title: Different expression of ceRNAs (lncRNAs, circRNAs and mRNAs) in peripheral blood exosomes from idiopathic short stature patients and healthy controls

status: Public on Jan 31 2023

city: Nanchang

first: xijuan

last: liu

state: Jiangxi

address: No. 1 Minde Road

institute: The Second Affiliated Hospital of Nanchang University

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

summary: Idiopathic short stature is diagnosed by a standing height of less than two standard deviation scores in a specific population adjusted for age and gender and the exclusion of identifiable diseases. A series of studies have confirmed that noncoding RNAs can regulate the chondrocyte proliferation, hypertrophy, and endochondral ossification in the growth plate. In order to analyze and find differentially expressed ceRNAs (lncRNAs, circRNAs and mRNAs in peripheral blood exosomes of idiopathic short stature and healthy controls, we aimed to explore whether differentially expressed ceRNAs (lncRNAs, circRNAs and mRNAs) in peripheral blood exosomes of idiopathic short stature. Three pairs of peripheral blood exosomes samples were subjected to microarray analysis using the SBC human ceRNA Microarray.

overall_design: Three pairs of peripheral blood exosomes specimens from idiopathic short stature patients and healthy controls were used for SBC human ceRNA microarray analysis. RNA samples were prepared for microarray hybridization using Eastep Super RNA simple Total RNA Kit according to the manufacturer’s protocol.

first: Xijuan

last: Liu

first: Jingyu

last: Jia

first: Jinghong


title: Cellular population dynamics shape the route to human pluripotency

city: Pozzuoli

first: Francesco

last: Panariello

state: Napoli

address: Via Campi Flegrei 34

country: Italy

institute: TIGEM

type: Expression profiling by high throughput sequencing

summary: Here we analyzed the gene expression dynamics of human cells reprogramming by using single cell RNA-seq (sc-RNAseq).

overall_design: Human BJ fibroblasts were reprogrammed to induced pluripotent stem cells in microfluidics chambers through mRNA transfections. Samples were harvested before the first transfection (D0), 3 days after transfection (D3) and then every 2 days (D5, D7, D9, D11, D13 and D15). All the samples were cryopreserved and finally analyzed through single cell RNA sequencing.

first: Panariello

last: Francesco

first: Gagliano

last: Onelia


title: Effects of L-BAIBA administration and sub-optimal mechanical loading on gene expression in osteocyte-enriched cortical bone

status: Public on Feb 01 2023

city: Indianapolis

first: Matt

last: Prideaux

state: Indiana

address: MS5055P, 635 Barnhill Dr

department: ICMH

country: USA

institute: Indiana University

summary: To investigate potential mechanisms for the synergism of L-BAIBA and mechanical loading on bone formation, RNA Seq was performed on osteocyte-enriched cortical bone from mice treated with L-BAIBA and sub-optimal mechanical loading (8.25N) for either long-term (2 weeks L-BAIBA and loading) or short-term (5 days L-BAIBA and a single bout of mechanical loading).

overall_design: Comparative gene expression profiling analysis of RNA-seq data from loaded and non-loaded osteocyte-enriched cortical bone from L-BAIBA and control treated mice.

first: Alberto

last: Smargiassi

first: Lynda

middle: F

last: Bonewald


title: TGFβ signaling in the uterine epithelium controls endometrial cell homeostasis and regeneration [RNA-Seq]

status: Public on Jan 30 2023

city: Houston

first: Peixin

last: Jiang

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: In this study, we define the epithelial-specific contribution of SMAD2/3 to endometrial function by conditionally ablating the Smad2 and Smad3 transcription factors using Lactoferrin-iCre (Ltf-cre). Using epithelial organoid cultures from the endometrium, we uncover the signaling mechanisms downstream of TGFβ that control endometrial cell regeneration and are critical for endometrial regeneration and homeostasis.

overall_design: The endometrial organoids generated from Smad2/3-FF or Smad2/3-LTF mice were cultured and treated with or without A83. Their mRNA was isolated using DirectZol kit and sequenced.

first: Maya

middle: L

last: Kriseman

first: Suni

last: Tang

first: Zian

last: Liao

first: Fei

last: Yuan

first: Sydney

last: Parks

first: Ramya

last: Masand

first: Patricia

last: Castro

first: Michael

last: Ittmann

first: Chad

last: Creighton

first: Zhi

last: Tan

first: Diana

last: Monsivais


title: TGFβ signaling in the uterine epithelium controls endometrial cell homeostasis and regeneration [CUT&RUN]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: We performed Cleavage Under Targets & Release Using Nuclease (CUT&RUN-seq) for SMAD4 in the mouse endometrial epithelium organoids.


title: Rhinoviruses and enterovirus-D68 replicate more robustly in respiratory tissues originating from asthmatic patients compared to non-asthmatic controls

status: Public on Feb 13 2023

city: Genève

first: Nicolas

last: Hulo

address: 1 rue Michel Servet

country: Switzerland

institute: Université de Genève

summary: Investigation of the mechanism leading to differential rhinovirus infection in airway epithelia from healty versus asthmatic patients

overall_design: Transcriptomic comparison of Human airway epithelia from healthy versus asthmatic patients infected with Rhinoviruses RV-48 or RV-15. Non-infected tissues from the same groups (mock) have been used as negative controls

first: Manel

last: Essaidi-Laziosi

first: Léna

last: Royston

first: Bernadett

last: Boda

first: Francisco

middle: J

last: Pérez-Rodriguez

first: Isabelle

last: Piuz

first: Song

last: Huang

first: Samuel

last: Constant

first: Laurent

last: Kaiser

first: Caroline

last: Tapparel


title: Village In a Dish: A Model System for Population-scale hiPSC Studies [Affymetrix]

status: Public on Feb 14 2023

city: Darlinghurst

first: Drew

last: Neavin

state: New South Wales

address: 384 Victoria St

department: Cellular Science

country: Australia

institute: Garvan Institute of Medical Research

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: The mechanisms by which DNA alleles contribute to disease risk, drug response, and other human phenotypes are highly context-specific, varying across cell types and under different conditions. Human induced pluripotent stem cells (hiPSCs) are uniquely suited to study these context-dependent effects, but to do so requires cell lines from hundreds or thousands of individuals. Village cultures, where multiple hiPSC lines are cultured and differentiated in a single dish, provide an elegant solution for scaling hiPSC experiments to the necessary sample sizes required for population-scale studies. Here, we show the utility of village models, demonstrating how cells can be assigned back to a donor line using single-cell sequencing and addressing whether line-specific signalling alters the transcriptional profiles of companion lines in a village. We generated single-cell RNA sequence data from hiPSC lines cultured independently (uni-culture) and in villages at three independent sites. Using a mixed linear model framework, we estimate that the proportion of transcriptional variation across cells is predominantly due to donor effects, with minimal evidence of variation due to culturing in a village system. We demonstrate that the genetic, epigenetic or hiPSC line-specific effects explain a large percentage of gene expression variation for many genes, not the village status. This is reiterated by replication of previously identified genetic effects. Finally, we demonstrate consistency in the landscape of cell states between uni- and village-culture systems. We demonstrate that village methods can effectively detect hiPSC line-specific effects, including sensitive dynamics of cell states.

overall_design: 20 total samples analyzed, no replicates

middle: R

first: Angela

middle: M

last: Steinmann

first: Nona

last: Farbehi

first: Han

middle: S

last: Chiu

first: Maciej

last: Daniszewski

first: Himanshi

last: Arora

first: Yasmin

last: Bermudez

first: Cátia

last: Moutinho

first: Chia-Ling

last: Chan

first: Monique

last: Bax

first: Mubarika

last: Tyebally

first: Vikkitharan

last: Gnanasambandapillai

first: Chuan

middle: E

last: Lam

first: Uyen

last: Nguyen

first: Damián

last: Hernández

first: Grace

last: Lidgerwood

first: Bob

last: Graham

first: Alex

middle: W

last: Hewitt

first: Alice

last: Pébay

first: Nathan

last: Palpant

first: Joseph

last: Powell


title: Increased expression of NKG2D ligands in BrafV600E-driven thyroid cancer cells with β-catenin ablation

status: Public on Feb 09 2023

city: Riyadh

first: yufei

last: shi

address: PO Box 3354

country: Saudi Arabia

institute: King Faisal Specialist Hospital and Research Centre

summary: BRAFV600E mutation frequently occurs in papillary thyroid cancer (PTC). β-catenin, encoded by CTNNB1, is a key downstream component of canonical Wnt signaling pathway and is often overexpressed in PTC. BRAFV600E-driven PTC tumors rely on Wnt/β-catenin signaling to sustain their growth and progression. In the present study, we investigated the tumorigenicity of thyroid cancer cells derived from BrafV600E PTC mice after Ctnnb1 ablation (BVE-Ctnnb1null). Remarkably, the tumorigenic potential of BVE-Ctnnb1null tumor cells was lost in nude mice. RNA-Seq analysis of the BVE-Ctnnb1null tumor cells showed up-regulation of  NKG2D receptor activating ligands (H60a, H60b, H60c, Raet1a, Raet1b, Raet1c, Raet1d, Raet1e and Ulbp1) and down-regulation of inhibitory MHC class I molecules H-2L and H-2K2 in the BVE-Ctnnb1null tumor cells. In vitro cytotoxicity assay demonstrated that BVE-Ctnnb1wt tumor cells were resistant to NK cell-mediated cytotoxicity whereas BVE-Ctnnb1null tumor cells were sensitive to NK cell-mediated killing. Furthermore, overexpression of any one of these NKG2D ligands in the BVE-Ctnnb1wt cell line resulted in significant reduction of tumor growth in nude mice. Our results indicate that active β-catenin signaling inhibits NK cell-mediated immune response against thyroid cancer cells.  Targeting β-catenin signaling pathway may have significant therapeutic benefit for thyroid cancer by not only inhibiting tumor growth but also enhancing host immune surveillance.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BRAFV600E-driven PTC cells with or without CTNNB1 knockout

first: Minjing

last: Zou

first: Huda

last: BinEssa

first: Yufei

last: Shi


title: Integrated mapping of the dog epigenome (RNA-seq)

city: Seoul

first: Je-Yoel

last: Cho

address: 1, Gwanak-ro, Gwanak-gu

department: Biochemistry

country: South Korea

institute: Seoul National University

summary: Dogs have become a valuable model in exploring multifaceted diseases and biology relevant to human health. Despite large-scale dog genome projects producing high-quality draft references, a comprehensive annotation of functional elements is still lacking. We addressed this through integrative next-generation sequencing of transcriptomes paired with five histone marks and DNA methylome profiling across 11 tissue types, deciphering the dog’s epigenetic code by defining distinct chromatin states, super-enhancer and methylome landscapes, and thus showed that these regions are associated with a wide range of biological functions and cell/tissue identity. In addition, we confirmed that the phenotype-associated variants are enriched in tissue-specific regulatory regions and, therefore, the tissue of origin of the variants can be traced. Ultimately, we delineated conserved and dynamic epigenomic changes at the tissue- and species-specific resolutions. Our study provides an epigenomic blueprint of the dog that can be used for comparative biology and medical research.

