title: TFE3-splicing factor fusions represent functional drivers and druggable targets in translocation renal cell carcinoma

status: Public on Sep 01 2023

city: Indianapolis

first: Ricardo

last: Cordova

state: IN

address: 635 Barnhill Drive, MS4067

institute: Indiana University School of Medicine

summary: TFE3 is a member of the basic helix-loop-helix leucine zipper MiT transcription factor family and its chimeric proteins are associated with translocation renal cell carcinoma (tRCC). Despite the variety of genes fusions, most of TFE3 fusions partner genes are related to spliceosome machinery. Dissecting the function of TFE3 fused to spliceosome machinery factors (TFE3-SF) could direct the development of effective therapies for this lethal disease, which is refractory to standard treatments for kidney cancer. Here, by using a combination of in silico structure prediction, transcriptome profiling, molecular characterization, and high-throughput high-content screening (HTHCS) we interrogated a number of oncogenic mechanisms of TFE3-SF-containing fusions. We demonstrate that inhibition of TFE3-SF dimerization reverses its oncogenic activity and represents a potential new target for therapeutic intervention.  Using HTHCS combined with FRET technology, we screened the FDA approved drugs library LOPAC and a small molecule library (Microsource) and identified compounds that inhibit TFE3-SF dimerization. Hit compounds were validated in 2D and 3D models utilizing patient derived xenolines and xenografts expressing TFE3-SF. The antihistamine terfenadine demonstrated decreased cell proliferation and reduced in vivo tumor growth. Overall, our results unmask synthetic vulnerabilities of TFE3-SF dimerization for novel therapeutic strategies in patients with this aggressive type of kidney cancer.

overall_design: Transcriptomic analysis was performed by RNA-seq in HEK293 cells expressing mRuby2 (Rb), SFPQmRuby2 (S), NONOmRuby2 (N), PRCCmRuby2 (P), TFE3mRuby2 (E), PRCCTFE3mRuby2 (PE),  SFPQTFE3mRuby2 (SE) or NONOTFE3mRuby2 (NE). RNAseq was also performed on IU-115 and IU-118 PDX tumors.

first: Nur

last: Damayanti

first: Christopher

last: Rupert

first: Ilaria

middle: D

last: Fontane

last: Shen

first: Sabrina

last: Orsi

first: Angela

last: Klunk

first: W

last: Linehan

first: Kirk

last: Staschke

first: Peter

last: Hollenhorst

first: David

last: Heppner

first: Roberto

last: Pili


title: FSHβ links photoperiodic signalling in the mediobasal hypothalamus and pituitary gland to seasonal reproduction in Japanese quail.

status: Public on Sep 04 2023

city: Glasgow

first: Tyler

last: Stevenson

address: Jarrett building

country: United Kingdom

institute: University of Glasgow

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: FSHβ links photoperiodic signalling in the mediobasal hypothalamus to seasonal reproduction in Japanese quail.

summary: Annual cycles in daylength provide an initial predictive environmental cue that plants and animals use to time seasonal biology. Seasonal changes in photoperiodic information acts to entrain endogenous programs in physiology to optimize an animal’s fitness. Attempts to identify the neural and molecular substrates of photoperiodic time measurement in birds have, to date, focussed on blunt changes in light exposure during a restricted period of photoinducibility. The objectives of these studies were first to characterise a molecular seasonal clock in Japanese quail and second, to identify the key transcripts involved in endogenously generated interval timing that underlies photosensitivity in birds. We hypothesized that the mediobasal hypothalamus (MBH) provides the neuroendocrine control of photoperiod-induced changes in reproductive physiology, and that the pars distalis of the pituitary gland contains an endogenous internal timer for the short photoperiod dependent development of reproductive photosensitivity. Here we report distinct seasonal waveforms of transcript expression in the MBH, and pituitary gland and discovered the patterns were not synchronized across tissues. Follicle-stimulating hormone-β (FSHβ) expression increased during the simulated spring equinox, prior to photoinduced increases in prolactin, thyrotropin-stimulating hormone-β and testicular growth. Diurnal analyses of transcript expression showed sustained elevated levels of FSHβ under conditions of the spring equinox, compared to autumnal equinox, short (<12L) and long (>12L) photoperiods. FSHβ expression increased in quail held in non-stimulatory short photoperiod, indicative of the initiation of an endogenously programmed interval timer. These data identify that FSHβ establishes a state of photosensitivity for the external coincidence timing of seasonal physiology. The independent regulation of FSHβ expression provides an alternative pathway through which other supplementary environmental cues, such as temperature, can fine tune seasonal reproductive maturation and involution.

overall_design: Male quail (N=54) were housed in a summer-like long-day (LD) photoperiod (16L:8D). To mimic the autumnal decline and subsequent spring increase in the annual photoperiodic cycle, birds were exposure to a sequential change in day length from 16L, to 14L, to 12L, to 10L, to 8L, then back to 10L, to 12L, to 14L and lastly 16L (Fig.1a). Each photoperiod treatment lasted for 2 weeks to minimize the impact of photoperiodic history effects (Stevenson et al., 2012a). At the end of each photoperiodic treatment a subset of quail (n=6) body mass was used as a measure to pseudo randomly select birds for tissue collection. Brain and pituitary stalk were rapidly dissected, frozen on powdered dry ice and stored at -80°C. RNA was extracted from the MBH and Oxford Nanopore Flow cells used to sequence the transcriptomes from individual birds

first: Calum

last: Stewart

first: Gaurav

last: Majumdar


title: Single-cell transcriptomic analysis of corneal organoids during development

status: Public on Sep 06 2023

city: Stanford

first: Ragini

last: Phansalkar

address: 291 Campus Drive

country: USA

institute: Stanford School of Medicine

summary: Corneal organoids are useful tools for disease modeling and tissue transplantation however they have not yet been well studied during maturation. We characterized human iPSC derived corneal organoids at 1, 2, 3 and 4 months of development using single-cell RNA sequencing to determine the cellular heterogeneity at each stage. We found pluripotent cell clusters committed to epithelial cell lineage at 1 month early corneal epithelial, endothelial and stromal cells markers at 2 months, keratocytes as the largest cell population at 3 months, and a large epithelial cell population at 4 months. We compared organoid to fetal corneal development at different stages and found that 4 month organoids closely resemble the corneal cellular complexity of the fetal (16 post conception week) and adult cornea. Using RNA velocity pseudotime trajectory analysis, we found that eye field primordial cells and limbal stem cells appear to give rise to corneal epithelial cells during development.

overall_design: Corneal organoids were characterized at 1, 2, 3 and 4 months during development using single cell RNAseq

first: Aditi

last: Swarup

first: Maurizio

last: Morri

last: Agarwal

first: Varun

last: Subramaniam

first: BaoXiang

last: Li

first: Albert

middle: Y

last: Wu


title: Dietary cystine restriction increases the proliferative capacity of the small intestine of mice

city: Utrecht

first: Saskia

middle: van

last: Mil

address: Universiteitsweg 100

department: Center for Molecular Medicine

country: Netherlands

institute: UMC Utrecht

summary: Cysteine is a semi-essential amino acid provided by dietary intake of mainly meat, eggs and whole grains or via the amino acid methionine. The majority of dietary cystine is absorbed in the small intestine and can be used for protein synthesis or converted to taurine and glutathione. Since there is a trend towards adopting a vegetarian/vegan diet, which is low in cysteine, in this study, we investigate the effect of dietary cystine restriction on intestinal epithelial layer function. Mice (8/group) received a normal diet or a diet low in cystine for 2 weeks. We observed no changes in plasma methionine, cysteine, taurine or glutathione levels after 2 weeks. Stem cell markers as well as the proliferation marker Ki67 were or tended to be increased upon cystine restriction. Gene set enrichment analysis reveals enrichment of Wnt signaling in the small intestine of mice on the low cystine diet. These proliferative effects were not observed in the colon, and are thus specific for the small intestine. In the colon, we observed that dietary cystine restriction results in an increase in the number of goblet cells but no significant changes in the thickness of the mucus barrier or in its protective capacity. There was no difference in the microbiome between the normal and low cystine diet. Overall, we cannot conclude if dietary cystine restriction is beneficial, since increased proliferation and goblet cells can indicate a potential for damage repair, nevertheless hyperproliferation has the potential to induce cancer as well.

overall_design: To identify whether dietary cystine restriction would induce differences in gene expression in small intestine, RNA was isolated from tissue and send for sequencing. 3 mice for low cysteine and 4 mice for ctrl/normal cysteine were used.

first: Judith

middle: C

last: de Jong

first: Noortje

last: Ijssennagger

middle: W

last: van Mil


title: Discrete chromatin alterations and deregulated gene expression upon PROTAC-induced rapid loss of the trithorax protein ASH2L [RNA-Seq]

status: Public on Sep 12 2023

city: Aachen

first: Mirna

last: Barsoum

state: North Rhine Westphalia

address: Pauwelsstrasse 30

department: Institute of Biochemistry and Molecular Biology

country: Germany

institute: Uniklinik RWTH Aachen

summary: The trithorax protein ASH2L is essential for organismal and tissue development and for cell proliferation. ASH2L is a subunit of KMT2/COMPASS methyltransferase complexes that catalyze the methylation of histone H3 lysine 4 (H3K4). Tri- and mono-methylation of H3K4 (H3K4me3 and H3K4me1) are associated with active promoters and enhancers, respectively. The molecular relevance of these modifications is not fully understood. We have used mouse embryo cells with a PROTAC-sensitive, degradable ASH2L to assess the functional consequences of KMT2 complex inactivation. The rapid loss of ASH2L resulted in a sequential alterations of histone marks at promoters, first a decrease of H3K4me3, then an increase of H3K4me1, and a decrease of H3K27ac during the first 16 hrs, while an increase in H3K27me3 was very slow. These consequences were most prominent at CpG island promoters within a window of ±1 kb of the transcription start sites. Despite the the rapid loss of ASH2L, the effect on transcription in the first 8 hrs was minimal. This was accompanied with an alterations in gene expression and associated proliferation stop and cell cycle arrest. These findings suggest an order series of events upon loss of ASH2L that requires considerable amount of time to unfold.

overall_design: We have generated a conditional knockout mouse, in which we can delete exon 4 of Ash2l. This prevents production  of Ash2l protein, however due to the long half-life of Ash2l, it requires days before the protein is depleted. From these animals we established mouse embryo fibroblasts (MEF). Upon knockout of the endogenous alleles, the cells stop proliferating and enter senescence. We have now introduced into these cells a construct that expresses an FKBP-ASH2L fusion protein. Upon knockout of the endogenous alleles, the MEF cells proliferate dependent on FKBP-ASH2L. We find that this fusion protein is sensitive to PROTACs (Proteolysis Targeting Chimeras) and is degraded by more than 99% within 30 minutes after addition  of a PROTAC.

