title: A Novel Piperine Derivative Inhibits Colorectal Cancer Progression by Modulating EMT Signaling Pathways: An Integrated Transcriptomic and Machine Learning Analysis

city: Lianyungang

first: wenhao

last: cheng

state: Jiangsu

address: 59 Cangwu Road, Haizhou District

department: College of Pharmacy

institute: Jiangsu Ocean University

summary: Colorectal cancer (CRC) is one of the most prevalent and lethal malignancies worldwide. The epithelial-mesenchymal transition (EMT) plays a critical role in tumor invasion and metastasis. Piperine, a natural alkaloid, has demonstrated antitumor activity; however, its low bioavailability limits clinical application. HJJ_3_5, a novel piperine derivative synthesized and validated by our research group, exhibits potent antitumor effects against colorectal cancer cells. In addition to its strong cytotoxicity, HJJ_3_5 disrupts key metastatic processes, including DNA replication, cell migration, invasion, and adhesion, showcasing its multifaceted mechanism of action. In vivo, HJJ_3_5 shows significant efficacy in the CAM model, effectively inhibiting tumor growth and angiogenesis, underscoring its potential as a powerful anti-cancer agent. At the molecular level, comprehensive transcriptomic analysis reveals that HJJ_3_5 significantly downregulates the EMT pathway. Notably, machine learning algorithms identify six core EMT-related genes (COL12A1, PJA2, VCAN, MEF2C, DPYD, and DDR2) as pivotal drivers of cancer progression, with their expression strongly associated with poor clinical outcomes. Single-cell RNA sequencing further reveals that these genes are predominantly expressed in fibroblasts and myofibroblasts, key players in the EMT process and metastasis. These findings position HJJ_3_5 as a promising therapeutic candidate, offering a targeted and potent approach to halting the relentless progression of colorectal cancer.

overall_design: In order to investigate the role and mechanism of HJJ_3_5 in colon cancer, we treated HCT116 cells with HJJ_3_5 and without treatment. Then, we performed gene expression profiling analysis using RNA seq data from HJJ_3_5 and DMSO cells.

first: Wenhao

first: Bin

last: Liu


title: Transcriptome analysis reveals anti-Cancer effects of fenbendazole on ovarian cancer: in vitro and in vivo study

status: Public on Aug 23 2024

city: Kunming

first: Xin

last: Wang

state: Yunnan

address: 519 Kunzhou Road,  Kunming, Yunnan, P. R. China

country: China

institute: Kunming Medical University, The Third Affiliated Hospital

type: Expression profiling by high throughput sequencing

summary: We reported the transcriptome profiling of FBZ-treated SKOV3 ovarian cancer cells. A total of 1747 differentially expressed genes (DEGs) were identified, including 944 downregulated and 803 upregulated genes. KEGG enrichment and reactome enrichment showed that DEGs were mainly associated with mitosis and cell cycle associated pathway

overall_design: The effect of Fenbendazole (FEN OR FBZ) on transcriptome of the SKOV3 cell line

first: Yue

last: Jia

first: Hongying

last: Yang

first: Hongping

last: Zhang


title: Transcriptomic analysis of TGFβ-mediated fibrosis in primary human Tenon’s fibroblasts

city: Melbourne

first: antony

last: boynes

state: Victoria

address: Parkville

department: Ophthalmology

country: Australia

institute: University of Melbourne

summary: Glaucoma filtration surgery (GFS) is performed to slow down disease progression in glaucoma, a leading cause of irreversible blindness worldwide. Following surgery, pathological wound healing may lead to conjunctival fibrosis and filtering failure. Myofibroblasts are the key cells responsible for postoperative conjunctival scarring.  This study aims to further understand the molecular mechanisms of conjunctival fibrosis following GFS. We utilised RNA-sequencing (RNA-seq) to delineate the TGFβ1 induced changes in the transcriptome of human Tenon’s fibroblasts (HTFs). RNA sequencing was performed on HTFs after 5 days of TGFβ1 treatment. Following quality control, 3,362 differentially expressed genes were identified, of which 1,532 were upregulated and 1,820 were downregulated. We identified signaling pathways associated with the pathogenesis of conjunctival fibrosis. The DEGs (differentially expressed genes) were enriched in pathways including myofibroblast differentiation, TGFβ-signaling, collagen and extracellular matrix organization, epithelial to mesenchymal transition, and cell cycle regulation. The results of this study identified the transition from HTF to myofibroblast is characterised by the upregulation of key genes including  LDLRAD4, CDKN2B, FZD8, MYOZ1, and the downregulation of SVIL, LTBP4,  and TNXB. This unprecedented insight into the transcriptional landscape of HTFs and myofibroblast differentiation is essential to understand the pathophysiology of conjunctival scarring and develop new therapeutic agents.

overall_design: HTFs were propagated from explanted subconjunctival Tenon’s capsules collected during GFS performed in three human patients. HTFs were assigned to either the control (medium alone) or the TGFβ1 (10 ng/mL) treatment group. RNA-sequencing was performed on samples after 5-days of treatment. RNA was extracted using the illustra RNAspin Mini Kit and sequenced using Novaseq 6000 with 100bp single-end sequencing at a depth of 20million reads per sample.

first: Antony

last: Boynes

first: Zoe

last: Pasvanis

first: Raymond

last: Wong

first: Jennifer

middle: F

last: Gaskin

first: Elsa

last: Chan

first: Roy

last: Kong


title: Identifying transcriptomic profiles after repetitive vaccination in ovine spleen

city: Leioa

first: Begoña

middle: M

last: Jugo

state: Basque Country

address: Sarriena auzoa s/n

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

summary: Aluminum hydroxide, has long been employed as a vaccine adjuvant for its safety profile, although its precise mechanism of action remains elusive. In this study, we investigated the transcriptomic responses in sheep spleen following repetitive vaccination with aluminum adjuvanted vaccines and aluminum hydroxide alone. Notably, this work represents the first exploration of the sheep spleen transcriptome in such conditions. A total of 18 high-depth RNA-seq libraries were sequenced, resulting in a rich dataset which allowed isoform-level analysis also. The comparisons between vaccine-treated and control groups (V vs C) as well as between vaccine-treated and adjuvant-alone groups (V vs A) revealed significant alterations in gene expression profiles, including protein coding genes and long non-coding RNAs. Among the differentially expressed genes, many were associated with processes such as endoplasmic reticulum (ER) stress, immune response, cell cycle, and cellular senescence. The analysis of co-expression modules further indicated a correlation between vaccine treatment and genes related to ER stress and unfolded protein response. Surprisingly, adjuvant-alone treatment had little impact on the spleen transcriptome. Additionally, the role of alternative splicing in the immune response was explored. We identified isoform switches in genes associated with immune regulation and inflammation, potentially influencing protein function. In conclusion, this study provides valuable insights into the transcriptomic changes in sheep spleen following vaccination with aluminum adjuvanted vaccines and aluminum hydroxide alone. These findings shed light on the molecular mechanisms underlying vaccine-induced immune responses and emphasize the significance of antigenic components in aluminum adjuvant mechanism of action. Furthermore, the analysis of alternative splicing revealed an additional layer of complexity in the immune response to vaccination in a livestock species.

overall_design: Total RNA profiles were generated by deep sequencing on an Illumina NovaSeq 6000 sequencer, of the spleen of 18 age-matched Rasa Aragonesa sheep divided in three experimental groups of 6 lambs. One group received aluminum-based subcutaneous commercial vaccines (the vaccine group). Another group (the adjuvant group) received equivalent doses of aluminum hydroxide (Alhydrogel, CZ Veterinaria, Spain). The control group only received phosphate-buffered saline (PBS). A total of 19 inoculations were administered in each group during a period of 475 days (from February 2015 to June 2016), following the recommended vaccination schedule. For this study 18 libraries were sequenced (all samples where sequenced in two different sequencing runs).

