title: Dads matter, too: The behavioural and neurogenomic effects of receiving paternal care

city: University Park

first: Jason

last: Keagy

state: PA

address: 410 Forest Resources Bldg

department: Ecosystem Science and Management

institute: Penn State University

summary: Offspring are often influenced by the care they receive from their parents. However, we know little about the underlying neurogenomic mechanisms. Using a half-sib design, threespine stickleback fish were either raised by their fathers or hand-reared (“orphaned”). As offspring developed, they were tested in one of three behavioural assays: an open field assay with a simulated predator attack, a social behaviour assay with a simulated predator attack, and a scototaxis assay. Offspring that received parental care were bolder, more social, and less anxious. Fish in the open field assay had their brains sampled one hour following the simulated attack; brains were sampled at the same time from full-sib controls. These brains were processed for gene expression (via Tag-seq) and chromatin accessibility (via ATAC-seq). Experiencing paternal care affected brain gene expression, but sex was also a major factor, despite the fish being reproductively immature. The predator attack in the open field assay affected expression of fewer genes. Sex, and to lesser extent, paternal care, also influenced chromatin accessibility at a whole genome scale. Our findings further our understanding of the mechanistic basis for offspring response to variation in the care they receive from their parents.

overall_design: Using a half-sib design, threespine stickleback fish were either raised by their wild-caught fathers (from Putah Creek, CA = Day 10) or hand-reared (“orphaned” = Day 0). Prior to sexual maturity, when these offspring were 6-8 months old, a subset were individually introduced to an open field assay (= open-field) and allowed to explore for 10 minutes. At 10 minutes, a model sculpin was moved through the pool in one complete circuit simulating a predatory attack. The subsequent behaviour of the juvenile fish was observed for an additional 10 minutes. Following this observation, the fish was left in the open field assay without any more disturbance. Sixty minutes after the attack, the juvenile fish was gently captured, euthanized via decapitation and its brain quickly dissected. Half of the brain was placed in RNAlater for subsequent RNA extraction for 3'TagSeq and the other half was placed in cold PBS and Roche cOmplete Mini Protease Inhibitor Cocktail (PIC) for processing for ATAC-seq. Each fish that went through the open field assay was paired with a full-sibling who was gently removed from its home tank and acted as a ‘baseline control’ (= baseline). This fish did not go into the pool, but had its brain dissected within 30 minutes of the fish with which it was paired. Fish were sexed with a DNA marker.

first: Alison

last: Bell


title: BMAL1 represses transposable elements independently of CLOCK in pluripotent cells [Hi-C]

status: Public on Aug 14 2025

city: Granada

first: Ivan

middle: Fernández

last: Rengel

address: Avenida de la Ilustración 114

country: Spain

institute: GENyO

summary: Genome profiling of BMAL1,TRIM28 and H3K9me3 analyzed by ChIP-seq in JM8+/+ and Bmal1-/- mESCs. Genome profiling of FlagBMAL1 in mESCs. High throughput capture chromosome conformation analysis (Hi-C) in  JM8+/+ and Bmal1-/- mESCs. mRNA-seq analysis of JM8+/+ and Clock-/- mESCs

overall_design: In situ Hi-C (High-throughput Chromosome Conformation Capture) assays were performed in two biological replicates of mutant and wild-type cells to assess the 3D genome structure changes upon BMAL1 depletion

first: Amador

last: Gallardo

first: María

last: Martí-Marimon

first: Marc

middle: A

last: Martí-Renom

first: David

last: Landeira


title: The effect of NDUFA5 expression on bystander cells cultured in conditioned media of chemotherapy-induced senescent cells

status: Public on Aug 13 2025

city: Pittsburgh

first: Katherine

last: Aird

address: 5051 Centre Ave.

country: USA

institute: University of Pittsburgh School of Medicine

type: Expression profiling by high throughput sequencing

summary: Cellular senescence has been shown to contribute to deliterious cancer phenotyores through modulation of the tumor microenvironment through the senescence assosciated sectretome (SAS). Senescence is induced in ovarian cancer by chemotherapy. We found that bystander cells exposed to the SAS from chemotherapy indiuced cells weakens adhesion and and promotes dissemination. We further identified expression of the complex I subunit NDUFA5 is required for this process. Understanding how the SAS modulates gene expression downstream of NDUFA5 expression is important to linking complex I activity to adhesion and may lead to novel targets to exploit to increase chemotherapeutic efficacy.

overall_design: To determine the role the SAS regulating bystander cell transcription downstream of NDUFA5 expression, control or NDUFA5 knockout (two independant sgRNA) cells were cultured in the conditioned media of cisplatin chemotherapy-induced senescent cells (SCM) or DMF control treated proliferative cells (PCM). All samples were done in triplicate.

middle: M

first: Aidan

middle: R

last: Cole


title: AI662270-GRP94 axis couples the unfolded protein response to mitochondrial dynamics during acute myocardial infarction

city: Shanghai

first: Xiangdong

last: Yang

address: Xietu Road

country: China

institute: Zhongshan Hospital Affiliated to Fudan University

summary: Endoplasmic reticulum stress (ERS) response, triggered by myocardial ischemia, contributes to cardiac injury through unresolved mechanisms. Our study reveals that the chaperone GRP94 attenuates mitochondrial fragmentation and ischemic damage by inhibiting OPA1 hydrolysis to S-OPA1 post-acute myocardial infarction (AMI). Mechanistically, hypoxia induces a transcriptional switch where transcription factor YY1 dissociates from lncRNA Oip5os1 and binds lncRNA AI662270, promoting GRP94 transcription. Cardiac-specific GRP94 overexpression reduced infarct size and improved cardiac function. Conversely, GRP94 or AI662270 knockdown exacerbated injury. Furthermore, GRP94-Anxa2 interaction (identified by Co-IP/MS) activates AKT signaling to stabilize long-form OPA1 (L-OPA1), preserving mitochondrial integrity. Targeting the AI662270/GRP94/OPA1 axis thus offers a novel therapeutic strategy for acute ischemic cardiomyopathy by modulating ER-mitochondria crosstalk.

overall_design: Total RNA was isolated from WT and Hdc-/- mouse hearts at one and seven days post-surgery using TRIzol reagent (Takara) for RNA-seq analysis. Sequencing read quality was initially assessed with FastQC (version 0.11.9) following preliminary quality control (version 0.20.1). Gene expression was quantified by aligning reads to the reference genome using HISAT2 (version 2.1.0) and counting with HTSeq-count (version 0.11.2). Expression values were normalized to FPKM to account for gene length and sequencing depth.


title: Interferon-sensitized hematopoietic progenitors dynamically alter organismal immunity [scRNA-seq]

city: New York

first: Dr. Shruti

last: Naik

state: NY

address: 1425 Madison Ave

department: Immunology and Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

summary: Inflammation has enduring impacts on organismal immunity. However, the precise mechanisms by which tissue-restricted inflammation conditions systemic responses are poorly understood. Here, we leveraged a highly compartmentalized model of skin inflammation and identified a surprising type I interferon (IFN)-mediated activation of hematopoietic stem/progenitor cells (HSPCs) that results in profound changes to systemic host responses. Post-inflamed mice were protected from atherosclerosis and had worse outcomes following influenza virus infection. This IFN-mediated HSPC modulation was dependent on IFNAR signaling and could be recapitulated with the administration of recombinant IFNα. Importantly, the transfer of post-inflamed HSPCs was sufficient to transmit the immune suppression phenotype. IFN modulation of HSPCs was rooted both in long-term changes in chromatin accessibility and the emergence of an IFN-responsive functional state from multiple progenitor populations. Collectively, our data reveal the profound and enduring effect of transient inflammation and more specifically type I IFN signaling and set the stage for a more nuanced understanding of HSPC functional modulation by peripheral immune signals.

overall_design: 8-week old female, C57BL/6J mice were treated topically with imiquimod (post-inflamed; PI) or petrolium jelly (as control) for 7 days. Mice were then allowed to recover for 23 more days, at which point animals were fed a Western-Diet for 1 or 4 weeks. Mice were then euthanized and bone marrow harvested. LSK (Lin-/Sca+/Kit+) cells were flow-sorted and single cell RNA-seq performed.

first: Ikjot

last: Sidhu

first: Aleksandr

last: Prystupa

first: Ada

last: Weinstock

first: Shruti


title: The effect of Ndufa5 expression on bystander cells cultured in conditioned media of chemotherapy-induced senescent cells

summary: Cellular senescence has been shown to contribute to deliterious cancer phenotyores through modulation of the tumor microenvironment through the senescence assosciated sectretome (SAS). Senescence is induced in ovarian cancer by chemotherapy. We found that bystander cells exposed to the SAS from chemotherapy indiuced cells weakens adhesion and and promotes dissemination. We further identified expression of the complex I subunit Ndufa5 is required for this process. Understanding how the SAS modulates gene expression downstream of Ndufa5 expression is important to linking complex I activity to adhesion and may lead to novel targets to exploit to increase chemotherapeutic efficacy.

overall_design: To determine the role the SAS regulating bystander cell transcription downstream of Ndufa5 expression, control or Ndufa5 knockdown (two independant shRNA) cells were cultured in the conditioned media of cisplatin chemotherapy-induced senescent cells (SCM) or DMF control treated proliferative cells (PCM). All samples were done in triplicate.


title: Epigenome-wide association study of blood DNA methylation and markers of physical performance indicates subtle differences across levels of cardiovascular fitness

city: Budapest

first: Ferenc

last: Torma

state: Pest

address: Alkotas st. 42-48

department: Research Institute of Sport Science

country: Hungary

institute: Hungarian University of Sports Science

type: Methylation profiling by genome tiling array

summary: An EWAS study investigating the associations between DNA cytosine methylation status in blood and human physical performance measures in a cross-sectional setting among senior-aged male and female individuals.

overall_design: This EWAS, conducted in a cross-sectional cohort design, aimed to investigate potential associations between VO2max, maximal hand grip force, maximal jump height, and cardiorespiratory fitness categories with DNA methylation status in circulating blood.


title: Transcriptomic profiling of irradiated senescent IMR90 cells treated with CDK4/6 or JAK inhibitors

city: La Jolla

first: Xue

last: Lei

state: CA

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

summary: Human fetal lung fibroblasts (IMR90) were induced to undergo senescence via ionizing radiation (IR). Ten days post-IR, RNA was collected from proliferating, senescent+DMSO, senescent+Palbociclib (2 µM), and senescent+Ruxolitinib (2 µM) conditions. Cells were treated on Days 4, 6, 8 and 10 after IR. This dataset examines how CDK4/6 or JAK inhibition affects gene expression in senescent cells.

overall_design: IMR90 cells were exposed to ionizing radiation to induce senescence. Treatments began on Day 4 post-irradiation and were repeated on Days 6, 8 and 10. Cells were harvested on Day 11 for RNA-seq. Experimental groups include: 1) proliferating control, 2) senescent+DMSO, 3) senescent+Palbociclib (2 µM), 4) senescent+Ruxolitinib (2 µM). RNA was isolated and sequenced using the Illumina platform.

first: Peter

middle: D

last: Adams

first: Adarsh

last: Rajesh


title: Hepatocyte‑specific Ccnd1 knockout in aged mice reduces inflammatory signaling

summary: We performed hepatocyte‑specific knockout of Ccnd1 in 17‑month‑old C57BL/6J mice using AAV8‑TBG‑saCas9 with Ccnd1‑targeting sgRNA versus Rosa26 control. After 3 weeks, livers were harvested for bulk RNA‑seq to assess effects of elevated Ccnd1 with age.

overall_design: Upon receipt, mice were rested for ≥2 weeks and maintained on normal chow. At 17 months, mice received retro‑orbital AAV8‑TBG‑saCas9–U6-sgCcnd1 (3×10¹¹ vg/mouse) or Rosa26 control; livers (m‑lobe) were harvested 3 weeks later for bulk RNA‑seq.


title: RNA Sequencing of Mycobacterium tuberculosis-infected macrophages treated with meclizine.

