title: Single cell RNA sequencing to study the in vivo behaviour of allogeneic HSC-derived MCAR-engineered NKT cells

city: Los Angeles

first: Lili

last: Yang

state: California

address: 610 Charles E. Young Dr. East

department: Microbiology Immunology & Molecular Genetics

institute: University of California, Los Angeles

summary: Ovarian cancer (OC) poses a significant challenge due to frequent recurrence linked to tumor heterogeneity and an immunosuppressive tumor microenvironment (TME). Targeting both OC cells and TME simultaneously holds promise for effective treatment. This study comprehensively analyzed 17 chemonaive and 18 refractory/recurrent OC samples, identifying mesothelin (MSLN) and natural killer receptor (NKR) ligands as tumor targets and CD1d as an OC TME target. Leveraging hematopoietic stem cell (HSC) gene engineering and feeder-free differentiation culture, we generated allogeneic MSLN-targeting CAR (MCAR)-engineered invariant natural killer T (MCAR-NKT) cells, demonstrating high-yield and high-purity production, potent antitumor efficacy, multiple tumor targeting mechanism, and significant in vivo expansion and persistence. Notably, these cells selectively deplete immunosuppressive TAMs and MDSCs, counteract tumor immune evasion, display a favorable safety profile with low risks of GvHD and CRS, and exhibit a stable “hypoimmunogenic” phenotype attributed to epigenetic and signaling regulations. These findings underscore the feasibility and therapeutic potential of allogeneic MCAR-NKT cell products for OC, laying a foundation for further translation and clinical development.

overall_design: Gene expression profiling of tumor cells in an in vivo study using an OVCAR8-FG human OC xenograft NSG mouse model

first: Yan-Ruide

last: Li

first: Zhe

first: Miao

first: Yuning

last: Chen

first: Yichen

last: Zhu


title: H3K4 methylation-promoted transcriptional memory supports faithful zygotic genome activation and development

status: Public on Jul 29 2025

city: Munich

first: Eva

last: Hoermanseder

state: Bavaria

address: Feodor-Lynen-Str. 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Center Munich

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Accurately established transcriptional programs are paramount for successful embryonic development. At zygotic genome activation, gene expression is initiated for the first time in the life of an embryo. Pioneer transcription factors present in the embryo are essential for this process, however, the role of active chromatin modifications is less clear. It is unknown if active chromatin modifications established in the gamete are propagated in the embryo as epigenetic memory to support zygotic genome activation and development. Here, we provide evidence that in Xenopus laevis, H3K4 methylation contributes to epigenetic memory of active chromatin states, which is required for faithful zygotic genome activation and successful embryonic development. We find that chromatin configurations of promoters displaying high H3K4me3 intensity and breadth, alongside DNA hypomethylation and increased GC content, are maintained from the gametes to the embryo across multiple cell divisions and a transcriptionally quiescent phase in early development. We show that this maintenance of H3K4 methylation is essential for precise zygotic genome activation. Finally, we demonstrate that Kmt2b and Cxxc1 facilitate transcription-independent maintenance of H3K4me3 and proper zygotic gene expression. In summary, our study establishes a role for H3K4 methylation for memory of active chromatin states in embryos and reveals its importance for successful embryonic development.

overall_design: Profiling of H3K4me3 occupancy using CUT&RUN of H4K4me3-depleted Xenopus laevis embryos via Kdm5b-wt and H3.3-K4M mRNA mutant overexpression  at mid-ZGA stage (6.5hpf). Kdm5b-ci (catalytically inactive) plus H3.3-wt were overexpressed as the respective control conditions. Treatments were performed either in a developmental "window" from zygote to ZGA, or "persistently" from zygote onwards.

first: Meghana

middle: S

last: Oak

first: Marco

last: Stock

first: Matthias

last: Mezes

first: Tobias

last: Straub

first: Antony

middle: M

last: Hynes-Allen

first: Jelle

last: van den Ameele

first: Ignasi

last: Forne

first: Andreas

last: Ettinger

first: Axel

last: Imhof

first: Antonio

last: Scialdone

last: Hörmanseder


title: Human DICER1+/- RMS tumors are enriched for neutrophils [bulk RNA-seq]

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hospital

type: Expression profiling by high throughput sequencing

summary: We used RNA-seq from to compare the transcriptome of human FFPE diagnostic DICER1+/+ and DICER1+/- RMS tumor samples. We observed that human DICER1+/- RMS tumor were enriched for neutrophil transcripts.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human FFPE diagnostic DICER1+/+ and DICER1+/- RMS tumor samples

first: Randolph

middle: K

last: Larsen

first: Mark

middle: E

last: Hatley

first: Kris

middle: A

last: Schultz


title: Non-cell autonomous tumor promotion in DICER1 cancer predisposition

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series

last: Larson


title: ASD+/+ and ASD+/- tumor stroma gene expression microarray comparison [microarray]

summary: We used a microarray to compare bulk gene expression differences between ASD+/+ and ASD+/- tumor stroma. We observed enrichment for neutrophil transcripts in ASD+/- stroma compared to ASD+/+

overall_design: Tumors were digested and then isolated by Fluorescence-activated cell sorting (FACS) into Tumor (PECAM1-;tdTomato+) and Stroma (PECAM1-;tdTomato-) cells prior to gene expression microarray

first: Jason

last: Hanna

first: Catherine

middle: J

last: Drummond

first: David

last: Finkelstein


title: An IFN/STAT1/CYBB Axis Defines Protective Plasmacytoid DC to Neutrophil Crosstalk in Aspergillus fumigatus Infected mice

city: New York

first: YAHUI

last: GUO

state: NY

address: 407 East 68th street, ZRC1641

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center (MSKCC)


title: An IFN/STAT1/CYBB Axis Defines Protective Plasmacytoid DC to Neutrophil Crosstalk in Aspergillus fumigatus - Infected mice [ATAC-seq]

summary: Aspergillus fumigatus is the most common cause of invasive aspergillosis (IA), a devastating infection in immunocompromised patients. Plasmacytoid dendritic cells (pDCs) regulate host defense against IA by enhancing neutrophil antifungal properties in the lung. Here, we define the pDC activation trajectory during A. fumigatus infection and the molecular events that underlie the protective pDC - neutrophil crosstalk. Fungus-induced pDC activation begins after bone marrow egress and results in pDC-dependent regulation of lung type I and type III IFN levels. These pDC-derived products act on type I and type III IFN receptor-expressing neutrophils and control neutrophil fungicidal activity and reactive oxygen species production via STAT1 signaling in a cell-intrinsic manner. Mechanistically, neutrophil STAT1 signaling regulates the transcription and expression of Cybb, which encodes one of five NADPH oxidase subunits. Thus, pDCs regulate sterilizing immunity against inhaled molds by controlling the local expression of a subunit required for functional NADPH oxidase assembly and activity in the lung.

overall_design: lung pDCs and neutrophils sorted from indicated genotype mice, at naïve or infected (72h pi) status

first: Yahui

last: Guo

first: Mariano

last: Aufiero

first: Kathleen

last: AMills

first: Simon

last: Grassmann

first: Hyunu

last: Kim

first: Mergim

last: Gjonbalaj

first: Paul

last: Zumbo

first: Audrey

last: Billips

first: Katrina

middle: B

last: Mar

first: Yao

last: Yu

first: Laura

last: Tirado

first: Lena

last: Heung

first: Amariliz

last: Rivera

first: Doron

last: Betel

first: Joseph

middle: C

last: Sun

last: Hohl


title: Identification of candidate long non-coding RNAs and mRNAs associated with heart aging in mice

city: Shanghai

first: Zheng

last: Kuai

address: No180 fenglin Road

country: China

institute: Zhongshan Hospital Fudan University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To further development of our gene expression approach to aging, we have employed lncRNA/mRNA microarray expression profiling as a discovery platform to identify genes with the potential to distinguish cardiac aging. We collected hearts from 3-month-old and naturally aged 20-month-old mice, respectively. Age-related differentially expressed lncRNAs and mRNAs were obtained by the method of RNA sequencing microarray of mouse heart tissue.

overall_design: Age induced gene expression was measured in 3-month-old mouse heart and 20-month-old mouse heart . Five independent experiments were performed at each group（3m and 20m） using different donors for each experiment.

first: Yu

last: Hu


title: BRD9 Dictates Oncolytic Virus Resistance in Glioblastoma

city: Hangzhou

first: Zhilin

last: Long

address: No. 600 Dunyu Road Sandun Town

institute: Westlake University

summary: Glioblastoma multiforme (GBM) treatment is a persistent challenge for oncologists, and this challenge has motivated the exploration of novel therapeutic strategies such as oncolytic virus therapy. Despite recent advancements in oncolytic virus therapy clinical trials for glioblastoma, a substantial number of patients have shown limited responses to this treatment. Here, we performed CRISPR‒Cas9 knockout screening and identified non-canonical BRG1/BRM-associated factor (ncBAF) complex as a pivotal determinant of oncolytic virus resistance. Knockout of the ncBAF-specific subunit Bromodomain-containing protein 9 (BRD9) markedly augmented the antitumor efficacy of oncolytic herpes simplex virus type 1 (oHSV1), as evidenced by our in vitro and in vivo studies. Mechanistically, BRD9 bound to RELA, a key transcription factor in the nuclear factor-κB (NF-κB) signaling pathway, to potentiate the expression of downstream antiviral genes. The application of a small molecule inhibitor targeting BRD9 (IBRD9) significantly enhanced oHSV1 activity against GBM across various models, including cell lines, patient-derived organoids, ex vivo cultured primary tumor slices, and mouse models. Moreover, reduced BRD9 levels correlated with improved patient outcomes in oHSV1 clinical trials. These findings highlight BRD9 as a prospective target for augmenting the effectiveness of oncolytic virus therapy against glioblastoma, providing insights for the development of novel combination treatments.

