title: Single Cell RNA Sequencing Before and After Light Chain Escape Reveals Intra-patientMultiple Myeloma Subpopulations with Divergent Osteolytic Gene Expression

city: Aurora

first: Dan

last: Sherbenou

state: CO

address: 12700 E 19th Ave Box B170

institute: UC Denver Hematology

summary: High-risk multiple myeloma (MM) is genomically unstable, comprised of heterogeneous populations of tumor cells that evolve over time. Lightchain escape (LCE) is a clinical phenomenon observed when light chains rise separately from M-spike values,  implying divergent tumor evolution. We sought to understand LCE by performing high depth transcriptomic and phenotypic studies. We performed single cell RNA sequencing and ex vivo drug sensitivity profiling on serial bone marrow biopsies from a patient with LCE at diagnosis, first  relapse and relapsed/refractory timepoints. Single cell RNA sequencing uncovered distinct transcriptomic subpopulations with phenotypes that could be tracked separately by clinical serum light chain and M-spike values. Genes differentially expressed between subpopulations were assessed for generalizable effects on prognosis from the MMRF CoMMpass and GSE24080 datasets. Notably ,the LCE subpopulation exhibited gene expression profile featuring prominentLAMP5-overexpression, which was associated with risk for osteolytic bone lesions. Ex vivo drug sensitivity testing displayed differential sensitivity of the subpopulations. Copy Number Variant inference showed that the transcriptomic subpopulation underlying LCE was related to a genetic subclone that evolved overtime. Our findings illustrate that malignant subpopulations underly light chain escape in multiple myeloma. These studies implied that LCE and LAMP5 gene overexpression portends for increased risk of osteolytic bone disease and adverse prognosis, findings that were confirmed in the subset of patients in the CoMMpass database with light chain escape.

overall_design: Bone marrow aspirates from one patient at three timepoints (diagnosis, first relapse, relapse/refractory) were collected at the University of Colorado Anschutz Medical Campus after informed consent and protocol approval. Mononuclear cells were isolated using SepMate Ficoll tubes (Stemcell Technologies) and cryopreserved in Iscove M odified Dulbecco medium with 45% fetal bovine serum and 10% dimethyl sulfoxide. Bone marrow samples were thawed, resuspended in DNAse and washed in PBS . A sort using a BD FACSAria (BD) was performed to remove dead cells. Single cells were captured using Chromium X Series (10X G enomics ) and sequen ced on a NovaSeq6000 (Illumina). Feature - barcode matrix was produced from reads using C ellranger v.3.1.0 (10X Genomics).

first: Denis

last: Ohlstrom

first: Zachary

last: Walker

first: Abhishek

last: Pandey

first: Lorraine

last: Davis

first: Krysta

middle: L

last: Engel

first: Zenggang

last: Pang

first: Peter

last: Forsberg

first: Tomer

last: Mark

first: Austin

middle: E

last: Gillen

first: Daniel


title: Expanding the cytokine receptor alphabet reprograms T cells into diverse cell states: RNAseq of orthogonal chimera transduced T cells

status: Public on Dec 09 2024

city: Stanford

first: Yang

last: Zhao

state: CA

address: Beckman B169B, 279 Campus Drive

department: MCP

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

summary: Cytokines signal through specific cell surface receptor dimeric pairings that have been selected over the course of evolution to activate canonical JAK/STAT signaling pathways and gene expression programs. However, the potential combinatorial diversity of JAK/STAT cytokine receptor pairings is much greater than what is utilized in nature, raising questions about the untapped biology of alternative 'non-natural' pairings. Here we exploited common γ chain (γc) receptor as a shared signaling hub on T cells and enforced the expression of both natural and non-natural heterodimeric JAK/STAT receptor pairings using an orthogonal cytokine receptor platform, followed by a comparative analysis of the resulting T cell phenotypes in vivo. We tested receptors from γc cytokines as well as interferon, IL-10, and other homodimeric receptor families that do not normally pair with γc or are not naturally expressed on T cells. These synthetic receptors induced unique gene expression programs, and led to distinct T cell fates in tumors, including naturally occurring states (type 2 cytotoxic T (Tc2) cell and type 2 helper T (Th2) cell differentiation driven by orthogonal IL-4R) and synthetic states (myeloid-like phagocytic T cells driven by orthogonal GSCFR). T cells armed with orthogonal IL-22R (o22R) and oGCSFR exhibited transcriptional, and chromatin landscapes associated with stemness and resistance to exhaustion, which enhanced anti-tumor properties. Non-native JAK/STAT signals open a path to diversifying T-cell states beyond those induced by the menu of natural cytokines.

overall_design: WT mouse T cells transduced with orthogonal receptors were sorted using an Aria II sorter (BD Biosciences) at the Stanford Shared FACS Facility. Non-ICD o2R-transduced cells were sorted as controls. Following sorting, cells were recovered in MSA-mIL-2 (100 U ml−1) for 24 hours, subjected to IL-2 starvation for another 24 hours, and then stimulated with 5 μM MSA-oIL2 or 10 nM recombinant cytokines (IL-2, IL-4, IL-7, IL-21, IL-10, IFN-α, Peprotech) for 6 hours. Total RNA was extracted using the Quick-RNA 96 Kit (Zymo Research). mRNA was isolated using poly-T magnetic beads, fragmented, and converted into cDNA using random hexamer primers. After second-strand synthesis, libraries were prepared through end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Libraries were pooled and sequenced on the NovaSeq X Plus Series (PE150).


title: The MeaB bZIP transcription factor is needed for proper nitrosative stress response induced by nitrite in Aspergillus fumigatus

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary: The function of the Aspergillus fumigatus MeaB bZIP-type transcription factor was investigated using a transcriptomics-based approach. Deletion of the meaB gene increased nitrite and menadione-sodium bisulfite, but not terc-butyl hydroperoxide or H2O2 stress sensitivity. When the transcriptome of the DmeaB strain was compared with the wild-type strain (Af293), genes involved in siderophore biosynthesis or glucanases were enriched in the up-regulated gene set, whereas genes encoding heme-binding proteins or chitinases were enriched in the down-regulated gene set. The 90 mM NaNO2-induced stress elicited a response in the  DmeaB gene deletion mutant that was very similar to that of the wild-type strain in the presence of 135 mM NaNO2. These stress responses included downregulation of mitotic cell cycle, and ribosomal protein genes, upregulation of nitrosative stress response (fhpA, fhpB, gnoA), nitrate utilization (niaD, niiA), several iron acquisition, ergosterol biosynthesis genes and the alternative oxidase gene aoxA, and altered the transcriptional activity of the secondary metabolite cluster and CAZyme genes. Nitrite treatment upregulated arginine metabolism genes only in the wild-type strain. The observed transcriptional changes were associated with reduced growth, increased redox imbalance and increased sterol content in both strains. Here, we discuss our hypothesis that MeaB affects (endogenous) NO production through fine-tuned regulation of arginine metabolism genes, and that disrupted NO homeostasis was responsible for the altered phenotype of the meaB mutant.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mycelia of Aspergillus fumigatus reference strain, and DmeaB mutant under Na-nitrite treated and untreated conditions with three biological replicates.

first: Kinga

last: Varga

first: Tamás

first: Károly

last: Antal

first: István

last: Pócsi


title: Gene transcriptomics reveals that PAK5 regulates the pathogenesis of Esophageal Squamous Cell Carcinoma

city: Haikou

first: Yue

last: Zeng

address: Longhua District Yehai Avenue

country: China

institute: The Second Affiliated Hospital of Hainan Medical University

summary: Abstract Background Esophageal Squamous Cell Carcinoma (ESCC) is one of the leading causes of cancer death worldwide, especially in Asia. Because the early symptoms are not obvious, most patients are already in an advanced stage when diagnosed, which greatly limits the effectiveness of treatment and affects the patient's prognosis. Therefore, it is of great significance to explore the occurrence and development mechanism of ESCC and to search for effective biomarkers and therapeutic targets for improving patient prognosis. P21 activated protein kinase 5 (PAK5) belongs to the mitogen-activated protein kinase family, which has been extensively studied in recent years and is thought to play an important role in a variety of malignant tumors. PAK5 promotes tumor development by regulating processes such as cell cycle, cell migration and invasion. However, the specific role of PAK5 in ESCC and its potential mechanisms have not been fully elucidated. Methods We initially employed immunohistochemical techniques to assess PAK5 expression levels in ESCC tissue samples and compared these levels with those in normal esophageal tissues. Kaplan-Meier survival analysis was subsequently conducted to evaluate the correlation between PAK5 expression levels and patient survival in ESCC. To further investigate the functional role of PAK5 in ESCC cells, we constructed PAK5 overexpression (PAK5-OE) and PAK5 silencing (PAK5-si) ESCC cell models.  The effects of PAK5 on cell proliferation, clonogenicity, migration, and invasion were assessed using CCK-8 assays, Cell Plate Cloning assays, and Transwell assays. Additionally, transcriptomic analyses were performed using mRNA sequencing techniques to identify downstream effector molecules and signaling pathways influenced by PAK5. Results The results showed that the expression of PAK5 in ESCC tissue was significantly higher than that in normal esophageal tissue, and high PAK5 level was closely associated with poor prognosis in ESCC patients.  Functional experiments showed that PAK5 could significantly enhance the proliferation, clonal formation, migration and invasion of ESCC cells.  Further transcriptomic analysis revealed multiple downstream genes and signaling pathways regulated by PAK5, particularly those related to cell cycle progression and anti-apoptosis. Most notably, this study found that PAK5 forms a new signaling axis by interacting with GAREM1, which is critical for maintaining the transfer behavior of ESCC cells.These findings underscore PAK5's tumorigenic potential in ESCC, positioning it as a promising prognostic marker and therapeutic target. Keywords: PAK5, Esophageal squamous cell carcinoma, GAREM1

overall_design: The KYSE-150 cell line, modified with either PAK5 overexpression or PAK5 silencing, was used for mRNA sequencing to identify differentially expressed genes (DEGs). Sequencing was performed by Beijing Novozymes Biotechnology Co., Ltd. using standard protocols. DEGs between PAK5-si-KYSE-150 and WT-KYSE-150 cells were analyzed using the DESeq2 R package, with significance thresholds set at FDR < 0.05 and |log2(Fold Change)| ≥ 1.