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

summary: The ability of Mycobacterium tuberculosis (Mtb) to tolerate antibiotics is a major impediment in the treatment of tuberculosis. This antibiotic tolerance is influenced by the host cells in which the bacteria reside, as Mtb senses host cues, and the bacterial response can provide an enhanced ability to withstand anti-TB drugs. Previouslyt, we have shown that Mtb exhibits redox heterogeneity in terms of its mycothiol redox potential (EMSH) giving rise to three broad subpopulations  EMSH-reduced, EMSH-basal, and EMSH-oxidized Mtb specifically inside the macrophages. Among these, the EMSH-reduced Mtb exhibit enahnced tolerance to several anti-TB drugs while the EMSH-basal and EMSH-oxidized subpopulations  are more susceptible. In this study, we have discovered a novel host-directed therapy molecule- meclizine, which enhances the drug susceptible population and diminishes the tolerant population.

overall_design: Bone marrow-derived macrophages were infected with Mtb expressing Mrx1-roGFP2 and were treated with 20uM meclizine or equivalent amount of DMSO (0.2%). At 24h post-infection, infected macrophages were flow-sorted using GFP as a marker for infection and RNA-Seq was performed for these sorted macrophages.

first: Vikas

last: Yadav

first: Sarthak

last: Sahoo

first: Nitish

last: Malhotra

first: Mohit

last: Jolly

first: Aswin Sai Narain

last: Seshasayee


title: Bulk RNA‑seq of IMR90 fibroblasts in IR‑induced senescence with siRNA knockdowns of CCND1, CDK4, CDK6 and controls

summary: We profiled transcriptomes of IR‑induced senescent IMR90 fibroblasts subjected to siRNA‑mediated knockdown of CCND1, CDK4, CDK6 (and CDK4+6), alongside two non‑targeting controls. Transfections occurred on days 4/5 and 7/8 post‑IR; all samples were harvested day 10 for RNA extraction. Differential expression identifies kinase‑specific roles in sustaining inflammatory and DNA damage responses in senescence.

overall_design: Conditions (n=3 each): • Proliferating (No IR) • Senescent + NT1 • Senescent + NT2 • Senescent + CCND1 KD • Senescent + CDK4 KD • Senescent + CDK6 KD • Senescent + CDK4+CDK6 KD Harvest day 10 post‑IR/transfections


title: Identification of SOK1-dependent transcriptome changes under anaerobic conditions in the yeast Candida albicans

city: Houston

first: Jose

middle: Christian

last: Perez

state: TX

address: 6431 Fannin

institute: UTHealth Houston

summary: Dietary components influence microbial composition in the digestive tract. Although often viewed as energy sources, dietary components are likely to shape microbial determinants of intestinal colonization beyond metabolism. Here, we report that a dietary long-chain fatty acid enhances the yeast Candida albicans colonization of the murine gut partly by eliciting modifications to the fungal cell surface. Mice fed an oleic acid-rich diet were readily colonized by C. albicans and exhibited higher fungal load in feces compared to rodents fed an isocaloric control diet. Surprisingly, β-oxidation, a catabolic process to break down fatty acids for energy production, was dispensable for C. albicans to colonize the high-oleic acid diet-fed mice. We identified SOK1 as an oleic acid-induced kinase. RNA-Seq was employed to identify SOK1-dependent transcriptome changes. We found that SOK1 influences multiple cellular functions and components in C. albicans, including oxidoreductase activity, metabolism, and cell periphery.

overall_design: Comparison of the transcriptome of the two Candida albicans strains SC5314 (= WT) and JCP_1525 (Δsok1) in YNB with final concentration of 0.2% oleic acid (OE). The strains were grown anerobically at 30°C for 24 hours. RNA purification was performed from cells harvested from liquid cultures. Directional mRNA library preparation (with poly A enrichment) and sequencing using NovaSeq PE150 mode was executed at Novogene Corporation Inc.

first: Musfirat

last: Shubaita

first: Elena

last: Lindemann-Perez

middle: C


title: Polycomb Repressive-Deubiquitinase Complex Safeguards Oocyte Epigenome and Female Fertility by Restraining Polycomb Activity [RNA-Seq]

city: Cincinnati

first: Zhiyuan

last: Chen

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: Polycomb group proteins are essential for oogenesis, yet mechanisms underlying the non-canonical Polycomb landscapes in oocytes remain unclear. Here we report BAP1, a core component of the Polycomb Repressive-Deubiquitinase (PR-DUB) complex, as a key negative regulator of Polycomb activity during oogenesis. BAP1 restricts pervasive H2AK119ub1 accumulation in oocytes and protects oocyte-specific broad H3K27ac, particularly within gene-poor regions, from ectopic H3K27me3 deposition. While PR-DUB has been linked to gene repression, in oocytes BAP1 primarily promotes transcription and contributes minimally to Polycomb-mediated silencing. BAP1-deficient oocytes cannot support preimplantation development due to impaired maternal-to-zygotic transition and defective embryonic enhancer activation. Notably, aberrant H3K27me3 landscape established in BAP1-null oocytes persists into early embryos. Together, these findings reveal a critical role for PR-DUB in safeguarding the oocyte epigenome by protecting euchromatin from ectopic Polycomb activity, rather than enforcing transcriptional repression.

overall_design: This study is to investigate how loss of BAP1 may impact transcriptome and chromatin states of mouse oocytes and early embryos. Total RNA-seq and H2AK119ub1/H3K27me3/H3K27ac CUT&RUN were performed for control (Bap1 flox/flox) and conditional KO (Gdf9-iCre, Bap1 flox/flox) fully grown oocytes. The control and conditional KO oocytes were fertilized with wild type sperm, resulting control and maternal KO embryos. Total RNA-seq were performed for control and maternal KO embryos at late 1-cell, early 2-cell, and late 2-cell stages. H3K27me3/H3K27ac CUT&RUN were performed for both groups at late 2-cell stage.

first: Jinwen

last: Kang

first: Peiyao

last: Liu

first: Shoko

last: Ichimura

first: Lauryn

last: Cook


title: Identification of oleic acid-induced transcriptome changes under anaerobic conditions in the yeast Candida albicans

summary: Dietary components influence microbial composition in the digestive tract. Although often viewed as energy sources, dietary components are likely to shape microbial determinants of intestinal colonization beyond metabolism. Here, we report that a dietary long-chain fatty acid enhances the yeast Candida albicans colonization of the murine gut partly by eliciting modifications to the fungal cell surface. Mice fed an oleic acid-rich diet were readily colonized by C. albicans and exhibited higher fungal load in feces compared to rodents fed an isocaloric control diet. Surprisingly, β-oxidation, a catabolic process to break down fatty acids for energy production, was dispensable for C. albicans to colonize the high-oleic acid diet-fed mice. RNA-Seq was employed to identify oleic acid-induced transcriptome changes under anaerobic conditions. We identified SOK1 as an oleic acid-induced kinase that dictates cell wall mannan exposure and binding to intestinal mucin under anaerobic conditions. Furthermore, oleic acid induced the expression of several C. albicans transcription factors that positively regulate intestinal colonization via remodeling of the fungal cell surface.

overall_design: Comparison of the transcriptome of the Candida albicans strain AHY940 (= WT) in YNB either with final concentration of 0.2% oleic acid (OE) or 0.02% glucose (dextrose, DX). The strains were grown anerobically at 30°C for 24 hours. RNA purification was performed from cells harvested from liquid cultures. Directional mRNA library preparation (with poly A enrichment) and sequencing using NovaSeq PE150 mode was executed at Novogene Corporation Inc.


title: Alveolar Macrophages Maintain Tissue Localization and Gain Enhanced Anti-Tumor Activity in Lewis Lung Carcinoma-Reprogrammed Lung Microenvironment

city: 安徽省

first: Liqin Ma

middle: Liqin

last: Ma

state: 合肥市

address: 安徽省合肥市蜀山区宿松路与观海路交口西北角

institute: 合肥综合性国家科学中心大健康研究院

summary: The role of alveolar macrophages (AMs) in lung carcinogenesis has been extensively studied, yielding significant insights. However, the status of AMs in tumor-bearing lungs remains incompletely characterized. Using orthotopic Lewis Lung Carcinoma (LLC) mouse models, we found that tumors induced an inflammatory extra-tumoral lung microenvironment (ETLME), distinct from the immunosuppressive tumor microenvironment (TME). T cells with an exhaustion phenotype and tumor-associated macrophages (TAMs) mainly accumulated in the TME rather than the ETLME. Surprisingly, AMs were absent from the tumor lesions and remained in the lung tissues, but they displayed a more active dynamic balance between proliferation and death in ETLME. Furthermore, AMs presented an activated phenotype characterized by upregulation of CD11b and downregulation of Siglec-F, elevated expression of inflammatory genes, and enhanced phagocytic and efferocytotic activity. Notably, AMs in ETLME retained their lipid metabolism capacity and responsiveness to external stimuli. More importantly, LLC-experienced AMs display enhanced anti-tumor ability. These findings indicate that AMs maintain their tissue localization and functional integrity within the ETLME.

overall_design: BAL fluid was collected from the tumor-bearing and control mice. AMs were resuspended at a density of 1×10⁵ cells/mL in complete DMEM (supplemented with 10% FCS), seeded into a 24-well plate (1 mL/well). Non-adherent cells were then removed after incubating for 30 min. AMs were stimulated for 4 hours with DMEM medium containing 400 ng/mL lipopolysaccharide (LPS) from E. coli 055:B5 (InvivoGen, tlrl-b5lps) or in LPS-free medium (as control) for 4 hours. RNA-seq samples were generated from 2-3 mice.

first: Mengfei

last: Ren

first: Jiaxiang

last: Dou

first: Qian

last: Yue

first: Liqin

first: Hang

last: Yu

first: Shengwen

last: Shang

first: Shijie

last: Wang

first: Jian

first: Tingting

last: Li

first: Fengqi


title: Polycomb Repressive-Deubiquitinase Complex Safeguards Oocyte Epigenome and Female Fertility by Restraining Polycomb Activity [CUT&RUN]

type: Genome binding/occupancy profiling by high throughput sequencing


title: Gene expression profiling of the CD33+ myeloid population of PBMCs following co-culture with HDBCLs or recombinant MIF/IL-10 stimulation.

