title: Chronic Aducanumab-mediated clearance of amyloid plaques decreases microglial activation and induces a unique microglial phenotype associated with antigen presentation

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: Anti-amyloid β-peptide (Aβ) immune therapy was developed as treatment for Alzheimer’s disease (AD) to reduce and prevent amyloid plaque pathology. This approach has proven successful in phase 3 clinical trials  of Aducanumab, Lecanemab and Donanemab. These antibodies induce robust amyloid plaque clearance, slow memory decline, and have beneficial effects on daily living activities.  The therapeutic effects correlate with the efficacy of plaque removal. Treatment is associated with adverse side-effects, such as oedema and haemorrhages (ARIA-E and -H), which are potentially linked to the induced immune response. To improve therapeutic safety, it is therefore imperative to understand the effects of anti-Aβ antibody treatment on immune cell function. We investigated the effects of long-term chronic Aducanumab treatment on amyloid plaque pathology and microglial response in the APP-SAA triple knock-in mouse model. Mice were treated weekly with Aducanumab from 4-8 months of age. Long-term treatment with Aducanumab results in a robust and dose-dependent removal of amyloid plaque pathology. Analysis of the CSF proteome indicates a reduction of markers for neurodegeneration including tau and α-synuclein. Consistent with a reduction of glucose uptake, the therapeutic effects were accompanied by reduced microglial activation. RNAseq confirmed a dose-dependent decrease in the disease-associated microglia (DAM) transcriptional signature of microglia, which is supported by a parallel decrease of Trem2 protein. However, genes associated with antigen-presentation were still increased after treatment. IHC confirms that Aducanumab treatment increases microglial clustering, as well as MHC-II expression around plaques and ELISA confirmed increased cytokine levels. These findings demonstrate that long-term chronic Aducanumab-mediated removal of Aβ leads to a dose dependent decrease in microglial activation and neurodegeneration, but induces a unique antibody treatment-related microglial phenotype associated with antigen presentation, which may be related to plaques still present after the 4 months treatment period.

overall_design: Homozygous APP-SAA knock-in mice were randomized into 5 treatment groups: (1) Untreated (4 months); (2) Isotype control, 10 mg/kg (8 months); (3) Aducanumab, 1 mg/kg (8 months); (4) Aducanumab, 3 mg/kg (8 months); (5) Aducanumab, 10 mg/kg (8 months). Each group (N=6) contained both male and female animals. Animals in the "Untreated" group were sacrificed at 4 months of age, when the 16-week treatments of the other groups began. Primary microglia were collected from the brain of each animal using magnetic activated cell sorting (MACS) with Cd11b microbeads.

first: Lis

last: de Weerd

first: Connie

last: Ha

first: Dan

last: Xia

first: Joseph

middle: W

last: Lewcock

last: Monroe

first: Christian

last: Haass


title: SPATIAL TRANSCRIPTOMICS IDENTIFY HOMOLOGOUS MECHANISMS IN THE PATHOPHYSIOLOGY OF HUMAN AND E4FAD MOUSE CEREBRAL MICROBLEEDS

status: Public on Aug 20 2025

city: Chicago

first: Federico

last: Salas-Lucia

state: IL

department: Endocrinology Department

country: USA

institute: University of Chicago

type: Non-coding RNA profiling by high throughput sequencing

summary: INTRODUCTION: Cerebral microbleeds (CMBs) are age-related vascular lesions, predisposing patients to a lifetime risk of stroke and cognitive decline. Little is known about the cellular architecture of the CMB lesional milieu as well as CMB pathobiological mechanisms. Understanding common histopathologic and transcriptomic signatures across heterogenous CMBs can aid in biomarker feature selection.  METHODS: These knowledge gaps were first addressed through the morphological and quantitative assessment of human CMB autopsy tissue and E4FAD mouse CMB tissue for cell types previously implicated in neurovascular diseases. Following, assessment of human and mouse lesional differentially expressed genes (DEGs) and pathway enrichment discovered important common and differential mechanisms in CMB pathogenesis. These findings facilitated identification of circulating proteins, which were quantified and underwent feature selection to identify the strongest diagnostic biomarker candidate molecules. In addition, a circulating DE miRNome found mechanistically-relevant homologous miRNA between human subjects and E4FAD mice as candidates.  RESULTS: Histopathologic studies identified significant increases in normalized counts of astrocytes and macrophages in human CMBs, as well as astrocytes and microglia in E4FAD murine CMBs. Spatial transcriptomics identified 781 human CMB DEGs and 448 mouse CMB DEGs, with 47 common DEGs (p<0.05, FDR-corrected). Pathway enrichment identified 110 common pathways related to vascular permeability, endothelial dysfunction, and inflammation (p<0.05, FDR-corrected). A supervised literature search then found 10 blood circulating proteins that had previously been assessed in CMB patients and healthy controls. Protein levels were assessed, and elastic net feature selection identified 7 circulating protein biomarker candidates. Through miRNome sequencing, two miRNAs (p<0.1, FDR-corrected) were discovered common between human CMB patients and E4FAD mice with mechanistic ties to IPA pathways enriched from the respective transcriptomes.  CONCLUSION: This is the first report to characterize the CMB microenvironment, provide mechanistic insight into its pathobiology, and identify biologically plausible circulating diagnostic biomarker features. Future studies should identify specific mechanisms related to lesion genesis, maturation, and progression to hemorrhagic stroke. In addition, studies aimed at validation of these features, and model validation in large multi-site cohorts are needed. The framework applied here paves the way for biomarker discovery in CMBs and other cerebrovascular diseases across varying contexts of use.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 12 microRNA samples from mouse blood plasma.Obtained from 6 E4FAD mice (5xFAD+/-; human APOE4+/+, C57BL/6 background) emulating Cerebral Microbleeds (CMB) and 6 wild-type mice (C57BL/6 background).

first: Abhinav

last: Srinath

first: Diana

last: Vera Cruz

first: Dorothy

last: DeBiase

first: Akash

last: Bindal

first: Ying

last: Li

first: Geetha

middle: P

last: Yeradoddi

first: Mannan

last: Bhola

first: Rhonda

last: Lightle

first: Justine

last: Lee

first: Agnieszka

last: Stadnik

first: Kristina

last: Piedad

first: Robert

last: Shenkar

first: Peter

last: Pytel

first: Yuanyuan

last: Zhu

first: Sharbel

last: Romanos

last: Moore

first: Sean

last: Polster

first: Yuan

first: Xiaoxi

last: Zhuang

first: Christopher

last: Gomez

first: Sangram

last: Sisodia

first: Romuald

last: Girard

first: Issam

middle: A

last: Awad


title: PRMT5-mediated SRSF1 methylation promotes virus-positive Merkel cell carcinoma tumorigenesis by increasing Tip60 exon inclusion [JNJvsDMSO_raw]

city: Durham

first: Joseph

middle: L

last: Sevigny

state: NH

address: 35 Colovos Rd.

institute: Hubbard Center for Genome Studies

type: Expression profiling by high throughput sequencing

summary: Protein Arginine Methyltransferase 5 (PRMT5) is a key regulator of gene expression and RNA splicing, with its therapeutic potential demonstrated through synthetic lethality in MTAP-deleted cancers. Emerging evidence also suggests that MYC-driven or p53 wild-type tumors may be more sensitive to PRMT5 inhibition, though the underlying mechanisms remain unclear. Virus-positive Merkel cell carcinoma (MCC) serves as an ideal model to explore this question, as it is driven by the MYC paralog MYCL, and most virus-positive MCCs retain wild-type p53. In this study, we investigated PRMT5’s impact on the Tip60-EP400 complex, given MCC’s reliance on the interaction between MYCL and this complex. We used second-generation sequencing (Illumina) to characterize PRMT5-mediated bulk gene expression and long-read RNA sequencing (PacBio Iso-Seq) to analyze PRMT5-mediated alternative splicing. The mechanism underlying PRMT5 deficiency's selective impact on specific splice sites while leaving others unaffected remains unclear. Our findings suggest that PRMT5-mediated methylation of SRSF1 enhances its recruitment to m6A-modified RNA, ensuring proper splicing of Tip60 and maintaining Tip60-EP400 activity. In contrast, PRMT5 inhibition disrupts this recruitment, leading to widespread splicing defects, including both exon skipping and intron retention. These results provide new insights into PRMT5’s role in splicing regulation in cancer cells and may have broader implications for targeting splicing dysregulation in MYC-driven cancers.

overall_design: RNA-seq analyses of MKL-1 cells treated with DMSO or the PRMT5 inhibitor JNJ-64619178

first: Evelyn

last: Proctor

first: Heather

last: Adams

first: Kelley

last: Thomas

first: Jingwei

last: Cheng


title: NRF2 ACTIVATORS FOR AGE-RELATED CHRONIC DISEASES: THEORETICAL LIMITATIONS AND PRACTICAL APPROACHES (HPPE and protoporphyrins)

city: Moscow

first: Sergey

last: Nikulin

address: 7, Vavilova st.

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

summary: One of the major metabolic responses to counteract aging, inflammation, and various chronic diseases including neurodegeneration, is the so call antioxidant pathway controlled by Nrf2 transcription factor. Nrf2 protein stability is regulated via interaction with the redox sensor Keap1, an adapter protein in Cullin III ubiquitin ligase complex. The search for Nrf2 activators is mainly focused on compounds that either chemically modify sensor thiols in Keap1 or competitively displace Nrf2 from the ubiquitin ligase complex. The latter approach is considered as the most appropriate one for continuous administration without side effects, which are unavoidable in case of non-specific chemical modifiers of Keap1. However, true displacement activators show a significant offset, by many orders of magnitude, when switched from homogeneous assay to cell-based assays. This phenomenon originates, as we show here, from high micromolar intracellular concentrations of Keap1. A guarantee for high specificity of an alkylating Nrf2 activator is its targeted delivery. A transcriptomic analysis for a cell-permeable Nrf2-peptide bearing a fumarate moiety shows the activation of the antioxidant program only, confirming the high specificity of such approach. However, aging-linked neurodegeneration is also known to build-up Bach1, an Nrf2 target gene and competitive transcriptional repressor for Nrf2. Therefore, an ideal combination could be a benign Nrf2 activator and Bach1 inhibitor in one molecule, as represented by the recently developed HPPE. HPPE demonstrates an intersection of the activated antioxidant pathway with the Nrf2 peptide, and, in addition to that, shows a big pool of genes overlapping with the known inhibitors of Bach1 - zinc and tin protoporphyrins.  Hence, at present moment, HPPE presents a unique combination of the two desired activities beneficial for age-related neurodegeneration.

overall_design: Total mRNA profiles of SH-SY5Y cells treated with HPPE, zinc and tin protoporphyrins.

first: Irina

last: Gazaryan


title: Estrogen and obesity synergistically suppress Protein S via HIF1α, enhancing thrombotic potential

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

summary: Venous thromboembolism (VTE) is a leading cause of morbidity and mortality, with risk heightened in premenopausal women who are obese or use estrogen-based oral contraceptives. When both risk factors are present, thrombosis risk increases substantially. Protein S (PS), an essential anticoagulant cofactor, is downregulated by both estrogen and obesity, but the molecular basis for this suppression remains poorly defined. We investigated the impact of estrogen and obesity on PS expression using plasma samples from 157 women stratified by body mass index and contraceptive use, alongside 40 mice categorized as lean or obese with or without estrogen pellet. The levels of PS were reduced by either estrogen or obesity alone, and the combined effect increased thrombin generation. In HepG2 hepatocytes, hypoxic conditions (1%–10% O₂) mimicking obesity, with or without 17 β-estradiol, suppressed PROS1 transcription and promoter activity. Chromatin immunoprecipitation confirmed direct binding of hypoxia-inducible factor 1α (HIF1α) to the PROS1 promoter, repressing gene expression. These findings define a mechanistic pathway through which estrogen and obesity converge to suppress PS synthesis, providing insight into the elevated thrombotic risk observed in obese women using estrogen-based contraceptives.

