title: Integrated proteomic and multi-mic characterizations of the synapse reveal RNA processing factor and ubiquitin ligases associated with neurodevelopment disorders

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: The molecular composition of the excitatory synapse is incompletely defined due to its dynamic nature across developmental stages and neuronal populations. To address this gap, we apply proteomic mass spectrometry to characterize the synapse in multiple biological models including the fetal human brain and hiPSC-derived neurons. To prioritize the identified proteins, we develop an orthogonal multi-omic screen of genomic, transcriptomic, interactomic, and structural data. This data-driven framework identifies proteins with key molecular features intrinsic to the synapse, including characteristic patterns of biophysical interactions and cross-tissue expression. The integrated proteomic and multi-omic analysis captures synaptic proteins across developmental stages and experimental systems, including 492 proteins that have not been documented previously. We further investigate three such proteins that are associated with neurodevelopmental disorders – the CUL3 E3 ubiquitin ligase, the DDX3X and YBX1 nucleic-acid binding factors – by mapping their networks of physically interacting synapse proteins or transcripts. Our study demonstrates the potential of an integrated multi-omic approach to systematically and more comprehensively resolve the synaptic architecture.

overall_design: Investigation of RNA targets of RNA-binding proteins YBX1 and DDX3X in the human iPSC-derived neurons

first: Yuan

last: Mei

first: Maya

last: Gosztyla

first: Hema

last: Kopalle

first: Xinzhu

last: Tan

first: Lara

middle: E

last: Dozier

first: Brent

last: Wilkinson

first: Justin

last: McKetney

first: John

last: Lee

first: Michael

last: Chen

first: Marina

last: Gritsenko

first: Nicolas

last: Hartel

first: Nicholas

last: Graham

first: Charlotte

last: Curtis

first: Sophie

middle: N

first: Dylan

last: Fong

first: Jing

first: Kate

last: Licon

first: Derek

last: Hong

first: Sarah

last: Wright

first: Jason

last: Kreisberg

first: Alexi

last: Nott

first: Richard

middle: D

last: Smith

first: Wei-Jun

last: Qian

first: Danielle

last: Swaney

first: Lilia

last: Iakoucheva

first: Nevan

last: Krogan

first: Gentry

last: Patrick

first: Yang

last: Zhou

first: Guoping

last: Feng

first: Marcelo

middle: P

last: Coba

middle: W

first: Trey

last: Ideker


title: The CoREST complex inhibitor, corin, leads to decreased tumor growth, increased cellular differentiation and extended lifespan in atypical teratoid rhabdoid tumor xenograft models [ATAC-seq]

status: Public on Mar 27 2025

city: Boston

first: Robert

last: Fisher

state: MA

address: 609 Albany St

department: Dermatology

country: USA

institute: Boston University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Background. Atypical teratoid rhabdoid tumor (ATRT) is the most common malignant brain tumor in infants, and more than 60% of children with ATRT die from their tumor. ATRT is associated with mutational inactivation/deletion of SMARCB1, a member of the SWI/SNF chromatin remodeling complex, suggesting that epigenetic events play a critical role in tumor development and progression. Moreover, disruption of SWI/SNF allows unopposed activity of epigenetic repressors, which contribute to tumorigenicity. We therefore explored the role of the CoREST repressor complex in ATRT. Methods. We evaluated the effects of the bifunctional LSD1/HDAC1/2 small molecule CoREST inhibitor, corin, on ATRT tumor cell growth, apoptosis, differentiation, gene expression and chromatin accessibility. Results. We found that corin inhibited the growth of ATRT cells regardless of their epigenetic subgroup, and was associated with increased tumor cell apoptosis and differentiation. ATAC-seq showed increases in chromatin accessibility in corin-treated ATRT cells, with changes seen at genes associated with neuronal differentiation and synaptic function. RNA-seq confirmed increased expression of neuronal differentiation genes and decreased DNA replication/cell cycle-associated genes in ATRT cells treated with corin. Corin suppressed orthotopic ATRT tumor growth, leading to significant extension of lifespan. In addition, increased histone acetylation (H3K9ac, H3K27ac) and methylation (H3K4Me1) was seen in corin-treated ATRT orthotopic xenografts, consistent with on-target pharmacodynamics. Conclusion. The CoREST inhibitor, corin, suppresses tumor growth, induces differentiation, and promotes apoptosis in ATRT, leading to significantly increased survival of mice bearing ATRT orthotopic xenografts. Our results suggest a potential application of CoREST complex inhibitors in patients with ATRT.

overall_design: 100,000 cells were seeded and treated with corin or DMSO. DNA was extracted, tagmented, purified, and adapter ligated using the ATAC-seq Kit (ActiveMotif #53150) according to the manufacturer’s instructions. Sequencing was done by Azenta Life Sciences (MA, USA), and reads were trimmed using the fastp command in fastp v.0.23.4.

first: Anupa

last: Geethadevi

first: Nikhil

last: Vaidya

middle: J

first: Tyler

last: Findlay

first: Yiming

last: Deng

first: Khoa

last: Pham

first: Vikas

last: Kumar

first: Samuel

last: Beck

first: Lucas

middle: G

last: Calixto-Hope

first: Charles

last: Eberhart

first: Jinchong

last: Xu

first: Philip

middle: A

last: Cole

first: Jeffrey

last: Rubens

first: Marianne

last: Collard

first: Eric

middle: H

last: Raabe

first: Rhoda

middle: M

last: Alani


title: Lung expression data from young and old mice at ZT0 and ZT12

city: Lille

first: Joel

last: Haas

address: 1 Rue du Professeur Calmette

country: France

institute: Institut Pasteur de Lille

summary:
Circadian rhythms control the diurnal nature of many physiological, metabolic and immune processes. Circadian rhythms are tighly controlled by positive and negative transcriptional loops; This circuitry is altered during aging altering tissue daily function.
We used microarrays to detail the global programme of gene expression underlying age-mediated alteration of the transcriptional progarm in lungs.

overall_design: Lungs from 2-month-old and 18-month-old male mice were harvested at ZT0 (light on) and ZT12 (light off). RNA were then extracted and hybridised on a Affymetrix microarrays.

first: Benoit

last: Pourcet

middle: T


title: Phase separation-based screening identifies arsenic trioxide as the N-Myc-DNA interaction inhibitor for neuroblastoma therapy

city: Hangzhou

first: Xuejing

last: Shao

address: 866, Yuhangtang Road

department: Zhejiang University

country: China

institute: College of Pharmaceutical Sciences

type: Expression profiling by high throughput sequencing

summary: Transcription factors (TFs) like N-Myc are crucial in disease including cancer. MYCN amplification is a pivotal biomarker for stratifying high-risk neuroblastoma patients. The difficulty in targeting N-Myc poses a significant challenge for treating high-risk neuroblastoma. Since transcription factors activate transcription by binding to DNA, inhibiting this DNA-binding could disrupt their function and offer a therapeutic approach.  Herein, we develop a high-throughput in vivo model to screen for inhibitors of protein-DNA interaction (PDI), utilizing phase separation and DNA-binding properties. Base on this, we identify arsenic trioxide (ATO) as the first N-Myc-DNA interaction inhibitor. ATO directly binds to N-Myc to disrupt its interaction with DNA, thereby destroying its transcriptional activity and reducing the expression of its target genes. Consistently, ATO significantly inhibits the cell proliferation and clone formation ability of MYCN-amplified neuroblastoma cells. More importantly, we used 5 patient-derived neuroblastoma cells to evaluate the therapy clinical value of ATO. Finally, we found ATO synergizes with the chemotherapy drug cisplatin in treating neuroblastoma in vitro and in vivo. Together, we not only construct a PDI inhibitor screening model for transcriptional factor and uncover ATO as the first DNA binding inhibitor of N-Myc, but also identify ATO as a promising therapeutic regimen for MYCN-amplified neuroblastoma, especially in refractory patients.

overall_design: SK-N-Be(2) cells treated with ATO (2, 4 μM) for 12 h.

first: Meidan

last: Ying

first: Aixiao


title: The gain of function mutation blf13 in the barley orthologue of the rice growth regulator NARROW LEAF1 is associated with increased leaf width.

city: Potsdam

first: Michael

last: Lenhard

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

country: Germany

institute: Universität Potsdam

summary: Canopy architecture in cereals plays an important role in determining yield. The width of leaves represents one key aspect of this canopy architecture. However, our understanding of leaf width control in cereals remains incomplete. Classical mutagenesis studies in barely identified multiple morphological mutants, including those with differing leaf widths. Of these, we characterized the broad leaf13 (blf13) mutant in detail. Mutant plants form wider leaves due to increased post-initiation growth and cell proliferation. The mutant phenotype perfectly co-segregated with a semi-dominant, missense mutation in the HvHNT1 gene which affected a highly conserved region of the encoded protein, orthologous to the rice NARROW LEAF1 (NAL1) protein. Causality of this mutation for the blf13 phenotype is further supported by correlative transcriptomic analyses and protein-protein interaction studies showing that the mutant HvNHT1 protein interacts more strongly with a known interactor than wild-type HvHNT1. The mutant HvHNT1 protein also showed stronger homodimerization compared to wild type HvHNT1homodimerization, with a dimer between mutant and wildtype HvHNT1intermediate. Thus, the blf13 mutation parallels known gain-of-function NAL1 alleles in rice that increase leaf width and grain yield, suggesting the blf13 mutation may have a similar agronomic potential in barley.

overall_design: Differential gene expression analysis between the barley mutants blf13 and nal1 and their wild types Bonus and Sebastian. Three biological replicates each.

first: Moritz

last: Jöst

first: Ouad

last: Soltani

first: Christian

last: Kappel

first: Agnieszka

last: Janiak

first: Beata

last: Chmielewska

first: Miriam

last: Szurman-Zubrzycka

first: Sarah

last: McKim


title: Interleukin-34-dependent perivascular macrophages promote vascular function in the brain [10X_IL34KOandWT_macrophages_vascular_cells]

city: Zurich

first: Hannah

middle: Jade

last: Van Hove

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

summary: The development of most macrophages depends on the colony-stimulating factor 1 (CSF-1) receptor, which has two ligands: CSF-1 and interleukin-34 (IL-34). While IL-34 is required for the homeostasis of microglia, the parenchymal macrophages in the central nervous system (CNS), it is unclear whether brain border-associated macrophages (BAMs) also depend on this cytokine. Here, we demonstrated that the embryonic development of murine BAMs in the choroid plexus, leptomeninges, and perivascular spaces required CSF-1, while IL-34 was critical for their maintenance in adulthood. In the brain, Il34 was expressed by mural cells and perivascular fibroblasts, and its transgenic deletion in these cells interrupted BAM maintenance. Il34-deficiency coincided with transcriptional changes in vascular cells, leading to increased flow velocity and vasomotion in pial and penetrating arterioles. Similarly, Mrc1CreCsf1rfl/fl mice lacking CD206+ perivascular BAMs exhibited increased hemodynamics in arterial networks. These findings reveal a crosstalk between vascular cells and CNS macrophages regulating cerebrovascular function.

overall_design: scRNA-seq of FACS-sorted mural cells (MCs) and fibroblasts (FBs) (CD13+ and/or CD140a+O4- cells), endothelial cells (ECs) (CD31+), astrocytes (AC) (ACSA-2+), BAMs (CD11bhiF4/80+) and microglia (CD11b+F4/80hi) from adult IL34LacZ/+ and IL34LacZ/LacZ mice.


