title: Effects of daridorexant on gene expression in the hypothalamus of LPS-induced mice.

status: Public on Feb 25 2025

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

summary: Acute inflammatory processes disrupt hypothalamic homeostatic systems, leading to a preference for sleep over wakefulness. Orexin knockout mice exhibit faster recovery from LPS-induced sickness, possibly due to enhanced sleep during inflammation. The reduction in orexin activity limits physical activity and encourages sleep, though it remains uncertain whether these responses are pathological or protective. In this study, to investigate the effects of daridorexant, a dual orexin receptor antagonist, on brain inflammation and sleep quality, we employed a systemic inflammatory model in C57BL/6J mice. LPS treatment resulted in significant decreases in REM sleep and wakefulness, while non-REM sleep increased. Here, we provide gene expression profiling of hypothalamus tissues using the RNA sequencing for identifying changes by daridorexant in gene expression of the LPS-treated mice.

overall_design: mRNA profiles of  hypothalamus were generated by RNA sequencing using the Illumina NextSeq 500  (Illumina).

first: Dai

last: Horiuchi

first: Koichiro

last: Tatsumi


title: Single-nuclei RNA/ATAC-seq of healthy and injured human kidney nephrectomy tissue

status: Public on Mar 25 2025

city: Ediburgh

first: Maximilian

last: Reck

address: 47 Little France Crescent

country: United Kingdom

institute: University of Edinburgh

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Improved understanding of the renal cell phenotypes and intercellular signaling pathways that mediate chronic kidney disease is required to develop novel therapeutics. To this end, we performed simultaneous single nuclear RNA and ATAC-sequencing on kidney tissue from patients undergoing tumour nephrectomy, where the ureter was either obstructed by tumour or remained unobstructed. In obstructed kidneys a discrete subset of proximal and ascending thin limb of loop of Henle tubular cells acquired a pro-inflammatory phenotype enriched in senescence markers.

overall_design: We performed single-nuclei RNA and ATAC sequencing using the 10x Genomics Multiome kit to profile gene expression and chromatin changes during kidney injury. Nuclei were isolated from human kidney nephrectomy tissue and 3-5 samples were pooled and processed simultaneously.

first: Bryan

middle: R

last: Conway


title: A Novel Rescue Strategy for Bone Marrow Hematopoietic Failure via Microenvironment Reconstruction with Reduced HSC Dependency

status: Public on Feb 14 2025

city: chongqing

first: Debao

last: Li

address: No. 13, Tianchi Avenue, Mudong Town, Banan District, Chongqing

country: China

institute: Chongqing International Institute for Immunology

summary: Hematopoietic stem cell transplantation (HSCT) represents the most effective therapeutic approach for hematopoietic malignancies, bone marrow (BM) failure syndromes, and primary immunodeficiency diseases. However, the clinical demand for HSCT is constrained by current limitations in HSC sources and expansion technologies. The BM niche is crucial providing a supportive microenvironment for the self-renewal and differentiation of HSCs, and its rejuvenation is essential for rapid and effective hematopoietic recovery. In this study, we demonstrate that costal-cartilage-derived stem cells (CDSCs) can achieve hematopoietic reconstruction comparable to HSCT, even with a significantly reduced number of hematopoietic stem and progenitor cells (HSPCs), while exhibiting low chimerism. We further show that transplanted CDSCs differentiate into various cell types, including bone marrow stromal cells (BMSCs), endothelial cells, and osteoblasts, and secrete pro-hematopoietic factors that restore the damaged BM niche. Moreover, in vitro-expanded CDSCs exhibit elevated expression of BMSC markers and enhance hematopoietic recovery in injury models. Notably, the combination of CDSCs with cyclosporine A is effective in treating aplastic anemia in mouse models. Collectively, these findings propose a novel strategy for treating BM hematopoietic failure through microenvironmental restoration and broaden the potential therapeutic scope of HSCT.

overall_design: The primary and cultured CDSCs at passaged P2-P3 underwent single cell RNA-seq (scRNA-seq) (MobiDrop, China).

first: Rui

last: Dong

first: zhiguo

last: Ling


title: Flagellin nebulization enhances respiratory immune responses in the porcine model

status: Public on Feb 19 2025

city: LILLE

first: Florence

last: MAURIER

address: 1 rue du Professeur Calmette BP 245

department: Plateformes Lilloises en Biologie & Santé

country: France

institute: Institut Pasteur de Lille

summary: Respiratory delivery of the Toll-like receptor 5 agonist FLAMOD, a recombinant flagellin, offers a promising approach for treating bacterial pneumonia. FLAMOD stimulates the airway epithelium, mobilizing and activating immune cells and effectors to combat infections. While previous evidences were obtained in mouse models, this study represents the first comprehensive assessment of FLAMOD delivered by nebulization in pigs. Our results demonstrate that a single nebulization of FLAMOD did not cause any adverse effects on clinical parameters. Histological analysis supported that FLAMOD treatment led to immune cell infiltration in the lung tissue, indicative of an active immune response. Flow cytometry confirmed granulocyte recruitment in conducting airways. RNA sequencing established immune activation across the respiratory tract, from the nose, trachea, bronchi to the lungs, highlighting innate immunity, bacterial defense, cytokine and chemokine signaling, and granulocyte chemotaxis as key biological pathways. These findings demonstrated FLAMOD’s capacity to induce a robust and common immune response throughout the porcine respiratory system as well as specific compartmentalized immune signature. This study establishes FLAMOD as a potent activator of innate immunity, providing a proof-of-concept for inhalation-based therapeutic strategies to combat bacterial pneumonia in clinical setting.

overall_design: Twelve male six-week-old pigs (Sus scrofa domestica, line LRxLW TOPIGS 20, Lelystad) were nebulized with diluent buffer for 24h, flagellin for 4h and flagellin for 24h (n=4 per group).  Nose, trachea, bronchus, and lung tissue as well as blood were sampled and processed for RNA isolation and sequencing.

first: Jean-Claude

last: Sirard

first: David

last: Hot

first: Mara

last: Baldry

first: Arndt

last: Benecke


title: Differential expression of lncRNAs enriched in coronary thrombus-derived exosomes from AMI patients relative to serum patients with AMI and their functional differences

city: Guiyang City

first: Youfu

last: He

state: Guizhou Province

address: No.83 Zhongshan East Road, Nanming District, Guiyang City, Guizhou Province, China

institute: Guizhou Provincial People's Hospital

summary: Purpose: to detect the expression differences of Long chain non coding RNA(Lnc RNA) in exosomes derived from Thrombus-derived exosomes in AMI patients, healthy human serum-source exosomes and AMI patients serum-source exosomes.  Methods: Total RNA containing Long chain non coding RNA was extracted from Thrombus-derived exosomes in AMI patients. Use Agilent lncRNA array for lncRNA analysis. Each lncRNA was repeatedly detected by the probe 30 times. The array also contains 2164 Agilent control probes. Agilent Feature Extraction (Agilent) was used to analyze the lncRNA array data for data aggregation, standardization and quality control. Perform the default 90th percentile normalization method for date preprocessing. To select differentially expressed genes, we used thresholds of ≥2 and ≤−2 fold change, and the Benjamini-Hochberg corrected p vlaue was 0.05.  Results: Compared with the Normal group, there were 2148 lncRNAs up-regulated and 2415 lncRNAs down-regulated in the serum group, and 2615 lncRNAs up-regulated and 452 lncRNAs down-regulated in the thrombus group. Compared with the serum group, there were 1374 lncRNAs up-regulated and 1218 lncRNAs down-regulated in the thrombus group.  Conclusion: The 2615 lncRNAs upregulated relative to the Noormal group are candidates for regulatory targets of thrombosis-related regulatory pathways.

overall_design: A total of 11 samples were taken. Among them, 3 were exosomes from healthy human serum, 4 were coronary thrombus-derived exosomes from AMI patients, and 4 were serum exosomes from AMI patients (from the same patient as the thrombus-derived exosomes were extracted).

first: Y

first: Q

last: Wu

first: Z

last: Yu

first: J

last: Huang

first: L

last: Ai

first: X

last: Long


title: A Novel Rescue Strategy for Bone Marrow Hematopoietic Failure via Microenvironment Reconstruction with Reduced HSC Dependency [RNA-Seq]

status: Public on Feb 13 2025

overall_design: This experiment was categorized into three groups, namely BM transplantation (BMT), novel transplantation involving CDSCs, and normal mice of the same age (Health). Cell samples were collected from the BM of these mice two weeks after transplantation and subjected to RNA-seq (Haplox, China).

first: Zhiguo


title: DISC1 Protects Against Zika Virus Infection and Long-Term Neurological Damage Through AMPK-mTOR-Mediated Autophagy

status: Public on Feb 17 2025

city: Shenzhen

first: Shengze

last: Zhang

state: Guangdong

address: No. 66, Gongchang Road

institute: Sun Yat-sen University

summary: Disrupted in Schizophrenia 1 (DISC1) is essential for neuronal development and has been implicated in various psychiatric disorders. However, its role in Zika virus (ZIKV) infection, particularly in congenital Zika syndrome (CZS) and ZIKV-induced long-term neurodevelopmental defects, remains unexplored. In this study, we demonstrate that DISC1 suppresses ZIKV infection in human placental and neuroglia cells, as well as in murine macrophages. DISC1 also limits ZIKV dissemination from peripheral tissues to key organs of mice, including the uterus, testis, and brain, thereby reducing fetal abortion rates and intrauterine growth restriction. Notably, DISC1 is associated with long-term ZIKV effects, including memory loss, reduced anxiety and depression, declines in sociability and social novelty. Mechanistically, DISC1 activates autophagy by enhancing AMPKα phosphorylation and reducing mTOR phosphorylation, protecting against ZIKV infection. Additionally, DISC1 interacts with LC3 to further activate autophagy, partially contributing to inhibit ZIKV infection. In conclusion, DISC1 plays a critical factor in controlling ZIKV infection and mitigating CZS and ZIKV-induced neurocognitive decline.

overall_design: U251 cells were infected with ZIKV GZ01 (MOI of 1.0) post pcDNA or HA-DISC1 transfection for 24 hours.


title: Reduced TBX5 dosage causes human atrial disease by undermining developmental gene regulation of atrial cardiomyocyte identity [scRNA-seq]

status: Public on Feb 18 2025

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens St

country: USA

institute: Gladstone Institutes

summary: In a TBX5-linked human cellular model of atrial disease, we examined the gene networks controlled by TBX5 during human atrial differentiation using single-cell RNA and ATAC sequencing.

