title: Transcriptional regulation of albumen biosynthesis in the magnum of broiler breeder hens

city: Honolulu

first: Birendra

last: Mishra

state: HI

address: 1955 East west road

department: Department of Human Nutrition Food and Animal Sciences

institute: University of Hawaii at Manoa

summary: Broiler chicken production is crucial to meet the increasing global food demand. Hyperphagic and obese broiler breeder hens have a short production cycle, which is challenged by age-associated egg quality and fertility decline, affecting hatchability. A fertilized egg is a comprehensive set of essential elements to nurture and develop a healthy chick. Egg albumin occupies most of the egg content, which is synthesized and secreted by the magnum. The genetic regulation of albumin biosynthesis in broiler breeder hens and its alteration with age might reveal the genetic marker that will produce quality eggs in subsequent generations. Hence, the objective of the study is to determine the differentially expressed genes (DEGs) and pathways involved in albumin biosynthesis in the magnum (young vs aged). The magnum tissues were collected from the broiler breeder hens at peak production, identified as the young group (35 weeks, N=30), and from the declined production, recognized as the aged group (50 weeks, N=30). Five samples from each group (n=5) were used for RNA sequencing and analyzed to get DEGs and associated pathways. The significantly upregulated genes with a putative function in quality egg formation were confirmed using qPCR. Seventy-five up-regulated and 52 down-regulated genes were determined. The top 20 most upregulated genes and top 20 most downregulated genes, based on their putative function, were categorized into five groups: egg white synthesizing (AMDHD1, FER, CTNNA3), molecular communication (VAPA), oviduct tissue regeneration (ADAM19, CFAP100, AMD1, TM4SF19, SLC39A13, VMO1), and defense (ZBTB46, STAM2, OVoDA3). “Post-translational protein phosphorylation” was the most significantly enriched Reactome pathway involving DNAJC3, PPP3CA, TF, SPARCL1, PDIA6, SGPP2, HSP90B1, and PNPLA2 genes.  The study successfully identified DEGs, genetic networks, and pathways that can be used as genetic markers to select quality egg producing broiler breeder hens.

overall_design: RNA sequencing of the broiler breeder magnum to compare between peak (35 weeks) and declining (50 weeks) production to see the traanscriptomic variation of the magnum.

first: Prem

middle: L

last: Mahato

first: Vedbar

last: Khadka

first: Ken

last: Macklin

first: Rajesh

last: Jha


title: Functional maps of a genomic locus reveal confinement of an enhancer by its target gene [Region-capture Micro-C (RCMC)]

status: Public on May 16 2025

city: Amsterdam

first: Christina

last: Moene

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Genes are often activated by enhancers located at large genomic distances. The importance of this positioning is poorly understood. Here, by relocating different promoter-reporter constructs into >1,000 alternative positions within a single locus, we dissected the positional relationship between the mouse Sox2 gene and its distal enhancer. This revealed an intricate, sharply confined activation landscape, in which the native Sox2 gene occupies an optimal position for its activation. Deletion of the gene relaxes this confinement and broadly increases reporter activity. Surprisingly, this confining effect of the Sox2 gene on reporter activity is partially conferred by its ~1 kb coding region. Our local relocation approach provides high-resolution functional maps of a genomic locus and reveals that a gene can strongly constrain its enhancer’s realm of influence.

overall_design: Allele specific micro-C with capture of the Sox2 locus in different mouse embryonic stem cell lines containing a Sox2 reporter at different genomic locations in the presenc and absence of the endogenous Sox2::mCherry (S129) allele.

first: Mathias

last: Eder

middle: J

first: Mikhail

last: Magnitov

first: Jamie

last: Drayton

first: Elzo

last: de Wit

first: Anders

middle: S

last: Hansen

first: Bas

last: van Steensel


title: Synthetic oligonucleotide-based sequencing of off-target regions for a guide RNA targeting EMX1

city: Cambridge

first: Gary

last: Ge

state: Massachusetts

address: 100 Cambridgepark Dr #101

department: QBio

country: USA

institute: Vor Biopharma Inc

summary: To generate a test data to facilitate development of toolkit for off-target nomination data analysis, a library consisting >81K in silico predicted on- and off-target regions for an EMX1 gRNA are synthesized and cleaved in vitro with SpCas9. The cleaved products are used to build NGS library followed by sequencing leading to >13 million reads. About 99% of examined regions are covered by 10 or more valid UMIs. More than 90% of valid UMIs from on-target region support cleavage. About 500 off-target regions have a score greater than 0.1, including 7 off-target regions with score exceeding one.

overall_design: Off-target normination study of a guide RNA targeting EMX1 gene using synthetic oligonucleotide-based sequencing technology

first: Shu

last: Wang

first: Huan

last: Qiu

first: Ruijia

first: Eric

last: Anderson

first: Huanying Gary


title: Effect of exercise at different loads in gene expression of both atria in male rats

city: Barcelona

first: Eduard

last: Guasch

state: Catalonia

address: Rosselló 149

country: Spain

institute: Hospital Clinic Barcelona, IDIBAPS

summary:
Strenuous exercise increases the risk of atrial fibrillation, while moderate physical activity has been suggested to decrease its risk, Data from animal models suggest that intensive exercise, but not moderate training, increases atrial fibrosis and could be on the basis of the increased atrial fibrillation risk. The impact of the transition from moderate to strenuous exercise on atrial fibrillation risk and its underlying mechanisms remain poorly understood. We aimed to analyze biatrial remodeling after moderate and strenuous exercise.
We conducted an RNA microarray of right and left atria of sedentary, mdoeratel-trained, and intensively-trained rats to uncover the mechanisms leading to atrial fibrosis in intensively trained rats.

overall_design: A group of male Wister rats were randomized into a moderate exercise (mod, 35 cm/s for 45 min, 5 days/week), strenuous exercise (int, 60 cm/s for 60 min, 5 days/week), or a sedentary group for 16 weeks.

first: Montserrat

last: Batlle

first: Cira

last: Rubies

first: Anna

last: Alcarraz

first: Aline

last: Meza-Ramos


title: Age-associated dysregulation of post-synaptic mitochondria perturbs re-innervation kinetics

city: Ann Arbor

first: Susan

middle: V

last: Brooks

state: Michigan

address: 109 Zina Pitcher Pl

department: Molecular and Integrative Physiology

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: Age-associated degeneration of neuromuscular junctions (NMJs) contributes to sarcopenia and motor decline, yet the mechanisms linking mitochondrial dysfunction to impaired NMJ regeneration in aging remain poorly defined. Here, we demonstrate that post-synaptic mitochondria are significantly diminished in both quantity and bioenergetic function in aged skeletal muscle, correlating with increased denervation and delayed reinnervation following nerve injury. Single-nucleus RNA sequencing of myofibers before and after sciatic nerve crush revealed that sub-synaptic myonuclei in aged muscle exhibit attenuated induction of mitochondrial gene programs, including oxidative phosphorylation, biogenesis, and import. To test whether these deficits are causal, we developed a muscle-specific CRISPR genome editing approach targeting CHCHD2 and CHCHD10—two nuclear-encoded mitochondrial proteins that localize to the intermembrane space and interact with the mitochondrial contact site and cristae organizing system (MICOS). Knockout of CHCHD2/CHCHD10 in young muscle recapitulated aged phenotypes, including mitochondrial disorganization, reduced ATP production, NMJ fragmentation, and delayed reinnervation. Transcriptional profiling of NMJ nuclei from knockout muscles revealed impaired pseudotime progression, failure to activate mitochondrial remodeling programs, and elevated stress signatures. These findings establish a critical role for sub-synaptic mitochondrial integrity in sustaining NMJ stability and regenerative capacity and identify CHCH domain-containing proteins as key regulators of post-synaptic mitochondrial function during aging and injury.

overall_design: Tibialis anterior muscles from young (2–5 months) and aged (23–29 months) mice were collected at 0, 7, and 14 days after sciatic nerve crush injury. Samples include uninjured and post-injury timepoints. Experimental groups consist of age-matched controls and injured muscles, with additional groups receiving intramuscular injections of AAV targeting CHCHD2/CHCHD10 or saline (PBS). All conditions include biological replicates. Young and aged timepoints include 2–3 biological replicates per group, and AAV vs. PBS conditions include 3–4 replicates per timepoint. Both multiplexed and non-multiplexed libraries were generated across batches.

first: Steve

middle: D

last: Guzman

first: Paula

middle: M

last: Fraczek

first: Klimentini

last: itsani

first: Esraa

middle: K

last: Furati

first: Grace

last: Kenney

first: Joe

last: Chakkalakal

first: Carlos

middle: A

last: Aguilar


title: Characterization of the aryl hydrocarbon receptor as a potential candidate to improve cancer T cell therapies

city: Besançon

first: Valentine

last: De Castro

state: Franche-Comté

address: 8 rue du Dr JFX Girod

country: France

institute: Université de Franche-Comté

summary: T cell-based cancer therapies efficacy can be limited by the tumor microenvironment which can lead to T cell dysfunction. Multiple studies, particularly in murine models, have demonstrated the capacity of the aryl hydrocarbon receptor (AhR) to negatively regulate antitumor T cell functions. AhR is a cytoplasmic receptor and transcription factor that was originally identified as a xenobiotic sensor, but has since been shown to play a significant role in the gene regulation of various immune cells, including T cells. Given the insights from murine studies, AhR emerges as a promising candidate to invalidate for optimizing T cell-based cancer therapies. However, the lack of studies on the role of AhR in human T cells underscores the need for comprehensive characterization of AhR expressing T cells. This study aims to investigate the regulatory mechanisms of AhR in human T cell biology to better understand its impact on reducing antitumor immune responses. By using the CRISPR-Cas method, knockout was performed on human T cells in order to characterize Ahr knocked-out T cells using an in vitro chronic stimulation model. Engineered T cells exhibited enhanced effector- and memory-like profiles and expressed reduced amount of CD39 and TIGIT. Ahr knockout enhanced human CAR-T cells’ functionality and persistence upon tumor chronic stimulation. Collectively, these results highlight the role of AhR in human CAR-T cells efficiency.

overall_design:
To investigate the role of the aryl hydrocarbon receptor (AhR) on T cells' biology, we knocked-out Ahr by CRISPR-Cas9.
We performed gene expression profiling analysis using data obtained from RNA-Seq of 3 donors at two different timepoints (either restimulated once or four times using dynabeads) in presence of AhR' ligand.

first: Oumaïma

last: Abdellaoui

first: Barbara

last: Dehecq

first: Babacar

last: Ndao

first: Alexandra

last: Dauvé

first: Olivier

last: Adotévi

first: Romain

last: Loyon

first: Yann

last: Godet


title: Inhibition of TGF-beta signalling during zebrafish larval tail regeneration.

city: Sheffield

first: Henry

middle: H

last: Roehl

address: Firth Court, Western Bank

country: United Kingdom

institute: University of Sheffield

summary: This study investigates the role of TGF-beta signalling during tail regeneration in 72-96 hour old zebrafish. The inhibitor SB431542 was used to inhibit TGF-beta signalling with and without larval tail excision. Control larvae were treated with DMSO. The study identifies candidate differentially expressed genes (DEGs) after injury; TGF-beta-dependent, injury regulated DEGs; TGF-beta-dependent DEGs in the absence of injury; and TGF-beta-independent injury-dependent DEGs.

