title: Intersecting impact of CAG repeat and Huntingtin knockout in stem cell-derived cortical neurons [cortical_bulkRNASeq]

city: Irvine

first: Ricardo

last: Miramontes

address: 845 Health Sciences Rd

institute: UC Irvine

summary: Huntington’s Disease (HD) is caused by a CAG repeat expansion in the gene encoding Huntingtin (HTT). While normal HTT function appears impacted by the mutation, the specific pathways unique to CAG repeat expansion versus loss of normal function are unclear. To understand the impact of the CAG repeat expansion, we evaluated biological signatures of HTT knockout (HTT KO) versus those that occur from the CAG repeat expansion by applying multi-omics, live cell imaging, survival analysis and a novel feature- based pipeline to study cortical neurons (eCNs) derived from an isogenic human embryonic stem cell series (RUES2). HTT KO and the CAG repeat expansion influence developmental trajectories of eCNs, with opposing effects on the growth. Network analyses of differentially expressed genes and proteins associated with enriched epigenetic motifs identified subnetworks common to CAG repeat expansion and HTT KO that include neuronal differentiation, cell cycle regulation, and mechanisms related to transcriptional repression and may represent gain-of-function mechanisms that cannot be explained by HTT loss of function alone. A combination of dominant and loss-of-function mechanisms are likely involved in the aberrant neurodevelopmental and neurodegenerative features of HD that can help inform therapeutic strategies.

overall_design: Profiling an isogenic embryonic stem cell line series containing two expanded repeat lines (56 and 72 CAG repeats in exon 1 of HTT), two control length repeat lines (20 and 22 CAG repeats in exon 1 of HTT), and one HTT knockout line differentiated down a cortical nueron lineage.

first: Jennifer

last: Stocksdale

first: Matthew

last: Leventhal

first: Keona

middle: Q

last: Wang

first: Charlene

last: Smith

first: Jie

last: Wu

first: Ernest

last: Fraenkel

first: Leslie

last: Thompson


title: DNA methylation profiling of pituitary neuroendocrine tumors identifies distinct clinical and pathological subtypes based on epigenetic differentiation

status: Public on Apr 29 2025

city: New York

first: Varshini

last: Vasudevaraja

state: New York

address: 240 East 38th street

country: USA

institute: NYU Langone Health

type: Methylation profiling by genome tiling array

summary: Pituitary neuroendocrine tumors (PitNETs) are the most common intracranial neuroendocrine tumors. PitNETs are difficult to classify, and current recommendations include a large immunohistochemical panel to differentiate among 14 WHO-recognized categories. In this study, we analyzed 118 PitNETs to develop a clinico-molecular approach to classifying PitNETs. Comparison of clinical, immunohistochemical, and DNA methylation showed that PitNETs can be classified into distinct clinical and molecular subgroups. Unsupervised DNA methylation separated PitNETs into two major clusters. The first major cluster was composed of tumors currently labeled as gonadotrophs, which form a biologically distinct group of PitNETs characterized by clinical silence, weak hormonal expression on immunohistochemistry, and simple copy number profile. The second major cluster was composed of Corticotrophs and Pit1 lineage PitNETs, which could be further classified using DNA methylation into distinct subclusters that correspond to clinically active and silent tumors and consistent with degree of differentiation. Analysis of promoter methylation patterns correlates with lineage for corticotrophs and Pit1 lineage subtypes. However, the gonadotrophic genes do not show a distinct promoter methylation pattern in gonadotroph tumors compared to other lineages. Promoter of the NR5A1 gene, which encodes SF1, was hypermethylated across all PitNETs clinical and molecular subtypes including gonadotrophs with strong SF1 protein expression indicating alternative epigenetic regulation. These findings suggest that future classification of PitNETs may need to include DNA methylation for clinicopathological stratification.

overall_design: In this study, we performed integrated analysis of clinical status, pathologic immunophenotyping, and DNA methylation analysis. In addition, DNA methylation data was further analyzed to investigate the status of relevant genes and regulatory domains.

first: Sarra

last: Belakhoua

first: Chanel

last: Schroff

first: Kristyn

last: Galbraith

first: Misha

last: Movahed-Ezazi

first: Jonathan

last: Serrano

first: Yiying

last: Yang

first: Daniel

last: Orringer

first: John

middle: G

last: Golfinos

first: Chandra

last: Sen

first: Donato

last: Pacione

first: Nidhi

last: Agrawal

first: Matija

last: Snuderl


title: RARb and Huntington Disease

city: ILLKIRCH

first: Wojciech

last: Krezel

address: 1 rue L.Fries

country: France

institute: IGBMC

type: Expression profiling by high throughput sequencing

summary: Our working hypothesis is that two genetic factors A (compromized Rarβ expression in Rarβ+/- mice) and B (mutant form of huntingtin; R6/1 Tg/0) can synergise in generating physiopathology of Huntington disease. To address this point we performed comparative transcritomics in the nucleus accumbens (NAc) for  4 experimental groups : 1) R6/1 Tg/0 ; Rarβ+/-, (n=3); 2) R6/1 Tg/0 ; Rarβ+/+, (n=3); 3) R6/1 0/0 ; Rarβ+/-, (n=3); 4) R6/1 0/0 ; Rarβ+/+ (n=2).

overall_design: RNAs were extracted from 12 samples (as described in the summary) collected from 8-week-old mice to evaluate transcriptional changes associated with decreased Rarβ signaling in the context of HD-causing mutation. Sample 10 (male 80, R6/1 0/0 ; Rarβ+/+) did not pass the quality control and was excluded. Samples were sequenced according to the attached protocol

first: Nicolas

last: Zinter


title: Intersecting impact of CAG repeat and Huntingtin knockout in stem cell-derived cortical neurons

first: Ricardo

last: Miramontes

overall_design: Profiling an isogenic embryonic stem cell line series containing two expanded repeat lines (56 andd 72 CAG repeats in exon 1 of HTT), two control length repeat lines (20 and 22 CAG repeats in exon 1 of HTT), and one HTT knockout line at the pluripotent stage by RNAseq.

first: Jennifer

middle: T

last: Stocksdale

first: Matthew

middle: J

last: Leventhal

first: Keona

last: Wang

first: Charlene

last: Smith

first: Jie

last: Wu

first: Ernest

last: Fraenkel

middle: M


title: Neuron-targeted caveolin-1 enhances the neuroprotective, neuronal and synaptic plasticity transcriptome and improves cognitive function in symptomatic Alzheimer’s Disease models

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

summary: Previous work demonstrated that hippocampal delivery of AAV9-synapsin-promoted Cav-1 (SynCav1) to presymptomatic PSAPP mice alleviate neurodegeneration. Thus, the current study further investigated the effect of SynCav1 delivery at post-symptomatic age in the  PSAPP mice. Transcriptional analysis revealed that SynCav1-treated PSAPP mice exhibited a gene profile that more closely resembled age-matched wild-type (WT) mice. Gene Ontology (GO) enrichment analysis identified decreased neurodegeneration-specific pathways together with enhanced synaptic and cognitive-related transcriptome pathways in SynCav1-treated animals.

overall_design: We delivered SynCav1 into hippocampus of the PSAPP mice at 6 months age. Six months later, total RNA from hippocmpaus was used for RNAsequence and gene expression profilling was done to determining the effect of SynCav1 delivery.

first: Dongsheng

middle: V

first: Ryan

last: Lam

first: Hongxia

first: Wenxi

last: Li

first: Xiaojing

first: Tiffany

last: Duong

first: Shanshan

first: Brian

middle: P

last: Head


title: Tranposable Element Control by TRIM28 Safeguards PGC Sex Determination Program [RNA-Seq]

city: Los Angeles

first: Jonathan

last: DiRusso

state: California

address: 615 Charles E. Young Drive

department: Molecular, Cell and Developmental Biology

institute: University of California Los Angeles

summary: Transposable elements are increasingly appreciated as regulatory elements in early mammalian development, especially in cells which exhibit pluripotency. Mammalian primordial germ cells (PGCs) must exit latent pluripotency in a process termed determination before they are competent to differentiate and enter sex-specific developmental programs. Here, we find that determination is marked by large changes to the transposable element (TE) repertoire, a phenomenon driven by TRIM28, after which testicular and ovarian PGCs exhibit district transposable element repertoires. We find that loss of TRIM28 perturbs entry into determination as marked by expression of DAZL in a sex-specific manner, but does not result in a failure to downregulate markers of latent pluripotency, including SOX2 and NANOG in either sex. Despite downregulation of some early PGC markers, both ovarian and testicular PGCs fail to properly enter into their meiotic germ cell or prospermatogonial programs, respectively. Thus, we show that TRIM28-mediated reorganization of the TE repertoire is necessary to establish a PGC epigenome competent for proper germline commitment and gametogenesis.

overall_design: Prdm1-cre, Trim28 Δ/flox, males were paired with Trim28 flox/flox, oct4-eGFP females for time mated breeding. Day of plug was marked as E0.5. Resulting embryos were genotyped and control (prdm1-cre -, trim28 +/flox) and TIRM28 knockout (prdm1-cre +, Trim28 Δ/Δ) kept for library preparation. At the dissected end point, embryos were removed and the embryonic gonads dissected and dissociated before isolation of PGCs via FACS.

first: Lingyu

last: Zhan

first: Tao

last: Yu

first: Amander

last: Clark


title: Tranposable Element Control by TRIM28 Safeguards PGC Sex Determination Program

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Tranposable Element Control by TRIM28 Safeguards PGC Sex Determination Program [ChIP-Seq]

overall_design: Embryonic gonads from 10 time-mated CD1 mice were collected according to visual sex of the embryonic gonad. Gonads were processed as below.


title: Emergence of a transferable daptomycin resistance mechanism in Gram-positive bacteria

city: Wurzburg

first: Wilma

last: Ziebuhr

address: Josef-Schneider-Strasse 2

department: Institute of Molecular Infection Biology

country: Germany

institute: University of Wurzburg

summary: Daptomycin represents a reserve antibiotic effective against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Daptomycin resistance (Dap-R) and clinical treatment failure has been associated with adaptive chromosomal mutations, but so far not with acquisition of specific resistance genes. We previously isolated Staphylococcus/Mammaliicoccus sciuri strain TS92, which displays high-level Dap-R but lacks reported adaptive mutations. To identify the underlying resistance mechanism, we performed transcription profiling upon daptomycin exposure of TS92, with subsequent subcloning and mutational analysis of candidate genes. In TS92, Dap-R is mediated by a novel two-gene operon (named drcAB), controlled by an adjacent two-component regulatory system (drcRS). Heterologous drc expression demonstrated drcAB to be required and sufficient to mediate Dap-R in S. aureus (including clinically relevant MRSA) and Bacillus subtilis via inactivation of the antibiotic. The drc genes and proteins show homologies to membrane-associated antimicrobial peptide (AMP) transporters of Gram-positive bacteria but are distinct from currently known systems. In TS92, drc is flanked by insertion sequences (IS) and integrated near a staphylococcal cassette chromosome (SCC) element, suggesting mobility and acquisition of the locus from another species. Consistent with this hypothesis, IS-flanked drc was identified in various bacterial backgrounds in database searches. Here we report for the first time a horizontally acquired Dap-R mechanism that appears to circulate among Gram-positive bacteria, including staphylococci and enterococci. Increasing clinical daptomycin usage increases the likelihood that drc may enter S. aureus and other pathogens, which calls for vigilant monitoring of drc spread and prudent use of the antibiotic.

