title: Gene Editing of Hematopoietic Stem Cells Restores T Cell Response in a Familial Hemophagocytic Lymphohistiocytosis Model [Amplicon]

city: Freiburg

first: Gianni

last: Monaco

address: Breisacher Straße

institute: Freiburg Medical Center

summary: Hemophagocytic lymphohistiocytosis (HLH) is a hyperinflammatory disorder characterized by a life-threatening cytokine storm and immunopathology. Familial HLH type 3 (FHL3) accounts for 30% of all inborn HLH cases worldwide. It is caused by mutations in the UNC13D gene, which result in impaired processing of cytotoxic vesicles and hence compromised T and NK cell-mediated killing. Current treatment protocols, including allogeneic hematopoietic stem cell (HSC) transplantation, still show 30-40% mortality. As a first step to meet this medical need, we developed and tested a curative genome editing strategy in the FHL3 Jinx mouse model. Jinx mice harbor a cryptic splice donor site (cSD) in Unc13d intron 26 and develop the clinical symptoms of human FHL3 upon infection with lymphocytic choriomeningitis virus (LCMV). Here, we employed CRISPR-Cas technology to delete the disease-underlying mutation in HSCs, and transplanted the Unc13d-edited stem cells into busulfan-conditioned Jinx recipient mice. Genotyping, phenotyping and CAST-Seq based off-target analyses of cells isolated from transplanted mice revealed efficient gene editing (>95%), polyclonality of the T cell receptor repertoire, and neither signs of off-target effects nor leukemogenesis. Unc13d transcription levels of edited and wildtype cells were comparable. LCMV challenge of the transplanted mice resulted in acute HLH in Jinx mice transplanted with mock-edited HSCs, while Jinx mice grafted with Unc13d-edited cells showed rapid virus clearance and protection from HLH. In sum, our study demonstrates that transplantation of CRISPR-Cas edited HSCs supports the development of a functional polyclonal T cell response in the absence of genotoxicity-associated clonal outgrowth or leukemogenesis.

overall_design: Mouse bone marrow HSPCs were treated with two RNP complexes (1:3 molar ratio of Cas9:sgRNA). Genotyping was performed on various tissues pre and post transplantation.

first: Viviane

last: Dettmer-Monaco

first: Kristoffer

last: Weißert

first: Manuel

last: Rhiel

first: Peter

last: Aichele

first: Toni

last: Cathomen


title: Gene Editing of Hematopoietic Stem Cells Restores T Cell Response in a Familial Hemophagocytic Lymphohistiocytosis Model [TCR]

status: Public on Jul 04 2023

country: Germany

overall_design: Mouse splenocytes/CD8 T cells from various treatment groups were subjected to transcript T cell repertoire analysis.


title: Precision RNAi using synthetic shRNAmir target sites

city: Vienna

first: Alexandra

last: Popa

state: Austria

address: Doktor-Boehringer-Gasse 5-11

country: Austria

institute: Boehringer Ingelheim

type: Expression profiling by high throughput sequencing

summary: Loss-of-function genetic tools are widely applied for validating therapeutic targets, but their utility remains limited by incomplete on- and uncontrolled off-target effects. We describe artificial RNA interference (ARTi) based on synthetic, ultra-potent, off-target-free shRNAs that enable efficient, inducible, and reversible suppression of any gene upon introduction of a synthetic target sequence into non-coding transcript regions. ARTi establishes a scalable loss-of-function tool with full control over on- and off-target effects.

overall_design: EGFRdel19::dsRed::ARTi engineered PC-9 cells harboring the Dox-inducible ARTi-shRNAmir were treated with Dox to elicit the knock-down of the EGFR transgene. KRASG12R-ARTi engineered MIA PaCa2 cells harboring the Dox-inducible ARTi-shRNAmir were treated with Dox to elicit the knock-down of the KRAS transgene. Differences in gene expression were monitored.

first: Ralph

last: Neumüller

last: Hörmann

first: Anna

last: Köferle


title: Gene Editing of Hematopoietic Stem Cells Restores T Cell Response in a Familial Hemophagocytic Lymphohistiocytosis Model

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

overall_design: Mouse bone marrow HSPCs were treated with two RNP complexes (1:3 molar ratio of Cas9:sgRNA). Genotoxicity was assesed via CAST-Seq.

first: Melanie

last: Börries


title: Chromosome arm length, and a species-specific determinant, define chromosome arm width

city: Tokyo

first: Yasutaka

last: Kakui

address: 1-21-1 Nishiwaseda, Shinjuku-ku

country: Japan

institute: Waseda Institute for Advanced Study

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

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Refer to individual Series


title: Digital Spatial Profiling of tumor microenvironment of classic Hodgkin lymphoma.

status: Public on Jul 03 2023

city: Krume

first: Koichi

last: Ohshima

state: Fukuoka

address: Asahimachi 67

department: Pathology

institute: Kurume University

summary: Classic Hodgkin lymphoma (CHL) harbors a small number of Hodgkin-Reed-Sternberg (HRS) cells scattering among numerous lymphocytes. HRS cells are surrounded by distinct CD4+ T cells in a rosette-like manner. These CD4+ T cell rosettes play an important role in tumor microenvironment (TME) of CHL. To elucidate the interaction between HRS cells and CD4+ T cell rosettes, we performed digital spatial profiling (DSP) and compared gene expression profile between CD4+ T cell rosettes and other CD4+ cells separated from HRS cells. programed cell death-1 (PD-1) and tumor necrosis factor receptor superfamily member (TNFRSF) 4 were significantly highly expressed in CD4+ T cell rosettes than others. Immunohistochemistry confirmed PD-1 and TNFRSF4-expressing CD4+ T cell rosettes. This study introduced the new pathological approach to TME and provided deeper insight to CD4+ T cells in CHL.

overall_design: Total 12 areas of interest from a case of CHL were sequenced using GeoMx Digital Spatial Profiler (Nanostring Technologies), with the Human Whole Transcriptome Altas (18,000+ genes)

first: M

last: Takeuchi

first: H

last: Miyoshi

first: K


title: Chromosome arm length, and a species-specific determinant, define chromosome arm width [S. cerevisiae]

summary: Mitotic chromosomes in different organisms adopt various dimensions. What defines chromosome dimensions is scarcely understood. Here, we compare budding and fission yeasts that harbor similarly sized genomes distributed amongst 16 or 3 chromosomes, respectively. Budding yeast chromosomes are thinner and characterized by shorter mitotic chromatin interactions. This remains the case even following chromosome fusions to form three fission-yeast-length entities, revealing a species-specific organizing principle that correlates with condensin binding site spacing. Unexpectedly, within each species, longer chromosome arms are always thicker, a trend also observed with human chromosomes. Arm length as a chromosome width determinant informs mitotic chromosome formation models.

overall_design:
3 biological replicates of Hi-C in G1 phase and mitosis using budding yeasts with different chromosome numbers; two fusion strains of cerev (SY7 and SY12) that were from the BY4742 strain
SY7 (8 chromosomes):
1+2, 3+4, 7+8, 9+10, 11, 13+12, 15 and 16+5+6+14
SY12 (3 chromosomes):
1+2+3+4+7+8+9+10, 13+12+15+11 and 16+5+6+14

first: Christopher

last: Barrington


title: Arl4c is involved in tooth germ development through osteoblastic differentiation

status: Public on Jul 01 2023

city: Fukuoka

first: Kana

last: Hasegawa

address: 3-1-1 Maidashi, Higashi-ku

institute: Kyushu University

summary: Murine tooth germ development proceeds in continuous and sequential steps with reciprocal interactions between the odontogenic epithelium and the adjacent mesenchyme, and several growth factor signaling and their activation are required for tooth germ development. The expression of ADP-ribosylation factor (Arf)-like 4c (Arl4c) has been shown to induce cell proliferation, thereby involving in epithelial morphogenesis and tumorigenesis. However, other functions of Arl4c except for cellular growth are largely unknown. Although we recently demonstrated the involvement of the upregulated expression of Arl4c in cell proliferation of ameloblastoma, which has the same origin as odontogenic epithelium, its effect on tooth germ development remains unclear. Herein, single-cell RNA sequencing (scRNA-seq) analysis revealed that the expression of Arl4c, among 17 members of the Arf-family members, was specifically detected in odontogenic epithelial cells, such as stratum intermedium, stella reticulum and outer enamel epithelium, of postnatal day 1 (P1) mouse molar. In addition, scRNA-seq analysis showed higher expression of Arl4c in non-ameloblast and inner enamel epithelium, which include immature cells. In the mouse tooth germ rudiments culture, treatment with SecinH3 (an inhibitor of ARNO/Arf6 pathway) reduced the size, width and cusp height and the thickness of eosinophilic layer, which would involve the synthesis of dentin and enamel matrix organization. In addition, loss-of-function experiments using siRNAs and shRNA revealed that Arl4c expression was involved in cell proliferation and osteoblastic cytodifferentiation in odontogenic epithelial cells. Finally, RNA-seq analysis with gene set enrichment analyses (GSEA) and Gene Ontology (GO) analysis showed that osteoblastic differentiation-related gene set and/or GO terms were downregulated in shArl4c expressing odontogenic epithelial cells. These results suggest that the Arl4c-ARNO/Arf6 pathway axis contributes to tooth germ development through osteoblastic differentiation.

overall_design: RNA-seq was performed using RNAs extracted from mDE6 expressing shControl or shArl4c.

first: Thinh

middle: T

last: Truong

first: Shinsuke

last: Fujii

first: Ryoko

last: Nagano

first: Megumi

last: Kokura

first: Yuta

last: Chiba

first: Keigo

last: Yoshizaki

first: Satoshi

last: Fukumoto

first: Tamotsu

last: Kiyoshima


title: HDAC1/2/3 Are Major Histone Desuccinylase Critical for Promoter Desuccinylation [RNA-seq]

city: ShangHai

first: Jialun

last: Li

address: NO. 500 Dongchuan Road, Minhang distinct

country: China

institute: WuHu Hospital, East China Normal University

summary: Lysine succinylation is one of the major post-translational modifications occurred on histones and is believed to have significant roles in regulation of chromatin structure and function. Currently, histone desuccinylation is widely believed to be exerted by the members of SIRT family deacetylases. Here, we report that histone desuccinylation is in fact primarily catalyzed by the class I HDAC1/2/3. Inhibition or depletion of HDAC1/2/3 resulted in marked increase of global histone succinylation, whereas ectopic expression of HDAC1/2/3 but not their deacetylase inactive mutants downregulated global histone succinylation. We demonstrated that the class I HDAC1/2/3 complexes have robust histone desuccinylase activity in vitro. Genomic landscape analysis revealed that histone succinylation is highly enriched at gene promoters and inhibition of HDAC activity results in marked elevation of promoter histone succinylation. Furthermore, integrated analysis revealed that the promoter histone succinylation positively correlates with the transcriptional activity. Collectively, we demonstrate that the class I HDAC1/2/3 but not the SIRT family proteins are the major histone desuccinylases particularly important for promoter histone desuccinylation. Our study thus sheds new light on the role of histone succinylation in transcriptional regulation.

overall_design: For RNA-seq analysis, an equivalent number (5 × 106) of DMSO/TSA-treated, control, HDAC1/2/3 knockout or SIRT7 knockout HeLa cells were used for total RNA preparation using Trizol reagent and phenol-chloroform-isopropanol extraction. Library preparation and sequencing were performed by Illumina Hiseq 2500 platform with three independent biological replicates.

