title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_A549_batchC

summary: This study aimed to identify transcript expression induced by digestion-related herbal medicines (DHM) and modes of action (MOA) of DHM in A549 cell line. For the production of THM-induced transcripts, digestion herbal medicines water extract (THW) and digestion herbal medicines ethanol extract (THE) were used.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for THW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), THE (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), positive control (wortmannin 10uM), and vehicle control (2% DMSO). However, in extracts with IC20 of less than 500ug/mL, the concentration at IC20 and the concentration diluted to 1/5 and 1/25 of the IC20 concentration were used, respectively.
Please note that the processed data 'RCM_digestion_A549.txt' contains the data from all batchA-batchE datasets.


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_SW1783_batchD

status: Public on Nov 13 2025

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

type: Expression profiling by high throughput sequencing

summary: This study aimed to identify transcript expression induced by digestion-related herbal medicines (DHM) and modes of action (MOA) of DHM in SW1783 cell line. For the production of THM-induced transcripts, digestion herbal medicines water extract (THW) and digestion herbal medicines ethanol extract (THE) were used.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), THE (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), positive control (wortmannin, LY294002, and thioridazine 10uM, respectively), and vehicle control (2% DMSO). However, in extracts with IC20 of less than 500ug/mL, the concentration at IC20 and the concentration diluted to 1/5 and 1/25 of the IC20 concentration were used, respectively.


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HT29_batchD

summary: This study aimed to identify transcript expression induced by digestion-related herbal medicines (DHM) and modes of action (MOA) of DHM in HT29 cell line. For the production of THM-induced transcripts, digestion herbal medicines water extract (THW) and digestion herbal medicines ethanol extract (THE) were used.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), THE (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), positive control (wortmannin 10uM), and vehicle control (2% DMSO). However, in extracts with IC20 of less than 500ug/mL, the concentration at IC20 and the concentration diluted to 1/5 and 1/25 of the IC20 concentration were used, respectively. As a result of RNA sequencing analysis, outlier values that did not produce results due to low RNA concentration were excluded from the sample.


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_A549_batchD


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_A549_batchE


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_A549_batchB


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HT29_batchA


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HT29_batchE


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_A549_batchA


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HepG2_batchA

summary: This study aimed to identify transcript expression induced by tonifying herbal medicines (THM) and modes of action (MOA) of THM in A549 cell line. For the production of THM-induced transcripts, digestion herbal medicines water extract (THW) and digestion herbal medicines ethanol extract (THE) were used.


title: Nascent RNA profiling reveals genome-wide productive reiterative initiation regulating gene transcription in bacteria

city: Tianjin

first: Zhe

last: Sun

address: 32 West 7th Ave

country: China

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: Productive reiterative initiation at promoters is an alternative transcription mechanism characterized by RNA slippage relative to the template DNA and RNA polymerase, resulting in the incorporation of extra nucleotides into transcripts. A comprehensive understanding of the mechanisms underlying productive reiterative initiation, and its functional implications has been hindered due to the complexity of heterogeneous slippage transcripts. Here, we develop and employ 5’ Terminal Native Elongating Transcript Sequencing (5’TNET-seq) to identify and quantify productive reiterative initiation events in Escherichia coli. Using this method, we reveal that more than half of promoters exhibit productive reiterative initiation. The conserved promoter –10 region, an appropriate spacer between the –10 region and the TSS, and the transcription initiation region associated with weak RNA-DNA hybrid stability, particularly “AAA” and “TTT” trinucleotide tracts, contribute to high productive reiterative initiation. In addition, up to four consecutive nucleotides can be added in a single cycle of productive reiterative initiation. A smaller transcription bubble is observed during productive reiterative initiation, which may stabilize the transcription initiation complex to stimulate gene transcription. Our results suggest that productive reiterative initiation emerges as an inherent transcription process regulating biological processes independent of protein regulators.

sample_organism: Escherichia coli str. K-12 substr. W3110

overall_design: To identify the genome-wide productive reiterative initiation,5prime terminal native elongating transcript sequencing (5primeTNET-seq) was designed and developed. 5primeTNET-seq was performed using the E. coli strain β'-WT with His-tag fusion to RpoC (β’) collected at log phase and stationary phase. Nascent RNA in the native elongating ternary complexes pulled down were extracted and size fractioned. The short nascent RNA was purified, treated with or without 5’-monophosphate-dependent terminator exonuclease, and applied to construct library for high-throughput sequencing. RNA-seq was performed using the same strains and conditions to monitor the changes of gene transcription.

first: Sun

last: Zhe

first: Mikhail

last: Kashlev


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HT29_batchC


title: Lethal giant larvae gene family functions as a tumor suppressor in skin epidermis

city: Seattle

first: Valeri

last: Vasioukhin

state: WA

address: 1100 Fairview Ave N

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Center

summary: Loss of cell polarity and tissue disorganization occurs in majority of epithelial tumors. The role of cell polarity mechanisms in cancer is not completely understood. Here we analyzed the mammalian orthologs of drosophila apical-basal polarity gene lethal giant larvae (lgl), which also functions as a tumor suppressor in flies. There are two mammalian orthologs of lgl (Llgl1 and Llgl2). To determine the role of the entire Lgl signaling pathway in mammals we generated mice with ablation of both Llgl1 and Llgl2 in skin epidermis (Llgl1/2-/- cKO mice). Surprisingly, we found that ablation of Llgl1/2 does not impact epidermal polarity. However, old Llgl1/2-/- cKO mice develop skin lesions which are missing epidermal layer and ripe with inflammation. To determine the role of Llgl1/2 in cancer we generated Trp53-/-/Llgl1/2-/- and Trp53-/+/Llgl1/2-/- cKO mice. Loss of Llgl1/2 promoted squamous cell carcinoma (SCC) development in Trp53-/- cKO and caused SCC in Trp53-/+ cKO mice, while no cancer was observed in Trp53-/+ cKO controls. Mechanistically, we show that ablation of Llgl1/2 activates aPKC-NF-B-RelA signaling pathway and epidermis-specific deletion of only one allele of RelA rescues SCC phenotype in Trp53-/+/Llgl1/2-/- cKO mice. We conclude that Lgl signaling pathway functions as a tumor suppressor in mammalian skin.

overall_design: To investigate the changes in gene expression in skin epidermis with mutation of Llgl1/2 genes with and without the deletion of one allele of Trp53, we isolated skin epidermises from 3 control, 3 Llgl1/2 cKO, 3 Trp53 +/- cKO and 3 Llgl1/2 + Trp53 +/- cKO newborn mice. Total RNA was extracted and analyzed using RNA-Seq.

first: Victor

last: Bii


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HT29_batchB


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HepG2_batchE


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HepG2_batchD


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HepG2_batchC


title: Transcription factor ZNF263 primes human embryonic stem cells for pluripotency dissolution and early differentiation [CUT&Tag]

city: shanghai

first: shao

last: zhen

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Conventional human embryonic stem cells (hESCs) are capable of self-renewal and simultaneously poised for differentiation, and thus have been considered to resemble a primed pluripotent state. But the underlying regulatory mechanisms remain largely underexplored. Especially, little was known about the pivotal transcription factors (TFs) driving hESCs through the naïve-to-primed transition to prepare for differentiation. Here, we conduct a large-scale in-silico screening and identify ZNF263 as a new key TF in primed hESCs, as evidenced by its extensive binding capacity at the active and poised genes. Genetic and functional assays reveal that ZNF263 directly initiates the incipient expression of early differentiation genes and concurrently dampens the core pluripotency circuitry in hESCs, greatly tilting the balance from pluripotency maintenance to lineage priming. Importantly, ZNF263 deficiency in hESCs further led to clear defects in pluripotency dissolution and lineage commitment, suggesting it’s indispensably required for the whole process. Together, our results demonstrate a pivotal role of ZNF263 in coordinating the establishment of primed pluripotency state in hESCs and facilitating the differentiation into primary germ layer lineages, which opens a new gate for understanding the central regulatory network governing human early development.

overall_design: We established H1 KO hESCs in which ZNF263 has been deleted using cas9 technology. Cleavage Under Targets & Tagmentation (CUT&Tag) of H1 KO hESCs (1-10) for ZIC2 transcription factor was performed to explore the ZIC2 chromatin binding changes upon ZNF263 loss.

first: Zhen

last: Shao


title: Transcription factor ZNF263 primes human embryonic stem cells for pluripotency dissolution and early differentiation [MEKi RNA-Seq]

overall_design: To investigate the role of ZNF263 in the regulation of hESC pluripotency dissolution, we treated H1 KO (1-10) and WT hESCs with MEK inhibitor, and then performed gene expression profiling using RNA-seq.


title: Transcription factor ZNF263 primes human embryonic stem cells for pluripotency dissolution and early differentiation [scRNA-seq]

overall_design: We established H1 KO hESCs in which ZNF263 has been deleted using cas9 technology, then cell population heterogeneity of WT and KO hESCs was analyzed using scRNA-seq.


title: Transcription factor ZNF263 primes human embryonic stem cells for pluripotency dissolution and early differentiation [RNA-seq]

overall_design: To investigate the role of ZNF263 in the regulation of hESC pluripotency, we established H1 and H9 KO hESCs in which ZNF263 has been deleted using cas9 technology. We then performed gene expression profiling using RNA-seq data of two cell lines. Comparative analysis was conducted between wildtype hESCs and its KO derivatives (1-5, 1-10, 9-1, 9-D).


title: An FXR-Casp6 axis-mediated bile acid/gut microbiota sensing modulates neonatal β-cell mass expansion [scRNA-Seq]

city: Shanghai

first: Chenyang

last: Fu

address: 197 Ruijin Road II

department: Department of Endocrine and Metabolic Diseases

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Weaning diet switch brings gut microbiome maturation along with postnatal formation of sufficient matured β-cell mass. The matured gut microbiota elevated agonistic components of bile acid (BA) pool towards farnesoid X receptor (FXR) that was paralleling with the declined β-cell FXR expression. To investigate whether BA/FXR could link postnatal β-cell development and gut microbiota maturation, we forced persistent FXR expression in β cells (βFxrKI) and found decreased neonatal β-cell mass growth and increased glycemia in weaned βFxrKI mice, which could be partially recovered by ablating gut microbiota before weaning. scRNA and scATAC seq analysis showed different β cell growth trajectories with suppressed intrinsic cell proliferation and elevated cell apoptosis in βFxrKI. Caspase-6 was then identified as a dominant β-cell FXR downstream effector to mediate its regulation. The negative regulation of the FXR-Casp6 axis on postnatal β-cell mass expansion reflected a programmed cellular response to gut microbiota maturation in neonatal mice.

overall_design: We constructed a mouse model of β-cell-specific FXR overexpression (βFxrKI). The overall goal of this study was to define the transcriptome alterations for pancreatic islet cells in control and βFxrKI mice from postnatal 1 week to 3 weeks, and we further identified dominant FXR targets in β cells. For the construction of  βFxrKI mice, a cassette of Fxr (Nr1h4) cDNA sequence with a 3xflag in N terminal followed a sequence containing the CAG promoter and loxp-PGK-Neo-polyA-loxp and was knocked in the first intron of the Rosa26 site. Fragment of loxp-PGK-Neo-polyA-loxp prevents the transcription of Nr1h4 cDNA as a “STOP” sequence. When mice with this knock-in fragment were mating with Ins2-Cre mice, the floxed sequence was cut off, Nr1h4 can be driven to express, and the mice with specifically forced Fxr expression in β cells were generated.