first: Chuanji

last: Zhou

first: Xingqun

last: Cai

first: Lijun

last: Gao

first: Mengyanan

last: Luo

first: Wenling

last: Wu

first: Yuecan


title: Nuclear expansion drives chromatin structure remodeling in aging neurons

city: Moscow

first: Ekaterina

last: Khrameeva

address: Bolshoy Boulevard 30, bld. 1

department: Center of Life Sciences

country: Russia

institute: Skolkovo institute of science and technology

summary: Aging, particularly in the brain, involves impairments in multiple cellular and molecular functions, many of which are regulated at the nucleus. Chromatin structure plays a critical role in the regulation of gene expression and the maintenance of genomic stability. During differentiation, chromosomes acquire their unique topology depending on the cell type that should be kept for a lifetime, but this may deteriorate as we age. However, the effects of aging on the chromatin 3D structure of neurons remain largely unknown and much has been inferred from senescent cells. By combining chromosome conformation capture and microscopy techniques, we investigated cortical neurons of young and aged mice and discovered neuronal nuclear expansion during neuronal aging, leading to increased distances between chromosomes. This expansion alters the topology of compartments, topologically associating domains (TADs) and chromatin loops. While larger TADs tend to dissociate, smaller TADs and loops exhibit strengthened interactions to maintain the cohesiveness of chromatin in aged neurons. These topological changes impact the borders of TADs, resulting in their overall weakening. Interestingly, we attribute these alterations to changes in the physical forces of an expanding nucleus, filling a growing nuclear area, affecting downstream gene expression and chromatin topology, further contributing to the functional declines observed during aging.

overall_design: We performed Hi-C in neurons isolated using FACS from the cortex tissue of the aging, adult, and control mice.

first: Deborah

last: Toiber

first: Dmitrii

last: Kriukov


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

city: Houston

first: Michael

middle: T

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

middle: P

last: Souto

first: Ping

last: Gong

first: John

middle: D

last: Landua

first: Ramakrishnan

last: Rajaram Srinivasan

first: Abhinaya

last: Ganesan

first: Lacey

last: Dobrolecki

first: Stephen

middle: C

last: Purdy

first: Xingxin

last: Pan

first: Anna

last: Chung

last: Zeosky

first: S

middle: S

last: Yi

first: Heide

last: Ford


title: Polygenic trait SNPs in noncoding genomic regions: using chromatin maps to elucidate potential regulatory mechanisms in blood pressure [ATAC-seq]

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8797 Watertown Plank Rd

department: Stem Cell Transriptional Regulation

institute: Versiti Blood Research Institte

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Many polygenic traits are associated with hundreds of single nucleotide polymorphisms (SNPs), which predominantly (>95%) reside within noncoding genomic regions, making it difficult to understand how they regulate complex traits, such as blood pressure (BP). Given the central role of the kidney in regulating BP, we hypothesized that chromatin-accessible regions in renal tissue would be enriched for BP-associated SNPs (bpSNPs). We developed chromatin state and transcriptomic maps of the proximal tubules (PT) and medullary thick ascending limbs (mTAL) isolated from humans and rats. These maps revealed shared cis-regulatory elements (CREs) across humans and rats, including upstream transcriptional regulators. Notably, bpSNPs were significantly enriched within open chromatin regions, suggesting they potentially alter the activity of CREs and near genes critical to renal development and function. Collectively, this work lays a foundation for interrogating how intergenic SNPs may regulate polygenic traits such as BP.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: We used manually dissected human and rat kidney segments; proximal tubule (PT) and medullary thick ascending limb (mTAL).  We have performed bulk ATAC-seq analysis to delinate the chromatin map, and bulk RNA-seq analysis to analyze the transcriptome of these two segments.  For ATAC seq analysis, we have used three replicates of mTAL samples and four replicates PT samples from both human and rat. For RNA-seq analysis, we have used three and six replicates of mTAL and PT from human and rat, respectively.

first: Atrayee

last: Ray

first: Chun

last: Yang

first: Cary

last: Stelloh

first: Monika

last: Tutaj

first: Pengyuan

last: Liu

first: Yong

first: Qiongzi

last: Qiu

first: Paul

last: Auer

first: Chien-wei

last: Lin

last: Widlansky

first: Aron

middle: M

last: Geurts

first: Allen

last: Cowley

first: Mingyu

last: Liang

first: Anne

last: Kwitek

first: Andrew

last: Greene


title: Transcriptome-wide  changes in the Substantia Nigra following Deep Brain Stimulation in the Subthalamic Nuecleus of a PD rat model.

city: Wuerzburg

first: Rhonda

last: McFleder

address: Josef-schneider-strasse 11

country: Germany

institute: Neurologische Klinik und Poliklinik des Universitaetsklinikum Wuerzburg

summary: In this study we identify the gene espression changes that occur in the substantia nigra in a Parkinson's Disease (PD) rat model with and without deep brain stimulation (DBS). A rat model of PD was created as previously described by stereotacticaly injecting an AAV-expressing the human A53T_mutated form of a-Synuclein into the Substantia Nigra of adult rats, while control rats were injected with empty vector (EV). These mice exhibit neurodegeneration in the Substantia Nigra and Parkinson-like behaviour phenotypes. Sixteen weeks after the injection, RNA was isolated from the Substantia Nigra and Striatum. Single-end 75nt high throughput sequencing were performed on libraries prepared from the RNA. We identified over 200 genes that were differentially expressed between control and Parkinson's ratswith a log2 fold-change > |0.6|. These genes were enriched for terms related to immune activation. The genes associated with these GO terms tended to be up-regulated in the Parkinson's rats suggesting that brain-localized immune cells are more activated in Parkinson's disease. Interestingly in the rats treated with DBS, these immune-related genes were comparable to control animals.

overall_design: Every sample represents RNA isolated from the ipsilateral SN of one animal six weeks after injection of either control virus (EV) or haSyn virus (haSyn). Three weeks after viral injection all animals were implanted with an electrode in the subthalamic nucleus however only (DBS) animals received high frequency stimulation. No DBS animals were not stimulated.

first: Chi

last: Wang Ip

first: Thomas

last: Musacchio

first: Susanne

last: Knorr


title: Human tri-tissue organoids model neuromusculoskeletal development and disease [bulk RNA-Seq]

city: Shanghai

first: Jinkui

last: Zhu

state: Shanghai

address: 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China.

department: School of Life Science and Technology

institute: ShanghaiTech University

summary: The development and function of the human body involves the crosstalk between the central nervous system (CNS) and its innervated peripheral targets. One such essential crosstalk involves the connections between neural, muscular, and skeletal tissues, which have not yet been modeled with human cells. Here, we generate three-dimensional, tri-tissue organoids from human pluripotent stem cells that contain spinal cord, muscular, and skeletal components. The three distinct lineages co-develop in each single organoid and differentiate in a spatially-organized manner. The neural, muscular, and skeletal regions undergo maturation and can establish functional connections during organoid development. Using this system, we find that skeletal support is essential for human skeletal muscles’ structural and functional development. We also show that proinflammatory stimulation in skeletal regions, which resembles the pathological trigger in arthritis-associated conditions, leads to skeletal tissue degeneration, notably, causes neuromuscular structure and function deterioration. We anticipate that our tri-tissue organoids will provide a valuable model for future studies of human neuromusculoskeletal crosstalk and disease.

overall_design: Bulk RNA sequencing profiles from day86 hNMSOs.

first: Yao

last: Yin

first: Wei

last: Zhou

first: Yangfei

last: Xiang


title: Burn Injury-Induced G-CSF Secretion Depletes Spi-C+ Erythroblastic Island Macrophages and Impairs Medullary Erythropoiesis.

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: University of Cincinnati, 160 Panzeca Way

institute: University of Cincinnati

summary: The erythroblastic island (EBI) functions as a niche where erythroblastic island macrophages (EBIMφ) are positioned within rings of erythroblasts, providing support and signals that orchestrate efficient erythropoiesis. Herein, we postulated burn injury impacts the EBI, given the nearly universal presence of anemia and inflammation in burn patients, and a divergent myeloid transcriptional signature we observed in murine bone marrow following burn injury, where G-CSF secretion increased neutrophil and monocyte transcripts but reduced EBIMφ transcripts. We utilized flow cytometry to investigate EBIMφ after imaging flow cytometry confirmed the heme induced transcription factor Spi-C as a robust marker of EBIMφ in Spicigfp/igfp mice. Two populations referred to as Spic+ macrophages and Spic+ Gr1 low monocytes possessed cell intrinsic GFP, with Spic+ macrophages distinguished by higher levels of GFP, F4/80, autofluorescence, and negligible CD115 staining compared to Gr1 low monocytes. Further, at least 50% of the Spic+ macrophages stained for CD163 while staining was negligible on Gr1 low monocytes. Since CD163 distinguished the populations and macrophage remnants could convolute flow cytometry analysis, total CD163 protein was quantified in marrow aspirates to corroborate results. Application of Spicigfp/igfp mice in studies revealed a G-CSF dependent reduction of Spic+ macrophages in post burn marrow that coincided with a loss of erythroid cells and that recombinant G-CSF alone was sufficient to reduce Spic+ macrophages in the marrow. These results provide the first evidence that burn injuries impact the EBI niche through G-CSF dependent depletion of EBIMφ and support the use of Spicigfp/igfp mice in investigation of EBIMφ.

overall_design: Sham or flame burn injured mice were adminstered isotype or anti-G-CSF antibodies 12 hours prior to injury, at the time of injury, and each day prior to harvest of whole bone marrow cells on day 7 post injury.

first: Jason

last: Gardner


title: Polygenic trait SNPs in noncoding genomic regions: using chromatin maps to elucidate potential regulatory mechanisms in blood pressure [RNA-seq]

first: Sridhar

last: Rao

first: Atrayee

last: Ray

first: Chun

last: Yang

first: Cary

last: Stelloh

first: Monika

last: Tutaj

first: Pengyuan

last: Liu

first: Yong

first: Qiongzi

last: Qiu

first: Paul

last: Auer

last: Lin

first: Michael


title: Characterization of Human Melanoma Skin Cancer Models: Paving the Way for Model-Based Melanoma Research and Drug Discovery

city: Odense

first: Jakob

middle: Rask

last: Tornby

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: The need for advanced tissue models in medical research and drug development is more critical than ever. Recent changes in EU law to reduce animal testing and U.S. regulation allowing the FDA to approve drugs without animal trials highlight the importance of these models in advancement of medical science. For the models to be applicable in preclinical studies, it is essential that models are thoroughly characterized so as to understand their applicability and limitations to avoid misinterpretation caused by their limited replication of the biological functions.  In this study, we applied bioimaging and RNA sequencing to assess and contrast the architecture and gene expression profiles of various skin models, including melanoma skin models. Our results indicate that these models closely emulate actual skin morphology and gene expression, with the full-thickness (FT) models exhibiting superior resemblance to human skin, especially in the formation of the basement membrane and cellular interactions. These characteristics make the FT model particularly useful for research that focuses on these aspects. Furthermore, the integrity of the skin-like properties and genetic signatures, of both skin and melanoma cell lines, was maintained upon integration of melanoma cells, establishing these models as robust platforms for cancer research and pharmacological development. The responsiveness of the FT melanoma models to vemurafenib was successfully monitored through live imaging, demonstrating their validity as a reliable, reproducible, and humane tool for cancer research and drug development.

overall_design: We investigated gene expression in various artificially grown skin models, including melanoma skin models. These models include epidermis, dermis, full-thickness (containing both epidermis and dermis), melanoma full-thickness models (with melanoma spheroids grown from both the A375 and SK-MEL-28 cell lines).

