title: Heterologous ChAdOx1-BNT162b2 vaccination in Korean cohort induces robust immune and antibody responses that includes Omicron

summary: Heterologous ChAdOx1-BNT162b2 vaccination induces a stronger immune response than BNT162b2-BNT162b2. Here we investigated the molecular transcriptome, germline allelic variants of immunoglobulin loci, and anti-Omicron antibody levels in 46 office and lab workers from the Republic of Korea following ChAdOx1-BNT162b2 vaccination. Anti-spike-specific IgG antibody levels against the ancestral SARS-CoV-2 strain increased from 70 AU/ml to 14,000 AU/ml to 142,000 AU/ml one, three and seven days following the second vaccination. Titers against VOC, including Omicron, were two- to three-fold lower, yet higher than those measured following BNT162b2-BNT162b2 vaccination. RNA-seq of peripheral immune cells demonstrated activation of interferon pathways with increased IGHV clonal transcripts encoding neutralizing antibodies. scRNA-seq revealed enriched B cell and CD4+ T cell responses in both ChAdOx1-BNT162b2 and BNT162b2-BNT162b2 recipients, but a stronger clonal expansion of memory B cells with ChAdOx1-BNT162b2. In summary, heterologous ChAdOx1-BNT162b2 provides an innate and adaptive immune response that exceeds homologous BNT162b2 vaccination.


title: High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails [Ampli-seq]

status: Public on May 21 2022

city: San Francisco

first: Vivasvan

last: Vykunta

state: CA

address: 513 Parnassus Avenue HSW901

country: USA

institute: Gladstone-UCSF Institute of Genomic Immunology

summary: Enhancing site-specific transgene insertion efficiency by homology-directed repair (HDR) using high concentrations of double-stranded DNA (dsDNA) with Cas9 target sequences (CTSs) can be toxic to primary cells. Here, we develop single-stranded DNA (ssDNA) HDR templates (HDRTs) incorporating CTSs with reduced toxicity that boost knock-in efficiency and yield by an average of 2–3-fold relative to dsDNA CTSs. Using small-molecule combinations that enhance HDR, we could further increase knock-in efficiencies by an additional 2–3-fold on average. Our method works across a variety of target loci, knock-in constructs, and primary human cell types, reaching HDR efficiencies of >80–90%. We demonstrate application of this approach for both pathogenic gene variant modeling and gene-replacement strategies for IL2RA and CTLA4 mutations associated with Mendelian disorders. Finally, we develop a good manufacturing practice (GMP)-compatible process for non-viral chimeric antigen receptor (CAR)-T cell manufacturing, with knock-in efficiencies (46–62%) and yields (>1.5×109 modified cells) exceeding those of conventional approaches.

overall_design: Amplicon sequencing for detection of insertions and deletions after CRISPR-Cas9 mediated DNA modifications at arrayed target sites.

first: Brian

middle: R

last: Shy

middle: S

first: Alexander

last: Marson

first: Theodore

middle: L

last: Roth

first: Eric

last: Shifrut


title: Single-cell RNA sequencing reveals molecular features of postnatal maturation in the murine retinal pigment epithelium

status: Public on May 19 2022

city: Bar Harbor

first: Gregory

middle: W.

last: Carter

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

type: Expression profiling by high throughput sequencing

summary: Transcriptomic analysis of the mammalian retinal pigment epithelium (RPE) aims to identify cellular networks that influence ocular development, maintenance, function, and disease.  However, available evidence points to RPE cell heterogeneity in the native tissue, which adds complexity to transcriptomic analysis. Here, to assess cell heterogeneity, we performed single-cell RNA sequencing of RPE cells from two young adult male C57BL/6J mice. Following quality control to ensure robust transcript identification limited to cell singlets, we detected 13,858 transcripts among 2,667 and 2,846 RPE cells, respectively. Dimensional reduction by principal component analysis and uniform manifold approximation and projection revealed six distinct cell populations. All clusters expressed transcripts typical of RPE cells; the smallest (C1, containing 1–2% of total cells) exhibited hallmarks of stem and/or progenitor cells. Placing C1–6 along a pseudotime axis suggested a relative decrease in melanogenesis and stem/progenitor gene expression, and a corresponding increase in visual cycle gene expression upon RPE maturation. K-means testing of all detected transcripts identified additional expression patterns that may advance understanding of RPE stem/progenitor cell maintenance and the evolution of cellular metabolic networks during development. This work provides new insights into the transcriptome of the mouse RPE and a baseline for identifying experimentally induced transcriptional changes in future studies of this tissue.

overall_design: 2 replicates

first: Ravi

last: Pandey

first: Mark

middle: P

last: Krebs

first: Mohan

middle: T

last: Bolisetty

first: Jeremy

last: Charette

first: Jürgen

middle: K

last: Naggert

first: Paul

last: Robson

first: Patsy

middle: M

last: Nishina

middle: W


title: Heterologous ChAdOx1-BNT162b2 vaccination in a Korean cohort induces a robust genetic immune and antibody response that includes Omicron [RNA_seq]

status: Public on May 20 2022

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: Heterologous ChAdOx1-BNT162b2 vaccination induces a stronger immune response than two doses of BNT162b2. Yet, the molecular transcriptome, the germline allelic variants of immunoglobulin loci and anti-Omicron antibody levels induced by the heterologous vaccination have not been formally investigated. Moreover, there is a paucity of COVID-19 vaccine studies including diverse genetic populations. Here, we show a robust molecular immune transcriptome and antibody repertoire in 46 office and lab workers from the Republic of Korea after heterologous vaccination, ChAdOx1 followed by BNT162b2. Anti-spike-specific IgG antibody levels against the ancestral SARS-CoV-2 strain increased from 70 AU/ml immediately following the first vaccination to 14,000 U/ml within three days after the second vaccination and 142,000 AU/ml after seven days. Antibody titers against more recent variants, including Omicron, were two- to three-fold lower, yet higher than those obtained after the second dose of a BNT162b2-BNT162b2 homologous vaccination. RNA-seq conducted on peripheral immune cells demonstrated a strong activation of interferon-induced genetic programs in the heterologous cohort and an increase of specific IGHV clonal transcripts encoding neutralizing antibodies was detected. Enrichment of B cell and CD4+ T cell responses was observed following both ChAdOx1-BNT162b2 heterologous and BNT162b2-BNT162b2 homologous vaccination using scRNA-seq, but clonally expanded memory B cells were relatively stronger in the heterologous cohort. In summary, a heterologous vaccination with ChAdOx1 followed by BNT162b2 provides an innate and adaptive immune response exceeding that seen in homologous BNT162b2 vaccination.

overall_design: RNA-seq were performed with peripheral blood mononuclear cells (PBMCs) from individuals who had received the ChAdOx1 or BNT162b2 mRNA vaccines.

first: Hye-Kyung


title: Impaired interferon-γ signaling promotes the development of silicosis

city: Changsha

first: Zhouyangfan

last: Peng

address: No.138 Tongzipo Road

country: China

institute: Third Xiangya Hospital, Central South University

summary: Silicosis is caused by inhalation of crystalline silica dust particles and known as one of the most serious occupational diseases worldwide. However, little is known about intrinsic factors leading to disease susceptibility. Using single-cell sequencing of bronchoalveolar lavage fluid (BALF) of mine workers with silicosis and their co-workers who did not develop silicosis, we found that the impaired interferon (IFN)-γ signaling in myeloid cells was strongly associated with the occurrence of silicosis. In a murine model of silicosis, global or myeloid cell-specific deletion of interferon γ receptor (IFN-γR) markedly enhanced the silica crystals-induced pulmonary interstitial fibrosis and respiratory dysfunction in wild-type but not in mutant mice deficient in NOD-like receptor family pyrin domain-containing 3 (NLRP3). In vitro, IFN-γ priming of macrophages suppressed the crystalline silica-induced NLRP3 inflammasome activation partly by inducing the formation of spacious phagosomes with relatively reduced ratio of crystalline silica/phagosomal areas/volumes through the RAB20-dependent membrane trafficking pathway. RAB20 deficiency was associated with the elevated susceptibility to silicosis as well as the elevated NLRP3 inflammasome activation in a manner similar to the impaired IFN-γ signaling. Thus, these findings provide novel molecular insights into the intricate mechanisms underlying innate immunity-mediated host responses to environmental irritants, and shed light on the future development of novel therapies for the prevention of silicosis.

overall_design:
Bronchoalveolar lavage fluid cells from 2 exposure and 3 silicosis patients were counted and loaded onto the 10x device (10x Genomics). Cells were processed the manufacturer’s protocol and sequenced on Illumina NextSeq sequencer. Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of sequencing runs were performed using the Cell Ranger analysis pipeline (V4.1).

>>>Submitter states that raw data are unavailable due to patient privacy concerns.<<<

first: Fang

last: Liang

first: Ben

last: Lu


title: Olfactory epithelium transcriptomes of the Nycticorax nycticorax and Egretta garzetta

status: Public on May 16 2022

city: Xiamen

first: Haoran

last: Luo

state: Fujian

address: Xiang'annan Road, Xiang'an District

institute: Xiamen University

summary: To understand the expression leves of the olfactory receptor genes, We sequenced transcriptomes of 12 olfactory epithelium samples of the Nycticorax nycticorax and Egretta garzetta.

sample_organism:
Nycticorax nycticorax
Egretta garzetta

platform_organism:
Nycticorax nycticorax
Egretta garzetta

overall_design: We sequenced transcriptomes of 12 olfactory epithelium samples of the Nycticorax nycticorax and Egretta garzetta. The nestling BC-Night Heron group included 3 individuals whose body length were less than 15cm, with brown mottled feather and olfactory bulbs were not developed. The adult group included another three individuals whose body length were more than 40cm, with the metallic green-black feather, and olfactory bulbs developed to reach the normal adult heron size (4.1 mm)(Cobb 1968). For Six Little Egrets individuals, the nestling Little Egret group included 3 individuals whose body length were less than 15cm and olfactory bulbs were not developed. The adult Little Egret group included another three individuals whose body length were more than 50cm and olfactory bulbs developed to reach the normal size.

first: Xiaolin

last: Chen

first: Xiaoping

last: Zhou


title: Effect of hemin and of HAP1 on C. albicans expression pattern

city: Haifa

first: Daniel

last: Kornitzer

address: 1, Efron St

department: Faculty of Medicine

country: Israel

institute: Technion - IIT

summary: To test the effect of hemin and of HAP1 in C. albicans, a hap1 mutant and it's reintegrant (wild-type) strain were grown in YPD to log phase, and then exposed or not to 50 microM hemin for 30'.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hap1-/- cells with vector or with HAP1 reintegrant, with or without hemin, 3 biological replicates each (12 total).


