title: Comparable levels of innate immune responses between low DIPs and high DIPs LAIV inoculations in the mouse upper respiratory tract revealed by scRNA-seq

status: Public on Sep 13 2024

city: Changchun

first: Weiheng

last: Su

state: Jilin

address: No. 2699, Qianjin Street

department: School of Life Sciences

institute: Jilin University

summary: To investigate the extent of replication and strength of innate immune responses of low DIPs and high DIPs H3N2 LAIVs in mouse turbinate tissues, the 48-hpi transcriptomes were analyzed using scRNA-seq.

overall_design: Female 6–8-week-old BALB/c mice were intranasally immunized with of low DIPs LAIV, high DIPs LAIV or placebo. The turbinate and adjacent mucosal tissues were isolated at 48 hpi for scRNA-seq.

first: Min

last: Wu

first: Peihan

last: Wang

first: Fei

last: Chen


title: Beyond Glucose: The Crucial Role of Redox Signaling in β-Cell Metabolic Adaptation

status: Public on Sep 15 2024

city: Praha

first: Blanka

last: Holendova

address: Videnska 1083

country: Czech Republic

institute: Institute of Physiology, CAS

type: Expression profiling by high throughput sequencing

summary: Objective: Redox signaling mediated by reversible oxidative cysteine thiol modifications is crucial for driving cellular adaptation to dynamic environmental changes, maintaining homeostasis, and ensuring proper function. This is particularly critical in pancreatic β-cells, which are highly metabolically active and play a specialized role in whole organism glucose homeostasis. Glucose stimulation in β-cells triggers signals leading to insulin secretion, including changes in ATP/ADP ratio and intracellular calcium levels. Additionally, lipid metabolism and reactive oxygen species (ROS) signaling are essential for β-cell function and health. Methods: We employed IodoTMT isobaric labeling combined with tandem mass spectrometry to elucidate redox signaling pathways in pancreatic β-cells. Results: Glucose stimulation significantly increases ROS levels in β-cells, leading to targeted reversible oxidation of proteins involved in key metabolic pathways such as glycolysis, the tricarboxylic acid (TCA) cycle, pyruvate metabolism, oxidative phosphorylation, protein processing in the endoplasmic reticulum (ER), and insulin secretion. Furthermore, the glucose-induced increase in reversible cysteine oxidation correlates with the presence of other post-translational modifications, including acetylation and phosphorylation. Conclusions: Proper functioning of pancreatic β-cell metabolism relies on fine-tuned regulation, achieved through a sophisticated system of diverse post-translational modifications that modulate protein functions. Our findings demonstrate that glucose induces the production of ROS in pancreatic β-cells, leading to targeted reversible oxidative modifications of proteins. Furthermore, protein activity is modulated by acetylation and phosphorylation, highlighting the complexity of the regulatory mechanisms in β-cell function.

overall_design: Isolated islets were cultivated in CMRL medium at non/stimulating glucose concentration for 24 h. The islets were washed with PBS and used immediately for RNA extraction.  Subsequent comparative gene expression profiling analysis of RNA-seq data was performed for WT islets treated with non/stimulating glucose.

first: Barbora

last: Salovska

first: Stepanka

last: Benakova

first: Lydie

last: Plecita


title: Hepatocyte identity and zonal position determine tumourigenic potential of mutant β-catenin

status: Public on Sep 12 2024

city: Glasgow

first: Joseph

middle: Alexander

last: Waldron

address: Switchback road

country: United Kingdom

institute: Beatson Institute for Cancer Research

summary: Oncogenic mutations in otherwise normal tissue are common in many adult tissues. This suggests multiple events need to converge to drive tumourigenesis and that many processes such as tissue differentiation may be protective against carcinogenesis. Within the liver Wnt/β-catenin signalling maintains zonal differentiation during liver homeostasis. However, the CTNNB1 oncogene—encoding β-catenin—is also frequently mutated in hepatocellular carcinoma, resulting in aberrant Wnt signalling that promotes cell growth. Here we investigated the antagonistic interplay between Wnt-driven growth and differentiation in zonal hepatocyte populations during liver tumorigenesis. In a model that acutely recombined mutant Wnt (Ctnnb1-ex3) and MYC alleles, we found that β-catenin mutants transiently stimulated growth in zone-1 and -2 hepatocytes within the Wnt-low region of the liver lobule – before inducing a differentiated zone-3 fate. To investigate the role of translation in this model of wnt and myc driven growth we performed Ribosome sequencing of whole liver at the early proliferative stage and the later differentiated stage. We found that Mutamt B-Catenin and MYC livers had a unique tanslational efficiency , which promted translation of RNA transcripts associated with growth.

overall_design: RPFs represent ribosome protected fragments and Totals represents the paired cytoplasmic RNA control, which was extracted with TRIzol from the lysate, prior to RNase digestion. For example, WT_day4_1_RPFs and WT_day4_1_Totals represents the RPFs and total cytoplasmic RNA sample from the first replicate of the day4 WT samples. Each sample represents an individual mouse and therefore a unique biological replicate. Day4 and Day10 mice were induced at different times so that all mice could be sacrificed and harvested at the same time.

middle: A

first: June

last: Munro

first: Alex

last: Raven

first: Martin

last: Bushell

first: Owen

middle: J

last: Sansom


title: Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade [scRNA-seq]

city: BALTIMORE

first: Daniel

middle: H

last: Shu

state: Maryland

address: CRB1, RM 416, 1550 ORLEANS ST.

department: Oncology

country: USA

institute: Johns Hopkins Sidney Kimmel Cancer Center

summary: Tertiary lymphoid structures (TLS) are associated with improved response in solid tumors treated with immune checkpoint blockade (ICB), but understanding of their clinical significance and the circumstances of their resolution remains incomplete. Here, we found that in hepatocellular carcinoma (HCC) treated with neoadjuvant immunotherapy, high intratumoral TLS density at the time of surgery is associated with pathologic response and improved relapse free survival. In areas of tumor regression, we further identified a non-canonical involuted morphology of TLS marked by dispersion of the B cell follicle, persistence of a T cell zone enriched for T cell-mature dendritic cell interactions, and increased expression of T cell memory markers. Collectively, these data suggest that TLS may serve be both a prognostic and predictive marker of response to immunotherapy in HCC and suggest a functional role for late-stage TLS T cell memory formation after elimination of viable tumor.

overall_design:
We utilized surgical resection specimens and peripheral blood obtained from patients with locally advanced hepatocellular carcinoma receiving neoadjuvant immune checkpoint blockade based therapy. Bulk RNA sequencing was performed on post-treatment tumor resection specimens to characterize differences in gene expression between tumors with high and low density of tertiary lymphoid structures. Tumor associated tertiary lymphoid structures were microdissected and subjected to bulk TCR and BCR sequencing using the Adaptive Biotechnologies ImmunoSEQ platform (shared separately). Single cell RNA, TCR, and BCR sequencing was performed on matched peripheral blood and tumor specimens to infer the identity of T and B cells identified in tertiary lymphoid structures.

*** Submitters state that raw data is being submitted to dbGap (phs003672.v1.p1)***

first: Mark

last: Yarchoan


title: Dnmt3a Controls Hematopoietic Stem Cells via DNA Methylation-Independent Regulation of Telomeres

status: Public on Sep 10 2024

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

type: Methylation profiling by high throughput sequencing

summary: Dnmt3a is the most recurrently mutated gene in clonal hematopoiesis (CH) and it is a critical regulator of hematopoietic stem cells (HSCs). Conditional deletion of Dnmt3a in mouse HSC results in enhanced self-renewal but impaired differnetiation. Dnmt3a encodes for a de novo DNA methyltransferase enzyme but both mouse and human cells with loss of Dnmt3a show minimal change in DNA methylation levels which do not correlate with gene expression differences. To understand if these changes are due to non-canonical function of Dnmt3a, we generated varying levels of DNA methyaltion-impared Dnmt3a mouse models. Our data depicts that DNA methyaltion-impaired Dnmt3a phenocopy wild-type in serial transplant. And Dnmt3a methyltransferase-deficient HSCs showed differntially methylated regions (DMRs) and gene expression  pattern that overlapped with Dnmt3a-null HScs. Suggesting that Dnmt3a has important non-canonical function that partially regulates HSC fate. Dnmt3a-null HSC increased HSC self-renwal and can be transplanted indefinitely and increase longevity with no erosion of telomere length. Dnmt3a-null HSCs showed increased telomere at baseline and maintained overa serial transplant and increased telomerase activity. The role of Dnmt3a in telomere maintenance was not strictly linked to elongated telomere length but in regulation of DNA damage response that occurs at stressed telomeres. These data show a unidentified role of Dnmt3a in HSC telomere maintenance that is note related to DNA methylation function.

overall_design: To investigate the diffential DNA methylation and gene expression patterns in hematopoietic cells expressing Dnmt3a-variants with varying DNA methyltransferase activity, we established Cre-mediated knockin mouse models. Competitive HSC transplantation was performed.  Post-transplant cells were isolated 18-weeks post transplant for analysis of gene expression patterns by RNA sequencing and DNA methylation patterns by whole genome bisulfite sequencing.

first: Infencia

middle: X

last: Raj

first: Won

middle: K

last: Koh

first: Christine

middle: R

last: Zhang

first: Jessica

last: Harrison

first: Barbara

last: Soares

first: Nancy

last: Issa

first: Hassan

last: Bjeije

first: Tyler

middle: M

last: Parsons

first: Wentao

last: Han

first: Ting

first: Luis

middle: F

last: Batista

first: Grant

last: Challen


title: Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells.

city: Baltimore

first: Annukka

last: Antar

state: MD

address: 733 North Broadway Room 869

department: Medicine - Infectious Diseases

institute: Johns Hopkins School of Medicine

summary: The latent reservoir of HIV persists for decades in people living with HIV (PWH) on antiretroviral therapy (ART). To determine if persistence arises from the natural dynamics of memory CD4+ T cells harboring HIV, we compared the clonal dynamics of HIV proviruses to that of memory CD4+ T cell receptors (TCRβ) from the same PWH and from HIV-seronegative people. We show that clonal dominance of HIV proviruses and antigen-specific CD4+ T cells are similar but that the field’s understanding of the persistence of the less clonally dominant reservoir is significantly limited by undersampling. We demonstrate that increasing reservoir clonality over time and differential decay of intact and defective proviruses cannot be explained by mCD4+ T cell kinetics alone. Finally, we develop a stochastic model of TCRβ and proviruses that recapitulates experimental observations and suggests that HIV-specific negative selection mediates approximately 6% of intact and 2% of defective proviral clearance. Thus, HIV persistence is mostly, but not entirely, driven by natural mCD4+ T cell kinetics.

