title: Neural Crest Cell Signatures Drive TSC and LAM Tumorigenesis [human]

first: Uchenna

last: Unachukwu

address: 630 West 168th Street, P&S 7-430

department: Anesthesiology

institute: Columbia University Medical Center

summary: This study was performed to test the hypothesis that neural crest cells (NCCs) are causative cells for multi-systemic neoplasms occurring in Tuberous Sclerosis Complex (TSC) and Lymphangioleiomyomatosis (LAM) disorders. The hypothesis stemmed from the mesenchymal phenotypes of TSC and LAM neoplasms and their occurrence in patients at known ontogenetic destinations for maturing neural crest cells. We determined differential gene expression between single cell populations in wildtype mice renal cortical tissues versus renal cystadenomas of the tuberous sclerosis mice model by RNA sequencing, and validated our findings by immunohistochemistry, RT-qPCR, western blots, and tumorigenicity assays. Based on our results, we pioneer the characterization of cranial NCC-induced tumorigenesis in TSC and LAM and identify the crucial role of novel neurocristopathic markers: secreted phosphoprotein (SPP1) and cytokeratin 18 (Krt18) in disease pathogenesis. Genetic inhibition of Spp1 yields an anti-tumorigenic phenotypes in NCCs.

overall_design: Neoplastic lesions were excised from fresh lung tissues biopsied from de-identified Lymphangioleiomyomatosis (LAM) patients (N=4) and supplied by the National Disease Research Interchange (NDRI) in DMEM containing  1% penicillin-streptomycin, 48 hrs after surgery. Tissues were minced under sterile conditions, enzymatically digested, and single cells sequenced on a NovaSeq6000 System (Illumina, San Diego, CA) using the 10x Genomics 3’ Single Cell Gene Expression (GEX) workflow. Cell type classifiers in the CLC Genomics knowledgebase (Qiagen, CA) were trained to annotate neural crest cells in pulmonary neoplastic cell populations based on identifying markers in the study by Soldatov et al. (2019) (PMID: 31171666). Differential gene expression based on the generalized linear model (GLM) fit was performed for cell clusters within pulmonary LAM tumors, cell types within resolved clusters, and cranial neural crest cells (CNCCs) versus other cell types in clusters and whole tumors to identify novel neurocristopathic tumor markers in LAM.

first: Jeanine

last: D'Armiento


title: Alu repeat-containing RNA spatially organizes actively transcribed genomic regions around nuclear speckle

status: Public on Mar 03 2026

city: Beijing

first: Zhongyang

last: Chen

address: No.5, Dongdan Santiao, Dongcheng District

country: China

institute: School of Basic Medicine, Peking Union Medical College (PUMC)

type: Expression profiling by high throughput sequencing

summary: Nuclear speckles are nuclear bodies enriched with RNA processing proteins. Highly transcribed genes and their nascent premRNAs are organized around nuclear speckles, facilitating co-transcriptional RNA processing. However, the mechanism underlying this spatial organization remains unclear. Here, we identified a class of Alu repeat-containing RNAs that are highly enriched in nuclear speckles. These RNAs interact with actively transcribed genes through their Alu elements, partially via R-loop formation. They also engage with nuclear speckle proteins promoting their aggregation, phase separation and assembly of nuclear speckles, thereby orchestrating the spatial organization of actively transcribed genes around these structures. Depleting these RNAs reduces speckle size, displaces active genes and impairs RNA processing. Moreover, this mechanism is critical for high expression of many erythroid differentiation genes during erythropoiesis. Our findings highlight the pivotal role of Alu repeat-containing RNAs in nuclear speckles assembly and their function in mediating spatial co-transcriptional RNA processing.

overall_design: RIP-seq, GRO-seq, RNA-seq datasets.

first: Siqi

last: Liu

first: Xinyan

last: Shen

first: Yanni

last: Ma

first: Jia

last: Yu


title: AF9/KLF2 gene regulatory circuit links histone lactylation to breast cancer metastasis [CUT&Tag]

first: Huida

address: No. 30 Shuangqing Road, Haidian District

institute: Tsinghua University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone lysine L-lactylation (hereafter referred to as histone Kla) is a novel epigenetic mark induced by glycolytic metabolism, serving as a link between metabolic reprogramming and epigenetic regulation. In this study, we uncover an epigenetic-genetic transcriptional regulatory circuit involving AF9 and KLF2 that drives luminal breast cancer progression. AF9, identified as a reader of histone H3 lysine 9 lactylation (H3K9la), promotes KLF2 expression, while KLF2, functioning as a transcription factor for AF9, forms a positive feedback loop that amplifies lactylation-dependent effects. This circuit activates tumor-associated pathways, including TGFβ1, glucose and lactate transporters, and metabolic enzymes essential for glycolysis and serine biosynthesis, driving tumorigenesis and metastasis. Spatial and single-cell transcriptomics show AF9-positive tumor cells enriched in regions of active lactylation, correlated with immune evasion through interactions with M2 macrophages. Together, AF9, H3K9la, and KLF2 integrate metabolism, epigenetics, and signaling to promote tumor growth and metastasis, highlighting AF9's central role as a histone lactylation reader and a potential therapeutic target in breast cancer.

overall_design: CUT&Tag samples in MCF7 breast cancer cell line.

first: Ming

last: Yuan

first: Chenxuan

last: Yang

first: Yuchen

first: Xin

last: Wang

first: Zhonghui

last: Tang

first: Haitao

last: Li


title: AF9/KLF2 gene regulatory circuit links histone lactylation to breast cancer metastasis [RNA-seq]

overall_design: RNA-seq samples in MCF7 breast cancer cell line, as well as knockdown and overexpression derivates (shAF9 and AF9OE).


title: Proteoglycan Mimetics-based Bioactive Microneedles with Regulation Capacities of Inflammatory Microenvironment and Lipid Metabolism for Acne Treatment

city: Wuhan

first: Zhuo-ran

state: Hubei

address: No. 1037 Luoyu Road, Hongshan District

department: Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering

institute: Huazhong University of Science and Technology (HUST)

summary: Acne is a common skin disease, closely involving bacterial infection, impaired lipid metabolism and host inflammatory response. Although microneedles (MNs) can deliver bacteriostats for acne treatment, the limited regulation of inflammatory microenvironment and lipid metabolism hinders the therapeutic effect on severe acne. Herein, we develop antimicrobial and anti-inflammatory peptides-laden MN (HMC-PEP MN) with a proteoglycan-mimetic peptide-grafted comb polymer as MN matrix, which effectively treats acne via regulation of both inflammatory microenvironment and lipid metabolism. Specifically, HMC-PEP MN inhibits the expression of pro-inflammatory factors by decreasing TREM2/M2 macrophage ratio in rabbit ear acne model. Integrative analyses of transcriptomic and metabolomic reveal that HMC-PEP MN effectively reduces sebaceous secretion, pro-inflammatory signal transduction, sustained proliferation and differentiation of keratinocytes via inhibition of the IGF1/IGF1R/PI3K/AKT/mTOR signaling pathway. The improved lipid metabolism of sebaceous glands is potential for inhibition of acne recurrence, which provides broad clinical application prospect.

overall_design: To evaluate the effect of microneedle (HMC-PEP MN) on acne in rabbit ear acne model. Microneedles were applied to the acne area (once daily for five sessions). The animals were sacrificed on day 7. Microneedle treated and untreated rabbit ear acne tissues and normal skin were collected for RNA-Seq.

first: Zhuo-Ran

first: Kehan

last: Du

first: Hao

last: Jiang

first: Jintao

last: Zhu


title: Characterization of resistance to the KRAS inhibitor sotorasib in KRASG12C-positive non-small cell lung cancer (NSCLC) cells

city: Osaka-Sayama

first: Toshiyuki

last: Takehara

state: Osaka

address: 377-2, Ohno-Higashi

department: Faculty of Medicine

country: Japan

institute: Kindai Universty Hospital

summary:
Inhibitors of KRAS show clinical efficacy for non–small cell lung cancer (NSCLC) positive for the G12C mutation of KRAS, but primary and acquired resistance to these drugs remains a major clinical problem. Activation of EGFR signaling via the MAPK pathway is a key mechanism of such resistance.
We used expression data to understand the gene expression profile and identified distinct charactersitics on resistance cells.

overall_design: The KRASG12C-mutant NSCLC cell lines NCI-H2122 were obtained from American Type Culture Collection (Manassas, VA). H2122 cells were cultured under a humidified atmosphere of 5% CO2 at 37°C in RPMI 1640 (Sigma-Aldrich, St. Louis, MO) supplemented with 10% FBS and 1% penicillin-streptomycin.  And also, we generated resistant clones of KRASG12C-mutant NSCLC (H2122) cells by exposing the parental cells to increasing concentrations of sotorasib over 10 months. Charactristics analysis was perfomed to investigate and compare the gene expression profile in two samples.

first: Hiroaki

last: Kanemura

first: Takeshi

last: Teramura

first: Hidetoshi

last: Hayashi

first: Kimio

last: Yonesaka


title: Transforming growth factor-β1 induces super-enhancers at the loci of the epithelial-mesenchymal transition-related genes in human keratinocyte HaCaT cells

city: Fukuoka

first: Mitsutoki

last: Hatta

state: Fukuoka

address: 2-15-1 Tamura Sawara-ku

institute: Fukuoka Dental College

summary: An enhancer is a genomic DNA sequence that substantially enhances the transcriptional activity of a target gene by recruiting transcription factors. The large clusters of enhancers identified through the ChIP-seq analysis of histone H3 lysine 27 acetylation (H3K27ac) are called super-enhancers (SEs). This study examined the dynamics of SEs during transforming growth factor (TGF)-β1-mediated epithelial-mesenchymal transition (EMT) in the human keratinocyte cell line HaCaT. Initially, we identified the constitutive and the TGF-β1 signal-dependent SE regions across the HaCaT genome. The TGF-β1-induced SEs were detected at the loci of genes associated with the cell cycle, cell death, and extracellular matrix organization. Notably, the EMT-related mesenchymal genes such as FN1 and SERPINE1 gained the SEs on their loci in response to TGF-β1. Next, we investigated the functional role of BRD4, a transcriptional mediator that binds to the SEs, in the expression of TGF-β1-induced SE-associated genes. JQ-1, a potent inhibitor of BRD4, effectively reduced the TGF-β1-induced mRNA expression of FN1 and SERPINE1. In conclusion, this study demonstrated that the rearrangement of SEs is crucial for the transcriptional regulation of the TGF-β1-induced EMT in HaCaT cells.

overall_design: ChIP-seq of the histone modification H3K27ac in HaCaT cells under the control and TGF-β1-treated conditions.

first: Kana

last: Takeda

first: Yoshiyuki

last: Nagaoka

first: Sachio

last: Tamaoki


title: Impact of SLC39A9 knockdown in murine melanoma tumors with Cdkn2a knockdown

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

country: USA

institute: The Wistar Institute

summary: This dataset includes  scRNA-Seq data from Yumm5.2 murine melanoma cells with Cdkn2a knockdown, either alone or in combination with Slc39a9 knockdown

overall_design: Yumm5.2 murine melanoma cells were infected with shRNAs targeting Cdkn2a, either alone or in combination with shRNAs targeting Slc39a9 (hairpins #1 and #2). Cdkn2a-targeting shRNAs were cloned into the pLKO.1 vector expressing blasticidin resistance, while Slc39a9-targeting shRNAs were cloned into the pLKO.1 vector expressing puromycin resistance. Infected cells were selected with puromycin and blasticidin for 3 days, after which 350,000 cells were implanted into the right flank of C57BL/6 mice. Once palpable mice were randomized and assigned to corresponding treatment (200ug of anti-PD1 or IgG , three times a week, i.p). When tumors reached 0.5cm3 were harvested, dissagregated and libraries were prepared and samples sequenced.

