title: ERK signaling expands mammalian cortical radial glial cells and extends the neurogenic period

status: Public on Aug 09 2023

city: Shanghai

first: Guoping

last: Liu

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary: The molecular basis for cortical expansion during evolution remains largely unknown. Here, we report that fibroblast growth factor (FGF)-extracellular signal-regulated kinase (ERK) signaling promotes the self-renewal and expansion of cortical radial glial (RG) cells. Furthermore, FGF-ERK signaling induces bone morphogenic protein 7 (Bmp7) expression in cortical RG cells, which increases the length of the neurogenic period. We demonstrate that ERK signaling and Sonic Hedgehog (SHH) signaling mutually inhibit each other in cortical RG cells. We provide evidence that ERK signaling is elevated in cortical RG cells during development and evolution. We propose that the expansion of the mammalian cortex, notably in human, is driven by the ERK-BMP7-GLI3R signaling pathway in cortical RG cells, which participates in a positive feedback loop through antagonizing SHH signaling. We also propose that the relatively short cortical neurogenic period in mice is partly due to mouse cortical RG cells receiving higher SHH signaling that antagonizes ERK signaling.

overall_design:
① scRNA-Seq of the E14.5 cortex of control mice (Map2k1 and Map2k2 flox), E14.5 cortex of Emx1-Cre; Map2k1/2-dcko mice, E14.5 cortex of hGFAP-Cre; RosaSmoM2 mice.
The whole mouse cortex at E14.5 was dissected out under a microscope for scRNA-Seq analysis. Briefly, mouse embryos were dissected out and immediately submerged in fresh ice-cold Hanks balanced salt solution (Gibco 12175-095). The cortex was then cut into pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit (Miltenyi Biotec, catalog no. 130-092-628) according to the manufacturer’s instructions. The Chromium droplet-based sequencing platform (10X Genomics) was employed to generate scRNA-Seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C). Cellular quality control thresholds were set at 750-5000 genes and <10% mitochondrial transcripts per cell. After filtering, the number of cells in our dataset were as follows: E14.5 control cortex, 8649 cells, 1390 genes/cell; E14.5 Emx1-Cre; Map2k1/2-dcko cortex, 5811 cells, 1713 genes/cell; E14.5 hGFAP-Cre; RosaSmoM2 cortex, 11868 cells, 2663 genes/cell.
② Bulk RNA-Seq data of E14.5 cortex of control mice (n =5), E14.5 cortex of hGFAP-Cre; RosaFgf8 mice (n = 5), E14.5 cortex of hGFAP-Cre; RosaMEK1DD mice (n = 4).
The whole cortex from E14.5 control mice (n = 5), from E14.5 hGFAP-Cre; RosaFgf8 mice (n = 5), and from E14.5 hGFAP-Cre; RosaMEK1DD mice (n = 4) was dissected. Total RNA was purified with a mini RNA isolation kit (ZymoGenetics). RNA-seq was performed as recommended by the manufacturer (Illumina). Levels of gene expression were reported in fragments per kilobase of exon per million fragments mapped (FPKM). A gene was considered to be expressed when it had FPKM > 1. For a gene to be called as differentially expressed, it required p < 0.05.

first: Mengge

last: Sun

first: Yanjing

last: Gao

first: Zhenmeiyu

last: Li

first: Zhengang

last: Yang


title: RNA-sequencing of 69 cell lines in the Human Protein Atlas database

status: Public on Aug 21 2023

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

type: Expression profiling by high throughput sequencing

summary: Cell lines are valuable resources as model for human biology and translational medicine. It is thus important to explore the concordance between the expression in various cell lines vis-à-vis human native and disease tissues. In this study, we investigate the expression of all human protein-coding genes in more than 1,000 human cell lines representing 27 cancer types by a genome-wide transcriptomics analysis. The cell line gene expression is compared with the corresponding profiles in various tissues, organs, single-cell types and cancers. Here, we present the expression for each cell line and give guidance for the most appropriate cell line for a given experimental study. In addition, we explore the cancer-related pathway and cytokine activity of the cell lines to aid human biology studies and drug development projects. All data are presented in an open access cell line section of the Human Protein Atlas to facilitate the exploration of all human protein-coding genes across these cell lines.

overall_design: A total of 141 cell line samples corresponding to 69 human cell lines were sequenced.

first: Cheng

last: Zhang

first: Martin

last: Zwahlen

first: Kalle

last: von Feilitzen

first: Mathias

last: Uhlén

first: Adil

last: Mardinoglu


title: GSK3a/b restrains IFNg-inducible costimulatory molecule expression in alveolar macrophages, limiting CD4+ T cell activation

status: Public on Aug 16 2023

city: Lansing

first: Kayla

middle: N

last: Conner

state: Michigan

address: 4125 Beaumont Rd

country: USA

institute: Michigan State University

summary: Macrophages play a crucial role in eliminating respiratory pathogens. Both pulmonary resident alveolar macrophages (AMs) and recruited macrophages contribute to detecting, responding to, and resolving infections in the lungs. Despite their distinct functions, it remains unclear how these macrophage subsets regulate their responses to infection, including how activation by the cytokine IFNg is regulated. This shortcoming prevents the development of therapeutics that effectively target distinct lung macrophage populations without exacerbating inflammation. We aimed to better understand the transcriptional regulation of resting and IFNg-activated cells using a new ex vivo model of AMs from mice, fetal liver-derived alveolar-like macrophages (FLAMs), and immortalized bone marrow-derived macrophages (iBMDMs). Our findings reveal that IFNg robustly activates both macrophage types; however, the profile of activated IFNg-stimulated genes varies greatly between these cell types. Notably, FLAMs show limited expression of costimulatory markers essential for T cell activation upon stimulation with only IFNg. To understand cell type-specific differences, we examined how the inhibition of the regulatory kinases GSK3a/b alters the IFNg response. GSK3a/b controlled distinct IFNg responses, and in AM-like cells, we found GSK3a/b restrained the induction of type I IFN and TNF, thus preventing the robust expression of costimulatory molecules and limiting CD4+ T cell activation. Together, these data suggest that the capacity of AMs to respond to IFNg is restricted in a GSK3a/b-dependent manner and that IFNg responses differ across distinct macrophage populations. These findings lay the groundwork to identify new therapeutic targets that activate protective pulmonary responses during infection without driving deleterious inflammation.

overall_design: Cells were treated with IFNy and CHIR for 24 hours. RNA was extracted and libraries were prepared for bulk RNA sequencing. Following sequencing, we carried out differential gene expression analysis to understand how the inhibition GSK3a/b alters IFNg responses in alveolar-like macrophages and immortalized bone marrow derived macrophages.

first: Laurisa

last: Ankley

first: Taryn

last: Vielma

first: Mahima

last: Thapa

first: Andrew

middle: J

last: Olive


title: SLE Antibody-Secreting Cells Are Characterized by Enhanced Peripheral Maturation and Survival Program.

status: Public on Aug 08 2023

city: Atlanta

first: Weirong

last: Chen

state: GA

address: 615 Michael Street

department: School of Medicine

institute: Emory University

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

overall_design: Refer to individual Series


title: SLE Antibody-Secreting Cells Are Characterized by Enhanced Peripheral Maturation and Survival Programs [AIRR]

summary: Systemic Lupus Erythematosus (SLE) is an autoimmune disease characterized by multiple autoantibodies, some of which are present in high titers in a sustained, B cell-independent fashion consistent with their generation from long-lived plasma cells (LLPC). Active SLE displays high numbers of circulating antibody-secreting cells (ASC). Understanding the mechanisms of generation and survival of SLE ASC would contribute important insight into disease pathogenesis and novel targeted therapies. We studied the properties of SLE ASC through a systematic analysis of their phenotypic, molecular, structural, and functional features. Our results indicate that in active SLE, relative to healthy post-immunization responses, blood ASC contain a much larger fraction of newly generated mature CD19-CD138+ASC similar to bone marrow (BM) LLPC. SLE ASC were characterized by morphological and structural features of premature maturation. Additionally, SLE ASC express high levels of CXCR4 and CD138, and molecular programs consistent with increased longevity based on pro-survival and attenuated pro-apoptotic pathways.Notably, SLE ASC demonstrate autocrine production of APRIL and IL-10 and experience prolonged in vitro survival. Combined, our findings indicate that SLE ASC are endowed with enhanced peripheral maturation, survival and BM homing potential suggesting that these features likely underlie BM expansion of autoreactive PC.

overall_design:
To investigate the question of whether different types of ASC arise from distinct B cell precursors or whether a common precursor might generate different ASC progeny through separate differentiation pathways, or instead through sequential maturation.
Sorted ASC populations (Pop 2, Pop 3, Pop 4 and Pop 5) from active SLE patients were used to extract the total cellular RNA by using the RNeasy Mini Kit (Qiagen, Inc. Valencia, CA) according to the manufacturer's protocol.
Approximately 400 pg of RNA was subjected to reverse transcription using the iScript RT kit. Resulting cDNA products were combined with 50 nM VH1- VH6 specific primers and 250 nM Ca, Cm, and Cg specific primers in a 25 μl PCR reaction.

first: Chris

last: Tipton


title: Acquired immunotherapy resistance in PDA (RNA-seq)

city: Philadelphia

first: Ben

middle: Z

last: Stanger

state: PA

address: 421 Curie Blvd

institute: Perelman School of Medicine

summary: 36 samples were sequenced with duplicates or triplicates

overall_design: RNA-seq

first: Salina

last: Yuan


title: Acquired immunotherapy resistance in PDA (ATAC-seq)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: 4 samples were sequenced in duplicate.

overall_design: ATAC-seq


title: SLE Antibody-Secreting Cells Are Characterized by Enhanced Peripheral Maturation and Survival Programs [RNA-seq]

overall_design: We performed RNA-seq of ASC Populations (Pop 2, Pop 3 and Pop5) as well as naive B cells to gain insights into disease-specific developmental and survival programs that may contribute to the observed phenotypic and morphological differences between SLE and HC ASC.

last: Scharer


title: Acquired immunotherapy resistance in PDA


title: Sox4 in adult hepatocytes

status: Public on Aug 10 2023

first: Takeshi

last: Katsuda

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania


title: RNA-Seq of human colorectal cancer (CRC) cell lines with or without METTL17 knockdown

city: Xiamen

first: yongyou

last: zhang

state: Fujian

address: Xiang'an South Road

country: China

institute: Xiamen University

summary: To investigate the mRNA profiling in RKO and SW620 cells with or without shRNA-mediated METTL17 knockdown, we performed RNA-seq with the total RNA extracted from the CRC cells.

overall_design:
We used lentivirus-mediated gene knockdown to construct cell lines with or without METTL17 stable knockdown. Then, the RNAs of RKO or SW620 cells were collected and RNA-Seq was performed