overall_design: Wildtype, TBX5 heterozygous and homozygous mutant iPSCs were differentiated to atrial cardiomyocytes. At day 20 or day 45 of differentiation, cells were harvested for single-cell RNA sequencing and analyzed using Seurat. Two replicates per genotype per timepoint were harvested.

first: Kavitha

middle: S

last: Rao

first: Irfan

last: Kathiriya

middle: G


title: Gene expression analysis of T-cell leukemia/lymphoma associated mutations of PLCG1 in Hut78 cells

status: Public on Feb 12 2025

city: New Haven

first: Longhui

last: Zeng

state: CT

address: Yale University, 333 Cedar Street, SHM-C-434 Su lab

department: Cell biology

institute: Yale University

summary: The most frequently mutated gene PLCG1 was identified in Adlut T-cell leukemia/lymphoma patients. Here, we employed bulk RNA-seq analysis to clariy regulated genes and signaling pathways of PLCG1 mutations in Hut78 cells. We further defined unique genes and pathways for PLCG1 mutation by comparing to T cell receptor stimulation group.

overall_design: PLCG1-GFP wild type (WT), R48W, S345F, and D1165H mutations were respectally introduced into human T-cell lymphoma Hut78 cell line by lentivirus.  Flow cytometry was used to sort satble expression cell lines using GFP channel. T cell receptor stimulation group: PLCG1 wild type Hut78 cells were activated by anti-CD3/CD28 antibodies for 3 days.

first: Xiaolei

last: Su


title: Transcriptional profiling of piriform cortex from a mouse model of Huntington's disease (Q140)

status: Public on Feb 10 2025

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: Piriform cortex were isolated from 12-month old wild type and Q140 knock-in (KI) HD mice. Transcriptomic analysis (RNASeq) was performed on 2 genotypes: WT and Q140, 6 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the piriform cortex tissues of 12 months old wild type and Q140 mice. N = 6 per group (3M/3F)

middle: W

last: Yang

last: Wang


title: Transcriptional profiling of striatum and cortex from a mouse model of Huntington's disease (Q140) crossed with Pms1 heterozygous and homozygous mice

summary: Cerebral cortex and striatum were isolated from 6-month old Pms1+/- and Pms1-/- mice crossed with the Q140 knock-in (KI) mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 6 genotypes: WT, Q140, Psm1+/-, Q140 X Psm1+/-, Psm1-/-, and Q140 X Psm1-/-, 8 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the cerebral cortex and striatum tissues of 6 months old wild type, Q140, Psm1+/-, Q140 X Psm1+/-, Psm1-/-, and Q140 X Psm1-/- mice. N = 16 per group (8M/8F)

first: William


title: Transcriptional profiling of striatum from a mouse model of Huntington's disease (Q140) crossed with Pms2 heterozygous and homozygous mice [Pms2_striatum]

summary: Striatum was isolated from 6-month-old Pms2+/- and Pms2-/- mice crossed with the Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 6 genotypes: WT, Q140, Pms2+/-, Q140 X Pms2+/-, Pms2-/-, and Q140 X Pms2-/-, 6-12 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the striatum tissues of 6-month-old wild type, Q140, Pms2+/-, Q140 X Pms2+/-, Pms2-/-, and Q140 X Pms2-/- mice. N = 6-12 per group.

first: Jim

last: Rosinski


title: Transcriptional profiling of cerebral cortex and striatum from a mouse model of Huntington's disease (Q140) crossed with Msh6 heterozygous and homozygous mice

summary: Cerebral cortex and striatum were isolated from 6-month old Msh6+/- and Msh6-/- mice crossed with the Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 6 genotypes: WT, Q140, Msh6+/-, Q140 X Msh6+/-, Msh6-/-, and Q140 X Msh6-/-, 8 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the cerebral cortex and striatum tissues of 6 months old wild type, Q140, Msh6+/-, Q140 X Msh6+/-, Msh6-/-, and Q140 X Msh6-/- mice. N = 8 per group (4M/4F)


title: Transcriptional profiling of cortex from a mouse model of Huntington's disease (Q140) crossed with Ccdc82 heterozygous and homozygous mice [Ccdc82]

summary: Cortex was isolated from 6-month-old Ccdc82+/- and Ccdc82-/- mice crossed with the Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 6 genotypes: WT, Q140, Ccdc82+/-, Q140 X Ccdc82+/-, Ccdc82-/-, and Q140 X Ccdc82-/-, 7-8 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the cortex tissues of 6-month-old wild type, Q140, Ccdc82+/-, Q140 X Ccdc82+/-, Ccdc82-/-, and Q140 X Ccdc82-/- mice. N = 7-8 per group.


title: Transcriptional profiling of cortex from a mouse model of Huntington's disease (Q140) crossed with Pms2 heterozygous and homozygous mice [Pms2]

summary: Cortex was isolated from 6-month-old Pms2+/- and Pms2-/- mice crossed with the Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 6 genotypes: WT, Q140, Pms2+/-, Q140 X Pms2+/-, Pms2-/-, and Q140 X Pms2-/-, 8 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the cortex tissues of 6-month-old wild type, Q140, Pms2+/-, Q140 X Pms2+/-, Pms2-/-, and Q140 X Pms2-/- mice. N = 8 per group (4F/4M).


title: Transcriptional profiling of striatum from a mouse model of Huntington's disease (Q140) crossed with Msh3 heterozygous and homozygous mice [Msh3_striatum_6m]

summary: Striatum was isolated from 6-month-old Msh3+/- and Msh3-/- mice crossed with the Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 6 genotypes: WT, Q140, Msh3+/-, Q140 X Msh3+/-, Msh3-/-, and Q140 X Msh3-/-, 7-8 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the striatum tissues of 6-month-old wild type, Q140, Msh3+/-, Q140 X Msh3+/-, Msh3-/-, and Q140 X Msh3-/-, and wild-type mice. N = 7-8 per group.


title: Transcriptional profiling of striatum from a mouse model of Huntington's disease (Q140) crossed with Ccdc82 heterozygous and homozygous mice [Ccdc82]

summary: Striatum was isolated from 6-month-old Ccdc82+/- and Ccdc82-/- mice crossed with the Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 6 genotypes: WT, Q140, Ccdc82+/-, Q140 X Ccdc82+/-, Ccdc82-/-, and Q140 X Ccdc82-/-, 7-8 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the striatum tissues of 6-month-old wild type, Q140, Ccdc82+/-, Q140 X Ccdc82+/-, Ccdc82-/-, and Q140 X Ccdc82-/- mice. N = 7-8 per group.


title: Transcriptional profiling of cortex from a mouse model of Huntington's disease (Q140) crossed with Mlh1 heterozygous and homozygous mice [Mlh1_4m]

summary: Cortex was isolated from 4-month-old Mlh1+/- and Mlh1-/- mice crossed with the Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 6 genotypes: WT, Q140, Mlh1+/-, Q140 X Mlh1+/-, Mlh1-/-, and Q140I X Mlh1-/-, 7-9 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the cortex tissues of 4-month-old wild type, Q140, Mlh1+/-, Q140 X Mlh1+/-, Mlh1-/-, and Q140I X Mlh1-/- mice. N = 7-9 per group.


title: Transcriptional profiling of cerebral cortex from a mouse model of Huntington's disease (Q140) crossed with Msh3 heterozygous and homozygous mice [Msh3_cortex]

summary: As part of collaboration between UCLA and CHDI, UCLA is creating knockouts (KOs) of 123 genes, implicated in Huntington’s disease (HD) through various computational modeling efforts. Cerebral cortex was isolated from 12-month-old Msh3+/- mice and Msh3-/- (KO) crossed with the Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 6 genotypes: WT, Msh3+/-, Msh3-/-, Q140, Q140 X Msh3+/- and Q140 X Msh3-/-, 8 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the cerebral cortex tissues of 12-month-old Msh3+/-, Msh3-/-, Q140, Q140 X Msh3+/- and Q140 X Msh3-/-, and wild-type mice. N = 8 per group (4F/4M).


title: Transcriptional profiling of cortex from a mouse model of Huntington's disease (Q140) crossed with Msh3 heterozygous and homozygous mice [Msh3_cortex_6m]

summary: Cortex was isolated from 6-month-old Msh3+/- and Msh3-/- mice crossed with the Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 6 genotypes: WT, Q140, Msh3+/-, Q140 X Msh3+/-, Msh3-/-, and Q140 X Msh3-/-, 7-9 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the cortex tissues of 6-month-old wild type, Q140, Msh3+/-, Q140 X Msh3+/-, Msh3-/-, and Q140 X Msh3-/- mice. N = 7-9 per group.


title: Genomic profiling of striatum from a mouse model of Huntington's disease (Q140) crossed with Msh3 knockout mice [ATACSeq]

summary: Striatum was isolated from 12-month-old Msh3-/- mice crossed with the Q140 knock-in (KI) HD mice and their respective controls. Genomic analysis (ATACseq) was performed on 4 genotypes: WT, Msh3-/-, Het (Q140) KI, and Het (Q140) KI X Msh3-/-, 6 replicates per genotype.

overall_design: ATACseq analysis was performed on samples from the striatal tissue of 12-month-old Msh3-/-, Het(Q140) KI, Het (Q140) KI X Msh3 -/-, and Wild type mice. N = 6 per group (3F/3M).


title: Transcriptional profiling of striatum and cortex from a mouse model of Huntington's disease (Q140) crossed with Tcerg1 heterozygous mice [Tcerg1]

summary: As part of collaboration between UCLA and CHDI, UCLA is creating knockouts (KOs) of 123 genes, implicated in Huntington’s disease (HD) through various computational modeling efforts. Striatum and cortex were isolated from 6-month-old Tcerg1+/- mice crossed with the Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 4 genotypes: WT, Tcerg1+/-, Q140, and Q140 X Tcerg1+/-, 8 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the striatum and cortex tissues of 6-month-old Tcerg1+/-, Q140 KI, Q140 X Tcerg1+/-, and wild-type mice. N = 8 per group (4F/4M).


