title: Splicing factor CWC22 prevents tetraploidy formation and mitotic slippage through maintenance of the BubR1 expression and CDK1 activity

first: Ryuzaburo

last: Yuki

address: 5 Misasagi-Nakauchi-cho, Yamashina-ku

institute: Kyoto Pharmaceutical Univeristy

summary: Splicing factors play a fundamental role in the process of gene expression. Several splicing factors are highly expressed in cancers and promote the proliferation. Although targeting of splicing factors prolong the duration of G2 phase and mitosis, the involvement of splicing factors in regulation of cell ploidy remains unclear. In this study, we found that knockdown of CWC22, a splicing factor, increased not only the population of G2 phase and mitosis but also tetraploid cells. Notably, CWC22 knockdown induces mitotic slippage, which exhibits rapid mitotic exit without SAC satisfaction after prolonged prometaphase duration. CWC22 knockdown led to cyclin B1 degradation and accumulation of inactive CDK1 having the inhibitory phosphorylation at Tyr15 in mitosis. The cyclin B1 overexpression and Wee1 blockage mitigated the shortage of mitotic duration by CWC22 knockdown. RNA-seq analysis indicated that CWC22 knockdown down-regulated SAC-regulatory genes, including BubR1. The shortage of mitotic duration caused by CWC22 knockdown was also mitigated by both overexpression of BubR1 and Wee1 blockage. Furthermore, CWC22 was highly expressed in pancreatic or cervical cancers, and the higher expression negatively correlated with patients’ prognosis. CWC22 knockdown induced cancer cell death after miotic slippage and prolonged G2 phase due to DNA damage accumulation. These results suggest that CWC22 not only supports proper progression of G2/M phase but also prevents mitotic slippage and tetraploid cell formation via regulation of checkpoint signaling by contributing to the proper expression of BubR1 and the CDK1 activity. These findings reveal a novel splicing factor function in genome stability.

overall_design: 4 RNA-seq samples were analyzed. 2 controls samples, 2 samples with shRNA depletion of CWC22.

first: Youhei

last: Saito

first: Yuji

last: Nakayama


title: Mutant p53 binds RNA to drive mitochondrial dysfunction [CLIP-seq]

status: Public on Nov 25 2025

city: Jupiter

first: Wuyue

last: Zhou

address: 110 Scripps Way

country: USA

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

summary: Tumor suppressor protein 53 (p53) is a transcription factor that is deregulated in 50% of cancers. Often termed the guardian of the genome, p53 is responsible for maintenance of genomic stability, cell cycle arrest, DNA repair, senescence, and apoptosis. In cancer cells, deregulation of p53 often occurs through mutations in the DNA binding domain which lead to a loss of the transcriptional activity. While 100’s of somatic mutations in the DNA binding domain are known, a small number of mutants are enriched in cancer, suggesting a gain-of-function role. Here we deploy an intein-based approach to localize µMap photoproximity labeling to p53 to define novel interactions contributing to the loss and gain of function roles of 5 separate hotspot mutants. These data revealed that G245S and R273H binds to RNA through its C-terminal domain. We show through CLIP experiments that mutant p53 has an RNA binding motif that conserved across mutants and is enriched in 3’UTRs, promoting ribosomal localization and labeling of proteins at the mitochondrial surface. We further demonstrate that the RNA binding ability of mutant p53 promotes altered miRNA processing and mitochondrial dysfunction providing mechanistic rationale for historically reported but poorly understood phenotypes.

overall_design: CLIP-seq of p53 bound RNA from HEK cells stably expressing wild-type or mutant p53 constructs. Materials were collected in biological duplicates. HEK cells stably expressing wild-type p53 served as the control.

first: Alice

last: Long

first: Cameron

middle: J

last: Douglas

first: Dalila

last: Gallegos

first: James

middle: M

last: Burke

first: David

last: MacMillan

first: Ezgi

last: Hacisuleyman

first: Ciaran

middle: P

last: Seath


title: Gene expression in wild-type or miR-71 KO animals with or without sodium azide stress

city: St Lucia

first: Steven

last: Zuryn

state: QLD

address: The University of Queensland

country: Australia

institute: Queensland Brain Institute

type: Expression profiling by high throughput sequencing

summary: Kirmes et al. identify the microRNA miR-71, which coordinates the suppression of both cell-autonomous and cell-non-autonomous mitochondrial stress signalling, thereby promoting cellular function under conditions of chronic mitochondrial damage.

overall_design: RNA-seq of whole populations of N2 or MT12993 strains treated with or without sodium azide

first: Ina

last: Kirmes


title: Affymetrix SNP-array data for fetal tissue from recurrent pregnancy loss patients

city: Jiaxing

first: Luming

last: Wang

state: Zhejiang

address: NO.2468 Zhonghuan East Road

country: China

institute: Jiaxing Maternity and Child Health Care Hospital

summary: Background. Recurrent pregnancy loss (RPL) is often associated with genetic factors. This study investigates chromosomal abnormalities in RPL by analyzing copy number variations (CNVs) and single nucleotide variants (SNVs).  Methods. We conducted a retrospective analysis of 400 RPL patients, with 393 successfully analyzed using CNV-seq and SNP-array after excluding maternal cell contamination (MCC). Additionally, 16 families with normal results underwent whole exome sequencing (WES).  Results. Among the patients, 187 (47.6%) showed normal results, while 206 (52.4%) exhibited abnormalities, including 152 aneuploidies (73.8%), 37 CNVs (18.0%), and 17 triploidies (8.3%). Statistical analysis revealed a significant increase in chromosomal abnormalities with advancing maternal age, but no significant differences in rates were observed before 24 weeks of pregnancy in patients with two or more miscarriages. We identified 28 pathogenic (P) / likely pathogenic (LP) CNVs and 6 P / LP SNVs, implicating 808 morbid genes. Enrichment analysis and protein-protein interaction (PPI) network construction revealed 69 key genes in critical pathways, with IL6, TNF, and ACTB as hub genes.  Discussion. These findings contribute to establishing genetic markers for RPL screening in the Chinese population, enhancing our understanding of miscarriage etiology and facilitating prenatal diagnosis.

overall_design: This study analyzed 66 samples (from Recurrent Pregnancy Loss patients with miscarriage at >12 weeks, no maternal cell contamination) using the CytoScan 750K Suite SNP-array platform. No biological/technical replicates, control samples, or reference samples were included; the 66 samples were solely tested via SNP-array to detect chromosomal abnormalities (e.g., CNVs, ROHs) associated with RPL.


title: Mesothelioma location influences the tumour microenvironment and immune checkpoint therapy response in preclinical models

city: Crawley

first: M. Lizeth

last: Orozco Morales

state: WA

address: 35 Stirling Hwy

institute: University of Western Australia

summary: Mesothelioma is a cancer derived from mesothelial cells, most commonly arising from the pleura or the peritoneum. Immune checkpoint therapy (ICT) has shown survival benefit for pleural mesothelioma, but little is known about the response in peritoneal mesothelioma. Most preclinical mesothelioma models involve subcutaneous cancer cell implantation, which lacks the relevant tumour microenvironment of peritoneal mesothelioma and does not resemble the clinical presentation. We therefore set out to explore the influence of location on the mesothelioma tumour microenvironment, comparing pleural, peritoneal, and subcutaneous models using identical cell line-derived syngeneic mesotheliomas. We found that the peritoneal location conferred an anti-inflammatory tumour microenvironment, characterised by low IFN, TNFα, and STAT signalling activity, low immune cell infiltration and a gene signature associated with non-response to ICT. ICT was effective in subcutaneous models, but the same cell line-derived tumours were irresponsive when inoculated intraperitoneally. Together, these findings show that peritoneal location is associated with an immune suppressive tumour microenvironment.

overall_design: RNA-seq profiling of AB1-mCherry mesothelioma tumours (whole tumours and CD45-mCherry+ sorted cancer cells) implanted in three different anatomical locations: pleural, peritoneal, and subcutaneos space, at day 10 after tumour inoculation

first: Mariana Lizeth

first: Sally

last: Lansley

first: Wee Loong

last: Chin

first: Caitlin

last: Tilsed

first: Nicola

last: Principe

first: Connull

last: Leslie

first: Breana

last: Vitali

first: Francois

middle: X

last: Rwandamuriye

first: Emma

last: de Jong

first: Joel

last: Kidman

first: Rachael

last: Zemek

first: Catherine

middle: A

last: Rinaldi

first: Timo

last: Lassmann

first: Anthony

last: Bosco

first: Y C Gary

last: Lee

first: Richard

last: Lake

first: Jonathan

last: Chee

first: Willem Joost

last: Lesterhuis


title: Retinoic Acid treatment of Xenopus laevis foregut endoderm explants during developmental window of NF15-25

city: Cincinnati

first: Aaron

last: Zorn

state: OH

address: 240 Albert Sabin Way, Bld S

department: Developmental Biology

institute: Cincinnati Children's Hospital and Medical Center

summary: To define Retinoic Acid regulated genes in Xenopus laevis foregut endoderm during developmental window of NF15 to NF25, we treated micro-dissected foregut endoderm explants with 3 doses of Retinoic Acid (25nM, 200nM, 500nM) and performed bulk-RNA seq analysis.

overall_design: Foregut endoderm was micro-dissected from wild-type Xenopus laevis embryos at stage NF15 and cultured to stage NF25, a period of approximately 16 hours at 15 degrees C (Adult Xenopus NXR_0031 obtained from National Xenopus Resource Stock Center,  Woods Hole, MA; RRID:SCR_013731).  Pools of n=8 foregut endoderm explants were harvested at NF25 as 1 biological replicate.  3 such biological replicates per condition were generated (0.1% DMSO treated, 25nM Retinoic Acid (RA, Sigma cat.no. R2625) treated, 200nM RA treated, or 500nM RA treated). RNA was extracted using the Machery-Nagel RNA isolation kit (740955) according to manufacturer's instructions.

first: Scott

last: Rankin

first: Jacek

last: Biesiada


title: PARG regulates the proteasomal degradation of TARG1

city: Oxford

first: Callum

last: Henfrey

address: Sir William Dunn School of Pathology, South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

summary: ADP-ribosylation is a reversible modification of macromolecules critical for the regulation of genome stability, stress responses, and proteostasis. While the roles of ADPr transferases such as PARP1/2 and TNKS1/2 are well established, the functions and regulatory mechanisms of ADPr hydrolases are still poorly understood. Here, we identify a previously uncharacterized function of the poly(ADP-ribose) glycohydrolase PARG in regulating protein degradation. Using quantitative proteomics, we show that PARG inhibition depletes protein levels of the mono-ADPr hydrolase TARG1. We demonstrate that this TARG1 depletion is both PAR- and proteasome-dependent, and identify the E3 ubiquitin ligases HUWE1 and TRIP12 as mediators of this process. Our findings establish TARG1 as a substrate of PAR-dependent protein degradation and uncover a PARG-dependent mechanism controlling its stability. This work highlights a new dimension of interplay between the two ADP-ribosyl hydrolases, with implications for the refinement of PARG-targeted therapeutic strategies.

