title: Acetylcholine derived from B lymphocytes controls liver regeneration [scRNA-Seq]

city: Toronto

first: Liam

last: Hendrikse

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

institute: University Health Network

summary: Humans recover from hepatic injury largely by liver regeneration. This complicated process requires hepatocyte proliferation driven by collaboration amongst multiple hepatic cell types. Immune cells also contribute, with some producing mitogenic cytokines such as IL-6 but others damaging hepatocytes by secreting IFNγ. A better understanding of immune cell functions in liver regeneration is necessary to improve clinical interventions. Here, we demonstrate that B cells expressing choline acetyltransferase (ChAT), the enzyme synthesizing acetylcholine (ACh), are specifically required for liver regeneration.  Mice lacking ChAT+ B cells subjected to partial hepatectomy (PHX) display greater mortality due to failed liver regeneration. We show that both Kupffer cells and hepatic CD8+ T cells express the α7 nicotinic ACh receptor (nAChR; encoded by Chrna7), and that liver regeneration is also disrupted in mice lacking α7 nAChR. Thus, two regulatory axes promoting hepatocyte proliferation operate following PHX: one where hepatic ChAT+ B cells and α7 nAChR+ Kupffer cells interact to drive IL-6 production by Kupffer cells, and another where ChAT+ B cells and α7 nAChR+ hepatic CD8+ T cells interact to reduce IFNγ production by CD8+ T cells. Our work offers novel insights into liver regeneration mechanisms that may point to new therapies for liver damage.

overall_design: scRNA-seq profiling of liver cells in ChATflox or ChATflox;Mb1-Cre mice; derived from 2 hours, 4 hours, or 24 hours post-PHX, or from sham treated mice. Eight samples total were collected and sequenced in 4-plex pooled reactions.

first: Nastaran

middle: F

last: Modares

first: Tak

last: Mak


title: H3 Acetylation promotes H2A.Z incorporation into chromatin through SWR1 recruitment to stimulate expression [RNA-Seq]

status: Public on May 02 2025

city: Xianyang

first: Mingming

last: Zhao

address: Taicheng Road,Yangling District

country: China

institute: Northwest A&F University China

type: Expression profiling by high throughput sequencing

summary: Following DNA replication, canonical H2A in eukaryotes is frequently replaced by histone variants, such as the conserved H2A.Z. Chromatin remodelers like the SWR1 complex facilitate this process, substituting the H2A histone with H2A.Z in an ATP-dependent manner. However, the precise mechanisms that recruit SWR1 to specific loci remain partially studied. In this study, we investigate the role of H3 acetylation in mediating the incorporation of H2A.Z into the chromatin to promote gene expression. Our results show that artificially induced hyperacetylation is associated with higher levels of H2A.Z and a decrease in H2A.W (HTA6 and HTA7). This phenomenon is also observed in histone deacetylases HDA6 and HDA9 defective backgrounds. Moreover, H2A.Z is required for the phenotype observed in hda6-1 and hda9-1

overall_design: RNA-Seq of Columbia nrp1-1 nrp2-2 double mutant、 hda6-1 mutant 、hda6-1 nrp1-1 nrp2-2 triple mutant 、hda9-1 mutant and hda9-1 nrp1-1 nrp2-2 triple mutant.RNA-Seq of Columbia and Columbia after TSA treatment.  RNA-Seq data presented in this study were generated from three or five independent biological replicates: TSA-treated tissues were analyzed using five biological replicates, while mutant samples were evaluated with three biological replicates.

first: Yafei

last: Wang

first: Israel

last: Ausin

first: Han

last: Jiang

first: Min

last: Liu

first: Wenshuo

last: Zhang

first: Junjie

last: Xu


title: A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing

city: Solna

first: Rodrigo

middle: A.

last: Morales Castro

state: Stockholms län

address: Karolinska Universitetssjukhuset, CMM L8:03

country: Sweden

institute: Karolinska Institutet

summary: To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish, we performed single-cell (sc)RNA-seq from dissected intestines.

overall_design: Intestines from control and Mtz-treated zebrafish larvae were dissected at 4 days post fertilization (dpf) and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation, and DAPI- live cells were sorted by FACS.

middle: A

first: Bianca

middle: C

last: Kern

first: Angélica

last: Díaz-Basabe

first: Eveline

middle: R

last: Meinen

first: Danxia

first: Yuqing

last: Zhou

first: Francisca

last: Castillo

first: Gustavo

last: Monasterio

first: Vlad

last: Farcas

first: Myra

middle: N

last: Chávez

first: Jennifer

last: Fransson

first: Eduardo

middle: J

last: Villablanca


title: scRNA-seq and genomic reference of PBMC upon TNF Inhibitor Response in Ankylosing Spondylitis

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

overall_design:
To identify molecular factor that can predicts TNF inhibitor responsiveness for Ankylosing spondylitis patients. We performed scRNA-seq and CITE-seq before and after TNF or IL17 inhibitor treatment.

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

first: Seongwan

last: Park

first: Baekgyu

last: Choi

first: Jeong

middle: S

last: Lee


title: Acetylcholine derived from B lymphocytes controls liver regeneration

first: Liam

middle: D

last: Hendrikse

country: Canada

overall_design: RNA-seq profiling of sorted GFP positive and GFP negative B cells isolated from the liver 4 hours after sham or PHX treated Chat-GFP reporter mice (B6.Cg-Tg(RP23-268L19-EGFP)2Mik/J).

first: Nastaran

last: Modares

first: Tak

middle: W

last: Mak


first: Song

last: Woogil

address: KAIST, Daejeon 34141, Korea

department: Graduate School of Medical science and engineering

summary: The study identifies allograft inflammatory factor-1 (AIF-1) as a key marker of interferon (IFN) signature, which differentiates TNF inhibitor (TNFi) responders from non-responders in ankylosing spondylitis (AS)

overall_design: Peripheral blood mononuclear cells from AS patients were subjected to single-cell RNA sequencing to investigate differential gene expression, focusing on AIF-1 and IFN-related genes between TNFi responders and non-responders.

first: Woogil

last: Song

first: Eunyoung

middle: E

first: Jeong Seok

first: Eun Young


title: Solid stress compression enhances breast cancer cell migration through the upregulation of Interleukin-6

city: Singapore

first: Cheng Gee

last: Koh

state: Singapore

address: 60, Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: Apart from biochemical signals, tumour cells respond to biophysical and mechanical cues from their environment. The mechanical forces from the tumour microenvironment could be in the form of shear stress, tension, or solid stress compression. In this study, we explore the effects of solid stress compression on tumour cells. Solid stress compression, a prevalent biomechanical stimulus accumulated during tumour growth, has been shown to enhance invasive and metastatic phenotypes in cancer cells. However, the underlying molecular mechanism that elicits this aggressive metastatic phenotype, especially in breast cancer, is not well understood. Using an established 2D in vitro setup to apply incremental solid stress compression, we found that migratory and invasive capacities of aggressive breast cancer cells were enhanced in a biphasic manner. We also found that Interleukin-6 (IL-6) and SNAI1 transcripts and proteins were upregulated in response to solid stress. The resultant increased secretion of IL-6 could in turn lead to autocrine activation of downstream signalling pathways and impact on cancer cell migration and invasion.

overall_design: RNA-seq profiling of MDA-MB-231 cells under different compressive stresses (Uncompressed 0 Pascals, 386.5 Pascals, 773 Pascals and 1546 Pascals) post 16 hours of compression.

first: Farouq

last: Azizan

first: Ryna Shireen

last: Sheriff

first: Corinna Jie Hui

last: Goh

first: Keng Hwee

last: Chiam


title: AGED CD8+ T CELLS DRIVE COGNITIVE DECLINE VIA GZMK [parabiosis]

city: San Francisco

first: Juliana

last: Sucharov Costa

state: CA

address: 505 Parnassus Ave

department: Anatomy

country: USA

institute: UCSF

summary: Changes in peripheral CD8+ T cells are a prominent hallmark of immune aging. While infiltrating CD8+ T cells are implicated in aging and neurodegenerative disease-related pathology in the brain, the role of aged non-infiltrating CD8+ T cells has yet to be fully defined. Here, we show that targeting activated aged peripheral CD8+ T cells rescues age-related cognitive decline. Using heterochronic parabiosis and single cell transcriptomics analysis we observed that aged peripheral CD8+ T cells maintain properties intrinsic to their age, being refractory to the effects of a young or aged systemic milieu. Systemic exposure of young mice to aged CD8+ T cells elicited synaptic-related aging transcriptional signatures in the hippocampus and impaired cognition. Inhibiting migration of aged peripheral CD8+ T cells to lymph nodes mitigated pro-aging effects on the young hippocampus. Conversely, targeting aged CD8+ T cells restored synaptic-related signatures in the aged hippocampus and ameliorated cognitive impairments. Mechanistically, we identified granzyme k (GZMK) as a secreted age-associated CD8+ T cell-derived factor that impairs cognitive function. Together, our data identify activated aged CD8+ T cells and their secreted factors as potential therapeutic targets to rescue cognition in old age.

overall_design: Considering the pro-aging effects observed in the hippocampus following both heterochronic parabiosis and transplantation of an aged hematopoietic system into young mice, we first assessed changes in peripheral CD8+ T cell trafficking and transcriptional responses to a young and aging systemic milieu using heterochronic parabiosis. Young (4 months) and aged (20 months) mice were surgically joined into isochronic (young-young and old-old) and heterochronic (young-old) parabiotic pairings for 28 days. To distinguish young versus aged cells in heterochronic parabionts, young CD45.1 B6/BoyJ and aged CD45.2 B6 mice were joined. We performed single cell RNA seq analysis on splenocytes of young isochronic, aged isochronic, young heterochronic and aged heterochronic parabionts after separation of CD45.1+ or CD45.2+ cells to analyze donor versus recipient immune cells.

last: Sucharov

first: Karishma

last: Pratt

first: Saul

last: Villeda


title: AGED CD8+ T CELLS DRIVE COGNITIVE DECLINE VIA GZMK [transfer]

overall_design: We sought to investigate functionally how aged CD8+ T exerted their pro-aging effects on the young hippocampus. Activation of memory CD8+ T cells is dependent on G?i/o-coupled G protein-coupled receptor (GPCR)-mediated migration to lymph nodes. Correspondingly, we pre-treated aged CD8+ T cells with pertussis toxin (PTx), a known inhibitor of Gi/o protein signaling, to block migration into lymph nodes following adoptive transfer. Specifically, we performed an adoptive transfer of PTx or vehicle treated aged (26 months) CD8+ T cells into young (5 months) mice, and vehicle treated young CD8+ T cells into age-matched young animals as a baseline control for age-related changes. PTx pre-treatment has been shown to prevent T cell migration to lymph nodes without altering migration to open circulation tissues such as spleen, bone marrow, or liver, Moreover, the timeframe used for our studies was selected in line with previous reports showing minimal entry into the brain parenchyma with no impact on migration to the brain by PTx treatment. To investigate the impact on the young hippocampus, we performed single nucleus RNA seq (snRNAseq) analysis. Having observed pro-aging effects of aged circulating CD8+ T cells in the young hippocampus, we conversely explored the possibility that targeting CD8+ T cells can rescue cognitive function in aged mice. To selectively target aged peripheral CD8+ T cells late in life, aged (22 months) mice were given intraperitoneal injections of a CD8a depleting antibody or IgG2b isotype control. To investigate molecular changes elicited in the aged hippocampus following depletion of aged peripheral CD8+ T cells, we performed snRNAseq.


