title: Formyl peptide receptor 2 contributes to intestinal epithelium homeostasis by regulating intestinal stem cell proliferation and differentiation [scRNA-seq]

status: Public on Mar 31 2025

city: Shanghai

first: shuting

last: Yu

address: 320 Yueyang Road, Xuhui District

country: China

institute: Shanghai Institute of Nutrition and Health

type: Expression profiling by high throughput sequencing

summary: To investigate the contribution of formyl peptide receptor 2 (FPR2) to intestinal epithelium homeostasis and the underlying mechanisms, we isolated small intestinal crypts from intestinal epithelial-specific knockout (Fpr2VKO) and control (Fpr2f/f) mice, isolated epithelial cells from the crypts and performed single-cell RNA sequencing (scRNA-Seq). The transcriptome profiles of Fpr2VKO and Fpr2f/f mice were compared.

overall_design: Epithelial cells were isolated from small intestinal crypts of Fpr2f/f and Fpr2VKO mice and gene expression was analyzed by single-cell RNA sequencing (scRNA-seq).

first: Shuting

first: Yingying

last: Le


title: Exonic enhancers are a widespread class of dual-function regulatory elements

city: Marseille

first: Benoit

last: Ballester

address: 162 Avenue de Luminy

country: France

institute: INSERM

summary: This study aimed to interrogate enhancer activity within a custom library of 11,999 exons enhancers candidate regulatory sequences in the K-562 cell line using the STARR-seq approach.

overall_design: A library of 11,999 candidate enhancer sequences was cloned into a STARR-seq vector and transfected into K-562 cells in five replicates, with an empty-vector control. After 24 hours, total RNA and corresponding gDNA were isolated. Libraries were constructed from mRNA-derived cDNA and from gDNA, then sequenced to identify and quantify active regulatory sequences.

first: Jean-Christophe

last: Mouren

first: Magali

last: Torres

first: Antoinette

last: Van Ouwerkerk

first: Iris

last: Manosalva

first: Frederic

last: Gallardo

first: Salvatore

last: Spicuglia


title: RIPK2-Regulated Gene Signature Associated with Poor Prognosis in Prostate Cancer

city: Stony Brook

first: Wei

last: Yang

state: NY

address: Lauterbur Drive, MART 8M-0832

department: Pathology

country: USA

institute: Stony Brook University

summary: Receptor-interacting protein kinase 2 (RIPK2) has emerged as a promising drug target in various cancers, including prostate cancer (PC). However, the absence of reliable biomarkers to assess RIPK2 activity limits patient selection for anti-RIPK2 therapies and treatment monitoring. To address this gap, we performed RNA-Seq analysis on PC cancer cell lines (22Rv1, DU145, and PC3) with CRISPR/Cas9-mediated RIPK2 knockout (RIPK2-KO) using two independent guide RNAs. This analysis identified 13 candidate RIPK2-regulated genes. Reverse transcription quantitative PCR (RT-qPCR) validated eight of these genes. Furthermore, treatment with two distinct RIPK2 inhibitors significantly reduced RIPK2 signature scores in four independent PC cell lines in a dose- and time-dependent manner. Clinical association analyses revealed that high RIPK2 signature scores correlate with metastasis and worse biochemical recurrence-free, progression-free, disease-free, and overall survival, outperforming RIPK2 mRNA levels as a prognostic biomarker. This study establishes, for the first time, a RIPK2-regulated gene signature as a potential biomarker for RIPK2 activity and PC prognosis, warranting further validation in clinical specimens to provide a much-needed tool for patient stratification and response monitoring in RIPK2-targeted therapies.

overall_design: RNA-Seq analysis of control and RIPK2-knockout 22Rv1, DU145, and PC3 cells

first: Qian

first: Sungyong

last: You


title: Adenine Nucleotide translocase 1 (ANT1) Deficiency Impairs Macrophage Metabolism and Migration, Protecting Against Emphysema in COPD [6 months]

city: Pittsburgh

first: Justin

last: Sui

state: PA

address: 200 Lothrop Street

institute: University of Pittsburgh School of Medicine

summary: Macrophage-mediated inflammation drives various lung diseases, including chronic obstructive pulmonary disease (COPD). COPD macrophages have dysfunctional mitochondrial metabolism and function which lead to a chronic inflammatory lung environment. However, the factors regulating this altered metabolism have not been elucidated. Adenine nucleotide translocase 1 (ANT1) is a mitochondrial ATP transporter critical to mitochondrial metabolism. We demonstrate that human alveolar macrophages from patients with moderate COPD (GOLD stage 2)  have reduced ANT1 expression while macrophages from very severe COPD (GOLD stage 4) has elevated ANT1 compared to normal control subjects. Ant1-deficient mice were protected against cigarette smoke (CS)-induced emphysema with failure of recruited immune cells to migrate into alveoli. Ant1-null alveolar macrophages had reduced ATP production and mitochondrial respiration, upregulated fewer inflammatory pathways after CS and reduced migratory capacity. Conditional Ant1 knockout in Cx3cr1-positive monocytes and adoptive transfer of Ant1-deficient bone marrow into CS-treated mice phenocopied the migratory defect in the lung. Our data indicate that ANT1 is a critical regulator of lung macrophage inflammatory signaling and CS-triggered cell migration in the lung, suggesting that metabolic modulation may be a promising therapeutic avenue for COPD

overall_design: C57BL WT or Ant1 null mice (gift from Douglas Wallace, Children's Hospital of Philadelphia) (female mice at 10-12 weeks of age, n = 3-4 per group) were subjected to the smoke of 4 unfiltered cigarettes per day (lot# 3R4F; University of Kentucky), 5 days a week for a duration of 6 months, using a smoking apparatus that delivers targeted cigarette smoke to single mice isolated in individual chambers. The controls in each group were exposed to room-air alone. Whole lung single cell suspensions were created and single cell RNA seq was performed.

first: Corrine

middle: R

last: Kliment


title: Expression of CREB3L1 blocks key cancer pathways and suppresses metastasis of lung squamous cell carcinoma cells

city: Saskatoon

first: Deborah

last: Anderson

state: Saskatchewan

address: 107 Wiggins Road

country: Canada

institute: University of Saskatchewan

summary: Lung cancer is the leading cause of death due to cancer, with higher mortality rates than cancers of the colon, breast and prostate combined. About one quarter of lung cancers are lung squamous cell carcinomas (LUSC), with a five-year survival rate of only 16%. We discovered that the majority of LUSCs have reduced expression of a key transcription factor CREB3L1 (cAMP responsive element binding protein 3 like 1), known to function as a metastasis suppressor in breast, bladder and ovarian cancers. In this report, we set out to determine if CREB3L1 functions as a metastasis suppressor in LUSCs. A differential gene expression analysis showed that ectopic expression of CREB3L1 in NCI-H2170 and NCI-1703 cells caused significant reductions in many signaling pathway genes involved in promoting cell viability, survival, migration and angiogenesis. Expression of CREB3L1 was able to reduce cell migration and anchorage-independent growth in soft agar in NCI-H2170, NCI-H1703 and NCI-H226 LUSC cells. Expression of CREB3L1 had less impact on the growth of primary xenograft tumors for NCI-H2170 and NCI-H1703 cells, the latter of which formed atypical masses filled with blood. In contrast, xenografts of NCI-H226 expressing CREB3L1 showed significant reductions in primary tumor growth. Finally, in a mouse metastasis assay, expression of CREB3L1 in NCI-H2170 cells significantly reduced the formation of liver metastases and in NCI-H226 cells, lung metastases, as compared to their respective CREB3L1-deficient parental LUSC cells. Taken together, these results strongly support a role for CREB3L1 as a metastasis suppressor in lung squamous cell carcinoma cells.

overall_design: Whole transcriptome shotgun sequencing (RNA-Seq) was used to compare gene expression between the parental human LUSC cells (NCI-H1703, NCI-H2170) and two stable cell lines each expressing HA-CREB3L1 (NCI-H1703 +HA-CREB3L1 #1 and #2; NCI-H2170 #7 and #10) via levels of polyadenylated RNA.

first: Paul

last: Mellor

first: Stephanie

last: Kendall

first: Austin

last: Hammond

first: Riley

last: Plett

first: Anurag

last: Saxena


title: Adenine Nucleotide translocase 1 (ANT1) Deficiency Impairs Macrophage Metabolism and Migration, Protecting Against Emphysema in COPD

overall_design: C57BL WT or Ant1 null mice (gift from Douglas Wallace, Children's Hospital of Philadelphia) (female mice at 10-12 weeks of age, n = 3-4 per group) were subjected to the smoke of 4 unfiltered cigarettes per day (lot# 3R4F; University of Kentucky), 5 days a week for a duration of 2 months, using a smoking apparatus that delivers targeted cigarette smoke to single mice isolated in individual chambers. The controls in each group were exposed to room-air alone. Whole lung single cell suspensions were created and single cell RNA seq was performed.


title: Mechanisms of drugs-resistance in small cell lung cancer III

city: Toyoake

first: Juntaro

last: Yamasaki

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake-cho

country: Japan

institute: Fujita Health University

summary: Lung cancer is the leading cause of cancer mortality and is classified by the World Health Organization into two broad histological subtypes. Non–small cell lung cancer (NSCLC), including adenocarcinoma, squamous cell carcinoma, and large cell carcinoma, accounts for ~85% of all lung cancer cases, with the remaining 15% of cases being due to small cell lung cancer (SCLC), which arises from neuroendocrine cells in the lung. Although most SCLC tumors are initially responsive to chemotherapy and radiation, patients often experience relapse, with the tumor acquiring an aggressiveness and therapeutic resistance that lead to a poor clinical outcome. Improvement of overall survival in individuals with SCLC will require the identification of novel therapeutic targets based on a better understanding of the changes in intracellular signaling of aggressive SCLC cells. The malignant progression of SCLC often occurs concomitantly with the acquisition of chemoresistance, suggesting that phenotypic malignant change is related to adaptation to the stresses induced by chemotherapy. In order to analyze gene expression changes associated with malignant transformation in SCLC, we established a cisplatin-resistant SCLC cell line and performed RNA sequencing.

overall_design: Cisplatin-resistant DMS273 and SBC5 cells were generated by exposing the parental cell lines to stepwise increases in the concentration of cisplatin. RNAs were isolated from parental and cisplatin-resistant cells and subjected RNA-sequencing analysis.

first: Kentaro

last: Suina


title: Biochemical Profiling and Structural Basis of ADAR1-Mediated RNA Editing

city: Houston

first: Yi-Lan

last: Weng

state: Texas

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

summary: ADAR1-mediated RNA editing suppresses the immunostimulatory potential of endogenous RNA. Deficiency in ADAR1 triggers inflammatory responses; however, the underlying mechanisms remain unclear. In this study, we overexpressed wild-type ADAR1 (ADAR1 WT) and various disease-associated ADAR1 variants in 293T cells to examine transcriptomic RNA editing events. We further compared how disease-associated ADAR1 variants fail to edit specific RNA substrates, potentially contributing to the activation of inflammatory pathways.