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for BRD9 in human glioblastoma stem cell line MGG4.

first: Chen

last: Guo

first: Qi

last: Xie


title: Effect of ADAR1 and MDA5 knock down by siRNA on human SMC phenotypic modulation and calcification in vitro

city: Stanford

first: Chad

last: Weldy

state: CA

address: 870 Quarry Road, CVRC Falk

department: Medicine, Cardiovascular Medicine

institute: Stanford University

summary: Mapping the genomic architecture of complex disease has been predicated on the understanding that genetic variants influence disease risk through modifying gene expression1. However, recent discoveries have revealed that a significant burden of disease heritability in common autoinflammatory disorders and coronary artery disease is mediated through genetic variation modifying post-transcriptional modification of RNA through adenosine-to-inosine (A-to-I) RNA editing2. This common RNA modification is catalyzed by ADAR enzymes, where ADAR1 edits specific immunogenic double stranded RNA (dsRNA) to prevent activation of the double strand RNA (dsRNA) sensor MDA5 (IFIH1)3,4. Multiple lines of human genetic data indicate impaired RNA editing and increased dsRNA sensing to be an important mechanism of coronary artery disease (CAD) risk2,5. Here, we provide a crucial link between observations in human genetics and the mechanistic cell biology leading to progression of CAD. Through analysis of human atherosclerotic plaque, we implicate the vascular smooth muscle cell (SMC) to have a unique requirement for RNA editing, and that MDA5 activation occurs in SMC phenotypic modulation — demonstrating a cell type and context specific role of RNA editing. We further show Adar1 controls SMC phenotypic state, is required to maintain vascular integrity, and controls progression of vascular calcification. Through this work, we describe a fundamental mechanism of CAD, where cell type and context specific RNA editing and sensing of dsRNA mediates disease progression, bridging our understanding of human genetics and disease causality.

overall_design: To investigate the role of ADAR1 and IFIH1 (MDA5) in regulating SMC phenotype in vitro, first we performed an in vitro assay using primary human coronary artery smooth muscle cells (HCASMC) and performed a phenotypic modulation assay with siRNA KD of ADAR1 or ADAR1 and IFIH1 and performed bulk RNA sequencing in both mature SMC phenotype (serum starved) and modulated SMC phenotype (serum stimulated). Second, we performed an in vitro assay of SMC calcification by culturing immortalized HCASMC cells in control or pro-calcification media for 7 days following siRNA KD of ADAR1, ADAR1 and IFIH1, or IFIH1 alone and performed bulk RNA sequencing.


title: Transcriptomes of somatic and germ line cells in the developing larval ovary of Drosophila melanogaster in wild type, hpoRNAi and ykiRNAi conditions.

city: Cambridge

first: Shreeharsha

last: Tarikere

state: Massachusetts

address: 16 Divinity Avenue, Biolabs

department: Organismic and Evolutionary Biology

institute: Harvard University

summary: Adult insect ovaries are made up of egg production structures called ovarioles, whose number is directly linked to fecundity and fitness. Ovariole number is directly determined by the number of cell stacks called terminal filaments in the larval ovary, which in turn is determined by the number of terminal filament cells available to form terminal filaments. Elucidating the developmental and genetic regulation of terminal filament cell proliferation is thus key to understanding the regulation of adult ovariole number and fitness. Our previous work showed that the Hippo signaling pathway, including the kinase hippo and the transcription factor yorkie, regulate terminal filament cell number in Drosophila melanogaster. To identify the specific transcriptional responses of ovarian cells to Hippo signaling during ovary development, we systematically measured mRNA expression in isolated pools of somatic and germ line cells from the Drosophila larval ovary at the beginning, middle and end of terminal filament formation using RNA-seq. We performed these RNA-seq experiments in wild type, hippoRNAi and yorkieRNAi genetic backgrounds at each of these three developmental stages.

overall_design:
We extracted RNA from Fluorescence Activated Cell Sorted (FACS) GFP-expressing somatic or germ line cells from the larval ovaries of Drosophila melanogaster at three stages - the beginning (72 hours After Egg Laying, h (AEL)), middle (96h AEL) and end (120h AEL) of terminal filament formation. We specifically marked either somatic or germ cells with GFP using somatic- and germ line-specific GAL4 drivers (w[*];P{w[+mW.hs]=GawB}bab1[PGAL4-2]/TM6B,Tb[1], abbreviated herein as bab:GAL4; Bloomington Drosophila Stock Center (BDSC) #6803 and P{w[+mC]=UAS-Dcr-2.D}1,w[1118];P{w[+mC]=GAL4-nos.NGT}40,  abbreviated herein as nos:GAL4; BDSC #25751 respectively). RNA-seq data from FACS-sorted somatic and germ line cells from wild type ovaries were previously reported in Bioproject PRJNA721702. In the present dataset we report RNA-seq data from FACS-sorted cells in loss of function conditions for two members of the hippo signaling pathway. We knocked down either hippo (using hpo:RNAi line BDSC #33614) or yorkie (using yki:RNAi line BDSC #34067) in either germ line or somatic cells at each of the three developmental stages. The targeted cells also expressed GFP, which was used to separate somatic and germ cells using FACS. Total RNA was isolated from each genetic background/stage/cell type in both control and knockdown conditions. In three biological replicates of each unique experimental condition, cDNA libraries were prepared for each sample from Poly-A enriched-RNA using PrepX kit (Takara 640096). These cDNA libraries were sequenced using a single end 50bp protocol in an Illumina HiSeq 2500 sequencer. Sequences obtained were checked for quality and replicates with 10 million or more reads were used for downstream differential expression analysis. Only one replicate each of sufficient quality was obtained for the early-stage germ line knockdown conditions. Data from these samples were not included in the final analysis but are deposited here.

Please note that the following control samples from GSE172015 have been re-used:

BioProject accession: PRJNA721702

GEO Sample  SRA Runs  BioSample   Title
==========  ========  =========   =====
GSM5239772  SRR14231550,SRR14231551 SAMN18736523  S_ctrl_Early_1
GSM5239773  SRR14231552,SRR14231553 SAMN18736522  S_ctrl_Early_2
GSM5239774  SRR14231554,SRR14231555 SAMN18736521  S_ctrl_Early_3
GSM5239775  SRR14231556,SRR14231557,SRR14231558,SRR14231559 SAMN18736535  S_ctrl_Mid_1
GSM5239776  SRR14231560,SRR14231561 SAMN18736534  S_ctrl_Mid_2
GSM5239777  SRR14231562,SRR14231563 SAMN18736533  S_ctrl_Mid_3
GSM5239778  SRR14231564   SAMN18736532  S_ctrl_Late_1
GSM5239779  SRR14231565   SAMN18736520  S_ctrl_Late_2
GSM5239780  SRR14231566   SAMN18736519  S_ctrl_Late_3
GSM5239781  SRR14231567,SRR14231568 SAMN18736518  G_ctrl_Early_1
GSM5239782  SRR14231569,SRR14231570 SAMN18736517  G_ctrl_Early_2
GSM5239783  SRR14231571,SRR14231572 SAMN18736516  G_ctrl_Early_3
GSM5239784  SRR14231573,SRR14231574 SAMN18736515  G_ctrl_Mid_1
GSM5239785  SRR14231575,SRR14231576,SRR14231577,SRR14231578 SAMN18736514  G_ctrl_Mid_3
GSM5239786  SRR14231579,SRR14231580 SAMN18736513  G_ctrl_Mid_4
GSM5239787  SRR14231581,SRR14231582,SRR14231583,SRR14231584 SAMN18736512  G_ctrl_Late_2
GSM5239788  SRR14231585,SRR14231586 SAMN18736511  G_ctrl_Late_3
GSM5239789  SRR14231587,SRR14231588 SAMN18736510  G_ctrl_Late_4

first: Guillem

last: Ylla

first: Cassandra

middle: G

last: Extavour


title: Single-cell gene expression profile of cultured mouse islet cells

city: Maebashi

first: Jun

last: Shirakawa

state: Gunma

address: 3-39-15, Showa-machi

department: Department of Diabetes and Metabolic Disorders

country: Japan

institute: Institute for Molecular and Cellular Regulation, Gunma University

summary: Dysregulated α-cell function contributes to the onset and progression of diabetes. Here, we report that the treatment with imeglimin, an anti-diabetes drug, prevents glucagon release and promotes α-to-β cell transdifferentiation through direct action on α-cells. Mechanistically, imeglimin reduces Gsα expression to attenuate EPAC2-mediated glucagon secretion induced by glucose or GIP in an insulin-independent fashion. MafB expression is downregulated by imeglimin to make α-cell transdifferentiate to β-cell. Imeglimin also upregulates CHOP expression, which partly contributes to the reduction in both Gsα and MafB expression to reduce glucagon secretion and induce α-cell dedifferentiation, without alteration of protein translation. Those pleiotropic effects of imeglimin on glucagon secretion and α-cell identity can be recapitulated by mouse models of diabetes in vivo. These data implicate the imeglimin-mediated regulation of α-cell plasticity as a novel component in diabetes therapy to correct islet functions.

overall_design: Pancreatic islets were isolated  from 8 weeks old male C57BL6J mice. The islets were cultured for 24 hours with or without 1 mM imeglimin under 3.9 mM  or 11.1 mM glucose.

first: Takahiro

last: Tsuno


title: Glioblastoma induce bone remodeling and dynamic change in the immune landscape of skull marrow and ACP5 macrophages

city: Bronx

first: Jinan

last: Behnan

state: New York

address: 1300 Morris Park Avenue

department: The Leo M. Davidoff Department of Neurological Surgery, Department of Microbiology & Immunology

institute: Albert Einstein College of Medicine

summary: We explore GBM induced changes in the immune landscape of skull marrow using single-cell RNA seq.

overall_design: Single-cell RNA-seq of skull marrow samples obtained from sham and brain tumor bearing mice.


title: Systematic characterization of single-cell full-length RNA isoforms in human colorectal cancer

city: Beijing

first: Ping

last: Lu

address: 5 Yiheyuan Road

institute: Peking University

summary: Dysregulated RNA splicing is a well-recognized characteristic of colorectal cancer (CRC); however, its intricacies remain obscure, partly due to challenges in profiling full-length transcript variants at single-cell level. Here, we employ high-depth long-read scRNA-seq to define the full-length transcriptome of colorectal epithelial cells in 12 CRC patients, revealing extensive isoform diversities and splicing alterations. Cancer cells exhibited increased transcript complexity, with widespread 3'-UTR shortening and reduced intron retention. Distinct splicing regulation patterns were observed between intrinsic-consensus molecular subtypes (iCMS), with iCMS3 displaying even higher splicing factor activities and more pronounced 3'-UTR shortening. Furthermore, we revealed substantial shifts in isoform usage that result in alterations of protein sequences from the same gene with distinct carcinogenic effects during tumorigenesis of CRC. Allele-specific expression analysis revealed dominant mutant allele expression in key oncogenes and tumor suppressors. Moreover, mutated PPIG was linked to widespread splicing dysregulation, and functional validation experiments confirmed its critical role in modulating RNA splicing and tumor-associated processes. Our findings highlight the transcriptomic plasticity in CRC and suggest potentially novel targets for splicing-based therapeutic strategies.

overall_design:
To investigate the heterogeneities of full-length transcriptome in CRC, we performed long-read scRNA-seq on CD45-EPCAM+ cells isolated from primary tumors (PT) and adjacent normal tissues (NT) of 12 CRC patients.