overall_design: RNA-seq in biological triplicates of U2OS WT cells treated with either DMSO or PARGi

first: Joséphine

last: Groslambert

first: Sara

middle: C

last: Buch-Larsen

first: Ivo

last: Hendriks

first: Robert

last: Kurzbauer

first: Jonas

middle: D

last: Elsborg

first: Chatrin

last: Chatrin

first: Thomas

last: Agnew

first: Michael

last: Tellier

first: Evgeniia

last: Prokhorova

first: Song

last: Huang

last: Barrosso-Gonzalez

first: Roderick

last: O'Sullivan

first: Tim

last: Clausen

last: Nielsen

first: Ivan

last: Ahel


title: Mutant p53 binds RNA to drive mitochondrial dysfunction [miRNA-Seq]

first: Wuyue

last: Zhou

type: Non-coding RNA profiling by high throughput sequencing

overall_design: miRNA-seq of HEK cells transiently expressing wild-type or mutant p53, collected in biological triplicates. Untranfected HEK cells served as the control.

first: Alice

last: Long

first: Cameron

last: Douglas

first: Dalila

last: Gallegos

first: James

last: Burke

first: David

last: MacMillan

first: Ezgi

last: Hacisuleyman

first: Ciaran

last: Seath


title: Commensal-derived short-chain fatty acids disrupt lipid membrane homeostasis in Staphylococcus aureus

city: Minneapolis

first: Ryan

last: Hunter

state: MN

address: 689 23rd Ave SE

institute: University of Minnesota

summary: We used a custom Nanostring codeset targeting 33 transcriptional regulators, virulence factors, and metabolic genes to gain insight into differential gene expression in Staphylococcus aureus JE2 when grown in LB supplemented with either propionate or butyrate relative to LB alone.

overall_design: 4 sample types, 3 biological replicates

first: Joshua

middle: R

last: Fletcher


title: SLC25A45 mediates mitochondrial import of methylated mitochondrial amino acids and carnitine biosynthesis

city: New York

first: Artem

last: Khan

state: NY

address: 1230 York Ave

institute: Rockefeller University

summary: Solute carriers (SLCs) regulate cellular and organismal metabolism by transporting small molecules and ions across membranes, yet the physiological substrates of ~20% remain elusive. To address this, we developed a supervised machine learning platform to predict and prioritize gene-metabolite associations. This approach identifies UNC93A and SLC45A4 as candidate plasma membrane transporters for acetylglucosamine and polyamines, respectively. Additionally, we uncover SLC25A45 as a mitochondrial transporter linked to serum levels of methylated basic amino acids, products of protein catabolism. Mechanistically, SLC25A45 is necessary for the mitochondrial import of methylated basic amino acids, including ADMA and TML, the latter serving as a precursor for carnitine synthesis. In line with this observation, SLC25A45 loss impairs hepatic carnitine synthesis and upregulation of carnitine-containing metabolites under fasted conditions. By facilitating mitochondrial TML import, SLC25A45 connects protein catabolism to carnitine production, sustaining β-oxidation during fasting.  Altogether, our study identifies putative substrates for three SLCs and provides a resource for transporter deorphanization.

overall_design: 7-week-old male Slc25a45-/- vs. Slc25a45+/-, Slc25a45+/+ mice were transferred into a clean cage with or without the food access for 24 hours. At the beginning of experiment as well as 24 hours after, the blood was collected for serum analysis. Subsequently, the liver tissues were harvested, immediately flash frozen and stored at −80°C for subsequent metabolomic profiling by liquid chromatography-mass spectrometry (LC-MS). Total RNA was extracted from the livers harvested as described above from Slc25a45-/- vs. Slc25a45+/-, Slc25a45+/+ mice using the RNeasy Mini Kit (Qiagen #74104) in accordance with the manufacturer's protocol. Library preparation and RNA-sequencing was performed by Genewiz.

first: Birsoy

last: Kivanc


title: Cytokine-driven glycosphingolipid metabolism modulates endoplasmic reticulum calcium homeostasis in primary human renal mesangial cells

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

summary: Glycosphingolipids (GSLs), including hexosylceramides (HexCers), lactosylceramides (LacCers), and gangliosides composed of one or more sugar residues attached to ceramide, are essential components of cell membranes. Dysregulated GSL metabolism has been implicated in various inflammatory and autoimmune diseases, including lupus nephritis; however, its contribution to renal cell dysfunction remains largely unexplored. In this study, we demonstrate that in primary human renal mesangial cells (hRMCs), proinflammatory cytokines relevant to lupus elicit significant upregulation and secretion of inflammatory mediators that parallel intracellular and extracellular accumulation of HexCers and elevated cytosolic calcium (Ca2+) levels. The increase in cytosolic Ca2+ was attributed to a decrease in endoplasmic reticulum (ER) Ca2+ store capacity. Pharmacological inhibition of GSL synthesis with eliglustat significantly reduced HexCers levels and restored ER Ca2+ stores, but did not impact cytokine-induced cytokine/chemokine secretion or cell viability/proliferation. Together, these data suggest that elevated GSL synthesis modulates cytokine-induced ER Ca²⁺ dysregulation in mesangial cells and may play a role in the pathogenesis of lupus nephritis.

overall_design: hRMCs (lots 12445, 17544, and 20018) were treated in quadruplicate wells in 6-well plates with vehicle, 25 ng/ml IL-1b, or 25 ng/ml IL-1b +20 nM eliglustat for 24, 48, or 72 hrs. Media was collected for ELISAs and GSL quantification, cell viability was measured by the alamar blue assay, and cells scraped into DPBS and replicate wells combined. The cell suspension was split into two tubes, centrifuged, and DPBS removed. Half the cells were used for GSL quantification, and the other half were used for RNA isolation.

first: Mariia

last: Stefanenko

first: Tessa

last: Ortiz

first: Sandra

middle: G

last: Mungaray

first: Mykhailo

last: Fedoriuk

first: Oleg

last: Palygin

first: Drew

last: Moore

first: Tamara

middle: K

last: Nowling


title: Chronobiology of Neurotropic Viruses: Rhythmic Viral Entry and Arrhythmic Host Clocks

city: 武汉市

first: Shaowei

last: Zeng

state: 湖北省

address: 水果湖街道

institute: wuhan university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Neurotropic viruses invade neural tissues, resulting in severe diseases such as poliomyelitis, rabies, herpesviral encephalitis, and viral meningitis. Given this neurotropism, we investigated whether the infection of the host by these viruses is under circadian control. Here we show that the expression of most neurotropic virus receptors exhibits rhythmicity across cells, cerebral organoids, and animal models, with host cell susceptibility modulated by the circadian clock. We identify E2F8 as a clock-controlled gene that mediates the indirect regulation of the circadian clock on neurotropic viruses. Notably, E2F8 regulates the expression of core clock components by binding directly to the promoters of REV-ERBα and PER2, suggesting its role as a potential modulator of circadian rhythms. Additionally, we uncovered a seldom-recognized viral strategy to accelerate its own replication in the host: rabies virus disrupts the host circadian clock system primarily through its glycoprotein hijacks the E3 ubiquitin ligase HUWE1 to inhibit proteasomal degradation of REV-ERBα. These findings enhance our understanding of circadian systems' interaction with neurotropic viral dynamics and highlight chronotherapy's potential for improved antiviral treatments.

overall_design: CUT&Tag-seq of BMAL1 in Cerebral organoids synchronized with 100 nM hydrocortisone at CT7

first: Qian

last: Zhang

first: Bishi

last: Fu


title: Salivary Extracellular Vesicle RNA Profiling Reveals Biomarkers for Sjögren’s

city: Framingham

first: Shuran

last: Xing

state: MA

address: 16 Chubb Rd

institute: Bio-Techne

summary: Sjögren’s is a chronic autoimmune disease affecting exocrine glands and is subclassified into SSA-positive (SSA+) and SSA-negative (SSA-) subtypes, with a complex diagnostic journey and an average diagnostic delay of almost 4 years. While SSA+ cases can be detected via serological testing, current assays lack specificity. For SSA-patients, no non-invasive diagnostic tools exist, and diagnosis often requires invasive lip biopsy. A saliva-based liquid biopsy capable of diagnosing both subtypes is therefore of high clinical interest. However, saliva poses challenges due to its abundant oral microbiome, which complicates unbiased biomarker discovery. In this study, we present a novel RNA sequencing workflow that efficiently depletes microbial content, enabling deep profiling of long RNAs within salivary extracellular vesicles (EVs). This approach identified both known and novel RNA biomarkers capable of diagnosing SSA+ and SSA-subtypes with high sensitivity and specificity. Moreover, we uncovered distinct RNA signatures that allow molecular stratification of Sjögren’s subtypes. Pathway analysis in SSA+ cases revealed enrichment of immune and glandular pathways consistent with prior tissue-based studies, supporting the utility of salivary EVs as a non-invasive surrogate for tissue biopsy. Importantly, our data provides new molecular insights into the under-characterized SSA-subtype, laying the foundation for future mechanistic studies and facilitating their broader inclusion in clinical trials.

overall_design: RNA sequencing using whole exome squencing of extracellular vesicles extracted from saliva


title: Plasma Proteome Pilot in KOREF

city: Ulsan

first: Jong

middle: Hwa

last: Bhak

address: 50, UNIST-gil

country: South Korea

institute: UNIST

summary: This study used SomaScan v 4.1 to profile>7000 proteins in human plasma KOREF1.

overall_design: 5 samples of KOREF1-P (including 2 technical replicates) and 3 samples of KOREF2-P are analyzed.

first: Changhan

last: Yoon

first: Hyomin

last: Lee

first: Youngmin

last: Park

first: Sangsoo

first: Sungwon

last: Jeon


title: Differential gene expression in C. difficile rough and smooth colony variants is partially determined by CmrRST regulation

city: Chapel Hill

first: Anchal

last: Mehra

state: North Carolina

address: 125 Mason Farm Rd, 6th Floor, CB 7290, Marsico Hall

department: Department of Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

summary: Clostridioides difficile introduces phenotypic heterogeneity into populations via phase variation. C. difficile modulates phase variation through invertible DNA sequences containing regulatory information, termed switches. Inversion of a switch controls expression of the adjacent genes in an ON/OFF manner, resulting in phenotypic switching. The C. difficile cmr switch (for ‘colony morphology regulator’) coordinates several phenotypes. When cmr is ON, C. difficile displays a rough colony morphology, surface motility, and cell chaining and elongation. When cmr is OFF, colonies are smooth, and high levels of swimming motility and biofilm formation are observed. Prior work has also linked colony morphology and cmr switch orientation to virulence in the hanster model of infection (Garrett et al., PLoS Biology, 2019). The cmr-ON orientation results in the expression of cmrRST, an operon encoding a signal transduction system. CmrS is a predicted histidine kinase, and CmrR and CmrT are response regulators. We have shown that CmrR and CmrT are responsible for the observed cmr-associated phenotypes (Garrett et al., PLoS Biology, 2019). The goal of this study is to identify the genes that are regulated by CmrR and CmrT and determine how these genes contribute to colony morphology and the other cmr-associated phenotypes. To identify genes important for C. difficile colony morphology, we conducted a multi-pronged RNA-Seq study comparing the following transcriptomes: (1) Rough vs. smooth colony variants of wild-type, (2) cmr-ON vs. cmr-OFF phase-locked strains, (3) Rough, smooth, cmr-ON, and cmr-OFF vs. a ΔcmrRΔcmrT mutant, and (4) Wild-type overexpressing either cmrR or cmrT vs. a no-overexpression condition. Transcription analyses revealed that CmrRST accounts for some, but not all, transcriptional differences between rough and smooth colony morphotypes. Fewer than 20 genes were differentially expressed by CmrR and/or CmrT (≥4-fold change, p<0.05). Most of those genes appeared in the rough vs. smooth and cmr-ON vs. -OFF datasets as well, and further phenotypic analyses of CmrRST-regulated genes revealed multiple genes that mediated rough colony development.