city: Kamigyo-ku, Kyoto

first: Yu

last: Inoue

state: Kyoto

address: 465 Kajii-cho, Kawaramachi-Hirokoji

department: Division of Hematology and Oncology, Department of Medicine

country: Japan

institute: Kyoto Prefectural University of Medicine

summary:
Human diffuse large B-cell lymphoma cell lines (HDBCLs) induce monocytic myeloid-derived suppressor cells (M-MDSCs) from healthy peripheral blood mononuclear cells (PBMCs) through the secretion of macrophage migration inhibitory factor (MIF) and interleukin-10 (IL-10).
This dataset explores molecular changes induced by these cytokines and the time-dependent transcriptomic alterations during M-MDSC induction by co-culture with HDBCLs.

overall_design: PBMCs were treated with recombinant (r) MIF and/or rIL-10, and were co-cultured with KPUM-UH1 or KPUM-MS3 for 24, 48, 96 hours, and 96 hours along with rIL-10. CD33+ myeloid cells were isolated from each condition and subjected to gene expression profiling to investigate molecular changes underlying M-MDSC induction.

first: Yuji

last: Shimura


title: A cell-type specific surveillance complex represses cryptic promoters during differentiation in an adult stem cell lineage [ChIP-seq]

city: Stanford

first: Neuza

last: Reis Matias

address: 279 Campus Drive

department: Developmental Biology

institute: Stanford University

summary: Regulators of chromatin accessibility play key roles in cell fate transitions, triggering onset of novel transcription programs as cells differentiate. In the Drosophila male germ line stem cell lineage, tMAC, a master regulator of spermatocyte differentiation that binds thousands of loci, is required for local opening of chromatin, allowing activation of spermatocyte-specific promoters. Here we show that a cell-type specific surveillance system involving the multiple zinc finger protein Kmg and the pipsqueak domain protein Dany dampens transcriptional output from weak tMAC dependent promoters and counteracts tMAC binding at thousands of additional cryptic promoters, thus preventing massive expression of aberrant protein-coding transcripts. ChIP-seq showed Kmg enriched at the tMAC-bound promoters it repressed, consistent with direct action. In contrast, Kmg and Dany did not repress highly expressed tMAC dependent genes, where they colocalized with their binding partner, the chromatin modeler Mi-2 (NuRD), along the transcribed regions rather than at the promoter. We discuss a model where Kmg, together with Dany and Mi-2, dampen expression from weak or ectopic promoters, while allowing robust transcription from highly expressed Aly-dependent genes.

overall_design: ChIPseq experiments in testes

last: Matias


title: A cell-type specific surveillance complex represses cryptic promoters during differentiation in an adult stem cell lineage [3'-seq]

overall_design: 3'end-seq from control (bamGAL4) and Kmg KD testes

first: Lorenzo

last: Gallicchio


title: A cell-type specific surveillance complex represses cryptic promoters during differentiation in an adult stem cell lineage [RNA-seq]

overall_design: RNAseq experiments in Drosophila testes, in different genetic backgrounds


title: Nuclear phosphatase PfNIF2 governs erythrocyte invasion and genome integrity through invasion-related proteins and SR1 dephosphorylation

city: Shenyang

first: Xiaotong

last: Zhu

state: Liaoning

address: No. 77 Puhe Road Shenyang North NEW AREA

department: Department of Immunology

institute: China Medical University

summary: PfNIF2 is a nuclear protein phosphatase belonging to the NIF family in Plasmodium falciparum. It is characterized by a conserved ‘DLDET’ motif, which is essential for its catalytic activity. PfNIF2 primarily localizes to the perinuclear or nuclear compartment and shows peak expression during the schizont stage of the parasite's lifecycle. Genetic disruption of the pfnif2 gene significantly impaired the efficiency of merozoite invasion, resulting in a 1.65-fold reduction (P < 0.05). It also increased susceptibility to artemisinin derivatives, with the IC50 of dihydroartemisinin decreasing from 12.5 nM to 7.9 nM (P < 0.001), although the asexual development of the parasites remained viable. Site-directed mutagenesis confirmed that aspartate 65 within the ‘D63LD65ET’ motif is critical for enzymatic function and invasion competence. Transcriptomic profiling revealed extensive dysregulation of invasion-related genes, including RON4 and MSP1, in schizont-stage PfNIF2Del parasites. Integrated co-immunoprecipitation, LC-MS/MS, and phosphoproteomic analyses demonstrated that PfNIF2 interacts with DNA repair machinery, such as SR1, SUN2, and MSH2-1. It plays a role in dephosphorylating RNA-binding proteins and invasion effectors. Notably, the expression of a phosphoablative variant of serine/arginine-rich splicing factor 1 (SR1-S205A/S208A) in PfNIF2Del parasites substantially rescued defects in DNA damage repair, alternative splicing fidelity, artemisinin sensitivity, and erythrocyte invasion. These findings establish PfNIF2 as a multifunctional regulator that bridges nuclear RNA processing, genome integrity maintenance, and host cell invasion in malaria parasites.

overall_design: type (WT) 3D7 and PfNIF2Del parasites using TRIzol reagent (Thermo Fisher). To ensure biological replicates, the experiments were repeated at three-week intervals. mRNA was enriched through the application of poly(dT) oligonucleotide-conjugated magnetic beads, followed by reverse transcription employing SuperScript II (Thermo Fisher) in conjugation with random hexamer primers. RNA templates were subsequently removed via RNase H treatment, and cDNA was purified using a DNA Clean and Concentrator Kit (Zymo Research, CA, USA). Indexed libraries were constructed using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina, CA, USA) and sequenced on an Illumina platform. Raw sequencing reads underwent quality filtering in fastq format and were subjected to adapter trimming using cutadapt v1.13. High-quality reads were aligned to the Plasmodium falciparum 3D7 reference genome (PlasmoDB-68) employing HISAT2 v2.0.4]. Deduplication of reads was conducted with UMI-tools v1.0.0 [52], and quantification was achieved through HTSeq v0.9.1. Differential expression analysis was carried out using DESeq (v1.18.0), with P-values adjusted for false discovery rate (FDR <0.05) following the Benjamini-Hochberg method. Gene Ontology (GO) enrichment analysis was performed using GOseq.

first: Geping

last: Pang

first: Yonghui

last: Feng

first: Chengqi

first: Duo

first: Sicong

first: Jingjing

first: Xuemeng

last: Zhang

first: Liwang

last: Cui

first: Yaming

last: Cao


title: A cell-type specific surveillance complex represses cryptic promoters during differentiation in an adult stem cell lineage [Long Read]

overall_design: PacBio Long-Read RNA sequencing (Iso-seq) on Control (bamGal4) and KmgKD testes

first: Angela

last: Detweiler


title: Drug-induced metabolic remodeling of immune cell repertoire generates an effective broad-range antimicrobial effect [scRNA-Seq 2]

city: Rīga

first: Bhupesh

last: Prusty

address: Rātsupītes iela 5

country: Latvia

institute: Rīga Stradiņš University

summary: Multiple mechanisms of immunity must be coordinated for the successful defense against a comprehensive range of pathogens, yet how broad-spectrum antipathogens act through these mechanisms remains largely elusive. Here, we used systems biology approaches to understand human immune cell reorganization at the single-cell level using a novel silane derivative, K21, which is effective against viruses, bacteria, and fungal infections. K21 significantly induced pro-inflammatory macrophages originating from both M1 and M2c macrophages without changing their ability to secrete respective cytokines. K21 decreased a specific subtype of M1 macrophages and CXCL4-induced M2-like macrophages, currently referred to as M4 macrophages, that play a critical role in solid cancers and fibrosis. K21-mediated immune cell remodeling was observed only in a complex multicellular co-culture environment, suggesting the interplay of various cell-derived components. K21 improved mitochondrial health by enhancing mitochondrial recycling via mitophagy. Similar treatment of the in vivo model organism C. elegans induced mitophagy and extended lifespan, suggesting evolutionary conservation of the mechanism. Our work demonstrates that a drug that remodels metabolism can shape the immune cell repertoire, which could aid in the development of more effective antimicrobials and potentially prevent the emergence of drug-resistant pathogens.

overall_design: Single-cell SLAM-seq profiling of human PBMCs exposed to a drug, K21 for 2 hours.

first: Prusty

last: Bhupesh


title: A cell-type specific surveillance complex represses cryptic promoters during differentiation in an adult stem cell lineage [ATAC-seq]

overall_design: ATACseq on Kmg KD testes, with 4 replicates

first: Dan

last: Lu


title: Long non-coding RNAs Kcnq1ot1 and Lncpint are involved in skeletal muscle atrophy induced by the space exposome

city: Stockholm

first: Alen

last: Lovric

address: Nobels väg 5

country: Sweden

institute: Karolinska Institutet

summary: Long non-coding RNAs (lncRNAs) play an important role in the regulation of skeletal muscle transcriptional processes, but their involvement in spaceflight- or inactivity-induced muscle atrophy remains poorly understood. To address this gap, we simulated the space environment by combining microgravity, irradiation and stress in a mouse model. Our results provide novel insights into the contribution of lncRNAs to muscle atrophy caused by the space exposome and has broader implications for understanding and combating muscle atrophy in clinical scenarios of prolonged inactivity.

overall_design: Entire soleus muscle of one of the hind-limbs from a two-group experimental design. Each group had 10 mice and the experimental group was subjected to 14-d HLU, radiation and stress (through diet). The control group was sham-radiated and kept under similar conditions.

first: Sergio

last: Pérez-Díaz

first: Bjorn

last: Baselet

first: Tommy

last: Lundberg

first: Mieke

last: Neefs

first: Lisa

last: Daenen

first: Eric

last: Rullman

first: Rodrigo

last: Fernandez-Gonzalo


title: Nuclear RNA cap-chaperones eIF4E and NCBP2 elicit distinct fates for 1000s of RNAs uncovering an unexpected regulatory point in gene expression cells [ribodeplete]

city: Chicago

first: Katherine

last: Borden

address: 675 N St Claire Street

department: Pharmacology/ Cancer Center

institute: Northwestern University

summary: Nuclear mRNA processing occurs in a stepwise manner to generate the protein blueprints required for cellular function. The addition of the methyl-7-guanosine (m7G) cap on the 5’end of mRNAs is conserved in humans, plants and fungi.  The m7G cap recruits the nuclear cap-binding protein NCBP2 co-/peri-transcriptionally where it mediates interactions between capped-RNAs and the processing machinery. Convention posits that NCBP2 is the sole cap-binding protein in the nucleus positioning cap-chaperoning as an important constitutive, housekeeping function. However, the eukaryotic translation initiation factor eIF4E is also found in the nucleus across Kingdoms. Both eIF4E and NCBP2 employ highly similar structural strategies to directly bind the m7G cap. The presence of two cap-binding factors in the nucleus could arise to provide redundancy to ensure gene expression security or it could provide the basis for tandem regulation of selected subsets of capped-mRNAs driving distinct gene expression programmes.  To dissect these possibilities, we compared the spatial localizations, interactomes and impacts on gene expression of eIF4E and NCBP2. We found that like NCBP2, eIF4E physically and spatially associated with active sites of transcription and splicing machinery. However, contrary to expectations, eIF4E and NCBP2 drove distinct transcription and splicing signatures impacting ~1000 transcripts which in turn elicit different biological programmes. RNAs segregated with specific cap-binding proteins with only an overlap of only ~130 transcripts between eIF4E and NCBP2. Clearly, the cap-interaction was not sufficient to elicit sensitivity to these cap-binding proteins given the absence of generalized impacts on the transcriptome. We uncovered the molecular mechanism for cap-chaperone selectivity which lay in differences in conserved sequences motifs within introns of selected mRNAs, their mainly distinct spatial localizations, and differences in the capacity to alter splice factor production. Relevant to the 130 common targets, a fraction of eIF4E and NCBP2 did interact and spatially overlap.  Despite their common m7G cap-binding activity, eIF4E and NCBP2 elicit substantively different impacts on gene expression. In contrast to the conventional paradigm, our data support a model whereby cap-chaperones direct processing of distinct subsets of mRNAs thereby eliciting diverse biological programmes.  Differential programming by cap-chaperones reveals an unexpected regulatory point in gene expression..

