title: 68Ga-FAPI PET imaging assesses tumor immunity and guides TGF-β inhibition to sensitize metastatic colorectal cancer to immunotherapy

city: Shanghai

first: Jiwei

last: Chen

address: 130 DongAn Road

institute: Fudan University

summary: BACKGROUND. Improving and predicting tumor response to immunotherapy remains challenging. Combination therapy with a transforming growth factor β (TGF-β) inhibitor that targets cancer associated fibroblasts (CAFs) is promising to enhance efficacy of cancer immunotherapies. However, the effect of this approach in clinical trials is limited, requiring in vivo methods to better assess tumor responses to combination therapy. METHODS. We measure CAFs in vivo using gallium 68-labeled fibroblast activation protein inhibitor (68Ga-FAPI) for PET/CT imaging to guide TGF-β inhibition and sensitize metastatic colorectal cancer (CRC) to immunotherapy. A total of 131 patients with metastatic CRC underwent 68Ga-FAPI and 18F-fludeoxyglucose (18F-FDG) PET/CT imaging. Fourteen patients underwent surgery after the imaging. Relationship between uptake of 68Ga-FAPI and tumor immunity was analyzed. Mouse cohorts of metastatic CRC were treated with TGF-β receptor (TGF-βR) inhibitor combined with KN046 which blocks PD-L1 and CTLA4, followed with 68Ga-FAPI and 18F-FDG micro-PET/CT imaging to assess tumor responses. RESULTS. Patients with metastatic CRC demonstrated high uptakes of 68Ga-FAPI, along with suppressive tumor immunity and poor prognosis. TGF-βR inhibitor enhanced tumor infiltrating T cells and significantly sensitized metastatic CRC to KN046. 68Ga-FAPI PET/CT imaging accurately monitored the dynamical changes of CAFs and tumor response to combined TGF-βR inhibitor with immunotherapy. CONCLUSION. 68Ga-FAPI PET/CT imaging is powerful in assessing tumor immunity and response to immunotherapy in metastatic CRC. This study supports future clinical application of 68Ga-FAPI PET/CT to stratify and guide patients with CRC for precise TGF-β inhibition plus immunotherapy, recommending 68Ga-FAPI and 18F-FDG dual PET/CT for CRC management.

overall_design: RNA-seq on tumor tissues isolated from mice bearing MC38 liver metastasis treated with PBS control, TGF-βR1 inhibitor SB525334, PD-L1/CTLA4 inhibitor KN046, combination of SB525334 and KN046.

first: Ke

last: Li

first: Shuang

last: Tang


title: Inhibition of UV-Induced Stress Signaling and Inflammatory Responses in SKH-1 Mouse Skin by Topical Small Molecule PD-L1 Blockade

status: Public on Dec 19 2023

city: Tucson

first: Georg

middle: Thomas

last: Wondrak

state: Arizona

address: UA Cancer Center, 1515 N Campbell Ave, Room 3971

department: Pharm/Tox

country: USA

institute: University of Arizona

summary: The immune checkpoint ligand PD-L1 has emerged as a molecular target for skin cancer therapy and might also hold promise for preventive intervention targeting solar ultraviolet light-induced skin damage. Topical application of the small molecule PD-L1 inhibitor BMS-202 significantly modulates UV-induced inflammation in SKH-1 mouse skin as substantiated by NanoString CounterTM transcriptomic analysis.

overall_design: Differential expression between murine full thickness skin exposed to UV (n=3) and skin exposed to UV plus BMS-202 (n=3) was assessed using the Mouse nCounter Inflammatory V2 Panel code set.

first: Jana

last: Jandova

middle: T

first: Sally

middle: E

last: Dickinson


title: Gene expression profile at single cell level of murine B cells from different compartments of naive young adult mice

status: Public on Dec 20 2023

city: Munich

first: Thomas

last: Korn

email: thomas.korn@tum.de, c.sie@tum.de

address: Ismaninger Str. 22

department: Experimental Neuroimmunology

country: Germany

institute: Technical University of Munich

type: Expression profiling by high throughput sequencing

summary: In the context of understanding thymic T cell selection facilitated by local B cells, we sought to compare thymic B cells with their counterparts from other compartments in naive young adult mice.

overall_design: B cells from spleen, inguinal lymph nodes, bone marrow, thymus and blood (each pooled from two mice) were isolated by fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq (10x).

first: Ali

last: Afzali

first: Lucy

last: Nirschl

first: Christopher

last: Sie


title: Minimal requirements for the epigenetic inheritance of engineered silent chromatin domains

city: BOSTON

first: Andy

last: Yuan

state: MA

address: 240 Longwood Avenue

department: Cell Biology

institute: Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mechanisms enabling genetically identical cells to differentially regulate gene expression are complex and central to organismal development and evolution. While gene silencing pathways involving DNA sequence–specific recruitment of histone-modifying enzymes are prevalent in nature, examples of sequence-independent heritable gene silencing are scarce. Studies of the fission yeast Schizosaccharomyces pombe indicate that sequence-independent propagation of heterochromatin can occur but requires numerous multisubunit protein complexes and their diverse activities. Such complexity has so far precluded a coherent articulation of the minimal requirements for heritable gene silencing by conventional in vitro reconstitution approaches. Here, we take an unconventional approach to defining these requirements by engineering sequence-independent silent chromatin inheritance in budding yeast Saccharomyces cerevisiae cells. The mechanism conferring memory upon these cells is remarkably simple and requires only two proteins, one that recognizes histone H3 lysine 9 methylation (H3K9me) and catalyzes the deacetylation of histone H4 lysine 16 (H4K16), and another that recognizes deacetylated H4K16 and catalyzes H3K9me. Together, these bilingual “read–write” proteins form an interdependent positive feedback loop that is sufficient for the transmission of DNA sequence–independent silent information over multiple generations.

overall_design: Chromatin immunoprecipitate DNA-sequencing (ChIP-seq) for H3K9me2 and FLAG epitope-tagged Sir3-SET in Saccharomyces cerevisiae cells

middle: H

first: Danesh

last: Moazed


title: Bulk RNA-seq analysis of primary CML CD34+ cells (n=3) treated with idasanutlin alone or in combination with nilotinib in vitro

city: Glasgow

first: David

last: Vetrie

address: Wolfson Wohl Cancer Research Centre

department: Institute of Cancer Sciences

country: United Kingdom

institute: Glasgow University

summary: Bulk RNA-seq was performed on primary human CML CD34+ cells to understand the molecular consequences of treatment with the MDM2 inhibitor idasanutlin alone and in combination with the tyrosine kinase inhibitor nilotinib for 24 hrs and 72 hrs.

overall_design: Primary CD34+ CML cells isolated from peripheral blood of 3 unrelated chronic phase CML patients were treated with nilotinib (3 µM), idasanutlin (166 nM), or a combination for 24 hrs or 72 hrs. RNA-seq analysis was performed at each time point for each drug treatment arm of each sample. CML CD34+ samples used in the study were randomly chosen without prior knowledge of age, sex, clinical outcome or response to tyrosine kinase inhibitors.

last: Stevens

first: Mary

last: Scott

first: Wei

last: Liu


title: Single cell RNA-seq analysis of the effects of idasanutlin and/or nilotinib on primary human CML cells engrafted into the bone marrow of immunocompromised mice

summary: Single cell RNA-seq was performed on primary human CML cells engrafted into the bone marrow of immunocompromised mice to understand the molecular consequences of treatment with the tyrosine kinase inhibitor nilotinib alone and in combination with the MDM2 inhibitor idasanutlin.

overall_design: CML CD34+ cells were engrafted into the BM of irradiated immuno-compromised mice (cohort sizes 3 mice per arm per experiment). Eight to twelve weeks post-transplantation, mice were treated with nilotinib (NIL) (50 mg/kg QD) for 7-14 days after which the cohorts received NIL for a further 14 days +/- IDASA (150 mg/kg BD) for the first 5 days. At the end of 28 day treatment or after a further 28 days treatment-free period mice were analyzed for human cell engraftment in the murine bone marrow and scRNA-seq was performed on huCD45+ or huCD34+ cells.


title: Single cell RNA-seq analysis of haemopoietic stem cells and CML stem cells isolated from human peripheral blood

summary: To identify differences in the transcriptomes of normal haemopoietic stem cells (HSC) and leukaemic stem cells (LSC) found in patients with chronic myeloid leukaemia (chronic phase) we performed single cell RNA-seq.

overall_design: Single cell RNA-seq was performed for HSC isolated from CD34+ cell samples obtained by mobilization with granulocyte-colony stimulating factor (G-CSF) from 5 unrelated individuals with no BM disease involvement. Single cell RNA-seq was performed on LSC isolated from CML CD34+ samples from 5 unrelated chronic phase patients that were randomly chosen without prior knowledge of age, sex, clinical outcome or response to tyrosine kinase inhibitors.


title: ChIP-seq analysis to determine p53 binding profiles in the BV173 cell line before and after treatment with the MDM2 inhibitor idasanutlin

summary: We performed ChIP-seq analysis in order to determine the transcriptional targets of p53 in the CML cell line BV173 as a result of p53 activation using the MDM2 inhibitor idasanutlin.

overall_design: We cultured one bioreplicate of 1 x 10^7 BV173 cells with and without idasanutlin (300 nM) for 6 hrs and then performed ChIP using a ChIP-grade antibody for p53. We isolated ChIP DNA from the p53 ChIP conditions. In parallel, we treated one bioreplicate of BV173 cells with and without idasanutlin (300 nM) and prepared input genomic DNA (control) from cross-linked cells. In total, we had four experimental conditions.


title: Single-cell multi-omics decodes regulatory programs during development of mouse secondary palate

city: HOUSTON

first: Zhongming

last: Zhao

state: Texas

address: 7000 Fannin St

department: School of Biomedical Informatics

institute: UTHealth

summary: The abnormal perturbation in gene regulation during palatogenesis may lead to cleft palate. Here, we performed single-cell multiome sequencing (snRNA-seq and snATAC-seq simuteneously from same cells) from mouse secondary palate across 4 developmental stages.

overall_design: Palatal shelves were isolated from time-mated C57BL/6J mice (Jackson Laboratory) at embryonic day (E) 12.5, E13.5, E14.0, and E14.5 and subjected to single-cell multiome sequencing. All mice were maintained in the animal facility of UTHealth. The protocol was approved by the Animal Welfare Committee (AWC) and the Institutional Animal Care and Use Committee (IACUC) of UT Health (AWC 19-0079).

first: Fangfang

last: Yan

first: Akiko

last: Suzuki

first: Chihiro

last: Iwaya

first: Guangsheng

last: Pei

first: Xian

first: Hiroki

last: Yoshioka

first: Meifang

last: Yu

first: Lukas

last: Simon

first: Junichi

last: Iwata


title: miRNA expression data from Sus scrofa BM-MSC

city: Valencia

first: Rubén

last: Salvador-Clavell

state: Valencia

address: 13 Blasco Ibanez Av.

country: Spain

institute: University of Valencia

summary:
Gene expression of characteristic chondrogenic markers and miRNA expression were analyzed in cells cultured in differentiation medium and significant differences were found between gelation/PRP microgels and those containing only pure gelatin.
We used microarrays to detail the miRNA expression in studied cell cultures for identification the expression of miRNA and study the up- and down-regulated miRNA associated.