overall_design: RNA-Seq profiling of C. difficile strains grown on agar (wildtype rough and smooth colony variants,  cmr-ON and cmr-OFF phase-locked mutants, and a ΔcmrRΔcmrT mutant), and grown in broth (wildtype overexpressing either cmrR or cmrT or a no-expression control).

first: Elizabeth

last: Garrett

first: Rita

last: Tamayo


title: The effect of the two-component system GrtK and GrtR proteins of Burkholderia glumae on the metabolic detoxification of intracellular ammonia.

city: Jinju-si

first: Yongsung

last: Kang

state: Gyeongsangnam-do

address: 1 Gyeongsangdae-ro

department: Institute of Agriculture and Life Science

institute: Gyeongsang National University

summary: This study demonstrates that the two-component system, consisting of the sensor kinase GrtK and the response regulator GrtR, plays a crucial role in detecting and neutralizing toxic environmental ammonia produced as waste by Burkholderia glumae, a rice pathogen. The growth of grtK or grtR null mutants was inhibited by ammonia produced as waste in amino acid-rich media, such as Luria-Bertani broth, but no growth inhibition was observed in amino acid-free minimal media, where ammonia production is limited. Transcriptomic analysis of grtK and grtR mutants also indicated that GrtK and GrtR are involved in the metabolic detoxification of intracellular ammonia. These results suggest that GrtK is not a member of the ammonia transporter protein family but acts as an external ammonia sensor, working in conjunction with the response regulator GrtR to respond to the dangers posed by its own metabolism.

overall_design: A comparative analysis of RNA-seq profiles was performed on Burkholderia glumae wild-type BGR1 and its grtK and grtR null mutants during 12 hours of growth in amino acid-rich media, such as Luria-Bertani broth.

first: Gi-Young

last: Kwak

first: Yewon

last: Nam

first: Ingyu

last: Hwang


title: Dac6 affects thermotolerance and pathogenicity of Cryptococcus neoformans by modulating utilization of host infection-related amino acids

city: Chongqing

first: XinDi

last: Gao

state: Chongqing

address: No.183 Xinqiaozheng Street, Shapingba District, Chongqing, China.

institute: Army Medical University

summary: Thermotolerance of fungal pathogens is critical for host adaptation, and most fungi cannot survive at mammalian body temperatures, making heat stress a key host defense. Cryptococcus neoformans, a leading cause of fungal meningitis, must overcome host fever and nutrient limitation to establish infection. However, the metabolic adaptations enabling C. neoformans to overcome this barrier remain unclear. Here, we investigated the role of a protein deacetylase Dac6 in C. neoformans thermotolerance and pathogenicity, focusing on its metabolic regulation under heat stress. We found that Dac6 is a thermotolerance regulator, distinct from its yeast homolog Rpd3, and its expression correlates with heat resistance in clinical strains. Multi-omics analyses reveal that Dac6 modulates histone acetylation and gene expression to reprogram amino acid metabolism under heat stress, particularly lysine and threonine. Notably, lysine and threonine are also the major altered metabolites in host during cryptococcal infection, and Dac6 deletion impaired fungal utilization of lysine and threonine under heat stress in vitro and in vivo. Consequently, Dac6 deficiency leads to reduced lung and brain colonization, and attenuated virulence in mice. Our study uncovers a metabolic adaptation mechanism by which Dac6 links nutrient utilization to thermotolerance and virulence, providing new insights into fungal survival strategies in high-temperature host environments.

sample_organism:
Saccharomyces cerevisiae
Cryptococcus neoformans

overall_design: For Cryptococcus neoformans, performed paired-end RNA-seq of fungal strains in 100ml YPD broth  at OD600=1 at 30°C or 39°C, respectively in biological triplicates.  For Saccharomyces cerevisiae, performed paired-end RNA-seq of fungal strains in 100ml YPD broth  at OD600=1 at 39°C, respectively in biological triplicates.


title: Hippo signaling regulates cuticle pigmentation and dopamine metabolism in Drosophila

city: Houston

first: Shinya

last: Yamamoto

state: TX

address: 1250 Moursund St

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Pigmentation plays multiple important roles in development, physiology and evolution. Melanization of the insect cuticle requires dopamine as a precursor of melanin and involves key enzymes in dopamine biosynthesis including Tyrosine hydroxylase (TH) and Dopa decarboxylase (Ddc). Some studies have hinted that disruption of the evolutionarily conserved Hippo signaling pathway, which has been primarily studied in the context of tissue growth, may lead to changes in cuticle pigmentation in the fruit fly Drosophila melanogaster. However, there have not been any systematic investigations into their potential mechanistic links. In this study, we identified that all genes that comprise the canonical Hippo signaling pathway [hippo (hpo), salvador (sav), mats, warts (wts), yorkie (yki) and scalloped (sd)] are involved in cuticle pigmentation in the fly notum based on tissue-specific gene knock-down/out experiments and epistatic analysis. Despite the notable divergence of pigmentation mechanisms between invertebrates and vertebrates, these phenotypes can often be rescued by the human orthologs of corresponding fly genes. While we find that manipulation of Hippo signaling in dopaminergic neurons does not affect global dopamine levels in the fly brain, developmental inhibition of this pathway can increase dopamine levels in the fly head, indicating that the mechanism by which dopamine levels are regulated in the nervous system is distinct from that in epithelial cells. Through single nuclei RNA sequencing of the developing fly nota and subsequent functional studies of differentially expressed genes that are altered upon inhibition of Hippo signaling, we found four genes [ciboulot (cib), transaldolase (taldo), yellow (y) and Insulin-like receptor (InR)] that contribute to cuticle pigmentation downstream of wts. Finally, we provide multiple pieces of evidence that indicate that the function of Hippo signaling in cuticle pigmentation and tissue growth can be genetically uncoupled and also identify beaten path Vc (beat-Vc) as a novel tissue growth regulator that acts downstream of wts but is not required for cuticle pigmentation. We conclude that regulation of cuticle pigmentation by canonical Hippo signaling acts through multiple downstream genes rather than directly through TH and Ddc. We also propose that the Drosophila melanogaster cuticle may serve as a useful platform to identify previously uncharacterized mediators of Hippo signaling as well as an in vivo experimental system to test the functionality of rare genetic variants found in human Hippo signaling orthologs associated with a variety of diseases.

overall_design: Single-nucleus RNA-sequencing


title: YAP1 dysfunction promotes molecular properties linked to breast cancer susceptibility

city: Duarte

first: Tara

last: Fresques

state: CA

address: 1500 East Duarte Rd.

department: Beckman Research Institute

institute: City of Hope

summary: YAP1 is a co-transcription factor that promotes malignant and stem cell properties in cancer. We previously found that YAP1 dysregulation is associated with aging in human mammary epithelia. With increased age, YAP1 expression changes in luminal epithelial cells, the prospective breast cancer cell of origin. Because age is a significant risk factor for breast cancer, we tested if YAP1 dysregulation acted early in cancer progression by conferring cellular states associated with increased cancer susceptibility. Here we find, that with increased age and genetic risk for developing cancer, human breast tissues showed significantly increased YAP1 expression and cultured primary human mammary epithelial cells (HMEC) showed significantly increased expression of both YAP1 and its transcriptional targets. Increased YAP1 expression in cultured HMEC induced gene expression changes associated with increased cancer susceptibility such as genes associated with: a stem cell fate, cells with increased telomerase activity, breast cancer progression, and increased age and genetic breast cancer risk. Further, overexpression of YAP1 in post-stasis HMEC- finite lifespan cells which have bypassed a retinoblastoma-mediated senescence barrier- promoted properties related to an increased growth potential. We found that YAP1 dysregulation in finite post-stasis epithelial cells allows for access to gene programs and functions that are typically thought to be restricted to stem cells. We hypothesize that YAP1 acts early in breast cancer progression, before development of a tumor, to impose cancer susceptible molecular states.

overall_design: General experimental design: Post-stasis human mammary epithelial cells (HMEC) were cultured in tissue culture plastic in M87A media. YAP1 or control constructs were transduced into cells to determine the effect of YAP1 on post-stasis HMEC. In some samples, MYC was further added to induce immortalization. In some samples, clonal immortalization events occurred. Cells were collected at different passages during post-stasis and immortal growth. Experiments were done with 2 different biological specimens: 184D and 240LB. Biological Replicate 1: Specimen 240LB. Cells were transduced with p16sh to make cells post-stasis. Control post-stasis cells were collected at passage 11. YAP1 was transduced into cells at passage 10 and cells were collected at passage 12. YAP1 transduced cultures underwent clonal immortalization around passage 18 when they were collected. Fully immortal YAP1 transduced cells were collected at passage 25. Biological Replicate 2: Specimen 240LB. Cells were transduced with p16sh to make cells post-stasis. YAP1 or control virus was transduced into cells at passage 10 and cells were collected at passage 12. YAP1 transduced cultures underwent clonal immortalization around passage 16 when they were collected. Fully immortal YAP1 transduced cells were collected at passage 22. Biological Replicate 3 (All samples collected in triplicate): Specimen 184D. Cells were transduced with p16sh to make cells post-stasis. YAP1 or control virus was transduced into cells at passage 10 and cells were collected at passage 12. Control cells approached replicative senescence at passage 18; control and YAP1 transduced cells were collected at passage 17. YAP1 transduced cultures underwent rare immortalization event(s) around passage 18 when they were collected. Fully immortal YAP1 transduced cells were collected at passages 20 and 24. Control and YAP1 post-stasis cells were also transduced with MYC at passage 12 and immortalized cells were collected at passages 15 and 21.

first: Debbie

last: Hussey

first: Jennifer

last: Lopez

first: Masaru

last: Miyano

first: James

last: Garbe

first: Stefan

last: Hinz

first: Rosalyn

last: Sayaman

first: Aimin

last: Li

first: Serenity

last: Van Bedford

first: Daniel

last: Schmolze

first: Martha

last: Stampfer

first: Mark

last: LaBarge


title: Head-to-head comparison of targeted transcriptome methods: HTG vs TempO-Seq

city: Valencia

first: Antonio

last: Fernandez-Serra

address: Profesor Beltran Baguena, 8

country: Spain

institute: Fundacion Instituto Valenciano de Oncologia

summary: In this work this HTG Edgeseq targeted RNA-seq technology is compared with another analogous approach (TempO-Seq) in order to establish its suitability in a research molecular oncology setting. Comparison was proposed at different levels of biomarkers ranging from single mRNA to more complexes including ten to thousands of genes.

overall_design: The same samples and RNA universal human controls (C1, C2 and C3) were assayed by using both approaches HTG edgeseq Human Transcriptome Panel and TempO-Seq from Biospyder. Their performance was benchmarked with different common biomarkers used in oncology

first: Raquel

last: Lopez-Reig

first: Jose Antonio

last: Lopez-Guerrero


title: The cervicovaginal microbiome associates with spatially restricted host transcriptional signatures throughout the human ectocervical epithelium and submucosa