title: The histone lysine methyltransferase MLL1 regulates the activation and functional specialization of regulatory T cells [RNA-seq]

city: Beijing

first: Ting

last: Wang

address: No.1 Beichen West Road, Chaoyang District, Beijing, China

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: The activation and specialization of regulatory T cells (Tregs) are crucial for maintaining immune self-tolerance, but the epigenetic regulation of these processes remains largely unexplored. Here, we show that T-cell-specific deletion of the lysine methyltransferase MLL1 results in a spontaneous lymphocyte proliferation phenotype in aged mice without disturbing the development of conventional T cells and Tregs. Treg-specific MLL1 ablation leads to a systemic autoimmune disease associated with Treg dysfunction. RNA sequencing demonstrated that the induction of multiple genes involved in Treg activation, functional specialization and tissue immigration is defective in MLL1-deficient Tregs. This dysregulation is associated with defects in H3K4 trimethylation at the transcription start sites (TSSs) of these genes. Finally, using a T-bet fate-mapping mouse system, we determined that MLL1 is required to establish stable Th1-type Tregs. Thus, MLL1 plays an essential role in optimal Treg function by providing a coordinated epigenetic context for activation and specialization.

overall_design: Lymphocytes were isolated from the spleen and lymph nodes of 6- to 8-week-old Foxp3RFP-Cre.RosaYFPMll1fl/fl male mice and enriched for CD4+ T cells using magnetic beads. RFP+YFP+ and RFP+YFP- Tregs (3 x 105) were sorted to a typical purity of > 95 for RNA sequencing.  RNA was extracted using the RNeasy MicroRNA Kit (QIAGEN 74004). RNA sequencing (RNA-seq) and bioinformatics analysis were conducted by Novogene as described previously.Differential expression analysis of two conditions was performed using the DEGSeq R package (1.16.1). The p values were adjusted using the Benjamini-Hochberg method. Corrected q value = 0.05 and log2 (fold change) = 1 were set as the threshold for significantly differential expression.

first: Xuyu

last: Zhou


title: The histone lysine methyltransferase MLL1 regulates the activation and functional specialization of regulatory T cells

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The inflammatory micro-environment induced by targeted CNS radiotherapy is underpined by disruption of DNA methylation [RNA-seq]

city: London

first: Silvia

last: Marino

address: 4 Newark Street

department: Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

summary: Although targeted radiotherapy (RT) is integral to the increasing survival of cancer patients, it has significant side-effects, the cellular and molecular mechanisms of which are not fully understood. During RT epigenetic changes occur in neoplastic tissue, but few studies have assessed these in non-neoplastic tissue and results are highly variable. Using bulk DNA methylation and RNA sequencing as well as spatial transcriptomics (ST) in a unique cohort of patient tissue samples, we show distinct differences in DNA methylation patterns in irradiated brain tissue, whilst ST characterisation identifies specific micro-environmental niches present after irradiation and highlights neuropeptides that could be propagating neuroinflammation. We also show that in a cerebral organoid (CO) model of early changes in neurons after irradiation there are similar DNA methylation alterations and disruption of the DNA methylation machinery, suggesting that early but persistent epigenetic dysregulation plays a role in neurotoxicity. We provide a link between radiotherapy induced neuroinflammation and disruption of DNA methylation for the first time and suggest possible driving mechanisms for this chronic neuroinflammation.

overall_design: RNA sequencing was performed on brain tissue from surplus FFPE surgical materials of patients who received radiotherapy for the treatment of cerebral lesions. The experimental samples comprised cases where neurosurgical removal of a brain lesion occurred following radiotherapy, and the control samples included peri-lesional CNS tissue that had not received radiotherapy. H&E and subsequent unstained sections were obtained from the representative FFPE blocks and healthy brain tissue was morphologically identified and marked. Extraction of nucleic acids was performed from the delineated healthy tissue. Expression profiles were compared between the irradiated and non-irradiated cases.

first: Thomas

middle: O

last: Millner

first: Yunchen

last: Xiao


title: The histone lysine methyltransferase MLL1 regulates the activation and functional specialization of regulatory T cells [ChIP-seq]

overall_design: Lymphocytes were isolated from the spleen and lymph nodes of 6- to 8-week-old Foxp3-Cre.RosaYFP and Foxp3-Cre.RosaYFPMll1fl/fl male mice or Foxp3RFP-Cre.RosaYFPMll1fl/fl male mice and enriched for CD4+ T cells using magnetic beads. YFP+Tregs or RFP+YFP+ and RFP+YFP- Tregs (1 x 105) were sorted to a typical purity of > 95 for CUT&TAG sequencing. Histone H3K4me3 CUT&TAG sequencing (anti-H3K4me3 CUT&TAG-seq) was performed as described in regents kits of Hyperactive pG-MNase CUT&RUN Assay Kit for Illumina (Vazyme) as described previously.Briefly, 50,000 cells for each CUT&Tag library were incubated with 100 μL balanced concanavalin A-coated magnetic beads at RT for 10 min. The bead-bound cells were resuspended with 50 μL of antibody buffer. Then added 1 ug anti-H3K4me3 antibody (Abcam, ab8580) to the bead-bound cells. After 2 h incubation at RT, the primary antibody was discarded carefully and 0.5 μg goat anti-rabbit IgG (Vazyme, Ab206-10-AA) diluted with 50μL Dig-wash buffer was added to the cells at RT for 1 h. Afterward, samples were washed gently with 800 μL Dig-wash buffer, and 2 μL pG–Tn5 together with 100 μL Dig-300 buffer was added to the samples. After 1 h incubation at RT, samples were washed gently with 800 μL Dig-300 buffer. 10 μL tagmentation buffer together with 40 μL Dig-300 buffer was then added to each sample and the samples were incubated at 37°c for 1 h. The interactions were quenched by adding 10 μL 0.5 M EDTA, 3 μL 10% SDS, and 2.5 μL 20 mg/mL Proteinase K and incubating the samples at 50°c for 1 h. Phenol–chloroform and ethanol precipitation, as well as PCR and size selection, were performed as described in Hi-C library construction. All CUT&Tag libraries were sequenced on Illumina Nova Seq 6000 platform at PE150 mode subsequently.


title: SAS cell line ChIP and RNA-seq

city: Hsinchu

first: Wen-Ching

address: NO.101, Sec. 2, Kuang-Fu Road, Hsinchu 300044, Taiwan (R.O.C)

department: Insitute of Molecular & Cellular Biology

country: Taiwan

institute: National Tsing Hua University


title: Mouse cancer cells and bone-marrow macrophages expressing or silenced for IKKA and IKKB

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholz Zentrum Munich

summary: In this study we used bioluminescent reporter mice to discover that transplantable tumors cause nuclear factor-kappa B activation in host macrophages. This effect is mostly aggravated in mouse models of malignant pleural effusion, is dependent on KRAS mutation status of tumor cells, and is delivered via secretory versican, a toll-like receptor 2 ligand. Versican, in turn activates nuclear factor-kappa B in host macrophages via the canonical inhibitor of nuclear factor-kappa B kinase beta (IKKbeta), resulting in release of myeloid-secreted interleukin-1beta in the tumor microenvironment. Silencing of versican in cancer cells or conditional deletion of IKKbeta in macrophages abrogates myeloid nuclear factor-kappa B activation as well as tumor progression.

overall_design: Compare differential gene expression between mouse cancer cells and bone-marrow macrophages expressing or silenced for IKKA and IKKB

first: Magda

last: Spella

first: Mario

last: Pepe

first: G


title: Gene expression data from a Brazilian cohort of pediatric adrenocortical tumors

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

summary: Adrenocortical tumors in children are rare, but 10-15 times more incident in Southern Brazil than in the rest of the world. However, reliable biomarkers capable of establishing a well-defined prognostic correlation or predicting relapse risk of the disease are still challenging. Herein, we aimed to compare the expression profiles of pediatric adrenocortical tumors of patients with favorable and unfavorable clinical outcomes.

overall_design: Gene expression profiles from pediatric adrenocortical tumor samples (n=14) using high throughput sequencing.

first: L

middle: G

last: Tone

first: C

first: E

last: Valera

last: Carlotti

first: R

last: Queiroz

first: J

last: Yunes

first: S

last: Brandalise


title: Analysis of miRNA/mRNA profile of neurons infected with latent and reactivated PRV

city: Chongqing

first: Zhang

last: Chen

address: No. 160 Xueyuan Road, Changyuan Street

institute: Southwest University

type: Non-coding RNA profiling by high throughput sequencing


title: Kozak sequence libraries for characterizing transgenes across expression levels

status: Public on May 01 2025

city: Cleveland

first: Kenneth

last: Matreyek

state: OH

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University

summary: Typical mammalian overexpression systems test protein sequence variants with little control over expression levels and steady-state protein abundances, hindering interpretations of how protein sequence and expression converge to yield phenotypic outcomes. We explored the translation initiation sequence, commonly referred to as the Kozak sequence, as a means to modulate protein steady-state abundance and cellular function. We performed sort-seq on a randomized library of the 6 nucleotides preceding the start codon, amounting to 4,042 sequences. Calibrating the scores revealed a ~100-fold range of protein steady-state abundances possible through manipulation of the Kozak sequence. We identified human germline variants with predicted expression-reducing Kozak substitutions in disease-associated genes. Modulating the cell surface abundance of the host cell receptor ACE2 controlled the rate at which those cells became infected by SARS-like coronavirus spike pseudotyped particles. We demonstrated the potential of the approach by simultaneously testing Kozak libraries with a small panel of coding variants for ACE2 and STIM1. This approach lays the methodological groundwork for linking the causal relationships between protein sequence, abundance, and functional outcome.