title: Nat10-mediated N4-acetylcytidine modification enhances Nfact1 translation to exacerbate osteoclastogenesis in postmenopausal osteoporosis [acRIP-seq]

city: Guangzhou

first: Yuke

last: Meng

state: Guangdong

address: 1023-1063, South Shatai Road, Baiyun dictrict

institute: Southern Medical University

summary: Increased differentiation or activity of osteoclasts is the key pathogenic factor of postmenopausal osteoporosis (PMOP). N4‐acetylcytidine (ac4C) modification, catalyzed by Nat10, is a novel post-transcriptional mRNA modification related to many diseases. However, its impact on regulating osteoclast activation in PMOP remains uncertain. Here, we initially observed that Nat10-mediated ac4C positively correlates with osteoclast differentiation of monocytes and low bone mass in PMOP. The specific knockout of Nat10 in monocytes and remodelin, a Nat10 inhibitor, alleviates ovariectomized (OVX)-induced bone loss by downregulating osteoclast differentiation. Mechanistically, epitranscriptomic analyses reveal that the nuclear factor of activated T cells cytoplasmic 1 (Nfatc1) is the key downstream target of ac4C modification during osteoclast differentiation. Subsequently, translatomic results demonstrate that Nat10-mediated ac4C enhances the translation efficiency of Nfatc1, thereby inducing Nfatc1 expression and consequent osteoclast maturation. Cumulatively, these findings reveal the promotive role of Nat10 in osteoclast differentiation and PMOP from a novel field of RNA modifications and suggest that Nat10 can be a target of epigenetic therapy for preventing bone loss in PMOP.

overall_design: To investigate the role of NAT10-mediated ac4C modification in osteoclastogenesis, we utilized acRIP-seq to detect differences in osteoclast differentiation between WT and Nat10 conditional knockout mice BMDMs.

first: Zhongmin

last: Zhang


title: Nat10-mediated N4-acetylcytidine modification enhances Nfact1 translation to exacerbate osteoclastogenesis in postmenopausal osteoporosis [RNA-seq]

summary: Increased differentiation or activity of osteoclasts is the key pathogenic factor of postmenopausal osteoporosis (PMOP). N4-acetylcytidine (ac4C) modification, catalyzed by Nat10, is a novel post-transcriptional mRNA modification related to many diseases. However, its impact on regulating osteoclast activation in PMOP remains uncertain. Here, we initially observed that Nat10-mediated ac4C positively correlates with osteoclast differentiation of monocytes and low bone mass in PMOP. The specific knockout of Nat10 in monocytes and remodelin, a Nat10 inhibitor, alleviates ovariectomized (OVX)-induced bone loss by downregulating osteoclast differentiation. Mechanistically, epitranscriptomic analyses reveal that the nuclear factor of activated T cells cytoplasmic 1 (Nfatc1) is the key downstream target of ac4C modification during osteoclast differentiation. Subsequently, translatomic results demonstrate that Nat10-mediated ac4C enhances the translation efficiency of Nfatc1, thereby inducing Nfatc1 expression and consequent osteoclast maturation. Cumulatively, these findings reveal the promotive role of Nat10 in osteoclast differentiation and PMOP from a novel field of RNA modifications and suggest that Nat10 can be a target of epigenetic therapy for preventing bone loss in PMOP.

overall_design: To investigate the role of NAT10-mediated ac4C modification in osteoclastogenesis, we utilized mRNA-seq to detect differences in osteoclast differentiation between WT and Nat10 conditional knockout mice BMDMs.


title: Nat10-mediated N4-acetylcytidine modification enhances Nfact1 translation to exacerbate osteoclastogenesis in postmenopausal osteoporosis

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

overall_design: Refer to individual Series


title: Chromatin Modification Abnormalities by CHD7 and KMT2C Loss Promote Medulloblastoma Progression [scRNA-seq]

status: Public on Mar 30 2025

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

country: Japan

institute: Japanese Foundation for Cancer Research

summary: Medulloblastoma, a common malignant pediatric brain tumor that typically originating from the cerebellum, is characterized by mutations in chromatin modifiers, highlighting the significance of epigenomic abnormalities in their progression. To prove this significance, the development and use of animal models that closely recapitulate the disease have been highly effective. However, due to substantial time and cost limitations of developing genetically engineered mouse models, a complete understanding of the oncogenic potential of chromatin modifiers’ mutations found in human medulloblastomas is still elusive. In this study, we address this by CRISPR-mediated gene editing platform to knock out chromatin modifiers mutated human in SHH-subgroup medulloblastoma as well as the Ptch1 gene in cerebellar granule neuron progenitors. We functionally screened molecules involved tumor formation, identifying CHD7 and KMT2C as tumor suppressor genes. Multi-layered omics analysis revealed that these molecules epigenetically regulate the expression of Neurod1 that encodes a transcription factor crucial for neuronal differentiation, through histone H3 modification. Mutations impairing these factors suppress Neurod1, accelerating tumor growth. Conversely, forced expression of Neurod1 inhibits proliferation and promotes differentiation, underscoring its role as a key regulator in medulloblastoma aggressiveness. These findings not only demonstrate converging epigenomic abnormalities in SHH-subgroup medulloblastoma but also hold significant potential for evaluating epigenetic drugs targeting medulloblastoma, advancing the development of novel treatments.

overall_design: 10X Chromium Single-Cell Gene Expression for mouse medulloblastoma GEMM model (double knockout)

first: Wanchen

last: Wang

first: Reo

last: Maruyama

first: Daisuke

last: Kawauchi


title: UUO-rUUO single population RNA seq, Denby lab 2019

city: Edinburgh

first: Laura

last: Denby

state: Midlothian

address: Queen's Medical Research Institute, 47 Little France Cres

country: United Kingdom

institute: University of Edinburgh

summary: RNA sequencing of sorted cell types, isolated from mice kidneys, after unilateral ureteral obstructive (UUO) surgery after 2 days, 7 days and a reversible (rUUO) 14 day model with corresponding sham operated mice. The goal of the study was to identify temporal gene expression changes in different cell types corresponding with kidney injury, in order to understand cell specific transcriptomic changes in the context of kidney injury and repair.

overall_design: Each group was sequenced from 4 mice, and 4 cell types. 2 day UUO kidneys were sorted into PDGFRβ+, F480+, LTL+ and CD31+ cell types before the RNA was extracted and small RNA sequenced for 4 mice. The same protocol was followed for 7 day UUO mice, rUUO mice, as well as sham operated mice for reference.

first: Oliver

last: Teenan

first: Katie

last: Connor

first: James

last: O'Sullivan


title: Daily lung expression data from young and old mice

first: Joel

last: Haas

summary: Circadian rhythms control the diurnal nature of many physiological, metabolic and immune processes. Circadian rhythms are tighly controlled by positive and negative transcriptional loops; This circuitry is altered during aging altering tissue daily function.

overall_design: Lungs from 2-month-old and 22-month-old male mice were perfused with PBS and harvested every 4 hours from ZT0 (Light onn) to ZT24 with ZT12 corresponding to light off.

first: Benoit

last: Pourcet

first: Jimmy

last: Vandel

first: Marie

last: Fourcot


title: Stromal lipid species dictate melanoma metastasis and tropism [MeWo_RNA_seq]

status: Public on Mar 26 2025

city: Manchester

first: Amaya

last: Viros

address: Wilmslow Road

department: Skin Cancer Ageing

institute: Cancer Research UK

summary: Cancer cells adapt to signals in the tumor microenvironment (TME), but the TME cues that impact metastasis and tropism are unknown. We show that stromal lipids from young adipocytes are taken up by melanoma cells, and lipids increase melanoma oxidative phosphorylation (OXPHOS) and oxidative stress, which decreases metastatic burden. In contrast, the aged TME provides fewer lipids, leading to lower OXPHOS and higher metastatic capacity. Young adipocytes transfer phosphatidylcholine (PC) to melanoma cells, where PC upregulates PI3K/AKT and mitochondrial OXPHOS. Melanoma cells with high OXPHOS predominantly seed the lung and brain, but do not colonise the liver, and decreasing oxidative stress with antioxidant supplements shifts tropism from the lung to the liver. In contrast, although the aged stroma has fewer total lipids, it has more ceramides, which activate the S1P/STAT3/IL6 signalling axis to direct melanoma liver tropism. Inhibiting OXPHOS in the young stroma and blocking IL6 receptor in the aged stroma reduces the age-specific patterns of metastasis imposed by stromal lipids.

overall_design: RNA sequencing of MeWo cells exposed to serum free (control), old adipocytes secretome (OA) and young adipocyte secretome (YA). All treated for 24 hours.

last: Virós

first: Shilpa

last: Gurung

first: Fabio

last: Amaral


title: Stromal lipid species dictate melanoma metastasis and tropism [A375_RNA_seq]

overall_design: RNA sequencing of A375 cells exposed to serum free (control), old adipocytes secretome (OA) and young adipocyte secretome (YA). All treated for 24 hours.


title: SIRT1-FOXO3 Pathway reprograms fatty acid metabolism to Mitigate Ferroptosis and Fibrosis

first: haixia

last: chen

state: Zhejiang

address: Research Building, School of Medicine, Zijingang Campus, Zhejiang University

institute: epartment of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine

summary: Targeting ferroptosis with reductive agents has emerged as a promising strategy to mitigate fibrotic diseases in various pathological conditions. However, while the NAD+/NADH redox pair plays a crucial role in biological processes, its connection to ferroptosis beyond FSP1 remains poorly understood. To explore underappreciated NAD+/NADH-dependent factors in the ferroptosis cascade, we conducted a compound screening of 138 NAD+ enzyme modulatory molecules and identified Sirtuin-1 (SIRT1) activators as critical regulators of ferroptosis. SIRT1 activators, such as SRT1720, broadly inhibit ferroptosis by reducing lipid peroxidation without affecting labile iron levels. Moreover, SRT1720 effectively alleviates pulmonary and liver fibrosis in mouse models. Using ChIP-seq and validation assays, we demonstrated that FOXO3 binds to gene loci involved in fatty acid elongation and arachidonic acid metabolism in ferroptosis. SRT1720 disrupts this binding, thereby restraining fatty acid metabolism and limiting lipid peroxides production. Our findings establish the SIRT1-FOXO3 axis as a key inhibitory pathway against ferroptosis and highlight its therapeutic potential for ferroptosis-associated diseases, including fibrosis.

overall_design: RNA-seq data of CTL, RSL3 and RSL3+SRT in MEFs

first: Haixia

last: Chen

first: Yanqi

last: Guo

first: Ruixin

last: Jia

first: Xinwei

last: Geng

first: Fang

last: Ji

first: Fei

last: Li

first: Dongyu

first: Gaoying

first: Xinyi

first: Beibei

last: Sun

first: Jiaqi

last: Huang

first: Yuejue

first: Qian

last: Wu

first: Wen

first: Songmin

last: Ying


title: Time series analysis of transcriptomic responses to iron and zinc stress in Sorghum

city: Cold Spring Harbor

first: Sunita

last: Kumari

state: New York

address: One Bungtown Road

institute: Cold Spring Harbor Lab

summary: Micronutrient stress impacts growth, biomass production, and grain yield in crops. Multi-omics studies are valuable resources for identifying genes for functional studies for trait improvement such as accumulation of Fe or Zn under deficient or excess conditions for bioenergy or grain agriculture. We conducted transcriptomics and ionomics analyses on Sorghum bicolor BTx623, grown under Fe and Zn limiting and excess conditions over a 21-day time-period. To identify early and late transcriptional response in roots and leaves, 180 RNAseq libraries were sequenced for differential expression and coexpression network analyses. Fe and Zn accumulation was measured using ICP-MS at each time point and a fluorometer was used to estimate chlorophyll content in leaves. Among the four treatments, Fe limiting and Zn excess resulted in the largest phenotypic effects and transcriptional response in roots and leaves.