overall_design: 22 RNA-seq generated from 11 adult normal tissue types of 3 beagles

first: Keun Hong

last: Son

first: Mark Borris

last: Aldonza

first: A-reum

last: Nam


title: Integrated mapping of the dog epigenome (ChIP-seq)

overall_design: 131 ChIP-seq (110 histone and 21 input data) generated from 11 adult normal tissue types of 3 beagles


title: Resolvin D1 improves allograft osteointegration and directly enhances osteoblasts differentiation

status: Public on Feb 08 2023

city: Jerusalem

first: Noy

last: Pinto

address: Refael Dela Pergula 18 Jerusalem

country: Israel

institute: Hadassah Hebrew University Jerusalem

overall_design: Maxillae were pulverized in a homogenizer, and total RNA was isolated from bones lysates or from cultured cells with TriZol (1000 ul per sample; Thermo Fisher Scientific). RNA purity was detected with a Nanodrop. DNA-free RNA was obtained by using and RNeasy Mini Kit (QIAGEN) with DNase treatment according to the manufacturer’s instructions. For quality control of RNA extraction yield, an RNA Screen Tape kit (Agilent Technologies), a D1000 Screen Tape kit (Agilent Technologies), Qubit RNA HS Assay kit (Invitrogen) and a Qubit DNA HS Assay kit (Invitrogen) were used for each specific step. RNA samples from Allograft vs Spon. Healing groups were all passed quality control analysis on a Bioanalyzer 2100 (Agilent Technologies). The 3 biological replicates with the highest RNA were used for mRNA library preparation and bioinformatics analysis as described previously.

first: Yehuda

last: Klein

first: Yechezkel

last: Barenholz

first: Stella

last: Chaushu


title: Meis1 establishes the pre-hemogenic endothelial state prior to Runx1 expression

status: Public on Feb 02 2023

city: Vancouver

first: Aly

last: Karsan

state: British Columbia

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre

summary: Hematopoietic stem and progenitor cells (HSPCs) originate from an endothelial-to-hematopoietic transition (EHT) during embryogenesis. Characterization of early hemogenic endothelial (HE) cells is required to understand what drives hemogenic specification and to accurately define cells capable of undergoing EHT. Using Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), we defined the early subpopulation of pre-HE cells based on both surface markers and transcriptomes. We identified the transcription factor Meis1 as an essential regulator of hemogenic cell specification in the embryo prior to Runx1 expression. Meis1 is expressed at the earliest stages of EHT and distinguishes pre-HE cells primed towards the hemogenic trajectory from the arterial endothelial cells that continue towards a vascular fate. Endothelial-specific deletion of Meis1 impaired the formation of functional Runx1-expressing HE which significantly impeded the emergence of pre-HSPC via EHT. Our findings implicate Meis1 in a critical fate-determining step for establishing EHT potential in endothelial cells.

overall_design: CD31+CD117-CD45-Runx1+23GFP- cells were FACS-isolated from Runx1+23GFP transgenic embryos and compared to bulk EC FACS-isolated from WT littermates

first: Patrick

last: Coulombe

first: Amanda

last: Fentiman

first: Jeremy

middle: D

last: Parker

first: Derek

last: Tam

first: Eric

last: Yung

first: R

middle: K

last: Humphries


title: Glimepiride Compared to Liraglutide Increases Plasma Levels of miR-206, miR-182-5p, and miR-766-3p in Type 2 Diabetes: A Randomized Controlled Trial

status: Public on Jan 26 2023

city: Örebro

first: Robert

last: Kruse

address: Södra Grev Rosengatan 32

department: Kliniskt forskningslaboratorium

country: Sweden

institute: Örebro University

type: Non-coding RNA profiling by high throughput sequencing

summary: In the current study we evaluated the effect of glimepiride, liraglutide on the expression of the circulating miRNAs. Univariate analyses show that treatment with glimepiride altered expression of three miRNAs in patient serum, miR-206, miR-182-5p, and miR-766-3p. Both miR-182-5p and miR-766-3p were also picked up among the top contributing miRNAs with penalized regularised logistic regressions (Lasso). The highest-ranked miRNAs with respect to Lasso coefficients were miR-3960, miR-31-5p, miR-3613-3p, and miR-378a-3p. Liraglutide treatment did not significantly influence levels of circulating miRNAs. Present study indicates that glucose-lowering drugs differently affect the expression of circulating miRNAs in serum in individuals with T2DM. More studies are required to investigate possible mechanisms by which glimepiride is affecting the expression of circulating miRNAs.

overall_design: The present study is a post hoc trial from a previously randomized control trial comparing liraglutide versus glimepiride both in combination with metformin in subjects with T2DM, and subclinical heart failure. miRNAs were determined in the subjects’ serum samples with next generation sequencing. Expression patterns of the circulating miRNAs were analyzed using bioinformatic univariate and multivariate analyses.

first: Nikolai

last: Scherbak

first: Thomas

last: Nyström

first: Johan

last: Jendle


title: The transcriptomic response of two basidiomycetes to plant biomass is modulated by temperature to a different extent

status: Public on Feb 03 2023

city: Utrecht

first: Ronald

last: de vries

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: westerdijkinstitute

summary: In this study, we compared the transcriptomeic profiles of two recently sequenced white-rot wood-decaying mushrooms, Trametes pubescens and Phlebia centrifuga, during their growth on two common plant biomass substrates at different temperatures.

sample_organism:
Hermanssonia centrifuga
Trametes pubescens

overall_design: We compared transcriptome of the T. pubescens and P. centrifuga during their growth on two common plant biomass, wheat straw (WS) and spruce (SP) for 3 weeks, at two temperatures (15 °C and 25 °C).

first: Mao

last: Peng

first: Zoraide

last: Granchi

first: Thommas

last: Chin-A-Woeng

first: Kristiina

last: Hildén

first: Miia

last: Mäkelä

middle: P

last: de Vries


title: Single cell analysis in mouse tissues after Tie2 or Tie1Tie2 deletion

status: Public on Jan 23 2023

city: Helsinki

first: Andrey

last: Anisimov

address: Haartmaninkatu 8

department: Faculty of medicine

country: Finland

institute: University of Helsinki

summary: To analyze genetic changes in arterial, pulmonary and bone marrow cells during atherosclerosis development

overall_design: We analyzed total aortic, pulmonary and bone marrow cells from arterial Tie2 (or Tie1/Tie2) deleted mice during atheroclerosis development. For total aortic cells and total bone marrow cells from Tie2-deleted mice, the analysis was done after 4 weeks since the start of high-fat (western) diet feeding the mice. For analysis of total cells from the lung we used mice with combined simultaneous deletion of both Tie1 and Tie2, and high-fat (western) diet feeding has lasted for 20 weeks.

first: Kari

last: Alitalo


title: RNA sequencing of Tie2 (TEK) silencing in Tie2+ Fibrolast like cells (TF) from the aorta of wild type C57Bl/6J mice.

summary: Purpose: Our objective is to compare the gene expression pattern in the TF cells transfected with LV-SCR or LV-shTEK-A or LV-shTEK-D invitro.

overall_design:
The TF cell population from the aorta of  wild type C57Bl/6J mice were isolated and sorted by FACS, cultured in the 0.1% gelatin coated petri dish containing growth media, at passage #6 transfected with the lenti viral vector (LV-SCR or LV-shTEK-A or LV-shTEK-D) and analyzed by RNA sequencing.
cDNA library was synthesized using BGI DNBSeq Stranded mRNA KIT (BGI, Hongkong), The library quality was determined using bioanalyzer and sequenced using MGISEQ-2000 System with the following specifications: 1 X 100bp, 20M paired end reads.


title: TGFβ signaling in the uterine epithelium controls endometrial cell homeostasis and regeneration

first: Peixin

last: Jiang

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

overall_design: Refer to individual Series


title: Single cell analysis in the adult aorta after Tie2 deletion

summary: To analyze the Angiopoietin receptor Tie2 on the arterial endothelial cells during atheroclerosis

overall_design: We analyzed total aortic cells from arterial Tie2 deleted mice during homeostasis and during atheroclerosis. To understand the difference between Tie2 and Tie1 during plaque formation, we also analyzed total aortic cells from both aortic arch and throcic/abdominal aorta during atheroclerosis


title: Integrated mapping of the dog epigenome

first: Je-Yoel

last: Cho

type: Methylation profiling by high throughput sequencing


title: Integrated mapping of the dog epigenome (MBD-seq)

overall_design: 33 MBD-seq (22 MBD and 11 input data) generated from 11 adult normal tissue types of 3 beagles

first: Keun Hong

last: Son

first: Mark Borris

last: Aldonza

first: A-reum

last: Nam


title: RNA-seq time course in response to lipo-chitooligosaccharides in hybrid poplar roots

status: Public on Jan 20 2023

city: Gainesville

first: Matias

last: Kirst

state: MA

address: 2033 Mowry Road, Room 320

department: School of Forest, Fisheries, and Geomatics Sciences

institute: University of FLorida

summary: We treated Populus tremula x alba roots with rhizobial LCOs. We analyzed gene expression by RNA sequencing at seven time-points: 0 hr (control treatment), 15, 30 min, 1, 2, 4, 8, 24 hours over the following 24 hours.

overall_design: Shoot tips (about 10-15 mm long) cut from in vitro grown Populus tremula × alba INRA clone 717-1B4 were placed aseptically on Murashige and Skoog media with vitamins (PhytoTech Labs-M519) supplemented with 0.1 g/L myo-inositol (PhytoTech Labs-I703), 0.25 g/L MES (PhytoTech Labs-M825), 2% (w/v) sucrose (PhytoTech Labs-S391) and solidified with 0.8% agar (PhytoTech Labs-A296). The pH of the medium was adjusted to 5.8 with KOH before autoclaving. Explants were placed in a growth chamber under long-day conditions (16 hours light/8 hours darkness, 24 °C, 65% relative humidity, and 100 μmol m−2 s−1 photosynthetic photon flux). Once the shoot tips were rooted, and the root was at least 25 mm long, plantlets were transferred to square plates (22.5 x 22.5 cm) containing Woody Plant Medium with reduced nitrogen (0.5 mM) and phosphate (7 μM), and 1.3 g/l calcium gluconate (Lloyd and McCown 1980). Plantlets were grown vertically for ten days in the growth chamber. Next, 3 hours after growth chamber dawn, plates were flooded to immerse roots in a 10-8 M solution of purified Rhizobium sp. IRBG74 LCOs or a control solution (0.005% ethanol) for 1 hour. After 1 hour, the solution was poured off, and plants returned to the growth chamber. Roots were collected immediately (control), 15 minutes, 30 minutes, 1, 2, 4, 8, and 24 hours after the LCO treatment. Roots were snap-frozen in liquid nitrogen, and roots from four plants were pooled for each of three biological replicates used in RNA sequencing. For each RNA extraction, roots from four plants were pooled and ground while keeping the sample frozen. RNA extraction was performed as described previously (Chang et al. 1993). Libraries were prepared using 0.5 μg of RNA in the NEBNext® UltraTM Directional RNA Library Prep Kit following the supplier’s instructions (New England Biolabs, Ipswich, MA, USA). Sequencing was conducted with an Illumina HiSeq3000 (2×100 cycles) at the Interdisciplinary Center for Biotechnology Research at the University of Florida (Gainesville, FL, USA).

