title: Single cell RNAseq of brian cells in the cortical amygdala with social transmitted food memory

status: Public on Mar 09 2024

first: Wenfei

last: Sun

address: 318 Campus Dr.

institute: Stanford University

summary: Social communication guides decision making that is essential for survival. Social transmission of food preference (STFP) is an ecologically relevant memory paradigm in which an animal learns a desirable food odor from other animals in a social context. How food-preference memory is acquired, consolidated, and stored is unclear. Here, we identify a circuit involving the posteromedial nucleus of the cortical amygdala (COApm) as a computational center that integrates social and sensory olfactory inputs for long-term STFP memory consolidation. Blocking synaptic signaling by the COApm circuit selectively abolished STFP memory consolidation without impairing memory acquisition, storage, or recall. STFP memory consolidation by the COApm depends on synaptic inputs from the accessory olfactory bulb and on synaptic outputs to the anterior olfactory nucleus and requires protein synthesis, suggesting a gene expression mechanism. Deep single-cell and spatial transcriptomics revealed robust but distinct gene expression signatures induced by STFP memory formation in the COApm consistent with synapse restructuring. Our data thus define a neural circuit for consolidation of a socially communicated long-term memory, thereby mechanistically distinguishing protein synthesis-dependent memory consolidation from memory acquisition, storage, or retrieval.

overall_design: To study the molecular and cellular basis of memory consolidation, we applied social transmitted food memory paradigm on C57BL/6J mice with tdTomato-expressing retro AAVs injected into the accessory Olfactory bulb and performed single cell RNAseq for the posteromedial nucleus of the cortical amygdala.

first: Zhihui

last: Liu

first: Stephen

last: Quake

first: Thomas

last: Südhof


title: PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiations and Function [scRNA-seq]

status: Public on Mar 01 2024

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

country: USA

institute: Cincinnati Children's Hospital Medical Center

type: Expression profiling by high throughput sequencing

summary: Differential chromatin accessibility accompanies and mediates transcriptional control of diverse cell fates and their differentiation during embryogenesis. While the critical role of NKX2-1 and its transcriptional targets in lung morphogenesis and pulmonary epithelial cell differentiation is increasingly known, mechanisms by which chromatin accessibility alters the epigenetic landscape and how NKX2-1 interacts with other co-activators required for alveolar epithelial cell differentiation and function are not well understood. Here, we demonstrate that the paired domain zinc finger transcriptional regulators PRDM3 and PRDM16 regulate chromatin accessibility to mediate cell differentiation decisions during lung morphogenesis. Combined deletion of Prdm3 and Prdm16 in early lung endoderm caused perinatal lethality due to respiratory failure from loss of AT2 cell function. Prdm3/16 deletion led to the accumulation of partially differentiated AT1 cells and loss of AT2 cells. A combination of single cell RNA-seq, bulk ATAC-seq, and CUT&RUN demonstrated that PRDM3 and PRDM16 enhanced chromatin accessibility at NKX2-1 transcriptional targets in peripheral epithelial cells, with all three factors binding together at a multitude of cell-type specific cis-active DNA elements. Network analysis demonstrated that PRDM3/16 regulated genes critical for perinatal AT2 cell differentiation, surfactant homeostasis, and innate host defense. Lineage specific deletion of PRDM3/16 in AT2 cells led to lineage infidelity, with PRDM3/16 null cells acquiring a partial AT1 fate. Together, these data demonstrate that NKX2-1-dependent regulation of alveolar epithelial cell differentiations is mediated by epigenetic modulation via PRDM3/16.

overall_design:
Floxed alleles of Prdm16 and Prdm3 were knocked out using the sonic hedgehog CRE transgene. Whole lungs were harvested from fetal control and PRDM3/16 knockout mice at E18.5.
We investigated differential gene expression and cell population changes between control mice and those lacking functional Prdm16 and Prdm3 genes

first: Hua

last: He

first: Shelia

middle: M

last: Bell

first: Ashley

middle: K

last: Davis

first: Shuyang

last: Zhao

first: Anusha

last: Sridharan

first: Cheng-Lun

first: Minzhe

last: Guo

first: John

last: Snowball

first: William

middle: J

last: Zacharias

first: Daniel

middle: T

last: Swarr

first: Mineo

last: Kurokawa

first: Susumu

last: Goyama

first: Jeffery

middle: A

last: Whitsett


title: PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiations and Function [bulk RNA-seq]

overall_design:
Floxed alleles of Prdm16 and Prdm3 were knocked out using the sonic hedgehog CRE transgene. Lungs were harvested from fetal mice at E17.5 and EpCAM+ lung epithelial cells were isolated with microbeads.
We investigated changes in gene expression between wild type mice and those lacking functional Prdm16 and Prdm3 genes in EpCAM+ sorted lung epithelial cells at the E17.5 timepoint.


title: Effects of formalin-fixation on FAIRE-Seq and MNase-Seq signatures in yeast

city: Canberra

first: Erin

middle: Elizabeth

last: Hahn

state: ACT

address: Clunies Ross

department: National Research Collections Australia

country: Australia

institute: CSIRO

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we first sought to understand the effect of prolonged formalin fixation on the read alignment signatures resulting from FAIRE and MNase treatment. Here we cultured yeast (Saccharomyces cerevisiae) under normal and heat-shock conditions then fixed the cells with formalin for 15 minutes, 1 hour, 6 hours, and 24 hours. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and enables semi-quantitative estimates of relative gene expression in this yeast model.

overall_design: FAIRE and MNase treatment of Saccharomyces cerevisiae (strain BJ5464 auxotroph ΔURA3) in a formalin-fixation time series

middle: E

first: Jiri

last: Stiller

first: Marina

last: Alexander

first: Alicia

last: Grealy

first: Jennifer

last: Taylor

first: Nicola

last: Jackson

first: Celine

middle: H

last: Frere

first: Clare

last: Holleley


title: RNA-seq and ChIP-seq H3K4me1 H3K4me2 H3K4me3 for Col-0

status: Public on Feb 26 2024

city: Shanghai

first: Wenhao

last: Xie

state: Shanghai

address: No. 2005, Songhu Road

department: School of Life Science

country: China

institute: Fudan University

summary: To investigate the relationship between H3K4me1/H3K4me2/H3K4me3 and transcription levels and  in Arabidopsis thaliana,we anlysis the RNA-seq and ChIP-seq data to quantified the transcription and modification levels on  Arabidopsis genes.We then performed H3K4 methylation occupancy analysis in different RNA transcription levels using data obtained from ChIP-seq and RNA-seq.

overall_design: Quantify the RNA transcription level and H3K4 methylation level on wild-type Arabidopsis genes, analyze the distribution of H3K4 methylation on genes at different transcription levels, and calculate the correlation between RNA transcription level and H3K4 methylation level

first: Aiwu

last: Dong

first: Chengzhang

last: Li

first: Bing

last: Liu

first: Xiang

first: Jiachen

last: Wang


title: ChIP-seq to test histone methylation in Bd21-3 and the jmj1-1 mutant.

summary: To investigate the impact of BdJMJ1 on H3K4me1, H3K4me2, H3K4me3, and H3 at the genome-wide level.

overall_design: ChIP-seq for Bd21-3 and jmj1-1 plants using H3K4me1/2/3 and H3 antibodies.

first: Richard

last: Amasino


title: SMYD5 regulates mRNA translation to promote gastric adenocarcinoma (GAC)

city: Stockholm

first: Krzysztof

middle: Jan

last: Szkop

state: Solna

address: SciLifeLab, Tomtebodavägen 23

department: Department of Oncology and Pathology

country: Sweden

institute: Karolinska Institutet

summary: Dysregulated transcription due to disruption in histone lysine methylation dynamics is an established contributor to tumorigenesis. However, whether analogous pathologic epigenetic mechanisms act directly on the ribosome to advance oncogenesis is unclear. Here we find that trimethylation of the core ribosomal protein L40 at lysine 22 (rpL40K22me3) by the lysine methyltransferase (KMT) SMYD5 regulates mRNA translation output to promote gastric adenocarcinoma (GAC) malignant progression with lethal peritoneal ascites. A biochemical-proteomic strategy identifies the mono-ubiquitin fusion protein partner rpL40 as the principal physiologic substrate of SMYD5 across diverse samples. Inhibiting the SMYD5-rpL40K22me3 axis in GAC cell lines reprograms protein synthesis to attenuate oncogenic gene expression signatures. SMYD5 and rpL40K22me3 are upregulated in GAC patient samples and negatively correlate with clinical outcomes. SMYD5 ablation in vivo in familial and sporadic mouse models of malignant GAC blocks metastatic disease including peritoneal carcinomatosis (PC). Suppressing SMYD5 methylation of rpL40 inhibits human cancer cell and patient-derived GAC xenograft growth and renders them hypersensitive to PI3K/mTOR inhibitors. Finally, combining SMYD5 depletion with PI3K/mTOR inhibition and CAR-T administration cures an otherwise lethal in vivo mouse model of aggressive GAC-derived PC. Together, our work uncovers a ribosome-based epigenetic mechanism that facilitates evolution of malignant GAC and nominates SMYD5 targeting as part of a potential cornerstone combination therapy to treat a deadly cancer.

overall_design: Analysis of total and polysome-associated RNA-sequencing of Control and SMYD5 knockout samples (3 vs 3)

first: Juhyung

last: Park

first: Jibo

last: Wu

first: Jinho

last: Jeong

first: Dylan

last: Husmann

first: Natasha

last: Flores

first: Joel

middle: W

last: Francis

first: Ying-Jiun

middle: C

last: Chen

first: Ana

last: Morales Benitez

first: Emily

last: Zahn

first: Shumei

last: Song

first: Jaffer

last: Ajani

first: Linghua

first: Kamini

last: Singh

first: Ola

last: Larsson

first: Benjamin

last: Garcia

first: Ivan

last: Topisirovic

first: Pawel

last: Mazur

first: Or

last: Gozani


title: Functional characterization of genetic variants associated with upper digestive cancers [HiChIP]

status: Public on Feb 25 2024

city: Salt Lake City

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

institute: University of Utah

summary: Using H3K27ac HiChIP assays to link genetic variants to target genes in upper digestive cancers

overall_design: H3K27ac HiChIP was done to identify enhancer-promoter interactions in upper digestive cancer cell lines, including the gastric cancer cell line AGS and the upper disgestive squamous cell carcinoma cell lines BICR16 and BICR31.

first: Swneke

middle: D

last: Bailey


title: Single-cell RNA sequencing analysis according to the clinical course of Mycobacterium avium complex pulmonary disease

city: Seoul

first: Su-Young

last: Kim

address: 81, Irwon-ro, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

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

overall_design: Refer to individual Series


title: Loss of PPARα function promotes epigenetic dysregulation of lipid homeostasis driving ferroptosis and pyroptosis lipotoxicity in Metabolic Dysfunction Associated Steatotic Liver Disease (MASLD)

city: Wilrijk

first: Claudia

last: Theys

state: Antwerpen (nl)

department: FBD

country: Belgium

institute: Universiteit Antwerpen

type: Methylation profiling by genome tiling array


title: RNA-Seq analysis of mouse neural stem cells with or wihtout Rad21 knockdown.

