title: Pancreatic islet β-cell subtypes are derived from biochemically-distinct and nutritionally-regulated islet progenitors

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: Endocrine islet beta cells comprise heterogenous cell subsets. Yet the origin, stability, and physiological significance of these subsets remain largely unknown. Using combinatorial cell lineage tracing, scRNA-seq, and DNA methylation analysis, we show here that embryonic islet progenitors with differential gene expression and DNA methylation produce stable beta-cell subtypes of different function and viability in adult mice. Differentially expressed genes, including the Myt transcription factors, voltage-gated channels, and Ca2+-sensor synaptotagmins, contribute to the functional differences of these subtypes. Maternal overnutrition, a major diabetes risk factor, reduces the proportion of endocrine progenitors of the better-functionality beta-cell subtype. Intriguingly, the gene signature that defines mouse beta-cell subtypes can reliably divide human cells into two populations, with the proportion of better-functionality beta cells reduced in diabetic donors. These results establish that some beta-cell subtypes are determined via DNA methylation in embryonic islet progenitors, which is regulated by diabetes-causing maternal factors. The implication is that modulating DNA methylation in islet progenitors can be explored to improve beta-cell function in the prevention and therapy of diabetes.

overall_design: Mice with a genotype of Myt1cCre; Ngn3nCre; Ai9 (MNA) will be derived via routine crossing.  This allows the activation of islet progenitors that co-express Ngn3 and Myt1 to be labeled with tdTomato permanently. When MNA mice were at postnatal day 2 (P2) and 2-months, they will be used for islet isolation. Islets were then washed with Ca2+/Mg2+ free HBSS and dissociated into single cells (~3-5 minutes). They were then used for InDrop RNAseq.

first: Monica

middle: E

last: Brown

first: Alan

last: Simmons

first: Yanwen

last: Xu

first: Yilin

last: Yang

first: Guoqiang

last: Gu

first: Ruiying

last: Hu


title: The conserved splicing factor PRP21 regulates abscisic acid response and seed germination in Arabidopsis

status: Public on Apr 21 2025

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

type: Expression profiling by high throughput sequencing

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: Gene-expression profiling of a polyostotic-DLBCL and primary bone-DLBCL cohort compared to a nodal DLBCL GCB.

status: Public on Apr 22 2025

city: Leiden

first: Ruben

last: de Groen

address: Albinusdreef 2

department: Hematology

country: Netherlands

institute: Leiden University Medical Center

summary: This study  performed an in-depth investigation of the immune-molecular profiles of an unique cohort of extranodal diffuse large B-cell lymphoma (DLBCL) of the bone, with single primary bone (PB-)DLBCL and multiple localizations (polyostotic-DLBCL). A similar DLBCL cohort with nodal localizations only and germinal center B-cell (GCB) phenotype (nodal-DLBCL-GCB) was used as comparator. With comprehensive genomic mutational and gene gene-expression profiling (GEP), in total 103 DLBCLS were analyzed.  Both molecular techniques revealed a shared mutational genomic and gene-expression transcriptomic profile for PB-DLBCL (n=51) and polyostotic-DLBCL (n=18), justifying a collective analysis as bone-DLBCL. Differential incidences of EZH2, IRF8, and HIST1H1E, and MYC mutations/rearrangements (p<0.05) confirmed the distinct oncogenic evolution of bone-DLBCL and nodal-DLBCL-GCB (n=34).   Bone-DLBCL primarily exhibited an intermediate/rich immune TME GEP signature (p≤<0.005), based on published gene sets. Further unsupervised clustering identified two distinct groups, establishing a notable ‘immune-rich’ cluster dominated by bone-DLBCL (754%, p=0.0062).  This immune-rich cluster demonstrated superior survival (p=≤0.0263) compared to the ‘immune-low’ cluster, which consisted mostly of nodal-DLBCL-GCB cases (61%). Gene-set enrichment analysis illustrated variations in cell proliferation and immune systemreceptor pathways for the immune-rich cluster (p<0.001), indicating a crucial role for the tumor microenvironment (TME) in disease behavior and outcome. Further supported by deconvolution applications (CIBERSORTx and single-sample gene-set enrichment analysis), The immune-rich cluster highlighted highlighting an abundantmainly  regulatory T cells in immune-rich and cell proliferation in immune-low. infiltrate of NK/T, Treg, TFH and follicular dendritic cells (p<0.001).    Conclusively, PB-DLBCL and polyostotic-DLBCL shared similar TME features and immune-molecular profiles. This study delineates tThe distinct immune-rich TME profile of bone-DLBCL, which  is associated with a superior survival. These findings suggest that bone-DLBCL patients with immune-rich GEP might benefit from less intensive polychemotherapies  and this could further shape targeted immunomodulatory strategies.

overall_design:
The nanoString probeset (BLYM-777) consists out of 797 probes with 13 housekeeping genes. The probes were selected based on several published signatures important for B-cell lymphomas, indicative for survival, or marks different tumor microenvironment. The inclusion of selected signatures is discussed in the following review by de Groot et al. (PMID: 35454765)
In total, 17 polyostotic-DLBCL (multiple osseous localizations), 42 primary bone DLBCL (one osseous localization with or without locoregional lymphodenopathy), and 34 nodal DLBCL with GCB-phenotype were collected for RNA isolation and consecutively analysis with the nanoString nCounter system and the BLYM-777 custom probeset.

first: R

middle: A

first: J

middle: S

last: Vermaat


title: Effect of GRPR activation on gene expression in melanoma cells

city: Orsay

first: Lionel

last: Larue

address: Centre universitaire Bat 101B-110-111-112 Rue Henri Becquerel CS 90030

department: CNRS UMR3347, INSERM  U1021

country: France

institute: Institut Curie

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: CircCDYL association with hnRNPL modulates CDYL isoform switching in Breast Cancer cells

status: Public on Apr 18 2025

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

summary: Circular RNAs (circRNAs) are covalently closed transcripts involved in the regulation of different cellular processes, and their dysregulation has been frequently observed in cancer. In this study, we investigated the role of circCDYL, a circRNA generated from the CDYL gene, in modulating alternative splicing (AS) and isoform switching in breast cancer cells. Analysis of circRNA profiles in breast cancer cells showed that circCDYL expression increased in estrogen receptor alpha (ERα)-downregulated cells, suggesting a potential link between circCDYL-mediated regulation and ERα signaling pathways. RNA-Sequencing analysis following circCDYL knock-down in MCF-7 cells revealed significant alterations in the splicing pattern, with over 2,900 splicing events significantly affected. Through RNA immunoprecipitation and RNA pull-down assays, we found evidence of an association between circCDYL and the splicing factor hnRNPL. To explore the consequences of this association, we performed AS and isoform switching analysis after circCDYL and hnRNPL silencing, revealing significant effects on AS and a weaker modulation of isoform switching events. Furthermore, we observed that circCDYL and hnRNPL modulated CDYL isoform expression, as confirmed by isoform-specific qRT-PCR analysis. Chromatin immunoprecipitation assays also indicated changes in chromatin marks at the CDYL locus upon knock-down of circCDYL and hnRNPL. These results suggested a possible association between circCDYL and hnRNPL, which contributed to the regulation of alternative splicing in breast cancer cells and may be involved in the modulation of isoform expression and chromatin dynamics of CDYL gene.

overall_design: To analyze the role oh hnRNPL and circCDYL in transcriptional and splicing control, we performed total RNA-Seq on MCF-7 cells after circCDYL and hnRNPL siRNA-mediated silencing.

first: Serena

last: Bernardi

first: Giorgia

last: Risso

first: Lorenzo

last: Franchitti

first: Alessandro

last: Camandona

first: Jean-Marie

last: Robbin

first: Isabella

last: Tarulli

first: Lucia

last: Coscujuela

first: Valentina

last: Miano

first: Michele

last: De Bortoli

first: Ymera

last: Pignochino

first: Santina

last: Cutrupi


title: Effect of GRPR activation on gene expression in mouse melanoma cell lines

summary: The consequences of the activation of GRPR on gene expression were assessed by RNA-seq. GRPRpos and GRPRneg mouse melanoma cell lines were treated with GRPR agonist (GRP) or antagonist (RC-3095) for four hours.

overall_design: Comparative gene expression profiling analysis of RNA-seq from mouse melanoma cell lines treated with GRPR ligands/

first: Jérémy

middle: H

last: Raymond

first: Valérie

last: Petit

first: Véronique

last: Delmas


title: Inflammation-induced epigenetic erosion drives stem cell ferroptosis during aging (CUT&Tag)

city: Madiosn

first: Romeo

last: Blanc

state: WI

address: 1111 Highland Ave, WIMR II, 4th floor, Blanc Lab

department: CRB

country: USA

institute: University of Wisconsin-Madison

summary: Aging is a complex process associated with multiple events that lead to the decline in stem cell number and function. However, the relationship between these events and their initiation in biological systems remains ambiguous. Here, we investigate the effects of sustained, low-grade systemic inflammation on muscle stem cells (MuSCs) during aging. We show that the slow rise in inflammation during aging causes long-lasting epigenetic remodeling in MuSCs, leading to premature exit of quiescence followed by rapid ferroptotic cell death. The elevation of circulating cytokines results in erosion of histone H4 lysine 20 methylation, fine-tuning of the MuSC transcriptome for future injury response that resembles the Galert state. Prolonged exposure to inflammatory signals during aging results in the loss of H4K20me1 maintenance by lysine methyltransferase 5a (Kmt5a), leading to a disruption of key transcriptional programs required to preserve MuSC quiescence and survival. Mechanistically, we established that Kmt5a genetic deletion prematurely activates MuSC through Notch signaling. Activated cells cannot cycle properly as they display aberrant iron metabolism and repressed Gpx4, resulting in the accumulation of reactive oxygen species, genomic instability, lipid peroxidation, and ultimately, cell death by ferroptosis. Notably, a lifelong reduction in inflammation restores the MuSC number and function and rejuvenates MuSC iron homeostasis. Our findings demonstrates that chronic systemic inflammatory signals reprogram the MuSC epigenome into a primed state, which drives premature cell cycle re-entry and ferroptosis during aging.

overall_design: Comparative CUT&Tag mapping of H4K20me1 in muscle stem cells derived from 3 adult (4mo) mice and 3 aged (24mo) mice.

first: Patrick

last: Murphy

first: Fanju

last: Meng


title: The “play transcriptome” is sex-specific in the juvenile rat medial amygdala: a role for inhibitory neurons

city: Baltimore

first: Mahashweta

last: Basu

state: MD

address: 670 W. Baltimore Street

institute: Institute for Genome Sciences

summary: Social play is a well-conserved, dynamic behavior known to be sexually differentiated. In most species, males play more than females, a sex difference largely driven by the medial amygdala (MeA) yet the full mechanism establishing this bias is unknown. Here, we explore “the transcriptome of playfulness” in both sexes for the first time, demonstrating that the transcriptomic profile in the juvenile rat MeA associated with playfulness is markedly distinct in males and females. Parallel single-cell RNA-sequencing experiments from newborn rats suggest that inhibitory neurons drive this sex difference. Furthermore, we show that inhibitory neurons comprise the majority of play-active cells in the juvenile MeA, with males having more play-active cells than females, of which a greater proportion are GABAergic. Through integrative bioinformatic analyses, we further explore the expression, function, and cell-type specificity of key play-associated gene modules, providing valuable insight into the sex-biased mechanisms underlying this fundamental social behavior.

