title: Sequence-specific RNA recognition drives Restrictor-mediated termination of extragenic transcription [ChIP-Seq]

first: Gaurav

last: Mandana

overall_design: The genomic distribution of ZC3H4 was analyzed by ChIP-seq and compared with that of RNA polymerase II phosphorylated at either Ser5 or Ser2 of the CTD. Genomic distribution of mutant ZC3H4 constructs was also analyzed by ChIP-seq.

first: Danilo

last: Polizzese

last: Madappa Mandana

first: Viviana

last: Piccolo

first: Marta

last: Russo

first: Sara

last: Polletti

first: Elena

last: Prosperini

first: Gioacchino

last: Natoli


title: Immune Dynamics in Palmoplantar Pustulosis Unveiled by Single-Cell and High-Resolution Spatial Transcriptomics [scRNA-seq]

status: Public on Mar 09 2026

city: Seoul

first: Hanjae

last: Lee

address: 103, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

type: Expression profiling by high throughput sequencing

summary: Palmoplantar pustulosis (PPP) is a chronic and relapsing inflammatory skin disorder marked by the appearance of sterile pustules on the palms and/or soles, with an underlying pathogenesis that remains only partially understood. In this study, we mapped the immune landscape underlying PPP progression using single-cell RNA sequencing (scRNA-seq) integrated with high-resolution spatial transcriptomics (ST). Keratinocytes and fibroblasts in PPP showed enhanced activation of the JAK–STAT signaling pathway, alongside a progressive accumulation of myeloid dendritic cells and Th17 cells across disease stages—from healthy control (HC) to non-pustular lesion (NPL), and then to pustular lesion (PL). Cell–cell interaction analysis revealed CCL19–CCR7 signaling between fibroblastic reticular cell (FRC)-like fibroblasts and LAMP3⁺/CCR7⁺ migratory dendritic cells, as well as CCL22/CCL17–CCR4 signaling between these dendritic cells and CD4⁺ T cells, including Th17 subsets. These interactions were spatially validated, with dendritic cells localized both within pustules and in the upper dermis. Within the CCL19⁺ dermal compartment, activated antigen-presenting cells and lymphocytes coalesced into a lymphoid-like immune structure. Moreover, pustular and surrounding keratinocytes emerged as key sources of CXCL1/6/8–ACKR1 signaling, promoting neutrophil infiltration via endothelial engagement. These coordinated cellular interactions contribute to the establishment of a spatially organized and densely populated immune niche during PPP progression. Lastly, transcriptome-based drug prediction analysis highlighted JAK inhibitors and phosphodiesterase-4 (PDE4) inhibitors as promising therapeutic candidates capable of targeting multiple components of PPP pathology. Overall, this work provides an integrative view of immune dynamics in PPP and offers potential avenues for more targeted and effective therapies.

overall_design:
Full-thickness human skin samples from patients with PPP were obtained from the sole via punch biopsies, and healthy sole skin was collected as dog-ear tissue during surgical excision of an atypical nevus.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************


title: YAP Induces a Pro-Renewal Metabolic State in Cardiomyocytes: Cardiomyocyte-enriched Datasets

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

country: USA

institute: Cincinnati Children's Medical Hospital Center

summary: Cardiomyocyte (CM) maturation is characterized by a change in energy metabolism from glucose to fatty acid catabolism, which poses a barrier to CM proliferation and cardiac regenerative repair. YAP, a transcriptional cofactor that is regulated by the Hippo signaling pathway, induces cardiac regenerative repair. We investigated YAP function in postnatal metabolic maturation and remodeling and found that YAP inhibits fatty acid catabolism and shifts fatty acid catabolism to anabolism with phospholipid biosynthesis. Moreover, YAP induced metabolic remodeling enhances CM carbohydrate utilization. Functional experiments using maternal dietary fat challenge, which stimulates fatty acid oxidation (FAO) and induces CM maturation, counteracts YAP-induced metabolic remodeling. Mechanistically, we discover that YAP inhibits the MEF2A directed maturation program leading to a neonatal-like CM metabolic state. We provide a transcriptional framework by which YAP induces neonatal CM metabolic remodeling to reverse CM metabolic maturation, thereby promoting heart regeneration.

overall_design: Wildtype ICR mice were injected with AAV9:cTnT-hMEF2A, AAV9:cTnT-YAP5SA, or both AAV9:cTnT-hMEF2A and AAV9:cTnT-YAP5SA at a dose of 1E11 GC per virus at P7 by intraperitoneal. Controls did not receive AAV. 5 days later at P12, the animals were sacrificed and the hearts were collected. Nuclei isolation and PCM1-enrichment was performed to enrich for cardiomyocyte nuclei. RNA was isolated using the Qiagen AllPrep RNA+DNA isolation kit. Isolated RNA was processed and library generation with Novogene Inc using polyA enriched, non-directional libraries and sequenced on Illumina NovaSeq XPlus.

first: Lin

last: Liu

first: James

middle: F

last: Martin


title: A Neuronal GPCR Modifies Neuropeptide Signaling to Suppress Proteostasis in distal tissues

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: The proteostasis network (PN) safeguards the integrity of proteins by the promotion of various cellular activities. However, with aging the competence of the PN declines and aggregated proteins accrue within cells. This process can underlie the development of neurodegenerative disorders, such as Alzheimer’s and Huntington’s diseases. Although the activities of the PN occur within the cell, this network is regulated across the organism by inter-tissue communication, which is partially governed by neurons. We discovered previously, that reducing the expression of gtr-1, which encodes a neuronal GPCR, protects worms from the toxicity of the Alzheimer’s-causing, Aβ peptide. Here we investigated the mechanism that is acted upon the knockdown of gtr-1 and found that gtr-1 RNAi treatment modulates the expression of neuropeptide-coding genes, differentially modifies the aggregation of proteotoxic proteins, and enhances protein degradation. These findings highlight the roles of neuropeptides as coordinators of proteostasis across the organism.

overall_design: three sets of Six thousand synchronized CL2006 worms were grown on IPTG induced bacteria expressing either EV or gtr-1 3’UTR RNAi. At day 1 of adulthood, the worms were bleached and eggs were placed on the same RNAi as their parental generation. Worms of the second generation were washed daily to get rid of progeny, harvested at day 6 of adulthood and RNA was extracted using kit (Macherey-Nagel # 740961) according to the manufacturer’s instructions, RNA integrity was tested and the samples were submitted for Nova-seq RNA sequencing.

first: Joud

last: Hirbawi

first: Ehud

last: Cohen

first: Adam

last: Zeretsky

first: Huadong

last: Zho

first: Emmanuelle

last: Merquiol

first: Atif

middle: A

last: Siddiqui

first: Irit

first: Galia

last: Blum

first: Gourab

last: Dey


title: m6A Methylation Suppresses anti-tumour immune responses in Colorectal Cancers by Inhibiting Double-stranded RNA accumulation from Alu Repeats [RNA-Seq1]

city: Oxford

first: Yucheng

last: Wang

state: Oxfordshire

address: Roosevelt Drive, Headington

country: United Kingdom

institute: University of Oxford

summary: How cancer cells evade immune detection despite expressing immunostimulatory retroelement (RE) transcripts remains an open question in tumour immunology. In cancer cells, endogenous REs that escape histone and DNA silencing are transcribed into RNA and can form double-stranded RNA (dsRNA), triggering innate immune responses through a process known as viral mimicry. However, RNA-level checkpoints can limit this effect. Here, we identify the m6A RNA methyltransferase METTL3 as a key regulator of this suppression in colorectal cancer (CRC). Targeting METTL3 enhances the accumulation of dsRNA derived from both pre-existing and newly transcribed REs, thereby amplifying immunostimulatory signalling and activating cell-intrinsic anti-tumour immunity. Notably, CRCs exhibit differential sensitivity to METTL3 inhibition: tumours with high basal dsRNA levels and RNA methylation respond robustly to METTL3 blockade alone, whereas those with low endogenous dsRNA require combination therapy to achieve comparable immune activation. Co-treatment with DNA methyltransferase inhibitors (DNMTis) restores immune activation in these otherwise resistant tumours. Together, these findings uncover a novel mechanism by which METTL3 functions as an RNA-level immune checkpoint and suggest that combining METTL3 and DNMT inhibition may overcome resistance and serve as an effective therapeutic strategy in CRC.

overall_design: CTRL (TGFP) or/and METTL3KD colorectal cancer cells were treated with Decitabine (300 nM) or mock-treated (MT). 5-days post-treatment the cells were collected, washed in PBS and used for RNA extraction. Total RNA was extracted for RNA-seq profiling .


title: Defining the chromatin-associated protein landscapes on Trypanosoma brucei repetitive elements using synthetic TALE proteins

city: Edinburgh

first: Robin

last: Allshire

address: Max Born Crescent,

institute: Edinburgh university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Kinetoplastids, such as Trypansoma brucei, are eukaryotes that likely separated from the main lineage at an exceptionally early point in evolution. Consequently, many aspects of kinetoplastid biology differ significantly from other eukaryotic model systems, including yeasts, plants, worms, flies and mammals. As in many eukaryotes the T. brucei genome contains repetitive elements at various chromosomal locations including centromere- and telomereassociated repeats and interspersed retrotransposon elements. T. brucei also contains intermediate-sized and mini- chromosomes that harbor abundant 177 bp repeat arrays, and 70 bp repeat elements implicated in Variable Surface Glycoprotein (VSG) gene switching. In many eukaryotes repetitive elements are assembled in specialised chromatin such as heterochromatin, however, apart from centromere- and telomere-associated repeats, little is known about chromatin-associated proteins that decorate these and other repetitive elements in kinetoplastids. Here we utilize affinity selection of synthetic TALE DNA binding proteins designed to target specific repeat elements to identify enriched proteins by proteomics. Validating the approach, a telomere repeat binding TelR-TALE identifies many proteins previously implicated in telomere function. Furthermore, the 70R-TALE designed to bind 70 bp repeats indicates that proteins involved in DNA repair are enriched on these elements that reside adjacent to VSG genes. Interestingly, the 177 bp repeat binding 177R-TALE enriches for many kinetochore proteins suggesting that intermediate-sized and mini- chromosomes assemble kinetochores related in composition to those located on the main megabase chromosomes. This provides a first insight into the chromatin landscape of repetitive regions of the trypanosome genome with relevance for their mechanisms of chromosome integrity, immune evasion and cell replication.

first: Roberta

last: Carloni

first: Tadhg

last: Devlin

first: Pin

last: Tong

first: Tania

last: Auchynnikava

first: Christos

middle: R

last: Spanos

first: Juri

last: Rappsilber

first: Keith

last: Matthews

middle: C


title: m6A Methylation Suppresses anti-tumour immune responses in Colorectal Cancers by Inhibiting Double-stranded RNA accumulation from Alu Repeats [MDA5]

overall_design: To identify the primary ligand for MDA5 in colorectal cancer cells which were wild-type (transduced with control pLKO1 plasmid) or Knock-downed (KD) for METTL3 and mock-treated or treated with Decitabine ( DAC-treated), we used the RNase A protection assay followed by RNA sequencing as previously described


title: Radiation triggers a clinically relevant profibrotic p53-mediated DNA damage response in an ex vivo human skin model