first: Daniel

last: Conde

first: Henry

last: Schmidt

first: Christopher

last: Dervinis

first: Sara

last: Knaack

first: Lucas

last: Gontijo Silva Maia

middle: B

last: Irving

first: Sushmita

last: Roy

first: Jean-Michel

last: Ané


title: Functionally and Metabolically Divergent Melanoma-Associated Macrophages Originate from Common Bone-Marrow Precursors

city: New Haven

first: Miller-Jensen

last: Lab

address: 55 Prospect St

department: Biomedical Engineering

institute: Yale University

summary: Melanomas display high numbers of tumor-associated macrophages (TAMs), which correlate with worse prognosis but also retain the potential to restore anti-tumor activity. Harnessing macrophages for therapeutic purposes has been particularly challenging due to their heterogeneity, based on their ontogeny and function and driven by the tissue-specific niche. In the present study, we used the YUMM1.7 murine melanoma model to better understand melanoma TAM origin and dynamics during tumor progression, with potential therapeutic implications. We identified distinct TAM subsets based on F4/80 expression, with the F4/80high fraction increasing over time and displaying tissue-resident-like phenotype. While skin-resident macrophages showed mixed ontogeny, F4/80+ TAM subsets in i.d. YUMM1.7 tumors originated almost exclusively from bone-marrow precursors. Multiparametric analysis of macrophage phenotype showed a temporal divergence of F4/80+ TAM subpopulations, which also differed from skin-resident subsets, and from their monocytic precursors. Overall, F4/80+ TAMs displayed co-expression of M1- and M2-like canonical markers, and RNA-seq and pathway analysis showed differential immunosuppressive and metabolic profiles. GSEA showed F4/80high TAMs to rely on oxidative phosphorylation, with increased proliferation and protein secretion while F4/80low cells had high pro-inflammatory and intracellular signaling pathways, with lipid and polyamine metabolism. Overall, the present in-depth characterization provides further evidence of the ontogeny of the evolving melanoma TAMs. Some of these gene profiles matched recently-identified TAM clusters in other tumor models and human cancers, which in turn can lead to more effective therapies targeting specific immunosuppressive cells in advanced tumor stages.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for F4/80+ macrophages (TAMs) sorted from YUMM1.7 murine melanomas. F4/80high- and F4/80low-expressing TAM profiles were compared using 3 samples from each subset.

first: Gabriela

middle: A

last: Pizzurro

first: Kate

last: Bridges

first: Xiaodong

first: Aurobind

last: Vidyarthi

first: Kathryn

last: Miller-Jensen

first: Oscar

last: Colegio


title: Modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches

status: Public on Jan 16 2023

city: Washington

first: Xiaolong

last: Cheng

state: DC

address: 7144 13th Place NW

institute: Children's National

summary: We conducted a two-vector CRISPR/Cas13d proliferation screening experiment. The screening library contains 10,830 sgRNAs targeting 192 protein-coding genes and 234 lncRNAs, and the screening experiment was performed using a melanoma cell line A375. It provides a unique dataset to model Cas13d sgRNA efficiency and specificity. We designed a deep learning model, named DeepCas13, to predict the sgRNA on-target activity with high accuracy from sgRNA sequences and RNA secondary structures.

overall_design: The gRNA lentiviral library-infected cas13d-expressing A375 cells harvested in day 0 and day 28 were used for DNA extraction, gRNA enrichment by PCR amplification and deep sequencing.

first: Zexu

last: Li

first: Teng

last: Fei

first: Wei


title: SAYSD1 senses UFMylated ribosome to safeguard co-translational protein translocation at the endoplasmic reticulum

city: Bethesda

first: Yihong

last: Ye

state: MD

address: 5 Center Drive

country: China

institute: NIH

summary: Translocon clogging at the endoplasmic reticulum (ER) as a result of translation stalling triggers ribosome UFMylation, activating Translocation-Associated Quality Control (TAQC) to degrade clogged substrates. How cells sense ribosome UFMylation to initiate TAQC is unclear. We conduct a genome-wide CRISPR/Cas9 screen to identify an uncharacterized membrane protein named SAYSD1 that facilitates TAQC. SAYSD1 associates with the Sec61 translocon, and also recognizes both ribosome and UFM1 directly, engaging a stalled nascent chain to ensure its transport via the TRAPP complex to lysosomes for degradation. Like UFM1 deficiency, SAYSD1 depletion causes the accumulation of translocation-stalled proteins at the ER and triggers ER stress. Importantly, disrupting UFM1- and SAYSD1-dependent TAQC in Drosophila leads to intracellular accumulation of translocation-stalled collagens, defective collagen deposition, abnormal basement membranes, and reduced stress tolerance. Thus, SAYSD1 acts as a UFM1 sensor that collaborates with ribosome UFMylation at the site of clogged translocon, safeguarding ER homeostasis during animal development.

overall_design: 293T cells stably expressing ERGFP_K20 were infected with GeckoV2 libraries. GFP high (1% of cells) and GFP low (80%) were sorted by a FACS Ariall cell sorter. Genomic DNA was extracted for amplification of sgRNAs by PCB.  Amplified sgRNAs were deep-sequenced by an Illumina platform.

first: Lihui

last: Wang

first: Yue

last: Xu

first: Sijung

last: Yun

first: Quan

last: Yuan

first: Prasanna

last: Satpute-Krishnan


title: Osteoclast-derived exosomal miR-5134-5p interferes with alveolar bone homeostasis by targeting the JAK2/STAT3 axis

status: Public on Jan 04 2023

city: Hangzhou

first: Lai

last: Pan

state: Zhejiang

address: Jiefang Road 88

institute: The second affiliated hospital of Zhejiang University

summary: The specific mirnas in the exosomes of mature osteoclasts were found by exosome sequencing, and their functions were identified by acting on osteoblasts to observe the differentiation and osteogenesis of osteoblasts

overall_design: Source: RAW264.7. In the T75 culture bottle, 100W cells were cultured in Gibco DMEM+10%FBS for 24h, then the supernatant was abandoned. After washing with PBS, the supernatant was changed to α-MEM+10%FBS (control group), α-MEM+10%FBS+50ng/mlRANKL (induction group), respectively. Cells in the supernatant were removed by centrifugation at 300g for 9min at 4 ° C and 2000g for 20min, and the precipitate was discarded

first: Jingyi

last: Tan

first: Chenyi

last: Zhang

first: Haizheng


title: Characterization of dynamic p300 enhancers in murine cardiomyocyte development [RNA-seq]

status: Public on Jan 19 2023

city: Boston

first: Pingzhu

last: Zhou

address: 320 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

summary: We report the application of bioChIP-seq, bulk RNA-seq, Hi-C, and Massively parallel reporter assays (MPRAs) to characterize the p300-bound regulatory regions in murine cardiomyocytes (CMs). By obtaining ChIP-seq data of coactivator p300 from seven developmental stages of mouse CMs, we defined the dynamic p300 enhancers from embryonic CMs to adult CMs. We then validated the activity of dynamic p300 enhancers with AAV9-based MPRAs, we found dynamic p300 enhancers show dynamic activity from postnatal day 0 (P0) CMs to 4-week-old CMs. In addition, MRPA results suggest nuclear receptor motifs are required for the activity of some p300 late enhancers. With Hi-C data of E12.5, P0 and adult CMs, we identified chromatin structure changes such as chromatin loops, compartment switch, and new TAD boundaries are associated with dynamic p300 binding. This study provides data source of CM-selective p300 enhancers, chromatin 3D structure and gene expression during CM development and maturation.

overall_design: Identification and characterization of p300 enhancers by CM-selective p300 bioChIP-seq and MPRAs.

first: Nathan

last: Vandusen

first: Yanchun

first: William

middle: T

last: Pu


title: SAPS3 is an AMPK inhibitor and controls metabolic homeostasis upon dietary challenge

status: Public on Jan 18 2023

city: Duarte

first: Haiqing

state: CA

address: 1500 E Durate Rd

department: Shared Resources Department

institute: City of Hope National Medical Center

summary: Inhibition of AMPK is tightly associated with metabolic perturbations upon over nutrition, yet the molecular mechanism underneath that is not clear. Here, we demonstrate serine/threonine-protein phosphatase 6 regulatory subunit 3, SAPS3, is an essential negative regulator of AMPK. SAPS3 is induced under high fat diet (HFD) and recruits the PP6 catalytic subunit to deactivate phosphorylated-AMPK, thereby inhibiting AMPK-controlled metabolic pathways. Remarkably, either whole-body or liver-specific deletion of SAPS3 protects mice against the HFD-induced detrimental consequences and reverses HFD-induced metabolic and transcriptional alterations while loss of SAPS3 has no effects on mice under balanced diets. Furthermore, genetic inhibition of AMPK is sufficient to block the protective phenotype in SAPS3 knockout mice under HFD. Together, our results reveal that SAPS3 is a critical negative regulator of AMPK and suppression of SAPS3 functions as a guardian when metabolism is perturbed and represents a potential therapeutic strategy to treat metabolic syndromes.

overall_design: To investigate the gene expression profiling exhibited in the livers of mice lacking serine/threonine protein phosphatase 6 regulatory subunit 3, SAPS3, and fed an high fat diet (HFD), we performed RNA sequencing using liver tissues that were collected from ppp6r3fl/fl (FF) mice and liver-specific SAPS3 knockout mice (LKO) following 16 weeks on HFD.

first: Ying

last: Yang

first: Michael

last: Reid

first: Eric

last: Hanse

first: Yuanding

first: Bryan

middle: I

last: Ruiz

first: Mei

last: Kong


title: Multi-omics profiling of cholangiocytes reveals chromatin state dynamics during hepatic cystogenesis in polycystic liver disease

status: Public on Jan 27 2023

city: Tianjin

first: Jiayuan

last: Chen

state: State...

address: Heping

institute: Tianjin Medical University


title: Transcriptome profile of intestinal epithelium in conditional Ifnar1 ko and wt mice following Cryptosporidium parvum Infection

city: Omaha

first: Xianming

state: NE

address: 2500 california plaza

institute: creighton university

summary: This study aims to measure the transcriptome profile of ilium tissues from intestinal epithelial conditional Ifnar1 KO and control littermates following cryptosporidial infection. Neonates of the conditional intestinal epithelial Ifnar1 knockout mice and control littlermates were exposed to C. parvum infection for 48 and 72h. Ilium tissues were collected and total RNA was isolated for the genome-wide analysis.

overall_design: The conditional intestinal epithelial type I IFN receptor Ifnar1 knockout mice (Villin.Ifnar1-/- mice) were generated from cross-breeding of the Ifnar1fl/fl mice [B6(Cg)-Ifnar1tm1.1Ees/J, Jackson] with the Villin.Cre transgenic [B6.Cg-Tg(Vil1-cre)1000Gum/J, Jackson].  Neonates of Villin.Ifnar1-/- mice and littlemates (5 days after birth) were administrated with C. parvum oocysts through oral administration. Neonates received oral adminstration of PBS were used as control.  At 48h and 72h after parasite (or PBS) adminstration, ilium tissues were collected and total RNAs were isolated with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction. High-throughput sequencing service was provided by the BGI Americas.


