title: Comprehensive testing of chemotherapy and immune checkpoint blockade in preclinical cancer models identifies additive combinations

city: Nedlands

first: Nicola

last: Principe

state: WA

address: 6 Verdun St

country: Australia

institute: University of Western Australia

summary:
Background: Antibodies that target immune checkpoints such as cytotoxic T lymphocyte antigen 4 (CTLA 4) and the programmed cell death protein 1/ligand 1 (PD-1/PD-L1) are now a treatment option for multiple cancer types. However, as a monotherapy, objective responses only occur in a minority of patients. Chemotherapy is widely used in combination with immune checkpoint blockade (ICB). Although a variety of isolated immunostimulatory effects have been reported for several classes of chemotherapeutics, it is unclear which chemotherapeutics provide the most benefit when combined with ICB.
Methods: We investigated 10 chemotherapies from the main canonical classes dosed at the clinically relevant maximum tolerated dose in combination with anti CTLA-4/anti-PD-L1 ICB. We screened these chemo-immunotherapy combinations in two murine mesothelioma models from two different genetic backgrounds, and identified chemotherapies that produced additive, neutral or antagonistic effects when combined with ICB. Using flow cytometry and bulk RNAseq, we characterized the tumor immune milieu in additive chemo-immunotherapy combinations.
Results: 5-fluorouracil (5-FU) or cisplatin were additive when combined with ICB while vinorelbine and etoposide provided no additional benefit when combined with ICB. The combination of 5-FU with ICB augmented an inflammatory tumor microenvironment with markedly increased CD8+ T cell activation and upregulation of IFN𝛾, TNF𝛼 and IL-1β signaling. The effective anti tumor immune response of 5-FU chemo-immunotherapy was dependent on CD8+ T cells but was unaffected when TNF𝛼 or IL 1β cytokine signaling pathways were blocked.
Conclusions: Our study identified additive and non-additive chemotherapy/ICB combinations and suggests a possible role for increased inflammation in the tumor microenvironment as a basis for effective combination therapy.

overall_design: 28 AB1HA tumor samples in total: 4 samples treated with PBS, 5 samples treated ICB (anti-CTLA-4/anti-PD-L1), 5 samples treated with 5-FU, 5 samples treated with Cisplatin, 5 samples treated with 5-FU+ICB, 5 samples treated with Cisplatin+ICB. Each sample represents an individual biological replicate (i.e. no duplicate samples from the same mouse). Tumors for all mice were collected 7 days after the administration of MTD Chemo and/or ICB


title: Transcriptional adaptation of olfactory sensory neurons to GPCR identity and activity [scRNAseq_MOE_rest]

status: Public on May 02 2022

city: Geneva

first: Ivan

last: Rodriguez

address: 30 quai Ernest Anrsermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

type: Expression profiling by high throughput sequencing

summary: In mammals, chemoperception relies on a diverse set of neuronal sensors able to detect chemicals present in the environment, and to adapt to various levels of stimulation. The contribution of endogenous and external factors to these neuronal identities remains to be determined. Taking advantage of the extensive parallel coding lines present in the olfactory system, we explored the potential variations of neuronal identities before and after olfactory experience. We found that at rest, the transcriptomic profiles of mouse olfactory sensory neuron populations are already highly divergent, specific to the olfactory receptor they express, and are surprisingly associated with the sequence of these latter. These divergent profiles further evolve in response to the environment, as odorant exposure leads to massive reprogramming via the modulation of transcription. These findings highlight a broad range of sensory neuron identities that are present at rest and that adapt to the experience of the individual, thus adding to the complexity and flexibility of sensory coding.

overall_design: Characterizing the genetic diversity of olfactory sensory neurons at rest in adult mice using single-cell RNA sequencing

first: Luis

last: Flores-Horgue

first: Alexis

last: Assens

first: Leon

last: Fodoulian

first: Leonardo

last: Marconi-Archinto

first: Joël

last: Tuberosa

first: Alexander

last: Haider

first: Madlaina

last: Boillat

first: Alan

last: Carleton


title: Transcriptional adaptation of olfactory sensory neurons to GPCR identity and activity

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

overall_design: Refer to individual Series


title: Transcriptional adaptation of olfactory sensory neurons to GPCR identity and activity [MOR23]

overall_design: Unravelling odorant-induced transcriptional modulation in single OSN populations using FAC-sorting followed by bulk RNA sequencing.


title: SGPL1 stimuates VPS39 recruitment to the mitochondria in MICU1deficient cells

status: Public on May 01 2022

city: Bonn

first: Daniele

last: Bano

state: NRW

address: Venusberg Campus 1, Gebaeude 99

country: Germany

institute: DZNE, German Center for Neurodegenerative Diseases

summary: Global transcriptome analysis was performed in adult wildtype, micu-1 and micu-1; mcu-1 mutant Caenorhabditis elegans in order to gain insight into the transcriptional regulation of stress response pathways that confer longevity.

overall_design: RNA-seq analysis of adult wildtype, micu-1 and micu-1; mcu-1 mutant Caenorhaditis elegans.

first: Kristian

last: Händler

first: Antonia

last: Piazzesi

first: Lena

last: Wischhof


title: Immunopeptidomic analyses of colorectal cancers with and without microsatellite instability

city: Montreal

first: Pierre

last: Thibault

state: Quebec

address: 2950 Chem. de Polytechnique

country: Canada

institute: Institute of Research in Immunology and Cancer (IRIC)

summary: Colorectal cancer is the second leading cause of cancer death worldwide, and the incidence of this disease is expected to increase as global socioeconomic changes occur. Immune checkpoint inhibition therapy is effective in treating a minority of colorectal cancer tumors; however, microsatellite stable tumors do not respond well to this treatment. Emerging cancer immunotherapeutic strategies aim to activate a cytotoxic T cell response against tumor-specific antigens, presented exclusively at the cell surface of cancer cells. These antigens are rare and are most effectively identified with a mass spectrometry-based approach, which allows the direct sampling and sequencing of these peptides. While the few tumor-specific antigens identified to date are derived from coding regions of the genome, recent findings indicate that a large proportion of tumor-specific antigens originate from allegedly noncoding regions. Here, we employed a novel proteogenomic approach to identify tumor antigens in a collection of colorectal cancer-derived cell lines and biopsy samples consisting of matched tumor and normal adjacent tissue. The generation of personalized cancer databases paired with mass spectrometry analyses permitted the identification of more than 30 000 unique MHC I-associated peptides. We identified 19 tumor-specific antigens in both microsatellite stable and unstable tumors, over two-thirds of which were derived from non-coding regions. Many of these peptides were derived from source genes known to be involved in colorectal cancer progression, suggesting that antigens from these genes could have therapeutic potential in a wide range of tumors. These findings could benefit the development of T cell-based vaccines, in which T cells are primed against these antigens to target and eradicate tumors. Such a vaccine could be used in tandem with existing immune checkpoint inhibition therapies, to bridge the gap in treatment efficacy across subtypes of colorectal cancer with varying prognoses. Data are available via ProteomeXchange with identifier PXD028309.

overall_design: RNA-seq

first: Jenna

last: Cleyle


title: Transcriptional adaptation of olfactory sensory neurons to GPCR identity and activity [M71]


title: Methanol fixed feeder layers altered the pluripotency and metabolism of bovine pluripotent stem cells

city: Hohhot

first: wen

middle: qiang

last: xu

state: Inner Mongolia autonomous region

address: Yuquan District

country: China

institute: Inner Mongolia University

summary: The pluripotency maintenance of pluripotent stem cells (PSCs) cultured in vitro requires the suitable microenvironment, which is commonly provided by the feeder layer. However, the preparation of feeder layer is time consuming and labor exhaustive. More importantly, the feeder cells treated with mitomycin or gamma-ray irradiation brings heterologous contamination to stem cells. The feeder-free PSC cultures are associated with high costs because of the requirement for additional supplements and special media. In this study, we characterize the pluripotency and metabolic status of bovine ESCs-F7 (classic bESCs lines, abbreviated as F7), which were cultured on methanol fixed mouse embryonic fibroblasts (MT-MEFs) or mitomycin C treated MEFs (1M-MEFs). MT-MEFs could be reused several times and were highly resistant to digestive enzymes. The relative expression levels of pluripotent markers were different between F7 cultured on MT-MEFs (marked as MT-F7) and those cultured on the 1M-MEFs (1M-F7). The long-term cultured MT-F7 cells formed embryoid bodies in vitro, showing the ability to differentiate into endodermal, ectodermal, and mesodermal germ layers like 1M-F7. RNA-sequencing analysis showed that the replacement of the feeder layer from 1M-MEFs to MT-MEFs lead to a novel steady transition of the F7, which included alteration of the expression patterns of genes that regulate pluripotency and metabolism. Further, the long-term cultured bovine expanded pluripotent stem cells (bEPSCs) on MT-MEFs (MT-bEPSCs) formed classical colonies, maintained pluripotency, and demonstrated elevated level of metabolic activity. In conclusion, this study demonstrated that methanol-fixed MEFs were efficient feeder layer that maintain the unique pluripotency and the distinctive metabolic characteristics of the bPSCs cultured in vitro.

overall_design: Pluripotent stem cells mRNA profiles of 15 passages in 1M-F7 and MT-F7,  NOTE: 1M equal to MC,   1M-F7 equal to MC-F7

first: Wenqiang

last: Xu

first: Ruifeng

last: Hao

first: Jing

last: Wang

first: Lingna

last: Gao

first: Xuejie

last: Han

first: Chen

last: Li

first: Hui

last: Zhang

first: Xueling


title: Human pluripotent stem cell-derived cells endogenously expressing follicle-stimulating hormone receptors: modeling the function of an inactivating receptor mutation

city: Helsinki

first: Karolina

last: Lundin

address: Haartmaninkatu 8

department: Department of Obstetrics and Gynecology

country: Finland

institute: University of Helsinki

summary: Follicle-stimulating hormone (FSH) is crucial in the development and regulation of reproductive functions. The actions of human FSH and its receptor (FSHR) and mutations therein have mainly been studied using in vivo models, primary cells, cancer cells and cell lines ectopically expressing the FSHR. To allow studies of endogenous FSHR function in vitro, we differentiated FSHR-expressing cells from human pluripotent stem cells. FSH stimulation of the wild-type (WT), but not the inactivating Finnish founder mutant (A189V) receptor, activated the canonical cAMP-dependent signaling pathway and downstream mediators. Interestingly, the WT and A189V mutant receptors activated distinct pathways in a G-protein-coupled receptor signaling assay. FSH stimulation of WT FSHR-expressing cells induced phosphorylation of PI3Kp85a/g, MAPKAPK2 and proteins involved in calcium-dependent signaling, among others, while in the A189V mutant cells FSH induced phosphorylation of e.g., P90RSK, ERK3, and focal adhesion kinase. Lastly, we expressed FSHR in HEK293 cells followed by affinity purification mass spectrometry analyses, to investigate protein-protein interaction partners of FSHR at resting state and upon FSH stimulation. We found 19 specific high-confidence interacting proteins for WT FSHR and 14 for A189V FSHR, several of which have been linked to infertility. In conclusion, our protocol allows detailed studies of FSH action and disease modeling in human cells endogenously expressing FSHR.

overall_design: Two samples (separate experiments) of human cells endogenously expressing FSHR (follicle stimulating hormone receptor) derived by 8-day directed differentiation of human embryonic stem cells (H9).


title: Clonal evolution in multiple myeloma after treatment pressure: heterogenous genomic aberrations and transcriptomic convergence

city: Trondheim

first: Kristine

last: Misund

address: Prinsesse Kristinas gate 1

department: Department of Clinical and Molecular Medicine

country: Norway

institute: NTNU

summary: Multiple myeloma (MM) is still an incurable plasma cell malignancy that generally responds well to treatment intitially, but eventually becomes refractory. In the present study, genomic and transcriptomic changes were investigated in paired early and late tumor samples of MM patients .

overall_design:
RNA sequencing (RNA Seq) were performed on longitudinal tumor samples taken from multiple myeloma (MM) patients to identify genomic and transcriptomic changes during disease progression. The own-institutional cohort consisted of sequential tumor samples (n=51) from 21 MM patients, of whom two or more samples had been obtained during their disease course, from the MM biobank of St. Olavs Hospital, Norway or Erasmus MC Cancer Institute, Netherlands.