overall_design:
To test whether the natural physiology of memory CD4+ T cells (e.g., HIV as inert “passenger” hypothesis) is sufficient to explain reservoir clonality and dynamics or whether selective factors related to HIV infection itself are required to explain these observations, we generated longitudinal clonality data from memory CD4+ T cells in HIV seronegative individuals and from HIV proviruses and CD4s simultaneously from PWH on ART. We compared the longitudinal (~10 year) clonality of HIV proviruses (intact and defective) from resting CD4+ T cells with the longitudinal clonality of their putative carrier cells, resting memory CD4+ (rmCD4) T cells from the same blood samples from PWH on ART. We also compared proviral clonality of the replication competent reservoir at single time points from PWH on long-term ART with the clonality of rmCD4s from the same blood samples. To determine whether suppressed HIV infection itself is associated with significantly different mCD4 clonality, we compared the longitudinal cohort of PWH on ART to HIV-seronegative people matched on age, race, and sex. We identified antigen specific (CMV and HIV) mCD4 cells in a subset of people and compared their clonality and decay rates with that of HIV-infected cells and all mCD4s. To make these comparisons, we modeled clonotype abundance distributions and calculated clonality and diversity metrics.
***Adaptive Biotechnologies does not release raw data.***

middle: B

last: Reeves


title: Effect of isolated neutrophils from Cd177 knockout mice post-SCI on macrophages in a co-culture system

city: Nanjing

first: Siming

last: Dai

address: No. 300, Guangzhou Road, Nanjing

department: Department of Orthopedic

country: China

institute: The First Affiliated Hospital of Nanjing Medical University

summary: To investigate the transcriptional effects of CD177+ neutrophils on macrophages in spinal cord injuries (SCI), we adapted a co-culture system containing isolated neutrophils from Cd177 WT or KO mice post-SCI and bone marrow-derived macrophages (BMDMs). Each group had a biological repeat (n=3).

overall_design: Briefly, we isolated neutrophils in injured lesions at 3 dpi from Cd177 KO or WT mice by magnetic-activated cell sorting (MACS) and co-cultured them with BMDMs. After co-culturing for 24h, We isolated macrophages by fluorescence-activated cell sorting (FACS, gated on Ly6G-) for further testing.

first: Ziyang

last: Zheng

first: Shujie

last: Zhao

first: Guoyong

last: Yin


title: Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

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

overall_design: Refer to individual Series


title: Effect of isolated neutrophils from Cd177 knockout mice post-SCI on microglia in a co-culture system

summary: To investigate the transcriptional effects of CD177+ neutrophils on microglia in spinal cord injuries (SCI), we adapted a co-culture system containing isolated neutrophils from Cd177 WT or KO mice post-SCI and isolated microglia. Each group had a biological repeat (n=3).

overall_design: Briefly, we isolated neutrophils in injured lesions at 3 dpi from Cd177 KO or WT mice by magnetic-activated cell sorting (MACS) and co-cultured them with microglia. After co-culturing for 24h, We isolated microglia by fluorescence-activated cell sorting (FACS, gated on Ly6G-) for further testing.


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [Embryo genomic DNA]

city: Beijing

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

institute: Tsinghua University

summary: X chromosome inactivation (XCI) triggers a drastic reprogramming of gene activities and chromosome architecture. However, how the 3D organization of the inactive X chromosome (Xi) is de novo established in vivo in mammals remains poorly understood. By comprehensive stage- and lineage- specific Hi-C mapping, we identified a unique Xist-separated megadomain structure (X-megadomains) on the Xi in mouse early embryos. X-megadomains emerge in extraembryonic lineages during imprinted XCI, in derived extraembryonic endoderm (XEN) cells, and transiently in the embryonic lineages during random XCI, before Dxz4-delineated megadomains (D-megadomains) occur at later stages in a strain-specific manner. Mechanistically, the emergence of X-megadomain boundary coincides with developmentally regulated enhancer activities and cohesin binding in a regulatory region near Xist (XRR). We pinpointed a subregion XRRa that is critical for the X-megadomain boundary. X-megadomains are impaired when XRRa is removed or cohesin is degraded in XEN cells. Importantly, this is accompanied by ectopic activation of regulatory elements and genes near Xist, suggesting that cohesin loading at regulatory elements promotes X-megadomains and confines local gene activities. Finally, the knockout of XRRa in mouse preimplantation embryos severely impairs the activation of Xist and the initiation of XCI. Hence, our data not only reveal stepwise chromosome folding during de novo XCI in vivo, but also support a model that regulatory element-dependent gene activation and cohesin loading simultaneously promote essential transcription activities and subsequent self-insulation amid global silencing during the early stage of XCI.

overall_design: Genomic DNA libraries for various genotypes of morula embryos.

first: Zhuoning

last: Zou

first: Liangjun

last: Hu

first: Zihan

last: Li

first: Wei

last: Xie


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [XEN cells CUT&RUN]

overall_design: CUT&RUN for CTCF and SMC3 in WT and mutant XEN cells


title: Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade [bulk RNA-seq]

first: Daniel

last: Shu

first: Mark

last: Yarchoan


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [XEN cells ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: STAR ChIP-seq for H3K27ac in WT and mutant XEN cells


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [XEN cells RNA-seq]

overall_design:
RNA-seq data for WT and mutant XEN cells

Please note that, in the *allelic_FPKM.txt.gz files, the "_Xa" and "_Xi" columns contain the FPKM values of genes in the active X chromosome and in the inactive X chromosome, respectively.


title: Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [Embryo CUT&RUN]

overall_design: CUT&RUN for CTCF and SMC3 in various stages of embryos


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [Embryo ChIP-seq]

overall_design: STAR ChIP-seq for H3K27ac in E6.5 extraembryonic tissues


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [XEN cells HiC]

summary: X chromosome inactivation (XCI) triggers drastic reorganization of chromatin architecture, which in turn facilitates XCI. However, how the 3D organization is de novo established during XCI in vivo remains poorly understood. Mouse embryos present an ideal model, as they undergo imprinted XCI, X chromosome reactivation (XCR) and subsequent random XCI. Using low-input Hi-C, we revealed a unique chromatin structure of the inactive X chromosome (Xi) during both imprinted and random XCI in early mouse embryos. A bipartite structure featured by two megadomains separated by Xist (X-megadomains), emerges in extraembryonic lineages, derived extraembryonic endoderm (XEN) cells, and also transiently in embryonic lineages. X-megadomains then diminish in adult tissues, where previously reported Dxz4-delineated megadomains (D-megadomains) appear in a strain-specific manner. Mechanistically, X-megadomains coincide with developmentally controlled activities of regulatory regions near Xist (XRRs), and loss of XRR disrupts X-megadomains. CUT&RUN revealed strong enrichment of CTCF and cohesin near Xist, despite global depletion, on Xi in embryos and XEN cells. X-megadomains are also impaired when Xist is silenced, accompanied by global cohesin restoration, or when residual cohesin is degraded, suggesting that X-megadomain formation is promoted by both global cohesin depletion and local cohesin loading. Importantly, the loss of cohesin leads to ectopic activation of regulatory elements and genes near Xist. Hence, these data reveal programming of chromatin architecture during de novo establishment of mammalian XCI in vivo, and suggest that cohesin mediates self-insulation of gene activity of essential escapees amid global silencing.

overall_design: Small scale in situ high throughput chromatin conformation capture (sisHi-C) for WT and mutant XEN cells


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [Embryo HiC]

overall_design: Small scale in situ high throughput chromatin conformation capture (sisHi-C) for various stages of embryos or tissues.


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [MEF RNA-Seq]

overall_design: RNA-seq data for MEF cell lines.


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [MEF HiC]

overall_design: Small scale in situ high throughput chromatin conformation capture (sisHi-C) for MEF cell lines.


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [Embryo RNA-seq]

overall_design:
RNA-seq data for female embryos in various stages

Please note that in the rna_embryo_all_stages_merged_allelic_FPKM.txt file of "GEO_embryo_data", the "_m" and "_p" columns contain the FPKM values of genes in the maternal allele and in the paternal allele, respectively.


title: Translational profiling of stress-induced small proteins uncovers a connection among distinct signaling systems

status: Public on Sep 05 2024

city: Piscataway

first: Srujana

middle: Samhita

last: Yadavalli

state: NJ

address: 190 Frelinghuysen Rd

institute: RUTGERS UNIVERSITY

summary: Bacteria utilize sophisticated mechanisms to detect and adapt to challenging environmental conditions by activating specific genes that help counteract stressors. Over 150 small proteins (≤ 50 amino acids long) are documented in Escherichia coli, but only a fraction of them are well-studied. Many of these proteins do not have an associated phenotype and their biological roles remain elusive. Here, we investigate small proteins induced in response to magnesium limitation using ribosome profiling, RNA sequencing, and transcriptional reporter assays. We uncover 17 small proteins with increased translation initiation, a majority of which are transcriptionally upregulated by the PhoQ-PhoP two-component signaling system, central for magnesium homeostasis. Next, we describe small protein-specific deletion and overexpression phenotypes, which underscore the significance of their expression to cellular physiology in low magnesium stress. Most remarkably, our study reveals the small protein YoaI as a connector of the major signaling networks – PhoR-PhoB and EnvZ-OmpR in E. coli.

overall_design: To investigate low magnesium stress induced small proteins in E. coli K-12 MG1655 strain, we utilized translation initiation profiling (Ribo-RET) and RNA-Seq under conditions of magnesium starvation and no stress. Code for processing the data can be found at https://github.com/yadavalli-lab/Small-proteins-induced-under-low-magnesium-stress

first: Sangeevan

last: Vellappan

first: Junhong

last: Sun

first: John

last: Favate

first: Pranavi

last: Jagadeesan

first: Debbie

last: Cerda

first: Premal

last: Shah


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [MEF ChIP]

overall_design: STAR ChIP-seq for H3K27ac in MEF cells


title: Stepwise de novo establishment of inactive X chromosome architecture in early development [MEF Cut&Run]

overall_design: CUT&RUN for CTCF and SMC3 in MEF cells


title: Comprehensive Profiling of Peripheral Blood Mononuclear Cells Reveals Monocyte-CD8+ T cell-B cell Communication as Central Cell-cell Interaction and pathogenesis in IgA Vasculitis

city: Wuhan

first: Zhaohui

last: Tang

state: Hubei

address: no.1095 Jiefang Avenue

department: Division of Trauma & Surgical Critical Care, Department of Surgery

institute: Tongji Hospital

summary: IgA vasculitis (IgAV) is a common vasculitis which often occurs in children. IgAV is characterized by the vasculitis caused by IgA deposition in the walls of small vessels. The mechanisms of immune disorders in IgAV, as well as the innmue network regulation between immune cells is still unclear. Dissecting the IgA-secreting B cells is crucial for understanding the pathegenesis mechanisms of IgA deposition in IgA vasculitis (IgAV). Here, we used single-cell RNA sequencing to profile immune cells in peripheral blood mononuclear cells of IgAV. MIF induced IgA secretion in IgAV, and monocyte-CD8+ T cell-B cell communication regulated MIF pathway. ICAMs pathway regulated monocyte-CD8+ T cell-B cell communication, and promoted B cells adhension in IgAV. CD8+ T cell was the key cell in monocyte-CD8+ T cell-B cell communication. TCR repertoire analysis identified a specific CD8+ Temra cluster with specific TCR clonetypes. BCR repertoire analysis revealed the existence of IgA Fc-specific IgG in serum of IgAV nephritis. These findings reveals complicated immune regulation in IgAV, emphrazing the importance of MIF and ICAMs pathways in cell-cell interaction, discovering CD8+ T cells’ crucial function for IgAV pathogenesis, and bringing new insights into the pathegenesis of IgA deposition in IgAV.