overall_design: Sorghum seedlings were  grown in a hydroponic growth system for one week and then transplanted into modified Hoagland’s solution for acclimation. After three-week acclimation in hydroponics, seedlings were randomized and transplanted into modified Hoagland’s solutions with different zinc sulphate and ferric sodium  EDTA concentrations for low, medium and high iron and zinc stress treatments. For RNA tissue sampling, leaf and root samples were collected from three individual plants to represent three biological replicates. Root tissues were sampled at 7 time points starting from untreated control and after individual stress treatments on 1hour, 2 days, 4 days, 7 days, 14 days, and 21 days for each low, medium and high iron and zinc stress treatments. Leaf discs were sampled from the young leaf from the same plant at 6 time points starting from untreated control and 2 days, 4 days, 7 days, 14 days, and 21 days after individual stress treatments of iron and zinc stress.

first: Ankita

last: Mishra

first: Aditi

last: Bhat

first: Reena

last: Sharma

first: Janeen

last: Braynen

first: Dimiru

last: Tadesse


title: TOP2B is required for compartment strength changes upon retinoic acid treatment in SH-SY5Y cells

city: Worcester

first: Job

last: Dekker

address: 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School/HHMI

summary: DNA topoisomerase II beta (TOP2B), is required for correct execution of certain developmental transcriptional programs and for signal-induced transcriptional activation, including transcriptional activation by nuclear hormone ligands such as retinoic acid. In addition, TOP2B is enriched at genomic locations occupied by CTCF and cohesin (RAD21) suggesting a role in chromosome looping and/or establishing or maintaining aspects of chromosome 3D structure. This led us to investigate the effect of TOP2B inactivation on patterns of intra- and inter- chromosomal interaction that reflect the higher-level 3D architecture of the genome. Using the retinoic acid responsive SH-SY5Y neuroblastoma cell line model, we had previously demonstrated a large number of gene expression changes upon retinoic acid treatment and upon depletion of TOP2B. However, we report here that these expression changes are accompanied by only subtle changes in chromosome organization. While there was no evidence for changes in cohesin loops or topologically associating domains, lack of TOP2B did affect compartment strength changes that occur upon ATRA treatment.

overall_design: Hi-C experiments in SH-SY5Y cell line before and after 5 days of ATRA induced differentiation, with or without TOP2B KO, 2 replicates of each condition.

first: Erica

last: Hildebrand

first: Ian

last: Cowell

first: Mushtaq

last: Khazeem

first: Snehal

last: Sambare

first: Ozgun

last: Uyan

first: Caroline

last: Austin


title: Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force-responsive genes. FAC sorted tenocytes from 36 hpf vs. 48 hpf zebrafish embryos bulk RNAseq dataset

city: Irvine

first: Pavan

last: Nayak

address: 4462 Natural Sciences 2

institute: UC Irvine

summary: Mechanical forces play a critical role in tendon development and function, influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix (ECM) remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome-wide bulk RNA sequencing of FAC-sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction.

overall_design: FAC sorted mCherry+ cells from 36 hpf and 48 hpf Tg(scxa:mCherry) zebrafish embryos, labeling tendon fibroblasts (tenocytes). 36 hpf embryos have not yet begun active muscle contraction, and 48 hpf embryos are freely swimming, indicating active muscle contraction onset.

middle: K

first: Arul

last: Subramanian

first: Thomas

middle: F

last: Schilling


title: Mycobacterium tuberculosis MutT4 is an RNA pyrophosphohydrolase that forms biomolecular condensates and sensitizes mRNAs to degradation

first: Junpei

last: Xiao

address: 100 Institute Rd

institute: Worcester Polytechnic Institute

summary: Bacterial adaptation to stress involves changes in transcription and mRNA degradation rates. In Escherichia coli, the Nudix hydrolase RppH initiates mRNA degradation by removing pyrophosphate from mRNA 5’-ends, converting 5’-triphosphates to 5’-monophosphates. We aimed to identify the RppH homolog in the globally important pathogen Mycobacterium tuberculosis (Mtb). We deleted each non-essential Nudix gene from Mtb to determine their impacts on mRNA 5’-phosphorylation. Deletion of mutT4 (Rv3908) increased the relative abundance of 5’-triphosphates on myriad mRNAs across the transcriptome. Purified MutT4 converted mRNA 5’-triphosphates into monophosphates, and stimulated degradation by RNase E and RNase J. MutT4 has intrinsically disordered regions (IDRs), a common domain for biomolecular condensate formation. Microscopy showed that MutT4 forms condensates that dissociate upon addition of rifampicin, and that the N-terminal IDR is sufficient for condensate formation. These MutT4 condensates localize with RNase E and RNase J. Deletion of mutT4 in Mtb leads to a higher outer membrane permeability and resistance to oxidative stress. We conclude that MutT4 is the RppH of Mtb, assembling in condensates that may act as degradation hubs. Our data indicate that MutT4 is unlikely to participate in DNA repair or nucleotide pool cleansing, and as such would more accurately be called RppH.

overall_design: The mutT4 gene of M. tuberculosis strain mc26030 (H37Rv ΔRD1 ΔpanCD) was partially replaced by a zeocin resistance gene by recombineering. Care was taken to disrupt the function of mutT4 without disrupting adjacent genes. The deletion strain was complemented by integration of a plasmid containing mutT4 with its native promoter and 5' UTR into the Giles phage integration site. Triplicate cultures of the parental, deletion, and complemented strains strains were grown to log phase in 7H9 media supplemented with OADC (0.05 g/L oleic acid, 5 g/L bovine serum albumin fraction V, 2 g/L glucose, 0.85 g/L NaCl, and 4 mg/L catalase), 0.2% glycerol, 0.05% Tween 80, and 24 μg/mL pantothenate. RNA was harvested and rRNA was depleted as described in (Culviner, P.H., Guegler, C.K. and Laub, M.T. (2020) A simple, cost-effective, and robust method for rRNA depletion in RNA-sequencing studies. MBio, 11, 10.1128/mbio. 00010-00020.). Samples were then treated with E. coli RppH or mock-treated, and 5'-end directed RNAseq libraries were constructed as described (Martini, M.C., Sun, H. and Shell, S.S. (2021) RNA Sequencing for Transcript 5'-End Mapping in Mycobacteria. Methods Mol Biol, 2314, 513-531).

first: Juan Hilario

last: Cafiero

first: Irene

last: Lepori

first: Abigail

middle: R

last: Rapiejko

first: Manchi

last: Reddy

first: Louis

last: Roberts

first: M Sloan

last: Siegrist

first: James

middle: C

last: Sacchettini

first: Scarlet

middle: S

last: Shell


title: Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force-responsive genes. FAC sorted tenocytes from 48 hpf zebrafish embryos WT vs. aBTX injected paralyzed bulk RNAseq dataset

overall_design: FAC sorted mCherry+ cells from uninjected control 48 hpf and aBTX (alpha-bungarotoxin) injected paralyzed 48 hpf Tg(scxa:mCherry) zebrafish embryos, labeling tendon fibroblasts (tenocytes).


title: Human Induced Pluripotent Stem Cells derived Neutrophils Display Strong Anti-microbial Potencies

first: Xing

last: Hu

institute: GIBH

summary: Neutrophils are essential innate immune cells with unusual anti-microbial properties while dysfunctions of neutrophils lead to severe health problems such as lethal infections. Generation of neutrophils from human induced pluripotent stem cells (hiPSCs) is highly promising to produce off-the-shelf neutrophils for transfusion therapies. However, the anti-microbial potencies of hiPSCs derived neutrophils (iNEUs) remain less documented. Here, we develop a scalable approach to generate iNEUs in a chemical defined condition. iNEUs display typical neutrophil characters in terms of phagocytosis, migration, formation of neutrophil extracellular traps (NETs), etc. Importantly, iNEUs display a strong killing potency against various bacteria such as K.pneumoniae, P.aeruginosa, E.coli and S.aureus. Moreover, transfusions of iNEUs in mice with neutrophil dysfunction largely enhance their survival in lethal infection of different bacteria. Together, our data show that hiPSCs derived neutrophils hold strong anti-microbial potencies to protect severe infections under neutrophil dysfunction conditions.

overall_design: We compared the transcriptome of   peripheral blood derived neutrophils and iPSCs derived neutrophils by RNA-Seq

first: Yanling

last: Zhu

first: Huaisong

last: Lin

first: Guangjin

last: Pan

first: Baoqiang

last: Kang


title: Stromal lipid species dictate melanoma metastasis and tropism [MFP_RNA_seq]

first: Amaya

last: Viros

overall_design: RNA sequencing of c57bl/6j female mammary fat pads of young (8 weeks) and aged (14 months) animals.

last: Virós

first: Shilpa

last: Gurung

first: Fabio

last: Amaral


title: HINT1 Aggravates Aortic Aneurysm by Targeting ITGA6/FAK Axis in Vascular Smooth Muscle Cells

city: Nanjing

first: Wencheng

last: Wu

address: Longmian Street

institute: Nanjing Medical University

summary: We analyzed differentially expressed genes in mouse aortic smooth muscle cells (MASMCs)  from wild-type or Hint1-/- mice treated with 20ng/ml PDGF-BB for 24h to explore the mechanism that HINT1 triggers VSMC phenotypic switching.

overall_design: Identification of differentially expressed genes in MASMCs from wild-type or Hint1-/- mice treated with 20ng/ml PDGF-BB for 24h (n=4 per group).

first: Yan

last: Zhang

first: Xuehui

last: Yang

first: Shanshan

last: Luo

first: Yong

last: Ji


title: Inhalable Stem Cell Exosomes Promote Heart Repair After Myocardial Infarction

city: New York

first: Ke

last: Cheng

state: NY

address: 3960 Broadway

institute: Columbia University

summary: Abstract  BACKGROUND:  Exosome therapy shows potential for cardiac repair after injury. However, intrinsic challenges such as short half-life and lack of clear targets hinder the clinical feasibility. Here, we report a noninvasive and repeatable method for exosome delivery through inhalation after myocardial infarction (MI), which we called stem cell–derived exosome nebulization therapy (SCENT). METHODS:  Stem cell–derived exosomes were characterized for size distribution and surface markers. C57BL/6 mice with MI model received exosome inhalation treatment through a nebulizer for 7 consecutive days. Echocardiographies were performed to monitor cardiac function after SCENT, and histological analysis helped with the investigation of myocardial repair. Single-cell RNA sequencing of the whole heart was performed to explore the mechanism of action by SCENT. Last, the feasibility, efficacy, and general safety of SCENT were demonstrated in a swine model of MI, facilitated by 3-dimensional cardiac magnetic resonance imaging. RESULTS:  Recruitment of exosomes to the ischemic heart after SCENT was detected by ex vivo IVIS imaging and fluorescence microscopy. In a mouse model of MI, SCENT ameliorated cardiac repair by improving left ventricular function, reducing fibrotic tissue, and promoting cardiomyocyte proliferation. Mechanistic studies using single-cell RNA sequencing of mouse heart after SCENT revealed a downregulation of Cd36 in endothelial cells (ECs). In an EC-Cd36fl/− conditional knockout mouse model, the inhibition of CD36, a fatty acid transporter in ECs, led to a compensatory increase in glucose utilization in the heart and higher ATP generation, which enhanced cardiac contractility. In pigs, cardiac magnetic resonance imaging showed an enhanced ejection fraction (Δ=11.66±5.12%) and fractional shortening (Δ=5.72±2.29%) at day 28 after MI by SCENT treatment compared with controls, along with reduced infarct size and thickened ventricular wall. CONCLUSIONS:  In both rodent and swine models, our data proved the feasibility, efficacy, and general safety of SCENT treatment against acute MI injury, laying the groundwork for clinical investigation. Moreover, the EC-Cd36fl/− mouse model provides the first in vivo evidence showing that conditional EC-CD36 knockout can ameliorate cardiac injury. Our study introduces a noninvasive treatment option for heart disease and identifies new potential therapeutic targets.