overall_design: To investigate the targets and RNA editing activity of ADAR1 and its mutants in the transcriptome, we overexpressed these ADAR1 variants in HEK293 cells. After 48 hours overexpression, we conducted RNA sequencing to identify adenosine-to-inosine (A-to-I) RNA editing events.

first: Deng

last: Xiangyu

first: Gao

first: Weng

last: Yi-Lan

first: Sun

last: Lina


title: Transcriptome mapping of unfertilized flowers under high temperature unveils the regulatory network of genes during pollen/flower development and provides genomics resource in pea

city: Uttarakhand

first: Harsh

last: Chauhan

state: Haridwar

address: Roorkee-Haridwar Highway, Roorkee

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Roorkee

summary: Pea (Pisum sativum L.) cultivar Arka Chaitra (AC) is considered heat tolerant variety, whereas cultivar Matar Ageta (MA) the heat sensitive variety. In this study, we initially report the repertoire of morpho-physiological traits namely pod number (PNP), weight of pods (PW), seed number/pod (SNP) and weight of seed/pod (SW) during high temperature environment in AC and MA. Subsequently, we conducted pollen viability assay to further examine the pollen behaviour under heat stress (HS). Morpho-physiological analysis revealed that cultivar AC exhibited greater number of pods and seeds, as well as higher pod and seed weights, compared to MA under HS. Furthermore, pollen viability in cultivar AC was reduced by 23%, whereas in cultivar MA, it was reduced by 41%, indicating that AC possess robust tolerance mechanisms under high temperature conditions. Based on these observations, we delve deeper to investigate the regulatory mechanisms by profiling the transcriptomes of cultivars AC and MA using RNA Sequencing under HS. We identified 1922 DEGs in the ACCON-ACHS cluster, 411 DEGs in the MACON-MAHS cluster, and 11,129 DEGs in the ACHS-MAHS cluster indicating substantial transcriptional reprogramming induced by HS. Further, the identified DEGs were annotated through gene ontology (GO) analysis, revealing a significant GO term associated with pollen and flower development, heat stress proteins, and plastid development in tolerant variety, in contrast, the sensitive variety was enriched with GO terms related to cell morphogenesis, cell growth, and cell wall biogenesis. These findings provide in-depth analysis of genes and pathways involved in imparting thermotolerance across pea cultivars AC and MA.

overall_design: In this study, we initially measured morpho-physiological traits such as the pods number per plant, weight of pods per plant, seed number per pod, and seed weight per pod in the heat-tolerant pea (Pisum sativum) cultivar Arka Chaitra (AC) and the susceptible cultivar Matar Ageta (MA). Furthermore, we analyzed pollen behaviour in contrasting cultivars under stress conditions. Based on above results, we profiled the transcriptome of two pea cultivars using RNA sequencing (RNA-Seq) at the pre-anthesis stage under CON and transient HS conditions. Both cultivars were subjected to short-term heat episode of 35 C for two hours in a growth chamber under ambient light conditions and stressed tissues were harvested immediately following the two-hour heat episode.

first: Chanderkant

last: Chaudhary

first: Meenakshi

last: Kanwar

first: Parul

last: Sirohi

first: Kumar Ankit

last: Anand

first: Sohini

last: Barua

first: Jaswinder

last: Singh


title: The Impact of HYOU1 Knockdown on Gene Expression in Hep3B Liver Cancer Cells

city: hefei

first: xiao

last: du

state: anhui

address: Anhui Medical University, 81 Meishan Road, Shushan District, Hefei City, Anhui Province

institute: first affiliated hospital of anhui medical university

summary: In order to explore the role of HYOU1 in liver cancer cells and identify its downstream target genes,  we utilized lentiviral technology to knock down HYOU1 expression and established a stable HYOU1 knockdown Hep3B liver cancer cell line. Gene expression profiling was then performed using two groups of cells: the control group and the stable knockdown group (n=3).

overall_design: Comparative Gene Expression Profiling of Hep3B Cell RNA-Seq Data (sh-NC,  sh-HYOU1)

first: Xiao

last: Du

first: Guoping

last: Sun


title: roboA and anosmin-1 restrict fate boundaries in planarian stem cells via foxA

city: ITHACA

first: Carolyn

last: Adler

address: 930 Campus road

institute: Cornell University

summary: Stem cells integrate extracellular cues with downstream transcriptional responses to channel their differentiation, but the underlying mechanisms responsible remain unclear. Planarians possess distinct organs embedded in a vast pool of pluripotent stem cells that maintain tissue turnover and drive whole-body regeneration. This unique configuration provides an ideal model for exploring how pluripotent stem cells sense tissue boundaries, guiding appropriate differentiation. Here, we use the planarian pharynx to define the cell lineages that originate from stem cells expressing the pioneer transcription factor foxA. The anatomical restriction of pharynx-specific lineages is disrupted by knockdown of the Roundabout receptor roboA, leading to ectopic pharynx neurons (EPNs) emerging in the brain. An RNAi screen for genes that phenocopy roboA identifies the extracellular protein anosmin-1, a gene responsible for Kallmann syndrome, as a potential partner of roboA. Aberrant induction of EPNs in the brain requires foxA, while knockdown of foxA induces head-specific neurons in the pharynx, revealing a latent plasticity in stem cells to adopt alternative fates. Together, we propose that RoboA and Anos1 act as fate-reinforcing genes (FRGs) that suppress inappropriate cell fates, maintaining organ integrity and enabling stem cell plasticity during regeneration.

overall_design: 10X 3'single-cell RNA sequencing from control and foxA(RNAi) planarian cells.

first: Kuang-Tse

last: Wang

first: Yu-Chia

last: Chen

first: Fu-Yu

last: Tsai

first: Catherine

middle: P

last: Judy

middle: E


title: Mettl14 deficiency promotes Fam32a expression via m6A modifications to facilitate the hepatocyte G1/S transition

city: Nanjing

first: WenHan

last: Zhou

address: No. 1 Weigang, Xuanwu District

department: college of animal science & technology

institute: Nanjing Agricultural University

summary: Mettl14, a key component of the m6A methyltransferase complex, plays a crucial role in regulating mRNA stability and splicing. Reduced expression of Mettl14 is associated with hepatocellular carcinoma and liver regeneration, yet the molecular mechanisms by which it regulates the hepatocyte cell cycle remain unclear. Using RNA-Seq and MeRIP-Seq in liver-specific Mettl14 knockout mice, we found that Mettl14 deficiency stabilizes Fam32a mRNA through m6A modifications, resulting in increased Fam32a protein levels. Elevated Fam32a expression accelerates the G1/S transition by modulating Cdkn1a splicing, specifically downregulating its variant 2. These findings uncover a novel m6A-dependent mechanism that regulates hepatocyte cell cycle progression and highlight the previously unrecognized role of Fam32a in promoting the G1/S transition.

overall_design: This experiment involved two sets of sequencing analyses: the first compared RNA-seq  between Mettl14-KO mice and wild-type mice, while the second analyzed RNA-seq data from AML12 cells overexpressing Fam32a versus empty vector controls.

first: Chengyu

last: Li

first: Wenhan

first: Dayu

first: Zhaojun

last: Liu

first: Ming

last: Shen

first: Linjie

last: Zhu

first: Hongmin


title: B4GALT5 and B3GNT3 downregulate MHC-I levels on tumor cells, thereby suppressing CD8+ T cell responses in pancreatic ductal adenocarcinoma.

first: Shiqi

last: Yin

address: 上海市奉贤区南桥新城南奉公路6600号

institute: 奉贤区中心医院

summary: Immune evasion is a critical event in the progression of pancreatic ductal adenocarcinoma (PDAC), where the expression of MHC-I molecules is frequently suppressed in the majority of PDAC cells, serving as a strategy for tumor cells to evade immune surveillance. Reduced MHC-I expression allows tumor cells to escape recognition and killing by CD8+ T cells, thereby promoting their growth and dissemination within the body. In this study, we identified a significant negative correlation between the expression of B3GNT3 and B4GALT5 and the levels of MHC-I on tumor cells.

overall_design: We separately knocked down the expression of B4GALT5 and B3GNT3 in a pancreatic ductal adenocarcinoma (PDAC) cell line and compared them with the control group (NC group), with three samples per group, followed by RNA sequencing analysis.


title: Nurr1 orchestrates claustrum development and functionality

city: Berlin

first: Andrew

last: Newman

address: Charitéplatz 1

department: Institute for Cell and Neurobiology

country: Germany

institute: Charité Universitätsmedizin Berlin

summary: Claustrum is the part of the forebrain known to be most widely interconnected tissue with almost all global regions. It is believed to be involved in coordinating multiple cognitive behaviors including consciousness formation. However, little is known about the molecular mechanisms underlying its development and involvement in behavioral control. Here we show that Nurr1 (Nr4a2) is the key transcription factor orchestrating claustral morphogenesis, functional connectivity and thus behaviors. Nurr1 deficient claustral cells aberrantly migrate into insular cortex, shaping claustrum into an abnormal wing-like structure, and ectopically turn on insular cortex genetic program. Accordingly, functional connectivity of the claustrum is not properly formed and relevant behaviors are dysregulated in Nurr1 deficient mice. We show that Nurr1 regulates claustral neuron positioning by suppressing G-protein signaling.

overall_design: P0 anterior claustro-insular parts of mouse cerebral cortices (amygdala, hippocampal and posterior cortical tissues were manually excluded) were dissociated. Approximately 10,000 nuclei were prepared for single-nuclei encapsulation using a 10X single cell controller for each genotype.10x Genomics 3' v3 gene expression (GEX) libraries were prepared and sequenced on a single Novaseq sequencing system. Sex was not discriminated in this project or single cell transcriptomic analysis.

first: Kuo

last: Yan

middle: G

first: Pauline

last: Lange

first: Susanne

last: Mueller

first: Marco

last: Foddis

first: Stefan Paul

last: Koch

first: Philipp

last: Boehm-Sturm

first: Maron

last: Mantwill

first: Carsten

last: Finke

first: Penghui

last: Deng

first: Melissa

last: Long

first: Victor

last: Tarabykin


title: Identification of phloem-specific proteinaSEOus structure heterogeneity in sieve element of Populus trichocarpa

city: Poznań

first: Karolina

last: Kulak

address: Uniwersytetu Poznanskiego 6

department: Department of General Botany

country: Poland

institute: Adam Mickiewicz University

summary: Phloem proteins (P-proteins) may play crucial role in phloem transporting cell function. We used single-nucleus RNA sequencing (snRNA seq) to analyze P-protein expression in Populus trichocarpa root.