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: Radiation therapy is a cornerstone of cancer treatment which frequently leads to cutaneous side effects. In a significant proportion of patients, this can progress to debilitating radiation-induced skin fibrosis (RISF). To investigate the early molecular events underlying RISF, we employed a novel human ex vivo model utilizing discarded human skin from elective surgical procedures. This dataset is comprised of irradiated and control skin from 6 human donors post-panniculectomy.

overall_design: Skin was irradiated with 0 Gy (control) or 3.5 Gy (irradiated) using a benchtop irradiator. A paired experimental design was employed, with irradiated and non-irradiated (control) samples from the same donor were maintained at an air-liquid interface and collected at various time points post-irradiation: Immediate (Day 0), Day 1, Day 2, Day 5, Day 7.

first: Caroline

last: Dodson

first: Sophie

middle: M

last: Bilik

first: Rivka

last: Stone


title: RNA profiling of BCLAF1 knock-down MOLM-13 cell line

city: SEVILLA

first: Gonzalo

last: Millán-Zambrano

address: Avenida Américo Vespucio, 24

country: Spain

institute: CSIC

summary: Acute myeloid leukemia (AML) is driven by a combination of genetic alterations and non-mutational mechanisms that disrupt normal hematopoiesis and support leukemic cell survival. While the mutational landscape of AML is well characterized, the non-genetic processes that sustain leukemic maintenance remain comparatively less understood. Using murine models of AML and human AML cell lines, we identify BCL2-associated transcription factor 1 (BCLAF1) as a critical regulator of leukemic progression through control of mRNA processing. BCLAF1 physically associates with core spliceosome components and regulates alternative splicing, with a predominant effect on intron retention. We demonstrate that BCLAF1 is required for the productive splicing of activating transcription factor 4 (ATF4) mRNA, thereby sustaining ATF4 protein expression. Loss of BCLAF1 reduces ATF4 protein levels, leading to downregulation of amino acid metabolic target genes essential for leukemic cell survival. Consistently, depletion of BCLAF1 sensitizes AML cells to venetoclax, which is known to disrupt amino acid uptake and metabolism in leukemia cells. Together, these findings uncover a previously unrecognized role for BCLAF1 in coordinating mRNA splicing and metabolic adaptation in AML, highlighting its potential as a therapeutic target.

overall_design: RNA-seq profiling of shCONTROL and shBCLAF1 at 4 days of DOX treatment. BCLAF1 RIP-seq data from shCONTROL cells at 4 days of DOX treatment.

first: Laura

last: López-Hernández

first: Ricardo

last: de Arellano

first: Patrick

last: Toolan-Kerr


title: m6A Methylation Suppresses anti-tumour immune responses in Colorectal Cancers by Inhibiting Double-stranded RNA accumulation from Alu Repeats [MeRIP]

first: Yucheng

last: Wang

overall_design: MeRIP sequencings were peformed for wild type and METTL3 knock down HT29 cell line, as well as wild type HCT116 cell line.


title: m6A Methylation Suppresses anti-tumour immune responses in Colorectal Cancers by Inhibiting Double-stranded RNA accumulation from Alu Repeats [CUT&Run]

overall_design: CUT&RUN assays were performed on CTRL and METTL3KD CRC cells using the Cell Signaling Technology (CST) CUT&RUN Assay Kit (#86652) according to the manufacturer’s protocol


title: Sequence-specific RNA recognition drives Restrictor-mediated termination of extragenic transcription [HeLa__4sU-RNAseq]

city: Milano

first: Gaurav

last: Mandana

address: Via Adamello 16

country: Italy

institute: European Institute of Oncology

summary: Mammalian genomes harbour hundreds of thousands of RNA Polymerase II (Pol II) landing pads, enhancers and promoters, from which transcription can initiate bidirectionally. Nevertheless, processive transcription is largely restricted to the small gene-containing fraction of the genome. A highly conserved and essential metazoan complex, Restrictor, composed of WDR82 and ZC3H4, restrains processive Pol II activity at thousands of extragenic transcription units, thus representing a critical enforcer of genome utilization. However, because of the widespread recruitment of Restrictor to both genic and non-genic transcription sites, the identification of the mechanistic basis for its exquisite selectivity for extragenic transcription has remained elusive thus far. Here, we show that while WDR82 tethers Restrictor to sites of transcription initiation, the three C3H1-type zinc fingers of ZC3H4 make sequence-specific interactions with short motifs selectively enriched at the 5’ end of extragenic transcripts, with such interactions being required for transcription termination. Hence, while Restrictor recruitment relies on WDR82-dependent tethering to the initiating Pol II, its selectivity mainly arises from sequence-specific RNA recognition.

overall_design: 4sU-RNA seq was performed in HeLa cells following acute CRISPR/Cas9-mediated domain-specific deletion of ZC3H4, where two single guide RNAs were used to precisely excise functional domains while preserving the open reading frame

first: DDanilo

last: Polizzese

first: DGaurav

last: Madappa Mandana

first: DMarta

last: Russo

first: DSara

last: Polletti

first: DElena

last: Prosperini

first: DGiuseppe

last: Ciossani

first: DSilvia

last: Monzani

first: DLuigi

last: Scietti

first: DSimona

last: Rodighiero

first: DFrancesco

last: Gualdrini

first: DViviana

last: Piccolo

first: DGioacchino

last: Natoli


title: A human organoid model of alveolar regeneration reveals distinct epithelial responses to interferon-gamma

city: Utrecht

first: Carla

last: Pou Casellas

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Chronic obstructive pulmonary disease (COPD) is characterized by inflammation and emphysema, leading to progressive alveolar destruction. Currently, no therapies effectively regenerate the alveolar epithelium. Here, we developed and characterized a feeder- and serum-free primary adult human organoid model to investigate how inflammatory conditions influence alveolar regeneration. Using Wnt activation and heregulin-β, we achieved long-term expansion of progenitor cells, while AT2 maturation protocols enhanced surfactant production, including the formation of tubular myelin. Introducing a LATS inhibitor to the expansion conditions induced an AT1 differentiation program without eliminating AT2 cells. Single-cell RNA-sequencing revealed multipotent progenitor-like populations, reflecting a state of heightened plasticity associated with regeneration. To model the effects of inflammation, we exposed these organoids to cytokines elevated in COPD. Notably, interferon-gamma (IFN-γ) exerted distinct effects on AT1 and AT2 cells: while it was cytotoxic to AT1 cells, it promoted growth in regenerating AT2 cells in a dose- and time-dependent manner. These findings underscore the nuanced influence of pro-inflammatory cytokines on alveolar regeneration. Our organoid model provides a reductionist platform for mechanistic studies in human cells, aiming to identify therapies that prevent alveolar destruction and improve alveolar regeneration in COPD

overall_design: Human primary tissue-derived alveolar organoids from three different donors (Lu37, Lu38, Lu39) were cultured in three media conditions: ALVO-EM (expansion), AT2-MM (AT2-maturation), and AT1/2-M (mixed AT1/2-differentiation). After 17 days in culture, organoids were dissociated into single cell suspensions and live cells (DAPI-/DRAQ5+) were sorted into PBS using a BD FACSAria Fusion. Cells from the same condition but different donors were mixed in equal parts and 25,000 cells per condition were subjected to droplet-based scRNA-seq using the 10x Genomics platform

first: Antonella

last: Dost

first: Hans

last: Clevers


title: RNAseq analysis of human neutrophils from healthy controls, people with frailty and people with rheumatoid arthritis

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

institute: University of Liverpool

summary: We report gene expression profiles of blood neutrophils from (1) people with frailty (2) healthy older people (>60Y), (3) healthy younger people (18-25Y), (4) people with rheumatoid arthritis.

overall_design: Neutrophils (purity >97%) were isolated from peripheral blood by separation of leukocytes from erythrocytes using HetaSep, then centrifugation through density-gradient reagent (HetaSep). Remaining erythrocytes were removed by hypotonic lysis using ammonium chloride buffer. RNA was isolated using Trizol:chloroform, cleaned up by Qiagen RNeasy kit including on-column DNase digest and sequenced on the DNBseq platform.

middle: L

first: Genna

last: Abdullah

first: Marie

last: Phelan

first: Asangaedem

last: Akpan


title: Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [YY1]

city: Chicago

first: Long

last: Zhao

state: Il

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

summary: Intrinsically disordered regions (IDRs) are well-known facilitators of chromatin regulation, but their role as regulatory restraints remains underexplored. Here, we reveal that the C-terminal IDR of mammalian ALKBH5 anchors its main activity to mRNA, limiting chromatin engagement in mouse embryonic stem cells (mESCs). IDR deletion redirects ALKBH5 to chromatin-associated non-coding RNAs, driving widespread chromatin opening and transcriptional activation. This mechanism extends to histone demethylases, where IDR deletion also results in broad removal of repressive histone marks, leading to increased chromatin accessibility and activation of transposable elements. Leveraging these insights, we engineered ALKBH5 and its plant homologs with IDR deletion. Overexpression of these IDR-deleted ALKBH5 demethylases could promote Arabidopsis root growth and increase rice yield. Our findings uncover a conserved role for IDRs in restraining chromatin access by RNA and histone demethylases and establish a new strategy of chromatin programming for crop engineering using plant proteins.

overall_design: Experiment Description: This dataset contains genomic binding profiles of YY1 and P300 in WT and Alkbh5-ΔcIDR mESCs, generated using CUT&RUN.

first: Liudan

last: Jiang

first: Chuan

last: He


title: Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [Histone_ALKBH]

overall_design: Experiment Description: This dataset contains chromatin state profiling data generated using CUT&Tag for H3K4me3 and H3K27ac, as well as CUT&RUN for H3K9me3 in WT and Alkbh5-ΔcIDR mESCs.


title: Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [Histone_LCD_RNA]

overall_design: Experiment Description: This dataset contains chromatin-associated RNA-seq (caRNA-seq) data from mESCs ectopically expressing full-length (FL) and ΔIDR variants of KDM4A, KDM4B, KDM6A, and KDM6B.


title: Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [ATAC-seq]

overall_design: Experiment Description: This dataset contains chromatin accessibility profiling data generated using ATAC-seq in WT, Alkbh5-/-, and Alkbh5-ΔcIDR mESCs.


title: Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [m6a]

overall_design: Experiment Description: This dataset contains mRNA m6A profiling data generated using MeRIP-seq to study m6A changes in WT, Alkbh5-/-, and Alkbh5-ΔcIDR mESCs.


title: Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [caRNA m6A]

overall_design: Experiment Description: This dataset contains caRNA m6A profiling data generated using MeRIP-seq in the chromatin-associated fraction of WT, Alkbh5-/-, and Alkbh5-ΔcIDR mESCs.