status: Public on Feb 20 2024

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

summary: The precise regulation of neural stem cell quiescence and activation is crucial for normal brain development and lifelong neurogenesis. However, the mechanisms that control neural stem cell activation remains poorly understood. In this study, we investigate the role of Rad21 in this process.

overall_design: RNA-seq analysis of neural stem cells that are derived from E13.5 wild type (Phf2f/f) control mice without and with treatment  shRNAs against mouse Rad21

middle: V

first: Jia

last: Feng

first: Derrick

middle: S

last: Ong


title: Functional characterization of genetic variants associated with upper digestive cancers

status: Public on Feb 24 2024


title: RNA-Seq analysis of mouse neural stem cells with or without Phf2 knockout

status: Public on Feb 14 2024

summary: The precise regulation of neural stem cell quiescence and activation is crucial for normal brain development and lifelong nwurogenesis. However, the mechanisms that control neural stem cell activation remains poorly understood. In this study, we investigate the role of Phf2 in this process.

overall_design: RNA-seq analysis of neural stem cells that are derived from E13.5 wild type (Phf2f/f) control mice and conditional KO (Nestin-Cre Tg, Phf2flox/flox) mutant mice.


title: Catabolism of b-5 linked aromatics by Novosphingobium aromaticivorans

status: Public on Feb 29 2024

city: Madison

first: Kevin

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: Aromatic compounds are an important renewable source of commodity chemicals traditionally produced from fossil fuels. Aromatics derived from plant lignin can potentially be converted into commodity chemicals through depolymerization followed by microbial funneling of monomers and low molecular weight oligomers. This study investigates the catabolism of the b-5 linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) by the bacterium Novosphingobium aromaticivorans. We used genome wide screens to identify candidate genes involved in DC-A catabolism. Subsequent in vivo and in vitro analyses of these candidates elucidated a catabolic pathway composed of four required gene products and several partially redundant dehydrogenases that convert DC-A to aromatic monomers that can be funneled into the central aromatic metabolic pathway of N. aromaticivorans. Specifically, a newly identified γ-formaldehyde lyase, PcfL, opens the phenylcoumaran ring to form a stilbene and formaldehyde. A lignostilbene dioxygenase, LsdD, then cleaves the stilbene to generate the aromatic monomers, vanillin and 5-formylferulate (5-FF). We also show that an aldehyde dehydrogenase FerD oxidizes 5-FF before it is decarboxylated by LigW, yielding ferulic acid. We found that some enzymes involved in b-5 catabolism pathway can act on multiple substrates and that some steps in the pathway can be mediated by multiple enzymes, providing new insights into the robust flexibility of aromatic catabolism in N. aromaticivorans.  We performed a comparative genomic analysis to predict that key enzymes in the newly discovered b-5 aromatic catabolic pathway are common among Sphingomonads.

sample_organism: Novosphingobium aromaticivorans DSM 12444

overall_design: RNA-seq comparison of transcript abundance in a PDC-producing N. aromaticivorans strain (12444PDC) grown in the presence of dehydrodiconiferyl alcohol (DC-A) and glucose, vanillin and glucose, ferulic acid and glucose, or glucose alone

first: Fletcher

last: Metz

first: Abigail

last: Olsen

first: Fachuang

last: Lu

first: Marco

middle: N

last: Allemann

first: Joshua

last: Michener

first: Daniel

middle: R

last: Noguera

first: Timothy

last: Donohue


title: The effects of Eupalinolide B on PANC-1 cells.

status: Public on Feb 28 2024

city: Qingyuan

first: Qingtian

last: Huang

address: 35 Yinquan North Road, Qingcheng District

institute: Guangzhou Medical University

summary: Eupalinolide B (EB), a compound isolated from Eupatorium lindleyanum, has been evaluated for its anticancer effects on pancreatic cancer cells and xenograft models. Our research presents a multi-faceted investigation of EB, including assessments of its impact on cell viability, proliferation, migration, invasion, and potential mechanisms of action.

overall_design: We divided the samples into two groups, four each: a control group and a group treated with 10μM EB. After 24 hours of treatment, we extracted RNA using Trizol for mRNA sequencing.

first: Jie

last: Yang

first: Yanfen

last: Wang

first: Ling

last: Qi


title: GDNF/GFRA1 signaling contributes to chemo- and radioresistance in glioblastoma

status: Public on Feb 13 2024

city: København Nv

first: Inès

middle: CN

last: Avenel

address: Ole Maaløes Vej 5

country: Denmark

institute: BRIC

summary: Glioblastoma (GBM) is the most common primary brain tumor in adults, characterized by an inherent aggressivity and resistance to treatment leading to poor prognoses. While some resistance mechanisms have been elucidated, a deeper understanding of these mechanisms is needed to increase therapeutic efficacy. In this study we first discovered glial-cell derived neurotrophic factor (GDNF) to be upregulated in patient-derived glioblastoma spheroid cultures after chemotherapeutic temozolomide (TMZ) treatment, through RNA-Seq experiments. Therefore, we investigated the role of the GDNF/GDNF receptor alpha 1 (GFRA1) signaling pathway as a resistance mechanism to chemotherapy with temozolomide and lomustine as well as irradiation using patient-derived glioblastoma spheroid cultures. With qPCR experiments we showed a consistent upregulation of GDNF and its primary receptor GFRA1 following all three lines of treatment. Moreover, CRISPR/Cas9 knock-outs of GDNF in two patient-derived models sensitized these cells to chemotherapy treatment, but not radiotherapy. The increased sensitivity was completely reversed by the addition of exogeneous GDNF, confirming the key role of this factor in chemoresistance. Finally, a CRISPR KO of GFRA1 demonstrated a similar increased sensitivity to temozolomide and lomustine treatment, as well as radiotherapy. Together, our findings support the role of the GDNF/GFRA1 signaling pathway in glioblastoma chemo and radioresistance.

overall_design:
To uncover potential genes of interest in glioblastoma treatment resistance we used 3 patient-derived primary glioblastoma cell lines, treated each one with either the alkylating agent Temozolomide or a DMSO control and compared control/post treatment gene expression through an RNA-Seq experiment.

***************************************************************
no raw files due to patient privacy issues (RNASeq experiment was done on patient-derived samples)
***************************************************************

first: Burton

last: Mark

first: Thesbjerg

last: Martin

first: Thomassen

last: Mads


title: NanoString immune profiling of pediatric brain tumors

status: Public on Feb 19 2024

city: Toronto

first: Cynthia

last: Hawkins

state: ON

address: 555 University Ave.

department: Pediatric Laboratory Medicine

country: Canada

institute: The Hospital for Sick Children

summary: With the increasing use of immunotherapy in cancer, understanding the tumor immune microenvironment (TIME) has become increasingly important. There has been great success in treatment of some pediatric high-grade gliomas with immune checkpoint inhibition, however overall, the immune microenvironment in pediatric brain tumors remains poorly understood. Accordingly, we developed a clinical immune-oncology gene expression assay and used it to profile a diverse range of pediatric brain tumors with detailed clinical and molecular annotation, including a total of 1379 cases. Our findings demonstrate the critical importance of understanding the TIME to guide the prognosis and management of pediatric brain tumors. In pediatric low-grade gliomas we identified distinct patterns of immune activation with prognostic significance in BRAF V600E mutant tumors. In pediatric high-grade gliomas, we observed elevated inflammation and T cell infiltrates in tumors that have historically been considered immune cold, as well as genomic correlates of inflammation levels. In our cohort of mismatch repair deficient high-grade gliomas treated with immune checkpoint inhibition, we found that high tumor inflammation signature was a significant predictor of treatment response. Furthermore, we demonstrated the potential for multimodal biomarkers to improve the treatment stratification of these patients. Importantly, while overall patterns of immune activation were observed for histologically and genomically defined tumor types, there was nonetheless significant variability within each diagnostic entity, indicating that the immune response must be evaluated as an independent feature. In sum, in addition to the histology and molecular profile, this work establishes the importance of assessing and reporting on the tumor immune microenvironment as an essential axis of cancer diagnosis in the era of personalized medicine.

overall_design: This study analyzed frozen or formalin-fixed paraffin-embedded (FFPE) tissue from 571 patient samples, including 559 pediatric brain tumors and 12 non-tumor brain control samples. Gene expression profiling was carried out using the NanoString nCounter system with a customized CodeSet composed of a total of 103 genes focused on the tumor-immune microenvironment.

first: Uri

last: Tabori


title: Dietary folate limitation late in life

status: Public on Feb 09 2024

city: College Station

first: Michael

last: Polymenis

state: Texas

address: 2128 TAMU

department: Biochemistry and Biophysics

institute: Texas A&M Univ

summary: Folate is a vitamin essential for cell growth and has been used to prevent congenital abnormalities. However, little is known about how folate affects health in older adults. We examined healthspan as a function of dietary folate intake. To begin to measure such effects, we performed a small (2x2; sex-by-diet) pilot study in the long-lived inbred mouse strain C57BL/6.

overall_design: There were  20 mice per group. At 52w of age, half the mice were maintained on the standard diet (AIN-93G), and the other half were placed on a folate/choline-deficient (F/C-) diet. The standard diet contains 2mg/kg of folic acid and 2.5g/kg choline bitartrate (F/C+), while the F/C- diet contains 0mg/kg of folic acid and choline bitartrate. The mice were sacrificed at 120w. At that point, only 39 mice were alive, from both sexes and groups. Samples from liver tissue were used to prepare the libraries described here, for RNAseq.


title: Rapid DNA methylation-based classification of pediatric brain tumours from ultrasonic aspirate specimens

status: Public on Feb 08 2024

city: Berlin

first: Luis

middle: Philipp

last: Kuschel

address: Robert-Koch-Platz 4

department: Abteilung für experimentelle Neurologie

country: Germany

institute: Charité Universitätsmedizin Berlin

type: Methylation profiling by high throughput sequencing

summary: Cavitating ultrasonic aspirator devices are frequently used in pediatric neurosurgery for efficient microsurgical resection of brain tumours while minimizing tissue damage to surrounding healthy brain. Within this study molecular diagnostics using methylation-based classification of ultrasonic aspirated samples was performed and performance against routine microarray diagnostics was assessed.

