title: Peroxisomes are critical for a unique metabolic demand and survival of alveolar macrophages

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

institute: ETH Zürich

summary: Tissue-resident macrophages (TRMs) populate throughout various tissues, and their homeostatic metabolism is heavily influenced by these microenvironments. Peroxisomes are organelles that contribute to lipid metabolism. However, the involvement of these organelles in the bioenergetics of TRMs remains undetermined. We conducted a developmental screen of TRMs using a conditional peroxisomal biogenesis factor 5 (Pex5) knockout mouse model that lacks functional peroxisomes in all immune cell subsets. Pulmonary alveolar macrophages (AMs) appeared as the only subset of TRMs that required functional peroxisomes for their development. Pex5-deficiency resulted in reduced AM survival due to increased sensitivity to lipotoxicity, in line with excess accumulation of ceramides. The absence of peroxisomes had a significant effect on overall mitochondrial fitness and altered their metabolic program, allowing them to engage in glycolysis in addition to oxidative phosphorylation. Our results revealed that AMs have a unique metabolic regulation, where peroxisomes play a central role for their homeostatic development and maintenance.

overall_design: Bulk RNA Sequencing of BAL AMs isolated from Pex5fl/fl and Vav1cre/+ and Pex5fl/fl mice

first: Mai

last: Matsushita

first: Jonathan

last: Muri

first: Ivan

last: Berest

first: Fengqi

last: Li

first: Huan

last: Liu

first: Basak

last: Corak

first: Nicola

last: Zamboni

first: Joerg

last: Buescher

first: Alaa

last: Othman

first: Mauro

last: Corrado

first: Jovana

last: Cupovic

first: Sabine

last: Werner

first: Werner

last: Kovacs


title: Transcriptome analysis of Hela cells treated with the PARP inhibitor Olaparib.

status: Public on Jun 01 2025

city: Kashiwa

first: Akihiro

last: Ohashi

state: Chiba

address: 6-5-1 Kashiwanoha

department: Exploratory Oncology Research and Clinical Center

country: Japan

institute: National Cancer Center Japan

type: Expression profiling by high throughput sequencing

summary: In total, 17,118 and 16,786 transcripts were detected in olaparib- and DMSO-treated cells, respectively. Analysis of differentially expressed genes (DEGs) revealed 866 genes, including 503 upregulated and 363 downregulated genes in olaparib-treated cells). Volcano plots indicated the upregulation of inflammatory cytokine-related genes . Enrichment analyses using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database20,21 identified inflammation-related pathways as prominently upregulated in olaparib-treated cells, with five of the top 10 pathways involving inflammation-related genes. Dot plot analyses also confirmed the upregulation of inflammatory hallmarks, such as TNFA signaling via NFκB, inflammatory response, IL2-STAT5 signaling and interferon gamma response, in olaparib-treated cells. Furthermore, the GSEA determined significant enrichment of inflammatory cytokine-related KEGG pathways, including cytokine–cytokine receptor interaction, JAK-STAT signaling, and Rig I like receptor signaling pathways, as well as inflammatory hallmarks such as TNFA signaling via NFκB, interferon alfa response, and interferon gamma response in olaparib-treated cells.

overall_design: HeLa cells were treated with 10 μM olaparib or DMSO for 72 h, where moderate anti-proliferation with considerable DNA damage was observed, and were subjected to RNA sequencing (RNA-seq)

first: Ryo

last: Kamata

first: Misato

last: Kamii

first: Hitoshi

last: Saito


title: Exploring an essential biomarker in pulmonary fibrosis: an integrated and cross-disease approach with spatial transcriptomics and single-cell RNA sequencing

status: Public on Jun 02 2025

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

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

overall_design: Refer to individual Series


title: Single-Cell Transcriptomic Profiling of Xenotransplanted Retinal Organoids Derived from the WA09 CRX-tdTomato Human Embryonic Stem Cell Line

city: Philadelphia

first: Raghavi

last: Sudharsan

address: 3900 Delancey Street

country: USA

institute: University of Pennsylvania

summary: Single-cell gene expression profiles were generated for human retinal organoids derived from the WA09 CRX-tdTomato human embryonic stem cell line. Fragmented organoids were transplanted into the subretinal space of normal canine retinas and analyzed three days post-transplantation. In parallel, fragmented organoids from the same batch, maintained in culture for the same duration, were used as controls. Comparative single-cell transcriptomic analysis provided insights into the early molecular changes associated with the transplanted environment versus in vitro culture conditions, shedding light on the cellular responses and adaptation of retinal organoids post-transplantation.

overall_design: Retinal organoids (ROs) derived from the WA09 CRX-tdTomato human embryonic stem cell line were cultured for 113–126 days. These ROs were mechanically triturated into smaller fragments and subsequently injected into the subretinal space of normal canine retinas. Fragments from the same batch of ROs, subjected to identical trituration, were maintained in culture as controls. After three days, both the transplanted RO fragments and their cultured counterparts were collected and processed for single-cell RNA sequencing (scRNAseq). This process was repeated across three independent experiments to ensure reproducibility and robustness of the findings.

first: William

last: Beltran


title: Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues [bulk RNA-seq]

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: Institute of Molecular Medicine, College of Future Technology

country: China

institute: Peking University

summary: RNA-binding proteins (RBPs) are essential regulators of RNA fate and function. A long-standing challenge in studying RBP regulation has been mapping RNA interactomes within the dynamic transcriptomic landscape, especially in single-cell contexts and primary tissues. Here we introduce MAPIT-seq (modification added to RBP interacting transcript-sequencing), which uses an antibody-directed editing strategy to map genome-wide in situ RBP–RNA interactions and gene expression concurrently. We demonstrate MAPIT-seq’s robustness across multiple RBPs and systematically analyze RNA substrates associated with core polycomb repressive complex 2 (PRC2) components. MAPIT-seq is also applicable to frozen tissue sections, enabling the mapping of RBP roles during brain development. Importantly, we develop high-throughput single-cell MAPIT-seq (scMAPIT-seq) to reveal cell stage-specific RBP regulation. In summary, MAPIT-seq expands multi-omics profiling, providing an effective framework to study post-transcriptional regulation in dynamic biological processes and clinically relevant scenarios.

overall_design: We developed Modification Adjacent to RNA-binding Protein Interaction Targets Sequencing (MAPIT-seq), a versatile method for in situ RNA-protein interaction profiling. Initial validation was performed in YTHDF2-FLAG-overexpressing HeLa cells, followed by optimization for target detection of endogenous protein G3BP1 in HEK293T cells. We refined formaldehyde crosslinking conditions and pAG-deaminase constructs to enhance specificity and sensitivity. Then, we evaluated its general applicability by extending to additional canonical RBPs and further selected RBFOX2 and PUM1, two RBPs with well-defined recognition sequences, for an in-depth evaluation of MAPIT-seq resolution. Demonstrating remarkable sensitivity, we scaled MAPIT-seq down to 500 cells, a 1000-fold reduction from the initial 500,000-cell protocol. We further advanced the technique to a high-throughput single-cell format, uncovering cell cycle-specific G3BP1 targets and revealing heterogeneity in RNA-protein interactions at single-cell resolution.

first: Qi-Xuan

last: Cheng

first: Gang

last: Xie


title: Integration of whole genome sequencing analysis with unique patient-derived models reveals clinically relevant drug targets in TFCP2 fusion-defined intraosseous rhabdomyosarcoma

city: SYDNEY

first: Diego

last: Chacon-Fajardo

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

summary: Here we present comprehensive, multi-omic and functional analysis, to discover and preclinically validate novel actionable molecular targets for a rare case of intraosseus rhabdomyosarcoma with TFCP2-rearrangement. Whole genome sequencing analyses of matched patient tumour and xenograft material revealed alterations in gene networks associated with the oncogenic, potentially targetable PI3K/AKT pathway. Preclinical assessments revealed that targeting the pathway with a small molecule PI3K/mTOR inhibitor dactolisib presents a promising treatment approach for this rare cancer, decreasing cancer cell viability in vitro and significantly reducing tumour growth in vivo. Parallel identification of the codeletion of adjacent genes CDKN2A and MTAP in these tumours, led us to further explore PRMT5 inhibition as a potential therapeutic approach.

overall_design: RNA-seq profiling to understand the transcriptional mechanisms that underpin the ecosystem of Intraosseous spindle cell Rhabdomyosarcoma (IORMS).

first: Patrick

last: Bergsma

first: Marina

last: Pajic


title: Single-Cell Transcriptomic Profiling of Canine Neuroretina Following Transplantation of Human ESC-derived Retinal Organoids [retina]

summary: This study aimed to identify transcriptomic changes in the host retina following subretinal xenotransplantation. Single-cell gene expression profiles were generated from the neuroretina of normal canine eyes in regions directly overlying subretinally transplanted retinal organoids, which were derived from the WA09 CRX-tdTomato human embryonic stem cell (hESC) line. For comparison, single-cell gene expression profiles were also obtained from neuroretinal regions without graft exposure.

overall_design: Retinal organoids (ROs) derived from the WA09 CRX-tdTomato human embryonic stem cell line were transplanted into the subretinal space of immunosuppressed normal canine retinas. Three days post-transplantation, 5 mm neuroretinal punches were collected from the canine retina in two distinct areas: one directly overlying the subretinal graft and another from a graft-free region. These retinal punches were processed for single-cell RNA sequencing (scRNAseq) analysis. Data were generated from three independent experiments to ensure reproducibility and reliability of the findings.


title: Heterogeneity of Purkinje cells orchestrates cerebellar development.

city: Farmington

first: Nagham

last: Khouri-Farah

state: Connecticut

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

summary: In this study, we performed single-cell RNA sequencing of E6, E7, E8 and E9 chick cerebella to analyze diversity in in Purkinje cells during development.

overall_design: Single-cell  suspensions of embryonic chick cerebellum were prepared following the protocols recommended by 10x Genomics. Subsequently, samples were processed using  the Evercode WT Mini Kit (Parse Bioscience).

first: James

last: Li


title: Deubiquitinase USP6 stabilizes oncogenic RUNX1 fusion proteins to promote the leukemic progression

city: Hangzhou

first: Xuejing

last: Shao

address: 866, Yuhangtang Road

department: Zhejiang University

institute: College of Pharmaceutical Sciences

summary: RUNX1-rearranged leukemia is one of the most common subtypes of patients with recurrent genetic abnormalities. Although a majority of RUNX1-rearranged patients are likely to respond well to standard chemotherapy, the risks of relapse and long-term adverse effects still persist. RUNX1 fusions generated by rearrangement are pivotal oncogenic drivers, with over 70 distinct fusions involving various partners including RUNX1/ETO and ETV6/RUNX1 having been characterized. Thus, elucidating their regulatory mechanism may help to find novel therapeutic strategies. Herein, we first clarify a universal deubiquitinase USP6-involved mechanism that enhances the protein stability of RUNX1 fusions with different partners. Importantly, In RUNX1-rearranged leukemia, USP6 is specially upregulated in RUNX1-rearranged leukemia and strongly linked to poor patient outcomes. Mechanically, USP6 stabilizes RUNX1 fusions to facilitate the formation of phase separation, leading to robust transcriptional activation of differentiation inhibitory and stemness maintenance pathways. Depletion of USP6 dramatically inhibits proliferation and induced differentiation of RUNX1-rearranged leukemia in vitro and in vivo. Subsequent phenotypic screening identifies marketed drug Auranofin as the first USP6 inhibitor, which induces significant degradation of different RUNX1 fusions. Furthermore, Auranofin effectively induced myeloid differentiation of RUNX1-rearranged cells and arrested xenograft tumor growth. Notably, Auranofin selectively showed a strong therapeutic effect on RUNX1-rearranged patients-derived leukemia blasts. Together, these findings not only uncover a new biological function of deubiquitinase USP6 in regulating transcriptional activity of RUNX1 fusions, but also validates USP6 as well as Auranofin as the promising drug target and candidate for RUNX1-rearranged leukemia.