title: Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [CLIP-seq]

overall_design: Experiment Description: This dataset comprises RNA-binding profiles obtained through eCLIP-seq for endogenous full-length mALKBH5 in WT mESCs and mALKBH5-ΔcIDR in Alkbh5-ΔcIDR mESCs.


title: Breast Cancer samples of Mexican patients

city: Ciudad de Mexico

first: Martha-Eugenia

last: Ruiz-Tachiquin

state: Ciudad de Mexico

address: Av. Cuauhtemoc No.330, Col. Doctores, Alcaldia Cuauhtemoc

department: Unidad de Investigacion Medica en Enfermedades Oncologicas

country: Mexico

institute: Instituto Mexicano del Seguro Social

type: Genome binding/occupancy profiling by SNP array

type: Genome binding/occupancy profiling by genome tiling array

summary: Breast Cancer is a multifactorial disease with an important genetics background, example copy number variants (CNV). Microarray data analysis were performed to identify CNV that could be contributing to those Mexican patient's clinical phenotypes and genotypes

overall_design: Affymetrix CytoScan HD arrays were performed according to the manufacturer's instructions. Copy Number Analysis of Cytoscan Affymetrix arrays was performed with ChAS software for adult samples, five adyacent tumor tissue, four leukocites and five tumor tissue.

last: Ruiz-Tachiquín

first: Violeta

last: Larios-Serrato


title: AMBRA1 as a novel positive regulator of the SHH pathway in medulloblastoma [scRNA-seq]

city: Paris

first: Jacob

last: Torrejon Diaz

address: 26 Rue d'Ulm

country: France

institute: Curie Institute

summary: AMBRA1 (Autophagy and Beclin 1 Regulator 1) is a versatile scaffold protein involved in disparate processes including autophagy, cell cycle regulation, and tumorigenesis. While AMBRA1 is primarily recognized as a tumor suppressor, its dual function as a tumor promoter has garnered increasing attention. However, the role of AMBRA1 remains largely unexplored in many malignancies, particularly in brain tumors. Leveraging multiomic analysis of the largest human medulloblastoma (MB) cohort, we identify significantly elevated AMBRA1 protein levels in the Sonic Hedgehog subgroup (MBSHH) compared to other MB variants. Notably, AMBRA1 protein abundance, independent of its mRNA expression, correlates with poor prognosis, positioning AMBRA1 as a biomarker for MBSHH. Mechanistically, AMBRA1 enhances SHH signaling by stabilizing GLI1, the pathway's final effector, by inhibiting the βTrCP-mediated degradation of GLI1. Additionally, AMBRA1 protein stability is modulated by the REN E3 ubiquitin ligase, a tumor suppressor gene and antagonist of the SHH pathway. Genetic inhibition of AMBRA1 significantly blocks MBSHH  growth in murine and patient-derived pre-clinical models, highlighting its therapeutic potential. Moreover, combining AMBRA1 knock-down with FDA-approved SHH inhibitors amplifies tumor suppression. These findings uncover the AMBRA1/βTrCP/REN axis as a key regulatory mechanism in SHH signaling, providing actionable insights into targeted therapies for MBSHH.

overall_design: To get insights into the effects of AMBRA1 on cellular heterogeneity of Sonic Hedgehog medulloblastoma (SHH-MB), we performed  knockdown of this gene using shRNAs in human SHH-MB PDX model. After 3 days of infection, AMBRA1-depleted SHH-MB PDX cells were orthotopically injected in nude/nude mice. When neurological symptoms became apparent, tumor masses, from the shAMBRA1 group and shCTR group, were surgically excised from the recipient mice and dissociated prior to single cell RNA-seq analysis.


title: Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [Histone LCD]

summary: Intrinsically disordered regions (IDRs) are well-known facilitators of chromatin regulation, but their role as regulatory restraints remains underexplored. Here, we reveal that the C-terminal IDR of mammalian ALKBH5 anchors its main activity to mRNA, limiting chromatin engagement in mouse embryonic stem cells (mESCs). IDR deletion redirects ALKBH5 to chromatin-associated non-coding RNAs, driving widespread chromatin opening and transcriptional activation. This mechanism extends to histone demethylases, where IDR deletion also results in broad removal of repressive histone marks, leading to increased chromatin accessibility and activation of transposable elements. Leveraging these insights, we engineered plant ALKBH5 homologs with IDR deletion. Overexpression of these IDR-deleted plant RNA demethylases could promote Arabidopsis root growth and significantly increase rice yield. Our findings uncover a conserved role for IDRs in restraining chromatin interaction to control chromatin state and establish a new strategy of crop engineering using plant proteins to increase biomass and yield.

overall_design: This dataset includes chromatin accessibility profiling (ATAC-seq) and genomic binding profiles of HA-tagged variants in mESCs ectopically expressing full-length (FL) and ΔIDR variants of KDM4A, KDM4B, KDM6A, and KDM6B. It also includes H3K27me3 genomic occupancy data (CUT&Tag) for mESCs expressing full-length (FL) and ΔIDR variants of KDM6A and KDM6B, as well as H3K9me3 genomic occupancy data (CUT&RUN) for mESCs expressing full-length (FL) and ΔIDR variants of KDM4A and KDM4B.


title: m6A Methylation Suppresses anti-tumour immune responses in Colorectal Cancers by Inhibiting Double-stranded RNA accumulation from Alu Repeats

first: Yucheng

last: Wang

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

overall_design: Refer to individual Series


title: Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [MeRIP-seq]

type: Methylation profiling by high throughput sequencing

overall_design: This dataset contains m6A profiling data of chromatin-associated RNA (caRNA) generated using MeRIP-seq. The study examines m6A changes in the chromatin-associated fraction of Col-0, full-length hALKBH5, and hALKBH5-ΔcIDR transgenic Arabidopsis thaliana lines, along with their respective inactive mutant lines.


title: AMBRA1 as a novel positive regulator of the SHH pathway in medulloblastoma [RNA-Seq]

overall_design: To define alterations in global gene expression following AMBRA1 knockdown by shRNAs in the context of Sonic Hedgehog medulloblastoma (SHH-MB), we performed issue-high-quality bulk RNA-seq data from a PDX SHH model and checked which genes were differentially expressed.


title: Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [EU]

overall_design: This dataset contains EU labelled nascent RNA profiling data in WT, Alkbh5-/-, and Alkbh5-ΔcIDR mESCs.


title: CD47 activates ROBO2 signaling to regulate glioblastoma cell plasticity and metabolism

city: Adelaide

first: John

last: Toubia

address: Frome Rd

country: Australia

institute: Centre for Cancer Biology

summary: CD47 inhibits phagocytosis by myeloid cells, contributing to immune evasion by cancer cells. Although CD47-blocking antibodies have shown promise in treating various malignancies, their efficacy in glioblastoma (GBM) remains limited, and the role of CD47 beyond immune escape is poorly understood. Here, we show that CD47 is highly expressed at the invasive edge of GBM tumours, with elevated expression correlating with poorer patient survival. We demonstrate that CD47 loss reduces proliferation, migration, and invasion, independently of immune activity leading to decreased GBM tumour burden and prolonged survival in vivo. Mechanistically, our study reveals that CD47 regulates ROBO2 signaling and enhances mitochondrial respiration. Furthermore, we demonstrate that combined loss of CD47 or ROBO2 with inhibition of mitochondrial function significantly increases GBM cell death. These findings highlight CD47 as a key regulator of GBM cell and metabolic plasticity, offering a novel therapeutic strategy by targeting CD47 or ROBO2 in combination with mitochondrial inhibitors.

overall_design:
To investigate the role of CD47 in regulating GBM cell plasticity, we knocked out CD47 in U-87MG GBM cells using CRISPR/Cas9 technology.
We then performed gene expression profiling analysis using RNA-seq data from wild-type (WT) and CD47-CRISPR-Knockout (KO) cells, with three biological replicates per group.
Comparative transcriptomic analysis between the WT and CD47 KO groups was performed to identify differentially expressed genes and pathways regulated by CD47.

first: Ruhi

last: Polara

first: Nirmal

last: Robinson


title: Microbiome-produced nicotinic acid controls colon regional identity and injury susceptibility (scRNAseq)

city: Los Angeles

first: Dario

last: Boffelli

state: CA

address: 700 N San Vicente Blvd

department: Pediatrics

institute: Cedars Sinai

summary: The gut epithelium exhibits regional specialization critical for its function and susceptibility to disease, as gut diseases localize to specific regions of the organ. However, how regionalization is established and its influence on disease susceptibility remain poorly understood. Here, we investigate the role of the gut microbiome—which comprises all microorganisms residing in the gut lumen and is itself regionalized—in regulating regionalization of the colon. We demonstrate that the regional identity of colonocytes is disrupted in mice lacking a microbiome. Mechanistically, we show that the proximal colonic microbiome produces high levels of nicotinic acid, which induces Pparα expression to establish proximal colonocyte identity. Furthermore, we find that microbiome-driven proximal identity confers protection against tissue injury in the mouse. Finally, we show that colon regionalization and the loss of proximal identity during disease are also present in human.

overall_design: We performed scRNAseq on sorted epithelial cells from the entire mouse colon of control, antibiotic-treated and germ-free mice.

first: Jeremie

last: Rispal

first: Dedeepya

last: Vaka

first: Ophir

last: Klein


title: Harnessing microglia capacity to facilitate myelin regeneration in chronically demyelinated brain lesions

city: Winnipeg

first: Soheila

last: Karimi-Abdolrezaee

state: MB

address: 629-Basic Medical Sciences Building, 745 Bannatyne Avenue

department: Department of Physiology and Pathophysiology

country: Canada

institute: University of Manitoba

summary: Failure in remyelination is a key feature of progressive multiple sclerosis (MS) that drive neurodegeneration and accumulation of disabilities. Microglia crucially facilitate oligodendrocyte remyelination in MS lesions through myelin phagocytosis, and subsequent cholesterol metabolism and release. However, microglia lose this capacity in chronic demyelinated lesions, as they acquire a dysfunctional phenotype characterized by intracellular accumulation of lipid droplets due to impaired cholesterol processing of myelin debris. Given the abundance of microglia in chronic MS lesions, revitalizing their pro-remyelination capacity represents a critical repair strategy for progressive MS. Here, we reveal that dysregulation of neuregulin-1 underlies impaired remyelination in chronically demyelinated brain lesions. Therapeutic restoration of neuregulin-1 supports remarkable myelin regeneration by augmenting microglia capacity for clearance of myelin debris, cholesterol metabolism and efflux. Altogether, we demonstrate the promise of neuregulin-1 as an endogenous target to facilitate microglia reparative functions in progressive MS in which there is an unmet critical need for new treatments.

overall_design: The samples are microglia isolated from corpus callosum of mice using magnetic-activated cell sorting (MACS) of CD11b+ cells. Each sample is the result of pooling of the brains of 2 mice. The treatment groups include: 1- Control mice. 2- Cuprizone for 10 weeks + 2 weeks of recovery period and Vehicle (0.1% BSA in saline) treatment. 3- Control mice. 2- Cuprizone for 10 weeks + 2 weeks of recovery period and Neuregulin 1 beta 1 (30µg/kg/day) treatment.


