title: Microglia in the rostral ventromedial medulla mediate synaptic pruning via the C1q/C3-CR3 signaling pathway – a mechanism for the chronic orofacial pain

city: Chongqing

first: Cong

address: No. 426 Songshi North Road, Yubei District

department: Anesthesiology

institute: The stomatology hospital affiliated chongqing medical university

summary: The mechanism of chronic orofacial pain was investigated by examining the interaction between activated microglia, C1q and neurons in RVM of rats with orofacial pain caused by temporomandibular joint injection of CFA. The results demonstrated that the pain threshold in CFA group exhibited a continuous decline, reaching its lowest point on the third day. During the modeling process, administered daily stereotactic injections of ANX-005 and minocycline into the RVM, which resulted in a notable recovery in the rats' pain threshold and a significant increase in C1q/C3 and microglia in RVM of CFA rat. The application of ANX-005 or minocycline resulted in a reduction in the expression of C1q/C3 and microglia. Notably, the expression of excitatory presynaptic membrane markers reduced and the length and density of dendritic spines decreased on neurons in RVM. Additionally, C1q was abundantly localized on excitatory presynaptic membranes and expressed in microglial lysosomes. Treatment with ANX-005 or minocycline resulted in a reduced number of immunofluorescence colocalizations and an elevated dendritic spine density. These findings indicate that initial orofacial pain induced by CFA, microglia in RVM are involved in the pruning of excitatory presynaptic membranes through the complement C1q/C3-CR3 signaling pathway. This process results in a reduction in the proportion of excitatory synapses and a disruption in the physiological balance between RVM descending facilitation and descending inhibition. This leads to the predominance of descending facilitation in pain transmission in the RVM, which in turn facilitates the chronification of orofacial pain.

overall_design: RNA sequencing analysis in RVM of CON rats and CFA rats on the third day.

first: Xilu

last: Huang

first: Jie

last: Zeng

first: Zhanwei

last: Hu

first: Yujia

last: Wu

first: Guangyan

last: Zhang

first: Chao

first: Min

last: Song


title: RiboTag RNA Sequencing Identifies Local Translation of HSP70 In Astrocyte Endfeet After Cerebral Ischemia

status: Public on Jan 27 2025

city: Baltimore

first: Prajwal

last: Ciryam

state: MD

address: 670 W. Baltimore St.

country: USA

institute: University of Maryland School of Medicine

type: Expression profiling by high throughput sequencing

summary: Brain ischemia causes disruption in cerebral blood flow and blood–brain barrier integrity, which are normally maintained by astrocyte endfeet. Emerging evidence points to dysregulation of the astrocyte translatome during ischemia, but its effects on the endfoot translatome are unknown. In this study, we aimed to investigate the early effects of ischemia on the astrocyte endfoot translatome in a rodent cerebral ischemia and reperfusion model of stroke. To do so, we immunoprecipitated astrocyte-specific tagged ribosomes (RiboTag IP) from mechanically isolated brain microvessels. In mice subjected to middle cerebral artery occlusion and reperfusion and contralateral controls, we sequenced ribosome-bound RNAs from perivascular astrocyte endfeet and identified 205 genes that were differentially expressed in the endfoot translatome after ischemia. The main biological processes associated with these differentially expressed genes included proteostasis, inflammation, cell cycle/death, and metabolism. Transcription factors whose targets were enriched amongst upregulated translating genes included HSF1, the master regulator of the heat shock response. The most highly upregulated genes in the translatome were HSF1-dependent Hspa1a and Hspa1b, which encode the inducible HSP70. Using qPCR, Western blot, and immunohistochemistry, we confirmed that HSP70 is upregulated in astrocyte endfeet after ischemia. This coincided with an increase in ubiquitination across the proteome that suggests that ischemia induces a disruption in proteostasis in astrocyte endfeet. These findings suggest a robust proteostasis response to proteotoxic stress in the endfoot translatome after ischemia. Modulating proteostasis in endfeet may be a strategy to preserve endfoot function and BBB integrity after ischemic stroke.

overall_design: Astrocyte-specific RiboTag RNA sequencing from 10-12 week old male mice undergoing middle cerebral artery occlusion (2h ischemia, 6 hours reperfusion). Paired contralateral and ipsilateral tissue was obtained from 3 biological replicates.

first: Bosung

last: Shim

first: Cigdem

last: Tosun

first: Riccardo

last: Serra

first: Natalya

last: Tsymbalyuk

first: Kaspar

last: Keledjian

first: Volodymyr

last: Gerzanich

first: J

middle: M

last: Simard


title: A novel conserved transcription factor Mycth_90344 regulates cellulase genes expression through controlling the Hac-1 and Cbh-1 in thermophilic fungus Myceliophthora thermophila

status: Public on Jan 28 2025

city: Tianjin

first: Liu

last: Qian

address: Xi 7 Dao No.32 Airport Economic Area

country: China

institute: TIB CAS

summary: In thermophilic fungi, work on the ER stress and UPR signalling is largely unknown,we here identified a new Cys2His2 transcription factor and found its knockout strain with significantly decreased cellulases production on crystalline cellulose.Here, we show that loss-of-function mutations of this regulator resulted in the reduced expression of Mthac-1 via RNA-seq under Avicel and artificial ER-stress.

sample_organism: Thermothelomyces thermophilus ATCC 42464

overall_design: mRNA profiles of Myceliophthora thermophila cells exposed to 4h Avicel.

first: Qian

last: Liu

first: Defei

first: Chaoguang

last: Tian


title: Analysis of SFTS pathogenesis based on single-cell RNA sequencing of monocytes

city: Hefei

first: Yin

state: Anhui

address: No. 218 Jixi Rd

institute: First Affiliated Hospital of Anhui Medical University

summary: Severe fever with thrombocytopenia syndrome (SFTS) is a newly identified tick-borne viral disease with a high mortality rate. Monocytes are known to play an important role in the pathogenesis of SFTS, but the distinct subpopulations of monocytes associated with the disease progression and their roles in inflammatory responses remain poorly elucidated. In this study, we used single-cell RNA sequencing (scRNA-seq) to explore the specific monocyte subpopulations correlated with the progression of SFTS and their involvement in inflammatory processes.

overall_design: We performed scRNA-seq analysis on isolated monocytes obtained from seven SFTS patients, complemented by flow cytometry for cell identification. Three normal monocyte samples were sourced from public databases for comparative analyses. Bioinformatic tools including Cell Ranger, Seurat, Monocle 2, GSEA, SCENIC, and NicheNet were utilized to identify distinct cell populations and transcriptional patterns.

first: Yuanhong

last: Xu


title: The genome of Pseudotaxus chienii, a relict conifer endemic  to China, provides insights into the origin and evolution of  taxane biosynthesis

city: Hangzhou City

first: M

middle: R

last: Y

address: Hangzhou Normal University, Hangzhou City, Zhejiang Province

institute: Hangzhou Normal University

summary: As a sister genus to Taxus, Pseudotaxus holds significant importance for studying the origin and evolution of the taxane biosynthesis pathway. However, the reference genome of P. chienii, the sole species of Pseudotaxus, is not yet available. We have completed a chromosome-level genome assembly of P. chienii, with a total length of 15.6 Gb. P. chienii possesses only a partial pathway for Taxol biosynthesis, which terminates before the enzyme taxane 2α-O-benzoyl transferase (TBT), a crucial enzyme responsible for the production of 10-deacetylbaccatin III. With the emergence of the Taxus genus, the limitation posed by TBT is overcome, allowing for the extension of the existing taxane biosynthesis pathway into a complete Taxol biosynthesis pathway. Protein structure analysis revealed that the structure of metal ion catalysis sites in taxadiene synthase (TS) is conserved across the Pseudotaxus and Taxus genera, providing potential sites for enhancing TS activity through enzyme engineering. This comparative genomic analysis contributes to our understanding of the origin and evolution of taxane biosynthesis within the Taxaceae family.

overall_design: In this study, we successfully assembled the Pseudotaxus genome and presented a reference-grade genome sequence of P. chienii, which contains 16.79 giga-bases (Gb) of data, 15.45 Gb of which was assigned to 12 pseudochromosomes. Our comparative genomic analysis contributes to our understanding of the origin and evolution of taxane biosynthesis and provides insights into the genome structure and organization of the Taxaceae family.

first: Mingshuang

last: Wang

first: Ruoyun

last: Ma

first: Zijin

last: Fang

first: Lingxiao

first: Yibo

first: Mengyin

last: Zheng

first: Enhui

last: Bai

first: Wanting

last: Lin

first: Yanyan

last: Pei

first: Yue

last: Zang

first: Huijie

first: Shangguo

last: Feng

first: Xiaori

last: Zhan

first: Chunna

last: Yu

first: Shuling

first: Huizhong

first: Chenliang

first: Chenjia

last: Shen


title: Effect of kinsenoside on bone marrow-derived macrophages during acute pancreatitis

city: Shanghai

first: Ruiyan

address: 650 New Songjiang Road

department: Department of Gastroenterology

institute: Shanghai General Hospital

summary: Studies have shown that the small molecular compound kinsenoside (KD) can inhibit the M1 polarization of macrophages and inhibit the expression of proinflammatory genes. However, the role of kinsenoside in acute pancreatitis is unclear. Our study showed that intraperitoneal injection of kinsenoside can alleviate acute pancreatitis in mice. In order to find out the main mechanism by which kinsenoside affects the polarization of macrophages in acute pancreatitis, we further performed transcriptomic analysis of bone marrow-derived macrophages (BMDMs) stimulated by injured pancreatic acinar cell conditioned media (PAC-CM) treated with or without kinsenoside. This work provides a potential therapeutic approach for acute pancreatitis.

overall_design: RNA-seq profiling of bone marrow-derived macrophages stimulated by injured pancreatic acinar cell conditioned media with or without kinsenoside

first: Jing

last: Jiang

first: Pengli

last: Song

first: Qi

last: Peng

first: Xuerui

last: Jin

first: Jianbo

last: Ni

first: Guoyong

last: Hu


title: New insights into the cis-regulation of the CFTR gene in pancreatic cells [4C-seq]

city: BREST

first: Clara

last: Blotas

address: 22 rue Camille Desmoulins

country: France

institute: INSERM 1078

summary: To understand the role of 3D chromatin architecture in establishing tissue-specific expression of the CFTR gene, we mapped chromatin interactions using Circular Chromosome Conformation Capture (4C) and epigenomic data such as H3K27ac and Assay for Transposase-Accessible Chromatin (ATAC-seq) on Capan-1 pancreatic cells.

overall_design: We used 4C to detect chromatin interactions with the promoter of the CFTR gene in Capan-1 cells. Caco-2 and HepG2 cells were used as controls for 4C interaction mapping.

first: Stéphanie

last: Moisan


title: DNA virus infections shape transposable element activity in vitro and in vivo (DUX4 knockout)

city: Freiburg

first: Florian

last: Full

address: Hermann-Herder-Str. 11

country: Germany

institute: institute of Virology, University Medical Center Freiburg

summary: We show strong activation of TEs in the context of DNA virus infection and investigate the molecular mechanisms of how TEs are induced. We demonstrate that herpesvirus infection leads to a robust expression of the MLT and THE1-class of LTR containing retrotransposons as well as a subset of long-interspersed nuclear elements-1 (LINEs), Alu-elements and some HERVs. Mechanistically we demonstrate that this TEs upregulation is induced by two pathways that act synergistically: de-repression of KAP1/TRIM28 mediated by phosphorylation and expression of the pioneer factor double-homeobox 4 (DUX4).