overall_design: Gene expression profiling analysis of RNA-seq data for KASUMI-1 cells  treated with lentivirus-USP6

first: Meidan

last: Ying

first: Xingya

last: Zhang


title: Fibroblast starvation activates ECM remodeling gene transcription and putative enhancers despite inducing quiescence [bruseq]

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Depletion of growth factors and nutrients induces cellular quiescence, which often accompanies transcriptional silencing and chromatin compaction. Paradoxically, such depletion occurs in pathological microenvironments in which fibroblasts are activated to orchestrate tissue remodeling. The relationship between fibroblast activation and growth factor and nutrient depletion remains unclear. Here, we report that serum depletion in cell culture, a model for growth factor and nutrient depletions, extensively activates transcription in fibroblasts, despite inducing quiescence. Activated genes were enriched for extracellular matrix (ECM) structural components and proteases. The ECM-related transcription accompanied activation of putative distal enhancers, but not promoters. The activated putative enhancers were enriched for non-coding variants associated with inflammatory bowel disease (IBD) risk, suggesting an alteration in the ECM remodeling gene regulatory network in IBD. This study implicates nutrient and growth factor depletion in activating the ECM remodeling gene program in fibroblasts, challenging the prevailing view linking such depletion to transcriptional dormancy.

overall_design: To define the transcriptional state of fibroblasts undergoing nutrient deprivation, primary dermal fibroblasts (GM07492) maintained in 10% serum (“proliferation”) were subjected to 1% serum for 48 hours (“starvation”). Starved cells were then subjected to a recovery phase with 10% serum for 24 hours ("recovery"). To determine genes transcribed during proliferation, starvation, and recovery, we performed Bru-seq, in which nascent transcripts are labeled with 5-bromouridine (BrU) in cell culture, purified by anti-BrU immunoprecipitation, and quantified by high-throughput sequencing. We labeled transcripts for 2 hours, either during proliferation, at the end of starvation, or at the end of recovery.


title: ELAV mediates circular RNA biogenesis in neurons

city: Freiburg

first: Valérie

last: Hilgers

address: Stübeweg 51

country: Germany

institute: MPI of Immunobiology and Epigenetics


title: Effects of excessive iodine intake on brain development

city: Maebashi

first: Izuki

last: Amano

state: Gunma

address: 3-9-22 Showa-machi

department: Department of Integrative Physiology, Graduate School of Medicine

institute: Gunma University

summary: To evaluate the impact of perinatal iodine excess intake on neurodevelopment, we conducted a gene expression profiling assessment using microarray technology. This evaluation was performed on the hippocampus of adult female offspring mice from both the 20-fold iodine intake group and the control group, which exhibited statistically significant differences in learning and memory-related behavioral experiments. Despite the observed behavioral differences, no significant differences were found in the gene expression profiles.

overall_design: Total RNA was extracted from dorsal hippocampus after behavioral test battery. Total RNA from female control group and 20-fold iodine intake group were used for microarray.


title: ELAV mediates circular RNA biogenesis in neurons [RNA-seq, dm]

summary: Circular RNAs (circRNAs) arise from back-splicing of precursor RNAs and accumulate in the nervous system of animals, where they are thought to regulate gene expression and synaptic function. Here, we show that neuronal circRNA biosynthesis is mediated by the pan-neuronal RNA-binding protein ELAV. In Drosophila embryos, we characterize the circRNA landscape in normal and elav mutant neurons. We find that neuronal circRNAs are globally depleted upon ELAV knockout, and induction of ELAV expression drives ectopic RNA circularization. In fly brains, ELAV binds to pre-mRNA introns flanking putative circRNAs and decreases efficiency of linear splicing in favor of intron pairing at reverse complementary matches, inducing circularization. Together, our data demonstrate that ELAV directly modulates splicing decisions to generate the neuronal circRNA landscape.

first: Carlos

last: Alfonso-Gonzalez

first: Mengjin

last: Shi

first: Sakshi

last: Gorey

first: Sarah

last: Holec

first: Judit

last: Carrasco

first: Michael

last: Rauer

first: Stylianos

last: Tsagkris

first: Fernando

last: Mateos


title: Combined ANA and IDA treatment is an innovative and promising therapeutic strategy for AML patients with high PDE3A expression

city: Suzhou

first: Zimu

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: Acute myeloid leukemia (AML) is an invasive hematopoietic malignancy requiring novel treatment strategies. The PDE3A inhibitor anagrelide (ANA) profoundly suppresses the proliferation of high PDE3A-expressing AML cells while showing minimal impact on those with low PDE3A expression. Moreover, synergistic effect of ANA with other chemotherapeutic drugs in high PDE3A expression AML cells was observed. The ANA-idarubicin (IDA) combination showed the most remarkable synergistic effect among all ANA-chemotherapeutic drugs commonly used in AML cell line models. Our findings suggest that combined ANA and IDA treatment is an innovative and promising therapeutic strategy for AML patients with high PDE3A expression.

overall_design: mRNA profiles of HEL cells transfected with DMSO, IDA or/and ANA were generated by RNA sequencing using Illumina NovaSeq6000.

first: Chenwei

last: Yang

first: Shaoyan

last: Hu


title: ELAV mediates circular RNA biogenesis in neurons [RIP-seq]

overall_design: RNA Immunoprecipitation and sequencing (RIP-seq) of fruit fly heads. 2 different RIP experiments : one with FLAG antibody on elavFLAG flies (4 input samples and 4 IP samples), one with ELAV antibody on wild-type flies (3 input samples and 3 IP samples). The control samples are IP with FLAG antibody on wild-type flies (3 samples for input, 3 for IP).


title: Fibroblast starvation activates ECM remodeling gene transcription and putative enhancers despite inducing quiescence [chipseq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design:
To define the transcriptional state of fibroblasts undergoing nutrient deprivation, primary dermal fibroblasts (GM07492) maintained in 10% serum (“proliferation”) were subjected to 1% serum for 48 hours (“starvation”). Starved cells were then subjected to a recovery phase with 10% serum for 24 hours ("recovery"). To define the mechanism underlying the transcriptional changes during starvation, we performed ChIP-seq for histone H3 lysine 27 acetylation (H3K27ac) and histone H3 lysine 4 trimethylation (H3K4me3) in proliferating, starved (48 hours into starvation), and recovering fibroblasts (24 hours into recovery).

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The table below lists GEO accessions reused/reanalyzed for this study.
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title: A histone methyltransferase, EARLY FLOWERING IN SHORT DAYS (EFS) is required for reproductive organs development via histone H3K36 methylation in the oil-seed type Brassica rapa (B. rapa var. trilocularis) plant.

city: Anseong-si, Gyeonggi-do

first: Heewon

last: Moon

address: 4726,Seodong-daero, Daedeok-myeon

country: South Korea

institute: Chung-ang university

summary: We report here NGS RNA-seqencing datasets for two different organ of Brassica rapa plant

overall_design: Two different organ (leaves and inflorescences) of B.rapa plant

first: Dong-Hwan

last: Kim


title: RNA-Seq of allotetraploid wild potato Solanum acaule and autotetraploid potato Solanum tuberosum cv. Atlantic

status: Public on May 31 2025

city: Sainte-Anne-de-Bellevue

first: Juan Carlos

last: Camargo-Tavares

state: Quebec

address: 21111 Lakeshore Road

country: Canada

institute: McGill University

summary: Potato wild relatives (Solanum section Petota) are a source of genetic diversity for improving traits in modern cultivars (S. tuberosum) to meet climate challenges. Potatoes are susceptible to multiple abiotic and biotic stresses and have undergone constant improvement through breeding programs worldwide. The allotetraploid S. acaule Bitter has been used to introgress cold tolerance into potato breeding germplasm. The cold challenged transcriptome of S. acaule was compared with that of autotetraploid S. tuberosum cv. Atlantic, and was found to have fewer differentially expressed genes than the latter. Specifically, subgenome 1 has less downregulated alleles compared to subgenome 2 and S. tuberosum.

sample_organism:
Solanum tuberosum
Solanum acaule

platform_organism:
Solanum tuberosum
Solanum acaule

overall_design: S. acaule (ACA) and S. tuberosum cv. Atlantic (ATL) plants underwent freezing exposure to compare transcription against control conditions. For freezing conditions (F), shoot explants were placed in a freezing growth chamber where the temperature gradually decreased from 22 °C to -4 °C at a rate of 2°C per hour. Long-day conditions were used as control (C). Three biological replicates were analyzed (F1-F3).

first: S

last: Achakkagari

first: J

middle: C

first: D

last: Praslickova

first: C

last: Martini

first: B

last: Bizimungu

first: N

middle: L

last: Anglin

last: Manrique-Carpintero

first: H

last: Lindqvist-Kreuze

middle: H

last: Tai

first: M

middle: V

last: Strömvik


title: Ephrin-B2 Deletion in GABAergic Neurons Induces Cognitive Deficits Associated with Single-Nucleus Transcriptomic Differences in the Prefrontal Cortex

city: Shanghai

first: Peijun

last: Ju

state: 上海市 - Shanghai Shi

address: Room 306, Research Building Humin Road 3210

institute: Shanghai Mental Health Center, Shanghai Jiaotong University School of Medicine

summary: A total of 11,308 single nuclei were sequenced. After quality filtering (Methods, Supplementary Fig. 3A, 4A-4C), 11,090 high-quality nuclei were obtained, including 5,336 cells from EB2-flox mouse and 5,754 from EB2-vGATCre mouse. These nuclei were grouped into 17 cell clusters (Supplementary Fig. 4D-4H), which were further assigned to 9 major cell types based on cell-type-specific markers: excitatory neurons (Slc17a7+), inhibitory neurons (Gad2+), astrocytes (Gja1+), microglia (C1qa+), oligodendrocytes (Aspa+), oligodendrocyte precursors (Pdgfra+), smooth muscle cell (Uaca+), endothelial (Flt1+) and ependymal (Dynlrb2+) cells (Fig. 4A, 4C, supplementary Fig. 3B).

overall_design: We dissociated cells from brain slices per brain (+2.1-+1.1 AP to bregma) from the individual mouse.

first: Jianhua

last: Chen

first: Yu

last: Fang

first: Siying

last: Xiang


title: ELAV mediates circular RNA biogenesis in neurons [RNA-seq, S2]

first: Valérie

last: Hilgers

overall_design: RNA-seq from Schneider 2 cells (S2cells) from Drosophila melanogaster : 4 replicates of cells transfected with empty vector (control) and 3 replicates ELAV CDS vector (condition).

