title: Fangji Dihuang formulation ameliorated DNCB-induced atopic dermatitis-like skin lesions by IL-17 signaling pathway: Integrating network analysis and experimental validation

city: Hong Kong

first: chunhao

last: cao

address: Hong Kong

department: School of Chinese Medicine

country: Hong Kong

institute: Hong Kong Baptist University

summary: Background: Fangji Dihuang formulation (FJDHF) is a well-known Traditional Chinese Medicine (TCM) formula with a reported clinical therapeutic effect in the treatment of inflammatory skin diseases.  However, there is a lack of pharmacological research on its anti-atopic dermatitis (AD) activity. Methods: To investigate the potential anti-AD activity of FJDHF, DNCB was used to induce AD-like skin inflammation in the back of mice.  Following successful modeling, the mice were administered FJDHF orally.  The extent of the inflammatory skin lesions was recorded at day 4, 7, 14 and 28.  UHPLC-Q-Exactive Orbitrap MS was used to identify and match the compounds present in FJDHF with ITCM, TCMIP and TCMSID.  In silico predictions of potential target proteins of the identified compounds were obtained from SwishTargetPrediction, ITCM and TargetNet databases.  AD-related genes were identified from GSE32924 data set, and FJDHF anti-AD hub genes were identified by MCODE algorithm.  ClueGo enrichment analysis was employed to identify the core pathway of FJDHF's anti-AD effect.  To further investigate the anti-AD effect of FJDHF, single-cell RNA sequencing data set (GSE148196) from AD patients was analyzed to determine the target cells and signaling pathways of FJDHF in AD.  Finally, rt-PCR, flow cytometry, and mouse back skin RNA sequencing were utilized to validate our findings. Results: FJDHF was found to be effective in improving the degree of the AD-like lesions in the mice.  Network pharmacological analysis revealed the core pathway of FJDHF to be the IL-17 signaling pathway, which is interactively associated with cytokines.  Single-cell RNA sequencing analysis suggested that FJDHF may play an anti-AD role by influencing dendritic cells.  Flow cytometry and rt-PCR results showed that FJDHF can reduce the influence of AD sample of IL-4, IFN-γ and the expression of IL-17.  The RNA sequencing of mouse back skin also confirmed our conclusion. Conclusion: FJDHF may inhibit DNCB-induced AD-like skin inflammation in mice by inhibiting the IL-17 signaling pathway.  Thus, FJDHF can be considered as a potential therapeutic agent for AD.

first: Xianyu

last: Zeng

first: Wenting

last: Zhao

first: Honghong

last: Jiang

first: Weiming

last: Zhang


title: Distinct mesenchymal cell states mediate prostate cancer progression (mouse)

status: Public on Oct 10 2023

city: New York

first: Mohamed

last: Omar

state: New York

address: 413 East 69th Street

department: Department of Pathology and Laboratory Medicine

country: USA

institute: Weill Cornell Medicine

type: Expression profiling by high throughput sequencing

summary: We sought to determine whether molecular alterations in tumor stroma influence prostate cancer progression and metastatic potential. To accomplish this, we compared mesenchymal cells from four genetically engineered mouse models (GEMMs) of prostate cancer representing different stages of the disease to their wild-type (WT) counterparts by single-cell RNA sequencing (scRNA-seq) and, ultimately, to human tumors with comparable genotypes. We identified 8 transcriptionally and functionally distinct stromal populations responsible for both common and GEMM-specific transcriptional programs. These are conserved between mouse models and human prostate cancers with the same genomic drivers. The transcriptional profiles of the stroma of murine models of advanced disease were similar to those of human prostate cancer bone metastases, with periostin expression by stromal cells influencing invasion and neuroendocrine differentiation. These profiles were then used to build a robust gene signature that can predict metastatic progression in localized disease independent of Gleason score. Taken together, this offers new evidence that the stromal microenvironment mediates prostate cancer progression.

overall_design: scRNA-seq profiles were obtained from primary prostate samples from mouse models of prostate cancer. These models include: TMPRSS2-ERG (T-ERG) fusion, Pten knock-out (NP),Tg(ARR2/Pbsn-MYC)7Key (Hi-MYC), Cre4 +/-;Pten f/f; Rb1 f/f;LSL-MYCN +/+ (PRN), FVB/N , C57BL/6 and B6129SF2/J.

first: Hubert

last: Pakula

first: Ryan

last: Carelli

first: Filippo

last: Pederzoli

first: Giuseppe

middle: N

last: Fanelli

first: Tania

last: Pannellini

first: Fabio

last: Socciarelli

first: Lucie

last: Van Emmenis

first: Silvia

last: Rodrigues

first: Caroline

last: Fidalgo-Ribeiro

first: Pier

middle: V

last: Nuzzo

first: Nicholas

middle: J

last: Brady

first: Wikum

last: Dinalankara

first: Madhavi

last: Jere

first: Itzel

last: Valencia

first: Christopher

last: Saladino

first: Jason

last: Stone

first: Caitlin

last: Unkenholz

first: Richard

last: Garner

first: Mohammad

middle: K

last: Alexanderani

first: Francesca

last: Khani

first: Francisca

last: de Almeida

first: Cory

last: Abate-Shen

first: Matthew

middle: B

last: Greenblatt

first: David

middle: S

last: Rickman

middle: E

last: Barbieri

first: Brian

middle: D

last: Robinson

first: Luigi

last: Marchionni

first: Massimo

last: Loda


title: Distinct mesenchymal cell states mediate prostate cancer progression

first: Mohamed

last: Omar

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Longitudinal modeling of human neuronal aging reveals the contribution of the RCAN1-TFEB pathway to Huntington's disease neurodegeneration

city: Saint Louis

first: Youngmi

last: Oh

state: MO

address: 660 S. Euclid Avenue

department: Development department

institute: Washington University in St. Louis

summary: Aging is a common risk factor in neurodegenerative disorders and the ability to investigate aging of neurons in an isogenic background would facilitate discovering the interplay between neuronal aging and onset of neurodegeneration. Here, we perform direct neuronal reprogramming of longitudinally collected human fibroblasts to reveal genetic pathways altered at different ages. Comparative transcriptome analysis of longitudinally aged striatal medium spiny neurons (MSNs), a primary neuronal subtype affected in Huntington's disease (HD), identified pathways associated with RCAN1, a negative regulator of calcineurin. Notably, RCAN1 undergoes age-dependent increase at the protein level detected in reprogrammed MSNs as well as in human postmortem striatum. In patient-derived MSNs of adult-onset HD (HD-MSNs), counteracting RCAN1 by gene knockdown (KD) rescued HD-MSNs from degeneration. The protective effect of RCAN1 KD was associated with enhanced chromatin accessibility of genes involved in longevity and autophagy, mediated through enhanced calcineurin activity, which in turn dephosphorylates and promotes nuclear localization of TFEB transcription factor. Furthermore, we reveal that G2-115 compound, an analog of glibenclamide with autophagy-enhancing activities, reduces the RCAN1-Calcineurin interaction, phenocopying the effect of RCAN1 KD. Our results demonstrate that RCAN1 is a potential genetic or pharmacological target whose reduction-of-function increases neuronal resilience to neurodegeneration in HD through chromatin reconfiguration.

overall_design: To investigate age-related differences in reprogrammed MSNs from longitudinally collected fibroblasts from three independent healthy individuals, we carried out comparative transcriptome analysis between the age groups. We designate fibroblasts initially collected during middle age as “young” and samples subsequently collected approximately 20 years later from three independent individuals as “old” groups (Coriell NINDS and NIGMS Repositories: AG10049 (48 years), AG16030 (68 years); AG10047 (53 years), AG14048 (71 84 years); AG04456 (49 years), AG14251 (68 years). RNA-seq analysis in both longitudinally collected fibroblasts and corresponding reprogrammed MSNs revealed differentially expressed genes (DEGs) between young and old samples.

first: Seong Won

last: Lee

first: Young Mi

first: Andrew

last: Yoo


title: Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by non-coding CRISPR screens [RNA-Seq sgCDK6]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: Accumulating evidence indicates that HOXA9 dysregulation is sufficient and necessary for leukemic transformation. Leukemia subtypes showing HOXA9 overexpression include those carrying MLL gene rearrangements (MLL-r), NPM1c mutations, and other genetic alterations. HOXA9 protein is a poor therapeutic target as it lacks targetable pocket domains. Therefore, understanding HOXA9’s functional downstream genes and its regulation might provide alternative therapeutic targets. However, it remains largely unknown how HOXA9, as a homeobox transcriptional factor, binds to noncoding regulatory sequences and controls the downstream genes in MLL-r leukemia and across leukemias of other genetic subtypes. In this study, we have successfully conducted dropout CRISPR screens in the MLL-r SEM cell line stably expressing Cas9 against ~1,800 HOXA9 binding peaks. Integrative data analysis identified six reproducible noncoding hits, including a positive control located in the distal enhancer of FLT3. Cas9-editing and dCas9-KRAB silencing HOXA9’s binding site in distal region of FLT3 reduced transcription and impaired cell proliferation in vitro and in vivo. In addition, RNA-seq and Q-PCR analysis further identified the functional relevant downstream genes upon CRISPR editing of other candidate HOXA9-bound noncoding segments, including survival essential genes as XBP1, JUN and BAHCC1. In summary, the work is significant as it will advance our understanding of how HOXA9-associated transcription programs reconstruct the regulatory network specifying MLL-r dependency. Moreover, our study will promote the future development of HOXA9-mediated noncoding regulation, and alternative therapeutic targets in HOXA9-driven (including HOXA9 and possibly NUP98-HOXA9 subtype) leukemia in patients.

overall_design: Using RNA-seq to confirm the CRISPRi-mediated targeting effect against HOCA9-bound peak at the intron of CDK6

first: Shaela

last: Wright

first: Xujie

last: Zhao

first: Wojciech

last: Rosikiewicz

first: Judith

last: Hyle

first: Shelby

last: Mryncza

first: Chunliang

last: Li


title: Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by non-coding CRISPR screens [ATAC-Seq II]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ATACseq were performed in SEM for different sgRNA target region to check chromatin accessibility


title: H3K27me3 is vital for fungal development and secondary metabolite gene silencing, and substitutes for the loss of H3K9me3 in the plant pathogen Fusarium proliferatum

city: Tulln

first: Harald

last: Berger

state: NOE

address: Konrad-Lorenzstraße 43

department: DAGZ

country: Austria

institute: Universität f. Bodenkultur Wien

summary: Facultative heterochromatin marked by histone H3 lysine 27 trimethylation (H3K27me3) is an important regulatory layer for secondary metabolite (SM) gene silencing and important for fungal development in the genus Fusarium. While this histone mark is essential in some (e.g., the rice pathogen Fusarium fujikuroi), it appears dispensable in other fusaria. Here, we show that deletion of FpKMT6 is detrimental but not lethal in the plant pathogen Fusarium proliferatum, a member of the Fusarium fujikuroi species complex (FFSC). Loss of FpKmt6 results in aberrant growth, and expression of a large set of previously H3K27me3-silenced genes is accompanied by increased H3K27 acetylation (H3K27ac) and an altered H3K36me3 pattern. Next, H3K9me3 patterns are affected in ∆fpkmt6, indicating a crosstalk between both heterochromatic marks that became even more obvious in a strain deleted for FpKMT1 encoding the H3K9-specific histone methyltransferase. In ∆fpkmt1, all H3K9me3 marks present in the wild-type strain are replaced by H3K27me3, a finding that likely explains the subtle phenotype of ∆fpkmt1 strains which stands in marked contrast to other filamentous fungi. A large proportion of SM-encoding genes is allocated with H3K27me3 in the wild-type strain, and loss of H3K27me3 result in elevated expression of 49% of them. Interestingly, genes involved in the biosynthesis of the phytohormones gibberellins (GA) are among the most upregulated genes in ∆fpkmt6. Although several FFSC members harbor GA biosynthetic genes, its production in planta is largely restricted to F. fujikuroi with few exceptions. We show that GA gene silencing is mediated by H3K27me3 in F.proliferatum and in at least one additional FFSC member, possibly outlining the distinct lifestyles of these notorious plant pathogens.

