title: Unveiling the Clinical Significance of RNA Pseudouridylation in Colorectal Cancer

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

summary: Colorectal cancer is a common malignant tumor worldwide, and its morbidity and mortality are increasing year by year. RNA pseudouracil modified synthetase is closely related to the development of colorectal cancer, but the whole transcriptomic level of pseudouridine（ψ） in colorectal cancer has not been fully explored. This study examined the extent of RNA ψ modification in 21 pairs of colorectal cancer tissues and adjacent normal tissues, as well as 10 blood samples from patients, utilizing RNA ψ modification sequencing technology. These findings underscore the significance of RNA ψ modification events in colorectal cancer and offer insights into its application for clinical detection and treatment.

overall_design: This study comprehensively assessed the alterations and consistency of RNA ψmodification in colorectal cancer tissues and blood samples from 21 patients recruited at Zhongnan Hospital of Wuhan University, along with ψ sequencing data from 10 colorectal cancer patients and 13 healthy controls. Utilizing the ψ sequencing results, we investigated differential pseudouridylated genes across various RNA types and elucidated their correlation with clinical characteristics

first: Jiehua

first: Shaoqing

last: Han

first: Yafen

last: Wang

first: Xiaocheng

last: Weng

first: Xiang

last: Zhou


title: Effect of root secretions on the transcriptome of Bacillus subtilis

status: Public on Jul 31 2025

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

type: Expression profiling by high throughput sequencing

summary: We tested the gene expression following association witht the root, exposure to secretions and regrowth in LB

sample_organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

overall_design: The bacteria were grown in liquid MSgg with either A. thaliana, or its secretions, and evaluated for gene expression. Cells were also transferred to LB and analyzed for their gene expression versus untreated bacteria that also were regrown in LB

first: Omri

last: Gilhar

first: Liat

middle: R

last: Navi

first: Ilana

last: Kolodkin-Gal


title: The antigen-specific T cell vaccine reduces mature neutrophil accrued in the spleen to induce immune tolerance in rheumatoid arthritis

city: 北京

first: aking

last: Eco

state: 北京

address: 11# Xizhimen South Street, Xicheng District

department: Rheumotology and Immunology

country: China

institute: Peking University People's Hospital

summary: RA, an autoimmune disease characterized by debilitating pain and joint damage, poses challenges in current treatments due to their non-specific nature and potential for systemic side effects. This study introduces a novel therapeutic approach – Antigen-Specific T Cell Vaccine (AgTCV), targeting the root cause of RA by selectively suppressing autoantigen-specific cells without compromising overall immunity. Utilizing a citrullinated self-peptide derived from collagen II, we developed AgTCV through selective expansion and inactivation of autoreactive T cells. In vivo experiments using a collagen-induced arthritis (CIA) mouse model demonstrated the sustained efficacy of AgTCV, reducing inflammation, cartilage damage, and bone erosion. The vaccine also modulated immune responses, decreasing pro-inflammatory cytokines and pathogenic autoantibody levels. AgTCV's subcutaneous delivery showcased prolonged persistence, efficient recruitment in draining lymph nodes, and enhanced dendritic cell maturation at the injection site. Single-cell transcriptome analysis revealed dynamic changes induced by AgTCV, emphasizing the pivotal role of neutrophils in remodeling inflammatory tissue towards immune homeostasis. These findings propose AgTCV as a promising, cost-effective, and targeted immunotherapy for RA, with implications for broader applications in autoimmune disorders.

overall_design: This study investigates the mechanism of the Antigen-specific T Cell Vaccine (AgTCV) in RA. The preparation of AgTCV involves a chemotherapeutic drug-based method, selectively expanding pathogenic antigen-specific T cells using a joint-specific self-peptide. Spleen samples are collected after AgTCV, TCV or Saline administration, and single-cell transcriptomic analysis is conducted to explore its impact on the immune system. The experimental design includes three replicates for each treatment group.

first: Shanzhao

last: Jin

first: Lulu

last: Cao

first: Xiaolin

last: Sun

first: Zhanguo

last: Li


title: The mechanism of FSTL3 in the progression of colon cancer

city: Nanjing

first: Leqian

last: Ying

state: Jiangsu

address: Ding Jiaqiao street

department: Oncology

institute: Southeast University

summary: FSTL3 is a multifunctional protein, and its role in cancer has attracted considerable attention. Firstly, overexpression of FSTL3 has been found to be closely associated with the occurrence and development of various tumors. The expression levels of FSTL3 are significantly elevated, which is linked to its role in promoting tumor cell proliferation, migration, and invasion. Additionally, the expression levels of FSTL3 are associated with the grading and prognosis of tumors, where high expression of FSTL3 is often correlated with the malignancy and adverse prognosis of tumors. Therefore, this study primarily explores the mechanisms by which FSTL3, acting as an exosomal cytokine, promotes the progression of colon cancer.

overall_design: In order to investigate the mechanistic role of FSTL3 in the progression of colon cancer, the study involved the exogenous addition of humanized FSTL3 protein to the culture medium of HCT116 cells. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells after 24 hours. This aimed to explore its impact on the biological functions of colon cancer cells and underlying mechanisms.


title: High-resolution Hi-C reveals increased chromatin looping with senescence associated with hypomethylation and retrotransposon derepression [RNA-seq]

city: Providence

first: Nicola

last: Neretti

state: RI

address: 225 Dyer St.

country: USA

institute: Brown University

summary: This study presents the highest-resolution chromatin map of cellular senescence to date, shedding light on how genomic architecture is altered with this damaging phenotype. Senescence, a driver of aging, is a pro-inflammatory state of proliferative arrest caused by DNA damage; it is associated with epigenetic changes, including those to chromatin organization. We created ~3kb Hi-C contact maps of proliferating, quiescent, and replicative senescent lung fibroblasts, and also compared these to oncogene-induced senescence. Our findings confirm a loss of heterochromatin, with a shift towards the A compartment and A subcompartments. We establish a novel loop analysis framework, revealing the ~six times more unique loops with senescence, which lose methylation at their anchors. Additionally, we present a custom long-read reference genome highlighting structural changes supporting retrotransposon derepression, particularly at a defined ‘hotspot’. These architectural changes contribute to senescence, as they promote cell cycle arrest and inflammation, as well as epigenetic drift.

overall_design: To investigate the role of genomic structure in cellular senescence we generated Hi-C data, total RNA-seq, and long-read DNA sequencing for proliferating and late replicative senescent human diploid lung fibroblasts (LF1). We also generated Hi-C and total RNA-seq for quiescent cells. We compared the proliferating, quiescent, and senescent cell data to determine characteristic architectural features of senescence.

first: Audrey

last: Dalgarno

first: Shane

middle: A

last: Evans

first: Maxfield

middle: G

last: Kelsey

first: Thomas

last: Nunez

first: Azucena

last: Rocha

first: Kelly

last: Clark

first: John

middle: M

last: Sedivy


title: Multiple Origins of Chalcone Synthase Short Interfering RNAs in Glycine max Revealed by Genome Assemblies of Mutant Alleles

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: With long-read assemblies, we delineate three origins of short interfering RNAs for chalcone synthase (CHS siRNAs) in Glycine max. Mutations from ii (yellow seed coat with black hilum) to i (fully pigmented) lack either a single antisense CHS1 gene by deletion or the partial 5’ subtilisin fragment-CHS1 gene region by a large inversion mutation. On the other hand, we show that the dominant I allele, with fully yellow seed coats, arose from the i black, wild soybean genome by an inverted duplication that places a partial 5’ DnaJ fragment next to slightly truncated CHS genes. In a direct I to i mutation, the two CHS genes are further truncated, destroying their capacity to produce siRNAs. The two-color saddle pattern of the ik allele arose by an inverted duplication event that places a partial 5’ P450 fragment in front of two inverted repeat CHS genes. Despite the importance of the three different 5’ promoters that abut inverted repeat CHS genes as drivers of precursor expression, the profiles of cognate gene family members for subtilisin, DnaJ, and P450 are not always limited to the seed coat as tightly as CHS siRNAs, implying that transcriptional or processing events for CHS dsRNA or siRNAs differ in other tissues.

overall_design:
High-throughput RNA sequencing was performed on different tissues and genotypes of soybean as listed in each sample.

High-throughput RNA sequencing was performed on dissections of the hilum versus the seed coat without the hilum for two stages of seed coat development with two biological repeats from the cultivar Williams which has black hilum on a yellow seed coat.

middle: O

first: Young

middle: B

last: Cho

first: Sarah

middle: I

last: Jones


title: Analysis of differential genes in osteogenic induction of alveolar bone derived MSCs under TNFα-induced inflammation in Ccrl2-KO mice and WT mice.

city: Shanghai

first: Yongliang

last: Chen

state: Shanghai

address: No 399. Middle Yanchang Road, JingAn District.

department: Stomatological Hospital and Dental School

institute: Tongji University

summary: In order to explore the effect of Ccrl2 knockout on the osteogenic differentiation of MSCs under inflammatory conditions, MSCs derived from the alveolar bones of Ccrl2-KO mice and WT mice were extracted, and total cellular RNA was extracted after 2 days of osteogenic induction under TNFα-induced inflammation, and carried out RNA-Seq to identify the potential mechanism by which Ccrl2 regulates osteogenic-related signals.

overall_design: MSCs derived from the alveolar bones of Ccrl2-KO mice and WT mice under TNFα-induced inflammation were extracted and RNA-Seq was performed. Each group had three biological replicates, with a total of 6 samples.

first: Yong

last: Liang


title: CTNNB1-dependent molecular pathways are disrupted proportional to gene-dosage in a human embryonic stem cell model of early neural differentiation

city: Adelaide

first: Mark

last: Corbett

state: South Australia

address: Adelaide Health and Medical Sciences, University of Adelaide, North Tce

department: Adelaide Medical School

country: Australia

institute: University of Adelaide

summary: CTNNB1 encodes β-catenin, a multifunctional protein which acts as a WNT responsive transcriptional co-activator in the nucleus, and separately as a component of cell-cell adhesion complexes. Heterozygous loss-of-function variants of CTNNB1 cause a defined neurodevelopmental disorder. To explore the gene-dosage dependent effects of CTNNB1 on embryonic neural development, we performed CRISPR/Cas9-mediated genome editing of the H1 human embryonic stem cell line to engineer either mono- or bi-allelic CTNNB1 null alleles. During directed neural differentiation, bi-allelic CTNNB1 knockout lines displayed an overt prematurity of neurogenesis which was subtly mirrored in the mono-allelic loss lines. RNA sequencing revealed impact on the expression of genes involved in both cell-cell adhesion, mediated through cadherins and protocadherins, as well as WNT signaling. These stem cells with loss of CTNNB1 provide human-specific insight into the early role of CTNNB1 in neural differentiation

overall_design: We aimed to model haploinsufficiency of CTNNB1 in hESCs using CRISPR/Cas9 genome editing in the most frequently studied hESC line, H1. We introduced bi-allelic 77 bp frameshifting deletions into exon 3 of CTNNB1 in hESC using two independent sgRNAs. To generate hESC clones that retain one wild-type copy of CTNNB1, we performed homology-directed repair to correct a mutant CTNNB1 allele (NM_001904.4: c.184delG:p.Val62Serfs*18) that was found in one of the sequenced compound heterozygous clones (initially presumed to be a mono-allelic CTNNB1 77 bp deletion), back to the wild-type allele.  to investigate the impact of heterozygous and complete CTNNB1 KO on the early stages of neural development. Three wild-type empty vector controls, heterozygous and complete CTNNB1 KO clones each, along with the H1 parental hESC line, were directed to differentiate into cortical neurons for 26 days using dual SMAD inhibition. The experiments were performed in two batches with replication of one heterozygous CTNNB1 clone #20 and one complete CTNNB1 KO clone #9 between each batch. We performed RNA-sequencing on the parental H1 hESC line (n=1), empty vector control (n=3), heterozygous (n=3) and complete CTNNB1 KO (n=3) clones at the undifferentiated (ESC; day 0), neuroepithelial sheet (NE; day 10), neural rosette (NR; day 13) and neural progenitor cell (NPC; day 23) stages of neural differentiation.