overall_design: Both IgAV patients and controls were collected from Wuhan Children's Hospital.

first: Chaohong

last: Liu

first: Jingzhi

last: Yang

first: Lu


title: A system for functional studies of the major virulence factor of malaria parasites [WGS]

status: Public on Sep 01 2024

city: Hamburg

first: Johannes

last: Allweier

address: Bernhard-Nocht-Straße 74

country: Germany

institute: Bernhard Nocht Institute for Tropical Medicine

summary: PfEMP1 is a variable antigen displayed on red blood cells (RBCs) infected with the malaria parasite Plasmodium falciparum. PfEMP1 mediates binding of the infected cell to the endothelium of blood vessels, a major cause of severe manifestations of malaria. Each parasite encodes ∼60 different PfEMP1 variants of which only one is expressed at a time and switching between variants underlies immune evasion in the host and variant-specific severity of disease. PfEMP1 expression heterogeneity between parasites complicates its study and hampers genetic modification approaches as in many cells the modified locus is not expressed. Here we used selection linked integration to generate parasites all expressing the same PfEMP1 variant and permitting genomic modification of the expressed locus. Using this system, we study PfEMP1 trafficking, generate cell lines binding to all major endothelial receptors, survey the protein environment from functional PfEMP1 in the host cell and identify new proteins needed for PfEMP1 mediated sequestration. Overall, these approaches facilitate the study of the molecular and cellular biology of the key virulence factor of malaria parasites.

overall_design: Whole genome sequencing samples of erythrocytes infected with the P. falciparum transgenic parasites IT4var01-BirA*Pos1endo, IT4var01-BirA*Pos1endo + TryThrA-TGD or IT4var01-BirA*Pos1endo + EMPIC3-TGD

first: Jakob

last: Cronshagen

first: Paolo

last: Mesén-Ramírez

first: Jan

last: Stäcker

first: Anna

last: Viktoria Vaaben

first: Gala

last: Ramón-Zamorano

first: Isabel

last: Naranjo

first: Susann

last: Ofori

first: Pascal

last: WTC Jansen

first: Joëlle

last: Hornebeck

first: Florian

last: Kieferle

first: Agnes

last: Murk

first: Carolina

last: Castro-Peña

first: Richárd

last: Bártfai

first: Thomas

last: Lavstsen

first: Iris

last: Bruchhaus

first: Tobias

last: Spielmann


title: Single cell RNA seq of 8 week old wild-type mouse choroid-RPE tissue

status: Public on Sep 04 2024

city: Chicago

first: Benjamin

last: Thomson

state: IL

address: 303 E Superior St. SQ8-500

department: Feinberg Cardiovascular and Renal Research Institute

institute: Northwestern University Feinberg School of Medicine

summary: Whole choroids/RPE complexes were dissected from wildtype ICR mice at 8 weeks of age, dissociated and subjected to single cell RNA sequencing using the 10x Chromium platform

overall_design: Enucleated eyes from 8 week old mice were dissected to collect Choroid-RPE complexes. Each sample consists of pooled eyes from 1 male and 1 female mouse.


title: Stepwise de novo establishment of inactive X chromosome architecture in early development

first: Zhenhai

last: Du

overall_design: Refer to individual Series


title: CRISPRi/a screen of doxorubicin induced cardiotoxicity

city: palo alto

first: Chun

last: Liu

state: CA

address: 1291 Welch Road BMI building, 3200-CVI Rm

institute: stanford

summary: Druggable genome of CRISPRi/a sgRNA libraries for druggable genes protecting doxorubicin induced cardiomyocyte toxicity using human induced pluripotent stem cell (iPSC) derived cardiomyocytes.

overall_design: Vehicle (DMSO) and doxorubicin treated iPSC differentiated cardiomyocytes (iCMs). iCMs were transfected with sgRNA libraries and CRISPRi (dCas9-KRAB) or CRISPRa (dCas9-VPR). Two biological replicates were used in both CRISPRi and CRISPRa screens.

first: Mengcheng

last: Shen


title: High expression of oleoyl-ACP-hydrolase predicts mortality in patients hospitalized with avian A(H7N9) influenza

status: Public on Sep 02 2024

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

summary: Although respiratory viral infections cause significant morbidity and mortality, it is still not fully clear why some individuals succumb to severe disease. In patients hospitalized with avian A(H7N9) influenza, we investigated early drivers underpinning hypercytokinemia and fatal disease. Our transcriptomics studies identified differential expression of 10 early host genes, defined by 16 probe sets, between patients who recovered and died. Seven probe sets were specific for the same host gene encoding for a key enzyme mediating free fatty acid production, oleoyl-ACP-hydrolase (OLAH). High olah transcript levels in fatal A(H7N9) patients were detected early after hospital admission and persisted until patients died. Conversely, patients who recovered had minimal olah transcript expression throughout their hospital stays.

overall_design: Blood samples were obtained from 8 patients hospitalized with avian A(H7N9) influenza, including 4 patients who survived and 4 who succumbed to disease during hospitalization. For 7 of these patients, we have paired samples obtained early after disease onset and late after disease onset. For 1 patient, data are only available for the late time point.

middle: C

first: Zhongfang

last: Wang

first: Jianqing

last: Xu

first: Xiaoxiao

last: Jia

first: Brendon

middle: Y

last: Chua

first: Katherine

last: Kedzierska


title: ETV5 accelerates therapy-induced neuroendocrine prostate cancer development by inducing neural stem-like cell differentiation [ChIP-seq]

city: Pohang

first: Jongeun

last: Lee

address: 77 Cheongam-ro

country: South Korea

institute: POSTECH

summary: Neuroendocrine prostate cancer (NEPC) is an aggressive subtype induced by hormone therapy, presenting significant therapeutic challenges due to the lack of effective treatments. In this study, we explored the role of ETV5 in NEPC development. Analysis of multiple prostate cancer datasets revealed significantly elevated ETV5 expression in NEPC compared to other subtypes. ETV5 expression increased progressively under hormone therapy conditions through epigenetic modifications. ETV5 overexpression induced NEPC-like features in LNCaP cells and facilitated their differentiation into NEPC under hormone treatment conditions, both in vitro and in vivo. Our molecular mechanism study identified PBX3 and TLL1 as ETV5 target genes, contributing to castration resistance and stemness induced by ETV5 overexpression. Notably, obeticholic acid, identified as an ETV5 inhibitor in this study, exhibited promising efficacy in suppressing NEPC development. This study highlights ETV5 as a key transcription factor driving NEPC development and underscores its potential as a therapeutic target for this aggressive cancer subtype.

overall_design: Chromatin immunoprecipitation (ChIP) sequencing for ETV5 in control and ETV5-overexpressing LNCaP cells.

first: Yoontae


title: Generation of Human Expandable Limb Bud Cells via Chemically Induced Dedifferentiation Strategy [scRNA-seq]

first: Jingxiao

last: Cao

state: Beijing

address: No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing

department: Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.

institute: Peking University

summary: Here, we introduce a novel chemically induced dedifferentiation approach that reverses the cellular development from a differentiated state to progenitor state with reduced senescence features, conferring the generation of limb bud progenitors from human adult mesenchymal stromal cells and dermal fibroblasts. These chemically induced limb bud cells (hCiLB cells) show a high degree of transcriptomic similarity to human embryonic limb bud cells. We found that hCiLB cells can undergo extensive expansion, while maintaining population homogeneity and long-term self-renewal capacity. Moreover, hCiLB cells exhibit increased osteochondrogenic differentiation ability than their parental cells, providing a new platform for the development of authentic articular cartilage. These results also highlight a potential therapeutic approach for the repair of damaged human tissues through reversal of developmental pathways from mature cells to expandable progenitor cells.

overall_design: we use small-molecule combiantions to induce the dedifferentiation of human somatic cells to progenitors and then characterized the features of the progenitors.


title: Generation of Human Expandable Limb Bud Cells via Chemically Induced Dedifferentiation Strategy [bulk RNA-seq]

summary: Here, we introduce a novel chemically induced dedifferentiation approach that reverses the cellular development from a differentiated state to progenitor state, conferring the generation of limb bud progenitors from human adult mesenchymal stromal cells and dermal fibroblasts. These chemically induced limb bud cells (hCiLB cells) show a high degree of transcriptomic similarity to human embryonic limb bud cells. We found that hCiLB cells can undergo extensive expansion, while maintaining population homogeneity and long-term self-renewal capacity. Moreover, hCiLB cells exhibit increased osteochondrogenic differentiation ability than their parental cells, providing a new platform for the development of authentic articular cartilage. These results also highlight a potential therapeutic approach for the repair of damaged human tissues through reversal of developmental pathways from mature cells to expandable progenitor cells.


title: Generation of Human Expandable Progenitors with Limb-Bud Features via Chemically Induced Dedifferentiation


title: Genomic Characterization of Papillary Thyroid Carcinoma: Age Differences in Tumor Aggressiveness and Immune Infiltration

status: Public on Aug 31 2024

city: Fuzhou

first: Bo Wang

state: Fujian province

address: 29 XinQuan Rd

department: Department of Thyroid and Parathyroid Surgery

institute: Fujian Medical University Union Hospital

summary: Adolescents and Young Adults (AYA) with papillary thyroid carcinoma (PTC) tend to exhibit more aggressive metastatic features compared to Adults (AD), despite low overall tumor proliferation. This study statistically analyzed clinical data from 501 PTC patients in The Cancer Genome Atlas (TCGA), categorized as Adolescents and Young Adults (AYA) and Adults (AD), to uncover differential clinical features between the two age groups.An independent cohort of 13 patients (7 AYA, 6 AD) was used to screen for differentially expressed genes (DEGs) through RNA sequencing. Functional enrichment and topology analyses identified core molecules associated with the heightened aggressiveness of age-related tumors, which were subsequently validated using immunohistochemistry (IHC). Among the 239 core DEGs identified between AYA and AD PTC, key genes such as CXCR4, OPCML, and S100A2 were upregulated in AYA, while ATP1A3, CHL1, HLA-DRA, and IL-1 Beta were downregulated. These genes play a crucial role in tumor invasion and are linked to immune cell infiltration. These findings suggest that integrating age-specific molecular markers into clinical management could enhance diagnostic accuracy and enable personalized treatment strategies for AYA patients, with further research needed to validate these results in larger cohorts and explore their therapeutic potential.

overall_design: An additional cohort of 13 PTC patients was recruited. Patients were categorized as AYA (n=7) or AD (n=6).

first: Wei

last: Ao

first: Bo

first: Wen-Xin

last: Zhao


title: Global  analysis of H3K36 methylation in  the  MM  genome

city: Yakushiji

first: NAOKI

last: OSADA

address: Tochigi

department: Center for Molecular Medicine

country: Japan

institute: Jichi Medical University

summary: We analyzed histone H3K36 methylation in multiple myeloma using ChIP-seq.