overall_design:
To identify potential resistance genes, we treated M. sciuri TS92 bacterial cells with daptomycin for 30 minutes and extracted total RNA. Total RNA was also extracted from untreated cells.
We performed transcriptional profiling comparing treated samples with control samples including three biological replicates each.

first: Tessa

last: Marciniak

first: Thorsten

last: Bischler

first: Justin

last: Nyasinga

first: Tom

last: Gräfenhan


title: Phylotranscriptomics reveals the convergent evolution of aggression is associated with both shared and unique patterns of gene expression evolution in cavity nesting songbirds

city: Bloomington

first: Kimberly

middle: A

last: Rosvall

state: IN

address: Dept of Biology, Indiana Univ., 1001 E. 3rd St, Jordan Hall

institute: Indiana University

summary: Uncovering the genomic regulation of phenotypic adaptation is a major goal in biology, but this has been hard to achieve for complex behavioral traits. Here, we leverage the repeated evolution of obligate cavity-nesting in birds to test the hypothesis that the shared pressure to compete for a limited breeding resource drives convergent behavioral evolution via convergent gene regulatory changes in the brain. Using behavioral assays in the field, hormonal measures, and transcriptome-wide analyses in 10 focal species, we examined females and males in five avian families, each including one obligate cavity-nesting species and a related species with a more flexible nesting strategy. Results support the hypothesis of behavioral convergence, with high levels of territorial aggression in obligate cavity-nesters, particularly among females. Levels of testosterone were not associated with nesting strategy for either sex, but phylogenetic analyses of individual genes and co-regulated gene networks revealed some shared patterns of gene expression, with functional enrichment related to metabolic and mitochondrial processes. Though this gene regulatory convergence may contribute to behavioral convergence, concordance in gene expression did not scale across multiple families. These observations indicate that replicated evolutionary increases in aggression arise via largely lineage-specific changes in brain gene expression.

sample_organism:
Passer montanus
Turdus migratorius
Hirundo rustica
Passer domesticus
Troglodytes aedon
Tachycineta bicolor
Thryothorus ludovicianus
Setophaga petechia
Sialia sialis
Protonotaria citrea

overall_design:
To evaluate the role of nesting strategy in shaping avian behavior, hormones, and gene expression, we compared 10 species of birds with obligate versus more flexible nesting strategies.
We conducted simulated territorial intrusion to measure aggression, conducted enzyme immunoassay to measure testosterone from blood plasma, and used RNA-seq to measure gene expression in the ventromedial telencephalon.

first: Sara

last: Lipshutz

first: Mark

last: Hibbins

first: Aaron

last: Buechlin

first: Tara

last: Empson

first: Elizabeth

last: George

first: Matthew

last: Hahn

last: Hauber

first: Doug

last: Rusch

first: Wendy

last: Schelsky

first: Quinn

last: Thomas

first: Sam

last: Torneo

first: Abbigail

last: Turner

first: Sarah

last: Wolf

first: Mary

last: Woodruff


title: Hematopoietic Stem Cell Transplant and Healthy Donor Single cell RNA-seq (scRNA-seq) combined with T Cell Receptor (TCR) and B Cell Receptor (BCR) sequencing on Timepoints Surrounding SARS-CoV-2 Vaccination and Infection

city: New Haven

first: Jennifer

last: VanOudenhove

state: CT

address: 300 George St RM 786

department: Internal Medicine - Section of Hematology

institute: Yale University

summary: Single cell RNA-seq (scRNA-seq) combined with T Cell Receptor (TCR) and B Cell Receptor (BCR) sequencing on pre- and post-vaccination (2nd dose) samples, as well as post-infection samples when available, from 4 alloSCT recipients and 3 healthy controls.

overall_design: Human blood was ficoll-separated to generate mononuclear cells that were then bead enriched for CD3 and CD19 positive cells at time points pre and post two doses of the SARVS-CoV-2 Vaccine and Surrounding SARS-CoV-2 Infection. 10X libraries were generated using the 10X 5' Single Cell Library Kits with paired VDJ libraries generated.

first: Stephanie

last: Halene


title: Ancestry and fetal sex differences in human placental transcriptome in spontaneous early preterm birth

city: Philadelphia

first: Blanca

middle: E

last: Himes

state: PA

address: 423 Guardian Dr

department: Department of Biostatistics, Epidemiology and Informatics

institute: University of Pennsylvania

summary: Black women have highest risk of spontaneous preterm birth (SPTB) than other race, and placental insufficiency is implicated in SPTB. We performed RNA-seq study in male and female placentas from White and Black women (self-identified) with early SPTB (< 32 weeks gestation) compared to normal pregnancies (≥ 38 weeks gestation) to assess the alterations in gene expression profiles as well as ancestry and fetal sex differences. The mid-trimester placentas (19-23 weeks gestation) were used as gestational controls.

overall_design: Examination of transcriptomes in 12 experimental conditions (SPTB White males, SPTB White females, SPTB Black males, SPTB Black females, Term White males, Term White females, Term Black males, Term Black females, Mid-trimester White males, Mid-trimester White females. Mid-trimester Black males, and Mid-trimester Black females)

first: Yu-Chin

last: Lien

first: Rebecca

last: Simmons

first: Samuel

last: Parry

first: Jerome

middle: F

last: Strauss III

first: Mengyuan

last: Kan


title: Human umbilical cord mesenchymal stem cell-derived exosomes deliver miRNA-451a targeting ATF2 to inhibit rheumatoid arthritis [small RNA-seq]

city: Taiyuan

first: Liangyu

last: Mi

state: Shanxi

address: 99 Longcheng Street

country: China

institute: Third Hospital of Shanxi Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background and aim:
Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic inflammation of the joints. Synovial fibroblasts (SFs) play a key role in the pathogenesis of RA. Dysregulation of MicroRNAs (miRNAs) expression in SFs mediates the development of RA. Exosomes (Exos) can transfer miRNAs between cells and have been validated as carriers for the delivery of therapeutic molecules.This study aimed toinvestigate the therapeutic potential of human umbilical cord mesenchymal stem cells (hUCMSC)-Exos deliveringmiR-451a to regulate ATF2 for RA both in vivo and in vitro.
Methods:
In this study, hUCMSC and RASF were isolated and identified, and hUCMSC-EXOs were extracted and characterized. The influence of hUCMSC-Exos on RASF was detected. hUCMSC-Exos RNA was labeled and hUCMSC-Exos targeting RA-SFs was traced. AGO2 promoted miRNA maturation, and hUCMSCKD-AGO2 was prepared by knocking down AGO2 in hUCMSC. hUCMSCKD-AGO2-Exos was extracted and characterized,and their influence on RASFs was detected. mRNA and miRNA profiles before and after hUCMSC-Exos intervention in RASFs were mapped to identify differential miRNAs. RT-qPCR was used to verify the differential miRNAs, with miR-451a finally selected as the target gene.The effect of miR-451a on SFs was detected. The latent binding of miR-451a to activating transcription factor 2 (ATF2)was analyzed. The effect of hUCMSC-ExosmiR-451a on SFs was detected, and the expression of miR-451a and ATF2 was measured by RT-PCR.In vivo, hUCMSC-ExosmiR-451a was injected into the ankle joint of CIA rats, and arthritis index, joint imaging and synovial pathology were assessed. The expression of miR-451a and ATF2 in synovial tissue was detected. Finally, the safety of hUCMSC-ExosmiR-451a in CIA rats was evaluated.
Results:
This study revealed that hUCMSC-Exos can inhibit RASF proliferation, migration and invasion through miRNAs. High throughput sequencing detected 13 miRNAs that could be transmitted from hUCMSC to RASF via hUCMSC-EXOs. MiR-451a inhibited RASF proliferation, migration and invasion by regulating ATF2. hUCMSC-Exos loaded with miR-451a targeted ATF2 to inhibit RASF proliferation, migration and invasion, and improve joint inflammation and imaging findings in CIA rats.
Conclusions:
This study demonstrates that miR-451a carried by hUCMSC-Exos canplay a role ininhibiting RASF biological traits and improving arthritis in CIA rats by inhibiting ATF2. The findings study suggest a promising treatment for RA and provide insights into the mechanism of action of hUCMSC-Exo in RA.

overall_design:
To investigate which miRNAs were delivered to RA SFs by hUCMSC-Exos, we divided 6 RASFs derived from various genotypes into the blank control group and the hUCMSC-Exos intervention group. The blank control group was treated with complete medium while the hUCMSC-Exos intervention group was treated with 150μg/ml hUCMSC-Exos. After 48 hours of intervention, RASFs were collected.
We identified the miRNAs in hUCMSC-Exos and detected the miRNAs and mRNAs in the RASFs of both the blank control group and the hUCMSC-Exos intervention group. Subsequently, the gene expression profiles were analyzed using RNA-seq data. To identify differentially expressed genes, a comparative analysis of the RNA-seq data was conducted.
We intersected miRNAs that were differentially upregulated in RASFs after hUCMSC-Exos intervention with miRNAs in hUCMSC-Exos. The resulting differentially expressed miRNAs were further used to predict target genes. From the predicted target genes, we selected the ones that overlapped with the down-regulated mRNAs identified through transcriptome sequencing. Finally, GO function annotation and KEGG pathway analysis were performed for the selected intersection mRNAs.

last: Li

first: Jinfang

last: Gao

first: Ke

last: Xu


title: Human umbilical cord mesenchymal stem cell-derived exosomes deliver miRNA-451a targeting ATF2 to inhibit rheumatoid arthritis [RNA-seq]


title: Human umbilical cord mesenchymal stem cell-derived exosomes deliver miRNA-451a targeting ATF2 to inhibit rheumatoid arthritis.


title: Study of the role of circPVT1 circRNA knockdown in cardiomyocytes

city: Milan

first: Fabio

last: Martelli

address: Via Olgettina 58

country: Italy

institute: IRCCS Policlinico San Donato

summary: circPVT1, a circRNA derived from the circularization of the second exon of the long-non coding RNA PVT1, was found upregulated in ischemic heart failure patients. We performed RNA-Seq to assess the molecular changes that occurr upon circPVT1 knockdown in AC16 cells, a human cardiomyocyte cell line. Transcriptome analysis identified differentially expressed genes mainly involved in extracellular matrix formation, fibrosis and cellular senescence, suggesting the involvement of circPVT1 in cardiac remodeling.

overall_design: We used siRNAs to knockdown the expression of circPVT1 or linear PVT1 in AC16 cells. A non-targeting siRNA was used as a control. Each condition was done in quadruplicate and samples were collected 72h after siRNA transfection. We analyzed the differential expressed genes in circPVT1 knockdown cells in comparison to cells transfected with non-targeting siRNA control (FDR < 0.01)  and in circPVT1 knockdown cells in comparison with linear PVT1 knockdown samples (FDR < 0.01). To identify genes specifically modulated by circPVT1 knockdown, we compared these two differential expression analyses and only overlapping genes were taken into account.