first: Yanyun

last: Gu


title: Transcription factor ZNF263 primes human embryonic stem cells for pluripotency dissolution and early differentiation [ChIP-seq]

overall_design: We established H1 KO hESCs in which ZNF263 has been deleted using cas9 technology. Chromatin immunoprecipitation DNA sequencing (ChIP-seq) of H1 KO hESCs (1-10) for histone modifications (H3K4me3, H3K27ac and H3K27me3) were performed to elucidate the chromatin state changes upon ZNF263 loss. Genomic occupancy profiling of ZNF263 was conducted in wildtype H1 hESCs with an endogeneous antibody or in H1 KO hESCs that expressed a FLAG-tagged version of ZNF263 with a FLAG antibody.


title: An FXR-Casp6 axis-mediated bile acid/gut microbiota sensing modulates neonatal β-cell mass expansion [scATAC-Seq]


title: Bovine Formative Embryonic Stem Cell Plasticity in Embryonic and Extraembryonic Differentiation [ bulk RNA-seq]

city: Storrs

first: Yue

last: Su

address: 1390 Storrs Road

institute: University of Connecticut

summary: Bovine embryonic stem cells (bESCs) can greatly enhance understanding of bovine embryonic development and applications for disease-resistance, biomedical and zoonotic pre-clinical models. However, formative bESCs with distinct morphology and complete differentiation capacity are still unreported. We document here the generation of bESCs which are pluripotent both in vitro and in vivo, and efficiently converted into neural progenitor cells (NPCs) and primordial germ cell-like cells (PGCLCs) by direct differentiation. These cells exhibited distinct metabolic features from human and mouse ESCs and early embryos. Formative bESCs contributed to a wide range of cell types within embryonic and extraembryonic tissues after aggregating with mouse and bovine embryos. The establishment of bovine formative ESCs with dual developmental plasticity represents a milestone for agricultural biotechnology and decoding the underlying mechanism of bona fide bovine pluripotency.

overall_design: To investigate the pluripotency of our bESCs, we performed RNA-seq of 6 formative bESC lines.

first: Ruifeng

last: Zhao

first: Yifei

last: Fang

first: Guangsheng

last: Li

first: Liangliang

last: Jin

first: Jiaxi

last: Liu

first: Jiaqi

last: Zhu

first: Neha

last: Mishra

first: Deborah

last: Kaback

first: Siu

middle: P

last: Yee

first: Chuzhao

last: Lei

first: Jingyue

middle: E

last: Duan

first: Xiuchun

middle: C

last: Tian

first: Young

last: Tang


title: Bovine Formative Embryonic Stem Cell Plasticity in Embryonic and Extraembryonic Differentiation [scRNA-seq]

overall_design: scRNA seq data of D25 bESC-incorporated bovine chimeric embryos.


title: Dermal adipocytes activate hair follicle stem cells through metabolic communication [SDS]

city: Taipei

first: Kang-Yu

last: Tai

address: Yonglin Biomedical Engineering Hall, No.49, Fanglan Rd.

department: Genome and Systems Biology Degree Program

country: Taiwan

institute: National Taiwan University

summary: The ability of tissue stem cells to sense and respond to their surroundings enables them to adapt their activity to meet the needs of the organism. External irritation has long been observed in humans to cause acquired hypertrichosis, but the mechanism is unknown. We discovered that external irritation activates hair follicle stem cells (HFSCs), leading to substantial hair regeneration in mice. The external irritation is sensed by niche adipocytes, which undergo lipolysis to activate HFSCs, rather than by the HFSCs themselves. Fatty acids released by adipocytes are taken up by HFSCs and activate them by priming them for fatty acid oxidation and increasing the mitochondrial oxidative phosphorylation capacity for ATP production. Inhibiting lipolysis, fatty acid uptake, or fatty acid oxidation restricts irritation-induced hair regeneration. As a result, adipocytes create an injury-sensing niche, allowing HFSCs to respond to external irritation by initiating a new round of hair growth to protect the skin.

overall_design: To determine the mechanism of the influence of irritant contact dermatitis induced by SDS on the whole skin, four groups of comparisons were performed. The control group is day 0, and the experimental group is treated with SDS on days 1, 3, and 5, respectively. The processed whole skin samples are collected, and total RNA is extracted.

first: Sung-Jan

last: Lin


title: Immune-Epithelial Interactions and Tissue Remodeling in the Inflammatory Respiratory Nasal Tract [scRNA-seq]

city: Boston

first: Guanrui

last: Liao

state: Massachusetts

address: 3 Blackfan Circle

institute: BIDMC

summary: Chronic rhinosinusitis (CRS) is a common inflammatory disease of the nasal cavity and sinuses that affects millions of individuals worldwide. The complex pathophysiology of CRS remains poorly understood, with emerging evidence implicating diverse immune and epithelial cell types in the disease process. We employed single-cell RNA sequencing (scRNA-seq) in dissociated tissues to investigate the cellular and molecular heterogeneity of CRS with and without nasal polyps.

overall_design: Samples from patients with CRS with and without nasal polyps and healthy controls were collected and analyzed using single-cell RNA sequencing (scRNA-seq).

first: Jayakar

middle: V

last: Nayak


title: DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID. [RNA-Seq]

city: Montréal

first: Javier

middle: M

last: Di Noia

state: QC

address: 110 Pine Avenue West

country: Canada

institute: Institut de recherches cliniques de Montréal (IRCM)

summary: Activation-induced deaminase (AID) initiates class switch recombination (CSR) and somatic hypermutation of immunoglobulin genes, which are required for efficient antibody responses. Collaterally, AID can also mutate a set of off-target genes with oncogenic consequences. The mechanisms that make such loci susceptible to AID are not fully understood. We find that the H3K79 histone methyltransferase DOT1L is located close to AID in the nucleus. Not only does DOT1L activity facilitate CSR, but it also facilitates AID off-target activity, including Igh-cMyc translocations. Genes mutated by AID display high DOT1L activity. DOT1L deficiency causes mostly increased nascent transcription, accompanied by a modest reduction in RNAPII occupancy. By integrating different genomic approaches, we discovered that DOT1L restricts the velocity of transcription elongation proportionally to the level of higher order H3K79 methylation (H3K79me2/3) and favors RNAPII pausing. These transcriptional conditions enhance AID occupancy and, consequently, its activity. Our data indicate a role for DOT1L and H3K79me2/3 in limiting transcription and highlight stronger RNAPII pausing and attenuated RNAPII elongation velocity as critical steps for productive AID association and mutagenesis at target loci. Furthermore, increased transcription elongation velocity could explain both upregulation and downregulation of genes in DOT1L-deficient cells.

overall_design:
To investige gene expression changes upon Dot1l depletion, CH12F3-G Dot1l knockout cells were generated by CRIPSR.
We then perform paired-end RNA-seq of unstimulated WT and Dot1l-/- CH12F3 cells, using Kc167 cells as spike-in controls.
Differential gene expression for WT vs Dot1l-/- CH12F3-G cells. Normalized counts, log2 fold changes and DESeq2 padj values are in the supplementary file "norm_counts.txt".

first: Poorani

middle: G

last: Subramani

first: Noé

last: Seija

first: Jana

last: Ridani

first: Jonathan

last: Boulais

first: Paul

middle: A

last: Donnelly

first: Mélanie

last: Provencher

first: Halil

last: Bagci

first: Christian

last: Poitras

first: Jean-François

last: Côté

first: François

last: Robert


title: Mast cells act as pro-angiogenic and pro-tumorigenic players in pituitary gonadotroph tumors

city: Lyon

first: Philippe

last: BERTOLINO

address: 28 rue Laennec

country: France

institute: INSERM

summary:
Background: The tumor microenvironment (TME) represents a promising avenue to understand gonadotroph tumors and develop therapeutic tools. Here, we aimed to gain insight into the tumorigenesis mechanisms driven by the gonadotoph TME. Methods: Single-cell and spatial-omics were combined with histological analysis. Mice engrafted with tumor cells were used for functional validation. Results: using single-cell and spatial transcriptomic data from gonadotroph tumors and normal tissues, we identified mast cells in the microenvironment of gonadotroph tumors and confirmed their physical and functional interaction with endothelial cells. Quantification of mast cells in 40 patients suggested their pro-tumoral role as tumors relapsing after surgery harbored more mast cells. More interestingly, the distribution of mast cells was associated with the presence of a higher number of blood vessels, with an increased microvessel density (MVD), and with blood vessels with thicker walls. Ligand-receptor network analysis highlighted VEGFA as a modulator of mast/endothelial cell communication, a result confirmed by the identification of intratumoral mast cells expressing VEGFA in mouse and human gonadotroph tumors. Finally, using mice engrafted with gonadotroph tumor cells, we demonstrated that the depletion of mast cells reduces tumor volume through increased apoptosis. These observations were associated with increased hemorrhagic areas and a significant reduction of the number of blood vessels and MVD as evidenced in human gonadotroph tumors.
Conclusion: we demonstrate that mast cells represent a new actor of the gonadotroph TME, and highlight their pro-angiogenic and pro-tumorigenic roles as potential targets for the therapeutic treatment of gonadotroph tumors.

overall_design: 6 surgically resected gonadotroph adenomas were dissociated and analyzed using scRNAseq with 10X Genomics. Generation of the library was done using a Chromium controller and v3 reagent kit (10xGenomics). 2 Cryospeserved gonadodotoph adenomas embeded in tissue-TEK were sectioned and sequenced using a Visium Kit (10xGenomics)

last: Bertolino

first: Gerald

last: Raverot

first: Franck

last: Picard

first: Emmanuel

last: Jouanneau

first: Alexandre

last: Vasiljevic


title: Immune-Epithelial Interactions and Tissue Remodeling in the Inflammatory Respiratory Nasal Tract [NanoString GeoMx spatial transcriptomics]

first: Guanrui

last: Liao

summary: Chronic rhinosinusitis (CRS) is a common inflammatory disease of the nasal cavity and sinuses that affects millions of individuals worldwide. The complex pathophysiology of CRS remains poorly understood, with emerging evidence implicating diverse immune and epithelial cell types in the disease process. We employed NanoString GeoMx spatial transcriptomics in both intact tissues to investigate the cellular and molecular heterogeneity of CRS with and without nasal polyps.

overall_design:
Samples from patients with CRS with and without nasal polyps and healthy controls were collected and analyzed using NanoString GeoMx spatial transcriptomics.

