title: Restoring Tumor Immunogenicity with Dendritic Cell Reprogramming [scRNA-seq]

summary: Decreased antigen presentation contributes to the ability of cancer cells to evade the immune system. We used the minimal gene regulatory network of type 1 conventional dendritic cells (cDC1) to reprogram cancer cells into professional antigen- presenting cells (tumor-APCs). Enforced expression of the transcription factors PU.1, IRF8, and BATF3 (PIB) was sufficient to induce cDC1 phenotype in 36 cell lines derived from human and mouse hematological and solid tumors. Within 9 days of reprogramming, tumor-APCs acquired transcriptional and epigenetic programs associated with cDC1 cells. Reprogramming restored the expression of antigen presentation complexes and costimulatory molecules on the surface of tumor cells, allowing the presentation of endogenous tumor antigens on MHC-I, and facilitating targeted killing by CD8+ T cells. Functionally, tumor-APCs engulfed and processed proteins and dead cells, secreted inflammatory cytokines, and cross- presented antigens to naïve CD8+ T cells. Human primary tumor cells could also be reprogrammed to increase their capability to present antigen and to activate patient-specific tumor-infiltrating lymphocytes. In addition to acquiring improved antigen presentation, tumor-APCs had impaired tumorigenicity in vitro and in vivo. Injection of in vitro generated melanoma-derived tumor-APCs into subcutaneous melanoma tumors delayed tumor growth and increased survival in mice. Antitumor immunity elicited by tumor-APCs was synergistic with immune checkpoint inhibitors. Our approach serves as a platform for the development of immunotherapies that endow cancer cells with the capability to process and present endogenous tumor antigens.

overall_design: Single-cell mRNA sequencing (scRNA-seq) was performed in T98G cells or patient-derived tumor cells transduced with hPIB-eGFP or with eGFP lentiviral particles. On 3,5,7 and 9 days after reprogramming was initiated, 5,000–10,000 transduced EGFP+ cells expressing at least one of the reprogramming markers (CD45 and HLA-DR), were separated by FACS and and subjected to sequencing.

first: Olga

last: Zimmermannova

first: Carlos-Filipe

last: Pereira


title: Spatial heterogeneity of integrins and their ligands in primary breast tumors

status: Public on Sep 08 2023

city: Tomsk

first: Tashireva

last: Liubov

address: 5 Kooperativny Street, Tomsk

department: Cancer Research Institute

country: Russia

institute: Tomsk National Research Medical Center

summary: The diversity of cell-cell interactions in different regions of a tumor reflects the functional heterogeneity of cancer, which poses challenges in early diagnosis, selection of treatment strategies, and prognosis of breast cancer. Cancer cells interact with each other to form different morphological structures in the tumor and stromal host cells via integrins. The objective of this study was to characterize the morphological and spatial heterogeneity of primary breast tumors in the context of expression profiles of integrins and their ligands. We studied spatial transcriptomics using the 10X Visium approach and the NICHES algorithm to map ligand-receptor signaling pathways and visualize the heterogeneity of signaling archetypes in tumor clusters. Cluster analysis of the expression profiles of tumor spots from the samples indicated pronounced inter-tumoral heterogeneity. Integrin-ligand functional clusters were associated with intratumoral heterogeneity, which was manifested by the presence of several morphological loci as observed in histological tumor samples. Inter-tumoral heterogeneity was manifested by a different number of functional clusters, ranging from 2 to 9 for each tumor sample. The main characteristic of these clusters was the significant predominance of non-complementary integrin subunits. Of the 42 functional integrin-ligand pairs in 21 clusters of five samples, 41 pairs occurred only once. The exception was the LAMA5-ITGB4 pair, which was detected in two clusters of different samples. The spatial heterogeneity of integrin-ligand expression clusters in breast cancer contributes significantly to the functional heterogeneity of the tumor, which sets the stage for many scenarios of parenchymatous-stromal relationships, some of which may be effective in the emergence of metastasizing tumor seed cells. The intra- and inter-tumoral spatio-functional heterogeneity of the tumor tissue that we discovered may largely explain why it is difficult to achieve success in most patients with breast cancer using any therapeutic strategy targeting one molecule of the vast array, regardless of the importance of its pathogenetic significance.

overall_design: Six breast cancer samples were included in this study. Spatial transcriptomics using the 10X Visium approach and the NICHES algorithm to map ligand-receptor signaling pathways and visualize the heterogeneity of signaling archetypes in tumor clusters.

first: Liubov

last: Tashireva

first: Evgeniya

last: Grigorieva

first: Vladimir

last: Alifanov

first: Pavel

last: Iamshchikov

first: Marina

last: Zavyalova

last: Perelmuter


title: Crosstalk between myeloid and B cells shapes the distinct microenvironments of primary and secondary liver cancer

status: Public on Jun 19 2023

city: Guangzhou

first: Guopei

last: Zhang

address: 58 Zhongshan Road 2

country: China

institute: Sun Yat-sen University

type: Expression profiling by high throughput sequencing

summary: The tumor microenvironment is distinctive in primary and secondary liver cancer. B cells represent an important component of immune infiltrates. Here, we demonstrated that B cells are an important regulator in hepatocellular carcinoma (HCC) and colorectal cancer liver metastasis (CRLM) microenvironments. B cells displayed distinct developmental trajectories in HCC and CRLM. Single-cell analysis revealed that IgG+ plasma cells preferentially accumulated in HCC while IgA+ plasma cells were preferentially enriched in CRLM. Mechanistically, IgG+ plasma cells in HCC were recruited by tumor-associated macrophages via the CXCR3-CXCL10 axis, whereas IgA+ plasma cells in CRLM were recruited by metastatic tumor cells via CCR10-CCL28 signaling. Functionally, IgG+ plasma cells preferentially promoted pro-tumorigenic macrophages formation in HCC, and IgA+ plasma cells preferentially induced granulocytic myeloid-derived suppressor cells activation in CRLM. Clinically, increased infiltration of IgG+ plasma cells and macrophages in HCC was correlated to worse survival, while increased intratumoral IgA+ plasma cells and neutrophils in CRLM indicated poor prognosis. Taken together, this study demonstrated plasma and myeloid cell-mediated immunosuppression in HCC and CRLM, suggesting that selectively modulating primary or secondary tumor-related immunosuppressive regulatory networks might reprogram the microenvironment and provide an immunotherapeutic strategy for treating liver cancer.

overall_design:
In this study, single-cell analysis of more than 20000 single B cells isolated from HCC tumor and peri-tumor tissues, and nine CRLM tissues, enabled us to demonstrate the subset composition and biological functions of B cells in HCC and CRLM.
** Please note that raw data have been deposited in the Genome Sequence Archive for Human under accession HRA004767***

first: Sui

last: Peng


title: Transcriptional profiling of EHMT1/2 depletion and overexpression in various high grade serous ovarian cancer models

status: Public on Jun 14 2023

city: Denver

first: Lily

last: Nguyen

state: CO

address: 220 Roslyn Street, Apt 706

country: USA

institute: UNIVERSITY OF COLORADO DENVER

summary: Euchromatin methyltransferase1/2 (EHMT1/2) have been correlated with tumorigenesis and therapy resistance through unknown mechanisms of action. Using a combination of experimental and bioinformatic analyses in several PARP inhibitor resistant ovarian cancer models, we demonstrate that combinatory EHMT and PARP inhibition is effective in treating PARP inhibitor resistant ovarian cancers. Our in vitro studies show that combinatory therapy reactivates transposable elements and increased immunostimulatory dsRNA formation and several immune signaling pathways. Our in vivo studies show that single EHMT and combinatory EHMT and PARP inhibition reduces tumor burden and that this reduction is dependent on CD8 T cells. Together, our results show a direct mechanism by which transposable elements are regulated and how an epigenetic therapy can be used as a fine tune agent to treat cancers with specific genetics.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Transcriptional profiling (RNA-seq) of patient-derived ex vivo tissues, PEO1-R, Kuramochi-R, OVCAR420-R, and ID8-R cells that were treated with DMSO, a PARP inhibitor (olaparib), an EHMT1/2 inhibitor (UNC0642 or EZM8266) or combinatory PARP/EHMT inhbitors. There is also a set of PEO1 cells with EHMT1 or EHMT2 overexpressed

first: Zachery

last: Watson

first: Ortega

last: Raquel

first: Edward

last: Chuong

first: Benjamin

last: Bitler

first: Arnoult

last: Nausica


title: Single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) from Kimura disease patient treated with dupilumab

status: Public on Jun 01 2023

city: Chiba

first: Takahiro

last: Kageyama

address: 1-8-1, Inohana

country: Japan

institute: Chiba University

summary: We performed single-cell RNA sequencing of PBMCs from Kimura disease patient succesfully treated with dupilumab to explore the mechanism of action of dupilumab treatment.

overall_design: We collected PBMCs seven days before the first administration of dupilumab and 14 months after the initiation of dupilumab, respectively.

first: Kensuke

last: Suga

first: Masahiro

last: Kiuchi

first: Kota

last: Kokubo

first: Shigeru

last: Tanaka

first: Arifumi

last: Iwata

first: Kotaro

last: Suzuki

first: Kiyoshi

last: Hirahara

first: Hioroshi

last: Nakajima


title: Expression profiling in exosomal miRNAs of health individuals and newly diagnosed multiple myeloma

city: Changsha

first: Liwen

last: Wang

state: Hunan

address: 138 Tongzipo road

department: Department of Hematology

institute: Third Xiangya Hospital, Central South University

type: Non-coding RNA profiling by high throughput sequencing

summary: Multiple myeloma (MM) is a hematopoietic malignancy.Based on its laboratory and clinical presentation it can be summarized as MGUS, smoldering myeloma, and multiple myeloma. Previous studies have shown that the expression levels of miRNAs in different stages of the disease are different and exosomes are involved in modulating the progression and the metastasis of cancers through miRNAs. This study analyzes the expression levels of miRNAs in healthy individuals and myeloma bone marrow serum exosomes.

overall_design: BM samples were obtained from 4 MM patients and 2 healthy individuals .The exosomes from bone marrow were isolated by ultracentrifugation. Exosomal miRNA profiling was sequencing on Illumina NextSeq 500.

first: Xin

last: Chen

first: Qian

last: Cheng

last: Li


title: An inflammatory memory of COVID-19 in airway basal stem cells impairs mucociliary differentiation

city: Boston

first: Xingbin

last: Ai

state: MA

address: 55 Fruit St

department: Pediatrics

institute: MASSACHUSETTS GENERAL HOSPITAL

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: A tracheal aspirate-derived airway basal cell model reveals a proinflammatory epithelial defect in congenital diaphragmatic hernia (ATAC-Seq)

status: Public on Jun 30 2023

summary: Congenital diaphragmatic hernia (CDH) is characterized by incomplete closure of the diaphragm and lung hypoplasia. The pathophysiology of lung defects in CDH is poorly understood. To establish a translational model of human airway epithelium in CDH for pathogenic investigation and therapeutic testing, we developed a robust methodology of epithelial progenitor derivation from tracheal aspirates of newborns. Basal stem cells from CDH patients and preterm and term, non-CDH controls were derived and analyzed by bulk RNA-sequencing, ATAC-sequencing, and air-liquid-interface differentiation. Transcriptomic and epigenetic profiling of CDH and non-CDH basal stem cells reveals a disease-specific, proinflammatory signature independent of severity or hernia size. In addition, CDH basal stem cells exhibit defective epithelial differentiation in vitro that recapitulates epithelial phenotypes found in fetal human CDH lung samples and fetal tracheas of the nitrofen rat model of CDH. Furthermore, steroid treatment normalizes epithelial differentiation phenotypes of human CDH basal stem cells in vitro and in nitrofen rat tracheas in vivo. Our findings have identified an interplay between a proinflammatory signature and BSC differentiation as a potential therapeutic target for airway epithelial defects in CDH.