***************************************************************
The raw data have been deposited at The Genome Sequence Archive for Human (GSA-Human) under accession codes HRA006041 and HRA010639 (BioProject accession: PRJCA021256) and are publicly available at https://ngdc.cncb.ac.cn/gsa-human.
***************************************************************

first: Fuchou

last: Tang


title: Effect of conditional SMC specific deletion of ADAR1 on mouse aortic single cell transcriptomic profile and effect on atherosclerosis

overall_design: To investigate the role of SMC specific ADAR1 on vascular function and progression of atherosclerosis, we used the Adar1 flox mouse crossed onto an Myh11 CreERT2 background, that has additional hyperlipidemia with ApoE-/- and SMC lineage tracing with ROSA tdTomato alleles. First, we performed homozygous deletion of Adar1 by treating 8 week old male mice with tamoxifen (Adar1 fl/fl, Myh11CreERT2, ApoE-/-,  tdTomato+/+). These mice develop severe disease and single cell RNAseq was performed of the ascending aorta and aortic root at 2 weeks post tamoxifen. Control mice were wild type for the Adar1 fl/fl allele ( Myh11CreERT2, ApoE-/-,  tdTomato+/+) and were similarly treated with tamoxifen at 8 weeks of age. To then evaluate the effect of SMC Adar1 haploinsufficiency in atherosclerosis, we treated mice that were heterozygous for the Adar1 flox allele (Adar1 fl/WT, Myh11CreERT2, ApoE-/-,  tdTomato+/+) with tamoxifen at 8 weeks of age, and then put on a high fat diet for 16 weeks to induce atherosclerosis. We then performed single cell RNAseq of the ascending aorta/aortic root for these Adar1 het mice along with controls to evaluate how Adar1 haploinsufficiency modifies atherosclerosis


title: Transcriptome analysis of the binucleate ciliate Tetrahymena thermophila cells after mating and re-feeding.

city: Bryan

first: GEOFFREY

last: KAPLER

state: TX

address: 4209B Medical Research Education Building II

institute: Texas A&M University

summary: During macronuclear development the five germline chromosomes undergo massive rearrangement, and the entire epigenome is remodeled from an obligate heterochromatic to obligate euchromatic state. The ~180 unique macronuclear chromosomes undergo two development waves of endo-reduplication to achieve a final copy number of ~45C, while the 21 kb rDNA minichromosome is amplified to ~9000C. The first period (endoreplication phase I) involves two rounds of DNA replication and generates an 8 C macronucleus (6–18 h after mating). Upon re-feeding, a second re-replication period (endoreplication phase II) is initiated generating a macronuclear DNA content of 32–64 C.  This study focused on RNA expression profile of cell in endoreplication phase II.

overall_design: Cell of different mating types were induced to conjugate by mixng after overnight starvation (19 hours).  RNA was isolated at 2 hours after refeeding cells that were mated for 24 hours (endoreplication phase II). Non-mating cells that were starved for 24 hours and then refed for 2 hours were used as control (vegetative cell cycle, early S phase).

first: Linying

last: Zhang

first: Marcella

last: Cervantes

first: Simin

last: Pan


title: Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels. [scRNA-Seq]

status: Public on Jul 28 2025

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

summary: Evolutionary adaptation to diurnal vision in ground squirrels has led to the development of a cone-dominant retina, in stark contrast to the rod-dominant retinas of most mammals. The molecular mechanisms driving this shift remain largely unexplored. Here, we perform single-cell RNA sequencing (scRNA-Seq) and chromatin accessibility profiling (scATAC-Seq) across developmental retinal neurogenesis in the 13-lined ground squirrel (13LGS) to uncover the regulatory basis of this adaptation. We find that 13LGS cone photoreceptors arise not only from early-stage neurogenic progenitors, as seen in rod-dominant species like mice, but also from late-stage neurogenic progenitors. This extended period of cone generation is driven by a heterochronic shift in transcription factor expression, with cone-promoting factors such as Onecut2, Pou2f1, and Zic3 remaining active in late-stage progenitors, while cone-differentiation factors Thrb, Rxrg, and Mef2c are expressed precociously in cone specification. Functional analyses reveal that Zic3 and Mef2c promote cone specification, acting through species-specific regulatory elements that drive their expression in late-stage progenitors. These results demonstrate that evolutionary modifications to gene regulatory networks underlie the development of cone-dominant retinas, providing insight into mechanisms of sensory adaptation and potential strategies for cone photoreceptor regeneration in vision disorders.

overall_design: In 13LGS, retinal neurogenesis begins around embryonic day 18 (E18), with birth occurring at E27 (blue-dotted line in Fig. 1A), and concludes by postnatal day 17 (P17)27. To comprehensively profile cellular-level changes in gene expression and chromatin accessibility, we conducted scRNA-Seq and scATAC-Seq analyses across ten developmental time points, spanning the full course of neurogenesis and the immediate post-neurogenesis period (E18–P21).

first: Kurt

last: Weir

first: Sangeetha

last: Kandoi

first: Roujin

last: An

first: Nicole

last: Pannullo

first: Isabella

last: Palazzo

first: Jared A.

last: Tangeman

last: Shi

first: Steven H.

last: DeVries

first: Dana K.

last: Merriman

first: Jiang

last: Qian

first: Seth

last: Blackshaw


title: Sequential adaptive changes in a c-Myc-driven model of hepatocellular carcinoma

city: pittsburgh

first: Huabo

last: Wang

state: PA

address: 4401 Penn Avenue

institute: Children hospital of pittsburgh

summary: Hepatocellular carcinoma (HCC) is a common cancer that frequently overexpresses the c-Myc (Myc) oncoprotein. Using a mouse model of Myc-induced HCC, we studied the metabolic, biochemical, and molecular changes accompanying HCC progression, regression, and recurrence. These involved altered rates of pyruvate and fatty acid β-oxidation and the likely re-directing of glutamine into biosynthetic rather than energy-generating pathways. Initial tumors also showed reduced mitochondrial mass and differential contributions of electron transport chain complexes I and II to respiration. The uncoupling of complex II's electron transport function from its succinate dehydrogenase activity also suggested a mechanism by which Myc generates reactive oxygen species. RNA sequence studies revealed an orderly progression of transcriptional changes involving pathways pertinent to DNA damage repair, cell cycle progression, insulin-like growth factor signaling, innate immunity, and further metabolic re-programming. Only a subset of functions deregulated in initial tumors was similarly deregulated in recurrent tumors thereby indicating that the latter can “normalize” some behaviors to suit their needs. An interactive and freely available software tool was developed to allow continued analyses of these and other transcriptional profiles. Collectively, these studies define the metabolic, biochemical, and molecular events accompanyingHCCevolution, regression, and recurrence in the absence of any potentially confounding therapies.

overall_design: Liver tissues were collected from a genetically engineered mouse model of hepatocellular carcinoma (FVB/N-Tg(tetO-MYC)36aBop/J × LAP-tTA) under seven experimental conditions. Mice were maintained on doxycycline (100 μg/ml) to suppress Myc expression. Tumor initiation was triggered by doxycycline withdrawal, and tissues were collected at day 3 (D3) and day 7 (D7) post-withdrawal, prior to visible tumor formation. Additional mice were maintained off doxycycline for 3–4 weeks until aggressive HCCs developed, after which tumors were sampled (Tumor group). Doxycycline was then reintroduced to induce regression, and tissues were collected after 3 days (R3) and 7 days (R7). A final group underwent long-term regression (2–3 months) followed by doxycycline withdrawal to induce tumor recurrence (Recurrence group). RNA-seq was performed on liver samples from each condition to profile gene expression during tumor progression, regression, and recurrence.

first: Edward

middle: V

last: Prochownik


title: Multi-Omics Integration Implicates Rac/Rho GTPase Cycling in Vascular Cognitive Impairment and Dementia Pathogenesis

city: Vilnius

first: Milda

last: Milčiūtė

address: Antakalnio st. 17, 12th building

country: Lithuania

institute: VUGENE

summary: Background: Vascular cognitive impairment and dementia (VCID) represents a spectrum of cognitive disorders linked to cerebrovascular pathology, yet its molecular underpinnings remain misunderstood. Methods: We conducted a multi-omics analysis of post-mortem brain tissue from the superior parietal lobe (Brodmann area 7) in 19 individuals with neuropathologically confirmed VCID and 21 age-matched controls. Whole genome sequencing, genome-wide DNA methylation profiling, transcriptomic analysis, and metabolomics profiling were performed to identify molecular signatures and integrated pathways involved in VCID pathogenesis. Results: Epigenome-wide association analysis revealed widespread hypermethylation in VCID, with significant enrichment of genes involved in the Rac/Rho GTPase cycle and cytoskeletal remodeling. Transcriptomic analysis confirmed dysregulation of small GTPase signaling, oxidative stress responses, and lipid metabolism. Metabolomic profiling identified altered levels of diacylglycerols (DAGs) and phosphatidylethanolamines (PEs), which showed strengthened associations with Rac/Rho pathway genes in VCID compared to controls. Conclusions: Our integrative multi-omics study identifies the Rac/Rho GTPase cycle as a convergent pathway disrupted at the genomic, epigenomic, transcriptomic, and metabolic levels in VCID. Lipid metabolism, particularly involving DAGs and PEs, emerged as a key downstream effector contributing to VCID. These findings offer mechanistic insights into VCID pathogenesis and suggest lipid signaling pathways as promising therapeutic targets for intervention.

overall_design: RNA-seq profilling of post-mortem brain tissue from the superior parietal lobe (Brodmann area 7) in 19 individuals with neuropathologically confirmed VCID and 21 age-matched controls.

last: Vishweswaraiah

first: Nadia

last: Ashrafi

first: Romana

last: Mimi

first: Nazia

last: Saiyed

first: Abdullah

last: Khalid

first: Ceyda

last: Buyuker

first: Boran

last: Aksakal

first: Lorena

last: Gomes

first: Migle

last: Gabrielaite

first: Ingrida

last: Olendraitė

first: Vilija

last: Lomeikaitė

first: Juozas

last: Gordevicius

first: Ali

last: Yilmaz

first: Stewart

middle: F

last: Graham


title: A Human iPSC-derived Organoid System to Model Myelin Destruction and Repair

city: Parkville

first: Samantha

last: Barton

address: Parkville Campus 30 Royal Parade

country: Australia

institute: The Florey

summary: We engineered a novel human iPSC-derived organoid system enriched with mature, myelinating oligodendrocytes and functionally reactive microglia. This model enables the study of human CNS remyelination following a demyelinating insult, encapsulating: myelin fragmentation, microglial clearance of myelin debris and oligodendrocyte genesis, differentiation, and axon ensheathment. This system provides a powerful and unparalleled capacity to interrogate complex human cell behaviour, relevant to those studying glial biology and neurological disease mechanisms.

overall_design: Dissociation of organoids into single cells for transcriptomic analysis was performed as per manufacturer’s protocol using a Papain Dissociation System (Worthington Biochemical). Briefly, 16 organoids per group were incubated in 20 U/mL papain enzyme solution at 37°C for 60 min. Every 15 min, gentle trituration was applied to each sample to break up cell clusters into a single cell suspension. After the digestion, DNase-protease inhibitor solution was added to single cell suspensions followed by centrifugation at 300 x g for 5 min. Cell pellets were then processed with the Chromium Gene Expression Flex Library Prep kit (10x Genomics) as per manufacturer’s protocol. Briefly, single cells were fixed overnight at 4 °C using 4 % PFA (ProSciTech) diluted in Concentrated Fix & Permealisation buffer (from Chromium Gene Expression Flex Library Prep kit). After fixation, cells were pelleted at 850 x g for 5 min. Cell pellets were quenched with Quenching and Enhancer buffer (from Chromium Gene Expression Flex Library Prep kit). Glycerol was added to each sample to a final concentration of 25 % prior to storing in -80 °C. Library preparation and sequencing were performed by AGRF sequencing facility (Australia). A single-cell suspension (~24,000 cells) was captured from all isolated cells per sample, without selection. Data was generated with the Illumina BCL Convert 4.1.5 pipeline.

first: Shwathy

last: Ramesan

first: Joel

last: Mason

first: Molly

last: EV Swanson

first: Samuel

last: A Mills

first: Sandeep

last: S Kumar

first: Heejung

last: Shim

first: Denis

last: Korneev

first: Georg

last: Ramm

first: Aaron

last: Andres

first: Lijun

last: Loh

first: Katherine

last: N Lewis

first: Francois-Xavier

last: E Beau

first: Stephanie

last: Chua

first: Miran

last: Mrkela

first: Bradley

last: Turner

first: Matthew

last: Rutar

first: David

last: G Gonsalvez

last: K Barton


title: IL-25-induced effector-memory ILC2s mediate small intestinal adaptation [scRNA-Seq 2]

city: San Francisco

first: Victor

last: Cortez

address: 513 Parnassus Avenue

department: Medicine

institute: University of California, San Francisco

summary: This study used single cell RNA sequencing of small intestinal ILC2s +50 days after an IL-25 regimen or PBS regimen in wild type and Il25-/- mice to study memory ILC2 gene signatures.