title: PTBP1 controls intestinal epithelial regeneration through post-transcriptional regulation of gene expression

city: URBANA

first: Ullas

middle: Valiya

last: Chembazhi

state: Illinois

address: 600 S Mathews Avenue

institute: UIUC

summary: The intestinal epithelial regeneration is driven by intestinal stem cells under homeostatic conditions. Differentiated intestinal epithelial cells, such as Paneth cells, are capable of acquiring multipotency and contributing to regeneration upon loss of intestinal stem cells. Paneth cells also support intestinal stem cell survival and regeneration. We report here that depletion of an RNA-binding protein named polypyrimidine tract binding protein 1 (PTBP1) in mouse intestinal epithelial cells causes intestinal stem cell death and epithelial regeneration failure. Mechanistically, we show that PTBP1 inhibits neuronal-like splicing programs in intestinal crypt cells, which is critical for maintaining intestinal stem cell stemness. This function is achieved at least in part through promoting the non-productive splicing of its paralog PTBP2. Moreover, PTBP1 inhibits the expression of an AKT inhibitor PHLDA3 in Paneth cells and permits AKT activation, which presumably maintains Paneth cell plasticity and function in supporting intestinal stem cell niche. We show that PTBP1 directly binds to a CU-rich region in the 3’ UTR of Phlda3, which we demonstrate to be critical for downregulating the mRNA and protein levels of Phlda3. Our results thus reveal the multifaceted in vivo regulation of intestinal epithelial regeneration by PTBP1 at the post-transcriptional level.

overall_design: Investigate the role of PTBP1 in regulating intestinal epithelial cell regeneration

middle: V

first: Auinash

last: Kalsotra

first: Wenyan

last: Mei


title: The Human Pre-replication Complex is an Open Complex

status: Public on Dec 31 2022

city: Paris

first: Chunlong

address: 26 rue d’Ulm

country: France

institute: Institut Curie

summary: In eukaryotes, DNA replication initiation requires assembly and activation of the minichromosome maintenance (MCM) 2-7 double hexamer (DH) to melt origin DNA strands. However, the mechanism for this initial melting is unknown. Here, we report a 2.59-Å cryo-electron microscopy structure of the endogenously purified human MCM-DH (hMCM-DH), also known as the pre-replication complex. In this structure, the hMCM-DH shows a constricted central channel with a diameter of only 13 Å at the hexamer interface. This unusual conformation untwists and stretches the DNA strands such that almost a half turn of the bound duplex DNA is distorted with one-base pair completely separated, generating an initial open structure (IOS) at the hexamer junction. This IOS is captured and stabilized by zinc fingers (ZFs) of MCM2 and MCM5 from opposing hexamers. Disturbing the interaction between MCM5-ZF and the IOS demonstrably inhibits DH formation and replication initiation. High-resolution mapping of hMCM-DH footprints indicates that IOSs are distributed across the human genome in large clusters aligning perfectly with initiation zones to safeguard robust stochastic origin firing. This work unravels an intrinsic mechanism that couples DH formation with initial DNA melting to license replication initiation in human cells.

overall_design: Mapping of the hMCM-DH footprints in human cells

first: Jian

last: Li

first: Weitao

last: Wang

first: Claire

last: Lee

first: Bik

last: Tye

first: YuanLiang

last: Zhai

first: Chun-Long


title: Next-generation sequencing facilitates quantitative analysis of transcriptome profile in IEC 4.1 cells in response to CSpV1 RNA transfection

status: Public on Jan 05 2023

summary: The Cryptosporidium parvum virus 1 (CSpV1) is a member of the family Partitiviridae, genus Cryspovirus that infects C. parvum. This study aims to measure the impact of CSpV1 on the transcriptome profile in cultured IEC 4.1. Cells were treated with specific dsRNAs encoding CSpV1 viral capsid protein (CA) and RNA dependent RNA polymerase (RdRp). Cells treated with a scrambled non-specific siRNA were used as the control. Total RNA was collected for the genome-wide analysis, for sequencing using BGISEQ-500 platform.

overall_design: The IEC 4.1 murine intestinal epithelial cells were grown to 80% confluence for four groups: the siRNA control (Group B, cells treated with a non-specific scrambled siRNA control), the dsCA transfected (Group C, cells treated with the double-strand RNA encoding CSpV1 capsid protein), dsRdRp transfected (Group D, cells treated with the double-strand RNA encoding CSpV1 RNA dependent RNA polymerase), and dsCA/dsRdRp transfected (Group F, cells treated with double-strand RNA encoding CSpV1 capsid protein plus double strand RNA encoding RNA dependent RNA polymerase). Cells were treated with the transfection for 24h. Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.


title: Transcriptome Profiling of Distinct Stromal Cell Populations in Skeletal Muscle Following Acute Injury

status: Public on Jan 02 2023

city: Ankara

first: Cetin

last: Kocaefe

state: Sihhiye

address: Hacettepe University School of Medicine

department: Dept. of Medical Biology

country: Turkey

institute: Hacettepe University School of Medicine

summary: Skeletal muscle regeneration is primarily accomplished through the concerted action of the myoblasts as well as the supporting stromal cells. Following accomplishment of injury repair, activated stromal cells disappear via apoptosis. In the case of muscle dystrophies where in a chronic inflammatory environment is present, activated stromal cells are transformed into a myofibroblastic state with the deposition of extracellular matrix components. Excessive accumulation of ECM leads to irreversible fibrosis and tissue deterioration. A distinct stromal cell population named fibro-adipogenic precursors (FAPs) are known to be responsible for contribution to fibrosis and fatty infiltration. Fibrosis is also evident in disuse atrophy and sarcopenia without any significant inflammation. This study aims to analyze the heterogeneous population of FAPs comparatively in the course of acute damage and immobilization models.   We isolated and analyzed the mononuclear cell population of skeletal muscles following tenotomy and denervation models in mice. Immunophenotyping of the FAPs was conducted based on exclusion of CD45, CD31 and CD11b and a comparative analysis was accomplished on three different subpopulations of i) CD140a(+), Sca1(+) ii) CD140a(+), Sca1(-) iii) CD140a(-), Sca1(+). High-throughput transcriptome analysis was employed to further characterize the transcriptome of these three cell populations and compare their quiescent and activated states.  Results: Investigated sub-populations exhibited diverse activation properties and kinetics for each studied model. While CD140a(+), Sca1(+) was the predominating activated population along with tenotomy, denervation majorly stimulated the proliferation of CD140a(+), Sca1(+) cells. Both immobilization models lacked myofiber damage and exhibited a minute inflammatory response compared to the acute damage. Transcriptome analysis supports commonalities in upregulation of ECM components in diverse subpopulation of cells as well as discriminating candidate cell surface markers.  Skeletal muscle regeneration is primarily accomplished through the concerted action of the myoblasts as well as the supporting stromal cells. Following accomplishment of injury repair, activated stromal cells disappear via apoptosis. In the case of muscle dystrophies where in a chronic inflammatory environment is present, activated stromal cells are transformed into a myofibroblastic state with the deposition of extracellular matrix components. Excessive accumulation of ECM leads to irreversible fibrosis and tissue deterioration. A distinct stromal cell population named fibro-adipogenic precursors (FAPs) are known to be responsible for contribution to fibrosis and fatty infiltration. Fibrosis is also evident in disuse atrophy and sarcopenia without any significant inflammation. This study aims to analyze the heterogeneous population of FAPs comparatively in the course of acute damage and immobilization models.   We isolated and analyzed the mononuclear cell population of skeletal muscles following tenotomy and denervation models in mice. Immunophenotyping of the FAPs was conducted based on exclusion of CD45, CD31 and CD11b and a comparative analysis was accomplished on three different subpopulations of i) CD140a(+), Sca1(+) ii) CD140a(+), Sca1(-) iii) CD140a(-), Sca1(+). High-throughput transcriptome analysis was employed to further characterize the transcriptome of these three cell populations and compare their quiescent and activated states.  Results: Investigated sub-populations exhibited diverse activation properties and kinetics for each studied model. While CD140a(+), Sca1(+) was the predominating activated population along with tenotomy, denervation majorly stimulated the proliferation of CD140a(+), Sca1(+) cells. Both immobilization models lacked myofiber damage and exhibited a minute inflammatory response compared to the acute damage. Transcriptome analysis supports commonalities in upregulation of ECM components in diverse subpopulation of cells as well as discriminating candidate cell surface markers.

overall_design: RNASeq was performed on freshly isolated stromal cell populations of the control and injured (three days) skeletal muscle based on three different immunophenotypes.

first: C

last: Özdemir

first: D

last: Akçay

last: Yöyen Ermiş

first: E

last: Taşkıran

first: R

last: Soylu

first: G

last: Esendağlı

first: Y

middle: C


title: Local IL-17 orchestrates skin aging

city: Badalona

first: Elisabetta

last: Mereu

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

summary: Skin aging is characterized by structural and functional changes that lead to slower wound healing and higher rate of infections, which contribute to age-associated frailty. This likely depends on synergy between alterations in the local microenvironment and stem cell–intrinsic changes, underscored by pro-inflammatory microenvironments that drive pleotropic changes. To date, little is known about the precise nature and origin of the proposed age-associated inflammatory cues, or how they affect different tissue resident cell types. Based on deep single-cell RNA-sequencing of the entire dermal compartment, we now provide a comprehensive understanding of the age-associated changes in all skin cell types. We show a previously unreported skew towards an IL-17–expressing phenotype of Th cells, γδ T cells and innate lymphoid cells in aged skin. Aberrant IL-17 signaling is common to many autoimmune (e.g., rheumatoid arthritis and psoriasis) and chronic inflammatory diseases. Importantly, in vivo blockade of IL-17–triggered signaling during the aging process reduces the pro-inflammatory state by affecting immune and non-immune skin cells of both dermis and epidermis. Strikingly, IL-17 neutralization significantly delays the appearance of age-related traits, such as decreased epidermal thickness, increased cornified layer thickness and ameliorated hair follicle stem cell activation and hair shaft regeneration. Our results indicate that the aged skin shows chronic and persistent signs of inflammation, and that age-associated increased IL-17 signaling could be targeted as a strategy to prevent age-associated skin ailments in elderly.

overall_design: single-cell RNA sequencing 3' (scRNA-seq)

first: Paloma

last: Solà

first: Salvador

last: Aznar


title: Compressed Perturb-seq: highly efficient screens for regulatory circuits using random composite perturbations

status: Public on Jan 01 2023

city: Cambridge

first: Douglas

last: Yao

address: 1350 Massachusetts Ave

institute: Harvard University

summary: Pooled CRISPR screens with single-cell RNA-seq readout (Perturb-seq) have emerged as a key technique in functional genomics, but are limited in scale by cost and combinatorial complexity. Here, we reimagine Perturb-seq’s design through the lens of algorithms applied to random, low-dimensional observations. We present compressed Perturb-seq, in which we measure multiple perturbations per cell or multiple cells per droplet, and decompress these measurements by leveraging the sparse structure of regulatory circuits. Applying compressed Perturb-seq to 598 genes in the immune response to bacterial lipopolysaccharide, we achieve the same accuracy as conventional Perturb-seq at 4 to 20-fold reduced cost, with greater power to learn genetic interactions. We identify known and novel regulators of immune responses and uncover evolutionarily constrained genes with downstream targets enriched for immune disease heritability, including many missed by existing GWAS or trans-eQTL studies. Our framework enables new scales of interrogation for a foundational method in functional genomics.

overall_design: scRNA-seq of THP-1 cells expressing Cas9 or dCas9-KRAB transduced with sgRNA libraries targeting 598 genes as well as non-targeting controls, using both the conventional Perturb-seq experimental protocol as well as our modifications for compressed Perturb-seq. Cells were treated with LPS for 3 hours before sequencing.