overall_design: Comparative chromatin opening profiling analysis of ATAC-seq data for basal stem cells from CDH patients and term and preterm controls.

first: Richard

last: Wagner

first: Gaurang

middle: M

last: Amonkar

first: Wei

first: Paul

middle: H

last: Lerou


title: An inflammatory memory of COVID-19 in airway basal stem cells impairs mucociliary differentiation (RNA-Seq)

summary: Airway basal stem cells (BSCs) in chronic lung diseases accumulate memories to promote disease-specific pathogenesis. Whether acute lung infection also endows BSCs with an inflammatory memory to impair epithelial regeneration is unknown. Here, we derived multiple BSC lines from patients with and without COVID-19 (CoV19) using tracheal aspirate (TA) as a viable source of bronchial BSCs. While tested negative for SARS-CoV-2, BSC lines from CoV19 patients bore a proinflammatory gene signature, exhibited early cell cycle exist, and displayed goblet cell hypoplasia following differentiation in air-liquid interface (ALI). These phenotypes reproduced, at least partially, changes in BSCs in patients with CoV19 assessed by bioinformatic analysis of preexisting single cell transcriptomes of BSCs and by staining of lung sections for select markers. Such a memory in BSCs previously exposed to CoV19 was mediated by increases in chromosomal accessibility at key inflammatory gene loci associated with gene dysregulation and sustained STAT3 activation. Blockade of STAT3 hyperactivation in CoV19-exposed BSCs restored mucociliary differentiation in ALI. Taken together, BSCs acquire an epigenetic memory of CoV19 to impair epithelial regeneration. BSC derivation from TA provides a versatile approach to model airway epithelium in health and lung diseases.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for basal stem cells from CDH patients and term and preterm controls.

first: Kamakshi

last: Bankoti


title: An inflammatory memory of COVID-19 in airway basal stem cells impairs mucociliary differentiation (ATAC-Seq)

overall_design: Comparative chromatin opening profiling analysis of ATAC-seq data for basal stem cells from CoV19 patients and controls.


title: Equine tissue miRNA profiling

city: Balice near Krakow

first: Klaudia

last: Pawlina-Tyszko

address: Krakowska 1

department: Deaprtment of Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

summary:
Purpose: Identification of miRNA expression profiles of selected horse tissues.
Methods: miRNA-seq analysis was performed on lung, heart and liver samples collected from 4 horses. The miRNA libraries were constructed from total RNA using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer protocol. The quantification of the obtained libraries was performed on a Qubit 2.0 spectrophotometer (Invitrogen, Life Technologies), while a quality control on a TapeStation 2200 instrument (D1000 ScreenTape; Agilent). 75 single-end cycle sequencing was performed on the NextSeq 500/550 platform (Illumina) with the use of NextSeq High Output Reagents v2 (Illumina).
Results: The comparison of miRNA profiles between the investigated tissues revealed 185 differentially expressed microRNAs (p adj≤0.05) in the heart samples versus the liver samples, 172 DE miRNAs (p adj ≤0.05) in the lung samples in comparison to the liver samples, and 155 in the lung samples versus the heart samples.
Conclusions: Obtained results show varied miRNA expression profiles characteristics for each investigated hore tissue.

overall_design: MicroRNA next generation sequencing of selected equine tissues was performed using the Illumina NextSeq 500/550 platform.

first: Ewelina

last: Semik-Gurgul

first: Tomasz

last: Szmatoła


title: Accumulating DNA damage and insufficient DNA repair in senescent cells underlie persistent DNA damage signaling

city: Stanford

first: Leighton

middle: Harrison

last: Daigh

state: CA

address: 318 Campus Dr, Clark W200

department: Chemical and Systems Biology

institute: Stanford University

summary: Senescent cells are a major cause of organismal aging and a key target for anti-aging therapies. Persistent DNA damage signaling is a primary driver of the induction and maintenance of cellular senescence. However, many DNA damaging stimuli that induce senescence, such as irradiation or transient exposure to genotoxic drugs, are transient. The mechanisms underlying persistent damage signaling in senescent cells, and why senescent cells fail to repair damaged DNA, remain unknown. Here, we were able to assess the mechanisms underlying persistence of DNA damage and senescence maintenance by designing a precisely controllable senescence system that does not require potent stressors to induce senescence. We demonstrate that sustained mTORC1 signaling in senescent cells causes gradually accumulating DNA damage and an inflammatory response that maintains cell-cycle arrest. Markedly, activation of E2F transcription, which promotes expression of DNA repair proteins, can reverse accumulated DNA damage. Thus, persistent DNA damage signaling arises in senescent cells by uncoupling of mTORC1 and E2F signaling, whereby prolonged mTORC1 activity causes gradually increasing DNA damage that cannot be sufficiently repaired without induction of protective E2F target genes.

overall_design: Transcriptomics data from MCF-10A cells arrested expressing either inducible mVenus,  mVenus-p21 or mVenus-p16. Mvenus-p16 expressing cells were  treated with DMSO or Torin2. Four conditions  with three biological replicates for a total of 12 samples

first: Tobias

last: Meyer


title: Full-length single-cell BCR sequencing paired with RNA sequencing reveals convergent responses to vaccination

status: Public on May 19 2023

city: CAMBRIDGE

first: Duncan

middle: Matthew

last: Morgan

address: 500 Main St

department: Koch Institute

institute: MIT

summary: Single-cell RNA sequencing can to resolve transcriptional features from large numbers of individual immune cells, but techniques capable of resolving the variable regions of B cell receptors (BCR) – defining features that confer antigen specificity to B cells – remain limited, especially from widely-used 3`-barcoded libraries. Here, we report a method that for recovering paired, full-length variable region sequences of the BCRs from 3`-barcoded single-cell whole transcriptome libraries. We first verified this method could produce accurate, full-length BCR sequences. We then applied this method to profile antigen-specific B cell responses elicited against the capsular polysaccharide of Streptococcus pneumoniae serotype 3 (ST3) by glycoconjugate vaccines in infant rhesus macaques. Using our method, we defined features of the BCR associated with specificity for the ST3 antigen and showed that these sequence characteristics are present in multiple vaccinated monkeys, indicating a convergent response to vaccination. These results demonstrate the utility of our method to resolve key features of the B cell repertoire and for profiling antigen-specific responses elicited by vaccination.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: B cells of interest were isolated from PBMC using either fluorscence associated cell sorting or immunomagnetic selection and analyzed with the Seq-Well platform for single-cell RNA sequencing.

first: Yiming

last: Zhang

first: Jin-Hwan

last: Kim

first: MaryAnn

last: Murillo

first: Suddham

last: Singh

first: Jakob

last: Loschko

first: Naveen

last: Surendran

first: Sarita

middle: U

last: Patil

first: I

last: Kanevsky

first: L

last: Chorro

first: J

middle: C

last: Love


title: PTEN inhibition dedifferentiates long-distance axon-regenerating intrinsically photosensitive retinal ganglion cells and upregulates mitochondria-associated DYNLT1A and LARS2

status: Public on Apr 11 2023

city: Farmington

first: Ephraim

middle: F

last: Trakhtenberg

state: CT

address: 263 Farmington Ave. RM L4005

department: Neuroscience

institute: University of Connecticut School of Medicine

summary: The central nervous system (CNS) projection neurons fail to spontaneously regenerate injured axons. Targeting the developmentally regulated genes in order to reactivate embryonic intrinsic axon growth capacity, or targeting tumor suppressor genes such as Pten, promote axon regeneration in a subset of injured retinal ganglion cells (RGCs). The subset of RGCs that regenerate axons in response to inhibition of Pten was narrowed-down to the Opn4+ intrinsically photosensitive (ip) and α subtypes of RGCs. Here, we used single cell RNA-sequencing (scRNA-seq) to investigate why only a subset of injured RGCs regenerate axons in response to Pten knockdown (KD), and to characterize the relationship between axon regeneration promoted by targeting Pten and the developmental decline in intrinsic axon growth capacity. We found that, only the most similar to embryonic state ipRGC subtypes C33 and C40 regenerated axons in response to Pten KD, which dedifferentiated them even further towards an embryonic state. We also found that genes downstream of Pten KD, specifically in the RGCs that regenerated axons, include mitochondria-associated developmentally regulated and non-developmentally regulated Dynlt1a and Lars2, respectively, which promoted axon regeneration on their own. Overall, we show that injury itself reverts transcriptome towards an embryonic state only in some neuronal subtypes and not sufficiently close to embryonic state to confer response to Pten KD, whereas certain mature neuronal subtypes are similar to embryonic state even without injury, which primes them to regenerate axons in response to Pten KD, that dedifferentiates them further towards an embryonic state and upregulates mitochondria-associated Dynlt1a and Lars2.

overall_design: Pten was KD in the adult RGCs using an intravitreally injected adeno-associated virus serotype 2 (AAV2) vector. The regenerating RGCs were FACS-isolated from the retinal single cell suspension 2 weeks after ONC injury, based on the expression of an mCherry reporter (identifying the transduced cells) and a signal of Alexa Fluor 488 conjugated to the Cholera toxin subunit B (CTB). After sorting, cells were processed by plate-based droplet scRNA-seq. The transcriptomes of 101 regenerating RGCs passed quality control.

first: Bruce

middle: A

last: Rheaume

first: Jian

last: Xing


title: MODELLING GENETIC POLYCYSTIC KIDNEY DISEASE USING HUMAN PLURIPOTENT STEM CELL- DERIVED KIDNEY ORGANOIDS

status: Public on May 08 2023

city: Singapore

first: Meng

last: Liu

state: Singapore

address: 11 Mandalay road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

summary:
To investigate the transcriptional features during cystogenesis, we performed bulk-RNA sequencing on ARPKD organoids.
We then performed gene expression profiling and Gene Set Enrichment Analysis using data obtained from bulk RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ARPKD DMSO and ARPKD FSK groups.

first: Liu

last: Meng

first: Zhang

last: Chao

first: Gong

last: Ximing

first: Xia

last: Yun


title: 5P-Seq analysis of wt and new1-knockout yeast strain as well as New1:80S pull-down samples

status: Public on Apr 12 2023

city: Lund

first: Vasili

last: Hauryliuk

address: BMC, Sölvegatan 17

department: Experimental Medical Science

country: Sweden

institute: Lund University

summary: We present two sets of 5P-Seq experiments: i) comparison of wt and new1-KO S. cerevisiae ii) analysis of New1:80S pulldown samples. Collectively our results unravel codon-dependent nature of ribosomal stalling in S. cerevisiae lacking New1.