*** FASTQ raw data files are unavailable (cannot be located). ***

first: Jayakar

last: Nayak


title: DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID. [CUT&RUN]

first: Javier

last: Di Noia

overall_design: CUT&RUN for Rpb1 and CTCF in WT and Dot1l-/- CH12F3-G cells; and CUT&RUN for H3K27me3 in WT CH12F3-G cells.

first: Poorani

last: Subramani

last: Seija


title: The Function of Tetrameric MADS-box Transcription Factors in Floral Fate Determination [RNA-seq]

city: Berlin

first: Manuel

last: Neumann

address: Philippstr. 13

country: Germany

institute: HU Berlin

summary: MADS-domain transcription factors (TF) are critical in determining floral cell fate and floral organ identities. However, their function molecular mechanisms are still poorly understood. Here, we show that effective DNA-binding in closed chromatin and target gene regulation of APETALA1 (AP1), a  key floral MADS-box TF requires tetramerisation, indicating the fundamental role of tetrameric MADS-box TFs in floral cell fate programming.

overall_design:
ChIP-seq, ATAC-seq and RNA-seq datasets were generated with seedling tissues at different time points (2, 8, 24 and 48 hours) after dexamethasone induction. In addition, mock-treated seedlings were collected at different time points as a control. Two biological replicates were generated for each time point.
Please note that each processed data file was generated from both replicates and is linked to the corresponding *r1 sample records.

first: Kerstin

last: Kaufmann

first: Xiaocai

last: Xu


title: Dermal adipocytes activate hair follicle stem cells through metabolic communication

first: Kang-Yu

last: Tai

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

overall_design: Refer to individual Series

first: Kang-Yu Tai

first: Sung-Jan

last: Lin


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_HepG2_batchB

first: Musun

last: Park

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), THE (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), positive control (wortmannin 10uM), and vehicle control (2% DMSO). However, in extracts with IC20 of less than 500ug/mL, the concentration at IC20 and the concentration diluted to 1/5 and 1/25 of the IC20 concentration were used, respectively. As a result of RNA sequencing analysis, outlier values that did not produce results due to low RNA concentration were excluded from the sample.


title: Dermal adipocytes activate hair follicle stem cells through metabolic communication [HFSC]

overall_design: To determine the mechanism of the influence of unsaturated fatty acids versus saturated fatty acids on hair follicle stem cells, three groups of comparisons were performed. The control group is ETOH alone, the unsaturated fatty acid treatment group is C18:1, and the saturated fatty acid treatment group is C18:0. Hair follicle stem cells were extracted for examination three days after the mouse dorsal skin was treated using Cd34+/Lgr5GFP+/Sca1- fluorescence-activated cell sorting


title: DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID


title: The Function of Tetrameric MADS-box Transcription Factors in Floral Fate Determination [ChIP-seq]

overall_design:
ChIP-seq, ATAC-seq and RNA-seq datasets were generated with seedling tissues at different time points (2, 8, 24 and 48 hours) after dexamethasone induction. In addition, mock-treated seedlings were collected at different time points as a control. Two biological replicates were generated for each time point.
Please note that each processed data file was generated from all replicates and is linked to the corresponding *r1 sample records.


title: A nanounit strategy enhance Wee1 targeting potential by promoting ferroptosis sensitivity [II]

city: Hefei

first: Peijie

last: Zhou

state: Anhui

address: Lujiang road

department: Department of Radiation Oncology, The First Affiliated Hospital of USTC

institute: University of Science and Technology of China

summary: To investigate the novel biological function of Wee1 inhibition, we conducted RNA-seq for 4T1 derived tumor samples with different drugs.

overall_design: We performed gene expression profiling analysis using data obtained from  RNA-seq of PBS control,Free-MK1775, Free-MK1775+NLG919,  Lipo-MK1775, Lipo-MK1775+NLG919 .

first: Ruijie

last: Huang


title: scRNAseq to understand hormonal control on pubertal transcription in the medial preoptic area

first: Koichi

last: Hashikawa

address: 1959 NE Pacific St. HSB J135

institute: University of Washington

summary: Pubertal maturation aids developments in emotion, cognition and reproduction. The conserved roles of elevated circulating gonadal sex steroids for the continued maturation of the nervous system via steroid hormone receptor mediated gene regulation is well documented. However, critical transcriptional dynamics mediated by steroids throughout puberty in molecularly defined circuitry remains elusive. We investigated pubertal transcriptional dynamics in the medial preoptic area (MPOA), a hypothalamic center for reproductive behaviors, in male and female mice at single cell resolution (scRNAseq).

overall_design: scRNAseq on the MPOA tissues from pre-, mid and post puberty mice of both sex


title: RNA-seq analysis of perichondral tissues obtained from rabbit

status: Public on Nov 12 2025

first: Hai

last: Tang

address: 507 Zhengmin Road, Yangpu District, Shanghai, China

institute: Shanghai Pulmonary Hospital affiliated to Tongji University

summary: RNA sequencing for 6 samples

overall_design: Examing 2 conditions, each with 3 replicates

first: Chang

last: Chen


title: The Function of Tetrameric MADS-box Transcription Factors in Floral Fate Determination [ATAC-seq]


title: A nanounit strategy enhance Wee1 targeting potential by promoting ferroptosis sensitivity


title: A nanounit strategy enhance Wee1 targeting potential by promoting ferroptosis sensitivity [I]

summary: To investigate the novel biological function of Wee1 inhibition, we conducted RNA-seq for 4T1 cell lines with Wee1 knock down.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of MK1775 and Wee1-siRNA, compared to NC group.


title: CDK4/6 Inhibition reprograms the Breast Cancer immunopeptidome via Rb-Dependent chromatin and transcriptomic remodeling

first: Robin

last: Minati

state: Québec

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: The Cyclin-dependent kinase 4/6 inhibitors (CDK4/6is) are standard-of-care therapies for metastatic hormone receptor-positive (HR+) breast cancer, yet their immunomodulatory effects remain underexplored. Here, we demonstrate that CDK4/6 inhibition with Abemaciclib reprograms the tumor antigen landscape by increasing MHC-I presentation and reshaping the immunopeptidome in HR+ and triple-negative breast cancer (TNBC) cells. Through multiomics integration, we reveal that this remodeling is driven by retinoblastoma protein (Rb)-dependent transcriptional and chromatin reprogramming, reflected by increased H3K27ac deposition and enhanced chromatin accessibility revealed by ATAC-seq. CDK4/6 inhibition dephosphorylates Rb, enhancing its interaction with BET family proteins and inducing chromatin remodeling that upregulates antigen-source transcripts. We identify immunogenic Abemaciclib-induced MHC-I peptides, including antigens derived from non-coding genomic regions, which can enhance tumor immunogenicity. These findings reveal a previously unrecognized role of CDK4/6is in shaping tumor antigenicity and suggest that combining CDK4/6is with immunotherapy could broaden antigenic targets in breast cancer.

overall_design: Abemaciclib (Cat#A115153) was procured from Toronto Research Chemicals Inc. The powder was dissolved in DMSO to prepare a 5 mM stock solution, filtered through a 0.22 µm filter for sterility, aliquoted, and stored at -20°C for no more than 6 months. For Abemaciclib treatment, the 5 mM stock was diluted in complete culture media to the indicated final concentrations. Cells were treated with the indicated final concentration of Abemaciclib or DMSO for 96 h before collection. Total RNA was isolated using TRIzol reagent (Thermo Scientific, cat#15596018) followed by RNeasy purification (Qiagen, Cat. #74104). RNA was quantified using Qubit (Thermo Scientific), and quality was assessed with the 2100 Bioanalyzer (Agilent Technologies). Transcriptome libraries were generated using the KAPA RNA HyperPrep (Roche) using a poly-A selection (Thermo Scientific). Sequencing was performed on the Illumina Novaseq 2000.

first: Maxime

last: Cahuzac

first: Julie

last: Perrault

first: Véronique

last: Lullier

first: Anca

last: Apavaloaei

first: Eric

last: Bonneil

first: Mathieu

last: Courcelles

first: Joel

last: Lanoix

first: Eralda

last: Kina

first: Claude

last: Perreault

first: Pierre

last: Thibault


title: Bioengineered Extracellular Vesicles Co-delivering PD-L1 and miR-27a-3p Synergistically Reprogram T cells To Treat Inflammatory Bowel Disease [scRNA-Seq]

city: Seoul

first: Mi-Kyung

last: Oh

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences

institute: Seoul National University

summary: Current treatments for inflammatory bowel disease (IBD) primarily rely on systemic immunosuppression, which often exhibits limited efficacy and off-target toxicity. Here we present a bioengineered extracellular vesicle (EV) platform designed for inflammatory bowel-targeted delivery of dual-action therapeutics, enabling precise modulation of T cell responses to enhance IBD treatment efficacy. EVs derived from Wharton’s jelly mesenchymal stem cells ( WJ-MSCs) were engineered to display membrane-bound PD-L1 and encapsulate miRNA 27a-3p (miR-27a-3p). The platform leverages WJ-MSCs’ intrinsic immunomodulatory properties and CXCR4-mediated recruitment to inflamed tissues. PD-L1 not only promotes immunosuppression of effector T cells, but also may enhance EV retention within inflamed sites. Meanwhile, miR-27a-3p shifts the Th17/Treg balance from a pro-inflammatory Th17 phenotype toward an anti-inflammatory Treg phenotype by targeting prohibitin 1. Bulk RNA sequencing of human CD4⁺ T cells treated with the EVs revealed downregulated of Th1/Th17-associated transcripts. In a humanized mouse model of colitis, EV treatment significantly reduced disease severity, diminished intestinal T cell infiltration, and restored mucosal integrity. Single-cell RNA sequencing demonstrated expansion of Treg cells and contraction of effector memory subsets, indicating durable immune modulation. This engineered EV platform represents a novel therapeutic paradigm that combines inflamed tissue targeting and dual immunomodulatory mechanisms to restore immune tolerance in IBD, addressing key limitations of conventional immunosuppressive approaches.

overall_design: RNA sequencing was performed on CD4⁺ T cells from spleens of IBD humanized mouse models (human graft), CD4⁺ T cells from human PBMCs, WJ-MSCs, and WJ-MSC–derived exosomes. The study includes single-cell RNA-seq, bulk mRNA-seq, and small RNA-seq to assess transcriptomic and miRNA profiles in the context of IBD and engineered exosome therapy.

first: Hyun Sung

last: Park

first: Kyung-Rok

last: Yu


title: Simultaneous Targeting of KRAS and CDK4 Synergistically Induces Durable Growth Arrest in Pancreatic Cancer Cells [51T-2D_RNA_Seq]

city: Göttingen

first: Maj-Britt

last: Paulsohn

address: Justus-von-Liebig-Weg 11

department: Department of Molecular Oncology

institute: University Medical Center Göttingen

summary: We report that the KRAS-G12C inhibitor Sotorasib synergizes with the CDK4/6 inhibitor Palbociclib to eliminate pancreatic ductal adenocarcinoma (PDAC) cells (51T-2D cells) harboring KRAS-G12C mutations. This synergy was especially pronounced following drug washout, indicating a durable cellular response. Mechanistically, the combinations induced sustained cell cycle arrest.

overall_design: RNA-Sequencing of 51T-2D cells treated for 48 h with DMSO, Palbociclib (5 µM), Sotorasib (2.5 µM) or the combination (day3), or 48 h treatment + 4 days of recovery in normal cultivation medium (Day7).

first: Matthias

last: Dobbelstein


title: Mutation Detection in p210 kinase domain

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

summary: Mutations in the BCR-ABL1 kinase domain (BCR-ABL1 KD) are among the most common causes of tyrosine kinase inhibitor (TKI) resistance in patients with chronic myeloid leukemia (CML). High-throughput DNA sequencing targeting the BCR-ABL1 KD revealed a higher frequency of mutations in patients with short treatment-free remission (TFR) compared to those with long TFR.