overall_design: To characterize gene expression changes underlying the treatment efficacy of SCENT in MI mice, we performed droplet-based single-cell RNA sequencing on whole mouse hearts from the treatment group and control group

first: Junlang

last: Li

first: Shenghuan

last: Sun

first: Atul

last: Butte


title: Multi-omics analysis reveals Jianpi formula-derived bioactive peptide-YG-22 potentially inhibited colorectal cancer via regulating epigenetic reprogram and signal pathway regulation [ChIP-Seq]

city: Shanghai

first: Baohui

last: Han

address: 227 South Chongqing Road

department: Department of Respiratory and Critical Care Medicine

institute: Shanghai Chest Hospital

summary: Colorectal cancer (CRC) is a prevalent malignancy worldwide, often treated with chemotherapy despite its limitations, including adverse effects and resistance. Chemotherapy combined with the traditional Chinese medicine (TCM) Jianpi formula has been demonstrated to improve efficacy. In this study, we aim to screen bioactive peptides derived from the blood of CRC patients through peptidomics and explore the molecular mechanisms of the candidate peptides in HCT116 cells using multi-omics analysis. Differential peptides were identified in plasma samples from patients treated with chemotherapy alone and those receiving the combined therapy. Among these, YG-22 exhibited the strongest cytotoxic effect on HCT116 cells, reducing viability in a dose- and time-dependent manner. Transcriptome analysis highlighted the modulation of key pathways involved in lysosome-mediated degradation and apoptosis, while metabolomic profiling indicated disruptions in tumor-supportive metabolic pathways. Additionally, chromatin accessibility and histone modifications suggested epigenetic reprogramming induced by YG-22. These findings demonstrate that combining chemotherapy with TCM enriches the molecular landscape and generates bioactive peptides with strong antitumor activity. Furthermore, this study also lays the foundation for further development of peptide-based therapies and highlights the value of combining traditional and modern therapeutic strategies for CRC management.

overall_design: For treatment group, the HCT116 cells were incubated with YG-22 (1.769 mg/mL) for 48 hours. For control group, the HCT116 cells were incubated with normal medium for 48 hours. 1 × 10⁵ HCT116 cells for each group were collected for ChIP-seq. ChIP-seq analysis for H3K4Me3 profiling and NF-κB protein-DNA interactions was conducted using a combination of chromatin immunoprecipitation and high-throughput sequencing. HCT116 cells (5 × 106) were fixed with 1% formaldehyde to crosslink proteins and DNA, followed by quenching with glycine and lysis to isolate chromatin. The chromatin was sonicated to fragment DNA, and immunoprecipitation was performed using specific antibodies for H3K4Me3 and NF-κB, coupled with Protein A+G magnetic beads. The immunoprecipitated complexes were reverse crosslinked, and DNA was purified. High-throughput sequencing libraries were prepared through end repair, A-tailing, adapter ligation, and PCR amplification, targeting fragment sizes of 100-300 bp. Sequencing was performed on the Illumina NovaSeq 6000 platform.

first: Jun

last: Lu

first: Qin

last: Shi


title: Multi-omics analysis reveals Jianpi formula-derived bioactive peptide-YG-22 potentially inhibited colorectal cancer via regulating epigenetic reprogram and signal pathway regulation [RNA-Seq]

overall_design: For treatment group, the HCT116 cells were incubated with YG-22 (1.769 mg/mL) for 48 hours. For control group, the HCT116 cells were incubated with normal medium for 48 hours. 1 × 10⁵ HCT116 cells for each group were collected for RNA-seq. Total RNA is extracted using RNA isolation kit (Qiagen, Germany) following the manufacturer's instructions. Total RNA samples were prepared with an initial concentration of at least 20 ng/μL and a total quantity of at least 2 μg, ensuring an A260/A280 ratio between 1.9 and 2.1 for quality control. mRNA was isolated using oligo-dT beads to capture polyA-tailed transcripts, followed by thermal fragmentation into 200-300 bp fragments. Reverse transcription was performed using a strand synthesis master mix to generate cDNA. Library preparation involved end-repair, A-tailing, and ligation of sequencing adapters, followed by PCR amplification and size selection for fragments of 300-400 bp, including adapter sequences. The prepared libraries underwent high-throughput sequencing on the Illumina NovaSeq 6000 platform, producing comprehensive transcriptomic data for downstream bioinformatics analysis.


title: Host immune response in brains of mouse model of cryptococcal post-infectious inflammatory response syndrome (cPIIRS), cPIIRS mice treated with Ruxolitinib, and naïve control mice

city: Bethesda

first: Jessica

middle: Caroline

last: Hargarten

state: MD

address: 10 Center Drive

department: LCIM

institute: NIAID/NIH

summary:
Transcriptional profiling of host immune response in brains of mouse model of cryptococcal post-infectious inflammatory response syndrome (cPIIRS), cPIIRS mice treated with Ruxolitinib, and naïve control mice using the NanoString nCounter Mouse Neuroinflammation Panel v1.0.
NanoString nCounter assay was performed to measure the expression of neuroinflammatory genes in the brains of cPIIRS mice (C57BL/6Tac, 21 day post-infection) compared to cPIIRS mice treated with Ruxolitinib, and naïve mice.

overall_design: In this study, RNA was isolated from whole brains of cPIIRS mice (female C57BL/6Tac, 21 day post-infection), cPIIRS mice treated with Ruxolitinib (female C57BL/6Tac, 21 day post-infection, 1 g/kg in Nutragel diet per day), and naïve mice (female C57BL/6Tac) and the expression of 757 genes was measured.

first: Peter

last: Williamson


title: A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression,

city: Cincinnati

first: Anne

last: Slavotinek

state: OH

address: 3333 Burnet Ave, Room E5.253

institute: Cincinnati Children's Hospital Medical Center

summary: We c ompared gene expression in dissected whole eyes from crim1-/- zebrafish compared to wildtype contros at 72 hpf.  This work will be published as Le et al., 2025: A zebrafish model of crim1 loss of function has small and misshapen lenses with dysregulated clic4 and fgf1b expression. Heterozygous deletions predicting haploinsufficiency for the Cysteine Rich Motor Neuron 1 (CRIM1) gene have been identified in two families with macrophthalmia, colobomatous, with microcornea (MACOM), an autosomal dominant trait. Crim1 encodes a type I transmembrane protein that is expressed at the cell membrane of lens epithelial and fiber cells at the stage of lens pit formation. Decreased Crim1 expression in the mouse reduced the number of lens epithelial cells and caused defective adhesion between lens epithelial cells and between the epithelial and fiber cells. We present three patients with heterozygous deletions and truncating variants predicted to result in haploinsufficiency for CRIM1 as further evidence for the role of this gene in eye defects, including retinal coloboma, optic pallor, and glaucoma. We used Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 to make a stable Danio rerio model of crim1 deficiency, generating zebrafish that were homozygous for a 2 basepair deletion, c.339_340delCT p.Leu112Leufs*3, in crim1. Homozygous, crim1-/- larvae demonstrated smaller eyes and small and misshapen lenses compared to controls, but we did not observe colobomas. Bulk RNA-Seq using dissected eyes from crim1-/- larvae and controls at 72 hours post fertilization showed significant downregulation of crim1 and chloride intracellular channel 4 (clic4) and upregulation of fibroblast growth factor 1b (fgf1b) and complement component 1, q subcomponent (c1q), amongst other dysregulated genes. Our work strengthens the association between haploinsufficiency for CRIM1 and eye defects and characterizes a stable model of crim1 loss of function for future research.

overall_design: We c ompared gene expression in dissected whole eyes from crim1-/- zebrafish compared to wildtype contros at 72 hpf. Wildtype and crim1-/- have two replicates.

first: Baranzini

last: Sergio

first: Yihui

first: Slavotinek

last: Anne


title: Spatial Metabolomics Reveals Metabolic reprogramming dynamics during ductal carcinoma in situ progression to invasive ductal carcinoma

city: Chengdu

first: Hong

last: Chen

state: Sichuan

address: Keyuan South Road

institute: West China Hospital, Sichuan University

summary: Elucidating the progression mechanism from ductal carcinoma in situ (DCIS), a non-obligate precursor of invasive ductal carcinoma (IDC), remains a critical challenge in oncology. Metabolic profiling of lesions with differential invasiveness may help reveal key drivers underlying DCIS progression. This study employed mass spectrometry imaging to delineate the small-molecule metabolic profiles of DCIS, DCIS with synchronous IDC, and IDC lesions. Key metabolic alterations driving DCIS-to-IDC progression were identified, including elevated fatty acid biosynthesis in tumor tissues. Comparative analyses revealed that IDC exhibited significantly higher accumulation of polyunsaturated fatty acids (PUFAs) than DCIS (P<0.05), consistent with immunohistochemical validation showing upregulated fatty acid desaturase 2 expression in IDC. DCIS lesions predominantly accumulated phosphatidylinositols with saturated/monounsaturated acyl chains, while IDC exhibited a marked enrichment of phosphatidylinositols with PUFA (P<0.01). Furthermore, IDC showed significantly reduced levels of antioxidant molecules (taurine, ascorbic acid, glutathione) and the detoxification enzyme glutathione S-transferase mu 2 compared to DCIS (P<0.05), indicating dysregulation of redox homeostasis. Strikingly, DCIS with synchronous IDC displayed metabolic signatures closely aligned with IDC, suggesting its role as a transitional state during malignant progression. These findings indicate that DCIS malignant progression exhibits metabolic dependency on PUFAs/phosphatidylinositols with PUFA and depletion of antioxidants. Therapeutic targeting of PUFA biosynthesis or redox homeostasis regulators may offer novel translational approaches for tracking and intercepting DCIS progression.