first: Nicoline

last: Daugaard

first: Rikke

last: Tholstrup

middle: R

first: Jonathan

last: Brewer


title: Generation of human neuromusculoskeletal tri-tissue organoids [Spatial Transcriptomics]

first: Jinkui

last: Zhu

summary: The human body function requires the crosstalk between the central nervous system and its innervated peripheral targets. One such essential crosstalk involves the connections between neural, muscular, and skeletal tissues, which have not yet been modeled with human cells. Here, we describe the generation of three-dimensional, neuromusculoskeletal tri-tissue organoids (hNMSOs) from human pluripotent stem cells. Staining, single-nucleus RNA-sequencing, and spatial transcriptome profiling revealed the co-emergence and spatially confined organization of neural, muscular, and skeletal lineages relevant to human tissues within individual organoids. The neural, muscular, and skeletal regions of hNMSOs exhibited maturation and established functional connections during development, and skeletal support benefited skeletal muscles’ structural and functional development. Modeling with hNMSOs also unveiled the neuromuscular alterations following pathological skeletal degeneration. Together, our study provides an experimental model for future studies of human neuromusculoskeletal crosstalk and disease.

overall_design: Spatial transcriptome profiles of hNMSOs from day 39 to day 44.

first: Yao

last: Yin

first: Wei

last: Zhou

first: Yangfei


title: Reversal of neuronal tau pathology, metabolic dysfunction, and electrophysiological defects via adiponectin pathway-dependent AMPK activation.

city: Madison

first: Rozalyn

last: Anderson

address: 2500 Overlook Terrace

institute: University of Wisconsin-Madison

summary: Changes in brain mitochondrial metabolism are coincident with functional decline; however, direct links between the two have not been established. Here, we show that mitochondrial targeting via the adiponectin receptor activator AdipoRon (AR) clears neurofibrillary tangles (NFTs) and rescues neuronal tauopathy-associated defects. AR reduced levels of phospho-tau and lowered NFT burden by a mechanism involving the energy-sensing kinase AMPK and the growth-sensing kinase GSK3b. The transcriptional response to AR included broad metabolic and functional pathways. Induction of lysosomal pathways involved activation of LC3 and p62, and restoration of neuronal outgrowth required the stress-responsive kinase JNK. Negative consequences of NFTs on mitochondrial activity, ATP production, and lipid stores were corrected. Defects in electrophysiological measures (e.g., resting potential, resistance, spiking profiles) were also corrected. These findings reveal a network linking mitochondrial function, cellular maintenance processes, and electrical aspects of neuronal function that can be targeted via adiponectin receptor activation.

overall_design: To investigate the therapeutic benefit of adiponectin receptor signaling in AD, we treated transgenic (hTau P301S) and WT neurons with 10uM AdipoRon (or DMSO control) for 24 hours.

first: Eric

last: McGregor

first: Danny

middle: J

last: Lasky

first: Olivia

last: Rippentrop

first: Josef

last: Clark

first: Samantha

last: Wright

first: Mathew

middle: V

last: Jones


title: Generation of human neuromusculoskeletal tri-tissue organoids [snRNA-seq]

overall_design: Single nucleus RNA sequencing from day 38 and day 75 of hNMSOs.

last: Xiang


title: Murine MPC5 Cells: Interference_vs_Model

city: Hefei

first: Ling

last: Jiang

state: Anhui

address: Meishan Road

institute: AHMU

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

summary: M6A-mRNA&lncRNA Epitranscriptomic Microarray of MPC5 cells comparing HG stimulated cells with HG stimulated cells with METTL3 knockdown.

overall_design:
Two-condition experiment, HG-METTL3KD vs. HG cells. Biological replicates: 3 HG replicates, 3 HG-METTL3KD replicates.
Please note that each raw data file contains raw data for both IP (Cy5) and Sup (Cy3) sample, and is linked to the corresponding IP sample records

first: Yonggui

last: Wu


title: Bulk RNA sequencing data of rice roots protoplasted for 2.5 hours and 3 hours, as well as rice roots grown in gel, non-compacted soil and compacted soil conditions

status: Public on Dec 08 2024

city: Los Angeles

first: Rachel

last: Shahan

state: California

address: 610 Charles E. Young Dr. S

institute: University of California, Los Angeles

summary: We report raw bulk RNA sequencing data rice roots (X.kitaake) protoplasted for 2.5 hours and 3 hours to eliminate the effects of protoplasting duration on our scRNA-seq analysis,  as well as rice roots grown in gel, non-compacted soil and compacted soil conditions to verify our findsing with scRNA-seq studies

overall_design: Bulk RNA-seq of 4 wild type (X.kitaake) grown in gel conditions, 3 wilde type grown in non-compacted soil conditions and 3 wild type grown in compacted soil conditions, 2 wild type with 2.5 hours protoplasting and 3 wild type with 3 hours protoplasting.

first: Mingyuan

first: Che-Wei

last: Hsu

first: Ogorek

last: Lucas

first: Isaiah

middle: W

last: Taylor

first: Medhavinee

last: Mijar

first: Trevor

last: Nolan

first: Ari

last: Sadanandom

first: Malcolm

last: Bennett

first: Philip

middle: N

last: Benfey

first: Bipin

middle: K

last: Pandey


title: Identification of clinical and molecular features for recurrent serous borderline ovarian tumor

first: Cenxi

last: Liu

address: Songhu Road 2005

institute: Fudan University

summary: Serous borderline ovarian tumor (SBOT) is the most common type of BOT with favorable prognosis upon radical hysterectomy. But this surgery is not applicable to many SBOT patients, because they are at reproductive age and wish for future fertility. The major issue of performing fertility sparing surgery (FSS) on SBOT patients is the recurrence of tumors. Based on a cohort with 319 SBOT patients from 2009 to 2019, we identified five first-class and one second-class risk factors for recurrence in Han population. A random forest based online recurrence prediction tool was established and validated by internal cohort and an independent external cohort for SBOT patients. The multi-omics analysis on the original SBOT samples reveals that its recurrence is related to metabolism regulated immunological suppression. Our study identified several important clinical and molecular features of recurrent SBOT, which will contribute to develop personalized and targeted therapies to improve its prognosis.

overall_design: SBOT non-recurrence and recurrence samples

first: Ziyang

last: Lu

first: Fanghe

last: Lin

first: Tao

last: Li

first: Guangxing


title: RNA-Sequencing of Acute interstitial pneumonia compared with Control Lung

city: Yangsan-si

first: Donghee

last: Kwak

address: 49, Busandaehak-ro

country: South Korea

institute: Pusan national university

summary: Acute Interstitial Pneumonia (AIP) represents a severe form of diffuse lung injury within the idiopathic interstitial pneumonia spectrum. Given the limited understanding of its molecular basis, this study aims to elucidate AIP's transcriptomic profiles to uncover its pathophysiological underpinnings and identify potential therapeutic targets.

overall_design: To determine the common and unique molecular features of AIP, transcriptome analysis of lung samples from AIP (N=15), controls (N=5) was conducted. Differential gene expression was determined using p-value to control for comparison.

first: Junho

last: Kang

first: Yun Hak

last: Kim

first: Hye Ju

last: Yeo

first: Woo Hyun

last: Cho


title: The Deubiquitylase USP52 Regulates Cell Proliferation and Ferroptosis through Stabilizing SLC7A11/xCT in Bladder Cancer

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

summary: Ferroptosis, a recently coined non-apoptotic form of cell death, is triggered by lethal accumulation of iron-dependent lipid peroxidation. SLC7A11/xCT, acts as a central hub in ferroptosis, is closely related to the development of multiple human diseases. However, the specific functions and potential regulatory mechanisms of ferroptosis, especially xCT protein, in bladder cancer (BLCA) remain poorly understood. Herein, through an unbiased siRNA screen targeting 96 deubiquitinases (DUBs), we identified USP52/PAN2 as a top regulator essential for xCT protein translational activity and ferroptosis process. Functionally, loss of USP52 inhibits glutathione (GSH) synthesis through xCT degradation, leading to elevated lipid peroxidation and ferroptosis, thereby suppresses BLCA progression. Mechanistically, USP52 physically interacts with xCT through its WD40 domain, biochemically hydrolyzes the K48-conjugated ubiquitin chains of xCT at K4 and K12, thereby promotes its protein stability. Importantly, USP52 expression demonstrates a positive correlation with xCT expression in clinical BLCA samples, and high USP52 expression is linked to a worse progression and prognosis. Additionally, USP52 depletion and IKE synergistically restrained the progression of BLCA by triggering ferroptosis in vivo. Collectively, our findings reveal a molecular mechanism of USP52-xCT axis in ferroptosis, and uncover a previously unappreciated role of USP52 in BLCA tumorigenesis.

overall_design: To investigate the downstream mechanism of USP52 regulation of bladder cancer, we performed RNA sequencing on three repeated siNC and siUSP52-treated T24 cells.

first: Jianmin

first: Xinghuan

last: Wang


title: Generation of human neuromusculoskeletal tri-tissue organoids

first: Jinkui

last: Zhu

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

overall_design: Refer to individual Series


title: Mouse embryonic kidney transplantation identifies maturation defects in the medulla

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

summary: Kidney organoids are connected to the host circulation and mature after transplantation. However, they are still immature compared to the adult kidneys, and their precise maturation stages remain unclear. By transplanting the mouse embryonic kidney as a model system for organoid transplantation, we report here the maturation defects of the graft, especially in the medulla. Single cell profiling of the developing kidneys in vivo identified gene sets associated with the maturation of the collecting duct epithelium and medullary stroma. These data revealed an upregulation of genes associated with channel/transporter functions and immune defense, as well as a downregulation of neuronal genes. Using these marker genes, we found that the maturation of the collecting duct and medullary stroma in the grafts barely corresponds to the perinatal stage, which was confirmed histologically by using representative genes. Thus, the gene sets obtained serve as maturation coordinates for the renal medulla and will be helpful in analyzing its maturation defects after transplantation. They will also provide a useful basis for further maturation of transplanted kidney organoids.

overall_design: Kidney mRNA profiles of embryonic day  E15.5, E17.5, postnatal day 0 and Day7 at single cell resolution

first: Hiroshi

last: Ide

first: Koichiro

last: Miike

first: Tomoko

last: Ohmori

first: Ryuichi

last: Nishinakamura


title: MEK Inhibitor Trametinib combined with RTK Inhibitor Anlotinib in KRAS-Mutant Lung Cancer

first: Baohui

last: Han

address: 227 South Chongqing Road

department: Department of Respiratory and Critical Care Medicine

institute: Shanghai Chest Hospital

summary: Oncogenic KRAS mutations frequently detected in non-small cell lung cancer (NSCLC) have been considered undruggable until recent development of inhibitors, e.g., sortorasib, adagrasib or divarasib, specifically targeting KRASG12C. However, it still remains as a big challenge to target all the KRAS mutants besides KRASG12C. We here found that MEK inhibitor trametinib treatment results in the feedback activation of multiple receptor tyrosine kinases (RTKs) in NSCLC, and combined treatments with trametinib and anlotinib, a pan-RTK inhibitor, effectively inhibited KRAS-mutant lung cancer progression.