first: Carlos

last: Alfonso-Gonzalez

first: Mengjin

last: Shi

first: Sakshi

last: Gorey

first: Sarah

last: Holec

first: Judit

last: Carrasco

first: Michael

last: Rauer

first: Stylianos

last: Tsagkris

first: Fernando

last: Mateos


title: Uncovering the Molecular Mechanism of A Novel Near-infrared Fluorescence Imaging Drug Caba-780 in Bladder Cancer

city: Xi'an

first: wen

last: liu

address: New temple Road num 1

institute: Tangdu Hospital of Air Force Medical University

summary:
To investigate the molecular mechanism by which Caba-780 inhibits the progression of bladder cancer, we treated bladder cancer cells with Caba-780 for 24 hours
We then used RNA-seq data from T-24 cells for gene expression profiling

overall_design: Compare the gene expression profiles of RNA-seq data from control group and administration group of T24 cells.

first: Dongen

first: Ying

last: Liang

last: Zhen

first: Jianlin

last: Yuan


title: ELAV mediates circular RNA biogenesis in neurons [RNA-seq, RNaseR]

overall_design: RNA-seq of Rnase R treated RNA from Drosophila melanogaster. 5 samples from embryos (3 treated replicates, 2 non-treated controls), 4 samples from heads (2 treated replicates, 2 non-treated control replicates)


title: ELAV mediates circular RNA biogenesis in neurons [RNA-seq, sm]

overall_design: RNA-seq from sorted cells of Drosophila melanogaster embryos, aged 14 to 16h after egg laying : 3 replicates of non-neuronal cells sample, of wild-type neurons sample (mixed sex and female), and of Δelav mutant neurons sample respectively


title: Single-cell RNA sequencing of the kidneys from kidney-resident macrophage deplated mice [D42]

status: Public on May 30 2025

city: Seoul

first: Donghwan

last: YUN

state: Jongno-gu

address: 103 Daehakro

institute: Seoul National University Hospital

summary: This study investigates the role of kidney-resident macrophages (KRMs) in modulating susceptibility to tubulointerstitial nephritis (TIN) by selectively depleting KRMs and examining the resulting immunological and pathological changes in the kidney using single-cell RNA sequencing.

overall_design: scRNA-seq datasets were generated from kidneys of mice treated with either αCSF1R Ab or control Ab, harvested at 42 days post-injection to assess temporal changes associated with KRM depletion.

first: Minki

last: Hong

last: Yun

first: Seung Seok

last: Han


city: ST LOUIS

first: Iris

last: Lee

state: MO

institute: Washington University in St. Louis School of Medicine

summary: Marginal zone (MZ) B cells bridge innate and adaptive immunity by sensing bloodborne antigens and producing rapid antibody and cytokine responses. When unregulated, MZ B cells are associated with autoimmunity. CD55 is a membrane-bound complement regulator that interferes with complement activation and is another important component of innate and adaptive immunity. MZ B cells express low CD55 in both mice and humans, but the role of CD55 in MZ B cell function is unknown. Using germline knockout mice, we found that similar numbers of MZ B cells were initially established in 3-week-old CD55-deficient mice compared to wild-type (WT) mice. However, MZ B cells failed to accumulate as mice aged and underwent increased apoptosis independent of alternative complement activation. Following ex vivo stimulation of MZ B cells through Toll-like receptor 9 (TLR9), we observed increased IL-6 expression in CD55 KO MZ B cells. In addition, CD55 KO mice exhibited reduced total IgG response with in vivo administration of TLR9 agonist. These findings provide new insights to the role of CD55 in MZ B cell survival and B cell function.

overall_design: Bulk RNA-seq of MZ B cells after negative selection for B cells, then flowsorting for MZ B cells from 14-week-old WT C57BL/6 and CD55 KO mice

first: Xi

last: Wang

first: Ivana

last: Ling

first: Sonam

last: Verma

first: Cassaundra

last: Eck

first: Wumei

last: Blanche

first: Christine

last: Pham

first: Peggy

last: Kendall


title: The genomic landscape of monocytes and CD4+ T cells after BCG vaccination in Malawian infants

city: Chapel Hill

first: Kristina

last: De Paris

state: North Carolina

address: Mary Ellen Jones Building , 116 manning Drive

department: Department of Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

summary: The Bacille Calmette-Guérin (BCG) vaccine administration studies in human adults determined that BCG-mediated mechanisms of protection include epigenetic reprogramming of innate immune cells and heterologous T cell immunity. The current study aimed to confirm that BCG immunization similarly impacts the functionally distinct infant immune system. Towards this goal, we applied RNA  sequencing to assess molecular changes in circulating monocytes and CD4+ T cells of Malawian infants prior to and 2 to 13 weeks after BCG immunization. We identified 168 differentially expressed genes (DEGs), 14 upregulated and 152 downregulated, in monocytes after BCG vaccination. The upregulated monocyte DEGs were enriched in genes associated with metabolic pathways, in particular glycolysis and lipid metabolism. In CD4 T cells, 322 DEGs (95 upregulated and 226 downregulated) were identified after BCG vaccination, and these DEGs were representative of activation, proliferation, differentiation, and cell survival. These findings are consistent with data reported in BCG vaccinated adults and contribute to the understanding of molecular changes in monocytes and CD4 T cells that may explain the improved capacity of the infant immune system to respond to pathogens after BCG vaccination.

overall_design: RNA sequence profiling of circulating monocytes and CD4+ T cells of Malawian infants prior to and 2 to 13 weeks after BCG immunization.

last: DeParis


title: Spatial transcriptomic analysis reveals increased adipogenesis and non-alcoholic fatty liver disease pathway in pig-to-NHP islet transplantation recipient liver during early post-transplantation period

city: Jongno-gu

first: Yoon Ji

last: Bang

state: --- Select One ---

address: 103 Daehak-ro

institute: Seoul National University

summary: Pancreatic islet transplantation stands out as a promising therapeutic avenue for type 1 diabetes patients grappling with glycemic instability and hypoglycemia unawareness. Given the persistent scarcity of donor organs, there is growing anticipation that pig-to-human islet xenotransplantation will emerge as the definitive beta cell replacement therapy for this condition. The liver is the site of preclinical pig-to-NHP islet transplantation as well as allogeneic clinical transplantation, yet there’s still a lack of understanding on the pathology of the liver after the transplantation procedure. Based on our observations of post-transplantation periportal pathologic changes in primate models, we have conducted a retrospective study examining the hepatic pathology in pig-to-NHP islet recipients with short-term graft survival, employing a state-of-the-art spatial transcriptomic platform within the vicinity of the islet implantation site. Post-transplantation liver tissue could be easily distinguished into three regions based on transcriptional profiles, consistent with its histology. A notable elevation in adipogenesis and non-alcoholic fatty liver disease (NAFLD) pathways could be identified, which included increased expression of SREBF1, CEBPA, IGF1, and TNFRSF12A. We furthermore discovered that, despite the decreased severity of the multifocal white lesions indicated by gross examination at 33 days post-transplantation, there was still evidence of NAFLD at the transcriptional level. These results prompt further research into the relationship between intrahepatic islet transplantation and hepatic microenvironment.

overall_design: A total of 18 AOIs were categorized into three groups as follows: steatohepatitic area and a non-steatohepatitic area on DPT8, as well as the recovered area on DPT33.

first: Hyunwoo

last: Chung

first: Jong-Min

last: Kim

first: Hyun-Je

first: Chung-Gyu

last: Park


title: Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease

city: Hamburg

first: Robin

last: Khatri

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

summary: Rapidly progressive glomerulonephritis (RPGN) is the most aggressive group of autoimmune kidney disease with the worst prognosis. Anti-neutrophil cytoplasmic antibody (ANCA) associated vasculitis, anti-glomerular basement membrane (anti-GBM) and lupus nephritis are the most common causes of RPGN and are characterized by the formation of glomerular crescents and infiltration of leukocytes that eventually lead to glomerulosclerosis and kidney failure.    In this work, we used high-resolution spatial transcriptomics of 32 ANCA, 19 lupus nephritis, 6 anti-GBM, and 6 control patients to understand how intercellular signaling between immune and renal tissue cells leads to renal inflammation and glomerular injury. Using 3,218,210 immune and kidney cells, we observed that the biological pathways involved in the sequence of glomerular crescent formation are similar across the diseases. While innate immune cells infiltrated the glomerular compartment relatively early, later increases in adaptive immune cells were largely restricted to the periglomerular regions. These changes in immune cells temporally correlated with increases in glomerular parietal epithelial (PEC) and fibrotic mesangial cells, suggesting disease-relevant functional signaling between these immune and renal cells. Cell communication analysis revealed early disease PDGF signaling from epithelial and mesangial cells to PECs, causing their activation and proliferation. At later stages, TGF-β signaling from macrophages, T cells, epithelial cells, and mesangial cells to PECs triggered the expression of extracellular matrix components resulting in glomerulosclerosis.    Our results highlight a spatio-temporally conserved progression into glomerular crescents and sclerosis for ANCA, lupus nephritis, and anti-GBM disease, which is driven by consecutive PDGF and TGF-β signaling to PECs.

overall_design: 8 slides containing 63 samples (biopsies from 32 ANCA, 19 lupus nephritis, 6 anti-GBM, and healthy tissues from tumor nephrectomies of 6 control patients) were analyzed with Xenium to capture RNA. One additional slide (Sample: 0011186) was used for Xenium + phenocycler run.

first: Zeba

last: Sultana

first: Saskia-Larissa

last: Jauch-Speer

first: Ulf

last: Panzer

first: Stefan

last: Bonn

first: Christian

last: Krebs


title: Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish

city: Durham

first: Leah

last: Wehmas

state: NC

address: 109 T.W. Alexander Drive

institute: US EPA

summary: Changes in resident microbiota may have wide-ranging effects on human health. Previous research found axenic zebrafish (Danio rerio) exhibit hyperactivity at 10 days post fertilization (dpf). This abnormal neurobehavioral response can be prevented with re-colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA-sequencing of pooled 10 dpf larval head tissue from axenic, conventionally colonized controls, and axenic zebrafish recolonized with microbes at 1 dpf.

overall_design: 10 days post fertilization (dpf) axenic (microbe free), conventionally colonized (normal), and axenic Danio rerio embryos recolonized with microbes at 1 dpf (control for axenic derivation process) were submitted for RNA-sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.

first: Luisa

last: Bertotto

first: Carmen

last: Wood

first: Tamara

last: Tal


title: Inducing bacterial calcification for systematic treatment and immunomodulation against Methicillin-resistant Staphylococcus aureus

first: Wanying

last: Zhang

state: Select...

address: 88 Jiefang Road, Hangzhou 310009, China;

institute: Zhejiang university

summary: Methicillin-resistant Staphylococcus aureus (MRSA) has become one of the deadliest bacteria globally due to antibiotic resistance. In this study, we crosslinked antigen-binding fragments of monoclonal antibodies against the wall-teichoic acid of S. aureus with polysialic acid (PSA) to form an antibody‒PSA conjugate (APC), which can effectively target and induce calcification on the surface of MRSA. This process eliminates bacteria by hindering the energy metabolism and multiple essential metabolic pathways of MRSA. We find thatbacterial calcification leads to increased expression of calprotectin, S100A8/S100A9, in macrophages and monocytes in vivo and can stimulate the activation of macrophages to an inflammatory state, thereby promoting bacterial eradication as an immunomodulator. Systemic administration of APC demonstrates high efficacy and safety for treating chronic lung infections and chronic osteomyelitis caused by MRSA in mice. This study offers a promising therapy for treating drug-resistant bacteria and related refractory pathogenic infections.

overall_design: Following MRSA-infection and treatment with PBS (control) or APC (treat), lung cells of BALB/c mice  were isolated by Fluorescence-activated cesorting (FACS) and analyzed using scRNA-seq.

