2). RNA m5C methylation, in turn, promotes RNA stability for those genes modulating mitochondrial function. When DNMT1 RFTS domain is mutated in the case of ADCA-DN disorder, it triggers aberrant DNMT1-RNA interaction and significantly elevated m5C RNA methylation and RNA stability for a portion of metabolic genes. Consequently, increased levels of metabolic RNA transcripts contribute to cumulative oxidative stress, mitochondrial dysfunction, and neurological symptoms. Collectively, our results highlight a novel role for DNMT1 in regulating both DNA and RNA methylation as well as mitochondrial function, shedding light on the pathogenic mechanism of DNMT1 mutation-induced neurodegeneration.

overall_design: HeLa cells were transfected with small interfering RNA (siRNA) targeting NSUN2 using Lipofectamine RNAiMAX (Thermo Fisher Scientific) according to the manufacturer's instructions. Following transfection, cells were collected for RNA extraction and RNA bisulfite sequencing (RNA-BS-seq).

first: Jing

last: Wang

first: Xiaoqian

last: Deng


title: Exploring the Role of DNMT1 in RNA m⁵C Methylation (Ribo-seq)

overall_design: Ribosome profiling libraries and the corresponding mRNA-seq were prepared on the DNMT1 knockdown HeLa cells as well the control HeLa  cells


title: Effect of iPS cell culture medium on the differentiation potential of induced cardiac tissues

city: Kyoto

first: Yoshiki

last: Nakashima

state: Kyoto

address: Kyoto Research Park KISTIC Building Room 501, 5th floor, KISTIC building,  134 Chudoji Minami-cho, Shimogyo-ku

department: Research and Development Center

institute: Kyoto University Center for iPS Cell Research and Application Foundation (CiRA Foundation)

summary:
The quality of iPSCs was compared using two types of culture media. PluriTest scores were 27.4 ± 1.1 for iMatrix511+StemFit and 35.2 ± 0.5 for LN521+mTeSR. n = 3. LN521+mTeSR was significantly higher than iMatrix511+StemFit.
The quality of iPSCs was compared using two types of culture media. KaryoStat assays revealed no genetic or karyotypic mutations in both iMatrix511+StemFit and LN521+mTeSR. n = 3.

overall_design: iMatrix511+StemFit (n = 3), LN521+mTeSR (n=3)

first: Masayoshi

last: Tsukahara


title: Transcriptomic profiling of CD11b+F4/80+CD206+ TAMs isolated from tumor-bearing mice treated with vehicle or TP-18.

city: shanghai

first: Yao

last: Zhang

address: No. 500, Dongchuan Road

institute: East China Normal University

summary: To investigate the antitumor mechanisms of the dual EP2/EP4 antagonist TP-18, Tumor-associated macrophages were isolated from CT26 tumors, with or without TP-18 treatment, and subjected to RNA-seq–based transcriptomic profiling.

overall_design: Female BALB/c mice (6–8 weeks old) bearing subcutaneous CT26 tumors were treated with either vehicle or TP-18 (50 mg/kg, QD, orally) for 3 weeks.  Following treatment, mice were euthanized via cervical dislocation, and subcutaneous tumors were harvested and processed into single-cell suspensions. CD11b+F4/80+CD206+ TAMs were isolated using Fluorescence-Activated Cell Sorting.  Total RNA was extracted using TRIzol reagent and stored in liquid nitrogen for subsequent sequencing.

first: Weiqiang

last: Lu

first: Mingyao

last: Liu


title: Exploring the Role of DNMT1 in RNA m⁵C Methylation (SLAM-seq)

overall_design: Slam-seq were performed on the HeLa cells and Human NPC in different coditions


title: Molecular and genetic characterization of sex-linked orange coat color in the domestic cat [C4F1]