overall_design:
This study included 5 IDC, 5 DCIS, 5 DCIS with coexisting IDC, 5 DCIS with microinvasion, and 5 distant surrounding tissues (DSTs; >5 cm from tumor bed). These samples were collected from West China Hospital, Sichuan University between November 2020 to December 2021. All patients had no evidence of distant metastasis and did not receive neoadjuvant therapy.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
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title: SIRT1-FOXO3 Pathway reprograms fatty acid metabolism to Mitigate Ferroptosis and Fibrosis [ChIP-seq]

first: haixia

last: chen

overall_design: ChIP-seq data of CTL, RSL3 and RSL3+SRT in HT1080

first: Haixia

first: Yanqi

last: Guo

first: Ruixin

last: Jia

first: Xinwei

last: Geng

first: Fang

first: Fei

first: Dongyu

first: Gaoying

first: Xinyi

first: Beibei

first: Jiaqi

last: Huang

first: Yuejue

last: Wang

first: Qian

last: Wu

first: Wen

first: Songmin

last: Ying


title: Multi-omics analysis reveals Jianpi formula-derived bioactive peptide-YG-22 potentially inhibited colorectal cancer via regulating epigenetic reprogram and signal pathway regulation [ATAC-seq]

first: Baohui

last: Han

overall_design: For treatment group, the HCT116 cells were incubated with YG-22 (1.769 mg/mL) for 48 hours. For control group, the HCT116 cells were incubated with normal medium for 48 hours. 1 × 10⁵ HCT116 cells for each group were collected for ATAC-seq. HCT116 cells (5 × 10⁵) to isolate nuclei using a lysis buffer containing RSB, NP-40, Tween-20, and digitonin, followed by centrifugation to remove supernatant. The isolated nuclei are treated with a transposase mix containing Tn5 transposase at 37°C for 30 minutes to fragment accessible chromatin regions and insert sequencing adapters. The DNA is then purified using MinElute kits (Qiagen, Germany) and subjected to PCR amplification to optimize library quality, with purified libraries dissolved in 10 mM Tris buffer. Following library preparation, high-throughput sequencing is conducted using the Illumina NovaSeq 6000 platform.

first: Jun

first: Qin


title: Towards an integrated cellular and molecular classifier for glioblastoma

city: Philadelphia

first: Dana

last: Silverbush

state: PA

address: 421 curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

type: Methylation profiling by genome tiling array

summary: The recognition of tumor heterogeneity has highlighted the necessity of examining tumor samples through the lens of single-cell genomics. In glioblastoma (GBM), a highly heterogeneous tumor, single-cell analysis is critical to assist in assessing tumor composition and in the longitudinal analysis of response to therapies. However, single-cell genomic approaches face practical challenges for broad implementation, underscoring the importance of developing deconvolution methods that may assist in the interpretation of bulk profiles and can be deployed at scale. Bulk DNA methylation data, a stable and widely used diagnostic tool in gliomas and central nervous system tumors, provides a promising substrate for deconvolution. However, the limited availability of cell state-specific references in DNA methylation, coupled with low-coverage single-cell DNA methylation data, poses significant challenges. We present a hierarchical non-negative matrix factorization approach to deconvolute bulk DNA methylation profiles, initially resolving cell types and subsequently refining cell states within a cell type. By integrating multi-omics single-cell data, we mapped DNA methylation components to their transcriptional counterparts, enabling accurate predictions of transcriptional cellular composition from bulk DNA methylation. This methodology allows the decomposition of GBM bulk DNA methylation into glial, immune, neuronal, and malignant cell types, with further distinction into malignant stem-like and malignant differentiated cell states. Our findings reveal that low cancer cell fractions can distort classification, prompting the development of an in-silico purification method to enhance diagnostic accuracy. Additionally, we provide a framework to assist in quantifying the influences of the immune micro-environment on GBM bulk classification, unmasking the underlying genetic heterogeneity and tumor subtype. Our work provides a blueprint to reconcile DNA methylation, bulk transcription-based and single-cell classifications of GBM.

overall_design: Illumina Infinium MethylationEPIC (850K)  for 11 samples of 9 GBM tumors. Out of the 11 samples 4 are FFPE and 7 Fresh, for two tumors we sequenced matched FFPE and Fresh tissue.

first: Liv

last: Jürgensen

first: Channing

last: Pooley

first: Fabio

last: Boniolo

first: Federico

last: Gaiti

first: Mario

middle: L

last: Suvà

first: Volker

last: Hovestadt


title: Estrogen-induced circFAM171A1 regulates sheep myoblast proliferation through the oar-miR-485-5p/MAPK15/MAPK pathway

city: Beijing

first: Runqing

last: Chi

address: 2 Yuanmingyuan West Rd

institute: State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences

summary: Estrogen is an important hormone that affects muscle development in female animals. Previous studies have shown that estrogen can protect muscle cells from apoptosis by inhibiting the MAPK signaling pathway. However, the molecular mechanisms by which estrogen-induced MAPK signaling regulates myoblast growth and development remain unclear. In this study, RNA-seq was performed on ovariectomized small-tailed Han (OR-STH) sheep and sham surgery small-tailed Han (STH) sheep to analyze the effects of estrogen on muscle growth and development in female animals. There were 8,721 differentially expressed circRNAs (DECs), 143 differentially expressed miRNAs (DEMs) and 2,238 differentially expressed mRNAs (DEGs) in the longissimus dorsi between the OR-STH and STH groups. Bioinformatics analysis revealed that the differentially expressed gene MAPK15 was significantly enriched in the MAPK signaling pathway, which is important for muscle development. Therefore, we constructed the ceRNA network circFAM171A1/oar-miR-485-5p/MAPK15 and explored its effect on muscle growth and development. The results of the molecular mechanism experiments indicated that circFAM171A1 can sponge oar-miR-485-5p to regulate MAPK15. The addition of the exogenous hormone estradiol (E2) to sheep myoblasts could induce circFAM171A1, regulate the expression of oar-miR-485-5p and MAPK15, and promote the proliferation of sheep myoblasts. The results showed that MAPK15 and circFAM171A1 significantly promoted the proliferation of myoblasts and inhibited the apoptosis of myoblasts in sheep, whereas oar-miR-485-5p inhibited the expression of MAPK15 and circFAM171A1, inhibited myoblast proliferation and promoted apoptosis. Furthermore, circFAM171A1 attenuated the inhibitory effect of oar-miR-485-5p on myoblasts. In summary, estrogen induced the expression of circFAM171A1 in sheep myoblasts, and circFAM171A1 can act as a sponge for oar-miR-485-5p to promote the expression of the target gene MAPK15 and ultimately regulate the proliferation of sheep myoblasts. This study provides new insights into the molecular mechanism of estrogen regulation of muscle growth and development in female animals.

first: Yufang

last: Liu

first: Peng

first: Fan

last: Yang

first: Xiangyu

first: Ran

last: Di

first: Xiaoyun

last: He

first: Mingxing

last: Chu


title: Transcriptome profiling of urothelial cells after exposure to low-grade oxidative stress

city: Ljubljana

first: Tadeja

last: Kuret

state: Slovenia

address: Vrazov trg 2

department: Faculty of Medicine

country: Slovenia

institute: University of Ljubljana

summary: In this study, we aimed to determine the overall effect of glucose oxidase (GO) on transcriptomic profile of urothelial cells using RNA sequencing. Our study represents a reference database that could lead to a better understanding of the link between oxidative stress and innate immune response of urothelial cells leading to continuous cycle of inflammation in IC/BPS pathology. Furthermore, the study sets grounds for future studies exploring potential biomarkers and therapeutic targets for IC/PBS diagnosis and treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SV-HUC1 normal urothelial cell line (untreated vs glucose oxidase-treated, four independent experiments).

first: Peter

last: Veranič

first: Mateja

middle: E

last: Kreft


title: Clinical progression of clonal hematopoiesis is determined by a combination of mutation timing, clonal fitness, and structure

city: Rochester

first: Neil

middle: Alistair

last: Robertson

state: MN

address: 200 1st Street

department: Quantitative Health Sciences

institute: MAYO CLINIC ROCHESTER

summary: Clonal hematopoiesis (CH) is characterized by expanding blood cell clones carrying somatic mutations in healthy aged individuals and is associated with various age-related diseases and all-cause mortality. While CH mutations affect diverse genes associated with myeloid malignancies, their mechanisms of expansion and disease associations remain poorly understood. We investigate the relationship between clonal fitness and clinical outcomes by integrating data from three longitudinal aging cohorts (n=713). We demonstrate pathway-specific fitness advantage and clonal composition significantly influence clonal dynamics. Further, the timing of mutation acquisition is necessary to determine the extent of clonal expansion reached during the host individual's lifetime. We introduce MAC120, a metric combining mutation context, timing, and variant fitness to predict future clonal growth, outperforming traditional variant allele frequency measurements in predicting clinical outcomes. Our unified analytical framework enables standardized clonal dynamics inference across cohorts, advancing our ability to predict and potentially intervene in CH-related pathologies.

overall_design: Our expanded cohort longitudinally sampled from the LBC1936 was processed as per our previous work. Briefly, DNA was extracted from whole blood with Ethylenediaminetetraacetic acid (EDTA) using the Nucleon BACC3 kit (Sigma-Aldrich, GERPN8512), according to the manufacturer’s protocol. Libraries were generated from 200 ng of each DNA sample using the Invitea/Archer VariantPlex® 75 Myeloid gene panel and the VariantPlex® Somatic Protocol for Illumina sequencing (Invitae, AB0108, and the VariantPlex®-HCG Myeloid Kit; see Supplementary Table 2), with adaptations for detecting low variant allele frequencies. Sequencing was performed on the NextSeq 550 platform (Illumina) using the NextSeq 500/550 High-Output version 2.5 kit (300 cycles). Two ‘Genome in a Bottle’ (GIAB) DNA samples (NA12878, Coriell Institute) were included in each sequencing batch to ensure reproducibility and support background error modeling and batch correction.

first: Eric

last: Latorre-Crespo

first: Gozde

last: Kosebent

first: Linus

last: Schumacher

first: Tamir

last: Chandra

first: Kristina

last: Kirschner


title: Asymmetric Histone Inheritance Regulates Differential Transcription Re-initiation and Cell Fate Decisions in Mouse Olfactory Horizontal Basal Cells

city: Baltimore

first: Guanghui

address: 3400 North Charles Street

department: Biology

institute: Howard Hughes Medical Institute/The Johns Hopkins University

summary: Histones, major carriers of epigenetic information, play critical roles in regulating gene expression patterns and cell fate decisions. While asymmetric histone inheritance has been shown to regulate distinct cell fates in Drosophila adult stem cells, its relevance in mammals remains unclear. In this study, we investigated cell division modes and histone inheritance patterns in horizontal basal cells (HBCs) of the mouse olfactory epithelium following injury. We found that approximately 40% of telophase HBCs show asymmetric division, with a corresponding asymmetric segregation of histone H4. In primary cultured HBCs, we observed asymmetric cell division accompanied by asymmetric distribution of histones, including H4, H3, and H3.3, but not H2A-H2B. Asymmetric histone segregation leads to asymmetric association of a key ‘stemness’ transcription factor p63 and asynchronous transcription re-initiation during mitotic exit. Single-cell RNA sequencing of paired daughter cells further revealed asymmetric cell fate priming in cultured HBCs. Disruption of asymmetric cell division abolished asymmetric transcription re-initiation, asymmetric histone inheritance in culture HBCs and further caused regeneration defects in OE. These findings reveal the conservation of asymmetric histone inheritance in mammalian adult stem cells and highlight its biological significance in tissue regeneration.

overall_design: Single daughter cells were individually picked using mouth pipette soon after division of ex vivo cultured mouse horizontal basal cells (HBCs). The pairing information were noted and RNA profiles in each cell were examined using the Smart-seq2 method.