first: Liang

last: Liu

first: Qingyan

first: Huidan

last: Lu

first: Anyao

last: Li

first: Yuqiao

last: Huang

first: Wenting

first: Hanhui

first: Xiaoyan

first: Xinliang

last: Ming

first: Ze

last: Yang

first: Hao

last: Shou

first: Yiling

last: Wang

first: Jingyan

last: Xia

first: Feng

last: Xu

first: Ben


title: White-Brown switching controls phenotypic plasticity and virulence of Candida auris [1]

city: Vienna

first: Trinh

last: Phan-Canh

email: phancanht99@univie.ac.at, phancanhtrinh@gmail.com, karl.kuchler@univie.ac.at, karl.kuchler@univie.ac.at

state: Vienna

address: Dr.-Bohr-Gasse 9

department: Max Perutz Labs Vienna, Campus Vienna Biocenter

country: Austria

institute: Medical University of Vienna

summary: Comparative transcriptomic profiling of Candida auris White and Brown cells from two clinical strains (1133/P/13R and 462/P/14) and their HYR3, WOR1, and MSN4 null mutants

overall_design: RNA Sequencing was conducted on Candida auris White and Brown cells from two clinical strains (1133/P/13R and 462/P/14) and their HYR3, WOR1, and MSN4 null mutants. The cells were cultivated to the exponential phase in YPD at 37°C with agitation at 200rpm. Subsequently, cultures were harvested, and RNA isolation was performed, followed by the preparation of sequencing libraries for three biological replicates.

first: Karl

last: Kuchler


title: Single-cell RNA sequencing of the kidneys from kidney-resident macrophage deplated mice

first: Donghwan

last: YUN

summary: The purpose of this study is to investigate the long-term depletion of kidney-resident macrophages (KRMs) and their role in regulating tubulointerstitial nephritis (TIN) through specialized efferocytosis and interaction with neighboring T cells.

overall_design: We prepared scRNA-seq datasets from KRM-depleted mouse 6 weeks after anti-colony stimulating factor 1 receptor antibody (αCSF1R Ab) injection.

first: Hong

last: Minki

first: Yun

last: Donghwan

first: Han

last: SeungSeok


title: Astrocytes and Neurons cell-specific transcriptomics

city: Philadelphia

first: Utham Kashyap

last: Valekunja

state: PA

address: 3400 Civic Center Boulevard,

department: Department of Systems Pharmacology & Therapeutics, Perelman School of Medicine,

institute: University of Pennsylvania

summary: Sleep regulation follows a homeostatic pattern. The mammalian cerebral cortex is the repository of homeostatic sleep drive and neurons and astrocytes of the cortex are principal responders of sleep need. The molecular mechanisms by which these two cell types respond to sleep loss are not yet clearly understood. By combining cell-type specific transcriptomics and nuclear proteomics we investigated how sleep loss affects the cellular composition and molecular profiles of these two cell types in a focused approach. The results indicate that sleep deprivation regulates gene expression and nuclear protein abundance in a cell-type-specific manner. Our integrated multi-omics analysis suggests that this distinction arises because neurons and astrocytes employ different gene regulatory strategies under accumulated sleep pressure. These findings provide a comprehensive view of the effects of sleep deprivation on gene regulation in neurons and astrocytes.

overall_design: Experimental design and sleep deprivation: Animals were divided into ad libitum Normal Sleep (NS) and Sleep Deprived (SD) groups. The NS group was left undisturbed SD group was sleep deprived by using a device that applied tactile stimulus with a horizontal bar sweeping just above the cage floor (bedding), as described previously 13. Once the sweeper was on, animals needed to step over it to continue their normal activities. Sleep deprivation began at the start of the light cycle (Zeitgeber Time 0 (ZT0)) and lasted for 12 h, with continuous sweeping mode (approximately 7.5 s cycle time). We made additional attempts to maintain wakefulness during the second half of the sleep deprivation period by occasionally tapping on the cage or gently touching the animals with a brush. Following sacrifice by cervical dislocation, whole brains were isolated at ZT12 (i.e. lights off). Isolated whole brains were placed in ice-cold Hibernate EB (BrainBits LLC, HEB) media, and the cerebral cortex was quickly dissected for the preparation of single-cell suspensions.

first: Akhilesh

middle: B

last: Reddy


title: ALK2/3 are components of the immune synapse crucial for T cell activation and death

city: Wuhan

first: Zilun

last: RUAN

state: Hubei

address: Donghu Road, No. 115, Wuchang District

department: Department of Infectious Diseases, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University

institute: Wuhan University

summary: Antigen recognition by TCR triggers T cell activation and activation-induced cell death (AICD). To investigate additional mechanisms beyond the classical model of T cell activation and death, we conducted a survival-based kinome-wide CRISPR-Cas9 knockout screens and identified the BMP receptors ALK2 and ALK3 as components required for AICD. ALK2 and ALK3 were interdependently required for induction of a subset of effector genes and AICD in activated T cells, and the functions of ALK2/3 in these processes are independent of their BMP ligands. Upon T cell activation, ALK2/3 were recruited to the immunological synapse and phosphorylated by PKC-θ at the conserved T203, resulting in their enhanced kinase activities. The activated ALK2/3, in the absence of BMP, phosphorylated SMAD1/5 at S57, which is reciprocally antagonistic to BMP-induced phosphorylation of SMAD1/5 at S463/465. The S57-phosphorylated SMAD1/5 associated with c-Fos to induce effector genes upon T cell activation. Disruption of Alk2 in T cells attenuated T cell–mediated immunity to Listeria, whereas blocking BMPs enhanced host defense to Listeria in wild-type but not Alk2-deficient mice. Our findings suggest that the BMP-independent ALK2/3-SMAD1/5 axis plays essential roles in T cell activation and AICD, which is reciprocally antagonistic with BMP-triggered inhibition of T cell-mediated immunity.

overall_design: For sample NM1, NM2, NA1, NA2, AA1, AA2, BA1, BA2, edited or control Jurkat cells were treated with PHA (400 ng/ml) for 2 h before RNA-seq transcriptome analysis. For sample E5, E6, E7, E8, Jurkat cells were left untreat or treat with BMP4 (40 ng/ml) and BMP7 (100 ng/ml), and then stimulated with PHA for 2 h (400 ng/ml) before RNA-seq profiling.

first: Jun-Ge

last: Shi

first: Zi-Lun

last: Ruan

first: Hong-Bing

last: Shu

first: Shu


title: White-Brown switching controls phenotypic plasticity and virulence of Candida auris [3]

summary: Comparative transcriptomic profiling of Parent, White and Brown clones derived from Candida auris 1333/P/13R

overall_design: RNA Sequencing was conducted on the Parent, White and Brown clones from Candida auris 1133/P/13R. The cells were cultivated to the exponential phase in YPD at 30°C with agitation at 200rpm. Subsequently, cultures were harvested, and RNA isolation was performed, followed by the preparation of sequencing libraries for three biological replicates (except ClaI-1P with two replicates).


title: White-Brown switching controls phenotypic plasticity and virulence of Candida auris [2]

summary: Comparative transcriptomic profiling of Candida auris WT 1333/P/13R and CRZ2 null mutant

overall_design: RNA Sequencing was conducted on a multidrug resistant Candida auris 1133/P/13R and its CRZ2 null mutant. The cells were cultivated to the exponential phase in YPD at 37°C with agitation at 200rpm. Subsequently, cultures were harvested, and RNA isolation was performed, followed by the preparation of sequencing libraries for three biological replicates.


title: Common cell lysis procedures distort ribosome profiling analyses of gene expression

city: Cork

first: Gary

last: Loughran

address: Bioinnovation Hub, FSB 330, College Rd,

country: Ireland

institute: EIRNA Bio

summary: Ribosome profiling is a powerful technique used to study gene expression on a transcriptome-wide scale. It involves sequencing of mRNA fragments protected by ribosomes from ribonuclease digestion. The initial steps commonly involve cell lysis followed by centrifugation and ribonuclease digestion. We find that centrifugation depletes 329 translated mRNAs in HEK293T cells. Many of these mRNAs encode cytoskeleton proteins. This suggests that the expression of a subset of mRNAs may be significantly underestimated in most ribosome profiling experiments. We show that omitting the centrifugation step after cell lysis can resolve this issue.

overall_design: We investigated how sample preparation protocols affect Riboseq perfomance. This include the effect of Triton-X100 concentration in cell lysis buffer and the effect of lysate centrifugation.

first: Aoife

last: O’Connell

first: Alla

middle: D

last: Fedorova

first: Patrick

last: O’Connor

first: Alexander

last: Zhdanov

first: Pavel

last: Baranov

first: Dmitry

middle: E

last: Andreev


title: TAS-seq enables subcellular single-stranded adenosine profiling by signal peptide-assisted adenosine deamination

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA structure critically facilitates RNA function and undergoes alterations from transcription into its ultimate functional destination in different subcellular compartments. To enhance our understanding of RNA structural dynamics, we develop TAS-seq, which locates deaminase TadA-8e to specific subcellular compartments and modifies adenosine in single-strand structures, particularly within the hairpin loop, to profile the RNA secondary structure of subcellular RNAs. We identified variations across three subcellular components (nucleus, cytoplasm, and endoplasmic reticulum membrane) and two cell lines (HEK293T and K562), and investigated the interplay between RNA structural changes and RBP binding. We also performed TAS-seq at the single-cell level, achieving the first full-length RNA structure heterogeneity profiling of individual cells.

overall_design: To profile the structure of subcellular RNAs, we expressed adenosine deaminase TadA-8e in human cells. TadA-8e is anchored into subcellular compartments (nucleus, cytoplasm, and endoplasmic reticulum membrane) by signal peptides (NLS, NES, and ERM). Then the total RNAs, poly(A) RNAs, and Ribo-RNAs were extracted and sequenced, separately. Adenosines in specific RNA structures were modified by TadA-8e resulting in A-to-G substitution in high-throughput data.

first: Lixia

last: Wang

first: Yangfan

last: Zhou

first: Zhenxing

last: Yu

first: Panfeng

last: Wu

first: Zhike

last: Lu


title: Identification of immune signatures associated with both SARS-CoV-2 infection and lung transplantation

city: Chicago

first: Huiping

last: Liu

state: IL

address: 303 E Superior St Room 5-250

department: Pharmacology

institute: Northwestern University

summary: We used single-cell RNA sequencing to analyze immune cells in COVID-19 patients. We drew blood from convalescent patients and examined PBMCs, monocytes and regulatory T cells.

overall_design: Monocytes and Tregs were sorted using fluorescence activated sorting (FACS). All samples were sequenced using a 10X genomics library preparation kit and an Illumina HiSeq sequencer.