overall_design: Cell nuclei were isolated from pioneer root fragments of Populus trichocarpa, stained with DAPI and sorted using a BD FACSAria™ Fusion flow cytometer

first: Anna

last: Samelak-Czajka

first: Malgorzata

last: Marszalek-Zenczak

first: Magdalena

last: Trybus

first: Paulina

last: Jackowiak

last: Kułak

first: Kornel

last: Michalak

first: Agnieszka

last: Bagniewska-Zadworna


title: Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery

city: San Diego

first: Melodi

last: Tastemel

address: 9500, Gilman drive

department: CMME

institute: UCSD

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Loop-extrusion machinery, comprising the cohesin complex and CTCC-binding factor CTCF, organizes the interphase chromosomes into topologically associating domains (TADs) and loops, but acute depletion of components of this machinery results in variable transcriptional changes in different cell types, highlighting the complex relationship between chromatin organization and gene regulation. Here, we systematically investigated the role of 3D genome architecture in gene regulation in mouse embryonic stem cells under various perturbation conditions. We found that acute depletion of cohesin or CTCF disrupts the formation of TADs, but affects gene regulation in a gene-specific and context-dependent manner. Furthermore, the loop extrusion machinery was dispensable for transcription from most genes in steady state, consistent with prior results, but became critical for a large number of genes during transition of cellular states. Through a genome-wide CRISPR screen, we uncovered multiple factors that can modulate the role of loop extrusion machinery in gene regulation in a gene-specific manner. Among them were the MORF acetyltransferase complex members (Kat6b, Ing5, Brpf1), which could antagonize the transcriptional insulation mediated CTCF and cohesin complex  at developmental genes. Interestingly, inhibition of Kat6b partially rescues the insulator defects in cells lacking the cohesin loader Nipbl, mutations of which are responsible for the developmental disorder Cornelia de Lange syndrome. Taken together, our findings uncovered interplays between the loop extrusion machinery and histone modifying complex that underscore the context-dependent and gene-specific  role of the 3D genome.

overall_design: Examination of insulator activity of CTCF binding seqences and their effects on chromatin topology upon perturbations to chromatin structural proteins in mouse embryonic cells  Chromosome coordinates of variants: '4CBS' was inserted between chr3:34,726,762-34,727,258; mm10

first: Adam

last: Jussila

first: Bing

last: Ren

first: Bharath

last: Saravanan

first: Hui

last: Huang

first: Yang

last: Xie

first: Quan

last: Zhu

first: Yifan

last: Jiang

first: Ethan

last: Armand


title: Phosphoproteomics reveals a crucial role of FLT3 in BCR::ABL1 independent resistant chronic myeloid leukemia

city: Rome

first: Francesca

last: Sacco

address: Via della Ricerca Scientifica, 1

country: Italy

institute: University of Rome Tor Vergata

summary: BCR::ABL1 drives chronic myeloid leukemia (CML) disease and treatment, as revealed by the success of tyrosine kinase inhibitor (TKI) therapy. However, additional poorly characterized molecular pathways, acting as BCR::ABL1 independent nechanisms,  play crucial roles in CML, contributing to leukemic stem cells (LSCs) persistence, TKI resistance and disease progression. Here, by combining high sensitive mass spectrometry (MS)-based phosphoproteomics with the SignalingProfiler pipeline, we obtained two signaling maps offering a comprehensive description of the BCR::ABL1 dependent and independent pro-survival signalling mechanisms. We leveraged these maps to unbiasedly and systematically discover therapeutic vulnerabilities, by implementing the Druggability Score computational algorithm. By this strategy, and in combination with in vitro and in ex vivo functional assays, we show a crucial role of acquired FLT3-dependency in resistant CML models. In conclusion, we reposition FLT3, one of the most frequently mutated drivers of acute leukemia, as a potential therapeutic target for TKI resistant CML patients.

overall_design: RNA was sequenced from peripheral blasts of 4 non responder and 3 responder chronic myeloid leukemia patients

first: Valeria

last: Bica

first: Veronica

last: Venafra

first: Giorgia

last: Massacci

first: Simone

last: Graziosi

first: Sara

last: Gualdi

first: Gessica

last: Minnella

first: Federica

last: Sorà

first: Patrizia

last: Chiusolo

first: Maria Elsa

last: Brunetti

first: Gennaro

last: Napolitano

first: Massimo

last: Breccia

first: Dimitrios

last: Mougiakakos

first: Martin

last: Boettcher

first: Thomas

last: Fischer

first: Livia

last: Perfetto


title: An Improved Human 3D Skin Model for Aging Research

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

institute: University of Ulm

summary:
Current models used to study skin aging, including in vivo murine models, ex vivo human skin, and in vitro 2D cell cultures, present significant limitations in replicating the complexity of chronological human skin aging. To address this gap, we developed a novel 3D human full-thickness skin aging model using primary dermal fibroblasts and epidermal keratinocytes harvested from the same aged donors (average age 80 years). Comprehensive histological, immunostaining, and transcriptomic analyses of this aging model, compared to a young 3D skin model (average age 20 years), revealed distinct hallmarks of chronological skin aging, including reduced epidermal and dermal thickness, decreased extracellular matrix content, diminished cell proliferation, and increased cellular senescence. Furthermore, 3D aging skin model also showed reduced IGF-1 expression and induction of AP1/JunB, which were consistent with observations in aged human skin. Transcriptomic profiling further identified upregulated pathways associated with extracellular matrix degradation, cellular senescence, and immune responses, aligning closely with published data from human aged skin. This novel in vitro model faithfully recapitulates several key features of chronological skin aging, offering a robust platform for studying aging mechanisms and testing therapeutic interventions.
We have used microarray to study the gene expression profile of 3D skin models

overall_design: Total RNA was isolated from 3D skin models at day 14 and day 21 of culture and used for microarray

first: Sebastian

last: Huth


title: Coupling ER stress to STAT1-mediated immunity against bacterial infection

city: Clayton

first: Kathleen

last: McCaffrey

state: VIC

address: 25-31 Wright Street

country: Australia

institute: Hudson Institute of Medical Research

summary: Endoplasmic reticulum (ER) stress and activation of the unfolded protein response (UPR) are hallmarks of pathogen infection. The UPR drives pro-inflammatory responses to ER stress but its role in interferon signaling is unknown. Using metabolomics approaches, we observed that pharmacological ER stress reprogrammed macrophage metabolism to a pro-inflammatory “M1-like” phenotype and enhanced the microbicidal activity of these cells to restrict bacterial infection. Phospho-proteomics analysis showed that this anti-microbial response was mediated via the UPR serine/threonine-protein kinase/endoribonuclease IRE1 (ERN1) and activation of signal transducer and transcription activator 1 (STAT1) required for interferon signaling. We also demonstrated that blockade of IRE1 signaling by the bacterial pathogen Legionella pneumophila inhibited STAT1-mediated immune responses to infection. These findings reveal the potential for ER stress to initiate anti-microbial STAT1 signaling in the absence of other pro-inflammatory stimuli and how this response is inhibited by a bacterial pathogen during infection.

overall_design: To investigate the role of Legionella effector proteins on host mRNA expression, THP-1 macrophages were infected with the Legionella pneumophila 130b strain (WT) or a mutant strain lacking four genes encoding Lgt1-3, SidI and SidL (delta4). We then performed comparitive gene expression profiling of RNA-seq data from WT versus delta4 infected cells from three independent experiments.

first: Elizabeth

middle: L

last: Hartland


title: Prolactin Regulates Seasonal Changes in Water Rheostasis in Siberian Hamsters (Phodopus sungorus)

city: Glasgow

first: Sayantan

last: Sur

address: University of Glasgow, Vet School, Garscube Campus, Bearsden Road

department: School of Biodiversity, One Health & Veterinary Medicine

country: United Kingdom

institute: University of Glasgow

summary: Prolactin (PRL) is a multifunctional hormone involved in diverse physiological processes, including lactation, reproduction, growth, and renal function. However, its effects on kidney morphology in seasonal mammals remain largely unexplored. The Siberian hamster (Phodopus sungorus), a seasonally breeding species, exhibits distinct physiological adaptations in response to photoperiod-driven changes in prolactin levels. Previous studies have demonstrated that PRL treatment significantly increases kidney mass, yet the underlying molecular mechanisms remain unclear. This study aimed to investigate the impact of PRL on kidney morphology and the associated molecular pathways. Histological analysis using Hematoxylin and Eosin (H&E) staining revealed that PRL treatment significantly increased convoluted tubule width (CTW). To elucidate the molecular basis of these morphological changes, transcriptome analysis was performed, identifying 19 significantly enriched pathways that were negatively correlated with CTW. These findings provide novel insights into the role of PRL in regulating seasonal kidney morphology and highlight key molecular pathways involved in this process.Our results contribute to a deeper understanding of PRL’s role in renal adaptations to seasonal changes, paving the way for future research into the endocrine regulation of kidney structure and function in seasonal mammals.

overall_design: Two experiments were conducted to assess seasonal changes in water rheostasis and the role of prolactin in kidney physiology.  1. Experiment 1: Seasonal Changes in Water Rheostasis Adult male Siberian hamsters (N = 54) were housed under long photoperiod (LP; 16L:8D). A subset (N = 6) remained under LP, while the rest were transferred to short photoperiod (SP; 8L:16D) and euthanized at 4-week intervals (N = 6 per time point, up to 32 weeks). Kidney dimensions were recorded using a vernier caliper, and kidney volume was estimated. Kidneys were weighed and stored at -80°C. 2. Experiment 2: Prolactin’s Role in Kidney Physiology Adult female hamsters (N = 12) housed in LP were exposed to SP for 8 weeks and assigned to two groups: control (N = 6; vehicle injections) and prolactin-treated (N = 6; 18 µg PRL daily for 3 days). Injections were administered at mid-light phase. Hamsters were euthanized 2–4 hours after lights-on. Kidney volume and mass were recorded and stored at -80°C for further analysis.Kidney samples from Experiment 1 (LP, SP12wk, SP28wk; N = 4 per group) and Experiment 2 (SAL, PRL; N = 6 per group) underwent transcriptome sequencing. RNA was extracted using the QIAGEN RNeasy Plus Mini Kit, and quality was assessed via Nanodrop ND-1000 (260/280 ~2.0).Oxford Nanopore Direct cDNA Native Barcoding (SQK-DCS109, EXP-NBD104) was used for cDNA synthesis. Sequencing was performed on MinION Mk1B using R9 Spot-ON Flow Cells (FLO-MIN106D), with 12 samples per flow cell. Runs lasted 72 hours at −180 mV, generating fast5 files for downstream analysis.

first: Tyler

middle: J

last: Stevenson


title: Characteristics between porcine bone marrow-derived mesenchymal stem and peripheral blood mononuclear cells

city: Jeongeup-Si

first: Ju Young

last: Lee

address: 30 Baekhak 1 Gil,

country: South Korea

institute: Korea institute of toxicology

summary: Mesenchymal stem cells (MSCs) have been isolated from various organs and extensively studied for their potential in regulating transplantation. MSCs from different mammalian species are well characterized; however, the properties and therapeutic potential of porcine bone marrow-derived MSCs (BM-MSCs) remain unclear. In this study, we aimed to profile the characteristics of porcine BM-MSCs by comparing their gene expression patterns and immunomodulatory properties with those of porcine peripheral blood mononuclear cells (PBMCs) and bone marrow-attached cells (BMACs). Using quantitative polymerase chain reaction, flow cytometry, immunocytochemistry, and RNA sequencing, we confirmed the expression of key MSC markers, including CD105, CD73, and CD90, in porcine BM-MSCs, and aligned them closely with human MSCs. We found significant differences in gene expression between BM-MSCs and PBMCs, with BM-MSCs exhibiting a distinct expression pattern similar to that of BMACs. Gene ontology enrichment analysis revealed the pathways involved in immune modulation and tissue repair, underscoring the potential of BM-MSCs to enhance immune regulation. Notably, BM-MSCs exhibited higher transforming growth factor-beta levels than PBMCs, suggesting a central role in their immunosuppressive function. These findings indicate the immunomodulatory capabilities of porcine BM-MSCs and support their application in xenotransplantation, where they may help mitigate graft rejection and promote tissue regeneration.

