title: Genome-wide evaluation of altered chromatin looping in the post-stroke mouse cortex using Hi-C chromatin conformation capture

city: Tampa

first: Ashutosh

last: Dharap

state: FL

address: 4001 E Fletcher Ave

department: Molecular Medicine

institute: University of South Florida

summary: Recent advances in high-throughput transcriptomics have revealed extensive gene expression changes during cerebral ischemia. However, the changes in 3D chromatin architecture and long-range chromatin looping between genes and distal regulatory elements that drive these gene expression changes remain virtually unexplored. In this study, we mapped the landscape of altered 3D chromatin looping the in the ischemic cortex and evaluated its contributions to post-stroke transcriptional changes. We used genome-wide chromatin conformation capture (Hi-C) to profile changes in the 3D chromatin architecture in the cerebral cortex of adult mice following a 1 h middle cerebral artery occlusion and 6 h of reperfusion, or sham surgery. We identified a total of 15,592 loops in the stroke group with a mean enrichment core of 6.108, and these included 1973 promoter-promoter contacts, 7857 enhancer-enhancer contacts, and 5762 enhancer-promoter contacts. In the sham group, there were 14,779 chromatin loops with a mean enrichment score of 5.473, including 1714 promoter-promoter contacts, 8597  enhancer-enhancer contacts, and 4468 enhancer-promoter contacts. Together, our study represents the first genome-wide evaluation of 3D chromatin looping following stroke.

overall_design: Genome-wide Hi-C was performed on ipsilateral cortices isolated from mice subjected to 1 h middle cerebral artery occlusion (MCAO) using the intraluminal filament model followed by 6 hours of reperfusion, as well as from sham animals that underwent the full surgical procedure except filament insertion.

first: Ankit

last: Patel


title: Single-cell RNA sequencing of the kidneys from kidney-resident macrophage deplated mice [D7]

status: Public on May 30 2025

city: Seoul

first: Donghwan

last: YUN

state: Jongno-gu

address: 103 Daehakro

country: South Korea

institute: Seoul National University Hospital

type: Expression profiling by high throughput sequencing

summary: This study investigates the role of kidney-resident macrophages (KRMs) in modulating susceptibility to tubulointerstitial nephritis (TIN) by selectively depleting KRMs and examining the resulting immunological and pathological changes in the kidney using single-cell RNA sequencing.

overall_design: scRNA-seq datasets were generated from kidneys of mice treated with either αCSF1R Ab or control Ab, harvested at 7 days post-injection to assess temporal changes associated with KRM depletion.

first: Minki

last: Hong

last: Yun

first: Seung Seok

last: Han


title: High protein intake causes gene-length-dependent transcriptional decline, shortens lifespan and accelerates ageing in progeroid DNA repair‐deficient mice

city: Utrecht

first: Wilbert

last: Vermeij

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center

summary: Dietary composition can significantly influence health and lifespan, however, robust knowledge on which food components, at what concentration exert which long-term health effects is still incomplete. Here, we explored the effects of dietary protein intake on Ercc1Δ/- DNA-repair-deficient mice, which are an excellent model for accelerated ageing and are hyperresponsive to the anti-ageing effect of dietary restriction. Restricting dietary protein by 50% extended lifespan in male mice, but not in females. Restricting protein levels beyond 80% improved various neurological health parameters, while a further reduction to 95% affected appetite and became distinctly detrimental. Conversely, a near doubling of protein intake and isocaloric compensatory lowering with carbohydrates significantly shortened lifespan in both sexes. Gene expression analysis of liver from mice on a high-protein, low-carbohydrate diet to those on high-carbohydrate, low-protein revealed increased expression of oxidative phosphorylation, enrichment of processes associated with tissue injury, inflammation, and gene-length-dependent transcriptional decline (GLTD), recently shown to be indicative of DNA damage accumulation causing transcription stress, and cellular ageing. Finally, GLTD was also identified by reanalysis of publicly available data of wild-type mice, rats and humans on high-protein diets, suggesting that increased dietary protein enhances GLTD and accelerates systemic ageing. Together, our findings have implications for nutritional guidelines for progeroid DNA-repair-deficient human syndromes, caution against excessive protein intake in the context of sustaining health, and suggest GLTD as a sensitive read-out of overall health and a predictor of biological ageing.

overall_design:
4 different groups (n=4 per group):
Ercc1Δ/− progeroid 11 weeks ad libitum standard AIN93G;
Ercc1Δ/− progeroid 11 weeks ad libitum Low-protein (70%), High-carbohydrate (~112%);
Ercc1Δ/− progeroid 11 weeks ad libitum Low-carbohydrate (70%), High-protein (~194%);
Ercc1Δ/− progeroid 11 weeks ad libitum Low-fat (70%), High-carbohydrate (~112%);
Diets were isocalorically compensated. Please see the associated research paper for exact dietary compositions.

first: Ivar

last: van Galen

first: Rutger

middle: A

last: Ozinga

first: Ricfrid

middle: W

last: van der Marel

first: Jan

middle: H

last: Hoeijmakers

first: Martijn

middle: E

last: Dollé

middle: P


title: Spatial constraints and cell surface molecule depletion structure a randomly connected learning circuit

city: Ann Arbor

first: Maria

last: Ahmed

address: 1105 North University

country: USA

institute: University of Michigan

summary: The brain can represent almost limitless objects to “categorize an unlabeled world”. This feat is supported by expansion layer circuit architectures, in which neurons carrying information about discrete sensory channels make combinatorial connections onto much larger postsynaptic populations. Combinatorial connections in expansion layers are modeled as randomized sets. The extent to which randomized wiring exists in vivo is debated, and how combinatorial connectivity patterns are generated during development is not understood. Non-deterministic wiring algorithms could program such connectivity using minimal genomic information. Here, we investigate anatomic and transcriptional patterns and perturb partner availability to ask how Kenyon cells, the expansion layer neurons of the insect mushroom body, obtain combinatorial input from olfactory projection neurons. Olfactory projection neurons form their presynaptic outputs in an orderly, predictable, and biased fashion. We find that Kenyon cells accept spatially co-located but molecularly heterogeneous inputs from this orderly map, and ask how Kenyon cell surface molecule expression impacts partner choice. Cell surface immunoglobulins are broadly depleted in Kenyon cells, and we propose that this allows them to form connections with molecularly heterogeneous partners. This model can explain how developmentally identical neurons acquire diverse wiring identities

overall_design: Pupal Kenyon cells at 3 stages (36h, 48h, and 60hAPF) were genetically labeled with GFP, using the drivers MB247 or OK107, and isolated by Fluorescence-activated cell sorting. Sorted Kenyon cells were then sequenced to generate 6 scRNA-Seq libraries.

first: Donnell

middle: L

last: Williams

first: Eleanor

middle: J

last: Clowney


title: Transcriptomic analysis of neuroblastoma cells in response to Earle's balanced salt solution treatment

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

country: China

institute: Union Hospital of Tongji Medical College

summary: Neuroblastoma, the most common extracranial solid malignancy in infants and young children, originates from aberrant neural crest cells and accounts for 10-15% of childhood cancer deaths. However, the underlying mechanisms regulating neuroblastoma progression remain to be determined. To investigate the mechanisms regulating tumorigenesis and aggressiveness, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human neuroblastoma SH-SY5Y cells in response to treatment with Earle's balanced salt solution (EBSS) free of amino acids. The results showed that 1118 and 1392 genes were respectively elevated or reduced in SH-SY5Y cells after EBSS treatment. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to EBSS treatment in human neuroblastoma cells, and these findings will help us understand the pathogenesis of neuroblastoma progression.

overall_design: Total RNA of cells treated with control complete medium or EBSS was extracted using the TRIzol® reagent according to the manufacturer's instructions. RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on an Illumina HiSeq X Ten platform were performed by Wuhan SeqHealth Technology Co., Ltd. (Wuhan, China), and 100 bp paired-end reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.

first: Liduan

last: Zheng


title: Silencing TET1 expression alters the epigenomic landscape and amplifies transcriptomic responses to allergen in airway epithelial cells [ATAC-seq]

city: Davis

first: Hong

last: Ji

state: CA

address: 1 Shields Ave

department: California National Primate Research Center

institute: University of California, Davis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Previous studies have demonstrated that TET1 plays a protective role against house dust mite (HDM)-induced allergic airway inflammation. TET1 transcriptionally responded to HDM extract and regulated the expression of genes involved in asthma in human bronchial epithelial cells (HBECs). How TET1 regulates expression of these genes, however, is unknown. To this end, we measured mRNA expression, DNA methylation, chromatin accessibility and histone modifications in control and TET1 knockdown HBECs treated or untreated with HDM extract. Throughout our analyses of multi-omics data, we detected significant similarities between the effects of TET1 knockdown alone and the effects of HDM treatment alone, all enriched for asthma-related genes and pathways. One especially striking pattern was that both TET1 knockdown and HDM treatment generally led to decreased chromatin accessibility at many of the same genomic loci. Transcription factor enrichment analyses indicated that altered chromatin accessibility following the loss of TET1 may affect, or be affected by, CTCF and CEBP binding. Analysis of H3K27ac levels and comparison with existing datasets suggested a potential impact of TET1 on enhancer activity. TET1 loss also led to changes in DNA methylation, but these changes were generally in regions where accessibility was not changing. Lastly, more significant transcriptomic changes were observed in HBEC cells with TET1 knockdown compared to control cells following HDM challenges. Collectively, our data suggest that TET1 regulates gene expression through distinct mechanisms across various genomic regions in airway epithelial cells, restricting transcriptomic responses to allergen and potentially protecting against the development of asthma.

overall_design:
To investigate the role of TET1 in mediating responses to HDM-induced inflammation, we performed ATAC sequencing in control and TET1 knockdown human bronchial epithelial cells treated or untreated with house dust mite extract. Initially there were 3 control samples (WTSal), 3 TET1 knockdown samples (KDSal, knocked down with siRNA), 3 HDM treated, TET1 intact samples (WTHDM), and 3 TET1 knockdown, HDM treated samples (KDHDM).
We performed three pairwise comparisons of chromatin accessibility: 1) KDSal vs WTSal, 2) WTHDM vs WTSal, 3) KDHDM vs WTHDM

first: Anthony

last: Brown

first: Sreeja

last: Parameswaran

first: Lucy

last: Cai

first: Sweeney

last: Elston

first: Chi

last: Pham

first: Artem

last: Barski

first: Matthew

middle: T

last: Weirauch


title: Silencing TET1 expression alters the epigenomic landscape and amplifies transcriptomic responses to allergen in airway epithelial cells [RNA-seq]

overall_design:
To investigate the role of TET1 in mediating responses to HDM-induced inflammation, we performed RNA-sequencing in control and TET1 knockdown human bronchial epithelial cells treated or untreated with house dust mite extract. There were 4 control samples (WTSal), 4 TET1 knockdown samples (KDSal, knocked down with siRNA), 2 HDM treated, TET1 intact samples (WTHDM), and 2 TET1 knockdown, HDM treated samples (KDHDM).
We performed three pairwise comparisons of expression: 1) KDSal vs WTSal, 2) WTHDM vs WTSal, 3) KDHDM vs WTHDM


title: Macrophages expressing Macrophage Receptor with Collagen Structure Attenuate Liver Fibrosis Through a Tissue Restoration Phenotype [macrophage_liverFibrosis_GeoMx_spatial-seq]

city: ROCHESTER

first: William

last: Sherman

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: Liver macrophages are central in maintaining hepatic homeostasis and mediating immune responses during liver injury, including fibrosis. Macrophages may have proinflammatory or anti-inflammatory properties, but which properties influence fibrosis remains unclear. To explore the role of macrophages in liver fibrosis, we performed single-cell RNA sequencing in a mouse model of liver injury and found that macrophage diversity was increased. A subset of macrophages expressing high levels of Marco gene was the most significantly upregulated after injury but was spatially segregated to non-fibrotic areas. The macrophage receptor with collagenous structure (MARCO) protein is a scavenger receptor expressed by specific subsets of macrophages, and its role in liver fibrosis is unclear. In vitro induction of Marco in bone marrow-derived macrophages decreased proinflammatory gene expression, increased anti-inflammatory and antifibrotic gene expression, and enhanced phagocytosis, indicating a restorative phenotype. Adoptive transfer of MARCO-positive macrophages in a mouse model of liver fibrosis reduced the expression of extracellular matrix (ECM)-associated genes in hepatic stellate cells (HSCs) and reduced collagen deposition, which did not occur with the transfer of MARCO-negative macrophages. Therefore, MARCO-positive macrophages have a tissue restorative role in the liver and attenuate fibrogenesis through interaction with HSCs, thereby providing a novel therapeutic pathway for liver fibrosis.