overall_design:
21 pediatric brain tumor cases acquired by an ultrasonic-cavitating aspirator were submitted to DNA extration, quality control and library preparation with subsequent six hour nanopore sequencing. Classification of cases was performed using a neural network classification model and classification calls were compared to routine microarray diagnostics.
***Submitter declares that the raw data has been deposited at European Genome Archive due to local regulations***

first: Michèle

last: Simon

middle: P

first: Katja

last: von Hoff

first: Dongsheng

last: Yuan

first: Pablo

last: Driever

first: Elisabeth

middle: G

last: Hain

first: Arend

last: Koch

first: David

last: Capper

first: Matthias

last: Schulz

first: Ulrich-Wilhelm

last: Thomale

first: Philipp

last: Euskirchen


title: Nanoligomers targeting NF-κB and NLRP3 reduce neuroinflammation and improve cognitive function with aging and tauopathy

status: Public on Feb 07 2024

city: Fort Collins

first: Devin

last: Wahl

state: Colorado

address: 1582 Campus Delivery, Moby Reception

institute: Colorado State University

summary: Neuroinflammation contributes to impaired cognitive function in brain aging and neurodegenerative disorders like Alzheimer’s disease, which is characterized by the aggregation of pathological tau. One major driver of both age- and tau-associated neuroinflammation is the NF-κB and NLRP3 signaling axis. However, current treatments targeting NF-κB or NLRP3 may have adverse/systemic effects, and most have not been clinically translatable. Here, we tested the efficacy of a novel, nucleic acid therapeutic (Nanoligomer) cocktail specifically targeting both NF-κB and NLRP3 in the brain for reducing neuroinflammation and improving cognitive function in old wildtype mice, and in a mouse model of tauopathy. We found that 4 weeks of NF-κB/NLRP3-targeting Nanoligomer treatment strongly reduced neuro-inflammatory cytokine profiles in the brain and improved cognitive-behavioral function in both old and tauopathy mice. These effects of NF-κB/NLRP3-targeting Nanoligomer treatment were associated with reduced glial cell activation in old wildtype mice, less pathology in tauopathy mice, favorable changes in transcriptome signatures of inflammation (reduced) and neuronal health (increased) in both mouse models, and no adverse systemic effects. Collectively, our results provide a basis for future translational studies targeting NF-κB/NLRP3 in the brain, perhaps using Nanoligomers, to inhibit neuroinflammation and improve cognitive function with aging and neurodegenerative disease.

overall_design: RNA-seq on hippocampus isolated from C57/B6 Mice aged 9 and 20 months.  RNA-seq on hippocampus tissue isolated from male and female rTg4510 mice aged 3 months.

first: Thomas

middle: J

last: LaRocca


title: Transcriptomics-based points of departure for Daphnia magna exposed to 18 per- and polyfluoroalkyl substances.

status: Public on Feb 22 2024

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

summary: Per- and polyfluoroalkyl substances (PFAS) represent a large group of contaminants of concern based on their widespread use, distribution and persistence in the environment, and potential toxicity. Many of the traditional models for estimating toxicity, bioaccumulation, and other relevant toxicological properties are not well suited for PFAS. Consequently, there is a need to generate hazard information for a large number of PFAS in an efficient and cost-effective manner. In the present study, Daphnia magna were exposed to multiple concentrations of 22 different PFAS for 24 h, in a 96-well plate format. Following exposure, whole body RNA was extracted and pooled extracts, each representing five exposed individuals, were subjected to RNA sequencing. Following analytical measurements to verify PFAS exposure concentrations in-well, and quality control on processed cDNA libraries for sequencing, concentration-response modeling was applied to the data sets for 18 of the tested compounds, and the concentration at which a concerted molecular response occurred (transcriptomic point of departure; tPOD) was calculated. The tPODs, based on average measured concentration of PFAS in the exposure wells, generally ranged from 0.03-0.58 µM (9.9-350 µg/L; interquartile range). In most cases, these concentrations were two orders of magnitude lower than similarly calculated tPODs for human cell lines exposed to PFAS. They were also lower than apical effect concentrations reported for seven PFAS for which some crustacean or invertebrate toxicity data were available, although there were a few exceptions. However, despite being lower than most other available hazard benchmarks, the Daphnia magna tPODs were, on average, four orders of magnitude greater than the maximum aqueous concentrations of PFAS measured in Great Lakes tributaries. Overall, this high throughput transcriptomics assay with Daphnia magna holds promise as a component of a tiered hazard evaluation strategy employing new approach methodologies.

overall_design: Test chemicals were sourced through contract with Evotec (Branford, CT, USA; Contract #EP-D-12-034). Substances were provided solubilized in dimethylsulfoxide (DMSO) at two stock concentrations, 30 mM and 9.5 mM. Stock solutions were shipped frozen at -20° C, and stored at -80°C until thawed for use in the bioassays. A dilution series for each assay was prepared using a Biomek i5 liquid handler (Beckman Coulter, Brea, CA, USA). Stock solutions of two PFAS at 30 mM and 9.5 mM (nominal) were pipetted into designated wells of a 96 well plate (300 µl; catalog #650101; Greiner Bio-One, NC, USA). Ten-fold serial dilutions in DMSO (or methanol) were then prepared from each stock solution to yield a total of 8 concentrations with ½ log spacing for each chemical. Stocks from the dilution plate were then diluted to 0.33% in sand-filtered and UV-treated Lake Superior Water amended with 94 µM Na2SO4; 24 µM NaCl; 23 µM KCl; 15 µM CaCl2; 48 µM MgCl2 (hereafter amended LSW) yielding a nominal concentration range from 100-0.03 µM (1/2 log spacing) and distributed to a dosing plate (2 ml deep-well plates; catalog # 503162; NEST Scientific, NJ, USA), such that each concentration of an individual PFAS to be tested was represented by five wells on each plate, with two wells for each concentration on the perimeter of the plate (edge wells) and the remaining three wells for each concentration positioned on the interior. A concentration response series for two PFAS, with a shared set of controls, was present on each 96-well plate and three replicate plates were prepared for each pair of two PFAS tested. Control wells contained the same concentration (0.33%) of either DMSO or methanol as the wells treated with PFAS. Daphnia magna were obtained from an onsite culture unit at the U.S. EPA Great Lakes Toxicology and Ecology Division, Duluth, MN. For use in the assays, Daphnia magna were reared in mass culture in amended LSW and held at 20° C until they were 72 hours old. They were fed a diet of yeast-Cerophyll-trout chow and algae (USEPA 2016d) until ready for use in the assays. All procedures involving animals were approved by a local animal care and use committee. Bioassays were conducted using the same experimental design. All assays were conducted in 96-well plate format using 1 ml volume deep-well plates (Catalog # 502162, NEST Scientific). Uniform age (72 ± 6 h) Daphnia magna were manually loaded to each well of three replicate 96-well plates using a P1000 pipet with the end of the tip cut off to a one cm bore diameter. The volume in each well was reduced to a uniform volume of 50 µl using the Biomek i5 liquid handler. Assays were initiated by adding 550 µl of exposure solution from the dosing plate to the three replicate exposure plates for each assay. Immediately after dosing, each plate was covered with a silicone sealing mat (catalog #506065; NEST Scientific) and then placed in a 20°C incubator for 24 h. At test termination, each well was inspected and all mortalities (immobile with gentle prodding) were recorded and removed. Live daphnia were also examined for phenotypic abnormalities, although none were noted at sublethal concentrations. The Biomek i5 was then used to transfer 100 µl of exposure solution to an “exposure verification plate”, where the n=5 samples for each treatment concentration were subsequently pooled together into a total volume of 500 on a per-plate basis. The pooled exposure solution for each treatment, per plate, was diluted 1:1 in acetonitrile (with the exception of PFTeDA, PFUdA, PFTrDA, and PFNA which were diluted 3:1 in acetonitrile and FHxSA, N-EtFOSA-M, 8:2 FTS, and PFTDoDA diluted 3:1 in methanol) for subsequent use in exposure verification. The remaining volume of exposure medium in each well was replaced with 60 µl of Trizol (Zymo Research, CA, USA). A 2.3 mm stainless steel bead was added to each well, then the plate was homogenized at 30 Hz for two minutes using an Omni-Bead Ruptor bead mill. Homogenates of individual Daphnia magna from the same treatment group were pooled together, on a per plate basis to generate one pooled sample per treatment, per plate (three biological replicates per treatment). Only live daphnia were included in the homogenate pools.

middle: L

first: Brett

last: Blackwell

first: Kendra

last: Bush

first: Joshua

last: Harrill

first: Felix

last: Harris

first: Monique

last: Hazemi

first: Michelle

last: Le

first: Emma

last: Stacy

first: Kevin

middle: M

last: Flynn


title: Protective Renalase-deficiency in beta cells shapes immune metabolism and function in autoimmune diabetes

status: Public on Feb 27 2024

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Type 1 diabetes (T1D) is caused by the immune-mediated loss of pancreatic beta cells that produce insulin. The latest advances in stem cell (SC)-beta cell differentiation methods have made a cell replacement therapy for T1D feasible. However, recurring autoimmunity would rapidly destroy transplanted SC-beta cells. A promising strategy to overcome immune rejection is to genetically engineer SC-beta cells. We previously identified Renalase (Rnls) as a novel target for beta cell protection. Here we show that Rnls deletion endows beta cells with the capacity to modulate the metabolism and function of immune cells within the local graft microenvironment. We used flow cytometry and single-cell RNA sequencing to characterize beta cell graft-infiltrating immune cells in a mouse model for T1D. Loss of Rnls within transplanted beta cells affected both the composition and the transcriptional profile of infiltrating immune cells in favor of an anti-inflammatory phenotype with decreased antigen presenting capacity. We propose that changes in beta cell metabolism mediate local immune regulation and that this feature could be exploited for therapeutic goals.

overall_design: WT and Rnls mutant NIT-1 cells (1.5 x 10e7 each) were injected subcutaneously (s.c.) into opposite flanks of immunodeficient NOD.scid mice. Four days later, autoreactive splenocytes from recently diabetic NOD mice were isolated and red blood cell were lysed using 5 ml of ACK lysing buffer (cat # A1049201; Thermo Fisher Scientific) for 4 min at RT. Lysis was stopped using 5 ml of PBS/ 10 % FCS followed by two washing steps using PBS only. Splenocytes were filtered two times in total through a strainer with 70 μm pore size to obtain a single cell solution for counting.  Splenocytes (1 x 10e7) were injected intravenously (i.v.) into NIT-1 cell-bearing NOD.scid mice to transfer autoimmune beta cell killing for 10 or 17 days. NIT-1 beta cell grafts were isolated and scaled on an analytical balance at indicated time points. Grafts were cut into small pieces and digested using HEPES buffered RMPI 1640 (cat # R4130-10L; Sigma-Aldrich) supplemented with 1mg/ml Collagenase D ( cat # 11088858001; Sigma-Aldrich), 20 μg/ml DNase I (cat # EN0521; Thermo Fisher Scientific), 2% FCS and 50 μg/ml Lipopolysaccharide neutralizing agent Polymyxin B sulfate (cat # 1405-20-5; Sigma-Aldrich) for 45 min at 37°C while shaking by maximum speed on a heating block. Digested grafts were further disaggregated and filtered through a strainer with 70 μm pore size two times to obtain a single cell solution. Cells were stained with anti-CD45 and PI in combination with one of four TotalSeq anti-mouse Hashtag antibodies (A0301, A0302, A0303 or A0304) (cat # 15580-1/3/5/7, clone M1/42 and 30-F11; Biolegend) to distinguish immune cells derived from individual NIT-1 beta cell grafts. Single cell RNA sequencing were then performed.

last: Bode

first: Peng

last: Yi

first: Stephan

last: Kissler


title: Transcriptome analysis of the jmj1 mutant

first: Wenhao

last: Xie

summary: To investigate the effects BdJMJ1 on gene transcription at a genome-wide level

overall_design: RNA-seq for Bd21-3 and jmj1-1 plants.