overall_design: To compare DEG profiles between BMAC, BM-MSC and PBMCs

first: Youngkyu

last: Kim

first: Juyoung

first: Jiwoo

last: Shin

first: Jeongho

last: Hwang


title: De novo genome assembly of faba bean (Vicia faba L.) leaf transcriptome provide novel insights into the drought stress tolerance mechanisms

city: Gembloux

first: Yordan

last: Muhovski

address: Chaussee de Charleroi

department: Life Sciences

country: Belgium

institute: CRAW

summary: Drought is a major limiting constraint to faba bean production worldwide, including Tunisia. However, molecular mechanisms underlying faba bean responses to drought stress are not well understood. In this context, transcriptome analysis by RNA-seq was performed to investigate drought-related genes and construct a network of faba bean drought stress response and tolerance. De novo assembly of the transcriptome generated 26,728 differentially expressed genes (DEGs). Of these, 13,920 were up-regulated and 12,808 down-regulated in faba bean drought-stressed leaves. Moreover, a total of 10,800 simple sequence repeats (SSRs) and 2130 transcription factors involved in major metabolic pathways including abscisic acid (ABA)-dependent and -independent signaling pathway were identified. GO, KOG and KEGG enrichment analyses revealed that these DEGs were involved in several important processes including photosynthesis, flavonoid biosynthesis, response to stimulus and abiotic stress, reactive oxygen species (ROS) scavengers, signal transduction, biosynthesis of secondary metabolites and transporters, suggesting the involvement of these important pathways in faba bean response to water deficit. Various stress proteins such as late embryogenesis abundant proteins (LEA), dehydrins (DHNs) and heat shock proteins (HSPs) have been identified and their expression was robustly upregulated in drought-stressed leaves, indicating their key contribution to drought response and adaptation by conferring protection and providing stability to faba bean plant cellular processes under water deficit. The reliability of the RNA-seq results was confirmed by the analysis of 10 randomly selected genes using qRT-PCR. Taken together, these findings help advancing our knowledge and can guide breeding programs aimed at improving the tolerance of faba bean to drought stress.

overall_design: The goal of the study was to investigate the leaf transcriptomic changes of faba bean (Vicia faba) in response to drought stress and to perform de novo assembly. The collected leaf samples (stressed and control) were ground in liquid nitrogen and the resulting powder was then used for RNA extraction using NucleoSpin RNA Plant kit (Macherey-Nagel, Germany). Library construction and  RNA sequencing were carried out at Beijing Genomics Institute (BGI), China, at a sequencing depth of 40 million paired end reads.

first: Ghassen

last: Abid

first: Khaled

last: Sassi

first: Frédéric

last: Debode

first: Benjamin

last: Dubois

first: Rim

last: Nefiss-Ouertani

first: Emna

last: Ghouili

first: Souhir

last: Abdelkrim

first: Zhengguo

last: Li

first: Salwa

last: Harzalli-Jabara

first: Moez

last: Jabara


title: Mapping and quantifying nascent transcript start sites using TT-TSS-seq

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

institute: Francis Crick Institute

summary: Transcription initiation is a highly dynamic and tightly regulated process involving the coordinated action of transcription factors, chromatin remodelers, and RNA polymerase which determine where and when transcription begins. Accurately mapping and quantifying transcription start sites (TSSs) from nascently transcribed RNAs remains a key area of interest, as it provides critical insights into transcription dynamics. Here, we combined transient transcriptome sequencing with transcription start site sequencing (TT-TSS-seq) to accurately map and quantify transcription initiation sites from nascent transcripts. Since transient metabolic labelling yields low-input RNA, we optimized the TSS-seq protocol to enhance sensitivity and accuracy. Specifically, we refined enzymatic reactions for decapping and RNA ligation and incorporated 5' oligonucleotides including unique molecular identifiers (UMIs) and barcodes to enable accurate quantification and sample multiplexing. The TT-TSS-seq approach detected transcription initiation of unstable transcripts, such as enhancer RNAs. Moreover, we identified that a large fraction of genes use multiple transcription initiation sites, yet often produce only a single stable transcript. Overall, TT-TSS-seq provides precise mapping and quantification of transcription initiation sites, offering new insights into transcriptional dynamics and expanding the toolkit for studying gene regulation.

sample_organism:
Saccharomyces cerevisiae
Mus musculus

platform_organism:
Saccharomyces cerevisiae
Mus musculus

overall_design: S288C S. cerevisea, and HM1 mESC cells.

first: Eleanor

last: Elgood Hunt

first: Claudia

last: Vivori


title: Expression data from ZBEE -treated SH-SY5Y cell

city: Tsukuba

first: sharmin

last: Aktar

state: 茨城県

department: Life and Environmental Science

institute: University of Tsukuba

summary:
Gene expression profiling reveals anti-inflammatory effects of RBEE  and 2-AB on lipopolysaccharide (LPS)-induced Human neuronal SH-SY5Y cells
We evaluated the pretreatment effect of RBEE  and 2-AB on LPS-induced inflammation in SH-SY5Y cells.

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). Clariom S assay system (Thermo Fisher, Japan) was used on duplicate RNA samples of each group. In accordance with the user manual, complementary DNA (cDNA) for microarray was generated using the GeneChip WT Plus Reagent kit (Thermo Fisher Science, Japan). Samples were hybridized using Clariom S GeneChip microarray kit (Thermo Fisher Science, Japan). After washing and staining, images were captured, and then CEL data were generated using the GeneChip Scanner 3000 (Thermo Fisher Science, Japan). The raw CEL data were normalized using the transcriptome analysis console (TAC) software ver.4.0.1 following the SST-robust multichip average (SST-RMA) algorithm (Thermo Fisher Scientific, Japan).

first: Sharmin

first: Ayumi

last: Kato


title: Gene expression profile at single cell level of mouse lung cancer cell-line tumors grown subcutaneously in adult male C57BL/6 mice with and without high-fat diet-induced obesity

city: Buffalo

first: Santosh

last: Patnaik

address: Elm and Carlton

institute: Roswell Park Cancer Center

summary: Obesity affects the progress of lung cancer. To understand this more, we performed single-cell RNA sequencing of dissociated tumors of four mouse lung cancer cell-lines grown subcutaneously in adult male C57BL/6 mice with and without high-fat diet-induced obesity.

overall_design: Groups (n = 6-8) of male C57BL/6 mice of about 4 months age had been kept on ad libitum for about 3 months on high-fat or control diet (Bioserv products S3282 and F4031, with 60% and 10% fat calories respectively), when they were injected subcutaneously in body flank with 100k cells of one of four mouse lung cancer cell-lines (four separate experiments, one per cell-line). All tumors were dissected after euthanizing mice when the largest tumor reached a maximum dimension of 2 cm. Tumor ulcerations occurred in case of the firefly luciferase-expressing Lewis lung carcinoma (LLC-Luc) cell-line. KPN1.1 cells were from Joshi lab of Yale University. CMT167 cell-line clones engineered with a CRISPR-Cas system for Stk11 knockout (ko) and its negative control were from Yau lab of Roswell Park Cancer Center. Tumors were dissociated with enzymatic and mechanical means in GentleMACS device with Miltenyi Bio reagents. Dissociated tumors were enriched for live cells using magnetic cell separation of dead cells, fixed using Parse Biosciences Cell Fixation Kit, and stored at -80 ºC until all experiments were completed. In all, 24 dissociated tumors were subjected to single-cell RNA sequencing with Parse Biosciences Evercode Whole Transcriptome v3 Kit – the samples underwent three rounds of combinatorial barcoding together (5k cells per sample) resulting in a single library that was sequenced and demultiplexed. For barcoding, 2 neighboring wells (total 5213 projected barcoded cells) were used for each sample, with wells A1 to D12 of the barcoding plate used in order of sample listing in the samples.tsv file.

middle: K


title: 5hmC-profiles in Puerto Rican Hispanic/Latino men with aggressive prostate cancer

city: Tampa

first: Manishkumar

middle: S

last: Patel

state: FL

address: 12902 USF Magnolia Drive

department: Tumor Microenvironment and Metastasis

institute: H. Lee Moffitt Cancer Center and Research Institute

type: Methylation profiling by high throughput sequencing

summary: Puerto Rican (PR) Hispanic/Latino (H/L) men are an understudied population that has the highest prostate cancer (PCa) specific mortality among other Hispanic populations. Little information is known about the higher mortality in PR H/L men. It is thought that epigenetic changes in key genes may play a critical role in aggressive tumors. We aimed to identify key 5-hydroxymethylcytosine (5hmC) changes in PR H/L men with aggressive PCa. We performed sequencing analysis using the 5hmC-enriched DNA from 22 prostate tumors and 24 adjacent normal FFPE samples. We identified 808 differentially methylated genes (DMGs) in tumors compared to adjacent normal tissues. These genes suggest key mechanisms, including upregulated signatures of negative Androgen Receptor (AR) regulation, Wnt/β-catenin pathway activation, and downregulation of tumor suppressor genes. Pathway analysis of DMGs demonstrated that DNA repair pathway was most upregulated in tumors. Since 5hmC abundance positively correlates with gene expression levels, we further investigated 808 DMGs in TCGA PCa gene expression data. Further, we identified 59 DMGs with significant gene expression changes in the same direction. Additionally, we identified 111 aggressiveness-related DMGs, of which, two hypomethylated genes (CCDC122, NUDT15) and four hypermethylated genes (PVT1, RPL30, TRMT12, UBR5) were found to be altered at transcriptomic level in a concordant manner in PR H/L PCa patients. Aberrant 5hmC and GE changes in these six genes were also associated with progression-free survival in the mixed PCa population. The 5hmC modifications and associated gene expression changes in these six genes could be linked to the highest prostate cancer (PCa)-specific mortality in PR H/L men. In conclusion, our study identified 59 DMGs showing concordant epigenetic and transcriptomic changes in tumor tissues and 111 DMGs showing association with aggressive PCa among PR H/L men. Our findings have significant implications for understanding these key genes’ molecular mechanisms, which may drive PCa progression and mortality in this population. This will help in developing potential biomarkers or therapeutic targets for personalized treatment strategies in this high-risk subgroup. Future research will explore how these genes contribute to PCa-specific mortality through molecular analyses, with plans to validate them in a larger validation cohort.

overall_design: We performed sequencing using the 5hmC-enriched DNA from 22 prostate tumors and 24 adjacent normal FFPE samples from PR H/L men with Prostate Cancer.