title: Metabolic reprogramming of macrophages via engineered nanoparticles after volumetric muscle loss

status: Public on Jan 31 2025

city: Ann Arbor

first: Carlos

middle: Andres

last: Aguilar

state: MI

address: 2200 Bonisteel Blvd

department: Biomedical Engineering

institute: University of Michigan

summary: Volumetric muscle loss (VML) injuries are characterized by an exacerbated and chronic inflammatory state that inhibits muscle stem-cell mediated repair, leading to fibrosis and attenuation of neuromuscular strength. The excessive infiltration of myeloid cells in VML injuries leads to the depletion of nutrients needed by myogenic progenitors for tissue repair. Mitigating the inflammatory response and fibrosis are potential approaches to enhance therapies for VML. The adenosine monophosphate-activated protein kinase (AMPK) pathway plays a critical role in myeloid responses to injury by regulating cellular metabolism, suppressing glycolysis, and attenuating fibrosis-inducing pathways such as transforming growth factor-beta (TGFβ). AMPK Activation reduces fibrosis and promotes muscle stem cell differentiation, however, a limiting factor of AMPK agonists such as AICAR (5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside) is that these therapies display low bioavailability. As such, there remains an unmet need for strategies to target AMPK in skeletal muscle to enhance therapeutic efficacy and prevent muscle degeneration. To address this need, we used synthetic protein nanoparticles (SPNPs) to encapsulate AICAR. SPNPs can have high drug loading (>10wt%), allow for a sustained release of the packaged drug (72 hours), and have a demonstrated targeting capacity. Increasing the bioavailability of AICAR through packaging into SPNPs would be enabling for improving metabolism after trauma and extensible to other AMPK agonists and small molecules, which in turn can further augment existing regenerative therapies to promote healing

overall_design: Quadriceps muscles from mice were given a VML injury and treated with either AICAR and Vehicle loaded SPNPs (x1011 particles) at 1,4,7 days post-injury (dpi). Muscles were collected at 8 dpi, digested into single cell suspensions, FACS sorted to obtain live cells and processed for single cell sequencing.

first: Jesus

middle: A

last: Castor-Macias

first: Celeste

last: Piotto

first: Albert

last: Cheng

first: Steve

last: Guzman

first: Jacqueline

last: Larouche

first: Joerg

last: Lahann


title: Transcriptional profiling of striatum from a mouse model of Huntington's disease (Q140) crossed with Msh3 heterozygous and homozygous mice [Msh3_striatum]

summary: As part of collaboration between UCLA and CHDI, UCLA is creating knockouts (KOs) of 123 genes, implicated in Huntington’s disease (HD) through various computational modeling efforts. Striatum was isolated from 12-month-old Msh3+/- mice and Msh3-/- (KO) crossed with the Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 6 genotypes: WT, Msh3+/-, Msh3-/-, Q140, Q140 X Msh3+/- and Q140 X Msh3-/-, 8 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the striatum tissues of 12-month-old Msh3+/-, Msh3-/-, Q140, Q140 X Msh3+/- and Q140 X Msh3-/-, and wild-type mice. N = 8 per group (4F/4M).


title: ZRSR2-loss causes aberrant splicing in a JAK2V617F-driven myeloproliferative neoplasm but is not sufficient to drive disease progression

status: Public on Feb 02 2025

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptional profiling of striatum and cortex from a mouse model of Huntington's disease (Q140) crossed with Rgs9 heterozygous mice and Msh2 knockout mice [Msh2_6mon]

summary: As part of collaboration between UCLA and CHDI, UCLA is creating knockouts (KOs) of 123 genes, implicated in Huntington’s disease (HD) through various computational modeling efforts. Striatum and cortex were isolated from 6-month-old Msh2-/- (KO) mice crossed with the Rgs9+/- and Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 4 genotypes: WT, Het (Q140) KI X Rgs9+/-, Q140, and Het (Q140) KI X Rgs9+/- X Msh2-/-, 8 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the striatum and cortex tissues of 6-month-old Het (Q140) KI X Rgs9+/- X Msh2-/-, Q140 KI, Het (Q140) KI X Rgs9+/-, and wild-type mice. N = 8 per group (4F/4M).


title: Zalfermin and semaglutide have beneficial effects liver histology and fibrotic gene in a murine model of NASH

status: Public on Feb 01 2025

city: Oxford

first: Maria

last: Dermit

state: Oxfordshire

institute: Novo nordisk research centre oxford

summary: The potential clinical benefits of FGF21 analogues for the treatment of NASH has evolved significantly within the last years. However, despite clinical meaningful effect on NASH resolution and fibrosis the body weight loss in humans have been less impressive. Thus, a combination of an FGF21 analogue with a GLP-1 receptor agonist may add additional benefit to the treatment of NASH due to complimentary mode of action compared to stand alone therapies

overall_design: RNA-sequencing data. CHOW diet: Vehicle n=8; AMLN diet: Vehicle  n=8, AMLN diet:  Zalfermin low dose (n=8), high dose  (n=8); Semaglutide low dose (n=8, one sample highlighted excluded during quality control)   high dose (n=8). Combination Zalfermin high and Semaglutide high (n=8).

first: Jenny

last: Norlin

first: Nikos

last: Sidiropoulos

first: Matthew

middle: P

last: Gillum

first: Elisabeth

middle: D

last: Galsgaard

first: Markus

last: Latta

first: Birgitte

last: Andersen


title: The Alb-R26Met liver cancer mouse model recapitulates molecular features and heterogeneity of hepatocellular carcinoma patients

status: Public on Feb 07 2025

city: Marseille

first: Abdessamad

last: EL KAOUTARI

state: France

address: 27 boulevard Lei Roure

institute: INSERM

summary: We have generated an inside-out genetic mouse model of liver cancer, the Alb-R26Met mice, in which slightly increased levels of the wild-type form of the MET Receptor Tyrosine Kinase (RTK) occurs specifically in the liver following the deletion of a stop cassette by the Cre recombinase. This genetic combination is obtained by crossing the R26stopMet with Alb-Cre mice. The Alb-R26Met mice spontaneously develop liver tumours and model the whole tumorigenic program. These tumours correspond to HCC patients belonging to the proliferative-progenitor subset. Importantly, the Alb-R26Met model recapitulates several features of HCC patients, including the molecular heterogeneity, the temporal heterogeneity of tumour onset, and the resistance to RTK inhibitors used in the clinic for HCC treatment. This unique genetic setting offered us the possibility to compare the transcriptomic profile of  Alb-R26Met non-tumoral livers with Alb-R26Met advanced liver tumours. Outcomes offer an overall vision of how gene expression switches during a tumorigenic process modelled by the Alb-R26Met mice. Importantly, as tumorigenesis in the Alb-R26Met genetic setting occurs in an immune-competent context, outcomes offers as well the possibility to explore the profound changes in the immune microenvironment in the liver tumours, by performing deconvolution of RNAseq data.

overall_design: mRNA of a total of 6  non-tumoral livers from  Alb-R26Met mice, and 12 advanced stage tumours from Alb-R26Met, were submitted for bulk RNA-sequencing.

first: Floriane

last: Cannet

first: Celia

last: Sequera

first: Paula

last: Michea Veloso

last: El Kaoutari

first: Jean-Paul

last: Borg

first: Flavio

last: Maina


title: EWS-FLI1 Expression in Human Embryonic Mesenchymal Stem Cells Leads to Defective DNA Damage Repair and Ewing Sarcoma

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute


title: EWS-FLI1 in embryonic hMSCs induces DNA damage and Ewing sarcoma tumorigenesis [ChIP-seq]

summary: Ewing sarcoma (ES) is an aggressive bone and soft tissue neoplasm, unique to humans, characterized by EWSR1/ETS rearrangements and whose cellular origin remains unclear. Expression of EWS-FLI1 in pediatric human mesenchymal stem cells (hMSCs) induced a transcriptional profile more resembling ES than its expression in adult hMSCs, but did not confer tumorigenic capacity. We have isolated human mesenchymal stem-like cells (hMSLCs) from experimental human embryonic stem cell (hESC)-derived teratomas. EWS-FLI1 expression in hMSLCs results in the acquisition of an ES signature through its preferential binding to microsatellites of intergenic and intronic regions. In hMSLCs, EWS-FLI1 directly regulates BRCA1 expression, although oncogene-expressing cells show defects in DNA damage repair (DDR). Xenografting in mice of EWS-FLI1-transduced hMSLCs resulted in the formation of tumors expressing characteristic ES markers. In summary, EWS-FLI1 enforces an aberrant transcriptome and endows in vivo transforming capacity when expressed in an undifferentiated early embryonic hMSC. Our approach represents an innovative experimental method for understanding critical aspects of the biology of developmental tumors, from leukemia to sarcomas, in which few (even single) genetic alterations are able to transform a fetal stem cell.

overall_design: human Mesenchymal Stem Like Cells (hMSLCs) line 1 was infected with flag-tagged EWS-FLI1 or with control lentivirus

first: Hernández-Muñoz

last: Inmaculada


title: Atovaquone-induced oxidative stress activates pentose phosphate pathway and immunogenic cell death in ovarian cancer

city: Madison

first: Alexander

middle: J

last: Fagan

state: WI

address: 1300 University Ave Room 1220

department: Department of Statistics

institute: UW-Madison

summary: Atovaquone, an FDA-approved oxidative phosphorylation (OXPHOS) inhibitor, has shown promise in treating epithelial ovarian cancer (EOC), the deadliest gynecologic malignancy. However, the precise mechanisms underlying its antitumorigenic effects remain unclear. We employed a longitudinal transcriptomic approach to characterize the molecular effects of atovaquone on EOC cells. Our findings demonstrate that atovaquone disrupts cellular homeostasis and metabolism, activates stress responses, and primes immune recognition. We observed temporal downregulation of genes and pathways involved in key cellular processes, such as cell cycle and DNA replication, correlating with reduced proliferative capacity. Atovaquone also downregulated both OXPHOS and glycolysis, while upregulating the pentose phosphate pathway, suggesting a metabolic shift toward redox homeostasis restoration in response to severe oxidative stress. Consistent with oxidative stress, we found that atovaquone activated endoplasmic reticulum (ER) stress, which is linked to immunogenic cell death. During ER stress, calreticulin, a Damage-Associated Molecular Pattern (DAMP), translocates to the plasma membrane, where it promotes immune recognition. We observed that calreticulin was upregulated on the plasma membrane of atovaquone-treated EOC cells. Additionally, we detected increased levels of other DAMPs, such as High Mobility Group Box 1 (HMGB1) and Mitochondrial Transcription Factor A (TFAM), in the supernatant of atovaquone-treated cells, indicating the release of immunogenic molecules. Moreover, increased expression of ligands for activating receptors of NK cells was observed and co-culture experiments showed enhanced NK cell activity toward atovaquone-treated cells. These results highlight atovaquone’s potential as an adjuvant therapy that activates immune responses, offering a new avenue for combination therapies in EOC treatment.