overall_design: The miRFP670 Kozak library was recombined and sorted in four separate instances to create the four replicates analyzed in our dataset. For the first biological replicate, 120,000 HEK 293T cells were plated per well in a 24-well plate, and each well was transfected with a mixture of 2 μg ACE2 Kozak library plasmid and 8 μL Fugene transfection reagent (Promega, E2692), diluted in 60 μL Opti-MEM (Gibco, 31985070). Eight wells were transfected per attempt and subsequently pooled. Flow cytometry analysis prior to selection showed 2.5% mCherry-positive cells, suggesting that approximately 24,000 cells were independently recombined, corresponding to an estimated 6 independent events per Kozak sequence variant. Following positive and negative selection, sequencing revealed that some key Kozak sequences necessary for calibrating our results with our panel of individual variants were missing. To address the coverage limitations observed in the first replicate, a modified approach was taken for the second replicate. For this replicate, 1 million cells were seeded in a 6-well plate one day before transfection. Cells were transfected with a mixture containing 4 μg ACE2 Kozak library plasmid, 30 ng G790A plasmid, and 1.2 μL Xfect reagent, following the manufacturer’s instructions. After positive and negative selection, approximately 8,500 cells from each of the following clonal plasmid-expressing cell lines, G1100A [TTCATCATG], G1101F [GACGACATG], G1102A [CGTCCAATG], G1103A [GCGCGCATG], G1104B [TGGTCAATG], and G1106A [TTGCACATG], were mixed with 10 million library-expressing cells to achieve a diverse range of protein abundance. For the third biological replicate, 1 million cells were seeded in a 6-well plate one day before transfection. Cells were transfected with a mixture containing 4 μg ACE2 Kozak library plasmid, 30 ng G790A plasmid and 30 ng of each Kozak sequence plasmids (G1100A, G1101F, G1102A, G1103A, G1104B, and G1106A), and 1.2 μL Xfect reagent, following the manufacturer’s protocol. Following recombination, cells were subjected to positive and negative selection as described before. This approach was designed to enhance the diversity of protein abundance linked to Kozak sequence variations. For both of these replicates, ~ 170,000 cells were collected during each 4-way sort and the cells were cultured for ~48hrs before their genomic DNAs were extracted. The fourth recombination experiment used an independent miRFP670 Kozak library, where miRFP670 was C-terminally fused to the hygromycin resistance gene. Here, cells were transfected in two separate wells of a 6-well plate using Xfect reagent. Each well containing 1 million cells was transfected with 4 μg of Hygromycin Kozak library plasmid mixed with 1.2 μL Xfect reagent.Following recombination, cells underwent positive and negative selection as mentioned above. Roughly 130,000 cells were collected in each bin during 4 way sorting and were cultured for ~48hrs before collecting them for gDNA isolation.

first: Nidhi

last: Shukla


title: Revealing Transcriptomic Responses in Escherichia coli During Early Antibiotic Exposure

city: San Diego

first: Yuan

last: Yuan

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

summary: The earliest stages of bacterial adaptation to antibiotics are critical for survival, as the responses initiated in these moments shape the path toward tolerance and resistance. While long-term adaptations have been extensively studied, much less is known about the immediate, complex transcriptional changes that unfold in the first moments after antibiotic exposure. Here, we applied iModulon analysis to time-resolved transcriptomic data from Escherichia coli exposed to subinhibitory concentrations of two antibiotics, capturing regulatory changes within the first 30 minutes of exposure. This analysis reveals an integrated, three-phase framework of adaptation: an immediate and sustained primary response that broadly activates stress programs, a transient secondary response that restores redox balance, and a tertiary response that supports long-term survival through metabolic remodeling and antibiotic-specific defenses. This model provides new insight into how metabolic, redox, and stress responses are integrated to manage the physiological challenges of antibiotic stress, revealing a highly coordinated and dynamic regulatory strategy. By disentangling these overlapping transcriptional programs, our work offers a systems-level understanding of early bacterial adaptation and highlights new opportunities to investigate how survival mechanisms unfold during the critical moments following antibiotic exposure.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: RNA-seq profiling of E. coli MG1655 in the first 30 minutes after exposure to ampicillin and ciprofloxacin

first: Ying

last: Hefner

first: Richard

last: Szubin

first: Jaemin

last: Sung

first: Bernhard

last: Palsson


title: Single nucleus RNA sequencing of the cortex of antibiotic and vehicle treated APPPS1-21 mice

city: CHICAGO

first: Sidhanth

last: Chandra

state: IL

address: Tarry Building Room 8-711 300 E Superior

institute: Northwestern University Feinberg School of Medicine

summary: Previously, we and others have shown that broad spectrum antibiotic treatment from postnatal day 14-21 reduces neuroinflammation in the APPPS1-21 model of AD-related amyloidosis. In the current study, we used single-nucleus RNA sequencing (snRNAseq) to assess cell-type specific transcriptional changes in antibiotic treated mice and controls. We also assessed changes in astrocyte subclusters in these groups.

overall_design: We treated antibiotic and vehicle treated APPPS1-21 male mice (N=4/group) with broad spectrum antibiotics (4 mg/ml kanamycin, 0.35 mg/ml gentamicin, 8,500 U/ml colistin, 2.15mg/ml metronidazole, 0.45 mg/ml vancomycin in autoclaved water) or vehicle control from postnatal day 14-21. Mice were transcardially perfused at 3 months of age and following perfusion, the  the right cortex was sub-dissected and flash frozen in liquid nitrogen. The cortex was used to generate single nucleus suspensions for downstream sequencing and analysis

first: Chandra

last: Sidhanth

first: Salvo

last: Miranda

first: Ramakrishnan

last: Abhi

first: Piehl

last: Natalie

first: Watson

last: James

first: Gate

last: David

first: Vassar

last: Robert


title: The effect of antibiotics and propionate treatment on astrocyte transcription in APPPS1-21 mice

summary: Previously, we have shown that broad spectrum antibiotic treatment reduces reactive astrocyte phenotypes in the APPPS1-21 model of AD-related amyloidosis. We have also found that antibiotics selectively increases propionate levels and exogenous propionate treatment recapitulates phenotypes observed in antibiotic treated mice. In the current study, we wanted to assess astrocyte transcriptional state using bulk RNA sequencing. To accomplish this we used translating ribosome affinity purification (TRAP) sequencing, a ribosomal protein L10a is fused to eGFP under the control of a cell type specific promoter in a transgenic mouse model. We crossed APPPS1-21 mice to the Aldh1l1-eGFP/Rpl10a bacTRAP mouse model and progeny were treated with antibiotics, propionate, or VHL and performed bulk TRAPseq.

overall_design: APPPS1-21 male were treated with broad-spectrum antibiotics, propionate, or water vehicle (N=5/group). Mice were perfused at 3 months of age. The cortex was collected and flash frozen in liquid nitrogen. Cortex was processed for TRAPSeq as previously described by Heiman et al 2014. Quality of RNA isolated from TRAP purifications was assessed using Agilent Bioanalyzer. All RNA used for downstream sequencing had a RIN score above 7. mRNA libraries were generated from TRAP-purified RNA using the Illumina Stranded mRNA prep kit. Prepared libraries were sequenced on an Illumina HighSeq 4000. The quality of reads, in FASTQ format, was evaluated using FastQC.  Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt (Martin, 2011).  Trimmed reads were aligned to the Mus musculus genome (mm39) using STAR (Dobin et al, 2013).  Read counts for each gene were calculated using htseq-count (Anders et al, 2015) in conjunction with a gene annotation file for mm39 obtained from Ensembl (http://useast.ensembl.org/index.html).  Normalization and differential expression were calculated using DESeq2 that employs the Wald test (Love et al, 2014). The cutoff for determining significant DEGs was an FDR-adjusted p-value less than 0.1 using the Benjami-Hochberg method. Pathway analysis was performed using Metascape.


title: Genome-wide screen uncovers novel host factors for L-A virus maintenance and a mutualistic-symbiosis relationship in yeast

city: Taipei

first: Tien-Hsien

last: Chang

address: 128 Academia Road, Section 2, Nankang

department: Genomics Research Center

institute: Academia Sinica

summary: Background:  Viruses are traditionally viewed as intracellular parasites that exploit host resources to propagate, often at the host’s expense.  However, emerging evidence suggests more nuanced interactions, including potential mutualism.  The L-A double-stranded RNA (dsRNA) virus, a non-lytic, cytoplasmic virus commonly found in Saccharomyces cerevisiae, presents an intriguing case, as it lacks clear pathogenic effects in the absence of its M1 satellite. Results:  To address how and why L-A persistently resides in its yeast host, we conducted a genome-wide screen using yeast deletion and temperature-sensitive mutant collections, covering approximately 93% of annotated genes, to identify host factors essential for L-A maintenance.  This screen revealed 96 genes spanning diverse biological processes. Transcriptomic profiling indicated that L-A presence alters the host stress-response gene expression.  Furthermore, competitive fitness assays under stress conditions demonstrated that L-A can enhance host resilience, suggesting a mutualistic relationship. Conclusion:  Our findings uncover a previously unrecognized virus-host mutualism, wherein L-A benefits its host under environmental stress.  These results not only expand our understanding of persistent viral infections in eukaryotes but also challenge the canonical view of viruses as purely parasitic, offering new insights into virus-host co-evolution and endogenous viral persistence.

overall_design: RNA-Seq profiling of nine wildtype (WT) yeast Saccharomyces cerevisiae BY4741 strains that endogenous harboring different expression of L-A virus (without L-A , mid level of L-A, highly expression level of L-A virus strains).  Librart construction using rRNA depleted and poly(A) RNA enriched method respectively.

first: Wan-Yi

last: Hsiao


title: RNA-seq transcriptomes of E. coli K-12 MG1655 under diverse conditions for regulatory network analysis

summary: This dataset contains RNA-seq profiles of Escherichia coli K-12 MG1655 collected under a variety of conditions to enable transcriptional regulatory network (TRN) analysis using the iModulon framework.

overall_design: RNA-seq profiling of E. coli MG1655 under various conditions


title: Bioresponsive lysosome-targeting chimeras for targeted protein degradation

city: Yiwu

first: Huiping

last: Liu

state: Zhejiang

address: Futian Sub-district

institute: Zhejiang University

summary: Lysosome-mediated degradation of extracellular proteins represents an emerging therapeutic paradigm that exploits cellular waste-disposal machinery to eliminate pathogenic targets. Despite its promise, achieving selective degradation of disease-associated proteins remains constrained by the scarcity of discovering highly effective disease-specific lysosome-targeting receptors. To address this limitation, we engineered NeuroTAC, a lysosome-targeting chimera (LYTAC) that bridges a sortilin-binding ligand-neurotensin (NT) to a disease-specific antibody targeting proteins overexpressed in tumors and inflammatory disorders. NeuroTAC demonstrated robust degradation efficacy against both membrane-bound and extracellular proteins in experimental models. Leveraging the dysregulated activity of matrix metalloproteinases (MMPs), a characteristic feature of tumor and inflammatory microenvironments, we further developed BioresTAC as an innovative bioresponsive LYTAC variant. This advanced construct integrates an MMP-cleavable linker and terminal RGD peptides, enabling MMP-triggered activation and spatial precision in MMP-enriched pathological niches. Systematic validation demonstrated that NeuroTAC and BioresTAC mediate broad-spectrum protein degradation with microenvironmental selectivity, enhancing therapeutic efficacy in cancer and psoriasis models. These findings advance the translational potential of lysosome-engaging biologics, offering a dual strategy for precision degradation through receptor recruitment and microenvironmental sensing.

overall_design: RNA sequencing indicated the differences in the gene expression profiles of HepG2 cells treated with LYTAC and those untreated, with three duplicate samples in each group.