**Due to patient privacy concerns, raw data are not provided**

first: Pieter

last: Sonneveld


title: RNA sequencing analysis of embryonic yolk sacs from wildtype and Etv2 mutant embryos at E8.5

city: San Francisco

first: Tanvi

last: Sinha

state: California

address: 555 Mission Bay blvd. S, Apt 1608

country: USA

institute: UCSF

summary: Transcriptomic analyses of yolk sacs from mouse embryos at E8.5 was performed to assess the dosage dependent effects of varying Etv2 dosage on early endothelial and hematopoietic development.

overall_design: Mouse embryonic yolksacs were collected across 6 different Etv2 genotypes with varying Etv2 dosage levels from 100% to 0%. Samples were somite-matched and littermates were included as controls. Samples from both sexes were used in the analysis. 4-6 biological replicates were used per group.

first: Brian

last: Black


title: BMP4 Signaling Plays a Critical Roles in Self-renewal of R2i Mouse Embryonic Stem Cells

city: Daegu

first: Ji Hwan

last: Park

state: Gyeongbuk

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Newbiology

country: South Korea

institute: DGIST

summary: Mouse embryonic stem cells (mESCs) can be maintained in a pluripotent state under R2i culture conditions that inhibit the TGF-β and ERK signaling pathways. BMP4 is another member of the TGF-β family that plays a crucial role in maintaining the pluripotency state of mESCs. It has been reported that inhibition of BMP4 caused the death of R2i-grown cells. In this study, we used the loss-of-function approach to investigate the role of BMP4 signaling in mESC self-renewal. Inhibition of this pathway with Noggin and dorsomorphin, two bone morphogenetic protein (BMP) antagonists, elicited a quick death of the R2i-grown cells. We showed that the canonical pathway of BMP4 (BMP/SMAD) was dispensable for self-renewal and maintaining pluripotency of these cells. Transcriptome analysis of the BMPi-treated cells revealed that the p53 signaling and two adhesion (AD) and apoptotic mitochondrial change (MT) pathways could be involved in the cell death of the BMPi-treated cells. According to our results, inhibition of BMP4 signaling caused a decrease in cell adhesion and ECM detachment, which triggered anoikis in the R2i-grown cells. Altogether, these findings demonstrate that endogenous BMP signaling is required for survival of mESCs under the R2i condition.

overall_design: Examination of BMP4 signaling role in mESC self-renewal

first: Sara

last: Taleahmad

first: Hossein

last: Baharvand

first: Ghasem

middle: H

last: Salekdeh


title: RNA Sequencing analysis of melanomas isolated from TN GEM models

status: Public on Apr 30 2022

city: Columbus

first: Brandon

middle: M

last: Murphy

state: Ohio

address: 460 W. 12th Ave, BRT 940E

institute: The Ohio State University

summary: RNA sequencing was peformed on RNA isolated from melanomas collected from TN GEM models upon reach exclusion criteria.

overall_design: Melanomas sequenced: 6 NRAS 61R/R, 6 NRAS 61K/K, 6 NRAS 61L/L, 6 NRAS 61H/H

first: Christin

middle: E

last: Burd


title: The Plasmodium falciparum CCCH zinc finger protein ZNF4 (PF3D7_1134600) plays an important role in gametocyte exflagellation through the regulation of male gametocyte enriched genes.

city: Aachen

first: Che

middle: Julius

last: Ngwa

address: Worringerweg 1

department: Cellular and Applied Infection Biology

institute: RWTH University

summary:
Purpose: To carryout comparative transcriptomics between the ZNF4-K0 and the wild type in the ring and mature gametocyte stage of Plasmodium falciparum
Methods: Total RNA was isolated from ring stage and percoll- enriched mature (stage V) gametocytes from the ZNF4-KO and NF54 wildtype using the Trizol reagent (Invitrogen) according to the manufacturer’s protocol. .  RNA sequencing was performed at the Genomic Facility of the University Clinic at the RWTH University Aachen, Germany. Briefly, the quality of the isolated total RNA samples from ring stage and mature gametocytes of the ZNF4-KO and the wildtype were evaluated by Tapestation 4200 (Agilent).  Libraries were generated with TruSeq Stranded mRNA Library Preparation kit (Illumina) from high quality total RNA samples according to the manufacturer´s protocol. The generated libraries, which pass the QC check on Tapestation 4200 (Agilent) were sequenced on a NextSeq 500 (Illumina) with High output Kit v2.5 (150 cycles) for paired-end sequencing according to standard procedure provided by Illumina.
Results:Comparative transcriptomics between wildtype and ZNF4-KO in ring and mature gametocyte stages show only 66 genes de-regulated by greater than 2-fold in the ZNF4-KO ring stage while about 473 (274- upregulated and 199 down-regulated) were deregulated in mature gametocytes.
Conclusions: Our combine data therefore reveal that ZNF4 plays an important role in male gametocyte exflagellation through the regulation of male gametocyte genes

overall_design: Total RNA was isolated from ring stage and percoll- enriched mature (stage V) gametocytes from the Plasmodium faciparum ZNF4-KO and NF54 wildtype using the Trizol reagent (Invitrogen) according to the manufacturer’s protocol. Quality of RNA samples were assessed using a ND-1000 (NanoDrop Technologies, Thermo Scientific) and by agarose gel electrophoresis.RNA sequencing was performed at the Genomic Facility of the University Clinic at the RWTH University Aachen, Germany.

first: Borja

last: Hanhsen

first: Fabian

last: Bick

first: Afia

last: Farrukh

first: Gabriele

last: Pradel

middle: J


title: Gene expression data in the human non-small cell lung cancer cell line NCI-H1975 and osimertinib-resistant OR1 and OR2 cells

status: Public on Apr 28 2022

city: Kurume

first: Yuichi

last: Murakami

address: Tsubukuhonmachi 422

country: Japan

institute: St Mary's Institute of Health Sciences

summary: Osimertinib, a third-generation EGFR-TKI, has applied to non-small cell lung cancer harboring activated EGFR mutation with or without T790M. However, the appearance of tumors resistant to osimertinib has been reported. We established and characterized osimertinib-resistant cells derived from NCI-H1975 cells harboring activating EGFR and T790M mutation.

overall_design: The gene expression profile to osimertinib-resistant OR cells was compared to that of osimertinib-sensitive parental NCI-H1975 cells.

first: Daiki

last: Kusakabe

first: Kosuke

last: Watari

first: Akihiko

last: Kawahara

first: Koichi

last: Azuma

first: Jun

last: Akiba

first: Masahiko

last: Taniguchi

first: Michihiko

last: Kuwano

first: Mayumi

last: Ono


title: Single cell RNA Sequencing Identifies G-protein Coupled Receptor 87 as a Basal Cell Marker Expressed in Distal Honeycomb Cysts in Idiopathic Pulmonary Fibrosis

city: Pittsburgh

first: Melanie

last: Königshoff

state: Pennsylvania

address: 200 Lothrop St

institute: University of Pittsburgh

summary: Idiopathic Pulmonary Fibrosis (IPF) is a devastating and life-threatening lung disease characterized by epithelial reprogramming and increased extracellular matrix deposition leading to loss of lung function. A prominent histopathological structure in the IPF lung are aberrant bronchioles filled with mucus, referred to as honeycomb cysts. These heterogeneous bronchiolized areas feature clusters of simple epithelium with Keratin (KRT)5+ basal-like cells interspersed with pseudostratified epithelium containing differentiated, hyperplastic epithelial cells as well as aberrant ciliated cells. Recent single-cell RNA sequencing studies of the lung epithelium shed further light into cellular subtypes unique to IPF, including basaloid KRT5-/KRT17+ cells present in the distal lung. However, IPF distal bronchiole cell subtypes still remain poorly characterized and their disease contribution remains underinvestigated. Using single-cell RNA sequencing of enriched EpCAM+ lung cells of the distal IPF lung, we identified G-protein coupled receptor (GPR) 87, as a marker of distal bronchioles and KRT5+ IPF basal cells contributing to impaired airway differentiation and honeycombing.

overall_design:
Single-cell suspensions from three donor lungs and three lungs from patients with IPF were enriched into Epcam+ cells and went through single cell RNA-seq analysis.
***Raw data not available due to patient privacy concerns***

first: Katharina

last: Heinzelmann

first: Qianjiang

last: Hu

first: Yan

first: Evgenia

last: Dobrinskikh

first: Meshal

last: Ansari

first: M Camila

last: Melo-Narváez

first: Henrik

last: Ulke

first: Colton

last: Leavitt

first: Carol

last: Mirita

first: Tammy

last: Trudeau

first: Maxwell

middle: L

last: Saal

first: Pamela

last: Rice

first: Bifeng

last: Gao

first: William

last: Janssen

first: Ivana

middle: V

last: Yang

first: Herbert

middle: B

last: Schiller

first: Eszter

middle: K

last: Vladar

first: Mareike

last: Lehmann


title: RNA sequencing analysis of Nras mutant MEFs

first: Brandon

last: Murphy

summary:
Purpose: Emerging evidence in the field of RAS biology is beginning to illustrate that RAS mutations are functionally distinct. To elucidate functional differences between NRAS mutants we performed RNA-sequencing on mouse embryonic fibroblasts (MEFs) expressing different NRAS codon 61 variants from the endogenous gene locus
Methods: MEFs were isolated from Tyr::CRE-ERT2 LSL-Nras mouse models containing different Nras variants in the endogeous gene locus. NRAS expression was induced in MEFs using an Adenoviral Cre delivery system. RNA was isolated from MEFs six days post-NRAS induction and submitted for RNA-sequencing
Results: Differential expression and gene set enrichment analysis (GSEA) between NRAS variants revealed enrichment of transcripts associated with cellular proliferation between all mutant Nras alleles versus wild-type Nras. Further, MEFs expressing NRAS mutants capable of driving melanoma formation were enriched for transcripts associated with RAS-MYC signaling axis.
Conclusion: While all NRAS mutants are capable of enhancing cellular proliferation versus wild-type NRAS, the melanomagenic potential of these mutants correlates with the ability to enhance activation of the RAS-MYC signaling axis

overall_design: RNA-Seq analysis MEFs expressing different Nras variants from the endogenous gene locus (Q61R, Q61H, Q61P, Q61Q)