first: Raquel

last: Buj

first: Katherine

middle: M

last: Aird

first: Jayamanna

first: Andrew

middle: V

last: Kossenkov


title: Hepatocyte-specific CEBPA-ORM1 axis restricts alcohol-associated liver disease

city: Bethesda, MD

first: Frank

last: Gonzalez

address: Bldg. 37 National Institutes of Health

department: Center for Cancer Research

institute: National Institutes of Health, National Cancer Institute

summary: Alcohol-associated liver disease (ALD) affects millions of people worldwide, while pharmacological therapies are limited. CCAAT/enhancer binding protein α (CEBPA) in hepatocytes is known to regulate the progression of liver fibrosis; however, the role of hepatocyte-specific CEBPA in modulating the ALD progression is still unknown. Here, hepatic CEBPA expression was found to be decreased during ALD progression in humans. CebpaΔHep mice had enhanced ALD induced both in short-term and long-term alcohol feeding. Temporal and spatial hepatocyte-specific CEBPA loss at the later stage of ALD in CebpaΔHep,ERT2 mice functionally promoted ALD. Mechanistically, hepatocyte CEBPA loss directly deactivated Orm1 expression in hepatocytes that resulted in reduced secretion of ORM1 and enhancement of ALD progression. Both hepatocyte ORM1 expression and serum ORM1 levels were found to be negatively correlated with the ALD progression in humans, while loss of hepatocyte ORM1 in mice sharply enhanced ALD. Both forced hepatocyte-specific CEBPA overexpression and hepatocyte-specific ORM1 overexpression by adeno-associated viruses rescued the progression of ALD in CebpaΔHep mice. Notably, treatment of recombinant ORM1 protein improved the progression of ALD in CebpaΔHep mice. These results reveal a key role for hepatocyte-specific CEBPA-ORM1 axis in ALD progression, which supports hepatocyte CEBPA to be a novel therapeutic target for the treatment of ALD.

overall_design: Ten-week-old, body weight-matched Cebpafl/fl and CebpaΔHep mice were acclimated to a liquid control diet (F1259SP, BioServ) for 5 days first, followed by a 5% (vol/vol) ethanol liquid diet (F1258SP, BioServ) feeding for 4 weeks. Samples were collected for further analysis.

first: Yan

last: Nana

first: Tingting

last: Yan

first: Vorthon

last: Sawaswong


title: Chromatin accessibility dynamics and transcriptional regulation in Tetrahymena thermophila

city: Hefei

first: Zhengyu

last: Luo

address: huanshang

institute: USTC

summary: Chromatin accessibility dynamics and their relationship to gene expression remain poorly understood in ciliated protozoa. Here, we investigate these dynamics in Tetrahymena thermophila by optimizing ATAC-seq to map chromatin accessibility across its transcriptionally active macronucleus during distinct life cycle stages. We demonstrate that chromatin accessibility at transcription start sites (TSSs) strongly correlates with gene expression levels. Intriguingly, partitioning ATAC-seq signals into nucleosome-free (NFR) and nucleosome-associated (NUC) regions revealed conserved TSS-proximal features: NFR signals peak upstream of TSSs, while phased +1 nucleosome arrays detected via NUC signals align with MNase-seq profiles. Temporal analysis uncovered stage-specific chromatin accessibility patterns, with global accessibility fluctuating dynamically across developmental phases. While most differentially accessible loci mirrored expression changes, subsets exhibited discordant regulation, suggesting context-specific chromatin-transcriptional coupling. Pharmacological inhibition of transcription using flavopiridol (FLV) triggered upstream chromatin compaction, elevated gene body accessibility, and enhanced nucleosome phasing, implicating transcription-coupled processes in shaping chromatin states. Cross-species comparisons of TSS-proximal accessibility across 13 eukaryotes revealed three conserved architectural modes (upstream-biased, symmetric, or upstream-restricted), with divergent spacing of +1 nucleosomes relative to TSSs. Our work establishes Tetrahymena as a model for studying chromatin dynamics in single-celled eukaryotes and provides evolutionary insights into the interplay between nucleosome organization, chromatin accessibility, and transcriptional regulation.

overall_design:
ATAC-seq of T. thermophila at different life cycle stages: vegetative growth, starvation, conjugation 1.5hpm, 3hpm, 8hpm, 12hpm, 24hpm, and Refeeding.
RNA-seq of T. thermophila at different life cycle stages: vegetative growth, starvation, conjugation 1.5hpm, 3hpm, 8hpm, 12hpm, 24hpm, and Refeeding.
ChIP-seq and ATAC-seq of H3K36me3 with DMSO control and FLV treated WT T. thermophila cells.

first: Tengfei

last: Hu

first: Xiaoyuan

last: Song


title: The molecular mechanism of on-demand sterol biosynthesis at organelle contact sites

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: The effect of Yet3 knock out or overexpression on RNA expression profiles.

overall_design: Yeast strains overexpressing or missing Yet3 were created and processed for RNA sequencing.

last: Zung

first: Gilad

last: Yaakov

first: Felix

last: Jonas

first: Maya

last: Schuldiner


title: Multiomic Study of Cutaneous T-Cell Lymphoma Reveals Single Cell Clonal Evolution in Progression and Therapy Resistance

city: St. Louis

first: Jacqueline

last: Payton

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: Cutaneous T-cell lymphoma (CTCL) remains a challenging disease due to its significant heterogeneity, therapy resistance, and relentless progression. Multi-omics technologies offer the potential to provide uniquely precise views of disease progression and response to therapy. We present here a comprehensive multi-omics view of CTCL clonal evolution, incorporating exome, whole genome, epigenome, bulk-, single cell (sc) VDJ-, and scRNA- sequencing of 114 clinically annotated serial skin, peripheral blood, and lymph node samples from 35 CTCL patients. We leveraged this extensive dataset to define the molecular underpinnings of CTCL progression in individual patients at single cell resolution with the goal of identifying clinically useful biomarkers and therapeutic targets. Our studies identified a large number of recurrent progression-associated clonal genomic alterations; we highlight mutation of CCR4, PI3K signaling, and PD-1 checkpoint pathways as evasion tactics deployed by malignant T cells. We also identified a gain of function mutation in STAT3 (D661Y) and demonstrated by CUT&RUN-seq that it enhances binding to transcription start sites of genes in Rho GTPase pathways, which we previously reported to have activated chromatin and increased expression in HDACi-resistant CTCL. These data provide further support for a previously unrecognized role for Rho GTPase pathway dysregulation in CTCL progression. A striking number of progression-associated mutations occurred in chromatin methylation modifiers, including EZH2, suggesting that EZH1/2 inhibition may also benefit patients with CTCL. Knowledge of these molecular changes should be leveraged for improved disease monitoring, biomarker-informed clinical trial design, and new therapeutic strategies in this challenging and incurable cancer.

overall_design: Bulk and single cell (sc)RNA sequencing were performed on Cutaneous T-cell Lymphoma (CTCL) samples, including skin and lymph node biopsies of CTCL, peripheral blood mononuclear cells, purified malignant and non-malignant T cells and matched normal monocytes or NK cells from peripheral blood, as well as peripheral blood T cells from healthy donors.


title: Derivation of elephant induced pluripotent stem cells [ATAC-seq]

city: Boston

first: Evan

middle: Michael

last: Appleton

state: MA

address: 75 Kneeland St.

institute: Colossal Biosciences

summary:
The crisis of biodiversity loss in the present era requires new tools for studying non-model organisms. Elephants are both an endangered species and excellent models for studying complex phenotypes including body size, social behavior, and longevity. Here we report here the first derivation of (Elephas maximus) induced pluripotent stem cells (emiPSCs). We achieved emiPSCs using two approaches: (1) a two-step process of chemical-media induction and colony selection followed by overexpression of elephant transcription factors; and (2) a one-step process with the same transgenes but without the chemical induction step and including an additional HRAS mutant transgene, HRASG12V. For both protocols, we inhibited TP53 expansion genes, which are hypothesized to confer unique cancer resistance in elephants. To confirm their reprogrammed state, we generated a functional genomics catalog of the modified cells with RNA-seq, ATAC-seq, and single-molecule direct RNA-sequencing. While these emiPSCs are transgene-dependent, we inactivated them to differentiate emiPSCs into all three germ layers via tri-lineage differentiation, embryoid body generation, and direct differentiation into putative cell types from all three layers. These methods will open new frontiers for cellular
models of non-model organisms, including for genetic rescue and conservation.

overall_design: ATACseq of elephant induced pluripotent stem cells

first: Nataly

last: Korover

first: Kyunghee

last: Hong

first: Xochitl

last: Ambriz-Peña

first: Yoshiaki

last: Tanaka

first: Asaf

last: Ashkenazy-Titelman

first: Cody

last: Rasmussen-Ivey

first: Cristina

last: Rodriguez-Caycedo

first: Ketaki

last: Bhide

first: Hao

last: Bai

first: Ana

last: Queiroz

first: Jorgen

middle: W

last: Nelson

first: Grishma

last: Rathod

first: Miles

last: Morgan

first: Anthony

last: Mastracci

first: Theodore

first: Greg

last: Knox

first: Brody

last: McNutt

first: Nandini

last: Malviya

first: Kairui

last: Zhang

first: Amanda

last: Kowalczyk

first: Austin

last: Bow

first: Bryan

last: McLendon

first: Jaroslav

last: Slamecka

first: Krista

last: Ryon

first: Jackie

last: Proszynski

first: Nadia

last: Houerbi

first: Ashley

middle: S

last: Kleinman

first: Chi-Lam

last: Poon

first: Wendy

last: Kiso

first: Matt

last: James

first: In-hyun

last: Park

first: Charles

last: Gray

first: Virginia

middle: R

last: Pearson

first: Christopher

middle: E

last: Mason

first: Brandi

last: Cantarel

first: Karl

last: Koehler

first: Beth

last: Shapiro

first: James

last: Kehler

first: Ben

last: Lamm

first: Georga

last: Church

first: Eriona

last: Hysolli


title: Transcriptome analysis of Kdm7a-deficient RAW264.7 cells during macrophage polarization.

city: Kumamoto

first: Mitsuyoshi

last: Nakao

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary: Transcriptome analysis of Kdm7a-deficient RAW264.7 cells revealed that Kdm7a suppresses excessive polarization toward M2 macrophages.

overall_design: Using CRISPR/Cas9 and gRNA, we generated a Kdm7a-deficient cell line in mouse macrophage RAW264.7 cells. The Kdm7a-deficient RAW264.7 cells were then stimulated under M1 and M2 polarization conditions for 48 hours, followed by mRNA-seq analysis.