overall_design: The F. proliferatum strain NRRL62905, FpWT, was used as parental strain and compared to the deletion strain of fpkmt6: FpKMT6. For fungal liquid cultivations, mycelia were pre-cultured in 100 mL Darken medium   in a 300 mL Erlenmeyer flask for 3 days in the dark (30°C, 180 rpm). Then, 0.5 mL of the pre-culture was transferred to ICI media supplemented  with either 6 mM  glutamine  sole nitrogen source .  Fungal cultures were incubated on an orbital shaker at 180 rpm, 30°C for 3 dpi . Total RNA for subsequent sequencing was extracted using TRIzol Reagent as described above, and sent to the Vienna BioCenter (Vienna, Austria) for quality control, library preparation and sequencing. Experiments were performed in duplicates. Library prep and sequencing was performed using poly-A enrichment kit (NEB) and Nextera Library prep kit.  75 bp single end sequencing was performed using a NextSeq550 Illumina sequencer. Obtained sequences were de-multiplexed, quality controlled, filtered using trimmomatic 0.36   and mapped on the new genome assembly (needs also to be submitted). Mapping was performed using BWA   and reverse transcripts were counted using python script HTSeq .   Normalization and statistics were done using R/Bioconductor and the limma and edgeR packages, using mean-variance weighting (voom) and TMM normalisation .  A significance cut-off of p < 0.01 and differential expression of +/-1 (2-fold) was applied for analysis.  Transcription levels are log2 read counts per kilobase of exon per million library reads (RPKM).

first: Lena

first: Anna

last: Atanasoff-Kardjalieff

first: Celine

last: Petersen

first: Simone

last: Bachleitner

first: Michael

last: Sulyok

first: Alica

last: Fischle

first: Hans-Ulrich

last: Humpf

first: Svetlana

last: Kalinina

first: Teis

last: Esben Søndergaard


title: Distinct mesenchymal cell states mediate prostate cancer progression (human)

first: Mohamed

last: Omar

overall_design: Human prostate tissue specimens were obtained from patients undergoing radical prostatectomy at Weill Cornell Medicine. These included 9 samples; 3 ERG-negative and 6 ERG-positive cases.

first: Hubert

last: Pakula

first: Ryan

last: Carelli

first: Filippo

last: Pederzoli

first: Giuseppe

last: Fanelli

first: Tania

last: Pannellini

first: Fabio

last: Socciarelli

first: Lucie

last: Van Emmenis

first: Silvia

last: Rodrigues

first: Caroline

last: Fidalgo-Ribeiro

first: Pier

last: Nuzzo

first: Nicholas

last: Brady

first: Wikum

last: Dinalankara

first: Madhavi

last: Jere

first: Itzel

last: Valencia

first: Christopher

last: Saladino

first: Jason

last: Stone

first: Caitlin

last: Unkenholz

first: Richard

last: Garner

first: Mohammad

last: Alexanderani

first: Francesca

last: Khani

first: Francisca

last: de Almeida

first: Cory

last: Abate-Shen

first: Matthew

last: Greenblatt

first: David

last: Rickman

last: Barbieri

first: Brian

last: Robinson

first: Luigi

last: Marchionni

first: Massimo

last: Loda


title: Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by non-coding CRISPR screens [CRISPR]

first: Beisi

last: Xu

overall_design: Dropout CRISPR Screen for sgRNA designed at HOXA9 peaks, SEM or MOLM13 cells harvested at Day 0, Day 7, Day14 and Day 21. CRISPRi also performed in SEM.

first: Shaela

last: Wright

first: Xujie

last: Zhao

first: Wojciech

last: Rosikiewicz

first: Siqi

last: Yi

first: Yong

last: Cheng

first: Chunliang

last: Li


title: Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by non-coding CRISPR screens [ATAC-Seq]

overall_design: ATAC-seq was conducted in SEM cells targeted with sgNT and sgFLT3-DE-1 to investigate the specific editing effect of CRISPRi and genome-wide influence.

first: Wright

last: Shaela

first: Zhao

last: Xujie

first: Rosikiewicz

last: Wojciech

first: Yi

last: Siqi

first: Cheng

last: Yong

first: Xu

last: Beisi

first: Li

last: Chunliang


title: Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by non-coding CRISPR screens [ChIP-seq]

overall_design: H3K27ac ChIPseq were performed to check enhancers for Patient-Derived Xenograft for 4 MLL-r leukemia cell lines.


title: 35S:TRAP of S. lycopersicum and S. pennellii roots under phosphate-deprivation

city: Davis

first: Siobhan

last: Brady

state: California

address: One Shields

department: Plant Biology and Genome Center

institute: UC Davis

summary: Phosphate is a necessary macronutrient for basic biological processes, plant growth, and agriculture. Plants modulate their root system architecture and cellular processes to adapt to phosphate deprivation albeit with a growth penalty. Excess application of phosphate in the form of fertilizer can lead to eutrophication and has negative environmental impact. Moreover, phosphate mined from rock reserves is a finite and non-recyclable resource and its levels are nearing complete depletion. Here, we show that Solanum pennellii, a wild relative of tomato, is partially insensitive to phosphate deprivation. Furthermore, it mounts a constitutive response under phosphate sufficiency. We demonstrate that activated brassinosteroid signaling through a tomato BZR1 ortholog gives rise to the same constitutive phosphate deficiency response which is dependent on over-accumulation of zinc. Collectively, these results reveal an additional strategy by which plants can adapt to phosphate starvation.

sample_organism:
Solanum lycopersicum
Solanum pennellii

platform_organism:
Solanum lycopersicum
Solanum pennellii

overall_design: 35S:TRAP construct-containing tomato seedlings were harvested between eight and ten days after germination. Two tissues were extracted for analysis, the root tip and the root midsection. A total of 4 biological replicates for each genotype and treatment were used with between 30 and 40 plants in each biological replicate.

first: Don

last: Gibson

first: Gozde

last: Demirer

middle: M


title: Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by non-coding CRISPR screens [RNA-Seq]

first: Beisi

last: Xu

overall_design: To identfiy the direct downstream targets of HOXA9, we devised a doxycycline-Tet-On inducible system to express HOXA9-AID cassette in MLL-r leukemia cell lines (SEM and MOLM13) to reveal transcriptome changes associated with HOXA9 expression. Overexpression of the HOXA9-AID fusion protein can be induced by doxycycline, and the fusion protein can also be rapidly degraded by auxin treatment without affecting the mRNA level of HOXA9. Combination of differentially expressed genes from these datasets will provide hits for candidate downstream genes of HOXA9.


title: Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by non-coding CRISPR screens


title: Association between Altered Tryptophan Metabolism, Plasma Aryl Hydrocarbon Receptor Agonists, and Inflammatory Chagas Disease

status: Public on Oct 09 2023

city: CORDOBA

first: JUAN

middle: NAHUEL

last: QUIROZ

state: CORDOBA

address: HAYA DE LA TORRE Y MEDINA ALLENDE S/N

department: CLINICAL BIOCHEMISTRY

country: Argentina

institute: CIBICI

summary: Chagas disease causes a cardiac illness characterized by immunoinflammatory reactions leading to myocardial fibrosis and remodeling. The development of Chronic Chagas Cardiomyopathy (CCC) in some patients while others remain asymptomatic is not fully understood, but dysregulated inflammatory responses are implicated. The Aryl hydrocarbon receptor (AhR) plays a crucial role in regulating inflammation. Certain tryptophan (Trp) metabolites have been identified as AhR ligands with regulatory functions. We investigated AhR expression, agonist response, ligand production, and AhR-dependent responses, such as IDO activation and regulatory T (Treg) cells induction, in two T.cruzi-infected mouse strains (B6 and Balb/c) showing different polymorphisms in AhR. Furthermore, we assessed the metabolic profile of Trp catabolites and AhR agonistic activity levels in plasma samples from patients with chronic Chagas disease (CCD) and healthy donors (HD) using a luciferase reporter assay and liquid chromatography-mass spectrophotometry (LC-MS) analysis. T. cruzi-infected B6 mice showed impaired AhR-dependent responses compared to Balb/c mice, including reduced IDO activity, kynurenine levels, Treg cell induction, CYP1A1 up-regulation, and AhR expression following agonist activation. Additionally, B6 mice exhibited no detectable 34 AhR agonist activity in plasma and displayed lower CYP1A1 up-regulation and AhR expression upon agonist activation. Similarly, CCC patients had decreased AhR agonistic activity in plasma compared to HD patients and exhibited dysregulation in Trp metabolic pathways, resulting in altered plasma metabolite profiles. Notably, patients with severe CCC specifically showed increased N-acetylserotonin levels in their plasma. The methods and findings presented here contribute to a better understanding of CCC development mechanisms and may identify potential specific biomarkers for T. cruzi infection and the severity of associated heart disease. These insights could be valuable in designing new therapeutic strategies. Ultimately, this research aims to establish the AhR agonistic activity and Trp metabolic profile in plasma as an innovative, non-invasive predictor of prognosis for chronic Chagas disease.

overall_design:
Bone marrow macrophages (BMDM) from C57BL/6 mice were cultured for 24h with Trypanosoma cruzi (Tulahuen Strain, TcVI). Cell to parasite ratio was set to 1:3. Total RNA was harvested according to the Qiagen RNeasy Mini Kit protocol.  Only Samples that passed the purity cutoff (Abs 260/Abs 280 = 1,7-2) were selected for downstream processing. Libraries were processed by the Broad Institute's Broad Technology Labs and the Broad Genomics Platform.
Expression profiling analysis by bulk-RNAseq was carried out across 2 experimental groups, each consisting of four replicates: Ctrl (non-infected BMDM) and Tc-infected BMDM.

first: Laura

middle: F

last: Ambrosio

first: Ximena

last: Volpini

first: Claudia

middle: C

last: Motran

first: Juan

last: Quiroz


title: Zfp335 establishes eTreg lineage and neonatal immune tolerance by targeting Hadha-mediated fatty acid oxidation

city: xian

first: Cangang

last: Zhang

state: State...

address: Yanta district, xi 'an city, shaanxi province

country: China

institute: xian jiaotong university

summary: We utilized single-cell RNA sequencing (scRNA-seq) to carry out comparative transcriptome analysis in Tregs from the spleens of WT and KO (Zfp335fl/flFoxp3-Cre).