title: tRForest: a novel random forest-based algorithm for tRNA-derived fragment target prediction

city: Birmingham

first: Anindya

last: Dutta

state: AL

address: 720 20th Street South, Kaul 230

department: Genetics

institute: University of Alabama at Birmingham

summary: tRNA fragments (tRFs) are a novel class of small RNAs comparable to the size and function of miRNAs. We and others have shown that tRFs are generally Dicer independent, can be found in abundance in the miRNA effector protein Ago, and can repress expression of specific genes that have complementarity to their 5’ seed-sequences. Given that this greatly expands the repertoire of small RNAs capable of post-transcriptional gene expression, it is important to predict tRF targets with confidence. Some attempts have been made to predict tRF targets, but are limited in the scope of tRF classes used in prediction or limited in feature selection. We hypothesized that established miRNA target prediction features applied to tRFs through a random forest machine learning algorithm will immensely improve tRF target prediction. Using this approach, we show significant improvements in tRF target prediction for all classes of tRFs and validate our predictions in two independent cell lines. Finally, using Gene Ontology analysis, we provide evidence that tRF-3009a targets may be involved in neural development. These improvements to tRF target prediction further our understanding of tRF function broadly across species and tRF types, and provide avenues for testing novel roles for tRFs in biology.

overall_design: mRNA sequencing was performed on U87 cells transfected with either tRF-3009a mimic or control single stranded siGL2 mimic.

first: Zhangli

last: Su

first: Rohan

last: Parikh

first: Briana

last: Wilson

first: Shekhar

last: Saha


title: Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients

status: Public on May 13 2022

city: Singapore

first: Lih Feng

last: Cheow

address: 4 Engineering Drive 3

department: Biomedical Engineering

country: Singapore

institute: National University of Singapore

type: Methylation profiling by high throughput sequencing

summary: Genome-wide analysis of cell-free DNA (cfDNA) methylation profile has been recognized as a promising approach for sensitive and specific detection of many cancers. However, scaling such genome-wide assays for clinical translation is impractical due to the high cost of whole genome bisulfite sequencing. We have shown that the small fraction of GC-rich genome is highly enriched in CpG sites and disproportionately harbors the majority of cancer-specific methylation signature. Here, we report on the simple but effective Heat enrichment of CpG-rich regions for Bisulfite Sequencing (Heatrich-BS) platform that allows for focused methylation profiling in these highly informative regions. Our novel method and bioinformatics algorithm enable accurate tumor burden estimation with high sensitivity and quantitative tracking of colorectal cancer patient’s response to treatment, at much reduced sequencing cost suitable for frequent monitoring. We also show, for the first time, tumor epigenetic subtyping from cfDNA using Heatrich-BS, which could enable patient stratification from non-invasive liquid biopsy. As such, Heatrich-BS holds great potential for highly scalable screening and regular monitoring of cancer using liquid biopsy.

overall_design: Analysis of GC content, CpG enrichment and methylation status in K562 genomic DNA

first: Elsie

last: Cheruba

first: Ramya

last: Viswanathan

first: Pui-Mun

last: Wong

first: Howard

middle: J

last: Womersley

first: Shuting

last: Han

first: Brenda

last: Tay

first: Yiting

last: Lau

first: Anna

last: Gan

first: Polly

last: Poon

first: Anders

last: Skanderup

first: Sarah

middle: B

last: Ng

first: Aik

middle: Y

last: Chok

first: Dawn

middle: Q

last: Chong

first: Iain

last: Tan

first: Lih

middle: F


title: Recapitulation of the pro-inflammatory signature of monocytes with ACVR1 mutation using FOP patient-derived iPSCs

status: Public on May 12 2022

city: Kyoto

first: Hirotsugu

last: Maekawa

address: 54 Shogoin-Kawaharacho, Sakyo-ku

country: Japan

institute: Kyoto Universiy

summary: Fibrodysplasia ossificans progressiva (FOP) is a rare genetic disease characterized by progressive heterotopic ossification (HO) in soft tissues due to a heterozygous mutation of the ACVR1A/ALK2 gene (FOP-ACVR1A), which erroneously transduces the BMP signal by Activin-A. Although inflammation is known to trigger HO in FOP, the role of FOP-ACVR1A on inflammatory cells remains to be elucidated. Here we investigated this issue using immortalized monocytic cell lines from FOP-iPSCs (FOP-ML) and mutation-rescued iPSCs (resFOP-ML). Without any stimulation, FOP-ML showed the pro-inflammatory signature of CD16+ monocytes with an up-regulation of INHBA gene, and treatment of resFOP-ML with Activin-A induced an expression profile consistent with FOP-ML at baseline. Treatment of FOP-ML with Activin-A further induced the inflammatory profile with the up-regulation of inflammation-associated genes, some of which were suppressed by corticosteroid. Experiments using an inhibitor for TGFβ or BMP signals demonstrated that Activin-A-induced genes, such as CD16 and CCL7, were regulated by both signals, indicating Activin-A transduced dual signals in FOP-ML. A comparison with resFOP-ML identified several down-regulated genes in FOP-ML, including LYVE-1, which is known to suppress matrix-formation in vivo. The down-regulation of LYVE-1 in HO tissues was confirmed in FOP model mice, verifying the in vitro experiments. These results indicate that FOP-ML faithfully recapitulated the phenotype of primary monocytes in FOP and its combination with resFOP-ML is useful for investigating the molecular events at the initial inflammation stage of HO in FOP.

overall_design: To investigate the effect of mutant ACVR1, monocytic cell lines established from fibrodysplasia ossificans progressiva patient derived induced pluripotent stem cells and those mutation corrected were stimulated by Activin A or Lipopolysaccharide

first: Junya

last: Toguchida


title: Transcriptomics data on E. coli lacking queuosine tRNA modification (tgt deficient strain) exposed or not to nickel stress.

status: Public on May 15 2022

city: Gainesville

first: Leticia

last: Pollo-Oliveira

state: FL

address: 1355 Museum Dr

department: Microbiology and Cell Science

institute: University of Florida

summary:
Purpose: to observe differences in E. coli transcripts levels due to the absence of the tRNA modification queuosine and due to exposure to excess nickel.
Methods: RNAseq was performed using the total RNA isolated from E. coli MG1655 WT and Δtgt strains grown in LB medium only or in LB added by 2 mM NiCl2.
Results: in nickel-treated WT compared to untreated WT (WT_Ni/WT_LB) 734 genes were found up-regulated and 1,642 genes down-regulated in the treated cells; in the tgt mutant compared to the WT strain (tgt_LB/WT_LB), 417 genes were found up regulated and 1,053 genes down regulated in the tgt mutant.
Conclusions: the gene expression pattern of the tgt deficient cell in LB medium resembles the one of the WT strain exposed to nickel, showing repression of iron-import genes and genes associated to anaerobic metabolism; increased resistance to nickel stress observed in the tgt mutant is explained by the repression of the nickel import system nikABCCDE.

overall_design: mRNA profiles of E. coli K-12 MG1655 wild type (WT) and tgt mutant, in LB medium and LB supplemented with 2 mM nickel (Ni), in triplicate, were generated by deep sequencing, using HiSeq 2500 System (Illumina).

last: Pollo de Oliveira

first: Cécile

last: Pereira

first: Ana

last: Conesa

first: Valérie

last: de Crécy‐Lagard


title: Constitutive activity of the cation channel TRPM8 regulates the function and differentiation of human monocytes

city: London

first: Hamish

last: King

address: 4 Newark St

department: Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

summary: This study investigated the impact of TRPM8 activity on human monocyte differentiation and function.   CD14+ peripheral blood monocytes were isolated from healthy volunteers and differentiated into macrophages using M-CSF, in the presence or absence of 10μM AMTB (TRPM8 antagonist).  RNA seq was performed on CD14+ monocytes and macrophages differentiated in vehicle(Mo-M-DMSO) or AMTB (Mo-M-AMTB).  To assess the transcriptional changes that normally occur in monocyte to macrophage differentiaiton we compared the Mo-M-DMSO and CD14+ monocyte samples. 3109 genes were significantly down-regulated and 3403 up-regulated in Mo-M-DMSO samples compared to CD14+ monocytes. To investigate the impact of AMTB upon macrophage differentiation we compared the Mo-M-DMSO and Mo-M-AMTB.  556 genes were significantly lower and 421 genes were significantly higher in Mo-M-AMTB samples compared to Mo-M-DMSO samples. 331 out of the 556  genes lower in Mo-M-AMTB samples were genes that were normally up-regulated during differentiaiton and  253 out of the 421 genes higher in the Mo-M-AMTB samples were genes that were normally down-regulated during differentiation indicating that AMTB predominantly acts to inhibit aspects of the differentiation programme.

overall_design: Peripheral blood CD14+ monocytes from 5 healthy donors were differentiated into macrophages (Mo-M) by 6 days culture with M-CSF, in the presence of 10μM AMTB or vehicle (DMSO). PolyA+ RNA seq was performed on CD14+ monocytes, Mo-M-DMSO and Mo-M-AMTB samples.

first: Eve

last: Hornsby

first: Andrew

last: Stagg


title: Transgenic expression of Nrf2 in the mouse

status: Public on May 09 2022

first: Arun

last: Jyothidasan

state: ALABAMA

summary:
NFE2L2, nuclear factor, erythroid 2 like 2 (Nrf2), is a transcription factor that protects cells through maintaining a homeostatic redox state during stress. Constitutive expression of Nrf2 (CaNrf2-TG) was previously shown to be pathological to the heart over time.
We tested a hypothesis that the cardiac-specific expression of full length Nrf2 (mNrf2-TG) would moderately increase the basal antioxidant defense, triggering a pro-reductive environment leading to adaptive cardiac remodeling.

overall_design: Cardiac-specific full-length Nrf2 transgenic (mNrf2-TG) and non-transgenic (NTG) mice hearts on the C57/BL6 background at 7-8 months of age were used to analyze the transcriptome and cardiac structure/function. Next generation sequencing (NGS) for RNA profiling (n=3/4group) and qPCR-based validation (n=5/group) of the NGS data were accomplished. Myocardial redox levels and imaging (echocardiography) were performed

first: Namakkal

last: Rajasekaran


title: Large-scale multi-omics analysis suggests an important role of intragenic cohesin in tissue-specific transcription.

first: Jiankang

last: Wang

state: Hunan

address: Lushan

institute: School of biology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cohesin is a protein complex that is essential for chromosome segregation. Cohesin regulates gene expression by insulation and chromatin domain formation with insulation factor CTCF. It was also reported that CTCF-independent cohesin-binding sites co-localize with transcription factors (TFs) for enhancer-promoter interaction. However, it is not a trivial task to assign whole-genome cohesin-binding regions into various functions. Also, the context-specific roles of cohesin-mediated interactions, especially on intragenic region, remains unsolved. To this end, we performed a comprehensive characterization of DNA-binding sites for cohesin and transcription factors (TFs) in MCF-7 cells with and without transcription stimulus. We integrated these epigenomic data with transcriptomic and chromatin interactions data to analyze context-specific cohesin function in genome-wide manner. As a result, we extracted a new subset of cohesin-binding sites named decreased intragenic cohesin sites (DICs), which were different from previous known functions of cohesin. DICs were negatively correlated with transcriptional regulation: a part of them were related to enhancer markers and “paused” RNA polymerase 2, while others contributed to chromatin architectures. The intron enriched DICs also showed chromatin de-compaction and special genomic bindings. Further conventional machine learning approach also captured similar DICs with distinguishable features. More importantly, DICs could be found in various tissues and cell lines, including cohesinopathy patient cells, to play a role in the disturbed transcription. These results suggested a novel function of cohesin on intragenic regions for gene transcription regulation.