overall_design: Mice (wild type and Il25-/-) were injected i.p. with IL-25 (500ng) or PBS 3x a week for 4 weeks and then rested for 50+ days. ILC2s (KLRG1+, CD3-, CD8a-, CD4-, CD19-, NKp46-, NK1.1-, F4/80-, Gr1-, CD11b-, CD11c-, Ter119- ) were then sort purified from the small intestine lamina propria. Cells were then used for single cell RNA sequencing using the 10x Genomics platform.

first: Andrew

last: Schroeder

first: Richard

last: Locksley


title: IL-25-induced effector-memory ILC2s mediate small intestinal adaptation [scRNA-seq]

summary: This study used single cell RNA sequencing of small intestinal epitheilal cells +50 days after an IL-25 regimen or PBS regimen in wild type mice to study long-term changes in gene expression by epitheilal cells.

overall_design: Mice (wild type) were injected i.p. with IL-25 (500ng) or PBS 3x a week for 4 weeks and then rested for 50+ days. Epitheilal cells (EpCAM+, CD45- ) were then sort purified from the small intestine. Cells were then used for single cell RNA sequencing using the 10x Genomics platform.


title: IL-25-induced effector-memory ILC2s mediate small intestinal adaptation [scRNA-Seq 1]

summary: This study used single cell RNA sequencing of small intestinal ILC2s +60 days after helminth infection (Nippostrongylus brasiliensis-Nb. or Heligmosomoides polygyrus, Hp.) and in age matched naïve mice (Ctrl) to study memory ILC2 gene signatures after helminth infection.

overall_design: Mice were infected with a given helminth (Nb, Hp) and allowed to rest for +60 days or age matched naïve mice (Ctrl). ILC2s (KLRG1+, CD3-, CD8a-, CD4-, CD19-, NKp46-, NK1.1-, F4/80-, Gr1-, CD11b-, CD11c-, Ter119- ) were then sort purified from the small intestine (proximal 1/3) lamina propria. Cells were then used for single cell RNA sequencing using the 10x Genomics platform.


title: RNA sequencing of Primary urothelial carcinoma (UC)

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: HER2 is an oncogenic driver in multiple cancers and a predictive biomarker for HER2-targeted therapies. While HER2-directed therapies like fam-trastuzumab deruxtecan (T-DXd) are approved for HER2-positive breast and other solid tumors, the landscape of HER2 expression in advanced prostate cancer (PC) and urothelial carcinoma (UC) remains inadequately characterized.This study demonstrates that HER2 is rarely overexpressed in metastatic prostate cancer but is more common and consistent in urothelial carcinoma. These findings highlight the need for HER2 testing in urothelial cancer.

overall_design: RNASeq of Primary Urothelial carcinoma samples

first: Hung-Ming

last: Lam

first: Gavin

last: Ha

first: Michael

last: Haffner

last: Hsieh

first: Rubin

last: Raychaudhuri


title: IL-25-induced effector-memory ILC2s mediate small intestinal adaptation [ATAC-seq]

summary: This study used bulk ATAC sequencing of either small intestinal ILC2s or Lgr5+ epithelial stem cells +50 days after an IL-25 regimen or PBS regimen in wild type (ILC2s) or Lgr5DTR-EGFP (epithelial stem cells) mice to study chromatin accessibility.

overall_design: Mice (wild type and Lgr5DTR-EGFP) were injected i.p. with IL-25 (500ng) or PBS 3x a week for 4 weeks and then rested for 50+ days. ILC2s (KLRG1+, CD3-, CD8a-, CD4-, CD19-, NKp46-, NK1.1-, F4/80-, Gr1-, CD11b-, CD11c-, Ter119- ) were then sort purified from the small intestine lamina propria. Lgr5+ intestinal stem cells (Lgr5GFP+, CD44+, EpCAM+, CD45-) were then sort purfied from the small intestine epithelium. Cells were then used for bulk ATAC sequencing.

first: Nathan

last: Kochhar


title: Mutations in TAC1B drive increased CDR1 and MDR1 expression and azole resistance in Candida auris

last: Barker

address: 262 Danny Thomas Place, Mail Stop 313, Room I5200

department: Pharmacy & Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary: Objective: Candida auris has emerged as a fungal pathogen of particular concern owing in part to its propensity to exhibit antifungal resistance, especially to the commonly prescribed antifungal fluconazole. In this work we aimed to determine how mutations in the transcription factor gene TAC1B, which are common among resistant isolates and confer fluconazole resistance, exert this effect. Methods: Selected TAC1B mutations from clinical isolates were introduced into a susceptible isolate and reverted to the wild-type sequence in select clinical isolates using CRISPR Cas9 gene editing. Disruption mutants were likewise generated for select genes of interest. TAC1B mutants were subjected to transcriptional profiling by RNA-seq, and relative expression of specific genes of interest was determined by qRT-PCR. Antifungal susceptibilities were determined by modified CLSI broth microdilution. Results: TAC1B mutations leading to A640V, A657V, and F862_N866del conferred fluconazole resistance, as well as increased resistance to other triazoles, when introduced into a susceptible isolate. RNA-seq revealed that the ATP-Binding Cassette (ABC) transporter gene CDR1 as well as the Major Facilitator Superfamily (MFS) transporter gene MDR1 were both up-regulated by these TAC1B mutations. Disruption of CDR1 greatly abrogated resistance in strains with TAC1B mutations whereas disruption of MDR1 had little to no effect. However, disruption of both CDR1 and MDR1 resulted in an additional reduction in resistance as compared to disruption of either gene alone. Conclusion: TAC1B mutations leading to A640V, A657V, and F862_N866del all result in increased resistance to fluconazole and other triazole antifungals, and increased expression of both CDR1 and MDR1 in C. auris. CDR1 is the primary driver of resistance conferred by these TAC1B mutations.

overall_design: Strains were constructed by CRISPR-Cas9 gene editing from a Candida auris Clade Ic clinical isolate (Kw2999) in order to correct the endogenous ERG11 mutation and then modify the endogenous TAC1B gene to either the wildtype sequence or to harbor one of the following amino acid substitutions: A640V, A657V, or F682_N866del. Each of the strains examined in this study were grown to mid-log phase in YPD at 35degC. For RNA-seq expression analysis, strain 1c (ERG11-WT/TAC1B-WT) was used as the control comparator for each of the TAC1B mutant strains.

first: Darian

last: Santana

first: Qing

last: Zhang

first: Tracy

middle: L

last: Peters

first: Jeffrey

last: Rybak

first: Joachim

last: Morschhauser

first: Christina

last: Cuomo

last: Rogers


title: Identification of Myeloid Protein Kinase C Epsilon as a Novel Atheroprotective Gene

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

summary:
Background: Atherosclerosis is a chronic inflammatory disease driven by macrophages. PKCɛ (protein kinase C epsilon) is a serine/threonine kinase involved in diverse cellular processes including migration, growth, differentiation, and survival. PKCɛ acts in a context-dependent manner within the heart; however, its role in atherosclerosis is unknown.

Methods: Bone marrow-derived macrophages from global PKCɛ knockout mice were tested for lipid retention and cytokine secretion. Public gene set analysis assessed raw counts of PRKCE in human atheromas to determine translational relevance. A LysM Cre PKCɛfl/fl (myeloid-selective PKCɛ knockout [mɛKO]) mouse was developed to study the impact of myeloid PKCɛ on atherosclerosis. After confirming myeloid-selective PKCɛ deletion, human-like hypercholesterolemia was induced, and multiple metrics of atherosclerosis were compared in wild-type (WT) and mɛKO plaques. RNA sequencing was used to provide unbiased insight into possible mechanisms by which PKCɛ regulates atherosclerosis.

Results: Public gene set analysis of human atherosclerotic plaque tissue revealed that PKCɛ expression is inversely correlated with plaque vulnerability. Similarly, peritoneal macrophages from WT hypercholesterolemic mice have significantly lower PKCɛ expression, providing a translational rationale for the generation of the mɛKO mouse. Quantitative polymerase chain reaction revealed no differences between genotypes in the expression of genes related to atherosclerosis, at either steady state or on lipid loading, suggesting that loss of PKCɛ does not fundamentally change the basal state and that differences seen are a result of a more complex pathway. Comparing descending aorta and aortic root plaques from WT and mɛKO hypercholesterolemic mice revealed that mɛKO plaques are larger, have larger foam cells and regions of necrosis, and thinner collagen caps. On lipid loading in vitro and in vivo, mɛKO macrophages retained significantly more cholesterol and lipid droplets than WT; Gene Ontology suggests higher expression of genes related to endocytosis in mɛKO macrophages compared with WT.

Conclusions: PKCɛ expression is decreased in vulnerable human plaques and decreases in mouse macrophages on lipid loading. mɛKO plaques are larger and exhibit markers of vulnerability. With no differences in SR (scavenger receptor) expression, the impact of PKCɛ deletion is more subtle than simple SR dysregulation. RNA sequencing implicates higher expression of genes involved in endocytosis, and mɛKO macrophages have significantly more lipid-containing endosomes. The data define the atherophenotype of mɛKO mice and demonstrate that PKCɛ restricts lipid uptake into macrophages by a mechanism independent of SR expression. Taken together, these studies identify PKCɛ as a novel atheroprotective gene, laying the foundation for mechanistic studies on the endocytic signaling networks responsible for the phenotype.

overall_design: 8 week old mice (8 WT, 8 meKO) were injected with AAV8PCSK9 to remove LDL receptor from hepatocytes.  Combined with a high fat ("Western") diet, these animals become hypercholesterolemic.  4 WT and 4 meKO animals were fed the high fat diet; control animals (r of each genotype) remained on a chow diet.  4 weeks after AAV8/high fat diet, macrophages were recruited to the peritoneum with sterile thioglycolate and the elicited macrophages harvested by peritoneal lavage

first: Alexis

middle: T

last: Wells

first: Michelle

last: Shen

first: Redwan

middle: H

last: Binrouf

first: Anna

last: Swinegar

middle: R

last: Lennartz


title: Circulating immune cell signature analysis in HFpEF across species [scRNA-Seq - mouse]

city: Leipzig

first: Jes-Niels

last: Boeckel

address: Johannisallee 30

department: Klinik und Poliklinik für Kardiologie

institute: Universitätsklinikum Leipzig

summary: Background: HFpEF is a heterogeneous clinical picture that is closely related to extracardiac comorbidities such as obesity, hypertension and diabetes and is associated with chronic, low-grade systemic inflammation. Previous studies on myocardial biopsies of HFpEF patients showed intramyocardial inflammatory activity, suggesting that the inflammatory processes in HFpEF are predominantly systemic and exhibit compartment specific-patterns. Methods: We performed single cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) of HFpEF patients (n=6), HFrEF patients (n=8) and healthy controls (n=7) taking obesity status into account. For validation, bulk RNA sequencing was performed on whole blood samples. In parallel, the systemic immune cell response was investigated in a HFpEF mouse model (induced by a high-fat diet plus L-NAME), with one group additionally administered the anti-inflammatory agent nitro-oleic acid (NO₂-OA). Results: Analysis of human PBMCs revealed a HFpEF-specific inflammatory fingerprint, which manifested in obesity-related increased expression of cytokine signaling genes (e.g. CCL2, TNF) and obesity-independent increases in mitochondrial-associated activity. In the mouse model, HFpEF animals showed a comparable increase in inflammatory markers, with treatment with NO₂-OA leading to a partial normalization of immunological signatures and a significant improvement in diastolic function. Conclusion: Our results demonstrate that the immune cells of patients with HFpEF are characterized by a distinct transcriptional immune signature that differs from that of patients with HFrEF. The conserved immunological signatures between humans and mice, and the beneficial effect of NO₂-OA in a preclinical model, provide important translational insights and generate hypotheses for personalized interventions in HFpEF.