first: Binbin

last: Ma

first: Haiqing

last: Zhao

first: Xin

last: Chen


title: The effect of nanoseond laser on murine retinal pigment epithelial cells

city: Melbourne

first: Andrew

middle: Ian

last: Jobling

state: Victoria

address: Medical Building, Cnr Grattan St and Royal Pde

department: Anatomy & Physiology

country: Australia

institute: University of Melbourne

summary: Ophthalmic laser treatment using short pulse lasers has shown promise as a treatment for certain eye diseases such as Age related macular degeeneration. In this study we treated C57BL/6J mice at 9 months of age with 10 laser spots delivered by the 2RT nanosecond laser. Animal were allowed to recover and were aged a further 3 months (12 months old) before retinal pigment epithelial (RPE) cells were isolated. Totsal RNA samples from laser-treated and control animals were isolated and  preamplified using the SMARTSeq v4 low RNA input kit. After library preparation a 50bp single end read was performed at a depth of 19-34 million reads per sample using the Illumina HiSeq. Constructs were mapped to the murine genome and differential expression calculated between the laser-treated and control groups.  underwent RNAseq o

overall_design: 3months after nanosecond laser treatment of the mouse eyes, two groups were examined  - laser treated and age-matched untreated controls.

first: Erica

last: Fletcher

middle: I


title: Targeting tumor-intrinsic S100A1 augments antitumor immunity and potentiates immunotherapy efficacy

first: yufeng

last: guo

address: No. 17 Panjiayuan Nanli, Chaoyang District

institute: Cancer Hospital Chinese Academy of Medical Sciences

summary: Immune checkpoint blockade (ICB) has revolutionized cancer treatment, but the therapeutic response is highly heterogeneous. A potential mode of resistance is tumor-intrinsic mechanisms leading to an immunosuppressive tumor microenvironment. However, the underlying interactive network remains elusive and the generalizable biomarkers and targeting strategies are still lacking. Here, we uncovered the potential of plasma S100 calcium-binding protein A1 (S100A1) in determining ICB efficacy based on liquid biopsy of patients with lung cancer. Muti-omics and functional studies suggested that tumor-intrinsic S100A1 expression correlates with an immunologically cold TME and resistance to ICB. Mechanistic investigations demonstrated that interfering with tumor-intrinsic S100A1/ubiquitin-specific protease 7/p65/granulocyte-macrophage colony-stimulating factor (GM-CSF) modulatory axis could potentiate an inflamed TME via promoting M1-like macrophage polarization and T cell function. GM-CSF priming was sufficient to enhance ICB response in tumors with high S100A1 expression. These findings defined S100A1 as a potential biomarker and a novel synergistic target for cancer immunotherapy.

overall_design: Mouse orthotopic models via intravenous injection of LLC cells stably transfected with S100a1 shRNA or scramble control were constructed. Single-cell suspensions were generated. The sequencing reads were examined by quality metrics, and transcripts were mapped to a reference mouse genome (mm10) and assigned to individual cells of origin according to the cell-specific barcodes using the Cell Ranger pipeline (10x Genomics).

first: Yufeng

last: Guo

first: Rui

last: Wan

first: Jianchun

last: Duan

first: Li

last: Yuan

first: Zhijie

last: Wang

first: Hua

last: Bai

first: Jie


title: Effect of psilocybin on visual cortex

city: Rehovot

first: Amir

last: Szitenberg

address: 234 Herzl St

department: INCPM

country: Israel

institute: Weizmann Institute

summary: Effect of psilocybin on visual cortex

overall_design: Experimentation took place in the dark cycle. The mice were split into four experimental groups: mice placed into light (light group), mice kept in dark (dark group), mice treated with 5mg/kg psilocybin, followed by immediate placement in light (psilocybin-light group), mice treated with 5mg/kg psilocybin and kept in the dark (psilocybin-dark group). Two and a half hours after placement of mice in the light (or maintaining in dark), mice were sacrificed by decapitation, brains were isolated, and the visual cortex (V1) was removed and stored immediately on dry ice.

first: Evan

last: Elliott

first: Ram

last: Harari


title: snRNA-seq  of the hippocampus of Mr1+/+ P301S mice and Mr1-/- P301S mice

city: New Brunswick

first: Qi

last: Yang

state: NJ

address: 89 French St

institute: Rutgers RWJMS

summary: We performed snRNA-seq  using 10xgenomics platform to study the role of MAIT cells in regulating neuroinflammation in mice with neurodegenerative tau pathology. MAIT cells are a type of innate-like T cells that are present in the meninges of mice carrying neurodgenerative human tau mutant transgene. This is the first study to examine single nucleus transcriptome profiles of human tau mice lacking MAIT cells.

overall_design: Nuclei was extracted from 4 Mr1-/- P301S mice that lack MAIT cells and 4 control Mr1+/+ P301S mice. Single-nucleus RNA-seq was performed using 10xgenomics GEM 3' gene expression kit. Libraries were sequenced using a Novaseq.

first: Yuanyue

last: Zhang


title: Actin polymerization by WASp limits nuclear envelope rupture and inflammation in macrophages

city: Trieste

first: Roberto

last: Amadio

address: Padriciano 99

country: Italy

institute: ICGEB Trieste

summary: Mutations in the immune-specific actin regulator WASp induce a proinflammatory state in myeloid cells, whose underlying causes remain poorly defined. Here, we applied microfabricated tools that mimic tissue mechanical forces to explore the role of WASp in connecting mechano-sensing to the activation of inflammatory responses in macrophages. We show that WASp-deficient macrophages carry nuclear structure alterations and undergo increased blebbing and nuclear rupture when exposed to mechanical confinement. High-resolution imaging indicates that WASp drives the formation of protective perinuclear actin structures in response to confinement. Functionally, WASp null macrophages respond to mechanical confinement by inducing a transcriptional profile consistent with the release of immunogenic DNA in the cytosol. The proinflammatory state of mechanically confined WASp-deficient macrophages depends, in part, on the cGAS-STING pathway of cytosolic DNA sensing. Together, these data uncover a WASp-dependent mechanism to restrict activation of inflammatory signalling in tissue macrophages and provide hints to target unabated inflammation in Wiskott-Aldrich Syndrome.

overall_design: RNA-seq profiling of WT and WASp KO (WKO) bone marrow-derived macrophages (BMDM) in unconfined conditions and after 1h of confinement at 3 µm of height.

first: Giulia Maria

last: Piperno

first: Federica

last: Benvenuti


title: Enhanced or Reversible RNA N6-Methyladenosine Editing by Red/Far-red Light induction

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

type: Methylation profiling by high throughput sequencing

summary: The RNA N6-methyladenosine (m6A) modification is a critical regulator of various biological processes, but precise and dynamic control of m6A remains a challenge. In this work, we present a red/far-red light-inducible m6A editing system that enables efficient and reversible modulation of m6A levels with minimal off-target effects. By engineering the CRISPR dCas13 protein and sgRNA with two pairs of light-inducible heterodimerizing proteins, ΔphyA/FHY1 and Bphp1/PspR2, we achieved targeted recruitment of m6A effectors. This system significantly enhances m6A writing efficiency, and allows dynamic regulation of m6A deposition and removal on specific transcripts, such as SOX2 and ACTB. Notably, reversible m6A editing was achieved through cyclic modulation at a single target site, demonstrating the ability to influence mRNA expression and modulate the differentiation state of human embryonic stem cells. This optogenetic platform offers a precise, versatile tool for cyclic and reversible m6A regulation, with broad implications for understanding RNA biology and its potential applications in research and medicine.

overall_design: This study comprehensively assessed the alterations and consistency of RNA m6A modification in HEK293T cells.  Utilizing the m6A sequencing results, we investigated differential  genes across various RNA types.

first: Heng

last: Tang

first: Shaoqin

last: Han

first: Yang

last: Jie

first: Wei

last: Jiang

first: Xiaocheng

last: Weng


title: A new soluble CSF1R-dimeric mutein with enhanced trapping of both CSF-1 and IL-34 reduces suppressive tumor-associated macrophages in mesothelioma.

city: Nantes

first: Christophe

last: Blanquart

address: 8 Quai Moncousu

institute: INSERM UMR 1307/CNRS UMR 6075

summary: Background: Signalling through the colony stimulating factor-1 receptor (CSF-1R) upon binding of its ligands CSF-1 and IL-34 has tumorigenic effects in several cancers through both induction of suppressive macrophages, and survival/proliferation of tumor cells. In addition, IL-34 tumorigenic effect can also be mediated by signalling through its other receptors, protein-tyrosine phosphatase zeta (PTPzeta), Syndecan-1 (CD138) and triggering receptor expressed on myeloid cells 2 (TREM2). Inhibition of CSF-1R signalling with small tyrosine kinase inhibitors or neutralization of CSF-1 and/or IL-34 using antibodies have been proposed to be used in cancer but their effect is limited, they have drawbacks since they only partially inhibit CSF-1 or IL-34 activity and in the case of small tyrosine kinase inhibitors lead to secondary effects due to lack of specificity. Thus, there is a need for a more specific and yet integrative approach. Methods: A human mutated form of the extracellular portion of CSF-1R was in silico modelized to trap both IL-34 and CSF-1 with higher affinity than the wild-type CSF-1R by replacing the methionine residue at position 149 by a Lysine (M149K). The extracellular portion of the mutated CSF-1R M149K was dimerized using the immunoglobulin Fc sequence of a silent human IgG1 (sCSF-1RM149K-Fc). Signalling through CSF-1R, survival of monocytes and differentiation of suppressive macrophages were analyzed using mesothelioma patient’s samples and mesothelioma/macrophage spheroids in the presence of sCSF-1RM149K-Fc or sCSF-1R-Fc wild type control (sCSF-1RWT-Fc). Results: We defined that the D1 to D5 domains of the extracellular portion of CSF-1R were required for efficient binding to IL-34 and CSF-1. The mutein sCSF-1RM149K-Fc trapped with higher affinity than sCSF-1RWT-Fc both recombinant CSF-1 and IL-34 added in culture and naturally produced in mesothelioma pleural effusions. This was shown by inhibition of CSF-1R signalling, survival and differentiation of human suppressive macrophage in vitro and in vivo induced by mesothelioma cells. Neutralization of IL-34 and CSF-1 resulted in higher killing of mesothelioma cells by a tumor-specific CD8+ T cell clone in mesothelioma/macrophage spheroids. Conclusions: sCSF-1RM149K-Fc efficiently inhibited CSF-1R signalling, monocyte survival and suppressive macrophage differentiation induced by mesothelioma cells producing CSF-1 and IL-34 as well as restored cytotoxic T cell responses. sCSF-1RM149K-Fc efficiently and simultaneously trap both CSF-1 and IL-34 with high therapeutic potential versus other therapies under development targeting single components of this complex cytokine pathway involved in cancer.