overall_design: For the combinational analysis, A549 cells were treated with trametinib (10nM) or anlotinib (1μM) or combination treatments for 24 hours in 6-well plates.


title: Mechanism of pyroptosis of pancreatic cancer induced by arachidonic acid

city: Chang Chun

first: Tongjia

last: Chu

state: Jilin

address: The First Bethune Hospital of Jilin University, No. 1 Xinmin Street, Chaoyang District, Changchun , Jilin Province

summary: Pancreatic cancer is one of the most deadly malignant tumors, and its treatment is scarce. This study found that arachidonic acid can induce pyroptosis of pancreatic cancer both in vitro and in vivo, and can cause immune cell infiltration.  Arachidonic acid can be used as a tumor killing drug and an immunotherapy activator, which provides a new idea for the treatment of pancreatic cancer.

overall_design: We found that tumor cells could pyroptosis only under the condition of  high concentrations of arachidonic acid treatment, but not at low concentrations. Therefore, RNA-seq was performed on three groups of samples, including Control, 40μM AA treatment group and 120μM AA treatment group, to find out the specific mechanism of arachidonic acid-induced pyroptosis in tumor cells.

first: Feng

last: Wei

first: Ziyu

last: Liu

first: Huan


title: Mechanisms of Treg cell dysfunction in activated mtDNANZB mice.

city: Philadelphia

first: Jeffrey

middle: Allen

last: Haltom

state: PA

address: 3501 Civic Center Blvd

department: Center for Mitochondrial and Epigenomic Medicine

institute: Children's Hospital of Philadelphia

summary: To investigate the underlying mechanisms of Treg cell dysfunction in the mtDNANZB mice during activation, we compared the gene expression profiles of resting and activated  Treg cells from mtDNAB6 and mtDNANZB mice.

overall_design: We compared the gene expression profiles of resting and activated  Treg cells from mtDNAB6 and mtDNANZB mice.


title: Disease type and Pathogenic Mechanism induced by PM2.5 in five Human Systems using omics and Human Disease Database

city: chongqin

first: xiaomeng

last: li

state: nanchong

address: 266 Fangzheng Avenue, Shuitu Street

institute: Chinese Academy of Sciences


title: Disease type and Pathogenic Mechanism induced by PM2.5 in five Human Systems using omics and Human Disease Database [EA.hy926]

summary: PM2.5 can harm various systems in the human body. However, due to the limitations of epidemiology and toxicology, the disease types, shared and specific pathogenic mechanisms induced by PM2.5 in various human systems are not comprehensive and in-depth revealed. Thus, this study conducted an analysis on the aforementioned issues in respiratory, circulatory, endocrine, female, and male urogenital systems. According to this study, PM2.5 was more likely to induce pulmonary emphysema, reperfusion injury, malignant neoplasm of thyroid, endometriosis of ovary, nephritis in above each system respectively. FOS, extracellular matrix, urogenital system development, extracellular matrix structural constituent conferring tensile strength, and ferroptosis was the most important co-existing gene, cellular component, biological process, molecular function, and pathway in five systems targeted by PM2.5. Furthermore, BTG2, BIRC5, NFE2L2, TBK1, and STAT1 were significantly uniquely targeted by PM2.5 in each system respectively. Important disease related cellular component, biological process, and molecular function were highly specially induced by PM2.5, such as response to wounding, blood vessel morphogenesis, body morphogenesis, negative regulation of response to endoplasmic reticulum stress, and response to type I interferon were the top 1 uq-existing biological processes in each system respectively. PM2.5 highly specially acted on the key disease related pathway, such as PD-L1 expression and PD-1 checkpoint pathway in cancer (respiratory), cell cycle (circulatory), apoptosis (endocrine), antigen processing and presentation (female), and neuroactive ligand-receptor interaction (male). This study provides a new analysis method to clarify PM2.5-related disease types, which is an important supplement to epidemiological investigation. Furthermore, this study has clarified the risks of PM2.5 exposure, elucidated the pathogenic mechanisms, and provided scientific support for promoting precise prevention and treatment of PM2.5-related diseases.

overall_design: To investigate the pathogenic molecular mechanism of cardiovascular diseases induced by PM2.5, we performed transcriptome sequencing on EA.hy926 cell models.


title: Bulk RNA-seq expression data isolated from early L4 stage C. elegans larvae

city: Worcester

first: Kellianne

last: Alexander

state: Massachusetts

address: 365 Plantation St

department: Neurobiology

institute: University of Massachusetts Chan Medical School

summary:
During development C. elegans GABAergic dorsal D-class (DD) motor neurons reverse polarity such that the axonal and dendritic compartments are switched. We found that the gene DVE-1 is important for this process.
To elucidate potential targets of dve-1 transcriptional regulation we conducted bulk RNA sequencing of total RNA from L4 stage wild type and dve-1 mutant animals

overall_design: Comparative gene expression profiling analysis of RNA-seq data for L4 stage wild type and dve-1(uf171) mutant animals

first: Michael

last: Francis


title: Characterization of Risks and Pathogenesis of Respiratory Diseases Caused by Rural Atmospheric PM2.5

city: Nanchong

first: Ronghua

last: Zhang

address: Sichuan Province Nanchong City Gaoping District North SiChuan Medical College

institute: North SiChuan Medical College

summary: Forty-six percent of the world's population resides in rural areas, the majority of whom belong to vulnerable and low-income groups. They mainly use cheap solid fuels for cooking and heating, which release a large amount of PM2.5 and cause adverse effects to human health. PM2.5 exhibits urban-rural differences in its health risk to the respiratory system. However, the majority of research on this issue has focused on respiratory diseases induced by atmospheric PM2.5 in urban areas, while rural areas have been ignored for a long time, especially the pathogenesis of respiratory diseases. This is not helpful for promoting environmental equity to aid low-income and vulnerable groups under PM2.5 pollution. Thus, this study focuses on rural atmospheric PM2.5 in terms of its chemical components, toxicological effects, respiratory disease types, and pathogenesis, represented by PM2.5 from rural areas in the Sichuan Basin, China (Rural SC-PM2.5). In this study, organic carbon is the most significant component of Rural SC-PM2.5. Rural SC-PM2.5 significantly induces cytotoxicity, oxidative stress, and inflammatory response. Based on multiomics, bioinformatics, and molecular biology, Rural SC-PM2.5 inhibits ribonucleotide reductase regulatory subunit M2 (RRM2) to disrupt the cell cycle, impede DNA replication, and ultimately inhibit lung cell proliferation. Furthermore, this study supplements and supports the epidemic investigation. Through an analysis of the transcriptome and human disease database, it is found that Rural SC-PM2.5 may mainly involve pulmonary hypertension, sarcoidosis, and interstitial lung diseases; in particular, congenital diseases may be ignored by epidemiological surveys in rural areas, including tracheoesophageal fistula, submucous cleft of the hard palate, and congenital hypoplasia of the lung. This study contributes to a greater scientific understanding of the health risks posed by rural PM2.5, elucidates the pathogenesis of respiratory diseases, clarifies the types of respiratory diseases, and promotes environmental equity.

overall_design: To investigate the pathogenic molecular mechanism of respiratory diseases induced by rural atmospheric PM2.5, the key gene RRM2 was identified by combining transcriptome and proteome sequencing with A549 and BEAS-2B cell models, and its function was further clarified by biological toxicity experiments


title: hnRNPA is a novel regulator of a mitochondrial microprotein expression

first: Su Jeong

last: Kim

address: 3715 McClintock Ave

institute: USC

summary: Mitochondrial-derived peptides (MDPs) are microproteins that are encoded by short open reading frames within the mitochondrial genome. Several MDPs have been identified in recent years; however, the transcriptional and translational regulation of MDPs remain poorly understood. Here we discovered an RNA binding protein of an MDP called humanin. By conducting RNA pull-down assays from mitochondrial extracts, we confidently pinpointed three humanin RNA binding partners that regulate translation:  heterogeneous nuclear ribonucleoproteins A1 (hnRNPA1), hnRNPA2, and hnRNPA3. We also identified a novel post-translational modification in the form of succinylation in hnRNPA1 at lysine residue K-106. Succinylation of hnRNPA1 plays an important role in mitochondrial translocation and binding affinity of hnRNPA1 to humanin mRNA. Furthermore, hnRNPA1 and humanin are highly co-expressed in prostate cancer. We provide the first evidence of mRNA binding proteins modulating the expression of a mitochondrial microprotein. This study articulates important new roles of ribonucleoproteins in modulating microprotein expression in mitochondria.

overall_design:
Examine RNAs bound to hnRNPA1 in cytosol, mitochondria, and total cell lysates by using RIPseq.
Examine differential gene expression  by hnRNPA1 knockdown using RNA sequencing

first: Su-Jeong

first: Pinchas

last: Cohen


title: Gene expression changes in in vitro equivalents of DC progenitors from uninfected or LCMV Cl13-infected mice upon Gmeb1 knockdown and treatment with glucocorticoid

status: Public on Dec 07 2024

city: Berkeley

first: Yeara

last: Jo

address: 485 Weill Hall

institute: University of California, Berkeley

summary: Gmeb1 and glucocorticoids suppress pDC development. To address which genes are involved in regulation of pDC development downstream of Gmeb1 and/or glucocorticoids, we investigated the gene expression profiles of pro-DCs (in vitro equivalents of DC progenitors) from bone marrow Flt3L culture from uninfected or LCMV Cl13-infected mice after knockdown of Gmeb1 or treatment with corticosterone.

overall_design: 7 weeks old C57Bl/6J mice were intravenously infected with 2x10^6 plaque forming units of lymphocytic choriomeningitis virus strain Clone-13. Bone marrow cells from 4-5 pooled mice were harvested to generate one single replicate per group. Bone marrow cells were harvested in duplicates at 8 days post infection and cultured in the presence of 100ng/ml Flt3L. For Gmeb1 knockdown, BM cells were enriched by using an EasySep Mouse Streptavidin Rapidspheres isolation Kit and biotin-conjugated anti-CD11b. Franctions unbound to streptavidin beads were cultured in the presence of Flt3L, and at day 2 post culture, the culture was enriched by using an EasySep Mouse Streptavidin Isolation Kit, biotin-conjugated anti-Gr-1, anti-CD19, and anti-CD127. Fractions unbound to streptavidin beads were transduced with retroviral particles encoding Gmeb1-targeting or control shRNA at days 2 and 3 post culture. For corticosterone treatment, bone marrow cells were cultured in the presence of vehicle or 50nM corticosterone. At 3.5 days post culture, pro-DCs were defined as Lin-CD11b-/loCD11c- cells (Lin includes B cells (CD19, B220), T cells (Thy1.2, CD3, CD4, CD8, CD127), NK cells (NK1.1), red blood cells (Ter119), granulocytes (Gr-1), monocytes (CD11b), and dendritic cells (MHCII)) were purified by using fluorescence-activated cell sorting (FACS). Pro-DCs transduced with retroviruses encoding control or Gmeb1-targeting shRNA were subsequently analyzed on a HiSeq 4000 instrument using a single read 100bp protocol. Pro-DCs treated with vehicle or 50nM corticosterone was sequenced using NOVA-seq with a paired end 50bp protocol.