first: Roksaneh

last: Sayadi Boroujeni

first: Alexander

middle: T

last: Stenzel

first: Philip

last: Bussmann

first: Juliane

last: Lüscher-Firzlaff

first: Bernhard

last: Lüscher


title: Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina [snRNA-seq]

status: Public on Aug 31 2023

city: Baltimore

first: Pin

last: Lyu

address: 400 N Broadway

institute: JHU

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Following acute retinal damage, zebrafish possess the ability to regenerate all neuronal subtypes. This regeneration requires Müller glia (MG) to reprogram and divide asymmetrically to produce a multipotent Müller glia-derived neuronal progenitor cell (MGPC). This raises three key questions.  First, does loss of different retinal cell subtypes induce unique MG regeneration responses? Second, do MG reprogram to a developmental retinal progenitor cell state? And finally, to what extent does regeneration recapitulate retinal development? We examined these questions by performing single-nuclear and single-cell RNA-Seq and ATAC-Seq in both developing and regenerating retinas. While MG reprogram to a state similar to late-stage retinal progenitors in developing retinas, there are transcriptional differences between reprogrammed MG/MGPCs and late progenitors, as well as reprogrammed MG in outer and inner retinal damage models. Validation of candidate genes confirmed that loss of different subtypes induces differences in transcription factor gene expression and regeneration outcomes. This work identifies major differences between gene regulatory networks activated following the selective loss of different subtypes of retina neurons, as well as between retinal regeneration and development.

overall_design: To investigate the molecular mechanisms controlling injury-induced neurogenesis, we performed both single-cell RNA-Seq (scRNA-Seq) and single-nuclei RNA-Seq (snRNA-Seq) and ATAC-Seq multiomic analysis to comprehensively profile injury-induced changes in gene expression and chromatin accessibility seen in both injury models, and to determine how closely these MGPCs resembled retinal progenitor cells (RPCs) in developing retinas.

first: Maria

last: Iribarne

first: Dmitri

last: Serjanov

first: Yijie

last: Zhai

first: Thanh

last: Hoang

first: Jiang

last: Qian

first: David

middle: R

last: Hyde

first: Seth

last: Blackshaw


title: A Proteomic Atlas of Atherosclerosis: The Contribution of Proteoglycans to Sex Differences, Plaque Phenotypes and Outcomes

status: Public on Aug 29 2023

city: London

first: Konstantinos

last: Theofilatos

address: 125 Coldharbour Lane

institute: King's CollegeLondon

summary: Background. Using proteomics, we aimed to reveal molecular types of humanatherosclerotic lesions and study their associations with histology, imaging andcardiovascular outcomes. Methods. 219 carotid endarterectomy samples were procured from 120 patients. A sequential protein extraction protocol was employed in conjunction with multiplexed, discovery proteomics. To focus on extracellular proteins, parallel reaction monitoring was employed for targeted proteomics. Proteomic signatures were integrated with bulk, single-cell, and spatial  RNA-sequencing data, and validated in 200 patients from the Athero-Express Biobank study. Results. This extensive proteomics analysis identified plaque inflammation and calcification signatures, which were inversely correlated and validated using targeted proteomics. The inflammation signature was characterized by the presence of neutrophil-derived proteins, such as S100A8/9 and myeloperoxidase, while the calcification signature included fetuin-A, osteopontin, and gamma-carboxylated proteins. The proteomics data also revealed sex differences in atherosclerosis, with large-aggregating proteoglycans versican and aggrecan being more abundant in females and exhibiting an inverse correlation with estradiol levels. The integration of RNA sequencing data attributed the inflammation signature predominantly to neutrophils and macrophages, and the calcification and sex signatures to smooth muscle cells, except for certain plasma proteins that were not expressed but retained in plaques, such as fetuin-A. Dimensionality reduction and machine learning techniques were applied to identify four distinct plaque phenotypes based on proteomics data. A protein signature of 4 key proteins (calponin, protein C, serpin H1, and versican) predicted future cardiovascular mortality with an area under the curve of 75% and 67.5% in the discovery and validation cohort, respectively, surpassing the prognostic performance of imaging and histology. Conclusions. Plaque proteomics redefined clinically relevant 55 patient groups with distinct outcomes, identifying subgroups of male and female patients with elevated risk of future cardiovascular events.

overall_design: Visium for formalin-fixed paraffin-embedded (FFPE) spatial gene expression slide and reagent kit was used according to manufacturer instructions (PN: 1000338; 10X Genomics). Each capture area (6.5 x 6.5 mm2) contains 5,000 barcoded spots that are 55 μm in diameter (100 μm center-to-center distance) providing an average resolution of 1 to 10 cells. A 5μm tissue section from one carotid plaque sample was placed onto one capture area of a Visium Spatial Gene  Expression slide. Two carotid plaque samples were selected from Asymptomatic male patients who undergone carotid endrarterectomy for spatial RNA-seq. Deparaffinization, DAPI immunofluorescence staining, image acquisition and decrosslinking were performed as specified in the Visium Spatial Gene Expression for FFPE – Deparaffinization, Decrosslinking, Immunofluorescence Staining & Imaging protocol (CG000410) and performed at the Core Facility Imaging, Medical University of Vienna. Fluorescent images were acquired with an Olympus IX83 microscope equipped with a Hamamathsu Orca FLash camera for fluorescence image capture. and parameters following those specified in the Visium Spatial Gene Expression Reagent Kits for FFPE User Guide sequencing instructions (read 1: 28 cycles; i7 index read: 10 cycles; i5 index read: 10 cycles; and read 2: 50 cycles) yielding 149 million sequenced reads. The FASTQ files and the manually aligned histology images were analyzed with Space Ranger 1.3.1 and the human probeset provided by 10X genomics (Visium Human Transcriptome Probe Set v1.0 GRCh38-2020-A). Visualization of spatial cluster output from Space Ranger as well as differential gene expression analysis to determine cluster- pecific up- or downregulated genes was performed on Loupe Browser 6.0.0 (10X Genomics).

first: Stefan

last: Stojkovic

last: Hasman

first: Sander

last: van der Laan

first: Ferheen

last: Baig

first: Javier

last: Barallobre-Barreiro

first: Lukas

last: Schmidt

first: Siqi

last: Yin

first: Xiaoke

first: Sean

last: Burnap

first: Bhawana

last: Singh

first: Jude

last: Popham

first: Olesya

last: Harkot

first: Stephanie

last: Kampf

first: Maja

last: Nackenhorst

first: Andreas

last: Strassl

first: Christian

last: Loewe

first: Svitlana

last: Demyanets

first: Christoph

last: Neumayer

first: Kurt

last: Huber

first: Gerarl

last: Pasterkamp

first: Johann

last: Wojta

first: Manuel

last: Myr


title: A MYOD-SKP2 axis boosts tumorigenesis in fusion negative rhabdomyosarcoma by preventing differentiation through p57Kip2 targeting [RNA-seq]

status: Public on Aug 30 2023

city: Rome

first: Matteo

last: Cassandri

address: Viale di San Paolo 15

department: Department of Oncohematology

country: Italy

institute: Bambino Gesù Children's Hospital

summary: Rhabdomyosarcoma (RMS) is a pediatric mesenchymal-derived malignancy encompassing Fusion Positive (FP)-RMS expressing PAX3/7-FOXO1 and Fusion Negative (FN)-RMS often mutated in the RAS pathway. RMS expresses the master myogenic transcription factor MYOD that, paradoxically, is unable to support differentiation while essential for tumor cell survival. We identify here SKP2, an oncogenic E3-ubiquitin ligase, as a critical driver of tumorigenesis in FN-RMS. SKP2 is overexpressed in RMS at the highest levels among several adult and pediatric cancers and its expression is maintained by MYOD through an intronic enhancer within the gene. In FN-RMS SKP2 promotes cell cycle progression and prevents differentiation directly targeting p27Kip1 and p57Kip2, respectively, unlocking a transcriptional myogenic program, partly MYOD-dependent, resulting in de novo expression of terminal muscle differentiation markers. SKP2 depletion strongly affects stemness and tumorigenic features in vitro and prevents in vivo tumor growth. The in vitro effects are mirrored by the SKP2 inhibitor SMIP004. Moreover, the investigational NEDDylation inhibitor MLN4924 hampers SKP2 functions restraining FN-RMS cell survival and tumor growth. Our results uncover a MYOD-SKP2 axis crucial for the crosstalk between transcriptional and post-translational mechanisms that contribute to FN-RMS tumorigenesis and broaden the understanding of MYOD function. Furthermore, they suggest inhibition of NEDDylation as a potential therapeutic approach in this tumor.

overall_design:
To investigate the function of SKP2 in the regulation of myogenic differentiation, senescence and tumor growth in RMS, we infected JR1 and RD cell lines with lentiviral vectors expressing an shRNA targeting human SKP2 (shSKP2.2) or a non-targeting control shRNA (shSCR).
We then perfomed gene expression profiling analysis using data from RNA-seq of JR1 and RD cell lines expressing shSKP2 and compared the results with their correspondant shSCR controls.

first: Silvia

last: Pomella

first: Berkley

middle: E

last: Gryder

first: Rossella

last: Rota


title: Role of mitochondria in intestinal epithelial cells

city: Cologne

first: Ulrike

last: Göbel

state: NRW

address: Joseph Stelzmann Strasse, 26

department: Bioinformatics Core Facility

institute: CECAD Research Center

summary: We aimed to study the role of mitochondria in intestinal epithelial cells by generating and analyzing mice with tamoxifen-inducible intestinal epithelial cell (IEC)-specific knockout of DARS2. DARS2 ablation caused severe mitochondrial dysfunction in IECs and resulted in suppression of epithelial cell proliferation and accumulation of lipids within large lipid droplets in enterocytes. To gain insight into the mechanism underlying the lipid processing defect, we used Lexogen 3' mRNA sequencing to compare the gene expression profiles of the proximal small intestine from mice with IEC-specific DARS2 knockout and control littermates at three days after tamoxifen induction, when the mice do not display yet lipid accumulation, and at seven days after tamoxifen induction, when enterocytes are filled with lipids.

overall_design: 8-12 week-old DARS2tamIEC-KO and control mice received daily tamoxifen injections for five consecutive days and were sacrificed three or seven days after the last tamoxifen injection. A piece of a proximal small intestinal tissue was collected for RNA extraction and subsequent 3´ mRNA sequencing.

first: Chrysanthi

last: Moschandrea

first: Manolis

last: Pasparakis


title: Integrative functional genomic analyses identify novel genetic variants influencing skin pigmentation in indigenous Africans [Cut&Run, ATAC-seq]

city: Philadelphia

first: Yuanqing

last: Feng

state: Pennsylvania

address: 430 Clinical Research Building, 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

summary:
Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. We identified 1,157 candidate variants influencing skin pigmentation in indigenous Africans by genome-wide association studies and scans of natural selection based on differentiation in allele frequencies between lightly pigmented southern African Khoesan populations and other darkly pigmented African populations. We applied massively parallel reporter and chromosome conformation capture assays to identify novel regulatory variants and their target genes related to skin pigmentation in melanocytic cells. We identified 165 SNPs showing strong differential regulatory activities between alleles. Combining CRISPR-mediated genome editing, transcriptome profiling and melanin assays, we identified causal regulatory variants impacting pigmentation near MFSD12/HMG20B, MITF, OCA2, and DDB1/CYB561A3/TMEM138. We identified CYB561A3 as a novel gene regulating pigmentation by impacting genes involved in oxidative phosphorylation and melanogenesis. Our results broaden our understanding of the genetic basis of human skin color diversity and human adaptation.
To identify candidate enhancers and regulatory regions in skin pigmentation, we performed CUT&RUN and ATAC assays in  two melanocytic cell lines (MNT-1 and WM88). We used the darkly pigmented MNT-1 cell line because it is widely used for studying skin pigmentation and it has a transcription pattern similar to normal melanocytes. We used the WM88 cell line because the cells are lightly pigmented and may have a different trans-environment (e.g., different levels of transcription factors and open chromatin regions) compared with MNT-1 cells. To identify regulatory regions in MNT-1 cells, we conducted CUT&RUN assays using antibodies against H3K4me3, H3K27ac, MITF and SOX10. We further performed ATAC-seq in both MNT-1 and WM88 cells to identify open chromatin regions.