overall_design: Two 5P-Seq experiments: i)  wt and new1Δ; ii) New1:80S pulldown and lysate. The libraries were sequenced, resulting in 12 and 8 datasets for i and ii experiments, respectively.

first: Kathryn

last: Turnbull

first: Esther

last: von der Weth

first: Yujie

last: Zhang

first: Lilit

last: Nersisyan

first: Marcus

middle: J

last: Johansson

first: Tõnu

last: Margus

first: Vicent

last: Pelechano

first: Gemma

last: Atkinson

first: Artyom

last: Egorov


title: PARP1-mediated circRNA detection in RNA-seq data

status: Public on May 03 2023

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: PARP1 has been shown to play roles in alternative splicing yet the role of PARP1 in circRNA biogenesis is unknown. Here we determine PARP1’s role in backsplicing.

overall_design: Three conditions, wild type (WT), PARylation inhibition using PJ34 (PARPi), and PARP-1 knockdown (KD), were examined with three replicates per condition.

first: Rebekah

last: Eleazer

first: Kandauda

last: De Silva

first: Kalina

last: Andreeva

first: Yvonne

last: Fondufe-Mittendorf


title: Experimental gene expression of developmentally downregulated Crmp1, Crmp4, and Crmp5 promotes axon regeneration and retinal ganglion cell survival after optic nerve injury.

status: Public on Apr 10 2023

first: Ephraim

last: Trakhtenberg


title: Experimental gene expression of developmentally downregulated Crmp1, Crmp4, and Crmp5 promotes axon regeneration and retinal ganglion cell survival after optic nerve injury [bulk RNA-seq]

summary: Collapsin response mediator proteins (Crmps) play roles in neuronal development and axon growth. However, neuronal-specific roles of Crmp1, Crmp4, and Crmp5 in regeneration of injured central nervous system (CNS) axons in vivo are unclear. Here, we analyzed developmental and subtype-specific expression of Crmp genes in retinal ganglion cells (RGCs), tested whether overexpressing Crmp1, Crmp4, or Crmp5 in RGCs through localized intralocular AAV2 delivery promotes axon regeneration after optic nerve injury in vivo, and characterized developmental co-regulation of gene-concept networks associated with Crmps. We found that all Crmp genes are developmentally downregulated in RGCs during maturation. However, while Crmp1, Crmp2, and Crmp4 were expressed to a varying degree in most RGC subtypes, Crmp3 and Crmp5 were expressed only in a small subset of RGC subtypes. We then found that after optic nerve injury, Crmp1, Crmp4, and Crmp5 promote RGC axon regeneration to varying extents, with Crmp4 promoting the most axon regeneration and also localizing to axons. We also found that Crmp1 and Crmp4, but not Crmp5, promote RGC survival. Finally, we found that Crmp1, Crmp2, Crmp4, and Crmp5's ability to promote axon regeneration is associated with neurodevelopmental mechanisms, which control RGC’s intrinsic axon growth capacity.

overall_design: Bulk-mRNA-seq samples from different age RGCs were purified by immunopanning for Thy1 (after immunopanning depletion of macrophages and amacrine cells), cDNA libraries prepared using polyA-selected RNA (TruSeq RNA Library Prep Kit, Illumina), paired reads sequenced 100 bp from each end on HiSeq 2000 Sequencer (Illumina), passed QC filters, mapped to the mm10 genome and transcriptome by Hisat2, and analyzed by Cufflinks/CuffDiff, as we previously described.

first: William

last: Theune

first: Jian

last: Xing


title: Effect of modified H2A.Z protein to gene expression in DT40 cells.

status: Public on Feb 23 2023

city: Debrecen

first: Gabor

last: Szabo

address: Egyetem ter 1

department: Biophysics and Cell Biology

country: Hungary

institute: University of Debrecen

summary: H2A.Z-nucleosomes participate in both euchromatin and heterochromatin and it has proven difficult to reveal how the disparate roles and stability features imparted by H2A.Z are connected. Using an in situ assay of nucleosome stability in nuclei of DT40 cells expressing engineered forms of the variant we show that H2A.Z is released from nucleosomes of peripheral heterochromatin at unusually high salt concentrations, compared to cells expressing C-terminally truncated H2A.Z. Binding of the tail-peptide (C9) to reconstituted nucleosomes, DNA and the nuclear lamina were detected. Upon treatment of HeLa nuclei with C9, the H2A.Z-nucleosomes assumed canonical stability, the peripheral heterochromatin became dispersed and overall nuclease sensitivity increased, recapitulating tail-dependent differences in DT40. When introduced into live cells, C9 elicited chromatin reorganization and transcriptional down-regulation of ~600 genes. Thus, large-scale epigenetic modulation can be achieved by targeting or making advantage of molecular interactions involving the C-terminal tail of H2A.Z.

overall_design: Gene expression profile in DT40 cell line was measured in Wild Type, double knock-out (DKO) +DKO H2A.Z1 or DKO +H2A.Z1ΔC mutant H2A.Z protein containing cell lines. One experiment was performed per sample.

first: Harata

last: Masahiko


title: AGXT overexpression during nonalcoholic steatohepatitis in mice

status: Public on Feb 19 2023

city: Shreveport

first: Oren

last: Rom

state: LA

address: Biomedical Research Institute Rm F4-27 1501 Kings Hwy

institute: LSU Health Shreveport

summary: To investigate the effects of AAV8-mediated overexpression of AGXT in mice with diet-induced nonalcoholic steatohepatitis compared to AAV8-GFP

overall_design: Comparative gene expression profiling analysis of RNA-seq data from mice with diet-induced nonalcoholic steatohepatitis (24 weeks) injected with AAV8-TBG-GFP or AAV8-TBG-AGXT

first: Zhipeng

last: Liu

first: Alexandra

last: Finney


title: The E. coli pathobiont LF82 encodes a unique variant of sigma 70 that results in global gene expression changes and altered phenotypes

status: Public on Jan 10 2023

city: Bethesda

first: Melissa

last: Arroyo-Mendoza

state: MD

address: 8 CENTER DR RM 2A11

department: LBG

institute: NIDDK

summary:
Purpose: To investigave how a unique rpoD variant of LF82 contributes to its biology by seeing how it affects phenotype and global gene expression
Method: Isogenic E. coli MG1655 and D445V mutant were grown to a cell density of OD600 ~0.5-0.6 in LB broth at either 37oC or 23oC. RNA was isolated at 5  post-infection using method II of (Hinton 1989).  rRNA subtraction was performed with the bacterial RiboMinus Kit (Ambion) according to manufacturer instructions.  cDNA was prepared using the NEBNext strand specific kit (New England BioLabs) according to manufacturer instruction for libraries with 300-450 bp insert size with the following modifications.  Illumina adaptors sequences based on TruSeq HT Sample Prep Kits were purchase from Integrated DNA Technologies and used in the ligation step.  TruSeq-1 and TruSeq-2 primer were used for PCR enrichment of adaptor ligated DNA.  Library size was verified with a Bioanalyzer using an Agilent High Sensitivity DNA kit.  The concentration of each library was determined using the KAPA Library Quantification Kit for Illumina platforms.  Sequencing was performed by the NIDDK Genomics Core facility using a MiSeq system with the MiSeq 2 x 250 bp Sequencing Kit (Illumina).
Result: RNA-seq data revealed that the single D445V subsitition changes the expression of multiple genes in E. coli. We see a total of 137 genes up-regulated at 23oC  and 75 gene up-regulated at 37oC in the mutant compared the WT. We saw an increase in genes that lead to beta-lactam resistance, biofilm formation, methionine biosynsesis. We saw a total of 236 genes that were down regulated at 23oC and 57 genes down-regulated at 37oC in the mutant compared to the WT, including a decrease in flagella gene expression.
Conclusion: The rpoD D445V mutation affects the expression level of multiple specific genes, consistent with the LF82 lifestyle.

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

last: Proctor

first: Abraham

last: Correa-Medina

first: Meghan

middle: W

last: Brand

first: Leslie

last: Knipling

first: Virginia

middle: R

last: Acosta

first: Michael

last: Wannemuelher

first: Gregory

last: Phillips

first: Deborah

last: Hinton


title: Experimental gene expression of developmentally downregulated Crmp1, Crmp4, and Crmp5 promotes axon regeneration and retinal ganglion cell survival after optic nerve injury [third-party re-analysis]

last: Trakhtenberg

relation:
SubSeries of: GSE228487
Reanalysis of: GSM3907320
Reanalysis of: GSM3907321
Reanalysis of: GSM3907322
Reanalysis of: GSM3907323
Reanalysis of: GSM3907324
Reanalysis of: GSM3907325
Reanalysis of: GSM3907326
Reanalysis of: GSM3907327
Reanalysis of: GSM3907328
Reanalysis of: GSM3907329
Reanalysis of: GSM4078555
Reanalysis of: GSM4078556
Reanalysis of: GSM4078557
Reanalysis of: GSM4078558
Reanalysis of: GSM3177677
Reanalysis of: GSM3177678
Reanalysis of: GSM3466902
Reanalysis of: GSM3466903

overall_design:
Normalized matrices and cell metadata (e.g., type assignment) for embryonic, adult uninjured, and adult injured RGCs, are available from the GEO accession numbers GSE122466 and GSE137400. Postnatal RGC scRNA-seq dataset we previously generated is available under the Gene Expression Omnibus (GEO) accession number GSE115404.
data processing step:
Cell-counts matrices were obtained from the GEO submissions from the previously published data. Matrices were loaded as seurat objects in R.
Seurat objects were merged and expression was normalized. A cell counts matrix for the merged dataset was then generating by extracting counts matrix from seurat object.
The condition each cell belongs to was appended to the cell ID in the columns of the matrix
genome build/assembly: mm10
processed data files format and content: One CSV files: Containg RGC embyonic, postnatal, adult and injured cells' normalized expression values for each gene.


title: Effects of Chemotherapy on Human Pancreatic Adenocarcinoma and its Tumor Microenvironment

status: Public on Jan 09 2023

city: San Diego

first: Diane

last: Simeone

address: 3855 Health Sciences Drive

institute: UCSD Health

summary: Single-cell RNA-seq analysis of primary and metastatic (liver) human PDAC tumors, some pre-treatment and some post-chemotherapy. (Please note that although the file has "RAW" in the name these are the filtered results from CellRanger.)

first: Gregor

last: Werba

first: Daniel

last: Weissinger

first: Emily

last: Kawaler

first: Aristotelis

last: Tsirigos


title: The rice pseudo phosphotransfer proteins are negative regulators of endogenous cytokinin signaling and affect multiple aspects of growth and development.