overall_design: Larvae were maintained at 28.5C in E3 buffer. Larval tails were excised at the pigment gap (approximately 200um from the end of the tail) at 72 hours post fertilisation (hpf). 18 hours later another 200um of tissue was removed for RNA analysis. For unoperated samples, the same region of tissue was removed at 90hpf. SB431542 treatments were at 50uM and were from 72-90hpf. DMSO was used at 0.1%.


title: Role of ATF3 in the transcription of GI-SINEs (growth inducing B2-SINEs) in DRG neurons in response to sciatic nerve crush

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: Injury of the sciatic nerve upregulates a specific subset of B2-SINE RNAs in Dorsal Root Ganglia (DRG) neurons that enhances axon regeneration, which we termed GI-SINEs (growth inducing SINEs). Based on ATAC-seq and transcription factor binding site analysis and in-culture perturbation of AP-1 TFs, we hypotheiszed that GI-SINEs specifically regulated by injury activated AP-1 TFs. Here we experimentally tested the role of ATF3, a CREB TF that belongs to the AP-1 TF superfamily, in the transcriptional upregulation of GI-SINEs. ATF3 was previously identified and characterized as a key activator of nerve-injury induced regeneration associated genes (RAGs) mRNA. Cre recombinase expressed under the Advillin promoter was used for ATF3-exon3 excision in a broad and specific manner in the DRG. Sciatic nerve injury was carried on on mice with a conditional knockout of ATF3 in sensory neurons and ATF3-wt mice and total RNAseq was carried on RNA extracred from on sciatic innervating DRGs (L4-L6) from the injured side ("Inj") and non-injured side (naive / "Na").

overall_design: Homozygous ATF3(exon3)-floxed (Cre-negative) female mice were bred with Advillin-Cre/ heterozygous ATF3(exon3)-flox mice to yield sensory neuron specific knockout of ATF3 ("ATF3 cKO": Adv-Cre+/ATF3-fl_homo). As control mice, either Cre-negative or ATF3-flox null from the same colony were used ("ATF3 wt"). Sciatic nerve crush injury was carried on the left side of 8-12 weeks old: 8 mice were included in the ATF3 cKO group and 9 mice in the ATF3-wt control group. Mice were euthanized 3 days later and sciatic-innervating DRGs L4-L6 were excised from both injured and non-injured (naive) sides. Dissociated DRG cells were passed on Percoll gradient for neuronal enrichment and RNA was extracted and purified using Qiagen RNeasy micro kit.

first: Michael

last: Fainzilber

first: Eitan

last: Zahavi


title: Targeting GI-SINE (Growth inducing B2-SINE) RNA in DRG neurons by Antisense Oligonucleotides (ASO)

summary: We identified 2 specific motifs that are enriched in GI-SINE RNA expressed in sciatic-nerve injured DRG neurons compared to non-regulated B2-SINE RNAs. We designed a mix of 5 ASOs (21nt phosphorothioate DNA with LNA-flanks) that target these motifs and transfected those into cultured dorsal root ganglia (DRG) neurons. Control ASO was based on a 21nt non-targetting sequence from shControl backbone (addgene plasmid #85741). Primary DRG neurons were transfected using Dharmafect-4 with ASO at 50nM final concentration 1 hour after plating. Cultures were processed for RNA extraction 48h after transfection for RNA sequencing to identify changes in B2-SINE expression.

overall_design: Each replicate (1-4) is based on indepdendent total DRG culture preparation, from 1 mouse in each repeat that was distributed between experimental conditions. Experimental conditions are: ASO control 50nM, ASO mix (GI-SINE ASOs) and untransfected cultures.


title: Single-cell gene expression profiling of oncogenically transformed small intestinal organoids upon treatment with TGF-β1

city: Freiburg im Breisgau

first: Andreas

last: Hecht

address: Stefan-Meier-Str. 17

department: Institute of Molecular Medicine and Cell Research

country: Germany

institute: Albert Ludwig University of Freiburg

summary: Colorectal cancer (CRC) cells infiltrating surrounding tissue commonly undergo partial epithelial-mesenchymal transitions (pEMT) and employ a collective mode of invasion. How these phenotypic traits are regulated and possibly interconnected remains underexplored. Here, we used intestinal organoids with CRC driver mutations as model system to investigate the mechanistic basis of TGF‑β1-induced pEMT and collective invasion. By scRNA-seq we identified multiple cell subpopulations representing a broad pEMT spectrum, where the most advanced pEMT state correlated with the transcriptional profiles of leader cells in collective invasion and a poor prognosis mesenchymal subtype in human CRC. Bioinformatic analyses pinpointed Sox11 as a transcription factor whose expression peaked in the potential leader/pEMThigh cells. Immunofluorescence staining confirmed Sox11 expression in cells at the invasive front of TGF‑β1-treated organoids. Loss-of-function and overexpression experiments showed that Sox11 is necessary, albeit not sufficient, for TGF-β1-induced pEMT and collective invasion. In human CRC samples, elevated Sox11 expression was associated with advanced tumor stages and worse prognosis. Unexpectedly, aside from orchestrating the organoid response to TGF-β1, Sox11 controlled expression of genes related to normal gut function and tumor suppression. Apparently, Sox11 is embedded in several, distinct gene regulatory circuits, contributing to intestinal tissue homeostasis, tumor suppression, and TGF-β-mediated cancer cell invasion.

overall_design: Mouse small intestinal organoids (line 931-TKA; Apc-/-, KrasG12D/+, Trp53R172H/+ ) were treated with solvent  or TGF-β1 for 0, 24, 48, and 72 h, followed by 10x Genomics scRNA-seq analysis.

first: Yu-Hsiang

last: Teng

first: Bismark

last: Appiah

first: Geoffroy

last: Andrieux

first: Monika

last: Schrempp

first: Katja

last: Rose

first: Angelika

last: Hofmann

first: Manching

last: Ku

first: Sven

last: Beyes

first: Melanie

last: Boerries


title: Sciatic nerve crush regulation of RNA alternative poly-adenylation [DRGinjury_2019-QuantSeq_Rev_24h]

summary: Poly-adenylation regulates post-transcriptional processing and localization of mRNA. To  study the effect of nerve injury on poly-adenylation across the transcriptome, 3'-end RNAseq was carried on DRG neurons following sciatic nerve injury. Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.

overall_design: Mice were subjected to crush injury on in one sciatic nerve. Corresponding DRG (Lumbar L4-L6) were dissected 24 h after injury and total RNA was extracted using Qiagen RNEasy Mini kit. Injured and naive (contralateral side) ganglia were extracted from two mice per repeat.

first: Indrek

last: Koppel


title: Blood single cell transcriptome of paradoxical eczema in psoriasis patients treated with biologics

city: Manchester

first: Ali

last: Al-Janabi

address: Oxford Road

institute: University of Manchester

summary: Biologics targeting the tumour necrosis factor (TNF) and interleukin (IL)-17/23 axis are highly effective treatments for psoriasis but can result in cutaneous adverse events. The pathogenesis of paradoxical eczema, the occurrence of an atopic dermatitis phenotype after biologic initiation in people with psoriasis, is unknown. Using single cell RNA-seq and mass cytometry, we found increased expression of TNF, interferon (IFN)-γ and IFN-α and their signalling pathways in paradoxical eczema case cell clusters compared with matched psoriasis controls. Genetic variants influencing expression of TNF pathway genes were associated with paradoxical eczema in a separate genotyped cohort, and this association was independent of known atopic risk loci. This suggests that paradoxical eczema has a predominantly type 1 systemic inflammatory signature, and that genetic susceptibility to aberrant TNF pathway signalling could contribute to development of this phenotype during biologic treatment.

overall_design: Peripheral blood mononuclear cells (PBMCs) were obtained from 3 patients with psoriasis who developed paradoxical eczema, and 3 matched psoriasis controls, and analysed with single cell (sc)RNA-seq.

first: Paul

last: Martin

first: Catherine

last: Simpson

first: Hefin

last: Rhys

first: Adnan

middle: R

last: Khan

first: Steve

last: Eyre

first: Maria

last: Christofi

first: Amy

middle: C

last: Foulkes

first: Andrew

last: Skelton

first: Sebastien

last: Viatte

first: Anne

last: Barton

middle: P

last: Morris

last: Smith

first: Christopher

middle: E

last: Griffiths

first: Richard

middle: B

last: Warren


title: Sciatic nerve crush regulation of ribosome-associated  RNA in DRG neurons, alternative polyadenylation analytsis [DRGinjuryRiboTag2018-QuntSeq72h]

first: Riki

last: Kawaguchi

summary: Nerve injury alters transcription and translational processes in cell-type specific manner.Here we probe the effect of sciatic nerve injury on alternative polyadenylation of ribosome associated RNA specifically in sensory neurons.Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.

overall_design: Adv-Cre//Ribotag mice were subjected to crush injury on in one sciatic nerve. Corresponding DRG (Lumbar L4-L6) were extracted 3 days after injury. Injured and naive ganglia was extracted from each animal and subjected to immunoprecipitation (IP) of Ribotag ribosomal marker (HA-tagged Rpl22) to isolate intact ribosomes from sensory neurons. RNA was extracted from the input (prior to immunoprecipitation) and post-IP fraction. 3 replicates were used, combining DRG tissue from 4 mice per repeat for RNA isolation.

first: Michael

last: Fainzilber


title: Transcriptional profiles of mouse retinal ganglion cells after optic nerve crush [RGC_injury_2019-9205_He]

summary: The removal of the Structure Specific Recognition Protein 1 (Ssrp1) gene from retinal ganglion cells has been shown to improve their survival after acute optic nerve injury in mice. To investigate the transcriptional mechanisms underlying the negative regulation of neuronal survival by Ssrp1, we obtained the bulk transcriptome of pooled RGCs at several time points (1, 2, 3, and 4 days) after optic nerve injury.

overall_design: Expression of Ssrp1 was disrupted in RGCs using an AAV based CRISPR-Cas9 system and its impact on RGC survival gene expression programs were investigated after optic nerve crush.

first: Aboozar

last: Monavarfeshani

first: Feng

last: Tian

first: Songlin

last: Zhou

first: Zhigang

last: He


title: GI-SINEs - non-coding RNA regulators of neuronal growth and regeneration [DRG_injury_2019-9047_Tuzsynski]

summary: How are axonal signaling and soma responses coordinated in enruonal growth and regeneration?

overall_design: At indicated times after bilateral sciatic nerve crush,L4-5 DRGs were isolated and RNA extracted as previously described.

first: Indrek

last: Koppel

first: Eitan

last: Zahavi

first: Erna

last: van Niekerk


title: Transcriptome-guided GLP-1 receptor therapy rescues metabolic and behavioral disruptions in a Bardet-Biedl Syndrome mouse model

city: London

first: Naila

last: Haq

state: London

address: Room HB4.2E, 2nd Floor, Hodgkin Building, Guy's Campus, London Bridge,

institute: King's College London

summary: Bardet-Biedl Syndrome (BBS), a ciliopathy characterized by obesity, hyperphagia, and learning deficits, arises from mutations in Bbs genes. More exacerbated symptoms occur with mutations in genes encoding the BBSome, a complex regulating primary cilia function. We investigated the mechanisms underlying BBS-induced obesity using a Bbs5 knockout (Bbs5-/-) mouse model. Bbs5-/- mice displayed hyperphagia, learning deficits, glucose/insulin intolerance, and disrupted metabolic hormones, phenocopying human BBS. They displayed an unique immunophenotype in white adipose tissue with increased proinflammatory macrophages and dysfunctional regulatory T cells, suggesting a distinct mechanism for adiposity compared to typical obesity models. Additionally, Bbs5-/- mice exhibited pancreatic islet hyperplasia but failed to normalize blood glucose, suggesting defective insulin action. Hypothalamic transcriptomics revealed dysregulated endocrine signaling pathways with functional analyses confirming defects in insulin, leptin, and cholecystokinin (CCK) signalling, while preserving glucagon-like peptide-1 receptor (GLP-1R) responsiveness. Notably, treatment with a GLP-1R agonist effectively alleviated hyperphagia, body weight gain, improved glucose tolerance, and circulating metabolic hormones in Bbs5-/- mice. This study establishes Bbs5-/- mice as a valuable translational model of BBS to understand the pathogenesis and develop better treatments. Our findings highlight the therapeutic potential of GLP-1R agonists for managing BBS-associated metabolic dysregulation, warranting further investigation for clinical application.

overall_design:
RNASeq was performed on 5 samples (UCLA Scientific Core Services) from 2 wildtype and 3 Bbs5-/- male mice at 12 weeks of age (post-obesity phase).