overall_design: ChIP-seq and RNA-seq in MCF-7, RPE, Fibrolast and other cell lines

first: Masashige

last: Bando

first: Katsuhiko

last: Shirahige

first: Ryuichiro

last: Nakato


title: Melanoma Addiction to GCDH is Mediated by NRF2

city: La Jolla

first: Ze'ev

middle: A.

last: Ronai

address: 10901 North Torrey Pines Road

department: Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: We identify melanoma addiction to the mitochondrial protein Glutaryl-CoA dehydrogenase (GCDH), which functions in lysine metabolism and controls protein glutarylation. GCDH knockdown promoted ATF4-ATF3 signaling and cell death programs in melanoma cells, an activity blocked by knockdown of the upstream lysine catabolism enzyme DHTKD1. Correspondingly, reduced GCDH expression correlated with improved survival of melanoma patients. We show that a key mediator of GCDH-dependent melanoma cell death programs is the transcription factor NRF2, which induces ATF4, ATF3, DDIT3, and CHAC1 transcription, linking lysine catabolism with apoptotic signaling

overall_design: Gene expression comparison of siGCDH and siControl in A375 (melanoma), SK_Hep1 (liver cancer), and SKBR3(breast cancer) using RNA-seq.

first: Sachin

last: Verma

middle: A


title: Pre-encoded responsiveness to type I interferon in the peripheral immune system defines outcome of PD1 blockade therapy

status: Public on May 30 2022

city: Toronto

first: David

last: Brooks

address: 610, University Ave

country: Canada

institute: Princess Margaret Cancer Centre

summary: This repository contains single-cell RNA and single-cell ATAC sequencing data of peripheral blood mononuclear cells (PBMCs) from melanoma patients at baseline (prior to receiving anti-PD1 therapy) and healthy donors. Patients were selected based on their IFN-I response capacity (measured by mass cytometry), which is associated with patient survival after therapy. The purpose of the experiment was to better understand the mechanisms underlying the differences in outcome observed betwee the two patient groups.

overall_design: 8 patient PBMCs (4 with high IFN-I response capacity (IRC) and 4 with low IRC) and 2 healthy donor PBMCs were sequenced through multiome (scRNA + scATAC) sequencing. Briefly, cryopreseved PBMCs were thawed and 10X multiome seuqencing workflow was performed following DNAse treatment according to the manufacturer's protocol. Processing and sequencing was performed by the Princess Margaret Cancer Center Genomics Core.

first: Giselle

last: Boukhaled

first: Ramy

last: Gadalla

first: Heidi

last: Elsaesser

first: Diala

last: Abd-Rabbo

first: Rene

last: Quevedo

first: Cindy

last: Yang

middle: G


title: Cellular identity loss occurring during both iPS cells generation and malignant transformation can be followed using the somatic markers Thy1 and Bcl11b [RNA-seq]

status: Public on May 06 2022

city: Lyon

first: Fabrice

last: Lavial

address: 28 rue Laennec

country: France

institute: CRCL

summary: Coordinated changes of cellular plasticity and cellular identity are critical for pluripotent reprogramming and oncogenic transformation. However, the sequences of cellular/molecular events that orchestrate these intermingled modifications have never been comparatively dissected. Here, we deconvoluted the cellular trajectories of reprogramming (via Oct4/Sox2/Klf4/c-Myc) and transformation (via Ras/c-Myc) at the single-cell resolution and revealed how the two processes intersect prior to bifurcate. This approach also led to identify the transcription factor (TF) Bcl11b as a broad-range regulator of cell fate changes, as well as a pertinent marker to capture early cellular intermediates that emerge simultaneously during reprogramming and transformation. Multi-omics characterization of these intermediates led to unveil a c-Myc/Atoh8/Sfrp1 regulatory axis that constrains rodent and human reprogramming but also cancer cell plasticity and neuron transdifferentiation. Mechanistically, we found that the TF Atoh8 restrains cellular plasticity, independently of cellular identity, by binding a specific enhancer network. This study provides insights into the partitioned control of cellular plasticity and identity for both regenerative and cancer biology.

overall_design: R-BLTL and T-BLTL intermediates being more prone to reprogram / transform, we FACS-sorted R-BLTL/T-BLTL and R-BHTH/T-BHTH in their way to pluripotency or malignancy to identify new regulators. RNA-seq analyses were conducted on untreated MEFs alongside R-BLTL and T-BLTL  (both Bcl11blow/thy1low), R-BHTH and T-BHTH (both Bcl11bhigh/thy1high) at 5 days of reprogramming or transformation and in iPS and transformed cells (TC).

first: Aurélia

last: Huyghe

first: Giacomo

last: Furlan


title: Bcl11b and Atoh8 binding on chromatin in MEFs

overall_design: ChIP-sequencing assay targeting the Atoh8 factor presenting an AM tag peptide or the endogenous Bcl11b transcription factor. As a control an empty AM tag pulldown as well as a whole cell extract input control has been also generated.

first: Jan

last: Schroeder

first: Jean

last: Studer

first: Florine

last: Mugnier

first: Léa

last: De Matteo

first: Juexuan

first: Yong

last: Yu

first: Nicolas

last: Rama

first: Benjamin

last: Gibert

first: Janice

last: Kielbassa

first: Pauline

last: Wajda

last: Gadot

first: Marie

last: Brevet

first: Maha

last: Siouda

first: Peter

last: Mulligan

first: Robert

last: Dante

first: Pentao

last: Liu

first: Hinrich

last: Gronemeyer

first: Marco

last: Mendoza-parra


title: Chromatin accessibility after 5 days of reprogramming and transformation

first: Fabrice

last: Lavial

overall_design: ATAC-seq analyses were conducted on bulk cells after 5 days of reprogramming and transformation

first: Aurélia

last: Huyghe

first: Giacomo

last: Furlan


title: Cellular identity loss occurring during both iPS cells generation and malignant transformation can be followed using the somatic markers Thy1 and Bcl11b [scRNA-seq]

overall_design: single cell RNA-seq analyses were conducted on untreated MEFs and in a kinetic manner during reprogramming and transformation alongside iPS and transformed cells (TC).


title: Cellular identity loss occurring during both iPS cells generation and malignant transformation can be followed using the somatic markers Thy1 and Bcl11b (ATAC-seq)

overall_design: R-BLTL and T-BLTL intermediates being more prone to reprogram / transform, we FACS-sorted R-BLTL/T-BLTL and R-BHTH/T-BHTH in their way to pluripotency or malignancy to identify new regulators. ATAC-seq analyses were conducted on untreated MEFs alongside R-BLTL and T-BLTL (both Bcl11blow/thy1low), R-BHTH and T-BHTH (both Bcl11bhigh/thy1high) at 5 days of reprogramming or transformation and in iPS and transformed cells (TC).


title: Identification of genes upregulated and downregulated in mouse embryonic fibroblasts (MEFs) upon Atoh8 depletion

summary: Upon Atoh8 downregulation by shRNA, cells were cultivated for 5 days and RNA extracted for sequencing.

overall_design: Comparison of transcriptomes of sh#control MEFs and sh#Atoh8 MEFs after 5 days upon lentiviral infection.


title: Identification of genes upregulated and downregulated in transformed cells (TCs) derived upon Atoh8 depletion

summary: Upon Atoh8 downregulation by shRNA in MEFs, KRas512D mutation c-Myc over-expression and depletion of p53 were induced in mouse embryonic fibroblasts. After 10 passages, cells were collected and RNA extracted.

overall_design: Comparison of transcriptomes of sh#control TCs and sh#Atoh8 TCs 10 passages after malignant transformation induction.


title: The comparative roadmaps of reprogramming and transformation unveiled that cellular plasticity is broadly controlled by Bcl11b and Atoh8

summary: Coordinated changes of cellular plasticity and cellular identity are critical for pluripotent reprogramming and oncogenic transformation. However, the sequences of cellular/molecular events that orchestrate these intermingled modifications have never been comparatively dissected. Here, we deconvoluted the cellular trajectories of reprogramming (via Oct4/Sox2/Klf4/c-Myc) and transformation (via Ras/c-Myc) at the single-cell resolution and revealed how the two processes intersect prior to bifurcate. This approach also led to identify the transcription factor (TF) Bcl11b as a broad-range regulator of cell fate changes, as well as a pertinent marker to capture early cellular intermediates that emerge simultaneously during reprogramming & transformation. Multi-omics characterization of these intermediates led to unveil a c-Myc/Atoh8/Sfrp1 regulatory axis that constrains rodent and human reprogramming but also cancer cell plasticity and neuron transdifferentiation. Mechanistically, we found that the TF Atoh8 restrains cellular plasticity, independently of cellular identity, by binding a specific enhancer network. This study provides insights into the partitioned control of cellular plasticity and identity for both regenerative and cancer biology.

overall_design: Refer to individual Series


title: An imbalance of tumour-suppressing and tumour-promoting hepatic stellate cell populations in liver fibrosis contributes to hepatocarcinogenesis

status: Public on May 01 2022

city: Edinburgh

first: John

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

summary: Hepatocellular carcinoma (HCC) develops almost exclusively in patients with chronic liver disease (CLD) and advanced fibrosis. Here we interrogated functions of hepatic stellate cells (HSC), the main source of fibroblasts in the injured liver, during hepatocarcinogenesis. Genetic depletion, activation, or inhibition established HSC as tumour-promoting in different HCC models. HSC were enriched in the non-tumour environment, where they closely interacted with hepatocytes and modulated hepatocarcinogenesis by regulating hepatocyte proliferation and death. Surprisingly, further analysis of mouse and human HSC subpopulations by single cell and single nucleus RNA-sequencing and their associated mediators revealed dual functions of HSC in hepatocarcinogenesis. Hepatocyte growth factor, enriched in quiescent and cytokine-producing HSC (cyHSC), protected from hepatocyte death and HCC development. In contrast, type I collagen, enriched in highly activated myofibroblastic HSC (myHSC), increased stiffness, TAZ activation, and subsequent hepatocyte proliferation, thereby promoting HCC development. An increasing HSC imbalance with decreased protective cyHSC and increased myHSC during liver disease progression was associated with elevated HCC risk in patients. In summary, our data suggest that the dynamic shift of HSC subpopulations during CLD and their mediators is associated with a switch from HCC protection to HCC promotion.

overall_design: Single, live nuclei were isolated from liver explants (n=2 healthy, n=2 NAFLD).