overall_design: Isolated regions of interest via IF with differential MARCO expression for macrophage populations from mice livers that underwent 6 weeks of Carbon tetrachloride administration to induce fibrosis were subjected to spatial transcriptomic sequencing using NanoString GeoMx.

first: Sofia

last: Jerez

first: Shawna

last: Cooper

first: Usman

last: Yaqoob

first: Bushra

last: Arif

first: Maleeha

middle: F

last: Kalaiger

first: Abid

last: Anwar

first: Mandy

last: Wong

first: Nidhi

last: Jalan-Sakrikar

first: Ying

last: Li

first: Moira

middle: B

last: Hilscher

first: Enis

last: Kostallari

first: Sheng

last: Cao

first: Vijay

last: Shah


title: Corticothalamic Neurons in Motor Cortex Have a Permissive Role in Motor Execution

city: New York

first: Vilas

last: Menon

state: NY

department: Neurology

institute: Columbia University Medical Center

summary: The primary motor cortex (M1) is a central hub for motor learning and execution. M1 is composed of heterogeneous cell types with varying relationships to movement. Here, we tagged active neurons at different stages of motor task performance in mice and characterized cell type composition. We identified corticothalamic neurons (M1CT) as consistently enriched with training progression. Using two-photon calcium imaging, we found that M1CT activity is largely suppressed during movement, and this negative correlation augments with training. Increasing M1CT activity through closed-loop optogenetic manipulations during forelimb movement significantly hinders execution, an effect that became stronger with training. Similar manipulations, however, had little effect on locomotion. In contrast, M1 corticospinal neurons positively correlate with movement, with an increase during training. We uncovered that M1CT neurons suppress corticospinal activity via feedforward inhibition, also scaling with training. These results identify a permissive role of corticothalamic neurons in movement execution through disinhibition of corticospinal neurons.

overall_design: Mice were injected with and AAV expressing CaMPARI to label neurons in the primary motor cortex. CaMPARI labeling was performed by delivering light as mice learned a motor task. Only active neurons (CaMPARI, red fluorescent) were isolated for sequencing.

first: Lina

middle: M

last: Carmona

first: Anders

last: Nelson

first: Lin

last: Tun

first: An

last: Kim

first: Rani

last: Shiao

first: Michael

middle: D

last: Kissner

first: Rui

last: Costa


title: Silencing TET1 expression alters the epigenomic landscape and amplifies transcriptomic responses to allergen in airway epithelial cells

first: Hong

last: Ji

type: Methylation profiling by high throughput sequencing

overall_design:
To investigate the role of TET1 in mediating responses to HDM-induced inflammation, we performed whole genome bisulfite sequencing in control and TET1 knockdown human bronchial epithelial cells treated or untreated with house dust mite extract. There were 2 control samples (WTSal), 2 TET1 knockdown samples (KDSal, knocked down with siRNA), 2 HDM treated, TET1 intact samples (WTHDM), and 2 TET1 knockdown, HDM treated samples (KDHDM).
We performed three pairwise comparisons of methylation: 1) KDSal vs WTSal, 2) WTHDM vs WTSal, 3) KDHDM vs WTHDM

first: Anthony

last: Brown

first: Sreeja

last: Parameswaran

first: Lucy

last: Cai

first: Sweeney

last: Elston

first: Chi

last: Pham

first: Artem

last: Barski

first: Matthew

last: Weirauch


title: Macrophages expressing Macrophage Receptor with Collagen Structure Attenuate Liver Fibrosis Through a Tissue Restoration Phenotype [macrophage_liverFibrosis_scRNA-seq]

first: William

last: Sherman

overall_design: Isolated primary cells from mice livers that underwent 6 weeks of Carbon tetrachloride administration to induce fibrosis were subjected to Single Cell RNA sequencing.

first: Sofia

last: Jerez

first: Shawna

last: Cooper

first: Usman

last: Yaqoob

first: Bushra

last: Arif

first: Maleeha

last: Kalaiger

first: Abid

last: Anwar

first: Mandy

last: Wong

first: Nidhi

last: Jalan-Sakrikar

first: Ying

last: Li

first: Moira

last: Hilscher

first: Enis

last: Kostallari

first: Sheng

last: Cao

first: Vijay

last: Shah


title: TREM2 supports neuronal protection and microglial reactivity independently of affecting misfolded protein deposition in chronic neurodegenerative prion disease

city: Edinburgh

first: Barry

last: McColl

address: 49 Little France Crescent

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

summary: TREM2 (triggering receptor expressed on myeloid cells-2) variants have been identified as risk factors for neurodegenerative disease including Alzheimer’s disease. TREM2 is a cell surface receptor on microglia that regulates homeostatic and immunomodulatory functions including phagocytosis of apoptotic debris and the resolution of damage-associated inflammation. It remains unclear how TREM2 may mediate an influence on neurodegenerative disease, particularly in relation to key neuropathological hallmarks such as neuronal loss and proteinopathy.  We used the ME7 prion disease model to assess the role of TREM2 in the progression and pathology of neurodegenerative disease. Prion diseases are characterised by the accumulation of misfolded prion protein and provide a highly tractable platform to determine if TREM2 has disease-modifying effects. Trem2-/- and wild type mice were inoculated intracerebrally with mouse-passaged ME7 scrapie prions and effects on CNS disease pathogenesis determined. Although the accumulation of prion disease-specific PrP was similar in the brains of mice from each group, the severity of the neuropathology was increased in Trem2-/- mice. Morphometric analysis of the microglia also indicated blunted disease-induced reactivity in the brains of infected Trem2-/- mice compared to wild type (WT) controls. The expression of genes involved in myelination were reduced in prion-infected Trem2-/- mice compared to infected WT mice. We conclude that during infection of the brain with prions, TREM2 supports microglial reactive changes that are associated with resilience to neuronal loss independently of affecting misfolded PrP deposition. These data imply that TREM2 status may be an important influence on the downstream response to CNS proteinopathy that alters the susceptibility of neurons and brain tissue to proteinopathy-induced degenerative changes.

overall_design: Transcriptional profiles of brain tissue from WT and Trem2-/- mice inoculated intracerebrally with either normal brain homogenate (NBH) or brain homogenate from mice terminally infected with mouse-passaged ME7 scrapie prion strain. Dataset includes a total of of 14 samples, including biological replicates for two different genotypes (WT and Trem2-/-) and 2 treaments (NBH and ME7).

first: Sarah

last: Carpanini

last: Bradford

first: Alessio

last: Alfieri

first: Pedro

last: Piccardo

first: Jimena

last: Monzón-Sandoval

first: Deborah

last: Brown

first: Aileen

last: Boyle

first: Neil

last: Mabbott

first: Jean

last: Manson


title: Defining the networks that connect RNase III and RNase J-mediated regulation of primary and specialized metabolism in Streptomyces venezuleae [RNAseq-induced]

city: Hamilton

first: Marie

last: Elliot

state: Ontario

address: 1280 Main Street W

department: Biology

country: Canada

institute: McMaster University

summary: RNA metabolism involves coordinating RNA synthesis with RNA processing and degradation. Ribonucleases play fundamental roles within the cell, contributing to the cleavage, modification, and degradation of RNA molecules, with these actions ensuring appropriate gene regulation and cellular homeostasis. Here, we employed RNA-sequencing to explore the impact of RNase III and RNase J on the transcriptome of Streptomyces venezuelae. Differential expression analysis comparing wild type and RNase mutant strains at distinct developmental stages revealed significant changes in transcript abundance, particularly in pathways related to multicellular development, nutrient acquisition, and specialized metabolism. Both RNase mutants exhibited dysregulation of the BldD regulon, including altered expression of many cyclic-di-GMP-associated enzymes. We also observed precocious chloramphenicol production in these RNase mutants and found that in the RNase III mutant, this was associated with PhoP-mediated regulation. We further found that RNase III directly targeted members of the PhoP regulon, suggesting an interesting connection between RNA metabolism and a regulator that bridges primary and specialized metabolism. We connected RNase J function with translation through the observation that RNase J directly targets multiple ribosomal protein transcripts for degradation. These findings establish distinct, but complementary roles for RNase III and RNase J in coordinating the gene expression dynamics critical for S. venezuelae development and specialized metabolism.

overall_design: RNA sequencing samples from Streptomyces venezuelae, where RNase III and RNase J are induced in their respective mutant backgrounds. For these samples there are induced and control strains (empty vector) collected pre-induction, and 20- and 40-minutes post-induction in biological duplicate.

first: Meghan

last: Pepler

first: Emma

last: Mulholland

first: Freddie

last: Montague


title: RpoS mutations mediate Enterobacter endophytic life style switch from alkaline desert soil to acidic host apoplast

city: Jeddah

first: Sabiha

last: Parween

address: Thuwal

department: Hirt lab

country: Saudi Arabia

institute: KAUST

summary: Enterobacter sp. SA187 is a facultative endophytic bacterium conferring multi-abiotic stress tolerance to various plant hosts. Upon interaction with plant tissues, a significant proportion of the typically yellow SA187 lose pigmentation. This phenotypic shift becomes more prominent with extended host plant colonization and under stress conditions, such as salinity. To explore the underlying mechanisms and ecological significance of this variation, we employed genome sequencing, comparative genomics, transcriptomics, and metabolic characterization. In all white SA187 variants, weidentified consistent point mutations in the rpoS gene, which encodes a global regulatory sigma factor. These rpoS loss-of-function mutations lead to alterations in gene regulation, affecting growth, morphology, biofilm formation, motility, oxidative stress responses and carotenoid production. Notably, the rpoS mutants demonstrated enhanced adaptability from a free living to an endophytic life style. Whereas the desert soil is characterized by highly alkaline conditions, the apoplast of the host plant is an acidic environment accompanied with the availability of distinct carbon sources. RpoS mutants allow life in the acidic and sucrose-rich apoplastic compartment, underscoring the role of genetic variation in bacterial adaptation to colonize plants.

