title: PAF1 N-terminal extension-generated PAF1c-SKIP-CDKB module regulates plant-specific cell cycle in the plant kingdom

city: Beijing

first: Yan

last: Li

address: Haidian

institute: Capital Normal University

summary: Through systematic biochemical analyses, we identified a novel protein-protein interaction between PAF1 and SKIP in Chlamydomonas reinhardtii.  To investigate the functional significance of this interaction, we generated targeted mutants using CRISPR-Cas9 genome editing technology.  Phenotypic characterization revealed that both PAF1 and SKIP mutants exhibit coordinated regulation of the cell cycle progression.  To elucidate the molecular mechanism underlying PAF1-SKIP mediated cell cycle regulation, we employed an integrated multi-omics approach.  RNA sequencing (RNA-seq) analysis was performed to identify differentially expressed genes, while chromatin immunoprecipitation sequencing (ChIP-seq) was utilized to map the genomic loci directly bound by the PAF1-SKIP protein complex.  This comprehensive strategy enabled us to delineate the transcriptional network governed by the PAF1-SKIP regulatory module.

overall_design: The Chip experiment was conducted using three materials: CrWT, CrPAF1-HA, and CrSKIP-HA. Chlamydomonas cells were cultured and harvested, then cross-linked with 1% formaldehyde. After terminating the cross-linking with Gly, the cells were sonicated in lysis buffer, followed by immunoprecipitation (IP) using HA antibody. The resulting products were subjected to DNA recovery and subsequent Chip-seq sequencing analysis.

first: Renshen

last: Yuan


title: Beta‑blockers prolong response to androgen deprivation therapy in prostate cancer through modulation of the neuro‑immuno‑oncology axis

status: Public on Jun 25 2025

city: Gothenburg

first: Bart

last: Edelbroek

address: Medicinaregatan 3B

department: Bioinformatics and Data Centre, Core Facilities

country: Sweden

institute: University of Gothenburg

type: Expression profiling by high throughput sequencing

summary: Background: The therapeutic impact of beta-blockers (BB), beta-adrenergic receptor antagonists, on prostate cancer remains controversial. The underlying health conditions of BB users complicate the ability to isolate and evaluate the specific effects of these drugs on the tumour cells. This study investigated whether BBs, by inhibiting sympathetic nerve signalling, extended the duration of androgen deprivation therapy (ADT) effectiveness in patients with de novo metastatic hormone sensitive prostate cancer and in prostate cancer xenograft models, while also uncovering the molecular mechanisms involved. Methods: An analysis was conducted on prospectively collected data from the Cancer Registry of Norway, Norwegian Prescription Database, and Norwegian Cause of Death Registry focusing on patients with de novo metastatic prostate cancer undergoing ADT using the commencement of second-line treatment as the endpoint. In addition, the causal effect of BB treatment was studied in two different hormone-sensitive prostate cancer xenograft mouse models. Prior to treatment, mice were surgically castrated, to mimic ADT, and tumour progression was tracked by measuring serum PSA levels. RNA sequencing was performed on xenografted orthotopic tumours to investigate the underlying mechanisms, utilizing annotation based on human data and protein levels were validated by the Protein Simple Immunoassay. Immune-related effects were evaluated using immunohistochemistry on tumour tissue and measuring neopterin levels, along with 92 analytes, using the OLINK proximity extension assay on serum samples from xenografted mice and prostate cancer patients, both BB users and non-users. Results: A competitive risk analysis indicated that BB treatment postponed the initiation of second-line treatment in prostate cancer patients on ADT. Additionally, in both prostate cancer xenograft models, BB treatment reduced tumour burden and delayed progression to castration-resistant prostate cancer (CRPC). Mechanistically, BB treatment suppressed androgen receptor signalling and induced a metabolic shift by up-regulating oxidative phosphorylation transcripts and down-regulating those involved in fatty acid synthesis and the PI3K/AKT/mTOR pathway. Additionally, BB treatment increased serum pro-inflammatory cytokines, such as the IL23/IL17 axis, in both xenografted mice and in patient samples. Enhanced intra-tumoral CD68+ immune cell infiltration was also observed in the tumours. Conclusion: The data suggest that BB combined with ADT delay the progression to castration-resistant prostate cancer. This may be achieved by influencing androgen receptor activity, adjusting energy metabolism and fostering a pro-inflammatory antitumoral microenvironment.

overall_design: RNA seq profiling of LNCaP orthotopic xenografts from mice treated with Propranolol, Propranolol+SR59230A or vehicle.

first: Malin

last: Hagberg Thulin

first: Håkon

last: Ramberg

first: Kristin

last: Austlid Taskén


title: Life long effects of radiation and high fat dieat on the mouse right ventricular tissue

city: New York

first: Davit

middle: A.

last: Goukassian

state: NY

address: One Gustave L. Levy Place, Box 1014

department: Cardiovascular Research Institute

country: USA

institute: Icahn School of Medicine at Mount Sinai

summary: We studied the long-term effects of single whole-body gamma and simulated GCR irradiation (IR) and consumption of a Western Diet (WD) on the heart's right ventricle (RV). Three-month-old C57Bl/6J wild-type male and female mice were assigned to the following groups: 1) Gamma-irradiated with follow-up at 440(males and females) and 660(males)/550(females) days post-IR; 2) simGCRsim-irradiated with follow-up at 440(males and females) and 660(males)/550(females) days post-IR; 3) 270-days WD-fed animals with followup at 530 (males and females) and 750(males)/640(females). Control groups consisted of non-irradiated (non-IR) mice and normal diet-fed mice. Control groups were followed up similarly to the treatment groups. RV tissues were collected at follow-up and subjected to bulk RNA sequencing analysis. Total RNA was extracted from RV tissues using the RNeasy Mini Kit (Qiagen, USA) according to the manufacturer’s protocol and stored at -80°C until further use. A poly-A selected mRNA library was prepared using the NEBNextUltra™II RNA Library Prep Kit. The sequencing was performed on the Illumina NovaSeq-6000 platform to collect an average of 48 million 2x150bp paired-end reads per sample. FastQC (version 0.11.9) was used for the quality assessment of raw sequencing reads (Q30% was greater than 94%). Next, we aligned the reads to the mouse reference genome (mm39) with STAR aligner (version 2.7.8a) with gene count quantification mode and obtained raw gene counts. Differential gene expression analysis and functional annotation were performed using DESeq2 and fgsea R packages. The results of the study provide insights into the long-term transcriptomic disturbances in response to irradiation and a Western diet and their association with structural and functional changes in the RV. Furthermore, the findings highlight pronounced sex-specific and irradiation type-dependent pathophysiological and transcriptomic alterations in the RV.

first: Siras

last: Hakobyan

first: Roksana

last: Zakharyan

first: Ani

last: Stepanyan

first: Arsen

last: Arakelyan

first: David

middle: A


title: Characterizing heterogeneous cis-regulatory elements in gene regulatory programs associated with breast cancer

city: Tokyo

first: Kohei

last: Kumegawa

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

country: Japan

institute: Japanese Foundation for Cancer Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Background: Cis-regulatory elements (CREs) control oncogene expression and malignant phenotypes. The high clinicopathological heterogeneity of cancer cannot be explained by gene expression alone, being attributed to CRE heterogeneity. However, characterizing cancer-associated CRE is challenging. To address this issue, we performed a single-cell epigenomic analysis of clinical specimens.
Methods: To map the multicellular ecosystem of BC and identify candidate CREs (cCREs), we performed a single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq) of 38 prospectively collected breast cancer (BC) samples with various clinicopathological characteristics.
Results: First, we performed single-cell chromatin accessibility profiling of a high-quality set of 22,775 cells from BC samples. Cells were accurately annotated using marker gene accessibility and integration with existing single-cell RNA sequencing data. By predicting copy number variants, epithelial cells were classified into non-malignant and malignant cells. The chromatin accessibility patterns exhibited by malignant cells were consistent with the clinicopathological features of each tumor. We identified 224,585 cCREs across the BC ecosystem. By identifying cluster-specific differentially accessible cCREs (DA-cCREs) and constructing a putative enhancer-promoter network, we mapped the cis-regulatory landscape for cancer cells and the tumor microenvironment. In this dataset, we identified changes in the cis-regulatory landscape associated with cancer progression. In particular, estrogen receptor (ER)-positive tumors have increased accessibility of ER binding motifs during the cell transition from non-cancerous to cancerous and increased accessibility of Kruppel like factor motifs during the transition from cancerous to metastatic. Furthermore, the accessibility of putative enhancers targeting the same gene differed within or between tumors, highlighting intra- and inter-cis-regulatory tumor heterogeneity.
Conclusions: This study provides a valuable resource for future epigenetic research on BC and highlights the diverse regulatory landscape within or among tumor(s), suggesting that cCREs regulate tumor progression and intra- and inter-tumor heterogeneity.

overall_design:
Single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq) of 38 prospectively collected breast cancer (BC) samples with various clinicopathological characteristics.

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

last: Hori

first: Reo

last: Maruyama


title: bulk RNAseq from the medial amygdala of male and female mice

city: Jerusalem

first: Tamar

last: Licht

address: Hadassah ein karem

department: Medical Neurobiology

country: Israel

institute: Hebrew University

summary: Sexual dimorphism in the brain is well-documented, yet clear binary features akin to genital differences remain elusive. Using the TRAP2 transgenic mouse line to track cFos-driven neuronal activity, we identified a distinct cluster of neurons (~200 µm) in the posterodorsal medial amygdala—termed the DIMPLE—that exhibited binary activation: consistently labeled in females but absent in adult virgin males. This pattern was unaffected by gonadectomy but was present in juvenile males before weaning and re-emerged in adult males after mating. Public RNA-seq data showed prolactin receptor enrichment in this region, and exogenous prolactin administration activated DIMPLE in virgin males. We propose that DIMPLE may support neural mechanisms related to female-typical behavior or paternal readiness.

overall_design: Medial amygdala (MeA) tissue containing the DIMPLE—comprising approximately 18–40% of the extracted area—was collected from TRAP2-Ai9 mice, including 3 adult females and 4 adult males that were labeled with tamoxifen at postnatal day 24 (P24).

first: Dan

last: Rokni


title: A Transcriptomics-Based Computational Drug Repositioning Pipeline Identifies Simvastatin And Primaquine As Novel Therapeutics For Endometriosis Pain

city: San Francisco

first: Marina

last: Sirota

state: CA

address: 490 Illinois St.

institute: UCSF

summary: Endometriosis is a disease with limited medical treatment options and a strong need for new therapeutic strategies. We previously applied a transcriptomics-based computational drug repositioning pipeline to publicly available bulk transcriptomic data to identify potential therapeutics for endometriosis. The drug candidates identified in silico includes fenoprofen, primaquine, and simvastatin. Validation of these drugs in our rat endometrial model determined that they significantly reduced endometriosis-associated vaginal hyperalgesia, a surrogate marker for endometriosis-related pain. The signatures of DEGs from uteri and lesions demonstrated reversal of the endometriosis disease signature with simvastatin and primaquine treatment.