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Submitter states that missing raw files are due to file loss.
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first: Arashdeep

last: Singh

first: Mingxin

last: Yang

first: Shelby

last: Luckey

first: Samira

last: Mansouri

first: Martha

last: Campbell-Thompson

first: Lei

last: Jin

first: Sofia

last: Christou-Savina

first: Guillaume

last: deLartigue


title: Identification of transcriptome markers in blue catfish cryopreserved sperm to predict male reproductive performance for catfish aquaculture

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

summary: Catfish is the most important species in US aquaculture, accounting for 70% of freshwater production. The production of hybrids of female channel catfish (Ictalurus punctatus) and male blue catfish (I. furcatus) constitutes over 50% of the total harvest due to their superior production traits and enhanced disease resistance. However, hybrids cannot be produced naturally, and male must be euthanized for sperm collection. An appropriate storage condition is essential to preserve the sperm’s ability to fertilize eggs during the female spawning season. Cryopreservation is a widely used method for sperm storage. However, it has been shown to affect sperm gene expression in many vertebrate species. A high degree of individual variability among cryopreserved sperm was reported, resulting in huge variations in hatch rate. Since high-quality gametes are the prerequisites for hybrid catfish reproduction, in this study, we investigate the molecular mechanisms underlying male reproductive performance, which is critical for the accurate prediction of hatching rate and offspring performance in hatchery environments.

overall_design: The sperm samples from 30 male blue catfish have been collected and divided into tow groups, the fresh one, which has been directly stored in -80℃ freezer, and the cryopreserved one, which exprerienced the cryopreserved procedures. And then the cryopreserved sperm samples have been thawed for fertilization. The embryo harch success rate and viability rate (40 days post-hatch) were documented. RNA was extracted from each sample and libraries were constructed, followed by the RNA sequencing. Differentially expressed genes (DEGs) were identified between the cryopreserved samples with high hatch rate and low hatch rate. The correlation between the expression level of DEGs and the hatch success rates were assessed to determine the potential gene markers which can serve as the predictors for hatch performance. Futhermore, a machine learning model was developed integrating the gene markers and physiological parameters to enable accurate prediction of hatch success rate.


title: Single cell gene expression profile of corneal endothelial cells from 2-month-old and 11-month-old murine cornea

city: Davis

first: Raneesh

last: Ramarapu

state: California

institute: UC Davis School of Veterinary Medicine

summary: Corneal endothelial cells are highly metabolically active and generally non-proliferative cells required for their corneal barrier and ionic pump. With age, corneal morphology and density changes; however, the transcriptional changes driving this is unknown. We used single cell RNA-sequencing (scRNA-seq) to assess the transcriptional changes in aging mouse corneal endothelial cells.

overall_design: Wildtype mice corneas from 2-month-old and 11-month-old were dissected, papain dissociated and analyzed using single cell RNA-sequencing. Only corneal endothelial cells and epithelial cells were enriched for.

first: Sangwan

last: Park

first: Brian

last: Leonard

first: Nayeli

last: Echeverria

first: Vijaykrishna

last: Raghunathan

first: Panteleimon

last: Rompolas

first: Sara

last: Thomasy


title: Sciatic nerve crush regulation of ribosome-associated RNA in DRG neurons

first: Riki

last: Kawaguchi

summary: Nerve injury alters transcription and translational processes in cell-type specific manner.Here we probe the effect of sciatic nerve injury on ribosome associated RNA specifically in sensory neurons.Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.

overall_design: Adv-Cre//Ribotag mice were subjected to crush injury on in one sciatic nerve. Corresponding DRG (Lumbar L4-L6) were extracted 3 days after injury. Injured and naive ganglia was extracted from each animal and subjected to immunoprecipitation (IP) of Ribotag ribosomal marker (HA-tagged Rpl22) to isolate intact ribosomes from sensory neurons. RNA was extracted from the input (prior to immunoprecipitation) and post-IP fraction. 4 mice (replicates) were used.

first: Michael

last: Fainzilber

first: Indrek

last: Koppel


title: Sciatic nerve crush upregulation of B2-SINE expression at specific genomic loci

summary: To map the loci of B2-SINE expressed in DRG which are regulated by sciatic nerve injury, paired-end RNAseq was carried on DRG neurons following sciatic nerve injury at 24h and 72h (3d) after injury. Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.

overall_design: Mice were subjected to crush injury on in one sciatic nerve. Corresponding DRG (Lumbar L4-L6) were extracted at two time points: 24h and 3 days after injury. For each time point, injured and naive ganglia was extracted from each animal. 4 mice (replicates) were used for each time-point.


title: GI-SINE Analyses

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

overall_design: Refer to individual Series


title: RNA-seq data of 293T cells trasfected with long non-coding RNA Lnc#61 or vehicle pcDNA3.1, and then infected or non-infected with the H5N1 avian influenza virus CK10 strain

city: Yangzhou

first: Jiao

last: Hu

address: 48 Wenhui Road

country: China

institute: Yangzhou University

summary:
Lnc#61 is a Long non-coding RNA that inhibits the replication of H5N1 subtype of influenza A virus
However, the mechanism of  role of Lnc#61 against highly pathogenic avian influenza virus (HPAIV) H5N1 subtype in mammalian cells is largely unknown.
By functional analysis, we want to investigate host factors involved in Lnc#61's antiviral activity in infected or non-infected 293T cells

overall_design: Cell samples were collected 24h after CK10 infection, a total of three biological samples were analyzied, each of them had triplication.The samples are named 011-1-1, 011-1-2, 011-1-3,  C1-1-1,  C1-1-2, C1-1-3, wei011-1, wei011-2,  wei011-3,  weiC1, weiC2, weiC3, repectively. As for the sample name, 011-1means transfected with Lnc#61 and then infected with CK10, C1-1 means transfected with pcDNA3.1 and then infected with CK10, while wei011 means transfected with Lnc#61 but non-infection, weiC1 means transfected with pcDNA3.1 but non-infection.

first: Xinxin

last: Zheng


title: AP-1 inhibition in DRG neurons by A-Fos dominant negative construct

summary: Prior analysis suggsted that that AP-1 TFs play a role in expression of specific B2-SINE following in-vivo nerve injury. We thus sought to experimnetally test the role of AP-1 transcription factors in upregulation of B2-SINE RNA expression in DRG neurons.  Neurons were transduced with PHP.S-AAV vectors expressing either A-Fos (dominant negative construct that targets Fos-interacting transcription factors), GFP control or were left untransduced. RNA was extracted 7 days later and analyzed to identify effects on B2-SINE expression and known AP-1 targetted mRNAs.

overall_design: Primary cultures from neuron-enriched DRG tissues were transduced using sensory-neuron specific AAV vector (PHP.S). Experimental conditions were DN (A-Fos AP-1 dominant negative), GFP control and untransduced control. Experiment replicates are cultures from separate mice and were divided between the 3 experimental conditions.

first: Eitan

last: Zahavi


title: Sciatic nerve crush regulation of RNA alternative poly-adenylation

overall_design: Mice were subjected to crush injury on in one sciatic nerve. Corresponding DRG (Lumbar L4-L6) were extracted 3 days after injury. Injured and naive ganglia was extracted from each animal. 4 mice (replicates) were used.


title: Identification of Key Pathways and Genes in the Progression of Silicosis Fibrosis Based on WGCNA

city: Beijing

first: Jiaqi

last: Lv

address: Nanwei Road, Xicheng District

institute: Chinese Center for Disease Control and Prevention

summary: Silicosis, induced by inhaling silica particles in workplaces, is one of the most common occupational diseases. The prognosis of silicosis and its consequent fibrosis is extremely poor due to limited treatment modalities and lack of understanding of the disease mechanisms.  In this study, a Wistar rat model for silicosis fibrosis was convincingly established by intratracheal instillation of silica (0, 50, 100 and 200 mg/mL, 1 mL) with the evidence of Hematoxylin and Eosin (HE) and Masson staining and the expressions of inflammatory and fibrotic proteins of rats’ lung tissues. RNA of lung tissues of rats exposed to 200 mg/mL silica particles and normal saline for 14 d and 28 d was extracted and sequenced to detect differentially expressed genes (DEGs) and to identify silicosis fibrosis-associated modules and hub genes by Weighted gene co-expression network analysis (WGCNA). Predictions of gene functions and signaling pathways were conducted using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. In this study, it has been demonstrated the promising role of Hippo signaling pathway in silicosis fibrosis, which will be conducive to elucidating the specific mechanism of pulmonary fibrosis induced by silica and to determining molecular initiating event (MIE) and adverse outcome pathway (AOP) of silicosis fibrosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for lung tissues of Wistar rats exposed to 200 mg/mL silica and normal saline.

first: Jingwei

last: Xiao

first: Qiang

last: Jia

first: Hua

last: Shao

first: Bin

last: Li


title: Transcriptomics provides novel insights into the regulatory mechanism of Panax notoginseng exosome-like nanoparticles

city: Wuhan

first: Wenying

last: Zhong

address: Shizi Street No.1

institute: Huazhong Agricultural University


title: TimeLapse-seq after translation inhibition in YTHDF-depleted Hela cells

status: Public on May 15 2025

city: New York

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

summary: Degradation of mRNA containing N6-methyladenosine (m6A) is essential for cell growth, differentiation, and stress responses. Here, we show that m6A markedly alters ribosome dynamics and that these alterations mediate the degradation effect of m6A on mRNA. We find that m6A is a potent inducer of ribosome stalling, and these stalls lead to ribosome collisions that form a unique conformation unlike those seen in other contexts. We find that the degree of ribosome stalling correlates with m6A-mediated mRNA degradation, and increasing the persistence of collided ribosomes correlates with enhanced m6A-mediated mRNA degradation. Ribosome stalling and collision at m6A is followed by recruitment of YTHDF m6A reader proteins to promote mRNA degradation. We show that mechanisms that reduce ribosome stalling and collisions, such as translation suppression during stress, stabilize m6A-mRNAs and increase their abundance, enabling stress responses. Overall, our study reveals the ribosome as the initial m6A sensor for beginning m6A-mRNA degradation.