first: Lu

last: Lu

first: Lingling

last: Liu

first: Jiemin

last: Wong


title: Genome-wide RNA structure changes during human neurogenesis modulate gene regulatory networks

city: SINGAPORE

first: Yue

last: Wan

address: 60 Biopolis Street, Genome, #07,

country: Singapore

institute: GIS, A*STAR

summary: RNAs structures play central roles in various cellular processes, and can be remodeled upon binding to cellular factors such as RNA binding proteins (RBP). However, how widespread this remodeling is and whether structural changes can serve as additional regulatory steps for other regulators remains under-explored. Here, we assayed RNA structural dynamics, gene expression, translation and decay during different stages of human neuronal differentiation to understand the impact of RNA structures in stem cell regulation. RBP binding resulted in wide-spread RNA structure changes during early neuronal differentiation.  Structure changes act as a common mechanism for RBPs to modulate the binding of additional RBPs and miRNAs to coordinate gene expression temporally.  In particular, we showed that PUM2 binding on LIN28A resulted in RNA structure changes that enabled miR-30 binding, leading to downregulation of LIN28A. Compensatory mutagenesis experiments that lock specific structural states confirmed the importance of PUM2-induced structure changes in miR-30 regulation. This systematic study broadens our understanding of RNA structural dynamics during human neuronal differentiation and illustrates the wide-spread and complex role of RBPs in regulating RNA structures for gene regulation during human development.

overall_design: High throughput RNA structure probing experiments in vivo using icSHAPE in hESCs (Day 0, D0), neuronal precursor cells (Day 7, D7), early neurons (Day 8, D8) and neurons (Day 14, D14).

first: Jiaxu

last: Wang

first: Tong

last: Zhang

first: Yu


title: Effect of autophagy deficiency in endothelial cells

city: Paris

first: Olivia

last: Lenoir

address: 56 rue Leblanc

country: France

institute: Inserm

summary: Dysregulated autophagy is associated with cardiovascular and metabolic diseases, where impaired flow-mediated endothelial cell responses promote cardiovascular risk. The mechanism by which the autophagy machinery regulates endothelial functions is complex. We applied multi-omics approaches and in vitro and in vivo functional assays to decipher the diverse roles of autophagy in endothelial cells. We demonstrate that autophagy regulates VEGF-dependent VEGFR signaling and VEGFR-mediated and flow-mediated eNOS activation. Endothelial ATG5 deficiency in vivo results in selective loss of flow-induced vasodilation in mesenteric arteries and kidneys, along with increased cerebral and renal vascular resistance. We found a crucial pathophysiological role for autophagy in endothelial cells in flow-mediated outward arterial remodeling, prevention of neointima formation following wire injury, and recovery after myocardial infarction. Together, these findings unravel a fundamental role for autophagy in endothelial function, linking cell proteostasis to mechanosensing.

overall_design: HUVEC were transduced with lentivirus encoding a shRNA against human ATG5 or shRNA scramble. Comparative gene expression of RNAseq data.

first: O

first: B

last: Saintpierre


title: Individual variation in preference behavior in sailfin fish refines the neurotranscriptomic pathway for mate preference

city: Austin

first: Rebecca

middle: L

last: Young

state: TX

address: 2415 Speedway

department: Integrative Biology

country: USA

institute: University of Texas at Austin

summary: Social interactions can drive distinct gene expression profiles which may vary by social context. Here we use female sailfin molly fish (Poecilia latipinna) to identify genomic profiles associated with preference behavior in distinct social contexts: male-interactions (mate choice) versus female-interactions (shoaling partner preference). We measured behavior of 15 females interacting in a non-contact environment with either two males or two females for 30 minutes followed by whole brain transcriptomic profiling by RNA sequencing. We profiled females that exhibited high levels of social affiliation and great variation in preference behavior to identify an order of magnitude more differentially expressed genes associated with behavioral variation than by differences in social context. Using linear modeling (limma), we took advantage of the individual variation in preference behavior to identify unique gene sets that exhibited distinct correlational patterns of expression with preference behavior in each social context.  By combining limma and weighted gene co-expression network analyses (WGCNA) approaches we identify a refined set of 401 genes robustly associated with mate preference that is independent of shoaling partner preference or general social affiliation. While our refined gene set confirmed neural plasticity pathways involved in moderating female preference behavior, we also identified a significant proportion of discovered that our preference-associated genes were enriched for ‘immune system’ gene ontology categories. We hypothesize that the association between mate preference and transcriptomic immune function is driven by the less well-known role of these genes in neural plasticity which is likely involved in higher-order learning and processing during mate choice decisions.

overall_design: Gene expression profiles (RNAseq) were associated with preference behavior in distinct social contexts: male interactions (mate choice) versus female interactions (shoaling partner preference) in female sailfin molly fish (Poecilia latipinna).

first: Sarah

middle: M

last: Price

first: Molly

last: Schumer

first: Silu

middle: E

last: Cummings


title: Inhibition of microsomal prostaglandin E2 synthase reduces collagen deposition in melanoma tumors and may improve immunotherapy efficacy by reducing T cell exhaustion

status: Public on Jul 02 2023

city: Houston

first: Suhendan

last: Ekmekcioglu

address: 1515 Holcombe Blvd

department: Melanoma Medical Oncology

institute: University of Texas, MD Anderson Cancer Center

summary: The arachidonic acid pathway participates in immunosuppression in various types of cancer. Our previous observation detailed that microsomal prostaglandin E2 synthase 1 (mPGES-1), an enzyme downstream of cyclooxygenase 2 (COX-2), limited antitumor immunity in melanoma; in addition, genetic depletion of mPGES-1 specifically enhanced immune checkpoint blockade therapy. The present study set out to distinguish the roles of mPGES-1 from those of COX-2 in tumor immunity and determine the potential of mPGES-1 inhibitors for reinforcing immunotherapy in melanoma. Genetic deletion of mPGES-1 showed different profiles of prostaglandin metabolites from that of COX-2 deletion. In our syngeneic mouse model, mPGES-1–deficient cells exhibited similar tumorigenicity to that of COX-2–deficient cells, despite a lower ability to suppress PGE2 synthesis by mPGES-1 depletion, indicating the presence of factors other than PGE2 that are likely to regulate tumor immunity. RNA sequencing analysis revealed that mPGES-1 depletion reduced the expressions of collagen-related genes, which have been found to be associated with immunosuppressive signatures. In our mouse model, collagen was reduced in mPGES-1–deficient tumors, and phenotypic analysis of tumor-infiltrating lymphocytes indicated that mPGES-1-deficient tumors had fewer TIM3+ exhausted CD8+ T cells compared with COX-2–deficient tumors. CAY10678, an mPGES-1 inhibitor, was equivalent to celecoxib, a selective COX-2 inhibitor, in reinforcing anti–PD-1 treatment. Our study indicates that mPGES-1 inhibitors represent a promising adjuvant for immunotherapies in melanoma by reducing collagen deposition and T cell exhaustion.

overall_design: In order to evaluate the specific roles of mPGES-1 in melanoma, we established ptgs1, ptgs2, and ptges genes (corresponding to COX-1, COX-2, and mPGES-1 proteins, respectively) knockout murine BrafV600E melanoma cells derived from C57BL/6 Braf+/LSL-V600E;Tyr::CreERT2+/o;p16INK4a-/- mouse using CRISPER/CAS9 system.

first: Sun-Hee

last: Kim

first: Yasunari

last: Fukuda

first: Matias

last: Bustos

first: Dave

last: Hoon


title: PPARα activation promotes liver progenitor cell-mediated liver regeneration by suppressing YAP signaling in zebrafish

city: Pittsburgh

first: Donghun

last: Shin

address: 3501 5th Ave

institute: University of Pittsburgh

summary: To elucidate the role of PPARα activation in liver progenitor cell-mediated liver regeneration, we used Tg(fabp10a:pt-β-catenin) zebrafish transgenic line where liver progenitor cell-mediated liver regeneration is induced by oncogene overexpression

overall_design: We performed gene expression profiling analysis using data from RNA-seq of DMSO- and GW7647-treated livers.

first: Minwook


title: Emergence of Disease Specific Cardiac Macrophages in Immune Checkpoint Inhibitor Myocarditis

city: Saint Louis

first: Pan

last: Ma

state: United States

address: CSRB, Room 9918, 425 S Euclid, Saint Louis, MO, 63110

institute: Washington University in Saint Louis

summary: Immune checkpoint inhibitors (ICIs), antibodies targeting PD-1/PD-L1 or CTLA4 have revolutionized cancer management but are associated with devastating immune-related adverse events (irAEs) including myocarditis. The main risk factor for ICI myocarditis is the use of combination PD-1 and CTLA4 inhibition. ICI-myocarditis is often fulminant and is pathophysiologically characterized by myocardial infiltration of T lymphocytes and macrophages. While much has been learned regarding the role of T-cells in ICI-myocarditis, little is understood regarding the identity, transcriptional diversity, and functions of infiltrating macrophages. We employed an established murine ICI myocarditis model (Ctla4+/-Pdcd1-/- mice) to explore the cardiac immune landscape using single-cell RNA-sequencing, immunostaining, and molecular imaging. We observed marked increases in CCR2+ monocyte-derived macrophages and CD8+ T-cells in this model. The macrophage compartment was heterogeneous and displayed marked enrichment in an inflammatory CCR2+ subpopulation expressing Cxcl9, Cxcl10, Gbp2b, and Fcgr4 that originated from CCR2+ monocytes.  Importantly, a similar macrophage population expressing CXCL9, CXCL10, and CD16α (human homologue of mouse FcgR4) were found selectively in patients with ICI myocarditis compared to other forms of heart failure and myocarditis. In silico prediction of cell-cell communication suggested interactions between T-cells and Cxcl9+Cxcl10+ macrophages via IFN-γ and CXCR3 signaling pathways. Depleting CD8+T-cells and blockade of IFN-γ signaling blunted the emergence of Cxcl9+Cxcl10+ macrophages in the heart and attenuated myocarditis suggesting that this interaction was necessary for disease pathogenesis. Collectively, these data demonstrate that ICI-myocarditis is associated with the emergence of a specific population of inflammatory macrophages and suggest the possibility that IFN-γ blockade may serve as an effective treatment for this devastating condition.

overall_design: To reveal the cardiac  immune landscape of immune chechpoint inhibitors (ICI) myocarditis, we performed single-cell RNA-sequencing (scRNA-seq) of heart tissue from control (Ctla4+/+Pdcd1-/-, n=4) and ICI myocarditis (Ctla4+/-Pdcd1-/-, n=10) mice. We constructed five libraries (control: L1, L2; disease: L3, L4, L5) from DRAQ5+DAPI- cells purified from pooled enzymatically digested hearts by FACS.