first: Richard

last: Amasino

first: Bing

last: Liu

first: Aiwu

last: Dong

first: Chengzhang

last: Li

first: Xiang

first: Jiachen

last: Wang


title: HeLa, Gene expression under normoxia (20%) vs hypoxia (<0.1% oxygen)

status: Public on Feb 05 2024

city: Kyoto

first: Peter

middle: Wai Tik

last: LEE

address: Sakyo Ward, Yoshidakonoecho

department: Graduate School of Biostudies

country: Japan

institute: Kyoto University

summary: Hypoxic cancer cells are known to acquire malignance like invasiveness and therapy resistance. In order to identify the candidate genes responsible for the malignant properties of hypoxic cancer cells, gene expression profile of hypoxic cancer cells is investigated herein.

overall_design: To characterise the genes that are related to malignance and simultaneously can be induced under hypoxia, total RNA samples from HeLa cells cultured under severely hypoxic conditions (<0.1% oxygen) and under normoxic conditions (20% oxygen) were subjected to RNA sequencing. Gene expression profiles of normoxic and hypoxic cells were compared in order to identify the relevant differentially expressed genes.

last: Lee

first: Christalle

last: Chow

first: Minoru

last: Kobayashi

first: Hiroshi

last: Harada


title: TsrA regulates gene expression of horizontally acquired elements in Vibrio cholerae via both H-NS dependent and independent mechanisms [RNA-Seq]

city: Ann Arbor

first: Yulduz

last: Rakibova

state: MI

address: 1150 W Medical center drive

department: Biological Chemistry

institute: University of Michigan

summary: Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in different environments. H-NS, the histone-like nucleoid structuring protein, is the best studied xenogeneic silencer of HAEs in gamma-proteobacteria. Although H-NS and other highly abundant nucleoid-associated proteins (NAPs) have been shown to play important roles in regulating HAEs and virulence in model bacteria, we still lack a comprehensive understanding of how different NAPs modulate transcription in V. cholerae. By obtaining genome-wide measurements of protein occupancy and active transcription in a clinical isolate of V. cholerae, harboring recently-discovered HAEs encoding for phage defense systems, we show that lack of H-NS causes a robust increase on the expression of genes found in many HAEs. We further found that TsrA, a protein with partial homology to H-NS, regulates virulence genes primarily through modulation of H-NS activity, but we also found a few sites that are affected by TsrA independently of H-NS. Our results demonstrate how the combinatorial activity of NAPs is employed by a clinical isolate of an important pathogen to regulate recently-discovered HAEs.

overall_design: IPOD-HR (in vivo protein occupancy display at high resolution (see method below or manuscript for details of the method), which consists of three sample types (IPOD, INPUT and RNA polymerase ChIP-seq) per sample) of V. cholerae strains: 4 replicates (reps.) of clinical isolate KDS1, and mutant strains: 2 reps. ∆hns::frt-spec-frt, 2 reps. ∆ihfA, 3 reps. ∆tsrA::frt-kan-frt, 3 reps. ∆tsrA::frt-kan-frt +∆hns::frt-spec-frt, and 2 reps. ∆vctA as a control. Additionally, IPOD-HR was performed on wild type KDS1 with Mitomycin C treatment in 3 replicates. RNA-sequencing was performed on wild type of KDS1 in 4 reps., 3 reps. of ∆ihfA, 4 reps. of ∆hns::frt-spec-frt, 4 reps. of ∆tsrA::frt-kan-frt, 4 reps. of ∆tsrA::frt-kan-frt +∆hns::frt-spec-frt.

first: Drew

middle: T

last: Dunham

first: Kim

last: Seed

first: P

last: Freddolino


title: Epidermal barrier impairment predisposes for excessive growth of the allergy-associated yeast Malassezia on murine skin

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: The skin barrier is vital for protection against environmental threats including insults caused by skin-resident microbes. Dysregulation of this barrier is a hallmark of atopic dermatitis (AD) and ichthyosis, with variable consequences for host immune control of colonizing commensals and opportunistic pathogens. While Malassezia is the most abundant commensal fungus of the skin, little is known about the host control of this fungus in inflammatory skin diseases. Here we show that in barrier-impaired skin, Malassezia acquires enhanced fitness and overt growth properties. By using four distinct and complementary murine models of atopic dermatitis and ichthyosis we provide evidence that structural and metabolic changes in the dysfunctional epidermal barrier environment provide increased accessibility and an altered lipid profile, to which the lipid-dependent yeast adapts for enhanced nutrient assimilation. These findings reveal fundamental insights into the implication of the mycobiota in the pathogenesis of common skin barrier disorders.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine ear skin that was pretreated with MC903 or EtOH (control) for 10 days and associated with Malasseia pachydermatis or olive oil (vehicle) for 4 or 7 days.

first: Fiorella

last: Ruchti

first: Salomé

last: LeibundGut-Landmann


title: Mouse mammary cells at single cell level from regeneration

status: Public on Feb 02 2024

city: xiamen

first: feng

last: deyi

state: xiamen

address: Xiamen University

institute: xiamen university

summary: By transplanting mammary cells into the mammary fat pad in vitro to regenerate the whole mammary gland, we can study the interaction between mammary epithelial cells at single cell level

overall_design: Control (Fgfr2+/+) and mutant (Fgfr2∆/∆) basasl cells mixed with luminal cells were transplanted into the cleared fat-pads of immune-deficient nude mice

first: Deyi

last: Feng

first: Rongze

last: Ma


title: Ursolic acid attenuates oligospermia in busulfan-induced mice by promoting motor proteins

status: Public on Feb 17 2024

city: nantong

first: Jin

last: Dong

address: No. 9 Qixiu Road, Chongchuan District

institute: nantong university

summary: This investigation scrutinizes the implications and mechanistic underpinnings of ursolic acid's effect on busulfan-induced oligospermia in mouse models. A single intraperitoneal injection at a dose of 30mg/kg of busulfan induced oligospermia, and two weeks later, the mice were treated with varied dosages of ursolic acid (10, 30, and 50 mg/kg w.t., respectively) daily for four consecutive weeks. Following this, a meticulous analysis of epididymal sperm parameters encompassing concentration and motility were undertaken using a computer-assisted sperm analysis system. The histopathology of the mice testes was performed utilizing hematoxylin and eosin staining, and the cytoskeleton regeneration of the testicular tissues was analyzed via immunofluorescent staining. Serum hormone levels (including testosterone, luteinizing hormone, and follicle-stimulating hormone) and reactive oxygen species levels (inclusive of reactive oxygen species and malondialdehyde) were gauged employing corresponding specific enzyme-linked immunosorbent assay kits. Differentially expressed genes of testicular mRNA between oligospermia and ursolic acid treatments were identified by RNA sequencing analysis. The results revealed that a dosage of 50 mg/kg ursolic acid treatment could increase the concentration of epididymal sperm in oligospermia mice, promote the recovery of testicular morphology, regulate hormone levels and ameliorate oxidative damage. The mechanism research results indicated that ursolic acid increased the expression level of genes related to motor proteins in oligospermia mice.

overall_design: Twenty five mice were randomly divided into five groups, each consisting of 5 individuals: normal group, BUS group, BUS + ULA low dose group, BUS + ULA medium dose group and BUS + ULA high dose group.


title: Effect of androgen on aldosterone and high salt induced aortic aneurysms in mice

city: Lexington

first: Xufang

last: Mu

state: KY

address: 900 S. Limestone St

institute: University of Kentucky

summary: Aortic aneurysm is a highly age- and sex-dependent cardiovascular disease in human, which men are at 4 to 6 times higher risk than women. We recently established an age-dependent animal model in which aldosterone and high salt administration induces aortic aneurysms in 10-month-old wildtype male mice. But whether it exhibits sex differences as in human remains unknown. The current study reports that androgen is a main driver for the sexual dimorphic response to aldosterone and high salt induced aortic aneurysms in mice. To explore the mechanism, aortas were isolated from three groups of mice as described below for transcriptomic profiling.

overall_design: To investigate the androgen effect, we isolated whole aortas from 10-month-old male C57BL/6 mice administered aldosterone and salt for seven days with following conditions: 1) sham-operated mice to serve as control; 2) orchiectomized mice to study androgen deprivation effects; and 3) orchiectomized mice given dihydrotestosterone pellet to restore androgen level

first: Shu

last: Liu

first: Tim

last: McClintock

first: Zhenheng

last: Guo


title: The longitudinal kinetics of AAV5 vector integration profiles and evaluation of clonal expansion in mice

status: Public on Feb 01 2024

city: San Rafael

first: Evan

last: Witt

state: California

address: 791 Lindaro Street

institute: Biomarin Pharmaceutical

summary: Recombinant adeno-associated virus (AAV)-based vectors are used clinically for gene transfer and persist as extrachromosomal episomes. A small fraction of vector genomes can integrate into the host genome, but the theoretical risk of tumorigenesis may depend on vector regulatory features. A mouse model was used to investigate long-term kinetics and integration profiles of an AAV serotype 5 (AAV5) vector that mimics key features of valoctocogene roxaparvovec (AAV5-hFVIII-SQ), a gene therapy for severe hemophilia A. The majority (95%) of vector genome reads identified by target enrichment sequencing were derived from episomes, and mean integration frequency was 2.70 (standard deviation, 1.24) integrations per 1000 cells. Longitudinal integration analysis suggested AAV5 vector integrations occur primarily within 1 week, at low frequency, and their abundance was stable over time. Integration profiles were polyclonal, and only 5.46% of integrations had a common integration site order ≥5, suggesting random distributions when looking at a 50-kb genomic window. No integrations were associated with clonal expansion. Integrations were enriched near transcription start sites of genes highly expressed in the liver (P = 1x10−4) and less enriched for genes with low or no liver expression. We found no evidence of tumorigenesis or fibrosis caused by the vector integrations.

overall_design: mice were treated with AAV5 vector produced with either HEK293 cells or sf9 cells and subjected to liver ATAC-seq to compare integration profiles with open chromatin

first: Ashrafali

last: Mohamed Ismail

first: Taren

last: Bouwman

first: Wyatt

last: Clark

first: Bridget

last: Yates

first: Matteo

last: Franco

first: Sylvia

last: Fong


title: Targeting cancer heterogeneity by breaking a stem cell and epithelial niche interaction loop

summary: BMP7 promotes luminal INHBA production to expand mammary stem cell pool

overall_design: We stimulated the HC11 cells using medium with or without BMP7 protein

first: Jing

last: Chen


title: Use-dependent synaptic plasticity associates with modulation of blood-brain-barrier permeability in the somatosensory cortex

status: Public on Jan 31 2024

city: Berkeley

first: Lynn

middle: T.

last: Yang

state: CA

address: 1951 Oxford Street, 430E

department: Integrative Biology, Helen Wills Neuroscience Institute

institute: UC Berkeley

summary: The effect of neuronal activity on blood-brain barrier function and whether it plays a role in plasticity in the healthy brain remains unclear. We show that neuronal activity induces modulation of microvascular permeability in the healthy brain and that it has a role in local network reorganization. Combining simultaneous electrophysiological recording and vascular imaging with transcriptomic analysis in rats, and functional and BBB-mapping MRI in human subjects we show that prolonged stimulation of the limb induces a focal increase in BBB permeability in the corresponding somatosensory cortex that is associated with long-term synaptic plasticity. We further show that the increased microvascular permeability depends on neuronal activity and involves caveolae-mediated transcytosis and transforming growth factor beta signaling. Our results reveal a role of BBB modulation in cortical plasticity in the healthy brain, highlighting the importance of neurovascular interactions for sensory experience and learning.