overall_design: Cut&Run, ATAC-seq data in two melanoma cell lines (MNT-1 and WM88).

first: Sarah

last: Tishkoff


title: Transcriptomic and Translatomic Analyses Reveal Insights into the Signaling Pathways of the Innate Immune Response in the Spleens of SPF Chickens Infected with Avian Reovirus

status: Public on Aug 27 2023

city: chengdu

first: tengda

last: huang

address: gaopeng road

country: China

institute: sichuan university

summary: Avian reovirus (ARV) infection is prevalent in farmed poultry, causes viral arthritis and severe immunosuppression. The spleen plays an important role in host defense against pathogen infection. In this study, transcriptome and translatome sequencing technology were combined to investigate the mechanisms of transcriptional and translational regulation in the spleen after ARV infection. On a genome-wide scale, ARV infection can significantly reduce the translation efficiency (TE) of splenic genes. Differentially expressed translational efficiency genes (DTEGs) were identified, including 15 upregulated DTEGs and 396 downregulated DTEGs. These DTEGs were mainly enriched in immune regulation signaling pathways, which indicates that ARV infection reduces the innate immune response in the spleen. In addition, combined analyses revealed that the innate immune response involves the effects of transcriptional and translational regulation. Moreover, we discovered the key gene IL4I1, the most significantly upregulated gene at both the transcriptional and translational levels. Further studies in DF1 cells showed that overexpression of IL4I1 could inhibit the replication of ARV, while inhibiting the expression of endogenous IL4I1 with siRNA promoted the replication of ARV. Overexpression of IL4I1 significantly downregulated the mRNA expression of IFN-β, LGP2, TBK1 and NF-κB; however, the expression of these genes was significantly upregulated after inhibition of IL4I1, suggesting that IL4I1 may be a negative feedback regulator of innate immune signaling pathways. In addition, the IL4I1 protein may interact with the ARV σA protein, and we speculate that the IL4I1 protein plays a regulatory role by interacting with the σA protein. This study not only provides a new perspective on the regulatory mechanisms of the innate immune response after ARV infection but also enriches the knowledge of the host defense mechanisms against ARV invasion and the outcome of ARV evasion of the host innate immune response.

overall_design: High-throughput sequencing of avian reovirus infected or not infected SPF chicken spleen tissue.

first: Sheng

last: Wang

first: Tengda

last: Huang

first: Zhixun

last: Xie

first: Lijun

last: Wan

first: Hongyu

last: Ren

first: Tian

last: Wu

first: Liji

first: Sisi

last: Luo

first: Meng

last: Li

first: Zhiqin

first: Qing

last: Fan

first: Jiaoling

first: Tingting

last: Zeng

first: Yanfang

last: Zhang

first: Minxiu

first: You

last: Wei


title: A MYOD-SKP2 axis boosts tumorigenesis in fusion negative rhabdomyosarcoma by preventing differentiation through p57Kip2 targeting

first: Matteo

last: Cassandri


title: Whole genome methylation sequencing for daughter fertility DNA mehylation biomarker

status: Public on Aug 23 2023

city: quebec

first: ying

last: zhang

address: 735 Ave.Neree tremblay

country: Canada

institute: UNIVERSITY LAVAL

type: Methylation profiling by high throughput sequencing

summary: high daughter fertility and low daughter fertility bulls were screened from the private bull database and then identify the sperm-derived DMR and DMC that associated with daughter fertility via whole genome methylation sequencing

overall_design: methylation characteristic of the bull sperm that associated with daughter fertility

first: Ying

first: Remi

last: Labrecque

first: Camila

last: Bruna de Lima

first: Marc

middle: A

last: Sirard


title: Effect of mce3R deletion on Mycobacterium tuberculosis response to acidic pH and cholesterol

city: Boston

first: Shumin

last: Tan

state: MA

address: 150 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

summary: The purpose of this study was to determine (i) the interplay between Mycobacterium tuberculosis response to acidic pH and cholesterol, two signals experienced concurrently by the bacterium during host colonization, and (ii) the role of the transcription factor Mce3R in regulation of this response.

overall_design: Log-phase Mycobacterium tuberculosis (Mtb) strain CDC1551 (streptomycin-resistant) or its isogenic mce3R deletion mutant (OD600 ~0.6) were used to inoculate standing T25 flasks with filter caps at an OD600 = 0.3, containing 10 ml of the following media: (i) 7H9, pH 7.0, (ii) 7H9, pH 5.7, (iii) cholesterol, pH 7.0, or (iv) cholesterol, pH 5.7. After four hours of exposure to the specific environmental conditions in a humidified, 37°C, 5% CO2 incubator, Mtb samples were collected and RNA isolated. Library preparation was with the Illumina stranded total RNA with Ribo-Zero Plus kit, and barcoded samples were pooled and sequenced on an Illumina HiSeq 2500 (single-end 100 bp reads). Two biological replicates were prepared for each condition.

first: Yue

last: Chen


title: Human Adult Glial Progenitors Are Transcriptionally Distinct from Their Fetal Counterparts.

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center


title: Transcriptome analysis for LMP1 depletion rescue with Wildtype LMP1 or individual TES mutant LMP1 in GM12878 Lymphoblastoid cell line (LCL)

status: Public on Aug 25 2023

first: Bidisha

last: Mitra

address: 181 Longwood Avenue, 8th floor

department: Medicine

institute: Brigham and Women's Hospital

summary: RNA-seq was used  to characterize the LMP1 mediated regulation of host target gene regulation. Here, we stably expressed doxycycline-induced HA-tagged wildtype (WT) LMP1 or TES1 mutant (TES1m) oe TES2 mutant(TES2m) in GM12878 LCL. We then depleted LMP1 from these cells using CRISPR-Cas9 approach and treated the cells with 400ng/ml of doxycycline to induce expression of WT, TES1m or TES2m LMP1 to rescue from the LMP1 depletion mediated effects  (including loss of cell viability) to understand and differenciate the role of LMP1 TES1 vs TES2 domains in LCL.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in GM12878 LCL upon rescue of CRISPR-Cas9-mediated LMP1 depletion with induced expression of wildtype LMP1, TES1mutant LMP1or TES2m LMP1.  The GM12878 LCL substituting LMP1 depletion with stable expression of wildtype LMP1 was used as the control.

first: Rui

last: Guo

first: Nina

last: Beri

first: Laura

last: Murray-Nerger

first: Benjamin

last: Gewurz


title: FSHβ links photoperiodic signalling in the pituitary gland to seasonal reproduction in Japanese quail.

first: Tyler

last: Stevenson

overall_design: Male quail (N=54) were housed in a summer-like long-day (LD) photoperiod (16L:8D). To mimic the autumnal decline and subsequent spring increase in the annual photoperiodic cycle, birds were exposure to a sequential change in day length from 16L, to 14L, to 12L, to 10L, to 8L, then back to 10L, to 12L, to 14L and lastly 16L (Fig.1a). Each photoperiod treatment lasted for 2 weeks to minimize the impact of photoperiodic history effects (Stevenson et al., 2012a). At the end of each photoperiodic treatment a subset of quail (n=6) body mass was used as a measure to pseudo randomly select birds for tissue collection. Brain and pituitary stalk were rapidly dissected, frozen on powdered dry ice and stored at -80°C. RNA was extracted from the pituitary gland and Oxford Nanopore Flow cells used to sequence the transcriptomes from individual birds

first: Calum

last: Stewart

first: Gaurav

last: Majumdar

first: Ana

last: Monteiro


title: Characterizing Influence of rCHOP Treatment on Diffuse Large B-Cell Lymphoma Microenvironment through In Vitro Microfluidic Spheroid Model

status: Public on Aug 21 2023

first: Matthew

middle: Ryan

last: Sullivan

state: Massachusetts

address: 140 The Fenway

department: Pharmaceutical Sciences

institute: Northeastern University

summary: We explored a novel hydrogel spheroid-based microfluidic model for screening lymphoma treatments. We utilized primary patient DLBCL cells in combination with NK cells and rCHOP treatment, and used ranscriptomic sequencing to determine the biological relevance of this approach.  Our results showed complex changes in the transcriptomic response to treatment stimuli, including numerous metabolic and immunogenic changes. These findings support this model as an optimal platform for comparative screening of novel treatments.

overall_design: Samples contained DLBCL and NK cells recollected from a hydrogel-based 3D culture platform. We extracted two replicates of two different treatment conditions, Rituximab and Rituximab+CHOP. RNA was extracted via Rneasy, then sent to Novogene for their Ultra-low input RNA seq pipeline.

first: Rachel

last: White

first: Ravi

last: Dashnamoorthy

first: Andrew

last: Evens

first: Tania

last: Konry


title: Epigenetics profiling of malignant uveal melanocytes reveals novel  molecular features of uveal melanoma

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: To elucidate if regulation of gene expression could be linked to chromatin organization and DNA folding, chromatin structure and DNA topology were investigated

overall_design: ChIPSeq against H2AUb, H3K4me and H3K27me3 were conducted in simplicate in NM, and in duplicate in MP41 and MP46.  ChIpSeq against H3K27Ac and CTCF, were conducted in duplicate in MP41 and MP46 to implement multiomics analysis.

first: David

last: Gentien

first: Pierre

last: de la Grange

first: Joshua

last: Watterfall


title: BACH1 is a central regulator of glutathione metabolism, cellular necrosis and host resistance in Mycobacterium tuberculosis infection

status: Public on Sep 07 2023

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz

summary: Background. An exacerbated oxidative stress response can regulate cellular necrosis by triggering lipid peroxidation in an iron-dependent manner and this form of necrotic death has been implicated in Mycobacterium tuberculosis (Mtb) pathogenesis. Here we examined the role of Bach1, a transcription factor that represses a major set of antioxidant genes, in regulating host resistance to Mtb. We found that BACH1 expression is associated with and predicts active pulmonary tuberculosis in humans. In response to Mtb infection in vitro and in vivo, ablation of Bach1 increased the levels of glutathione as well as enhanced the expression of Gpx4, an enzyme that regulates lipid peroxidation. Consistent with these observations, Bach1-/- macrophages exhibited increased resistance to Mtb-induced cell death and infected Bach1-deficient mice displayed a striking reduction in bacterial loads as well as pulmonary necrosis and lipid peroxidation accompanied by enhanced survival. In addition, single-cell RNAseq analysis of the lungs of Mtb-infected Bach1-/- mice revealed an enrichment of genes associated with suppression of ferroptosis. Finally, deletion of Bach1 in B6.Sst1S mice, an inbred strain that exhibits the necrotic lung pathology similar to that seen in human TB, enhanced host resistance to Mtb while significantly reducing tissue necrosis. These findings identify Bach1 and its regulation of the oxidative stress response as an important modulator of cellular and tissue necrosis as well as host resistance in Mtb infection.