first: Jing

last: Liu

first: Lulu

last: Lai

first: Juan

last: Qin

first: Deborah

last: Sultan

first: Andrea

last: Bredemeyer

first: Geetika

last: Bajapa

first: Guoshuai

last: Feng

first: Junedh

last: Amrute

first: Ana

last: Villanueva

first: Inessa

last: Lokshina

first: Yongjian

first: Chieh-Yu

last: Lin

first: Matthias

last: Mack

first: Javid

last: Moslehi

first: Kory

middle: J

last: Lavine


title: Antioxidants improve the proliferation and efficacy of hUC-MSCs against H2O2 induced senescence

city: Shanghai, China

first: Liming

last: Ouyang

state: Shanghai

address: East China University of Science and Technology, 130 Meilong Road, Xuhui District, Shanghai, China

summary: Human umbilical cord mesenchymal stem cells (hUC-MSCs) are broadly applied in clinical treatment due to easy availability, low immunogenicity, and no ethical issues involved. However, the microenvironment of inflammatory tissues may cause oxidative stress and induce senescence in transplanted hUC-MSCs, which will further reduce the proliferation, migration ability, and the final therapeutic effects of hUC-MSCs. Beta-nicotinamide mononucleotide (NMN), and coenzyme Q10 (CoQ10) are famous antioxidants and longevity medicines that could reduce intracellular reactive oxygen species levels by different mechanisms.Transcriptomic analysis revealed that NMN and CoQ10 both increased DNA repair ability and cyclin expression, and downregulated TNF and IL-17 inflammatory signaling pathways, thereby contributed to the proliferation of advanced stem cells and aging due to oxidative stress. These findings suggest that antioxidants can improve the survival and efficacy of hUC-MSCs in stem cell therapy for inflammation-related diseases.

overall_design: Comprehensive evaluation of the effects of NMN and coenzyme Q10 on hUC-MSCs of passage 12. Cells without treatment were set as control group.

first: Zhaojuan

last: Zheng

first: Xia

last: Wang

first: Wenxia

last: Cheng


title: Chromatin regulation of transcriptional enhancers and cell fate by the Sotos syndrome gene NSD1

city: New York

first: Zhen

last: Sun

state: NY

address: 408 E 69th street, Z619

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing


title: Combinatorial treatment with PARP and MAPK inhibitors to overcome phenotype switch-driven drug resistance in advanced melanoma

city: Geneva

first: Phil

middle: Fang

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

country: Switzerland

institute: Hopitaux universitaires de Geneve

summary: The prognosis for most patients with advanced malignant melanoma is traditionally very poor, as the disease is either intrinsically resistant or rapidly acquires resistance to targeted therapy treatments. Here, using a drug screen targeting chromatin regulators in patient-derived 3D melanoma cell cultures, we discovered that PARP inhibitors are capable of restoring MAPKi sensitivity. This synergy was found to be independent of DNA damage repair pathways and was effective both in vitro and in vivo in patients-derived xenografts.  Strikingly, through integrated transcriptomic, proteomic and epigenomic analysis, we discovered that PARPi induces lysosomal autophagy which was accompanied by enhanced mitochondrial lipid metabolism that, ultimately, increased antigen presentation and T-cell cytotoxicity. Moreover, we also found that PARP inhibitors regulated EMT-like phenotype switching by dampening the mesenchymal phenotype via transcriptomic and epigenetic rearrangements. This, in turn, redirected melanoma cells towards a proliferative and, thus, MAPKi-sensitive state. Our study provides a scientific rational for treating patients with PARPi in combination with MAPKi to annihilate acquired therapy resistance

overall_design: RNAseq of spheroids of melanoma cell lines M121224 and M111031 were treated with Talazoparib (PARPi), Encorafenib (LGX818) and combination of Talazoparib and Encorafenib .

middle: F

first: Lorenza

last: Feretti


title: Single Cell RNA Sequencing of adult WT Zebrafish Retina

first: John

last: O'Brien

state: Texas

address: 4401 Martin Luther King Blvd

department: Vision Science

institute: University of Houston College of Optometry

summary: In this study, we have pooled 3 adult wild-type Zebrafish retinas and performed Single-Cell RNA Sequencing. We would like to see the transcriptomic signatures of each cell type in the retina. The data provided here will provide a foundation for other studies to further investigate the transcriptomic retinal enviromnent and compare how their models differ from WT.

overall_design: We have performed single-cell RNA Sequencing (sc-RNA Seq) of adult retina in the wild-type adult Zebrafish. We find that each cell type has a unique transcriptional signature, reflective of what is in the literature.

first: Abirami

last: Santhanam

first: Eyad

last: Shihabeddin

first: Haichao

last: Wei

first: Jiaqian

last: Wu


title: Sublethal necroptosis signaling promotes inflammation and liver cancer

city: Aachen

first: Mingbo

state: North Rhine-Westphal

address: Pauwelsstr. 19

institute: Uniklinik RWTH Aachen

summary: We developed a genetic mouse model of chronic necroptosis activation in hepatocytes (in the presence of basal NF-kB activity) that lead to hepatocellular carcinoma. Blocking Necroptosis (RIP3) or NF-kB-(IKKβ) activation in those mice blocked hepatocarcinogenesis.

overall_design: WT, combined conditional deletion of Traf2 and Caspase-8 in hepatocytes (DKO mice) (T2), inter-bred DKO mice with constitutive RIPK3 deficient mice RIP3-TKO(RIP3), interbred DKO mice with IKKβ-floxed mice to facilitate hepatocyte specific triple knockout mice IKKβ-TKO(IKK2)

first: Mihael

last: Vucur


title: Reduced fatty acid synthesis and enhanced oxidation promote human definitive endoderm differentiation

city: WuHan

first: chenchao

last: yan

state: Hubei Province

address: Donghu Road, No. 115

institute: WuHan university

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human definitive endoderm cells and its derivatives (C75-treatment, ETO-treatment;  C75: a fatty-acid synthase (FASN) inhibitor, ETO: a fatty-acid oxidation (FAO) inhibitor).

first: Ying

last: Yi

first: Chenchao

last: Yan

first: Wei

last: Jiang


title: Chromosome arm length, and a species-specific determinant, define chromosome arm width [S. pombe]

first: Yasutaka

last: Kakui

overall_design: 3 biological replicates of Hi-C in interphase and mitosis using fission yeast with fusion chromosome (i.e. 2 chromosomes: 1+2 and 3)

first: Christopher

last: Barrington


title: Dual inhibition of the endothelin and angiotensin receptor ameliorates renal and inner ear pathologies in Alport mice

city: San Diego

first: Tiziano

last: Pramparo

state: CA

address: 3611 Valley Centre Drive

department: R&D

institute: Travere

summary: Alport syndrome, a type IV collagen disorder, leads to glomerular disease and, in some patients, hearing loss. AS is treated with inhibitors of the renin-angiotensin system; however, a need exists for novel therapies, especially those addressing both major pathologies. Sparsentan is a single-molecule dual endothelin type-A and angiotensin II type 1 receptor antagonist (DEARA) under clinical development for focal segmental glomerulosclerosis and IgA nephropathy. We report the ability of sparsentan to ameliorate both renal and inner ear pathologies in an autosomal-recessive Alport mouse model. Sparsentan significantly delayed onset of glomerulosclerosis, interstitial fibrosis, proteinuria, and glomerular filtration rate decline. Sparsentan attenuated glomerular basement membrane defects, blunted mesangial filopodial invasion into the glomerular capillaries, increased lifespan more than losartan, and lessened changes in profibrotic/proinflammatory genes pathways in both the glomerular and renal cortical compartments. Notably, treatment with sparsentan, but not losartan, prevented accumulation of extracellular matrix in the strial capillary basement membranes in the inner ear and reduced susceptibility to hearing loss. Improvements in lifespan and in renal and strial pathology were observed even when sparsentan was initiated after development of renal pathologies. These findings suggest that sparsentan may address both renal and hearing pathologies in Alport syndrome patients.

overall_design: Alport mouse model was treated with sparsentan, a dual inhibitor of endothelin type-A and angiotensin II AT1 receptors, and gene expression changes were investigated at two location of the kidneys, the glomerulus and the cortex. From each location 4 samples in three mouse groups have been analyzed. These groups are Alport untreated (AS), Alport treated (AS_SP) and wild-type (WT).

first: Michael

middle: A

last: Gratton

first: Jacob

last: Madison

first: Denise

last: Vosik

first: Gina

last: Samuelson

first: Daniel

last: Meehan

first: Duane

last: Delimont

first: Grady

last: Phillips

first: Brendan

last: Smyth

first: Diana

last: Jarocki

first: Mai

last: Nguyen

first: Radko

last: Komers

first: Celia

last: Jenkinson


title: Neuronal diversity of neuropeptide signaling, including galanin, in the mouse locus coeruleus

city: Vienna

first: Tibor

last: Harkany

address: Spitalgasse 4

department: Department of Molecular Neurosciences (Center for Brain Research)

institute: Medical University of Vienna

summary:
Purpose:
The locus coeruleus (LC) is a small nucleus in the pons, with norepinephrine (NE) as its major transmitter. It plays key roles in wakefulness and is associated with disorders like depression. The study aims to analyze single-cell RNA-seq data to subdivide neurons in the LC and chart their neuropeptide, co-transmitter, and receptor profiles. It also seeks to build a precise map of galanin and its receptors in the mouse LC, and understand the role of neuropeptide expression and signaling.
Results:
The study identified 24 clusters in total, with 3 NE, 17 glutamate, and 5 GABA subtypes. NE neurons expressed at least 19 neuropeptide transcripts, mainly galanin (Gal) but not Npy, and >30 neuropeptide receptors. Among galanin receptors, Galr1 was expressed in ~19% of NE neurons, and highly expressed in GABA neurons surrounding the NE ensemble. Patch-clamp electrophysiology and cell-type-specific Ca2+-imaging using GCaMP6s revealed that a GalR1 agonist inhibits no more than ~35% of NE neurons, with the effect being direct and not relying on feed-forward GABA inhibition.
Conclusions:
The results define a role for the galanin system in NE functions and provide a conceptual framework for the action of many other peptides and their receptors. The study found that most NE neurons express mRNA transcripts for galanin, at least 19 neuropeptides (but not Npy), and >30 neuropeptide receptors, including Galr1 at low levels. Selective activation of GalR1 inhibited the spontaneous activity of a subset of NE neurons possibly through the activation of Kv currents. These findings offer new insights into the role of neuropeptide expression and signaling in mouse LC.

overall_design: The scRNA-seq experiment involved collecting cells from 3-4-week-old C57Bl/N mice of both sexes, dissociating the LC tissue, and fixing single cells in ice-cold methanol. cDNA libraries were prepared, and sequencing was performed using the 10x Genomics Chromium Single Cell Kit. Two independent samples were prepared and sequenced, resulting in a total of 2,578 cells. Data was analyzed using the Seurat pipeline, including quality control, filtering, and clustering.

first: Martino

last: Caramia

first: Roman

last: Romanov

first: Spyridon

last: Syderomenos

first: Zsofia

last: Hevesi

first: Ming

last: Zhao

first: Marharyta

last: Krasniakova

first: Zhi-Qing

middle: D

last: Xu

first: Tomas

last: Hökfelt


title: Development of a peptide drug restoring AMPK and adipose tissue functionality in cancer cachexia

city: Neuherberg

first: Maria

last: Rohm

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Cancer

institute: Helmholtz Munich

summary: Cancer cachexia is a severe systemic wasting disease that negatively affects quality of life and survival in patients with cancer. To date, treating cancer cachexia is still a major unmet clinical need. We recently discovered the destabilization of the AMPK complex in adipose tissue as a key event in cachexia-related adipose tissue dysfunction and developed an AAV-based approach to prevent AMPK degradation and prolong cachexia-free survival. Here, we show the development and optimization of a prototypic peptide, Pen-X-ACIP, where the AMPK stabilizing peptide ACIP is fused to the cell-penetrating peptide moiety penetratin via a propargylic glycine linker to enable late-stage functionalization using click chemistry. Pen-X-ACIP was efficiently taken up by adipocytes, inhibited lipolysis and restored AMPK signaling. Tissue uptake assays showed a favorable uptake profile into adipose tissue upon intraperitoneal injection. Systemic delivery of Pen-X-ACIP into tumor-bearing animals prevented the progression of cancer cachexia without affecting tumor growth, and preserved body weight and adipose tissue mass with no discernable side effects in other peripheral organs, thereby achieving proof-of-concept. As Pen-X-ACIP also exerted its anti-lipolytic activity in human adipocytes, it now provides a promising platform for further (pre)clinical development towards a novel, first-in-class approach against cancer cachexia.