overall_design: Bulk RNA-sequencing of rat sensorimotor cortex contralateral and ipsilateral to the stimulated limb. Tissue was harvested 1 hour and 24 hour post-stimulation for transcriptomic analysis of differentially expressed genes in the contralateral (“stimulated”) compared to the ipsilateral (“non-stimulated”) cortex. Corresponding striatum samples were likewise dissected and sequenced for RNA-sequencing validation and reference control.

first: Evyatar

last: Swissa

first: Daniela

last: Kaufer

first: Alon

last: Friedman


title: TsrA regulates gene expression of horizontally acquired elements in Vibrio cholerae via both H-NS dependent and independent mechanisms

first: Yulduz

last: Rakibova

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

overall_design: Refer to individual Series


title: Single nuclei RNAseq datasets supporting the impact of primary cilia deficiency on astrocytes’ intercellular connectivity and neuronal transcriptomes in the brain.

status: Public on Jan 24 2024

city: Calgary

first: Jiami

address: 2500 University Dr NW

department: Cell Biology and Anatomy

institute: University of Calgary

summary: Astrocyte diversity is greatly influenced by local environmental modulation. In this study, we analyzed the impact of ciliary deficient astrocytes on astrocytes’ intercellular communications and neuronal transcriptomes in the brain. Our analysis revealed a broad disturbance of astrocyte intercellular connectomes and profound changes in neuronal transcriptomic profiles induced by ciliary deficiency in astrocytes.

overall_design: Nuclei were isolated from mouse (P52) cortices with cell fixation and nuclei fixation kit (Parse Biosciences) from both Arl13bcKO (Arl13blox/lox; Aldh1l1-CreERT2, tamoxifen: P7 to P9) and control (Arl13b+/+; Aldh1l1-CreERT2, tamoxifen: P7 to P9) mice. Cortices of two male mice were combined in each group. A total of 10,000 cells per group were used for library construction using the EvercodeTM Whole Transcriptome Mini kit (Parse Bioscience) as per the manufacturer’s protocol. Sequencing was performed using NovaSeq 200 cycle SP. Alignment was performed with the pipeline provided by Parse Biosciences and the resulting gene expression matrix was analyzed using different packages in R.

first: Lizheng

last: Wang

first: Sandesh

last: Acharya


title: Single cell multiomics guided mechanistic understanding of Fontan-associated liver disease

city: Philadelphia

first: Liming

last: Pei

state: Pennsylvania

address: 3501 Civic Center Blvd. CTRB 6018

department: Pathology and Laboratory Medicine

institute: Children's Hospital of Philadelphia/University of Pennsylvania

summary: Liver biopsy samples were from patients with Fontan circulation (FC) and healthy patients undergoing resection or transplant for hepatoblastoma.  We used snRNA-ATAC-seq to generate the transcriptomic and epigenomic atlas of human FALD.

overall_design: Single nuclei of each sample were isolated using a homogenizer followed by filtering, washing, counting and analyzed by snRNA-ATAC-seq.

first: Po

last: Hu


title: Single-cell RNAseq datasets supporting the role of primary cilia to drive region-specific diversification of astrocytes within the developing brain

last: Guo

summary: Astrocyte diversity is greatly influenced by local environmental modulation. In this study, we analyzed how primary ciliary signaling modulates astrocyte subtype-specific maturation and accessed the impact of ciliary deficient astrocytes on neuronal programs and behaviours. Comparative single-cell transcriptomics revealed that primary cilia mediate canonical Shh signaling to modulate astrocyte subtype-specific core features in synaptic regulation, intracellular transport, energy and metabolism. Our results uncover a critical role for primary cilia in transmitting local cues that drive the region-specific diversification of astrocytes within the developing brain.

overall_design: Aldh1l1-CreERT2 (Control), Arl13blox/lox; Aldh1l1-CreERT2 (Arl13bcKO), Ift88lox/lox; Aldh1l1-CreERT2 (Ift88cKO), Smolox/lox; Aldh1l1-CreERT2 (SmocKO), and SmoM2lox/+; Arl13blox/lox; Aldh1l1-CreERT2 (SmoM2-Arl13bcKO) mice were administrated with tamoxifen from P7 to P9. Single cell suspension of Cortices and the cerebellum were obtained from two male mice of each genotype using papain-based protocol. Astrocytes were then labelled using ASCA2-PE antibody and live ASCA2+ cells were sorted using flow cytometry. A total of 15, 000 single cells of each sample were loaded for partitioning using 10x Genomics NextGEM Gel Bead emulsions (3’ gene expression kit, version 3.1) and processed according to the manufacturer’s protocol. Illumina Sequencing was performed on NovaSeq SP and Illumina NovaSeq S2 at the Centre for Health Informatics (CHGI) at University of Calgary. Alignment to the mouse reference genome was performed using the CellRanger 3.1.0 pipeline and the resulting gene-barcode matrix was further analyzed using different packages in R.

first: Nicole

last: Rosin

first: Elodie

last: Labit


title: RNA-seq of Hacat cells treated with TOPK inhibitor

status: Public on Jan 18 2024

city: wuhan

first: Zeng

last: Fanfan

address: No. 13, Hanghang Road, Qiaokou District, Wuhan

institute: Huazhong University of Science and Technology

summary: Hacat cells were treated with TOPK inhibitor to elucidate the effect of TOPK signaling on Hacat cells

overall_design: Hacat cells  were cultured in M5 cocktail, then treated with or without TOPK inhibitor for 24 h. Total RNA were then extracted and subjected to RNA-seq analysis

first: Fanfan

last: Zeng

first: Mengjun

last: Wu


title: TsrA regulates gene expression of horizontally acquired elements in Vibrio cholerae via both H-NS dependent and independent mechanisms [IPOD-HR]

first: Drew

last: Dunham

first: Kim

last: Seed

first: P

last: Freddolino


title: Single T-cell receptor profiling identifies distinct patterns of T-cell infiltration in nodal B-cell lymphoma entities

status: Public on Jan 28 2024

city: Düsseldorf

first: Sascha

last: Dietrich

address: Moorenstr. 5

department: Hematology

institute: University Hospital Düsseldorf

summary: The redirection of T-cells has emerged as an attractive therapeutic principle in B-cell non-Hodgkin lymphoma (B-NHL). However, a detailed characterization of lymphoma-infiltrating T-cells across B-NHL entities is missing. Here, we present single-cell transcriptome and T-cell receptor sequencing of lymph-node derived T-cells from patients with diffuse large B-cell, mantle cell, follicular, or marginal zone lymphoma, and from healthy controls. These data revealed quantitative aberrations of the T-cell microenvironment across and within B-NHL entities.

overall_design:
Lymph node-derived cells were isolated from patients with nodal B-cell lymphoma entities. Lymphocytes were forwarded to single-cell 5' RNA and T-cell receptor sequencing.

[UPDATE] 05-09-2024: The raw data and processed data were removed from this dataset due to patient privacy concerns.

All single-cell sequencing data have been deposited at the European Genome-phenome Archive (EGA) under accession number EGAS50000000342: https://ega-archive.org/studies/EGAS50000000342

first: Tobias

last: Roider

first: Donnacha

last: Fitzgerald

first: Harald

last: Vöhringer

first: Mareike

last: Knoll

first: Bianca

last: Faßbender

first: Maxime

last: Herbon

first: Marc

last: Seifert

first: Wolfgang

last: Huber


title: The Diversified Astrocyte Developmental Programs are Modulated by Primary Ciliary Signaling

first: Jiami

last: Guo

overall_design: Astrocyte diversity is greatly influenced by local environmental modulation. In this study, we analyzed how primary ciliary signaling modulates astrocyte subtype-specific maturation and accessed the impact of ciliary deficient astrocytes on neuronal programs and behaviours. Comparative single-cell transcriptomics revealed that primary cilia mediate canonical Shh signaling to modulate astrocyte subtype-specific core features in synaptic regulation, intracellular transport, energy, and metabolism. Independent of canonical Shh signaling, primary cilia are important regulators for astrocyte morphology and intracellular signaling balance. Dendritic spine analysis and transcriptomics revealed that perturbation of astrocytic cilia leads to disruption of neuronal development and global intercellular connectomes in the brain. Our results uncover a critical role for primary cilia in transmitting local cues that drive the region-specific diversification of astrocytes within the developing brain


title: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation

status: Public on Jan 10 2024

city: Brookline

first: Ramesh

middle: A

last: Shivdasani

state: Massachusetts

address: SM1052, Smith10, 450 Brookline Ave

department: Medical Oncology

institute: DFCI

summary: Enteroendocrine cells (EECs) secrete serotonin (enterochromaffin [EC] cells) or specific peptide hormones (non-EC cells) that serve vital metabolic functions. The basis for terminal EEC diversity remains obscure. By forcing activity of the transcription factor (TF) NEUROG3 in 2D cultures of human intestinal stem cells, we replicated physiologic EEC differentiation and examined transcriptional and cis-regulatory dynamics that culminate in discrete cell types. Abundant EEC precursors expressed stage-specific genes and TFs. Before expressing pre-terminal NEUROD1, post-mitotic precursors oscillated between transcriptionally distinct ASCL1+ and HES6hi cell states. Loss of either factor accelerated EEC differentiation substantially and disrupted EEC individuality; ASCL1 or NEUROD1 deficiency had opposing consequences on EC and non-EC cell features. These TFs mainly bind cis-elements that are accessible in undifferentiated stem cells, and they tailor subsequent expression of TF combinations that underlie discrete EEC identities. Thus, early TF oscillations retard EEC maturation to enable accurate diversity within a medically important cell lineage.

overall_design: Enteroendocrine differentiation was induced by transient (48h) NEUROG3 activation in 2D human ISCs. This triggered full and efficient EEC differentiation over a period of 6-8 days during which we examined step-wise dynamic profile of enhancers and genes at bulk and single-cell resolution. We identify the binding pattern of crucial intermediate factors ASCL1 and NEUROD1 using CUT&RUN and CRISPR-edited specific transcription factors to determine their role in differentiation program.

first: Pratik

last: Singh


title: The role of chorionic PGRMC2 and HLA-G in maintaining immune homeostasis at the chorio-decidual interface

status: Public on Jan 02 2024

city: Manila

first: Ryan

last: Lintao

address: 547 Pedro Gil Street

department: College of Medicine

country: Philippines

institute: University of the Philippines Manila

summary: The chorio-decidual interface (CDi) is formed by chorion trophoblasts (CTCs) and immune cell-rich decidua (DECs) cells. The roles of human leukocyte antigen (HLA)-G and progesterone receptor membrane component 2 (PGRMC2) in mediating innate immune homeostasis at this maternal-fetal interface interface were investigated.

overall_design: The CDi was recreated in a microfluidic device (CDi-on-chip) with an outer chamber of DECs and innate immune cells (70:30 ratio) and an inner chamber of wild-type (WT) or KO CTCs interconnected by microchannels. After device preparation and cell seeding, DECs were treated with LPS and pIC, respectively, for 48 hours. To mimic fetal (fOS) and maternal oxidative stress (mOS), CTCs and DECs were treated with CSE, respectively. Expression levels of inflammation and immunity genes were determined via targeted RNA sequencing.