first: Andrew

last: Hoffmann

first: Hannah

middle: F

last: Almubarak

first: Radhika

last: Iyer

first: Sam

last: Weinberg

first: Joshua

middle: R

last: Squires

first: Chengsheng

last: Mao

first: Juncheng

last: Wei

first: Shuvam

last: Chadhuri

first: Lamiaa

last: El-Shennawy

first: Nurmaa

middle: K

last: Dashzeveg

first: Yuzhi

last: Jia

first: Alexis

last: Demonbreun

first: Matthew

middle: J

last: Schipma

first: Yuan

last: Luo

first: Suchitra

last: Swaminathan

first: Michael

middle: G

last: Ison

first: Deyu

last: Fang


title: Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo [RNA-seq]

city: Columbus

first: Genevieve

last: Kendall

state: Ohio

address: 575 Children's Crossroads

department: Center for Childhood Cancer Research

institute: Nationwide Children's Hospital

summary: Fusion-positive rhabdomyosarcoma is an aggressive pediatric cancer molecularly characterized by arrested myogenesis. The defining genetic driver, PAX3::FOXO1, encodes a chimeric gain-of-function transcription factor. An incomplete understanding of PAX3::FOXO1’s in vivo chromatin regulatory mechanisms has hindered therapeutic development. Here, we establish a PAX3::FOXO1 zebrafish injection model and a semi-automated ChIP-seq normalization strategy to evaluate how PAX3::FOXO1 initially interfaces with and modulates chromatin in a developmental context. We find that PAX3::FOXO1 interacts with inaccessible chromatin through partial/homeobox motif recognition consistent with pioneering activity. However, PAX3::FOXO1-genome binding through a composite paired box/homeobox motif alters chromatin accessibility and redistributes H3K27ac to activate neural transcriptional programs. We uncover neural signatures that are highly representative of clinical rhabdomyosarcoma gene expression programs that are enriched following chemotherapy. Overall, we identify partial/homeobox motif recognition as a key mode for PAX3::FOXO1 pioneer function and identify neural signatures as a potentially critical PAX3::FOXO1 tumor initiation event.

overall_design: Examination of RNA-seq transcriptional profiles in developmentally 6 hour old zebrafish embryos injected with PAX3::FOXO1-2A-sfGFP mRNA compared to embryos injected with a control sfGFP mRNA. Each sample is a pool of 30-40 embryos at that time-point, with quadruplicates collected across 2 injection days.

first: Jack

last: Kucinski

first: Alexi

last: Tallan

first: Cenny

last: Taslim

first: Andrew

middle: M

last: Vontell

first: Katherine

last: Silvius

first: Meng

last: Wang

last: Cannon

first: Benjamin

middle: Z

last: Stanton


title: Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo [ATAC-seq]

overall_design: Examination of chromatin accessibility by ATAC-seq in developmentally 6 hour old zebrafish embryos injected with PAX3::FOXO1-2A-sfGFP mRNA compared to embryos injected with a control sfGFP mRNA. Each sample from 50,000 live zebrafish cells at that time-point, with duplicates collected across two injection days.


title: A Mechanistic basis of fast myofiber vulnerability in neuromuscular diseases [snRNA-seq]

status: Public on May 29 2025

city: Dallas

first: Matthieu

last: Dos Santos

state: Texas

address: 5323 Harry Hines Blvd

institute: UtSouthwestern

summary: Skeletal muscle denervation is a characteristic feature of neuromuscular diseases such as amyotrophic lateral sclerosis (ALS) and sarcopenia, leading to atrophy, loss of muscle strength, and poor patient outcomes. Myofibers are typically classified into slow oxidative and fast glycolytic types based on their contractile and metabolic properties. Neuromuscular diseases predominantly affect fast myofibers, while slow myofibers are relatively spared. However, the mechanisms underlying the heightened susceptibility of fast myofibers to disease and atrophy remain unclear. To investigate this, we analyzed the transcriptional profiles of innervated and denervated myonuclei. Our findings revealed that the fast muscle gene program and the transcription factor Maf are repressed during denervation.  Notably, overexpression of Maf in the skeletal muscles of mice prevented loss of muscle mass and myofiber atrophy caused by denervation. Single-nucleus RNA sequencing and ATAC sequencing demonstrated that Maf overexpression reprogrammed denervated myonuclei by repressing atrophic gene programs and reactivating fast muscle gene expression. Similar repression of fast muscle genes and Maf was observed in muscles from mice and humans with ALS. Consistent with these findings, Maf overexpression in human skeletal muscle cells induced the expression of fast muscle genes while suppressing atrophic gene expression. Our findings highlight a key role for Maf in maintaining muscle mass and demonstrate that its repression contributes to the progression of neuromuscular diseases in both mice and humans. Modulating Maf activity could offer a promising therapeutic strategy to preserve skeletal muscle function during disease, aging, or injury.

overall_design: Single nuclei RNAseq of WT and 7 days denervated gastrocnemius

first: Svetlana

last: Bezprozvannaya

first: John

last: R. McAnally

first: Chunyu

last: Cai

first: Ning

last: Liu

first: Eric

last: N. Olson


title: Comprehensive serum metabolic snapshots enable diagnosis, prognosis, and monitoring for brainstem gliomas [I]

city: SHANGHAI

first: Ruimin

state: SHANHAI

address: 1954 hUASHAN ROAD

institute: Shanghai Jiao Tong University

summary: Brainstem gliomas (BSG) is a highly malignant central nervous system childhood tumors with a poor prognosis of a 5-year survival rate of < 10%. Metabolism during radiotherapy is a dynamic and precisely programmed process, improving clinical outcomes and guiding therapy decisions of BSG. Here, we for the first time construct diagnostic and prognostic assays of BSG via circulating metabolites based on both cross-sectional study and longitudinal cohort study with 106 BSG patients. We employ nanoparticle enhanced laser desorption/ionization mass spectrometry to characterize high-resolution static and dynamic snapshots of metabolites during BSG radiotherapy. We show that this serological tool reaches the area under the curve of 0.933 for BSG diagnosis in an independent blind test and predicts risk of patients with significant differences (p < 0.05) in prognostic outcomes. We further identify eight distinct temporal patterns of metabolite regulation associated with radiotherapy responses and tracked the metabolic trajectory via dynamic metabolic snapshots throughout radiotherapy process. If further validated, this framework could be extended to derive comprehensive metabolic pictures for cancers including but not limited to BSG.

overall_design: SPF-grade female BALB/c nude mice, aged 5-6 weeks and weighing 18-20 g, were used as experimental subjects in this study, following refinement of the experimental methods based on previous study. In the case of the orthotopic tumor model, the inoculation site was the right caudate nucleus of the mouse brain. When anesthetizing mice with isoflurane, a concentration of 1-2% was maintained once the mice are confirmed to have entered the anesthetized state, in order to sustain the anesthetic effect throughout the experiment. The trypsinized U87MG-Luc cells were resuspended in cold phosphate-buffered saline at 1.0 × 105 cells/μL. A 10 μL microsyringe was used to inject 5 μL of the cell suspension into the right hemisphere of the mouse brain (0.5 mm anterior to the bregma, 2 mm lateral to the midline, and 3.5 mm depth from the skull) at a rate of 1 μL/min. Following the injection, the bone hole was sealed with bone wax, and the incision was sutured. The mice were placed on thermostatic electric blankets and closely monitored until fully resuscitated. Three days post tumor cell injection, tumor implantation and growth were evaluated using the IVIS Lumina Series III in vivo imaging system (PerkinElmer, USA). At the humane endpoint, mice were euthanized. Five brain tumor tissue and four adjacent non-cancerous tissue were collected and subjected to RNA sequencing. To establish the subcutaneous tumor model, mice were inoculated with U87MG-Luc cells (3.0 × 106 cells/site) suspended in Matrigel, and were injected into the axillary region of the right forelimb. Tumor volume was measured using a vernier caliper, and radiotherapy was initiated once the average tumor size exceeded 100 mm3. Mice in the radiotherapy group were administered a daily radiation dose of 2 Gy at the tumor site for five consecutive days. Four brain tumor samples were collected before and five days after radiotherapy, and then subjected to  RNA sequencing, respectively.

first: Keke

last: Li

first: Zhengying

last: Gu

first: Wenyun

last: Weng


title: Excessive HIF-1α driven by phospholipid metabolism causes septic cardiomyopathy through cytopathic hypoxia

city: Fukuoka

first: Masataka

last: Ikeda

state: Fukuoka

address: 3-1-1, Maidashi, Higashiku

institute: Kyushu University

summary: To elucidate the molecular mechanism by which LPS treatment increases HIF-1α expression, lipopolysaccharide was added to cultured cardiomyocytes derived from neonatal SD rats, and changes in gene expression were evaluated 24 h after LPS treatment.

overall_design: Cardiomyocytes were isolated from neonatal SD rats and cultured for several days. Subsequently, LPS (100 ng/mL) was added, and total RNA was extracted 24 hrs later for microarray analysis.


title: Targeting G1–S-checkpoint-compromised cancers with cyclin A/B RxL inhibitors

city: Boston

first: Yixiang

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: Cancer cell proliferation requires precise control of E2F1 activity; excess activity promotes apoptosis. We developed cell-permeable and bioavailable macrocycles that selectively kill small cell lung cancer (SCLC) cells with inherent high E2F1 activity by blocking RxL-mediated interactions of cyclin A and cyclin B with select substrates.  This work uncovers gain-of-function mechanisms by which cyclin A/Bi induce apoptosis in cancers with high E2F activity, and suggests cyclin A/Bi as a therapeutic strategy for SCLC and other cancers driven by high E2F activity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in a human SCLC patient-derived xenograft (PDX) tumor model treated with a cyclin A/B RxL inhibitor (CIRc-014) or vehicle, and a human SCLC cell line NCI-H1048 after treatment with DMSO (vehicle), cyclin A/B RxL inhibitor (CIRc-004 or CIRc-014), inactive enantiomer (CIRc-005) or a Cdk2 inhibitor (PF-07104091). The SCLC PDX model DFCI393 was grown in NSG mice and established tumors were treated with the orally bioavailable cyclin A/B RxL inhibitor CIRc-014 at 100 mg/kg PO TID or vehicle (30% PEG400, 20% Solutol HS15, 50% Phosal 53 MCT) three times a day for 4 days and tumors were collected 8 hours after the morning dose on the last day of treatment and snap frozen for RNA-seq. 6 independent tumors from 6 independent mice were used for CIRc-014 and 5 independent tumors from 5 independent mice were used for vehicle. For cell line experiments, NCI-H1048 cells were plated at 500,000 cells/mL density in presence of DMSO (vehicle), cyclin A/B RxL inhibitor (CIRc-004 or CIRc-014, 200nM), inactive enantiomer (CIRc-005, 200nM) or a Cdk2 inhibitor (PF-07104091, 500nM). 24 hours after treatment with drugs, cells were harvested for RNA. The NCI-H1048 cell line experiments were done in 2 biological replicates.

first: Singh

last: Shilpa

first: Oser

last: Matthew


title: A Mechanistic basis of fast myofiber vulnerability in neuromuscular diseases [Multiome]

overall_design: Multiome single nuclei RNAseq and single nuclei ATACseq of WT and denervated gastrocnemius overexpression GFP or Maf


title: Triglyceride metabolism controls inflammation and microglial phenotypes associated with APOE4 [RNA-seq]

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Microglia modulate their cell state in response to various stimuli. Changes to cellular lipids often accompany shifts in microglial cell state, but the functional significance of these metabolic changes remains poorly understood. In human induced pluripotent stem cell-derived microglia, we observed that both extrinsic activation (by lipopolysaccharide treatment) and intrinsic triggers (the Alzheimer’s disease-associated APOE4 genotype) result in accumulation of triglyceride-rich lipid droplets. We demonstrate that lipid droplet accumulation is not simply concomitant with changes in cell state. In fact, both triglyceride biosynthesis and catabolism are necessary for the activation-induced transcription and the secretion of inflammatory cytokines and chemokines as well as the changes in phagocytosis of many substrates including the amyloid-beta peptide. In microglia harboring the Alzheimer’s disease risk APOE4 genotype, inhibiting triglyceride biosynthesis modifies the transcription of immune response genes and attenuates disease-associated transcriptional states. In addition, this inhibition rescues microglial surveillance defects observed in slices from APOE4 humanized transgenic mice. Together, our findings establish that modulating triglyceride metabolism can be used to tune microglial immunometabolism in response to extrinsic activation and in APOE4-associated disease.