overall_design: To obtain a systemic overview of the genes regulated by Pen-X-ACIP in aWAT, we performed RNA sequencing in aWAT of tumor bearing mice treated with either Pen-X-ACIP or its scrambled control. (n=4 in each group)

first: Honglei

last: Ji


title: Effect of overexpression and depletion of CCDC137 on miRNA expression in hepatocellular carcinoma cells [miRNA-seq]

city: Guang zhou

first: Shuang

last: Tao

address: 2693 Kaichuang Avenue

institute: Sun Yat-sen University

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the function of CCDC137 in the regulation of miRNA expression, we established CCDC137-overexpressing and CCDC137-knockdown cells.We then performed miRNA expression profiling analysis using data obtained from miRNA-seq of CCDC137-overexpressing and CCDC137-knockdown cells.

overall_design: Comparative miRNA expression profiling analysis of miRNA-seq data from CCDC137-overexpressing cells, CCDC137-knockdown cells and their specific control cells.

first: Zhen-Dong

last: Xiao

first: Shu-Juan

last: Xie

first: Li-Ting

last: Diao


title: RNA-seq of CCDC137-APOBEC1 expressing HCCLM3 cells [APOBEC1-seq]

summary: We established GFP/CCDC137-APOBEC1 transfected HCCLM3 cells.Then doxycycline was added to induce the expression of GFP/CCDC137-APOBEC1.We then performed gene expression profiling analysis using RNA obtained from GFP/CCDC137-APOBEC1 overexpressing HCCLM3 cells with or without doxycycline treatment.

overall_design: Gene expression profiling analysis of mRNA-seq data from GFP/CCDC137-APOBEC1 expressing HCCLM3 cells with or without doxycycline treatment.


title: Effect of overexpression and depletion of CCDC137 on gene expression in hepatocellular carcinoma cells [RNA-seq]

summary: To investigate the function of CCDC137 in the regulation of gene expression, we established CCDC137-overexpressing and CCDC137-knockdown cells.We then performed gene expression profiling analysis using data obtained from RNA-seq of CCDC137-overexpressing and CCDC137-knockdown cells.

overall_design: Comparative gene expression profiling analysis of mRNA-seq data from CCDC137-overexpressing cells, CCDC137-knockdown cells and their specific control cells.


title: CCDC137 in HCC cells

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

overall_design: Refer to individual Series


title: Affymetrix gene expression profiling of GEMM uteri with perturbation of Pten and Fbxw7 at 8 weeks age

city: Oxford

first: David

last: Church

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

summary:
Mice with (i) PR-Cre; (ii) PR-Cre, Fbxw7 R482Q/+; (iii) PR-Cre, Pten fl/fl; (iv) PR-Cre, Pten fl/fl, Fbxw7 R482Q/+
Uterine RNA was harvested at 8 weeks age and expression profiling done by Affymetrix Clariom S Mouse HT array

overall_design: GEMM experiment (BL6)

middle: N


title: Digital Spatial Profiling of CD4+ cells in classic Hodgkin lymphoma.

city: Krume

first: Koichi

last: Ohshima

address: Asahimachi 67

institute: Kurume University

summary: Classic Hodgkin lymphoma (CHL) harbors a small number of Hodgkin-Reed-Sternberg (HRS) cells scattered among numerous lymphocytes. HRS cells are surrounded by distinct CD4+ T cells in a rosette-like manner. These CD4+ T cell rosettes play an important role in the tumor microenvironment (TME) of CHL. To elucidate the interaction between HRS cells and CD4+ T cell rosettes, we completed digital spatial profiling to compare the gene expression profiles of CD4+ T cell rosettes and other CD4+ T cells separated from the HRS cells. Tumor necrosis factor receptor superfamily member (TNFRSF) 4 or OX40 showed significantly higher expression in CD4+ T cell rosettes when compared with other CD4+ T cells. Programed cell death-1 (PD-1) and cytotoxic T lymphocyte associated protein 4 (CTLA-4) tended to be highly expressed in CD4+ T cell rosettes compared to other CD4+ T cells. Immunohistochemistry revealed variable expression of these immune checkpoint molecules in the CD4+ T cell rosettes. This study introduced a new pathological approach to the TME and provided deeper insight into CD4+ T cells in CHL.

overall_design: Total 24 areas of interest from 8 CHL were sequenced using GeoMx Digital Spatial Profiler (Nanostring Technologies), with the Human Whole Transcriptome Altas (18,000+ genes)

first: M

last: Takeuchi

first: H

last: Miyoshi

first: K


title: Reduced fatty acid synthesis and enhanced oxidation promote human definitive endoderm differentiation by mediating SMAD3 nuclear localization via acetylation

first: chenchao

last: yan

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hESCs and its KO derivatives (CPT2-KO).

first: Ying

last: Yi

first: Chenchao

last: Yan

first: Wei

last: Jiang


title: Effect of S. epidermidis phenol-soluble modulins on  murine dorsal skin (24h)

city: La Jolla

first: Michael

middle: R

last: Williams

address: 9500 Gilman Drive

department: Dermatology

institute: UC San Diego

summary:
To investigate the effect of both S. epidermidis  phenol-soluble modulins (PSMs)  and EcpA genetic knockouts on murine back skin.
We then performed gene expression profiling analysis using data obtained from RNA-seq of  5 conditions (n=3 per condition).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for murine back skin after 24h application of live S. epidermidis 1457 WT or PSM/EcpA knockout strains (n=3 per condtion).

first: Richard

last: Gallo


title: HSV-1 exploits host heterochromatin for nuclear egress

city: Seattle

first: Daphne

last: Avgousti

state: WA

address: 1100 Fairview Avenue North C1-201

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

sample_organism:
Homo sapiens
Human alphaherpesvirus 1

platform_organism:
Homo sapiens
Human alphaherpesvirus 1


title: Effect of high fat diet (HFD) on gene expression profile of regulatory T cells (Tregs) in the skin

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: We found that HFD inhibit the homeostasis of skin Tregs. The goal of this study is to investigate the mechanism by which HFD dysregulates skin Tregs

overall_design: 6-8-week-old Pparg-Tdt Foxp3-thy1.1 mice were fed on normal chow diet (NCD) or HFD for 16 weeks. Tregs from the ears were sorted for RNA-Seq.

first: Christopher

first: Pulavendran

last: Sivasami

first: Chaoran

last: Li


title: Effect of Palmitic acid on the transcriptional profile of skin regulatory T cells (Tregs)

summary: We found that palmitic acid inhibits proliferation and cell death of Tregs in the skin. The goal of this study is to investigate how Palmitic acid drives lipid toxicity in skin Tregs

overall_design: Tregs were sorted from skin of 2-3-week-old Pparg-tdTKI/KI Foxp3-thy1.1KI/KI mice that were injected with 100ng/g body weight recombinant mouse IL-33 twice in a week, and were cultured in the presence of 2000 U/ml recombinant human IL-2 and 20 ng/ml IL-33 with 300uM BSA or BSA-conjugated PA for 3 days. Live Tregs were sorted again for RNA-Seq


title: Effect of SIRT7 deletion on gene expression of aged mouse liver

city: Kumamoto

first: Tomonori

last: Tsuyama

state: Kumamoto

address: 1-1-1, Honjo Chuo-ku

department: Faculty of Life Sciences

institute: Kumamoto university

summary: Male Sirt7 KO mice exhibit an lifespan extension and increased FGF21 expression in liver. To reveal the mechanism of the increase of hepatic FGF21 expression in aged male Sirt7 KO mice, we performed RNA-seq analysis of the liver.

overall_design: RNA-seq data for liver from 24-month-old WT and SIRT7 KO male mouse.

first: Masaya

last: Yamazaki

first: Tomoya

last: Mizumoto

first: Kazuya

last: Yamagata


title: Gene expression profile at single cell level of whole melanoma tumor dissociations taken from sedentary or exercised mice

city: Houston

first: Keri

last: Schadler

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: Exercise reduces tumor growth in certain models but the mechanisms driving this is unknown. Tumors from sedentary or exercised mice were removed and processed for single cell sequencing to explore transcriptional changes in the tumor microenvironment induced by exercise.

overall_design: 600,000 YUMMER1.7 melanoma cells were injected subcutaneously into male C57Bl/6 mice. After tumor establishment, mice were randomized into sedentary or exercise treatment. Exercising mice ran at 12meters/min, 45min/day for 14 consectutive days. Tumors were harvested, digested, and single cell suspensions were submitted for scRNA-seq

first: Hannah

last: Savage

first: Darlan

last: Conterno Minussi

first: Jerome

last: Lin


title: The miR-23-27-24 Clusters Drive Lipid-Associated Macrophage Proliferation in Obese Adipose Tissue II

status: Public on Jun 30 2023

city: Nashville

first: Heather

last: Pua

state: Tennessee

address: 1161 21st Avenue South

department: Pathology, Microbiology, and Immunology

institute: Vanderbilt Medical Center

summary:
Bone marrow isolated from control and cluster KO mice were differentiated to macrophages
Macrophages were subsequently metabollically-activated for 24 h to encourage an obese-like ATM phenotype. Cells were harvested for bulk RNA-seq

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and knockout metabollically-activated bone marrow-derived macrophages  (4 biological replicates per genotype; 8 total)

first: Neil

last: Sprenkle

middle: H


title: Strength of CD28 costimulation directs self-renewal or differentiation of TCF-1+ PD-1+ CD8 T cells through metabolic regulation

first: Dan

last: Filipescu

state: New York

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: During persistent antigen stimulation, such as in chronic infections and cancer, T cells differentiate into a hypofunctional exhausted state to survive. Exhausted PD-1+ CD8 T cell responses are sustained by TCF-1+ precursors (Tpex) that self-renew or differentiate into exhausted T cells (Tex) that retain some effector function. Tpex have high expression of the costimulatory molecule CD28 and are the cells that respond to PD-1 targeted immunotherapy. Here, we demonstrate that abrogation of CD28 signaling impairs maintenance of anti-viral T cell responses during chronic infection. Low-level CD28 signaling was required to preserve mitochondrial fitness and self-renewal of Tpex, whereas stronger CD28 signaling enhanced glycolysis and promoted Tpex differentiation. Our findings show that CD28 signaling is essential for long-term maintenance of antigen-specific T cells during chronic stimulation, and suggest that the activation status of antigen presenting cells determines Tpex differentiation into more functional effector-like Tex cells.