overall_design: High-dimensional single-cell RNA sequencing (10X Genomics) was used to profile the transcriptomes of YFP+ Tregs from the spleens of WT and KO (Zfp335fl/flFoxp3-Cre).

first: Baojun

first: Xin

last: Wang

first: Lina

last: Sun


title: Genome-wide MNase hypersensitive sites in soybean

city: East Lansing

first: Jiming

last: Jiang

state: MICHIGAN

address: 612 WILSON ROAD

department: Department of Plant Biology

institute: Michigan State University

summary: We investigated MNase hypersensitive sites (MHSs) in four soybean tissues (leaf, flower, seed and root) by MH-seq. The MHSs were highly overlapped with ATAC-seq peaks from previous study. In addition, we detected many MHSs, which is not identified by ATAC-seq. Through comparing MHSs among three tissues, we identified tissue-specific MHSs, which contributed to tissue specific expression of their cognate genes. As analyzing MHSs between duplicated genes, we found the divergence of MHSs between duplicated genes were highly related with their gene expression divergence.

overall_design: Chromatin are lightly digested by MNase to identify open chromatin regions in soybean.

first: Chao

last: Fang

first: Hainan

last: Zhao

first: Fanli

last: Meng


title: SINGLE CELL ANALYSIS OF POLYCYSTIC KIDNEY DISEASE USING HUMAN PLURIPOTENT STEM CELL- DERIVED KIDNEY ORGANOIDS

city: Singapore

first: Meng

last: Liu

state: Singapore

address: 11 Mandalay road

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

summary: To reveal the key pathways involved in kidney cystogenesis. We performed single nuclei gene expression and ATAC profiling using kidney organoids  from ARPKD patients-iPSCs derived organoids.

overall_design: Firstly, we generated ARPKD patient-derived kidney organoids (E17), gene-corrected kidney organoids (C15) and ARPKD KIF3A (E173A) mutation kidney organoids. After 3 days foskolin treatment. Organoids were collected for multiomics library construction and downstream analysis.

first: Liu

first: Zhang

last: Chao

first: Gong

last: Ximing

first: Xia

last: Yun


title: High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis

city: Pleasanton

first: Stephen

middle: Richardson

last: Williams

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics


title: High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis [scRNA-seq and Visium]

summary: Single-cell and spatial technologies that profile gene expression across a whole tissue are revolutionizing the resolution of molecular states in clinical tissue samples. Current commercially available technologies provide whole transcriptome single-cell, whole transcriptome spatial context, or high resolution in situ targeted gene expression analysis. Here, we combine these technologies to explore tissue heterogeneity in large, FFPE human breast cancer sections. In one sample, we identify three molecularly distinct tumor subtypes, enabling us to define cell neighborhoods and biomarkers in the progression towards invasive carcinoma. In another sample, we identify rare boundary cells that sit at the critical myoepithelial border confining the spread of malignant cells. We demonstrate that each technology alone provides information about molecular signatures relevant to understanding cancer heterogeneity. However, it is the integration of these technologies that leads to even deeper insights, ushering in discoveries that will progress oncology research and the development of diagnostics and therapeutics.

overall_design: Two formalin-fixed & paraffin-embedded (FFPE) breast cancer tissue blocks were obtained from Discovery Life Sciences. Sample #1 was annotated by a pathologist to be T2N1M0, Stage II-B, ER+/HER2+/PR−. Sample #2 was characterized as stage pT2 pN1a pMX, ER−/HER2+/PR−. Corresponding dissociated tumor cells for Sample #1, fresh frozen (FF) in liquid nitrogen, were also sampled from the same 2.5 cm biopsy. For the Chromium Flex workflow, two 25 μm curls were pooled as a single replicate. 5 μm sections from Sample #1 were taken from the FFPE tissue using a microtome. Two replicate 5 μm sections were taken each for Visium CytAssist and Xenium. A 5 μm section was also taken from Sample #2 for Xenium.

first: Amanda

last: Janesick

first: Robert

last: Shelansky

first: Andrew

last: Gottscho

first: Florian

last: Wagner

middle: R

first: Morgane

last: Rouault

first: Ghezal

last: Beliakoff

first: Carolyn

middle: A

last: Morrison

first: Michelli

last: Faria de Oliveira

first: Jordan

middle: T

last: Sicherman

last: Kohlway

first: Jawad

last: Abousoud

first: Tingsheng

middle: Y

last: Drennon

first: Seayar

middle: H

last: Mohabbat

first: Sarah

last: Taylor


title: High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis [Xenium]


title: CD8 TIL subsets isolation from early-stage, untreated NSCLC

city: Paris

first: Sebastian

last: Amigorena

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: The overall objective of this study was to characterize the diversity and ontogeny of CD8 T cells in untreated lung tumors. This was accomplished by performing bulk RNAseq and flow cytometry analysis on CD8+ T cell subsets isolated from tumor tissue, normal adjacent to tumor (juxta0 tissue samples from patients undergoing surgical resection for early-stage, untreated non-small-cell lung cancer (NSCLC).

overall_design: Subsets of tissue-resident, circulating precursor and late-dysfunctional CD8 T cells are sorted from early-stage, untreated NSCLC tumor-and juxta-tumor-tissue samples. Upon RNA purification and cDNA amplification using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Taqara), sampels are prepared for bulkRNAseq.

first: Christina

last: Metoikidou

first: Pierre-Emmanuel

last: Bonté


title: Functional Dissection of Variant Polycomb Repressive Complex 1 Subunits RYBP and YAF2 during Neural Differentiation of Embryonic Stem Cells [ChIP-Seq]

city: guangzhou

first: gongcheng

last: Hu

state: guangdong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: Chromatin immunoprecipitation sequencing (ChIP-seq) for RING1B, RYBP, YAF2, PRC2 complex (EZH2, MTF2 and JARID2) as well as the histone modifications H2AK119ub, H3K27me3 and H3K27ac in mESCs and the neural differentiated cells.

overall_design: Rybp-/- and Yaf2-/- mESC lines were generated by using CRISPR/Cas9 technique. ChIP samples obtained from wild-type, Rybp-/- and Yaf2-/- mESCs and the neural differentiated cells.

first: Gongcheng

first: Yanjiang

last: Liu

first: Hongjie

last: Yao


title: Functional dissection of PRC1 subunits RYBP and YAF2 during neural differentiation of embryonic stem cells

summary: Polycomb repressive complex 1 (PRC1) comprises two different complexes: CBX-containing canonical PRC1 (cPRC1) and RYBP/YAF2-containing variant PRC1 (vPRC1). RYBP and its paralog YAF2 recruit vPRC1 to catalyze H2AK119ub through a positive-feedback model. Here, we show that expression of RYBP and YAF2 decreases and increases, respectively, during neural differentiation of embryonic stem cells (ESCs). Rybp knockout impairs neural differentiation by activating Wnt signaling and derepressing nonneuroectoderm-associated genes. However, Yaf2 knockout promotes neural differentiation and leads to redistribution of RYBP binding, increases enrichment of RYBP and H2AK119ub on the RYBP-YAF2 co-targeted genes, and prevents ectopic derepression of nonneuroectoderm-associated genes in neural-differentiated cells. Furthermore, the phase separations mediated by RYBP alone or together with RING1B are easier and more stable than those by YAF2, which might facilitate the deposition of H2AK119ub more abundantly by RYBP-PRC1 than YAF2-PRC1. Together, this study reveals that RYBP might maintain repressed chromatin more strongly and function differentially in regulating mESC neural differentiation compared with YAF2.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in wild-type, Rybp-/- and Yaf2-/- mESCs and their neural differentiated cells.


title: Functional Dissection of Variant Polycomb Repressive Complex 1 Subunits RYBP and YAF2 during Neural Differentiation of Embryonic Stem Cells [ATAC-Seq]

summary: ATAC-seq was used to investigate the impact of Rybp knockout on chromatin accessibility in 46C mESCs.

overall_design: Rybp-/-  mESC lines were generated by using CRISPR/Cas9.


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

status: Public on Oct 08 2023

city: Montreal

first: Arthur

middle: Jules

last: Gouhier

state: Quebec

address: 110 Avenue des Pins

country: Canada

institute: IRCM

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

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

first: Justine

last: Dumoulin-Gagnon

first: Vincent

last: Lapointe-Roberge

first: Juliette

last: Harris

first: Aurelio

last: Balsalobre

first: Jacques

last: Drouin


title: Dual roles of the Arabidopsis PEAT complex in histone H2A deubiquitination and H4K5 acetylation [ChIP-seq]

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: Histone H2A monoubiquitination is associated with transcriptional repression and needs to be removed by deubiquitinases to facilitate gene transcription in eukaryotes. However, the deubiquitinase responsible for genome-wide H2A deubiquitination in plants has yet to be identified. We found that UBP5, an ubiquitin-specific protease, interacts with a previously identified PEAT (PWWP-EPCR-ARID-TRB) complex to form a larger version of PEAT complex in Arabidopsis thaliana. UBP5 functions as an H2A deubiquitinase in a nucleosome substrate-dependent manner in vitro and mediates H2A deubiquitination at the whole-genome level in vivo. Moreover, our results indicated that the histone acetyltransferases HAM1 and HAM2 (HAM1/2), catalytic subunits of the NuA4 histone acetyltransferase complex, are also part of the PEAT complex at PEAT target genomic loci. Within the PEAT complex, the PWWP components (PWWP1, PWWP2 and PWWP3) directly interact with UBP5 and are necessary for UBP5-mediated H2A deubiquitination, while the EPCR components (EPCR1 and EPCR2) directly interact with HAM1/2 and are required for HAM1/2-mediated H4K5 acetylation. This study identifies previously unknown regulators of H2A deubiquitination and H4K5 acetylation and illustrates how these processes collaborate at the whole-genome level.

overall_design: Examination of protein binding levels in transgenic plants; Examination of H4K5Ac, H2Aub level in wild type and mutants; Examination of H3K27me3 level in wild type.

first: Xin-Jian


title: Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [hDC RNA-seq]

city: Guangzhou

first: Zhu

last: Xiaofeng

address: 107 Yan Jinag West Road

institute: Sun Yat-Sen University

type: Non-coding RNA profiling by high throughput sequencing

summary: By using RNA-seq, we report circRNA stimulates DCs.

overall_design: Ribo-seq of human DCs.

first: Erwei

last: Song

first: Xiaofeng

last: Zhu


title: Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [circRNA-Seq breast cancer]

summary: By using circRNA-seq, we report tumor special circRNA from breast cancer tissues and normal tissues.

overall_design: circRNA-seq of breast cancer tissues and normal tissues.


title: Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [Ribo-Seq]

summary: By using Ribo-seq, we report tumor special antigen from breast cancer tissues and normal tissues.

overall_design: Ribo-seq of breast cancer tissues and normal tissues.