overall_design: Bulk RNA-Seq profiling of 25 human iPSC samples representing either APOE3 or APOE4 under no treatment condition or treatment with LPS, DGAT1 and DGAT2 inhibitor, or DGAT1 and DGAT2 inhibitor and LPS

first: Roxan

middle: A

last: Stephenson

first: Jordy

last: Sepulveda

first: Adrian

last: Lita

first: Jaanam

last: Gopalakrishnan

first: Dominic

last: Acri

first: Alexandra

last: Beilina

first: Linling

last: Cheng

first: Linda

last: Yang

first: Jessica

middle: T

last: Root

first: Michael

last: Ward

first: Christian

last: Combs

first: William

last: Skarnes

first: Mark

last: Cookson

first: Mioara

last: Larion

first: Han-Yu

last: Shih

first: G

middle: W

last: Rebeck

first: Priyanka

middle: S

last: Narayan


title: PROCR diminishes the efficacy of radiation by impairing T cell-mediated antitumour immunity

city: Guangzhou

first: Xiaoyu

last: Liang

address: 651 Dongfengdongroad, Guangzhou, Guangdong

institute: Sun Yat-sen University Cancer

summary: We found that PROCR promotes IL-6 secretion, which is magnified after radiation, leading to inhibition of antitumour immunity. Next, we investigated the mechanism by which PROCR upregulated IL-6. To this end, we performed RNA sequencing on irradiated HONE1 cells with or without PROCR knockout.

overall_design: High-throughput RNA sequencing analysis was performed in irradiated sgGFP (WT) or sgPROCR (KO)  human nasopharyngeal carcinoma cell line  HONE1

first: Wei-peng

last: Chen


title: Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo [ChIP-seq]

first: Genevieve

last: Kendall

overall_design: Determination of PAX3::FOXO1 binding sites and H3K27ac localization by ChIP-seq in developmentally 6 hour old zebrafish embryos injected with PAX3::FOXO1-2A-sfGFP mRNA compared to embryos injected with a control sfGFP mRNA. PAX3::FOXO1 ChIP-seq used 2,000,000 injected zebrafish cells with 250,000 RH30 cells for spike-in normalization. H3K27ac ChIP used 1,000,000 injected zebrafish and 1,000,000 RH30 cells for spike-in normalization.

first: Jack

last: Kucinski

first: Alexi

last: Tallan

first: Cenny

last: Taslim

first: Andrew

last: Vontell

first: Katherine

last: Silvius

first: Meng

last: Wang

first: Matthew

last: Cannon

first: Benjamin

last: Stanton

middle: C


title: GPNMB is a marker of invasive quiescent differentiated melanoma cells driven by tumor niche reprogramming.

city: Milano

first: Marine

last: Melixetian

address: via Adamello 16

country: Italy

institute: European Institute of Oncology

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

overall_design: Refer to individual Series


title: GPNMB is a marker of invasive quiescent differentiated melanoma cells driven by tumor niche reprogramming

summary: We provide evidence of the existence of a slow cycling melanoma population isolated in vivo from melanoma PDXs using the H2B-GFP system. Single cell transcriptomic analysis unveils a significant transcriptional heterogeneity of GFP-retaining slow cycling cells, defining a quiescent subpopulation of cells. These cells show a different phenotype in primary tumors and matched metastases, suggesting that tumor niche pressure drives a transcriptional reprogramming of quiescent cells during melanoma progression.

overall_design: Metastatic melanoma PDX  MM13 cells were stained with anti-KI67 antibody, KI67- positive and -negative cell populations were sorted by FACS and used for RNAseq library preparation.

first: Fiorenza

last: Lotti

last: Meliksetyan

first: Luisa

last: Lanfrancone


title: Modulation of infiltrating CD206-positive macrophages restricts progression of pulmonary lymphangioleiomyomatosis (LAM)

first: Remi

last: Diesler

state: MA

address: 75 Francis Street

department: Pulmonary Division

institute: Brigham and Women's Hospital

summary: Lymphangioleiomyomatosis (LAM) is a very rare disease affecting women of childbearing age, either sporadically or in association with tuberous sclerosis complex (TSC). The proliferation of TSC2 null LAM cells in the lung results in cystic destruction, airflow obstruction, respiratory insufficiency and eventually death. In the LAM lung, the tumor immune microenvironment (TME) plays a role in the progression of LAM lesions. Macrophages can be polarized into inflammatory M1 macrophages or protumorigenic immunosuppressive M2 macrophages. Macrophages are an important component of the TME, and we hypothesized that CD206+ M2 macrophages could facilitate LAM progression and represent a potential therapeutic target.

overall_design: To study the effect of TSC2 null cells on the macrophage polarization, we cocultured RAW264.7 macrophages with Tsc2-null TTJ cells derived from an angiomyolipoma of a murine model of tuberous sclerosis complex. We perfomed gene expression analysis using RNA-seq data from FACS-sorted control RAW264.7 cells or RAW264.7 cells cocultured for 48h with TTJ cells.

first: Heng-Jia

last: Liu

first: Joelle

last: Chami

first: Elizabeth

last: Henske


title: Identifying downstream targets of ankrd1a in skeletal muscle injury repair in adult zebrafish

city: Belgrade

first: Mirjana

last: Novkovic

address: Vojvode Stepe 444a

country: Serbia

institute: Institute of Molecular Genetic and Genetic Engineering

summary: The ANKRD1 gene is responsive to different forms of mechanical stress, including injury, stretching, resistance exercise, and eccentric contractions. We showed that ankrd1a, zebrafish homologue of mammalian ANKRD1, gets activated in the heart, after cryoinjury of the ventricle and in skeletal muscle after stab wound, suggesting its role in muscle healing processes. To identify targets of ankrd1a involved in skeletal muscle repair we performed RNA-seq of injured adult ankrd1a mutant and wt zebrafish muscle at 5 days post injury. Non-injured skeletal muscle of both genotypes were used as controls. The loss of ankrd1a function affected the expression of genes involved in muscle contraction, muscle cell differentiation, MAPK and integrin-mediated signaling pathways, and cell-substrate adhesion. Our findings offer novel insights into the ankrd1a function and skeletal muscle repair in adult zebrafish.

overall_design: The ankrd1abns502 mutant zebrafish line was generated by CRISPR/Cas9 genome editing. Muscle injury was performed by needle stab into the dorsal myotome of the tail. After 5 days of recovery, RNA was isolated from the muscle tissue around the injury, anterior and posterior to the needle lesion or corresponding non-injured region in control fish. Four experimental groups (injured wt, non-injured wt, injured mutant, and non-injured mutant) were subjected to RNA-seq. Each experimental group comprised four biological samples and one sample contained RNA isolated from the skeletal muscle of one fish.

first: Emilija

last: Milosevic

first: Jovana

last: Jasnic

first: Andjela

last: Milicevic

first: Snezana

last: Kojic


title: Irx3 controls a sumoylation-dependent epigenetic switch between adipogenesis and osteogenesis

city: Oslo

first: Pierre

last: Chymkowitch

address: Blindernveien 31

department: Biosciences

country: Norway

institute: University of Oslo

summary: Background IRX3 is implicated in genetic predisposition to obesity via the FTO variant locus. IRX3 shows FTO risk allele-dependent upregulation specifically during early adipogenesis, leading to a shift from energy dissipation to fat storage in mature adipocytes. However, how changes in IRX3 expression at one developmental stage affect cellular phenotype at a later stage remains unclear. We here hypothesize that IRX3 regulates adipocyte development via transcriptional modulation of epigenetic reprogramming factors. Methods We combined ChIP-, ATAC- and RNA-sequencing to map direct Irx3 target genes in regions of open chromatin during early adipogenesis of wild-type and Irx3-KO preadipocytes. Gene ontology analyses was performed to identify significantly enriched biological pathways. Denaturing western blotting was used to assess sumoylation levels, and the inhibitor ML-792 was used to specifically block sumoylation. Luciferase assays were performed to estimate effects of ML-792 on Pparγ activity. Bodipy lipid staining, immunofluorescence and qPCR were employed to assess adipogenic differentiation in 3D culture. Alkaline phosphatase and Alizarine Red S staining, as well as immunofluorescence and qPCR were used to assess osteogenic differentiation in 3D culture. Results We identified more than 300 Irx3 binding sites in preadipocytes, and these were almost exclusively restricted to promoter regions, with a strong enrichment of genes related to sumoylation, histone modifications and chromatin remodeling. Genes from every step of the sumoylation cycle were bound by Irx3 and differentially expressed in response to Irx3-KO, leading to increased global sumoylation levels in the KO cells. Irx3 ablation and elevated sumoylation inhibited Pparγ activity and adipogenic differentiation in preadipocytes, both of which could be restored by pharmacological inhibition of sumoylation. The Irx3-KO cells demonstrated reduced epigenetic suppression against osteogenesis, resulting in increased osteogenesis in 3D culture. Finally, osteogenesis induced by Irx3 ablation could partially be reversed by inhibition of sumoylation. Conclusions Our study has uncovered IRX3 as a novel upstream regulator of sumoylation, and a potent controller of epigenetic regulators, both directly and indirectly via suppressing global sumoylation levels. This study indicates that the FTO locus promotes obesity via IRX3-mediated suppression of sumoylation, which promotes adipogenic commitment and differentiation through epigenetic programming.

overall_design: Adipogenesis was induced in WT and IRX3-KO ME3 cells. Chromatin was prepared from uninduced (day -1) and induced (day 1) cells before performing SUMO2/3 ChIP-seq. All procedures as decribed in Zhao et al., NAR, 2022.

first: Bjune

last: Jan-Inge

first: Dankel

last: Simon

first: Mellgren

last: Gunnar


title: The role of the DRW1 mutation on the DNA 6mA abundance in rice grains. [6mA IP-seq]

city: Beijing

first: Xiaofeng

last: Gu

address: Zhongguancun south street

institute: Chinese Academy of Agricultrual Sciences

summary: DRW1  modulates the DNA 6mA levels at loci involved in hormone pathway, photosynthesis, carbon metabolism as well as cell division and proliferation .

overall_design: Genomic DNA was extracted from ZH11 and drw1 seeds at 3 DAP, treated with RNase A and sonicated to produce ~250 bp fragments, which were incubated with 6mA antibody. After extensive washing, bound DNA fragments were eluted. These DNA fragments were used to construct DNA 6mA library, and high-throughput DNA 6mA IP-seq was conducted using the Illumina nova6000 platform.

first: Liwen

last: Yang


title: The role of the DRW1 mutation on H3K27me3 levels in rice grains. [H3K27me3 cut tag]

summary: DRW1  controls H3K27me3 abundance contributed to hormone pathway, photosynthesis, carbon metabolism as well as cell division and proliferation .

overall_design: Samples were collected from ZH11 and drw1 grains at 3 days after pollination. Nuclei was extracted, and high-throughput cut&tag was conducted using the Illumina nova6000 platform.


title: The role of the DRW1 mutation on chromatin accessibility in rice. [ATAC-Seq]

summary: DRW1  controls chromatin accessibility around DNA 6mA- and H3K27me3-modified regions in rice.