overall_design: Knowing that pre-menopausal women who use estrogen-based oral contraceptives have higher incidence of venous thromboembolism, and that venous thromboembolism is associated with obesity, we used in vivo and in vitro systems to investigate the molecular mechanisms responsible for estrogen- and obesity-induced Protein S downregulation, under lean and obese conditions.

first: Mohammad

last: Mohammad

first: Narender

last: Kumar

first: Sonali

last: Ghosh

first: Ashley

last: Paysee

first: Claudia

last: Leonardi

first: Vijaya

middle: S

last: Pilli

first: Ma.

last: Duhaylungsod

first: Eric

last: Lazartigues

first: Diana

middle: C

last: Polania-Villanueva

first: Sadaf

last: Khan

first: Logan

last: Barrios

first: Rima

last: Chattopadhyay

first: Rafika

last: Yasmin

first: Alaina

last: Guilbeau

first: Manoj

first: Tina

last: Nguyen

first: Li

last: Li

first: Luis

last: Del Valle

first: Mallory

last: Barbier

first: Samarpan

last: Majumder

first: Laurent

middle: O

last: Mosnier

first: Rinku


title: Escalated oxycodone self-administration is associated with activation of specific gene networks in the rat dorsal striatum

city: Baltimore

first: Atul

last: Daiwile

state: MD

address: 251 Bayview Blvd,

department: MNRB

institute: NIDA

summary: The number of individuals diagnosed with opioid use disorder (OUD) has risen steeply because of the increased prescribing of opioid drugs like oxycodone for chronic pain relief. OUD is characterized by loss of control of drug taking, continued drug use in the presence of adverse consequences, and repeated relapses to drug taking. Repeated exposure to oxycodone self-administration can lead to addiction in certain rats while others remain unaffected. Understanding the molecular mechanisms between these two groups holds promise for developing strategies to combat addiction. To identify signaling pathways associated with oxycodone addition, this study used male Sprague-Dawley rats to self-administer oxycodone for 20 days according to short-(ShA, 3 h) and long-access (LgA, 9 h) paradigms. Animals were euthanized after 2 hours of self-administration cessation and their dorsal striata were used for RNA sequencing analysis. LgA rats escalated their oxycodone intake and developed into 2 phenotypes, named long-access high (LgA-H, addicted) and long-access lower (LgA-L, non-addicted) rats, based on the level of escalation and drug taken during the self-administration experiment. RNA sequencing revealed many differentially expressed genes in the oxycodone-addicted rats in comparison to other groups. DAVID analysis indicated that some of these genes were involved in potassium transport, ATP binding, and regulation of synaptic processes. Ingenuity pathway analysis (IPA) revealed previous involvement of some genes in OUD and cognitive processes. RNA sequencing and RT-PCR analysis of dorsal striatum samples unveiled a significant upregulation of potassium channel genes Kcnma1, Kcnk9, Kcnq1, Kcnd3, and Kcng3 in LgA-H rats, which was corelated with oxycodone intake. We also identified increased expression for Cldn3, Serping1, and Serpinh1 in ShA rats. Taken together, these observations identified potassium channels as potential targets for the treatment of oxycodone use disorder.

overall_design: Herein we Long-access (LgA) and Sal rats were trained to self-administer for three sessions: one 3-h session during days 1–5, followed by two 3-h sessions during days 8–14, and then for three 3-h sessions during the rest of the study (days 15–20). Short-access (ShA) rats were trained to self-administer oxycodone for only one 3-h session for the entirety of the study (days 1–20).

first: Ammanuel

middle: Y

last: Wabreha

first: Michael

middle: T

last: McCoy

first: Jean Lud

last: Cadet


title: Aging compromises terminal differentiation program of cytotoxic effector lineage and promotes exhaustion in CD8+ T cells responding to coronavirus infection [scRNA-seq]

city: Dallas

first: Chen

last: Yao

state: Texas

address: 5901 FOREST PARK RD, NS6 218

institute: UT Southwestern Medical Center

summary: T cell aging increases the risk of viral infection-related morbidity and mortality and reduces vaccine efficacy in the elderly. A major hallmark of T cell aging is the loss of quiescence and shift towards terminal differentiation during homeostasis. However, how aging alters the differentiation program of virus-specific T cells during infection is unclear. Here, in a murine coronavirus (MHV) infection model with age-associated increased mortality, we demonstrate that aging impairs, instead of promoting, the terminal differentiation program of virus-specific CD8+ T cells. Upon infection, CD8+ and CD4+ T cells in old mice showed marked reduction in clonal expansion and upregulation of immune checkpoints associated with T cell exhaustion. Bulk and single-cell transcriptomics showed that aging upregulated T cell exhaustion transcriptional program associated with TOX in virus-specific CD8+ T cells and shift the myeloid compartment from immunostimulatory to immunosuppressive phenotype. In addition, aging downregulated the transcriptional program of terminally differentiated effector CD8+ T cells and diminished CX3CR1+ cytotoxic effector lineage. Mechanistically, virus-specific CD8+ T cells from infected aged mice displayed defects in inducing transcription factors ZEB2 and KLF2, which were required for terminal differentiation of effector CD8+ T cells. Together, our study shows that aging impairs terminal differentiation and promotes exhaustion of virus-specific CD8+ T cells responding to coronavirus infection through dysregulating expression of lineage-defining transcription factors.

overall_design: We performed single-cell RNA sequencing on leukocytes isolated from the lung, as well as S598 tetramer-positive CD8 T cells isolated from the spleen and lung of young and old mice on day 7 post-MHV infection.

first: Tuoqi

last: Wu

first: Ziang

last: Zhu

first: Guohua

last: Lou


title: The SAMD1 transcription factor coordinates hematopoietic lineage differentiation and H3K4 methylation status [RNA-seq]

city: Omaha

first: Meg

last: Schaefer

state: Nebraska

address: 985805 Nebraska Medical Center

department: Genetics Cell Biology and Anatomy

institute: University of Nebraska Medical Center

summary: Cell progenitor to progeny transitions depend on precise transcriptional mechanisms to adjust gene expression. The sterile alpha motif-containing 1 protein (SAMD1) regulates a shift in transcriptional activity during embryonic stem cell exit from pluripotency. SAMD1 interacts with and facilitates the activity of the histone H3 lysine demethylating enzyme LSD1. SAMD1 is expressed throughout many biological systems, but its role in hematopoiesis is unknown. In human and mouse hematopoietic stem/progenitor cells, we tested the role of SAMD1 in hematopoiesis and erythropoiesis using loss-of-function approaches. We discovered that SAMD1 promotes expression of critical drivers of hematopoiesis, including the GATA2 transcription factor, while opposing erythroid programs. Loss of SAMD1 in ex vivo differentiating cells increased erythroid differentiation and altered the landscape of histone H3K4 methylation genome-wide. Cohorts of SAMD1-repressed genes are linked to erythropoietic activities. SAMD1 expression promoted ERK signaling via SCF/Kit stimulation in progenitor populations. In erythroid precursor cells, SAMD1 co-occupies chromatin with LSD1 and GATA factors. Whereas SAMD1 downregulates H3K4me2 levels genome-wide, contributing to gene repression, SAMD1 elevates transcription at select sites. To test Samd1 function in hematopoiesis, we performed competitive transplant experiments in mice using shRNA knockdown HSCs. Samd1 knockdown contributed more to peripheral blood mononuclear cells versus control HSCs. Our results establish SAMD1 as a coordinator of H3K4 methylation and stem/progenitor activity in hematopoiesis and erythropoiesis.

overall_design: On day 12 of erythroid differentiation, gene expression profiling was performed on Kit+ primary human CD34+ hematopoietic stem and progenitor cells to compare gene expression of scramble and SAMD1 knockout cells by RNA-seq.

first: Venkatasai

middle: R

last: Dogiparthi

first: Yichao

last: Zhou

first: Kyle

middle: J

last: Hewitt


title: Gene expression profile at single cell level of an orthotopic mouse model with ZEB1 knockdown  in the KPC cell line and control group mouse [spatial transcriptomic]

city: Peking

first: Mingyang

last: Liu

address: No.17, Panjiayuan South, Chaoyang District

country: China

institute: State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital

summary: Pancreatic cancer is characterized by high resistance to chemotherapy and immunotherapy and there are no effective drugs which leads to poor overall survival for pancreatic cancer patients. The transcription factor ZEB1 promotes cellular plasticity and tumor metastasis in pancreatic cancer. We employed single-cell RNA sequencing and spatial transcriptomic sequencing to analyze ZEB1-mediated remodeling of the tumor microenvironment in pancreatic cancer.

overall_design: Spatial transcriptomic sequencing of an orthotopic mouse model injected with KPC-shV and KPC-shZEB1 cells.

first: Shaobo

last: Zhang

first: Yumeng

last: Hu

first: Zhijun

first: Gaoyuan

last: Lv


title: An acid-oxidizing solution containing hypochlorous acid reduces Staphylococcus aureus and improves bacterial diversity in epidermolysis bullosa wounds

first: Ziyou

last: Ren

address: 303 E Chicago Ave

institute: Northwestern University

summary: Epidermolysis bullosa (EB) is a group of rare inherited skin disorders characterized by mechanobullous skin fragility and painful wounds that are readily infected by bacteria, particularly Staphylococcus (S.) aureus. More effective approaches for decreasing wound colonization and infection by pathogenic bacteria are necessary to reduce EB morbidity and mortality. To assess the ability of a low pH, hypochlorous acid (HOCl)-based spray to reduce S. aureus burden, promote wound healing, and restore a healthier skin microbiome. Pilot 12-week open-label study of APR-TD011, a low pH (2.5-3) acid-oxidizing spray containing HOCl (0.0038%), on chronic wounds of EB patients. Patients used the spray daily for 8 weeks on designated wounds. Wounds were assessed clinically and swabbed for microbiome analysis using full-length 16S rRNA sequencing before, at Weeks 4 and 8 of treatment, and at 4 weeks post-treatment. Thirteen of 15 enrolled patients, most of whom had dystrophic EB, were culture-positive for S. aureus at baseline. Sequencing data showed S. aureus had the highest relative abundance (34%), followed by Acinetobacter guillouiae and Pseudomonas poae. S. aureus relative abundance was reduced by Weeks 4 (to 11%), 8 (primary endpoint; to 10%, p<0.01), and still at Week 12 (to 9.7%), including for methicillin-resistant S. aureus. Overall, bacterial diversity increased with treatment and wound sizes decreased, correlating with reduction in S. aureus (p=0.64). These findings suggest that acid-oxidizing HOCl sprays may be an effective adjunctive therapy to reduce bacterial dysbiosis and infection risk in EB wounds, while promoting wound healing.