city: Huntsville

first: Christopher

middle: Bryan

last: Kaelin

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: The Sex-linked orange mutation in domestic cats causes variegated patches of reddish/yellow hair and is a defining signature of random X-inactivation in female tortoiseshell and calico cats. Unlike the situation for most coat color genes, there is no apparent homolog for Sex-linked orange in other mammals. We show that Sex-linked orange is caused by a 5 kb deletion that leads to ectopic and melanocyte-specific expression of the Rho GTPase Activating Protein 36 (Arhgap36) gene. Single cell RNA-seq studies from fetal cat skin reveal that red/yellow hair color is caused by reduced expression of melanogenic genes that are normally activated by the Melanocortin 1 receptor (Mc1r)—cyclic adenosine monophosphate (cAMP)—protein kinase A (PKA) pathway, but Mc1r and its ability to stimulate cAMP accumulation is intact. Instead, we show that expression of Arhgap36 in melanocytes leads to reduced levels of the PKA catalytic subunit (PKAC); thus, Sex-linked orange is genetically and biochemically downstream of Mc1r. Our findings resolve a longstanding comparative genetic puzzle, provide in vivo evidence for the ability of Arhgap36 to inhibit PKA, and reveal a molecular explanation for a charismatic color pattern with a rich genetic history.

overall_design: Single-cell preparations from fetal cat skin at a mid-gestation time point, isolated from a male cat with the derived (orange) Arhgap36 allele.

first: Gregory

last: Barsh


title: Exploring the Role of DNMT1 in RNA m⁵C Methylation (eCLIPseq II)

overall_design: eCLIP-seq of human NSUN2 and DNMT1 in HeLa or 293T cells.


title: Clu regulate myeloid bias in aged hematopoietic stem cells

first: Ninghe

last: Sun

state: Massachusetts

address: 200 Longwood Avenue

institute: Harvard Medical School / Boston Children's Hospital

summary: Clu is upregulated in aged HSCs and its knockout diminishes the myeloid bias.

overall_design: We performed RNA sequencing and studied transcriptome changes in old HSCs after transplantation.


title: Ceramide-FGF13 axis regulate nutrient sensing

city: Iowa city

first: Bhagirath

last: Chaurasia

state: Iowa

address: 431 Newton Road

institute: University of Iowa

summary: Ceramide accumulation impairs adipocytes’ ability to efficiently store and utilize nutrients, leading to energy and glucose homeostasis deterioration. Using a comparative transcriptomic screen, we identified the non-canonical, non-secreted fibroblast growth factor FGF13 as a ceramide-regulated factor that impairs adipocyte function. Obesity robustly induces FGF13 expression in adipose tissue in mice and humans and is positively associated with glycemic indices of type 2 diabetes. Pharmacological or genetic inhibition of ceramide biosynthesis reduces FGF13 expression. Using mice with loss and gain-of-function of FGF13, we demonstrate that FGF13 is both necessary and sufficient to impair energy and glucose homeostasis independent of ceramides. Mechanistically, FGF13 exerts these effects by inhibiting mitochondrial content and function, metabolic elasticity, and caveolae formation, which cumulatively impairs glucose utilization and thermogenesis. These studies suggest the therapeutic potential of targeting FGF13 to prevent and treat metabolic diseases.

overall_design: To investigate the molecular targets of fgf13 in adipose tissue, RNA seq was performed on the adipose tissue obtained from obese control and Fgf13∆Adipo [inducible (ieWAT and isWAT) and constitutive (sWAT and BAT)] mice fed a high fat diet for 20 weeks. Differentially gene expression analysis was done on RNA-Seq data obtained from  obese control and  obese Fgf13 knockout mice.

first: Jamal

last: Naderi

first: Amanda

middle: K

last: Johnson


title: A Dominant mutation in Dnmt1 leads epigenetic changes (RNA-BS-seq Mouse Cortex)

summary: We report the application of rnaseq on the Dnmt1 A560V mice

overall_design: Examine the epigenetic changes and gene expression changes due to Dnmt1 mutation


title: Gene expression profiling of WT and Aldh1a1 KO mouse lung tissues exposed to naphthalene

city: Suita

first: Daisuke

last: Motooka

address: 3-1, Yamadaoka

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

summary: To explore potential impact of Aldh1a1 deficiency in the retinoic acid signaling in the lung, gene expression levels were compared between wildtype and Aldh1a1 deficient lung tissues. The expression levels of retinoic acid responsive genes were very similar between wildtype and Aldh1a1 deficient lungs, suggesting that Aldh1a1 deficiency has minimal impact on retinoic acid signaling.

