title: An inflammatory single-cell RNA sequencing signature driven by metabolic stress in a new mouse model of heart failure with preserved ejection fraction and its reversion by the SGLT2 inhibitor dapagliflozin [scRNA-Seq cd45+]

status: Public on Dec 22 2023

first: Bioinformatics

last: Unit

summary: Heart failure with preserved ejection fraction (HFpEF) is a public health problem with increasing incidence and prevalence. Different phenotypes have been identified based on related risk factors, cardiac structural alterations, biomarkers and prognosis. Among these, the one with the worst prognosis is characterized by metabolic dysfunction . This clinical phenotype exhibits high levels of biomarkers related to  dysregulated metabolism and TNF-a–mediated inflammation, thus underlying its close association with metabolic dysfunction and inflammation. The aim of our work is to better comprehend the involvement of the immune cells in the pathogenesis of metabolic HFpEF and  to determine whether treating metabolic dysfunction with SGLT2i could ameliorate HFpEF by decreasing myocardial inflammation.

overall_design: 7–8-week-old male C57BL/6J (RRID:IMSR_JAX:000664) and ApoE KO (B6.129P2-Apoe tm1Unc/J) mice (Charles River, France) were fed with standard chow (CD) or a high fat (HFD) (Western diet, high fat/high cholesterol 0.21%; Sniff EF D12079) diet for 7 or.  After 8 weeks, mice were randomly assigned to either treatment or control group. The treatment group received intragastric dapagliflozin (AstraZeneca) through gavage, 1.0 mg/kg/d for 12-weeks, while mice in the control group and in another group of wild-type (WT) C57BL/6J mice were given vehicle.

first: Paolo

last: Kunderfranco

first: Cristina

last: Panico

first: Arianna

last: Felicetta

first: Gianluigi

last: Condorelli

first: Carolina

last: Greco


title: Single-Cell RNA Sequencing Reveals Metabolic Stress-Dependent Activation of Cardiac Macrophages in a Model of Dyslipidemia-Induced Diastolic Dysfunction

city: Pieve Emanuele (MI)

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: An inflammatory single-cell RNA sequencing signature driven by metabolic stress in a new mouse model of heart failure with preserved ejection fraction and its reversion by the SGLT2 inhibitor dapagliflozin [RNA-Seq macrophages]

summary: Heart failure with preserved ejection fraction (HFpEF) is a public health problem with increasing incidence and prevalence. Different phenotypes have been identified based on related risk factors, cardiac structural alterations, biomarkers and prognosis. Among these, the one with the worst prognosis is characterized by metabolic dysfunction . This clinical phenotype exhibits high levels of biomarkers related to dysregulated metabolism and TNF-a–mediated inflammation, thus underlying its close association with metabolic dysfunction and inflammation. The aim of our work is to better comprehend the involvement of the immune cells in the pathogenesis of metabolic HFpEF and  to determine whether treating metabolic dysfunction with SGLT2i could ameliorate HFpEF by decreasing myocardial inflammation.

middle: M


title: mouse lung endothelial single cell transcriptomics

status: Public on Dec 10 2023

city: Philadelphia

first: Gan

last: Zhao

state: PA Pennsylvania

address: 384E Old Vet Quad 3800 spruce street

country: USA

institute: University of Pennsylvania

summary: Disruption of pulmonary vascular homeostasis is a central feature of viral pneumonia, wherein endothelial cell (EC) death and subsequent angiogenic responses represent critical determinants of the outcome of severe lung injury. A more granular understanding of the fundamental mechanisms driving reconstitution of the lung endothelium is necessary to facilitate therapeutic targeting of vascular repair. Here, we applied single-cell RNA sequencing (scRNA-seq) to profile lung ECs from mice on D0, D20 and D30 post influenza infection. Our data revealed the dynamics of endothelial subsets during influenza injury.

overall_design: Influenza virus A/H1N1/PR/8 was administered intranasally at 50 to 60 TCID50 units to C57BL/6 mice as our previously described (Zhao et al, 2020). Mouse lung ECs sorted from uninjured (D0) and on 20 and 30 days after influenza infection.

first: Andrew

middle: E

last: Vaughan


title: An inflammatory single-cell RNA sequencing signature driven by metabolic stress in a new mouse model of heart failure with preserved ejection fraction and its reversion by the SGLT2 inhibitor dapagliflozin [RNA-seq cardiomyocytes]

summary: Heart failure with preserved ejection fraction (HFpEF) is a public health problem with increasing incidence and prevalence. Different phenotypes have been identified based on related risk factors, cardiac structural alterations, biomarkers and prognosis. Among these, the one with the worst prognosis is characterized by metabolic dysfunction . This clinical phenotype exhibits high levels of biomarkers related to  dysregulated metabolism and TNF-a–mediated inflammation, thus underlying its close association with metabolic dysfunction and inflammation. The aim of our work is to better comprehend the involvement of the immune cells in the pathogenesis of metabolic HFpEF and  the effect of local inflammatory activation on cardiomyocyte function.

overall_design: 7–8-week-old male C57BL/6J (RRID:IMSR_JAX:000664) and ApoE KO (B6.129P2-Apoe tm1Unc/J) mice (Charles River, France) were fed with standard chow (CD) or a high fat (HFD) (Western diet, high fat/high cholesterol 0.21%; Sniff EF D12079) diet for 7 or.


title: Gene expression profile at single cell level of trigeminal ganglion non-neuronal cells

status: Public on Dec 07 2023

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: Trigeminal ganglion non-neuronal cells contain glial, endothelila, smooth muscle, immune cells and fibroblasts.

overall_design: These cells were isolated from wild-type naïve male C57black/B6 maice using liberase-dispase treatment and FACS sorting for live cells

first: Jennifer

last: Mecklenburg

first: Yi

last: Zou

first: Anahit

last: Hovhannisyan

first: Korri

last: Weldon

first: Zhao

last: Lai

first: Sergey

middle: A

last: Shein

first: Shivani

last: Ruparel

first: Alexei

middle: V

last: Tumanov

first: Armen

middle: N

last: Akopian


title: Spatial transcriptomics reveals the pharmacological effects on tumors and TME structural heterogeneity under MASK vaccine treatment

status: Public on Dec 01 2023

city: Tianjin

first: Heng

last: Zhang

address: 38 Rd.Tongyan

country: China

institute: Nankai University

summary: To explore the pharmacological effects on tumors and TME structural heterogeneity under Magnetic Sculpture-liKe (MASK) Cells vaccine treatment, we performed spatial transcriptomics (ST) with B16F10 xenograft receiving MASK vaccine and magnet treatment.

overall_design: C57BL/6 mice subcutaneously inoculated with B16-F10-Luciferase cells were randomly divided into two groups: PBS and MASK. Sample MASK1 was collected on the 7 days after MASK vaccine treatment,  Sample MASK2 was collected on the 13 days after MASK vaccine treatment. Magnet processing group according to the previous method. After the treatment periods, tumor samples were collected, and spatial transcriptomics was performed.

first: Qingqing

last: Li

first: Kaiwen

last: Wang

first: Shanbin

last: Cheng


title: Activation of estrogen receptor beta signaling reduces stemness of glioma stem cells

summary: We examined the transcriptional changes altered by ERβ agonist LY500307 treatment in glioma stem cells (GSCs) by performing global transcriptome analysis. Patient-derived GBM cells (GSC-111010) were subjected to CD133 sorting, and isolated GSCs were treated with either vehicle or LY500307 (5 µM) for 24 h. The RNA was isolated and utilized for RNA-seq analysis. Our results demonstrated that the top pathway altered by LY500307 was the glutamate receptor pathway. Other pathways altered by LY500307 treatment include unfolded protein response, CREB signaling, death receptor signaling, PCP pathway, p53 signaling, and NRF2-mediated oxidative stress response which are known to be involved in stemness and apoptosis. Further, Gene Ontology (GO) analysis revealed that differentially expressed genes were enriched in biological processes, such as regulation of programmed cell death, glutamate receptor signaling pathway, cell communication, and response to unfolded protein. In terms of molecular function, the differentially expressed genes were mainly enriched in glutamate receptor activity, glutamate-gated and transmitter-gated ion channel activity.

overall_design: GSC11 cells were treated with either vehicle or LY500307 (5 µM) for 24 h. Total RNA was isolated using RNeasy mini kit according to the manufacturer's instructions (Qiagen, Valencia, CA).  Illumina TruSeq RNA Sample Preparation was performed following the manufacturer's protocol. Samples were run on an Illumina HiSeq 2000 in duplicate. The combined raw reads were aligned to UCSC hg19, and genes were annotated by Tophat. Genes were annotated and quantified by the HTSeq-DESeq pipeline.

first: Gangadhara

middle: R

last: Sareddy

first: Yidong

last: Chen

first: Ratna

middle: K

last: Vadlamudi


title: Stepwise Neofunctionalization of c-Rel during Vertebrate Evolution

status: Public on Dec 02 2023

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

type: Genome binding/occupancy profiling by high throughput sequencing


title: Stepwise Neofunctionalization of c-Rel during Vertebrate Evolution (ChIP-Seq)

status: Public on Nov 29 2023

summary: Adaptive immunity and the five vertebrate NF-kB/Rel family members first appeared in cartilaginous fish, suggesting that NF-kB family expansion allowed the acquisition of new functions to regulate adaptive immune responses. Transcriptome profiling revealed that, even in macrophages, the NF-kB family member, c-Rel, most potently regulates a cytokine gene linked to adaptive immunity, Il12b, with limiting roles at key regulators of innate immunity. Neofunctionalization of c-Rel to regulate Il12b depends on its unique DNA-binding properties, which we examined using structural, biochemical, functional, and genomic approaches. Among our findings was functional c-Rel homodimer binding to motifs with little resemblance to canonical NF-kB motifs. To determine whether c-Rel’s unique binding properties drove c-Rel-RelA divergence, we compared binding properties in various vertebrate species. c-Rel-RelA binding properties diverged in mammals and amphibians but were comparable in earlier vertebrates, suggesting that divergent DNA binding emerged relatively late during vertebrate evolution to support increasing complexity of adaptive immune regulation.

overall_design: To investigate differences in NF-kB dimer binding genome-wide, we performed p50, RelA, and cRel ChIP-seq in bone marrow-derived macrophages stimulated with Lipid A for 1.0h.

first: Allison

last: Daly

first: George

last: Yeh

first: Ann-Jay

last: Tong


title: Transcriptomes of Chlamydia trachomatis L2 with Conditional GrgA deficiency

first: YI

last: ZOU

summary:
To determine the role that GrgA plays in chlamydial physiology, we constructed a Chlamydia trachomatis mutant that we term L/cgad-peig, in which the chromosomal grgA (ctl0766 or ct504) has been disrupted by Targetron mutagenesis, and the plasmid carries an inducible grgA under the control of anhydrotetracycline (ATC).
RNA-Seq analysis was performed for L2/cgad-peig grown with and without ATC.

overall_design: Total RNA was prepared from the midcycle and earlylate developmental stage.