overall_design: Single-cell RNA sequencing (scRNA-seq.) was performed on PBMCs of a HFpEF mouse model. Cardio metabolic syndrome was induced in C57BL/6N mice by HFD combined with eNOS inhibitor L-NAME for 15 weeks. A subgroup of the mice subjected to the HFpEF-inducing regimen were additionally treated with NO2-OA for the last 4 weeks. Control mice were fed regular chow.

first: Jasmin

last: Kneuer

first: Marion

last: Müller

first: Stephan

last: Erbe


title: Circulating immune cell signature analysis in HFpEF across species

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

overall_design: Refer to individual Series


title: Intrauterine hyperglycemia impairs primordial germ cell development and fertility by sex-specific epigenetic reprogramming interference in mice offspring [ATAC-seq]

first: Jiangshan

last: Cong

address: No.130,Dongan Road

institute: Fudan University

summary: Adverse intrauterine environments, such as hyperglycemia, impair the sexual reproduction and species continuous, yet the underlying mechanisms remain poorly understood. In this study, we demonstrated that intrauterine hyperglycemia significantly disrupted primordial germ cell (PGC) development, especially in female offspring and thus reduced fertility. Using Oct4-EGFP transgenic mice with intrauterine hyperglycemia exposure, we revealed that hyperglycemia compromised sexually specific chromatin accessibility and DNA methylation reprogramming during PGC development. Particularly, in female PGCs, hyperglycemia leads to the aberrant retention of chromatin accessibility at pluripotency gene promoters such as Nanog and Tfap2c, inhibiting proper gene silencing and blocking the initiation of meiosis, which ultimately hinders oocyte maturation. Conversely, male PGCs exhibit less severe changes in chromatin accessibility and gene transcription. Intriguingly, the global DNA methylation reconstruction is impaired in male PGCs, particularly in key imprinted gene regions, suggesting potential developmental ramifications for later stages and even subsequent generations. Particularly, our findings indicate that intrauterine hyperglycemia adversely affects sex differentiation in PGCs by disrupting the expression of critical sex-determining transcription factors. Collectively, these findings highlight how intrauterine hyperglycemia interferes with sex-specific epigenetic reprogramming during PGC development, leading to abnormal germ cell development, reduced fertility, and adverse intergenerational effects.

overall_design: RNA-seq profiling of control group and  IUHG (intrauterine hyperglycemia) group gonads (E13.5 female) and PGCs (E12.5, E13.5 female, E13.5 male, E16.5 female, and E16.5 male) at development stage.

first: Hefeng

last: Huang

first: Yu

first: Yangyang

last: Li


title: Repressive Cytosine Methylation is a marker of Viral Gene Transfer across distant eukaryotes

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

type: Methylation profiling by high throughput sequencing

summary: Cytosine DNA methylation patterns vary widely across eukaryotes, with its ancestral roles being understood to have had roles in both transposable element silencing and host gene regulation. To further explore these claims, in this study, we reevaluate the evolutionary origins of DNA methyltransferases and characterise the roles of cytosine methylation on underexplored lineages, including the amoebozoan Acanthamoeba castellanii, the glaucophyte Cyanophora paradoxa, and the heterolobosean Naegleria gruberi. Our analysis of DNA methyltransferase evolution reveals a complex ancestral eukaryotic repertoire, with several eukaryotic lineages encoding enzymes likely acquired through lateral gene transfer (LGT). In the three species examined, DNA methylation is enriched on young transposable elements and silenced genes, suggesting an ancestral repressive function, without the transcriptionally linked gene body methylation of plants and animals. Notably, the closest homologues of many of the silenced, methylated genes in diverse eukaryotes belong to viruses, including giant viruses. Given the widespread occurrence of this pattern across diverse eukaryotic groups, we propose that cytosine methylation was a mechanism originally acquired from bacterial donors to mitigate the expression of both transposable and viral elements, and that this function may persist in creating a permissive atmosphere for LGT in diverse eukaryotic lineages. These findings further highlight the importance of epigenetic information to annotate eukaryotic genomes, as it helps delimit potentially functional LGTs from silenced parasitic elements, less likely to be actively contributing to organism adaptations.

sample_organism:
Cyanophora paradoxa
Acanthamoeba castellanii
Naegleria gruberi

overall_design: We generated Enzymatic Methyl-seq for 3 distantly related microbial eukaryotes grown axenically in laboratory conditions, including the amoebozoan Acanthamoeba castellanii, the heterolobosean Naegleria gruberi and the glaucophyte Cyanophora paradoxa. Moreover, both A. castellanii and N. gruberi were treated with cytidine analogues (5-Azacytidine, Decitabine, Zebularine) known to interfere with 5mC deposition, and compared to DMSO treated control samples. Effects on 5mC levels were measured by EM-seq and RNA-seq was used to characterise the transcriptional response. A. castellanii and N. gruberi were also sequenced with Whole Genome Bisulphite Sequencing.

first: Luke

last: A Sarre

first: Giselle Azucen

last: Gastellou Peralta


title: single cell RNA-seq of CD45+ cell from DSS induced colitic

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

summary:
Objective: Inflammatory bowel disease (IBD), encompassing ulcerative colitis (UC) and Crohn’s disease (CD), represents a challenging group of chronic gastrointestinal inflammatory disorders. While trained immunity, a form of innate immune memory, has shown promise in combating infection and cancer, its role in chronic inflammatory diseases, particularly inflammatory bowel disease (IBD), remains relatively underexplored. This study aims to investigate the potential of trained immunity to ameliorate IBD.
Results: BG induced trained immunity significantly ameliorates DSS-induced colitis. Mechanistically, β-glucan primed the hematopoietic compartment, leading to a profound shift in monocyte fuction. Both bone marrow transplantation from trained donors to naïve recipients and adoptive transfer of trained peripheral monocytes provided protection against DSS colitis. Notably, trained mice displayed enhanced bactericidal activity against intestinal bacterial infections. Furthermore, single-cell RNA sequencing revealed that β-glucan-induced trained immunity resulted in an expansion of reparative Cx3cr1 intestinal macrophages originating from Ly6Chi monocytes, facilitating faster recovery of the colon epithelium.
Conclusion: Our findings demonstrate that β-glucan effectively induces trained immunity, leading to a multifaceted protective response against experimental colitis. These findings provide compelling evidence for the therapeutic potential of harnessing trained immunity to treat IBD and offer a novel approach to modulating intestinal inflammation and restoring gut homeostasis。

overall_design: Mice were i.p. injected with one dose of BG (1 mg) on day -7 (designated day0, D ), Then, Mice received 3% indicated DSS (36,000 to 50,000 molecular weight; MP Biomedicals) in their drinking water for 5 days, followed by 2 days(D7).

first: Yinyin

last: Lv

first: Qiongyun

last: Chen


title: Circulating immune cell signature analysis in HFpEF across species [RNA-Seq - mouse]

overall_design: Bulk RNA sequencing (RNA-seq.) was performed on PBMCs of a HFpEF mouse model. Cardio metabolic syndrome was induced in C57BL/6N mice by HFD combined with eNOS inhibitor L-NAME for 15 weeks. A subgroup of the mice subjected to the HFpEF-inducing regimen were additionally treated with NO2-OA for the last 4 weeks. Control mice were fed regular chow.


title: Global identification and regulatory network analysis reveal the significant roles of lncRNAs during anther and pollen development in Arabidopsis

city: Guangzhou

first: Dong

last: Zhou

address: wushan street

institute: south china agricultural university

type: Non-coding RNA profiling by high throughput sequencing

summary: Long non-coding RNAs (lncRNAs) are important regulatory molecules involved in various biological that function in numerous processes. YetHowever, their roles in male reproductive development and their interactions with miRNAs remained elusive. In this study, a high-throughput sequencing was performed forof anthers at different developmental stages in Arabidopsis, which identified 1283 lncRNAs including 524 differentially expressed lncRNAs (DELs) among different developmental stages. Most of these DELs exhibited positive correlations with thein their expression patterns with of adjacent protein-coding genes. Additionally, wWeighted gene co‐expression network analysis (WGCNA) analysis showedrevealed that protein-coding genes targeted by DELs in four modules associated withrelated to the tetrad stage were annotated for functions related toassociated with functions such as pollen wall formation, pollen germination, or pollen tube growth, respectively. Furthermore, five, 10, and 11 lncRNAs were predicted as miRNAs’ endogenous target mimics (eTMs), precursors, and natural antisense transcripts of pri-miRNA, respectively. Remarkably, one of the lncRNA,s, host gene of ath-miR167a (ath-miR167aHG) was , predicted to beas the precursor of miR167a, and  was selected for function validation. Its Ooverexpression of ath-miR167aHG led toresulted in the up-regulation of miR167a and the subsequent down-regulation of miR167a’s target genes ARF6 and ARF8, demonstrating a functional interaction between ath-miR167aHG and miR167a. The transgenic plants showed delayed flowering, shorter filaments, abnormal anther dehiscence, and undeveloped siliques ultimately, suggesting an a involvement role of ath-miR167aHG during in male reproductive development. Collectively, our research shed new light onprovided a new insight into the roles functions of lncRNAs in male reproductive development and uncovered the unique interactions between lncRNAs and miRNAs.

overall_design: RNA-seq profiling of Arabidopsis anthers at four different developmental stages including tetrad, uninucleate microspore (UNM), bicellular pollen (BCP), and tricellular pollen (TCP) stage.

first: Ruiqi

last: Song

first: Yuan

last: Fang

first: Rui

last: Liu

first: Chenjiang

last: You

first: Yijie

last: Wang

first: Li


title: Intrauterine hyperglycemia impairs primordial germ cell development and fertility by sex-specific epigenetic reprogramming interference in mice offspring [Bisulfite-Seq]

city: Shanghai

first: Jiangshan

last: Zhang


title: Integrative assessment of RNA sequencing and in silico analysis to pinpoint mRNAs, lncRNAs, and circRNAs interactions with miRNAs underlying arsenic-induced neurotoxicity

city: Lucknow

first: Aditya

middle: Bhushan

last: Pant

state: Uttar Pradesh

address: vishvigyan Bhawan MG Marg

department: FEST

country: India

institute: CSIR-INDIAN INSTITUTE OF TOXICOLOGY RESEARCH

summary: The acquisition of neurodegeneration hallmarks necessitates molecular changes at multiple levels of functional genomics. Regulatory RNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) play crucial roles in modulating messenger RNAs (mRNAs) expression and are potential molecules that regulate multifactorial neurotoxicity mechanisms. Integrated studies of regulatory RNAs’ functions are still lacking to portray the complete picture. In this study, we carried out a detailed analysis of mRNA, lncRNA, and circRNA profiles in differentiated SH-SY5Y cells exposed to arsenic, a well-known neurotoxicant, using the Illumina Novaseq6000 platform. Subsequently, employing a bioinformatics approach, we identified specific interactions between these RNA molecules and potential miRNAs, unraveling intricate regulatory networks. Among significantly deregulated transcripts, we identified 2487 mRNA transcripts, 1192 lncRNA transcripts, and 20 circRNA transcripts in arsenic-treated cells compared to control. Functional enrichment analysis indicated their involvement in numerous pathways underlying neurotoxicity. Further, these regulatory molecules displayed strong interactions with multiple miRNAs implicated in neuronal damage. Our findings revealed intricate molecular alterations in response to arsenic exposure, emphasizing the crucial role of multi-omics technologies in understanding neurodegeneration. These findings pave the way for targeted therapeutic interventions, focusing on precise modulation of regulatory RNA networks to mitigate the effects of arsenic.