status: Public on Dec 31 2022

city: Chapel Hill

first: Charles

last: Hodgens

state: North Carolina (NC)

address: 250 Bell Tower Drive

department: GMB

institute: UNC Chapel Hill

summary: The phytohormone cytokinin plays a significant role in nearly all aspects of plant growth and development. Cytokinin signaling has primarily been studied in the dicot model Arabidopsis, with relatively little work done in monocots, which include rice (Oryza sativa) and other cereals of agronomic importance. The cytokinin signaling pathway is a phosphorelay comprised of the histidine kinase receptors (HKs), the authentic histidine phosphotransfer proteins (AHPs), and the type-B Response Regulators (ARRs). Two negative regulators of cytokinin signaling have been identified: the type-A ARRs, which are cytokinin primary response genes, and the pseudo histidine phosphotransfer proteins (PHPs), which lack the His residue required for phosphorelay. Here, we describe the role of the PHP genes from rice. Phylogenic analysis indicates that the PHPs are generally first found in the genomes of gymnosperms and that they arose independently in monocots and dicots. Consistent with this, the three rice PHPs fail to complement an Arabidopsis php mutant (ahp6). Disruption of the three PHPs results in a molecular phenotype consistent with these elements acting as negative regulators of basal cytokinin signaling, including the constitutive up-regulation of a number of type-A RR and cytokinin oxidase genes. The triple php mutant affects multiple aspects of rice growth and development, including shoot morphology, panicle architecture and seed fill. However, in contrast to Arabidopsis, disruption of the rice PHPs does not affect root vascular patterning, suggesting that while many aspects of key signaling networks are conserved between monocots and dicots, the molecular components regulating some processes are distinct.

overall_design: This project relates to SRA submission PRJNA589193 which contains the raw data files. SRA did not give me an SRP number. Kitaake control plants and php1,2,3 loss of function mutants treated with control media, 100 nM benzyl adenine (BA), or 5 uM BA. 8 developmentally matched seedlings collected for each replicate. Root and shoot tissue collected separately. 3 biological replicates collected. One library prepared from each replicate.

first: Joseph

last: Kieber

first: Christian

last: Burr

first: Samantha

last: Boeshore


title: Reduced representation bisulfite sequencing of equine tissue

city: Balice

first: Ewelina

last: Semik-Gurgul

department: Department of Animal Molecular Biology

type: Methylation profiling by high throughput sequencing

summary: The aim of the project was to identify the tissue-specific DNA methylation patterns of selected horse tissues, derived from two germ layers, endodermal (liver and lung) and mesenchymal (cardiac striated muscle) origin. The comparative analysis of DNA methylation patterns of the genome fraction rich in CpG dinucleotides was investigated using Reduced Representation Bisulfite Sequencing (RRBS) technique.

overall_design: One-condition experiment, heart vs. lung, heart vs. liver, liver vs. lung. Biological replicates: 4 heart  replicates, 4 lung replicates, 4 liver replicates.

last: Semik-Guegul

first: Tomasz

last: Szmatoła

first: Artur

last: Gurgul

last: Ząbek


title: β-catenin-controlled tubular cell-derived exosomes play a key role in fibroblast activation via the OPN-CD44 axis

status: Public on Dec 20 2022

city: Guangzhou

first: Shuangqin

last: Chen

state: Guangdong

address: 1838 North Guangzhou Avenue

department: Division of Nephrology

institute: Chen

summary: Tubular injury and peripheral fibroblast activation are the hallmarks of chronic kidney disease (CKD) and renal fibrosis, suggesting intimate communication between the two diseases. However, the underlying mechanisms remain to be determined. Exosomes play a role in shuttling proteins and other materials to recipient cells. In our study, we found that tubular cell-derived exosomes were aroused by β-catenin in kidney fibrogenesis. Osteopontin (OPN), especially its N-terminal fragments (N-OPN), was encapsulated in β-catenin-controlled tubular cell-derived exosome cargo, and subsequently passed to fibroblasts. Through binding with CD44, exosomal OPN promoted fibroblast proliferation and activation. Gene deletion of β-catenin in tubular cells (Ksp-β-catenin−/−) or gene ablation of CD44 (CD44−/−) greatly ameliorated renal fibrosis. Notably, N-OPN was secreted by exosome into the urine of patients with CKD, and negatively correlated with kidney function. The urinary exosomes from patients with CKD greatly accelerated renal fibrosis, which was blocked by CD44 deletion. These results suggest that exosome-mediated activation of the OPN/CD44 axis plays a key role in renal fibrosis, which is controlled by β-catenin.

overall_design: Three β-catenin knockout mice and wild-type mice underwent UUO surgery, and three CD44 knockout mice and wild-type mice underwent UIRI surgery


title: COVID-19 Vaccine Immune Responses Study (COVIRS)

status: Public on Jan 12 2023

city: Adelaide

first: Feargal

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

summary: Blood collected from adults pre vaccination and post vaccination to study the immune effects of COVID-19 vaccination and how they relate to antibody and T-cell responses.

overall_design: Total RNA sequenced from healthy adults pre vaccination (V0), 7 days after dose 1 (V1) and 2 days after dose 3 (V3A) for COVID-19 vaccines

first: David

last: Lynn


title: A novel HLA-G/SPAG9/STAT3 axis promotes brain metastases

status: Public on Jan 01 2023

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

summary: Transcriptomic analyses of early-stage brain metastatic cells reveals essential genes that promotes brain metastases, which are targetable.

overall_design: We utilized early passage brain metastasis cell lines derived from primary patient samples of lung-to-brain, breast-brain and melanoma-brain metastases in our work, as these samples are enriched for brain metastasis initiating cells (BMICs) that have already successfully completed the metastatic process. Previous work in our lab successfully established preclinical models of lung-to-brain BM(Nolte, et al., 2013; Singh, et al., 2017). We followed up on this work here by establishing preclinical models of breast-brain and melanoma-brain metastases. Briefly, we injected mice through fatpad and subcutaneous routes, which forms tumors that progresses through the breast-brain and melanoma-brain metastatic stages. Brains from these mice were harvested at orthotopic tumor endpoints that allowed for the identification and capture of pre-metastatic breast (BMFP)and melanoma (BMSC) BMICs respectively. RNA was extracted from these cells and submitted for RNA seq analysis. This work describes the role of a top hit (HLA-G) in brain metastases. HLA-G was identified through transcriptomic analyses of premetastatic lung, breast and melanoma BMICs.

first: BI

last: Bassey-Archibong

first: C

last: Chokshi

first: N

last: Aghaei

first: A

last: Kieliszek

last: Tatari

first: D

last: McKenna

first: M

middle: S

middle: K

last: Subapanditha

last: Parmar

last: Mobilio

last: Savage

first: F

last: Lam

first: T

last: Tokar

first: J

last: Provias

first: Y

last: Lu

first: S

last: Chafe

first: Ch

last: Swanton

first: R

middle: E

last: Hynds

last: Venugopal


title: Single-Cell Transcriptomics Identifies Brain Endothelium Inflammatory Networks in Experimental Autoimmune Encephalomyelitis

status: Public on Dec 01 2022

city: Montreal

first: Olivier

last: Tastet

address: 900 Saint-Denis

institute: crCHUM

summary: Multiple sclerosis (MS) is a neuroinflammatory and neurodegenerative disease characterized by infiltration of immune cells in multifocal areas of the central nervous system (CNS). The specific molecular processes allowing autoreactive immune cells to enter the CNS compartment through the blood-brain barrier (BBB) remain elusive. Using endothelial cells (ECs) enrichment and single-cell RNA sequencing (scRNA-Seq), we characterized the cells implicated in the neuroinflammatory processes in experimental auto-immune encephalomyelitis, an animal model of MS. We found an upregulation of genes associated with antigen presentation and interferon in most populations of CNS-resident cells, including ECs. Interestingly, a gradient of gene expression rather than distinct transcriptional profiles separated the arteriovenous zonation of the brain vasculature. However, differential gene expression analysis showed more transcriptomic alterations in venous ECs, suggesting their prominent role in neuroinflammation. Furthermore, analysis of ligand-receptor interactions identified important crosstalk between venous ECs and infiltrating immune subsets. To confirm the relevance of our observation in the context of human disease, we validated the protein expression of the most differentially expressed genes in MS lesions. Here, we demonstrate a landscape of the cellular heterogeneity involved in neuroinflammation and provide important molecular insights in unraveling specific cell processes that lead to the infiltration of the brain by immune cells in EAE.

overall_design: We extracted brains from myelin oligodendrocyte glycoprotein (MOG)-induced Experimental autoimmune encephalomyelitis (EAE) at peak of the disease and control (CTRL) mice to isolate single cells using an optimized protocol adapted from the Miltenyi Brain Dissociation Kit. Cells from each brain were subjected to scRNA-seq using a microdroplet-based method from 10X genomics.

first: Antoine

middle: P

last: Fournier

first: Marc

last: Charabati

first: Chloé

last: Hoornaert

first: Lyne

last: Bourbonière

first: Wendy

last: Klement

first: Sandra

last: Larouche

first: Fiona

last: Tea

first: Chang

last: Wang Yu

first: Catherine

last: Larochelle

first: Nathalie

last: Arbour

first: Ioannis

last: Ragoussis

first: Stephanie

last: Zandee

first: Alexandre

last: Prat


title: Hepatic PPARα dysfunction in porcine sepsis

status: Public on Nov 28 2022

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: Despite decades of research, sepsis remains one of the most urgent unmet medical needs. Clinical trials in sepsis have mainly focused on targeting the inflammatory pathway, however, recent data indicate that sepsis should also be seen as a metabolic disease. Targeting metabolic dysregulations that take place in sepsis might uncover novel therapeutic opportunities to treat human sepsis patients. The role of PPARα in liver dysfunction during sepsis has recently been described, and restoring PPARα signaling proves to be successful in murine sepsis. To find out whether this therapy might also be helpful in human sepsis patients, we analyzed metabolic perturbations in liver of a porcine fecal peritonitis model. Resuscitation with fluids, antimicrobial therapy and abdominal drainage were applied to the pigs in order to mimic human clinical care. By using RNA-seq, we detected problems with PPARα signaling in the livers of septic pigs and reduced PPARα levels correlated well with disease severity. As PPARα regulates the expression of many genes involved in FA oxidation, reduced expression of these target genes concomitant with increased FFAs in plasma and ectopic lipid deposition in the liver was observed. The results obtained in pigs are in agreement with earlier observations in mice and support the potential of targeting defective PPARα signaling in the clinic.

overall_design: Comparative gene expression profiling between livers from sham (3 biological replicates) and sepsis (9 biological replicates) pigs. Samples were taken between 14 and 18 hours after initiating the model for RNA-seq

first: Jolien

last: Vandewalle

first: Bruno

last: Garcia

first: Tineke

last: Vanderhaeghen

first: Lise

last: Van Wyngene

first: Melanie

last: Eggermont

first: Hester

last: Dufoor

first: Céline

last: Van Dender

first: Siska

last: Croubels

last: Herpain

first: Claude

last: Libert


title: Harnessing the Pre-metastatic Niche Macrophages through the Induction of Trained Immunity to control Metastasis.

status: Public on Nov 01 2022

first: Eric

last: Rouchka

summary: We demonstrate that a natural compund B-Glucan (WGP) can induce training of macrophages by upregulating the Sphingolipid biosynthesis pathway and more specifically, the accumulation of S1P, resulting in mitochondrial fission in macrophages. These trained macrophages upon re-stimulation with tumor cells or tumor-derived factors showed increased responsiveness by increased pro-inflammatory cytokine production, increased phagocytosis and cytotoxicity. In vivo training of mice with WGP resulted in the training of Lung Interstitial macrophages and controlled the metastasis to the lungs.