first: Loic

last: Binan

first: Jon

last: Bezney

first: Brooke

last: Simonton

first: Jahanara

last: Freedman

first: Chris

last: Frangieh

first: Alexander

last: Gusev

first: Aviv

last: Regev

first: Brian

last: Cleary


title: H3K27ac ChIP-seq analysis of genetically engineered  mouse models (GEMMs) of PDA with  KRAS and TP53 mutations

status: Public on Dec 20 2022

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

summary: We profile  H3K27ac signals   in WT, KC and KPC mice of pancreatic cancer

overall_design: Peaks bound by H3K27ac were obtained from WT, KC and KPC mice.

first: Shujun

last: Zhang


title: FOSL2 CUT-tag analysis of genetically engineered  mouse models (GEMMs) of PDA with  KRAS and TP53 mutations

summary: We profile  FOSL2 genome occupancy upon  KPC mice of pancreatic cancer

overall_design: Peaks bound by FOSL2 were obtained using CUT-tag-Seq from KPC mice.


title: RNA-Seq of genetically engineered  mouse models (GEMMs) of PDA with or without KRAS and/or TP53 mutations

summary: We profile gene expression upon WT, KC and KPC mice of pancreatic cancer

overall_design: The gene expression  changes are analysis by comparing WT, KC, and KPC  mice in pancreatic cancer.


title: Mapping genetic effects on cell type-specific chromatin accessibility and annotating complex trait variants using single nucleus ATAC-seq

status: Public on Jan 10 2023

city: La Jolla

first: Paola

last: Benaglio

address: 9500 Gilman Drive #0761

department: Pediatrics

institute: University of California San Diego

summary: Gene regulation is highly cell type-specific and understanding the function of non-coding genetic variants associated with complex traits requires molecular phenotyping at cell type resolution. In this study we performed single nucleus ATAC-seq (snATAC-seq) and genotyping in peripheral blood mononuclear cells from 13 individuals. Clustering chromatin accessibility profiles of 96,002 total nuclei identified 17 immune cell types and sub-types. We mapped chromatin accessibility QTLs (caQTLs) in each immune cell type and sub-type which identified ~6,000 total caQTL peaks, including those obscured from assays of bulk tissue such as with divergent effects on different cell types. For ~3,000 caQTLs we further annotated putative target genes of variant activity using single cell co-accessibility, and caQTL variants were significantly correlated with the accessibility level of linked gene promoters. We fine-mapped loci associated with 16 complex immune traits and identified immune cell caQTLs, including those with cell type-specific effects. At the 6q15 locus associated with type 1 diabetes, in line with previous reports, variant rs72928038 was a naïve CD4+ T cell caQTL linked to BACH2 and we validated the allelic effects of this variant on regulatory activity in Jurkat T cells. These results highlight the utility of snATAC-seq for mapping genetic effects on accessible chromatin in specific cell types and provide a resource for annotating complex immune trait loci.

overall_design: Single nucleus ATAC-seq (10x) of  peripheral mononuclear blood cells from human donors

first: Jacklyn

last: Newsome

first: Jee

middle: Y

last: Han

first: Joshua

last: Chiou

first: Anthony

last: Aylward

first: Sierra

last: Corban

first: Mei-Lin

last: Okino

first: Jaspreet

last: Kaur

first: David

middle: U

last: Gorkin

first: Kyle

last: Gaulton


title: Myoscaffolds reveal laminin scarring is detrimental for stem cell function while sarcospan induces compensatory fibrosis

status: Public on Dec 29 2022

city: Los Angeles

first: Yerbol

middle: Z.

last: Kurmangaliyev

address: 675 Charles E. Young Drive South

institute: University of California, Los Angeles

summary: We developed an on-slide decellularization approach to generate acellular extracellular matrix (ECM) scaffolds that can be repopulated with various cell types to interrogate cell-ECM interactions. Using this platform, we investigated whether fibrotic ECM scarring affected human skeletal muscle progenitor cell (SMPC) functions that are essential for myoregeneration. SMPCs exhibited robust adhesion, motility, and differentiation on healthy muscle-derived myoscaffolds. All SPMC interactions with fibrotic myoscaffolds from dystrophic muscle were severely blunted including reduced motility rate and migration. Furthermore, SMPCs were unable to remodel laminin dense fibrotic scars within diseased myoscaffolds. Proteomics and structural analysis revealed that excessive collagen deposition alone is not pathological, and can be compensatory, as revealed by overexpression of sarcospan and its associated ECM receptors in dystrophic muscle. Our in vivo data also supported that ECM remodeling is important for SMPC engraftment and that fibrotic scars may represent one barrier to efficient cell therapy.

overall_design: Sequencing pf total RNA prepared from SMPCs cultured (5 days) on WT and mdx myoscaffolds.

first: Kristen

last: Stearns-Reider

first: Rachelle

middle: H

last: Crosbie


title: AP-1 is a regulatory transcription factor of inflammaging in the murine kidney and liver

status: Public on Dec 30 2022

city: BEIJING

first: xiaojie

last: yu

state: China Mainland

address: NO.5 YIHEYUAN ROAD

institute: collage of life science

summary: Aging is characterized by a chronic low-grade inflammation in multiple tissues, also termed as “inflammaging”, which represents a significant risk factor for many aging-related chronic diseases. However, the mechanisms and regulatory networks behind inflammaging across different tissues have not been fully elucidated. Here, by profiling transcriptomes and epigenomes of the kidney and liver from young and aged mice, we found that activation of inflammatory response was the conserved signature across tissues. Through integrative analysis, we revealed links between transcriptome change and chromatin dynamics, and identified AP-1 and ETS family transcription factors (TFs) were potential regulators of inflammaging. Further in-situ validation showed AP-1 was mainly activated in aged hepatic and renal cells, while enhanced ETS was almost caused by elevated infiltration of macrophages, indicating these TFs had different mechanisms in inflammaging. Functional data showed genetic knockdown of Fos, a major member of AP-1, significantly attenuated inflammatory response in aged kidneys and livers. Taken together, our analysis revealed conserved signatures and regulatory TFs of inflammaging in the kidney and liver, providing novel targets for the development of anti-aging interventions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for kidneys and livers from aged mice treated with shNT and shFOS.

first: Xiaojie

last: Yu

first: Yuting

last: Wang

first: Yifan

last: Song


title: ATAC-seq analysis of genetically engineered  mouse models (GEMMs) of PDA with  KRAS and TP53 mutations

first: chuanxin

last: wang

summary: We profile chromatin accessibility signals   in WT, KC and KPC mice of pancreatic cancer

overall_design: Accessible regions were obtained from WT, KC and KPC mice.

first: Shujun

last: Zhang


title: A Multi-Organoid Platform Identifies CIART as a Key Factor for SARS-CoV-2 Infection [CUT&RUN]

status: Public on Dec 07 2022

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: COVID-19 is a systemic disease involving multiple organs. Human pluripotent stem cells (hPSCs) derived organoids/cells provide insight into cellular tropism and host response, yet the molecular mechanisms regulating SARS-CoV-2 infection remain poorly defined. Here, we systematically examined changes in transcript profiles caused by SARS-CoV-2 infection at different MOIs for airway organoids (AWOs), alveolar organoids (ALOs) and cardiomyocytes (CMs), and identified several genes, including CIART, that are generally implicated in controlling SARS-CoV-2 infection. AWOs, ALOs, and CMs derived from isogenic CIART-/- hPSCs were significantly resistant to SARS-CoV-2 infection, independent of viral entry. Single-cell RNA-seq further validated the decreased levels of SARS-CoV-2 infection in multi-ciliated cells of AWOs. CUT&RUN, ATAC-seq and RNA-seq analyses found that CIART controls SARS-CoV-2 infection at least in part through regulating NR4A1, a gene also identified from the multi-organoid analysis. Finally, transcriptional profiling and pharmacological inhibition revealed that the Retinoid X Receptor (RXR) pathway regulates SARS-CoV-2 infection downstream of CIART/NR4A1. The multi-organoid platform provides potential therapeutic targets for protection against COVID-19 across organ systems.

overall_design: CUT&RUN was performed to identify downstream targets regulated by CIART in human pluripotent stem cells-derived cardiomyocytes.

first: Xuming

last: Tang

first: Dongxiang

last: Xue

first: Tuo


title: Bacterial meningitis in the early postnatal mouse studied at single-cell resolution

status: Public on Dec 27 2022

city: Baltimore

first: Amir

last: Rattner

state: MD - Maryland

address: 725 North Wolfe St.

institute: Johns Hopkins University

summary: Single nuclei RNAseq was used to study the cells comprising the mouse meninges and their response to bacterial infection.

overall_design: single nuclei RNA-seq were preformed on control and  E. coli infected  P6 mice meninges.

first: Jie

first: Jeremy

last: Nathans


title: HCT116_SMARCA4 ATAC-seq

city: Nanjing

first: Xiangwei

last: Zeng

state: Jiangsu

address: Xianlin avenue

institute: Nanjing university

summary: To investigate the effect of SMARCA4-R1157W mutant on chromatin accessibility, we performed ATAC-seq experiments in HCT116 cells.

overall_design: ATAC-seq for SMARCA4 in HCT116_SMARCA4-Wildtype and HCT116_SMARCA4-R1157W mutant cells

first: Jianpeng

last: Liu

first: Quan

last: Zhao


title: A Multi-Organoid Platform Identifies CIART as a Key Factor for SARS-CoV-2 Infection [ATAC-seq]

overall_design: WT and CIART-/- human pluripotentstem cells were differentiated into cardiomyocytes and used for ATAC-seq analysis.


title: Three-dimensional genome re-wiring in loci with Human Accelerated Regions

status: Public on Dec 21 2022

city: San Francisco

first: Katherine

middle: S

last: Pollard

address: 1650 Owens St

department: Institute of Data Science and Biotechnology

institute: Gladstone Institutes

summary: Human Accelerated Regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 251 mammalian genomes. Combining deep-learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains (TADs) containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design:
Two human (WTC11 and HS1) and two chimpanzee (C3649 and Pt2a) induced pluripotent cell lines (iPSCs) were cultured in Matrigel-coated plates with mTeSR media (WTC11 and C3649 were cultured in StemFlex) in an undifferentiated state. Cells were propagated at a 1:3 ratio by treatment with 200 U/mL collagenase IV (or PBS-EDTA) and mechanical dissection.

WTC11 and C3649 iPSCs were differentiated to neural progenitor cells (NPCs) and validated as previously described (24). Briefly, 2-2.5×10⁵ cells per cm² were seeded on Matrigel-coated wells in StemFlex containing 2 μM Thiazovivin. The following day (Day 0), medium was replaced with E6 containing 500 nM LDN193189 (Selleckchem), 10 μM SB431542 (Selleckchem), and 5 μM XAV-939 (Selleckchem). Starting on Day 3, medium was replaced with E6 containing 500 nM LDN193189 and 10 μM SB431542 every 48 hrs. Starting on Day 12, medium was replaced with Neurobasal containing 2 mM GlutaMAX, 60 μg per ml L-Ascorbic acid 2-phosphate, N2, and B27 without Vitamin A every 48 hours. Around Day 16, cells were washed with PBS, dissociated with Accutase, pelleted and resuspended in Neurobasal containing 2 mM GlutaMAX, 60 μg per ml L-Ascorbic acid 2-phosphate, N2, and B27 without Vitamin A, 10 ng per ml fibroblast growth factor 2, and 10 ng per ml epidermal growth factor, and seeded on poly-L-ornithine-, fibronectin-, and laminin-coated wells. Cells were collected for HiC at passage 5-7.