overall_design: We have performed Illumina sequencing using the Novaseq6000 platform to identify differentially expressed microRNAs (mRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in differentiated SH-SY5Y cells in response to arsenic exposure.

first: AB

first: Sana

last: Sarkar

first: Anuj

last: Pandey

first: Bushra

last: Khan


title: Single cell RNA sequencing of the in vivo mouse TME

city: Los Angeles

first: Lili

last: Yang

address: 610 Charles E. Young Dr. East

institute: University of California, Los Angeles

summary: Ovarian cancer (OC) poses a significant challenge due to frequent recurrence linked to tumor heterogeneity and an immunosuppressive tumor microenvironment (TME). Targeting both OC cells and TME simultaneously holds promise for effective treatment. This study comprehensively analyzed 17 chemonaive and 18 refractory/recurrent OC samples, identifying mesothelin (MSLN) and natural killer receptor (NKR) ligands as tumor targets and CD1d as an OC TME target. Leveraging hematopoietic stem cell (HSC) gene engineering and feeder-free differentiation culture, we generated allogeneic MSLN-targeting CAR (MCAR)-engineered invariant natural killer T (MCAR-NKT) cells, demonstrating high-yield and high-purity production, potent antitumor efficacy, multiple tumor targeting mechanism, and significant in vivo expansion and persistence. Notably, these cells selectively deplete immunosuppressive TAMs and MDSCs, counteract tumor immune evasion, display a favorable safety profile with low risks of GvHD and CRS, and exhibit a stable “hypoimmunogenic” phenotype attributed to epigenetic and signaling regulations. These findings underscore the feasibility and therapeutic potential of allogeneic MCAR-NKT cell products for OC, laying a foundation for further translation and clinical development.

overall_design: Gene expression profiling of tumor cells in an in vivo study using an OVCAR8-FG human OC xenograft NSG mouse model

first: Yan-Ruide

last: Li

first: Zhe

first: Miao

first: Yuning

first: Yichen

last: Zhu


title: Spatial Touchstone: A Comprehensive Assessment of Imaging-Based Spatial Transcriptomics, Reproducibility and Best Practices

city: Memphis

first: Jasmine

last: Plummer

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

summary: Spatial transcriptomics is a rapidly advancing field, yet it lacks standardized metrics for evaluating imaging-based in situ hybridization technologies. In this study, we emphasize the importance of rigorous experimental design and standardized operating procedures (SOPs) in defining performance metrics across multiple modalities—from single-cell to spatial transcriptomics to spatial proteomics. Our Spatial Touchstone (ST) dataset, generated from six tissue types across three global sites (n=76 assays), provides a comprehensive evaluation of reproducibility, sensitivity, dynamic ranges, signal-to-noise ratio, false discovery rates, cell type annotation, and congruence with single-cell profiling. Using single-nucleus RNA sequencing (snRNA-seq) on the same formalin-fixed paraffin-embedded tissues, we created a reference for transcriptional profiles to assess cellular organization and biomarker localization. In the absence of an independent 'gold standard’ in the field, this study provides an objective assessment of technical performance through standardized protocols, Spatial Touchstone Protocols (STSOP). Our open-source software, SpatialQC, allows users to evaluate samples across all technical metrics and directly impute cell annotations from single-cell datasets. This study features the largest imaging-based spatial transcriptomics data repository available, with a total of 203 spatial profiles. It incorporates both public (n=127) and ST datasets (n=76) through the Spatial Touchstone Portal (STP), available at www.spatialtouchstone.org. This resource offers users easy access to analyze and compare their own data against an extensive collection of imaging-based datasets. We show that the ST datasets demonstrate high reproducibility (r=0.93 to 1.0) and set a new benchmark for the field. Finally, we establish metrics to evaluate and integrate imaging based multi omics data from single cell into spatial transcriptomics to spatial proteomics. The ST project provides a comprehensive, reproducible assessment across platforms and sites, establishing essential standards for imaging-based spatial multi omics (transcriptomics and proteomics) and paving the way for future research and technological advancements.

overall_design: The study utilized two leading spatial technologies, Xenium and CosMx SMI, as representative examples of cutting-edge commercial platforms for evaluating technical performance. These platforms were evaluated across six tissue types in both normal (appendix/AP, colon/CO, pancreas/PA, ileum/IL) and cancerous (breast/BR and prostate/PR) conditions, focusing on accuracy, precision, reproducibility, sensitivity, and specificity. It used commercially available panels for both RNA (CosMx Human Universal Cell Characterization RNA Panel targeting 950 human genes and a 50-target add-on panel set; Xenium Human Multi-Tissue and Cancer Panel targeting 377 human genes; Xenium Human Breast Panel targeting 380 human genes) and protein (NanoString 64-plex human protein panel). All samples were analyzed on both imaging-based platforms (full scan of the entire section) generating 76 profiles, subjected to snRNA-seq (snPATHO-seq, n=6) and hematoxylin and eosin (H&E) staining (n=44) (n=126 total).

first: Felipe

last: Segato Dezem

first: David

middle: P

last: Cook

first: Jiwoon

last: Park

first: Luke

first: Yutian

first: Maycon

last: Marcao

first: Hannah

last: DuBose

first: Arjumand

last: Wani

first: Kellie

last: Wise

first: Natalia

last: Morosini

first: Kirk

last: Jensen

first: Michael

last: Roach

first: Kate

last: Harvey

first: Taopeng

first: Roberto

last: De Gregorio

first: Alicia

last: Alonso

first: Shauna Lee

last: Houlihan

first: Robert

last: Schwartz

first: Erika

last: Hissong

first: Catherine

last: Snopkowski

first: Jeffrey

last: Wrana

first: Natalie

last: Ryan

first: Lisa

last: Butler

first: George

last: Church

first: Alex

last: Swarbrick

first: Christopher

last: Mason

first: Luciano

last: Martelotto


title: Single-cell analysis of human fibrous dysplasia bone reveals a fibrotic transcriptome and somatic, mosaic GNAS R201H/C mutations in endothelial, perivascular, and stromal cells

first: Edward

last: Hsiao

address: 505 Parnassus Ave

institute: UCSF

type: Genome variation profiling by high throughput sequencing

summary: Genetic mosaicism is a leading cause of human disease across the lifespan.  Improving the tools to detect somatic mosaicism and applying them to understand the cellular and molecular mechanisms that contribute to disease is of critical importance for improving human health.  Fibrous dysplasia (FD) is a prototypical disease of Gs-GPCR activation caused by somatic, mosaic GNAS R201H/C mutations that result in fibrotic bone.  Utilizing single-cell RNA sequencing and a unique GNAS genotyping strategy, we analyzed non-hematopoietic cells from FD and non-FD human bone. FD bone showed an altered fibroblast composition with a unique FD-specific osteoblastic cluster. Surprisingly, in addition to the skeletal stromal lineages, endothelial and perivascular cells also expressed GNAS R201H/C , which was confirmed using BaseScope, suggesting that GNAS R201H/C mutations are present in multiple non-osteogenic cell lineages.  We also identified a common fibrotic transcriptomic signature across FD cell lineages.  Our results highlight the effects of GNAS mosaicism on the cellular and transcriptomic landscapes of FD, identify previously unrecognized cell types that may be relevant to FD pathogenesis, and reframe our understanding of GNAS R201H/C function in bone.

overall_design: We performed single-cell RNA sequencing combined with single GNAS genotyping on non-hematopoietic cells from 4 (four)  fibrous dysplasia (FD) and 4 (four) non-FD human bone samples.

first: Kelly

last: Wentworth

first: Fernando

last: Fierro

first: Tania

last: Moody

first: Bryan

last: Le

first: Zachary

last: Michel

first: Alison

last: Boyce

last: Collins

first: Vardit

last: Kram

first: Luis

last: de Castro

first: Eric

last: Chow

first: Amir

last: Qorbani


title: Circulating immune cell signature analysis in HFpEF across species [RNA-Seq - human]

first: Jes-Niels

last: Boeckel

overall_design: Bulk RNA sequencing (RNA-seq.) was performed on PBMCs from healthy human donors which were pre-treated with increasing concentrations of NO2-OA [1 or 3 µM] before induction of inflammation using IL-1β [10 ng/ml].

first: Jasmin

last: Kneuer

first: Marion

last: Müller

first: Stephan

last: Erbe


title: Targeting nucleoporin 214 selectively eliminates leukemia stem cells by inducing ferroptosis

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University


title: RNA-seq of retinal microglia and non-microglial retina cells in  WT (Bmal1f/f) and microglial Bmal1-KO (Bmal1-mg/-mg) mice

city: Saint Louis

first: Charles

middle: W.

last: Pfeifer

state: Missouri

address: 660 S. Euclid Ave., Campus Box 8096

department: Ophthalmology and Visual Sciences

institute: Washington University School of Medicine in St. Louis

summary: We discovered that Bmal1 knockdown in retinal microglia alters their diurnal clock gene expression, inflammatory gene expression, and morphology. Furthermore, we found that this disruption of diurnal physiology in microglia results in reduced scotopic visual function, retinal neurodegeneration, and abnormal wheel running behavior in mice, suggesting that maintenance of the microglial clock contributes to retinal homeostasis. Subsequently, we investigated transcriptional alterations in retinal microglia and non-microglial cells in the retina to uncover gene expression patterns that may explain these clock-dependent phenotypes and potentially identify homeostatic neuro-glial signaling mechanisms dependent on microglial clock biology.

overall_design: We used tissue dissociation and fluorescent activated cell sorting methods to simulatenously isolate viable microglia (CD11b+, DAPI-) and non-microglia retina (CD11b-, DAPI-) cells from Bmal1f/f and Bmal1-mg/-mg mice and performed RNA-Sequencing on purified mRNA samples (n=4-5/condition).

middle: W

first: Rajendra

middle: S

last: Apte


title: RNA-seq based characterization of host responses to Brachyspira hyodysenteriae infection

city: León

first: Lucía

last: Pérez-Pérez

address: C/ Pedro Cárdenes s/n

country: Spain

institute: Universidad de León

summary: Using RNA-seq, we investigated for the first time the in vivo transcriptome of colonic mucosa in 16 control pigs and 16 pigs experimentally infected with Brachyspira hyodysenteriae, which were euthanized at different stages of the disease: 8 during a preclinical stage characterized by bacterial shedding without clinical signs (early  infection group), and 8 during an acute stage presenting with dysentery (acute infection group). No significant differences in gene expression were observed between the control and early infection groups, except for an overexpression of matrix metalloproteinases (MMPs), which may be associated with early ulceration of the colonic epithelium. The acute infection group showed a significant upregulation of the S100A8, S100A9 and S100A12 proteins, but most of the host biological processes were downregulated, particularly those related to the immune response, such as chemokines and cytokines signalling or immune cells chemotaxis and migration. Accordingly, the prediction of cell types associated with the detected transcripts revealed a depletion of immune cells, except neutrophils, and an enrichment of stromal cells in the acute infection group. Marked alterations in mucin gene expression were observed in this group, including overexpression of MUC5AC, MUC20, and GCNT3, a trend toward increased MUC2, and downregulation of MUC1 and MUC3. Although no significant changes were detected in the early infection group, a similar trend was observed. These findings suggest that B. hyodysenteriae may suppress host immune responses, particularly through inhibition of the IFNγ signalling pathway, accompanied by a depletion of cellular responses, except for neutrophils, and promotion of tissue damage via overexpression of multiple MMPs, even at early stages of the disease. Significant alterations in mucin composition were observed during the acute stage, likely driven by the overexpression of S100 proteins and activation of the SPDEF pathway. This study proposes several mechanisms associated with the pathophysiology of swine dysentery, revealing key aspects of host–pathogen interactions, particularly the host response to B. hyodysenteriae infection.