overall_design: We employed different in vivo models of Lung metastasis to demonstrate that training of the pre-metastatic lung interstitial macrophages with a natural compound, B-Glucan, induces the control of cancer metastasis to the lungs.

first: Jun

last: Yan

first: Rejeena

last: Shrestha

first: Chuanlin

last: Ding

first: Julia

last: Chariker


title: Improved outcome of contusive spinal cord injury in Bmal1-/- mice is associated with protection of the blood spinal cord barrier

status: Public on Jun 01 2023

summary: The purpose of the study is to understand the role of Bmal1 in spinal cord contusion.

overall_design: Bmal1 is also referred to as Arntl, and this RNA-seq analysis was undertaken to investigate the difference in the transcriptome between Arntl knockout and wild type mice 3 days after spinal cord contusion at the T9 level. Total RNA was purified from the epicenter of the injury of the spinal cord. Differential expression analysis was performed to compare the transcriptome of Arntl knockout mice vs. wild type mice.

first: Lukasz

last: Slomnicki

first: Scott

last: Myers

first: Sujata

last: Saraswat-Ohri

first: Molly

last: Parsh

first: Kariena

last: Andres

last: Whittemore

first: Michal

last: Hetman


title: IL-33 induces an antiviral signature in mast cells but enhances their permissiveness for human rhinovirus infection

city: Southampton

first: Anna

last: Willis

address: Southampton General Hospital, Tremona Road

country: United Kingdom

institute: University of Southampton

summary: Mast cells (MCs) are classically associated with allergic asthma but their role in antiviral immunity is unclear. Human rhinoviruses (HRVs) are a major cause of asthma exacerbations and can infect and replicate within MCs. The primary site of HRV infection is the airway epithelium and MCs localise to this site with increasing asthma severity. The asthma susceptibility gene, IL-33, encodes an epithelial-derived cytokine released following HRV infection but its impact on MC antiviral responses has yet to be determined. In this study we investigated the global response of LAD2 MCs to IL-33 stimulation using RNA sequencing and identified genes involved in antiviral immunity. In spite of this, IL-33 treatment increased permissiveness of MCs to HRV16 infection which, from the RNA-Seq data, we attributed to upregulation of ICAM1. Flow cytometric analysis confirmed an IL-33-dependent increase in ICAM1 surface expression as well as LDLR, the receptors used by major and minor group HRVs for cellular entry. Neutralisation of ICAM1 reduced the IL-33-dependent enhancement in HRV16 replication and release in both LAD2 MCs and cord blood derived MCs. These findings demonstrate that although IL-33 induces an antiviral signature in MCs, it also upregulates the receptors for HRV entry to enhance infection. This highlights the potential for a gene-environment interaction involving IL33 and HRV in MCs to contribute to virus-induced asthma exacerbations.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LAD2 mast cells treated with IL-33 (10ng/mL) compared to a control

first: Charlene

last: Akoto

first: Chiara

last: Banas

first: Joseph

last: Bell

first: Dean

last: Bryant

first: Cornelia

last: Blume

first: Donna

last: Davies

first: Emily

last: Swindle


title: Influence of diabetic retinopathy on peripheral blood gene expression

status: Public on May 26 2023

city: Shanghai

first: zhaoyu

last: xiang

state: Shanghai

address: No.85 Wujin Road

institute: Shanghai general hospital

summary: To understand the association between systemic factors and the diabetic retinopathy, blood samples were collected in 50 healthy controls, 74 diabetic patients without diabetic retinopathy (DM group), and 69 diabetic retinopathy (DR Group). T1DM and T2DM in this study was based on the diagnostic criteria for diabetes proposed by the WHO in 1999. The diagnosis of DR was based on the international clinical classification of DR proposed at the 2002 International Ophthalmology Conference. We then performed gene expression profiling analysis using data obtained from RNA-seq of three patient groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data between DR Group and healthy controls and between DR Group and DM group.

first: Haidong

last: Zou

first: Yi

last: Xu

first: Lina

last: Lu

first: Senlin

last: Lin

first: Zhaoyu

last: Xiang

first: Shuli

last: Chen

first: Xinran

last: Qin


title: The cellular basis for epithelial-mesenchymal interaction during mouse tooth development

city: Chengdu

first: Zhonghan

last: Li

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Science

institute: Sichuan University

summary: In this study, using mouse molar as the model, we developed a dual fluorescence reporter mouse to precisely track and analyze dental epithelium and mesenchyme at single-cell resolution from early embryonic to postnatal stages. Moreover, we constructed the virtual molar explorer (VMEx) to spatially map 15,967 molar-expressed genes and identified that Msx1+ Sdc1+ marked the developing dental papilla while surrounded by Msx1+ Sdc1- molar niche. Through tooth germ reconstitution and organoid culture in vitro and kidney capsule transplantation in vivo, we provided evidence that the Msx1+ Sdc1- dental follicle cells might function as the tooth organizers that promoted epithelium survival and tooth germ organization. Furthermore, the appearance of Msx1+ Sdc1+ dental papilla cells relied on the interaction between dental epithelium and Msx1+ Sdc1- dental follicle cells. Together, our results revealed the cellular dynamics of tooth development in mice and identified that the dental follicle might be the key driver of epithelial-mesenchymal interaction and tooth morphogenesis.

overall_design: Tooth germs were dissected and collected at different development stages, including bud stage (E12.5), cap stage (E14.5), bell stage (E16.5), postnatal day 1 (PN1) and day 7 (PN7). Epithelial and mesenchymal cells were enriched by FACS sorting using copGFP and tdTomato fluorescence. Cells were then used for single-cell RNA sequencing using 10X Genomics platform.

first: Yufeng

last: Duan

first: Huancheng

last: Fu

first: Hong

last: Hu

first: Yuansong

last: Liao

first: Fanchen

last: Kang

first: Ziwei

last: Zhang

first: Baiquan

first: Fangjun

last: Huo

first: Yike

last: Yin

first: Guoqing

first: Hongbo

first: Weidong

last: Tian


title: Transcriptome analysis of AAV-induced retinopathy models expressing human VEGF, TNF-α and IL-6 in murine eyes

status: Public on Nov 11 2022

city: Biberach an der Riß

first: Kolja

last: Becker

address: Birkendorfer Str. 65

department: Global Computational Biology and Digital Sciences

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

summary: High-throughput sequencing of murine retina and RPE/Choroid (eye cup) tissue following mueller-cell mediated expression of either hVEGFA, hTNFa, or hIl6 by adeno-associated viruses (AAV)

overall_design: We intravitreally injected mouse eyes with AAVs expressing one of the three human transgenes VEGF, TNFa, or IL6. As controls, we used AAV-stuffer injected eyes at matching concentrations and non-injected eyes. From all treatment groups total RNA was extracted from the retina and the posterior eye cup, including retinal pigment epithelium (RPE), choroid, sclera and the ciliary body. Sample collection was followed by RNA sequencing.

first: Carina

last: Weigelt


title: Acquisition of alveolar fate and differentiation competence by human fetal lung epithelial progenitor cells

status: Public on Sep 30 2022

city: Cambridge

first: Kyungtae

last: Lim

address: Tennis Court Road

department: The Wellcome Trust/Cancer Research UK Gurdon Institute

institute: University of Cambridge

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

overall_design: Refer to individual Series


title: Post-injury born oligodendrocytes incorporate into the glial scar and contribute to the inhibition of axon regeneration

status: Public on Mar 27 2023

city: Farmington

first: Ephraim

last: Trakhtenberg

address: 263 Farmington Ave. RM L4005

institute: University of Connecticut School of Medicine

summary: Pathologies of the central nervous system (CNS) white matter often result in permanent functional deficits because mature mammalian projection neurons fail to regenerate long-distance axons after injury. A major barrier to axonal regenerative research is that the CNS axons that regenerate in response to experimental treatments stall growth before reaching their post-synaptic targets. Here, we test the hypothesis that interaction of regenerating axons with live oligodendrocytes, which were absent during developmental axon growth, stalls axonal growth. To test this hypothesis, first, we used single cell RNA-seq (scRNA-seq) and immunohistological analysis to investigate whether post-injury born oligodendrocytes incorporate into the glial scar after optic nerve injury. Then, we administered demyelination-inducing cuprizone (used in studies of multiple sclerosis), concurrently with the stimulation of axon regeneration by Pten knockdown (KD) in projection neurons after optic nerve injury. We found that post-injury born oligodendrocyte lineage cells incorporate into the glial scar, where they are susceptible to the demyelination diet treatment, which reduced their presence in the glial scar. We further found that the demyelination diet enhanced Pten KD-stimulated axon regeneration, and localized injection of cuprizone promoted axon regeneration. We also present a website for comparing the gene expression of scRNA-seq-profiled optic nerve oligodendrocyte lineage cells under physiological and pathophysiological conditions. Annotation of oligodendrocyte lineage cell subtypes, and normal or injured condition, are indicated in the last two rows of the cell matrix CSV file.

overall_design: Cells were purified from uninjured (n = 5) and injured (n = 5) optic nerves of both sexes 10-week old mice. ONC injury was performed at 8 weeks. 6,000 cells from each sample were loaded in parallel for capture onto the Chromium System using the v2 single cell reagent kit (10X Genomics). Following capture and lysis, cDNA was synthesized and amplified (12 cycles) as per manufacturer's protocol (10X Genomics).

first: Jian

last: Xing

first: Bruce

last: Rheaume


title: Directed protein evolution of an RNA editor for single molecule RNA-binding protein co-occupancy (I)

status: Public on Oct 28 2022

city: San Francisco

first: Yizhu

last: Lin

address: 513 Parnassus

department: Cell and Tissue Biology

institute: University of California, San Francisco

summary: RNA base editors have become powerful tools for both therapeutic and research purposes. However, currently available RNA editors such as ADAR or APOBEC family proteins have limitations due to RNA structure and sequence dependence. Here, we designed a protein engineering platform for putative RNA editor screening and directed enzyme evolution. We engineered an RNA A-to-I base editor (rABE) that has high activity, low local sequence or structure bias, and low background. Utilizing rABE, we present REMORA (RNA Encoded Molecular Recording in Adenosines), a new strategy to measure RNA-binding events on single RNA molecules in cells. In REMORA, adenosine deamination serves as a molecular record of RNA-protein interactions that are identified by mutations by sequencing. By combining our improved A-to-I RNA deaminase with the C-to-U deaminase APOBEC1 and long-read RNA sequencing, our approach enables simultaneous recording of the locations two RNA binding proteins on single mRNA molecules. Orthogonal RNA molecular recording of two Pumilio family proteins, PUM1 and PUM2, reveals that PUM1 competes with PUM2 for some but not all Pumilio binding sites in cells, despite having the same in vitro binding preferences. Our work thus measures competition between RNA-binding proteins for RNA sites in cells, and our genetically encodable RNA deaminase enables single-molecule identification of RNA-protein interactions with cell type specificity.

overall_design: Stable HEK293T cell lines expressing RBP-rABE, RBP-APOBEC1 or the deaminase only controls were generated with lentivral infection. Expression was driven by doxycycline promoters and cells were treated for 0, 50 or 1000 ng/ml doxycycline for 48 hours.

first: Samentha

last: Kwok

first: Stephen

middle: N

last: Floor


title: Characterization and reduction of non-endocrine cells accompanying islet-like endocrine cells differentiated from human iPSC

status: Public on Sep 16 2022

city: Fujisawa

first: Hideyuki

last: Hiyoshi

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-Chome

institute: Takeda Pharmaceutical Company Limited

summary: The differentiation of pancreatic endocrine cells from human pluripotent stem cells has been thoroughly investigated for their application in cell therapy against diabetes. Although non-endocrine cells are inevitable contaminating by-products of the differentiation process, a comprehensive profile of such cells is lacking. Therefore, we characterized non-endocrine cells in iPSC-derived pancreatic islet cells (iPIC) using single-cell transcriptomic analysis. We found that non-endocrine cells consist of 1) heterogeneous proliferating cells, and 2) cells with not only pancreatic traits but also liver or intestinal traits marked by FGB or AGR2. Non-endocrine cells specifically expressed FGFR2, PLK1, and LDHB. We demonstrated that inhibition of pathways involving these genes selectively reduced the number of non-endocrine cells in the differentiation process. These findings provide useful insights into cell purification approaches and contribute to the improvement of the mass production of endocrine cells for stem cell-derived cell therapy for diabetes.

overall_design:
Single-cell mRNA sequencing of cadaveric human islet, and pluripotent stem cells differentiating in vitro towards pancreatic islet like cells.