**Raw data not provided for GSM7663201, GSM7663202, GSM7663203

first: Hao

last: Li


title: Characterizing transcriptomic changes at different stage of hepatobiliary reprogramming in the adult mouse liver

summary: Recent studies have demonstrated that hepatocytes can be reprogrammed into biliary epithelial cell-like cells. Here, by RNA-seq, we dissect the transcriptomic changes involving the reprogramming process at different stages.

overall_design: Mice were injected with AAV8-TBG-Cre for lineage trace hepatocytes. One week after AAV injection, biliary reprogramming was induced by challenging the mice with diet supplemented with 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC). After 8 weeks, cells were harvested, FACS-sorted, and RNA was isolated from them.

first: Jonathan

last: Sussman


title: A ubiquitous GC content signature underlies multimodal post-transcriptional regulation by DDX3X

city: Berlin

first: Lorenzo

last: Calviello

address: Robert-Rössle-Straße 10, MDC, Haus 89

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

summary: The road from transcription to protein synthesis is paved with many obstacles, allowing for several modes of post-transcriptional regulation of gene expression. A fundamental player in mRNA biology, DDX3X is an RNA binding protein that regulates mRNA translation. By monitoring dynamics of mRNA abundance and translation following DDX3X depletion, we observe stabilization of translationally suppressed mRNA. We used interpretable statistical learning models to uncover GC content in the coding sequence as the major feature underlying RNA stabilization. GC content-related mRNA regulation is detectable in other studies, including hundreds of ENCODE datasets and recent work focusing on mRNA dynamics in the cell cycle. We provide further evidence for mRNA stabilization by detailed analysis of RNA-seq profiles in hundreds of samples, including a recently published Ddx3x conditional mouse model exhibiting cell cycle and neurogenesis defects. Our study identifies a ubiquitous feature underlying mRNA regulation and highlights the importance of quantifying multiple steps of the gene expression cascade, where RNA abundance and protein production are often uncoupled.

overall_design: RNA-seq, Ribo-seq (Ribosome footprints) and SLAM-seq following DDX3X inactivation

first: Ziad

last: Jowhar

first: Albert

last: Xu

first: Srivats

last: Venkataramanan

first: Mariah

middle: L

last: Hoye

first: Debra

last: Silver

first: Stephen

last: Floor


title: Transcriptomic comparisons and allele specific expression reveals the electric signal duration divergence in radiative mormyrid electric fish evolution

status: Public on Aug 31 2023

city: Potsdam

first: Feng

last: Cheng

address: Meistersingerstr., 5

institute: University of Potsdam

summary: Electric fishes have independently evolved six times. Most of these fish are weakly electric and they use their discharge mainly for orientation and communication. In the African weakly electric fish genus Campylomormyrus, electric organ discharge (EOD) signals are strikingly different in shape and duration among closely related species, they contribute to pre-zygotic isolation and may have triggered an adaptive radiation. We performed mRNA sequencing on electric organs (EOs) and skeletal muscle (SMs; from which the EOs derive) from three species with short (0.4 ms), medium (5 ms), and long (40 ms) EODs and two different cross-species hybrids. Using pairwise comparison of differential gene expression between EOs and SMs, we identified 1,444 up regulated genes in EO shared by all five species/hybrids cohorts, rendering them candidate genes for EO-specific properties in Campylomormyrus. To understand how gene expression contributes to the variation in EOD duration, we made cross species comparisons among species and tissue. We identified three types of EOD-duration-related expression patterns and several candidate genes, including KCNJ2, KLF5 and SLC24a2, their upregulation may contribute to increased EOD duration, along with a down-regulated gene KCNK6. Hybrids between a short (C. compressirostris) and a long (C. rhynchophorus) discharging species exhibit EODs of intermediate duration and showed imbalanced expression of KCNJ2 alleles. The preferential expression of the C. rhynchophorus allele is in line with a higher expression level in that parental species and points towards a cis-regulatory difference at this locus, relative to EOD duration. A further candidate gene, KLF5, is a transcription factor potentially balancing potassium channel gene expression, a crucial process for the formation of an EOD. Unraveling the genetic basis of the species-specific modulation of the EOD in Campylomormyrus is crucial for understanding the adaptive radiation of this emerging model taxon of ecological (perhaps even sympatric) speciation.

sample_organism: Campylomormyrus compressirostris x Campylomormyrus tshokwe

sample_organism: Campylomormyrus compressirostris x Campylomormyrus rhynchophorus

overall_design: C. tshokwe samples were collected from Brazzaville, Congo river in 2012. Other samples were artifically bred and raised at the Univerrsity of Potsdam. Those fish were anesthetized by a lethal dose of clove oil, and dissected on cold 99% ethanol.  Electric organ and skeletal muscle tissue from each specimen were flash frozen in liquid nitrogen, and further preserved in -80°C.

first: Alice

middle: B

last: Dennis

first: Otto

last: Baumann

first: Frank

last: Kirschbaum

first: Salim

last: Abdelilah-Seyfried

first: Ralph

last: Tiedemann


title: Immunological Signatures Driving COVID-19 Severity in Ghanaians: Insights from Upper Airway Transcriptome Analysis

status: Public on Aug 07 2023

city: Accra

first: JOHN

middle: DEMBY

last: SANDI

address: Legon Boundary

department: Biochemistry, Cell and Molecular Biology

country: Ghana

institute: West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana

summary:
The immunological signatures driving COVID-19 severity in Ghanaians are not well understood. We, therefore, performed bulk transcriptome sequencing of nasopharyngeal samples from SARS-CoV-2-infected Ghanaians with mild and severe COVID-19 and healthy controls to characterize immune signatures at the primary SARS-CoV-2 infection site and identified drivers of disease severity. Generally, a heightened antiviral response was observed in SARS-CoV-2-infected Ghanaians compared with uninfected controls. COVID-19 severity was associated with a dysregulated inflammatory response occasioned by overexpression of IL1A, S100A7, CRNN, and IL23A proinflammatory cytokines and hyperactivation of the NF-κB pathway through MAL signaling. SAMD9L was also among the differentially regulated interferon-stimulated genes (ISGs) in our mild and severe disease cohorts, suggesting that it may be playing a critical role in SARS-CoV-2 pathogenesis. We noted differences in antiviral gene expression by comparing our data with a publicly available dataset from a non-African (Indians) (GSE166530) cohort. Overall, the study identifies immune signatures driving COVID-19 severity in Ghanaians that could serve as potential prognostic markers. It further provides preliminary evidence suggesting differences in antiviral response at the upper respiratory interface in sub-Saharan Africans (Ghanaians) and non-Africans (Indians), which could be contributing to the differences in disease outcomes. Further studies using a larger dataset from different populations will expand on these findings.

Keywords: Nasopharyngeal swab, SARS-Cov-2, RNA-Seq, Ghanaians, immunological signatures

overall_design:
Profiling upper airway transcriptome differences in SARS-CoV-2 infected Ghanaians with mild and severe clinical phenotypes
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Authors state "I am currently   limited on the type of data I should make publicly available as per my current study protocol since human subjects are involved."

first: John

middle: D

last: Sandi

first: Josh

middle: I

last: Levy

first: Kesego

last: Tapela

first: Mark

last: Zeller

first: Joshua

middle: A

last: Yeboah

first: Daniel

middle: F

last: Saka

first: Donald

middle: S

last: Grant

first: Kristian

middle: G

last: Andersen

first: Gordon

last: Awandare

first: Peter

middle: K

last: Quashie

first: Lily

last: Paemka


title: Liquid Application Dosing Alters the Physiology of Air-Liquid Interface Primary Bronchial Epithelial Cell/Lung Fibroblast Co-Cultures and In Vitro Testing Relevant Endpoints

city: Durham

first: Shaun

middle: David

last: McCullough

state: NC

address: 3040 E. Cornwallis Rd., PO Box 12194

department: Exposure & Protection

institute: RTI International

overall_design: Differential gene expression between differentiated primary human bronchial epithelial cells (dpHBEC) and IMR90 lung fibroblast co-cultulres submerged in medium compared being maintained under air-liquid interface conditions.

first: Nicholas

middle: M

last: Mallek

first: Elizabeth

last: Martin


title: Human iPSC-derived heart organoids modeling the etiology of pregestational diabetes induced congenital heart defects

city: East Lansing

first: Aitor

last: Aguirre

state: MI

address: 775 Woodlot Dr

department: Biomedical Engineering

summary: Human iPSC-derived organoids modeling the etiology of pregestational diabetes induced congenital heart defects

overall_design: 1 control sample of 4 pooled healthy organoids and 1 treatment sample of 4 pooled diabetic organoids

first: Yonatan

middle: R

last: Lewis-Israeli


title: Transcriptomics of pig vascular endothelial cells by D-malate treatment

status: Public on Aug 02 2023

city: Guangzhou

first: Penglin

last: Li

address: 483 Wushan Road, Tianhe District

institute: South China Agriculture University

summary: By transcriptomics analysis, we identified that the mechanism underlying the effects of D-malate is dependent on the elevated intra-cellular acetyl-CoA content and increased Cyclin A acetylation. This finding revealed a novel mechanism, by which gut microbes impair muscle angiogenesis, and may provide therapeutic target for skeletal muscle function and other vascular associated diseases, such as cancer or aging.

overall_design: We uesd pig vascular endothelial cell as samples, invided them into two group: control and D-malate treatment group (n=3 for each group). After 24 h treatment, cells were collected and uesd for transcriptomic sequencing.

first: Jinlong

last: Feng

first: Gang

last: Shu

first: Qingyan

last: Jiang


title: Essential role of PLD2 in hypoxia-induced stemness and therapy resistance in ovarian tumors

status: Public on Aug 06 2023

city: Seville

first: José

middle: M.

last: Santos-Pereira

address: Avda. Manuel Siurot s/n

country: Spain

institute: IBiS, Universidad de Sevilla-CSIC

summary: Ovarian cancer (OC) is the most lethal gynecological cancer due to its late diagnosis and, importantly, its high rate of chemoresistance. Hypoxia in solid tumors is an important source of chemoresistance that can determine poor patient prognosis. Such chemoresistance relies on the presence of cancer stem cells (CSCs), and hypoxia promotes their generation through transcriptional activation by HIF transcription factors. We use OC cell lines, xenograft models, OC patient samples, transcriptional databases, iPSCs and ATAC-seq. We show here that hypoxia induces the formation of ovarian CSCs through transcriptional activation of the PLD2 gene encoding phospholipase D2. HIF-1 activates PLD2 transcription through hypoxia response elements located within PLD2 promoter and an intronic enhancer. PLD2 overexpression leads to similar effects than hypoxia, increasing CSC-like features, stemness gene expression and enhancing cell reprogramming in OC cells, as well as chromatin accessibility around stemness genes detected by ATAC-seq. Conversely, PLD2 depletion in hypoxia partially suppresses these effects, indicating that PLD2 is a major determinant of hypoxia-induced CSC generation in OC. Indeed, PLD2 expression is high in OC patients leading to poor survival and a transcriptional switch in the genes related to the response to hypoxia and stemness. Finally, we demonstrate that PLD2 overexpression provokes resistance to platinum-based chemotherapy and that combination of cisplatin with pharmacological inhibition of PLD2 suppresses such resistance. Altogether, our work highlights the importance of the HIF-1-PLD2 axis for CSC generation and chemoresistance in OC and proposes an alternative treatment for patients with high PLD2 expression.