overall_design: To examine the link between Oxr1 and BCR-ABL1 kinase domain (KD) mutations in relation to TKI treatment outcomes, high-throughput sequencing was performed on peripheral blood mononuclear cells (PBMCs) from CML patients classified as short or long TFR. Samples were collected at TKI discontinuation (TKI-D) for all patients, and at relapse post-discontinuation for short TFR patients. RNA was enriched for the BCR-ABL1 KD region using nested RT-PCR for mutation analysis.

first: Weiqi

last: Huang

first: Elizabeth

last: Eklund


title: Simultaneous Targeting of KRAS and CDK4 Synergistically Induces Durable Growth Arrest in Pancreatic Cancer Cells [AsPC-1_RNA_Seq]

summary: We show that the KRAS-G12D inhibitor MRTX1133 synergizes with the CDK4/6 inhibitor Palbociclib to eliminate pancreatic ductal adenocarcinoma (PDAC) cells (AsPC-1) harboring KRAS-G12D mutations. This synergy was especially pronounced following drug washout, indicating a durable cellular response. Mechanistically, the combinations induced sustained cell cycle arrest.

overall_design: RNA-Sequencing of AsPC-1 cells treated for 24 h with DMSO, Palbociclib (5 µM), MRTX1133 (0.5 µM) or the combination.


title: NSUN7 is an RNA:m5C catalytically inactive protein that regulates sperm flagellum assembly [scRNA-seq]

first: Jing

last: Li

address: Haike Road 230

department: School of Life Science and Technology

institute: ShanghaiTech University

summary: Defects in Nsun7, a member of the main RNA:m5C modifying enzymes, known as the NOL1/NOP2/Sun domain (NSUN) family, cause male infertility. The NSUN family includes NSUN1-7, all possessing conserved motifs IV and VI essential for RNA:m5C formation. However, due to the controversy regarding the catalytic activity and RNA substrates of NSUN7, the pathogenic mechanism underlyingof NSUN7-related male infertility remains unclear. Here, we showed that NSUN7 is predominantly enriched in adult mouse testes, particularly in elongated spermatids. Through m5C mass spectrometry detection and bisulfite sequencing, we found that knockout of Nsun7 has no impact on testicular RNA:m5C modification. Mechanistically, NSUN7 loses its ability to bind S-adenosylmethionine (SAM) due to sequence variations in motif IV compared towith the conserved residues observed in NSUN1-6. Notably, the key SAM-binding Asp in motif IV is replaced by Leu in NSUN7, thereby abolishing SAM binding. Nsun7 deficiency impairs sperm progressive motility, accompanied by defects in axonemes and mispositioning of longitudinal columns. Single-cell RNA sequencing showed that knockout of Nsun7 results in a significantly decrease in the levels of a cohort of mRNAs related to cilium organization in elongated spermatids. Collectively, our study demonstrateds that NSUN7 is the only RNA:m5C catalytically inactive member in the NSUN family, and that it regulates sperm flagellum assembly by modulating the expression of cilium organization-associated genes.

overall_design: single cell RNA sequencing of  WT and Nsun7 KO adult mouse testes

first: Wen-Yu

last: Zhu

first: Zhen

last: Wang


title: NSUN7 is an RNA:m5C catalytically inactive protein that regulates sperm flagellum assembly

type: Methylation profiling by high throughput sequencing

overall_design: ultrafast bisufite-seq profiling of m5C modification levels in mRNA, large RNA, and small RNA from  WT and Nsun7 KO adult mouse testes


title: Bioengineered Extracellular Vesicles Co-delivering PD-L1 and miR-27a-3p Synergistically Reprogram T cells To Treat Inflammatory Bowel Disease [RNA-Seq]


title: ChIP-seq analysis of Brachyury (T) in invitro derived NMPs

city: Frederick

first: Terry

last: Yamaguchi

state: Maryland (MD)

address: Building 560,  1050 Boyles St

department: Cancer and Developmental Biology

institute: NIH/NCI

summary: Brachyury (Tbxt or just T) is a T-box transcription factor and known target of the cnaonical Wnt signalling pathway. Brachyury is an important gene in the regulation of neuromesodermal progenitors, a stem cell-like population of cells that drive axial elongation during mouse embryogenesis. The goal of the project was to investigate the binding pattern of brachyury in in vitro derived NMPs.

overall_design: ES cells were differentiated in serum free N2B27 media and treated with bFGF (12ng/ml) from Day0 to Day2 followed by 3uM CHIR and 12ng/ml bFGF from Day2 to day3. Cells were harvested and fixed in 1% formaldehyde solution for 15min, quenched in 0.125M glycine and flash-frozen. Nuclear extracts were incubated with Goat IgG and anti-T/Brachyury antibodies (AB-108-C, AF2085, R&D systems, Inc respectively) for chromatin immunoprecipitation followed by sequencing.

first: Chalamalasetty

last: Ravi

first: Kelly

last: Ryan

first: Yamaguchi

last: Terry


title: Single-Cell Mapping Reveals Age-Related Alterations in Periosteal Progenitor Cells and Immune Microenvironment Impairing Bone Regeneration

first: Lei

last: Zhao

state: Shanghai

address: 500 Zhennan Road

institute: Tongji University

summary: Aging profoundly impacts bone homeostasis and regeneration, yet the cellular and molecular mechanisms underlying periosteal aging remain poorly understood. Using single-cell RNA sequencing, we profiled the periosteum of 3-, 9-, and 18-month-old mice, revealing age-related shifts in progenitor, neutrophil, and macrophage subpopulations. Aging reduced mesenchymal cell populations and impaired osteogenic potential, disrupting periosteal homeostasis. Periosteal progenitor subsets exhibited distinct aging trajectories: Dpt⁺ fibrous-layer cells undergoing early senescence, while Postn⁺ progenitors showed osteogenic decline. Aging also shifted immune profiles, increasing inflammatory Cd38hi macrophages and dysfunctional Nlrp3hi neutrophils, further disrupting bone homeostasis. Notably, aged progenitor cells upregulated CSF1 and CXCL signaling, driving macrophage and neutrophil infiltration, exacerbating bone loss. Our findings provide a comprehensive periosteal aging atlas, highlighting disrupted progenitor-immune crosstalk as a key driver of bone homeostasis imbalance and impaired regeneration, offering potential therapeutic targets for age-related bone disorders.

overall_design: Long bones were harvested from wild-type C57BL/6 J mice across three age groups: 3 months, 9 months, and 18 months, with six males per group (Aniphe Biolaboratory Inc.). The acquisition protocol was as follows: following cervical dislocation for euthanasia, the animals were sterilized by external application of 75% ethanol. The lower limbs were then aseptically dissected, and the overlying skin, muscles, fat, and other soft tissues were meticulously removed. The intact femur and tibia were subsequently isolated for further processing.

first: Chao

last: Wu


title: Supplementation with short-chain fatty acids and a prebiotic improves clinical outcome in Parkinson’s disease: A randomized double-blind prospective study

city: Ramat Gan

first: Nissan

last: Yissachar

address: Bar-Ilan University

country: Israel

institute: Bar-Ilan University

summary: Background: Parkinson’s disease is associated with a dysbiotic, proinflammatory gut microbiome, disruptions to intestinal barrier functions, and immunological imbalance. Microbiota-produced short-chain fatty acids, such as propionic and butyric acid promote gut barrier integrity and immune regulation, but their impact on Parkinson’s disease pathology remains mostly unknown .Methods: In a randomized double-blind prospective study, 72 people with Parkinson’s disease received propionic and butyric acid and/or the prebiotic fiber 2′-fucosyllactose supplementation over 6 months in combination with existing Parkinson’s disease-specific therapy. Patients underwent complete neurological assessment and provided blood and stool samples before as well as 3 and 6 months after supplementation. Results: We observed improvement in motor and nonmotor symptoms, in addition to modulation of peripheral immunity and improved mitochondrial respiration in immunocytes. Postintervention microbiota remodeled inflammatory and barrier-related gene sets in gut organ cultures and improved in vitro barrier functions. Treatment response was associated with microbiome composition, distinct patterns of colonic transcription and permeability ex vivo. Multiobjective analysis revealed immune parameters associated with an optimal response to supplementation. Conclusion: Short-chain fatty acids ameliorate clinical symptoms in Parkinson’s disease patients and modulate intestinal and peripheral immunity.

overall_design: CaCo-2 cells were cultured to full confluency with penicillin/streptomycin for 4 days. Fecal samples were resuspended in cell culture media without antibiotics to a concentration of 15 mg/ml. Suspensions were passed through a sterile cell strainer and then added to CaCo-2 cells. Following incubation for 30 min, cells were washed 3 times with PBS to remove nonadherent bacteria. DNA was extracted using the PureLink™ Microbiome DNA Purification Kit (Invitrogen).

first: Tobias

last: Hegelmaier

first: Alexander

last: Duscha

first: Christiane

last: Desel

first: Sabrina

last: Fuchs

first: Michal

last: Shapira

first: Sivan

last: Amidror

first: Qihao

last: Shan

first: Gabriele

middle: I

last: Stangl

first: Frank

last: Hirche

first: Stefan

last: Kempa

first: András

last: Maifeld

first: Lisa-Marie

last: Würtele

first: Jana

last: Peplinski

first: Diana

last: Jauk

first: Gitali

last: Naim

first: Nuphar

last: Shidlovsky

first: Adva

last: Cohen

first: Yifat

last: Bennet

first: Lisa

last: Paschold

first: Claudia

last: Dumitru

first: Ute

last: Obermüller-Jevic

first: Svein-Olaf

last: Hustvedt

first: Nina

last: Timmesfeld

first: Ralf

last: Gold

first: Antonia

last: Zapf

first: Mascha

last: Binder

first: Ibrahim

last: Sandalcioglu

first: Sanaz

last: Mostaghim

first: Horst

last: Przuntek

first: Eran

last: Segal

first: Aiden

last: Haghikia


title: DUX4-induced HSATII RNA accumulation drives protein aggregation impacting RNA processing pathways

first: Stephen

last: Tapscott

state: Washington

address: 1100 Fairview Ave N, Room C3-123

institute: Fred Hutchinson Cancer Research Center

summary: RNA-driven protein aggregation leads to cellular dysregulation by sequestering regulatory proteins, disrupting normal cellular processes, and contributing to the development of diseases and tumorigenesis. Here, we show that double homeobox 4 (DUX4), an early embryonic transcription factor and causative gene of facioscapulohumeral muscular dystrophy (FSHD), induces the accumulation of stable intranuclear RNAs, including nucleolar-associated RNA and human satellite II (HSATII) repeat RNA. Stable intranuclear RNAs drive protein aggregation in DUX4-expressing muscle cells. Specifically, HSATII RNA sequesters m6A and m5C RNA methylation factors. Furthermore, HSATII-YBX1 ribonucleoprotein (RNP) complex formation is mediated by HSATII RNA accumulation, NSUN2 activity and RNA methylation. YBX-1 specifically associates with HSATII double-stranded RNA. Aberrant HSATII-RNP complexes affect key RNA processing pathways, including mRNA splicing. Differential splicing of genes mediated by HSATII-RNP complexes are associated with pathways known to be dysregulated by DUX4 expression. These findings highlight the broader influence of DUX4 on nuclear RNA dynamics and suggest that HSATII RNA could be a critical mediator of RNA processing regulation in DUX4-expressing cells. Understanding the impact of HSATII-RNP formation on RNA processing pathways provides valuable insight into the molecular mechanisms underlying FSHD.