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

country: Sweden

institute: Karolinska Institutet

summary: The cervicovaginal microbiome is a key biological determinant of human immunodeficiency virus (HIV) susceptibility, but its underlying impact on the ectocervical transcriptional landscape is unclear. Ectocervical tissue samples from Kenyan female sex workers were categorized into pre-defined cervicovaginal microbiome groups based on dominant compositions: Lactobacillus crispatus, Lactobacillus iners, Gardnerella, and ‘highly diverse’. The tissue samples (n=21) were assessed using spatial transcriptomics, revealing three epithelial, one mixed border, and nine submucosal gene clusters. Differential gene expression analysis across the microbiome groups and gene clusters identified 3,771 unique genes. The highly diverse microbiome group exhibited the largest differences, mostly located near the epithelial basal membrane, encompassing genes involved in epithelial maintenance, submucosal extracellular matrix structures, and immune function. The L. crispatus- dominated group was identified by genes involved in active immune engagement, supporting mucosal barrier integrity. Weighted gene co-expression analysis confirmed tissue-wide altered gene expression associated with all microbiome groups and with individual bacterial taxa. Despite the assumption that microbiome colonization is restricted to the luminal surface, the transcriptional landscape was affected throughout the mucosa, with the most pronounced effect near both sides of the basal membrane. This broad impact on the mucosal barrier integrity is likely to affect susceptibility to HIV acquisition.

overall_design:
In this study we compared gene expression between ectocervical tissue samples (n=21) from women with pre-defined groups of microbiome profiles (L. crispatus: 4, L. iners: 6, Gardnerella: 6, highly diverse: 5) using visium spatial transcriptomics. Ectocervical tissue were obtained as part of our broader longitudinal investigation within the Sex Worker Outreach Program in Pumwani, Nairobi, Kenya

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Due to patient privacy concerns, the raw data cannot be held in a public database.
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title: Co-targeting EZH2 and TEAD elicits apoptosis through tumor-intrinsic innate immune signaling in Hippo pathway-mutated cancers - RNA-seq data from genetic disruption of EZH2

city: Boston

first: Zhaorong

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: TEA/TEF-domain [TEAD] inhibitors are being evaluated in clinical trials for cancers with alterations in the Hippo pathway including mesothelioma. We recently developed and showcased the potency of TEAD palmitoylation inhibitors MYF-03-69 and MYF-03-176 in mesothelioma cell lines. However, TEAD inhibition results in cell cycle arrest in cell line models with Hippo pathway alterations without inducing cell death, potentially limiting their long-term clinical efficacy. Using a genome-wide CRISPR/Cas9 screen, we identified EZH2 as a critical modulator of the cellular response to TEAD inhibition. Compared to single agent treatments, EZH2i/TEADi robustly triggered apoptosis and suppressed the growth of Hippo-mutated cells in vitro and in vivo. Mechanistically, EZH2i/TEADi-treated cells exhibited heightened activation of tumor-intrinsic innate immune signaling which resulted in DNA damage and subsequent apoptosis. Taken together, we propose this novel combinatorial strategy as a potential approach to enhancing the anti-tumor efficacy of single agent TEAD targeting therapies in Hippo pathway altered tumors. This GEO accession includes the data series associated with RNA-seq derived from pharmacologic disruption of EZH2.

overall_design: MSTO-211H malignant pleural mesothelioma cells were transiently transfected with Cas9 and either an sgRNA control guide (sgCTRL) or a guide targeting EZH2 (EZH2-KO). RNA-seq profiling of sgCTRL and EZH2-KO cells  treated with DMSO or a TEAD inhibitor, MYF-03-69 for 24h, was then performed.

first: Antja-Voy

last: Hartley

first: Matthew

last: Booker

first: Nicholas

last: Tourtillot

first: Pasi

last: Jänne


title: BRD4 inhibition suppresses histone H4 UFMylation to drive ferroptosis sensitivity through TXNIP

city: Nanjing

first: Tao

last: Wu

address: 24 Tongjiaxiang

institute: China Pharmaceutical University

summary: BRD4 inhibition selectively changes gene transcription which defines cell responses to BET inhibitors. Altered genes driving cell cycle arrest in solid tumor upon BET inhibitor treatment are far from clear. Here, we find that BET inhibitor JQ1 upregulates TXNIP which mediates the anti-tumor effects of JQ1. Mechanistically, JQ1 reduces histone H3K9 trimethylation at TXNIP promoter, facilitating its transcription in the presence of glucose. Increased TXNIP inhibits Histone H4 UFMylation by interfering the interaction between H4 and UFBP1. Instead of regulating cMYC expression, H4 UFMylation promotes the chromatin binding of cMYC to facilitate the transcription of cell-cycle related genes. Additionally, TXNIP prevents proteasomal degradation of P27, a CDK inhibitor. JQ1-treated solid cancer cells thus enter dormant state which is associated with cancer relapse and drug tolerance. However, these arrested cells are sensitive to ferroptosis, suggesting enhancing the functions of ferroptosis inducers with BET inhibitors. Together, our studies reveal regulators of protein UFMylation and cMYC activity, which modulate cell responses to BET inhibitors and ferroptosis inducers in solid cancer cells.

overall_design: RNA-Seq profiling of DMSO and JQ1 treated HepG2 cells

first: Zhen

last: Yang


title: IRF3 attenuates hypoxia signaling by retaining HIF-α in the cytoplasm

city: Wuhan

first: Hongyan

last: Deng

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: Interferon regulatory factor 3 (IRF3) functions as a key transcription factor in the innate antiviral immune response, which is depended on its nuclear localization. However, its function in the cytoplasm during non-infection states remains largely unknown. In this study, we found that resting cytoplasmic IRF3 interacts with HIF-1α and HIF-2α, two master regulators of hypoxia signaling. This interaction retains HIF-α in the cytoplasm under hypoxic conditions, preventing it from exerting their transcription factor function and attenuating hypoxia signaling. Disruption of IRF3 in both mice and zebrafish resulted in increased expression of hypoxia response genes and enhanced tolerance to hypoxia. These findings suggest that, in the absence of viral infection, cytoplasmic IRF3 modulates hypoxia signaling by retaining HIF-α in the cytoplasm under hypoxic conditions.

overall_design: THP-1 cells infected without or with VSV or HSV-1 for 8 hours. IRF3-deficient or wild-type H1299 cells under normoxia (21% O2) or hypoxia (1% O2) for 24 hours.

first: Shuke

last: Jia

first: Chunchun

last: Zhu

first: Jiale

last: Hua

first: Zixuan

last: Wang

first: Xueyi

last: Sun

first: Wen

last: Liu

first: Liyun

last: Shi

first: Wenhua

first: Jian-Fang

last: Gui

first: Xing

first: Wuhan

last: Xiao


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from human iPSC-derived Hepatocyte-like cells

city: Aurora

first: Matthew

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

summary: Analysis of steady-state mRNA levels in Hepatocyte-like cells differentiated from human iPSCs originating from donors with and without Down syndrome. This dataset is part of the Human Trisome Project - Trisomy 21 Model Atlas run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/

overall_design: Hepatocyte-like cells differentiated from a panel of iPSCs reprogrammed from urine-derived kidney epithelial cells of human donors - comparison of cells with trisomy 21 (T21, n = 6) to euploid controls (D21, n = 6).

first: Kelly

last: Sullivan

first: Brian

last: Niemeyer


title: Dp16 liver transcriptome

institute: University of Colorado Anschutz Medical Campus

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from adult WT and Dp16 mouse liver tissue ± high fat diet

summary: Analysis of steady-state mRNA levels in mouse liver tissue at 13-15 weeks from wild-type C57BL/6J and Dp(16)1Yey mice fed control or high fat diet.

overall_design: Comparison of control diet to high fat diet for wild-type (n=10/14) and Dp16 (n=8/13) animals.

first: Lauren

last: Dunn


title: Genomic Microarray data from two siblings affected with Schizophrenia

city: Mumbai

first: Dhanjit

middle: Kumar

last: Das

state: Maharashtra

address: JM Street

department: Stem Cell Biology

country: India

institute: ICMR-NIRRCH

type: Genome variation profiling by genome tiling array

summary:
Schizophrenia is a polygenic, multifactorial chronic neuropsychiatric disorde. Due to its polygenic and complex nature, traditional genetic approaches like GWAS or candidate gene studies are often insufficient to capture rare or novel mutations.
We have used genomic microarray to find large deletion in the Schizophrenic patients which are difficult to find from whole exome sequencing

overall_design: Genomic DNA was isolated from the two Schizophrenia affected siblings and microarray was performed using Affymatrix platform.

first: Bipin

last: Shekhar

first: Shyla

last: Menon

first: Shailesh

last: Pande


title: EBF1 and PAX5 exert dose dependent epigenetic repression of T-lineage potential [RNA-seq]

city: Linköping

first: Mikael

last: Sigvardsson

address: Lab1, Level 13

department: Department of Biomedical and Clinical Sciences

institute: Linköping University

summary: B-lymphocyte development is dependent on the coordinated action of transcription factors controlling the expression of stage and lineage specific genes. To better understand gene regulation and changes in the epigenetic landscape in early B-cell development, we conducted combined SC-RNA/ATAC seq analysis of bone marrow progenitor populations, allowing us to build a developmental trajectory based on changes in epigenetic accessibility. This analysis identified a rapid shift in DNA accessibility, where T-lineage primed progenitors gained the epigenetic landscape of B-lymphocytes. The epigenetic switch correlated well with initiation of EBF1 and PAX5 transcription as well as their functional activity. As ectopic expression of EBF1 in Pax5-/- pro-B cells was not sufficient to mediate either the full activation of the B-lineage program of silencing of T-lineage associated genes, we conclude that PAX5 and EBF1 are independently essential for the establishment of the epigenetic landscape in normal B-cell development. This idea was supported by the finding that pro-B cells from mice with combined heterozygote deletion of the Ebf1 and Pax5 genes, carried a non-differentiated epigenetic landscape and expressed T-lineage associated genes. The importance of epigenetic silencing for the preservation of B-cell fate was supported by the finding that inhibition of the histone methylases EZH1 and EZH2 in pro-B cells, allowed for the activation of T-lineage genes and generation of T-lineage cells in response to Notch signaling. Hence, B-lymphoid commitment is associated with a transcription factor dose dependent epigenetic switch, silencing an inherent T-lineage potential in early lymphoid progenitors.

overall_design: RNA-seq of WT, Ebf1+/-, Pax5+/- and Ebf1+/-Pax5+/- (Total, CD25-, CD25+) exvivo sorted BM proB cells.

first: Johanna

last: Tingvall-Gustafsson

first: Kim

last: Hellerstedt

first: Jonas

last: Ungerbäck


title: EBF1 and PAX5 exert dose dependent epigenetic repression of T-lineage potential [ChIPmentation]

overall_design: H3K4me3, H3K27ac and H3K27me3 ChIPmentation of WT and Ebf1+/-Pax5+/- c-Kit enriched BM proB cells.


title: EBF1 and PAX5 exert dose dependent epigenetic repression of T-lineage potential [ATAC-seq]

overall_design: ATAC-seq of Ebf1KO/Pax5KO FL B cell progenitor cells transduced with Mig-Ctrl or Mig-Ebf1. ATAC-seq of WT and Ebf1+/-Pax5+/- BM proB cells either exvivo sorted or expanded followed by culturing on Op9/Op9DL1 for 24h.


title: Restoring mechanophenotype reverts malignant properties of ECM-enriched vocal fold cancer

city: Turku

last: Ivaska

address: Tykistökatu 6

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

summary: Increased extracellular matrix (ECM) and matrix stiffness promote solid tumor progression. However, mechanotransduction in cancers arising in mechanically active tissues remains underexplored. Here, we report upregulation of multiple ECM components accompanied by tissue stiffening in vocal fold cancer (VFC). We compare non-cancerous (NC) and patient-derived VFC cells – from early (mobile, T1) to advanced-stage (immobile, T3) cancers – revealing an association between VFC progression and cell-surface receptor heterogeneity, reduced laminin-binding integrin cell-cell junction localization and a flocking mode of collective cell motility. Mimicking physiological movement of healthy vocal fold tissue (stretching /vibration), decreases oncogenic nuclear β-catenin and YAP levels in VFC. Multiplex immunohistochemistry of VFC tumors uncovered a correlation between ECM content, nuclear YAP and patient survival, concordant with VFC sensitivity to YAP-TEAD inhibitors in vitro and in vivo. Our findings present evidence that VFC is a mechanically sensitive malignancy and restoration of tumor mechanophenotype or YAP/TAZ targeting, represents a tractable anti-oncogenic therapeutic avenue for VFC.