overall_design: We isolated fixed chromatin from KMS34 cells and performed immunoprecipitation with anti-histone H3K36me2 antibody, followed by deep sequencing.

first: Sae

last: Matsuoka

first: Jiro

last: Kikuchi


title: Human Early Postnatal Thymus [CITE-seq]

status: Public on Aug 30 2024

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

summary: Within the thymus, regulation of the cellular cross-talk directing T cell development is dependent on spatial interactions within specialized niches. To create a holistic, spatially defined map of tissue niches guiding postnatal T cell development we employed the multidimensional imaging platform CO-detection by indEXing (CODEX), as well as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) and Assay for Transposable-Accessible Chromatin (ATAC-seq). We generated age-matched 4–5-month-old postnatal thymus datasets for both male and female donors, and describe signaling and cell-cell interaction networks in sequential thymocyte developmental niches. Together, these data represent a unique age-matched spatial multiomic resource to investigate how sex-based differences in thymus regulation and T cell development arise, and provide an essential resource to understand the mechanisms underlying immune function and dysfunction in males and females.

overall_design: 4-5 month old sex-matched human thymus + a 33-month-old human thymus samples were processed prior to sequencing to enrich for CD45- and CD25+CD8- cells. See Stankiewicz et al. 2023 (BioRxiv) for experimental details.

first: Laura

middle: N

last: Stankiewicz

first: Kevin

last: Salim

first: Megan

last: Levings

first: Peter

middle: W

last: Zandtsra


title: Developmental regulation of endothelial-to-hematopoietic transition from iPSCs [10X 3' sc-RNA-seq]

status: Public on Aug 23 2024

city: Seattle

first: Sergei

last: Doulatov

state: Washington

address: 1959 NE Pacific St K259

institute: University of Washington

summary: Hematopoietic stem cells (HSCs) arise in mid-gestation from a specialized hemogenic endothelium (HE). In this process, HE cells undergo a unique fate change termed endothelial-to-hematopoietic transition, or EHT. While induced pluripotent stem cells (iPSCs) give rise to HE with robust hemogenic potential, the generation of bona fide HSCs from iPSCs remains a challenge. Here, we map single cell dynamics of EHT during embryoid body differentiation from iPSCs and integrate it with human embryo datasets to identify key transcriptional differences between in vitro and in vivo cell states. We further map ligand-receptor interactions associated with differential expression of developmental programs in the iPSC system. We found that the expression of endothelial genes was incompletely repressed during iPSC EHT. Elevated FGF signaling by FGF23, an endothelial pathway ligand, was associated with differential gene expression between in vitro and in vivo EHT. Chemical inhibition of FGF signaling during EHT increased HSPC generation in the zebrafish system, while an FGF agonist had the opposite effect. Consistently, chemical inhibition of FGF signaling increased hemogenic output from iPSCs. In summary, we map the dynamics of EHT from iPSCs at single cell resolution and identify ligand-receptor interactions that can be modulated to improve iPSC differentiation protocols. We show, as proof of principle, that chemical inhibition of FGF signaling during EHT improves hematopoietic output in zebrafish and the iPSC system.

overall_design: iPSCs were formed into embryoid bodies (day 0) and treated with 100ng/ml hSCF, 100ng/ml hFLT3, 50ng/ml hG-CSF, 25ng/ml IL-6 and 10ng/ml IL-3 starting on day 1 and throughout the rest of any given experiment. Unsorted cells from each time point (days 7, 8, 11, 18 and 21 of differentiation) were used for single-cell combinatorial indexing RNA-seq (sci-RNA-seq) samples.  CD34+, CD43+ or CD45+ were sorted using FACS for the 10X 3' sc-RNA-seq day 8 sample.

first: Rachel

last: Wellington

first: Xiaoyi

last: Cheng

first: Clyde

last: Campbell

first: Cole

last: Trapnell

first: Raquel

last: Espin-Palazon

first: Brandon

last: Hadland


title: Doxorubicin and protective inhibitor treated iPSC derived cardiomyocytes

first: Chun

last: Liu

summary: Investigation of drug and gene rescues doxorubicin induced alterations of transcriptomic and metabolic profiles

overall_design: RNA-seq analysis on 1) WT and CA12 KO iCMs treated with vehicle or doxorubicin (0.5 µM) and 2) WT iCMs treated with doxorubicin plus indisulam to gain a comprehensive understanding of their genome-wide transcriptomic changes.

first: Mengcheng

last: Shen


title: ETV5 accelerates therapy-induced neuroendocrine prostate cancer development by inducing neural stem-like cell differentiation [RNA-seq]

first: Jongeun

last: Lee

overall_design: mRNA profiles of control and ETV5-overexpressing LNCaP cells.

first: Yoontae


title: Recording morphogen signals reveals mechanisms underlying gastruloid symmetry breaking

status: Public on Aug 19 2024

city: Princeton

first: Harold

middle: Michael

last: McNamara

address: Carl Icahn Laboratory, South Drive

department: Lewis-Sigler Institute

institute: Princeton University

summary: We engineered mouse embryonic stem cells to express reporters and recorders developmental signals, and traced how early signaling states predict cell fates.

overall_design: For single cell sequencing analysis, we collected and dissociated gastruloids at both 96 hours after aggregate ("t96") and 120 hours after aggregation ("t120"). For the 120 h sample, we also recording Wnt signaling activity earlier at 96 h, and used fluorescence activated cell sorting (FACS) to separate Wnt-recorded cells based on a GFP signal ("G") from those in which Wnt was not recorded ("R")


title: Flame retardant tetrabromobisphenol A (TBBPA) disrupts histone acetylation and zygotic transcription during zebrafish embryogenesis

city: Clemson

first: Subham

last: Dasgupta

state: South Carolina

address: 142 Long Hall

department: Biological Sciences

institute: Clemson University

summary: 3,3’,5.5’-Tetrabromobisphenol A (TBBPA) is a widely used brominated flame-retardant utilized in the production of electronic devices and plastic paints. The objective of this study is to use zebrafish as a model and determine the effects of TBBPA exposure on early embryogenesis. We initiated TBBPA exposures (0, 10, 20 and 40μM) at 0.75 h post fertilization (hpf) and monitored early developmental events such as cleavage, blastula and epiboly that encompass maternal-to-zygotic transition (MZT) and zygotic genome activation (ZGA). Our data revealed that TBBPA exposures induced onset of developmental delays by 3 hpf (blastula). By 5.5 hpf (epiboly), TBBPA-exposed (10-20 μM) embryos showed concentration-dependent developmental lag by up to 3 stages or 100% mortality at 40 μM. Interestingly, while continued 0.75- 48 hpf TBBPA exposures (10 μM) led to severely deformed embryos, replacing exposure solution with chemical-free media at 6 hpf mitigated this effect, with 100% normal embryos at 48 hpf. To examine the genetic basis of TBBPA-induced delays, we conducted mRNA-sequencing on embryos exposed to 0 or 40 μM TBBPA from 0.75 hpf to 2, 3.5 or 4.5 hpf. Read count data showed that while TBBPA exposures had no overall impacts on maternal or maternal-zygotic genes, collective read counts for zygotically activated genes were lower in TBBPA treatment at 4.5 hpf compared to time-matched controls, suggesting that TBBPA delays ZGA. Gene ontology assessments for both time- and stage-matched differentially expressed genes revealed TBBPA-induced inhibition of chromatin assembly- a process regulated by histone modifications. Since acetylation is the primary histone modification system operant during early ZGA, we hypothesized that TBBPA inhibits histone acetylation, resulting in lack of open chromatin within promoters of zygotic genes and delaying ZGA. Therefore, we co-exposed embryos to 20 μM TBBPA and 100 μM N-(4-Chloro-3-(trifluoromethyl)phenyl)-2-ethoxybenzamide (CTB) -a histone acetyltransferase activator that promotes histone acetylation- and showed that TBBPA-CTB co-exposures from 0.75- 3 hpf significantly reversed TBBPA-only developmental delays, suggesting that TBBPA-induced phenotypes are indeed driven by repression of histone acetylation. Collectively, our work demonstrates that TBBPA disrupts ZGA and early developmental morphology, potentially by inhibiting histone acetylation. Future studies will focus on mechanisms of TBBPA-induced chromatin modifications.

overall_design: Zebrafish embryos were exposed to 0 or 40 uM TBBPA from 0.75 to 2, 3.5 or 4.5 hpf, followed by sample collection, RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 (Illumina, San Diego, CA) (2x150 bp, ~40m reads/sample).

first: Rosemaria

last: Serradimigni

first: Alfredo

last: Rojas

first: Madeline

last: Bryan

first: Connor

last: Leong

first: Uttam

last: Pal

first: Sunil

last: Sharma

first: Maria

last: Baltazar


title: Quercus glauca transcriptome project

status: Public on Aug 16 2024

city: Fukuoka

first: Akiko

last: Satake

address: Motooka 744

institute: Kyushu University

summary: In the family Fagaceae, fertilization is delayed by several weeks to more than one year after pollination, leading to one- or two-year fruiting species depending on whether fruiting occurs in the same or the next year of flowering. Although delayed fertilization was recorded over a century ago, underlying mechanisms remain to be explored. To uncover the key genes associated with delayed fertilization, we obtain and analyze the comparative molecular phenology data over two years in one-year (Quercus glauca) and two-year fruiting species (Lithocarpus edulis).

overall_design: Lead and bud samples were collected from May 2017 to February 2019 from Quercus glauca (Qg). Samples were collected from three individuals. Sample title indicates "year_month and day_individual ID".

first: Kayoko

last: Ohta

first: Noriko

last: Takeda-Kamiya

first: Kiminori

last: Toyooka

first: Junko

last: Kusumi


title: Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler

status: Public on Aug 26 2024

city: Ithaca

first: Justin

middle: Sungsoo

last: Cha

state: NY

address: 526 Campus Rd

department: Computational Biology

institute: Cornell University

summary: The SWR1 chromatin remodeling complex (SRCAP in humans) is recruited to +1 nucleosomes downstream of transcription start sites of eukaryotic promoters, where it exchanges histone H2A for the specialized variant H2A.Z. Here we use cryo-EM to resolve the structural basis of the SWR1 interaction with free DNA, revealing a distinct open conformation of the Swr1 ATPase that enables sliding from accessible DNA to nucleosomes. A complete structural model of the SWR1-nucleosome complex illustrates critical structure-function roles for Swc2 and Swc3 subunits in oriented nucleosome engagement by SWR1. Moreover, an extended DNA-binding α -helix within the Swc3 subunit enables sensing of nucleosome linker length and is essential for SWR1 promoter-specific recruitment and activity. The previously unresolved N-SWR1 subcomplex forms a flexible extended structure enabling multivalent recognition of acetylated histone tails by reader domains to further direct SWR1 towards the +1 nucleosome. Altogether, our findings provide a generalizable mechanism for promoter-specific targeting of chromatin and transcription complexes.