overall_design: To investigate the genetic changes occurring to SA187 upon plant colonization and defining the genetic and biochemical basis of the phenotypic variation observed.

first: Wiam

last: Alsharif

first: Heribert

last: Hirt

first: Maged

last: Saad

first: Cristina

last: Andrés-Barrao

first: Abdulrahman

last: Hashim

first: Kirti

last: Singh

first: Michael

last: Abrouk

first: Jian

middle: Y

last: Wang

first: Ramona

last: Marasco

first: Simon

middle: G

last: Krattinger

first: Daniele

last: Daffonchio

first: Salim

last: Al-Babili


title: Defining the networks that connect RNase III and RNase J-mediated regulation of primary and specialized metabolism in Streptomyces venezuleae [RNAseq]

first: Marie

last: Elliot

summary: RNA metabolism involves coordinating RNA synthesis with RNA processing and degradation. Ribonucleases play fundamental roles within the cell, contributing to the cleavage, modification, and degradation of RNA molecules, with these actions ensuring appropriate gene regulation and cellular homeostasis. Here, we employed RNA-sequencing to explore the impact of RNase III and RNase J on the transcriptome of Streptomyces venezuelae. Differential expression analysis comparing wild type and RNase mutant strains at distinct developmental stages revealed significant changes in transcript abundance, particularly in pathways related to multicellular development, nutrient acquisition, and specialized metabolism. Both RNase mutants exhibited dysregulation of the BldD regulon, including altered expression of many cyclic-di-GMP-associated enzymes. We also observed precocious chloramphenicol production in these RNase mutants and found that in the RNase III mutant this was associated with PhoP-mediated regulation. We further found that RNase III directly targeted members of the PhoP regulon, suggesting an interesting connection between RNA metabolism and a regulator that bridges primary and specialized metabolism. We also connected RNase J function with translation through the observation that RNase J directly targets multiple ribosomal protein transcripts for degradation. These findings establish distinct, but complementary roles for RNase III and RNase J in coordinating the gene expression dynamics critical for S. venezuelae development and specialized metabolism.

overall_design: RNA sequencing samples from Streptomyces venezuelae wild tpye, RNase III, and RNase J mutant strains. Wild type strains were sampled at 10h and 14h (vegetative and reproductive stages of development, respectively) in biological duplicate. RNase III and RNase J mutant strains were sampled at vegetative, reproductive/aerial, and sporulating stages of developent (10h/14h/20h for the RNase III mutant, and 12h/18h/24h for the RNase J mutant) in biological duplicate.


title: Human endothelial colony forming cells (ECFCs) require endothelial protein C receptor (EPCR) for cell cycle progression and angiogenic activity

city: Milan

first: Edoardo

last: Pedrini

state: Lombardy

address: Via Olgettina 60

department: Division of Neuroscience

country: Italy

institute: Hospital San Raffaele

summary: Vascular repair and regeneration are critical for tissue homeostasis. Endothelial colony forming cells (ECFCs) are vessel-resident progenitors with vasoreparative capacity and they offer an important avenue for allogeneic cytotherapy to achieve perfusion of ischemic tissues. Endothelial Protein C Receptor (EPCR) has been proposed as a reliable marker for vascular endothelial stem cells, but its precise role in ECFC biology remains unknown. The current study has investigated the biological relevance of EPCR in ECFC function. Our data shows that over 95% of ECFCs exhibit high EPCR expression. These levels surpassing CD34 and CD157, positions EPCR as a new robust ECFC immunophenotypic marker, alongside established markers CD31 and CD105. Functionally, depleting ECPR expression in ECFCs significantly diminished angiogenic activity, including proliferation, migration and tube formation. This knockdown also altered normal ECFC barrier function. Transcriptomic analysis indicated that knockdown of EPCR led to enrichment of gene signatures for cell cycle, TGF beta, and focal adhesion kinases and cell cycle arrest in G1 was confirmed ECFCs in which EPCR was depleted. Mechanistically, EPCR knockdown led to increased release of TGFB2 and SMAD2/3 activation, coupled with increased p21, decreased pFAK, and increased transgelin. Additionally, we showed that quiescent ECFCs showed significantly lower EPCR expression when compared to proliferating ECFCs. In agreement with this, cell sorting experiments demonstrated that ECFCs with the highest EPCR expression exhibited the highest clonogenic capacity. In summary, our findings highlight that EPCR expression in ECFCs is critical for their angiogenic activity, by modulating processes such as cell cycle progression, barrier function, and endothelial to mesenchymal transition.

overall_design: ECFCs were Transfected at 70% confluency with siRNA for PROCR or control for 16 hrs. Cells were passaged and used for experiments after 48 hrs. 6 clones per condition (paired) were profiled for RNAseq

first: Sarah

last: Chambers

first: Jasenka

last: Guduric-Fuchs

first: Pietro

last: Bertelli

first: Judith

last: Lechner

first: Elisa

last: Peixoto

first: Alan

last: Stitt

first: Reinhold

last: Medina


title: N-6 adenine-specific DNA methyltransferase 1 is essential for meiosis prophase I progression during spermatogenesis

city: Xi'an

first: Luo

last: Yuru

state: Shannxi

address: 28 Xianning West Road

department: Health Science Center

institute: Xi'an Jiaotong University

summary: Mammalian sexual reproduction critically relies on the generation of haploid gametes through a specialized cell division process known as meiosis. Here, we demonstrate that N-6 Adenine-Specific DNA methyltransferase 1 (N6AMT1) plays a crucial role in the progression of meiosis during spermatogenesis, as follows. Gene expression profiling revealed that N6AMT1 was expressed in germ cells throughout the entire process of spermatogenesis, with a peak in expression levels in spermatocytes at the prophase I stage of meiosis. Germ cell-specific deletion of N6amt1 in mice resulted in male subfertility as well as a significant reduction in sperm count. Notably, N6amt1-null spermatocytes exhibited meiotic arrest at prophase I and extensive apoptosis. Chromosome spreading assays revealed that N6amt1 loss impaired meiotic sex chromosome inactivation (MSCI) and delayed DNA double-strand break (DSB) repair, both crucial for proper meiotic progression. Correspondingly, transcriptomic analysis identified a substantial upregulation of genes mapping to sex chromosomes in N6amt1-null mutants, consistent with failures in MSCI. Moreover, N6AMT1 deficiency significantly augmented the expression of genes involved in the p53 pathway. Incorporating single-cell analysis, we found that the differentially expressed genes following the knockout of N6amt1 were primarily high-variability genes in pachytene stage spermatocytes, indicating that the absence of N6AMT1 leads to gene expression disorders during the pachytene stage. Taken together, our findings demonstrate that N6AMT1 is crucial to male fertility in mice, through molecular mechanisms for meiotic progression during spermatogenesis, including MSCI and DSB repair.

overall_design: To further elucidate the molecular mechanism through which N6AMT1 regulates the spermatogensis, testes from the CTL and N6amt1-SKO mice were sent to RNA-seq analysis.

first: Yuru

last: Luo

first: Shuang

last: Liu


title: Effects of deletion Rack7 on gene expression in primary astrocyte during mouse postnatal development [RNA-Seq]

city: Shanghai

first: jiao

last: fangfang

address: DongAn Road 131

institute: fudan university

summary: Dysregulation of epigenetic mechanisms play crucial roles in brain development and disease. Emerging evidence suggests that RACK7, an epigenetic reader protein, may play a role in brain development, but in vivo exploration of RACK7 in neural development and the underlying mechanisms are still lacking. Here, we established a conditional knock-out Rack7 mouse model and show that Rack7-deficient mice exhibit overt developmental defects. Multicomplex immunofluorescence staining (mIF) of cell-type specific markers indicates that the developmental defects are associated with compromised astrocyte development. Mechanistically, we surprisingly found RACK7 interacts with PRC2 complex, which acts as the histone H3K27 methyltransferase. Our results suggest RACK7 binding with PRC2 complex helps to establish the proper genomic location of histone H3K27me3 modification. Deletion of Rack7 in astrocyte leads to a remarkable decrease of H3K27me3 chromatin enrichment. genome-wide?. Functionally, we found RACK7 works together with H3K27me3 to prevent overactivation of Wnt signaling pathway and other astrocyte differentiation genes. Collectively, our study provides new insights into the cellular and molecular mechanisms underlying brain development regulated by RACK7.

overall_design: In order to determine the impact of Rack7 loss on the transcriptome during astrocyte development, we extracted and cultured primary astrocyte from WT and Rack7-cKO mice brain at three time points, including neonatal (P1), P6 and P8, and performed RNA-seq analysis.

first: Fangfang

last: Jiao

first: Rui

last: Guo

first: Yang

last: Shi


title: Chromatin distribution alterations of histone modifacations and PRC2 complex caused by Rack7 deletion in primary astrocyte [ChIP-Seq]

overall_design: To gain insight into the molecular mechanisms underlying Rack7 function in astrocytes, we performed chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) to analyze the chromatin distribution of histone modifations related to Rack7,including enhancer marker (H3K4me1/H3K27ac), H3K4me3,  and H3K27me3. We also analyzed the genome occupancy of PRC2 complex using ChIP-seq in primary astrocyte, which acts as the histone H3K27 methyltransferase.


title: Identification of prognostic biomarkers for endometrioid endometrial carcinoma based on the miRNA and mRNA co‐expression network regulated by estradiol [miRNA]

city: Beijing

first: Li

last: Jin

state: -- None selected --

address: Department of Obstetrics and Gynecology

institute: peking union medical college hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Endometrioid endometrial carcinoma (EEC), an estradiol-related disease, remains a serious health threat to women because of its high incidence and trend of rejuvenation. Accumulating evidence has highlighted that microRNAs (miRNAs) and messenger RNAs (mRNAs) play important roles in various biological processes involved in the pathogenesis of EEC. This study aimed to identify the potential prognostic biomarkers associated with EEC regulated by estradiol.

overall_design: To investigate the pathway through which estrogen participates in the the pathogenesis of EEC, microRNA sequencing were performed on EEC samples treated with or without estradiol (250 nM). We then performed gene expression profiling analysis of RNA-seq obtained from above two groups.

first: Qiu

last: Xie


title: Dose-dependent CHCHD10 dysregulation affects motor neuron disease severity and creatine metabolism

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

summary: Dominant defects in CHCHD10, a mitochondrial intermembrane space protein, lead to a range of neurological and muscle phenotypes including amyotrophic lateral sclerosis. Many patients present with spinal muscular atrophy Jokela type (SMAJ), which is caused by a heterozygous p.G66V variant. While most disease variants lead to aggregation of CHCHD10 and activation of proteotoxic stress responses, the pathogenic mechanisms of the p.G66V variant have been less investigated. We report here the first homozygous CHCHD10 patient, with variant p.G66V. We compare the metabolic findings in heterozygous and homozygous SMAJ patient skin fibroblasts, and in motor neurons differentiated from patient-specific stem cells as well as a novel mouse model of SMAJ. Our findings show that p.G66V variant leads to dose-depended reduction of the CHCHD10 protein in a cell type specific manner. In addition, CHCHD10 p.G66V dysregulates energy metabolism, leading to altered redox balance and energy buffering by creatine metabolism.

overall_design: We analyzed the effect of a pathogenic mutation p.G66V in CHCHD10 gene in homozygous and heterozygous mouse muscle using RNA-seq.