overall_design: Briefly, 32 females crossbred 7 weeks-old piglets (commercial hybrids of Landrace × Large White × Pietrain) from a SD-free farm were randomly assigned to either the control or infected group (n = 16 per group). The infected group was orally challenged for three consecutive days with 30 mL of broth containing B. hyodysenteriae B-204 (ATCC 31212) strain at a concentration of 5 × 10^8 bacteria/mL. Half of the infected pigs (n = 8) were euthanised 24 hours after the first B. hyodysenteriae q-PCR positive in faeces (early infection group), while the other half (n = 8) were euthanised after two consecutive days of mucohaemorrhagic diarrhoea (acute infection group). Non-infected controls (control group) were euthanised and necropsied in parallel, one to one, with the challenged pigs.

first: Héctor

last: Arguello

first: María

last: de Toro

last: Puente

first: Juan

middle: M

last: Ortiz Sanjuán

first: Cristina

last: Galisteo

first: Ana

last: Carvajal


title: KRAS-mediated upregulation of CIP2A promotes suppression of PP2A-B56a to initiate pancreatic cancer development [ATAC-seq]

city: West Lafayette

first: Brittany

middle: L.

last: Allen-Petersen

state: IN

address: 201 S. University St., HANS 215

institute: Purdue University

summary: Oncogenic mutations in KRAS are present in approximately 95% of patients diagnosed with pancreatic ductal adenocarcinoma (PDAC) and are considered the initiating event during the development of pancreatic intraepithelial neoplasia (PanIN) precursor lesions. While it is well established that KRAS mutations can drive the initiation of pancreatic oncogenesis, the effects of oncogenic KRAS signaling on regulation of phosphatases during this process is not fully appreciated. Protein Phosphatase 2A (PP2A) has been implicated in suppressing KRAS-driven cellular transformation. However, low PP2A activity is observed in PDAC cells compared to non-transformed cells, suggesting that suppression of PP2A activity is an important step in the overall development of PDAC. In the current study, we demonstrate that KRASG12D induces the expression of both Cancerous Inhibitor of PP2A (CIP2A), an endogenous inhibitor of PP2A activity, and the PP2A target, c-MYC. Consistent with these findings, KRASG12D sequestered the specific PP2A subunit responsible for c-MYC degradation, B56a, away from the active PP2A holoenzyme in a CIP2A-dependent manner. During PDAC initiation in vivo, knockout of B56a promoted KRASG12D tumorigenesis by accelerating acinar-to-ductal metaplasia (ADM) and the formation of PanIN lesions. The process of ADM was attenuated ex vivo in response to pharmacological re-activation of PP2A utilizing direct small molecule activators of PP2A (SMAPs). Together, our results suggest that suppression of PP2A-B56a through KRAS signaling can promote Myc-driven initiation of pancreatic tumorigenesis.

overall_design: 5-6W old PDX1-Cre; LSL-KRASG12D (KC) mice or KC mice with B56a loss (KCB) were used for experiment. Pancreata were harvested and then isolated using the Fleming-Martinez and Storz JOVE 2019 protocol. Isolated acinar clusters were plated in a collagen matrix and cultured at 37*C and 5% O2 for 24, 48, or 72H. Structures were digested out of collagen using collagenase, washed in PBS, and then resulting cell pellets after final centrifgation were resuspended in 10%DMSO/90%FBS and stored at -80*C until used for ATAC-seq processing.

first: Samantha

last: Tinsley

first: Alisha

last: Dhiman

first: Emily

last: Dykhuizen


title: SLIT2 regulates the skeletal stem cell niche through sympathetic innervation

city: Xiamen

first: zuoxing

last: wu

address: Xiang’an South Road

institute: Xiamen university

summary: Sympathetic tone has long been known as a central signaling axis inhibiting osteogenesis. However, the mechanism of this nerve to bone influence remains elusive, especially regarding the specific cellular targets of sympathetic activity. Recently, a bona fide tissue-resident stem cell giving rise to skeletal cell types, skeletal stem cells (SSCs), have been identified. To explore if and how nerves impact SSCs, we utilized mice with conditional deletion of SLIT2, a classic axonal repellent, finding that neural (Slit2syn1 mice) and sympathetic (Slit2th mice) but not bone stem/progenitor (Slit2prx1 mice) or sensory (Slit2adv mice) deletion of Slit2, led to osteopenia due to impaired bone formation associated with an increase in sympathetic innervation and a decrease in the numbers of SSCs. Consistent with this, pharmacological or surgical sympathectomy caused expansion of the SSC pool. More directly, wild type (WT) SSCs transplanted orthotopically into the bones of Slit2th mice with increased sympathetic innervation displayed impaired osteogenic capability, demonstrating that sympathetic nerves functionally contribute to the SSC niche. In line with these findings, the increased sympathetic innervation in Slit2th mice disrupted bone regeneration and bone fracture healing by reducing SSC expansion. Transcriptomic profiling in sympathetic neurons identified Follistatin-like 1 (FSTL1) as a SLIT2-regulated soluble factor that suppressed SSC self-renewal and osteogenic capacity. Accordingly, ablation of Fstl1 in sympathetic neurons enhanced SSC-driven osteogenesis and attenuated the bone loss seen in Slit2th mice in vivo. Altogether, our study both newly establishes SLIT2 as a regulator of skeletal sympathetic innervation and establishes sympathetic nerves as a key component of the SSC niche, providing new therapeutic opportunities to augment SSC function to treat skeletal disorders.

overall_design: We next focused on identifying the mechanism by which slit2-mediated sympathetic innervation constitutes part of the SSC niche regulating osteogenesis, we performed RNA sequencing (RNA-seq) and filtered for secreted factors the list of genes exhibiting lower expression in the absence of slit2.


title: Profound effect of asparagine-linked glycosylation protein 11 (TgALG11) on genomic expression of Toxoplasma gondii

status: Public on Jul 27 2025

city: Wenzhou

first: Ya-Ni

last: Mou

state: China

address: Chashan University Town, Ouhai District, Wenzhou City, Zhejiang Province

institute: Wenzhou Medical University

summary: Toxoplasma gondii is an intracellular parasite that relies on complex molecular mechanisms to support its proliferation and survival. In this study, we investigate the role of TgALG11 in these processes and explore the underlying regulatory network. Our data demonstrate that TgALG11 is essential for maintaining T. gondii proliferation and for normal N-glycosylation. To further elucidate the molecular mechanisms underlying the essential functions of TgALG11, we performed transcriptome sequencing to identify the genes regulated by this factor. Total RNA was extracted from iTgALG11 strains cultured with 0.5 μg/ml ATc (knockdown strain) and DMSO (control), and subjected to deep sequencing using the Illumina Novaseq™ 6000 platform. The sequence reads were subsequently mapped to the T. gondii genome, resulting in a comprehensive transcriptome encompassing 8,948 genes. Among these, 934 genes were differentially expressed due to TgALG11 deficiency, including 315 downregulated and 5 upregulated genes (DESeq, |log2(FoldChange)| ≥ 1, padj ≤ 0.05). Functional enrichment analysis revealed that these genes were associated with various Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Our findings provide novel insights into the profound impact of TgALG11 on the T. gondii transcriptome, underscoring its critical role in parasite biology.

overall_design: Three replicates of iTgALG11 transgenic parasites cultured with 0.5 μg/ml ATc (knockdown strain) and DMSO (control) were prepared and sent to Novo gene (Beijing, China) for TgALG11-specific transcriptome construction and analysis. .

first: Feng

last: Tan

first: Yani

first: Siyu

last: Tian


title: scATAC-seq of murine B cells post NP-OVA immunization

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary: To determine the role of p52:ETS1 function in activated B cells.

overall_design: Spleen were harvested from WT and p52ki/ki mice (1 each) on day 9 post immunisation with NP-OVA and alum. B cells were isolated from total splenocytes and stained for FACs. Naive (CD19+IgD+) and activated B cells  (CD19+IgD-) were sorted and mixed at 1:3 ratio. These sorted B cells (1 wt and 1 p52 ki/ki) were sent to immunogenomics facility at SIgN to be processed for single cell ATAC-seq on the 10x Genomics Chromium platform. Their protocol: Briefly, nuclei were prepared from sorted cells as per the 10x Genomics Demonstrated Protocol CG000169 followed by processing with the Chromium Single Cell ATAC Kit v2 following the manufacturer’s protocol, targeting the capture of up to 5000 nuclei. After quantification on the Agilent Bioanalyzer, ATAC-seq libraries were pooled for sequencing on the Illumina NovaSeq X, with the cycle configuration of Read 1N-151 cycles; i7 index-8 cycles, i5 index-16 cycles; Read 2N-151 cycles, targeting about 200 million reads-pairs/sample.

first: Dhakshayini

last: Morgan

first: Biyan

last: Zhang


title: Caulerpin alleviates cyclophosphamide -induced ovarian dysfunction by modulating macrophage-associated granulosa cells senescence in breast cancer

city: 广州市

first: 心怡

last: 任

state: 广东省

address: 黄埔大道601号

institute: 暨南大学

summary: In this study, xenograft tumors of the breast cancer cell line MDA-MB-231 in female BALB/c nude mice model were established. It demonstrates that cyclophosphamide (CTX) alone caused a remarkable ovarian damage, including irregular estrous cycles, follicle loss and reduced expression in anti-Mullerian hormone (AMH) and follicle-stimulating hormone receptor (FSHR), while the ovarian toxicity can be largely reduced after caulerpin treatment in mice and in vitro.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumor-bearing mice and  tumor-bearing mice  by using cyclophosphamide (CTX)-induced

first: Ping

last: Li

first: Xiyi

last: Ren


title: Intrauterine hyperglycemia impairs primordial germ cell development and fertility by sex-specific epigenetic reprogramming interference in mice offspring [RNA-seq]

first: Jiangshan

last: Cong

overall_design: RNA-seq profiling of control group and  IUHG (intrauterine hyperglycemia) group gonads (E13.5 female) and PGCs (E12.5, E13.5 female, E13.5 male, E16.5 female, and E16.5 male) at development stage.

first: Hefeng

last: Huang

first: Yu

first: Yangyang


title: Single cell RNA sequencing of embryonic thymuses from 22q11.2 DS mouse models following in utero drug treatments.

