title: Gene expression profile of S-180 tumour cells after treated with Fluoxetine 20uM for 12hr.

city: Purulia

first: Sankar

last: Bhattacharyya

state: West Bengal

address: Ranchi Road Sainik School

department: Zoology

country: India

institute: Sidho Kanho Birsha University

summary: To understand changes in  gene expression profile of S-180 cells in response to Fluoxetine treated for 12hr.

overall_design: S-180 tumor cells were treated with 20uM Fluoxetine for 12hr and compare the difference in gene expression profile between control counter part of S-180 cells which is not treated with Fluoxetine.  Whole cell mRNA were isolated using TRIzol reagent (ambionÒ, life technologiesTM). Each group of sample represents two biological replicates. 2 groups of samples as control and Fluoxetine treated S-180 cells with replicates, total 4 samples were analysed.

first: Krishna

last: Mahanti

first: Jayasree

last: Saha

first: Debanjan

last: Sarkar

first: Anik

last: Pramanik


title: DNA Methylation Profiling of Hepatic Insulin Response  in Young and Aged Mice

status: Public on May 14 2025

city: New Haven

first: Jessica

middle: Yuki

last: Kasamoto

state: CT

address: 300 George Street

department: Computational Biology and Bioinformatics

country: USA

institute: Yale University

type: Methylation profiling by genome tiling array

summary: To investigate age-related differences in hepatic insulin response at the epigenetic level, we profiled genome-wide DNA methylation in liver tissue from young (6-month-old) and old (20-month-old) male C57BL/6J mice following a hyperinsulinemic-euglycemic clamp. Mice underwent detailed metabolic phenotyping, including body composition analysis and indirect calorimetry, followed by surgical catheterization and a standardized insulin clamp procedure with stable isotope tracer infusions.  Liver tissue was collected immediately after the clamp, and DNA was extracted for methylation profiling using Illumina Infinium arrays. The tracer studies enabled quantification of hepatic fluxes through pyruvate dehydrogenase, fatty acid oxidation, citrate synthase, and pyruvate carboxylase.

platform_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus

overall_design: This study investigates age-related differences in hepatic DNA methylation in response to insulin stimulation using methylation array profiling. Male C57BL/6J mice aged 6 months (young) and 20 months (old) were obtained from The Jackson Laboratory (stock number: 000664). Mice were maintained under standard housing conditions and underwent comprehensive metabolic phenotyping.    Body composition was assessed using Bruker’s Minispec Whole Body Composition Analyzer. Mice were acclimated to single housing before being placed in metabolic cages (Columbus Instruments CLAMS) for measuring. Following phenotyping, mice underwent jugular vein catheterization and recovery. After a 14-hour overnight fast, a 150-minute hyperinsulinemic-euglycemic clamp was performed, during which [2H7]glucose was infused to maintain euglycemia (~115 mg/dL), along with continuous infusion of metabolic tracers [3-13C]lactate and [U-13C]palmitate to assess substrate flux (results contained in metadata).    After the clamp, mice were euthanized, and liver tissues were collected and snap-frozen. Genomic DNA was extracted from liver tissue, and genome-wide DNA methylation profiling was performed using Illumina Infinium arrays.    The design comprises two biological groups: young (6-month-old, n=8) and old (20-month-old, n=10) insulin-stimulated mice.

first: John

middle: T

last: González

first: Olivia

middle: H

last: Scharfman

first: Wanling

last: Zhu

first: Victoria

last: Gould

first: Rachel

middle: J

last: Perry

first: Albert

last: Higgins-Chen


title: Cytokine-induced memory-like responses in endothelial cells link chronic inflammation to vascular disease risk

city: Nijmegen

first: Nick

last: Keur

address: Geert Grooteplein Zuid 10

department: Internal medicine

country: Netherlands

institute: Radboudumc

type: Expression profiling by high throughput sequencing

summary: Chronic inflammation plays a central role in the progression of both infectious and vascular diseases, yet its impact on endothelial cells (ECs), which form the interface between blood and tissue, remains poorly understood. Given their constant exposure to inflammatory cytokines such as TNF-α and IFN-γ, we set out to investigate how cytokine induced inflammation shapes EC function at the molecular level. Using primary human umbilical vein endothelial cells (HUVECs), we modeled repeated cytokine exposure to simulate a chronically inflamed microenvironment. Transcriptomic and epigenetic profiling revealed that ECs respond to this chronic stimulation with durable transcriptional and chromatin changes. These responses included phenotypes resembling immune cell priming, training, and tolerance, which are commonly associated with innate immune memory, a phenomenon whereby innate immune cells mount altered response following previous stimulation. Although we did not observe classical trained immunity pathways, several genes known to mediate immune training, including TLR2, IL1B, and HDAC9, exhibited persistent activation following TNF-α re-exposure. IFN-γ stimulation uniquely induced sustained expression and chromatin accessibility at MHC class II loci, suggesting cytokine-specific modes of reprogramming. Functionally, re-stimulated ECs exhibited enhanced monocyte adhesion in a 3D vessel-on-chip model, highlighting the relevance of these molecular changes to vascular inflammation. Moreover, the regulatory regions altered by cytokine exposure were enriched for disease-associated SNPs, particularly those linked to COVID-19, sepsis, and cardiovascular disorders. In summary, these findings reveal that repeated exposure to cytokines as seen in chronic inflammation can induce memory-like responses in ECs and suggest that endothelial reprogramming may contribute to vascular dysfunction.

overall_design: Restimulation of endothelial cells with cytokines to investigate the immunological memory using RNAseq and ATACseq

first: Kieu

last: Le

first: Heleen

last: Middelkamp

first: Thuy

middle: L

last: Do

last: van den Berg

first: Valeria

last: Orlova

first: Leo

middle: A

last: Joosten

first: Mihai

middle: G

last: Netea

first: Iris

last: Jonkers

first: Sebo

last: Withoff

first: Andries

middle: D

last: Van der Meer


title: Developmental features and unique characteristics of peptide-specific PLZF+ innate-like T cells

city: Hannover

first: Ahmed

last: Hassan

address: Carl-Neuberg-Straße 1

country: Germany

institute: Hannover Medical School

summary: Innate-like T cells are considered a family of T lymphocytes capable of mounting quick responses, yet restricted to conserved antigens of non-peptide nature. Here, we performed single-cell transcriptomic analyses of peptide-specific PLZF+ innate-like T (PILT) cells and compared them to other members of the innate-like T cell family. Our data revealed that PILT cells share similar transcriptional profiles and overlapping developmental trajectories with invariant Natural Killer T (iNKT) cells as well as mucosal-associated invariant T (MAIT) cells. Yet, in contrast to iNKT and MAIT cells, PILT cells displayed a polyclonal T cell receptor (TCR) repertoire closely resembling the one of conventional CD8 T cells, inferring MHC I restriction and a broader range of antigen specificity. We further show that artificial thymic organoid cultures (ATOC) support selection and development of PILT cells in vitro exhibiting similar transcriptional profiles to their counterparts maturing in the thymus. Lastly, using an “on-time” T-cell receptor retrogenic ATOC system, we demonstrate that PILT1 derived TCR clonotypes favour acquisition of PILT1 innate-like phenotype during T cell development in vitro suggesting an instructive role of TCR specificity in PILT cell lineage commitment and  functional differentiation.

overall_design: Experiment 1. Single-cell suspensions of thymocytes were prepared from 3 WT mice and 3 MHC-T mice (10 weeks old). All samples were subjected to CD8 depletion, stained with appropriate antibody mix followed by FACS sorting. Sorted cells were mixed in a ratio of 1:4 (iNKT:PILT enriched population) and 20,000 cells were used for GEM1 generation.     Experiment 2. Single-cell suspensions of thymocytes were prepared from 3 WT mice and 3 MHC-T mice (10 weeks old) and then split into two equal parts. Part 1 was depleted for CD8 (as in Experiment 1) and Part 2 was not. Both parts were stained with appropriate antibody mix followed by FACS sorting. Sorted cell fractions were then mixed in a ratio of 1:4 (iNKT:PILT-enriched population) and 40,000 cells were used for GEM2 (CD8 depleted) and GEM3 (non-deplete) generation.   Experiment 3. Single-cell suspensions of thymocytes were prepared from 3 CD1d-/- mice (10 weeks old), stained with appropriate antibody mix followed by FACS sorting. Sorted cells were then mixed and 40,000 cells were used for GEM4 generation.   Experiment 4. For samples week1:5, we collected and pooled three organoids per time point in organoid collection buffer. The sample was then split into two equal parts. Part 1 was stained with an appropriate antibody mix and subjected to FACS sorting for iNKT cells (Live/CD19-/TCRβ+/CD1d-PBS57+). Part 2 was stained with an appropriate antibody mix and subjected to FACS sorting for PILT-enriched population (Live/CD19-/TCRb+/CD1d-PBS57-/TCRβ+/CD44+ and/or PD-1+). All sorted iNKT cells were then pooled with 40,000 cells from the PILT-enriched population and used for GEM5 generation.  Experiment 5. For week 0 sample, FACS sorted DN1-3 thymocytes from 3 WT mice (10 weeks old) were used as shown in (Supplementary Fig. 6B). Samples for weeks 1:5 were collected from the corresponding organoids in an organoid collection buffer and then stained using Zombie Green™ Fixable Viability Kit.  FACS sorted live thymocytes from samples from weeks 0:5 were then mixed in equal numbers and 40,000-pooled cells were then used for GEM6 generation.   For experiments 1, 2, and 3 the GEMs were generated by Chromium controller (10x Genomics) using Chromium Single Cell V(D)J Reagent Kits (v1.1). For experiments 4 and 5 the GEMs were generated by Chromium Xi (10x Genomics) using Chromium Single Cell 5' Reagent Kits (v2 - Dual Index). The library preparation was carried out as per manufacturer recommendations for each of the kits. Generated sequencing libraries were either sequenced by Illumina’s NextSeq 550, NovaSeq 6000 or NovaSeqX with an average read per cell of 40,000 for gene expression libraries and an average of 10,000 reads per cell for VDJ and hashtag libraries. Schematic representation of the layout of all single-cell RNA sequencing experiments is depicted in (Supplementary Fig. 1B and C).

first: Hristo

last: Georgiev


title: Occupancy of synaptonemal complex at mouse genome

city: Wuhan

first: Li-quan

last: Zhou

state: Hubei

address: 13 Hangkong road

department: Tongji Medical College

country: China

institute: Huazhong University of Science and Technology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: As the vital components of synaptonemal complex, SYCP3 plays an important role in meiosis by self-assembling into a special bilayer structure. Although SYCP3 has been widely studied, the genome-wide binding of SYCP3 remains largely unknown. In this study, we identified specific binding of SYCP3 in mouse spermatocytes and studied how its binding dynamics is regulated.

overall_design: Mouse spermatocytes were collected from male mouse testis, followed by ChIP-seq assay to identify specific protein occupancy.

first: Ying

last: Yin


first: Vinod

last: Kumar


title: Hochuekkito accelerates recovery from cisplatin induced-muscle atrophy accompanied by slow-twitch fiber-specific microRNA upregulation in mice

status: Public on May 15 2025

city: Inashiki-gun

first: Hitomi

last: Sekine

state: Ibaraki

address: 3586, Yoshiwara, Ami-machi

department: TSUMURA Kampo Research Laboratories Kampo Research & Development Division

country: Japan

institute: TSUMURA & CO.