first: Sayaka

last: Kayumi

first: Lachlan

last: Jolly

first: Louise

last: Korte

first: Wendy

last: Waters

first: Alastair

middle: H

last: MacLennan

first: Jozef

last: Gecz


title: Differential gene analysis of extraction sockets in periodontitis in mice

summary: In order to determine the mechanism of the effect of periodontitis on the healing of tooth extraction sockets in mice, the mandibular first molar extraction models of mice in the periodontitis group and the control group were constructed respectively, and samples were taken for RNA-Seq at three time points: 0d, 3d, and 7d. Analysis of key genes in periodontitis regulating tooth extraction socket healing was conducted.

overall_design: The mandibular first molar extraction models of mice in the periodontitis group and the control group were constructed respectively, and samples were taken for RNA-Seq at three time points: 0d, 3d, and 7d, with three biological replicates in each group. 18 samples in total.


title: Effect of loperamide on transcriptional profile of Raw264.7 cells infected with Salmonella

city: Changchun

first: Jiazhang

last: Qiu

address: Xi'an Road 5333

institute: Jilin University

summary: Our previous  screening allowed us to identify the loperamide (LPD) as a potent inhibitor of S. Typhimurium intracellular proliferation. LPD treatment of infected cells markedly promoted the host autophagic response and lysosomal activity. A mechanistic study revealed that the elevated host autophagy and elimination of intracellular bacteria were dependent on the high expression of glycoprotein nonmetastatic melanoma protein B (GPNMB) induced by LPD. In addition, LPD treatment could effectively protect S. Typhimurium-infected LPD Galleria mellonella and mouse models. Thus, our study suggests that LPD may be used for the treatment of diseases caused by intracellular bacterial pathogens. Moreover, LPD may serve as a promising lead compound for the development of anti-infection drugs based on the HDT strategy.

overall_design: The assay was divided into 4 groups: untreated Raw264.7 cells (Blank), Salmonella infected  Raw264.7 cells (ST), LPD treated  Raw264.7 cells (LPD), and LPD treated  Raw264.7 cells with Salmonella infection (ST-LPD)

first: Hongtao

last: Liu

first: Siqi

last: Li


title: Biomimetic multifunctional nanodrugs enable regulating abnormal tumor metabolism and amplifying PDT-induced immunotherapy for synergistically enhanced tumor ablation

city: Beijing

first: yanghong

last: liu

address: No.2 Nanwei Road, Xicheng District

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Aberrant tumor metabolic activities not only promotes the aggressiveness and proliferation of tumor cells in the harsh microenvironment in vivo, but also contributes to immune cell dysfunction and immunosuppressive TME. This phenomenon poses a major challenges to cancer immunotherapy. Thus, tumor metabolic interventions might be a promising strategy to reverse immune suppression for boosting anti-tumor immunotherapy. Herein, biomimetic multifunctional nanodrugs (CM-ZIF8 at Ce6/Lon) were constructed for collaborative tumor metabolic regulation and photodynamic (PDT) amplified immunotherapy. These nanodrugs were prepared by homotypic tumor cell membrane (CM)-camouflaged zeolitic imidazolate framework-8 (ZIF-8) nanoparticles embedded with photosensitizer (Chlorin e6, Ce6) and metabolic modulator (Lonidamine, Lon). We carried out a series of experiments to explore the possible mechanism of CM-ZIF8 at Ce6/Lon for tumor metabolic regulation. Firstly, CM-ZIF8 at Ce6/Lon could actively metastasis towards tumor cells based on the homotypic targeting property. Subsequently, the nanodrugs blocked tumor metabolic pathways and reduced metabolites accumulation, therefore reversing the immunosuppressive TME through releasing Lon. Meanwhile, the released Ce6 from these nanodrugs triggered PDT efficiency on the tumor suppression, and induced ICD effect to activate the cascade immune response. The regulation of tumor metabolism disorders synergistically augmented PDT-mediated immunotherapy through reduction of regulatory T cells, enhancement of CD8+ T cell infiltration and upregulation of inflammatory factors. As a result, CM-ZIF8 at Ce6/Lon efficiently inhibited the primary and metastatic tumor. Overall, our study explored mechanism of tumor metabolic regulation to reverse the immunosuppressive TME and demonstrated the important potential of the synergistic anti-tumor. This multifunctional nanodrug may provide new insight for developing a promising therapeutic tool to reverse immunosuppression and boost anti-tumor immunotherapy

overall_design: To develop breast cancer-bearing orthotopic mouse model, 4T1 cells (2×106) in PBS were injected into the left mammary gland of each mouse. Tumor volumes were calculated using the following equation: volume = 0.5×L×W×W, in which L and W represented the tumor length and width, respectively.

first: Yanhong

first: Zhonggao

last: Gao

first: Wei

last: Huang


title: OXPHOS driven by glycolysis through the malate aspartate shuttle is required for cardiomyocyte re-differentiation and long-term fish heart regeneration [Astyanax_mexicanus_RNAseq]

city: Oxford

first: Mathilda

last: Mommersteeg

address: | Institute of Developmental and Regenerative Medicine (IDRM) | IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive

department: Department off Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

summary: In contrast to humans after myocardial infarction, fish can fully regenerate their hearts. However, not all fish are equally able to regenerate, allowing comparative inter- and intra-species analysis to identify novel mechanisms controlling successful heart regeneration. Here, we report a differential regenerative response to cardiac cryo-injury between seven different wild-type zebrafish strains. Correlating this data to single cell and bulk RNAseq data, we identify oxidative phosphorylation (OXPHOS) as a positive regulator of long-term regenerative outcome. OXPHOS levels, driven by Glycolysis through the Malate aspartate shuttle (MAS), increase as soon as cardiomyocyte proliferation decreases, and this increase is required for cardiomyocyte re-differentiation and successful long-term regeneration. We confirm these findings in Astyanax mexicanus and link it to a dynamic temporal sarcomere gene expression programme during cardiomyocyte re-differentiation. These findings challenge the current stance that OXPHOS inhibits regeneration and provide new targetable pathways to enhance heart repair in humans after myocardial infarction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the Astyanax mexicanus surface fish and Pachon cavefish populations.  The fish underwent cryo-injury of the cardiac ventricle and hearts were isolated at 6 hours, 1, 3, 7, 14 and 30 days post cryo-injury as well as 6 hours, 1 and 3 days post sham and uninjured controls.

first: Zhilian

last: Hu


title: OXPHOS driven by glycolysis through the malate aspartate shuttle is required for cardiomyocyte re-differentiation and long-term fish heart regeneration [WT_ZF_strain_RNAseq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 7 different wild-type zebrafish strains (AB, KCL, NA, SAT, TL, TU and WIK). Zebrafish underwent cryo-injury of the cardiac ventricle and hearts were isolated at 1 and 7 days post cryo-injury as well as uninjured control.

middle: T

first: Konstantinos

last: Lekkos


title: Tissue specificity of chalcone synthase short interfering RNAs (CHS siRNAs) that control seed color

first: Lila

last: Vodkin

type: Non-coding RNA profiling by high throughput sequencing

summary: We previously showed CHS siRNAs levels to be high in immature seed coats of seed with dominant alleles of the I locus that controls seed color (Tuteja et al., Plant Cell 2009; Cho et al., Plos One, 2013) and to be much lower in several other tissues sampled (Zabala et al., BMC Plant Biology 2012).  Here, we examined 15 additional small RNA populations by high-throughput sequencing of developing seed coats of various stages from cultivars with the dominant I and i-i alleles that specify yellow seed coats or from spontaneous mutations to pigmented seed coats. The CHS siRNAs were tissue specific and found at high levels of up to 5700 normalized RPMs (reads per millions) in immature seed coats but were less than 6 RPMs in libraries from 21 non-seed coat samples including the embryonic axis, different stages of seedlings cotyledons, vegetative buds, and shoot tips, illustrating the tightly controlled tissue-specific expression of the CHS siRNAs in seed coats.

overall_design: High-throughput sequencing was performed on different tissues and genotypes of soybean as listed in each sample.

first: Young

last: Cho

first: Sarah

last: Jones


title: Histone modification-dependent production of peptide hormones facilitates acquisition of pluripotency during leaf-to-callus transition in Arabidopsis

city: Seoul

first: Cheljong

last: Hong

address: Gwanak-ro 1

department: Chemistry

country: South Korea

institute: Seoul National University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin configuration is critical for establishing tissue identity and changes substantially during tissue identity transitions; the leaf-to-callus transition is of particular interest because. the crucial scientific and agricultural technology of in-vitro tissue culture exploits callus formation from diverse tissue explants and tissue regeneration via de novo organogenesis. We analyzed changes in the global distribution of H3ac and H3K4me3 during the leaf-to-callus transition, with focus on open chromatin regions in calli relative to leaf explants, defined by increased accumulation of both H3ac and H3K4me3. Signaling peptides were identified as genes with accumulation of both H3ac and H3K4me3, and exogenous treatment of the identified peptide enhanced callus proliferation and de novo shoot regeneration.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3ac and H3K4me3 in mature leaf and callus cells.

first: Kyounghee

last: Lee

first: Sangrea

last: Shim

first: Oksun

last: Park

first: Pil

middle: J

last: Seo


title: The mRNA expression profile of THP1 cells with hsa_circRNA_103124 overexpressed

city: Suzhou

first: Juan

last: Yin

address: 80 Tian'e Dang Road

department: Suzhou Key Laboratory of Gut Microecology

institute: The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University

summary: To investigate the possible molecular biological function of hsa_circRNA_103124, THP1 cells  were overexpressed with  hsa_circRNA_103124 by recombinant lentivirus infection.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of THP1 cells transfected with hsa_circRNA_103124 overexpressed recombinant lentivirus  (n=3) or control lentivirus (n=3).