first: Sebastian

last: Wallace

first: Ross

last: Dobie

first: Neil

middle: C

last: Henderson

middle: R


title: DNA Methylation-Based Prediction of Post-Operative Atrial Fibrillation I

status: Public on May 05 2022

city: Los Angeles

first: Matthew

last: Fischer

address: 650 Charles Young Dr

department: Anesthesiology and Perioperative Medicine

institute: University of California, Los Angeles

summary: Background: Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia and post-operative atrial fibrillation (POAF) is a major healthcare burden, contributing to an increased risk of stroke, kidney failure, heart attack and death. Genetic studies have identified associations with AF, but no molecular diagnostic exists to predict POAF based on pre-operative measurements. Such a tool would be of great value for perioperative planning to improve patient care and reduce healthcare costs. In this pilot study of epigenetic precision medicine in the perioperative period, we carried out bisulfite sequencing to measure DNA methylation status in blood collected from patients prior to cardiac surgery to identify biosignatures of POAF. Methods: We enrolled 221 patients undergoing cardiac surgery in this prospective observational study. DNA methylation measurements were obtained from blood samples drawn from awake patients prior to surgery. After controlling for clinical and methylation covariates, we analyzed DNA methylation loci in the discovery cohort of 110 patients for association with POAF. We also constructed predictive models for POAF using clinical and DNA methylation data. We subsequently performed targeted analyses of a separate cohort of 101 cardiac surgical patients to measure the methylation status solely of significant methylation loci in the discovery cohort. Results: A total of 47 patients in the discovery cohort (42.7%) and 43 patients in the validation cohort (42.6%) developed POAF. We identified 12 CpGs that were statistically significant in the discovery cohort after correcting for multiple hypothesis testing. Of these sites, 6 were amenable to targeted bisulfite sequencing and chr16:24640902 was statistically significant in the validation cohort. In addition, the methylation POAF prediction model had an AUC of 0.79 in the validation cohort. Conclusions: We have identified DNA methylation biomarkers that can predict future occurrence of POAF associated with cardiac surgery. This research demonstrates the use of precision medicine to develop models combining epigenomic and clinical data to predict disease.

overall_design: Identification of DNA methylation biomarkers in pre-operative whole blood samples that predict post-operative atrial fibrillation after cardiac surgery

first: Douglas

last: Chapski

first: Thomas

last: Vondriska


title: DNA Methylation-Based Prediction of Post-Operative Atrial Fibrillation

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


title: Physiological Calcium Combined with Electrical Pacing accelerates Maturation of Human Engineered Heart Tissue

status: Public on Apr 28 2022

city: New Haven

first: Stuart

last: Campbell

state: CT

address: 55 Prospect Street, Malone 301

institute: Yale University

summary: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have wide  potential application in basic research, drug discovery, and regenerative medicine, but  functional maturation remains challenging. Here, we present a simple method whereby  maturation of hiPSC-CMs can be accelerated by simultaneous application of  physiological Ca  2+  and frequency-ramped electrical pacing in culture. This  combination produces realistic force-frequency relationship, physiological twitch  kinetics, robust β-adrenergic response, improved Ca  2+  handling, and cardiac  troponin I expression within 25 days. This study provides insights into the role of Ca  2+  in hiPSC-CM maturation and offers a scalable platform for translational and clinical  research.

overall_design: Gene expression profile analysis of 4 experimental groups of engineered heart tissues (EHTs). The four groups are: High Calcium Ramp Pacing (HCRP), High Calcium No Pacing (HCNP), Low Calcium Ramp Pacing (LCRP) and Low Calcium No Pacing (LCNP)

first: Shi

last: Shen

first: Lorenzo

last: Sewanan

first: Stephanie

last: Shao

first: Saiti

last: Halder

first: Xia

last: Li


title: Myristic acid alleviates hippocampal aging via regulating GABAergic expressions

status: Public on Apr 21 2022

city: Guangzhou

first: Qi

last: Shang

state: Guangzhou

address: No.16, Airport road, BaiYun Road, Guangzhou City,

institute: Guangzhou University of Chinese Medicine

summary:
To evaluate differentially expressed genes and pathways in hippocampus between young (3-month-old, 3M) and aging (22-month-old, 22M) group.
We then performed gene expression profiling analysis using data obtained from mRNA-seq in hippocampus of 3M and 22M group.

overall_design: Comparative gene expression profiling analysis of mRNA-seq data in hippocampus of 3M and 22M group.

first: Hui

last: Ren


title: Swc4 protects nucleosome free chromatin of telomeres, tRNA genes and rDNA loci to inhibit genome instability [ATAC-seq]

status: Public on May 14 2022

city: Shanghai

first: Yue

last: Pan

address: 320 Yue Yang Road

department: Center for Excellence in Molecular Cell Science, CAS

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: In the baker’s yeast Saccharomyces cerevisiae, Swc4, Yaf9, Arp4, and Act1 form a submodule shared by histone acetylation NuA4 complex and chromatin remodeling SWR1 complex (SWR1-C). Act1 and Arp4 are essential for cell survival. Deletion of SWC4, but not YAF9, results in severe growth defect, however, the underlying mechanism remains largely unknown. Here, we show that swc4Δ, but not yaf9Δ, eaf1Δ, or swr1Δ cells display mitotic defects in both faithful chromosome segregation and DNA ploidy, suggesting that the defects observed in swc4Δ cells are independent of the integrity of either NuA4 or SWR1-C. Additionally, loss of Swc4 function results in chromosomal breakage and spindle assembly check-point activation. Swc4 binds to telomeres, tRNA and rDNA regions in genome, which represent nucleosome free regions (NFRs) of chromatin. Notably, telomeres, tRNA genes and rDNA loci, in swc4Δ cells become unstable and are highly susceptible to recombination. Taking together, we conclude that the chromatin associated Swc4 protects nucleosome-free chromatin from breakage to ensure genome integrity.

overall_design: ATAC-seq assays to examine the chromatin accessibility using hyperactive Tn5 transposase in logarithmic wide-type and swc4Δ cells

first: Lin-Jun

last: Hou

first: Jia-Cheng

last: Liu

first: Jin-Qiu

last: Zhou


title: BARD1 loss enhances GBP1 expression and tumor sensitivity to DNA damage in Ewing sarcoma

city: Pittsburgh

first: Kelly

last: Bailey

state: PA

address: Rangos Research Building 4401 Penn Ave

department: Pediatrics

institute: University of Pittsburgh

summary: This experiment examined the transcriptional changes present upon reduction of BARD1 expression in Ewing sarcoma cells

overall_design: A673 Ewing sarcoma cells were transfected with BARD1siRNA (versus controlsiRNA)


title: Impact of an Immune Modulator Mycobacterium-w on Adaptive Natural Killer Cells and Protection Against COVID-19

status: Public on Apr 25 2022

city: Kolkata

first: Suparno

last: Chakrabarti

state: West Bengal

address: PGH Shah Road

department: Cellular Therapy and Immunology

country: India

institute: Manashi Chakrabarti Foundation

summary: Whole transcriptome Differential Gene Expression (DGE) analysis was carried out on four biological replicates of both Mw (0.1 ml Mw administrated intradermally in each arm) and Control group at 6 months following exposure to Mycobacterium-w. Sequencing was done through Direct cDNA Sequencing (oxford nanopore technologies, Oxford, UK) using RNA isolated from Peripheral blood mononuclear cells (PBMC) by Trizol method. Native barcoding and adaptor ligation was done according to the manufacturer’s instructions. Ligated cDNA was loaded on the flow cell (R9.4.1) in MinION and were sequenced specifying 72 hours protocol. MinKNOW (v21.06.10, Microsoft Windows OS based) was used to generate FAST5 files. FAST5 files were base-called with CPU based Guppy basecaller (v.5.0.11) (ONT) to generate FASTQ files. DGE analysis was done using “pipeline-transcriptome-de” (https://github.com/nanoporetech/pipeline-transcriptome-de) pipeline. DGE analysis confirmed that upregulation of ANK pathway was evident at 6 months in the Mw group. Apart from upregulation of KLRC2 and B3GAT1 and downregulation of KLRC1, the key transcription factor in the ANK pathway, BCL11b, was persistently upregulated. Downregulation of EAT-2 and PLZF further corroborated the classic gene expression signature of ANK cells. Moreover, increased expression of AT-rich interaction domain 5B (ARID5B), as demonstrated in the Mw group plays an important role in enhanced metabolism in ANK cells as well as increased IFN-γ release and survival.  DGE analysis also revealed an enhancement of ANK mediated ADCC pathway, with significant upregulation of CD247 along with downregulation of FCER1G, which is a typical signature of ANK-ADCC. Both CD247 and FCER1G are adapter molecules for FCGRIIIA (CD16) with CD247 possessing 3 ITAMs against one ITAM of FCER1G, increasing the ADCC several folds. It is possible that Mw induced augmentation of NK-ADCC might potentiate the efficacy of SARS-CoV2 vaccines as well.

overall_design: Comparative whole gene expression analysis between four Mycobacterium-w treated and four control biological replicates

first: Sarita

last: Jaiswal

first: Jaganath

last: Arunachalam

first: Ashraf

last: Saifullah

first: Rohit

last: Lakhchaura

first: Dhanir

last: Tailor

first: Anupama

last: Mehta

first: Gitali

last: Bhagawati

first: Hemamalini

last: Aiyer

first: Bhakulesh

last: Khamar

first: Sanjay

middle: V

last: Malhotra


title: RNA sequencing unveils very small RNAs with potential regulatory functions in bacteria

status: Public on Apr 16 2022

city: Quebec

first: Patrick

last: PROVOST

state: QUEBEC

address: 2705 , Boulevard Laurier, Bloc T

department: Centre Hospitalier de l'Université Laval (CHUL) - Microbiology, Infectious diseases, Immunology

institute: CRCHU of Québec City - Université LAVAL

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA sequencing (RNA-seq) is the gold standard for the discovery of small non-coding RNAs. Following a long-standing approach, reads shorter than 16 nucleotides (nt) are removed from the small RNA sequencing libraries or datasets. The serendipitous discovery of a 12 nt-long RNA species capable of modulating the microRNA from which they derive prompted us to challenge this dogma, and by expanding the window of RNA sizes down to 8 nt, to confirm the existence of functional very small RNAs (vsRNAs <16nt). Here we report the profiling of vsRNAs in Escherichia coli (with different experimental conditions), E. coli-derived outer membrane vesicles (OMVs) and five other bacterial strains (Pseudomonas aeruginosa PA7, P. aeruginosa PAO1, Salmonella Typhimurium 14028S, Legionella pneumophila JR32 Philadelphia-1 and Staphylococcus aureus HG001).