overall_design: In this study, we generated single-cell RNA-seq (scRNA-seq) data from the amygdala of 4-day-old male and female rats. Amygdala tissue from 3 animals per sex were pooled into each of two samples (Male_A, Male_B, Female_A, Female_B) submitted for sequencing.

first: Ashley

last: Marquardt

first: Jonathan

middle: W

last: VanRyzin

first: Seth

last: Ament

first: Margaret

middle: M

last: McCarthy


title: Therapeutic Restoration of miR-96 Prevents Hearing Loss in Mice through Modulation of Noise-Induced and Genetic Pathways

city: Yangpu

first: Changgeng

last: Peng

state: Shanghai

address: Siping Road 1239

department: School of Medicine

institute: Tongji University

summary: Hearing loss often arises from impairments in multiple genes, complicating therapeutic development. MicroRNAs, as master regulators, offer promising targets for complex diseases. We explored miR-96’s roles in hair cell (HC) function and noise-induced hearing loss (NIHL), finding that miR-96-/-, not miR-96+/-, mice exhibited progressive hearing loss due to gene regulatory network dysregulation from miR-96 loss in HCs not spiral ganglion neurons (SGNs). Viral-mediated delivery of miR-96 into the inner ear partially rescued hearing of miR-96-/- mice. Tamoxifen-induced depletion of miR-96 in adult UBCCreERT2/+; miR-96fl/fl mice led to hearing loss, with Bach2, Gabra2, Gabra4, Grk1 up-regulation, and Tnn, Col11a1, Gjb3 and Hnf4a down-regulation. Furthermore, noise trauma reduced miR-96, altering Bach2, Bcl2l1, Slc26a9, Gabrb1, Grk1, Nos2 and Cyp1a1 expression, while miR-96 overexpression protected hearing against noise by reversing the expression of Bach2, Bcl2l1 and Cyp1a1. Our findings underscore miR-96’s essential role in adult hearing maintenance and NIHL prevention, presenting it as a promising therapeutic target.

overall_design:
Experiment1: Bulk RNA of inner ear profiling data from 4 P28 wild type, 4  miR-96 knock-out mice.
Experiment2: Bulk RNA of inner ear profiling data from 3 6 months old UBCCreERT2/+, 4  UBCCreERT2/+; miR-96fl/fl mice.

first: Ruilong

last: Xia

first: Chenxi

last: Jin

first: Yong

last: Tao


title: Effect of GRPR activation on gene expression in human melanoma cells

first: Lionel

last: Larue

summary: To investigate the consequences of GRPR activation on the cell signaling, Dauv-1, MDA-MB-435S and 501-Mel GRPR human GRPRpos melanoma cell line were treated with GRPR agonist (GRP) and/or antagonist (RC-3095) and gene expression was analysed after four hours of stimulation in low serum conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  Dauv-1, MDA-MB-435S and 501-Mel GRPR human melanoma cells after stimulation with agonist and antagonist of GRPR.


title: Treehouse compendium of ribosomal-depletion RNA-Seq gene expression data from 2079 tumors

city: Santa Cruz

first: Olena

middle: Morozova

last: Vaske

state: CA

address: 1156 High Street

department: MCD Biology Department

institute: UCSC

summary: We uniformly analyze sequence data to generate a resource for comparative gene expression studies. Specifically, we obtained access to primary RNA sequence data from repositories and clinical partners, consistently processed the data, harmonized metadata, and released the expression values and metadata without access restrictions

overall_design:
The data contains 2079 consistently processed gene expression datasets from 16 studies. TPM values are log transformed (specifically, log2(TPM+1)) and are associated  with Hugo identifiers. Expected counts are not transformed and are associated with Ensemble gene identifiers. Transcript enrichment was performed via ribosomal depletion.
Gene expression in each sample is uniformly quantified using the dockerized TOIL RNA-Seq pipeline versions from 3.2 to 3.4.1 (Vivian et al., 2017); all of these versions produce bitwise identical RSEM gene expression outputs. The pipeline uses RSEM Version 1.2.25 (Li and Dewey, 2011) for quantification after aligning reads with STAR v 2.4.2a (Dobin et al., 2013) using indices generated from the human reference genome GRCh38 and the human gene models GENCODE 23 as described at https://github.com/UCSC-Treehouse/pipelines. Quality is assessed with the MEND pipeline https://github.com/UCSC-Treehouse/mend_qc (Beale et al., 2021).

first: Holly

middle: C

last: Beale

first: Katrina

last: Learned

first: Ellen

middle: T

last: Kephart

first: A

middle: G

last: Lyle

first: Anouk

last: van den Bout

first: Molly

last: McCabe

first: Kathryn

last: Echandia-Monroe

first: Mansi

middle: J

last: Khare

first: Elise

middle: Y

last: Huang

first: Sheha

last: Jariwala

first: Reyna

last: Antilla

first: Allison

last: Cheney

first: Alex

last: Lee

first: Leanne

last: Sayles

first: Stanley

last: Leung

first: Yvonne

last: Vasquez

first: Lauren

last: Sanders

first: David

last: Haussler

first: Sofie

middle: R

last: Salama

first: E

last: Sweet-Cordero


title: Imlunestrant: A next-generation oral SERD overcomes ESR1 mutant resistance in estrogen receptor-positive breast cancer

city: Boston

first: Rinath

last: Jeselsohn

state: MA

address: 450 Brookline Ave.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Estrogen receptor alpha (ER) is a critical driver of tumorigenesis and tumor progression in most breast cancers. Endocrine therapies targeting the ER are the cornerstone treatments in hormone receptor-positive breast cancer. Resistance to these therapies poses a significant clinical challenge and is due to diverse mechanisms. Some of these mechanisms, particularly through estrogen independent activity and the ESR1 mutations, remain dependent on the estrogen axis providing a rationale for the development of next-generation endocrine therapies. This study investigates the preclinical efficacy of imlunestrant, a next-generation oral selective estrogen receptor degrader, in ER-positive breast cancer pre-clinical models, including models harboring the Y537S ESR1 mutation, a prevalent and potent ER activating mutation. Imlunetsrant demonstrated pure antagonistic activity and effective degradation of both wild-type and mutant ER, significantly suppressing cell growth. In vivo, imlunestrant outperformed fulvestrant leading to tumor regression in a patient derived xenograft harboring the Y537S ESR1 mutation. Cyclic multiplexed immunofluorescence and transcriptomic analysis revealed enhanced cell cycle arrest and downregulation of estrogen-responsive genes with imlunestrant treatment. Additionally, a genome wide CRISPR knock-out screen identified several vulnerabilities that were either persistent or gained after imlunestrant treatment, which provides a rational for future studies of combination treatments with imlunestrant. In summary, these results highlight the on target and selective potent activity of imlunestrant, which can circumvent resistance engendered by the Y537S ESR1 mutation and support the clinical development of imlunestrant.

overall_design: Cell lines (MCF7 or T47D) with doxycycline-induclible expression of ER-Y537S were hormone-deprived and treated with or without DMSO, E2, Fulvestrant, or Imlunestrant for 6 or 12 hours. Following treatment cells were processed for mRNAseq.

first: Shira

last: Sherman

first: Zachary

last: Sandusky

first: Douglas

last: Russo


title: Treehouse compendium of polyA selected RNA-Seq gene expression data from 932 cell lines

first: Olena

last: Vaske

overall_design:
The data contains 932 consistently processed gene expression datasets from 9 studies of cancer cell lines. TPM values are log transformed (specifically, log2(TPM+1)) and are associated  with Hugo identifiers. Expected counts are not transformed and are associated with Ensemble gene identifiers. Transcript enrichment was performed via polyA selection.
Gene expression in each sample is uniformly quantified using the dockerized TOIL RNA-Seq pipeline versions from 3.2 to 3.4.1 (Vivian et al., 2017); all of these versions produce bitwise identical RSEM gene expression outputs. The pipeline uses RSEM Version 1.2.25 (Li and Dewey, 2011) for quantification after aligning reads with STAR v 2.4.2a (Dobin et al., 2013) using indices generated from the human reference genome GRCh38 and the human gene models GENCODE 23 as described at https://github.com/UCSC-Treehouse/pipelines. Quality is assessed with the MEND pipeline https://github.com/UCSC-Treehouse/mend_qc (Beale et al., 2021).

first: Holly

last: Beale

first: Katrina

last: Learned

first: Ellen

last: Kephart

first: A

last: Lyle

first: Anouk

last: van den Bout

first: Molly

last: McCabe

first: Kathryn

last: Echandia-Monroe

first: Mansi

last: Khare


title: Treehouse compendium of polyA selected RNA-Seq gene expression data from 13,359 tumors

overall_design:
The data contains 13359 consistently processed gene expression datasets from 42 studies. TPM values are log transformed (specifically, log2(TPM+1)) and are associated  with Hugo identifiers. Expected counts are not transformed and are associated with Ensemble gene identifiers. Transcript enrichment was performed via polyA selection.
Gene expression in each sample is uniformly quantified using the dockerized TOIL RNA-Seq pipeline versions from 3.2 to 3.4.1 (Vivian et al., 2017); all of these versions produce bitwise identical RSEM gene expression outputs. The pipeline uses RSEM Version 1.2.25 (Li and Dewey, 2011) for quantification after aligning reads with STAR v 2.4.2a (Dobin et al., 2013) using indices generated from the human reference genome GRCh38 and the human gene models GENCODE 23 as described at https://github.com/UCSC-Treehouse/pipelines. Quality is assessed with the MEND pipeline https://github.com/UCSC-Treehouse/mend_qc (Beale et al., 2021).

first: Elise

last: Huang

first: Sheha

last: Jariwala

first: Reyna

last: Antilla

first: Allison

last: Cheney

first: Alex

last: Lee

first: Leanne

last: Sayles

first: Stanley

last: Leung

first: Yvonne

last: Vasquez

first: Lauren

last: Sanders


title: Treehouse compendium of polyA selected RNA-Seq gene expression data from 33 PDX

first: Olena

last: Vaske

overall_design:
The data contains 33 consistently processed gene expression datasets from 3 studies. TPM values are log transformed (specifically, log2(TPM+1)) and are associated  with Hugo identifiers. Expected counts are not transformed and are associated with Ensemble gene identifiers. Transcript enrichment was performed via polyA selection.
Gene expression in each sample is uniformly quantified using the dockerized TOIL RNA-Seq pipeline versions from 3.2 to 3.4.1 (Vivian et al., 2017); all of these versions produce bitwise identical RSEM gene expression outputs. The pipeline uses RSEM Version 1.2.25 (Li and Dewey, 2011) for quantification after aligning reads with STAR v 2.4.2a (Dobin et al., 2013) using indices generated from the human reference genome GRCh38 and the human gene models GENCODE 23 as described at https://github.com/UCSC-Treehouse/pipelines. Quality is assessed with the MEND pipeline https://github.com/UCSC-Treehouse/mend_qc (Beale et al., 2021).