overall_design: RNA profiling on a rat model of endometriosis with a WT (no endo+no drug) group and five treatment groups: vehicle, fenoprofen, primaquine, simvastatin, and ibuprofen (positive control). Each group included six rats.

first: Tomiko

middle: T

last: Oskotsky

first: Xinyu

last: Tang

first: Erin

last: Arthurs

first: Arpita

last: Govil

first: Linda

middle: C

last: Giudice

first: Stacy

middle: L

last: McAllister


title: Canonical Hedgehog Signaling Controls Astral Microtubules and Mitotic Spindle Orientation in Neural Progenitors and iPSCs

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

summary: Mitotic spindle orientation is crucial for cell fate determination and tissue organization. Although the intracellular machinery governing spindle orientation is well characterized, whether and how secreted factors, such as morphogens, regulate this process remains poorly understood. This study investigated the role of Hedgehog (HH) signaling in modulating mitotic spindle orientation in neural progenitor cells and in induced pluripotent stem cells (iPSCs). Time-lapse microscopy of cerebral organoids and iPSCs revealed that HH signaling increases the angle of the mitotic spindle relative to the apical surface, prolongs mitosis, and enhances spindle rotation. Mechanistically, HH signaling reduces both the number and the length of astral microtubules, key regulators of spindle orientation. This reduction correlates with increased spindle angle in iPSCs. Furthermore, we show that canonical HH signaling, involving GLI-dependent transcriptional regulation, contributes to these effects. RNA sequencing and gene set enrichment analysis (GSEA) revealed that HH signaling upregulates genes associated with microtubule depolymerization, suggesting a transcriptional mechanism by which HH signaling influences astral microtubule dynamics and, consequently, mitotic spindle orientation. These findings highlight a novel link between a morphogen, transcriptional regulation, and the control of mitotic spindle orientation, with implications for development and tissue homeostasis.

overall_design: RNA-seq profiling of induced pluripotent stem cells (AICS-0012) that were treated with DMSO, SAG (400 ng), or SAG (400 nM) + Forskoling (10 mM) for 24 hours.

first: Fengming

last: Liu

first: Young-Goo

last: Han


title: Mutations in PSEN1 predispose inflammation in an astrocyte model of familial Alzheimer’s disease through disrupted regulated intramembrane proteolysis

city: London

first: Oliver

last: Ziff

address: Institute of Neurology, Queen Square

country: United Kingdom

institute: University College London

summary: Mutations in PSEN1 cause familial Alzheimer’s disease with almost complete penetrance. Age at onset is highly variable between different PSEN1 mutations and even within families with the same mutation. Current research into late onset Alzheimer’s disease implicates inflammation in both disease onset and progression. PSEN1 is the catalytic subunit of gamma-secretase, responsible for regulated intramembrane proteolysis of numerous substrates that include cytokine receptors. For this reason, we tested the hypothesis that mutations in PSEN1 impact inflammatory responses in astrocytes, thereby contributing to disease progression. We developed patient-derived models of iPSC-astrocytes, representing three lines harbouring PSEN1 mutations and six control lines (including two isogenic controls). Transcriptomic and biochemical assays were used to investigate differential inflammatory responses to TNFa, IL1a and C1q. We show that PSEN1 is upregulated in response to inflammatory stimuli, and this upregulation is disrupted by pathological PSEN1 mutations. Using transcriptomic analyses, we demonstrate that PSEN1 mutant astrocytes have an augmented inflammatory profile in their basal state, concomitant with gene expression signatures revealing dysregulated  intramembrane proteolysis and JAK-STAT signalling. Detailed investigation of the JAK-STAT2 signalling pathway showed reduced cell surface expression of IFNAR2, lower STAT2 phosphorylation cascades and delayed NFκB nuclear localisation in PSEN1 mutant astrocytes in response to inflammatory stimuli, thereby implicating the notion of altered cytokine signalling cascades. Finally, we use small molecule modulators of gamma-secretase to confirm a role for PSEN1/gamma-secretase in regulating the astrocytic response to inflammatory stimuli. Together, these data suggest that mutations in PSEN1 enhance cytokine signalling via impaired regulated intramembrane proteolysis, thereby predisposing astrocytic inflammatory profiles. These findings support a two-hit contribution of PSEN1 mutations to fAD pathogenesis, not only impacting APP and Abeta processing but also altering the cellular response to inflammation.

overall_design: iPSC-derived cortical neurons and iPSC-derived astrocytes derived from healthy controls, PSEN1 mutation carriers and isogenic corrected controls. Samples were either untreated or treated with TNFa + IL1a + C1q as an inflammatory stimulus.

middle: J

first: Gustavo

last: Morrone Parfitt

first: Sarah

last: Jolly

first: Jackie

middle: M

last: Casey

first: Lucy

last: Granat

first: Satinder

last: Samra

first: Nuria

last: Seto-Salvia

first: Argyro

last: Alatza

first: Leela

last: Phadke

first: Benjamin

last: Galet

first: Philippe

last: Ravassard

first: Marie-Claude

last: Potier

first: John

last: Hardy

first: Dervis

last: Salih

first: Paul

last: Whiting

first: Fiona

last: Ducotterd

first: Rickie

last: Patani

first: Selina

last: Wray

first: Charles

last: Arber


title: Transcriptomic profile at single cell level of adult lungs expressing exogenous BCL2 driven by three mesenchymal cell-specific drivers

city: Cincinnati

first: Jichao

last: Chen

address: 3333 Burnet Avenue

department: Pediatrics

institute: University of Cincinnati and Cincinnati Children's Hospital Medical Center

summary: A transient mesenchymal cell in the lung called alveolar myofibroblast (AMF) plays a key role in alveolar formation during postnatal development. However,  AMFs are cleared from the alveoli upon lung maturation. We induce exogenous BCL2 expression in these cells using three lineage-specific drivers (Myh11-CreER, PdgfraCreER, and PdgfrbCreER) to prevent AMF clearance. We use scRNA seq to analyze the transcriptomic changes of AMFs upon BCL2 expression and subsequent persistence in the lung. Additionally, we evaluated the consequences driven by persistent AMFs in other cell lineages at a transcriptional level.

overall_design: Lung cells from mice that overexpressed the prosurvival protein BCL2 (Rosa26 Bcl2/+) in mesenchymal cells were compared to control littermates. Epithelia (ECAD+), endothelial (ICAM2+), immune(CD45+) and mesenchymal cells (ECAD-/ICAM-/CD45-) from adult mouse lungs were isolated using Fluorescence-activated cell sorting (FACS). The transcriptome of each lineage was analyzed using RNA -single cell sequencing.

first: Maria Jose

last: Gacha-Garay

first: Hui

last: Liu

first: Scott

last: Evans

first: Tingting

last: Mills


title: Single-cell RNA sequencing of mouse epidermal Langerhans cells under injured and healthy conditions

city: East Lansing

first: Artem

last: Kiselev

state: Michigan

address: 775 Woodlot Dr

department: The Institute for Quantitative Health Science & Engineering

institute: Michigan State University

summary: Langerhans cells (LCs) are a specialized subset of dendritic cells that reside in the basal layer of the epidermis. LCs form a dense network across the skin, where LCs serve as key sentinels by detecting antigens from the environment and sensing damage to the epidermis. Despite extensive and persistent research, many immunological and physiological aspects of LCs functioning remain incompletely understood. In our study, we combined the advantages of single-cell RNA sequencing, intravital microscopy, and deep experimental approach to create protocols for the mass activation of LCs and the rapid isolation of the maximum viable LCs number. We present a high-resolution single-cell transcriptomic dataset of over 22,000 epidermal LCs, including injured and homeostatic conditions. We have, for the first time, clearly identified and characterized the distinct populations of LCs present in both homeostatic and injured epidermis. Most notably, we discovered a specific population of activated LCs that displays several unique features, including the activation of the complement system, a key component of the skin’s innate immune response.

overall_design: Single-cell RNA libraries were generated using the 10x Genomics platform from Langerhans cells isolated from mouse ear epidermis. Samples included untreated sample, skin treated with multiple microneedle-array punches and skin treated with a mixture of acetone, croton oil and olive oil. Libraries were sequenced on the Illumina NovaSeq X using 100 bp single-end reads (10B 100 SR).

first: Sangbum

last: Park


title: Circulating Cell-free DNA Methylation Biomarkers for Hepatocellular Carcinoma Risk Prediction in HIV-Positive Nigerian Population

city: Chicago

first: Yinan

last: Zheng

state: Illinois

address: 680 N Lake Shore Drive, Suite 1400

department: Department of Preventive Medicine

institute: Northwestern University

type: Methylation profiling by genome tiling array

summary: Hepatocellular carcinoma (HCC) is a leading cause of cancer mortality globally, with particularly high burdens among people living with HIV (PLWH) in low-resource settings like Nigeria. Effective early detection remains a major challenge due to limited access to imaging-based surveillance and the low sensitivity of current biomarkers such as alpha-fetoprotein (AFP). We conducted an epigenome-wide association study (EWAS) of circulating cell-free DNA (ccfDNA) methylation in a Nigerian cohort of HIV-positive individuals (n = 245), spanning HCC, cirrhosis, fibrosis, and HCC-free groups. Using random forest modeling, we developed and evaluated a ccfDNA methylation classifier (ccfDNAmRF) for HCC risk prediction. We identified 73 CpG sites significantly associated with HCC (false discovery rate <0.01). The ccfDNAmRF model demonstrated strong discriminatory power, achieving 100% sensitivity and 81–91% specificity for distinguishing HCC from cirrhosis, fibrosis, and HCC-free groups (area under the curve [AUC]: 92–97%). Combining ccfDNA methylation risk scores with AFP further improved classification accuracy (AUC up to 98.5%). Notably, ccfDNA methylation patterns displayed clear dose–response relationships across the disease spectrum, supporting their utility for early-stage detection and risk stratification. Our findings highlight the promise of ccfDNA methylation biomarkers as a minimally invasive, blood-based screening tool for improving early HCC detection among PLWH in resource-limited settings. These biomarkers may help address critical gaps in current surveillance strategies, offering scalable solutions adaptable to high-risk populations.

overall_design:
In this study, we focus on identifying circulating cell-free epigenetic markers for HCC among Nigerian population living with HIV, and then build and evaluate a machine-learning-based model to predict the risk of HCC. The study encompassed four groups of participants:
HIV Positive without Hepatocellular Carcinoma
HIV Positive Hepatocellular Carcinoma
HIV Positive Cirrhosis
HIV Positive Fibrosis

first: Lifang

last: Hou

first: Robert

last: Murphy

first: Folasade

last: Ogunsola

first: Atiene

middle: S

last: Sagay


title: Raw datas of the transcriptome in livers of Hezuo pigs and Bama pigs

city: Lanzhou

first: Jihong

last: Yan

state: Gansu

address: Yintan Road Subdistrict, Yingmen Village, No. 1

country: China

institute: Gansu Agricultural University

summary: This study selected cooperative pigs and Baoma pigs as the experimental subjects. By integrating the whole-transcriptome sequencing technology, the ceRNA network related to cold stress-induced anti-injury in the livers of cooperative pigs was screened. The aim was to reveal the molecular mechanism of maintaining liver functional homeostasis in cooperative pigs under cold stress conditions, and to provide new theoretical basis and technical support for cold resistance breeding and liver injury protection of livestock.