first: Zhi

last: Pang

first: Yulan

last: Ye

first: Tong


title: High-resolution Hi-C reveals increased chromatin looping with senescence associated with hypomethylation and retrotransposon derepression [Hi-C]

first: Nicola

last: Neretti

first: Audrey

last: Dalgarno

first: Shane

last: Evans

first: Maxfield

last: Kelsey

first: Thomas

last: Nunez

first: Azucena

last: Rocha

first: Kelly

last: Clark

first: John

last: Sedivy


title: Genome-wide analysis of replication initiation in a TXR1 (Histone H3 K27  monomethyltranferase) overexpression strain in Tetrahymena

city: Bryan

first: GEOFFREY

last: KAPLER

state: TX

address: 4209B Medical Research Education Building II

institute: Texas A&M University

summary: We mapped Tetrahymena macronuclear replication origins in TXR1 overexpression strain on a genome-wide scale using Okazaki fragments sequencing (OK-seq). Replication initiation sites of TXR1 overexpression strain followig cadmium induction of MMT1 promoter driven-TXR1 were studied compare to the uninduced TXR1 overexpression strain without cadmium using OK-seq.

overall_design: Asynchronous exponentially growing Tetrahymena cells were labelled by EdU (5-ethynyl-2’-deoxyuridine, ThermoFisher) for 5 min to label newly synthesized DNA.  Cells were washed and collected. Genomic DNA was extracted. Okazaki fragment were isolated and biotinylated using ClickIt chemstry. Sequencing adaptor were ligated and Okazaki fragment capture using streptavidin magnetic beads (Petryk et al. 2016).

first: Zhang

last: Linying

first: Dang

last: Hung

first: Pan

last: Simin


title: Genome-wide identification and characterization of circular RNA m6A modification in pancreatic cancer

city: Guangzhou

first: Jian

last: Zhen

address: 651 Dongfeng East Road

department: State Key Laboratory of Oncology in South China

institute: Sun Yat-sen University Cancer Center

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A) is the most abundant modification of RNA in eukaryotic cells and play critical roles in cancer. While most related studies focus on m6A modifications in linear RNA, transcriptome-wide profiling and exploration of m6A modification in circular RNAs in cancer is still lacking. Here, we proposed a high-performance tools named Circm6A for the detection of m6A-circRNAs. Based on Circm6A results, we revealed the m6A-circRNAs genomic landscape of PDAC for the first time and shed new light on the regulatory aspect of circRNAs at the RNA epigenetic level.

overall_design: 77 tissue samples were collected from PDAC patients for m6A-seq, including 53 tumor samples and 24 normal samples.  *** The GEO submission contains only processed data (raw counts tables). Raw data has been submitted to GSA (The Genome Sequence Archive, China), due to patient privacy concerns and human genetic resources policy in China.

last: Zheng

first: Ying


title: Genome-wide analysis of replication initiation in Tetrahymena

summary: We mapped Tetrahymena macronuclear replication origins on a genome-wide scale using Okazaki fragments sequencing (OK-seq). OK-seq permits a high-resolution, quantitative analysis of replication fork initiation on a genome-wide scale that is dependent on the depth of coverage within a population of molecules. Replication initiation sites of the TXR1 (Histone H3 K27  monomethyltranferase) deletion strain were also studied compare to wild type using OK-seq.


title: Enhancer priming role of FOXO1 sustains pro-survival BCR signaling in lymphoma

status: Public on Jul 30 2025

city: Valhalla

first: Seungha

middle: Alisa

last: Lee

state: New York

address: 15 Dana Road

institute: New York Medical College

summary: Mantle cell lymphoma (MCL) remains incurable requiring new actionable targets. Forkhead Box O1 (FOXO1) exhibits lineage-specific bivalent function as an oncogenic transcription factor that regulates MCL lineage survival function, contrasting with its tumor-suppressor role in other cancer types. Acute degradation of FOXO1-FKBP12F36V by degrader TAG (dTAG) molecules potently induces MCL cell death. Cell cycle restricted degradation of FOXO1 reveals that its function in G1 phase is critical for MCL cell survival. Mechanistically, FOXO1 rapidly reactivates lineage enhancers in the early G1 phase of the cell cycle following the cell division through collaborating with SWI/SNF chromatin remodelers. This interaction facilitates binding and activation of transcription factor PAX5-driven oncogenic MCL lineage gene regulatory networks. Multiomic analysis of FOXO1-dependent transcriptomic changes shows that BCR signaling pathway depends on functional FOXO1 expression. BTK inhibitor combination accelerates G1-specific degradation of FOXO1-caused MCL cell death. Consistently, combined FOXO1 and BTK inhibitors effectively suppress progression of primary MCL cells and MCL xenografts. Our results uncover the molecular networks through which FOXO1 drives MCL lineage survival that can serve as a rationale for a combinatorial targeting of FOXO1 network components with Bruton’s tyrosine kinase inhibitors and explain the mechanism underlying its lineage-restricted oncogenic bivalent activity.

overall_design: Nascent RNA sequencing of mantle cell lymphoma cell lines with FOXO1 degron and P300 or SMARCA-1 inhibitors

first: Soo Yeon

last: Hwang

first: Jihye

last: Paik

first: Hojoong

last: Kwak

first: Jeongbin

last: Heo


title: Dynamic change of immune microenvironment in ovarian cancer following neoadjuvant chemotherapy [scRNA-seq]

city: Hangzhou

first: Lv

last: Fei

address: The First People's Hospital of Hangzhou, Zhejiang Province

institute: Zhejiang Chinese Medical University

summary: Initial surgery and platinum-based chemotherapy is extensively applied to ovarian cancer. Although the majority of patients were sensitive, most relapse at later stage, highlighting the urgent need to understand the tumor microenvironment in ovarian cancer following NACT (neoadjuvant chemotherapy). Through analyzing the published scRNA-seq on human high-grade serous ovarian cancer and performing several in vitro and in vivo experiments, we found prostaglandins-mediated immunosuppressive microenvironment formation is a critical contributor to chemotherapy-resistant upon cisplatin treatment. In mechanisms, cisplatin-treated ovarian cancer cells induce the formation of MDSCs, which passivates the cytotoxicity of CD8+T cell. Moreover, we also carried out scRNA-seq on mice ovarian cancer intraperitoneal injection model to confirm our findings. Notably, Collaborative application of cisplatin and prostaglandins-specific inhibition boosts the cytotoxicity of CD8+T cell and greatly improves the effective rate compared to cisplatin monotherapy.

overall_design: Female mice (6-8 weeks old) were intraperitoneally injected with ID8 cells. Two weeks later, cisplatin (2.5mg/kg) was used in CS group for twice a week. For another four weeks, peritoneal irrigation fluid and metastatic nodes in mesentery, omentum and peritoneum were collected as primary and metastatic tumor samples, respectively. Then, we performed scRNA-seq in four groups (C/ P/ CT/ PT, Control/ cisplatin/ Control metastasis/ cisplatin metastasis) including peritoneal irrigation fluids and metastasis with or without cisplatin therapy.

first: Shuai

last: Wang

first: Ruoyao

last: Zou

first: Fei

last: Lv

first: Yi

last: Jin

first: Xiaoye

last: Ye

first: Yongfeng

last: Wu

first: Jinyi

last: Tong


title: Changes in macrophages and endothelial cells mechanics treated with native LDL from donors with CVD

city: Moscow

first: Diana

last: Kiseleva

address: 2, Abricosovskiy Pereulok

country: Russia

institute: Petrovsky National Research Center of Surgery

summary: Atherosclerosis is a progressive and multifactorial vascular disorder characterized by lipid accumulation, chronic inflammation, and structural alterations in the arterial wall. This condition disrupts normal endothelial function, including the biomechanical properties of endothelial cells, which play a crucial role in maintaining vascular homeostasis. Mechanical dysfunction in these cells contributes to increased vascular permeability and topographical irregularities that disturb hemodynamic flow, fostering an environment conducive to plaque development. A growing body of evidence suggests that low-density lipoprotein (LDL) exacerbates these dysfunctions by increasing cellular stiffness. As endothelial cells act as primary mechanosensors within blood vessels, their altered mechanical state is a critical factor in early atherogenesis.  In this study, we explored the molecular pathways by which native LDL, derived from individuals with cardiovascular disease, affects the mechanical and structural properties of endothelial cells and macrophages. Our analyses revealed that exposure to native LDL triggers a pronounced reorganization of the actin cytoskeleton, primarily mediated through Rho GTPase signaling, along with notable augmentation of the tubulin network. These cytoskeletal changes were accompanied by compromised cell adhesion, weakened intercellular connectivity, and impaired extracellular matrix integrity—all of which are pivotal to endothelial barrier function. Furthermore, gene expression profiling indicated a significant upregulation of LOX, HMOX1, RND1, RUNX1, and TFRC in LDL-treated endothelial cells, suggesting a disruption in iron metabolism. This dysregulation likely contributes to oxidative stress through reactive oxygen species (ROS) production, thereby accelerating atherosclerotic plaque formation.

overall_design: RNA-seq profiling of PMA-induced THP-1 macrophages and EA.hy926 cell lines treated with native LDL from donors with CVD. Control samples were incubated with culturing media and test samples were incubated with 100 μg/mL of LDL for 24 hours.

first: Ulyana

last: Khovantseva

first: Vadim

last: Cherednichenko

first: Denis

last: Fotin

first: Evgeny

last: Denisov

first: Anton

last: Fedorov

first: Pavel

last: Iamshchikov

first: Elizaveta

last: Prostakishina

first: Yulia

last: Markina

first: Alexander

last: Markin


title: Microarray Expression Analysis of Circular RNA in Perineural Invasion of Pancreatic Ductal Adenocarcinoma

first: Rufu

last: Chen

address: No. 106, Zhongshan 2nd Road, Guangzhou

institute: Guangdong Provincial People's Hospital

summary: This study aimed to investigate the expression profile of circular RNAs (circRNAs) in pancreatic cancer and evaluate their potential as reliable biomarkers and novel diagnostic and therapeutic targets, with a specific focus on molecular characteristics associated with perineural invasion. We employed Arraystar Human circRNA Array Analysis to detect circRNA expression levels in 3 pancreatic cancer tissues with perineural invasion and 3 pancreatic cancer tissues without perineural invasion. The results revealed significant differences in circRNA expression between the two groups, with distinctly different expression patterns observed in the samples. This study analyzed the expression profile of circRNAs and their potential value as reliable biomarkers and potential novel diagnostic and therapeutic targets for pancreatic cancer, particularly in the context of perineural invasion.

overall_design: To clarify the exact mechanism of circular RNAs (circRNAs) in the process of perineural invasion in pancreatic cancer, total RNA was extracted from 3 pancreatic cancer tissues with perineural invasion and 3 pancreatic cancer tissues without perineural invasion in this study. Next-generation sequencing was performed to explore the differences in circRNA expression profiles between the two groups.