first: Harjuhaahto

last: Sandra

first: Jokela

last: Manu

first: Rajendran

last: Jayasimman

first: Rokka

last: Minea

first: Hu

last: Bowen

first: Kvist

last: Jouni

first: Zhang

last: Fuping

first: Zárybnický

last: Tomáš

first: Haimilahti

last: Kimmo

first: Pirinen

last: Eija

first: Huber

last: Nadine

first: Herukka

last: Sanna-Kaisa

first: Haapasalo

last: Annakaisa

first: Kuuluvainen

last: Emilia

first: Gopalakrishnan

last: Swetha

first: Katajisto

last: Pekka

first: Hietakangas

last: Ville

first: Huang

last: Xiaoping

first: Narendra

last: Derek

first: Kuure

last: Satu

first: Ylikallio

last: Emil

first: Tyynismaa

last: Henna


title: 6PPD induces cerebrovascular defects by triggering oxidative stress and ferroptosis in zebrafish

city: Guiyang

first: Mengzhu

last: Lv

address: No. 6, Ankang Avenue, Gui'an New District

institute: Guizhou Medical University

summary: N-(1,3-dimethylbutyl)-N′-phenyl-p-phenylenediamine (6PPD), which is widely used as an antiozonant in rubber tires, has recently got much attention for its acute aquatic toxicity. However, the developmental toxicity of 6PPD in cerebrovascular network remains unknown. Here, we investigated the effects of 6PPD exposure in cerebral vascular using the larvae of zebrafish. 6PPD would not affect the body length and shape of zebrafish larvae at the concentrations ranging from 20 μg/L to 1000 μg/L. 6PPD induced developmental defects in the brain in a concentration-dependent manner. The trunk vascular development would not be affected while the cerebrovascular network was disrupted upon 6PPD exposure. 6PPD would trigger excessive Reactive Oxygen Species (ROS) in the brain, indicating abnormal oxidative stress. Mechanistically, brain-specific transcriptome analysis showed that 6PPD could potentially cause the blockage of arachidonic acid (AA) metabolism-related genes and the upregulation of ferroptosis-related genes. Besides, treatment with ferroptosis inhibitor N-Acetyl-L-cysteine (NAC) attenuated oxidative damage and improved the construction of cerebrovascular network upon 6PPD exposure. Moreover, using a human vascular endothelial cell line, we further confirmed that 6PPD could trigger abnormal oxidative stress and defective expansion capacity, implying the conserved toxicity cross species. These findings are useful for the elucidation of toxicity underlying 6PPD in cerebrovascular systems of both zebrafish and humans.

overall_design: To investigate the effects of 6PPD on zebrafish development, embryos were treated with 500 μg/L 6PPD from 10 hours post-fertilization (hpf) until 2 days post-fertilization (dpf). For transcriptomic analysis, three biological replicates were prepared for both the 6PPD treatment group and the DMSO control group. For each replicate, the heads of 150 embryos at 2 dpf were dissected, flash-frozen in liquid nitrogen, and sent for transcriptomic sequencing. The raw data analysis was performed to identify differentially expressed genes between the 6PPD-treated and control groups.

first: Xiaoyu

last: Mao

first: Zheng

last: Lu

first: Yanzhu

last: Yang

first: Jiangtao

last: Huang

first: Chuan

last: Ye

first: Zhixu

last: He

first: Liping

last: Shu

first: Dashuang

last: Mo


title: RNA sequencing analysis of doxorubicin-treated mice after administration with Akkermansia muciniphila

city: ningbo

first: Hui

last: Lin

state: zhejiang

address: The Affiliated Lihuili Hospital of Ningbo University, Healthy Science Center, Ni

summary: Doxorubicin (DOX) is considered as the major culprit in chemotherapy-induced cardiotoxicity, which limits its clinical application. Akkermansia muciniphila (AKK) shows a beneficial role as a probiotic in the treatment of metabolic syndrome. However, the changes of AKK during DIC and whether it mediates cardioprotective effects remains unclear. Cardiac transcriptomics certified by in vitro experiments demonstrated that AKK administration effectively improved mitochondrial function and alleviated DIC, by activation of PPARα/PGC1α signaling pathway. These findings provide a therapeutic strategy for DIC through supplementation with AKK.

overall_design: To investigate the cardioprotective effects of AKK on DIC and its potential mechanisms, we established a mouse model of doxorubicin-induced cardiotoxicity was established by intraperitoneally injecting C57BL/6 mice with doxorubicin at a dose of 5 mg/kg weekly for 4 consecutive weeks, resulting in a cumulative dose of 20 mg/kg. Colonization with Akkermansia muciniphila was achieved by administering 150 μl of the bacterial suspension at a concentration of 1*10^10 CFU/mL via gavage twice a week for 4 weeks. At the end of the experiments, Mouse hearts were rapidly harvested, rinsed in ice-cold phosphate-buffered saline (PBS), and flash-frozen in liquid nitrogen. The differentially expressed genes were analyzed by RNA-sequencing and clustering analyses.


title: ZNF574 is a Quality Control Factor for Defective Ribosome Biogenesis Intermediates [RNA-Seq]

city: Kansas City

first: Hua

last: Li

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

summary: Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs, 80 ribosomal proteins, and over 200 biogenesis factors that take part in numerous interdependent steps. The complexity and essentiality of this process creates opportunities for deleterious mutations to occur, accumulate, and impact downstream cellular processes. “Dead-end” ribosome intermediates that result from biogenesis errors are rapidly degraded, affirming the existence of quality control pathway(s) that monitor ribosome assembly. However, the factors that differentiate between on-path and dead-end intermediates are unknown. We engineered a system to perturb ribosome assembly in human cells and discovered that faulty ribosomes are degraded via the ubiquitin proteasome system. We identified ZNF574 as a key component of a novel quality control pathway, which we term the Ribosome Assembly Surveillance Pathway (RASP). In an animal model, loss of ZNF574 leads to developmental defects, further emphasizing the importance of RASP in organismal health.

overall_design:
To identify differentially expressed genes following the loss of znf574, we in-crossed znf574+/- animals.
znf574 wild-type (znf574+/+ or +/-) and znf574 mutant (znf574-/-) larvae were phenotypically identified seven days post-fertilization. Whole animals were used for this experiment.
We performed RNA-Seq followed by differential expression analysis with DESeq2, comparing differentially expressed genes between ZNF574 mutant and wild-type animals.

first: Kostova

last: Kamena


title: Effect of non-structural protein 1 (NS1) of H5N1 on CK2 expression, p53 signaling pathway and cell proliferation

city: Shenyang

first: Man

last: Zhang

state: Liaoning

address: No. 66, Chongshan Zhonglu

institute: Liaoning University

summary: NS1 (Non-structuralprotein1) is a non-structural protein of avian influenza viruses that can interact with a variety of host proteins. Our previous studies have demonstrated the interaction between NS1 and NOLC1 (nucleolus and coiled-coil phosphoprotein 1). To continue to investigate the mechanism of interaction, we constructed a cell line (A549-Flag-GFP-NS1) that stably expresses NS1. The expression of NS1, p53 and NOLC1 proteins was analysed by co-immunoprecipitation. The p53 signalling pathway in A549-Flag-GFP-NS1 cells was enriched for differentially expressed genes as analysed by transcriptome sequencing. qPCR experiments further verified that endogenous expression of NS1 altered the mRNA expression levels of p53 signalling-related genes (Bcl-2, CDK4, MDM2, cell cycle protein D, etc.). Meanwhile, endogenous expression of NS1 in A549 cells not only led to elevated expression of CK2, but also resulted in a significant increase in the phosphorylation levels of Ser46 and Ser392 as well as the acetylation level of Lys120 in p53 protein. The expression of relevant apoptotic factors in the p53 signalling pathway was further affected. These new findings provide new targets for pathogenic mechanism studies and drug screening.

overall_design: samples A549 cell  and A549-Flag-GFP as normal control, and the A549-Flag-GFP-NS1 as over expressed H5N1 NS1

first: Junfeng

last: Zhu

first: Yingyue

last: Zeng


title: ZNF574 is a Quality Control Factor for Defective Ribosome Biogenesis Intermediates [CRISPRi_FLOW]

overall_design:
To identify quality control factors targeting defective large subunits, we generated K562 dCas9-KRAB cells that stably express RFP-tagged mutant uL16.
The CRISPRi compact library (hCRISPRi_dual_1_2 pooled library, Addgene, Cat#187246) was transduced in duplicate into K562 CRISPRi cells stably expressing uL16mut-RFP at an MOI < 1 (percentage of transduced cells 2 days after transduction: 20%–40%). Replicates were maintained separately in four T125 flasks per replicate for the course of the screen. Two days after transduction, the cells were selected with 1 mg/mL puromycin for 3 days, at which point transduced cells accounted for 80%–95% of the population. Cells were allowed to recover to >80% cell viability, as measured with a Cell Countess (Invitrogen). The cells were maintained in T125 flasks by daily dilution to 0.5 × 10^6 cells/mL at an average coverage of greater than 1000 cells per sgRNA for the duration of the screen. Cells were sorted using BD FACS Aria3 two days after recovery, based on the RFP fluorescence of the uL16mut-RFP reporter. Cells with the highest (~30%) and lowest (~30%) RFP expression were collected and snap-frozen. Approximately 10 million cells were collected per bin.


title: Hepatic PKA Mediates the Liver and Pancreatic Alpha-Cell Crosstalk

city: Tarrytown

first: Kehan

last: Bao

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

summary: Objective: Activation of the liver glucagon receptor (GCGR) promotes amino acid catabolism, which provides substrate for glucose production. Inhibition of the receptor downregulates hepatic amino acid catabolism, leading to increases in circulating amino acid levels. Amino acids serve as a potent growth factor for pancreatic alpha cells, where glucagon is produced. Thus, GCGR inhibition-induced hyperaminoacidemia causes alpha cell hyperplasia. This liver-alpha cell feedback loop, mediated by glucagon and amino acids, has been demonstrated across species, including humans. This study was designed to delineate hepatic signaling molecules that lie downstream of GCGR and mediate the liver-alpha cell loop.  Methods: We used AAV8-shRNA to knock down GCGR signaling molecules, the G-coupled protein GNAS and two GNAS downstream effectors, PKA and EPAC2 (RAPGEF4), in the liver of diet-induced obese (DIO) mice. We monitored plasma amino acid and blood glucose levels and conducted pancreas histology to derive alpha and beta cell mass. We performed liver RNA-sequencing to assess expression of glucose and amino acid metabolism genes. To examine the contribution of PKA in changes associated with GCGR inhibition, we knocked down PRKAR1A, a major inhibitory subunit of PKA, to activate PKA in liver of mice administered with GCGR blocking or control antibody. Results: Comparable suppression of hepatic amino acid catabolism gene expressions, increases in plasma amino acid levels and alpha cell hyperplasia were observed in mice with hepatic knockdown of GCGR, GNAS, and PKA. Hepatic EPAC2 knockdown did not affect amino acid metabolism or alpha cell mass in mice. Mice with hepatic PKA activation alone developed hypoaminoacidemia, hypoglucagonemia and reduced alpha cell mass. Administering GCGR blocking antibody to the mice did not alter the abnormalities.  Conclusions: Hepatic PKA activation in mice fully overrides the effect of GCGR inhibition on amino acids and alpha cells. In the liver, GCGR signals through PKA to control amino acid metabolism and pancreatic alpha cell mass. Hepatic PKA plays a critical role in the liver-alpha cell loop, mediated by circulating glucagon and amino acids.