overall_design: Using the cooperative pigs and Baoma pigs treated with cold stress for 15 days as the experimental subjects, the normal-temperature groups of both types of pigs were respectively set as controls. High-throughput sequencing technology was employed to analyze the expression differences of mRNA, LncRNA, circRNA and miRNA in the livers of the cooperative pigs and Baoma pigs, to explore their biological functions, and to screen out the key genes and ncRNAs related to cold resistance of the cooperative pigs.

first: Shuangbao

last: Gun

first: Pengfei

last: Wang


title: The TET protein family interactor PROSER1 sustains hematopoietic stem cell function [RNA-Seq]

city: Dundee

first: Kasper

middle: Dindler

last: Rasmussen

address: Dow Street

department: Division of Molecular, Cellular, and Developmental Biology (MCDB)

institute: School of Life Sciences, University of Dundee

summary: Ten-Eleven-Translocation (TET) enzymes are epigenetic regulators important for prevention of hematological malignancies. PROSER1, a known TET protein interactor, has a critical role in modulating TET-mediated DNA demethylation during development. However, the potential involvement of PROSER1 in regulation of hematopoiesis and leukemogenesis remains unknown. Here, we demonstrate that the leukemia suppressive functions of TET2 are preserved in the absence of PROSER1. Nonetheless, we find that loss of PROSER1 partially recapitulates the aberrant enhancer DNA methylation phenotype observed upon TET2 knockout, suggesting that PROSER1 and TET2 play both cooperative and distinct roles in the regulation of DNA methylation in hematopoiesis. Importantly, using serial hematopoietic stem cell (HSC) transplantation assays, we find progressive exhaustion of HSC activity and reduction in hematopoietic lineage output upon loss of PROSER1. Our findings imply that, beyond the established role of TET2 loss-of-function mutations in promoting HSC expansion and leukemic transformation, accurate TET activity, regulated by PROSER1, is equally important to prevent HSC exhaustion and sustain normal hematopoiesis.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) in wildtype and PROSER1 KO immortalised hematopoietic progenitor cells (HOXB8-FL) for the following histone modifications: H3K27ac, H3K4me1, H3K27me3. Enzymatic methyl-seq (EM-seq) in wildtype, PROSER1 KO and TET2 KO HOXB8-FL cells. RNA-seq in LSK cells (Lin-Sca1+cKit+) FACS purified from lethally irradiated recipient mice transplanted with wildtype or PROSER1 knockout bone marrow.

first: Elena

middle: V

last: Knatko

first: Anna

last: Fleming

first: Xiang

last: Li

first: Phoebe

last: Crawley

first: Ieva

last: Budriunaite

middle: D


title: Identification of human macrophage tissue signatures at homeostasis and during polarization

first: Donna

last: Farber

address: 701 West 168th Street

institute: Columbia University Irving Medical Center

summary: Human macrophages (MΦs) reside in tissues and develop tissue-specific identities. Murine studies have dissected molecular signatures of tissue MΦ differentiation, but the translatability of these findings to human systems and the maintenance of these identities during MΦ activation is relatively unexplored. Here, we use multimodal single-cell sequencing and ex vivo stimulation to uncover MΦ tissue signatures in human lung, small intestine, spleen, bone marrow, and lymph nodes. Tissue-adapted gene and protein profiles were specific to MΦs, not monocytes isolated from the same sites, and biased populations to distinct metabolomic, adhesion, and immune profiles which were concordant with previous murine signatures. Tissue-adapted MΦs remained responsive to distinct cytokine polarization ex vivo, upregulating gene signatures and producing cytokines consistent with monocyte polarization. Despite this plasticity, MΦs maintain their tissue-specific phenotypes ex vivo, demonstrating memory and persistence of their tissue-specific programs in the absence of continuous external signaling.

overall_design: CITE-seq of human macrophages and monocytes isolated from different human organ donor tissues and cultured for 12 hours in media, or stimulated with LPS+IFNγ or IL-4

first: Daniel

middle: P

last: Caron

first: William

last: Specht

first: David

last: Chen

first: Peter

last: Sims


title: Beneficial and detrimental consequences of AHR stimulation in intestinal infection

city: Solna

first: Oscar

last: Diaz Perez

address: Nobels väg 13

institute: Karolinska Institutet

summary: The ligand dependent transcription factor aryl hydrocarbon receptor (AHR) is an environmental sensor whose activation can have physiologically beneficial or detrimental consequences for host immune responses depending on the ligand. Here we investigated the hypothesis that prolonged AHR activation either due to inefficient ligand metabolism or due to genetic manipulation may underlie the distinction between beneficial and detrimental effects. Our data indicate that prolonged AHR activation caused toxic endpoints for liver and thymus but was not per se interfering with the host response to infection with the intestinal pathogen C.rodentium. Genetically driven constitutive AHR activation improved resistance to infection, whereas prolonged AHR activation by the pollutant TCDD resulted in delayed clearance of C.rodentium. This was associated to a suppression in antibody production. Combined single cell RNAseq and ATAC-seq analysis provided evidence that TCDD, but not genetic AHR overactivation, affected dendritic cell functions such as activation, maturation and antigen presentation. Thus, the detrimental impact of environmental pollutants such as TCDD on immune responses cannot solely be attributed to aberrantly prolonged activation of AHR.

overall_design: Single nuclei were extracted on day 5 after infection with Citrobacter rodentium. Mice were treated with Vehicle or TCDD 6 days before infection. Joint snRNA-seq and scATAC-seq libraries were prepared using the 10x Genomics platform

middle: E

last: Diaz

first: Christopher

last: Barrington

first: Liang

last: Zhou

first: Dennis

last: Lindquist

first: Frederike

last: Graelmann

first: Emma

last: Wincent

first: Brigitta

last: Stockinger


title: Maternal Vitamin C Deficiency and Genetic Risk Factors Contribute to Congenital Malformations through Dysregulation of DNA Methylation. [WGBS E8.5]

city: Leuven

first: Bernard

middle: Klaas

last: van der Veer

state: Vlaams-Brabant

address: Herestraat 49 - box 804

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

type: Methylation profiling by high throughput sequencing

summary: Maternal dietary insufficiencies can reshape the offspring epigenome during gestation, contributing to birth defects and developmental disorders. Vitamin C (VitC) is a critical co-factor for Ten-Eleven-Translocation (TET) DNA demethylases, but the impact of its deficiency on embryonic development remains unclear. Here, we show that insufficient maternal VitC combined with genetic susceptibility can give rise to congenital malformations, including neural tube defects (NTDs), through dysregulation of DNA methylation. We previously reported NTDs in Tet1 knockout (KO) mice at low penetrance in C57BL/6J (B6) congenic inbred strains, but at two- to three-fold higher rates when outbred or highly backcrossed (incipient congenic) on a 129S6.B6 background. Similarly, maternal VitC deficiency in L-gulonolactone oxidase (Gulo) KO mice, which like humans are unable to synthesize VitC, resulted in highly penetrant congenital malformations in non-inbred mice, during a vulnerable window coinciding with gastrulation. DNA hypermethylation is a signature of VitC-deprived 129S6.B6-Gulo-/- embryonic headfold tissues, being absent in B6 embryos which are grossly normal. In outbred Gulo-/- embryonic brains, genomic regions harboring hypermethylation – hallmarks of TET dysfunction - increased with the severity of embryonic pathologies. A moderate reduction in VitC status is sufficient to induce hypermethylated regions and cause NTDs. Severe embryonic defects in VitC-deprived embryos can be rescued by timely re-supplementation of VitC at the onset of gastrulation, which normalized DNA methylation at most loci. Our results suggest that promoting timely VitC supplementation by at-risk pregnant mothers may prevent many birth defects currently refractory to folic acid supplementation and enhance the “health-span” of future generations.

overall_design: WGBS in E8.5 headfolds, collected from B6 and 129S6.B6-Gulo<-/-> embryos, with or without VitC supplementation.

first: Kian

last: Koh


title: High burden of premature ventricular contractions upregulates transcriptional markers of inflammation linked with adverse cardiac remodeling and cardiomyopathy.

first: Jose

last: Gomez-Arroyo

state: Ohio

address: 3333 Burnet Ave

department: Pulmonary and Critical Care Medicine

institute: University of Cincinnati

summary: Premature ventricular contractions (PVCs) are the most prevalent ventricular arrhythmia in adults. High PVC burden can lead to left ventricular (LV) systolic dysfunction, eccentric hypertrophy, and an increased risk of heart failure (HF) and sudden cardiac death (SCD). Deficient angiogenesis is a key determinant in the transition from adaptive to maladaptive cardiac hypertrophy and fibrosis is a risk factor for arrhythmias and SCD. Here,  the primary objective was to quantitatively assess the structural remodeling and transcriptional alterations associated with PVC-induced cardiomyopathy (PVC-CM). Canines were implanted with modified pacemakers to reproduce bigeminal PVCs (200-220 ms coupling interval) for 12 weeks. Collagen deposition and interstitial ultrastructure were visualized using light and transmission electron microscopy, respectively, in LV samples. Morphometric studies of pericytes, fibroblasts, myocytes, smooth muscle and endothelial cells were performed using confocal microscopy and quantified with an artificial intelligence-based segmentation analysis and compared using hierarchical statistics. Transcriptional changes were assessed via RNAseq. Although the cardiomyocytes were hypertrophied in PVC-CM LV samples, capillary rarefaction was not observed due to an increase in capillary-to-myocyte ratio. Additionally, thicker blood vessels were more abundant in PVC-CM. Fibroblast-to-myocyte ratio more than doubled, interstitial collagen fibers increased, and the interstitial space thickened in PVC-CM. Transcripts involved in interstitial remodeling, inflammatory response, and alarmins were strongly elevated in PVC-CM. While the angiogenic response meets the metabolic demands of cardiac hypertrophy, upregulated markers of inflammation and cardiomyopathy linked to reactive fibrosis collectively represent an adverse remodeling that heightens the risk of HF and SCD in PVC-CM.

overall_design: Female mongrel canines (>10 months old, ~21 Kg) were implanted with a modified dual-chamber epicardial pacemaker. After a 2-week surgical recovery, animals were randomized into 2 groups: 1) PVC-CM group, receiving bigeminal PVCs (50% burden) with a 200-220 ms coupling interval for 12 weeks, and 2) sham group where PVCs were not enabled. Echocardiographic recordings were obtained at baseline and at 12-weeks of chronic PVCs to evaluate the development of cardiomyopathy. Euthanasia was performed at week 12, via exsanguination during final left thoracotomy surgery under general anesthesia. The harvested heart was immediately rinsed with ice-cold phosphate-buffered saline (PBS), which was injected directly through the left main coronary artery to remove blood. Segments of the anterior LV were snap frozen and snap-frozen myocardial tissue from randomly selected regions of the left ventricular (LV) free wall was used for RNA extraction and downstream analysis.