overall_design:
Genomic DNA was extracted using a Maxwell 16 LEV Blood DNA Kit (Promega, Madison, WI) implemented on a Maxwell 16 Instrument, following the manufacturer’s instructions with minor modifications: a lysozyme incubation (10 ng/μl lysozyme; Thermo Fisher Scientific, Waltham, MA) for 30 minutes at 37°C and bead beating (5 min at 30 Hz twice, 2 min rest in between) using a TissueLyser III (Qiagen, Germantown, MD). Homogenized samples were transferred to the Maxwell cartridges for final DNA purification.
Genomic DNA was prepared for sequencing on a PacBio Revio sequencer using a two-stage PCR protocol, similar to that described for Illumina amplicon library preparation.15 In the first stage of PCR, DNA was PCR amplified with primers 27F and 1492R using domain-level bacterial primers as described by PacBio. The underlined regions, however, represent Oxford Nanopore Universal sequences for tailing PCR primers’ linker sequences. In the second stage of PCR, amplicons from the first stage were used as a template and amplified with primers that contained PacBio Kinnex adapter sequences, combinatorial dual indices, and the ONT linker sequences at the 3’ ends of the primers). Kinnex adapters are bolded, combinatorial indices are indicated with “NNNNNNNNNN”, and ONT linkers are underlined. PCR products from the 2nd stage of amplification were pooled, purified, and subjected to Kinnex library preparation and loading on the Revio instrument. Two-stage library preparation was performed at the Genomics and Microbiome Core Facility (GMCF) at Rush University.  Kinnex library preparation and PacBio sequencing was performed at the DNA Services Facility at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign. Library preparation was performed using a two-stage PCR amplification protocol but with primers targeting the full 16S rRNA gene.16,17 Genomic DNA was initially amplified with an annealing temperature of 50°C for 24 cycles. Barcoding was performed during the 2nd stage, as described previously.

first: Xiaolong

middle: B

last: Burns

first: Elise

last: Stagaman

first: Stefan

last: Green

first: Ashley

first: Lynna

last: Yang

first: Stephanie

last: Rangel

first: Lydia

last: Rabbaa

first: Amy

last: Paller


title: The SAMD1 transcription factor coordinates hematopoietic lineage differentiation and H3K4 methylation status [CUT&RUN]

first: Meg

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Cleavage Under Targets & Release Using Nuclease (CUT&RUN) DNA-sequencing for SAMD1, LSD1, H3K4me2, H3K4me3, H3K27me3, and IgG in control and SAMD1 knockout HUDEP2 cells.

first: Venkatasai

first: Sandipan

last: Brahma


title: Gene expression profile at single cell level of an orthotopic mouse model with ZEB1 knockdown  in the KPC cell line and control group mouse [scRNA-seq]

first: Mingyang

overall_design: Single-cell RNA sequencing of an orthotopic mouse model injected with KPC-shV and KPC-shZEB1 cells.


title: BCLAF1 restrains stress responses in hematopoietic stem cells to support expansion and repopulation [RNA-seq]

city: St. Louis

first: Jeffrey

last: Bednarski

state: Missouri

address: 660 S. Euclid Ave.

department: Pediatrics

institute: Washington University School of Medicine

summary: Hematopoietic stem cells (HSC) rapidly expand during fetal development and after stress. Here, we identify BCLAF1 as a regulator of HSC repopulation activity with functions in propagation of fetal HSCs and hematopoietic reconstitution after stem cell transplantation. Using mice with hematopoietic-specific and inducible deletion of Bclaf1, we find that BCLAF1 promotes fetal HSC expansion but is dispensible for maintenance of adult HSCs at steady state. Loss of BCLAF1 in either fetal or adult HSCs significantly impairs their self-renewal and multi-lineage reconstitution activity after stem cell transplantation. Single-cell RNA sequencing of fetal hematopoietic progenitors reveals that loss of BCLAF1 reduces long-term HSCs and restrains expression of stress response genes. BCLAF1 associates with chromatin throughout the genome of fetal and adult hematopoietic cells, likely through indirect mechanisms, to regulate transcriptional programs. These results establish a novel function for the transcriptional regulator BCLAF1 in limiting stress responses in HSCs to preserve their expansion during embryogenesis and after stem cell transplant.

overall_design:
To investigate the role of BCLAF1 in HSC transcriptional regulation, we generated Vav:Bclaf1f/f mice.
We then performed RNAseq of FACS-sorted HSCs (Lineage- Sca1+ c-Kit+ CD150+ CD48-) and MPP3/4s (Lineage- Sca1+ c-Kit+ CD150- CD48+) cells from E17.5 fetal livers of Bclaf1f/f and Vav-Cre:Bclaf1f/f mice.

first: Stephanie J

last: Crowley

first: Wei

first: Lynn S

last: White

first: Jun

last: Wu

first: Yanan

last: Li

first: Haley

last: Schmidt

first: Kyunghee

last: Choi

first: Jeffrey A

last: Magee

first: Jeffrey J


title: Systems Biology-Based Assessment of Immune Responses to Whole Cell and Acellular Pertussis Vaccines: Rationale, Methodology and Enrollment Procedures for Omics Workflows

city: Rockville

first: Johannes

last: Goll

address: 401 N Washington St

department: Bioinformatics Service Group

institute: The Emmes Company

summary: Given the local and systemic adverse reactions associated with whole cell pertussis vaccines combined with diphtheria and tetanus toxoids (DTP), acellular pertussis vaccines combined with the same toxoids (DTaP) were developed in the 1990s. In comparison to DTP, DTaP vaccines demonstrated reduced reactogenicity and equivalent or improved immunogenicity and efficacy. However, there has been a resurgence of pertussis disease, particularly in DTaP-vaccinated children, suggesting that immunity wanes more quickly with DTaP vaccination. To elucidate the differences in immune responses to DTP and DTaP vaccines, we employed a systems biology-based strategy to compare global changes in gene expression following primary vaccination with either DTP or DTaP. We used RNA-Seq and ribosome profiling (RP) to identify transcriptional and translational signatures, respectively, in peripheral blood mononuclear cells (PBMCs) collected from 50 infant recipients of DTP or DTaP at two time-points (baseline (pre-vaccination at Day 1) and either Day 2 or 8 post-vaccination). We also used standard serologic methods to assess immunogenicity and correlated these results with the transcriptional and translational signatures. Here, we provide a detailed description of the rationale, experimental design, methodology and enrollment procedures used. Given the technical complexity of our approach, our objective is to fill knowledge gaps, describe key quality metrics, and support future publications. In brief, we recovered 4-12 million PBMCs (average 8.9 million) with 99% viability per 2.5 mL blood sample, enabling excellent nucleic acid recovery yields for preparation of high-quality sequencing libraries. In turn, these generated RNA-Seq and RP datasets with sufficient genome coverage, breadth, and depth to enable differential gene expression analyses, demonstrating the validity of our approach to study pertussis vaccine immunology specifically, and its utility to characterize mechanisms of the human immune response to vaccination generally.

overall_design:
To establish basic metrics of quality for RNA-Seq and RP workflows, as our approach had no precedent and working in the context of a vaccine study where the participants were infants presented several significant challenges.
To measure post-vaccination changes in gene expression at two different time points (24 hours and 7 days post-vaccination), and to compare changes in gene expression between vaccine groups (DTP and DTaP) following the first vaccine dose administered at ~2 months of age.
To compare the gene-expression responses measured by RNAseq and RP with those obtained using traditional immunological tools, like antibody responses, inflammatory cytokine production, cell-mediated immunity, and B-cell antibody repertoires.

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

first: Mariana

last: Leguia

first: Antón

last: Vila-Sanjurjo

first: Diana

last: Juarez

first: Alejandra

last: Garcia-Glaessner

first: Ana

middle: I

last: Gil

first: Mayita

last: Alvarez

first: Rubelio

last: Cornejo

first: Sami

last: Cherikh

first: Casey

middle: E

last: Gelber

first: Leigh

middle: M

last: Howard

first: Natalia

last: Jimenez-Truque

first: Kathryn

last: Edwards

first: C

last: Creech

first: Claudio

middle: F

last: Lanata


title: Evolution of the human autopod skeleton [ATAC-seq]

city: Cambridge

first: Terence

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

summary: We investigate the genetic architecture of autopod development at the regulatory and transcriptomic level.

overall_design: Examination of open chromatin regions (ATAC-seq) and differentially expressed genes (RNA-seq) in the developing autopod skeleton.

first: Alexander

last: Okamoto

middle: D


title: BCLAF1 restrains stress responses in hematopoietic stem cells to support expansion and repopulation [CITE-seq]

first: Jeffrey

last: Bednarski

overall_design: E17.5 fetal liver LSK (Lineage- Sca1+ c-Kit+) cells were FACS-sorted from Bclaf1f/f and Vav-Cre:Bclaf1f/f mice. The cells were stained with CITE-seq antibodies (ADTs).

first: Stephanie J

last: Crowley

first: Wei

last: Yang

first: Lynn S

last: White

first: Jun

last: Wu

first: Yanan

last: Li

first: Haley

last: Schmidt

first: Kyunghee

last: Choi

first: Jeffrey A

last: Magee

first: Jeffrey J


title: IGFBP-7 transforms hepatic stellate cells into an HCC-promoting phenotype in MASLD.

city: Tsu city

first: Naoto

last: Fujiwara

state: Mie

address: 2-174 Edobashi

country: Japan

institute: Mie University

summary: Hepatic fibrosis is the strongest contributor to hepatocarcinogenesis in metabolic dysfunction-associated steatotic liver disease (MASLD); however, the underlying mechanisms have yet to be fully elucidated. In 94 human MASLD biopsy samples, artificial intelligence-based morphological phenotyping of hepatic fiber and multi-omics analyses revealed that insulin growth factor-binding protein 7 (IGFBP-7) secreted from senescent periportal endothelial cells might transform stellate cells into a hepatocarcinogenesis-promoting phenotype. To test the effect of IGFBP-7 on HSC, a hepatic stellate cell line, LX-2, was cultured with recombinant IGFBP-7 (100ng/mL), resulting in their transformation to a more activated form than the control.

overall_design: Hepatic stellate cell (HSC) line LX-2 (Merck Sigma-Aldrich, #SCC064) was cultured with DMEM and 2% fetal bovine serum (FBS). After incubation without FBS for 18 hours, cells were treated with IGFBP-7 (100ng/mL, R&D, #1334-B7) or phosphate-buffered saline and were incubated for an additional 24 hours. The total RNA of the treated cells was extracted using TRI Reagent (Sigma-Aldrich) and subjected to RNA sequencing. Library preparation was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequencing was performed with NovaSeq 6000, according to the manufacturer’s instructions.

first: Hayato

last: Nakagawa


title: Evolution of the human autopod skeleton


title: Effects of Ancestral SARS-CoV-2 versus Variants of Concern Delta and Omicron on Megakaryocyte Activation and Transcriptome

city: New York City

first: Florencia

last: Schlamp

state: New York

address: 435 East 30th Street

institute: NYU Langone Health

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is associated with a hyperreactive platelet phenotype, which is thought to contribute to the high incidence of thrombosis in COVID-19 patients. Mutations of SARS-CoV-2 resulted in several virus variants with differences in transmissibility, infectivity and mortality. This study was designed to investigate how SARS-CoV-2 variants of concern, delta and omicron, affect the transcriptome and function of megakaryocytes (MKs) relative to the ancestral WA1 strain.

overall_design: Human CD34+-derived megakaryocytes from 4 unvaccinated COVID-19 donors were infected with WA1, Delta or Omicron SARS-CoV-2 variants or vehicle control for 24 hours.