To differentiate HS1 and Pt2a iPSCs into NPCs, cells were split with EDTA at 1:5 ratios in culture dishes coated with matrigel and culture in N2B27 medium (comprised of DMEM/F12 medium (Invitrogen) supplemented with 1% MEM-nonessential amino acids (Invitrogen), 1 mM L-glutamine, 1% penicillin-streptomycin, 50 ng/mL bFGF (FGF-2) (Millipore), 1x N2 supplement, and 1 x B27 supplement without Vitamin A (Invitrogen)) supplemented with 100 ng/ml mouse recombinant Noggin (R&D systems). Cells at passages 1-3 were split by collagenase into small clumps, and continuously cultured in N2B27 medium with Noggin. After passage 3, cells were plated at the density of 5×10⁵ cells/cm² after disassociation by TrypLE express (Invitrogen) into single-cell suspension, and cultured in N2B27 medium supplemented with 20 ng/mL bFGF and EGF. Cells were maintained and collected at passage 18-20. Our use of two differentiation protocols reflects rapid progress in stem cell research during the course of this study. Cells from the same populations were validated and used in a previous study (24). We verified that the chromatin interactions in the resulting Hi-C data did not show a batch effect across protocols.

Hi-C was performed using the Arima Hi-C kit (Arima Genomics) according to the manufacturer’s instructions. 10 million cells were used. The sequencing library was prepared using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) according to the manufacturer's protocol. Two independent biological replicates were prepared for each cell line. In total eight libraries were pooled and sequenced with paired-end 150-bp reads using two lanes of a NovaSeq6000 S2 (Illumina) at the Chan Zuckerberg Biohub.

first: Kathleen

last: Keough

first: Sean

last: Whalen

first: Fumitaka

last: Inoue

first: Pawel

middle: F

last: Przytycki

first: Tyler

last: Fair

first: Hane

last: Ryu

first: Nadav

last: Ahituv

first: Alex

last: Pollen

first: Chengyu

last: Deng

first: Marilyn

last: Steyert

first: Kerstin

last: Lindblad-Toh

first: Elinor

last: Karlsson

first: Tomasz

last: Nowakowski


title: Genomic landscapes of ovarian clear cell carcinoma from Latin countries reveal aberrations linked to survival and progression

status: Public on Dec 14 2022

city: Ottawa

first: Martin

last: Roffe

state: ON

address: 401 Smyth Rd

institute: CHEO Research Institute

summary:
Background: Ovarian clear cell carcinomas (OCCCs) are rare, aggressive and chemoresistant tumors. Geographical and ethnic differences in the incidence of OCCC have been reported with a higher incidence in Asiatic countries. There is a paucity of information regarding OCCC in Latin America (LA) and other countries.

Methods: Here, we characterized two cohorts of 33 patients with OCCC from LA (24 from Brazil and 9 from Costa Rica) and a cohort of 27 patients from Spain. Genomic analysis was performed for 26 OCCC using the OncoScan platform. Tumors were classified according to their genomic landscapes into subgroups. Clinical parameters were related to the frequency of genomic aberrations.

Results: The median overall survival (OS) was not significantly different between the cohorts. Genomic landscapes were characterized by different homologous recombination deficiency (HRD) levels. No difference in the distribution of genomic landscapes profiles was detected between patients from the different cohorts. OCCCs with MYC-amplified tumors harboring a concomitant loss of a region in chromosome 13q12-q13 that includes the BRCA2 gene had the longest OS. In contrast, patients carrying a high number (> 30) of total copy number (CN) aberrations with no concomitant alterations in MYC and BRCA2 genes presented the shortest OS. Furthermore, amplification of the ASH1L gene was also associated with a shorter OS. Initial-stage OCCCs with early progression were characterized by gains in the JNK1 and MKL1 genes.

Conclusions: Our results provide new data from understudied OCCC populations and reveal new potential markers for OCCCs.

overall_design: Sixty patients older than 18 years old with a histological diagnosis of OCCC between 2000 and 2015 were recruited from institutions in three different countries: 7 patients from Hospital das Clínicas de Ribeirão Preto (HCRP) - Brazil; 17 patients from A.C.Camargo Cancer Center (ACCCC) - Brazil; 9 patients from Hospital México (HM) – Costa Rica; and 27 patients from Instituto Valenciano de Oncología (IVO) – Spain. Fifty-seven samples were obtained from the primary tumor, and 4 corresponded to metastatic tissue after recurrence. The samples were reviewed by two pathologists to confirm the diagnosis of pure OCCC histology. DNA extracted from 26 primary tumors and one recurrent tumor was subjected to the SNP array OncoScan® FFPE (Thermo)

first: Mariana

last: de Paiva Batista

first: Eduardo

middle: M

last: Rego


title: A Multi-Organoid Platform Identifies CIART as a Key Factor for SARS-CoV-2 Infection [scRNA-seq]

first: Shuibing

last: Chen

overall_design: WT and CIART-/- hPSC-AWOs were infected with mock or SARS-CoV-2 (MOI=0.1). Samples were collected at 24hpi.

first: Xuming

last: Tang

first: Dongxiang

last: Xue

first: Tuo

last: Zhang

first: Benjamin

last: Nilsson-Payant


title: Glioblastoma stem cells after RNF8 overexpression

status: Public on Dec 10 2022

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

summary: RNF8 is downregulated in glioblastoma and low RNF8 expression correlates with poor patient prognosis. Overexpression (OE) of RNF8 in glioblastoma stem cell (GSC) impairs its proliferation and tumorigenicity, and the anti-cancer effects of RNF8 are dependent on both its FHA and RING domains. Paradoxically, transcriptomic analysis of RNF8 OE GSC reveals cell cycle as the top upregulated pathway. Mechanistically, RNF8 interacts with the mitotic checkpoint protein MAD2 in a RING domain-dependent manner to induce spindle assembly checkpoint (SAC) activation. RNF8 OE GSC displays increase level of aneuploidy and micronuclei formation, suggesting that RNF8 promotes chromosomal instability (CIN) in GSC through persistent SAC activation.

overall_design: TS543 cells were transduced with either GFP vector or GFP RNF8 overexpression construct.

first: Xue

last: Tay

first: You

last: Chuah

first: Sek

last: Ong


title: RGS4 impacts carbohydrate and siderophore metabolism in Trichoderma reesei

status: Public on Dec 12 2022

city: Tulln

first: Miriam

last: Schalamun

address: Konrad Lorenz Strasse 24

country: Austria

institute: Austrian Institute of Technology

summary: We investigated the function of the SNX/H-type regulator of G-protein signaling (RGS) protein RGS4 and found alterations in enzyme regulation, stress response, siderophore production and metabolism of several carbon sources in light and darkness

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for Trichoderma reesei QM6a (WT) and deletion mutant QM6aΔrgs4
---------------------------
QM6a_transcript_seq.fa from Li WC, Huang CH, Chen CL, Chuang YC, Tung SY, Wang TF. Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters. Biotechnol Biofuels. 2017;10():170. doi: 10.1186/s13068-017-0825-x

first: Eva-Maria

last: Molin

first: Monika

last: Schmoll


title: A Multi-Organoid Platform Identifies CIART as a Key Factor for SARS-CoV-2 Infection.

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

overall_design: Refer to individual Series


title: Prominin-1 promotes restitution of the murine extrahepatic biliary luminal epithelium following cholestatic liver injury

status: Public on Dec 05 2022

first: Allen

middle: Charles

last: Zhong

address: 200 West 108th Street

institute: Icahn School of Medicine at Mount Sinai

summary: Restitution of the extrahepatic biliary luminal epithelium in cholangiopathies is poorly understood. Prominin-1 (Prom1) is a key component of epithelial ciliary body of stem/progenitor cells. Given that intrahepatic Prom1-expressing progenitor cells undergo cholangiocyte differentiation, we hypothesized that Prom1 may promote restitution of the extrahepatic bile duct (EHBD) epithelium following injury. Utilizing various murine biliary injury models, we identified Prom1-expressing cells in the peribiliary glands (PBGs) of the EHBD. These Prom1-expressing cells are progenitor cells which give rise to cholangiocytes as part of the normal maintenance of the EHBD epithelium. Following injury, these cells proliferate significantly more rapidly to re-populate the biliary luminal epithelium. Null mutation of Prom1 leads to significantly more than ten-fold dilated PBGs following rhesus rotavirus-mediated biliary injury. Cultured organoids derived from Prom1 knockout mice are comprised of biliary progenitor cells with altered apical-basal cellular polarity, significantly fewer and shorter cilia, and decreased organoid proliferation dynamics consistent with impaired cell motility. We, therefore, conclude that Prom1 is involved in biliary epithelial restitution following biliary injury in part through its role in supporting cell polarity.

overall_design: Biliary epithelial organoids were grown from murine wild-type and Prominin-1 (Prom1, CD133) knock-out extrahepatic bile ducts, which were then collected and then sequenced for gene expression.


title: High Fat Diet (HFD)-Induced Obesity Augments the Deleterious Effects of Estrogen Deficiency on Bone: Evidence from ovariectomized Mice.

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

summary: There is an increasing clinical evidence that obesity exerts deleterious effects on the skeleton. While obesity coexists with estrogen deficiency in postmenopausal women, their combined effects on the skeleton are poorly studied. Thus, we investigated the impact of high-fat diet (HFD) on bone and metabolism of ovariectomized (OVX) female mice (C57BL/6J). OVX or sham operated mice were fed either HFD (60%fat) or normal diet (ND) (10%fat) for 12 weeks. HFD-OVX group exhibited pronounced increase in body weight (~86% in HFD and ~122% in HFD-OVX, p<0.0005) and impaired glucose tolerance. Bone microCT-scanning revealed a pronounced decrease in trabecular bone volume/total volume (BV/TV) in HFD-OVX (15.6±0.48% in HFD and 37.5±0.235% in HFD-OVX, p<0.005) and expansion of bone marrow adipose tissue (BMAT) (+60.7±9.9% in HFD vs +79.5±5.86% in HFD-OVX, p<0.005). Mechanistically, HFD-OVX treatment led to upregulation of genes markers of senescence, bone resorption, adipogenesis and inflammation and downregulation of gene markers of bone formation and bone development. Similarly, HFD- OVX treatment resulted in significant changes in bone tissue levels of Purine/Pyrimidine and Glutamate metabolisms, known to play a regulatory role in bone metabolism. Obesity and estrogen deficiency exert combined deleterious effects on bone resulting in accelerated cellular senescence, expansion of BMAT and impaired bone formation leading to decreased bone mass. Our results suggest that obesity may increase bone fragility in post-menopausal women.

overall_design: Gene expression analysis in stromal progenitors from female wild type mice undergoing either  ovarioectomy,  high fat diet feeding or both.