overall_design: RNA-sequencing was performed from DUX4 KO cells upon HSV-1 infection.

first: Jiang

last: Tan

first: Vedran

last: Franke

first: Eva

last: Neugebauer

first: Justine

last: Lagisquet

first: Anna

last: Katharina Kuderna

first: Stephanie

last: Walter

first: Armin

last: Ensser

first: Markus

last: Landthaler

first: Thomas

last: Stamminger

last: Gramberg

first: Altuna

last: Akalin

first: Emanuel

last: Wyler


title: IL-2 Mutein Promotes Antigen-Specific Acceptance of Transplanted Organs by Activating ST2+ Tissue-Resident Regulatory T Cells

city: Boston

first: Leonardo

middle: V.

last: Riella

state: MA

address: 149 13th Street

department: Medicine

institute: Massachusetts General Hospital

summary: Transplantation is the preferred treatment for most patients with end-stage organ disease, but long-term outcomes are hindered by immunosuppressive drug toxicity and immune-mediated injury. Developing therapies that promote immune tolerance while minimizing systemic immunosuppression is essential to improve graft health and survival. Regulatory T cell (Treg)-based therapies offer promise for inducing antigen-specific transplant tolerance, with recombinant IL-2 analogs emerging as potentially effective tools to selectively expand Tregs while minimizing adverse effects. mIL-2 therapy combined with co-stimulation blockade significantly prolonged allograft survival in an antigen-specific manner without adverse events. The immunomodulatory effects of mIL-2 persisted even after treatment cessation at 60 days after transplantation, with sustained graft function and preservation of histopathological integrity. Treatment with mIL-2 increased graft-infiltrating Tregs and decreased effector T cell activation. Donor-specific antibody production was reduced in mIL-2-treated recipients, which correlated with an enhanced follicular regulatory T-cell proportion. These findings were consistent across fully mismatched kidney and haplo-mismatched heart transplant models. Transcriptional profiling revealed the expansion of an ST2-positive, tissue-resident Treg population critical for long-term graft survival. Accordingly, the mIL-2-induced Treg suppression was abrogated in Treg-specific ST2 knockout graft recipients.

overall_design: We investigated the effects of a novel IL-2 mutein molecule (mIL-2) with enhanced receptor specificity and extended half-life in experimental models of solid organ transplantation. Following fully mismatched heart or kidney transplantation (BALB/c to C57BL/6), mIL-2 was administered biweekly with a single dose of CTLA-4 Ig co-stimulation blockade. Graft survival, immune cell phenotyping of graft-infiltrating cells and splenocytes, and donor-specific antibody production were assessed. Mechanistic insights into Treg function were obtained through functional suppression assays and RNA sequencing, while the role of ST2+ Tregs was studied using Treg-specific ST2 knockout mice.

first: Yoshikazu

last: Ganchiku

first: Guilherme

last: T. Ribas

first: Thiago

last: J. Borges

last: V. Riella


title: Genetic network profiles associated with established resistance to ionizing radiation in leukemia cell line HL60

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: Radiation-resistant of acute myeloid leukemia cell present challenges to treatment, and the acquisition of resistance to ionizing radiation (IR) is a matter of clinical concern. However, little information is available on the behavior of radio-resistant leukemia in terms of gene expression profiles and intercellular communication. In this study, mRNA microarray was used to analyze the intracellular genetic network in the established radio-resistant HL60 (Res-HL60) cell line. Significant changes in the expression of 7,309 known mRNAs were observed in Res-HL60 relative to control. In addition, 7 mRNAs were determined as targets because significant changes in the expression were observed using Ingenuity analysis software, confirming the quantitative RT-PCR. However, extracellular vesicles from Res-HL60 cells did not include these target mRNAs. These results suggest that radio-resistant leukemia model is regulated by the expression and suppression of specific mRNAs, and these molecules are not transferred between cells by extracellular vesicles.

overall_design: Human acute myeloid leukemia cell line HL60 was prepared after frequent irradiation (4Gy X-irradiation ×4 fractions per 4 weeks) with confirmed radiation-resistance characteristics.  The extracted total RNA in wild type cell and radiation-resistant cell were performed messenger RNA (mRNA) microarray and calculate the expression of mRNAs.

first: Satoru

last: Monzen

first: Yoichiro

last: Hosokawa


title: New insights into the cis-regulation of the CFTR gene in pancreatic cells [CUT&Run]

first: Clara

last: Blotas

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: We used CUT&RUN with H3K27ac to identify active enhancer regions in Capan-1 cells. We also mapped CTCF, H3K27ac and H3K27me3 binding site in Caco-2 cells.

first: Stéphanie

last: Moisan


title: New insights into the cis-regulation of the CFTR gene in pancreatic cells [ATAC-seq]

overall_design: We used ATAC-seq to map DHS in Capan-1 cells. Caco-2 cells were used as controls.


title: Genetic Variation in Gut Microbes as a Key Regulator of Host Social Behavior

city: Xuzhou

first: Dianshuang

last: Zhou

state: Jiangsu

address: 209 Tongshan Road

institute: Xuzhou Medical University

summary: The gut-brain axis allows gut microbes to influence host social behavior, yet the specific role of microbial genetic variation in this process and its potential transgenerational effects remains poorly understood. Using C. elegans as a model, we identified 77 E. coli strains among 3,983 mutants that markedly enhanced C. elegans aggregation behavior. Our findings reveal that mutant bacteria modulate C. elegans social behavior through distinct neurobehavioral pathways, demonstrating a synergistic regulatory mechanism between microbial genetics and host heredity. Mechanistically, ycgJ mutant bacteria were found to impact C. elegans social behavior via the mitochondrial pathway. Additionally, even F2 offspring of parent C. elegans exposed to these mutant bacteria exhibited enhanced social behavior within their populations. These insights underscore the significance of investigating microbial genetic variation in relation to host behavior, particularly for the development of genetically engineered probiotics, aimed at promoting well-being across generations.

overall_design: C. elegans mRNA profiles of  wild type C. elegans (N2) fed BW25113 and  mutant bacteria

first: Zuobin

last: Zhu

first: Ying

last: Li

first: Ruijie

last: Bai

first: Yao

first: Peng

last: Shi


title: Dual Biological Role and Clinical Impact of De Novo Chromatin Activation in Chronic Lymphocytic Leukemia

city: Barcelona

first: Vicente

last: Chapaprieta

address: C/Rosselló 149-153

country: Spain

institute: IDIBAPS

summary: Previous studies have reported that chronic lymphocytic leukemia (CLL) shows a de novo chromatin activation pattern as compared to normal B cells. Here, we explored whether the level of chromatin activation is related to the clinical behavior of CLL. We identified that in some regulatory regions, increased de novo chromatin activation is linked to clinical progression whereas, in other regions, it is associated with an indolent course. We next developed two prognostic scores for progressive and indolent disease, respectively, calculated a single score representing the balance between them, and further generated surrogate scores based on gene and protein expression of the target genes. The balance score outperformed the clinical impact of the two individual scores, as it seemed to capture the prognostic information provided by each of them. Biologically, CLLs with higher balance score showed increased activation of TNF-α/NF-κB and mTOR signaling pathways. Regulatory programs related to progression were predominantly activated in the lymph node microenvironment, whereas those linked to indolent disease appeared to be microenvironment-independent. Finally, we thoroughly validated the balance score as a powerful and independent quantitative prognostic factor for time to first treatment across independent CLL cohorts and data modalities such as chromatin, transcriptome or proteome data. Our findings support the concept that de novo acquisition of chromatin changes in CLL cells plays a dual biological role, and that the balance between pro-progression and pro-indolence is a strong independent determinant of CLL prognosis.

overall_design: RNA-seq data from lymph node samples collected from five chronic lymphocytic leukemia patients

first: Alba

last: Maiques-Diaz

first: Ferran

last: Nadeu

first: Guillem

last: Clot

first: Ramon

last: Massoni-Badosa

first: Pablo

last: Mozas

first: Judith

last: Mateos-Jáimez

first: Anna

last: Vidal

first: Stella

last: Charalampopoulou

first: Martí

last: Duran-Ferrer

first: Romina

last: Royo

first: Núria

last: Russiñol

first: Laura

last: Llaó-Cid

first: Juan

middle: A

last: Piñeyroa

first: Neus

last: Villamor

first: Holger

last: Heyn

first: Sophie

last: Herbst

first: Junyan

last: Lu

first: Dean

middle: J

last: Bryant

first: Jonathan

middle: C

last: Strefford

first: Sascha

last: Dietrich

first: Thorsten

last: Zenz

first: Julio

last: Delgado

first: Armando

last: López-Guillermo

first: Elias

last: Campo

first: Jose

middle: I

last: Martin-Subero


title: Mouse embryoid body differentiation of wild-type embryonic stem cells

city: San Francisco

first: Carolyn

last: Sangokoya

state: CA

address: 35 Medical Center Way

department: Pathology

institute: UCSF

summary:
This dataset reports mouse embryoid body differentiation of wild-type embryonic stem cells in support of multiple studies.
The coordinated actions of post-transcriptional regulation are essential for stem cell differentiation.

overall_design: To investigate transcriptomic expression within mouse embryoid body differentiation of wild-type mouse embryonic stem cells.


title: Single-cell and spatial transcriptomics of vulvar lichen sclerosus reveal multi- compartmental alterations in gene expression and signaling cross-talk

city: Irvine

first: Christina

last: Kraus

address: 118 Medical Surge 1

department: Dermatology

institute: University of California, Irvine

summary: Vulvar diseases are a critical but often overlooked issue in women's health, impacting many women and frequently causing long-term physical and emotional challenges. Lichen sclerosus (LS) is a chronic inflammatory skin disease that causes scarring of the vulva and is associated with an increased risk of malignancy. The molecular pathogenesis of vulvar LS (VLS) is not well understood, preventing development of any FDA-approved therapies. Here, we utilize single-cell and spatial transcriptomics to analyze lesional and non-lesional skin from VLS patients, as well as healthy control vulvar skin. Our studies, which reveal histologic, cellular, and molecular heterogeneities within VLS, also identify unifying molecular changes across fibroblasts, immune cells, keratinocytes, and melanocytes in lesional skin. The findings depict a scenario of cellular stress and damage affecting both fibroblasts and keratinocytes, along with a complex immune landscape indicating enhanced CD8+ T cell cytotoxicity but also signs of exhaustion. They further suggest aberrant cell-cell signaling across, and increased activation of IFN, JAK/STAT, and p53 pathways in specific cell types. Using monolayer and organotypic culture models, we demonstrate that the depletion of select genes, which are downregulated in VLS lesional skin keratinocytes, partially recapitulates VLS-like stress-associated changes. Collectively, these data provide novel insights into the pathogenesis of VLS, identifying potential biomarkers and therapeutic targets for future research.

overall_design: We performed scRNA-seq on patient-matched LE and NL vulvar skin samples collected from punch biopsies of patients with biopsy-proven VLS, using the 10x Genomics Chromium platform.