first: Marcin

last: Sowa

first: Michael

last: Tuen

first: Marie

last: Samanovic

first: Mark

last: Mulligan

last: Berger

first: Tessa

last: Barrett


title: Synergistic Exacerbation of Oral Streptococci-induced pneumonia due to Prevotella intermedia

city: Nagasaki

first: Naoki

last: Iwanaga

address: Sakamoto, 1-7-1

institute: Nagasaki University

summary: Anaerobic bacteria in the oral cavity can cause respiratory infections. However, their precise mechanisms of action remain elusive. Unexpectedly, bacterial flora analysis using 16s rRNA revealed ‘hidden’ mixed infections of anaerobic bacteria and commensal oral Streptococcus species in community-acquired pneumonia. The purpose of this study is to elucidate the mechanisms by which Prevotella intermedia exacerbates oral streptococcal pneumonia.

overall_design: Total RNA of lungs extracted from 12 hours post infection with Streptococcus anginosus and the supernatants of Prevotella intermedia (OMA.14) or control medium (GAM) were compared.

first: Hiroki

last: Ashizawa


title: BCLAF1 restrains stress responses in hematopoietic stem cells to support expansion and repopulation [CUT&RUN]

first: Jeffrey

last: Bednarski

overall_design: CUT&RUN for BCLAF1 on FACS-sorted E17.5 fetal liver HSCs or LSK cells. LSK cells were either native or fixed.

first: Stephanie J

last: Crowley

first: Wei

last: Yang

first: Lynn S

last: White


title: The effects of PD-L1 and SCE over-expression on CAR-NK cell cytotoxicity against tumor cells

first: Fuguo

last: Liu

address: 500 Main Street

department: Koch Institute For Integrative Cancer Research at MIT

institute: Massachusetts Institute of Technology

summary: This experiment aims to investigate how the overexpression of PD-L1 and SCE enhances the cytotoxic activity of CAR-NK cells against tumor cells. Pathway enrichment analysis revealed that CAR-NK cells with reduced HLA-ABC and overexpressed PD-L1 showed enrichment in proliferation and pro-inflammatory pathways. In contrast, CAR-NK cells with reduced HLA-ABC and overexpressed SCE exhibited enrichment in homeostasis-related pathways. On the other hand, cellular stress pathways were more prominently enriched in HLA-ABC reduced CAR NK cells following co-culture with target cells.

overall_design: To elucidate the mechanisms underlying the enhanced NK cell cytotoxicity following PD-L1 and SCE overexpression, NK cells isolated from 4 unrelated donors were transduced with lentivectors expressing shRNA #1+MLSN CAR, shRNA #1+MLSN CAR+PD-L1, or shRNA #1+MLSN CAR+SCE. NK cells from the same donors but without transductions were used as controls. NK cells were labeled with CTV and then cocultured with OVCAR8 target cells or in the media alone for 18 hours in triplicates. The cocultured NK cells were purified by cell sorting and processed for RNAseq.

first: Yiming J

last: Zhang

first: Rizwan

last: Romee

first: Jianzhu

last: Chen


title: Engineered vasculature induces functional maturation of pluripotent stem cell-derived islet organoids

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

summary: Blood vessels play a critical role in pancreatic islet function, yet current methods for deriving islet organoids from human pluripotent stem cells (SC-islets) lack vasculature. We engineered 3D vascularized SC-islet organoids by assembling SC-islet cells, human primary endothelial cells (ECs) and fibroblasts in a non-perfused model and a microfluidic device with perfused vessels. Vasculature improved stimulus-dependent Ca2+ influx into SC-β-cells, a hallmark of β-cell function that is blunted in non-vascularized SC-islets. Furthermore, vascularization accelerated diabetes reversal post-engraftment of a subtherapeutic SC-islet dose. We show that vasculature leads to formation of an islet-like basement membrane that contributes to functional improvement of SC-β-cells. Furthermore, scRNA-seq data predicted BMP2/4-BMPR2 signaling from ECs to SC-β cells, and correspondingly, BMP4 enhanced the SC-β cell Ca2+ response and insulin secretion. Vascularized SC-islets will enable further studies of crosstalk between β-cells and ECs and will serve as an in vitro platform for disease modeling and therapeutic testing.

overall_design: In this analysis, we used single-cell RNA-seq (scRNA-seq) to profile 9197 cells from control and 5 ng/ml BMP4-treated stem cell-derived islets (SC-islets) derived from the H1 human embryonic stem cell line. To characterize gene expression changes in stem-cell β-cells (SC-β-cells), we identified different cell populations by clustering and performed pair-wise comparison of gene expression between control and BMP-4 treated SC-β-cells.

first: Sander

last: Maike


title: STING is crucial for the survival of AML1-ETO leukemia cells

city: Shanghai

first: Yue

last: Sun

address: 131 Dongan Road

institute: Institutes of Biomedical Sciences, Medical College of Fudan University

summary: Even though acute myeloid leukemia (AML) patients with a RUNX1::RUNX1T1 (AE) fusion have a relatively favorable prognosis, approximately 50% relapse within 2.5 years and develop resistance to subsequent chemotherapy1. It is therefore imperative to identify novel therapeutic targets for AE leukemia to improve outcomes. In this study, we unveil that targeting STING effectively suppresses the growth of AE leukemia cells. Both genetic and pharmacological inhibition of STING lead to the diminish of AE leukemia cells. Importantly, in a mouse primary AE leukemia model, STING deletion significantly attenuates leukemogenesis and prolongs the animals' lifespan. Blocking the downstream inflammatory pathway of STING yields similar effects to STING inhibition in AE leukemia cells, highlighting the pivotal role of STING-dependent inflammatory responses in sustaining the survival of AE leukemia cells. Moreover, through a genome-wide CRISPR screen, we identified fatty acid desaturase 2 (FADS2) as a non-canonical factor downstream of STING inhibition that mediates cell death. Inhibition of STING releases FADS2 activity, consequently inducing the synthesis of polyunsaturated fatty acids (PUFAs) and triggering lipid peroxidation-associated cell death2. Taken together, these findings reveal a critical function of STING in the survival of AE-positive AML cells and suggest STING to be a potential therapeutic target for clinical intervention in these patients.

overall_design: To gain insights into the molecular mechanism of STING inhibition in AE leukemia cells,we performed Switching Mechanism at the 5' end of the RNA Transcript sequencing (SMART-Seq) to analyze the mRNA profiles of WT and AE9a c-Kit+ cells treated with DMSO or C-176

first: Yushuang

last: Wu

first: Guozheng

last: Pang

first: Jingru

last: Huang

first: Mengyao

last: Sheng

first: Jiaying

last: Xie

first: Pingyue

first: Yin

last: Wang

first: Dongrui

last: Yin

first: Guangjie

last: Zhao

first: Stefan

middle: K

last: Bohlander

first: Jian

first: Guo-Liang

last: Xu

first: Hai

last: Gao

first: Dan

last: Zhou

first: Yuheng

last: Shi


title: Epigenetic control of the master regulator fumarate nitrate reductase (FNR) contributes to survival of Haemophilus influenzae during lung infection

city: Mutilva Baja

first: Junkal

last: Garmendia

address: Pamplona, 123

country: Spain

institute: Instituto de Agrobiotecnologia, Consejop Superior de Investigaciones Científicas

summary: Regulatory elements that dictate how Haemophilus influenzae adapts to the airways of COPD patients are poorly understood. In this work, global fitness profiling of H. influenzae mutants by transposon mutagenesis/sequencing (Tn-seq) within the mouse lung identified Dam methyltransferase as an in vivo requirement, even though dam mutants grow normally during in vitro culture. In turn, methylation sequencing found that genome-wide Dam methylation patterns were undermethylated at GATC motifs with putative regulatory elements. This was confirmed for the htpG heat-shock chaperone gene, making it the first case of phenotypic variation controlled by variable Dam methylation for H. influenzae. Moreover, RNA sequencing revealed a novel multifactorial regulatory network, in which Dam methyltransferase activity is coordinated with the FNR and Fur transcriptional regulators to control the expression anaerobic defences against host-produced reactive species. Our results indicate key bacterial pathways for survival in diseased environments with high nitrosative stress, where damage to the airways reduces the amount of oxygen in the lungs as is encountered in COPD.

overall_design: To study how H. influenzae adapts to the airways of COPD patients. A key factor, Dam methyltransferase, was studied in aerobic and anaerobic conditions with the comparison of gene expression (RNA-seq) of wild type samples and Dam mutants.

first: Celia

last: Gil-Campillo

first: Begoña

last: Euba

first: Irene

last: Rodríguez-Arce

first: David

last: San León

first: Javier

last: Asensio-López

first: Nahikari

last: López-López

first: Joshua

last: Mell

first: Gabriel

last: Gutiérrez

first: Jeroen

last: Langereis

first: María Antonia

last: Sánchez-Romero


title: An aberrant resurrection of endogenous retrovirus prompts acute myocarditis and heart failure

city: shanghai

first: Junhao

last: Xiong

address: *800 Rd dongchuan

institute: shanghai jiao tong university

type: Methylation profiling by high throughput sequencing

summary: The abberant resurgence of which have been recently found to link to some critical pathologies. To evaluate the occurrence and role of ERV resurrgenece in heart and heart failure (HF), we conducted heart total RNA-seq analysis from mice ischemia-reperfusion (I/R) heart failure models and found that ERVs were activated which is similar in various cross-species models of heart failure. To explore the mechanism of ERVs resurgence we profiled trimethylation at lysine 9 of histone H3 (H3K9me3) ChIP- and MeRIP-seq of cardiomyocytes specific TRIM28 knockout mice heart. The deprivation of TRIM28 in the mouse myocardium attenuated the epigenetic surveillance of H3K9me3 and N6-methyladenosine (m6A), and revived the ERVs, which consequently activated the intracellular antiviral innate immune pathways of TLR7-9 and NF-kappaB and lead to the myocarditis and acute heart failure.

overall_design: For total RNA-seq of I/R mice, ischemia was created by temporarily ligating the left anterior descending coronary artery for 45 min and reperfusion for 24h. Hearts were collected and then extracted and total RNA sequencing was performed. For total RNA-seq, H3K9me3 ChIP-seq and MeRIP-seq of TRIM28 iCKO mice, the genomic deletion of TRIM28 was introduced via an intraperitoneal administration of 25mg/kg tamoxifen dissolved in corn oil for a consecutive five days. After 1week, hearts were extracted then total RNA, ChIP and MeRIP sequencing was performed.

first: Bing

last: Zhang

first: Zilong

last: Geng


title: Dysregulation of histone methylation in SV40 chromosomes during replication results in aberrant transcription and chromatin structure

city: Grand Forks

first: Barry

last: Milavetz

state: North Dakota

address: 1301 N Columbia Rd Stop 9037 RM W129

institute: University of North Dakota School of Medicine and Health Sciences

summary: Since early and late transcription are both regulated from the same central regulatory region in SV40 chromatin, the location of nucleosomes carrying histone modifications may contribute to controlling the direction of transcription from the regulatory region. This could occur through the generation of active chromatin in the direction of transcription and repressive chromatin in the opposite direction. In order to test this hypothesis, we have characterized the products of SV40 transcription and location of nucleosomes carrying histone modifications in SV40 chromatin following treatment of infected cells with inhibitors of histone methylation metabolism. The inhibitors used included GSK-LSD1 to inhibit demethylation of H3K4me1 and H3K9me1, A366 to inhibit the introduction of H3K9me1, and UNC1999 to inhibit the introduction of H3K27me3. The results are consistent with a regulatory model in which nucleosomes carrying H3K9me1 and H3K27me3 located at the ends of the SV40 regulatory region act to regulate transcription.