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

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

overall_design: We analyzed by small RNA-seq the 8- to 30-nt window of RNA length of the gram-negative E. coli MG1655 model organism and 5 other bacterial strains (P. aeruginosa PA7, P. aeruginosa PAO1, S. Typhimurium 14028S, L. pneumophila JR32 Philadelphia-1 and S. aureus HG001).

first: Idrissa

last: Diallo

first: David

last: Lalaouna

first: Eric

last: Massé

last: Provost


title: RNA sequencing of MM.1S and U266 cell lines after IT848 treatment

status: Public on Apr 10 2022

city: Nutley

first: Johannes

last: Zakrzewski

state: New Jersey

address: 111 Ideation Way

institute: Hackensack Meridian Health

summary: IT848 is a small molecule inhibiting DNA binding of all five NF-kB subunits. In vitro treatment of lymphoma or multiple myeloma cells with IT848 suppresses NF-kB transcriptional activity, cell growth, and indices apoptosis.

overall_design: Multiple myeloma cell lines MM.1S and U266 were treated with the NF-kB inhibitor IT848 versus empty vehicle for 6 hours, followed by RNA extraction and whole exome sequencing to identify alterations in transcriptional signatures.

first: Zakrzewski

last: Johannes

first: Cassella

last: Elena


title: Microarray data of CACTg/Tg;APC580S mouse model exposed to 1, 2, and 5 mg/kg;bw/day of E171 via intragastric administration for 2, 7, 14, and 21 days.

status: Public on Apr 12 2022

city: Maastricht

first: Danyel

last: Jennen

address: Universiteitssingel 40

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

summary: Titanium dioxide (TiO2) is present in many different food products as food additive E171 and is currently scrutinized, due to its potential adverse effects, including the stimulation of tumor formation in the gastrointestinal tract. We developed a transgenic mouse model to examine the effects of E171 on colorectal cancer (CRC), using the Cre-LoxP system to create an Apc-gene-knockout model which spontaneously develops colorectal tumors. In phase I of this study, tumor formation was studied following the exposure to 5 mg/kgbw/day of E171 for 9 weeks. E171-exposure increased the number of transgenic mice with colorectal tumors as well as the average number and size of these tumors. Colorectal adenocarcinomas were accompanied by enhanced hyperplasia in epithelial cells and lymphatic nodules at the base of the polyps. In phase II, gene expression changes in the colon were analyzed after exposure to 1, 2, and 5 mg/kgbw/day of E171 for 2, 7, 14, and 21 days. Whole-genome mRNA analysis revealed the modulation of genes in pathways involved in the regulation of gene expression, cell cycle, post-translational modification, nuclear receptor signaling, and circadian rhythm. The processes associated with these genes might be involved in the enhanced tumor formation and suggest that E171 may contribute to tumor formation and progression by modulation of events related to inflammation, activation of immune responses, cell cycle, and cancer signaling.

overall_design: Total of 99 samples. Per time point (2, 7, 14, and 21 days) and dose (1, 2, and 5 mg/kg:bw/day) there was 3 female and 4 male mice assigned, which were exposed to E171 via intragastric gavage. Dose was administered 5 days a week, Mo-Fr.

first: Nicolaj

middle: S

last: Bischoff

first: Héloïse

last: Proquin

first: Marlon

last: Jetten

first: Yannick

last: Schrooder

first: Marloes

last: Jonkhout

first: Jacob

last: Briedé

first: Simone

last: van Bred

first: Estefany

middle: I

last: Medina-Reyes

first: Norma

middle: L

last: Delgado-Buenrostro

first: Yolanda

last: Chirino

first: Henk

last: van Loveren

first: Theo

last: de Kok


title: Transcriptomic Analysis of Canine Osteosarcoma from a Precision Medicine Perspective Reveals Limitations of Differential Gene Expression Studies

city: Auburn University

first: Xu

last: Wang

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

summary: Despite significant advances in cancer diagnosis and treatment, osteosarcoma (OSA), an aggressive primary bone tumor, has eluded attempts at improving patient survival for many decades. The difficulty in managing OSA lies in its extreme genetic complexity, drug-resistance, and heterogeneity, making it improbable that a single-target treatment would be beneficial for the majority of affected individuals. Precision medicine seeks to fill this gap by addressing the intra- and inter-tumoral heterogeneity to improve patient outcome and survival. Characterization of differentially expressed genes (DEGs) unique to the tumor provides insight into the phenotype and can be useful for informing appropriate therapies as well as development of novel treatments. Traditional DEG analysis combines patient data to derive statistically inferred genes that are dysregulated in the group; however, the results from this approach are not necessarily consistent across individual patients, thus contradicting the basis of precision medicine. Spontaneously occurring OSA in the dog shares remarkably similar clinical, histological, and molecular characteristics to the human disease and therefore serves as an excellent model. In this study, we use transcriptomic sequencing of RNA isolated from primary OSA tumor and patient-matched normal bone from seven dogs prior to chemotherapy to identify DEGs in the group. We then evaluate the universality of these changes in transcript levels across patients to identify DEGs at the individual level. These results can be useful for reframing our perspective of transcriptomic analysis from a precision medicine perspective by identifying variations in DEGs among individuals.

overall_design: This study uses transcriptomic sequencing of RNA derived from seven primary canine osteosarcoma tumors with patient-matched normal bone harvested from the phalanges prior to chemotherapy or evidence of macrometastatic lung disease

first: Rebecca

last: Nance

first: Bruce

last: Smith


title: AG- and AP3- domain specific FANS RNA-seq

status: Public on Apr 09 2022

city: Berlin

first: Jose

middle: M.

last: Muino

address: Max-Dohrn-Str. 8-10

country: Germany

institute: German Federal Institute for Risk Assessment

summary: We characterized the nuclear trasncriptome of AG- and AP3- domains.

overall_design: In this study, we characterized the nuclear transcriptome of the  AG- and AP3- flower domains by  using FANS RNA-seq at stage 5 of flower development

first: Manuel

last: Neumann

first: Xiaocai

last: Xu

first: Cezary

last: Smaczniak

middle: M

first: Kerstin

last: Kaufmann


title: Contraction band necrosis and dephosphorylated cardiac connexin 43 in rat myocardium after 14 days cocaine administration

status: Public on Apr 07 2022

city: Tokyo

first: Shuheng

last: Wen

address: 1-5-45 Yushima

department: Forensic Science

institute: Tokyo Medical and Dental University

summary:
To obtain insight of the changes of myocardium after repeated cocaine administration, we performed transcriptiome analysis.
Total RNAs from the control and cocaine groups (day 14) were subjected to DNA microarray analysis.

overall_design: We analyzed myocardium from 1 control rat and 1 cocaine-administered rat (20 mg/kg, daily for 14 days via tail vein) using the ClariomS platform.

first: S

middle: H

first: K

last: Unuma

first: T

last: Funakoshi

last: Aki

last: Uemura


title: snRNA-seq of Arabidopsis thaliana flower meristems

summary: In order to decipher the transcriptome heterogeneity of the the flower meristem, we perfomed single-nuclei RNA-seq in flower mersitems

overall_design:
In this study, we use the  pAP1::AP1-GR ap1 cal system to synchronize flower development, and we characterized the nuclear transcriptome for
stage 5 flowers after 4 days of DEX induction of the flower meritem
stage 4 flowers after 3 days of DEX induction of the flower meritem


title: Transcriptional profiling of Regulatory T cells isolated from mice exposed to Smoke, Morphine and Smoke plus Morphine

status: Public on Apr 14 2022

city: Philadelphia

first: Ying

last: Shao

state: Pennsylvania

address: 3500 N Broad St, MERB1083A

institute: Temple University

summary: Purpose: The goals of this study were to identify gene expression signatures that are unique to Tregs from mice upon treatments with smoke, morphine and smoke plus morphine  Methods and results: Wild-type mice were treated with cigarette smoke (SM) for a period of eight weeks, and/or the chronic continuous administration of  morphine (M) via mini-pumps for the final four weeks CD4+CD25highCD127low Tregs from spleen were purified by cell sorting to generate mRNA transcription. Transcriptional profiling revealed a unique Treg signatures in SM, M or SM + M relative to control mice.  Conclusion: Our study represents the first detailed analysis of splenic Treg transcriptome in mice exposure to smoke plus morphine.

overall_design: Spleen treg mRNA profiles of mice treated with smoke, morphine, or smoke plus morphine.

first: Xiaofeng

last: Yang


title: CASK mutation Disrupts Neural Connectivity in Human Neurons

status: Public on Apr 03 2022

city: Cincinnati

middle: J

last: Aronow

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics, Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Loss-of-function mutations in CASK cause severe developmental phenotypes including microcephaly with pontine and cerebellar hypoplasia (MICPHC), X-linked intellectual disability and autism. Modeling of CASK-related disorders has been challenging due to limited human cellular models to study the multifaceted roles of this protein during neuronal and synapse development. Here, we generated two independent CASK knockout (KO) isogenic cell lines from human embryonic stem cells (hESCs) using CRISPR/Cas9 and performed a detailed characterization of gene expression, morphology and neuronal function during neuronal differentiation and synapse development. While immature neurons showed an upregulation of gene networks related neuronal cell adhesion, projection and outgrowth, concomitant with increased neuronal complexity in CASK KO neurons, mature neurons displayed severe defects in neuronal spiking, spontaneous synaptic transmission and synchronized burst firing patterns without significant changes in neuronal morphology and synapse numbers. In developing human cortical neurons, CASK functions to promote both structural integrity and establishment of cortical excitatory neuronal networks. These results lay the foundation for future studies identifying suppressors of such phenotypes relevant to human patients.

overall_design: Day 7 human cortical excitatory neurons were collected for bulk RNAseq from 4 independent culture replicates of WT, CASK KO#1 and CASK KO#2 hESC lines. Day 28 human cortical excitatory neurons cultured with mouse glia were also collected for bulk RNAseq from 4 independent culture replicates of WT, CASK KO#1 and CASK KO#2. Differential gene expression analysis was carried out.

first: ChangHui

last: Pak

first: Kang

last: Jin

first: Danny

last: McSweeney


title: Identification and characterization of putative targets of VEGETATIVE1/FULc, a key regulator of development of the compound inflorescence in pea and related legumes

city: Valencia

first: Marcos

last: Serra

state: Comunidad Valenciana

address: Carrer de l'Enginyer Fausto Elio

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas Primo Yúfera (IBMCP) CSIC

summary: Inflorescence architecture contributes to essential plant traits. It determines plant shape, contributing to morphological diversity, also determines position and number of the flowers and fruits produced by the plant, influencing seed yield. Most legumes have compound inflorescences, where flowers are produced in secondary inflorescences (I2), formed at the flanks of the main primary inflorescence (I1), in contrast to simple inflorescences of plants like Arabidopsis, in which flowers are directly formed on the I1. The pea VEGETATIVE1/ FULc (VEG1) gene, and its homologues in other legumes, specify the formation of the I2 meristem, a function apparently restricted to legumes. To understand the control of I2 development it is important to identify the genes working downstream of VEG1. In this study, we adopted a novel strategy to identify genes expressed in the I2 meristem, as potential regulatory targets of VEG1. To identify pea I2-meristem genes we compared the transcriptomes of inflorescence apices from wild type and mutants affected in I2 development, proliferating inflorescence meristems (pim - with more I2 meristems), veg1 and vegetative2 (both without I2 meristems). Analysis of the differentially expressed genes using Arabidopsis genome databases combined with RT-qPCR expression analysis in pea, allowed the selection of genes expressed in the pea inflorescence apex. In situ hybridization of four of these genes showed that all four genes are expressed in the I2 meristem, proving our approach to identify I2-meristem genes successful. Finally, analysis by VIGS in pea identified one gene, PsDAO1, whose silencing lead to small plants and another gene, PsHUP54, whose silencing leads to plants with very large stubs, meaning that this gene controls activity of the I2 meristem. PsHUP54-VIGS plants also are large and, more importantly, produce large pods with almost double of seeds than the control. Our study shows a new useful strategy to isolate I2-meristem genes and identifies a novel gene, PsHUP54, which seems a promising tool to improve yield in pea and another legumes.