overall_design: Chromatin Immunoprecipitation DNA-sequencing with exonuclease treatment (ChIP-exo) for histone variant H2A.Z and chromatin remodeler Swr1 in S. Cerevisiae with genetic modifications in the SWR1 complex

first: Louder

last: Robert

first: Park

last: Giho

first: Ye

last: Ziyang

first: Cha

last: Justin

first: Gardner

last: Anne

first: Lei

last: Qin

first: Ranjan

last: Anand

first: Höllmüller

last: Eva

first: Stengel

last: Florian

first: Pugh

last: B Franklin

first: Wu

last: Carl


title: Lymphocyte activation gene 3 (Lag3) supports Foxp3+ Treg cell function by restraining c-Myc-dependent aerobic glycolysis

first: Booki

last: Min

address: 300 E. Superior Street

department: Microbiology-Immunology

institute: Northwestern University

summary: Lymphocyte activation gene 3 (Lag3) has emerged as the next-generation immune checkpoint molecule due to its ability to inhibit effector T cell activity. Foxp3+ regulatory T (Treg) cells, a master regulator of immunity and tolerance, also highly express Lag3. While Lag3 is thought to be necessary for Treg cell-mediated regulation of immunity, the precise roles and underlying mechanisms remain largely elusive. In this study, we report that Lag3 is indispensable for Treg cells to control autoimmune inflammation. Utilizing a newly generated Treg cell specific Lag3 mutant mouse model, we found that these animals are highly susceptible to autoimmune diseases, suggesting defective Treg cell function. Genome wide transcriptome analysis further uncovered that Lag3 mutant Treg cells upregulated genes involved in metabolic processes. Mechanistically, we found that Lag3 limits Treg cell expression of Myc, a key regulator of aerobic glycolysis. We further found that Lag3-dependent Myc expression determines Treg cells’ metabolic programming as well as the in vivo function to suppress autoimmune inflammation. Taken together, our results uncovered a novel function of Lag3 in supporting Treg cell suppressive function by regulating Myc-dependent metabolic programming.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of regulatroy T cells and its Lag3 knockout phenotype.

first: Dongkyun

last: Kim

first: Giha

first: Rongzhen

last: Yu

first: Juyeun

last: Lee

first: Sohee

first: Kevin

last: Qiu

first: Elena

last: Montauti

first: Deyu

last: Fang

first: Navdeep

middle: S

last: Chandel

first: Jaehyuk

last: Choi


title: The RNA binding protein HNRNPA2B1 regulates RNA abundance and motor protein activity in neurites

status: Public on Aug 20 2024

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

summary: RNA molecules are localized to subcellular regions through interactions between localization-regulatory cis-elements and trans-acting RNA binding proteins (RBPs). However, the identities of RNAs whose localization is regulated by a specific RBP as well as the impacts of that RNA localization on cell function have generally remained unknown. Here, we demonstrate that the RBP HNRNPA2B1 acts to keep specific RNAs out of neuronal projections. Using subcellular fractionation, high-throughput sequencing, and single molecule RNA FISH, we find that hundreds of RNAs demonstrate markedly increased abundance in neurites in HNRNPA2B1 knockout cells. These RNAs often encode motor proteins and are enriched for known HNRNPA2B1 binding sites and motifs in their 3′ UTRs. The speed and processivity of microtubule-based transport is impaired in these cells, specifically in their neurites. HNRNPA2B1 point mutations that increase its cytoplasmic abundance relative to wildtype lead to stronger suppression of both RNA mislocalization and transport defects than seen with wildtype HNRNPA2B1. We further find that the subcellular localizations of HNRNPA2B1 target RNAs are sensitive to perturbations of RNA decay machinery, suggesting that it is HNRNPA2B1’s known role in regulating RNA stability that may explain these observations. These findings establish HNRNPA2B1 as a negative regulator of neurite RNA abundance and link the subcellular activities of motor proteins with the subcellular abundance of the RNAs that encode them.

overall_design: We profiled subcellular transcriptomes of neuronal cells with and without HNRNPA2B1.

first: Taliaferro

last: Matthew


title: Single-cell RNA sequencing revealed the role of the Th17 pathway in the development of anti HLA antibodies in a highly sensitized mouse model

status: Public on Aug 15 2024

city: Seoul

first: Hanbi

address: 222 Banpo-daero, Seocho-gu

department: Division of Nephrology, Department of Internal Medicine

institute: Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea

summary: The aim of this study is to investigate the specific pathway involved in HLA sensitization using single-cell RNA sequencing analysis and an allo-sensitized mouse model developed with an HLA.A2 transgenic mouse. For sensitization, wild-type C57BL/6 mouse received two skin grafts from C57BL/6-Tg (HLA-A2.1)1Enge/J mouse (allogeneic mouse (ALLO)). For syngeneic control (SYN), skin grafts were transferred from C57BL/6 to C57BL/6. We performed single-cell RNA sequencing analysis on splenocytes isolated from ALLO and SYN mice and compared the gene expression between them. We generated 9,190 and 8,890 single-cell transcriptomes from ALLO and SYN control mice, respectively. Five major cell types (B-cells, T-cells, NK cells, macrophages, and neutrophils) and their transcriptome data were annotated according to the representative differentially expressed genes of each cell cluster. The percentage of B-cells was higher in allogeneic mouse than it was in syngeneic control mouse. KEGG enrichment analyses indicated that the highly expressed genes in the B-cells from ALLO mouse were mainly associated with antigen processing and presentation pathways, allograft rejection, and the Th17 cell differentiation pathway. Upregulated genes in the T-cells of ALLO mouse were involved in the IL-17 signaling pathway. The ratio of Th17 cluster and Treg cluster was increased in the ALLO mouse. On flow cytometry, the percentage of Th17 (IL-17+/CD4+ T) cells was higher and regulatory T cells (FOXP3+/CD4+ T) was lower in the ALLO mouse compared to those in the SYN mouse. Our results indicate that not only the B cell lineage, but also the Th17 cells and their cytokine (IL-17) are involved in the sensitization to HLA.

overall_design: For sensitization (Allogeneic (ALLO) mouse), wild-type C57BL/6 mouse was sensitized twice with skin allografts from C57BL/6-Tg(HLAA2.1)1Enge/J mouse (0 and 5 weeks). Syngeneic (SYN) mouse received skin transplants from wild-type C57BL/6 mouse using the same procedure. Both the donor and recipient mice were anesthetized with intraperitoneal (i.p.) injections of Zoletil®50 (Tiletamine and Zolazepam) 30 mg/kg and Rompun® (Xylazine) 10 mg/kg. Tail skin, segmented into 8 × 8 −10 mm2 sizes, was obtained from the donor mice and grafted onto the dorsal area of the recipient mice. The mice were sacrificed using a CO2 chamber at four weeks after the second skin transplant, and mice spleens were harvested for scRNA-seq analysis.

first: Yoo-Jin

last: Shin

first: Xianying

first: Sheng

last: Cui

first: Sun

last: Lim

first: Sang

last: Eum

first: Ji-Won

first: Chang-Won

last: Hong

first: Hae-Ock

first: Eun-Jee

last: Oh

first: Chul

last: Yang

first: Byung

last: Chung


title: Developmental regulation of endothelial-to-hematopoietic transition from iPSCs [sci-RNA-seq]

first: Sergei

last: Doulatov

first: Rachel

last: Wellington

first: Xiaoyi

last: Cheng

first: Clyde

last: Campbell

first: Cole

last: Trapnell

first: Raquel

last: Espin-Palazon

first: Brandon

last: Hadland


title: Cerebral hypoperfusion exacerbates traumatic brain injury in male mice

status: Public on Aug 14 2024

city: Morgantown

first: Zachary

last: Weil

state: WV

address: 108 Biomedical Road, 313 BMRC

institute: WVU

summary: Traumatic brain injury (TBI) has been postulated to initiate a disease process that interacts with vascular dysfunction. However, the combined effects of preexisting cerebral hypoperfusion and TBI remain poorly explored. This study aimed to investigate the combined effects of bilateral carotid artery stenosis (BCAS) and mild-moderate TBI on cerebral blood flow (CBF), cognitive function, histology, and transcriptomics in Swiss-Webster mice. Male and female mice underwent BCAS using steel microcoils around the carotid arteries, followed by TBI 30 days post coil implantation. CBF, spatial learning and memory, axonal damage, and gene expression profiles were assessed. BCAS led to a ~10% reduction in CBF, while TBI caused a similar decrease. However, mice exposed to both BCAS and TBI exhibited more pronounced reductions in CBF, associated with marked spatial learning and memory deficits, particularly in males. Axonal damage in male mice was also exacerbated by the combination of BCAS and TBI. Notably, females demonstrated differential vascular and cognitive responses to BCAS and TBI, suggesting sex-specific protective mechanisms. Single nuclei RNA sequencing revealed unique, cell type-specific gene expression alterations due to BCAS, TBI, or the combination. Moreover, BCAS and TBI induced significant gene expression changes in various cell types, hinting at complex cellular interactions following vascular challenges and trauma. The cellular and molecular interplay between hypoperfusion and TBI points to intricate vascular-neuronal interactions and potential avenues for targeted interventions.

overall_design: A 2mm cube of perilesional forebrain tissue was dissected from male Swiss Webster mice that underwent control, BCAS, TBI, or a combination of BCAS+TBI surgeries and frozen in liquid nitrogen. Frozen tissue was submitted to Genewiz for 10X snRNA sequencing on the 10X Genomics Chromium System.

first: Bailey

last: Whitehead

first: Corbin

last: Deborah

first: Alexander

last: Megan

first: Bumgarner

last: Jacob

first: Zhang

last: Ning

first: Kate

last: Karelina


title: Genome-wide identification of ZCCHC10 targets in acute myeloid leukemia cells

city: Changsha

first: Jianlin

last: Zhou

state: Hunan

address: 36 Lushan road

department: College of Life Science

institute: Hunan Normal University

summary: To explore which pathways ZCCHC10 is involved in acute myeloid leukemia (AML), we constructed ML-2 cells stably expressing ZCCHC10 (ML2-Zh10) or empty vector (ML2-Vec). Then, RNA-seq was performed to compare the mRNA profilings of ML2-ZH10 and ML2-Vec cells.

overall_design: Comparing the mRNA profilings of ML-2 cells stably expressing ZCCHC10 (ML2-Zh10) and empty vector (ML2-Vec)

first: Yichong

first: Hao


title: Olig1/2 Coordinately Control Oligodendrocyte Versus Interneuron Fate Acquisition in Normal Brain and H3.3G34R/V-mutant Gliomas

status: Public on Aug 10 2024

city: SHANGHAI

first: YU

last: TIAN

state: SHANGHAI

address: 131 DONGAN ROAD

institute: FUDAN UNIVERSITY

summary: The co-opting of the developmental gliogenesis program is a hallmark characteristic of glioblastoma (GBM). The bHLH transcription factors Olig1/2 are co-expressed in tri-potential intermediate progenitors (tri-IPCs) and GBM cells, yet their functions in these cells remain largely unknown. Here, we demonstrate that Olig1/2 coordinately promote the generation of oligodendrocytes while repressing the generation of olfactory bulb interneurons in tri-IPCs and GBM. Mechanistically, Olig1/2 directly bind to multiple enhancers, such as hs687, DSG (downstream from Gsx2) and a putative enhancer to regulate the expression of Gsx2, thereby regulating the fate determination process of tri-IPCs during gliogenesis. Furthermore, we provide compelling evidence that human histone H3.3G34R/V-mutation tumors, a subtype of pediatric high-grade gliomas, originate from cortical-derived tri-IPCs. Altogether, our findings suggest that the molecular mechanism of Olig1/2 in gliogenesis and gliomagenesis are conserved, which will deepen our understanding of the gaps between normal development and tumorigenesis.