first: Yuxuan

first: Andrew

first: Huizhou

last: Fan

first: Yi

last: Zou

first: Korri

last: Weldon


title: Combined RNAinterfering and gene therapy targeting MFN2 for the treatment of Charcot-Marie-Tooth type 2A

first: Bioinformatics

last: Unit

summary:
Mitofusin-2 (MFN2) is an outer mitochondrial membrane protein essential for mitochondrial networking in most cells. Autosomal dominant mutations in the MFN2 gene cause Charcot-Marie-Tooth type 2A disease (CMT2A), a severe and disabling sensory-motor neuropathy with impact on the entire nervous system. To date, no curative treatment is available. In the paper we propose a novel therapeutic strategy tailored to correct the root genetic defect of CMT2A. In our approach, while mutant and wild-type MFN2 mRNA are inhibited by RNA interference (RNAi), the wild-type protein is restored by overexpressing a cDNA encoding a functional MFN2, modified to be resistant to RNAi. This strategy allows proper MFN2 molecular correction in vivo in the MitoCharc1 CMT2A transgenic mouse model after cerebrospinal fluid (CSF) delivery of the constructs via adenoassociated virus 9 (AAV9) in newborn mice. To identify the therapeutic molecular mechanisms and the pathway that are modulated, we have compared the bulk RNA expression profile of spinal cord from one month old wild type (WT) mice and MitoCharc1 transgenic mice (B6;D2-Tg(Eno2-MFN2*R94Q)L51Ugfm/J) which encode the mutant human MFN2*R94Q under the neuron specific rat enolase (Eno2) promoter, as potential mouse model to test the therapeutic approach.
We performed gene expression profiling analysis  using data (RNA-seq) obtained from 4 wild type mice and 8 MitoCharch1 transgenic mice at one time point.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from WT mice and its derivatives (CMT2A).

first: Paolo

last: Kunderfranco

first: Federica

last: Rizzo

first: Monica

last: Rizzardo

first: Stefania

last: Corti

first: Simona

last: Lodato


title: SIRT1 prevents R-loops during chronological aging by modulating DNA replication at rDNA loci

status: Public on Nov 27 2023

city: Bethesda

first: Christophe

last: Redon

state: MD

address: 37 Convent Drive

institute: NIH

summary: In metazoans, the largest sirtuin, SIRT1, is a nuclear protein implicated in epigenetic modifications, circadian signaling, DNA recombination, replication and repair. Our previous studies have demonstrated that SIRT1 binds replication origins and inhibits replication initiation from a group of potential initiation sites (dormant origins). We studied the effects of aging and SIRT1 activity on replication origin usage and the incidence of transcription-replication collisions (creating R-loop structures) in adult human cells obtained at different time points during chronological aging and in cancer cells. In primary, untransformed cells, SIRT1 activity declined, and the prevalence of R-loops rose with chronological aging. Both the reduction of SIRT1 activity and the increased abundance of R-loops were also observed during the passage of primary cells in culture. All cells, regardless of donor age or transformation status, reacted to short-term, acute chemical inhibition of SIRT1 with the activation of excessive replication initiation events coincident with an increased prevalence of R-loops. However, only cancer cells showed genome-wide activation of dormant origins during long-term proliferation with mutated or depleted SIRT1, whereas in primary cells, aging-associated SIRT1-mediated activation of dormant origins was restricted to rDNA loci. These observations suggest that chronological aging and the associated decline in SIRT1 activity relaxes the regulatory networks that protect cells against excess replication and that the mechanisms protecting from replication-transcription collisions at the rDNA loci manifest as a differentially enhanced sensitivity to SIRT1 decline and chronological aging.

overall_design: Nascent strands were purified with the lambda exonuclease methods from human fibroblasts.

first: Bhushan

middle: L

last: Thakur

first: Nana

last: Kusi

first: Sara

last: Mosavarpour

first: Roger

last: Zhu

first: Haiqing

last: Fu

first: Anjali

last: Dhall

first: Lorinc

middle: S

last: Pongor

first: Robin

last: Sebastian

first: Fred

last: Indig

first: Mirit

middle: I

last: Aladjem


title: Therapeutic efficacy of INX-315, a selective CDK2 inhibitor, in solid tumors [OVCAR3 RNAseq]

status: Public on Nov 22 2023

city: Melbourne

first: Shom

last: Goel

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

summary: We performed RNA sequencing on OVCAR3 parental cells treated with either control vehicle for 4 days or 300 nM INX-315 for 7 days.

overall_design: OVCAR3 parental cells were treated with either control DMSO for 4 days or 300 nM INX-315 for 7 days. 3 replicates per group were collected.


title: Therapeutic efficacy of INX-315, a selective CDK2 inhibitor, in solid tumors [OV5398PDX RNAseq]

summary: We performed RNA sequencing on tumors harvested from OV5398 (ovarian) PDX treated for 40-50 days with either control vehicle (PEG), 100 mg/kg BID INX-315 or 200 mg/kg QD INX315.

overall_design: Mice with OV5398 (ovarian) PDX tumours were treated with either control vehicle (PEG), 200 mg/kg QD INX-315 or 100 mg/kg BID INX-315. cells were collected 2 hours following final treatment. 3-5 replicates were collected per group.


title: Therapeutic efficacy of INX-315, a selective CDK2 inhibitor, in solid tumors [Gastric mouse (GA0103) RNAseq]

summary: We performed RNA sequencing on tumours harvested from GA0103 (gastric cancer) PDX treated for 40-50 days with either control vehicle or 100 mg/kg BID INX-315.

overall_design: Mice with GA0103 gastric PDX tumours were treated with either control vehicle (G1) or 100 mg/kg BID INX-315 (G2). Tumors were collected wither 2hr or 8hr following final treatment (as denoted on file name).


title: Time course single-cell multiome sequencing data from mESCs treated with Activin A/Lithium Chloride

status: Public on Nov 25 2023

city: Stanford

first: Jingxue

last: Xin

state: California

address: JAMES CLARK CENTER E100A

institute: Stanford University

summary: This study generated multiome profiling of scRNA-seq and scATAC-seq data from ∼11,000 differentiating mouse embryonic stem cells over a time course. It demonstrates scTIE achieves effective data integration while preserving more biological signals than existing integration methods.

overall_design: Embryoid bodies from mESCs were treated with Activin A/Lithium Chloride for up to 6 days. The EBs were collected at Day 2, 4, and 6 after treatment. Nuclei were isolated to generate single cell multiome data using 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle Kit.

first: Wing

middle: H

last: Wong

first: Xi

last: Chen


title: Therapeutic efficacy of INX-315, a selective CDK2 inhibitor, in solid tumors [MCF7 and T47D RNAseq]

summary: We performed RNA sequencing on T47D and MCF7 cells, both parental and abema- or abema/fulvestrant- resistant, treated with either control vehicle or 300 nM (MCF7) or 100 nM (T47D) INX-315 for 7 days

overall_design: Both parental (PAR) and abema-(LYR) or abema/fulvestrant-(LYFR) resistant, treated with either control vehicle or 300 nM (MCF7) or 100 nM (T47D) INX-315 for 7 days. Three replicates per group were collected. 'DMSO' groups denote controls.


title: Therapeutic efficacy of INX-315, a selective CDK2 inhibitor, in solid tumors [HER2mouse upfront RNAseq]

summary: We treated tumour-bearing MMTV-rtTA/tetO-HER2 female mice with either  vehicle (veh), INX-315 (INX), Abemaciclib (LY) or both INX-315 and Abema in combination (LY.INX) for 7 days. Resistant tumors were collected and RNA sequencing performed

overall_design: MMTV-rtTA/tetO-HER2 tumors treated with either vehicle, INX-315, Abemaciclib or Abemaciclib + INX-315 were collected. Replicates are included for each group with tumours collected at 7 days post- beginning of treatment. Each replicate was obtained from a separate tumor.


title: Therapeutic efficacy of INX-315, a selective CDK2 inhibitor, in solid tumors [HER2mouse resistant RNAseq]

summary: We treated tumour-bearing MMTV-rtTA/tetO-HER2 female mice with 75 mg/kg Abemaciclib for ~4 weeks (or until point of resistance, where tumours have started to grow again). Mice were then divided into treatment groups, receiving vehicle (veh), INX-315 (INX), Abemaciclib (LY) or both INX-315 and Abema in combination (LY.INX). Resistant tumors were collected and RNA sequencing performed.

overall_design: Abemaciclib-resistant MMTV-rtTA/tetO-HER2 tumors treated with either vehicle, INX-315, Abemaciclib or Abemaciclib + INX-315 were collected. Replicates are included for each group with tumours collected at different times post- beginning of treatment (as referenced in days on each sample). Each replicate was obtained from a separate tumor.


title: Therapeutic efficacy of INX-315, a selective CDK2 inhibitor, in solid tumors

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Translation Regulation of the Prolactin Receptor Defines Sexually Dimorphic Pain Responses to Prolactin

status: Public on Nov 17 2023

first: YI

last: ZOU

summary: Transcriptional control by gonadal hormone nuclear receptors is the foundation for sex-dependent physiological processes, including pain. Our current findings point to sex-dependent translation control as a new mechanism for sexual dimorphisms in pain. We show that hindpaw or spinal administration of exogenous prolactin (PRL) induces thermal and mechanical hyperalgesia in a female-selective fashion. Unexpectedly, PCR and transcriptomic analysis of hindpaw and dorsal root ganglion (DRG) tissues reveal no differences in PRL receptor (Prlr) mRNA between sexes. Variance in overall hindpaw and DRG transcriptomes between females and males were minor. We find that Prlr mRNA and protein is mainly expressed by peptidergic nociceptors as shown by profiling using Prlr reporter mice and electrophysiology, but there are far more peptidergic neurons with functional Prlr in females than in males. In line with this, exogenous PRL increased excitability only in female neurons. Moreover, in male DRG neurons, 6-24 hr estrogen exposure establishes PRL sensitivity in Prlr mRNA+ male neurons that do not show PRL responses under other conditions. PRL-induced behavioral hypersensitivity as well as sensitivity to PRL in female DRG neurons can be ablated by treatment with cap-dependent translation inhibitor 4EGI-1. Spinal cord immunohistochemistry of Prlr reporter mice highlight that Prlr protein is only found in female DRG neurons, but Prlr mRNA localizes to central terminals of male and female sensory neurons. Based on these findings, we propose a novel mechanism for sex-dependent regulation Prlr mRNA translation that renders female DRG neurons uniquely responsive to PRL.

overall_design: Paw and DRG tissue from 18 males and 12 females are sequenced.

first: Mayur

last: Patil

first: Anahit

last: Hovhannisyan

first: Jennifer

last: Mecklenburg

first: Yi

last: Zou

first: Andi

last: Wangzhou

first: Vincent

last: Goffin

first: David

last: Grattan

first: Ulrich

last: Boehm

first: Zhao

last: Lai

first: Gregory

last: Dussor

first: Theodore

middle: J

last: Price

first: Armen

last: Akopian


status: Public on Nov 03 2023

city: Xiamen

first: Yipeng

last: Rao

address: Xiangan Campus, Xiamen University, Xiangan Road, Xiangan District, Xiamen City, Fujian Province, China

institute: national insititute of diagnostics and vaccine development in infectious diseases（xiamen university）

summary: Gene expression profiles of oHSV-infected GBM cell lines (U-251 MG and U-87 MG)  in the presence or absence of LRRK2-IN-1.

overall_design: Gene sets from oHSV-infected GBM cell lines (U-251 MG and U-87 MG)  in the absence of LRRK2-IN-1 were compared against oHSV-infected GBM cell lines (U-251 MG and U-87 MG)  in the presence of LRRK2-IN-1.

first: Chenhao

last: Huang


title: Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon [scrna-seq]

status: Public on Oct 31 2023

city: Cincinnati

first: Daniel

middle: O.