overall_design: TimeLap-seq was performed as previously described.  Briefly, cells were grown to 80% confluency.  Cells were treated for 1.5 h with 500 µM 4-thiouridine (4sU, SigmaAldrich, T4509).  After 1.5 h, total RNA was collected using Qiagen RNeasy Mini kit RLT buffer (Qiagen, 74104) supplemented with 1% 𝛽-mercaptoethanol (BME).  Cells were lysed by passing through a 25 1/2-gauge needle, and RNA was isolated following the manufacturer’s instruction with RPE buffer supplemented with 1% BME.  10 µg total RNA was treated with 2,2,2-trifluoroethylamine (TFEE) and sodium periodate (NaIO4) at 45 °C for 1 h to convert 4sU to N4-trifluoroethylcytosine.  RNA was then purified twice using RNAClean beads (Beckman Coulter, A63987). 1 µg of treated RNA was used for RNA-seq library preparation using NEBNext® rRNA Depletion Kit (NEB, E6310X) and NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB, E7760L).  Library quality was assessed on Agilent TapeStation4200 using D1000 ScreenTape (Agilent, 5067-5584).  Library was quantified on Qubit4 Fluorometer using Qubit 1X dsDNA HS Assay Kit (ThermoFisher, Q33231).  Libraries were sequenced with pair-end 2x100 cycles on Illumina NovaSeq 6000.

first: Shino

last: Murakami


title: Transcriptomics provides novel insights into the regulatory mechanism of Panax notoginseng exosome-like nanoparticles in HSF

summary: In current study, we observed that Panax notoginseng exosome-like nanoparticles successfully inhibited apoptosis and promoted proliferation in HSF. Moreover, transcriptomics was implemented to uncover its underlying mechanism. A total of 7924 differentially expressed genes (DEGs) were identified, with some of them enriched in apoptosis, proliferation related pathways. Intriguingly, some DEGs were annotated in skin aging development or coagulation function pathways. In view of this, we suggested Panax notoginseng exosomes may delay skin aging. Lastly, RT-qPCR confirmed the veracity and reliability of RNA-sequencing results.

overall_design: Examination the overexpression of Panax notoginseng exosome-like nanoparticles in HSF.

first: Zhaowei

last: Teng


title: Latent EBV impairs immune cell signaling and enhances the efficacy of anti-CD3 mAb in Type 1 Diabetes.

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Teplizumab is approved for delay of diagnosis of type 1 diabetes and may modulate new onset disease. Compared to EBV seronegative patients, those who were EBV seropositive prior to treatment had a more robust response to drug in two clinical trials. We compared the phenotypes, transcriptomes, and development of peripheral blood cells before and after teplizumab treatment. Higher number of Tregs and partially exhausted CD8+ T cells were found in EBV seropositive individuals at the baseline in the TN10 and AbATE trials. Single cell transcriptomics and functional assays identified downregulation of NFkB and other pathways after treatment in treated EBV seropositive patients. Among diabetes antigen specific CD8+ T cells, T cell receptor and mTOR signaling were also reduced. Impairments in function of adaptive immune cells were enhanced by teplizumab treatment in EBV seropositive individuals. Our data indicate that EBV can impair signaling pathways in immune cells, that broadly redirect cell differentiation.

overall_design:
Islet autoantigen  and EBV tetramer positive CD8 cells were single cell sorted for scRNA-Seq analysis. Comparisions between placebo controls and teplizumab anti-CD3 treated patients were compared at baseline and 18 months with and without EBV seropositivity
Please note that the indivisual sample information (for total 3668 samples) is provided in the 'sample_metadata.xlsx'.

first: Eddie

last: James

first: Hai

last: Nguyen

first: Alex

first: Ana

last: Delgado


title: TRAF6 integrates innate immune signals to regulate glucose homeostasis via Parkin-dependent and -independent mitophagy

first: Scott

last: Soleimanpour

state: MI

address: 1000 Wall St

department: Metabolism, Endocrinology, and Diabetes

summary: Elevated or chronic innate immune activation plays a role in the progression of metabolic diseases such as diabetes, yet the influence of innate immune signaling on pancreatic β-cells is not well characterized. Here we report that TRAF6, an E3 ubiquitin ligase downstream of TLR signaling, maintains β-cell function during diet-induced obesity. Deletion or inhibition of TRAF6 impairs glucose homeostasis, mitochondrial function, and mitophagy during metabolic stress in both mouse and human islets. The combination of TRAF6 deficiency and palmitate exposure reduces localization of mitophagy machinery, such as BNIP3, to the mitochondria. Interestingly, co-deletion of Parkin restores glucose-stimulated insulin section, mitochondrial bioenergetics, and mitophagy. These findings suggest that Parkin-independent mitophagy mechanisms may be important for maintenance of β-cell function during metabolic stress.

overall_design: RNA-seq profiling of pancreatic islets isolated from either control or beta-cell specific Traf6 KO mice fed a 15-week HFD.

first: Elena

last: Levi-D'Ancona


title: Patient-derived kidney organoids recapitulate ADPKD and enable the identification of RHO signaling inhibitors as candidate therapeutics

city: Jinan

first: liqiang

last: guo

state: Shandong

address: No. 107, Wenhua West Road

department: Shandong University

institute: Qilu Hospital

summary: Current renal organoid models, typically derived from pluripotent stem cells, recapitulate aspects of kidney development but are constrained by cellular immaturity and off-target populations. Here, we establish an expandable renal organoid system from adult patient kidney tissues, comprising proliferative epithelial progenitors and differentiated proximal tubule and collecting duct lineages. Leveraging this system, we generated “petal-like” polycystic organoids from PKD1 or PKD2 mutant tissues that faithfully mimic the morphological and functional hallmarks of ADPKD. Mechanistic investigation revealed that RHO signaling may serve as a candidate component of the cilia-dependent cyst activation (CDCA) mechanism that drives cystogenesis. Subsequent drug screening identified RHO GTPase inhibitors as selective suppressors of cyst growth across multiple organoid lines. This patient tissue-derived organoid platform offers a physiologically relevant and robust model for investigating cytogenic mechanisms and enabling precision therapeutic discovery and drug screen in polycystic kidney disease.

overall_design: Comparative gene expression profiling analysis of scRNA-seq data for kidney organoids.

first: Guo

last: Liqiang

first: Fan

last: Yujia

first: Du

last: Haoran

first: Zhang

last: Xinyan

first: Jiang

last: Shan

first: Guan

last: Yong

first: Ren

last: Lingtong

first: An

last: Yachun

last: Xiaohui

first: Sun

last: Huixian

first: Kong

last: Feng

first: Shi

last: Benkang

first: Yi

last: Fan

first: Hu

last: Huili

first: Zhao

last: Shengtian


title: Transcriptomic analysis of sulfur dioxide stress-resistant Saccharomyces cerevisiae strain obtained by evolutionary engineering

city: Istanbul

first: Halil

middle: ibrahim

last: KISAKESEN

state: Istanbul

address: ITU MOBGAM, SARIYER

department: Molecular Biology, Genetics and Biotechnology

country: Turkey

institute: Istanbul Technical University

summary:
In this study, we have developed a highly SO2-stress-resistant yeast (Saccharomyces cerevisiae) strain [F3] using evolutionary engineering, by successive batch selection at gradually increased SO2 levels. The evolved F3 strain was resistant to 1.0 mM SO2 stress, which was strongly inhibitory to the reference strain. Whole-transcriptomic analysis of F3 was performed with respect to its reference strain to determine differences in gene expression levels between the two strains.
Saccharomyces cerevisiae

overall_design: Agilent Yeast One-Color DNA microarray systems were used for comparative whole-genome transcriptomic analysis of the selected mutant F3 and its reference strain. Prior to gene expression analysis, each culture was grown in triplicate in yeast minimal medium (YMM) at 30°C and 150 rpm. Total RNA isolation was carried out, using RNeasy Mini Kit (Qiagen) at early exponential phase of growth (OD600 ~1.0).

middle: I

last: Kisakesen

first: Zeynep

last: Canbay

first: Aziz

last: Korkmaz

first: Alican

last: Topaloğlu

first: Ömer

last: Esen

first: Mevlüt

last: Arslan

first: Can

last: Holyavkin

last: Çakar


title: In vitro and in vivo induction of fetal hemoglobin with two potent and orally bioavailable LSD1 inhibitors

first: Kaiwen

last: Deng

address: 3305 NCRC Building 520

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Pharmacological small molecules that target fetal hemoglobin (HbF) repressors serve as potent, cost-effective, and accessible therapeutic strategies to β-globinopathies such as sickle cell disease (SCD). LSD1 inhibition has been shown to induce HbF levels both in vitro and in vivo. However, all potent LSD1 inhibitors in HbF induction in vivo are covalent irreversible compounds, which can cause some adverse effects. In this study, we utilized structure-aided drug design based on the scaffold of a reversible LSD1 inhibitor GSK-690, and developed potent new reversible LSD1 inhibitors that induce robust γ-globin expression in human primary erythroid differentiation culture. Moreover, in a transgenic mouse model of SCD, oral administration of the novel LSD1 inhibitors induces significant elevation of HbF levels and alleviates the disease pathologies resulted from SCD. In addition, combined treatment of an BRD4 degrader, BD-9136 with the LSD1 inhibitors represses the induction of RUNX1 and PU.1, therefore rescues the yield of erythroid cells caused by LSD1 inhibition. Our data indicate that our novel LSD1 inhibitors can effectively induce HbF levels and reduce disease pathologies in SCD mice, and are well-tolerated by oral administration. We anticipate that these new compounds will offer new therapeutic possibilities for treating SCD.

overall_design: To examine the chromatin occupancy of BRD4 in adult erythroid cells, CUT&RUN was performed in adult erythroid cells differentiated from CD34+ hematopoietic stem and progenitor cells (HSPCs) isolated from peripheral blood (PB) (purchased from Fred Hutchinson Cancer Center). PB-CD34+ HSPCs were differentiated in a standard 3-phase erythroid differentiation culture for 11 days before collection for CUT&RUN. CUT&RUN experiments were carried out using either BRD4 antibody or IgG antibody (negative control) to examine the BRD4 chromatin occupancy. All experiments were carried out in independent duplicates from 2 different CD34+ cell donors.

first: Yu

last: Wang

first: Yuanfang

last: Guan

first: James

last: Engel


title: The LSD1 inhibitor RN1 rescues Congenital Dyserythropoietic Anemia type II

summary: Congenital dyserythropoietic anemia type II (CDAII) is an autosomal recessive disease resulting from loss-of-function mutations in SEC23B, which encodes a component of coat complex protein II (COPII) vesicles. We have previously shown that the expression of SEC23A, a paralogous protein for SEC23B, is significantly lower than that of SEC23B in human erythroid cells and that increased SEC23A expression rescues CDAII. In this study, we generated a human erythroid cell line that expresses eGFP from the endogenous genomic locus of SEC23A and performed a small molecule screen to identify compounds that increase the SEC23A-eGFP level. The top compound passing all filters was an LSD1 inhibitor. We validated that LSD1 inhibition with RN1 i) results in increased SEC23A mRNA and protein levels in primary erythroid cells derived from CD34+ human hematopoietic stem and progenitor cells (HSPCs), at doses that do not impair erythroid cell growth or differentiation and ii) rescues the defect resulting from SEC23B deletion in primary human erythroid cells. We validated LSD1 as the target of RN1 by showing that genetic downregulation of LSD1 also led to a profound induction of SEC23A mRNA levels in HPSC-derived erythroid cells. Subsequently, we validated our findings in vivo, demonstrating that deletion of Lsd1 in mouse erythroid cells results in increased Sec23a expression and that RN1 treatment rescues the erythroid defect observed in CDAII mice. Finally, using CUT&RUN, we found that LSD1 occupies a sequence in the SEC23A promoter, which when deleted, results in increased SEC23A expression and rescue of CDAII. These finding suggest that LSD1 occupies the SEC23A promoter, repressing SEC23A transcription and that in the setting of LSD1 inhibition, SEC23A expression is de-repressed, resulting in CDAII rescue. Therefore, using an unbiased screen, we have identified and validated a novel promising therapeutic strategy for CDAII, using a compound that inhibit LSD1 or a genetic approach based on deleting the SEC23A promoter sequence that is occupied by LSD1.