overall_design: RNAseq profiling of triplicata of two different clones of U2-OS cells overexpressing the cap binding protein NCBP2. The comparison is made with three different clones obtained identically but with an empty vector.

first: Jean-Clement

last: Mars

first: Caleb

last: Embree

first: Biljana

last: Culjkovic-Kraljacic

first: Aidan

middle: W

last: Carlile

first: Patrick

last: Gendron

middle: L


title: Drug-induced metabolic remodeling of immune cell repertoire generates an effective broad-range antimicrobial effect [scRNA-Seq]

first: Bhupesh

last: Prusty

overall_design: Single-cell RNA-seq profiling of human monocyte-derived macrophages exposed to a drug, K21 for 2 hours.


title: Disruption of mitochondrial integrity induced by MCL-1 targeting enhances the pro-angiogenic phenotype of breast cancer-associated fibroblasts

city: Nantes

first: jennifer

last: Derrien

address: 8 quai moncousu

country: France

institute: INSERM

summary: Breast cancer-associated-fibroblasts (bCAFs) consist of two pro-tumoral populations:  inflammatory CAFs (iCAF) releasing pro-inflammatory cytokines, and myofibroblastic CAFs (myCAF) known for their extensive production of extracellular matrix proteins and immunosuppressive features. We have previously shown that targeting the anti-apoptotic protein MCL-1 in primary culture of bCAFs directly derived from human samples reduces their myofibroblastic characteristics linked to actomyosin cytoskeleton disorganization and mitochondrial fragmentation. In this study, we explore the involvement of this protein in phenotypic differentiation and plasticity of bCAFs. Single-cell RNA-sequencing analysis reveals a shift from wound-myCAF to IL-iCAFs phenotype expressing genes involved in inflammation like IL-8, IL-1β, CXCL1, CXCL3, CCL2 and in angiogenesis like VEGF after MCL-1 gene silencing in bCAFs. In vitro, targeting of MCL-1 in bCAFs induces an increase of VEGF secretion associated with enhanced endothelial cell tubulogenesis. In ovo, using chicken chorioallantoic membrane model, we engrafted breast cancer cells and bCAFs to study vascularization. Our data suggest that a low level of MCL-1 expression in bCAF is associated with greater peritumoral vascular density in a VEGF-dependent manner.

overall_design: In the study, we explore the role of the anti-apoptotic protein MCL-1 in primary cultures of cancer-associated fibroblasts obtained from treatment-naive patients with invasive breast carcinoma after surgical resection, by genetically targeting of this protein by CRISPR/Cas9.

first: Chloé

last: Lefebvre

first: Fréderique

last: Souaze

first: Philippe Paul

last: Juin

first: Jennifer

first: Elise

last: Douillard


title: A cell-type specific surveillance complex represses cryptic promoters during differentiation in an adult stem cell lineage [CAGE]

first: Neuza

last: Reis Matias

overall_design: CAGEseq from control (bamGAL4) and Kmg KD testes

last: Matias

first: Dan

last: Lu


title: Profiling RNA Cargo in Extracellular Vesicles from hiPSC-Derived Neurons of Alzheimer’s Disease Patients

city: Baltimore

first: Vasiliki

last: Machairaki

state: Maryland

address: 733 N. Broadway, Edward D. Miller Research Building

department: Department of Genetic Medicine

institute: Johns Hopkins University

type: Non-coding RNA profiling by high throughput sequencing

summary: Alzheimer’s disease (AD) is a major neurodegenerative disorder that affects more than 55 million people, with an incidence that is projected to triple by 2050. Despite continuous advancements in the field, reliable treatment and early detection strategies remain elusive. Extracellular vesicles (EVs) play a major role in cellular communication throughout the body. In this study, we assessed the cargo of neuronal-specific EVs for their potential as AD biomarkers. We isolated EVs released from iPSC-derived excitatory glutamatergic neurons generated from eight AD patients (ADiNEVs) and six healthy controls (iNEVs). We performed RNA-sequencing and identified significant differences in RNA cargo between ADiNEVs and iNEVs. Notably, fewer small nuclear RNAs (snRNAs) were found in ADiNEVs. RNA transcripts significantly more abundant in ADiNEVs included MT-CO1, PRR32, and IGSF8 messenger RNAs. We also observed fewer XIST long noncoding RNAs and miR-7-5p microRNA content in ADiNEVs. These findings suggest that precision medicine approaches, such as characterizing the content of EVs from a patient’s own cells, could advance early detection and management of AD.

overall_design: We generated iPSC-derived excitatory glutamatergic neurons from 14 human participants, including 8 individuals diagnosed with sporadic Alzheimer’s disease (sAD) and 6 age-matched healthy controls. Then we collected EVs from neuronal culture supernatants on Day 21 of differentiation, extracted RNAs from EVs, and performed small RNA sequencing on these EVs using the NovaSeq 6000 platform and S4 Reagent Kit v1.5.

first: Ram

last: Sagar

first: Yiyao

last: Huang

first: Daiyun

last: Dong

first: Rachel

middle: J

last: Boyd

first: Waqar

last: Ahmed

first: Kenneth

last: Witwer

last: Mahairaki


title: AUTOPHAGY INHIBITION IMPROVES SENSITIVITY TO THE MULTI-KINASE INHIBITOR REGORAFENIB IN PRECLINICAL MOUSE COLON TUMOROIDS

city: Brussels

first: Marie-Isabelle

last: Garcia

address: route de lennik 808

department: IRIBHM-Jacques E. Dumont

country: Belgium

institute: Universite Libre de Bruxelles

summary: Colorectal cancer (CRC) remains the third leading cause of cancer-related deaths worldwide, with its incidence continuing to rise. Regorafenib, a multi-kinase inhibitor approved as a palliative treatment, extends survival in patients with metastatic CRC (mCRC) who have failed standard therapies. However, the clinical benefit of regorafenib is limited to a subset of patients, is typically short-lived, and is often accompanied by significant toxicity. The mechanisms by which CRC cells develop resistance to regorafenib remain poorly understood.In this study, we investigated resistance mechanisms to regorafenib using a preclinical mouse colon organoid model. Transcriptomic analysis of Apc wild-type and Apc-deficient organoids treated with regorafenib revealed an upregulation of epithelial-to-mesenchymal transition (EMT), accompanied by alterations in the secretome and increased activation of phosphorylated Erk1/2. Notably, co-treatment with an autophagy inhibitor suppressed regorafenib-induced EMT and its associated secretory phenotype, resulting in reduced cell proliferation and enhanced apoptosis in mouse organoids. The effectiveness of this drug combination was further supported by cell viability assays in human CRC cell lines. In contrast, primary mouse colon fibroblasts displayed greater resistance to both single-agent and combination regorafenib treatments. In summary, our findings using a preclinical organoid model suggest that autophagy inhibition may offer a promising strategy to mitigate chemoresistance and reduce toxicity associated with regorafenib treatment in mCRC patients.

overall_design: Mouse colon organoids (Apc WT or Apc deficient) with  3 biological  replicates per genotype were treated with regorafenib or vehicle (DMSO) for 6 days. Mouse primary fibroblasts with 43-4 biological replicates were treated for 7 days with regorafenib, vehicle (DMSO), autogramin-2 or combined regorafenib and autogramin-2.

first: Giulia

last: Agostini

first: Morgane

last: Leprovots

first: Jérôme

last: Jendriens

first: Anne

last: Lefort

first: Frédérick

last: Libert

first: Francesco

last: Sclafani

first: Ingrid

last: Langer

first: Alain

last: Hendlisz


title: Drug-induced metabolic remodeling of immune cell repertoire generates an effective broad-range antimicrobial effect

city: Piscataway

first: Christopher

last: Rongo

state: NJ

address: 190 Frelinghuysen Rd

department: Genetics

institute: Waksman Institute / Rutgers University

summary: Multiple mechanisms of immunity must be coordinated for the successful defense against a comprehensive range of pathogens, yet how broad-spectrum antipathogens act through these mechanisms remains largely elusive. Here, we used systems biology approaches to understand human immune cell reorganization at the single-cell level using a novel silane derivative, K21, which is effective against viruses, bacteria, and fungal infections. K21 significantly induced the differentiation of monocytes into macrophages and dendritic cells (MoDCs), as well as the differentiation of natural killer cells (NK cells). K21 decreased a specific subtype of M1 macrophages and CXCL4-induced M2-like macrophages, currently referred to as M4 macrophages, that play a critical role in solid cancers and fibrosis. K21-mediated immune cell remodeling was observed only in a complex multicellular co-culture environment, suggesting the interplay of various cell-derived components. K21 improved mitochondrial health by enhancing mitochondrial recycling via mitophagy. Similar treatment of the in vivo model organism C. elegans induced mitophagy and extended lifespan, suggesting evolutionary conservation of mechanism. Our work demonstrates that a drug that remodels metabolism can shape the immune cell repertoire, which could help develop more effective antimicrobials and potentially prevent the development of drug-resistance pathogens.

overall_design: RNA-seq of L4-stage C. elegans nematodes following treatment (from embryogenesis through L4) with either K21 quaternary ammonium silane or vehicle control.

first: Park

last: Eunchan

first: Nourollahi

last: Faye

first: Dietz

last: Jonathan

first: Vora

last: Mehul

first: Rongo

last: Christopher


title: Crotonate-activated histone H3K14 crotonylation enhances intestinal regeneration after injury

city: Beijing

first: Ye-Guang

last: Chen

state: China

address: Haidian  District

institute: Tsinghua University

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

overall_design: Refer to individual Series


title: Acclimation of the Escherichia coli transcriptome after 10 hours of incubation in the presence of tetrachloroauric acid at sublethal levels.

city: Calgary

first: Daniel Armando

last: Salazar-Alemán

state: Alberta

address: 2500 University Drive NW

department: Department of Biological Sciences

country: Canada

institute: University of Calgary

summary:
Tetrachloroauric acid has been explored as an FDA-approved alternative to treat antibiotic-resistant bacterial strains. Questions remain as it relates to the full-systems response elicited to counteract its toxic effects, especially in the context of a non-lethal exposure.
We explored the transcriptomic response profile of Escherichia coli K12 BW25113 when challenged to grow planktonically for 10 hours in M9-glucose minimal media spiked with a sublethal concentration of tetrachloroauric acid (10 µM, 3.39 µg/mL).
Our results yielded significant changes in gene expresson levels: 1028 genes were up-regulated, while 1025 were down-regulated in our tetrachloroauric acid treatment. Several biological processes became dysregulated to cope with the presence of this metal stressor, including iron metabolism, ribosome assembly, sulfur metabolism, cysteine biosynthesis, zinc uptake, and the copper homeostasis system Cue.
Altogether, this work provides a valuable snapshot of how our indicator strain adapts to metal-induced stress. This is a significant step in understanding how bacteria can adjust their physiology to coexist with sublethal concentrations of metal-based antimicrobials.