title: Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [genomic occupancy]

overall_design: This dataset includes chromatin accessibility profiling (ATAC-seq), genomic occupancy of H3K4me3 and H3K27ac (CUT&Tag), and genomic binding profiles of Flag-tagged full-length hALKBH5 and hALKBH5-ΔcIDR (Flag CUT&RUN) in Col-0, full-length hALKBH5, and hALKBH5-ΔcIDR transgenic Arabidopsis thaliana lines.


title: DNA methylation stochasticity is linked to transcriptional variability and identifies convergent epigenetic disruption across genetically-defined subtypes of AML [scRNAseq]

city: Baltimore

first: Andrew

middle: P

last: Feinberg

state: MD

address: 855 North Wolfe Street

department: Center for Epigenetics

institute: Johns Hopkins University

summary: Epigenetic regulators are frequently mutated in acute myeloid leukemia (AML). We applied the CPEL method to publicly-available ERRBS data to investigate DNA methylation stochasticity in genetic subtypes of AML, and identified transcriptional dysregulation related to methylation entropy using single-cell RNA-seq data.

overall_design: Single-cell RNA-seq of primary patient acute myeloid leukemia samples and normal CD34+ progenitor samples.

first: Eleanor

last: Hilgart

first: Michael

last: Koldobskiy


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_pSR_SF3B1_FLASH]

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

country: Germany

institute: Max-Planck-Institut für molekulare Genetik

summary: Nuclear Speckles are large, multi-component condensates in the mammalian nuclei that are thought to be involved in various stages of gene expression, including transcription, splicing, and export. Investigating the direct role of Speckles in these processes have been intractable due to their heterogeneous, multi-component nature. Here we show that Speckles are necessary for the splicing of GC-rich, levelled intron/exon architecture. Acute removal of Speckles leads to a drastic downregulation of GC-rich genes which are clustered within GC-rich isochores. Genes outside these domains are physically away from Speckles and are not affected from loss of Speckles. Animal genomes that do not have GC-rich isochores, do not have GC-rich levelled intron/exon architecture and do not have Speckles. Our results suggest that the expansion of Speckles core proteins’ intrinsically disordered domains during vertebrate evolution facilitated GC-content elevation in Amniotes by creating a condensate necessary to splice the by-products of this process: GC-rich, levelled intron/exon architecture.

overall_design: FLASH libraries of p-SR (mAb 1H4) and SF3B1 in HCT116_SON-HaloTag cells that were either treated with DMSO as a control or HaloPROTAC-3 for 16hr to deplete SON protein.

first: Ibrahim

last: Ilik

first: Michal

last: Malszycki

first: Tugce

last: Aktas


title: Bulk RNA sequencing analysis of a iPSC-derived neurons, microglia and astrocytes models of mitochondrial unfolded protein response (UPRmt) activation.

first: Michela

last: Deleidi

address: 24 boulevard du Montparnasse

institute: Institut Imagine, INSERM UMR1163

summary: Mitochondria have developed a specialized unfolded protein response (UPRmt) to maintain proteostasis and promote recovery under stress conditions. Research in simpler organisms has demonstrated that UPRmt activation in glial cells promotes protein homeostasis through beneficial cell-nonautonomous communication to neurons. To address the role of mitochondrial stress responses in the human brain we profiled the cell-type-specific role of human UPRmt using human induced pluripotent stem cell (iPSC)-derived neurons, astrocytes and microglia. We found that UPRmt activationinduces a cell-type specific response characterized by microglial senescence.

overall_design: We developed a human iPSC-derived neuron, astrocytes and microglia from a control line. Monocultures were independently cultured and treated with 1 µM CDDO-Me for 6 hours (microglia and astrocytes) and 24 hours (for neurons). Cells were dissociated using accutase, and RNA was generated using RNeasy Mini Kit (Cat. number: 74106, Qiagen, Germany) according to the manufacturer’s instructions. High-quality RNA samples were subjected to bulk RNA sequencing (RNA-seq) at GENEWIZ GmbH (Leipzig, Germany)

first: Maria Jose

last: Perez J


title: Embryonic Origin Dictates Functional Heterogeneity and Neoplastic Potential in Adult Intestinal Stem Cells [scRNA-seq_adult_SI_crypts]

city: Mainz

first: Natalia

last: Soshnikova

address: Langenbeckstr. 1

department: Institute for Molecular Medicine

institute: University Medical Centre of the Johannes Gutenberg University

summary: Adult intestinal stem cells (ISCs) are the primary source of all differentiated cell types within the intestine and also the cells-of-origin of intestinal cancer. Traditionally, ISCs were viewed as a functionally uniform population. Here, we show that ISCs derived from Axin2+ embryonic progenitors are a functionally distinct group. During homeostasis, Axin2+-derived ISCs exhibit an increased capacity to differentiate into tuft and enteroendocrine cells, but are markedly less efficient at generating Paneth cells. Mechanistically, ISC differentiation potential is established during embryogenesis and shaped by a combination of cell-intrinsic factors, including WNT signaling and transcriptional regulators, as well as external BMP cues from the surrounding microenvironment. Consequently, the differentiation potential of adult ISCs into secretory lineages can be altered by temporary suppression of BMP signalling during embryonic development. We further demonstrate that Axin2+-derived ISCs display a higher propensity for neoplastic transformation in the Apcmin/+ mouse model for intestinal cancer. Moreover, a marker of Axin2+-derived epithelial cells, CSRNP3 is overexpressed in the inflamed and cancerous epithelium of patients with IBD and colorectal cancer. Our study reveals the cell-intrinsic nature of ISC differentiation potential, defined during embryogenesis, and underscores the importance of embryonic signaling cues in determining the functional outcomes of adult ISCs.

overall_design: Epithelial cells from small intestinal crypts were isolated at P120 from Axin2-CRE-ERT_Rosa-tdTomato mice by FACS based on the presence or absence of tdTomato signal and analyzed by scRNA-sequencing


title: Microbiome-produced nicotinic acid controls colon regional identity and injury susceptibility (Bulk-RNAseq)

overall_design: We performed bulk-RNAseq on organoids cultured in control (proliferative) or differentiation media derived from proximal, mid and distal mouse colon


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_SRRM2_dTAG_pA]

overall_design: Gene expression profiling of HCT116 cells subject to SRRM2-depletion, SON-depletion, SRRM2+SON-depletion or control treatment.. Libraries were prepeared from pA(+)-selected RNA, 12 libraries in total.


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_4sU_pulse]

overall_design: Gene expression profiling of HCT116 cells subject to control vs SON-depletion. Libraries were prepared from cells incubated with 1mM 4sU for 15 minutes. Ribo-depleted total RNA was used to construct 4 libraries in total.

first: Lisa

last: Martina


title: Charting the transition from in vitro production through in vivo diversification of human glial progenitor cells

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_SRRM2_dTAG_PoreC]

overall_design: Pore-C data of HCT116 cells subject to SON-depletion for 0, 6, 12 or 18hrs.

first: Daniela

last: Salgado Figueroa

first: Ferhat

last: Ay


title: spatial transcriptomics of mouse brain before and after activation

city: Beijing

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

country: China

institute: Chinese Academy of Sciences

summary: to unravel the intricate neural mechanisms that underpin the brain's complex functions through neural circuit, we selected two important neural circuits,  using optogenetic technology to activate specific circuits and applying spatial transcriptomics technology to explore the molecular mechanisms under the activation process

overall_design: we collect control and activated mice brain samples respectively for spatial transcriptomics to explore the molecular changes after neural circuit activation.


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_CR_H3K9_H327me3]

overall_design: Profiling of H3K9me3 and H3K27me3 in HCT116 cells subject to SON-depletion, or control treatment using CUT & RUN.


title: Small RNA sequencing of serum identifies circulatory microRNAs as biomarkers of coronary artery disease

city: Delhi

first: Neeru

last: Khanna

state: Delhi

address: Mall road

department: Functional Genomics Unit

country: India

institute: CSIR-IGIB

type: Non-coding RNA profiling by high throughput sequencing

summary: Coronary artery disease (CAD) remains the leading cause of morbidity in developing countries like India. It is crucial to identify reliable biomarkers for early detection and risk stratification of the disease. Nucleic acids like microRNAs have emerged as promising candidates for reliable biomarkers due to their stable presence in circulation. Our aim was to determine the potential of circulating miRNA as biomarkers in CAD. To achieve this we utilized next-generation RNA sequencing to profile the miRNome in the serum samples obtained from 8 angiographically proven CAD patients and 4 control subjects. This approach allowed for a comprehensive analysis of the miRNA expression, identifying 12 differentially expressed miRNAs.

overall_design:
Collected serum from 4 Control subjects and 8 CAD patients which includes  2 Acute coronary syndrome (ACS) and 6 Chronic coronary syndrome (CCS) patients.
Isolated RNA from the serum samples and performed next-generation sequencing to profile the miRNome in the collected serum samples.

first: Raj Rajeshwar

last: Choudhury

first: Harshi

last: Gupta

first: Sudha

last: Bhushan

first: Archna

last: Singh

first: Ambuj

last: Roy

last: Saini


title: Identification of a human hematopoietic stem cell subset that retains memory of inflammatory stress [CB]

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

institute: University Health Network

summary: Hematopoietic stem cells (HSCs) survive a lifetime of infection to sustain life-long blood production. Inflammation activates many blood cell types, driving aging and malignancy. To understand HSC adaptation to inflammation, we performed single cell multi-omics on human HSC in xenograft inflammation-recovery models. Two transcriptionally and epigenetically distinct HSC subsets expressing canonical HSC programs were identified. Only one showed sustained transcriptional and epigenetic changes after recovery from inflammatory treatments. This HSC inflammatory memory (HSC-iM) program is enriched in memory T cells and HSC from recovered COVID-19 patients. Importantly, HSC-iM accumulates with age and in clonal hematopoiesis. Overall, heritable molecular alterations in a subset of human HSCs, an adaptation to long-term inflammatory stress, may predispose to heightened age related risk of blood cancer and infection.

overall_design:
All samples were stored as viable cryopreserved cell products. Bone marrow samples were collected from patients undergoing hip replacement surgery for middle and older aged samples, and were purchased from a vendor for younger adult donors. Xenograft samples were pooled from multiple mice treated with the same conditions (as listed) from three separate cord blood engraftment pools. Fresh cord blood was collected from multiple donors. 10x Multiome was performed on cells sorted by FACS after thawing and processing as necessary. For LT-HSC, cells from a large number of donors (>20) were pooled and subjected to scRNAseq (BD Rhapsody).