first: Hongwei

last: Wu

first: Zhengcheng

last: He

first: Longguang

last: Tang


title: Fibulin-5, an integrin-binging matricellular protein, maintains epidermal stem cell heterogeneity during skin aging

city: Fukuoka

first: Aiko

last: Sada

address: 3-1-1 Maidashi, Higashi-ku, Fukuoka City, Fukuoka 812-8582, Japan

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

summary: The extracellular matrix (ECM) plays a crucial role in building the extracellular environment and translating extracellular information into biochemical signals that sustain organ functions. Fibulin-5 is a multifunctional ECM protein essential for the formation of elastic fibers and the regulation of cellular functions through integrin binding. Fibulin-5 expression decreases with aging in human skin; however, its functional significance remains unknown. To address the roles of fibulin-5 in regulating epidermal stem cells during skin aging, Fbln5 knockout mice were examined for changes in their cellular and molecular phenotypes. Loss of Fbln5 in mice results in early impairments of epidermal stem cell properties, similar to the chronological aging of the skin. Fibulin-5 deficiency results in the suppression of integrins and other cell junctional molecules, leading to the inactivation of YAP signaling in epidermal stem cells. The reduced YAP signal is associated with the down-regulation of the fast-cycling epidermal stem cell marker, SLC1A3, in human skin and primary keratinocytes. These findings underscore the important role of fibulin-5 in governing the balance of epidermal stem cell populations during skin aging via crosstalk between the extracellular environment and intracellular signaling.

overall_design: RNA sequencing was performed on FACS-sorted epidermal stem cells from 12-month-old Fbln5 wild-type and knockout mice tail skin to investigate gene expression changes associated with Fibulin-5 deficiency in aging skin.

first: Wenxin

last: Fan

first: Mizuho

last: Ishikawa

first: Erna

last: Raja

first: Ahmed

middle: M

last: Hegazy

first: Yen Xuan

last: Ngo

first: Hiromi

last: Yanagisawa


title: Transcriptome analysis of Generalized Pustular Psoriasis (GPP) versus Palmoplantar Pustular Psoriasis (PPP) uncovers raised potential markers of severity, atopy and anxiety in GPP

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

institute: University of Ulm

summary: Background. Generalized pustular psoriasis (GPP), palmoplantar pustular psoriasis (PPP) and Acrodermatitis continua suppurativa Hallopeau (ACH) are 3 prototypes of pustular psoriasis. Treating them with the established psoriasis armamentarium of immunomodulating therapies is more or less a trial-and-error game because pathophysiology has not been uncovered in detail yet. Objectives. To promote the decoding of immunological pathways in GPP as the maximal variant of pustular psoriasis. Methods. Focusing on transcriptomic differences in GPP versus PPP, bulk RNA sequencing of affected skin and healthy skin of 3 GPP and 3 PPP patients was performed, and results were compared to each other and to matching healthy skin samples. Results. Analysis of heatmaps confirmed the expected up-regulation of Interleukin (IL-) 17, IL-23 and IL-36 pathways, especially in GPP. Interestingly, in our GPP patients we detected an unexpected marked atopic-like milieu with an upregulated T-helper cell (Th) type 2 profile. This raises the bar concerning personalized medicine as recently introduced IL-36 blockage will probably not be able to succeed as a monotherapy in GPP. In PPP-patients the ‚typical‘ immune signatures, although differentially regulated, struck with a notable heterogeneity. The atopic markers were not as overregulated as in GPP. Further findings might elucidate clinical features of GPP: Severity of symptoms was accompanied by up-regulated SERPIN B4 and L-selectin. And, an overexpression of KYNU and TDO2 as a sign for imbalance in tryptophan metabolism could deliver an explanation for psychological findings like anxiety and depression during an acute flare of GPP. Conclusions. GPP has an atopic component next to notorious drivers of classical psoriasis and IL-36. Key factors for aggressiveness of disease and psychological distress during flares could be overexpression of SERPIN B4/L-selectin respectively KYNU/TDO2. Trials with a greater number of patients and even more meticulous transcriptome analysis possibly supported by artificial intelligence should be considered.

overall_design: RNA-Seq of healthy and diseased skin of GPP and PPP patients

first: Maity

last: Pallab


title: Host aging induces a senescent-like phenotype in neutrophils with altered transcriptional responses to Streptococcus pneumoniae infection

city: Buffalo

first: Michael

last: Battaglia

state: NY

address: 955 Main St

department: Microbiology and Immunology

institute: SUNY at Buffalo

summary: Streptococcus pneumoniae is a Gram-positive commensal of the nasopharynx and highly virulent opportunistic pathogen in the respiratory tract. Despite the availability of multiple vaccines, S. pneumoniae remains a significant health burden especially in aged adults resulting in higher rates of serious disease progression, hospitalization, and death following infection. Polymorphonuclear leukocytes (PMNs) are among the first responders in the lung following S. pneumoniae infection. However, studies have indicated that PMNs of human and murine origin are dysfunctional in aged individuals. To identify mechanisms underlying this dysfunction and if it displays characteristics of immunosenescence previously observed in lymphocytes, we conducted RNA sequencing on PMNs in the lungs of young and old mice at 12 and 24 hours post pulmonary infection with S. pneumoniae. Our analysis indicated significant transcriptomic differences between the young and aged cohorts associated with decreased expression of many genes important for effector function including significant metabolic changes. These metabolic changes indicated that PMNS in the lungs of aged mice fail to upregulate glycolysis, which is necessary for anti-pneumococcal activity. Analysis of the transcription factors that may be regulating these differential transcriptomic changes to pneumococcal infection indicated differential regulation by E2f2 in aged mice, which appears to negatively regulate PMN differentiation. Importantly, analysis of PMNs in aged mice display context dependent senescent-like characteristics. Together this would suggest that in aged hosts PMNs display altered maturation and can adopt a senescent-like phenotype in the periphery, which contributes to defective gene expression changes required for normal anti-pneumococcal effector functions.

overall_design: Bulk RNA-seq of murine neutrophils (PMNs) in the lungs of animals 12- and 24-hour post intratracheal infection with Streptococcus pneumoniae

first: Elsa

last: Bou Ghanem

first: Manmeet

last: Bhalla

first: Brandon

last: Marzullo


title: Gene expression profile characteristics of patients with ulcerative colitis

city: Hangzhou

first: Shaopeng

last: Sun

address: No. 54, Youdian Road, Shangcheng District

department: Department of Gastroenterology

institute: The First Affiliated Hospital of Zhejiang Chinese Medical University

summary: Gene expression patterns of ulcerative colitis (UC) colonic specimens were analyzed using Transcriptome Sequencing

overall_design: Active UC patients(n=3) and healthy volunteers(n=3) provided intestinal mucosal tissue. Total RNA obtained from intestinal biopsies were analyzed using Transcriptome Sequencing

first: Bin

last: Lv

first: Yihong


title: Modular Design of T Cell Nanoengagers for Tumor Immunotherapy via Genetically Engineered Lipid-Tagged Antibody Fragments

city: Tianjin

first: Helong

last: Kang

state: 选择一个

address: 94 Weijin Road

institute: Nankai University

summary: T cell engagers, which bind tumor-associated antigens and T cell specific molecules, represent a promising class of immunotherapies for enhancing targeted immune responses. Here, we introduce a “plug-and-display” platform for engineering T cell nanoengagers by anchoring antibody fragments into lipid-based nanoparticles. This approach utilizes a genetically engineered lipoprotein fused with single-chain variable fragments (scFv) and nanobodies, which spontaneously integrated into lipid bilayer of the nanoparticles, achieving a high surface density of at least 0.102 scFv/nm2 (approximately 3200 scFv per particle). We designed modular bi-specific (Lipo-BiTE) and tri-specific (Lipo-TriTE) immunoliposomes to enhance anti-tumor T cell immune responses. The Lipo-BiTE, integrating anti-CD3 and anti-HER2 scFv at an optimized surface density of 1.28 × 10-3 scFv/nm2, exhibited enhanced CD8+ T cell-mediated cytotoxicity in HER2-positive tumor models by simultaneously engaging tumor cells and T cells. Incorporating anti-PD-L1 nanobodies to create Lipo-TriTE further addressed T cell exhaustion. This modular platform provides a robust foundation for designing immune cell engagers, with broad applications in targeted immunotherapy.

overall_design: To elucidate the underlying mechanisms of treatment response, RNA-seq analysis was performed on tumor-infiltrating CD3+ T cells isolated from mice treated with PBS, Lipo-BiTE, or Lipo-TriTE. Tumors were harvested at the experimental endpoint, and CD3+ T cells were sorted for transcriptomic profiling.


title: The stringent response does not influence ribosome pausing in Bacillus subtilis [Ribo-Seq]

city: Amsterdam

first: Yaozu

last: Han

address: Science Park 904

country: Netherlands

institute: Unversity Of Amsterdam

summary: The stringent response represses translation and is activated when amino acid levels drop, for example during the stationary phase. Bacillus subtilis, a well-known industrial enzyme production organism, secretes most enzymes during the stationary phase. We were curious whether the stringent response affects ribosome pausing, and whether its absence improves protein production yields in the stationary phase. To investigate this, genome-wide ribosome profiling was used using a stringent response mutant that overexpressed the α-amylase AmyM. Although, blocking the stringent response did increases overall protein synthesis, the secretion of AmyM was actually reduced. The ribosome profiling data revealed that this was not caused by a reduction in translation. In fact, absence of the stringent response did not seem to markedly influence ribosome pausing. However, late in stationary phase an increased ribosome pausing at tryptophane codons emerges, suggesting a depletion of tryptophane. A strong suppression of tryptophane biosynthesis and acquisition genes, under control of the trp RNA-binding attenuation protein TRAP, likely accounts for this, although TRAP does not belong to the stringent response regulon of B. subtilis. Finally, the ribosome profiles revealed several genes with unusually low translation activities, illustrating the importance of translation initiation as a regulatory element of expression.

overall_design: A high-copy expression plasmid was used to overexpress the heterologous α-amylase AmyM from G. stearothermophilus. Throughout this study this strain is referred to as the wild type (WT) strain. To eliminate the stringent response, we took this strain and deleted rel, sasA and sasB. This mutant is referred to as the ppGpp0 strain. Both strains were grown in rich medium for 16 h at 30 °C with continuous shaking.

first: Alberto

last: Agnolin

first: Frans

last: van der Kloet

first: Christopher

last: Sauer

first: Paul

last: Igor Costea

first: Max

last: Fabian Felle

first: Mathis

last: Appelbaum

first: Leendert

last: Hamoen


title: The stringent response does not influence ribosome pausing in Bacillus subtilis

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

overall_design: Refer to individual Series


title: The stringent response does not influence ribosome pausing in Bacillus subtilis [RNA-Seq]


title: Nucleosome dynamics render heterochromatin generally accessible in living human cells (MNase-seq in MCF7 nuclei, cells were transduced by Ad-Dam-3HA-eGFP for 72h)

city: Bethesda

first: David

middle: J.

last: Clark

state: MD

address: 6 Center Drive

department: NICHD

institute: NIH

summary: The eukaryotic genome is packaged into chromatin, which resembles beads on a string. Each bead consists of a nucleosome containing ~147 bp of DNA wrapped around a histone octamer. The nucleosomal filament undergoes additional folding to create a complex genomic organisation which is thought to restrict the access of gene-regulatory transcription factors to the genome. Consequently, it is widely accepted that DNA accessibility, modulated by chromatin architecture, is pivotal in gene regulation. Here, we measure genome accessibility at all GATC sites in living human MCF7 and MCF10A cells, using an adenovirus vector to express the sequence-specific dam DNA adenine methyltransferase. We find that the human genome is globally accessible in living cells, unlike in isolated nuclei. Active promoters are methylated somewhat faster than gene bodies and inactive promoters. Remarkably, both constitutive and facultative heterochromatic sites are methylated only marginally more slowly than euchromatic sites. In contrast, sites in centromeric chromatin are methylated slowly and are partly inaccessible. We conclude that nucleosomes in euchromatin and heterochromatin are highly dynamic in living cells, whereas nucleosomes in centromeric asatellite chromatin are static. A dynamic chromatin architecture implies that simple occlusion of transcription factor binding sites is unlikely to be critical in gene regulation.