first: Alessia

last: Bibi


title: Tranposable Element Control by TRIM28 Safeguards PGC Sex Determination Program [ATAC-Seq]

first: Jonathan

last: DiRusso

first: Amander

last: Clark


title: MYLK-AS1 Enhances Glutamine Metabolism to Promote EGFR Inhibitor Resistance in Non-Small Cell Lung Cancer

status: Public on Apr 28 2025

city: Nanjing

first: Erbao

last: Zhang

state: Jiangsu

address: longmian da dao

department: Department of Epidemiology

institute: Nanjing Medical University

summary: Here we identified a role for the lncRNA MYLK-AS1 promoting acquired TKI resistance of lung cancer in vitro and in vivo. MYLK-AS1 bound and directly drove phase separation of interleukin enhancer binding factor 3 (ILF3), thus interacting with the 3’UTR of glutamate dehydrogenase 1 (GLUD1) to post-transcriptionally promote its mRNA stability, thus enhancing mitochondrial glutamine catabolism, promoting TKI resistance. The MYLK-AS1/ILF3/GLUD1 may be a target for overcoming TKI resistance in lung cancer.

overall_design: RNA-seq analysis was performed after knockdown of MYLK-AS1 in PC9/GR cell line.

first: Tianyu

last: Qu

first: Lei

last: Song

first: Jiali

first: Xiyi

last: Lu

first: Dandan

last: Yin

last: Dai

first: Chen

first: Renhua

last: Guo


title: CNOT7 Promotes Radiation Resistance in Colorectal Cancer via XRCC6-Mediated NHEJ DNA Repair Pathway

city: Harbin

first: Binbin

last: Cui

state: Heilongjiang

address: Baojian Road

institute: Harbin Medicial University

summary: In this study, we identified CNOT7 as a key protein influencing the radiotherapy sensitivity of rectal cancer through proteomic sequencing of patient tissues. Patients with high CNOT7 expression often exhibit poorer prognoses during radiotherapy. We explored the potential mechanisms by which CNOT7 affects radiotherapy sensitivity in CRC. CNOT7 reduces polyubiquitination of K48 linked lysine 526 on XRCC6 by regulating TRIM21. This enhances DNA damage repair primarily mediated by the NHEJ pathway, thereby conferring radiotherapy resistance to colorectal cancer cells. Our study suggests that targeting CNOT7 could serve as a potential therapeutic strategy for rectal cancer patients

overall_design: To investigate the function of CNOT7 in the CCR4-Not complex, we established a stable CNOT7 knockdown cell line in the CRC cell line SW480 using shRNA, and performed RNA-seq to identify downstream differentially expressed target genes.

first: Yien

first: Luying


title: Single-cell transcriptomes of CD27− or CD27+ ESLAMSK hematopoietic stem cells under homeostatic conditions

city: Tianjin

first: Caiying

last: Zhu

address: Heping District, Nanjing Road, 288

institute: Institute of Hematology and Blood Disease Hospital

summary: Single-cell RNA-seq of CD27− or CD27+ hematopoietic stem cells (HSCs) isolated from 8-week-old wild-type mice

overall_design: Cells were first isolated from bone marrow of 8-week-old wild-type mice(LSKCD150+CD48-CD201+, ESLAMLSK), single hematopoietic stem cells ((LSKCD150+CD48-CD201+, ESLAMLSK) were then sorting based in expression levels of CD27 (CD27- or CD27+) and processed for STRT-seq (single-cell tagged reverse transcription sequencing) to generate high-resolution transcriptomic data.

first: Fang

last: Dong

first: Ping

first: Tao

last: Cheng


title: A Germline Heterozygous Dominant Negative IKZF2 Variant Causing Syndromic Primary Immune Regulatory Disorder and ICHAD

city: Vancouver

first: Stuart

last: Turvey

state: British Columbia

address: A5-122 950 W 28th Avenue

department: Pediatrics

country: Canada

institute: The University of British Columbia

summary: Monogenic defects that impair the control of inflammation and tolerance lead to profound immune dysregulation, including autoimmunity and atopy. Studying these disorders reveals important molecular and cellular factors that regulate human immune homeostasis and identifies potential precision medicine targets. Here, we provide a detailed immunological assessment of a pediatric patient with a recently discovered syndrome causing Immunodysregulation, Craniofacial anomalies, Hearing impairment, Athelia, and Developmental delay (or ICHAD syndrome). The immunodysregulation resulted in autoimmune hemolytic anemia (AIHA) and atopic dermatitis. The patient carried a de novo germline heterozygous c.406+540_574+13477dup;p.Gly136_Ser191dup variant in IKAROS family zinc finger 2 (IKZF2), which encodes HELIOS. This variant led to reduced HELIOS protein expression and dominant interference of wild-type HELIOS-mediated repression of the IL2 promoter. Multi-parameter flow cytometric analyses of patient peripheral blood mononuclear cells revealed strongly impaired natural killer cell differentiation and function, and increased CD8+ T cell activation and cytokine secretion. Strikingly, patient CD4+ T cells were hyperactive, produced elevated levels of nearly all T helper (TH) cytokines, and readily proliferated in response to stimulation. Patient regulatory T cells (Tregs) developed normally but aberrantly produced high levels of many TH cytokines. Single-cell RNA sequencing revealed largely normal Tregs (albeit mostly memory), but naïve CD4+ T cells that were more enriched in genes related to activation, proliferation, metabolism, and TH differentiation. This work describes the immunological phenotype of one of the first reported cases of germline dominant negative HELIOS deficiency, expands our understanding of the pathogenesis of AIHA on a single cell level, and provides valuable insights into HELIOS function in a variety of lymphocyte subsets.

overall_design: CD3+CD4+CD25+CD127lo regulatory T cells (Tregs) and CD3+CD4+CD25-CD127hi conventional T cells (Tconv) were sorted from the index patient (P1) and two age-matched and sex-matched controls (HC1 and HC2) and analyzed using scRNA-seq

first: Henry

middle: Y

first: Mehul

last: Sharma


title: Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations II

city: Urbana

first: Sihang

last: Zhou

state: IL

address: 601 S Goodwin Ave

institute: University of Illinois Urbana-Champaign

summary: RNA polymerase III (Pol III) transcription in cancer is linked with the emergence of snaR-A (small NF90-associated RNA isoform A), a hominid-specific ncRNA shown to enhance cell proliferation, migration, and invasion. Here, we investigate snaR-A-protein interactions to delineate its role as a putative driver of cancer progression. At the molecular level, we discover that snaR-A interacts with mRNA splicing factors, including SF3B2 - a core component of the U2 small nuclear ribonucleoprotein (snRNP) - and localizes to subnuclear foci enriched for splicing factors. Ectopic snaR-A overexpression leads to increased intron retention, a hallmark of inefficient splicing, whereas depletion of endogenous snaR-A reduces intron retention in mRNA subpopulations associated with 3’ intron-exon U2 snRNP residency and nuclear speckle proximity. We further show that high levels of snaR-A promotes cell migration in cells linked with increased intron retention, consistent with evidence supporting snaR-A as a negative prognostic factor in cancer. Taken together, these findings establish snaR-A as a molecular disruptor of splicing. We propose that snaR-A-related splicing disruption may phenocopy previously reported splicing defects and consequences attributed to mutations in U2 snRNP in cancer, eliciting an alternate, non-mutational pathway during tumorigenesis.

overall_design: To investigate the effect of snaR-A on splicing of mRNAs, we performed snaR-A overexpression and SF3B2 overexpression in HEK293T and A549 cells and deep sequenced the samples. The experiment included three biological replicates for scramble, snaR-A, GFP, and SF3B2 overexpression. Raw mRNA signal counts were extracted.

first: Kevin

last: Van Bortle


title: Slowed epigenetic aging in Olympic champions compared to non-champions

city: Budapest

first: Zsolt

last: Radák

address: Alkotás Street 44, building L3

country: Hungary

institute: Research Center for Molecular Exercise Science, Hungarian University of Sports Science

summary: The lifestyle patterns of top athletes are highly disciplined, featuring strict exercise regimens, nutrition plans, and mental preparation, often beginning at a young age. Recently, it was shown that physically active individuals exhibit slowed epigenetic aging and better age-related outcomes. Here, we investigate whether the extreme intensity of physical activity of Olympic champions still has a beneficial effect on epigenetic aging. To test this hypothesis, we examined the epigenetic aging of 59 Hungarian Olympic champions and of the 332 control subjects, 205 were master rowers. We observed that Olympic champions exhibit slower epigenetic aging, applying seven state-of-the-art epigenetic aging clocks. Additionally, male champions who won any medal within the last 10 years showed slower epigenetic aging compared to other male champions, while female champions exhibited the opposite trend. We also found that wrestlers had higher age acceleration compared to gymnasts, fencers, and water polo players. We identified the top 20 genes that showed the most remarkable difference in promoter methylation between Olympic champions and non-champions. The hypo-methylated genes are involved in synaptic health, glycosylation, metal ion membrane transfer, and force generation. Most of the hyper-methylated genes were associated with cancer promotion. The data suggest that rigorous and long-term exercise from adolescence to adulthood has beneficial effects on epigenetic aging.

overall_design:
In this study, we analyzed four methylation batches (we referred to them as MET2019, MET2020, MET2022, and MET2023). MET2019 batch contained 263 control samples, MET2020 batch contained 33 control and 59 Olympic champion samples and the MET2023 batch contained also 33 control samples. The MET2019 and MET2020 batches were measured by the Infinium MethylationEPIC (850 k) BeadChip and the MET2023 batch was measured by the Infinium MethylationEPIC v2.0 BeadChip.  For our analysis, we converted the CpG sites in the MET2023 batch back to the EPIC v1 array format and merged all four batches. Due to patient privacy concerns, raw data idat files could not be provided.
***Due to patient privacy concerns, raw data idat files could not be provided***
Methylation array gene mapping file: olympic_gmap.csv.gz

first: Iván

last: Fejes

first: Csaba

last: Kerepesi


title: In vivo CRISPRi screen reveals lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth [RNASeq_knockdown]

city: Stanford

first: Luca

last: Ducoli

address: 269 Campus Drive CCSR 2150

institute: Stanford University

summary: Cutaneous squamous cell carcinoma (cSCC) accounts for 20% of all skin cancer mortality globally, making it the second-highest subtype of skin cancer. The high prevalence of cSCC in humans highlights the need to uncover alternative actors and mechanisms influencing skin cancer development. Significant advances have been made to better understand some key factors in cSCC growth. However, little is known about the role of noncoding RNAs, particularly of a specific subclass termed long noncoding RNA (lncRNA). By performing pseudobulk analysis of single-cell sequencing data from normal and cSCC human skin tissues, we determined a global portfolio of lncRNAs specifically expressed in keratinocyte subpopulations. Integration of CRISPR interference screens in vitro and the xenograft model identified several lncRNAs impacting the growth of cSCC cancer lines both in vitro and in vivo. Among these, we further validated LINC00704 and LINC01116 as proliferation-regulating lncRNAs in cSCC lines and potential biomarkers of cSCC growth. Taken together, our study provides a comprehensive signature of lncRNAs with roles in regulating cSCC growth.

overall_design: Bulk RNA-seq in A431 cells after antisense oligonucleotide (ASO) treatment including non-targetin ASO, two different LINC00704-ASO, two different LINC01116-ASO.