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title: Medullary cavity expansion is mediated by distinct cell populations during fetal bone development [bulk RNA-seq]

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

summary: RNA-sequencing was performed to examine the transcriptional characteristics of cells involved in osteoclast induction in murine fetal bone.

overall_design:
For analysis of cells marked by CD55 and CD90, tdTomato positive cells isolated from the diaphysis of embryonic day 15.5 (E15.5) Tnfsf11-tTA; LC1; R26-tdTomato mouse bones were further subdivided into CD55+CD90+, CD55+CD90-, CD55-CD90+ and CDCD-CD90- populations and sorted respectively. Two biological replicates were obtained.
For analysis of cells marked by RANKL-tdTomato and Csf1-EGFP, diaphyseal cells isolated from E15.5 Csf1-VCre; Tnfsf11-tTA; LC1; R26-tdTomato; R26-VSV-EGFP mouse bones were subdivided into tdTomato+EGFP+, tdTomato+EGFP-, tdTomato-EGFP+ and tdTomato-EGFP- populations and sorted respectively. Three biological replicates were obtained.
RNA from 14-200 cells were reverse transcribed and amplified for library construction using SMART-Seq kit (Takara Bio).

first: Eriko

last: Sumiya


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_CR_Ser2P]

first: IBRAHIM

last: ILIK

overall_design: Profiling of RNAPII ser2p in HCT116 cells subject to SON-depletion, or control treatment using CUT & RUN.

first: Ibrahim

last: Ilik

first: Michal

last: Malszycki

first: Tugce

last: Aktas


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [HCT116_wt_TRA2AB_KD_pA]

overall_design: Gene expression profiling of HCT116 cells subject to TRA2A/B  or control siRNA for 48hrs. Libraries were prepeared from pA(+)-selected RNA. Control siRNA treatment of this experiment was published: GSM7824617, GSM7824618, GSM7824619


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_Fractionation]

overall_design: Gene expression profiling of HCT116 cells subject to control vs SON-depletion. Libraries were prepeared from ribo-depleted total RNA (whole-cell extract), nuclear RNA or cytoplasmic RNA, 18 libraries in total.


title: Nuclear Speckles enable processing of RNA from GC-rich Isochores [SON_Halo_4sU_chase]

overall_design: Gene expression profiling of HCT116 cells subject to control vs SON-depletion. Libraries were prepeared from cells incubated with 1mM 4sU for 15 minutes, then chased with medium without 4sU for 45 minutes. Ribo-depleted total RNA was used to construct 4 libraries in total.

first: Lisa

last: Martina


title: Identification of a human hematopoietic stem cell subset that retains memory of inflammatory stress [Xenograft]


title: Single cell analysis of a iPSC-derived glial-neurons triculture model of mitochondrial unfolded protein response (UPRmt) activation.

first: Michela

last: Deleidi

summary: Mitochondria have developed a specialized unfolded protein response (UPRmt) to maintain proteostasis and promote recovery under stress conditions. Research in simpler organisms has demonstrated that UPRmt activation in glial cells promotes protein homeostasis through beneficial cell-nonautonomous communication to neurons. To address the role of mitochondrial stress responses in the human brain we profiled the cell-type-specific role of human UPRmt using human induced pluripotent stem cell (iPSC)-derived neuronal and glial tricultures. We found that UPRmt activation disrupted intercellular communication among neuronal and glial cells, leading to  microglial phagocytic pathways dysfunction and increased inflammatory signaling.

overall_design: We developed a human iPSC-derived  triculture system, consisting of 30% iPSC-derived neurons, 60% astrocytes, and 10% microglia. Tricultures were cultured for 7 days before being treated with 1 µM CDDO-Me for 6 hours. Cells were dissociated using accutase and single cell transcriptomic analysis was performed using 10X Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Cat. number 1000128, 10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s instructions

first: Maria Jose

last: Perez J.


title: Medullary cavity expansion is mediated by distinct cell populations during fetal bone development

overall_design: Refer to individual Series


title: Medullary cavity expansion is mediated by distinct cell populations during fetal bone development [scRNA-seq]

summary:
Single-cell RNA-sequencing was performed to examine the transcriptional landscape of murine fetal primary ossification center in early bone and bone marrow development.
We particularly focused on the identification of potential osteoclast-inducing cells in the developing bone and aimed to analyzed its cellular fates.

overall_design:
For whole bone analyses, cells were sorted from bone and bone marrow of embryonic day 15.5 (E15.5) or 9-week-old mice.
For analysis of early primary ossification center, tdTomato positive cells were sorted from the diaphysis of Tnfsf11-tTA; LC1; R26-tdTomato mice or Col10a1-Cre; R26-tdTomato mice at E15.5.
For cell lineage tracing experiments, tdTomato positive cells were sorted from bone and bone marrow of E17.5 or postnatal day 3 Tnfsf11-tTA; LC1; R26-tdTomato mice which were treated with doxycycline from E15 onwards.
Sorted cells were subjected to scRNA-sequencing based on 10x Genomics Chromium Single Cell 3' Gene Expression Profiling version 3.1 platform.


title: A low-input Micro-C protocol for high-resolution 3D genome mapping

status: Public on Mar 08 2026

city: shenzhen

first: Chongren

last: Pei

state: guangdong

address: Gaoke Innovation Center, Guangming District

department: Institute of Molecular Physiology

institute: Shenzhen Bay Laboratory

summary: Standard Micro-C protocols typically require millions of cells, which limits their application to rare cell populations. Here, we present an optimized low-input Micro-C workflow that requires only 100,000 cells. By comparing 30 G of sequencing data from 100,000 cells with that from 5 million G1E-ER4 cells, we demonstrate that all key architectural features—compartments, TADs, and chromatin loops—are reliably detected. Applying this method to investigate acute CTCF degradation, we observed the loss of loops and TAD boundaries in CTCF-degraded samples, consistent with previous reports. Our optimized protocol enables nucleosome-resolution 3D genome mapping for sample-limited studies.

overall_design: To evaluate the feasibility of performing Micro-C (micrococcal nuclease chromosome conformation capture) using 100,000 G1E-ER4 cells, the following experimental procedure was conducted. Cells were first cross-linked with formaldehyde and EGS, followed by chromatin digestion with MNase. The digested chromatin, fragmented into nucleosome, was then ligated using T4 DNA ligase in the presence of biotin-labeled nucleotides. After reverse cross-linking, DNA was purified with DNA clean beads. Biotin-containing DNA fragments were subsequently pulled down using streptavidin C1 beads to construct the DNA library for sequencing.

first: Fengnian

last: Shan

first: Sijian

last: Xia

first: Fei

last: Ling


title: Identification of a human hematopoietic stem cell subset that retains memory of inflammatory stress [LTHSC]


title: Massively parallel reporter assay reveals promoter-, position-, and strand-specific effects in transcription start sites

city: Ann Arbor

first: Stephen

middle: CJ

last: Parker

state: Michigan

address: 1000 WALL ST, BREHM TOWER,RM 5474

department: Gilbert S. Omenn Department of Computational Medicine & Bioinformatics

institute: University of Michigan

summary: Massively parallel reporter assays (MPRA) are a high-throughput method of assessing the activity of candidate cis-regulatory sequences, and can be used to detect allelic differences at disease-associated variants. Previous MPRA studies have screened thousands of functional SNPs associated with various complex traits and conditions. Most MPRA libraries utilize a single plasmid configuration, a single minimal promoter to drive expression, and a single-strand orientation, which may fail to capture the context-dependent activity of disease-associated cis-regulatory elements. We interrogate the potential regulatory differences introduced by variable MPRA plasmid promoters and positions. We used an MPRA library to quantify the activity of 1,305 pancreatic islet-derived transcription start sites generated from Cap analysis of gene expression profiling. We cloned fragments upstream or downstream of a reporter gene along with either the human insulin (INS) promoter or a synthetic housekeeping promoter (SCP1). We used elastic net regression to predict position-specific fragment activity based on enrichment of transcription factor binding site motifs, and generalized linear models to predict position-specific fragment activity from tissue-specific chromatin state regulatory annotations. Our results support the use of MPRA strategies that account for context-dependent factors when assaying candidate regulatory elements in pursuit of understanding complex genetic diseases.

sample_organism:
Homo sapiens
Rattus norvegicus
synthetic construct

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

first: Maya

last: Bose

first: Adelaide

last: Tovar

first: Yasuhiro

last: Kyono

first: Arushi

last: Varshney

first: Jacob

middle: O

last: Kitzman


title: H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs [RNA-seq]

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

institute: McGill University

summary: Polycomb Repressive Complex 2 (PRC2) deposits H3K27me3 to recruit canonical PRC1 (cPRC1) that establishes repressive heterochromatin. Higher order cPRC1-mediated chromatin interactions characterize early development and resolve during cell differentiation. Here, we use two opposing models of H3K27me3 dysregulation to elucidate how these long-range loops affect gene expression and cellular phenotypes. Aggressive gliomas driven by histone H3 Lys-27-Met (H3K27M) mutations or EZH-Interacting Protein (EZHIP) expression confine H3K27me3 deposition to PRC2 nucleation sites, while loss of the H3K36 methyltransferase NSD1 in pluripotent stem cells leads to its unrestrained spread from these sites.  In H3K27M mutant tumours, focal H3K27me3 deposition concentrates chromatin occupancy of cPRC1 complexes, which results in long-range chromatin interactions anchored in polycomb bodies, mirroring patterns found in stem cells. Conversely, spread of H3K27me3 due to NSD1 loss dilutes cPRC1 deposition and disrupts polycomb body architecture. In H3K27M cells, H3K27me3 confinement sustains repression of genes tethered to the polycomb bodies, promoting self-renewing progenitor states required for tumour development. Maintenance of progenitor states depends on cPRC1 interaction with H3K27me3, as chemical allosteric modulation of chromodomains alleviates repression of transcription and promotes differentiation. These results suggest that H3K27me3 spread from CGIs modulates cPRC1 gene expression programs to orchestrate developmental transitions through the maintenance or dissolution of repressive 3D loop architecture at polycomb bodies. Imbalances in the spread of H3K27me3 altering chromatin architecture in disease including H3K27M-expressing neoplasms or following NSD1 loss contribute to explain pathogenic states.

overall_design: Hi-C, ChIP-seq, bulk and single-cell RNA-seq on model systems with altered H3K27me3 spread

first: Nada

last: Jabado

first: Chao

last: Lu


title: Whole-Genome Bisulfite Sequencing (WGBS) Analysis of Tail Tip Tissues from F2 Generation Mice

city: Guangzhou

first: Qi

last: Li

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

department: Developmental biology

institute: Southern Medical University

summary: Here, we include data on the transmission of DNA methylation patterns to the F2 generation, which are derived from F1 progeny sired by either in vivo or O-Torgs-derived  spermatids.

overall_design: Whole-Genome Bisulfite Sequencing (WGBS) Analysis of  tail tip tissues from F2 generation mice.