first: Aitor

last: Guisasola

first: Martin

last: Bilbao Arribas

first: Endika

last: Varela Martínez

first: Naiara

last: Abedaño

first: Marta

last: Pérez

first: Lluis

last: Luján


title: GPR40 Agonist ameliorates neurodegeneration and motor impairment by regulating NLRP3 inflammasome in Parkinson’s disease animal models.

city: Incheon

first: TAEYOUNG

last: HA

address: 155 Gaetbeol-ro Yeonsu-gu Incheon, Korea

country: South Korea

institute: Lee Gil Ya Cancer And Diabetes Institute

summary: Parkinson's disease (PD) is characterized by the progressive degeneration of dopaminergic neurons in the substantia nigra pars compacta (SN) and accumulation of intracellular α-synuclein aggregates known as Lewy bodies and Lewy neurites.   Levels of polyunsaturated fatty acids (PUFAs) are reduced in the SN of PD patients and G protein-coupled receptor 40 (GPR40) serves as a receptor for PUFAs, playing a role in neurodevelopment and neurogenesis. Additionally, GPR40 is implicated in neuropathological conditions such as apoptosis and inflammation, suggesting its potential as a therapeutic target in PD.   In this study, we investigated the neuroprotective effects of the GPR40 agonist, TUG469, in PD models. Our results demonstrate that TUG469 reduces neurotoxicity induced by 6-OHDA in SH-SY5Y cells. In the 6-OHDA-induced PD model, TUG469 treatment improved motor impairment, preserved dopaminergic fibers and cell bodies in the striatum (ST) or SN, and attenuated 6-OHDA-induced microgliosis and astrogliosis in the brain. Furthermore, in a PD model involving the injection of mouse ɑ-syn fibrils into the brain (mPFFs-PD model), TUG469 treatment reduced the level of phosphorylated Ser129 ɑ-synuclein and decreased microgliosis and astrogliosis in mPFFs-PD model. Our investigation also revealed that TUG469 modulates inflammasome activation, apoptosis, and autophagy in the 6-OHDA-PD model, as evidenced by RNA-seq analysis and western blotting.  In summary, our findings highlight the neuroprotective effects of GPR40 agonist on dopaminergic neurons and their potential as therapeutic agents for PD. These results underscore the importance of targeting GPR40 in PD treatment, particularly in mitigating neuroinflammation and preserving neuronal integrity.

overall_design: To investigate the mechanisms of TUG469, we performed an animal experiment in which we treated the striatum of C57BL6 mice with 4 μg of 6-OHDA and administered TUG469 for 3 weeks. Subsequently, we extracted RNA from the striatum and sustantianigra, and performed RNA-seq.

first: Tae-Young

last: Ha

first: Jae-Bong

last: Kim

first: Yeji

first: Sang

last: Park

first: Keun-A

last: Chang


title: Transcriptomic analysis of synovial cells derived from collagen-induced arthritis mice treated with a JAK inhibitor, upadacitinib

city: Tokyo

first: Noriko

last: Komatsu

address: 7-3-1, Hongo, Bunkyo-ku

country: Japan

institute: The Univ of Tokyo

summary: In rheumatoid arthritis (RA), inflammation and joint destruction are exacerbated by a complicated interaction among immune cells, synovial fibroblasts and bone cells. It remains to be elucidated which cell-cell interaction critically drives the pathogenesis of RA and serves as a therapeutic target for synthetic disease modifying antirheumatic drugs (DMARDs) such as janus kinase (JAK) inhibitors. we performed a scRNA-seq analysis of the synovium of collagen-induced arthritis (CIA) mice treated with JAK inhibitor, followed by a computational analysis to identify the drug target cells and signaling pathways in vivo

overall_design: scRNA-seq analysis was performed on synovial cells which were isolated from the knee joints of CIA mice treated with a JAK inhibitor, upadacitinib (n=6). Alignment, quantitation and aggregation of the sample count matrices were performed using the 10x Genomics Cell Ranger pipeline (v.3.0) according to the manufacturer’s protocol (GENEWIZ).

first: Nam

last: Cong-Nhat Huynh

first: Hiroshi

last: Takayanagi


title: Single-cell lineage tracing uncovers unique skin adipose hierarchy and Sox9-mediated differentiation of adipocyte precursors

city: St. Louis

first: Samantha

middle: A

last: Morris

state: Missouri

address: 660 S Euclid Ave

country: USA

institute: Washington University in St. Louis

summary: White adipose tissue is essential to various physiological functions, with adipocyte precursor cells (APCs)—comprised of progenitors and preadipocytes—playing a pivotal role in generating mature adipocytes during the expansion of adipose depots. Here, using single-cell RNA sequencing-based lineage tracing, we characterize APC populations in the skin, a depot distinguished by its uniquely rapid and efficient adipogenesis relative to other sites, such as inguinal adipose. We identify a previously uncharacterized population of immature preadipocytes and reveal a biased differentiation potential among APCs. Contrary to the step-wise differentiation paradigm proposed to yield mature adipocytes, progenitor cells represent the primary source of committed preadipocytes, while preexisting preadipocytes accumulate in immature states with distinct potential. We use this framework of cell heterogeneity and lineage in skin adipose to investigate the mechanisms of APC differentiation, identifying Sox9 as a crucial regulator of precursor proliferation and differentiation. Finally, via cross-depot transplantation, we define intrinsic and extrinsic factors that influence the behavior of skin progenitors, highlighting the contrasting dynamics between skin and inguinal depots. These findings provide a deeper understanding of the specific dynamics and molecular mechanisms underlying rapid adipogenesis in skin adipose tissue.

overall_design: Skin adipocyte precursors were isolated by Fluorescence-activated cell sorting (FACS) according to markers of subpopulations, CellTagged, transplanted into P21 mice, and analyzed by scRNA-seq.

first: Guillermo

last: Rivera-Gonzalez

first: Emily

middle: G

last: Butka

first: Carolynn

middle: E

last: Gonzalez

first: Rachel

middle: L

last: Mintz

first: Violet

last: Josephson

first: Wenjun

first: Kunal

last: Jindal

first: Kenji

last: Kamimoto

first: Brett

last: Shook

first: Matthew

middle: S

last: Rodeheffer


title: NOTCH, ERK and SHH signaling respectively control the fate determination of cortical astrocytes, oligodendrocytes, and olfactory bulb interneurons

city: SHANGHAI

first: MENGGE

last: SUN

address: FENGLIN ROAD

institute: FUDAN UNIVERSITY

summary: During cortical development, radial glial cells, known as neural stem cells, initially generate a large number of cortical glutamatergic pyramidal neurons through a process called neurogenesis. This is followed by the generation of a diversity of cortical astrocytes, oligodendrocytes, and olfactory bulb interneurons, known as gliogenesis. However, the molecular mechanisms underlying the switch from cortical neurogenesis to gliogenesis, and the subsequent fate determination of cortical astrocytes, oligodendrocytes, and olfactory bulb interneurons, remain unclear. Here, we report that extracellular signal-regulated kinase (ERK) signaling plays a fundamental role in promoting cortical gliogenesis and the generation of cortical glial progenitors. Additionally, SHH-SMO-GLI activator signaling has an auxiliary function to ERK during these processes. We further demonstrate that NOTCH signaling is absolutely required for the fate determination of astrocytes, while ERK signaling plays a prominent role in oligodendrocyte fate specification, and SHH signaling is crucial for the fate determination of olfactory bulb interneurons from cortical progenitors. We provide evidence suggesting that this mechanism is conserved in both mice and humans. Finally, we propose a unifying principle of mammalian cortical gliogenesis.