overall_design: Gene expression analysis on Mtb-infected and uninfected B6.Sst1s and  B6.Sst1sBach1-/- mice

first: Eduardo

middle: P

last: Amaral

first: Sivaranjani

last: Namasivayam

last: Fukutani

first: Kerry

middle: L

last: Hilligan

first: Kate

last: Aberman

first: Logan

last: Fisher

first: Caio

last: Bomfim

first: Keith

last: Kauffman

first: Jay

last: Buchanan

first: Leslie

last: Santuo

first: Pedro

middle: H

last: Gazzinelli-Guimaraes

first: Diego

last: Costa

first: Mariane

last: Teixeira

first: Beatriz

last: Barreto-Duarte

first: Clarissa

middle: G

last: Rocha

first: Monique

middle: F

last: Santana

first: Marcelo

last: Cordeiro-Santos

first: Daniel

last: Barber

first: Robert

middle: J

last: Wilkinson

first: Igor

last: Kramnik

first: Kazuhiko

last: Igarashi

first: Thomas

last: Scriba

first: Katrin

last: Mayer-Barber

first: Bruno

middle: B

last: Andrade

first: Alan

last: Sher


title: RNA sequencing of an optimized shuttle cell line for intranasal delivery

status: Public on Aug 18 2023

city: Tübingen

first: Ali

last: El-Ayoubi

address: otfried müller straße 27

institute: Hertie Institute for Clinical Brain Research

summary: We generated  cell lines from LX-2 hepatic stellate cells that are otpimzed for intranasal delivery of the oncolytic adenovirus XVir-N-31  to treat glioblastoma. One cell line migrates faster, the next in addition expressed HSV-TK as a safety gene to eliminate cells in case of adverse events.

overall_design: RNA sequencing has been performed to analyze changes in gene expression between the parental (PAR) and the two optimized cell lines (FR and FR/TK). RNA sequencing was performed on mRNA generated from the three cell lines (n=3)

first: Ulrike

last: Naumann

first: Lusine

last: Danielyan

first: Arsen

last: Arakelyan


title: Multi-omics comparison of malignant and normal uveal melanocytes reveals novel molecular features of uveal melanoma

first: Nicolas

last: Servant

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

overall_design: Refer to individual Series


title: 6 small intestinal macrophage subsets (CD4–Tim4–CD163–, CD4+Tim4–CD163–, CD4+Tim4+CD163–, CD4–Tim4–CD163+, CD4+Tim4–CD163+, CD4+Tim4+CD163+ ) from adult male C57BL/6J mice

city: Manchester

first: Ian

middle: Edward

last: Prise

state: Select state

address: Oxford Road

institute: University of Manchester

summary: To better determine functional heterogenity of small intestinal macrophages, 6 subsets of were sorted for RNA sequencing based on expression of CD4, Tim4, and CD163

overall_design: 25,000 - 50,000 small intestinal macrophages were isolated by fluorescence-activated cell sorting (FACS) from a single cell suspension, generated  by mechanical disruption and enzymatic digest. Live CD45+Lin–(TCRb,B220,SiglecF,Ly6C,Ly6G)CD11b+MHCII+CD64+ cells were sorted into CD4–Tim4–CD163–, CD4+Tim4–CD163–, CD4+Tim4+CD163–, CD4–Tim4–CD163+, CD4+Tim4–CD163+, CD4+Tim4+CD163+ populations, directly into RLT buffer, frozen on dry ice and stored at –80C until RNA extraction using a Qiagen RNeasy micro kit

first: Tovah

last: Shaw

first: John

last: Grainger

first: Verena

last: Kästele


title: Role of EGR1 in vasculogenic mimicry of MDA-MB-231 cells

status: Public on Aug 15 2023

city: Seoul

first: Soon Young

last: Shin

address: 120, Neungdong-ro, Gwangjin-gu

department: Department of Biological Sciences

country: South Korea

institute: Konkuk University

summary: Vasculogenic mimicry (VM) is an intriguing phenomenon observed in tumor masses, in which cancer cells organize themselves into capillary-like channels that closely resemble the structure and function of blood vessels. Although VM is believed to contribute to alternative tumor vascularization, the detailed regulatory mechanisms controlling these cellular processes remain poorly understood. Our study aimed to investigate the role of Early Growth Response 1 (EGR1) in regulating VM in aggressive cancer cells, specifically MDA-MB-231 triple-negative breast cancer cells.

overall_design: To identify the genes that regulated by EGR1, we examined the gene expression profile of control shRNA- or shEGR1-transfected MDA-MB-231 cells using an Agilent human whole genome microarray. Additionally, TNF-a was treated to obtain information about cytokine-dependent transcriptomic changes.

first: Euitaek

last: Jung

first: Soon

middle: Y

first: Young

last: Lee


title: Identification of state-specific proteomic and transcriptomic signatures of microglia-derived extracellular vesicles [bulk rna-seq]

status: Public on Aug 12 2023

city: Atlanta

first: Srikant

last: Rangaraju

state: GA

address: 615 Michael St

department: Neurology

institute: Emory University

summary: Microglia are resident immune cells of the brain that play important roles in mediating inflammatory responses in several neurological diseases via direct and indirect mechanisms. One indirect mechanism may involve extracellular vesicle (EV) release, so that the molecular cargo transported by microglia-derived EVs can have functional effects by facilitating intercellular communication. The molecular composition of microglia-derived EVs, and how microglial activation states impacts EV composition and EV-mediated effects in neuroinflammation, remain poorly understood. We hypothesize that microglia-derived EVs have unique molecular profiles that are determined by microglial activation state. Using size-exclusion chromatography to purify EVs from BV2 microglia, combined with proteomic (label-free quantitative mass spectrometry or LFQ-MS) and transcriptomic (mRNA and non-coding RNA seq) methods, we obtained comprehensive molecular profiles of microglia-derived EVs. LFQ-MS identified several classic EV proteins (tetraspanins, ESCRT machinery, and heat shock proteins), in addition to over 200 proteins not previously reported in the literature. Unique mRNA and microRNA signatures of microglia-derived EVs were also identified. After treating BV2 microglia with lipopolysaccharide (LPS), interleukin-10, or transforming growth factor beta, to mimic pro-inflammatory, anti-inflammatory, or homeostatic states, respectively, LFQ-MS and RNA seq revealed novel state-specific proteomic and transcriptomic signatures of microglia-derived EVs. Particularly, LPS treatment had the most profound impact on proteomic and transcriptomic compositions of microglia-derived EVs. Furthermore, we found that EVs derived from LPS-activated microglia were able to induce pro-inflammatory transcriptomic changes in resting responder microglia, confirming the ability of microglia-derived EVs to relay functionally-relevant inflammatory signals. These comprehensive microglia-EV molecular datasets represent important resources for the neuroscience and glial communities, and provide novel insights into the role of microglia-derived EVs in neuroinflammation.

overall_design: We equally dosed individual wells of BV2 cells with EVs secreted from control and LPS treated BV2 cells to assess gene expression changes in recipient microglia using RNA sequencing. Resting microglia were treated with extracellular vesicles for 24 hours.

first: Juliet

middle: V

last: Santiago

first: Aditya

last: Natu

first: Christina

middle: C

last: Ramelow

first: Sruti

last: Rayaprolu

first: Hailian

last: Xiao

first: Vishnu

last: Kumar

first: Nicholas

last: Seyfried


title: Effects of Testosterone and GH on liver transcriptome

city: Las Palmas de Gran Canaria

first: Leandro

last: Fernández-Pérez

state: Las Palmas

address: Blas Cabrera Felipe s/n

department: Clinical Sciences

country: Spain

institute: University of Las Palmas de Gran Canaria (ULPGC-IUIBS)

summary: Transcriptional profiling of the effects of testosterone and growth hormone on hypothyroid-orquidectomized rat (TXOX) liver

overall_design: Five-condition experiment: hypothyroid-orquidectomized rats (TXOX; Cy3); euthyroid testis-intact rats (INTACT; Cy5);  GH-treated TXOX rats (TXOXGH; Cy5); Testosterone Propionate-treated TXOX rats (TXOXTP; Cy5); TP plus GH-treated TXOX rats (TXOXTPGH; Cy5). Biological replicates: 4 TXOX (references), 4 INTACT; 4 TXOXGH, 4 TXOXTP, 4 TXOXTPGH.

last: Fernandez-Perez

first: Borja

last: Guerra

first: Amilcar

last: Flores-Morales


title: Identification of state-specific proteomic and transcriptomic signatures of microglia-derived extracellular vesicles [rna-seq]

middle: T


title: Identification of state-specific proteomic and transcriptomic signatures of microglia-derived extracellular vesicles [mirna-seq]

type: Non-coding RNA profiling by high throughput sequencing


title: A MYOD-SKP2 axis boosts tumorigenesis in fusion negative rhabdomyosarcoma by preventing differentiation through p57Kip2 targeting [ChIP-seq]

first: Matteo

last: Cassandri

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27ac and for MYOD in RD FN-RMS cells, previously infected with vectors expressing an shRNA targeting human SKP2 (shSKP2) or a non-targeting control shRNA (shSCR).

first: Silvia

last: Pomella

first: Berkley

last: Gryder

first: Rossella

last: Rota


title: Identification of state-specific proteomic and transcriptomic signatures of microglia-derived extracellular vesicles


title: Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans

status: Public on Aug 11 2023

first: Yuanqing

last: Feng

summary: Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. Here we applied massively parallel reporter assays to screen 1,157 candidate variants influencing skin pigmentation in Africans and identified 165 single-nucleotide polymorphisms showing differential regulatory activities between alleles. We combine Hi-C, genome editing and melanin assays to identify regulatory elements for MFSD12, HMG20B, OCA2, MITF, LEF1, TRPS1, BLOC1S6 and CYB561A3 that impact melanin levels in vitro and modulate human skin color. We found that independent mutations in an OCA2 enhancer contribute to the evolution of human skin color diversity and detect signals of local adaptation at enhancers of MITF, LEF1 and TRPS1, which may contribute to the light skin color of Khoesan-speaking populations from Southern Africa. Additionally, we identified CYB561A3 as a novel pigmentation regulator that impacts genes involved in oxidative phosphorylation and melanogenesis. These results provide insights into the mechanisms underlying human skin color diversity and adaptive evolution.


title: TBX5 overexpression in ventricle

first: William

middle: T.

last: Pu

state: Ma

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

summary: Understanding how the atrial and ventricular chambers of the heart maintain their distinct identity is a prerequisite for treating chamber-specific diseases. Here, we selectively inactivated the transcription factor Tbx5 in the atrial working myocardium of the neonatal mouse heart to show that it is required to maintain atrial identity.  Atrial Tbx5 inactivation downregulated highly chamber specific genes such as Myl7 and Nppa, and increased  expression of ventricular identity genes including Myl2. Using combined single nucleus transcriptome and open chromatin profiling, we assessed genomic accessibility changes underlying the altered atrial identity expression program, identifying 1846 genomic loci with greater accessibility in control atrial cardiomyocytes compared to KO aCMs. 69% of the control-enriched ATAC regions were bound by TBX5, demonstrating a role for TBX5 in maintaining genomic accessibility. These regions were associated with genes that had higher expression in control aCMs compared to KO aCMs, suggesting they act as TBX5-dependent enhancers. To confirm this hypothesis we analyzed chromatin looping of enhancers marked by H3K27Ac using HiChIP and found 510 chromatin loops that were sensitive to TBX5 dosage. Of the loops enriched in control aCMs, 73.7% contained anchors in control-enriched ATAC regions. Conversely, Tbx5 overexpression in the ventricular myocardium drove atrial gene expression. Together, these data demonstrate a role for TBX5 in maintaining the atrial gene expression program by binding to atrial enhancers to preserve tissue-specific chromatin architecture. We highlight this phenomenon at major atrial identity genes including Nppa, Bmp10 and Myl7.