type: Non-coding RNA profiling by high throughput sequencing

summary: Hochuekkito (HET) increased locomotor activity and muscle weight in cisplatin induced muscle atrophy model mice, probably by enhancing myogenesis in slow-twitch fibers, which was related to miRNA expression changes. Thus, HET may be useful in treating cisplatin-induced muscle atrophy.

overall_design:
Eight-week-old male C57BL/6J mice were administered with cisplatin (3 mg/kg/day, intraperitoneally) from Day0 to Day3 and provided with hochuekkito (HET) -containing food from 2 weeks before cisplatin administration until Day14.
The red regions of gastrocnemius muscle were harvested on Day 14 for microRNA sequence analysis.
The analysis was conducted using three groups: Vehicle group (saline + control diet); n = 10, cisplatin group (cisplatin + control diet); n = 15, and 3% HET group (cisplatin + 3% HET-containing diet); n = 15.

first: Chinami

last: Matsumoto

first: Naoki

last: Fujitsuka

first: Sachiko

last: Mogami

first: Shunsuke

last: Ohnishi

first: Hiroshi

last: Takeda


title: Regulation of MORC-1 is key to the CSR-1-mediated germline gene licensing mechanism in C. elegans

city: Los Angeles

first: Colette

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

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

overall_design: Refer to individual Series


title: First Generation Tools for the Modeling of Capicua-Family Fusion Oncoprotein-Driven Cancers (February 2025 Dataset)

status: Public on May 13 2025

city: San Francisco

first: Ross

last: Okimoto

address: 513 Parnassus Ave

institute: University of California, San Francisco

summary: The rearrangement of separate genes into neomorphic fusion oncogenes can occur after chromosomal damage and repair, causing cancer. In the case of sarcomas, several tumor types are driven by fusion oncogenes comprised of various partner genes. We study fusions involving capicua (CIC), a developmental transcriptional repressor whose fusion to 3' partner genes including DUX4, NUTM1, and LEUTX drives devastating tumors of the soft tissue, central nervous system, and spine. Here we develop the first tools to investigate previously understudied fusions of CIC and ATXN1 and express them in 293T cells to uncover convergent/divergent biology between various CIC-family fusions depending on what the specific partner genes are.

overall_design: polyA-selected bulk RNAseq of 293T cells transfected with empty vector, HA-ATXN1::DUX4, or HA-ATXN1::DUX4 delAXH expressing constructs, 48 hours post transfection.

first: Cuyler

last: Luck

first: Kyle

last: Jacobs

first: Julia

last: Riad

first: Christopher

last: Macaraig

first: Rovingaile Kriska

middle: M

last: Ponce


title: Multi-omics analyses construct an inflammatory response based prognostic gene signature for cervical cancer and suggest tumor infiltrating monocytes subgroups as key players

city: Beijing

first: Yidong

last: Zhang

state: Bijing

address: No 1. Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: A multi-gene model based on inflammatory response relevant genes was constructed for cervical cancer patients. The association of patients’ scores for the model and the characteristics of tumor microenvironment as well as patients’ predicted response to anti-cancer treatments was analyzed. Based on the single-cell RNA-sequencing (scRNA-seq) data, two tumor infiltrating monocytes (TIM) clusters were found to be associated with the inflammatory response in the tumor microenvironment. The tumour tissues of 23 cervical adenocarcinoma patients in our hospital were collected and bulk RNA-sequencing was carried out. The correlation of marker genes of the two TIM clusters and patients’ score of the multi-gene model was analyzed to validate the findings on the scRNA-seq data.

overall_design: The Pearson correlation of marker genes of TIM clusters and patients' inflammtion score was calculated to validate the findings on the scRNA-seq data.

first: Jiawei

last: Zhu

first: Ke

last: Hu

first: Jie

last: Qiu

first: Fuquan


summary: The Argonaute CSR-1 is essential for germline development in C. elegans. Loss of CSR-1 leads to the downregulation of thousands of germline-expressed genes, supporting a model in which CSR-1 “licenses” gene expression via a poorly understood mechanism. In contrast, a small subset of genes is upregulated in csr-1 mutants, including morc-1, which encodes a conserved GHKL-type ATPase. We show that morc-1 is overexpressed in csr-1 mutants and accumulates over CSR-1 licensed targets, coinciding with aberrant gain of H3K9me3, reduced H3K36me3, and transcriptional repression. Strikingly, loss of morc-1 fully rescues these chromatin defects and partially restores gene expression and fertility in csr-1 mutants. Conversely, ectopic overexpression of MORC-1 in the wild-type germline is sufficient to repress CSR-1 licensed targets and severely compromise fertility. These findings support a model in which CSR-1 prevents MORC-1 overexpression and consequent misregulation of CSR-1 licensed genes.

overall_design: RIP-seq to assess the population of sRNAs bound by CSR-1, and how this is altered in the CSR-1(G560R) mutant. Each sample includes an IP and matched input control, and experiment was performed in triplicate.

first: Jessica

last: Kirshner

first: Natasha

middle: E

last: Weiser

first: Nicita

last: Mehta

first: Suhua

last: Feng

first: Victoria

middle: N

last: Murphy

first: Anna

last: Vakhnovetsky

first: Amelia

middle: F

last: Alessi

first: Connie

last: Xiao

first: Kai

last: Inoki

first: Sonia

last: El Mouridi

first: Christian

last: Frøkjær-Jensen

first: Steven

last: Jacobsen

first: John

middle: K

last: Kim


title: First Generation Tools for the Modeling of Capicua-Family Fusion Oncoprotein-Driven Cancers (April 2023 Dataset)

first: Ross

last: Okimoto

overall_design: polyA-selected bulk RNAseq of 293T cells transfected with empty vector, HA-CIC::DUX4-, or HA-CIC(ex20)::NUTM1(ex6)-expressing constructs, 48 hours post transfection.

first: Cuyler

last: Luck

first: Kyle

last: Jacobs

first: Julia

last: Riad

first: Christopher

last: Macaraig

first: Rovingaile Kriska

last: Ponce


title: First Generation Tools for the Modeling of Capicua-Family Fusion Oncoprotein-Driven Cancers (May 2024 Dataset)

overall_design: polyA-selected bulk RNAseq of 293T cells transfected with empty vector or one of several CIC-fusion full length/mutant expressing constructs, 48 hours post transfection.


title: Metastatic site influences driver gene function in pancreatic cancer

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center


title: Sex-specific transcriptome dynamics of Anopheles gambiae during embryonic development [Ag55 CUT&Tag]

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

institute: Institute of Molecular Biology (IMB)

summary: Malaria-transmitting mosquitoes are extremely sexually dimorphic in their anatomy and behaviour. Sex-specific gene expression in Anopheles gambiae is well-studied in adult stages, but its onset during embryogenesis, apart from sex-determination factors like Yob, remains largely unknown. Here, we report a comprehensive single-embryo transcriptome atlas of A. gambiae males and females to understand the earliest stages of establishing the sex-specific expression networks. Our dataset reveals embryonic RNA isoform diversity including a global shift towards distal alternative polyadenylation (APA) events sites during the maternal-to-zygotic genome transition. Sex-biased gene expression and alternative splicing are limited during embryogenesis, with most sex-specific patterns emerging post-embryonically. X chromosome dosage compensation is established shortly after zygotic genome activation concomitant with direct binding of the master regulator protein SOA to X-linked promoters. In contrast to DC regulators in Drosophila and mammals, we find rather weak evidence in Anopheles for early binding sites or distance-dependent patterns. Instead, both compensation and binding tend to occur locally and uniformly across genes and developmental stages. The most highly expressed genes tend to show the strongest SOA binding. We propose that the Anopheles dosage compensation system represents an extreme case of a gene-by-gene regulatory mechanism that operates at the chromosome-wide level.

overall_design: CUT&Tag samples are analyzed. Each group has two biological replicates. The IgG antibody is a negative control for unspecific binding of the antibodies.

first: Agata

middle: I

last: Kalita

first: Eric

last: Marois

first: Claudia

last: Keller Valsecchi


title: DNA G-quadruplex structures act as functional elements in α- and β-globin enhancers

city: Cambridge

first: Larry

last: Melidis

state: Not US or Canada

address: Robinson Way

department: CRUK-CI

country: United Kingdom

institute: University of Cambridge

summary:
Enhancer elements interact with target genes at a distance to modulate their expression, but the molecular details of enhancer-promoter interaction are incompletely understood. G-quadruplex DNA secondary structures (G4s) have recently been shown to co-occur with 3D chromatin interactions, however, the functional importance of G4s within enhancers remains unclear.
Results: In this study we identify novel G4 structures within two locus control regions at the human α- and β- globin loci. We find that mutating G4 motifs by genome editing prevents their folding into G4 structures in cells and disrupts 3D enhancer-promoter interactions and target gene expression in a manner comparable to whole enhancer deletion. Furthermore, restoration of G4 structure formation using a dissimilar G4-forming primary sequence recovers specific enhancer-gene interactions and gene expression. Through proteomic, biophysical, and genomic profiling, we find that enhancer G4s are tightly linked to the maintenance of an active chromatin state and RNA polymerase II recruitment to regulate target gene expression.

overall_design: CUT&Tag, RNA-seq, 4C

first: Colm

last: Doyle

first: Krzysztof

last: Herka

first: Sean

last: Flynn

first: Somdutta

last: Dhir

first: David

last: Tannahill

first: Shankar

last: Balasubramanian


title: Sex-specific transcriptome dynamics of Anopheles gambiae during embryonic development [Ag55 ChIP-Seq]

overall_design: ChIP-Seq samples are analyzed with two biological replicates per group. Input controls were used as negative controls for unspecific background signal.


title: Human Endothelial Cell Effects on Human Neural Stem/Progenitor Cells

city: Irvine

first: Lisa

last: Flanagan

state: CA

address: 845 Health Sciences Rd

institute: University of California, Irvine

summary: Endothelial cells and neural stem/progenitor cells communicate during development and in adult neural stem cell niches. However, much remains unclear regarding the coordinated regulation of these cells, particularly in humans. We used single cell RNA sequencing (scRNA-seq) to determine how human endothelial cells (hECs) affect human neural stem/progenitor cells (hNSPCs). We assessed hNSPC gene expression and cell phenotype after hEC contact or exposure to hEC secreted factors via conditioned media. HEC contact increases the percentage of type B hNSPCs and upregulates Notch downstream signaling, identifying a new mode of hNSPC regulation by hECs. Furthermore, hECs increase hNSPC expression of vessel promoting genes, providing a mechanism by which hNSPCs stimulate hEC vessel formation. This human scRNAseq dataset is crucial for deciphering hEC-hNSPC communication.

overall_design: Human neural stem/progenitor cells (hNSPCs) were grown on laminin-coated plates in media control, with human endothelial cell (hEC) conditioned media, or with hECs in co-culture for 5 days for scRNA-seq analysis. HECs alone were also cultured for 5 days in media control. Cells were harvested and sequences using the 10x Genomics platform.