first: Xiaoyang

last: Zhao

first: Fang

last: Luo

first: Kai

last: Miao

first: Cong

last: Wan


title: H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs [ChIP-seq]

overall_design: Hi-C, ChIP-seq, bulk and single-cell RNA-seq on isogenic model systems with altered H3K27me3 spread


title: Transcriptomic analyses of labial glands and gut tissue from two wax moths, Achroia grisella and Galleria mellonella

city: Acton

first: Gunjan

last: Pandey

address: Clunies Ross Street

department: Environment

institute: Commonwealth Scientific and Industrial Research Organisation

summary: Plastics are highly stable materials with widespread applications, but their resistance to degradation poses a significant environmental challenge, often resulting in accumulation in landfills or pollution in the form of microplastics. Biodegradation using insect larvae has recently emerged as a promising strategy to address this issue, though the molecular basis of plastic degradation in these organisms remains poorly understood due to limited genomic resources. In this study, we present a complete genome of the lesser wax moth, Achroia grisella, and tissue-specific RNA-Seq data of both the lesser and the greater wax moth, Galleria mellonella, two species known to consume various plastics. Our analyses reveal several highly expressed secretory enzymes in gut and labial tissues. Orthologous comparisons of differentially expressed genes also identified five enzymes (three hexamerins and two monooxygenases) from the lesser wax moth that have been shown or are predicted to have plastic-degrading potential in the greater wax moth. We also identified enzymes that may potentially be involved in polyethylene and polystyrene degradation based on their identities with known bacterial enzymes that have been experimentally validated and are involved in plastic degradation pathways. Together, these genomic and transcriptomic resources provide a foundation for understanding plastic degradation in wax moths and highlight candidate genes for future functional validation.

overall_design: RNA-Seq analysis of digestive tissue (gut, labial glands) of penultimate instar A. grisella larvae to identify candidate catabolic enzymes potentially capable of acting on long-chain hydrocarbons. Fat body was also sequenced and used as the reference tissue. Tissue from five individual specimen were collected and pooled for the whole gut and labial gland tissues whilst tissue from three individual specimen were collected and pooled for the fat body.

first: Reginald

last: Young

first: Khandaker

last: Ahmed

first: Leon

last: Court

first: Rahul

last: Rane

first: Tom

last: Walsh


title: Peripheral modulation of Pumilio in intestinal stem cells and the corpus allatum affects sleep latency in Drosophila

city: San Juan

first: Jose

last: Agosto-Rivera

state: Puerto Rico

address: 14 Ave. Universidad Ste. 1401

department: Biology

institute: University of Puerto Rico, Rio Piedras

summary: While central circuits governing sleep are well-studied, the contribution of signaling from peripheral tissues remains a critical yet less understood aspect of sleep regulation. The highly conserved RNA-binding protein Pumilio (Pum) is a post-transcriptional regulator expressed in multiple tissues that influence systemic physiology, but its role in modulating basal sleep has not been established. Although Pumilio’s function in central neurons has been linked to sleep homeostasis following deprivation, whether it regulates sleep through peripheral mechanisms remains unknown. Here, we use conditional genetic tools in the fruit fly Drosophila melanogaster to demonstrate that genetic manipulation of Pumilio targeting the intestinal stem cells (ISCs) and the endocrine corpus allatum (CA) regulates the transition to sleep. Reducing Pumilio function in either the ISCs or the CA independently and significantly accelerates nighttime sleep onset, while overexpression produces the opposite effect. This behavioral change is accompanied by widespread transcriptional alterations in the head, characterized by a robust upregulation of genes involved in cellular stress responses. Our findings reveal a previously unrecognized gut-endocrine-brain signaling axis and identify peripheral post-transcriptional regulation as a key input to the central control of sleep behavior.

overall_design: RNA-seq profiling by high-throughput sequencing of Drosophila heads (10 per sample) following transgene expression at 29°C using the TARGET system. Comparative analysis between pum knockdown and mCherry control groups.

first: Josué

last: Rodríguez-Cordero

first: Marialena

last: Dorta-Avilés

first: Imilce

last: Rodriguez-Fernandez

first: Alfredo

last: Ghezzi

first: José

middle: E

last: Lizardi-Ortiz


title: Autophagy controls neuronal differentiation by regulating the WNT/DVL signal pathway

city: Bongmyeongdong

first: Vincencius

last: Vidyawan

state: Cheonan

address: 25, Bongjeong-ro, Dongnam-gu, Cheonan-si, 31151, Korea

department: Department of Integrated Biomedical Science

institute: Soonchunhyang Institute of Medi-bio Science (SIMS)

summary: Development of human embryonic stem cells (hESCs) technology provides a powerful tool to understand the mechanism of various diseases, as well as a model for human developmental study in vitro. In this study, we generated neurons from hESCs with previously established protocol and we observed that autophagy-related genes were upregulated at neuroepithelial/NPC stage. To check the importance of autophagy activation, bafilomycin was treated at a specific time point. We found that inhibition of autophagy at NPC stage delayed neuronal differentiation, as indicated by the downregulation of neuronal marker TUJ1 and upregulation of NPC marker NESTIN. Further investigation revealed that WNT signaling might be involved as part of the underlying mechanisms. Autophagy negatively regulates WNT signaling by promoting Disheveled-2 (DVL-2) degradation. Disruption of autophagy might lead to failure in the downregulation of WNT signaling and consequently, delaying neuronal differentiation. Dysregulation of autophagy has been associated with a variety of neurological diseases, including Vici syndrome. Here, we developed cerebral organoids culture to model Vici syndrome by introducing loss of function mutation in EPG5 gene. Mutation in EPG5 gene disturbed autophagy process, subsequently induced defect in progenitor cells migration and cortical layer generation in organoids. The results showed how damaged autophagy leads to smaller organoids, recapitulating Vici syndrome-associated microcephaly, and therefore validating the disease relevance of our study.

overall_design: To investigate role of autophagy RNA sequencing analysis was performed  the transcriptome profiles of EPG5 Knockout cell line (CL5; day 11 of differentiation)

first: Lesly

last: Puspita

first: Virginia

middle: B

last: Juwono

first: Magdalena

last: Deline

first: Mi-Yoon

last: Chang

first: Sang-Hun

last: Lee

first: Jae-won

last: Shim


title: Muscleblind-like proteins dimerize by forming disulfide bonds to influence regulation of alternative splicing

city: Atlanta

first: Adam

last: Kosti

state: GA

address: 615 Michael St

department: Cell Biology

institute: Emory University

summary: Muscleblind-like (MBNL) RNA-binding proteins (RBPs) possess modular domains that contribute to their regulation of alternative splicing and RNA localization. MBNL dimerization may play a role in these functions, but the mechanism is not well understood. Here we identify a cysteine residue in the unstructured carboxy-terminal domain of MBNL1 that enables dimerization by forming intermolecular disulfide bonds. We also demonstrate that MBNL2 likewise dimerizes by forming disulfide bonds between multiple cysteines in its carboxy-terminal tail. Nucleocytoplasmic fractionation revealed a greater proportion of MBNL1 dimer in the nucleus, suggesting a nuclear function for the MBNL1 dimer. We investigated a connection between MBNL1 dimerization and MBNL1-mediated regulation of alternative splicing. To accomplish this, we mutated the MBNL1 cysteine in question to alanine (C325A) and performed RNAseq. We uncovered numerous novel splicing events sensitive to MBNL1 dimerization.

overall_design: RNA-seq profiling of WT MEFs, Double Knockout (DKO) MBNL1/2 MEFs, DKO MEFs transfected with WT-MBNL1 and DKO MEFs transfected with MBNL1 that has a conserved cysteine mutated to an alanine.

first: Luke

last: Knudson

first: Gary

middle: J

last: Bassell


title: Reconstitution of spermatogenesis and continuous generation of functional haploid germ cells in mouse testicular organoids

first: Qi

last: Li

summary: Testicular organoids that support spermatogenesis and generate functional haploid germ cells are still lacking. Here, we developed a formation-differentiation culture approach to generate optimized testicular organoids (O-Torgs) derived from neonatal mouse primary testicular cells. These O-Torgs could essentially recapitulate the seminiferous tubule morphogenesis, Sertoli cell maturation and testosterone secretion. Importantly, O-Torgs not only support spermatogenesis but also sustain proliferative undifferentiated spermatogonia and continuous generation of functional haploid cells for up to three months, with offspring derived from these haploid cells displaying normal growth and reproductive capability to F2 generation. Mechanistically, we found that the formation stage enhanced the reconstruction of tubule-like structures and subsequent spermatogenesis by providing a more conducive extracellular matrix niche. Finally, O-Torgs were proved to be effective in modeling male infertility and drug screening, with BTT-3033 acting as a potential drug in protecting busulfan-mediated germ cell loss. Overall, our work establishes a strategy to obtain functional testicular organoids, offering promising avenues for male infertility modeling and drug discovery.

overall_design: scRNA - seq profiling of testicular organoids cultured with the traditional system and optimized system at Day6 and Day40

first: Xiaoyang

last: Zhao

first: Fang

last: Luo

first: Kai

last: Miao

first: Cong

last: Wan


title: Two mycorrhiza-responsive MADS transcription factors, OsMADS61 and OsMADS26, regulate both direct and mycorrhizal nitrate transport pathways

status: Public on Mar 07 2026

city: Jinan

first: Yuhan

last: Ren

address: 2 Wenbo Road, Zhangqiu District, Jinan, Shandong, P.R.China

department: School of Life Sciences

institute: Qilu Normal University

summary: Most land plants have evolved both a direct root uptake pathway and a symbiotic pathway, via association with arbuscular mycorrhizal (AM) fungi, to facilitate nutrient acquisition, particularly of phosphorus (P) and nitrogen (N), from soil. Recently, we revealed a highly efficient symbiotic pathway for nitrate uptake, mediated by an AM-specific NPF/NRT1 transporter, OsNPF4.5, in rice. However, the regulatory mechanism controlling the AM-specialized expression of OsNPF4.5 remains unclear. Here, we demonstrate that two cis-acting elements, the CArG and GCC-box, are essential for activating the expression of OsNPF4.5 in rice mycorrhizal roots. Deletion of either of the two motifs in its promoter caused almost complete abolition of the promoter activity of OsNPF4.5. An AM-responsive MADS (MCM1, AG, DEFA, and SRF) transcript factor, OsMADS61, could positively regulate OsNPF4.5 and another nitrate transporter gene, OsNRT2.2, involved in direct nitrate uptake. Knockout of OsMADS61 decreased root biomass, N accumulation and mycorrhization efficiency in its mutants. OsMADS61 could be directly regulated by another AM-upregulated OsMADS paralogue, OsMADS26, which itself can also activate OsNPF4.5, OsNRT2.2, and OsNAR2.1, encoding a nitrate transporter activating protein. Together, our results reveal a dual regulatory role for OsMADS61 and OsMADS26 in governing both direct and symbiotic nitrate uptake pathways.

overall_design: To gain further insights into the mechanism of OsMADS61-mediated regulation of nitrate transport under asymbiotic condition, we performed RNA sequencing (RNA-seq) analysis of the roots collected from both WT and Osmads61 mutants grown in hydroponic solution containing 2.5 mM nitrate.

first: Congfan

last: Yang

first: Haoyan

last: Ji

first: Kun

last: Xie

first: Haoran

last: Mao

first: Dechao

last: Zeng

first: Lingxiao

last: Wang


title: H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs [Hi-C ]

first: Jacek

last: Majewski

first: Nada

last: Jabado

first: Chao

last: Lu


title: tRNA m1A modification enhances anti-tumor immunity in macrophages by promoting translation of key interferon associated genes

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

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


title: Single-cell transcriptome analysis of individual embryos.