overall_design: In order to study miRNA expression related to chondrogenic differentiation, Sus scrofa Bone Marrow Mesenchymal Stem Cells (pBM-MSC) were seeded in gelatin/gelatin-PRP (GEL/PRP) microspheres and cultured with proliferation (PROLI) and chondrogenic differentiation (DIFFER) media for 6 weeks (6w).

first: Manuel

last: Mata

first: Joaquín

last: Ródenas Rochina

first: María

last: Sancho-Tello

first: Gloria

last: Gallego Ferrer

first: José

middle: L

last: Gómez Ribelles


title: RNA-seq analysis reveals modulation of inflammatory pathways by an enriched-triterpene natural extract in mouse and human macrophage cell lines

status: Public on Dec 18 2023

city: Medellin

first: alejandro

last: mejia garcia

state: antioquia

country: Colombia

institute: Universidad de Antioquia

summary: Chronic Inflammation has a key role in the development of insulin resistance and type 2 diabetes. Previously, we demonstrated that OBE100, a natural extract from the leaves of Eucalyptus tereticornis, has anti-inflammatory properties. Three pentacyclic triterpenoids, ursolic acid, oleanolic acid, and ursolic acid lactone are the major compounds present in OBE100. These molecules have shown multiple biological activities. In this study we analyzed how the compounds of OBE100 modify macrophage gene expression using RNA sequencing. Triterpenoids regulate the inflammatory program in activated macrophages inhibiting the expression of many cytokines, chemokines, and inflammatory mediators. However, the OBE100 extract has a more powerful immunomodulatory effect than the triterpene mixture increasing the number of genes regulated, both in mouse and human models. Our study shows that OBE100 is a promising extract for the treatment of diabetes that can break the link between inflammation and insulin resistance.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
To establish the effect and molecular mechanisms of the OBE100 extract, we bought J774A.1 (TIB-67™) mouse monocyte; macrophage cells and U-937 (CRL-1593.2) human monocytic (pre-macrophage line), we differentiated them to macrophages using 100 nM phorbol myristate acetate (PMA), and  we treated the samples with Crude extract OBE100, M1 (mixture of UA, OA and UAL), UA, OA, and UAL
We then performed RNA seq profiling using data obtained from RNA-seq. We compared activated macrophages againts each control (OBE100, M1, UA, OA, UAL) and we also included a monocyte control, to verify that the activation to macrophage was successfull

first: Norman

last: Balcazar

first: Sergio

last: Acin

first: Geysson

middle: J

last: Fernandez

first: Alejandro

last: Mejia-Garcia

first: Luis

middle: F

last: Echeverri


title: laser-captured chondrocyte transcriptomes from cranial base

city: Saskatoon

first: Brian

last: Eames

state: Saskatchewan

address: 107 Wiggins Road

department: Anatomy and Cell Biology

country: Canada

institute: University of Saskatchewan

summary: similar methods as in Gomez-Picos et al. (2022) and Nguyen et al. (2023)

overall_design: mRNA profiles of wild type Danio rerio chondrocytes

first: B


title: Neuroretina of young and old mice treated with UA or vehicle

city: Madrid

first: Juan Ignacio

last: Jiménez-Loygorri

state: Madrid

address: Ramiro de Maeztu 9

department: Cellular and Molecular Biology

institute: Centro de Investigaciones Biológicas Margarita Salas

summary: Macroautophagy decreases with age, and this change is considered a hallmark of the aging process. It remains unknown whether mitophagy, the essential selective autophagic degradation of mitochondria, also decreases with age. In our analysis of mitophagy in multiple organs in the mito-QC reporter mouse, mitophagy was either increased or unchanged in old versus young mice. Transcriptomic analysis showed marked upregulation of the type I interferon response in the retina of old mice, an effect that correlated with increased levels of cytosolic mtDNA and activation of the cGAS/STING pathway. Crucially, these same alterations were replicated in primary human fibroblasts from elderly donors. In old mice, pharmacological induction of mitophagy with urolithin A attenuated cGAS/STING activation and ameliorated deterioration of neurological function. These findings point to induction of mitophagy as a novel strategy to decrease age-associated inflammation and increase healthspan.

overall_design: Young (6-8 months) or old (22-24 months) C57BL/6J mice were treated daily with 2.3 mg/kg/day of Urolithin A (UA) or Vehicle

first: Juan

middle: I

first: Patricia

last: Boya


title: CUT&RUN profiling of Tfap2a binding genome-wide using zebrafish embryos at 24hpf

city: Iowa City

first: Colin

last: Kenny

state: Iowa

address: 5269B CBRC Newton Road

department: Surgery

institute: University of Iowa

summary: The purpose of this study was to identify Tfap2a binding genome-wide in zebrafish embryos at 24hpf. Tfap2 transcription factors are essential regulators of neural crest development, melanocyte differentiation, and melanoma progression. We aimed to identify Tfap2a-occupied genes to determine direct Tfap2a-regulated transcriptional networks.

overall_design: Zebrafish embryos at 24hpf were used to profile Tfap2a occupied genes genome-wide using CUT&RUN followed by sequencing

first: Coin

first: Robert

last: Cornell


title: A chromatin-associated long non-coding RNA is required for effective replication stress signaling [RNAseq_HUtreatment]

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

institute: Centro de Investigación Médica Aplicada

summary: Despite the well-characterized protein network involved in replication stress response, several regulatory RNAs have been shown to be involved in this process; however, it has remained elusive the presence of such RNAs on the replication fork, and how they locally act in this critical process. Here, we identified lncREST, a previously uncharacterized lncRNA among a set of chromatin-associated transcripts induced by hydroxyurea. We show that lncREST localizes on stressed replication forks. Specifically, during replication stress, lncREST interacts with NCL in the nucleus, to help engage its interaction with RPA. Consequently, lncREST loss is associated to reduction of NCL-RPA interaction and decreased RPA on chromatin, leading to a defective replication stress signaling. lncREST depleted cells suffer sustained replication fork progression and accumulate un-signaled DNA damage. These findings uncover a structural function of a lncRNA acting as anchoring point for replication proteins foci on sites of DNA replication.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for chromatin and total RNA fractions of HCT116 cells treated with hydroxyurea versus control non-treated

first: Luisa

last: Statello

first: Jose

middle: M

last: Fernández-Justel

first: Enrique

last: Goñi

first: Jovanna

last: González

first: Alessia

last: Ranieri

first: Aina

last: Mas


title: A chromatin-associated long non-coding RNA is required for effective replication stress signaling

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

overall_design: Refer to individual Series


title: RNA polymerase II pausing is essential for appropriate gene expression and meiosis during spermatogenesis

city: Boston

first: Geoffrey

last: Nelson

address: 45 Shattuck St

department: BCMP

summary: Male germ cell development requires precise regulation of gene activity, in a cell-type and stage-specific manner, with perturbations in gene expression during spermatogenesis associated with infertility. Here, we use both steady-state and nascent RNA sequencing strategies to comprehensively characterize gene expression across male germ cell populations, to dissect the mechanisms of gene control and provide new insights towards therapy. We discover a requirement for pausing of RNA Polymerase II (Pol II) at the earliest stages of sperm differentiation to establish the landscape of gene activity across development. Accordingly, genetic knockout of the Pol II pause-inducing factor NELF in immature germ cells impairs differentiation to mature spermatids. Moreover, our work reveals unanticipated roles for Pol II pausing in the regulation of meiosis during spermatogenesis, with the presence of paused Pol II influencing double strand break formation by Spo11, and disruption of Spo11 expression in germ cells lacking NELF.

overall_design: Investigation of single cell RNA-seq on whole testis in Control (N=4), NELF-B cKO (N=2), and TDP-43 cKO (N=3) C57BL/6 mice.

first: Emily

middle: G

last: Kaye

first: Helena

last: Zomer

first: Debarun

last: Roy

first: Irene

last: Infancy

first: Prabhakara

last: Reddi

first: Karen

last: Adelman


title: RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis[PRO-Seq]

address: 45 Shattuck Street

summary: Male germ cell development requires precise regulation of gene activity in a cell-type and stage-specific manner, with perturbations in gene expression during spermatogenesis associated with infertility. Here, we use steady-state, nascent and single-cell RNA sequencing strategies to comprehensively characterize gene expression across male germ cell populations, to dissect the mechanisms of gene control and provide new insights towards therapy. We discover a requirement for pausing of RNA Polymerase II (Pol II) at the earliest stages of sperm differentiation to establish the landscape of gene activity across development. Accordingly, genetic knockout of the Pol II pause-inducing factor NELF in immature germ cells blocks differentiation to spermatids. Further, we uncover unanticipated roles for Pol II pausing in the regulation of meiosis during spermatogenesis, with the presence of paused Pol II associated with double strand break (DSB) formation, and disruption of meiotic gene expression and DSB repair in germ cells lacking NELF.

overall_design: Investigation of active polymerase position using PRO-seq on three cell types present during spermatogenesis (3 biological replicates of spermatogonia, spermatocytes, and round spermatids isolated from wild type C57BL/6 mice).

first: Kavyashree

last: Basavaraju

middle: D

last: Infancy Joseph

first: Reza

last: Rajabi-Toustani

first: Huanyu

last: Qiao

middle: P


title: RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis [RNA-Seq]

overall_design: Investigation of steady-state bulk RNA-seq on three cell types present during spermatogenesis (3 biological replicates of spermatogonia, spermatocytes, and round spermatids isolated from wild type C57BL/6 mice).


title: Single-cell analysis of isoform switching and transposable element expression during preimplantation embryonic development

status: Public on Dec 17 2023

city: Guangzhou

first: Zhuoxing

last: Shi

state: GD

address: #7 Jinsui Road, Tianhe District

department: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center

country: China

institute: Sun Yat-sen University

summary: This study explores alternative splicing's role in embryo development. Using single-cell direct isoform sequencing, we detected an abundance of 3-prime partial transcripts lacking stop codons in oocytes and zygotes, potentially influencing the maternal-to-zygote transition. Long-read sequencing identified dynamic changes in 3894 transposable element loci throughout preimplantation, impacting nearby gene expression and shedding light on early embryonic transcriptional regulation.

overall_design: The experiment involved 6-8-week-old female C57BL/6J and male DBA/2NCrl mice. Post-mating, embryos were collected at specific intervals post-hCG injection: 20 hours (MII oocytes, non-mated), 22-24 hours (fertilized eggs), 30-32 hours (early 2-cell stage), 46-48 hours (late 2-cell stage), 54-56 hours (4-cell), 68-70 hours (8-cell), 78-80 hours (16-32-cell), 88-90 hours (early blastocyst). Subsequently, the same amplification process as SCAN-seq was used, except a 10x gel bead was used in each single-cell embryo reaction. Following this, the PacBio sequencing library was constructed following the HIT-scISOseq process, sequenced in HiFi mode. We sequenced a total of 4 PacBio Sequel II SMRT 8M chips, each representing a different experimental replicate.