first: Mousa

last: Almubarak

first: Jaime

last: Matta

first: Carmen

last: Ortiz-Sanchez

first: Jarline

last: Encarnacion

first: Gilberto

last: Ruiz-Deya

first: Julie

last: Dutil

first: Jasreman

last: Dhillon

first: Kosj

last: Yamoah

first: Anders

last: Berglund

first: Hyun

last: Park

first: Deepak

last: Kilari

first: Yoganand

last: Balagurunathan

first: Liang

last: Wang

first: Jong

middle: Y


title: YAP1 promotes adipogenesis by regulating negative feedback mechanism of the hippo pathway via LATS2

city: Hohhot

first: Dongjun

last: Liu

state: Inner Mongolia

address: 235 Daxue west road  Saihan District

institute: Inner Mongolia University

summary: Adipose-derived mesenchymal stem cells (ADSCs) originating from adipose tissue are an important source of mesenchymal stem cells (MSCs) with multidirectional differentiation potential. YAP, a key effector of the Hippo signaling pathway, can control and regulate the differentiation of MSCs to certain types of mature cells. However, the specific mechanism of ADSCs' lipidogenic differentiation has not been clearly concluded. In this study, we used Capra hircus ADSCs (gADSCs) from Albas in Inner Mongolia as experimental materials. YAP1 promoted the differentiation of ADSCs into adipocytes. YAP1 overexpression activated the negative feedback regulation of the Hippo signaling pathway. LATS2 phosphorylation levels in the cells increased after YAP1 overexpression, leading to YAP phosphorylation, which reduces YAP and TAZ levels in the nucleus while promoting their accumulation in the cytoplasm. YAP1 overexpression increased the expression of LATS2, and overexpression of LATS2 promoted the differentiation of ADSCs to adipocytes. The promotion of ADSCs adipose differentiation by YAP1 was affected by the activity of LATS2 kinase. Therefore, overexpression of YAP1 promotes ADSCs adipogenic differentiation by regulating the expression of LATS2 and activating the negative feedback of Hippo pathway. Elucidating the molecular mechanism of YAP in ADSCs lipogenic differentiation is of great significance for the regulation of stem cell differentiation homeostasis, disease treatment and hair follicle growth.

overall_design: To investigate the effect of YAP on adipogenesis of gADSCs, we constructed gADSCs cell lines OE-TAZ. RNA-seq was performed with OE-TAZ and Control cells. Based on the RNA-seq data, an expression profile was generated.


title: decemedip: hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylome

city: Vancouver

first: Ning

last: Shen

state: BC

address: 2875 Osoyoos Crescent, Apt 124

institute: University of British Columbia

summary: MeDIP-seq is an enrichment-based DNA methylation profiling technique that measures abundance of methylated DNA. While this technique offers efficiency advantages over direct methylation profiling, it does not provide absolute quantification of DNAm necessary for cell type deconvolution. We introduce decemedip, a Bayesian hierarchical model for cell type deconvolution of methylated sequencing data that leverages reference atlases derived from direct methylation profiling. We demonstrate its accuracy and robustness through simulation studies and validation on cross-platform measurements, and highlight its utility in identifying tissue-specific and cancer-associated methylation signatures using MeDIP-seq profiling of patient-derived xenografts and cell-free DNA. decemedip is available at \url{https://github.com/nshen7/decemedip}.

overall_design: The submitted samples were DNA from the LuCaP PDXs extracted using the DNeasy Blood and Tissue Kit (QIAGEN). Genomic DNA was sheared using a Covaris Sonicator E220, and AMPure XP beads (Beckman Coulter) were used to size select 150 to 250 bp DNA fragments. Library preparation was performed using the KAPA HyperPrep Kit (KAPA Biosystems) according to the manufacturer's protocol. We then performed end-repair, A-tailing, and ligation of NEBNext adaptors (NEBNext Multiplex Oligos for Illumina kit, New England BioLabs). Libraries were digested using the USER enzyme (New England BioLabs). Lamda DNA, consisting of unmethylated and in vitro methylated DNA, was added to prepared libraries to achieve a total amount of 100 ng DNA. Methylated and unmethylated Arabidopsis thaliana DNA (Diagenode) was added for quality control. MeDIP was performed using the MagMeDIP Kit (Diagenode anti-5-methylcytosine (5-mC) antibody, specifically the 33D3 clone) following the manufacturer's protocol. Samples were purified using the iPure Kit v2 (Diagenode). Success of the immunoprecipitation was confirmed using qPCR to detect recovery of the spiked-in Arabidopsis thaliana methylated and unmethylated DNA.

first: Ze

last: Zhang

first: Sylvan

last: Baca

first: Keegan

last: Korthauer


title: TNFα Downregulates STX17 Blocking Autophagy and Impairing Platelet Metabolism and Clot Contraction

city: Sheridan

first: Kenneth

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

summary: Platelets are key players in hemostasis and thrombosis. In inflammatory conditions, platelets are hyperreactive and patients have an overal increased thrombotic risk. Our previous research demonstrated that TNFα significantly increases mitochondrial mass and platelet reactivity, emphasizing the crucial role of TNFα in modulating platelet metabolism and function.We hypothesized that TNFα disrupts platelet metabolism and function by inhibiting autophagy and mitophagy, which are critical processes for preserving mitochondrial mass, integrity, and energy production. We investigated the function, metabolism, and autophagy of human and mouse platelets in myeloproliferative neoplasms, rheumatoid arthritis, and aseptic inflammation. Our analysis reveled a blocked

overall_design: RNA was extracted from platelets of three TNFdARE mice, and three control littermates. Bulk RNA sequencing was performed to determine transcriptional differences in platelets due inflammatory conditions mediated by TNFα

first: Guadalupe

last: Rojas-Sanchez

first: Jorge

last: Calzada-Martinez

first: Ken

first: Pavel

last: Davizon-Castillo


title: TNF-α promotes TNBC aggressiveness by upregulating miR-5001-5p and inhibiting MNK2a–p38 MAPK signaling

city: jinan

first: shujuan

last: sun

state: jinan

address: jiyan road 440,jinan ,china

department: Shandong Cancer Hospital and Institute

institute: Shandong First Medical University and Shandong Academy of Medical Sciences

summary: Triple-negative breast cancer (TNBC) has a greater invasive and metastatic potential than non-TNBC, leading to a poorer prognosis because of the absence of viable therapeutic targets. Tumor necrosis factor-alpha (TNF-α), which is aberrantly activated in TNBC, plays a pivotal role in TNBC metastasis and progression. The ability of TNF-α to promote TNBC progression is unique when compared with its ability to promote non-TNBC progression; however, the underlying mechanism remains unclear. TNF-α specifically enhanced the invasive and metastatic potential of TNBC compared with that of non-TNBC. Analysis of the differentially expressed miRNAs showed that TNF-α upregulated miR-5001-5p expression in TNBC cells. The results of transcriptomic sequencing combined with subsequent verification analysis indicated that MNK2a was significantly downregulated following miR-5001-5p overexpression. Evidence from dual-luciferase reporter assays confirmed that miR-5001-5p bound to the MNK2a 3' UTR region and inhibited the activation of the p38 MAPK pathway. Our results provide novel insights into the molecular mechanism by which TNF-α promotes epithelial–mesenchymal transition in TNBC through the TNF-α–miR-5001-5p–MNK2a–p38 MAPK signaling axis, eventually enhancing the invasive and metastatic potential of TNBC. We discovered a novel mechanism of invasion and metastasis in TNBC whereby TNF-α upregulated the expression of miR-5001-5p, which downregulated MNK2a by binding to its 3' UTR region. This inhibited the activation of the p38 MAPK pathway, following which MNK2a promoted epithelial–mesenchymal transition in TNBC. This mechanism offers a theoretical basis for TNBC-targeted therapy and also serves as a novel therapeutic target.

overall_design: Cell lines transfected with mimic and control cell lines were sent for transcriptome sequencing in order to find key downstream target genes and related pathways


title: Next Generation Sequencing of BAT Transcriptomes in young and aged mice

city: Osaka

first: Yung-Ting

last: Hsiao

address: 6-1 Kishibe-Shimmachi, Suita

institute: National Cerebral and Cardiovascular Center

summary: To investigate the mechanism in BAT in young and aged male mice, we performed RNA-seq analysis with BAT tissue from 12-13 weeks of age and 79 weeks of age mice.

overall_design: BAT tissue were collected from 12-13 weeks of age mice and 79 weeks of age mice, and were generated by RNA-seq using Illumina NextSeq500.


title: Global transcription factors analyses reveal hierarchy and synergism of regulatory networks and master virulence regulators in Pseudomonas aeruginosa 2

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: The transcription factor regulatory network (TRN) in Pseudomonas aeruginosa is complicated and involves multiple regulators responding to various environmental signals and physiological cues by regulating gene expression. P. aeruginosa utilizes versatile virulent determinants to exert its virulence, including biofilm formation, quorum sensing (QS), Type III (T3SS) and Type IV (T6SS) secretion system, motility, siderophore production, oxidative stress resistance, and antibiotic resistance, which under the control of TRN. Herein, ChIP-seq was applied to investigate the binding sites of 158 TFs in P. aeruginosa PAO1 strain. The results revealed a total of 30,481 significant binding peaks in the genome, more than half of which were located in the promoter regions. To furthermore decode diverse regulatory relationships among TFs, the hierarchical network was assembled into three levels: top, middle, and bottom. Thirteen ternary regulatory motifs revealed flexible relations of TFs in small hubs, and a comprehensive co-association atlas was established and enriched three high-associated clusters. A total of 32 TFs were identified as master regulators in regulating virulence-related pathways, and 34 TFs were involved in four metabolism pathways significantly. These results will provide significant insight into understanding the pathogenesis mechanisms of P. aeruginosa and relevant bacteria and contributing to developing effective therapies for diseases caused by infection.

overall_design: ChIP-seq analyses of genomic regulators in Pseudomonas aeruginosa

first: X

last: Deng


title: Substained DNA demethylation and discordant chromatin accessibility dynamics define enhancer regulation during neural progenitor cell differentiation [ATACme]

city: Nashville

first: Lindsey

last: Guerin

state: Tennessee

address: 2215 Garland Ave, 673B Light Hall

department: Biochemistry

institute: Vanderbilt University

summary: Epigenetic mechanisms govern the transcriptional activity of lineage-specifying enhancers; but recent work challenges the dogma that both chromatin accessibility and DNA hypomethylation are prerequisites for transcription, highlighting a need to understand their coordinated dynamics. We established a highly-resolved timeline of DNA demethylation, chromatin accessibility, and transcription factor (TF) occupancy during early human cell differentiation. We show >30,000 lineage-specifying enhancers undergo rapid and transient accessibility changes associated with distinct periods of TF expression. By contrast, enhancer DNA methylation changes are prolonged, unidirectional and delayed relative to chromatin dynamics, creating discordant epigenetic states. Using 6-base sequencing to detect methyl-intermediate, 5hmC, revealed that, for a subset of enhancers, TET-mediated, active demethylation begins prior to, and is maintained independently of, TF binding. In fact, machine learning models trained on 5-hydroxymethylation can predict of future chromatin states. Complete demethylation persists long after TF binding and accessibility have dissipated, suggesting that long-lasting hypomethylation of certain enhancers is a historical record of previous activity.