first: Brenda

last: Gutierrez


title: Diversity and complexity of auditory representation in the hearing systems of Aedes aegypti mosquitoes

status: Public on May 12 2025

city: Nagoya

first: Takuro

middle: S

last: OHASHI

address: E-324, Science building, Furo-cho, Chikusa-ku

institute: Nagoya University

summary: While low-frequency sounds have been reported to stimulate dispersal responses in male and female mosquitoes, only males show attraction to sound. Male attraction to female flight tones is important during courtship; however, groups of males show diverse responses to acoustic stimuli, suggesting auditory processing can vary drastically between the sexes and individual males. To investigate diversity in auditory representation within and between the sexes, we utilised molecular and functional analyses to explore Aedes aegypti mosquito auditory processing. We identified shared and dimorphic neurons connecting mosquito ears to the brains’ primary auditory processing center. Calcium imaging from this brain region facilitated definition of multiple neuronal clusters based on auditory stimulation responses. More clusters with greater complexity were identified in males than females, with these clusters highly differentiated amongst males. Transcriptomic and proteomic analyses found enrichment of ciliary-related factors in male ears compared to females, potentially underlying sexual dimorphisms in hearing systems.

overall_design: RNA-seq profiling of head and pedicel in males and females. Groups of virgin Liverpool male or non-blood fed female mosquitoes were flash-frozen in liquid nitrogen at ZT12 after entrainment in an incubator for two days. Five repeats of pedicels and heads were collected, and RNA extracted from homogenized samples.

last: Ohashi

first: Yifeng

middle: Y

last: Xu

first: Shunsuke

last: Shigaki

first: Yukiko

last: Nakamura

first: Tai-Ting

last: Lee

first: YuMin

last: Loh

first: Emi

last: Mishiro-Sato

first: Daniel

last: Eberl

first: Matthew

middle: P

last: Su

first: Azusa

last: Kamikouchi


first: Colette

last: Picard

overall_design: To check if our csr-1 mutants affect CSR-1-bound sRNAs, we performed sRNA-seq of our csr-1 mutants and matched controls (control for csr-1(G560R) is N2, control for aid::csr-1 1mM auxin in aid::csr-1 0mM auxin), all samples done in triplicate.

first: Jessica

last: Kirshner

first: Natasha

last: Weiser

first: Nicita

last: Mehta

first: Suhua

last: Feng

first: Victoria

last: Murphy

first: Anna

last: Vakhnovetsky

first: Connie

last: Xiao

first: Kai

last: Inoki

first: Sonia

last: El Mouridi

first: Christian

last: Frøkjær-Jensen

first: Steven

last: Jacobsen

first: John

last: Kim


title: Transcriptomic analysis reveals genetic factors underlying impaired symbiotic nitrogen fixation in lines derived from crosses between cultivated peanut (Arachis hypogaea L.)  and its wild ancestors

city: Dakar

first: Darius

last: Tchoutang Nzepang

address: Route des hydrocarbures

country: Senegal

institute: IRD

summary: Symbiotic nitrogen fixation (SNF) is a complex process regulated by numerous genes extensively studied in legumes that undergo intracellular infection, such as Lotus japonicus, Medicago truncatula, and Glycine max. However, the molecular and genetic mechanisms of SNF in legumes that rely on the intercellular infection pathway, such as peanut (Arachis hypogaea L.), remain poorly understood. In a previous study, we identified two chromosome segment substitution lines (CSSLs), 12CS_051 and 12CS_044, each contains a wild segment on homeologous regions of chromosomes A02 and B02 respectively, that are severely impaired in nitrogen fixation. In this study, we have compared the transcriptomes of those lines with that of their recurrent parent, Fleur11, in roots inoculated with the effective Bradyrhizobium vignae strain ISRA400 to identify candidate genes associated with the reduced nitrogen fixation observed in these CSSLs. A comparative analysis of the transcriptome profiles of the CSSLs and Fleur11 revealed significant changes in the expression of genes involved in plant immune signaling and key symbiotic genes, such as NIN, EFD, FEN1 or SNF-related transporters. These results align with the phenotypic differences observed during the symbiotic process in the CSSLs. When focusing on each QTL region, we found that only the orthologs of the symbiotic gene FEN1, which is responsible for the failure in the enlargement of infected cells in L. japonicus, exhibited a lack of expression in the two CSSLs compared to Fleur11. FEN1 encodes a homocitrate synthase that is essential for the nitrogenase activity. We hypothesize that changes in the expression of FEN1 could affect the nitrogenase activity, potentially leading to the unfair SNF observed in these lines. In this study, we analyzed the expression profiles of two ineffective nitrogen-fixing chromosome segment substitution lines and identified FEN1 as a suitable candidate gene involved in peanut symbiosis. This research provides valuable insights into understanding and improving SNF in peanut.

overall_design: RNA-Seq profiling of two CSSLs (12CS_051 and 12CS_044) and their recurent parent Fleur11 at 0, 12, and 21 days post-inoculation

last: Nzepang T.

first: Maimouna

last: Cissoko

first: Djamel

last: Gully

first: Valérie

last: Hocher

first: Jean-François

last: Rami

first: Saliou

last: Fall

last: Fonceka

first: Sergio

last: Svistoonoff


title: Transcriptome analysis of fat globules in milk of cows with differential genotype for β-casein

city: Pamplona

first: Olaia

last: Urrutia

state: Navarra

address: Campus Arrosadia S/N

department: Agronomy, Biotechnology and Nutrition

country: Spain

institute: Public University of Navarre

summary: In the framework of A2 milk production, a better understanding of the molecular mechanisms of the milk synthesis is needed. The transcriptome profiling  of mamamry gland of Holstein cows with A1A1 genotype (n = 7) and A2A2 genotype (n = 7) for β-casein was analysed by RNA-seq technology. Total RNA was isolated from milk fat globules (non-invasive source of mammary RNA). Out of the 11,180 and 11,257 genes expressed in milk fat globules (identified with DESeq2 and EdgeR packages, respectively), only two genes were detected as differentially expressed between A1A1 and A2A2 genotype cows, indicating that both groups had very similar mammary gland transcriptome profiles. The majority of the highly expressed genes in milk fat globulesduring lactation (FPKM ≥500) were involved in biological process and molecular functions related to protein synthesis and energy production, as lactation is one of the most energetically demanding process for female mammals.

overall_design: To investigate the milk fat globules transcriptome of two groups of cows with differential genotype for β-casein, a total of 14 milk fat globule RNA samples from Holstein cows were analysed. 7 milk samples were collected from cows with A1A1 genotype for β-casein and 7 samples were collected from cows with A2A2 genotype.

first: Lucía

last: Jiménez-Montenegro

first: Leo

last: Alfonso

first: Beatriz

last: Soret

first: José

last: Mendizabal


title: Herpes simplex virus type 1 reshapes the host chromatin architecture via transcription machinery hijacking

city: Guangzhou

first: Alvaro

last: Castells-Garcia

state: Guandong

address: 106 Zhongshan Er Road, Yuexiu district

department: Medical Research Department

institute: Guandong Peoples Hospital

summary: To discover the mechanism by which herpes simplex virus type 1 (HSV-1) widely reshapes the structure of host chromatin during lytic infection, we used chromosome capture technologies (HiC). We infected A549 cells with HSV-1, and analized its chromatin structure before infection and at 1, 3 and 8 hours post infection. We report both Human-Human contacts and Human-Virus trans-contacts.

overall_design: HiC-seq samples from A549 cells and A549 cells infected with Herpes Simplex Virus type 1 (HSV1), at 1, 3 and 8 hours post infection.

first: Esther

last: Gonzalez Almela

first: Francois

last: le Dily

first: Davide

last: Carnevali

first: Maria

last: Cosma


title: Herpes simplex virus type 1 reshapes the host chromatin architecture via transcription machinery hijacking [RNA-seq]

summary: To discover the mechanism by which herpes simplex virus type 1 (HSV-1) drastically reshapes the host cell transcriptional patterns during infection, we performed RNAseq. We infected A549 cells with HSV-1, and analized host and viral expression at 1, 3 and 8 hours post infection. We report both a drastical human transcription shutoff parallel with an increase in viral transcription.

overall_design: RNAseq samples from A549 cells and A549 cells infected with Herpes Simplex Virus type 1 (HSV1), at 1, 3 and 8 hours post infection.


title: Bone marrow neutropoiesis bias underlies inflammatory comorbidities [smart_seq2]

first: Yuman

last: Li

address: No.22 , Zhongguancun South Avenue, Haidian District, Beijing

institute: Peking University School and Hospital of Stomatology

summary: Local chronic inflammation exacerbates the prevalence and severity of associated distal organ comorbidities, causing catastrophic consequences for patients. However, the underlying mechanisms remain unclear. Here, we found that periodontitis increased the circulating pro-inflammatory neutrophils, which could be easily recruited to rheumatoid arthritis (RA) joints and aggravated articular destruction. Single-cell multiomics sequencing has revealed that periodontitis induces transcriptomic and epigenomic rewiring of hematopoietic stem and progenitor cells (HSPCs), which display skewed differentiation toward the neutrophil lineage, resulting in an increase in pro-inflammatory neutrophils. We further identified that periodontitis-elevated type I interferons are responsible for guiding the continuous neutropoiesis bias in the bone marrow. Resolution of periodontitis can reverse the differentiation bias of HSPCs and alleviate the progression of RA. This study indicated that neutropoiesis bias induces the progression of inflammatory comorbidities and emphasizes the necessity of controlling local chronic inflammation in the management of inflammatory comorbidities.

overall_design: Neutrophils from the peripheral blood of mice, which underwent 14-day silk ligation or remained untreated for 14 days, were isolated by fluorescence-activated cell sorting (FACS) and analyzed using smart-seq2.

first: Yuting

last: Niu

first: Chenyu

last: Deng

first: Yue

last: Yang

first: Shiyu

last: Sun

first: Yao

first: Yiming

last: Chen

first: Bo

last: Hu

first: Ying

last: He

first: Xuehui

last: Zhang

first: Wenwen

last: Liu

first: Yan

last: Wei

first: Mingming

last: Xu

first: Lili

first: Guojun

last: Han

last: Huang

first: Xuliang


title: Bone marrow neutropoiesis bias underlies inflammatory comorbidities

overall_design: Refer to individual Series


title: Bone marrow neutropoiesis bias underlies inflammatory comorbidities [RNA-Seq]

overall_design: Neutrophils from the bone marrow of mice, which underwent 14-day silk ligation or remained untreated for 14 days, were isolated by fluorescence-activated cell sorting (FACS) and analyzed using RNA-seq.


title: Gene expression profile at single cell level from rhesus macaque fetal brain prefrontal cortex and human organotypic dlPFC slices.

city: madison

first: Xinyu

last: Zhao

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin-Madison

summary: The dorsolateral prefrontal cortex (dlPFC) is a derived cortical area in primates that is involved in myriad high-cognitive functions and is associated with several neuropsychiatric disorders. Here, we performed patch-seq and single-nucleus multiomic analyses of the rhesus macaque dlPFC to identify genes governing neuronal maturation during midfetal to late-fetal development. We also employed patch-seq analysis to assess the impact of CHD8 knockdown on human midfetal neuronal development with human organotypic dlPFC slices.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Nuclei were isolated from the prefrontal cortex of rhesus macaque fetal brains and subsequently subjected to single-nuclear ATAC-seq(snATAC-seq) and single-nuclear RNA-seq(snRNA-seq) using the 10X Genomics platform. The rhesus macaque acute slice cells obtained from the prefrontal cortex of the fetal brain were patched, and the nucleus of each cell was subsequently isolated for single-nuclear SAMRT-seq(patch-seq). Also, We performed patch-seq on cells from human organotypic dlPFC slices that contained both CHD8 knockdown(infected by lentivirus expressing both mScarlet and shRNA against CHD8) and control cells(infected by lentivirus expressing both mNeon and control shRNA).