first: Kamil

last: Khanipov

first: George

last: Golovko

first: Ramkumar

last: Menon


title: NFKBIE-mutated CLL cells reshape the immune microenvironment and display selective resistance to BTK inhibitor treatment

status: Public on Jan 29 2024

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

summary: Inactivating mutations in the NF-kB inhibitor NFKBIE are frequent in chronic lymphocytic leukemia (CLL) and have been associated with accelerated disease progression and inferior responses to chemotherapy. To further understand the role of NFKBIE mutations in CLL, we disrupted by CRISPR/Cas9 editing the NFKBIE gene in CLL cells derived from the Eμ-TCL1 transgenic mouse model and investigated how this will affect CLL growth and response to B cell receptor inhibitor treatment. In vitro and adoptive transfer experiments showed that NFKBIE-mutated cells have a growth advantage over NFKBIE-wild type cells when exposed to microenvironmental signals that activate the canonical NF-kB pathway and can induce alterations within the tumor microenvironment that may allow for escape from immune surveillance, including the expansion of CD8+ T cells with an exhausted phenotype and increased expression of PD-L1 on the malignant B cells. Consistent with these findings, significantly greater expression of the exhaustion markers PD1 and TIGIT was observed on T cells from CLL patients with NFKBIE-mutated compared to NFKBIE-wild type leukemia. In addition, in vitro and in vivo experiments showed that NFKBIE-mutated murine CLL cells are selectively resistant to BTK inhibitor treatment while remaining sensitive to treatment with a PI3K or SYK inhibitor. Reduced sensitivity to BTK inhibitor treatment was also observed in a series of 229 ibrutinib-treated CLL patients showing inferior outcomes for the NFKBIE-mutated cases. These findings provide evidence that NFKBIE-mutated CLL cells reshape and are selected by the tumor microenvironment and may account for suboptimal ibrutinib responses.

overall_design: In the study presented here, the RNA-seq profile was analyzed in NFKBIE-wild type and NFKBIE-mutated TCL1-355 TKO cells. These were first separately propagated for 21 days in two C57BL/6 mice and then transplanted via intraperitoneal injection in two groups of C57/BL6 recipient mice (5 mice per group). The leukemic cells were recovered after 10 days from the spleen and peritoneal cavitiy of the transplanted mice and 4 samples from each group were analyzed by RNA sequencing. We also analyzed NFKBIE-mutated and NFKBIE-wild type TCL1-355 TKO cells that were isolated from spleens of three different mice and separately cultured for two weeks prior to RNA isolation.

first: Alice

last: Bonato

first: Supriya

last: Chakraborty

first: Dimitar

last: Efremov

first: Giulia

last: Canarutto


title: Tumor cell-intrinsic ATP6V0A1 drives immunosuppressive reprogramming in colorectal cancer

status: Public on Jan 01 2024

city: Shenzhen

first: Tuxiong

last: Huang

address: 1066 Xueyuan Avenue

institute: Shenzhen University

summary: The roles of V-ATPase subunits in regulating CRC immune evasion remain unclear. By analyzing the Tumor and Immune System Interaction Database (TISIDB) for correlations between V-ATPases subunits and immune activities, we found that subunit ATP6V0A1 was inversely correlated with immune activities, especially with the proportions of effective or memory T cells in colon adenocarcinoma (COAD), suggesting an immunosuppressive role. With Atp6v0a1/ATP6V0A1 knockdown CRC cells and CRC syngeneic and xenograft mouse models, we confirmed that tumor cell-intrinsic ATP6V0A1 promotes the growth of CRC in an immune-dependent manner. To determine the type of immune cells contributing to ATP6V0A1-mediated immune evasion, we used single-cell transcriptome sequencing (sc-RNA seq) to analyze the ATP6V0A1-edited immune microenvironment in murine MC38 tumors. Holistic immune profiles in Atp6v0a1 knockdown and control MC38 tumors were compared. The results showed that Atp6v0a1 interference in MC38 cells increased the percentages of naïve T, effector T, and memory-like T-2 cells in the total T cell population while decreasing the percentages of exhausted T, Treg, and memory-like T-1 cells. Moreover, the percentages of granulocytes, monocytes, and dendritic cells within the myeloid population were increased in Atp6v0a1 knockdown-derived tumors, whereas the percentage of macrophages was decreased. Of all the immune cell subclusters, memory-like T-2 cells exhibited the most significantly increased cell count ratio in shv0a1 tumors vs. control tumors. In addition, memory-like T-2 cells expressed more effector markers than memory-like T-1 cells. These data suggest that MC38-derived ATP6V0A1 induced immunosuppressive tumor microenvironment (TME) and suppression of the effectiveness of memory-like T cells may play important roles in ATP6V0A1-regulated CRC immune evasion. The study provides directions to investigate the roles and mechanisms of ATP6V0A1 regulating anti-tumor immunity and thus shed light on the potential for ATP6V0A1-targeted immunotherapy in CRC.

overall_design: To investigate the suppressive reprogramming in TME induced by ATP6V0A1, we established CRC syngeneic mouse models with MC38 shNTC cells and MC38 shv0a1 cells separately. Five tumor tissue samples from each group were mixed in equal proportions and used for single-cell sequencing.

first: Huisi

first: Shaowei

last: Dong

first: Qiaoyun

last: Long


title: Multimodal single-cell profiling identifies distinct patterns of T-cell infiltration in nodal B-cell lymphoma entities

first: Sascha

last: Dietrich

summary: The redirection of T-cells has emerged as an attractive therapeutic principle in B-cell non-Hodgkin lymphoma (B-NHL). However, a detailed characterization of lymphoma-infiltrating T-cells across B-NHL entities is missing. Here, we present cellular indexing of transcriptomes and epitopes of lymph-node derived T-cells from patients with diffuse large B-cell, mantle cell, follicular, or marginal zone lymphoma, and from healthy controls. These data revealed quantitative aberrations of the T-cell microenvironment across and within B-NHL entities.

overall_design:
Lymph node-derived cells were isolated from patients with nodal B-cell lymphoma entities. Lymphocytes were forwarded to cellular indexing of transcriptomes and epitopes (CITEseq). An panel of 70 different antibodies was used.

[UPDATE] 05-09-2024: The raw data and processed data were removed from this dataset due to patient privacy concerns.

All single-cell sequencing data have been deposited at the European Genome-phenome Archive (EGA) under accession number EGAS50000000342: https://ega-archive.org/studies/EGAS50000000342

first: Tobias

last: Roider

first: Donnacha

last: Fitzgerald

first: Harald

last: Vöhringer

first: Mareike

last: Knoll

first: Wolfgang


title: Effect of G6PD loss on gene expression in LKB1 deficient KRAS-driven lung tumor

status: Public on Jan 23 2024

city: New Brunswick

first: Jessie

middle: Yanxiang

last: Guo

state: NJ

address: 195 Little Albany Street, Room 3039, Lab 3029

department: Rutgers Cancer Institute of New Jersey

institute: Rutgers, The State University of New Jersey

summary: Cancer cells heavily rely on nicotinamide adenine dinucleotide phosphate (NADPH) to counteract oxidative stress and facilitate reductive biosynthesis. One crucial route for NADPH production operates through the oxidative pentose phosphate pathway, with a pivotal step at glucose-6-phosphate dehydrogenase (G6PD). This study delves into the repercussions of G6PD ablation on the development of lung tumors driven by the KRAS oncogene and deficient in LKB1 (KL). The research involved comparing the growth of KL lung tumors with or without G6PD, revealing a significant inhibition of KL lung tumor growth upon G6PD loss. Subsequently, RNA-seq analysis was employed to identify the alterations in gene expression following G6PD deletion, providing insights into the underlying mechanisms.

overall_design: To tumor-specificly knock out G6PD in KL lung tumor, we crossed KrasG12D;Lkb1flox/flox mice with G6pdflox/flox mice to generate G6pdflox/flox;KrasLSL-G12D/+;Lkb1flox/flox mice and G6pdWT;KrasLSL-G12D/+;Lkb1flox/flox mice. Following this, Lenti-cre infection was utilized to induce tumor formation and simultaneously delete Lkb1/G6pd. After 12 weeks of tumor induciton, lung tumors were dissected from the mice, RNA-Seq then was employed  to analyze the gene expression in KL lung tumors, comparing those with and without G6PD.

middle: Y


title: MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer

city: New York

first: Theodoros

last: Sakellaropoulos

address: 550 1st Avenue

institute: NYU Langone


title: MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer [Perturb-seq]

summary: We present MethNet, a pipeline that integrates large-scale DNA methylation and gene expression data across multiple cancers, to uncover novel cis regulatory elements (CREs) in a 1Mb region around every promoter in the genome. MethNet identifies highly ranked CREs, referred to as ‘hubs’, which contribute to the regulation of multiple genes and strongly affect patient survival. Promoter-capture Hi-C confirmed that highly ranked associations involve physical interactions between CREs and their gene targets, and CRISPRi based scRNA Perturb-seq validated the functional impact of CREs. Thus, MethNet represents a valuable resource for unraveling complex mechanisms underlying gene expression, and for prioritizing the verification of predicted non-coding disease hotspots.

overall_design: CloneTracker XP CRISPR Barcode pooled lentiviral libraries expressing barcoded sgRNAs, the puromycin selection gene as well as an RFP reporter were purchased from Cellecta®. The A549 cells were transduced with lentiviruses expressing dCas9-KRAB-MECP2 plasmids as described in Yeo et al. Cells were then grown in DMEM medium (Gibco/Invitrogen) + 10% FBS + 100 units/ml penicillin + 100 μg/ml streptomycin + 5% CO2 at 37℃. The 248 sgRNAs targeting high-confidence MethNet hubs and 5 non-targeting sgRNAs (negative controls) were designed using CRISPick for the Human GRCh37 (hg19) assembly using parameter settings: CRISPRi, SpyoCas9/Chen (2013) tracrRNA (Suppl. Table 1). The lentiviral libraries were transduced into the A549-dCAS9-KRAB-MeCP2 cells according to Cellecta® protocols. Briefly, 105 cells/well were seeded into a 6 well-plate. The optimal MOI of viral particles (to reach ~30-40% of infected cells) were added. On day 3, 2 ug/ml of puromycin was added, resulting in >90% transduced cell selection as confirmed by cytofluorometry using RFP (Figure S7). Cells were expanded under puromycin selection until day 14. For scRNA-seq using the 10X Genomics technology, 25,000 cells were harvested. For optimal multiplet detection and optimal signal-to-noise ratios, cells were hashtagged using 5 cell multiplexing oligos purchased from 10X Genomics. The sequencing library was, then, prepared using the Chromium Next GEM Single Cell 3ʹ Kit according to the manufacturer’s protocol and sequenced by NYU Langone's Genome Technology Center.