first: Peng

last: Sun

first: Wei

last: Zhao

first: Quy

last: Nguyen

first: Arjun

last: Nair

first: Melanie

last: Oakes

first: Qing

last: Nie

first: Xing

last: Dai


title: The effects of Erastin on the proliferation of Staphylococcus aureus in mouse macrophages

city: 绵阳

first: Anlong

last: Li

state: 四川

address: 四川省绵阳市涪城区教育中路1号

institute: 四川中医药高等专科学校

type: Non-coding RNA profiling by high throughput sequencing

summary: This study mainly explores the effects of Erastin on the proliferation of Staphylococcus aureus in mouse macrophages and seeks potential host-directed therapeutic targets for S. aureus. High-throughput sequencing technology was used to detect the expression of mRNAs and microRNAs in mouse macrophages infected with S. aureus after being treated with Erastin. The differentially expressed genes and miRNAs were ultimately selected for further scientific research.

overall_design: Erastin (20 μM) was applied to infected macrophages for 6 hours, followed by total RNA extraction and high-throughput sequencing.

first: Jiajia

last: Bao

first: Lili

last: Wang


title: Single-cell and spatial transcriptomics of vulvar lichen sclerosus reveal multi-compartmental alterations in gene expression and signaling cross-talk

address: 825 Health Sciences Road

department: Biological Chemistry

institute: UC Irvine

summary: Vulvar diseases are a critical but often overlooked issue in women's health, impacting many women and frequently causing long-term physical and emotional challenges. Lichen sclerosus (LS) is a chronic inflammatory skin disease that causes scarring of the vulva and is associated with an increased risk of malignancy. The molecular pathogenesis of vulvar LS (VLS) is not well understood, preventing development of any FDA-approved therapies. Here, we utilize single-cell and spatial transcriptomics to analyze lesional and non-lesional skin from VLS patients, as well as healthy control vulvar skin. Our studies, which reveal histologic, cellular, and molecular heterogeneities within VLS, also identify unifying molecular changes across fibroblasts, immune cells, keratinocytes, and melanocytes in lesional skin. The findings depict a scenario of cellular stress and damage affecting both fibroblasts and keratinocytes, along with a complex immune landscape indicating enhanced CD8+ T cell cytotoxicity but also signs of exhaustion. They further suggest aberrant cell-cell signaling across, and increased activation of IFN, JAK/STAT and p53 pathways in, specific cell types. Using monolayer and organotypic culture models, we demonstrate that the depletion of select genes, which are downregulated in VLS lesional skin keratinocytes, partially recapitulates VLS-like stress-associated changes. Collectively, these data provide novel insights into the pathogenesis of VLS, identifying potential biomarkers and therapeutic targets for future research.

overall_design: We performed siRNA knockdown of ATF3, APOE, and CXCL14 in N/TERT-2G keratinocytes and bulk RNA-seq analysis.

first: Jiahui

last: Xu


title: 3D Intercellular Assembly of Decellularized Matrix  Recapitulates In Vivo Tumor Heterogeneity

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

summary: The tumor microenvironment consists of resident tumor cells organized within a compositionally diverse, three-dimensional (3D) extracellular matrix (ECM) network that cannot be replicated in vitro using bottom-up synthesis. We report a new self-assembly system to engineer ECM-rich 3D MatriSpheres wherein tumor cells actively organize and concentrate microgram quantities of decellularized ECM dispersions which modulate cell phenotype. 3D colorectal cancer (CRC) MatriSpheres were created using decellularized small intestine submucosa (SIS) as an orthotopic ECM source that had greater proteomic homology to CRC tumor ECM than traditional ECM formulations such as Matrigel. SIS ECM was rapidly concentrated from its environment and assembled into ECM-rich 3D stroma-like regions by mouse and human CRC cell lines within 4-5 days via a mechanism that was rheologically distinct from bulk hydrogel formation. Both ECM organization and transcriptional regulation by 3D ECM cues affected programs of malignancy, lipid metabolism, and immunoregulation that corresponded with an in vivo MC38 tumor cell subpopulation identified via single cell RNA sequencing. This 3D modeling approach stimulates tumor specific tissue morphogenesis that incorporates the complexities of both cancer cell and ECM compartments in a scalable, spontaneous assembly process that may further facilitate precision medicine.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: MatriSpheres (SIS ECM) and traditional cells alone spheroids (CA) (n = 5-6/group) generated from mouse (MC38, CT26) and human (HT-29) colorectal cell lines and cultured for 7 days. RNA was isolated at day 7 and sent for Bulk RNA Sequencing. The intercellular role of the ECM biomaterial (decellularized SIS ECM) on cancer cells within the 3D MatriSpheres were evaluated based upon their transcriptome profiles when compared to traditional cells alone spheroids.

first: Michael

last: Buckenmeyer

first: Elizabeth

last: Brooks

first: Madison

middle: S

last: Taylor

first: Liping

last: Yang

first: Ronald

last: Holewinski

first: Melissa

last: Galloux

first: Marcial

last: Garmendia-Cedillos

last: Pohida

first: Thorkell

last: Andresson

first: Brad

last: St Croix

first: Matthew

middle: T

last: Wolf


title: Cardiac differentiation roadmap for analysis of plasticity and balanced lineage commitment

city: Nijmegen

first: Rebecca

middle: Regina

last: Snabel

state: Gelderland

address: Geert Grooteplein 26-28

department: Molecular Developmental Biology

country: Netherlands

institute: RIMLS

summary: Stem cell-based models of human heart tissue and cardiac differentiation employ monolayer and 3D organoid cultures with different properties, cell type composition, and maturity. Here we show how cardiac monolayer, embryoid body, and engineered heart tissue trajectories compare in a single-cell roadmap of atrial and ventricular differentiation conditions. Using a multiomic approach and gene-regulatory network inference, we identified regulators of the epicardial, atrial and ventricular cardiomyocyte lineages. We identified ZNF711 as a regulatory switch and safeguard for cardiomyocyte commitment. We show that ZNF711 ablation prevents cardiomyocyte differentiation in the absence of retinoic acid, causing progenitors to be diverted more prominently to epicardial and other lineages. Retinoic acid rescues this shift in lineage commitment and promotes atrial cardiomyocyte differentiation by regulation of shared and complementary target genes, showing an interplay between ZNF711 and retinoic acid in cardiac lineage commitment.

overall_design:
RNA-seq experiments used to build an integrated scRoadmap of in vitro cardiac differentiation.
Embryoid Body (EB) cardiomyocyte differentiation cultures of different KOs.

first: Carla

last: Cofiño-Fabrés

first: Marijke

last: Baltissen

first: Verena

last: Schwach

first: Robert

last: Passier

first: Gert-Jan

last: Veenstra


title: The PHR2-DGP1 Signaling Integrates Carbon and Nitrogen Assimilatory Metabolisms under Phosphorus Deficiency Stress in Rice Plants [ChIP-Seq]

city: Yangzhou

first: Mingnan

last: Qu

address: Pazhou Dadao Rd, 17-19

institute: Yangzhou Univerisity

summary: Carbon (C), nitrogen (N) and phosphorus (Pi) are crucial macronutrients for plants. While substantial knowledge exists on C/N balance signaling physiological and molecular perspectives, the core regulatory mechanism governing C/N and Pi balance remains largely unexplored. This study reveals that C/N assimilatory metabolisms matching the Pi-deficiency stress is integrated by a DEEP GREEN PANICLE1 (DGP1)-mediated regulatory network in rice (Oryza sativa). We found that low-Pi stress triggers DGP1 expression in a dose-responsive manner, facilitated by the PHOSPHATE STARVATION RESPONSE REGULATOR (PHR2). Intriguingly, DGP1 interacts with transcription factors (GLK1 and GLK2) and mitochondrial factors (GDCH and QCR9), modulating their roles in photosynthetic gene expression, the glycine cleavage system and the mitochondrial electron transport chain (mETC), respectively. Additionally, DGP1 influences aminoacyl-tRNA synthetases and ribosomal subunits, impacting protein biosynthesis, and intervenes in various metabolic pathways, including glycolysis and the citrate cycle. Phenotypically, we observed that under short-term Pi-deficiency, wild-type plants exhibit compromised photosynthesis, photorespiration and mETC-driven ATP synthesis, whereas dgp1 and phr2 mutants display reduced sensitivity to these conditions. Conversely, DGP1 overexpressors show decreased yield under normal conditions due to altered cell metabolomes and protein biosynthesis inadequacy, despite unaffected 15NO3– uptake and transport. In conclusion, the PHR2-DGP1 module orchestrates a comprehensive signaling network, harmonizing C and N metabolic fluxes under Pi limitation through coordinated interactions among cytoplast, chloroplast and mitochondria.

overall_design: ChIP-seq assay of the combined GLK1 and GLK2 binding signals in the leaves of phr2 mutant under normal condition or after Pi-deficiency stress.

first: Zhan

last: Xu

first: Mengmeng

last: Hou

first: Jemaa

last: Essemine

first: Peng

last: Wang


title: Age-dependent differences in the tumor microenvironment of preclinical models of triple-negative breast cancer: challenges and opportunities for efficacy studies.

city: Vienna

first: Stephan

last: Gruener

address: Borschkegasse 8a

department: Center for Cancer Research

country: Austria

institute: Medical University of Vienna

summary: The immune system orchestra suffer a deficit of function during aging, and the incidence of most cancer types is significantly increased in elderly humans. Although breast cancer (BC) can occur in young women, it is way more common in middle-age and elderly women. There is evidence that a tonic immune system is pivotal for the success of therapies aimed at awakening a dormant or exhausted immunological response against cancer cells by mean of checkpoint inhibitors (CI). However, current cancer models in rodents use very young mice of a few weeks of age, which have a fully functional and tonic immune system and thymus, and thus might be poorly representative of adult human cancer patients. We have recently reported that that a triple therapy (TT) involving antigen-presenting cell activation by vinca alkaloids and the generation of new TCF1+ stem cell-like T cell (scT) clones by an alkylating agent can significantly improve the efficacy of the CI anti-PD-1 in models of cancer known to be otherwise CI-resistant such as TNBC and lymphoma (PMIDs: 33268528, 37048617). TT effect was due to T cells, as it was abrogated by their in vivo depletion. In the present study we investigated differences in TNBC growth kinetics, TT preclinical activity and tumor microenvironment (TME, including intratumoral immune and stroma cells) in young (6-8w, representative of a 6y old human) versus adult (12m, representative of 40y humans) mice. Models included 4T1 and EMT6 TNBC cells, the former generating a mostly lymphoid TME and the latter generating a mostly myeloid TME (PMID: 33268528). In both models, TT efficacy was similar in young and in adult mice, as the treatment abrogated TNBC local and metastatic growth. CD8+ (but not CD4+) scTs, likely crucial players in TT efficacy, were only slightly reduced in adult mice despite age-related thymus involution. This notwithstanding, single-cell transcriptomics, IHC and flow cytometry analyses of immune (CD45+EPCAM-) and stroma (CD45-EPCAM-) cell populations indicated major differences in the TME of young vs adult mice. Adults had significantly less CD4+ scTs, B naïve and NK cells and significantly increased memory B cells. Cancer-associated fibroblasts with a matrix deposition signature (matrix CAF) were skewed in young, while pro-inflammatory stromal populations and myofibroblasts were skewed in adults. Matrix CAFs down regulated a signature involved in different ECM-remodeling abilities, and up regulated metabolic and hypoxic pathways. Expression of genes encoding for glycoproteins, basement membrane components, and collagens were also upregulated. Our data indicate profound differences between young and adult mice TMEs that should be taken into consideration when selecting the age of orthotopic immune competent mice to be used in preclinical efficacy studies.