first: Yu

last: Gao

first: Qiping

last: Dong

first: Kalpana

last: Arachchilage

first: Daifeng

last: Wang

first: Qiang

last: Chang

first: André

last: Sousa


title: scATAC-seq data of pig brains

status: Public on May 11 2025

first: yi

last: huang

address: No.1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: Pig brains are valuable models for studying brain diseases due to their structural similarities to human brains. However, understanding the regulatory mechanisms in pig brains is challenging due to cellular heterogeneity. This study aimed to investigate the heterogeneity of pig brains and uncover the underlying regulatory mechanisms at single-cell resolution. We created the first single-cell chromatin accessibility atlas of the cerebral cortex and cerebellum in domestic pigs and wild boars using single-cell ATAC-seq (scATAC-seq). We profiled 71,798 cells, identifying nine cell types, and integrated single-cell RNA sequencing (scRNA-seq) data to characterize cell type-specific regulatory landscapes and oligodendrocyte development. Our analysis revealed that oligodendrocyte progenitor cells exhibit the fastest evolutionary rate between domestic pigs and wild boars. Additionally, cross-species comparison showed that pig regulatory elements are more conserved with humans than those in mice. Notably, genetic variant enrichment studies found that regulatory elements associated with Alzheimer’s disease were significantly enriched in pigs but not in mice, suggesting pigs as a potentially superior model for this condition. Conversely, neurological diseases like schizophrenia and bipolar disorder showed higher enrichment in mice.

overall_design: We dissected the cerebral cortex and cerebellum of a duroc pig and a wild boar. The cerebral cortex was further subdivided into the frontal, parietal, occipital, and temporal lobes. scATAC-seq experiments were performed on these samples.

first: Yue

last: Xiang

first: Saixian

first: Yi

first: Zhuqing

last: Zheng

first: Jiahui

last: Sun

first: Qiulin

first: Peng

last: Zhou

first: Xiaolong

last: Qi

first: Jingjin

last: Li

first: Fuyang

last: Xiong

first: Jing

first: Shengquan

first: Liangliang

last: Fu

first: Xinyun


title: Cancer-induced FOXP1 disrupts and reprograms skeletal muscle circadian transcription in cachexia [skeletal muscle overexpression of FoxP1 RNA-seq]

city: Gainesville

first: Andrew

middle: R

last: Judge

state: FL

address: 1275 Center Drive, Biomedical Sciences Building RM J303

institute: University of Florida

summary: Cancer cachexia is a debilitating metabolic disorder characterized by involuntary loss of body and muscle mass, leading to increased morbidity and mortality. We previously found that Forkhead box P1 (FoxP1) upregulation in skeletal muscle causes muscle wasting and is required for muscle wasting in response to cancer. However, transcriptional networks targeted by FoxP1 in skeletal muscles undergoing cancer-induced wasting remain largely unknown. Here, we identify FoxP1 as a key disruptor of the skeletal muscle clock in response to cancer, that reprograms circadian patterns of gene expression at cachexia onset. Specifically, we show that cancer-induced FoxP1 rewires the skeletal muscle circadian transcriptome towards pathways associated with muscle wasting and disrupts the temporal patterning of pathways governing glucose, lipid, and oxidative metabolism. These findings thus implicate cancer/disease-specific functions of FOXP1 in the disruption and reprograming of the skeletal muscle circadian transcriptome which may contribute to muscle wasting and the development of cachexia.

overall_design: Tibialis anterior (TA) muscles were isolated and flash frozen in liquid nitrogen from 13- to 18-week-old female mice genetically modified to enable tamoxifen-inducible skeletal muscle-specific FoxP1 overexpression (FoxP1iSkmOE / FoxP1iSkmTG) and aged matched Control mice (n = 5 mice/group). RNA isolation was performed by homogenization of TA muscles in Trizol followed by extraction with chloroform, precipitation with isopropanol, and treatment with DNAse. RNA sequencing was performed by Novogene (Novogene Co, Ltd., Sacramento, CA).

first: Sarah

first: Jeremy

middle: B

last: Ducharme


title: Cancer-induced FOXP1 disrupts and reprograms skeletal muscle circadian transcription in cachexia [ChIP-seq]

overall_design: Gastrocnemius-plantaris muscle complexes were isolated and pooled from the hind limbs of 10-week-old C57BL/6J male mice following a 30-hour fast (n=2), and 12-week-old C57BL/6J male mice with or without KPC pancreatic tumors (n=2 mice/group). Isolated whole muscle samples were sent to Active Motif (Carlsbad, CA) for ChIP-sequencing. A ChIP reaction was carried out using 15 µg of skeletal muscle chromatin and anti-FoxP1 antibody (Millipore, ABE68, RRID:AB_10631734). ChIP DNA sequences generated by a standard Illumina ChIP-sequencing library were aligned to the mouse genome (mm10). Binding events were called and identified using MACS with the manufacturer default cutoff of P < 1 × 10-7. De novo motifs were identified via HOMER.


title: Bone marrow neutropoiesis bias underlies inflammatory comorbidities [multiomics]

first: Yuman

overall_design: HSPCs (Lin-cKit+) from the bone marrow of mice, which underwent 14-day silk ligation or remained untreated for 14 days, were isolated by fluorescence-activated cell sorting (FACS) and analyzed using single-cell multiomics sequencing.

first: Yuting

last: Niu

first: Chenyu

last: Deng

first: Yue

last: Yang

first: Shiyu

first: Yao

first: Yiming

last: Chen

first: Bo

last: Hu

first: Ying

last: He

first: Xuehui

last: Zhang

first: Wenwen

last: Liu

first: Yan

last: Wei

first: Mingming

last: Xu

first: Lili

first: Guojun

last: Han

last: Huang

first: Xuliang


title: Delayed forebrain excitatory and inhibitory neurogenesis in STRADA-related  megalencephaly via mTOR hyperactivity

status: Public on May 09 2025

city: Frederick

first: Tomozumi

last: Imamichi

state: MD

address: Frederick National Laboratory for Cancer Research

department: Applied and Developmental Research Directorate

institute: National Institutes of Health

summary: Biallelic pathogenic variants in STRADA, an upstream regulator of the mechanistic target of rapamycin (mTOR) pathway, result in megalencephaly, drug-resistant epilepsy, and severe intellectual disability. This study seeks to understand how mTOR pathway hyperactivity alters cell fate specification in dorsal and ventral forebrain development using STRADA knock-out human stem cell derived brain organoids. In both dorsal and ventral forebrain STRADA knock-out organoids, neurogenesis is delayed, with a predilection for stem cell maintenance and an increase in outer radial glia. Ventrally, interneuron subtypes shift to an increase in neuropeptide-Y expressing cells. Inhibition of the mTOR pathway with rapamycin results in rescue for most phenotypes. When mTOR pathway variants are present in all cells of the developing brain, overproduction of interneurons and altered interneuron cell fate may underlie mechanisms of megalencephaly, epilepsy, and cognitive impairment. Our findings suggest mTOR inhibition during fetal brain development as a potential therapeutic strategy in STRADA deficiency.

overall_design: The four iPSC lines used for this study (C1, C2, M1, M2) were derived from a commercially available source of male foreskin fibroblasts using CRISPR gene editing of STRADA. C1 and C2 lines were unedited and carried the wild-type sequence of STRADA (NM_001003787.4). M1 was a compound heterozygote, with c.632_636del (p.Leu211Argfs*45) on one allele and c.636del (p.Gly213Valfs*8) on the other. M2 was also a compound heterozygote, with two variants, c.635_636del (p.Ser212Trpfs*45) and c.631C>G (p.Leu211Val) on one allele, and c.636_637insA (p.Gly213Argfs*45) on the other allele.

first: Tong

last: Pan

first: Grace

last: Lin

first: Xuan

last: Li

first: Debora

last: VanHeyningen

first: John Clay

last: Walker

first: Sahej

last: Kohli

first: Aiswarya

last: Saravanan

first: Amrita

last: Kondur

first: Daniel C

last: . Jaklic

first: Saul

last: Pantoja-Gutierrez

first: Shivanshi

last: Vaid

first: Julie

last: Sturza

first: Ken

last: Inoki

first: Weizhong

last: Chang

first: Louis

last: T Dang


title: Multiomics analysis unveils key biomarkers during dynamic progress of IAV infection in mice

status: Public on May 08 2025

city: chengdu

first: HUAN

last: LEI

state: Sichuan

address: No.1166 Liutai Avenue, Wenjiang District, Chengdu

institute: Chengdu university of traditional Chinese medicine

summary: Murine IAV infection models are vital for influenza research, but biomarker progression during the disease is unclear. This study aims to help improve disease surveillance and treatment outcome assessment by understanding viral infection dynamics and biological shifts from mild to severe symptoms in mouse models. The physiological parameters, viral load, inflammatory responses, and histopathological changes were evaluated in Balb/c mice infected with IAV over 14 days period. Intervention within 6 days after influenza virus infection is crucial to prevent severe illness. Using DIABLO multi-omics analysis, we analyzed transcriptomic and metabolomic data from mouse lung tissues and serum metabolomic data at 4, 6, 8, and 10 days post-infection. Several key biomarkers like Ccl8, Pdcd1, Gzmk, Kynurenine, L-Glutamine were identified during influenza infection. The serum-based influenza progression scoring system developed in this study provides precise treatment strategies and personalized plans for clinical management. This scoring system detects when the levels of L-Glutamine, adipoyl-carnitine, triacetic acid lactone, and isopropanol in the serum exceed 2.5 times the normal range, indicating that the patient is in the influenza infection phase (days 4-6). Intervening during this phase can effectively prevent the condition from deteriorating into a critical stage.

overall_design: RNA-seq profiling of lung tissues from Balb/c mice on days 4, 6, 8, and 10 post-infection with influenza A virus.

first: Huan

last: Lei

first: Yixi

last: Xu

first: Hao

last: Zhang

first: Bin

first: Shijun

first: Ping

last: Wang


title: LIFR-mediated ERBB2 signaling is essential for successful embryo implantation in mice.

city: Sagamihara

first: Junya

last: Ito

state: Kanagawa

address: 1-17-71 Fuchinobe, Chuo-ku

department: School of Veterinary Medicine

institute: Azabu university

summary: To investigate the molecular mechanism underlying LIFR in the endometrium during embryo implantation, we generated mice with uterine-specific deletion of LIFR. We report the sequencing of the uterine transcriptome of control and uterine-specific Lifr-deficient mice at day 4 (1600h) of pregnancy.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine endometrium at day 4 (1600h) of pregnancy between control and uterine-specific Lifr-deficient mice.