overall_design: Comparing the expression of TBX5 overexpressing left ventricle to WT left ventricle in mice.

first: Ozanna

last: Burnicka-Turek

first: Carlos

last: Perez-Cervantes

first: Mason

last: Sweat

first: Ivan

last: Moskowitz


title: Bulk RNA seq of P0 aCMs and P28 aCMs

summary: Understanding how the atrial and ventricular chambers of the heart maintain their distinct identity is a prerequisite for treating chamber-specific diseases. Here, we selectively inactivated the transcription factor Tbx5 in the atrial working myocardium of the neonatal mouse heart to show that it is required to maintain atrial identity. Atrial Tbx5 inactivation downregulated highly chamber specific genes such as Myl7 and Nppa, and conversely, increased the expression of ventricular identity genes including Myl2. Using combined single nucleus transcriptome and open chromatin profiling, we assessed genomic accessibility changes underlying the altered atrial identity expression program, identifying 1846 genomic loci with greater accessibility in control atrial cardiomyocytes compared to KO aCMs. 69% of the control-enriched ATAC regions were bound by TBX5, demonstrating a role for TBX5 in maintaining atrial genomic accessibility. These regions were associated with genes that had higher expression in control aCMs compared to KO aCMs, suggesting they act as TBX5-dependent enhancers. We tested this hypothesis by analyzing enhancer chromatin looping using HiChIP and found 510 chromatin loops that were sensitive to TBX5 dosage. Of the loops enriched in control aCMs, 74.8% contained anchors in control-enriched ATAC regions. Together, these data demonstrate a genomic role for TBX5 in maintaining the atrial gene expression program by binding to atrial enhancers and preserving tissue-specific chromatin architecture of atrial enhancers.

overall_design: We isolated and sequenced RNA from aCMs at different stages


title: Structure of the ISW1a complex bound to the dinucleosome

status: Public on Aug 09 2023

city: Beijing

first: Youyang

last: Sia

address: Haidian district

institute: Tsinghua University

summary: Nucleosomes are basic repeating units of chromatin, and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes, and are vital in regulating chromatin organization and gene expression.  Here we report the cryoEM structure of chromatin remodeler ISW1a complex bound to the dinucleosome. Each subunit of the complex recognizes a different nucleosome. The motor subunit binds to the mobile nucleosome and recognizes the acidic patch through two arginine residues, and the DNA-binding module interacts with the entry DNA at the nucleosome edge. This nucleosome-binding mode provides the structural basis for linker DNA sensing of the motor. Notably, the Ioc3 subunit recognizes the disk face of the adjacent nucleosome through interacting with the H4 tail, the acidic patch and the nucleosomal DNA, which plays a role in the spacing activity in vitro, and in nucleosome organization and cell fitness in vivo. Together, these findings support the nucleosome spacing activity of ISW1a, and add a new mode of nucleosome remodeling in the context of a chromatin environment.

overall_design: To generate three independent datasets, sample preparation were repeated three times by different people at different times. Each dataset includes three biological replicates of the WT samples, and one set of the Ioc3 mutants.

first: Lifei

last: Li

first: Kangjing

last: Chen

first: Pengjing

last: Hu

first: Youpi

last: Ye

first: Zhucheng


title: TBX5 KO multiome

overall_design: We performed 10x combined snRNA-seq and snATAC-seq to understand gene expression changes in atria after inactivating TBX5 and genomic accessibility changes regulating altered gene expression.


title: TBX5 KO HiChIP

summary:
Understanding how the atrial and ventricular chambers of the heart maintain their distinct identity is a prerequisite for treating chamber-specific diseases. Here, we selectively inactivated the transcription factor Tbx5 in the atrial working myocardium of the neonatal mouse heart to show that it is required to maintain atrial identity.  Atrial Tbx5 inactivation downregulated highly chamber specific genes such as Myl7 and Nppa, and increased  expression of ventricular identity genes including Myl2. Using combined single nucleus transcriptome and open chromatin profiling, we assessed genomic accessibility changes underlying the altered atrial identity expression program, identifying 1846 genomic loci with greater accessibility in control atrial cardiomyocytes compared to KO aCMs. 69% of the control-enriched ATAC regions were bound by TBX5, demonstrating a role for TBX5 in maintaining genomic accessibility. These regions were associated with genes that had higher expression in control aCMs compared to KO aCMs, suggesting they act as TBX5-dependent enhancers. To confirm this hypothesis we analyzed chromatin looping of enhancers marked by H3K27Ac using HiChIP and found 510 chromatin loops that were sensitive to TBX5 dosage. Of the loops enriched in control aCMs, 73.7% contained anchors in control-enriched ATAC regions. Conversely, Tbx5 overexpression in the ventricular myocardium drove atrial gene expression. Together, these data demonstrate a role for TBX5 in maintaining the atrial gene expression program by binding to atrial enhancers to preserve tissue-specific chromatin architecture. We highlight this phenomenon at major atrial identity genes including Nppa, Bmp10 and Myl7.
HiChIP for H3K27Ac from atria of TBX5KO and control animals

overall_design: Nuclei were purified using PCM1 and then used for HiChIP

first: Yangpo

last: Cao


title: WT and Ccr2-/- small intestinal macrophages

first: Ian

last: Prise

summary: To better determine heterogeneity of small intestinal macrophages, CD64+ macrophages were sorted for single cell RNA sequencing

overall_design: Live CD45+Lin-(CD3,TCRb,B220,SiglecF,Ly6C,Ly6G)CD11b+MHCII+CD64+ cells were FACS sorted from 3-4 pooled mouse small intestines and loaded on to the 10X Genomics single cell platform for subsequent sequencing

first: Tovah

last: Shaw

first: John

middle: R

last: Grainger

first: Charlotte

last: Scott


title: COVD-19 infection during pregnancy induces a hematopoietic stem cell signature in cord blood fetal cells

status: Public on Aug 10 2023

city: PARIS 14EME ARRONDISSEMENT

first: Qui Trung

last: NGO

address: 24 rue du Faubourg Saint Jacques

institute: Institut Cochin (U1016 Inserm/UMR8104 CNRS/UMR-S8104)

summary: Pregnant women and their fetuses are particularly susceptible to respiratory pathogens. How they respond to SARS-CoV-2 infection is still under investigation. Here, we studied the transcriptome and phenotype of umbilical cord blood cells in pregnant women infected or not with SARS-CoV-2. We found that symptomatic maternal COVID-19 was associated with a transcriptional erythroid cell signature as compared with asymptomatic and uninfected mothers. We observed an expansion of fetal hematopoietic progenitors skewed towards erythroid differentiation and displaying increased clonogenicity. We found no difference in inflammatory cytokines in the cord blood upon SARS-CoV-2 infection. Interestingly, we showed an activation of hypoxia pathway in cord blood cells from symptomatic COVID-19 mothers, suggesting that maternal hypoxia may be triggering this fetal stress erythropoiesis. Overall, these results show a fetal hematopoietic response to symptomatic COVID-19 in pregnant mothers in the absence of vertically transmitted SARS-CoV-2 infection, which is likely to be a mechanism of fetal adaptation to maternal infection and reduced oxygen supply.

overall_design: Comparative differences gene expression in cord blood mononuclear cells between COVID- and asymptomatic COVID+ and severe COVID+

first: Mansour

last: Alkobtawi

first: Qui

last: Ngo

first: Nicolas

last: Chapuis

first: Romain

last: Fontaine

first: Mira

last: El khoury

first: François

last: Delhommeau

first: Michaela

last: Fontenay

first: Vassilis

last: Tsatsaris

first: Sélim

last: Aractingi

first: Bénédicte

last: Oulès


title: Tbx5 maintains atrial identity by regulating an atrial enhancer network

first: William

last: Pu


title: The C9ORF72 Repeat Epansion Impairs Neurodevelopment

city: Los Angeles

first: Justin

last: Ichida

state: California

address: 1425 San pablo Street, BCC Room 209

institute: USC

summary: RNA sequencing analysis of human iPSC-derived neural stem cells generated from Control, C9ORF72 FTD/ALS, an isogenic control, and a C9ORF72 knockout line. The goal of this study is to determine the effects of the C9ORF72 repeat expansion on neural stem cell proliferation and differentiation.

overall_design: Neural stem cells were generated by exposing iPSCs to dual smad inhibition using a 10 day protocol. The neural stem cell population was enriched at day 10 using magnetic activated cell sorting (MACS) purification of polysialic acid-neural cell adhesion molecule (PSA-NCAM)+. The enriched population was lysed in RLT buffer and sent to Amaryllis Nucleics for 3'DGE RNA sequencing.

middle: K


title: Small RNA of EVs from MH-S cells

status: Public on Aug 08 2023

city: Guangzhou 510275

first: Weiyang

last: Fan

address: School of Life Sciences, Sun Yat-sen University, No. 135 Xingang West Road, Guangzhou

department: School of Life Sciences

institute: Sun Yat-sen University

summary: EV RNA samples from MH-S cells were prepared for small RNA sequencing by TruSeq Small RNA Sample Prep Kits (Illumina, San Diego，USA), using a minimum of 1 μg RNA per sample.

overall_design: total samples = 15, and n = 5

first: Peibo

last: Li


title: Towards a human brain EV atlas: Characteristics of EVs from different brain regions, including small RNA and protein profiles

status: Public on Aug 07 2023

city: Baltimore

first: Kenneth

middle: W.

last: Witwer

state: MD

address: 733 N. Broadway

department: Department of Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

summary: Brain derived EVs (bdEVs) from eight brain regions, including orbitofrontal gyrus(ORB), postcentral gyrus (POSTC), hippocampus (HIPPO), thalamus (THAL), occipital gyrus (OCC), medulla (MED), corpus callosum (CORP), and cerebellum (CBLM)  were separated and characterized by small RNA sequencing. We aim to provide an atlas of bdEV molecular profiles with brain region specificity.

overall_design: RNA was extracted from bdEVs of eight brain regions and small RNA libraries construction by the D-Plex Small RNA-seq Kit (Diagenode C05030001). Sequencing data of bdEVs from eight different regions were then compared.

middle: W

first: Yiyao

last: Huang

first: Tanina

last: Arab

first: Andrey

last: Turchinovich


title: The mRNA-lncRNA-circRNA network profiling of Turner syndrome patient-derived induced pluripotent stem cells and their derived cardiomyocytes

status: Public on Aug 06 2023

city: Guangzhou

first: Detu

last: Zhu

state: Guangdong

institute: The Third Affiliated Hospital of Guangzhou Medical University

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

summary: Heart deformity is the leading cause of mortality in Turner syndrome (TS) patients. To investigate the dysregulated ceRNA network in cardiomyocytes (CMs) of TS patients, we employed a ceRNA microarray to profile the mRNA-lncRNA-circRNA network in induced pluripotent stem cells (iPSCs) and their derived CMs from healthy donors (WT) and TS patients.

overall_design: 3 WT and 3 TS patient-derived iPSC lines were generated from PBMCs. CMs were derived from these iPSC lines, respectively. The mRNA-lncRNA-circRNA networks in the WT and TS-derived iPSC and CM lines were examined with ceRNA microarrays that were capable of profiling 18k mRNAs, 68k lncRNAs and 88k circRNAs.