first: Juana

last: Medina-Contreras

first: Jaime

last: Balderas-Villalobos

middle: F

last: Huizar

last: Eltit


title: RNA binding proteins PCBP1 and PCBP2 regulate pancreatic β cell translation

city: Philadelphia

first: Doris

last: Stoffers

state: PA

address: 3400 Civic Center Blvd

department: IDOM

institute: University of Pennsylvania

summary: Tight control of β cell mRNA translation plays a central role in regulating glucose homoeostasis and β cell health. RNA binding proteins (RBPs) impact translational dynamics and function in networks to achieve their regulatory outcomes, yet an understanding of the RBPs and nature of their interplay in directing β cell translation remain limited. We recently established that the RBP PCBP2 is a key post-transcriptional regulator of β cell function. Here, we investigate the relationship of PCBP2 and its sister-isoform PCBP1 in shaping β cell homeostasis and translation. Pcbp co-deletion in primary β cells gave rise to a severe diabetic phenotype due to compromised β cell viability. Single-cell RNA sequencing of Pcbp co-deficient β cells revealed downregulation of a network of core translation initiation factors and ribosomal mRNAs. Motif enrichment analysis, mRNA-protein interaction, and mRNA stability studies identified that the PCBPs co-impact these mRNAs in part through binding and stabilization. Accordingly, protein translational monitoring demonstrated a requirement for the PCBPs in sustaining global mRNA translation in β cells. Together, these findings demonstrate a requirement for the PCBPs in sustaining the global rates of mRNA translation critical for β cell control of glucose homeostasis.

overall_design: Islets were isolated from 4-5 week old, male Pcbp1/2Fl/Fl or Pcbp1/2βKO mice, hand-picked clean of acinar, and recovered for 3 days in RPMI 1640 medium.

first: Matthew

middle: W

last: Haemmerle

first: Kirill

last: Batmanov


title: Maternal Vitamin C Deficiency and Genetic Risk Factors Contribute to Congenital Malformations through Dysregulation of DNA Methylation.

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

overall_design: Refer to individual Series


title: Maternal Vitamin C Deficiency and Genetic Risk Factors Contribute to Congenital Malformations through Dysregulation of DNA Methylation. [RNA-Seq E8.5]

overall_design: RNA-seq in E8.5 headfolds, collected from B6 and 129S6.B6-Gulo<-/-> embryos, with or without VitC supplementation.


title: A Silk-Based Patch with Temporary Adhesion and Detachability on the Ocular Surface for Inflammatory Mediator Removal

first: Yilin

last: Zhang

address: XueYuan Road No.37, HaiDian District

institute: Beihang University

summary: Corneal alkali burns cause persistent inflammation, leading to corneal vascularization and fibrosis, which severely impair vision. Here, we developed a temporary adhesive silk-based patch to capture and remove inflammatory mediators from the ocular surface. The patch utilizes photocrosslinkable silk for mechanical support, chitosan as the adhesive, hyaluronan for lubrication, and polyamidoamine (PAMAM) dendrimers with heparin to enhance adsorption. After water annealing, the patch exhibited excellent transparency, mechanical strength, and resistance to swelling, remaining attached to the rat ocular surface for 3–5 days. Adsorption tests confirmed that the patch effectively captured small-molecule dyes, proteins, and free DNA. In the rat corneal alkali burn model, imaging and histological evaluations showed significant reductions in vascularization and fibrosis after 3 days of treatment, along with improved corneal transparency. RNA sequencing revealed that patch treatment effectively inhibited the PI3K–AKT inflammatory pathway. This inflammation-removing patch represents an innovative treatment for corneal alkali burns with significant clinical potential.

overall_design: After the corneas were ground, cell lysis buffer was added, and the samples were collected for reverse transcription. Double-stranded cDNA was quantified using a Qubit4 fluorometer (Thermo Fisher, USA). The fragment size of the double-stranded cDNA was assessed using an Agilent 4150 Bioanalyzer (Agilent, China). A sample was considered qualified if the concentration was greater than 1.6 ng/μL and if the main peak was concentrated between 750 and 1500 bp. The library was sequenced on the Illumina HiSeq high-throughput sequencing platform. First, the raw reads in FASTQ format were processed using fastp1 to remove low-quality reads and obtain clean reads for subsequent analysis. The fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated for each gene, and the read counts for each gene were obtained using HTSeq-count. PCA was performed using R (v 4.4.1) to assess sample reproducibility. The differential expression analysis was conducted using DESeq2. A q value < 0.05 and a fold change > 2 or < 0.5 were considered significant. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) pathway enrichment analyses were performed using R (v 4.4.1), with significantly enriched terms filtered by R (v 4.4.1). Bar plots and bubble plots for the significantly enriched terms were generated using R (v 4.4.1) and GraphPad Prism 9.

first: Dongyan

last: Li

first: Linhao

first: Jing

last: Ji

first: Yubo

last: Fan


title: single-cell transcriptomes of meningeal and CP T cells in young and aged mice

city: New Brunswick

first: Qi

last: Yang

state: NJ

address: 89 French St

institute: Rutgers RWJMS

summary: The effects of aging on brain-associated T cells remain incompletely understood. We sorted CD4 and CD8 T cells from meninges and choroid plexus of young and aged mice, and compared their single-cell transcriptomes. The results provide insights into the changes of brain-associated T cells with aging, and identify unique aging-associated T cells.

overall_design: Meninges and choroid plexus samples were obtained from young and aged mice. CD4 and CD8  T cells were sorted by FACS. scRNA-seq were performed using the 10xgenomics 5' gene expression kit. Libraries were sequenced by a NextSeq.

first: Yuanyue


title: Aggresomes protect mRNA under stress in Escherichia coli

city: Wuhan

first: linsen

last: pei

state: Hubei

address: Shui guohu

institute: Wuhan University

summary: Membraneless droplets formed through liquid-liquid phase separation of ribonucleoprotein particles contribute to mRNA storage in eukaryotic cells. How such aggresomes contribute to mRNA dynamics under stress, and their functional role, is less understood in bacteria. Here we used multiple approaches including imaging, modelling and transcriptomics to show that prolonged stress leading to ATP depletion in Escherichia coli results in increased aggresome formation, their compaction, and enrichment of mRNA within aggresomes compared to the cytosol. Transcript length was longer in aggresomes compared to the cytosol. Mass spectrometry showed exclusion of mRNA ribonucleases from aggresomes, which was due to negative charge repulsion. Experiments with fluorescent reporters and disruption of aggresome formation showed that mRNA storage within aggresomes promoted translation and associated with reduced lag phases during growth after stress removal. Our findings suggest that mRNA storage within aggresomes confers an advantage for bacterial survival and recovery from stress.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: We treated the cells with arsenite for 30 min, and extracted the aggresome RNA and cytol RNA respectively, and then analyzed the RNA SEQ.


title: Maternal Vitamin C Deficiency and Genetic Risk Factors Contribute to Congenital Malformations through Dysregulation of DNA Methylation. [RNA-Seq E11.5]

overall_design: RNA-seq E11.5 brains, collected from CD1-Gulo<-/-> embryos, supplemented with various doses of VitC


title: NOTCH2 disrupts the synovial fibroblast identity and the inflammatory response of epiphyseal chondrocytes [scRNA-Seq]

city: Farmington

first: Ernesto

last: Canalis

state: CT

address: 263 Farmington Avenue

department: Orthopaedic Surgery

institute: UConn Health

summary: Notch signaling plays a fundamental role in the inflammatory response and has been linked to the pathogenesis of osteoarthritis in murine models of the disease and in humans, but the mechanisms are poorly understood. We examined the effects of NOTCH2 in chondrocytes from Notch2tm1.1Ecan mice harboring a NOTCH2 gain-of-function mutation and from R26-NICD2 mice, a conditional gain-of-NOTCH2 function model, expressing the NOTCH2 intracellular domain (NICD2) from the Rosa26 locus. Bulk RNA-Sequencing (Seq) revealed increased expression of pathways associated with the phagosome, the role of osteoclasts in rheumatoid arthritis signaling and pulmonary fibrosis signaling in Notch2tm1.1Ecan and NICD2-expressing cultures. Collagen degradation was enhanced in Notch2tm1.1Ecan chondrocytes and the osteoarthritis pathway in NICD2-expressing cells. Single cell (sc)RNA-Seq analyzed 7,845 control and 7,141 Notch2tm1.1Ecan cells and used to define cell clusters. The more prevalent ones were constituted by limb mesenchyme, chondrogenic cells and fibroblasts including articular synovial fibroblasts. Pseudotime trajectory finding revealed a good association among clusters in control cultures, but this was disrupted in the articular/synovial cluster from Notch2tm1.1Ecan mice. scRNA-Seq of R26-NICD2 mice analyzed 9,957 cells in control and 9,924 in NICD2-expressing cultures. Neither the cluster distribution nor the pseudotime trajectory analysis revealed substantial differences between NIDC2-expressing and control cells except for an altered progression in an undefined cluster in NICD2-expressing cells. In conclusion, NOTCH2 enhances the activity of pathways associated with inflammation in epiphyseal chondrocytes and disrupts the transcriptome profile of articular/synovial fibroblasts.

overall_design: Chondrocyte-enriched cells were isolated from the epiphyses of long bones of the hind and fore limbs from 3- to 4-day-old C57BL/6 mice.

first: Canalis

last: Ernesto

first: Guzzo

last: Rosa

first: Schilling

last: Lauren

first: Denker

last: Emily


title: Evaporative cooling signals for wound healing in plants

city: Piracicaba

first: Paulo

last: Teixeira

state: SP

address: Av. Pádua Dias, 11

department: Biology

country: Brazil

institute: University of São Paulo (ESALQ/USP)

summary: Repairing a damaged body part is critical for the survival of an organism. Tissue damage induces rapid responses to activate downstream events including defense, regeneration and wound healing. Despite accumulating knowledge of early wound signaling including the orchestrated actions of phytohormones, electric circus and reactive oxygen species, our knowledge about the end point of a wound response - wound healing, is still limited. We observed that a local temperature reduction associated with the activation of cold-responsive genes occurred at wounding site on Arabidopsis leaves, which was likely caused by evaporative cooling. The disappearance of localized cooling and restoration of cold responsive genes to a steady state could be used as a quantitative readout of wound healing. Based on these observations, we developed a deep learning pipeline to monitor the dynamics of wound healing. We found that CBFs transcription factors relay injury-induced cooling signal to wound healing. Thus, our work provides a tool to quantify wound healing in plants and advances our understanding of tissue repair in plants.

overall_design: Arabidopsis thaliana (Col-0 ecotype) seeds were sown on Sungro Propagation Mix Question soil and placed in 4°C cold room for 3 days prior to being transferred to a short-day growth room with 23°C/19°C day/night temperatures and 45% humidity. Plants were watered weekly and placed in random block design to reduce the impact of environmental factors. Total RNA was extracted from leaf samples subjected to wounding stress. Samples were harvested at three time points: prior to the treatment (time 0), 30 minutes post-wounding, and 60 minutes post-wounding. The experiment included three biological replicates per condition.