overall_design: Bulk RNA-seq profiling of OVCAR3 cancer cells in the presence of DMSO, 30μM Atovaquone, and 45μM Atovaquone at 1, 8, 24, and 48 hours, as well as untreated OVCAR3 cells at 24 hours. Samples were sent in three batches at different times. All observations at 48 hours were in the third batch, batch C, and all samples in batch C were taken at 48 hours. This batch had 3 replicates each of DMSO-, 30μM-, and 45μM-treated samples. The first and second batch, A and B respectively, contained each of 1, 8, and 24 hours combined with each of 30μM, 45μM, and DMSO, as well as untreated cells observed at only 24 hours. For each such experimental condition, batch A had one biological replicate, and batch B had two.

first: Mayra

last: Betancourt Ponce

first: Nicha

last: Boonpattrawong

first: Michael

last: Newton

first: Manish

last: Patankar

first: Lisa

last: Barroilhet


title: Clonal cell states link gastroesophageal junction tissues, metaplasia, and cancer [Spatial transcriptomics]

city: Philadelphia

first: Sydney

last: Shaffer

state: PA

address: 421 Curie Boulevard

department: Penn Medicine

institute: University of Pennsylvania

summary: Barrett's esophagus is a common type of metaplasia and a precursor of esophageal adenocarcinoma. However, the cell states and lineage connections underlying the origin, maintenance, and progression of Barrett’s esophagus have not been resolved in humans. Here, we performed single-cell lineage tracing and transcriptional profiling of patient cells isolated from metaplastic and healthy tissue. Our analysis unexpectedly revealed that the squamous esophagus and gastric cardia contained cells belonging to common lineages that also included transitional basal progenitor cells; both esophageal and gastric tissues were also related to Barrett's esophagus. Barrett’s esophagus biopsies consisted of multiple clones, with lineages that contained all progenitor and differentiated cell types. In contrast, precancerous dysplastic lesions were initiated by the expansion of a single molecularly aberrant Barrett’s esophagus clone. Together, these findings provide a comprehensive view of the cell dynamics of Barrett's esophagus, linking cell states along the disease trajectory, from its origin to cancer.

overall_design: Performed single-cell lineage tracing and transcriptional profiling of patient cells isolated from metaplastic and healthy tissue.

first: Rodrigo

last: Gier

first: Raúl

last: Reyes Hueros

first: Jiazhen

last: Rong

first: Maureen

last: DeMarshall

last: Bracht

first: Tatiana

last: Karakasheva

first: Amanda

middle: B

last: Muir

first: Gary

last: Falk

first: Nancy

last: Zhang

middle: M


title: ZRSR2-loss causes aberrant splicing in a JAK2V617F-driven myeloproliferative neoplasm but is not sufficient to drive disease progression I.

first: Jasmin

last: Straube

summary: Myeloproliferative neoplasms (MPN), including polycythemia vera (PV), essential thrombocythemia (ET) and primary myelofibrosis (PMF), are clonal disorders driven by mutations in hematopoietic stem cells (HSCs). JAK2V617F is the most recurrent driver mutation in MPN and results in the constitutive activation of the JAK-STAT pathway. ZRSR2-loss is reported to cause mis-splicing of U12-type introns in myelodysplastic syndromes (MDS). Loss of function mutations in ZRSR2 have been found in a JAK2V617F-driven MPNs and are associated with disease progression and poor prognosis. However, the functional contribution of ZRSR2-loss to the pathogenesis and disease progression of MPN remains unknown. Using CRISPR-Cas9, we generated concomitant ZRSR2-loss in a JAK2V617F-driven human cell line and mouse model of MPN. RNA-Seq data demonstrates that ZRSR2-loss causes aberrant splicing in both human and murine cells, with the affect being more subtle in the murine context. Gene expression analysis in murine HSCs indicates that Zrsr2-loss biases lineage differentiation priming to megakaryocytes. However, Zrsr2-loss did not alter the severity or phenotype of the MPN in Jak2V617F mice. These results indicate that Zrsr2 mutations have limited impact on disease progression of Jak2V617F -driven MPN in vivo. Consistent with this, we find that ZRSR2 mutations are more frequently identified in genetically complex MPN patients carrying other high molecular risk mutations. In total, our findings demonstrate that ZRSR2-loss causes subtle mis-splicing in JAK2V617F-driven MPN that is not sufficient to drive disease progression in the absence of other high-risk mutations.

overall_design: At terminal time point, GFP and mCherry double positive LSK (Lineage- Sca1+ Kit+) cells from bone marrow of mouse expressing either Jak2V617F alone or in combination with Zrsr2 loss were enriched and sorted by BD FACS ARIA IIIu.

first: Ranran

first: Megan

last: Bywater

first: Steven

last: Lane


title: EWS-FLI1 in embryonic hMSCs induces DNA damage and Ewing sarcoma tumorigenesis [Spatial_transcriptomics]

first: Júlia

last: Perera-Bel

overall_design: Two different samples from mice inoculated with human mesenchymal stem cells infected with EWS-FLI1, one of which corresponded to a soft mass in the abdominal cavity and the other to a lung metastasis, were analyzed by spatial transcriptomics.

first: Hernández-Muñoz

last: Inmaculada


title: Transcriptional profiling of striatum from a mouse model of Huntington's disease (Q140) crossed with Msh3 heterozygous and homozygous mice [Msh3 snRNA-seq]

first: Jeff

last: Aaronson

summary: Striatum was isolated from 12-month-old Msh3+/- and Msh3-/- mice crossed with the Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (snRNASeq) was performed on 6 genotypes: WT, Q140, Msh3+/-, Q140 X Msh3+/-, Msh3-/-, and Q140 X Msh3-/-, 4 replicates per genotype.

overall_design: snRNASeq analysis was performed on samples from the striatum tissues of 12-month-old wild type, Q140, Msh3+/-, Q140 X Msh3+/-, Msh3-/-, and Q140 X Msh3-/- mice. N = 4 per group (2M/2F).

first: X

last: Yang

first: Jim

last: Rosinski


title: Transcriptional profiling of striatum and cortex from a mouse model of Huntington's disease (Q140) crossed with Polq heterozygous mice [Polq]

summary: As part of collaboration between UCLA and CHDI, UCLA is creating knockouts (KOs) of 123 genes, implicated in Huntington’s disease (HD) through various computational modeling efforts. Striatum and cortex were isolated from 6-month-old Polq+/- mice crossed with the Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 4 genotypes: WT, Polq+/-, Q140, and Q140 X Polq+/-, 8 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the striatum and cortex tissues of 6-month-old Polq+/-, Q140 KI, Q140 X Polq+/-, and wild-type mice. N = 8 per group (4F/4M).


title: Drug and single-cell gene expression integration identifies sensitive and resistant glioblastoma cell populations [PDX GBM22 orthotopic xenografts]

city: Washington, DC

first: Nagi

last: Ayad

state: District Of Columbia

address: 3970 Reservoir Rd NW

department: Department of Oncology

institute: Georgetown University

summary: Glioblastoma (GBM) remains the most common and lethal adult malignant primary brain cancer with few treatment options. One of the most significant issues hindering GBM therapeutic development is intratumor heterogeneity. GBM tumors consist of multiple neoplastic cell types with distinct transcriptional profiles. Identifying compounds that target these different cell types requires a platform that predicts differential sensitivity and resistance of cells within GBM tumors. To address this, we developed a novel framework to generate tumor cell-type-specific disease signatures and their predicted drug sensitivity. We performed single-cell RNA sequencing of newly diagnosed and recurrent GBM tumors and identified compounds from the LINCS L1000 database with transcriptional response signatures selectively discordant with distinct single-cell transcriptional states within GBM tumors. We then validated in silico predictions with in vivo findings in mice as the aurora kinase inhibitor alisertib induced a shift from NPC-like to MES-like transcriptional states upon treatment. To allow other investigators to predict selective tumor cell type drug sensitivity in silico we developed a platform termed ISOSCELES (Inferred cell Sensitivity Operating on the integration of Single-Cell Expression and L1000 Expression Signatures).  Our studies suggest that ISOSCELES is a novel platform to identify cell populations that are sensitive and resistant to targeted therapies in GBM, which can inform treatment decisions in future clinical trials.

overall_design: Single-cell RNA sequencing analysis of PDX GBM22 orthotopic xenografts treated with the aurora kinase inhibitor alisertib or a DMSO vehicle control.

first: Robert

middle: K

last: Suter

first: Anna

last: Jermakowicz


title: ZRSR2-loss causes aberrant splicing in a JAK2V617F-driven myeloproliferative neoplasm but is not sufficient to drive disease progression II.

overall_design: SET-2 cells were transduced with PLKO5 GFP virus containing sgRNAs targeting human ZRSR2 (sg1: TGACGTTTCCCGAGAAACCA, sg2: ACAGTTCCTAGACTTCTATG, sg3: CTTCCAGCCACAAAAAGTAC) and non-targeting sgRNAs control (NTG1: GACGGAGGCTAAGCGTCGCAA, NTG2: GCGCTTCCGCGGCCCGTTCAA) and subjected to RNA-sequencing.

middle: E

last: Marneth

first: Charles

last: Laurore

first: Ann

last: Mullally


title: Prior vaccination prevents overactivation of innate immune responses during COVID-19 breakthrough infection

status: Public on Jan 30 2025

city: Stanford

first: Leslie

last: Chan

address: 300 Pasteur Dr Bldg S131, Grant

institute: Stanford University

summary: At this stage in the COVID-19 pandemic, most infections are 'breakthrough' infections that occur in individuals with prior immunity to SARS-CoV-2 through infection or vaccination. Understanding both innate and adaptive immune induction in the setting of breakthrough infection is critical to refining vaccine strategies to ensure long-term efficacy against emerging variants, yet existing studies have primarily focused on adaptive immune responses. Here, we performed single-cell transcriptomic, proteomic, and functional profiling of innate and adaptive immunity during primary and breakthrough COVID-19 infections by comparing immune responses between unvaccinated and vaccinated individuals during the SARS-CoV-2 Delta wave. Breakthrough infections were characterized by a significantly less activated transcriptomic profile in CD56dim NK cells and monocytes, with induction of pathways limiting NK cell proliferation and monocyte migratory potential. Furthermore, we observed a female-specific trend of increased transcriptomic activation of CD16+ monocytes and  type-2 conventional dendritic cells (cDC2s) during breakthrough infections. Despite these differences, antibody-dependent cellular cytotoxicity responses were similar between breakthrough and primary infection groups. These insights suggest that prior vaccination prevents overactivation of innate immune responses during breakthrough infections with discernible sex-specific patterns and underscore the potential of harnessing vaccines in mitigating pathologic immune responses resulting from overactivation.