title: Neural extracellular matrix regulates visual sensory motor integration

city: Bochum

first: Jacqueline

last: Reinhard

address: Universitätsstrasse 150

department: Cell Morphology and Molecular Neurobiology

institute: Ruhr University

summary: Visual processing depends on sensitive and balanced synaptic neurotransmission. Extracellular matrix proteins in the environment of cells are key modulators in synaptogenesis and synaptic plasticity. In the present study, we provide evidence that the combined loss of the four extracellular matrix components brevican, neurocan, tenascin-C and tenascin-R in quadruple knockout mice leads to severe retinal dysfunction and diminished visual motion processing in vivo. Remarkably, impaired visual motion processing was accompanied by a developmental loss of cholinergic direction-selective starburst amacrine cells. Additionally, we noted imbalance of inhibitory and excitatory synaptic signaling in the quadruple knockout retina. Collectively, the study offers novel insights into the functional importance of four key extracellular matrix proteins for retinal function, visual motion processing and synaptic signaling.

overall_design: Our dataset includes the expression data obtained from adult dissected Bcan, Ncan, Tnc and Tnr (quadruple) knockout and wildtype mouse retinae. In total, 8 retina samples from 4 control wildtype and 4 quadruple knockout mice were analyzed.

first: Andreas

last: Faissner

first: Lin

last: Gan

first: Chao-Chung

last: Kuo

first: Julia

last: Franzen


title: A chromatin-associated long non-coding RNA is required for effective replication stress signaling [RNAseq_cell_cycle]

first: Maite

last: Huarte

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT116 cells synchronized in G1 with thymidine and released at different stages of the cell cycle

first: Luisa

last: Statello

first: Jose

last: Fernández-Justel

first: Enrique

last: Goñi

first: Jovanna

last: González

first: Alessia

last: Ranieri

first: Aina

last: Mas


title: RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis

first: Emily

last: Kaye


title: eIF3B CLIP-sequencing in prostate cancer

status: Public on Dec 22 2023

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: The role of eIF3B in advanced therapy resistant lethal stages of prostate cancer remains unknown. To gain insight into how eIF3B regulates the translation of specific mRNAs we performed Genome-wide eIF3B enhanced cross-linking immunoprecipitation sequencing (eCLIP-seq). this analysis showed specialized binding to a UC-rich motif present in subsets of 5’-UTRs. Indeed, translation of the androgen receptor (AR) and major histocompatibility complex I (MHC-I) through this motif are sensitive to eIF3B amount. These results suggest that eIF3B by regulating specific mRNA translation may play key role in the pathogenesis of lethal prostate cancer.

overall_design: eIF3B eCLIP-Seq in human prostate cancer cell line 22Rv1

first: Sandra

last: Santasusagna

first: Shijia

last: Zhu

first: Vijayakumar

last: Jawalagatti

first: Josep

last: Domingo-Domenech

first: Asim

last: Hassan


title: Role of SREBP1 in macrophages during muscle regeneration

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

summary: The purpose of this study is to investigate how SREBP1a in macrophages regulates cellular function during muscle regeneration process after injury.  We report that the systemic deletion of Srebf1, encoding SREBP1, and macrophage-specific deletion of Srebf1a, encoding SREBP1a, delays the resolution of inflammation, and impairs skeletal muscle regeneration after injury. Srebf1 deficiency impairs mitochondrial function of macrophages and suppresses the accumulation of reparative macrophages to the injured site.

overall_design: mRNA profiles of CD45+CD11b+ myeloid cells obtained from muscle 3 days after cardiotoxin-induced injury of control (Srebf1af/f) and LysM-Cre: Srebf1af/f mice were analyzed.

first: Oishi

last: Yumiko

first: Manabe

last: Ichiro


title: The effects of periodic restricted feeding on Rhesus Macaques

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

summary: Dietary restriction has shown benefits in physiological, metabolic, and molecular signatures associated with aging. In mice, periodic dietary restriction, that accompanies cyclical periods of reduced calories, mitigates aging phenotypes, yet the effects of this periodic restriction in higher order, genetically heterogenous mammals, have not been investigated. Reducing caloric intake in middle-aged Rhesus Macaques for four days followed by ad libitum eating for ten days, repeated for six cycles, led to significant changes in body composition, metabolome, and microbiome of the restricted monkeys compared to their ad libitum fed (age and sex matched) controls. These changes were also associated with stabilized blood parameters. The changes in metabolome, microbiome, and body compositions were additive, with consistent but increasingly pronounced changes in later cycles, suggesting sustaining benefits in non-human primates. These results suggest this type of cyclical dietary restriction, that is easy to adhere to, will also have translational benefits in humans while enhancing aging-associated parameters.

overall_design: Adlib diet vs PRF diet, primate gut microbiome sample analysis

first: Hagai

last: Yanai

first: Hyunwook

last: Koh

first: Isabel

last: Beerman


title: ATG5-regulated MCP-1 production in myeloid cells selectively modulates anti-malarial CD4+ Th1 responses

status: Public on Dec 16 2023

city: Chongqing

first: taiping

last: Liu

address: Gaotanyan zhengjie 30, Shapingba district, Chongqing

institute: Department of Pathogenic Biology, Army Medical University (Third Military Medical University)

summary: Induction of parasite-specific CD4+ Th1 cell responses is a promising strategy for designing effective blood-stage malaria vaccines; however, the underlying regulatory mechanisms remain largely unknown. This study demonstrated that ATG5 deficiency in myeloid cells can significantly inhibit the growth of rodent blood-stage malarial parasites by enhancing parasite-specific CD4+ Th1 cell responses. This effect was independent of ATG5-mediated canonical and non-canonical autophagy. Mechanistically, ATG5 deficiency promoted myeloid cell (Ly6G-CD11b+F4/80-) survival and subsequently increased MCP-1 production in parasite-infected mice. Ly6G-CD11b+F4/80- cell-derived MCP-1 interacted with CCR2 on CD4+ Th1 cells for their optimized responses through the JAK2/STAT4 pathway. Notably, recombinant MCP-1 significantly improved parasite-specific CD4+ Th1 responses of the whole-killed blood-stage vaccine. Conclusively, our study highlights the previously unrecognized role of ATG5 in modulating myeloid cell survival via MCP-1 production, which selectively promotes CD4+ Th1 cell responses. Our findings provide new insights into the development of effective antimalarial vaccines.

overall_design: scRNA-seq analysis of CD11b+ cells isolated from splenocytes of P. yoelii 17XNL-infected mice at day 0 and day 3 post-infection.

first: Wenyue

last: Xu

first: Taiping

first: Yuanli

last: Gao


title: Compromised THOC2, a TREX mRNA export complex scaffold protein, leads to R-loop accumulation, DNA damage and adverse neurodevelopmental outcomes in mice and men

status: Public on Dec 15 2023

city: Adelaide

first: Alison

last: Gardner

state: SA

address: AHMS, Uni of Adelaide, North Terrace

department: Faculty of Health and Medical Sciences

country: Australia

institute: University of Adelaide

summary: TREX (Transcription-Export) is a highly conserved multi-subunit protein complex that, besides its established role in mRNA export from nucleus to cytoplasm, is involved in transcriptional regulation, stem cell maintenance, 3’ mRNA processing, mitotic progression, and genome stability in eukaryotic cells. TREX is composed of a six subunit THO core complex (THOC1, THOC2, THOC3, THOC5, THOC6 and THOC7) and eight accessory proteins. We have implicated the X-chromosome THOC2 gene, which encodes the scaffold protein of the THO complex, in a clinically variable neurodevelopmental disorder (NDD) with intellectual disability (ID) as the core phenotype. To study the function of this essential eukaryotic gene and the mechanisms underlying its NDD outcomes, we generated a clinically-relevant mouse model based on a hypomorphic Thoc2 exon37-38 deletion variant of a patient with ID, speech delay, hypotonia, and microcephaly. The Thoc2 exon37-38 deletion male (Thoc2Δ/Y) mice recapitulate the core phenotypes of THOC2 syndrome including smaller size and weight, and significant deficits in spatial learning, working memory and sensorimotor functions. The Thoc2Δ/Y mice brain development is significantly impacted by compromised THOC2/TREX function resulting in R-loop accumulation, DNA damage and consequent cell death. Differentiated cortical neurons of Thoc2Δ/Y mice show perturbed synaptic and electrophysiological properties underlined by increased DNA damage comparable to the primary cells of patients with THOC2 pathogenic variants. Altogether, our data suggest that perturbed R-loop homeostasis, in stem cells and/or differentiated cells in mice and men, and DNA damage-associated functional alterations are at the root of THOC2 syndrome. Overall, we suggest that THOC2 is a major, conserved player in the efficient resolution of R-loops, a process essential for normal brain development and function.

overall_design: Total RNAs were extracted from the E14.5, E18.5 and P10 Thoc2Δ/Y and Thoc2+/Y mouse brain dorsal cortices (we refer to it as ‘brain’ in the text for simplicity) with each genotype having 5 biological replicates. The Strand-specific sequencing at 80 million 2×150bp paired-end reads per sample was sequenced in an Illumina NovaSeq 6000 (Illumina, USA).

first: Rudrarup

last: Bhattacharjee

first: Raman

last: Sharma


title: DNA methylation profiling of phyllodes tumours determines a signature of malignancy and delineates from metaplastic breast carcinoma

city: Sydney

first: Braydon

last: Meyer

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genetics and Epigenetics

institute: Garvan Institute of Medical Research

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of phyllodes tumour, fibroadenoma and metaplastic breast cancer samples. The Illumina Infinium Methylation EPIC v1.0 BeadChip Array was used to obtain DNA methylation profiles across approximately 866,000 CpGs from primary tumours. Samples included a range of grades of phyllodes tumours (n=29), fibroadenoma (n=2), and metaplastic breast cancer (n=2).

overall_design: Bisulphite converted DNA from the 33 samples were hybridised to the Illumina Infinium MethylationEPIC v1.0 BeadChip Array

first: Ruth

last: Pidsley


title: Extracellular miRNAs in serum and feces of mice exposed to high-dose radiation

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

institute: Hirosaki University

summary: Exposure to high-dose radiation causes life-threatening serious intestinal damage. Histological analysis is the most accurate method for judging the extent of intestinal damage after death. However, it is difficult to predict the extent of intestinal damage to body samples. Here we focused on extracellular microRNAs (miRNAs) released from cells and investigated miRNA species that increased or decreased in serum and feces using a radiation-induced intestinal injury mouse model. A peak of small RNA of 25–200 nucleotides was detected in mouse serum and feces 72 h after radiation exposure, and miRNA presence in serum and feces was inferred. MiRNAs expressed in the small intestine and were increased by more than 2.0-fold in serum or feces following a 10 Gy radiation exposure were detected by microarray analysis and were 4 in serum and 19 in feces. In this study, miR-375-3p, detected in serum and feces, was identified as the strongest candidate for a high-dose radiation biomarker in serum and/or feces using a radiation-induced intestinal injury model.

overall_design: In this study, miRNAs expression was examined in the small intestine, serum, and feces of mice exposed to high doses of radiation.


title: Using single-cell transcriptomics to characterise early mechanisms of psoriasis resolution

city: London

first: Luc

last: Francis

address: Guy's Hospital, Great Maze Pond

institute: King's College London

summary: We obtained full-thickness skin biopsies from five individuals with severe psoriasis who were receiving risankizumab treatment. Skin biopsies were taken from lesional and non-lesional sites at baseline, and from lesional sites at day 3 and day 14 of therapy. Single-cell RNA sequencing was performed using a 10x Genomics platform.