first: Li

first: Nathália

last: Dias

first: Joseph

last: Balem


title: Lymphatic dysfunction drives inflammatory temporomandibular joint osteoarthritis (TMJOA) and pain

city: Los Angeles

first: Ziying

last: Lin

address: 2250 Alcazar St. CSA Clinical Sciences Annex

institute: University of Southern California

summary: Temporomandibular joint (TMJ) arthritis is a craniofacial disorder characterized by joint dysfunction and orofacial pain. Despite of its established roles in fluid and immune regulation, lymphatic regulation, and function in TMJ remain unknown. Using genetic report mouse, uDISCO tissue clearing, and 3D volume imaging, we defined lymphatic vessel morphology, structure, anatomic location in adult mouse TMJ. We demonstrate in a mouse model of TMJ osteoarthritis (TMJOA) that arthritis induces inflammatory lymphangiogenesis and leads to impaired synovial lymphatic functions, including decreases in synovial influx and lymph node fluid drainage. To establish the causative link between lymphatic remodeling and TMJOA, we performed lymphatic loss- and gain-of-function studies. Lymphatic deficiency exacerbated cartilage defects, bone loss, synovitis, synovial fibrosis, and pain behaviors in TMJOA mice. Conversely, lymphatic activation via a hydrogel-mediated VEGF-C delivery to TMJ reduced TMJ pain, inflammation, and arthritis-like pathogenesis. Therefore, we defined lymphatic structure in TMJ and found that lymphatic dysfunction drives TMJOA pathogenesis and pain, suggesting its potential as a therapeutic target.

overall_design: To elucidate the role of lymphatic vessels in TMJ arthritis, we employed a lymphatic loss-of-function approach using Prox1 mutant mice. TMJ arthritis was induced by intra-articular injection of complete Freund’s adjuvant (CFA). Subsequently, TMJs from both wild-type and Prox1 mutant mice were harvested. Single-cell suspensions were prepared from dissected TMJ tissues and subjected to scRNA-seq for transcriptomic profiling and comparative analysis.


title: NOTCH2 disrupts the synovial fibroblast identity and the inflammatory response of epiphyseal chondrocytes


title: Maternal Vitamin C Deficiency and Genetic Risk Factors Contribute to Congenital Malformations through Dysregulation of DNA Methylation. [WGBS E11.5]

first: Bernard

last: van der Veer

overall_design: WGBS in E11.5 brains, collected from CD1-Gulo<-/-> embryos, supplemented with various doses of VitC

first: Kian

last: Koh


title: Type 2 cytokines act on enteric sensory neurons to regulate neuropeptide-driven host defense [RNA-Seq 2]

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

state: MA

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

summary: Enteric nervous system (ENS)-derived neuropeptides modulate immune cell function, yet our understanding of how inflammatory cues directly influence enteric neuron responses during infection is considerably lacking. Here, we characterize a primary enteric sensory neuron (PSN) subset that produces the neuropeptides neuromedin U (NMU) and calcitonin gene-related peptide beta (CGRPβ) and co-expresses receptors for the type 2 cytokines IL-4 and IL-13. Type 2 cytokines were sufficient to upregulate NMU and CGRPβ expression in PSNs, in vitro and in vivo, which was abrogated by PSN-specific Il13ra1 deletion. Importantly, PSN-specific Il13ra1 deletion impaired host defense to the gastrointestinal helminth H. polygyrus, diminished enteric sensory neuron populations, and blunted muscularis immune responses. Co-administration of NMU23 and CGRPβ rescued helminth clearance deficits and restored anti-helminth immunity. Mechanistically, we show that CGRPβ signaling synergizes with IL-4 in intestinal macrophages, inducing alternatively-activated macrophage defense responses, altogether illustrating the critical role of bi-directional neuro-immune crosstalk in regulating intestinal type 2 immunity.

overall_design: Bulk RNA-seq was performed on enteric neuro-glial cultures treated with or without indicated cytokines or cytokine combinations (50 ng/mL per cytokine) for 24 hours. Each neuro-glial culture replicate is derived from a distinct mouse (n = 5 to 9 mice).

first: Rocky

last: Barilla

first: Ramnik

last: Xavier

first: Vijay

middle: K

last: Kuchroo


title: Type 2 cytokines act on enteric sensory neurons to regulate neuropeptide-driven host defense [RNA-Seq]

overall_design: Bulk RNA-seq was performed on FACS-purified muscularis and lamina propria (LP) ILC2s from the ilea of Calb2-cre; Il13ra1 flox/flox (Calb2ΔIl13ra1) cKO mice (n = 4) and littermate control Il13ra1 flox/flox mice (n = 5) infected with H. polygyrus (7 days post-infection)


title: Type 2 cytokines act on enteric sensory neurons to regulate neuropeptide-driven host defense


title: Type 2 cytokines act on enteric sensory neurons to regulate neuropeptide-driven host defense [scRNA-Seq]

overall_design: Single-cell RNA-seq was performed on the ileal muscularis propria and duodenal epithelium of Calb2-cre; Il13ra1 flox/flox (Calb2ΔIl13ra1) cKO mice (n = 2) and littermate control Il13ra1 flox/flox mice (n = 2) after H. polygyrus infection (7 days post-infection).

first: Jacques

last: Deguine

first: Sumiti

last: Sandhu


title: Hope for Others: Research Results from the University of Pittsburgh Rapid Autopsy Program for Breast Cancer

city: Pittsburgh

first: Alexander

middle: Chih-Chieh

last: Chang

address: 5051 Centre Ave

institute: University of Pittsburgh

summary: Breast cancer affects 1/8 of women throughout their lifetimes, with over 90% of cancer deaths being caused by metastasis. However, metastasis poses unique challenges to research, as complex changes in the microenvironment in different metastatic sites and difficulty obtaining tissue for study hinder the ability to examine in depth the changes that occur during metastasis. Rapid autopsy programs thus fill a unique need in advancing metastasis research. Here, we describe our protocol and processes for establishing and improving the US-based Hope for OTHERS (Our Tissue Helping Enhance Research and Science) program for organ donation in metastatic breast cancer. As of August 2024, we consented 114 patients and performed 37 autopsies, from which we collected 551 unique metastatic frozen tumor samples, 1244 FFPE blocks, 90 longitudinal liquid biopsy samples and developed 14 patient-derived organoid and 8 patient-derived xenograft models. We report in-depth clinical and histopathological information and discuss extensive new research and novel findings in patient outcomes, metastatic phylogeny, and factors in successful living model development. Our results reveal key logistical and protocol improvements that are uniquely beneficial to certain programs based on identifiable features, such as working closely with patient advocates, methods to rescue RNA quality in cases where tissue quality may degrade due to time delays, as well as guidelines and future expansions of our program.

overall_design: Single nuclei sequencing of liver metastases using fixed or frozen techniques.

first: Neil

last: Carleton

first: Kai

last: Ding

first: Adrian

last: Lee

first: Steffi

last: Oesterreich


title: Geniposide suppressed tumor progression through DUOX1-mediated ferroptosis in hepatocellular carcinoma

city: Chengdu

first: Jike

last: Li

address: Traditional Chinese Medicine Laboratory , Chengdu Public Health Clinical Center, Chengdu,610061, PR China

institute: Chengdu Public Health Clinical Center

summary: Hepatocellular carcinoma (HCC) poses a formidable challenge within the spectrum of digestive system cancers due to its poor prognosis. Geniposide, an iridoid glucoside extracted from the fruits of Gardenia jasminoides Ellis, exhibits a diverse array of biological activities. The objective of this study is to delineate the specific roles and underlying mechanisms of geniposide on the progression of HCC.

overall_design: Huh7 and HepG2 cells were subjected to treatment with or without geniposide for 48 h, after which they were collected for transcriptome sequencing


title: Differential impact of inflammatory microglia signals and chronic HIV-1 Tat exposure on A1-like polarization of astrocytes

first: Micheal

last: Nonnemacher

address: 245 N Broad St

institute: Drexel University

summary: In the context of neurodegeneration, activated microglia facilitate inflammation via secretion of TNF-α, IL-1α, and C1q. Astrocytes exposed to this signaling array polarize to a reactive inflammatory phenotype, termed A1 or A1-like. Astrocytes are essential for neuronal survival, synaptic support, and blood-brain barrier (BBB) function, but A1-like astrocytes upregulate inflammatory gene expression, downregulate neurotrophic factors, and secrete neurotoxic signals. The consequences of A1-like polarization on BBB function are unknown but may have etiological implications for some diseases. Frequently identified by upregulation of complement component 3 (C3), A1-like astrocytes have been characterized in neurodegenerative disorders like Alzheimer’s disease, with polarization correlated with disease progression and severity. However, the role of A1-like astrocytes in neurodegeneration associated with chronic viral infections, like HIV-1-associated neurocognitive disorder (HAND), remains unclear. An in vitro system using primary human astrocytes, as well as a BBB model featuring primary human brain microvascular endothelial cells (BMECs) co-cultured with astrocytes, was used to elucidate cellular and molecular consequences of chronic astrocyte activation. As measured by whole transcriptome analysis and protein expression assays, repeated treatment with TNF-α, IL-1α, and C1q induced A1-like polarization of astrocytes both in monoculture and in a BBB model, resulting in increased secretion of pro-inflammatory signals. No substantial change to BBB permeability was observed. In contrast, exposure to HIV-1 viral protein Tat did not independently induce A1-like polarization. Ongoing investigations into the effect of astrocyte polarization on BBB integrity and treatment with pathogenic proteins may provide insights into the role of neurotoxic astrocytes in neuroviral pathologies.

overall_design: To study these facets of astrocyte reactivity, an in vitro model of pro-inflammatory astrocyte polarization was developed using primary human fetal cells, both in monoculture and in a co-culture BBB model. An array of analyses, from RNA transcriptional profiles to changes in signal secretion, were used to characterize an A1-like phenotype in stimulated primary human astrocytes.

first: Jill

last: Lawrence

first: Will

last: Dampier

first: Joshua

last: Mell

first: Diehl

middle: R

last: De Souza

first: Kayla

last: Schardien

first: Kyle

last: Yeakle

first: Jordan

last: Barnett

first: Bhaswati

last: Sen

first: Azad

last: Ahmed

first: Michael

last: Bouchard

first: Brian

last: Wigdahl


title: Identification of Differentially Expressed Long non-Coding RNAs in Renal Cancer Tissues: A Comparative Analysis of Cancerous and Adjacent Non-Cancerous Samples

city: sheng yang

first: li

middle: rui

last: ming

address: san hao jie

institute: china medical school

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

summary: This study aims to investigate the role of Long non-coding RNAs (lncRNAs) in renal cell carcinoma (RCC). By analyzing differential expression of lncRNAs between three pairs of RCC and adjacent non-cancerous tissues, the study seeks to identify lncRNAs that are specifically expressed in RCC. These findings could provide insights into the molecular mechanisms of RCC and potential biomarkers for diagnosis or therapeutic targets.

overall_design: Samples of cancerous and adjacent non-cancerous tissues were collected from clinical renal cancer patients to measure the differentially expressed Long non-coding RNAs.