***Raw data was returned to private due to patient privacy concerns***

first: Kensuke

last: Sakuma

first: Noriko

last: Tsubooka-Yamazoe

first: Shinya

last: Asano

first: Taisuke

last: Mochida

first: Junji

last: Yamaura

first: Shuhei

last: Konagaya

first: Ryo

last: Fujii

first: Hirokazu

last: Matsumoto

last: Ito

first: Taro

last: Toyoda


title: Single-cell RNA-seq reveals immune landscape of pancreatic cancer

status: Public on Sep 13 2022

city: Beijing

first: Kai

last: Chen

address: 8th Xishiku Street

department: General Surgery

institute: Peking University First Hospital

summary: Pancreatic ductal adenocarcinoma (PDAC) has complex tumor immune microenvironment (TIME), the clinical values of which remains to be explored. This study aimed to delineate the immune landscape of PDAC and determine the clinical value of immune features in TIME. There was a significant difference in immune profiles between PDAC and adjacent normal pancreatic tissues. Several novel immune features were captured by quantitative pathology analysis on mIHC, some of which were significantly correlated to the prognosis of PDAC patients. A risk score-based prognostic model was developed according to these immune features. We also drew a user-friendly nomogram plot to predict the overall survival of patients by combining risk score and clinicopathologic features. Both mIHC and scRNA-seq analyses showed the expression of PD-L1 was scarce in PDAC. We found that PD1+ cells were distributed in different T cell subpopulations, not enriched in a specific subpopulation. In addition, there were other conserved receptor-ligand pairs (CCL5-SDC1/4) besides PD1-PD-L1 interaction between PD1+ T cells and PD-L1+ tumor cells. Our findings reveal the immune landscape of PDAC and highlight the significant value of combined application of mIHC and scRNA-seq in uncovering TIME, which might provide new clues for developing immunotherapy strategies.

overall_design: All H&E stained slides from eighty patients were reviewed for confirming PDAC diagnosis by a pathologist. The corresponding tumor and adjacent noncancerous areas were carefully marked. Duplicated 1.5 mm diameter tissue cores were selectively punched and transferred to recipient tissue array blocks. The tissue microarray (TMA) was set up. For scRNA-seq analysis, a total of six PDAC and six adjacent noncancerous resection specimens were obtained from the Department of General Surgery at Peking University First Hospital. All patients with PDAC did not receive any treatments before collecting specimens.


title: Reference Short-Read Transcriptomes of Human Peripheral Blood Lymphocytes (Illumina RNA-Seq, Matched to PacBio Iso-Seq Data)

city: Louisville

first: Eric

last: Rouchka

address: 522 East Gray Street

institute: University of Louisville

summary: Long-read sequencing technologies such as Iso-Seq (PacBio Inc.) generate highly accurate sequences of full-length mRNA transcript isoforms. Long-read transcriptomics may be especially useful in the context of lymphocyte functional plasticity as it relates to human health and disease. However, no long-read isoform-aware reference transcriptomes of human circulating lymphocytes seem to be publicly available despite being valuable as benchmarks in a variety of transcriptomic studies. To begin to fill this gap, we purified four lymphocyte subsets (CD4 T, CD8 T, NK, and Pan B cells) from the peripheral blood of a healthy male donor and obtained high-quality RNA (RIN>8) for PacBio Iso-Seq analysis and parallel RNA-Seq analysis.

overall_design: Four lymphocyte subsets (CD4 T, CD8 T, NK, and Pan B Cells) were purified from peripheral blood mononuclear cells of a healthy male donor. RNA was extracted from each purified subset and used for Pacific Biosciences Iso-Seq long-read sequencing in parallel with Illumina RNA-Seq short-read sequencing. The resulting datasets are offered here as reference transcriptomes for studies of circulating human lymphocytes.

first: Cassandra

last: Woolley

first: Julia

middle: L

last: Chariker

first: Easton

last: Ford

first: Elizabeth

last: Hudson

first: Vennila

last: Arumugam

first: Sabine

last: Waigel

first: Melissa

last: Smith

first: Thomas

last: Mitchell


title: Targeted NKX2.1 DamID sequencing data from human fetal lung organoids recapitulating differential developmental features of human lung development

first: Kyungtae

last: Lim

summary: Human fetal  lung tip cells were purifed from developing human lungs at pseudoglandular and canalicular stages and in vitro cultured; pseudoglandular organoids and LinPOS organoids, respectively. Alveolar organoids were differentiated from LinPOS organoids in the alveolar differentiation condition. Differential NKX2.1 binding patterns in each organoid were profiled  by targeted DamID-seq.

overall_design: 1) CD44+ tip population from pseudoglandular organoids, 2) CD36+CD44+ population from LinPOS organoids, 3) Alveolar organoids (three biological replicates for each cell type)

first: Alex

last: Donovan

first: Andrea

middle: H

last: Brand

first: Emma

last: Rawlins


title: Multifactorial chromatin regulatory landscapes at single cell resolution

status: Public on Sep 14 2022

city: Chapel Hill

first: Michael

last: Meers

state: NC

address: 250 Bell Tower Dr.

summary: Chromatin profiling at locus resolution uncovers gene regulatory features that define cell types and developmental trajectories, but it remains challenging to map and compare distinct chromatin-associated proteins within the same sample. Here we describe a scalable antibody barcoding approach for profiling multiple chromatin features simultaneously in the same individual cells, Multiple Target Identification by Tagmentation (MulTI-Tag). MulTI-Tag is optimized to retain high sensitivity and specificity of enrichment for multiple chromatin targets in the same assay. We use MulTI-Tag to resolve distinct cell types using multiple chromatin features on a commercial single-cell platform, and to distinguish unique, coordinated patterns of active and repressive element regulatory usage in the same individual cells. Multifactorial profiling has allowed us to detect novel associations between histone marks in single cells and holds promise for comprehensively characterizing cell-specific gene regulatory landscapes in development and disease.

overall_design: We used Multiple Target Identification by Tagmentation (MulTI-Tag) to produce libraries for paired-end DNA sequencing.

first: Derek

last: Janssens

first: Steven

last: Henikoff


title: Genome-wide chromatin accessibility data from cultured human fetal lung tip-derived organoids at different stages of lung development

summary: Human fetal  lung tip cells were purifed from developing human lungs at pseudoglandular and canalicular stages and in vitro cultured as organoids. Chromatin accessibility data for each organoid line at different stages were profiled  by ATAC-seq.

overall_design: Two types of human  lung tip organoids of two biological replicates at different stages

first: Walfred

last: Tang


title: Transcriptomic data from cultured human fetal lung tip-derived organoids at different stages of lung development

summary: Human fetal  lung tip cells were purifed from developing human lungs at pseudoglandular and canalicular stages and in vitro cultured as organoids. Whole transcriptomic data for each organoid line at different stages were profiled  by RNA seq.

overall_design: Three types of human  lung tip organoids of two biological replicates at different stages


title: Single cell transcriptomic and T cell repertoire analysis reveals trajectory of tumor - infiltrating lymphocyte states in pancreatic cancer

status: Public on Sep 06 2022

city: Houston

first: Anil

last: Sood

state: TX

address: 6767 Bertner Ave

department: genetics

institute: MDACC

summary: The CD8+ TIL contained a putative transitional GZMK+ population based on TCR clonotype sharing, and cell-state trajectory analysis showed similarity to a GZMB+PRF1+ cytotoxic and a CXCL13+ dysfunctional population. Statistical analysis suggested that certain TIL states, such as dysfunctional and inhibitory populations, often occurred together. Finally, analysis of cultured TIL revealed that high-frequency clones from effector populations were preferentially expanded. These data provide a framework for understanding the PDAC TIL landscape for future TIL use in immunotherapy for PDAC.

overall_design: we profiled 80,000 T cells from 57 PDAC, 22 uninvolved/normal samples, and cultured TIL using single-cell transcriptomic and T-cell receptor analysis.

first: Aislyn

last: Schalck

first: Nicholas

last: Navin

first: Chantale

last: Bernatchez


title: A cryptic transactivation domain of EZH2 binds AR and its splice variant promoting oncogene activation and prostate tumorigenesis

status: Public on Aug 29 2022

city: Nanjing

first: jun

last: wang

state: Jiangsu

address: No. 163 Xianlin Avenue, Qixia District

department: IMB

institute: Nanjing University


title: A cryptic transactivation domain of EZH2 binds AR and AR’s splice variant promoting oncogene activation and prostate tumorigenesis [CUT&RUN]

summary: Enhancer of Zeste Homolog 2 (EZH2) and androgen receptor (AR) are both crucial for the development and progression of prostate tumor, including advanced castration-resistant prostate cancer (CRPC). Previously, it was reported that, in order to sustain tumorigenicity of prostate cancer, EZH2 has noncanonical functions in interaction with AR for mediating gene activation, in addition to its canonical role as a transcriptional repressor and enzymatic subunit of Polycomb Repressive Complex 2 (PRC2). However, the molecular basis underlying non-canonical activities of EZH2 in prostate cancer remains far from clear, and therapeutic strategies for targeting EZH2:AR-mediated gene-activation activities are also lacking.  Here, we report that a hidden transactivation domain of EZH2 (EZH2TAD) binds both AR and AR’s variants enriched in CRPCs, notably AR splice variant 7 (AR-V7), mediating the assembly and/or recruitment of a gene-activation-related complex at genomic sites that lack PRC2 binding. Such noncanonical targets of EZH2:AR/AR-V7:(co)activators are enriched for the clinically-relevant prostate oncogenes. EZH2TAD is crucial for EZH2-mediated transactivation of oncogenes and for CRPC growth in vitro and in vivo. To completely block EZH2’s multifaceted oncogenic activities in prostate cancer, we employed MS177, a recently developed proteolysis targeting chimera (PROTAC) of EZH2.  MS177 achieved on-target depletion of both EZH2’s canonical (EZH2:PRC2) and noncanonical (EZH2TAD:AR/AR-V7:coactivators) complexes in prostate tumor, eliciting much more potent antitumor effects than the existing catalytic inhibitors of EZH2. Overall, this study reports previously unappreciated requirements of EZH2TAD for mediating EZH2’s noncanonical recruitment and gene-activation functions in prostate tumor and suggests EZH2-targeting PROTACs as potentially attractive therapeutics for the treatment of aggressive prostate tumors that reply on circuits wired by EZH2 and AR.