first: Yumei

last: Luo


title: Integrated multi-omics analyses identify key anti-viral host factors and pathways controlling SARS-CoV-2 infection

city: Houston

first: Weiyi

last: Peng

state: TX

address: 3455 Cullen Blvd., Suite 342

department: Department of Biology and Biochemistry

institute: University of Houston

summary: Anti-viral host factors are essential for controlling SARS-CoV-2 infection but remain largely unknown due to the biases of previous large-scale studies toward pro-viral host factors. To fill this gap, we performed a genome-wide CRISPR dropout screen and integrated analyses of the multi-omics data of the CRISPR screen, genome-wide association studies, single-cell RNA-seq, and host-host/viral protein-protein/RNA interactome. We identified many anti-viral host genes that were missed by previous studies, including the components of V-ATPases, ESCRT, and N-glycosylation pathways that inhibited viral entry/replication. We also identified the cohesin complex as a novel antiviral pathway, supporting an important role of three-dimensional chromatin organization in mediating host-viral interaction. Furthermore, we discovered an anti-viral transcription factor KLF5, a regulator of sphingolipid metabolism, which was up-regulated and harbored genetic variations linked to COVID-19 patients with severe symptoms. Our analyses provide a resource for understanding the host antiviral network for combating SARS-CoV-2 and may help develop new therapeutic strategies.

overall_design: We performed a genome-wide LOF screen based on virus-induced cytopathic effect. Our LOF screen was optimized to identify depleted hits with potential anti-viral activities. This screen employed a SARS-CoV-2-permissive lung epithelial cell line, A549-AC, which constitutively expresses human ACE2 and Cas-9. Cells with gRNAs targeting anti-viral host factors would be significantly depleted after SARS-CoV-2 infection, whereas gRNAs targeting pro-viral host factors would be enriched.To achieve 50-80% of cell killing (an optimal selection condition for dropout screens), we infected A549-AC cells with MOI 5 for 48-hour (h) post infection. Cells with gRNA library without virus infection were used as the negative control.

first: Yiwen

last: Chen

first: Jiakai

last: Hou

first: Yanjun

last: Wei


title: Multimodal spatiotemporal transcriptomic resolution of embryonic palate osteogenesis

city: Bethesda

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

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

overall_design: Refer to individual Series


title: Cdo1-Camkk2-AMPK axis confers the protective effects of exercise against NAFLD in mice

city: Shanghai

first: Min

address: YangPu

institute: Shanghai University of sports

summary: Cysteine dioxygenase type 1 (Cdo1) is a key enzyme for cysteine catabolism that is enriched in liver, whose role in NAFLD remains poorly understood. Here, we show that exercise induces the expression of hepatic Cdo1 via the cAMP/PKA/CREB signaling pathway. Hepatocyte-specific knockout of Cdo1 (Cdo1LKO) impairs the effect of exercise against NAFLD, whereas hepatocyte-specific overexpression of Cdo1 (Cdo1LTG) and exercise synergistically ameliorates NAFLD in male mice. Mechanistically, Cdo1 facilitates the binding between AMPK and kinase active Camkk2, which activates AMPK signaling. This promotes fatty acid oxidation and mitochondrial biogenesis in hepatocytes to attenuate hepatosteatosis. Therefore, by promoting hepatic Camkk2-AMPK signaling pathway, Cdo1 acts as an important downstream effector of exercise to combat against NAFLD

overall_design: Total RNA was obtained from liver of HFD-fed control mice and Cdo1LKO mice.

first: Liang

last: Guo

first: Jie-Ying

first: Wang-Jing

last: Mu


title: A somatic cell cloned rhesus monkey obtained by trophoblast replacement [WGBS II]

status: Public on Aug 01 2023

first: Liao

last: Zhaodi

address: 500, Qiangye Road

department: Institute of Neuroscience

institute: Chinese Academy of Sciences

summary: Somatic cell nuclear transfer (SCNT) has been used to clone cynomolgus monkeys (Macaca fascicularis), but the cloning of other non-human primate species remains to be achieved. On the other hand, our histological examination indicated severe calcification of the placenta of SCNT fetuses. Additionally, we found that some of the maternal-biased imprinting genes were aberrantly lost in the cloned embryos by multi-omics analysis. We thus developed a trophoblast replacement (TR) method, providing an ICSI-derived placenta for the SCNT fetus, to support the full-term development of the cloned embryos after implantation. By combining this TR method with treatment with epigenetic modification factors, we obtained a healthy somatic cell cloned rhesus monkey. Thus, TR represents a useful approach for rhesus monkey cloning.

overall_design: Whole genome bisulfite sequencing of the trophoblast cells of monkey ICSI and SCNT embryos

first: Zhaodi

last: Liao


title: A somatic cell cloned rhesus monkey obtained by trophoblast replacement [RNA-seq]

overall_design: RNA sequencing of the trophoblast cells of monkey ICSI and SCNT embryos


title: p16 epimutation modulates the tumor microenvironment and promotes malignancy  of Apc-mutant colon cancer

status: Public on Aug 02 2023

first: Lanlan

last: Shen

state: Texas

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

summary:
We previously generated a mouse model of p16 epimutation (named as p16cis/cis) through targeted knock-in of a 140-bp Alu-related DNA sequence (cis-element) that facilitates the spread of DNA methylation at promoter CpG islands (CGIs) in cis (Yu et al. JCI, 2014).
We generated primary mouse embryonic fibroblasts (MEFs) from p16cis/cis  and control mice. By whole genome bisulfite sequencing (WGBS) for comprehensive DNA methylation profiling, we showed that cis-element-mediated approach specifically induces p16 promoter hypermethylation.

overall_design: Genome-wide DNA methylation profiling by WGBS was performed in primary ctr-MEF at passage 7 and cis-MEF at passage 12

first: Li

last: Yang


title: Inhibiting NLRP3 Signaling in Aging Podocytes Improves Their Life- and Health-span

city: Cleveland

first: Oliver

last: Wessely

state: OH

address: 9500 Euclid Avenue/NC10

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic Foundation

summary: The decrease in the podocyte’s lifespan and health-span that typify healthy kidney aging cause a decrease in their normal structure, physiology and function. The ability to halt and even reverse these changes becomes clinically relevant when disease is superimposed on an aged kidney. RNA-sequencing of podocytes from middle-aged mice showed an inflammatory phenotype with increases in the NLRP3 inflammasome, signaling for IL2/Stat5, IL6 and TNF, interferon gamma response, allograft rejection and complement, consistent with inflammaging. Furthermore, injury-induced NLRP3 signaling in podocytes was further augmented in aged mice compared to young ones. The NLRP3 inflammasome (NLRP3, Caspase-1, IL1ß IL-18) was also increased in podocytes of middle-aged humans. Higher transcript expression for NLRP3 in human glomerular was accompanied by reduced podocyte density and increased global glomerulosclerosis and glomerular volume. Pharmacological inhibition of NLRP3 with MCC950, or gene deletion, reduced podocyte senescence and the genes typifying aging in middle-aged mice, which was accompanied by an improved podocyte lifespan and health-span. Moreover, modeling the injury-dependent increase in NLRP3 signaling in human kidney organoids confirmed the anti-senescence effect of MC9950. Finally, the impact of NLRP3 also impacted liver aging. Together, these results suggest a critical role for the NLRP3 inflammasome in podocyte and liver aging.

overall_design: We performed mRNA-seq of podocytes from young (4-month-old) mice, middle-aged mice (19.5-month-old) treated with saline, and middle-aged mice (19.5-month-old)  mice treated with the NLRP3 inhibitor MCC950. All mice were male.

first: Jeffrey

last: Pippin

first: R

middle: A

last: Schweickart

first: Stuart

last: Shankland


title: A somatic cell cloned rhesus monkey obtained by trophoblast replacement

sample_organism:
Macaca fascicularis
Macaca mulatta

platform_organism:
Macaca fascicularis
Macaca mulatta


title: Measuring the effect of deoxycholate on Bacteroides fragilis gene expression

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

summary: We used RNAseq as an approach to assess the B. fragilis strain p207 response to the bile salt, deoxycholic acid (DC). A 6min DC exposure dramatically remodeled the transcriptome with approximately 20% of transcripts exhibiting significant changes. Chaperones and efflux systems were among the most highly induced genes, while protein synthesis genes were strongly repressed by DC.

overall_design: RNA-seq data were collected on triplicate samples of B. fragilis RNA from: 1) cells not exposed to deoxycholate (DC), 2) cells exposed to 0.01% DC for 6 minutes, and 3) cells exposed to 0.01% DC for 20 minutes.

first: Aretha

last: Fiebig

first: Murat

last: Eren

first: Mitch

last: Sogin

first: Eugene

last: Chang


title: A somatic cell cloned rhesus monkey obtained by trophoblast replacement [WGBS I]

overall_design: Whole genome bisulfite sequencing


title: Expression of PVRL4, a molecular target for cancer treatment, is transcriptionally regulated by FOS family protein

status: Public on Jul 31 2023

city: Tokyo

first: Kiyoshi

last: Yamaguchi

address: 4-6-1 Shirokanedai, Minato-ku

department: Division of Clinical Genome Research

country: Japan

institute: The University of Tokyo

summary: Nectin-4 or PVRL4 is a promising therapeutic target because its augmented expression has been found in a wide range of human cancers. It is of note that Enfortumab Vedotin, an ADC for PVRL4 is clinically used for the treatment of urothelial bladder cancer. In addition, rMV-SLAMblind, a genetically engineered oncolytic measles virus, can infect cancer cells and induce apoptosis through an interaction with PVRL4. Although the transcripts of PVRL4 are elevated in breast, lung and ovarian cancer, the mechanism(s) of its overexpression has not been uncovered. To clarify the regulatory mechanism(s) of its elevated expression in breast cancer cells, we searched for its regulatory region(s) using ATAC-seq and ChIP-seq data. Using breast cancer cells, we identified an enhancer region. Additional analyses disclosed that FOS interacted with the enhancer region, and the alterations of the FOS-binding motifs decreased the reporter activity. Consistent with these data, exogenous expression of FOS enhanced not only the reporter activity but also PVRL4 expression in breast cancer cells. Furthermore, RNA-seq analysis using breast cancer cells treated with PVRL4-siRNA revealed its possible involvement in cytokine response and immune systems. These data suggest that FOS is involved, at least partly, in the regulation of PVRL4 expression in breast cancer cells, and that elevated PVRL4 expression may regulate response of the cancer cells to cytokines and immune systems.

overall_design: mRNA expression profiles of SKBR3 treated with siCTRL or siPVRL4

first: Tomoyuki

last: Nanamiya

first: Kiyoko

last: Takane

first: Yoichi

last: Furukawa


title: Longitudinal Analysis of Influenza Vaccines on DNA methylation Identifies the RIG-I Signaling Pathway

first: Matteo

last: Pellegrini

address: 610 Charles E. Young Drive South TLSB room 5146, Pellegrini Lab

department: Molecular, Cell, and Developmental Biology

institute: University of California, Los Angeles

summary: Influenza virus infection was previously found to alter the promoter DNA methylation of key immune response-related genes, including type-1 interferons and proinflammatory cytokines. However, less is known about the effect of the influenza vaccine on the epigenome. Therefore, we utilized a targeted DNA methylation to study the longitudinal effects (day 0 pre-vaccination and day 28 post-vaccination) of influenza vaccination responses in peripheral blood mononuclear cells. We found that baseline methylation profiles are associated with protective immunity and immune conversion prior to influenza vaccination. Moreover, we identified 481 differentially methylated sites 28 days post-vaccination. These sites were enriched for genes involved in the regulation of the RIG-I signaling pathway, an important regulator of viral response. Our results suggest that DNA methylation changes to components of the RIG-1 pathway may impact vaccine effectiveness.