overall_design: Liver RNA-seq was performed in mice injected with AAV8-shRNA to knockdown GCGR downstream pathway components, or to activate PKA with/without GCGR inhibition

first: Jason

last: Berger

first: Erqian

first: Qi

last: Su

first: Gabor

last: Halasz

first: Mark

last: Sleeman

first: Haruka

last: Okamoto


title: Physiological, transcriptomic, and metabolomic analyses uncover crucial factors enhancing cadmium stress tolerance in centipedegrass

city: Nanjing

first: Ling

address: Zhongshanmenwai, Qianhuahoucun No.1

institute: nstitute of Botany, Jiangsu Province and Chinese Academy of Sciences

summary: This study analyzed the physiological, transcriptomic, and metabolomic changes in centipedegrass to elucidate the pivotal mechanisms involved in Cd tolerance. Centipedegrass exhibited a heightened capacity for Cd absorption and transportation. Moderate Cd concentrations had no significant impact on plant growth, whereas elevated Cd concentrations inhibited growth. Higher Cd levels led to decreased photosynthetic efficiency, elevated lignin, abscisic acid (ABA), and salicylic acid (SA) contents, increased activity of antioxidant enzymes, and malondialdehyde (MDA) levels. The integrated analysis of the transcriptome and metabolome revealed the potential critical roles of phenylpropanoid biosynthesis, plant hormones, and ABC transporters in Cd detoxification in centipedegrass. Overexpression of the metal transporter ATP−binding cassette B11 (EoABCB11) in Arabidopsis conferred high Cd tolerance. These findings indicate that centipedegrass possesses robust resistance and transport capabilities against Cd toxicity, potentially attributed to ABA−, SA−, and lignin−mediated positive defense responses, primarily involving enhanced antioxidant enzyme activity and cell wall reinforcement.

overall_design: These pots were filled with red soil containing varying cadmium concentrations: 0 (CK), 50 (Cd50), 100 (Cd100), and 200 mg kg−1 (Cd200) (CdCl2).

first: Hailong

last: Lu

first: Dongli

last: Hao

first: Rongrong

last: Chen


title: AKT1E17K-interacting lncRNA SVIL-AS1 promotes AKT1 oncogenic functions by sustaining its phosphorylation

city: Guangzhou

first: Jingyi

last: Wang

state: Guangdong

address: Yingfeng

institute: Sun Yat-sen Memorial Hospital

summary: AKT1 E17K, occurring at low frequency in a broad range of cancer types, is a gain-of-function mutation that constitutively activates the PI3K-AKT pathway. However, how AKT1E17K is regulated in cancer pathogenesis remains elusive. Here, we interrogate the AKT1E17K-interacting lncRNAs and identify that SVIL-AS1 preferentially binds to AKT1E17K rather than AKT1WT proteins. We find that SVIL-AS1 enhances AKT1 phosphorylation and downstream signaling. SVIL-AS1 knockdown dramatically inhibits the growth of AKT1E17K cells in intro and in vivo. Notably, AKT1 and SVIL-AS1 interaction is AKT1 phosphorylation-dependent. SVIL-AS1 also interacts with PPP2R2A, a subunit of phosphatase PP2A holoenzyme, and blocks the binding of PPP2R2A to AKT1E17K to prevent AKT1 dephosphorylation. Moreover, AKT1E17K cells are not effectively inhibited by the allosteric AKT inhibitor, whereas silencing SVIL-AS1 sensitizes AKT1E17K cells to AKT1 allosteric inhibitor, as well as the PI3K inhibitor. In breast cancer tissues, SVIL-AS1 is highly expressed and associated with p-AKT1 level and poor prognosis of patients. Together, our findings highlight a previously unappreciated role of lncRNA SVIL-AS1 in regulating AKT1 dephosphorylation, which serves as a promising therapeutic target for AKT1E17K tumors.

overall_design: To identify lncRNAs binding to the AKT1 E17K mutant protein, we transfected Flag-tagged AKT1 wild-type (AKT1WT) or E17K mutant (AKT1E17K) plasmids into breast cancer cell line MDA-MB-231. RNA immunoprecipitation (RIP) using negative control IgG or anti-FLAG antibody respectively was then performed and deep sequencing showed that several lncRNAs preferentially bound to the AKT1 E17K mutant protein.

first: Man-Li

last: Luo

first: Hai

last: Hu

first: Wenyin


title: Extended abstinence from morphine normalizes sperm small RNA expression and prevents transmission of multigenerational phenotypes

city: Philadelphia

first: Mathieu

last: Wimmer

state: PA

address: 1701 N 13th Street

institute: Temple University

summary: We examined the impact of paternal abstinence following morphine self_administration on the transmission of multigenerational factors from the F0 to the F1 generation. Previously, we found that offspring of non_abstinent, morphine administering male rats showed increased morphine_taking, diminished adolescent social play, and reduced sensitivity to morphine analgesia. Here, we show that these phenotypes are normalized in the offspring of fathers who were 90 days abstinent from morphine at the time of breeding. We further compared the small RNA content of sperm collected from non_abstinent versus 90 days abstinent F0 males to identify candidate molecules correlated with transmission of morphine_induced multigenerational phenotypes.

overall_design: Mature sperm collected from cauda epididymus of male rats from 4 experimental treatment groups: Morphine IVSA, no abstinence; Morphine IVSA + abstinent 90 days; Saline IVSA, no abstinence; Saline IVSA + abstinent 90 days.

first: Dana

last: Zeid

first: Drew

last: Peterson

first: Reza

last: Karbalaei


title: ZNF574 is a Quality Control Factor for Defective Ribosome Biogenesis Intermediates [CRISPRi_growth]

first: Hua

last: Li

overall_design:
To identify quality control factors targeting defective large subunits, we generated K562 dCas9-KRAB cells that stably express wild-type or mutant uL16.
We transduced these cells with a whole-genome CRISPRi library, selected infected cells by treating them with puromycin for three days, and then maintained the cells at 0.5 × 10^6 cells/ml with viability over 90% for ten cell doublings.
After ten cell doublings, we harvested the cells, isolated genomic DNA, and constructed a sequencing library.

first: Kostova

last: Kamena


title: Defective DcpS Decapping Manifests in Creatine Deficiency Syndrome and Neurological impairment

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Biallelic mutations in the DCPS gene that disrupt the decapping activity of the DcpS scavenger decapping enzyme lead to neurodevelopmental deficiencies and intellectual disability. However, how the neurogenesis defects arise in these individuals remains unknown. Here we show that cells derived from DCPS mutant individuals have a metabolic deficiency in their creatine biosynthetic pathway.  The cells possess reduced levels of creatine and a corresponding elevation of the creatine precursor, guanidinoacetate (GAA), due to reduced levels of guanidinoacetate methyltransferase mRNA and protein. Importantly, the compromised neurogenesis as well as neurite outgrowth observed in DcpS mutant induced pluripotent stem cell differentiation into neurons was reversed upon supplementation of creatine monohydrate into the culture medium. These findings suggest creatine deficiency as the underlying etiology of the neurogenetic defect in DcpS mutant cells and a potential driver of the neurological deficienciesin affected individuals.

overall_design: Total RNA sequencing was performed on induced excitatory neuron cultures prepared from patient-derived iPSC.  Three samples each of DcpS mutant or control cells were compared.

first: Jun

last: Yang

first: Megerditch

last: Kiledjian


title: Single-cell RNA sequencing of the kidneys from adult Axl WT and KO mice

city: Seoul

first: Donghwan

last: YUN

address: 103 Daehakro

institute: Seoul National University Hospital

summary: This study aims to delineate the effects of AXL deletion on kidney development and cellular heterogeneity by analyzing single-cell RNA transcriptomic datasets from 11-week-old male Axl wild type (WT) and heterozygous (het) knockout mice.

overall_design: We prepared scRNA-seq datasets from whole kidneys of male Axl WT and heterozygous KO mice (n=3 each; 11 weeks old)

first: Minki

last: Hong

last: Yun

first: Seung

middle: S

last: Han


title: The effects of Lycorine on PANC-1 cells.

first: Xiaoyan

last: Xu

address: No. 21, Yinquan South Road

institute: Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital

summary: Lycorine (LY) is a natural alkaloid extracted from the Amaryllidaceae plant, it has been evaluated for its anticancer effects on pancreatic cancer cells and xenograft models. Our research presents a multi-faceted investigation of LY, including assessments of its impact on cell viability, proliferation, migration, invasion, and potential mechanisms of action.

overall_design: We divided the samples into two groups, four each: a control group and a group treated with 20μM LY. After 24 hours of treatment, we extracted RNA using Trizol for mRNA sequencing.

first: Jiaxing

last: Zhang

first: Xiangzong

last: Zeng

first: Ling

last: Qi


title: UV irradiation or Lkb1 loss allows the identification of target genes preventing BRAFV600E-induced growth arrest in melanoma cells.

city: Barcelona

first: Paula

last: Nieto

state: Spain

address: Barcelona Science Park, Carrer de Baldiri Reixac, 4, tower I, 08028 Barcelona

department: CNAG

country: Spain

institute: CNAG

summary: BRAFV600E-induced cell growth arrest in melanocytic nevus is on debate where only one third of melanomas arise directly from nevi. We showed that simultaneous neonatal oncogene (BRAFV600E) activation and UVB irradiation prevent BRafV600E-induced growth arrest in melanocytes, allowing melanoma development. A meta-analysis of gene expression profiles of melanocytes isolated from different mouse models and numerous studies revealed multiple common genes and processes involved in preventing BRafV600E-induced growth arrest. In humans, many of these genes are associated with poor survival and are upregulated during melanoma progression and in many RAS pathway activation-driven tumors. Single-cell profiling confirmed that BRAFV600E and the identified genes cooperate in melanocyte transformation, including the acquisition of multidrug resistance features. Depletion of these genes in vitro and in vivo revealed the utility of the encoded proteins as therapeutic targets. These results support the existence of BRAFV600E-mutated melanomas unassociated with nevus progression and identify targets for melanoma treatment

overall_design: Human neonatal melanocytes (MEL-F-NEO) were simultaneously transduced with two different lentiviral constructs: pLenti-hPGK-rtTA2-p2A-mCherry-TRE-BRAFV600E and pLenti-hPGK-rtTA2-TREUPP1/ CHTF18/BNC1-IRES-GFP. The expression of BRAFV600E, UPP1, CHTF18 and BNC1 was induced by the addition of doxycycline (1 μM) to the culture medium. After 27 days of induction, cells exhibiting red fluorescence (expressing BRAFV600E) and cells exhibiting both red and green fluorescence (expressing BRAFV600E and UPP1, CHTF18/, or BNC1) were sorted by flow cytometry using Aurora CS spectral technology (Cytek).