last: Kechele

state: OH

address: 3333 Burnet Ave Location R3.034

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Most organs have tissue resident immune cells that function during tissue development, homeostasis and disease. Human organoids, derived either from adult tissues or from pluripotent stem cells (PSCs), have been lacking these immune cells, which limits their utility to model many normal and disease processes. Here we describe that human PSC-derived colonic organoids (HCOs) co-develop a diverse population of immune cells. Comparisons to the developing human hematopoietic cells, demonstrate that HCO cultures developed hemogenic endothelium and erythromyeloid progenitors that undergo stereotypical steps in differentiation, resulting in the generation of macrophages. HCO macrophages acquired a transcriptional signature most similar to human fetal small and large intestine tissue-resident macrophages. Functional analyses demonstrate that HCO-macrophages modulate cytokine secretion in response to pro- and anti-inflammatory signals. In addition, macrophages were able to phagocytose and mount a robust response to pathogenic bacteria. In HCOs that were transplanted into mice, macrophages expanded within the colonic organoid tissue, established a close association with the colonic epithelium and were not displaced by the host bone marrow-derived macrophages. These studies support the conclusion that hemogenic endothelium in HCOs gives rise to multipotent hematopoietic progenitors and functional tissue-resident macrophages.

overall_design: Human colonic organoids from day 22 (two biological replicates), 37 in vitro and 15 wk in vivo grown under mouse kidney capsule were dissociated to single cells and along with hematopoietic floaters from day 28 human colonic organoids or day 14 hPSC-derived macropahges, were subjected to 10X sequencing.

first: Jorge

last: Munera

middle: O

first: Jacob

last: Enriquez

first: Praneet

last: Chaturvedi

first: Xinghao

last: Zheng

first: J

middle: G

last: Sanchez

first: James

last: Wells


title: Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon


title: Bexmarilimab activates human tumor-associated macrophages to support adaptive immune responses in interferon-poor immune microenvironments

status: Public on Oct 30 2023

city: Turku

first: Maija

last: Hollmén

address: Tykistökatu 6A 4th floor

country: Finland

institute: University of Turku

summary: Immune checkpoint inhibitors (ICI) show substantially greater efficacy in inflamed tumors characterized by preexisting T-cell infiltration and IFN signaling than in noninflamed “cold” tumors, which often remain immunotherapy resistant. The cancer immunotherapy bexmarilimab, which inhibits the scavenger receptor Clever-1 to release macrophage immunosuppression and activate adaptive immunity, has shown treatment benefit in subsets of patients with advanced solid malignancies. However, the mechanisms that determine bexmarilimab therapy outcome in individual patients are unknown. Here we characterized bexmarilimab response in ovarian cancer ascites macrophages ex vivo using single-cell RNA-sequencing and demonstrated increased IFN signaling and CXCL10 secretion following bexmarilimab treatment. We further showed that bexmarilimab was most efficacious in macrophages with low baseline IFN signaling, as chronic IFNγ priming abolished bexmarilimab-induced TNFα release. These results highlight an approach to target immunologically cold tumors and to increase the likelihood of their subsequent response to ICIs.

overall_design: Ovarian cancer patient ascites cells were treated ex vivo with bexmarilimab or isotype control IgG4 for 48h, after which the cells were analyzed by scRNA-seq.

first: Jenna

last: Rannikko


title: Single cell multi-omic dissection of response and resistance to chimeric antigen receptor T cells against BCMA in relapsed multiple myeloma

status: Public on Dec 15 2023

city: Leipzig

first: Maximilian

last: Merz

address: Liebigstr. 22

department: Department for Hematology, Cell Therapy and Hemostaseology

country: Germany

institute: University Hospital Leipzig

summary: Markers predicting response and resistance to chimeric antigen receptor (CAR) T cells in relapsed/refractory multiple myeloma are currently missing. We subjected cells isolated from peripheral blood and bone marrow before and after the application of CAR T cells directed against B cell maturation antigen to single cell multi-omic analyses to identify markers associated with resistance and early relapse.

overall_design: Peripheral Blood Mononuclear Cells (PBMC) and Bone Marrow Mononuclear Cells (BMMC) collected at day of leukapheresis and approximately 30 days after CAR T cell infusion were subjected to Single Cell RNA, T Cell Receptor, B Cell Receptor and Surface Proteome Sequencing

first: Nora

last: Grieb


title: Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon [bulk rna-seq]

overall_design:
Human pluripotent stem cell derived intestinal and colonic organoids were grown in vitro for 21 and 35 days  and total RNA was extracted from pooled organoids and subjected to bulk 3' RNA-sequencing. All conditions were done in biological triplicate.
Human pluripotent stem cell derived intestinal and colonic organoids were generated using modified clumps (mod) or human colonic organoids using standard grown 35 days  and total RNA was extracted from pooled organoids and subjected to bulk 3' RNA-sequencing. All conditions were done in biological triplicate except HIO (mod) was performed in biological duplicate.

last: Qu


title: Senescent astrocytes derived from human pluripotent stem cells reveal age-related changes and implications for neurodegeneration

status: Public on Oct 28 2023

city: Seongbuk-gu

first: Gyu-Bum

last: Yeon

state: Seoul

address: 145, Anam-ro

department: Department of Biodtechnology

country: South Korea

institute: Korea University

summary: In this study, we present evidence for the first time of senescent astrocytes derived from human pluripotent stem cells (hPSCs) induced by an extended culture.

overall_design: RNA-Seq

first: DongYun

last: Kim

first: Dae-Sung


title: Bexmarilimab-induced macrophage activation leads to treatment benefit in solid tumors: the phase I/II first-in-human MATINS trial

status: Public on Oct 26 2023

summary: Macrophage Clever-1 contributes to impaired antigen presentation and suppression of anti-tumor immunity. This first-in-human trial investigates the safety and tolerability of Clever-1 blockade with bexmarilimab in patients with treatment-refractory solid tumors and assesses preliminary anti-tumor efficacy, pharmacodynamics and immunologic correlates. Bexmarilimab shows no dose-limiting toxicities in part I (n=30) and no additional safety signals in part II (n=108). Disease control (DC) rates of 25%-40% are observed in cutaneous melanoma, gastric, hepatocellular, estrogen receptor-positive breast, and biliary tract cancers. DC associates with improved survival in a landmark analysis and correlates with high pre-treatment intratumoral Clever-1 positivity and increasing on-treatment serum interferon γ (IFNγ) levels. Spatial transcriptomics profiling of DC and non-DC tumors demonstrates bexmarilimab-induced macrophage activation and stimulation of IFNγ and T cell receptor signaling selectively in DC patients. These data suggest that bexmarilimab therapy is well tolerated and show that macrophage targeting can promote immune activation and tumor control in late-stage cancer.

overall_design: Spatial transcriptomics profiling of pre- and post-treatment biopsies from MATINS trial patients with observed disease control (DC, n = 3) and without observed disease control (nDC, n = 3). Transcriptomes of macrophages (CD68+), vessels (CD31+) and remaining tumor area (CD68-CD31-) were analyzed separately from each region of interest using GeoMx Digital Spatial Profiler and GeoMx Human Whole Transcriptome Atlas (NanoString).

first: Yujuan

last: Xiang

first: Sinem

last: Karaman


title: Therapeutic efficacy of INX-315, a selective CDK2 inhibitor, in solid tumors [MCF7 ATACseq]

first: Shom

last: Goel

summary: We performed the Assay for Transposase-Accessible Chromatin with Sequencing (ATAC-Seq) on (i) parental MCF7 cells treated with control vehicle or abemaciclib (ii) abemaciclib- and abemaciclib/fulvestrant-resistant cells treated with control vehicle or INX-315.

overall_design: MCF7 parental cells were treated for 7 days with either DMSO control (DMSO), Abemaciclib (LY; 500nM), INX-315 (INX; 300nM) or both Abemaciclib and INX-315 (LYplusINX). All samples include in duplicate as reference on the name. LYR denotes Abemaciclib-resistant cells, LYFR denotes Abemaciclib/Fulvestrant-resistant cells.


title: Regulation of the Alveolar Epithelial Transitional State in Murine and Human Pulmonary Fibrosis

status: Public on Oct 18 2023

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: Idiopathic Pulmonary Fibrosis (IPF) is a progressive scarring disease arising from impaired regeneration of the alveolar epithelium after injury. During regeneration, type 2 alveolar epithelial cells (AEC2s) differentiate into AEC1s via a transitional state that upregulates keratin 8. In IPF, transitional AECs persist with ineffectual AEC1 differentiation. However, whether keratin 8 regulates transitional state persistence and fibrosis is unclear. Here, we isolated AEC2s from WT or keratin 8 KO mice and harvested RNA from freshly isolated cells or from cells cultured for 1, 3, or 7 days. RNAseq was performed.

overall_design: AEC2s were isolated from WT or KO mice. RNA was harvested from freshly isolated cells (Day 0 or D0). Cells were cultured, and RNA was harvested at Day 1, 3, and 7 (D1, D3, D7). This was done 3 times, on 6/17/2021, 7/14/2021, and 8/3/2021, for 3 independent biological replicates. RNAseq was performed.

first: Rachel

last: Zemans

first: Fa

last: Wang


title: DPEP INHIBITS CANCER CELL GROWTH AND SURVIVAL VIA SHARED AND CONTEXT-DEPENDENT TRANSCRIPTOME PERTURBATIONS

status: Public on Oct 10 2023

city: NEW YORK

first: LLOYD

middle: A.

last: GREENE

state: NEW YORK

address: 650 W. 168TH STREET

department: PATHOLOGY AND CELL BIOLOGY

institute: COLUMBIA UNIVERSITY

summary: Dpep is a cell-penetrating peptide targeting transcription factors ATF5, CEBPB and CEBPD that selectively promotes apoptotic death of multiple tumor cell types in vitro and in vivo.  To better understand its mechanism of action, we compared transcriptomes of 6 cancer cell lines of varying origins before and after Dpep exposure. This revealed a context-dependent pattern of regulated genes that was unique to each line, but that exhibited a number of shared elements with other lines. This included upregulation of pro-apoptotic genes and tumor suppressors as well as enrichment of genes associated with responses to hypoxia and interferons.  Downregulated transcripts included oncogenes and dependency genes and enriched genes associated with different phases of the cell cycle as well as with DNA repair.  In each case, such changes have the potential to lie upstream of apoptotic cell death. We also detected regulation of unique as well as shared sets of transcription factors in each line, suggesting that Dpep may initiate a cascade of transcriptional responses that culminate in cancer cell death. Such death thus appears to reflect context-dependent, yet shared disruption of multiple cellular pathways as well as of individual survival-relevant genes.

overall_design: To illuminate the potential mechanisms by which Dpep promotes death of a wide range of tumor cell types, we carried out PLATE-seq (a technology that permits high throughput transcriptomic analysis on multiple samples) on 6 diverse human tumor cell lines: HCT116 (colorectal carcinoma), MDA-MB-231 (triple -negative breast cancer), MCF7 (breast cancer), T98G (glioblastoma) A375 (BRAF mutated melanoma), and A549 (non-small-cell lung cancer). In each case, the cells were treated with or without 20 µM Dpep for 48 hrs prior to analysis. This Dpep concentration is near the IC50 for each line and under these treatment conditions, appreciable cell death only becomes apparent by about 72 hrs, with little at 48 hrs.  Six replicate cultures were assessed for each condition.