first: Naofumi

last: Funagura

first: Tomoaki

last: Koga


title: Derivation of elephant induced pluripotent stem cells [RNA-seq]

first: Evan

last: Appleton

sample_organism:
Elephas maximus
Procavia capensis

platform_organism:
Elephas maximus
Procavia capensis

overall_design: Short-read sequencing of elephant induced pluripotent stem cells

first: Nataly

last: Korover

first: Kyunghee

last: Hong

first: Xochitl

last: Ambriz-Peña

first: Yoshiaki

last: Tanaka

first: Asaf

last: Ashkenazy-Titelman

first: Cody

last: Rasmussen-Ivey

first: Cristina

last: Rodriguez-Caycedo

first: Ketaki

last: Bhide

first: Hao

last: Bai

first: Ana

last: Queiroz

first: Jorgen

last: Nelson

first: Grishma

last: Rathod

first: Miles

last: Morgan

first: Anthony

last: Mastracci

first: Theodore

first: Gregory

last: Knox

first: Brody

last: McNutt

first: Nandini

last: Malviya

first: Kairui

last: Zhang

first: Amanda

last: Kowalczyk

first: Austin

last: Bow

first: Bryan

last: McLendon

first: Jaroslav

last: Slamecka

first: Krista

last: Ryon

first: Jackie

last: Proszynski

first: Nadia

last: Houerbi

first: Ashley

last: Kleinman

first: Chi-Lam

last: Poon

first: George


title: Neural Crest Cell Signatures Drive TSC and LAM Tumorigenesis

city: New York

first: Uchenna

last: Unachukwu

state: New York

overall_design: Single-cell isolates from renal cortical tissues of the B6129SF2/J wildtype mice and spontaneously occurring renal cystadenomas in the Tuberous Sclerosis Tsc2+/- mice model were sequenced on a NovaSeq6000 System (Illumina, San Diego, CA) using the 10x Genomics 3’ Single Cell Gene Expression (GEX) workflow. Cell type classifiers in the CLC Genomics knowledgebase (Qiagen, CA) were trained to annotate neural crest cells in renal tissue/tumor cell populations based on identifying markers in the study by Soldatov et al. (2019) (PMID: 31171666). Differential gene expression and signaling pathway analyses were used to resolve NCC-induced tumorigenic pathways and novel neurocristopathic markers in TSC and LAM. CRISPR/Cas9-mediated gene recombination was used to perform loss-of-function tests assessing the role of identified NCC markers and pathogenic pathways.

first: Jeanine

last: D'Armiento


title: Estrogen-mediated gene expression in the arcuate (ARC) and paraventricular (PVN) nuclei of the hypothalamus and the nucleus of the solitary tract (NTS) in female rats (Rattus norvegicus)

city: Tulsa

first: Dusti

last: Sloan

state: Oklahoma

address: 1111 West 17th Street

department: Pharmacology and Physiology

institute: Oklahoma State University Center for Health Sciences

summary: A microarray analysis (transcriptome analysis) was conducted to examine estrogen-mediated gene expression in the arcuate nucleus (ARC) and paraventricular nucleus (PVN) of the hypothalamus, as well as the nucleus of the solitary tract (NTS) in female rats (Rattus norvegicus). All procedures were approved by the Oklahoma State University - Center for Health Sciences IACUC (protocol #2021-1278). Rats underwent ovariectomy, recovered, and were then treated with either 17β-estradiol (EB) or an oil vehicle (Oil). Following euthanasia, mRNA was extracted and submitted to Thermo Fisher Scientific for microarray analysis using the Clariom S Rat Pico Assay.

overall_design: Microarray analysis of brain tissue from the arcuate nucleus (ARC), paraventricular nucleus (PVN), and nucleus of the solitary tract (NTS), collected following administration of 17β-estradiol (EB) in oil vehicle or oil vehicle alone.

first: Kaitlin

last: Burch

first: Henry

last: Lang


title: The OsCCT22- OsSh1-OsCAD2 module facilitate seed shattering by suppress lignin biosynthesis in rice [RNA-seq]

first: He

last: wei

state: Beijing

address: China agriculture university

institute: China agriculture university

summary: OsCCT22, physically interacted with OsSh1 to regulate the abscission development.

overall_design: Total RNA was isolated from 0 DAH AZ of the WT, sh1 mutant ,oscct22 mutant and CK, with three biological replicates each containing five plants. Samples were sequenced using BGISEQ PE150, averagely generating about 6.69G Gb bases per sample and used HISAT2

first: Wei

last: He


title: Multiomic Study of Cutaneous T-Cell Lymphoma Reveals Single Cell Clonal Evolution in Progression and Therapy Resistance [bulk RNA-seq]

first: Jacqueline

last: Payton


title: Effect of deoxynivalenol and acrylamide on gene expression on IEC-6 intestinal cells

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

country: France

institute: INRAE

summary: To investigate the effect of co-treatment with deoxynivalenol and acrylamide, rat IEC-6 intestinal cells were treated during four hours with different concentrations of compound alone or together.

overall_design: IEC-6 cells were seeded in 60mm dishes at a density of 1,10e6 cells per well. After 24h of culture, treatment of IEC-6 cells with vehicule, deoxynivalenol (3 and 10µM) or acrylamide (6mm) during 4 hours before ARN extraction. N= 4 biological replicates

first: Isabelle

last: Oswald

first: Delphine

last: Payros

first: Sylvie

last: Puel

first: Marie

last: Penary

first: Claire

last: Naylies

first: Gaëlle


title: ESCRT-mediated machinery directly drives cardiac T-tubule formation

city: Hangzhou

first: Xinjian

last: Wang

address: No. 866, yuhangtang Road, Xihu District

department: School of Medicine

institute: Zhejiang University

summary: Cardiac transverse tubules (T-tubules) are regular spaced plasma membrane invaginations that play an essential role in establishing excitation-contraction coupling of cardiomyocytes, yet the molecular machinery that controls T-tubule formation remains elusive. The endosomal sorting complex required for transport (ESCRT) proteins are involved in a variety of cellular events primarily through regulating membrane deformation in a reverse topology mode (budding away from cytosol). Strikingly, we find ESCRT directly controls the inward budding of cardiomyocyte plasma membrane to form T-tubules. Visualization of postnatal cardiomyocytes uncovers the gradual localization of charged multivesicular body protein 4b (Chmp4b), the key ESCRT-III filament component, to T-tubules.

overall_design: To achieve targeted ablation of Chmp4b, postnatal-day-0 (P0) MCM; Chmp4bF/F mice received subcutaneous injections of 0.1 mg/g tamoxifen for two consecutive days. As a control, MCM; Chmp4bF/F mice were injected with corn oil.  Hearts were harvest at P10, we then performed gene expression profiling analysis using data obtained from RNA-seq, 5 mice per group.

first: Hongkun

last: Wu

first: Peidong

last: Han


title: TWEAK-induced alternative NF-κB signaling regulates Cxcl10 and Mymx to promote myoblast-to-myotube fusion

city: Ottawa

first: Neena

last: Lala-Tabbert

state: Ontario

address: 401 Smyth Rd

country: Canada

institute: CHEO Research Insitute

summary: Repair of adult skeletal muscle relies on molecular and cellular mechanisms that sustain tissue homeostasis during regeneration of injured myofibers. The NF-κB pathway has emerged as an important signaling network in skeletal muscle. Depending on the type of stimulus, activation of NF-κB signaling can occur through the classical or alternative pathway. TWEAK is a membrane bound and soluble cytokine that signals through Fn14, a highly inducible cell-surface receptor that is upstream of numerous signaling pathways including NF-κB. Upregulation of Fn14 signaling is associated with the progression of several chronic atrophic muscle disorders. In contrast, TWEAK/Fn14 signaling has also been suggested to play a beneficial role during muscle regeneration by promoting myoblast proliferation and fusion. In this study, we demonstrate that TWEAK promotes secondary fusion through direct transcriptional activation of Myomixer and CXCL10 by alternative NF-κB. Overall, our study demonstrates that TWEAK is beneficial for myoblast fusion and may be a potential approach to improve muscle regeneration in degenerative disorders.

overall_design: To examine the molecular mechanism by which TWEAK stimulates myoblast-to-myotube fusion we treated nascent C2C12 myotubes (differentiated for 3 days) with 10ng/ml TWEAK for 12 hours. Untreated cells were used as controls. We performed RNA-Sequencing to examine differential gene expression between untreated and treated myotubes.

first: Robert

middle: G

last: Korneluk


title: Brain endothelial cells with inflammatory signature in CCM disease in hypoxia and normoxia conditions

city: La Jolla

first: Miguel

middle: Alejandro

last: Lopez Ramirez

state: CA

address: 9500 Gilman Dr

department: Medicine

institute: University of California, San Diego

summary: The CCM endothelium is hypersensitive to angiogenesis and can induce a hypoxic program associated with changes in angiogenesis, inflammation, and endothelial-cell metabolism under normoxic conditions. It has been suggested that environmental, genetic, or biological factors act as disease modifiers. However, the underlying mechanisms are not entirely understood. To assess whether mild hypoxia accelerates CCM, we employed a CCM mouse model (Pdcd10BECKO;Aldh1l1-EGFP/Rpl10a). Brain endothelial cells (BECs) were isolated from Slco1c1-iCreERT2;Pdcd10fl/fl;Aldh1l1-EGFP/Rpl10a mice to as previously described. BECs mRNAs were from isolated microvesels from cerebral tissue of mice age P50 exposed to hypoxia or normoxia conditions.

overall_design: Brain endothelial cell-specific conditional Pdcd10-knockout mice were generated by crossing a brain endothelial tamoxifen-regulated Cre recombinase (Slco1c1-iCreERT2) strain with loxP-flanked Pdcd10 (Slco1c1-iCreERT2; Pdcd10 fl/fl). We generated Slco1c1-iCreERT2;Pdcd10fl/fl;Aldh1l1-EGFP/Rpl10a and controls littermate Pdcd10fl/fl;Aldh1l1-EGFP/Rpl10a. On a postnatal day 1 (P1), mice were administered 50 μg of 4-hydroxy-tamoxifen (H7904, Sigma-Aldrich) by intragastric injection to induce genetic inactivation of endothelial CCM3 gene in littermates with Slco1c1-iCreERT2;Pdcd10fl/fl; Aldh1l1-EGFP/Rpl10a (Pdcd10BECKO; Aldh1l1-EGFP/Rpl10a) and Pdcd10fl/fl;Aldh1l1-EGFP/Rpl10a mice were used as littermate controls. Non-injected animals with Cre recombinase were also used as littermate controls, whose gene expression and histology were the same as in Pdcd10fl/fl; Aldh1l1-EGFP/Rpl10a mice. Hypoxic conditions consisted in 12% O2,  for seven days and normoxic conditions consisted in 21% O2.mRNAs from BECs collection was performed using the protocol and instructions as previously described. BECs mRNAs were from brains of mice age P57. Total RNA was assessed for quality using an Agilent Tapestation 4200, and 50 nanograms of RNA from samples with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA-seq libraries using the Illumina® Stranded mRNA Prep (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions.

first: Eduardo

last: Frias-Anaya

first: Brendan

last: Gongol

first: Helios

last: Gallego-Gutierrez

first: Catherine

middle: C

last: Lai

middle: A

last: Lopez-Ramirez


title: 3D Chromatin Remodeling in B-cell Development and B-cell Acute Lymphoblastic Leukemia [Hi-C]

first: Yohana

last: Ghebrechristos

state: NY

address: 550 1st Ave.

department: Pathology

institute: NYU Grossman School of Medicine

summary: The identification of molecular subgroups of B-cell progenitor acute lymphocytic leukemia (B-ALL) have proven to be a powerful tool in understanding the derivation of ALL while also providing essential prognostic information. Several studies have also shown changes in epigenetic landscape including differences across B-ALL subtypes. However, the state of the 3D genome across subtypes and how they compare to healthy B-cell progenitors remains unexplored. Here we use Hi-C and RNA-seq to profile early B-cell progenitors from healthy donors and a number of B-ALL samples harboring the most frequent and prognostic structural variations, including KMT2A::AFF1 and BCR::ABL. We show that B-ALLs undergo subtype-specific changes in 3D genome organization that indicate the differentiation stage of the disease. Additional analysis shows B-ALLs acquire aberrant chromatin configurations and expression of oncogenic drivers compared to normal progenitors. We also find that the TF ERG is aberrantly activated in ETV6::RUNX1 B-ALL, and it aids in the establishment of a differentiation block. Overall, the findings from our study show the impact of altered chromatin folding on the leukemogenic state of B-ALL.