first: Kai

first: Trever

last: Greene

first: Simone

last: Dallari

first: Nuha

last: Marooki

first: Wei

last: Wang

first: Elina

middle: I

last: Zuniga


title: Breasi-CRISPR Ccnd2 Thr280Ala mutation E13.5-E15.5 embryonic mouse cortex

city: Sioux Falls

first: Louis-Jan

last: Pilaz

state: SD

address: 2301 E 60th Street North

department: Pediatrics and Rare Disease

institute: Sanford Research

summary: Here we demonstrate the ability to model patient variants associated with two different NDDs in vivo using Breasi-CRISPR. We first model periventricular nodular heterotopia (PVNH), a neuronal migration disorder (Heinzen et al., 2018; Walters et al., 2018). We use Breasi-CRISPR to insert two patient analogous protein truncating variants in MAP1B, resulting in a significant defect in migration. We were able to validate that MAP1B fragments are being produced from these protein truncating variants, but the fragments do not act as a dominant negative. Next, we modeled a patient variant in CCND2 (encoding the protein cyclin D2) associated with megalencephaly postaxial polydactyly polymicrogyria hydrocephalus (MPPH) syndrome (Mirzaa et al., 2014). The unifying pathogenic mechanism underlying MPPH syndrome is believed to be excessive cyclin D2, a cell cycle regulator known to promote cell cycle progression. Modeling the repeated variant Thr280Ala caused an increase in the number of cells in S phase, an increase in progenitor numbers, an accumulation of cyclin D2 protein, and a tangential expansion of the cortex. We wondered if Breasi-CRISPR would be efficient enough to notice transcriptomic changes via bulk RNA sequencing of the targeted area. Indeed, we found that introduction of the MPPH syndrome variant caused an upregulation of genes and pathways important in tissue growth and a downregulation of those important in cell differentiation. Taken together we demonstrate that Breasi-CRISPR is efficient enough to model patient analogous variants, mirroring patient phenotypes and enabling investigation of NDDs.

overall_design: Breasi CRISPR in utero electroporation inserting the Ccnd2 Thr280Ala variant in embryonic mouse brains was performed at E13.5, and RNA from the transfected regions was collected at E15.5

first: L

first: Claire

last: Kittock

first: Brandon

last: Meyerink


title: METTL3-Mediated m6A Modification of TIMP2 mRNA Promotes Podocyte Injury in Diabetic Nephropathy [RNA-seq]

first: Ling

last: Jiang

summary: Epigenetic changes present in many physiological and pathological processes. The N6-methyladenosine (m6A) modification is the most common modification in eukaryotic mRNA. However, the role of m6A modification in diabetic nephropathy (DN) is still elusive. Here, the level of m6A modification was significantly upregulated in podocytes stimulated by high glucose (HG), which was caused by elevated levels of METTL3. The results were consistent in the streptozotocin (STZ)-induced experimental model of type 1 diabetes and db/db type 2 diabetes mice. Knocking out METTL3 significantly reduced the inflammation and apoptosis of HG-stimulated podocytes, while its overexpression significantly aggravated these responses. More importantly, silencing METTL3 both in type 1 and type 2 diabetic mice in vivo significantly reduced urinary albumin excretion and histopathological injury. Mechanistically, METTL3 modulated Notch signaling via the m6A modification of its target gene, TIMP2, and exerted pro-inflammatory and pro-apoptotic effects. Moreover, METTL3 enhanced the stability of TIMP2 in an insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2)-dependent manner. In summary, this study suggested that METTL3-mediated m6A modification is an important mechanism of podocyte injury in DN. Targeting m6A through the writer enzyme METTL3 is a potential approach for the treatment of DN.

overall_design: Two-condition experiment, HG-METTL3KD vs. HG cells. Biological replicates: 3 HG replicates, 3

first: Yonggui

last: Wu


title: Bulk RNA-seq expression data isolated from early L1 stage C. elegans larvae

first: Kellianne

summary:
During development C. elegans GABAergic dorsal D-class (DD) motor neurons reverse polarity such that the axonal and dendritic compartments are switched. We found that the gene DVE-1 is important for this process.
To elucidate potential targets of dve-1 transcriptional regulation we conducted bulk RNA sequencing of total RNA from early L1 stage wild type and dve-1 mutant animals

overall_design: Comparative gene expression profiling analysis of RNA-seq data for L1 stage wild type and dve-1(uf171) mutant animals

first: Michael


title: The Epigenetic Regulator UTX Imposes An Effector Differentiation Trajectory in Autoimmune CD8+ T Cell Stem-like Progenitors

first: Ho Chung

last: Chen

address: 609 Charles E Young Dr E

department: MIMG

summary: Recent findings suggest that long-lived CD8+ progenitors can continuously replenish CD8+ mediators in pancreatic lymph node (pLN). The mechanism controlling this conversion is still unclear. T cell specific UTX-deficiency NOD mice harbor increased frequency of islet-specific progenitors population and decreased frequency of islet-specific mediators. Thus, we analyzed pLN CD8+ T cells of UTXTCD mice and WT mice in 8- and 13-week old NOD mice by scRNAseq.

overall_design: We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 13-week-old NOD WT vs UTXTCD females to compare their transcriptome profile.

first: Ho-Chung

first: Shirley

first: Lisa

last: Kohn

first: Hsing Hui

first: David

last: Sailer

first: Ethan

last: McCarthy

first: Maryam

last: Seyedsadr

first: Zikang

last: Zhou

first: Xihui

last: Yin

first: Nicole

last: Wilkinson

first: Melissa

last: Lechner

first: Willy

last: Hugo

first: Maureen

middle: A

last: Su


title: The role of KLF family members, KLF4, KLF9, KLF11, KLF16 and KLF17 in human adipose derived stem cells (hADSC)

city: Houston

first: Paul

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

summary:
Analysis of change in transcriptosome after KLF4, KLF9, KLF11, KLF16 and KLF17 knockdown in hADSC.
Analysis of effects of siRNA transfection (siCtrl, siKLF4, siKLF9, siKLF11, siKLF16 and siKLF17) in hADSC at gene expression level.The hypothesis tested in the present study was that different KLF members have distinctive roles in these cells.

overall_design: Total RNA was obtained from hADSC,transfected with siCtrl, siKLF4, siKLF9, siKLF11, siKLF16 and siKLF17. siKLF samples were compared to siCtrl samples.

first: P

first: A

last: Cvoro


title: Epigenome analysis of ALKBH5 knocked down HCT116 cell

city: Guangzhou

first: Dingcheng

last: Shen

address: 26 Yuancun Erheng Road

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

type: Methylation profiling by genome tiling array

summary: ALKBH5 is one of the important m6A demethylases and is reported to be closely associated with tumorigenesis.In this study, we investigated whether ALKBH5 could affect genome-wide DNA methylation pattern. We investigated DNA methylation profile of ALKBH5 deleted HCT116 cell with control cell. The Illumina Infinium HumanMethylation 850K BeadChip was used. Samples included 2 HCT1116 shNC and 4 HCT116 shALKBH5.

overall_design: Genome-wide DNA methylation profiling of ALKBH5 KD and control HCT116 cell line.

first: Yanxin

last: Luo

first: Huichuan

last: Yu


title: Epigenetic modulation through BRD8 impairs conversion of primed EpiSCs to naïve ESCs

city: Shenzhen

first: Andrew

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology


title: Bulk RNA-seq expression data isolated from early L1 and L4 stage C. elegans larvae

first: Kellianne

last: Alexander


title: Global analysis of H3K36 methylation in the MM genome

status: Public on Dec 06 2024

city: Shimotsuke

first: Sae

last: Matsuoka

state: Tochigi

department: Center for Molecular Medicine

institute: Jichi  Medical  University

summary: We analyzed histone H3K36 methylation in multiple myeloma using ChIP-seq.

overall_design: We isolated fixed chromatin from KMS34 cells and performed immunoprecipitation with anti-histone H3K36me2 antibody, followed by deep sequencing.

first: Sae Matsuoka

last: MD

first: Jiro Kikuchi

last: PhD


title: Dendritic Cell Immunotherapy with Homologous Antigenic Loading as Adjuvant Treatment for Glioblastoma: Phase I Trial Analysis [RNA-seq]

first: Briana

middle: Amicarella

last: Burns

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Glioblastoma is a devastating CNS tumor for which median survival remains only 14-18 months. Homologous antigenic loading provides a powerful PAMP signal that initiates cDC1-like skewing of monocyte-derived DC and downstream development of tissue-homing, cytolytic memory effectors. Here we report results of a phase I trial in which DC vaccines prepared through homologous antigenic loading were administered principally to newly-diagnosed MGMT unmethylated GBM patients. AEs were mild, with none >grade 2 attributable to the regimen. Enrolled patients exhibited post-vaccination elevations in central memory and MPEC cells in peripheral blood, evidence of in situ immune responses by spatial transcriptomics, and a vaccine cell gene signature that correlated with outcomes. One-year OS of the 15/16 MGMT unmethylated newly-diagnosed cohort was 87.5%. Among nine patients who did not receive reoperation, GBM-specific OS was 88.9% with median OS yet-to-be-reached after 17.2 months follow-up among this group and late pseudoprogression notable among long-term survivors.

overall_design: Paired DC vaccine, doubly-loaded loaded with both amplified tumor mRNA and lysate, and autologous control samples loaded only with amplified tumor mRNA were normalized to read count, and statistically significant alterations to gene expression between homologous loaded vaccine and autologous, non-homologous control (mRNA-loaded only) were determined across the 18 paired samples.