first: Kimberley

last: McGrail

first: Ginevra

last: Caratù

first: Holger

last: Heyn


title: AGEs induce MMP-9 promoter demethylation to promote breast cancer metastasis in patients with diabetes

city: Tianjin

first: Liyan

last: Zhou

address: Huanhu West Road

institute: Tianjin Medical University Cancer Institute and hospital

summary: To evaluate the involvement of transcriptional mechanisms of AGEs in breast cancer cells, we treated MDA-MB-231 cells with AGEs or BSA (as a control group) and  performed gene expression profiling analysis using data obtained from RNA-seq of the two groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AGEs-treated or BSA-treated (as a control group) breast cancer MDA-MB-231 cell (n=3 per group).


title: Scale Up Manufacturing Approach for Production of Human Induced Pluripotent Stem Cell-Derived Islets Using Vertical Wheel®Bioreactors

city: Edmonton

first: Nidheesh

last: Dadheech

state: Alberta

address: 5-126C LKS centre for research and innovation, Alberta diabetes institute, University of Alberta, 112 St, 87 AV, NW

department: Surgery

institute: University of Alberta

summary: We utilized the 10x Genomics Chromium Single Cell 3’ RNAseq platform to examine the genomic makeup of human induced pluripotent stem cell-derived islets following their differentiation under full suspension conditions using PBS vertical wheel bioreactors. Our investigation aimed to assess the efficacy of the SC-islet differentiation process in suspension, transitioning from a 0.1L to a scaled-up 0.5L volume. Our primary objective was to showcase the effectiveness of a modified protocol for pancreatic endocrine differentiation, with a specific focus on the final stage of maturation during scale-up. To gain a comprehensive understanding of these developmental changes, we integrated our transcriptomic analyses post the final maturation process with transcript data from human donor islets and existing SC-islet datasets.

overall_design: total 2 scRNAseq samples were analyzed

first: James

last: Shapiro


title: scRNA-seq of muscles with different metabolic states

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University

summary: Transcriptional regulation of Csf1 expression in fibroblasts has been described to regulate macrophage numbers, at least in vitro. Thus, we examined the expression of Csf1 in fibroblasts across muscles with different metabolic states and macrophage densities.

overall_design: Leukocytes, stromal and endothelial cells from heart, diaphragm, soleus and tibialis anterior from CkmCRE and CkmCRE; Mapk14fl/fl mice were isolated by FACS and analyzed using scRNAseq

first: Jose

middle: A

last: Nicolas-Avila

first: Laura

last: Pena-Couso

first: Jon

last: Sicilia


title: GPATCH4 functions as a regulator of nucleolar R-loops in hepatocellular carcinoma cells

city: shanghai

first: yiming

last: zhao

address: 320 Yue Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences

summary: Emerging evidence suggests that dysregulated RNA-binding proteins (RBPs) are associated a variety of cancers. However, the exact roles of RNA-binding proteins during the tumorigenesis of hepatocellular carcinoma (HCC) remain largely unknown. Here, we systematically searched for RBP candidates with potential oncogenic functions in HCC through multi-omics data integration strategies and identified that GPATCH4 gene is amplified and its high expression predicts a poor prognosis. We mapped the in vivo RNA binding sites of GPATCH4 by iCLIP-seq and characterized that GPATCH4 mainly bound rRNAs with a GC-rich consensus sequence. GPATCH4 promoted HCC cell proliferation and transformation both in vitro and in vivo through increasing rRNA transcription and global protein synthesis.

overall_design: In this study, we performed  iCLIP-seq using Huh7 cells to characterize the RNA binding sites of GPATCH4.

first: Yiming

last: Zhao

first: Jingyi

last: Hui


title: Sexually dimorphic effects of ADNP mutation and Davunotide treatment on mice hippocampal transcriptome

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

summary: ADNP haplo-insufficient (Adnp +/- ) mice or CRSIPR/Cas9 edited to carry the most prevalent neurodevelopmental ADNP syndrome mutation, p.Tyr718*. A subgroup was treated the ADNP fragment, investigational drug, NAP (davunetide).

overall_design: RNA was extracted from 2.5-month-old Tyr mouse hippocampi, treated, handled, sequenced on NextSeq500 (Illumina, CA, USA).

first: Gidi

last: Karmon

first: Illana

last: Gozes


title: CO2 sensing pathway controls drug resistance and skin tropism in Candida auris

city: Vienna

first: Trinh

last: Phan-Canh

email: phancanht99@univie.ac.at, phancanhtrinh@gmail.com, karl.kuchler@univie.ac.at, karl.kuchler@univie.ac.at

state: Vienna

address: Dr.-Bohr-Gasse 9

department: Max Perutz Labs Vienna, Campus Vienna Biocenter

country: Austria

institute: Medical University of Vienna

summary: Comparative transcriptomic profiling of Candida auris RCA1 and EFG1 null mutants in comparison to the Wild-Type Strain

overall_design: RNA Sequencing was conducted on clinical isolates of Candida auris, including the wild-type (WT) strains and deletion mutants in RCA1 or EFG1. The cells were cultivated to the exponential phase in YPD at 37°C with agitation at 200rpm. Subsequently, cultures were harvested, and RNA isolation was performed, followed by the preparation of sequencing libraries for three biological replicates. Specifically, for the rca1∆ mutant, sequencing was conducted on two distinct clinical strains labeled as R1 and R2. For the efg1∆ mutant, sequencing analysis was performed on the R1 strain.

first: Karl

last: Kuchler


title: Improvement of hepatocellular carcinoma  using hepatocyte-derived liver progenitor-like cells (HepLPCs): therapeutic, proliferation arrest, malignant biological behavior changes，signal pathway screening

city: Shanghai

first: hexin

last: Yan

address: Pujian Road

institute: Shanghai Reji Hospital

summary: We employed a co-culture experiment and found that human hepatocyte-derived liver progenitor-like cells (HepLPCs) significantly inhibited the proliferation of hepatocellular carcinoma (HCC) in a specific manner and altered their malignant biological behavior without affecting cell aging, autophagy, apoptosis and so on. To evaluate the mechanism of action, HepG2 and Hep3B after co-cultured with HepLPCs gene profiling were performed, and we observed, in addition to proliferative blockade induction, that cascade events originated from mitochondrial dysfunction.

overall_design: Global expression analysis of RNA sequencing data of expression levels of HepG2 and Hep3B in the presence or absence of hepatocytes derived liver progenitor-like cells (HepLPCs), and the global expression of HepG2 and Hep3B genes after combined inhibition of Notch1 and STAT3.

first: Liu

last: Wen-ming

first: Yan

last: He-xin


title: Tauroursodeoxycholic Acid (TUDCA) Reduces ER Stress and Lessens Disease Activity in Ulcerative Colitis

city: St. LOuis

first: Vladimir

last: Lamm

address: 660 S. Euclid Avenue

department: Gastroenterology

institute: Washington University

summary: Background and Aims: In inflammatory bowel disease, protein misfolding in the endoplasmic reticulum (ER) potentiates epithelial barrier dysfunction and impairs mucosal healing. Tauroursodeoxycholic acid (TUDCA), a naturally occurring bile acid, acts as a chemical chaperone to reduce protein aggregation and colitis severity in preclinical models. We conducted an open label trial evaluating oral TUDCA as therapy in patients with active ulcerative colitis (UC). Methods: Patients with moderate-to-severely active UC (Mayo score ≥6, endoscopic subscore ≥1) received oral TUDCA at 1.75 or 2 g/day for 6 weeks. Exclusion criteria included known hepatic disorders or change in UC therapy within 60 days. Clinical disease activity questionnaires, endoscopy with biopsy, blood, and stool were collected at enrollment and after 6 weeks. The primary outcome measure was change in ER stress markers while safety, tolerability and change in UC disease activity were secondary outcomes. Results: Thirteen participants completed the study with eleven evaluable for clinical response. TUDCA was well-tolerated with transient dyspepsia being the most common side effect. Mucosal biopsies revealed significant reductions in ER stress and inflammation as well as an increase in markers of epithelial restitution. Clinical, endoscopic, and histologic disease activity were significantly improved at week 6 (mean total Mayo Score: 9 to 4.5, p<0.001). Conclusions:  Six weeks of oral TUDCA promoted mucosal healing, lessened ER stress, and reduced UC clinical disease activity. TUDCA was safe and well-tolerated in patients with active UC.  A randomized controlled trial of adjunctive TUDCA therapy in patients with UC is warranted. ClinicalTrials.gov (NCT04114292).

overall_design: Biologic comparisons were made between pre-and post-treatment biopsy samples from the colon. RNA was isolated by RNAeasy kit (Qiagen) and sequencing (RNA-seq) performed by the Genome Technology Access Center at Washington University using Illumina NovaSeq 2x150 with a 30M read target. Bioinformatics included the R/Bioconductor package Limma using the voomWithQualityWeights function for differential expression analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database for pathway analysis.

first: Katherine

last: Huang

first: Ruishu

last: Deng

first: Siyan

last: Cao

first: Miao

last: Wang

first: Saeed

last: Soleymanjahi

first: Thanyarat

last: Promlek

first: Rachel

last: Rodgers

first: Deanna

last: Davis

first: Darren

last: Nix

first: Guadalupe

last: Oliva Escudero

last: Xie

first: Chien-Huan

last: Chen

first: Anas

last: Gremida

first: Richard

last: Rood

first: Ta-Chiang

last: Liu

first: Megan

last: Baldridge

first: Parakkal

last: Deepak

first: Nicholas

middle: O

last: Davidson

first: Randal

last: Kaufman

first: Matthew

last: Ciorba


title: Redirecting glucose flux during in vitro expansion generates epigenetically and metabolically superior anti-tumor T cells for adoptive cell therapies (RNA-Seq)

city: Pittsburgh

first: Aaron

last: Yang

address: 4401 Penn Ave

institute: University of Pittsburgh

summary: Cellular therapies are uniquely living drugs that must survive and persist within the body to achieve anti-tumor efficacy.  In vitro culture of therapeutic T cells often relies on hypermetabolic conditions to maximize expansion. We show that this non-physiologic environment generates metabolically and functionally impaired T cells that more readily rely on aerobic glycolysis than T cells found in vivo. To target this shift in glycolytic metabolism, we employ dichloroacetate (DCA) during in vitro expansion resulting in elevated mitochondrial capacity and stemness properties pre-infusion - ultimately improving anti-tumor efficacy. DCA-conditioned T cells surprisingly show no elevated intratumoral function, but have an immediate and long-term survival benefit. DCA conditioning decreases reliance on extracellular glucose by promoting the usage of more physiologic carbon sources. This metabolic shift increases histone acetylation at key longevity genes dependent on citrate export from mitochondria. Blockade of mitochondrial citrate export – and thus formation of cytosolic acetyl-coA – reverses the beneficial effects of DCA. Our data suggest a simple means of correcting in vitro expansion of adoptive cell therapies for enhanced anti-tumor efficacy.

overall_design: Gene expression analysis of bulk RNA-seq of Pmel-1 T cells from 3 separate mice expanded with or without DCA for 7 days

first: Andrew

last: Frisch


title: Redirecting glucose flux during in vitro expansion generates epigenetically and metabolically superior anti-tumor T cells for adoptive cell therapies (CUT&Tag)

overall_design: CUT&Tag analysis of H3K9Ac, H3K9Lac, H3K27Ac of Pmel-1 T cells from 3 separate mice expanded with or without DCA for 7 days


title: Exploring the roles of Notch inhibitors and STAT3 inhibitors in the regulation of liver cancer proliferation

first: hexin

last: Yan

summary: We discovered that the inhibition of both the Notch and STAT3 signaling pathways effectively suppressed the proliferation of liver cancer cells, which aligns with the results obtained from co-culturing with human hepatocyte-derived liver progenitor-like cells (HepLPCs).