overall_design: Two treatment groups were set up: a non-metal control with M9-glucose minimal media, and a metal challenge using the same culture media but spiked with a sublethal concentration of tetrachloroauric acid (10 µM, 3.39 µg/mL). Both treatments were inoculated with Escherichia coli K12 BW25113, with three biological trials each. RNA extraction took place after an incubation time of 10 hours at 37 ºC 150 rpm. Differential gene expression was identified by contrasting both treatments, using p-adj value < 0.05 and absolute fold-change (FC) of at least 2 (|log2 FC| > 1) as significance thresholds.

first: Daniel

first: Ashley

last: McGibbon

first: Raymond

last: Turner


title: Acclimation of the Escherichia coli transcriptome after 10 hours of incubation in the presence of copper sulfate at sublethal levels.

summary:
Copper sulfate has been explored as an FDA-approved alternative to treat antibiotic-resistant bacterial strains. Questions remain as it relates to the full-systems response elicited to counteract its toxic effects, especially in the context of a non-lethal exposure.
We explored the transcriptomic response profile of Escherichia coli K12 BW25113 when challenged to grow planktonically for 10 hours in M9-glucose minimal media spiked with a sublethal concentration of copper sulfate (39 µM, 6.22 µg/mL).
Our results yielded changes in gene expresson levels: 80 genes were up-regulated, while 76 were down-regulated in our copper sulfate treatment. Some biological processes became dysregulated to cope with the presence of this metal stressor, including iron metabolism, sulfur metabolism, cysteine biosynthesis, and the copper homeostasis systems Cue and Cus.
Altogether, this work provides a valuable snapshot of how our indicator strain adapts to metal-induced stress. This is a significant step in understanding how bacteria can adjust their physiology to coexist with sublethal concentrations of metal-based antimicrobials.

overall_design: Two treatment groups were set up: a non-metal control with M9-glucose minimal media, and a metal challenge using the same culture media but spiked with a sublethal concentration of copper sulfate (39 µM, 6.22 µg/mL). Both treatments were inoculated with Escherichia coli K12 BW25113, with three biological trials each. RNA extraction took place after an incubation time of 10 hours at 37 ºC 150 rpm. Differential gene expression was identified by contrasting both treatments, using p-adj value < 0.05 and absolute fold-change (FC) of at least 2 (|log2 FC| > 1) as significance thresholds.


title: Nuclear RNA cap-chaperones eIF4E and NCBP2 elicit distinct fates for 1000s of RNAs uncovering an unexpected regulatory point in gene expressioncells

first: Katherine

last: Borden

first: Jean-Clement

last: Mars

first: Caleb

last: Embree

first: Biljana

last: Culjkovic-Kraljacic

first: Aidan

last: Carlile

first: Patrick

last: Gendron


title: Acclimation of the Escherichia coli transcriptome after 10 hours of incubation in the presence of silver nitrate at sublethal levels.

summary:
Silver nitrate has been explored as an FDA-approved alternative to treat antibiotic-resistant bacterial strains. Questions remain as it relates to the full-systems response elicited to counteract its toxic effects, especially in the context of a non-lethal exposure.
We explored the transcriptomic response profile of Escherichia coli K12 BW25113 when challenged to grow planktonically for 10 hours in M9-glucose minimal media spiked with a sublethal concentration of silver nitrate (7 µM, 1.18 µg/mL).
Our results yielded significant changes in gene expresson levels: 131 genes were up-regulated, while 558 were down-regulated in our silver nitrate treatment. Some biological processes became dysregulated to cope with the presence of this metal stressor, including iron metabolism and protein folding at the inner membrane and periplasm.
Altogether, this work provides a valuable snapshot of how our indicator strain adapts to metal-induced stress. This is a significant step in understanding how bacteria can adjust their physiology to coexist with sublethal concentrations of metal-based antimicrobials.

overall_design: Two treatment groups were set up: a non-metal control with M9-glucose minimal media, and a metal challenge using the same culture media but spiked with a sublethal concentration of silver nitrate (7 µM, 1.18 µg/mL). Both treatments were inoculated with Escherichia coli K12 BW25113, with three biological trials each. RNA extraction took place after an incubation time of 10 hours at 37 ºC 150 rpm. Differential gene expression was identified by contrasting both treatments, using p-adj value < 0.05 and absolute fold-change (FC) of at least 2 (|log2 FC| > 1) as significance thresholds.


title: Optimal pairing of binder and costimulatory domains improves dual CAR T cell efficacy

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary: We explore whether introducing two chimeric antigen receptor (CAR) molecules with distinct signaling motifs into a single T cell improves CAR T cell (CART) efficacy against leukemia and lymphoma. RNA expression profiling demonstrated that T cells co-expressing two CARs that recognize the same target in which one CAR was linked to CD28 costimulation and the other was linked to 4-1BB costimulation augmented canonical NF-κB, non-canonical NF-κB, and Th17 differentiation pathways equivalently upon target engagement. Interestingly, multitargeted CARTs transcriptional profile favored the costimulatory domain linked to the binder of the more robustly expressed CD19 rather than one linked to the binder of the less expressed CD22 upon tumor engagement. In vivo and T cell exhaustion assays found that multitargeted T cells with distinct signaling domains led to greater durable control of B-ALL than single targeted Dual CAR T cells with T cells co-expressing CD19.BBζ and CD22.28ζ being the most potent. Together, this data indicates that optimal pairing of CAR binder domain with signaling cassette bolsters anti-tumor efficacy by improving both T cell durability and effector function.

overall_design: RNAseq comparisons analysis of STS,STD and MTD CARTs after stimulation to check expression changes after CAR engagement.Three replicates were used for each condition

first: James

last: Riley

first: Divanshu

last: Shukla

first: Shuguang

last: Jiang

first: Sasikanth

last: Manne

first: John

middle: E

last: Wherry


title: Single nucleus analysis of post-mortem brain tissues from Adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) patients

city: Saint Louis

first: Siling

last: Du

address: 4515 Mckinley Ave

institute: Washington University in St. Louis

summary: Microglia, the brain's resident macrophages, depend on interleukin 34 (IL-34) and colony-stimulating factor 1 (CSF1) for their development and maintenance, engaging the CSF1 receptor (CSF1R). Adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP), a neurodegenerative disorder affecting the brain's white matter, is caused by heterozygous pathogenic mutations in the CSF1R gene. Neuropathological studies of postmortem ALSP brains have shown widespread depletion of microglia, demyelination of cerebral white matter, axonal swellings, and pigmented glial cells. In this study, we investigated how individual brain cell populations respond to microglia depletion and contribute to ALSP progression. To do this, we analyzed post-mortem specimens from patients wirth ALSP using single-nucleus RNA-seq (snRNA-seq).

overall_design: Compare the transcriptomics of occipital cortex of ALSP patients with controls

first: Yingyue

last: Zhou

first: Marco

last: Colonna


title: PTEN restrains tumor expansion through cell autonomous and non-autonomous mechanisms

city: New York

first: Yinwen

last: Liang

email: liangy@mskcc.org, liangyinwen@gmail.com

state: New York

address: 1275 york avenue

institute: Memorial Sloan Kettering Cancer Center

summary: To gain insight into transcriptional changes that occur in SmoM2 SHH-MB tumor cells that lack Pten and could account for the cell autonomous changes we observed in tumors of a mouse model, we performed single cell RNA-sequencing (scRNA-seq) of whole tumors dissected from P22 SmoM2 (Atoh1-FlpoER/+; R26MASTR/LSL-SmoM2) and P16 SmoM2-Ptenfl/fl (Atoh1-FlpoER/+; R26MASTR/LSL-SmoM2; Ptenfl/fl) mice (n = 2 per genotype).

overall_design: To investigate transcriptome differences of SmoM2 and SmoM2-Ptenfl/fl tumor tissues, we performed scRNA-seq analysis of SHH-MBs of P16 SmoM2-Ptenfl/fl mice and P22 SmoM2 mice. Two replicates per genotype. For each library, tumor cells were treated with EasySep Dead Cell Removal kit (STEMCELL technologies,17899) to filter out dead cells before loading to 10x Chip for single cell sequencing.

first: Salsabiel El

last: Nagar

first: Alexandra L

last: Joyner


title: Gene expression-based, treatment response analyses using Nanostring nCounter

city: Banjul

first: Ismaila

middle: L.

last: Manneh

address: Atlantic Blvd

department: VIT

country: Gambia

institute: MRCG at LSHTM

summary: Background: Despite availability of effective treatment regimens for drug-susceptible TB, some patients still experience poor treatment outcomes. Currently tools for monitoring treatment outcomes are dependent on detection of mycobacteria in sputum, which are slow, expensive and poor at predicting relapse and failure. This study aims to identify new blood-derived markers for predicting treatment response and outcomes.  Methods: Whole blood was collected in PAXgene tubes from patients with microbiologically confirmed TB at diagnosis, week 2, and at month 2, 4 and 6. Treatment response and outcomes were determined by culture and gene expression was compared between slow and fast responders; and between patients with good (cured) and poor treatment outcomes (failure and recurrent TB) using targeted RNA gene expression. Gene signatures were developed using random forest classification models.  Results: Significant changes in gene expression were detected over the course of the TB treatment. Notably, major gene expression differences were observed at diagnosis between subsequently cured patients and patients who experienced poor treatment outcomes while minimal changes were detected between slow and fast responders among cured patients at diagnosis. A 7-gene end of treatment signature distinguished patients with good outcomes from those with poor treatment outcomes with AUCs of 0.91, 0.98, and 1.0 at baseline, month 2 and month 6 respectively. Additionally, a 6-gene month 2 signature discriminates slow from fast responders with AUCs of 0.49, 0.57, and 0.93 at diagnosis, week 2 and month 2 respectively.  Conclusion: The study identified genes signatures associated with TB treatment response and outcomes suggesting potential utility for treatment monitoring

first: Jayne

middle: S

last: Sutherland


title: Ultra-deep bulk RNA-seq from hESC-derived thyroid follicular cells

first: Xiaoyan

last: Yi

state: Brussels

address: Route de Lennik 808

department: Medical Faculty

institute: Université libre de Bruxelles

summary: This study provides ultra-deep bulk RNA-seq data from human embryonic stem cell (hESC)-derived thyroid follicular cells. The NKX2-1GFP+ population was isolated using fluorescence-activated cell sorting (FACS) and subjected to RNA extraction. Library preparation was performed using the Ovation Solo RNA-seq System, followed by high-output sequencing on the Illumina HiSeq 1500 platform. Each sample generated approximately 400 million reads. These data enable transcriptomic analysis of differentiated thyroid lineage cells exposed to IFN-α and IFN-γ.

overall_design: Human embryonic stem cell-derived thyroid follicular cells were differentiated in vitro. NKX2-1GFP+ cells were isolated using FACS and immediately lysed in Qiazol. Total RNA was extracted using the miRNeasy Micro Kit. Libraries were prepared with the Ovation Solo RNA-seq System (NuGen), and sequencing was performed on the Illumina HiSeq 1500 platform, generating ~400 million reads per sample. The experimental conditions included IFN-α, IFN-γ, and untreated controls. The dataset supports transcriptome profiling and differential expression analysis between these groups.