overall_design: ATAC-seq assays SKOV3 ovarian cancer cells, in normoxia and hypoxia, with PLD2 or shPLD2 expression

first: Sandra

last: Muñoz-Galván

first: Eva

last: Verdugo-Sivianes

first: Purificación

last: Estévez-García

first: Amancio

last: Carnero


title: Transcriptomic analysis of early IFALD in preterm piglets receiving parenteral nutrition

city: Boston

first: Scott

middle: C

last: Fligor

state: MA

address: 300 Longwood Ave

department: Surgery

institute: Boston Children's Hospital

summary: Preterm Yorkshire piglets were provided parenteral nutrition for 14 days and developed cholestasis and histologic liver injury. Bottle-fed age-matched controls were provided sow milk replacer every 2-3 hours for 14 days.

overall_design: RNA-Seq was performed on liver tissue obtained at sacrifice on day of life 15 from all treatment (parenteral nutrition) and control animals (sow milk replacer).

first: Savas

middle: T

last: Tsikis

first: Thomas

last: Hirsch

first: Mark

last: Puder


title: Histidine re-sensitizes acute lymphoblastic leukemia cells to 6-mercaptopurine through tetrahydrofolate consumption and SIRT5-mediated desuccinylation

status: Public on Jul 27 2023

city: Jinan

last: Dong

state: Shandong Province

address: No. 107 Wenhua West Road

department: Department of Pediatrics

institute: Qilu Hospital of Shandong University

summary: Given the progressive improvements in the efficacy of multiagent chemotherapy and the survival rate of pediatric acute lymphoblastic leukemia (ALL), concerted efforts are required to eradicate chemoresistance-induced disease progression and relapse. Our present study coupled chemoresistance in B-ALL with histidine metabolism deficiency. We provide evidence that histidine supplementation significantly shifts the 6-MP dose response in 6-MP-resistant B-ALL cell lines and xenograft mice model. Moreover, we prove that the THF consumption through histidine degradation pathway and SIRT5-mediated desuccinylation of HINT1 are required for the histidine combination therapy to promote B-ALL cells against 6-MP resistance. Collectively, our results demonstrated that histidine supplementation and SIRT5-HINT1 axis activators might be rational strategies to overcome chemoresistance, thus protect B-ALL patients from disease progression or recurrence.

overall_design: To provide insight into the genes that contribute to the response of leukemia cells to 6-MP and histidine, we performed RNA-seq in the Reh-6-MPR cells after treatment with vehicle, histidine, 6-MP, or both histidine and 6-MP.

first: Hui-Xian

last: Ma

first: Xue-Qin

last: Liu

first: Dong

first: Ling-Hong

first: Qing

last: Shi

first: Xiu-Li

last: Ju


title: Pityriasis rubra pilaris transcriptomics implicate IL-17 signaling and correlate with response to IL-17A inhibition

status: Public on Jul 28 2023

city: Salt Lake City

first: Robert

last: Judson-Torres

state: Utah

institute: University of Utah

summary: Pityriasis rubra pilaris (PRP) is a rare inflammatory skin disorder associated with significant patient morbidity. To further characterize the molecular landscape of PRP, we conducted a transcriptomic analysis of epidermis and dermis collected from patients with moderate-to-severe PRP compared to matched healthy controls, on no systemic therapy and then following 24 weeks of treatment with the IL17A inhibitor, ixekizumab. Patients with PRP not only experienced clinical improvements, but also correction of their cutaneous transcriptome dysregulation after therapy. Moreover, those who has >50% improvement in PASI score after treatment demonstrated distinct transcriptomic profiles when compared to those who failed to respond, despite the lack of a discernable phenotypic difference. Pathway enrichment was strongest among DEGs belonging to inflammatory processes for patients with PRP – in particular, enrichment of the Th17 immune response was seen both prior to and following treatment with IL17A inhibition. Positive regulation of natural killer cell chemotaxis was also seen pre- and post-treatment, however, the pathway’s odds of enrichment decreased following treatment in both epidermis and dermis. Additionally, negative regulation of IL-12 production was highly enriched following therapy, suggesting decreased activity of the Th1 axis. Several individual genes of interest similarly displayed marked differential expression by response status. In parallel with their overall normalization in gene expression, responders had a greater normalization toward healthy control skin than non-responders in the Th17 family genes IL17C, IL23A, CCL20, as well as IL36A and IL36F (implicated in pustular psoriasis), Phospholipase A2 group IVD, and the antimicrobial protein S100A7, all of which remained elevated in non-responders. Intriguingly, responders had higher baseline levels of IL17A and IL17F than non-responders. Whereas dermal IL17A/F levels improved in responders, epidermal expression remained high despite the clinical response to IL17A inhibition. In contrast, non-responder IL17A/F epidermal levels normalized and dermal levels were significantly suppressed compared to healthy controls, despite the lack of clinical improvement. This suggests alternative pathways such as specific targeting of IL17C or IL36 may be preferred in some subsets of PRP.

overall_design: The study cohort consisted of 11 adults with moderate-to-severe PRP (as defined by a Psoriasis Area and Severity Index [PASI] ≥ 10) undergoing 24 weeks of IL17A inhibitor therapy and 14 matched healthy controls. All studies were approved by the Oregon Health & Science University Institutional Review Board (#18031), and subjects gave written informed consent. Lesional PRP and matched healthy control punch biopsy specimens were separated into epidermis and dermis, and RNA was extracted, as previously described (Haynes et al., 2020). Short read sequencing assays were performed by the OHSU Massively Parallel Sequencing Shared Resource and postprocessed with standard pair-end trimming via Trimmomatic-0.36 and alignment to the human genome version GRCh38.89 using STAR (v2.5.3a). A counts matrix was generated using FeatureCounts (Subread package v2.0.1) and gencode v38 alignment. Differential expression analysis was conducted with DESeq2 (v1.34.0) (Love et al., 2014) and results filtered by adjusted p value < 0.05 and absolute log2 fold change (log2FC) > 2. Gene expression was compared between healthy controls and PRP patients, with delimitations by tissue depth (epidermis vs. dermis) as well as time on therapy (prior to receiving therapy [pre] vs. week-24 of therapy [post]) and response to therapy (≥50% improvement in PASI [responder] vs. <50% improvement [non-responder]) for PRP patients. Two models were generated, one combining all PRP patients, and another separating responders from non-responders. Pathway enrichment analysis was conducted using Enrichr (adjusted p value < 0.05) (Xie et al., 2021) separated by genes that were increased or decreased in abundance; Gene Ontology (GO) biological process terms (Ashburner et al., 2000) were selected for publication, sorted by the top 3 largest odds ratios per condition. A literature review was also performed to identify individual differentially expressed genes (DEGs) with biological relevance to PRP.

first: Teri

last: Greiling

first: Dylan

last: Haynes

first: Taylor

last: Reiter

first: Rose

last: Velasco

first: Matthew

last: Chang

first: Rajan

last: Kulkarni

first: Gail

last: Kent

first: Jennifer

last: Strunck

first: Pamela

last: Cassidy


title: The anti-cancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3' processing machinery

status: Public on Jul 22 2023

city: Irvine

first: Yongsheng

address: 811 Health Sciences Rd, Med Sci B262

institute: University of California, Irvine

summary: JTE-607 is a small molecule compound with anti-inflammation and anti-cancer activities. Upon entering the cell, it is hydrolyzed to Compound 2, which directly binds to and inhibits CPSF73, the endonuclease for the cleavage step in pre-mRNA 3' processing. Although CPSF73 is universally required for mRNA 3' end formation, we have unexpectedly found that Compound 2-mediated inhibition of pre-mRNA 3' processing is sequence-specific and that the sequences flanking the cleavage site (CS) are a major determinant for drug sensitivity. By using massively parallel in vitro assays, we have measured the Compound 2 sensitivities of over 260,000 sequence variants and identified key sequence features that determine drug sensitivity.  A machine learning model trained on these data can predict the impact of JTE-607 on poly(A) site (PAS) selection and transcription termination genome-wide. We propose a biochemical model in which CPSF73 and other mRNA 3' processing factors bind to RNA of the CS region in a sequence-specific manner and the affinity of such interaction determines the Compound 2 sensitivity of a PAS. Together, our study not only characterized the mechanism of action of a compound with clinical implications, but also revealed a previously unknown sequence-specificity of the mRNA 3' processing machinery.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design:
(1). N23 MPIVA on in vitro synthesized RNA library to study sequence specificity of Compound 2, the active form of JTE-607.
(2). 4sU-seq to study transcription termination in HepG2 cells treated with DMSO or JTE-607.
(3). PAS-seq to study poly(A) site usage in HepG2 cells treated with DMSO or JTE-607

first: Liang

first: Angela

last: Yu

first: Xiuye

last: Wang

first: Georg

last: Seelig


title: Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish

status: Public on Jul 19 2023

city: xinxiang

first: chune

last: zhou

address: jian she east road 46

institute: henan normal university

summary: Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues, but their identification and organogenesis-related function have not elucidated. In this study, high-throughput sequencing was performed at three different organogenesis stages of zebrafish embryos, which were important for zebrafish muscle development. The three stages were 10 hpf (hours post fertilization) (T1), 24 hpf (T2) and 36 hpf (T3).

overall_design: To investigate the function of lncRNAs during organogenesis stages in zebrafish. We then performed gene expression profiling analysis using RNA-seq during three key organogenesis stages (10, 24, 36hpf). Differentially expressed lncRNAs were screened out and lncRNA gas5 was selected as the next research target.

first: Chune

last: Zhou

first: Xiaoyu

last: Li

first: Yaoyi

last: Sun

first: Mengting


title: ChIP-Seq analysis of switchgrass  transcriptome in response to single drought and combinations of drought and heat stress

status: Public on Jul 23 2023

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

institute: Purdue University

summary:
The combined heat and drought stress influence the plant growth and development. Switchgrass is an economically important crop due to the availability of high biomass with little water and nutrient requirements. Earlier reports suggested that switchgrass growth and yield highly influenced by heat and drought. The mechanism behind heat and drought stress is not fully understood in switchgrass. This study has undertaken to analyze the epigenetic modification using ChIP-Seq analysis with the activation histone mark H3K4me3.
Conclusion: Our study provides the first epigenomic analysis of heat and drought response in switchgrass. This comprehensive resource will provide other epigenomic regulated information in non-model plant species.

overall_design: Method: We conducted solely drought treatment in switchgrass plant Alamo AP13 by withholding water after 45 days of growing. For the combination of drought and heat effect, heat treatment (35 °C/25 °C day/night) was imposed after 72 h of the initiation of drought. Samples were collected at 0 h, 72 h, 96 h, 120 h, 144 h, and 168 h after treatment imposition, genomic DNAwas extracted, and ChIP-Seq conducted.