first: Gyuhyeon

last: Kim

first: Paul

last: Khavari


title: In vivo CRISPRi screen reveals lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth [in_vivo_CRISPRi]

overall_design: In vivo CRISPR-interference (CRISPRi) screen using squamous carcinoma cells (A431, Cal27) grown in nude mice as flank injected tumors harvested after few weeks comparing to week 0 (pre-tumor injection) samples.

first: Zurab

last: Siprashvili

first: Xue


title: In vivo CRISPRi screen reveals lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth [s3DRAS_scRNAseq]

overall_design: Single cell RNA-seq of spheroid of transformed human Keratinocyte with CDK4(R24C) and Ras(G12V)

first: Jordan

last: Meyers


title: In vivo CRISPRi screen reveals lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth [in_vitro_CRISPRi]

overall_design: In vitro CRISPR-interference (CRISPRi) screen using two sublibraries (KC and TSK) in squamous carcinoma cells (A431, Cal27) at Week 0 and Week 3, and normal Keratinocytes at Week 0 and Week 1.5.


title: mRNA/sRNA Co-Sequencing Reveals Multiple New Targeted Therapy Candidates in Rhabdomyosarcoma [miRNA-seq]

city: Norwich

first: Maisie

last: Evans

address: Norwich Research Park

country: United Kingdom

institute: UEA

summary: There have been few studies investigating the transcriptional-driver landscape of rhabdomyosarcoma (RMS). In this study, we performed genome-wide mRNA and sRNA co-sequencing from the same RMS and wildtype tissues to identify differentially expressed and differentially regulated genes involved in the molecular pathology of RMS. One key finding is the upregulation of RUNX2 transcription factor, which is normally under the negative control of HDAC4 transcriptional silencer, but this is lost in these tissues. Similar to bone sarcomas, we propose that HDAC4 itself was under the negative regulated of miR-140, i.e., upregulation of miR-140 silences HDAC4, allowing for the expression of RUNX2. The data showed that most miRNAs known to target HDAC4 (e.g. miR-1, miR-206) including miR-140 were downregulated, with the exception of miR-155. There might be the possibility that  miR-140/HDAC4/RUNX2 signalling pathway is specific to bone sarcoma but here, the miR-155/HDAC4/RUNX2 signalling pathway is specific to muscle sarcomas. Further studies are required to test this hypothesis.

overall_design: In total, 14 human biopsy samples were used; 5 alveolar RMS, 4 embryonal RMS and 5 control skeletal muscle samples. Total RNA was extracted and then sRNA was sequenced. This contains the sRNA-seq data while the mRNA-seq data, which includes the same samples and additional RMS/control samples, is provided separately.

first: Darrell

last: Green

first: Archana

last: Singh


title: A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination

city: Cambridge

first: Caroline

middle: Anne

last: Martin

state: Massachusetts

address: 455 Main St

institute: Whitehead Institute

summary: Successful seed development is essential for flowering plant reproduction and requires the coordination of three genetically distinct tissues: the embryo and endosperm, which are the products of fertilization, and the maternal seed coat. Understanding of transcriptional programs that underlie tissue-specific functions and coordination in Arabidopsis seeds is incomplete. To address this, we performed single nucleus RNA-sequencing on seeds at 3, 5, and 7 days after pollination. We characterize all major seed cell types, further refine transcriptional states in the endosperm, and report previously transcriptionally undefined cell types in the seed coat. Among other findings, our analyses reveal the compartmentalization of genes involved in brassinsteroid-responsive transcription factor activation and nutrient transport. Additionally, we identify abundant cell-type specific expression of genes that encode rapidly evolving short, secreted peptides (SSPs) in the micropylar and chalazal endosperm, suggesting that SSP activity is an unexplored but potentially significant contributor to Arabidopsis seed development.

overall_design: Two biological replicates, (different plants hand pollinated and processed for snRNA-seq on different days) each containing seeds dissected from 10-15 Arabidopsis thaliana col-0 siliques (500-800 seeds), were collected for each timepoint (3, 5, and 7 days after pollination), producing six replicates total. Each biological replicate was processed individually using one Chromium Next GEM Single Cell 3’ Kit (v3.1) reaction with a target nuclei recovery of 10k, except for one 3DAP biological replicate, which was split across two reactions. In total, 7 libraries were generated in this study.

first: Martin

last: Caroline

first: Cogdill

last: Kylee

first: Pusey

last: Alesandra

first: Gehring

last: Mary


title: mRNA/sRNA Co-Sequencing Reveals Multiple New Targeted Therapy Candidates in Rhabdomyosarcoma

overall_design: In total, 26 human biopsy samples; 5 Alveolar RMS (ARMS), 4 Embryonal RMS (ERMS), 3 Spindle Cell/Scelorising RMS, 1 Pleomorphic RMS and 13 control skeletal muscle samples. Total RNA was extracted and then mRNA-seq and sRNA-seq were carried out. This contains the mRNA-seq data, while the sRNA-seq data, which includes some of the RMS/control samples is provided separately. Some samples (R09, R11, R12, R13, R14, R17, R18, R21, R22, R24, R25, R26) were resequenced due to quality of the samples.


title: Insights into the Cellular and Molecular Mode of Action behind the Anti-Fibrotic Effects of Nerandomilast

city: Biberach an der Riss

first: Christoph

middle: H

last: Mayr

address: Birkendorfer Str. 65

department: Immunology & Respiratory Diseases Research

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

summary: The quest for innovative pharmacologic interventions in idiopathic pulmonary fibrosis (IPF) is a challenging journey. The complexity of the disease demands a comprehensive approach that targets multiple cell types and pathways. In this study, we explored the anti-fibrotic properties of nerandomilast, a preferential phosphodiesterase 4B inhibitor, focusing on its effects on myofibroblasts (MFs) and endothelial cells. Our findings demonstrate that nerandomilast induces the dedifferentiation of human lung MFs and diminishes their contractility in vitro by interfering with TGFβ and GPCR signaling pathways. Moreover, nerandomilast effectively mitigates features of vascular dysfunction, such as increased vascular permeability and immune cell infiltration, both in vitro and in vivo. This is accomplished by strengthening endothelial junctions and inhibiting the expression of adhesion molecule proteins. Furthermore, in a rat model of bleomycin-induced pulmonary fibrosis, nerandomilast normalizes the specialization of endothelial cell types. The results of this study significantly contribute to the growing knowledge around the potential therapeutic use of nerandomilast in the treatment of IPF by providing valuable insights into its cellular and molecular mode of action

overall_design: To examine the molecular mechanisms behind Myofibroblast dedifferentiation upon treatment with nerandomilast, we performed NGS of Myofibroblasts. IPF-HLF were pre-stimulated with TGFβ1 for 48h to induce Myofibroblast differentiation, with nerandomilast and/or high-dose PGE2 added in the continued presence of TGFβ1 for a further 24h.

first: Dennis

last: Reininger

first: Felix

last: Wolf

first: Susanne

middle: L

last: Wespel

first: Nadine

last: Laufhaenger

first: Kerstin

last: Geilinger-Kästle

first: Alec

last: Dick

first: Florian

last: Gantner

first: Peter

last: Nickolaus

first: Franziska

last: Herrmann


title: Tyrosinase in melanoma inhibits anti-tumor activity of PD-1 deficient T cells

city: Xinxiang

first: Tianhan

last: Li

state: Henan

address: No.601, Hualan Road

institute: Xinxiang Medical University

summary: Melanoma is one of the most commonly diagnosed malignancies and serves as a model for studying immunotherapy. The B16 melanoma model is characterized by low T cell infiltration in the tumor, and blocking the PD-1 pathway shows no significant anti-tumor activity, mirroring melanoma patients with a cold tumor immunophenotype. Therefore, understanding the molecular basis that prevents T cell-mediated anti-tumor activity in B16 melanoma is of great significance. In this study, we generated Tyr knockout B16 melanoma cells using CRISPR/Cas9 and discovered that tyrosinase in melanoma significantly inhibits the anti-tumor activity of T cells. Tyrosinase deficiency significantly increases T-cell infiltration and activation within the tumor. Single-cell RNA sequencing reveals an altered cold tumor immunophenotype in tyrosinase-deficient B16 melanoma. In wild-type mice, T cells in tyrosinase-deficient tumors express elevated levels of PD-1 and Foxp3. However, strikingly, in PD-1 deficient mice, the loss of tyrosinase in B16 melanoma unleashes the anti-tumor activity of PD-1 deficient T cells. This enhanced anti-tumor activity is explained by significantly increased tumor T cell infiltration accompanied by reduced frequencies of Tregs in PD-1 knockout mice. Targeting tyrosinase may enhance the anti-tumor efficacy of PD-1 blockade in cold tumors, offering a novel strategy to render cold tumors responsive to immunotherapy. Clinically, higher levels of tyrosinase expression in human melanoma are associated with a poorer prognosis, indicating that our findings could potentially improve the efficacy of immunotherapy in melanoma patients.

overall_design: For scRNA-seq analysis of tumor-infiltrating immune cells (TIICs), wildtype (WT) , oca2 knockout and Tyr knockout B16F10 melanoma cells were implanted in the right flank of female C57BL/6 mice (n=3). At the endpoint, the tumors were dissected from the surrounding fascia, and single cell suspensions were prepared from both the Tyr knockout and the WT melanoma cells. TIICs were isolated using the FACSAria Ⅱ cell sorter (BD Biosciences, USA) and stained with anti-mouse CD45.2 PE-cy7 (eBioscience). CD45+ TIICs were labeled with the BD Single-Cell Multiplexing Kit (BD Biosciences) according to the manufacturer’s protocol. Cells from each group were labeled with sample tags, washed, and pooled. The pooled sample was then counted, resuspended, and subjected to single-cell capture and cDNA Synthesis using the BD Rhapsody Express Single-Cell Analysis System (BD Biosciences). cDNA libraries were prepared using the mRNA Targeted and Sample Tag Library preparation method along with the BD Rhapsody Targeted mRNA Amplification and BD Single-Cell Multiplexing Kits and protocols from BD Biosciences. The libraries were sequenced on the Illumina Novaseq platform (Novogene), and clustering analysis and high-dimensional visualization were performed using the SeqGeqTM software.

first: Rong

last: Huang

first: Yingbin

last: Wang

first: Yinming

last: Liang

first: Liaoxun

last: Lu

first: Lichen

last: Zhang


title: Topoisomerase 1 is required for the development and function of thymus

city: Bangalore

first: Kushagra

last: Bansal

state: Karnataka

address: Jakkur

department: MBGU

country: India

institute: JNCASR

summary: Thymus organogenesis is critical for proper maturation of developing T cells. In this study, we identified Topoisomerase 1 (Top1) as a novel gene involved in thymus development and function. We created a mouse line with deletion of Top1 in thymic epithelial cells (TECs) and our results demonstrate that biallelic loss of Top1 in TECs causes congenital thymic aplasia, precipitating T cell immunodeficiency. Transcriptomic analysis provides insights into the molecular mechanism of Top1 in thymus development as we identify key genes involved in thymus organogenesis as the transcriptional targets of Top1 in TECs. Analysis of peripheral immunological compartments revealed severe loss of ab T cells complemented with a disproportionate accumulation of gd T cells and myeloid cells upon deletion of Top1 in TECs. The residual ab T cells in Top1 knock-out mice were effector and oligoclonal in nature highlighting their possible self-reactivity. These results reveal a previously unknown role of Top1 in thymus development and T cell homeostasis. We propose Top1 as a genetic target for altered thymic development and T cell lymphopenia.