overall_design: RNAseq from apice inflorescences of pea WT plants and pim, veg1 and veg2 pea mutants

last: Serra-Picó

first: Valerie

last: Hecht

first: James

last: Weller

first: Reyes

last: Benlloch

first: Francisco

last: Madueño


title: Human Milk Oligosaccharide Utilization in Intestinal Bifidobacteria is Governed by Global Transcriptional Regulator NagR

status: Public on Apr 02 2022

city: La Jolla

first: Aleksandr

last: Arzamasov

state: CA

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Bifidobacterium longum subsp. infantis (B. infantis) is a prevalent beneficial bacterium that colonizes the human neonatal gut and is uniquely adapted to efficiently use human milk oligosaccharides (HMOs) as a carbon and energy source. Multiple studies have focused on characterizing the elements of HMO utilization machinery in B. infantis; however, the regulatory mechanisms governing the expression of these catabolic pathways remain poorly understood. A bioinformatic regulon reconstruction approach used in this study implicated NagR, a transcription factor from the ROK family, as a negative global regulator of genomic loci encoding lacto-N-biose/galacto-N-biose (LNB/GNB), lacto-N-tetraose (LNT), and lacto-N-neotetraose (LNnT) utilization pathways in B. infantis. This conjecture was corroborated by transcriptome profiling upon nagR genetic inactivation and experimental assessment of binding of recombinant NagR to predicted DNA operators. The latter approach also implicated N-acetylglucosamine (GlcNAc), a universal intermediate of LNT and LNnT catabolism, and its phosphorylated derivatives as plausible NagR effectors. Reconstruction of NagR regulons in various Bifidobacterium lineages revealed multiple regulon expansion events, suggesting evolution from a local regulator of GlcNAc catabolism in ancestral bifidobacteria to a global regulator controlling foraging of mixtures of GlcNAc-containing host-derived glycans in mammalian gut-colonizing B. infantis and Bifidobacterium bifidum.

overall_design: Three biological replicates were analyzed for each of 4 conditions (two nagR genotypes; two carbon sources)


title: Transcriptome analysis of rMSCs cultured for 4 hours in differerent substrate (TCP, PCL film, ISB-P fIlm)

status: Public on Apr 01 2022

city: Cheonansi

first: Ji-Young

last: Yoon

state: Chungnam

address: Dandaero 119

department: Nanbiomedical science

country: South Korea

institute: Dankook University

summary: We developed new isosorbide derivatives (propoxylated or ethoxylated isosorbide) which have more reactivity in PCL-PU copolymer synthesis than the original isosorbide. PCL-PU copolymer incorporated propoxylated isosorbide (ISB-P) exhibited notable mechanical performance (50 MPa tensile strength and 1150% elongation with hyperelasticity under cyclic load), ultra-cell-adhesive property, and enhanced osteogenic differentiation. There was no significant difference in surface characteristics between ISB-P and PCL), however, mRNA profiles showed higher expressions of heat shock proteins which have been reported to promote osteogenic differentiation at 4 h after cell seeding in rMSC cultured on ISB-P compared to PCL. In conclusion, the engagement of heat shock protein to the ISB-P surface during cell attachment may promote osteogenic differentiation in ISB-P.

first: Jung-Hwan

last: Lee

first: Hae-Won

last: Kim


title: O-GlcNAc-modified proteins leaked from dead cells suppress fibrosis

status: Public on Mar 30 2022

city: Fukuoka

first: Hirohiko

last: Ise

address: Motooka 744

department: IMCE

institute: Kyushu University

summary: Tissue fibrosis is induced by chronic inflammation accompanied by repeated injuries. Chronic inflammation alters fibroblasts and stellate cells, maintaining the tissues in myofibroblasts and activating stellate cells. This activation promotes the augmentation of these cells and the abundant production of extracellular matrices, such as collagen. Fibrotic tissue dysfunction is eventually induced by expelling parenchymal cells with these abundant collagen depositions. To recover from tissue fibrosis, the activation of myofibroblasts and stellate cells is suppressed by selectively targeting these cells. Here we show that O-N-acetylglucosamine (GlcNAc)-modified proteins leaked from dead cells and GlcNAc-bearing polymers mimicking the GlcNAc moiety of these proteins suppress the activation of these cells; administration of the GlcNAc-bearing polymer into carbon tetrachloride-treated mice can improve liver fibrosis. We found that a multivalent GlcNAc moiety structure elicited antifibrotic activities in myofibroblasts by interacting with cell surface vimentin and desmin. Therefore, since these cells highly express cytoskeletal proteins, vimentin and desmin, on the cell surface and have GlcNAc-binding activity, we suggest that O-GlcNAc-modified proteins leaked from dead cells can function as suppressors of fibrosis and hyperplasia in spontaneous recovery. Moreover, we anticipate that GlcNAc-bearing polymers mimicked by O-GlcNAc-modified proteins will be useful as new therapeutic tools for fibrosis and hyperplasia.

overall_design: TGFb- stimulated NHDFs were control. The data showed comparison between TGFb- stimulated NHDFs and TGFb- stimulated NHDFs supplemented with AC-GlcNAc10 and comparison between TGFb- stimulated NHDFs and TGFb- stimulated NHDFs supplemented with cell debris from dead HeLa cells.


title: Comprehensive analysis for gene expressions of normal human dermal fibroblasts supplemented with N-acetylglucosamine -bearing polymers

summary: To reveal the comprehensive gene expression of normal human dermal fibroblasts (NHDFs) based on the interaction of GlcNAc-bearing polymer, AC-GlcNAc10, with cell surface vimentin at 24 h, we performed a DNA microarray for NHDFs treated with AC-GlcNAc10. The DNA microarray analysis revealed altered expression of approximately 1000 genes in NHDF vs. NHDF treated with AC-GlcNAc10 by extracting differentially expressed genes with the ratio of >1.5 and <0.66-fold changes between the gene expressions of NHDF vs. NHDF treated with AC-GlcNAc10, and Z-score >2.0 and <-2.0. We observed the downregulation of gene expression related to cell cycle progression, such as baculoviral IAP repeat-containing protein 5 (BIRC5; survivin), and the upregulation of gene expression related to cell cycle arrest, such as cyclin-dependent kinase inhibitor 1A (CDKN1A; p21).

overall_design: NHDFs are control. The data showed comparison between NHDFs (control) and AC-GlcNAc10-treated NHDFs


title: Targeted DamID to understand transcription factor genomic occupancy in human foetal lung progenitor cells

status: Public on Apr 30 2022

city: Cambridge

first: Dawei

last: Sun

address: Tennis Court Road

department: The Gurdon Institute

institute: University of Cambridge

summary: In order to study the genomic occupancy of transcription factors, including SOX9, ETV4 and ETV5, in human foetal lung tip progenitor cells, we have introduced Targeted DamID system via lentivirus in a human foetal lung tissue derived organoid culture (Nikolic et al., 2017). We were able to identify the corresponding TF motif enrichment and discovered a potential co-regulation function of SOX9 and ETV factors in human feotal lung progenitor cells. This study has pioneered the use of targeted DamID approach in tissue derived organoid system.

overall_design: We used 4 different independent organoid lines treated as replicates, all of which are around 8 pcw. We introduced the SOX9 targeted DamID into organoids via lentiviral transduction and compared with the results from organoids with Dam only controls. In a following-up experimental setting, we introduced ETV4 and ETV5 targeted DamID into organoids via lentiviral transduction and compared with the results from organoids with Dam only controls.

first: Oriol

last: Llorà-Batlle

first: Jelle

last: Van Den Ameele

first: Andrea

last: Brand

first: Emma

last: Rawlins


title: Transcriptional profiling of multiple system atrophy cerebellar tissue highlights differences between the parkinsonian and cerebellar sub-types of the disease

status: Public on Mar 29 2022

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

summary:
Multiple system atrophy (MSA) is a rare adult-onset neurodegenerative disease of unknown cause, with no effective therapeutic options, and no cure. Limited work to date has attempted to characterize the transcriptional changes associated with the disease, which presents as either predominating parkinsonian (MSA-P) or cerebellar (MSC-C) symptoms. We report here the results of RNA expression profiling of cerebellar white matter (CWM) tissue from two independent cohorts of MSA patients (n = 66) and healthy controls (HC; n = 66). RNA samples from bulk brain tissue and from oligodendrocytes obtained by laser capture microdissection (LCM) were sequenced. Differentially expressed genes (DEGs) were obtained and were examined before and after stratifying by MSA clinical sub-type.
We detected the highest number of DEGs in the MSA-C group (n = 747) while only one gene was noted in MSA-P, highlighting the larger dysregulation of the transcriptome in the MSA-C CWM. Results from both bulk tissue and LCM analysis showed a downregulation of oligodendrocyte genes and an enrichment for myelination processes with a key role noted for the QKI gene. Additionally, we observed a significant upregulation of neuron-specific gene expression in MSA-C and enrichment for synaptic processes. A third cluster of genes was associated with the upregulation of astrocyte and endothelial genes, two cell types with a key role in inflammation processes. Finally, network analysis in MSA-C showed enrichment for β-amyloid related functional classes, including the known Alzheimer’s disease (AD) genes, APP and PSEN1.
This is the largest RNA profiling study ever conducted on post-mortem brain tissue from MSA patients. We were able to define specific gene expression signatures for MSA-C highlighting the different stages of the complex neurodegenerative cascade of the disease that included alterations in several cell-specific transcriptional programs. Finally, several results suggest a common transcriptional dysregulation between MSA and AD-related genes despite the clinical and neuropathological distinctions between the two diseases.

overall_design: RNA sequencing case-control study between MSA patients and controls (samples from cohort 1 as indicated in the manuscript)

first: Christiane

last: Bleul

first: Isabelle

last: Schrauwen

first: Joshua

last: Talboom

first: Llorida

last: Llaci

first: Matthew

middle: D

last: DeBoth

first: Marcus

last: Naymik

first: Glenda

last: Halliday

first: Conceicao

last: Bettencourt

first: Janice

last: Holton

first: Geidy

middle: E

last: Serrano

first: Lucia

last: Sue

first: Thomas

last: Beach

first: Nadia

last: Stefanova

last: Huentelman


title: RNAseq of MDA-MB-231 siCon and siCD81 cells

status: Public on May 01 2022

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

summary: We conducted an RNA sequencing analysis comparing MDA-MB-231 siCon and siCD81 cells.

overall_design: MDA-MB-231 cells were transfected with non-targeting siRNA (siCon) and siCD81 using Dharmafect in triplicate. After 48 hours, the cells were harvested and total RNA of MDA-MB-231 cells was isolated using Trizol, phase separated by chloroform, and extracted by alcohol. Samples were sent to Northwestern University’s Center for Genetic Medicine Sequencing core facility for deep sequencing analysis.

first: Erika

middle: K

last: Ramos


title: Rpd3 regulates single-copy origins independently of the rDNA array by opposing origin stimulation by Fkh1 [BrdU-IP-seq]

status: Public on Apr 06 2022

city: Los Angeles

first: Yiwei

last: He

address: 1050 Childs Way RRI 203

department: Molecular Biology

institute: University of Southern California

summary: The replication of eukaryotic genomes is highly regulated to ensure faithful transmission of all genetic information through cell divisions. In addition to stringent control of origin initiation by cell cycle controls and DNA damage checkpoints, spatial and temporal control of origins serves to stage and balance replication of different genomic regions, with potential implications for development and genome stability. Replication of highly repetitive sequences creates stressful competition between genomic regions for sufficient replication resources. Here, we examined histone deacetylases Rpd3 and Sir2 in balancing replication between unique sequences and the multi-copy ribosomal DNA gene cluster(s), which has emerged as an evolutionarily conserved node of genomic instability.  We elucidate Rpd3's mechanism of origin regulation, which is distinct and independent of Sir2.