first: Jumpei

last: Terakawa

first: Sakura

last: Nakamura

first: Hironobu

last: Murakami


title: Differences between human male and female neutrophils with respect to which RNAs are present in polysomes

city: College Station

first: Darrell

last: Pilling

state: Texas

address: 301 Old Main Drive

department: Biology

institute: Texas A&M University

summary: Human males and females show differences in the incidence of neutrophil-associated diseases such as systemic lupus erythematosus, rheumatoid arthritis, and multiple sclerosis, and differences in neutrophil physiological responses such as responses to infection, tissue damage, and chemotactic factors. However, little is known about the basis of sex-based differences in human neutrophils. Starting with human neutrophils from healthy donors, we used RNA-seq to examine total RNA profiles, RNAs not associated with ribosomes and thus not being translated, RNAs in monosomes, and RNAs in polysomes and thus heavily translated. There were sex-based differences in the levels of RNAs across free RNA, monosome, and polysome fractions. Male neutrophils had increased levels of mRNAs encoding mitochondrial proteins in the free RNA fractions, indicating low levels of translation. The polysomes of male neutrophils were enriched for mRNAs encoding cytoskeletal organization, cell motility, and phosphatases. The polysomes of female neutrophils were enriched for mRNAs associated the regulation of RNA, metabolic processes, responses to interferon, and mitochondrial proteins.These data indicate that male and female neutrophils have different expression patterns and different translation efficiency of some mRNAs. This may contribute to the observed sex-based differences in neutrophil behavior and neutrophil-associated disease incidence and severity.

overall_design: RNA-seq of human neutrophils from male and female donors. Also RNA-seq after isolation of RNA from polysome profiling

first: Kristen

last: Consalvo

first: Sara

last: Kirolos

first: Richard

middle: H

last: Gomer


title: Role of SREBP1 in chronic endometritis

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

summary: The aim of this study was to investigate the role of SREBP1a in the regulation of inflammation in endometrial tissue after LPS injection.  We report that systemic deletion of Srebf1, which encodes SREBP1, resulted in persistent endometrial inflammation and CD138-positive plasma cell infiltration. In addition, Srebf1 knockout mice exhibited pregnancy loss and placental insufficiency in the endometritis model.

overall_design: mRNA profiles of endometrial tissue obtained from WT and Srebf1 knockout mice 7 days after LPS-induced inflammation were analyzed.

first: Oishi

last: Yumiko

first: Manabe

last: Ichiro


title: Cancer-induced FOXP1 disrupts and reprograms skeletal muscle circadian transcription in cachexia [circadian RNA-seq]

first: Andrew

last: Judge

overall_design: Following an acclimation period to ensure entrainment to 12-hour light/dark cycle (lights on: 6 am), mice were kept in constant darkness for 18 hours (circadian time 0: CT0) in light-tight circadian cabinets. Tibialis anterior muscles were isolated and flash frozen in liquid nitrogen for RNA-sequencing from 39- to 55-week-old male homozygous FoxP1fl/fl x ACTA1-Cre (FoxP1SkmKO) mice and FoxP1fl/fl mice, as a FoxP1-expressing control and are referred to as wild type (WT) hereafter, with and without orthotopic murine KPC pancreatic tumors at CT 18, 22, 26, 30, 34, and 38 (n = 2 mice/condition/genotype/time point). RNA isolation was performed by homogenization of TA muscles in Trizol followed by extraction with chloroform, precipitation with isopropanol, and treatment with DNAse. RNA sequencing was performed by Novogene (Novogene Co, Ltd., Sacramento, CA).

first: Sarah

first: Jeremy

last: Ducharme


title: A gatekeeper mechanism of the noradrenergic neural control of tear secretion via the NA-Adra1a-Ucp2 pathway

city: Qingdao

first: Bin

state: Shandong

address: Yanerdao Road 5

institute: Shangdong Eye Institue

summary: Tears are mainly secreted from the lacrimal gland under precise controls by autonomic neural response to external sensory and psychogenic emotional stimulation. Dynamic volume and compositional changes of tears may lead to development of dry eye disease. The role of sympathetic nerve system (SNS) in controlling tear secretion and the noradrenergic neural circuit projecting from brain to lacrimal gland remain unexplored. Here, we discovered the dense sympathetic innervation of mouse lacrimal gland and investigated its physiological role in regulating tear production. In response to dry eye stimuli, SNS became overactivated with high noradrenaline (NA) in the lacrimal gland. Using gain- and loss-of-functional approaches, including pharmacologic, surgical, chemogenetic manipulations, and genetic knockout mice of specific adrenergic receptors, we demonstrated that both SNS ablation and NA blockage markedly increased tear volume and alleviated dry eye diseases. Mechanistically, activation of SNS released NA to reduce tear secretion through binding to α1a-adrenergic receptor (Adra1a) that targeted mitochondrial Ucp2 in the acinar and myoepithelial cells of the lacrimal gland. Consequently, antagonization of NA and Ucp2 markedly increased tear secretion. Using a retrograde neuronal tracing technique in combination with physiologic experiments of tear reduction and hypersecretion, we identified a novel noradrenergic neural circuit projecting from the brain locus coeruleus to the lacrimal gland and the orchestrated controlling of parasympathetic and sympathetic nervous system for tear secretion. Together, our data define a novel NA-Adra1a-Ucp2 signaling pathway as a gatekeeper mechanism for controlling tear secretion from the lacrimal gland. These findings provide novel mechanistic insights into sympathetic role in tear secretion and potential therapeutic options for treatment of dry eye disease.

overall_design: RNA-seq analysis of mouse lacrimal gland

first: Qun

first: Qingjun

last: Zhou

first: Lixin

last: Xie


title: NUDT21 lactylation reprograms alternative polyadenylation to promote cuproptosis resistance

first: Jinlong

last: Lin

address: Dongfeng dong road

institute: Sun Yat-sen university cancer center

summary: Alternative polyadenylation (APA) serves as a critical mechanism for shaping transcriptome diversity and modulating cancer therapeutic resistance. While lactate is a well-established metabolic signal in cancer progression, its role in APA regulation remains unclear. Here, we demonstrate that L-lactate-induced lactylation of NUDT21 drives transcriptomic reprogramming through APA modulation. NUDT21 lactylation enhances its interaction with CPSF6, facilitating CFIm complex formation and inducing 3′ untranslated region (UTR) lengthening of FDX1. Extension of the FDX1 3′ UTR attenuates its protein output, thereby conferring resistance to cuproptosis in esophageal squamous cell carcinoma (ESCC). Furthermore, we identify AARS1 as the lactylation “writer” catalyzing NUDT21 K23 lactylation, and HDAC2 as its enzymatic “eraser”. Clinically, elevated LDHA and NUDT21 levels correlate with reduced FDX1 expression and worse prognosis in ESCC patients. Notably, combined targeting of the lactate-NUDT21-FDX1-cuproptosis axis with the clinical LDHA inhibitor stiripentol and the copper ionophore elesclomol synergistically suppressed tumor growth. Collectively, our work identifies lactylated NUDT21 as a critical factor linking cellular metabolism to APA and proposes a promising therapeutic strategy for ESCC treatment.

overall_design: To explore whether lactate affects APA regulation, we treated ESCC cells with lactate and conducted PAS-seq.

first: Yixin

last: Yin

first: Jinghua

last: Cao

first: Dan

last: xie


title: RNAi screen in tumor cells identifies artificial microRNAs that improve oncolytic virus replication

city: Montreal

first: Dominic

middle: Guy

last: Roy

state: Quebec

address: 333 rue St-Antoine E, CRCHUM, Room R10.720

country: Canada

institute: Centre de Recherche du CHUM

summary: Gene expression data from CT26WT cells transfected with VSV replication-enhancing siRNAs and infected with VSV

overall_design: CT26 cells were cultured for 24h in DMEM+10%FBS followed by transfection with 50uM of the indicated siRNAs. Cells were infected with VSV 48h post-transfection. Samples were collected 16h post-infection.


title: Interaction of BCL11A and CHD8 in triple negative breast cancer [ChIP-seq]

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary: BCL11A interacts with and recruits the chromatin remodeller, CHD8 and this interaction is essential for mediating the oncogenic activity of BCL11A.

overall_design:
BCL11A shRNA sequences ((TRCN0000033449) mCHD8 (TRCN0000217316) were obtained from TRC consortium and cloned into a piggyBac transposon vector (PB-H1-shRNA-GFP) as describe previously (Khaled 2015). 4T1 were transfected with 4.0ug of respective vector or control (scramble) using Lipofectamine LTX (Invitrogen). Cells were treated with G418 (400 ug/mL) (Gibco) for 5 days after which GFP+ve cell were sorted and cultured.
CHIP-assays of using antibodies against BCL11A and CHD8 were performed as below using cultured cells.

first: Kyren

last: Lazarus

first: Eleanor

last: Williams

first: Mark

last: Waterhouse

first: Walid

last: Khaled


title: Interaction of BCL11A and CHD8 in triple negative breast cancer [RNA-seq]

overall_design:
BCL11A shRNA sequences ((TRCN0000033449) mCHD8 (TRCN0000217316) were obtained from TRC consortium  and cloned into a piggyBac transposon vector (PB-H1-shRNA-GFP) as describe previously (Khaled 2015). 4T1 were transfected with 4.0ug of respective vector or control (scramble) using Lipofectamine LTX (Invitrogen). Cells were treated with G418 (400 ug/mL) (Gibco) for 5 days after which GFP+ve cell were sorted and cultured.
RNA was extracted as below and submitted for sequencing. To control for variation, three independent cell lines with independent KD experiments were used.


title: Interaction of BCL11A and CHD8 in triple negative breast cancer [ATAC-seq]

overall_design:
BCL11A shRNA sequences ((TRCN0000033449) mCHD8 (TRCN0000217316) were obtained from TRC consortium  and cloned into a piggyBac transposon vector (PB-H1-shRNA-GFP) as described previously (Khaled 2015). 4T1 were transfected with 4.0ug of respective vector or control (scramble) using Lipofectamine LTX (Invitrogen). Cells were treated with G418 (400 ug/mL) (Gibco) for 5 days after which GFP+ve cell were sorted and cultured.
ATACseq assay was performed on cultured cells as below


title: Identification of Prognostic Biomarkers of Ovarian High Grade Serous Carcinoma through Spatial Transcriptome Analysis and Multispectral imaging

status: Public on May 07 2025

city: Seongnam City

first: Doo Hyun

last: Koh

address: Yatap-ro 64

country: South Korea

institute: CHA university

summary: The identification of reliable predictive biomarkers is crucial for assessing optimal therapeutic responsiveness in high grade serous ovarian carcinoma (HGSC). The immune profile of the tumor microenvironment (TME) influenced the prognosis of HGSC patients. Using spatial transcriptome analysis, We investigated the characteristics of the tumor microenvironment associated with treatment response and identified multiple biomarkers associated with treatment benefit in HGSC patients.

overall_design: 12 HGSC patients who were treated with platinum-based chemotherapy were selected for this analysis.Among the 12 patients, 2 ROIs (region of interset) were obtained from each of 11 patients, while 1 ROI was obtained from patient P12. A total of 23 ROIs were obtained from 12 patients. Each ROI consisted of 3 Areas of Interest (AOIs) of morphologic markers (PanCK, SMA, CD45). PanCK was for epithelial tumor area, SMA was for stroma, and CD45 was for pan-immune cells. A total of 69 AOIs were generated for this analysis.

first: Doohyun

first: Sohyun

last: Hwang

first: Hee Jung

last: An


title: EV-microRNA Signatures in Pregnant Women with Idiopathic Recurrent Pregnancy Loss: Deciphering MicroRNAome Pathway Networks at Feto-Maternal Interface

city: Chandigarh

first: Priyanka

last: Srivastava

state: Chandigarh

address: PGIMER, Sector-12

department: Pediatrics

institute: PGIMER

summary: Despite extensive research in the past decade, the exact pathogenesis of recurrent pregnancy loss (RPL) remains unknown. At the time of pregnancy, human placenta releases microRNAs (miRNAs) enclosed in extracellular vesicles (EVs), which enter into maternal circulation and play an important role at feto-maternal interface to sustain a successful pregnancy. Aberrant expression of these miRNAs often results in adverse pregnancy complications. Therefore, studying the expression of these EV-miRNAs in maternal circulation could provide insights into the pathogenesis of RPL. miRNA sequencing revealed 66 (44 known and 22 novel) significantly DE miRNAs between RPL and healthy pregnant women.