overall_design: RNA-seq profiling of HaCat, UT-SCC-11 and UT-SCC-103 cells subjected 30 min or 6h hours of vibration or no vibration (control condition; CTRL)

first: Jasmin

last: Kaivola


title: EBF1 and PAX5 exert dose dependent epigenetic repression of T-lineage potential [scMultiome]

overall_design: sc-multiome (ATAC/GEX) of overlapping BM progenitor populations spanning early B cell development (LSK, FLT3+, IL7RA+, CD19+IgM/IgD-.


title: DNA interactions of transcriptional co-regulator SEUSS (SEU) during Arabidopsis flower development.

city: Berlin

first: Cezary

last: Smaczniak

address: Philippstr. 13

department: Institute for Biology

country: Germany

institute: Humboldt-Universität zu Berlin

summary: Transcriptional co-regulators are key modulators of gene expression, often functioning in complexes with transcription factors to regulate chromatin dynamics. LEUNIG_HOMOLOG (LUH) is a member of the conserved Groucho/Tup1 family of co-regulators in Arabidopsis, yet its role in flower development remains poorly understood. While LEUNIG (LUG), a homolog of LUH, has been extensively studied in floral organ identity specification, contributions of LUH appear to be both overlapping and distinct from LUG. Other co-regulators, such as SEUSS (SEU) and its homologs SEUSS-LIKE1-3 (SLK1-3), function as bridge proteins that stabilize the interactions between transcription factors and cofactors from the LUG/LUH family. Using high-throughput DNA occupancy analyses, we identify SEU target genes during flower development in Arabidopsis. Our findings contribute to understanding how LUH modulates transcriptional responses and chromatin state to fine-tune flower development in Arabidopsis.

overall_design: To study the high-throughput DNA occupancy of SEU protein during flower development in Arabidopsis, we conducted chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments using inflorescences of the proSEU:SEU-GFP seu-1 plant line. Two biological replicates were prepared with the input samples as controls. We used μMACS Anti-GFP MicroBeads (Miltenyi Biotec) for the immunoprecipitation.

first: Rosario

last: Vega-Léon

first: Jose

last: Muino

first: Maurizio

last: Pimentel

first: Kerstin

last: Kaufmann


title: A metabolism-chromatin axis promotes ribosome heterogeneity in the human malaria parasite

city: Paris

first: Sebastian

last: Baumgarten

address: 25, Rue du Dr. Roux

department: Parasites and Insect Vectors

country: France

institute: Institut Pasteur

summary: The transmission of the most virulent human malaria parasite, Plasmodium falciparum, relies on the survival in the contrasting environments of the human host and mosquito vector. One of the most fascinating adaptations to this lifestyle is the specific silencing of individual rDNA genes in the human host that are de-repressed following host-to-vector transmission. In this study, we characterized the epigenetic signatures of active and silent rDNA loci and found that rDNA silencing  relies on aerobic glycolysis, the sole energy-generating pathway in the human host. We show that disruption of NAD+ regeneration during lactate fermentation promotes rDNA de-repression and identify Sir2 as the mediator between fluctuating NAD+ levels and a functional transcriptional outcome. Hence, rDNA activation appears to be coupled to the metabolic state of the parasite as it transitions from aerobic glycolysis to mitochondrial respiration during host-to-vector transmission.

overall_design: ChIP sequecing of H3K9ac, H3K14ac, H4K12ac and H4K16ac in Plasmodium falciparum wild-type (strain 3D7) and Sir2a-KO parasites.

first: Couble

last: Justine

first: Vignolini

last: Tiziano

first: Dore

last: Gregory

first: Lombard

last: Bérangère

first: Richard

last: Michael

first: Loew

last: Damarys

first: Büttner

first: Dueñas-Sánchez

last: Rafael

first: Poschet

last: Gernot

first: Bryant

last: Jessica

first: Baumgarten

last: Sebastian


title: snRNA-seq dataset of 17 treatment-naive human PDAC patient-derived tumors

city: Munich

first: Julian

last: Frädrich

address: Ismaninger Strasse 22

department: Institute of Experimental Oncology & Therapy Research

institute: TUM School of Medicine and Health

summary: This is a human single nucleus RNA sequencing (snRNAseq) dataset of human primary pancreatic ductal adenocarcinoma (PDAC) tumor tissues of 17 (deidentified) treatment-naive patients. The goal of this study was to thoroughly characterize the tumor microenvironment in human primary PDAC.

overall_design: single-nucleus RNA-seq (snRNA-seq) profiling of human PDAC patient-derived primary tumors using the 10xGenomics Chromium Next GEM Single Cell 3’ Kit v3.1.

first: Achim

last: Krüger

first: Carmen

last: Mota Reyes

first: Ihsan Ekin

last: Demir


title: Effect of TIMP1 depletion on gene expression in MIA PaCa-2 cell line by CRISPR/Cas9-based targeting of exon 4

summary: This is a bulk RNA sequencing dataset of MIA PaCa-2 cells with or without genetic manipulation of the TIMP1 gene. A two-guide RNA system was used and designed to target two sites of exon 4, introducing a 64-bp deletion, leading to a frameshift and premature stop-codon. This led to the generation of two TIMP1 KO cell lines, as well as a CRISPR control cell line that acquired only a silent point mutation (g.64C>T) without altering the amino acid sequence. To measure the impact of TIMP1 on MIA PaCa-2 gene expression, bulk RNAseq was performed for all four cell lines (WT, CRISPR Control, KO 1, and KO 2) in triplicates.

overall_design: All four cell lines were culltured to 70% confluency. Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) and RNAseq was performed on a NovaSeq X Plus platform (Illumina).


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: Single cell fixed RNA profiling from 4-month old WT and Dp16 mouse liver tissue

first: Matthew

last: Galbraith

summary: Analysis of single cell steady-state mRNA levels in fixed cells from mouse liver tissue at 4 months from wild-type C57BL/6J and Dp(16)1Yey mice.

overall_design: Comparison of cells from wild-type (n=4) and Dp16 (n=4) animals.

first: Kelly

last: Sullivan

first: Lauren

last: Dunn

first: Ariel

last: Timkovich


title: Deletion of CNTNAP2 Gene Leads to Dendritic Spine Abnormalities in Familial Schizophrenia: Insights from induced Pluripotent Stem Cells-Derived Patients’ Neurons

first: Dhanjit

last: Das

summary: Schizophrenia, a complex neuropsychiatric disorder, exhibits a wide range of genetic diversity. Multiple Genome-wide studies have identified several Copy Number Variations (CNVs) associated with Schizophrenia. One of the significant CNVs, comprising an intragenic deletion of the CNTNAP2 gene, has been associated with various neuro-developmental and neuro-psychiatric disorders. However, the molecular mechanism leading to the pathogenesis of Schizophrenia remained unclear. In this study, we report a 7q35-36.1del encompassing the entire CNTNAP2 gene in two affected siblings. Human induced Pluripotent Stem Cells (hiPSCs) were generated from both affected individuals. Neurons derived from the patient's hiPSCs lines have revealed that the dendritic length & arborization, spine number & density, soma area & volume were decreased in the patient’s neurons, while axon length was increased. Further classifying the dendritic spines, it was observed that the percentage of filopodia spines was increased, whereas stubby, mushroom and long thin spines were decreased in the patient’s neurons. Transcriptomics of hiPSCs-derived neurons has revealed eight significant dysregulation genes that interact directly or indirectly with CNTNAP2. Of these eight genes, Schizophrenia associated genes, PADI2 and LHX2 were observed to be significantly dysregulated. Overall, this study has identified abnormalities in neuronal architecture in hiPSCs-derived patients’ neurons harbouring CNTNAP2 gene deletion, confirming the disease pathophysiology of Schizophrenia.

overall_design: RNA-seq profiling of 2 Schizophrenia patient hiPSCs derived cortical neurons maintained for 120 days in culture along with 2  age and sex matched controls who do not have any mental disorder

first: Bipin

last: Shekhar

first: Shyla

last: Menon

first: Shailesh

last: Pande


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from adult WT and Dp16 mouse liver tissue

summary: Analysis of steady-state mRNA levels in mouse liver tissue at 19-26 weeks from wild-type C57BL/6J and Dp(16)1Yey mice.

overall_design: Comparison of wild-type (n=6) and Dp16 (n=6).


title: Crosstalk between the polycomb repressive complex 2 and DNA methylation mediates neuroendocrine prostate cancer lineage plasticity [RRBS]

city: New York City

first: Richa

last: Singh

address: 413 East, 69th street

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

type: Methylation profiling by high throughput sequencing

summary: Acquired changes in DNA methylation have been proposed as a mechanism underlying epigenetic plasticity in several cancer types. In prostate cancer, methylation changes are dynamic, with preclinical studies pointing to a tumor suppressor role of the DNA methyltransferase DNMT1 in early stage, in contrast to an oncogenic function of DNMT1 in later stage. The importance of DNA methylation dynamics during normal development and cell lineage fate decisions also points to DNA methylation having a critical function in lineage plasticity, yet the mechanisms by which DNA methylation changes drives lineage transitions in prostate cancer is not well understood. DNA methylation can directly repress gene expression but also cooperate with other epigenetic pathways to modulate downstream transcriptional activity. The enhancer of zeste homolog 2 (EZH2) protein is a subunit of the polycomb repressive complex 2 (PRC2) and catalyzer of the repressive histone 3 lysine 27 tri-methylation (H3K27me3) mark that also acts to suppress downstream transcriptional activity and has also been implicated in lineage plasticity. EZH2 is overexpressed in castration-resistant prostate cancer (CRPC) including NEPC and is an emerging therapeutic target. Although, the compensatory relationship between DNA methylation and EZH2 has been shown in embryonic stem cell studies and in some cancer types during acquired treatment resistance or immune evasion, how DNA methylation and EZH2/PRC2 interact to modulate prostate cancer lineage plasticity has not been characterized. In this study, we address the potential crosstalk between epigenetic pathways in advanced prostate cancer and demonstrate how DNA methylation and H3K27me3 profiles overlap and cooperate to reprogram the epigenome during prostate cancer lineage plasticity. Using both mouse and patient-derived models, we highlight the compensatory roles of these two repressive machineries during progression of CRPC towards a NE-lineage state. We predict their specific impact on NEPC progression by assessing the associated molecular alterations following genetic and pharmacological perturbations of each.