first: Priscila L.

last: Zimath

first: Sabine

last: Costagliola

first: Mirian

last: Romitti

first: Decio L.

last: Eizirik


title: Analysis of (MC38) tumor infiltrating T regulatory cells From ERT2Cre control and ERT2CreTIM-3(FLEX4) KO mouse.

city: Pittsburgh

first: Lawrence

middle: P.

last: Kane

address: 5051 Centre Ave.

department: Immunology

institute: University of Pittsburgh

summary: Increased activity or number of regulatory T cells (Treg) serves as a barrier to effective anti-tumor immunity. Although manipulation of Treg cells is a promising anticancer strategy, doing so while sparing general immune tolerance has been a challenge. Thus, identifying factors specifically expressed in tumor-infiltrating Treg is important for better understanding cancer pathogenesis and identifying novel therapeutic targets that enhance anti-tumor immunity. We show that Tim-3 expression on tumor Treg is required for the function and survival of these cells, in part through Akt activation and FOXO1 inactivation. Knocking out Tim-3 in Treg also leads to delayed CD8 T cell exhaustion and lower tumor burden, without altering peripheral homeostasis. Thus, Tim3-expressing Treg are a promising target to modulate tumor-specific immune responses.

overall_design: Treg cells (CD4+Foxp3ERT2CreGFP+CD25+) cells from MC38 tumors day 12 post tumor implantation were sorted using FACS ARIA into RNA isolation buffer and mRNA was sequenced.

first: Hridesh

last: Banerjee

first: Hector

last: Nieves-Rosado

first: Benjamin

last: Murter

middle: P


title: Inhibiting the RNA helicase DDX3X in Burkitt lymphoma induces oxydative stress and impedes tumor progression in xenografts

city: Montreal

first: Tarik

last: Moroy

state: QC

address: 110, West Pine Avenue, 597

institute: Institut de recherches cliniques de Montréal

summary: Burkitt Lymphoma (BL), an aggressive B-cell lymphoma driven by MYC translocations, requires intensive chemotherapy treatments which deliver high effectiveness yet increase future risks of developing secondary malignancies. We have previously shown that DDX3X, an RNA helicase frequently mutated in BL, is essential for B cell lymphomagenesis in mice. To assess if DDX3X could therefore represent a promising therapeutic target, we tested two DDX3X inhibitors, the well characterized RK-33 and the more potent newly developed C1, in three BL cell lines (CA46, Raji, Daudi). We found that the three cell lines exhibited differential sensitivities to the drugs in vitro, with Daudi being the most susceptible and Raji the most resistant. In vivo, RK-33 treatment in a xenograft BL model reduced tumor progression in all cell lines, with the Daudi cells being the most responsive to the treatment, albeit with variable efficacy compared to the clinical drug Pevonedistat. Transcriptomic and proteomic analyses indicated that RK-33-mediated inhibition of DDX3X and DDX3X ablation through siRNA affects oxidative phosphorylation among other pathways and leads to an increase of intracellular reactive oxygen species (ROS). A CRISPR chemogenomic screen to identify synthetic lethalities linked to RK-33 implicated enzymes of the glutathione synthesis pathway. We therefore tested the inhibition of the glutathione pathway with buthionine sulfoximine and showed that it reduced the CC50 of RK-33 in BL cells lines. Our findings not only support DDX3X as a therapeutic target in BL, but also provide evidence for a combinatorial strategy to improve the efficacy of current treatments.

overall_design: RNA-seq profiling of Raji, CA47 and Daudi cell lines, as well as primary human B cells treated with DDX3X inhibitor RK-33 or DMSO, and siRNA-mediated knockdown of DDX3X, DDX3Y, both, or scramble control siRNA.

first: Hugues

last: Beauchemin

first: Zeinab

last: Dalloul

first: Virginie

last: Calderon

first: Thierry

last: Bertomeu

last: Möröy


title: The Multiomics Landscape of Plasma Exosomes in First-Episode Drug-Naïve of Schizophrenia

city: Tianjin

first: Shuo

last: Wang

address: No.13 Liu Lin Road

institute: Tianjin Anding Hospital

summary: Background: Schizophrenia (SZ) is a debilitating mental illness with uncertain etiology and challenges in early diagnosis and treatment outcomes. For the first time, we applied a multiomics techniques to explore plasma exosomal markers of SZ and underlying molecular mechanisms. Methods: Exosomes were separated and identified from ten drug-naive first-episode SZ patients and ten healthy controls. Then small RNA-seq and high-performance liquid chromatography-tandem mass spectrometry technology were used to detect the profiles of microRNAs (miRNAs) and proteomics, respectively. The integrative multiomics analysis was further performed. Results: A total of 167 differentially expressed miRNAs (DE miRNAs) were identiﬁed in plasma exosomes from drug-naive first-episode SZ patients. The potential target genes of DE miRNAs were predicted, and GO and KEGG enrichment analysis showed that they were associated with RNA catabolic process, proteasome-mediated ubiquitin-dependent protein catabolic process, etc. Proteomic analysis identified 274 differentially expressed proteins (DEPs), and DEPs were mainly enriched in immune response and some signaling pathways. The combination of Top 10 DE miRNAs/ DEPs both had good values to diagnose SZ. Importantly, miRNA-protein ceRNA networks were constructed by integrating multiomics, one consisting of 21 downregulated DE miRNAs and 21 upregulated DEPs and the other consisting of 64 upregulated DE miRNAs and 86 downregulated DEPs in SZ patients. Conclusions: Our study for the ﬁrst time describes the multiomics landscape of plasma exosomes in first-episode drug-naïve of SZ, and provides novel insights into the molecular alterations of SZ. These findings hold promise for advancing diagnostic and therapeutic strategies in SZ management.

overall_design: A total of 20 plasma samples were collected for miRNA profiling. These include 10 samples from patients diagnosed with schizophrenia and 10 from healthy control subjects. Exosomes were isolated from the plasma to enrich for miRNAs, and all samples were processed under uniform conditions to ensure consistency. This dataset is designed to facilitate the comparison of miRNA expression profiles between schizophrenia patients and healthy individuals, potentially providing insights into the molecular underpinnings of the disorder.

first: Jie

last: Li


title: Sex dimorphic impact of maternal Zika infection on offspring neutrophil functions

city: Detroit

first: Gil

middle: G.

last: Mor

state: Michigan

address: 275 E. Hancock

department: C.S. Mott Center for Human Growth and Development

institute: Wayne State University School of Medicine

summary: To investigate the impact of Zika infection during pregnancy on the placenta and offspring immune response

overall_design: Pregnant C57/BL6 mice were exposed to 50PFU Zika virus on E8.5. Placentas were collected on E12.5. And in another cohort, pups were delivered and sacrificed on PND35, bone marrow neutrophils of offspring from Zika-exposed dams were isolated and sent for RNAseq.

first: Jiahui

last: Ding

first: Anthony

last: Maxwell

first: Aditi

last: Singh

first: Grace

last: Loedeman

first: Nicholas

last: Adzibolosu


title: Evaluating the Link Between Efflux Pump Expression and Motility Phenotypes in Pseudomonas aeruginosa Treated with Virulence Inhibitors

city: Minneapolis

first: Hannah

last: Lembke

state: MN

address: 207 Pleasant St SE

institute: University of Minnesota

summary: Antibiotic resistance continues to rise as a global health threat. Novel anti-virulence strategies diminish the drive for evolutionary pressure, but still hinder a pathogen’s ability to infect a host. Treatment of the highly virulent Pseudomonas aeruginosa strain PA14 with virulence inhibitors (R-2 and R-6) elicited widely varying transcriptional profiles. Of interest, expression of a family of resistance-nodulation-division (RND) efflux pumps implicated in the intrinsic drug resistance of P. aeruginosa, was significantly altered by R-2 and R-6 treatment. While structurally similar, these inhibitors caused differential expression of various RND efflux pumps within the Mex family—R-2 treatment stimulated expression of mexEF-oprN while R-6 treatment led to increased mexAB-oprM expression. Further expansion into a small library of virulence inhibitors revealed chemical motifs that trigger increases in RND efflux pump expression. Additionally, activation of these efflux pumps suggests low accumulation of virulence inhibitors in WT PA14. Treatment of an efflux pump-deficient strain with R-2 or R-6 resulted in inhibition of several virulence factors, for example R-2 was found to abolish swimming motility. Collectively, treatment with either R-2 or R-6 gives rise to a convoluted transcriptomic response, confounded by the impact of efflux pump expression on the system. However, understanding the moieties that lead to high expression of the efflux pumps enables further rational design of novel virulence inhibitors that do not cause RND efflux pump activation.

overall_design: PA14 diluted from overnight cultures were diluted into fresh LB media containing DMSO, R-2 or R-6 (200 uM) and grown to OD600 ~0.9 or ~1.2. Four biological replicates were grown for every treatment condition. RNA extracted and sequenced to evaluate differences in transcriptome profiles under each inhibitor at different growth phases.

last: K. Lembke

first: Kelsie

last: M. Nauta

first: Ryan

last: C. Hunter

first: Erin

last: E. Carlson


title: Gut microbiota modualtes innate anxiety via the neuron activity of medial prefrontal cortex in mice

city: Guangzhou

first: Jing

last: Ren

address: shatai road

institute: southern medical university

summary: Anxiety disorders are the most common mental illness with a lifetime prevalence of up to 33.7%, the mechanisms of which have been only partially elucidated. Recent observations have revealed the gut microbiota contributes to the regulation of anxiety. However, little attention has been given to innate anxiety, which excluded genetic background and environmental factors. Herein, we investigate causal mechanisms of gut microbiota in modulating innate anxiety. First, specific pathogen-free (SPF) C57BL/6J mice were divided into high-anxiety (HA) and low-anxiety (LA) subgroups in the top or bottom 44%, respectively (ie, the middle 12% was excluded) in the elevated plus maze (EPM). We transplanted the microbiota from high or low anxiety mice, which was identified by 16S rRNA sequencing to be of a differential composition, to antibiotic (ABX)-treated C57 mice. Strikingly, ABX treatment produced anxiolytic effects and HA-FMT recipients exhibited anxiety-like behaviors. We moreover defined that the neuron activity of medial prefrontal cortex (mPFC) was activated identified by increased c-Fos expression and GCaMP6 signals in the HA-FMT recipients. Finally, RNA-seq suggested that transcriptional reprogramming, modification of proteins, and synaptic plasticity modulation were involved in the gut microbiota-brain axis mechanism. We conclude that the microbiota influences the innate anxiety-like behavior and affects the neuron activity of mPFC involving transcriptional reprogramming, modification of proteins, and synaptic plasticity modulation.

overall_design: RNA-seq analysis of  medial prefrontal cortex from high- and low-anxiety mice

first: Xiao-Ying

last: Lian

first: Wan-Qian

last: Ye

first: You-Lu

last: Wen

first: Cheng-Lin

last: Lu

first: Xiong

last: Cao


title: Single-cell and spatial transcriptome analysis revealed the immunomodulatory role of T cells in the colon cancer tumor microenvironment

city: Suzhou

first: YingXi

last: Guo

address: No. 199, Renai Road, Industrial Park

department: IBMS

institute: Soochow University

summary: The purpose of this study was to explore the dynamic changes of tumor microenvironment and its effects on immune cell function in different TNM stages of colon cancer, identify key genes and signaling pathways related to tumor progression, and provide a basis for accurate diagnosis and personalized treatment.