overall_design: mRNA from Meso13 (n=3), Meso13 + monocytes (n=3), Meso34 (n=3) and Meso34 + monocytes (n=3) MCTS were analyzed using 3'RNA sequencing

first: Noémie

last: Joalland

first: Agnès

last: Quéméner

first: Sophie

last: Deshayes

first: Romain

last: Humeau

first: Mike

last: Maillasson

first: Héloïse

last: LeBihan

first: Apolline

last: Salama

first: Judith

last: Fresquet

first: Séverine

last: Remy

first: Erwan

last: Mortier

first: Carole

last: Guillonneau

first: Ignacio

last: Anegon


title: FOXL2 drives the differentiation of supporting gonadal cells in early ovarian development

city: Helsinki

first: Juha

middle: Samuli

last: Tapanainen

state: Uusimaa

address: Haartmaninkatu 8

department: Obstetrics and Gynaecology

country: Finland

institute: University of Helsinki

summary: Forkhead box L2 (FOXL2) is a forkhead box transcription factor expressed in the pituitary, ovaries, and eyelids. Human mutations in FOXL2 associate with the blepharophimosis, ptosis epicanthus and inversus syndrome (BPES), which can be linked to primary ovarian insufficiency, and are indirectly linked with differences of sex development (DSD). Animal studies have shown the crucial role that FOXL2 plays in the development, function, and maintenance of the ovary as well as in sex determination. However, the role of FOXL2 in early human somatic cell ovarian development is largely unknown. In this study, using CRISPR/Cas9 genome activation and a previously published in-house 14-day gonadal differentiation protocol, we show that FOXL2 downregulates coelomic epithelial markers GATA4 and LHX9, female gonadal markers RSPO1 and WNT4, and male gonadal markers SOX9 and NR0B1. Differentially expressed genes were mostly associated with Kyoto encyclopaedia of genes and genomes (KEGG) pathways relating to cell adhesion molecules and gene ontology (GO) pathways relating to extracellular matrix and junction formation. Moreover, comparative analysis with existing single cell RNA sequencing data from human in vivo-derived data elucidated that FOXL2 initiates downregulation of coelomic epithelial genes GATA4, LHX9 and UPK3B at day 6. At day 8, the genes ARX and GATA2 are transiently upregulated by FOXL2 induction and then downregulated as the genes LGR5, TSPAN8, OSR1 and TAC1 become upregulated. Thus, FOXL2 seems to support the exit of the differentiating cells from coelomic epithelium and first drives the cells towards a transitional identity and then into early supporting gonadal-like cells. The findings of this study will help largely in understanding normal gonadal development which can be used as a basis to elucidate pathological gonadal development underlying BPES.

overall_design: A total of 11 samples with 3 technical replicates each were collected at days 4, 6, 8, 10, 12 and 14 of differentiation of human embryonic stem cells (H9-DDdCas9VP192-FOXL2 clone 24) into gonadal-like cells. At days 6, 8, 10, 12 and 14 the samples were collected separately from both FOXL2 induced (IND) and non-induced (CTRL) treatment conditions.

first: Laura

last: Danti

first: Karolina

last: Lundin

first: Petra

last: Nedeczej-Ruszák

first: Timo

last: Tuuri


title: Rescue of the bag-of-marbles hypomorph fertility defect by Wolbachia pipientis is associated with expression changes in genes associated with ubiquitin and histone lysine methylation.

city: Ithaca

first: Catherine

middle: Herminia

last: Kagemann

address: 215 Tower Rd, Ithaca, NY, Room 233

department: Molecular Biology and Genetics

institute: Cornell University

summary: Wolbachia pipientis are maternally transmitted endosymbiotic bacteria commonly found in arthropods and nematodes. These bacteria manipulate reproduction of the host to increase their transmission using mechanisms, such as cytoplasmic incompatibility, that favor infected female offspring. The underlying mechanisms of reproductive manipulation by W. pipientis continue to be the subject of ongoing research. Interestingly, W. pipientis infection partially rescues female fertility in flies containing hypomorphic mutations of bag of marbles (bam) in D. melanogaster, which functions in germline stem cell (GSC) maintenance and differentiation. Our RNA-seq analysis using the W. pipientis infected relative to uninfected bam hypomorph genotype showed differential expression for many of bam’s genetic and physical interactors. The  bam hypomorph showed enrichment of ubiquitination and histone lysine methylation genes, some of which have fertility rescue by W. pipientis when knocked down in the WT genotype. Our results show that W. pipientis interacts with ubiquitination and histone lysine methylation genes which could be integral to the bam hypomorph fertility rescue.

overall_design: To study whether the rescue of bam hypomorph (partial loss of function of bam) fertility by Wolbachia pipientis variants (wMel2a, wMel3, wMelCS2a, and wMelCS2b) in D. melanogaster occurs at the  gene expression level, we conducted RNA-seq in bam hypomorph and WT ovaries followed by a differential expression analysis using uninfected controls.. We used unmated three-day old, mated three-day old and mated-six day old flies from each genotype to determine if the age-dependent rescue by W.pipientis of the bam hypomorph is due to gene expression differences in the host.

middle: H

first: Jaclyn

last: Bubnell

first: Gabriela

last: Colocho

first: Daniela

last: Arana

first: Charles

last: Aquadro


title: Gene expression profile at single cell level of immune cells infiltrating iPS cell-derived teratoma

city: Sapporo

first: Tomoki

last: Kamatani

address: Kita-15, Nishi-7, Kita-ku

institute: Hokkaido University

summary: Currently, most cell or tissue transplantations using induced pluripotent stem cells (iPSCs) are anticipated to involve allogeneic iPSCs. However, the immunological properties of iPSCs in an allogeneic setting are not well understood. We previously established a mouse transplantation model of MHC-compatible/minor antigen-mismatched combinations, assuming a hypoimmunogenic iPSC-setting. Here, we found that iPSCs subcutaneously inoculated into MHC-compatible allogeneic host mice resisted rejection and formed teratomas without immunosuppressant administration. Notably, when skin grafts were transplanted onto hosts more than 40 days after the initial iPSCs inoculation, only the skin of the same strain as the initial iPSCs was engrafted. Therefore, donor-specific immune tolerance was induced by a single iPSC inoculation. Diverse analyses, including single-cell RNA-sequencing after transplantation, revealed an increase in regulatory T cell (Treg) population, particularly CD25+ CD103+ effector Tregs within the teratoma and skin grafts. The removal of Tregs or CD25+ cells suppressed the increase in effector Tregs and disrupted graft acceptance, indicating the importance of these cells in the establishment of immune tolerance. Within the teratoma, we observed an increase in TGF-β2 levels, suggesting an association with the increase in effector Tregs. Our results provide important insights for future applications of allogeneic iPSC-based cell or tissue transplantation.

overall_design: Teratomas from each mouse were collected at 10 (n = 33), 20 (n = 20), and 40 days (n = 20) after subcutaneous administration of CBA/N iPS into B6C3F1 mice and processed collectively at each time point. Single-cell suspensions were obtained using BD Horizon™ Dri Tumor & Tissue Dissociation Reagent (BD Biosciences), and infiltrated immune cells were collected through sorting of CD45-positive cells by FACSAria II (BD Biosciences). We followed the 10x Genomics protocol for Next GEM Single Cell 3′ Gene Expression v3.1 (CG000315 Rev C) and used cell suspensions with ≥70% viability to generate complementary DNA and prepare scRNA-seq libraries

first: Satoshi

last: Ikeda

first: Makoto

last: Inoue

first: Ken-ichiro

last: Seino


title: Psychological stress-induced ALKBH5 deficiency promotes tumour innervation and pancreatic cancer progression via extracellular vesicle transfer of m6A-modified RNAs

city: Guangzhou

first: Zhou

last: yifan

state: 周一帆

address: 74 Zhongshan Second Road

institute: Sun Yat-sen University Cancer Center

summary: Pathological role and the mechanism of psychological stress in cancer progression are little known. Here, we show in a mouse model that psychological stress drives pancreatic ductal adenocarcinoma (PDAC) progression via stimulating tumor nerve innervation. We demonstrate that nociception and other stressors activate sympathetic nerve to release Noradrenaline, downregulating tumor cell RNA demethylase alkB homolog 5 (Alkbh5). Alkbh5 deficiency causes cancer cell aberrant m6A modification of RNAs, which are packed to extracellular vesicles and delivered to neurons in the tumor microenvironment, enhancing hyperinnervation and PDAC progression. ALKBH5 levels are reversely correlated with tumor innervation and survival time in PDAC patients. Animal experiments identify a natural flavonoid Fisetin preventing neurons from taking in m6A-RNA contained EVs and suppress PDAC tumor excessive innervation and progression. Together, our study shed light on a novel molecular mechanism for neuro-cancer crosstalk linking psychological stress and cancer progression and raise a potential strategy for PDAC therapy.

overall_design: Chromatin immunoprecipitation DNA-sequencing ( ChIP-seq ) for H3K27ac and Chd4 in KPC cells

first: Jian

last: Zheng

first: Ziming

last: Chen


title: Cisplatin exposure dysregulates pancreatic islet function in male mice

city: Ottawa

first: John

last: Stead

state: ON

address: 1125 Colonel By Drive

department: Department of Neuroscience

country: Canada

institute: Carleton University

summary: Cancer survivors have an increased risk of developing new-onset Type 2 diabetes compared to the general population. Moreover, patients treated with cisplatin, a commonly used chemotherapeutic agent, are more likely to develop metabolic syndrome and Type 2 diabetes compared to age- and sex-matched controls. Insulin-secreting β-cells—located within pancreatic islets—are critical for maintaining glucose homeostasis, and dysregulated insulin secretion is central to Type 2 diabetes pathophysiology. Surprisingly, the impact of cisplatin treatment on pancreatic islets has not been reported. In this study, we aimed to determine if murine islet function is adversely affected by direct or systemic exposure to cisplatin. In vivo cisplatin exposure led to  deficits in glucose-stimulated insulin secretion in both male and female mice. In vitro cisplatin exposure to both male and female mouse islets profoundly dysregulated insulin release and reduced oxygen consumption in a non-sex specific manner. Male mouse islets exposed to cisplatin had altered the expression of genes related to insulin production, oxidative stress, and the Bcl-2 family and numerous DEGs related to the insulin secretion pathway. Our data suggest both direct and systemic cisplatin exposure cause acute defects in insulin secretion and may have lasting effects on islet health in mice.

overall_design: To investigate the effects of cisplatin on gene expression, pancreatic islets were isolated from 3 male C57Bl/6 mice. Half of the islets isolated from each mouse were treated with vehicle control, and the other half with 10 uM cisplatin for 48 hours, leading to 3 biological replicates per treatment group. Islets were then collected for TempO-Seq analysis.

first: Lahari

last: Basu

first: Ma. Enrica Angela

last: Ching

first: Lili

last: Grieco-St-Pierre

middle: D

first: Antonio

middle: A

last: Hanson

first: Jana

last: Palaniyandi

first: Erin

middle: P

last: van Zyl

first: Myriam

last: Hoyeck

first: Kelsea

last: McKay

first: Kyle

last: van Allen

first: Hyojin

last: Lee

first: Xiao-Qing

last: Dai

first: Austin

last: Bautista

first: Evgenia

last: Fadzeyeva

last: Muvihill

first: Carole

last: Yauk

first: Patrick

last: MacDonald

first: Jan

last: Mennigen

first: Jennifer

last: Bruin


title: PP2A attenuates thoracic aneurysm and dissection in mouse models of Marfan syndrome [RNA-seq]

city: Atlanta

first: Qian

last: Xu

state: GA

address: 101 Woodruff Circle

institute: Emory University

summary: Recent studies show that hyperactivation of mTOR signaling plays a causal role in the development of thoracic aortic aneurysm (TAA) and dissection (AAD). Modulation of Protein phosphatase 2A (PP2A) activity has been shown to be of significant therapeutic value. In light of the effects that PP2A can exert on mTOR pathway, we hypothesized that PP2A activation by small molecule activators of PP2A (SMAPs) could mitigate AA progression in Marfan Syndrome (MFS).

overall_design: Fbn1mgR/mgR mice, which has under-expression of Fbn1 gene, were obtained from the Jackson Laboratory (JAX stock #005704). A 5mg/kg dose of DT-061 was given orally twice a day to mice starting at the age of 5 weeks (Fbn1mgR/mgR). DT-061 was prepared in a N,N-dimethylacetamide/Kolliphor HS-15/diH20 solution. The control mice were orally given vehicle solution along the same schedule. After 4 weeks of treatment, total RNAs were extracted from ascending aortas in mice and was sent for bulk RAN-seq.