first: Kefeng

last: Wang


title: Setdb2 Regulates Inflammatory Trigger-Induced Trained Immunity of Macrophages Through Two Different Epigenetic Mechanisms

city: New York

first: Laszlo

last: Halasz

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

summary: "Trained immunity" of innate immune cells occurs through a two-step response pattern where an initial pathogenic or sterile inflammatory trigger is followed by an augmented response to a later un-related secondary pathogen challenge. The memory effect is mediated at least in part through epigenetic modifications of the chromatin landscape. Here, we investigated the role of the epigenetic modifier Setdb2 in microbial (β-glucan) or sterile trigger (Western-diet-WD/oxidized-LDL-oxLDL)-induced trained immunity of macrophages. Using genetic mouse models and genomic analysis, we uncovered a critical role of Setdb2 in regulating proinflammatory and metabolic pathway reprogramming. We further showed that Setdb2 regulates  trained immunity through two different complementary mechanisms: one where it positively regulates glycolytic and inflammatory pathway genes via enhancer-promoter looping, which is independent of its enzymatic activity; and a second mechanism that requires its SET domain and is associated with both elevated H3K9 methylation changes and repression of interferon response pathway gene promoters. Interestingly, while both mechanisms occur in response to pathogenic training, only the chromatin-looping mechanism operates in response to the sterile inflammatory stimulus. These results reveal a previously unknown bifurcation in the downstream pathways that distinguishes between pathogenic and sterile inflammatory signaling responses associated with the innate immune memory response and may provide potential therapeutic opportunities to target cytokine vs. interferon these pathways to limit complications of chronic inflammation.

overall_design: Gene expression (RNA-seq, n = 24) and chromatin accessibility (ATAC-seq, n = 24) were analyzed in wild-type (WT) and Setdb2 knockout (Setdb2KO) bone marrow-derived macrophages (BMDMs) under four different treatment conditions: control (CTRL), β-glucan (GLU), lipopolysaccharide (LPS), and a combination of β-glucan and lipopolysaccharide (GLULPS).

first: Anant

last: Jaiswal

first: Timothy

last: Osborne


title: The Intronic Structure Variation of Rapeseed BnaC3.LEAFY Regulates the Timing of Inflorescence Formation and Flowering

city: Hangzhou

first: Mengjie

last: Gong

address: Yuhangtang Road-866

institute: Zhejiang University

summary: Rapeseed (Brassica napus L.) is a globally significant oil-producing crop, and its structural variations (SVs) are fundamental to the enhancement and domestication of important agronomic traits. However, the effects of SVs on agronomic traits in allotetraploid rapeseed are still largely unexplored. Here, we conducted a whole-genome identification of SVs based on 300 re-sequenced rapeseed accessions and found 42,384 high-quality SVs consisted of 34,442 deletions, 6,653 insertions, 828 duplications and 461 inversions. Onset of inflorescence formation and subsequent flower opening at the proper time is crucial for successful propagation. To uncover significant SVs associated with inflorescence development, we performed genome-wide association study based on SVs (SV-GWAS) and identified seven significant SVs. Through analysis of each SV and referencing previous studies, we explored the SV in the second intron of LEAFY on Chromosome C3 (BnaC3.LFY), which is one of homologs of Arabidopsis floral identification gene LFY (AtLFY). BnaC3.LFY Hap1 is significantly related to early inflorescence development due to increased gene expression of BnaC3.LFY. By the CRISPR/Cas9 application in the wild-type spring accession Westar, multiple deletions in intron 2 region of BnaC3.LFY were received and the phenotype of delayed flowering opening was observed. Additionally, we discovered the conserved function of the second intron in Arabidopsis. This study demonstrates the whole-genome layout of SVs in Brassica napus genomes and highlights the conserved role of the second intron of BnaC3.LFY in influencing the timing of inflorescence formation and flower opening, with significant agronomic implications.

overall_design: To compare the intron 2 region of BnaC3.LFY in regulating inflorescence formation, we generated intron 2-deleted mutants and performed the RNA-seq analysis to compare their transcriptomes with that of the wild type.

first: Tao

last: Zhou


title: m6A-modified lncRNA Profiling in RCC Tumor and Adjacent Normal Tissues

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

summary: The total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody.   The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”.   The unmodified RNAs were recovered from the supernatant as “Sup”.   The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.   The cRNAs were combined together and hybridized onto Arraystar Human mRNA&lncRNA Epitranscriptomic Microarray (8x60K, Arraystar).   After washing the slides, the arrays were scanned in two-color channels by an Agilent Scanner G2505C.


title: Spatial proteo-transcriptomic profiling reveals the molecular landscape of borderline ovarian tumors and their invasive progression

city: Chicago

first: CRI

last: Bioinformatics

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

summary: Epithelial serous borderline tumors (SBT) are non-invasive neoplastic ovarian lesions that may recur as chemo-resistant low-grade serous cancer (LGSC). While genetic alterations suggest a common origin, the transition from SBT to LGSC remains poorly understood. Here, we integrate cell-type resolved spatial proteomics and transcriptomics to elucidate the evolution from SBT to LGSC and its corresponding metastasis in both the stroma and the tumor. We show that the transition of SBT to LGSC occurs in the epithelial compartment through an intermediary stage with micropapillary features. LGSC overexpressed the c-Met receptor tyrosine kinase and several CNS-specific proteins. In the tumor microenvironment, interconnectivity between cancer and tumor cells and enzymes degrading a packed extracellular matrix suggests functional collaboration between various cells in the tumor organ. Integrating spatial transcriptomics and proteomics, we functionally validate 16 drug targets.

overall_design: ROIs of a total of four cohort groups were studied in the epithelial and stromal compartment on ovarian cancer: serous borderline tumors (SBT), micropapillary SBT (SBT-MP), low-grade serous cancer primary tumors (LGSC-PT) and corresponding metastases (LGSC-Met).

first: Lisa

last: Schweizer

first: Hilary

middle: A

last: Kenny

first: Rahul

last: Krishnan

first: Lucy

last: Kelliher

first: Agnes

last: Bilecz

first: Aasa

last: Shimizu

first: Andreas

last: Metousis

first: Rachelle

last: Mendoza

first: Thierry

last: Nordmann

first: Sarah

last: Rauch

first: Janna

last: Heide

first: Sabrina

last: Richter

first: Yan

last: Li

first: Florian

last: Rosenberger

first: Maximillian

middle: T

last: Strauss

first: Katherine

middle: C

last: Kurnit

first: Marvin

last: Thielert

first: Edwin

last: Rodriguez

first: Johannes

middle: B

last: Müller-Reif

first: Seiko

last: Yamada

first: Fabian

last: Theis

last: Mund

first: Ricardo

last: Lastra

first: Matthias

last: Mann

first: Ernst

last: Lengyel


title: Transcriptome analysis of NK92 treated with deferoxamine or PPMX-T003

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

institute: Saga University

summary: Although several types of iron deprivators are available in laboratory, the differences of them in transcriptome alterations remains unclear. In this study, we performed RNA-seq analysis of NK92 cells treated with deferoxamine (DFO; an iron chelator) and PPMX-T003 (an anti-transferrin receptor 1 inhibitory antibody) to investigate the differences in transcriptomic alterations between them.

overall_design: NK92 cells were  treated with 500 µM of DFO or 10 µg/mL of PPMX-T003 for 24 hours, followed by RNA extraction using Qiazol. cDNA library was constructed using TruSeq Standard mRNA Library Prep. Sequencing was performed using NovaSeq-6000 with 101 bp paired end mode. Reads were mapped into hg38 using HISAT2 version 2.2.1 after trimmed with fastp version 0.21.0, followed by conting them using StringTie version 2.1.6 with RefSeq gene annotation file of hg38.

first: Ai

last: Kotani


title: Identifying downstream targets of ankrd1a in heart regeneration after cryoinjury in adult zebrafish

city: Belgrade

first: Mirjana

last: Novkovic

address: Vojvode Stepe 444a

country: Serbia

institute: Institute of Molecular Genetic and Genetic Engineering

summary: In contrast to humans, zebrafish have a remarkable ability to regenerate injured heart through a complex and highly orchestrated process involving all cardiac structures. During regeneration, the major source of new myocardial cells are resident cardiomyocytes, which dedifferentiate and reinitiate proliferation, invading the area of injury to replace the lost myocardium. The response of the myocardium and the coronary vasculature is preceded by activation of epi- and endocardium, which form active scaffolds to provide mechanical and paracrine support to guide regeneration.Zebrafish ankrd1a was found activated in differentiated and proliferating cardiomyocytes restricted to the border zone, as well as in protrusions of cardiomyocytes that invade the scar. The TgBAC(ankrd1a:EGFP) transgene was not detected in epicardial or endocardial cells of regenerating zebrafish heart. Transcriptomic analysis of cryoinjured ventricles showed that lack of functional ankrd1a at 7 dpci leads to change in expression of genes involved in antigen processing and presentation of peptide or polysaccharide antigen via MHC class II, cellular extravasation, cell-cell adhesion and heart valve development.

overall_design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Heart cryoinjury was performed after the incisions made in the body wall and pericardial sac and the exposed ventricles were placed in contact with the cryoprobe previously cooled in liquid nitrogen. After 7 days of recovery, RNA was isolated from the heart ventricle of cryoinjured or sham operated fish. Four experimental groups (cryoinjured wt, sham wt, cryoinjured mutant, and sham mutant) were subjected to RNA-seq. Each experimental group comprised four samples and one sample contained RNA isolated from ventricles of three fish.

first: Emilija

last: Milosevic

first: Jovana

last: Jasnic

first: Andjela

last: Milicevic

first: Snezana

last: Kojic


title: LSMEM2, localized at the neuromuscular junction, modulates mitochondrial integration in skeletal muscles

city: Suita

first: Yasunori

last: Shintani

state: Osaka

address: 6-1, Kishibe Shimmachi

department: Molecular Pharmacology

institute: National Cerebral and Cardiovascular Center

summary: In addition to the canonical metabolism-regulating function, AMP-activated protein kinase (AMPK) has non-canonical functions, in which AMPK spatiotemporally phosphorylates specific sets of substrates. Recently, we identified LSMEM2, a novel substrate of AMPK in the heart. LSMEM2 is a membrane protein localized at the intercalated disc (ICD), whose function is currently under investigation. Interestingly, LSMEM2 is also expressed in the skeletal muscles. As skeletal muscles lack a homophilic intercellular junction corresponding to the ICD in the heart, predicting the role of LSMEM2 in skeletal muscles is difficult. In this study, we identified that LSMEM2 is expressed in skeletal muscles, specifically at the neuromuscular junction (NMJ). LSMEM2-knockout mice showed no histological abnormalities, suggesting that LSMEM2 is not essential for skeletal muscle development. The overexpression of full-length wild-type or C-del mutant of LSMEM2 led to the tubular aggregate formation with functional abnormality in male mice. RNA sequence analysis revealed that the genesets of mitochondrial oxidative phosphorylation and vesicle-mediated transport are enriched in LSMEM2 overexpression. Furthermore, histological analysis demonstrated the accumulation of swollen subsarcolemmal mitochondria in LSMEM2-overexpressing skeletal muscles. The study findings suggest that LSMEM2 may play a role in the pathogenesis of skeletal muscle diseases.

overall_design: To examine the role of LSMEM2 in skeletal muscles in vivo, we overexpressed LSMEM2 C-del or EGFP (mock) using AAV6 in the hindlimb of adult male and female C57BL/6 mice. Total RNA was extracted from the TA after 2 months post injection, then RNA-sequencing was performed.