overall_design: exp1: sample 1-12; exp2: sample 13-16; exp3: sample 17-24; And each experiment was divided into 'IP' and the corresponding 'Total'.

first: Jared

last: Peace

first: Oscar

last: Aparicio


title: Csf2ra deletion attenuates acute lung injuries induced by intratracheal inoculation of aerosolized ricin in mice

status: Public on Mar 28 2022

city: Beijing

first: Fuliang

last: Zong

state: China

address: Feitai region Dongda road

institute: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

summary: The global transcriptome profile of lung tissue in WT and Csf2ra knockout mice after exposure to aerosolized ricin

overall_design: Lung mRNA profiles of 6-8 week-old females Csf2ra knockout mice and wild type (WT) mice treated with lethal dose aerosolized ricin

first: Sha

last: Li

first: Lingfei

last: Hu

first: Huiying

last: Yang


title: Gene expression profiling of human colorectal cancer cell lines KM12SM and SW620

status: Public on Mar 26 2022

city: Madrid

first: Javier

last: Robles

state: Madrid

address: Calle Ramiro de Maetzu 9

department: Biomedicine

institute: Biological Research Centre Margarita Salas

summary: Colorectal cancer (CRC) is the second leading cause of cancer death in developed countries, mainly as a consequence of metastatic spread. A significant number of diagnosed and treated patients relapse after a few years and may eventually die from metastasis. Our goal was to develop and validate a gene-based risk score algorithm for patient stratification in stages II and III based on metastasis-related secreted proteins

overall_design: Affymetrix (Clariom S) array-based mRNA expression profiles generated for KM12SM and SW620 colorectal cancer (CRC) cell lines cultured in vitro under standard conditions. Three replicates of each cell line were performed.

first: Laura

last: Pintado

first: Issam

last: Boukich

first: Juan

last: Imbaud

first: José

last: Casal


title: Transcriptional profiling of macrophages in situ in metastatic melanoma reveals localization dependent phenotypes and function

city: Farmington

first: Jianan

last: Lin

address: 10 discovery dr

institute: The Jackson Laboratory

summary: Therapeutic interventions modulating immune function at the tumor site could improve outcomes in cancer. Here we analyzed metastatic melanoma; a tumor type highly responsive to T-cell based therapies, and found that the tumor-infiltrating T cells are localized closely to CD14+ monocytes/macrophages rather than to melanoma cells. Using customized immunofluorescence-guided laser capture micro-dissection, we analyzed transcriptome of CD3+ T cells, CD14+ monocytes/macrophages and melanoma cells in non-dissociated tissue. CD14+ cells localized in tumors beds displayed specific transcriptional signature distinct from CD14+ cells that were localized in tumor stroma. When applied to TCGA cohorts, the gene module of stromal macrophages distinguished patients with significantly prolonged survival in cutaneous melanoma and as well as other cancers including uveal melanoma, bladder urothelial carcinoma and lower grade glioma. This gene module contained CD14; Ly75, a gene linked with antigen capture and regulation of tolerance and immunity; and CD2; altogether a signature of monocyte-derived dendritic cells (DCs). Thus, stromal CD14+ cell signature represents a novel candidate biomarker and targeted reprogramming of stromal macrophages to acquire DC function might offer a therapeutic opportunity for metastatic cancer.

overall_design:
We analyzed 64 samples in total, which include 16 iCD14+, 16 sCD14+, 16 cancer cells, 8 iCD3+ and 8 sCD3+ cell samples. The samples are from 8 different patients. For CD14+ and cancer cell samples, we have 2 samples per patient. For CD3+ samples, we have 1 sample per patient.

**The raw data are deposited in dbGaP (phs002564) due to patient privacy concerns**

first: Jan

last: Martinek

first: Kyung

last: Kim

first: Victor

last: Wang

first: Te-Chia

last: Wu

first: Hannah

last: Boruchov

first: Ananya

last: Gulati

first: Shamreethaa

last: Seeniraj

first: Lili

last: Sun

first: Florentina

last: Marches

first: Paul

last: Robson

first: Anthony

last: Rongvaux

first: Micheal

last: Chiorazzi

first: Richard

last: Flavell

first: Joshy

last: George

first: Jeffrey

last: Chuang

first: Jacques

last: Banchereau

first: Karolina

last: Palucka


title: E0771 cultured mouse mammary tumor cell RNA-seq gene expression profiling: impact of activated cyclophosphamide versus interferon-beta, and the role of interferon signaling in cyclophosphamide responses

status: Public on Mar 17 2022

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: RNA-seq analysis of polyA-selected RNA isolated from cultured E0771 mouse breast cancer cells, with or without treatment with activated cyclophosphamide (4HC, 4-hydroperoxy-cyclophosphamide), interferon-beta, and antibody to the type-I interferon receptor IFNAR1. These RNA samples were part of a study where we investigated the role of type-I interferon signaling in therapeutic responses to cyclophosphamide in mouse models of breast cancer [Vergato et al, Canc Res Communic].

overall_design: RNA-seq libraries were prepared from cultured tumor cell-extracted RNA obtained from n=3 independent cultures for each condition tested.

first: Cameron

last: Vergato


title: Cyclophosphamide treatment experiments in mouse models of breast cancer: 4T1 and E0771

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

overall_design: Refer to individual Series


title: T cells

status: Public on Apr 04 2022

city: New York

first: Peter

last: Smibert

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center


title: Next Generation Sequencing of Transcriptomes of human cells expressing the human gene LY6S which is the TransMap and phylogeneticlly predicted homolog to murine Ly6a also known as T-cell Activating Protein, Sca1, Stem Cell Antigen-1, Ly6A2/E1 [M12 YDFR]

status: Public on Mar 15 2022

city: Tel-Aviv

first: Daniel

last: Wreschner

address: Ramat Aviv

institute: Tel Aviv University

summary: We discovered a new human gene, LY6S, coding for an LY6-like protein. TransMap and phylogenetic studies reveal that LY6S is the homolog of the murine Ly6a gene known as Ly6A.2/Ly6E.1, Sca1 (Stem Cell Antigen-1) and TAP (T-cell activating protein) which codes for a cell-surface protein used extensively as a hematopoietic stem cell marker. LY6S is interferon-inducible and codes for both GPI-linked membrane and secreted proteins. The LY6S cell-surface protein, contains only 9 cysteines distinguishing it from all other LY6-like proteins that have 10 consensus cysteine residues.  LY6S is most highly expressed in cells of the human spleen that constitute a unique spleen cell lineage. Expression of the GPI-linked LY6S protein in various human cell lines leads to profound changes in cell morphology and cell growth, neither of which are affected by expression of the secreted LY6S protein. RNA-Seq analyses presented here show distinct shifts in patterns of gene expression, particularly of genes coding for inflammatory and immune response proteins, were associated with these changes. Our findings reveal the presence of a previously non-annotated human gene, LY6S, which is the Ly6a homolog and that codes for proteins expressed in  spleen cells representing a new cell lineage, are associated with a florid inflammatory phenotype and  regulate immune responses and cell growth.

overall_design: mRNA profiles of human M12 or YDFR human melanoma cells that were stably transfected with either control pQCXIP expression vector or with the same vector coding for the GPI-linked, cell membrane located human LY6-iso1 protein  were generated by deep sequencing, in triplicate.

first: Avital

last: Sarusi-Portuguez


title: Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases

status: Public on Mar 09 2022

city: Stanford

first: Sean

last: Wang

address: 1291 Welch Rd

institute: Stanford University

summary: We present a joint single-cell atlas of gene expression and chromatin accessibility of the adult human retina. We integrate this atlas with a HiChIP enhancer connectome, expression quantitative trait loci (eQTL) data, and base-resolution deep learning models to predict noncoding variants with causal roles in eye disease.

overall_design:
Single-cell RNA-seq, single-cell ATAC-seq, and HiChIP
Please note that the processed data for the ATAC-seq and RNA-seq samples were generated from all replicates and are linked to the corresponding rep1 sample records.

first: Howard

middle: Y

last: Chang


title: Microglial-oligodendrocyte interactions in myelination and neurological function recovery after traumatic brain injury

city: Pittsburgh

first: Md Nabiul

last: Hasan

address: 3501 Fifth Avenue

department: Neurology

institute: University of Pittsburgh

summary: Differential microglial inflammatory responses play a role in regulation of differentiation and maturation of oligodendrocytes (OLs) in brain white matter. How microglia-OL crosstalk is altered by traumatic brain injury (TBI) and its impact on axonal myelination and neurological function impairment remain poorly understood. In this study, we investigated roles of a Na+/H+ exchanger (NHE1), an essential microglial pH regulatory protein, in microglial proinflammatory activation and OL survival and differentiation in a murine TBI model induced by controlled cortical impact. Similar TBI-induced contusion volumes were detected in the Cx3cr1-CreERT2 control (Ctrl) mice and selective microglial Nhe1 knockout (Cx3cr1-CreERT2;Nhe1flox/flox, Nhe1 cKO) mice. Compared to the Ctrl mice, the Nhe1 cKO mice displayed increased resistance to initial TBI-induced white matter damage. The cKO brains presented increased anti-inflammatory phenotypes of microglia and infiltrated myeloid cells, with reduced proinflammatory transcriptome profiles. Moreover, the cKO mice exhibited accelerated post-TBI sensorimotor and cognitive functional recovery than the Ctrl mice. These phenotypic outcomes were recapitulated in C57BL6J wild-type mice which were subjected to TBI and received treatment of a potent NHE1 inhibitor HOE642 for 1-7 days post-TBI. Taken together, these findings collectively demonstrated that blocking NHE1 protein stimulates restorative microglial activation and oligodendrogenesis, which contributes to accelerated white matter repair and neurological function recovery after TBI.

overall_design: Examination of effect of deletion of Nhe1 in microglia on post-TBI white matter repair and neurological function recovery

first: Md

middle: N

first: Susan

last: Song

first: Dandan

last: Sun


title: 4T1 cultured mouse mammary tumor cell RNA-seq gene expression profiling: impact of activated cyclophosphamide versus interferon-beta treatment, and the role of interferon signaling in cyclophosphamide responses

summary: RNA-seq analysis of polyA-selected RNA isolated from cultured 4T1 mouse breast cancer cells, with or without treatment with activated cyclophosphamide (4HC, 4-hydroperoxy-cyclophosphamide), interferon-beta, and antibody to the type-I interferon receptor IFNAR1. These RNA samples were part of a study where we investigated the role of type-I interferon signaling in therapeutic responses to cyclophosphamide in mouse models of breast cancer [Vergato et al, Canc Res Communic].

overall_design: RNA-seq libraries were prepared from cultured tumor cell-extracted RNA obtained from n=2-3 independent cultures for each condition tested.