overall_design: ScRNA-seq were performed on FACS sorted tdT+ cells from the P1 Olig1/2f/f;IS-reporter mice cortex which were electroporated of pCAG-Cre plasmid at E15.5.Emx1-CRE;Olig1/2f/f mice cortex were dissected out at P7 and immediately submerged in fresh ice-cold Hanks balanced salt solution. The cortex was then cut into pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit according to the manufacturer’s instructions.

first: Yu

last: Tian

first: Ziwu

last: Wang

first: Feihong

last: Yang

first: Wen

last: Zhang

first: Jialin

last: Li

first: Lin

first: Tongye

last: Fu

first: Wenhui

last: Zheng

first: Zhejun

last: Xu

first: Yan

last: You

first: Xiaosu

first: Jiangang

last: Song

first: Yunli

last: Xie

first: Zhengang

first: Zhuangzhi


title: Gene expression profiling of corneal and limbal epithelial cells in young and aged mice

city: Kensington

first: Alexander

last: Richardson

state: NSW

address: Crn Botany and High St

country: Australia

institute: UNSW Sydney

summary: Using the K14CreERT2-Confetti transgenic mouse, we analyzed differential gene expression between Confetti+ and Confetti- cells  in an attempt to uncover novel limbal epithelial stem cell markers

overall_design:
Confetti+ and Confetti- cells were isolated from the corneal epithelium of 6, 18 and 60-week-old mice, then sorted into 96-well plates and analyzed using scRNA sequencing.
Please note that the raw data R2 mate file for the 'Corneolimbal, 60 week old, Confetti- 9' sample is corrupted and thus only R1 file is included as raw data.

first: Susan

last: Corley

first: Naomi

last: Delic

first: Hui

first: Andrew

last: Lloyd

first: Nick

last: Di Girolamo


title: Single-cell RNA-seq profiling of cardiopharyngeal progenitor maturation in Ciona Robusta

status: Public on Aug 12 2024

city: Qingdao

first: WEI

last: WANG

state: Shandong

address: 23 Hongkong east road haier building G zone

institute: Ocean University of China

summary: During development, stem and progenitor cells divide and transition through germ layer- and lineage-specific multipotent states to generate the diverse cell types that compose an animal. Defined changes in biomolecular composition underlie the progressive loss of potency and acquisition of lineage-specific characteristics. For example, multipotent cardiopharyngeal progenitors display multilineage transcriptional priming, whereby both the cardiac and pharyngeal muscle programs are partially active and coexist in the same progenitor cells, while their daughter cells engage in a cardiac or pharyngeal muscle differentiation path only after cell division. Here, using the tunicate Ciona, we studied the acquisition of multilineage competence and the coupling between fate decisions and cell cycle progression. We showed that multipotent cardiopharyngeal progenitors acquire the competence to produce distinct Tbx1/10 (+) and (-) daughter cells shortly before mitosis, which is necessary for Tbx1/10 activation. By combining transgene-based sample barcoding with single cell RNA-seq (scRNA-seq), we uncovered transcriptome-wide dynamics in migrating cardiopharyngeal progenitors as cells progress through G1, S and G2 phases. We termed this process “transcriptome maturation”, and identified candidate “mature genes”, including the Rho GAP-coding gene Depdc1, which peak in late G2. Functional assays indicated that transcriptome maturation fosters cardiopharyngeal competence, in part through multilineage priming and proper oriented and asymmetric division that influences subsequent fate decisions, illustrating the concept of “behavioral competence”. Both classic feedforward circuits and coupling with cell cycle progression drive transcriptome maturation, uncovering distinct levels of coupling between cell cycle progression and fateful molecular transitions. We propose that coupling competence and fate decision with the G2 and G1 phases, respectively, ensures the timely deployment of lineage-specific programs.

overall_design: Samples from 5-14hpf Ciona embryos were tagged with a pair of sample barcoding (SBC) constructs as unique labels for the multiplexing strategy. Singel-cell suspensions were prepared as described in the manuscripts. FACS-purified B7.5 lineage cells were used to generate single-cell libraries following a modified 10X protocol to capture the sequencing reads from both the transcriptome and SBC transcripts.

first: Wei

first: Lionel

last: Christiaen


title: Zebrafish genetic model of accelerated muscle atrophy associated with Fbxo32/Atrogin-1 expression

status: Public on Aug 09 2024

city: Portland

first: Thomas

middle: Dexter

last: Morse

state: ME

address: 154 New Island Ave

institute: MDIBL

summary: The degenerative loss of muscle associated with aging leading to muscular atrophy is called sarcopenia. Currently, practicing regular physical exercise is the only efficient way to delay the onset of sarcopenia. To identify therapeutic targets to suppress the symptoms of aging, there is a need for in vivo model organisms of accelerated muscle degeneration and atrophy. The zebrafish harbors hallmarks of aging, notably mitochondrial dysfunction, telomeres shortening and accumulation of senescent cells. Unfortunately, zebrafish aged slowly, and no specific zebrafish models of accelerated muscle atrophy associated with aging or sarcopenia are currently available. We have developed a new genetic tool to efficiently accelerate muscle fibers degeneration and muscle tissue atrophy in zebrafish larvae and adults. We used a gain-of-function strategy with a molecule that has been shown to be necessary and sufficient to induce muscle atrophy and a sarcopenia phenotype in mammals: Atrogin1 (also named Fbxo32). We report the generation, validation, and characterization of a zebrafish genetic model of accelerated muscle atrophy, the sarcofish. We demonstrated that specific expression of Atrogin1 in skeletal muscle tissue induces a muscle atrophic phenotype associated with locomotion dysfunctions in both larvae and adult fish. We identified that degradation of the myosin light chain as an event occurring before the degeneration of muscle fibers. Biological processes associated with muscle aging such as inflammation, proteolysis, apoptosis and stress response are upregulated in the sarcofish. Surprisingly, we observed a strong correlation between muscle fibers degeneration and a reduction of neuromuscular junctions in the peripheral nervous system, as well as neuronal cell bodies in the spinal cord, suggesting that muscle atrophy could underly a neurodegenerative phenotype in the central nervous system. Finally, while sarcofish larvae harbor regeneration of muscle fibers, spinal neurons and recover locomotive functions, adult sarcofish have impaired regenerative capacities as observed in mammals during muscle aging. In the future, the sarcofish could open new strategies in the fight against the sarcopenia disease to test therapeutic molecules aiming to treat or alleviate the symptoms of muscle aging.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for zebrafish sarcopinia phenotype (Fbxo32 over-expressed) vs wild-type at time points 6d and 8d post induced muscle attrophy

first: Romain

last: Menard

first: Elena

last: Morin

first: Marko

last: Pende

first: Caroline

last: Halluin

first: Dexter

first: Frederic

last: Bonnet

first: Jijia

first: Laetitia

last: Lancelot

first: Prayag

last: Murawala

first: Cedric

last: Dray

first: Jean-Philippe

last: Pradere

last: Madelaine


title: Molecular differentiation between complete and incomplete responders to neoadjuvant therapy in rectal cancer

city: Birmingham

first: Fengyuan

last: Huang

state: AL

address: University Blvd

department: Genetics

institute: University of Alabama at Birmingh

summary: Neoadjuvant chemoradiotherapy (nCRT) is the standard treatment for locally advanced rectal cancer, but less than half of patients have a clinical complete response to this treatment. To define the molecular features that are associated with response to neoadjuvant therapy, we generated and collected genomic and transcriptomic data from 712 cancers prior to treatment from our own data and from publicly available data. We found that patients with a complete response have decreased risk of local recurrence and future metastasis. We identified multiple differences in DNA mutations and transcripts between complete and incomplete responders. Complete responder tumors have a higher tumor mutation burden and many more significant co-occurring mutations than the incomplete responder tumors. In addition, mutations in DNA repair genes (across multiple mechanisms of repair) were enriched in complete responders and they also had lower expression of these genes indicating that defective DNA repair is associated with complete response to nCRT. Using logistic regression, we identified three significant predictors of complete response: tumor size, mutations within specific network genes, and the existence of three or more concurrent mutations. In tumors that do not completely respond to nCRT, abnormal cell-cell interaction and increased cancer associated fibroblasts were associated with recurrence. Additionally,gene expression analysis identified a subset of immune hot tumors with worse outcomes and upregulation of immune checkpoint proteins. Overall, our study provides a comprehensive understanding of the molecular features associated with response to nCRT and the molecular differences in non-responder tumors that later reoccur. This knowledge may provide critical insight into the development of precision therapy for rectal cancer.

overall_design: To investigate the transcriptomic differences between complete and incomplete responders to neoadjuvant therapy in rectal cancer,  we collected pre-treatment biopsy samples and isolated RNA from the samples. We then perfored gene expression profiling analysis using data obtained from RNA-seq of 15 samples from 7 patients.

first: Karin

last: Hardiman

first: Zechen

last: Chong

first: Marshall

last: McLeod

first: Regin

last: Irwin

first: Mary

last: Smithson

first: Zongliang

last: Yue

first: Min

last: Gao


title: Feedback regulation between ALKBH3-mediated glycolysis and histone lactylation promotes age-related macular degeneration

city: Nanjing

first: Ying

last: Wang

address: Guangzhou Road

institute: NanJing Medical University

summary: Age-related macular degeneration (AMD) is a leading cause of blindness among the elderly. Using clinical samples and knockout mice, we reported that the m1A eraser ALKBH3 reshaped retinal metabolism to promote AMD. In retinal pigment epithelium (RPE), the dm1ACRISPR system demonstrated that ALKBH3 demethylated the glycolytic enzyme HK2 to activate anaerobic glycolysis, producing excessive lactate. The lactate promoted histone lactylation at H3K18, which in turn bound to ALKBH3 to amplify its transcription, establishing a positive feedback loop. The ALKBH3 inhibitor HUHS015 disrupted this loop, effectively mitigating RPE degeneration. Furthermore, ALKBH3 directly targeted the pro-angiogenic factor VEGFA to modulate the metabolic cross-talk between RPE and choroidal capillaries, thus promoting choroidal neovascularization (CNV). HUHS015 inhibited CNV synergistically with the anti-VEGF drug Aflibercept. Our study provides critical insights into the molecular mechanisms and metabolic events facilitating the progression from RPE degeneration to CNV in AMD, laying the groundwork for new treatments of AMD.