overall_design: FlashTag (CellTrace Yellow, Life Technologies, #C34567, 0.5 μl of 10 mM) was injected into the cortical lateral ventricle of control mice (Map2k1 and Map2k2 flox), Emx1-Cre; MAP2k1/2-dcko and hGFAP-Cre; MAP2k1/2-dcko mice at E18.0. P2 pups were sacrificed, and the brains were immediately removed and submerged in fresh ice-cold Hanks’ balanced salt solution (Gibco 14175-095). The dorsal cortices were cut into small pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit by following the manufacturer’s instruction. The tdTomato+ (tdT+) cells were captured and harvested through fluorescence-activated cell sorting (FACS). The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-Seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina Novaseq 6000.

first: Yanjing

last: Gao

first: Mengge

last: Sun

first: Tongye

last: Fu

first: Zhengang

last: Yang


title: Gene expression of human bone marrow-derived stem cells on liquid crystalline self-assembed hydroxyapatite nanorods for bone regeneration

city: London

first: Jishizhan

last: Chen

address: 10 Pond St

department: Division of Surgery & Interventional Science

country: United Kingdom

institute: University College London

summary: Liquid crystal-like, low-dimensional and long-range ordered structures (LC) are found in human tissues including bones.  The excellent mechanical and biological functions of natural bones entail the well-orchestrated nano-scale hydroxyapatite (HAp) crystals within collagen fibres matrix.  However, the understanding of the self-assembling of HAp nanocrystals and formation of hierarchically ordered bone structure are still elusive.  Our study aims to develop an in situ traceable anisotropic HAp nanorods doped with citrate and terbium (Cit/Tb-HAp NRs), investigate their self-assembling behaviour and illuminate their potential and pathway of guiding ordered osteogenesis at multi-scale in vitro.

overall_design: Human bone marrow-derived stem cells (hBMSCs, ScienCell, Carlsbad, US) were culture on coated coverslips. Different groups were set up based on the coating substrates, which are hydroxyapatite nanorods (HAp NRs) with or without 4 mol% terbium (Tb) doping, in short- or long-range ordered patterns (fixed by PDMS). The coverslips coated with only PDMS were utilised as the control. Three biological replicates were set for each condition. On day 21 of osteogenic differentiation in the Mesenchymal Stem Cell Osteogenic Differentiation Medium (MODM, ScienCell, Carlsbad, US), total RNA extraction was performed using a Monarch Total RNA Miniprep Kit (New England Biolabs, Ipswich, US), according to the manufacturer’s protocol. The RNA-Seq was carried out at the UCL Genomics facility. RNA concentration was measured on a Nanodrop spectrometer and 500 ng of RNA was used for cDNA synthesis and library preparation using the Kapa mRNA HyperPrep assay (Roche, Basel, Switzerland) and xGen UDI-UMI adapters (Integrated DNA Technology, Shanghai, China). Sequencing of these libraries was performed on the NextSeq 2000 (Illumina, San Diego, US) P2 flow-cell with 56bp paired-end reads.

first: Wenhui

last: Song

first: Martin

last: Birchall

first: Alexander

middle: J

last: MacRobert


title: B7-H3-Targeted CAR-Vδ1T Cells Exhibit Potent Broad-Spectrum Activity Against Solid Tumors

status: Public on Aug 22 2024

city: Suzhou

first: Licui

last: Jiang

state: None Selected

address: Dushuhu Campus, Soochow University, No. 199, Ren'ai Road/Street

institute: Soochow University

summary: Vδ1T cells, a rare subset of γδT cells, hold promise for treating solid tumors. Unlike conventional T cells, they recognize tumor antigens independently of the MHC antigen-presentation pathway, making them a potential “off-the-shelf” cell therapy product. However, isolation and activation of Vδ1T cells is challenging, which has limited their clinical investigation. Here, we developed a large-scale clinical-grade manufacturing process for Vδ1T cells and validated the therapeutic potential of B7-H3-CAR-modified Vδ1T cells in treating solid tumors. Co-expression of interleukin-2 with the B7-H3-CAR led to durable anti-tumor activity of Vδ1T cells in vitro and in vivo. In multiple subcutaneous and orthotopic mouse xenograft tumor models, a single intravenous administration of the CAR-Vδ1T cells resulted in complete tumor regression. These modified cells demonstrated significant in vivo expansion and robust homing ability to tumors, akin to natural tissue-resident immune cells.Additionally, the B7-H3-CAR-Vδ1T cells exhibited a favorable safety profile. In conclusion, B7-H3-CAR-modified Vδ1T cells represent a promising strategy for treating solid tumors.

overall_design: To investigate the molecular mechanisms underlying the superior efficacy of IL-2-expressing AQ-CAR-IL2-Vδ1T cells compared to AG-CAR-Vδ1T cells, we performed single-cell RNA sequencing on cells after repeated antigen stimulation with Raji-B7-H3 cells in vitro for four consecutive days.

first: Lin

first: Fengtao

last: You


title: Molecular and pathological characterisation of diffuse large B-cell lymphomas in children with Nijmegen breakage syndrome

city: Łódź

first: Jędrzej

last: Chrzanowski

state: łódzkie

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

summary:
Nijmegen-breakage syndrome (NBS, OMIM #251260) is an autosomal recessive chromosomal instability syndrome characterized by a very distinct phenotype (microcephaly, growth retardation, immunodeficiency) associated with increased predisposition to develop malignancies, particularly of lymphoid origin (by the age of 20 years, over 40% of NBS patients develop cancer). Immunological lineage of lymphomas in NBS significantly differs from Non-Hodgkin Lymphomas (NHL) entities observed in general pediatric population as well as in primary immunodeficiencies. There is a strong predominance of diffuse large B-cell lymphoma (DLBCL) and T cell lymphoblastic lymphoma (T-LBL/ALL), all showing clonal Ig/TCR rearrangements.
In the current study we aimed to examined gene expression signature of metabolic pathways in DLBCL cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 41 human FFPE samples, of which 8 had confirmed Nijmegen breakage syndrome and 22 presented immunohistochemistry-confirmed Germinal center B-cell like sub-type of diffuse large B-cell lymphoma

first: Agata

last: Pastorczak

first: Marcin

last: Braun

first: Joanna

last: Madzio

first: Szmyd

last: Bartosz

first: Kamila

last: Wypyszczak

first: Pawel

last: Sztormwasser

first: Marzena

last: Wojtaszewska

first: Jedrzej

first: Wieslawa

last: Grajkowska

first: Hanna

last: Gregorek

first: Anna

last: Wakulinska

first: Bernarda

last: Kazanowska

first: Zdenka

last: Krenova

first: Dilys

last: Weijer

first: Roland

last: Kuiper

first: Wojciech

last: Mlynarski


title: Paired VDJ and transcriptome single cell sequencing in LMP2 multimer-positive human T cells treated with anti-PD-L1 and anti-TIM3 antibodies.

city: Montreal

first: Jean-Sebastien

last: Delisle

state: Quebec

address: 5415 Boulevard de l'Assomption

country: Canada

institute: Centre de recherche de l'Hôpital Maisonneuve-Rosemont

summary: We report the change in gene expression profile paired to clonotype profiling in single cells from LMP2 multimer-positive human T cells generated following weekly stimulations with antigen-pulsed dendritic cells and subjected or not to PD-L1/TIM3 double blockade.

overall_design: VDJ and transcriptome scRNA-sequencing at day 21 and 28 in LMP2 multimer FACS-sorted positive fractions of human T cells cultured with or without anti-PD-L1 and anti-TIM3 antibodies from 3 healthy donors.