first: Holly

last: Beale

first: David

last: Haussler

first: Sofie

last: Salama

first: E

last: Sweet-Cordero


title: DNA demethylating agents represent a therapeutic opportunity for synovial sarcoma

city: Salt Lake City

first: Li

last: Li

state: Utah

address: 201 PRESIDENTS CIRCLE

institute: University of Utah

summary: Synovial sarcoma is an aggressive soft tissue cancer driven by the chimeric SS18::SSX fusion oncoprotein, which disrupts chromatin remodeling by combining two antagonistic transcriptional regulators. SS18 participates in BAF complexes that open chromatin, while the SSX genes are cancer-testis antigens that interface with chromatin decorated with monoubiquitinated histone H2A placed by Polycomb repressive complexes (PRCs) activity. Because KDM2B brings PRC to unmethylated CpG islands, it is plausible that methylation directly determines the distribution of SS18::SSX to target loci. Given that synovial sarcoma is also characterized by a peculiarly low DNA hypomethylation profile, we hypothesized that further disturbance of DNA methylation would have a negative impact on synovial sarcoma growth. DNMT1 disruption by CRISPR/Cas9 targeting or pharmacologic inhibition with cytidine analogs 5-aza-2ʹ-deoxycytidine (decitabine) and 5-azacytidine led to decreased genome-wide methylation, redistribution of SS18::SSX, and altered gene expression profiles, most prominently including upregulation of tumor suppressor genes, immune-related genes, and mesenchymal differentiation-related genes. These drugs suppressed growth of synovial sarcoma cell lines and drove cytoreduction in mouse genetic models. DNMT1 inhibitors, already approved for treating myelodysplastic syndromes, warrant further clinical investigation for synovial sarcoma as repurposed, targeted treatments exploiting a vulnerability in the intrinsic biology of this cancer.

overall_design: Calibrated Chromatin immunoprecipitation DNA-sequencing (cChIP-seq) for KDM2B and SS18-SSX in mouse synovial sarcoma tumors harvested after DAC and 5-AZA in mice.

first: Nobuhiko

last: Hasegawa

first: Nezha

last: Benabdallah

first: Ana

last: Banito

first: Kevin

middle: B

last: Jones


title: DNA demethylating agents represent a therapeutic opportunity for synovial sarcoma [Methylation array]

platform_organism:
Mus musculus
Strix uralensis

overall_design: Analyses of genome-wide methylation arrays to identify epigenetic changes associated with these therapeutic responses.


title: DNA demethylating agents represent a therapeutic opportunity for synovial sarcoma [ChIP-Seq]

overall_design: calibrated Chromatin immunoprecipitation DNA-sequencing (cChIP-seq) for KDM2B and endegeneously tagged HA-SS18-SSX in human synovial sarcoma cells HS-SY-II after 12 days of DMSO or 500nM Decitabine treatment.


title: DNA demethylating agents represent a therapeutic opportunity for synovial sarcoma [RNA-Seq 2]

overall_design: Explore the mechanisms by which decitabine and azacytidine inhibit tumor growth, we evaluated their effects on the transcriptome in HS-SY-II and SYO-1 cell lines. We next evaluated the effects of hypomethylation agents in SS tumors genetically-induced in mice with conditional expression of the SS18::SSX2 fusion gene.RNAseq was performed on tumors harvested after DAC and 5-AZA in mice.


title: Characterization of human healthy i3 lower motor neurons exposed to CSF from ALS patients stratified by UNC13A and C9ORF72 genotype

city: Worcester

first: Alberto

last: Brusati

address: N Lake Ave 55

department: Neurology

institute: UMass Chan Medical School

summary: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease affecting upper and lower motor neurons. Neurodegeneration in ALS might be driven by proteotoxicity or neuroinflammation, which have also been proposed to be promoted by toxic components of the cerebrospinal fluid (CSF). We investigated the possible toxicity of ALS CSF on healthy induced pluripotent stem cells (iPSC)-derived integrated, inducible, and isogenic lower motor neurons (i3LMNs). CSFs were obtained from ALS patients homozygous for the risk UNC13A rs12608932 single nucleotide polymorphism (CC) and for the corresponding major allele (AA), ALS patients with C9ORF72 hexanucleotide repeat expansion, and individuals affected by normal pressure hydrocephalus (NPH), a non-degenerative condition, as controls (ND). Chronic sodium arsenite (ARS) treatment was used as positive control of oxidative stress. We found that 10 % ALS CSF treatment for 48 h was not sufficient to induce significant alterations in viability, autophagic flux, axonal degeneration, DNA damage, and Golgi apparatus integrity in healthy i3LMNs, in contrast to ARS treatment. Only UNC13A CC CSF significantly increased protein aggregation and Golgi apparatus fragments dimension. RNA-sequencing revealed that all ALS and ND CSFs induced expression changes of few genes, while chronic ARS deregulated the expression of thousands of genes, mostly involved in inflammation and synapse biology. In this work, we demonstrated that in our experimental settings only UNC13A CC CSF induced some ALS-associated pathological features in healthy i3LMNs. Further studies will be required to elucidate the mechanistic link between the risk UNC13A genotype and CSF composition and toxicity.

overall_design: RNA-seq profiling of i3 lower motor neurons treated with 10% CSF from UNC13A CC, UNC13 AA or C9ORF72 ALS patients, ND controls or chronic ARS, as well as their untreated counterparts.

first: Valeria

last: Casiraghi

first: Enrico

last: Pellegrini

first: Silvia

last: Peverelli

first: Sabrina

last: Invernizzi

first: Serena

last: Santangelo

first: Claudia

last: Colombrita

first: Federico

last: Verde

first: Nicola

last: Ticozzi

first: Vincenzo

last: Silani

first: Antonia

last: Ratti


title: Topological velocity inference from spatial transcriptomic data

city: Ann Arbor

first: Joshua

last: Welch

state: MI

address: 100 Washtenaw Ave

institute: University of Michigan

summary: Cell fate transition is a spatiotemporal process, however, previous work has largely neglected the spatial dimension. Incorporating space and time into models of cell fate transition would be a key step toward characterizing how interactions among neighboring cells, local niche factors, and cell migration contribute to tissue development. Here, we developed topological velocity inference (TopoVelo), a computational tool to infer spatial and temporal dynamics of cell fate transition from spatial transcriptomic data. We show that TopoVelo significantly improves the accuracy and spatial coherence of inferred cell ordering compared to previous methods. TopoVelo also reveals spatial cell state dependencies of ligand-receptor genes, spatial signatures of mouse neural tubes, and patterns of early differentiation in 3D cell culture.

overall_design: Embryoid bodies (EBs) differentiation was performed using induced pluripotent stem cells (WTC11) using the EB formation media. After 21 days of seeding, EBs were embedded in OCT compound. 10-micron EB sections were placed on 3 mm x 3 mm CurioSeeker (Slide-seq) tiles for processing.

first: Yichen

last: Gu

first: Jialin

last: Liu

first: Kun H.

last: Lee

first: Chen

first: Jaimee

last: Moline

first: Renxiang

last: Guan


title: Charaterization of potential roles and mechanisms of ACBP/DBI in NASH/MASH-dirven HCC mouse models

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

institute: Centre de Recherche des Cordeliers

summary: We demonstrated that ACBP/DBI inhibition impaired hepatocarcinogenesis in NASH/MASH-driven HCC models. To further investigate its potential mechanisms at transcriptional level in NASH/MASH-driven HCC models, we performed Bulk RNA-seq analyses with liver tissues from the following three models, namely, (i) WD/CCl4 with tamoxifen inducible ACBP/DBI knout mice (Dbi-/- mice, Dbi+/+ mice as control) for in total  27 weeks; (ii) WD/CCl4 with KLH/KLH-ACBP immunized mice for in total 34 weeks; and (iii) HFD/DEN with KLH/KLH-ACBP immunized miceI for a total of 36  weeks.

overall_design: (i) WD+CCl4 with Dbi+/+ and Dbi-/- mice, tamoxifen was i.p.injected with a dose of 75 mg/kg/day, for 5 consecutive days. After 3 days, mice received a western diet, high-sugar water (23.1 g/L D-fructose plus 18.9 g/L D-glucose), and weekly i.p. injections of carbon tetrachloride (CCl4) for 26 weeks; (ii)WD/CCl4 with KLH/KLH-ACBP immunized mice, the 5-week old mice were i.p. vaccinated with the mixture of KLH/Montanide or KLH-ACBP/Montanide on days 0 (30 μg), 7 (30 μg), 14 (30 μg), and 21 (10 μg of KLH-ACBP) to induce anti-ACBP autoantibodies, then mice received a western diet, high-sugar water (23.1 g/L D-fructose plus 18.9 g/L D-glucose), and weekly i.p. injections of carbon tetrachloride (CCl4) for 30 weeks; (iii)HFD/DEN with KLH/KLH-ACBP immunized mice, mice (15 dpp) were treated with a single dose of diethylnitrosamin (DEN) dissolved in saline at a dose of 25 mg/kg body weight by i.p. injectionthe, after 2 weeks,  mice started the KLH/KLH-ACBP vaccination plus HFD for 34 weeks. All mice in the above mouse models are male, C57BL/6 background. Four to five samples are incuded in each treatment group.

first: Sijing

last: Li


title: Treehouse compendium of ribosomal-depletion RNA-Seq gene expression data from 43 PDX

first: Olena

last: Vaske

overall_design:
The data contains 43 consistently processed gene expression datasets from 1 study.  TPM values are log transformed (specifically, log2(TPM+1)) and are associated  with Hugo identifiers. Expected counts are not transformed and are associated with Ensemble gene identifiers. Transcript enrichment was performed via ribosomal depletion.
Gene expression in each sample is uniformly quantified using the dockerized TOIL RNA-Seq pipeline versions from 3.2 to 3.4.1 (Vivian et al., 2017); all of these versions produce bitwise identical RSEM gene expression outputs. The pipeline uses RSEM Version 1.2.25 (Li and Dewey, 2011) for quantification after aligning reads with STAR v 2.4.2a (Dobin et al., 2013) using indices generated from the human reference genome GRCh38 and the human gene models GENCODE 23 as described at https://github.com/UCSC-Treehouse/pipelines. Quality is assessed with the MEND pipeline https://github.com/UCSC-Treehouse/mend_qc (Beale et al., 2021).