first: Lloyd

last: Greene

first: Qing

last: Zhou


title: Unveiling alterations of epigenetic modifications and chromatin architecture leading to lipid metabolic reprogramming during the evolutionary trastuzumab adaptation of HER2-positive breast cancer

status: Public on Oct 08 2023

city: Nanjing

first: Nignjun

last: Duan

address: 300 Guangzhou Road

institute: JSPH

summary: Secondary trastuzumab resistance represents an evolutionary adaptation of HER2-positive breast cancer during anti-HER2 treatment. Most current studies have tended to prioritize HER2 and its associated signaling pathways, often overlooking broader but seemingly less relevant cellular processes, along with their associated genetic and epigenetic mechanisms. Here, transcriptome data is not only characterized but also examined epigenomic and 3D genome architecture information in both trastuzumab-sensitive and secondary-resistant breast cancer cells. The findings reveal that the global metabolic reprogramming associated with trastuzumab resistance may stem from genome-wide alterations in both histone modifications and chromatin structure. Specifically, the transcriptional activities of key genes involved in lipid metabolism appear to be regulated by variant promoter H3K27me3 and H3K4me3 modifications, as well as promoter-enhancer interactions. These discoveries offer valuable insights into how cancer cells adapt to anti-tumor drugs and have the potential to impact future diagnostic and treatment strategies.


title: Unveiling alterations of epigenetic modifications and chromatin architecture leading to lipid metabolic reprogramming during the evolutionary trastuzumab adaptation of HER2-positive breast cancer [RNA-Seq]

summary: Secondary trastuzumab resistance represents an evolutionary adaptation of HER2-positive breast cancer during anti-HER2 treatment. Most current studies have uncovered the alternations of HER2 and associated signaling pathways but pay less attention to broader cellular processes and their relevant genetic and epigenetic mechanisms. Here we have not only characterized transcriptome data but also examined epigenomic and 3D genome architecture information in both trastuzumab-sensitive and secondary-resistant breast cancer cells. Our findings reveal that the global metabolic reprogramming associated with trastuzumab resistance may stem from genome-wide alterations in both histone modifications and chromatin structure. Specifically, the transcriptional activities of key genes involved in lipid metabolism appear to be regulated by variant promoter H3K27me3 and H3K4me3 modifications, as well as promoter-enhancer interactions. These discoveries offer valuable insights into how cancer cells adapt to anti-tumor drugs and have the potential to impact future diagnostic and treatment strategies.

overall_design: To investigate the gene expression changes of HER2 positive breast cancer cells during secondary trastuzumab resistance formation, we treated SKBR3 cells with raising trastuzumab concentration in 30 weeks.

first: Ningjun

first: Yijia

last: Hua

first: Xueqi

last: Yan

first: Yaozhou

last: He

first: Tianyu

last: Zeng

first: Jue

last: Gong

first: Ziyi

last: Fu

first: Wei

last: Li

first: Yongmei

last: Yin


title: Pediatric T-cell acute lymphoblastic leukemia blast signature and MRD associated immune environment changes defined by single cell transcriptomics analysis.

status: Public on Sep 27 2023

city: Atlanta

first: Swati

last: Bhasin

state: GA

address: 615 Michael Street, Whitehead Biomedical Research Building

department: Department of Pediatrics

institute: Emory University

summary: Different driver mutations and/or chromosomal aberrations and dysregulated signaling between leukemia cells and the immune microenvironment have been implicated in the development of T-cell acute lymphoblastic leukemia (T-ALL). To better understand the changes in the bone marrow microenvironment and signaling pathways in pediatric T-ALL, bone marrows collected at diagnosis (Dx) and end of induction therapy (EOI) were profiled for 11 T-ALL patients (10 Dx, 5 paired EOI, 1 relapse) by single cell transcriptomics. T-ALL blasts were identified by comparison with healthy bone marrow cells. T-ALL blast-associated gene signature included SOX4, STMN1, CD99, HES4, and ARMH1 among the highest dysregulated genes, all of which together associated with poor prognosis in children with T-ALL (HR=2.7, LR P value=0.008)). The transcriptome profiles of the blast cells exhibited significant inter-patient heterogeneity. Post induction therapy, expression profiles of the immune cells revealed significant changes. Residual blast cells in MRD+ EOI samples exhibited significant upregulation (P <0.01) of PD-1 and RhoGDI signaling pathways. Differences in cellular communication were noted in the presence of residual disease in T cell and hematopoetic stem cell compartments in the bone marrow. Together, these studies generate new insights and expand our understanding of the bone marrow landscape in pediatric T-ALL.

overall_design:
A total of 16 samples were collected from 11 T-ALL patients. 10 at diagnosis (Dx), 5  after therapy (EOI) and 1 at relapse.
NOTE FROM SUBMITTER: raw data are not available due to patient privacy concerns.

first: Beena

last: Thomas

first: Ryan

last: Summers

first: Debasree

last: Sarkar

first: Hope

last: Mumme

first: William

last: Pilcher

first: Mohamed

last: Emam

first: Sunil

last: Raikar

first: Sunita

last: Park

first: Sharon

last: Castellino

first: Douglas

last: Graham

first: Manoj

first: Deborah

last: DeRyckere


title: Pioneer factor Pax7 initiates two-step cell-cycle dependent chromatin opening (ChIP-seq)

city: Montreal

first: Arthur

middle: Jules

last: Gouhier

state: Quebec

address: 110 Avenue des Pins

country: Canada

institute: IRCM

summary: Pioneer transcription factors direct cell differentiation by deploying new enhancer repertoires through their unique ability to target and initiate remodelling of closed chromatin. The initial steps of their action remain undefined although pioneers were shown to interact with nucleosomal target DNA and with some chromatin remodelling complexes. We now define the sequence of events that enable the pioneer Pax7 with its unique abilities. Chromatin condensation exerted by linker histone H1 is the first constraint on Pax7 recruitment, and this establishes the initial speed of chromatin remodelling. The first step of pioneer action involves recruitment of the KDM1A (Lsd1) H3K9me2 demethylase for removal of this repressive mark, as well as recruitment of the MLL complex for deposition of the activating H3K4me1 mark. Further progression of pioneer action requires passage through cell division, and this involves dissociation of pioneer targets from perinuclear lamin B. Only then, the SWI/SNF remodeling complex and the coactivator p300 are recruited, leading to nucleosome displacement and enhancer activation. Thus, the unique features of pioneer actions are those occurring in the lamin-associated compartment of the nucleus. This model is consistent with prior work that showed a dependence on cell division for establishment of new cell fates.

overall_design: ChIP-seq in mouse corticotrope AtT-20 cells with Pax7 or ER-Pax7 ectopic expression. Treated with tamoxifen (tam, ER-Pax7 activation) or mimosine (mim, cell cycle arrest).

first: Justine

last: Dumoulin-Gagnon

first: Vincent

last: Lapointe-Roberge

first: Juliette

last: Harris

first: Aurelio

last: Balsalobre

first: Jacques

last: Drouin


title: Pioneer factor Pax7 initiates two-step cell-cycle dependent chromatin opening


title: Single-cell RNA sequencing distinctly characterizes the wide heterogeneity in pediatric mixed phenotype acute leukemia

address: 1760 Haygood Dr NE

summary: We analyzed over 40,000 cells from nine pediatric MPAL BM samples to generate a single-cell transcriptomic landscape of B/Myeloid (B/My) and T/Myeloid (T/My) MPAL blasts and associated microenvironment cells. Cell clusters were identified using principal component analysis and uniform manifold approximation and projection (UMAP). Supervised differentially expressed gene (DEG) analysis was performed to identify B/My and T/My MPAL blast-specific signatures. MPAL sample transcriptome profiles were compared with normal BM stem and immune cells to identify MPAL-specific dysregulation. We have for the first time described the single-cell transcriptomic landscape of pediatric MPAL and have demonstrated that B/My and T/My MPAL have unique scRNA-seq profiles distinct from each other with expected overlap with AML and their respective ALL subtype.

overall_design:
We generated scRNA-seq data from cryopreserved bone marrow (BM) samples using 10x Genomics 3' Single-Cell RNA profiling approach.
*** Raw data not included due to patient privacy concerns. ***

first: Swati

last: Bhasin

first: Beena

last: Thomas

first: Taylor

last: Lawrence

first: Elizabeth

middle: P

last: Weinzierl

first: Yakun

last: Pang

first: Chuck

last: Gawad

first: Daniel

last: Wechsler

first: Christopher

middle: C

last: Porter

middle: M


title: Intrahepatic CD69+ Vd1 T cells recirculate in the blood of patients affected by liver metastatic colorectal cancer and predict their overall survival

status: Public on Oct 03 2023

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

institute: IRCCS Humanitas Research Hospital

summary: More than 50% of all patients with colorectal cancer (CRC) develop liver metastasis (CLM) that are characterized by poor prognosis and lack of reliable prognostic markers. Vd1 T cells are gd T innate-like lymphocytes endowed with a broad array of antitumor functions at peripheral tissues, but little is known about their impact in the pathophysiology of CLM. We assessed the phenotype and functions by flow cytometry, clonotype by gdTCR-sequencing, transcriptional profiles by single cell RNA-sequencing and clinical impact of human Vd1 T cells isolated from peripheral blood (PB), tumor-free liver parenchyma surrounding CLM (TFLP) and metastatic tumor (MT) from a large cohort of CLM patients. We show here that CLM tissue is highly enriched of CD69+ Vd1 T effector (TEF) cells in the TFLP area. These cells have a peculiar phenotype, high anti-tumour potential and correlate with a better clinical outcome in terms of lower numbers of liver metastatic lesions and longer overall survival (OS). Moreover, the specific terminally differentiated (TEMRA) CD69+ Vd1 cells can egress CLM tissue to re-circulate in the bloodstream, where they retains high effector functions and show phenotypic/transcriptional and gdTCR profiles that resemble their liver origin. Importantly, high frequencies of CD69+TEMRA Vd1 cells in PB predict a longer OS of CLM patients that is not affected by the neo-adjuvant chemotherapy/immunotherapy regimens administered to CLM patients. The presence at high frequencies of liver memory CD69+TEMRA Vd1 cells in CLM homing to PB represents a new important target to better predict CLM clinical outcomes and to develop novel protocols of adoptive cell transfer therapies.

overall_design: A total of three blood samples deriving from three CLM patients

first: R

last: Carriero

first: P

last: Kunderfranco

first: J

last: Mikulak

first: D

last: Mavilio


title: Intrinsic tumor resistance to CAR T-cells is a dynamic transcriptional state that can be exploited with low dose radiation

city: St. Louis

first: Carl

last: DeSelm

state: MO

address: 325 S. Euclid Ave

department: Radiation Oncology

institute: Washington University in St. Louis

summary:
Purpose: High tumor burden prior to CAR T-cell therapy predicts poor outcome, however it is unclear if this is driven more by cell number or underlying biology. It is also unclear if tumor intrinsic properties that confer CAR T-cell resistance can be clinically manipulated to improve response. Here we capitalize on radiation’fering effects by dose in vivo to examine the relative importance of tumor quantity versus quality prior to CAR T-cell therapy.
Experimental Design: Using Nalm6 ALL tumor-bearing mice, we investigate the impact of high dose (20Gy in 5 fractions) radiation to focal bulky disease, versus less cytotoxic low-dose (1.8Gy) to all disease (total tumor irradiation; TTI) on CAR T-cell efficacy. We characterize the dynamics of predictive transcriptional states in mice and patients using tumor RNA-seq under conditions of excellent vs poor response.
Results: We find the in vivo sensitivity of leukemia cells to CAR T-cells is not only predicted by a transcriptional score, but this score can be temporarily increased by low dose TTI, which is associated with significantly improved survival. Focal high dose radiation (as is currently done clinically) was more debulking but did not improve survival. The tumor transcriptional state induced by low dose radiation was found in >80% of long-term CAR T-cell survivors.
Conclusions: These findings provide a path to 1) identify patients unlikely to respond to CAR T_x0002_cells due to potentially reversible tumor-intrinsic resistance, and 2) potentially improve response using low dose TTI to adjust a tumor’s unfavorable transcriptional state prior to CAR T-cell delivery.