overall_design: Infections and treatment with inhibitors


title: Whole transcriptome analysis of control human fibroblasts, TGFβ-induced human fibroblasts, and fibroblasts co-cultured with normal lung decellularized scaffolds and fibroblasts co-cultured with bleomycin-induced lung decellularized scaffolds.

city: Wenzhou

first: Chan

last: Chen

state: Zhejiang

address: Nanbaixiang, Ouhai District

department: Department of Geriatric Medicine

institute: The First Affiliated Hospital of Wenzhou Medical University

summary: Fibrosis refers to the abnormal proliferation and excessive accumulation of fibrous tissue in an organ or tissue, typically caused by chronic injury or inflammation. Fibroblasts play a crucial role in the initiation and progression of fibrosis, with their excessive activation and overproduction of ECM being key mechanisms in fibrotic diseases. In this study, we constructed decellularized lung scaffolds from normal mice and bleomycin-induced lung decellularized scaffolds to analyze and compare the differential gene expression in control human fibroblasts, TGFβ-induced human fibroblasts, fibroblasts co-cultured with normal lung decellularized scaffolds, and fibroblasts co-cultured with bleomycin-induced lung decellularized scaffolds. This investigation aims to explore the impact of ECM on fibroblast activation and its underlying mechanisms.

overall_design: We divided human fibroblasts into four groups: control group, TGFβ-induced group, co-culture with normal lung decellularized scaffold group, and co-culture with bleomycin-induced lung decellularized scaffold group. After three days of co-culture, RNA was extracted from the human fibroblasts.

first: Zhiyi

last: Wang

first: Jingwen

last: Yang

first: Peisen

last: Zhou


title: A highly conserved sRNA downregulates multiple genes, including a Sigma-54 transcriptional activator, in the virulence mode of Bordetella pertussis

city: Bethesda

first: Hernan

last: Lorenzi

state: Maryland

address: 8 Center Dr, Bldg 8A

department: National Institutes of Diabetes and Digestive and Kidney Diseas

institute: National Institutes of Health

summary: Bacterial sRNAs together with the RNA chaperone Hfq post-transcriptionally regulate gene expression by affecting ribosome binding or mRNA cleavage. In the human pathogenBordetella pertussis, the causative agent of whooping cough, hundreds of sRNAs have been identified, but their roles inB. pertussisbiology are mostly unknown. We have performed RNA-seq analyses to determine gene expression changes forB. pertussisTohama Ivs.its derivative with a deletion of the Hfq-dependent sRNA S17, whose level increases dramatically in the virulence (Bvg+) mode.

overall_design:
WT and delS17 strains were grown under nonmodulating conditions (no MgSO4; Bvg+ mode).  This is the mode in which the level of S17 sRNA is enhanced.
We then performed differential gene expression analysis between WT and delS17 samples.

first: Minji

last: Sim

first: Qing

first: Kyung

last: Moon

first: Deborah

last: Hinton


title: CD45+ Epcam- poluation scRNAseq analysis in control and Goblet-Y/T-Scgb1a1CreERT mouse lung tissues.

city: Boston

first: Xaralabos

last: Varelas

address: 72 E. Concord St

department: Department of Biochemistry and Cell biology

institute: Boston University Chobanian & Avedisian School of Medicine

summary: The gole of this experiment is to get an in depth understanding of the immune population responses in mouse lungs presented with goblet cell metaplasia in the airway upon Yap/Taz deletion in Scgb1a1+ cells.

overall_design: Three Scgb1a1CreERT+ and three Scgb1a1CreERT- animals received daily tamoxifen injection for five consecutive days by intraperineal injection. 7 days after the last dosage of tamoxife, mouse lungs were harvested, prepared into single cell suspension. Cells were stained with fluorescent-conjugated CD45 and Epcam antibodies. Consequently, CD45+/Epcam- cells were collected for scRNA-seq.

last: Cheng


title: Effect of Cardiac LIM Protein (CSRP3) on human proximal tubule epithelial cells

city: Portland

first: Michael

last: Hutchens

state: OR

address: 3710 SW US Veterans Hospital Road R&D5

department: Anesthesiology, Nephrology

institute: Oregon Health & Science University

summary: Cardiac LIM protein (CSRP3) is released from the heart after cardiac injury and transits the plasma to the renal filtrate. CSRP3 has a well described transcriptionally-active role in myocardiocyte development and response to stress. Although it appears in endocytic vesicles within tubular epithelial cells in vivo it is unknown whether it alters tubular epithelial cell transcription.  Therefore to test the hypothesis that CSRP3 alters PTEC transcription, human primary PTEC were exposed to physiologic concentration of CSRP3 (10nM) for 6h prior to bulk RNA sequencing.

overall_design: For bulk RNA sequencing, hPTECs were treated with 10 nM rCSRP3 for 6h following 24h serum starvation. After rCSRP3 treatment, cells were harvested, then total RNA was extracted. hPTEC were treated with either PBS or CSRP3 and then subjected to RNA isolation and bulk RNA sequencing.

first: Yoshio

last: Funahashi

first: Tahnee

last: Groat


title: AFF4 RNA-seq in A549 cell line

city: Anhui

first: Xueyi

last: Feng

address: TangHe street

department: College of Life Science

institute: Anhui Medical University

summary: We aimed to detect the mRNA expression levels in stable-transfected A549 cells after transfection with AFF4 knockdown or control virus.

overall_design: Extract total RNA from  A549 cell line after transfection with AFF4 over-expression or control virus, each sample use one well in 6 wells plate A549 cells.

first: Dai

last: Qian

first: Xufeng

last: Yao


title: FUS controls muscle differentiation and structure through LLPS mediated recruitment of MEF2 and ETV5 [RNA-Seq]

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

summary: FUS, a major RNA binding protein with prominent roles in transcription and splicing, is mutated in agressive forms of amyotrophic lateral sclerosis (ALS), a neurodegenerative disease characterized by muscle weakness and motor neuron degeneration. We show here that ALS-associated FUS mutations lead to ultrastructural defects in muscle biopsies of ALS-FUS patients, in particular in sarcomeres and mitochondria, that are recapitulated in iPSC-derived myocytes. Studies in mouse and Drosophila models demonstrate an evolutionary-conserved cell autonomous function of FUS in muscle development. Mechanistically, FUS is required for transcription of MEF2 dependent pathways and directly binds to the promoter of a subset of genes with binding sites for PEA3 family ETS transcription factors, in particular ETV5. We further show that FUS co-activates transcription of MEF2 dependent genes with ETV5. Importantly, FUS phase separates with ETV5 and MEF2A, and MEF2A binding to FUS is potentiated by ETV5. Last, Etv5 haploinsufficiency exacerbates muscle weakness in a knock-in model of ALS-FUS. Thus, FUS is required for muscle structure through its phase separation-dependent recruitment of ETV5 and MEF2, and this pathway is compromised in ALS-FUS.

overall_design: RNA-Seq in siCT and siFUS C2C12 myoblast cells

first: Gina

last: Picchiarelli

first: Anne

last: Zienand

first: Salim

last: Megat

first: Amr

last: Aly

first: Marije

last: Been

first: Saskia

last: Hutten

first: Erin

last: Sternburg

first: Stéphane

last: Dieterle

first: Marica

last: Catinozzi

first: Valérie

last: Demais

first: Laura

last: Tzeplaeff

last: Huebers

first: Dagmar

last: Zeuschner

first: Albert

last: Ludoplh

first: Anne-Laurence

last: Boutilier

first: Tobias

last: Boesckers

first: Dorothee

last: Dormann

first: Maria

last: Demestre

first: Chantal

last: Sellier

first: Clotilde

last: Lagier-Tourenne

first: Eric

last: Storkebaum

first: Luc

last: Dupuis


title: Effect of depletion of RNH1 on gene expression in KYSE510 cell

first: He

last: Zhang

state: Shanghai

address: Tongji University, 1239 Siping Road, Yangpu District, Shanghai

institute: School of Life Science and Technology, Tongji University

summary: Accumulation of R-loops causes DNA breaks and genome instability, as well as regulates tumorigenesis in a mechanism that remains poorly understood. We knockdown the ribonuclease RNase H1 (RNH1) to generate a cell model of induced R-loop accumulation. We showed that the expression of a large number of genes was disturbed after RNH1 knockdown, including 961 genes with more than twofold differences . The KEGG pathway indicates that the target genes are enriched in the Hippo signaling pathway, Wnt signaling pathway, and other tumor-associated biological processes .

overall_design: To establish a novel induced R-loop model, we knocked down the ribonuclease RNH1 in KYSE510 cells with shRNA.

first: Jixing


title: Single cell transcriptional landscape of liver transplant rejection reveals tissue persistence of clonally expanded, treatment-resistant T cells

city: Cincinnati

first: Erica

last: DePasquale

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology

institute: Cincinnati Children's Hospital

summary: T cell mediated rejection (TCMR) affects ∼50% of pediatric liver transplant recipients within 5 years, and late TCMR is associated with graft failure due to ineffective treatment. Although CD8+ T cells promote late TCMR, their clonal expansion, intragraft persistence, localization, and gene expression remain largely undefined. Herein, single-cell RNA sequencing and immune repertoire profiling of 30 cryopreserved liver biopsies from rejecting and non-rejecting pediatric patients identified expanded intragraft CD8+ T cell clonotypes (CD8EXP) and their gene expression profiles. Expanded CD8+ clonotypes (CD8EXP) bore markers of effector and CD56hiCD161- 'NK-like' T cells, retaining their clonotype identity and phenotype in serial biopsies despite histologic TCMR resolution. CD8EXP clonotypes localized to portal infiltrates during active TCMR and persisted in the lobule after histologic TCMR resolution. MultiNicheNet analysis revealed differential crosstalk between Kupffer cells (KC) and CD8EXP, with activation of TGFß and downregulation of CD47 immune checkpoint signaling. Therefore, persistenting intragraft CD8EXP clones remain active despite TCMR treatment and may contribute to long-term allograft fibrosis and failure of operational tolerance.

overall_design: 10X Genomics Chromium Next GEM Single Cell V(D)J Reagent Kit was used on needle biopsies from human liver rejection patients and associated healthy controls (pre-transplantation donors).

first: Anna

last: Peters

middle: A

first: Gousia

last: Begum

first: Krishna

last: Roskin

first: Michael

last: Kotliar

first: Artem

last: Barski

first: Nathan

last: Salomonis

first: Tiffany

last: Shi

first: Sarangarajan

last: Ranganathan

first: E

last: Woodle

first: David

last: Hildeman


title: RNA interactome capture identifies key proteins for herpesviral gene expression

city: Haifa

first: Tamar

last: Lahav

address: Zor

department: Biology

country: Israel

institute: Technion

summary: The primary mRNA sequence determines its secondary structure and the repertoire of interacting RNA-binding proteins (RBPs). The resulting mRNA ribonucleoprotein complex (mRNP) then influences all stages of the life of an mRNA. Here, we determined the mRNP composition of individual Kaposi Sarcoma Herpesviral (KSHV) mRNAs. In KSHV, the viral RNA regulator ORF57 ensures the translation of viral mRNAs by increasing mRNA stability and nuclear export. By optimizing an LNA/DNA mixmer RNA capture protocol to both transfection and virus replication settings, we identified the RBPome of specific ORF57-dependent viral transcripts. Both capture and eCLIP experiments robustly detected ORF57 as a direct RNA binder to an AU-rich motif, which may enable ORF57 to discriminate viral from cellular RNAs. Furthermore, we identified the RNA processing factor SRSF3 as a key regulator of viral replication. This work facilitates RNA-interactome studies of specific mRNAs and sheds light on how the mRNP composition orchestrates gene expression.