overall_design: RRBS in mouse prostate tumors, patients' tumor derived organoids and LNCaP cells

first: David

middle: S

last: Rickman


title: Excitatory Neuronal ErbB4 Drives Early Pathophysiology of Alzheimer's Disease

city: Daejeon

first: Se Young

last: Lee

address: Daehakro 291

institute: KAIST

summary: Neuroinflammation and synapse loss synergistically contribute to cognitive decline in Alzheimer’s disease (AD). Although microglial hyper-phagocytic activity has been shown to mediate synapse loss, the exact mechanisms underlying these pathologies remain obscure. Here, we first demonstrate that astrocytes and microglia increase the phagocytic elimination of excitatory synapses, but significantly decrease their elimination of inhibitory synapses during AD progression, suggesting neuroinflammation may be dispensable for early AD synapse loss. Instead, through single-nucleus RNA sequencing (snRNAseq), we identified Disease-Initiating Excitatory Neurons (DIENs), characterized by ectopic Erbb4 expression, as the earliest alteration in an AD mouse model. Notably, specific deletion of Erbb4 in 5XFAD excitatory neurons abrogated abnormal neuro-network activities and synapse loss, as well as reactive gliosis, amyloid plaque deposition, and cognitive deficits. Conversely, overexpression of Erbb4 in wild-type excitatory neurons recapitulated key AD phenotypes, including cognitive impairment. Subsequent snRNAseqs following Erbb4 deletion and overexpression confirm that excitatory neuronal Erbb4 is both sufficient and necessary to induce DIEN and reactive gliosis. Together, these findings reveal that the early pathophysiology of AD arises largely due to aberrant Erbb4 expression in excitatory neurons, and that targeting excitatory neuronal Erbb4 may thus represent a novel therapeutic strategy for mitigating AD progression.

overall_design: For 2-month-old 5XFAD and 3-month-old WT and 5XFAD, hippocampi were isolated and analyzed by snRNAseq. For 4-month-old WT and 5XFAD, 3 weeks after AAV injection, hippocampal CA1 were isolated and analyzed.

first: SeYoung

first: Won-Suk

last: Chung


title: A metabolism-chromatin axis promotes ribosome heterogeneity in the human malaria parasite [II]

first: Sebastian

last: Baumgarten

overall_design: Protein-DNA proximity labelling approach using the bacterial M.EcoGII 6mA DNA methyltransferase fused to Sir2a. Sir2a interaction with histones leads to 6mA modification of nearby adenines that are identified using direct DNA ONT sequencing

first: Justine

last: Couble

first: Tiziano

last: Vignolini

first: Gregory

last: Dore

first: Bérangère

last: Lombard

first: Michael

last: Richard

first: Damarys

last: Loew

last: Büttner

first: Rafael

last: Dueñas-Sánchez

first: Gernot

last: Poschet

first: Jessica

last: Bryant


title: OTX2 inhibits human pluripotent stem cell reprogramming toward 8-cell-like and morula-like states

city: luzhou

last: Jiang

state: sichuan

address: 1st xianglinlu

institute: southwest medical university

summary: In human embryos, major zygotic genome activation (ZGA) initiates at the 8-cell (8C) blastomere stage, marking the initiation of the ontogenesis program. Recent advancements have demonstrated that human pluripotent stem cells (hPSCs) can revert to 8C-like cells (8CLCs) with totipotency in vitro. However, the key regulators involved this transition remain largely unexplored. In this study, we identified OTX2 as a novel regulator repressing the induction of 8C-like cells (8CLCs) from hPSCs. Our findings reveal that OTX2 depletion facilitates the generation TPRX1-EGFP+ totipotent-like stem cells (TLSCs), which closely resemble the transcriptomic profile and chromatin accessibility of 8C blastomeres. Notably, TLSCs with OTX2 depletion exhibit bidirectional embryonic and extraembryonic differentiation potential in forming chimeric embryos. OTX2 influences totipotent state transition by binding at loci of key 8CLC regulator, which function in parallel with DUX4. Collectively, our findings reveal a previously unrecognized function of OTX2 in regulating totipotency and establish a new framework for generating TLSCs from hPSCs in vitro, offering significant insights for stem cell biology and regenerative medicine.

overall_design: Total of 38 samples were analyzed, which included primed hPSCs, naive hPSCs and TLSCs. We conducted RNA-seq to analyzed the transcriptome difference between different samples during the transition from primed hPSCs to TLSCs.

first: Bingqing

last: Xie


title: Effect of depletion of ISG20 on gene expression in EMT6 mouse breast cancer cells with RNA-Seq.

city: Baltimore

first: YONGKANG

last: YANG

state: Maryland

address: Room 673, MRB, 725 North Broadway

department: ICE

institute: Johns Hopkins University

summary: Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype with the highest rates of recurrence, metastasis and patient mortality due to lack of effective targeted therapies. In this study, we demonstrate that ISG20 expression is induced by hypoxia and directly targeted by HIF-1 for transcription in TNBC cells. ISG20 functions as RNA exonuclease to target mRNAs for degradation, resulting in breast cancer stem cell specification and lung metastasis, and also cancer cell immune evasion. Mostly importantly, ISG20 silencing could markedly increase the sensitivity of TNBC to anti-PD1 immune checkpoint blockade (ICB) in a mouse model. Our data suggested that, in combination with immunotherapy, targeting ISG20 might be an effective strategy for TNBC treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for EMT6 subclone of NTC and ISG20 knockdown that were exposed in 20% or 1% oxygen condition for 48 hours.

first: Yongkang

last: Yang

first: Gregg

middle: L

last: Semenza


title: DNA interactions of transcriptional co-regulator LEUNIG_HOMOLOG (LUH) during early stages of Arabidopsis flower development.

first: Cezary

last: Smaczniak

summary: Transcriptional co-regulators are key modulators of gene expression, often functioning in complexes with transcription factors to regulate chromatin dynamics. LEUNIG_HOMOLOG (LUH) is a member of the conserved Groucho/Tup1 family of co-regulators in Arabidopsis, yet its role in flower development remains poorly understood. While LEUNIG (LUG), a homolog of LUH, has been extensively studied in floral organ identity specification, contributions of LUH appear to be both overlapping and distinct from LUG. Here, we investigate the LUH regulome, uncovering its dynamic protein interactions with transcriptional cofactors, histone-modifying enzymes, chromatin remodelers, and transcription factors, including MADS-domain proteins APETALA1 and SEPALLATA3. Using high-throughput DNA occupancy and transcriptomic analyses, we identify LUH target genes and their expression dynamics across floral developmental stages. Comparative transcriptome profiling of luh and lug mutants in floral induction system reveals unique regulatory functions of LUH. Furthermore, we provide some evidence for a dual role of LUH in transcriptional activation and repression. Our findings contribute to understanding how LUH modulates transcriptional responses and chromatin state to fine-tune flower development in Arabidopsis.

overall_design: To study the high-throughput DNA occupancy of LUH protein at various stages of flower development, we conducted a series of chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments using the LUH-GFP in floral induction system (FIS) plant line (pLUH:LUH-GFP in pAP1:AP1-GR ap1 cal). We focused on four time points after the induction of flowering corresponding to: undifferentiated inflorescence meristem (0 days after induction, 0 DAI), meristem specification (2 DAI), organ specification (4 DAI), and organ differentiation (8 DAI). At least two biological replicates of each time point were prepared with the input samples as controls. We used GFP antibodies (#ab290, Abcam) for the immunoprecipitation.

first: Rosario

last: Vega-Léon

first: Jose

last: Muino

first: Maurizio

last: Pimentel

first: Kerstin

last: Kaufmann


title: Pancreatic gene expression patterns during PDAC development in mice

first: Julian

last: Frädrich

summary: This is a bulk RNA sequencing dataset of pancreatic tumors of varying disease grades from genetically engineered PDAC-bearing KPC mice (Pdx-1+/Cre; Kras+/LSL-G12D; Trp53+/LSL-R172H) (n = 24), and healthy controls (n = 11). KPC-derived tissues comprised early PDAC (only pancreatic remodeling and/or preinvasive lesions) to advanced disease (PDAC grades 2, 3, and 4). Mice resulting from KPC strain breeding, which did not carry Pdx-1+/Cre but only Kras+/LSL-G12D and/or Trp53+/LSL-R172H-mutations, or which carried no mutation at all, served as control animals. To identify the changes in pancreatic gene expression during PDAC development, bulk RNAseq was performed on harvested pancreatic tissues.

overall_design: Total RNA was isolated from banked frozen pancreatic tissues using the RNeasy Plus Mini Kit (Qiagen) and RNAseq was performed on a NovaSeq X Plus platform (Illumina).

first: Achim

last: Krüger


title: Crosstalk between the polycomb repressive complex 2 and DNA methylation mediates neuroendocrine prostate cancer lineage plasticity [RNA-Seq]

first: Richa

last: Singh

overall_design: RNA-Seq in mouse prostate tumors

first: David

last: Rickman


title: Crosstalk between the polycomb repressive complex 2 and DNA methylation mediates neuroendocrine prostate cancer lineage plasticity [ChIP-Seq]

overall_design: H3K27me3 and H3K4me3 ChIP-Seq in mouse prostate tumors and in decitabine-treated NEPC patients' tumor derived xenografts


title: Transcriptome profiling of leunig_homolog (luh) and leunig (lug) mutants in floral induction system (FIS) during early stages of Arabidopsis flower development

overall_design: RNA-seq profiling of luh and lug mutants in floral induction system (FIS) plant line (pAP1:AP1-GR ap1 cal). We focused on four time points after the induction of flowering corresponding to: undifferentiated inflorescence meristem (0 days after induction, 0 DAI), meristem specification (2 DAI), organ specification (4 DAI), and organ differentiation (8 DAI). Three biological replicates of each time point were prepared.


overall_design:
Total of 12 samples were analyzed, which included primed hPSCs, naive hPSCs and TLSCs. We conducted Cuttag  to analyzed the epigeneitc difference between different samples during the transition from primed hPSCs to TLSCs.
Total of 6 samples were analyzed, which included H3K4me3, H3K27me3 and H3K9me3 in WT and OTX2-KO me4CL cells. We conducted Cuttag  to analyzed the epigeneitc difference between WT and OTX2-KO condition in me4CL cells.Total of 6 samples were analyzed, which included H3K4me3, H3K27me3 and H3K9me3 in WT and OTX2-KO me4CL cells. We conducted Cuttag  to analyzed the epigeneitc difference between WT and OTX2-KO condition in me4CL cells.


overall_design: Total of 12 samples were analyzed, which included primed hPSCs, naive hPSCs and TLSCs. We conducted ATAC-SEQ  to analyzed the epigeneitc difference between different samples during the transition from primed hPSCs to TLSCs.


title: scRNA-seq transcriptomic profiles of cochlear and vestibular hair cells from adult mice [10_weeks_CBAJ]

city: Omaha

middle: Z

last: He

state: NE

address: 2500 California Plaza

department: Biomedical Science

institute: Creighton University

summary: The cochlear and vestibular sensory epithelia contain four different hair cell (HC) types for detecting sound and motion. There are substantial differences in morphology and function among them. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of HCs in the inner ear.

overall_design: HCs from cochlear and vestibular sensory organs were isolated. cDNA library were constructed using the 10x Genomics Chromium Single Cell 3’ Reagent Kits V3.1.  7 mice were used for each biological replicate, and 6 biological replicates for cochlear sensory epithelium and 4 biological replicates vestibular sensory epithelia were prepared. Illumina NextSeq 6000 sequencer was used for sequencing.

first: Zhenhong

last: Xu

first: Samadhi

last: Kulasooriya

first: Huizhan

last: Liu


title: Streptavidin mediated CLEAR-CLIP in desmoplakin-BirA overexpressing mouse keratinocyte

city: Chicago

first: Rui

last: Yi

state: IL

address: 303 E. Chicago Avenue

institute: Northwestern University

summary: Argonautes were found to be located at desomosal plaque. To specifically identify Argonaute binding microRNA-RNA species, Desomoplakin fused biotin ligase BirA was overexpressed in mouse keratinocytes. By pulling down Biotin labled proteins using streptavidin, we examines the functions of Argonautes at desmosomal plaques.