overall_design: To profile 3D chromatin rewiring during leukemia emergence and differences across B-ALL subtypes, we performed Hi-C, RNA-sequencing and ATAC-sequencing on primary B-ALL patient samples and healthy sorted B-cell progenitors.

first: Nikki

last: Evensen

first: Soobeom

last: Lee

first: Finnegan

last: Clark

first: Stanley

last: Clarke

first: Matthew

middle: T

last: Witkowski

first: Ziyan

last: Lin

first: Hua

last: Zhou

first: Elizabeth

last: Raetz

first: David

last: Teachey

first: Timothée

last: Lionnet

first: Aristotelis

last: Tsirigos

first: William

middle: L

last: Carroll

first: Iannis

last: Aifantis


title: Alu repeat-containing RNA organizes actively transcribed genomic regions around nuclear speckle for co-transcriptional RNA processing

city: Beijing

first: Zhongyang

last: Chen

address: No.5, Dongdan Santiao, Dongcheng District

institute: School of Basic Medicine, Peking Union Medical College (PUMC)

summary: It has long been known that nuclear speckle is a nuclear body that contains numerous RNA splicing and processing proteins. Accumulating evidences have shown that the genomic regions of highly transcribed genes and their corresponding nascent premRNAs are organized around nuclear speckles to achieve co-transcriptional RNA processing. But, how the actively transcribed genes are organized around nuclear speckle is unknown. Here, we identified RNAs localized in nuclear speckles and found that a class of Alu-repeat RNAs were highly enriched around the nuclear speckle. These RNAs tend to directly bind to the genomic regions of actively transcribed genes via its Alu element and form R-loops. Meanwhile, they can interact with nuclear speckle protein components and promote their aggregation and phase separation, synchronously mediating the formation of nuclear speckle and organization of the actively transcribed genes around them. Depletion of these Alu-repeat RNAs results in a significant reduction in the size of nuclear speckle, far away of active genes from nuclear speckle, and the consequent reduction in RNA processing. This mechanism is essential for the high expression of a large number of erythroid specific genes during erythrocyte development, which would be severely impeded in the absence of these repeat-containing RNAs. Our work highlights the emerging role of Alu-repeat RNAs in assembling nuclear speckles and mediating spatial co-transcriptional RNA processing.

overall_design: RIP-seq, CUT&Tag, ChIRP-seq, DRIP-seq and Poly(A)+ RNA-seq datasets.

first: Siqi

last: Liu

first: Xinyan

last: Shen

first: Yanni

last: Ma

first: Jia

last: Yu


first: Xinjian

last: Wang

summary: Cardiac transverse tubules (T-tubules) are regular spaced plasma membrane invaginations that play an essential role in establishing excitation-contraction coupling of cardiomyocytes, yet the molecular machinery that controls T-tubule formation remains elusive. The endosomal sorting complex required for transport (ESCRT) proteins are involved in a variety of cellular events primarily through regulating membrane deformation in a reverse topology mode (budding away from cytosol). We demonstrate that  Chmp4b is essential for T-tubule formation, a process dependent on the ESCRT-I component Tsg101. Our results uncover that the spatiotemporal organization of ESCRT can orchestrate invaginations of cardiomyocyte plasma membrane.

overall_design: For the deletion of Tsg101 in postnatal hearts, postnatal-day-0 (P0) Tsg101F/F mice were injected with 2×1010 vg/g AAV9-cTnT-Cre-T2A-EGFP at P0 (called after TCK), with controls receiving an equivalent dose of AAV9-cTnT-EGFP (called after TNC). Hearts were harvest at P10, we then performed gene expression profiling analysis using data obtained from RNA-seq, 5 mice per group.

first: Hongkun

last: Wu

first: Peidong

last: Han


title: The OsCCT22- OsSh1-OsCAD2 module facilitate seed shattering by suppress lignin biosynthesis in rice [ChIP-seq]

first: He

last: wei

overall_design: ChIP-seq analysis of OsSh1-GFP transgene transgene line using GFP antibody.

first: Wei

last: He


title: 3D Chromatin Remodeling in B-cell Development and B-cell Acute Lymphoblastic Leukemia [ChIP-seq]

first: Yohana

last: Ghebrechristos

first: Nikki

last: Evensen

first: Soobeom

last: Lee

first: Finnegan

last: Clark

first: Stanley

last: Clarke

first: Matthew

last: Witkowski

first: Ziyan

last: Lin

first: Hua

last: Zhou


title: Inhibition of circulating glycocholic acid-regulated signaling potentiates immune checkpoint therapy in colorectal cancer immune evasion and resistance to anti PD1 immunotherapy by suppressing FBXW7 mediated CD73 degradation

city: Shanghai

first: Senlin

last: Zhao

address: 270 Dong An Road

department: Colorectal Surgery

institute: Cancer Hospital, Fudan University

summary: Serum bile acids (BAs) (1) are an important risk factor for the initiation and progression of cancer, but their roles in colorectal cancer (CRC) remain largely unknown. The present study showed that glycocholic acid (GCA), a primary BA, was highly accumulated in the serum of patients with CRC. In a mouse model of CRC, GCA diet promoted programmed death-ligand 1 (PD-L1) expression in tumors, which attenuated CD8+ T cell-mediated antitumor responses in the tumor microenvironment (TME) (2), and promoted the occurrence and development of CRC. Increased PD-L1 expression was caused by the reduction in activity of the BA receptor farnesoid X receptor (FXR). Mechanistically, FXR acted as transcriptional repressor for the transcription factor SRY-box transcription factor 14 (SOX14), and suppressed the palmitoylation and stabilization of PD-L1 by inhibiting the SOX14-mediated expression of zinc finger DHHC-type palmitoyl transferase 9 (DHHC9). Notably, genetically silencing SOX14 and DHHC9 in cancer cells or administering an FXR agonist synergized with anti-PD-1 therapy, leading to reduced tumor growth in GCA-fed mice. Together, the present findings reveal a previously unrecognized mechanism of BA in remodeling the TME to mediate CRC resistance to immunotherapy, which may have clinical implications for developing immunotherapy strategies for patients with CRC.

overall_design: 6-week-old C57BL/6Jmice were injected subcutaneously into the right flank with 1.0x106 MC38 cells, then  were treated with ot without GW4064 twice per week after 6 days.  Then, tumors  were  sheared and isolated into single-cell suspensions.  Goblet cells were considered as a homogeneous population and analyzed using scRNAseq.

first: Jing

last: Zhang

first: Yushuai

last: Mi

first: Zijuan

last: Hu

first: Xinyang

last: Zhong

first: Ye

last: Xu

first: Sanjun

last: Cai

first: Xinxiang

last: Li

first: Ping

last: Wei

first: WanJun

last: Chen

first: Dawei


title: 3D Chromatin Remodeling in B-cell Development and B-cell Acute Lymphoblastic Leukemia [RNA-seq]

first: Yohana

last: Ghebrechristos

first: Nikki

last: Evensen

first: Soobeom

first: Elizabeth

last: Raetz

first: David

last: Teachey

first: Timothée

last: Lionnet

first: Aristotelis

last: Tsirigos

first: William

last: Carroll

first: Iannis

last: Aifantis


title: SEP3 Tetrameric Complexes Promote Flower Development

city: Berlin

first: Kerstin

last: Kaufmann

address: Philippstr. 11-13 (House 22)

department: Plant Cell and Molecular Biology

country: Germany

institute: Humboldt-Universitaet zu Berlin

summary: Being able to tetramerize has dramatically expanded the functional diversity of the MADS transcription factor family in plants. A key MADS, SEPALLATA3 (SEP3), functions as a "glue", mediating tetramerization with other MADS TFs. Here, we use a SEP3 tetramerization deficient mutation, SEP3tet, which decouples SEP3 tetramerization and DNA-binding activities to study the significance of tetramerization in target gene regulation.

overall_design: ChIP-seq datasets have been generated from rescue lines of wildtype SEP3 (SEP3wt) and a tetramerization deficient SEP3 (SEP3tet) in the sep1,2,3 background. ChIP-seq was done using SEP3 native antibody. Two biology replicates were generated for each line. In addition, the pre-immune serum of SEP3 was used to generate the mock reference dataset for each line.

first: Xiaocai

first: Jose

last: Muino


title: Transcriptomic profiling of ZFTA ependymoma cell line after 5-Azacytidine treatment.

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

summary: Transcriptomic profiling of ZFTA ependymoma cell line was treated with the hypomethylating (5-Azacytidine) for a period of 96 hours to assess global transcriptional response. The focus of these transcriptional studies were identified changes in gene expression following treatment with hypomethylating agent, such as, pathways and biological functions alterations to defining novel promoters genes regulated by DNA methylation and potential demethylation therapy.

overall_design: Therapeutic induced gene expression changes were assayed in human cell line (BXD-1425) after 96 hours of continuos in vitro exposure to control (0uM) and 5-Azacytidine (3uM).

first: L

last: Tone

first: C

first: E

last: Valera

last: Carlotti

first: R

last: Queiroz


title: 3D Chromatin Remodeling in B-cell Development and B-cell Acute Lymphoblastic Leukemia

first: Yohana

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

overall_design: Refer to individual Series


title: Effect of COQ6 D316Y homozygosity on BMDM transcriptome

first: Sharon

middle: Celeste

last: Morley

address: 625 S Euclid

institute: Washington University in St. Louis

summary: To investigate the effect of the COQ6 D316Y SNV on BMDM function, we performed RNA-seq on BMDMs from WT and homozygous D316Y mice at baseline and 24h after LPS stimulation

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and D316Y BMDMs with and without stimulation

first: Emma

last: Walker


title: Microinjection of human ESC-derived trophoblast stem cells (hES-TSCs) to mouse blastocysts

city: Taipa, Macau

first: Siyi

last: FU

state: Taipa, Macau

address: Room 2003,  N22 Building

department: FHS

country: Macau

institute: University of Macau

summary:
Purpose: 1. Characterize hESCs and hESC-derived trophoblast stem cells
Results: 1. hESCs have high level of most pluripotency markers; 2. hESC-derived trophoblast stem cells specifically express trophoblast markers.

overall_design: Examination mRNA profiles of human ESCs and ESC-derived trophoblast stem cells

last: Fu


title: Targeting the EWS::FLI1 Transcription Factor for Ewing Sarcoma: A Phase 1/2 Study of Trabectedin and Low Dose Irinotecan (SARC037)

status: Public on Mar 02 2026

city: Ann Arbor

first: Patrick

last: Grohar

state: MI

address: 1600 Huron Parkway

institute: University of Michigan Medical School

summary: The EWS::FLI1 transcription factor drives the growth of Ewing sarcoma (ES). Trabectedin above a threshold concentration reverses the activity of EWS::FLI1, which is potentiated in vivo by low dose irinotecan. This open label phase 1/2 trial of trabectedin with irinotecan enrolled 37 relapsed/refractory ES patients (SARC037; NCT04067115). The recommended phase 2 dose (RP2D) was trabectedin 1.0 mg/m2 over 1 hour (Day 1) and irinotecan 25 mg/m2 (Days 2 & 4) of 21-day cycle. Toxicities were manageable with >Grade 3 toxicities (>15%) of myelosuppression and ALT elevations at RP2D. The phase 2 objective response rate was 33% (39%, including RP2D phase 1 patients) and 6-month PFS was 48%. Transcriptional profiling demonstrated reversal of the EWS::FLI1 transcriptome in tumors from a subset of patients. Additional correlative objectives captured molecular profiling, ctDNA levels, and 18F-FLT PET avidity. The combination of trabectedin and irinotecan is active in ES and suppresses its driver, EWS::FLI1.