overall_design: We generated Top1-cKO mice having deletion of Top1 in thymic epithelial cells (TECs), to investigate the thymus-intrinsic role of TOP1 in T cell development. Top1-cKO mice had thymic aplasia with no visible thymus present in thoracic cavity at the age of 6-weeks. Since Top1-cKO mice did not have thymic tissue, we performed RNA-seq-based transcriptomic analysis on cTEChi and mTEChi from Top1-WT and Top1-cHet mice (2-weeks old) to understand the molecular mechanism of Top1 in thymus development. Loss of thymus in Top1-cKO mice affected the peripheral T cell populations in the spleen and lymph nodes. We could detect a minor proportion (<5%) of ab T cells in both spleen and MLN of Top1-cKO mice. To understand the impact of loss of TOP1 in TECs on the biology of the residual T cells in the periphery, we performed RNA-seq-based transcriptomic analysis on splenic CD4+ helper T cells from Top1-cKO mice and compared it with control (Top1-WT) littermates.

first: Amit

last: Kumar

first: Pallawi

last: Choubey

first: Harshdeep

last: Kaur

first: Prerana

last: Muralidhara


title: Transcriptome analysis of the uterovaginal junction containing sperm storage tubules in heat-stressed breeder hens

city: Muang District

first: Satoshi

last: Kubota

state: Nakhon Ratchasima

address: 111 University Avenue, Suranaree Sub-District,

country: Thailand

institute: Suranaree University of Technology

summary: Sperm storage tubules (SSTs) in the uterovaginal junction (UVJ) of the oviduct are major sites of sperm storage after artificial insemination or mating. Female birds may regulate sperm motility in the UVJ. Heat stress can decrease the reproductive ability of broiler breeder hens. However, its effects on UVJ remain unclear. Changes in gene expression aid in understanding heat stress-affected molecular mechanisms. Herein, we wanted to conduct a comparative transcriptomic analysis to identify the differentially expressed genes (DEGs) in the UVJ of breeder hens under thermoneutral (23°C) and heat stress (36°C for 6 h) conditions.

overall_design: RNA-seq profiling of the uterovaginal junction of breeder hens under thermoneutral (23°C) and heat stress (36°C for 6 h) conditions.

first: Phocharapon

last: Pasri

first: Supattra

last: Okrathok

first: Orapin

last: Jantasaeng

first: Sitthipong

last: Rakngam

first: Pascal

last: Mermillod

first: Sutisa

last: Khempaka


title: Low input ATAC-seq of CD27− or CD27+ ESLAMSK cells under homeostatic conditions [ATAC-seq]

first: Caiying

last: Zhu

summary: CD27− or CD27+ ESLAMSK cells isolated from 8-week-old wild-type mice

overall_design: Cells were first isolated from bone marrow of 8-week-old wild-type mice, hematopoietic stem cells (EPCR+Lin-Sca1+cKit+CD150+CD48-CD201+, ESLAMLSK) were then sorting based in expression levels of CD27 (CD27- or CD27+) and processed for ATAC-seq library preparation by using Hyperactive ATAC-Seq Library Prep Kit for Illumina.

first: Fang

last: Dong

first: Junren

last: Chen

first: Ping

first: Tao

last: Cheng


title: Transcranial ultrasound stimulation ameliorates DSS-induced colitis and behavioral disorders by suppressing the inflammatory response in the brain

city: Taipei

first: Feng-Yi

last: Yang

state: Taiwan

address: No. 155, Sec. 2, Li-Nong St.

department: Department of Biomedical Imaging and Radiological Sciences

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: This study explores the efficacy of transcranial ultrasound stimulation (TUS) in mitigating dextran sulfate sodium (DSS)-induced colitis and associated behavioral abnormalities in mice. TUS treatment significantly reduced colon inflammation and tissue damage while improving histological scores. Additionally, TUS alleviated anxiety- and depression-like behaviors, possibly by suppressing neuroinflammation via the downregulation of pro-inflammatory cytokines in both the colon and the brain. These findings suggest TUS as a promising non-invasive therapy for managing gut inflammation and associated behavioral disorders, highlighting its potential clinical implications.

overall_design: There are four groups: Sham, DSS, DSS+LIPUS 0.5W, and DSS+LIPUS 1.0W. Sham group are the animals with no treatment. DSS group are animals were treated with DSS. DSS+LIPUS groups are animals treated DSS and LIPUS (0.5W/1.0W).

first: Feng-YI

first: Yu-Chen

last: Lin


title: IL-17 links the tumor suppressor LKB1 to gastrointestinal inflammation and polyposis

city: Grand Rapids

first: Russell

last: Jones

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: Loss-of-function mutations in the tumor suppressor liver kinase B1 (LKB1) promote the development of Peutz-Jeghers Syndrome (PJS), a chronic disease characterized by the development of gastrointestinal (GI) polyps. Treatment options for patients are extremely limited due to a poor understanding of how LKB1 mutations lead to the development of GI polyps. Here, we reveal a role for CREB-regulated transcription coactivator 2 (CRTC2) signaling in the regulation of inflammatory potential in LKB1 mutant T cells. We also demonstrate that targeting CRTC2 and pathogenic T helper 17 (Th17) cells reduces GI polyp growth in LKB1 mutant mice. Our data reveal a critical role for CRTC2 in LKB1-mediated T cell inflammatory responses that we hypothesize predisposes PJS patients harboring LKB1 mutations to GI polyp development.

overall_design: RNA-seq was performed on GI polyp tissue from 12-month-old LKB1-mutant mice (whole-body heterozygosity for Stk11) or control stomach tissue from 12-month-old wild type mice. RNA-seq was also performed on Lkb1+/-, Lkb1+/-/Crtc2-/-, and A485-treated Lkb1+/- T cells differentiated under pathogenic Th17 conditions.

first: Shelby

last: Compton


title: Big data-driven target identification by machine learning: DRD2 as a therapeutic target for psoriasis.

city: Yufu-shi

first: Takashi

last: Sakai

state: Oita

address: 1-1, Idaigaoka, Hasama-machi

department: Dermatology

country: Japan

institute: Oita University

summary: We developed a new machine learning method to predict therapeutic target molecules by searching for potential target proteins of preventive drugs derived from clinical medication history reports and molecular data, and successfully identified DRD2 as a novel therapeutic target for psoriasis.

overall_design: Investigation of the effects of quinpirole on imiquimod (IMQ)-induced psoriasis in mice: We employed the IMQ-induced psoriasis mouse model, widely recognized as a representative model for studying psoriasis, to investigate the effects of an agonist for DRD2 on this condition. Female BALB/c mice, aged 10-11 weeks, were utilized. Daily, topical application of IMQ (5% cream) was applied to the shaved dorsal skin of the mice for five consecutive days. Following this procedure, mice were euthanized according to approved protocols, and samples of skin were collected. Quinpirole was used as a DRD2 agonist and was administered intraperitoneally to the mice five times concurrently with the topical IMQ application.

first: Ryusuke

last: Sawada

first: Otoha

last: Ichinose

first: Takeshi

last: Terabayashi

first: Yutaka

last: Hatano

first: Yoshihiro

last: Yamanishi

first: Toshimasa

last: Ishizaki


title: Bi-directional immunosuppressive interactions between astrocytes and glioblastoma cells identified by barcoded viral tracing [Mouse Bulk RNA-Seq Dataset of Monocytes, T Cells and Astrocytes 63FG]

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

summary: Glioblastoma (GBM) is the most lethal primary brain malignancy. Immunosuppression in the GBM tumor microenvironment (TME) presents a major barrier to immune-targeted therapies. However, our understanding of mechanisms of immunomodulation in the GBM TME is still limited. To address this challenge, we developed a viral barcode interaction tracing approach for the analysis of cell-cell communication in the TME in GBM samples and preclinical models with single-cell resolution, which we combined with single-cell and bulk RNA-seq analyses of GBM clinical samples and pre-clinical models, human organotypic GBM slice cultures, in vivocell-specific CRISPR/Cas9-driven genetic perturbations and human and mousein vitroexperimental systems to identify a novel bi-directional communication pathway between ANXA1 expressed inastrocytes and its receptor FPR1 expressed by GBM cells that limits anti-tumor immune responses. ANXA1 expression in astrocytes and FPR1 expression in cancer cells are associated with shorter survival and earlier recurrence in GBM patients. The inactivation of astrocyte-glioma ANXA1/FPR1-signaling enhanced tumor specific CD4+ and CD8+ T-cell responses, increasing tumor infiltration by neoantigen-specific CD8+ T cells while limiting transcriptional modules linked to T-cell exhaustion; ANXA1/FPR1-signaling inactivation also boosted tumor-associated macrophage responses. Using pre-clinical models and human GBMin vitroexperimental systems, we established that FPR1 inhibits immunogenic necroptosis in tumor cells, while ANXA1 retrograde signaling suppresses NF-kB and inflammasome activation within astrocytes. In summary, we developed a new barcoding approach to analyze TME cell-cell interactions with single-cell resolution in clinical samples and pre-clinical models, and used it to identify a novel pathway of bidirectional ANXA1–FPR1 astrocyte-GBM communication which promotes immunoevasion and cancer progression.

overall_design: Bulk RNA-Seq dataset which includes 33 samples from 4 different cell types sorted from Mice

first: Brian

last: Andersen

first: Camilo

last: Akl

first: Francisco

last: Quintana


title: Bi-directional immunosuppressive interactions between astrocytes and glioblastoma cells identified by barcoded viral tracing [Human Single Cell Dataset]

overall_design: Single Cell RNA-Seq dataset which includes 12 samples obtained from 3 patients


title: Bi-directional immunosuppressive interactions between astrocytes and glioblastoma cells identified by barcoded viral tracing [Mouse Bulk RNA-Seq Dataset of Monocytes, T Cells and Astrocytes 5OLJ]


title: Immunometabolic dysregulation in microglia drives brain ageing via neuroimmune cGAS-STING

city: Shanghai

first: Erlin

last: Wang

state: Shanghai

address: 748 Zhongshan Middle Road, Songjiang District, Shanghai

department: Songjiang Hospital

institute: Shanghai Jiao Tong University School of Medicine

summary: Ageing and age-related brain disorders are typically concomitant with cellular mitochondrial dysfunction and metabolic dysregulation in immune cells. However, whether and how immunometabolic dysregulation in the brain affects neurological function are incompletely understood. Here we reveal the presence of metabolic dysregulation within microglia, the brain-resident immune cells, in aged mice. We discover that microglia with dysregulated immunometabolism, induced by dysfunctional mitochondria, initially act as triggers of brain ageing-related neurological dysfunctions in mice, which are mechanistically driven by microglial immunometabolic disturbance-induced inflammaging response depending on neuroimmune cGAS-STING pathway. We present evidence that a combined treatment targeting both metabolism and neuroinflammation partially rescues brain ageing in mice. These findings establish a causal link between immunometabolism, neuroimmunity, and brain ageing, underscoring the significance of tightly regulated immunometabolism in age-associated neurological diseases.

overall_design: To assess the impact of Tfam knockout on microglial cell function, we employed CRISPR-Cas9 technology to knockout Tfam in BV2 cells, and evaluated its effect on the cellular transcriptome through RNA-seq analysis.