first: Eman

last: Elrefaei

first: Satoru

last: Yamazaki

first: Issei

last: Yazawa

first: Yusuke

last: Takahashi

first: Naoki

last: ito

first: Nozomi

last: Hayashiji

first: Ichizo

last: Nishino

first: Seiji

last: Takashima


title: LKB1 regulates ILC3 postnatal development and effector function through metabolic programming

city: 黄浦区

first: Lin

last: Hu

state: 上海市

address: 重庆南路280号

institute: 基础医学院

summary: Group 3 Innate Lymphoid Cells (ILC3s) is important for maintaining intestinal homeostasis and host defense. Emerging studies have shown that metabolic regulation plays a crucial role in regulating ILC3 activation and function. However, the role of Liver Kinase B1 (LKB1), key metabolic regulator, in regulating ILC3 function and intestinal immunity remains poorly understood. In this study, we show that LKB1 is essential for ILC3 postnatal development, effector function, and intestinal immunity. Ablation of LKB1 in ILC3s results in reduced cell number due to increased apoptosis and reduced proliferation, which occurs at 2 -3 weeks after birth. In addition, LKB1 deletion leads to diminished IL-22 production and less protection against C.rodentium infection. Mechanistically, LKB1 deficiency led to impaired mitochondrial metabolism, as indicated by reduced glycolysis and oxidative phosphorylation and less mitochondrial mass. Together, our data demonstrate that LKB1 promotes ILC3 postnatal development and effector function to maintain intestinal immune homeostasis.

first: Lei

last: Shen

first: Jiping

last: Sun

first: Huasheng

last: Zhang

first: Hongshen

last: Niu

first: Linfeng

last: Zhao

first: Qingbing


title: Inactivated Rothia nasimurium promotes a persistent antiviral immune status in porcine alveolar macrophages

city: Bellaterra, Catalonia

first: Jordi

last: Argilaguet

address: Campus de la Universitat Autònoma de Barcelona (UAB)

department: Sanitat animal

country: Spain

institute: IRTA-CReSA

summary: Globalization has increased in the incidence of infectious diseases in livestock, further aggravated by the reduction of antibiotic consumption. To minimise the resulting economic consequences to the meat production industry, as well as the higher risk of zoonotic events, immunostimulants have risen as a potential strategy to enhance animal resilience to diseases. The capability of bacterial-based immunostimulants to modulate innate immune cells functionality makes them cost-effective candidates to be used in livestock, whether as vaccine adjuvants, as antimicrobials, or as preventive immunostimulators inducing long-term innate immune memory. Here we characterized in vitro the immunostimulatory properties of a strain of Rothia nasimurium isolated from warthog fecal microbiota. Stimulation with heat-inactivated bacteria induced cytokine production by porcine immune cells, and a robust innate immune transcriptomic signature in porcine alveolar macrophages. Interestingly, the bacteria induced inflammasome activation and IL1b production, thus confirming its proinflammatory properties, and suggesting its potential as vaccine adjuvant. Importantly, this immunostimulatory status functionally resulted in an antimicrobial state, hampering the replication levels of two major porcine viral pathogens: the porcine reproductive and respiratory syndrome virus (PRRSV) and the African swine fever virus (ASFV). Moreover, alveolar macrophages showed an enhanced cytokine response upon ASFV infection several days after heat-inactivated bacteria stimulation, suggesting the induction of an innate immune memory phenotype. This nonspecific response resulted in a significant reduction of ASFV replication kinetics, demonstrating the capacity of the bacteria to induce a more resistant state in macrophages against a highly lethal virus infection. Altogether, these results demonstrate the immunostimulatory capability of heat-inactivated Rothia nasimurium in porcine macrophages, showing potential to enhance animal resilience to diseases through the modulation of innate immune cells responsiveness to infections.

overall_design: Four lots of PAMs were seeded at 5x10^6 cells/well in a 24-well flat-bottom plate with RPMI supplemented with 10% FCS, 1% of P/S, 1% of L-glutamine, and 0.5% of nystatin, and left overnight at 37ºC and 5% CO2. Cells were then stimulated for 6 or 24 hours with LPS (tlrl-eblps InvivoGen) at 10 ug/ml, Pam3CKS (InvivoGen tlrl-pm2s-1) at 10 ug/ml, or heat-inactivated Rothia nasimurium (HI-Ro) at MOI 50. Non-stimulated cells were used as a reference.

first: Aida

last: Tort-Miró

first: Uxia

last: Alonso

first: Beatriz

last: Martín-Mur

first: Anna

last: Cardona-Coma

first: Jordana

last: Muñoz-Basagoiti

first: Yan

last: Zeng

first: David

last: Marín-Moraleda

first: Enrique

last: Ezcurra

first: Sergio

last: Montaner

first: Maria Jesus

last: Navas

first: Marta

last: Muñoz

first: Paula

last: Monleón

first: Esmeralda

last: Cano

first: Carles

last: Vilalta

first: Marc

last: Caballé

first: Lourdes

last: Criado

first: Karl

last: Kochanowski

first: Francesc

last: Accensi

first: Virginia

last: Aragón

first: Flor

last: Correa

last: Esteve-Codina

first: Fernando

last: Rodríguez


title: Identification of Asporin as a HER3 ligand that exposes a therapeutic vulnerability in metastatic prostate cancer

city: Nashville

first: Hong Yuen

last: Wong

state: Tennessee

address: 2220 Pierce Ave # PRB648, Preston Research Building

department: Medicine

institute: VUMC

summary: Cancer-associated fibroblasts (CAF) are part of the tumor microenvironment that enable cancer cells to establish metastases, but the mechanisms of these interactions are not fully known. Herein, we identify a novel paracrine mechanism in which CAF-secreted asporin (ASPN) activates ErbB signaling and subsequent migration of adjacent metastatic prostate cancer cells. Our data support that ASPN binds directly to HER3 to induce HER2/HER3 heterodimerization and activation of the PI3-kinase and MAP-kinase pathways. Genetic and therapeutic inhibition of HER2/HER3 ablated ASPN-induced signaling and migration. Small molecule and antibody-drug conjugates targeting HER2/HER3 demonstrated efficacy in vitro, with near complete resolution of tumors in vivo. Clinically, over 50% of human prostate cancer metastases show expression of HER2/HER3, along with ASPN expressing CAF.  Collectively, these findings support ASPN functions as a HER3 ligand to induce cellular migration which can be targeted with anti-HER2/HER3 therapies, highlighting the potential clinical benefit for patients with metastatic prostate cancer.

overall_design: 1 million proliferative human PC3 cells in a 1:1 mixture of ice-cold PBS and Matrigel were subcutaneously injected into the flanks of 11-week-old NSG male mice (100 μL/mouse). Mice were monitored and tumor measurements obtained three times a week using electronic calipers once tumors were palpable. Tumor volume was calculated by [(length)2 x width]/2. When tumors were 90 mm3, mice were randomized and treated with 5 mg/kg T-DXd or P-DXd, or Vehicle Control (PBS) once a week via retro-orbital injection for 5 cycles. Tumors were harvested for analysis at experimental endpoint.

first: Amanda

last: Hesterberg

middle: J

last: Hurley


title: The Intronic Structure Variation of Rapeseed BnaC3.LEAFY Regulates the Timing of Inflorescence Formation and Flowering [ChIP-Seq]

first: Mengjie

last: Gong

overall_design: To identify the genomic binding sites of the BnaC3.LFY transcription factor in Brassica napus, DAP-seq was performed using inflorescence tissue to map its genome-wide binding profile.


title: MicroRNA (miR) profiling of the MERLIM-TIMI 36 cohort

first: Worawan

last: Limpitikul

address: 55 Fruit Street

institute: Massachusetts General Hospital

summary: This study aims to identify circulationg miR that could predict cardiovascular outcomes in patients who developed acute coronary syndrome.

overall_design:
Plasma samples from 4,541 participants was used in quantification of 21 candidate miRs. Primary outcome include hospitalization for heart failure and cardiovascular death.
21 candidate miRNAs:  hsa-mir-22-3p, hsa-mir-320a, hsa-mir-100-5p, hsa-mir-194-5p, hsa-mir-146a-5p, hsa-mir-146b-5p, hsa-mir-150-5p, hsa-mir-151a-3p, hsa-mir-21-5p, hsa-mir-223-3p, hsa-mir-29c-3p, hsa-mir-30a-5p, hsa-mir-30d-5p, hsa-mir-378c, hsa-mir-423-5p, hsa-mir-92a-3p, hsa-mir-106b-5p, hsa-mir-29a-3p, hsa-let-7g-5p, hsa-mir-103a-3p, hsa-mir-140-3p

first: Michael

last: Silverman

first: Nedyalka

last: Valkov

last: Camacho Garcia


title: BCAT1 activation reprograms branched-chain amino acids (BCAAs) metabolism and epigenetically promotes inflammation in diabetic retinopathy

city: Shanghai

first: Jingyi

last: Wang

state: --None--

address: Shanghai General Hospitol

department: School of Medicine

institute: Shanghai Jiao Tong University

summary: Branched-chain amino acids (BCAAs) metabolism is dysregulated in diabetic retinopathy. Retina Müller cells maintain various metabolic processes and immune homeostasis. Here, we found that branched-chain aminotransferase 1 (BCAT1), which catalyzes the first step of BCAAs metabolism, was predominantly expressed in retina Müller cells. Under diabetic conditions, BCAT1 showed increased enzymatic activity in Müller cells, which drove the remodeling of BCAAs catabolism, and upregulated the expression of inflammatory genes such as interleukin 6 (IL6) and tumor necrosis factor-α (TNF-α). Mechanistically, BCAT1 activity was negatively regulated by Polo-like kinase 4 (PLK4) via phosphorylation at threonine 333. Increased BCAT1 activity further reduced α-ketoglutarate (α-KG) levels, a critical substrate for histone demethylation, resulting in higher H3K4me3 levels at inflammatory gene promoters, and further upregulated inflammation genes. Treatment with chemical BCAT inhibitor significantly reduced inflammatory gene expression and vascular leakage in diabetic retinas in vivo. These findings reveal a crucial role of BCAT1 in metabolic remodeling and inflammatory regulation, which indicates that BCAT1 could be used as a target for diabetic retinopathy.