overall_design: We examined genome-wide binding of EZH2 or H3K27me3 in the 22Rv1 CRPC cells. Also, the genome-wide binding of an HA-tagged EZH2, with either wildtype (WT) TAD or the TAD-transactivation-dead mutant (FA), was also examined. Lastly, the genomic binding sites of EZH2, H3K27me3 and AR were assessed after treatment of 22Rv1 cells with MS177 versus DMSO.

first: Jun

last: Wang

first: Greg

first: Ling

last: Cai


title: Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease [RNA-Seq]

status: Public on Jul 26 2022

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

institute: Institute of Clinical Molecular Biology

summary: We investigated the dynamics of gene expression in blood samples of IBD patients treated with infliximab and vedolizumab and analyzed the predictive potential regarding therapy outcome.

overall_design: We performed a longitudinal, blood-based multi-omics study in two prospective IBD patient cohorts receiving first time infliximab therapy (discovery: 14 patients, replication: 23 patients) and one prospective IBD patient cohort receiving first time vedolizumab therapy (17 patients). Samples were collected at up to 7 timepoints (from baseline to 14 weeks after therapy induction).

first: Konrad

last: Aden

first: Nathan

last: Baran

first: Philip

last: Rosentiel


title: RNA-seq comparing Cushing's disease adenomas and surrounding normal tissues

status: Public on Jul 16 2022

city: Bethesda

first: Prashant

last: Chittiboina

address: 3D20, 10 Center Drive

department: NINDS

institute: NIH

summary:
To investigate transcriptomic differences between Cushing's disease adenomas and adjacent normal tissues
We performed RNAseq analysis on CD adenomas versus their adjacent normal tissues

overall_design: CD adenomas and adjacent normal glands were analyzed for transcriptomic changes

first: David

last: Asuzu


title: Cushing's disease adenomas


title: Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease

type: Methylation profiling by genome tiling array


title: Single cell RNA-sequencing of Cushing's disease adenomas

summary: Cushing's disease causes severe morbidity and mortality, yet its underlying mechanisms are poorly understood. We used scRNAseq to compare the transcriptomes of CD adenomas to their normal adjacent pituitary glands

overall_design: Cushing's disease adenomas and their adjacent normal cells were dissociated into single cells and scRNAseq was performed


title: Refined molecular taxonomy and treatment remodeling of pancreatic cancer using single-cell resolution

status: Public on May 18 2022

first: Karthik

last: Jagadeesh

state: MA

address: 415 Main St

department: Human Cell Atlas

institute: Broad Institute

summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet inform clinical management or therapeutic development. Here we construct a high-resolution molecular landscape of the multicellular subtypes and spatial communities that compose PAC using single-nucleus RNA-seq and whole-transcriptome digital spatial profiling (SP) of 43 primary PDAC tumor specimens that either received neoadjuvant therapy or were treatment-naïve. We uncovered expression programs across malignant cells and fibroblasts, including a newly-identified neural-like progenitor malignant cell program that was enriched after chemotherapy and radiotherapy and associated with poor prognosis in independent cohorts. Integrating spatial and cellular profiles revealed three multicellular communities: classical, squamoid-basaloid, and treatment-enriched. Our refined molecular and cellular taxonomy can advance precision oncology in PAC through stratification in clinical trials and as roadmap for therapeutic targeting of specific cellular phenotypes and multicellular interactions.

overall_design: 18 specimens received no treatment prior to resection; 25 specimens received neoadjuvant chemoradiation therapy (e.g. CRT = FOLFIRINOX), losartan (L), and/or nivolumab (N) prior to resection; 2 specimens were non-malignant

first: William

last: Hwang

first: Jimmy

last: Guo

first: Hannah

middle: I

last: Hoffman

first: Carina

last: Shiau

first: Jennifer

last: Su

first: Tyler

last: Jacks

first: Aviv

last: Regev


title: BMX Kinase Mediates Gilteritinib Resistance in FLT3-mutated AML through Microenvironmental Factors

status: Public on Jul 07 2022

city: Columbus

first: Bradley

middle: Wayne

last: Blaser

state: OH

address: 400 W 12th Ave

department: Comprehensive Cancer Center

institute: Ohio State University

summary: While clinical benefit has been observed with gilteritinib, most patients relapse through unknown mechanisms.  To investigate mechanisms of gilteritinib resistance, we performed targeted genomic sequencing and single cell (sc) RNASeq on primary FLT3-ITD-mutated AML samples.  Co-occurring mutations in RAS pathway genes were the most common.  In gilteritinib-unresponsive patients, increased expression of bone marrow-derived hematopoietic cytokines and chemokines was observed after treatment compared to gilteritinib-sensitive patients.  Expression of the TEK-family kinase, BMX, was higher in gilteritinib-unresponsive patients after treatment compared to gilteritinib-sensitive patients. BMX contributed to gilteritinib resistance in FLT3-mutant cells lines in a hypoxia-dependent manner by promoting pSTAT5 signaling, which was reversed with pharmacological inhibition and genetic knockout. In primary FLT3-mutated AML samples, pharmacological inhibition of BMX enhanced the antileukemic activity of gilteritinib and decreased chemokine expression.  Gene module analysis associated gilteritinib responsiveness with lymphocyte differentiation and myeloid leukocyte activation. By contrast, unresponsiveness to gilteritinib associated with upregulation of cell-cycle, DNA/RNA metabolic processes, and protein translation.  Together, these data support a role for microenvironment-mediated factors modulated by BMX in the escape from targeted therapy and gilteritinib resistance.  This analysis provides a deeper understanding of targets and pathways for potential therapeutic intervention to restore gilteritinib sensitivity.

overall_design: 20 Samples were analyzed from 7 individuals before (n = 7 samples) and after (n = 13 samples) treatment with gilteritinib.  Patients were classified according to gilteritinib response.  Patients with 50% or greater decrease in myeloblast percentage after starting gilteritinib were considered "sensitive" (n = 4 patients, n = 11 samples).  The remaining patients were considered "unresponsive" (n = 3 patients, n = 9 samples).

first: Daelynn

last: Buelow

first: Bhavana

last: Bhatnagar

first: Shelley

last: Orwick

first: Jae

middle: Y

last: Jeon

first: Eric

middle: D

last: Eisenmann

first: Jack

last: Stromatt

first: Navjot

last: Pabla

first: James

last: Blachly

first: Sharyn

last: Baker


title: Gene Expression profiling of wild type (WT) and Allograft inflammatory factor-1 deficient (Aif1-/-) immortalized bone marrow derived macrophages by RNA-seq.

status: Public on Jun 22 2022

city: Bronx

first: Prameladevi

last: Chinnasamy

state: New York

address: Golding 105

department: Medcine-Cardiology

institute: Albert Einstein College of Medicine

summary:
Purpose: Identification of cellular pathways regulated by AIF1 in bone marrow derived macrophages, based on gene expression patterns identfied by RNA seq.
Methods: Imortalized macrophage cell lines were generated from bone marrow of 8 week old WT and Aif1-/- mice. These cells were subject to RNA sequencing in triplicate, using Illumina Nextseq 500, single end read with high output. The sequence reads that passed quality filters were analyzed as follows; Aligned to GRCm38 mouse genome with Tophat (v2.0.13); Gene hits were counted with HTseq(v0.6.1) under default parameters using release 84 of the Mus_musculus.GRCm38; Differential expression analysis was performed in R/Bioconductor following the DESeq2 workflow and annotated with biomaRt.
Results: Using an optimized data analysis workflow, we mapped about 35 million sequence reads per sample to the mouse genome (build GRCm38) and identified 26,934 transcripts in WT and Aif1-/-  macrophages with a tophat/htseq/DESeq2 workflow. Approximately 4% of the transcripts showed differential expression between the WT and Aif1-/- macrophages, with a fold change ≥1.0 and p value <0.05. Aif1 transcript expression was confirmed in WT and Aif1-/- macrophages. Using qRT–PCR, we validated altered expression of 5 genes involved in the noradrenaline degradation pathway. Unsupervised hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to macrophage AIF1-mediated immune activation and inflammation. Data analysis revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study represents the first detailed analysis of transcriptomes of WT and Aif1-/- macrophages, with technical replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that Next generation sequencing offers a comprehensive and accurate quantitative and qualitative evaluation of mRNA content within a cell. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: mRNA profiles of bone marrow-derived WT and  and Aif1l-/- mice were generated by RNA sequencing, in triplicate, using Illumina Next seq 500.

first: Nicholas

last: Sibinga


title: Gene expression data from the brain of adult autism model marmosets

status: Public on May 01 2022

city: Kodaira

first: Satoshi

last: Watanabe

state: Tokyo

address: 4-1-1 Ogawa Higashi

institute: National Center of Neurology and Psychiatry

summary:
Autism spectrum disorder (ASD) affects gene expression in adult ages. We used valproic acid (VPA)-induced ASD model marmosets.
Gene expression modulations in VPA-exposed and unexposed (UE) marmosets were analyzed at adult ages. We revealed modulations in neuron- and glia-related genes.

overall_design: Tissues from two cortical areas (area 12 and TE) of UE and VPA marmosets were isolated. RNA was extracted and hybridized on custom-made microarrays. We sought to obtain differentially expressed genes.

first: Tomofumi

last: Oga

first: Tetsuya

last: Sasaki

first: Kayo

last: Sumida

first: Kohei

last: Hoshino

first: Koichi

last: Saito

first: Izuru

last: Miyawaki

first: Keiko

last: Nakagaki

first: Jun

last: Noguchi

first: Noritaka

last: Ichinohe


title: RNA-sequencing of liver tissue from corn oil and TCDD treated Fmo3+/+ and Fmo3-/- mice

status: Public on Apr 27 2022

city: Cleveland

first: Ernest

last: Chan

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary:
Purpose: The goals of this study are to compare the hepatic transcriptome profiles of Fmo3+/+ and -/- mice injected weekly with either corn oil vehicle or 25ug/kg TCDD for 6 weeks data analysis.
Methods: RNA was isolated from frozen liver tissue. RNA-Seq libraries were generated using the Illumina mRNA TruSEQ Directional library kit and sequenced using an Illumina NovaSeq 6000 (both according to the manufacturer’s instructions). RNA-Seq was performed by the University of Chicago Genomics Facility.
Conclusions: Our study represents the first report of the role of Fmo3 in response to TCDD and finds that genes associated with the acute phase response and detoxification are significantly altered in the absence of Fmo3.

overall_design: Hepatic mRNA profiles of Fmo3+/+ and -/- mice injected weekly with either corn oil vehicle or 25ug/kg TCDD for 6 weeks.