overall_design: 5 replicates each of Nalm6 leukemia cells irradiated with 1.8gy sequenced at 24 hours and 7 days post-treatment and a set of Nalm6 that received sham treatment, 3 sequenced at pre-treatment, 4 at 24 hours, and 1 at 21 days post-treatment.

first: Alexander

middle: B

last: Kim

first: Ssu-Yu

last: Chou

first: Solomon

last: Kang

first: Eric

last: Kwon

first: Matthew

last: Inkman

first: Jeff

last: Szymanski

first: Colin

last: Willoughby

first: Neal

last: Andruska

first: Cian

last: Colgan

first: Jin

last: Zhang

first: Joanna

last: Yang

first: Nathan

last: Singh


title: IL-6 Trans-Signaling in a Humanized Mouse Model of Scleroderma

status: Public on Sep 20 2023

city: New Haven

first: Ian

last: Odell

state: CT

address: 330 Cedar St. LMP-5040

department: Dermatology

institute: Yale University

summary: Fibrosis is regulated by interactions between immune and mesenchymal cells. However, the capacity of cell types to modulate human fibrosis pathology is poorly understood due to lack of a fully humanized model system. MISTRG6 mice were engineered by homologous mouse/human gene replacement to develop an immune system like humans when engrafted with human hematopoietic stem cells (HSC) (1, 2). We utilized MISTRG6 mice to model scleroderma by transplantation of healthy or scleroderma skin from a patient with pansclerotic morphea to humanized mice engrafted with unmatched allogeneic HSC. We discovered that scleroderma skin grafts contained both skin and bone marrow derived human CD4 and CD8 T cells along with human endothelial cells and pericytes. Unlike healthy skin, fibroblasts in scleroderma skin were depleted and replaced by mouse fibroblasts. Furthermore, HSC engraftment alleviated multiple signatures of fibrosis, including expression of collagen and interferon genes, and proliferation and activation of human T cells. Fibrosis improvement correlated with reduced markers of T cell activation and expression of human IL-6 by mesenchymal cells. Mechanistic studies supported a model whereby IL-6 trans-signaling driven by CD4 T cell derived soluble IL-6 receptor complexed with fibroblast derived IL-6 promoted excess ECM gene expression. Thus, MISTRG6 mice transplanted with scleroderma skin demonstrated multiple fibrotic responses centered around human IL-6 signaling, which was improved by the presence of healthy bone marrow derived immune cells. Our results highlight the importance of IL-6 trans-signaling in pathogenesis of scleroderma and the ability of healthy bone marrow derived immune cells to mitigate disease.

overall_design: we performed scRNA-Seq on 3 of the HSC-engrafted (+HSC) compared to 3 HSC unengrafted (-HSC) scleroderma skin grafts 4 weeks after transplantation onto MISTRG6 humanized mice.


title: Hypoxia-inducible factor-2 (HIF2) regulates alveolar regeneration after repetitive injury

status: Public on Sep 18 2023

city: Nashville

first: Jonathan

middle: A

last: Kropski

state: TN

department: Medicine

institute: Vanderbilt University Medical Center

summary: Idiopathic Pulmonary Fibrosis (IPF) is a progressive and often fatal chronic respiratory disease thought to result from repetitive injury and failed repair of the lung alveoli, and recent studies have identified a number of disease-emergent intermediate/transitional cell states in the IPF lung supporting this concept. In this study, we found that persistent activation of hypoxia-inducible factor (HIF)-signaling in airway-derived, repair-associated cell types/states is a hallmark of dysfunctional epithelial repair in the IPF lung epithelium and experimental models of recurrent lung epithelial injury. Disrupting Hif-signaling attenuated experimental lung fibrosis, reduced mucous-secretory cell polarization, and promoted functional alveolar regeneration following repetitive injury. Mouse and human organoid studies demonstrated that small-molecule-based HIF2 inhibition promoted alveolar epithelial cell proliferation and maturation while preventing the emergence of maladaptive intermediate/transitional states analogous to those in IPF. Together, these studies indicate that targeted HIF2-inhibition represents a novel and effective therapeutic strategy to promote functional lung regeneration, and could be readily translated into human studies of IPF and other chronic interstitial lung diseases with disease modifying effect.

overall_design: scRNA-sequencing ofsorted lung epithelial cells from WT, epithelial Hif1/2 deficient, Sftpc-CreER-tDtomato and Scgba1-CreER-tDtomato mice after repetetive intratracheal bleomycin; scRNA-seq of human alveolar organoids with and without HIF2 inhibitor

first: Kropski

last: Jonathan

first: McCall

last: A Scott

first: Blackwell

last: Timothy


title: Gene expression changes in leaves, roots and Laccaria bicolor mycorrhiza of Poplar treated with ozone or stopped watering.

status: Public on Sep 12 2023

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

country: France

institute: INRAE

summary: Illumina  technology was used to generate mRNA profiles of leaves, roots and Laccaria bicolor mycorrhiza of Poplar treated with ozone or stopped watering.   Total RNA was extracted separately from each plant and pooled to 4 biological replicates per condition.TruSeq mRNA Stranded libraries were constructed and   and sequenced using Illumina HiSeq 3000 at the Genotoul sequencing facilities (Toulouse, France).    Raw reads were filtered and trimmed using erne-filter command.   Filtered reads from each library were aligned to P. trichocarpa (https://phytozome-next.jgi.doe.gov/info/Ptrichocarpa_v4_1)   using TopHat2 v2.12.

sample_organism:
Populus trichocarpa
Laccaria bicolor

platform_organism:
Populus trichocarpa
Laccaria bicolor

overall_design: mRNA profiles of leaves, roots and Laccaria bicolor mycorrhiza of Poplar treated with ozone or stopped watering were generated by Illumina HiSeq 3000 (2x150bp). Four biological replicates were sequenced.

first: Maíra

last: de Freitas Pereira

first: David

last: Cohen

first: Irene

last: Hummel

first: Marie

middle: N

last: Vaultier

first: Claire

last: Veneault-Fourrey


title: Single-cell analysis reveals altered tumor microenvironments of relapse- and remission-associated pediatric acute myeloid leukemia

status: Public on Sep 05 2023

first: Hope

last: Mumme

summary: Pediatric acute myeloid leukemia (AML) bone marrow (BM) samples from diagnosis (Dx), end of induction (EOI), and relapse timepoints were analyzed by single-cell RNA sequencing (scRNA-seq). Analysis of matched Dx, EOI scRNA-seq datasets and TARGET AML RNA-seq datasets revealed a novel AML blasts-associated 7-gene signature (CLEC11A, PRAME, AZU1, NREP, ARMH1, C1QBP, TRH) that was validated in two independent datasets. Distinct clusters of relapse- and continuous complete remission (CCR)-associated AML-blasts were observed at Dx, with differential expression of genes associated with survival. At Dx, relapse-associated samples had more exhausted T cells while CCR-associated samples had more inflammatory M1 macrophages. Post-therapy EOI residual blasts overexpressed fatty acid oxidation, tumor growth, and stemness genes. Also, a post-therapy T-cells cluster present in relapse-associated samples exhibited downregulation of MHC Class I and T-cell regulatory genes. Altogether, this study deeply characterizes pediatric AML relapse- and CCR-associated samples to provide novel insights into BM microenvironment landscape.

overall_design:
We generated scRNA-seq data from cryopreserved bone marrow (BM) samples using 10x Genomics 3' Single-Cell RNA profiling approach.
------------------------------------
Authors state:
Raw data is not included due to patient privacy concerns.

first: Beena

middle: E

last: Thomas

first: Swati

last: Bhasin

first: Upaasana

last: Krishnan

first: Bhakti

last: Dwivedi

first: Pruthvi

last: Permualla

first: Debasree

last: Sarkar

first: Gulay

last: Ulukaya

first: Himalee

last: Sabnis

first: Sunita

last: Park

first: Deborah

last: DeRyckere

first: Sunil

last: Raikar

first: Melinda

last: Pauly

first: Ryan

last: Summers

first: Sharon

last: Castellino

first: Daniel

last: Wechsler

first: Christopher

last: Porter

first: Douglas

middle: K

last: Graham

first: Manoj


title: Independent and temporally separated dynamics for RORγt and Foxp3 during Th17 differentiation

status: Public on Sep 10 2023

city: Rehovot

first: Stav

last: Miller

address: Herzl

country: Israel

institute: Weizmann Institute of Science

summary: T helper 17 and Regulatory T cells (Th17 and Treg, respectively) are two well-described lymphocyte subsets with opposing actions. The divergent fates of Th17 and Treg cells are accounted for, at least in part, by molecular antagonism that occurs between their respective specific transcription factors, RORγt and Foxp3. An imbalance between Th17 and Treg cells may lead to tissue inflammation and is associated with certain types of autoimmunity. In order to understand the heterogeneity and dynamics of the differentiation process, we studied Th17/Treg cell differentiation of naïve cells in vitro, using RORγtGFPFoxp3RFP dual-reporter mouse. Flow cytometry revealed the consistent emergence of a population of double positive RORγt+Foxp3+ (DP) cells during the early stages of Th17 cell differentiation. These DP cells are closely related to RORγt+ single positive (SPR) cells in terms of global gene expression. Nevertheless, for some genes, DP cells share an expression pattern with Foxp3+ single positive (SPF) Treg cells, most importantly by reducing IL17 levels. Using time-lapse microscopy, we could delineate the expression dynamics of RORγt and Foxp3 at a clonal level. While the RORγt expression level elevates early during differentiation, Foxp3 rises later and is more stable upon environmental changes. These distinct expression profiles are independent of each other. During differentiation and proliferation, individual cells transit between SPR, DP, and SPF states. Nevertheless, the differentiation of sister cells within a clone progeny was highly correlated. We further demonstrated that sorted SPR and DP populations were not significantly affected by changes in their environment, suggesting that the correlated fate decision emerged at early time points, before the first division. Overall, this study provides the first quantitative analysis of differentiation dynamics during the generation of DP RORγt+Foxp3+ cells. Characterizing these dynamics and the differentiation trajectory could provide a profound understanding and be used to better define the distinct fates of T cells, critical mediators of the immune response.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for differentiated T cells sorted by their RORƴt and Foxp3 expression.

first: Jacob

last: Rimer


title: Single cell profiling of primary and paired metastatic lymph node tumors and adjacent normal thyroid in a papillary thyroid carcinoma patient

status: Public on Aug 18 2023

first: Shanliang

last: Zhong

address: Baiziting 42

summary: In the present study, we measured gene expression levels of 3 tissue samples from a young female patient with papillary thyroid carcinoma (PTC) using scRNA-seq technology and tried to uncover the mechanisms of promoting lymph node metastasis of PTC.