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

summary: Background: Single-cell RNA sequencing (scRNA-seq) integration methods remove technical variation while preserving biological signal, yet systematic frameworks for evaluating how parameter choices influence biological interpretation remain limited. Traditional benchmarking approaches evaluate single-parameter configurations per method, potentially missing systematic patterns in functional outcomes and method convergence. A framework for systematic integration parameter evaluation was developed and applied to bovine embryo development. Results: Six integration methods (FastMNN, CCA, RPCA, scVI, Harmony, STACAS) combined with multiple parameters, including those for neighbor identification and clustering, yielded 8232 combinations. The main outputs evaluated were specific cell counts and marker identification. After filtering for extremely poor cell and marker identification, 4,287 integration parameter combinations were retained for analysis. There were three major patterns (clusters) with integration methods distributed non-randomly across clusters and distinct biological outcomes. One pattern emerged, composed of scVI and STACAS integration, dominated by the lack of identification of epiblast cells. Cluster 2 (n=29), also composed of scVI and STACAS integration, identified the most epiblast markers (n=7, 8, or 9) but had a limited number of epiblast cells (median=10). Cluster 1 (n=4,120 combinations) had the highest method diversity. Across clusters, trophoblast and mesoderm showed high functional distinctness, while epiblast and hypoblast showed moderate overlap in gene ontology classes. Conclusions: The approach reveals that parameter choices influence cell type classification, functional interpretation, and the degree of method convergence, with implications for identifying specific biological inferences for further orthogonal validation. A systematic approach to evaluating integration methods, along with other parameters, is advisable for accurate biological inference.

overall_design: Cattle embryos were produced in vitro and collected on days 12 and 16 post fertilization.


title: Mild cold exposure mitigates ischemic heart injury through indole-3-acetamide–AHR-mediated SMAD2 proteolysis

city: Jiangsu Province

first: cunzhong

last: Fan

address: No. 2, Southeast University Road, Jiangning District, Nanjing, Jiangsu, China.

institute: Southeast University

summary: Ambient temperature profoundly influences organismal metabolism, physiology, and disease. While cold exposure is a well-recognized risk factor for the onset of myocardial infarction (MI), its impact on the injured heart after MI remains unexplored. Here, we demonstrate that a mild cold exposure (MCE) regimen at 16oC improved mice systolic function post-MI compared to the controls kept at room temperature. Integrative multi-omics analyses revealed a critical link between a cold-inducible tryptophan metabolite indole-3-acetamide (I3AM) and cardiac fibrosis in post-MI hearts. MCE elevated I3AM levels in serum and heart tissue and upregulated gut indole-related metabolic pathways; which was necessary to attenuate cardiac fibrotic remodeling by inhibiting SMAD2/3 signaling and fibroblast activation. Mechanistically, I3AM acts as a ligand for the aryl hydrocarbon receptor (AHR). I3AM-bound AHR promoted ubiquitination and proteasomal degradation of SMAD2. Treatment with I3AM recapitulated the cardioprotective effects of MCE, while genetic or pharmacological inhibition of AHR abolished the benefits of both MCE and I3AM in MI mice. In patients with and without heart failure, serum I3AM levels correlated positively with cardiac function, underscoring its clinical relevance. Our findings unveil a previously unrecognized metabolic-proteolytic axis triggered by MCE and identify the temperature responsive I3AM-AHR-SMAD pathway as a potential therapeutic target for ischemic hearts.

overall_design: Bulk RNA sequencing analysis was performed on heart tissues from myocardial infarction (MI) mice treated at room temperature (RT) or with mild cold exposure (MCE).


title: Bulk RNA-seq Analysis of Testis Tissues from Normal and Model Mice

first: Qi

last: Li

summary: We provide bulk RNA-seq data generated from testicular tissue samples of mice treated with Vehicle, BU+PBS, and BU+BTT-3033.

overall_design: Bulk RNA-seq of testis tissues from normal and model mice treated with Vehicle, BU+PBS, and BU+BTT-3033.

first: Xiaoyang

last: Zhao


title: Expression profiling by high throughput sequencing of breast cancer

city: Guiyang

first: Tao

state: Guizhou

address: #83 zhongshandong road

institute: Guizhou Provincial People's Hospital

summary: This study comprises 158 clinical samples diagnosed as breast carcinoma in situ. Total RNA was extracted from fresh-frozen tissue specimens and subjected to high-throughput RNA sequencing to characterize the transcriptomic landscape and identify molecular signatures associated with disease progression and heterogeneity.

overall_design:
Gene expression profiling analysis of RNA-seq data for breast cancer.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************


overall_design: Refer to individual Series

first: Fang

last: Luo

first: Kai

last: Miao

first: Cong


title: Evolutionary expansion of the corticospinal system is linked to dexterity in Peromyscus mice

city: Cambridge, MA

first: KT

last: Tyssowski

state: Massachusetts

address: 16 Divinity Ave

institute: Harvard University

summary: While the central nervous system is perpetually reshaped by evolution, the principles governing how such changes promote ecologically relevant behaviors without breaking established functions are poorly understood. The expansion of neuron number is a potential mechanism by which the nervous system evolves to support changes in behavior without disrupting existing circuit function. Corticospinal neurons (CSNs) are a classic example: an expansion in the corticospinal system in the primate lineage has been hypothesized to underlie their exceptional dexterity. However, the role of CSN number in behavior has been difficult to assess due to the lack of a tractable model system. We compared two closely related subspecies of deer mice (Peromyscus maniculatus): forest mice, which evolved the ability to adeptly climb, presumably to support a semi-arboreal lifestyle, and prairie mice, which are less proficient climbers. We find that forest mice have about two-fold larger corticospinal tracts (CSTs) driven by an increase in CSN number in secondary motor and sensory cortical areas (M2 and S2). Furthermore, forest mice display greater manual dexterity than their prairie counterparts in a reach-to-grasp task, consistent with the idea that an increase in CSN number supports more dexterous behavior. High-throughput neural recordings during this task revealed a difference in the timing of neural activity between forest and prairie mice, specifically in M2: in forest mice, the peak of activity was shifted towards the grasping phase of the behavior. Forest mice also outperform their prairie counterparts on an ecologically relevant climbing task, where they spend more time upright crossing a thin rod, move faster, and right themselves more quickly when they fall, suggesting a general difference in motor dexterity not restricted to hand use. Finally, we use F2 hybrid animals to show that CST size is correlated with climbing dexterity, providing support for the long-standing hypothesis that corticospinal system expansion supports the evolution of dexterity. Together, our work establishes the forest-prairie deer mouse system as a model to investigate the role of neuron number expansion, and CSNs in particular, in dexterous movement.

sample_organism:
Peromyscus maniculatus bairdii
Peromyscus maniculatus nubiterrae

overall_design: We used the frontal cortex of five animals of each subspecies (P.maniculatus bairdii, BW; P.maniculatus nubitarrae, NB). The anterior half of the cortex was extracted from both hemispheres for each animal (this includes all of sensorimotor cortex, as well as other areas) and flash-frozen in liquid nitrogen.

first: Kelsey


title: Restoring Circadian Rhythms in the Paraventricular Nucleus Reverses the Epigenetic Clock of Multi Tissues in Aging Mice. [RRBS]

city: Beijing

first: Meimei

last: Liao

address: 7 Science Park Road ZGC Life Science Park, Beijing

institute: National Institute of Biological Sciences, Beijing.

summary: The decline of behavioral and metabolic rhythms with aging underscores the critical role of circadian regulation in health and longevity. Restoring circadian rhythms has recently emerged as a promising strategy to combat aging-associated disorders. Epigenome remodeling and gene expression changes during cellular senescence. These epigenomic changes have been widely recognized as hallmarks of aging. Therefore, we examined the DNA methylation levels in aging mice with 3dA treatment and chemogenetic manipulation in PVN. Our results suggest that enhancing circadian rhythm amplitude in paraventricular nucleus (PVN) neurons by 3’-deoxyadenosine (3dA) and chemogenetics significantly reverses the epigenetic clock of multi tissues in aging mice.

overall_design: Reduced representation bisulfite sequencing (RRBS) profiling of liver, lung and muscle tissues in aging mice treated with 3dA and chemogenetic manipulation in PVN.

first: Haijiao

first: Dapeng

last: Ju

first: Eric Erquan

last: Zhang


first: Gunjan

last: Pandey

overall_design: RNA-Seq analysis of digestive tissue (gut, labial glands) of penultimate instar G. mellonella larvae to identify candidate catabolic enzymes potentially capable of acting on long-chain hydrocarbons. Fat body was also sequenced and used as the reference tissue. Tissue from five individual specimen were collected and pooled for the whole gut and labial gland tissues whilst tissue from three individual specimen were collected and pooled for the fat body.

first: Reginald

last: Young

first: Khandaker

last: Ahmed

first: Leon

last: Court

first: Rahul

last: Rane

first: Tom

last: Walsh


title: LIF induced tumor plasticity establishes an immunosuppressive myeloid niche in LKB1 mutant lung cancer [antiLif_CITEseq]

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

summary: Single Cell RNA-seq analysis (5' CITE-seq) of immune Cells from Murine Lkb1 mutant KP Lung Tumors  with deletion of Lif or Lifr (Figure 3)

overall_design: Eight weeks after tumor initiation, mice with Lkb1 mutant tumors were treated with an isotype control or anti-LIF therapy for 3 weeks. 11 weeks after tumor initiation, immune cells from the lungs of KP GEMM mice were isolated (sorted live, CD45 positive, extravascular CD45 negative). 10% sorted tumor cells were spiked in (GFP positive CD45 negative). 2 samples per lane individually hashed. N=2 per tumor genetic condition.

first: Ray

last: Pillai

first: Ali

last: Rashidfarrokhi

first: Aristotelis

last: Tsirigos

first: Sergei

last: Koralov

first: Thales

last: Papagiannakopoulos


title: LIF induced tumor plasticity establishes an immunosuppressive myeloid niche in LKB1 mutant lung cancer [10x_scRNAseq]

summary: Single Cell RNA-seq analysis (3' 10x) of immune Cells from Murine Lkb1 wildtype or mutant KP Lung Tumors (Figure 1A, 1B, 1C)

overall_design: Immune cells from the lungs of KP GEMM mice were isolated (sorted live, CD45 positive, extravascular CD45 negative). 2 samples per lane individually hashed. N=2 per tumor genetic condition.