overall_design: Timecourse NPC differentiation with collection of chromain at nine timepoints over 12 days to be used for ATAC-Me-seq

middle: N

first: Emily

last: Hodges


title: Substained DNA demethylation and discordant chromatin accessibility dynamics define enhancer regulation during neural progenitor cell differentiation [scRNAseq]

overall_design: Timecourse NPC differentiation with collection of single cells at three timepoints over 6 days to be used for scRNA-seq

last: Lau

first: Alan

last: Simmons

first: Yilin

last: Yang


title: Twist1-induced suppression of oncogene-induced senescence in non-small cell lung cancer requires the transactivation domain of Twist1

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

summary: Non-small cell lung carcinoma (NSCLC) is a major cause of cancer mortality. High expression of the epithelial-to-mesenchymal transition transcription factor (EMT-TF) Twist1 is strongly associated with metastatic cancers and with treatment resistance. Twist1 can also upregulate O-GlcNAcylation to suppress fail-safe programs such as KrasG12D oncogene-induced senescence (OIS) that accelerates NSCLC tumorigenesis. We wanted to decipher the critical domains and transcriptional targets required for Twist1 acceleration of lung tumorigenicity. We created a novel genetically-engineered mouse model for autochthonous lung cancer through lung epithelial expression of KrasG12D oncogene (CR) concomitantly with Twist1wt (CRT) or a Twist1F191G transactivation-null mutant (CRF191G). Compared to CR and CRF191G, CRT mice had shorter tumor-free survival and more aggressive tumors histologically. CRT lung tumors also showed higher proliferation and lower cell-cycle arrest suggesting that the Twist1 transactivation-domain is important for OIS suppression. Supporting these data, we observed in non-cancer human bronchial epithelial cells (HBECs) that the co-expression of human TWIST1wt enhanced tumorigenic/invasive programs and could suppress HRasG12V-induced senescence while co-expressing TWIST1F187G transactivation-null mutant could not. TWIST1wt co-expression with HRasG12V in HBECs differentially modulated MYC downstream transcriptional programs. Finally, OIS induction in HBEC-HRasG12V-TWIST1wt was rescued by O-GlcNAcylation inhibition or by treatment with a novel MYC inhibitor MYCi975. Altogether, these results indicate that the Twist1 transactivation domain is required for Twist1-dependent acceleration of lung tumorigenesis via MYC and nominate MYCi975 as a means to activate latent OIS programs. MYC targeting strategies could limit pro-tumorigenic programs and serve as a therapeutic for TWIST1-overexpressing NSCLCs.

overall_design: Structure-functions studies of TWIST1 domains may allow for more precise targeting of pro-oncogenic downstream transcriptional programs/targets involved in NSCLC aggressiveness. TWIST1 is a pleiotropic basic helix-loop-helix (bHLH) transcription factor that can activate or repress E-box-regulated target genes. TWIST1 contains four main domains: (1) an amino-terminal Twist domain, (2) a glycine-rich region domain, (3) a bHLH domain responsible for DNA binding and dimerization, and (4) a highly conserved carboxy-terminal Twist-box domain responsible for transactivation of gene targets. In the present study, we set out to determine whether the transactivation function of TWIST1 was important for the acceleration of tumorigenesis in NSCLC, and we developed and characterized a novel genetically-engineered mouse model (GEMM) of KrasG12D-driven lung tumors that also overexpresses mouse Twist1wt or Twist1 transactivation-null point mutant (phenylalanine 191 to glycine - F191G). We complemented these GEMM experiments with in vitro human bronchial epithelial cell (HBEC) models co-overexpressing HRasG12V along with human TWIST1wt or TWIST1 transactivation-null point mutant (phenylalanine 187 to glycine - F187G).   We used RNA sequencing analyses on HBEC expressing or not Twist1wt or Twist1F87G and co-expressing HRasG12V-EGFP or EGFP to determine differentially expressed genes and programs between the different conditions.

first: Audrey

last: Lafargue

first: Hailun

last: Wang

first: Sivarajan

middle: T

last: Chettiar

first: Rajendra

last: Gajula

first: Amol

middle: C

last: Shetty

first: Yang

last: Song

first: Brian

middle: W

last: Simons

first: Triet

last: Nguyen

first: Christine

last: Lam

first: Francesca

middle: A

last: Carrieri

first: Caleb

last: Smack

first: Nick

last: Connis

first: Dipanwita

last: Dutta Chowdhury

first: Jinhee

last: Chang

first: Danielle

last: Council

first: Katriana

last: Nugent

first: Ismaeel

last: Siddiqui

first: Kekoa

last: Taparra

first: Mohammad

last: Rezaee

first: Natasha

last: Zachara

first: Zachary

last: Morris

first: Christopher

last: McFarland

first: Sarki

last: Abba Abdulkadir

last: Hann

first: Phuoc

last: Tran


title: SNX10 deficiency confers resistance to anti-HER2 antibody-drug conjugates via regulating endosomal trafficking

city: Shanghai

first: Keda

last: Yu

address: 270 Dongan road

institute: Fudan university Shanghai cancer center

summary: Antibody-drug conjugates (ADCs) are a rapidly developing therapeutic approach in cancer treatment that has shown remarkable efficacy in breast cancer. Despite the promising efficacy of anti-HER2 ADCs, many patients are still experiencing disease progression under treatment. Here, by analyzing the transcriptome data from patient-derived organoid models, I-SPY2 trial, and resistant cell lines, we identified that SNX10 deficiency conferred anti-HER2 ADCs resistance. Low levels of SNX10 attenuated HER2 recycling and promoted HER2 trafficking into lysosomes. We also noticed that the lack of interaction between SNX10 and the transcription factor STAT1 inhibited its activation, while STAT1 binds to the promoter region of RAB11A and regulates its transcription. Thus, the lack of SNX10 inhibited HER2 recycling by downregulating RAB11A, decreased cell-surface HER2, and caused anti-HER2 ADC resistance.

overall_design: This study analyzed the transcriptome data from patient-derived organoid models, I-SPY2 trial, and resistant cell lines to explore the underlying mechanisms of anti-HER2 ADC resistance.


title: Paneth cell SIRT1 deficiency protects against DSS-induced colitis

city: Durham

first: HAMED

last: BOSTAN

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: Paneth cells, intestine-originated innate immune-like cells, are important for maintenance of the intestinal stem cell niche, gut microbiota, and gastrointestinal barrier.  Dysfunctional Paneth cells under pathological conditions are a site of origin for intestinal inflammation. However, mechanisms underlying stress-induced Paneth cell dysregulation remains unclear. We have previously reported that deletion of SIRT1 in the intestinal epithelium (SIRT1 iKO) leads to hyperaction of Paneth cells along with an increased sensitivity to Dextran sodium sulfate (DSS)-induced colitis. We recently generated a Paneth-cell specific SIRT1 KO mouse model (SIRT1 PKO). Similar to mice with SIRT1 iKO mice, SIRT1 PKO mice had increased abundance as well as hyperactivation of Paneth cells in vivo and in cultured intestinal organoids. However, in contrast to the hypersensitivity of SIRT1 iKO mice to chemical- or age-induced inflammation, SIRT1 PKO mice were protected from Dextran sodium sulfate (DSS)-colitis.

overall_design: Nine-month old Flox control and SIRT1 PKO female mice were challenged with a chronic colitis model by feeding mice with two cycles of 7-day 2.5% DSS drinking water separated by a 14-day regular water break. Body weights and rectal bleeding were monitored daily during the DSS treatment and one week immediately after DSS treatment. According to the animal protocol, mice with more than 20% loss of their initial body mass were sacrificed during the experiments.

first: Alicia

last: Wellman

first: Ming

last: Ji

first: Xiaoling

last: Li

first: Hamed

last: Bostan


title: Substained DNA demethylation and discordant chromatin accessibility dynamics define enhancer regulation during neural progenitor cell differentiation [6base]

first: Lindsey

last: Guerin

overall_design: Timecourse NPC differentiation with collection of genomic DNA at three timepoints over 8 days to be used for evoC 6-base-seq

first: Emily

last: Hodges


title: Substained DNA demethylation and discordant chromatin accessibility dynamics define enhancer regulation during neural progenitor cell differentiation [RNAseq]

overall_design: Timecourse NPC differentiation with collection of RNA at nine timepoints over 12 days to be used for RNAseq


title: Generation of mandibular prominence ectomesenchyme (mdEM) from human induced pluripotent stem cell (iPSC)-derived neural crest cell (NCC) aggregates

city: Kyoto

first: Makoto

last: Ikeya

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

institute: Kyoto University

summary: To clarify the changes in cell properties during the differentiation process from iPSCs into mdEM through NCC aggregates, we sampled iPSCs and cell aggregates during the differentiation process and compared gene expression patterns.

overall_design: RNA sequencing profiles of 1231A3 iPSCs, NCC aggregates (day 5), and mdEM (day 9).

first: S

last: Motoike

first: M


title: Methotrexate affects brain development by regulating serum-glucocorticoid inducible protein kinase 3 (SGK3) signal pathway in brain organoids.

city: Deajoen

first: Onju

last: Ham

address: 141 Gajeong-ro

institute: Korea Institute of Toxicology

summary: Neurological toxicity, including brain atrophy, is a commonly observed side effect of chemotherapy, often referred to as "chemotherapy brain," particularly prevalent among young cancer patients with developmental disorders. Methotrexate (MTX), a widely used chemotherapeutic reagent and immunosuppressive medication, is associated with a spectrum of adverse effects. While many researchers have highlighted neurotoxic-related issues in both cancer patients and animals treated with MTX, the mechanism of chemotherapy's impact on brain development, including in children or fetuses, remains poorly understood. In this study, we investigate the effects of MTX exposure on brain cortical organoids (COs), three-dimensional in vitro models designed to mimic human cortex development. Our primary objective is to assess their potential for exhibiting developmental toxicity when exposed to MTX. We observed a significant decrease in both the size and viability of COs morphologically and statistically after MTX exposure (MTX COs) on day 45 of differentiation. Additionally, compared with control COs, the MTX COs showed increased expression of immature neuron and GABAergic neuron-related genes. Furthermore, we detected a significant increase in intracellular ROS levels and the expression of ER-stress, cell cycle, and DNA damage-related genes in MTX COs. The expression of the apoptosis-related protein, cleaved caspase-3, was also significantly elevated in the MTX COs. Moreover, through RNA sequencing analysis, we found a significant decrease in SGK3 (serum/glucocorticoid-regulated kinase family member 3), a regulator gene of proliferation, in MTX COs. Consequently, our findings suggest that MTX could impact cortex development in the brain by increasing intracellular ROS and ER stress, ultimately inducing apoptosis, possibly through the inhibition of the SGK3 pathway. Understanding the developmental neurotoxicity of MTX in brain COs is crucial, as it provides valuable insights into the risk factors associated with prenatal exposure to the drug.