first: Holly

last: Beale

first: Katrina

last: Learned

first: Ellen

last: Kephart

first: A

last: Lyle

first: Anouk

last: van den Bout

first: Molly

last: McCabe

first: Kathryn

last: Echandia-Monroe

first: Mansi

last: Khare

first: Elise

last: Huang

first: Sheha

last: Jariwala

first: Reyna

last: Antilla

first: Allison

last: Cheney

first: Alex

first: Leanne

last: Sayles

first: Stanley

last: Leung

first: Yvonne

last: Vasquez

first: Lauren

last: Sanders

first: David

last: Haussler

first: Sofie

last: Salama

first: E

last: Sweet-Cordero


title: Near-infrared light-driven metabolic reprogramming of synoviocytes for the treatment of rheumatoid arthritis

status: Public on Apr 17 2025

city: Changchun

first: Hugang

last: Zhang

address: Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun

institute: Jilin University

summary: Rheumatoid arthritis is a common autoimmune disease characterized by chronic synovial inflammation and joint destruction, primarily driven by imbalance cellular metabolism and inflammatory microenvironment. While gene therapy offers a promising therapeutic approach, its effectiveness is limited by the challenges of non-specific gene expression in healthy tissues. In the present study, we developed a gene delivery system (namely APPC), in which near-infrared (NIR)-responsive gold nanorods (AR) were coated with chondroitin sulfate-modified polyethyleneimine (CS-PEI) to facilitate the heat-responsive targeted delivery of heme oxygenase 1 (HO-1) gene. The APPC showed favorable transfection efficiency due to its targeting ability and significantly facilitate the HO-1 expression under NIR irradiation. The combination of APPC/pHO-1 and NIR could effectively reprogram the cellular metabolism and repolarize the macrophages and fibroblast-like synoviocytes (FLSs), thereby inhibiting the inflammation by suppressing the glycolysis. Meanwhile, APPC could specifically enhance the HO-1 expression in inflamed tissues through NIR-mediated the activation of HSP70 promoter, ensuring the precise gene expression via photothermal conversion. In a collagen-induced arthritis (CIA) model, APPC/pHO-1 under NIR irradiation exhibited potent therapeutic efficacy, restoring the articular microenvironmental homeostasis and mitigating the symptoms of RA. These findings highlighted the potential of APPC/pHO-1 nanoparticles in the gene therapy of RA and other inflammatory diseases.

overall_design: RNA-seq profiling of RAW264.7, LPS-stimulated RAW264.7cells and NIR-induced HO-1 expression mediated by the APPC/pHO-1 nanocomplex.

first: Jiaxin

last: Jia

first: Hanyu

last: Liu

first: Haobo

last: Han

first: Quanshun

last: Li


title: Human CLOCK enhances cognitive flexibility by altering cortical excitatory neuron function

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

summary: A BAC containing human CLOCK gene with flanking regulatory region was transferred to mice. The humazied  (HU) mice outperformed wildtype (WT) in a reversal learning task, and hence suggested enhanced cognitive flexibility in HU mice. IHC of frontal cortex suggested that the enhanced cognitive flexibility in HU mice might result from the increased neuronal density, dendritic arborization, and spine density. In order to determine the molecular mechanism, we conducted single-nuclei RNA-seq on frontal cortex from postnatal 7 day (P7) and P56 mice. In the excitatory neuron, genes that upregulated in HU mice were enriched for  dendritic growth (e.g. Tenm2 and Flrt2), spine formation (e.g. Cntn5 and Sorcs2), and energy metabolism (e.g. Suclg1 and Cox8a).

overall_design: P7 and P56 of humanized (CLOCKhum;Clock-/-, HU), knockout (Clock-/-, KO), and wildtype (Clock+/+, WT) mice were harvested rostral part of frontal cortex which is corresponding to the cortex part of Coronal level 22-36 in Allen Brain Atlas: Reference Atlas, Version 2 (2011), and extracted single nuclei for sequencing.

first: Joseph

last: Takahashi

first: Yuxiang

first: Ashwinikumar

last: Kulkarni

first: Miles

last: Fontenot


title: Thymic mimetic cells in various mouse strains

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: We profiled a subset of medullary thymic epithelial cells from three mouse strains by scRNA-seq to investigate the composition of the mimetic cell compartment.

overall_design: scRNA-seq of mouse thymic mimetic cells from C57BL/6, BALB/c, and NOD mice (cells from two mice of each strain)

first: Chong

last: Zuo

first: Brooke

last: Huisman

first: Diane

last: Mathis


title: Measles oncolytic virus as an immunotherapy for recurrent/refractory pediatric medulloblastoma and atypical teratoid rhabdoid tumor: results from PNOC005

city: San Francisco

first: Aaron

last: Diaz

institute: UCSF

summary: Pediatric recurrent medulloblastoma (MB) and atypical teratoid rhabdoid tumor (ATRT) are largely incurable and warrant novel therapies. We investigated a) the safety of a measles virus variant, MV-NIS, in a pediatric phase 1 study and b) the mechanisms of MV-NIS and potential benefit of combination with immune checkpoint inhibition (ICI). Pediatric patients with recurrent MB or ATRT were treated with intratumoral injections for local recurrence or via lumbar puncture for disseminated recurrence. We evaluated local immune responses to MV-NIS with and without ICI via single-cell and bulk RNA sequencing in an intracranial, immunocompetent, syngeneic murine model. MV-NIS given intratumorally or via repeat intrathecal dosing was safe. MV-NIS prolonged survival in murine models but did not demonstrate additive benefit with ICI. No changes in tumor-infiltrating immune-cell composition or activation were observed in response to MV-NIS treatment; however, MV-NIS induced local expression of neutralizing antibodies, complement cascade, and phagocytosis-related genes.

overall_design:
Single-cell and bulk RNA sequencing were performed to characterize tumor and immune responses to oncolytic measles virus (MV-NIS) therapy in medulloblastoma (MB) and atypical teratoid rhabdoid tumor (ATRT). Single-cell RNA sequencing was used to profile tumor-infiltrating cells from MB PDX tumors derived from CSCG, treated with MV-NIS alone or in combination with anti-PD1. Bulk RNA sequencing was performed on PDX tumors across treatment conditions, including PBS control, heat-inactivated control, mid-treatment, and resistance. In parallel, bulk RNA sequencing was conducted on whole blood and PBMCs from pediatric patients enrolled in the PNOC005 clinical trial, across different MV-NIS treatment regimens.

***************************************************************
Due to the human privacy concern we have submitted the raw fastq files to  European Genome-phenome Archive (EGA), that can be access through this EGAS50000000811.
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first: Bohyeon

last: Yu


title: SHROOM3 Deficiency aggravates Adriamycin-induced nephropathy accompanied by Focal Adhesion disassembly and stress fiber disorganization

city: Shanghai

first: Li-nan

last: Xu

address: No.399, Wanyuan Load, Minhang district, Shanghai.

institute: Children's Hospital of Fudan University

summary: This RNA-sequencing study investigates the role of SHROOM3 in podocyte function and its contribution to renal pathophysiology. Podocytes are highly specialized epithelial cells critical for glomerular filtration barrier integrity. The study explores how SHROOM3 deficiency affects podocyte cytoskeletal architecture and focal adhesion dynamics in the context of Adriamycin-induced nephropathy, a widely used experimental model of podocyte injury and proteinuric kidney disease.  We performed transcriptome analysis using RNA-sequencing on human podocyte cell lines, comparing Control (n=4) and SHROOM3 knockdown (KD) podocytes (n=4). Our objective was to identify the molecular mechanisms and signaling pathways through which SHROOM3 regulates podocyte cytoskeletal organization, with particular focus on stress fiber formation and focal adhesion assembly/disassembly. The dataset provides comprehensive gene expression profiles revealing how SHROOM3 deficiency exacerbates podocyte injury, disrupts actin cytoskeleton dynamics, and impairs focal adhesion stability during nephropathy progression.

overall_design: This RNA-seq dataset includes samples from cultured human podocyte cell lines under two experimental conditions: Control podocytes (n=4) and SHROOM3 knockdown (KD) podocytes (n=4). The study investigates the transcriptomic changes associated with SHROOM3 deficiency in human podocytes to understand its role in podocyte cytoskeletal organization and focal adhesion dynamics.  Each biological replicate (n=4 per condition) represents an independent culture of immortalized human podocytes either expressing normal levels of SHROOM3 (Control) or with stable knockdown of SHROOM3 expression (SHROOM3 KD). All samples were cultured under identical conditions and harvested at the same level of confluence to minimize technical variation. Total RNA was extracted from each sample and subjected to RNA sequencing to compare gene expression profiles between the two groups.


title: T-cell dysfunction during blinatumomab therapy in pediatric acute lymphoblastic leukemia

city: Duarte

first: chintan

last: parekh

state: California

address: 1500 east duarte

department: Pediatrics

institute: Children's Hospital Los Angeles

summary: Despite the high response rate to the T-cell engager blinatumomab in B-cell acute lymphoblastic leukemia (B-ALL), maintaining persistent efficacy is a challenge. Limited data from adults with relapsed B-ALL and high disease burden suggest T-cell dysfunction with continuous blinatumomab treatment contributes to loss of response; T-cell function in patients with low disease burden or pediatric B-ALL are uncharacterized. Given the recent adoption of blinatumomab in frontline post-remission pediatric B-ALL therapy and the existence of age and leukemia burden-related immune differences, a comprehensive assessment of T-cells is needed to inform optimal continuous treatment duration. Hence, we assessed T-cell function and phenotype during a 28-day continuous intravenous blinatumomab cycle in a pediatric leukemia cohort of 11 patients aged 1-21 years; 8 received blinatumomab in minimal residual disease-negative first remission. By day 14, T-cells exhibited impairments in cytotoxicity (baseline, day 14, day 28 = 72%, 56%, 54%; p = 0.008), IFN-γ production (p = 0.0004), and T-cell receptor (TCR) signaling (mTOR and MEK) that persisted through day 28. The frequency of stem cell memory T-cells declined (p = 0.0004) while those of terminally differentiated (p = 0.012) and TIM3+ (p < 0.0001) cells were elevated at day 14. T-cells at day 14 were marked by exhaustion and terminal differentiation transcriptional signatures; genes encoding inhibitory receptors and negative regulators of TCR signaling were upregulated. Overall, multimodal T-cell dysfunction occurs by day 14. These findings could inform studies to optimize cycle duration and reveal candidate targets for functional studies aimed at ameliorating T-cell dysfunction.

overall_design: RNA-Seq profiling of T-cells prior to and on days 14 and 28 days of continuous intravenous blinatumomab

first: Julie

last: Ma

first: Annie

last: Luong

first: Andrew

last: Doan

first: Tsen-Yin

last: Lin

first: Lingyun

last: Ji

first: Cassandra

last: Wang

first: Seon-Jae

last: Yoon

first: Teresa

last: Rushing

first: Anh

last: Duong

first: Miguel

last: Villa

first: Chintan

last: Parekh


title: A multimorphic variant in ThPOK causes a novel human disease characterized by T cell abnormalities, immunodysregulation, allergy, and fibrosis

city: Toronto

first: Arttu

last: Jolma

state: Ontario

address: 160 College Street, Room 1350

department: Donnelly Centre

country: Canada

institute: University of Toronto

summary: The role of the transcription factor ThPOK, encoded by ZBTB7B, has not been formally established in humans since individuals with ThPOK deficiency or dysfunction have not yet been identified. We report the first case of a human with a damaging variant in ThPOK causing a syndrome encompassing CD4 T cell deficiency, allergic disease, severe fibrotic interstitial lung disease, global developmental delay, and growth failure. Trio whole-genome sequencing revealed a de novo variant (NM_001256455.2:c.1080A>C, p.K360N) in ZBTB7B. Despite normal expression, ThPOKK360N exhibited dysfunctional multimorphic activity. It demonstrated dominant-negative effects by hindering the capacity of ThPOKWT to regulate target gene expression (antimorph). Protein-DNA interaction assays showed inability of  ThPOKK360N to bind to WT consensus sequences (amorph) and revealed a novel DNA-binding specificity (neomorph). Single-cell sequencing confirmed the patient's CD4 T cell deficiency, revealing that most T cells were less mature compared to healthy controls. Furthermore, naive CD4 and CD8 T cells showed diminished activation after stimulation. The link between ThPOKK360N and the patient’s symptoms was confirmed through lentiviral transduction experiments in healthy T cells and pulmonary fibroblasts. While T cells expressing ThPOKWT upregulated genes involved in activation, proliferation, and interferon responses, those with ThPOKK360N did not. When overexpressed in fibroblasts, ThPOKK360N significantly increased expression of pro-fibrotic genes implicated in pulmonary fibrosis. This description of a novel human disease caused by a multimorphic variant in ThPOK confirms its role in CD4 T cell development in an intact human context, while also revealing an unanticipated role for ThPOK in T cell function and fibrosis.