overall_design: Gene expression analysis of bulk sorted Tpex (CD73+) or Tex (Tim3+) P14 CD28flox CREert2+ (CD28neg) or creERT2neg (CD28+) from mice chronically infected with LCMV cl13 and 2 weeks post tamoxifen treatment to understand the molecular impact of CD28 loss in maintenance and differentiation of virus-specific T cells.

first: Etienne

last: Humblin

first: Alice

last: Kamphorst


title: CD133+ Intercellsome Mediates Direct Cell-Cell Communication to Offset Intracellular Signaling Deficit

first: Yan

last: Liang

address: 9500 Gilman Drive, BRFII Room 1220 Bay B

summary: We performed single-cell RNAseq and bulk RNAseq analysis to investigate the function of CD133 and a new mechanism of intercellular comminication for cell proliferation, in mouse liver, following partial hepatectomy (PHx).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For single-cell RNAseq, hepatocytes were isolated from wild type (WT) and hepatocyte-specific Shp2 knockout (SKO) livers at 4 hours and 2 days following PHx, and Shp2/Prom1 double knockout (DKO)  livers at 2 days following PHx. For bulk RNA-seq, total RNA was isolated from CD133+ vesicle, extracellular vesicle and whole cells.

first: Kota

last: Kaneko

first: Qing

last: Liu

first: Wendy

middle: S

last: Chen

first: Gen-Sheng

last: Feng


title: Nuclear GRP78 on transcription regulation

city: Los Angeles

first: Ze

address: 1441 Eastlake Ave. NOR 5306

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary: To investigate the role of nuclear GRP78 on transcriptional activity

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H1975 cells and its knockdown and overexpressed derivatives

first: Justin

last: Wang

first: Dat

last: Ha

first: Amy

last: Lee


title: Single-cell transcriptomic analysis of sorted CD8+ T cell subsets isolated from the spleen of C57BL/6 mice treated with aCD137 or an Ig control.

city: Toulouse

first: Liliana

middle: Elisa

last: Lucca

address: 2 Avenue Hubert Curien

department: Immunology

institute: CRCT

summary: We report the single cell RNA sequencing of mouse CD8+ T cells sorted from the spleen into three differentiation subsets: effector, precursor exhausted and terminally exhausted. CD8 T cells from mice treated with anti-CD137 or an isotype control are compared.

overall_design: Five C57BL/6 mice were treated with anti-CD137 (10ug, clone 3H3) twice a week for 14 days. Ten C57BL/6 mice were treated with an Ig control (100ug, clone HRPN) also twice a week for 14 days. Mice were sacrificed and spleens were harvested for T cell sort. Teff cells were sorted as CD44hiPD1-, precursor exhausted T cells were sorted as CD44hiPD1+Slamf6+Tim3-, and exhausted T cells as CD44hiPD1+Slamf6-Tim3+.

first: Ludovic

last: Martinet


title: Effects of Huatan Jiangzhuo Decoction and Poria cocos - Alismatis Rhizoma on gene expression in liver of rats with hyprelipidemia

city: Guangzhou

first: Xiaowen

last: Zhou

state: Guangdong

address: No.232, East Waihuan Road, Guangzhou Higher Education Mega Centre, Panyu District

institute: Guangzhou University of Chinese Medicine

summary: Huatan Jiangzhuo Decoction, a traditional Chinese medicine composition, has been used to treat patients with hyperlipidemia (HLP). To investigate the therapeutic mechanism of Huatan Jiangzhuo decoction(HTJZD) and  Poria cocos (PC) - Alismatis Rhizoma (AR) on gene expression in liver of rats with HLP, this study performed gene expression profiling analysis using data obtained from RNA-seq technology. It’s predicted that the potential role of regulating the expression of differentially expressed genes in the treatment of HLP by HTJZD and PC-AR separately.

overall_design: Firstly, the rat model of HLP was established by the fed with high-fat diet (HFD). Next, In the intervention phase, the rats in control group were fed with normal diet and the rat model were continuously supplied with HFD but regrouped into three groups: model group, HTJZD group and PC-AR group. Liver samples of rats which was used in RNA-seq to explore the underlying mechanism of effects of HTJZD and PC-AR in HLP. 4 experimental conditions, 1 time point

first: Qi

last: Ren

first: Xiantao

last: Li

first: Xiaoqi

first: Zhenqian

last: Yan

first: Yaxin

first: Ge

last: Fang

first: Bin

first: Shuxian

first: Jiangbiao

last: Luo


title: Lipid Nanoparticles Allow Efficient and Harmless Ex Vivo Gene Editing of Human Hematopoietic Cells [RNAseq_lnps]

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

summary: Ex vivo gene editing in T cells and hematopoietic stem/progenitor cells (HSPCs) holds promise for treating diseases. Gene editing encompasses delivery of a programmable editor RNA or ribonucleoprotein, often achieved ex vivo by electroporation and, when aiming to homology-driven correction, of a DNA template often provided by viral vectors together with a nuclease editor. Whereas HSPCs activate robust p53-dependent DNA damage response (DDR) upon nuclease-based editing, the responses triggered in T cells remain poorly characterized. Here, we performed comprehensive multi-omics analyses and found that electroporation is the main culprit of cytotoxicity in T cells, causing death and cell cycle delay, perturbing metabolism and inducing inflammatory response. Nuclease RNA delivery by lipid nanoparticles (LNPs) nearly abolished cell death and ameliorated cell growth, improving tolerance to the procedure and yielding higher number of edited cells compared to electroporation. Transient transcriptomic changes upon LNP treatment were mostly caused by cellular loading with exogenous cholesterol, whose potentially detrimental impact could be overcome by limiting exposure. Notably, LNP-based HSPC editing dampened p53 pathway induction and supported higher clonogenic activity and similar or higher reconstitution by long-term repopulating HSPCs compared to electroporation, reaching comparable editing efficiencies. Overall, LNPs may allow efficient and harmless ex vivo gene editing in hematopoietic cells for treatment of human diseases.

overall_design: Whole transcriptomic analysis 24 hours after treatment of CD4+ T cells from 3 healthy donors and of HSPC (from 3 replicates) for CD40LG editing treated with LNPs. As controls, cells untreated (UT), mock electroporated or treated with LNPs formulated without RNA (Empty LNPs) were employed.

first: Valentina

last: Vavassori

first: Samuele

last: Ferrari

first: Ivan

last: Merelli

first: Luigi

last: Naldini


title: Ssdp influences neurodevelopment and autism-like behaviors in Drosophila melanogaster

city: Doha

first: Safa

last: Salim

state: Qatar

address: 21, Kuwari Building, Khaleel Bin Ahmed Street, Umm-Ghuwailina

country: Qatar

institute: Hamad Bin Khalifa University

summary: To investigate the alterations in gene expression in Ssdp transgenic overexpressing flies compared with controls. We then performed gene expressing profiling from the RNA-seq data to determine if any genes are dysregulated.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Ssdp[2082-G4]-Gal4/+ flies compared to w1118 controls

first: Mohammad

last: Farhan


title: Single-cell analysis of human fetal epicardium reveals its cellular composition and identifies CRIP1 as a modulator of EMT

status: Public on Jun 29 2023

city: Leiden

first: Anke

last: Smits

address: Einthovenweg 20

department: Cell and Chemical Biology

country: Netherlands

institute: Leiden University Medical Center

summary: Epicardial cells can undergo epithelium-to-mesenchymal transition (EMT) upon which the epicardium-derived cells (EPDCs) migrate into the myocardium and deliver growth factors or differentiate into smooth muscle cells or fibroblasts. The cell fate of EPDCs has been proposed to be determined by the persistence of subpopulations found in the proepicardial organ, but findings regarding this epicardial heterogeneity have been inconsistent. In the human heart, the composition of the developing epicardium is largely unknown. Here we performed a direct analysis of the human fetal epicardium through single cell RNA sequencing to investigate its composition and to search for regulators of developmental processes

overall_design: Isolated epicardial cells of human fetal hearts (14-15 weeks) were sorted by Fluorescence-Activated Cell Sorting (FACS) based on viability and analyzed using scRNA seq

first: Thomas

last: Streef

first: Esmee

last: Groeneveld

first: Tessa

last: van Herwaarden

first: Jesper

last: Hjortnaes

first: Marie

last: Goumans


title: Metabolic competition between lipid metabolism and histone methylation regulates sexual differentiation in human malaria parasites

city: New York

first: Bjorn

middle: FC

last: Kafsack

address: 1300 York Avenue

department: Microbiology & Immunology

institute: Weill Cornell Medicine

summary: Like most pathogens, malaria parasites balance persistence in the current host with transmission to the next. For Plasmodium falciparum, the most widespread and virulent human malaria parasite, persistence depends on continuous asexual replication in red blood cells while transmission requires differentiation into non-replicating gametocytes, the male and female cells able to infect the mosquito vector. This developmental decision is controlled via stochastic derepression of a heterochromatin-silenced locus encoding the transcription factor PfAP2-G, which acts as the master switch for sexual differentiation. Recent work showed that the frequency of pfap2-g derepression is responsive to extracellular levels of phospholipid precursors. However, the regulatory mechanisms linking these metabolites to epigenetic regulation of pfap2-g was hitherto unknown. Using chemical, metabolomic, and genetic approaches, we show that this response is mediated by metabolic competition for the methyl donor S-adenosylmethionine between histone methyltransferases and phospho-ethanolamine methyltransferase, a critical enzyme in the parasite’s pathway for de novo phosphatidyl-choline synthesis. When phosphatidyl-choline precursors are scarce, increased consumption of S-adenosylmethionine for de novo synthesis of phosphatidyl-choline results in a decrease in histone methylation marks that mediate silencing of pfap2-g, thereby up-regulating its transcription and increasing the frequency of sexual differentiation. Our findings reveal a key connection between metabolite utilization and gene expression in malaria parasites that forms the mechanistic link between phosphatidyl-choline metabolism and the frequency of sexual commitment.

overall_design: We performed Cut&RUN for H3K9me3 and H3K4me3 on P. falciparum nuclei under different growth media conditions

first: Chantal

last: Harris


title: Effect of depletion of USF1 or USF2 on Jurkat Tat mHIV-Luciferase T cell gene expression.

city: Vancouver

last: Sadowski

state: British Columbia

address: 2350 Health Sciences Mall

country: Canada

institute: University of British Columbia

summary:
To investigate the cooperative function USF factors for the regulation of T cell transcriptom, we established Jurkat mHIV-Luciferase cells in which USF1 or USF2 was knocked out by CRISPR-Cas9.
We then performed gene expression profiling analysis using data obtained from RNA-seq of cell lines either left untreated or stimulated by PMA and Ionomycin co-treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wildtype, USF1 KO, and USF2 KO cell lines under basal or activated conditions.

first: Horvath

last: Riley

first: Sadowski

last: Ivan


title: CSF1R inhibition by PLX5622 affects multiple immune cell compartments with tissue-specific metabolic effects

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

summary: We found that long-term CSF1R-inhibition by PLX5622 depleted tissue resident macrophages in different organs. This alteration resulted in a dual impact on glucose homeostasis with improved insulin sensitivity predominantly in the liver, combined with an insulin secretion defect in the islets of Langerhans. RNA-Seq analysis of islets of mice treated with PLX5622 compared to control mice hinted at a role of IL-1β in supporting insulin secretion,

overall_design: RNA-sequencing was performed of pancreatic islets (islets of Langerhans) from mice on PLX5622 or control diet for 5.5 or 8.5 months.