first: Joseph

middle: F

last: Georges

first: Christina

last: Clay

first: Sabina

last: Amin

first: Ashley

last: Goralczyk

first: Corey

last: Mossop

first: Christopher

last: Bilbao

first: Amber

last: Valeri

last: Ifrach

first: Mazen

last: Zaher

first: Lindsey

last: Colman

first: Lynne

last: Kohler

first: Thuy

last: Cao

first: Kennisha

last: Okereke

first: Cathy

last: Schilero

first: Rahul

last: Garg

first: Nicholas

last: Troy

first: Eva

middle: H

last: Schumann

first: Mia

last: Vu

first: Akshar

last: Trivedi

first: Wei

last: Liu

first: Madhuri

last: Namekar

first: Colby

last: Hofferek

first: Keenan

last: Ernste

first: Damilola

last: Oyewole-Said

first: Nalini

last: Bisht

first: Jonathan

last: Vazquez-Perez

first: Sharon

middle: B

last: Amanya

first: Victoria

last: Rodriguez

first: Daniel

last: Kraushaar

first: Vinod

last: Ravi

first: Deancy

last: Okoebor

first: Ian

last: Bellyar

first: Jay

last: Hartenbach

first: Matthew

last: Halpert

first: Laura

last: Aguilar

first: Sigmund

last: Hsu

last: Zhu

first: Roderick


title: Long-Read Single-Cell Sequencing Confirms the Synaptic Disruptions and Developmental Delays in Neurabin I+/- iNeurons: Molecular Rescue via Gene-based Approaches

city: Dubai

first: Muhammad

last: Kumail

state: Dubai

address: Al Razi road

department: CATG

country: United Arab Emirates

institute: Mohammad Bin Rashid University

summary: Neurodevelopmental disorders (NDDs) are often associated with mutations that disrupt synaptic function and neuronal differentiation, but the mechanisms linking these genetic alterations to cellular phenotypes remain elusive. Here, we investigate the role of Neurabin I (PPP1R9A), a scaffolding protein critical for synaptic plasticity, in human neurons derived from induced pluripotent stem cells (iPSCs) with CRISPR/Cas9-mediated heterozygous mutation (Neurabin I+/-). We observed that, although mutant neurons exhibit dense and elongated neuritic extensions, they fail to form connections and display disrupted action potentials, as observed in electrophysiological studies. Employing a multi-omics approach that integrates long-read transcriptomics, including single-cell and bulk RNA sequencing, and proteomics, we revealed profound transcriptional, structural, and functional deficits associated with Neurabin I haploinsufficiency. We observed that Neurabin I+/- iNeurons revealed downregulation of key neurogenesis genes and ion channel components, while pathway enrichment highlighted dysregulation in synaptic signaling and axon guidance. Long-read sequencing provided isoform-specific insights, revealing altered expression of Neurabin I isoforms, particularly in cortical excitatory neuron subtypes, implicating isoform-specific regulatory mechanisms in the pathophysiology of NDDs. Proteomic profiling identified differentially expressed proteins enriched in pathways related to synaptic vesicle cycle, neurotransmitter release, and neurodegeneration, further substantiating the functional impact of Neurabin I deficiency. Furthermore, single-cell RNA sequencing delineated distinct neuronal differentiation trajectories, showing that Neurabin I+/- neurons exhibit stalled progression and accumulate in intermediate states, suggesting impaired maturation. Gene-based molecular rescue experiments using Neurabin I overexpression (OE) and antisense oligonucleotides (ASO) partially restored neuronal morphology, transcriptomic profiles, and synaptic protein expression, demonstrating the therapeutic potential of targeting Neurabin I in NDDs. This comprehensive multi-omics study elucidates the critical role of Neurabin I in neuronal differentiation and synaptic function, providing a mechanistic link between Neurabin I mutations and neurodevelopmental pathologies, with implications for therapeutic intervention.

overall_design: We performed long-read sequencing on the neural progenitor cells (NPCs) and iPSCs-derived neurons (iNeurons) from both wild type and mutant origins, i.e. wild type NPCs, wild type iNeurons, Neurabin I+/- NPCs, and Neurabin I+/- iNeurons. The EPI2ME pipeline was utilized to generate a transcript expression matrix for downstream analysis.

first: Zehra

last: Binte

first: Mohammed

last: Nesrin

first: Uddin

last: Mohammed

first: Berdiev

last: Bakhrom K.


title: The role of KLF family members, KLF2 and KLF8 in human adipose derived stem cells (hADSC)

first: Paul

last: Webb

summary:
Analysis of change in transcriptosome after KLF2 and KLF8 knockdown in hADSC.
Analysis of effects of siRNA transfection (siCtrl, siKLF2 or siKLF8) in hADSC at gene expression level.The hypothesis tested in the present study was that different KLF members have distinctive roles in these cells.

overall_design: Total RNA was obtained from hADSC,transfected with siCtrl,  siKLF2 or siKLF8. siKLF2 or siKLF8 samples were compared to  siCtrl samples.

first: Aleksandra

last: Cvoro


title: A biologic- and chemical-induced rat model of glomerular and tubular injury

city: Groton

first: Thomas

last: Lanz

state: CT

address: Eastern Point Rd

department: Multi-Omics & Biomarkers

institute: Pfizer

summary: Nonsurgical rodent chronic kidney disease (CKD) models for both glomerular and tubular injuries are currently limited. This study aimed to develop a rat model of CKD by combining anti-Fx1A with N(ω)-nitrophenyl-L-arginine methyl ester (L-NAME) administration. The rats were assigned to groups receiving L-NAME, anti-Fx1A, anti-Fx1A + L-NAME, or vehicle. Renal function, stiffness, injury biomarkers, histopathology and genome-wide transcriptomic changes were evaluated. Protein and renal injury biomarker levels in the urine were elevated in the anti-Fx1A alone and combination groups. Shear wave elastography revealed increased stiffness of the kidneys in all treatment groups. Histopathological evaluation revealed glomerular injury, characterized by enlarged glomeruli with increased hyaline materials in both anti-Fx1A groups and tubular degeneration/regeneration in the renal cortex of all treated groups, with the highest incidence and severity in the combination group. These tubular changes were sometimes accompanied by interstitial mononuclear cell infiltrates and interstitial fibrosis. Proteinuria and mild changes in blood, urine renal injury biomarkers and imaging endpoints were noted in association with these histopathologic changes. The concurrence and higher incidence and/or severity of glomerular and tubular injuries in the combination group indicate that this would be a useful and relevant CKD model suitable for mechanistic, pharmacologic and toxicological investigations.

overall_design: Kidneys were processed by RNAseq from rats following 7 weeks of treatment with L-NAME, anti-Fx1A, or a combination of the two drugs.

first: Seo-Kyoung

last: Hwang

first: Leah

last: Newman

first: Jessie

last: Qian

first: Thomas A

first: Chang-Ning

last: Liu


title: Single-nucleus RNA sequencing of human periventricular white matter in vascular dementia [snRNA-Seq]

city: New Haven

first: Sebastian

last: Diaz

state: Connecticut

address: 300 George St

department: Immunobiology

institute: Yale University

summary: Single-nucleus RNA sequencing of human periventricular white matter comparing healthy age-matched controls with vascular dementia patients.

overall_design: Human postmortem periventricular white matter adjacent to the frontal horn was subjected to nuclei isolation and subsequent snRNAseq.

first: Sebastián

last: Díaz-Pérez

first: Jonathan

last: DeLong

first: Cyprien

last: Rivier

first: Chia-Yi

last: Lee

first: Michael

last: Askenase

first: Biqing

first: Le

last: Zhang

first: Kristen

last: Brennand

first: Andrew

last: Martins

first: Lauren

last: Sansing


title: Single-nucleus RNA sequencing of human periventricular white matter in vascular dementia [scRNA-Seq]

summary: Single-cell RNA sequencing of human iPSC-derived microglia (iMGL) exposed to normoxia, hypoxia or oxygen-glucose deprivation (OGD) for 24 hrs.

overall_design: Human iPSCs were differentiated into microglia prior to experimental treatment and single-cell RNA sequencing.

last: Zhu


title: Pericardial adipose tissue promotes transition to heart failure with reduced ejection fraction upon pressure-overload in mice

city: Munich

first: Sabine

last: Steffens

address: Pettenkoferstrasse 9b

department: Clinical Pathobiochemistry

institute: Institute for Cardiovascular Prevention-LMU Klinikum

summary: Aims: In humans, secretome of pericardial (PAT) and epicardial adipose tissue (EAT) contribute to establishment of heart failure (HF) with preserved ejection fraction (HFpEF) originating from pressure-overload due to metabolic disorder. We examined whether PAT affects also manifestation and progression of pressure-induced HF in the absence of metabolic burden in mice. Methods and results: Progressive remodelling was assessed in C57BL/6J males, aged 9 wks, randomly assigned to sham surgery or transverse aortic constriction (TAC) for 1 week (early pressure-overload), 8 (chronic pressure-overload), or 12 weeks (HFrEF) with or without concomitant PAT excision. PAT removal did not affect early (1 wk TAC), and chronic (8 wks) pressure-overload induced concentric remodelling. However, the initial PAT excision prevented TAC-induced expansion of pro-inflammatory macrophages during early pressure-overload and attenuated the persistent LV expression of pro-hypertrophic, pro-inflammatory and pro-fibrotic factors as well as the drastic LV dilation and progressive systolic dysfunction in the long-term and thereby protected against the transition to HFrEF. This protection was associated with significant reduction of microscar and perivascular fibrosis. The latter was, at least in part, attributed to reduced accumulation of pro-fibrotic CD206+ macrophages around the coronaries 12 wks post-surgery in the absence of PAT compared to mice with intact PAT. In addition, PAT bulk RNA sequencing revealed the initiation of an extracellular matrix deposition programme in the PAT early upon TAC surgery, which might trigger fibrotic responses in the underlying myocardium. Indeed, isolated naive adult cardiac fibroblasts exposed to PAT lysate from 12 wks TAC mice increased collagen production and cell viability/proliferation. Conclusion: Our data suggest PAT to play divergent roles in the chronically pressure overloaded heart versus HFrEF - while widely not affecting concentric hypertrophy, PAT removal counteracts manifestation of HFrEF in mice, at least in part, by preventing excessive fibrotic and macrophage responses.

overall_design: To investigate the impact of pericardial adipose tissue (PAT) on pressure-overload induced heart failure progression, we subjected male wild-type mice to TAC or sham surgery for different time periods with or without additional surgical PAT removal and characterized the PAT-dependent phenotypes. Vice versa we examined the impact of TAC-mediated pressure-overload and duration of pressure-overload on the PAT itself. Herein, we excised PAT 1 wk after TAC/Sham and 12 wks post -TAC in n=6-7/group for subsequent bulk PAT RNA sequencing. Comparative gene expression analyses were performed ( 1wk Sham vs. 1 wk TAC; 1 wk TAC vs. 12 wks. TAC).

first: Guo

last: Li

first: Sarah-Lena

last: Puhl


title: Transcriptional changes in PC12 cells induced by repetitive transcranial magnetic stimulation (rTMS) in MSCs-inhibited inflammatory conditions

city: Guang Zhou

first: Shimei

last: Cheng

state: Guang Dong

address: Guang Zhou, Guang Dong, China

department: Department of Rehabilitation Medicine

institute: The Third Affiliated Hospital of Sun Yat-sen University

summary: Neuronal death is the primary cause of poor outcomes in cerebral ischemia. The Inflammatory infiltration in the early phase of ischemic stroke plays a vital role in triggering neuronal death. Either transplantation of mesenchymal stem cells (MSCs) derived from humans or repetitive transcranial magnetic stimulation (rTMS) have respectively proved to be neuroprotective and anti-inflammatory in cerebral ischemia. However, either treatment above has its limitations. Whether these two therapies have synergistic effects on improving neurological function and the underlying mechanisms remains unclear.Using an in vitro model of PC12 nerve cell co-culture with MSCs, we demonstrated a transcriptional response pattern, including REST, in which rTMS inhibited PANoptosis of PC12 cells in a low-inflammation environment induced by MSCs. This molecular investigation is helpful in providing a basis for sorting out the complex molecular mechanism of combination of rTMS and MSCs in treating ischemic stroke.

overall_design: Gene expression microarray analysis of 20 sequential in vitro PC12 cells from four deprivation/reoxygenation (OGD/R), four mesenchymal stem cells (OGD/R+MSCs), and four MSCs+rTMS (OGD/R+MSCs+rTMS) at the 48 hours time point after either MSCs and/or 10Hz repetitive transcranial magnetic stimulation (rTMS) treatment.