overall_design: Single-cell RNA-seq of FACS-sorted cancer and TME cells from xenografts obtained from 4T1 cell lines, captured using 10x Chromium and subjected to high-throughput sequencing.

first: P

last: Falvo

first: S

last: Orecchioni

first: F

last: Pisati

first: G

last: Talarico

last: Mitola

first: D

last: Lombardi

last: Bravetti

first: J

last: Winkler

first: I

last: Barozzi

last: Bertolini


title: Gene expression of Aif-1 knock out and wild type mice-kidney macrophages after ischemic injury

city: DURHAM

first: Irma

last: Husain

state: North Carolina

address: 2 Genome Ct, MSRBII, Rm 2019

department: Medicine (Nephrology)

institute: Duke University Hospital

summary:
RNA was isolted from immunomagnetically sorted macrophages from kidneys of mice 4 day after 30 minutes of IRI, 100ng of Rna per sample was used for Nanostring hybridization
Gene expression was measured using nCounter Mouse Myeloid Innnate Immunity V2 Panel

overall_design: Macrophages from 3 mice each from both KO and WT mice kidneys were processed. Contralateral right kidney from each mouse served as its own respective control.

first: Xunrong

last: Luo


title: Modeling human limb skeletal development using human pluripotent stem cell-derived skeletal assembloids [scRNA-seq]

status: Public on Jan 26 2025

city: Okayama

first: Takeshi

last: Takarada

institute: Okayama University

summary: Despite recent advances in pluripotent stem cell-based approaches to induce skeletal cells, recapitulating human limb skeletal development in terms of structure and longitudinally oriented growth remains an unresolved challenge. Here, we report a method to differentiate human pluripotent stem cells into region-specific skeletal organoids harboring GDF5+PRG4+ interzone/articular chondrocyte　progenitors (IZ/ACPs) and SP7+ growth plate chondrocytes (GPCs) via PRRX1⁺ limb-bud mesenchymal cells. Comparative analysis demonstrated marked similarities of IZ/ACP and GPC organoids to the human embryonic limb, and graft fate and regenerative capacity in vivo were further characterized. We also mimicked the limb skeletal developmental process in a spatially structured manner by vertically positioning two IZ/ACP organoids at both ends of a GPC organoid to generate a human skeletal assembloid. Notably, this human skeletal assembloid recapitulated endochondral ossification with longitudinal skeletal growth upon transplantation. In summary, our study provides a novel research platform for human limb skeletal development and disease.

overall_design: induced cells: ExpLBM, Organoid:IZ/ACP and GPC organoids. Assembloid:assembloid after transplantation, each sample is N=1


title: Identification of phthalate mixture exposure targets in the human and mouse ovary in vitro

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary: Chemical health risk assessment is based on single chemicals, but humans and wildlife are exposed to extensive mixtures of industrial substances and pharmaceuticals. Such exposures are life-long and correlate with multiple morbidities, including infertility. How combinatorial effects of chemicals should be handled in hazard characterization and risk assessment are open questions. Further, test systems are missing for several relevant health outcomes including reproductive health and fertility in women. Here, our aim was to screen multiple ovarian cell models for phthalate induced effects to identify biomarkers of exposure.  We used an epidemiological cohort study to define different phthalate mixtures for in vitro testing. The mixtures were then tested in five cell models representing ovarian granulosa or stromal cells, namely COV434, KGN, primary human granulosa cells, primary mouse granulosa cells, and primary human ovarian stromal cells. Exposures at epidemiologically relevant exposure level did not markedly elicit cytotoxicity or affect steroidogenesis in short 24-hour exposure. However, significant effects on gene expression were discovered by RNA-sequencing. Altogether, the exposures changed the average expression of 124 genes (9-479 genes per exposure) in human cell models, without obvious concentration or mixture-dependent effects on gene numbers. The mixtures stimulated distinct changes in different cell models. Despite differences, our analyses suggest commonalities in responses towards phthalates, which forms a starting point for follow-up studies on identification and validation of candidate biomarkers that could be developed to novel assays for regulatory testing or even into clinical tests.

overall_design: Samples from five different cell models (COV434 (three passages), KGN (three passages), primary human granulosa cells (three patients), primary human stromal cells (three patients) and primary mouse granulosa cells (four animals)), with nine different treatments in total (DMSO, WQS-m 1x, WQS-m 100x, EPIDEM 1x, EPIDEM 100x, EQUI 1x, EQUI 100x, MEHHP 1x and MEHHP 100x)

first: Pauliina

last: Damdimopoulou


title: Modeling human limb skeletal development using human pluripotent stem cell-derived skeletal assembloids [bulkRNA-seq]

overall_design: induced cells:  Organoid:IZ/ACP and GPC organoids. each sample are duplicate.


title: Modeling human limb skeletal development using human pluripotent stem cell-derived skeletal assembloids [ATAC-seq]

overall_design: cells: hiPSC, LPM, LBM, ExpLBM, GPC organoids from hiPSCs (no TP), IZ/ACP organoids from hiPSCs (no TP).  ExpLBM and GPC organoids from hiPSCs (no TP)are triplicate. Other samples are each duplicate.


title: Single-oocyte mRNA sequencing reveals that AMH-overexpression alters oocyte gene expression

city: Dunedin

first: Michael

last: Pankhurst

state: Otago

address: 270 Great King St

department: Department of Anatomy

country: New Zealand

institute: University of Otago

summary: Research Question: Does over-expression of AMH lead to changes in oocyte gene expression in mice? Design: Naturally ovulated oocytes were dissected from the oviduct of wild-type, and AMH-overexpressing (Thy1.2-AMHTg/0) mice and single oocytes underwent transcriptome sequencing (n=11 and n=10, respectively). Results: Oocytes from Thy1.2-AMHTg/0 females displayed 39 significantly expressed differentially expressed genes (DEGs) compared to wild-type mouse oocytes. The most prominent gene expression changes were a 70-fold increase in Rpsa3a, a 22-fold increase in Hormad1 and a 5.6-fold increases in Fnip2 in the oocytes from Thy1.2-AMHTg/0 mice. Gene ontology analysis indicated that among the DEGs, the most enriched pathways were mitochondrial genes and DNA repair genes. Conclusions: These data show that overexpression of AMH, through its actions on granulosa cells, can lead to changes in the expression of specific genes in mouse oocytes.

overall_design: RNA-seq profiling of individual, naturally ovulated oocytes obtained from either wild-type or Thy1.2-AMHTg/0 (AMH-overexpressing) female mice.

first: Timothy

last: Hore

middle: W


title: DNA topological regulation by topoisomerase IIβ-DNA-PK interaction is important for controlled hypoxia-inducible gene expression [RNA-Seq]

city: Cheonan

first: Jihye

last: Park

address: 119 Dan-daero, Dongnam-gu

country: South Korea

institute: Dankook University

summary: Hypoxic stress responses are crucial for cellular and organismal survival and provoke gene regulation in diverse biological pathways including cell cycle progression and energy metabolism. Here, we identified that topoisomerase IIβ (TOP2B) regulates DNA topology and transcription in hypoxiainducible genes (HIGs) in a DNA-PK-dependent manner. Cellular, mutational, and genomic analyses showed antagonistic relation between TOP2B and DNA-PK. TOP2B associates with HIGs and represses transcription by suppressing negative supercoiling formation under normoxic conditions.Under hypoxia, TOP2B is released, whereas DNA-PK and HIF1a are recruited to and activate HIGs.

overall_design: Transcriptomic profiling analysis of WT and DNA-PK KO cells with or without CoCl2-induced hypoxic stress (200 µM CoCl2 supplemented for 12 h)

first: Heeyoun

last: Bunch

first: Minseok

last: Seu

first: Jasmin

middle: K

last: Farmakes

first: Jeongho

last: Lee

first: Huiming

last: Lu

first: Ji-Seung

last: Yoo

first: Caroline

last: Austin

first: Young

last: Yoon

first: Jae-Han

last: Jeon

first: Anthony

last: Davis

first: Matthew

last: Schellenberg

first: Stuart

last: Calderwood

first: Keunsoo

last: Kang


title: DNA topological regulation by topoisomerase IIβ-DNA-PK interaction is important for controlled hypoxia-inducible gene expression [TMP-seq]

summary: Hypoxic stress responses are crucial for cellular and organismal survival and provoke gene regulation in diverse biological pathways including cell cycle progression and energy metabolism. Here, we identified that topoisomerase IIβ (TOP2B) regulates DNA topology and transcription in hypoxiainducible genes (HIGs) in a DNA-PK-dependent manner. Cellular, mutational, and genomic analyses showed antagonistic relation between TOP2B and DNA-PK. TOP2B associates with HIGs and represses transcription by suppressing negative supercoiling formation under normoxic conditions.Under hypoxia, TOP2B is released, whereas DNA-PK and HIF1a are recruited to and activate HIGs.Intriguingly, DNA-PK is responsible for TOP2B to be repressive because DNA-PK knockout overturns both TOP2B activity and release and increases the expression of a number of HIGs. Mutational and genomic analyses confirmed that DNA-PK phosphorylates TOP2B at T1403 to stimulate TOP2B catalysis for DNA topological relaxation, which is important for controlled HIG transcription. Collectively, our findings suggest a novel role of TOP2B and DNA-PK-mediated TOP2B regulation as important transcriptional elements in HIG expression. We propose that TOP2B catalysis modulated by protein phosphorylation is coordinated with transcriptional activation and determines DNA topology to stimulate Pol II transcription in response to hypoxic stresses.

overall_design: TMP-seq data from SH-SY5Y cells were generated. The samples consist of wild-type (WT), TOP2B knockout (KO), and TOP2B mutant-expressing SH-SY5Y cells, with and without CoCl2-induced hypoxic stress. Each condition was prepared in biological triplicates to ensure reproducibility and reliability.


title: Transcriptome comparison of Arabidopsis and rice responses to fungal infection under different Fe availability periods.

city: Cerdanyola del Vallès

first: ANTONI

last: GARCIA-MOLINA

state: Barcelona

address: Campus UAB - CRAG Building

department: Plant Development and Signal Transduction

institute: Centre for Research in Agrigenomics

summary: Iron (Fe) is an essential nutrient for virtually all plants that modulate immune responses. However, whereas low and high Fe availalbility confers susceptibility to the fungus Colletotrichum higgisianum, the same conditions lead to rice tolerance to Magnaporthe oryzae. To better understand the systemic responses behind this antagonistic pattern, transcriptome profiling on  fungal infected Arabidopsis and rice plants has been conducted. To consider the signaling component and avoid the interference of tissues experiencing necrosis, samples were conducted on aerial tissues 48h post-infection, when both pathogens remain in the biotrophic phase. Collectively, our data support that Arabidopsis employs a defence strategy based on glucosinolates and other secondary metabolites, whereas rice uses oxidative stress based mechanisms. A different usage of Fe pools during infection is also proposed.