overall_design: Single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) from 25 unvaccinated, infected participants and 25 vaccinated, infected participants

first: Catherine

last: Blish


title: Clonal cell states link gastroesophageal junction tissues, metaplasia, and cancer [MAESTER]

status: Public on Jan 27 2025

first: Sydney

last: Shaffer

first: Rodrigo

last: Gier

first: Raúl

last: Reyes Hueros

first: Jiazhen

last: Rong

first: Maureen

last: DeMarshall

last: Bracht

first: Tatiana

last: Karakasheva

first: Amanda

last: Muir

first: Gary

last: Falk

first: Nancy

last: Zhang


title: Drug and single-cell gene expression integration identifies sensitive and resistant glioblastoma cell populations [patient glioblastoma tumors]

last: Ayad

overall_design: Single-cell RNA sequencing analysis of 3 newly diagnosed and 3 recurrent (treated with RT & TMZ) patient glioblastoma tumors.

last: Suter


title: Transcriptional profiling of striatum from a mouse model of Huntington's disease (Q140) crossed with Mlh1 heterozygous and homozygous mice [Mlh1_4m]

first: Jeff

last: Aaronson

summary: Striatum was isolated from 4-month-old Mlh1+/- and Mlh1-/- mice crossed with the Q140 knock-in (KI) HD mice and their respective controls. Transcriptomic analysis (RNASeq) was performed on 6 genotypes: WT, Q140, Mlh1+/-, Q140 X Mlh1+/-, Mlh1-/-, and Q140I X Mlh1-/-, 7-9 replicates per genotype.

overall_design: RNASeq analysis was performed on samples from the striatum tissues of 4-month-old wild type, Q140, Mlh1+/-, Q140 X Mlh1+/-, Mlh1-/-, and Q140I X Mlh1-/- mice. N = 7-9 per group.

first: X

last: Yang

first: Jim

last: Rosinski


title: Drug and single-cell gene expression integration identifies sensitive and resistant glioblastoma cell populations

first: Nagi


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

city: Baltimore

first: Prajwal

last: Ciryam

state: MD

address: 670 W. Baltimore St.

institute: University of Maryland School of Medicine

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

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

first: Bosung

last: Shim

first: Cigdem

last: Tosun

first: Riccardo

last: Serra

first: Natalya

last: Tsymbalyuk

first: Kaspar

last: Keledjian

first: Volodymyr

last: Gerzanich

first: J

last: Simard


title: Zmiz1-dependent Native Stem Cell Transcriptional Circuits in Normal and Malignant Immature T cells

status: Public on Jan 23 2025

first: Mark

middle: Yat-fung

last: Chiang

address: 109 Zina Pitcher Place

department: Internal Medicine/Heme-onc

overall_design: Refer to individual Series


title: microRNA profile of high-grade B-cell lymphoma with 11q aberration

status: Public on Jan 15 2025

city: Warsaw

first: Michalina

last: Zajdel

address: Roentgena 5

department: Department of Experimental Oncology

country: Poland

institute: Maria Sklodowska-Curie National Research Institute of Oncology

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: High-grade B-cell lymphoma with 11q aberration (HGBCL-11q) is a rare germinal centre lymphoma with a typical gain/loss pattern on chromosome 11q, but without MYC translocation and with some features resembling Burkitt lymphoma (BL) and HGBCLs or germinal centre derived diffuse large B-cell lymphoma, not otherwise specified (GCB-DLBCL-NOS). The microRNA expression profile of HGBCL-11q is not characterised. We aim to analyse miRNA expression profile in HGBCL-11q, BL and in GCB-DLBCL-NOS.
Methods: Next generation sequencing (NGS)-based microRNA profiling was performed for HGBCL-11q (n=6), BL (n=8), and also GCB-DLBCL-NOS without (n=3) and with MYC rearrangement (MYC-R) (n=7).
Results: We identified 39 and 64 miRNAs differentiating HGBCL-11q from BL, and from GCB-DLBCL-NOS without MYC-R, respectively. We found that the expression level of miR-223-3p, miR-193b-3p, miR-29b-3p and miR-146a-5p simultaneously differentiated HGBCL-11q from BL, as well as from GCB-DLBCL-NOS without MYC-R. We found higher miRNA profile heterogeneity in HGBCL-11q than in BL. The analysis of MYC-regulated miRNA showed different profile in HGBCL-11q and in BL but demonstrated separation of HGBCL-11q and BL from GCB-DLBCL-NOS cases.
Conclusion: microRNA profile of HGBCL-11q is different than that of BL and of GCB-DLBCL-NOS but more heterogeneous compared to BL.

overall_design: To investigate the profile of microRNA expression in HGBL-11q in comparison with BL, and also with GCB DLBCL,NOS without and with MYC rearrangement (MYC-R) we have used total RNA isolated from freshly frozen cell aspirates of above mentioned aggressive lymphomas tumours and performed next generation sequencing.


title: Native nucleosome-positioning elements for the investigation of nucleosome repositioning.

status: Public on Jan 16 2025

city: State College

first: Shane

middle: Douglas

last: Stoeber

state: Pennsylvania

address: 406 South Frear Building

department: BMMB

institute: Penn State

summary: Nucleosome repositioning is essential for establishing nucleosome-depleted regions (NDRs) to initiate transcription. This process has been extensively studied using structural, biochemical, and single-molecule approaches, which require homogenously positioned nucleosomes. This is often achieved using the Widom 601 sequence, a highly efficient nucleosome positioning element (NPE) selected for its unusually strong binding to the H3-H4 histone tetramer. Due to the artificial nature of 601, a library of native NPEs is needed to explore the role of DNA sequence in nucleosome repositioning. Here, we characterize the position distributions and nucleosome formation free energy for a set of yeast native nucleosomes (YNNs) from Saccharomyces cerevisiae. We show these native NPEs can be used in biochemical studies of nucleosome repositioning by transcription factors (TFs) and the chromatin remodeler Chd1. TFs could directly reposition a fraction of nucleosomes containing native NPEs, but not 601-containing nucleosomes. In contrast, partial unwrapping was similar for 601 and native NPE sequences. The rate of ATP-dependent remodeling by Chd1 was within the range of the fast and slow directions of the 601 nucleosomes. This set of native NPEs provides an alternative to the 601 NPE that can be used for probing the repositioning of nucleosomes that contain native DNA sequences.

overall_design: MNase-seq to determine nucleosome positioning of YNN candidates or 601 with and without yeast transcription factors.

first: Ruo-Wen

last: Chen

first: Ilana

last: Nodelman

first: Hengye

first: Lloyd

first: Gregory

last: Bowman

first: Lu

last: Bai

first: Michael

last: Poirier


title: Maternal cause of early-onset preeclampsia: excessive endometrial gland-derived apolipoprotein D induces placental ferroptosis and developmental abnormalities

city: Hong Kong

first: Jianlin

last: Li

address: L 7-08, Department of Obstetrics and Gynecology  Laboratory block, 21th Sassoon Road, Hong Kong

country: Hong Kong

institute: The University of Hong Kong

summary: Early-onset pre-eclampsia (ePE) is a severe pregnancy complication affecting millions of pregnancies worldwide, resulting in significant maternal and fetal morbidity. The etiology of ePE is associated with defective trophoblast functions, leading to abnormal placental development. Regulatory factors released by endometrial glands are crucial for proper placental development. While circumstantial evidence indicates that defective endometrial gland development or function may lead to defective placental development and ePE in humans, direct evidence has been lacking. This study explored the role of endometrial gland-derived factors both in vitro and in vivo and correlated the findings with the clinical phenotypes of ePE. Our findings revealed that the secretome of organoids derived from the endometrial tissues of ePE patients impeded spiral artery remodeling and thus disrupted proper placental perfusion. Transcriptomic and proteomic analyses identified an increased apolipoprotein D (APOD) production in ePE organoids and decidual tissues compared to their normotensive (NT) counterparts. Overexpression of endometrial APOD impaired the vascular remodeling functions of extravillous trophoblasts (EVT) and endothelial cells in vitro. These findings were corroborated using an endometrial-specific APOD knock-in mouse model. APOD-induced ferroptosis through the PI3K/Akt pathway in both human ePE placentas and the mouse model. Moreover, elevated APOD levels were detected in the first-trimester serum of pregnant women who subsequently developed ePE. These results provide the first direct evidence that dysregulated endometrial gland secretome is a maternal cause of defective placental development and ePE. Clinically, APOD could serve as a biomarker for early detection of ePE, enabling early intervention with  the potential to improve outcomes for both mothers and their babies.

overall_design: Study the effect of pre-eclampsia  endometrial organoid secretion on the functions on EVTs in vivo and in vitro.

first: Yang

last: Dong

first: Cheuk-Lun

last: Lee

first: Philip C.N.

last: Chiu


title: Classes of Lamin-Associated Domains are Defined by Distinct Patterns of Repressive Histone Methylation [ChIP-seq]

city: Columbus

last: Parthun

state: Ohio

address: 1060 Carmack Rd.

department: Biological Chemistry and Pharmacology

institute: The Ohio State University

summary: A large fraction of the genome interacts with the nuclear periphery through lamina-associated domains (LADs), repressive regions which play an important role in genome organization and gene regulation across development. Despite much work, LAD structure and regulation remain incompletely understood, and a mounting number of studies have identified numerous genetic and epigenetic differences within LADs, demonstrating they are not a uniform group. Here we profile Lamin B1, HP1β, H3K9me3, H3K9me2, H3K27me3, H3K14ac, H3K27ac, and H3K9ac in MEF cell lines derived from the same mouse colony and cluster LADs based on the abundance and distribution of these features across LADs. We find that LADs fall into 3 groups, each enriched in a unique set of histone modifications and genomic features. Each group is defined by a different heterochromatin modification (H3K9me3, H3K9me2, or H3K27me3), suggesting that all three of these marks play important roles in regulation of LAD chromatin and potentially of lamina association. We also discover unique features of LAD borders, including a LAD border-specific enrichment of H3K14ac. These results reveal important distinctions between LADs and highlight the rich diversity and complexity in LAD structure and regulatory mechanisms.