first: Qiying

last: Lu

first: Qiuli

first: Yuanchen

last: Ma

first: Jinshuo

last: Chen

first: Di

first: Mudan

last: Huang

first: Yinong

first: Erming

last: Zhao

first: Jing

last: Luo

first: Haiqing

last: Zheng


title: Impact of LINE-1 overexpression on gene expression in human induced pluripotent stem cell-derived microglia

city: New York

first: Falak

last: Sher

state: New York

address: 630 W 168th street

institute: Columbia University

summary: The aberrant expression of the transposable element LINE-1 is posited to impact cellular function and contribute to disease. We report that LINE-1 overexpression in these microglial cells drives significant functional and transcriptomic changes, including altered expression of genes associated with antigen presentation.

overall_design: To investigate the impact of increased LINE-1 expression on human microglia, we utilized the CRISPR activation system to establish human iPSC-derived microglial cell lines over expression LINE-1, as well as a corresponding non-targeting control. We generated three independent cell lines for each condition, and performed bulk RNA-seq on the differentiated microglia to examine how LINE-1 over expression impacted the microglial transcriptome.

first: Nainika

last: Roy


title: Analysis of differential gene expression in the Streptococcus sanguinis comC mutant

city: Richmond

first: Ping

last: Xu

state: VA

address: 521 North 11th street

department: Philips Institute for Oral Health Research

institute: Virginia Commonwealth Univ. School of Dentistry

summary: Gene expression profile of the Streptococcus sanguinis comC deletion mutant compared to the wild-type strain SK36

overall_design: Experiment: comC mutant vs. wild-type SK36. Biological replicates independently grown and prepared for each sample.

first: Bin


title: Custom-designed lipid-based nanoparticles efficiently deliver mRNA to reverse the pathogenesis of LAL deficiency in a preclinical model

city: Montreal

first: Simon-Pierre

last: Gravel

state: QC

address: 2940 ch. de la polytechnique

department: Faculty of pharmacy

country: Canada

institute: University of Montreal

summary: Lysosomal acid lipase (LAL) is a crucial enzyme responsible for the hydrolysis of triglycerides (TGs) and cholesteryl esters (CEs) in the lysosomes. LAL deficiency results in the extensive storage of CEs and TGs in the liver and the spleen, inducing hepatosplenomegaly, and can be a life-threatening condition with patients rarely surviving beyond 6 months of age in the most aggressive form. Using messenger ribonucleic acid (mRNA) for protein replacement is an innovative approach to treating LAL deficiency. Here, we describe the development of a new lipid-based nanoparticle (LNP) formulation capable of efficiently delivering LAL mRNA and restoring LAL activity in affected organs mediating significant reversal of the pathological progression in a highly predictive preclinical model.  A combinatorial library of mRNA-LNPs was generated and screened both in vitro and in vivo to yield a new formulation with a higher potency than an FDA-approved MC3-based nano-formulation. In vivo evaluation revealed that the new formulation could promote a more sustained and superior LAL expression. Multiple injection regimen was able to mitigate hepatosplenomegaly and reduce the lipid accumulation of CEs and TGs by 20-30% in the liver and 50% in the spleen. Furthermore, liver inflammation processes and development of fibrosis were significantly diminished. These findings provide strong evidence that mRNA-LNP is a very promising approach for the chronic treatment of LAL deficiency and support the clinical translation of mRNA therapy to overcome side effects and challenges encountered with traditional enzyme replacement therapies.

overall_design: An efficacy study in LAL knockout (LAL-/-) mice was performed to investigate the effect of mRNA therapy for treating LAL deficiency. 3 sex- and age-matched groups with equal number of mice  were treated for 8 weeks at a 5-day interval. Wild-type (WT) mice received empty nanoparticles (WT+Blank), untreated LAL-/- mice received also blank nanoparticles (LAL-/-+Blank) and the last group was treated with mRNA-LNP formulation F23 (LAL-/-+F23). 1.0 mg/kg body weight. During the treatment period, 1 LAL-/-+Blank mice died, and one WT mice was excluded from the study yielding at the end point to a total of 28 mice. From each mouse, liver was harvested and RNA extracted for RNA sequencing analysis. PCA analysis showed that one sample (Sample 28, 7121-0629) was wrongly clustered and was therefore withdrawn from subsequent differential gene expression analyses. This mouse was treated at a later age than all other mice, whcih minimized the impact of treatment.

first: Davide

last: Brambilla

first: Matthias

last: Zadory

first: Dagmar

last: Kratky

first: Nemanja

last: Vujic


title: RNA genome expansion up to 64 kb in nidoviruses: role of host, genome segmentation, translation elongation and replicase expression

city: Würzburg

first: Redmond

last: Smyth

state: Bayern

address: Josef-Schneider-Straße 2, D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: Positive-strand RNA viruses of the order Nidovirales have the largest known RNA genomes of vertebrate and invertebrate viruses with 36.7 and 41.1 kb, respectively. The acquisition of a proofreading exoribonuclease (ExoN) locus by an ancestral nidovirus enabled crossing of the 20 kb barrier. Other factors constraining genome expansions in nidoviruses remain poorly defined. Here, we assemble 76 genome sequences of invertebrate nidoviruses from >500.000 published transcriptome experiments and triple the number of known nidoviruses with >36 kb genomes, including the largest known 64 kb RNA genome. Many of the novel viral lineages acquired putative enzymatic domains that were inserted in open reading frame (ORF) 1a and ORF1b or equivalent regions and may constitute cofactors of the viral replicase or modulate infection otherwise. We classify multi-cistronic ExoN-encoding nidoviruses into seven groups and four subgroups, according to canonical and non-canonical modes of viral polymerase expression by ribosomes and genomic organization (reModes). The largest group employing the canonical reMode comprises invertebrate and vertebrate nidoviruses, including coronaviruses, with genomes ranging from 20 to 36 kb. Six groups with non-canonical reModes include giant invertebrate nidoviruses with 31 to 64 kb genomes. Among them are viruses with segmented genomes and viruses utilizing dual ribosomal frameshifting that we validate experimentally. Moreover, polyprotein length and genome size in nidoviruses show reMode- and host phylum-dependent relationships. We demonstrate that the largest polyproteins in nidoviruses may be close to an upper limit that we hypothesize to be determined by the host-inherent translation fidelity, further constraining nidovirus genome size. Thus, expansion of giant RNA virus genomes, the vertebrate/invertebrate host division, the control of viral replicase expression, and translation fidelity are interconnected.

overall_design: DMS-MaP analysis of in vitro transcribed RNA

first: Benjamin

last: Neuman

first: Alexandria

last: Smart

first: Orian

last: Gilmer

first: Josef

last: Vaas

first: Nicolai

last: Böker

first: Dmitry

last: Samborskiy

first: Ralf

last: Bartenschlager

first: Stefan

last: Seitz

first: Alexander

last: Gorbalenya

first: Neva

last: Caliskan

first: Chris

last: Lauber


title: Splicing Correction as a Therapeutic Approach for Acetylation-Defective p53 K120R mutation

city: Daejeon

first: Doyeong

last: Kim

institute: Chungnam Natl' University

summary: The TP53 c.359A>G mutation severely impairs expression of the major TP53 transcript variant encoding p53 K120R by creating a new splicing donor site. Antisense morpholino oligomer (AMO) targeting the mutation site restored normal splicing and expression of the major variant. Despite the recovery of mutant TP53 mRNA levels, the functional restoration as the tumor suppressor of p53 K120R was unclear. Given that p53 exerts its tumor suppressor function through regulation of target genes that mediate growth arrest or apoptosis, the p53 K120R mutant exhibits impaired transcriptional regulation of CDKN1A, a key target gene in growth arrest, while maintaining normal induction of the pro-apoptotic BBC3 gene. Consequently, the p53 K120R mutant protein demonstrates a phenotype characterized by defective cell growth arrest but retained apoptotic induction capacity, suggesting that the p53 K120R mutant protein may retain some tumor suppressor functionality. In addition, Lysine 120 provides a critical acetylation site linked to p53 activation. Although other studies of the oncogenic effects of p53 K120R highlight the relevance of acetylation for tumor suppression, our findings indicate that targeting mutant TP53 mRNA is a prerequisite for restoration of p53 function. In particular, despite the presence of mutations, it showed sufficient corrective effect to restore p53 functions, including apoptosis induction. In conclusion, this study highlights the potential of AMO-mediated splice correction as a therapeutic approach for TP53 mutations.

overall_design: The splicing issue caused by the TP53 c.359A>G mutation was treated with an antisense morpholino oligonucleotide, and its effects were studied.

first: Sun-Ku

last: Chung

first: Sang-Min

last: Park

first: Jin-Chul


title: ALFIN-like proteins link histone H3K4me3 with H2A ubiquitination and coordinate diverse chromatin modifications in Arabidopsis

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: The Arabidopsis H3K4me3-binding ALFIN-like proteins are components of the PRC1 complex and promote H2A ubiquitination, thereby establishing a connection between H3K4me3 and H2A ubiquitination across the genome. Additionally, the ALFIN-like proteins interact with various chromatin-related proteins involved in H2A.Z deposition, H3K27me3 demethylation, histone deacetylation, and chromatin accessibility. The ALFIN-like proteins play a crucial role in coordinating H3K4me3 with diverse other chromatin modifications.

overall_design: Refer to individual Series


title: Deep phenotyping the right ventricle to establish translational MRI biomarkers for characterization of adaptive and maladaptive states in pulmonary hypertension

city: London

first: Lan

last: Zhao

address: Du Cane road

department: NHLI

country: United Kingdom

institute: Imperial College London

summary: We performed molecular phenotyping of RV remodelling in pulmonary hypertension (PH), using transcriptome analysis of RV tissue obtained from SuHx-induced male rats.When compared to human RV decompensated PH, the molecular characterisation of these rats showed that ECM and collagen fibrillar organisation were highly upregulated in SuHx rats and human profiles along with responses to cytokines. Moreover, growth differential factor was found common in SuHx and RV human samples.

overall_design: RNA sequencing was performed on rat RV tissues which were classfied as maladaptive SuHx (n=3) as well as healthy RV from control rats (n=3).