overall_design: RNA sequencing from MB135 iDUX4ca inducible DUX4 myoblasts treated with either HSATII or control gapmers.

first: Sean

last: Bennett

first: Tessa

last: Arends


first: Robin

last: Minati

summary: The Cyclin-dependent kinase 4/6 inhibitors (CDK4/6is) are standard-of-care therapies for metastatic hormone receptor-positive (HR+) breast cancer, yet their immunomodulatory effects remain underexplored. Here, we demonstrate that CDK4/6 inhibition with Abemaciclib reprograms the tumor antigen landscape by increasing MHC-I presentation and reshaping the immunopeptidome in HR+ and triple-negative breast cancer (TNBC) cells. Through multiomics integration, we reveal that this remodeling is driven by retinoblastoma protein (Rb)-dependent transcriptional and chromatin reprogramming, reflected by increased H3K27ac deposition and enhanced chromatin accessibility revealed by ATAC-seq. CDK4/6 inhibition dephosphorylates Rb, enhancing its interaction with BET family proteins and inducing chromatin remodeling that upregulates antigen-source transcripts. We identify novel Abemaciclib-induced MHC-I peptides, including antigens derived from non-coding genomic regions, which can enhance tumor immunogenicity. These findings reveal a previously unrecognized role of CDK4/6is in shaping tumor antigenicity and suggest that combining CDK4/6is with immunotherapy could broaden antigenic targets in breast cancer.

overall_design: Abemaciclib (Cat#A115153) was procured from Toronto Research Chemicals Inc. The powder was dissolved in DMSO to prepare a 5 mM stock solution, filtered through a 0.22 µm filter for sterility, aliquoted, and stored at -20°C for no more than 6 months. For Abemaciclib treatment, the 5 mM stock was diluted in complete culture media to the indicated final concentrations. Cells were treated with the indicated final concentration of Abemaciclib or DMSO for 96 h before collection. Total RNA was isolated using TRIzol reagent (Thermo Scientific, cat#15596018) followed by RNeasy purification (Qiagen, Cat. #74104). RNA was quantified using Qubit (Thermo Scientific), and quality was assessed with the 2100 Bioanalyzer (Agilent Technologies). Transcriptome libraries were generated using the KAPA RNA HyperPrep (Roche) using a poly-A selection (Thermo Scientific). Sequencing was performed on the Illumina NextSeq500 or Novaseq. For each triplicate, one sample was sequenced at 160-280M paired-end reads per sample (80-140M clusters) for database generation and the others at 50-70M paired-end reads per sample (35-25M clusters) for RNAseq analysis.

first: Maxime

last: Cahuzac

first: Julie

last: Perrault

first: Veronique

last: Lullier

first: Anca

last: Apavaloaei

first: Eric

last: Bonneil

first: Mathieu

last: Courcelles

first: Joel

last: Lanoix

first: Eralda

last: Kina

first: Claude

last: Perreault

first: Pierre

last: Thibault


title: TerryYamaguchi_CS037981_32ChIP_101624

first: Terry

last: Yamaguchi

summary: Sp5 is a zinc-finger transcription factor that postively regulates canonical Wnt signaling and binds to key Wnt-signaling components such as TCF7. TCF7, also known as T-cell factor 1, is a transcription factor that binds to DNA via its high mobility group (HMG) domain. Importantly, TCF7 forms protein-protein complex with other cofactors, such as TLE, to regulate canonical Wnt signaling. TLE is a transcriptional-linked enhancer/repressor protein that binds TCF7 to repress canonical Wnt signaling. The goal of the project was to investigate the binding pattern of Sp5 in in vitro derived NMPs. Additionally, we investigated whether the binding patterns of TCF7 and TLE factors changed in the presence and absence of Sp5 and Sp8 in in vitro derived NMPs.

overall_design: ES cells were differentiated in serum free N2B27 media and treated with bFGF (12ng/ml) from Day0 to Day2 followed by 3uM CHIR and 12ng/ml bFGF from Day2 to Day3. For dox-inducible Sp5 overexpression cells, 1ug/mL dox was added from Day2 to Day3. Cells were harvested and fixed in 1% formaldehyde solution for 15min, quenched in 0.125M glycine and flash-frozen. Nuclear extracts were incubated with anti-Flag, anti-TCF7, and anti-TLE antibodies (F3165 Sigma-Aldrich, C63D9 Cell Signaling,TLE(C-19):sc-13373 Santa Cruz, respectively) for chromatin immunoprecipitation followed by sequencing.

first: Haley

last: Tran

first: Sara

last: Thomas

first: Ravi

last: Chalamalasetty

first: Moonsup

last: Lee


title: Oxidation Resistance 1 (Oxr1) Dysregulation Promotes TKI Resistance and Blast Crisis in Chronic Myeloid Leukemia [dataset 3]

first: Priyam

last: Patel

summary: To unravel the intricate interplay among Oxr1, ROS-induced genetic changes, and dynamics influencing TKI resistance and CML progression

overall_design: We conducted high-throughput sequencing analyses, including RNA-Seq, whole exome sequencing (WES), and p210 KD mutation detection.

first: Weiqi

last: Huang

first: Elizabeth

last: Eklund


title: CIRCADIAN MODULATION OF NEUTROPHIL FUNCTION DETERMINES CEREBRAL PERFUSION AND STROKE OUTCOME

city: Madrid

first: María

middle: Ángeles

last: Moro

address: C. de Melchor Fernández Almagro, 3

department: Cardiovascular Risk Factors and Brain Health

country: Spain

institute: CNIC

summary: Stroke is a leading cause of mortality and disability, driven by complex and time-dependent mechanisms that aggravate ischemic damage. Recent evidence indicates that infarct volumes fluctuate according to diurnal oscillations, both in mice and humans, with worse outcomes during the inactive phase of their circadian cycle. Here, we show that neutrophils are responsible for these circadian variations. By depleting neutrophils or blocking their circadian clock, differences in infarct volumes were abolished, suggesting that both the number of neutrophils and their circadian phenotype contribute to ischemic damage. Mechanistically, these differences were linked to the collateral circulation: cerebral blood flow measurements at different times after ischemia showed differential perfusion in the ipsilesional area. We found that, during the inactive mouse phase, neutrophil extracellular traps (NETs), were markedly elevated, coinciding with a reduction in ipsilesional blood flow, a higher percentage of intravascular neutrophils, and an increase in infarct volumes compared with the active phase. These findings underscore a crucial role of neutrophils, their circadian dynamics, and NET release as key drivers of ischemic damage, suggesting novel personalized therapeutic strategies based on circadian rhythms for the treatment of stroke.

overall_design: To elucidate whether circadian rhythms affect the transcriptional landscape of neutrophil heterogeneity during stroke in mice, we conducted single-cell RNA sequencing of DAPI-CD11b+Ly6G+ cells obtained from ischemic brain of mice under different conditions.

first: Sandra

last: Vazquez-Reyes

last: Cuartero

first: Alicia

last: García-Culebras


title: Supplementation with short-chain fatty acids and a prebiotic improves clinical outcome in Parkinson’s disease: A randomized double-blind prospective study [RNA-Seq]

first: Nissan

last: Yissachar

overall_design: Colon organ cultures were infused with microbiota samples collected from PD patients at baseline and 6 months postintervention (n=8, all intervention groups included) or with sterile medium as an internal control.

first: Tobias

last: Hegelmaier

first: Alexander

last: Duscha

first: Christiane

last: Desel

first: Sabrina

last: Fuchs

first: Michal

last: Shapira

first: Sivan

last: Amidror

first: Qihao

last: Shan

first: Gabriele

last: Stangl

first: Frank

last: Hirche

first: Stefan

last: Kempa

first: András

last: Maifeld

first: Lisa-Marie

last: Würtele

first: Jana

last: Peplinski

first: Diana

last: Jauk

first: Gitali

last: Naim

first: Nuphar

last: Shidlovsky

first: Adva

last: Cohen

first: Yifat

last: Bennet

first: Lisa

last: Paschold

first: Claudia

last: Dumitru

first: Ute

last: Obermüller-Jevic

first: Svein-Olaf

last: Hustvedt

first: Nina

last: Timmesfeld

first: Ralf

last: Gold

first: Antonia

last: Zapf

first: Mascha

last: Binder

first: Ibrahim

last: Sandalcioglu

first: Sanaz

last: Mostaghim

first: Horst

last: Przuntek

first: Eran

last: Segal

first: Aiden

last: Haghikia


title: Genome-wide binding profiles of Sp8 in differentiation mouse embryonic stem cells

first: Terry

last: Yamaguchi

summary: We have determined the genome-wide binding profile of the transcription factor Sp8. We found that Flag-Sp8 prefentially bound to promoters associatd with several growth factor signalling pathways, but most prominently with the Wnt/beta-catenin pathway to selectively promote mesoderm differentiation over neural. These data implicate Sp8 as new regulator of Wnt/beta-catenin target expression to promotes ES cell differentation into the mesoderm lineage.

overall_design: Cells were fixed for 15mins in 1% formaldehyde, quenched with glycine. Cells were lysed to extract nuclei which were then sonicated to obtain sheared genomic DNA ~100-300bp in size for sequencing. The libraries were prepared according to standard Illumina's TruSeq Chip protocol. The ChIP DNA is blunt-ended and phosphorylated. A single 'A' nucleotide is added to the 3' ends of the fragments in preparation for ligation to an adapter that has a single-base 'T' overhang. The ligation products are purified and size-selected. The size-selected DNA is purified and PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product is then quantitated by qPCR before cluster generation and sequencing.

first: Ravi

last: Chalamalasetty

first: Mark

last: Kennedy

first: Ryan

last: Kelly


title: MSS2-mediated ROS and calcium are essential for Candida albicans invasive behavior and virulence

first: Ching-Hsuan

last: Lin

state: Taiwan

address: National Taiwan University, 1 Roosevelt Rd. Sec. 4

department: Department of Biochemical Science and Technology

institute: National Taiwan University

summary: Mitochondrial function is essential for virulence in Candida albicans, yet the mechanism by which mitochondria influence invasive behavior remains largely undefined. Here, we uncover a novel, mitochondria-centered mechanism in which the mitochondrial-associated gene MSS2 controls invasive growth through the regulation of calcium–ROS homeostasis. Deletion of MSS2 exhibits impaired invasive growth on solid agar without affecting hyphal formation in liquid, suggesting a unique contact-specific regulatory program. Indeed, we found that the regulation of these processes by Mss2 is linked to the regulation of cytosolic calcium levels and cellular ROS production. Furthermore, transcriptomic profiling identified the MSS2-regulated genes, UME6, SAC1, RIM8, and ORF19.1841, whose expression is dependent on calcium and ROS levels. Restoration of invasive phenotypes through exogenous ROS confirms the functional significance of this calcium-ROS circuit. In systemic infection models., mutants lacking MSS2 or its downstream genes exhibit severe host cell invasion and virulence defects. Together, this work is the first to reveal that mitochondrial regulation of a coordinated calcium-ROS circuit is indispensable for invasive hyphal growth in C. albicans. These findings further refine the current model of fungal invasive progression and may provide useful information for future studies aiming to target mitochondrial signaling in pathogenic fungi.