overall_design:
Longitudinal single-cell RNA-sequencing of skin biopsies obtained from 5 individuals with severe psoriasis. Samples were taken at day 0 (non-lesional and lesional skin) day 3 and day 14 (lesional skin only) of risankizumab treatment.
Submitter states that raw data will be submitted to dbGaP due to patient privacy concerns.

first: Satveer

last: Mahil

first: Francesca

last: Capon


title: Sexual dimorphism in melanocyte stem cell behavior reveals combinational therapeutic strategies for cutaneous repigmentation

city: ithaca

first: Luye

last: An

address: 618 tower road

department: biomedical sciences

institute: cornell university


title: Self-organization of human gastrulation upon in vitro attachment

city: New York

first: Riccardo

last: De Santis

address: 1230 York Ave

institute: The Rockefeller univeristy

summary: Single cell RNA-seq profiling distinguished extra-embryonic populations and derivatives of three germ layers that match with the human gastrula at 16-19 days post fertilization.

overall_design: scRNA-seq profiling of in vitro attched human blastoids at 7 and 10 days post attachment

first: Ali

last: Brivanlou


title: Direct Comparison of Canine and Immune Responses Using Transcriptomic and Functional Analyses

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

summary: The canine spontaneous cancer model is increasingly utilized to evaluate new combined cancer immunotherapy approaches. While the major leukocyte subsets and phenotypes are closely related in dogs and humans, the functionality of T cells and antigen presenting cells in the two species has not been previously compared in detail. Such information would be important in interpreting immune response data and evaluating the potential toxicities of new cancer immunotherapies in dogs. To address this question, we used in vitro assays to compare the transcriptomic, cytokine, and proliferative responses of activated canine and human T cells, and also compared responses in activated macrophages. Transcriptomic analysis following T cell activation revealed shared expression of 515 significantly upregulated genes and 360 significantly downregulated immune genes. Pathway analysis identified 33 immune pathways shared between canine and human activated T cells, along with 34 immune pathways that were unique to each species. Activated human T cells exhibited a marked Th1 bias, whereas canine T cells were transcriptionally less active overall. Despite similar proliferative responses to activation, canine T cells produced significantly less IFN-g than human T cells. Moreover, canine macrophages were significantly more responsive to activation by IFN-g than human macrophages, as reflected by co-stimulatory molecule expression and TNF-a production. Thus, these studies revealed overall broad similarity in responses to immune activation between dogs and humans, but also uncovered important key quantitative and qualitative differences, particularly with respect to T cell responses, that should be considered in designing and evaluating cancer immunotherapy studies in dogs.

sample_organism:
Homo sapiens
Canis lupus familiaris

platform_organism:
Homo sapiens
Canis lupus familiaris

overall_design: Following Ficoll separation, PBMC for both species were washed with PBS, counted and added to 24-well plates in triplicate cultures, at a cell density of 2 X 10^6 cells per mL in complete culture medium. For T cell activation, phytohemagglutinin (PHA) (Sigma-Aldrich, St. Louis, MO) was added to cultures at a concentration of 5 ug/ml for 72 hours (cytokine and proliferation measurement) or for 24h (RNA sequencing).

first: Lyndah

last: Chow


title: Transplantation of Committed Pre-adipocytes from Brown Adipose Tissue improves Whole-body Glucose Homeostasis

status: Public on Dec 13 2023

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

summary: Obesity and its co-morbidities including type 2 diabetes are increasing at epidemic rates in the U.S. and worldwide. Brown adipose tissue (BAT) is a potential therapeutic to combat obesity and type 2 diabetes. Increasing BAT mass by transplantation improves metabolic health in rodents, but its clinical translation remains a challenge. Here, we investigated if transplantation of 2-4 million differentiated brown pre-adipocytes from mouse BAT stromal fraction (SVF) or human pluripotent stem cells (hPSCs) could improve metabolic health. Transplantation of differentiated brown pre-adipocytes, termed ‘committed pre-adipocytes’ from BAT SVF from mice or derived from hPSCs improves glucose homeostasis and insulin sensitivity in recipient mice under conditions of diet-induced obesity, and this improvement is mediated through the collaborative actions of the liver transcriptome, tissue AKT signaling and FGF21. These data demonstrate that transplantation of a small number of brown adipocytes has significant long-term translational and therapeutic potential to improve glucose metabolism.

overall_design: Transplantation of differentiated pre-adipocytes from stromal fraction of brown adipose tissue into high-fat diet fed recipient mice using silk scaffolds to determine metabolic changes, including changes to liver transcriptome

first: Revati

middle: S

last: Dewal

first: Falko

last: Noé

first: Estella

last: Puchulu-Campanella

first: Huabao

last: Wang

first: Pearlly

last: Yan

first: Kristin

last: Stanford


title: RNA Sequencing of Peribiliary Mesenchymal Cells

status: Public on Dec 14 2023

city: New Haven

first: Vikas

last: Gupta

address: 1 Gilbert Street

institute: Yale School of Medicine

summary: These datasets look are bulk RNA sequencing of sorted peribiliary mesenchymal cells from the murine extrahepatic bile duct under wild type, 4 days post bile duct ligation, Smo gain and loss of function, Ctnnb1 loss of function, and Gli2/Gli3 loss of function

overall_design: Peribiliary mesenchymal cells were isolated from the murine extraheptic bile ducts and purified by flow cytometry prior under normal, injured, and genetic gain or loss function


title: Sexual dimorphism in melanocyte stem cell behavior reveals combinational therapeutic strategies for cutaneous repigmentation [RNA-Seq]

summary: Vitiligo is an autoimmune skin disease caused by cutaneous melanocyte loss. Although phototherapy and T cell suppression therapy have been widely used to induce epidermal re-pigmentation, full pigmentation recovery is rarely achieved due to our poor understanding of the cellular and molecular mechanisms governing this process. Here, we identify unique melanocyte stem cell (McSC) epidermal migration rates between male and female mice, which is due to sexually dimorphic cutaneous inflammatory responses generated by ultra-violet B exposure. Using genetically engineered mouse models, and unbiased bulk and single-cell mRNA sequencing approaches, we determine that manipulating the inflammatory response through cyclooxygenase and its downstream prostaglandin product regulates McSC proliferation and epidermal migration in response to UVB exposure. Furthermore, we demonstrate that a combinational therapy that manipulates both macrophages and T cells (or innate and adaptive immunity) significantly promotes epidermal melanocyte re-population. With these findings, we propose a novel therapeutic strategy for repigmentation in patients with depigmentation conditions such as vitiligo.

overall_design: Male and female dorsal skin with 3x UVB irradiation were collected for bulk RNA sequencing. Male and female non UVB irradiated skin were used as control

first: Dahihm

last: Kim

first: Leanne

last: Donahue

first: Menansili

last: Abraham Mejooli

first: Chi-Yong

last: Eom

first: Nozomi

last: Nishimura

first: Andrew

middle: C

last: White


title: Effect of Galectin-8 treatment on gene expression of human peripheral blood mononuclear cells

city: Shanghai

first: Yiting

address: Dongfang Road 1630

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

summary:
Galectin-8 is an identified ligand of LILRB4, which is an immune checkpoint receptor expressed on monocytic cells.Human PBMCs were treated with or without Galectin-8 to test transcriptome alteration.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 replicates from each group.

overall_design: Comparative gene expression profiling analysis of RNA-seq data fohumanPBMCs with or without Galectin 8 treatment.

first: Jie

last: Xu


title: Study of PRMT5 mediated H3R2me2s in Th1-like iTregs

city: Amherst

first: Nidhi

last: Jadon

address: 661 N plesant St

department: Veterinary and Animal Sciences

institute: University of Massachusetts Amherst

summary: In this study, we have studied the genes associated with PRMT5 mediated histone methylation (H2R2me2s) in Th1-like iTregs. This particular epigenetic markers is upregulated in Th1 cells, and Th1-like iTregs. Therefore, we wanted to identify the genes H3R2me2s is regulating in Th1-like iTregs as compared to iTregs or Th1 cells. The goal of this sequencing was to identify if H2R2me2s is important for increased suppressive capacity of Th1-like iTregs or not.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for symmetric histone arginine methylation (H3R2me2s) in Th1-like iTregs, iTregs and Th1 cells of C57BL\6 mice

first: Sudarvili

last: Shanthalingam

first: Lisa

last: Minter

first: Gregory

middle: N

last: Tew

first: Zhiyi

last: Liu


title: Effect of Gal-8 treatment on gene expression of human CD14+ monocytes

summary:
Galectin-8 is an identified ligand of LILRB4, which is an immune checkpoint receptor expressed on monocytic cells.Isolated human CD14+ cells from human PBMC were treated with or without Galectin-8 to test transcriptome alteration.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 replicates from each group.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Isolated human CD14+ cells with or without Galectin 8 treatment.


title: Postnatal persistence of hippocampal Cajal-Retzius cells has a crucial role in the establishment of the hippocampal circuit

city: Trondheim

first: Giulia

last: Quattrocolo

address: Olav Kyrres gate 9

department: Kavli Institute for Systems Neuroscience

country: Norway

institute: NTNU

summary:
Cajal-Retzius (CR) cells are a transient type of neurons that populate the postnatal hippocampus. The role of transient cell types and circuits have been vastly addressed in neocortical regions, but poorly studied in the hippocampus.
To understand how CR cells persistence influences the maturation of hippocampal circuits, we specifically ablated CR cells from the postnatal hippocampus.

overall_design: Our results highlighted a layer-specific effects on dendritic spines and synaptic-related genes and revealed a critical role of CR cells on the establishment of the hippocampal network.

first: Ingvild

last: Glærum

first: Keagan

last: Dunville


title: Modeling early pathophysiological phenotypes of diabetic retinopathy in a human inner blood-retinal barrier-on-a-chip

status: Public on Dec 12 2023

city: Basel

first: Thomas

middle: Luc

last: Maurissen

address: Grenzacherstrasse 124

institute: Roche

summary:
We developed a diabetic iBRB-on-a-chip that produces novel pathophysiological phenotypes and disease pathways in vitro that are representative of clinical diagnoses.
Diabetic stimulation of the iBRB-on-a-chip mirrors DR features including pericyte loss, vascular regression, ghost vessels, and production of pro-inflammatory factors.
We also report transcriptomic data from diabetic iBRB MVNs that may reveal novel targets, and examine pericyte-endothelial cell stabilizing strategies.

overall_design: Differential gene expression analysis of RNA-seq data for primary human retinal microvascular endothelial cells, pericytes and astrocytes in an iBRB-on-a-chip obtained for different timepoints and treatment conditions, from 3 replicate experiments.