first: Vasudevan

last: Ayyappan

first: Malay

last: Saha

first: Rita

last: Hayford

first: Desalegn

last: Serba

first: Venkateswara

last: Sripathi

first: Mayavan

first: Jyothi

last: Thimmapuram

first: Venu

last: Kalavacharla


title: Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrids

status: Public on Jul 18 2023

city: Wuhan

first: Wenying

last: Zhong

address: Lion Rock Street

institute: Huazhong Agricultural University

summary: Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.

overall_design: Brassica napus; epigenetic; gene expression; heterosis; histone modification.


title: Nuclear Localization of Argonaute is affected by Cell Density and May Relieve Repression by microRNAs

status: Public on Jul 17 2023

city: DALLAS

first: David

middle: Reid

last: Corey

state: TX

address: 6001 Forest Park Rd

department: Pharmacology

institute: UT Southwestern Medical Center

summary: In this study, we grew WT HCT116 cells to different levels of cell density by growing them for 3 Days (50% confluent), 5 Days (250% confluent), and 7 Days (400% confluent), and we extracted whole cell RNA from cells at these different growth conditions for small RNA and whole transcriptome sequencing.

overall_design: Comparative gene expression profiling analysis of whole transcriptome sequencing data and small-RNA-sequencing data for whole cell RNA from HCT116 cells grown to varying levels of cell density or cell confluency.

first: Krystal

last: Johnson


title: Plasma microRNA ratios associated with breast cancer detection: results from a nested case-control study in an Italian population-based mammography screening cohort

status: Public on Jul 26 2023

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

type: Non-coding RNA profiling by high throughput sequencing

summary:
Mammographic breast cancer screening is effective in reducing breast cancer mortality. Nevertheless, several limitations are known. The objective of this study was to identify circulating microRNAs (miRs) ratios associated with BC in women attending mammography screening.
A nested case-control study was conducted within the ANDROMEDA cohort (women of age 46-67 attending BC screening in northern Italy), where pre-diagnostic plasma samples, information on life-styles and common BC risk factors were collected.
Small RNA sequencing was carried out on plasma samples from 65 cases and 66 controls. miR-ratios associated with BC were selected by two-sample Wilcoxon test and lasso logistic regression.
Subsequent assessment by RT-qPCR of the miRs contained in the selected miR-ratios was carried out as a platform validation. Penalized logistic regression was further applied to candidate miR-ratios alone, or in combination with non-molecular factors, to build a diagnostic model.

overall_design: Small RNA sequencing for discovery of microRNA ratios associated with BC detection analysed between BC cases and controls obtained in a screening setting. Candidate biomarker miR ratios were then validated using qRT-PCR

first: Giovanna

last: Chiorino

first: Elisabetta

last: Petracci

first: Emir

last: Sehovic

first: Ilaria

last: Gregnanin

first: Elisa

last: Camussi

first: Maurizia

last: Mello-Grand

first: Emilia

last: Riggi

first: Viviana

last: Vergini

first: Alessia

last: Russo

first: Enrico

last: Berrino

first: Andrea

last: Ortale

first: Francesca

last: Garena

first: Tiziana

last: Venesio

first: Federica

last: Gallo

first: Giuseppe

last: Matullo

first: Nereo

last: Segnan

first: Livia

last: Giordano


title: Efferocytosis by bone marrow mesenchymal stromal cells disrupts osteoblastic differentiation via mitochondrial remodeling

status: Public on Jul 14 2023

city: Rochester

first: Laura

last: Calvi

state: New York

address: 601 Elmwood Avenue

institute: University of Rochester

summary: The efficient clearance of dead and dying cells, also known as efferocytosis, is critical to maintain tissue homeostasis. In the bone marrow microenvironment (BMME), this role is primarily fulfilled by professional bone marrow macrophages, but recent work has shown that mesenchymal stromal cells (MSCs) act as a non-professional phagocyte within the BMME. However, little is known about the mechanism and impact of efferocytosis on MSCs in the BMME and on their function. To investigate this, we performed flow cytometric analysis of neutrophil uptake by ST2 cells, a murine bone marrow-derived stromal cell line, and in murine primary bone marrow-derived stromal cells. Transcriptional analysis showed that MSCs possess the necessary receptors and internal processing machinery to conduct efferocytosis, with Axl and Tyro3 serving as the main receptors, while MerTK was not expressed. Moreover, the expression of these receptors was modulated by efferocytic behavior, regardless of apoptotic target.  MSCs derived from human bone marrow also demonstrated efferocytic behavior, showing that MSC efferocytosis is conserved. In all MSCs, efferocytosis impaired osteoblastic differentiation. Transcriptional analysis and functional assays identified downregulation in MSC mitochondrial function upon efferocytosis. Experimentally, efferocytosis induced mitochondrial fission in MSCs. Pharmacologic inhibition of mitochondrial fission in MSCs not only decreased efferocytic activity but also rescued osteoblastic differentiation, demonstrating that efferocytosis-mediated mitochondrial remodeling plays a critical role in regulating MSC differentiation. This work describes a novel function of MSCs as non-professional phagocytes within the BMME and demonstrates that efferocytosis by MSCs plays a key role in directing mitochondrial remodeling and MSC differentiation. Efferocytosis by MSCs may therefore be a novel mechanism of dysfunction and senescence. Since our data in human MSCs show that MSC efferocytosis is conserved, the consequences of MSC efferocytosis may impact the behavior of these cells in the human skeleton, including osteoporosis in aging.

overall_design: ST2 cells, a bone marrow derived mesenchymal stromal cell line, were plated at 2x10^4 per cm2 in αMEM without ascorbic acid (Gibco)+ 10% FBS+1% pen-strep and incubated in normoxia at 37°C until 80% confluent.  Neutrophils were isolated from human peripheral blood via Mono-Poly resolving medium (MP Biomedicals, Inc)  according to manufacturer’s instructions and incubated at -80°C in FBS+ 10% DMSO for a minimum of 18hrs. End-stage neutrophils were washed with PBS and fluorescently labeled with 20μM eFluor670 dye (eBioscience) in PBS at 37°C for 20 min and then washed with RPMI+10% FBS+10mM HEPES to bind free dye. End-stage neutrophils were then given in excess (10:1) to plated MSCs for 3 or 24hrs. Cells were then washed 3x with PBS and collected for isolation via sorting flow cytometry analysis (BD FACSAriaII). ST2 cells and isolated neutrophils were FACS-isolated directly in RLT Plus buffer (Qiagen). RNA extraction was performed with Qiagen RNeasy PLUS Micro kit following standard operating procedures of the URMC Genomic Core. RNA quality was assessed using Agilent Bioanalyzer 2100. One nanogram of high-quality (RNA integrity number >8.0) total RNA from each sample was reverse-transcribed into cDNA using the Clontech SMART-Seq v4 Ultra Low Input RNA Kit. Final Illumina libraries were constructed using 150 pg of cDNA with the Illumina Nextera XT DNA Library Preparation Kit.

first: Emily

last: Quarato

first: Noah

last: Salama

first: Allison

middle: J

last: Li

first: Charles

middle: O

last: Smith

first: Jane

last: Zhang

first: Yuko

last: Kawano

first: Matthew

last: McArthur

first: Michael

middle: W

last: Becker

last: Elliott

first: Roman

last: Eliseev


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

overall_design: Refer to individual Series


title: Stimulation of PSTPIP1 to trigger proinflammatory responses in asymptomatic SARS-CoV-2 infections

status: Public on Jul 11 2023

first: Jinbao

last: Gu

address: No.1023, South Shatai Road

institute: Southern Medical University

summary: A hyperinflammatory response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection gravely worsens the clinical progression of coronavirus disease 2019 (COVID-19). Although the undesirable effects of inflammasome activation have been correlated to the severity of COVID-19, the mechanisms of this process in the asymptomatic infection and disease progression have not yet been clearly elucidated. Our results indicate potential preventive targets for COVID-19 disease development and progression.

overall_design: We performed strand-specific RNA sequencing in 39 peripheral blood mononuclear cell (PBMC) samples from asymptomatic individuals, symptomatic patients and healthy donors.

first: Ruili

last: Ji

first: Yue

last: Wu

first: Yuhua

last: Ye

first: Yanling

first: Yizhe

first: Guojiu

last: Zhong

first: Wentao

last: Fan

first: Chengjuan

last: Feng

first: Hui

last: Chen

first: Xiangyun

last: Teng

first: Yunli

first: Jianhua

last: Xu


title: Protein arginine methyltransferase 5 (PRMT5) is an actionable therapeutic target in CDK4/6 inhibitor-resistant ER+/RB-deficient breast cancer [RNA-seq_siPRMT5]

city: Dallas

first: Chang-Ching

last: Lin

address: 4554 Glenwick Ln, Apt 2203

department: Harold C. Simmons Comprehensive Cancer Center

summary: CDK4/6 inhibitors (CDK4/6i) have improved survival of patients with estrogen receptor-positive (ER+) breast cancer. However, patients treated with CDK4/6i eventually develop drug resistance and progress. RB1 loss-of-function alterations confer resistance to CDK4/6i, but the optimal therapy for these patients is unclear. Through a genome-wide CRISPR screen, we identified protein arginine methyltransferase 5 (PRMT5) as a molecular vulnerability in ER+/RB1-knockout (RBKO) breast cancer cells. Inhibition of PRMT5 blocked the G1-to-S transition in the cell cycle independent of RB, leading to growth arrest in RBKO cells. Proteomics analysis uncovered fused in sarcoma (FUS) as a downstream effector of PRMT5. Inhibition of PRMT5 resulted in dissociation of FUS from RNA polymerase II (Pol II), which led to Ser2 Pol II hyperphosphorylation, intron retention, and subsequent downregulation of proteins involved in DNA synthesis. Furthermore, treatment with the PRMT5 inhibitor pemrametostat and a selective ER degrader fulvestrant synergistically inhibited growth of ER+/RB-deficient cell-derived and patient-derived xenografts. These findings highlight the potential of dual ER and PRMT5 blockade as a novel therapeutic strategy to overcome resistance to CDK4/6i in ER+/RB-deficient breast cancer.

overall_design: To investigate suppresion of G1-to-S cell cycle progression upon inhibition of PRMT5, total RNA of RBKO cells transfected with a PRMT5 siRNA or control siRNA were extracted and then subjected to RNA-seq.