title: Inhibition of the SLC35B2-TPST2 axis of tyrosine sulfation attenuates the growth and metastasis of pancreatic ductal adenocarcinoma

city: Pittsburgh

first: Wen

last: Xie

state: Pennsylvania

address: 10068 Salk Hall, 3501 Terrace St

institute: University of Pittsburgh

summary: Background & Aims: Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer deaths in the United States. Tyrosine sulfation, catalyzed by the tyrosylprotein sulfotransferase 2 (TPST2), is a post-translational modification essential for protein-protein interactions and cellular functions. SLC35B2 is a key transporter that transports the universal sulfate donor 3’-phosphoadenosine 5’-phosphosulfate (PAPS) into the Golgi apparatus where the protein sulfation occurs. The goal of this study is to determine whether and how SLC35B2-TPST2 axis of tyrosine sulfation plays a role in PDAC.   Methods: Gene expression was analyzed in PDAC patients and mice. Human PDAC MIA PaCa-2 and PANC-1 cells were used for in vitro studies. TPST2 deficient MIA PaCa-2 cells were generated to assess xenograft tumor growth in vivo. Mouse PDAC cells derived from the KrasLSL-G12D/+;Tp53L/+;Pdx1-Cre (KPC) mice were used to generate Tpst2 KO KPC cells to evaluate tumor growth and metastasis in vivo.   Results: High expressions of SLC35B2 and TPST2 were correlated with poor PDAC patient survival. Knockdown of SLC35B2 or TPST2, or pharmacological inhibition of sulfation inhibited PDAC cell proliferation and migration in vitro. TPST2 deficient MIA PaCa-2 cells exhibited inhibited xenograft tumor growth. Orthotopic inoculation of Tpst2 KO KPC cells in mice showed inhibition of primary tumor growth, local invasion, and metastasis. Mechanistically, the integrin ITGB4 was found to be a novel substrate of TPST2. Inhibition of sulfation destabilizes ITGB4 protein, which may have accounted for the suppression of metastasis.  Conclusions: Targeting the SLC35B2-TPST2 axis of tyrosine sulfation may represent a novel approach for therapeutic intervention of PDAC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MIA PaCa-2 cells and its KD derivatives (sgGFP and sgTPST2).

first: Xinran

last: Cai

first: Sihan

last: Li

first: Da

last: Yang


title: Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by non-coding CRISPR screens [Capture-C]

first: Beisi

last: Xu

summary: Accumulating evidence indicates that HOXA9 dysregulation is sufficient and necessary for leukemic transformation. Leukemia subtypes showing HOXA9 overexpression include those carrying MLL gene rearrangements (MLL-r), NPM1c mutations, and other genetic alterations. HOXA9 protein is a poor therapeutic target as it lacks targetable pocket domains. Therefore, understanding HOXA9’s functional downstream genes and its regulation might provide alternative therapeutic targets. However, it remains largely unknown how HOXA9, as a homeobox transcriptional factor, binds to noncoding regulatory sequences and controls the downstream genes in MLL-r leukemia and across leukemias of other genetic subtypes. In this study, we have successfully conducted dropout CRISPR screens in the MLL-r SEM cell line stably expressing Cas9 against ~1,800 HOXA9 binding peaks. Integrative data analysis identified six reproducible noncoding hits, including a positive control located in the distal enhancer of FLT3. Cas9-editing and dCas9-KRAB silencing HOXA9’s binding site in distal region of FLT3 reduced transcription and impaired cell proliferation in vitro and in vivo. In addition, RNA-seq and Q-PCR analysis further identified the functional relevant downstream genes upon CRISPR editing of other candidate HOXA9-bound noncoding segments, including survival essential genes as XBP1, JUN and BAHCC1. In summary, the work is significant as it will advance our understanding of how HOXA9-associated transcription programs reconstruct the regulatory network specifying MLL-r dependency. Moreover, our study will promote the future development of HOXA9-mediated noncoding regulation, and alternative therapeutic targets in HOXA9-driven (including HOXA9 and possibly NUP98-HOXA9 subtype) leukemia in patients.

overall_design: Capture-C used to check the loop change from FLT3 enhancer

first: Shaela

last: Wright

first: Xujie

last: Zhao

first: Wojciech

last: Rosikiewicz

first: Siqi

last: Yi

first: Yong

last: Cheng

first: Chunliang


title: Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [RNA-Seq 2]

summary: By using RNA-seq, we report  mRNA or lncRNA profilings from breast cancer tissues and normal tissues.

overall_design: RNA-seq of breast cancer tissues and normal tissues


title: Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [circRNA-seq of mouse]

summary: By using RNA-seq, we report circRNA  profilings from B16F10 and melan-a, circRNA  profilings from 4T1 and Eph4-ev.

overall_design: CircRNA-seq of B16F10 and melan-a, circRNA -seq of 4T1 and Eph4-ev

first: Shicheng

last: Su

first: Di

last: Huang


title: Tumor-specific cicrRNAs elicit anti-tumor immune response via encoding cryptic peptides

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

overall_design: Refer to individual Series


title: Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [circRNA-seq]

summary: By using RNA-seq, we report  circRNA or lncRNA profilings from breast cancer tissues and normal tissues.


title: Real-time quantitative PCR analysis of Wild-type p53 (Wtp53) and Mutant p53 (Mutp53) transiently overexpressed in HEK-293T cells

status: Public on Oct 07 2023

city: Taichung

first: Wei-Chien

address: 9F, No.6, Hsueh-Shih Road

department: Graduate Institute of Cancer Biology

country: Taiwan

institute: China Medical University

summary: To identify a novel lncRNA regulated by mutp53. Wtp53 and 5 different hotspots mutation of p53 were transiently transfected into HEK-293T cells and compared with plasmid vector (pcDNA6A-Flag).

overall_design: Use LncRNA qPCR profiling to define differences in 90 LncRNAs expression patterns between wtp53 and mutp53 expressing samples.


title: Functional Dissection of Variant Polycomb Repressive Complex 1 Subunits RYBP and YAF2 during Neural Differentiation of Embryonic Stem Cells

first: gongcheng

last: Hu

summary: Polycomb repressive complex 1 (PRC1) comprises two different complexes: CBX-containing canonical PRC1 (cPRC1) and RYBP/YAF2-containing variant PRC1 (vPRC1). RYBP-vPRC1 or YAF2-vPRC1 catalyzes H2AK119ub through a positive-feedback model; however, whether RYBP and YAF2 have different regulatory functions is still unclear. Here, we show that the expression of RYBP and YAF2 decreases and increases, respectively, during neural differentiation of embryonic stem cells (ESCs). Rybp knockout impairs neural differentiation by activating Wnt signaling and derepressing nonneuroectoderm-associated genes. However, Yaf2 knockout promotes neural differentiation and leads to redistribution of RYBP binding, increases enrichment of RYBP and H2AK119ub on the RYBP-YAF2 cotargeted genes, and prevents ectopic derepression of nonneuroectoderm-associated genes in neural-differentiated cells. Taken together, this study reveals that RYBP and YAF2 function differentially in regulating mESC neural differentiation.

overall_design: Rybp-/- and Yaf2-/- mESC lines were generated by using CRISPR/Cas9 technique. RNA-seq, ChIP-seq and ATAC-seq data were obtained in wild-type, Rybp-/- and Yaf2-/- mESCs and their neural differentiated cells.


title: Transcriptomic analysis predicts the risk of progression of premalignant lesions in in human tongue.

city: New York

first: Xiaohan

last: Tang

address: 1300 York Ave.

institute: Weill Cornell Medicine

summary: The 5-year survival rate for patients with oral squamous cell carcinomas (SCC), including tongue SCC, has not significantly improved over the last several decades. Oral potentially malignant disorders (OPMD), including oral dysplasias, are oral epithelial disorders that can develop into oral SCCs. To identify molecular characteristics that might predict conversion of OPMDs to SCCs and guide treatment plans, we performed global transcriptomic analysis of human tongue OPMD (n=9) and tongue SCC (n=11) samples with paired normal margin tissue from patients treated at Weill Cornell Medicine.  Compared to margin tissue, SCCs showed more transcript changes than OPMDs.  OPMDs and SCCs shared some altered transcripts, but these changes were generally greater in SCCs than OPMDs. Both OPMDs and SCCs showed altered signaling pathways related to cell migration, basement membrane disruption, and metastasis. We suggest that OPMDs were on the path towards malignant transformation.  Based in patterns of gene expression, both OPMD samples and SCC samples can be categorized into subclasses (mesenchymal, classical, basal, and atypical) similar to those seen in human head and neck SCC (HNSCC).  These subclasses of OPMDs the potential to be used to stratify patient prognosis and therapeutic options for tongue OPMDs. Lastly, we developed Firth logistic regression models to classify OPMDs and SCCs using a signature gene set ELF5, RPTN, IGSF10, HTR3A, and CRMP1, and this predictive model is amenable to testing as data sets become available. We suggest that changes in these five transcripts relative to paired normal tissue could be used to predict of the likelihood of an OPMD developing into a SCC.

overall_design: RNA-seq analysis of human tongue oral potentially malignant disorders (OPMD) and squamous cell carcinomas (SCC)

first: Xiao-Han

first: Lorraine

middle: J

last: Gudas

first: Tuo

last: Zhang

first: David

last: Kutler


title: Nucleoporin downregulation modulates keratinocyte differentiation independent of nuclear pore numbers

status: Public on Oct 06 2023

city: Evanston

first: Xiaomin

last: Bao

state: IL

address: 633 Clark St

institute: Northwestern University

summary: We determined the target gene sets controlled by NUP93 in maintaining in undifferentiated state of primary human keratinocytes.

overall_design: We use primary human keratinocytes pooled from 6 donors. RNA-seq data comparing keratinocytes with NUP93 knockdown (2 independent shRNAs) vs control (2 independent control shRNAs) were generated.

first: Amy

last: Neely


title: Targeting the non-coding genome and temozolomide signature enables CRISPR-mediated glioma oncolysis

status: Public on Oct 05 2023

city: San Francisco

first: I-Li

last: Tan

address: 1650 Owens St

institute: Gladstone Institutes

summary: Glioblastoma (GBM) is the most common lethal primary brain cancer in adults. Despite treatment regimens including surgical resection, radiotherapy, and temozolomide (TMZ) chemotherapy, growth of residual tumor leads to therapy resistance and death. At recurrence, a quarter to a third of all gliomas have hypermutated genomes 5, with mutational burdens orders of magnitude greater than in normal tissue. Here, we quantified the mutational landscape progression in a patient’s primary and recurrent GBM, and uncovered Cas9-targetable repeat elements. We show that CRISPR-mediated targeting of highly repetitive loci enables rapid elimination of GBM cells, an approach we term “Genome Shredding”. Importantly, in the patient’s recurrent GBM, we identified unique repeat sequences with TMZ mutational signature and demonstrate that their CRISPR targeting enables cancer-specific cell ablation. “Cancer Shredding” leverages the non-coding genome and therapy-induced mutational signatures for targeted GBM cell depletion and provides an innovative paradigm to develop treatments for hypermutated glioma.

overall_design: Validation of Cancer-Specific sgRNA Prediction through a CRISPR Screen in SF11411, a Patient-Derived Hyper-Mutated GBM Cell Line, and Normal Human Astrocytes (NHAs). Our objective is to identify sgRNAs that are specifically depleted in SF11411, a patient-derived hyper-mutated glioblastoma multiforme (GBM) cell line, compared to normal human astrocytes (NHAs) by utilizing a CRISPR library and next-generation sequencing (NGS). Both SF11411 and NHAs will be transduced with the CRISPR library, and samples will be collected at two time points: day 1 (T0) and day 28 (D28) post-transduction, equivalent to approximately 14 cell doublings. Subsequently, NGS will be employed to sequence the sgRNAs in both cell populations, and the resulting data will undergo analysis to pinpoint sgRNAs that exhibit specific depletion in SF11411 cells when compared to NHAs, thereby validating the prediction of cancer-specific sgRNAs.