first: Héloïse

last: Ragelle


title: Sexual dimorphism in melanocyte stem cell behavior reveals combinational therapeutic strategies for cutaneous repigmentation [scRNA-seq]

first: Luye

last: An

overall_design: Male dorsal skin with no UVB, 3xUVB and Cox-2 overexpression male dorsal skin with 3xUVB were collected for enriched immune cell scRNA-seq

first: Dahihm

last: Kim

first: Leanne


title: Next-generation sequencing of wild type and CD4 conditional Bob1 deficient follicular helper T cells

city: Sapporo

first: Ippei

last: Ikegami

state: Hokkaido

address: S1 W17, Chuo-ku

department: Department of Human Immunology

institute: Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine

summary: Accumulating evidence has shown that a transcriptional coactivator of B-cell Oct-binding protein-1 (Bob1), in which Oct represents a DNA binding molecule specific to the octamer motif with an 8-bp element, ATTTGCAT, is preferentially expressed in human and mouse foollicular helper T (Tfh) cells. Meanwhile, the mechanism of how Bob1 contributes to the control of Tfh cells remains to be addressed. Studies using T-dependent antigens further showed that Bob1 would control the maintenance and development of memory Tfh cells from the central memory T-cell pool to sustain specific humoral responses. This was probably attributable to the regulatory program by Bob1 in energy metabolism as well as the expression of ICOS and IL-4. Collectively, Bob1 has the fundamental capacity to regulate long-term responses of Tfh cells to maintain specific humoral immunity.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild type Tfh cells and Bob1 KO Tfh cells.

first: Masahiro

last: Yanagi

first: Shingo

last: Ichimiya


title: TISSUE-LOCATION SPECIFIC TRANSCRIPTIONAL PROGRAMS IN COLON DETERMINE MOLECULAR DEPENDENCIES FOR TUMOR INITIATION [RNA-Seq]

first: Lijing

last: Yang

state: MD

address: 3400 N. Charles St.

institute: Johns Hopkins university

summary: It is not known why cancers arising in anatomically distinct locations but within the same tissue type can exhibit stark differences in molecular, pathological and clinical features. Cancers arising in proximal and distal sites of the colon are emblematic of these above differences as the proximal and distal colon cancers harbor differences in key molecular features, with BRAFV600E oncogene predominantly occurring in proximal colon cancers in the context of the increased promoter DNA methylation phenotype (CIMP-high), while distal colon cancers lack these molecular features. We determined the molecular basis of tissue-location specificity of driver mutations using normal mouse derived organoid models for colon cancer initiation. We show that the homeobox transcription factor, Cdx2, which is downregulated by DNA methylation in proximal colon cancers, plays distinct roles in regulating stem cell and differentiation in proximal compared to distal colon stem cells. Loss of Cdx2 altered the differentiation and stem cell programs and result in transformation by BRAFV600E specifically in the proximal but not distal colon stem cells. Analyses of RNA expression and Cdx2-binding to target genomic regions revealed that Cdx2 was a key effector of the transcriptional response to differentiation cues in proximal colon cells. This proximal colon-specific transcriptional program concurrently is tumor suppressive, and its loss sufficiently creates permissive state for oncogenic-BRAF mutations. The transcriptional program associated with Cdx2 loss in mouse proximal organoids matches that of human proximal colon cancers with downregulated CDX2 expression due to epigenetic silencing. Our analyses reveal that developmental and lineage-restricted transcription factors maintain tissue-location specific transcriptional programs which create critical dependencies for tumor initiation.

overall_design: Proximal and distal colon organoids were generated from 3 mice and cultured in WENR-plus medium for 4 months before collecting sample for ChIP-seq. We applied Chipmentation to identify Cdx2 bound genomic regions in the organoids, with minor adaptions(Schmidl et al., 2015). For WENR-plus group, organoids were cultured in WENR-plus medium, while for WENR-minus group, organoids were cultured in WENR-plus medium for 2 day first after plating in 150 μl of Matrigel, followed with 3 days treatment of WENR-minus medium. RNA was extracted subsequently.

first: Sara-Jayne

last: Thursby

first: Stephen

middle: B

last: Baylin

first: Hariharan

last: Easwaran


title: Profiling The Compendium Of Changes In Saccharomyces cerevisiae Due To Mutations That Alter Availability Of The Main Methyl Donor S-Adenosylmethionine

city: Highland Heights

first: Erin

last: Strome

state: KY

address: Nunn Drive, Northern Kentucky University

department: Department of Biological Sciences

institute: Northern Kentucky University

summary: The SAM1 and SAM2 genes encode for S-AdenosylMethionine (AdoMet) synthetase enzymes, with AdoMet serving as the main cellular methyl donor.  We have previously shown that independent deletion of these genes alters chromosome stability and AdoMet concentrations in opposite ways in Saccharomyces cerevisiae. To characterize other changes occurring in these mutants, we grew wildtype, sam1∆/sam1∆, and sam2∆/sam2∆ strains in 15 different Phenotypic Microarray plates with different components and measured growth variations. RNA-Sequencing was also carried out on these strains and differential gene expression determined for each mutant. We explored how the phenotypic growth differences are linked to the altered gene expression, and hypothesize mechanisms by which loss of the SAM genes and subsequent AdoMet level changes, impact pathways and processes. We present six stories, discussing changes in sensitivity or resistance to azoles, cisplatin, oxidative stress, arginine biosynthesis perturbations, DNA synthesis inhibitors, and tamoxifen, to demonstrate the power of this novel methodology to broadly profile changes due to gene mutations. The large number of conditions that result in altered growth, as well as the large number of differentially expressed genes with wide-ranging functionality, speaks to the broad array of impacts that altering methyl donor abundance can impart. Our findings demonstrate that some cellular changes are directly related to AdoMet-dependent methyltransferases and AdoMet availability, some are directly linked to the methyl cycle and its role in production of several important cellular components, and others reveal impacts of SAM gene mutations on previously unconnected pathways.

overall_design: To explore similarities and differences due to the loss of the paralogous S-adenosylmethionine synthetase genes, SAM1 and SAM2, we deleted each gene indepdendently and explored gene expression and phenotype differences.

first: McKayla

last: Remines

first: Makailyn

last: Schnoonover

first: Zoey

last: Knox

first: Kailee

last: Kenwright

first: Kellyn

last: Hoffert

first: Amila

last: Coric

first: James

last: Mead

first: Joseph

last: Ampfer

first: Serigne

last: Seye


title: TISSUE-LOCATION SPECIFIC TRANSCRIPTIONAL PROGRAMS IN COLON DETERMINE MOLECULAR DEPENDENCIES FOR TUMOR INITIATION [ChIP-Seq]

city: Baltimore

overall_design: Proximal and distal colon organoids were generated from 3 mice and cultured in WENR-plus medium for 4 months before collecting sample for ChIP-seq. We applied Chipmentation to identify Cdx2 bound genomic regions in the organoids, with minor adaptions(Schmidl et al., 2015). For WENR-plus group, organoids were cultured in WENR-plus medium, while for WENR-minus group, organoids were cultured in WENR-plus medium for 2 day first after plating in 150 μl of Matrigel, followed with 3 days treatment of WENR-minus medium. Samples were subsequently processed or ChIP-seq (ChIP-mentation) analyses.


title: Effect of Aging on the Human Myometrium at Single-Cell Resolution

city: Paterna

first: Raul

last: Pérez-Moraga

address: Rda. de Narcís Monturiol, 11, Bloque C

institute: Carlos Simon Foundation, INCLIVA Health Research Institute

summary: The myometrial dysfunction associated with aging can prompt complications during pregnancy and labor, causing a 7.8-fold increase in maternal mortality in women over 40. Using single-cell/single-nucleus RNA sequencing and spatial transcriptomics, we constructed a cellular atlas of the aging myometrium from 186,120 cells across twenty peri- and post-menopausal women. We identified 23 myometrial cell subpopulations, including novel contractile capillary, venous capillary, immune-modulated fibroblasts, and nervous system regulatory fibroblasts. Myometrial aging leads to fewer contractile capillary cells, a reduced level of ion channel expression in smooth muscle cells, and impaired gene expression in endothelial, smooth muscle, fibroblast, perivascular, and immune cells. We observed altered myometrial cell-to-cell communication as an aging hallmark associated with the loss of 25/229 signaling pathways, including those related to angiogenesis, tissue repair, contractility, immunity, and nervous system regulation. These insights may contribute to a better understanding of the complications faced by older women during pregnancy and labor

overall_design:
This series includes 20 female donors, both living and deceased, ranging from 46 to 79 years old. Donors were divided into two groups based on age: perimenopausal group (between 46 and 54 years old) and postmenopausal (> 55 years old)

>>>Submitter states: Raw data are unavailable due to patient privacy concerns.<<<

first: Paula

last: Punzón-Jiménez

first: Alba

last: Machado-Lopez

first: Raúl

first: Jaime

last: Llera-Oyola

first: Daniela

last: Grases

first: Marta

last: Gálvez-Viedma

first: Mustafa

last: AlSibai

first: Elena

last: Satorres

first: Rafael

last: Badenes

first: Carolina

last: Ferrer

first: Eduard

last: Porta-Pardo

first: Beatriz

last: Roson

first: Carlos

last: Simon

first: Aymara

last: Mas


title: Characterization of CD8+ T cells in immune-privileged organs of ZIKV-infected Ifnar1-/- mice

status: Public on Dec 11 2023

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

summary: Zika virus (ZIKV) infection caused neurological complications and male infertility, leading to the accumulation of antigen-specific immune cells in immune-privileged organs (IPOs). Thus, it is important to understand the immunological responses to ZIKV in IPOs. We extensively investigated the ZIKV-specific T-cell immunity in IPOs in Ifnar1-/- mice, based on an immunodominant epitope E294-302 tetramer. The distinct kinetics and functions of virus-specific CD8+ T cell infiltrated into different IPOs were characterized. The E294-302-specific TCRαβs are featured within the IPOs in different infection phases with the majority of clonotypes utilizing TRAV9N-3 paired with diverse TRBV chains. Specific chemokine receptors, Ccr2 and Ccr5, were selectively expressed in the E294-302-specific CD8+ T cells within the brain and testicle, indicating an IPO-orientated migration of virus-specific T cells after infection. Overall, this study adds to the understanding of virus-specific CD8+ T cell responses for controlling and clearing ZIKV infection in IPOs.

overall_design: We applied E294–302 tetramer selection to dissect virus-specific CD8+ T cells within different tissues of ZIKV infected Ifnar1-/- mice, including spleen, PBMCs, brain and testicle, at different onset times (7 and 30 dpi), and then performed single TCR sequencing and single-cell RNA sequencing (scRNA-seq) with 10× Genomics platform. Moreover, we also sequenced TCRs of general CD8+ T cells from the spleen at 0 dpi. After quality control processing and removing non-T cells, 40,371 high-quality single T cells were retained for the downstream analysis.


title: 6ThiodG induces anti-tumor immunity in SCLC

city: Dallas

first: Mingrui

last: zhu

address: 5323 Harry Hines Blvd

department: Pathology

institute: UTSouthwestern Medical Center

summary: There are few effective treatments for small cell lung cancer (SCLC). We explored a major dependency of small cell lung cancer as a therapeutic target. Nearly all of SCLCs have telomerase activity and they are dependent on this enzyme for their ability to continuously divide. We utilized a nucleoside analog, 6-Thio-2’-deoxyguanosine (6TdG), that is preferentially recognized by telomerase to promote telomere dysfunction. Low and intermittent doses of 6TdG inhibited tumor growth and metastasis from the primary tumors. Anti-tumor activity of 6TdG was associated with decrease in cancer initiation cell (CIC) markers L1CAM/CD133 and increase in visibility to innate and adaptive immunity. Mechanistically, 6TdG depleted CICs and induced type-I interferon signaling by activating tumor STING. We confirmed the functional essential role of CIC markers L1CAM/CD133 in SCLC tumor initiation. We also observed dramatic synergy between 6TdG and irradiation in both syngeneic and humanized SCLC models that was dependent on immune cells.