overall_design: Samples were collected from ZH11 and drw1 panicles at 3 days after pollination. Nuclei was extracted, and high-throughput ATAC-seq was conducted using the Illumina nova6000 platform.


title: The role of the DRW1 overexpression on the gene expression levels and RNA m5C levels in rice grains.

address: Zhongguancun sourth no.12

department: Biotechnology Research Institute

institute: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences

summary:
DRW1  controls gene expression contributed to hormone pathway, photosynthesis, carbon metabolism as well as cell division and proliferation .
DRW1  controls RNA m5C levels of  transcripts contributed to hormone pathway, photosynthesis, carbon metabolism.

overall_design:
Samples were collected from ZH11 and DRW1-OE grains at 3 days after pollination. Total RNA was extracted using a Plant RNA Kit (RP3302; Bioteke, Beijing, China), and high-throughput RNA-sequencing (RNA-seq) was conducted using the Illumina nova6000 platform.
Samples were collected from ZH11 and DRW1-OE1 seedlings at 3 weeks after germination.~300 μg total RNA was fragmentated by ZnCl2, and  RNA fragments are used for m5C immunoprecipitation. High-throughput RNA-sequencing (RNA m5C IP-seq) was conducted using the Illumina nova6000 platform.


title: The role of the DRW1 mutation on the gene expression levels in rice grains. [RNA-Seq]

summary: DRW1  controls gene expression contributed to hormone pathway, photosynthesis, carbon metabolism as well as cell division and proliferation .

overall_design: Samples were collected from ZH11 and drw1 grains at 3 days after pollination. Total RNA was extracted using a Plant RNA Kit (RP3302; Bioteke, Beijing, China), and high-throughput RNA-sequencing (RNA-seq) was conducted using the Illumina nova6000 platform.


title: The role of the DRW1 gene in rice.


title: Single dose of CD137-Antibody Drug Conjugate protects non-human primate allogeneic HCT recipients against acute GVHD

status: Public on May 28 2025

first: Victor

last: Tkachev

address: 55 Fruit Street

department: Center for Transplantation Sciences

institute: Mass General Research Institute

summary: Rapid CD137 upregulation on alloreactive T-cells upon allogeneic stimulation suggests that their selective elimination could prevent acute graft-versus-host disease (aGVHD) after allogeneic hematopoietic stem cell transplantation (HCT). Here, we developed a novel aGVHD prophylactic regimen consisting of a single dose of an anti-CD137 antibody-drug conjugate (CD137-ADC) administered on the day of transplant without additional immunosuppression. The CD137-ADC depleted both human and non-human primate (NHP) activated T-cells and proved highly effective in preventing xenogeneic aGVHD in mice receiving human peripheral blood mononuclear cells (PBMC), as well as in NHP undergoing MHC-haploidentical HCT. Flow cytometry analysis of NHP T-cells indicated specific depletion of activated PD-1+ CD4 and CD8 T-cells, while sparing naïve and PD-1-OX40+ memory T-cell subsets during the first week after HCT. CD137-ADC-treated NHP recipients demonstrated robust hematopoietic and immune reconstitution. Hallmarks of T-cell recovery after CD137-ADC, which were associated with long-term aGVHD-free survival, included reconstitution of CD4 memory T-cells expressing TRAIL, terminally-differentiated CD8 T-cells expressing CX3CR1, and CD4 FoxP3+ Tregs – cell types not expected to be involved in aGVHD pathogenesis. CD137-ADC-treated recipients demonstrated a higher risk of reactivation of rhLCV (the rhesus macaque EBV analogue), which was associated with reconstitution of follicular helper T-cells, interferon signaling-associated memory, and gamma-delta T-cell subsets. This reactivation was controllable with rituximab administration. These results document effective depletion of alloreactive T-cells and prevention of aGVHD following a single dose of CD137-ADC, suggesting that clinical translation should be carefully explored.

overall_design: This study contains data of two cohorts of GVHD model Non-human Primates, one given a-CD137 4 hours after HCT, the other given placebo. At timepoint, samples were frozen. Later, these were thawed and T cells were isolated by Fluorescence-activated cell sorting (FACS) for CD3+ CD20- cells, then analyzed using scRNA-seq.

first: Ulrike

last: Gerdemann

first: Kyle

last: Kimler


title: Fc-optimized CD40 Agonistic Antibody Induces Tertiary Lymphoid Structures and Systemic Antitumor Immunity in Metastatic Cancer Patients [Human]

city: New York

first: Ning

last: Yao

address: 321 E 61st St

institute: Memorial Sloan Kettering Cancer Center

summary: Human peripheral blood mononuclear cells (PBMC) from participants of the clinical study were isolated and thawed using prewarmed BD BSA stain buffer (BD Biosciences), washed twice with ice-cold buffer and counted and CD45+ cells were sorted for RNA sequencing.

overall_design: Human CD45+ PBMCs isolated by FACS and analyzed by scRNAseq to determine the gene expression profile and T-cell receptor repertoire.

first: Yao

last: Ning

first: Osorio

last: Juan

first: Jeffrey

last: Ravetch


title: Fc-optimized CD40 Agonistic Antibody Induces Tertiary Lymphoid Structures and Systemic Antitumor Immunity in Metastatic Cancer Patients

summary: These studies were performed to understand the transcriptional profile of immune cells following treatment with 2141-V11, the main comparison was injected tumors versus non-injected ones. In summary: hCD40/hFcγR mice were inoculated bilaterally with E0771 tumors (5*105). IT 2141-V11 or isotype-matched control Abs were given into one tumor (the largest of the two) on days 14 and 17. Both tumors were excised on day 18 for scRNAseq and TCR-seq of CD45+ cells.

overall_design: Murine CD45+ cells isolated by FACS and analyzed by scRNAseq to determine the gene expression profile and T-cell receptor repertoire.


title: The targets of the DRW1 in rice grains. [DRW1-Flag cut tag]

summary: DRW1  binds genes contributed to hormone pathway, photosynthesis, carbon metabolism as well as cell division and proliferation .

overall_design: Samples were collected from ZH11 and DRW1-OE grains at 3 days after pollination. Nuclei was extracted, and high-throughput cut&tag was conducted using the Illumina nova6000 platform.


title: Short Tandem Repeats of Single-Stranded (ATTCC)n in Neutrophil Extracellular Traps Bind Thrombin

first: Tao

last: Pan

address: 929E 57th street

institute: The University of Chicago

summary: DNA-protein interactions play a pivotal role in a variety of cellular processes. Despite the considerable research dedicated to understanding these interactions, the specific role of single-stranded DNA (ssDNA) remains largely unexplored. Our study aimed to uncover the role of ssDNA in the interplay between neutrophil extracellular traps (NETs) and thrombin, a crucial enzyme involved in both blood clot formation and immune response. Using chromatin immunoprecipitation sequencing (ChIP-seq) and kethoxal-assisted ssDNA sequencing, we identified a specific short tandem repeat (STR) sequence, ss(ATTCC)n, that is highly enriched and forms an iI-motif structure crucial for its interaction with thrombin. We further observed that the binding affinity between ss(ATTCC)n and thrombin is increased under acidic conditions, a condition frequently linked to diseases such as cancer. Our findings not only shed light on the unexplored area of sequence-dependent ssDNA-protein interactions but also pave the way for targeted interventions in thrombosis and coagulation disorders.

overall_design: Pull down thrombin binding DNA and do DNA seq to reveal the binding sites in 4 replicates. Do KAS-seq to reveal all single stranded DNA as a comparison.

first: Weijie

last: Guo

first: Sihao

last: Huang

first: Xiangli

last: Shao

first: Yuting

last: Wu

first: Yuan

last: Ma

first: Shuya

last: Lu

first: Hanlin

last: Ren

first: Zhenglin

first: Mingkuan

last: Lyu

first: Whitney

last: Lewis

first: Yiwei

last: Liu

first: Yi


title: Senolytic-Resistant Senescent Cells Have a Distinct SASP Profile and Functional Impact: The Path to Developing Senosensitizers

city: Rochester

first: Alexandra

last: Krivonos

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

summary: The senescent cell (SC) fate is linked to aging, multiple disorders and diseases, and physical dysfunction. Senolytics, agents that selectively eliminate 30-70% of SCs, act by transiently disabling the senescent cell anti-apoptotic pathways (SCAPs), which defend those SCs that are pro-apoptotic from their own senescence-associated secretory phenotype (SASP). Consistent with this, a JAK/STAT inhibitor, Ruxolitinib, which attenuates the pro-apoptotic SASP of senescent human preadipocytes, caused them to become “senolytic-resistant”. Administering senolytics to obese mice selectively decreased abundance of the subset of SCs that is pro-inflammatory. In cell cultures, the 30-70% of human senescent preadipocytes or human umbilical vein endothelial cells (HUVECs) that are senolytic-resistant (to Dasatinib or Quercetin, respectively) had increased p16INK4a, p21CIP1, senescence-associated β-galactosidase (Saβgal), γH2AX, and proliferative arrest similar to the total SC population (comprising senolytic-sensitive plus -resistant SCs). However, the SASP of senolytic-resistant SCs entailed less pro-inflammatory/apoptotic factor production, induced less inflammation in non-senescent cells, and was equivalent or richer in growth/ fibrotic factors. Senolytic-resistant SCs released less mitochondrial DNA (mtDNA) and more highly expressed the anti-inflammatory, immune evasion signal, glycoprotein non-melanoma-B (GPNMB). Transplanting senolytic-resistant SCs intraperitoneally into younger mice caused less physical dysfunction than transplanting the total SC population. Since Ruxolitinib attenuates SC release of pro-apoptotic SASP factors while pathogen-associated molecular pattern factors (PAMPs) can amplify release of these factors rapidly (acting as “senosensitizers”), senolytic-resistant and senolytic-sensitive SCs appear to be interconvertible.

overall_design: Preadipocytes (also known as adipose-derived stromal cells or adipose mesenchymal “stem” cells [MSCs]) were isolated from abdominal subcutaneous fat biopsies obtained from subjects donating kidneys for transplantation. In human preadipocytes, senescence was induced by 20 Gy X-irradiation and experiments were performed 30 days after radiation. Cells were treated with DMSO or 800 nM dasatinib and incubated for 24 hrs. Next, the remaining cells were washed with PBS 4X and subsequently incubated 3 days and analyzed via RNA SEQ

first: Utkarsh

last: Tripathi

first: Masayoshi

last: Suda

first: Vagisha

last: Kulshreshtha

first: Bryan

last: Piatkowski

first: Allyson

last: Palmer

first: Nino

last: Giorgadze

first: Christina

last: Inman

first: Nathan

last: Gasek

first: Ming

last: Xu

first: Kurt

middle: O

last: Johnson

first: Tamara

last: Pirtskhalava

first: Selim

last: Chaib

first: Larissa

last: Langhi Prata

last: Zhu

first: Renuka

last: Kandhaya-Pillai

first: Stefan

last: Tullius

first: Saranya

middle: P

last: Wyles

first: Rambabu

last: Majji

first: Hari

last: Yalamanchili

first: David

last: Allison

last: Tchkonia

first: James

middle: L

last: Kirkland


title: Mammalian queuosine tRNA modification impacts codon usage preferences to enhance cell proliferation and MHC-II expression [BMDC_0v100Q_mRNA-seq]