first: Liu

last: Wen-ming

first: Yan

last: He-xin


title: Silencing of long noncoding RNA P53RRA suppressed ferroptosis in prostate cancer by activating the AKT signaling pathway

first: chen

middle: wei

last: fen

address: 4F, Building 1, Standard Property Unit 3, International Biotech Island

institute: Forevergen

summary: Background: Investigations regarding the function of ferroptosis in prostate cancer (PCa) progression are still rare. Therefore, this study revealed the function of long noncoding RNA P53RRA (P53RRA)-mediated ferroptosis in PCa. Methods: The levels of P53RRA, TFR1, IREB2, SLC7A11, and GPX4 in DU145 cells were examined by quantitative real-time PCR and Western blot. Besides, cell proliferation was tested by Cell Counting Kit-8; GSH, MDA, and reactive oxygen species (ROS) levels were examined using the corresponding kits, flow cytometry, or fluorescence. Additionally, P53RRA silenced DU145 cells were treated with an AKT inhibitor to confirm the role of the AKT signaling pathway in P53RRA-mediated ferroptosis. Then, transcriptome RNA sequencing (RNA-seq) obtained the mRNA expression profiling.  Results: P53RRA was down-expressed in PCa cells compared with normal human prostate epithelial cells. Silencing of P53RRA decreased the levels of TFR1 and IREB2 while promoted the expression of SLC7A11 and GPX4. Knockdown of P53RRA promoted the proliferation ability and GSH level while decreased ROS and MDA levels. Additionally, the bioinformatics analysis showed that P53RRA silencing enriched in phosphatidylinositol 3-kinase (PI3K)-AKT signaling pathway causes the aberrantly expressed mRNAs. Besides, P53RRA silencing induced the phosphorylation of AKT. Interestingly, AZD5363 treatment increased TFR1 and IREB2 levels inhibited by P53RRA silence and decreased SLC7A11 and GPX4 levels stimulated by P53RRA silence. Besides, AZD5363 administration partly reversed the silencing of P53RRA-mediated proliferation promotion, increased the level of GSH, and inhibition on MDA/ROS levels. Conclusions: Silencing of P53RRA suppressed ferroptosis by activating the AKT signaling pathway to modulate the development of prostate cancer.

overall_design:
The human prostate cancer cell lines DU145 (HTB-81) were obtained from the American Type Culture Collection.
To investigate whether P53RRA promotes ferroptosis in PCa, we used siRNA to deplete P53RRA levels in DU145 cells.

first: Junhao

last: Liao

first: Gaohuang

first: Lilin

last: Zhou

first: Jinpeng

last: Gu

first: Sihua

last: Zhu

first: Chunling

last: Li

first: Tengyu

first: Chonghe

last: Jiang


title: PSPC1 selectively controls tumorigenesis and oncogenic transcription in acute myeloid leukemia

city: San Antonio

first: Pinpin

last: Sui

state: TX

address: 8403 Floyd Curl Dr., STRF

institute: UT health San Antonio

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

overall_design: Refer to individual Series


title: Redirecting glucose flux during in vitro expansion generates epigenetically and metabolically superior anti-tumor T cells for adoptive cell therapies (ATAC-Seq)

overall_design: Chromatin accessibility analysis of bulk ATAC-seq of Pmel-1 T cells from 3 separate mice expanded with or without DCA for 7 days


title: Redirecting glucose flux during in vitro expansion generates epigenetically and metabolically superior anti-tumor T cells for adoptive cell therapies


title: mbdIL-7 CAR19 versus traditional CAR19 long term antigen exposure

city: Charlestown

first: Michael

middle: C

last: Kann

state: MA

address: 149 13th Street

department: CCR

institute: MGH

summary: CAR+ cells were sorted out of co-culture after 4weeks of continuous exposure to CD19 expressing K562 in order to determine the effects of mbdIL-7 on CAR19 performance and transcriptome

overall_design: 2 CAR, 2 treatments (drug or control), 3 samples each --  total of 12 samples.

first: Max

last: Jan


title: Changes in Gut, Microbiome, and Cognition after Doxorubicin, Cyclophosphamide, and Paclitaxel Chemotherapy Treatment

status: Public on May 29 2025

city: Little Rock

last: Robeson

state: Arkansas

address: 4301 W. Markham St., Slot 782

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: Chemotherapy induced cognitive impairment (CICI), or “chemobrain”, is defined as an impairment in memory, learning, executive function, and attention following chemotherapy treatment. In this study, 12-week-old female C57/BL6 mice were treated with 8 once weekly intraperitoneal injections (IP) of the following chemotherapeutic treatment groups: 1) Doxorubicin (Dox), Cyclophosphamide (CYP), and Paclitaxel (PTX) (AC-T) or 2) saline. At 30 days after the last AC-T or Saline injection, mice underwent the three-chamber sociability test to assess social behavior and social memory. AC-T treated mice spent equal time with both the novel and the stranger mouse, indicating a deficit in social memory. RNA sequencing showed changes in networks associated with neurogenesis, axonal guidance and neurotransmission.

overall_design: Whole brains were harvested and flash frozen in 2-methylbutane. Hippocampal samples were collected from coronal slices using a 0.2mm tissue punch and were sent to the RNA Sequencing Core for processing. There were 6 samples for each treatment group: AC-T and Saline. RNA was extracted from samples using the Zymo Quick-DNA/RNA miniprep Plus Kit (Cat # D7003). mRNA Library was constructed using the Illumina TruSeq Stranded mRNA Library Prep kit (Cat # 20020594). Samples were run on a 200-cycle NextSeq 2000 P2 flow cell. Dragen (v 4.3.6) was used for binary base call conversion and FastQC (v 0.11.9) was used for quality control. Quantification was done using Salmon (v 1.9.0). Fastq files were uploaded into Qiagen Ingenuity Pathway Analysis (IPA) via the RNA-Seq Analysis Portal (https://digitalinsights.qiagen.com/IPA).

first: Bailey

last: Cronin

first: Sangam

last: Kandel

first: Taylor

last: McElroy

first: Sofia

last: Syed

first: Chase

last: Swinton

first: Christa

last: Corley

first: Vijayalakshmi

last: Sridharan

first: Antiño

last: Allen


title: Splenic accumulation of PD-1+ TIGIT+ CD4+ T cells and elevated of IL1R2 expression suppress antibody production during aging

city: Beijing

first: fang

last: wu

address: Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

summary: Aging populations and infectious diseases are posing increasingly significant global challenges. The the immune system’s changes, particularly in the spleen, are crucial for elderly individuals to combat infections. However, the underlying mechanism of aging changes in the spleen remains unclear. In this study, we observed that IgE and IgG1 production was suppressed following OVA stimulation in 18-month-old mice. Using CyTOF, we identified a notable accumulation of exhausted PD-1+TIGIT+CD4+ T cells in the spleens of aging individuals. These cells influenced B cells IgG1 production via the il1r2-CD40L pathway. Our findings revealed how immunity declines with age and offers specific targets for enhancing elderly immunity through nutritional interventions and vaccine development.

overall_design: The exhausted PD-1+TIGIT+CD4+ T cells detected by CyTOF detection were sorted and then subjected to transcriptome sequencing to discover differentially expressed genes and pathways that affect the immune response function.

first: Fang

last: Wu

first: Ming

last: Zhang

first: Bing

last: Fang


title: JC virus propagation is potentiated by glial replication and accelerated by demyelination-associated glial proliferation [scRNA-seq]

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

summary: Progressive multifocal leukoencephalopathy (PML) is a demyelinating infection of the brain of immunosuppressed individuals, mediated by the gliotropic polyomavirus JCV. JCV replicates in mitotically-competent human glial progenitor cells and astrocytes, which are triggered to divide in the setting of viral T antigen-mediated cell cycle entry, allowing viral replication; the death of mitotically-incompetent oligodendrocytes occurs secondarily, largely through T antigen-mediated apoptosis. This observation suggested that JCV infection might be potentiated by astrocytic replication, and hence accelerated in the setting of mitotic gliogenesis. To test this hypothesis, we tagged dividing human glia in vitro with bromodeoxyuridine (BrdU), then infected them with JCV MAD1, and confirmed that proliferating human astrocytes are more supportive of JCV propagation than mitotically quiescent cells. In vitro, scratch assays confirmed that viral propagation was greatly enhanced in peri-scratch regions of dividing glia. JCV infection of human glial chimeras established that infection was greatly accentuated by cuprizone-mediated demyelination, which was associated with increased glial progenitor cell proliferation. JCV infection in vivo was associated with caspase3-defined death of uninfected as well as infected oligodendrocytes, suggesting the contribution of bystander death to JCV-associated demyelination.  These results suggest that JCV propagation in PML may be potentiated by glial cell division, and that the accentuated glial cell division and hence DNA replication attending acute demyelination might provide an especially favorable environment for JCV propagation and PML progression. These data thus argue for the aggressive prevention of new demyelinating events in patients at risk for PML.

overall_design: Infected primary fetal astrocytes were collected at different stages. At three different time points (day 0, day 4, and day 14 post infection), cells were washed with HBSS-/- and detached with TryplE at 37ºC for 5-10min. We transferred all the cells to 50 mL tube and set the volume to 30 mL. Aliquots of 5e5 cells in 15 mL tubes were preserved for single cell RNA-seq. Cells were suspended in 100 µL Miltenyi washing buffer and incubated with cell hashing antibody (1 µL, BioLegend, USA). Cells from different groups were independently stained with one of the barcodes labeled antibody pools. Samples were pooled at equal concentration, then loaded on a 10x Genomics Chromium instrument to generate single-cell gel beads in emulsion (GEMs). Libraries were prepared using Chromium Single Cell v3 Reagent Kit (10x GENOMICS) according to the manufacturer’s protocols.

first: Cui

last: Li

first: Nguyen

middle: P

last: Huynh

last: Schanz

first: Martha

last: Windrem


title: Single cell RNA sequencing CD45+ tumor-infiltrating lymphocytes (TILs) samples from glioma mouse model treated with PBS or ibudilast.

city: guangzhou

first: Fan

last: Xing

address: Zhongshan Road

institute: Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences

summary: We report the analysis of tumor infiltrating lymphocytes from a GL261 mouse glioma model that were treated with PBS or ibudilast.

overall_design: 2 conditions, PBS treated, ibudilast

first: Zixi

last: Qin


title: LncRNA RPPH1 regulated gene expression changes in breast cancer MDA-MB-231 cells

city: Nanjing

first: Yi

last: Pan

address: 24 Tongjiaxiang Avenue

institute: China Pharmaceutical University

summary: LncRNA RPPH1 has been reported to be highly expressed in a variety of cancers. In order to determine the function and mechanism of lncRNA RPPH1 in breast cancer, we overexpressed lncRNA RPPH1 in breast cancer MDA-MB-231 cells, and analyzed the gene expression changes in these RPPH1 overexpressed cells compared with the control cells by RNA-seq.

overall_design: Gene expression profiles from RNA-sequencing were generated from lncRNA RPPH1 overexpressed MDA-MB-231 cells and the control MDA-MB-231 cells. There are three replicates in each group.