overall_design: Tumor needle biopsies from five patients with relapsed, treatment-refractory, Ewing sarcoma and documented EWS::FLI1 fusion/breakpoint, before and after treatment with 1h trabectedin infusion and prior to irinotecan administration.

first: Gretchen

middle: Y

last: Lam


title: 3D Chromatin Remodeling in B-cell Development and B-cell Acute Lymphoblastic Leukemia [ATAC-seq]

last: Ghebrechristos

first: Nikki

last: Evensen

first: Soobeom

last: Lee

first: Finnegan

last: Clark

first: Stanley

last: Clarke

first: Matthew

last: Witkowski

first: Ziyan

last: Lin

first: Hua

last: Zhou

first: Elizabeth

last: Raetz

first: David

last: Teachey

first: Timothée

last: Lionnet

first: Aristotelis


title: Single cell RNAseq of whole lungs extracted from Bleomycin-induced pulmonary fibrosis models of wild type and Kdm7a KO mice.

first: Mitsuyoshi

last: Nakao

summary: Bleomycin-induced pulmonary fibrosis is more severe in Kdm7a KO mice than in wild type mice, with this exacerbation being driven by excessive M2 polarization of interstitial macrophages.

overall_design: Bleomycin (0.75 mg/kg body weight) dissolved in PBS was administered intratracheally to three wild-type and three Kdm7a KO mice. Mice were sacrificed on day 21 post-administration, and their lungs were harvested. The lungs were then enzymatically digested and processed into single-cell suspensions.

first: Naofumi

last: Funagura

first: Tomoaki

last: Koga


title: Transcriptome analysis of wild type and MafB knockout macrophages stimulated for 24 h with IL-4

city: Seoul

first: June

last: Yang

address: 145, Anam-ro, Seongbuk-gu, Seoul, Republic of Korea

department: Biotechnology

country: South Korea

institute: Korea University

summary: The functional polarity of macrophages driven by specific cues within local milieu can play a pivotal role in the pathogenesis of various human diseases. Identifying a key regulator to control macrophage polarization is of great importance in the therapeutic strategies for modulating macrophage function to improve clinical outcome. Here, we identify MafB as an essential transcription factor to induce M2 macrophage polarization. The myeloid-specific genetic ablation of Mafb in mice causes a severe defect in M2 macrophage polarization, ultimately leading to a deterioration of inflammatory diseases such as experimental sepsis or colitis.

overall_design: Wild type and MafB-deficient macrophages stimulated for 24 h with IL-4 were profiled for mRNA expression by RNA-sequencing analysis.

first: Jun


title: Targeting the EWS::FLI1 Transcription Factor for Ewing Sarcoma: A Phase 1/2 Study of Trabectedin and Low Dose Irinotecan (SARC037) - RNA-Seq

first: Patrick

middle: J

last: Grohar

first: Rebecca

last: Kaufman

first: Gretchen


title: The role of Galectin-8 in mouse stomach maturation

first: Jeffrey

middle: Wade

last: Brown

address: 660 S. Euclid

summary: We compare the RNA expression profiles of the stomachs from Lgals8–/– to wild-type C57BL/6J mice at 3 weeks and 8 weeks of age to search for differences that could explain an observed delay in maturation of the chief cell population

overall_design: RNA-seq profiling of Lgals8–/– and wild-type C57BL/6J at 3 weeks and 8 weeks of age.

first: Xiaobo


title: LKB1 functions as a checkpoint for neuronal-glial balance during enteric nervous system development

city: La Tronche

first: Chantal

last: Thibert

address: Site Santé - Allée des Alpes

institute: Institute for Advanced Biosciences

summary: How the energy status of enteric progenitors controls neurogliogenesis and the subsequent formation of the complex enteric nervous system (ENS) remains poorly understood. We previously showed that the tumor suppressor kinase LKB1 is essential for postnatal ENS maintenance through amino acid homeostasis. Here, we investigated LKB1’s functions during embryonic ENS formation using a genetically engineered mouse model with conditional Lkb1 inactivation in neural crest progenitors during gut colonization. Using advanced 3D imaging techniques on cleared tissue including lightsheet microscopy and adaptive optics confocal microscopy, we found that Lkb1 loss impairs early neuronal differentiation followed by progressive glial degeneration, leading to hypoganglionosis and compromised digestive tissue integrity. Notably, Lkb1 inactivation induced a transient upregulation of the glial stress marker S100 at mid-gestation, suggestive of a reactive glial state preceding glial loss. Consistent with this response, Lkb1 loss elevated oxidative stress in the digestive tract and in neural crest progenitors and their glial derivatives, triggering DNA damage and p53 activation. Although p53 ablation rescued glial specification in vitro and glial maintenance in vivo, it only partially restored ENS architecture in vivo without rescuing enteric neuron numbers. Together, these findings establish LKB1 as a critical metabolic checkpoint governing neuronal-glial balance during ENS development and suggest that dysregulated LKB1 signaling may contribute to human enteric neurogliopathies.

overall_design: To identify the downstream effectors of Lkb1 loss, we performed transcriptomic profiling (bulk RNAseq) of JoMa1.3 progenitors following Lkb1 knockdown using siRNA

first: Jordan

last: Allard


title: Differential Expression and Target Gene Analysis of PBMC-Derived microRNAs as diagnostic / disease-associated biomarkers in Acute Lymphoblastic Leukemia

city: Riyadh

first: Ghaida

last: Almuneef

address: KSA-Riyadh

country: Saudi Arabia

institute: King Abdullah International Medical Research Center

summary:
Clinical specimens were collected from patients with Acute Lymphoblastic Leukemia (ALL) and from non-leukemic controls. Total RNA (including small RNA) was profiled using the Affymetrix GeneChip miRNA 4.0 array to identify differentially expressed miRNAs between ALL and controls
Raw CEL files were generated using standard Affymetrix GeneChip scanning and feature extraction (AGCC or equivalent). Expression values were obtained in R using RMA normalization, followed by probe filtering was applied. Differential expression was assessed with limma using an ALL vs CTRL contrast with Benjamini–Hochberg FDR correction.

overall_design: Case–control study comparing ALL vs non-leukemic controls, one microarray per sample (Affymetrix GeneChip miRNA 4.0). miRNA differential expression was tested between groups

first: Hadil

last: Alahdal

first: Fatemah

last: Basingab

first: Kawther

last: Zaher

first: Alia

middle: M

last: Aldahlawi


title: Brassinosteroids mediate proper coordination of sepal elongation [Spatial Transcriptomics]

city: Ithaca

first: Byron

last: Rusnak

email: bzr5@cornell.edu, ahr75@cornell.edu

address: 237 Tower Rd

department: Plant Biology

institute: Cornell University

summary: Arabidopsis sepals must grow in a coordinated and robust fashion to a consistent size and shape to close and protect the developing flower bud. To understand how this robust coordination occurs, we use the loss of robustness mutant development related myb-like1 (drmy1), which exhibits variable sepal initiation and growth, causing failure of the sepals to close the flower bud. Specifically, drmy1 has overgrown outer (abaxial) sepals and undergrown inner (adaxial) sepals, leading to a large discrepancy in the sizes of different sepals within individual flower buds. Using single cell and spatial RNA-seq, we found changes in expression of key genes related to brassinosteroid (BR) signaling in drmy1, particularly in cell types important to young flower bud development such as epidermal cells, boundary cells, and meristematic cells. Confocal imaging of a BRI1-EMS-SUPPRESSOR1 (BES1) ratiometric reporter confirms that BR signaling is upregulated and more variable in young drmy1 sepals. Subsequently, we found that altering BR signaling in drmy1 by crossing with BR mutants or adding brassinolide (a potent brassinosteroid) or brassinazole (a brassinosteroid biosynthesis inhibitor) can partially rescue this elongation defect by differentially altering the relative growth of the inner and outer sepals. Increasing BR signaling rescues by increasing the growth of the inner sepal but not the outer sepal, while decreasing BR signaling rescues by decreasing the growth of the outer sepal but not the inner sepal. These results suggest that brassinosteroids mediate the robust coordination of the growth rates between inner and outer sepals during early development, ensuring proper flower bud closure.

overall_design: 108 hours after induction with dexamethasone, WT and drmy1 in the ap1cal 35S::AP1-GR background was harvested by cutting off the cauliflower-like clusters of flower buds and embedded in OCT compound and flash frozen in liquid nitrogen cooled isopentane (2-methylbutane). 10 micron thick cryosections were then taken on a cryostat and placed on 10x Visium spatial transcriptomic capture areas

last: Rusank

first: Lilijana

last: Oliver

first: Kyle

last: Procopio

first: Adrienne

last: Roeder


title: Glomerulus-enriched RNA-seq of BALB/cAjcl and BALB/cByJcl mice at baseline and Day 5 after Adriamycin administration

city: Towada

first: Masaki

last: Watanabe

department: School of Veterinary Medicine

institute: Kitasato University

summary: This dataset contains glomerulus-enriched RNA sequencing (RNA-seq) data from two BALB/c mouse substrains, BALB/cAjcl (Ajcl) and BALB/cByJcl (ByJcl). Glomeruli were isolated using a Dynabeads-based perfusion method. Samples were collected from untreated (baseline) mice and from mice on Day 5 after a single intravenous administration of adriamycin (doxorubicin hydrochloride; 10 mg/kg; retro-orbital injection under isoflurane anesthesia). Total RNA was extracted from isolated glomeruli, and only samples with RNA integrity number (RIN) ≥ 7.0 were used. RNA-seq libraries were prepared using poly(A) selection for strand-specific sequencing and sequenced on an Illumina NovaSeq 6000 platform to generate 2 × 150 bp paired-end reads (approximately 6 Gb per sample). Primary processing included quality control (FastQC), trimming (Trimmomatic), alignment to the Mus musculus reference genome (GRCm39) with STAR, and gene-level read summarization with featureCounts. Gene-level raw count matrices (tab-delimited) are provided as processed data files.

overall_design: Glomerulus-enriched RNA-seq was performed on two BALB/c mouse substrains, BALB/cAjcl (Ajcl) and BALB/cByJcl (ByJcl). Glomeruli were isolated using a Dynabeads-based perfusion method. Samples were collected from untreated (baseline) mice and from mice on Day 5 after a single intravenous administration of adriamycin (10 mg/kg). For baseline comparisons, glomeruli were isolated from untreated Ajcl (n = 3) and ByJcl (n = 3) mice. For post-ADR comparisons, glomeruli were isolated from Ajcl (n = 3) and ByJcl (n = 3) mice at Day 5 after treatment. All libraries were prepared using poly(A) selection and sequenced as 2 × 150 bp paired-end reads.