sample_organism:
Arabidopsis thaliana
Oryza sativa Japonica Group

overall_design: Arabidopsis thaliana and Oryza sativa japonica were cultivated on semi-hydroponic conditions irrigated with 1/10 Hoagland media adapted for low (20 µM Fe-EDTA, -Fe), sufficient (20 µM Fe-EDTA, suf) and high (20 µM Fe-EDTA, +Fe) iron availability. Plants were either mock treated or infected by spraying with Colletotrichum higgisianum (Arabidopsis) or Magnaporthe oryzae (rice) suspensions at 10^6 and 10^5 spores/mL, respectively. Shoot samples were harvested 48h post-infection and used for RNA-Seq profiling.

first: Antoni

last: Garcia-Molina


title: VRN2-PRC2 facilitates light-triggered repression of PIF signaling to coordinate growth in Arabidopsis

city: Birmingham

first: Rory

last: Osborne

address: Edgbaston

country: United Kingdom

institute: University of Birmingham

summary: To identify putative targets of the Polycomb protein VERNALIZATION2 (VRN2) we performed mRNA sequencing in arabidopsis seedlings and rosettes. We then performed comparative H3K27me3 ChIP sequencing between Col-0 and vrn2 seedings. We then performed protein ChIP sequencing on VRN2-YFP expressing seedlings

overall_design: Comparative gene expression profiling analysis of RNA-seq data from Arabidopsis thaliana (Col-0, vrn2-5, prt6-1, vrn2-5prt6-1, pif4-2, vrn2-5pif4-2). H3K27me3 (in Col-0 and vrn2-5) and VRN2-YFP ChIP sequencing data to identify direct binding targets of the Polycomb repressive complex 2


title: Differential gene expression analysis in French bulldog high grade

city: Saint Paul

first: Susan

last: Arnold

state: MN

address: 1352 Boyd Avenue

department: Veterinary Clinical Sciences

institute: University of Minnesota

summary: Several canine breeds, including boxers, Boston terriers, and French bulldogs, belong to the same phylogenetic clade and have a higher risk for high-grade oligodendroglioma (HGO) than the general canine population. Despite their shared increased risk for HGO, French bulldogs treated with immunotherapy have experienced worse survival outcomes compared to boxers and Boston terriers. Given the narrow genetic pools of purebred dogs, we hypothesized that the French bulldog HGO transcriptome differs from those of boxers and Boston terriers, which may account for the disparity in survival. We performed RNA sequencing on formalin-fixed, paraffin-embedded tissue from French bulldogs, boxers, and Boston terriers to determine differentially expressed genes (DEGs) between French bulldogs and the other evaluated breeds. We identified 31 DEGs in HGO samples from French bulldogs compared to boxers and Boston terriers. Gene set enrichment analysis revealed activated enrichment of 15 cell cycle progression, oncogene, and immune pathways, including E2F targets, mTOR signaling, IL2-STAT 5 signaling, and allograft rejection. These data confirm the presence of breed- specific canine HGO transcriptomes that can be used to advance our understanding of canine glioma, its translational capacity for human glioma, and precision-based therapies for individual canine patients.

overall_design: Samples included in this study are surgically resected canine high grade glioma samples that were subjected to bulk RNA sequencing.

first: Juan

middle: E

last: Abrahante

first: Jonah

last: Cullen

first: Eva

last: Furrow

first: Walter

last: Low

first: Elizabeth

middle: G

last: Pluhar


title: single cell RNA-seq data for MOC1 tumors

city: Madison

first: Scot

middle: Carson

last: Callahan

state: WI

address: 600 highland ave

institute: UW Health

summary: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, with 5-year survival of ~50%. Genomic profiling studies have identified important somatic mutations in this disease which presents an opportunity for precision medicine. We demonstrate that KMT2D, a histone methyltransferase harbors somatic mutations in ~17% of HNSCC and is associated with 2-year recurrence in TCGA data. Consistent with algorithmic prediction of bring a driver tumor-suppressor event, its loss results in larger oral tumors in immune-proficient orthotopic models. Mechanistically, we find that KMT2D knockdown or KMT2D mutation causes loss of H3K4me1-marked enhancers harboring IRF7/9 binding sites, which is known to regulate interferon signaling. Indeed, KMT2D loss in human and murine cell lines deregulated transcriptional levels of cytokine expression and impacted numerous immune signaling pathways, including interferon signaling. Consistently, Kmt2d knockdown in murine tumors exhibited decrease in IFN-producing effector T cells and an increase in T-cells with an exhausted phenotype. Epistasis experiments showed that exogenous treatment with IFN abrogated the increased tumor growth in Kmt2d-deficient oral tumors. Together, these results support the role of KMT2D as a tumor suppressor in HNSCC that regulates the tumor microenvironment by modulating H3K4me1-marked enhancers controlling interferon signaling.

overall_design: Please note that the mixed sample represents 4 samples, 2 each (rep1 and rep2) of control (MOC1 shNT with doxycycline) and Kmt2d knockdown (MOC1 shKmt2d with doxycycline).

first: S

first: Kunal

last: Rai


title: RNA sequencing analysis of genes related to manganese toxicity in Vibrio parahaemolyticus

status: Public on Jan 25 2025

first: Yu

last: Zhang

address: No. 48, Wenhui East Road

institute: Yangzhou University

summary: RNA sequencing analysis was used to compare the transcriptome of the wild strains under normal conditions and manganese stress conditions. The data showed that some genes, such as mneA and terC, were significantly differentially expressed under manganese stress.

overall_design: The transcription profiles of wild type strains incubated under H2O and 1 mM Mn2 + conditions were compared. Three biological replicates were set for each condition.

first: Chengkun

last: Zheng

first: Xiaoya

last: Zhu

first: Furong

last: Ma


title: Identification of insertion sites for the integrative and conjugative element Tn916 in the Bacillus subtilis chromosome

city: Cambridge

first: Alan

middle: D

last: Grossman

address: 31 Ames St.

department: Biology

institute: Massachusetts Institute of Technology

summary: Integrative and conjugative elements (ICEs) are found in many bacterial species and are mediators of horizontal gene transfer. Tn916, an ICE found in several Gram-positive species, can integrate into many sites in the host chromosome, in contrast to the many ICEs that preferentially integrate into a single site. The consensus integration motif for Tn916, based on analyses of approximately 200 independent insertions, is an ~16 bp AT-rich sequence. Here, we describe the identification and mapping of approximately 105 independent Tn916 insertions in the Bacillus subtilis chromosome. The insertions were distributed between 1554 chromosomal sites, and approximately 99% of the insertions were in 303 sites and 65% were in only ten sites. One region, between ykuC and ykyB (kre), was a 'hot spot' for integration with ~22% of the insertions in that single location. In almost all of the top 99% of sites, Tn916 was found with similar frequencies in both orientations relative to the chromosome and relative to the direction of transcription, with a few notable exceptions. Using the sequences of all insertion regions, we determined a consensus motif which is similar to that previously identified for Clostridium difficile. The insertion sites are largely AT-rich, and some sites overlap with regions bound by the nucleoid-associated protein Rok, a functional analog of H-NS of Gram-negative bacteria. Rok functions as a negative regulator of at least some horizontally acquired genes. We found that the presence or absence of Rok had little or no effect on insertion site specificity of Tn916.

overall_design: Transposon-Directed Insertion Site (TraDIS) sequencing pipeline was used to sequence a library of Tn916-chromosome junctions

first: Emily

middle: L

last: Bean

first: Janet

last: Smith


title: Measuring the effect of ROCK inhibition on microtubule destabilization response

city: Boston

first: Lillian

middle: Jessica

last: Horin

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

summary: In this study, we sought to measure what changes cells experienced upon microtubule destabilization after inhibiting Rho effector: ROCK. We used human pulmonary microvascular endothelial cells (HPMECs) as a model to measure cell response to microtubule depolymerization in a sensitive cell type.

overall_design: RNA-seq profiling of primary human pulmonary microvascular endothelial cells (HPMECs). First, cells were pre-treated with 10 uM Y-27632 (ROCK inhibitor, hereafter labeled ROCKi) for 1 hour. Following pre-treatment, cells were treated with either 0.1% DMSO or 100 nM vinblastine for 6 hours. Cells from three donors were purchased from PromoCell. Donor identification between the metadata and data file names corresponds as follows: donor 1 = donor 1, donor 2 = donor 4, donor 3 = donor 6.

first: Timothy

last: Mitchison


title: Measuring the effect of pan-Rho inhibition on microtubule destabilization response

summary: In this study, we sought to measure what changes cells experienced upon microtubule destabilization after inhibiting Rho GTPases. We used human pulmonary microvascular endothelial cells (HPMECs) as a model to measure cell response to microtubule depolymerization in a sensitive cell type.

overall_design: RNA-seq profiling of primary human pulmonary microvascular endothelial cells (HPMECs). First, cells were pre-treated with 1 µg/ml cell-permeable C3 transferase (Rho inhibitor, hereafter labeled RHOi) for 4 hours. Following pre-treatment, cells were treated with either 0.1% DMSO or 100 nM vinblastine for 6 hours, while concurrently adding an additional 0.5 µg/ml C3 transferase (RHOi) booster dose. Cells from three donors were purchased from PromoCell. Donor identification between the metadata and data file names corresponds as follows: donor 1 = donor 1, donor 2 = donor 4, donor 3 = donor 6.


title: The PHR2-DGP1 Signaling Integrates Carbon and Nitrogen Assimilatory Metabolisms under Phosphorus Deficiency Stress in Rice Plants [RNA-seq]

first: Mingnan

last: Qu

overall_design: RNA-seq assay in the leaves of dgp1 and phr2 mutants and WT ZH11 under normal condition or after Pi-deficiency stress.

first: Zhan

last: Xu

first: Mengmeng

last: Hou

first: Jemaa

last: Essemine

first: Peng

last: Wang


title: Time lapse RNA-Seq of UIR kidney in mice

city: Nanjing

first: Mengqiu

last: Wu

address: Children’s Hospital of Nanjing Medical University

summary: Unilateral kidney ischemia-reperfusion(UIR) surgery was induced，kidney  were harvested at 3 time points  and RNA-Seq were performed.

overall_design: UIR surgery was induced as described in the previous section (n = 3 in each group). Sham treated mice served as controls. Mice were sacrificed at 1 day, 3 days and 21 days after surgery. Kidney tissues were harvested and perform RNA-Seq.

first: Weiyi

last: Chen

first: Mi

last: Bai


title: Gene expression of combretastatin A4 on quiescent retinal pigment epithelial cells

summary: In this study, we seek to measure the effect that 6 hours of treatment with combretastatin A4 has on an immortalized cell line, quiescent hTert retinal pigment epithelial cells (RPE1s). The ultimate goal of this data set is to compare it to the corresponding human primary cell data set to find overlap in response.

overall_design: RNA-seq profiling of three replicates of quiescent hTert retinal pigment epithelial cells (RPE1s) treated with either 0.1% DMSO or 100 nM combretastatin A4 for 6 hours. RPE1s were made quiescent by cultivation at 100% confluency for 5 days before treatment.


title: Comparative profile of microtubule destabilizers, a microtubule stabilizer, and TNF-α in human pulmonary microvascular endothelial cells

summary: This study is a comparative analysis to examine whether there are significant gene expression changes after 6 hours of treatment with three diverse microtubule destabilizers: combretastation A4 (CA4), vinblastine (VB), and plinabulin (PL). Other comparators include baseline control DMSO, microtubule destabilizer docetaxel (DTXL), and inflammatory cytokine TNF-α. We use primary human pulmonary microvascular endothelial cells as a model for a cell sensitive to microtubule perturbations.