overall_design: Enhanced crosslinking and immunoprecipitation (eCLIP) for RBM42 upon DNA damage and mock treatment on HCT116 cells. For each treatment we performed 2 replicates and comapred the eCLIP to size match input control

first: Carolin

last: Vogt

first: Marco

last: van Ham

first: Ruchira

last: Bhowmik

first: Amir

last: Argoetti

first: Daniel

middle: P

last: Depledge

first: Lars

last: Steinbrück

first: Jasper

last: Götting

first: Carolina

last: Henkel

first: Andrea

last: Cuadra Granados

first: Yael

last: Mandel-Gutfreund

first: Lothar

last: Jänsch

first: Jens

last: Bohne


title: Gene expression profile in single cell level of Drosophila brain associated with different gut microbial condition

city: Gainesville

first: Adam

last: Wong

state: Florida

address: 1881 Natrual Area Drive, Steinmetz Hall

department: Entomology and Nematology Department

institute: University of Florida

summary: The gut microbial community is closely linked to the host's brain function. In this study, we created adult Drosophila melanogaster flies with a germ-free gut and utilized single-cell RNA sequencing to compare brain gene expression between axenic and conventional flies.

overall_design: Axenic flies were produced by chlorinating the egg surface and maintaining the treated eggs on an axenic diet. Brains from both axenic and conventional flies were dissected, with 20 brains collected for each sample. The study included flies that were one-week-old and four-week-old. The difference in gene expression level was analzyed by single-cell RNA sequencing.

first: Dianshu

last: Zhao


title: Differential effects of lithium on metabolic dysfunction in astrocytes derived from bipolar disorder patients

city: Daejeon

first: Dayeon

last: Kim

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

summary: Metabolic alterations have been observed in the brains of patients with bipolar disorder (BD), a neuropsychiatric disorder characterized by biphasic mood episodes of mania and depression. However, the specific contributions of glial cells to these metabolic changes in BD patients remain largely unknown and have not been extensively studied. Here, we investigate the metabolic characteristics of induced astrocytes (iAstrocytes) derived from induced pluripotent stem cells of BD patients and their responses to lithium treatment. The gene expression profiles of iAstrocytes from BD patients (BD iAstrocytes) indicate dysregulation of metabolic processes in BD iAstrocytes. Compared to iAstrocytes from control subjects, BD iAstrocytes showed decreased mitochondrial respiration, increased glycolysis, and elevated lactate secretion. These changes in metabolic pathways suggest impaired mitochondrial function.  Additionally, we observed reduced protein expression within the oxidative phosphorylation complex and decreased reactive oxygen species production, further supporting the impaired mitochondrial function in BD iAstrocytes. Intriguingly, BD iAstrocytes showed an accumulation of lipid droplets (LDs) in both volume and number, possibly reflecting metabolic stress-induced LD accumulation. Lithium, a commonly prescribed treatment for BD, selectively attenuated LD accumulation exclusively in BD iAstrocytes from lithium responders, while it failed to restore mitochondrial dysfunction and increased lactate secretion. Our findings provide novel insights into understanding the metabolic dysfunction in the brains of BD patients and shed light on molecular mechanisms of lithium action, particularly regarding astrocytes. The LDs in BD iAstrocytes from lithium non-responders may serve as a useful readout for drug screening to identify suitable medications for these patients.

overall_design: To investigate the phenotype of BD astrocyte, control and BD patients' iPSCs were differnetitated into iAstrocytes. Then. we performed total RNA sequencing using the obtained iAstrocytes.

first: Jinju

last: Han


title: Developmental toxicity of the fungicide Boscalid and primary metabolite M510F01 in zebrafish embryos

city: East Lansing

first: Karilyn

last: Sant

state: MI

address: 1355 Bogue St., Life Science B440

department: Pharmacology & Toxicology

institute: Michigan State University

summary: Succinate Dehydrogenase Inhibitors (SDHIs) have been used for decades, with new formulations cropping up as fungi evolve. Boscalid was introduced to United States agriculture in 2003 and was determined to be effective for fungal management and safe for aquatic discharge and human consumption. Recent studies have found Boscalid’s primary metabolite, M510F01, on crops and in irrigation runoff as well. However, limited information is available about the aquatic and developmental toxicity of M510F01. The goal of our study was to compare and contrast the developmental toxicity of Boscalid with its metabolite, M510F01. Zebrafish (AB, wild-type strain) embryos were exposed to Boscalid or M510F01 from 3-96 hours post fertilization (hpf) at concentrations of 0.03, 0.3, or 3 µg/L. Embryos were examined for aberrant morphologies at 96 hpf using microscopy. Boscalid exposures at concentrations of 3 µg/L increased incidence of blue sac disease by 72%, craniofacial malformation by 97%, pericardial edema by 69%, delayed swim bladder inflation by 35%, and yolk edema by 83% (p<0.001 for all morphologies). 3 µg/L M510F01 increased the incidence of blue sac disease by 25% and yolk edema by 17% (p=0.005). Additionally, Boscalid exposures at 3 µg/L indicated a significant effect on fish length at 96 hpf (p<0.05).To assess whether Boscalid and M510F01 impact Cytochrome P450 1a (Cyp1a) activity, embryos were exposed to Boscalid or M510F01 (0.03 µg/L) from 96-100 hpf concurrently to 7-ethoxyresorufin (EROD)—a fluorometric indicator of Cyp1a activity. There is no significant change in acute EROD activity for Boscalid or M510F01; however, chronic exposure of Boscalid and M510F01 at 0.03 µg/L indicated a significant decrease in Cyp1a activity in the gut and M510F01 additionally reflected a significant decrease in Cyp1a activity in the liver at 0.03 µg/L. RNA sequencing and pathway analysis were performed to assess the mechanisms of xenobiotic response to Boscalid and M510F01 exposures (0.03 µg/L). Boscalid significantly upregulated pathways involved in ATP production including oxidative phosphorylation, glycolysis, and TCA cycle. Overall, this research suggests that M510F01 exhibits reduced aquatic and developmental toxicity when compared to Boscalid.

overall_design: Zebrafish embryos were exposed to Boscalid or M510F01 from 3-96 hpf at concentrations of 0.03, 0.3, or 3 µg/L, with exposures renewed daily. Embryos were monitored for survival and hatching, and imaged to assess structural anomalies and malformations. RNA was isolated and sequenced at 96 hpf.

first: Julia

last: Goebel

first: Ashley

last: Schwartz

first: Angus

last: Fletcher


title: NRF2 ACTIVATORS FOR AGE-RELATED CHRONIC DISEASES: THEORETICAL LIMITATIONS AND PRACTICAL APPROACHES (Nrf2 peptide)

city: Moscow

first: Sergey

last: Nikulin

address: 7, Vavilova st.

department: Faculty of Biology and Biotechnology

institute: HSE University

summary: One of the major metabolic responses to counteract aging, inflammation, and various chronic diseases including neurodegeneration, is the so call antioxidant pathway controlled by Nrf2 transcription factor. Nrf2 protein stability is regulated via interaction with the redox sensor Keap1, an adapter protein in Cullin III ubiquitin ligase complex. The search for Nrf2 activators is mainly focused on compounds that either chemically modify sensor thiols in Keap1 or competitively displace Nrf2 from the ubiquitin ligase complex. The latter approach is considered as the most appropriate one for continuous administration without side effects, which are unavoidable in case of non-specific chemical modifiers of Keap1. However, true displacement activators show a significant offset, by many orders of magnitude, when switched from homogeneous assay to cell-based assays. This phenomenon originates, as we show here, from high micromolar intracellular concentrations of Keap1. A guarantee for high specificity of an alkylating Nrf2 activator is its targeted delivery. A transcriptomic analysis for a cell-permeable Nrf2-peptide bearing a fumarate moiety shows the activation of the antioxidant program only, confirming the high specificity of such approach. However, aging-linked neurodegeneration is also known to build-up Bach1, an Nrf2 target gene and competitive transcriptional repressor for Nrf2. Therefore, an ideal combination could be a benign Nrf2 activator and Bach1 inhibitor in one molecule, as represented by the recently developed HPPE. HPPE demonstrates an intersection of the activated antioxidant pathway with the Nrf2 peptide, and, in addition to that, shows a big pool of genes overlapping with the known inhibitors of Bach1 - zinc and tin protoporphyrins.  Hence, at present moment, HPPE presents a unique combination of the two desired activities beneficial for age-related neurodegeneration.

overall_design: Total mRNA profiles of SH-SY5Y cells treated with Nrf2-peptide-linked fumarate.

first: Irina

last: Gazaryan

first: Andrey

last: Poloznikov


title: BRRIAR lncRNA alters breast cancer risk by modulating interferon signaling in cis and in trans through BHLHE40 and RIG-I

status: Public on Aug 19 2025

city: Brisbane

first: Juliet

last: French

address: 300 Herston Rd

country: Australia

institute: QIMRB

summary: Interferons (IFNs) are key regulators of cell proliferation and anti-tumor immunity. We identified a breast cancer-associated long noncoding RNA (lncRNA), BRRIAR, that modulates IFN signaling in estrogen receptor-positive (ER+) breast cancer. BRRIAR is transcribed from an 11 kb enhancer cluster at 3p26, and its reduced expression is linked to breast cancer GWAS risk variants. Primarily expressed in ER+ breast tumors, BRRIAR exhibits dual functionality, acting both in cis and in trans. Nuclear BRRIAR regulates BHLHE40 expression through its enhancer, while cytoplasmic BRRIAR binds to the pattern recognition receptor RIG-I, modulating its activation. BRRIAR RNA overexpression activates RIG-I signaling, inducing IFN responses that selectively trigger apoptosis in ER+ breast tumor cells in vitro and in vivo, while promoting immune activation in human peripheral blood mononuclear cells. These findings emphasize the complex regulatory mechanisms at GWAS risk regions, reveal the critical role of lncRNAs as modulators of tumor immunity and identify BRRIAR as a promising RNA-based therapeutic for ER+ breast cancer.

overall_design: H3K27ac ChIPseq data in T47D cells after CRISPRi-BRRIAR or using gRNAs targeted to the 3’ end of the enhancer cluster. T47D cells were cross-linked with 1% formaldehyde (Merck) at 37oC for 10 min, rinsed with phosphate buffered saline (PBS; TMO) containing 5% bovine serum albumin (BSA; Scientifix) and harvested in PBS containing protease inhibitor cocktail (PIC; Roche). Harvested cells were centrifuged for 2 min at 3,000 rpm. Cell pellets were resuspended in lysis buffer (1% sodium dodecyl sulfate (SDS; Merck), 10 mM EDTA (TMO), 50 mM Tris-HCl, pH 8.1, PIC) and sonicated three times for 15 s at 70% duty cycle (Branson SLPt) then centifuged at 13,000 rpm for 15 min. Supernatants were resuspended in dilution buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, pH 8.1). Antibodies detecting H3K27ac (2 μg; Abcam) or an IgG control (2 μg; Abcam) were prebound for 6 h to protein G Dynabeads (TMO), then incubated with the chromatin for 16 h. The complexes were then washed six times in RIPA buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1% IGEPAL CA-630, 0.5% sodium deoxycholate (Merck), 0.1% SDS, 1 mM DTT, PIC). To reverse cross-links, the complexes were incubated at 65oC for 16 h in elution buffer (1% SDS, 0.1 M NaHCO3), then DNA fragments purified using the QIAquick spin kit (Qiagen). Libraries were prepared using the NEBNext Ultra II DNA library prep kit (NEB), according to manufacturer’s instructions.