overall_design:
A female patient aged 17 years with PTC was enrolled from The Affiliated Cancer Hospital of Nanjing Medical University. The thyroid tumor (TT), adjacent normal thyroid (NT) and lymph node metastasized tumor (LN) were collected and digested into single-cell suspensions for 10×Genomics single cell sequencing (scRNA-seq).
*** The raw data files are protected by submitter's institution and not available at SRA.***

first: Wei

last: Chen


title: KDM1A/LSD1 inhibition enhances estrogen receptor beta-mediated tumor suppression in ovarian cancer

status: Public on Oct 16 2023

city: SAN ANTONIO

first: YI

last: ZOU

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: We examined global transcriptional changes in ES2-control and ES2-KDM1A knockout (KO) cells that are treated with vehicle or estrogen receptor beta agonist LY500307 using RNA-sequencing.

overall_design: ES2-control and ES2-KDM1A knockout cells were treated with vehicle or LY500307 (5 µM) for 48 hours. Total RNA was isolated using RNeasy mini kit according to the manufacturer's instructions (Qiagen, Valencia, CA).  Illumina TruSeq RNA Sample Preparation was performed following the manufacturer's protocol. Samples were run on an Illumina HiSeq 3000 in duplicate. The combined raw reads were aligned to UCSC hg19 by Tophat2. Genes were annotated and quantified by the HTSeq-DESeq pipeline.

first: Prabhakar

last: Venkata

first: Gangadhara

middle: R

last: Sareddy


title: Quantification of intrinsic regulatory factors refines human hematopoietic progenitor definitions and reveals early erythroid lineage priming

status: Public on Aug 20 2023

city: Palo Alto

first: Reema

last: Baskar

address: 3373 Hillview Ave

institute: Stanford University

summary: Hematopoietic stem and progenitor cell (HSPC) transplantation is an essential therapy for the treatment of hematological conditions, but finer definitions of human HSPC subsets with associated function could enable better tuning of grafts and more routine application in patients with lower risks. To deeply characterize human HSPCs, we quantified 41 surface proteins and functional regulators on millions of CD34+ and CD34- cells, spanning four primary human hematopoietic tissues: bone marrow, mobilized peripheral blood, cord blood, and fetal liver. We propose more granular definitions of HSPC subsets and provide new, detailed differentiation trajectories of erythroid and myeloid lineages. These aspects of our revised human hematopoietic model were validated with corresponding epigenetic analysis and in vitro clonal differentiation assays. Overall, we demonstrate the utility of using molecular regulators as surrogates for cellular identity and functional potential, providing a framework for description, prospective isolation, and cross-tissue comparison of HSPCs in humans.

overall_design: Chromatin accessibility profiling through ATAC sequencing of human bone marrow progenitors after sorting for specific populations in the erythrocyte and myeloid development stages

first: Patricia

last: Favaro

first: David

last: Glass

first: Luciene

last: Borges


title: Profound effect of a ubiquitin activating enzyme (UAE1) on genomic expression of Toxoplasma gondii

status: Public on Aug 16 2023

city: Wenzhou

first: Ya-Ni

last: Mou

state: China

address: Chashan University Town, Ouhai District, Wenzhou City, Zhejiang Province

institute: Wenzhou Medical University

summary: Toxoplasma gondii is an intracellular parasite that relies on intricate molecular mechanisms for its proliferation and survival. Here, we investigate the role of TgUAE1 in these processes and shed light on the underlying regulatory network. We demonstrate that TgUAE1 is crucial for maintaining the proliferation of T. gondii and the normal morphology of mitochondria. To elucidate the molecular basis of TgUAE1's essential functions, we conducted transcriptome sequencing to identify the genes regulated by this factor. Total RNA was extracted from TATi-3HA-TgUba1 strains cultured under 0.5 μg/ml ATc (knockout strain) and DMSO (wild strain), and subjected to deep sequencing using the Illumina Novaseq TM 6000 platform. Subsequently, sequence reads were mapped to the T. gondii genome, resulting in a comprehensive transcriptome containing 8637 detected genes. Among these genes, 934 were dysregulated in the absence of TgUAE1, comprising 60 downregulated and 874 upregulated genes. Functional enrichment analysis revealed their involvement in various GO categories and KEGG pathways. Our findings provide novel insights into the profound impact of TgUAE1 on the expression landscape of the T. gondii genome, highlighting the significance of this factor in parasite biology.

overall_design: RNA profiles of TgUAE1 knockdown and wild-type strains.

first: Tan

last: Feng

first: Yani

first: Daiqiang

last: Lu

first: Qixin

last: Zhou


title: Hepatitis B virus X protein contributes to hepatocellular carcinoma via upregulation of KIAA1429 methyltransferase and mRNA m6A hypermethylation of HSPG2/Perlecan

status: Public on Aug 09 2023

city: Suzhou

first: Enakshi

last: Sivasudhan

address: 111, Ren'ai Road, Suzhou Industrial Park

institute: Xi'an Jiaotong Liverpool University

type: Methylation profiling by high throughput sequencing

summary: Chronic hepatitis B virus (HBV) remains to be the most common risk factor of hepatocellular carcinoma (HCC). While previous work has primarily focussed on understanding the direct and indirect mechanisms of Hepatitis B virus X protein (HBx)-mediated hepatocarcinogenesis, from genetic and epigenetic perspectives, its influence on RNA modification mediated onset of liver malignancies is less well understood. This study explored the role of HBV-encoded HBx in altering the m6A methylome profile and its implications on the pathogenesis of HCC. We established HBx-expressing stable HCC cell lines, Huh7-HBx and HepG2-HBx, and explored the transcriptomic and epitranscriptomic profiles by RNA-seq and MeRIP-seq, respectively. Preliminary results suggest that HBx promotes liver cell proliferation, migration, survival and overall m6A methylation in HCC cells and is involved in modulating the extracellular matrix. We show that HBx mediates liver cell transformation by upregulating KIAA1429 methyltransferase. HBx also drives the expression and hypermethylation of the extracellular matrix protein HSPG2/Perlecan and promotes tumourigenesis. Furthermore, we observed a potential interaction between KIAA1429 and HSPG2 in HCC liver cancer cells and demands further investigation.

overall_design: Refer to individual Series


title: Astrocyte-Derived Estrogen Regulates Reactive Astrogliosis and is Neuroprotective Following Ischemic Brain Injury

status: Public on Jul 13 2023

summary: We examined the transcriptional changes modulated in ischemic brain of astrocyte specific aromatase knockout mice (GFAP-ARO-KO) by performing global transcriptome analysis.Total RNA was isolated from FLOX and GFAP-ARO-KO mice that underwent 20-minute CCA occlusion, followed by 24-hour reperfusion. The collected hippocampi samples were subjected to RNA isolation and Illumina TruSeq RNA sample preparation and sequencing was done using UT Health San Antonio genomics core facility protocol. We observed that that the ischemic GFAP-ARO-KO mouse hippocampus failed to upregulate a group of genes, which have been suggested to represent the “A2” neuroprotective signature of astrocytes. In addition, the JAK-STAT3 pathway, which is critical for the induction of reactive astrogliosis, was significantly down-regulated in the GFAP-ARO-KO hippocampus following GCI.  Additional pathways that altered in GFAP-ARO-KO hippocampus were related to cytokine, chemokine and inflammatory signaling pathways.

overall_design: Total RNA was isolated from female FLOX and GFAP-ARO-KO mice that underwent 20-minute CCA occlusion, followed by 24-hour reperfusion. RNA was isolated from the hippocampi using the RNeasy mini kit. Illumina TruSeq RNA sample preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 3000 in duplicate. The combined raw reads were aligned to UCSC mm9 and genes were annotated by Tophat. Genes were annotated and quantified by HTSeq-DESeq pipeline.

first: Yidong

first: Ratna

last: Vadlamudi


title: KDM1A inhibition is effective in reducing stemness and treating triple negative breast cancer

summary: We examined the transcriptional changes modulated by lysine-specific histone demethylase 1 (KDM1A/LSD1) by perfroming global transcriptome analysis. MDA-MB-231 cancer stem cells (CSCs) were transduced with control shRNA or KDM1A shRNA lentiviral particles and the RNA was isolated and utilized for RNA-seq analysis. Our results demonstrated that differentially expressed genes were enriched in biological processes of regulation of organismal processes, cell migration, cell motility, cell proliferation and cell differentiation. In terms of molecular function, the differentially expressed genes were enriched in growth factor activity, cytokine activity, and cytokine receptor binding. Importantly, GSEA results demonstrated that KDM1A regulated genes showed a negative correlation with the gene sets of IL6-JAK-STAT3 signaling and epithelial mesenchymal transition (EMT) pathways.

overall_design: Total RNA was isolated from MDA-MB-231 CSCs expressing either control shRNA or KDM1A shRNA. Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 3000 in duplicate. The combined raw reads were aligned to UCSC hg19 and genes were annotated by Tophat. Genes were annotated and quantified by HTSeq-DESeq pipeline.


title: Heart (Left Ventricle) RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org)

status: Public on Sep 17 2023

city: Aurora

first: Laura

last: Saba

state: CO

address: 12850 E. Montview Blvd

department: Skaggs School of Pharmacy and Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

summary: As part of the PhenoGen Project (https://phenogen.org), heart(left ventricle) RNA-Seq data has been/will be collected from strains of the Hybrid Rat Diversity Panel (HRDP). RNA expression levels were estimated using high throughput RNA sequencing (RNA-Seq) on long (>200 nucleotides) RNAs, i.e., total RNA where ribosomal RNA was depleted. These data can be used to examine predisposition phenotypes in the HRDP. Processed data and interactive graphics are also available through the PhenoGen website. Additional data from additional strains will be added as they become available.

overall_design: RNA expression data has been gathered over several tissues (e.g., brain, liver, heart, kidney) on rats from the Hybrid Rat Diversity Panel (HRDP) as part of the RGAP: The heritable transcriptome and alcoholism project funded by NIAAA R24 AA013162. For each strain, RNA from 3 naive male biological replicates is extracted and a separate RNA-Seq library is generated fro each replicate. rRNA-depleted total RNA is used to generate libraries and libraries are sequenced using Illumina sequencing technology. All rats used in this study were alcohol and drug naive and were NOT subjected to any behavioral testing. Therefore, these data represent a predisposition database that can be used for integrative systems genetics studies.

first: Boris

last: Tabakoff

first: Paula

last: Hoffman


title: Somatic mutations in SLC30A1 lead to aldosterone-producing adenomas  and primary aldosteronism

status: Public on Jul 03 2023

first: Antonio

middle: Marcondes

last: Lerario

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

summary: Primary aldosteronism (PA), the most common form of endocrine hypertension, is characterized by inappropriately elevated aldosterone production via renin-independent mechanisms. Driver somatic mutations for aldosterone excess have been found in approximately 90% of aldosterone-producing adenomas (APAs) using an aldosterone synthase (CYP11B2)-guided sequencing approach. Herein, using CYP11B2-guided whole-exome sequencing (WES) and targeted amplicon sequencing, we detected two closely-stationed somatic variants in SLC30A1 in five APAs (p.L51_A57del, n=3; p.L49_L55del, n=2) that were devoid of any of the known aldosterone-driver mutations. SLC30A1 encodes the ubiquitous zinc efflux transporter ZnT1 (zinc transporter 1). PA cases with SLC30A1 mutations showed male dominance and demonstrated increased serum aldosterone concentration compared with age-matched male controls. We tested functional effects of the variant SLC30A1L51_A57del in a doxycycline-inducible system using the human adrenocortical HAC15 cell line. Functional in vitro studies following doxycycline treatment indicated increased adrenal cell aldosterone production, CYP11B2 mRNA expression, CYP11B2 promoter activity, depolarization of the resting membrane potential and increased cytosolic Ca2+ levels in the SLC30A1L51_A57del cells. Collectively, these data support a pathological role for mutant SLC30A1 on the development of PA.