overall_design: Single-cell RNA sequencing (scRNA-seq), single-cell VDJ sequencing (scVDJ-seq) and spatial transcriptomics (stRNA-seq) were used to analyze colon cancer and adjacent tissues, systematically study the changes in immune function of T cells, especially CD8⁺ T cells, in the tumor microenvironment, and explore the role of key genes and signaling pathways in combination with TNM staging.

first: Hebin

last: Liu

first: Xiaodong

last: Yang

first: Tengfei

last: Jia

first: Yingxi


title: PV-10 triggers immunogenic cell death in head and neck squamous cell carcinoma via endoplasmic reticulum stress and apoptosis

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

summary: Primary risk factors of head and neck squamous cell carcinoma (HNSCC) include human papillomavirus (HPV) infection and exposure to tobacco and excessive alcohol. Despite currently available treatments, patients with recurrent HNSCC still have poor survival, highlighting the need for innovative therapies. PV-10, also known as rose bengal sodium (RBS, 4,5,6,7-tetrachloro-2′,4′,5′,7′-tetraiodofluorescein disodium), is a small molecule being developed as an intralesional (IL) therapeutic agent, exhibiting substantial anti-tumor activity across diverse cancer types, but current knowledge regarding the molecular mechanisms involved in response to PV-10 remains limited. We evaluated the cytotoxic effects of PV-10 in HNSCC and explored its molecular mechanisms. In vitro, we found that PV-10 induced cytotoxicity in mEER and MTE-RAS cell lines, primarily by increasing the production of reactive oxygen species and leading to apoptosis through a caspase-dependent mechanism. Additionally, we observed that PV-10 treatment increased the release of damage-associated molecular pattern molecules such as HMGB1 and ATP and enhanced expression of calreticulin, HSP-70, and HSP-90 indicating potent immunogenic cell death (ICD). In vivo, IL PV-10 injections led to significant tumor regression in both mEER and MTE-Ras models. Complete responses (CR) were observed in 7 of 21 (33%) mice in mEER although no CR was observed in MTE-Ras. Our data suggests that one of the possible mechanisms by which PV-10 triggers ICD is by inducing endoplasmic reticulum stress, autophagy, and apoptosis. Our findings contribute to further understanding of the underlying mechanisms of PV-10 induced cytotoxicity and to develop future clinical trials in locally recurrent HNSCC.

overall_design: RNA-sequencing and data analysis For RNA-sequencing MTE-Ras cells were injected subcutaneously into the right flank of C57BL/6 mice. Total RNA was isolated from three mouse tumors each from PBS and PV-10 treated mice using the RNeasy Mini Kit (Qiagen, #74104) according to the manufacturer's protocol, followed by DNase treatment using RNase-Free DNase Set (Qiagen, #79254). The RNA extracted from tumors was quantitated with the Qubit Fluorometer (ThermoFisher Scientific, Waltham, MA) and screened for quality on the Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA). The samples were then processed for RNA-sequencing using the NuGEN Universal RNA-Seq Library Preparation Kit with NuQuant (Tecan Genomics, Redwood City, CA). Briefly, 100 ng of RNA was used to generate cDNA and a strand-specific library following the manufacturer’s protocol. Quality control steps were performed, including TapeStation size assessment and quantification using the Kapa Library Quantification Kit (Roche, Wilmington, MA). The final libraries were normalized, denatured, and sequenced on the Illumina NovaSeq 6000 sequencer with the SP-200 cycle reagent kit to generate 100-150 million 100-base read pairs per sample (Illumina, Inc., San Diego, CA). All work was performed by the Moffitt Cancer Center Molecular Genomics Core Facility (RRID:SCR_012333). Read adapters were detected using BBMerge (v37.02) (RRID:SCR_016970) and subsequently removed with cutadapt (v1.8.1) (RRID:SCR_011841). Processed raw reads were then aligned to mouse genome mm10 using STAR (v2.7.7a) (RRID:SCR_004463). Gene expression was evaluated as read count at the gene level using RSEM (v1.3.0) (RRID:SCR_000262) with the Gencode gene model vM21. Normalization and differential expression analysis between the experimental and control groups were performed using DESeq2 (RRID:SCR_015687) (27). Gene set enrichment analysis (GSEA) was performed on the ranked gene list, based on fold change between experimental and control groups, using the gseGO function from the cluster Profiler R package (v 4.6.2). The analysis focused on Gene Ontology (GO) terms.

first: Sowjanya

last: Thatikonda

first: Ritu

last: Chaudhary

first: Yeva

last: Meshkovska

first: Maria

middle: I

last: Biernacki

first: Robbert

last: Slebos

first: Xiaofei

last: Song

first: MacLean

last: Hall

first: Kenneth

last: Lilley

first: Shari

last: Pilon-Thomas

first: Jose

middle: A

last: Guevara-Patino

first: Philippe

last: Spiess

first: Jad

last: Chahoud

first: Antonio

last: Amelio

first: Eric

last: Wachter

first: Dominic

last: Rodrigues

first: Christine

middle: H

last: Chung


title: Construction of a Diagnosis Model for Tuberculosis based on Long Non-coding RNA

first: Xiuxiu

last: Ji

address: No. 1, Beiguang Street, Tongzhou District

institute: Department of Molecular Biology, Beijing Chest Hospital, Capital Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Tuberculosis (TB) remains a significant global public health threat, this study aimed to systematically identify potential long non-coding RNAs (lncRNAs) as biomarkers and construct a diagnostic model for TB. The study revealed the lncRNA expression profile associated with TB in peripheral blood mononuclear cells (PBMCs) through microarray analysis and identified key modules and lncRNAs using weighted gene co-expression network analysis (WGCNA). The expression levels of candidate lncRNAs were validated by real-time quantitative PCR (RT-qPCR), and characteristic variables were selected using the least absolute shrinkage and selection operator (LASSO) regression. The findings suggest that a diagnostic model based on five host-derived lncRNAs combined with the AdaBoost algorithm can serve as a potential tool for TB diagnosis.

overall_design: Genome-wide lncRNA profiling of peripheral blood mononuclear cells (PBMCs) from tuberculosis (TB) patients, latent TB infection (LTBI) individuals, and healthy controls (HCs) was conducted using the Agilent microarray technique. Eight independent samples were included in each group (TB, LTBI and HCs).

first: Siyu

last: Yao

first: Qi

last: Sun

first: Yingchao

last: Wang

first: Xuetian

last: Shang

first: Zeqi

first: Mailing

last: Huang

first: Lanyue

last: Zhang

first: Chuanzhi

last: Zhu

first: Zongde

first: Hongyan

last: Jia

first: Qiuyue

last: Liu

first: Liping

last: Pan


city: Shanghai

first: Minwen

last: Zou

address: 800 Dongchuan Road, Shanghai

institute: Shanghai Jiao Tong University

summary: PGC1α regulates the mitochondrial metabolism response to cyclic stretch, which inhibits neointimal hyperplasia microscopy revealed that intimal injury disrupted the balance of vascular energy metabolism and impaired the mitochondrial ultrastructure in vivo. The human carotid plaque and femoral artery plaque samples also exhibited alterations in mitochondrial morphology. Vascular smooth muscle cells (VSMCs) are the main components of neointimal hyperplasia and are subjected to cyclic stretch resulting from pulsatile pressure. In this study, we found that the application of cyclic stretch in vitro increased VSMC mitochondrial mass and function. In addition, peroxisome proliferator-activated receptor gamma coactivator-1α (PGC1α) played an important role in regulating VSMC mitochondrial function in response to physiological stretch via the phosphorylation of Smad3. Increasing the activation of PGC1α by ZLN005 treatment effectively inhibited VSMC hyperproliferation after intimal injury in vivo. These results suggested that the regulation of PGC1α by p-Smad3 in response to physiological cyclic stretch may effectively alleviate neointimal hyperplasia by promoting mitochondrial function. PGC1α may be a potential therapeutic target for the prevention and treatment of neointimal hyperplasia.

overall_design: RNA-seq profiling of left carotid artery (injury group) and right carotid artery (control group) in 4-week carotid intimal injury model rats

first: Kaichuang

last: Ye

first: Jing

last: Yan

first: Shoumin

first: Han

last: Bao

first: Zhiyin

last: Li

first: Yue

last: Han


first: Tengfei

address: 199 Renai Road

department: Institutes of Biology and Medical Sciences

first: Hebin

first: Xiaodong

last: Yang

first: Yingxi

last: Guo


title: Activating NRF2^E79Q mutation alters the differentiation of human non-small cell lung cancer

city: Camden

first: Samera

last: Hamad

address: 401 South Broadway

institute: Cooper Medical School of Rowan University

summary: The NRF2 signaling pathway promotes tumor initiation, progression and resistance to chemotherapy, radiation therapy and immune checkpoint inhibitors. The mechanisms underlying the biology of NRF2-active tumors are varied, and include altered cellular metabolism, a reductive shift in redox state, and immunosuppression. Here we determined the molecular and phenotypic impact of NRF2 activation on two human non-small cell lung cancer (NSCLC) cell models. Inducible expression of NRF2^E79Q, a common activating NRF2 mutation, in H358 lung adenocarcinoma (LUAD) cells altered cellular morphology and increased xenograft tumor growth in mice but not in 2D cell culture. In contrast, NRF2^E79Q expression in H596 lung adeno-squamous cell carcinoma altered cellular morphology, increased neuroendocrine marker gene expression, but did not impact tumor growth in 2D or in xenografts. Gene expression profiling revealed shared and unique NRF2 transcriptional programs between these models, some of which were shared in primary lung tumors. Collectively, our findings reveal context-dependent effects of NRF2 activation on the growth and differentiation-state of two human NSCLC models, supporting a new differentiation-centric mechanism of NRF2-driven tumor progression and therapeutic resistance.

overall_design: Two human NSCLC cell lines (H358 and H596) with doxycycline inducible NRF2 activating mutations (E79Q) were used to generate mouse xenograph tumors. Tumors were profiled with RNAseq analysis comparing NRF2 activated tumors from dox induced mice vs NRF2 normal tumors  from mice with no dox induction. Biological replicates are provided by tumors sourced from different mice in each treatment group.

first: Hansa

last: Joshi

first: T

last: Hess

first: Stuart

middle: R

last: Jefferys

first: Zena

last: Saleh

first: Rani

last: Sellers

first: Gord

first: Travis

last: Shrank

first: Rayvon

middle: T

last: Moore

first: David

last: Corcoran

first: Jeremy

middle: M

last: Simon

first: Francis

last: Spitz

last: Shersher

first: Ben

last: Major

first: Bernard

last: Weissman


title: Murine anaphylaxis to food requires cysteinyl leukotriene-mediated absorption of allergens in the gut.