first: Christin

last: Burd


title: Post-mitotic G1 phase survivin drives mitogen-independent cell divisions of B lymphocytes

status: Public on Apr 29 2022

city: Baltimore

first: Amit

last: Singh

state: MD

address: 251 Bayview Blvd, BRC, NIA-NIH

department: LMBI

institute: NIA-NIH

summary: The prevailing dogma is that renewed mitogenic signaling is essential to traverse G1 phase of the cell cycle after each division. B lymphocytes undergo multiple mitotic divisions, termed clonal expansion, to expand antigen-specific cells that mediate effective immunity. We explored mechanisms by which primary murine B lymphocytes make cell division decisions. We demonstrate that commitment to DNA replication _S phase_ programs B cells to divide multiple times in the absence of overt mitogenic signaling. The extent of division is limited by cell death rather than by return to quiescence, and circumventing cell death permits up to 4 rounds of division in 72h. Mitogen-independent cell cycle progression is driven by unique S- and G2/M- like characteristics of the G1 phase of cells that have divided once, such as, large cell size, low levels of p27, phosphorylated Rb and expression of G2/M markers survivin, Cenp-A and Aim1/Aurora B. Pharmacologic inhibition of survivin blocked G1 progression in a B cell line and in primary B cells undergoing mitogen-independent division. These observations indicate that, in contrast to textbook models of the cell cycle, B cells inherit a partially active G1 phase after cell division that permits them to move quickly to the next S phase in the absence of exogenous G1 progression signals. Our studies provide direct evidence for Pardee’s hypothesis that retention of features of G2/M in post-mitotic cells could trigger a second round of cell cycle progression. We propose that these mechanisms may assist in rapid cell division without differentiation that is required for clonal expansion in response to antigens.

overall_design: RNA-seq from mouse splenic B cells. Naïve, activated and not-divided vs activated and divided

first: Matthew

last: Spitzer

first: Jaimy

middle: P

last: Joy

first: Mary

last: Kaileh

first: Xiang

last: Qiu

first: Garry

last: Nolan

first: Ranjan

last: Sen


title: H3K27ac BL HiChIP and GRID-seq data of LW and MS

city: Wuhan

first: Shuhong

last: Zhao

address: No. 1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: For Large White (LW) and Meishan (MS) skeletal muscle, we performed H3K27ac BL HiCHIP to establish enhancer-promoter interaction maps. We also performed GRID-seq which uses a bivalent linker to ligate RNA to DNA in situ.

overall_design: H3K27ac anchored chromatin-chromatin interaction and RNA-chromatin interactome of LW and MS skeletal muscle.

first: Liangliang

last: Fu

first: Xiaolong

last: Qi

first: Jingjin

last: Li

first: Lu

last: zhang

first: Yue

last: Xiang

first: Peng

last: Zhou

first: Zhuqing

last: Zheng

first: Qiulin


title: Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

city: Stanford

first: Winston

last: Becker

state: CA

address: 1291 Welch Road, B259 Beckman Center

department: Genetics

institute: Stanford University


title: Effect of cancer cell knockdown of EphB4 in a Moc2 tumor model

city: Aurora

first: Sana

last: Karam

state: CO

address: 1665 Aurora Court Suite 1032

institute: University of Colorado Denver Anschutz Medical Campus

summary: To investigate the functional significance of EphB4, we generated cancer cell-specific knockdown of EphB4 in a head and neck cancer cell line, Moc2, using shRNA approach. These cells along with the controls were orthotopically implanted in a C57BL/6 murine model and tumors for harvested for RNA-seq analysis

overall_design: To compare the gene expression profiling of RNA-Seq data for Moc2 control sh, and Moc2 EphB4 sh tumors

middle: D


title: The long noncoding RNA ADIPINT is a gatekeeper of pyruvate carboxylase function regulating human fat cell metabolism

city: Huddinge

first: hui

last: Gao

address: Novum

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary: The pleiotropic function of long noncoding RNAs (lncRNAs) is well recognized, but their direct role in governing metabolic homeostasis is less understood. Here, we describe a human adipocyte-specific lncRNA, ADIPINT, that regulates pyruvate carboxylase (PC), a pivotal enzyme in energy metabolism. With a novel approach, Targeted RNA-protein identification using Orthogonal Organic Phase Separation (TROOPS), and validation with electron microscopy, we show that ADIPINT binds to PC. ADIPINT knockdown alters the interactome and decreases the abundance and enzymatic activty of PC in the mitochondria. Reduced ADIPINT or PC expression lowers adipocyte lipid synthesis, breakdown, and lipid content.

overall_design: Knockdown of ADIPINT was carried out on day 8 of differentiation (when the cells showed adipocyte features), using a Neon™ transfection system MPK5000 (Invitrogen) with 2 pulses of 710 ms at 1300 V. Details of the Antisense LNA GapmeRs (Qiagen) used for ADIPINT knockdown and control conditions are following: GapmeR_1: TCTTGATTGCTGCAGA; GapmeR_2: TACTTTGCCTCTTAGA; GapmeR_3: CGAAGATTCATGGTCA; GapmeR NC: Negative Control A (Cat#  LG00000002). Cell viability was assessed using Alamar blue fluorescence (ThermoFisher) as per manufacturers’ recommendations. All hADSC analyses were performed at day 13 of differentiation for RNA extraction. 4 replicates for each Gapmer and 7 replicates for the sicontrol group.   Total RNA was extracted for microarray analysis.

first: Alastair

last: Kerr

first: Hui


title: Transcriptomic analysis of peripheral blood mononuclear cells (PBMC) in psoriasis patients treated with guselkumab

status: Public on Apr 27 2022

city: Shanghai

first: Ning

last: Yu

state: Shanghai

address: Baode Road 1278

institute: Shanghai Skin Disease Hospital

summary: Psoriasis is a worldwide chronic inflammatory skin disease. The treatment is usually designed according to its severity. In this research, RNA-seq was performed on the peripheral blood mononuclear cells (PBMCs) of 12 patients with psoriasis before and after treatment (4 week) of guselkumab.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for peripheral blood mononuclear cells (PBMCs) from 12 psoriasis patients, before and 4 weeks after treatment of gulselkumab

first: Jiajing

last: Lu

first: Yuling

last: Shi


title: Analysis of Age-Dependent Transcriptomic Changes in Response to Intracerebral Hemorrhage in Mice

city: Chongqing

first: Xinhui

address: NO1 Youyi Road, Yuzhong District

institute: Chongqing Medical University

summary:
To investigate  age-dependent transcriptomic changes between young or aged intracerebral hemorrhage mice, we established collagenase IV-induced intracerebral hemorrhage mice models.
Intracerebral hemorrhage was induced by infusion of sterile collagenase IV in ipsilateral caudate putamen of brain. We then performed gene expression profiling analysis using data obtained from RNA-seq of brain perihematomal tissues from young or aged ICH mice 24 hours after intracerebral hemorrhage.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for young or aged intracerebral hemorrhage mice and their corresponding sham controls.


title: Low-dose anti-HIV drug efavirenz mitigates retinal vascular lesions in a mouse model of Alzheimer's disease

city: Cleveland

first: David

last: Buchner

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: A small dose of the anti-HIV drug efavirenz (EFV) was previously discovered to activate CYP46A1, a cholesterol-eliminating enzyme in the brain, and mitigate some of the manifestation of Alzheimer’s disease in 5XFAD mice. Herein, we investigated the retina of these animals, which were found to have genetically determined retinal vascular lesions associated with deposits within the retinal pigment epithelium and subretinal space. We established that EFV treatment activated CYP46A1 in the retina, enhanced retinal cholesterol turnover, and diminished the lesion frequency >5-fold. In addition, the treatment mitigated fluorescein leakage from the aberrant blood vessels, deposit size, activation of retinal macrophages/microglia, and focal accumulations of amyloid b plaques, unesterified cholesterol, and Oil Red O-positive lipids. Studies of retinal transcriptomics and proteomics identified biological processes enriched with differentially expressed genes and proteins. We discuss the mechanisms of the beneficial EFV effects on the retinal phenotype of 5XFAD mice. As EFV is an FDA-approved drug, and we already tested the safety of small-dose EFV in patients with Alzheimer’s disease, our data support further clinical investigation of this drug in subjects with retinal vascular lesions or neovascular age-related macular degeneration.

overall_design: RNA-Seq expression analysis of efavirenz treated vs control retina in 5XFAD mice

first: Nicole

last: El-Darzi

middle: A

first: Irina

last: Pikuleva


title: Long-term changes in adipose tissue gene expression following bariatric surgery

summary: In order to identify mechanisms underlying the long-term beneficial effect of bariatric surgery on abdominal subcutaneous WAT, we performed gene microarray analyses on adipose tissue from a cohort of obese women. Adipose tissue biopsies were obtained before RYGB, and then 2 and 5 years thereafter. To evaluate the long-term effect of  Roux-en-Y gastric bypass (RYGB) surgery on WAT, we also compared the WAT gene expression at 5 years postsurgery with that of age-matched nonoperated women.

overall_design: Transcriptomic profiling by gene microarray was performed in abdominal subcutaneous WAT from women before (n = 50) and two (n = 49) and five (n = 38) years after Roux-en-Y gastric bypass (RYGB) surgery as well as in 28 age-matched nonoperated women.

first: Ingrid

last: Dahlman


title: Genome-wide CRISPR Knockout Screen Identified PLAC8 as an Essential Factor for SADS-CoVs Infection

city: Chapel Hill

first: Rita

last: Meganck

state: North Carolina

address: 135 Dauer Drive

department: Epidemiology

institute: UNC Chapel Hill

summary: Zoonotic transmission of coronaviruses poses an ongoing threat to human populations. Endemic outbreaks of Swine Acute Diarrhea Syndrome Coronavirus (SADS-CoV) have caused severe economic losses in the pig industry and have the potential to cause human outbreaks. Currently, there are no vaccines or specific antivirals against SADS-CoV, and our limited understanding of SADS-CoV host entry factors could hinder prompt responses to a potential human outbreak. Using a genome-wide CRISPR knockout screen, we identified placenta-associated 8 protein (PLAC8) as an essential host factor for SADS-CoV infection. Knockout of PLAC8 abolished SADS-CoV infection, which was restored by complementing PLAC8 from multiple species, including human, rhesus macaques, mouse, pig, pangolin, and bat, suggesting a conserved infection pathway and susceptibility of SADS-CoV among mammals. Mechanistically, PLAC8 knockout does not affect viral entry; rather, knockout cells displayed a delay and reduction in viral subgenomic RNA expression. In a swine primary intestinal epithelial culture (IEC) infection model, differentiated cultures have high levels of PLAC8 expression and support SADS-CoV replication. In contrast, expanding IEC have low levels of PLAC8 expression and are resistant to SADS-CoV infection. PLAC8 expression patterns translate in vivo; immunohistochemistry of swine ileal tissue revealed high levels of PLAC8 protein in neonatal compared to adult tissue, mirroring the known SADS-CoV pathogenesis in neonatal piglets. Overall, PLAC8 is an essential factor for SADS-CoV infection and may serve as a promising target for antiviral development for the potential pandemic SADS-CoV virus.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Huh7.5 cells and its PLAC8 KO derivative, with or without SADS-CoV infection.