overall_design: MNase-seq experiment for MCF7 nuclei: Illumina paired-end data. Two biological replicate experiments.

first: Hemant

middle: K

last: Prajapati

first: Zhuwei

last: Xu

first: Peter

last: Eriksson


title: Nucleosome dynamics render heterochromatin generally accessible in living human cells (qDA seq in MCF7 nuclei in buffer without spermidine)

overall_design: Dam titrations for MCF7 nuclei: Illumina paired-end data. Two biological replicate experiments.


title: Nucleosome dynamics render heterochromatin generally accessible in living human cells (RNA-seq)

summary:
The eukaryotic genome is packaged into chromatin, which resembles beads on a string. Each bead consists of a nucleosome containing ~147 bp of DNA wrapped around a histone octamer. The nucleosomal filament undergoes additional folding to create a complex genomic organisation which is thought to restrict the access of gene-regulatory transcription factors to the genome. Consequently, it is widely accepted that DNA accessibility, modulated by chromatin architecture, is pivotal in gene regulation. Here, we measure genome accessibility at all GATC sites in living human MCF7 and MCF10A cells, using an adenovirus vector to express the sequence-specific dam DNA adenine methyltransferase. We find that the human genome is globally accessible in living cells, unlike in isolated nuclei. Active promoters are methylated somewhat faster than gene bodies and inactive promoters. Remarkably, both constitutive and facultative heterochromatic sites are methylated only marginally more slowly than euchromatic sites. In contrast, sites in centromeric chromatin are methylated slowly and are partly inaccessible. We conclude that nucleosomes in euchromatin and heterochromatin are highly dynamic in living cells, whereas nucleosomes in centromeric asatellite chromatin are static. A dynamic chromatin architecture implies that simple occlusion of transcription factor binding sites is unlikely to be critical in gene regulation.
We performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF7 cells transduced by Ad-eGFP or Ad-Dam-3HA-eGFP adenoviral vector.


title: Beta-cell dependence to alpja-cell signals for proper insulin secretion in mouse pancreatic islets

city: Paris

first: Alexis

last: Fouque

address: 123 boulevard de Port-Royal

country: France

institute: Inserm

summary: The islets of Langerhans play a central role in detecting and regulating blood glucose levels. While insulin-producing beta-cells are well-characterized, much remains to be studied about the other cell types in pancreatic islets (alpha-, delta-, PPY-, and epsilon-cells). In this context, we have developed chimeric organoids that we use to understand the interactions between the different cell populations present in pancreatic islets. We previously developed an efficient approach to purify the major cell populations present in pancreatic islets (alpha, beta, and delta) using flow cytometry. We have now developed a technique to re-aggregate these sorted cell populations, enabling the production of clusters (pseudo-islets) in which we can modulate the proportion of each cell population on demand. We generated clusters devoid of delta cells or both alpha and delta cells and confirmed this depletion at the gene and protein levels. We then evaluated the function of these pseudo-islets by measuring glucose-stimulated insulin secretion. The absence of delta-cells did not affect insulin secretion. However, the insulin secretory capacity of pseudo-islets lacking both alpha- and delta-cells was significantly reduced. Transcriptomic analysis of these pseudo-islets did not reveal a loss of beta-cell identity as the cause of the observed functional impairment but highlighted potential new signaling pathways influenced by alpha- and delta-cells. This demonstrates the importance of interactions among different endocrine cell types within the islet for the function of pancreatic beta-cells. It represents a new and effective tool for identifying signaling pathways and compounds that directly or indirectly (via other endocrine cell types) modulate the identity and function of pancreatic endocrine cells.

overall_design: RNAseq profiling of mouse pancreatic beta-cells from clusters cultured for 5 days with all other endocrine cells or culture alone

first: Masaya

last: Oshima

first: Chloe

last: ourenco

first: Marine

last: De-Brghgrave

first: Latif

last: Rachdi

first: Raphael

last: Scharfmann


title: Targeting p85β condensates by RNA therapy inhibits liver cancer progression

city: Shanghai

first: Yujun

last: Hao

address: No. 25, Lane 2200, Xietu Road

institute: Medicine for Cancer, Shanghai Cancer Institute, School of Medicine, Shanghai Jiao Tong University

summary: PI3K complex consists of catalytic subunit p110s and regulatory subunit p85s. Emerging evidence indicates that p110-free p85 subunits play pivotal roles in diverse biological processes, including cancer progression. In this study, we demonstrate the oncogenic function and underlying mechanism of p110-free p85β in hepatocellular carcinoma (HCC) development. PIK3R2/p85β is highly expressed in HCC tissues and correlates with worse overall survival of HCC patients. Nuclear p85β, but not its cytoplasmic counterpart, exhibits oncogenic activity. In the nucleus of HCC cells, p85β undergoes liquid-liquid phase separation (LLPS) and specifically accumulates in the fibrillar centers of nucleoli, where it drives HCC progression. Within the nucleolar compartment, p85β directly interacts with and stabilizes POLR1A, the catalytic core subunit of RNA polymerase I, thereby enhancing rRNA biosynthesis and maintaining HCC stemness. Furthermore, we develop an engineered circular RNA that encodes a peptide containing p110α ABD domain, which effectively suppresses HCC tumor growth by simultaneously disrupting p85β/POLR1A condensates and inhibiting PI3K/AKT signaling pathway. Our findings not only elucidate the critical role of p85β biomolecular condensates in HCC  tumorigenesis but also establish a novel RNA-based therapeutic strategy for HCC intervention.

overall_design: RNA-seq profiling of Huh cell treated with NC or ABD circular RNA overnight


title: Lipid Droplet-Enriched Luminogens Enable Adoptive Macrophage Transfer for Treatment of Bacterial Sepsis

city: Singapore

first: Xianglong

last: Liu

address: College of Design and Engineering, National University of Singapore, 5A Engineering Drive 1, T-Lab 03-01

institute: National University of Singapore

summary: MRSA-induced sepsis poses a significant threat to human health. In clinical practice, the primary approach for sepsis treatment remains the use of antibiotics to control bacterial infections. However, the widespread and prolonged use of antibiotics has led to increased bacterial resistance, rendering conventional antibiotics less effective. Here, we report the design and development of a novel antibiotic that differs from traditional bactericidal mechanisms. This antibiotic employs a dual-targeting strategy by disrupting bacterial membrane integrity and binding to bacterial DNA, thereby effectively eliminating bacteria. This approach enhances antibacterial efficacy while reducing the likelihood of resistance development.

overall_design: The impact of the novel antibiotic TPA2PyPh on gene expression in methicillin-resistant Staphylococcus aureus (MRSA) was investigated. MRSA (~10⁵ CFU/mL) was incubated in LB culture medium containing 0.5 μM TPA2PyPh (1/2 × MIC) at 37 °C for 24 hours. Following incubation, the bacteria were harvested for total RNA extraction using the TRIzol reagent (Invitrogen, CA, USA). The control group was subjected to the same conditions without TPA2PyPh treatment.

first: Guobin

last: Qi

first: Minyang

last: Zhao

first: Min

last: Li

first: Bowen

first: Duo

last: Mao

first: Bin


title: The Urinary eccDNA Landscape in Prostate Cancer Reveals Associations with Genome Instability and Vital Roles in Cancer Progression [Circle-Seq]

city: Hangzhou, Zhejiang

first: Zhimin

last: Zhou

address: No. 866, Yuhangtang Road, Xihu District, Hangzhou City, Zhejiang Province

summary: Introduction: Extrachromosomal circular DNA (eccDNA) plays significant roles in cancer progression and prognosis. However, it remains unclear whether cell-free eccDNA, considered more stable than linear DNA, possesses cancer-specific genomic features. Furthermore, the biogenesis and function of eccDNAs are not yet fully understood. Objectives: This study aims to characterize the genomic landscape of urinary cell-free eccDNAs in prostate cancer (PCa) and non-cancer (NC) individuals, elucidate their biogenesis and PCa-specific genomic features, and investigate their roles in PCa progression. Methods: We conducted urine Circle-seq for 21 PCa patients and 16 NC individuals, performed integrated analysis with other omics datasets, and finally validated the function of eccDNA by in vitro transfection and RNA-seq. Results: We pioneered the profiling of urinary cell-free eccDNAs landscape in PCa and uncovered a high association between eccDNA generation and active chromatin status as well as gene transcription. Double strand breaks and R-loops, which preferentially occur in active genomic sites and cause genome instability, can promote eccDNA generation. Genome instability frequently results in genomic mutations, and our study further established a link between eccDNA generation and oncogenic mutations. Additionally, genes specifically exhibiting high eccDNA generation frequency (HFGs) in PCa contributed to PCa progression and were associated with poorer survival outcomes in PCa patients. Finally, we demonstrated that eccDNAs derived from PCa-specific HFGs, in contrast to intergenic eccDNAs, could suppress PCa cell proliferation and migration, which was independent of their host gene expression. Conclusion: Our study illustrated the biogenesis of eccDNAs from DSBs in active genes, revealed PCa-specific eccDNA features and suggested new mechanisms underlying eccDNA function.

overall_design: Urine Circle-seq for 21 prostate cancer (PCa) patients and 16 non-cancer (NC)  individuals

first: Shengcai

last: Chen

first: Jindan

last: Luo

first: Liang

last: Gong

first: Yanfen

last: ZHU


title: The Urinary eccDNA Landscape in Prostate Cancer Reveals Associations with Genome Instability and Vital Roles in Cancer Progression [R-loop CUT&Tag]

overall_design: R-loop identification of ISO-induced PC-3 cell line


title: RNA Sequencing of Nalm-6 SF3B1 K700E MT and Nalm-6 SF3B1 WT cells

city: Greenwood

first: Austin

last: Herbert

state: South Carolina

address: 114 Gregor Mendell Circle

department: Genetics and Biochemistry

institute: Clemson University

summary: SF3B1, a core component of the spliceosome involved in branch point recognition and 3’ splice site selection is frequently mutated in hematopoietic malignancies. Though its associations with clinical outcomes are unclear, mice and zebra fish with conditional SF3B1 knock-in mutations develop macrocytic anemia. A hallmark of SF3B1 mutation is an increase to cryptic 3’ splice site (C3SS) usage, a finding that is recapitulated across multiple isogenic and patient cell types. Mechanisms contributing to cryptic splice site choice and the influence of mis-splicing on posttranscriptional isoform regulation in SF3B1 mutants remains unclear. Our data indicate that SF3B1 K700E mutant Nalm-6 cells carry a significantly different set of cryptic 3’ splice sites than ones utilized in wild type cells.