title: AP2Ⅺ-3 is critical for the cell cycle of Toxoplasma to progress through the G1 phase

city: Wuhan

first: Fan

last: Fuqiang

address: 1 Shizishan St

institute: Huazhong Agricultural University

summary: Toxoplasmosis caused by the Apicomplexan parasite Toxoplasma gondii is a significant health threat to immunocompromised individuals and newborns. This parasite has a complex life cycle that is well controlled to achieve optimal transmission and pathogenesis. Acute phase of the disease is caused by rapid proliferation of tachyzoites, which has a highly coordinated and tightly regulated cell cycle to allow parasite propagation. Tachyzoite cell cycle has five partially overlapping phases (G1, S, G2, M and C) with distinct gene expression patterns and cellular activities, yet the underlying regulatory mechanisms are not well understood. In this study, we show that the AP2 family transcription factor AP2Ⅺ-3 has important roles in regulating the cell cycle to progress through the G1 phase. Depletion of AP2Ⅺ-3 resulted in cell cycle retention at G1 and impaired parasite division, leading to growth inhibition of tachyzoites. RNA-Seq and CUT&Tag analyses revealed that AP2Ⅺ-3 regulates the transcription of genes involved in nucleic acid metabolism, RNA biogenesis and processing, which are consistent with the cellular activities of G1 phase in preparing biomass for cell cycle progression. Moreover, AP2XI-3 binds to the conserved DNA motif, TRP-2, a sequence widely distributed in the promoters of genes that exhibit peak expression during the G1 phase. Together, these findings underscore the essential role of AP2Ⅺ-3 in the tight regulation of the G1 phase, highlighting its potential as a therapeutic target for drug development.

overall_design: Cut&TAG of RH iAP2XI-3 and parental RH Tir1 to detect genome occupancy of AP2XI-3 in tachyzoites.

first: Fuqiang

last: Fan

first: Bang

last: Shen


title: Identification of BET Inhibitors (BETi) Against Solitary Fibrous Tumor (SFT) Through High-Throughput Screening (HTS)

city: Madrid

first: Jose

last: Mondaza-Hernandez

address: Av Reyes Católicos, 2

institute: Health Research Institute Fundacion Jimenez Diaz

summary: Solitary Fibrous Tumor (SFT) is a rare mesenchymal tumor driven by the NAB2-STAT6 fusion oncogene. To investigate transcriptional changes induced by BET inhibition in SFT models, we performed bulk RNA sequencing of INT-SFT and IEC139 cell lines treated with the BET inhibitors Mivebresib (ABBV-075) or BMS-986158 (50 nM for 24 h). Total RNA was extracted and libraries were sequenced on the Illumina NovaSeq X platform. Gene-level expression was quantified using Salmon against the GRCh38 reference genome with GENCODE annotation. Differential expression and pathway enrichment analyses were performed to characterize transcriptional programs associated with BET inhibitor treatment.

overall_design: Two SFT cell line models (INT-SFT and IEC139) were treated with either vehicle control, Mivebresib (50 nM), or BMS-986158 (50 nM) for 24 hours. For each condition, three independent biological replicates were collected, except where one replicate was excluded as an outlier (INT-SFT BMS-986158 rep1). Total RNA was extracted and subjected to bulk RNA sequencing. Differential gene expression analysis was performed comparing treated versus control samples within each cell line.

first: Yi

last: Li

first: Jesus

last: Marti


title: A Positive Feedback Loop Between TKT and c-Myc Drives TACE Resistance In Hepatocellular Carcinoma

city: Nantong

first: Yifu

last: Xiao

address: xisi Road

institute: Affiliated Hospital of Nantong University

summary: Hepatocellular carcinoma (HCC) often receives transarterial chemoembolization (TACE), yet clinical benefit is limited by resistance driven by ischemia-induced adaptations. This study explains how transketolase (TKT) in the pentose phosphate pathway (PPP) modulates HCC progression and TACE refractoriness, and clarifies its mechanistic connection to oncogenic signaling.

overall_design: We integrated transcriptomic screening with analyses of TACE patient specimens, and  performed  gain  and  loss  of  function  experiments  across  HCC  cell  lines. Functional assays, RNA-seq with pathway enrichment, western blotting, immunofluorescence,cycloheximide-chase and ubiquitination assays, and an orthotopic VX2 rabbit TACE model with imaging and immunohistochemistry were used.TKT emerged as a hub gene, was elevated in TACE-resistant patients, and promoted proliferation, migration, invasion, epithelial–mesenchymal transition, and apoptosis resistance.Mechanistically, TKT associates with RAF1, promoting phosphorylation of c-Raf at Ser338 and subsequent ERK activation, and stabilizes c-Myc by enhancing Ser62 phosphorylation and reducing ubiquitin-mediated degradation. Additionally, c-Myc enhances the transcriptional expression of TKT, creating a positive feedback loop between TKT and c-Myc.These findings identify a TKT/c-Myc positive feedback loop that underlies TACE resistance and HCC progression, nominating TKT as a biomarker of refractoriness and a therapeutic target to improve locoregional treatment outcomes.


title: Exploring the mechanism of Jia Wei Xing Bi Gel nasal drops on Children with Allergic Rhinitis based on Transcriptomics and Network Pharmacology

city: Fuzhou

first: si

last: ai

state: Fujian

address: No. 602 Middle 817 Road, Taijiang District

institute: The People's Hospital Affiliated to Fujian University of Traditional Chinese Medicine

summary: Objective: This study combines transcriptomics and network pharmacology to explore the mechanism of action of Jia Wei Xing Bi Gel nasal drops in treating allergic rhinitis (AR) in children. Methods: A total of 56 AR children were randomly divided into Jia Wei Xing Bi Gel nasal drops(JWXBGND) group and mometasone furoate nasal spray (MFGS) group, with 28 cases in each group, and a healthy control group of 20 cases. After 4 weeks of treatment, efficacy was evaluated, and RNA-seq, database mining, and bioinformatics analysis methods were employed. Results: In terms of clinical efficacy, the TCM group showed better improvement in nasal itching, ocular symptoms, non-nasal ocular symptoms, and behavioral issues compared to the western medicine group, with a more significant decrease in TCM syndrome scores; transcriptomic analysis revealed 2776 differentially expressed genes when comparing AR children with healthy children, and 441 differential genes were identified between JWXBGND group and MFGS group; combined analysis of transcriptomics and network pharmacology identified 195 active components and 493 targets of action for Jiawei Xingbi Gel, with core components including ferulic acid, fexofenadine, and curcumin A, and core targets involving TNF, IL-6, IL-1β, AKT1, ALB, SRC, etc.; KEGG pathway analysis mainly enriched in caffeine metabolism, linoleic acid metabolism, Th17 cell differentiation, HIF-1 signaling pathway, etc.; molecular docking results indicated that key active components of Jia Wei Xing Bi Gel nasal drops bind stably to targets such as ALB, AKT1, SRC, TP53, etc. Conclusion: Jia Wei Xing Bi Gel nasal drops can effectively alleviate AR symptoms, and its mechanism may be related to the regulation of inflammatory signaling pathways through multiple components and multiple targets

overall_design: Identification of differentially expressed genes via RNA-seq of PBMCs in 5 pediatric rhinitis patients pre- and post-treatment

first: Si

last: Ai

first: Zhuoyang

last: Jiang

first: Shiwei

last: Kang

first: Xueqi

first: Yuqin

last: Zhang

first: Xiong

last: Lin

first: Jian

last: Zheng


title: Nitric Oxide Synthase 2-Dependent Metabolic Dysregulation, Immunosuppression, and Genomic Instability in Metastatic Triple-Negative Breast Cancer

city: Tucson

first: William

last: Montfort

state: AZ

address: 1041 E Lowell St

institute: University of Arizona

summary: Chronic inflammation drives many diseases, including cancer, where inflammation is associated with metastasis, the cause of death in 90% of cancer fatalities.  Tumor inflammation drives inducible nitric oxide synthase (NOS2 or iNOS) and cyclooxygenase 2 (COX2) expression, each of which is associated with poor outcomes in cancer.  Here, we knocked out the NOS2 gene in the murine triple negative breast cancer allograft tumor model 4T1 and examined metastatic spread from primary mammary tumors to lung in BALB/c mice with intact immune systems.  Remarkably, while the parental 4T1 tumors were highly metastatic, metastasis from 4T1 NOS2-/- tumors was nearly eliminated.  In cell culture, we find that nitric oxide from NOS2 induces a glycolytic phenotype, epitrascriptomic dysregulation, DNA damage, and prostaglandin E2 synthesis by stimulating COX2.  Human colorectal cancer cell line DLD1 yielded similar results.  RNA sequencing revealed NOS2-dependent loss of mRNA associated with regulation of chromosome and DNA replication, including cell cycle checkpoints, as well as mRNA associated with RNA demethylation, including tRNA demethylation.  Immunoprofiling of the tumor microenvironment revealed immunosuppressed tumors that were low in T cells and high in myeloid derived suppressor cells expressing interferon gamma, which induces NOS2 expression.  Others have shown nitric oxide from immune cells suppresses tumor immunity.  Here, we show nitric oxide from tumor cells plays a critical role in metastasis.  Taken together, these data suggest high NOS2 in tumor cells drives metastasis through a broad accumulation of cancer-associated factors – including metabolic dysregulation, genetic instability, and immunosuppression – all of which contribute to aggressive metastasis.

overall_design: RNA-seq analysis of 4T1 (murine) cells and DLD1 (human) cells in tissue culture.  A cytokine mixture was used to induce NOS2 expression.  4T1 WT, 4T1 NOS2 KO1, and 4T1 NOS2 KO2, were compared +/- cytokine and NOS2 inhibitor. DLD1 WT was compared +/- cytokine and NOS2 inhibitor.


title: Dissecting the mechanism of circZNF827-mediated transcriptional regulation of neuronal differentiation (CUT&RUN)

city: Aarhus

first: Ivan

last: Zaporozhchenko

address: Universitetsbyen 83, 1874-356

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary: Circular RNAs (circRNAs) originate from backsplicing of numerous genes in animals, but the functions of most circRNAs remain elusive. We previously demonstrated that circZNF827 forms a complex with hnRNPL/K and its host gene-encoded protein ZNF827 that acts in the nucleus to transcriptionally repress the nerve growth factor receptor (NGFR/p75NTR) gene during neuronal differentiation (Hollensen, 2020) [1]. To explore the mechanism of action, and to assess a potential role of the circZNF827-hnRNP complex on additional loci, we scrutinized the genome-wide consequences of circZNF827 and/or hnRNPL knockdown at the transcriptomic and epigenetic level. RNA-sequencing and CUT&RUN confirmed that NGFR and additional loci are transcriptionally repressed by the circZNF827-protein complex, and that these are primarily enriched for H3K27me3 signatures. Only a fraction of the massive transcriptomic changes could be ascribed a direct circZNF827 transcription-regulated phenotype, suggesting that initial key regulatory events elicited by the circZNF827-hnRNP complex likely lead to a secondary response, which further augments neuronal differentiation.

overall_design: CUT&RUN profiling of H3K4me3, H3K27me3 and H3K27ac in retinoic acid treated neuroblastoma L-AN-5 cells after circZNF827 and/or hnRNPL knockdown

first: Anne

middle: K

last: Hollensen

first: Christian

last: Damgaard