first: Theodore

first: Guimei

last: Jiang

first: Peter

last: Meyn

first: Adrianna

last: Heguy

first: Aristotelis

last: Tsirigos

first: Catherine

last: Do

first: Jane

last: Skok


title: A Blood-based Multi-omic Landscape for the molecular characterization of Kidney Stone Disease

first: Yuhao

last: An

state: Guangdong Province

address: 16 Lanjing Road, Kengzi Street, Pingshan District

institute: Shenzhen Bay Lab

summary: Kidney stone disease (KSD, also named renal calculi, nephrolithiasis, or urolithiasis) is a common urological disease entailing the formation of minerals and salts that form inside the urinary tract, frequently caused by diabetes and high blood pressure, hypertension, and monogenetic components in most patients. 10% of adults worldwide are affected by KSD, which incidence continues to be highly prevalent and increasing. For the identification of novel therapeutic targets in KSD to deal with this situation, we adopted high-throughput sequencing and mass spectrometry (MS) techniques in this study and carried out an integrative analysis of exosome proteome and DNA methylation data from blood samples of normal and KSD patients. Our study described the profiling of serum exosome and DNA methylation in blood from both normal individuals and those with Kidney Stone Disease (KSD), finding the overexpressed proteins and the demethylated DNA genes in KSD samples are related to immune reactions. The consistency of the results in proteomics and epigenetics supports the feasibility of the comprehensive strategy. Our understanding of the molecular landscape of KSD provides an opportunity for more information on the pathogenic mechanism, precise diagnosis, and treatment for KSD.

overall_design: we collected 5 normal and 9 KSD blood samples for both of LC-MS/MS data and DNA methylation data generation. Based on SEPs matrix, we performed differential expression analysis and biological terms enrichment.


title: MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer [pcHiC]

overall_design: Promoter Capture Hi-C data was generated in K562 and A549 cell lines using the Arima Hi-C+ kit, the Arima Promoter Capture Module, and the Arima Library Prep Module according to the Arima Genomics manufacturer’s protocols. The A549 and K562 cell lines were purchased from ATCC. Two replicates of the Hi-C were performed in each cell line, and for each replicate 1 million cells were collected and double cross-linked using 3mM DSG (disuccinimidyl glutarate), followed by 1% formaldehyde. Samples were sequenced with Illumina Novaseq 6000 technology according to standard protocols with around 300 million (150bp paired-ends) reads per sample. The library preparation and sequencing were conducted by NYU Langone's Genome Technology Center.

first: Giulia

last: Cova

first: Dacia

last: Dimartino

first: Sitharam

last: Ramaswami


title: Investigating iRhom2-associated transcriptional changes in Tylosis with Esophageal Cancer

city: London

first: Keat-Eng

last: Ng

state: England

address: William Harvey Heart Centre

country: United Kingdom

institute: Queen Mary University of London

summary:
BACKGROUND AND AIMS: Survival rates for esophageal squamous cell carcinoma (ESCC) are extremely low due to the late diagnosis of most cases. An understanding of the early molecular processes that lead to ESCC may facilitate opportunities for early diagnosis; however, these remain poorly defined. Tylosis with esophageal cancer (TOC) is a rare syndrome associated with a high lifetime risk of ESCC and germline mutations in RHBDF2, encoding iRhom2. Using TOC as a model of ESCC predisposition, this study aimed to identify early-stage transcriptional changes in ESCC development.

METHODS: Esophageal biopsies were obtained from control and TOC individuals, the latter undergoing surveillance endoscopy, and adjacent diagnostic biopsies were graded as having no dysplasia or malignancy. Bulk RNA-Seq was performed, and findings were compared with sporadic ESCC vs normal RNASeq datasets.

RESULTS: Multiple transcriptional changes were identified in TOC samples, relative to controls, and many were detected in ESCC. Accordingly, pathway analyses predicted an enrichment of cancer-associated processes linked to cellular proliferation and metastasis, and several transcription factors were predicted to be associated with TOC and ESCC, including negative enrichment of GRHL2. Subsequently, a filtering strategy revealed 22 genes that were significantly dysregulated in both TOC and ESCC. Moreover, Keratin 17, which was upregulated in TOC and ESCC, was also found to be overexpressed at the protein level in ‘normal’ TOC esophagus tissue.

CONCLUSION: Transcriptional changes occur in TOC esophagus prior to the onset of dysplasia, many of which are associated with ESCC. These findings support the utility of TOC to help reveal the early molecular processes that lead to sporadic ESCC.

overall_design: 10 TOC and 6 normal (control / wildtype) esophageal biopsies were processed for bulk RNA-Seq in this study

first: Stephen

last: Murtough

first: David

last: Kelsell


title: Effect of neutrophil extracellular vesicles treatment on the K/BxN mouse model of arthritis

first: Trinidad

last: Montero

address: Charterhouse Square

department: Biochemical Pharmacology

institute: Whilliam Harvey Research Institute, Bart's and The London School of Medicine; Queen Mary University of London

summary: Arthritis was induced in C57BL/6 mice by injection of arthritogenic serum. This study aims to evaluate the transcriptomic profile of the K/BxN model of arthritis in knee joints, as well as he anti-inflammatory/tissue pro-repair effect of the intra-articular administration of neutrophil extracellular vesicles (EVs).

overall_design: Four study groups were included: Disease (arthritic, n=4); Naive (healthy, n=4); Treated (arthritic, treated with EVs, n=8); Control (arthritic, treated with vehicle, n=8). Arthritis was induced with two injections of K/BxN arthritigenic serum on days 0 and 2. Treatments were applied on day 3. Mice were sacrificed on day 10.

first: Bethan

last: Thomas

last: Montero-Melendez

first: Mauro

last: Perretti

first: Lucy

middle: V

last: Norling


title: ATM and 53BP1 regulate alternative end joining-mediated V(D)J recombination

status: Public on Dec 31 2023

city: Stanford

first: Jinglong

last: Wang

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford Medicine

summary: The critical role of the alternative end joining (AEJ) repair mechanism in V(D)J recombination for B and T lymphocyte development, particularly in the absence of the key non-homologous end joining (NHEJ) component Ku70, is not well understood. AEJ involves functionally redundant factors such as Parp1 vs Polθ and Lig3 vs Lig1, making it unclear which factors are responsible for repairing V(D)J recombination. Additionally, the regulatory mechanism of AEJ remains enigmatic. In this study, we utilized the murine Igκ antigen locus as a model and employed gene editing and HTGTS-Seq pipelines to systematically evaluate potential factors involved in V(D)J recombination. We assessed various aspects of recombination, including efficiency, V gene usage, end resection, joining fidelity, repair patterns, and inter-chromosome translocation. Our findings highlight the Parp1-XRCC1-Lig3 axis as a key mediator of V(D)J recombination, regulated by 53BP1 and ATM. This study advances our understanding of AEJ in DNA damage repair and contributes to our knowledge of lymphocyte development in immunology.

overall_design: Various murine proB cells including WT, Ku70-/-, Ku70-/- 53BP1-/-, Ku70-/- XRCC1-/-, Ku70-/- Parp1-/-, Ku70-/- ATM-/-, Ku70-/- Exo1-/-, etc, with/without indicated inhibitors  were arrested by STI-571 to induce V(D)J recombination, the V-J recombination in IgK locus were systematically captured using JK1CE and JK1SE by HTGTS.

first: Cheyenne

last: Sadeghi

first: Richard

last: Frock


title: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation [scRNA-seq]

status: Public on Jan 11 2024

first: Ramesh

last: Shivdasani

summary:
To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines.
We then performed gene expression profiling analysis at single cell level using data obtained from single cell RNA-seq of at various  time points.

first: Pratik

middle: N

last: Singh


title: Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation [Multiome-seq]

summary:
To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines.
We then performed simultaneous gene expression profiling and chromatin analysis at single cell level using data obtained from Multiome-seq at various  time points.

overall_design:
Multiome-seq at various  time points
Please note that processed data generated from both RNA and ATAC is linked to the corresponding  *Multiome-seq, RNA sample records.
barhash.csv.gz
filteredinbarcodes.csv.gz


title: CLIP-seq analysis of hnRNPA1-RNA interactions

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: MO

address: 660 S. Euclid Avenue, Campus Box 8230

institute: Washington University School of Medicine

summary: hnRNPA1 CLIP-seq experiments were conducted on HEK293T cells transiently expressing WT hnRNPA1 and hnRNPA1-DSB mutant

overall_design: hnRNPA1 CLIP-seq experiments were conducted by immunoprecipitation of hnRNPA1-RNA complexes (using an anti-myc antibody against the tag) from HEK293T cells transiently expressing WT hnRNPA1 and a DSB mutant bearing R75D/R88D mutations. Libraries of RNA molecules bound by hnRNPA1 were generated and sequenced by Illumina Next-Seq500 platform.

middle: B


title: Retinoic acid enhances HIV-1 reverse transcription and transcription in macrophages via mTOR-modulated mechanisms

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

institute: Université de Montréal

summary: The intestinal environment facilitates HIV-1 infection via mechanisms involving the gut-homing vitamin A-derived retinoic acid (RA), which transcriptionally reprograms CD4+ T cells for increased HIV-1 replication/outgrowth. Consistently, colon-infiltrating CD4+ T cells carry replication-competent viral reservoirs in people with HIV-1 (PWH) receiving antiretroviral therapy (ART). Intriguingly, integrative infection in colon macrophages, a pool replenished by monocytes, represents a rare event in ART-treated PWH, thus questioning the effect of RA on macrophages. Here, we demonstrate that RA enhances R5 but not X4 HIV-1 replication in monocyte-derived macrophages (MDMs). RNA sequencing, gene set variation analysis, and HIV interactor NCBI database interrogation reveal RA-mediated transcriptional reprogramming associated with metabolic/inflammatory processes and HIV-1 resistance/dependency factors. Functional validations uncover post-entry mechanisms of RA action including SAMHD1-modulated reverse transcription and CDK9/RNA polymerase II (RNAPII)-dependent transcription under the control of mammalian target of rapamycin (mTOR). These results support a model in which macrophages residing in the intestine of ART-untreated PWH contribute to viral replication/dissemination in an mTOR-sensitive manner.

overall_design: Monocyte-derived macrophages (MDMs) from 6 HIV-uninfected donors; 2 conditions: M-CSF . M-CSF + ATRA

first: Jonathan

last: Dias

first: Amélie

last: Cattin

first: Laurence

middle: R

last: Marchand

first: Augustine

last: Fert

first: Tomas

last: Wiche Salinas

first: Christ-Dominque

last: Ngassaki Yoka

first: Etiene

last: Moreira Gabriel

first: Jean-Pierre

last: Routy

first: Petronela

last: Ancuta


title: Regulated the AEJ -mediated V(D)J recombination by 53BP1 and ATM

state: CA California

address: 1291 Welch Rd, CCSR Room 1240

institute: Stanford University


title: A pumpless liver-on-a-chip for drug hepatotoxicity analysis

city: Beijing

first: Dian

last: Jiao

state: Beijing

address: Tsinghua University Beijing China

institute: Tsinghua University

summary: This study presents the development and validation of an innovative microfluidic liver-on-a-chip device utilizing gravity-driven perfusion for the evaluation of drug hepatotoxicity. This research involved the construction of a hydrogel-based coculture chip that integrates liver parenchymal and stellate cells within a tri-channel configuration. The assembly and operation of the liver-on-a-chip and its accompanying custom rocker were straightforward. The chip maintained high cell viability and continuous liver albumin synthesis over extended culture durations. Acetaminophen, a hepatic injury-inducing drug, was utilized as a positive control in hepatic toxicity assays on the chip. The liver chip exhibited hepatotoxic responses comparable to those observed in 2D models. Furthermore, in this study we evaluated the effects of two plant-derived natural compounds, aristolochic acid I (AA) and its ana-log aristolactam AII (AL), in both 2D cell models and the liver-on-a-chip system. Aristolochic acid I, known for its hepatorenal toxicity, was observed to cause hepatotoxicity in both the 2D models and on the chip. Flow cytometry and mRNA sequencing results confirmed the propensity of these compounds to induce liver cell apoptosis. Notably, aristolactam AII, previously consid-ered nontoxic, provoked a significant decrease in the hepatic functionality marker albumin exclusively in the liver chip but not in 2D models, indicating the liver chip's enhanced sensitivity to toxic substances. In summary, this pumpless liver-on-a-chip offers a simple yet powerful tool for drug hepatotoxicity studies.