first: William

last: Massey

first: E

first: J

middle: M

last: Brown


title: GLUTag cell line transcriptomic profiling

status: Public on Apr 08 2022

city: Oxford

first: Thomas

last: Monfeuga

address: Innovation Building, Old Road Campus, Roosevelt Drive

institute: Novo Nordisk Research Centre Oxford

summary: We sequenced cells from the GLUTag enteroendocrine murine cell line to characterize its transcriptome

overall_design: GLUTag cell line 3' mRNA-sequencing (6 replicates)

first: Malgorzata

last: Cyranka

first: Natascia

last: Vedovato

first: Chelsea

last: Larabee

first: Anandhakumar

last: Chandran

first: Enrique

last: Toledo

first: Heidi

last: de Wet


title: Identification of prognostic-related key genes and their impact on immune response based on high-throughput RNA sequencing

status: Public on May 25 2022

city: Chongqing

first: xiaomao

last: Tian

address: Zhongshan 2nd Road, Yuzhong District, Chongqing 400014, P.R. China

institute: Children’s Hospital of Chongqing Medical University, Chongqing, P.R. China

summary: Wilms tumor is the most common type of renal malignancy in children. Accumulating evidence introduces that dysregulation of genes contributes to tumorigenesis. To explore potential therapeutic targets for WT, a more detailed and comprehensive investigation of gene expression profiles is warranted. We used high-throughput RNA sequencing to analyze the mRNA expression of the WT tissues and adjacent normal tissues.

overall_design: we used 8 paired WT samples and high-throughput RNA sequencing to identify differentially expressed mRNAs. The PPI network of differential genes was constructed based on the STRING database, and top 10 HUB genes were further identified. Then, a three-gene prognostic signature for WT patients was constructed by LASSO regression analysis. In addition, we analyzed the mutational characteristics of key HUB genes and predicted the effect of immunotherapy.

first: Xiao-Mao

first: Bin

last: Xiang

first: Feng

last: Liu

first: Guang-Hui

last: Wei


title: Changes in gene expression of mouse-derived glioma stem cells (005), Tumor derived endothelial cells (TDEC) differentiated from 005, and TDEC under sertraline treatment

status: Public on Mar 30 2022

city: Okayama City

first: Nobushige

last: Tsuboi

state: Okayama Prefecture

address: 2-5-1 Shikata-cho Kita-ku

department: Neurological Surgery

institute: Okayama University

summary: Comparison of gene expression between glioma stem cells and endothelial cells differentiated from them and endothelial cells under drug administration.

overall_design: RNA extracted from 005, 005-differentiated TDECs, Sertraline-treated TDECs, and mouse brain microvascular endothelial cells (MBMECs)

first: Hiroyuki

last: Michiue


title: Hatching is modulated by microRNA-378a-3p derived from extracellular vesicles secreted by blastocysts (mRNA)

status: Public on Mar 10 2022

city: Merelbeke

first: Krishna Chaitanya

last: Pavani

state: Gent

address: Salisburylaan 133, Merelbeke, Belgium

institute: Ghent Univeristy

summary: The current study is aimed on determine the functional impact of microRNA-378a-3p and microRNA-146b on embryo development. For such purpose,  we supplemented miR-378/miR-146b mimics or inhibitors to the culture medium containing presumed zygotes at 1 dpi and cultured them until day 8, thus allowing miR-378/miR-146b mimics or inhibitors to influence further embryo development and quality. Further on, to gain more in-depth molecular insights, we performed transcriptome profiling of blastocysts cultured in the presence of miR-378/miR-146b mimics or inhibitors.

overall_design: Examining the effects of supplementing microRNA-378a-3p/146b mimics and inhibitors to embryos  on the transcriptomic level

first: Krishna

middle: C

first: Tim

last: Meese

first: Katrien

last: Smits

first: Filip

last: Van Nieuwerburgh

first: Ann

last: Van Soom


title: Hatching is modulated by microRNA-378a-3p derived from extracellular vesicles secreted by blastocysts (miRNA)

summary: The current study is focused on Isolating EVs and their cargo content (miRNAs) from culture medium conditioned by individual embryos that can differentiate between the blastocyst and non-blastocyst embryos. We were able to isolate EVs from both blastocyst and non-blastocyst group with size exclusion chromatography (Izon’s™ qEV single column) and characterize them with Western blotting, nanoparticle tracking analysis, and Transmission electron microscopy.  Further, we could isolate total RNA (including small RNAs) from the blastocyst and non-blastocyst EVs for miRNA sequencing.

overall_design: Examination of miRNA content between the blastocyst and non-blastocyst conditioned media derived EVs


title: Hatching is modulated by microRNA-378a-3p derived from extracellular vesicles secreted by blastocysts

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

overall_design: Refer to individual Series


title: RNA-Seq Analysis of Dose-Dependent TCDD-Elicited Colonic Gene Expression in Male Mice

status: Public on Dec 31 2021

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

summary: Dose-dependent colonic gene expression was examined following repeated exposure (every 4 days for 28 days) to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). These data were used to examine the effect of repeated TCDD exposure on gene expression in the intestinal epithelium of C57BL/6 male mice.

overall_design: Three biological replicates for each dose (0.01, 0.03, 0.1, 0.3, 1, 3, 10, 30) of TCDD and sesame oil vehicle

first: Kelly

middle: A

last: Fader

first: Timothy

last: Zacharewski


title: small non-coding RNA expression profile of human lung tissue explants infected with bacteria/virus by RNAseq

status: Public on Jan 04 2022

city: Hannover

first: Frank

last: Pessler

address: Feodor-Lynen-Str. 7-9

department: Experimental Infection Research

institute: Center for Experimental and Clinical Infection Research GmbH

summary: small non-coding RNA-seq was performed to study the transcriptomic changes in human lung tissue post infection with either Influenza A virus (IAV), or Pseudomonas aeruginosa (PA) or Mycobacterium bovis (BCG)

overall_design: Human lung tissue explants tissue were further dissected into small pieces with an average size of approx. 27 mm3 (3x3x3 mm) and an average weight of approx. 30 mg. These pieces (HLTEs) were cultured in RPMI wither either of infection. Followed by 24 hour incubation with either of pathogens, tissue were collected for RNA extraction and sequencing.

first: Aaqib

last: Sohail

first: Robert

last: Geffers


title: Gene expression profile of human lung tissue explants infected with bacteria/virus by RNAseq

status: Public on Dec 30 2021

summary: RNA-seq was performed to study the transcriptomic changes in human lung tissue post infection with either Influenza A virus (IAV), or Pseudomonas aeruginosa (PA) or Mycobacterium bovis (BCG)


title: Effects of Nogo-A deletion in the dental epithelium of the continuously growing mouse incisor

status: Public on Jan 01 2022

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

summary: Nogo-A is a major player in the regulation of neural development and regeneration, and it is the target of several clinical trials. Despite its high clinical relevance, the functions of Nogo-A outside the central nervous system are mostly unknown. In this work, we investigated the role of Nogo-A in tooth development in mouse transgenic models. We observed that Nogo-A is expressed in ameloblasts, the cells responsible for the formation of enamel. We show that the deletion of Nogo-A in the dental epithelium leads to the formation of defective enamel. By RNA sequencing we showed  that this phenotype is associated with the overexpression of clusters of genes involved in cell differentiation and production of enamel.

overall_design: The posterior half of the dental epithelium of incisors isolated from newborn K14cre; Nogo-A flox/flox mice and wild type controls was analyzed by RNA sequencing. The left and the right lower incisors of a single animal were pooled to generate 1 sample. A total of n = 4 wild type and n = 4 K14cre; Nogo-A flox/flox animals was analyzed

first: Pierfrancesco

last: Pagella

first: Thimios

last: Mitsiadis


title: Single Cell RNA Sequencing of MIC WT and B1KO early invasive breast carcinoma

status: Public on Oct 19 2021

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

institute: Canadian Centre for Computational Genomics (C3G)

summary: The goal of this study is the compare the tumour compositions between B1 integrin-proficient and -deficient dormant lesions based on single cell transcripts. Tumours were dissociated and pooled into single cell suspension, passed multi-stage quality checks, and sequenced by Génome Québec Innovation Tumour. Clustering visualization by UMAP and differential gene expression analyses show that B1 integrin-deficient dormant lesions have significantly more cancer-associated fibroblasts by depleted of antitumourigenic immune cells, altogether promoting dormnacy exit and recurrence.

overall_design: Sequencing on viable single cell suspension from pooled mouse mammary early invasive lesions (B1 integrin-proficient or -deficient)

first: Yu

last: Gu

first: Tung

last: Bui

first: William

last: Muller


title: Cellular and transcriptional immune responses induced by neoadjuvant PD-1 blockade in glioblastoma patients

status: Public on Oct 18 2021

city: Los Angeles

first: Willy

last: Hugo

state: California

address: 10833 Le Conte Ave

department: Medicine

institute: University of California, Los Angeles

summary: The differentiation and effector function of tumor infiltrating lymphocytes and macrophages in the tumor microenvironment is critical for productive anti-tumor immune responses, although direct evidence for this remains poorly characterized in brain cancer patients.  Using mass cytometry, single-cell RNA sequencing, and quantitative multiplex immunofluorescence, we comprehensively characterized the phenotype and single-cell transcriptome of myeloid cells and T lymphocytes that infiltrated malignant gliomas, and identified how such populations changed following neoadjuvant PD-1 checkpoint blockade in recurrent glioblastoma patients.  Cells of the myelo-monocytic lineage represented approximately three quarters of the immune cell infiltrate, with T lymphocytes representing the next major immune cell subset by density and percentage, but following neoadjuvant PD-1 antibody blockade, the ratio of myeloid cells to T cells significantly decreased.  We then used single-cell RNA sequencing to comprehensively define the transcriptional profiles of lymphoid and myeloid populations in these tumors.  Recurrent GBM patients treated with neoadjuvant PD-1 checkpoint inhibition possessed a greater fraction of CD8+ T cells with an effector T cell transcriptional program. The increased effector T cell populations were associated with the distinct upregulation of the chemokines, CXCL9 and CXCL10 by an interferon-responsive macrophage cluster.  Importantly, we also identified that neoadjuvant PD-1 blockade was associated with significantly increased cellular interactions specifically between CD8+ T cells and tumor associated macrophages within the tumor microenvironment. Together, these findings suggest that effector T cell infiltration and differentiation are increased with neoadjuvant PD-1 blockade but impeded by adaptive resistance and immunosuppression from tumor associated macrophages.  Future therapeutic strategies to target this dominant immunosuppressive myeloid cell population may be needed to achieve true, therapeutic interventions in this patient population.

overall_design: This dataset contains a total of 40 single cell transcriptomes of new and recurrent glioblastoma with/without neoadjuvant anti-PD1 treatment.

first: Alexander

last: Lee

first: Lu

last: Sun

first: Aaron

last: Mochizuki

first: Jeremy

middle: G

last: Reynoso

first: Joey

last: Orpilla

first: Frances

last: Chow

first: Jenny

last: Kienzler

first: Richard

last: Everson

first: David

last: Nathanson

first: Steven

last: Bensinger

first: Linda

last: Liau

middle: F

last: Cloughesy

last: Prins