overall_design: The samples in our study were from the University of Georgia (UGA) cohorts. The influenza vaccines administered by the University of Georgia had four different cohorts, with partially overlapping participants. In this study, we focused on the third and the fourth cohorts. Peripheral blood mononuclear cells were collected, and targeted bisulfite sequencing was then performed on 63 individuals for day 0 (before influenza vaccine injection) and 96 individuals for day 28 (28 days after vaccine injection with FluZone). 55 samples were paired between pre-vaccination and post-vaccination. We sequenced approximately 5000 targeted regions within the genome that were selected based on previous evidence that they were associated with viral infections. In total, we quantified levels of DNA methylation at approximately 70,000 CpG sites.

first: Hongxiang

last: Fu

first: Harry

last: Pickering

first: Liudmilla

last: Rubbi

first: Ted

middle: M

last: Ross

first: Elaine

last: Reed


title: Uncovering the hidden threat: single-organoid analysis reveals clinically relevant treatment-resistant and invasive subclones in pancreatic cancer

city: Wilrijk

first: Maxim

last: Le Compte

state: Antwerp

address: Campus Drie Eiken, Universiteitsplein 1, T457

country: Belgium

institute: University of Antwerp, Center for Oncological Research

summary: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal diseases, characterized by a treatment-resistant and invasive nature. In line with these inherent aggressive characteristics, only a subset of patients shows a clinical response to the standard of care therapies, thereby highlighting the need for a more personalized treatment approach. In this study, we comprehensively unraveled the intra-patient response heterogeneity and intrinsic aggressive nature of PDAC on bulk and single-organoid resolution. We leveraged a fully characterized PDAC organoid panel (N=8) and matched our artificial intelligence-driven, live-cell organoid image analysis with retrospective clinical patient response. In line with the clinical outcomes, we identified patient-specific sensitivities to the standard of care therapies (gemcitabine-paclitaxel and FOLFIRINOX) using a growth rate-based and normalized drug response metric. Moreover, the single-organoid analysis was able to detect resistant as well as invasive PDAC organoid clones, which was orchestrates on a patient, therapy, drug, concentration and time-specific level. Furthermore, our in vitro organoid analysis indicated a strong correlation with the matched patient progression-free survival (PFS) compared to the current, conventional drug response readouts. This work not only provides valuable insights on the response complexity in PDAC, but it also highlights the potential applications (extendable to other tumor types) and clinical translatability of our approach in drug discovery and the emerging era of personalized medicine.

overall_design:
The identification of patient-specific responses to the standard of care regimen using organoids ans an artificial intellegence driven live cell analysis
To assess the transcriptional heterogeneity between the included patients (N=8), we performed a baseline bulk RNA seq analysis
To assess the effect of Gemcitabine-paclitaxel, we performed a bulk RNA seq analysis of 2 patients after treatment.

first: Christophe

last: Deben


title: Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies to widely expressed self-antigens

city: Woodbury

first: Jonathan

last: Preall

state: NEW YORK

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

summary: Intratumoral B cell responses are associated with more favorable clinical outcomes in human pancreatic ductal adenocarcinoma cancer (PDAC). However, the antigens driving these B cell responses are largely unknown. We sought to discover these antigens by using single-cell RNA (sc-RNASeq) and immunoglobulin (Ig) sequencing of tumor-infiltrating immune cells from seven primary PDAC samples. We identified activated T and B cell responses and evidence of germinal center reactions. Ig sequencing identified plasma cell (PC) clones expressing isotype-switched and hyper-mutated Igs, suggesting the occurrence of T cell-dependent B cell responses. We assessed the reactivity of 41 recombinant antibodies that represented the products of 235 PCs and 12 B cells toward multiple cell lines and PDAC tissue, and identified frequent staining of intracellular self-antigens. Three of these antigens were identified: the filamentous actin (F-actin), the nucleic protein, RUVBL2, and the mitochondrial protein, HSPD1. Antibody titers to F-actin and HSPD1 were frequently elevated in the plasma of PDAC patients, and also detectable in healthy donors. Thus, PCs in PDAC frequently produce auto-antibodies reacting with intracellular self-antigens, which may result from promotion of pre-existing autoreactive B cell responses. These observations indicate that the chronic inflammatory microenvironment of PDAC can support the adaptive immune responses.

overall_design: single-cell RNA-seq and BCR-seq

first: Min

last: Yao

first: Douglas

last: Fearon


title: Immune and stromal transcriptional patterns in cHL

status: Public on Jul 30 2023

city: MADRID

first: Juan F

last: Garcia

state: MADRID

address: C/ ARTURO SORIA 270

institute: MD ANDERSON CANCER CENTER MADRID

summary: Gene-expression profiling from 31 cHL FFPE samples using the NanoString technology, with the PanCancer Immune Profiling Panel with 30 extra custom genes, up to 800 total genes

overall_design: 31 FFPE tumor samples of lymph nodes affected by classical Hodgkin lymphoma (cHL); PanCancer Immune Profiling Panel with 30 extra custom genes, up to 800 total genes

first: Juan

last: García

first: Victoria

last: Menéndez


title: RA-induced prominence-specific response resulted in distinctive regulation of Wnt and osteogenesis [mRNA-seq]

status: Public on Jul 29 2023

first: Yi

last: Zou

address: West Huangpu Avenue

institute: Jinan University

summary: Proper retinoic acid (RA) signaling is essential for normal craniofacial development. Both excessive RA and RA deficiency in early embryonic stage led to a variety of craniofacial malformations, e.g., cleft palate, which have been investigated extensively. Dysregulated Wnt and Shh signaling were shown to underlie the pathogenesis of RA-induced craniofacial defects. In our present study, we showed a spatiotemporal-specific effect of RA signaling in regulating early development of facial prominences. While inhibited the Wnt activities in E12.5/E13.5 mouse palatal shelves, early exposure of excessive RA induced Wnt signaling and Wnt-related gene expression in mouse embryonic Frontonasal/Maxillary processes. A conserved regulatory network of miR-484-Fzd5 was identified to play critical roles in RA regulated craniofacial development using RNA-seq.

overall_design: In this work we investigated the changes in gene expression profile in the developing craniofacial prominences of RA induced CLP mouse model. Multiple dosages of all-trans RA (atRA) were applied to pregnant mice between early gestation (from E8.5 to E 10.5) to induce full penetrance of CL/P. The frontonasal prominence (FnP), a pair of maxillary processes (MxP) and a pair of mandibular processes (MdP) at E12.5 were collected and subjected to mRNA-sequencing. To minimize the chance of variance due to casualness in sampling, each of the fetus was collected from an independent conception with (n=4) or without RA exposure (n=4). The dysregulated craniofacial development was confirmed by morphological analysis before sampling.

first: Chao

last: Song


title: RA-induced prominence-specific response resulted in distinctive regulation of Wnt and osteogenesis


title: RA-induced prominence-specific response resulted in distinctive regulation of Wnt and osteogenesis [miRNA-seq]

overall_design: In this work we investigated the changes in gene expression profile in the developing craniofacial prominences of RA induced CLP mouse model. Multiple dosages of all-trans RA (atRA) were applied to pregnant mice between early gestation (from E8.5 to E 10.5) to induce full penetrance of CL/P. The frontonasal prominence (FnP), a pair of maxillary processes (MxP) and a pair of mandibular processes (MdP) at E12.5 were collected and subjected to miRNA-sequencing. To minimize the chance of variance due to casualness in sampling, each of the fetus was collected from an independent conception with (n=4) or without RA exposure (n=4). The dysregulated craniofacial development was confirmed by morphological analysis before sampling.


title: PCSK9, a promising novel target for age-related cardiovascular dysfunction

city: Gothenburg

first: Muhammad

last: Arif

state: Västra Götaland

address: Blå Straket 5/WLAB

department: Department of Molecular and Clinical Medicine

country: Sweden

institute: University of Gothenburg

summary: Cardiovascular diseases (CVD) are the leading cause of death among elderly people. Proprotein convertase subtilisin/kexin type 9 (PCSK9) is an important regulator of cholesterol metabolism. Herein, we investigated the role of PCSK9 in age-related CVD. Both in humans and rats, sPCSK9 correlated positively with increasing age and the development of cardiovascular dysfunction. Network analysis identified PCSK9 as an important factor in age-associated lipid alterations and it correlated positively with intima media thickness, a clinical parameter of CVD risk. PCSK9 inhibition with alirocumab effectively reduced the CVD progression in aging rats suggesting that PCSK9 plays an important role in cardiovascular aging.

overall_design: A population-based screening program and the iNetModels database were used to explore the PCSK9’s role in cardiovascular aging in humans. A rat model of advanced aging was applied to study age-related cardiovascular/hepatic changes and to investigate the effects of PCSK9 inhibition on cardiovascular aging.

first: Csaba

last: Matyas

first: Eszter

last: Trojnar

first: Suxian

last: Zhao

first: Partha

last: Mukhopadhyay

first: Attila

last: Kovacs

first: Alexandra

last: Fabian

first: Marton

last: Tokodi

first: Zsolt

last: Bagyura

first: Bela

last: Merkely

first: Laszlo

last: Kohidai

last: Lajko

first: Angela

last: Takacs

first: Yong

last: He

first: Bin

last: Gao

first: Janos

last: Paloczi

first: Falk

last: Lohoff

first: Gyorgy

last: Hasko

first: Wen-Xing

last: Ding

first: Pal

last: Pacher


title: Cytosine methylation profiling in small and large for gestational age newborns

status: Public on Jul 26 2023

city: Halifax

first: Alejandro

last: Lomniczi

state: NS

address: 5850 College Street

department: Physiology and Biophysics

institute: Dalhousie University

summary: In 1990, David Barker proposed that prenatal nutrition is directly linked to adult cardiovascular disease. Since then, the relationship between adult cardiovascular risk, metabolic syndrome and birth weight has been widely documented. Here we used the TruSeq Methyl Capture EPIC platform to compare the methylation patterns in cord blood from large for gestational age (LGA), small for gestational age (SGA) and  adequate for gestational age/Control (AGA/Ctl) newborns. We found several differentially methylated CpGs (DMCs) and differentially methylated regions (DMRs) between LGA, SGA and AGA groups. A system biology approach identified several biological processes significantly enriched with genes in association with DMCs including Regulation of transcription, Regulation of epinephrine secretion, Norepinephrine biosynthesis, Receptor transactivation, Forebrain regionalization and several terms related with kidney and cardiovascular development. Gene ontology analysis of the genes in association with the DMRs identified several significantly enriched biological processes related with kidney development including Mesonephric duct development and Nephron tubule development. Furthermore, our dataset identified several DNA methylation markers enriched at gene networks involved in biological pathways and rare diseases of the cardiovascular system, kidneys and metabolism. Our study identified several DMCs/DMRs in association with fetal growth patterns. The use of cord blood as material for the identification of DNA methylation biomarkers gives us the possibility to perform follow up studies on the same patients as they enter childhood and puberty. These studies will not only help us understand how the methylome responds to continuum postnatal growth but also link early alterations of the DNA methylome with later clinical markers of growth and metabolic fitness.