title: PD-1 regulates tumor-infiltrating CD8+ T cells in both a cell-intrinsic  and cell-extrinsic fashion [scRNA-seq]

city: Boston

first: Samuel

middle: Cyrus

last: Markson

address: 77 Ave Louis Pasteur

department: Immunology

institute: Harvard Medical School

summary: Although PD-1 inhibitors are FDA-approved for over 25 different cancers, the mechanisms contributing to response remain incompletely understood. To elucidate the impact of PD-1 deleted CD8+ T cells on PD-1-expressing CD8+ T cells in the same tumor microenvironment, we developed an inducible PD-1 knockout (KO) model in which PD-1 is deleted on approximately 50% of cells. PD-1 deletion beginning at day 7 after implantation of MC38 tumor cells induced robust tumor control. Remarkably, PD-1-expressing CD8+ T cells in the tumor had increased functionality similar to PD-1 KO CD8+ T cells. Using single cell RNA seq and TCR seq, we found that the major transcriptional changes following PD-1 deletion were shared by PD-1 KO and PD-1-expressing CD8+ T cells, though PD-1 KO clones preferentially expanded. These data suggest PD-1 inhibitors not only exert cell-intrinsic effects but also may promote increased T cell function via non-cell autonomous mechanisms, which has important implications for design of PD-1-based cancer immunotherapies.

overall_design: Cre+ and Cre- PD-1 fl/fl mice bearing subcutaneous MC38 tumors were treated with tamoxifen such that roughly 50% of cells experienced deletion of exons 2-4 of Pdcd1. CD8+ T cells were obtained and use to generate gene expression, V(D)J, and feature barcoding libraries.


title: IL-6 Evades KSHV-Mediated Hyperadenylation repression via CRM1-Dependent Nuclear Export.

city: Lausanne

first: Mandy

last: Muller

address: Rue du Bugnon 48

department: Institute of Microbiology

country: Switzerland

institute: University Hospital of Lausanne

summary: RNA turnover is critical for regulating gene expression and cellular homeostasis, with nuclear export representing a key step in mRNA fate. During lytic reactivation of Kaposi’s Sarcoma-associated Herpesvirus (KSHV), widespread host mRNA decay is mediated by the viral endonuclease SOX, which depletes cytoplasmic transcripts and induces secondary nuclear RNA processing defects. One such defect includes transcript hyperadenylation, which typically promotes nuclear retention and decay. However, a subset of host mRNAs escapes both SOX-mediated degradation and nuclear retention, raising questions about their export mechanisms and stability. Here, we investigate the impact of KSHV infection on mRNA poly(A) tail length and nuclear export dynamics using high-throughput poly(A)-sequencing of nuclear and cytoplasmic RNA fractions from KSHV-positive cells. Our data confirm a global increase in poly(A) tail length during KSHV lytic infection, consistent with transcript hyperadenylation. Nevertheless, we identified a group of hyperadenylated transcripts that remain cytoplasmically localized, suggesting active evasion of nuclear retention. Notably, we focused on interleukin-6 (IL-6), a known SOX escapee, which retains cytoplasmic expression during lytic infection despite acquiring a longer poly(A) tail. Using G/I tailing and sPAT assays, we confirmed IL-6 hyperadenylation and demonstrate that its export is CRM1-dependent rather than through the canonical NXF1-NXT1 pathway, which is suppressed during host shutoff. Pharmacological inhibition of CRM1 impairs IL-6 nuclear export and reduces steady-state RNA levels, implicating CRM1 export in the stabilization of this transcript. Our findings reveal a previously unrecognized mechanism by which select host mRNAs, including IL-6, bypass KSHV-imposed nuclear export blocks and escape nuclear decay, thereby preserving their function during viral infection. This study highlights viral manipulation of RNA processing and export pathways as a critical determinant of transcript fate and identifies CRM1 as a key mediator of selective host transcript preservation during KSHV lytic reactivation.

overall_design: iSLK-WT Cells, either latent or 24hr lytic reactivation, Cytoplasmic and Nulcear RNA fractionation, subjected to PolyA-seq

first: Jacob

last: Miles

first: Samantha

last: Schultz

first: Will

last: Dwyer

first: Daniel

last: MacVeigh-Fierro


title: Self and parasite-derived peptides selected upon DERAA-bearing HLA-DRB1 alleles activate CD4+ T cells from Chagas cardiomyopathy patients and are associated with ventricular dysfunction

city: Belo Horizonte

first: Thaiany

last: Goulart de Souza-Silva

address: Avenida Antônio Carlos

department: Morphology

country: Brazil

institute: Federal University of Minas Gerais

summary: Human infection with the protozoan Trypanosoma cruzi causes Chagas disease, which may lead to a deadly dilated cardiomyopathy resulting from T-cell-mediated inflammation. We found that specific HLA-DRB1 alleles (*0103, *0402, *1301, and *1302) that display the DERAA motif are linked to this severe clinical manifestation of Chagas disease. We employed computational analysis, in vitro functional assays, and single-cell RNA sequencing to determine the response of CD4+ T cells from indeterminate (IND) and cardiac (CCC) Chagas patients to peptides selected on DERAA-bearing alleles. We observed that these alleles display binding affinity towards host-derived peptides with sequence similarity to parasite-derived proteins. These peptides can activate and induce proliferation of CD4+ T-cells from CCC, but not IND. Importantly, the magnitude of this response correlated with the severity of ventricular dysfunction and increased production of soluble factors associated with myocardial fibrosis. Analysis of differentially expressed genes (DEGs) in activated CD4+ T-cells from individuals with the DERAA-DRB1 alleles demonstrated a high expression of cytotoxic, chemotactic and proapoptotic genes, linking these cells with pathogenic functions. Finally, we observed the upregulation of genes that code for the host proteins that contain the potentially pathogenic peptides in the cardiac tissue of CCC, suggesting their involvement in cardiomyopathy. Our findings highlight the ability of CD4+ T-cells from CCC patients to recognize and react to foreign and self-peptides, thereby emphasizing the importance of HLA-DRB1 alleles in the presentation of potentially pathogenic antigens and in the amplification of CCC pathology.

overall_design: PBMCs from 24 patients with Chagas disease (Asymptomatic=10, CCC=14) were sequecing. CD45-positive PBMCs were isolated and stained with oligonucleotide-conjugated Sample Tags following the manufacturer’s instruction using the BDTM Single-Cell Multiplexing Kit, BD-Biosciences. Single-cell capture and cDNA library preparation was performed using the BD Rhapsody Express Single-cell analysis system (BD Biosciences), using the BD Rhapsody cDNA (BD Biosciences, cat# 633663) and Target amplification (BD Biosciences, cat# 633664) kits, according to the manufacturer’s instructions. Sequencing was performed on Nova SeqTM 6000 (Illumina, San Diego, CA). Data processing was initially conducted through the Seven Bridges Genomics platform, using BD Rhapsody Target Analysis Pipeline (version CWL-v1.2) to identifies and correct artifacts of sequencing, ensuring accurate molecule counting pre cell. DBEC (Distribution-based error correction) files were imported into SeqGeq version 1.6.0 (BD, Ashland, OR). Normalization was performed considering all genes, 10,000 counts per cell as a scaling factor. Quality control of samples was performed considering both cell and gene quality. Quality control for cell removes outlier events or doublets based on number of expressed genes relative to the library size. Gene quality control considered the total expression of each gene versus the cells expressing each gene, as well as the expression dispersion (Supplementary Figure 1D). The Lex BDSMK plugin was employed to identify Sample Tags. Data analyses were performed on sample-normalized and quality-controlled cells. Differentially expressed genes (DEGs) were identified using the FindMarker function, applying a Log2 fold change threshold (≥ 1.5 or ≤ -1.5) and a Bonferroni-adjusted p value<0.05.

first: Thaiany G

last: Souza-Silva

first: Eula GA

last: Nenes

first: Andrea

last: Teixeira-Carvalho

first: Amanda B

last: Figueiredo

first: Katia LP

last: Morais

first: Juliana

last: Apóstólico

first: Hélcio

last: Rodrigues

first: Jorge

last: Kalil

first: Maria A

last: Juliano

first: Luiz

first: Silvana S

last: Araújo

first: Alexandre N

last: Pantaleao

first: Antonio

last: Mutarelli

first: Maria CP

last: Nunes

first: Kenneth J

last: Gollob

first: Walderez O

last: Dutra


title: ISG15-Mediated Suppression of Type I Interferon Signaling Leads to Susceptibility to Epstein-Barr Virus Infection  (Early_Infection_day7_BulkRNAseq)

city: Durham

first: Nicolas

middle: Martin

last: Reinoso-Vizcaino

state: North Carolina

address: 213 Research Drive

department: Molecular Genetics & Microbiology

institute: Duke University

summary: Epstein-Barr Virus (EBV), the first identified human oncogenic virus, is linked to numerous malignancies, including gastric cancer, nasopharyngeal cancer and multiple B-cell Lymphomas. However, the host-virus interactions that regulate EBV-driven cell transformation and pathogenesis remain incompletely understood. Here, employing a Cas9–ribonucleoprotein (RNP)-based screen in primary B cells, we identified 11 host factors that promote and 35 that restrict EBV-driven outgrowth. Notably, ISG15, a ubiquitin-like, type I interferon-induced antiviral protein, exhibited a dependency role for growth in early stages of infection but not in LCLs. Mechanistically, we found that the regulation of free ISG15 levels greatly impacts the proliferation capacity of EBV-infected B-cells, by modulating the activation of type I IFN signaling. Finally, we identified rare germ-line variants in UBA7, the ISG15 E1 enzyme, in patients with EBV severe disorders, that impair the ISG15 conjugation process. This highlights a critical role of ISG15 in the control of EBV infections.

overall_design: Bulk RNAseq of CD46- sorted from CD46-only knockout, and CD46 with ISG15 or STAT1 knockout EBV-infected cells, 7 days post infection.

first: Micah

last: Luftig


title: JC virus propagation is potentiated by glial replication and accelerated by demyelination-associated glial proliferation

first: Steven

last: Goldman

overall_design: Infected primary fetal astrocytes were collected at different stages. At three different time points (day 0, day 4, and day 14 post infection), cells were washed with HBSS-/- and detached with TryplE at 37ºC for 5-10min. We transferred all the cells to 50 mL tube and set the volume to 30 mL. Aliquots of 5e5 cells in 15 mL tubes were preserved for single cell RNA-seq. The remaining cell portion was subsequently isolated for polyA+ RNAs, and libraries were made with Illumina TruSeq Stranded mRNA Library Prep Kit (n = 3 independent sets).

first: Cui

last: Li

first: Nguyen

last: Huynh

middle: J

last: Schanz

first: Martha

last: Windrem


title: Expression of RNA in serum EV from PDAC patient

city: Asahikawa

first: Kenji

last: Takahashi

state: Hokkaido

address: 2-1-1-1, Midorigaokahigashi

department: Department of Medicine

country: Japan

institute: Asahikawa Medical University

summary: Expression profiling of over 60000 RNAs was performed using cDNA microarray. The profiling was performed using serum EV RNA from PDAC patients compared with healthy individuals.

overall_design: EV RNAs derived from 3 PDAC patients compared with 3 healthy individuals were processed for use on the microarray.

first: Kazuya

last: Koyama