overall_design: RNA-seq profiling of primary human pulmonary microvascular endothelial cells (HPMECs) treated for 6 hours with either 0.1% DMSO, 1 ng/ml TNF-α, 100 nM combretastatin A4, 100 nM vinblastine, 100 nM plinabulin, or 100 nM docetaxel. Cells from three donors were purchased from PromoCell. Donor identification between the metadata and data file names corresponds as follows: donor 1 = donor 1, donor 2 = donor 4, donor 3 = donor 6.


title: Triple-Negative Breast Cancer Shapes the Systemic Immune Landscape and Alters Neutrophil Functionality [bulkRNA-seq]

city: Amsterdam

first: Iris

last: de Rink

address: Plesmanlaan 121

institute: NKI

summary: Cancer dysregulates intratumoral innate-adaptive immune cell crosstalk, but it remains largely unknown how the systemic immune landscape is modified during breast cancer progression. Here, we comprehensively profiled the circulating immune profile of patients with stage I-III or stage IV triple-negative breast cancer (TNBC) and healthy donors (HDs). We showed that patients with metastatic TNBC (mTNBC) exhibited decreased numbers of circulating T cells, dendritic cell subsets and differentiated B cells compared to patients with stage I-III TNBC and HDs, which was partially associated with prior chemotherapy. Moreover, increased IL17 production by vδ1 γδ T cells was observed in patients with mTNBC compared to HDs. Classical monocytes and neutrophils were increased in patients with mTNBC compared to HDs, irrespective of prior chemotherapy. Transcriptional and proteomic analysis, alongside ex vivo functionality assays, revealed increased migratory capacity, increased abundance of granule proteins, and elevated ROS production in circulating neutrophils from mTNBC patients. Some of these systemic immune alterations, including decreased levels of non-switched B cells and increased migratory capacity of neutrophils, were already evident in patients with stage I-III TNBC. Our data underscore the significant impact of TNBC disease stage on the systemic immune composition and function.

overall_design: Freshly isolated neutrophils from patients with mTNBC and age and BMI matched HDs were used for bulk RNA seq experiments.

first: Noor

middle: A

last: Bakker

first: Hannah

last: Garner

first: Ewald

last: van Dyk

first: Elisa

last: Champanhet

first: Chris

last: Klaver

first: Maxime

last: Duijst

first: Leonie

last: Voorwerk

last: Nederlof

first: Rosie

last: Voorthuis

first: Marte

last: Liefaard

first: Marja

last: Nieuwland

first: Onno

last: Bleijerveld

first: Hendrika

middle: M

last: Oosterkamp

first: Lodewyk

middle: F

last: Wessels

first: Marleen

last: Kok

first: Karin

last: de Visser


title: Modeling human limb skeletal development using human pluripotent stem cell-derived skeletal assembloids [CUT&Tag]

first: Takeshi

last: Takarada

summary: Despite recent advances in pluripotent stem cell-based approaches to induce skeletal cells, recapitulating human limb skeletal development in terms of structure and longitudinally oriented growth remains an unresolved challenge. Here, we report a method to differentiate human pluripotent stem cells into region-specific skeletal organoids harboring GDF5+PRG4+ interzone/articular chondrocyte　progenitors (IZ/ACPs) and SP7+ growth plate chondrocytes (GPCs) via PRRX1⁺ limb-bud mesenchymal cells. Comparative analysis demonstrated marked similarities of IZ/ACP and GPC organoids to the human embryonic limb, and graft fate and regenerative capacity in vivo were further characterized. We also mimicked the limb skeletal developmental process in a spatially structured manner by vertically positioning two IZ/ACP organoids at both ends of a GPC organoid to generate a human skeletal assembloid. Notably, this human skeletal assembloid recapitulated endochondral ossification with longitudinal skeletal growth upon transplantation. In summary, our study provides a novel research platform for human limb skeletal development and disease.

overall_design: cells: hiPSC, LPM, LBM, ExpLBM, GPC organoids from hiPSCs (no TP), IZ/ACP organoids from hiPSCs (no TP). All samples are each duplicate.


title: Microglia aggravate white matter injury via C3/C3aR pathway after experimental subrachnoid hemorrhage

city: Luzhou

first: lei

last: yang

state: Sichuan

address: Xianglin Road

institute: southwest medical university

summary: Activation of microglia induces neuroinflammation in acute and chronic phase is closely related to the white matter injury (WMI) pathophysiologyafter subrachnoid hemorrhage (SAH). The complement C3a receptor (C3aR) has a dual role in regulating inflammation and plays a role in neurodevelopment, neuroplasticity and neurodegeneration, but it’s effect on WMI during SAH re'mairemains unknown. In this study, 175 male C57BL/6J mice received SAH by endovascular perforation. oxy-Hb was used to simulate SAH in vitro. Multiple technical approaches, including immunohistochemistry, transcriptome sequencing, neurological function assessment, and various molecular biotechnologies, were used to assess the activation of the C3-C3aR pathway after SAH and its effects on microglial polarizations and WMI after SAH. The results showed that abnormal microglial activation after SAH was accompanied by upregulation of complement C3 and C3aR. C3aR inhibition reduced abnormal microglial activation, attenuated neuroinflammation, ameliorated WMI and cognitive deficits after SAH. RNA-Seq revealed that C3aR inhibition downregulated several immune and inflammatory pathways and ameliorated cellular injury by downregulating Pidd1 expression. The adverse effects of C3-C3aR in SAH may be related to Endoplasmic reticulum (ER) stress-dependent cellular injury and formation of inflammasome. PERK agonists exacerbate cellular injury and neuroinflammation attenuated by C3aR inhibition. Intranasal C3a treatment during the subacute phase of SAH helps to reduce astrocyte reactivity and ameliorate cognitive deficits after SAH. In conclusion, these findings suggest that C3aR plays a critical role in the regulation of neuroinflammation and WMI after SAH, providing new therapeutic targets to ameliorate WMI and cognitive deficits after SAH.

overall_design: microglia treated with oxy-Hb and C3aRA for RNA-seq

last: Yang


title: Pancreatic STAT5 activation promotes KrasG12D- and inflammation- induced acinar-to-ductal metaplasia and pancreatic cancer

city: Shanghai

first: Yuli

last: Lin

address: 上海市徐汇区东安路130号

institute: Fudan University

summary: Pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal malignancy due to its predilection for late-stage presentation. Signal transducer and activator of transcription 5 (STAT5) is a transcription factor implicated in the progression of various cancer types. However, its functional role in KRAS-driven pancreatic tumorigenesis remains unclear. We found that high levels of STAT5 in tumor cells were associated with a poorer prognosis in patients. The loss of Stat5 in acinar cells significantly reduced the development of acinar-to-ductal metaplasia (ADM) and PDAC lesions driven by KRAS mutation and pancreatitis. IL-22 signaling, induced by chronic inflammation, enhanced KRAS-mutant mediated STAT5 phosphorylation and the tumor-promoting function of IL-22 depends on the activation of STAT5. Chromatin immunoprecipitation assays revealed that STAT5 was directly bound to the promoters of ADM mediators HNF4a.

overall_design: Acinar cells from KC and KCS mouse pancreata tissues infected with Ad5-Cre or Ad5 to induce KRAS mutation were obtained for RNA-seq to analyze the role of STAT5 in PDAC development.


title: Akkermansia muciniphila reduces lipid absorption through activating AMPK in the jejunum

city: Guangzhou

first: Shiqi

last: Jia

address: Huangpu Avenue West 613

institute: Jinan University

summary: Akkermansia muciniphila (Akk) associated with multiple metabolic diseases and administration of Akk can improve the metabolic disorders. However, little is known about the effect of Akk on jejunal epithelial cells which absorb lipid and interact with oral administrated Akk. We oral administrated Akk to mice and measured the lipid absorption and gene expression in small intestinal epithelial cells. The long-term effect of Akk treatment reduced lipid deposits in the liver and adipocytes with improved the glucose metabolism. This is particularly caused by reduced lipid absorption in jejunal epithelia. Akk feeding reduced the expression of those genes that regulate synthesis and cell cycles, characters of the host cell responding to energy deficiency. In fact, we detected increased AMPK-alpha phosphorylation levels in Akk-treated jejunal epithelial cells both in vivo and in vitro. Furthermore, activating AMPK inhibits lipids absorption in jejunum. Thus, we conclude that oral administration of Akk activates the AMPK pathway and represses the lipid absorption in jejunal epithelial cells, which contributes to the metabolic benefits of oral Akk administration.

overall_design: The mice were fed with normal chow diet. At the age of 8 weeks old, we orally administrated 4x10^8 Akk to mice dailly for 7 weeks. Then, the intestine epithelial cells were collected followed by RNA extraction and RNAseq. The control group oraaly administrated with PBS.

first: Qiming

last: Ma

first: Qingyu

last: Wang

first: Xincheng

last: Zhou


title: MicroRNA expression profiling of hepatocellular carcinoma tissues derived exosomes

city: fuzhou

first: xiaoyun

last: chen

address: 福建省福州市闽侯县上街镇学园路1号

institute: Fujian Medical University

summary: In this study, we isolated exosomes from liver cancer tissues and exosomal miRNA expression was profiled by high-throughput sequencing to investigate the potential of exosomal contents as biomarkers for HCC.

overall_design: Fresh tumor and adjacent normal tissue samples were gently cut into small pieces and incubated at 37 ◦C for 30–60min in DMEM/F12 media supplemented with collagenase I, collagenase Ⅳ, hyaluronidase and DNase I under continuous rotation. The cell suspension containing the diffusing tissue exosomes was filtered through a 70-μm filter and centrifuged at 300×g for 10 min, followed by centrifugation at 2000×g for 20 min to eliminate cells and tissue debris. The exosomes were extracted by ultra-high speed centrifugation. RNA was isolated from exosome using Trizol reagent. small RNA library was constructed and then sequenced using the Illumina NextSeq 500 platform.

first: Wansong

first: Jieyu

last: Li

first: Zhifeng


title: MicroRNA expression profiling of tumor cells derived exosomes

address: 福建省福州市闽侯县上街镇学园路1号

summary: In this study, we isolated exosomes from liver cancer cell lines and exosomal miRNA expression was profiled by high-throughput sequencing to investigate the potential of exosomal contents as biomarkers for HCC.

overall_design: 97H or HepG2 cells were cultured using DMEM medium containing 10% exosom-free serum. The exosomes were extracted from the culture supernatant by ultra-high speed centrifugation.  Exosomes were identified and verified using transmission electron microscopy, nano-flow cytometry analysis, and western blotting. Total RNA, including miRNA, was isolated from exosome using Trizol reagent. RNA was applied for small RNA library construction using the NEB Multiplex Small RNA Library Prep Set for Illumina. The purified library was examined using the Agilent 2100 Bioanalyzer and the Agilent DNA 1000 chip kit for quality control and then sequenced using the Illumina NextSeq 500 platform.


title: Gene expression of KYSE150 cells and CAFs in coculture system

city: beijing

first: di

last: zhao

address: 52 Fucheng Road, Haidian District, Beijing

institute: beijng cancer hospital

summary:
KYSE150 cells and CAFs were cocultured in transwell apparatus with 0.4 μm pore size. In different groups, KYSE150 cells or CAFs plated in the lower chamber were collected for gene expression analysis using Agilent SurePrint G3 Human Gene Expression v3 (8×60K).
Investigation of the critical gene participating the crosstalk between ESCC cells and cancer-associated fibroblasts (CAFs).