overall_design: Stable cell lines for each TF was established via Flp recombination of EGFP-tagged TF plasmid in HEK293 Flp-In-TRex. Cells were treated with doxycyclin and after 24 hours, ChIP is performed using anti-GFP antibody.

first: Maryam

last: Vaseghi-Shanjani

first: Mehul

last: Sharma

first: Pariya

last: Yousefi

first: Simran

last: Samra

first: Kaitlin

middle: U

last: Laverty

first: Rozita

last: Razavi

first: Ally

last: Yang

first: Mihai

last: Albu

first: Liam

last: Golding

first: Anna

middle: F

last: Lee

first: Ryan

last: Tan

first: Phillip

last: Richmond

first: Marita

last: Bosticardo

first: Jonathan

last: Rayment

first: Connie

middle: L

first: Kyla

last: Hildebrand

first: Rae

last: Brager

first: Michelle

middle: K

last: Demos

first: Yu

last: Lau

first: Luigi

middle: D

last: Notarangelo

first: Timothy

last: Hughes

first: Rémy

last: Bosselut

first: Catherine

last: Biggs

first: Stuart

last: Turvey


title: Molecular signatures define BAP1-altered meningioma as a distinct CNS tumor with deregulation of Polycomb repressive complex target genes

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

summary:
Background: Meningiomas are the most common primary intracranial neoplasms, with highly variable patient outcomes. While most meningiomas are benign, a significant subset recurs postoperatively, presenting substantial treatment challenges. BAP1 gene inactivation has been suggested as a marker for aggressive meningiomas, although its precise molecular and clinical roles remain poorly understood.

Methods: To comprehensively investigate BAP1-altered meningiomas, we used six meningiomas with known BAP1 alterations as a discovery set. Genome-wide DNA methylation profiling of these samples, along 11,151 reference meningiomas, identified a distinct molecular cluster (n = 42) using unsupervised visualization approaches. These tumors were further characterized by DNA/RNA sequencing, histopathological examination, and a retrospective review of clinical data, compared to reference meningioma cohorts, providing a thorough characterization of this rare tumor subtype.

Results: Our integrative analysis revealed BAP1-altered meningiomas as a distinct CNS tumor subtype, characterized by recurrent loss of chromosome 3p21 and driven by various BAP1-inactivating alterations. Although rhabdoid morphology is present in some cases, it is not exclusive and should not be used as a grading criterion. Progression-free survival analysis showed a median of 21 months (95% CI: 12-NA), with a 2-year overall survival rate of 79% (95% CI: 60%-100%), highlighting the aggressive nature of these tumors. Gene expression profiling revealed upregulation of PRC target genes, dysregulated Polycomb signaling, and elevated expression in several cellular and growth factor pathways.

Conclusions: BAP1-altered meningiomas represent a distinct and aggressive CNS tumor subtype associated with PRC dysregulation and recurrent 3p chromosome loss. These findings support the designation "meningioma, BAP1-altered."

overall_design: Bisulphite converted DNA from the 42 samples were hybridised to the Illumina EPIC array

first: Philipp

last: Sievers

first: Felix

last: Sahm


title: mRNA expression profiling analysis in  AGS cells after RBM8A knockdown [RNA-Seq]

city: Xi'an

first: Hang

last: Peng

address: No. 256 Youyi West Road

institute: Shaanxi Provincial People’s Hospital

summary: In this study, we aimed to investigate the impact of RBM8A knockdown on mRNA expression in gastric cnacer cells. We used RNAi technology to specifically knock down RBM8A expression in AGS cells, establishing two experimental groups: siNC and siRBM8A. Each group had three biological replicates. Subsequently, mRNA-seq was performed to comprehensively analyze the mRNA expression profiles of the cells after RBM8A knockdown. Our results may provide insights into the biological functions of RBM8A in gastric cancer and potential therapeutic targets.

overall_design: AGS cells were transfected with siNC or siRBM8A, respectively. Then total RNA was extracted, with three replicates of each group of samples. mRNA expression profiles of the experimental (siRBM8A) and control (siNC) groups were subsequently detected using mRNA-seq, and differentially expressed genes between the two groups were analysed using bioinformatics methods.

first: Chen

last: Huang

first: Jianhua

last: Wang


title: Single Nuclear RNAseq and MultiOme of IPF and Control Lung Tissue

city: New Haven

first: Naftali

last: Kaminski

state: CT

address: 300 Cedar Street

department: PCCSM

institute: Yale School of Medicine

summary: Differentially affected regions of Idiopathic Pulmonary Fibrosis (IPF) lungs were assessed for changes in cell composition, gene expression and chromatin accessibility.

overall_design: Frozen tissue cores from IPF lungs following transplant and unused donor control lungs were analyzed by microCT as previously described (PMID:22029978, PMID:31600171). Nuclei were isolated from frozen tissue and profiled with either snRNAseq or assays of paired snRNAseq and snATACseq data.

first: Taylor

last: Adams

first: Jonas

last: Schupp


title: Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila [Hi-C]

city: Montpellier

first: Bernd

last: Schuettengruber

address: 141, rue de la cardonille

institute: Institute de Génétique Humaine

summary: The tight correlation between topologically associating domains (TADs) and epigenetic domains in Drosophila suggests that the epigenome contributes to define TADs. However, it is still unknown whether histone modifications are essential for TAD formation and structure. By either deleting or shifting key regulatory elements needed to establish the epigenetic signature of Polycomb TADs, we show that the epigenome is not a major driving force for the establishment of TADs. On the other hand, physical domains have an important impact on the formation of epigenetic domains, as they can restrict spreading of repressive histone marks and looping between cis-regulatory elements.

overall_design: Hi-C experiments of wild type imaginal leg discs or imaginal leg discs carrying PRE deletions or insertion

first: Sandrine

last: Denaud

first: Gonzalo

last: Sabaris

first: Marco

last: Di Stefano

first: Giorgio-Lucio

last: Papadopoulos

first: Giacomo

last: Cavalli


title: Understanding TAK1 deficiency in microglia: Dual mechanisms for photoreceptor protection in a mouse model of retinitis pigmentosa

city: Hong Kong

first: Jing

last: Zhang

address: 11 Yuk Choi Rd, The Hong Kong Polytechnic University, Hung Hom, Hong Kong.

country: Hong Kong

institute: The Hong Kong Polytechnic University

summary: Retinitis pigmentosa (RP) is a group of inherited retinal disease characterized by the progressive loss of photoreceptors. Neuroinflammation has been implicated in the pathophysiology of RP and its progression. Previous studies have suggested that the transforming growth factor-beta-activated kinase 1 (TAK1) plays a pivotal role in regulating acute and chronic neuroinflammation. However, the functional role of TAK1 in neuroinflammation remains unclear in RP. Here, we observed TAK1 upregulation in activated microglia of the rd10 mouse model of RP. To create the conditional deletion of TAK1 in microglia, we backcrossed Cx3cr1CreER/CreER mice and Tak1fl/fl mice onto rd10 background. We found that both heterozygous (rd10;Cx3cr1CreER/+;Tak1fl/+) and homozygous (rd10;Cx3cr1CreER/+;Tak1fl/fl) deletion of microglial TAK1 slowed down photoreceptor degeneration but with distinct mechanisms. The heterozygous TAK1 deficiency resulted in a reduction in the activation and proliferation of microglia and the release of proinflammatory cytokines by inhibiting STAT3 signaling. In contrast, the homozygous TAK1 deficiency induced apoptosis in microglia via the TNF/RIPK1/CASP3 signaling pathway, contributing to the reduction of microglia-mediated neurotoxicity and subsequent preservation of photoreceptors in RP. Overall, our findings highlight the crucial role of TAK1 in the survival and activation of microglia. We propose that targeting microglial TAK1, considering its expression levels and subsequent signal transduction, could offer a promising personalized therapeutic strategy for individuals with RP regardless of underlying genetic causes.

overall_design: RNA-seq profiling of sorted microglia from 2-month-old TAK1 knockout and control mice

first: Bin

last: Lin


title: Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila [Cut&Run]

overall_design: Cut&Run experiments of wild type imaginal leg discs or imaginal leg discs carrying PRE deletion or insertions


title: Detection RNA targets interacting with RBM8A in AGS cells

summary: RBM8A is an RNA-binding protein. To identify RNAs interacting with RBM8A, we employed RNA immunoprecipitation (RIP) to enrich associated RNAs, followed by high-throughput sequencing and bioinformatics approaches to characterize the RBM8A-bound RNA profile.

overall_design: Comparative gene profiles analysis of RIP-seq data for anti-RBM8A antibody-enriched RNA and control input RNA in AGS cells.


title: DNA demethylating agents represent a therapeutic opportunity for synovial sarcoma [RNA-Seq]

first: Li

last: Li

summary: Synovial sarcoma is an aggressive soft tissue cancer driven by the chimeric SS18::SSX fusion oncoprotein, which disrupts chromatin remodeling by combining two antagonistic transcriptional regulators. SS18 participates in BAF complexes that open chromatin, while the SSX genes are cancer-testis antigens that interface with chromatin decorated with monoubiquitinated histone H2A placed by Polycomb repressive complexes (PRCs) activity. Because KDM2B brings PRC to unmethylated CpG islands, it is plausible that methylation directly determines the distribution of SS18::SSX to target loci. Given that synovial sarcoma is also characterized by a peculiarly low DNA hypomethylation profile, we hypothesized that further disturbance of DNA methylation would have a negative impact on synovial sarcoma growth. DNMT1 disruption by CRISPR/Cas9 targeting or pharmacologic inhibition with cytidine analogs 5-aza-2ʹ-deoxycytidine (decitabine) and 5-azacytidine led to decreased genome-wide methylation, redistribution of SS18::SSX, and altered gene expression profiles, most prominently including upregulation of tumor suppressor genes, immune-related genes, and mesenchymal differentiation-related genes. These drugs suppressed growth of synovial sarcoma cell lines and drove cytoreduction in mouse genetic models. DNMT1 inhibitors, already approved for treating myelodysplastic syndromes, warrant further clinical investigation for synovial sarcoma as repurposed, targeted treatments exploiting a vulnerability in the intrinsic biology of this cancer.

overall_design: For high throughput RNA sequencing, total RNA from two independent experiments was extracted using a RNeasy mini kit (Qiagen). Cells transduced with the indicated sgRNAs or treated with DAC were collected 12 days post-infection. RNA-Seq library preparation and sequencing were performed at the High Throughput Sequencing Unit of the Genomics & Proteomics core facility of DKFZ using TruSeq Stranded Total RNA Library Prep kit (Illumina) and HiSeq 2000 v4 single-read 50bp sequencing system.