overall_design: To investigate gene expression in the retinas of wild-type and db/db mice


title: Danshenol B alleviates central post-stroke pain by regulating PIK3CG/NLRP3 signaling pathway

city: ZHENGZHOU

first: Sen

last: Zhao

state: HENAN

address: 100 Science Avenue

institute: ZHENGZHOU UNIVERSITY

summary: Background: Central post-stroke pain (CPSP) severely impairs quality of life and is challenging to manage, potentially leading to self-harm or suicide. Although Compound Salvia miltiorrhiza (Danshen) is effective against neuropathic pain, its specific active components and mechanisms remain unclear. Study design and methods: We established a CPSP mouse model and performed RNA sequencing on the ipsilateral Ventral posterolateral thalamic nucleus and Ventral posteromedial thalamic nucleus (VPL/VPM) to identify differentially expressed genes (DEGs). DEGs were analyzed through network pharmacology and molecular docking to assess interactions with 42 Danshen components. We evaluated the effects of varying Danshenol B concentrations, administered daily into the VPL/VPM, on CPSP. Changes in PIK3CG and NLRP3 were monitored to determine Danshenol B’s analgesic effects. Additionally, we overexpressed and knocked down PIK3CG to examine its role in CPSP and assessed NLRP3 to explore if it acts downstream of PIK3CG. Results: In the CPSP model, 409 DEGs were identified in the VPL/VPM, involved in pathways like signal transduction and NOD-like receptor signaling. Network pharmacology linked 21 Danshen components to 11 DEGs. Molecular docking showed strong binding affinities (≤ −7.00 kcal/mol) between four Danshen components—tanshinaldehyde, sclareol, MOL007155, and Danshenol B—and proteins including BTK, CASP1, MMP9, and PIK3CG. Danshenol B (0.5 μM) significantly alleviated CPSP and reduced PIK3CG and NLRP3 protein. PIK3CG overexpression increased NLRP3 and counteracted Danshenol B’s effects, while its knockdown induced CPSP and reduced NLRP3 expression. Conclusion: Danshenol B alleviates CPSP by suppressing the PIK3CG/NLRP3 signaling pathway, clarifying its therapeutic mechanism, and highlighting its potential in analgesic drug development.

overall_design: To investigate differentially expressed genes in the CPSP model, we established this model by injecting 0.01 U/10 nL of type IV collagenase into the right VPM/VPL of C57 mice; controls received 10 nL saline. Fourteen days post-injection, VPM/VPL tissues were harvested for transcriptomic sequencing to identify DEGs. We then predicted Danshen components and target genes, analyzing their interactions with DEGs and evaluating their therapeutic effects on CPSP.

first: Panyang

last: Li

first: Linna

last: Yu

first: Jinzhong

last: Yao

first: Tingting


title: Gonadotropins regulate cell adhesion and spermiation through a cross-talk between oxytocin and relaxin pathways in Senegalese sole

city: Valencia

first: Jose Vicente

last: Roig Genovés

address: Calle Moratín 17

institute: Rara Avis Biotec S.L.

summary: Our understanding of semi-cystic spermatogenesis in the Senegalese sole (Solea senegalensis), specifically the process where spermatids are released and undergo differentiation in the lumen, remains limited. Previously, we demonstrated that Luteinizing hormone (Lh) has the ability to penetrate the blood-testis barrier and reach released spermatids expressing the Lh receptor, thereby stimulating spermiogenesis. To deepen our knowledge, the current study aims to investigate how gonadotropins regulate the release of spermatids from Sertoli cells, known as spermiation. We conducted a six-week experiment exposing male Senegalese sole to recombinant gonadotropins (Follicle-stimulating hormone, rFsh, or rLh) via weekly injections at a dose of 6 μg/kg. Following treatment, we performed transcriptomic analysis using RNA-seq to identify differentially expressed genes (DEGs). We found that rLh significantly regulated 1316 genes, while rFsh regulated 717 genes, with 357 DEGs common to both. Pathway analysis revealed that both gonadotropins influenced the expression of cell-cell junctions and adhesion proteins. Notably, other affected pathways included those involving oxytocin (OXT) and relaxin (RLN), suggesting their potential roles in regulating spermiation. Immunohistochemistry (IHC) and in situ hybridization (ISH) were employed to investigate the cellular localization of OXT and RLN receptors in the testicular cortex and medulla, primarily finding them in Sertoli cells and spermatids. Proteins associated with cell adhesion identified through RNA-seq, such as CTNNB1, PARD3, GJA3, TJP2, CLDN4, TMEM47, and ITBG1, were observed in either spermatids or Sertoli cells, with their expression mainly repressed by gonadotropins. This repression indicates a disruption in Sertoli cell-spermatid junctions, potentially responsible for active spermiation and the enhanced permeability of the blood-testis barrier. Furthermore, we conducted an in vitro assay where testes explants were incubated with OXT, RLN, OXT inhibitor (L-371), RLN inhibitor (AT001), in combination with rFsh and rLh. Subsequent qPCR analysis indicated a trend towards decreased expression of cell adhesion genes by OXT and RLN, most notably by Lh by acting through the OXT and RLN pathways. In summary, our findings suggest that gonadotropins regulate cell adhesion and spermiation through a cross-talk between OXT and RLN pathways. These insights lay the groundwork for further research aimed at unraveling the process of spermiation in fish species.

overall_design: Two-year-old male Senegalese sole, F1 generation offspring from wild-caught parents, were acquired from the commercial supplier Stolt Sea Farm S.A. (Spain) and transferred to the IRTA fish research center in Sant Carles de la Ràpita (Spain). The fish were housed in 10 m³ fiberglass tanks with a recirculating system (IRTAmar1) and were fed five times a week with 0.75% of wet feed (mussels and polychaetes) and 0.55% of dry feed (balanced diet) based on total biomass. They were maintained for three months before the experiments under natural light cycles and regulated simulated natural temperatures. The experiment was conducted over six weeks from November to January to examine the specific impact of recombinant Fsh and Lh (rFsh and rLh) on testicular development. Males (347±9 gr) received intramuscular injections once a week with saline (control, n=8), rFsh (18 μg/kg, n=8) or rLh (18 μg/kg, n=8). The animal care and sample collection procedures were conducted in compliance with protocols approved by the Ethics Committee (EC) of the Institut de Recerca i Tecnologìa Agroalimentàries (IRTA) following the European Union Council Guidelines (86/609/EU). The study received specific approval from the IRTA EC.

first: Noelia

last: Lopez-Fortún

last: Roig-Genovés

first: Ignacio

last: Gimenez

first: Joan

last: Cerdá

first: François

last: Chauvigné


title: VGF-derived TLQP21 peptide ameliorates tumor progression, pain and depression-like behaviors in an orthotopic mouse model of pancreatic ductal adenocarcinoma

city: Guangzhou

first: Huang

last: Shuying

address: 中国广州市中山二路74号中山大学广州校区北校园

institute: Sun Yat-Sen University

summary: In summary, we report that the VGF-derived TLQP21 is a promising target for pharmaceutical interventions in pancreatic ductal adenocarcinoma (PDAC) with dual promise of improving survival outcomes and quality of life in patients with PDAC. Combining bioinformatic analysis of clinical datasets with experimental validations, our study reveals that high VGF expression is correlated with improved survival of PDAC patients. Furthermore, using RNA-Seq analysis and behavioral experiments we found that TLQP21 administration effectively hinders PDAC progression by modulating Tumor-associated macrophages (TAMs), alongside with alleviating depression-like behaviors and allodynia in an orthotopic mouse model of PDAC. Collectively, these findings underscore TLQP21 not only suppresses PDAC progression by modulating TAMs in the tumor microenvironment, but also alleviates pain and depression-like symptoms, highlighting its multifaceted therapeutic potential.

overall_design: To delve into the molecular mechanisms underlying TLQP21-mediated PDAC growth inhibition, we performed whole transcriptome sequencing on tumor tissues harvested from mice two weeks post-KPC cell implantation, where TLQP21 treatment significantly reduced tumor growth.

first: Shuying

last: Huang

first: Pei

last: Xia

first: Yixiu

last: Zeng

first: Qiuyi

last: Chen

first: Wenbao

last: Cai

first: Yuying

last: Yang

first: Yangyang

last: Ou

first: Jun

first: Wei-Jye

last: Lin

first: Xiaojing

last: Ye


title: Immunosuppressive microenvironment restrains chemotherapy efficacy in liver metastases of triple-negative breast cancer

city: Nanjing

first: Mingduo

last: Liu

address: 300 Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

summary: This study investigates the role of the immune microenvironment in the efficacy of chemotherapy for triple-negative breast cancer (TNBC) liver metastases compared to primary tumors. Using  mouse models, we assessed chemotherapeutic efficacy  and characterized intratumoral T lymphocytes and macrophages via RNA sequencing, immunohistochemistry, and flow cytometry. We found that liver metastases had a less effective response to chemotherapy compared to subcutaneous tumors, linked to reduced CD8+ T cell infiltration and macrophage activation. Chemotherapy induced an immunosuppressive shift, with neutrophil extracellular traps (NETs) accumulating in liver metastases and macrophages and T cells showing impaired functionality in the primary tumors. Combining macrophage activators or NETs inhibitors with chemotherapy improved outcomes. Our findings highlight the importance of tumor site-specific immune microenvironmental differences in chemotherapy responses and suggest that targeted therapies could enhance chemotherapy efficacy.

overall_design: To assess the efficacy of chemotherapy,  mouse models harboring TNBC liver metastases or primary tumors were utilized. RNA sequencing (RNA-seq) was conducted to analyze gene expression profiles in both subcutaneous tumors and liver metastases before and after chemotherapy treatment.

first: Shui

last: Wang

first: Wenbin

last: Zhou

first: Mengjia

last: Qian


title: CSF1-R inhibition attenuates posttraumatic osteoarthritis and quadriceps atrophy following ligament injury II

city: Lexington

first: Alexander

middle: Romano

last: Keeble

state: KY

address: 900 S Limestone st

institute: University of Kentucky

summary: Knee osteoarthritis contributes substantially to worldwide disability. Post-traumatic osteoarthritis (PTOA) develops secondary to a joint injury, such as ligament rupture, and there is increasing evidence suggesting a key role for inflammation in the etiology of PTOA and associated functional deficits. Colony stimulating factor 1 receptor (CSF1-R) has been implicated in the pathogenesis of musculoskeletal degeneration following anterior cruciate ligament (ACL) injury. We sought to assess the efficacy CSF1-R inhibition to mitigate muscle and joint pathology in a mouse model of PTOA. Four-month-old mice were randomized to receive a CSF1-R inhibitor and studied for 7 or 28 days after joint injury. Additionally, we profiled synovial fluid samples for CSF1-R from patients with injury to their ACL. Transcriptomic analysis of quadriceps muscle and articular cartilage in CSF1-R inhibitor-treated animals at 7 days after injury revealed elevated chondrocyte differentiation within articular cartilage and enhanced metabolic and contractile gene expression within skeletal muscle. At 28 days post-injury, CSF1-R inhibition attenuated PTOA severity and mitigated skeletal muscle atrophy. Patient synovial fluid CSF1-R levels correlated with matrix metalloproteinase 13, a prognostic marker and molecular effector of PTOA. Our findings support an opportunity for CSF1-R targeting to mitigate the severity of PTOA and muscle atrophy after joint injury.

overall_design: Comparative gene expression profiles were assessed in murne quadriceps before and after ACL transection. One group received a CSF1-R inhibitor, the other received a placebo control

first: Nicholas

last: Thomas

first: Peyton

last: Balawender

first: Camille

last: Brightwell

first: Sara

last: Gonzalez-Velez

first: Madeline

last: O’Daniel

first: Caitlin

last: Conley

first: Austin

last: Stone

first: Darren

middle: L

last: Johnson

first: Brian

last: Noehren

first: Cale

last: Jacobs

first: Christopher

middle: S

last: Fry

first: Allison

middle: M

last: Owen