overall_design: ChIP-seq for HP1β in two independently derived mouse embryonic fibroblast (iMEF) cell lines from one mouse colony.

first: Caden

last: Martin

first: Prabakaran

last: Nagarajan

first: Elizabeth

last: Oser

first: Liudmila

middle: V

last: Popova


title: Classes of Lamin-Associated Domains are Defined by Distinct Patterns of Repressive Histone Methylation [RNA-seq]

first: Mark

overall_design: RNA-seq in three independently derived mouse embryonic fibroblast (iMEF) cell lines from one mouse colony.


title: Classes of Lamin-Associated Domains are Defined by Distinct Patterns of Repressive Histone Methylation [CUT&Tag]

overall_design: Cleavage Under Target and Tagmentation (CUT&Tag) for H3K9me2, H3K9me3, H3K27me3, H3K14ac, H3K27ac, and H3K9ac in immortalized mouse embryonic fibroblast (iMEF) cells derived from three different mice from the same mouse colony.


title: Strategic timing of contralateral nephrectomy after ischemic AKI prevents CKD by enhancing epithelial progenitor proliferation while attenuating polyploidization

status: Public on Dec 31 2024

city: Aachen

first: Benjamin

middle: Arthur

last: Vervaet

address: Pauwelstrasse 30

country: Germany

institute: RWTH Uniklinik Aachen

summary: Kidneys have a limited ability to self-repair, and their response to injury not seldomly leads to chronic kidney disease (CKD). An intriguing phenomenon of successful recovery is observed in models of unilateral acute kidney injury (AKI) upon contralateral nephrectomy. Here we aimed to better understand the cellular mechanisms of this enhanced reparative effect.In a time-course study with different nephrectomy delay times, we found that the most effective rescue after injury was observed when contralateral nephrectomy was performed early during AKI in both rats and mice. This timely intervention led to full functional recovery and attenuation of tubular atrophy, fibrosis, and inflammation, averting AKI-to-CKD transition. Morphometry of histopathology using pathomics revealed distinct trajectories of structural alterations of kidney tubules, distinguishing between atrophy and repair, as adaptive signatures. These responses were corroborated by transcriptomics analysis, which indicated improved cellular energy metabolism after nephrectomy. Lineage tracing of tubular progenitor cells showed that nephrectomy robustly stimulated their clonal expansion, surpassing the levels observed during spontaneous self-repair. Live cell cycle/DNA-content analysis of tubular cells demonstrated a robust polyploid response immediately after the ischemic insult, and revealed that nephrectomy attenuated long term tubular cell polyploidization, a contributor to CKD. Altogether, our data revealed that early timing of nephrectomy in experimental AKI induces an efficient repair response, involving tubular epithelial regeneration while counteracting the progression towards CKD.

overall_design: Male mice of 8-10 weeks of age were randomly divided in 4 groups (n=6/group), All animals, except from control animals, underwent left renal unilateral ischemia-reperfusion injury (UIRI) for 21 minutes at 34°C core body temperature. The first group was euthanized on day 3 after UIRI, whilst the other groups underwent a contralateral Nx or sham-Nx of the unharmed kidney at day 3 after UIRI. These groups were euthanized 7 days after UIRI.

first: Lies

last: Moonen

first: Bart

last: Cuypers

first: Esther

last: Bartholomeus

first: Stuart

last: Maudsley

first: Kris

last: Laukens


title: Extensive length and homology dependent chimerism in pool-packaged AAV libraries

status: Public on Jan 14 2025

city: Montreal

first: Jean-Benoit

last: Lalanne

state: QC

address: 5155 Chem. de la Rampe

department: Biochemistry and Molecular Medicine

country: Canada

institute: University of Montreal

summary: Adeno-associated viruses (AAVs) have emerged as the foremost gene therapy delivery vehicles due to their versatility, durability and safety profile. Here we demonstrate extensive chimerism among complex AAV libraries that are packaged as a pool. The observed chimerism is length- and homology-dependent but capsid-independent, in some cases affecting >60% of packaged AAV genomes. These results have important implications for the design and deployment of functional AAV libraries in research and clinical settings.

overall_design: Barcoded plasmid dictionary generation and barcode swap assessment in long-read data.

first: Jean-Benoît

first: Chau

last: Huynh

first: John

last: Mich

first: Avery

last: Hunker

first: Troy

last: McDiarmid

first: Haedong

last: Kim

first: Boaz

last: Levi

first: Jonathan

last: Ting

first: Jay

last: Shendure


title: Eosinophils in Lung Allograft

city: Scottsdale

first: Elizabeth

middle: A.

last: Jacobsen

state: AZ

address: 13400 E. Shea Blvd.

institute: Mayo Clinic

summary: Eosinophils were isolated from the lungs of mice that were resting naïve or 7 or 30 days post-transplant with costimulatory blockade

overall_design: Lungs of 3 to 5 mice were pooled per sample. Lung eosinophils were isolated by flow cytometry sorting. RNA was prepared from Trizol and sequencing was performed at Genewiz (South Plainfield, NJ) using Ultra-Low Input RNA-Seq Service.

first: Elizabeth A.

first: Alexander

last: Krupnick


title: Overcoming Nanosilver Resistance: Resensitizing Bacteria and Targeting Evolutionary Mechanisms

city: Beijing

first: Rui

last: Sun

address: No.19, Xinjiekouwai St

department: School of Environment

institute: Beijing Normal University

summary: The rapid spread of antimicrobial resistance poses a critical threat to global health and the environment. Antimicrobial nanomaterials, including silver nanoparticles (AgNPs), are being explored as innovative solutions; however, the emergence of nanoresistance challenges their effectiveness. Understanding resistance mechanisms is essential for developing antievolutionary strategies. AgNPs exhibit diverse resistance mechanisms, and our findings reveal a dynamic transition between these mechanisms: from flagellin-mediated AgNP precipitation (state I) to activation of the copper efflux pump (CusCFBA) system (state II). We designed targeted physicochemical interventions to counteract these mechanisms. Energy supply blocking was effective for state I, while for state II, neutralizing intracellular acidic pH significantly reduced resistance. These strategies reduced nanoresistance/tolerance by up to 10,000-fold. Additionally, resistance evolution can be completely halted by disrupting the energy supply using carbonyl cyanide 3-chlorophenylhydrazone and overactivating sigma E, one of the key envelope stress regulators that govern resistance transitions. Our findings provide practical strategies to overcome nanoresistance, offering a groundbreaking approach to enhance nanoantimicrobials’ efficacy in medical therapies and combat resistance evolution.

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

overall_design: E. coli K12 MG1655  was subjected to 14 days of evolution under intermittent exposure to high concentrations of AgNPs. RNA-seq was performed on cells from days 0, 9, and 14.

first: Ruibin

last: Li

first: Radek

last: Zbořil

first: Chengdong

last: Zhang


title: scRNAseq gene expression profile of zebrafish jaw joint cells after complete resection of the synovial jaw joint

status: Public on Dec 16 2024

city: New York

first: Joanna

last: Smeeton

state: NY

address: 650 W 168TH ST, ROOM 1103A, William Black Building

department: Rehabilitation and Regenerative Medicine

institute: Columbia University Irving Medical Center

summary: Adult mammalian synovial joints have limited regenerative capacity, where injuries heal with mechanically inferior fibrotic joint tissues. Here we developed a unilateral whole-joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using single-cell RNA sequencing, we profile RNA expression from live-sorted jaw joint cells throughout the time course of joint regeneration (1 to 70 days-post-joint-resection (dpjr)). Our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage.

overall_design: scRNAseq was performed on live-sorted cells from uninjured jaw joints and regenerated jaw joint tissues at 6 timepoints post-joint-resection (1, 3, 7, 14, 28, and 70 dpjr) to capture the major stages of healing post-resection.

first: Maria

last: Blumenkrantz

first: Ernesto

last: Gagarin

first: Everett

last: Weinstein

last: Anderson

first: Julia

last: Mo

first: Desmarie

last: Sherwood


title: Aberrantly Expressed RECQL4 Helicase Supports Proliferation and Drug Resistance of Human Glioma Cells and Glioma Stem Cells

status: Public on Dec 26 2024

first: Bartosz

last: Wojtas

address: Pasteura 3

institute: Nencki Institute of Experimental Biology

summary: RECQL4 depletion in human glioma cells with genetic tools slightly impaired cell viability and DNA replication, induced changes in gene expression and increased sensitivity of glioma cells and glioma stem cells to chemotherapeutics

overall_design: RecQL4 knock-out and wild type LN18 and LN229 cell lines were used to the experiments.

first: Sylwia

last: Krol

first: Agnieszka

last: Kaczmarczyk

first: Kamil

last: Wojnicki

first: Bartoisz

first: Bartlomiej

last: Gielniewski

first: Wieslawa

last: Grajkowska

first: Katarzyna

last: Kotulska

first: Cezary

last: Szczylik

first: Ryszard

last: Czepko

first: Mariusz

last: Banach

first: Wojciech

last: Kaspera

last: Szopa

first: Andrzej

last: Marchel

first: Tomasz

last: Czernicki

first: Bozena

last: Kaminska


title: Host and rabies virus gene expression is shaped by human brain cell type and reveals a preexisting pro-viral transcriptional state in astrocytes

status: Public on Dec 14 2024

city: Portland

first: Arpiar

last: Saunders

state: OR

address: 3232 SW Research Dr

institute: Vollum Institute (Oregon Health and Sciences University)

summary: Rabies virus (RABV) proteins play dual roles during the infection of complex neural tissue, the generation and spread of new virions and the active inhibition of cellular innate immune pathways, both contributing to rabies’ lethality. While spatially-distinct RABV protein residues specializing in virus-centric and immune-inhibitory functions have been identified, how these dual functions interact to shape infection outcomes across diverse types of host brain cells is unknown. To “unmask” and study how innate immune inhibition affects the transcriptional regulation of the human and viral genome with cellular resolution, we performed single-cell RNA sequencing of co-cultured human brain cell types, comparing infection dynamics of a wild-type RABV isolate virus to a mutant virus in which six critical point mutations in the P and M RABV proteins selectively neuter antagonism of interferon- and NF-κB- dependent cellular responses. Our analysis reveals that RABV gene expression is shaped by host cell type and that wild-type RABV infection induces small-scale, cell-type conserved transcriptional programs that may support infection by hijacking transcriptional feedback systems that control pro-viral host cell factors while minimizing anti-viral responses. In contrast to accepted models, disinhibited innate immune signaling increases RABV transcriptional output across infected cell types. Most strikingly, we discovered a sub-population of “pro-viral” astrocytes that supports an average of 6-fold higher viral mRNA expression through a massive host cell transcriptional change involving ~38% of the astrocyte-expressed human genome. Our analysis suggests that “pro-viral”-like astrocytes are a rare subtype found in the human brain and are poised to play a protective role during viral infection by advertising pathogens to microglia.