overall_design: In order to evaluate the hepatotoxicity of two natural compounds aristolochic acid I (AA) and aristolactam AII (AL), these compounds at the concentration of 30 μM were used to treat two liver cell lines HepG2 and LX2. Each cell line has three groups: AA, AL and DMSO control group and each group has three replicates. mRNAs were sequenced after 48 hours of  compounds exposure.

first: Lan

last: Xie

first: Wanli

last: Xing


title: transcriptome-wide map of NCSTN-KD and NC Hacat cells

city: Nanjing

first: Yuanyuan

last: Zhang

state: Jiangsu

address: 12 Jiang Wang Miao Street

institute: Hospital for Skin Diseases (Institute of Dermatology), Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Acne inversa (AI) is an inflammatory skin disease associated with the nicastrin (NCSTN) mutations. Family history with autosomal dominant inheritance has heen reported in AI patients and are associated with mutations in the γ-secretase subunit, nicastrin (NCSTN), presenilin enhancer 2 (PSENEN), and presenilin-1 (PSEN1). Among them, NCSTN gene has the highest mutation rate. To detect the impact of NCSTN deficiency on AI keratinocytes. Here, using the short hairpin RNA (shRNA)-mediated gene knockdown and RNA sequencing technology, we explored the differentially expressed genes regulated by NCSTN deficiency  in HaCaT cells.

overall_design: Examination of gene expression alternation in Hacat NC and NCSTN-KD cells

first: Li

last: Chengrang

first: Zhang

last: Yuanyuan

first: Mao

last: Qiuxia

last: Wanlu


title: Temporal changes in mice hippocampus transcriptome after pilocarpine-induced seizure

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

type: Non-coding RNA profiling by high throughput sequencing

summary: We  mapped out temporal changes in mice hippocampus transcriptome as mRNA-seq and microRNA-seq after pilocarpine-induced SE to understand better molecular and cellular pathways that lead to neurodegenerative and neuroprotective processes after SE.

overall_design:
Hippocampal  mRNA-seq of  C57Bl/6J mice, control and  treated with pilocarpine, RNA collected at time points: 1 hour, 8 hours, 36 hours and 120 hours after start of seizure. 8 controls and 11 experimental.
Hippocampal  microRNA-seq of  C57Bl/6J mice, control and treated with pilocarpine, RNA collecte at time points: 1 hour, 8 hours, 24 hours and 120 hours after start of seizure. 8 controls and 8 experimental.

first: Evgenya

last: Popova

first: Ming

last: Leung

first: Colin

last: Barnstable


title: Pharmacogenomic eQTL mediated by androgen receptor modulators

city: Rochester

first: Liewei

last: Wang

state: MN

address: 200 2st Str SW

department: Neurology

institute: Mayo Clinic

summary: Endocrine therapy is the most important treatment modality of breast cancer patients whose tumors express the estrogen receptor  (ER).  The androgen receptor (AR) is also expressed in the vast majority (80-90%) of ER-positive tumors. However, AR-targeting drugs are not used in clinical practice, but have been evaluated in multiple trials and preclinical studies. We performed a genome-wide study to identify genetic context-dependent AR signaling induced by either AR agonist (dihydrotestosterone [DHT]), or AR antagonist (enzalutamide [Enz]), known as pharmacogenomic expression quantitative expression loci (PGx-eQTLs), utilizing a previously well characterized lymphoblastic cell line panel.

overall_design: 30 LCL panel were treated with DHT, enzalutamide, their combination, or Veh, and subjected to RNAseq

first: Huanyao

last: Gao

first: Lixuan

last: Wei


title: Development of an Epigenetic Clock Resistant to Changes in Immune Composition

status: Public on Dec 27 2023

city: Novato

first: Alan

last: Tomusiak

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: Epigenetic clocks are age predictors that use machine-learning models trained on DNA CpG methylation values to predict chronological or biological age. Increases in predicted epigenetic age relative to chronological age (epigenetic age acceleration) are connected to aging-associated pathologies, and changes in epigenetic age are linked to canonical aging hallmarks. However, epigenetic clocks rely on training data from bulk tissues whose cellular composition changes with age. We found that human naive CD8+ T cells, which decrease during aging, exhibit an epigenetic age 15–20 years younger than effector memory CD8+ T cells from the same individual. Importantly, homogenous naive T cells isolated from individuals of different ages show a progressive increase in epigenetic age, indicating that current epigenetic clocks measure two independent variables, aging and immune cell composition. To isolate the age-associated cell intrinsic changes, we created a new clock, the IntrinClock, that did not change among 10 immune cell types tested. IntrinClock showed a robust predicted epigenetic age increase in a model of replicative senescence in vitro and age reversal during OSKM-mediated reprogramming

overall_design: Bisulphite converted DNA from the 130 samples were hybridised to the Illumina MethylationEPIC chip. 11 different immune cell types were analyzed from  a total of 15 donors

first: Ariel

last: Floro

first: Ritesh

last: Tiwari

first: Rebeccah

last: Riley

first: Hiroyuki

last: Matsui

first: Nicolas

last: Andrews

first: Herbert

last: Kasler

first: Eric

last: Verdin


title: Neutrophils in the brain are sources of neuroprotective molecules and demonstrate functional heterogeneity during chronic Toxoplasma gondii infection

status: Public on Dec 30 2023

city: Riverside

first: Emma

middle: Harriet

last: Wilson

address: 900 University Avenue

institute: UC Riverside

summary: Infection with the protozoan parasite Toxoplasma gondii leads to the formation of lifelong cysts in neurons of the brain that can have devastating consequences in the immunocompromised. However, despite the establishment of a chronic inflammatory state and infection-induced neurological changes, there are limited signs of clinical neuropathology resulting in an asymptomatic infection in the immunocompetent. This suggests the work of neuroprotective mechanisms to prevent clinical manifestations of disease. However, such sources of neuroprotection during infection remain largely unknown. This study identifies a population of neutrophils chronically present in the brain during Toxoplasma infection that express the neuroprotective molecules NRG-1, ErbB4, and MSR1. Further phenotyping of this population via flow cytometry and singe-cell RNA sequencing reveals two distinct subsets of neutrophils based on age that display functional heterogeneity. This includes cells transcriptionally prepared to function both as anti-parasitic effector cells and in a more alternative protective manner. Chronic depletion of neutrophils results in increased parasite burden and infection-induced vascular pathology. Lack of neutrophils during chronic infection also deleteriously affects neuronal regeneration and repair mechanisms. In conclusion, this work identifies and demonstrates a functionally diverse chronic neutrophil population that plays a dynamic role in controlling infection outcome in the CNS by balancing classical responses with neuroprotective functions.

overall_design: We sequenced ~40,000 cells: brain mononuclear cells (labeled KB_Infected_BMNCs) (~10,000) from pooled infected brains (28 days post-infection); neutrophils (labeled KB_Naive_Spleen_Neutrophils) (~10,000) sorted from pooled naive spleens (28 days post-infection); neutrophils (labeled KB_Infected_Spleen_Neutrophils) (~10,000) sorted from pooled infected spleens (28 days post-infection); and neutrophils (labeled KB_Infected_Brain_Neutrophils) (~10,000) sorted from pooled infected brains (28 days post-infection).

first: Kristina

last: Bergersen

first: Bill

last: Kavvathas

first: Clement

last: David

first: Byron

middle: D

last: Ford

middle: H


title: Single-cell transcriptome analysis of small cell neuroendocrine tumor of the endometrium reveals ISL1 as a potential biomarker for diagnosis and treatment

city: Shanghai

first: Yin

last: Liu

state: Shanghai

address: Building #2, 507 Zhengmin Road

department: Department of Laboratory Medicine

institute: Shanghai Pulmonary Hospital, Tongji University School of Medicine

summary: In this study, we performed single-cell RNA sequencing on a specimen from a patient with endometrial neuroendocrine carcinoma pathologically diagnosed. By analyzing the data, we found that the expression of Islet-1 was significantly up-regulated in tumor cells. Furthermore, we verified it in neuroendocrine tumor cell lines, and obtained cells with high expression of Islet-1 and cells with low expression of Islet-1 by flow sorting. Cell function experiments were performed in vitro to verify that the cell proliferation and cell migration abilities of the high expression Islet-1 group were significantly higher than those of the low expression group. In summary, Islet-1 protein in neuroendocrine tumors could act as a promising biomarker for the tumorigenesis and progression of neuroendocrine tumors.

overall_design: NOT PROVIDED; REQUESTED

first: Cheng

last: Zhong

first: Yu-e

last: Guo

first: Yiran

last: Li


title: Arabidopsis thaliana: transgenic plants vs wild type

status: Public on Dec 25 2023

city: Irkutsk

first: Igor

last: Gorbenko

address: Lermontova st., 132

department: Cell biology and engineering

country: Russia

institute: SIPPB SB RAS

summary: Transcriptional profiling of Arabidopsis thaliana 12-days old seedlings comparing Col-0 wild type with transgenic plants with altered expression of dual-targetting plastid/mitochondrial organellar RNA-polymerase RPOTmp. Transgenic plants used for experiment were: overexpressor plants obtained by transformation of Col-0 WT plants with genetic constructs created in [Tarasenko et al., 2016] contained catalytic part of RPOTmp enzyme with transit peptides of RPOTm (mitochondrial) and RPOTp (plastid) by agrobacterial transformation; plants with complementation of RPOTmp functions in mitochondria or chloroplasts obtained from transformation of GABI_286E07 rpotmp knockout-mutant plants with genetic constructs created in [Tarasenko et al., 2016]. Goal was to determine the effects of RPOTmp knockout/overexpression on global Arabidopsis thaliana gene expression.

overall_design: Two-condition experiment, WT vs. transgenic seedlings. Analytical replicates: 3 control replicates, 3 replicates of knockout mutant, 3 replicates of each of overexpressor (4), 3 replicates of each of complementant(3).

first: Vladislav

middle: I

last: Tarasenko

first: Tatiana

last: Yakovleva

first: Alexander

last: Katyshev

first: Elena

last: Garnik

first: Vadim

last: Belkov

first: Yuri

last: Konstantinov

first: Milana

last: Koulintchenko