title: Utilizing a dual endogenous reporter system to identify functional regulators of aberrant stem cell and differentiation activity in colorectal cancer

status: Public on Jul 05 2023

first: David

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer (CRC). To identify functional mediators that regulate these key cellular programs in CRC, we developed an endogenous reporter system by genome-editing human CRC cell lines with knock-in fluorescent reporters at the SOX9 and KRT20 locus to report aberrant stem cell-like activity and differentiation respectively in pooled CRISPR screening formats. We then constructed a dual reporter system that simultaneously monitors aberrant stem cell-like and differentiation activity in the same CRC cell line, improving our signal to noise discrimination. Using a focused-library CRISPR screen targeting 78 epigenetic regulators with 542 sgRNAs, we identified factors that contribute to stem cell-like activity and differentiation in CRC. Perturbation single cell RNA sequencing (Perturb-seq) of validated hits nominated SMARCB1 of the SWI/SNF BAF complex as a negative regulator of differentiation across an array of neoplastic colon models. SMARCB1 is a dependency in CRC and required for human CRC cell line and patient-derived organoid growth in vivo. These studies highlight the utility of a biologically designed endogenous reporter system to uncover novel therapeutic targets for drug development.

overall_design: To monitor aberrant stem cell-like (SOX9) and differentiation (KRT20) programs within the same cell in colorectal cancer, we established a dual endogenous reporter cell lines by knocking in fluorescent reporters after marker genes (HT29 SOX9-mKate2/KRT20-GFP) for functional genetic screens. We then compared differential guide abundance using sgRNA read counts in each sorted cell fraction using flow cytometry (mKate2high/GFPhigh, mKate2high/GFPlow, mKate2low/GFPhigh, mKate2low/GFPlow).

first: Nilay

last: Sethi

first: Sandor

last: Spisak

first: Pornlada

last: Likasitwatanakul

first: Paul

last: Doan


title: DNA methylation changes in mice induced by mock parabiosis

status: Public on Jul 06 2023

first: Jesse

last: Poganik

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital, Harvard Medical School

summary: Aging is classically conceptualized as an ever-increasing trajectory of damage accumulation and loss of function, leading to increases in morbidity and mortality. However, recent in vitro studies have raised the possibility of age reversal. We characterized several models in which biological age, assessed primarily through analysis of DNA methylation, undergoes reversible changes. Heterochronic parabiosis is one such example.

platform_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus

overall_design: We studied a mouse model of mock parabiosis. Mouse pairs (either age-mismatched, heterochronic; or age-matched, isochronic) were subjected to sham parabiosis and maintained for 5 weeks. After this period, mice were euthanized and tissues were collected for analysis. We subjected DNA isolated from these samples to the HorvathMammalMethylChip320 for methylation profiling.

first: Bohan

last: Zhang

first: Gurpreet

last: Baht

first: Alexander

last: Tyshkovskiy

first: Amy

last: Deik

first: Csaba

last: Kerepesi

first: Sun

middle: H

last: Yim

first: Ake

last: Lu

first: Amin

last: Haghani

first: Tong

last: Gong

first: Anna

last: Hedman

first: Ellika

last: Andolf

middle: E

last: Lee

first: Alexandre

last: Trapp

first: Akshay

last: Bareja

first: Lauren

last: McKay

first: Anastasia

middle: V

last: Shindyapina

first: Sergey

last: Dmitriev

first: Gören

last: Pershagen

first: Catarina

last: Almqvist

first: Clary

middle: B

last: Clish

first: Steve

last: Horvath

first: James

middle: P

last: White

first: Vadim

middle: N

last: Gladyshev


title: Transgenic Ferret Models Define Pulmonary Ionocyte Diversity and Function

status: Public on Aug 01 2023

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

summary: Speciation leads to adaptive changes in organ cellular anatomy and physiology. These evolutionary changes create challenges for studying rare cell type functions that diverge between human and mice. Rare CFTR-rich pulmonary ionocytes exist throughout the cartilaginous airways of humans, but limited presence and divergent biology in the proximal trachea of mice has prevented the use of traditional transgenic models to elucidate ionocyte functions in the airway. Here we describe the creation and use of novel conditional genetic ferret models to dissect pulmonary ionocyte biology and function by enabling ionocyte lineage tracing (FOXI1-CreERT2::ROSA-TG), ionocyte ablation (FOXI1-KO), and ionocyte-specific deletion of CFTR (FOXI1-CreERT2::CFTRL/L). By comparing these models to cystic fibrosis (CF) ferrets, we demonstrate that ionocytes control airway surface liquid (ASL) absorption, secretion, pH, and mucus viscosity—leading to reduced ASL volume and impaired mucociliary clearance in CF, FOXI1-KO, and FOXI1-CreERT2::CFTRL/L ferrets. These processes were regulated by CFTR- dependent ionocyte transport of Cl– and HCO3–, as determined electrophysiologically and by single-cell imaging with a conditionally activated halide fluorescent sensor. Single-cell transcriptomics, using pulse-seq of lineage-traced ionocyte-enriched cultures, revealed three subtypes of pulmonary ionocytes with unique biologic functions and a common rare cell progenitor of ionocytes, tuft, and neuroendocrine cells. Thus, rare pulmonary ionocytes perform critical CFTR-dependent functions in the proximal airway that are hallmark features of CF airway disease. These studies provide a road map for using conditional genetics in the first non- rodent mammal to address gene function, cell biology, and disease processes that have greater evolutionary conservation between humans and ferrets.

overall_design: Airway epithelial cells were cultured in air-liquid interface from donor ferrets of 3 different genotypes and then isolated and profiled using single-cell RNA-sequencing. We profiled a total of 94,664 tracheal epithelial cells from WT (n=4), FOXI1-KO (n=4) and FOXI1-CreERT2::ROSA-TG (n=8) differentiated ALI cultures derived from 4 independent donor ferrets using 10X Chromium droplet-based 3’ scRNA-seq.

first: Feng

last: Yuan

first: Grace

last: Gasser

first: Evan

last: Lemire

first: Daniel

last: Montoro

first: Karthik

last: Jagadeesh

first: Yan

last: Zhang

first: Yifan

last: Duan

first: Vitaly

last: Ievlev

first: Kristen

middle: L

last: Wells

first: Pavana

middle: G

last: Rotti

first: Weam

last: Shahin

first: Michael

last: Winter

first: Bradley

last: Rosen

first: Idil

last: Evans

first: Qian

last: Cai

first: Miao

last: Yu

first: Susan

middle: A

last: Walsh

last: Acevedo

first: Darpan

last: Pandya

first: Vamsidhar

last: Akurathi

first: David

last: Dick

first: Thaddeus

last: Wadas

first: Nam

middle: S

last: Joo

first: Jeffrey

last: Wine

last: Birket

first: Courtney

last: Fernandez Petty

first: Hui

last: Leung

first: Guillermo

last: Tearney

first: Alan

last: Verkman

first: Peter

last: Haggie

first: Kathleen

last: Scott

first: Douglas

last: Bartels

last: Meyerholz

first: Steven

last: Rowe

first: Xiaoming

last: Liu

first: Ziying

last: Yan

first: Xingshen

last: Sun

first: John

middle: F

last: Engelhardt


title: RNA-seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos

city: Vienna

first: Laura

last: Lorenzo-Orts

address: Institute of Molecular Pathology (IMP), Campus Vienna Biocenter 1

country: Austria

institute: IMP

summary: To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c, we performed RNA immunoprecipitation (RIP) experiments using anti-GFP beads and transgenic embryos expressing GFP-eIF4E1b or GFP-eIF4E1c at the 8-cell stage.

overall_design: We performed differential expression gene analyses of eIF4E1b (n = 3 biological replicates) versus eIF4E1c (n = 2 biological replciates) RIP and input samples.

first: Marcus

last: Strobl

first: Andrea

last: Pauli


title: Protein arginine methyltransferase 5 (PRMT5) is an actionable therapeutic target in CDK4/6 inhibitor-resistant ER+/RB-deficient breast cancer

status: Public on Jul 10 2023

first: Chang-Ching

last: Lin


title: Ageing related deficiency of miR-708-5p in osteoarthritic cartilage lesions

city: Xi'an

first: Xu

last: Lingfeng

state: Shaanxi

address: 169 Changle West Road

institute: Air Force Medical University


title: Protein arginine methyltransferase 5 (PRMT5) is an actionable therapeutic target in CDK4/6 inhibitor-resistant ER+/RB-deficient breast cancer [pSer2 Pol II ChIP-seq]

overall_design: To investigate distribution of pSer2 Pol II bindings upon inhibition of PRMT5, ER+/RBKO cells were treated with pemrametostat or DMSO control. ChIP-seq was conducted using a pSer2 Pol II antibody.


title: TRPS1 modulates chromatin accessibility to regulate estrogen receptor (ER) binding and ER target gene expression in luminal breast cancer cells

status: Public on Jul 02 2023

city: Charlottesville

first: Thomas

state: VA

address: 1340 Jefferson Park Ave, Pinn Hall 6225

department: Biochemistry and Molecular Genetics

institute: University of Virginia


title: Assessing the impact of phagocytosis on mesenchymal-osteolineage cell function

last: Calvi

overall_design: Following sacrifice, soft tissue was removed from the bilateral tibiae, femora, and pelvic bones and bones were each cut into 3-4 pieces. Bone pieces were crushed with a mortar and pestle to release bone marrow (BM) into PBS+2%FBS. Bone marrow was passed through a 16G needle to disassociate clumps and pelleted by centrifugation of 1200 RPM for 5 min. Red blood cells were removed via incubation in RBC lysis buffer (156mM NH4Cl, 127μM EDTA, and 12mM NaHC3) for 5 minutes. BM was digested in HBSS containing collagenase type IV (1 mg/mL; Sigma), dispase (1mg/mL, Gibco), and DNase (10 units/mL, New England Biolabs) for 35 min at 37°C. Digested BM was filtered through a 100 µM cell strainer (Corning) and washed with PBS+2%FBS. Cell numbers were determined using the TC20 Automated Cell Counter (Biorad) and Trypan Blue (Sigma-Aldrich) to exclude dead cells. A two-step approach was used to remove hematopoietic cells, first via magnetic-depletion and second via fluorescence-activated cell sorting (FACS). For magnetic-depletion of hematopoietic populations, BM was labeled with biotinylated antibodies against CD45 and lineage markers (Ter119, B220, CD3e, and Gr1) followed by secondary labeling with streptavidin-conjugated magnetic particles (IMag Streptavidin Particles Plus-DM, BD Biosciences). BM was incubated on the BD IMagnet to magnetically separate CD45+ and lineage+ hematopoietic cells from the non-hematopoietic fraction enriched for stromal cells. The stromal cell-enriched fraction was then labeled with PE-CF594 streptavidin, PerCP-Cy5.5 lineage antibodies, APC-Cy7 CD45, FITC CD31, and PE CD51. Cells were labeled with DAPI to exclude dead cells and FACS-purified using a FACSAria II (BD Biosciences) to remove residual hematopoietic cells (lineage+ and/or CD45+) and endothelial cells (CD31+) to obtain lineage- CD45- CD31- CD51+ marrow stromal cells. Sorted marrow stromal cells were seeded in 12-well plates at 1000 cells/cm2 in αMEM (ascorbic acid-free) +10%FBS+1%P/S and incubated in 2%O2/5%CO2/37°C. Media was changed on day 4 of culture initiation and every 3-4 days thereafter. Upon reaching confluence, cells were passaged and expanded in 6-well plates. For passaging, cultures were washed with PBS and treated with TrypLE Express (ThermoFisher Scientific) to detach cells. Equivalent volume of culture media was added and cells were re-plated at ratios ranging from 1:5 to 1:10. Marrow stromal cells were used at passage 2 or 3 for experiments. In all stromal cultures, flow cytometry was used to assess expression of hematopoietic and macrophage markers (lineage, CD45, CD11b, F4/80), endothelial markers (CD31), and stromal markers (CD51, Sca1, CD140a) and confirmed lack of contamination with macrophages and endothelial cells (data not shown). Marrow stromal cultures were grown in 6-well plates prepared as described above. Each well was pre-treated with 1 mL of media containing 5x106 apoptotic thymocytes/well. Primary murine apoptotic thymocytes were isolated and prepared as previously published (46), fluorescently labeled with 20nM efluro670 (ThermFischer) according to manufacturer’s instructions. Culture plates were centrifuged for 40s at 100xg and incubated in 5%O2/5%CO2/37°C for 24hr. Control cultures received no target. Stromal cells were washed 3-6x with PBS to remove non-engulfed phagocytic targets. Treated and control cells were then washed 3x with PBS and then collected by FACS-isolated directly in RLT Plus buffer (Qiagen). Both populations were sorted and control as well as target+ cells were isolated.