overall_design: Single-cell RNA-seq data was generated from co-cultured human brain cell types following various infection conditions of Tha isolate rabies virus (RABV). One experimental axis was viral titer (either 0.5 or 5.0 MOI). The second experimental axis was the rabies virus infection condition, which included 1) "No Infection" (in which no rabies virus was introduced into the culture well) as well 2) wild-type "Tha" RABV or 3) Tha2P4M RABV ("2P4M" denotes six amino acid mutations in RABV P and M proteins that block antagonism of host cell innate immune pathways by P and M protein).

first: Lena

last: Feige

first: Karl

last: Young

first: Juan Pablo

last: Cerapio

first: Tatsuya

last: Kozaki

first: Lauriane

last: Kergoat

first: Valentina

last: Libri

first: Florent

last: Ginhoux

first: Milena

last: Hasan

first: Lamya

last: Ben Ameur

first: Gregory

last: Chin

first: Zach

last: Goode

first: Hervé

last: Bourhy


title: High-resolution whole-genome DNA methylation revealed unique signatures of painful diabetic neuropathy

city: Bologna

first: Paolo

last: Garagnani

state: BO

address: Via San Giacomo 12

department: Department of Medical and Surgical Sciences (DIMEC)

country: Italy

institute: Univeristy of Bologna

type: Methylation profiling by genome tiling array

summary: This work describes the DNA methylation signature and identifies genes associated with neuropathic pain in type 2 diabetes mellitus. Genome-wide methylation data for 315 DNA (WB) samples were generated using Illumina Infinium Methylation EPIC v1.0 BeadChip. Four different selection criteria were used to identify promising pain-related genes. The findings revealed significant differences in methylation patterns between painful and painless diabetic neuropathy and identified a set of individual CpG sites of unique candidate genes associated with the painful phenotype. Several of these genes, including GCH1, MYT1L and MED16, have been previously linked to pain-related phenotypes or diabetes. Through pathway enrichment analysis, we demonstrated that specific epigenetic signatures could contribute to the complex phenotype of diabetic neuropathy and cluster analyses highlighted significant epigenetic dissimilarities between painful and painless phenotypes. Our results uncovered epigenetic differences between painful and painless diabetic neuropathy patients and identified targeted genes linked to neuropathic pain through DNA methylation mechanisms. This approach holds promise for investigating other chronic pain conditions, such as secondary chronic pain from cancer treatment, thoracic surgery, and various transplant settings.

overall_design: Bisulphite converted DNA isolated from 315 whole blood samples were hybridised to the Illumina Infiniun MethylationEPIC BeadChip following manufacture's protocols.

first: Katarzyna M

last: Kwiatkowska


title: Pol II degradation activates cell death independently from the loss of transcription [CRISPR_screen]

status: Public on Dec 13 2024

city: Worcester

first: Michael

last: Lee

state: MA

address: 368 Plantation Street

institute: UMASS Chan Medical School

summary: Pol II-mediated transcription is essential for eukaryotic life. While loss of transcription is thought to be universally lethal, the associated mechanisms promoting cell death are not yet known. Here, we show that death following loss of Pol II is not caused by loss of gene expression. Instead, death occurs in response to the loss of Pol II protein itself. Loss of Pol II protein exclusively activates apoptosis, and using functional genomics, we identified a previously uncharacterized pathway, which we call the Pol II Degradation-dependent Apoptotic Response (PDAR). Using the genetic dependencies of PDAR, we identify clinically used drugs that owe their efficacy to a PDAR-dependent mechanism. Our findings unveil a novel apoptotic pathway that contributes to the efficacy of a wide array of anti-cancer therapies.

overall_design: Genome-wide CRISPR KO screen of U2OS-Cas9 cells treated with or without 1 µM triptolide for 32 hours. T0 samples were taken immediately prior to drugging. Drug treated cells were then mechanically separated into live and dead fractions.

first: Nicholas

last: Harper

first: Gavin

last: Birdsall

first: Megan

last: Honeywell

first: Athma

last: Pai


title: Hi-C Calibration by Chemically Induced Chromosomal Interactions

status: Public on Dec 11 2024

first: Yi

last: Li

address: 406 SOUTH FREAR, UNIVERSITY PARK

institute: Penn State University

summary: The genome-wide chromosome conformation capture method, Hi-C, has greatly advanced our understanding of genome organization. However, its quantitative properties, including sensitivity, bias, and linearity, remain challenging to assess. Measuring these properties in vivo is difficult due to the heterogenous and dynamic nature of chromosomal interactions. Here, using Chemically Induced Chromosomal Interaction (CICI) method, we create stable intra- and inter-chromosomal interactions in G1-phase budding yeast across a broad range of contact frequencies. Hi-C analysis of these engineered cell populations demonstrates that static intra-chromosomal loops do not generate Topologically Associated Domains (TADs) and only promote 3D proximity within ~50kb flanking regions. At moderate sequencing depth, Hi-C is sensitive enough to detect interactions occurring in a few percent of cells. It also shows no inherent bias toward intra- versus inter-chromosomal interactions. Furthermore, we observe a linear relationship between Hi-C signal intensity and contact frequency. These findings illuminate the intrinsic properties of the Hi-C assay and provide a robust framework for its calibration.

overall_design: Hi-C experiments are performed on three yeast strains with intra-chromosomal CICI pairs and two yeast strains with inter-chromosomal CICI pairs. For each strain, 5 populations with different absolute contact frequencies between CICI loci are generated and their Hi-C contacts are measured.

first: Christoph

last: Fischer

first: Fan

last: Zou

first: Manyu

last: Du

first: Lu

last: Bai


title: Pol II degradation activates cell death independently from the loss of transcription [Exosome_knockout_RNAseq]

overall_design: RNA-seq profiling of U2OS cells with CRISPR mediated knockout of either NUP93 or EXOSC5, or cells given a nontargeting sgRNA (NONT). Cells were treated with or without 1 µM triptolide for 8 hours.


title: Pol II degradation activates cell death independently from the loss of transcription [Fractionation_RNAseq]

overall_design: RNA-seq profiling of U2OS cells and U2OS-PTBP1-knockout cells following treatment with or without 1 µM triptolide for 8 hours. Samples were fractionated into cytoplasmic and nuclear compartments.


title: Pol II degradation activates cell death independently from the loss of transcription [Switchover_RNAseq]

overall_design: RNA-seq profiling of U2OS cells expressing a Dox-inducible RPB1 transgene (RPB1-N792D-∆CTD), referred to as "switchover" cells. Cells were incubated with or without 2 µg/mL Dox for 48 hours, followed by exposure to 10 µM ⍺-amanitin for 0, 12, or 24 hours.


title: MicroRNA-directed control of complex mRNA stability patterns across cell types

status: Public on Dec 12 2024

city: Seattle

first: Lukas

last: Oesinghaus

state: WA

address: 3946 W Stevens Wy NE

institute: University of Washington

summary: Limiting expression to target cell types or states is a longstanding goal in gene therapy, which could be met by sensing endogenous microRNA. However, an unclear association between microRNA expression and activity currently hampers such an approach. Here, we probe this relationship by measuring the stability of synthetic microRNA-responsive 3'UTRs across 10 cell lines in a library format. By systematically addressing biases in microRNA expression data and confounding factors such as microRNA crosstalk, we demonstrate that a straightforward model can quantitatively predict the stability of reporters containing full microRNA target sites purely from expression data. We use this model to design constructs with previously unattainable response patterns across our cell lines. We then generalize this approach to primary tissues and cells and show that mRNA can be engineered to be differentially active between rested and exhausted T cell states. The rules we derive for microRNA expression data selection and processing should apply to microRNA-responsive devices for any environment with available expression data.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Plasmid libraries containing reporters with microRNA target sequences in their 3'UTR were transiently transfected into either 4 (library 1) or 11 (library 2) cell lines for n=2 replicates. After two days, poly(A) RNA was extracted, reverse transcribed, and sequenced. The original plasmid libraries were also sequenced.

first: Sebastian

last: Castillo-Hair

first: Morgan

last: Bean

first: Nicole

last: Ludwig

first: Shusruto

last: Rishik

first: Hao Yuan

last: Kueh

first: Andreas

last: Keller

first: Georg

last: Seelig


title: scBiopsy-seq: a platform for temporal single-cell RNA-seq analysis

city: Xiamen

first: Xing

last: Xu

address: 422, Siming South Road

institute: Xiamen University

summary: The development of temporal single-cell RNA-seq (scRNA-seq) assay enabled us to systemically investigate the effects of various types of perturbations in a time course with single-cell resolution. However, the existing temporal scRNA-seq technologies have certain limitations in reliability, detection efficacy and detection diversity. In the current study, we develop scBiopsy-seq assay that combines a synergistic electroosmosis-electrophoresis extraction method for efficient RNA extraction and digital microfluidics with contamination-isolated hydrophobic interface for high-performance sample processing. scBiopsy-seq extracts the cytoplasm at well-controlled volume to detect >10K genes per extraction with 90% successful rate. Functional enrichment revealed that the genes robustly detected by scBiopsy-seq were associated to diverse biological processes, demonstrating its superb diversity of detection. scBiopsy-seq can perform the sequential extraction of the cytoplasm from the same cell multiple times, which allows us to associate the cell phenotypic responses with its transcriptic dynamics. We employed scBiopsy-seq to analyze the temporal response to BRD4 inhibition with single-cell resolution of SW480 cells and identified the key roles of fatty acid oxidation in this biological process. scBiopsy-seq with comparable data quality with scRNA-seq will dramatically expand the application of temporal scRNA-seq towards a broader spectrum of biological research.