first: Ryuya

last: Nakagawa

first: Nobuya

last: Sasaki


title: A Single-Cell and Spatial 3D-Epigenomic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons

city: Los Angeles

first: Chongyuan

last: Luo

address: 695 Charles E Young Drive South

department: Human Genetics

institute: University of California Los Angeles

summary: During human brain development, the basal ganglia arise from transient progenitor zones in the ventral telencephalon—the lateral, medial, and caudal ganglionic eminences (LGE, MGE, and CGE, respectively). These regions generate inhibitory projection neurons and interneurons that populate diverse brain regions, yet the developmental programs underlying this cellular diversity remain incompletely understood. This study aims to elucidate the epigenomic and 3D-genomic dynamics involved in the specification and maturation of GEs and GE-derived neurons, using single-nucleus methyl-3C sequencing (snm3C-seq), chromatin+RNA single-molecule imaging, and highly-multiplexed spatial transcriptomics. The multi-modal data support a heterogeneous temporal progression across GEs, with LGE showing declining neurogenic activity in mid-gestation and CGE exhibiting prolonged activity in infancy. We reconstructed the regulatory programs of MSN subtype specification and revealed an unusually synchronized maturation of the 3D-Epigenome across individual MSN cells. The differentiation of neurons and glial cells is associated with permanent Short-range Enriched (SE) and Long-range Enriched (LE) chromatin conformation, respectively 1. We found a reversible shift toward LE in projection neurons in early infancy, and a temporary SE conformation during transition between oligodendrocyte progenitors (OPCs) and oligodendrocytes (ODCs). Mapping genetic risk for neuropsychiatric disease to single brain cells highlights the critical role of MSNs in infancy. Our study provides a comprehensive 3D-Epigenomic map of human brain cell development in the basal ganglia and reveals highly complex and lineage-specific 3D genomic dynamics.

overall_design:
The study generated 155,225 new snm3C-seq profiles sampled from nine developing brains.  The dissected brain regions include the lateral ganglionic eminence (LGE), medial ganglionic eminence (MGE), caudal ganglionic eminence (CGE), putamen (Pu), caudate (Ca), globus pallidus (GP), ventricular zone (VZ), dorsallateral prefrontal (DFC), ventrolateral prefrontal (VFC), frontal (FCx), orbital frontal (OFC), temporal (TCx), cingulate (CCx), insular (ICx) cortices, postcentral gyrus (PoCG), and the hippocampus (HIP). Fastq files for the snm3C-seq data are available through the NeMO archive under accession nemo:dat-n5emc24 (https://assets.nemoarchive.org/dat-n5emc24).

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NeMO archive (https://assets.nemoarchive.org/dat-n5emc24) per NIH requirement
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first: Matthew

last: Heffel

first: Heng

last: Xu

first: Oier

last: Pastor-Alonso

first: Xinzhe

last: Li

first: Rayyan

middle: I

last: Ghoor

first: Runjia

first: Yi

last: Zhang

first: Joonho

last: Kum

first: Mohammad

last: Baig

first: Jon

last: Paino

first: Min Jen

last: Tsai

first: Zachary

last: von Behren

first: Mohini

last: Bhade

first: Siqian

first: Kadellyn

last: Sandoval

first: Jessica

last: Scholes

first: Felicia

last: Codrea

last: Calimlim

first: Emma

last: Liao

first: Gwyneth

last: Leung

first: Jaeyeon

last: Kim

first: Eleazar

last: Eskin

first: Jonathan

last: Flint

first: Bogdan

last: Pasaniuc

first: Eran

last: Mukamel

first: Jason

last: Ernst

first: Mercedes

middle: F

last: Parades


title: DNAJC17 regulates RNA splicing in auditory hair cells and is required for hearing

city: nanjing

first: wang

last: ziyang

address: 12 Xuefu Road, Pukou District

institute: nanjing university

summary: RNA splicing is essential for gene regulation, but its role in maintaining cochlear hair cell function remains incompletely understood. Here, we identified a heterozygous missense variant in DNAJC17 (c.401A>C, p.E134A), which encodes a spliceosome-associated protein, that segregates with adult-onset progressive hearing loss in a multigenerational family. Hair cell-specific deletion of Dnajc17 in mice resulted in profound deafness with progressive hair cell degeneration, establishing its essential role in cochlear maintenance. Hair cells lacking DNAJC17 exhibited marked stereocilia disorganization accompanied by widespread alternative splicing defects in the cochlea. Notably, the dual-specificity protein kinase Clk1 that regulates pre-mRNA splicing showed altered exon inclusion, consistent with disruption of splicing control networks. In addition, Dnajc17 p.E134A knock in mice developed adult-onset progressive hearing loss with stereocilia and mitochondria abnormalities but preserved hair cell survival, recapitulating the human phenotype. Together, these findings identify DNAJC17 as a gene for autosomal dominant hearing loss and identify RNA splicing regulation as a key mechanism required for long-term maintenance of cochlear hair cell integrity.

overall_design: To explore the effect of Dnajc17 on auditory function in mice, we generated a knockout strain to explore the changes in its transcriptome level.

first: Luping

last: Zhang

first: Ziyang

last: Wang

first: Qing

last: Liu

first: Guoqiang

last: Wan


title: Competition between commensal protists shapes gut mucosal immunity in mice

city: Madison

first: Marienela

middle: Yaritza

last: Heredia

state: WI

address: 1550 Linden Drive

department: Medical Microbiology & Immunology

institute: University of Wisconsin-Madison

summary: Intestinal protists are emerging as key modulators of host immunity and microbial ecology, yet their roles remain poorly defined. Here, we investigated the role of two distinct protists, the amoeba Entamoeba muris, and the parabasalid, Tritrichomonas, to determine how they shape gut immunity in vivo individually and together. Unlike the well-characterized inducer of type 2 immunity, Tritrichomonas, which activates the tuft cell–IL-25–ILC2 circuit in the small intestine, E. muris failed to elicit robust immune responses in the intestine or colon. However, introduction of E. muris into mice naturally colonized by Tritrichomonas spp., or co-infection with E. muris and Tritrichomonas spp. suppressed the Tritrichomonas-induced type-2 response in the small intestine. Fecal and cecal qPCR suggest that E. muris may outcompete Tritrichomonas spp., with reduced protist loads in the cecum and possibly diminished succinate-driven tuft cell activation. We also identified sex-specific differences in the intestinal response to primary Tritrichomonas spp. colonization which have not previously been described. These findings reveal that E. muris can dampen existing type-2 immune circuits without triggering overt inflammation, underscoring its role as an immunomodulatory agent. This work provides a framework for understanding how commensal protists interact within the gut ecosystem and shape mucosal immunity in the absence of pathogenicity.

overall_design: Bulk RNA-seq profiling of distal small intestine and proximal colon tissue segments harvested from uninfected mice, E. muris-infected mice, Tritrichomonas-infected mice, or mice co-infected with both E. muris and Tritrichomonas. All mice are of the C57BL/6J background. Tissues were harvested at 28 dpi.

first: Paul

last: Kuehnert

first: Kylie

last: March

first: Laura

last: Knoll

first: Claire

last: O'Leary


title: USP18 inhibits protective immune responses and the intracellular control of Mycobacterium tuberculosis in macrophages.

city: Stockholm

first: Martin

last: Rottenberg

address: Solna vägen 9

country: Sweden

institute: Karolinska Institutet

summary: We compared the transcriptome  profile of M. tuberculosis-infected murine bone marrow derived macrophages (BMM) treated with either the USP18 small molecule inhibitor BB7 or an inactive control (NC),   and uninfected controls as described below.   We identified 710 differentially expressed genes (DEGs) between uninfected and Mtb BMM and 243 DEGs comparing Mtb-BB7 vs Mtb BMM, 129 of these DEGs were upregulated. Gene ontology (GO) analysis showed enrichment of pathways related to antiviral responses, innate immune activation and inflammasome signalling when comparing Mtb-BB7 vs Mtb BMM. Conversely, genes associated with stress responses, hypoxia  and antioxidant activity were downregulated in Mtb-BB7.

overall_design: RNA seq was performed in triplicate independent cultures of BMM treated either with10 mM uM BB7 or NC , infected 4 h after treatment with M. tuberculosis  at a MOI of 5:1. RNA was extracted 8h after Mtb infection from uninfected BMM controls (Control), Mtb infected BMM treated with NC (Mtb), and MGO-treated, Mtb-infected BMM  (Mtb-BB7).

first: Zhen

last: Gong

first: Qiao


title: A multimodal characterization of the human uncinate fasciculus

city: Montreal

first: Naguib

last: Mechawar

address: 6875 Boulevard LaSalle

institute: Douglas Mental Health University Institute

summary: The uncinate fasciculus (UF) is a hook-shaped long-range association white matter tract that serves to bidirectionally transmit information between the anterior temporal lobe and the orbitofrontal cortex. Neuroimaging studies have suggested that changes in UF microstructure are involved in the neurobiological sequalae of childhood abuse (CA). Given that the UF is not present in rodents, it is vastly understudied with no cellular and molecular information available. To this end, we aimed to perform a multimodal characterization of the UF between individuals diagnosed with depression who died by suicide with (DS-CA) and without a history of severe CA (DS) and psychiatrically healthy individuals (CTRL). Fresh frozen UF tissue was obtained from the Douglas Bell-Canada Brain Bank, with phenotypic information collected via psychological autopsy. Immunohistochemistry with PDGFRα and NogoA was used to label oligodendrocyte precursor cell (OPC) and oligodendrocyte (OL), respectively, and stereology was performed to ascertain cell density and soma volume. Single nucleus RNA sequencing (snRNAseq) was used to generate a transcriptomic survey of the distinct cell types found in the UF. Finally, spectral focusing Coherent Anti-Stokes Raman Scattering (sf-CARS) microscopy was employed in tandem with a custom AxonDeepSeg segmentation model to measure axon diameter, myelin thickness, and g-ratio. No group differences were observed in histology or ultrastructure metrics, but nearly 50 differentially expressed genes (DEG) were identified between groups. Interestingly NECTIN3, the top DEG downregulated in OL1 and OL3 of DS-CA, is a computationally predicted target of the microRNA MIR646, the host gene of which was significantly downregulated in multiple clusters of DS-CA. Age-associated changes were pronounced and observed in all modalities, including an age-related increase in OL density, extensive changes in glial gene expression, as well as decreases in axon diameter and g-ratio. This study serves as a foundational resource on the molecular and cellular properties of the human UF. Our results suggest that observable myelin-related traces of depression or CA are limited in the UF and highlights the need for future research on the cellular and molecular properties of white matter tracts during aging.

overall_design: Single nucleus RNA sequencing of human postmortem uncinate fasciculus from Brodmann Area 38 comparing DS-CA (individuals with depression who died by suicide with a history of severe childhood abuse) versus CTRL (control).

first: Kelly

last: Perlman

first: Sarah

last: Barnett-Burns

first: John

last: Kim

first: Valérie

last: Pineau Noël

first: Armand

last: Collins

first: Justine

last: Major

first: Malosree

last: Maitra

first: Anjali

last: Chawla

first: Murielle

last: Mardenli

first: Sébastien

last: Jerczynski

first: Maria Antonietta

last: Davoli

first: Julien

last: Cohen-Adad

first: Daniel

last: Côté

first: Richard

last: Bazinet

first: Corina

last: Nagy

first: Gustavo

last: Turecki


title: Thermal adaptation cross-talks with azole response through lncRNA in Aspergillus fumigatus

city: Riverside

first: Jason

last: Stajich

address: 900 University Ave

department: Microbiology and Plant Pathology

institute: University of California-Riverside

summary: Newer fungal pathogens have emerged recently, attributed to their adaptation to higher environmental temperatures. With increasing earth’s temperatures, many existing fungal pathogens are adapting and show changes in host-pathogen interactions, disease pattern, and response to the antimicrobial drugs. Here, we show that thermal adaptation to 42C leads to reversible changes in fungal colony size, appearance, and azole drug response in human pathogenic fungus Aspergillus fumigatus. Importantly, this adaptation is mediated by a lncRNA, afu-182, whose RNA levels negatively correlate with temperature. Either growth back at lower temperature or ectopically increasing afu-182 RNA levels reverses the temperature adaptation. Global transcriptomic analyses show enrichment of pathogenesis associated genes at 37C and 42C compared to 25C. Interestingly, we show that small heat shock proteins and chaperones, but not ATP dependent heat-shock proteins are negatively regulated by afu-182 at 37C and 42C. Previously, we have shown that delta afu-182 strain produce worse disease outcomes in a murine model of invasive pulmonary aspergilllosis. Here, more importantly, we show that overexpression of afu-182 in clinically azole resistant isolates increased survival in a murine model of invasive pulmonary aspergillosis. Taken together, fungal adaptation to increased temperature leads to decrease in afu-182 RNA levels that is associated with worse disease outcomes upon azole treatment and an increase in MIC. This provides a framework, to take temperature into account when analyzing the rise in azole MIC in environmental and clinical isolates.