overall_design: To investigate the mechanism by which LSD1 inhibition induces SEC23A expression and rescues CDAII, we performed CUT&RUN using a well-established LSD1 antibody in day 11 and day 14 erythroid cells derived from human CD34+ HSPCs.

first: Lei

last: Yu

first: Rami

last: Khoriaty


title: A novel model for high-grade transformation in IDH mutant glioma (Methylation Analysis)

city: BETHESDA

first: Zachary

last: Sergi

address: 37 CONVENT DR

department: Neuro-Oncology Branch

institute: National Cancer Institute

summary: Background. High-grade transformation (HT) is common in IDH-mutant glioma, which is inevitable and unpredictable. Both genomic and metabolomic landscapes are going through dynamic processes during the transformation. Although HT phenomena have been observed clinically, the research of mechanisms underlying HT have been limited by the lack of preclinical models that can recapitulate the evolution of malignant transformation.      Methods. Here we established a unique pair of matched cell lines, 403L and 403H, by utilizing  tumor samples of an IDH-mutant astrocytoma from the same patient when the tumor was diagnosed as WHO grade 2 and  4, respectively. Using genetic, epigenetic, and metabolomic analyses, the two cell models have been characterized extensively. The cell lines have been used to establish orthotopic xenograft models of the disease.

overall_design: UMAP analysis was employed to investigate DNA methylation profiling of the tumors using methylation-based classifiers of the central nervous system (CNS) tumorsclustering using tSNE and UMAP analysis.  Next, a comprehensive examination of DNA methylation patterns across the genomes of the two cell lines, 403L and 403H, was conducted. The analysis covered over 742,000 CpG sites in both cell lines.

first: Zach


title: Metabolic transcriptional profile of virulent Mtb-infected human AM

city: Dublin

first: Aaron

last: Walsh

address: Trinity Translational Medicine Institute

department: Department of Clinical Medicine

country: Ireland

institute: Trinity College Dublin

summary: Mycobacterium tuberculosis (Mtb)-induced shifts in macrophage metabolism are an accepted central infection paradigm. Mtb-infected murine lung tissue exhibits gene expression changes consistent with classic Warburg metabolism and Mtb-infected murine macrophages undergo TCA cycle remodeling. Human macrophages also respond energetically to Mtb infection, however, interestingly the phenotypic nature of this response appears to vary depending on the viability of infection. Despite the overwhelming consensus that metabolic changes are critical to the host response to infection, we have little understanding of the metabolic transcriptional landscape of virulent Mtb-infected human alveolar macrophages (AM), the sentinel pulmonary immune cell during Mtb infection. Further still, whether the human AM undergoes glycolytic reprogramming and TCA cycle remodeling during virulent Mtb infection remains undefined; as is suggested to occur in circulating Mtb-infected human macrophages. Here, we aimed to characterise the metabolic transcriptional profile of virulent Mtb-infected human AM. We hypothesised that infection would induce the transcriptome of Warburg metabolism (characterised by aerobic glycolysis), TCA cycle remodeling, and reduce expression of genes involved in mitochondrial oxidative phosphorylation (OXPHOS).

overall_design: Human alveolar macrophages (AM) were harvested from 6 volunteers (3 never-smokers and 3 ex-smokers), who were undergoing clinically indicated bronchoscopy. AM were infected with live virulent H37Rv Mtb for 24 h using a multiplicity of infection of 1-10 bacilli per cell. AM were then lysed, and total RNA was collected and purified using silica-membrane column centrifugation. MTB-induced changes in gene expression were determined using the NanoString nCounter Platform Metabolic Pathways Panel and data were analysed using the NanoString nSolver Data Analysis software.

first: Joseph

last: Keane


title: CITE-Seq of tumors from 4T1-tumor bearing mice

city: Baltimore

first: Jose

last: Adrover

state: Maryland

address: 855 N Wolfe St

department: Cell Biology

institute: Johns Hopkins University

summary: CITE-Seq of sorted cells from the tumor of 4T1-bearing mice to study immune cell composition.

overall_design: CITE-Seq was performed on sorted cells from the tumors of 4T1-bearing mice. CITE-Seq was performed using TotalSeq-B Mouse Universal Cocktail, V1.0.

first: Mikala

last: Egeblad


title: Integrative miRNOMe profiling reveals the miR-195-5p-CHEK1 axis and its impact on luminal breast cancer outcomes

city: Prague 10

first: Veronika

last: Boušková

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

summary: The luminal subtype (estrogen receptor-positive, ER+) is the most common and the most heterogeneous type of breast carcinoma (BC) in women. During our study, we determined expression levels of all microRNAs (miRNOMe) in 101 ER+ BC samples and identified 25 miRNAs being associated with proliferative markers. Using comprehensive in silico analyses we prioritized CHEK1, CDC25A, and CCNE1 as candidate genes affecting the proliferation of ER+ BC, with two microRNAs from the miR-497∼195 cluster identified as their potential regulators. In a cohort of 217 patients, we found a significant association between low expression of CHEK1 and prolonged relapse-free survival (RFS) in luminal BC patients treated with adjuvant chemotherapy. In patients with luminal A subtype treated with neoadjuvant therapy, the opposite role for RFS was seen for hsa-miR-195-5p. Subsequently, we confirmed the potency of hsa-miR-195-5p to inhibit the expression of CHEK1 in vitro. Moreover, the specific Chk1 inhibitor rabusertib (LY2603618) significantly enhanced the efficacy of doxorubicin in ER+ MCF-7 cell line. In summary, we have identified the association of a miRNA profile with highly proliferative luminal BCs and demonstrated the ability of hsa-miR-195-5p to inhibit CHEK1 expression in BC in vitro, underlining the importance of CHEK1 expression and its inhibition for prognosis and treatment of patients with luminal BCs.

overall_design: Expression levels of all miRNAs (miRNOMe) were detected in 101 luminal (ER+) early breast carcinoma samples.

first: Marie

last: Ehrlichová

first: Alžběta

last: Spálenková

first: Ivona

last: Krus

first: Simona

last: Šůsová

first: Viktor

last: Hlaváč

first: Renata

last: Koževnikovová

first: Markéta

last: Trnková

first: David

last: Vrána

first: Jiří

last: Gatěk

first: Kateřina

last: Kopečková

first: Marcela

last: Mrhalová

first: Soňa

last: Měšťáková

first: Pavel

last: Souček


title: Pediatric Sickle Cell Disease Humoral Immunophenotype Alterations

city: Providence

first: Patrycja

last: Dubielecka

state: RI

address: 1 Hoppin St., Coro West, 5th Fl., Suite 5.36

department: Division of Hematology/Oncology, Department of Medicine

institute: Warren Alpert Medical School of Brown University and Rhode Island Hospital

summary: Sickle cell disease (SCD) is a red blood cell disorder associated with hemolysis and inflammation affecting hematopoietic system homeostasis. While both innate and T cell driven adaptive immune responses are involved in driving SCD-linked inflammation, the involvement of the B cell compartment in the pathophysiology of SCD, especially in pediatric patients, is much less understood. To determine the range of immune changes, we assessed the frequency of twelve immune populations via flow cytometry and levels of B cell related cytokines of the peripheral blood (PB) of pediatric (n=13) and adult (n=12) patients with SCD on hydroxyurea as compared to pediatric (n=5) and adult (n=10) race-matched controls. We also evaluated bulk RNA sequencing of the PB of pediatric SCD patients and controls. The majority of SCD patients carried the hemoglobin SS genotype (92.3% pediatrics and 66.7% adults). Mean Hydroxyurea dose was 23.4 mg/kg and 20.0 mg/kg for pediatric SCD (PSCD) and adult SCD (ASCD), respectively. Laboratory data revealed anemia with mean hemoglobin 9.4 g/dl in PSCD and 9.7 g/dl in ASCD with elevated hemolysis in pediatric and adult SCD with mean reticulocyte count of 7.1% in PSCD and 8.8% in ASCD with mean absolute reticulocyte count (ARC) 203 ± 94 for pediatric SCD and 214 ± 169 for adult SCD. Flow cytometry data revealed 1.9-fold increase (p value 0.012) of CD3+CD4+ cells in pediatric SCD versus pediatric controls; this change was not seen in adult SCD versus adult controls (decrease 17%, p value 0.302). Pediatric SCD patients had 3.5-fold increase (p=0.005) in CD19+ B cells without further increase in differentiated B cells, and this change was not seen in adult SCD versus adult controls (increase 7%, p value 0.815). We performed bulk RNA sequencing on the PB of pediatric patients with SCD as compared to the pediatric controls. Obtained transcriptomic data indicated significant changes in transcripts linked to humoral immunity. Over Representation Analysis (ORA) of cell type revealed upregulation of transcripts linked to pro-B cells (27 genes, top 3:E2F2,RAD51,ASPM) and plasma cells (37 genes, top 3:IGF1,TNFRSF17,DERL3). Analysis of B cell related cytokines revealed significant increase in IL2 (p value 0.013), IL4 (p value 0.026), TNFβ (p value 0.039), and IL13 (p value 0.034) inpediatric SCD versus pediatric controls withno significance for these cytokines in adult SCD versus adult controls. BAFF was elevated in both pediatric and adult SCD versus age-matched controls (p value0.041 and p value 0.005, respectively). In sum, our data indicate significant changes in CD4+ and CD19+ cells andsuggest significant alteration of the B cell maturation in pediatric SCD samples. Our findings point to previously unreported effect of SCD on the humoral immune system in children with SCD treated with hydroxyurea, warranting further investigation.

overall_design: To investigate the global transcriptome of pediatric sickle cell diseased patients, RNA was isolated from whole peripheral blood from 13 pediatric sickle cell patients and compared to 5 healthy pediatric controls.

first: E

last: Vistica Sampino

first: D

last: Bonal

first: J

last: Morgan

first: A

last: Chorzalska

first: L

last: Nguyen

first: C

last: Yu

last: Rodriguez

first: R

last: DeVito

first: S

last: Pels

first: P

middle: G

last: Sprinz

last: McGann

last: Lulla


title: Transcriptomic analysis of HIV-associated nephropathy (Tg26) mouse kidney treated with INT-747 and nicotinamide riboside

city: Bethesda

first: Teruhiko

last: Yoshida

address: 10 Center Drive, 9N208

department: NIDDK - KDB

institute: National Institutes of Health

summary: We analyzed the transcriptomic profiles of Tg26 mouse kidney cortex treated by FXR agonist (INT-747) or by nicotinamide riboside (NR) by bulk mRNA-seq.

overall_design: Transcriptomic profiling of Tg26 mouse kidney cortex treated by INT-747 or by nicotinamide riboside by bulk mRNA-seq.

first: Shashi

last: Shrivastav

first: Cheryl

last: Winkler

first: Jeffrey

last: Kopp


title: Patient-derived kidney organoids recapitulate ADPKD and enable the identification of RHO signaling inhibitors as candidate therapeutics [RNA-Seq]

first: liqiang

last: guo

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data for kidney organoids.