overall_design: RNA-Seq was performed to compare the alternative splicing differences between Nalm-6 SF3B1 mutant and Nalm-6 SF3B1 wild type cells. Three technical replicates were performed for SF3B1 K700E cells and three technical replicates for SF3B1 wild type cells.

first: Lela

last: Lackey

first: Abigail

last: Hatfield


title: Differential memory enrichment of cytotoxic CD4 T cells in Parkinson’s disease patients reactive to ⍺-synuclein

city: La Jolla

first: Emil

last: Johansson

state: California

address: 9420 Athena Cir

department: Center for Autoimmunity and Inflammation

institute: La Jolla Institute for Immunology

summary: Parkinson’s disease (PD) is a complex neurodegenerative disease with a largely unknown etiology. Although the loss of dopaminergic neurons in the substantia nigra pars compacta is the pathological hallmark of PD, neuroinflammation also plays a fundamental role in PD pathology. We have previously reported that PD patients have increased frequencies of T cell reactive to peptides from ⍺-synuclein (⍺-syn). However, not all PD participants respond to ⍺-syn. Furthermore, we have previously found that CD4 T cells from PD participants responding to ⍺-syn (PD_R) are transcriptionally distinct from PD participants not responding to ⍺-syn (PD_NR). To gain further insight into the pathology of PD_R participants, we investigated surface protein expression of 11 proteins whose genes had previously been found to be differentially expressed when comparing PD_R and healthy control participants not responding to ⍺-syn (HC_NR). We found that Cadherin EGF LAG seven-pass G-type receptors 2 (CELSR2) was expressed on a significantly higher proportion of CD4 effector memory T cells (Tem) in PD_R compared to HC_NR. Single-cell RNA sequencing analysis of cells expressing or not expressing CELSR2 revealed that PD_R participants have elevated frequencies of activated Tem subsets and an almost complete loss of cytotoxic Tem cells. Flow cytometry analyses confirmed that Granulysin+ CD4 cytotoxic Tem cells are reduced in PD_R. Taken together, these results provide further insight into the perturbation of T cell subsets in PD_R, and highlights the need for further investigation into the role of Granulysin+ CD4 cytotoxic Tem in PD pathology.

overall_design: We set out to perform single cell RNA sequencing to determine the impact of CELSR2 expression of CD4+ effector memory T cells in donors with Parkinsons's disease (PD) resonsive to alpha-synuclein (PD_R) and healthy donor not responsive to alpha-synuclein (HC_NR).  20x10^6 cells per participant were used. Fc receptors were blocked (BD Biosciences) before membrane staining with antibodies and a specific hashtag (TotalSeq B; Biolegend) for 20 min at 4C. Cells were washed and DAPI was added to stain dead cells. Two populations were sorted using a BD FACSAria II (BD Biosciences): DAPI-CD3+CD4+CD8-CD45RA-CCR7-CESLR2+ and DAPI-CD3+CD4+CD8-CD45RA-CCR7-CESLR2-.

first: Antoine

last: Freuchet

first: Alessandro

last: Sette


title: ENO1 couples HDAC1 to regulate histone lactylation and gene transcription

first: zilong

last: fan

address: 22 Weidai Road, Heping District

institute: Tianjin Medical University

summary: Histone deacetylases (HDACs) are essential transcriptional regulators that mediate gene expression through the complexes they are involved in. Thus, deciphering the HDAC-associated proteins is key to elucidating the underlying mechanisms. Here we present an efficient tool, termed heterobifunctional molecule-enabled proximity labeling strategy (BimPL), to investigate endogenous HDAC neighboring proteins in living cells. Leveraging BimPL and quantitative proteomics, we enable the robust capture of several known HDAC complexes as well as numerous putative HDAC interactors such as glycolytic enzyme enolase-1 (ENO1). Through biochemical studies and CUT&Tag analysis, we uncovered that nuclear ENO1 interacts with HDAC1, which in turn blunts the activity of HDAC1 via locally generated phosphoenolpyruvate (PEP), thereby mediating histone lysine lactylation (Kla) and gene transcription. Our study offers a versatile tool for systematic exploring endogenous protein complexes, as well as provides insight into the unidentified function of ENO1 in the regulation of histone Kla and liver tumor progression.

overall_design: We  implemented CUT&Tag assays in HepG2 cells to determine the impact of ENO1/HDAC1-mediated histone lactylation on gene transcription. To this end, the cells were  immunoprecipitated by H4K12la, ENO1 or HDAC1 antibodies, respectively, followed by high-throughput sequencing.


title: RNA sequencing of HGC - 27 and AGS cells that were treated with estradiol.

city: Wuhan

first: sheng

last: tian

address: 169 Donghu Road, Wuchang District, Wuhan City, Hubei Province.

institute: zhongnan hospital

summary:
Although it is established that chronic psychological stress significantly contributes to tumor development, the molecular mechanisms linking it to gastric cancer (GC) progression remain incompletely understood.
In this work, we analyzed depression-related gene expression profiles in relation to clinical prognosis and identified estradiol (E2) and NOTCH3 as key factors involved in GC progression under depression conditions. The impact of depression on GC was verified using a chronic unpredicted stress (CUS)-stimulated tumor bearing mouse model. Furthermore, the underlying molecular mechanisms were elucidated through various biological techniques, including western blotting, immunofluorescence, flow cytometry and immunohistochemistry.
Depression significantly promoted GC growth in our mouse model, accompanied by decreased estrogen levels and an upregulation of NOTCH3 expression. Notably, exogenous estrogen supplementation effectively mitigated depression-induced tumor growth. In vitro studied consistently demonstrated that E2 treatment suppressed NOTCH3 expression in HGC and YTN3 cell lines, with NOTCH3 regulating intracellular ROS levels by modulating SOD2 activity to affect cell proliferation.
This work identified the estrogen-regulated NOTCH3 as a key link between chronic stress and GC, offering promising therapeutic strategies to enhance the outcome for GC patients suffering from comorbid depression.

overall_design: RNA-seq profiling of HGC-27 and AGS cells and those treated with 10 nM estradiol for 1 day.

first: Yixin

last: Liu

first: Yongchang

last: Wei


title: Porcine respiratory coronavirus as a model for acute respiratory disease: mechanisms of different infection outcomes

city: Pirbrigh

first: liu

last: yang

address: Ash Rd

institute: The Pirbright Institute

summary: Porcine respiratory coronavirus (PRCV) is a naturally occurring pneumotropic coronavirus in the pig, providing a valuable large animal model to study acute respiratory disease. PRCV pathogenesis and the resulting immune response was investigated in pigs, the natural large animal host. We compared two strains, ISU-1 and 135, which induced differing levels of pathology in the respiratory tract to elucidate the mechanisms leading to mild or severe disease. The 135 strain induced greater pathology which was associated with higher viral load and stronger spike-specific antibody and T cell responses. In contrast, the ISU-1 strain triggered mild pathology with a more balanced immune response and greater abundance of T regulatory cells. A higher frequency of putative T follicular helper cells was observed in animals infected with strain 135 at 11 days post-infection. Single-cell RNA-sequencing of bronchoalveolar lavage revealed differential gene expression in B and T cells between animals infected with 135 and ISU-1 at 1 day post infection. These genes were associated with cell adhesion, migration, and immune regulation. Along with increased IL-6 and IL-12 production, these data indicate that heightened inflammatory responses to the 135 strain may contribute to pronounced pneumonia. Among BAL immune cell populations, B cells and plasma cells exhibited the most gene expression divergence between pigs infected with different PRCV strains, highlighting their role in maintaining immune homeostasis in the respiratory tract. These findings indicate the potential of the PRCV model for studying coronavirus induced respiratory disease and identifying mechanisms that determine infection outcomes.

overall_design: For scRNA-seq two group of animals were used. First group received low pathogenic PRCV ISU-1 and second group received high pathogenic PRCV 135 intranasally. 4 animals from each group were humanly culled at day 1 and 20 post infection and subsequently bronchoalveolar lavage were obtained. To account for the strong domination of macrophages in BAL cell preparations, we sorted major leukocyte to reresent equal proportion of each major cell types. In brief, cryopreserved BAL cells were thawed and labelled with antibodies against CD4 (clone 74-12-4, PerCP-Cy5.5-conjugated, BD Biosciences), CD8β (clone PPT23, FITC-conjugated, Bio-Rad), CD3 (clone PPT3, APC-conjugated, Southern Biotech), CD16 (clone G7, AF647-conjugated, Bio-Rad), CD172a (clone 74-22-15, PE-conjugated, Bio-Rad) and Fixable Viability Dye eFluor780 (ThermoFisher) and sorted on a FACSAria UIII (BD Biosciences). This allowed the sorting of CD4+ (CD4 T cells), CD8β+ (CD8 T cells), CD16+CD172a+ (Macrophages) and CD3-CD16- (B cells) cells.  12,000 of each cell types were collected. Cells from each fraction were processed for partitioning and barcoding using a 10x Genomics Chromium iX Controller.

first: Ehsan

last: Sedaghat-Rostami

first: Brigid

last: Veronica Carr

first: Liu

last: Yang

first: Sarah

last: Keep

first: Fabian Z X

last: Lean

first: Isabella

last: Atkinson

first: Albert

last: Fones

first: Basudev

last: Paudyal

first: James

last: Krik

first: Eleni

last: Vatzia

first: Simon

last: Gubbins

first: Erica

last: Bickerton

first: Emily

last: Briggs

first: Alejandro

last: Nunez

first: Adam

last: McNee

first: Katy

last: Moffat

first: Graham

last: Freimanis

first: Christine

last: Rollier

first: Andrew

last: Muir

first: Arianne

last: C Richard

first: Nicos

last: Angelopoulos

first: Wilhelm

last: Gerner

first: Elma

last: Tchilian


title: Quantitative analyses of structure-function heterogeneity of individual mitochondrial components reveal an early role of small-mitochondrial-networks in priming neoplastic transformation

city: Sonipat

first: Kasturi

last: Mitra

state: Haryana

address: RGEC Sonipat Delhi NCR

department: Biology

country: India

institute: Ashoka University

summary: We elucidate a biological mechanism of cancer initiation involving stem cell specification. Based on data from experimentation with a model carcinogen, we propose that conversion of large ‘Hyperfused Mitochondrial Networks’ (HMNs) to heterogenous ‘Small Mitochondrial Networks’ (SMNs) primes non-transformed cells towards stem cell driven neoplasticity. Mechanistically, the SMNs, enriched by modulation of the physical nodes and edges of mitochondrial networks, tunes the mitochondrial redox balance to establish transcriptomic interactions required to maintain a stem cell state to support neoplastic transformation.

overall_design: The scRNAseq data of HaCaT keratinocyte line exposed to model carcinogen TCDD (1nM and 10nM) at the 2.5 hour timepoint

first: Swati

last: Agarwala

first: Brian

last: Spurlock


title: Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection-induced enteritis in zebrafish

first: dahai

last: Yang

address: No.130, Meilong Road, Xuhui District

institute: East China University of Science and Technology

summary: Infectious enteritis is often accompanied with immuno-disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long-term functional reprogramming of innate immune cells to combat infectious diseases. However, whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here, through establishing an in vivo β-glucan training and E. piscicida infection model in zebrafish, we observe that induction of trained immunity could alleviate bacterial infection-caused enteritis. Moreover, we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore, we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3-dependent manner to alleviate infectious enteritis. Taken together, our results uncover the role of complement C3-mediated trained immunity in maintaining Th17 cells and intestine homeostasis, and provide a theoretical strategy for immunotherapies of infectious enteritis.