overall_design: We designed this experiment to screen for gene whose expressions participate the crosstalk between ESCC cells and cancer-associated fibroblasts (CAFs).

first: Di

last: Zhao

first: Qimin

last: Zhan


title: Inherited KDM6AA649T facilitates tumor-immune escape and exacerbates colorectal signet-ring cell carcinoma outcomes

city: Jinan

first: Maoxiao

last: Feng

address: Beiyuan Street 247

institute: Department of Clinical Laboratory

summary: Childhood onset of colorectal signet ring cell carcinoma (CR-SRCC) is extremely rare and featured as highly malignant with poor prognosis. Here we reported a CR-SRCC case of 11-year-old boy with a novel inherited X-linked KDM6AA694T mutation. The H3K27me2/3 demethylase KDM6A was frequently mutated in varieties of tumors and acts as a tumor suppressor. In vivo H3K27me3 demethylation assay demonstrated that KDM6AA694T had dampened H3K27me3 demethylase activity. Overexpression of KDM6AA694T in SRCC cell line KATO3 promoted cell proliferation, invasion and migration, which were further confirmed in vivo by constructing orthotopic tumor growth and lung metastasis model. Besides, expression of KDM6AA694T in immune cells suppresses inflammatory macrophage response and effector T cell response. In conclusion, we characterized a novel inherited KDM6AA694T mutant from a childhood-onset SRCC case and demonstrated that the mutant with impaired H3K27me3 demethylase activity could potentiate tumor malignancy and suppress antitumor immunity.

overall_design: RNA sequencing was used to explore the mechanism of KDM6A A694T regulation and obtained 1029 and 1442 differentially expressed genes (DEGs) in Jurkat cells expressing EV (Empty Vector), KDM6AWT or KDM6AA694T.


title: A melanoma mutation panel for individualized treatment of patient-derived melanoma cell cultures

status: Public on Jan 24 2025

city: Leipzig

first: Maciej

last: Rosolowski

address: Härtelstr. 16-18

institute: Institute for Medical Informatics, Statistics and Epidemiology (IMISE)

summary: Purpose: To identify new targets in melanoma for targeted treatment based on a mutational analysis of melanoma cell lines and subsequent individualized treatment combinations. Experimental Design: A series of 57 melanoma cell lines (mostly short-term cultures) are analyzed for their mutation pattern based on a mutation panel of 83 genes selected from the most abundant mutations (more than 5 % of samples). Of these, 28 cell lines are treated with small molecule inhibitors either as single-agent or combination therapy. Most effective therapies are estimated by Chou Talaley method, applied to multiple drug treatments, based on growth characteristics of melanoma cells during life-cell imaging. Results: In a number of cell lines, combination treatment showed better treatment response rates than monotherapy. BRAFi and an inhibitor of a further pathway is more efficient to induce an anti-proliferative effect than the standard therapy with a BRAFi-MEKi combination. Among these are PI3K/mTOR inhibitor apitolisib either together with a BRAFi or as triple combination with BRAFi/MEKi. A combination of BRAFi and CDK4/6 inhibitor palbociclib also showed significant synergy. The most promising drug combinations in NRASmut cell lines is a triple combination of MEKi, ERKi and and PI3K/mTOR apitolisib, or a combination of MEKi, apitolisib and aurora A kinase inhibitor alisertib. Transcriptomic analysis showed that BRAF and NRAS mutant cell lines could be differentiated by ARHGAP42 and DLD expression, both higher expressed in BRAFmut cell lines, and ARHGAP42 being a putative new target for BRAFmut melanoma cells.  Conclusion: Combination treatment of melanoma cells with individual drug combinations based on mutational patterns are sometimes more effective than monotherapy or classical double-agent therapy and may thereby replace classical treatment approaches.

overall_design: A series of 57 melanoma cell lines (mostly short-term cultures) are analyzed for their mutation pattern based on a mutation panel of 83 genes selected from the most abundant mutations (more than 5 % of samples). Of these, 27 cell lines are treated with small molecule inhibitors either as single-agent or combination therapy. Most effective therapies are estimated by Chou Talaley method, applied to multiple drug treatments, based on growth characteristics of melanoma cells during life-cell imaging.

first: Franziska

last: Karras


title: The interferon/STAT1 signaling axis is a common feature of tumor-initiating cells in breast cancer [snRNA-Seq]

city: Houston

first: Michael

last: Lewis

state: TX

address: 1 Baylor Plaza N1210

department: Breast Center

institute: Baylor College of Medicine

summary: Gene expression profile of STAT-signaling tumor-initiating cells (TIC) in breast xenograft models

overall_design: Cell line- and patient-derived xenografts transduced with a STAT reporter or STAT lineage tracing system were FACS-enriched according to the presence/absence of EGFP (STAT reporter) and/or the presence of mNeptune2 or dsRed (lineage tracing system)

first: Eric P

last: Souto

first: Ping

last: Gong

first: John D

last: Landua

first: Ramakrishnan

last: Rajaram Srinivasan

first: Abhinaya

last: Ganesan

first: Lacey E

last: Dobrolecki

first: Stephen C

last: Purdy

first: Xingxin

last: Pan

first: Anna

last: Chung

last: Zeosky

first: S Stephen

last: Yi

first: Heide L

last: Ford

first: Michael T


title: The Drosophila histone variant H2Av facilitates Notch signaling activity in a two-tier regulatory fashion

city: Beijing

first: Yao

last: Chen

state: Beijing

address: No.2 Yuanmingyuan western road

department: College of Plant Protection

institute: China Agricultural University

summary: Background H2Av is evolutionarily conserved H2A variant protein involved in the regulation of transcription. The Tip60 complex is recruited by different transcription factors to facilitate the incorporation and acetylation of H2Av, thereby influencing target gene expression by modifying the stability of the nucleosome that occludes the transcription start site. The Tip60-H2Av module is involved in various developmental processes, though its precise roles are not yet fully understood. Methods RNA interference and gene knock-out technology were used screen essential genes in regulating Notch signaling pathway. We use immunostaining method to detect the protein level of H2Av, Tip60 complex as well as Notch signaling pathway components. Chromatin immunoprecipitation assay was performed to detect the specific bind of H2Av in E(spl)-Complex and Su(H) genes. Result Here we report that H2Av is required for Notch signaling activation during Drosophila wing development. H2Av depletion disrupts the expression of Notch target genes, resulting in wing marginal defects. Unexpectedly, we find that H2Av regulates the expression of Su(H) gene which encodes the transcription factor of the Notch signaling cascade. We further demonstrate that the Tip60 complex modulates the transcription of both Notch targets and Su(H) likely through H2Av. Based on these observations, we propose a model that the Tip60-H2Av module facilitates Notch pathway activation by simultaneously promoting the expression of both the target genes and the transcription factor. Conclusion This study offers insights into the diverse roles of the Tip60-H2Av module in Notch pathway activation by identifying a novel two-tier regulatory mechanism which may also be utilized by other chromatin remodeling factors. Key words H2Av, Notch, Su(H), Drosophila, Tip60

overall_design: Collect ChIP-seq sequencing experiments on the disc tissues of H2Av-EGFP strains with endogenous GFP knock in from winged adults.


title: Ablating VHL in Rod Photoreceptors Modulates RPE Glycolysis and Improves Preclinical Model of Retinitis Pigmentosa

city: New York

first: Salvatore

last: Caruso

state: New York

address: 701 West 168th Street, RM211E

institute: Columbia

summary: Neuroretinal degenerations including retinitis pigmentosa (RP) comprise a heterogeneous collection of pathogenic mutations that ultimately result in blindness. Despite recent advances in precision medicine, therapies for rarer mutations are hindered by burdensome developmental costs. To this end, Von Hippel-Lindau (VHL) is an attractive therapeutic target to treat RP. By ablating VHL in rod photoreceptors and elevating hypoxia-inducible factor (HIF) levels, we demonstrate a path to therapeutically enhancing glycolysis independent of the underlying genetic variant that slows degeneration of both rod and cone photoreceptors in a preclinical model of retinitis pigmentosa. This rod-specific intervention also resulted in reciprocal, decreased glycolytic activity within the retinal pigment epithelium (RPE) cells despite no direct genetic modifications to the RPE. Suppressing glycolysis in the RPE provided notable, non-cell-autonomous therapeutic benefits to the photoreceptors, indicative of metabolically sensitive crosstalk between different cellular compartments of the retina. Surprisingly, targeting HIF2A in RPE cells did not impact RPE glycolysis, potentially implicating HIF1A as a major regulator in mouse RPE and providing a rationale for future therapeutic efforts aimed at modulating RPE metabolism.

overall_design: RNA seq profiling of bulk neuroretina following VHL or VHL and HIF1A ablation in rod photoreceptors at 3 weeks of age compared to controls

first: Salvatore Marco

first: Xuan

last: Cui

first: Stephen H

last: Tsang


title: Nudt21 ablation in macrophages induces constitutive autophagy activation and diminishes inflammation in inflammatory diseases

first: Yunzhu

address: 280 South Chong Qing Rd

institute: Shanghai Jiao Tong University School of Medicine

summary: Macrophage hyperactivation is a hallmark of inflammatory diseases, yet the role of alternative polyadenylation (APA) in regulating innate immunity remains unclear. In this study, we demonstrate that Nudt21, a crucial RNA-binding component of the APA machinery, is significantly upregulated in various inflammatory settings. Utilizing myeloid-specific Nudt21-deficient mice, we reveal a protective effect of Nudt21 depletion against colitis and severe hyperinflammation, primarily through diminished production of proinflammatory cytokines. Notably, Nudt21 regulates the mRNA stability of key autophagy-related genes by mediating selective 3’UTR polyadenylation in activated macrophages. As a result, Nudt21-deficient macrophages display enhanced autophagic activity, which leads to reduced cytokine secretion.

overall_design: To identify the potential targets regulated by Nudt21 in inflammatory  macrophages,  we harvested bone marrow derived macrophages (BMDMs) from WT and Nudt21-cKO mice with and without IFNγ/LPS treatment (4hr) for deep RNA sequencing. Bioinformatic analysis revealed that Nudt21 deficiency results in alterations in mRNA levels and 3'UTR lengths of 354 genes, with enrichment observed in autophagy-related pathways.

first: Hua-bing

last: Li


title: C12orf43-NAT10 Enhance breast cancer proliferation and chemotherapy resistance via  BMI1-P53 signaling axis in a N4-acetylcytidine-dependent manner

city: Shen yang

first: siyu

last: jiang

state: Liaoning

address: 77 Puhe Road

department: School of Basic Medicine

institute: CHINA Medical University

summary: C12orf43-NAT10 interaction was found to accelerate breast cancer progression and chemotherapy resistance by activating the BMI-P53 signaling axis in a N4-acetylcytidine-dependent manner.


title: ANKRD11 Binds to Cohesin to Regulate Neural and Craniofacial Development

first: HongXin

last: Zhong

address: No. 190, Open Source Avenue, Luogang District, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: In this study, we analyzed gene expression changes in the E14 mESC wild-type cell line and the ANKRD11 Y347A mutant cell line using RNA-seq.

overall_design: Comparative gene expression analysis of RNA-seq data for the E14 mESC wild-type cell line and the ANKRD11 Y347A mutant cell line.