first: Guo

last: Liqiang

first: Fan

last: Yujia

first: Du

last: Haoran

first: Zhang

last: Xinyan

first: Jiang

last: Shan

first: Guan

last: Yong

first: Ren

last: Lingtong


title: Bisphenol A enhances retinoic acid-HOX genes signaling disrupting brain development: human

city: Kyoto

first: Akira

last: Hirasawa

state: Kyoto

address: 46-29 Yoshida Shimoadachi-cho, Sakyo-ku

department: Genomic Drug Discovery Science

country: Japan

institute: Kyoto University Graduate School of Pharmaceutical Sciences

summary: Plastic  pollution  and exposure to endocrine- disrupting chemicals (EDCs) like Bisphenol A (BPA) are emerging environmental concerns with potential impacts on human health and development. Despite evidence from epidemiological studies linking chemical exposure1,2 to neurodevelopmental disorders such as autism spectrum disorder and attention deficit hyperactivity disorder, the underlying causal mechanisms remain unclear3.  Here, we show quantitative evidence that chemical exposure and detrimental outcomes are mechanistically linked to  interference with retinoic acid (RA) signaling, a critical pathway in brain and neuronal development. Utilizing human induced pluripotent stem cells and zebrafish embryos, we found that BPA potentiated exogenous RA effects on 3′HOX gene expression and brain patterning, resulting in abnormalities such as duplication of Mauthner cell and abnormal craniofacial cartilage defects. Crucially, this potentiation effect was abolished by retinoic acid receptor antagonists but not estrogen receptor antagonists, suggesting a direct interaction with RA signaling pathways. Notably, the phenomenon was also observed with other chemicals, indicating a potential generalizable mechanism for a broader range of EDCs.  Our findings provide a causal link between chemical exposure and neurodevelopmental impairments, contributing to the potential adverse effects of plastic pollution on development processes.

overall_design: Human iPS cells (409B2, RBRC-HPS0076) were maintained on mitomycin C-treated SNL cell monolayer on gelatin-coated 6 cm dishes in human iPS medium consisting of DMEM/HAM-F12 (Nacalai Tesque) supplemented with 20% KnockOutTM Serum Replacement (Thermo Fisher Scientific), 2 mM L-Alanyl-L-Glutamine (Wako Pure Chemical Industries), 0.11 mM β-mercaptoethanol (Sigma-Aldrich), 1% non-essential amino acids (Nacalai Tesque), 5 ng/mL human recombinant basic fibroblast growth factor (hbFGF; Wako Pure Chemical Industries), and 0.5% penicillin-streptomycin (Nacalai Tesque). Before differentiation, iPS cells were transferred onto feeder-free conditions using E8 medium (Thermo Fisher Scientific) and reseeded onto a 24-well plate with 1.5 × 10^5 cells/well. The next day, the medium was replaced with E6 medium (Gibco), and chemicals were added for 3 d from the following day. The medium was changed every day, and the cells were collected on the fourth day after addition. To treat cells with 100 nM RA, we prepared 1 µM RA in E6 medium from 1 mM RA stock solution in DMSO by diluting 1:1000 with E6 medium. One-tenth volume (100 µL) of 1 µM RA solution was added into the well to make the final concentration to 100 nM. As a control, the same amount of DMSO solution (0.1% in medium) was added.

first: Kenya

last: Ueno

first: Keiko

last: Iida

first: Tatsuyuki

last: Takada


title: Opioid-driven disruption of the septum reveals a role for neurotensin-expressing neurons in withdrawal

city: Seattle

first: Rhiana

middle: Catherine

last: Simon

address: 1959 NE Pacific St

department: Anesthesiology & Pain Medicine

institute: University of Washington

summary: Because opioid withdrawal is an intensely aversive experience, persons with opioid use disorder (OUD) often relapse to avoid it. The lateral septum (LS) is a forebrain structure that is important in aversion processing, and previous studies have linked the LS to substance use disorders. It is unclear, however, which precise LS cell types might contribute to the maladaptive state of withdrawal. To address this, we used single-nucleus RNA-sequencing to interrogate cell type specific gene expression changes induced by chronic morphine and withdrawal. We discovered that morphine globally disrupts the transcriptional profile of LS cell types, but neurotensin-expressing neurons (Nts; LS-Nts neurons) are selectively activated by naloxone. Using two-photon calcium imaging and ex vivo electrophysiology, we next demonstrated that LS-Nts neurons receive enhanced glutamatergic drive in morphine-dependent mice and remain hyperactivated during opioid withdrawal. Finally, we showed that activating and silencing LS-Nts neurons during opioid withdrawal regulates pain coping behaviors and sociability. Together, these results suggest that LS-Nts neurons are a key neural substrate involved in opioid withdrawal and establish the LS as a crucial regulator of adaptive behaviors, specifically pertaining to OUD.

overall_design: Approximately 10,000 nuclei per experimental group were captured and single-nucleus cDNA libraries were constructed using the Chromium Single Cell 3' v3 (samples 1-3) and Chromium NextGEM platform (samples 4-5) according to manufacturer’s instructions. Libraries for samples 1-3 were sequenced using an Illumina 4400 HiSeq platform to a target output of ~ 350,000,000 reads, and libraries 4-5 were sequenced using an Illumina NovaSeq 6000 for a target output of ~350,000,000 reads

first: Koichi

last: Hashikawa

first: Garret

last: Stuber


title: Transcriptomics provides novel insights into the regulatory mechanism of panax notoginseng derived exosome-like nanoparticles on HUVECs cells

first: Wenying

last: Zhong

summary: In current study, we observed that panax notoginseng derived exosome-like nanoparticles successfully promoted proliferation, significantly inhibited apoptosis and greatly facilitated migration in HUVECs, further highlighting the robust therapy effects of HIF1A-AS1 to cardiovascular diseases (CVD). Moreover, transcriptomics was implemented to uncover its underlying mechanism. A total of 276 differentially expressed genes (DEGs) were identified, with some of them enriched in apoptosis, migration and cell cycle related pathways. Intriguingly, some DEGs were annotated in vascular development or coagulation function pathways. In view of this, we suggested panax notoginseng derived exosome-like nanoparticles mediated the progression of CVD by not only regulating the function of HUVECs, but also altering vascular development or coagulation function. Lastly, RT-qPCR confirmed the veracity and reliability of RNA-sequencing results.

overall_design: Examination the overexpression of panax notoginseng derived exosome-like nanoparticles in HUVECs.

first: Yirong

last: Teng


title: Orthotopic 4T1 tumors spatial transcriptomics

first: Jose

last: Adrover

summary: 4T1 tumors, 4 weeks after implantation were excised and analyzed using the 10X Visium technology.

overall_design: FFPE tissue blocks were cut down to approximately 6.5 mm x 6.5 mm in size and sectioned onto the capture areas of the Visium slide according to 10X Genomics Tissue Preparation Guide CG000408. Slides were then deparaffinized and H&E-stained according to the 10X Genomics Demonstrated Protocol CG000409 and imaged at the Animal & Tissue Imaging Core Facility at CSHL. After imaging, the tissue was decrosslinked and probe hybridization with the Visium Mouse Transcriptome Probe Kit (PN-1000365, 10X Genomics) was performed overnight at 50°C. Probe ligation, probe release and extension, and library preparation were performed according to manufacturer’s instructions, and final libraries were sequenced on a NextSeq 500 to target 20,000 reads per spot. Sequencing data were processed with Space Ranger version 2.0.0 (10X Genomics).

first: Mikala

last: Egeblad


title: TimeLapse-seq after translation inhibition in Mettl14 knockout mESC

first: Samie

last: Jaffrey

summary: Degradation of mRNA containing N6-methyladenosine (m6A) is essential for cell growth, differentiation, and stress responses. Here, we show that m6A markedly alters ribosome dynamics and that these alterations mediate the degradation effect of m6A on mRNA. We find that m6A is a potent inducer of ribosome stalling, and these stalls lead to ribosome collisions that form a unique conformation unlike those seen in other contexts. We find that the degree of ribosome stalling correlates with m6A-mediated mRNA degradation, and increasing the persistence of collided ribosomes correlates with enhanced m6A-mediated mRNA degradation. Ribosome stalling and collision at m6A is followed by recruitment of YTHDF m6A reader proteins to promote mRNA degradation. We show that mechanisms that reduce ribosome stalling and collisions, such as translation suppression during stress, stabilize m6A-mRNAs and increase their abundance, enabling stress responses. Overall, our study reveals the ribosome as the initial m6A sensor for beginning m6A-mRNA degradation.

overall_design: TimeLap-seq was performed as previously described.  Briefly, cells were grown to 80% confluency.  Cells were treated control or 200 μM emetine for 3 h with 250 µM 4-thiouridine (4sU, SigmaAldrich, T4509).  After 3 h, total RNA was collected using Qiagen RNeasy Mini kit RLT buffer (Qiagen, 74104) supplemented with 1% 𝛽-mercaptoethanol (BME).  Cells were lysed by passing through a 25 1/2-gauge needle, and RNA was isolated following the manufacturer’s instruction with RPE buffer supplemented with 1% BME.  10 µg total RNA was treated with 2,2,2-trifluoroethylamine (TFEE) and sodium periodate (NaIO4) at 45 °C for 1 h to convert 4sU to N4-trifluoroethylcytosine.  RNA was then purified twice using RNAClean beads (Beckman Coulter, A63987). 1 µg of treated RNA was used for RNA-seq library preparation using NEBNext® rRNA Depletion Kit (NEB, E6310X) and NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB, E7760L).  Library quality was assessed on Agilent TapeStation4200 using D1000 ScreenTape (Agilent, 5067-5584).  Library was quantified on Qubit4 Fluorometer using Qubit 1X dsDNA HS Assay Kit (ThermoFisher, Q33231).  Libraries were sequenced with pair-end 2x100 cycles on Illumina NovaSeq 6000.

first: Shino

last: Murakami


title: Metastatic site influences driver gene function in pancreatic cancer [scRNA-seq]

status: Public on May 14 2025

first: Yu-Jui

last: Ho

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Driver gene mutations can increase the metastatic potential of the primary tumor, but their role in sustaining tumor growth at metastatic sites is poorly understood. A paradigm of such mutations is inactivation of SMAD4 – a transcriptional effector of TGFβ signaling – which is a hallmark of multiple gastrointestinal malignancies. SMAD4 inactivation mediates TGFβ’s remarkable anti- to pro-tumorigenic switch during cancer progression and can thus influence both tumor initiation and metastasis. To determine whether metastatic tumors remain dependent on SMAD4 inactivation, we developed a mouse model of pancreatic ductal adenocarcinoma (PDAC) that enables Smad4 depletion in the pre-malignant pancreas and subsequent Smad4 reactivation in established metastases. As expected, Smad4 inactivation facilitated the formation of primary tumors that eventually colonized the liver and lungs. By contrast, Smad4 reactivation in metastatic disease had strikingly opposite effects depending on the tumor’s organ of residence: suppression of liver metastases and promotion of lung metastases. Integrative multiomic analysis and functional perturbations revealed that the divergent effects of Smad4 were underpinned by organ-specific differences in the tumor cells’ chromatin state that emerged in the premalignant pancreas and were distinguished by the dominance of KLF (liver-biased) or RUNX (lung-biased) transcription factors. Our results show how epigenetic states favored by the organ of residence can influence the output of driver gene mutations in metastatic tumors. This organ-specific gene–chromatin interplay invites consideration of anatomical site in the interpretation of tumor genetics, with implications for the therapeutic targeting of metastatic disease.

overall_design: To explore the origin of liver- and lung metastasis-biased chromatin states, we performed scRNA-seq on premalignant pancreata in the KC-shRen and KC-shSmad4 autochthonous model (at 8 weeks of age) +/– Dox after treatment with PBS or Cerulein (for 2 days). Cerulein treatment induces pancreatitis, which facilitates PDAC development.