overall_design: RNA-seq profiling of wildtype zebrafish in mock and PBS- or β-glucan-trained at Day 7 after secondary E. piscicida infection

first: Yanbo

last: Zhao

first: Xiaochuan

last: Mei

first: Jin

first: Zhuang

last: Wang

first: Dahai


title: NeuroD1-USP1-N-Myc axis drives tumor progression in neuroblastoma [ATAC-seq]

city: Suzhou

first: Gen

last: Li

state: Jiangsu

address: No. 92 Zhongnan Street

institute: Children's Hospital of Soochow University

summary: Neuroblastoma, derived from the sympathetic neural crest, represents the most prevalent extracranial solid tumor in children. Amplification of MYCN is widely recognized as a key indicator of unfavorable prognosis in neuroblastoma. However, the structural properties of the N-Myc protein encoded by MYCN have hindered the development of direct inhibitors with favorable drug-like properties. Therefore, uncovering the upstream regulatory mechanisms of N-Myc offers promising new targets for therapeutic intervention in MYCN-amplified neuroblastoma. In this study, we identified NeuroD1 as a critical regulator closely associated with MYCN amplification. NeuroD1 was shown to drive the proliferation of MYCN-amplified neuroblastoma cells both in vitro and in vivo. Mechanistically, NeuroD1 knockdown led to increased K48-linked polyubiquitination of N-Myc, resulting in its proteasomal degradation. Through transcriptional target screening, USP1 was identified as a key downstream effector of NeuroD1. Further investigation revealed that USP1 interacts with N-Myc, removing K48-linked polyubiquitin chains and stabilizing the protein. Importantly, Pimozide, an FDA-approved USP1 inhibitor, was found to effectively suppress USP1 expression, reduce N-Myc levels, and inhibit neuroblastoma cell proliferation. These findings highlight a novel oncogenic axis in MYCN-amplified neuroblastoma, where NeuroD1 transcriptionally upregulates USP1, facilitating N-Myc stabilization and tumor progression. Additionally, our results underscore the therapeutic potential of repurposing Pimozide as a viable treatment strategy for this aggressive tumor subtype.

overall_design: About 50,000 IMR-32 cells were obtained for ATAC-seq libraries.

first: Yanlin

last: Chen

first: Ran

last: Zhuo

first: Juanjuan

last: Yu


title: NeuroD1-USP1-N-Myc axis drives tumor progression in neuroblastoma [ChiP-seq]

overall_design: ChIP-seq of the NeuroD1 binding sites in IMR-32 cells

first: Jianping

last: Bao


title: NeuroD1-USP1-N-Myc axis drives tumor progression in neuroblastoma [CUT&TAG]

overall_design: CUT&Tag using antibody against H3K27ac in IMR-32 cells.


title: NeuroD1-USP1-N-Myc axis drives tumor progression in neuroblastoma [RNA-seq]

overall_design: Gene expression profiles of both parental and NeuroD1 knockdown IMR-32 cells were analyzed using RNAseq


title: PWS gene expression profiling of obese and non-obese patients

city: Yangsan

first: Ju Young

last: Yoon

address: Geumo-ro 20

institute: Pusan National University Children's Hospital

summary: We aimed to characterize genetic alterations in PWS using whole genome microarrays. We performed mRNA expression microarray analysis using RNA isolated from whole blood of 25 PWS patients and 25 age-matched controls.. After preprocessing the data to reduce heterogeneity, differentially expressed genes (DEGs) between groups were identified using a linear regression model package. Reactome pathway analysis was performed for upregulated and downregulated genes using EnrichR. Correlations between gene expression levels and clinical factors were estimated using Spearman’s rank correlation coefficient. Of 21,488 probes examined in the microarray analysis, 4,156 were detected. Fifty-two genes had different expression levels in children with PWS compared with healthy controls (36 genes upregulated and 16 downregulated). Twelve genes were upregulated and 13 were downregulated in obese PWS patients compared with normal-weight PWS (NW-PWS) patients. The C-Type Lectin Domain Family 4 Member D (CLEC4D) was upregulated in both PWS (vs. control) and obese-PWS (vs. NW-PWS) patients, and CLEC4D expression was also correlated with body mass index-standard deviation score in PWS patients. Among the genes upregulated in obese PWS vs. NW-PWS, Annexin A3 (ANXA3), Potassium Inwardly Rectifying Channel Subfamily J Member 15 (KCNJ15), and Selenium Binding Protein 1 (SELENBP1) were upregulated in obese-control vs. NW-control. Gene Ontology analysis revealed that upregulated DEGs were significantly enriched in biological processes, including pathways involved in myeloid dendritic cell activation associated with CLEC4D.This study revealed differences in gene expression between obese and NW-PWS patients. The regulation of macrophage infiltration by CLEC4D suggests a possible mechanism associated with obesity-related complications in PWS.

first: Juyoung

first: Yeuni

first: Chongkun

last: Cheon

first: Choongho

last: Shin


title: Enhancing Extracellular Polysaccharide Production under Nitrate Condition through the Silencing of the Transcription Factor AreA in Ganoderma lucidum

city: nanjing

first: xiaoyu

last: guo

address: xuanwu district

institute: nanjing agricultural university

summary: Fungal polysaccharides are not only important components of cell walls but also important for their applications in food and medicine. Nitrogen is crucial for physiological functions of fungi. However, studies on how nitrogen affect polysaccharides biosynthesis are relatively scarce. In this study, transcriptomic profiles of strains cultured with ammonium or nitrate as the nitrogen source were examined, respevtively, and their comparative analysis resulted in the enrichment of polysaccharide synthesis pathway. Further studies revealed that ammonium nitrogen promotes the extracellular polysaccharides (EPS) synthesis, whereas nitrate enhances the intracellular polysaccharides (IPS) synthesis. Subsequently, the function of AreA, an important nitrogen metabolism transcription factor, on polysaccharides synthesis was studied. Under nitrate condition, compared to the wild-type (WT), the content of EPS increased by approximately 33%, while the content of IPS, chitin, and ?-1,3-glucan in the areA-silenced strain was significantly reduced by 24%, 20%, and 20%-25%, respectively. Changes in content of chitin and ?-1,3-glucan affect the structure and integrity of the cell wall. Compared to ammonium condition, under nitrate condition, the cell wall thinned by approximately 23% following areA silencing, and sensitivity to cell wall perturbing agents increased by approximately 20%-30%. In summary, this study elucidates the impact of nitrogen sources on the polysaccharides synthesis, offering valuable insights into strategies for enhancing polysaccharide content in G. lucidum

overall_design: Analysis of differential genes in the transcriptome sequencing of Ganoderma lucidum wild-type treated with ammonium salts and nitrates.

first: yuzhen

last: yang

first: yanqiu

last: li

first: Bin

last: chen

first: Huajun

first: chen

last: zhang

first: jiping

last: ma


title: Nucleosome dynamics render heterochromatin generally accessible in living human cells (MNase-seq in MCF7 nuclei)

first: David

last: Clark

overall_design: MNase-seq experiment for MCF7 nuclei: Illumina paired-end data. Two biological replicate experiments.

first: Hemant

last: Prajapati

first: Zhuwei

last: Xu

first: Peter

last: Eriksson


title: Nucleosome dynamics render heterochromatin generally accessible in living human cells (qDA seq in MCF7 live cells and nuclei)

overall_design: Multiple time courses of DNA methylation by Dam methylase in MCF7 cells and Dam titrations for MCF7 nuclei: Illumina paired-end data. Two biological replicate experiments.


title: RNA-Sequencing Analysis of Type-I and Type-II Interferon Effects on an In-Vitro Human Thymic Epithelium Model

city: Palo Alto

first: Abdulvasey

last: Mohammed

address: 240 Pasteur Dr

institute: Stanford

summary: The thymus plays a critical role in instructing T cell immunity and establishing central tolerance, yet its therapeutic potential remains largely unexplored. Understanding the signals that govern thymic epithelial cell differentiation is essential for advancing regenerative applications. Here, we investigate the pathways that influence thymic epithelial development by introducing human recombinant interferon-alpha (IFNA2) and interferon-gamma (IFNG) during the final stage of differentiation in an in-vitro human thymic epithelium model. Using bulk RNA-sequencing, we examine signaling responses activated by interferons in the context of thymic development.

overall_design: To investigate the role of interferon in thymic epithelial development, we performed bulk RNA sequencing on an in-vitro human thymic epithelium model, introducing human recombinant interferon-alpha (IFNA2) and interferon-gamma (IFNG) during the final stage of differentiation.

first: Andrew

last: Gentles

first: Katja

last: Weinacht


title: Nucleosome dynamics render heterochromatin generally accessible in living human cells (qDA seq in MCF10A live cells)

summary: The eukaryotic genome is packaged into chromatin, which resembles beads on a string. Each bead consists of a nucleosome containing ~147 bp of DNA wrapped around a histone octamer. The nucleosomal filament undergoes additional folding to create a complex genomic organisation which is thought to restrict the access of gene-regulatory transcription factors to the genome. Consequently, it is widely accepted that DNA accessibility, modulated by chromatin architecture, is pivotal in gene regulation. Here, we measure genome accessibility at all GATC sites in living human MCF7 and MCF10A cells, using an adenovirus vector to express the sequence-specific dam DNA adenine methyltransferase. We find that the human genome is globally accessible in living cells, unlike in isolated nuclei. Active promoters are methylated somewhat faster than gene bodies and inactive promoters. Remarkably, both constitutive and facultative heterochromatic sites are methylated only marginally more slowly than euchromatic sites. In contrast, sites in centromeric chromatin are methylated slowly and are partly inaccessible. We conclude that nucleosomes in euchromatin and heterochromatin are highly dynamic in living cells, whereas nucleosomes in centromeric asatellite chromatin are static. A dynamic chromatin architecture implies that simple occlusion of transcription factor binding sites is unlikely to be critical in gene regulation.

overall_design: Multiple time courses of DNA methylation by Dam methylase in MCF10A cells; Illumina paired-end data. Two biological replicate experiments.


title: Resolvin E1/ChemR23 Protects Against Hypertension and Vascular Remodeling in Angiotensin II-Induced Hypertensive Mice

first: MENGMENG

last: Zhao

address: Wuhan University

institute: Wuhan University

summary: Inflammation plays a critical role in the development of hypertension and vascular remodeling. Resolvin E1 (RvE1), as one of the specialized proresolving lipid mediators, promotes inflammation resolution by binding with a G protein-coupled receptor, ChemR23 (chemerin receptor 23). However, whether RvE1/ChemR23 regulates hypertension and vascular remodeling is unknown. Aortic ChemR23 expression was increased in Ang II-induced hypertensive mice and that ChemR23 was mainly expressed on vascular smooth muscle cells (VSMCs). RvE1 lowered blood pressure, reduced aortic media thickness, attenuated aortic fibrosis, and mitigated VSMC phenotypic transformation and proliferation in hypertensive mice, which were all reversed by the knockdown of ChemR23. Moreover, RvE1 reduced the aortic infiltration of macrophages and T cells, which was also reversed by ChemR23 knockdown. RvE1 inhibited Ccl5 expression in VSMCs via the AMPKα (AMP-activated protein kinase α)/Nrf2 (nuclear factor E2-related factor 2)/canonical NF-κB (nuclear factor κB) pathway, thereby reducing the infiltration of macrophages and T cells. The AMPKα/Nrf2 pathway also mediated the effects of RvE1 on VSMC phenotypic transformation and proliferation. In patients with hypertension, the serum levels of RvE1 and other eicosapentaenoic acid-derived metabolites were significantly decreased

overall_design: Hypertension in mice was induced by Ang II (angiotensin II) infusion (750 ng/kg per minute), and RvE1 (2 µg/kg per day) was administered through intraperitoneal injection.