first: Guanqin

last: Ma

first: Xiaochun

last: Xie

first: Xiaoxu

last: Yan

first: Meng

last: Zhao

first: Xiangxiong

last: Xu

first: Xiaohong

first: Luxiu

last: Zang

first: Jianxiong

last: Zeng


title: Spatial-Temporal Analysis Revealed the Dynamic Changes of Leukemia Neighborhood After Receiving Pembrolizumab and Decitabine

city: Bethesda

first: Laura

last: Dillon

state: Maryland

address: Room 10CRC 6-5142, 10 Center Drive

department: Hematology Branch

institute: National Heart Lung and Blood Institute, NIH

summary: Acute myeloid leukemia (AML) is a genetically heterogeneous disease that is characterized by abnormal clonal proliferation of myeloid progenitor cells found predominately within the bone marrow (BM) and blood. Recent studies suggest that genetic and phenotypic alterations in the BM microenvironment support leukemogenesis and allow leukemic cells to survive and evade chemotherapy-induced death. However, despite substantial evidence indicating the role of tumor-host interactions in AML pathogenesis, little is known about the complex microenvironment of the BM. To address this, we performed novel proteomic profiling of the non-cellular compartment of the BM microenvironment in AML patients (n=10) and age- and sex-matched healthy controls (n=10) using an aptamer-based, highly multiplexed, affinity proteomics platform (SOMAscan). We demonstrate that proteomic assessment of blood or RNA-sequencing of BM are suboptimal alternate screening strategies to determine the true proteomic composition of the extracellular compartment of the AML marrow microenvironment. Proteomic analysis showed 168 proteins significantly differed in abundance, with 91 proteins up-regulated and 77 proteins down-regulated in leukemic BM. A highly connected signaling network of cytokines and chemokines, including IL-8, was found to be the most prominent proteomic signature associated with AML in the BM microenvironment. We report the first description of significantly elevated levels of the myelosuppressive chemokine CCL23 (MPIF–1) in both AML and MDS patients and perform functional experiments supportive of a role in the suppression of normal hematopoiesis. This unique paired RNA-sequencing and proteomics dataset provides innovative mechanistic insights into AML and healthy aging and should serve as a useful public resource.

overall_design: For bulk RNAseq: Total RNA sequencing of rRNA-depleted RNA was performed using the Illumina TruSeq Stranded Total RNA kit.  Sequencing was performed on RNA isolated from bone marrow PAXgene tubes of 10 acute myeloid leukemia patients at multiple follow-up time points. For single-cell: Bone marrow aspirate was collected from enrolled patients at different time points. The 10x Genomics 3’v3 Single Cell Immune profiling platform was used for scRNA-seq of BMMCs. cDNA amplification was performed according to manufacturer’s instructions with the addition of 1 ul 0.2 uM ADT additive primer per sample to amply ADT tags.

first: Gege

last: Gui

first: Christopher

middle: S

last: Hourigan

middle: W


title: Nuclear adenine activation of hnRNPA2B1 promotes IL-1 transcription in antibacterial innate immunity [Cut&Tag-seq]

city: Hangzhou

first: Shihao

last: Zhang

state: Zhejiang Province

address: 866 Yuhangtang Rd

institute: Zhejiang University School of Medicine

summary: Deciphering the rapid expression and the underlying mechanisms of antibacterial effectors is critical to host defense against bacterial infection. Bacterial infection can reprogram cellular metabolism, however, the immunometabolism and its cross-talk with epigenetics in the regulation of antibacterial innate immunity remain to be fully understood. Here we report that nuclear hnRNPA2B1 is required to antibacterial innate response by promoting Il1b transcription. Myeloid-specific Hnrnpa2b1-deficient mice are susceptible to bacterial infection, resulting from IL-1β production insufficiency. The screenings identify the metabolite adenine in the nucleus to be able to bind and activate hnRNPA2B1. Adenine directly recruits hnRNPA2B1 to Il1b enhancers for increasing chromatin accessibility to promote Il1b transcription through NCL and FTO-mediated DNA 6mA demethylation of Il1b gene enhancers. Furthermore, bacterial infection elevates nuclear adenine levels, and in vivo administration of adenine protects mice from bacterial infection through hnRNPA2B1-IL1 circuit. Our findings provide an undiscovered paradigm of cross-regulation between epigenetic and metabolic pathways in antibacterial innate immunity, adding insight and proposing new approach to the treatment of bacterial infections.

overall_design: Cleavage Under Targets and Tagmentation (Cut&Tag) sequencing of hnRNPA2B1 in RAW264.7 cells stimulated with LPS 100 ng/ml for 0, 1, 2 hours.

first: Xuetao

last: Cao


title: Nuclear adenine activation of hnRNPA2B1 promotes IL-1 transcription in antibacterial innate immunity [ATAC-seq]

overall_design: Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-Seq) in LPS 100 ng/ml stimulated 1 hour and unstimulated Hnrnpa2b1-KO and wild-type RAW264.7 cells


title: Pre-treatment of Interferon-α stimulates DHX58 to prevent hepatic ferroptosis [DHX58 RIP-Seq]

first: Jia

middle: Kai

last: W

address: 800 Xiangyin Road

institute: National Key Laboratory of Medical Immunology and Institute of Immunology

summary: Characterized by lethal iron accumulation and lipid peroxidation, ferroptosis plays critical roles in liver injury, especially caused by ischemia/reperfusion (I/R) of hepatic inflow occlusion during liver operation. Here, we found that the excessive production of reactive oxygen species could decrease the expression of Interferon (IFN)-stimulated gene DExH-box helicase 58 (DHX58) in hepatocytes, and then promote hepatic ferroptosis, while pre-treatment using IFN-α increased DHX58 expression and prevented ferroptosis during I/R injury. Mechanistically, DHX58 with RNA-binding activity could constitutively associate the mRNA of glutathione peroxidase 4 (GPX4), a crucial ferroptosis suppressor, and then recruit the m6A reader YT521-B homology domain containing 2 (YTHDC2) to promote the translation of Gpx4 mRNA in m6A-dependent manner, thus enhancing GPX4 protein level and preventing hepatic ferroptosis.

overall_design: DHX58 antibody RIP RNA

first: Jin

last: Hou


title: Single-cell multiomic comparison of mouse and rat spermatogenesis reveal gene regulatory networks conserved for over 20 million years.

city: Philadelphia

first: Eoin

middle: Christopher

last: Whelan

address: 3800 Spruce St

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

summary: Spermatogenesis is driven by dramatic temporal and spatial changes in chromatin regulation, gene transcription, and protein expression. To assess the mechanistic bases for these developmental changes, we utilized multiomic single-cell/single-nuclear RNA-sequencing (sc/snRNA-seq) and transposase-accessible chromatin (snATAC-seq) to identify chromatin changes associated with transcription along with cellular indexing of transcriptomes and epitopes (CITE-seq) to assess post-transcriptional control of expression in adult mouse and rat testes. We characterized similarities and variations between the transcriptomes of both species, including a difference in the expression of Id4 in spermatogonial stem cells. In both mice and rats, promoter accessibility and gene expression showed the greatest association during meiosis. We mapped cross-species conservation in putative regulatory regions for key spermatogenic genes, including Sdc4, Sycp3 and Spam1, and we found that the correlation between Cd9 chromatin states and CD9 protein abundance allowed for the isolation of distinct germ cell types with improved resolution. Using a gene regulatory network (GRN) model, we identified 40 key regulons conserved between mouse and rat germ cells, highlighting the relevance of chromatin-related factors in regulating the transcription and translation of key genes across spermatogenesis.  (iPSCs) into primordial germ cell-like cells that self-organize within xenogeneic reconstituted testes (xrTestes) generated from mouse fetal testicular cells. Subsequent transplant of xrTestes into immunodeficient mice resulted in efficient generation of undifferentiated and differentiated spermatogonia as well as preleptotene spermatocytes with striking similarities to their in vivo counterparts. As the fertilization competency of human iPSC-generated germ cells cannot be evaluated due to ethical constraints, we utilized a similar strategy to differentiate rhesus iPSCs through all fetal germ cell stages into spermatogonia-like cells. Together, these newly identified models of human gametogenesis will allow further mechanistic assessment of both germ cell development and genetic causes of infertility.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Single-cell 3' mRNA + CITE seq of rat and mouse adult testes alongside single-nucleus mRNA + ATACseq of the same tissues. Samples were unselected or selected with EPCAM to enrich for early germ cells or with CD9 to enrich specific fractions.

middle: C

first: John

last: Swain

first: Jonathan

last: Sussman

first: David

last: Smith

first: Fan

last: Yang

first: Antonia

last: Rotolo

first: Mary

middle: R

last: Avarbock

first: Clara

last: Malekshahi

first: Enrico

last: Radaelli

first: Daniel

last: Beiting

first: Ralph

last: Brinster


title: Pre-treatment of Interferon-α stimulates DHX58 to prevent hepatic ferroptosis [scRNA-seq]

overall_design: Hepatic global cells of the Dhx58f/f and Dhx58hep-/- mice were  analyzed using scRNAseq.


title: RBM47 Inhibits Hepatocellular Carcinoma Progression as a DNA/RNA Regulator [RIP-seq]

city: Weifang

first: Yingying

last: Jiang

state: Shandong

address: 7166 Baotong west Road

institute: Weifang Medical University

summary: By RIP sequencing, we determined that RBM47 modulated UPF1 by stabilizing its mRNA and addressed the novel motif in the UPF1 3’UTR with direct binding.

overall_design: RIP-seq of human HCC cells

first: Tao

last: Guo

first: Ke

last: You

first: Xi

last: Chen


title: Pre-treatment of Interferon-α stimulates DHX58 to prevent hepatic ferroptosis [m6A RIP]

first: Jia

last: W


title: Pre-treatment of Interferon-α stimulates DHX58 to prevent hepatic ferroptosis

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

overall_design: Refer to individual Series


title: RBM47 Inhibits Hepatocellular Carcinoma Progression as a DNA/RNA Regulator


title: Comparative RNA-seq analysis of Arabidopsis thaliana wild-type vs. autophagy atg5 mutant under water deprivation.