overall_design: Whole transcriptomic profiling of WT CEA10 and ∆afu-182 strains grown at 25C, 37C, and 42C stationary cultures for 72 hours.

first: Nava

middle: R

last: Poudyal

first: Ryan

last: Mehlem

first: Ritu

last: Devkota

first: Sourabh

last: Dhingra


title: microRNA-21 promotes dysregulated lipid metabolism and hepatocellular carcinoma [bulk RNA-Seq]

city: Salt Lake City

first: Kimberley

middle: Jane

last: Evason

state: UT

address: 2000 Circle of Hope

institute: University of Utah

summary: The prevalence of hepatocellular carcinoma (HCC) is rising in parallel with increasing obesity and metabolic dysfunction-associated steatohepatitis (MASH). MicroRNAs are key post-transcriptional regulators of gene expression and are attractive targets for HCC therapy. Here we sought to identify and characterize dysregulated microRNAs in MASH-driven HCC (MASH-HCC). We profiled microRNA expression in liver tissue from patients with MASH or MASH-HCC and in zebrafish HCC driven by activated β-catenin (ABC), one of the most commonly mutated oncogenes in MASH-HCC. We found overlap between dysregulated human and zebrafish miRNAs, including miR-21, which was increasingly upregulated from normal liver to MASH to MASH-HCC. We generated transgenic zebrafish that overexpress or sponge miR-21 in hepatocytes. We found that miR-21 overexpression caused larval liver overgrowth and increased HCC, while miR-21 sponge suppressed β-catenin-driven larval liver overgrowth. By performing histologic and lipidomic analysis, we found that overexpression of miR-21, like ABC, suppressed lipid accumulation in response to a high cholesterol diet and increased accumulation of acylcarnitines. Thus miR-21, which is similarly upregulated in human and zebrafish HCC, promotes lipid metabolic changes that may help drive hepatocarcinogenesis.

overall_design: The goal of this study was to profile mRNAs in liver tissues from 13 dpf zebrafish, with and without hepatocyte-specific overexpression of microRNA-21, fed either high cholesterol diet or normal control diet from 6 dpf to 13 dpf.

first: Chad

last: VanSant-Webb

first: Jessye

last: Castro

first: Audrey

last: Su

first: Kiandra

last: Hawkins

first: Aavrati

last: Saxena

first: Jillian

last: Wright

last: Smith

first: Marco

last: Fragoso- García

first: Yian

last: Chen

first: Carrie

last: Barton

first: Chris

last: Stubben

last: O'Connell

first: Gregory

middle: S

last: Ducker


title: Shen-yuan-dan capsule inhibits METTL3-mediated m6A methylation to restore autophagy homeostasis and attenuate post-myocardial infarction heart failure

city: Beijing

first: Shuaijie

last: Guo

state: None Selected

address: 23 Art Museum Back Street, Dongcheng District, Beijing, China

institute: Beijing Hospital of Traditional Chinese Medicine

summary: Heart failure (HF) after myocardial infarction (MI) is a serious health issue. This study investigates the therapeutic effects of Shen-Yuan-Dan Capsule (SYD) on post-MI HF and explores its mechanisms, particularly involving m6A modification and autophagy. Using network pharmacology and MeRIP-seq, we identified potential epitranscriptomic targets. In vitro, H9c2 cardiomyocytes were treated with Phenylephrine (PE) and SYD. MeRIP-seq analysis identified differential m6A peak distribution among control, PE-induced, and SYD-treated groups, revealing that SYD alleviates HF by regulating the mTOR/TFEB autophagy pathway through inhibition of METTL3-mediated m6A modification.

overall_design: To investigate the m6A epitranscriptomic changes and identify potential targets of Shen-Yuan-Dan (SYD) capsule, we performed m6A Methylated RNA Immunoprecipitation Sequencing (MeRIP-seq). H9c2 cardiomyocytes were divided into three experimental groups: Control group (no intervention), Model group (induced with 50 µM Phenylephrine for 24 h to induce hypertrophy), and SYD group (treated with 1 mg/mL SYD and 50 µM Phenylephrine for 24 h). Total RNA was extracted, fragmented, and subjected to immunoprecipitation using an m6A-specific antibody. RNA libraries for both the immunoprecipitated (IP) and Input (total RNA) samples were constructed and sequenced.

first: Siqi

first: Changxu

last: Xie

first: Sinai

last: Li

first: Hongxu

last: Liu

first: Lei

last: Zhang

first: Weihong

first: Mingxue

last: Zhou


title: microRNA-21 promotes dysregulated lipid metabolism and hepatocellular carcinoma [miRNA-Seq]

first: Kimberley

last: Evason

type: Non-coding RNA profiling by high throughput sequencing

overall_design: The goal of this study was to profile microRNAs in liver tissues from transgenic adult male zebrafish expressing hepatocyte-specific activated beta-catenin compared to non-transgenic sibling controls.

first: Chad

last: VanSant-Webb

first: Jessye

last: Castro

first: Audrey

last: Su

first: Richard

first: Ryan


title: Transcriptomic analyses of mortality in HIV-associated Pneumocystis pneumonia

city: London

first: Rachel

last: Lai

address: Du Cane Road

department: Infectious Disease

country: United Kingdom

institute: Imperial College London

summary: Pneumocystis jirovecii pneumonia (PCP) remains a leading cause of respiratory failure and mortality in individuals with advanced HIV. While severe disease is classically attributed to hyperinflammation, the specific biological determinants driving fatal outcomes in patients remain poorly understood. To address this, we employed an integrated systems biology approach, performing transcriptomics, proteomics, and metabolomics on bronchoalveolar lavage fluid from a prospective cohort of 42 patients with HIV-associated PCP. We demonstrate that mortality is not primarily driven by uncontrolled fungal burden or isolated hyperinflammation, but by profound immunometabolic failure. Non-survivors exhibited marked suppression of local humoral immunity, characterised by depletion of immunoglobulins and complement components, together with significant impairment of apolipoprotein E (ApoE)-mediated alveolar repair and dysregulation of arginine-nitric oxide metabolism. A predictive model combining ApoE and arginine achieved high prognostic accuracy. Crucially, using an ex vivo immunodeficient precision-cut lung slice model, we functionally reversed this opsonic deficit with intravenous immunoglobulin, which restored macrophage-mediated fungal clearance. These findings redefine fatal HIV-associated PCP as a syndrome of immunometabolic failure and provide a mechanistic rationale for evaluating immunoglobulin replacement as a host-directed adjunctive therapy.

overall_design: Bronchoalveolar lavage (BAL) samples were collected from 24 patients with confirmed or probable PCP, 4 of which have died. BALf were centrifuged and the cell pellet lysed in TRIzol reagent. Following total RNA extraction, RNA-seq libaries were prepared and sequenced.


title: Gene syntax defines supercoiling-mediated transcriptional feedback [CUT&Tag II]

city: Cambridge

first: Christopher

middle: Patrick

last: Johnstone

state: Massachusetts

department: Chemical Engineering

institute: Massachusetts Institute of Technology

summary: Gene syntax---the order and arrangement of genes and their regulatory elements---shapes the dynamic coordination of both natural and synthetic gene circuits. Transcription at one locus profoundly impacts the transcription of nearby adjacent genes, but the molecular basis of this effect remains poorly understood. Here, using integrated reporter circuits in human cells, we show that the reciprocal effects of transcription and DNA supercoiling, which we term supercoiling-mediated feedback, regulates expression of adjacent genes in a syntax-specific manner. Using a suite of chromatin state assays, we measure syntax- and induction-dependent formation of chromatin structures in human induced pluripotent stem cells. Applying syntax as a design parameter and without altering sequence or copy number, we built compact gene circuits, tuning the expression mean, noise, and stoichiometry across diverse delivery methods and cell types. Integrating supercoiling-mediated feedback into models of gene regulation will expand our understanding of native systems and enhance the design of synthetic gene circuits.

overall_design: CUT&Tag profiling of hiPSC lines containing integrated synthetic gene pairs. Gene pairs with one of the four possible syntaxes (divergent, convergent, upstream tandem, downstream tandem) were integrated homozygously at the CYLBL locus in hiPSCs. The two genes were mTagBFP2-T2A-rtTA expressed constitutively from the CAG promoter, and mScarlet expressed from the inducible TRE promoter. These four lines were split into plus and minus induction conditions. The induced condition was treated with treated with 1000 ng/mL doxycycline for three days. Around 500k cells were collected per condition and per antibody (for H3K27me3, H3K4me3, H3K27ac, Pol II (ser2)) and bound to ConA beads before processing with a CUT&Tag protocol.

middle: P

first: Kasey

last: Love

first: Sneha

last: Kabaria

first: Albert

last: Blanch-Asensio

first: Deon

last: Ploessl

first: Emma

last: Peterman

last: Lee

first: Jiyoung

last: Yun

first: Conrad

middle: G

last: Oakes

first: Christine

last: Mummery

last: Davis

first: Brandon

last: DeKosky

first: Peter

middle: W

last: Zandstra

first: Kate

middle: E

last: Galloway


title: A Proteostasis Checkpoint Governs EGFR Stability and Cell Fitness, Defined by an lncRNA

city: Shenzhen

first: Diansheng

last: Zhou

address: 1066 Xueyuan Road, Nanshan District

institute: Shenzhen University

summary: EGFR RNA immunoprecipitation (RIP) followed by RNA profiling in EGFR wild-type (WT) and EGFR knockout (KO) cells.

overall_design: Two-condition experiment, EGFR WT vs EGFR KO cells. Biological replicates: 2 EGFR WT, 2  EGFR KO, independently grown and harvested. One replicate per array.

first: Taewan

last: Kim


title: Transcriptomic Landscape of Microglia in Mouse Models of Social Dysfunction and Oxytocin-Mediated Recovery

city: Kobe

first: Masafumi

last: Tsurutani

state: Hyogo

address: 2-2-3 Minatojima minami, Chuo-ku

department: Center for Biosystems Dynamics Research (BDR)

institute: RIKEN

summary: Atypical social behaviors modeling autism spectrum disorder have been observed in various genetic mutants and after embryonic perturbations in mice. We previously showed selective vulnerability of parvocellular oxytocin (OT) neurons in the paraventricular hypothalamus (PVH) in mice with social deficits following embryonic exposure to valproic acid (VPA). Here, we demonstrate that VPA induces transcriptional abnormalities in PVH microglia.

overall_design: High throughput RNA in situ hybridization performed with Xenium protocols on healthy controls and VPA-treated mice hypothalamus of brain.