sample_organism:
Danio rerio
Homo sapiens
Mus musculus

platform_organism:
Danio rerio
Homo sapiens
Mus musculus

overall_design: scRNA-seq profiles of different cell lines

first: Linfeng

last: Cai

first: Shiyan

last: Lin

first: Minghao

last: Qiu

first: Li

first: Fuyuan

first: Jiajia

last: Liu

first: Yuning

first: Dianyi

last: Liang

first: Shanshan

first: Chaoyong

last: Yang

first: Jin


title: Classes of Lamin-Associated Domains are Defined by Distinct Patterns of Repressive Histone Methylation [CUT&RUN]

first: Mark

last: Parthun

overall_design: Cleavage Under Target and Release Using Nuclease (CUT&RUN) for Lamin B1, H3K9me2, H3K14ac, and IgG (control) in independently derived mouse embryonic fibroblast (iMEF) cell lines from one mouse colony. CUT&RUN for Lamin B1 and IgG was performed in 2 biological replicates and H3K9me2 and H3K14ac in one.

first: Caden

last: Martin

first: Prabakaran

last: Nagarajan

first: Elizabeth

last: Oser

first: Liudmila

last: Popova

middle: R


title: Pol II degradation activates cell death independently from the loss of transcription [DKO_wasting_RNAseq]

first: Michael

last: Lee

overall_design:
RNA-seq profiling of U2OS cells treated with 1 µM triptolide for 0 or 1 days, and U2OS-BAX-BAK1 -/- cells treated with 1 µM triptolide for 0, 2, 4, 6, 8, or 10 days.
RNA-seq profiling of U2OS and U2OS-BAX-BAK1 -/- cells treated with 1 µM triptolide short timecourse (0,4,8,24 hours).

first: Nicholas

last: Harper

first: Gavin

last: Birdsall

first: Megan

last: Honeywell

first: Athma

last: Pai


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

first: Yang

last: Zhao

state: CA

address: Beckman B169B, 279 Campus Drive

department: MCP

institute: Stanford University

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: Development of Fit Epidermal Resident Memory T Cells Requires Antigen Encounter in the Skin.

status: Public on Dec 10 2024

city: Boston

first: Liang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: CD8+ tissue resident memory T cells (TRM) develop from effectors that are recruited into peripheral tissues by infection or inflammation where they persist and provide defense against subsequent challenges.  Long-term persistence of epidermal TRM requires autocrine TGFβ that is transactivated by integrins expressed on keratinocytes.  In response to inflammation, the availability of TGFβ transactivation is limited.  Antigen-experienced TRM that encountered antigen in the epidermis during their development are more fit and outcompete bystander TRM for TGFβ transactivation resulting in their enrichment in the epidermis.  Transcriptomic analysis of endogenous epidermal TRM revealed that antigen-experienced TRM were enriched for TRM signature genes while bystander TRM retained the transcriptome of an earlier developmental state.  Following antigen recall, antigen-experienced TRM displayed accelerated proliferation kinetics compared with bystanders that was determined by the TCR signal-strength during their differentiation the skin.  Finally, antigen experienced TRM expressed TGFβRIII, which increases avidity of the TGFβRI/II receptor complex.  Selective ablation of Tgfbr3 from antigen experienced TRM reduced their capacity to persist when TGFβ activation was limited thus rendering them phenotypically like bystander TRM.  In sum, antigen-driven TCR signaling in the epidermis during TRM differentiation represents a required final step in ontogeny resulting in a lowered requirement on TGFβ transactivation for persistence and increased proliferation during recall responses that together result in the enhanced fitness of antigen-experience epidermal TRM.

overall_design:
Cohorts of wildtype C57BL/6 mice were infected on the left flank with VV by skin scarification.  DNFB was applied to the right flank 5 days post infection to recruit into the skin circulating CD8 effectors expanded by infection.  Mice were then rested for 50+ days to allow for the formation of TRM. Cells were pooled from 10 mice, enriched by percoll gradient centrifugation and purified by double FACSorting based on expression of CD90 and CD8.
On August 15, 2025, the Series was reorganized in order to include tissue-specific samples.

first: Eric

middle: S

last: Weiss

first: Toshiro

last: Hirai

first: Haiyue

last: Li

first: Andrew

last: Lui

first: Shannon

last: Baker

first: Ian

last: Magill

first: Jingyu

last: Fan

first: David

last: Masopust

first: Niroshana

last: Anandasabapathy

first: Harinder

last: Singh

last: Zemmour

first: Laura

last: MacKay

first: Daniel

middle: H

last: Kaplan


title: Latent Epigenetic Programs in Müller Glia Contribute to Stress, Injury, and Disease Response in the Retina [scRNA-seq]

status: Public on Dec 01 2024

city: Memphis

first: Michael

last: Dyer

state: Tennessee

address: 262 Danny Thomas

department: DNB

institute: St. Jude Children's Research Hospital

summary: Previous studies have demonstrated the dynamic changes in chromatin structure during retinal development that correlate with changes in gene expression. However, a major limitation of those prior studies was the lack of cellular resolution. Here, we integrate single-cell (sc) RNA-seq and scATAC-seq with bulk retinal data sets to identify cell type–specific changes in the chromatin structure during development. Although most genes’ promoter activity is strongly correlated with chromatin accessibility, we discovered several hundred genes that were transcriptionally silent but had accessible chromatin at their promoters. Most of those silent/accessible gene promoters were in the Müller glial cells. The Müller cells are radial glia of the retina and perform a variety of essential functions to maintain retinal homeostasis and respond to stress, injury, or disease. The silent/accessible genes in Müller glia are enriched in pathways related to inflammation, angiogenesis, and other types of cell-cell signaling and were rapidly activated when we tested 15 different physiologically relevant conditions to mimic retinal stress, injury, or disease in human and murine retinae. We refer to these as “pliancy genes” because they allow the Müller glia to rapidly change their gene expression and cellular state in response to different types of retinal insults. The Müller glial cell pliancy program is established during development, and we demonstrate that pliancy genes are necessary and sufficient for regulating inflammation in the murine retina in vivo. In zebrafish, Müller glia can de-differentiate and form retinal progenitor cells that replace lost neurons. The pro-inflammatory pliancy gene cascade is not activated in zebrafish Müller glia following injury, and we propose a model in which species-specific pliancy programs underly the differential response to retinal damage in species that can regenerate retinal neurons (zebrafish) versus those that cannot (humans and mice).

overall_design: Retina were dissected from the eye cup in Retinal Explant Media (REM). 1.5mm punches were taken from each eye using a biopsy punch and placed on a Nuclepore 1.0uM membrane floating on 2mL of REM (+/- stress) in a 12-well dish. 50uL of REM was removed from the dish and placed on the retinal punches. The retinal punches were incubated for 24 hours (37C, 5% CO2) for culture control retina. After culture, retinal punches dissociated in papain, spun down in a 4% BSA cushion and single cell RNA-sequencing was preformed using the 10x Genomics platform.

first: Jackie

last: Norrie


title: PD-1 Mediated Regulation of Unique Activated CD8+ T Cells by NK Cells in the Submandibular Gland

last: Yang

summary: The increasing use of anti-PD-1 immune checkpoint blockade has led to the emergence of immune-related adverse events (irAEs), including dysfunction of the submandibular gland (SMG). In this study, we investigated the immunoregulatory mechanism contributing to the susceptibility of the SMG to irAEs. Here, we found that the SMG of PD-1 deficient mice and anti-PD-L1 treated mice harbor an expanded population of CD8+ T cells. We demonstrate that NK cells expressing PD-L1 tightly regulate CD8+ T cells in the SMG. When this immunoregulation is disrupted, CD8+ T cells clonally expand and acquire a unique transcriptional profile consistent with TCR activation. These clonally expanded cells phenotypically overlapped with cytotoxic GzmK+ CD8+ T autoimmune cells identified in primary Sjögren’s syndrome patients. Understanding how NK cells modulate CD8+ T cell activity in the SMG opens new avenues for preventing irAEs in patients undergoing checkpoint blockade therapies.

overall_design:
T cells were extracted from the submandibular glands of WT and PD-1KO mice, and the spleen of WT mice for transcriptomic, proteomic, and TCR repertoire analysis
On August 15, 2025, the Series was reorganized in order to include tissue-specific samples.

first: Sam

last: Borys

first: Shanelle

last: Reilly

first: Laurent

last: Brossay


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

status: Public on Dec 07 2024

city: Los Angeles

first: Ho Chung

last: Chen

address: 609 Charles E Young Dr E

department: MIMG

institute: University of California, Los Angeles

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

last: Zhang

first: Lisa

last: Kohn

first: Hsing Hui

last: Wang

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

last: Su


title: Yeast elongation factor homolog New1 protects a subset of mRNAs from degradation by no-go decay

status: Public on Nov 26 2024

city: Mainz

first: Marie-Luise

last: Winz

address: Staudingerweg 5

institute: Johannes Gutenberg-University Mainz

summary: New1 is a homolog of fungal translation elongation factor 3 (eEF3) inSaccharomyces cerevisiae. Its absence has previously been described to lead to cold sensitivity, ribosome biogenesis defects, and ribosomal queues upstream of Stop codons on selected mRNAs. Here, we find that, especially in cold conditions, lack of New1 induces no-go decay (NGD) on specificmRNAs, leading, as a consequence, to decreased mRNA and protein levels of such genes.The effect correlates with the presence of specific Lysine and Arginine codons just upstream of the Stop codon. In total, more than 10% of yeast coding sequences end with the affected codons. We have confirmed NGD and subsequent downregulation at the protein level for the metabolic enzymes Pgk1, Gpm1, and Adh1, translation elongation factors EF-1 alpha and EF-1 beta (gamma-subunit), ribosomal protein Rps5, as well as ribosome biogenesis factor Nop1 and adenosine kinase Ado1.

overall_design: We performed UV crosslinking and analysis of cDNA (CRAC) for the collision sensor and E3 ubiquitin ligase Hel2 and for New1, in presence or absence of the respective other player. To this end,in yeast Saccharomyces cerevisiae, BY4741, we genomically tagged Hel2 or New1 (only version in the genome, single copy) with a His-TEV-ProteinA tag in either a wildtype or new1-deleted (for Hel2) or hel2-deleted (for New1) strain background. Cells were cultured at 30°C or 20°C, as mentioned, and UV-crosslinked.  The tagged protein was purified along with crosslinked RNA and sequencing libraries were prepared in a total of 4 replicates (2 at 30°C, 2 at 20°C). For each replicate, a control experiment was conducted in which no protein was tagged (BY), in the wildtype background, to assess background signals.

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