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

summary: A comparative analysis between wild-type Arabidopsis thaliana and autophagy´s atg5 mutant to discover differences between these two plants during normal growth and in relationship to water deficit

overall_design: Seeds were germinated in Normal medium o WSM during five days to compare differences in expression of genes during normal or water deciency

first: Luis

last: Castillo-Olamendi

first: Elsa

last: Quezada-Rodríguez

first: Jorge

last: Solís-Miranda

first: Gladys

last: Jiménez-Nopala

last: Vega-Alvarado

first: Patricia

last: León

first: Helena

last: Porta


title: RBM47 Inhibits Hepatocellular Carcinoma Progression as a DNA/RNA Regulator [ChIP-seq]

summary: After ChIP assay, DNA sequencing was conducted to analyze the specific loci binding by RBM47 in HCCLM3 cells.

overall_design: ChIP-seq of human HCC cells


title: The RNA-binding E3 ligase MKRN2 selectively disrupts IL-6 translation to restrain inflammation [RNA-seq]

status: Public on Apr 27 2025

city: Suzhou

first: Zhou

last: Yu

address: 100 Chongwen Road

institute: Chinese Academy of Medical Sciences /Suzhou Institute of Systems Medicine

summary: Dysregulation of proinflammatory cytokine production leads to autoimmune and inflammatory diseases. Although E3 ligases and RNA-binding proteins (RBPs) are critical in autoimmunity and inflammation, whether RNA-binding E3 ligases (E3-RBPs) can regulate proinflammatory cytokine expression to be involved in autoimmune disorders remains unclear. Here, we found that MKRN2, an E3-RBP, selectively inhibits IL-6 expression in LPS-activated macrophages. MKRN2-deficient mice have increased IL-6 serum levels at the untreated stage or after LPS treatment, and exhibit increased severity of experimental colitis which is associated with increased IL-6 levels. MKRN2 is negatively correlated with IL-6 expression in clinical samples from patients with ulcerative colitis and rheumatoid arthritis. Mechanistically, upon encountering Il6 mRNA, MKRN2 links K29 polyubiquitin to Lys179 of PAIP1 which blocks PAIP1-eIF4A interaction, thus inhibiting the translational efficiency of Il6 mRNA. Our findings provide new mechanistic insight and potential therapeutic strategies for inflammatory autoimmune diseases by disrupting translation process of specific proinflammatory cytokines.

overall_design: RNA-seq of mkrn2+/+ and mkrn2-/- BMDM treated with LPS (100ng/ml) for 8 hours

first: Xuelian

last: Li

first: Jiaying

last: Huang

first: Jueyu

last: Pan

first: Jiale

last: Cheng

first: Qian

last: Zhang

first: Xuetao

last: Cao


title: Expression data from mouse peritoneal macrophages

summary:
Biologic functions involved in innate immune response of macrophages rely on the precise regulation of kinds of immune molecular. In the LPS treatment procession, the macrophages are activated following a tightly controlled genetic programme where specific sets of genes are up-regulated or down-regulated.
We used microarrays to detail the global programme of gene expression underlying LPS treatment and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: Mouse peritoneal macrophages were selected with/without  LPS treatment for 6 hours for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain expression profiles. We selected macrophages according to LPS treatment at two time-points: uninfected macrophage(Mock) and LPS treatment for 6 hour macrophages(LPS).

first: Weilin

last: Chen


title: Single-cell RNAseq of T-HSCs.

city: Guangzhou

first: chen

last: minqi

state: Guangdong

address: No.74, 2nd Zhongshan Road

institute: Sun Yat-sen University

summary: T-HSCs were collected from Cd4-cre;R26Tdtomato mice, which were intravenously injected with 5×103 CFU LM for 6 weeks.

overall_design: Single-cell RNAseq on HSCs

first: Meng

last: Zhao

first: Xue

last: Han

first: Minqi


title: Chromatin structure predicts survival in glioma patients

city: Cincinnati

first: Matthew

last: Garrett

state: Ohio

address: 5061 myerdale drive

institute: Kettering Health

summary: The pathological changes in epigenetics and gene regulation that accompany the progression of low-grade to high-grade gliomas are under-studied. The authors use a large set of paired atac-seq and RNA-seq data from surgically resected glioma specimens to infer gene regulatory relationships in glioma. Thirty-eight glioma patient samples underwent atac-seq sequencing and 16 samples underwent additional RNA-seq analysis. Using an atac-seq/RNA-seq correlation matrix, atac-seq peaks were paired with genes based on high correlation values (|r2| > 0.6). Samples clustered by IDH1 status but not by grade. Surprisingly there was a trend for IDH1 mutant samples to have more peaks. The majority of peaks are positively correlated with survival and positively correlated with gene expression. Constructing a model of the top six atac-seq peaks created a highly accurate survival prediction model (r2 = 0.68). Four of these peaks were still significant after controlling for age, grade, pathology, IDH1 status and gender. Grade II, III, and IV (primary) samples have similar transcription factors and gene modules. However, grade IV (recurrent) samples have strikingly few peaks. Patient-derived glioma cultures showed decreased peak counts following radiation indicating that this may be radiation-induced. This study supports the notion that IDH1 mutant and IDH1 wildtype gliomas have different epigenetic landscapes and that accessible chromatin sites mapped by atac-seq peaks tend to be positively correlated with expression. The data in this study leads to a new model of treatment response wherein glioma cells respond to radiation therapy by closing open regions of DNA.

overall_design: 38 glioma samples (7 Grade II, 9 Grade III, 9 Grade IV primary, 13 Grade IV recurrent), ATAC-seq for all samples analyzed by IDH1 mutation status and survival

first: Rebecca

last: Albano

first: Troy

last: Carnwath

first: Sanjit

last: Shah

first: Daniel

last: Woo

first: Michael

last: Lamba

first: David

last: Plas

first: Aditi

last: Paranjpe

first: Krishna

last: Roskin

first: Chuntao

first: Richard

last: Lu


title: Transcriptomic profiling of primary human dermal fibroblasts treated with BoNTA

city: shanghai

first: Fangzhou

last: Xie

state: shanghai

address: 99 Haike Road, Pudong New Area, Shanghai

institute: 上海交通大学第九人民医院

summary: This study aimed to explore the transcriptomic changes in primary human dermal fibroblasts upon treatment with Botulinum toxin type A (BoNTA). BoNTA is a neurotoxin known for its clinical use in dermatology, and emerging evidence suggests potential antifibrotic and anti-inflammatory effects at the cellular level. We performed high-throughput RNA sequencing to assess the global gene expression profiles in fibroblasts treated with BoNTA (1 U/ml) for 24 hours, compared with vehicle control (PBS). This dataset provides valuable insights into the molecular mechanisms of BoNTA in skin-resident fibroblasts and offers a reference for future investigations into its therapeutic roles in fibrotic skin diseases.

overall_design: Total RNA was extracted from primary human dermal fibroblasts treated with BoNTA (1 U/ml, n = 3) and from control fibroblasts treated with an equivalent volume of PBS (n = 3). RNA-seq libraries were prepared and sequenced using the Illumina platform. Differential gene expression analysis was performed to identify transcriptional changes induced by BoNTA treatment. All samples were collected after 24 hours of treatment.

first: Jia

last: Liu

first: Yun


title: Using a modular massively parallel reporter assay to discover context-specific regulatory grammars in type 2 diabetes - Kyono library

city: Ann Arbor

first: Adelaide

middle: Erin

last: Tovar

state: Michigan

address: 100 Washtenaw Ave

department: Computational Medicine & Bioinformatics

institute: University of Michigan

summary: Recent genome-wide association studies have established that most complex disease-associated loci are found in noncoding regions where defining their function is nontrivial. In this study, we leverage a modular massively parallel reporter assay (MPRA) to uncover sequence features linked to context-specific regulatory activity. We screened enhancer activity across a panel of 198-bp fragments spanning over 10k type 2 diabetes- and metabolic trait-associated variants in the 832/13 rat insulinoma cell line, a relevant model of pancreatic beta cells. We explored these fragments’ context sensitivity by comparing their activities when placed up- or downstream of a reporter gene, and in combination with either a synthetic housekeeping promoter (SCP1) or a more biologically relevant promoter corresponding to the human insulin gene (INS). We identified clear effects of MPRA construct design on measured fragment enhancer activity. Specifically, a subset of fragments (n = 702/11,656) displayed positional bias, evenly distributed across up- and downstream preference. A separate set of fragments exhibited promoter bias (n = 698/11,656), mostly towards the cell-specific INS promoter (73.4%). To identify sequence features associated with promoter preference, we used Lasso regression with 562 genomic annotations and discovered that fragments with INS promoter-biased activity are enriched for HNF1 motifs. HNF1 family transcription factors are key regulators of glucose metabolism disrupted in maturity onset diabetes of the young (MODY), suggesting genetic convergence between rare coding variants that cause MODY and common T2D-associated regulatory variants. We designed a follow-up MPRA containing HNF1 motif-enriched fragments and observed several instances where deletion or mutation of HNF1 motifs disrupted the INS promoter-biased enhancer activity, specifically in the beta cell model but not in a skeletal muscle cell line, another diabetes-relevant cell type. Together, our study suggests that cell-specific regulatory activity is partially influenced by enhancer-promoter compatibility and indicates that careful attention should be paid when designing MPRA libraries to capture context-specific regulatory processes at disease-associated genetic signals.

sample_organism:
Rattus norvegicus
synthetic construct

platform_organism:
Rattus norvegicus
synthetic construct

overall_design: We obtained a pool of 79,511 full-length 230-bp fragments spanning variants associated with type 2 diabetes and related metabolic traits from Agilent. We cloned these sequences into the STARR-seq backbone plasmid and inserted 16-bp random barcodes into this library. We electroporated 10 ug of barcoded library into 25 million INS-1/832/13 rat insulinoma cells and harvested the cells 24 hours later. We isolated total RNA and enriched for mRNA using oligo(dT) beads. We generated sequencing libraries and performed paired-end sequencing on the Illumina HiSeq instrument.

first: Yasuhiro

last: Kyono

first: Kirsten

last: Nishino

first: Maya

last: Bose

first: Arushi

last: Varshney

first: Stephen

last: Parker

first: Jacob

middle: O

last: Kitzman


title: The RNA-binding E3 ligase MKRN2 selectively disrupts IL-6 translation to restrain inflammation

first: Zhou

last: Yu

overall_design: CLIP-seq of MKRN2 in RAW264.7 cell treated with LPS (100ng/ml) for 8 hours

first: Xuelian

last: Li

first: Jiaying

last: Huang

first: Jueyu

last: Pan

first: Jiale

last: Cheng

first: Qian

last: Zhang

first: Xuetao

last: Cao


title: Using a modular massively parallel reporter assay to discover context-specific regulatory grammars in type 2 diabetes - Tovar library

overall_design: We selected fragment sequences from the first library with strong INS promoter-biased activity that contained HNF1 motifs. We added barcodes to these fragments using PCR and cloned these fragments into an MPRA vector via Golden Gate cloning. We electroporated 30 ug of barcoded library into 30 million INS-1/832/13 rat insulinoma cells and harvested the cells 24 hours later. We isolated total RNA, generated sequencing libraries and performed paired-end sequencing on the Illumina NovaSeq instrument.


title: The circadian clock component REV-ERBs is an analgesic target for cancer-induced tactile pain hypersensitivity

city: Fukuoka

first: Satoru

last: Koyanagi

address: 3-1-1 Maidashim Higashi-ku

department: Pharmaceutical Sciences

institute: Kyushu University

summary: Neuropathic pain is one of the most intractable pain conditions associated with tumor growth compressing and damaging nerves. A troublesome hallmark symptom of neuropathic pain is hypersensitivity to innocuous stimuli, known as “tactile allodynia,” which is often refractory to currently available analgesics. Diurnal variations in pain hypersensitivity are common in patients with cancer, but the underlying mechanisms are enigmatic. Herein, we report that spinal expression of lipocalin-2 (LCN2) enhances pain sensitivity of NCTC2472 fibrosarcoma-implanted male mice during specific stages of the diurnal cycle. As the tumor grew, interleukin-6 (IL-6) levels increased in the spinal cord of the mice. Increased IL-6 levels stimulated LCN2 expression in spinal microglia, but this expression was periodically repressed by the circadian clock components REV-ERBα and REV-ERBβ. Notably, intra-spinal dorsal horn injection of lentiviral vectors expressing REV-ERBα or REV-ERBβ in tumor-bearing mice alleviated tactile allodynia. Furthermore, intrathecal injection of SR9009, a synthetic agonist of REV-ERBs, also attenuated cancer-induced pain hypersensitivity, accompanied by suppressing spinal LCN2 expression. These results suggest that temporal elevation of LCN2 expression decreases the threshold of tactile pain hypersensitivity induced by tumor growth. We propose that the circadian clock component of REV-ERBs is an effective target for alleviation of cancer-induced tactile allodynia, identifying a new class of analgesic agents.