overall_design: Extracted and purified total RNA was evaluated for quantity and integrity. Ideal RNA samples were sent for library construction using the Directional RNA Library Prep Kit (GenSeq, Shanghai, China), according to the manufacturer’s instructions. The mRNA is typically fragmented into pieces of ~300 nucleotides in length. cDNA synthesis form the mRNA fragments was then carried out using reverse transcriptase and random hexamer primers. The resulting cDNA fragments were subjected to end-repair and dA-tailing, followed by adapter ligation. These adapter-ligated cDNA samples were subsequently amplified via PCR and purified to yield sequencing libraries. Finally, the libraries were sequenced on an Illumina Novaseq 6000 platform (Illumina) using a paired-end 150 bp mode. Raw sequencing data were processed and filtered to produce clean reads, which were aligned to the human genome using the STAR software. To generate expression levels, we used the HTSeq v0.6.0 to calculate the fragments per kilobase per million mapped reads (FPKM) of each gene or transcript. The DESeq2 algorithm was applied to identify differentially expressed genes.

first: Xue

last: Chen

first: Qinghuai

last: Liu


title: Transcriptome sequencing of sheep hypothalamus tissue reveals the regulatory role of lncRNA in the mechanism of pubertal estrus initiation

city: Alar

first: Rong

last: Xuan

state: XinJiang

address: No. 1487, Tarim Avenue East, Alar City, Xinjiang

department: Tarim University

institute: College of Animal Science and Technology

summary: Improving the fertility of sheep is an important goal in sheep breeding as it greatly increases the productivity. Dolang sheep is a typical representative breed of lamb in Xinjiang and is the main local sheep breed and meat source in the region. To explore the genes associated with the initiation of puberty in Dolang sheep, the hypothalamic tissues of Dolang sheep prepubertal, pubertal, and postpubertal periods were collected for RNA-seq analysis on the Illumina platform.

overall_design: Dolang sheep maintained in the Tarim University experimental station were used as the model in this study. The ewes were observed at 10 o ‘clock, 14 o ‘clock, and 18 o ‘clock every day. The criteria for judging puberty in ewes were mental restlessness, the tendency to walk, the acceptance of ram riding, and the presence of mucus in the vulva. All sheep were in good health. Hypothalamus samples were collected from ewes that were first found to be undergoing puberty, immediately frozen in liquid nitrogen, and stored at −80°C for further analysis. The hypothalami were further collected from prepubertal and postpubertal ewes maintained in the same manner. A total of nine sheep’s hypothalamic tissues were collected. Three biological replicates were performed for each period and analyzed.

first: Feng

last: Xing

first: Zhishuai

last: Zhang

first: Zhiyuan

last: Sui


title: Parental Alcohol Exposures Promote Increased Susceptibility to Hepatocellular Carcinoma in Adult Male Offspring

status: Public on Aug 05 2024

city: College Station

first: MICHAEL

middle: C.

last: GOLDING

state: Texas

address: 4466 TAMU

department: Physiology

institute: Texas A&M UNiversity

summary: There is a growing interest in understanding how lifestyle choices and social factors affect life expectancy, healthspan, and the onset of chronic age-related diseases, including cancer. Although alcohol is a known carcinogen that accounts for roughly one-third of primary liver cancer cases worldwide, it is not yet known if chronic alcohol consumption by an individual’s parents heritably influences their predisposition to developing liver cancer. Here, we employed our established multiplex mouse model to compare sensitivities of the male offspring of maternal, paternal, and dual-parental alcohol exposures to the potent hepatocellular carcinoma inducer, Diethylnitrosamine (DEN), and determine their predisposition for tumor formation and growth. Our experiments reveal that chronic parental alcohol consumption programs a pro-tumor environment in the liver. This increased cancer susceptibility correlates with increased steatosis, hepatic fibrosis, inflammation, and oxidative stress. Interestingly, some of these changes display accumulative effects and are more pronounced when both parents are exposed to alcohol.

overall_design: Control Saline, Maternal Saline, Paternal Saline, Dual Saline, Control DEN, Maternal DEN, Paternal DEN, Dual DEN

first: A

last: Basel

first: M

last: Golding


title: A Trisomy 21 Lung Cell Atlas

city: Rochester

first: Soumyaroop

last: Bhattacharya

address: 601 Elmwood Ave Box 703

department: Pediatrics

institute: University of Rochester

summary: Trisomy 21 (T21), resulting in Down Syndrome (DS), is the most prevalent chromosomal abnormality worldwide. While pulmonary disease is a major cause of morbidity and mortality in DS, the ontogeny of pulmonary complications remains poorly understood. We recently demonstrated that T21 lung anomalies, including airway branching and vascular lymphatic abnormalities, are initiated in utero. Here, we aimed to describe molecular changes at the single cell level in prenatal T21 lungs. Our results demonstrate differences in the proportion of cell populations and detail changes in gene expression at the time of initiation of histopathological abnormalities. Notably, we identify shifts in the distribution of alveolar epithelial progenitors, widespread induction of key extracellular matrix molecules in mesenchymal cells and hyper-activation of IFN signaling in endothelial cells. This single cell atlas of T21 lungs greatly expands our understanding of antecedents to pulmonary complications and should facilitate efforts to mitigate respiratory disease in DS.

overall_design: human fetal lung tissue samples from Trsomy 21 subjects (n=5) and age matched controls (n=4)

first: Bhattacharya

last: Soumyaroop

first: Danopoulos

last: Soula


title: Inhibition of Notch4 with Novel Neutralizing Antibodies Reduces Tumor Growth in Multiple Tumor Types and Targets Endothelium and Tumor Associated Macrophages in a Mouse Breast Cancer Model  [RiboTag RNA-seq]

status: Public on Aug 08 2024

city: Chicago

first: Jan

last: Kitajewski

state: IL

address: 909 S. Wolcott Ave. MC 901

department: Dept. of Physiology and Biophysics

institute: University of Illinois at Chicago

summary: Endothelial Notch signaling is critical for tumor angiogenesis. Notch1 blockade reduces tumor vessel function but causes vascular dysfunction, hypoxia, and gastrointestinal toxicity. Notch4 expression is restricted to developing vasculature, where it promotes angiogenesis. Unlike other Notch proteins, Notch4 has rarely been targeted therapeutically. We developed highly specific Notch4-blocking antibodies, 6-3-A6 and humanized E7011, allowing therapeutic targeting of Notch4 in tumor models. E7011 treatment significantly delayed tumor growth and impaired tumor vessel perfusion in mouse models of breast, skin, and lung tumors. In a mouse orthotopic breast cancer model, Notch4 expression was confined to endothelial cells, but E7011 treatment significantly increased tumor-associated macrophages and increased macrophage expression of anti-tumor genes. Liposomal clodronate-mediated macrophage depletion reversed the anti-tumor effects of E7011, demonstrating that Notch4 supports tumor growth via angiocrine signaling to tumor macrophages. We conclude that targeting Notch4 alters tumor vessel function and tumor associated macrophage phenotype, leading to tumor inhibition.

overall_design: we examined endothelial translatomic changes using the Rpl22tm1.1Psam (RiboTag) system, which isolates cell-type specific polysome-bound mRNA(18), in combination with Cdh5TgCreERT2 to confer endothelial specificity (RiboTagEC mice). RiboTagEC expression was induced with tamoxifen by intraperitoneal injection at 3 weeks old (75mg/kg for 5 days), and orthotopically implanted with Py8119 tumors at 8 weeks. Once tumors reached an average of 50mm3, 6 3 A6 or control IgG was administered as above. Tumors were isolated 10 days after the start of treatment to examine endothelial gene expression changes.

first: Jason

last: Eng

first: Yu

last: Kato

first: Yusuke

last: Adachi

first: Bhairavi

last: Swaminathan

first: L

middle: A

last: Naiche

first: Rahul

last: Vadakath

first: Yoshimasa

last: Sakamoto

first: Youya

last: Nakazawa

first: Sho

first: Ken

last: Ito

first: Takanori

last: Abe

first: Yukinori

last: Minoshima

first: Kana

last: Hoshino-Negishi

first: Hideaki

last: Ogasawara

first: Tomomi

last: Kawakatsu

first: Miyuki

last: Nishimura

first: Masahiko

last: Katayama

first: Masashi

last: Shimizu

first: Kazuhiro

last: Tahara

first: Toshitaka

last: Sato

first: Katsuhisa

last: Suzuki

first: Kishan

last: Agarwala

first: Masao

last: Iwata

first: Kenichi

last: Nomoto

first: Yoichi

last: Ozawa

first: Toshio

last: Imai

first: Yasuhiro

last: Funahashi

first: Junji

last: Matsui


title: The unique proteasomal processing of viral ORF1 drives HEV-induced liver fibrosis

status: Public on Aug 01 2024

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: Hepatitis E virus (HEV) is a globally prevalent pathogen that causes 20 million infections and 60,000 fatalities annually, endangering particularly pregnant women and immunosuppressed individuals. Liver cirrhosis, which results from advanced fibrosis, is the primary symptom and leading mortality cause in chronic hepatitis E patients. However, the causation and process of liver fibrosis triggered by chronic HEV infection remain poorly understood. Here, we unexpectedly discovered that the viral multiple-domain replicase (ORF1) undergoes unique ubiquitin-proteasomal processing in HEV replicon hepatocytes, HEV-infected gerbil livers, and HEV-infected patient livers, which follows a CHIP-mediated K48 ubiquitination and produces the HEV-Derived Smad Activator (HDSA). Lacking putative helicase and RNA polymerase domains, this enriched viral polypeptide in hepatocytes and gerbil livers is non-HSP90-bound, stable, and exhibits exclusively nuclear localization. Surprisingly, HDSA markedly potentiates the fibrogenic TGF-β/Smad pathway in livers by facilitating promoter binding and coactivator recruitment of SMAD3, leading to profound liver fibrotic symptoms and damage. Thus, we have identified the first viral protein derived from the unique proteasomal processing of the host, defined its notable role in liver fibrosis, and highlighted the nature of complex host-HEV interactions that drives HEV pathogenesis.

overall_design: Bulk RNA sequencing performed with human HEK293 cell line treated with Vector-SB, Vector-TGFb and HDSA-TGFb respectively.