title: Inducible neuroblast differentiation into mature neurons reveals centrosome-spliceosome complex as a new splicing-modifying site

city: Benevento

first: Luca

last: Faretra

state: BN

address: Via dei Mulini

department: DST

country: Italy

institute: University of Sannio

summary: Nuclear transcriptional factors are key regulators of stem cell identity and differentiation, however whether extra-nuclear factors are involved in cell fate decisions remains unclear. Here we report that centrosome-associated spliceosome repression drives the differentiation of immature neuroblasts into neurons. Using neuroblastoma cells undergoing asymmetric division (ACD) as a model, we demonstrate that spliceosome components assemble preferentially at the mother centriole and undergo dynamic relocation in response to retinoic acid (RA) or centrosome ablation. ACD cells require selective Ninein splicing variants to promote the efficient formation of centrosome-associated spliceosome condensates. RA-induced neuron differentiation activates ciliogenesis and alternative splicing patterns, including cytoplasmic intron-retained transcripts in spliceosome-related genes. While pharmacological ablation of cilia impedes RA-dependent neuronal differentiation, inhibition of centriole duplication enhances synapse formation, recapitulating the molecular and morphological features of neurons.  Mechanistically, centrosome repression-mediated differentiation of ACD cells into neurons relocates spliceosome factors between the nucleus and centrosome, activating cytoplasmic intron retention and exon inclusion in genes essential for ciliogenesis and cerebral cortical development. Collectively, our findings establish a cellular model for programmed splicing control and a strategy to enhance cytoplasmic spliced genes critical for human brain development.

overall_design: RNA-seq profiling of SK-N-SH cells under three conditions—untreated control, retinoic acid treatment, and combined centrinone plus retinoic acid treatment—after 5 days of differentiation.

first: Giampiero

last: Cipolletta

first: Giovanni

last: Puopolo

first: Agostino

last: Mellone

first: Marco

last: Nigro

first: Paolo

last: Salerno

first: Antonio

last: Ammendola

last: d’Amati

first: Giuseppe

last: Ingravallo

first: Andrea

last: Remo

first: Rustem

last: Uzbekov

first: Hui

last: WU

first: Paola

last: Parente

first: Luigi

last: Ferrante

first: Brunella

last: Franco

first: Pietro

last: Carotenuto

last: Merla

first: Francesco

last: Napolitano

last: Cerulo

first: Massimo

last: Pancione


title: Gene Expression Profile of Synchronized Cells Identifies Alzheimer's Disease in Autopsy Validated Skin and Blood Samples

city: Morgantown

first: Florin

middle: V

last: Chirila

state: WV

address: 895 Vandalia Rd

department: Diagnostic

institute: Spot Dx

summary: A gene expression profile has not been identified for late-onset Alzheimer's Disease (LOAD) in more than 95% of cases. However, autosomal dominant genes are known for their early-onset (EOAD) characteristics. Moreover, the genetic convergences between familial EOAD and sporadic LOAD have not previously been identified despite the common neuropathology. Here, synchronized skin fibroblast samples from individuals with LOAD, confirmed by autopsy, revealed 36 statistically significant (P<0.05) LOAD-dysregulated genes, with 26 showing an essential gap with non-Alzheimer's disease (non-ADD) dementia patients. Notably, five LOAD-dysregulated genes in the skin—FAM149B, NHLH1, SHISA5, URB2, and WASF2—were also dysregulated in blood B-lymphocytes. Importantly, an additional 18 LOAD-dysregulated gene families in the skin were validated in the blood. In total, 23 LOAD-dysregulated gene families in the skin were confirmed in the blood. An intriguing and novel aspect is the genetic convergence between late-onset and early-onset Alzheimer's disease, as demonstrated by dysregulated gene families, including ADAM, IL, and RAB. The gene expression profile aligns remarkably well with prior autopsy-validated biomarkers: Morphometric Imaging, PKC epsilon, Cell Size, Growth Rate, and Protein Amount. Our findings suggest a promising potential for personalized genomic profiling in the diagnosis and treatment of LOAD, offering hope for more effective and targeted approaches.

overall_design: We aimed to uncover distinct gene expression patterns using NGS RNA-Seq in synchronized skin fibroblasts and blood B-lymphocytes from autopsy-confirmed Alzheimer's disease (AD) patients, comparing them to non-Alzheimer's disease dementia (non-ADD) patients and healthy controls (HC).

first: William

last: MacTurk

first: Jack

last: Wallace

first: Guang

last: Xu

first: Daniel

middle: L

last: Alkon


title: Transcriptional alterations in the brain using Eomes-Cre mouse line control animals at embryonic day 16.5 - WT only

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

country: Germany

institute: University of Freiburg

summary: During cerebral cortex development, neural stem cells (NSCs) require precise spatiotemporal signals to acquire the correct cell identity at the exact moment. Even though epigenetic regulation plays a central role in cell fate decisions, the exact mechanisms remain elusive. Thus, we focus our research on the H3K79 methyltransferase DOT1L, a key player in cell fate decisions. Our group has shown that DOT1L prevents NSC premature differentiation by increasing expression of genes that regulate asymmetric cell division (Franz et al. 2019). Using cell-lineage tracing and pharmacological inhibition, we confirmed that when DOT1L is inhibited apical progenitors (APs) switch to symmetric neurogenic divisions in detriment of asymmetric self-renewal (Appiah et al. 2023). However, the impact on basal progenitors (BPs), responsible for the evolutionary expansion of the cortex in both size and complexity (Nonaka-Kinoshita et al, 2013), is still unexplored. As DOT1L generally preserves NSC transcriptional programs of cells dividing multiple times, the restricted proliferation potential in BPs might bear potentially novel insights into how stem cells control the tight balance between proliferation and differentiation. We now analyse control (WT) mice for DOT1L using Eomes-Cre line during cortical neurogenesis (E16.5) using single cell RNA-seq to understand how the transcriptome changes.

overall_design: EomesDot control mouse embryos were harvested at E16.5. The cerebral cortex was dissected, dissociated into a cell suspension and analyzed using scRNA-seq.

first: Camila

last: Fullio


title: Transcriptional study in the brain using control animals from the Eomes-Cre mouse line at embryonic day 14.5 - WT only

summary: The specification of neural composition and of neuronal networks in the six-layered cerebral cortex is a highly organized and complex process. Neural stem cells (NSCs) and glutamatergic neurons of the cerebral cortex are born in different stem cell compartments, namely the ventricular (VZ) and the subventricular zone (SVZ). Embryonic VZ and SVZ-derived progenitors produce neurons of the upper layers (UL) and deep layers (DL) of the stratified neuroepithelium in an inside-out manner. Both cellular compartments seem to be associated with higher cognitive tasks that are observed in these species. Understanding of the molecular mechanisms that control cell fate within the SVZ is therefore of utmost interest to understand one basis of cognition. Furthermore, the SVZ is one of the stem cell niches of the adult nervous system and thus contributes to repair processes after CNS injuries in mice. Recent data from embryonic and neural stem cells (ESC, NSC) revealed that chromatin modifying enzymes (CME) and epigenetic modifications play a pivotal role in cell fate decisions such as proliferation/self-renewal and lineage differentiation. In addition, during development the balance between proliferation and differentiation is achieved through the activities of diverse transcription factors (TF) that are expressed in a time- and space-specific manner. The aim of this project is to further elucidate the role of neural stem cells that are residing in the SVZ with a focus on the implications of epigenetic modifications mediated by MLLT3 in transcriptional control and regulation of proliferation, survival and differentiation during brain development.

overall_design: EomesMllt3 control mouse embryos were harvested at E14.5. The dorsal telencephalon was dissected, dissociated into a cell suspension and analyzed using scRNA-seq.

first: Annalisa

last: Izzo


title: Identifying the role of DNMT1 in gene expression regulation in somatostatinergic interneurons during embryonic corticogenesis

city: Aachen

first: Geraldine

last: Zimmer-Bensch

address: Worringerweg 3

department: Biology 2

institute: RWTH Aachen University

summary: The establishment of neuronal circuits, made up of excitatory neurons and inhibitory interneurons, is a fine-tuned process during corticogenesis and is pivotal for a functional brain. Developmental aberrations affecting these circuits are implicated in several neuropsychiatric disorders. While excitatory neurons originate in cortical proliferative zones, inhibitory interneurons migrate from the basal telencephalon into the cortex. This migration is regulated by intrinsic genetic programs and extrinsic cues. Here, we aimed to identify the role of the DNA methyltransferase 1 (DNMT1) in controlling the expression of key genes implicated in mouse cortical interneuron development and the migration of somatostatin-expressing interneurons within the developing cortex.

overall_design: FAC-sorted somatostatinergic interneurons from the cortex were collected from the brains of multiple E14.5 mice, with or without a conditional knockout of Dnmt1 in somatostatinergic interneurons, and pooled per genotype. The samples were sequenced following an RNA extraction and library preparation.

first: Julia

last: Reichard

first: Philip

last: Wolff


title: Distinct effects of restricting individual branched-chain amino acids on the development and progression of Alzheimer’s disease in 3xTg mice

city: MADISON

first: REJI

middle: P

last: BABYGIRIJA

state: WI

address: 726 BEAR CLAW WAY, APT 211

institute: UW Madison

summary: Dietary protein is a critical regulator of metabolic health and aging in diverse species, and many of the benefits of low-protein diets are recapitulated by restriction of the three branched-chain amino acids (BCAAs), leucine, isoleucine, and valine. In mouse models of Alzheimer’s disease (AD), dietary supplementation with BCAAs worsens AD neuropathology, while restriction of any of the BCAAs improves cognitive deficits. We recently discovered that each BCAA has distinct metabolic effects, with the restriction of isoleucine alone being sufficient to improve metabolic health and extend lifespan and healthspan in genetically diverse mice. Here, we investigate the effect of restricting each individual BCAA on metabolic health and the development and progression of AD in the 3xTg mouse model. We find that restriction of isoleucine and valine, but not leucine, promotes metabolic health. Restricting any of the three BCAAs improved short-term memory in males, with isoleucine restriction having the strongest effect, while restricting valine has the greatest cognitive benefits in females. Restriction of each BCAA had distinct effects on AD pathology, mTOR signaling, autophagy, and survival. Transcriptomic analysis of the brain revealed both distinct and shared, and highly sex-specific, molecular impacts of restricting each BCAA, and we identify a set of significantly altered pathways strongly associated with reduced AD pathology and improved cognitive performance in males. Our findings suggest that restricting any of the BCAAs, particularly isoleucine or valine, may form the basis of a novel sex-specific approach to prevent or delay the progression of AD.

overall_design: Six month old Male and female 3xTg mice were placed on either of these 4 diets Amino acid defined diet , Isoleucine restricted diet, Leucine restricted diet or Valine restricted diet for 9 months. Brains were colelcted for rna sequencing from all the treatment groups.

first: Reji

last: Babygirija

first: Cara

last: Green

first: Dudley

last: Lamming


title: Histone H4 Lysine 20 Methylation Marks Genes Dynamically Regulated During Erythroid Maturation [CUT&Run_2]

city: Rochester

first: Laurie

last: Steiner

state: NY

address: 601 Elmwood Ave

department: Pediatrics

institute: University of Rochester

summary: We profiled H4K20 monomethylation and KMT5A during the well-characterized erythroid differentiation of human hematopoietic stem and progenitor cells.