first: Shirin

last: Lak

first: Valérie

last: Janelle

first: Anissa

last: Djedid

first: Gabrielle

last: Boudreau

first: Ann

last: Brasey

first: Véronique

last: Lisi

first: Cédric

last: Carli

first: Lambert

last: Busque

first: Vincent-Philippe

last: Lavallée

first: Jean-Sébastien


title: Toxoplasma gondii infection supports the infiltration of T cells into brain tumors

city: Charlottesville

first: Hui

last: Zong

state: Virginia

address: 7042 Pinn Hall

department: Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

summary: Primary brain tumors, residing behind the blood-brain-barrier (BBB), have few infiltrated T cells. We hypothesized that Toxoplasma gondii, a microorganism that naturally traffics to the brain to elicit a Th1 response, can promote T cell infiltration into brain tumors. Using a mouse genetic model for medulloblastoma, we found that T. gondii infection was well-controlled in tumor-bearing mice, induced robust infiltration of T cells into the tumor, and led to myeloid cell transcriptional reprogramming toward a T cell-supportive state. The study demonstrates that the immune modulatory capacity of T. gondii could be leveraged to promote brain tumor immunotherapy through future efforts.

overall_design: To study the effect of T. gondii infection over the transcriptional profile of the myeloid populations in the tumors, myeloid cells were enriched from the tumors of uninfected (injected with PBS) or infected tumor-bearing mice (n=5 per group). Gene expression analysis was then performed on the RNA-seq data obtained from the samples.

first: Yen

middle: T

last: Nguyen

first: Piotr

last: Przanowski

first: Shengyuan

last: Wang

first: Lydia

last: Sibley

first: Xiao-Yu

last: Zhao

first: Michael

last: Kovacs

first: Marieke

middle: K

last: Jones

first: Maureen

last: Cowan

first: Wenjie

last: Liu

first: Andrea

middle: R

last: Merchak

first: Alban

last: Gaultier

first: Kevin

last: Janes

first: Chongzhi

last: Zang

first: Tajie

last: Harris

first: Sarah

last: Ewald


title: Single cell RNA-sequencing reveals cellular heterogeneity and trajectories of lineage specification

city: Hangzhou

first: Fangling

state: Zhejiang province

address: Jie Fang Road NO.88

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

overall_design: The coordinated spatial and temporal regulation of gene expression in the murine hindlimb determines the identity of mesenchymal progenitors and the development of diversity of musculoskeletal tissues they form.   Hindlimb development has historically been studied with lineage tracing of individual genes selected a priori, or at the bulk tissue level, which does not allow for the determination of single cell transcriptional programs yielding mature cell types and tissues.  In order to study the regulatory mechanism of stem cell therapy for sarcopenia and the influence of related genes on sarcopeniawe used single cell mRNA sequencing (scRNA-seq) to profile the developing murine hindlimb.

first: Kelly

last: NH

first: Huynh

last: NP


title: ZMAT1 promotes osteoclast formation and bone loss through TRIM46 mediated YAP1 degradation II

city: Shanghai

first: Yijin

last: Hou

address: No. 168, Changhai Road

institute: Department of Traumatic Orthopedics, Changhai Hospital, Naval Medical University

summary: Osteoclasts and osteoblasts play a critical role in bone remodeling, and their dysregulation leads to pathological bone loss. However, precise regulation of their differentiation remains not fully elucidated. This study investigates the role of transcriptional regulator Zinc Finger Matrin-Type 1 (Zmat1) in both osteoclastogenesis and osteoblastogenesis. Zmat1 deficiency resulted in decreased osteoclast activity, and reduced bone resorption. Mechanististically, ZMAT1 was significantly upregulated during osteoclast differentiation and acted as a transcriptional repressor of the E3 ubiquitin ligase TRIM46, which then regulates YAP1 degradation via K48-linked ubiquitination. Furthermore, Zmat1 deficiency also enhanced osteoblast activity and bone formation. These findings highlight a novel ZMAT1/TRIM46/YAP1 axis, providing new insights into the transcriptional regulation of both osteoclast and osteoblast differentiation, and present potential therapeutic targets for osteoporosis.

overall_design: Extract bone marrow-derived macrophages from Zmat1 knockout mice and their wild-type littermate controls, and stimulate them with M-CSF for 3 days. Then, induce osteoclast development. The control groups are set as follows: 1WT-d0, 2WT-d0, 3WT-d0. The experimental groups are set up as follows: Without RANKL stimulation: 1KO-d0, 2KO-d0, 3KO-d0. After RANKL stimulation for 1 day: 1WT-d1, 2WT-d1, 3WT-d1; 1KO-d1, 2KO-d1, 3KO-d1. After RANKL stimulation for 3 days: 1WT-d3, 2WT-d3, 3WT-d3; 1KO-d3, 2KO-d3, 3KO-d3.

first: Xinyu

last: Chang


title: The enhancer RNA, AANCR, regulates APOE expression in astrocytes and microglia

city: Ann Arbor

first: Vivian

last: Cheung

state: MI

address: 210 Washtenaw Ave.

department: Pediatrics

institute: University of Michigan

summary: Enhancers, critical regulatory elements within the human genome, are often transcribed into enhancer RNAs. The dysregulation of enhancers leads to diseases collectively termed enhanceropathies. While it is known that enhancers play a role in diseases by regulating gene expression, the specific mechanisms by which individual enhancers cause diseases are not well understood. Studies of individual enhancers are needed to fill this gap. This study delves into the role of APOE-activating noncoding RNA, AANCR, in the central nervous system, elucidating its function as a genetic modifier in Alzheimer's Disease. We employed RNA interference, RNaseH-mediated degradation, and single-molecule RNA fluorescence in situ hybridization to demonstrate that mere transcription of AANCR is insufficient; rather, its transcripts are crucial for promoting APOE expression. Our findings revealed that AANCR is induced by ATM-mediated ERK phosphorylation and subsequent AP-1 transcription factor activation. Once activated, AANCR enhances APOE expression, which in turn imparts an inflammatory phenotype to astrocytes. These findings demonstrate that AANCR is a key enhancer RNA in some cell types within the nervous system, pivotal for regulating APOE expression and influencing inflammatory responses, underscoring its potential as a therapeutic target in neurodegenerative diseases.

overall_design: siRNA of AANCR and APOE in human astrocytes, and ASO knockdown of AANCR, followed by RNA-seq.


title: Evolution of T-Cell Fitness through AML Progression: Enhanced Bispecific T-Cell Engager-mediated Function of Bone Marrow T Cells at Remission Compared to Initial Diagnosis and Relapse [epigenome analysis]

city: Munich

first: Maryam

last: Kazerani

address: Feodor-Lynen-Strasse 25

country: Germany

institute: LMU Gene Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To date, bispecific antibodies designed to engage T cells have failed to show sustained responses in relapsed/refractory acute myeloid leukemia (R/R AML). Bispecific antibodies, including bispecific T-cell-engager (BiTE) molecules, predominantly recruit T cells from the local immune microenvironment. Because they are mainly applied in the R/R setting, understanding the fitness of T cells from bone marrow in AML progression, is fundamental for advancing this platform. Here, by flow cytometry analysis of bone marrow-derived T cells, we identified distinct differentiation stages and expression of inhibitory receptors at initial diagnosis (ID) and relapse (RL). Longitudinal transcriptional analyses of paired ID and RL T cells showed a senescent phenotype at ID, whereas an exhausted and memory phenotype was dominant at RL. In line with these observations, T cells at RL exhibited higher BiTE-mediated cytotoxicity than ID T cells. Finally, we provide evidence that T cells, both from ID and RL, exhibit limited functional capacity following continuous BiTE exposure compared to T cells from complete remission. Our study provides insights into the different stages of T-cell phenotype and function during AML evolution. Correlative biomarker studies in patients treated with T-cell-based immunotherapies are needed, to better understand resistance mechanisms and to advance the platform.