first: Mainá

last: Bitar

first: Stacey

last: Edwards

first: Jonathan

last: Beesley


title: Single-cell gene expression of neocortex after transient Yamanaka factor expression during brain development

city: Barcelona

first: Daniel

last: Toro Ruiz

address: C/Casanova 143

department: Dept Biomedical Sciences

institute: Universitat de Barcelona

summary: Yamanaka factors (YFs) can reverse some aging features in mammalian tissues, but their effects on the brain remain largely unexplored. Here, we used single cell RNA sequecing (scRNA-seq) to analyze the effects of YFs induction during cortical development.

overall_design: We used the conditional inducible-four factors (i4F) mouse line, which allows the induction of YFs in a Tet-ON system. This line was crossed with a Cre-dependent floxed rtTA and the nervous system-specific Nestin-Cre (Nes) mouse line. In this mouse model (i4F-Nes), YF expression was induced by administering doxycycline from E10.5 to E14.5. The rostral region of the mouse neocortex was collected at E15.5. Two i4F-Nes samples and two littermate control (CTR) samples were prepared for scRNA-seq analysis.

first: Yi-Ru

last: Shen

first: Rüdiger

last: Klein

last: del Toro


title: AFF4 promotes tumor progression by modulating PTEN/PI3K/AKT/mTOR axis to accelerate glycolysis in lung adenocarcinoma

city: Hefei

first: qian

last: dai

state: Anhui

address: Tanghe Road, Yaohai District

summary: Bioinformatics analysis and western blotting were used to examine AFF4 expression in lung adenocarcinoma cells and tissues. The changes in cell proliferation, migration, invasion and apoptosis were determined by loss- and gain-of-function assays. Metabolite determination assays of glucose and lactate were used to evaluate the glycolysis level. Transcriptome sequencing, cleavage under targets (CUT)&Tag, dual-luciferase report assay and a series of rescue experiments were used to explore the underlying mechanisms.

overall_design: AFF4 Cleavage under targets and tagmentation sequencing (CUT&Tag-seq) were performed in A549 and PC9 cells

first: xueyi

last: Feng


title: MicroRNA profiling of normal and imflammation induced nuclues pulposus and annulus fibrosis primary cells

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

summary: In order to investigate the changes and different function of normal and degenerated nuclues pulposus (NP) and annulus fibrosis (AF) derived exosomes, we take advantages of high through-put sequencing technology to fully reveal the small RNA content of both normal and degenerated NP and AF primary cell derived exosomes.

overall_design: We collect the normal NP and AF tissues samples from spine fracture patients who underwent discectomy. The collected samples were washed with PBS and subjected to primary culture immediately. The samples were first operated under magnifier to separate NP and AF tissue, the tissues were then lysed using type II collagenase and the lysed cells were put to culture flasks for primary culture. 10%FBS high-glucose DMEM were used as culture medium for primary cell culture. When cells reach 80% confluent, the cell were lysed with trypsin for passage. After 2 passages, the primary cells were ready to perform exosome collection. For exosome collection, we use 1% exosome-free FBS/DMEM for culture, the medium were collected at a 3-days interval, and the collected culture medium of  were subsequently subjected to ultracentrifugation. After the ultarcentrifugation, the pellet were washed with PBS and ultarcentrifugated again before use.

first: Wen

last: Yuan


title: CaSR activation triggers mandibular overgrowth in fMP patients and mice

city: chengdu

first: Han

last: Fang

state: yunnan

address: 四川省成都市武侯区人民南路三段17号四川大学华西校区东区

institute: 四川大学

summary: Mandibular prognathism (MP) is the most common type of dento-maxillofacial deformity in East Asian populations. Genetic studies have revealed several MP-associated loci, suggesting that MP could be inherited as familial MP (fMP). However, functional verifications and in-depth mechanistic investigations of these loci are limited. For this study, we recruited 5 fMP families with 17 fMP members and 7 normal members. We first compared the clinical features of the 17 fMP members with 31 non-familial MP patients, finding a stronger mandibular overgrowth phenotype in the fMP subjects. Next, we performed whole-exome sequencing (WES) analysis with members of the 5 fMP families and singled out a potential fMP-associated pathogenic variant in the CASR gene—namely, rs117375173—the mutation introduces an amino acid substitution (A601G) in exon 7 and confers gain-of-function in Calcium-Sensing Receptor (CaSR). The rs11735173 variant changes the CaSR protein structure toward a semi-active state, similar to CaSR activated by L-tryptophan (L-Trp). To verify the regulating roles of CASR in mandibular bone growth, we further generated different mouse models with abnormal CaSR function. L-Trp administration effectively activate CaSR/GNAQ expression in vivo and in vitro. The MC3T3-E1 cell line transfected with CaSR with rs117375173 showed increased osteogenic differentiation and collagen synthesis at transcriptional level. Local injection of L-Trp in the mandible of growing mice significantly increased the mandibular length and BMD, due to activated osteogenic activity and suppressed bone resorption. At the same time, loss-of-function of CaSR in osteogenic progenitors caused mandibular growth retardation in Gli1-CreER; Casrfl/fl; tdTomatofl/+ mice. In conclusion, our study reveals that abnormal functioning of CaSR affects mandibular bone development and may contribute to the pathogenesis of fMP, providing a theoretical and experimental basis for the early diagnosis of and therapeutic strategies for fMP in clinical practice.

overall_design: The MC3T3-E1 cells were plated at a cell density between 500,000 and 800,000 cells/well in a 6-well plate and cultured with Dulbecco’s modified Eagle’s medium + GlutaMAX (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. After 24 h, the CaSRmut plasmid and CaSRwt  plasmid were transfected into the cells with Lipofectamine 3000 (Thermo Fisher Scientific). After 48 h, cells were harvested, and RNA was extracted using TRIzol™  (Thermo Fisher Scientific). RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). And then bulk RNA sequencing.

first: Peiran

last: Li

first: Yali

last: Wei

first: Ruiye

last: Bi


title: Adenosine Kinase and ADAL Coordinate Detoxification of Modified Adenosines to Safeguard Metabolism

city: Sendai

first: Fan-Yan

address: Seiryo-machi 4-1

institute: Tohoku University

summary: RNA contains diverse post-transcriptional modifications, and its catabolic breakdown yields numerous modified nucleosides requiring correct processing, but the mechanisms remain unknown. Here, we demonstrate that three RNA-derived modified adenosines, N6-methyladenosine (m6A), N6,N6-dimethyladenosine (m6,6A), and N6-isopentenyladenosine (i6A), are sequentially metabolized into inosine monophosphate (IMP) to mitigate their intrinsic cytotoxicity. After phosphorylation by adenosine kinase (ADK) they undergo deamination by adenosine deaminase-like (ADAL). In Adal knockout mice, N6-modified adenosine monophosphates (AMPs) accumulate and allosterically inhibit AMP-activated protein kinase (AMPK), dysregulating glucose metabolism. Furthermore, ADK deficiency, linked to human inherited disorders of purine metabolism, elevates levels of the three modified adenosines, resulting in early lethality in mice. Mechanistically, excessive m6A, m6,6A, and i6A impairs lysosomal function by interfering with lysosomal membrane proteins, thereby disrupting lipid metabolism and causing cellular toxicity. Through this nucleotide metabolism pathway and mechanism, cells detoxify modified adenosines, linking modified RNA metabolism to human disease.

overall_design: To investigate the impact of ADK and ADAL-mediated metabolism of m6A, m6,6A, i6A, we generated constitutive ADK knockout mice and ADAL knockout mice. We performed RNA-seq using liver and brain from age-matched postnatal ADK KO mice and WT mice (P4), and liver, soleus, and gastrocnemius (GC) muscle of adult ADAL KO mice and WT mice at age of 10-weeks-old.


title: Maintenance of Fibroblast Identity During Cardiac Reprogramming and Heart Repair [ATAC-seq]

city: Baltimore

first: Chulan

last: Kwon

state: MD

address: 720 Rutland Ave, Ross 954

department: Medicine, Cardiology, Heart & Vascular Institute, Institute for Cell Engineering, and Cellular and Molecular Medicine

institute: Johns Hopkins University

summary: Direct cardiac reprogramming (CR) of fibroblasts into induced cardiomyocytes represents a promising therapeutic avenue to treat heart failure as it would use the injury by-product and transform fibroblasts into new cardiac muscle thereby achieving the unmet medical need of cardiac regeneration. However, low reprogramming efficiency limits its clinical potential. Our lab identified four transcription factors playing a conserved role as barriers to CR. Knock-down of these barriers increase CR five-fold compared to MGT (MEF2C; GATA4; TBX5) overexpression alone. Exploration of direct downstream targets of these barriers identified proteoglycan sulfation as potential pathway regulating cell fate stability.   Proteoglycan sulfation, specifically Carbohydrate Sulfotransferase 7 (CHST7), was identified as a conserved barrier to CR. Knockdown of Chst7 in mouse and human fibroblasts significantly enhances CR, increasing expression of cardiac-specific markers and promoting sarcomeric organization. Functional screening of proteoglycan core proteins identifies CD44 as a conserved barrier to reprogramming. Additionally, Chst7 and Cd44 functionally interact to mediate cell fate stability. RNA sequencing and transcription factor analysis identify Junb as the main TF mediating Chst7-regulated transcription during CR. Mechanistic studies of Chst7-regulated pathway genes demonstrate that Chst7 knockdown reduces Pip4k2c expression, establishing a novel regulatory axis between Chst7/Cd44/Junb and Pip4k2c. In vivo, shRNA-mediated Pip4k2c knockdown significantly enhances MGT-mediated CR, increasing cardiac muscle content and reducing fibrosis after myocardial infarction. These findings establish proteoglycan sulfation as a key regulator of cell fate stability, offering new opportunities to improve CR therapies. Thus, proteoglycan sulfation-associated genes might represent an innovative target space to enhance CR for therapeutic purposes.

overall_design: bulkATAC-seq of iMGT (Mef2c, Gata4, Tbx5)-Myh6-eGFP-MEF cell line reprogrammed into induced-cardiomyocytes at day 1 post-MGT overexpression comparing siControl and siChst7 conditions.

first: Michaela

last: Romero

first: Sean

last: Murphy

first: Yu-Ling

last: Chang

first: Alexandre

last: Colas


title: Histone Variants and H2A Ubiquitination [Cut&Tag]

city: Richmond

first: Hengbin

last: Wang

state: VA

address: 401 College Street

department: Massey Cancer Institute

institute: Virginia Commonwealth University

summary: Cut&Tag sequencing of mouse embryonic stem cell lines with knockin of tagged histone variants

overall_design: Established knockin cell lines for tagged H2BC1 and H2AZ2 histone variants.  To study distribution of these histone variants, performed Cut&Tag.


title: Efficient Induction of U87 Differentiation into Neurons by Small Molecules.