first: Alexendar

last: Perez

first: Rachel

last: Lew

first: Xiaoyu

last: Sun

first: Alisha

last: Baldwin

middle: K

last: Zhu

first: Mihir

last: Shah

first: Mitchel

last: Berger

first: Jennifer

last: Doudna

first: Christof

last: Fellmann


title: Single-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liver

city: Toronto

first: Diana

last: Nakib

state: ON

address: 101 College Street

institute: University of Toronto

summary: Primary sclerosing cholangitis (PSC) is a rare liver disease characterized by chronic inflammation and irreparable damage to the bile ducts. Due to a limited understanding of the underlying pathogenesis of disease, there remains a paucity of treatment options. As such, we sequenced healthy and diseased livers to compare the activity, interactions, and localization of immune and non-immune cells. This revealed that outside PSC scar regions, hepatocytes are transitioning to bile duct cells, whereas within the scars, there is an accumulation of immune cells. Of these cells, macrophages that typically contribute to tissue repair were enriched in immunoregulatory genes and were less responsive to stimulation. These cells are likely involved in maintaining hepatic inflammation and could be targeted in novel therapeutic development.

overall_design:
Spatial gene expression profiling by high throughput sequencing

The submitter states that the sample C73-D1 has already been uploaded as GSM5616008 that was uploaded as part of GSE185477.
The GSM7697871 (C73_D1_VISIUM) records were generated for the convenient retrieval of the complete raw data from SRA.

first: Tallulah

last: Andrews

first: Gary

last: Bader

first: Ian

last: McGilvray

first: Sonya

last: MacParland


title: T cell homeostasis and antitumor function require the Na+-K+-ATPase

city: Portland

first: Robert

last: Eil

state: Oregon

address: 3266 SW Research Drive

institute: Oregon Health and Science University

summary: The cancer-killing activity of T cells is often compromised within tumors, allowing disease progression. We previously found that intratumoral elevations in extracellular K+ constrain T cell antitumor function. Despite the relevance of K+abundance for T cell antitumor function and the importance of ion gradients for cellular physiology broadly, our understanding of T cell K+ transporters remains rudimentary7,8. Here, we report that the Na+-K+-ATPase is required for T cell quiescence, memory formation, and antitumor activity. Deletion of Atp1a1, the catalytic alpha subunit of the Na+-K+-ATPase, in CD8+ T cells induced constitutive activity in TCR, Akt-mTOR, and MAPK/ Erk signaling pathways. This state of tonic signal transduction was reflected in the acquisition of co-inhibitory surface receptors and terminal differentiation in T cells following Atp1a1 deletion. Mechanistically, we found that the Na+-K+-ATPase functions to support ROS homeostasis as its disruption produced ROS accumulation and the addition of antioxidants prevented the accelerated differentiation and acquisition of co-inhibitory receptors in T cells lacking Atp1a1. The in vivo behavior of T cells lacking Atp1a1 was also consistent with tonic signal transduction and stimulation-induced terminal differentiation. T cells lacking Atp1a1 could not achieve proliferative burst or form memory following pathogen challenge or perform tumor destruction in a syngeneic model of orthotopic murine melanoma. These results highlight the fundamental but underappreciated importance of monovalent ion transporters in T cell biology and have translational implications for the ongoing development of immune checkpoint blockade and T cell transfer therapies (i.e. CAR, TCR, TIL).

overall_design: Comparitive gene expression profiling of RNA-seq data for C57BL/6 murine CD8+ T cells electroporated with CRISPR-Cas9 molecules complexed to sgRNAs encoding Atp1a1 specific or scramble sequences

first: Eil

last: Robert

first: Collier

last: Camille


title: Transcriptional and post-transcriptional control of odorant receptor choice in ants

first: Wei

last: Wang

address: 1230 York Ave.

department: Bioinformatics Resource Center

institute: The Rockefeller University

summary: We generated snRNA-Seq for olfactory sensory neurons from late stage pupae of the clonal raider ant to study the chemosensory gene expression during development.

overall_design: Antennal clubs of pupae were dissected  and single nuclei extraction was done using a custom protocol for insect tissues. Library preparation was done using 10X Genomics 3' v3.1 kit. Sequencning was dine using Illumina NovaSeq S2 flowcell.

first: Anindita

last: Brahma

first: Daniel

last: Kronauer


title: Loss Of Function of Male-Specific Lethal 3 (Msl3) Does Not Affect Spermatogenesis in Rodents

city: Albany

first: Paolo

middle: Emanuele

last: Forni

state: NY

address: 1400 Washington Avenue

department: Biology

institute: University at Albany

summary:
Msl3 is a member of the chromatin-associated male-specific lethal MSL complex which is responsible for the transcriptional upregulation of genes on the X chromosome in males Drosophila. Although the dosage complex operates differently in mammals, the Msl3 gene is conserved from flies to humans.
Msl3 is required for meiotic entry during Drosophila oogenesis. Recent reports indicate that also in primates, Msl3 is expressed in undifferentiated germline cells before meiotic entry. However, if Msl3 plays a role in the meiotic entry of mammals has yet to be explored. To study this, we used mouse spermatogenesis as a study model. Analyses of single cells RNA-seq data revealed that in mouse, differently from what was reported in primates, Msl3 is expressed in meiotic cells.
To test the role of Msl3 in meiosis, we used a male germline-specific Stra8-iCre driver and a newly generated Msl3flox conditional knock-out mouse line. Msl3 conditional loss-of-function in spermatogonia did not cause spermatogenesis defects or changes in the expression of genes related to meiosis. Our data suggest that, in mice, Msl3 exhibits delayed expression compared to Drosophila and primates, and loss-of-function mutations disrupting the chromodomain or the MRG domain of Msl3 alone do not impede meiotic entry in rodents.

overall_design: P45 Testes from 3 Msl3 floxed conditional knock-out mice and 3 Msl3 wildtype mice were collected and RNA extraction was performed for whole RNA sequencing.

first: Tyler

last: Mitchell

first: Jen

last: Lin

first: Sawyer

last: Hicks

first: Joshua

last: James


title: Discovery of diverse DNA cytosine deaminases enables a single-enzyme method for base resolution methylation detection

city: Ipswich

first: Zhiyi

last: Sun

state: MASSACHUSETTS

address: 240 County Road

department: Research

institute: New England Biolabs

summary: Cytosine deaminases have important uses in the detection of epigenetic modifications and in genome editing. However, the range of applications of deaminases is limited by their substrate preference. To expand the toolkit of deaminases, we developed an in-vitro approach that bypasses a major hurdle with their severe toxicity in expression hosts. We screened 175 putative cytosine deaminases, primarily from bacteria, and found enzymes with strong activity on double- and single-stranded DNA in various sequence contexts, including some without any sequence constraints. We also found enzymes that do not deaminate modified cytosines. The remarkable diversity of cytosine deaminases opens new avenues for biotechnological and medical applications. As a demonstration, we developed a single-enzyme methylation sequencing (SEM-seq) method for 5-methylcytosine detection using a novel non-specific, modification-sensitive double-stranded DNA deaminase, MsddA. SEM-seq generated accurate base-resolution maps of 5-methylcytosine in human genome samples including cell free DNA and samples of 10 pg DNA, equivalent to single cell input. This simple and efficient protocol has the potential to allow high-throughput epigenome profiling of scarce biological material.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design: DNA sequencing of deaminated double-stranded and single-stranded E.coli genomic DNA plus other control DNAs with various DNA modification types. 2 replicates were conducted for each deaminase tested.

first: Romas

last: Vaisvila

first: Sean

last: Johnson

first: Bo

last: Yan


title: Synaptic-like transmission between neural axons and arterial smooth muscle cells drives cerebral neurovascular coupling

city: Shanghai

first: Dong-Dong

last: Zhang

state: Shanghai

address: 130 Dong'an Road

institute: Fudan University

summary: Normally functioning brains depend on neurovascular coupling (NVC) and its dysfunction underlies many neuropathologies. Although cell-type specificity has been implicated in NVC, how active neural information is specifically conveyed to the targeted arterioles in the brain remains poorly understood. Here, using two-photon focal optogenetics in the mouse cerebral cortex, we demonstrated that single glutamatergic axons dilate their innervating arterioles via synaptic-like transmission between neural-arteriolar smooth muscle cells junction (NsMJ). The presynaptic parental-daughter bouton makes dual innervations on postsynaptic dendrites and on arteriolar smooth muscles cells (aSMCs), which expressed many types of neuromediator receptors, including glutamate NMDA receptor subunit 1 (Grin1). Disruption of NsMJ transmission, by aSMC specific knockout of GluN1, diminished the optogenetic and whisker stimulation-caused functional hyperemia. Notably, the absence of GluN1 subunit in aSMCs protected the brain atrophy from cerebral ischemia by preventing Ca2+ overload in aSMCs during arteriolar constriction caused by the ischemia-induced spreading depolarization. Our findings reveal that NsMJ transmission drives neurovascular coupling and also open up a new avenue for studying stroke.

overall_design: mRNA profiles of arteriolar smooth muscle cell, cortical cell and astrocyte

first: Woo-Ping

last: Ge

first: Jie-Min

last: Jia


title: Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [singleCell-seq]

first: Zhu

last: Xiaofeng

summary: By using 10x GenomicsTM scRNA-seq, we defined putative clones by grouping cells having identical reconstruction of the TCRα or TCRβ chains.

overall_design: 10x Genomics scRNA-seq  of pentamer positive T cells and pentamer negative T cells

first: Erwei

last: Song

first: Shicheng

last: Su

first: Xiaofeng

last: Zhu

first: Di

last: Huang


title: PCMT1 knockdown attenuates malignant properties by globally regulating transcriptome profiles in triple-negative breast cancer cells

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Breast cancer is the most frequently diagnosed cancer in women, and has high mortality and metastasis rate, especially triple-negative breast cancer (TNBC). As an oncogene, Protein-L-Isoaspartate (D-Aspartate) O-Methyltransferase (PCMT1) is a prognostic biomarker in breast cancer and is highly expressed, while the underlying mechanisms remain unknown. In this study, we silenced PCTM1 in TNBC MDA-MB-231 cells by short hairpin RNA (shPCMT1) to investigate its cellular functions using cell proliferation, apoptosis, migration, and invasion experiments. Following this, the transcriptome sequencing (RNA-seq) experiment was performed to identify the molecular targets of PCMT1, including differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs). We found that shPCMT1 inhibited the proliferation, migration, and invasion of MDA-MB-231 cells. We obtained 1084 DEGs and 2287 RASEs between shPCMT1 and negative control (NC) groups through RNA-seq. The DEGs were highly enriched in immune or inflammation response and cell adhesion-associated pathways, pathways associated with PCMT1 cellular function in cell migration. The RASE genes were enriched in cell cycle-associated pathways and were associated with the altered cell proliferation rate. We finally validated the changed expression and splicing levels of DEGs and RASEs. We found that 34 RNA binding protein (RBP) genes were dysregulated by shPCMT1, including NQO1, S100A4, EEF1A2, and RBMS2. The dysregulated RBP genes could partially explain how PCMT1 regulates the global transcriptome profiles. In conclusion, our study identified the molecular targets of PCMT1 in the TNBC cell line, expands our understanding of the regulatory mechanisms of PCMT1 in cancer progression, and provides novel insights into the progression of TNBC. The identified molecular targets are potential therapeutic targets for future TNBC treatment.