overall_design:
scRNA-seq of SCLC-bearing mouse livers, control and 6ThiodG-treated.
Contacts for data availability:
Esra.Akbay@utsouthwestern.edu
Kenian.Chen@utsouthwestern.edu
Mingrui.r.Zhu@gmail.com

first: Buse

last: Eglenen-Polat

first: Ryan

last: Kowash

first: Hai-Cheng

last: Huang

first: Silvia

last: Siteni

last: Zhu

first: Kenian

last: Chen

first: Matthew

last: Bender

first: Ilene

last: Mender

first: Benjamin

last: Drapkin

first: Prithvi

last: Raj

first: Victor

last: Stastny

first: John

last: Minna

first: Lin

last: Xu

first: Jerry

middle: W

last: Shay

first: Esra

middle: A

last: Akbay


title: Single Cell Sequencing of Murine Common Bile Duct

first: David

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary: The goal of this study was to map out the populations of cells in the murine common bile duct using single cell RNA seuqencing

overall_design: One sample was used that was comprised of the common bile duct from two male animals

first: Vikas

last: Gupta


title: TISSUE-LOCATION SPECIFIC TRANSCRIPTIONAL PROGRAMS IN COLON DETERMINE MOLECULAR DEPENDENCIES FOR TUMOR INITIATION

first: Lijing

last: Yang

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

overall_design: Refer to individual Series


title: Gene expression changes in cutting and  inverted cutting in Populus yunnanensis at the primary and rapid growth stages respectively

status: Public on Dec 08 2023

city: kunming

first: Shaojie

last: MA

state: yunnan

address: panlongqu

institute: Southwest Forestry University

summary: Illumina technology was used to generate mRNA profiles of stem apex of Populus yunnanensis with cutting and  inverted cutting. Total RNA was extracted separately from each plant and pooled to three biological replicates per condition.  RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).

overall_design: 4-5 week-old Populus yunnanensis cuttings were treated with cutting and  inverted cutting.  harvested for RNAseq analysis at the primary and rapid growth stages respectively.

first: ChengZhong

last: He

first: Furui

last: Jiang

first: Dan

last: Zong

first: ShaoJie

last: Ma


title: Gene expression profiles of murine melanomas after treatment with STING agonist ADU-S100

status: Public on Dec 09 2023

city: Pittsburgh

first: Jessica

last: Filderman

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh


title: Gene expression profiles of murine melanoma after treatment with STING agonist ADU-S100 [I]

summary: Murine BPR melanomas were treated with either ADU-S100 or ADU-S100 + inhibitors of ARG2, COX2, and NOS2. Tumors were collected 7 days after treatment initiation and RNA was isolated and run on the Nanostring mouse Tumor 360 panel.

overall_design: Six tumors per treatment group (ADU-S100 vs ADU-S100 + ARG2i/COX2i/NOS2i) were analyzed.


title: Enhanced metabolic detoxification is associated with fluroxypyr resistance in Bassia scoparia

first: Todd

last: Gaines

address: 1177 Campus Delivery

department: Agricultural Biology

summary: Resistance to the synthetic auxin herbicide fluroxypyr has an unconfirmed non-target site resistance mechanism. An RNA-Seq experiment was used to align to a reference transcriptome for the weed species Bassia scoparia to quantify gene expression and to identify sequence variants in the alignments. High gene expression was found in several genes related to metabolic degredation of the parent fluroxypyr compound.

overall_design:
Young leaves were sampled for RNA extraction from four individuals from a resistant line (B3) and two susceptible lines (9425 and J01).
RNA was used for preparation of Illumina Hi-Seq libraries. Samples were collected from untreated plants sprayed with water, and the same plants treated with fluroxypyr 3 and 10 hours after treatment

first: Olivia

middle: E

last: Todd

first: Eric

last: Westra

last: Patterson

first: Scott

last: Nissen

first: Andre

last: Araujo

first: William

last: Kramer

first: Franck

last: Dayan


title: High-dimensional comparison of monocytes and T cells in post-COVID and idiopathic pulmonary fibrosis

status: Public on Dec 07 2023

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

summary: Up to 30% of hospitalized COVID-19 patients experience persistent sequelae, including pulmonary fibrosis (PF). We examined COVID-19 survivors with impaired lung function and imaging worrisome for developing PF and found within six months, symptoms, restriction and PF improved in some (Early-Resolving COVID-PF), but persisted in others (Late-Resolving COVID-PF). To evaluate immune mechanisms associated with recovery versus persistent PF, we performed single-cell RNA-sequencing and multiplex immunostaining on peripheral blood mononuclear cells from patients with Early- and Late-Resolving COVID-PF and compared them to age-matched controls without respiratory disease. Our analysis showed circulating monocytes were significantly reduced in Late-Resolving COVID-PF patients compared to Early-Resolving COVID-PF and non-diseased controls. Monocyte abundance correlated with pulmonary function forced vital capacity and diffusion capacity. Differential expression analysis revealed MHC-II class molecules were upregulated on the CD8 T cells of Late-Resolving COVID-PF patients but downregulated in monocytes. To determine whether these immune signatures resembled other interstitial lung diseases, we analyzed samples from Idiopathic Pulmonary Fibrosis (IPF) patients. IPF patients had a similar marked decrease in monocyte HLA-DR protein expression compared to Late-Resolving COVID-PF patients. Our findings indicate decreased circulating monocytes is associates with decreased lung function and uniquely distinguishes Late-Resolving COVID-PF from Early-Resolving COVID-PF, IPF, and non-diseased controls.

overall_design: Patients with IPF donated peripheral blood mononuclear cells (PBMCs) in the outpatient setting while in a stable clinical state. Three control PBMC samples from age-matched patients with no known pulmonary disease were prepared and sequenced at the Mayo Clinic (IRB #:19-012187). We recruited a subset of patients from the University of Virginia COVID-19 survivor clinic (IRB #:13166) with restrictive lung physiology on pulmonary function tests (PFTs) and features consistent with pulmonary fibrosis on chest CT performed at the associated visit. Radiographic features indicative of possible development of pulmonary fibrosis included bilateral reticulation, traction bronchiectasis, and/or honeycomb change in peripheral and basilar distribution, similar to the presently recognized progressive pulmonary fibrosis clinical radiologic phenotype, and similar to previously defined COVID-19 pulmonary fibrosis characteristics. PFT and chest imaging was performed in association with the patient's first visit to the outpatient COVID-19 survivor clinic. Early- and Late-Resolvers were identified by comparing chest imaging and PFT values from the patient's first and subsequent visit.  Patients with COVID-19 associated pulmonary fibrosis (COVID PF) were followed for 6 months or until the patient clinically improved. COVID PF patients were age-matched to IPF patients to control for age-related differences in peripheral immune signatures.

first: Grace

last: Bingham

first: Lyndsey

last: Muehling

first: Chaofan

last: Li

first: Yong

last: Huang

first: Shwu-Fan

first: Daniel

last: Abebayehu

first: Imre

last: Noth

first: Jie

last: Sun

first: Judith

last: Woodfok

first: Thomas

middle: H

last: Barker

first: Catherine

last: Bonham


title: CD62L expression marks a functionally distinct subset of memory B cells

city: St. Louis

first: Brian

last: Laidlaw

state: MO

address: 425 S Euclid Ave

institute: Washington University in St. Louis

summary: The memory B cell response consists of phenotypically distinct subsets that differ in their ability to respond upon antigen re-encounter. However, the pathways regulating the development and function of memory B cell subsets are poorly understood. Here we show that CD62L and CD44 are progressively expressed on mouse memory B cells and identify transcriptionally and functionally distinct memory B cell subsets. Bcl6 is important in regulating memory B cell subset differentiation with overexpression of Bcl6 resulting in impaired CD62L+ memory B cell development. Bcl6 regulates memory B cell subset development through control of a network of genes, including Bcl2 and Zeb2. Overexpression of Zeb2 impairs the development of CD62L+ memory B cells. Importantly, CD62L is also differentially expressed on human memory B cells following SARS-CoV-2 vaccination and identifies phenotypically distinct populations. Together, these data indicate that CD62L expression marks functionally distinct memory B cell subsets.

overall_design: We performed gene expression profiling using data obtained from RNA-seq analysis of memory B cell subsets defined based on their expression of CD44 and/or CD62L at day 15 and day 40 post acute LCMV infection.


title: Transcriptome analysis of colonic epithelial cells from Efhd2f/f Vil1cre/+ and Efhd2f/f mice during experimental colitis

city: Beijing

first: Jiacheng

last: Wu

address: 5 Dongdansantiao, Dongcheng District

institute: PUMC  & CAMS

summary: To determine how deficiency of Efhd2 in intestinal epithelial cells aggravates DSS-induced colitis in mice, we performed a transcriptional analysis.

overall_design: Colonic epithelial cells were isolated from Efhd2f/f Vil1cre/+ and Efhd2f/f mice with and without DSS administration. Total RNA was isolated with TRIzol.

first: Xuetao

last: Cao

first: Xiaoqing

last: Xu

first: Yangyang

last: Chai


title: Gene expression profiles of murine melanomas after treatment with STING agonist ADU-S100 [II]

first: Jessica

last: Filderman

summary: Two murine melanoma models (B16 and BPR) were treated with PBS or STING agonist ADU-S100 in vivo. Dose 1 was administered intratumorally on day 10, and a second dose was given on day 14. Tumors were collected 6 hours after the second dose and RNA was isolated. RNA was run on the Nanostring mouse PanCancer Immune Profiling Panel.

overall_design: Three mice per group (B16 untreated, B16 ADU-S100, BPR untreated, BPR ADU-S100) were treated and analyzed.


title: Pituitary  transcriptomic data in pigs to improve the understanding of heat stress adaptation mechanisms

status: Public on Dec 06 2023

city: Castanet-Tolosan

first: Laurence

last: Liaubet

address: 24 chemin de Borde Rouge

department: Animal genetics

country: France

institute: INRAE

summary:
This study aims to use omics data to understand the genetic pathways involved in heat stress adaptation.
Heat stress is one of the main limiting performance factors in the pig industry, and its importance is expected to grow with the consequences of warming climate. Different solutions to temper the influence of heat stress on the performance and well-being of pigs have been studied, and the genetic selection appear as a potential solution. Genetic mechanisms behind heat tolerance are still not well understood, but some differences between breeds have been shown, as well as an interaction between genetic and environment.

overall_design: To achieve this, transcriptomic data from pituitary gland were obtained in an experiment involving 36 pigs from 3 breeds slaughtered before (n=18) or after a 5-days exposure to 32°C (n=18).

first: David

last: Renaudeau

first: Guilhem

last: Huau

first: Jean-Luc

last: Gourdine

first: Laure

last: Gress

first: Katia

last: Feve

first: Yannick

last: Lippi

first: Yann

last: Labrune

first: Jérôme

last: Fleury

first: Juliette

last: Riquet


title: Muscle transcriptomic data in pigs to improve the understanding of heat stress adaptation mechanisms

overall_design: To achieve this, transcriptomic data from Longissimus dorsi muscle were obtained in an experiment involving 36 pigs from 3 breeds slaughtered before (n=18) or after a 5-days exposure to 32°C (n=18).