overall_design: The present study included idiopathic currently pregnant (<22 weeks of gestation) RPL women (n=10) and gestational-age-matched healthy pregnant women as control (n=5). Total RNA was isolated and subjected to miRNA sequencing on Illumina NovaSeq 6000 platform


title: Specialized Molecular Pathways Drive the Formation of Light-Scattering Assemblies in Leucophores

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

summary: Pigmentation plays a vital role in the survival of organisms, supporting functions such as camouflage, communication, and mate attraction. In vertebrates, these functions are mediated by specialized pigment cells known as chromatophores of which, uric acid crystal-forming leucophores remain the least understood, with little known about their molecular mechanisms. A key question in pigment cell biology is whether different crystal chemistries require distinct molecular pathways, or whether similar cellular processes drive the formation of diverse crystals. This study was designed to unravel the uncharacterized process of uric acid crystallization in leucophores and compare them to guanine crystal formation in iridophores and pterin formation in xanthophores. The results of our transcriptomic, ultrastructural, and metabolomic analyses, demonstrate that leucophores share molecular pathways with iridophores, particularly those connected to organelle organization and purine metabolism, but express discrete genes involved in uric acid biosynthesis and storage. Additionally, leucophores share intracellular trafficking and pterin biosynthesis genes with xanthophores, suggesting universally conserved processes. Ultrastructural studies reveal star-like fibrous structures in leucosomes, which likely serve as scaffolds for unique one-dimensional uric acid assemblies that radiate from the core and act as efficient light scatterers. These findings provide new insights into leucophore cell biology and the specialized mechanisms driving molecular crystalline assembly, and reveal that while some cellular processes are conserved, the specific chemistry of each crystal type drives the evolution of distinct molecular pathways.

overall_design: Cells were isolated from adult HdrR Medaka fish skin and scales and sorted via Fluorescence-Activated Cell Sorting (FACS),  pigment cells enrichment was done  according to the present of both GFP and mCherry signals.

first: Barzilay

last: Yuval

first: Olender

last: Tsviya

first: Kedmi

last: Merav

first: Gur

last: Dvir


title: Interaction of BCL11A and CHD8 in triple negative breast cancer

city: Cambridge

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

overall_design: Refer to individual Series


title: Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq

city: Tsukuba

first: Shodai

last: Taguchi

state: Ibaraki

address: #307 Health and Medical Science Innovation Laboratory, Tennohday, 1-1-1

department: Faculty of Medicine

institute: University of Tsukuba

summary: This study utilizes the robotic OT-2 platform to systematically investigate the effects of varying pipetting speeds on yeast growth and gene expression. By employing RNA-seq and growth assays, we observed no significant differences in yeast growth and gene expression within the range of pipetting speeds investigated. Our findings reveal the potential of robotic platforms for optimizing culture conditions and enhancing reproducibility and accuracy in biological experiments, thus providing valuable insights for future research.

overall_design: To investigate the effect of four different pipetting speeds controled by liquid handling robot on gene expression and growth speed, we performed RNA sampling and growth assays using liquid handling robot with four different pipetting speeds, two biological replicates, and three technical replicates. We then performed gene expression clusttering analysis using data obrained from RNA-seq of 24 samples.

first: Ryosuke

last: Matsuzawa

first: Yasuyuki

last: Suda

first: Kenji

last: Irie

first: Haruka

last: Ozaki


title: Microbiota-derived butyrate alleviates asthma via constraining Tfh13-mediated IgE production.

city: Shanghai

first: Baichao

last: Yu

state: Shanghai

address: NO.130,  Dong'an Road , Xuhui District

institute: Fudan University

summary: IgE production in type 2 immunity is strictly dependent on CD4+ T helper cells. To further elucidate whether butyrate affects IgE production via regulating CD4+ T cells, we took mediastinal lymph nodes (MedLN) from asthmatic mice with or without butyrate supplementation for single-cell RNA sequencing

overall_design: Total cells were sorted from MedLNs of C4-treated or -untreated OVA-induced asthma model. The single cells were obtained by the method of grinding through a 70 μm cell strainer.Then four mice were pooled into per group for scRNA-seq.

first: Luman

last: Wang

first: Yiwei

last: Chu


title: The endocannabinoid system drives eosinophil infiltration during eosinophilic esophagitis

city: Graz

first: Rudolf

last: Schicho

address: Neue Stiftingtalstraße 6

country: Austria

institute: Medical University of Graz

summary: Eosinophilic esophagitis (EoE) is a chronic, inflammatory, and antigen-driven disease of the esophagus. Total transcriptome data revealed alterations in the endocannabinoid system (ECS), in particular, downregulation of monoacylglycerol lipase (MGL) in biopsies of patients with active EoE. We investigated the consequence of MGL downregulation in mucosal biopsies of patients, and its implications for EoE development, such as recruitment of eosinophils. Levels of MGL substrate 2-arachidonoylglycerol (2-AG), MGL enzyme activity and MGL co-localization with epithelial cells were determined in mucosal esophageal biopsies of EoE patients. Supernatant of human primary esophageal epithelial cells was used to determine eosinophil migration and activation. An inducible mouse model of EoE was used to test MGL inhibition and cannabinoid (CB) receptor antagonism in vivo. MGL expression in esophageal epithelial cells from active EoE patients is decreased, while 2-AG is increased compared to controls. Inhibition of MGL in epithelial cells leads to a pro-inflammatory phenotype capable of attracting eosinophils via CB2. Similarly, the EoE mouse model indicates that absence of MGL results in higher eosinophil infiltration. Targeting CB2 reduced the number of infiltrating eosinophils in the esophagi of mice. This study is the first of its kind to investigate the involvement of altered expression of ECS components in EoE, and partly explains recent findings of more inflammatory features post EoE-treatment in cannabis users. Our findings could pave the way for research into alternative treatment options for EoE and call for caution regarding the use of cannabinoids in EoE.

overall_design: Mouse esophagi were isolated from MGL WT or KO mice, their total RNA was isolated and sequenced to compare basal changes between the genotypes.

first: Thomas

last: Bärnthaler

first: Eva

last: Gruden


title: Small RNA Landscape of Platelet Dust: Platelet-Derived Extracellular Vesicles from Patients with Non-Small-Cell Lung Cancer

city: Leiden

first: Danijela

last: Koppers-Lalic

address: Albinusdreef 2

department: Medical Oncology & Medical Microbiology

institute: Leiden University Medical Center

summary:
Abstract: Background: Platelet-derived Extracellular Vesicles, or “Platelet Dust” (PD), are
reported as the most-abundant extracellular vesicles in plasma. However, the PD
molecular content, especially the small RNA profile, is still poorly characterized. This
study aims to characterize PD and other extracellular vesicles (EVs) in patients with non-
small-cell lung cancer (NSCLC), focusing on their small RNA signatures and diagnostic
potential. Methods: The EVs were isolated directly from the plasma of healthy donors
and patients with NSCLC using the surface markers CD9, CD63, CD81 (overall EVs), and
CD61 (PD). Small RNA sequencing was then performed to comprehensively profile the
miRNAs. Results: Our analysis revealed distinct small RNA profiles in the EVs and the
PD from the patients with NSCLC. The EVs (CD9-, CD63-, and CD81-positive) showed
the enrichment of four miRNAs and the depletion of ten miRNAs, while the PD (CD61-
positive) exhibited a more complex profile, with nineteen miRNAs enriched and nine
miRNAs depleted in the patients with NSCLC compared to those of the healthy controls.
Conclusions: This exploratory study enhances our understanding of miRNA composition
within different plasma vesicle populations, shedding light on the biology of plasma
vesicles and their contents. Furthermore, utilizing an extracellular vesicle isolation
method with potential clinical applicability offers the prospect of improved cancer
characterization and detection by selecting the most informative subpopulation of plasma
vesicles.

overall_design: Total RNA profiling by high throughput sequencing

first: Mafalda

last: Antunes-Ferreira

first: Ilias

last: Glogovitis

first: Diogo

last: Fortunato

first: Silvia

last: D’Ambrosi

first: Mariona

last: Colom Saborit

first: Galina

last: Yahubyan

first: Vesselin

last: Baev

first: Michael

last: Hackenberg

first: Natasa

last: Zarovni

last: Wurdinger


title: A single-cell RNA-seq dataset of synovial fluid from rheumatoid arthritis treated with TNF-α/JAK inhibitor

status: Public on May 06 2025

city: Chengdu

first: Heng

last: Xu

address: 17#, section 3, South Renmin Road

institute: Sichuan University

summary: Although multiple single-cell RNA sequencing (scRNA-seq) based studies have explored rheumatoid arthritis (RA), most have focused on synovial tissue, limiting the ability to perform paired pre- and post-treatment comparisons and to elucidate dynamic changes. Moreover, the single-cell impact of TNF-α and JAK inhibitors on RA remains poorly understood, hindering effects toward precision medicine for RA. Here, we present a comprehensive scRNA-seq analysis of synovial fluid samples of RA patients treated with tofacitinib or adalimumab, both pre- and post-treatment. Following stringent quality control, we analyzed 106,506 high-quality cells, providing an in-depth characterization of cell composition, molecular signaling pathways, and functional properties. This rich dataset offers a valuable resource to address diverse research questions, from uncovering the mechanisms of action of TNF-α and JAK inhibitors, to identifying novel therapeutic targets for RA, and advancing our understanding of the pathogenesis of inflammatory diseases.

overall_design:
In this study, we collected SF samples from RA patients pre- and post-treated with TNF-α/JAK inhibitors and constructed a single-cell atlas of RA SF.