first: Long

last: Tse

first: Ralph

middle: S

last: Baric


title: Transcriptome response of murine alveolar epithelial cells to infection by three unrelated respiratory viruses commonly studied in mouse models II

status: Public on Apr 26 2022

city: Moscow

first: James

middle: Theodore

last: Van Leuven

state: ID

address: 709 S Deakin St

department: Center for Modeling Complex Interactions

institute: University of Idaho

summary: Rhinoviruses (RV) have been shown to inhibit subsequent infection by heterologous respiratory viruses, including influenza viruses and severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). To better understand the mechanisms whereby RV protects against pulmonary coronavirus infection, we used a native murine virus, mouse hepatitis virus strain 1 (MHV-1), that causes severe disease in the lungs of infected mice. We found that priming of the respiratory tract with RV completely prevented mortality and reduced morbidity of a lethal MHV-1 infection. Replication of MHV-1 was reduced in RV-primed mouse lungs although type I interferon (IFN-b) expression was more robust in mice infected with MHV-1 alone. We further showed that type I IFN signaling was required for survival of mice given a non-lethal dose of MHV-1. RV-primed mice had reduced pulmonary inflammation and hemorrhage and influx of leukocytes, especially neutrophils, in the airways. RV-mediated priming in the respiratory tract protects against a lethal pulmonary coronavirus infection in mice. This model can be used to understand how heterologous viruses impact each other during coinfection of the respiratory tract.

overall_design: Microarray analysis of mouse epithelial cells infected by combinations of three viruses. Infections done in triplicate. RNA extracted at 12 and 24 hours post infection.

first: Tanya

last: Miura

middle: T


title: Zfp281 inhibits the pluripotent-to-totipotent state trasition in mouse embryonic stem cells

city: HangZhou

first: hao

last: wu

address: YuHang street

institute: Zhejiang University

summary: We perform RNA-seq in sgZfp281/sgSV40 mESC to investigate the effect of Zfp281 during 2CLC transition.

overall_design: mRNA profile of sgZfp281/sgSV40 mESC within/without DOX

first: Xinpeng

last: Wen

first: Zesong

last: Lin

first: Hao

last: Wu

first: Lanrui

last: Cao

first: Xudong

last: Fu


title: Single-cell assay examining chromatin accessibility reveals transcriptional regulatory variation in the proinflammatory milieu of uremia

city: Guangzhou

first: Hongwei

address: Jinan University, No.601, West Huangpu Avenue ,Guangzhou, Guangdong, China

institute: Jinan University

summary: A single-cell assay for transposase-accessible chromatin with high-throughput sequencing (scATAC-seq) was applied to compare the single-cell chromatin accessibility profiles of peripheral blood mononuclear cells (PBMCs) that were obtained from healthy volunteers and uremia patients. Besides, we further revealed the biological functions and regulatory modes of the uremia-related transcription factors (TFs). We principally identified 8 leukocytic clusters using promoter sums of cell type-specific marker genes. Representative TF motifs related to immune cell phenotype identification were found. The comparison of cells from uremia patients and healthy individuals revealed differential candidate TF motifs driving the uremia-associated transcriptomic signature changes, thereby resulting in variation of multiple immune-inflammatory pathways, virus infection-related pathways, and tumor-associated pathways.Our findings reveal transcriptional regulatory variation in uremia-derived PBMCs from an epigenetic perspective, providing a foundational framework for studies examining proinflammatory mechanisms in uremia and establishing a foundation for future research investigating epigenetic therapy.

overall_design: Single-cell chromatin accessibility (scATAC) profiles of human peripheral blood mononuclear cells in the uremia milieu

first: Haiyan

last: Yu

first: Yong

last: Dai


title: p53-specific transcriptome under starvation

city: Graz

first: Andreas

last: Prokesch

state: Styria

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology, and Embryology

country: Austria

institute: Medical University Graz

summary: Signaling trough cytoplasmic or nuclear action of p53 is a major response mechanism to cellular stresses. Here we perform transcriptomics after p53 re-expression on a CRISPR/Cas9 knock out background to reveal a distinct starvation-specific transcriptome response and novel nutrient-dependent p53 target genes.

overall_design: In HepG2 cells, wild-type p53 was knocked out using CRISPR-Cas9. Cells were kept for 48 hours in normal growth medium (MC-medium change) or starvation medium (STV), 3 days after electroporation with p53-expression vector or empty vector (EV) as control.

first: Ellen

last: Heitzer


title: Gene expression comparison between yeast histone H2B WT and H2B R95A mutant without and with rapamycin treatment.

status: Public on Apr 25 2022

city: Doha

first: Dindial

last: Ramotar

state: Qatar

address: Education City, Qatar Foundation

department: Division of Biological and Biomedical Sciences, College of Health and Life Sciences

country: Qatar

institute: Hamad Bin Khalifa University

summary:
This microarray data is the Affymetrix array of RNA expressed by Wild Type and Mutant strains yeast that is untreated and treated with rapamycin.
In yeast, rapamycin inhibits the TORC1 kinase signaling pathway causing rapid alteration in gene expression and ultimately cell cycle arrest in G1 and this study provides a new insight whereby rapamycin signaling via the Torc1 kinase may exploit the pheromone pathway.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Wild Type and Mutant Yeast cultures were either untreated or treated with rapamycin and extracted using the hot phenol extraction protocol. Microarray analysis was performed using Affymetrix GeneChip® and the data was normalized using robust multi-array average (RMA) with FlexArray tool.


title: Tumor-associated and control mammary adipose tissue in lean and high fat diet-induced obese mice

city: Gothenburg

first: Ingrid

last: Wernstedt Asterholm

address: Box 432

institute: University of Gothenburg

summary: To investigate the crosstalk between a growing breast cancer tumor and adjacent adipose tissue, we set up an breast cancer mouse model and compared the gene expression between control and tumor-associated adipose tissue.

overall_design: Female mice, fed either regular chow or high fat diet for 16 weeks, were injected with E0771 cancer cells resuspended in PBS mixed with Matrigel into their left inguinal/mammary fat pad (tumor-associated inguinal adipose tissue) while their right inguinal fat pad (control inguinal adipose tissue) received PBS-Matrigel solution alone. Tumor-associated and control IWAT were collected two weeks after cancer cell injections.


title: Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome

city: Berlin

first: Lydia

last: Herzel

address: Takustr. 6

department: Biology, Chemistry and Pharmacy

institute: Freie Universität

summary: Bacterial mRNAs have short life cycles, in which transcription is rapidly followed by translation and degradation within seconds to minutes. The resulting diversity of mRNA molecules across different life-cycle stages impacts their functionality but has remained unresolved. Here we quantitatively map the 3’ status of cellular RNAs in Escherichia coli during steady-state growth and report a large fraction of molecules (median>60%) that are fragments of canonical full-length mRNAs. The majority of RNA fragments are decay intermediates, whereas nascent RNAs contribute to a smaller fraction. Despite the prevalence of decay intermediates in total cellular RNA, these intermediates are underrepresented in the pool of ribosome-associated transcripts and can thus distort quantifications and differential expression analyses for the abundance of full-length, functional mRNAs. The large heterogeneity within mRNA molecules in vivo highlights the importance in discerning functional transcripts and provides a lens for studying the dynamic life cycle of mRNAs.

sample_organism:
Escherichia coli
Bacillus subtilis
synthetic construct

overall_design: Nascent, total and polysome-associated RNA profiles by RNA sequencing with Illumina HiSeq and NextSeq technology.

first: Julian

last: Stanley

first: Gene-Wei

last: Li


title: The 3' Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies’ association with histone locus bodies

city: Yokohama

first: Hidefumi

last: Suzuki

address: Fukuura 3-9

institute: Yokohama City University

summary: The non-polyadenylated mRNAs of replication-dependent histones (RDHs) and small nuclear RNAs (snRNAs) are synthesized by RNA polymerase II at histone locus bodies (HLBs) and Cajal bodies (CBs), respectively. We previously showed that MED26-containing Mediator regulates the 3'-end processing of non-polyadenylated transcripts by recruiting Little Elongation Complex (LEC) to the genes. HLBs frequently associate with CBs, in which 3'-end processing factors for RDH genes are enriched; however, this association’s role has not been elucidated. Here, we show that disruption of the Mediator docking site for LEC by mutating the MED26-binding site of EAF1, a subunit of LEC, interferes with CBs’ association with HLBs, resulting in decreased inter-chromosome interaction between RDH gene clusters and increased aberrant unprocessed RDH gene transcripts. Our findings suggest a model in which LEC recruitment by Mediator plays a role in CBs’ association with HLBs to facilitate the 3'-end processing of RDH genes by supplying 3'-end processing factors.

overall_design: Experiment 1: RNA-seq of ribosome RNA-depleted libraries prepared from HEK293T WT and EAF1-mutant cells. Experiment 2: PRO-seq in HEK293T WT and EAF1-mutant cells using D. melanogastor S2 cells as spike-in control. Experiment 3: ELL ChIP-seq in HEK293T WT cells. Experiment 4: 4C-seq in HEK293T WT and EAF1-mutant cells. Experiment 5: Coilin antibody-based in situ biotinylation-seq in HEK293T WT and EAF1-mutant cells using D. melanogastor S2 cells as spike-in control. Experiment 6: PRO-seq in siRNA-transfected HEK293T cells using D. melanogastor S2 cells as spike-in control. Experiment 7: PRO-seq in HEK293T WT and MED26-mutant cells using D. melanogastor S2 cells as spike-in control. Experiment 8: PRO-seq in alpha-amanitin-treated HEK293T cells. The read counts were normalized with million rRNA reads.

first: Ryota

last: Abe

first: Yutaka

first: Atsushi

last: Toyoda

first: Hidehisa

last: Takahashi


title: Gene Regulation Dynamics during the Cell Cycle uncovered by RNA velocity and deep-learning

city: Illkirch

first: Andrea

last: Riba

address: 1 rue Laurent Fries

country: France

institute: IGBMC

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene Regulation Dynamics during the Cell Cycle uncovered by RNA velocity and deep-learning (mESCs)

summary: Investigation of the cell cycle regulations in mouse embryonic stem cells (mESCs)

overall_design: mESC

first: Attila

last: Oravecz

first: Nacho

last: Molina


title: Gene Regulation Dynamics during the Cell Cycle uncovered by RNA velocity and deep-learning (IMR90)

summary: Investigation of the cell cycle regulations in human fibroblasts (IMR90)

overall_design: Human fibroblast

first: Matej

last: Durik

first: Bill

last: Keyes


title: The metastatic spread of breast cancer accelerates during sleep

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

institute: ETH Zurich

summary: The metastatic spread of cancer is achieved by the haematogenous dissemination of circulating tumour cells (CTCs). Generally, however, the temporal dynamics that dictate the generation of metastasis-competent CTCs are largely uncharacterized, and it is often assumed that CTCs are constantly shed from growing tumours or are shed as a consequence of mechanical insults1. Here we observe a striking and unexpected pattern of CTC generation dynamics in both patients with breast cancer and mouse models, highlighting that most spontaneous CTC intravasation events occur during sleep. Further, we demonstrate that rest-phase CTCs are highly prone to metastasize, whereas CTCs generated during the active phase are devoid of metastatic ability. Mechanistically, single-cell RNA sequencing analysis of CTCs reveals a marked upregulation of mitotic genes exclusively during the rest phase in both patients and mouse models, enabling metastasis proficiency. Systemically, we find that key circadian rhythm hormones such as melatonin, testosterone and glucocorticoids dictate CTC generation dynamics, and as a consequence, that insulin directly promotes tumour cell proliferation in vivo, yet in a time-dependent manner. Thus, the spontaneous generation of CTCs with a high proclivity to metastasize does not occur continuously, but it is concentrated within the rest phase of the affected individual, providing a new rationale for time-controlled interrogation and treatment of metastasis-prone cancers.