first: Emily

middle: R

last: Quarato

first: Noah

last: Salama

first: Allison

last: Li

first: Charles

last: Smith

first: Jane

last: Zhang

first: Yuko

last: Kawano

first: Matthew

last: McArthur

first: Michael

last: Becker

last: Elliott

first: Roman

last: Eliseev

middle: M


title: Evaluating The Infinium Human MethylationEPIC v2 BeadChip

status: Public on Jul 04 2023

city: Philadelphia

first: Wanding

last: Zhou

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

type: Methylation profiling by genome tiling array

summary: We conducted a comprehensive evaluation of the updated Infinium MethylationEPIC v2 BeadChip (EPICv2). Our evaluation revealed that EPICv2 offers significant improvements over its predecessors, including expanded enhancer coverage, applicability to diverse ancestry groups, support for low-input DNA down to one nanogram, coverage of existing epigenetic clocks, cell type deconvolution panels, and human trait associations, while maintaining accuracy and reproducibility.

overall_design:
Cell line (GM12878, K562, LNCaP, HCT116 and derivative cell lines) DNA and methylation control DNA is run on EPIC and/or EPICv2 BeadChips to evaluate EPICv2 reproducibility, accuracy, performance at low input ranges, and capability at capturing biological methylation variation.

Please note that *control* samples are DNA ordered from EpigenDx. The exact cell line source is unknown (i.e. mixed cell line-derived DNA).

The study is published at
Comprehensive evaluation of the Infinium human MethylationEPIC v2 BeadChip
D Kaur, SM Lee, D Goldberg, NJ Spix, T Hinoue, HT Li, VB Dwaraka, ...
Epigenetics Communications 3 (1), 6

first: Diljeet

last: Kaur

first: Peter

last: Laird


title: TRPS1 modulates chromatin accessibility to regulate estrogen receptor (ER) binding and ER target gene expression in luminal breast cancer cells (ATAC-Seq)

last: Scott

summary: Breast cancer is the most frequently diagnosed cancer in women. The most common subtype is luminal breast cancer, which is typically driven by the estrogen receptor alpha (ER), a transcription factor (TF) that activates many genes required for proliferation. Multiple effective therapies target this pathway, but individuals often develop resistance. Thus, there is a need to identify additional targets that regulate ER activity and contribute to breast tumor progression. TRPS1 is a repressive GATA-family TF that is overexpressed in breast tumors. Common genetic variants in the TRPS1 locus are associated with breast cancer risk, and luminal breast cancer cell lines are particularly sensitive to TRPS1 knockout. However, we do not know how TRPS1 regulates target genes to mediate these breast cancer patient and cellular outcomes. We introduced an inducible degron tag into the native TRPS1 locus within a luminal breast cancer cell line to identify the direct targets of TRPS1 and determine how TRPS1 mechanistically regulates gene expression. We acutely deplete over eighty percent of TRPS1 from chromatin within 30 minutes of inducing degradation. We find that TRPS1 regulates transcription of hundreds of genes, including those related to estrogen signaling. TRPS1 directly regulates chromatin structure, which causes ER to redistribute in the genome. ER redistribution causes direct repression of ER targets and indirectly activates dozens of ER target genes. Downstream from these primary effects, TRPS1 depletion represses cell cycle-related gene sets and reduces cell doubling rate. Finally, we show that high TRPS1 activity, calculated using a gene expression signature defined by primary TRPS1-regulated genes, is associated with worse breast cancer patient prognosis. Taken together, these data suggest a model in which TRPS1 modulates the activity of other TFs, both activating and repressing transcription of genes related to cancer cell fitness.

overall_design: T47D cells with TRPS1 tagged with an inducible degron tag were treated with drugs to induce TRPS1 degradation for 0, 0.5, 1, 2, 4, and 24 hours, and collected for ATAC-seq

last: Guertin


title: Characterization of the distribution and dynamics of chromatin states in the C. elegans germ line reveals substantial H3K4me3 remodeling during oogenesis

status: Public on Jul 03 2023

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

summary: Chromatin organization in the C. elegans germ line is tightly regulated and critical for germ cell differentiation. While certain germline epigenetic regulatory mechanisms have been identified, how they influence chromatin structure and ultimately gene expression remains unclear, in part because most genomic studies have focused on data collected from whole worms. We therefore analyzed publicly available histone modification and chromatin accessibility data from isolated undifferentiated germ nuclei to define chromatin states. We then correlated these states with overall transcript abundance, spatio-temporal expression patterns, and the function of small RNA pathways. Because the essential role of the germ line is to transmit genetic information to the next generation and establish gene expression in the early embryo, we compared epigenetic and transcriptomic profiles from undifferentiated germ cells, oocytes, and embryos to define the epigenetic changes during this developmental transition. The active histone modification H3K4me3 exhibits particularly dynamic remodeling as germ cells differentiate into oocytes, with implications for establishing transcriptional activation of essential genes during early embryogenesis. Our results highlight the dynamism of the chromatin landscape in germ cells, and provide a resource for future investigation into epigenetic regulatory mechanisms.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K4me3 of early embryos in C. elegans.

first: Mazzetto

last: Mariateresa

first: Lauren

last: Gonzalez

first: Sanchez

last: Nancy


title: Non-coding autoimmune risk variant accelerates T peripheral helper cell development via ICOS

status: Public on Jul 01 2023

last: Nigrovic

address: 1 Blackfan Cir Bldg 10004C, Karp Research

department: Immunology

institute: Boston Children's Hospital

summary: Fine-mapping and functional studies implicate rs117701653, a common non-coding variant in the CD28/CTLA4/ICOS locus, as a contributor to risk for rheumatoid arthritis and type 1 diabetes.  Using DNA pulldown, mass spectrometry, genome editing and eQTL analysis, we establish that the disease-associated allele reduces affinity for the inhibitory chromosomal regulator SMCHD1 to drive expression of inducible T-cell costimulator (ICOS), enhancing memory CD4+ T cell ICOS expression in individuals bearing the risk allele. Higher ICOS expression is paralleled by an increase in circulating T peripheral helper (Tph) cells, and in rheumatoid arthritis patients, of blood and joint fluid Tph cells and circulating plasmablasts, suggesting a causal link. Indeed, ICOS ligation accelerates T cell differentiation into CXCR5-PD-1high Tph cells producing IL-21 and CXCL13, as does carriage of the rs117701653 risk allele. Thus, mechanistic dissection of a causal non-coding variant in human autoimmunity discloses a new pathway through which ICOS regulates Tph abundance.

overall_design:
To establish whether SNP rs117701653 is associated with transcription of a gene in the CD28/CTLA4/ICOS locus,  we performed Row-input RNA-seq in resting total CD4+ T cells from 24 healthy subjects with 8 A/A, 8 A/C, and 8 C/C genotypes at rs117701653.
----------------------------
Authors state:
We would like to submit the raw data to dbGAP as soon as possible. Therefore, we have not included the raw data in this GEO submission.

first: Taehyeung

last: Kim

first: Marta

last: Martínez-Bonet


title: Ageing related deficiency of miR-708-5p in osteoarthritic cartilage lesions [miRNA]

first: Xu

last: Lingfeng

summary: Aging is a major risk factors for osteoarthritis (OA), and cartilage of the elder are more sensitive to mechanical loading stress. Recently, cartilage progenitor cells (CPCs) arose much interests due to its important role in maintaining cartilage homeostasis. However, the potential mechanism of increased sensitivity to mechanical stress in CPCs has not been elucidated. The aim of this study was to investigate the potential links between aging and age-related OA through establish CPCs replicative senescence model and fluid flow shear stress (FFSS) stimulated degeneration model. Small RNA and mRNA sequence were conducted to investigate miRNA-related mechanisms in this process. By gain-and-lost strategy we investigated the age-related miRNAs and their impacts on exacerbating the progression of biomechanical stimulated TMJ-OA. miR-708-5p was identified as age-related miRNA in CPCs, and TLR4 was identified as its direct target through luciferase report assay. Age-related miR-708-5p deficiency increased sensitivity of CPCs for exposure to FFSS by liberating TLR4 expression. Intra-articular delivery agomiR-708-5p alleviated TMJ osteoarthritic cartilage lesions in mice. In conclusion, age-related miR-708-5p deficiency increases the sensitivity to mechanical loading stress and promotes CPCs senescence like degeneration via TLR4.

overall_design: To investigated the common mechanism between replicative senescence and abberant mechanical stress induced senescence like degeneration of cartilage progenitor cells (CPCs), we established replicative senescence model and flow fluid shear stress induced degeneration model of CPCs in vitro. We choosed CPCs of Passage 3 as control group, CPCs of passage 9 as replicative senescence group, and FFSS treated P3 CPCs as FFSS induced degeneration group. Then we performed RNA-seq and miRNA-seq .