overall_design: CUT&RUN

first: Kristin

middle: E

last: Murphy

first: Michael

last: Getman

first: Xiurui

last: Lv

first: Zachary

middle: C

first: Deanna

last: Adib

first: Nabil

last: Raman


title: CRISPR screen reveals genes with differential fitness with polyamines

city: Cambridge

first: Pushkal

last: Sharma

address: 455 Main Street

institute: Whitehead Institute

summary: Polyamine depletion using DFMO or sardomozide, inhibitors of the polyamine biosynthesis enzymes ODC1 and AMD1, respectively, exerts cytostatic effects without inducing substantial cell death. To identify genetic dependencies under varying polyamine levels, we conducted a genome-wide CRISPR-Cas9 knockout screen across conditions with differing intracellular polyamine concentrations.

overall_design: K562 cells were transduced with a CRISPR sgRNA library targeting ~20,000 protein-coding genes (5 sgRNAs per gene). Following 14 days of treatment with DFMO, sgRNA abundance was compared between DFMO-treated and control cells.


title: Transcriptional study in the brain  using control animals from the Eomes-Cre mouse line at embryonic day 16.5 - WT only

first: Tanja

last: Vogel

overall_design: EomesMllt3 control mouse embryos were harvested at E16.5. The cerebral cortex was dissected, dissociated into a cell suspension and analyzed using scRNA-seq.

first: Camila


title: Transcriptional study of the brain using Eomes-Cre mouse line control animals at embryonic day 14.5 - WT only

summary: During cerebral cortex development, neural stem cells (NSCs) require precise spatiotemporal signals to acquire the correct cell identity at the exact moment. Even though epigenetic regulation plays a central role in cell fate decisions, the exact mechanisms remain elusive. Thus, we focus our research on the H3K79 methyltransferase DOT1L, a key player in cell fate decisions. Our group has shown that DOT1L prevents NSC premature differentiation by increasing expression of genes that regulate asymmetric cell division (Franz et al. 2019). Using cell-lineage tracing and pharmacological inhibition, we confirmed that when DOT1L is inhibited apical progenitors (APs) switch to symmetric neurogenic divisions in detriment of asymmetric self-renewal (Appiah et al. 2023). However, the impact on basal progenitors (BPs), responsible for the evolutionary expansion of the cortex in both size and complexity (Nonaka-Kinoshita et al, 2013), is still unexplored. As DOT1L generally preserves NSC transcriptional programs of cells dividing multiple times, the restricted proliferation potential in BPs might bear potentially novel insights into how stem cells control the tight balance between proliferation and differentiation. We now analyse  control (WT) mice for DOT1L using Eomes-Cre line during cortical mid-neurogenesis (E14.5) using single cell RNA-seq to understand how the transcriptome changes.

overall_design: EomesDot control mouse embryos were harvested at E14.5. The dorsal telencephalon was dissected, dissociated into a cell suspension and analyzed using scRNA-seq.

last: Fullio


title: Urolithin A maintains primordial follicle dormancy and prevents cyclophosphamide-induced follicle loss by inhibiting the PI3K/Akt signaling

city: guangzhou

first: Weiyong Wang

last: Wang

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: south china university of technology

summary: Urolithin A, a natural gut microbial metabolite, exerts multiple beneficial effects upon supplementation, including prolonging lifespan, mitigating diseases, restoring the quality of aged oocytes and alleviating drug toxicity. The study aims to investigate the ovarian protective role of Urolithin A, focusing on its mechanisms for inhibiting primordial follicle activation and mitigating cyclophosphamide (CY)-induced follicle apoptosis. The results showed that Urolithin A significantly decreased the number of growing follicles, downregulated the expression of oocyte growth-related genes (Gdf9 and Zp3) and protein (DDX4), as well as Ki-67 and BrdU-positive signals. Further studies revealed that Urolithin A downregulated the levels of phosphorylated Akt and FOXO3a and decreased the percentage of oocytes with FOXO3a nuclear export. Molecular docking showed a strong binding ability between Urolithin A and its downregulated gene Pik3cg (PI3Kγ). Moreover, Urolithin A attenuated CY- and 4-HC-induced increases in Cleaved caspase-3 and cleaved PARP1 positive signals. Meanwhile, RNA-seq analysis indicated that Urolithin A downregulated CY-induced expression of DNA damage-related genes (Trp73 and Trim29). In short, Urolithin A inhibits primordial follicle activation by reducing PI3K/Akt pathway reactivity. Furthermore, Urolithin A prevents CY-induced follicle apoptosis. The study provides valuable insights into Urolithin A treatment for chemotherapy-induced infertility.

overall_design: Ovaries from 3 days postpartum (dpp) mice were cultured in Urolithin A (5-20 μM) for 4 days to determine the optimal concentration. For the in vitro chemotherapy model, ovaries were treated with vehicle, 4-Hydroperoxy cyclophosphamide (4-HC) or 4-HC + Urolithin A. For the in vivo chemotherapy model, 4 dpp mice received intraperitoneal injections of vehicle, Urolithin A, CY or CY + Urolithin A. Follicles were quantified using hematoxylin staining. RT-qPCR, RNA-seq, immunofluorescence and Western blotting were performed to detect activity of PI3K/Akt and mTOR pathways, as well as apoptotic signaling. Molecular docking analysis was used to predict the potential interactions between Urolithin A and PI3K/Akt.

first: Weiyong

first: Ren

last: Zhou

first: Yong

last: Ruan

first: Shuhao

last: Fan


title: Mandibular and Femur-Derived Ligated preosteoclasts from LSD1WT and cKO mice

city: Minneapolis

first: Kim

last: Mansky

state: MN

address: 515 Delaware St SE

institute: University of Minnesota

summary: The goal of this study was determine gene changes from LSD1WT and cKO mice that had ligature induced periodontal disease.

overall_design: Bone marrow was isoalted from 2 month old female LSD1WT and cKO mice who had ligature for 7 days.  Bone marrow from the mandible and femur was flushed and incubated with M-CSF and RANKL for 2 days to generate preostoeclasts.  RNA was isolated using a qiagen kit and sequenced.

first: Juan E.

last: Abrahante Llorens


title: Retinoic acid-regulated epigenetic marks identify Alx1 as a direct target gene required for optic cup formation [ChIP-seq]

city: La Jolla

first: Gregg

last: Duester

state: CA

address: 10901 North Torrey Pines Road

department: Center for Cardiovascular and Muscular Diseases

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Retinoic acid (RA) is a transcriptional control agent that regulates several aspects of eye development including invagination of the optic vesicle to form the optic cup, although a target gene for this role has not been previously identified. As loss of RA synthesis in Rdh10 knockout embryos affects the expression levels of thousands of genes, a different approach is needed to identity genes that are directly regulated by RA. Here, we combined ChIP-seq for epigenetic marks with RNA-seq on eye tissue from wild-type embryos and Rdh10-/- embryos that exhibit failure in optic cup formation. We identified a small number of genes with decreased expression when RA is absent that also have decreased presence of a nearby epigenetic gene activation mark (H3K27ac). One such gene was Alx1 that also has an RA response element (RARE) located near the RA-regulated H3K27ac mark, providing strong evidence that RA directly activates Alx1. In situ hybridization studies showed that Rdh10-/- embryos exhibit a large decrease in eye Alx1 expression. CRISPR/Cas9 knockout of Alx1 resulted in a failure in optic cup formation, thus demonstrating that RA directly activates Alx1 in order to stimulate this stage of eye development.

overall_design: H3K27ac ChIP-seq of WT and Rdh10 KO mouse embryonic craniofacial tissue

first: Marie

last: Berenguer


title: Microgravity Accelerates Skeletal Muscle Degeneration: Functional and Transcriptomic Insights from a Muscle Lab-on-Chip Model Onboard the ISS.

city: Orlando

first: Siobhan

last: Malany

state: FL

address: 6550 Sanger Rd

department: Department of Cellular and Systems Pharmacology

institute: UF Research and Academic Center at Lake Nona

summary: Global transcriptomic analysis revealed increased gene expression and particularly mitochondrial-related gene expression in microgravity for the electrically stimulated younger myobundles, while the older myobundles were less responsive. Young- and old-derived skeletal muscle myobundles were exposed to microgravity for 12 days and matching ground control group.

overall_design: CD56 myoblasts-derived from young active and old sedentary muscle biopsies, differentiated into functional myobundles, that exhibited classic skeletal muscle bio-functions, were subjected to microgravity. We report on the differences in gene expression  profiling between the flight young- vs old-derived electrically stimulated myobundles and ground young- vs old-derived myobundles. A minimum of three biological replicates was used for RNA seq.

first: Maddalena

last: Parafati

first: Zon

last: Thwin

first: Legrand K

first: Paul M

last: Coen


title: I-SPY2 TRIAL RPPA data for ganitumab arm (and control arm)

city: San Francisco

first: Denise

last: Wolf

address: 2340 Sutter st

institute: University of California, San Francisco

summary: Pre-treatment specimens from patients treated on the I-SPY2 neoadjuvant breast cancer trial were studied to identify predictive biomarkers associated with response to the regimen of paclitaxel, an anti-type I IGF receptor (IGF-1R) antibody ganitumab, and metformin (PGM) followed by doxorubicin and cyclophosphamide (AC) compared to control therapy (paclitaxel followed by AC). This record contains protein/phosphoprotein data from pre-treatment laser capture microdissected (LCM) tumor biopsies for up to 162 key signaling proteins/phosphoproteins in cancer for 221 HER2-negative patients from 2 arms of the neoadjuvant I-SPY2 TRIAL (NCT01042379) for aggressive early stage breast cancer [119 Control; 102 Ganitumab].   This record also contains clinical data for these patients, including HR, and HER2 status, response (pCR or no pCR), and treatment arm. RPPA endpoints assayed are from hormone receptor (n=4), HER family (n=14), cell cycle/proliferation (n=20), immune (n=18), DNA repair deficiency (DDR; n=15), AKT/mTOR/PI3K (n=7), apoptosis/autophagy (n=10), IGF1R (n=6), TIE/ANG (n=4), growth/survival/metabolism (n=22) and RTK (n=19) and other pathways.  For gene expresson data for these patients, see the GEO record/subseries GSE194040.

overall_design: Reverse phase protein array (RPPA) array run on isolates from pre-treatment breast cancer biopsy samples that were first LCM-enriched for epithelial cells.    The sample characteristics and their values represent:    HER2: the status of the HER2 gene. 1 = positive; 0 = negative.    HR: the status of hormone (estrogen and progesterone) receptors.  1 = positive; 0 = negative.    pCR: the status of a pathological complete response (pCR).  1 = complete response; 0 = failed complete response    Arm: arm of the trial per patient, detailing treatment during taxol-phase of protocol:  Paclitaxil (Control arm: HER2- subset); Paclitaxel + Ganitumab.  All patients also received subsequent doxorubicin + cyclophosphamide.     Arm (short name): abbreviated name of treatment arm in the trial per patient (n=2 arms) - Control, Ganitumab                                                                  RPPA Array:  Platform Array version.  Key to convert from raw to normalized data.