overall_design: BMMCs from AML patients at time of initial diagnosis (ID) and relapse (RL) were retrospectively collected. Bone marrow CD3+ T cells from matched ID and RL samples as well as healthy donors (HD) were sorted and subjected to epigenome analysis.

last: Terrasi

first: Helena

last: Domínguez Moreno

first: Tobias

last: Straub

first: Gunnar

last: Schotta

first: Marion

last: Subklewe


title: Evolution of T-Cell Fitness through AML Progression: Enhanced Bispecific T-Cell Engager-mediated Function of Bone Marrow T Cells at Remission Compared to Initial Diagnosis and Relapse [transcriptome analysis]

overall_design: BMMCs from AML patients at time of initial diagnosis (ID) and relapse (RL) were retrospectively collected. Bone marrow CD3+ T cells from matched ID and RL samples as well as healthy donors (HD) were sorted and subjected to transcriptome analysis.


title: Identification of XD23 as a potent inhibitor of osteosarcoma via downregulation of DKK1 and activation of the WNT/β-Catenin pathway

city: Shenzhen

first: jianhui

last: liang

state: Guangdong

address: 1068 Xueyuan Avenue, Nanshan District

institute: Shenzhen Institute of Science and Technology

summary: Osteosarcoma, the most prevalent malignant bone tumor, is notorious for its aggressive growth and invasiveness. The highly mutable genome of osteosarcoma has made identifying a key oncogene challenging, hindering the development of targeted treatments. Our study validates the effectiveness of XD23, an anti-cancer agent we previously identified, in curbing osteosarcoma proliferation, metastasis, EMT differentiation, and bone destruction and promoting osteosarcoma apoptosis.

overall_design: 143B cells were seeded in the 6-well plates and incubated for 48h after stimulated with 0.5 μM XD23. Then cells were lysed by TRIZOL reagent and sent to BGI Genomics institution for RNA extraction and bulk mRNA sequencing.

first: Qian

last: Xie

first: Huiren

last: Tao

first: Yan

last: Wang

first: Yanni

last: Shen

first: Yipei

last: Yang

first: Jianhui

last: Liang

first: Tailin

last: Wu

first: Chun

last: Hu


title: Single cell RNA and TCR sequencing reveals substantive similarities between synovial fluid and synovial tissue T-cells in inflammatory arthritis.

first: Lucy

last: Durham

address: 1st Floor, New Hunt's House, Guy's Campus, Newcommen Street

department: Centre for Inflammation Biology and Cancer Immunology

institute: King's College London

summary: Objective: Synovial fluid (SF) derived T-cells are frequently studied as a proxy for investigating the synovial tissue (ST) T-cell infiltrate in inflammatory arthritis. However, since ST is the primary site of inflammatory activity, there is debate as to whether SF provides a true reflection of the ST T-cell population.  Methods: In this study, we used single cell RNA sequencing paired with single cell TCR sequencing to directly compare memory T-cells from paired samples of SF and ST from 6 patients with inflammatory arthritis to investigate their similarity in terms of T-cell receptor (TCR) repertoire and T-cell subset composition. Results: The TCR repertoires of SF and ST T-cells were strikingly similar, particularly for CD8+ T-cells. A median of 49% of the total CD8+ TCR repertoire in SF was shared with ST, compared to 20% shared with blood and 47% of the ST CD8+ TCR repertoire was shared with SF compared to 25% with blood. Furthermore, once the effect of collagenase digestion on gene expression by ST T-cells had been accounted for, the frequencies of specific CD8+ and CD4+ T-cell subsets were, in general, very similar in SF and ST and were distinct from blood. Conclusion: Our results suggest that T-cells migrate and equilibrate between SF and ST and maintain similar phenotypes in both sites. We conclude that SF is an appropriate proxy for investigating the T-cell infiltrate in inflamed synovium using single cell RNA sequencing, particularly in terms of investigating the TCR repertoire.

overall_design: Single cell RNA and TCR sequencing analysis of memory T cells  from blood, synovial fluid and synovial tissue from patients with psoriatic arthritis

first: Frances

last: Humby

first: Nora

last: Ng

first: Sarah

last: Ryan

first: Rosamond

last: Nuamah

first: Kathy

last: Fung

first: Athul

last: Menon

first: Pawan

last: Dhami

first: Bruce

middle: W

last: Kirkham

first: Leonie

last: Taams


title: Predicting Antigen-Specificities of Orphan T Cell Receptors from Cancer Patients with TCRpcDist

city: Lausanne

first: Marta

middle: A. S.

last: Perez

address: Amphipôle, Quartier UNIL-Sorge

country: Switzerland

institute: SIB - Swiss Institute of Bioinformatics/ UNIL- University of Lausanne

summary: Approaches to analyze and cluster T-cell receptor (TCR) repertoires to reflect antigen specificity are critical for the diagnosis and prognosis of immune-related diseases and the development of personalized therapies. Sequence-based approaches showed success but remain restrictive, especially when the amount of experimental data used for the training is scarce. Structure-based approaches which represent powerful alternatives, notably to optimize TCRs affinity toward specific epitopes, show limitations for large-scale predictions. To handle these challenges, TCRpcDist is presented, a 3D-based approach that calculates similarities between TCRs using a metric related to the physico-chemical properties of the loop residues predicted to interact with the epitope. By exploiting private and public datasets and comparing TCRpcDist with competing approaches, it is demonstrated that TCRpcDist can accurately identify groups of TCRs that are likely to bind the same epitopes. Importantly, the ability of TCRpcDist is experimentally validated to determine antigen specificities (neoantigens and tumor-associated antigens) of orphan tumor-infiltrating lymphocytes (TILs) in cancer patients. TCRpcDist is thus a promising approach to support TCR repertoire analysis and TCR deorphanization for individualized treatments including cancer immunotherapies.

overall_design: CD45+-sorted cells from baseline tumors of  patients with melanoma and lung cancer.

first: Johanna

last: Chiffelle

first: David

last: Barras

first: Alexandre

last: Harari

first: Vincent

last: Zoete


title: HLH-30/TFEB-regulated autophagy mediates sexual dimorphism in immunity in Caenorhabditis elegans

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

institute: KAIST

summary: Sexual dimorphism affects diverse biological functions such as immune responses. However, mechanisms by which different sexes alter immunity remained largely unknown. By using Caenorhabditis elegans as a model, here we show that male animals exhibit enhanced immunity against various pathogenic bacteria via upregulating autophagy. We found that male C. elegans displayed upregulation of helix loop helix 30 (HLH-30)/transcription factor EB (TFEB), a transcription factor crucial for autophagy, which contributed to the enhanced anti-bacterial immunity. We showed that autophagy-related protein 2 (atg-2) that is upregulated by HLH-30/TFEB, mediated increased immunity in male animals. Thus, male C. elegans appear to be equipped with enhanced autophagy for increasing pathogen resistance, likely conferring prolonged mate search with less infection.

overall_design: RNA-seq profiling of hlh-30(tm1978) mutant and WT males and hermaphrodites.