***************************************************************
Raw files for human/patient samples are being made available in the Genome Sequence Archive (GSA) for human (https://ngdc.cncb.ac.cn/gsa-human) under the accession number HRA011646, for controlled access to the personally identifiable sequence data.
***************************************************************


title: Aurora B and INCENP co-overexpression severely disrupts mitosis and distinctly modifies the global transcriptional landscape

city: Sevilla

first: Fernando

last: Monje-Casas

state: Sevilla

address: CABIMER. Avda. Americo Vespucio, 24, P.C.T. Cartuja 93, CIF: Q2818002D

department: CABIMER

institute: CSIC


title: Aurora B and INCENP co-overexpression severely disrupts mitosis and distinctly modifies the global transcriptional landscape [RNA-seq]

summary: Aurora B kinase, as part of the chromosomal passenger complex (CPC), controls key processes during the cell cycle such as DNA compaction, genome partitioning or cytokinesis. Nonetheless, increased Aurora B levels are a potential threat for the cells and have been linked to different tumor types. We have carried out an exhaustive characterization of the global consequences of the overexpression of Aurora B and INCENP, the scaffold of the CPC and an activator of Aurora B kinase activity, in non-transformed human cells. Our data demonstrate, not only that an individual increase in the levels of Aurora B or INCENP have a different impact on the cells, but more importantly that their simultaneous overexpression stabilizes both CPC components, exacerbates Aurora B activity, severely impairs mitotic progression and chromosome dynamics, and has a distinctive and more dramatic effect on the transcriptional landscape of the cells.

overall_design:
In order to analyze the differential consequences of Aurora B and/or INCENP overexpression, we generated RPE-1 cells that conditionally expressed an extra copy of AURKB (AurkB), INCENP (INCENP),or a bi-cistronic construct that comprises both genes linked by a sequence encoding a P2A “self-cleaving” oligopeptide (Both), all under the control of the TET promoter.
Gene expression profiles of each line were analyzed by RNA-seq 32 hours after tetracycline addition to induce AurkB and/or INCENP overexpression. Two independent replicates were performed for each RNA-seq experiment.

first: María

last: Galindo-Moreno

first: Marta

last: Muñoz-Barrera

first: Chiara

last: Marcozzi

first: Federica

last: Bruno

first: Cristina

last: Maya-Álvarez

first: Felipe

last: Cortés-Ledesma

first: Rosa

last: Ríos

last: González-Aguilera


title: MODELING TISSUE-RESIDENT MACROPHAGE DEVELOPMENT FROM MOUSE PLURIPOTENT STEM CELLS

status: Public on May 05 2025

city: New York City

first: Ragavi

last: Vijayakumar

state: New York

address: 430 E 67th St

department: Developmental Biology

institute: Sloan Kettering Institute

summary: Tissue-resident macrophages (TRMs) are innate immune cells that participate in tissue development, homeostasis, and immune surveillance. Extensive efforts have been made to recapitulate TRM development from pluripotent stem cells (PSCs) in vitro to study molecular and cellular mechanisms of TRM development and to create cellular models of disease. However, available PSC models of mouse TRM development exhibit low overall efficiencies of TRM generation, generate heterogeneous off-target populations, and rely upon undefined media components, thus limiting their reproducibility, scalability, and widespread application as an experimental platform for TRM biology. To address these important limitations, we developed an efficient and reproducible protocol to faithfully recapitulate the stepwise differentiation of mouse PSCs (epiblast stem cells) into unspecialized, proliferative TRMs through the pro-definitive hematopoietic program under defined conditions. These immature TRMs can stably integrate into developing mouse neural organoids in vitro and acquire features of microglia, the TRMs of the brain. In addition, immature TRMs can stably engraft into the lung niche in vivo and adopt alveolar macrophage characteristics. This new platform for modeling mouse TRM development will enable paired in vitro and in vivo studies that leverage the full suite of mouse genetic tools, and thus should be a powerful experimental model system for studying TRM function and dysfunction in development and disease.

overall_design: RNA-seQ of day 16  CX3CR1 (+) tissue-resident macrophages differentiated from mouse epiblast stem cells and cultured as macrophages under 3 different conditions (immature TRM, B27-TIC, and TIC)

first: Ann

last: Baako

first: Daniel

last: Medina-Cano

first: Zhaoquan

last: Wang

first: Jesús

last: Romero Pichardo

first: Kelvin

last: Fadojutimi

first: Mohammed

last: Islam

first: Sanjana

last: Dixit

first: Stephanie

last: Do

first: Yuan

last: Lin

first: Alissa

last: Trzeciak

first: Justin

last: Perry

first: Thomas

last: Vierbuchen


title: Armoured CAR Tregs with PD1 promoter-driven IL-10 have enhanced suppressive function

city: Vancouver

first: Megan

last: Levings

state: BC

address: 938 W 28th Ave

institute: BC Children's Hospital Research Institute

summary: The potency of regulatory T cell (Treg) therapy has been transformed through use of chimeric antigen receptors (CAR). However, to date, CAR Treg therapy has not achieved long-lasting tolerance in mouse models, suggesting that additional engineering is required to unlock the full potential of these cells. We previously found that human Tregs produce minimal amounts of IL-10 and have a limited capacity to control innate immunity in comparison to type I regulatory (Tr1) cells. Seeking to create “hybrid” CAR Tregs that were engineered with Tr1-like properties, we examined whether the PDCD1 locus could be exploited to endow Tregs with the ability to secrete high levels of IL-10 in a CAR-regulated manner.

overall_design: Human Tregs, Tr1s, and conventional T cells (Tconvs) were engineered with an HLA-A2-specific CAR. CAR-Tregs were then edited via homology directed repair to knock-out PD1 and introduce IL10 under control of the PDCD1 promoter. All cell types were stimulated for 16 hours via their CAR, then harvested for RNA sequencing analysis.

first: Dominic

last: Boardman

first: Sonya

last: Mangat

first: Lorna

last: Leon


title: Aurora B and INCENP co-overexpression severely disrupts mitosis and distinctly modifies the global transcriptional landscape [ChIP-seq]

first: Fernando

last: Monje-Casas

overall_design:
In order to analyze the differential consequences of Aurora B and/or INCENP overexpression, we generated RPE-1 cells that conditionally expressed an extra copy of AURKB (AurkB), INCENP (INCENP),or a bi-cistronic construct that comprises both genes linked by a sequence encoding a P2A “self-cleaving” oligopeptide (Both), all under the control of the TET promoter.
Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for H3 Ser10 phosphorylation in each line, 32 hours after tetracycline addition to induce AurkB and/or INCENP overexpression. Two independent replicates were performed for each ChIP-seq experiment.

first: María

last: Galindo-Moreno

first: Marta

last: Muñoz-Barrera

first: Chiara

last: Marcozzi

first: Federica

last: Bruno

first: Cristina

last: Maya-Álvarez

first: Felipe

last: Cortés-Ledesma

first: Rosa

last: Ríos

last: González-Aguilera


title: Reversible proliferative arrest induced by rapid depletion of RNase MRP

city: Riverside

first: Shiyang

last: He

state: CA

address: 3401 Watkins Drive, Boyce Hall

department: Biochemistry

institute: UCR

summary: Cellular quiescence is a state of reversible proliferative arrest that plays essential roles in development, resistance to stress, aging, and longevity of organisms. Here we report that rapid depletion of RNase MRP, a deeply conserved RNA-based enzyme required for rRNA biosynthesis, induces a long-term yet reversible proliferative arrest in human cells. Severely compromised biogenesis of rRNAs along with acute transcriptional reprogramming precede a gradual decline of the critical cellular functions. Unexpectedly, many arresting cells show increased levels of histone mRNAs, which accumulate locally in the cytoplasm, and S-phase DNA amount. The ensuing proliferative arrest is entered from multiple stages of the cell cycle and can last for several weeks with uncompromised cell viability. Strikingly, restoring expression of RNase MRP leads to a complete reversal of the arrested state with resumed cell proliferation at the speed of control cells. We suggest that targeting rRNA biogenesis may provide a general strategy for rapid induction of a reversible proliferative arrest, with implications for understanding and manipulating cellular quiescence.

overall_design: RNase P alone or both RNase P and MRP were depleted in HEK293T cells (N21 and C40 lines, respectively) using dTAG-mediated targeted protein degradation for 3 or 24 hours. DMSO-treated cells were used as controls. Samples were prepared and sequenced in triplicates by RNA-seq, TTchem-seq, and Histone End-seq.

last: Liu

first: Kawon

last: Pyo

first: Reuben

last: Franklin

first: Ibrahim

last: Maaz

first: Chen

last: Cai

first: Kriti

last: Shah

first: Sihem

last: Cheloufi

first: William

last: Marzluff

first: Jernej

last: Murn


title: Elmo2 is an essential regulator of carotid artery development

city: Münster

first: Kai

last: Kruse

state: North Rhine-Westphalia

address: Roentgenstr. 20

institute: Max Planck Institute for Molecular Biomedicine

summary: Engulfment and cell motility 2 (ELMO2) is a cytoskeletal adaptor protein. Loss of function mutations in ELMO2 are associated with a life-threatening human disease called intraosseous vascular malformation (VMOS). This autosomal recessive disease manifests in the craniofacial area and has no effective treatment, in part due to the poor characterization of its physiopathology. In this study, we report the first detailed characterization of Elmo2 global deletion in mice and showcase the importance of Elmo2 during cardiovascular development. Elmo2 was found to be indispensable for normal morphogenesis of the third pharyngeal arch artery (3rd PAA) which gives rise to the common carotid artery, responsible for the blood supply to the craniofacial region. Global deletion of Elmo2 induces severe dilation in the 3rd PAAs and aneurism formation in the carotid arteries leading to embryonic lethality. Elmo2-deficient embryos showed impaired cytoskeletal organization in neural crest-derived vascular smooth muscle cells (VSMCs) and defects in the endothelial lining of the dilated arteries. Deletion of Elmo2 specifically in neural crest cells phenocopied all the relevant defects observed in the global knockout while gene inactivation in endothelial cells, sympathetic neurons and mature VSMCs had no effect or induced only minor changes in vessel diameter. Furthermore, time-controlled ubiquitous deletion of Elmo2 allowed us to conclude that early gene inactivation is necessary for recapitulating the major defects observed in Elmo2-null embryos. In addition, analysis of cultured neural crest-derived human brain VSMCs showed decreased active RAC1 and F-actin levels upon ELMO2 downregulation, which impair adhesion, spreading and cell contractility. These defects can be rescued in vitro through administration of the F-actin stabilizer Jasplakinolide. Altogether our results highlight a previously unappreciated role for Elmo2 in the physiology of neural crest-derived VSMCs. These findings might be relevant for understanding the cellular mechanisms responsible for VMOS.

overall_design: To investigate the function of Elmo2 in the development of the 3rd PAA, this vascular structure along with its surrounding mesenchyme was microdissected and processed for single-cell RNA sequencing. In order to reduce variability, samples from control (Elmo2+/+), heterozygous knockout (Elmo2+/-), and homozygous knockout (Elmo2-/-) E12.5 embryos were prepared following the same protocol. Each sample is the result of pooling together the microdissected tissue from 3-4 embryos from at least 2 different pregnancies in order to increase biological significance and reduce potential batch effects

first: Athira

last: Suresh

first: Rodrigo

last: Diéguez-Hurtado

first: Ralf

last: Adams


title: Defining the mechanisms-of-action of nitrofuranyl piperazines against Mycobacterium abscessus

city: East Lansing

first: Robert

last: Abramovitch

state: MI

address: 2215 Biomedical And Physical Sciences

institute: Michigan State University

summary: Defining the functions of the small molecule to inhibit M. abscessus growth and comparitive studies examining the mechanisms of action in M. tuberculosis vs. M. abscessus.

sample_organism:
Mycobacterium tuberculosis CDC1551
Mycobacteroides abscessus ATCC 19977

overall_design: Mab cultures were treated in two biological replicates with 10 μM of HC2210 and an equivalent volume of DMSO for 24 hours at T25 standing flasks in 37°C incubator (without 5% CO2). The same is done for Mtb cultures except that 2 μM of HC2210 is used and cultures were incubated in T25 standing flasks at 37°C, 5% CO2 for 24 hours. After treatment, the pellets were harvested, and the bacterial RNA was extracted using the TRIzol-based protocol as previously described(56). Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI). Sequencing was done on a NovaSeq X Plus, producing paired end 150bp reads. Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.1.5). The sequencing reads were analyzed using the commercially licensed CLC Genomics Suite and are presented in Dataset 3.1 (for Mab) and Dataset 3.2 (for Mtb).