first: Christina

last: Yau

first: Julia

last: Wulfkuhle

first: Emanuel

middle: F

last: Petricoin III

first: Douglas

last: Yee

first: Laura

last: van ‘t Veer


title: Multiomics analyses reveal the role of Glis3 in polycystic kidney disease

city: New Haven

first: Stefan

last: Somlo

state: CT

address: 333 Cedar Street

institute: Yale University

summary: We performed unbiased transcriptional profiling and chromatin accessibility analyses on adult kidney tissues from allelic series of Pkd1 and Glis3 inactivation mouse models. Glis3 is a modifer of cyst progression whose inactivation exacerbates polycystic kidney disease. Through the integration of multiomic datasets, we generated hypotheses to explain the worsening phenotype observed in Pkd1 and Glis3 double mutants.

overall_design: We performed RNA-Seq and ATAC-Seq on the same kidney tissues using the following genotypes: wild type, Glis3fl/fl; Pax8rtTA; TetOCre (Glis3KO), Pkd1fl/fl; Pax8rtTA; TetOCre (Pkd1KO), and Glis3fl/fl; Pkd1fl/fl; Pax8rtTA; TetOCre (Pkd1KO+Glis3KO). All mice received oral doxycycline from postnatal day 28 to 42 (P28-P42) and kidney tissues were harvested at P49 (7 weeks).

first: Zemeng

last: Wei


title: Benchmarking of Computational Demultiplexing Methods for Single-Nucleus RNA Sequencing Data [dataset 2]

city: Leuven

first: Llewelyn

last: Roderick

address: Herestraat 49

department: Department of Cardiovascular Sciences

country: Belgium

institute: KU Leuven

summary: Single-nucleus RNA sequencing enables high-resolution profiling of complex tissues, but its high cost limits large-scale studies. Sample pooling with genetic demultiplexing is a scalable solution, yet comparative benchmarks are lacking. We benchmarked four widely used tools using variants from SNP arrays or extracted from matched bulk RNA-Seq. Performance, including accuracy, runtime, robustness, and scalability, was evaluated. Real-world application to 10x RNA-Seq from human and multi-species heart tissue demonstrates the tools' utility for demultiplexing and doublet removal.

sample_organism:
Homo sapiens
Ovis aries

platform_organism:
Homo sapiens
Ovis aries

overall_design: snRNA-seq was applied to: 1) six patients for the simulated dataset (sequenced by 1-sample-per-lane); 2) four patients for the real-world dataset (sequenced by 2-sample-per-lane); 3) four patients for the application dataset (sequenced by 4-sample-per-lane); 4) 2 samples for the species-mixed dataset (1 human, 1 sheep).

first: Yile

last: Fu

first: Mohamad

last: Youness

first: Alessia

last: Virzì

first: Xinran

last: Song

first: Michiel

middle: R

last: Tubeeckx

first: Gilles

middle: W

last: De Keulenaer

first: Hein

last: Heidbuchel

first: Vincent

last: Segers

first: Karin

last: Sipido

first: Bernard

last: Thienpont

first: H


title: Benchmarking of Computational Demultiplexing Methods for Single-Nucleus RNA Sequencing Data [dataset 1]

overall_design: Six matching RNA-seq of the individual snRNA-seq experiments used for the simulated datasets


title: SGLT2 Inhibition Ameliorates Age-Dependent Renovascular Rarefaction

city: BAR HARBOR

first: CGDS

last: Data

state: ME

address: 159 OLD BAR HARBOR RD

institute: MDI Biological Laboratory

summary: Introduction: Aging is associated with progressive loss of renal function and vascular structure, with and without chronic kidney disease. However, the mechanisms driving renal vascular aging and potential therapeutic interventions remain poorly understood. Methods: To model this state-of-affairs, we used African turquoise killifish (Nothobranchius furzeri), a naturally short-lived vertebrate. We then inhibited the sodium-glucose co-transporter 2 inhibition (SGLT2i) to test a potential therapeutic intervention. Histological, immunofluorescent, and 3D vascular imaging were used to evaluate glomerular, tubular, and vascular changes. Single-nuclei transcriptomic profiling was performed on whole kidneys to identify age- and treatment-associated molecular signatures. Results: Aged killifish kidneys exhibited hallmark features of human renal aging, including glomerulosclerosis, tubular fibrosis, and vascular rarefaction. Functional changes included increased proteinuria and altered tubular transporter expression. Transcriptomic profiling revealed a metabolic shift from oxidative phosphorylation to glycolysis and upregulation of pro-inflammatory pathways. Aged vasculature also displayed a marked reduction in tight junctions and cell–cell contacts. Dapagliflozin attenuated age-related vascular rarefaction, preserved functional peritubular capillary networks, and reduced albuminuria by restoring a youthful transcriptional profile and enhancing intercellular signaling. However, fish lifespan was not extended. Conclusion: This study establishes the killifish as a translational model for investigating renal vascular aging. We show that SGLT2i preserves renal microvascular structure and function, reduces proteinuria, and reprograms the aged transcriptome. These results support a vascular-protective role of SGLT2i in mitigating age-related renal deterioration.

overall_design: Comparison betweeen young and old (untreated) and old treated killifish. Old untreated animals serve as control of physiological aging. Treatment was performed using the sodium-glucose-linked transporter 2 (SGLT2) inhibitor dapagliflozin. Male and Female fish were examined. The data presented is a pooled sample of approximatly 4-9 fish.

first: Anastasia

last: Paulmann

first: Matthew

middle: D

last: Cox

first: Tom

middle: Y

last: Boewer

first: Hannah

middle: M

last: Somers

first: Ryan

last: Seaman

first: Joel

last: Graber

first: Heath

last: Fuqua

first: Anchel

last: Mahajan

first: Cory

last: Johnson

last: Beverly-Staggs

first: Sonia

last: Sandhi

first: Heiko

last: Schenk

first: Hermann

last: Haller


title: Analysis of gene regulation by the TP63 isoforms deltaNp63alpha and deltaNp63beta in MCF10A cells

city: Albany

first: Morgan

middle: A

last: Sammons

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

summary: We analyzed the transcriptome changes of the basal mammary epithelial human cell line MCF10A in response to expression of the TP63 isoforms deltaNp63alpha or deltaNp63beta. The goal was to understand how these C-terminal isoforms of p63 might differentially regulate gene expression.

overall_design: PolyA+ RNAseq (in biological triplicate) of MCF10A cell lines expressing either control (vector only), human deltaNp63alpha, or deltaNp63beta in induced (+ doxycycline) conditions for 24hrs.

first: Morgan A.


title: Single cell immunophenotyping of the Lyme erythema migrans lesion

first: Hailong

last: Meng

address: 300 George Str

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

overall_design: Refer to individual Series


title: Viral Infection Induces Alzheimer’s Disease-Related Pathways and Senescence in iPSC-Derived Neuronal Models

city: Brno

first: Katerina

last: Amruz Cerna

state: Czech Republic

address: Kamenice 3

department: Department of Histology and Embryology

country: Czech Republic

institute: Faculty of Medicine, Masaryk University

summary:
The Pathogen Infection Hypothesis proposes that amyloid-β (Aβ) functions as an antimicrobial peptide, with pathogen-induced aggregation potentially contributing to Alzheimer’s disease (AD) pathology.
We used human iPSC-derived 2D neurons and 3D cerebral organoids from wild-type and familial AD (PSEN1/2 mutant) lines to model acute infections with HSV-1 and TBEV and Aβ aggregation.
Transcriptomic and proteomic analyses were performed to assess molecular responses.
HSV-1, but not TBEV, induced robust APP clustering in 2D and 3D models, dependent on extracellular Aβ levels. Transcriptomic profiling revealed widespread HSV-1-induced changes, including activation of neurodegeneration-related pathways.
Proteomic profiling confirmed the enrichment of neurodegeneration- and senescence-associated secretome signatures. PSEN1/2 mutations did not alter the acute infection response. Reanalysis of independent datasets confirmed our findings and revealed a limited protective effect of acyclovir.
HSV-1 infection triggers APP aggregation, neuroinflammation, and cellular senescence in human brain models, supporting a causal role in AD pathogenesis.

overall_design:
For transcriptomic analysis, total RNA was extracted from single organoids using the Direct-zol RNA Microprep Kit (R2062, ZymoResearch) after UV inactivation and PBS washing.
Biological replicates from six independent iPSC lines (WT1-3, AD1-3) were pooled per condition (non-treated=NTR, HSV-1, TBEV).
Only RNA samples with RINe ≥ 7.5 were processed for library preparation using the QuantSeq FWD 3’ mRNA Library Prep Kit (Lexogen), and sequencing was performed on a NextSeq 500 system (Illumina), generating ~10 million reads per sample.

first: Hana

last: Hribkova

first: Veronika

last: Pospisilova

first: Tereza

last: Vanova

first: Jan

last: Haviernik

first: Jiri

last: Sedmik

first: Ondrej

last: Bernatik

first: Jaroslav

last: Olha

last: Raska

first: Sona

last: Cesnarikova

first: Miriam

last: Satkova

first: Klara

last: Plesingrova

first: Petra

last: Strakova

first: Andrea

last: Fortova

first: Katarina

last: Gresova

first: Manolis

last: Maragkakis

first: Michaela

last: Sadibolova

first: Rudolf

last: Kupcik

first: Ivo

last: Fabrik

first: Marie

last: Vajrychova

last: Sheardova

first: Daniel

last: Ruzek

first: Dasa

last: Bohaciakova


title: Immune cell single-cell RNA sequencing analyses link an age-associated T cell subset to symptomatic benign prostatic hyperplasia

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

summary: Benign prostatic hyperplasia (BPH) is among the most common age-associated diseases in men. Whether age-related changes in immune cells, termed immunosenescence, contribute to BPH is not clear. Specific T cell populations, in particular a subset of CD8+ T cells with high Granzyme K (GZMKhi) and low Granzyme B (GZMBlow) gene expression, have been associated with aging; however, the precise function and biological significance of these cells in age-related diseases is not known. The current study determine that Taa cells infiltrate aged human prostates and positively correlate with International Prostate Symptom Score (IPSS). A velocity analysis indicated that CD8+ T cell differentiation is altered in large BPH prostates compared to small age-matched prostates. In vitro granzyme K treatment of human BPH patient-derived large prostate fibroblasts increased secretion of senescence-associated secretory phenotype (SASP)-associated cytokines. These data suggest that granzyme K-mediated stimulation of prostate stromal fibroblast SASP cytokine and chemokine production promotes prostate immune cell recruitment and activation. Overall, these results connect symptomatic BPH with immune aging.

overall_design: For aged prostate tissues, transitional zone (TZ) tissue was excised from each collected large (≥90 grams) and small (≤40 grams) prostates. Tissues were digested and RNA was extracted.  Poly A selection was employed to capture mRNA transcripts, which were then sequenced by Novogene. Bulk RNA-seq paired-end 150 bp reads were sequenced by Novogene.