overall_design: We isolated live circulating tumor cells (CTCs) from a breast cancer patient (number of CTCs = 36) and two breast cancer xenografts, NSG-CDX-BR16 (number of CTCs = 138) and NSG-LM2 (number of CTCs = 108) at different time points. Isolated CTCs were categorized into three different types : single CTC, CTC clusters and CTC-white blood cells (CTC-WBC) clusters. Amplified cDNA was prepared according to the Smart-seq2 protocol. Libraries were prepared using with Nextera XT (Illumina) and sequenced on Illumina NextSeq500 instrument in 75-bp single-read mode.

first: Zoi

last: Diamantopoulou

first: Fabienne

last: Schwab

first: Karin

last: Strittmatter

first: Ilona

last: Krol

first: Massimo

last: Saini

first: Selina

last: Budinjas

first: Marcus

last: Vetter

first: Christoph

last: Rochlitz

first: Christian

last: Kurzeder

first: Viola

last: Heinzelmann-Schwarz

first: Nicola

last: Aceto


title: Epigenomic analysis of eating disorders in children and adolescents of Mexican ancestry

city: Mexico City

first: José Jaime

last: Martínez Magaña

state: Mexico City

address: Av. Insurgentes Sur 3877, La Fama, Tlalpan,

country: Mexico

institute: Instituto Nacional de Medicina Genómica

summary: This study included whole-genome DNA methylation data from 64 whole-blood samples from patients recruited from the Hospital Psiquiatrico Infantil Juan N. Navarro in Mexico City. The project explored epigenetic changes associated with eating disorders in children and adolescents from a Mexican population.

overall_design: Bisulfite converted DNA from the 64 samples into the Illumina Infinium MethylationEPIC. The arrays' fluorescence intensity was processed with the GenomeStudio and transformed to idat files.

first: Humnerto

last: Nicolini

first: Alma

last: Genis Mendoza

first: José


title: Identification of metabolic pathways differentially regulated in somatic and zygotic embryos of maritime pine

status: Public on Apr 24 2022

city: Malaga

first: Vanessa

middle: Viviana

last: Castro Rodriguez

state: Malaga

address: Universidad de Malaga

country: Spain

institute: Universidad de Malaga

summary: Analysis of the transcriptome of developing somatic and zygotic embryos from maritime pine.

overall_design: Developing embryos samples from three somatic stages of line PN519 and three zygotic stages of pinus pinaster were isolated for the RNA-seq analyses.

first: Concepción

last: Avila

first: Maria

last: Llebres

last: Castro-Rodriguez

first: Cesar

last: Lobato-Fernandez

first: Jean-Francois

last: Trontin

first: Luc

last: Harvengt

first: Francisco

last: Canovas


title: LCL Capture-C

city: Oxford

first: Julia

last: Truch

address: John Radcliffe Hospital, Headley Way, Headington

department: RDM - WIMM

country: United Kingdom

institute: University of Oxford

summary: The chromatin remodeller ATRX interacts with the histone chaperone DAXX, to deposit the histone variant H3.3 at sites of nucleosome turnover. ATRX is known to bind repetitive, heterochromatic regions of the genome including telomeres, ribosomal DNA and pericentric repeats many of which are putative G-quadruplex forming sequences (PQS). At these sites ATRX plays an ancillary role in a wide range of nuclear processes facilitating replication, chromatin modification and transcription.  Here, using an improved protocol for chromatin immunoprecipitation, we show that ATRX also binds active regulatory elements in euchromatin. Mutations in ATRX lead to perturbation of gene expression associated with a reduction in chromatin accessibility, histone modification, transcription factor binding and deposition of H3.3 at the sequences to which it normally binds. In erythroid cells where down regulation of a-globin expression is a hallmark of ATR-X syndrome, perturbation of chromatin accessibility and gene expression occurs in only a subset of cells. The stochastic nature of this process suggests that ATRX acts as a general facilitator of cell specific transcriptional and epigenetic programmes, both in heterochromatin and euchromatin.

overall_design: To identify regulatory interactions at ATRX binding sites, we performed high resolution chromatin conformation capture (3C) using NG CaptureC (Davies 2016). NG CaptureC was performed in human lymphoblastoid cell lines derived from three unaffected donors and three patients with ATR-X syndrome. Capture was performed with biotinylated oligonucleotides targeting sequences adjacent to DpnII sites.

first: Damien

last: Downes


title: single cell RNA-seq

overall_design: Individuals with exactly the same mutation in the ATRX gene can have variable degrees of a-thalassaemia. This suggests that a-globin gene expression may not be affected in the majority of erythroid cells in ATR-X syndrome and that the presence of a-thalassaemia may be variable even with the same underlying mutation. To determine if there might be cellular heterogeneity in a-globin gene expression we performed single cell RNA-seq (scRNA-seq) on day10 of  CD34+ Haematopoietic Stem Cells differentiation derived from one ATR-X case with a-thalassaemia and one unaffected donor.

first: Caroline

last: Scott


title: Two steps cross-linking LCL ChIP-seq

overall_design: To identify the binding sites of ATRX and runx3, ChIP-seq was carried out on lymphoblastoid cell lines.


title: Association of gene expression with Creatine Riboside, A Prognostic Metabolite of Metabolome Imbalance in the NCI-MD Non-Small Cell Lung Cancer Cohort

city: Bethesda

first: Josh

last: Stone

address: 9000 Rockville Pike

department: CCR

institute: National Cancer Institue

summary: The metabolic dependencies of cancer cells have significant potential to be exploited to improve the diagnosis and treatment of cancer. Creatine riboside (CR) is a novel urinary metabolite associated with risk and prognosis in lung and liver cancer. However, the source of high creatine riboside levels in cancer patients, as well as its implications for the treatment of these aggressive cancers remain unclear.   By integrating RNA sequencing and whole exome sequencing of non-small cell lung cancer tissues we sought to understand the source of creatine riboside and the tumor biology associated with this novel metabolite. Utilising multiple lung and liver cancer cohorts, next generation sequencing data was combined with global metabolomics analysis of human tumors, and matched liquid biopsies together with functional studies to reveal that dysregulation of the mitochondrial urea cycle and nucleotide imbalance are associated with high creatine riboside levels and are indicators of poor prognosis. Creatine riboside-high cancer cells were auxotrophic for arginine, revealing a metabolic vulnerability that may be exploited therapeutically. This highlights the potential of creatine riboside not only as a poor prognosis biomarker but also as a companion biomarker to inform the administration of arginine-targeted therapies in precision medicine strategies to improve cancer patient survival.

overall_design: non-small cell lung cancer tissues were analysed by RNA sequencing.

first: Curtis

middle: C

last: Harris

first: Mohammed

last: Khan

first: Amelia

last: Parker


title: two steps cross-linking ChIP-seq

overall_design: To identify the binding sites of ATRX and GATA1, ChIP-seq was carried out at day10 of  CD34+ Hematopoietic Stem Cells differentiation.


title: Capture-C

overall_design: To identify regulatory interactions at ATRX binding sites, we performed high resolution chromatin conformation capture (3C) using NG CaptureC (Davies 2016). NG CaptureC was performed in Day 10 differentiating erythroid (Ery) cells from two unaffected donors and two patients with ATR-X syndrome. Capture was performed with biotinylated oligonucleotides targeting sequences adjacent to DpnII sites.


title: Erythroblasts


title: YTHDF2 suppresses the plasmablast genetic program and promotes germinal center formation

city: Rehovot

first: Ziv

last: Shulman

address: Herzl St 234

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Antibody-mediated immunity is initiated by B cell interactions with cognate antigen, followed by differentiation into multiple cell subsets, including plasmablast, memory, and germinal center (GC) cells. B cell differentiation trajectories are determined by specific transcription factors, yet very few mechanisms that determine B cell fate at the early stage of the response have been described. Here, we report an epigenetic mechanism that specifically suppresses the plasmablast genetic program and promotes GC B cell fate commitment. Single-cell RNA-seq analysis of antigen-specific B cells revealed activated B cell precursors at the pre-GC stage that express high levels of RNA binding proteins, including YTHDF2, which enhances the decay of methylated transcripts. Ythdf2-deficient B cells exhibited intact proliferation and upregulation of early activation markers in response to antigenic stimulation, whereas differentiation into GC B cells was blocked. Mechanistically, B cells required YTHDF2 to attenuate the plasmablast genetic program during GC seeding, and key transcripts of plasmablast-related genes, including Irf4 and Xbp1, were methylated and bound by YTHDF2. Modulation of YTHDF2-dependent gene expression by YTHDF1 and YTHDF3 was less pronounced, and no functional redundancy of these paralogs in GC seeding was observed. Collectively, this study reveals a novel epigenetic mechanism that specifically directs appropriate B cell fate commitment through post-transcriptional suppression of gene expression.

overall_design: Bulk and single-cell RNAseq of WT/CD23cre and Ythdf2 cKO B18-hi B cells, five days after immunization

first: Amalie

last: Grenov

first: Hadas

last: Hezroni


title: single step cross-linking ChIP-seq

overall_design: To characterize the epigenetic landscape and identify the chromatin modifications associated with ATRX binding sites, ChIP-seq was carried out at day10 of  CD34+ Hematopoietic Stem Cells differentiation. CD34+ Hematopoietic Stem Cells were differentiated from unaffected donors or ATR-X patients.


title: Osteocyte CIITA Aggravates Osteolytic Bone Lesions in Myeloma

status: Public on Apr 23 2022

city: Houston

first: Jing

last: Yang

address: 6550 Fannin St

institute: Houston Methodist Research Institute

summary: Osteolytic destruction is a hallmark of multiple myeloma, resulting from activation of osteoclast  mediated bone resorption and reduction of osteoblast-mediated bone formation. However, the  molecular mechanism underlying the differentiation and activity of osteoclasts and osteoblasts  within a myelomatous microenvironment remains unclear. Here, we demonstrate that the  osteocyte-expressed major histocompatibility complex class II transactivator (CIITA) contributes  to myeloma-induced bone lesions. CIITA upregulates the secretion of osteolytic cytokines from  osteocytes through acetylation at histone 3 lysine 14 in the promoter of TNFSF11 (encoding  RANKL) and SOST (encoding sclerostin), leading to enhanced osteoclastogenesis and decreased  osteoblastogenesis. In turn, myeloma cell–secreted 2-deoxy-D-ribose, the product of thymidine  catalyzed by the function of thymidine phosphorylase, upregulates CIITA expression in  osteocytes through the STAT1/IRF1 signaling pathway. Our work thus broadens the  understanding of myeloma-induced osteolysis and indicates a potential strategy for disrupting  tumor-osteocyte interaction to prevent, or treat patients with, myeloma bone disease.