first: Jishou

last: Zhang

first: Zheng

last: Yin

first: Yao

first: Juanjuan

last: Qin

first: Jun

last: Wan

first: Menglong

last: Wang


title: RNA-Sequencing of postnatal thymic epithelial and immune subsets

summary: To examine the role of key immune populations within the thymic stroma in interferon production, we conducted bulk RNA-sequencing on postnatal thymic epithelial cells, B cells, thymocytes, plasmacytoid dendritic cells, and myeloid dendritic cells.

overall_design: Bulk RNA-seq profiling of Fluorescence-Activated Cell-Sorted (FACS) populations from human postnatal (5 days, 3 month, and 4 month) thymus.


title: Microbiota-derived acetate protects against UPEC-epididymo-orchitis by improving the phagocytosis of testicular macrophages.

city: ZhengZhou

first: Ming

address: jianshe Road

institute: ZhengZhou university

summary: The gut microbiota is intimately associated with maintaining a stable intestinal immune balance. However, it remains unclear whether gut dysbiosis affects the homeostasis within the testes. In our DSS-induced colitis mouse model, we observed increased inflammatory cell infiltration within the mouse testes. Analysis of the gut microbiota in the feces of DSS colitis mice and mice treated with antibiotics revealed a significant decrease in the number of bacteria related to cellulose decomposition in the gut, as well as a decrease in the content of short-chain fatty acid salts in the peripheral blood of mice. In vitro experiments found that acetate can significantly improve the outcome of UPEC-induced bacterial epididymo-orchitis. Further in vitro experiments demonstrated that acetate can enhance the bacterial phagocytic ability of testicular macrophages (TM), accelerate the early clearance of bacteria within the testes, and thus reduce the degree of testicular inflammation. This study provides a link to explain the progression of bacterial epididymo-orchitis in relation to gut microbiota dysbiosis and offers new insights for the treatment of bacterial epididymo-orchitis.

overall_design: Transcriptome analysis of TM stimulated by UPEC and sodium acetate. Approximately 10^6 TM were isolated and inoculated into 6-well plates. Sodium acetate (10mM) was pre-treated for 30 minutes, followed by UPEC (MOI: 5) infection for 3 hours, after which the cells were collected for transcriptome sequencing; (C1-2: Control group. U1-2: UPEC infected. A1-2: UPEC infected + sodium acetate treatment).

first: Zhengguo

first: Zhongyu

last: Fan


title: Loss of Sarm1 Mitigates Axonal Degeneration and Promotes Neuronal Regeneration After Ischemic Stroke

city: Los Angeles

first: Yutaro

last: Komuro

address: 635 Charles E Young Dr S

department: Neurology

institute: University of California Los Angeles

summary: Axonal degeneration is a core feature of ischemic brain injury that limits functional recovery. The pro-degenerative molecule Sarm1 is required for Wallerian axon degeneration after traumatic and chemotoxic nerve injuries, however it is unclear if a similar mechanism mediates axonal degradation after ischemic injury. Here we show that loss of Sarm1 in male mice tested results in profound attenuation of axonal degeneration after focal ischemia to the subcortical white matter. Moreover, absence of Sarm1 significantly promotes the survival of neurons distal but connected to the infarct after ischemic injuries to the subcortical white matter as well as to the cortex. To further understand the mechanism of Sarm1-/- mediated neuronal protection, we performed differential gene expression analysis of male wildtype and Sarm1-/- stroke-injured neurons and found that that loss of Sarm1 activates a pro-regenerative molecular program that promotes new axon and synapse formation after white matter ischemia. Using a functional genomics approach to recapitulate such a molecular program in Sarm1-/- neurons, we identify molecular compounds sufficient to enhance cortical neurite outgrowth in vitro, and all of which elicit a conserved epigenetic signature promoting axonogenesis. These results indicate that Sarm1 concurrently promotes axonal degeneration and inhibits a regenerative program encoded at the level of the epigenome that can be modulated pharmacologically. Our findings thus reveal a novel role for Sarm1 as a crucial regulator of both axonal degeneration and axonal remodeling after ischemic stroke.

overall_design: Male C57BL/6 control mice and Sarm1 -/- mice were used at 3-6 months of age. Stroke was induced by focal injection of Lnio in subcortical white matter. 7 days after stroke induction, neurons were sorted via negative selection of CD11b and positive selection of NCAM using magnetic beads. RNA was isolated from the neurons and normalized using cell counts. This RNA was used for differential gene expression analysis between Sarm1 -/- neurons and wild-type neurons under stroke injury conditions.

first: Jack

first: Brian

last: Toh

first: Jennifer

last: An

first: Marlesa

middle: I

last: Godoy

last: Putman

first: S

last: Carmichael

first: Robert

last: Damoiseaux

first: Jason

last: Hinman


title: NeuroD1-USP1-N-Myc axis drives tumor progression in neuroblastoma

first: Gen

last: Li

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

overall_design: Refer to individual Series


title: ACSS2-mediated acetylation promotes BCAT1 aggradation to elevate branched-chain amino acid metabolism and development of pancreatic cancer

city: Xianyang

first: ZHUANGLI

middle: ZHUANGLI

last: ZHUANGLI

address: No. 3, Taicheng Road, Yangling District,Xianyang 712100，Shaanxi Province

institute: Northwest A&F University

overall_design: we selected NC and ACSS2-KO  PDAC samples to perform RNA sequencing

first: Haidi

last: Chen


title: KATNAL2 mutation cause hydrocephalus by impairing vesicular trafficking and ependymal cell polarity in ASD

first: Yao

last: Xue

address: 3663 North Zhongshan Rd

institute: East China Normal University

summary: Autism spectrum disorders (ASD) are characterized by intricate neurodevelopmental abnormalities, yet the molecular underpinnings remain elusive for many high-risk genes, including KATNAL2. Here, we identify KATNAL2 as a key regulator of the intracellular vesicular system in the ependymal epithelium, crucial for vesicle trafficking and ciliary function. We demonstrate that an ASD-associated mutation in KATNAL2 disrupts its molecular activity, impairing intracellular vesicle trafficking, which in turn alters planar cell polarity and ciliary motion in ependymal cells. These defects lead to compromised cerebrospinal fluid circulation and postnatal hydrocephalus in mice. Notably, ependymal-specific ablation of Katnal2 in neonatal mice recapitulated the hydrocephalic phenotype. Our findings uncover a previously unrecognized molecular role for the ASD risk gene KATNAL2 in ependymal cells, underscoring its essential function in vesicle trafficking and cell polarity regulation, and suggest new avenues for targeted therapeutic strategies for ASD.

overall_design: Differential gene expression analysis of RNA-seq data for Katnal2 WT/Mut P5 cortical tissues(one sample each, and three replicates per sample)


title: Gene Expression is Co-regulated by Non-nucleolar RNA Polymerase I [RNA-seq]

city: Evanston

first: vadim

last: backman

address: 2170 Campus Drive, Silverman Hall 3627

institute: Northwestern University

summary: Due to its role in mRNA synthesis, many studies of the relationship between transcription and chromatin organization have focused on the regulation of RNA polymerase II (Pol-II) function by supranucleosomal structure and vice-versa. In contrast, there is little work on the function of RNA polymerase I (Pol-I) in non-nucleolar chromatin. Prior work has shown that Pol-I engages with components of Pol-II on rDNA, but it’s role in global transcription and chromatin structure beyond the nucleolus has largely been ignored. By pairing auxin-inducible degron technology with nanoscopic imaging, RNA-Seq, and Hi-C, we found that Pol-I and Pol-II co-regulate conformationally defined chromatin domains and mRNA synthesis. Mechanistically, Pol-I maintains the positioning of intronic and intergenic chromatin within domains for the proper expression of exon elements. Consequently, Pol-I loss disrupts genome connectivity, in situ chromatin domains, and the expression of mRNA, genome-wide.

overall_design: To investigate the structure-function relationship between Pol-I and Pol-II transcription and genome organization,  we took advantage of two auxin inducible degron lines targeting either POLR1A or POLR2A. After treating 3 technical replicates (different plates, but treated on the same day) with auxin for 8 hours, DMSO for 8 hours, or 6 hour of ActD (5 µg/mL), we generated total RNA-seq for each set of samples. We performed diffrential expression analysis for coding and non-coding transcripts with this data.

first: Carter

last: Lucas

first: Backman

last: Vadim

first: Almassalha

last: Luay


title: Kinesin KIFC1 is essential for meiotic recombination and male fertility in mice

first: Xinrui

last: Wang

address: 197 Ruijin Rd II

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

summary: Purpose: KIFC1 functions a crucial role in the formation and structural maintenance of mitotic and meiotic spindles. Its loss is linked to reduced fertility and the production of polyploid offspring. This study determines the effects of KIFC1 deficiency on spermatogenesis and germ cell differentiation in mice, particularly during meiosis prophase I and metaphase. Methods: C57BL/6J mice with global KIFC1 knockout were generated using the CRISPR/Cas9 system. Histological and fluorescence imaging analyses revealed KIFC1's involvement in meiotic recombination. To further explore the effects of KIFC1 loss on fertility, RNA sequencing, liquid chromatography-mass spectrometry, and single-cell RNA sequencing were employed. Results: KIFC1 deficiency resulted in a significant reduction of germ cells in seminiferous tubules, decreased testicular volume, and disrupted meiosis. In severely affected mice, spermatocytes arrested at the zygotene-like stage. Although KIFC1 loss does not impact the initiation of DNA double-strand breaks, it is essential for homologous chromosome pairing and crossover formation. KIFC1-null spermatocytes exhibited delayed DNA recombination, leading to abnormal chromosome alignment and polyploid gametes. Conclusions: This study highlights KIFC1's critical role in homologous recombination and chromosome segregation during male germ cell meiosis. Multi-omics analyses reveal how KIFC1 deficiency affects spermatocyte differentiation and spermatogenesis, with additional evidence suggesting impairment of mitochondrial function.

overall_design: RNA sequencing identified differences in the transcriptional abundance of key reproductive genes between KIFC1 mutant and wild-type mice.

first: Ya-Lan

last: Wei

first: Xiao-Jing

last: Fan

first: Hai-Tao

last: Zhang

first: Xin-Chen

last: Lin

first: Li-Ping

last: Zhu

first: Zhen-Yu

last: She

first: Xin-Rui