overall_design: The human adrenocortical carcinoma cell line HAC15 containing a CYP11B2 promoter-driven secreted Gaussia luciferase reporter (HAC15-B2Luc)17,18, was used as parental cells. The HAC15-B2Luc cells were grown in DMEM-F12 containing 10% cosmic calf serum (CCS), 1% insulin-transferrin-selenium, and antibiotics (penicillin, streptomycin and gentamicin) and maintained in a 37°C humidified atmosphere (5% CO2), as previously described18. These cells were transduced8,18,19 with the SLC30A1WT and SLC30A151_57del lentiviruses to generate the cell lines HAC15B2Luc-Doxy-SLC30A1WT and HAC15B2Luc-Doxy-SLC30A151_57del respectively, followed by antibiotic selection with geneticin (Gaussia luciferase selection marker, 1 mg/mL) and blasticidin (SLC30A1 selection marker, 2 µg/mL).  Cells were plated at a density of 75,000 cells/well in a 48-well dish for 48 hours. After incubation in a low serum medium (DMEM/F-12 containing 0.1% CCS and antibiotics) for 24 hours, expression of SLC30A1WT and SLC30A151_57del in the cells was initiated by addition of 1 μg/mL Doxy (Sigma Aldrich, St. Louis, MO) for the indicated times.

first: Juilee

last: Rege

first: Kazutaka

last: Nanba

first: Carla

last: Kosmann

first: Sascha

last: Bandulik

first: Amy

last: Blinder

first: Chandan

last: Kumar-Sinha

first: Pankaj

last: Vats

first: Tobias

last: Else

first: Yuto

last: Yamazaki

first: Fumitoshi

last: Satoh

first: Hironobu

last: Sasano

first: Thomas

last: Giordano

first: Tracy

last: Williams

first: Martin

last: Reincke

first: Adina

middle: F

last: Turcu

first: Aaron

last: Udager

first: Richard

last: Warth

first: William

last: Rainey


title: Combinatorial targeting of a novel MET/EMT network components by macroH2A variants safeguards cell identity [ChIP-seq]

status: Public on Jun 21 2023

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

summary: The establishment and maintenance of cellular identity rely upon the precise coordination of regulatory pathways culminating to the proper execution of cell type-specific gene expression programs. Generation of induced pluripotent stem cells (iPSCs) from highly specialized cell types provides an excellent model system to study how cells maintain their stability through the functional interplay of transcription factors and chromatin structure, and how they can change identity, especially in the context of disease. Previous studies have shown that chromatin structure safeguards cell identity by acting as a barrier to reprogramming. Here, we investigated the mechanisms of how the histone variant macroH2A inhibits reprogramming by interfering with the mesenchyme to epithelial transition, a step that is a prerequisite for reprogramming of mouse embryonic fibroblasts. We found that each of the macroH2A isoforms regulates the expression of defined sets of genes, whose overall function is to stabilize the mesenchyme phenotype, thus resisting reprogramming. We identified a novel gene network (MSCN, mesenchyme network) composed of 63 macroH2A-regulated genes encoding proteins of the extracellular matrix, cell membrane, cytoplasmic signal integrators and the transcriptional regulators Id2 and Snai2, all of which can function as key controllers of the mesenchyme phenotype. Functional studies including ChIP-seq and KD experiments using any one of the individual macroH2A isoforms revealed an isoform-specific combinatorial targeting of the genes that reconstruct the MSCN. Our findings established that the combinatorial macroH2A targeting of the MSCN components safeguards cell identity and demonstrated its pivotal role in maintaining the differentiated cell phenotype by generating robustness in gene expression programs to resist cellular reprogramming.

overall_design:
ChIPseq
Please note that the antibodies are custom-made and is described in PMID: 24885602

last: Thanos

first: Dimitrios


title: Combinatorial targeting of a novel MET/EMT network components by macroH2A variants safeguards cell identity.

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


title: Cigarette smoke exposure alters innate immune signaling in macrophages

status: Public on Jun 23 2023

city: Santa Cruz

first: Susan

last: Carpenter

state: CA

address: Red Hill Rd, Biomedical Sciences

department: MCD

institute: UC Santa Cruz

summary: The goal of this project is to identify novel genes that contribute to inflammation in cigarette smoke induced chronic obstructive pulmonary disease  (COPD). Our lab is interested in a class of RNA genes called Long noncoding RNAs (lncRNAs). There are over 16,000 lncRNAs in the human genome and less than 3% have defined functions. Here we aim to identify inflammatory specific lncRNAs that are dysregulated following cigarette smoke exposure in macrophages.

overall_design: RNA-seq analysis of Bone Marrow Derived Macrophages from mice exposed to cigarette smoke.

first: Salih

last: Mays

first: Robinson

last: Elektra

first: Malekos

last: Eric

first: Carpenter

last: Susan


title: Adenovirus transducion of A4.eSPR on in vitro differentiated C57BL6 murine BMDM cells

status: Public on Jun 13 2023

city: Duarte

first: Siqi

last: Chen

address: E 1500 Duarte Rd.

department: Department of Immuno-Oncology

institute: City of Hope Beckman Research Institute

overall_design: In vitro transduced murine bone marrow derived macrophages on differentiation day 5 were replated, and transduced with adenovirus carrying A4.eSPR on day6. Cells were collected on day8 for RNA extraction

first: Mingye

last: Feng


title: Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fates [scRNA-seq and scATAC-seq coAssay]

status: Public on May 31 2023

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary: Longitudinal scRNA-seq and scATAC-seq  from LCMV-specific P14 CD8 T cells in LCMV-Armstrong and LCMV-Clone 13 infection

overall_design: LCMV-specific P14 cells were sorted from mice infected with LCMV-Arm or LCMV-Cl13 on days 8, 15, or 30 post infection. An additional group of mice was treated with anti-PDL1 every three days starting at day 16; cells were sorted at day 30. scRNA-seq and scATAC-seq libraries were prepared using 10x Genomics coAssay kits.

first: Josephine

last: Giles

middle: J

last: Wherry


title: Distinct SWI/SNF chromatin remodelling complexes act differentially to maintain stem-like exhausted CD8 T cells.


title: Distinct SWI/SNF chromatin remodelling complexes act differentially to maintain stem-like exhausted CD8 T cells [RNA-seq]

summary: Exhausted CD8 T cells (TEX) arise during chronic viral infections and cancer and limit disease control. Three major sequential epigenetic remodeling events occur as naïve CD8 T cells (TN) differentiate into TEX: initial activation, early bifurcation between effector (TEFF) and TEX precursors, and later differentiation of effector-like and terminal TEX subsets from progenitor TEX. The epigenetic factors mediating these transitions remain poorly understood. Here, we uncovered distinct roles for two versions of the SWI/SNF chromatin remodeling complex, BAF and PBAF, in TEX differentiation using in vivo CRISPR screening. Disruption of BAF ablated antigen-specific CD8 T cells early in chronic infection, suggesting a requirement for BAF-mediated remodeling in the early epigenetic remodeling events. In contrast, depletion of PBAF subunits enhanced TEX formation and promoted progenitor TEX differentiation into more differentiated TEX subsets by limiting accessibility of TCF-1 binding sites. Loss of PBAF improved tumor control alone and in combination with anti-PD-L1. Simultaneous depletion of BAF- and PBAF-specific subunits revealed that BAF is required for the beneficial impact of loss of PBAF on TEX differentiation. Thus, BAF and PBAF regulate epigenetic transitions in CD8 T cell differentiation, with PBAF acting at a later stage in exhaustion as a guardian to limit full TEX differentiation and preserve TEX progenitor populations with implications for cancer immunotherapy.

overall_design: LCMV-specific CD8 T cells (P14) from Day 15 clone 13 infection were analyzed by RNA sequencing to study gene expression. Three biological replicates were analyzed for sgAno9 controls. For PBAF-distrupted samples (sgArid2 and sgPbrm1), two guides were used, for two replicates per guide.

first: Amy

last: Baxter


title: Distinct SWI/SNF chromatin remodelling complexes act differentially to maintain stem-like exhausted CD8 T cells [ATAC-seq]

overall_design: LCMV-specific CD8 T cells (P14) from Day 15 clone 13 infection were analyzed by ATAC sequencing to study chromatin accessability changes. Two biological replicates were analyzed for sgAno9 controls. For PBAF-distrupted samples (sgArid2 and sgPbrm1), two guides were used, for two replicates per guide.


title: Single-cell transcriptome profiling reveals diverse immune cell populations and their responses to viral infection in the spleen of zebrafish

city: Hangzhou

first: Chongbin

last: Hu

state: Zhejiang Province

address: 866 Yuhangtang Rd

department: College of Life Sciences

institute: Zhejiang University

summary: Teleost fish are indispensable model organisms for comparative immunology research that should provide fundamental insights into the evolutionary history of vertebrate immunity and eventually lead to an improved understanding of the general principles of immune system design. Although numerous studies on ﬁsh immunology have been conducted, knowledge about the cell types that orchestrate piscine immune systems remains limited. In this study, we generated a comprehensive atlas of immune cell types in a zebrafish model on the basis of single-cell transcriptome profiling.

overall_design: Spleen leukocyte (PBS-administered (control), SVCV-infected (infected) and SVCV-vaccinated plus SVCV-infected (vaccinated+infected) groups) of the AB zebrafish were isolated byFicoll-Hypaque (1.080 g/mL) density-gradient centrifugation and analyzed using scRNAseq.

first: Jie

last: Wang

first: Yun

last: Hong

first: Hao

last: Li

first: Dongdong

last: Fan

first: Aifu

last: Lin

first: Lixin

last: Xiang

first: Jianzhong

last: Shao


title: High-resolution analysis of mononuclear phagocytes reveals clinically relevant markers in human colo-rectal liver metastasis II

status: Public on May 02 2023

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

summary: Macrophages (Mf) are the most abundant mononuclear phagocytes in tumor tissues and hold promise as therapeutic targets and indicators of disease progression. In this work, we mapped by single-cell analysis the distinct Mf populations infiltrating the invasive margin and normal adjacent regions of human colo-rectal liver metastasis (CLM), and we exploited this information to identify non redundant markers with clinical relevance. Different populations were enriched in the invasive margin, including early-mature, inflammatory Mf (MoMf) expressing the monocytic markers S100A12 and SERPINB2, and a more mature population (TAMs) expressing CD68, GPNMB and TREM2. TAMs were enriched in pathways of matrix degradation, angiogenesis and lipid metabolism, similarly to dysfunctional macrophages described in other tumors. Cell-cell interaction analysis with CD8+ T cells defined opposing roles of MoMf, predicted to interact via IL-15, and TAMs, engaging T cells via IL-20 and IL-10. By multiplex immunofluorescence in CLM sections, we confirmed that SERPINB2 and GPNMB are expressed by different Mf subsets, with distinct topographical distribution and opposite association with patient clinical outcome.

overall_design: A total of six samples. Three invasive margin tissues (IM) and three normal adjacent tissues (NA).