first: Broman

last: Meaghan

first: Lanman

last: Nadia A

first: Vickman

last: Renee

first: Cresswell

last: Greg

first: Kothandaraman

last: Harish

first: Kolliegbo

last: Andree

first: Sebastian Paez Paez

last: Juan

first: Glaser

last: Alexander

first: Helfand

last: Brian

first: Henry

last: Gervaise

first: Strand

last: Douglas

first: Franco

last: Omar

first: Hayward

last: Simon

first: Ratliff

last: Timothy


title: RNA sequencing reveals differential MYC-driven gene expression as a driver of a divergent cholangiocyte response to stress

first: Alexander

middle: Quinn

last: Wixom

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: In Primary Sclerosing Cholangitis (PSC), some cholangiocytes undergo cell cycle arrest (senescence) while others proliferate (ductular reaction). Our aim was to determine the mechanisms driving this divergent response. We used lipopolysaccharide (LPS) to stress normal human cholangiocytes (NHC) transfected with a senescence reporter, p16- promoter driven green fluorescent protein. We performed RNA sequencing to assess gene expression profiles on non-senescent (GFP-) and senescent (GFP+) cholangiocytes. Our analysis revealed a MYC-driven gene expression profile in non-senescent cholangiocytes and suggest that MYC may function as a "molecular switch" in determining cholangiocyte responses to stress.

overall_design: NHCs were stably transfected with a p16-promoter driven green fluorescent protein (GFP) reporter (p16-GFP-NHC) and cultured in the presence or absence of the cellular stressor LPS in our in vitro model of experimentally induced NHC senescence. The cells were collected and standard fluorescence activated cell sorting (FACS) analysis was performed. We then performed RNA sequencing analysis on the non-senescent (GFP-) and senescent (GFP+) cell populations.

first: Steven

last: O'Hara

first: Patrick

last: Splinter

first: Nicholas

last: LaRusso


title: Dnmt3a2 expression during embryonic development is required for phenotypic stability

city: Grand Rapids

first: Peter

last: Jones

state: MI

address: 333 Bostwick Ave NE

department: Center of Epigenetics

institute: Van Andel Research Institute

type: Methylation profiling by genome tiling array

summary: Proper function and switching of regulatory elements is essential for the development of vertebrates and is known to be controlled by DNA cytosine methylation. We used isoform-specific knockouts of the two known DNA methyltransferase variants, Dnmt3a1 and Dnmt3a2 to probe their roles in regulatory element methylation in embryogenesis and in postnatal development. Mouse embryos lacking Dnmt3a1 showed minimal loss of genomic methylation confirming that this isoform may not be directly involved in embryonic development. However, they were smaller than their littermates and died about 4 weeks after birth with considerable postnatal demethylation as has been previously reported. On the other hand, embryos lacking Dnmt3a2 showed widespread genomic hypomethylation which was particularly prevalent at enhancers, CTCF sites and imprinted  genes. Interestingly these methylation deficits were largely repaired after birth, presumably by the remaining Dnmt3a1 isoform. The mice lacking Dnmt3a2 were viable; however, they showed an increased prevalence of sporadic abnormalities as previously observed at a low frequency in laboratory mice, including anophthalmia, hydrocephalus, hydronephrosis and male infertility phenotypes. Interestingly, hypomethylation of several imprinted genes  was also observed in sperm which might explain the infertility phenotype.  Therefore, the interaction between the two isoforms is developmentally regulated, with Dnmt3a2 playing a key role in ensuring the methylation states of enhancers, CTCF sites and imprinted genes, thereby reducing the likelihood of stochastic phenotypes emerging after birth.

overall_design: We investigated the DNA methylation changes that might be associated with the stochastic developmental defects observed in Dnmt3a2-/- mice compared to their WT litter mates, focusing on two critical developmental windows: E15.5, and 21 days postnatal (PD 21). These time points were selected to capture methylation dynamics during peak embryonic DNA methylation establishment (E15.5) and during postnatal tissue maturation (PD 21). We also determined DNA methylation changes in Dnmt3a1-/- mice compared to their WT litter mates at these time points. To examine tissue-specific DNA methylation patterns, we isolated brain and liver tissues and used the Illumina MM285 Infinium Methylation EPIC array to perform genome-wide methylation analysis.

first: Minnin

last: Liu

first: Guillermo

last: Urrutia


title: Phenotypic and Functional Characterization of Oncohistone Mutations in Breast Cancers

city: Dallas

first: W. Lee

last: Kraus

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center


title: Phenotypic and Functional Characterization of Oncohistone Mutations in Breast Cancers [RNA-seq]

summary: Although mutations in genes encoding histones display a similar prevalence to that of some other somatic mutations in cancer, the underlying mechanisms by which histone mutations drive tumorigenesis have not been fully explored.  Herein, we curated missense mutations occurring in core histone genes in breast cancers using data from MSK-IMPACT and cBioPortal to identify high frequency breast cancer-associated histone gene mutations.  We characterized 17 high frequency oncohistone mutations in H2A H2B, and H3 that are enriched in breast cancer samples and occurred at glutamate (E), aspartate (D), serine (S), and arginine (R) residues.  Many of these mutants co-occur with PIK3CA mutations in breast cancer samples.  The oncohistone mutants were expressed in MCF-7 breast cancer cells or MCF10A mammary epithelial cells and screened for effects on oncogenic phenotypes in a variety of cell- and tumor-based assays (i.e., proliferation, migration, invasion, competitive outgrowth, transformation).  In addition, we examined the effects of selected mutants on DNA damage, gene expression, and posttranslational modification of histones (e.g., acetylation, phosphorylation, methylation, ADP-ribosylation).  Our results indicate that the collection of oncohistone mutants that we screened have varying phenotypic and functional effects.  Some can promote cancer-related phenotypes and may act as potential cancer drivers, with H2B-E76K/Q, H3-E97K, and H3-E105K eliciting strong cancer phenotypes.  These observations can be used as a resource to connect biological and molecular outcomes to oncohistones in breast cancers.

overall_design: RNA-seq for MCF-7 cells ectopically expressing oncohistone H2B and H3 mutants.

first: Andrea D

last: Edwards

first: Yangyang

last: Dai

first: Siddharth

last: Singh

first: Micah

last: Thornton

first: Tulip

last: Nandu

first: Ralf

last: Kittler

first: Cristel V

last: Camacho

first: Dan

last: Huang

first: W


title: The transitional cerebellar progenitor is a technical artifact driven by low-quality cells [re-analysis]

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: We reprocessed the raw FASTQ files from the published single-cell RNA-seq atlas of the developing human cerebellum (accession GSE198565) and, following rigorous quality control, removed low-quality cells and refined the cell-type annotations.

overall_design: Both raw scRNA-seq FASTQs and cellranger mapping outputs from the fetal human cerebellar atlas (accession GSE198565, sample GSM5952337), were obtained and reprocessed using the same parameters described in the publication. FASTQ files for GSM5952337 were provided by the submitter. FASTQ files were mapped with CellRanger (V3.2, the same as the cellranger outputs provided) and cell type annotations were adopted from the original publication (GSE198565). The dataset was composed of 95,542 cells collected from fetal cerebella of eight individual donors. Additional QC metrics were calculated for each sample utilizing CELLBENDE and DropletQC. UMAP coordinates were all calculated using cosine distance between the top 100 nearest neighbors based on the first 50 principal components. Unsupervised clustered were determined using leiden clustering at a resolution of 0.8 as implemented in scanpy.

first: Kyle

middle: S

last: Smith

first: Yiran

last: Li

first: Brian

last: Gudenas


title: Single cell immunophenotyping of the Lyme erythema migrans lesion (GEX)

first: Hailong

last: Meng

summary: The skin lesion erythema migrans (EM) is the first clinical sign of Lyme disease, an infection due to the tick-transmitted bacterium Borrelia burgdorferi (Bb). Previously we used single cell transcriptomics with B cell and T cell receptor sequencing to characterize the cutaneous immune response in the EM lesion, focusing on B cells. Here, in an expanded sample size, we profiled T cell responses in the EM lesions in comparison to autologous uninvolved skin. In addition to CD4+IFNG+ T cell subsets known to be abundant in the EM, we identified clonal expansion of CD8+GZMK+IFNG+ T cells that comprised the only T cell population with significant differential expression of interferon regulated genes.  This subset included IFNG+ cells with low cytotoxic gene expression, which may promote inflammation.  While FOXP3+ regulatory T cells also were increased in EM, we found that the CD4+FOXP3- effector T cell subset contained cells with the highest differential expression of IL-10.  Fibroblasts, endothelial cells, and pericytes expressed a broader array of chemokines than macrophages. These studies represent the first comprehensive interrogation of the cutaneous T cell response to Bb infection using single cell transcriptomics and provide insight into the orchestration of the skin immune response to this vector-borne pathogen.

overall_design:
we performed single-cell RNA sequencing using 10x Genomics on PBMCs and whole skin cell digests of biopsies of paired EM lesions and autologous uninvolved skin from 13 subjects with Lyme disease.

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

last: Edel

first: Meng

last: Hailong

first: Linda

last: Bockenstedt

first: Kleinstein

last: Steven


title: A molecular circuit regulates fate plasticity in emerging and adult AT2 cells [scRNA-seq]

first: Douglas

middle: Glenn

last: Brownfield

address: 200 First St. SW

summary: Alveolar AT1 and AT2 cells are vital for gas exchange in the lung and become compromised in several common and deadly diseases. While the signals driving differentiation of either cell type have been identified, it remains unclear when and how fate plasticity is regulated in the emerging and adult alveolar epithelium. Here we show AT2s first emerge as singletons at zones between the proximal stalks and distal tips of the embryonic lung that quickly extrude and can traverse the interstitium to connect with nearby epithelium, a process we term interlumenal junctioning. Throughout the late embryonic and early perinatal period, we find that a window of AT2 fate plasticity exists that is closed by the bZIP transcription factor C/EBPα, mediated by its transcriptional suppression of the Notch signaling regulator DLK1. C/EBPα acts on Dlk1 at a novel regulatory site. Further, both Dlk1 and Cebpa are regulated by the polycomb repressive complex (PRC2), and together constitute a novel incoherent feedforward loop that generates a Dlk1 pulse upon downregulation of PRC2. We propose these form a “pulse generator” circuit capable of generating a timed activation of Notch signaling, resulting in a “salt and pepper” pattern of AT1 and AT2 fate. Following injury in the adult lung, we found that C/EBPα downregulation is required for re-accessing AT2 fate plasticity and is mediated by the dominant negative C/EBP family member CHOP. Finally, we observe Cebpa loss also activates a “defender” AT2 state enriched in interferon-stimulated antipathogenic gene expression that is distinct from its reparative state and propose AT2s toggle between these states following infection to robustly protect and repair alveoli.