first: Nobuhiko

last: Hasegawa

first: Nezha

middle: S

last: Benabdallah

first: Ana

last: Banito

first: Kevin

last: Jones


title: Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila [RNA-seq]

overall_design: RNA-seq experiments of wild type imaginal leg discs or imaginal leg discs carrying PRE deletion


title: A non-syndromic orofacial cleft risk locus links tRNA splicing defects to neural crest cell pathologies [Ribo-seq]

city: Cambridge

first: Michaela

last: Bartusel

state: Massachusetts

address: 31 Ames St

institute: Massachusetts Institute of Technology

summary: Orofacial clefts are the most common form of congenital craniofacial malformations worldwide. The etiology of these birth defects is multifactorial, involving genetic and environmental factors. In most cases, however, the underlying causes remain unexplained, precluding molecular understanding of disease mechanisms. Here, we integrated genome-wide association data, targeted re-sequencing of case and control cohorts, cell type-specific epigenomic profiling, and genome architecture analyses, to functionally and molecularly dissect a genomic locus associated with an increased risk of non-syndromic orofacial cleft. We found that common and rare risk variants associated with orofacial cleft intersect with a conserved enhancer (e2p24.2) that becomes activated in cranial neural crest cells—the embryonic cell type responsible for sculpting the craniofacial complex. We mapped e2p24.2 long-range interactions to a topologically associated domain harboring MYCN and DDX1 and demonstrated that both MYCN and DDX1 are required for craniofacial development in chicken embryos. We found that e2p24.2 regulates the expression of MYCN, but not DDX1, in cranial neural crest cells. In turn, DDX1 is a target of the MYC family of transcription factors and a component of the tRNA splicing complex. The loss of DDX1 in cranial neural crest cells resulted in the accumulation of unspliced tRNA fragments, depletion of the mature pool of intron-containing tRNAs, and ribosome stalling at codons decoded by these tRNAs. These effects were accompanied by defects in both global protein synthesis and cranial neural crest cell migration. We further showed that the induction of tRNA fragments is sufficient to disrupt craniofacial development. Together, these results uncovered a molecular mechanism in which impaired tRNA splicing affects neural crest and craniofacial development and positioned MYCN, DDX1, and tRNA processing defects as risk factors in the pathogenesis of orofacial clefts.

overall_design: Ribosome profiling was performed as described (McGlincy and Ingolia, 2017) with minor modifications. cNCCs derived from three separate differentiations of DDX1-/-::TetON-HA-DDX1 hiPSCs were grown for 5 days with (DDX1-ON) or without (DDX1-OFF) DOX to ~80% confluency on 10 cm dishes, rapidly washed twice with ice-cold PBS supplemented with 100 μg/mL cycloheximide and lysed on-plate in 500 μL ice-cold Polysome Lysis Buffer (20mM HEPES pH 7.3, 100mM KCl, 5mM MgCl, 1% TritonX-100, 2 mM DTT, 100 μg/mL cycloheximide). Lysate was passed through a 26 gauge needle 10 times and clarified by centrifugation for 5 minutes at 1,300 x g, 4°C, and the supernatant was further clarified by centrifugation for 5 minutes at 20,000 x g, 4°C. Samples were normalized to the same concentration, as measured by NanoDrop Spectrophotometer, and treated with 350 U Ambion RNAseI (Invitrogen) per O.D. of absorbance at 260 nM per mL for 16 hours at 4°C. Samples were loaded on cold 10-50% sucrose gradients generated by layering 6 mL of 10% sucrose gradient buffer (20 mM HEPES pH 7.3, 100 mM KCl, 5 mM MgCl, 1 mM DTT, 100 μg/mL cycloheximide, 10% sucrose w/v) on 6 mL of 50% sucrose gradient buffer (20 mM HEPES pH 7.3, 100 mM KCl, 5 mM MgCl, 1 mM DTT, 100 μg/mL cycloheximide, 50% sucrose w/v) and mixed using a BioComp Gradient Station (BioComp, New Brunswick, Canada). Sample-loaded gradients were spun at 210,000 x g for 2.5 hours at 4°C using a SW-41 swinging-bucket rotor (Beckman Coulter) and Optima XPN Ultracentrifuge (Beckman Coulter). These gradients were fractionated on a BioComp Gradient Station and the monosome peaks were collected. RNA was extracted from the collected monosome peaks using Trizol LS (Invitrogen) and purified using a Direct-zol RNA Miniprep kit (Zymo Research). Fragments between 17-34 nt long were isolated and libraries were prepared from them as described in McGlincy and Ingolia, 2017, except with a depletion of rRNA immediately before reverse transcription using a mixture of rRNA-complementary biotinylated oligos (http://bartellab.wi.mit.edu/protocols.html). Reads were processed for downstream analysis as follows: Basic read quality control was performed using FastQC (Babraham Bioinformatics). Illumina libraries were demultiplexed, adapter sequences were trimmed using fastp (Chen, 2023). Libraries were demultiplexed by using UMI-tools to assign correctable barcodes to reads, and split into samples using SeqKit2 (Shen et al., n.d.; Smith et al., 2017). Reads aligning to rRNA were identified with BowTie and removed (Langmead et al., 2009). The remaining reads were aligned to the genome using human reference assembly (GRCh38.p13) with STAR (Dobin et al., 2013). STAR was run using the following relevant parameters: --outFilterType BySJout --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 --outFilterMatchNmin 16 --alignEndsType EndToEnd. Aligned reads were then deduplicated using the 7 nt unique molecular identifier with UMI-tools (Smith et al., 2017). Read lengths and their phasing were quantified on maximal spanning windows generated using plastid (Dunn and Weissman, 2016). Differential analysis was performed by counting the ribosome profiling reads aligned to the CDS of each gene with featureCounts (Liao et al., 2014). Differential expression analysis was performed on counts using DESeq2 (Love et al., 2014), excluding genes with fewer than one read in all samples. The DESeq2 results can be found in Supplementary Table 1. Principal component analysis was performed on regularized log-transformed count data using the rlog() and prcomp() functions in R (R Core Team, 2021). Codon analysis was performed as described previously with minor modifications (Darnell et al., 2018). Aligned reads were trimmed by 12 nt from both ends, and read coverage was calculated across each 300 nt window centered at each in-frame codon of all annotated CDSs in the transcriptome, excluding the first and last 150 nt of each CDS and those with less than 0.33 reads per nt. Read coverage at each position in each codon window was normalized to the mean coverage of their CDS of origin, and these ribosome densities at every position were averaged across all instances for each codon. These positional means were additionally normalized to the total summed ribosome density for each sample before subtracting densities of DDX1OFF samples from DDX1ON samples for each replicate to generate Δ ribosome densities.

first: Skylar

middle: X

last: Kim

first: Alicia

last: Darnell

first: Alvaro

last: Rada-Iglesias

first: Eliezer

last: Calo


first: Aaron

last: Diaz

first: Bohyeon

last: Yu


title: A non-syndromic orofacial cleft risk locus links tRNA splicing defects to neural crest cell pathologies [4C-seq]

summary: Orofacial clefts are the most common form of congenital craniofacial malformations worldwide. The etiology of these birth defects is multifactorial, involving genetic and environmental factors. In most cases, however, the underlying causes remain unexplained, precluding molecular understanding of disease mechanisms. Here, we integrated genome-wide association data, targeted re-sequencing of case and control cohorts, cell type-specific epigenomic profiling, and genome architecture analyses, to functionally and molecularly dissect a genomic locus associated with an increased risk of non-syndromic orofacial cleft. We found that common and rare risk variants associated with orofacial cleft intersect with a conserved enhancer (e2p24.2) that becomes activated in cranial neural crest cells—the embryonic cell type responsible for sculpting the craniofacial complex. We mapped e2p24.2 long-range interactions to a topologically associated domain harboring MYCN and DDX1 and demonstrated that both MYCN and DDX1 are required for craniofacial development in chicken embryos. Molecularly, we found that e2p24.2 regulates the expression of MYCN, but not DDX1, in cranial neural crest cells. In turn, DDX1 is a target of the MYC family of transcription factors and a component of the tRNA splicing complex. The loss of DDX1 in cranial neural crest cells resulted in the accumulation of unspliced tRNA fragments, and impaired both global protein synthesis and cranial neural crest cell migration. We further showed that the induction of tRNA fragments is sufficient to disrupt craniofacial development. Together, these results uncovered a molecular mechanism in which impaired tRNA splicing, and the concomitant accumulation of tRNA fragments, affect neural crest and craniofacial development and positioned MYCN, DDX1, and tRNA processing defects as risk factors in the pathogenesis of orofacial clefts.

sample_organism:
Gallus gallus
Homo sapiens

platform_organism:
Gallus gallus
Homo sapiens

overall_design: Circular Chromatin Conformation Capture (4C) was performed as previously described (Laugsch et al., 2019), based on a published protocol (Stadhouders et al., 2013) with minor modifications. 2-3x107 neural crest cells or 25 frontonasal prominences of stage HH24 chicken embryos were crosslinked with 1% formaldehyde. NlaIII (NEB, R0125) was used as the first restriction enzyme, DpnII (NEB, R0543) as the second restriction enzyme. The resulting 4C DNA was amplified by inverse PCR with the expand long template PCR system (11681842001, Roche) using 32 amplification cycles and primers designed as previously described (Stadhouders et al., 2013) (see Supplemental Table 1) Illumina adaptors P5 and P7 were added to the primers close to the NlaIII and the DpnII restriction site, respectively, with barcodes for multiplex sequencing. 4C-seq libraries were sequenced on the HiSeq2500 platform, generating reads of either 74 or 100 bp in length. As described in Laugsch et al. (2019), 4C-seq reads were assigned to samples based on the first 10 bases of the read. Then, the primer sequences were removed from the reads and the remaining sequence was trimmed to 36 bp. These 36 bases were then aligned to the human (hg19) or the chicken (galGal4) reference genome using Bowtie (Langmead et al., 2009). Finally, the resulting reads were analyzed with R3C-seq  to generate RPM-normalized bedgraph files for downstream visualization and analysis (Thongjuea et al., 2013).

first: Petros

last: Kolovos

first: Wilfred

last: van IJcken


title: Tripartite phosphorylation of SPT5 by CDK9 times pause release and tunes elongation rate of RNA polymerase II (RNA-Seq)

city: NYC

first: Rui

last: Sun

state: New York

address: 1425 Madison

institute: Icahn school of medicine at Mount Sinai

summary: The RNA polymerase II (RNAPII) transcription cycle is regulated throughout its duration by protein phosphorylation. Previously, two regions phosphorylated by cyclin-dependent kinase 9 (CDK9) in elongation factor SPT5—the linker between Kyrpides-Ouzounis-Woese (KOW) x-4 and 5 domains and carboxy-terminal repeat (CTR) 1—were implicated in promoter-proximal pausing and termination, respectively. Here, we show that phosphorylations in the linker, CTR1, and a third region, CTR2, coordinately control pause release, elongation speed, and termination in HCT116 human colon cancer cells. Pausing was unaffected or increased by mutations preventing CTR1 or CTR2 phosphorylation, respectively, but attenuated when both CTRs were mutated. Whereas loss of CTR1 phosphorylation slowed elongation and repressed nascent transcription, simultaneous CTR2 mutation partially reversed both effects. Nevertheless, mutating both CTRs had additive effects on splicing, termination, steady-state mRNA levels, and cell proliferation. Therefore, tripartite SPT5 phosphorylation times pause release and tunes RNAPII elongation rate to ensure productive transcription and cell viability.