overall_design: To assess the effects of MTX, brain organoids were differentiated from human embryonic stem cells, specifically H9 cells. A concentration of 0.5uM MTX was administered to the organoids on day 16 of differentiation, with treatments repeated every other day until sample harvest

first: Soontag

last: Jung

first: Wook-Joon

last: Yoo


title: The expression of regional markers in neural crest cell (NCC) aggregates treated with or without retinoic acid (RA).

summary: To evaluate the anterior-posterior axial identity of the NCC aggregates, we prepared aggregates treated with RA to induce posterior fates as a positive control and compared gene expression patterns among the aggregates.

overall_design: RNA sequencing profiles of 1231A3 iPSCs, day 5 aggregates, CD271high-sorted NCCs from day 5 aggregates, and RA-treated day 5 aggregates.


title: Gene expression in wildtype and Prxl2a knockout mouse

city: Dongguan

first: XUERONG

last: SUN

state: Guangdong Province

address: No. 1 Xincheng Avenue, Songshan Lake District

institute: Guangdong Medical University

summary: The function of Prxl2a gene is still not fully understood. To provide some new clues to investigate the function of Prxl2a, we collected multiple tissues from wildtype and homozygous Prxl2a knockout mice, including subcutaneous inguinal adipose tissue (IAT), dorsal brown adipose tissue (BAT), brain and liver tissue, and performed RNA-seq.

overall_design: The female wildtype and Prxl2a knockout mice in 12 weeks age were prepared. Each group contained 3 mice. Before tissues extraction, the mice were systematically perfused with PBS solution to remove the whole-body blood. Then IAT, BAT, brain and liver tissue were excised and fast cryopreserved with liquid nitrogen before RNA-seq.

first: Xuerong

last: Sun

first: Songbang

last: Ou

first: Jingyu

last: Lou

first: Jiayi

last: Ma

first: Xinxin

last: Yang


title: Gene sequencing analysis of mouse airway smooth muscle cells in co-culture environment with mouse airway epithelial cells and mouse smooth muscle cells in non-co-culture environment

city: 深圳

first: Yilun

last: Liu

state: Guangdong

address: 深圳市福田区深圳北京大学香港科技大学医学中心

institute: Shenzhen PKU-HKUST Medical Center

summary: Airway epithelial cells can promote the proliferation of airway smooth muscle cells in an undisturbed environment. We isolated airway epithelial cells and airway smooth muscle cells in mice and conducted co-culture experiments. The results showed that the proliferative phenotype of airway smooth muscle cells was significantly changed by co-culture of  epithelial cells after five day. Therefore, we conducted gene sequencing for ASMC in the co-culture group and ASMC in the non-co-culture group after 5 days of culture. The results show that Wnt pathway related genes are activated in ASMC, and the activation of this pathway may be the main reason why AEC stimulates the proliferation of ASMC

overall_design: In order to investigate the cause of smooth muscle proliferation phenotype, we co-cultured smooth muscle cells with epithelial cells in the experimental group and no epithelial cells in the control group, and then sent three samples of ASMC cells from each of the two groups for sequencing

first: Jiana


title: Time course gene expression pattern during neural crest cell (NCC) differentiation from induced pluripotent stem cells (iPSCs) in three-dimensional (3D) conditions

summary: To clarify the changes in cell properties during the differentiation process from iPSCs into NCC aggregates, we sampled iPSCs and each cell aggregate during the differentiation process and compared gene expression patterns.

overall_design: RNA sequencing profiles of 1231A3 iPSCs, cell aggregates at days 1-5, CD271high+ NCCs sorted from day 5 aggregates, and CD271high+ NCCs sorted from two-dimensional (2D) induction protocols.

first: D

last: Kamiya


title: 4D marmoset brain map reveals MRI and molecular signatures for onset of multiple sclerosis-like lesions [snRNA-seq]

city: Bethesda

first: Daniel

last: Reich

state: Maryland

address: 10 Center Drive Bldg 10 Rm 5C103

department: NINDS

institute: NIH

summary: Abstract: The cellular and molecular dynamics of multiple sclerosis (MS) lesion development and repair cannot be inferred through study of postmortem tissue harvested decades after lesion onset. Employing MRI-informed spatiotemporal RNA profiling and experimental autoimmune encephalitis (EAE) in the common marmoset — a faithful model for these processes — we identified five microenvironmental groups pertinent to neural function, immune and glial responses, tissue destruction and repair, and regulatory networks at brain borders during lesion evolution. Before visible demyelination, astrocytic and ependymal secretory signals delineated perivascular and periventricular regions, later becoming demyelination hotspots where MS-like lesions frequently grow. An MRI biomarker, the ratio of proton density-weighted signal to T1 relaxation time, captured the hypercellularity phase before apparent myelin destruction. At lesion onset, there was a global shift in cellular connectivity, especially in extracellular matrix-mediated signaling. Early responses included microglia and oligodendrocyte precursor cell proliferation and diversification, replaced by monocyte derivatives and lingering lymphocytes as lesions aged. Concurrent with demyelination, reparative signaling modules were found at the lesion edge as early as 10 days post-lesion establishment. Over-representation of senescence-associated secretory phenotype at the brain borders and the formation of concentric glial barriers at the lesion edge prompted model-based identification of potential treatments to reverse EAE-associated molecular pathology. Our study highlights the marmoset platform's potential for assessing MS treatment outcomes.

overall_design: From 11 marmosets, we derived a transcriptomic map with spatial and single-nucleus resolution and studied the heterogeneity of tissue damage at an individual lesion level. We developed a 10x Visium-compatible staining protocol to quantitatively integrate 16 regions of interest (ROI) and spatiotemporally dissect the significance of focal and global molecular changes as lesions evolve. Mapping the temporal sequence of cellular and molecular changes during lesion evolution, we retrospectively estimated lesion age through serial MRI (Methods). To pinpoint the cellular source of spatially resolved signals, we integrated single-nucleus RNA-seq (snRNA-seq) libraries (n = 43) from 8 animals with spatial transcriptomes (ST) (n = 16 ROI) from 6 animals. WM from healthy control (n = 13) and WM with T2-hyperintense demyelinated MRI features from EAE animals (n = 14) were the most extensively sampled groups. We used additional categories, including normal-appearing WM from EAE animals (n = 2), Gd-enhancing demyelinating WM lesions (n = 2), and resolved WM lesions that were no longer T2-hyperintense on the terminal MRI (n = 3), to group the remaining WM samples. In parallel, we included leukocortical T2-hyperintense lesions (n = 2) along with matching healthy (n = 2) and normal-appearing (n = 1) control tissue, and abnormal-appearing lateral geniculate nucleus tissue on MRI (n = 2) along with matching healthy control tissue (n = 2), to explore tissue-specific and shared responses. We implemented a hierarchical workflow comparing across cell classes (Level 1 analysis, L1) and cell clusters within a class (Level 2 analysis, L2) to better realize the source of each profile change.

first: Jing-Ping

last: Lin

first: Alexis

last: Brake

first: Maxime

last: Donadieu

first: Amanda

last: Lee

first: Riki

last: Kawaguchi

first: Pascal

last: Sati

middle: H

last: Geschwind

first: Steven

last: Jacobson

first: Dorothy

last: Schafer


title: Metabolic dysfunction mediated by HIF-1α contributes to epithelial differentiation defects in eosinophilic esophagitis. [HIF1A-KD]

city: Maynooth

first: Joanne

middle: Carol

last: Masterson

address: Biomedical Sciences Building, Maynooth University

department: Biology

country: Ireland

institute: Maynooth University

summary: Investigating the contributory role that epithelial cell metabolism plays in allergic inflammation is a key factor to understanding what influences dysfunction and the pathogenesis of the allergic disease eosinophilic esophagitis (EoE). Herein, we sought to define the role of HIF-1α-mediated metabolic dysfunction in esophageal epithelial differentiation processes and barrier function in EoE. In RNA-sequencing derived from EoE patient biopsies, we observed the expression pattern of key genes involved in mitochondrial metabolism/oxidative phosphorylation (OXPHOS) and glycolysis. Bioenergetics analysis using Seahorse was performed on EPC2-hTERT cells to decipher the metabolic processes involved in epithelial differentiation processes. In addition, air-liquid interface cultures were employed to delineate metabolic dependency mechanisms required for epithelial differentiation. Transcriptomic analysis identified an increase in genes associated with OXPHOS in patients with EoE. Bioenergetic analysis in vitro revealed thatdifferentiated epithelium was less reliant on OXPHOS compared withundifferentiated epithelium. Increased OXPHOS potential and reduced glycolytic capacity was mirrored in HIF1A-knockdown EPC2-hTERT cells which portray a significant absence of terminal markers of epithelial differentiation, including involucrin. Pharmacological glucose transport inhibition phenocopied this, while rescue of the HIF-1α-deficient phenotype using the pan-prolyl hydroxylase inhibitor DMOG resulted in restored expression of epithelial differentiation markers. An OXPHOS-dominated metabolic pattern in EoE patients, brought about largely by the absence of HIF-1α-mediated glycolysis, is linked with the deficit in esophageal epithelial differentiation.

overall_design:
Stable esophageal epithelial (EPC2-hTERT) cell lines were generated with a lentiviral-mediated shRNA HIF1A knockdown (HIF1A-KD) and shRNA controls (shCtrl).
To investigate changes in gene expression in functional epithelial processes, shCtrl and HIF1A-KD cells were cultured in 3D-air-liquid interface cultures.
RNA-seq was performed using these samples and comparative gene expression profiling of RNA-seq data was carried out.

first: Sinéad

last: Ryan


title: CD73 enhances hepatic Treg functions by enzymatic and non-enzymatic pathways in NAFLD development [RNA-Seq]

city: beijing

first: xinjie

last: zhong

address: No. 95 Yong 'an Road

institute: Beijing Friendship Hospital

summary: Regulatory T cells (Treg) have a critical role in immunosuppression to delay the course of NAFLD, and CD73 is known as a functional molecule highly expressed by Treg. However, the role and the mechanism of CD73 modulating Treg in the pathogenesis of NAFLD is still unknown.

overall_design: To investigate the role of CD73 on Treg in the progression of NAFLD, Treg from liver tissue of WT and CD73 KO mice which were fed with NCD (normal control diet) or MCD (methionine/choline-deficient diet) were performed transcript sequencing analysis.

first: Hua

last: Jin

first: Xinjie

last: Zhong

first: Guangyong

last: Sun

first: Dong

last: Zhang


title: Mitochondrial carrier SLC25A19 is required for respiratory chain function

city: Haining, Zhejiang Province

first: Zongsheng

last: Jiang

state: Select if applicable

address: Haizhou East Road, Haining, Zhejiang province

department: Zhejiang University-University of Edinburgh Institute

institute: Zhejiang University

summary: In this study, we investigate how mitochondrial thiamine pyrophosphate (TPP) transporter SLC25A19 regulates mitochondrial function and cell metabolism.