first: Ifeanyichukwu

last: Eke


title: Functional Validation of SAM Riboswitch Element A from Listeria monocytogenes

city: Ann Arbor

first: Chase

middle: Andrew

last: Weidmann

address: 1150 W. Medical Center Drive

department: Biological Chemistry

institute: University of Michigan

summary: SreA is one of seven candidate S-adenosyl methionine (SAM) class I riboswitches identified in Listeria monocytogenes, a saprophyte and opportunistic foodborne pathogen. SAM is essential to all domains of life, serving as a ubiquitous methyl donor and mediator of trans-sulfuration. SreA precedes genes encoding a methionine ATP- binding cassette (ABC) transporter, which imports methionine, a sulfur containing amino acid and substrate for sulfur metabolism. SreA is presumed to regulate transcription of its downstream genes in a SAM-dependent manner. The proposed role of SreA in controlling the transcription of genes encoding an ABC transporter complex may have important implications for how the bacteria senses and responds to the availability of the metabolite SAM in the diverse environments in which L. monocytogenes persists. Here we validate SreA as a functional SAM-I riboswitch through ligand binding studies, structure characterization, and transcription termination assays. We determined that SreA has both a similar structure and SAM binding properties to other well characterized SAM-I riboswitches. However, SreA regulates transcription at a distinctly lower (nM) ligand concentration but does not substantially terminate transcription, even in the presence of mM SAM.

overall_design: To evaluate structural properties of the SreA riboswitch, we performed SHAPE probing and Switch-MaP to obtain conformational flexibility measurements of the riboswitch aptamer domain in the presence or absence of SAM.

first: Ian

last: Hall

first: Sarah

last: Keane


title: Stromal vascular fraction inhibits inhibits kidney fibrosis and inflammation in UUO mice

city: Beijing

first: Yuandong

last: Tao

state: --- Select One ---

address: Beijing

institute: Chinese PLA General Hospital

summary: To understand the roles and mechanisms of stromal vascular fraction (SVF) in renal fibrosis induced by unilateral ureteral obstruction (UUO), we performed RNA sequencing of UUO kidneys from PBS- or SVF-treated mice. The transcriptome analysis revealed that SVF triggered significant metabolic reprogramming and improved mitochondrial function. Moreover, SVF treatment inhibited kidney inflammation as revealed by the downregulation of immune cell migration pathway. Furthermore, SVF contributed to the activation of PPAR signaling while inhibited TGF-beta signaling pathway.

overall_design: Bulk RNA sequencing was performed in UUO kidneys from PBS- or SVF-treated mice that were subject to UUO surgery.


title: Induction of hemodynamic traveling waves by glial-driven vasomotion in a rat model of neuroinflammation: implications for functional neuroimaging

status: Public on May 04 2025

city: Lyon

first: Guillaume

last: Marcy

address: 8 avenue Rockefeller

country: France

institute: Universite Lyon 1

summary: Cerebral hemodynamics are crucial for brain homeostasis and serve as a key proxy for brain activity. Although this process involves coordinated interaction between vessels, neurons and glial cells, its dysregulation in neuroinflammation is not well understood. We used in vivo mesoscopic functional ultrasound imaging to monitor cerebral blood volume changes during neuroinflammation in rats injected with lipopolysaccharide (LPS) in the visual cortex, under resting-state or visual stimulation, combined to advanced ex vivo techniques for glial cell reactivity analysis. Cortical neuroinflammation induced large oscillatory hemodynamic traveling waves in the frequency band of vasomotion (~0.1 Hz) in both anesthetized and awake rats. Vasomotor waves traveled through large distances between adjacent penetrating vessels, spanning the entire cortex thickness, and even extending to subcortical areas. Moreover, vasomotion amplitude correlated with microglial morphology changes and was significantly reduced by astrocytic toxins, suggesting that both microglia and astrocytes are involved in the enhancement of vasomotion during neuroinflammation. Notably, functional connectivity was increased under this oscillatory state and functional hyperemia was preserved or even exacerbated. These findings reveal new spatiotemporal properties and cellular mechanisms of cerebral vasomotion, and suggest that this is an important component of brain hemodynamics in pathological states. Moreover, reactive microglia and astrocytes are participating to increased vasomotion during neuroinflammation. These results call for a reassessment of vasomotion and traveling waves as major phenomena when imaging brain hemodynamic activity, particularly in conditions associated with neuroinflammation.

overall_design: Nuclei of rat visual cortex were isolated and then selected using Fluorescence-activated nuclei sorting (FANS) based on high DAPI intensity for analysis using snRNA-seq. Nuclei were individually barcoded trough split-seq technology used in the Evercode WT technology by PARSE Biosciences without equipment and libraries were prepared according to PARSE Biosciences protocol.

first: Mickaël

last: Pereira

first: Marco

last: Valdebenito

first: Benjamin

last: Vidal


title: Vimentin network dysregulation mediates neurite deficits in SNCA duplication 2 Parkinson’s patient-derived midbrain neurons [ATAC-seq]

status: Public on May 02 2025

city: La Jolla

first: Johannes

last: Schlachetzki

address: 9500 Gilman Drive

institute: UCSD

summary: Duplication of the SNCA gene (SNCADupl), linked to elevated levels of alpha-synuclein (aSyn), is a genetic cause of Parkinson's disease (PD). Our prior work with human-induced pluripotent stem cell (hiPSC)-derived midbrain neurons generated from PD SNCADupl patients identified neuritic deficits, accompanied by decreased levels of cytoskeletal element b-tubulin-III (bTubIII). To explore the underlying mechanisms for these effects in SNCADupl neurons, we employed CRISPR/Cas9 technology to generate isogenic control hiPSCs. Isogenic correction of SNCA dosage restored SNCADupl-induced neurite morphologic defects and decreased bTubIII levels. Multi-omics analyses revealed SNCADupl-induced upregulation of the cytoskeletal protein vimentin. Further characterization revealed heightened vimentin truncation, associated with altered distribution and organization. Similar changes in vimentin levels and truncation were observed in post-mortem putamen tissue from sporadic PD patients. Notably, interference with vimentin by okadaic acid and withaferin A restored bTubIII- and neurite-associated defects, suggesting that targeting vimentin potentially prevents aSyn-mediated neuritic degeneration.

overall_design: IPSC-derived neurons from a patient with duplication of the SNCA gene and isogenic neurons (n=4 per group)

first: Yanni

last: Schneider

first: Aron

last: Koller

first: Alina

last: Schweigert

first: Marie

last: Andert

first: Laura

last: Hoffmann

first: Sydney

last: O’Brien

first: Lukas

last: Seebauer

first: Sonja

last: Ploetz

first: Pavel

last: Kielkowsk

first: Jürgen

last: Winkler

first: Wei

last: Xiang


title: Dmrt2 and Hmx2 direct intercalated cell diversity in the mammalian kidney through antagonistic and supporting regulatory processes

status: Public on May 03 2025

city: Los Angeles

first: Riana

last: Parvez

address: 1425 San Pablo St.

department: Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

summary: Intercalated cells (ICs) in the mammalian kidney regulate circulatory pH through IC subtype restricted actions of bicarbonate transcporters: pH is elevated by Slc4a1 restricted to type A-ICs (A-ICs) and depressed by Slc26a4 in type B-IC (B-ICs). nonA-nonB-ICs (nA/nB-ICs) also produce Slc26a4 though their function is unclear. Though both nephron and ureteric progenitor lineages generate A-ICs, the former also generates nA/nB-ICs and the latter B-ICs. Lineage and subtype restricted transporter gene expression in the mouse and human kidney is preceded by expression of the transcriptional regulators Dmrt2/DMRT2 in A-ICs, and either, or both Hmx2/HMX2 and Hmx3/HMX3 in B- and nA/nB ICs. CRISPR/CAS9-directed removal of Dmrt2 and the linked Hmx2/Hmx3 genes resulted in IC-subtype switching. A-ICs adopted an Hmx2+/Slc26a4+ B-IC cell fate on Dmrt2 removal while B-ICs initiated a Dmrt2+/Slc4a1+ A-IC program on Hmx2/Hmx3 removal. Triple knockout of Dmrt2, Hmx2, and Hmx3 resulted in hybrid ICs expressing both Slc4a1 and Slc26a4. Thus, restricted expression of these regulators is essential for specifying IC subtypes. These data support a model in which mutually repressive interactions between Dmrt2 and Hmx2/3 establish distinct IC-identities and activity of these factors supports gene regulatory programs specific to each IC sub-type.

overall_design: To understand the role of Dmrt2, Hmx2, and Hmx3 in regulation of development of intercalated cell subtypes, we generated Dmrt2 knockout (KO) and Hmx3; Hmx2 knockout mice to look at gene expression. Whole embryonic day 18.5 knockout and control kidneys were sequenced from 1) Dmrt2 KO (n=3), 2) Hmx3; Hmx2 KO (n=6), and 3) Dmrt2; Hmx3; Hmx2 KO (n=3) samples as well as control littermates (n= matched for each KO condition).

first: Andrew

last: McMahon


title: Vimentin network dysregulation mediates neurite deficits in SNCA duplication 2 Parkinson’s patient-derived midbrain neurons [RNA-seq]


title: Sotorasib Resistance in KRAS G12C-Mutant Invasive Mucinous Adenocarcinoma with Implications for VEGF-A

city: Asahikawa

first: Hiraku

last: Yanada

institute: Asahikawa Medical University

summary: Invasive mucinous adenocarcinoma (IMA) is a rare subtype of lung adenocarcinoma with a poor prognosis. Compared to non-small cell lung cancer (NSCLCs), IMA more frequently harbors KRAS mutations in the order KRAS p.G12V, p.G12D, and p.G12C. This report describes a patient with KRAS p.G12C-mutant IMA treated with sotorasib. To date, no studies have investigated the therapeutic efficacy or resistance mechanisms of sotorasib in IMA. The patient was treated with carboplatin and pemetrexed, followed by sotorasib upon disease progression. While the primary lung lesions responded well, metastatic thoracic lymph node lesions continued to increase. A pathological autopsy was performed with the family’s consent to investigate potential resistance mechanisms. RNA sequencing and additional analyses revealed increased VEGF-A expression in metastatic lymph node lesions, suggesting a role in sotorasib resistance. These findings provide insights into the molecular mechanisms underlying treatment resistance in KRAS p.G12C-mutant IMA.

overall_design: Two lung lesion tissues and two thoracic lymph node lesion tissues were used for RNA-seq analysis.

first: Ryohei

last: Yoshida

first: Takaaki

last: Sasaki


title: The impact of wild environment on murine epigenetic aging

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

summary: The aging of mammalian epigenomes fundamentally alters cellular functions, implicating organismal fitness and disease risk. However, the studies of this process typically use mouse models in the laboratory environment and neglect the impact of variation in social, physical, microbial, and other aspects of the living environment. We examined the aging differences between lab mice and “re-wilded” mice, which are C57BL6/J mice reintroduced into a controlled field environment with enhanced realism. Systematic analysis of age-associated methylation dynamics in the liver tissues suggests a genomic region-conditioned, faster epigenetic aging rate in field mice than in lab mice, implicating a 3D genome conformation change. The predicted age of lab mice by epigenetic clocks is closer to their actual age than that of field mice. These observations underscore the overlooked role of the social and physical environment in epigenetic aging.

overall_design: 73 rewilded mouse liver methylome and 20 lab mouse methylome.

first: Matthew

last: Zipple

first: Sol Moe

last: Lee