title: LncRNAs regulate FBL to facilitate rRNA processing in cancer cells

first: Wen-Tao

last: Wang

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: sun yat sen university

summary: We identified lncRNA DNAJC3-AS1 can buffer the behavior of FBL condensation in cancer cell. In this study, we preformed the FBL-TurboID-RIP and Single-end Enhanced Cross-linking and Immunoprecipitation (seCLIP)  sequencing to to identify candidate RNAs that bind to FBL or its adjacent proteins. The FBL-binding regions distributed throughout the sequence of lncRNAs were also discovered.

overall_design: 1.  MOLM-13 and SW480 cells used in the  FBL-TurboID-RIP-seq. 2. HEK293T cells  used in the  FBL-seCLIP.

first: Yue-Qin

last: Chen

first: YU-Meng

last: Sun


title: Gene expression profile at single-cell level of myeloid cells from the liver of mice after vertical sleeve gastrectomy (VSG)

city: Minneapolis

first: Adam

last: Herman

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: We used droplet-based scRNA-seq to profile the gene expression of magnetically-sorted F4/80+ cells from the liver of Sham AL, Sham PF, and VSG mice.

overall_design: Two million F4/80+ cells from were individually labeled with cell multiplexing oligos (CMOs, 10X Genomics) to allow for the multiplexing of individual samples prior to pooling and gel bead-in-emulsion (GEM) preparation. Separate gene expression and CMO libraries were created and sequenced in a Novaseq S4 chip (2 x 150bp PE).

first: Revelo

last: Xavier

first: Ikramuddin

last: Sayeed


title: ac4C-seq in NAT10-knockdown PANC-1 cells

first: Leyi

last: Huang

address: 107 Yan Jiang West Road, Guangzhou, P.R. China

institute: Sun Yat-sen University

summary: Pancreatic cancer is a lethal diease with high tendency of metastasis. Howerver,  the mechanisms of pancreatic cancer are sitill unclear. To explore the roles of N4-acetylation (ac4C) RNA modification and its involved N-Acetyltransferase 10 (NAT10) in pancreatic ductal adenocarcinoma (PDAC), we performed profiling by high throughput sequencing. In this study, we investigate the effects of NAT10 knockdown on N4-acetylcytidine (ac4C) modification in mRNA within PANC-1 cells using ac4C-seq. By employing RNA interference to specifically knock down NAT10 expression in PANC-1 cells, we aim to elucidate its impact on ac4C RNA modifications, which have been implicated in various cellular processes and cancer progression. Total RNA was extracted and mRNA was captured and treated with sodium borohydride (NaBH4) for detection of ac4C sites.Following library preparation, sequencing was performed on an Illumina Novaseq 6000 platform. Bioinformatics analyses identified significant changes in ac4C modification patterns due to NAT10 depletion. This dataset provides a valuable resource for further exploration of ac4C modifications in mRNA and their role in PDAC.

overall_design: NAT10 knockdown or ctrl PANC-1 cells were used to investigate the genes with changes in ac4C sites regulated by NAT10.

first: Quanbo

last: Zhou


title: Integrated analysis of the anoikis-related signature identifies RAC3 as a novel therapeutic target in hepatocellular carcinoma

city: Xi'an

first: Dong

last: Wu

state: Shaanxi Province

address: Changle Road 169

institute: National Translational Science Center for Molecular Medicine, Fourth Military Medical University

summary:
Introduction: Anoikis is a form of programmed cell death. Anoikis resistance in hepatocellular carcinoma (HCC) promotes cancer cells shedding from the primary tumor site, thus contributing to survival and distant metastasis. However, the prognostic significance of anoikis-related genes (ARGs) and the biological functions of crucial genes in HCC have not been reported.
Objectives: This study aimed to construct a model for predicting the outcome of patients with HCC based on ARGs and to investigate the clinicopathological significance and function of Rac family small GTPase 3 (RAC3) in HCC.

overall_design: Three independent RNA samples from stable RAC3-overexpressing  Huh-7 cells and their corresponding negative controls were subjected to sequencing by Gene Denovo Biotechnology Co. (Guangzhou, China). Genes were considered differentially expressed when the fold change was greater than 1.5 or less than -1.5 with P < 0.05.


title: Mapping EGFR-mediated local invasion and response to Cetuximab in head and neck cancer

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary: Recurrent/metastatic head and neck squamous cell carcinoma (R/M-HNSCC) is a severe, frequently lethal condition. Targeted therapy includes epidermal growth factor receptor (EGFR) blockade, but overall response rates are low and predictive biomarkers amiss. Deepened understanding of molecular networks governing EGFR-driven progression are required to explore predictive markers and therapeutic targets. We have mapped EGFR-mediated local invasion in a 3D-model using photoconvertible cell-tracers and uncovered invasion-associated, differentially expressed genes (DEGs) correlated with EGFR/MAPK activity and epithelial-to-mesenchymal transition (EMT) in primary malignant cells. A gene regulatory network (GRN) of local invasion was defined, composed of the central hubs inhibin subunit beta alpha (INHBA) and SLUG, and druggable effectors integrin subunit beta 4 (ITGβ4), its ligand laminin 5 (LAMB3/LAMC2), sphingosine kinase 1 (SPHK1), and EGFR ligand amphiregulin (AREG). Blockade of INHBA repressed local invasion, which was rescued by Activin A, Laminin 5, and sphingosine-1-phosphate, proving functional interconnection of the GRN. Functional DEGs (fDEGs) and, most prominently, central hub IHNBA, were associated with tumor buds in TCGA-HNSCC. Newly defined EGFR-activity subtypes, primarily dictated by AREG and epiregulin (EREG), show enhanced fDEGs expression, EMT correlation, and prognostic value. Cell-communication revealed strong interactions of AREG/EREG-governed EGFR-activities with non-malignant cells, potentially impacting on tumor progression. High expression of fDEGs enriched in EGFR-activities (INHBA, ITGA3, ITGΒ4, LAMA3, LAMC2, MT2A, EREG) was associated with response to Cetuximab in PDX models and R/M-HNSCC patients. Thus, we describe a novel GRN of EGFR-mediated local invasion and define druggable effectors with predictive potential regarding the response to Cetuximab.

overall_design: In total 40 samples were included, 5 expertimtal groups: cell spheroids treated with high-dose EGF in combination with Cetuximab, cell spheroids treated with high-dose EGF_Photoconverted non-invasive cells, FaDu cell spheroids treated with high-dose EGF in combination with MEK-inhibitor and cell spheroids treated with high-dose EGF_Photoconverted invasive cells for the two cell lines FaDu and Kyse30.

first: Olivier

last: Gires


title: Pathways underlying selective neuronal vulnerability in Alzheimer's disease: contrasting the vulnerable locus coeruleus to the resilient substantia nigra

city: San Francisco

first: Alexander

middle: James

last: Ehrenberg

state: CA

address: 675 Nelson Rising Lane

department: Memory and Aging Center

institute: University of California, San Francisco

summary: Identifying factors underlying selective neuronal vulnerability is crucial for understanding Alzheimer's disease (AD) pathophysiology. The Neuromodulatory Subcortical System (NSS) includes nuclei that exhibit early, but varied vulnerability to tau accumulation and neuronal loss. This varied vulnerability represents a valuable opportunity to explore the underlying mechanisms of AD. In this study, we investigated factors contributing to selective neuronal vulnerability by comparing transcriptomic profiles of two similar NSS nuclei with differing vulnerabilities to AD, the locus coeruleus and substantia nigra. Using paired samples from well-characterized postmortem human tissue from individuals in early Braak stages and free of comorbid neuropathologic diagnoses, we identified pathways related to cholesterol homeostasis and antioxidant pathways response as key potential drivers of vulnerability.

overall_design:
The locus coeruleus and substantia nigra were sampled from human postmortem brains from Alzheimer's disease Braak stages 0-III.

Samples were frozen in RNAlater, were sent to a vendor (Novogene Inc., Davis, CA) for RNA extraction and sequencing. Tissue homogenization and cell lysis was performed in TRIzol. After cell lysis, impurities removal, and inhibition of RNAse activity, total RNA was extracted by using phase separation method from cell debris. An Agilent bioanalyzer 2100 was used to measure RNA quality and concentration. Samples with an RNA integrity number (RIN) greater than 4 and at least 0.1µg of RNA available was passed to library preparation and sequencing.

The quality of sequence files was assessed using the FastQC package before and after trimming steps. Trimmomatic (ILLUMINACLIP: TruSeq3-PE.fa:2:30:10:2:True, LEADING: 3, TRAILING: 3, SLIDINGWINDOW: 4:15, and MINLEN: 36) was used to remove adapter sequences and any sequences with low mean quality scores. Sequences were aligned to GRCh38 using STAR alignment and count matrices were generated using featureCounts. The count matrices were converted to counts per million (CPM) using the edgeR package.

middle: J

first: Cathrine

last: Petersen

first: Felipe

last: Pereira

first: Song

last: Li

first: Jessica

last: Buxton

first: Sonali

last: Langlois

first: Marena

last: Trinidad

first: Ian

last: Oh

first: Claudia

middle: K

last: Suemoto

first: Renata

last: Paraizo Leite

first: Roberta

last: Diehl Rodriguez

first: Vitor

last: Ribeiro Paes

first: Carlos

last: Pasqualucci

first: William

middle: W

last: Seeley

first: Salvatore

last: Spina

first: Daniela

last: Kaufer

first: Lea

middle: T

last: Grinberg


title: NAT10 and N4-Acetylcytidine restrain R-loop levels and related inflammatory responses II

city: Austin

first: Blerta

last: Xhemalçe

state: Texas

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

summary: N4-acetylcytidine (ac4C) is an evolutionarily conserved RNA modification that is deposited on diverse RNAs by N-acetyltransferase 10 (NAT10), a protein with high biological significance for aging and cancer. Here, we performed a comprehensive survey of ac4C using metabolic labeling, sodium cyanoborohydride chemical treatment coupled to next generation sequencing (NGS) and ac4C antibody-based cell and molecular biology techniques. Our NGS analysis confirms robust ac4C modification of rRNA and specific tRNA species in a NAT10-dependent manner, but suggests low or spurious ac4C acetylation in mRNA. Analysis of RNA-seq data also revealed an induction of inflammatory responses as well as mutagenesis at transcriptionally active sites in NAT10-KO cells. This finding led us to further explore the role of NAT10 in R-loops, which have recently been shown to induce APOBEC3B-mediated mutagenesis. Our analysis revealed that R-loops are modified with ac4C in a NAT10-dependent manner. Furthermore, NAT10 restrains the levels of R-loops at a subset of differentially expressed genes in a manner dependent on its catalytic activity. Together with cellular biology data showing ac4C containing RNA in endosomal structures, we propose that increased levels of ac4C-unmodified RNAs, likely derived from R-loops, in endosomal structures induce inflammatory responses.

overall_design: DRIP-seq: DNA/RNA hybrid Immunoprecipitation of HeLa-Flp-In-TREx+ Empty Vector (Control); NAT10-FLAG WT; NAT10-FLAG R628A, treated with either either or RNase H samples.

first: Turja

last: Debnath

first: Nathan

last: Abell

first: Yi

middle: R

first: Sravan

last: Devanathan

first: Enrique

last: Navedo