overall_design: Aldh1a1+/+ and Aldh1a1-/- mice were exposed to naphthalene (4 mg / 100µL corn oil, i.p.) and sacrificed on day 7 and 14. Lung tissues were isolated from two mice per group and enzymatically digested. Extracted and purified total RNA samples were used for RNA-seq analysis.

first: Yasutaka

last: Okabe

first: Noriko

last: Shinjyo


title: Molecular and genetic characterization of sex-linked orange coat color in the domestic cat [C96]

overall_design: Single-cell preparations from fetal cat skin at  late-gestation time points, isolated from male cats with either the ancestral (nonorange) or the derived (orange) Arhgap36 alleles, or from a female cat heterogzygous for both Arhgap36 alleles.


title: Identifying mechanisms for augmenting antitumour efficacy of PD-1 blockade therapy by gut microbiota

city: Kashiwa

first: Hiroyoshi

last: Nishikawa

state: Chiba

address: Kahiwanoha 6-5-1

department: Exploratory Oncology Research & Clinical Trial Center

institute: National Cancer Center

summary: The gut microbiota is related to the antitumour efficacy of immune checkpoint blockade, but the mechanism(s) of action have not been fully elucidated. Here, we show that a novel Ruminococcaceae strain (designated YB328) isolated from the faeces of patients who responded to programmed cell death 1 (PD-1) blockade primes/activates tumour-specific CD8+ T cells through stimulation/maturation of CD103+CD11b- conventional dendritic cells (cDCs) which migrate from the gut to the tumour microenvironment (TME). YB328 administration improved the antitumour efficacy of PD-1 blockade even when it was added to faecal transplantation from non-responder patients in animal models. YB328 promoted the IRF8-driven differentiation of CD103+CD11b- cDCs expressing multiple Toll-like receptors, which received additional stimulation/maturation signals from other bacteria, and the accumulation of these DCs in tumour lesions. These CD103+CD11b- cDCs prolonged engagement with cognate antigen-specific CD8+ T cells, which induced the activation of CD8+ T cells specific for diverse tumour antigens and fostered PD-1 expression through NFATc1 nuclear translocation, thereby leading to an increase in PD-1+CD8+ T cells harbouring a broader T-cell receptor repertoire in the TME. We propose that the gut microbiota augments antitumour immunity by accelerating the differentiation/maturation and migration of DCs to increase CD8+ T cells responding to diverse tumour antigens.

overall_design: RNA-seq profiling of YB328, P. vulgatus-treated and untreated BMDCs.

first: Nina Yi-Tzu

last: Lin


title: Exploring the Role of DNMT1 in RNA m⁵C Methylation (RNA-BS-SEQ DNMT1 knockdown)

first: Guoping

last: Fan

overall_design: HeLa cells were transfected with small interfering RNA (siRNA) targeting DNMT1 using Lipofectamine RNAiMAX (Thermo Fisher Scientific) according to the manufacturer's instructions. For the α-Amanitin treatment, HeLa cells in culture were treated with 15 μg/ml of the RNA polymerase II and III inhibitor α-Amanitin (Santa Cruz) for 12 h. Subsequently, the cells were washed twice with PBS, collected, and processed for RNA-bisulfite sequencing (RNA-BS-seq).

first: Jing

last: Wang

first: Xiaoqian

last: Deng


title: A Dominant mutation in Dnmt1 leads epigenetic changes (Bulk RNAseq)

overall_design: Examination the epigenetic changes and gene expression changes due to Dnmt1 mutation


title: A Dominant mutation in Dnmt1 leads epigenetic changes (scRNAseq and snRNAseq)

summary: We report the application of single cell and single nucleus rna -seq in the prefrontal cortex and retina from the Dnmt1 A560V mice

overall_design: Examination the epigeneitc changes and gene expression changes due to Dnmt1 mutation