first: Jooyeon

last: Sohn

first: Sujeong

last: Kwon

first: Gee-Yoon


title: Transcriptional analysis of transposon mutants disrupted in bacillithiol biosynthesis in Staphylococcus aureus

city: Fresno

first: Mamta

last: Rawat

state: CA

address: 2555 E. San Ramon Ave. MS S/B 73

department: Biology

institute: California State University, Fresno

summary: In this study we compare logrithmically grown Staphylococcus aureus SAUSA300 wildtype to a transposon mutant that is disrupted in bshC, the third step in bacillithiol biosynthesis using RNASeq to identify novel pathways where bacillithiol may be involved.

overall_design: RNASeq analysis of wildtype cells and bshC:Tn grown logarithmically at 37C while shaken.

first: Rawat

last: Mamta

first: Thomas

last: Jason


title: Secretory phenotype in PBMCs of elderly patients with rheumatoid arthritis

city: Guangzhou

first: Yanjuan

last: Chen

address: Guangzhou

department: Department of Geriatrics and Division of Rheumatology and Research

institute: The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital)

summary: Purpose: The senescence-associated secretory phenotype (SASPs) might increase risk of age-related diseases and concomitant diseases in elderly rheumatoid arthritis (ERA) patients. This study aims to investigate the SASPs in peripheral blood mononuclear cells (PBMCs) for ERA patients. Methods: We performed RNA-seq of the PBMCs from 5 aged RA (RA_A) and 4 young RA (RA_Y) patients. By comparing the differentially expressed genes (DEGs) of RA_Y and RA_A using DESeq package, we identified the senescent secretory phenotype of ERA. The Gene Ontology (GO) functional enrichment, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses and GSEA analysis were performed using clusterProfiler package. The significant protein–protein interaction (PPI) networks identified by Cytoscape. The proteomics data that investigate secretory phenotype of ERA was download from proteomics database. The overlapping SASPs at the intersection of proteomic and transcriptomic were then validated using real-time PCR (RT-PCR).  Results: The PBMCs of RA_A and RA_Y had heterogeneity transcriptomic feature. By comparing RA_A with RA_Y groups, 348 up-regulated and 363 down-regulated DEGs were identified. Gene functional enrichment indicated that up-regulated DEGs in RA_A, SASPs for ERA patients, enriched in PI3K-Akt signaling pathway, MAPK signaling pathway, toll-like receptor family, neutrophil degranulation and immune-related pathways and so on. GSEA analysis indicated, humoral immune response pathways were activated in RA_A. By performing RT-PCR, these five SASPs, SPTA1, SPTB, VNN1, TNXB, KRT1, in PBMCs of RA patients were finally validated. Conclusion: Our study revealed the aging phenotypes in PBMCs of RA patients, and validated five SASPs, which providing novel insights for targeting SASPs therapy.

overall_design: We performed RNA-seq on peripheral blood mononuclear cells (PBMCs) from aged RA patients (RA_A) and young RA patients (RA_Y). By comparing the differentially expressed genes (DEGs) between RA_A and RA_Y, the SASPs in PBMCs of ERA patients was revealed and validated by performing RT-PCR.

first: Wenlong

last: Wang

first: Yidi

last: Shen

first: Jian

first: Xiaoyang

last: Yao

first: Yongjun

last: Cheng

first: Jinzhong

last: Xu

first: Lisa

last: Ma

first: Yong

first: Chuanfu

last: Zhang


title: DNA sequences from two non-avian dinosaurs

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 0900 Euclid Ave.

institute: Case Western Reserve University

summary: Studies of ancient DNA have revolutionized our understanding of extinct organisms, but thus far the maximum estimated age of sequenced DNA is two million years. However, evidence for endogenous biomolecules, including proteins, lipids, and pigments have been found in much older fossils, dating to up to 195 million years. Amino acid sequence data consistent with ancient, endogenous biomolecules have been derived from specimens of the theropod Tyrannosaurus rex (MOR 1125) and the hadrosaur Brachylophosaurus canadensis (MOR 2598). Histochemical and immunological studies also identified a molecule consistent with DNA in these two ancient specimens, localized to a single point within preserved osteocytes. Here we report the sequencing and analysis of DNA extracted from osteocytes and blood vessels of T. rex and B. canadensis, liberated after demineralization of dense cortical bone. Usable sequence reads were obtained at a low recovery rate. After the removal of high-quality reads that mapped to the human genome, the remaining reads were highly fragmented, with similarities to multiple animal species including reptilian and avian genomes. Our findings support the hypothesis that DNA and histone signal from imaging, mass spectrometry, and DNA sequencing of dinosaur osteocytes are endogenously preserved biomolecules.

sample_organism:
Tyrannosaurus rex
Brachylophosaurus canadensis

overall_design: 12 samples

first: Berkley

last: Gryder

first: Mary

last: Schweitzer


title: Transcriptomic analysis of control and macrophage-conditioned meduim treated MCF-7 breast cancer cells to investigate the mechanism of macrophage-induced TNT formation.

city: Mumbai

first: Pooja

middle: Kamal

last: Melwani

state: Maharashtra

address: Mod Lab, Trombay

department: Radiation Biology & Health Science Division

country: India

institute: Bhabha Atomic Research Centre

summary: Tumor-associated macrophages (TAMs) secrete cytokines, chemokines, and growth factors in tumor microenvironment to support cancer progression. Previous studies have demonstrated role of macrophages in stimulating long range intercellular bridges referred as tunneling nanotubes (TNTs) in cancer cells. Intercellular communication between cancer cells via TNTs promote cancer growth, invasion, and therapy resistance. Given the important role of TNTs and macrophages in cancer, the mechanism of macrophage mediated TNT formation is elusive. In this study, it is shown that the macrophage-conditioned medium treated MCF-7 cells showed enrichment of NFκB and focal adhesion pathway as well as upregulation of genes involved in EMT, extracellular remodelling, and actin cytoskeleton reorganization. Interestingly, inhibition of PKC, Src, NFκB and p38 inhibited macrophage-induced TNT formation in MCF-7 cells. These results reveal novel role of PKC and Src in inducing TNT formation in cancer cells and suggest that inhibition of PKC and Src activity may likely contribute to reduced macrophage-breast cancer cell interaction and potential therapeutic strategy of cancer.

overall_design:
To investigate the mechanism of macrophage induced TNT formation in MCF-7 cells, we treated MCF-7 cells with macrophage conditioned medium derived from differentiated U937 cells.
We then performed transcriptomic analysis using RNA seq data from control and macrophage conditined medium treated MCF-7 cells amd identified key genes that regulate TNT formation.

first: B

middle: N

last: Pandey


title: iCLIP-Seq analyses of NSP12-bound RNAs

city: shanghai

first: ql

last: zheng

address: xiangyin

institute: immunity

summary: We known that NSP12 as an important RNA binding protein, but the potential substrate RNA of host cells remain elusive.