overall_design: We performed CRISPR-cas9 to knock out SLC25A19 in K562 cells using two different sgRNAs. Two knockout cell lines, SLC25A19-sg1 and SLC25A19-sg2, were selected and further used for phenotype analysis. We also used K562 cells with Non-targeting control sgRNA as a reference. RNA was collected after 48 h of culturing, and each cell line was performed in triplicate.


title: Isogenic iPSC-derived proximal and distal lung-on-chip models reveal tissue and virus-specific immune responses in human lungs [Airway Top]

city: Nishkyo ward

first: Ryuji

last: Yokokawa

state: Kyoto

address: Kyotodaigaku-katsura, Nishikyo-ku, c2N06, C cluster, Micro Biosystems Laboratory

department: Department of Microengineering

summary: MPS (Micro-physiological systems) are foreseen to play a crucial role in preclinical studies, particularly for future viral pandemics. However, the development of an MPS is often hindered by the shortage of reliable cell sources, especially different organs/tissues from a single patient to compare the host immune response. Here, we developed a human airway-on-chip and an alveolus-on-chip model using induced pluripotent stem cell (iPSC)-derived isogenic lung progenitor cells. Both chips showed replication of two different respiratory viruses, SARS-CoV-2 and Influenza virus, related cellular damage, and innate immune response on-chip. We report differential immune response against SARS-CoV-2 between the proximal and distal lung on-chip models. Airway chips elicit a robust IFN-dependent immune response whereas alveolus chips exhibit a dysregulated IFN activation but a significantly upregulated chemokine pathway. On the other hand, Influenza virus infection elicits an immune response and cellular damage of higher magnitude in both chips in comparison to SARS-CoV-2. The results show potential of the iPSC-derived lung-on-chip models to rapidly understand viral pathology and screening drugs for future pandemics.

overall_design: This study examined host transcriptome on-chip of hiPSC-derived airway epithelial cells following SARS-CoV-2 and IAV infection in respective chips at 3 days post infection

first: Sachin

last: Yadav

first: Kazuya

last: Fujimoto

first: Toru

last: Takenaga

first: Senye

last: Takahashi

first: Yukiko

last: Muramoto

first: Ryuta

last: Mikawa

first: Takeshi

last: Noda

first: Shimpei

last: Gotoh


title: Isogenic iPSC-derived proximal and distal lung-on-chip models reveal tissue and virus-specific immune responses in human lungs [Alveoli Top]

overall_design: This study examined host transcriptome on-chip of hiPSC-derived alveolus epithelial cells following SARS-CoV-2 and IAV infection in respective chips at 3 days post infection


title: Isogenic iPSC-derived proximal and distal lung-on-chip models reveal tissue and virus-specific immune responses in human lungs [Airway Bottom]

overall_design: This study examined host transcriptome on-chip of HUVECs in an airway-on-chip model following SARS-CoV-2 and IAV infection in respective chips at 3 days post infection


title: Isogenic iPSC-derived proximal and distal lung-on-chip models reveal tissue and virus-specific immune responses in human lungs

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

overall_design: Refer to individual Series


title: Effects of adipocyte ablation on RPE/choroid complex in mice

city: St. Louis

first: Ryo

last: Terao

state: MO

address: 517 S. Euclid Ave

department: Ophthalmology & Visual Sciences

institute: Washington University School of Medicine in St. Louis

summary: Adipocytes are essential for mainteining homeostatic status of multiple organs.  Here we report that adipocytes ablation leads to pro-inflammatory state of retinal pigent epithelium/choroid complex in the eye.

overall_design: iDTR (iDTR (C57BL/6-Gt(ROSA)26Sortm1(HBEGF)Awai/J) mice expressing adiponectin-Cre were treated with intraperitoneal injection of diphtheria toxin every day for 7 weeks.  RPE/choroid complex samples were collected from eyes.

first: Rajendra

last: Apte

first: Mitsukuni

last: Yoshida


title: Transcriptional profiles of ageing human pulmonary blood vessel endothelial cells after their exposure to human serum from healthy donors and idiopathic pulmonary fibrosis patients

city: Hull

first: Eamon

middle: Connor

last: Faulkner

address: Cottingham Road

department: Centre for Biomedicine

institute: University of Hull

summary: Human pulmonary microvascular endothelial cells (HPMEC) from older individual are considered a homogenous population in culture. We used single cell RNA sequencing (scRNAseq) to analyse transcriptional profiles of these cells in culture

overall_design: HPMEC were purified using magnet assisted cell sorting (MACS) to remove PDPN-positive human pulmonary lymphatic vessel endothelial cells (HPLEC), leaving PDPN-negative human pulmonary blood vessel endothelial cells (HPBEC). The HPBEC were then cultured using human serum from healthy donors and idiopathic pulmonary fibrosis patients to assess disease-associated changes in transcriptional profiles of these cells.

first: Adam

last: Moverley

first: Markus

last: Queisser

first: Simon

last: Hart

first: Leonid

last: Nikitenko


title: Isogenic iPSC-derived proximal and distal lung-on-chip models reveal tissue and virus-specific immune responses in human lungs [Alveoli Bottom]

first: Ryuji

last: Yokokawa

overall_design: This study examined host transcriptome on-chip of HUVECs in an alveolus-on-chip model following SARS-CoV-2 and IAV infection in respective chips at 3 days post infection


title: Mitochondrial Daed disambiguates Zuc endonucleolysis in Piwi-piRISC production to optimize its function in transposon repression

city: Bunkyo-ku,

first: Yuica

last: Koga

state: Tokyo

address: Faculty of Science Bldg.3, Rm126, 2-11-16 Yayoi,

department: Biological Sciences

institute: The University of Tokyo

type: Non-coding RNA profiling by high throughput sequencing

summary: In Drosophila ovarian somatic cells, Piwi and piRNA assemble Piwi-piRISC and protect the genome against transposons. The Piwi-piRISC precursor is produced in Yb bodies and translocates with Armi to mitochondria for Zuc-dependent maturation. Daed features in this maturation phase, but the details remain unclear. Here, we show that Daed stabilizes its partner Gasz through protein?protein interaction, and tethers Armi to mitochondria to allow Zuc to process substrates. Daed binds to Armi through two regions: the first ?-helix in the extended coiled-coil domain, which interacts with Armi?s N-terminus, and the SAM domain, which interacts with Armi?s UPF1-like helicase domain. Inhibition of the former interaction abolishes Piwi-piRISC generation. When the latter interaction is disrupted, Zuc obscures cleavage positions and Piwi-bound piRNAs elongate atypically. Consequently, Piwi-piRISC?s level is reduced, leading to transposon derepression. Thus, it is Daed that disambiguates Zuc cleavage in orchestrating with Gasz and Armi to optimize Piwi-piRISC production and its function.

overall_design: 12 smRNA-seq libraries (4 different samples with triplicates): PIWI-associated small RNA libraries were prepared from small RNAs associated with Piwi immunoprecipitates.

first: Sigeki

last: Hirakata

first: Mayu

last: Negishi

first: Hiroya

last: Yamazaki

first: Mikiko

last: Siomi


title: SINE-MIR enhancer rewiring by Esrrb architecturally reprogram the pluripotency spectrum [RNA-Seq 2]

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: Bulk RNA-seq were performed during EPSC differentiation to 3dESC

first: N

middle: O

last: Cipta

first: Y

first: H

last: Li

last: Loh


title: ADSC gene expression tendency depends on the medium which was used during cultivation

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Life and Environmental sciences

institute: University of Tsukuba

summary: The effect of culture media to the cultivated cells are not well understood. We evaluated to visualize the medium effects, related with signal pathways and gene expression tendencies by comprehensive gene analysis. The microarray analysis was conducted by using RNAs extracted from adipose derived stem cells in five independent media sets.

overall_design: Four types of xenofree MSC media were selected and used to cultivate ADSCs. These names of media were randomly anonymized and labeled as medium A, B, C and D in the quantitative results, to compare the other cell potency assay results.The actual names of media are listed without particular order; StemPro MSC SFM Xenofree Medium (Gibco/Thermo Fisher), KBM ADSC-4 (Kohjin-Bio), MesenCult ACF Plus culture Kit (STEMCELL technologies) and Cellartis MSC Xeno-Free Culture Medium (Takara Bio Europe AB). A growth-factor containing MSC medium, MesenPRO (MP), was also used to compare with these xenofree media. After cultivation with these media, cells were harvested and total RNAs were extracted from the cells. MSCGM condition(Sample 10 and 11)was a candidate condition as a positive control in this study, but we desided not to use this condition after evaluation because of its high variability in the tube formation assay results.

first: SongHo

last: Moon


title: DNA mutagenesis driven by transcription factor competition with mismatch repair

first: Raluca

last: Gordan

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

sample_organism:
Saccharomyces cerevisiae
Homo sapiens
synthetic construct


summary: The distribution of somatic mutations across the genome is not uniform. Recently, an unexpected pattern of hyper-mutation was reported at binding sites of transcriptional regulatory factors (TFs). In some human cells, a decrease in DNA repair activity was also observed at TF binding sites, leading to the hypothesis that TFs may increase mutagenesis by interfering with the recognition of DNA lesions by repair enzymes, and thus inhibiting repair. However, direct proof of this surprising TF-induced mutagenesis mechanism is lacking. Here, we show that TF binding to DNA mismatch lesions leads to increased mutation rates at TF binding sites by reducing the efficiency of lesion recognition by MutSα, the main enzyme that initiates mismatch repair in eukaryotic cells. We developed a yeast mutagenesis assay to directly observe the accumulation of mutations in a TF binding site. Upon TF overexpression, the binding site exhibited an increased mutation rate, specifically for mutations resulting from mismatches where the TF strongly reduced MutSα binding in vitro. This trend was amplified in cells with an increased rate of misincorporation errors, and it was not observed in mismatch repair-deficient cells. Analyses of human cancer somatic mutation data revealed a pattern similar to that observed in yeast, with mutations resulting from TF-bound mismatches being specifically enriched in mismatch repair-proficient tumors. Taken together, our results demonstrate that in addition to their well-known roles in gene regulation, TFs also play a role in DNA mutagenesis, by directly interfering with the repair of replication errors. Since a majority of cancer mutations originate from unrepaired replication errors, most commonly mismatches, our results suggest that TF interference with mismatch repair will shape the mutation landscape of regulatory DNA in cancer genomes.

overall_design: Competition DNA-binding experiments were performed for yeast MutS⍺ and yeast TF Cbf1, and human MutS⍺ and human TF MYC. Briefly, we designed DNA sequences to form a stem-loop structure that incorporates mismatched base pairs in the stem, and the DNA molecules were synthesized on an Agilent microarray. Then we measured the binding of MutS⍺ to the DNA, either by itself or under direct competition from Cbf1 or MYC. We also measured the binding of Cbf1 and MYC by themselves. For each Watson-Crick and mismatch-containing sequence except for the random sequences, ten replicate spots were used in each chamber, randomly distributed across the microarray surface. For the 200 random DNA sequences, five replicate spots were used. We report the PBM signal intensity of yeast MutS⍺, Cbf1, human MutS⍺, or MYC for each spot.