title: Liver transcriptomic data in pigs to improve the understanding of heat stress adaptation mechanisms

overall_design: To achieve this, transcriptomic data from Liver were obtained in an experiment involving 36 pigs from 3 breeds slaughtered before (n=18) or after a 5-days exposure to 32°C (n=18).


title: Thyroid gland transcriptomic data in pigs to improve the understanding of heat stress adaptation mechanisms

overall_design: To achieve this, transcriptomic data from thyroid gland were obtained in an experiment involving 36 pigs from 3 breeds slaughtered before (n=18) or after a 5-days exposure to 32°C (n=18).


title: Adrenal transcriptomic data in pigs to improve the understanding of heat stress adaptation mechanisms

overall_design: To achieve this, transcriptomic data from adrenal glands were obtained in an experiment involving 36 pigs from 3 breeds slaughtered before (n=18) or after a 5-days exposure to 32°C (n=18).


title: Changes in cognitive ability and serum microRNAs during aging in mice

city: Hirosaki

first: Mitsuru

last: Chiba

address: 66-1 Hon-cho

institute: Hirosaki University

summary: Mild cognitive impairment (MCI) is considered an early stage leading to dementia. MCI can be reversed, and early diagnosis at the MCI stage is vital to control the progression to dementia. Dementia is currently diagnosed based on interviews and screening tests. However, novel biomarkers must be identified to enable early detection of MCI. Therefore, this study aimed to discover novel biomarkers in the form of blood microRNAs (miRNAs) for the diagnosis of MCI or early dementia.

overall_design: Four-week-old (4w), 8-week-old (8w), 36-week-old (36w) and 58-week-old (58w) mice were used in this study (each n = 4). In this study, mice of various ages were used to search for microRNAs whose expression changes in serum with aging.

first: Keisuke

last: Yamamoto


title: Sub-Cutaneous Adipose Tissue (SCAT) transcriptomic data in pigs to improve the understanding of heat stress adaptation mechanisms

overall_design: To achieve this, transcriptomic data from Sub-Cutaneous Adipose Tissue (SCAT) were obtained in an experiment involving 36 pigs from 3 breeds slaughtered before (n=18) or after a 5-days exposure to 32°C (n=18).

first: Nathalie

last: Iannuccelli


title: Next Generation Sequencing Facilitates Quantitative Analysis of THP-1 cells under different stimulas.

city: HOUSTON

first: Chunxiao

last: Liu

state: Texas

address: 6565 MD Anderson Blvd., Zayed building. Z11.4000A

institute: MD Anderson Cancer center

summary:
To explore the role of human RNase1 on macrophage polarization, we induced human monocytes (THP-1) to differentiate into uncommitted macrophages and then polarized them to different phenotypes by lipopolysaccharide (LPS)/interferon (IFN)-γ, interleukin (IL)-4, or RNase1 as a stimulus.
We then performed gene expression profiling analysis using data obtained from RNA-seq of Nivolumab reponders and non-reponsers.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THP-1 cells under INF-γ plus LPS, IL-4 or RNase1 treatment.

first: Chenhao

last: Zhou

first: Mien-Chie

last: Hung


title: Transcriptomic data in pigs to improve the understanding of heat stress adaptation mechanisms.


title: Next Generation Sequencing Facilitates Quantitative Analysis of tumor samples from HCC patients receiving Nivolumab.

summary:
To identify critical tumor-secreting factors that may contribute to immunotherapy efficacy against HCC, we subjected tumor samples from 10 HCC patients to whole-transcriptome sequencing, and categorized the patients into two groups according to clinical response to nivolumab.
We then performed gene expression profiling analysis using data obtained from RNA-seq of Nivolumab reponders and non-reponsers.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Nivolumab reponders and non-reponsers.


title: Transcriptome profiling of Olaparib-resistant (OlapR) prostate cancer cell lines

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: Acquisition of resistance to the PARP inhibitor, Olaparib, constitutes a major challenge for the treatment of advanced prostate cancer. The purpose of this study was to identify molecular targets responsible for the development of acquired Olaparib resistance in advanced prostate cancer. Towards this goal, next-generation sequencing (NGS)-based gene expression profiling (RNA-Sequencing; RNA-Seq) was performed on castration-sensitive prostate cancer (CSPC)/Olaparib-sensitive LNCaP cells, castration-sensitive prostate cancer (CSPC)/Olaparib-resistant LN-OlapR cells, castration-resistant prostate cancer (CSPC)/Olaparib-sensitive C4-2B cells, and castration-resistant prostate cancer (CSPC)/Olaparib-resistant 2B-OlapR cells.

overall_design: A total of 4 samples were analyzed in this study. The study focused on castration-sensitive prostate cancer (CSPC) cell line, LNCaP, and the derived Olaparib-resistant cell line, LN-OlapR, and castration-resistant prostate cancer (CRPC) cell line, C4-2B, and the derived Olaparib-resistant cell line, 2B-OlapR. The cells were plated for 48 hours with no selection agent and total RNA was isolated (TRIzol) and then submitted for RNA-sequencing analysis.

first: Allen

last: Gao

first: Alan

last: Lombard

first: Amy

middle: R

last: Leslie


title: ChIP-seq analysis comparing WT, TAp63-/-, and ΔNp63-/- primary murine keratinocytes

city: Tampa

first: Elsa

middle: Renee

last: Flores

state: FL

address: 12902 USF Magnolia Drive

department: Department of Molecular Oncology

institute: Moffit Cancer Center

summary: The p53 family member TP63 encodes two sets of isoforms, TAp63 and ∆Np63 isoforms, which are characterized by different N-termini and have diverse biological functions in epidermal morphogenesis and in cancer. In the skin, where their activities are best characterized, TAp63 prevents premature aging by regulating cellular senescence and genomic stability of stem cells, while ∆Np63 controls terminal differentiation of the basal cells in the epidermis. This functional diversity is surprising given that these isoforms share a high degree of similarity, including an identical DNA binding domain. To understand the mechanisms involved in the transcriptional programs leading to these diverse biological functions, we performed genome-wide analyses using p63-ChIP-seq and RNA-seq of TAp63-/- and ∆Np63-/- compared to wild-type primary mouse epidermal cells. Our data indicate that TAp63 and ∆Np63 recognize significantly different response elements on DNA and can physically and functionally interact with distinct transcription factors for the downstream regulation of their target genes. Our findings unveil previously uncharacterized transcriptomes activated by the p63 isoforms to regulate diverse biological functions in epidermal morphogenesis and homeostasis and cancer.

overall_design: We performed a ChIP-seq analysis comparing differential bindings of p63 in 3 samples: WT, TAp63-/-, and ΔNp63-/- primary murine keratinocytes.

first: Marco

last: Napoli

first: Cristian

last: Coarfa


title: RNA sequencing for AML patients

status: Public on Dec 05 2023

city: Dalian

first: Jinsong

last: Yan

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary: We systematically evaluated osimertinib’s usage for treating AML patients from the subgroup with high level of CD34 and warrant clinical investigation in the treatment of refractory/resistant AML.

overall_design: Examination of osimertinib sensitivity for AML patients with different expression levels of CD34.


title: Smart-seq2 of spinal cord motoneurons in spinal cord injury model  after dual electrical stimulation with specific frequencies

city: Suzhou

first: Yaobo

state: Jiangsu

address: 199 Ren-Ai Road, Suzhou Industrial Park

department: Institute of neuroscience

institute: Soochow University

summary: Electrical stimulation can augment or modify neuronal function and can have therapeutic benefits for certain neurological disorders. There is evidence that enhancing spinal excitability with either epidural or transcutaneous stimulation can restore some volitional motor output after spinal cord injury (SCI). Lumbosacral epidural stimulation temporarily improves locomotor and autonomic function in both rodents and humans with SCI. When combined with overground locomotor training enabled by a weight-supporting device, epidural electrical stimulation (EES) promotes extensive reorganization of residual neural pathways that improves locomotion after stopping stimulation. However, the exact mechanism underlying the reconstruction of spinal cord neural circuits with electrical stimulation is not yet known. Thus, we developed a epidural electrical and muscle stimulation(EEMS) system at the interface of the spinal cord and muscle to mimic feedforward and feedback electrical signals in spinal sensorimotor circuits. Using methods of motor function evaluation, neural circuit tracing and neural signal recording, we discovered a unique stimulus frequency of 10-20 Hz under EEMS conditions that was required for structural and functional reconstruction of spinal sensorimotor circuits. Single-cell transcriptome analysis of EEMS activated motoneurons characterized molecular networks involved in spinal sensorimotor circuit reconstruction. This study provides insights into neural signal decoding during spinal sensorimotor circuit reconstruction, and indicates a technological approach for the clinical treatment of SCI.

overall_design: Spinal cord motoneurons of mice in the sham group (n = 3 mice), untrained group (n = 3 mice), 10-20 Hz MS group (n = 3 mice),  10-20 Hz SCS group (n = 3 mice), 10-20 Hz DES group (n = 3 mice), 1-40 Hz DES group (n = 3 mice) were labeled with TRDA and sacrificed 4 weeks after SCI (DES was renamed EEMS). The freshly isolated spinal cord was sliced on a vibratome (Leica, Germany) into 200- to 300-μm thick coronal sections.  Fluorescence-labeled motoneurons were visualized under a fluorescence microscope (Zeiss) using a miniature operating system (Eppendorf, Germany), and the motoneurons were aspirated by glass electrodes and placed in preservation solution (Invitrogen, USA).  TRDA-labeled neurons were individually homogenized in 1 ml TRIzol (Invitrogen), and RNA was extracted with a RNeasy Mini Kit (Qiagen) or equivalent.  Total RNA (1 μg) was used to synthesize double-stranded cDNA.

first: Kai

first: Wei

last: Wei

first: Dan

last: Yang


title: Tumor samples from HCC patients receiving Nivolumab; THP-1 cells under different stimulas.

overall_design: Refer to individual Series


title: Genetic suppressor screen identifies Tgp1 (glycerophosphocholine transporter), Plc1 (phospholipase C), and Kcs1 (IP6 kinase) as determinants of inositol pyrophosphate toxicosis in fission yeast

city: New York

first: Ana

last: Sanchez

state: NY

address: 430 E 67th Street, RRL-865

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: RNA-seq analysis compares gene expression of the STF6 (asp1-W386*), STF9 (asp1-W493*), kcs1-R332T, kcs1-L338R, and kcs1-E834K mutants to the wild-type fission yeast (Schizosaccharomyces pombe).

overall_design: 5 test sample and 2 control sample was processed (each sample has 3 replicate experiments).