overall_design: iCLIP-Seq analyses of NSP12-bound RNAs from three replicate of HEK293T cells

first: Qingliang

last: Zheng


title: Inherited functional regulatory risk variants for common human cancers [MPRA]

city: Stanford

first: Paul

last: Khavari

address: 269 Campus Drive, CCSR, Room 2150

department: Dermatology

institute: Stanford University

summary: Single nucleotide variants (SNVs) in regulatory DNA are linked to inherited cancer risk. Massively parallel reporter assays (MPRA) of 5,031 SNVs linked to 14 neoplasms comprising >90% of human malignancies were performed in pertinent diploid cell types then integrated with matching chromatin accessibility, looping, and eQTL data to identify 411 regulatory SNVs and their putative target eGenes. The latter highlighted specific protein networks in lifetime cancer risk, including mitochondrial translation, proliferation, signaling, adhesion, and immunity. This cancer SNV compendium underscores the importance of studying pathogenic variants in disease-relevant cells and implicates specific dysregulated gene networks in cancer predisposition. It also indicates that inherited cancer risk can impact the same gene via orthogonal genetic mechanisms of dysregulated expression as well as protein coding sequence alteration and demonstrates that a subset of germline-encoded risk genes also enable tumor growth of established cancers.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Massively parallel reporter assay of cancer associated risk variants in 14 cell types

first: Laura

last: Kellman


title: The landscape of H3K9me2 and CTCF in mice GV oocytes

city: Beijing

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: During oocyte growth, various epigenetic modifications are gradually established, accompanied by accumulation of large amounts of mRNAs and proteins. However, little is known about the relationship between epigenetic modifications and meiotic progression. Here, by using Gdf9-Cre to achieve oocyte-specific ablation of Ehmt2 (Euchromatic-Histone-Lysine-Methyltransferase 2) from the primordial follicle stage, we found that female mutant mice were infertile. Oocyte-specific knockout of Ehmt2 caused failure of homologous chromosome separation independent of persistently activated SAC during the first meiosis. Further studies revealed that lacking maternal Ehmt2 affected the transcriptional level of Ccnb3, while microinjection of exogenous Ccnb3 mRNA could partly rescue the failure of homologous chromosome segregation. Of particular importance was that EHMT2 regulated ccnb3 transcriptions by regulating CTCF binding near ccnb3 gene body in genome in oocytes. In addition, the mRNA level of Ccnb3 significantly decreased in the follicles microinjected with Ctcf siRNA. Therefore, our findings highlight the novel function of maternal EHMT2 on the metaphase I-to-anaphase I transition in mouse oocytes: regulating the transcription of Ccnb3.

overall_design:
H3K9me2 and CTCF ChIP-seq in mice GV oocytes
Please note that the processed data generated from both replicates is linked to the corresponding rep1 sample records.

first: Qing-Yuan

first: Zhen-Bo

first: Xiang-Hong

last: Ou

first: Shao-Rong

last: Gao

first: Tie-Gang

last: Meng

first: Xukun

last: Lu

first: Wen-Long

last: Lei

first: Zheng-Hui

last: Zhao


title: Transcriptional analysis of transposon mutants disrupted in glutathione biosynthesis in Pseudomonas aeruginosa

first: Mamta

last: Rawat

summary: In this study we compare logarithmically grown Pseudomonas aeruginosa wildtype to a transposon mutant that is disrupted in gshA, which is involved in glutathione biosynthesis using RNASeq to identify novel pathways where glutathione may be involved.

overall_design: RNASeq analysis of wildtype cells and gshA:Tn grown logarithmically at 37C while shaken.

first: Jason

last: Thomas


title: Inherited functional regulatory risk variants for common human cancers

overall_design: CRISPR knockout screen of genes implicated in colon cancer by massively parallel reporter assay


title: Machine learning-based prediction of the activity and specificity of Cas9 variants in gene editing

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

overall_design: This study aims to compare the activity and specificity of SpCas9 variants by deep learning at genome-scale. In this study, we have focused on the development of a system for evaluating the activity and specificity of SpCas9 variants by using >180,000 guide RNAs (gRNAs) covering ~20,000 protein-coding genes and ~10,000 non-coding genes in synthetic constructs with a high-throughput manner. With the help of deep learning algorithms in the field of artificial intelligence, eight prediction models with the best generalization performance now are constructed: AIdit_ON_HiFi, AIdit_ON_NG, AIdit_ON_Sniper, AIdit_ON_LZ3, AIdit_OFF_HiFi, AIdit_OFF_NG, AIdit_OFF_Sniper and AIdit_OFF_LZ3. Moreover, we found a novel Cas9 variant SuperFi Cas9 has a very low activity compared with other variants in vivo. Finally, we confirm that this study will greatly facilitate CRISPR-based genome editing.

first: Jianbo

last: Li

first: Zhoutao

last: Cao


title: Transcriptome analyses of HEK293T and VERO upon overexpression

first: ql

summary: NSP12 as the key RNA transcription polymerase of SARS-CoV-2, we intend to know whether NSP12 regulate the mRNA transcription of host cell upon viral infection

sample_organism:
Chlorocebus aethiops
Homo sapiens

platform_organism:
Chlorocebus aethiops
Homo sapiens

overall_design: we analyzed 8 samples in total, including two replicates of Control and NSP12 overexpression samples in HEK293T and VERO, respectively.

first: Qingliang


title: Valproic acid targets IDH1 mutants through alteration of lipid metabolism

status: Public on Aug 21 2024

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

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

overall_design: Refer to individual Series


title: MDM2 inhibition enhances immune checkpoint inhibitor therapy in melanoma

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: Immune checkpoint therapy has improved outcome of patients with advanced melanoma, however the tumor becomes refractory in a large number of patients. Therefore, novel combination therapies that enhance anti-melanoma immunity are highly desirable.  We studied the impact of MDM2 (mouse double minute 2) inhibition, leading to p53 activation, on response to anti-PD-1 immunotherapy in melanoma. MDM2 treatment caused upregulation of MHC II and IL-15 in melanoma cells in a p53 dependent manner. Survival of melanoma bearing mice improved upon combining anti-PD1 and MDM2 inhibition in vivo. Lack of IL-15Rα in T cells abrogated the beneficial effect of the combined treatment.  This gene expression study was performed to determine potential effects of MDM2 inhibition on genes in the melanoma microenvironment.

overall_design: Melanoma cells were subcutaneously injected into five mice, which were treated with anti-PD1. Every other day, two mice were treated with vehicle and three mice were treated with MDM2 inhibitor. The tumors were excised on day 13 and total RNA was isolated. For the gene expression study, a total of five samples were analysed, two of which were control samples from vehicle-treated mice and the other three samples were obtained from the mice treated with MDM2 inhibitor.

first: Marlene

last: Langenbach

first: Robert

last: Zeiser

first: Melanie

last: Boerries


title: A Dual-Payload Antibody-Drug Conjugate Targeting CD276/B7-H3 Elicits Cytotoxicity and Immune Activation in Triple-Negative Breast Cancer

city: COLUMBUS

first: Zhuoxin

last: Zhou

state: OH

address: Gateway Lofts Columbus, 2211 Dublin Rd

institute: Ohio State University

summary: Triple-negative breast cancer (TNBC) is a highly aggressive and heterogeneous disease that often relapses following treatment with standard radiotherapies and cytotoxic chemotherapies. Combination therapies have potential for treating refractory metastatic TNBC. Here, we aimed to develop an antibody-drug conjugate with dual payloads (DualADC) as a chemo-immunotherapy for TNBC. The overexpression of an immune checkpoint transmembrane CD276 (also known as B7-H3) was associated with angiogenesis, metastasis, and immune tolerance, in over 60% of TNBC patients. Development of a monoclonal antibody (mAb) capable of targeting the extracellular domain of surface CD276 enabled delivery of payloads to tumors, and a platform was established for concurrent conjugation of a traditional cytotoxic payload and an immunoregulating toll-like receptor 7/8 agonist to the CD276 mAb. The DualADC effectively killed multiple TNBC subtypes, significantly enhanced immune functions in the tumor microenvironment, and reduced tumor burden by up to 90-100% in animal studies. Single-cell RNA-sequencing, multiplex cytokine analysis, and histology elucidated the impact of treatment on tumor cells and the immune landscape. This study suggests that the developed DualADC could represent a promising targeted chemo-immunotherapy for TNBC.