title: A Hypothalamic Circuit that Modulates Feeding and Parenting Behaviors

status: Public on May 05 2025

city: Bethesda

first: Ivan

middle: Cedric

last: Alcantara

state: Maryland

address: 10 Center Dr, Room 5-5832

institute: NIDDK

summary: Female lactating mammals undergo many physiological and behavioral changes postpartum to care for newborn offspring and meet the increased caloric demands of milk production. To uncover the neural correlates of these postpartum adaptations, we investigated how gene expression in two hypothalamic regions -- the arcuate nucleus (ARC) and the medial preoptic area (MPOA) -- is regulated by food deprivation and lactation. To this end, we employed 10x Genomics scRNA-seq in the ARC and MPOA of 4 groups of age-matched female mice: sated virgins (VS), fasted virgins (VF), sated mothers (MS), and fasted mothers (MF).

overall_design: 4 groups (sated virgins, fasted virgins, sated lactating mothers, fasted lactating mothers) of 14-week-old female C57BL/6 mice (n = 3 mice pooled per group) were used for scRNA-seq. The litter size for the lactating groups was 8 pups and pups were 13-15 days old at the time of sample collection. The fasted groups were food-deprived overnight for 16-18 hours.

middle: C

first: Laura

middle: E

last: Mickelsen

last: Mazzone

first: Brian

last: Papas

first: Jian-Liang

last: Li

first: Guohong

last: Cui

first: Michael

middle: J

last: Krashes


title: Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation (human cell)

city: Kunming

first: Chao

last: Zhang

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

institute: Chinese Academy of Sciences

summary: ATP-dependent chromatin remodelers establish and arrange nucleosome distribution, modifying accessibility of DNA. Brg1 is exclusive ATPase subunit of mSWI/SNF complex. To understand the dosage dependent function of mSWI/SNF complex. We take an advantage of dTag system to precisely control abundancy of BRG1. We found overall Brg1-binding is sensitive to its abundance nevertheless OCT4-target or H3K27ac region, suggesting Brg1 genome-wide distribution rather than being actively recruited. We also reveal open chromatin dependency on BRG1. The chromatin accessibility of super enhancer shows buffered response on depletion of BRG1, whereas weak enhancer is sensitive. Finally, transcriptomic analysis identified that transcription shows buffered dependencies on BRG1 loss. Overall, our results highlight kinetics differences of BRG1-binding to transcriptome underline BRG1 dosage-sensitive mechanism.

overall_design: To study the kinetics of BRG1 binding, chromatin accessibility, and gene expression, we employed the dTAG system to precisely control Brg1 protein levels in BEAS-2B cell. We then used Cut&Run and ATAC-seq examine the kinetic changes under different Brg1 protein levels.

first: Hagihara

last: Yota

first: Zhang

last: Chao

last: Yi


title: Linear dicentric bacterial chromosomes in Agrobacterium tumefaciens natural isolates reveal common constraints for replicon fusion

city: Bloomington

first: Xindan

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

summary: Multipartite bacterial genome organization can confer advantages including coordinated gene regulation and faster genome replication, but is challenging to maintain. Agrobacterium tumefaciens lineages often contain a circular chromosome (Ch1), a linear chromosome (Ch2), and multiple plasmids. We previously observed that in some stocks of the lab model strain C58, Ch1 and Ch2 were fused into a linear dicentric chromosome. Here we analyzed Agrobacterium natural isolates from the French Collection for Plant-Associated Bacteria (CFBP) and identified two strains with fused chromosomes. Chromosome conformation capture identified integration junctions that were different from the C58 fusion strain. Genome-wide DNA replication profiling showed both replication origins remained active. Transposon sequencing revealed that partitioning systems of both chromosome centromeres were essential. Importantly, the site-specific recombinases XerCD are required for the survival of the strains containing the fusion chromosome. Our findings show that replicon fusion occurs in natural environments and that balanced replication arm sizes and proper resolution systems enable the survival of such strains.

overall_design: Hi-C and whole genome sequencing expriments were performed on environmental isolates of Agrobacterium tumefaciens growing in ATGN minimal medium.