first: Angela

last: Bosch

first: Claudia

last: Cavelti-Weder

first: Julien

last: Roux


title: Effect of ERI1 deficiency on gene expression during chondrogenic differentiation of human iPSCs

city: Tokyo

first: Long

last: Guo

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

institute: RIKEN

summary: To investigate the function of ERI1 in the regulation of chondrogenic differentiation, we established iPSC lines from the lymphoblastoid cells of the individuals with ERI1 mutations. We then performed gene expression profiling analysis using data obtained from RNA-seq of two cell lines (healthy mother-derived iPSCs and patient-derived iPSCs).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ERI1-deficient iPSC lines.

first: Jingyi

last: Xue

first: Juan

last: Wang

first: Shiro

last: Ikegawa


title: Lipid Nanoparticles Allow Efficient and Harmless Ex Vivo Gene Editing of Human Hematopoietic Cells

first: Stefano

last: Beretta

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

overall_design: Refer to individual Series


title: Repressed Blautia-acetate immunological axis underlies chronic stress promoted breast cancer progression

status: Public on Jun 27 2023

first: Wanyu

last: Hu

address: 1838 Guangzhou Avenue North

institute: Southern medical university

summary: To explore acetate wether exerted its effects on T cell recall function and metabolism via transcriptional regulation. We used the Easy sepTM Mouse CD8+ T Cell Isolation Kit for negative selection of CD8+ T cells. Then CD8+ T cells were cultured in complete RPMI-1640 culture medium with recombinant mouse IL-2 (15 ng/ml) and anti-CD28 (1 µg/ml) in plate pre-coated with anti-CD3 (2 mg/ml). CD8+ T cells (2×106 cells/ml) were treated with or without sodium acetate (5 mM) for 24 hour, and co-cultured with/without 4T1 cells (1×105 cells/ml) for 48 hours. Subsequently, we removed the dead cells with EasySepTM Dead cell Removal (Annexin V) Kit and collected CD8+ T cells for RNA sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD8+ T cells after different treatments.

first: Ling

last: Ye


title: Loss of the Atrial Fibrillation-related gene, Zfhx3, Results in Atrial Dilation and Arrhythmias by Disruption of Genes Essential for Cardiovascular Homeostasis

city: Cambridge

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

summary: Background: ZFHX3, a gene that encodes a large transcription factor, is the second-most significantly associated locus with AF, but its function in the heart is unknown. This study aims to identify causative genetic variation related to AF at the ZFHX3 locus and examine the impact of Zfhx3 loss on cardiac function in mice. Methods: CRISPR-Cas9 genome editing, chromatin immunoprecipitation, and luciferase assays in pluripotent stem cell-derived cardiomyocytes were used to identify causative genetic variation related to AF at the ZFHX3 locus. Cardiac function was assessed by echocardiography, MRI, electrophysiology studies, calcium imaging, and RNA sequencing in mice with heterozygous and homozygous cardiomyocyte-restricted Zfhx3 deletion (Zfhx3 Het and KO, respectively). Human cardiac single-nucleus ATAC-sequencing data was analyzed to determine which genes in atrial cardiomyocytes are directly regulated by ZFHX3. Results: We found SNP rs12931021 modulates an enhancer regulating ZFHX3 expression, and the AF risk allele is associated with decreased ZFHX3 transcription. We observed a gene-dose response in AF susceptibility withZfhx3KO mice having higher incidence, frequency, and burden of AF thanZfhx3Het and WT mice, with alterations in conduction velocity, atrial action potential duration, calcium handling and the development of atrial enlargement and thrombus, and dilated cardiomyopathy. Zfhx3 loss results in atrial-specific differential effects on genes and signaling pathways involved in cardiac pathophysiology and AF. Conclusions: Our findings implicate ZFHX3 as the causative gene at the 16q22 locus for AF, and cardiac abnormalities caused by loss of cardiac Zfhx3 are due to atrial-specific dysregulation of pathways involved in AF-susceptibility. Together, these data reveal a novel and important role for Zfhx3 in the control of cardiac genes and signaling pathways essential for normal atrial function.

overall_design: Total RNA was collected from left and right atria from Zfhx3 Het, KO, and wildtype (control) mice. Next, mRNA-seq libraries were generated and sequenced and differential expression analysis was performed.

first: Heather

last: Jameson

first: Patrick

last: Ellinor


title: Transcriptomic analysis of VK12653 Multiple Myeloma bone marrow microenvironmentupon treatment with anti-CD137 agonists

first: Liliana

last: Lucca

summary: We report the RNA sequencing of VK12653 Multiple Myeloma bone marrow microenvironment upon treatment with anti-CD137 agonists

overall_design: A global transcriptomic analysis of BM cells isolated from WT mice challenged with Vk12653 myeloma cells (2.106 cells, i.v) treated or not with anti-CD137 mAb (10 µg; 3H3, i.p twice a week) was performed by RNAseq using TruSeq Stranded mRNA Sample Preparation kit on a Novaseq 6000 S4 Illumina sequencing platform  generating in average 20 million pairs of reads per sample.

first: Ludovic

last: Martinet


title: PD-L1 Enhanced by cis-Urocanic Acid on Langerhans Cells Inhibits Vg4+ gdT17 Cells in Psoriatic Skin Inflammation

city: Taipei City

first: Yeh Fong

last: Tan

state: Taipei

address: No. 128, Section 2, Academia Rd, Nangang District

department: Institute of BioMedical Sciences

country: Taiwan

institute: Academia Sinica

summary:
To establish the role of PD-L1 expression on Langerhans cells and its influence on psoriatic skin inflammation, we isolated Langerhans cells from harvested ears of wild type mice treated with Vaseline or Imiquimod.
We then determined the gene expression profile of isolated Langerhans cells from the different groups at a single time point using data from RNA-seq. The experiment was performed in duplicate.

overall_design: Transcriptomic analysis of RNA-seq data of isolated Langerhans cells from ears of wild type mice treated with Vaseline (negative control) or Imiquimod (test).

first: Yeh

first: Chen-Yun

last: Yeh

first: Yungling

last: Lee


title: The PFYRE Subdomain in Master Growth Repressor DELLA is Essential for Its Association with Target Chromatin via Histone H2A Binding

city: Durham

first: Hao

last: Tian

state: North Carolina

address: Science drive 124

department: Biology

institute: Duke University

summary:
The DELLA genes encode conserved master growth repressors in plants, and they are also known as ‘Green Revolution’ genes because of their pivotal role in modulating stature of the high-yielding wheat varieties, which were crucial for the success of the ‘Green Revolution’ in the 1960s. At the cellular level, DELLA proteins are nuclear-localized transcription regulators, which play a central role in controlling plant development in response to internal and environmental cues. Recent studies indicate that DELLAs regulate expression of target genes via direct protein-protein interaction of their C-terminal GRAS domain with hundreds of key transcription factors (TFs) and epigenetic regulators. However, the molecular mechanism of DELLA-mediated transcription reprogramming remains unclear. Here, by characterizing missense alleles of an Arabidopsis DELLA, REPRESSOR OF ga1-3 (RGA), we unveil a novel function of the PFYRE subdomain within its GRAS domain for binding to histone H2A via pulldown and co-IP assays. ChIP-Seq analysis further show that this activity is essential for RGA association with its target chromatin globally. Our results indicate that although DELLAs are recruited to target gene promoters by binding to TFs via its LHR1 subdomain, DELLA-H2A interaction via its PFYRE subdomain is necessary to stabilize the TF-DELLA-H2A complex at the target chromatin. This study provides new insight into the two distinct key modular functions in DELLA for its genome-wide transcription regulation in plants.
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) for RGA vs rga-11 and RGA treated with GA or mock.

overall_design: Tai-ping Sun

first: Xu

last: Huang


summary:
The DELLA genes encode conserved master growth repressors in plants, and they are also known as ‘Green Revolution’ genes because of their pivotal role in modulating stature of the high-yielding wheat varieties, which were crucial for the success of the ‘Green Revolution’ in the 1960s. At the cellular level, DELLA proteins are nuclear-localized transcription regulators, which play a central role in controlling plant development in response to internal and environmental cues. Recent studies indicate that DELLAs regulate expression of target genes via direct protein-protein interaction of their C-terminal GRAS domain with hundreds of key transcription factors (TFs) and epigenetic regulators. However, the molecular mechanism of DELLA-mediated transcription reprogramming remains unclear. Here, by characterizing missense alleles of an Arabidopsis DELLA, REPRESSOR OF ga1-3 (RGA), we unveil a novel function of the PFYRE subdomain within its GRAS domain for binding to histone H2A via pulldown and co-IP assays. ChIP-Seq analysis further show that this activity is essential for RGA association with its target chromatin globally. Our results indicate that although DELLAs are recruited to target gene promoters by binding to TFs via its LHR1 subdomain, DELLA-H2A interaction via its PFYRE subdomain is necessary to stabilize the TF-DELLA-H2A complex at the target chromatin. This study provides new insight into the two distinct key modular functions in DELLA for its genome-wide transcription regulation in plants.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RGA, rga-11 as well as the negative control sly1 dP and sly1 dQ.

overall_design: Tai-ping, Sun

first: Jeongmoo

last: Park

first: Dong-Ha

last: Oh


title: Effect of Flavivirus infections (Kunjin, Zika, Yellow Fever) on gene expression and alternative splicing in U87 cells.

status: Public on Jun 28 2023

city: Sherbrooke

first: Martin

last: Bisaillon

state: QC

address: 3201 rue Jean-Mignault

department: Département de biochimie et de génomique fonctionnelle

institute: Université de Sherbrooke

summary: As obligate intracellular parasites, viruses rely heavily on their host cells for their replication, and therefore dysregulate several cellular processes for their benefit. In return, host cells activate multiple signaling pathways to limit viral replication and eradicate viruses. The present study explores the complex interplay between viruses and their host cells through next generation RNA sequencing. The coding transcriptome of human brain-derived U87 cells infected with Kunjin virus, Zika virus, or Yellow Fever virus were compared to the transcriptome of mock-infected cells. Changes in the abundance of several hundred mRNAs were found in each infection. Moreover, the alternative splicing of hundreds of mRNAs was found to be modulated upon viral infection.

overall_design: U87 cells were either infected (MOI=5) or treated with cell-conditioned media for 24h (n=3 for each virus and control). PolyA-RNAs were extracted and sequenced. Differential gene expression analysis as well as differential alternative splicing analysis were performed using DESeq2 and rMATS, respectively.

first: Carolin

last: Brand

first: Gabrielle

last: Deschamps-Francoeur

first: Kristen

last: Bullard-Feibelman

first: Michelle

last: Scott

first: Brian

last: Geiss


title: The miR-23-27-24 Clusters Drive Lipid-Associated Macrophage Proliferation in Obese Adipose Tissue

first: Heather

last: Pua

address: 1161 21st Avenue South

institute: Vanderbilt Medical Center

summary:
To determine how the miR-23-27-24 miRNA clusters regulate adipose tissue macrophage (ATM) programming in obesity, we placed control mice and mice containing a myeloid-specific deletion of the clusters on high-fat diet for 20weeks.
Following dietary intervention, we performed bulk RNA-seq on F4/80 bead-selected ATMs from obese adipose tissue of control and knockout mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and knockout ATMs from obese adipose tissue  (4 biological replicates per genotype; 8 total)

first: Neil

last: Sprenkle


title: Lipid Nanoparticles Allow Efficient and Harmless Ex Vivo Gene Editing of Human Hematopoietic Cells [RNAseq_electro]

first: Stefano

last: Beretta

overall_design: Whole transcriptomic analyses on human CD4+ T cells from 3 healthy donors, using a previously optimized culture/editing protocol and Cas9 reagents targeting the first intron of CD40LG gene. We compared untreated (UT) cells, mock electroporated cells (mock electro), cells electroporated with RNP without (RNP) or with AAV6 donor (RNP+AAV6), and AAV6-transduced cells (AAV6 only - no electroporation) derived from 3 healthy donors 12 hours after treatment, and at long term.