overall_design: Single Cell RNAseq of lineage label AT2s of wildtype and Cebpa floxed in perinatal day (day 11-25)

first: Amitoj

last: Sawhney

first: Junming

last: Cai

middle: G


title: Cell-type-specific contributions to impaired blood-brain barrier and altered cerebral metabolism in prodromal 5XFAD mice

last: Sun

state: MA

address: 455 Main St

department: EECS

summary: Single-nucleus RNA sequencing (snRNA-Seq) further revealed cell type-specific transcriptomic changes in the hippocampus of prodromal 5XFAD mice, including downregulation of synaptogenesis and synaptic transmission genes in the CA1 and dentate gyrus excitatory neurons, impaired endothelia gene expression linked to brain barrier function and angiogenesis, altered innate immune response genes in astrocytes, as well as upregulation of cholesterol biosynthesis and metabolism genes in the CA1 excitatory neurons.

overall_design: We performed snRNA-seq in mouse hipppcampus from 3 months old 5xFAD and wild type mice with and without blood vessel enrichment.

first: Wenzhen

last: Duan


title: FRA1 drives melanoma metastasis through an actionable transcriptional network

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

summary: Transcriptional dysregulation has emerged as a critical driver of melanoma progression, yet the molecular mechanisms governing this process and their potential as therapeutic targets remain inadequately characterized. Here, we identify FRA1 as a potent and actionable driver of melanoma metastasis. FRA1 enhanced both the initial seeding and subsequent outgrowth of metastatic lesions. Comprehensive multi-omics integration revealed transcriptional target genes of FRA1, with AXL, CDK6, and FSCN1 exhibiting increased expression in melanoma metastasis and a significant correlation with poor patient outcomes. Silencing AXL, CDK6, or FSCN1 abrogated FRA1-mediated invasion in vitro and reduced metastatic colonization. Furthermore, pharmacological inhibition of CDK6 and FSCN1, and to a lesser extent AXL, suppressed melanoma metastasis and prolonged overall survival. The expression of FRA1 and its target genes correlates with shortened survival across multiple cancer types, highlighting the broader clinical relevance of this pathway. This study unveils an actionable FRA1-mediated transcriptional network that drives cancer progression and metastasis, offering potential avenues for therapeutic interventions.

overall_design: RNAseq and Cut&Run profiling of A375 and 1205Lu cells treated with siRNAs targeting human FRA1.

first: Xiaonan

last: Xu

first: Manon

last: Chadourne

first: Zulaida

last: Soto-Vargas

first: Vinesh

last: Jarajapu

first: Jiqiang

last: Yao

first: Xiaoqing

last: Yu

first: Florian

last: Karreth


title: Divergent regulatory element programs steer sex-specific supporting cell differentiation along mouse gonadal development

city: Antwerp

first: Valeriya

last: Malysheva

state: Select State

address: Universiteitsplein 1, Building V

institute: VIB Center for Molecular Neurology

summary: Gonadal sex determination relies on tipping a delicate balance involving the activation and repression of several transcription factors and signalling pathways. This is likely mediated by numerous non-coding regulatory elements that shape sex-specific transcriptomic programs. To explore the dynamics of these in detail, we performed paired time-series of transcriptomic and chromatin accessibility assays on pre-granulosa and Sertoli cells throughout their development in the embryo, making use of new and existing mouse reporter lines. Regulatory elements were associated with their putative target genes by linkage analysis, and this was complemented and verified experimentally using promoter capture Hi-C. We identified the transcription factor motifs enriched in these regulatory elements along with their occupancy, pinpointing LHX9/EMX2 as potentially critical regulators of ovarian development. Variations in the DNA sequence of these regulatory elements are likely to be responsible for many of the unexplained cases of individuals with Differences of Sex Development.

overall_design: Capture Hi-C: 3 libraries of E13.5 Sox9IRES-GFP Sertoli cells and 2 libraries of E13.5 Enh8-mCherry pre-granulosa cells were generated from ~100,000 sorted cells.

first: Isabelle

last: Stévant

first: Elisheva

last: Abberbock

first: Meshi

last: Ridnik

first: Roni

last: Weiss

first: Linoy

last: Swisa

first: Christopher R

last: Futtner

first: Danielle

last: Maatouk

first: Robin

last: Lovell-Badge

first: Nitzan

last: Gonen


title: Single cell immunophenotyping of the Lyme erythema migrans lesion (TCR)

first: Hailong

last: Meng

overall_design: we performed single-cell RNA and B cell receptor sequencing using 10x Genomics on PBMCs and whole skin cell digests of biopsies of paired EM lesions and autologous uninvolved skin from 13 subjects with Lyme disease.

first: Aron

last: Edel

first: Meng

last: Hailong

first: Linda

last: Bockenstedt

first: Kleinstein

last: Steven


title: Hepatocyte FoxO1 depletion exacerbates hepatic inflammation in MASH

city: Guangzhou

first: Yongjian

last: zhou

address: No.1, Pan Fu Road, Yuexiu District

institute: Guangzhou First People’s Hospital

summary: The transcription factor Forkhead box protein O1 (FoxO1) is a well-established regulator of glucose and lipid metabolism, yet its role in metabolic dysfunction-associated steatohepatitis (MASH) pathogenesis remains debated. This study investigates hepatocyte-specific FoxO1 mechanisms driving hepatic inflammation in MASH. Using hepatocyte-specific FoxO1-knockout (KO) mice fed a methionine-choline-deficient diet and LPS-treated FoxO1-KO cells, we demonstrate FoxO1 depletion exacerbates hepatic inflammation, ballooning degeneration, and upregulates TNF-alpha, CXCL8, and CXCL2 in vivo and in vitro. Transcriptomics linked FoxO1 deficiency to enriched pro-inflammatory pathways and suppressed cysteine/methionine metabolism.

overall_design: HepG2 WT and FoxO1-KO cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum and 1% antibiotic . The cells were collected for transcriptome sequencing after treatment with 1μg/mL LPS for 24 h.

last: Zhou

first: Huiting

last: Chen

first: Chen

last: Huang

first: Hanqing

first: Yong-Qiang

last: Li

first: Jiemin

last: Cheng

first: Siqi

last: Yang

first: Jiawei


title: Gene expression profiling of human umbilical vein endothelial cells overexpressing CELF2 as diagnostic targets in diabetes-induced erectile dysfunction

city: Urumqi

first: daniyaer

last: nuerdebieke

state: 新疆

address: Urumqi

department: Urology Center

institute: People's Hospital of Xinjiang Uygur Autonomous Region

summary: Background: Erectile dysfunction (ED) is a common complication of diabetes mellitus (DM), and because of its complex neurovascular etiology, the associated molecular pathogenic mechanisms are not fully understood. This study investigated the important functions and potential molecular regulatory roles of CELF2 in DMED. Methods: An in vitro HUVEC model with CELF2 overexpression was successfully established via transfection with a CELF2-overexpressing lentiviral vector. The effects of CELF2 overexpression on cell proliferation and angiogenesis were assessed via CCK-8 and angiogenesis assays. RNA sequencing was employed to evaluate the gene expression profiles and alternative splicing events regulated by CELF2. An RNA-sequencing assay was performed to evaluate gene expression profiles and alternative splicing genes in HUVECs overexpressing CELF2, and an integration analysis was combined with GSE146078 data to detect potential target genes related to DMED. Results: The expression of genes related to angiogenesis and the immune response significantly increased with CELF2 overexpression, and the four hub genes associated with alternative splicing in aging and angiogenesis were CXCL2, CXCL10, IL-1A and IL-6. Conclusions: CELF2 appears to be a key factor in DMED, influencing gene expression and alternative splicing related to angiogenesis and immune responses. The identified hub genes (CXCL2, CXCL10, IL-1A, and IL-6) are closely related to DMED and warrant further investigation to understand the underlying mechanisms and potential therapeutic implications. Keywords: Diabetes mellitus; Erectile dysfunction; RBPs; CELF2; RNA sequencing

overall_design: This study utilized human umbilical vein endothelial cells (HUVECs) overexpressing the RNA-binding protein CELF2 to investigate its regulatory roles in gene expression, alternative splicing, and angiogenesis, identifying hub genes (CXCL2, CXCL10, IL-1A, IL-6) associated with diabetes-induced erectile dysfunction (DMED).

first: Daniyaer

last: Nuerdebieke

first: Lizhong

last: Yao

first: Lange

last: Guo

first: Jiuzhi

first: Hongliang

last: Jia

first: Yukui


title: Single-cell characterization of enterovirus infection of spinal cord organoids

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

summary: The mechanisms by which enteroviruses, particularly enterovirus D-68 (EV-D68) and enterovirus A-71 (EV-A71), contribute to acute flaccid myelitis (AFM), a severe neurological condition characterized by sudden muscle weakness and paralysis, remain poorly understood. To investigate the cellular tropism and infection dynamics of these enteroviruses, we utilized human spinal cord organoids (hSCOs) derived from induced pluripotent stem cells (iPSCs). We performed single-cell RNA sequencing (scRNA-seq) to profile the cellular composition of hSCOs and identify infected cell types post-infection. We found that hSCOs exhibit a diverse cellular landscape, including neurons, astrocytes, oligodendrocyte progenitor cells (OPCs), and multipotent glial progenitor cells (mGPCs), with astrocytes predominant in earlier developmental stages and neurons more abundant in later stages. Upon infection with two EV-D68 strains (US/IL/14-18952 and US/CO/18-23089) and one EVA71 strain (Tainan/4643/1998), we observed distinct viral tropism. EV-D68-18952 showed a significant increase in infected neurons, while EV-D68-23089 exhibited higher infection rates in cycling astrocytes and OPCs. In contrast, EVA71 demonstrated a broader tropism, with a statistically significant increase in infected mGPCs, suggesting enhanced infection efficiency across multiple cell types. These findings provide novel insights into the cell-type specificity of EV-D68 and EVA71 in the spinal cord, offering a deeper understanding of potential mechanisms underlying AFM pathogenesis. Understanding the dynamics of infection at single-cell resolution will inform future therapeutic strategies aimed at mitigating the neurological impact of enteroviral infections.

overall_design: Human spinal cord organoids (hSCOs) were infected in pools of 12 organoids each and inoculated with virus at 105 PFU/pool. After 1 hour of incubation at room temperature, hSCOs were washed 3X with PBS and moved to new wells before incubation with fresh medium. No further media changes were performed for the rest of the experiment. The EV-D68 infected pool was incubated at 33oC and EV-A71 at 37oC for 48 hours post infection (hpi). After 48hpi, the pools were dissociated to a single-cell suspension with Accumax (Invitrogen). They were incubated for 15 minutes in the water bath at 37℃, gently mixed, and then proceeded with the proposed 10X Genomics protocol (Cell Preparation Guide - CG00053 Rev C). Once the cell's concentration is achieved the cells are moved to analyze using scRNA-seq.

first: Nathânia

last: Dábilla

first: Sarah

last: Maya

first: Colton

last: McNinch

first: Taylor

last: Eddens

first: Patrick

middle: T

last: Dolan

first: Megan

last: Freeman