city: Dallas

first: Nicolai

last: van Oers

address: NA2.200, 6000 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

summary: 22q11.2 DS causes the formation of a hypoplastic thymus. Mouse models of 22q11.2 were used to study the impact of different drugs, administered in pregnant mice,  on the growth of the thymus.  Thymuses from the different treatments were processed for single cell RNA sequencing. These were from control (Tbx1+/+;+/neo2) and 22q mouse models (Tbx1neo2/neo2 )

overall_design: Sc-RNA seq is performed on thymus cells isolated at E13.5 GA from a wild type embryo, Tbx1neo2/neo2 embryo, Tbx1neo2/neo2 embryo exposed in utero to Minoxidil drug and Tbx1neo2/neo2 embryo exposed in utero to PGE.2

first: Pratibha

last: Bhalla

first: Ashwani

last: Kumar

first: Chao

last: Xing


title: Znf706 regulates germplasm formation and primordial germ cell development in zebrafish

city: Beijing

first: Xiaotong

last: Wu

address: Haidian

institute: Tsinghua University

summary: The cell fate of primordial germ cells (PGCs) in zebrafish is pre-determined by maternally deposited germplasm, which is packaged into ribonucleoprotein complex in oocytes and, after fertilization, inherited into PGCs promoting germline fate in embryos. However, the maternal factors regulating the assembly of germplasm and PGC development remain poorly understood. In this study, we report that the maternal transcription factor Znf706 regulates the assembly of germplasm factors into a granule-like structure localized perinuclearly in PGCs during migration. Maternal and zygotic mutants of znf706 (MZznf706) exhibited deficient germplasm at the early embryonic stage, decreased PGC numbers with ectopic PGC locations during PGC migration, and lower female ratio in adulthood. Notably, the implementation of Znf706 CUT&Tag and RNA-seq on immature oocytes uncovered that Znf706 in stage I oocytes may act as a transcriptional activator and mediate mRNA binding, translational regulation, and metabolic pathways of oocytes. Hence, we propose that Znf706 is crucial for germplasm assembly and PGC development in zebrafish.

overall_design: Wild-type and znf706(tsu7d/tsu7d) mutants generated by CRISPR/Cas9 were used for mRNA-seq and Znf706 CUT&Tag assaies.  In the context of the current investigation, a protocol for the isolation of oocytes from juvenile female fish was developed, aimed at maximizing yield and maintaining cellular integrity. The first step involved the euthanization of the WT and znf706-/- juvenile female fish (3-month-old) by submerging them in an ice-water mixture. After euthanization, the abdominal cavity of the fish was carefully opened using surgical scissors and the ovaries were bilaterally detached from the abdomen by utilizing forceps. The excised ovaries were promptly transferred into a 6-well plate preloaded with 2 ml digestive buffer (cell dissociation buffer, PCM, PC-33689) and incubated for 2-3 hrs at a temperature of 28.5℃. To enhance the efficacy of the digestive process, the 6-well plate was shaken every half hour during incubation. Once the digestion period was complete, the L-15 medium, which had been preheated to 28.5℃, was added to the digestive buffer to halt the digestion process effectively. To eliminate residual impurities, the oocytes were subjected to a series of washing steps involving the addition of fresh L-15 medium, followed by gentle resuspension of the oocytes, a process repeated 2-3 times to ensure thorough cleansing. Approximately 600 stage I oocytes and 150 stage II oocytes were collected manually with a pipette, with two biological replicates each for znf706-/- and WT through the aforementioned procedure and then transferred into RNase-free 1.5 ml tubes, for quick-frozen with liquid nitrogen and preserved at -80℃ for short-term storage. All the liquid nitrogen-freezing samples (stages I and II oocytes) were sent to Novogene for were sent to Novogene for RNA-seq library preparation and sequencing in the Hiseq-PE150 platform. The operation from the anesthetization of adult fish to oocyte digestion is the same as that for RNA-seq. It is worth noting that CUT&Tag is a technique capturing genomic DNA, thus, it is imperative to eliminate the contamination from the granulosa cells and other somatic cells that envelop the oocytes. In our study, we performed the digestion by cell dissociation buffer (PCM, PC-33689) to get rid of somatic cells. The oocyte surface exhibits a pronounced smoothness, signifying the removal of somatic cells, which would be further validated by DAPI staining. Then, the medium containing the oocytes was drawn through a 100 μm cell strainer using a pipette, followed by a 2-minute incubation period to allow for the gravitational sedimentation of the oocytes at the bottom of the plate. To remove impurities, the sample was thoroughly washed 2-3 times with a preheated L-15 medium. Approximately 5,000 WT stage I oocytes were collected, followed by library construction using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, TD904) and sequencing (Novogene, Hiseq-PE150 platform). The primary antibody used in the experimental group is rabbit anti-Znf706 (Aviva, arp32987-P050, 2.5μg / 50μl), while rabbit anti-IgG antibody (Cell Signaling Technology, 2729s, 2.5 μg / 50μl) in the control group. The secondary antibody was goat anti-rabbit IgG H&L (Abcam, ab6702, 1:100 dilution). The experimental group underwent two biological replicates.

first: Weiying

first: Yaqi

first: Han

last: li

first: Xin

last: Liu

first: Tao

last: Zheng

first: Guangyuan

first: Boqi

first: Tong

last: lv

first: Zihang

last: Wei

first: Anming

last: Meng


title: Next generation sequencing facilitates quantitative analysis of transcriptional profiling of  Candida albicans wild type

city: Jinan

first: Chen

last: He

address: Wenhua Road

institute: Shandong University

summary: Illumina NovaSeq 6000 was used to deeply sequenced the mRNA expression of the AMB treated group, the AMB and Rimonabant combined treatment group and the vehicle-treated Candida albicans SC5314, and three repeated mRNA expressions were obtained. The analysis was performed at the isoform level by sequence reading through a quality filter. SYBR Green method was used for QRT-PCR validation. We found that after Amb treatment, the regulatory genes MDM12, PSD2, OPI3, INO2 and PMP3 related to lipid synthesis were up-regulated, and INO2 and MDM12 were significantly down-regulated after combined treatment.Some genes involved in lipid modification and oxidative phosphorylation also changed accordingly

overall_design: mRNA Profiles of Candida albicans SC5314 processed by Amb，Amb and Rimonabant,and vehicle-treated were obtained by deep sequencing.

first: Wenqiang

last: Chang

first: Hongxiang

last: Lou


title: Single cell RNA sequencing of in vivo OVCAR8 tumor cells

first: Lili

last: Yang

state: California

department: Microbiology Immunology & Molecular Genetics

first: Yan-Ruide

last: Li

first: Zhe

first: Miao

first: Yuning

last: Chen

first: Yichen

last: Zhu


title: Understanding early human knee joint development with a single cell RNAseq approach

city: Pok Fu Lam

first: Peikai

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

summary: Mature synovial joints consist of cruciate ligament, articular cartilage, superficial membrane and mensicus.  During limb development, all these structures are developed from a transient joint anlagen called the interzone. Studies in mouse are relatively well established but less imformation is available for human joint. This study captured progenitors and committed joint and surrounding growth plate cartilage from 4 human fetuses (from 9w to 18wk gestation time).

overall_design: Skin, muscles and surrounding soft tissues (inlcuding patella, patella tendon and  collacteral ligaments) were removed from the collected fetal knee joints  (with minimal growth plate tissues). Tissues were digested to single cell with collagenase P and sent for 10x genomics encapsulation. These 4 samples covered stages of early joint lineage committment (9w) to lineage maturation (18w). Progenitors and committed cells in cruciate ligament, articular cartilage, superficial zone, and meniscus were captured in these dataset. As meniscus is a fibrocartilage structure, one horn of mensicus was dissected and sequenced seperately (h18WMC), and the remaining parts of the joint was sequenced as h18WKJ.

first: Wilson

last: Chan

first: Danny


title: Exploring transcriptomic change related to DNA damage response in CM-Leukemia

city: MONROVIA

first: Yahuei

last: Kuo

address: 1218 S 5TH AVE

department: Hem Malignancies Trans Sci

institute: City of Hope National Medical Center

summary: To explore the underlying changes during the DNA damage in CBFB-MYH11 (CM) preleukemic hematopoietic stem cell and progenitor cells, we performed RNA-seq for CM-LSK, and control (Ctrl)-LSK cells at no IR (NIR) and 24h after irridiation (IR).

overall_design: The LSK population (Lin-Sca1+ckit+) was sorted out from the bone marrow of preleukemic stage Cbfb-MYH11 mice and wild-type mice and exposed to irridiation (3.5Gy). Twenty-four hours after the irridiation, cells were harvested and sujected to RNA extraction. LSK cells went through the same incubation process without irridiation were collected as control.

first: Lianjun

last: Zhang

first: Yu-Hsuan

last: Fu

first: Ya-Huei


title: Adverse neonatal outcomes are associated with a sex-specific placental inflammatory profile

city: Rochester

first: Sylvie

last: Girard

state: Minnesota

address: 200 First Street

institute: Mayo Clinic

summary:
Background and objective: The placenta is crucial for fetal development; altered function is associated with complications and adverse neonatal outcomes. Our goal was to ascertain changes in the placental transcriptome in relation to neonatal outcome and fetal/placental sex.
Study Design: 72 mother-baby dyads were included. Demographic, obstetrical, neonatal and infant health data were obtained through medical charts. Adverse neonatal outcome was defined as the presence of a pulmonary, cardiac, neurological or other health complication. Bulk RNA-sequencing of placental biopsies was obtained. P-value < 0.05 was considered statistically significant.
Results: Neonates experiencing adverse outcomes were more likely to be premature or have lower birth weights. Analysis of the placental transcriptome revealed a predominant inflammatory profile in pregnancies associated with adverse neonatal outcomes with the top pathways being related to immune and inflammatory responses. Amongst differently expressed genes (DEGs), 1237 were upregulated and 239 were downregulated in adverse vs no adverse outcomes. Furthermore, sex-specific differences in gene expression were observed and indicated that male and female placentas displayed unique DEGs in association with adverse outcomes. Indeed, no DEG was observed in female placentas when comparing those without vs with adverse neonatal outcomes, as opposed to 1279 DEGs in male placentas, of which 91% were up-regulated in adverse subgroups.
Conclusions: These findings highlight that inflammatory pathways are upregulated in placentas in association with adverse neonatal outcomes, and showcase the importance of the fetal sex in understanding neonatal health. The placenta provides a unique tool for early identification of high-risk infants rapidly after delivery.

overall_design: Placental villus biopsies were collected rapidly after delivery and placed into RNA later for 24h before being stored at -80ºC until processing. mRNA was extracted using the RNeasy mini kit (Qiagen, Canada) following manufacturer instructions. RNA was quantified by spectrophotometry (Nanodrop 8000, Thermo Fisher Scientific, Canada) and the quality was assessed using the RNA Integrity Number (RIN ≥ 7; Agilent 2100 Bioanalyzer, USA). Libraries were done using the TruSeq RNA Library Kit v2 (Illumina, USA) and fragment size was validated on a Bioanalyzer (Agilent 2100, USA). Libraries were sequenced using the HiSeq 4000 system (Illumina, USA) at the “Integrated Clinical Genomics Centre in Pediatrics”at the CHUSJ.

first: Camille

last: Couture

first: Marie-Eve

last: Brien

first: Jacqueline

last: Piche

first: Elizabeth

last: Cervantes

first: Thuy Mai

last: Luu


title: KRAS-mediated upregulation of CIP2A promotes suppression of PP2A-B56a to initiate pancreatic cancer development

first: Brittany

last: Allen-Petersen

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

overall_design: Refer to individual Series