first: Aili

last: Saiding

first: Xinyu

last: Hu

first: Dilinuer

last: Maimaitiyiming

first: Minglan

first: Futian

first: Ping

last: Shi


title: RBM25 affects the immune and inflammatory progress by binding to and modulating alternative splicing levels of associated genes in rat H9C2 cells [ABL2020-10020-ABF_H9C2_RBM25_iRIP]

summary: Alternative splicing (AS) enables genes to be translated into a vast diversity of proteins while aberrant AS predisposes cells to abnormal biological processes. As is closely associated with AS, RNA binding proteins (RBPs) are gradually gaining attention. RBM 25 was reported to participate in the cardiac pathophysiological process via AS regulation. Nonetheless, gaps still existed in whether RBM 25 functions in heart failure by its splicing factor role. H9C2 cells with excessively expressed RBM25 were used to filtrate different expression genes (DEGs) and analyze for RBM25-regulated AS by RNA-seq. Next, iRIP-seq was performed to examine its binding targets. For genes screened, further RT-qPCR-based validation was conducted. RBM25 overexpression caused expressive alteration in 80 genes mainly involved in the inflammatory response and virus response. Notably, RBM25 partially modulated AS of differential genes enriched in the apoptotic process and bound to genes clustered at inflammation response. Further, qRT-PCR verified Slc38a9, IL-17RC, Csf1, and Coro6 as targets of RBM25 being bound to and AS-regulated.

first: Xin

last: Tian

first: Guangli

last: Zhou

first: Hao

last: Li

last: Yang


title: Effect of EZH2 and BET bromodomain inhibition, alone and combined, on NUT carcinoma gene expression

city: boston

first: Chris

last: French

state: MA

address: 75 francis st.

department: Pathology

institute: BWH

summary: To determine mechanisms of synergy between EZH2 and BRD4-NUT, we treated NUT carcinoma cell lines with EZH2 inhibitor, tazemetostat, and/or BET bromodomain inhibitors (ABBV075 pan-BET inhibitor or ABBV744 BD2-selective inhibitor). We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different NUT carcinoma cell lines at two time points, 6h and 96h.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PER-403 and 10-15 NUT carcinoma cells treated with ABBV-744 or ABBV075 alone for 6h, tazemetostat alone for 96h, or tazemetostat combined with ABBV075 for 96h.

first: Christopher

first: Dora


title: Identifying new cellular mechanisms of MCPH5

city: Laramie

first: Todd

last: Schoborg

state: Wyoming

address: 1000 E. University Ave, Department of Molecular Biology, #3944

department: Molecular Biology

institute: University of Wyoming

summary: The coordination of cellular behaviors during neurodevelopment is critical for determining the form, function, and size of the central nervous system. Mutations in the vertebrate Abnormal Spindle-Like, Microcephaly Associated (ASPM) gene and its Drosophila melanogaster ortholog abnormal spindle (asp) lead to microcephaly, a reduction in overall brain size whose etiology remains poorly defined. Here we provide the neurodevelopmental transcriptional landscape for a Drosophila model for autosomal recessive primary microcephaly-5 (MCPH5) and extend our findings into the functional realm to identify the key cellular mechanisms responsible for Asp-dependent brain growth and development. We identify multiple transcriptomic signatures, including new patterns of co-expressed genes in the developing central nervous system (CNS). Defects in optic lobe neurogenesis were detected in larval brains through downregulation of temporal transcription factors (tTFs) and Notch signaling targets, which correlated with a significant reduction in brain size and total cell numbers during the neurogenic window of development. We also found inflammation as a hallmark of asp mutant brains, detectable throughout every stage of CNS development, which also contributes to the brain size phenotype. Finally, we show that apoptosis is not a primary driver of the asp mutant brain phenotypes, further highlighting an intrinsic Asp-dependent neurogenesis promotion mechanism that is independent of cell death. Collectively, our results suggest that the etiology of the asp mutant brain phenotype is complex and that a comprehensive view of the cellular basis of the disorder requires an understanding of how multiple pathway inputs collectively determine tissue size and architecture.

overall_design: We sequenced bulk mRNA from the central nervous system (brain) of Drosophila melanogaster third instar larva, mid-pupal, and adult developmental stages. Three genotypes were included: Heterozygous control (aspt25/+), asp mutant (aspT25/aspDf), and a genetic resuce strain (AspMF/+; AspT25/AspDf)

first: Maria

last: Mannino

first: Mercedes

last: Cassidy

first: Steven

last: Florez

first: Zeid

last: Rusan

first: Shalini

last: Chakraborty


title: HMGA1 Chromatin Regulators Drive MPN Progression

city: BALTIMORE

first: Linda

last: Resar

state: Maryland

address: 720 Rutland Avenue

department: Department of Medicine / Division of Hematology

institute: Johns Hopkins University

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


title: Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [RNA-Seq]

first: Zhu

last: Xiaofeng

summary: By using RNA-seq, we report mutation and lncRNA from breast cancer tissues and normal tissues.

overall_design: RNA-seq of breast cancer tissues and normal tissues.

first: Erwei

last: Song

first: Shicheng

last: Su

first: Xiaofeng

last: Zhu

first: Di

last: Huang


title: Targeting BMI-1 to deplete antibody-secreting cells in autoimmunity

city: Clayton

first: Kim

last: Good-Jacobson

state: Victoria

address: Gr Fl Reception (Bldg 77) 23 Innovation Walk

country: Australia

institute: Monash University

summary: We measured genes expression differences in antibody secreting cells from LynKO mice in following treatment with a BMI-1 inhibitor (PTC-028) or a vehicle control. BMI-1 inhibition lead to a reduction in antibody secreting cells in LynKO mice and in humans donors. We performed RNA sequencing to understand the impact of BMI-1 inhibition on antibody secreting cells in LynKO mice.

overall_design: Antibody secreting cells (B220loCD138hi) were sort purified from LynKO mice 4 days after 12 consecutive days of PTC-028 treatment or vehicle control. RNAseq was undertaken on these cells.

first: Jack

last: Polmear

middle: L

last: Jacobson


title: HMGA1 Chromatin Regulators Drive MPN Progression [ATAC-Seq]

summary: Myeloproliferative neoplasms (MPN) transform to myelofibrosis (MF) and highly lethal acute myeloid leukemia (AML), although actionable mechanisms driving progression remain elusive. The HMGA1 chromatin regulator is up-regulated during MPN progression with highest levels after transformation. HMGA1 depletion in JAK2V617F MPN AML cell lines disrupts proliferation, clonogenicity, and leukemic engraftment. Surprisingly, loss of just a single Hmga1 allele prevents progression to MF in JAK2V617F transgenic mice, decreasing blood counts and expansion in stem and myeloid progenitors while preventing splenomegaly and fibrosis within the spleen and bone marrow. RNA sequencing revealed HMGA1-dependent transcriptional networks that govern proliferation (E2F, G2M, mitosis, MYC targets) and cell fate, including the GATA2 master regulatory gene. Silencing GATA2 recapitulates phenotypes observed with HMGA1 depletion whereas GATA2 re-expression partially rescues leukemogenesis. HMGA1 transactivates GATA2 through sequences near the developmental enhancer (+9.5), increasing chromatin accessibility and recruiting active histone marks. Further, HMGA1 transcriptional networks, including GATA2, are activated in human MF after leukemic transformation. Further, HMGA1 depletion synergizes with the JAK2 inhibitor, ruxolitinib, to prolong survival in murine MPN AML. These findings illuminate HMGA1 as a key epigenetic switch required for MPN transformation and promising therapeutic target to treat or prevent disease progression.

overall_design: ATAC sequencing (ATACseq) was performed with RNA from of DAMI and SET-2 cell lines with or without HMGA1 silencing.

first: Leslie

last: Cope


title: HMGA1 Chromatin Regulators Drive MPN Progression [RNA-Seq]

overall_design: RNA sequencing (RNAseq) was performed with RNA from of DAMI and SET-2 cell lines with or without HMGA1 silencing.


title: HMGA1 Chromatin Regulators Drive MPN Progression [scRNA-Seq]

overall_design: We used 10x genomics platform to profile single-cell transcriptome of LSK (Lineage-/Sca1+/Ckit+) hematopoietic stem/progenitor cells (HSPCs) derived from 2 JAK2V617F/V617F and 2 JAK2V617F/V617F-Hmga1+/- mice


title: RBM25 affects the immune and inflammatory progress by binding to and modulating alternative splicing levels of associated genes in rat H9C2 cells [ABL2020-10020-ABF_RBM25_OE]

first: Dong

last: Chen

summary: Alternative splicing (AS) enables genes to be translated into a vast diversity of proteins while aberrant AS predisposes cells to abnormal biological processes. As is closely associated with AS, RNA binding proteins (RBPs) are gradually gaining attention. RBM 25 was reported to participate in the cardiac pathophysiological process via AS regulation. Nonetheless, gaps still existed in whether RBM 25 functions in heart failure by its splicing factor role. H9C2 cells with excessively expressed RBM25 were used to filtrate different expression genes (DEGs) and analyze for RBM25-regulated AS by RNA-seq. Next, iRIP-seq was performed to examine its binding targets. For genes screened, further RT-qPCR-based validation was conducted. RBM25 overexpression caused expressive alteration in 80 genes mainly involved in the inflammatory response and virus response. Notably, RBM25 partially modulated AS of differential genes enriched in the apoptotic process and bound to genes clustered at inflammation response. Further, qRT-PCR verified Slc38a9, IL-17RC, Csf1, and Coro6 as targets of RBM25 being bound to and AS-regulated. Herein, our work demonstrated that by exerting its binding capability, RBM25 may serve as a regulator of related RNA expressive levels and AS process to confer negative impacts on cardiac inflammation in cardiomyocytes. Our study provided preliminary evidence regarding the understanding of RBM25 in heart failure complicated by inflammation.

first: Xin

last: Tian

first: Guangli

last: Zhou

first: Hao

last: Li

first: Ping

last: Yang


title: Prefoldin 6 mediates longevity response from heat shock factor 1 to FOXO in C. elegans

status: Public on Oct 04 2023

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

summary: Heat shock factor 1 (HSF-1) and forkhead box O (FOXO) are key transcription factors that protect cells from various stresses. InCaenorhabditis elegans, HSF-1 and FOXO together promote a long life span when insulin/IGF-1 signaling (IIS) is reduced. However, it remains poorly understood how HSF-1 and FOXO cooperate to confer IIS-mediated longevity. Here, we show that prefoldin 6 (PFD-6), a component of the molecular chaperone prefoldin-like complex, relays longevity response from HSF-1 to FOXO under reduced IIS. We found that PFD-6 was specifically required for reduced IIS-mediated longevity by acting in the intestine and hypodermis. We showed that HSF-1 increased the levels of PFD-6 proteins, which in turn directly bound FOXO and enhanced its transcriptional activity. Our work suggests that the prefoldin-like chaperone complex mediates longevity response from HSF-1 to FOXO to increase the life span in animals with reduced IIS.