first: Haruaki

last: Sato

first: Mitsue

last: Hagihara

first: Dooseon

last: Cho

first: Mitsutaka

last: Kadota

first: Takefumi

last: Kondo

first: Kazunari

last: Miyamichi


title: Gene syntax defines supercoiling-mediated transcriptional feedback [Micro-C]

first: Christopher

last: Johnstone

overall_design: Region Capture Micro-C profiling of hiPSC lines containing integrated synthetic gene pairs. Gene pairs with one of the four possible syntaxes (divergent, convergent, upstream tandem, downstream tandem) were integrated homozygously at the CYLBL locus in hiPSCs. The two genes were mTagBFP2-T2A-rtTA expressed constitutively from the CAG promoter, and mScarlet expressed from the inducible TRE promoter. These four lines were split into plus and minus induction conditions. The induced condition was treated with treated with 1000 ng/mL doxycycline for three days. Around 15M cells per condition were collected, crosslinked, and treated according to a Micro-C protocol. After library construction, a biotinylated oligo library was used to capture 3 loci: ~600 kb around the CLYBL locus, the region around the Rogi2 locus, and the region around the AAVS1 locus. The resulting capture libraries were amplified and sequenced.

first: Kasey

last: Love

first: Sneha

last: Kabaria

first: Albert

last: Blanch-Asensio

first: Deon

last: Ploessl

middle: L

last: Peterman

first: Rachel

last: Lee

first: Richard


title: Gene syntax defines supercoiling-mediated transcriptional feedback [CUT&RUN]

overall_design: GapRUN profiling of hiPSC lines containing integrated synthetic gene pairs. Gene pairs with one of the four possible syntaxes (divergent, convergent, upstream tandem, downstream tandem) were integrated homozygously at the CYLBL locus in hiPSCs. The two genes were mTagBFP2-T2A-rtTA expressed constitutively from the CAG promoter, and mScarlet expressed from the inducible TRE promoter. These four lines were split into plus and minus induction conditions. The induced condition was treated with treated with 1000 ng/mL doxycycline for three days. Two days prior to collection, the cells were transduced with a lentivirus expressing EGFP-GapR from an EF1a promoter. Around 500k cells were collected and bound to ConA beads. A fusion protein of MNase and a nanobody targeting EGFP was purified separately and added to the cells. After nanobody binding and wash steps, the MNase was activated to fragment the DNA, as in CUT&RUN. The resulting library was prepared as in CUT&RUN. The GapRUN protocol was derived from dx.doi.org/10.1016/j.molcel.2024.10.007; see the attached work here for protocol details.

first: Emma

first: Jiyoung

last: Yun

first: Conrad

last: Oakes

first: Christine

last: Mummery

last: Davis

first: Brandon

last: DeKosky

first: Peter

last: Zandstra

first: Kate

last: Galloway


title: Gene regulatory co-option drives birdsong neural circuit specialization [snRNA-seq]

city: San Francisco

first: Michael

last: Brainard

address: 675 Nelson Rising Ln

institute: University of California, San Francisco

summary: A defining feature of our species is the ability to manipulate our environment through the fine control of our hands and to communicate with others through the rapid and complex motor orchestration of human speech. The courtship song of songbirds shares a number of neural and behavioral similarities with human speech and other learned motor skills, providing a powerful model for understanding how enhanced motor skills develop at molecular and cellular levels. Birdsong is controlled by a specialized neural circuit whose properties enable high precision and speed. In particular, glutamatergic neurons in the birdsong motor region RA (Glut-RA) have higher spike rates and narrower action potentials than projection neurons in an adjacent motor region that does not control song, the dorsal intermediate arcopallium (Glut-AId). To identify candidate gene regulatory networks that establish the specialized properties of Glut-RA neurons, we performed single-nucleus profiling of gene expression and chromatin accessibility across song and non-song motor regions. We found that Glut-RA projection neurons and fast spiking interneurons (FSIs), a GABAergic type also characterized by high spike rates and narrow action potentials, share several transcriptional similarities. In particular, the transcription factor MAFB, which is essential for the development and fast-spiking physiology of FSIs in mice, is expressed in Glut-RA but no other projection neuron type. We found that MAFB transcription factor binding sites have enhanced chromatin accessibility specifically in glutamatergic neurons in RA relative to AId. Furthermore, gene regulatory network inference and in silico knockdown of MAFB expression reveal common MAFB targets in Glut-RA neurons and FSIs, and suggest that the transcription factor is necessary to specialize song Glut-RA neurons from non-song Glut-AId neurons. These data support a model in which birdsong projection neurons co-opt an interneuron gene regulatory program to enable the rapid physiological properties required for fast and precise birdsong performance.

overall_design: Several regions of the song system and comparator non-song regions were dissected from the brains of adult Bengalese finch (Lonchura striata domestica) males. The regions include, RA, HVC, and LMAN, and paired non-song regions, arcopallium, caudal nidopallium, and rostral nidopallium. Single-nucleus 3' RNA-seq libraries (10X Genomics) were prepared from these samples.

first: Bradley

last: Colquitt


title: Elucidation of a Potent Pro-Resolving Mediator of Inflammation-Resolution via Human Neutrophil-Vascular Endothelial Cell Interactions

city: Boston

last: Chiang

address: 60 Fenwood Rd. 3016Q

department: Anesthesiology

institute: Brigham and Women's Hospital

summary: We examined the impact of the new compound VL-Rv on TNF-stimulated HUVEC using RNAseq

overall_design: HUVEC (~1 million cells) were incubated with vehicle, TNF (10 ng/mL) and TNF plus VL-Rv (10 nM) for 48h. Cells were collected and total RNA prepared for RNAseq.

first: Charles

middle: N

last: Serhan

first: Robert

last: Nshimiyimana


title: Endothelial Fat4 regulates tumor angiogenesis and tumor immunity

city: St. Louis

first: Yoojung

last: Kwon

state: Missouri

address: 660 S Euclid Ave, BJCIH 8th floor, room 8302

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: The atypical cadherin FAT4 has mainly been studied as a tumor suppressor, but a pan-cancer analysis of its expression in human tumors suggests this view is likely oversimplified. Here, we identify that across multiple cancer types, FAT4 expression was enriched in cancer patients with high angiogenic activity and low T-cell immunity signatures and was predominantly observed in tumor endothelial cells. Consistently, endothelial Fat4 is required for both retinal and tumor angiogenesis in preclinical mouse models. Mechanistically, FAT4 governs endothelial planar cell polarity (PCP), which is essential for coordinated sprouting and vessel patterning. Strikingly, loss of endothelial FAT4 normalizes tumor vessels, enhances tumor immunity and responsiveness to immune checkpoint blockade, suggesting that targeting FAT4 can overcome endothelial cell anergy and restore anti-tumor immunity. These findings reposition FAT4 as a regulator that links angiogenesis to tumor immunity and extend its function beyond a tumor-cell-intrinsic suppressor. Targeting this pathway may offer an opportunity to normalize tumor vasculature and enhance immunotherapy, but its clinical success will hinge on recognizing the distinct and context-dependent roles of FAT4 in tumor cells and within the tumor microenvironment.

overall_design: RNA sequencing of wild type mouse cardiac endothelial cells and their Fat4 knockdown (ShFat4) cells.

first: Kyunghee

last: Choi


title: Gene regulatory co-option drives birdsong neural circuit specialization

overall_design: Several regions of the song system and comparator non-song regions were dissected from the brains of adult Bengalese finch (Lonchura striata domestica) males. The regions include the two region of the song motor pathway, RA and HVC, as paired non-song regions, arcopallium and caudal nidopallium. Joint single-nucleus RNA- and ATAC-seq libraries (10X Genomics Multiome-seq) were prepared from these samples.


title: An ITGA11 expressing subpopulation as predictor for the donor-specific osteogenic capacity of stromal cells

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

summary: Stromal progenitor cells of bone marrow origin are non-hematopoietic cells that give rise to osteoblasts and adipocytes in the postnatal organism. Marrow stromal cells (also known as mesenchymal stem cells - MSCs) are currently being employed in a large number of clinical trials for regenerative purposes post in vitro expansion. However, the clinical outcome has been variable, which might in part be due to the heterogeneity of the cells and the lack of a defined cell product with a molecular signature that favors tissue regeneration. In this study, we determined the cellular heterogeneity of primary stromal cultures and examined how inter-donor variation in subpopulation composition contributes to the differentiation potential of primary cultures. We profiled 136,014 stromal progenitors from 26 donors and identified 5 subpopulations that were linked to distinct bone-related pathways and genetic traits of bone mineral density and morphology. Abundancy of one cluster characterized by high expression of ITGA11 (integrin alpha-11) and genes related to matrix function, collagen organization, and elevated expression upon lineage commitment was positively correlated with osteoblastic differentiation capacity in vitro. In addition, ITGA11 protein expression in progenitor cells was a predictive marker for matrix mineralization in vitro and ectopic bone formation in vivo. Sorting stromal progenitors into ITGA11high and ITGA11low cells established cultures with high and low osteoblastic differentiation potential and revealed transcriptional differences reflective of the subpopulation-specific signature, which was not affected by siRNA mediated knockdown of ITGA11 expression. Our findings corroborate the presence of an extensive donor-dependent cellular heterogeneity that persists in cultured stromal cells, and that ITGA11 can be employed as a marker for isolating cells with high bone-forming potential, a feature likely to benefit clinical trials of bone regeneration.

overall_design: 10x Genomics single cell RNA-seq expression profiles of 21 primary cell cultures that have been tested for their osteogenic and adipogenic differentiation capacity in vitro. Bulk RNA-seq of primary cultures from 5 donors subjected to control or ITGA11 knockdown or subjected to sorting into low and high ITGA11 surface expression.

first: Ali Jasim

last: Jamil

first: Kaja

last: Madsen

first: Souad

last: Daamouch

first: Birgitte

last: Villadsen

first: Chao

last: Ma

first: Shakespeare

last: Jeromdesella

first: Mikkel

last: Nørgård

first: Emilie

last: Grupe

first: Maria

middle: B

last: Jakobsson

first: Yuting

last: Wang

first: Eri

last: Takematsu

first: Liming

last: Zhao

first: Stuart

last: Goodman

first: Lawrence

middle: H

last: Goodnough

last: Chan

first: Thomas

last: Andersen

first: Moustapha

last: Kassem


title: Molecular basis of target RNA cleavage by Cas13 I

city: Hong Kong

first: Joe

last: Lam

address: 21 Sassoon road

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: RNA-targeting CRISPR-Cas13 enzymes are robust RNA knockdown tools with both on-target and collateral cleavage activities. However, to this date, the in vivo RNA cleavage mechanisms remain poorly understood. Here, we combine in vitro and in vivo methods to elucidate the exact cleavage sites of Cas13. We reveal that some subtypes of Cas13, including Cas13b and Cas13bt, cleave the target RNA in predominant positions, and rational engineering of Cas13 further improves the precision. Building on this fact, we developed RNA segment editing (RSE), a targeted RNA cleavage and repair method, to restore dysfunctional RNA in cells. We anticipate that RSE will enable precision RNA engineering for therapeutics and basic research.

overall_design: Cleavage preference analysis of different Cas13 proteins with a random substrate library

first: SC

last: Kwon


title: Molecular basis of target RNA cleavage by Cas13 III

overall_design: Cleavage site and preference analysis of different PspCas13b mutants using in vivo adaptor ligation


title: Gene syntax defines supercoiling-mediated transcriptional feedback [RNA-seq]

first: Christopher

last: Johnstone

overall_design: RNA-seq profiling of hiPSC lines containing integrated synthetic gene pairs. Gene pairs with one of the four possible syntaxes (divergent, convergent, upstream tandem, downstream tandem) were integrated homozygously at the CYLBL locus in hiPSCs. The two genes were mTagBFP2-T2A-rtTA expressed constitutively from the CAG promoter, and mScarlet expressed from the inducible TRE promoter. These four lines were split into plus and minus induction conditions. The induced condition was treated with treated with 1000 ng/mL doxycycline for three days. Around 300k cells per condition were collected, then RNA was extracted and sequenced using poly(A) selection.

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