first: Lauren

last: Bednor

first: Angad

last: Garg

first: Stewart

last: Shuman

first: Beate

last: Schwer


title: VGLL1 drives therapy resistance in estrogen receptor positive breast cancer [RNA-Seq 2]

city: London

first: Carolina

last: Gemma

state: Greater London

address: Du Cane Road, Hammersmith Campus

department: Department of Surgery and Cancer

institute: Imperial College London

summary: To identify VGLL1 target genes we performed RNA-seq following siRNA-mediated VGLL1 downregulation in FULVR cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FULVR cells treated with VGLL1 siRNA or control siRNA (3 replicates per siRNA)

first: Simak

last: Ali


title: VGLL1 drives therapy resistance in estrogen receptor positive breast cancer [RNA-Seq 3]

summary: To investigate the function of VGLL1 in breast cancer and its role in the resistance to endocrine therapies we generated stable MCF7 cells overexpressing VGLL1 using CRISPR/Cas9 Synergistic Activation Mediator (SAM) method (MCF7 ActCas9-VGLL1 cells). MCF7 ActCas9-VGLL1 cells were also cultured in the presence of fulvestrant 100nmM or 1µM to develop fulvestrant resistant cells (MCF7 ActCas9-VGLL1-FULVR) and RNA-seq was performed in the different cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF7 ActCas9-VGLL1 cells, MCF7 ActCas9-VGLL1-FULVR cells and the parental MCF7 cells (3 replicates per cell line)


title: Blood transcriptomic data in pigs to improve the understanding of heat stress adaptation mechanisms.

first: Laurence

last: Liaubet

overall_design: To achieve this, transcriptomic data from blood were obtained in an experiment involving 36 pigs from 3 breeds slaughtered before (n=18) or after a 5-d exposure to 32°C (n=18).

first: David

last: Renaudeau

first: Guilhem

last: Huau

first: Jean-Luc

last: Gourdine

first: Laure

last: Gress

first: Katia

last: Feve

first: Yannick

last: Lippi

first: Yann

last: Labrune

first: Jérôme

last: Fleury

first: Juliette

last: Riquet


title: Scaffold RNA engineering in type V CRISPR-Cas systems: a potent way to enhance gene expression in the yeast Saccharomyces cerevisiae.

city: Tianjin

first: Lifang

middle: Li

last: Yu

state: Tianjin

address: Wei Jin road

institute: Tianjin University

summary: New, orthogonal transcription factors in eukaryotic cells have been realized by engineering nuclease-deficient CRISPR-associated proteins and/or their guide RNAs. In this work, we present a new kind of orthogonal activators, in Saccharomyces cerevisiae, made by turning type V CRISPR RNA into a scaffold RNA (ScRNA) able to recruit a variable number of VP64 activation domains. The activator arises from the complex between the synthetic ScRNA and DNase-deficient type V Cas proteins: dCas12e and denAsCas12a. The transcription activation achieved via the newly engineered dCas:ScRNA system is up to 4.7-fold higher than that obtained with the direct fusion of VP64 to Cas proteins. The new transcription factors have been proven to be functional in circuits such as Boolean gates, converters, multiplex-gene and metabolic-pathway activation. Our results extend the CRISPR-Cas-based technology with a new effective tool that only demands RNA engineering and improves the current design of transcription factors based on type V Cas proteins.

overall_design: To investigate the dCas12:ScRNA activation on endogenous regulation, we used S. cereviase endogenous gene GAL7, HED1, CYC1 as our target genes. And the dCas12:ScRNA activators will bind on the promoter on these target genes.

first: Mario

last: Marchisio


title: VGLL1 drives therapy resistance in estrogen receptor positive breast cancer [RNA-Seq 1]

summary: To investigate if the drug verteporfin can inhibit VGLL1 co-transcriptional activity in Fulvestrant resistant breast cancer cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FULVR cells treated with vertepotfin (2µM, 24 h) or vehicle (4 replicates per treatment)


title: PI3K signaling promotes formation of lipid-laden foamy macrophages at the spinal cord injury site

city: Miami

first: James

last: Choi

address: 1095 NW 14th Terrace

institute: University of Miami Miller School of Medicine

summary: After spinal cord injury (SCI), infiltrating macrophages undergo excessive phagocytosis of myelin and cellular debris, forming lipid-laden foamy macrophages. To understand their role in the cellular pathology of SCI, investigation of foamy macrophage phenotype in vitro revealed a unique inflammatory profile, increased reactive oxygen species (ROS) production, and mitochondrialdysfunction. Bioinformatic analysis identified PI3K as a regulator of inflammation in foamy macrophages, and pharmacological inhibition of this pathway decreased lipid content and inflammatory cytokine and ROS production in these cells. Macrophage-specific inhibition of PI3K using liposomes significantly decreased foamy macrophages at the injury site after a mid-thoracic contusive SCI in mice. RNA sequencing and in vitro analysis of foamy macrophages revealed increased autophagy after PI3K inhibition as a potential mechanism for reduced cellular lipid accumulation. Together, our data suggest that formation of pro-inflammatory foamy macrophages after SCI is due to activation of PI3K signaling that leads to decreased autophagy.

overall_design: We used an in vitro model of cultured macrophages treated with homogenized spinal cord, rather than purified myelin, since it is more representative of all the lipid sources driving foamy macrophage formation after SCI. To investigate the biological processes by which Torin-2 decreased lipid droplet accumulation, we incubated bone-marrow-derived macrophages in 1% w/v spinal cord homogenate for 24 hours and performed bulk RNA-seq on 3 biological replicates treated with vehicle, Torin-2, or rapamycin. Rapamycin, whcih does not affect lipid accumulation, was used as a control to account for the effects of mTORC1 inhibition by Torin-2.

first: Christine

last: Ryan

first: Brian

last: Kang

first: Claudia

last: Pereira

first: Carlos

last: Moraes

first: Hassan

last: Al-Ali

first: Jae

middle: K

last: Lee


title: VGLL1 drives therapy resistance in estrogen receptor positive breast cancer [ChIP-Seq]

first: Carolina

last: Gemma

summary: The transcriptional activity of the TEAD4 trascription factor requires co-activators. In this study we found that the expression of the TEAD coactivator VGLL1 is repressed in estrogen receptor positive breast cancer but upon resistance to endocrine threapies VGLL1 is expressed to high levels. To  elucidate the importance of the coactivator VGLL1 in breast cancer cells resistant to endocrine therapies and to identify the VGLL1 target genes, we performed ChIP-seq for VGLL1 in MCF7 breast cancer cells resistant to fulvestrant (FULVR) and ChiP-seq for TEAD4 in FULVR cells and the isogenic MCF7 cells.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for VGLL1 in the MCF7 cell line resistant to fulvestrant (FULVR) (3 replicates), ChIP-seq for TEAD4 in FULVR cells (2 replicates), ChIP-seq  for TEAD4 in the parental cell line MCF7 (2 replicates). ChIP-seq samples were also sequenced together with the input controls in MCF7 and FULVR cell lines

first: Simak

last: Ali


title: Rare, tightly-bound, multi-cellular clusters in the pancreatic ducts of adult mice function like progenitor cells and survive and proliferate after acinar cell injury

status: Public on Dec 04 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: Pancreatic ductal progenitor cells have been proposed to contribute to adult tissue maintenance and regeneration after injury, but the identity of such ductal cells remains elusive. Here, from adult mice, we identify a near homogenous population of ductal progenitor-like clusters, with an average of 8 cells per cluster. They are a rare subpopulation, about 0.1% of the total pancreatic cells, and can be sorted using a fluorescence-activated cell sorter with the CD133highCD71lowFSCmid-high phenotype. They exhibit properties in self-renewal and tri-lineage differentiation (including endocrine-like cells) in a unique 3-dimensional colony assay system. An in vitro lineage tracing experiment, using a novel HprtDsRed/+ mouse model, demonstrates that a single cell from a cluster clonally gives rise to a colony. Droplet RNAseq analysis demonstrates that these ductal clusters express embryonic multipotent progenitor cell markers Sox9, Pdx1, and Nkx6-1, and genes involved in actin cytoskeleton regulation, inflammation signaling, organ development and cancer. Surprisingly, these ductal clusters resist prolonged trypsin digestion in vitro, preferentially survive in vivo after a severe acinar cell injury and become proliferative within 14 days post-injury. Thus, the ductal clusters are the fundamental units of progenitor-like cells in the adult murine pancreas with implications in diabetes treatment and tumorigenicity.

overall_design: From adult murine pancreata, the CD133(hi)CD71(low)FSC(mid-high) (abbreviated as FSC-MH) or the CD133(hi)CD71(low)FSC(low) (abbreviated as FSC-L) sub-populations were sorted and subjected to a 10x Chromium device using a 10X V3 Single Cell 3’ Solution kit (10x Genomics, Chromium Single Cell 3’ Regent 00kit V3 Chemistry, Cat. PN-1000092). Approximately 0.1 million reads per cell/unit were sequenced. Raw sequencing data were aligned to the mouse genome (mm10) and the R package Seurat was used for data analysis. Units with <200 detectable genes and >15% mitochondrial genes were excluded.

first: Jacob

last: Tremblay

first: Jose

last: Ortiz

first: Heater

last: Zook

first: Janine

last: Quijano

first: Min-Hsuan

last: Chen

first: Xiwei

last: Wu

middle: T


title: RNA-seq profiling of epidermal tissues of visually younger and older women in the Youngster-Oldie (Y-O) study

city: Hamburg

first: Agata

last: Bienkowska

address: Beiersdorfstraße 1-9

institute: Beiersdorf AG

summary: Skin, with its distinctive features and visible signs of aging, provides a remarkable model for studying the aging process. The variable rate of skin aging among individuals provides a valuable opportunity to capture a wide range of age-related changes. In this study, we used bulk RNA sequencing (RNA-seq) to explore the diverse skin characteristics of individuals with both older and younger appearances.

overall_design: We examined samples from 25 women aged 41-51 years who appeared visually at least 5 years younger (n = 10 females) or older (n = 15 females) than their chronological age. Both groups of the Y-O study were similar in chronological age (Youngsters = 45.30 ± 2.11 years, Oldies = 46.40 ± 3.00 years), but different in expert-rated visual facial age (Youngsters = 40.24 ± 2.61 years, Oldies = 58.16 ± 5.39 years).

first: Cassandra

last: Falckenhayn

first: Jörn

last: Söhle

first: Boris

last: Kristof

first: Elke

last: Grönniger


title: Transcriptonal and epigenetic profiling of neuroblastoma cells based on CD49b expression

city: Boston

first: Allan

middle: M

last: Goldstein

state: MA

address: 185 Cambridge St

department: Pediatric Surgery

institute: Massachusetts General Hospital

summary: This study was undertaken to assess heterogeneity within neuroblastoma cell populations, and to assess whether the integrin CD49b can distinguish different neuroblastoma phenotypes. Methods: We performed bulk RNA sequencing on Neuro-2a and SH-SY5Y neuroblastoma cells sorted based on CD49b expression, and CUT&RUN for H3K4me1 and H3K27ac on Neuro-2a cells sorted based on CD49b expression. Results: We find that CD49b expression identifies transcriptionally distinct neuroblastoma cell populations. High CD49b expression marks cells expressing mesenchymal genes, while lack of CD49 denotes cells expression neuronal genes. CUT&RUN analysis shows that CD49b distinguishes cells with distinct enhancer and super enhancer profiles. Conclusion: RNA sequencing and CUT&RUN demonstrate that neuroblastoma cell lines include heterogeneous populations.

overall_design: Use of bulk RNA sequencing and CUT&RUN technologies to analyze transcription and enhancer status of neuroblastoma cell lines.