overall_design: A total of 36 newborns were included in the study: 13 were classified as SGA, 11 as LGA and 12 as AGA (Ctl). LGA: newborns ≥ 34 weeks of gestational age, whose weight and / or length were >+ 2 SDS (Z-score) according to sex-specific birth weight and birth length gestational age reference charts. SGA: newborns ≥ 34 weeks of gestational age, whose weight and / or length were <- 2 SDS according to sex-specific birth weight and birth length gestational age reference charts. AGA (Ctl): newborns ≥ 34 weeks of gestational age, whose weight and length were between – 2 and + 2SDS according to sex-specific birth weight and birth length gestational age reference charts. Umbilical cord blood was collected and genomic DNA was immediately extracted from whole umbilical cord blood using an automated DNA extractor (BioRobot EZ1, QIAGEN, Hilden, Germany).

first: Lomniczi

last: Alejandro

first: Soriano-Guillén

last: Leandro


title: Bioinformatics-driven discovery of silica nanoparticles induces apoptosis and renal damage via the unfolded protein response in NRK-52E cells and rat kidney

city: Changchun

first: Mindan

last: Sun

address: Street Xinmin 1

institute: the First Hospital of Jilin University

summary: Silica nanoparticles (SiNPs), a type of nanomaterial, have widespread applications in drug delivery and disease diagnosis. Despite their utility, SiNPs can lead to chronic kidney disease (CKD), which hinders their clinical translation. The molecular mechanisms responsible for SiNPs-induced renal toxicity are intricate and still need elucidation. To address this challenge, our study employed bioinformatics tools to predict potential mechanisms underlying renal damage caused by SiNPs. We identified 1627 up-regulated differentially expressed genes (DEGs) and 1334 down-regulated DEGs. Functional enrichment analysis and the protein-protein interaction (PPI) network revealed that SiNPs-induced renal damage is associated with apoptosis. Subsequently, we verified that SiNPs induce apoptosis in an in vitro model of NRK-52E cells via the unfolded protein response (UPR) in a dose-dependent manner. Furthermore, in an in vivo rat model, high-dose SiNPs administration via tracheal drip caused hyalinization in renal tubules, renal interstitial lymphocytic infiltration, and collagen fiber accumulation. Concurrently, we observed an increase in UPR-related proteins with the onset of renal damage. Thus, our study confirms that SiNPs induce apoptosis and renal damage through the unfolded protein response, adding to the theoretical understanding of SiNPs-related kidney damage and offering a potential target for preventing and treating kidney injuries in SiNPs clinical applications.

overall_design: To analyze the molecular mechanisms responsible for SiNPs-induced renal toxicity

first: Naimeng

last: Liu

first: Meng

last: Li

first: Huan

last: Pang

first: Tiantian

last: Tian

first: Xinyue

first: Yanchi

last: Su

first: Minghua

last: Jin

first: Hao

last: Wu

first: Chuyue

last: Qian


title: EBF2 links KMT2D-mediated H3K4me1 to suppress pancreatic cancer progression via upregulating KLLN.

status: Public on Jul 18 2023

city: Nanjing

first: Mengying

last: Xing

address: 163 Xianlin Avenue

department: The State Key Laboratory of Pharmaceutical Biotechnology

institute: Nanjing University

overall_design: Refer to individual Series


title: EBF2 links KMT2D-mediated H3K4me1 to suppress pancreatic cancer progression via upregulating KLLN [RNA-seq]

summary: We sought to elucidate the roles of KMT2D- and EBF2-regulated H3K4me1 in gene expression through profiling the gene transcription in PDAC cells overexpressed with EBF2 (EBF2-OE) or activated by GSK-LSD1, a selective inhibitor of KDM1A/LSD1 which can increase H3K4me1 level via blocking the histone H3K4 demethylase activity of KDM1A/LSD1

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SW1990 cells overexpressed with EBF2 (EBF2-OE) or activated by GSK-LSD1

first: Bing

last: Yao

first: Changyan

last: Ma


title: EBF2 links KMT2D-mediated H3K4me1 to suppress pancreatic cancer progression via upregulating KLLN [ChIP-seq]

summary: ChIP-seq revealed a strong reduction of KMT2D, H3K4me1 and EBF2 signals at the transcription start site (TSS) and promoter regions of genes that were downregulated in KMT2D-depleted (KMT2D-KD) cells

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChlP-seq) for KMT2D, EBF2 as well as the histone modifications H3K4me1 in negative control and KMT2D knowndown SW1990 cells.


title: EBF2 links KMT2D-mediated H3K4me1 to suppress pancreatic cancer progression via upregulating KLLN [Cut&Tag]

summary: CUT-Tag revealed a strong reduction of KMT2D, H3K4me1 and EBF2 signals at the transcription start site (TSS) and promoter regions of genes that were downregulated in KMT2D-depleted (KMT2D-KD) cells

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) for KMT2D, EBF2 as well as the histone modifications H3K4me1 in negative control and KMT2D knowndown SW1990 cells.


title: Effect of Cnn1 Knockout on Aortic Smooth Muscle Cell Transcriptome

status: Public on Jul 27 2023

city: Augusta

first: Joseph

last: Miano

address: 1460 Laney Walker Blvd, CL-3060

institute: Medical College of Georgia at Augusta University

summary: Smooth muscle cell (SMC) contraction and vascular tone are modulated by phosphorylation and multiple modifications of the thick filament. Thin filament regulation of SMC contraction has been reported to involve extracellular regulated kinase (ERK). Previous studies suggest that the actin-binding protein, calponin 1 (CNN1), acts as a scaffold linking protein kinase C (PKC), Raf, MEK, and ERK, promoting PKC-dependent ERK activation. To definitively test this hypothesis, and to gain further insight into the role of CNN1 in ERK activation and the regulation of SMC contractility, we generated a novel Calponin 1 knockout mouse (Cnn1 KO) by a single base substitution in an intronic CArG box that abolishes expression of CNN1 in a vascular SMC-restricted manner. Using this new Cnn1 KO mouse, we show that ablation of CNN1 has two effects, depending on the cytosolic free calcium level: (1) a reduced amplitude of stress and stiffness but an increase in agonist-induced ERK activation in the presence of elevated intracellular calcium caused by agonist stimulation; and (2) an increased duration of SM tone maintenance during intracellular calcium depletion, in the presence of an agonist. Together, these results indicate that CNN1 plays an important and complex modulatory role in SMC contractile tone amplitude and maintenance.

overall_design: Differential gene expression in the aorta of Cnn1 KO mice


title: Inhibition of PIK3CA by miR-203a-3p reduces hypertrophic scar formation via PI3K/AKT/mTOR signaling pathway

status: Public on Jul 15 2023

first: Julin

last: Xie

state: State...

address: Zhongshan 2nd Road, Yuexiu District, Guangzhou city, Guangdong Province, China

institute: First Affiliated Hospital of Sun Yat-sen University

summary: Hypertrophic scar (HS) is a skin fibroproliferative disease currently having no truly effective therapy. PIK3CA is a catalytic subunit of PI3K able to promote collagen synthesis in benign fibrotic diseases and to regulate cell survival, proliferation, and adhesion in malignancies. To explore PIK3CA’s functions in HS formation, we performed transcriptome sequencing and experimental validation. PIK3CA were overexpressed in HS tissues, and positively correlated with fibrosis. We then screened out miR-203a-3p as the most suitable endogenous inhibitor of PIK3CA through bioinformatics. Intriguingly, miR-203a-3p suppressed the proliferation, migration, collagen synthesis, and contractility, as well as trans-differentiation of fibroblasts into myofibroblasts in vitro, improved the morphology and histology of HS in vivo. Mechanistically, miR-203a-3p attenuated fibrosis by inactivating PI3K/AKT/mTOR pathway via directly targeting PIK3CA. In conclusion, Our findings identified that PIK3CA and PI3K/AKT/mTOR pathway were actively involved in HS formation and demonstrated that miR-203a-3p might serve as a potential strategy for HS therapy through targeting PIK3CA and inactivating PI3K/AKT/mTOR pathway.

overall_design: To investigate the function of miR-203a-3p in the regulation of hypertrophic scar fibroblasts (HSFs) fibrosis, we established HSFs cell lines in which miR-203a-3p has been overexpressed by lentivirus.

first: Shixin

last: Zhao

first: Hengdeng

first: Ronghua

last: Yang


title: Epigenetic profiles guide optimized CRISPR/Cas9-mediated gene knockout in human T cells

status: Public on Jul 14 2023

city: Shinjuku-ku

first: Yusuke

last: Ito

state: Tokyo

address: 35 Shinanomachi

department: Division of Tumor Immunology

institute: Keio University

summary: Short-term culture with IL-7 improves CRISPR/Cas9-mediated gene-editing efficiency in naïve T cells. In order to investigate the effect of culture with IL-7, we performed RNA sequencing analysis using human T cells.

overall_design: Human peripheral blood mononuclear cells derived from 2 healthy different donors (0309 and D110) were used. CD8+ naïve T cells (CD8+CD45+CCR7+), CD8+ unstimulated T cells cultured in the presence of IL-7 for 3 days (CD8+CD45+CCR7+), and CD8+ T cells which were stimulated and cultured in the presence of IL-2 and IL-15 for 3 days (CD8+) were isolated by flow cytometry and subjected to RNA sequencing.

first: Yuki

last: Kagoya


title: Dynamic phosphorylation of G9a by Plk1 and PP2A modulates its catalytic activity and chromosome accessibility during mitosis

status: Public on Jul 17 2023

city: Wuhan

first: Yueyu

last: Kong

state: Hubei

address: Wuhan University

institute: Wuhan University

summary: Phosphorylation of Ser10 of histone H3 (H3S10p), together with the adjacent dimethylation of Lys9 (H3K9me2), has been proposed to function as a ‘phospho-methyl switch’ to regulate mitotic chromosome dynamics and control peripheral heterochromatin localization (1, 2). Despite of immensely understanding the regulation of H3S10 phosphorylation, how this modification temporarily masks the H3K9me2 mark during mitosis is poorly understood. Herein, we report that the master mitotic kinase Plk1 phosphorylates G9a at Thr1045 (pT1045) in vitro and in vivo at early mitosis. T1045p inhibits G9a catalytic activity, leading to decrease H3K9me2 levels. RNA-sequencing analysis showed that the phospho-mimic T1045 mutant of G9a (T1045E) compromised its repressive activity on several targeted genes, which was confirmed by luciferase reporter assays. Using genome-wide epigenomic technologies, we found that T1045E mutant displayed reduced H3K9me2 level, accompanied with increased chromatin accessibility, compared to the wild-type G9a cells. Finally, we found that T1045 phosphorylation could be removed by the phosphatase PP2A at late mitosis, which inversely reactivated G9a activity on H3K9me2 level, correlated with lower levels of H3S10p. Therefore, our result may provide a mechanistic explanation for ‘phospho-methyl switch’ and highlight the importance of Plk1 and PP2A-mediated dynamic regulation of G9a during mitosis.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for HEK293T cells and its overexpression derivatives (T1045E G9a and WT G9a).
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K9me2 in HeLa S3 cells.
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) for the different treatments in HeLa S3 cells.

first: Qizhi

last: Geng