first: Hongxin

first: Hongjie

last: Yao


title: Coordinated immune networks in leukemia bone marrow microenvironments distinguish response to cellular therapy

first: Cameron

last: Park

state: NY

institute: Columbia University

summary: Understanding how intra-tumoral immune populations coordinate to generate anti-tumor responses following therapy can guide precise treatment prioritization. We performed systematic dissection of an established adoptive cellular therapy, donor lymphocyte infusion (DLI) by analyzing 348,905 single-cell transcriptomes from 74 longitudinal bone-marrow samples of 25 patients with relapsed myeloid leukemia; with a subset evaluated by protein-based spatial analysis. In acute myelogenous leukemia (AML) responders, diverse immune cell types within the bone-marrow microenvironment (BME) were predicted to interact with a clonally expanded population of ZNF683+GZMB+ CD8+ cytotoxic T lymphocytes (CTLs) which demonstrated in vitro specificity for autologous leukemia. This population, originating predominantly from the DLI product, expanded concurrently with NK and B cells. AML nonresponder BME revealed a paucity of crosstalk and elevated TIGIT expression in CD8+ CTLs. Our study highlights recipient BME differences as a key determinant of effective anti-leukemia response and opens new opportunities to modulate cell-based leukemia-directed therapy.

overall_design:
single-cell RNA sequencing and CITE protein sequencing from 9 AML patients and 16 CML patients, with mutliple time points before and after relapse and treatment with donor lymphocyte infusion

***************************************************************
Submitter states that missing raw data are being made available for controlled access in dbGaP.
***************************************************************

first: Katie

last: Maurer

middle: Y

first: Shouvik

last: Mani

first: Mehdi

last: Borji

first: Florian

last: Raths

first: Kenneth

middle: H

last: Gouin III

first: Livius

last: Penter

first: Yinuo

last: Jin

first: Jia

last: Zhang

first: Crystal

last: Shin

first: James

middle: R

last: Brenner

first: Jackson

last: Southard

first: Sachi

last: Krishna

first: Wesley

last: Lu

first: Haoxiang

last: Lyu

first: Domenic

last: Abbondanza

first: Channell

last: Magnum

first: Lars

last: Olsen

first: Michael

middle: J

last: Lawson

first: Martin

last: Fabani

first: Donna

last: Neuberg

first: Pavan

last: Bachireddy

first: Eli

middle: N

last: Glezer

first: Samouil

last: Farhi

first: Shuqiang

last: Livak

first: Jerome

last: Ritz

first: Robert

last: Soiffer

first: Catherine

last: Wu

first: Elham

last: Azizi


title: RNA-seq analysis of transcriptomic alterations in isogenic TF-1 leukemia cells harboring base-edited IDH mutations

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

institute: St. Jude Children's Research Hospital

summary: Recurrent IDH mutations catalyze NADPH-dependent production of oncometabolite R-2HG for tumorigenesis. IDH inhibition provides clinical response in a subset of acute myeloid leukemia (AML) cases; however, most patients develop resistance, highlighting the need for more effective IDH-targeting therapies. By comparing transcriptomic alterations in isogenic leukemia cells harboring base-edited IDH mutations, we identify the activation of adhesion molecules including CD44, a transmembrane glycoprotein, as a shared feature of IDH-mutant leukemia. R-2HG-mediated CD44 upregulation is found in IDH-mutant AML patients of different cohorts. CD44 is indispensable for IDH-mutant leukemia cells through activating pentose phosphate pathway and inhibiting glycolysis by phosphorylating G6PD and PKM2, respectively. This metabolic rewiring ensures efficient NADPH generation for mutant IDH-catalyzed R-2HG production. Combining IDH inhibition with CD44 blockade enhances killing of IDH-mutant leukemia cells and overcomes resistance to IDH inhibition. Hence, we uncover an oncogenic feedforward pathway involving CD44-mediated metabolic rewiring for oncometabolite production, representing a targetable dependency of IDH-mutant malignancies.

overall_design: RNA-seq was performed to determine the transcriptomic changes isogenic TF-1 leukemia cells harboring base-edited IDH mutations

first: Junhua

first: Yuxuan

last: Liu


title: Immune cell distribution and DNA methylation signatures differ between tumor and stroma enriched compartment in pancreatic ductal adenocarcinoma

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

institute: Medical University of Vienna

type: Methylation profiling by genome tiling array

summary: Background: The presence of abundant tumor stroma is a prominent characteristic of pancreatic ductal adenocarcinomas (PDAC) that potentially influences disease progression and therapy response. This study aims to investigate immune cell infiltration and epigenetic profiles in tumor cell enriched (“Tumor”) and stroma cell enriched (“Stroma”) regions within human PDAC tissue samples to identify regional-specific genetic alterations as a basis for novel drug target development.  Methods: Formalin-fixed paraffin-embedded (FFPE) tumor tissue samples were obtained initially from 15 patients who underwent PDAC resection. Tumor and Stroma regions were separately assessed for their immune cell composition by using immunohistochemistry (IHC) and epigenetic modifications based on DNA methylation obtained by Infinium MethylationEPIC microarrays. A tissue microarray cohort of additional 65 PDAC patients was included for validation of IHC findings and survival analysis.  Results: By comparing Tumor and Stroma defined regions of PDAC tumors, we identified 25,410 differentially methylated positions (DMPs) distributed across 6,963 unique genes. Pathway enrichment analysis using the top 2,000 DMPs that were either hyper- or hypomethylated, indicated that immune response pathways and the estrogen receptor pathway are epigenetically dysregulated in Tumor and Stroma regions, respectively. In terms of immune cell infiltration, we observed overall low levels of T cells in both regions. In Tumor regions however, occurrence of tumor-associated macrophages (TAMs) was higher than in Stroma regions (p=0.02) concomitant with a dualistic distribution that stratifies PDAC patients into those with high and low TAM infiltration. By categorizing TAM levels into quartiles, our analysis revealed that PDAC patients with more than 1,515 TAMs per mm², representing the upper quartile, exhibited significantly shorter overall survival (p=0.036).   Conclusions: Our data suggest that variations in inflammatory characteristics between the Tumor and Stroma defined compartments of PDAC may primarily stem from the presence of macrophages rather than lymphocytes. The abundance of TAMs within regions enriched with tumor cells correlates with patient survival, underscoring the potential significance of exploring therapeutic interventions targeting TAMs. Furthermore, directing attention towards the estrogen receptor pathway represents a promising strategy to address the stroma cell component within the PDAC tumor microenvironment.

overall_design: Compare Tumor and Stroma defined regions of PDAC tumors by EPIC methylation microarrays

first: Erwin

last: Tomasich

first: Anna

last: Berghoff


title: RNA-seq Provides Insights into Sucrose Signaling Re-sponses in White Lupin Roots

city: Hayward

first: Claudia

last: Uhde-Stone

state: CA

address: 25800 Carlos Bee Blvd

department: Biological Sciences

institute: California State University, East Bay

summary: White lupin (Lupinus albus) has become a model plant for understanding plant adapta-tions to phosphorus (P) and iron (Fe) deficiency, two major limiting factors for plant productivity. In response to both nutrient deficiencies, white lupin forms cluster roots, bottle-brush-like root structures that aid in P and Fe acquisition from soil. While cluster root function is well studied, not much is known about the signaling pathways involved in sensing and responding to P and Fe deficiency. Sucrose has been identified as a long-distance signal sent in increased concentrations from shoot to root in response to both P and Fe deficiency. Thus, sucrose plays a dual role both as a signal and as a major source of energy for the root. To unravel the responses to sucrose as a signal, we performed Illumina paired-end cDNA sequencing of white lupin roots treated with sucrose for 20, 40 or 80 minutes, compared to untreated controls. We identified 634 up-regulated and 956 down-regulated genes in response to sucrose. Twenty minutes of sucrose treatment showed the most responses, with the ethylene-activated signaling pathway as the most enriched GO (Gene Ontology) category. The number of up-regulated genes went down at 40 min and 80 minutes, and protein dephosphorylation became the most enriched category. Taken together, our findings indicate active responses to sucrose as a signal at 20 minutes after sucrose addition, but fewer responses and potential re-setting of signal transduction pathways by dephosphorylation of proteins at 40 and 80 minutes.

overall_design: To unravel responses to sucrose as a signal, we performed Illumina paired-end cDNA sequencing of white lupin roots treated with sucrose for 20, 40, and 80 minutes, compared to untreated controls.

first: Roy

last: Proyasha

first: Sethi

last: Shrey

first: New

last: James

first: Lorilla

last: Kristina Mae

first: Maleski

last: Karen

first: Ancheta

last: Allan

first: Uhde-Stone

last: Claudia


title: Single-cell RNA-seq Analyses of Oocytes and Zygotes Reveal Earlier Maternal to Zygote Transition in Mice and Rats

status: Public on Jan 23 2025

city: Stockton

first: Yangqi

last: Su

address: 4142 E Morada Ln, Apt 6303

department: Bioinformatics

institute: UNC Charlotte

summary: The maternal to zygote transition in mammals has been an area of intensive research over the past few decades, with an ever-changing landscape of understanding that has accompanied the rapid development of cell-profiling technology. Utilizing a full-length single cell RNA-seq protocol, we profiled mature oocytes and zygotes of mice and rats to uncover elusive transcriptomic dynamics during the maternal to zygote transition. We confirm the existence of early gene expression in the mouse zygote while revealing a similar chain of events occurring in the rat zygote. We observe an increase in nascent transcription in both species. Moreover, we find subtle but pervasive signals of differential splicing of genes related to key early zygotic activities occurring in both species. Meanwhile, we find distinct profiles of alternative polyadenylation between zygotes and oocytes in both species, particularly, in genes related to major processes within the zygotes. Finally, although a more dynamic transcriptomic landscape exists in the mouse zygote, the rat zygote also displays similar transcriptomic features, suggesting that minor zygotic activation in rat occurs earlier than originally thought.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: single cell RNA-seq was performed to compare transcriptomes of single oocytes vs zygotes in mice and rats

first: Jane

last: Kouranova

first: Jonathan

last: Shea

first: Xiaoxia

last: Cui

first: Zhengchang


title: scRNA-seq of tumor-infiltrating CD45+ cells from B16-F10 tumor-bearing mice treated with vehicle and DOPAC.

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

summary: To investigate how DOPAC suppresses tumors in vivo, we performed single-cell RNA sequencing (scRNA-seq) on CD45+ cells isolated from the tumor tissues of B16-F10-bearing mice.

overall_design: To perform single-cell RNA sequencing analysis, we treated mice under each treatment condition (Vehicle-treated and DOPAC-treated, n=4 biological replicates/group). Flow sorting was used to obtain tumor-infiltrating CD45+ cells and cell suspensions were dissociated and loaded into the 10x Chromium instrument.

first: Penghu

last: Han

first: Shuzheng

last: Chu

first: Yatai

last: Chen

first: Shiyang

last: Li

first: Detian

last: Yuan


title: Chip-seq of Nrf2 in vehicle and DOPAC-treated CD8+ T cells

summary: To further investigate how DOPAC regulates mitophagy in CD8+ T cells by rescuing Nrf2 from Keap1-driven degradation, we conducted chromatin immunoprecipitation sequencing (ChIP-seq) to identify genome-wide Nrf2-binding loci.

overall_design: ChIP assay was performed by using a ChIP assay kit (Beyotime).