first: R

last: Carriero

first: N

last: Cortese

first: P

last: Kunderfranco

first: F

last: Marchesi

first: A

last: Mantovani


title: High-resolution analysis of mononuclear phagocytes reveals clinically relevant markers in human colo-rectal liver metastasis

overall_design: A total of six samples; three margin invasive tissues (IM) and three normal adjacent tissues (NA)


title: Bioinformatics Analysis of Gene Expression Profiles for Diagnosing Sepsis and Risk Prediction in Patients with Sepsis

status: Public on May 19 2023

city: Seoul

first: kyeongman

last: Jeon

address: 81 Irwon-ro, Gangnam-gu

institute: Samsung Medical Center

summary: This study aimed to compare gene expression profiles between patients with sepsis and healthy volunteers, to determine the accuracy of these profiles in diagnosing sepsis, and to predict sepsis outcomes by combining bioinformatics data with molecular experiments and clinical information.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for patients with sepsis and healthy volunteer.

first: Hayoung

last: Choi

first: Jin Young

last: Lee

first: Hongseok

last: Yoo

first: Kyeongman


title: Characterisation of concurrent liver injury and oncogenes in a plasmid-based mouse model of liver cancer

city: Sydney

first: Vincent

middle: Lok Hang

last: Chiu

state: NSW

address: 1 Campbell St Liverpool

institute: Ingham Institute for Applied Medical Research

summary:
This experiment aimed to characterise transcriptomes of plasmid-based mouse models of liver cancer, hepatotoxin-induced chronic liver injury and the combination thereof.
In detail, C57BL/6JAusb mice received hydrodynamic tail vein injection (HTVI) of plasmids encoding Sleeping Beauty transposase (SB), alone or in combination with transposon plasmids encoding myristylated AKT1 (AKT), c-Met and NRasV12 (NRas), previously characterised by Ho et al. (2012) (Hepatology 55(3):833-45) and Hu et al. (2016) (Sci Rep 6:20484). 8-10 days post-HTVI, mice began biweekly intraperitoneal (i.p.) injections of saline or the hepatotoxin thioacetamide (TAA), 10-11 doses.

overall_design: There are 6 groups: 1) SB + saline (healthy control) (SB plasmid by HTVI and i.p. saline; 4 mice (180702, 180724, 180725, 180726)), 2) SB + TAA (Liver injury alone) (SB plasmid by HTVI, i.p. TAA; 4 mice (180704, 180705, 180706, 180727)), 3) SB/AKT/c-Met + saline, (Liver cancer model 1) (SB, AKT and c-Met plasmids by HTVI, i.p. saline; 3 mice (180707, 180708, 180748)) 4) SB/AKT/c-Met + TAA (Liver cancer model 1 + injury) (SB, AKT and c-Met plasmids by HTVI, i.p. TAA; 4 mice (180710, 180712, 180713, 180714)), 5) SB/AKT/NRas + saline (Liver cancer model 2) (SB, AKT and NRas plasmids by HTVI, i.p. saline; 4 mice (180715, 180716, 180717, 180749)) and 6) SB/AKT/NRas + TAA (Liver cancer model 2 + injury) (SB, AKT and NRas plasmids by HTVI, i.p. TAA; 5 mice (180719, 180720, 180721, 180722, 180723)).

middle: L


title: Spatial resolution of cellular senescence dynamics in colorectal liver metastasis

status: Public on May 16 2023

city: Pieve Emanuele (MI)

institute: IRCCS Humanitas Research Hospital

summary: Heterogeneity of senescent cancer cells have been dissected by Spatial Transcriptomic in human colorectal liver metastasis (CRLM).

overall_design: Comparative spatial gene expression profiling of senescent cancer cells subpopulations

first: Luca

last: Lambroia

first: Francesca

last: Faggioli


title: Oligoadenylate synthetase-like (OASL) aggravated newcastle disease virus (NDV)-induced necroptosis in glioma cells

status: Public on May 01 2023

city: Hangzhou China

first: Zecheng

last: Yu

address: 481 Binwen Road, Binjiang District, Hangzhou City, Zhejiang Province, China

institute: Hangzhou Medical College

summary: Newcastle disease virus (NDV) has emerged as an oncolytic agent in several cancers. Previous study has shown that NDV exerts cytolytic activity in glioma, however, the underlying mechanism has not been fully uncovered. Here the cytolytic activity of NDV in glioma and the associated mechanisms have been demonstrated. Infection with NDV inhibits cell proliferation and promotes cell apoptosis in LN229 cells. Further investigation showed that cytoplasmic organelle damage and cytoplasmic vacuolation were observed in LN229 cells after NDV infection. JC-1 staining assay proved that NDV caused cell apoptosis of LN229 cells by inducing mitochondrial dysfunction. We next speculated that NDV caused LN229 cells death through inducing necroptosis, but not ferroptosis, since the Fe2+ level did not alter after NDV infection. Furthermore, the NDV-caused cell death in LN229 cells was blocked by necroptosis inhibitor Nec1. Besides, RNA-seq analysis identified the different expression genes in NDV-infected LN229 cells. OASL, an antiviral gene, has been found to be directly induced by NDV infection. We also found that knockdown of OASL enhanced NDV infection-induced LN229 cells necroptosis. In summary, two aspects about cytolytic activity of NDV in glioma have been demonstrated. NDV presented cytolytic activity in glioma cells through inducing necroptosis. Additionally, targeting OASL may provide new strategy for enhancing necroptosis of glioma cells after NDV infection.

overall_design: The normal group of LN299 was controlled with the infected group of NDV rLa Sota-GFP strain, and the molecular mechanism of necrotizing apoptosis of LN299 killed by NDV infection was investigated by using EdU cell proliferation, flow cytometry, transmission electron microscopy, JC-1 staining, Fe2+ detection, RNA isolation and sequencing, and cell transfection to observe the changes in genome and protein levels and activation of signaling pathways before and after infection at the cellular level and transcriptome gene level.

first: Yangkun

last: Chen

first: Wei

last: Han


title: Single nucleus RNAseq of midbrain dopaminergic neuronal nuclei isolated by FACS

status: Public on Apr 26 2023

city: Chicago

first: Zachary

last: Gaertner

state: Illinois

address: 320 E Superior, Searle 7-450

department: Neurology

institute: Northwestern University, Feinberg School of Medicine

summary: While many studies have performed single cell profiling of dopamine (DA) neurons in mice, they have largely been limited by the number of DA neurons captured. Here, we performed single-nucleus RNAseq on DA neurons to refine the DA subtype landscape.

overall_design: Two replicates from a total of n=5 DAT-Cre mice with a nuclear GFP reporter. Samples contain tissue from midbrains after isolation of DAT+ nuclei via FACS.

first: Maite

last: Azcorra

first: Rajeshwar

last: Awatramani

first: Daniel

last: Dombeck


title: Adenovirus transducion of CV1.eSPR on in vitro differentiated human primary macrophages

first: Siqi

overall_design: Buffy coat was isolated from leukapheresis cones by Ficoll-Paque centrifugation. Monocytes were enriched from human PBMC by CD14 beads positive selection (Miltenyi Biotec) and cultured in IMDM supplanted with 10% human AB serum (omega scientific, Cat# HS-20) for 6 days. Cells were replated. On day7, cells were transduced with MOI=1000 CV1.eSPR carrying adenovirus. On day9, RNA were extracted.

first: Mingye

last: Feng


title: Reticulocalbin 3 is a Novel Mediator of Glioblastoma Progression

status: Public on Apr 19 2023

first: YI

last: ZOU

state: TX

summary: Patient-derived primary GSCs were established from discarded specimens obtained from glioblastoma (GBM) patients undergoing surgery at UT Health San Antonio. We examined global transcriptional changes by RNA-sequencing using patient derived glioma stem cells (GSCs) transduced with either control shRNA or Reticulocalbin-3 (RCN3) shRNA. RNA-seq studies showed downregulation of genes related to translation, ribosome, and cytokine signaling and upregulation of genes related to immune response, stem cell differentiation, and extracellular matrix.

overall_design: Patient derived GSC040815 cells were transduced with either control shRNA or RCN3 shRNA.  Total RNA was isolated using RNeasy mini kit according to the manufacturer's instructions (Qiagen, Valencia, CA).  Illumina TruSeq RNA Sample Preparation was performed following the manufacturer's protocol. Samples were run on an Illumina NextSeq 500 in triplicate. The combined raw reads were aligned to UCSC hg19, and genes were annotated by Tophat. Genes were annotated and quantified by the HTSeq-DESeq pipeline.

first: Salvador

last: Alejo

first: Yidong

first: Gangadhara

last: Sareddy


title: Blood cells with trisomy 21 overreact to heat shock stress [PRO-seq]

status: Public on Apr 21 2023

city: Boulder

first: Mary

middle: Ann

last: Allen

state: Co

address: UCB 596  JSCBB

department: BioFrontiers

institute: University of Colorado

summary: Lymphoblastoid cells trisomic for chromosome 21 activate the heat shock response more robustly than disomic cells.

overall_design: D21 and T21 lymphoblastoid cells derived from EBV infection of B cells from two brothers were assayed before and after heat shock using ATAC-seq, PRO-seq and scRNA-seq. Heat shock was 42C for 1 hour. This dataset includes the PRO-seq data.

first: Joseph

last: Cardiello

first: Robin

last: Dowell


title: Estradiol cycling drives female obesogenic adipocyte hyperplasia

status: Public on Apr 10 2023

city: New Haven

first: Matthew

middle: S

last: Rodeheffer

state: Connecticut

address: 316 Cedar St.

department: Comparative Medicine

institute: Yale University

summary: White adipose tissue (WAT) distribution is sex dependent. Adipocyte hyperplasia contributes to WAT distribution in mice driven by cues in the tissue microenvironment, with females displaying hyperplasia in subcutaneous and visceral WAT, while males and ovariectomized females have visceral WAT (VWAT)-specific hyperplasia. However, the mechanism underlying sex-specific hyperplasia remains elusive. Here, transcriptome analysis in female mice shows that high-fat diet (HFD) induces estrogen signaling in adipocyte precursor cells (APCs). Analysis of APCs throughout the estrous cycle demonstrates increased proliferation only when proestrus (high estrogen) coincides with the onset of HFD feeding. We further show that estrogen receptor α (ERα) is required for this proliferation and that estradiol treatment at the onset of HFD feeding is sufficient to drive it. This estrous influence on APC proliferation leads to increased obesity driven by adipocyte hyperplasia. These data indicate that estrogen drives ERα-dependent obesogenic adipocyte hyperplasia in females, exacerbating obesity and contributing to the differential fat distribution between the sexes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from adipocyte precursor cells (APCs) from female mice fed a control (SD) and high-fat diet (HFD) for 3 days.

first: Rocio

middle: D

last: Saavedra-Peña

first: Natalia

last: Taylor

first: Clare

last: Flannery


title: Genes regulated by CREB1 in LPS-primed THP1 monocytes

status: Public on Apr 14 2023

city: Changsha

first: Nian

last: Wang

state: Hunan

address: No.110 Xiangya Road

institute: Central south university

summary: To screen the genes and pathways regulated by CREB1 in the THP1 monocytes induced by LPS, THP1 monocytes were transfected by CREB1 shRNA and then treated by LPS for 3 hours.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THP1 monocytes and CREB1 shRNA with or without LPS treatment..

first: Daolin

last: Tang