first: Valentina

last: Vavassori

first: Samuele

last: Ferrari

first: Ivan

last: Merelli

first: Luigi

last: Naldini


title: Single cell Transcriptomic analysis of CD8+ T cells from bone marrow chimeras reconstituted with CD137 wild-type or knock out bone marrow, and implanted with B16K1 melanoma.

first: Liliana

last: Lucca

summary: We report the single cell RNA sequencing of mouse CD8+ T cells in bone marrow chimeras reconsitituted with equal amounts of CD137-/-tomato+ and CD137-/-tomato- bone marrow implanted with B16K1 melanoma. CD8 T cells from the spleen or the tumor infiltrate are compared.

overall_design: (CD137-/-tomato+) and (CD137+/+tomato-) mixed BM chimera were injected s.c. with B16K1 melanoma cells. tomato+ and tomato- spleen and tumor infiltrating CD8+ T cells were isolated using FACSaria™ Fusion (BD biosciences). Single-cell libraries (5′ gene expression) were generated from CD8 cell fractions from 7 mice per group hashed together, using the Chromium Controller Instrument and Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 according to the manufacturer’s protocol (10× Genomics). Single-cell library size and quality were confirmed on the Tapestation 4200 (Agilent) and pooled to reach at least 20,000 read pairs for 5’ Gene Expression Library; 10,000 read pairs of Protein Library. Libraries were sequenced twice on a NextSeq 550 (Illumina) in pair-end sequencing 26 bp (read1) × 91 bp (read2) and a single index 8 bp in length.

first: Ludovic

last: Martinet


title: E2F1 mediates SOX17 Deficiency-Induced Pulmonary Hypertension [scRNA-seq]

city: St. Louis

first: Zhiyu

last: Dai

state: MO

address: 4960 Childrens Place

institute: Washington University in St. Louis

summary: SRY-Box Transcription Factor 17 (SOX17) enhancers variants and mutations are found in patients with pulmonary arterial hypertension (PAH). In human PAH pulmonary endothelial cells, there is a significant downregulation of SOX17 expression. We hypothesized that SOX17 deficiency contributes to the pathogenesis of PAH and found that mice with endothelial specific disruption (ecKO Sox17) developed spontaneous pulmonary hypertension (PH) and exacerbated hypoxia-induced PH. Loss of SOX17 in lung ECs induced endothelial dysfunctions including upregulation of cell cycle programming and paracrine effect, proliferative and anti-apoptotic phenotypes, impaired cellular junction and BMP signaling. E2F Transcription Factor 1 (E2F1) signaling was showed to mediate the SOX17 deficiency-induced EC dysfunction. Pharmacological inhibition of E2F1 in ecKO Sox17 mice attenuated PH and cell cycle programming. Our study demonstrated that endothelial SOX17 deficiency induces PH through E2F1 and targeting E2F1 signaling represents a promising approach in PAH patients.

overall_design: WT and Sox17 cKO lung, WT Cell hashing oligo sequence: ACCCACCAGTAAGAC, cKO Cell Hashing oligo sequence: GGTCGAGAGCATTCA


title: Single cell Transcriptomic analysis of CD8+ T cells treated with anti-CD137 agonists within VK12653 Multiple Myeloma bone marrow microenvironment .

summary: We report the single cell RNA sequencing of mouse CD8+ T cells infiltrating VK12653 Multiple Myeloma lesions upon treatment with anti-CD137 agonists .

overall_design: C57BL/6 mice were injected with Vk12653 MM cells. After 10 days, mice were treated with anti-CD137 (100 µg, 3H3, BioXcell, twice a week) or with control IgG (100 µg, HRPN,BioXcell). At the indicated time points, CD8+ T cells were isolated from the BM using mouse CD8+ T cell isolation kit (Miltenyi Biotec) and FACSaria™ Fusion (BD biosciences). Single-cell libraries (3′ gene expression) were generated using the Chromium Controller Instrument and Chromium Single Cell 3′ Library & Gel Bead Kit v3 according to the manufacturer’s protocol (10× Genomics).  Single-cell library size and quality were confirmed on the Fragment Analyzer (Agilent). KAPA Quantification Kit for Illumina platforms (KAPA Biosystems, Roche) was used to quantify libraries. The libraries were sequenced on a NextSeq 550 (Illumina) in pair-end sequencing 28 bp (read1) × 91 bp (read2) and a single index 8 bp in length.


title: Transcriptome comparison of PMN-MDSCs and and normal neutrophils

status: Public on Jun 26 2023

city: Shanghai

first: Zhigang

last: Lu

address: 130 Dongan Road, Shanghai

department: IBS

institute: Fudan University

summary: Polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC), also named pathologically activated neutrophil, is a critical component of tumor microenvironment (TME), playing crucial roles in tumor progression and therapy resistance. Here, we compared the transcriptome of PMN-MDSCs from B16 tumor bearing mice and the neutrophils from tumor free mice.

overall_design: B16-F10 melanoma cells were inoculated subcutaneously into wild-type C57/BL6 mice. At day 15 post inoculation, PMN-MDSCs were isolated spleen of tumor bearing (TB) mice by AutoMACS with EasySep Mouse Neutrophil Enrichment Kit (Stem cell). Normal neutrophils were isolated from tumor free (TF) heathy control mice by the same methods. Total RNA was extracted by TRIZOL (Invitrogen) for RNAseq and comparison.

first: Min

last: Luo

first: Yun

last: Zhao


title: Transcription factor EGR2 controls homing and pathogenicity of TH17 cells in the central nervous system.

city: Arlington

first: Vanja

last: Lazarevic

state: VA

address: 1820 N Tuckahoe Street,

department: National Cancer Institute

institute: National Institutes of Health

summary: CD4+ T helper 17 (TH17) cells protect barrier tissues but also trigger autoimmunity. The mechanisms behind these opposing processes remain unclear. Here, we found that the transcription factor EGR2 controlled the transcriptional program of pathogenic TH17 cells in the central nervous system (CNS) but not that of protective TH17 cells at barrier sites. EGR2 was significantly elevated in myelin-reactive CD4+ T cells from patients with multiple sclerosis and mice with autoimmune neuroinflammation. The EGR2 transcriptional program was intricately woven within the TH17 cell transcriptional regulatory network and showed high interconnectivity with core TH17 cell-specific transcription factors. Mechanistically, EGR2 enhanced TH17 cell differentiation and myeloid cell recruitment to the CNS by upregulating pathogenesis-associated genes and myelomonocytic chemokines. T cell-specific deletion of Egr2 attenuated neuroinflammation without compromising the host’s ability to control infections. Our study shows that EGR2 regulates tissue-specific and disease-specific functions in pathogenic TH17 cells in the CNS.

overall_design: ATAC-seq of naïve CD4+ T cells or in vitro polarized TH17 cells from 2D2 WT or 2D2 Egr2ΔT mice. Each condition includes three biological replicates.

first: Y

last: Gao

last: Wang

first: D

last: Chauss

first: A

middle: V

last: Villarino

first: V

last: Link

first: H

last: Nagashima

first: C

last: Spinner

last: Koparde

first: N

last: Bouladoux

first: M

last: Abers

first: T

last: Break

first: L

middle: B

last: Chopp

first: J

last: Park

last: Zhu

last: Wiest

first: W

last: Leonard

last: Lionakis

last: O'Shea

first: B

last: Afzali

last: Belkaid


title: CD300ld regulates tumor immunity

first: Zhigang

last: Lu


title: CD300ld regulates tumor immunity - In vivo Crispr-Cas9 screening

summary: To identify surface proteins on myeloid cells involved in the establishment of the tumor immune microenvironment, we selected transmembrane protein encoding genes with a high myeloid/lymphoid expression ratio to construct a sgRNA library. The sgRNA pool was transduced into hematopoietic stem/progenitor cells of Cas9 mice to transplant the lethal irradiated mice for immune system reconstitution, then followed by B16-F10 tumor inoculation. Once the tumor was established, the tumor and bone marrow (BM) were collected for sgRNA deep sequencing and comparison.

overall_design: Lentiviral particles encoding sgRNA pool were transduced into freshly lineage negative HSC/progenitors isolated from fetal liver of Cas9-tdTomatao mice at a multiplicity of infection of 0.25. At 60 h post spin-infection, the transduced cells were retro-orbitally transplanted in lethally irradiated (X-ray, 9.5 gray) recipient mice (1 million cells per mouse). B16-F10 cells were injected s.c to recipient mice 4 weeks after transplantation. Mice were sacrificed at day-15 post tumor cell inoculation, and CD45+ cells were collected from bone marrow and tumor by flow cytometry. genomic DNA was isolated from all samples using Universal Genomic DNA Purification Mini Spin Kit (Qiagen). sgRNA encoding fragments were amplified for deep sequencing .

first: Min

last: Luo

last: Zhao


title: Transcriptome comparsion of WT and CD300ld KO PMN-MDSC

summary: Polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC), also named pathologically activated neutrophil, is a critical component of tumor microenvironment (TME), playing crucial roles in tumor progression and therapy resistance. CD300ld is specifically expressed in normal neutrophils and is upregulated in PMN-MDSCs upon tumor bearing. CD300ld knockout (KO) inhibits the development of multiple tumor types in a PMN-MDSC-dependent manner. Here, we compared the transcriptome of PMN-MDSCs from WT mice and CD300ld KO mice.

overall_design: B16-F10 melanoma cells were inoculated subcutaneously into wild-type (WT) or CD300ld KO mice. The mice were sacrificed at day 15 post inoculation, and PMN-MDSCs were isolated by AutoMACS with EasySep Mouse Neutrophil Enrichment Kit (Stem cell). PMN-MDSC-1 & 6 (WT), PMN-MDSC-11 &13 (KO). Total RNA was extracted by TRIZOL (Invitrogen) for RNAseq and comparison.

first: Yun


title: RNA-seq analysis of thick ascending limb (TAL) epithelium isolated from uromodulin (UMOD) deletion mutation mice and wild type (WT) mice at 16wks of age

status: Public on Jun 25 2023

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

summary: To gain insight into the mechanisms underlying the defective autophagic activity and its functional impact on the pathogenesis of disease, we performed RNA sequencing (RNA-seq) of mRNA isolated from TAL cells purified from heterozyous Umod deletion mutation mice (DEL/+) and Umod +/+ littermates at 16 weeks, the full-blown stage of the disease. Our analysis revealed that 9566 genes were significantly differentially expressed between mutant and WT TAL cells, including 4706 upregulated and 4860 downregulated.

overall_design: TAL mRNA profiles of 16-week old UMOD WT and deletion mutation mice were generated by RNA-seq.