overall_design: Desomoplakin fused with biotin ligase BirA was overexpressed in mouse keratinocytes. Streptavidin was used to pull down all biotinated proteins at the desmosomal plaque, including Argonautes. By sequencing microRNA-mRNA chimeras using CLEAR-CLIP technique, the function of Argonautes at desmosomal plaque could be inferred.

first: Glen

last: Bjerke


title: Type I Interferon Induced Apoptosis Drives Chronic Wounds in ISG15 deficiency

city: New York

first: Dusan

last: Bogunovic

state: NY

institute: Columbia Univesity

summary: Chronic exposure to IFN-I in ISG15 deficiency drives impaired wound healing, improper macrophage activation and enhanced Epithelial-to-Mesenchymal transition, likely causing fibrosis in multiple organ systems.

overall_design: This is a cross-sectional study involving the accrual of 3-4-mm skin punch biopsy samples from one healthy control and biologic naïve ISG15 deficient patients with skin lesions. The samples were then subjected to the protocols entailed by spatial transcriptomics platform.

first: Christos

last: Sazeides

first: Ikjot

last: Sidhu


title: MED19 Promotes 2’-O-methylation of rRNA to Facilitate IRES-Dependent c-Myc Translation

city: Shanghai

first: Yang

last: Ming

address: No.2005,Songhu Road

institute: Fudan Universitry

summary: The Mediator is an essential co-factor of Pol II-dependent transcription, and MED19 is a subunit of this complex. MED19 has been reported to overexpress in various cancers to promote cancer progression, although the underlying mechanism remains elusive. Here, we unexpectedly discovered that the MED19 protein can localize to the nucleolus independently of the Mediator complex. The nucleolus localization of MED19 depends on a patch of poly-lysine sequence at its C-terminus, which is important for MED19 to directly bind ribosomal RNA (rRNA) and FBL, the catalytic enzyme of 2'-O-methylation, thus promoting the 2'-O-methylation level of rRNA. Mature ribosomes with highly 2'-O-methylated rRNA can more effectively translate from the internal ribosome entry sites (IRES), while the oncogenic c-Myc contains a typical IRES-element at its 5’ UTR. We show that the knockdown of MED19 significantly reduces the protein abundance of c-Myc without affecting its mRNA level. Pan-cancer analyses further demonstrate a positive correlation between MED19 and c-Myc at the protein but not mRNA level. Collectively, our findings reveal an important role of the Mediator-independent MED19 in translational control of c-Myc, thus providing novel mechanistic insights into the c-Myc-driven tumorigenesis.

overall_design: CLIP-seq of MED19 in 293T cells

first: Wang

last: Gang


title: MED26 regulates H3K4Me3 by recruiting the COMPASS complex

summary: In the nucleus of cells, the regulation of gene expression is a sophisticated and finely tuned process, in which histone modifications play a crucial role. One such modification, H3K4me3 (the trimethylation of lysine 4 on histone H3), is associated with active transcription and typically occurs at promoter regions to facilitate gene expression. Recent studies have illuminated the mechanism by which MED26, a component of the Mediator complex, regulates H3K4me3 levels through the recruitment of the COMPASS (Complex Proteins Associated with Set1) complex.The COMPASS complex is responsible for catalyzing the methylation of histone H3 at lysine 4, an essential step in the activation of gene transcription. MED26 acts as a bridge between the Mediator complex, which is involved in the assembly of transcriptional machinery at gene promoters, and the COMPASS complex. By facilitating this interaction, MED26 ensures that the COMPASS complex is correctly positioned to modify histones, thereby influencing the chromatin structure and accessibility of genes for transcription. This regulatory mechanism underscores the importance of MED26 in coordinating the activities of different protein complexes during gene expression, contributing to cellular functions and development. Understanding the precise role of MED26 in this context provides valuable insights into the molecular mechanisms underlying gene regulation and may have implications for the treatment of diseases associated with aberrant gene expression.

overall_design: H3K4Me3 ChIP-seq and IgG ChIP-IP in WT 293T cells.

first: Zhou

last: Qing


title: RNA-seq Analysis of Sox9f/f and Sox9HKO Mouse Primary Hepatocyte Transcriptomes

city: 上海

first: shuqing

address: 415 Fengyang Road

department: gastroenterology

institute: shanghai changzheng hospital

summary: Purpose: To identify the alterations of genes transcriptional profile of hepatocytes obtained from Sox9f/f mice and Sox9HKO mice treated with partial hepatectomy (PHx). Methods: Sox9HKO mice were generated by Sox9f/f mice injected with AAV-TBG-Cre via tail. Sox9f/f mice and Sox9HKO mice were treated with PHx to induce liver regeneration. Liver mRNA profiles of 12-week-old Sox9f/f  and  Sox9HKO mice treated with PHx were generated by deep sequencing, using Illumina Novaseq 6000. We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05. RT–PCR validation was performed using SYBR Green PCR Kit. Results: We identified the transcripts in the hepatocytes of Sox9f/f and Sox9HKO mice. 1379 transcripts showed differential expression between Sox9f/f and Sox9HKO mouse hepatocytes, with a  |log2FC| > 1 and P value < 0.05. Altered expression of 4 genes was confirmed by qRT–PCR. Conclusion:  Our study represents the first detailed analysis of liver transcriptomes of Sox9HKO mice during liver regeneration. RNA-seq based transcriptome analysis would provide us with a better understanding of the complex biologic functions of Sox9 in the hepatocyte during the pricess of hepatocyte proliferation in mice.

overall_design: Examine the hepatocyte mRNA profiles of 12-week old Sox9f/f mice and Sox9HKO mice treated with PHx by RNA-seq technolodgy


title: snRNA-seq Analysis of Sox9f/f and Sox9HKO Mouse Liver Transcriptomes

summary: Purpose: To identify the alterations of genes transcriptional profile of livers obtained from Sox9f/f mice and Sox9HKO mice treated with partial hepatectomy (PHx). Methods: Sox9HKO mice were generated by Sox9f/f mice injected with AAV-TBG-Cre via tail. Sox9f/f mice and Sox9HKO mice were treated with PHx to induce liver regeneration. Liver mRNA profiles of 12-week-old Sox9f/f  and  Sox9HKO mice treated with PHx were generated by deep sequencing, using 10 × library preparation, each cDNA molecule was tagged on the 3’end of a mRNA transcript with unique molecular identifiers (UMI) and cell labels indicating its cell of origin on cDNA synthesis. We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05. Results: We identified the transcripts in the livers of Sox9f/f and Sox9HKO mice and identified the differential expression between Sox9f/f and Sox9HKO mouse hepatocytes, with a  |log2FC| > 1 and P value < 0.05. Conclusion:  Our study represents the first detailed analysis of liver transcriptomes of Sox9HKO mice during liver regeneration. snRNA-seq based transcriptome analysis would provide us with a better understanding of the complex biological functions of Sox9 in the hepatocyte during the process of hepatocyte proliferation in mice.

overall_design: Examine the hepatocyte mRNA profiles of 12-week old Sox9f/f mice and Sox9HKO mice treated with PHx by snRNA-seq technolodgy


title: Circadian Reprogramming by Timed Sodium Intake Reveals Transcriptional Pathways of Daily Salt Handling in the Colon.

city: Irvine

first: Kousha

last: Changizi

state: California

address: Donald Bren Hall

department: ICS/IGB

institute: University of California, Irvine

summary: The circadian gene expression in peripheral tissue displays rhythmicity which is reprogrammed by feeding rhythms and dietary composition in mammals. In this study, circadian transcriptome was performed to investigate how the circadian clock and mineralocorticoid receptor contribute to daily gene expression in the colon.

overall_design: 8- to 12-week-old, gut-specific Bmal1 knockout mice and MR knockout mice were subjected to ad libitum normal chow diet. 8-week-old male C57BL/6 mice were subjected to time-restricted feeding of low- or high-salt diet under 12hr light/ 12hr dark schedule. Tissues were harvested every 4 hours over the circadian cycle at ZT0, 4, 8, 12, 16, 20 (n=3 per time point per group). Total RNA was extracted from the colon, and used for RNA-seq.

first: Takuto

last: Torimitsu

first: Kenichiro

last: Kinouchi

last: Changizi Ashtiani

first: Sherif

last: Abdelkarim

first: Pierre

last: Baldi

first: Hiroshi

last: Itoh


title: Critical role for a high-plasticity cell state in lung cancer

first: Jason

middle: Earl

last: Chan

address: 1275 York Ave, Box 20

department: Medicine

institute: Memorial Sloan Kettering Cancer Center

summary: Plasticity—the ability of cells to undergo phenotypic transitions—drives cancer progression and therapy resistance. Recent studies have suggested that plasticity in solid tumors is concentrated in a minority subset of cancer cells, yet functional studies interrogating this high plasticity cell state (HPCS) in situ are lacking. Here, we develop mouse models enabling detection, longitudinal lineage tracing, and ablation of the HPCS in autochthonous lung tumors in vivo. Lineage tracing reveals that the HPCS cells possess high capacity for cell state transitions, giving rise to both early neoplastic (differentiated) and progressed lung cancer cell states in situ. Longitudinal lineage tracing using secreted luciferases reveals HPCS-derived cells harbor high capacity for growth when compared to bulk cancer cells or another cancer cell state with features of differentiated lung epithelium. HPCS ablation in early neoplasias abrogates benign-to-malignant transition, whereas ablation in established tumors by suicide gene or CAR T cells robustly reduces tumor burden. We further demonstrate that the HPCS gives rise to therapy-resistant cell states, whereas HPCS ablation suppresses resistance to chemotherapy and oncoprotein-targeted therapy. Interestingly, an HPCS-like state is ubiquitous in regenerating epithelia and in carcinomas of multiple other tissues, revealing a convergence of plasticity programs. Our work establishes the HPCS as a critical hub enabling reciprocal transitions between cancer cell states. Targeting the HPCS in lung cancer and in other carcinomas may suppress cancer progression and eradicate treatment resistance.

overall_design:
KP mice with either Slc4a11-FSF-MCD/+ with either Hipp11-FSF-GGCB/+ or Rosa26-FSFmTmG/+ reporter alleles or Hopx-FSF-MACD/+ mouse model with either Hipp11-FSF-GGCB/+ or Rosa26-FSF-mTmG/+ alleles were infected by adenoviral CMV-FlpO or lentiviral PGK-FlpO recombinase. Mice with tumors were treated as indicated and tumor cells were hashed with TotalSeq B and then isolated for single-cell mRNA sequencing after FACS purification. One dataset is KP Rosa26-tdTomato/+ with tumors harvested 14 weeks post tumor initiation. One dataset is a KP Slc4a11-MCD/+ iRFP670-GLuc cell line transplant.
Please note that GSM9193561/GSM9193562 are biological replicate of GSM8529536/GSM8529537, sequenced on separate lanes and have different featureref.csv files.