first: Fei

last: Zhang

last: Huang

first: Yinghao

last: Pan


title: YAP1 status defines two intrinsic subtypes of LCNEC with distinct molecular features and therapeutic vulnerabilities

city: Houston

first: Carl

last: Gay

state: TX

address: 1515 Holcombe Blvd

department: Thoracic-Head & Neck Med Onc

institute: The University of Texas MD Anderson Cancer Center

summary: Purpose: Large cell neuroendocrine carcinoma (LCNEC) is a high-grade neuroendocrine malignancy that, like the more common small cell lung cancer (SCLC), is associated with an absence of druggable oncogenic driver mutations, a clinically aggressive disease course, and dismal prognosis. In contrast to SCLC, however, there is little evidence to guide optimal treatment strategies which are often adapted from SCLC and non-small cell lung cancer (NSCLC) approaches. While there have been some efforts to describe the molecular landscape of LCNEC, to date there are few links between distinct biologic phenotypes of LCNEC and therapeutic vulnerabilities.  Experimental design: To better define the biology of LCNEC, we analyzed cell line and patient genomic data and performed immunohistochemistry and single-cell (sc)RNAseq of core needle biopsies from LCNEC patients and preclinical models. Results: Here, we demonstrate that the presence or absence of YAP1 distinguishes two subsets of LCNEC. The YAP1-high subset is mesenchymal and inflamed and characterized, alongside TP53 mutations, by co-occurring alterations in CDKN2A/B and SMARCA4. Therapeutically, the YAP1-high subset demonstrates vulnerability to MEK and AXL targeting strategies, including a novel preclinical AXL CAR-T cell, as well as predicted vulnerability to SMARCA2 degraders and CDK4/6 inhibitors. Meanwhile, the YAP1-low subset is epithelial and immune-cold and more commonly features TP53 and RB1 co-mutations, similar to those observed in pure SCLC. Notably, the YAP1-low subset is also characterized by expression of SCLC subtype-defining transcription factors - especially ASCL1 and NEUROD1 - and, as expected given its transcriptional similarities to SCLC, exhibits putative vulnerabilities reminiscent of SCLC, including Delta-like ligand 3 (DLL3) and CD56 targeting, as with novel preclinical DLL3 and CD56 CAR T-cells, and DNA damage repair (DDR) inhibition.  Conclusion: YAP1 defines distinct subsets of LCNEC with unique biology. These findings highlight the potential for YAP1 to guide personalized treatment strategies for LCNEC.

overall_design: Six patient derived xenograft tumors and six patient biopsies with a diagnosis of LCNEC or mixed histology, including LCNEC, were collected and analyzed by single-cell RNAseq.

first: Allison

last: Stewart

first: Yuanxin

last: Xi


title: Fagaceae transcriptome project

city: Fukuoka

first: Akiko

last: Satake

address: Motooka 744

institute: Kyushu University

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

sample_organism:
Quercus glauca
Lithocarpus edulis

platform_organism:
Quercus glauca
Lithocarpus edulis

overall_design: Refer to individual Series


title: Transcriptome analysis of cardiac tissue from Wild-type (WT) andsalvianolate-treated  Zebrafish

city: shanghai

first: Jianxuan

last: Li

address: No. 180 Fenglin Road, Xuhui District, Shanghai

department: Department of Cardiology, Zhongshan Hospital

institute: Fudan University

summary: We analyzed the transcriptome of Wild-type (WT) and salvianolate-treated Zebrafish  by bulk RNA-seq

overall_design: To investigate the underlying mechanism by which salvianolate inhibits cardiotoxicity, we performed a comparative RNA-seq analysis of salvianolate-treated zebrafish embryos. Compared with the control group, RNA-seq analysis found that the salvianolate group had significant changes in the transcription, of which 109 genes were up-regulated and 565 genes were down-regulated. Interestingly, GO and KEGG pathway analysis showed that membrane part and lysosomal pathway was enriched in our study.

first: Yuxiang

last: Dai

first: Yang

first: Zhi

last: Zuo


title: Host complement C3 promotes malaria transmission by killing symbiotic bacteria in the mosquito midgut

city: chongqing

first: Biao

last: He

state: chongqing

address: Gaotanyan street 30, Shapinba district

department: Department of Pathogen Biology

institute: Army medical university

summary: Host-derived factors are sucked into midgut of mosquitoes during natural malaria transmission, but their influence on malaria transmission is largely unknown. We reported that mouse complement C3 taken into mosquitoes significantly promoted malaria transmission either in laboratory or in field. This effect was attributed to the reduction of microbiota abundance in mosquito midgut by host-derived C3 through direct lyses the predominant symbiont bacteria Elizabethkingia anopheles. Elizabethkingia anopheles symbiont bacteria were demonstrated to be detrimental to malaria sexual stages in mosquitoes. Strikingly, the promoted effect of host C3 on malaria transmission was confirmed by laboratory mosquitoes membrane-feeding on Plasmodium falciparum. Therefore, we reveal a novel strategy of malaria parasite to utilize host complement C3 to promote its transmission, and the administration of C3 inhibitor would provide us a novel strategy to control malaria transmission.

overall_design: RNA-seq analysis of anopheles stephensi mosquito fed on P. yoelii-infected C57BL/6 or C3-/- mice after 12h and 24h

first: Wenyue

last: Xu


title: Human Early Postnatal Thymus [ATAC-seq]

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

institute: University of British Columbia

summary: Within the thymus, regulation of the cellular cross-talk directing T cell development is dependent on spatial interactions within specialized niches. To create a holistic, spatially defined map of tissue niches guiding postnatal T cell development we employed the multidimensional imaging platform CO-detection by indEXing (CODEX), as well as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) and Assay for Transposable-Accessible Chromatin (ATAC-seq). We generated age-matched 4–5-month-old postnatal thymus datasets for both male and female donors, and describe signaling and cell-cell interaction networks in sequential thymocyte developmental niches. Together, these data represent a unique age-matched spatial multiomic resource to investigate how sex-based differences in thymus regulation and T cell development arise, and provide an essential resource to understand the mechanisms underlying immune function and dysfunction in males and females.

overall_design: 4-5 month old sex-matched human thymus samples were processed prior to sequencing to enrich for CD45- and CD25+CD8- cells. See Stankiewicz et al. 2023 (BioRxiv) for experimental details.

first: Laura

last: Stankiewicz

first: Kevin

last: Salim

first: Megan

middle: K

last: Levings

first: Peter

last: Zandstra


title: Disentangling the mutational effects on protein stability and interaction of human MLH1

city: Copenhagen

first: Sven

last: Larsen-Ledet

state: N

address: Ole Maaloes Vej 5

country: Denmark

institute: University of Copenhagen

summary: Missense mutations can have diverse effects on proteins, depending on their location within the protein and the specific amino acid substitution. Mutations in the DNA mismatch repair gene MLH1 are associated with Lynch syndrome, yet the underlying mechanism of most disease-causing mutations remain elusive. To address this gap, we aim to disentangle the mutational effects on two essential  properties for MLH1 function: protein stability and protein-protein interaction. We systematically examine the cellular abundance and interaction with PMS2 of 4839 (94%) MLH1 variants in the C-terminal domain. Our combined data shows that most MLH1 variants lose interaction with PMS2 due to reduced cellular abundance. However, substitutions to charged residues in the canonical interface lead to reduced interaction with PMS2. Unexpectedly, we also identify a distal region in the C-terminal domain of MLH1 where substitutions cause both decreased and increased binding with PMS2. Our data successfully distinguish benign from pathogenic MLH1 variants and correlate with thermodynamic stability predictions and evolutionary conservation. This work provides mechanistic insights into variant consequences and may help interpret MLH1 variants.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: The C-terminal domain of human MLH1 was divided into seven tiles. In each tile, we generated site saturation mutagenesis libraries comprising all possible missense variants and cloned them into pDONR221. The libraries were subsequently cloned into pDEST-DHFR-PCA for the abundance assay and pDEST22 for the interaction assay and transformed into the wild-type BY4741 yeast strain and the MaV203 yeast strain, respectively. For the abundance assay, cells were plated on medium without uracil and with (selection) or without (control) methotrexate. For the interaction assay, cells were plated on medium with (control) or without (selection) histidine. After selection, cells were harvested and plasmids were isolated to prepare amplicons that was sequenced using the Illumina NextSeq 550 System. Based on the relative change in frequency of variants between the control and selection conditions compared to synonymous wild-type variants, we calcuated an abundance and interaction score for each variant.

first: Amelie

last: Stein


title: Post-prandial cardiac hypertrophy is sustained by mechanics, epigenetic, and metabolic reprogramming in pythons [RNA-Seq]

status: Public on Aug 04 2024

city: Boulder

first: Mary

middle: Ann

last: Allen

state: Co

address: UCB 596  JSCBB

department: BioFrontiers

institute: University of Colorado

summary: Constricting pythons, known for their ability to consume infrequent, massive meals, exhibit rapid and reversible cardiac hypertrophy following feeding. Our primary goal was to investigate how python hearts achieve this adaptive response after feeding. Isolated myofibrils increased force after feeding without changes in sarcomere ultrastructure and without increasing energy cost. Ca2+ transients were prolonged after feeding with no changes in myofibril Ca2+ sensitivity. Feeding reduced titin-based tension, resulting in decreased cardiac tissue stiffness. Feeding also reduced the activity of sirtuins, a metabolically-linked class of histone deacetylases, and increased chromatin accessibility. A transcription factor enrichment analysis on transposase-accessible chromatin with sequencing (ATAC-Seq) revealed the prominent role of transcription factors YY1 and NRF1 in post-feeding cardiac adaptation. Gene expression was also changed in favor of translation and metabolism. Finally, metabolomics analysis and ATP production assay demonstrated that cardiac adaptation after feeding not only increased energy demand but also energy production. These findings have broader implications for our understanding of cardiac adaptation across species and hold promise for the development of innovative approaches to address cardiovascular diseases.

overall_design:
To determine the gene expression profile of post-prandial python hearts, the hearts of fasted and 24 post fed Python regius were collected for RNA-sequencing analysis.
Three fasted and three fed pythons were included in the study.
Gene expression analysis was performed between fasted and 24 hour post fed python hearts.

first: Claudia

last: Crocini

first: Kathleen

last: Woulfe

first: Christopher

middle: D

last: Ozeroff

first: Stefano

last: Perni

first: Joseph

last: Cardiello

first: Cierra

middle: J

last: Walker

first: Kristi

last: Anseth

first: Leslie

last: Leinwand


title: Single-cell RNA-seq profiling of early  embryonic development in Ciona Robusta

status: Public on Aug 21 2024

first: WEI

last: WANG

overall_design: Samples from 5-14hpf Ciona embryos were tagged with a pair of sample barcoding (SBC) constructs as unique labels for the multiplexing strategy. Singel-cell suspensions were prepared as described in the manuscripts. Whole embryo cells were used to generate single-cell libraries following a modified 10X protocol to capture the sequencing reads from both the transcriptome and SBC transcripts.

first: Wei

last: Wang

first: Lionel

last: Christiaen


title: RNA-seq after knockdown of PhiKZ genes in PhiKZ-infected Pseudomonas aeruginosa PAO1 cells

status: Public on Jul 31 2024

city: Würzburg

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

institute: Würzburg University

summary: We aimed to illuminate the effects on the transcriptome upon translation knockdown (KD) of core genes and other characterised genes or early expressed genes in PHIKZ through anti-sense-based technology. We identified phage transcripts that are affected in level upon KD and clustering allowed to group these together that likely are expressed at a similar stage and dependency in the phage replication cycle. The read coverage can point to alterations in transcripts and mode of action for several candidates that were knocked down.

overall_design: PAO1 cells were pretreated with anti-sense-based molecules against the start codon and ribosome binding site of PHIKZ transcripts. Cells were infected with PhiKZ and at defined time-points post-infection, cells were harvested. RNA was extracted from cells and sequenced.

first: Milan

last: Gerovac