overall_design: We hypothesized that effects of SUPT5H mutations on cell proliferation would be reflected in steady-state mRNA levels, which we analyzed by RNA sequencing (RNA-seq).

first: Robert

last: Fisher


title: Cloche is a pro-regenerative platelet factor during zebrafish heart regeneration

city: Beijing

first: Yabing

last: Song

state: Beijing

address: Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

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

overall_design: Refer to individual Series


title: A non-syndromic orofacial cleft risk locus links tRNA splicing defects to neural crest cell pathologies [RNA-seq]

overall_design: Bulk-RNA-sequencing experiments were performed in triplicates for DDX1 KO cNCCs cultured with 0.4 ng/mL DOX (DDX1 ON) and without DOX for 4 days (DDX1 OFF). cDNA libraries were prepared using the RNA sample preparation kit (TruSeq v2; Ilumina) as previously described (Respuela et al., 2016) and sequenced with a 2x 100-bp strand-specific protocol on a HiSeq 2500 sequencer (Illumina).  Basic read quality control was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools. Reads (61-73 million per sample) were mapped to the human reference assembly (GRCh38.p13) using STAR Aligner (Dobin et al., 2013). Aligned reads were sorted with featureCounts (Liao et al., 2014), specifying for paired end reads. Differential expression analysis was performed using DESeq2 (Love et al., 2014), excluding low-count transcripts (<5).

first: Jade

last: Varineau


title: Dietary restriction mitigates vascular aging, modulates the cGAS-STING pathway and reverses macrophage-like VSMC phenotypes in progeroid DNA-repair-deficient Ercc1Δ/- mice

status: Public on Apr 16 2025

city: Rotterdam

first: Sanne

last: Stefens

address: Dr. Molewaterplein 40

department: Molecular Genetics

institute: Erasmus MC

summary: Aging is a major risk factor for cardiovascular diseases and the accumulation of DNA damage significantly contributes to the aging process. This study aimed to identify the underlying molecular mechanisms of vascular aging in DNA-repair-deficient progeroid Ercc1Δ/- mice and to explore the therapeutic effect of dietary restriction (DR). RNA sequencing analysis revealed that DR reversed gene expression of vascular aging processes including extracellular matrix remodeling in the Ercc1Δ/- aorta. Notably, this analysis indicated the presence of macrophage-like vascular smooth muscle cells (VSMCs) and suggested cGAS-STING pathway activation. The presence of macrophage-like VSMCs and increased STING1 expression were confirmed in Ercc1Δ/- aortic tissue and were both reduced by DR. In vitro, cisplatin-induced DNA damage activated the cGAS-STING pathway in Ercc1Δ/- VSMCs but not in wildtype VSMCs. These findings identify involvement of the cGAS-STING pathway in DNA damage driven vascular aging and underscore the therapeutic benefits of DR for vascular aging. Furthermore, upstream regulator analysis revealed compounds that may replicate the beneficial effects of DR, providing promising leads for further investigation.

overall_design: To investigate the underlying molecular mechanism of vascular aging and the effect of dietary restriction, we performed RNA sequencing on the aortic arch of Ercc1Δ/- mice and wildtype littermates at 6 weeks of age (ad libitum diet) and at 22 weeks of age (after either being subjected to an ad libitum diet or 30% dietary restriction). Next, differential expression analysis was performed to compare the RNA expression in Ercc1Δ/- aortas to the RNA expression in wildtype aortas at the different ages and to compare the RNA expression in aortas from mice on dietary restriction to the aortas of mice on an ad libitum diet.

first: SJM

first: J

last: van der Linden

first: JM

last: Heredia-Genestar

first: RMC

last: Brandt

first: S

last: Barnhoorn

first: N

last: van Vliet

first: I

last: van der Pluijm


title: A dendritic cell-like transition of T cells is associated with spontaneous remission of adult T-cell leukemia-lymphoma

city: Kumamoto

first: Osama

last: Hussein

state: Kumamoto Prefecture

address: 1-1-1 Honjo, Chuo-ku, Kumamoto City, Kumamoto Prefecture

department: Department of Haematology, Rheumatology, and Infectious Diseases

country: Japan

institute: Kumamoto University

summary: Spontaneous remission in patients with various cancers has been reported. Some patients with adult T-cell leukemia–lymphoma (ATL) have experienced spontaneous remission, although the mechanisms for this remain unknown. In this study, we analyzed ATL cells and human T-cell leukemia virus type 1 (HTLV-1)- infected cells using cytometry by time-of-flight mass spectrometry. We observed a small number (less than 5% on average) of ATL cells and HTLV-1–infected cells that expressed CD14 and other dendritic cell (DC)-associated molecules such as CD1c, CD11b, CD11c, and CD141. Single-cell analysis revealed that these T cells expressing DC markers also contained rearranged T-cell receptor genes, indicating that these cells are indeed derived from T cells. In a patient with ATL who entered remission after contracting coronavirus disease 2019, the number of DC-like T cells increased, and an enzyme-linked immunosorbent spot assay detected CTLs against the Tax protein in accordance with a regression of ATL. These findings suggest that DC-like ATL cells acquire antigen-presenting capability and induce spontaneous remission through enhanced immunity to the virus. Specifically, in an ATL cell line, enforced expression of IRF8 and PU.1, in addition to endogenous BATF3 expression, increased CD86 expression and enabled the cells to present Tax peptide antigens to T cells. Collectively, these data indicate that ATL cells acquire antigen-presenting activity when IRF8, PU.1, and BATF3 are expressed, suggesting that the transition of a subset of T cells to DC-like T cells can induce immune responses to viral antigens, resulting in spontaneous remission. Thus, the transition of T cells to DC-like T cells is a unique mechanism for spontaneous remission in ATL.

overall_design: Peripheral blood mononuclear cells (PBMCs) from adult T-cell leukemia/lymphoma (ATL) patients were processed for single-cell RNA sequencing (scRNA-seq) using the 10X Genomics Chromium Next GEM Single Cell 5' Reagent Kit v2 (Dual Index) according to the manufacturer's instruction. Briefly, a single-cell suspension was loaded onto the Chromium Next GEM Chip K for GEM generation. Following GEM formation, gel beads were dissolved, and co-partitioned cells were lysed. The transcripts present in the beads were barcoded and reverse-transcribed into full-length cDNA. The resulting cDNA was amplified via PCR, and then used to generate the 5' gene expression and T-cell receptor (TCR) V(D)J libraries according to the manufacturer's protocol. Finally, sequencing was performed on the DNBSEQ-G400RS platform.


title: Effect of GSK3 inhibition on the transcriptional signature of human monocytes

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

institute: Hospital General Universitario Gregorio Marañón

summary: We explored the molecular impact of blocking GSK3 on the gene expression profile in human monocytes. GSK3 inhibition by CHIR-99021 redirected monocytes towards acquiring an anti-inflammatory gene profile similar to M-CSF-primed monocyte-derived macrophages.

overall_design: mRNA profiles of purified human monocytes treated DMSO or 10 micromolar of GSK3a/β inhibitor (CHIR99021) or 10 ng/mL M-CSF for 16 hours.

first: Israel

last: Ríos

first: Cristina

last: Herrero

last: Puig-Kröger

first: Ángel

last: Corbí


title: Tripartite phosphorylation of SPT5 by CDK9 times pause release and tunes elongation rate of RNA polymerase II (CUT&RUN)

first: Rui

last: Sun

overall_design: The effects of CTR1 and CTR2 mutations on elongation index suggested complex regulation of RNAPII elongation velocity by CTR phosphorylation. To measure elongation rates directly in cells dependent on different SPT5 variants, we reversibly blocked RNAPII in the promoter-proximal region by a 3-hr treatment with the CDK inhibitor 5,6-dichloro-1-b-D-ribofuranosyl-benzimidazole (DRB), and monitored progression of the transcribing RNAPII wavefront by CUT&RUN at 0, 3 and 5 min after DRB washout.


title: Inflammation-induced epigenetic erosion drives stem cell ferroptosis during aging [scRNA-seq]

city: Madiosn

first: Romeo

last: Blanc

address: 1111 Highland Ave, WIMR II, 4th floor, Blanc Lab

institute: University of Wisconsin-Madison

summary: Aging is a complex process associated with multiple events that lead to the decline in stem cell number and function. However, the relationship between these events and their initiation in biological systems remains ambiguous. Here, we investigate the effects of sustained, low-grade systemic inflammation on muscle stem cells (MuSCs) during aging. We show that the slow rise in inflammation during aging causes long-lasting epigenetic remodeling in MuSCs, leading to premature exit of quiescence followed by rapid ferroptotic cell death. The elevation of circulating cytokines results in erosion of histone H4 lysine 20 methylation, fine-tuning of the MuSC transcriptome for future injury response that resembles the Galert state. Prolonged exposure to inflammatory signals during aging results in the loss of H4K20me1 maintenance by lysine methyltransferase 5a (Kmt5a), leading to a disruption of key transcriptional programs required to preserve MuSC quiescence and survival. Mechanistically, we established that Kmt5a genetic deletion prematurely activates MuSC through Notch signaling. Activated cells cannot cycle properly as they display aberrant iron metabolism and repressed Gpx4, resulting in the accumulation of reactive oxygen species, genomic instability, lipid peroxidation, and ultimately, cell death by ferroptosis. Notably, a lifelong reduction in inflammation restores the MuSC number and function and rejuvenates MuSC iron homeostasis. Our findings demonstrates that chronic systemic inflammatory signals reprogram the MuSC epigenome into a primed state, which drives premature cell cycle re-entry and ferroptosis during aging.

overall_design: Comparative single cell gene expression in muscle stem cells derived from 3 adult (4mo) mice, 3 aged (24mo) mice, 3 adult Kmt5a knockout mice 2wks post tmx-injection,  3 adult Kmt5a knockout mice 6wks post tmx-injection, and  3 aged (24mo) Kmt5a knockout mice 20mo post tmx-injection


title: Tripartite phosphorylation of SPT5 by CDK9 times pause release and tunes elongation rate of RNA polymerase II (TT-Seq)

overall_design: To try to reconcile the effects of CTR mutations on steady-state mRNA levels and pre-mRNA splicing with their impacts on RNAPII distribution, we analyzed nascent RNA synthesis in cells expressing wild-type or mutant Flag-SPT5 by transient transcriptome sequencing with chemical fragmentation of RNA (TTchem-seq)

first: Robert

last: Fisher


title: Integrated Molecular-Phenotypic Profiling Reveals Metabolic Control of Morphological Variation in Stembryos

city: Dresden

first: Ryan

middle: George

last: Savill

address: Pfotenhauer Strasse 108

institute: Max Planck Institute for Molecular Cell Biology and Genetics

summary: Mammalian stem-cell-based models of embryo development (stembryos) hold great promise in basic and applied research. However, considerable phenotypic variation despite identical culture conditions limits their potential. The biological processes underlying this seemingly stochastic variation are poorly understood. Here, we investigate the roots of this phenotypic variation by intersecting transcriptomic states and morphological history of individual stembryos across stages modeling post-implantation and early organogenesis. Through machine learning and integration of time-resolved single-cell RNA-sequencing with imaging-based quantitative phenotypic profiling, we identify early features predictive of the phenotypic end-state. Leveraging this predictive power revealed that early imbalance of oxidative phosphorylation and glycolysis results in aberrant morphology and a neural lineage bias that can be corrected by metabolic interventions. Collectively, our work establishes divergent metabolic states as drivers of phenotypic variation, and offers a broadly applicable framework to chart and predict phenotypic variation in organoid systems. The strategy can be leveraged to identify and control underlying biological processes, ultimately increasing the reproducibility of in vitro systems.