overall_design: The investigation of the changes of gene expression in daf-2(e1370) mutants on control RNAi or hsf-1 RNAi

first: Heehwa

middle: S

last: Son

first: Keunhee

last: Seo

first: Seokjin

last: Ham


title: RNA helicase HEL-1 promotes longevity by specifically activating DAF-16/FOXO transcription factor signaling in Caenorhabditis elegans

summary: The homeostatic maintenance of the genomic DNA is crucial for regulating aging processes. However, the role of RNA homeostasis in aging processes remains unknown. RNA helicases are a large family of enzymes that regulate the biogenesis and homeostasis of RNA. However, the functional significance of RNA helicases in aging has not been explored. Here, we report that a large fraction of RNA helicases regulate the lifespan ofCaenorhabditis elegans. In particular, we show that a DEAD-box RNA helicase, helicase 1 (HEL-1), promotes longevity by specifically activating the DAF-16/forkhead box O (FOXO) transcription factor signaling pathway. We find that HEL-1 is required for the longevity conferred by reduced insulin/insulin-like growth factor 1 (IGF-1) signaling (IIS) and is sufficient for extending lifespan. We further show that the expression of HEL-1 in the intestine and neurons contributes to longevity. HEL-1 enhances the induction of a large fraction of DAF-16 target genes. Thus, the RNA helicase HEL-1 appears to promote longevity in response to decreased IIS as a transcription coregulator of DAF-16. Because HEL-1 and IIS are evolutionarily well conserved, a similar mechanism for longevity regulation via an RNA helicase-dependent regulation of FOXO signaling may operate in mammals, including humans.

overall_design: The investigation of the changes of gene expression in wild-type worms and daf-2(e1370) mutants by hel-1 mutations

first: Mihwa


title: GRAMD2+ alveolar type I cell plasticity facilitates cell state transitions in organoid culture

city: Duarte

first: Crystal

middle: N

last: Marconett

email: cmarcone@usc.edu, cmarconett@coh.org

address: 1500 E Duarte Rd

department: Integrative Translational Sciences

institute: City of Hope

summary: Alveolar epithelial regeneration is critical for normal lung function and becomes dysregulated in disease. While alveolar type 2 (AT2) and club cells are known distal lung epithelial progenitors, determining if alveolar epithelial type 1 (AT1) cells also contribute to alveolar regeneration has been hampered by lack of highly specific mouse models labeling AT1 cells.  To address this, the Gramd2CreERT2 transgenic strain was generated and crossed to ROSAmTmG mice. Extensive cellular characterization, including distal lung immunofluorescence and cytospin staining, confirmed that GRAMD2+ AT1 cells are highly enriched for green fluoresecent protein (GFP).  Interestingly, Gramd2CreERT2 GFP+ cells were able to form colonies in organoid co-culture with Mlg fibroblasts. Temporal scRNAseq revealed that Gramd2+ AT1 cells transition through numerous intermediate lung epithelial cell states including basal, secretory and AT2 cell in organoids while acquiring proliferative capacity.  Our results indicate that Gramd2+ AT1 cells are highly plastic suggesting they may contribute to alveolar regeneration.

overall_design: Primary isolation of FACS sorted GFP+ cells were defined as day 0. On days 8, 13, and 20 of 3D culture, to obtain single cells, colonies were dissociated with dispase (#354235, BD Gibco) and TrypLE express (#12604013, Gibco). Biotinylated EpCAM Ab (#130-096-419, Miltenyi Biotec, San Diego, California), anti-biotin microbeads (#130-900-485, Miltenyi Biotec,) and MS columns (#130-042-201, Miltenyi Biotec) were used to enrich for epithelial cells. For each time point, cells were counted, and viability was measured using an automated cell counter (Countess 3, Thermo Fisher Scientific). Single cell suspensions were processed using Chromium Single Cell 3’ Reagent Kits v3.1 (10x Genomics, PN-1000128, PN-1000127 and PN-1000213). Briefly, cells resuspended in the reaction mix were loaded into the Chromium Single Cell Chip G, together with the 10x Barcoded Gel Beads and partitioning oil. The Chip G was placed into the 10x Chromium controller for cell partitioning, targeting a final number of 10,000 cells per sample. After partitioning, the GEMs (Gel Bead-In EMulsions) were transferred to the C1000 Touch Thermal Cycler for the first phase of reverse transcription followed by library preparation following the manufacturer’s instructions. Libraries were deep sequenced using the Illumina NovaSeq platform.

first: Shen

last: Hua

first: Chen

last: Weimou

first: Liu

last: Yixin

first: Castaldi

last: Alessandra

first: Castillo

last: Jonathan

first: Horie

last: Masafumi

first: Floody

last: Per

first: Sundar

last: Shivah

first: Li

last: Changgong

first: Minoo

last: Parviz

first: Ji

last: Yanbin

first: Marconett

last: Crystal N

first: Zhou

last: Beiyun

first: Borok

last: Zea


title: Bacteroides is increased in an autism cohort and induces autismrelevant behavioral changes in mice in a sex-dependent manner

city: Safed

first: Evan

last: Elliott

address: Henrietta Szold Street, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

summary: Autism Spectrum Disorder (ASD) is a neurodevelopmental condition which is defined by decreased social communication and the presence of repetitive or stereotypic behaviors. Recent evidence has suggested that the gut-brain axis may be important in neurodevelopment in general and may play a role in ASD in particular. Here, we present a study of the gut microbiome in 96 individuals diagnosed with ASD in Israel, compared to 42 neurotypical individuals. We determined differences in alpha and beta diversity in the microbiome of individuals with ASD and demonstrated that the phylum Bacteroidetes and genus Bacteroides were the most significantly over-represented in individuals with ASD. To understand the possible functional significance of these changes, we treated newborn mice with Bacteroides fragilis at birth. B. fragilis-treated male mice displayed social behavior dysfunction, increased repetitive behaviors and gene expression dysregulation in the prefrontal cortex, while female mice did not display behavioral deficits. These findings suggest that overabundance of Bacteroides, particularly in early life, may have functional consequences for individuals with ASD.

overall_design: in order to determine the difference in alpha and beta diversity in the microbiome, 96 individuals diagnosed with ASD in Israel, caompared to 42 neurotypical individualsa. In order to understand the possible functional significance of these changes,  newborn Wild-type mice (C57BL/6J) treated with Bacteroides fragilis at birth.

first: Natalia

last: Saleev

first: Dmitriy

last: Getselter

first: Omry

last: Koren

first: Tali

last: Bretler

first: Tanya

last: Kronos

first: Neta

last: Kevtani-Friedman

first: Alla

last: Kuzminsky

first: Saleh

last: Khatib

first: Mounia

last: Shaalan

first: Julie

last: Carmel

first: Sondra

last: Turjeman

first: Evgeny

last: Tikonov

first: Ipsita

last: Chaterjee

first: Rasha

last: Mayouf

first: Nasreen

last: Ghanayem


title: Key role for Rac in the early transcriptional response  to ECM stiffness and the stiffness-dependent repression of ATF3

city: Philadelphia

first: Richard

last: Assoian

address: 421 Curie Blvd

department: Systems Pharmacology

institute: University of Pennsylvania

summary: The Rho family GTPases, Rac and Rho, play critical roles in transmitting mechanical information contained within the extracellular matrix (ECM) to the cell. Rac and Rho have well described roles in regulating stiffness-dependent actin remodeling, proliferation and motility. However, much less is known about the relative roles of these GTPases in stiffness-dependent transcription, particularly at the genome-wide level. Here, we selectively inhibited Rac and Rho in mouse embryonic fibroblasts cultured on deformable substrata and used RNA sequencing to elucidate and compare the contribution of these GTPases to the early transcriptional response to ECM stiffness. Surprisingly, we found that the stiffness-dependent activation of Rac is dominant over Rho in the initial transcriptional response to ECM stiffness. We also identified Activating Transcription Factor 3 (ATF3) as a major target of stiffness/Rac-mediated signaling and show that ATF3 repression by ECM stiffness helps to explain how the stiffness-dependent activation of Rac results in the induction of cyclin D1.

overall_design: Spontaneously immortalized MEFs pre-incubated with EHT1864 (Rac inhibitor), CT04 (Rho inhibitor), or vehicle (untreated control) were plated on soft (2-4 kPa) or stiff (20-25 kPa) fibroenctin-coated polyacrylamide hydrogels for 1 hr before collection, isolation of total RNA and analysis of the transcriptomes by RNASeq.

first: R

first: Y

last: Bae


title: Reduced insulin/IGF1 signaling prevents immune aging via ZIP-10/bZIP–mediated feedforward loop

first: Seung-Jae

last: Lee

summary: A hallmark of aging is immunosenescence, a decline in immune functions, which appeared to be inevitable in living organisms, includingCaenorhabditis elegans. Here, we show that genetic inhibition of the DAF-2/insulin/IGF-1 receptor drastically enhances immunocompetence in old age inC. elegans. We demonstrate that longevity-promoting DAF-16/FOXO and heat-shock transcription factor 1 (HSF-1) increase immunocompetence in olddaf-2(−)animals. In contrast, p38 mitogen-activated protein kinase 1 (PMK-1), a key determinant of immunity, is only partially required for this rejuvenated immunity. The up-regulation of DAF-16/FOXO and HSF-1 decreases the expression of thezip-10/bZIP transcription factor, which in turn down-regulates INS-7, an agonistic insulin-like peptide, resulting in further reduction of insulin/IGF-1 signaling (IIS). Thus, reduced IIS prevents immune aging via the up-regulation of anti-aging transcription factors that modulate an endocrine insulin-like peptide through a feedforward mechanism. Because many functions of IIS are conserved across phyla, our study may lead to the development of strategies against immune aging in humans.

first: Yujin

first: Seokjin

last: Ham


title: Myeloid Cell Derived IL1b Contributes to Pulmonary Vascular Remodeling in Heart Failure with Preserved Ejection Fraction

status: Public on Oct 03 2023

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

summary: Goals and objectives of this study were to determine by bulk RNA-sequencing transcriptomic changes that occur in the lungs of a murine model of heart failure with preserved ejection fraction caused by administration of high fat diet and eNOS inhibitor L-NAME.

overall_design: Four C57/BL6 mice each were given either a combination of high fat diet and L-NAME or control (low fat diet with no L-NAME) for 5 weeks. Lungs were isolated after sacrifice, enzymatically digested, separately labeled with hashing antibodies, and submitted for single cell RNA sequencing.

first: Vineet

last: Agrawal


title: Transcriptomic profiling of 27-year cryopreserved umbilical cord blood HSCs/HPCs

city: Indianapolis

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

summary: Umbilical cord blood banking is critical for the success of umbilical cord blood transplants. Here we analyzed transcriptomic differences between 27-year cryopreserved umbilical cord blood hematopoietic stem cells (HSCs) and multipotent progenitor cells (MPPs) and those derived from fresh cord blood. We also leveraged differences in engraftment capacity to examine the transcriptomes of HSCs/HPCs defined by engraftment capacity, demonstrating the feasibility of this approach for identifying potency markers to aid in the selection of cord blood units for transplantation and revealing novel potential regulators of cord blood HSC/HPC engraftment.