middle: E

first: Chunhao

last: Pan

first: Doron

last: Betel

first: Tuomas

last: Tammela


title: CSF1R marks a subset of foetal LMPPs with Acute Myeloid Leukaemia propagation properties in a KMT2A-MLLT3 mouse model

city: Edinburgh

first: Giuseppina

last: Camiolo

state: Edinburgh

address: EDINBURGH BIOQUARTER

institute: CENTRE FOR REGENERATIVE MEDICINE - THE UNIVERSITYOF EDINBURGH

summary: As KMT2A-MLLT3 oncoprotein can give rise to ALL and AML in infants, we investigated whether such choice could lie in two subsets of foetal LMPPs, that express or not CSF1R, and found that CSF1R mark a more potent subpopulation with leukaemic-initiating

overall_design: Murine CSF1R+/-LMPPs (Lin- Sca1+ ckit+ CD45+ Flt3+CSF1R+/-) were sorted from KMT2AMLLT3-expressing E14.5 foetal livers. Cell populations were analysed by bulk RNA-Seq

first: Katrin

last: Ottersbach


title: Epigenetic profiling of prostate adenocarcinoma and neuroendocrine prostate cancer models to understand DNMT-EZH2 crosstalk. [RNA-Seq]

city: Boston

first: Varadha Balaji

last: Venkadakrishnan

state: MA

address: 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

summary: EZH2-DNMT crosstalk is diverse across prostate adenocarcinoma and neuroendocrine prostate cancer.

overall_design: Epigenetic profiling was performed in prostate cancer models upon DNMT1 silencing.

first: Venkadakrishnan

last: Varadha Balaji

first: Beltran

last: Himisha


title: Discovery of an HIV-1-encoded circular RNA that enhances viral transcription

city: New Haven

first: Grace

last: Chen

state: CT

address: 300 Cedar Street

institute: Yale School of Medicine

summary: Circular RNAs (circRNAs) are a class of transcripts that are formed when portions of a pre-mRNA molecule are spliced together in a closed loop. Here, we discover a novel HIV-1-encoded viral circRNA present in patient-derived plasma and infected T-cell lines, demonstrating that an RNA retrovirus can generate circRNAs. This HIV-1-encoded circRNA is packaged within HIV-1 virions, binds the HIV-1 Tat protein, and enhances transcription from the HIV-1 promoter. Our study sheds lights on a previously overlooked aspect of HIV-1 transcription and presents interactions between viral proteins and viral circRNAs as novel mechanisms underlying viral pathogenesis.

overall_design: Total RNA was isolated from uninfected Jurkat T-cells and two HIV-1 infected Jurkat-derived clones (8B10 and 5F9). Each clone contains stable integration of a modified HIV-1 provirus (NL4-3-d6-GFP) containing a GFP reporter gene and loss-of function mutations in all viral ORFs except for those encoding Tat and Rev. Following isolation, total RNA from each sample was further processed to yield three fractions with varying levels of circRNA enrichment: (i) poly(A)-enriched RNA, containing minimal circRNA enrichment, (ii) RNA depleted of both poly(A)-tailed and ribosomal RNAs, containing moderate circRNA enrichment (RR0), and (iii) RNA depleted of both poly(A)-tailed and ribosomal RNAs then further treated with the exonuribonuclease RNase R for for 2 hours (RR120), containing high circRNA enrichment. Of note, the RR0 fraction was also mock-digested with water in place of enzyme for 2 hours. Two replicates were generated for each RNA fraction for a total of 18 libraries (3 cell lines x 3 RNA fractions x 2 replicates). Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit and sequenced on an Illumina Next-Seq Machine (1x150bp reads, single-end).

first: Prisca

last: Obi

first: Ye


title: The PLK1 Inhibitor Onvansertib in Combination with FOLFIRI and Bevacizumab in Second-line Treatment of KRAS-mutant Metastatic Colorectal Cancer: A Single-Arm, Phase II Trial.

city: San Diego

first: Peter

last: Croucher

address: 11055 Flintkote Avenue

institute: Cardiff Oncology Inc

summary: Purpose: This phase II study evaluated the efficacy and tolerability of onvansertib, a polo-like kinase 1 (PLK1) inhibitor, combined with FOLFIRI + bevacizumab for the second-line treatment of KRAS-mutant metastatic colorectal cancer (mCRC).  Patients and Methods: This multicenter, open-label, single-arm study enrolled KRAS-mutated mCRC patients previously treated with oxaliplatin and 5-fluorouracil with or without bevacizumab. Patients received onvansertib 15 mg/m2 (days 1-5 and 15-19 of a 28-day cycle) and FOLFIRI + bevacizumab (days 1 and 15). The primary endpoint was the objective response rate (ORR), and secondary endpoints included progression-free survival (PFS), duration of response (DOR), and tolerability. Translational and preclinical studies were conducted in KRAS-mutant CRC.   Results: Among the 53 patients treated, the confirmed ORR was 26.4% (95% CI, 15.3 to 40.3). The median DOR was 11.7 months (95% CI, 9.4 to not reached). Grade 3/4 adverse events were reported in 62% of patients. A post hoc analysis revealed that patients with no prior bevacizumab treatment had a significantly higher ORR and longer PFS compared to patients with prior bevacizumab treatment: ORR of 76.9% versus 10.0% (odds ratio of 30.0, p<0.001) and median PFS of 14.9 months versus 6.6 months (hazard ratio of 0.16, p<0.001). Our translational findings support that prior bevacizumab exposure contributes to onvansertib resistance. Preclinically, we showed that onvansertib inhibited the hypoxia pathway and exhibited robust antitumor activity in combination with bevacizumab through the inhibition of angiogenesis.   Conclusion: Onvansertib combined with FOLFIRI + bevacizumab showed significant activity in the second-line treatment of KRAS-mutant mCRC patients, particularly in patients with no prior bevacizumab treatment. These findings led to the evaluation of the combination in the first line setting (ClinicalTrails.gov identifier: NCT06106308).

overall_design: KRAS-mutant CRC cell lines were treated with DMSO or onvansertib at two doses for 20 h and then exposed to hypoxia or kept in normoxia for 4h. RNA-seq data were examined for hypoxia related genes specifically regulated by onvansertib.

first: Daniel

middle: H

last: Ahn

first: Maya

last: Ridinger

first: Timothy

last: Cannon

first: Lawrence

last: Mendelsohn

last: Starr

first: Joleen

last: Hubbard

first: Anup

last: Kasi

first: Afsaneh

last: Barzi

first: Errin

last: Samuëlsz

first: Ramanand

last: Subramanian

first: Anju

last: Karki

first: Divora

last: Yemane

first: Roy

last: Kim

first: Chu-Chiao

last: Wu

middle: J

first: Tod

last: Smeal

first: Fairooz

middle: F

last: Kabbinavar

first: Heinz-Josef

last: Lenz


title: Remote limb ischemic conditioning alleviates nonalcoholic steatohepatitis via extracellular vesicle-mediated muscle-liver crosstalk [miR_181_RNAseq]

first: Yichao

last: Zhao

state: China

address: #160 Pujian Road, Shanghai,China

department: Renji Hospital

institute: Shanghai Jiaotong University

summary: Nonalcoholic steatohepatitis (NASH) is an advanced form of nonalcoholic fatty liver disease with adverse outcomes that currently lacks approved medication. Muscle-liver interaction has emerged as one of the critical determinants governing NASH progression. Here, we report that remote limb ischemic conditioning (RIC), a clinically validated therapy for distant ischemic organ protection by transient muscle ischemia, significantly alleviated NASH in different mouse models. The anti-NASH effect of chronic RIC treatment was mediated by the muscle-to-liver transfer of extracellular vesicles (EVs) and their cargo microRNAs, leading to elevation of miR-181d-5p in the liver. Hepatic miR-181d-5p overexpression faithfully mirrored the benefits of RIC treatment via suppression of nuclear receptor 4A3. Furthermore, administration of circulating EVs from human volunteers undergoing RIC treatment improved NASH phenotypes and transcriptomic perturbations in primary human hepatocytes and animal models. Our data underscore the translational potential of RIC treatment for NASH management and extend our understanding of muscle-liver crosstalk.

overall_design: Mice were fed a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) to induce nonalcoholic steatohepatitis (NASH), and were intravenously injected with control AAVs or AAVs encoding miR-181d-5p. Liver tissues were harvested and subjected to RNA-sequencing.


title: Satb2 gene dosage in cortical projection neurons impacts neuronal maturation and somatosensory processing [ChIP-seq]

city: Santa Cruz

first: Bin

last: Chen

address: 1156 High St.

department: MCD Biology

institute: University of California Santa Cruz

summary: SATB2 Associated Syndrome (SAS) is characterized by severe intellectual deficiency (ID) with limited or absence of speech, behavioral problems, and craniofacial abnormalities. It is caused by de novo heterozygote mutations in the Special AT-rich sequence-Binding Protein 2 (SATB2) gene, which encodes a DNA-binding protein involved in chromatin remodeling. In the brain, SATB2 expression is mostly restricted to the projection neurons in the cerebral cortex and hippocampus. Much of what is known about SATB2 function in brain development comes from studies using homozygous loss-of-function mutant mice. Nonetheless, the heterozygous loss of SATB2 negatively impacts brain development, as identified in SAS patients. Here, we report a dose-dependent requirement for Satb2 in regulating subtype specification for layer 5 subcerebral and all intra-telencephalic neurons, as a modulator of gene expression, through its binding to gene promoters and enhancers of many ID genes. Consequently, Satb2 haploinsufficiency in humans, and in mice as we show here, results in aberrations of cortical projection axons that impact mouse sensory behavior including discriminative touch and vocalization.  Our findings uncover fundamental mechanisms underlying the etiology of SAS.

overall_design: ChIP-seq using Satb2 antibodies with wild-type mouse cortices at post-natal day 0

first: Thomas

last: Finn

first: Jeremiah

last: Tsyporin

first: Gabrielle

last: Servito

first: Sol

last: Katzman


title: Satb2 gene dosage in cortical projection neurons impacts neuronal maturation and somatosensory processing

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

overall_design: Refer to individual Series


title: Remote limb ischemic conditioning alleviates nonalcoholic steatohepatitis via extracellular vesicle-mediated muscle-liver crosstalk [RIC Sham]

overall_design: Mice were fed a normal chow (NC) or a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) to induce nonalcoholic steatohepatitis (NASH), and were subjected to remote limb ischemic conditioning (RIC) or sham treatment. Liver tissues were harvested and subjected to RNA-sequencing.


title: OTX2 inhibits human pluripotent stem cell reprogramming toward 8-cell-like and morula-like states

last: Jiang

summary: In human embryos, major zygotic genome activation (ZGA) initiates at the 8-cell (8C) blastomere stage, marking the initiation of the ontogenesis program. Recent advancements have demonstrated that human pluripotent stem cells (hPSCs) can revert to 8C-like cells (8CLCs) with totipotency in vitro. However, the key regulators involved this transition remain largely unexplored. In this study, we identified OTX2 as a novel regulator repressing the induction of 8C-like cells (8CLCs) from hPSCs. Our findings reveal that OTX2 depletion facilitates the generation TPRX1-EGFP+ totipotent-like stem cells (TLSCs), which closely resemble the transcriptomic profile and chromatin accessibility of 8C blastomeres. Notably, TLSCs with OTX2 depletion exhibit bidirectional embryonic and extraembryonic differentiation potential in forming chimeric embryos. OTX2 influences totipotent state transition by binding at loci of key 8CLC regulator, which function in parallel with DUX4. Collectively, our findings reveal a previously unrecognized function of OTX2 in regulating totipotency and establish a new framework for generating TLSCs from hPSCs in vitro, offering significant insights for stem cell biology and regenerative medicine.

overall_design: Single-cell RNA sequencing (scRNA-seq) was performed using the 10x Genomics platform to profile cell subpopulations in 4CL and me4CL cells under both wild-type (WT) and OTX2 knockout (KO) conditions, comprising a total of four samples.

first: Bingqing

last: Xie