overall_design: Define a heretofore unrecognized role for osteocytes in genesis of myeloma-associated bone disease

first: Huan

last: Liu

first: Jin

last: He

first: Rozita

last: Bagheri-Yarmand

first: Zongwei

last: Li

first: Rui

first: Zhiming

last: Wang

first: Duc-hiep

last: Bach

first: Yung-hsing

last: Huang

first: Pei

last: Lin

first: Theresa

last: Guise

first: Robert

middle: F

last: Gagel


title: Epithelial-derived exosomes promote M2 macrophage polarization via Notch2/SOCS1 during mechanical ventilation

city: Wuhan

first: Yan

middle: Ting

state: Hubei

address: 1277 Jiefang Avenue, Kong Hon District

department: Department of Anesthesiology, Union Hospital, Tongji Medical College

institute: Huazhong University of Science and Technology

summary: To explore the downstream mechanisms of Notch2 induced M2 macrophage polarization during mechanical ventilation, the BMDMs-treated with exosomes for non-cyclical-stretched or cyclical-stretced epithelial cells for 12 h  were subjected to RNA-seq.

overall_design: Epithelial cells were cyclically stretched for 6 h or non-cyclically stretched. BMDMs were treated with exosomes (100 μg/ml) for non-cyclical-stretched or cyclical-stretced epithelial cells for 12 h.

first: Yanting

first: Zhenzhen

last: Xu

first: Yuyao


title: ChIP-seq of OsLEC1

city: Hangzhou

first: Fu

last: Guo

address: Yuhangtang Road 866

summary: Genome-wide identification of OsLEC1 binding sites was to find the OsLEC1 directly bound genes

overall_design: Examination of OsLEC1-binding genes using the callus of NIP and 35S:3*FLAG-OsLEC1

first: Hongwu

last: Bian

first: Peijing

last: Zhang

last: Wu


title: Detect-seq on transfected HEK293T cells [Detect-seq data]

status: Public on Apr 22 2022

city: Beijing

first: Hua-nan

last: Zhao

state: Beijing

address: 5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

summary: We used a new technology, named Detect-seq, to perform genome sequencing on transfected HEK293T cells to see DdCBEs' off-target mutations. Besides, targeted-amplicon sequencing and ATAC-seq data were applied to validate the results of Detect-seq.

overall_design: We applied DdCBEs to generate on-target editings on mt-DNA to see DdCBEs' editing performance and evaluate their effects on the whole mitochondrial genome. This is the Detect-seq part. Detect-seq utilized a dU-mapping strategy to profile on-target and off-target editing events by DdCBE at the whole-genome level.

first: Zhixin

last: Lei

first: Haowei

last: Meng

first: Lulu

first: Huanan


title: Study of three-dimensional structure of chromatin through a 4C-seq experiments in mouse

status: Public on Apr 21 2022

city: Barcelona

first: Marta

last: Vicioso Mantis

address: Carrer Baldiri Reixac, 15

institute: IBMB-CSIC

overall_design: Refer to individual Series


title: LCL ATAC-seq

first: Julia

last: Truch

overall_design: To characterise the epigenetic landscape and identify the nucleosome depleted regions associated with ATRX binding sites, ATAC-seq was carried out on lymphoblastoid cell lines derived from unaffected donors or ATR-X patients.


title: RIViTseq enables systematic identification of regulons of transcriptional machineries II

city: Berkeley

first: Hiroshi

last: Otani

address: 1 Cyclotron Road

department: DOE Joint Genome Institute

institute: Lawerence Berkeley National Laboratory

summary: Transcriptional regulation is a critical process to ensure expression of genes necessary for growth and survival in diverse environments. Transcription is mediated by multiple transcriptional factors including activators, repressors and sigma factors. Accurate computational prediction of the regulon of target genes for transcription factors is difficult and experimental identification is a laborious process and not scalable. Here, we demonstrate a new technology, RIViTseq, that enables systematic identification of regulons of transcription factors by combining an in vitro transcription assay and RNA-sequencing. Using this technology, target genes of 11 sigma factors were identified in Streptomyces coelicolor A3(2). The RIViTseq data expanded the transcriptional regulatory network in this bacterium, discovering new regulatory cascades and crosstalk between sigma factors. Implementation of RIViTseq with other transcription factors and in other organisms will improve our understanding of transcriptional regulatory networks across biology.

overall_design: RNA samples were prepared by incubating a mixture of a purified sigma factor, E. coli RNA polymerase core enzyme (NEB), digested genomic DNA and NTPs for 15 minutes at 30ºC. ERCC RNA Spike-in Mix was added as normalisation controls, genomic DNA was digested by DNase, and RNA samples were purified and sequenced on 6000 Sequencing System (Illumina) by paired-end 2 x 150 bp sequencing.

first: Nigel

last: Mouncey


title: SpotClean adjusts for spot swapping in spatial transcriptomics data

city: Madison

first: Zijian

last: Ni

address: 425 Henry Mall

institute: University of Wisconsin-Madison

summary: Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. We conduct chimeric experiments to evaluate the spot swapping effect in 10x Visium spatial transcriptomics protocol. We propose SpotClean to adjust for spot swapping and, in doing so, to increase the sensitivity and precision with which downstream analyses are conducted.

overall_design: Visium spatial transcriptomics experiments of three human and mouse chimeric samples

first: Aman

last: Prasad

first: Shuyang

last: Chen

first: Richard

last: Halberg

first: Lisa

last: Arkin

first: Beth

last: Drolet

first: Michael

last: Newton

first: Christina

last: Kendziorski


title: Detect-seq on transfected HEK293T cells [ATAC-seq data and in situ ChIP-seq data]

first: Howard

last: MENG

address: No.5 Yiheyuan Road Haidian District

summary: We used a new technology, named Detect-seq, to perform genome sequencing on transfected HEK293T cells to see DdCBEs' off-target mutations. Besides, targeted-amplicon sequencing, ATAC-seq and in situ ChIP-seq data were applied to validate the results of Detect-seq.

overall_design: We applied DdCBEs to generate on-target editings on mt-DNA to see DdCBEs' editing performance and evaluate their effects on the whole mitochondrial genome. These are the ATAC-seq part and in situ ChIP-seq part . ATAC-seq was performed as previously reported. 10,000 viable cells were pelleted, lysed and the genomic DNA was tagmented with 2.5μl self-assembled Tn5 transposase. The tagmented DNA was purified using the DNA Clean and Concentrator-5 Kit (Vistech) and eluted in 20μl ultrapure water. All 20μl eluate was amplified by 12 cycles in a total volume of 50μl and the final library was purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter). Low-input in situ ChIP was performed as previously described with minor modifications mentioned in our paper.

last: Liu


title: Study of three-dimensional structure of chromatin through a 4C-seq experiment in mouse NSC shControl and shJMJD3 upon TGFβ treatment [Chst8]

summary: In this study we analyzed how multiple enhancers arrange in the 3D-space to control the activation of a specific promoter. Specifically, we did a 4C-seq experiment on a ~374 Kb locus where enhancers abound, which revealed that the TGFβ pathway drives the establishment of contacts between cis-regulatory elements that facilitates the assembly of an enhancer-cluster and precise gene activation. We discovered that the TGFβ pathway coactivator JMJD3 is essential to maintain these 3D-structures, as when it is depleted the contacts are lost but they are restablished when re-expressing the protein. To do that, JMJD3 requires a proline-rich intrinsically disordered region, which is essential for proper gene activation due to its involvement in the formation of phase-separated biomolecular condensates. Overall, we uncover novel functions for the ubiquitous coactivator JMJD3, and we shed light on the relationships between the 3D-conformation of the chromatin, and their role in regulating the TGFβ-driven response during mammalian neurogenesis.

overall_design: 4C-seq of shControl and shJMJD3 was performed in NSCs non-treated or treated for three hours with TGFβ (in duplicates)

last: Vicioso-Mantis

first: Raquel

last: Fueyo

first: Claudia

last: Navarro

first: Sara

last: Cruz-Molina

first: Wilfred

last: van IJcken

first: Elena

last: Rebollo

first: Álvaro

last: Rada

first: Marian

last: Martínez-Balbás


title: Study of three-dimensional structure of chromatin through a 4C-seq experiment in mouse NSC shControl and shJMJD3 upon TGFβ treatment [Ldlrad4]

first: Marta

last: Vicioso Mantis

summary: In this study we analyzed how multiple enhancers arrange in the 3D-space to control the activation of a specific promoter. Specifically, we did three 4C-seq experiments on different genomic loci where enhancers abound - Chst8, Ldlrad4 and Aopep, which revealed that the TGFβ pathway drives the establishment of contacts between cis-regulatory elements. Furthermore, we discovered that the TGFβ pathway coactivator JMJD3 is essential to maintain these 3D-structures. Specifically, in the Chst8 locus JMJD3 requires a proline-rich intrinsically disordered region to properly induce these loops, and hence gene activation, due to its involvement in the formation of phase-separated biomolecular condensates. Overall, we uncover novel functions for the ubiquitous coactivator JMJD3, and we shed light on the relationships between the 3D-conformation of the chromatin, and their role in regulating the TGFβ-driven response during mammalian neurogenesis.


title: ATAC-seq

first: Julia

last: Truch

overall_design: To characterize the epigenetic landscape and identify the nucleosome depleted regions associated with ATRX binding sites, ATAC-seq was carried out at day10 of  CD34+ Hematopoietic Stem Cells differentiation. CD34+ Hematopoietic Stem Cells were differentiated from unaffected donors or ATR-X patients.

first: Damien

last: Downes

first: Matthew

last: Gosden

first: Caroline

last: Scott


title: SMYD5 catalyzes histone H3 lysine 36 trimethylation at promoters

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

summary: Histone mark, one carrier of epigenetic information, regulates the gene expression in cells. Studies have shown that H3K36me3 is mainly catalyzed by SETD2 to be deposited at gene body regions in mammalian cells. Here, we profile the distributions of H3K36me3 in native cells and uncover that H3K36me3 is also enriched at the promoters beyond the gene body regions. We identify SMYD5 as one methyltransferase responsible for the enrichment of H3K36me3 at promoters. Through RNA polymerase II, SMYD5 is recruited to chromatin to regulate H3K36me3 and gene expression. The enzymatic activity of SMYD5 is dependent on its C-terminal glutamic acid rich domain. Depletion of C-terminal domain reduces the reestablishment of H3K36me3 at promoters when Smyd5 is over-expressed in Smyd5 knockout cells. Furthermore, elevated Smyd5 expression contributes to the tumorigenesis of liver hepatocellular carcinoma. Together, our study reveals SMYD5 as the H3K36me3 methyltransferase at promoters to regulate the gene expression, providing important insights into the localization and function of H3K36me3.

overall_design: Examination of histone modifications and SMYD5 in mouse embryonic stem cells.

first: Yanjun

last: Zhang

first: Yuan

first: Yin

last: Tang


title: Single step cross-linking LCL ChIP-seq

overall_design: To characterise the epigenetic landscape and identify the chromatin modifications associated with ATRX binding sites, ChIP-seq was carried out on lymphoblastoid cell lines derived from unaffected donors or ATR-X patients.