city: Chicago

first: Aditi

last: Verma

state: IL

address: 300 East Superior Street Tarry 15-735

department: Department of Medicine

institute: Northwestern University

summary: Food-specific IgE triggers life-threatening anaphylaxis; however, some people with food-specific IgE are asymptomatic upon allergen consumption. Using murine food allergy models, we discovered an unexpected pathway regulating the ability of food allergens to trigger anaphylaxis. C57BL/6 mice are uniquely resistant to anaphylaxis when challenged orally; we show that goblet cells transport less food allergens relative to anaphylaxis-susceptible strains, even prior to allergic sensitization. In a forward genetic screen, oral anaphylaxis resistance correlated with Dipeptidase1 (Dpep1) allelic variants. DPEP1 is expressed in intestinal epithelium and catabolizes leukotriene D4 (LTD4). Blocking DPEP1 with cilastatin, genetically deleting Dpep1, or oral administration of LTD4 enhanced allergen transport in resistant mice. Conversely, pre-treatment of susceptible mice with a leukotriene synthesis inhibitor, zileuton, abrogated allergen absorption from the gut and subsequent oral anaphylaxis. Inhibiting leukotrienes may be a novel treatment for food allergy.

overall_design: Bulk RNA-seq profiling of jejenum from  naïve  C57BL/6 and C3H/Hej mice.

first: Stephanie

middle: C

last: Eisenbarth

first: Adam

last: Williams

first: Slim

last: Fourati

first: Darcae

last: Holmes


title: PV - Oligodendrocyte Interactions In the Infralimbic Cortex Promote Extracellular Plasticity after Safety Learning

first: Jia

last: Liu

state: NY

address: 85 Saint Nicholas Ter

department: Neuroscience

institute: CUNY Advanced Science Research Center

summary: The ability to differentiate between threat and safety cues is essential for adaptive behavior, yet this process is disrupted in psychiatric disorders such as post-traumatic stress disorder (PTSD), where safety cues fail to suppress fear expression. To uncover the neurobiological mechanisms of safety learning, we compared safety conditioning (SC) and contextual fear conditioning (CFC) in the infralimbic cortex (IL) of the medial prefrontal cortex (mPFC) across recent and remote memory retrieval in mice. We identify a novel mechanism whereby safety learning promotes neuro-glial interactions that may facilitate plasticity in the mPFC. SC promotes long-term suppression of contextual fear compared to CFC. At remote retrieval, SC animals show increased IL parvalbumin (PV) interneuron activity and reduced perineuronal net (PNN) density, suggesting that extracellular matrix (ECM) remodeling could support enhanced plasticity in this group. We further identify a critical role for oligodendrocyte lineage cells (OLCs) in PNN remodeling. Notably, safety retrieval recruits satellite oligodendrocyte lineage cells (i.e., satOlig2+ cells) to PV interneurons. In SC animals, this recruitment correlates with reduced PNN accumulation around PV-satOlig2 pairs, whereas CFC animals exhibit increased PNN density at remote retrieval. Open-source single-cell RNA sequencing reveals that oligodendrocyte precursor cells (OPCs) express PNN-building genes, mature oligodendrocytes (OLs) express PNN-degrading genes, and newly-formed oligodendrocytes (NFOLs) express both. Bulk RNAseq from SC animals shows reduced expression of OPC-related structural genes and increased expression of OL-related PNN-degrading genes in the mPFC. Notably, satOlig2 cells recruited during remote safety retrieval are predominantly CC1+ mature satellite OLs (satOLs), which we hypothesize degrade PNNs through expression of PNN degradation enzymes. Optogenetic inhibition of PV activity during safety learning blocks satOlig2 recruitment, maturation, and PNN degradation while restoring long-term contextual fear expression. These findings suggest a role for satOlig2 cells in promoting safety learning through dynamic PNN regulation. By maintaining PV interneuron activity and excitatory-inhibitory balance, satOlig2 cells may facilitate PNN remodeling, in support of fear suppression and adaptive behavior. This study provides critical insights into the mechanisms of safety learning and highlights potential OL- and ECM-based therapeutic targets for PTSD and related psychiatric disorders.

overall_design: Bulk RNAseq from the mPFC of CFC and SC animals after remote memory retrieval

first: Emma

last: Denholtz

first: Patrizia

last: Casaccia

first: Ekaterina

last: Likhtik


title: Pan-cancer single cell transcriptomic clustering reveals heterogeneous CD8+ exhausted T cell populations with different immune checkpoint inhibitor responses

last: Gutmann

address: 660 S. Euclid Ave

institute: Washington University in St. Louis School of Medicine

summary: In most cancers, T lymphocytes comprise an essential cellular component of the non-neoplastic microenvironment, where they have the capacity to both suppress and support tumor growth. One specialized T lymphocyte population is the CD8+ exhausted T cell, which has been intensely studied as an actionable therapeutic target. Unfortunately, there is currently no uniformly accepted classification scheme for these specialized T cells. To provide a potential model for classifying CD8+ exhausted T cells, we leveraged single cell transcriptomic analysis of a diverse collection of both human (n = 8) and mouse (n = 4) cancers to identify unique subpopulations shared across tumor types and species. By integrating data from both human and mouse cancer studies, as well as previously described CD8+ exhausted T cell subsets, we provide an integrated framework to characterize the heterogeneity of exhausted CD8+ T cells. As such, one of these subpopulations (cluster C1) increases following immune checkpoint inhibitor treatment in the setting of cancer in mice and patients. Taken together, this proposed classification scheme may be useful for the design and interpretation of current and future immune-based therapy studies.

overall_design: All experiments were performed under active Animal Studies Committee protocols at Washington University School of Medicine (Washington University in St Louis Institutional Animal Care and Use Committee). Mice harboring a neomycin cassette insertion in exon 31 (Nf1+/-) with GFAP-Cre-mediated Nf1 loss in neuroglial progenitors (Nf1flox/neo; GFAP-Cre, Nf1-OPG mice) (Bajenaru et al., 2003). Nf1+/−, WT or Nf1flox/flox mice were employed as controls.

first: Rui

last: Mu

first: Rasha

last: Barakat


title: Methylomes of healthy Polish women and women diagnosed with breast cancer with blood arsenic (As) measurements

city: Szczecin

first: Tomasz

middle: K

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

summary: Genome-wide DNA methylation patterns were quantified in peripheral blood samples collected from 90 individuals using the Illumina Infinium HumanMethylationEPIC BeadChip

overall_design: In this study, we recruited 56 Healthy Polish women with 12-years cancer free follow-up and 34 Polish women diagnosed with BC with blood samples collected 4.29 years prior to cancer diagnosis. From each participant we collected peripheral blood sample for DNA extraction and performed DNA methylation analyses using Illumina Infinium HumanMethylationEPIC BeadChip.

first: Katarzyna

last: Sokolowska

first: Jacek

last: Antoniewski

first: Marta

last: Sobalska-Kwapis

first: Wojciech

last: Marciniak

first: Dominik

last: Strapagiel

first: Jan

last: Lubiński


title: Dynamic compression improves chondrogenesis in the tissue engineered model of cartilage.

city: Newcastle upon Tyne

middle: Anna

last: Pirog

address: Biosciences Institute

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

summary: Hyaline cartilage is a dense avascular tissue with low regenerative potential, present at the ends of the diarthrodial joints and in the cartilage growth plate. Skeletal diseases often result from extracellular changes in this tissue; however, studies of these are hindered by the tissue complexity, the difficulty in obtaining human material, and the cost of generating animal models. Recent developments in tissue engineering are opening possibilities to develop mechanoresponsive zonally stratified models of cartilage in vitro. In this study, we optimised a 3D model of cartilage using chondroprogenitor cells cultured for 21 days in 2% agarose hydrogel constructs with daily dynamic compression. Our hydrogel constructs developed pericellular matrices with nanostiffness comparable to native murine tissue and showed increased production of extracellular matrix components and expression of chondrogenic and differentiation markers. Daily dynamic compression resulted in progressive increase in mechanoresponsive gene expression and promoted a juvenile cartilage phenotype, decreasing expression of dedifferentiation and cartilage degradation markers. Our study highlights the potential of hydrogel-enhanced chondrogenesis and proposes an adaptable and scalable in vitro model to study mechanoresponses, intracellular signals and pericellular matrix involvement in cartilage development and disease.

overall_design: To investigate the effect of 3D environment and dynamic compression on chondrogenesis of ATDC5 cells, we cultured 10x10^6 cells/ml in 2% w/v low melting agarose with or without daily dynamic compression for 30min at 10kPa 0.33Hz

first: Marc

middle: V

last: Farcasanu

first: Thais

last: de las Heras Ruiz

first: Francesca

last: de Sousa Brito

first: Jamie

last: Soul

first: Matthew

last: German

first: David

last: Young

first: Ana

last: Ferreira-Duarte


title: Profiling lamina specific pyramidal neurons using postmortem human formalin fixed paraffin embedded frontal cortex tissue in combination with digital spatial profiling

city: Orangeburg

first: Stephen

middle: D.

last: Ginsberg

address: 140 Old Orangeburg Rd

department: Center for Dementia Research

institute: Research Foundation for Mental Hygiene

summary: Digital spatial profiling (DSP) is an innovative approach to perform RNA sequencing (RNA-seq) and bioinformatic analysis combined with precise spatial information from individually identified regions or cell types, including neurons. This approach enables expression profiling linking RNA-seq data to spatially characterized samples utilizing tissue bound probes. We employ the GeoMx DSP system to allow spatial characterization of transcriptomic data from lamina specific pyramidal neurons as well as cortical laminar ribbons containing neurons and admixed cell types in human postmortem brain tissue. We optimized the protocol to establish a robust and reproduceable method in human postmortem formalin fixed paraffin embedded (FFPE) frontal cortex tissue using nondemented human control brains. Layer III (L3) and Layer V (L5) pyramidal neurons from Brodmann area 9 were identified with the neuronal marker Ca2+/calmodulin-dependent protein kinase II and selected for probe collection. The present protocol significantly reduced the amount of FFPE tissue needed for robust RNA-seq using the GeoMx DSP platform. We demonstrate ~20 identified L3 or L5 pyramidal neurons or  one lamina-specific cortical ribbon from a single 5 µm thick section is sufficient to generate RNA-seq results. Bioinformatic analysis of isolated neurons and ribbons showed notable similarities and differences, reflective of the single neuron and multiple admixed cell types within the former and latter, respectively. This revised DSP assay provided high resolution RNA-seq data demonstrating utility and versatility of GeoMx platform for individually characterized neurons as well as isolated cortical ribbons within postmortem FFPE human brain tissue for downstream analyses.

overall_design: This study is focused on profiling of layer III (L3) and layer V (L5) pyramidal neurons within their respective cortical laminae in non pathologic human postmortem FFPE frontal cortex brain tissue sections for gene expression analysis and downstream bioinformatic inquiry.

first: Aleksandra

last: Stanisavljevic

first: Kyrillos

middle: W

last: Ibrahim

first: Philip

last: Stavrides

first: Christopher

last: Bare

first: Melissa

middle: J

last: Alldred

first: Adriana

last: Heguy

first: Ralph

last: Nixon

middle: D


title: RNA-seq for TFPI2 overexpressing tumor pericytes

city: Shenzhen

first: zhou

last: hongzhong

state: Guangdong

address: No. 3002, Shangang West Road, Futian District, Shenzhen, Guangdong Province

department: Shenzhen Institute of Translational Medicine

institute: The Second People's Hospital of Shenzhen (The First Affiliated Hospital of Shenzhen University)

summary: This study aims to investigate genes regulated by TFPI2

overall_design: RNA sequencing data of human hepatocellular carcinoma cells overexpressing TFPI2 and overexpressing empty vector plasmid

first: Hongzhong

last: Zhou