first: Ying

last: Chen


title: OsNAR2.1 induced endogenous nitrogen concentration variation affects transcriptional expression of miRNAs in rice

status: Public on Jun 23 2023

city: Nanjing

first: Yong

last: Zhang

address: street of Zhongling 50

institute: Jiangsu Acdemy of Agricultural Sciences

summary: The studies of rice nitrogen concentration on the expression of miRNA so far are mostly limited to the exogenous nitrogen, leaving the effect of endogenous nitrogen largely unexplored. OsNAR2.1 is a high-affinity nitrate transporter partner protein which plays a central role in nitrate absorption and translocation in rice. The expression of OsNAR2.1 could influence the concentration of the endogenous nitrogen in rice. We showed that the expression and production of miRNA in rice can be influenced by manipulating the endogenous nitrogen concentration via OsNAR2.1 transgenic lines. The small RNA expressed differently in two transgenic rice lines (nitrogen efficient line with overexpression of OsNAR2.1 (Ov199), nitrogen-inefficient line with knockdown OsNAR2.1 by RNAi (RNAi)) compared to the wild-type (NP). Comparative hierarchical clustering expression pattern analysis revealed that the expression profiles of mature miRNA in both transgenic lines were different from NP.

overall_design: miRNA sequence of wild type of Nipponbare, OsNAR2.1 line and pUbi-OsNAR2.1 transgenic line

first: Xiaoru

last: Fan

first: Yulong

last: Wang

first: Pulin

last: Kong

first: Ling

first: Xiaorong

first: Yadong


title: Reduction of Nemo-like kinase increases lysosome biogenesis and ameliorates TDP-43-related neurodegeneration

status: Public on Jun 24 2023

city: New Haven

first: Leon

middle: L

last: Tejwani

state: CT

address: 295 Congress Ave, BCMM139

department: Neuroscience

institute: Yale University

summary: Protein aggregation is a hallmark of many neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS). Although mutations in TARDBP, encoding TDP-43, account for less than 1% of all ALS cases, TDP-43-positive aggregates are present in nearly all ALS patients, including patients with sporadic ALS (sALS) or carrying other familial ALS (fALS)-causing mutations. Interestingly, TDP-43 inclusions are also present in subsets of patients with frontotemporal dementia, Alzheimer’s disease, and Parkinson’s disease; therefore, methods of activating intracellular protein quality control machinery capable of clearing toxic cytoplasmic TDP-43 species may alleviate disease-related phenotypes. Here, we identify a novel function of Nemo-like kinase (Nlk) as a negative regulator of lysosome biogenesis. Genetic or pharmacological reduction of Nlk increased lysosome formation and improved clearance of aggregated TDP-43. Furthermore, Nlk reduction ameliorated pathological, behavioral, and lifespan deficits in two distinct mouse models of TDP-43 proteinopathy. Because many toxic proteins can be cleared along the autophagy-lysosome axis, targeted reduction of Nlk represents a potential approach to therapy development for multiple neurodegenerative disorders.

overall_design: RNA-sequencing was performed on isogenic wild-type (WT) and Nlk knockout (KO) mouse Neuro2a (N2a) cells (3 biological replicates per genotype) to examine the effect of Nlk loss.

first: Youngseob

last: Jung

first: Hiroshi

last: Kokubu

first: Janghoo

last: Lim


city: Nagoya

first: Hiroyuki

last: Tsuji

address: Furocho

department: Bioscience and Biotechnology Center

institute: Nagoya University

summary: Transcriptome analysis of axillary meristems of rice cultivar Takanari and a near isogenic line that have a chromosomal segment from rice cultivar Habataki.

overall_design: Axillary meristems were isolated from rice, RNA was extracted and RNA-seq library was prepared according to the method of CEL-seq2. The libraries were sequenced by illumina Hiseq pratform.


title: Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks VI

status: Public on Jun 21 2023

city: Rehovot

first: Noa

last: Bossel Ben-Moshe

address: Hertzl Street

country: Israel

institute: Weizmann

summary: Encounters between host cells and intracellular bacterial pathogens lead to complex phenotypes that determine the outcome of infection. Single-cell RNA-sequencing (scRNA-seq) are increasingly used to study the host factors underlying diverse cellular phenotypes. But current approaches do not permit the simultaneous unbiased study of both host and bacterial factors during infection. Here, we developed scPAIR-seq, an approach to analyze both host and pathogen factors during infection by combining multiplex-tagged mutant bacterial library with scRNA-seq to identify mutant-specific changes in host transcriptomes. We applied scPAIR-seq to macrophages infected with a library of Salmonella Typhimurium secretion system effector mutants. We developed a pipeline to independently analyze redundancy between effectors and mutant-specific unique fingerprints, and mapped the global virulence network of each individual effector by its impact on host immune pathways. ScPAIR-seq is a powerful tool to untangle bacterial virulence strategies and their complex interplay with host defense strategies that drive infection outcome.

overall_design: Examination of specific detection of tagged bacterial mutants in infected BMDMs

first: Ori

last: Heyman

first: Dror

last: Yehezkel

first: Neta

last: Blumberger

first: Gili

last: Rosenberg

first: Camilla

last: Mattioli

first: Aryeh

last: Solomon

first: Dotan

last: Hoffman

last: Ben-Moshe

first: Roi

last: Avraham


title: Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks III

overall_design: Validating our procedure for mapping bacterial mutant identity within single host cell by quantification of tagged SPI-2 mutants from matched bulk infected samples


title: Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks I

overall_design: Examination of specific detection of tagged bacterial mutants from pooled bacterial culture


title: scRNA-seq data from pancreatic cancer cell lines and tumors treated with MRTX1133 and MRTX849

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

summary: Here, we sought to evaluate the impact of KrasG12D and KrasG12C inhibitors on pancreatic cancer cells. A murine pancreatic cancer cell line with KrasG12D mutation was treated with MRTX1133 (KrasG12D inhibitor) and MRTX849 (KrasG12C inhibitor) and scRNA-seq performed to evaluate transcriptional changes. We further evaluated transcriptional changes in cancer cells, as well as in the tumor microenvironment of immunodeficient (NSG) and immunocompetent (C57BL6/J) mice orthotopically implanted with KPC689 cells and spontaneous KPPC tumors in response to MRTX1133 and MRTX849.

overall_design: KPC689 cells: untreated n=1, vehicle (DMSO) n=1, MRTX1133 (50 nM) n=1, MRTX849 (50 nM) n=1. C57BL6/J and NSG KPC689 tumors: VehicleMRTX1133, MRTX1133, VehicleMRTX849, MRTX849 n=1 sample per group, 3 pooled mice per sample for VehicleMRTX1133, VehicleMRTX849, MRTX849 and 6 mice pooled per sample for MRTX1133 and healthy pancreas. KPPC vehicle: n=1 mouse, KPPC MRTX1133: n=1 mouse

first: Raghu

last: Kalluri


title: Dynamics of chromatin marks and the role of EZH2/JMJD3/P300 during hepatoblast differentiation

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

summary: Bi-potential hepatoblasts give rise to hepatocytes with the default fate choice, while undergo a regulatory fate transition to cholangiocytes. We aimed to understand how the “default” vs “regulatory” cell fate differentiations were modulated at the chromatin level. We performed chromatin immunoprecipitation sequencing (ChIP-seq) of hepatobiliary lineages to profile promoter and enhancer associated histone modifications H3K4me3, H3K27me3, H3K27ac and H3K4me1. We also performed in vivo gene manipulation and ex vivo intervention of related histone modifiers were performed to validate their roles in hepatoblast differentiation. We discovered that removal of H3K27me3 from bivalency on promoters was associated with activation of genes related to hepatoblast-cholangiocyte fate transition. In vivo gene manipulation and ex vivo intervention with H3K27me3-modifying enzymes demonstrated that Ezh2 and Jmjd3 specifically regulated hepatoblast-cholangiocyte cell fate transition. In addition, establishments of active and primed enhancers were associated with the developmental processes of both hepatocytes and cholangiocytes, and knockout of P300 inhibited these lineages development.

overall_design: To investigate the dynamics of chromatin marks during hepatoblast differentiation, we dissected the Sox9-CreER;Rosa-tdTomato fetal livers in mouse E12.5 and E17.5 embryos. DLK+ and tdTomato+ cells were sorted by FACS for hepatic cells and cholangiocytes isolation. We performed Low-cell-number native ChIP-seq (N-ChIP) using antibodies against H3K4me3, H3K27me3, H3K4me1 and H3K27ac. We performed CUT&RUN ChIP-seq using antibodies against EZH2. We also performed bulk cell RNA-seq to E17.5 hepatocytes and cholangiocytes. To investigate the role of EZH2/JMJD3/P300 during hepatoblast differentiation, we dissected Alfp-Cre;Jmjd3-f/f, Alfp-Cre;Ezh2-f/f, Alfp-Cre;P300-f/f mouse livers and corresponding control groups at P0. DLK+ hepatocytes and EpCAM+ cholangiocytes were isolated by FACS. We also dissected mouse livers at E12.5 and cultured liver lobes for 2 days with treatment of DMSO (vehicle), 2 µM GSKJ4 or 1 µM GSK126. We performed single cell RNA-seq (scRNA-seq) to these cells using Smart-seq2 method.

first: Li

last: Yang

first: Xin

last: Wang

first: Zhen-Yu

last: Liu

first: Xin-Xin

last: Yu

first: Wei-Lin

last: Qiu

first: Lu

first: Jing

first: Cheng-Ran


title: Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks [CEL-Seq]

first: Noa

last: Bossel Ben-Moshe

overall_design: Comparing single infection with WT or ∆ssaV to pool infection with a mixture of WT & ∆ssaV

first: Ori

last: Heyman

first: Dror

first: Neta

last: Ciolli Mattioli


title: Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks

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

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: Gene expression profile at single-cell level of regenerating lizard (Anolis carolinensis) tail

status: Public on Jun 20 2023

city: Los Angeles

first: Thomas

middle: P

last: Lozito

state: CA

address: 1450 Biggy St NRT4513

department: Orthopaedic Surgery

institute: University of Southern California

summary: Lizards cannot naturally regenerate limbs but are the closest known relatives of mammals capable of epimorphic tail regrowth. However, the mechanisms regulating lizard blastema derivation and chondrogenesis remain unclear. We utilized single-cell RNA sequencing analyses of regenerating lizard tails throughout the course of regeneration to assess diversity and heterogeneity in  regeneating tail cell populations.

overall_design: Regenerating green anole lizard (Anolis carolinensis) tail samples were collected 0-28 days post amputation (DPA) and digested with physical and enzymatic dissociation to obtain single-cell suspensions for single-cell RNA sequencing analysis.

first: Ariel

last: Vonk

first: Xiaofan

last: Zhao

first: Zheyu

last: Pan

first: Megan

last: Hudnall

first: Conrad

middle: G

last: Oakes

first: Gabriela

last: Lopez

first: Sarah

last: Hasel-Kolossa

first: Alexander W

last: Kuncz

first: Sasha

last: Sengelmann

first: Darian

last: Gamble


title: Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks IV

overall_design: Analyzing transcriptional profile of BMDMs infected with S.Tm SPI-2 mutants

last: Yehezkel

last: Blumberger

first: Gili

last: Rosenberg

first: Camilla

last: Mattioli

first: Aryeh

last: Solomon

first: Dotan

last: Hoffman

last: Ben-Moshe

first: Roi

last: Avraham