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: Queuosine (Q) is a conserved tRNA modification in the wobble anticodon position of tRNAs that read codons of Tyr/His/Asn/Asp. Eukaryotic tRNA Q-modification requires the metabolite queuine – derived from diet or catabolism of the gut microbiome – and a host-genome encoded enzyme complex, QTRT1/QTRT2. tRNA Q-modification has been shown to regulate translational efficiency, but the response of the mammalian transcriptome and tRNAome to tRNA Q-modification in the context of cell proliferation has not been thoroughly investigated. Using cells that differ only in their tRNA Q-modification levels, we found that both human HEK293T cultures and the primary, murine bone marrow-derived dendritic cells (BMDCs) proliferate faster when tRNA Q-modification level is high. We carried out tRNA-seq and mRNA-seq to elucidate the molecular mechanisms underlying this phenotype, revealing distinct tRNA modification and transcriptome changes associated with altered proliferation. In both cell types, the m22G26 tRNA modification is positively correlated to Q-modification, consistent with its reported role in enhancing translational efficiency. We also find that elevated Q-modification levels result in transcriptome changes, but in a context-dependent manner. In HEK293T cells, upregulated genes are in catabolic processes and signaling pathway activation; whereas in BMDCs, upregulated genes are in immune response mediation, proliferation, and immunoglobulin diversification. Codon usage analysis of differentially expressed transcripts is consistent with Q-modification enhancing the translation of ribosomal proteins, which increases cell proliferation. We also find that tRNA Q-modification increases surface presentation of MHC-II in BMDCs. Our results provide insights into the broader implications of tRNA Q-modifications in regulating diverse biological functions.

overall_design: To investigate the effects of queuosine modification on mouse transcriptome, RNA from murine bone marrow-derived dendritic cells (BMDCs) underwent mRNA-seq. Cells grown in queuine-free (0Q) and 100 nM queuine-supplemented (100Q) conditions were grown in triplicate. Generated libraries were sequenced using NextSeq 550. Following quality control processing and demultiplexing, libraries were aligned to mm39 reference genome.

first: Olivia

middle: N

last: Pura Zbihley

first: Kate

first: Luke

last: Frietze

first: Wen

last: Zhang

first: Marcus

last: Foo

first: Hoang Anh

middle: V

last: Tran

first: Nicolas

last: Chevrier


title: Mammalian queuosine tRNA modification impacts codon usage preferences to enhance cell proliferation and MHC-II expression [BMDC_0v100Q_tRNA-seq]

type: Genome variation profiling by high throughput sequencing

overall_design: To investigate the effects of queuosine modification on mouse cytosolic and mitochondrial tRNA, RNA from murine bone marrow-derived dendritic cells (BMDCs) underwent multiplex small RNA-seq (MSRseq). Cells grown in queuine-free (0Q) and 100 nM queuine-supplemented (100Q) conditions were grown in triplicate. Generated libraries were sequenced using Illumina. Following quality control processing and demultiplexing, libraries were aligned to mm39 tRNA genes. Mutation profile and abundance were calculated using custom Python and R scripts.

last: Johnson


title: Disruption of Notch1 and Gata5 in mice leads to congenital aortic valve disease

first: Vidu

last: Garg

state: OH

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

summary: Congenital aortic valve disease (AVD) is one of the most common type of congenital heart defects whose molecular and genetic basis is poorly understood. Pathogenic variants in NOTCH1 and GATA5 have been associated with AVD including aortic valve stenosis (AVS) and bicuspid aortic valve (BAV). Whereas previous genetic mouse models of AVD with Notch1 haploinsufficiency or Gata5 deletion alone display limitations with regards to significant perinatal lethality or a partially penetrance, and here, we generate a new murine model by intercrossing Notch1 and Gata5 heterozygote mice. We demonstrate that Notch1;Gata5 compound mutant mice display highly penetrant and clinically relevant congenital AVS without early lethality. Echocardiographic examination shows progressive AVS and aortic dilatation in Notch1+/-;Gata5-/- compound mutant mice at 6 and 16 weeks of age. Histologic analysis of 16 week old Notch1;Gata5 compound mutant mouse hearts identifies myxomatous aortic valves with thickened and dysmorphic leaflets. Morphologic analysis reveals the presence of BAV in a subset of Notch1;Gata5 compound mice. Furthermore, histologic analysis demonstrates   AVS and aortic valve leaflet thickening with proteoglycan accumulation at embryonic day 18.5 and postnatal day 10, consistent with congenital disease. RNA-sequencing analysis of postnatal day 10 aortic valves demonstrates dysregulation of extracellular matrix (ECM) genes in Notch1+/-;Gata5-/- compound mutant mice. In conclusion, we demonstrate a novel genetic interaction between Notch1 and Gata5, which is critical for the proper aortic valve development, and show that Notch1+/-;Gata5-/- compound mutant mice represent a novel mouse model of congenital and progressive AVS.

overall_design: Comparative gene expression profiling analysis for wildtype, Notch1+/-;Gata5+/- and Notch1+/-;Gata5-/- aortic valves dissected at postnatal day 10

first: Jun

last: Yasuhara

first: Mona

last: Aljuhani

first: Talita

last: Choudhury

first: Anupama

last: Rao


title: H3K27 and H3K9 Methylation Mask Potential CTCF Binding Sites to Maintain 3D Genome Integrity [ChIP-Seq]

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

institute: RIKEN

summary: The three-dimensional (3D) genome structure is essential for gene regulation and various genomic functions. CTCF plays a key role in organizing Topologically Associated Domains (TADs) and promoter-enhancer loops, contributing to proper cell differentiation and development. Although CTCF binds the genome with high sequence specificity, its binding sites are dynamically regulated during development, and aberrant CTCF binding is linked to diseases such as cancer and neurological disorders, and aging. However, the mechanisms controlling CTCF binding remain unclear. Here, we investigated the role of repressive chromatin modifications in CTCF binding using H3K9 methyltransferase-deficient immortalized mouse embryonic fibroblasts (iMEFs) and H3K27 methyltransferase EZH1/2 inhibitor. We found that H3K9 and H3K27 methylation regulate CTCF binding at distinct genomic regions, and their simultaneous loss induces drastic changes in CTCF binding. These changes were associated with alterations in 3D genome architecture and gene expression, suggesting that repressive chromatin modifications preserve proper chromatin organization by preventing aberrant CTCF binding. Additionally, while CTCF binding sites repressed by H3K9 methylation were bound by CTCF in early mouse embryos, those repressed by both H3K9 and H3K27 methylation remained inaccessible, with early embryonic-specific H3K27 methylation forming at these sites. These findings implicate that H3K27 methylation prevents abnormal CTCF binding in early embryos, ensuring proper genome organization during development.

overall_design: ChIP-seq profiles of histone modifcations in immortalized mouse embryonic fibroblasts

first: Yoichi

last: Shinkai


title: Nascent RNA profiles of WT and MED23-KD 293T cells

city: Shanghai

first: Lu

last: CHENGJIANG

state: China, Mainland

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: To profile the nascent RNAs, we performed 4SU-seq. Briefly, WT or MED23-KD 293T cells were seeded at 50% confluence in a 10 cm dish and cultured overnight. The newly transcribed RNAs in living cells were then transiently labelled with 4SU at a final concentration of 1 mM for 15 minutes. The labelled cells were harvested immediately with TRIzol. Total RNA was extracted with phenol/chloroform/isoamyl alcohol. The 4SU-labelled RNAs were biotinylated and enriched using streptavidin beads. Finally, the enriched nascent RNAs were subjected to library construction using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina for sequencing.

overall_design: MED23 was knocked down by CRISPR-Cas9 in 293T cells. WT, MED23KD-1 and MED23KD-2 293T cells with two replicates were subjected to 4SU-seq.

first: Chengjiang

last: Lu

first: Xue

last: Bai


title: Mammalian queuosine tRNA modification impacts codon usage preferences to enhance cell proliferation and MHC-II expression [HEK293T_0v100Q_mRNA-seq]

first: Tao

last: Pan

overall_design: To investigate the effects of queuosine modification on human transcriptome, RNA from human HEK293T cells underwent mRNA-seq. Cells grown in queuine-free (0Q) and 100 nM queuine-supplemented (100Q) conditions were grown in triplicate. Generated libraries were sequenced using Illumina. Following quality control processing and demultiplexing, libraries were aligned to hg38 reference genome.

first: Olivia

last: Pura Zbihley


title: Differential effects of different time windows of postnatal perfluorooctane sulfonate exposure on cognitive development in mouse hippocampus

city: Maebashi

first: Izuki

last: Amano

state: Gunma

address: 3-9-22 Showa-machi

department: Department of Integrative Physiology, Graduate School of Medicine

institute: Gunma University

summary: Perinatal perfluorooctane sulfonate (PFOS) exposure of the next generation through placenta and breast milk has been highly concerned. Epidemiological and animal studies have reported that perinatal PFOS exposure is associated with neurodevelopmental disorders such as learning and autism spectrum disorders in children. However, the sensitive time window of perinatal PFOS exposure for neurodevelopment has yet to be elucidated. Here we examined differential effects of different time windows of postnatal PFOS exposure (postnatal day (PD) 1-7 or 8-14) on cognitive development and gene expression profiles in the hippocampus. Pups were exposed to PFOS from PD 1 to 7 (PD 1-7 group) or from PD 8-14 (PD 8-14 group) through breastfeeding by dams who received a daily gavage of 1 mg/kg body weight PFOS per day during each period. Object location test and object recognition test revealed the impairment in spatial memory in PD 1-7 group at PD 70. Learning ability was also retarded in visual discrimination test. According to RNA-seq analysis and real-time PCR, Serpina3g and Tmem91 were significantly downregulated in the hippocampus of PD 1-7 group at PD 21. These results suggest that the first 7 days after birth is critically vulnerable to PFOS exposure and consequent neurodevelopmental deficits rather than the late phase of postpartum. Our work puts a strong emphasis on the importance of monitoring PFOS concentration in pregnant women and potential impact on retardation of neurodevelopment in children.

overall_design:
To examine the sensitive time window of perinatal PFOS exposure for neurodevelopment, we generated 2 different mouse models with different PFOS exposure periods (PD 1-7 and 8-14). Pups were exposed to PFOS from PD 1 to 7 or from PD 8-14 through breastfeeding by dams who received a daily gavage of 1 mg/kg body weight PFOS per day during each period.
Pups were then assessed by behavior test battery for evaluating higher brain functions.
RNA-seq was performend using RNA samples extracted from mouse hippocampal tissues sampled at postnatal day 21 from each group to investigate the differential effects of lactaional PFOS exposure periods on gene expression profiles.

first: Ayane

last: Ninomiya

first: Asahi

last: Haijima

first: Yuki

last: Fujiwara

first: Reika

last: Kawabata-Iwakawa

first: Noriyuki

last: Koibuchi


title: The critical role of Toxoplasma gondii GRA1 in nutrient salvage

city: Wuhan

first: bolin

last: Fan

state: hubei

address: hubei

institute: Huazhong Agricultural University

summary: To investigate the transcriptional effects of TgGRA1 on type I Toxoplasma gondii (RH) in the tachyzoite stages.

overall_design: Gene expression profiling by high throughput sequencing

first: Bolin

first: Biyun

last: Qin

first: Mingjun

last: Li

first: Yuchao

last: Zhu

first: Fuqiang

first: Hao

last: Xu

first: Lilan

last: Xue

first: Yukun

last: Chen

first: Ming

first: Bang

last: Shen