first: Kaloyan

last: Tsanov

first: Scott

middle: W

last: Lowe


title: LLC cancer cells from primary tumors from Padi4f/f-Mrp8Cre- (WT) and Padi4f/f-Mrp8Cre+ (PAD4-DN) mice bulk RNA-seq data

overall_design: Tomato-expressing LLC cells sorted from primary tumors from WT (Mrp8Cre-, Padi4fl/fl) and PAD4-DN (Mrp8Cre+, Padi4fl/fl) mice and subjected to bulk RNAseq.


title: Effect of hypoxia on HIF-1α binding genes in SUM159 breast cancer cells with ChIP-Seq.

first: YONGKANG

last: YANG

address: Room 673, MRB, 725 North Broadway

department: ICE

summary: Brain metastasis is a major cause of breast cancer mortality, but the molecular basis and pathological mechanisms are poorly understood. Here, we determined that integrin β3 (ITGB3) expression mediated by hypoxia-inducible factor 1 (HIF-1) plays a critical role in brain metastasis of breast cancer. Hypoxia induces HIF-1-dependent expression of ITGb3, which is required for breast cancer cell migration and invasion. Knockdown of HIF-1a or ITGB3 expression impairs the colonization of breast cancer cells to brain after injection into the cardiac left ventricle. Mechanistically, ITGB3 protein expressed by breast cancer cells was incorporated into extracellular vesicles (EVs). The ITGb3+ EVs associated with brain endothelial cells, activated vascular endothelial growth factor receptor 2 signaling, and increased endothelial permeability to facilitate metastatic colonization of the brain.

overall_design: ChIP-seq for HIF-1α in SUM159 cells. Comparative HIF-1α binding gene profiling analysis of ChIP-seq data for SUM159 cells that were exposed in 20% or 1% oxygen condition for 16 hours.

first: Yongkang

last: Yang

first: Gregg

middle: L

last: Semenza


title: Unexpected combination of increased protein translation and decreased endoplasmic reticulum stress during pancreatic cancer initiation

city: Gosselies

first: Denis

middle: LJ

last: Lafontaine

state: Hainaut

address: Av Profs Jeneer & Brachet, 12

country: Belgium

institute: Universite libre de Bruxelles

summary: Background & Aims: Tumorigenesis is usually associated with increased protein synthesis rates coupled with increased endoplasmic reticulum (ER) stress. In the pancreas, acinar cells already exhibit a very high protein synthesis rate in normal condition, which raises the question as to how this cell type adapts during pancreatic tumor formation. Here, we characterize how acinar cells modulate their protein synthesis rate in metaplastic lesions, which are precursor lesions of pancreatic ductal adenocarcinoma (PDAC). Methods: We evaluated protein synthesis by puromycin incorporation assays and investigated the control of translation and ER stress by transcriptomic analyses and phenotyping of a mouse model of PDAC. We also assessed the level of ribosomal RNA (rRNA) methylation systematically using a deep-sequencing-based technique, RiboMethSeq. Results: During pancreatic tumorigenesis, protein synthesis levels in acinar-to-ductal metaplasia exhibited a significant increase as compared to normal acinar cells. This was associated with enhanced expression and activity of translation initiation factors, and with increased production of ribosomal components and ribosome assembly factors. We detected differential rRNA methylation at conserved ribosomal positions near the peptidyl-transferase center and the exit tunnel, suggesting a possible role in modulating translation and/or initial protein folding. Despite increased protein synthesis, ER stress was reduced, which was associated with an overall reduction in N-glycosylation and increased expression of proteasome components. Conclusions: Our work provides evidence for a pancreas-specific adaptation of the translation program during tumorigenesis, characterized by the production of differentially modified ribosomes and a rather unexpected combination of increased protein synthesis rate and decreased ER stress. This highlights the diversity of adaptive protein translation in transforming tissues.

overall_design: RiboMethSeq sequencing data from "Ela-K" and "Ela-K+cerulein" samples that refer to Fig.4 A and B

first: Maxime

last: Libert

first: Sophie

last: Quiquempoix

first: Leyre

last: Lopez

first: Christiane

last: Zorbas

first: Ludivine

last: Wacheul

first: Sabine

last: Cordi

first: Patrick

last: Jacquemin


title: Study on the Mechanism of Exosome circAP2B1 Promoting Proliferation and Metastasis of Esophageal Squamous cell carcinoma

city: Guangzhou

first: kai

last: lei

address: 107 Yan Jiang West Road

department: Department of Thoracic Surgery

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: Background: Esophageal squamous cell carcinoma (ESCC) has become an important global health issue. The M2 polarization of tumor-associated macrophages (TAMs) plays a key role in the occurrence and development of ESCC. It is reported that exosome circRNAs are involved in the regulation of the polarization state of TAMs, but the underlying mechanism remains unclear. In this study, we aim to identify novel exosome circrnas that regulate the progression of ESCC and explore their biological functions and regulatory mechanisms in ESCC.  Method: The highly expressed circRNAs in ESCC tissues and plasma were identified by circRNA microarray analysis. Transmission electron microscopy, differential centrifugation and Western blotting were used for the presence of exosome circAP2B, and the uptake of circAP2B1 by macrophages was determined by exosome tracing. The effects of exosome circAP2B1 on tumor proliferation and metastasis were investigated in vitro and in vivo. The role and molecular mechanism of exosome circAP2B1 in enhancing mitochondrial homeostasis of macrophages to induce M2 polarization were investigated by means of flow cytometry analysis, IP, LC-MS/MS, RIP, Pull down, CHIP, CHRIP and dual-luciferase reporter gene.  Result: We demonstrated that the upregulation of exosome circAP2B1 expression was positively correlated with lymph node metastasis and poor prognosis in patients with ESCC. Functionally, exosome circAP2B1 promotes the growth and metastasis of ESCC both in vitro and in vivo by inducing TMS-M2 polarization. Mechanism speaking, the tumor-derived exosome circAP2B1 enters macrophages to promote the nuclear translocation of the circAP2B1/ESRRA/KPNA1 ternary complex and mediate the transcriptional regulation of MFN2 to enhance the mitochondrial homeostasis of TAMs.  Conclusion: The exosome circAP2B1 derived from ESCC cells induces TMS-M2 polarization and tumor progression by regulating mitochondrial metabolic reprogramming in macrophages. Therefore, circAP2B1 targeting exosome packaging may provide potential diagnostic and therapeutic strategies for ESCC.

overall_design: The differentially expressed circRNAs in the plasma of three pairs of ESCC patients and normal Human plasma were analyzed using the Arraystar Human circRNA Array.

first: Kai

last: Lei

first: Minghui

last: Wang


title: Single-molecule simultaneous profiling of DNA methylation and DNA-protein interactions with Nanopore-DamID

city: St Lucia

first: Seth

last: Cheetham

state: Queensland

address: Australian Institute of Bioengineering and Nanotechnology

country: Australia

institute: University of Queensland

type: Methylation profiling by high throughput sequencing

summary: We present Nanopore-DamID, a method to simultaneously detect cytosine methylation and DNA-protein interactions from single molecules, via selective sequencing of adenine-labelled DNA. Assaying LaminB1 and CTCF binding with Nanopore-DamID, we identify escape from LAD-associated repression of hypomethylated promoters amidst generalised hypermethylation of LaminB1-associated regulatory elements. We detect novel CTCF binding sites in highly repetitive regions, and allele-specific CTCF binding to imprinted genes and the active X chromosome. Nanopore-DamID highlights the importance of DNA methylation to transcription factor activity.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Nanopore-DamID

first: Yohaann

last: Jafrani

first: Stacey

last: Andersen

first: Natasha

last: Jansz

first: Michaela

last: Kindlova

first: Adam

middle: D

last: Ewing

first: Geoffrey

middle: J

last: Faulkner


title: Contribution of UPF1  and RCOR1 to androgen response of prostate cancer cells.

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: The ligand-activated androgen receptor is a transcription factor that drives prostate cancer growth. Blocking androgen-activation of androgen receptor via androgen deprivation therapy is the default treatment for metastatic prostate cancer. Despite initial remissions, androgen deprivation invariably fails and prostate cancer progresses to castration-recurrent disease, which still relies on aberrantly activated androgen receptor. Alternative approaches are needed to inhibit androgen receptor action in prostate cancer that has failed androgen deprivation therapy. Our laboratory has been exploring the therapeutic potential of a non-canonical androgen receptor signaling mechanism wherein androgen receptor stimulates another transcription factor, Serum Response Factor. Serum Response Factor-mediated androgen receptor action correlates with prostate cancer progression and is enriched in castration-recurrent prostate cancer. Inhibiting Serum Response Factor-dependent androgen receptor action may be an effective treatment strategy following failure of androgen deprivation therapy but remains poorly understood. We have recently isolated UPF1 and RCOR1 as putative novel mediators of Serum Response Factor-dependent androgen receptor action.  Here, we perform RNA-Seq assays to determine the contribution of UPF1 and RCOR1 to the androgen response of prostate cancer cells.

overall_design: LNCaP cells were transfected with siGenome SmartPools (Horizon Discovery)  against UPF1, RCOR1 or non-targeting control siRNA. The next day, medium was changed to androgen-deprived medium. At 48h post transfection, androgen-deprived medium was refreshed and cells were treated with 5nM R1881 or vehicle (ethanol). Biological triplicates were included in each treatment group. Cells were harvested in Trizol reagent at 48h after treatment.

first: Hannelore

last: Heemers


title: VSIG4-EXPRESSING MACROPHAGES CONTRIBUTE TO ANTI-PARASITIC AND ANTI-METASTATIC RESPONSES IN THE PERITONEAL CAVITY

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

institute: Vrije Universiteit Brussel - VIB

summary: Large peritoneal macrophages (LPMs) play a role as gatekeepers of peritoneal homeostasis by providing a first line of defense against pathogens. A third of the LPMs express the surface receptor VSIG4, but it is unclear whether these cells differ from their VSIG4-negative counterparts and perform dedicated functions. We demonstrate that VSIG4+, but not VSIG4-, LPMs are in majority derived from embryonal precursors and their occurrence is largely independent from sex and microbiota but increases with age. Although their transcriptome and surface proteome are indistinguishable from VSIG4- LPMs at steady-state, VSIG4+ LPMs are superior in phagocytosing S. aureus bioparticles and colorectal carcinoma (CRC) cells. Anti-VSIG4 nanobody constructs that are ADCC-enabled allowed a selective elimination of the VSIG4+ LPM subset without affecting overall LPM abundance. This strategy uncovered a role for VSIG4+ LPMs in lowering the first peak of parasitemia in a Trypanosoma brucei brucei infection model and in reducing CRC outgrowth in the peritoneal cavity, a prime metastatic site in CRC patients. Altogether, our data uncover a protective role for VSIG4+ LPMs in infectious and oncological diseases in the peritoneal cavity.

overall_design: CITE-seq of CD45+ cells from peritoneal lavages of female C57BL/6 mice.  Three peritoneal lavages were pooled for each condition: HBSS-injected naive mice and mice 18 hours post-T. brucei brucei infection

first: Els

last: Lebegge

first: Jo

last: Van Ginderachter


title: Ly6C-low and Ly6C-high neutrophils bulk RNA-seq data

first: Jose

middle: M

last: Adrover

summary: Neutrophils (single cells - Ly6G+ cells) from 4T1 tumor bearing mice were sorted based on Ly6C high or low expression and sequenced.