first: Lin


title: A Meta-Atlas of the Developing Human Cortex Identifies Modules Driving Cell Subtype Specification [Chimeroid]

city: Los Angeles

first: Patricia

last: Nano

state: CA

address: 615 Charles E Young Dr S

institute: University of California, Los Angeles

summary: During development, the human brain orchestrates the generation of hundreds of diverse cell types, and recent transcriptomic atlases of the developing human cortex provide new opportunities to identify novel regulators of cell fate specification. We have conducted an integrated meta-analysis of seven recently published single-cell transcriptomic profiles of the developing human cortex, generating a meta-atlas of 225 meta-modules. By tracking the activity of these meta-modules throughout development and comparing this to datasets from the adult human as well as the developing and adult mouse, we identified modules with potential roles in the transition from neurogenesis to gliogenesis and neuronal subtype maturation. The cell type and developmental state at which these modules exist was validated in primary samples from the developing human brain. Of particular interest, we identified and validated a module associated with both developing human deep layer neurons and human adult deep layer neuronal subtypes expressing the terminal differentiation marker FEZF2. Though FEZF2 is neither a member of nor co-expressed with our deep layer-associated gene module, almost half of module genes are putative FEZF2 targets, including TSHZ3, a transcription factor associated with neurodevelopmental disorders such as autism. Knockdown experiments in human cortical organoid models confirm that both FEZF2 and TSHZ3 are necessary for deep layer neuron specification. Importantly, we observe that subtle manipulations of these transcription factors result in slight changes in module activity, but together yield strong differences in cell fate. Our analyses therefore reveal a gene network that required to generate deep layer neuronal subtypes, demonstrating the ability of our meta-atlas to engender further mechanistic analyses of cortical fate specification. We anticipate this resource being useful for the study of co-expression programs across diverse biological questions related to the developing neocortex.

overall_design: Human cortical organoid models were used to functionally interrogate the role of module 20 in the specification of human deep layer neurons. Stem cells were passaged in the presence of lentivirus expressing an shRNA construct and an mCherry coding sequence. One of four shRNA sequences were used: a scrambled (scram) sequence, two FEZF2-targeting sequences, and a TSHZ3-targeting sequence. After a minimum of 12 days in culture, stem cells were used to generate cortical organoids, in which a subset of cells express shRNA as indicated by mCherry fluorescence. The resulting FEZF2 or TSHZ3 knock-down organoids were maintained for a minimum of 7 weeks prior to characterization with single-cell RNA sequencing.

last: Rayos Nano

first: Aparna

last: Bhaduri


title: APE1 regulates the transcription of urea cycle genes through stabilizing DNA G-quadruplexes in lung adenocarcinoma [ATAC-seq]

city: Shanghai

first: Yanhao

last: Yu

address: Yueyang Street

institute: Center of Excellence in Molecular Cell Science

summary: Lung adenocarcinoma (LUAD) remains the leading cause of cancer deaths worldwide. Apurinic/apyrimidinic endonuclease 1 (APE1), an enzyme integral to DNA repair and redox signaling, is notably upregulated in various cancers, including LUAD. Here we reveal that APE1 amplification, primarily via allele duplication, correlates with poor prognosis in LUAD patients strongly. Using human LUAD cell models and a KRAS-driven genetically engineered mouse model (GEMM), we show that APE1 deletion hampers cell proliferation and tumor growth, highlighting its role in tumorigenesis. Mechanistically, APE1 promoted the transcription of urea cycle genes CPS1 and ARG2 by modulating the presence of G-quadruplex (G4) structures in their promoter regions. Loss of APE1 disrupts the urea cycle and pyrimidine metabolism, inducing metabolic reprogramming and growth arrest, which can be rescued by CPS1 or pyrimidine restoration. These findings uncover APE1’s role in metabolic regulation via G4-mediated transcription, providing a potential therapeutic target LUAD patients with elevated APE1 expression.

overall_design: ATAC-seq in WT and APE1 knockout A549 cells.

first: Yiqin

last: Wang


title: SenMayo transcriptomic senescence panel highlights glial cells in the ageing mouse and human retina

city: Camperdown

first: Katharina

last: Bell

state: NSW

address: Medical Foundation Building, Levels 4-6, 92-94 Parramatta Rd

country: Australia

institute: The University of Sydney

summary: There is a growing need to better characterise senescent cells in the CNS and retina. The recently published SenMayo gene panel was developed to identify transcriptomic signatures of senescence across multiple organ systems, but the retina was not included. While other approaches have identified senescent signatures in the retina, these have largely focused on experimental models in young animals. We therefore conducted a detailed single-cell RNA-seq analysis to identify senescent cell populations in the retina of different aged mice and compared these with five comprehensive human and mouse retina and brain transcriptome datasets. Transcriptomic signatures of senescence were most apparent in mouse and human retinal glial cells, with IL4, 13 and 10 and the AP1 pathway being the most prominent markers involved. Similar levels of transcriptional senescence were observed in the retinal glia of young and old mice, whereas the human retina showed significantly increased enrichment scores with advancing age.

overall_design: Mouse retina tissue from 3 different age groups was collected, sorted via MACS(R) and analysed via scRNA sequencing. 10x Genomics Cellranger output filtered feature-barcode matrices  available in sample wise supplementary information.

first: Samyuktha

last: Suresh

first: Gayathri

last: Karthik

first: John

last: Ouyang

first: Vicki

last: Chrysostomou

first: See

last: Tang

first: Enrico

last: Petretto

first: Jonathan

middle: G

last: Crowston

middle: C


title: Transcriptomic profiling of primary and unmatched lung metastatic clear cell Renal Cell Carcinoma

city: Boston

first: Yufei

state: MA

address: 450, Brookline Ave

institute: Dana-Farber Cancer Institute

summary: To understand the tumor immune microenvironment (TIME), we sequenced CD45+ tumor infiltrating leukocytes (TILs) isolated from three primary and three lung metastatic clear cell renal cell carcinoma (ccRCC) specimens.

overall_design: Comparison of unpaired primary and lung metastatic ccRCC

first: Michael

middle: P

last: Lynch

first: Hsien-Chi

last: Yuan

first: Aedin

last: Culhane

first: Wayne

last: Marasco


title: 3D Chromatin Structures Foreshadow the Drosophila Fate Map

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab

department: QCB

institute: Princeton

summary: 3D structure of chromatin is thought to be critical for the regulation of gene expression during development. Here we employ the Micro-C assay to achieve 100 bp resolution for the genome organization of Drosophila melanogaster throughout the first half of embryogenesis. The resulting contact maps enable the identification of fine-scaled structures such as individual loops and boundaries delineating TADs. We observe that 3D structures form prior to zygotic genome activation in precellular embryos, and many of these organizational features persist during successive mitotic cycles. 3D structures are classified through the use of 149 ChIP-seq datasets. We present evidence for specialized elements associated with housekeeping genes that are enriched for BEAF-32 but not CTCF. We also characterize a distinct class of elements associated with developmental gene regulation that are enriched with GAF and Zld binding. This binding is maintained during mitotic cycles and exhibits evolutionary conservation of both sequence and 3D structures. In sum, this work provides a comprehensive genome-wide characterization at unprecedented resolution of the role of 3D chromatin organization in gene regulation during development. We propose that the 3D organization of the pre-cellular embryo facilitates deployment of the developmental control genes defining the Drosophila fate map.

sample_organism:
Drosophila melanogaster
Drosophila virilis

overall_design: Micro-C in Drosophila embryos at stages nc1-8, nc12 (mitotic), nc14, and s10-12 with two biological replicates and two technical replicates.

first: Xinyang

last: Bing

first: Evan

last: Cofer

first: Gabriel

last: Dolsten

first: Benjamin

last: Brack

first: Marcus

last: Curlin

first: Chandra

last: Theesfeld

first: Olga

last: Troyanskaya

last: S Levine


title: The Multifaceted Role of Vitreous Hyalocytes: Orchestrating Inflammation, Angiomodulation, and Erythrophagocytosis in Proliferative Diabetic Retinopathy

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

summary: Despite great advancements in proliferative diabetic retinopathy (PDR) therapy over the last decades, one third of treated patients continue to lose vision. Vitreous macrophages called hyalocytes have been implied in the pathogenesis of vitreoretinal proliferative disease previously but little is known about their role in PDR. In this study, we address molecular and cellular alterations of the PDR vitreous, in order to assess the potential contribution of hyalocytes to PDR development. A total of 55 patients were included in this study encompassing RNA-Sequencing analysis of vitreous hyalocytes from PDR and control patients, multiplex immunoassay and ELISA analysis of undiluted vitreous samples and isolation and immunohistochemical staining of cultured porcine hyalocytes. Our transcriptional analysis revealed an enhanced inflammatory signature of hyalocytes contributing to the cytokine pool within the PDR vitreous by expressing, among others, interleukin-6. The data further indicate an expression shift, involving angiopoietin-2, in PDR hyalocytes converting them to a proangiogenic cellular component, which may mediate formation of retinal neovascularization, hallmark of PDR. Finally, our data suggest a role of vitreous macrophages in erythrophagocytosis and, thereby, removal of vitreous hemorrhage, a severe complication of PDR. Immunomodulation of hyalocytes may thus prove an essential novel therapeutical approach in diabetic vitreoretinal disease.

overall_design:
Hylalocytes from humans with proliferative diabetic retinopathy (n=8), macular hole (MH) (=control) (n=5) and macular pucker (MP) (=control) (n=4). 4 MH and 3 MP samples were used from a previously published dataset from our group (GSE147657)

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The table below lists GEO accessions reused/reanalyzed for this study.
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first: Stefaniya

last: Boneva

first: Julian

last: Wolf

first: Malte

last: Jung

first: Gabriele

last: Prinz

first: Jacqueline

last: Jauch

first: Anne

last: Drougard

first: Andrew

last: Pospisilik

first: Anja

last: Schlecht

first: Felicitas

last: Bucher

first: Hansjürgen

last: Agostini

first: Günther

last: Schlunck


title: Pericardial Fluid of Patients with Coronary Artery Disease Can Drive Fibrosis via TGF-Beta Signalling Pathway

city: Calgary

first: Paul

last: Gordon

state: AB

address: 3330 Hospital Drive NW

institute: University of Calgary

summary: Pericardial fluid (PF) helps maintain homeostatic conditions that facilitate optimal heart function. We have yet to understand how cardiovascular pathologies affect the profile of PF. We hypothesized that human PF contains immune markers that can be affected by different pathologies and contribute to inflammatory-mediated processes, such as fibrosis.   PF was collected from patients undergoing cardiac surgery. Multiplex analysis was performed to determine the composition of inflammatory markers and soluble mediators. A gel contraction assay was used to investigate the fibrotic potential of PF. RNA-sequencing was used to elucidate the mechanisms driving the pro-fibrotic properties of PF.  With the results of these multiple approaches we show that the acellular component of PF has pro-fibrotic characteristics and suggest putative mechanisms that can explain such observations.

overall_design:
Patients undergoing isolated CABG and valvular surgeries at Foothills Medical Centre (Calgary, Canada) were prospectively enrolled in the study after providing written informed consent. Native Pericardial Fluid (PF) was obtained from all patients before the institution of cardiopulmonary bypass (CPB) and the administration of heparin or steroids. Pericardial tissue and right atrial appendage were also collected from patients.
Human cardiac fibroblasts were isolated from right atrial appendage taken from consenting patients, then culture alone, with pericardial fluid supernatant, or with the supernatant plus TGF-β1 receptor inhibitor (TGF-βR1i).

first: Ali

last: Fatehi Hassanabad

first: Darrell

middle: D

last: Belke

middle: M

first: Guoqi

last: Teng

first: Jameson

last: Dundas

first: Anna

last: Zarzycki

first: Jeannine

last: Turnbull

first: Justin

last: Deniset

last: Fedak