overall_design: Total 4 samples were obtained from the spinal cord of [1] healthy control (Matrigel implanted) mice at ZT10 (late light phase), [2] healthy control (Matrigel implanted) mice at ZT22 (late dark phase), [3] NCTC tumor-bearing mice at ZT10 (late light phase), and [4] NCTC tumor-bearing mice at ZT22 (late dark phase).

first: Sai

last: Yasukochi

first: Wakaba

last: Yamakawa

first: Marie

last: Taniguchi

first: Sayaka

last: Itoyama

first: Akito

last: Tsuruta

first: Naoki

last: Kusunose

first: Tomoaki

last: Yamauchi

first: Risako

last: Nakamura

first: Naoya

last: Matsunaga

first: Shigehiro

last: Ohdo


title: Sequencing of human hepatocellular carcinoma huh7 cell line under the effect of disulfiram [m1A-seq]

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

summary: To detect the altered m1A in human hepatocellular carcinoma huh7 cell line under the condition of disulfiram and contorl.

overall_design: 6 samples were analyzed, two groups were divided with three samples each,including control group, disulfiram group.

first: Zhuoran

last: Qi

first: Feng


title: The effect of culture medium from apoptotic chondrocytes on macrophages

city: Nanjing

first: Ziyang

last: Zheng

address: Longmian Avenue NO.101

institute: The first affiliated hospital of nanjing medaical university

summary: To investigate the altered gene expression levels in macrophages treated with culture medium from apoptotic chondrocytes and normal chondrocytes. Each group had a biological repeat (n=3). Results provide insight into the effect of culture medium from apoptotic chondrocytes on macrophages.

overall_design: Three groups of macrophages treated with apoptotic chondrocytes culture medium(AC CM) versus three groups of macrophages treated with normal chondrocytes culture medium(C CM).

first: Shujie

last: Zhao

first: Guoyong

last: Yin


title: Glutamine recovers stress granules after cellular starvation to help mount cancer stress response

city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

summary: To investigate the effects of glutamine of cancer cell metabolism and its effects of Stress Granule formation during the stress response

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U2OS cells under various cellular stresses


title: Sequencing of human hepatocellular carcinoma huh7 cell line under the effect of disulfiram [transcriptome]

summary: To detect the altered gene expression in human hepatocellular carcinoma huh7 cell line under the condition of disulfiram, thalidomide and the combination of the two drugs.

overall_design: 12 samples were analyzed, four groups were divided with three samples each,including control group, disulfiram group, thalidomide group and combination group.


title: Human Dental Pulp Stem Cell derived exosomes as effective biomaterials for anti-inflammation and regeneration in pulpitis

status: Public on Apr 26 2025

city: Seoul

first: Ju Ri

last: Ye

address: Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: KyungHee university

summary: The study investigates the effects of exosomes derived from human dental pulp stem cells (hDPC-Exos) on pulpitis, an inflammatory dental condition. The research demonstrates that hDPC-Exos exhibit significant anti-inflammatory and regenerative properties, making them effective biomaterials for treating pulpitis. Exosomes were shown to downregulate pro-inflammatory cytokines and chemokines, such as interleukin-1β and tumor necrosis factor-alpha, thus suppressing inflammation. Additionally, hDPC-Exos promoted angiogenesis and odontogenesis, facilitating recovery and regeneration of pulp tissue. These effects were observed through various analyses, including RNA sequencing and histological evaluations in an in vitro pulpitis model and a rat model of pulpitis. The findings suggest that hDPC-Exos hold potential as a cell-free therapeutic approach for oral inflammation and tissue regeneration.

overall_design: The RNA sequencing (RNA-seq) procedure was conducted to explore the transcriptome-level effects of exosomes derived from human dental pulp cells (hDPC-Exos) in response to lipopolysaccharide (LPS) treatment.

first: Hyekyoung

last: You

first: Ok Hyung

last: Nam

first: Si Won

last: Kang

first: In Chol

first: Myeong-Kwan

last: Jih

first: Ok Joon

last: Kim

first: Young


title: RNAseq of CD4 T cells from female Rheumatoid arthritis patients [ConA + LPS]

city: Gothenburg

first: Maria

middle: I

last: Bokarewa

state: VG

address: Guldhedagatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: Gothenburg University

summary: RNAseq of CD4 cells from 3 female RA patients activated with ConA + LPS for 72h. Patients were collected crossectionally from the Rheumatology clinic during 2018.

overall_design: 3 women with  rheumatoid arthritis, CD4 cells  from human PBMC isolated by positive selection on Dynabeads (cat.11331D), stimulated with ConA+LPS for 72h

first: Karin

middle: M

last: Andersson

first: Malin

last: Erlandsson

first: Nina

last: Oparina


title: Transcriptome analysis of sunflower varieties with different petiole inclination angles

city: Hohhot

first: Kai

last: Cao

address: Inner Mongolia Agricultural University

department: agricultural college

institute: Inner Mongolia Agricultural University

summary: ( 1 ) The RNA-seq analysis of 6 samples was completed, and a total of 41.36 Gb Clean Data was obtained. The Clean Data of each sample reached 6.63 Gb, and the percentage of Q30 bases was 93.43 % and above.( 2 ) The Clean Reads of each sample were compared with the designated reference genome, and the alignment efficiency ranged from 87.86 % to 94.06 %. Based on the alignment results, alternative splicing prediction analysis, gene structure optimization analysis and new gene discovery were carried out, and 13,716 new genes were discovered, of which 6,959 were functionally annotated.( 3 ) In this project, Fold Change ≥ 1.5 and FDR < 0.01 were used as differential gene screening criteria. In each set of comparison groups, the results of differential expression gene list, differential expression gene function enrichment analysis, GSEA analysis, differential alternative splicing, and differential gene protein interaction were obtained. The detailed results are shown in each chapter of the text.

overall_design: In this study, based on the analysis of the petiole inclination angle of the leaf flat type ( large petiole inclination angle ) inbred line 19G and the leaf compact type ( small petiole inclination angle ) inbred line 20G, the Illumina Hi-Seq2500 high-throughput sequencing technology was used to sequence the transcriptome, and the differentially expressed genes were screened for GO and KEGG database comparison and annotation analysis.

first: Haizhu

last: Bao

first: Yanan

last: Zhou

first: Jiafeng

last: Lu

first: Juanyong

last: Qu

first: Chunguang

first: Mingyue

first: Yang

last: Huang

first: Xinrao

last: Fu

first: Shiyao

last: Wang


title: Expression data from keloid fibroblasts.

first: XIANGLAN

last: ZHANG

address: Yonsei roo

institute: Yonsei University

summary:
Hypoxic areas and a metabolic shift toward glycolysis are common features of keloids.
However, the roles and underlying molecular mechanisms of these features in keloid pathogenesis remain largely unknown.

overall_design: To investigate the role of proteins involved in the hypoxia–glycolysis–acidosis sequence in keloid pathogenesis, we performed gene expression profiling using the Affymetrix array platform. Among acidosis-related genes, CA9 expression was found to be overexpressed in keloid fibroblasts. Based on this finding, we further investigated the molecular function of CA9 in keloid fibroblasts.

first: Xianglan

last: Zhang

first: Mi

last: Roh


title: Large-scale tethering of RNA binding proteins discovers alternative splicing regulators [RIP-Seq]

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: To elucidate the role of large sets of RBPs, we developed a comprehensive and diverse plasmid resource3 of 765 RBPs fused to the MS2 bacteriophage coat protein. When systematically tethered to an intronic 4 MS2 hairpin downstream ofan alternative exon, we identified 55 RBPs that significantly induced exon 5 retention.

overall_design: RBPs were exogeneously expressed and immunoprecipitated by affinity tag and NGS was performed.

first: Tomas

last: Bos

first: Thai

last: Nguyen

first: John

last: Lapek

first: Brian

last: Yee

first: J

middle: P

last: Donahue


title: Design and Biological Activity of a Novel Urea Compound Against Glioblastoma [HK-374_bulkRNA-seq]

city: Los Angeles

first: Frank

last: Pajonk

address: 10833 Le Conte Ave

institute: UC Los Angeles

summary: Despite advances in surgery and radiotherapy, glioblastoma (GBM) remains the deadliest adult brain cancer with unacceptable low median survival rates. Targeted therapies and biologics have failed to improve outcome and the standard-of-care against GBM has not changed in two decades. GBM, like many solid tumors are thought to be organized hierarchically with a small number of radiation- and chemotherapy-resistant glioma stem cells (GSCs) producing more differentiated progeny and can repopulate tumors after sublethal treatment.In this study we sought to develop novel compounds that cross the blood-brain barrier (BBB), target existing GSCs and interfere with glioma cell plasticity to prevent the induction of GSCs in response to irradiation. We show that novel urea compounds target existing GSCs, prevent the radiation-induced conversion of non-stem glioma cells into GSCs and prolong the median survival in mouse models of GBM with minimal normal tissue toxicity.

overall_design: Primary HK-374 cells were treated with 10 µM MXC-017 one hour before a single dose of radiation (4 Gy), RNA was extracted at 48 hours using Trizol followed with RNeasy kit (Qiagen) isolation.

first: Ling

last: He


title: Design and Biological Activity of a Novel Urea Compound Against Glioblastoma [HK-390_scRNA-seq]

overall_design: HK-390 gliomaspheres were plated onto the Poly-D-Lysine/Laminin coated 6-well plate (#354595, Corning) and treated with MXC-017 at a concentration of 10 µM, one hour before receiving a single dose of 4 Gy the next day. Five days post-irradiation, the cells were collected for sequencing.


title: Temporal Mapping of Radiation-Induced Changes in Human Brain Organoids using single-cell RNA sequencing

summary: Radiation therapy (RT) is a standard-of-care oncological treatment for the central nervous system (CNS). However, during cranial RT, normal brain tissue adjacent to the tumors is inevitably irradiated, causing transient reversible abnormalities as well as progressive irreversible late toxicities. Approximately 100,000 patients with primary and metastatic brain tumors per year in the United States survive long enough (>6 months) to develop radiation-induced brain injury, including cognitive impairment and/or neurological sequelae, significantly impeding the quality of life. These symptoms occur in 50-90% of adult patients after treatment and can be seen without clinical and radiographic evidence of histological changes. Here we established a novel, robust, cell-based 3D brain organoid model that closely mimics the complexity of the human brain microenvironment, and explored the pathophysiologiacl processes and neuroinflammation induced by radiation in the normal brain tissue.

overall_design: Mature iPSC-derived brain organoids were exposed to fractionated irradiation, receiving 2 Gy per day for five consecutive days (total of 5 fractions). Control organoids underwent sham irradiation under identical conditions. Culture medium was refreshed every other day. Organoids were harvested and dissociated for single-cell RNA sequencing at two time points: 72 hours and 2 weeks following the final radiation dose.