title: 4T1 mouse mammary tumor RNA-seq gene expression profiling: impact of time course of metronomic cyclophosphamide treatment of triple negative breast cancer tumors implanted in female BALB/c mice

summary: RNA-seq analysis of polyA-selected RNA isolated from frozen tumor tissue excised from adult female BALB/c mice implanted with 4T1 tumors in the mammary fat pad. Mice were treated with cyclophosphamide given on a metronomic schedule (treatment every 6 days at 130 mg/kg, or PBS (vehicle control), for a total of 2, 4 or 7 treatment cycles) (lab experiment # TD227). These tumor RNA samples were part of a study where we investigated the role of type-I interferon signaling in mouse models of breast cancer [Vergato et al, Canc Res Communic].

overall_design: Tumor-derived RNA-seq libraries were prepared for n=2-3 independent pools for tumor-extracted RNA for each condition tested, with each pool comprised of RNA isolated from n=2-3 independent biological replicate tumors.

first: Kshama

middle: A

last: Doshi


title: Human PSCs determine the competency of cerebral organoid differentiation via FGF signaling and epigenetic mechanisms

first: Kent

last: Imaizumi

address: 318 Campus Drive


title: Effect of CRABP2 depletion and overexpression on thyroid cancer cell lines

status: Public on Mar 02 2022

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

summary: Cellular retinoic acid-binding protein 2, encoded by the CRABP2 gene, is a protein that facilitates retinoic acid binding to its cognate receptor complex and transport to the nucleus. Our analysis indicates that CRABP2 expression is upregulated in thyroid cancer and is involved in the invasiveness of thyroid cancer. Loss- and gain-of-function approaches were used to elucidate its oncogenic mechanisms.

overall_design: Human thyroid cancer cell lines BHT-101 and FTC-133 were transfected with CRABP2-specific siRNA or a control siRNA, whereas 8505C cell line was transfected with the CRABP2-overexpressing vector or an empty vector. Cellular RNA was submitted for RNA sequencing.


title: HIV-1 Tat modifies expression of host genes in B cells

status: Public on Mar 07 2022

city: Moscow

first: Anna

last: Valyaeva

address: Leninskiye Gory, MSU, 1-73

department: Faculty of Bioengineering and Bioinformatics

country: Russia

institute: Lomonosov Moscow State University

summary: We carried out genome-wide analysis of cellular gene expression changes in response to ectopic expression of HIV-1 Tat and mutant TatC22G proteins.

overall_design: Study of HIV-1 Tat and mutant TatC22G proteins influence on host genes expression in lymphoblastoid B cell line RPMI 8866. Mock RPMI 8866 cells and cells expressing EGFP were used as controls. Three replicates in each group.

first: Maria

last: Tikhomirova

first: Daria

last: Potashnikova

first: Eugene

last: Arifulin

first: Alexey

last: Penin

last: Logacheva

first: Alexandra

last: Bogomazova

first: Anastasia

last: Zharikova

first: Andrey

last: Mironov

first: Aleena

last: Saidova

first: Yana

middle: R

last: Musinova

first: Yegor

last: Vassetzky

last: Sheval


title: Mettl14-dependent m6A modification controls iNKT cells development and function by regulating p53-dependent apoptosis pathway and TCR signaling

status: Public on Mar 01 2022

first: Eva

last: Morgun

address: 320 N Superior St

department: Department of Microbiology and Immunology

summary: N6-methyladenosine (m6A) is the most common modification to mRNA in mammalian cells linked to development and disease. m6A controls CD4+ T cell homeostasis by targeting the IL-7/STAT5/SOCS family pathway and sustains Treg suppressive function. However, the role of m6A modification in non-conventional T cell development and function remains unknown. Here we showed that m6A modification was indispensable for NKT cell homeostasis using mice with T cell-specific deletion of RNA methylation writer METTL14 (T-Mettl14-/-). Loss of METTL14-dependent m6A modification led to the upregulation of p53-mediated apoptosis in double-positive (DP) thymocytes. The decreased lifespan of DP thymocytes reduced the efficiency of distal Va-Ja rearrangement, including the invariant Va14-Ja18 TCR, and therefore led to a profound decrease in the iNKT cell population. The residual iNKT cells in T-Mettl14-/- mice exhibited increased apoptosis and impaired maturation.  In addition, loss of METTL14 upregulated Cish expression, which contributed to decreased proliferative response to IL-2 and IL-15 and impaired cytokine production upon TCR stimulation in METTL14-deficient iNKT cells. Furthermore, knocking down METTL14 in mature iNKT cells diminished their cytokine production, correlated with increased Cish expression and decreased TCR signaling. Collectively, our data reveals a critical role for METTL14- dependent-m6A modification in iNKT cell development and function, highlighting the need to take this effect into consideration for targeting m6A pathway in therapeutic settings.

overall_design: DP thymocytes from Mettl14fl/fl/CD4-Cre+ (n=3) and littermate controls (n=3)

first: Liang

last: Cao

first: Samantha

last: Genardi

first: Lavanya

last: Visvabharathy

first: Chuan

last: He

first: Haochu

last: Huang

first: Chyung-Ru

last: Wang


title: Borrelia burgdorferi, the Lyme disease spirochete, possesses genetically-encoded responses to doxycycline, but not to amoxicillin.

status: Public on Mar 08 2022

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

summary:
Purpose: To determine whether Borrelia burgdorferi, the spirochetal agent of Lyme disease, responds to sub-lethal doses of antibiotics.
Methods: mRNA profiles of Borrelia burgdorferi were compared after subculturing in 0.2μg/mL amoxicillin, 0.2μg/mL doxycycline, or media control for 3h or 24h (n=3 per group) by paired-end sequencing using the Illumina NextSeq 500. The sequence reads were aligned using Salmon aligner followed by DESeq2 for differential expression analysis.
Results: After culturing for 24 h in a sub-lethal concentration of doxycycline, there were significant increases in a substantial number of transcripts for proteins that are involved with translation. Bacteria continued to elongate, but appeared to be defective in septation and formed filaments. In contrast, incubation with sublethal concentration of amoxicillin led to membrane blebbing and swelling, indicative of cell wall disruption, but no significant changes in levels of any bacterial transcript.
Conclusion: We conclude that B. burgdorferi has a mechanism(s) that detects translational inhibition by doxycycline, and increases production of translational machinery in compensation. In contrast, The absence of response to the inhibition of cell wall synthesis by amoxicillin implies that B. burgdorferi lacks a mechanism to assess cell wall integrity.

overall_design: Borrelia burgdorferi gene expression responses to sub-lethal concentrations of antibiotics.

first: Timothy

middle: C

last: Saylor

last: Casselli

first: Catherine

last: Brissette

first: Brian

last: Stevenson


title: Identification of Key Gene and Functional Pathways in Radioresistance of non-small cell lung cancer

status: Public on Feb 27 2022

city: Guangzhou

first: Jiaxin

last: Feng

address: No.151 Yanjiang West Road, Yuexiu District, Guangzhou , Guangdong Province

institute: The First Affiliated Hospital of Guangzhou Medical University

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

summary: For better understanding of radiotherapy resistance and its potential mechanism, we established radioresistance cell lines of non-small cell lung cancer (NSCLC) followed by microarray analysis. 529 differentially expressed genes (DEGs) were then screened between radiation resistant cell lines compared with the sensitive cell lines. The biological functions and enrichment pathways of the above DEGs were identified using Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) enrichment analyses. Gene Set Enrichment Analysis (GSEA) revealed that the radiation resistance group had the most gene sets enriched in altered immune response, such as TNF signaling pathway, when compared to the radiation sensitive group. Protein-protein interaction (PPI) network was carried out from the STRING database. Following that, by means of Cytoscape software, five hub genes (CXCL10, IFIH1, DDX58, CXCL11, RSAD2) were identified, and qRT-PCR confirmed the expression of the above hub genes. ChIP-X Enrichment Analysis showed that STAT1 might be the transcription factor of the above hub genes. Our results suggested that although immune system activation occurs followed by radiation resistance, the unregulated expression of PD-L1 ultimately leads to the exhaustion of anti-tumor immunity, which may be the possible mechanisms of tumor resistance to radiotherapy.

overall_design: The lung cancer cell line A549 in logarithmic growth phase was irradiated with 4 Gy for the first time and cultured for subculture. After cell adherence growth, the cells were irradiated again with 4 Gy, with a total dose of 60Gy. The radiotherapy resistance cell line A549-RR was obtained by further culture. Total RNA of cultured cells was isolated using TRIzol reagent (Invitrogen), there were three samples in each group and the samples were sent to Shanghai Kangcheng Biological Co LTD for RNA microarray analysis.

first: Shouying

last: Li


title: Single-cell RNAseq anaysis of 4-month-old brain organoids from feeder-free iPSCs with PD173074 treatment

first: Kent

last: Imaizumi

summary: Single-cell gene expression profiling of 4-month-old brain organoids from feeder-free iPSCs with PD173074 treatment

overall_design: 1 sample

first: Hirosato

last: Ideno

first: Hideyki

last: Okano


title: Single cell transcriptomics of hepatostellate organoids derived from DKC1 A353V mutant and DKC1 A353V corrected iPSCs

status: Public on Feb 28 2022

city: Philadelphia

first: Joshua

middle: .H

last: Rhoades

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

summary: We model liver phenotypes associated with telomere dysfunction using DC patient-derived iPS cells and isogenic controls with CRISPR/Cas9-mediated homology-directed repair correction of the disease-causing DKC1 mutation. Differentiation of these cells into hepatocyte-like cells or hepatic stellate cells indicates that the parenchymal hepatocytes are primarily affected by telomere dysfunction. We develop an admixed hepatostellate organoid culture model which further reveals that mutant hepatocytes exert dominant effects on hepatic stellate cells regardless of stellate cell genotype. Hepatostellate organoids containing DKC1-mutant hepatocytes exhibit hyperplasia in both the hepatocyte compartment and, remarkably, in stellate cells. Moreover, mutant hepatocytes can induce hallmarks of stellate cell activation independently of stellate cell genotype. Interestingly, mutant hepatostellate organoids also contain off-target PLVAP+ endothelial cells reminiscent of scar-associated endothelium observed in non-DC cirrhosis patients.

overall_design: Single cell sequecing analysis with HTO of hepatostellate organoids by admixing hepatocyte-like cells (HEPs) and hepatic stellate cells(HSCs).

first: Christopher

last: Lengner

first: Youngjun

last: Choi


title: Bach2 negatively regulates natural killer cell maturation and effector program

status: Public on Feb 10 2022

first: Shasha

state: MO

address: 660 S Euclid Avenue

department: Rheumatology

institute: Washington University in St.Louis

summary: Bach2 has been reported to regulate multiple immune cell development and function. Here we report that Bach2 is constitutively expressed in relatively immature NK subsets. Bach2 negatively regulates NK cell development and Bach2 deficiency results in NK cell with mature effector phenotype. Thus, Bach2 functions as a negative regulator of NK cell maturation and function.

overall_design: Fresh NK cells from spleen of Bach2-conditional knockout mice or wild-type mice were enriched by the EasySep Mouse NK cell isolation kit (STEMCELL Technologies). CD3-CD19-NK1.1+NKp46+ NK cells were then sorted from enriched cells. Total RNA were isolated by PureLink RNA Mini Kit (Ambion) and subjected to RNA-sequencing. The library was generated using low input Clontech method and NovaSeq 6000 was used for sequencing.

first: Benpeng

last: Miao

first: Wayne

last: Yokoyama