first: Lingfeng

last: Xu

first: Yuejiao

last: Zhang

first: Meiqing

last: Wang


title: TRPS1 modulates chromatin accessibility to regulate estrogen receptor (ER) binding and ER target gene expression in luminal breast cancer cells (Time course PRO-seq)

first: Thomas

overall_design: T47D cells with TRPS1 tagged with an inducible degron tag were treated with drugs to induce TRPS1 degradation for 0, 0.5, 1, 2, 4, and 24 hours, and collected for PRO-seq


title: Macrophages reprogramming improves immunotherapy of IL-33 in peritoneal metastasis of gastric cancer

status: Public on Jun 30 2023

city: Nanjing

first: Keying

last: Che

address: 321 Zhongshan Road

institute: Nanjing Drum Tower Hospital

summary: Peritoneal metastasis (PM) has a suppressive tumor immune microenvironment (TIME), which limits the effects of immunotherapy. This study aims to investigate the immunomodulatory effects of intraperitoneal administration of IL-33 on PM-associated TIME. Immunocompetent mice were used to investigate the role of IL-33 in development of abdominal dissemination and host outcome. Murine (m) and human (h) gastric cancer cells were tested for their response to IL-33 by qRT-PCR, flow cytometry, and immunofluorescence. Survival was significantly prolonged in patients with high Il-33 mRNA expression. Intraperitoneal administration of IL-33 could induce the celiac inflammatory environment, activate immunologic effector cells and reverse the immunosuppressive tumor microenvironment, which delayed tumor progression and peritoneal metastasis of gastric cancer. Mechanistically, IL-33 could induce M2 polarization by activating p38-GATA-binding protein 3 (GATA3) signaling pathway. IL-33 combined with anti-CSF1R or p38 inhibitor to regulate tumor-associated macrophages (TAMs) showed synergistic anti-tumor effect. Intraperitoneal administration of IL-33 inducing local inflammatory milieu provided a novel approach for the treatment of metastatic peritoneal malignancies, which combined with TAMs reprogramming to reshape TIME could achieve better treatment efficacy.

overall_design: To investigate the immunomodulatory effects of intraperitoneal administration of IL-33 on peritoneal metastasis-associated tumor immune microenvironment, we established abdominal dissemination tumor model by challenging 615-line mice with mouse forestomach carcinoma cells.

first: Jia

last: Wei


title: Protein arginine methyltransferase 5 (PRMT5) is an actionable therapeutic target in CDK4/6 inhibitor-resistant ER+/RB-deficient breast cancer [RNA-seq_RBKO vs WT]

first: Chang-Ching

last: Lin

overall_design: To compare gene expression profiles between RBKO and WT, total RNA of RBKO and WT cells were extracted and then subjected to RNA-seq.


title: Protein arginine methyltransferase 5 (PRMT5) is an actionable therapeutic target in CDK4/6 inhibitor-resistant ER+/RB-deficient breast cancer [RNA-seq_Pemrametostat]

overall_design: To investigate RNA splicing alteration upon inhibition of PRMT5, ER+/RBKO cells were treated with pemrametostat or DMSO control. Total RNA were then extracted and subjected to RNA-seq.


title: Ageing related deficiency of miR-708-5p in osteoarthritic cartilage lesions [RNA]


title: Next generation sequencing facilitates quantitative analysis of colonic tissue from miR-7 deficiency and WT mice with IBD mice, and human colonic epithelial cells transfected-with NC/miR-7 inhibitor/miR-7 inhibitor plus Erlotinib following LPS treatment

city: Zunyi

first: Juan

middle: Juan

last: Zhao

state: Guizhou

address: 6 Xuefu west Road

institute: Zunyi medical University

summary: Methods: Colon tissue from 8-10-Week wild-type (WT) and miR-7 deficiency mice with DSS treatment, and  miR-7 inhibitor/NC-transfected-FHC cells and Erlotinib plus miR-7 inhibitor-transfected-FHC cells  with LPS treatment,  mRNA profiles of which were generated by deep sequencing, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: mRNA profiles of colon tissue from 8-10-Week wild-type (WT) and miR-7 deficiency mice with DSS treatment, and mRNA profiles of miR-7 inhibitor/NC-transfected-FHC cells and Erlotinib plus miR-7 inhibitor-transfected-FHC cells  with LPS treatment,

first: Juanjuan

first: Lin


title: Epigenetic landscape of Human Brains by Single Nucleus DNA Methylation and Chromatin Conformation Profiling - pool117_h1930004_TH-TL

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating the cellular architecture of the human brain is critical to understanding its diverse functions and complex animal behaviors. Single nucleus methylation sequencing was applied to regions of human brains. we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster.

overall_design: Apply snmC-seq3 to brain regions to identify epigenomic landcape of the adult human brains

first: Wei

last: Tian

first: Anna

last: Bartlett

first: Hanqing

last: Liu

first: Jordan

last: Altshul

first: Rosa

last: Castanon

last: Nery

first: Huaming

last: Chen


title: Use of a combined antibacterial synergy approach and the ANNOgesic tool to identify novel targets within the gene networks of multidrug-resistant Klebsiella pneumoniae

city: Seodaemun-gu, Seoul

first: Dongeun

last: Yong

address: 50-1 Yonsei-ro

country: South Korea

institute: Yonsei University College of Medicine

summary: To investigate of phenotypic effects of antibacterial synergy and gene expression analysis

overall_design: 4 different conditions were analyzed without replicates (1 control, 2 single treatment, 1 combination treatment)

first: Sung-Huan

last: Yu

first: Jungeun

last: Shim

first: Hyunsook

last: Lee


title: G4-DNA Formation and Chromatin Remodelling are Interdependent in Human Cells [ATAC-seq]

status: Public on Jun 28 2023

city: Perth

first: Nicholas

last: Lawler

state: Western Australia

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

summary: DNA G-quadruplexes (G4s) have been identified as important biological targets for transcriptional, translational, and epigenetic regulation. The stabilisation of G4s with small molecule ligands has emerged as a technique to regulate gene expression and as a potential therapeutic approach for human diseases. Here, we demonstrate that ligand stabilisation of G4s causes altered chromatin accessibility dependant on the targeting specificity of the molecule. In particular, stabilisation of a target G4 using the highly specific GTC365 ligand resulted in differential accessibility of 61 genomic regions, while the broad targeted GQC-05 ligand stabilised many G4s and induced a global shift towards increased accessibility of gene promoter regions. Interestingly, while we observed distinct effects of each ligand on RNA expression levels and the induction of DNA double-stranded breaks, both ligands modified DNA damage response pathways. Our work represents the dual possibility of G4-stabilising ligands for specific or global chromatin modulation via unique targeting characteristics.

overall_design: To investigate the potential for G4 stabilisation to alter chromatin organisation and subsequent gene expression, we treated MCF-7 cells with GQC-05 and GTC365 G4-stabilising ligands and then performed ATAC- and RNA-seq.

first: Arnold

last: Ou

first: Jessica

middle: J

last: King

first: Cameron

last: Evans

first: K

last: Iyer

first: Nicole

last: Smith


title: Genomic profiling of the overlap phenotype between psoriasis and atopic dermatitis

status: Public on Jun 24 2023

city: Sacramento

first: JAEHWAN

last: KIM

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

summary: Clinical overlaps between psoriasis and atopic dermatitis are sometimes undiscernible, and there is no consensus whether to treat the overlap phenotype as psoriasis or atopic dermatitis. We enrolled patients diagnosed with either psoriasis or atopic dermatitis, and clinically re-stratified them into classic psoriasis, classic atopic dermatitis, and the overlap phenotype between psoriasis and atopic dermatitis. We compared gene expression profiles of lesional and nonlesional skin biopsy tissues between the three comparison groups. Global mRNA expression and T-cell subset cytokine expression in the skin of the overlap phenotype were consistent with the profiles of psoriasis and different from the profiles of atopic dermatitis. Unsupervised k-means clustering indicated that the best number of distinct clusters for the total population of the three comparison groups was two, and the two clusters of psoriasis and atopic dermatitis were differentiated by gene expression. Our study suggests that clinical overlap phenotype between psoriasis and atopic dermatitis has dominant molecular features of psoriasis, and genomic biomarkers can differentiate psoriasis and atopic dermatitis at molecular levels in patients with a spectrum of psoriasis and atopic dermatitis.

overall_design: Whole tissue samples of 20 atopic dermatitis (10 lesional and 10 nonlesional),  33 overlap phenotype of atopic dermatitis and psoriasis (17 lesional and 16 nonlesional), 16 psoriasis (9 lesional and 7 nonlesional), and 6 normal skin (including GSE78097 data) were obtained via skin biopsy and subjected to microarray analysis.

first: James

last: Krueger

first: Jaehwan

last: Kim

first: Jeong


title: A common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PDKCC during chondrogenesis [HiChIP]

status: Public on Jun 23 2023

city: Stanford

first: Jaaved

last: Mohammed

address: 265 Campus Drive

department: Chemical and Systems Biology

institute: Stanford University

summary: Genome-wide association studies (GWAS) identified thousands of genetic variants linked to phenotypic traits and disease risk. However, mechanistic understanding of how GWAS variants influence complex morphological traits and can, in certain cases, simultaneously confer normal-range phenotypic variation and disease predisposition, is still largely lacking. Here, we focus on rs6740960, a single nucleotide polymorphism (SNP) at the 2p21 locus, which in GWAS studies has been associated both with normal-range variation in jaw shape and with an increased risk of non-syndromic orofacial clefting. Using in vitro derived embryonic cell types relevant for human facial morphogenesis, we show that this SNP resides in an enhancer that regulates chondrocytic expression of PKDCC - a gene encoding a tyrosine kinase involved in chondrogenesis and skeletal development. In agreement, rs6740960 SNP is sufficient to confer a large difference in acetylation of its cognate enhancer preferentially in chondrocytes. By deploying dense landmark morphometric analysis of skull elements in mice, we show that changes in Pkdcc dosage are associated with quantitative changes in maxilla, mandible, and palatine bone shape that are concordant with the facial phenotypes and disease predisposition seen in humans. We further demonstrate that the frequency of the rs6740960 variant strongly deviated among different human populations, and that the activity of its cognate enhancer diverged in hominids. Our study provides a mechanistic explanation of how a common SNP can mediate normal-range and disease-associated morphological variation, with implications for the evolution of human facial features.

overall_design: We performed H3K27ac HiChIP experiments in order to identify enhancer-promoter 3D interactions in in vitro derived cranial neural crest cells (CNCCS) and cranial chondrocytes.

first: Neha

last: Arora

first: Tomek

last: Swigut

first: Joanna

last: Wysocka


title: A common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PDKCC during chondrogenesis

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

overall_design: Refer to individual Series


title: Functional identification of protocadherin alpha 9 (PCDHA9) as a candidate causative gene for amyotrophic lateral sclerosis

city: Beijing

first: Dan

last: Zhang

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: Genes associated with amyotrophic lateral sclerosis (ALS) are identified in ~15% of sporadic cases. Pcdhα9 mouse mutants carrying the corresponding point mutation or deletion mutation manifested a progressive decline in survival and motor function (paralysis) caused by loss of spinal motor neurons, significant muscle atrophy, and structural/functional abnormalities of the neuromuscular junction. Potential causes of defects in mutant mice predicted by single nucleus RNA-seq and ATAC-seq.

overall_design: scRNA-seq; snATAC-seq

first: Jie

last: Zhong

first: Chaodong

last: Wang

first: Xiaoli

last: Yao


title: Characterization of naive CD4 T cells deficient for Foxo1 expression in T cells

status: Public on Jun 21 2023

city: Paris

first: sebastien

last: jacques

address: 24 rue du faubourg saint jacques

department: Genomic

country: France

institute: Institut Cochin

summary: Naive CD4 T cells lacking Foxo1 expression exhibit an altered transcriptional signature.