overall_design: Ly6C-high and Ly6C-low neutrophils fom 4T1 tumor-bearing mice were sorted. Then total RNA was extracted using a Qiagen RNeasy Plus kit, according to the manufacturer’s instructions. We then measured the concentration of the total RNA using Qubit (Thermo Fisher) and Agilent RNA 6000 Nano kit (Cat. ID: 5067-1511) to analyze its quality. Libraries were made using the Kapa mRNA Hyper prep protocol: the mRNA is captured with oligo-dT beads and then fragmented using heat and magnesium. The first cDNA strand is synthesized using random priming. Then, this step is followed by a combined second strand synthesis and A-tailing, which converts the cDNA:RNA hybrid to double-stranded cDNA (dscDNA), incorporates dUTP into the second cDNA strand, and adds dAMP to the 3’ ends of the resulting dscDNA. The next steps are Illumina adaptor ligation and then library amplification using high-fidelity, low-bias PCR. The strand marked with dUTP is not amplified, allowing strand-specific sequencing. As starting material, we used 100 ng of total RNA in 50 μl of DNase-free water. For fragmentation, we incubated the samples 6 minutes at 85°C (fragments of 300–400 bp). For PCR enrichment, we used 13 cycles. Quality control for the final libraries was done using Qubit (DNA HS assay) and Bioanalyzer (DNA HS assay), then we pooled the samples and checked the final library using the Kapa qPCR. Sequencing was done using the Illumina NextSeq 500/550 Mid Output Kit v2.5 (~24M single-end 75-cycles reads for each sample).

first: Mikala

last: Egeblad


title: RNA-seq from Rag2-/-SiteI.3Pr-/-  primary pro-B cells

city: Chicago

first: Amy

last: Kenter

state: IL

address: 835 S Wolcott

institute: UIC

summary: We report the gene expression profile from the RNA-seq data generated from BM derived  Rag2-/-SiteI.3Pr-/-  pro-B cells.

overall_design: RNA-seq was performed on BM derived Rag2-/-SiteI.3Pr-/- murine pro-B cells following 5 days of ex vivo IL7 expansion. These samples are part of a series of RNA-seq analyses which were previously submitted (GSE203402).

first: Sarah

last: Naiyer

first: Saurabh

last: Priyadarshi

first: Ann

last: Feeney


title: Effect of shRNA-mediated knockdown of Eya3 in 66cl4 murine TNBC cells in vitro

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

summary: To investigate gene expression changes associated with Eya3 in the 66cl4 cell line

overall_design: Comparative gene expression profiling of 66cl4 SCR and shEya3 knockdown cells in biological triplicates

first: Connor

last: Hughes

last: Ferrara

first: Heide

last: Ford


title: Downregulation of SENP1 impairs nuclear condensation of MEF2C and deteriorates ischemic cardiomyopathy

city: Tianjin

first: Zhiqiang

last: Liu

address: 22 Qixiangtai Rd

department: Pathophysiology

institute: Tianjin Medical University

summary: Ischemic cardiomyopathy (ICM) is characterized by the insufficient capacity of the heart to effectively pump blood, which ultimately contributes to heart failure (HF). In this study, the down regulation of SNEP1 is identified in the cardiomyocyte of ICM mouse models and in patients. The depletion of SENP1 exacerbates hypoxia-induced apoptosis of cardiomyocytes in vitro and deteriorated cardiomyocyte injury of ICM mice in vivo. Mechanistically, SENP1 directly interacted and deSUMOylates the SUMO2-mediated modification of MEF2C at lysine 407, consequently promoting the protein stability and phase separation of MEF2C. When rescuing SENP1 expression using adeno-associated virus serotype 9, the attenuation of cardiomyocyte injury is discerned in the mouse model of ICM. Therefore, these finding elicits a previously unrecognized role and mechanism of SENP1 in safeguarding cardiomyocyte in ICM progression while establishing a basis for the development of SENP1 as a potential marker for ICM diagnosis and treatment.

overall_design: We conducted RNA-sequencing analysis on heart tissues at marginal zone of infarcted area in ICM mice compared with the sham controls.

first: Ying

last: Xie

first: Xin

last: Quan

first: Qiaoyuan

last: Li

first: Xiyun

last: Bian

first: Yan

last: Yin

first: Zhuo

last: Liang

first: Xu


title: Abundance of tRNA fragments in Tau-RNA complexes from Tau-mutant PS19 (human P301S Tau transgenic) mice hippocampus

city: Boston

first: Ami

last: Kobayashi

state: MA

address: 60 Fenwood Rd

department: Neurology

institute: Brigham & Women's Hospital

summary: We report the binding between tRNA fragments and Phosphorylated Tau pS396 from the hippocampus of WT controls and Tau-mutant PS19 (human P301S Tau transgenic) mice. We show tRNA fragments abundance in Tau-RNA complexes changes between the two groups. Specific tRNA fragment in the results of Real Time-qPCR were consistent with the small RNA microarray:5'tRF_GluCTC

overall_design: CLIP-Small RNA array on three pairs of hippocampus of PS19 mice and WT controls


title: RNA demethylase ALKBH5 regulates cell cycle progression in X-ray-induced DNA damage response

city: Hangzhou City

first: Jingyu

last: Hou

state: Zhejiang Province

address: Zhejiang University Student Apartment

institute: Zhejiang University

summary: RNA N6-methyladenosine (m6A) modification plays a crucial role in the DNA damage response, while the detailed mechanisms remain to be explored. In this study, we report the involvement of the m6A demethylase ALKBH5 in X-ray-induced DNA damage response. Depletion of ALKBH5 reduces X-ray-induced DNA damage, induces G2/M phase arrest and reduces cell apoptosis. RNA sequencing and m6A sequencing analysis reveal that ALKBH5 removes m6A modifications from its target mRNAs and suppresses their expression. A subset of mRNAs encoding cyclin dependent kinase inhibitors, such as CDKN1A and CDKN2B, show increased stability and expression upon ALKBH5 knockdown. Subsequently, the upregulation of CDKN1A and CDKN2B contributes to G2/M phase arrest to facilitate DNA repair. Our findings unveil the epigenetic regulation of cell cycle checkpoint by ALKBH5 in X-ray-induced DNA damage, offering potential targets for DNA damage-based therapy for cancers.

overall_design: 4 samples. m6A-seq of polyA+ RNA samples, including m6A input, m6A-IP in shCTL and shALKBH5 HEK293T cells after X-ray exposure


title: Beyond A and B Compartments: how major nuclear locales define nuclear genome  organization and function.

last: DCIC

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

summary: Models of nuclear genome organization often propose a binary division into active  versus inactive compartments yet typically overlook nuclear bodies. Here we  integrated analysis of sequencing and image-based data to compare genome  organization in four human cell types relative to three different nuclear  locales: the nuclear lamina, nuclear speckles, and nucleoli. Whereas gene  expression correlates mostly with nuclear speckle proximity, DNA replication  timing correlates with proximity to multiple nuclear locales. Speckle attachment  regions emerge as DNA replication initiation zones whose replication timing and  gene composition vary with their attachment frequency. Most facultative LADs  retain a partially repressed state as iLADs, despite their positioning in the  nuclear interior. Knock out of two lamina proteins, Lamin A and LBR, causes a  shift of H3K9me3-enriched LADs from lamina to nucleolus, and a reciprocal  relocation of H3K27me3-enriched partially repressed iLADs from nucleolus to  lamina. Thus, these partially repressed iLADs appear to compete with LADs for  nuclear lamina attachment with consequences for replication timing. The nuclear  organization in adherent cells is polarized with nuclear bodies and genomic  regions segregating both radially and relative to the equatorial plane. Together,  our results underscore the importance of considering genome organization relative  to nuclear locales for a more complete understanding of the spatial and  functional organization of the human genome.

overall_design:
Total 28 samples generated using TSA-seq in H. sapiens on condition2 - conditionE - anti-MKI67IP, input - condition2 - conditionE -  anti-MKI67IP, condition2 - conditionE - anti-SON, input - condition2 - conditionE - anti-SON, condition2 - conditionAI - anti-Lamin B1, input - condition2 - conditionAI - anti-Lamin B1.
(Note: 4 Samples used in this study were excluded from this GEO series as they were already added to GEO and SRA as part of another series: GSE81553. Please find details in attached supplementary file: excluded_samples.txt)

first: O

last: Gholamalamdari

first: T

last: van

first: Y

last: Wang

first: P

last: Kumar

first: L

last: Zhang

first: GAH

last: Gonzalez

first: AE

last: Vouzas

first: PA

last: Zhao

first: DM

last: Gilbert

first: J

last: Ma

first: B

first: AS

last: Belmont


title: Comparing the Effects of Taurine and 3-Sulfopropanoic Acid, a Metabolite of Tramiprosate, on ApoE4 Pathological Aggregation: Implications for Alzheimer's Disease

city: Brno

first: Katerina

last: Amruz Cerna

state: Czech Republic

address: Kamenice 3

department: Department of Histology and Embryology

institute: Faculty of Medicine, Masaryk University

summary:
Apolipoprotein E4 (ApoE4) is a major genetic risk factor for Alzheimer's disease.
Its pathological aggregation can be mitigated by tramiprosate and its metabolite 3-sulfopropanoic acid, along with their impact on the transcription of genes, expression of proteins, and production of lipids.
Taurine (TRN) is a close chemical analogue of tramiprosate (TMP) with an extra carbon atom , demonstrating protective effects against aging.
Using an integrated approach involving static light scattering, hydrogen-deuterium exchange mass spectrometry, molecular dynamics, and studies of cerebral organoids, we evaluated the effects of 3-sulfopropanoic acid
and taurine on ApoE4 aggregation, as well as their impact on organoid transcriptomics and proteomics.
Our results reveal that taurine effectively inhibits ApoE4 aggregation, comparable to 3-sulfopropanoic acid, and ameliorates the pathophysiological phenotype of ApoE4 in cerebral organoids, aligning it more closely with the ApoE3 phenotype.
These findings suggest that taurine may have potential as a therapeutic agent against Alzheimer's disease, particularly in ApoE4/E4 carriers.

overall_design: Comparative gene expression analysis of three biological replicates of cerebral organoids (Vanova et al., 2023; each condition sample consisted of several organoids ~10) treated with tramiprosate/taurine/untreated at D50 of cell culture to D100.

first: Anthony

last: Legrand

first: Sérgio

last: M. Marques

first: Naina

last: Verma

first: Jakub

last: Kopko

first: Tereza

last: Vanova

first: Madhumalar

last: Subramanian

first: Jaroslav

last: Bendl

first: Tomas

last: Henek

first: Pavel

last: Vanacek

first: Josef

last: Kucera

first: Joan

last: Planas-Iglesias

first: Jiri

last: Sedmik

first: Veronika

last: Pospisilova

first: Petr

last: Kouba

first: Aneta

last: Vaskova

first: Marketa

last: Nezvedova

last: Sedlar

last: Damborsky

first: Stanislav

last: Mazurenko

first: Martin

last: Marek

last: Sivic

first: Lenka

last: Hernychova

first: David

last: Bednar

first: Dasa

last: Bohaciakova

first: Zbynek

last: Prokop


title: The effects of sorafenib treatment on the T helper cell (Th9) population

city: Hangzhou

first: Shuowang

last: Wang

address: Yuhang Tang Street No.866

summary: To investigate the impact of sorafenib treatment on gene expression in Th9 cells, we performed RNA sequencing on Th9 cells treated with sorafenib and on control Th9 cells that were not treated with sorafenib. Here, we found that the up regulation of genes about Il-9.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for sorafenib treated Th9 cell and non-sorafenib treated cell.