overall_design: Stringently defined HSCs or MPPs were collected by flow cytometry sorting from 27-year cryopreserved cord blood units following thaw. HSCs/MPPs were also collected from fresh cord blood units to analyzed transcriptomic changes induced by cryopreservation and freeze-thaw. CD34+ cells, a population enriched in HSCs/HPCs, were transplanted to immune deficient mice for calculation of SCID repopulating cell frequency, and high SRC units were compared to low SRC units in the transcriptomic analysis model.


title: HOPX associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function

city: Wooloongabba

first: Seth

last: Cheetham

state: QLD

address: Level 4, 37 Kent St

institute: Mater Research Institute-University of Queensland

summary: Identification of HOPX genomic binding sites using DamID

first: Clayton

middle: E

last: Friedman

middle: W

last: Mills

first: Masahito

last: Ogawa

first: Han

last: Chiu

first: Yuliangzi

last: Sun

first: Romaric

last: Bouveret

first: Xichun

last: Li

first: Xiaoli

last: Chen

first: Scott

last: Paterson

first: Stacey

middle: B

last: Andersen

first: Sohye

last: Yoon

first: Geoffrey

last: Faulkner

last: Harvey

first: Enzo

last: Porrello

first: Benjamin

middle: M

last: Hogan

first: Quan

last: Nguyen

first: Kazu

last: Kikuchi

last: Hudson

first: Nathan

last: Palpant


title: Transcriptional profile of bone marrow mature neutrophils

city: Lille

first: Yasmine

last: Zeroual

state: Nord

address: 1 Rue du professeur Calmette, 59000 Lille (Institut pasteur de Lille)

institute: INSERM

summary: We analyzed the impact of amoxicillin on the transcriptional profile of bone marrow mature neutrophils from infected mice withStreptococcus pneumoniae

overall_design: Bone marrow mature neutrophils from amoxicillin (AMX)-treated infected mice (IAV/Sp/AMX)and infected mice left untreated (IAV/Sp) were sorted by FACS and analyzed using RNA-seq

first: Mondemé

last: Mélanie

first: Zeroual

last: Yasmine

first: Beury

last: Delphine

first: Faveeuw

last: Christelle


title: Neuron Navigator 1 Regulates Learning, Memory, and the Response to Multiple Potentially Addictive Drugs

city: Stanford

first: Zhuoqing

last: Fang

state: California

address: 300 Pasteur Drive

institute: Stanford

summary: Genetic variation accounts for much of the risk for developing a substance use disorder (SUD). Inbred mouse strains exhibit substantial and heritable differences in the extent of voluntary cocaine intravenous self-administration (IVSA). Computational genetic analysis of IVSA data obtained from an inbred strain panel identified Nav1, a member of the neuron navigator family that regulates dendrite formation and axonal guidance, as a candidate gene. To test this hypothesis, we generated and characterized Nav1 knockout (KO) mice. Nav1 KO mice exhibited increased cocaine intake during IVSA testing. Surprisingly, Nav1 KO mice also displayed a reduced susceptibility to become opioid dependent and to develop opioid-induced hyperalgesia after chronic morphine administration, and they had impaired spatial learning/memory. Immunohistochemistry and electrophysiology studies revealed that inhibitory synapse density in the cortex of Nav1 KO mice was reduced, and excitatory synaptic transmission was increased in the Nav1 KO cortex and hippocampus. Transcriptomic analysis revealed that Nav1 KO mice had a marked increase in layer 5 excitatory cortical neurons. Collectively, our results indicate that Nav1 regulates learning, memory, and the response to multiple addictive drugs, and that changes in the excitatory and inhibitory synaptic balance in the cortex and hippocampus could possibly mediate these phenotypic effects.

overall_design: snRNA-Seq was performed on high quality PFC cells obtained from Nav1 KO mice (14,056 cells) and from age-matched, isogenic C57BL/6J mice (14,630 cells), as well as BTBR T<+> Itpr3<tf>/J mice (15,238 cells).

first: Jared

middle: R

last: Bagley

first: Yalun

last: Tan

first: Zhuanfen

last: Cheng

first: Saori

last: Takeda

first: Zhouqing

first: Yuan

last: Guan

first: J

middle: D

last: Jentsch

first: Gary

last: Peltz


title: Cyclosporin A inhibits prostate cancer growth through suppression of E2F8

city: Seoul

first: Ju-Hong

last: Jeon

state: Seoul

address: 28 Yongon-Dong, Chongno-Gu

department: Department of Physiology and Biomedical Sciences

institute: Seoul National University College of Medicine

summary: Cyclosporin A (CsA) is a potent immunosuppressive agent used clinically in organ transplantation. In this study, we examined that CsA exerts anti-tumor activity against prostate cancer. We performed microarray experiments to investigate the effect of CsA on the transcriptome of prostate cancer cells. CsA potently induced transcriptome change and primarily affected cell cycle-related gene signatures. These results suggest that CsA can be used as a potential therapeutic agent or an intriguing tool for exploring prostate cancer biology and identifying novel therapeutic targets.

overall_design: Cells were cultured in RPMI1640 medium containing 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 ug/ml streptomycin. CsA was dissolved in 100% ethanol (vehicle) and treated to cells with 10 mM CsA for 24h

first: Da Young

last: Lee

first: Jung Nyeo

last: Chun

first: Sanghoon

first: Soonbum

last: Park


title: Gene expression profile at single cell level of murine air liquid interface cultures

status: Public on Oct 02 2023

city: Homburg

first: Felix

last: Ritzmann

address: Kirrberger Street

country: Germany

institute: Saarland University

summary: Alveolar type 2 (AT2) and club cells are part of the stem cell niche of the lung and their differentiation is required for pulmonary homeostasis and tissue regeneration. A disturbed crosstalk between fibroblasts and epithelial cells contributes to the loss of lung structure in chronic lung diseases. We used single cell RNA sequencing to analyze the interaction of fibroblasts and the alveolar epithelium modelled in air-liquid interface cultures.

overall_design: Lung epithelial cells were apically seeded in Transwells and fibroblasts in the basolateral compartment. The apical chamber medium was aspirated after 2 days. Single cell suspensions were obtained after 2 days post airlift and single cell transcriptome profiling was performed by BD Rhapsody™ Single-Cell Analysis System.

first: Christoph

last: Beisswenger

first: Yiwen

last: Yao

first: Robert

last: Bals


title: Gene expression profile at the single cell level of Gatad2b WT, Het and KO E16.5 embryos

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: We performed single-cell RNA sequencing (scRNA-seq) on cortical samples obtained fromGatad2bstop/+ and WT littermates at a single embryonic time point (E16.5) in order to explore underlying mechanisms  of Gatad2b function.  We also generated Gatad2bstop/stop scRNA-seq data to identify dosage sensitive targets of Gatad2b

overall_design: E16.5 whole cortices were isolated and used fresh for scRNAseq. 3 embryos of WT, 3 embryos of KO and 4 embryos of Het genotypes were used.

first: Juan

last: Young

first: Clemer

last: Abad

first: Katherina

last: Walz


title: Effector Memory T cells induce DC-intrinsic DNA damage and a non-canonical STING pathway during innate inflammation

city: Cincinnati

first: Chandrashekhar

last: Pasare

state: Ohio

address: 250 Albert Sabin Way

department: Immunology

institute: Cincinnati Children's Hospital Medical Center

summary: A breach in tolerance to self-antigens induces expansion of autoreactive T cells, ultimately leading to autoimmune inflammation. While autoreactive T cells are principal drivers of autoimmunity, tissue pathology is alternatively driven by innate cytokines, indicating that autoreactive T cells can induce innate inflammation. This study has led to the discovery that effector memory T (Tem) cells trigger double stranded breaks via mitochondrial ROS production in interacting DCs. Consequently, initiation of the DNA damage response leads to activation of a cGAS-independent, STING-TRAF6-NFkB signaling axis. STING deficient DCs display significant defects in transcriptional induction and functional production of IL-1b and IL-6 following their interaction with Tem cells, both in vitro and in vivo. The discovery of Tem induced innate inflammation through DNA damage and a non-canonical STING-mediated NFkB activation presents this pathway as a potential target to alleviate T cell driven autoimmune inflammation.

overall_design: WT or STING golden ticket BMDCs were co-cultured with in vitro generated effector memory T (Tem) cells + anti-CD3 for 1 hour. BMDCs were then sorted away from Tem cells and submitted for sequencing. Control samples include WT and STING golden ticket sorted BMDCs previously cultured with Tem cells - anti-CD3 (unstimulated).

first: Hannah

last: Meibers


title: RNA sequence (RNA-seq) profiling of Syn6.5 consolidation strain

city: New York

first: Jitong

last: Cai

address: 435 E 30th street

department: NYU Langone Health

institute: NYU Langone Health

summary: The Sc2.0 project is building a eukaryotic synthetic genome from scratch. A major milestone has been achieved with all individual Sc2.0 chromosomes assembled. Here, we describe consolidation of multiple synthetic chromosomes using advanced endoreduplication intercrossing with tRNA expression cassettes to generate a strain with 6.5 synthetic chromosomes. The 3D chromosome organization and transcript isoform profiles were evaluated using Hi-C and long-read direct RNA sequencing. We developed CRISPR Directed Biallelic URA3-assisted Genome Scan, or “CRISPR D-BUGS”, to map phenotypic variants caused by specific designer modifications, known as “bugs”. We first fine-mapped a bug in synthetic chromosome II (synII), and then discovered a combinatorial interaction associated with synIII and synX, revealing an unexpected genetic interaction that links transcriptional regulation, inositol metabolism and tRNASerCGA abundance. Finally, to expedite consolidation, we employed chromosome substitution to incorporate the largest chromosome (synIV), thereby consolidating >50% of the Sc2.0 genome in one strain.

overall_design: To assess the effects of synthetic genome design on gene expression levels, we performed stranded mRNA sequencing of Syn6.5 consolidation strain YZY463 against wildtype strain YZY597.

first: Yu

last: Zhao

first: Jef

last: Boeke


title: Expression data that were specifically regulated by  lncRNA-HELF (ENSMUST00000147617 ) in livers of mice undergoing CCl4-induced liver fibrosis

city: Tianjin

first: Kun

last: Zhang

address: Qixiangtai Road NO.22

department: Department of Histology and Embryology

institute: Tianjin medical university

summary: Long non-coding RNAs (lncRNAs) are involved in numerous biological functions and pathological processes. In this study, we have identified a novel lncRNA ENSMUST00000147617, named Highly Expressed in Liver Fibrosis (lnc-HELF), which is remarkably up-regulated in mouse and human fibrotic livers. To identify the roles of lnc-HELF in liver fibrosis, we performed RNA-seq to analyze the effect of lnc-HELF deficient on CCl4-induced liver fibrosis. The mice were divided in three groups:   mice treated with CCl4 in combination with injection of AAV8-NC (NC_CCl4, n=3), mice treated with CCl4 in combination with injection of AAV8-shRNA-lncHELF1# (sh1_CCl4, n=3) and mice treated with CCl4 in combination with injection of AAV8-shRNA-lncHELF2# (sh2_CCl4, n=3).

first: Wei

last: Hong

first: Tao

last: Han