overall_design: CD4 T cells from peripheral lymph-nodes of mice deficient (C57BL/6-Foxp3GFP Foxo1TKO) or proficient (C57BL/6-Foxp3GFP Foxo1Ctrl) for Foxo1 expression in T cells were first purified by depleting B cells and CD8 T cells. Then, Naive CD4 T cells were FACS-sorted as CD44-/low GFP- Lin- cells and mRNAs extracted.

first: Bruno

last: Lucas

first: Aurélie

last: Durand


title: The RNAome of the extracellular vesicles derived from THP-1 cells

status: Public on Jun 20 2023

city: Auckland

first: Xinyi

last: Sun

address: 85 Park Road, Grafton

country: New Zealand

institute: the university of auckland

summary: To investigate the cargos in extracellular vesicles derived from THP-1 cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for extracellular vesicles derived from first trimester placentae and THP-1 cells.

first: Qi

last: Chen


title: A spatially resolved single cell genomic atlas of the adult human breast [scRNA_cells]

status: Public on Jun 29 2023

city: Houston

first: Nicholas

last: Navin

address: 6767 Bertner Ave

department: System Biology

institute: MD Anderson Cancer Center

summary: The adult human breast comprises an intricate network of epithelial ducts and lobules that are embedded in connective and adipose tissue. While most previous studies have focused on the breast epithelial system, many of the non-epithelial cell types remain understudied. Here, we constructed a comprehensive Human Breast Cell Atlas (HBCA) at single-cell and spatial resolution.  Our single-cell transcriptomics data profiled 714,331 cells from 126 women, and 120,024 nuclei from 20 women, identifying 12 major cell types and 58 biological cell states.  These data revealed abundant pericyte, endothelial and immune cell populations, and highly diverse luminal epithelial cell states.  Spatial mapping using four different technologies revealed an unexpectedly rich ecosystem of tissue-resident immune cells, as well as distinct molecular differences between ductal and lobular regions.  Collectively, these data provide an unprecedented reference of the adult normal breast tissue for studying mammary biology and diseases such as breast cancer.

overall_design: This data provides an unprecedented atlas of the normal cell types and cell states in the human breast, that will serve as an important reference for studying breast development and diseases such as breast cancer.

first: T

last: Kumar

first: K

last: Nee

first: R

last: Wei

last: Kessenbrock

first: N


title: TRPS1 modulates chromatin accessibility to regulate estrogen receptor (ER) binding and ER target gene expression in luminal breast cancer cells (ChIP-Seq)

first: Thomas

last: Scott

overall_design: T47D cells with TRPS1 tagged with an inducible degron tag were treated with drugs to induce TRPS1 degradation (or a DMSO vehicle control) for 30 minutes, and collected for ChIP-seq

first: Michael

last: Guertin


title: A spatially resolved single cell genomic atlas of the adult human breast

first: Tapsi

first: Kevin

first: Runmin

first: Kai


title: Development of Drosophila Midgut

status: Public on Jun 13 2023

city: Windsor

first: Phillip

last: Karpowicz

state: ON

address: 401 Sunset Avenue

department: Biomedical Sciences

country: Canada

institute: University of Windsor

summary: Investigating circadian clock activity in the pupal and adult midgut

overall_design: Three experimental groups: pupa, immature adult, and adult

first: Kathyani

last: Parasram


title: Rapid Attenuation of B-Cell and Interferon Gamma Associated Chemokines in Clinical Responders to Janus Kinase Inhibition with Upadacitinib in Hidradenitis Suppurativa.

status: Public on Jun 18 2023

city: Liverpool

first: John

last: Frew

address: Elizabeth St

institute: Liverpool Hospital

summary: Serum Proteomic Analysis of patients with Hidradenitis Suppurativa treated with 15mg daily of Upadacitinib. Samples from Week 0 and Week 4 of therapy, Straficied by clinical response.

overall_design: Retrospective Cohort Study

first: J


title: mTert induction in p21-positive cells counteracts capillary rarefaction and pulmonary emphysema

city: MARSEILLE CEDEX 09

first: Christelle

last: Cayrou

address: 27 Boulevard Lei Roure

institute: CRCM

summary: Lung diseases develop when telomeres are shortened beyond a critical point. We have constructed a mouse model in which the catalytic subunit of telomerase (mTert), or its catalytically inactive form (mTertCI), is expressed from the p21Cdkn1a promoter. We found that this particular expression of mTert reduces senescence of endothelial cells (EC) in lungs of aged mice, as well as emphysema and pulmonary perivascular fibrosis. We also show that mTert counteracts the decline in capillary density in aged mice and promotes the maintenance of high numbers of Cd34+ cells, identified as a subclass of endothelial cells with proliferative capacity. In line with these results, young p21+/Tert mice treated with a VEGF receptor inhibitor combined with hypoxia are also protected against senescence and emphysema induced by this treatment. The catalytic activity of mTert is required for all the effects observed. However, and unexpectedly, we found that both mTert and mTertCI expression significantly reduced p21 levels in the lungs of aged mice. mTert thus protects against age-related and induced loss of capillary vessels and subsequent lung emphysema.

overall_design:
Droplet-based single-cell RNA-sequencing on 3 samples of total cells from mouse lung tissue. Three genotypes were simultaneously analyzed.

Single-cell 3'-RNA-Seq samples were prepared using single cell V2 reagent kit and loaded in the Chromium controller according to standard manufacturer protocol (10x Genomics, PN-120237) to capture 6.000 cells. Briefly, dissociated lung cells are encapsulated using microfluidic device. RNAs are captured on beads coated of oligos containing an oligo-dTTT, UMIs and a specific barcode. After reverse transcription, cDNAs are washed, PCR-amplified and washed again before analysis on a Bioanalyzer (Agilent) for quality control. Finally, libraries are prepared following standard Illumina protocol and sequenced on a NovaSeq sequencer (Illumina). Raw sequences are demultiplexed and reads are mapped onto the mm10 reference genome using the v2.3 Cell Ranger pipeline (10X Genomics) to generate a count matrix for each sample. The digital matrices were filtered by cell type (on clusters composed of the same cell type), to remove low-quality cells with low UMI counts and cells with relatively high mitochondrial DNA content. Outlier analysis was performed with perCellQCMetrics from the scatter package. An upper cutoff was manually determined for each sample based on a plot of gene count versus UMI count or % of mito-chondrial genes, to have at least 1000 UMIs, number of transcripts ranging between 1000 and 30000 and at most 14% mitochondrial transcripts. The quality was consistent across samples, and differences in RNA and gene content could be ascribed to cell-type-specific effects. DGE matrices from all sam-ples, sequenced at different time, were then merged and subsequently normalized using the deconvo-lution normalization method in the scran R package in order to correct for differences in read depth and library size inside and between samples.

first: Vincent

last: Geli

first: Charles

last: Fouillade

first: Sandra

last: Curras-Alonso


title: G4-DNA Formation and Chromatin Remodelling are Interdependent in Human Cells [RNA-seq]

first: Nicholas

last: Lawler

first: Arnold

last: Ou

first: Jessica

last: King

first: Cameron

last: Evans

first: K

last: Iyer

first: Nicole

last: Smith


title: Newly repopulated spinal cord microglia exhibit a unique transcriptome and contribute to pain resolution (mouse)

status: Public on Jun 09 2023

first: Vivianne

last: Tawfik

state: California

address: 1291 Welch Road, Grant Building S007

department: Anesthesiology, Perioperative and Pain Medicine

summary: Microglia contribute to the initiation of pain, however, a translationally viable approach addressing how or when to modulate these cells remains elusive. We used a targeted, inducible, genetic microglial depletion strategy at both acute and acute-to-chronic transition phases in the clinically-relevant tibial fracture/casting pain model to determine the contribution of microglia to the initiation and maintenance of pain. We observed complete resolution of pain which coincided with the timeframe of full repopulation of microglia after transient microglial depletion at the acute-to-chronic phase. These repopulated microglia were morphologically distinct from control microglia, signifying they may exhibit a unique transcriptome. RNA sequencing of repopulated spinal cord microglia identified genes of interest using weighted gene coexpression network analysis (WGCNA). We intersected these genes with a newly generated single nuclei microglial dataset from human spinal cord dorsal horn and identified human-relevant genes that may ultimately promote pain resolution after injury. This work presents a novel approach to gene discovery in pain and provides comprehensive datasets for the development of future microglial-targeted therapeutics.

overall_design: Cx3Cr1-Cre x Rosa26-iDTR mice were injected with tamoxifen followed by diphtheria toxin to transiently deplete microglia. Microglia were isolated via fluorescence activated cell sorting and then RNA sequencing was executed. Replicates per group ranged from n=2 to n=7.

first: Lauren

last: Donovan

first: Caldwell

last: Bridges

first: Amy

last: Nippert

first: Meng

last: Wang

first: Shaogen

last: Wu

first: Thomas

last: Forman

first: Elena

last: Haight

first: Sabrina

last: Bond

first: Nolan

last: Huck

first: Claire

last: Jordan

first: Aysha

last: Gardner

first: Ramesh

last: Nair

first: Tawfik

last: Vivianne


title: Activation of adult human pancreatic ductal and ductal progenitor-like cells requires extracellular matrix protein signaling [scRNA-seq]

status: Public on Jun 05 2023

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: Ductal progenitor-like cells are a subpopulation of ductal cells in the adult human pancreas that have the potential to contribute to regenerative medicine. However, the microenvironmental cues that regulate their activation are poorly understood. Here, we establish a 3-dimensional suspension culture system containing six defined soluble factors in which primary human ductal and ductal progenitor-like cells can survive but do not proliferate. Expansion and polarization occur when cells are provided with a low concentration (5% v/v) of Matrigel, a sarcoma cell product enriched in many extracellular matrix (ECM) proteins. Screening of ECM proteins identified that collagen IV is capable of partially recapitulating the effects of Matrigel. Inhibition of integrin α1β1, a major collagen IV receptor, negates collagen IV- and Matrigel-stimulated effects. These results demonstrate that collagen IV is a key ECM protein that stimulates the expansion and polarization of human ductal and ductal progenitor-like cells via integrin α1β1 receptor signaling.

overall_design: Single-cell RNA-sequencing of primary adult human pancreatic cells cultured in 3D suspension for 3 or 7 days. The cells were derived from a freshly dissociated, islet-depleted exocrine tissue that was either directly placed into culture or was first cryopreserved before culture.

first: Heather

last: Zook

first: Janine

middle: C

last: Quijano

first: Min-Hsuan

last: Chen

middle: T


title: Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development

city: Seville

first: José

middle: M.

last: Santos-Pereira

address: Avda. Manuel Siurot s/n

institute: IBiS, Universidad de Sevilla-CSIC


title: G4-DNA Formation and Chromatin Remodelling are Interdependent in Human Cells

first: Nicholas

last: Lawler