city: Suzhou

first: Hu

last: ya'nan

state: Jiangsu

address: 199 Ren-Ai Road, Suzhou Industrial Park

department: Department of Cell Biology

institute: Medical College of Soochow University

summary: The investigation of effective, prompt, and universally applicable strategies for inducing the differentiation of glioblastoma (GBM) into terminally differentiated cells, such as astrocytes or neurons that cease cell division, has become a crucial aspect of GBM differentiation therapy, aiming to reduce the risk of recurrence.The utilization of a small-molecule cocktail, known as YFSS (Y27632, Forskolin, SB431542, and SP600125), which selectively targets the ROCK, cAMP, TGF-β, and JNK signaling pathways, respectively, successfully induced differentiation in human GBM cell line U87 within 7 days.Transcriptome sequencing analysis provided insights into the signaling pathways implicated in YFSS-induced differentiation, encompassing both cellular proliferation and neuronal differentiation. This study, which delved into approaches to rapidly and efficiently induce neuronal differentiation of GBM cells, and provided a thorough understanding of the underlying molecular mechanisms, holds great promise as a novel and encouraging strategy for the treatment of GBM.

overall_design: In order to gain a deeper understanding of the molecular mechanism underlying the differentiation of GBM cells into neurons induced by YFSS, an intergroup correlation analysis (WGCNA, GO, KEGG and GSEA) was conducted on the differentially expressed gene sets within the U87 transcriptome at multiple time points (0, 1, 3, 5, and 7 days).

first: Ya'nan

last: Hu

first: Huanxiang

last: Zhang


title: JPF promotes repair of early nontraumatic osteonecrosis of the femoral head by inhibiting NAMPT/STK11/HMGCR/ACAT1 signal axis-mediated lipid production

city: Beijing

first: Li

last: tao

address: 16 Dongzhimen Inner South Street, Dongcheng District, Beijin

institute: Institute of Traditional Chinese Medicine, Chinese Academy of Traditional Chinese Medicine

summary: Jianpi Huogu Formula (JPF) has achieved good curative effects in nontraumatic osteonecrosis of the femoral head (NONFH) in clinical practice. However, its underlying pharmacological mechanisms remain unclear. Herein, chemical constituents of JPF were systematically identified by UPLC-Q-TOF-MS, and the putative targets were predicted using TCMIP v2.0 platform. Then, the transcriptomic profiling based on clinical cohorts were carried out to identify the early NONFH-related genes and JPF effective targets. Following network-based calculation and functional enrichment analysis, JPF candidate targets against early NONFH were screened and further validated by a series of in vivo experiments. As a result, a total of 299 chemical constituents in JPF were identified under positive and negative ion mode of mass spectrometry. Pharmacologically, JPF was demonstrated to effectively reduce the content of blood lipids and the number of adipocytes in bone marrow, decrease the serum levels of various inflammatory factors, relieve the joint pain, maintain the normal morphology of bone trabeculae and reduce bone loss of early NONFH rats. Mechanically, JPF markedly suppressed the activities of NAMPT, NMNAT1 and NMNAT3 in the affected femoral head tissues, leading to the reduce of NAD+ synthesis and its mediated ATP synthesis, subsequently promoted the combination of STK11 with energy receptor AMPK, which further reduced the accumulation of cholesterol esters in the liver and the amount of cholesterol esters transported to the blood. In conclusion, JPF may promote the repair of early NONFH with reducing lipid production, improving blood hypercoagulable state and restoring normal bone metabolism by regulating NAMPT/STK11/HMGCR/ACAT1 signal axis.

overall_design: The whole blood samples collected from human in different groups were used to detect the gene expression profiling which may represent the overall status of the body and the pathological characteristics of the affected tissues during early NONFH development and progression by RNA-seq. Differential genes among different groups were identified by the edge R package with Pvalue < 0.05 and fold change >1. Among them, the JPF effective targets (DEGs of JPF pre-treatment group vs. JPF post-treatment group) were identified.The JPF consists of Citrus reticulata Blanco, Paeonia lac tiflor a Pall., Codonopsis pilosula (Franch.) Nannf., Rehmannia glutinosa Libosch., Cinnamomum cassia Presl, Angelica sinensis (Oliv.) Diels, Cyathula officinalis Kuan, Ligusticum chuanxiong Hort., Atractylodes macrocephala Koidz., Poria cocos (Schw.) Wolf, and Deerhorn glue.

first: Tao

first: Zhaochen

last: Ma

first: Xueting

last: Liu

first: Chu


title: A dual histone code specifies the binding of heterochromatin protein Rhino to a subset of piRNA source loci [ChIP-seq]

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

summary: Animal germ cells deploy a specialized small RNA-based silencing system, called the PIWI-interacting RNA (piRNA) pathway, to prevent aberrant expression of transposable elements and maintain genome integrity.  In Drosophila germ cells, the majority of piRNA populations originate from dual-strand piRNA clusters, genomic regions highly enriched in transposon fragments, via an elaborate protein machinery centred on the heterochromatin protein 1 homolog, Rhino.  Although Rhino binds to peptides carrying trimethylated H3K9 in vitro, it is not fully understood why it only occupies a fraction of H3K9me3-decorated heterochromatin in vivo.  Recent work uncovered that Rhino is recruited to a subset of piRNA clusters by the zinc finger protein Kipferl.  Here we identify a Kipferl-independent mode of Rhino targeting that is dependent on the histone H3 lysine 27 methyltransferase Enhancer of Zeste and the presence of H3K9me3 and H3K27me3 marks.  At Kipferl-independent sites, we find that Rhino, through its dimeric chromodomain, specifically binds to loci marked by both H3K9me3 and H3K27me3.  These results expand our understanding of the characteristic binding profile of the heterochromatin protein Rhino and reveal a role for dual histone modifications in defining the specificity of a chromatin binding protein.

overall_design: ChIP-seq from ovaries in Drosophila melanogaster characterising H3K27me3, H3K9me3 or Rhino.

first: Abdou

last: Akkouche

first: Emma

last: Kneuss

first: Susanne

last: Bornelöv

first: Yoan

last: Renaud

first: Evelyn

middle: L

last: Eastwood

first: Jasper

last: van Lopik

first: Nathalie

last: Gueguen

first: Mingxuan

last: Jiang

first: Pau

last: Creixell

first: Stéphanie

last: Maupetit-Mehouas

first: Benjamin

last: Czech Nicholson

first: Emilie

last: Brasset

first: Gregory

last: Hannon


title: Nucleosome Positioning Shapes Cryptic Antisense Transcription [RNA-seq]

city: Vienna

first: Jian Yi

last: Kok

address: Dr.-Bohr-Gasse 3

country: Austria

institute: GMI - Gregor Mendel Institute of Molecular Plant Biology

summary: Maintaining transcriptional fidelity is essential for precise gene regulation and genome stability. Despite this, cryptic antisense transcription, occurring opposite to canonical coding sequences, is a pervasive feature across all domains of life. How such potentially harmful cryptic sites are regulated remains incompletely understood. Here, we show that nucleosome arrays within gene bodies play a key role in suppressing cryptic transcription. Using the fission yeast Schizosaccharomyces pombe as a model, we demonstrate that CHD1-family chromatin remodelers coordinate with the transcription elongation machinery, specifically the PAF complex, to position nucleosomes at sites of cryptic transcription initiation within gene bodies. In the absence of CHD1, AT-rich sequences within gene bodies lose nucleosome occupancy, exposing promoter-like sequences that drive cryptic initiation. While cryptic transcription is generally detrimental, we identify a subset of antisense transcripts that encode critical meiotic genes, suggesting that cryptic transcription can also serve as a source of regulatory innovation. These findings underscore the essential role of nucleosome remodelers in maintaining transcriptional fidelity and reveal their broader contributions to cellular homeostasis and evolutionary adaptability.

overall_design: To investigate the effect of different mutants on transcription, mRNA-seq was performed on either 11 remodeler single deletion mutants (expA), CHD1 mutants (expB), mutants where the C-terminal domains of Hrp1 and Hrp3 were swapped (expC) or mutants of Prf1 (expD).


title: Nucleosome Positioning Shapes Cryptic Antisense Transcription [Mnase-seq]

overall_design: To investigate the effect of S. pombe mutants on transcription, MNase-seq was performed on either 11 remodeler single deletion mutants (expA) or hrp1Δhrp3Δ and hrp1Δhrp3Δprf1Δ deletion mutants (expB).


title: Nucleosome Positioning Shapes Cryptic Antisense Transcription [ChIP-seq]

overall_design: To investigate the effect of the localization of H2A.Z/H3K36me3 (expA), Hrp1 or Hrp3 (expB) and H2BK119ub (expC) onto chromatin genome-wide, ChIP-seq was performed.


title: Differential expression of microRNA profiles of four induced pluripotent stem cells lines derived from distinct tissues

city: Bangkok

first: Chanatip

last: Metheetrairut

state: Bangkok

address: 2 Wanglang Rd.

department: Department of Biochemistry, Faculty of Medicine Siriraj Hospital

country: Thailand

institute: Mahidol University

summary: This study compared microRNA profiles of four iPSC lines derived from dermal fibroblasts, hair follicle keratinocytes, peripheral blood T cells, and exfoliated renal epithelial cells by copy number count method.

overall_design: In this study, total RNA were extracted from iPSC lines derived from distinct tissues, dermal fibroblasts, hair follicle keratinocytes, peripheral blood T cells, and exfoliated renal epithelial cells and their microRNA profiles were studied by copy number count method (nCounter® miRNA expression assay: Human v3 miRNA panel).

first: K

last: Trakarnsanga

first: N

last: Vorasan

last: Tantarungsee

first: M

last: Wattanapanitch

first: C

last: Vatanashevanopakorn

first: B

last: Suktitipat


title: RNA-sequencing analysis of colon RNA from mice with compound mutations of XBP1, caspase-8, TNFR1 and MLKL.

city: Cologne

first: Ulrike

last: Göbel

state: NRW

address: Joseph Stelzmann Strasse, 26

department: Bioinformatics Core Facility

institute: CECAD Research Center

summary: To purpose of this study was to assess how intestinal epithelial cell (IEC)-specific ablation of XBP1 or caspase-8 alone or in combination affected mucosal immune homeostastis and inflammation, and the role of TNFR1 and MLKL in the associated phenotypes. First, expression of colonic RNA from mice with combined IEC-specific XBP1 and caspase-8 ablation (Xbp1IEC-KO Casp8IEC-KO) was compared with Casp8IEC-KO, Xbp1IEC-KO, and wild-type mice. In addition, Xbp1IEC-KO Casp8IEC-KO Mlkl-/-  and  Xbp1IEC-KO Casp8IEC-KO Tnfr1IEC-KO mice were  compared with Xbp1IEC-KO Casp8IEC-KO, Casp8IEC-KO, Xbp1IEC-KO as well as wild-type control mice. For each mouse line 5 individual mice were analysed.

overall_design: RNAs from the colons of control, Xbp1IEC-KO, Casp8IEC-KO, Xbp1IEC-KO Casp8IEC-KO, Xbp1IEC-KO Casp8IEC-KO, Xbp1IEC-KO Casp8IEC-KO Tnfr1IEC-KO and Xbp1IEC-KO Casp8IEC-KO Mlkl-/- mice were isolated. Then RNA-sequencing-assisted gene expression analysis were performed from these isolated RNAs.

first: Kaya

last: Göksu Gökberk

first: Göbel

last: Ulrike

first: Pasparakis

last: Manolis


title: Nucleosome Positioning Shapes Cryptic Antisense Transcription

overall_design: To investigate the effect of CHD1 mutants on nascent transcription, PRO-seq was performed on hrp1Δ, hrp3Δ and hrp1Δhrp3Δ mutants.

first: Kok

last: Jian Yi