title: single cell ATAC-seq

overall_design: Individuals with exactly the same mutation in the ATRX gene can have variable degrees of a-thalassaemia. This suggests that a-globin gene expression may not be affected in the majority of erythroid cells in ATR-X syndrome and that the presence of a-thalassaemia may be variable even with the same underlying mutation. To determine if there might be cellular heterogeneity associated with changes in chromatin accessibility we performed single-cell ATAC-seq (scATAC-seq) on day10 of CD34+ Hematopoietic Stem Cells differentiation derived from two ATR-X cases with a-thalassaemia and two unaffected donors.


title: LCL Bio-CAP-seq

overall_design: To characterise the epigenetic landscape and identify the metylation status of the CpG clusters associated with ATRX binding sites, Bio-CAP-seq (Blackledge et al., 2011) was carried out on lymphoblastoid cell lines derived from unaffected donors or ATR-X patients.


title: p63 Directs Subtype Specific Gene Expression in HPV+ Head and Neck Squamous Cell Carcinoma

status: Public on Apr 19 2022

city: Buffalo

first: Satrajit

last: Sinha

state: NY

address: 955 Main Street

institute: University at Buffalo

summary: Gene expression analysis of p63 knockdown in 2 HPV+ HNSCC cell lines using RNA-seq, Genomic profiling of p63 binding across 2 HPV+ HNSCC cell lines, Epigenomic landscape of 2 HPV+ HNSCC cell lines

overall_design: RNA was collected and analyzed for two biological replicated from two different HPV+ HNSCC cell lines using RNA-seq, p63 bound chromatin and chromatin associated with different epigenomic marks were collected and analized using ChIP-seq

first: Alexandra

last: Glathar

first: Akinsola

last: Oyelakin

first: Christian

last: Gluck

first: Jonathan

last: Bard


title: Expression data from human lymphoblastoid cell lines (LCLs)

summary:
The X-linked alpha thalassaemia intellectual disability syndrome (ATRX) protein is a member of the SWI/SNF family of chromatin remodelling factors which acts as an ATP dependent molecular motor. Germline mutations in ATRX give rise to a severe form of syndromal intellectual disability (ATR-X syndrome). To date, only a small number of genes have been identified that are affected by pathogenic ATRX mutations in human.
We performed microarray experiments on LCLs  from normal individuals and  patients with diverse pathogenic ATRX mutations, to identify more genes regulated by ATRX.

overall_design: We used 20 LCLs  from unaffected individuals and  28 LCLs from patients for RNA extraction and hybridization on Affymetrix microarrays.

first: Emmanouela

last: Repapi


title: RIViTseq enables systematic identification of regulons of transcriptional machineries I

first: Hiroshi

last: Otani

overall_design: RNA samples were prepared by incubating a mixture of a purified sigma factor, E. coli RNA polymerase core enzyme (NEB), digested genomic DNA and NTPs for 15 minutes at 30ºC. ERCC RNA Spike-in Mix was added as normalisation controls, genomic DNA was digested by DNase, and RNA samples were purified and sequenced on MiSeq System (Illumina) by paired-end 2 x 150 bp sequencing.

first: Nigel

last: Mouncey


title: The cellular origin and differentiation status of glioblastoma by scRNA-seq

city: Solna

first: Yizhou

last: Hu

state: Stockholm

address: C6 , Biomedicum Karolinska, Solnavägen 9,

institute: Karolinska Institute

summary: Understanding the cellular origin and differentiation status of glioblastoma is critical to resolve the etiology of the disease. we profile 18 patient glioblastomas by single cell RNA sequencing (scRNAseq). From this, we uncovered two principal cell-of-origin relations. Each lineage displays unique directional differentiation trajectories  and  transcriptional cores from the naïve cell populations. Thus, glioblastoma is defined by robust cell lineage features which may provide insights into the cell origin of the diseases.

overall_design:
Single cell RNA-seq study of human glioblastoma cells
*** The raw data has been deposited in the European Genome-phenome Archive (EGAS00001006236) due to patient privacy concerns***

first: Yiwen

last: Jiang

first: Mikael

last: Svensson

first: Oscar

last: Persson

first: Patrik

last: Ernfors


title: Single cell transcriptomics of human brain epileptic lesions identifies pro-inflammatory immune mechanisms based on interlacing cellular immune networks

status: Public on Apr 20 2022

city: Singapore

first: Pavanish

last: Kumar

state: Not Applicable

address: 20 collage road, The Academia, Discovery Tower, Level-8 Translation Immunology Institute (TII)

country: Singapore

institute: Translational Immunology Institute (TII), SingHealth-DukeNUS

summary: We analysed 85780 single cells from epileptic brain tissues using Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) to dissect the architecture of the immuno-transcriptome of the diseased epileptic human brain. dissect the architecture of the immuno-transcriptome of the diseased epileptic human brain.  Our approach uncovered in all patients, well organized pro-inflammatory microenvironment pivoting on activated, pro-inflammatory microglia in a closely-knit network where resident cells attract and manipulate in a pro-inflammatory fashion infiltrating innate and adaptive immune cells. These findings were corroborated by ligand-receptor interactome analysis, which demonstrated potential mechanisms of infiltration and by evidence of direct interactions between microglia and T cells likely contributing to pathogenesis.

overall_design:
Immune cells Isolated from human brain tissue from epilepsy Patients analyzed
----------------------------------------------------------------
Authors state "We are not allowed to deposit Human Patients sequence data to archives."

first: Salvatore

last: Albani

first: Derrick

last: Chan


title: Immune and epithelial determinants of age-related risk and alveolar injury in fatal COVID-19

city: New York

first: Stuart

last: Weisberg

address: 650 W 168th Street

department: Pathology and Cell Biology

institute: Columbia University

summary: Respiratory failure in COVID-19 is characterized by widespread disruption of the lung’s alveolar gas exchange interface. To elucidate determinants of alveolar lung damage, we performed epithelial and immune cell profiling in lungs from 24 COVID-19 autopsies and 43 uninfected organ donors ages 18-92 years. We found marked loss of type 2 alveolar epithelial (T2AE) cells and increased peri-alveolar lymphocyte cytotoxicity in all fatal COVID-19 cases, even at early stages before typical patterns of acute lung injury are histologically apparent. In lungs from uninfected organ donors, there is also progressive loss of T2AE with increasing age which may increase susceptibility to COVID-19 mediated lung damage in older individuals. In the fatal COVID-19 cases, macrophage infiltration differed according to the histopathological pattern of lung injury. In cases with acute lung injury, we found accumulation of CD4+ macrophages that express distinctly high levels of T-cell activation and co-stimulation genes and strongly correlate with increased extent of alveolar epithelial cell depletion and CD8 T-cell cytotoxicity. Together, our results show that T2AE deficiency may underlie age-related COVID-19 risk and initiate alveolar dysfunction shortly after infection; and we define immune cell mediators that may contribute to alveolar injury in distinct pathological stages of fatal COVID-19.

overall_design: 24 samples of formalin fixed paraffin embedded lung are analyzed in total including 7 from COVID-19 cases with acute lung injury, 7 from COVID-19 cases without acute lung injury and 10 uninfected controls

first: Michael

last: Chait


title: STING Agonism Reprograms Tumor-associated Macrophages and Overcomes Resistance to PARP inhibition in BRCA1-deficient Models of Breast Cancer

city: Boston

first: Qiwei

last: Wang

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: PARP inhibitors (PARPi) have drastically changed the treatment landscape of advanced ovarian tumors with BRCA mutations. However, the impact of this class of inhibitors in patients with advanced BRCA-mutant breast cancer is relatively modest. Using a syngeneic genetically-engineered mouse model of breast tumor driven by Brca1 deficiency, we show that tumor-associated macrophages (TAMs) blunt PARPi efficacy both in vivo and in vitro. Mechanistically, BRCA1-deficient breast tumor cells induce pro-tumor polarization of TAMs, which in turn suppress PARPi-elicited DNA damage in tumor cells, leading to reduced production of dsDNA fragments and synthetic lethality, hence impairing STING-dependent anti-tumor immunity. STING agonists reprogram M2-like pro-tumor macrophages into an M1-like anti-tumor state in a macrophage STING-dependent manner. Systemic administration of a STING agonist breaches multiple layers of tumor cell-mediated suppression of immune cells, and synergizes with PARPi to suppress tumor growth. The therapeutic benefits of this combination require host STING and are mediated by a type I IFN response and CD8+ T cells, but do not rely on tumor cell-intrinsic STING. Our data illustrate the importance of targeting innate immune suppression to facilitate PARPi-mediated engagement of anti-tumor immunity in breast cancer.

overall_design: Transcriptome analysis were performed on mouse bone marrow-derived macrophages (BMDMs) after treatment with DMSO vehicle control, olaparib, DMXAA, olaparib-treated or untreated BRCA1-deficient mouse mammary tumor cells-derived conditioned medium (CM) with or without DMXAA.

first: Johann

last: Bergholz

first: Liya

last: Ding

first: Ziying

last: Lin

first: Shaozhen

last: Xie

first: Jean

last: Zhao


title: Study of three-dimensional structure of chromatin through a 4C-seq experiment in mouse NSC shControl and shJMJD3 upon TGFβ treatment [Aopep]

first: Marta

last: Vicioso Mantis

last: Vicioso-Mantis

first: Raquel

last: Fueyo

first: Claudia

last: Navarro

first: Sara

last: Cruz-Molina

first: Wilfred

last: van IJcken

first: Elena

last: Rebollo

first: Álvaro

last: Rada

first: Marian

last: Martínez-Balbás


title: Interleukin-4 receptor signaling modulates neuronal network activity [mouse]

status: Public on Apr 14 2022

city: Mainz

first: Samantha

last: Schmaul

address: Langenbeckstr 1

department: Neurology

country: Germany

institute: University Medical Centre Mainz

summary: Neuroimmune interaction influences essential CNS processes. Hanuscheck et al. report expression of interleukin-4 receptor alpha at presynaptic terminals in mouse and human brain. Modulation of neuronal IL-R signaling alters the neuronal transcriptome, impacts synaptic transmission and causes anxiety-related behavior.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Syn-Cre+ IL-4R fl/fl mice and littermates

first: Nicholas

last: Hanuscheck

first: Carine

last: Thalman

first: Micaela

last: Domingues

first: Muthuraman

last: Muthuraman

first: Mohammadsaleh

last: Oshaghi

first: Christina

last: Vogelaar

first: Frauke

last: Zipp


title: Fusion Genes in Prostate Cancer: A Comparison in Men of  African and European Descent

status: Public on Apr 16 2022

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

summary: Prostate cancer is one of the most prevalent cancers worldwide, particularly affecting men living a western lifestyle and of African descent, suggesting risk factors that are genetic, environmental, and socioeconomic in nature. In the USA, African American (AA) men are disproportionately af-fected, on average suffering from a higher grade of the disease and at a younger age compared to men of European descent (EA). Fusion genes are chimeric products formed by the merging of two separate genes occurring as a result of chromosomal structural changes, for example, inversion or trans/cis-splicing of neighboring genes. They are known drivers of cancer and have been identified in 20% of cancers. Improvements in genomics technologies such as RNA-sequencing coupled with better algorithms for prediction of fusion genes has added to our knowledge of specific gene fu-sions in cancers. At present AA are underrepresented in genomic studies of prostate cancer. The primary goal of this study was to examine molecular differences in predicted fusion genes in a cohort of AA and EA men in the context of prostate cancer using computational approaches. RNA was purified from prostate tissue specimens obtained at surgery from subjects enrolled in the study. Fusion gene predictions were performed using four different fusion gene detection pro-grams. This identified novel putative gene fusions unique to AA and suggested that the fusion gene burden was higher in AA compared to EA men.