first: Dalia

last: Ali

first: Florence

last: Figeac

first: Atenisa

last: Caci

first: Nicholas

last: Ditzel

first: Clarissa

last: Schmal

first: Greet

last: Kerckhofs

first: Jesper

last: Havelund

first: Nils

last: Færgeman

first: Michaela

last: Tencerova

first: Moustapha

last: Kassem


title: Targeting c-fos to suppresses metastasis in BRMS1v2 germline mutant lung adenocarcinoma patient derived cells

status: Public on Dec 01 2022

first: Yuan

last: Liu

address: 1275 York Avenue

country: USA

institute: Memorial Sloan Kettering Cancer Center

summary: Approximately 50% of patients with early-stage, surgically resected lung cancer will develop distant metastasis. There remains an unmet need to identify patients likely to develop recurrence and to design innovative therapies to decrease this risk. Two primary isoforms of BRMS1, v1 and v2 are present in humans. Using next generation sequencing of BRMS1 on matched human noncancerous lung tissue and NSCLC specimens we identified single-nucleotide polymorphism rs1052566 that results in an A273V mutation of BRMS1v2.  This SNP is  homozygous (BRMS1v2A273V/A273V) in 8% of the population and correlates with aggressive biology in lung adenocarcinoma (LUAD). Mechanistically we show that BRMS1v2 A273V abolishes the metastasis suppressor function of BRMS1v2 and promotes robust cell invasion and metastases by activation of c-fos-mediated gene-specific transcriptional regulation. Specifically, BRMS1v2 A273V increases cell invasion in vitro and increased metastases in both tail-vein injection xenografts and LUAD patient-derived organoid (PDO) intracardiac injection metastasis in vivo models. Moreover, we show that BRMS1v2 A273V fails to interact with nuclear Src, thereby activating intratumoral c-fos in vitro. Higher c-fos results in upregulation of CEACAM6, which drives metastases in vitro and in vivo. Using both xenograft and PDO metastasis models, we repurposed T5224, a c-fos pharmacologic inhibitor investigated in clinical trials for arthritis, and observed suppression of metastases in BRMS1v2A273V/A273V LUAD in mice. Collectively, we elucidate the mechanism of BRMS1v2A273V/A273V-induced metastases and offer a putative therapeutic strategy for patients with LUAD with this germline alteration.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of wild-type and isogenic cell lines with BRMS1v2 variant.
Comparative gene expression profiling analysis of RNA-seq data for WT, C1, and C2 cells.

first: Neel

last: Chudgar

first: Brooke

last: Mastrogiacomo

first: Di

last: He

first: Manendra

last: Lankadasari

first: Samhita

last: Bapat

first: Francisco

last: Sanchez-Vega

first: Kay

last: Tan

first: Nikolaus

last: Schultz

first: Semanti

last: Mukherjee

first: Kenneth

last: Offit

first: Yongdee

last: Bao

first: Matthew

middle: J

last: Bott

first: Natasha

last: Rekhtman

first: Prasad

last: Adusumilli

first: Bob

last: Li

first: Marty

middle: W

last: Mayo

first: David

middle: R

last: Jones


title: Specific exercise patterns generate an epigenetic molecular memory window that drives long-term memory formation and identifies ACVR1C as a bidirectional regulator of memory

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

summary: We utilized an unbiased RNA-sequencing approach to uncover genes in the dorsal hippocampus that are differentially expressed under conditions where exercise benefits are maintained throughout sedentary delay periods and enable the formation of long-term memory and synaptic plasticity. Engagement in different exercise parameters resulted in a diverse transcriptional profile as defined by differences in the number, pattern, and type of genes up and down-regulated. To identify genes that play a critical role in cognitive enhancement, we next focused our attention on exercise groups that enable robust long-term memory formation under inadequate subthreshold acquisition sessions of the hippocampus-dependent object location memory task. By intersecting up regulated genes when exercise facilitated learning, we identify potential regulators of learning and targets for memory enhancement. We identify a gene coding for a type 1 membrane receptor and kinase for the TGF-β family of signaling molecules, Acvr1c as one of few genes showing upregulation in conditions where exercise enabled the formation of long-term memory, indicating a gate-type role for Acvr1c in memory consolidation. In addition to overall gene expression levels, we identify potential regulators upstream of gene targets within the window for cognitive enhancement. Additionally, we use three complementary analyses to examine the mechanisms responsible for maintaining the ‘molecular memory window’ for exercise utilizing up regulated differentially expressed genes compared to sedentary controls. These analyses include: gene coexpression network analysis to identify potential hub genes for each exercise condition, predicted pathways altered by exercise, and gene ontology enrichment analysis of cellular components altered by exercise. Together, results identify Acvr1c as one of few genes up regulated only under conditions where exercise enabled the formation of long-term memory and synaptic plasticity, suggesting a role for Acvr1c in facilitation of memory consolidation. Follow up experiments manipulating ACVR1C function, find that it serves as an essential bidirectional regulator of long-term memory formation capable of alleviating impairments in hippocampus-dependent memory and synaptic plasticity associated with age and Alzheimer’s Disease.

overall_design:
We employed genome-wide RNA-sequencing to analyze transcriptional profiles underlying exercise-enhanced learning in the hippocampus. Adult male mice underwent different periods of exercise including: initial exercise (2 weeks), a sedentary delay period (1-2 weeks), and a brief 2-day period of reactivating exercise, followed by 3 min subthreshold training in an object location memory (OLM) task. We utilized these exercise parameters to examine effects of exercise on gene expression in the hippocampus occurring during memory consolidation, 1 hour following acquisition in a subthreshold version of the object location memory task (OLM).
Exercise Parameters (days of: initial exercise-sedentary delay-exercise re-introduction)
Harvest Cohort 1 or 2 (within 4 hour window, separated by 24hrs)

first: A

middle: A

last: Keiser

first: T

last: Dong

first: E

last: Kramár

first: C

last: Butler

first: S

first: D

middle: P

last: Matheos

first: J

last: Beardwood

last: Al-Shammari

first: V

last: Vera

first: L

last: Tong

first: N

last: Berchtold

first: M

last: Samad

last: Magnan

last: Shanur

first: P

last: Baldi

last: Cotman

last: Wood


title: Muscle-specific cellular and molecular adaptations to late-life voluntary concurrent exercise in mice [NovoGene]

city: Lexington

first: Yuan

last: Wen

state: Kentucky

address: 760 Press Ave

institute: University of Kentucky

summary: Aged mice (22-24 mo) underwent Progressive weighted wheel running (PoWeR) for 8 weeks. RNA-seq on soleus and plantaris muscles was conducted on untrained and PoWeR trained mice. RNA from soleus and plantaris of young mice (4-6 months old) was used as a comparator (Englund et al. 2021 Function)

overall_design: Mice underwent PoWeR for 8 weeks, and age-matched sedentary mice served as controls. Mice were euthanized after an overnight fast and 24 hour wheel lock for PoWeR mice. RNA from soleus and plantaris was isolated and sequenced at NovoGene.

first: Kevin

last: Murach

first: Chris

last: Fry

first: Cory

last: Dungan


title: Altered gene expression in plasma of patients with pneumonia-induced sepsis compared to pneumonia without sepsis and healthy people

status: Public on Nov 30 2022

city: Shanghai

first: Dianyin

last: Yang

address: 150, Jimo Road, Pudong District

institute: Shanghai East hospital

summary: To investigate the differentially expressed genes in the plasma of pneumonia-induced sepsis patients compared to pneumonia patients without sepsis and healthy people, we performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the plasma from healthy people, pneumonia patients without sepsis and pneumonia-induced sepsis patients

first: Lunxian

last: Tang

first: Dongyang

last: Zhao

first: Jinlu

last: Ji


title: Deciphering the functions of Stromal Interaction Molecule-1 in Amelogenesis using Amelx-iCre mice

city: Saskatoon

first: Raed Samir

last: Said

state: SK

address: University of Saskatchewan 107 Wiggins Road, S7N 5E5 Saskatoon, Canada

institute: University of Saskatchewan

summary:
STIM1 is an ER transmembrane protein that serve as the main intracellular calcium (iCa2+) sensors in several mammalian cells. Humans with mutated STIM1 present with severely defective enamel which suggests a critical role of STIM1 protein in enamel formation.
We  established an ameloblast specific (Amelx-iCre) Stim1 conditional deletion mouse model (Stim1 cKO). RNAseq  on micro-dissected ameloblasts from  4 weeks old mice  to evaluate changes in the gene expression levels of several key ameloblast genes.

overall_design:
Whole incisor enamel organ (EO) cell populations of 4 week old mice were extracted from 3 samples; 1 Stim1 cKO sample with complete deletion of Stim1, 1 Stim1 Heterozygous (Stim1 Het) sample with heterozygous deletion of one Stim1 allele and 1 sample with no Stim1 deletion as it was Cre negative.
The Stim1 Het and Cre negative samples were used as controls. RNAseq libraries were prepared and loaded on the HiSeq 2500 high output Sequencing System (Illumina).

first: Said

last: Raed

first: Mortazavi

last: Helyasadat


title: A Multi-Organoid Platform Identifies CIART as a Key Factor for SARS-CoV-2 Infection [bulk RNA-seq]

first: Shuibing

last: Chen

overall_design: RNA-seq was used to systematically profile transcriptional changes of hPSC-derived airway organoids, alveolar organoids and cardiomyocytes caused by SARS-CoV-2 infection.

first: Xuming

first: Dongxiang

last: Xue

first: Tuo

last: Zhang

first: Benjamin

last: Nilsson-Payant


title: Dynamics and variability of transcriptomic dysregulation in congenital myotonic dystrophy during childhood development

status: Public on Nov 17 2022

city: Richmond

first: Nicholas

middle: E

last: Johnson

state: VA

address: 1101 E Marshall St

institute: Virginia Commonwealth University

summary: Myotonic dystrophy type 1 (DM1) is the most common form of adult-onset muscular dystrophy caused by expansion of a CTG repeat microsatellite within DMPK. In 10-20% of individuals with DM1, symptomatic onset begins at birth; these patients are classified as congenital myotonic dystrophy (CDM). While dysregulation of RNA metabolism, specifically alternative splicing, has been linked to disease pathology in adult-onset DM1, little is known about the mechanism of CDM. Biopsies from individuals (CDM), age range 0.04-16 years, were subjected to total RNA-seq to quantify the transcriptomic dysregulation throughout pediatric development. To achieve this, they were compared against age matched pediatric controls which revealed a triphasic pattern of dysregulation not before seen observed in CDM. CDM samples were also compared to adult-onset (DM1) individuals which showcased a shared disease signature to seen in all individuals with myotonic dystrophy irrespective of disease age of onset.

overall_design:
Total RNA-seq on 36 skeletal muscle biopsies collected from CDM individuals, 22 adult biopsies from individuals with adult-onset DM1, 7 unaffected adult controls (AdCo), and 21 unaffected pediatric controls (PeCo). Biopsies were subjected to RNA-seq and analyzed for alternative splicing and gene expression changes.