overall_design: Total mRNA extracted from wild-type (WT) and mss2Δ strains in RPMI 1640 liquid medium or on RPMI 1640 agar plate for 24 hours at 30°C was analyzed using RNA sequencing.

first: Cai-Ling

last: Ke

first: Hsaio-Yen

last: Tsai

first: Ajinkya

last: Kulkarni

first: Richard

middle: J

last: Bennett


title: Transcription factor occupancy is affected by genetic variation in the white adipose tissue of C57BL6/j and 129S1/SvImJ mice [RNA-seq]

city: Kuopio

first: Juho

middle: Mikael

last: Mononen

address: Yliopistonranta 1E

department: Faculty of Health Sciences

country: Finland

institute: University of Eastern Finland

summary: Most of the disease associated genetic variants identified in genome wide association studies have been mapped to the non-coding regions of the genome. One of the leading mechanisms by which these variants are thought to affect disease susceptibility is by altering transcription factor (TF) binding. Even though inbred mouse strains have been commonly used to investigate polygenic diseases, less is known on how their genetic differences translate to the level of gene regulation and chromatin landscape. Here, we investigated how genetic variation affects chromatin accessibility, a commonly used proxy for TF binding, and how this relates to gene regulation in the epididymal white adipose tissue (eWAT) of C57BL/6J and 129S1/SvImJ mice fed either chow or high-fat diet. We show that differences in chromatin accessibility are almost exclusively strain-specific and driven by genetic variation. In addition, we integrate ATAC-seq (chromatin accessibility) and H3K27ac ChIP-seq (active regulatory regions) data to show that tissue-specific TFs are commonly found in the active regulatory regions hosting TF binding motif altering variants in eWAT. By incorporating footprint analysis, we also show that TF occupancy is consistent with TF binding motif scores at the genetically altered loci. In addition, we validate these findings by extending the footprint analysis to ATAC-seq and H3K27ac ChIP-seq data obtained from the liver. Also, we employ RNA-seq to show that differentially expressed genes are collocated with differentially accessible regions hosting genetic variants. Overall, our findings highlight the connection between differential chromatin accessibility, TF binding and genetic variation and their role in the gene regulation across metabolically central tissues of a mouse model for polygenic obesity.

overall_design: We generated 5-7 RNA-seq libraries from the 4 groups: 129S1/SvImJ and C57BL/6J on either chow or high-fat diet.

first: Mari

last: Taipale

first: Sami

last: Heikkinen


title: Transcription factor occupancy is affected by genetic variation in the white adipose tissue of C57BL6/j and 129S1/SvImJ mice [ChIP-seq]

overall_design: We generated 4 ChIP-seq libraries from the 4 groups: 129S1/SvImJ and C57BL/6J on either chow or high-fat diet for H3K27ac. For control, 4 libraries with IgG where generated.


title: Oxidation Resistance 1 (Oxr1) Dysregulation Promotes TKI Resistance and Blast Crisis in Chronic Myeloid Leukemia.

first: Priyam

last: Patel

type: Genome variation profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Oxidation Resistance 1 (Oxr1) Dysregulation Promotes TKI Resistance and Blast Crisis in Chronic Myeloid Leukemia [dataset 2]

first: Weiqi

last: Huang

first: Elizabeth

last: Eklund


title: The effects of IL-16 deficience on gene expression after 24 week high-fat diet in mice

city: Gui'an

first: Hailong

last: Ou

state: Guizhou

address: No.6 Ankang Avenue

institute: Guizhou Medical University

summary: IL16-/-ApoE-/- mice and ApoE-/- mice were fed with high-fat diet for 24 weeks. The aortas from the two group mice were isolated for RNA-sequencing. Results showed that IL16-/- deletion caused a total of 1201 genes was altered, of which 943 genes were upregulated and 258 genes were downregulated in mice. Genes encoding membrane and extracellular components were remarkably enriched by Gene Ontology (GO) analysis, such as Collagen I α1 (ColIα1), ColIα2, Elastin, Filamin-α (Flnα), integrin beta 1 (Itgb1) and TIMP-3.

overall_design: We generated double-mutant mice (IL-16-/-ApoE-/-). The mice and ApoE-/- mice were treated with high-fat diet for 24 weeks at the age of 8-week. Then, the aorta were isolated for RNA-sequencing.


title: GCN2 regulates paclitaxel-induced neuropathic pain

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

type: Non-coding RNA profiling by high throughput sequencing

summary: Neuropathic pain is a significant clinical challenge affecting patients treated with the chemotherapeutic paclitaxel. Current therapeutic options for paclitaxel-induced neuropathy are limited due to an incomplete understanding of its molecular mechanisms. Here, we demonstrate a critical role for the Integrated Stress Response (ISR) in paclitaxel-induced neuropathic pain. Paclitaxel robustly activates the ISR specifically in dorsal root ganglion (DRG) neurons via the upstream kinase GCN2. Activation of GCN2 alone is sufficient to sensitize DRG neurons to depolarization and produce pain-like behaviors in vivo. Critically, paclitaxel-induced DRG neuron sensitization and behavioral mechanical and cold hypersensitivity require GCN2 signaling. Finally, paclitaxel treatment reduces global tRNA charging and abundance, providing a mechanistic basis for GCN2 activation. These findings position GCN2 and the ISR as promising therapeutic targets for the management of paclitaxel-induced neuropathic pain.

overall_design: To investigate the mechanism of paclitaxel-induced neuropathic pain and GCN2 activation, Male C57BL/6 mice were injected with 4mg/kg paclitaxel injection or vehicle control. One day after injection, mice were sacrificed and DRGs were harvested. Libraries were prepared for multiplex small RNA-seq (MSRseq) and were sequenced using Illumina. Following quality control processing and demultiplexing, libaries  were aligned to Mus musculus tRNA genes. Charging and abundance were calculated using custom Python and R scripts.

first: Alexander

middle: R

last: Mikesell

first: Angela

last: Meyer

first: Guadalupe

last: Garcia

first: Luke

last: Frietze

first: Cheryl

last: Stucky

first: Zachary

middle: T

last: Campbell


title: Oxidation Resistance 1 (Oxr1) Dysregulation Promotes TKI Resistance and Blast Crisis in Chronic Myeloid Leukemia [dataset 1]


title: Editing DNA Methylation in vivo [WGBS]

city: New York

address: 1150 St Nicholas Ave

institute: Columbia University

summary: DNA methylation is an epigenetic mechanism essential for orchestrating gene expression. Precise editing of DNA methylation has emerged as a new method to dissect its biological function in a DNA sequence specific manner with great potential to treat human diseases. However, applications of DNA methylation editing are largely in vitro. An experimental system to systematically investigate in vivo DNA methylation editing is needed to reveal its full therapeutic potential. We generated two transgenic mouse lines carrying an inducible dCas9-Dnmt3a or dCas9-Tet1 editor to enable cell-type specific methylation editing in vivo. We demonstrated that targeted methylation of the Psck9 promoter in the liver of dCas9-Dnmt3a mice reduced Psck9 expression and lowered plasma low-density lipoprotein cholesterol level to reduce the risk for cardiovascular diseases. Targeted demethylation of the Mecp2 promoter by dCas9-Tet1 reactivated Mecp2 expression from the inactive X chromosome in the brain of Mecp2 heterozygous Rett syndrome mice, suggesting a promising therapeutic approach for Rett syndrome and other X-linked diseases. Genome-wide sequencing analysis showed no detectable off-target at the transcriptional level in the methylation edited mice. These results demonstrate the feasibility and versatility of methylation editing in vivo, to explore DNA methylation in normal physiology and develop treatments for human diseases.

overall_design: Evaluation of off target effects by dCas9-Dnmt3a with Pcsk9 targeting sgRNAs or dCas9-Tet1 with Mecp2 targeting sgRNAs by whole genome bisulfite sequencing

first: X Shawn

last: Liu


title: Editing DNA Methylation in vivo [ChIP-Seq]

overall_design: Evaluation of off target effects by dCas9-Dnmt3a with Pcsk9 targeting sgRNAs or dCas9-Tet1 with Mecp2 targeting sgRNAs by dCas9 ChIP Sequencing

first: Luis

last: Flores


title: Blocking 6PGD restricts immunosuppression driven by the innate immune response in cancer

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: The pentose phosphate pathway (PPP) has always been relegated to the background of cellular metabolism, but our research identifies its unique and provocative influence on cell function, specifically in myeloid-derived suppressor cells (MDSCs). We’ve uncovered that 6-phosphogluconate dehydrogenase (6PGD), a rate limiting enzyme in this pathway, is not just a metabolic enzyme but a crucial determinant of MDSC behavior. While the IL-6/STAT3 axis propels 6PGD activity, it also empowers MDSCs to exert their immune-suppressive prowess. When we disrupt 6PGD – either through genetic knockout or pharmacological inhibition – an astonishing transformation occurs. The accumulation of 6-phosphogluconate (6PG) sets off a cascade involving JNK1-IRS-1 interaction and PI3K-AKT-pDRP1 signaling pathway, triggering mitochondrial fragmentation and dismantling oxidative phosphorylation (OXPHOS). This change in metabolism doesn’t just disrupt MDSC function; it transforms it stimulatory, leading to a strong anti-tumor response and making anti-PD1 therapies much more effective. Our results suggest we need to completely rethink the role of the PPP in cell function, with 6PGD emerging as a key target that could change the future of cancer immunotherapy.

overall_design: CD45+ cells were isolated Pgdfl/fl LysmCre (KO) and Pgdfl/fl (WT) AT3 tumor bearing mice and their transcriptomics profile was evaluated by single cell RNA sequencing (scRNA-seq).

first: Saeed

last: Daneshmandi

first: Eduardo

last: Gomez

first: Hemn

last: Mohammadpour


title: Effect of elastin-deficiency on gene expression in murine aortic smooth muscle cells at embryonic day 15.5

city: New Haven

first: Junichi

last: Saito

state: CT

address: 300 George Street, 7th Floor

department: Internal Medicine

institute: Yale University

summary: Defective elastin induces aortic smooth muscle cell hyperproliferation. As elastin is expressed from embryonic day 14 in the murine aorta, we utilized bulk RNA-seq to reveal molecular differences between Eln(+/+) and Eln(-/-) aortic smooth muscle cells at  embryonic day 15.5.

overall_design: Acta2-GFP, Eln(+/-) mice were bred with each other and embryos were collected at embryonic day 15.5. Aorta was isolated from Acta2-GFP embryos carrying Eln(+/+) or Eln(-/-). After digestion with collagenase enzyme mixtures, GFP+, CD31-, DAPI- smooth muscle cells were sorted by FACS and incubated with RNA lysis buffer. Extracted RNA was subjected to bulk RNA-seq.