first: E

last: Hazard

first: Chanita

last: Hughes-Halbert


title: Transcriptomic analysis revealed an important role of PPARα signaling in SHP-1 insufficiency leading to the development of renal ischemia-reperfusion injury

city: Shanghai

first: Sijia

last: Yan

address: Huashan Road

department: Institute for Personalized Medicine

institute: Shanghai Jiaotong University

summary: In this study, we systematically analyzed differences in the expression profiles of three SHP-1 (encoded by Ptpn6)-insufficient mice and three wild-type mice after renal ischemia-reperfusion injury by RNA-sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  the kidney of SHP-1 (encoded by Ptpn6)-insufficient mice and wild-type mice after ischemia-reperfusion injury

first: Mingxing

last: Sui

first: Hongzhe

last: Tian

first: Li

last: Zeng

first: Xianting

last: Ding


title: Expression profiles of lncRNA and mRNA in the liver of Echinococcus multilocularis-infected mice

status: Public on Apr 17 2022

city: lanzhou

first: xiaofeng

last: nian

address: No.1 of xujiaping

institute: LVRI

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

summary: Echinococcus multilocularis (Em) infection and the growth and proliferation of its metacestode within the liver of hosts are related to complex host–parasite interactions at the molecular level. However, the profiles of long non-coding RNAs (lncRNAs) and mRNAs of mice in response to Em are poorly understood. In this study, we detected numerous differentially expressed lncRNAs (DELs) and mRNAs (DEMs) in the mouse liver at eight time points after Em infection. Some DEMs and DELs were found continuously dysregulated. These DEMs were notably enriched in the “antigen processing and presentation,” “Th1 and Th2 cell differentiation” and “Th17 cell differentiation” pathways.

overall_design: The profiles of long non-coding RNAs (lncRNAs) and mRNAs of mice in response to Em was measured at 2, 4, 8, 15, 30, 60, 90, 150 days post infection. Eight independent experiments were performed using CA group (n=4) and Con group (n=4) for each experiment.

first: Xiaofeng

last: Nian

last: Li

first: Xusheng

last: Ma

first: Xiurong

first: Wenhui

first: Nianzhang

last: Zhang

first: John

last: Ohiolei

first: Le

first: Guodong

last: Dai

first: Yanhong

last: Liu

first: Hongbin

first: Baoquan

last: Fu

first: Sa

last: Xiao

first: Wanzhong

last: Jia


title: ALTERATIONS IN THE SKIN MICROBIOTA ARE ASSOCIATED WITH SYMPTOM SEVERITY IN MYCOSIS FUNGOIDES

status: Public on Apr 11 2022

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

summary: We identified skin microbiota signatures related to different symptoms, i.e. pain, pruritus, in patients with Mycosis Fungoides.

overall_design: The study is a prospective exploratory study with intrapersonal comparison. Among 39 patients with mycosis fungoides, we compared the changes between the skin microbiota from the healthy contralateral skin to that from the affected skin by MF. Using the change in relative abudance from the control skin to the affected skin, we correlates the changes with the severity of various symptoms

first: Yumeng


title: Gene-expression data of female wild-type (WT) and knock-out (KO) bone marrow derived macrophages (BMDMs) from C57BL/7 mice

city: Epalinges

first: Nicolas

last: Fasel

address: Chemin des Boveresses 155

department: Department of Biochemistry

country: Switzerland

institute: University of Lausanne

summary: Leishmania are medically relevant protozoan parasites that cause leishmaniasis, a neglected tropical disease that can differently manifest depending on the species and the immune status of the host. Previously, it has been suggested that the presence of an endosymbiont double stranded RNA virus, Leishmania RNA Virus 1 (LRV1), within the parasite may leed to an exarcerbation of the disease outcome and represents an important factor for treatment failure and relapse. Here, we provide gene expression data of wild-type (WT) and various knock-out (KO) bone marrow derived macrophages (BMDMs) from mice (C57BL/6) in different conditions of infections and treatments. We included BMDMs from WT, Ifnar-/-, IFNg-/-, iNOs-/-, Nlrx1-/-, Nox2-/- and Prx5-/- mice. BMDMs were either infected with a human protozoan parasite Leishmania guyanensis with or without its endosymbiant dsRNA virus, LRV1 (LgyLRV1+ and LgyLRV1-, respectively). Alternatively BMDMs were treated with poly I:C, a synthetic dsRNA or a TLR2 agonist FSL1 to identify virus dependetn pathways or to explore the impact of co-exposure to additional agents, respectively.

overall_design: Transcriptomic analysis of female WT and 6 KO BMDMs. A total of 62 samples were included in triplicates (total 186).

first: Amel

last: Bekkar

first: Nathalie

last: Isorce

first: Filipa

last: Teixeira

first: Tiia

last: Snäkä

first: Dmitry

last: Kopelyanskiy

first: Florence

last: Prével

first: Marta

last: Reverte

first: Chantal

last: Desponds

first: Stéphanie

last: Claudinot

first: Ioannis

last: Xenarios


title: Testing different rRNA removal methods in 4 species of model halophilic archaea

city: Durham

first: Amy

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

summary: We tested a number of rRNA removal methods (Illumina RiboZero Plus, NEBNext, NEB Core Depletion Set with custom probes, siTools Panarchaea, siTools RiboPool) on 4 model halophile species: Halobacterium salinarum, Haloferax volcanii, Haloferax meditteranei, Haloarcula hispanica). It was found that methods using custom probes (NEB Core Depletion set with HVO probes, siTools RiboPool with HVO probes) efficiently remove rRNA in species they are targeted to, and that Panarchaea efficiently removes rRNA in all 4 tested species.

sample_organism:
Halobacterium salinarum
Haloferax volcanii
Haloferax mediterranei
Haloarcula hispanica

overall_design: Cells were grown to mid-exponential phase and cell pellets were extracted and immediately frozen in liquid N2. After 1-7 days at -80C, total RNA was extracted from frozen cell pellets using the Absolutely RNA Miniprep kit made by Agilent, with additional DNase treatment as necessary. 1-10ng of total RNA was used as input for rRNA removal methods, for which we followed manufacturer's protocols (with the exception of longer RNase digestion of 120 minutes instead of 30 minutes, for some samples of HBT treated with NEB Core Depletion set, labeled NEB_HVO_120). dsDNA libraries were created using NEBMultiplex Oligos (part of the NEBNext protocol for the relevant samples). They were quantified and quality-checked using DNA High Sensitivity Chip for the Agilent Bioanalyzer and were sent for sequencing to the Duke Center for Genomic and Computational Biology, where they were sequenced on Illumina NovaSeq 6000.

first: Mar

last: Martinez-Pastor

first: Saaz

last: Sakrikar


title: The cellular origin of perivasuclar glioblastoma by scRNA-seq

first: Yizhou

last: Hu

summary: Understanding the cellular origin and differentiation status of glioblastoma is critical to resolve the etiology of the disease. we profile control and genetically modified human brain perivasuclar fibroblasts by single cell RNA sequencing (scRNAseq). From this, we observed the potential tumorigenicity of brian perivascular fibroblasts.

overall_design:
Single cell RNA-seq study of genetically modified human brain vascular primary fibroblasts
*** The raw data has been deposited in the European Genome-phenome Archive (EGAS00001006236) due to patient privacy concerns***

first: Patrik

last: Ernfors


title: Transcriptomic analysis of the tomato plant response to Tuta absoluta herbivory

status: Public on Apr 18 2022

city: Vandoeuvre les nancy

first: Romain

last: Larbat

address: 2 avenue de la forêt de Haye

department: INRAE

institute: LAE

summary: Tomato plants are submitted to a high diversity of herbivory pests, among them the leafminer Tuta absoluta, considered as one of the most important threat on the tomato worldwide production. In spite of its susceptibility to this pest, a better understanding of the tomato plant response to T. absoluta herbivory will help defining plant resistance traits and enlarging the range of possibilities for an efficient integrated pest management strategy. We analyzed the transcriptomic response in leaves of tomato (cv. Better Bush) submitted to the herbivory of T. absoluta larvae after 5h and 24h.

overall_design: Six tomato plants were infested with 6 larvae deposited on the three terminal leaflets of the 3rd true leaf and six control plants were subject to mock deposition. Two harvests were conducted after 5 h and 24 h of herbivory. At both harvest time, the infested leaflets from which the larvae have been removed (and the corresponding leaflets of the control plant) were sampled, immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. Twelve RNA bank were created corresponding to 4 conditions in triplicates (Tuta infested 5h and 24h; control 5h and 24h)

first: Marwa

last: Roumani

first: Christophe

last: Robin

first: Frédérique

last: Hilliou

first: Arthur

last: Péré


title: Dissecting tissue compartment-specific protein signatures in primary and metastatic oropharyngeal squamous cell carcinomas

status: Public on Apr 12 2022

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

summary:
Head and neck squamous cell carcinoma (HNSCC) often present with locoregional or distant disease, despite multimodal therapeutic approaches, which include surgical resection, chemoradiotherapy, and more recently immunotherapy for metastatic, or recurrent HNSCC. Therapies often target the primary and nodal regional HNSCC sites, and efficacy at controlling occult distant sites remains poor. Whilst our understanding of the tumour microenvironment, conducive for effective therapies is increasing, the biology underpinning locoregional sites remains unclear. Here, we applied targeted spatial proteomic approaches to primary and lymph node metastasis from an oropharyngeal SCC (OPSCC) cohort, to understand the expression of proteins within tumour, and stromal compartments of the respective sites in both matched and unmatched patients’ samples. In unmatched analyses of n=43 primary and 11 nodal metastasis, our data indicated that tumour cells in nodal metastases had higher levels of Ki-67, PARP, BAD and cleaved caspase 9, suggesting a role for increased proliferation, DNA repair and apoptosis within these metastatic cells. Conversely, in matched analyses (n=7), pro-apoptotic markers BIM and BAD were enriched in the stroma of primary tumours. Univariate, overall survival (OS) analysis indicated CD25 in tumour regions of primary tumours to be associated with reduced survival (HR=3.3, p=0.003), while partial response (PR) was associated with an improved OS (HR=0.33, p=0.015). This study highlights the utility of spatial proteomics for delineating tumour and stroma compartment composition, and the utility towards understanding these properties in locoregional metastasis. These findings indicate the unique biological properties of lymph node metastases that may elucidate further understanding of the subsequent distant metastatic potential of OPSCC.
In this dataset, we applied GeoMx DSP protein profiling to tumour and tumour microenvironment regions of primary and lymphnode metastasis FFPE samples. The files here represent the Ncounter readout from this assay.

overall_design: This dataset contains protein expression of tumour and tumour microenvironment regions from 43 primary tumours, 11 nodal metastases, with 7 additional patient matched primary/metastases

first: Habib

last: Sadeghirad

first: James

last: Monkman

first: Ahmed

middle: M

last: Mehdi

first: Rahul

last: Ladwa

first: Kenneth

last: O'Byrne

first: Brett

middle: G

last: Hughes