Updates: [07-28-2023] The sex characteristics was changed for GSM6056748, and the age characteristics was changed for GSM6056756, GSM6056763, GSM6056766, GSM6056768, GSM6056770, GSM6056774, and GSM6056775.

first: Kameron

last: Bates

first: Melissa

last: Hale

first: Marina

last: Provenzano


title: Batch effect during human bone marrow stromal cell propagation prevails donor variation and culture duration impact on phenotype, transcriptome and function [RNA-seq]

status: Public on Nov 04 2022

city: Salzburg

first: Rodolphe

last: Poupardin

address: Strubergasse 22

summary: Donor variation is a prominent critical issue limiting applicability of cell-based therapies. We asked whether reference protocols for pre-clinical bone marrow stromal cell (BMSC) propagation using human platelet lysate (hPL) to replace xenogeneic fetal bovine serum (FBS) might also reduce donor variability for osteo-chondral regeneration. We therefore investigated the impact of donor variability, hPL- vs FBS driven propagation and exhaustive proliferation, on BMSC epigenome, transcriptome, phenotype, coagulation risk and osteochondral regenerative function. Polychromatic flow cytometry revealed maintained canonical fibroblastic phenotype in all cells tested. We confirmed significantly declining proliferative potential in FBS-expanded BMSC after proliferative challenge. Notably, BMSC propagation under the aegis of hPL, compared to FBS, significantly increased BMSC proliferation, created significantly different gene expression trajectories and diverging surface marker signatures, already after just one culture passage. We observed limited but measurable effects on DNA methylation irrespective of culture duration. Moreover, expansion under xenogenic serum conditions resulted in significant loss of function during 3D cartilage organoid-like disk formation and significantly increased clotting risk. Superior chondrogenic function under hPL conditions was maintained over culture duration. As an additional observation, platelet blood group and isoagglutinin levels showed phenotypic changes but only minor impact on BMSC chondrogenesis and clotting behaviour.

overall_design: RNA-seq analysis of Bone marrow derived Mesenchymal stromal cells from four different donors cultivated in either FBS medium or hPL at two different passages (p1 and p4/5)

first: Dirk

last: Strunk


title: Batch effect during human bone marrow stromal cell propagation prevails donor variation and culture duration impact on phenotype, transcriptome and function


title: Identification of altered miRNAs and their targets in Placenta Accreta

status: Public on Nov 01 2022

city: Jena

first: Emanuel

last: Barth

address: Leutragraben 1

department: Bioinformatics Core Facility FSU Jena

country: Germany

institute: Friedrich Schiller University Jena

summary: We aim to elucidate regulatory miRNA and target networks contributing to Placenta accreta spectrum  development using smallRNA-Seq.

overall_design: Following grades were included for small RNA-Seq expression comparison: accreta; increta; percreta.   Tissue samples (≤ 0.5 cm in any single dimension) were taken from central areas of control placentas (NP) and adherent tissue in Placenta Accreta Spectrum samples (PA).

first: José

last: Murrieta-Coxca

first: Paulina

last: Fuentes-Zacarias

first: Ruby

middle: N

last: Gutiérrez-Samudio

first: Tanja

last: Groten

first: Alexandra

last: Gellhaus

first: Angela

last: Köninger

first: Manja

last: Marz

first: Udo

last: Markert

first: Diana

last: Morales-Prieto


title: Branch point evolution controls species-specific alternative splicing and regulates long term potentiation

status: Public on Dec 02 2022

city: Berlin

first: Andreas

last: Franz

state: Berlin

address: Tarkustraße 6

department: Institut fuer Chemie, Biochemie, Pharmazie

institute: Freie Universität Berlin

summary: Regulation and functionality of species-specific alternative splicing has remained enigmatic for many years. Calcium/calmodulin-dependent protein kinase IIβ (CaMKIIβ) is expressed in several splice variants and plays a key role in learning and memory. Here, we identify and characterize several primate-specific CAMK2B splice isoforms, which show altered kinetic properties and changes in substrate specificity. Furthermore, we demonstrate that primate-specific Camk2β alternative splicing is achieved through branch point weakening during evolution. We show that reducing branch point and splice site strength during evolution globally renders constitutive exons alternative, thus providing a paradigm for cis-directed species-specific alternative splicing regulation. Using CRISPR/Cas9 we introduced the weaker human branch point into the mouse genome, resulting in human-like CAMK2B splicing in the brain of mutant mice. We observe a strong impairment of long-term potentiation in CA3-CA1 synapses of mutant mice, thus connecting branch point-controlled, species-specific alternative splicing with a fundamental function in learning and memory.

overall_design: A mouse model of humanized Camk2b alternative splicing was generated. Cerebellum tissue was extracted from the wild type strain (C57Bl/6) and heterozygous and homozygous mice of the mouse model. Total RNA was extracted using RNATri (Bio&Sell).

first: Markus

last: Wahl

first: Marco

last: Preussner

first: Florian

last: Heyd


title: Batch effect during human bone marrow stromal cell propagation prevails donor variation and culture duration impact on phenotype, transcriptome and function [MethylCap-seq]

overall_design: MethylCap-seq analysis of Bone marrow derived Mesenchymal stromal cells from four different donors cultivated in either FBS medium or hPL at two different passages (p1 and p4/5)


title: Gramd2+ alveolar type I cells can give rise to Kras-induced lung adenocarcinoma

status: Public on Oct 19 2022

city: Duarte

first: Crystal

last: Marconett

email: cmarcone@usc.edu, cmarconett@coh.org

address: 1500 E Duarte Rd

department: Integrative Translational Sciences

institute: City of Hope

summary: Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer and arises in the distal lung. LUAD encompasses several pathologic subtypes, including solid, lepidic, papillary, micropapillary, acinar and mixed subtypes, each with differing clinical outcomes or biological behavior. Specifically, lepidic histology is associated with improved survival relative to other LUAD histologies. Yet, the molecular and cellular underpinnings of these subtypes are largely unknown. Understanding which cell populations in the distal lung contribute to LUAD could provide insights for the marked heterogeneity in LUAD pathologic features, clinical presentation and responses to therapy.Recent studies have seen tumor-derived epithelial cells with an AT1 transcriptomic cell signature, suggesting AT1 cells may contribute to a subset of LUAD cases. We tested the ability of AT1 cells to give rise to LUAD by inducing KrasG12D, a known oncogenic driver in human LUAD. Activation of KrasG12D in Gram-domain containing 2 (Gramd2)+ AT1 cells gave rise to multiple LUAD lesions, primarily of papillary histology. In contrast, activation of KrasG12D in Sftpc+ AT2 cells resulted in LUAD lesions of lepidic histology. Immunohistochemistry established Gramd2:KrasG12D lesions were of primary lung origin and not metastatic events. Spatial transcriptomic profiling revealed distinct pathway alterations occurring within Gramd2- and Sftpc-derived LUAD. Immunofluorescence confirmed differences observed in the Spatial transcriptomic analysis in expression patterns and distribution of cell-specific markers between cell of origin, while universal upregulation of the Krt8 intermediate cell state marker was observed. Our results are consistent with Gramd2+ AT1 cells serving as a putative cell of origin for LUAD and suggest that LUAD may be a collection of adenocarcinomas that share a common location within the distal lung, but which arise from different cells of origin.

overall_design: Spatial transcriptomic profiling was performed at the Molecular Genomics Core, a part of the Norris Comprehensive Cancer Center and under manufacturer’s instructions. Briefly, three biological replicates (one block per mouse) of Gramd2:KrasG12D and Sftpc:KrasG12D underwent initial 10μM sectioning at the Tissue Pathology Core, part of the Norris Comprehensive Cancer Center. Sections were H&E stained (as above) and underwent pathology review. Regions of Interest (ROIs) then underwent sample preparation including test slide sample sequencing using the Visium Tissue Section Test Slide (PN-2000460, 10X Genomics, Dublin, CA, USA). H&E overlapping spatial transcriptomic regions was generated as part of the Cytassist pipeline. RNA quality assessment of test slides was determined by first extracting RNA using the Qiagen RNeasy FFPE kit (#73504, Qiagen, Hilden, Germany) and measuring RNA concentration using a Qubit fluorometer (#Q33238, ThermoFisher Scientific, Waltham, MA, USA). To determine The percentage of total fragments >200nt in length was determined by running the samples using a 4200 Tapestation (#G2991AA, Agilent, Santa Clara, CA). Once samples were determined to be of high enough quality to continue, 5μM FFPE sections were then placed in a 42C water bath and once rehydrated adhered to the Visium Spatial Gene Expression Slide (PN-2000233, 10X Genomics). Subsequently, samples were dried at 42C for 3hrs in a desiccation chamber and underwent deparrafinization using Qiagen Deparaffinization Solution (Cat # 19093) at 60C for 2 hr. Subsequently H&E staining (#MHS16, #HT110116 Millipore Sigma, Burlington MA, USA) was performed according to Visium technical parameters (CG000409) and images were captured with a Zeiss Axioscan2 microscope using a 10x objective. Decrosslinking was performed according to 10X standard protocol (CG000407) and immediately hybridized to the Visium Mouse Transcriptome probe set V1.0, which contained 20,551 genes targeted by 20,873 probes. Post-probe extension, sequencing library construction was performed using unique sample indices using the Dual Index Kit TS, Set A (PN-1000251) for Illumina-compatible sequencing. Paired-end sequencing (2x100) was performed on an Illumina instrument. Sequencing data was pre-processed using the Space Ranger pipelines (10x Genomics, https://cloud.10xgenomics.com/cloud-analysis). BCL data was demultiplexed and converted to FASTQ format using the spaceranger mkfastq pipeline. The spaceranger count pipeline was then used for read alignment to mouse genome reference mm10, Unique Molecular Identifier (UMI) counting, and generation of feature-spot matrices corresponding to the microscopic tissue image. The pipeline also performs automatic tissue detection and fiducial alignment from the image.

first: Minxiao

last: Yang

first: Hua

last: Shen

first: Per

last: Flodby

first: Michael

middle: D

last: Koss

first: Rania

last: Bassiouni

first: Yixin

last: Liu

first: Tea

last: Jashashvili

first: Aaron

last: Neely

first: Ezuka

last: Ogbolu

first: Jonathan

last: Castillo

first: Theresa

last: Stueve

first: Daniel

last: Mullen

first: Amy

middle: L

last: Ryan

first: John

last: Carpten

first: Alessandra

last: Castaldi

first: W

last: Wallace

first: Beiyun

last: Zhou

first: Zea

last: Borok


title: Early biomarkers of renal damage due to prolonged exposure to embedded metal.

first: Yuan

last: Wen

summary: Background: Prolonged exposure to toxic heavy metals leads to deleterious health outcomes such as kidney injury and irreversible progression to chronic kidney disease. For example, veterans return from the battlefield with increasing amounts of retained metal fragments. Certain community water sources in the US are contaminated with varying levels of heavy metals, including uranium and lead. One of the key challenges is to detect damage to kidney tissue before glomerular filtration rate is affected. Methods: High-throughput transcriptomics (HTT) has recently been demonstrated have high sensitivity and specificity as a rapid and cost-effective assay for detecting tissue toxicity. To better understand the molecular signature of early kidney damage, we performed RNA-seq analysis on renal tissue using a rat model of soft tissue-embedded metal exposure. We them performed small RNA-seq analysis on serum samples from the same animals in an effort to identify miRNA biomarkers of kidney damage. Results: We found that metals, especially lead and depleted uranium, induces oxidative damage that  mainly cause dysregulated mitochondrial gene expression. Utilizing publicly available single-cell RNA-seq datasets, we demonstrate that deep learning-based cell type decomposition effectively identified cells within the kidney that were affected by metal exposure. By combining random forest feature selection and statistical methods, we further identify miRNA-423 as a promising early systemic marker of kidney injury. Conclusion: Our data suggests that combining HTT and deep learning represents a promising approach for identifying cell injury in kidney tissue. We propose miRNA-423 as a potential serum biomarker for early detection of kidney injury.

overall_design: We investigated the effects of tungsten (W), cobalt (Co), aluminum (Al), lead (Pb), and depleted uranium (DU) compared to inert metal tantalum (Ta). Rats were randomly assigned to one of the metal implant groups (n=8/group). All metal “pellets” were cylinders 1 mm in diameter x 2 mm in length. We performed RNA sequencing on kidney samples embedded with W, Co, Al, Pb, DU, and Ta 12 months post-implant surgery.

first: Wen

last: Yuan

first: Charlotte

last: Peterson

last: McCarthy