first: Eunate

last: Gallardo-Vara

first: Rolando

last: Garcia Milian

first: Daniel

last: Greif


title: TOWARDS THE GENERATION OF A LASER CAPTURE MICRODISSECTION-BASED HUMAN ANAGEN HAIR FOLLICLE TRANSCRIPTOME ATLAS

city: Muenster

first: Markus

last: Fehrholz

address: Mendelstr. 17

institute: Monasterium Laboratory GmbH

summary: While this is available for murine HFs, systematic characterization of the transcriptome of specific human hair follicle (HF) compartments remains a major unmet challenge in human hair research. Here, we have aimed to initiate the generation of such an atlas to reveal HF compartment-specific transcriptome. We performed laser capture microdissection (LCM) on 8 selected compartments, i.e. bulge outer root sheath (ORS), suprabulbar ORS, inner root sheath (IRS), precortical hair matrix (HM), germinative HM, dermal papilla (DP), the lower dermal cup (DC), and the connective tissue sheath (CTS), of human anagen VI scalp HFs, and analysed these by RNA-seq. Principal component analysis (PCA) was used to validate the distinctness of the microdissected compartments. Biological replicates were clearly separated by HF compartments and a high degree of similarity of the distinct transcriptional profiles of each examined compartment was seen. Afterwards, we matched well-known signature genes to the correct HF compartments. For example, VCAN (versican) and ALPL (alkaline phosphatase) were correctly expressed in the DP, the lower DC, and suprabulbar CTS, while TCHH (trichohyalin) was solely found in the proximal IRS, and KRT85 (Keratin 85) and KRT31 (Keratin 31) were almost exclusively expressed in the precortical HM. These transcriptomic data were used to generate an easily accessible database for identifying and defining compartment-specific gene expression profiles, which can be ultimately made publicly accessible (“hair follicle MONasterium InteraCtive atlas – hairMONic”). This human HF transcriptomic map and the associated interactive database will support the identification of HF compartment-specific signature genes, and facilitates the development of compartment-specific, therapeutic interventions for the management of human HF disorders.

overall_design: We utilized laser capture microdissection (LCM)-based RNA-Seq from 8 defined HF compartments - bulge outer root sheath (bORS), suprabulbar ORS (sbORS), inner root sheath (IRS), germinative hair matrix (gHM), precortical HM (pcHM), dermal papilla (DP), lower dermal cup (DC), and connective tissue sheath (CTS) – of occipital scalp terminal anagen VI HFs from 7-10 male and female donors undergoing hair transplantation, followed by RNA-Seq analysis of 3-5 HFs per donor.

first: Lisa

last: Epping

first: Ilaria

last: Piccini

first: Ludovica

last: Timperi

first: Xiaolin

last: Li

first: Francisco

last: Jimenez

first: Daniela

last: Pinto

first: Ralf

last: Paus

first: Marta

last: Bertolini


title: Editing DNA Methylation in vivo [RNA-Seq]

first: Richard

last: Pan

overall_design: To evaluate off-target transcriptional effects of DNA methylation editing RNA seq was performed on samples edited with dCas9-Dnmt3a and Pcsk9 sgRNAs vs a non-targeting Scr sgRNA or samples edited with dCas9-Tet1 and Mecp2 Pool sgRNAs or Scr sgRNA

first: X Shawn

last: Liu


title: Bioengineered Extracellular Vesicles Co-delivering PD-L1 and miR-27a-3p Synergistically Reprogram T cells To Treat Inflammatory Bowel Disease [miRNA-Seq]

first: Mi-Kyung

last: Oh

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: Current treatments for inflammatory bowel disease (IBD) primarily rely on systemic immunosuppression, which often exhibits limited efficacy and off-target toxicity. Here we present a bioengineered extracellular vesicle (EV) platform designed for inflammatory bowel-targeted delivery of dual-action therapeutics, enabling precise modulation of T cell responses to enhance IBD treatment efficacy. EVs derived from Wharton’s jelly mesenchymal stem cells ( WJ-MSCs) were engineered to display membrane-bound PD-L1 and encapsulate miRNA 27a-3p (miR-27a-3p). The platform leverages WJ-MSCs’ intrinsic immunomodulatory properties and CXCR4-mediated recruitment to inflamed tissues. PD-L1 not only promotes immunosuppression of effector T cells, but also may enhance EV retention within inflamed sites. Meanwhile, miR-27a-3p shifts the Th17/Treg balance from a pro-inflammatory Th17 phenotype toward an anti-inflammatory Treg phenotype by targeting prohibitin 1. Bulk RNA sequencing of human CD4⁺ T cells treated with the EVs revealed downregulated of Th1/Th17-associated transcripts. In a humanized mouse model of colitis, EV treatment significantly reduced disease severity, diminished intestinal T cell infiltration, and restored mucosal integrity. Single-cell RNA sequencing demonstrated expansion of Treg cells and contraction of effector memory subsets, indicating durable immune modulation. This engineered EV platform represents a novel therapeutic paradigm that combines inflamed tissue targeting and dual immunomodulatory mechanisms to restore immune tolerance in IBD, addressing key limitations of conventional immunosuppressive approaches.

overall_design: RNA sequencing was performed on CD4⁺ T cells from spleens of IBD humanized mouse models (human graft), CD4⁺ T cells from human PBMCs, WJ-MSCs, and WJ-MSC–derived exosomes. The study includes single-cell RNA-seq, bulk mRNA-seq, and small RNA-seq to assess transcriptomic and miRNA profiles in the context of IBD and engineered exosome therapy.

first: Hyun Sung

last: Park

first: Kyung-Rok

last: Yu


title: Bulk-RNA sequencing of E8.25 posterior tissue +2 somites from controls and Sp5/8 double knockout or Wnt3a knockout embryos

first: Terry

last: Yamaguchi

summary: Sp5/8 are Zn finger downstream transcription factors of Wnt/b-catenin signaling pathway.  Deletion of Sp5/8 in mice result in severer posterior axis truncation by E9.5 closely resembling Wnt pathway mutants.  The goal of this project is to identify differentially expressed genes between controls and Sp5/8 double knockout mutants that could potentially reveal mechanisms of the role of Sp5/8 factors in self-renewal and differentiation of caudal progenitors.

overall_design: Posterior tissue + 2 somites were dissected out from E8.25 embryos (3-5 somites).  Total RNA was isolated using Trizol reagent according to the manufacturer's instructions (ThermoFisher Scientific) and genomic DNA was eliminated using Turbo-DNAse.  RNA quality was assessed using Agilent RNA bioanalyzer and samples with RNA integrity numbers greater than 9.0 were selected for sequencing.

first: Ravi

last: Chalamalasetty

first: Mark

last: Kennedy

first: Ryan

last: Kelly


title: Effect of elastin insufficiency on gene expression in cultured human aortic smooth muscle cells

first: Junichi

last: Saito

summary: Defective elastin induces aortic smooth muscle cell hyperproliferation. To elucidate gene expression changes with elastin insufficiency, bulk RNA-seq was performed on  cultured human aortic smooth muscle cells treated with siRNA targeting elastin.

overall_design: Cultured human aortic smooth muscle cells were treated with scrambled RNA or siRNA-targeting elastin. Total RNA was extracted 72 hours after siRNA transfection and subjected to bulk RNA-seq.

first: Jui

last: Dave

first: Daniel

last: Greif


title: Integrating whole-exome sequencing and scRNA-seq reveal the characteristic in one clear cell renal cell carcinoma sample arising in the setting of VHL disease

city: Nanning

first: Zhenyuan

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

summary: Clear cell renal cell carcinoma (ccRCC) arising in the setting of von Hippel–Lindau (VHL) disease is a rare type of kidney cancer and features VHL germline mutation. This type of ccRCC is rarely characterised at the single-cell level. In this work, whole-exome sequencing and single-cell RNA sequencing (scRNA-seq) were conducted on one ccRCC sample with VHL disease. Integrating scRNA-seq and whole-exome sequencing data by the Seurat package, we determined the relationship between single-cell transcriptome features and gene mutations. Immunohistochemistry and immunofluorescence were performed on one VHL germline mutation ccRCC and six non-VHL germline mutation ccRCC samples. We revealed the gene expression characteristics of ccRCC with VHL germline mutation. The frameshift mutations in OBP2A and BCR1, and the elevated expression of COX7A1 were most specific characteristics of ccRCC tumor cells with VHL mutation. And the extensive infiltration of exhausted T cells was the characteristic of tumor microenvironment. In addition, we discovered the relationship between genetic mutations and immune checkpoints. This work highlights the single-cell transcriptome and DNA-level information of this rare ccRCC and will provide more genetic insights and references into this rare disease.

overall_design: ccRCC arising in the setting of VHL disease was used for single-cell RNA sequencing by 10X Genomics.

first: Wenhao

last: Lu

first: Tingwei

last: Jin

first: Xiaoxiang

first: Yixuan

first: Shengzhu

last: Huang

first: Zheng

last: Wen

first: Cheng

last: Su

first: Yu

last: Ye

first: Ziyan

first: Zengnan

last: Mo


title: Discovery of novel circular RNAs through integration of short- and long-read RNA sequencing

city: St. Louis

first: Christopher

last: Maher

state: Missouri

address: 1 Brookings Dr

institute: Washington University in St. Louis

summary: Circular RNAs (circRNAs) have been reported to be associated in crucial hallmarks of tumorigenesis. The lack of open ends gives rise to their high stability, making them clinically significant as potential non-invasive as biomarkers for cancer diagnosis and prognosis. Select circRNAs contain open reading frames and impact tumorigenesis through encoded small peptides, though computational challenges remain in accurately profiling circular open reading frames. Currently circRNA sequencing projects rely heavily on detecting circRNA backsplice junctions, without accurate transcript reconstruction to differentiate circular isoforms that share backsplice junctions but contain different intermediate exons. We adopted a long-read RNA sequencing strategy that enriches for full-length circRNAs to generate an accurate reference to integrate with matched short-read sequencing samples of colorectal cancer cell lines and patient trio tissues. We further validated circRNAs detected in long-read sequencing with high-confidence support from short reads. We present CHRIS, an open-source bioinformatic workflow that maximizes the detection of novel circRNAs missed in existing tools. In addition, we performed an integrative proteogenomic analysis and discovered thousands of novel peptides encoded by circRNAs that previously eluded short-read based methods, published in an online database PepCircDB. Our unique findings revealed numerous novel circRNAs, non-canonical isoforms of known circRNAs, circRNAs altered in cancer metastasis, and candidates that encode small peptides. Overall, this research will improve existing computational methods for circRNA detection and provide valuable resources for future research of circRNAs in tumor biology.