overall_design: Expression profiling of individual gastruloids and trunk-like-structures at 48h, 72h, 96h and 120h post-aggregation using MULTI-Seq

first: Alba

middle: V

last: Luque

first: Natalia

last: Lopéz-Anguita

first: Adriano

last: Bolondi

first: Sumit

last: Garai

first: Seher

middle: I

last: Gassaloglu

first: Aayush

last: Poddar

first: Aydan

last: Bulut-Karslioglu

first: Jesse

last: Veenvliet


title: Tripartite phosphorylation of SPT5 by CDK9 times pause release and tunes elongation rate of RNA polymerase II (ChIP-Seq)

overall_design: To ask whether CTR1 and CTR2 mutations had similarly reinforcing effects on chromatin distribution of RNAPII, we performed ChIP-seq analysis in the Flag-SPT5-expressing cells after depletion of endogenous dTAG-SPT5.


title: Inflammation-induced epigenetic erosion drives stem cell ferroptosis during aging

overall_design: Comparative gene expression in muscle stem cells derived from 3 adult (4mo) mice, 3 aged (24mo) mice, 3 adult Kmt5a knockout mice 2wks post tmx-injection,  3 adult Kmt5a knockout mice 6wks post tmx-injection, and  3 aged (24mo) Kmt5a knockout mice 20mo post tmx-injection


title: Multimodal delineation of a layer of effector function among exhausted CD8 T cells in tumors

status: Public on Apr 28 2025

city: San Francisco

first: Arja

last: Ray

address: 513 Parnassus Avenue

institute: UCSF

summary: The anti-tumor function of CD8 T cells is limited through well-established pathways of T cell exhaustion (TEX). Strategies to capture emergent functional states amongst this dominant trajectory of dysfunction are necessary to find pathways to durable anti-tumor immunity. By leveraging transcriptional reporting (by the fluorescent protein TFP) of the T cell activation marker Cd69, related to upstream AP-1 transcription factors, we define a classifier for potent versus sub-optimal CD69+ activation states arising from T cell stimulation. In tumors, this delineation acts an additional functional readout along the TEX differentiation trajectory, within and across TEX subsets, marked by enhanced effector cytokine and granzyme B production. The more potent state remains differentially prominent in a T cell-mediated tumor clearance model, where they also show increased engagement in the microenvironment and are superior in tumor cell killing. Employing multimodal CITE-Seq in human head and neck tumors enables a similar strategy to identify Cd69RNAhiCD69+ cells that also have enhanced functional features in comparison to Cd69RNAloCD69+ cells, again within and across intratumoral CD8 T cell subsets. Refining the contours of the T cell functional landscape in tumors in this way paves the way for the identification of rare exceptional effectors, with imminent relevance to cancer treatment.

overall_design:
To identify patterns of gene expression within six broadly defined cell populations, we also performed cell sorting for bulk RNA-sequencing from freshly resected primary human tumors including compartments denoted: 1. “Live”: All viable cells at the time of sorting, 2. “Tconv”: sorted conventional CD4+ and CD8+ T cells, 3. “Treg”: CD25+ CD4+ (enriched for regulatory) T cells, 4. “Myeloid”: Lymphocyte-negative HLA-DR+ (enriched for myeloid) cells, 5. “Stromal”: CD45- CD44+Thy1+ cells, and 6. “Tumor”: all other CD45- cells. We use the bulk RNASeq data from the 'Tconv' compartment for this study

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
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first: Bushra

last: Samad

first: Alexis

last: Combes


title: ETMR stem-like state and chemo-resistance are supported by perivascular cells at single-cell resolution (human+murine organoids subset)

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

summary: To investigate the celluar heterogeneity of ETMR and the role of pericytes in the tumor microenvironment, we performed single-cell RNA sequencing of about 140,000 cells from primary human and murine ETMR as well as from 2D ETMR cultures and 3D models of ETMR-harboring forebrain organoids. We also analysed 3 ETMR human samples by spatial transcriptomics.

overall_design: scRNA-seq (10xGenomics) of fresh frozen samples: n=21 forebrain organoids harboring murine ETMR cell lines and controls

first: Flavia

middle: W

last: de Faria

first: Nicole

middle: C

last: Riedel

first: Marta

last: Interlandi

last: Göbel

first: Viktoria

last: Melcher

first: Christian

last: Thomas

first: Rajanya

last: Roy

first: Melanie

last: Schoof

first: Daniel

last: Münter

first: Ivan

last: Bedzhov

last: Moreno

first: Monika

last: Graf

first: Marc

last: Hotfilder

first: Dörthe

last: Holdhof

first: Wolfgang

last: Hartmann

first: Martin

last: Hasselblatt

first: Ann-Katrin

last: Bruns

first: Angela

last: Brentrup

first: Friederike

last: Liesche-Starnecker

first: Bruno

last: Maerkl

first: Sarah

last: Sandmann

first: Julian

last: Varghese

last: Dugas

first: Sebastian

last: Balbach

first: Claudia

last: Rössig

last: Ebinger

last: Schuhmann

first: Aysegül

last: Canak

first: Jens

last: Schnittenhelm

first: Michael

last: Frühwald

first: Ulrich

last: Schüller

first: Thomas

last: Alber

first: Jan

middle: M

last: Bruder

first: Kornelius

last: Kerl


title: SK4 potentially modulates the alternative splicing profile associated with papillary thyroid cancer development in BHT101 cells

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 888 Gaoxin Avenue

institute: Nissi Biotech

summary: Papillary thyroid cancer (PTC) is an ever-increasing cancer type worldwide, and greatly decreases the life quality and affects survival time of patients during its development and progression, but the underlying mechanisms and key factors for PTC progression are not clear. Recent studies demonstrated the potassium channel protein SK4, also named as KCNN4, participates in the progression of many cancers, while it lacks the molecular mechanism study for SK4 function. In this study, we performed functional and molecular explorations for SK4 by overexpressing its level in thyroid cancer BHT101 cells. Cellular proliferation and invasion experiments were performed to assess the influences of SK4 on cell behaviors. Further, whole transcriptome sequencing (RNA-seq) analysis helped us systematically investigated the down stream targets of SK4, including differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs). We finally validated several DEGs and RASEs associated with the functions of SK4 by RT-qPCR experiment. In thyroid cancer patients, SK4 expression was completely lost in normal tissues and significantly increased in every stage of tumor tissues compared with normal tissues, the reason of which probably results from the low DNA methylation level at its promoter region. Consistent with previous study, SK4 overexpression (SK4-OE) promoted proliferation level and invasion ability of BHT10 cells compared with negative control (NC). By analyzing the RNA-seq data, we detected dozens of DEGs and found that up DEGs were enriched in negative regulation of apoptotic progress, including VTCN1, MSX1, FATE1, TEK, and PRAMEF2. More importantly, we found SK4-OE globally changed the alternative splicing pattern and identified 1639 RASEs. The genes of RASEs were enriched in DNA damage/repair, viral process, translation, and mRNA splicing pathways, which were tightly associated with the pathogenesis and progression of cancers. The splicing regulatory genes from RASGs could partly explain the reason of global AS dysregulation by SK4-OE in BHT101 cells. Finally, we validated several DEGs and RASEs associated with PTC progression by RT-qPCR. We found the expression of VTCN1, EDN1, SLC29A4, RP11-473M20.16, and CH507-513H4.4 were validated by RT-qPCR, as well as the AS pattern of TMEM116, RBM39, and RBM6. In summary, our results deeply explored the molecular targets of SK4 associated them with SK4-induced progression of PTC. We highlight that SE4-regulated AS pattern probably is a novel regulatory mechanism for SK4 in PTC. The identified DEGs and RASEs, as well as SK4 itself, could be used as potential therapeutic targets for PTC treatment in future.

overall_design: By overexpressing SK4 in BHT101 cells, whole transcriptome sequencing (RNA-seq) analysis helped us systematically investigated the down stream targets of SK4, including differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs).

first: Alimujiang

last: Wupuer

first: Xuekelaiti

last: Kuerban

first: Gong

last: Ye


title: ETMR stem-like state and chemo-resistance are supported by perivascular cells at single-cell resolution (spatial transcriptomics subset)

first: Carolin

last: Walter

overall_design: Visium FFPE spatial transcriptomics of n=3 ETMR human samples derived from distinct patients

first: Flavia

last: de Faria

first: Nicole

last: Riedel

first: Marta

last: Interlandi

last: Göbel

first: Viktoria

last: Melcher

first: Christian

last: Thomas

first: Rajanya

last: Roy

first: Melanie

last: Schoof

first: Daniel

last: Münter

first: Ivan

last: Bedzhov

first: Natalia

last: Moreno

first: Monika

last: Graf

first: Marc

last: Hotfilder

first: Dörthe

last: Holdhof

first: Wolfgang

last: Hartmann

first: Martin

last: Hasselblatt

first: Ann-Katrin

last: Bruns

first: Angela

last: Brentrup

first: Friederike

last: Liesche-Starnecker

last: Maerkl

last: Sandmann

last: Varghese


title: Architecture mechanics mediated osteogenic progression in bone regeneration of artificial scaffolds

status: Public on Apr 15 2025

city: Chengdu

first: Siyu

last: Long

state: China Sichuan

address: Yihuan street

institute: Sichuan University

summary: Scaffold architecture exerts a considerable influence on the osteogenic effect through stress transmission, as the deformation of scaffolds alters the mechanical microenvironment of cells adhering to scaffold surface. Despite extensive researches on bone regeneration influenced by scaffold architecture, present studies have not addressed the biological mechanism underlying scaffold architecture-induced stress stimulation (SASS) on cells yet, posing a great challenge in revealing the biomechanical cues between scaffold architecture and osteogenic progression. Therefore, Graphite (GP), Fullerene (FL), and Diamond (DM) scaffolds with gradient stress-stimulation to cells after deformation were prepared. The cellular biomechanical mechanisms of SASS through single-cell RNA sequencing indicated that architectures providing SASS can induce the enrichment of focal adhesion and osteogenic differentiation pathways of bone mesenchymal stem cells, and balance bone resorption of osteoclasts and bone formation of osteoblasts. Besides, SASS enhances bone regeneration for repairing critical-sized defects in vivo. These results provide insights for artificial bone scaffold design and clarify the biomechanical cues between SASS and osteogenic progression.

overall_design: Our team designed three scaffolds based on the crystal structures of carbon, that is, graphite (GP), fullerene (FL), and diamond (DM) architectures. One month after the implantation of GP, FL, and DM scaffolds in the femur, the bone tissue at the defect site was removed and single-cell RNA sequencing was performed.

first: Si-Yu

first: Peng

last: Yu

first: Wei

last: Yang