overall_design: Integrative analysis using both short-read and long-read RNA-seq to profile novel circRNAs in CRC cell lines and patient samples

first: Sidi

last: Zhao

first: Amy

last: Ly

last: Fields


title: Exploration the role of INHBA in Hu sheep granulosa cells using RNA-Seq

city: nanjing

first: Yongjin

last: Bao

state: jinagsu

address: weigang No.1

institute: nanjing agricultural university

summary: Activin/inhibin is an important factor for the fecundity of Hu sheep, and it is involved in follicular development in ovaries. Inhibin subunit beta A (INHBA) participates in the synthesis of activin A and inhibin A. Here we investigated the effect and molecular mechanism of INHBA on cell cycle, apoptosis, activin A/inhibin A secretion in Hu sheep granulosa cells (GCs) based on RNA-Sequencing. A total of 1,687 differentially expressed genes (DEGs) were identified (Fold change ≥ 2 and FDR ≤ 0.01), of which 602 genes were upregulated and 1,087 genes were downregulated in the INHBA interference groups compared with the control groups. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in the regulation of cell cycle, protein serine/threonine kinase activity and actin cytoskeleton reorganization. Moreover, pathway analysis showed that DEGs were significantly enriched in 40 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including P53 pathway, progesterone-mediated oocyte maturation, PI3K-AKT signaling pathway. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) confirmed the differential expression of 7 selected DEGs. In addition, INHBA knockdown promoted GCs to G1 phase and decreased the S phase cell numbers, initiated GC apoptosis through P53 signal pathway, and decreased the concentration of activin A and inhibin A in medium. Above all, our findings may contribute to a better understanding on the law of follicular development and thus improve the reproductive performance of female animals.

overall_design: The ovaries of sexually mature Hu sheep were collected from Jiangsu Taicang slaughterhouse (Jincanghu Food Co., Ltd.) during the breeding season (November to January). Ovaries are clipped from connective tissue and adherent fallopian tubes, then immediately immersed in warm (30-37°C) sterile saline (160 IU/mL gentamicin) and transported to the laboratory within 2 hours. After washing with normal saline for 6 times, follicular fluid was aspirated from follicles ≥3 mm, and GCs were isolated for in vitro culture according to a previous study.Isolated GCs were seeded into a 6-well plate for culture, and when they grow to 70%-80% confluence, mix the lipid complexes containing NC and siRNA-INHBA according to the instructions of Lipofectamine 3000 (Thermo Scientific, MA, USA). After 24h transfection, the RNA of GCs was extracted with Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions. The concentration and purity of RNA were detected by the Nanodrop 2000 spectrophotometer (Thermo Scientific, MA, USA). After comfirming the purity of RNA, the RNA sample were sent to sequencing company.

first: M

last: EI-Samahy

first: Xiaodan

last: Li

first: Hua

last: Yang


title: The alteration of genome-wide gene expression as a result of PoxCxrE deletion in P. oxalicum under glucose or Avicel cultured condition

first: Di

last: Tian

address: DaXue east road

institute: College of Life Science and Technology,GuangXi university

summary: To investigate the effect of PoxCxrE on gene expression in P. oxalicum, we sequenced the transcriptomes from the parental strain ΔPoxKu70 and deletion mutant ΔPoxCxrE which were cultivated in Avicel medium or glucose medium for 24 h after transfer from glucose.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ΔPoxKu70 and ΔPoxCxrE under 2 different carbon sources

first: Xiong

last: Lin

first: Shuai


title: Comparative Eye Transcriptome Atlas

status: Public on Nov 11 2025

city: Aarhus C

first: Christian

last: Damsgaard

address: C F Møllers Alle 3

department: Department of Biology

country: Denmark

institute: Aarhus University

summary: The Comparative Eye Transcriptome Atlas provides transcriptomic resources to study retinal evolution and physiology across non-mammalian vertebrates. We profiled retinas from four species using two complementary high-throughput approaches. Eight 10x Genomics Visium spatial transcriptomics datasets were generated from Anolis carolinensis (n = 2), Taeniopygia guttata (n = 4), Columba livia (n = 1), and Gallus gallus (n = 1), capturing spatially resolved gene expression with matched histology images. In parallel, six 10x Genomics Chromium Single Cell 3′ RNA-seq datasets were obtained from zebra finch (T. guttata) retinas to resolve cell-type–specific transcriptomes. Raw sequencing data (FASTQ) and processed outputs from SpaceRanger (Visium) and CellRanger (Chromium) are provided. Downstream integrated and annotated datasets can be explored interactively at https://linlab.au.dk/Damsgaard_lab/CETA/ and full Seurat objects are available on request.

sample_organism:
Columba livia
Gallus gallus
Anolis carolinensis
Taeniopygia guttata

overall_design: Retinas were dissected from healthy adult animals of four species: the green anole (Anolis carolinensis; n = 2), zebra finch (Taeniopygia guttata; n = 4 for Visium, n = 6 for Chromium), rock pigeon (Columba livia; n = 1), and chicken (Gallus gallus; n = 1). For spatial transcriptomics, retinas were cryosectioned and processed with the 10x Genomics Visium Spatial Gene Expression kit v1 (55 µm spot resolution) and imaged at 20× magnification before library preparation. For single-cell transcriptomics, retinas from zebra finches were dissociated and processed with the 10x Genomics Chromium Single Cell 3′ v3 workflow. All libraries were sequenced on an Illumina HiSeq 4000 using paired-end 2 × 150 bp reads. Raw data were processed with SpaceRanger 3.1.1 (Visium) and CellRanger 7.1.0 (Chromium) against the following reference genomes: AnoCar3.1 (A. carolinensis), TaeGut1 (T. guttata), Cliv_2.1 (C. livia), and GRCg7b (G. gallus). The processed data deposited here are the standard filtered outputs of these pipelines without additional ambient RNA removal, doublet removal, or downstream QC filtering.

first: Lin


title: ZKSCAN3 promotes ovarian cancer cell proliferation through upregulating HSPB1

city: Wuhan

first: suli

last: LV

address: Wuhan, Hubei, China

institute: Huazhong University of Science and Technology

summary: Ovarian cancer has the worst prognosis in major gynecological cancers. Current therapies includes platinum, taxol, angiogenesis inhibitor, PARP inhibitor. However, most ovarian cancer patients develop resistance. Identification of more pro-tumor factors in ovarian cancer may shed insight into ovarian cancer biology and therapy. In this study, we find ZKSCAN3, a zinc-finger transcription factor is overexpressed in ovarian cancer. We show ZKSCAN3 promotes ovarian cancer cell proliferation. Through RNA-sequencing and ChIP-sequencing, HSPB1 is identified as a target gene of ZKSCAN3. HSPB1 expression is significantly decreased by suppressing ZKSCAN3. Suppressing HSPB1 expression inhibits ovarian cancer cell proliferation as well. In contrast, expressing exogenous HSPB1 partially rescues the cell proliferation in ZKSCAN3 knock-down cells. Collectively, our study uncovers a functional ZKSCAN3-HSPB1 axis that promotes ovarian cancer cell proliferation.

overall_design: To examine the effect on transcriptome by ZKSCAN3, we performed ChIP-Seq and RNA-Seq to identify ZKSCAN3 directly-regulated genes. For ChIP-Seq, we stably expressed HA-ZKSCAN3 in Hey ovarian cancer cells. HA antibody was used for Chromatin IP. ChIP DNA was analyzed with Next generation sequencing. For RNA-Seq, Hey cells were transduced with lentiviruses expressing ZKSCAN3-shRNA or control sequences. Total RNA was extracted for RNA-Seq.

first: Tanjing

last: Song

first: Lidong

last: Sun

first: Suli

last: Lv


title: The Splicing Factor PTBP1 Interacts with RUNX1 and is Required for Leukemia Cell Survival [Long Read]

city: Omaha

first: Jordan

last: Rowley

state: NE

address: 3828 Jones St, Apt 202

institute: University of Nebraska Medical Center

summary: Runt-related Transcription Factor 1 (RUNX1) is essential for definitive hematopoiesis and is among the most frequently mutated genes in leukemia. Previous work from our lab demonstrated that Histone Deacetylase 1 (HDAC1), a known RUNX1 partner, is unexpectedly required for active transcription suggesting a non-histone role for HDAC1 regulating components of the RUNX1 complex. Here, we use proteomics, genomics, and long-read transcriptomics to identify novel RUNX1 interacting partners and decipher their role in gene regulation and RNA splicing in leukemia cells. We demonstrate that Polypyrimidine Tract Binding Protein 1 (PTBP1) interacts with RUNX1 in an HDAC1-dependent manner. Chromatin profiling revealed extensive genome-wide overlap in sites occupied by RUNX1 and PTBP1, with significant enrichment at promoters of actively transcribed genes. Loss of PTBP1 in AML cells led to widespread alterations in RNA splicing and decreased expression of genes whose promoters are bound by both factors, including metabolic genes. In agreement with these findings, we found that loss of PTBP1 reduced glycolysis and glucose uptake and ultimately caused cell death. Based on our data, we propose that the interaction between RUNX1 and PTBP1 facilitates expression of metabolic proteins essential for leukemia cell growth and survival.

overall_design: Long-read RNA-seq of MOLM-13 cells with PTBP1 shRNA knockdown and control, treated with doxycycline for 9 days

first: Arjun

last: Dhir

first: Alexander

last: Ethell

first: Riley

last: Watkins

first: Calvin

last: Lam

first: Kevin

last: Tur-Rodriguez

first: Jimmie

last: Persinger

first: Kasidy

middle: K

last: Dobish

first: Sipra

last: Panda

first: Shannon

last: Buckley

first: Samantha

last: Swenson

first: Sandipan

last: Brahma

first: Katherine

last: Hyde


title: The Splicing Factor PTBP1 Interacts with RUNX1 and is Required for Leukemia Cell Survival [CUT&Tag]

overall_design: CUT&Tag of RUNX1 and PTBP1 and CUT&RUN of H3K27me3, with IgG controls, in MOLM-13 cells


title: A circadian checkpoint relocates neutrophils to minimize injury

first: Alejandra

last: Aroca-Crevillén

address: C/ Melchor Fernández Almagro 3

institute: Spanish National Center for Cardiovascular Research Carlos III (CNIC)

summary: Inflammation-driven injury, a significant source of morbidity and mortality worldwide, is largely mediated by the cytotoxic activity of neutrophils, which extend the initial lesion and jeopardize organ function. Intriguingly, inflammatory injury naturally declines at specific times of day, suggesting that circadian mechanisms exist that mitigate the destructive activity of neutrophils and protect the host. Here, we show that the periods of diurnal protection coincide with peaks in plasma CXCL12, a chemokine that inhibits a neutrophil-intrinsic circadian clock by signaling through CXCR4. Genetic deletion of this clock, or a hyperactive form of CXCR4, prevented the diurnal spikes of injury, and treatment with a synthetic CXCR4 agonist conferred protection from myocardial and vascular occlusion. In tissues, this protection was mediated by repositioning neutrophils in the wound core, thus sparing neighboring host cells from death. Thus, a circadian neutrophil checkpoint protects from exuberant inflammatory injury and can be activated to protect the host.

overall_design: To elucidate the transcriptional landscape of leukocyte heterogeneity during myocardial infarction in mice, we conducted single-cell RNA sequencing of DAPI-CD45+, DAPI-CD45-CD31+ and DAPI-CD45-CD31-PDGFRa+ cells obtained from control and infarcted heart of mice under different conditions. These conditions included vehicle-treated and ATI2341 treated mice, to elucidate the effect of a CXCR4 agonist (ATI2341) in leukocytes and other cell populations after an inflammatory insult such as myocardial infarction (45 min occlusion, 24h of reperfusion). Basal condition was also included as a control.

last: Aroca-Crevllén

first: Jon

last: Sicilia

first: Andrea

last: Rubio-Ponce

first: Andrés

last: Hidalgo