overall_design: The flash-frozen tissue samples (25 mg) were collected and stored at -80°C until processing. Chromium Next GEM RNA Profiling Sample Fixation Kit (PN-1000414, 10x Genomics, Pleasanton, CA, USA) was used to fix tissue by mixing 1 mL of fixation buffer with 25 mg of tissue, followed by fine mince and incubation at 4°C for 16-24 hours without agitation. After fixation, tissue samples were centrifuged, washed with chilled PBS, and resuspended in 1 mL of tissue resuspension buffer. The fixed tissues supplemented with pre-warmed dissociation buffer were dissociated using an Octo Dissociator according to the manufacturer's instructions. The dissociated tissue samples were filtered through a 30 µm filter, centrifuged and resuspended in 1 mL of chilled quenching buffer. Cell concentration was determined using an automated cell counter with fluorescent nucleic acid staining. The dissociated tumor samples were stored in 50% glycerol with enhancer at -80°C until single-cell library generation.


title: Translatome analyses of HEK293T upon NSP12 overexpression

last: zheng

summary: NSP12 of SARS-CoV-2 can recruit the elongation factor eEF1A, we intend to know whether NSP12 regulate the mRNA translation level of host cell upon viral infection

overall_design: We analyzed 4 samples in total, including two replicates of Control and NSP12 overexpression samples in HEK293T, respectively.

last: Zheng


title: NOTCH, ERK and SHH signaling respectively control the fate determination of cortical astrocytes, oligodendrocytes, and olfactory bulb interneurons [CUT&Tag]

city: SHANGHAI

first: MENGGE

last: SUN

address: FENGLIN ROAD

institute: FUDAN UNIVERSITY

summary: During cortical development, radial glial cells, known as neural stem cells, initially generate a large number of cortical glutamatergic pyramidal neurons through a process called neurogenesis. This is followed by the generation of a diversity of cortical astrocytes, oligodendrocytes, and olfactory bulb interneurons, known as gliogenesis. However, the molecular mechanisms underlying the switch from cortical neurogenesis to gliogenesis, and the subsequent fate determination of cortical astrocytes, oligodendrocytes, and olfactory bulb interneurons, remain unclear. Here, we report that extracellular signal-regulated kinase (ERK) signaling plays a fundamental role in promoting cortical gliogenesis and the generation of cortical glial progenitors. Additionally, SHH-SMO-GLI activator signaling has an auxiliary function to ERK during these processes. We further demonstrate that NOTCH signaling is absolutely required for the fate determination of astrocytes, while ERK signaling plays a prominent role in oligodendrocyte fate specification, and SHH signaling is crucial for the fate determination of olfactory bulb interneurons from cortical progenitors. We provide evidence suggesting that this mechanism is conserved in both mice and humans. Finally, we propose a unifying principle of mammalian cortical gliogenesis.

overall_design: CUT&Tag-Seq: The hGFAP-GFP mice were sacrificed at E18 or P1. The green brain dorsal cortices were collected, minced and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit by following the manufacturer’s instruction (Miltenyi Biotec, catalog no. 130-092-628). The GFP+ cells were captured and harvested through fluorescence-activated cell sorting (FACS).

first: Yanjing

last: Gao

first: Mengge

last: Sun

first: Tongye

last: Fu

first: Zhengang

last: Yang


title: ACE2 knockout hinders SARS-CoV-2 propagation in iPS cell-derived airway and alveolar epithelial cells

city: Kyoto

first: Ryo

last: Niwa

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo

department: Center for iPS Cell Research and Application

institute: Kyoto University

summary: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, continues to spread around the world with serious cases and deaths. It has also been suggested that different genetic variants in the human genome affect both the susceptibility to infection and severity of disease in COVID-19 patients. Angiotensin-converting enzyme 2 (ACE2) has been identified as a cell surface receptor for SARS-CoV and SARS-CoV-2 entry into cells. The construction of an experimental model system using human iPS cells would enable further studies of the association between viral characteristics and genetic variants. Airway and alveolar epithelial cells are cell types of the lung that express high levels of ACE2 and are suitable for in vitro infection experiments. Here, we show that human iPS cell-derived airway and alveolar epithelial cells are highly susceptible to viral infection of SARS-CoV-2. Using gene knockout with CRISPR-Cas9 in human iPS cells we demonstrate that ACE2 plays an essential role in the airway and alveolar epithelial cell entry of SARS-CoV-2 in vitro. Replication of SARS-CoV-2 was strongly suppressed in ACE2 knockout (KO) lung cells. Our model system based on human iPS cell-derived lung cells may be applied to understand the molecular biology regulating viral respiratory infection leading to potential therapeutic developments for COVID-19 and the prevention of future pandemics.

overall_design: We used the bulk RNA-Seq to compare gene expression profiles of differentiated airway and alveolar epithelial cells before and after ACE2 Knockout gene editing.

first: Shimpei

last: Gotoh

first: Knut

last: Woltjen


title: Okra polysaccharide activates PPAR-γ signaling to attenuate metabolic-associated fatty liver disease in mice

city: Nanchang

first: Yaojun

last: Cai

address: 1519 Dongyue Avenue

department: Department of Endocrinology and Metabolism

institute: The First Affiliated Hospital, Jiangxi Medical College, Nanchang University

summary: Okra (Abelmoschus esculentus (L.) Moench) serves as a botanical resource extensively utilized in ethnomedicine. Prior investigations revealed that okra polysaccharide (OP) ameliorated hepatocellular lipotoxicity in vitro context. Nonetheless, the curative efficacy and the precise molecular mechanisms implicated in metabolic-associated fatty liver disease (MAFLD) warrant further elucidation. To address this gap, two murine models of MAFLD, namely obese Ob/Ob mice and high fat/cholesterol/fructose (HFCF) fed mice, were employed. The therapeutic implications of OP supplementation were assessed through quantification of lipid specific biomarkers and hepatic histopathological examination. Complementary transcriptomic, phosphoproteomic, and in vitro analyses were conducted to decipher the molecular underpinnings. In the Ob/Ob mouse model, OP substantively mitigated both circulating and hepatic lipid concentrations, concurrently ameliorating hepatic steatosis. In the context of HFCF-induced MAFLD, OP not only attenuated hepatic lipidic sequestration but also abrogated concomitant inflammation and fibrosis. Subsequent RNA-sequencing analyses on hepatic tissues derived from HFCF-diet mice delineated that OP modulated MAFLD-associated transcriptional signatures. A synergistic assessment of transcriptomics and phosphoproteomics disclosed a salient effect of OP on the Peroxisome Proliferator-Activated Receptor (PPAR) pathway, particularly manifested by the upregulation of PPAR-γ signaling. In murine hepatocytes, OP counteracted steatosis and inflammation via the activation of PPAR-γ signaling. The effects induced by OP were nullified upon administration of the PPAR-γ-specific antagonist GW9662. Collectively, our empirical evidence furnishes the inaugural demonstration that OP mitigates MAFLD pathology through the activation of PPAR-γ signaling, thereby presenting a novel therapeutic avenue for MAFLD intervention.

overall_design: The present study aimed to interrogate the therapeutic potential and underlying mechanisms of OP in MAFLD progression across multiple experimental models.


title: Therapy of allergic rhinitis using ribavirin spray to clear nasal commensal viruses

city: Shanghai City

first: Yue

last: Dong

address: 800 Xiangyin Road

institute: Naval Medical University

summary: For analyzing the exploratory nasal commensal viruses, we performed the metatranscriptomic analysis of the nose swabs from the enrolled AR patients both before and after treatments, as well as sequenced the nose swabs from a set of healthy volunteers without AR history.Simultaneously, to assess the expression of interferon-stimulated genes in patients with allergic rhinitis, we analyzed the gene expression of host reads.

overall_design: We had designed and conducted a randomized, double-blind, parallel-controlled phase 2 clinical trial. Eligible patients diagnosed with AR based on the typical symptoms and either a positive skin prick test (SPT) or allergen-specific IgE level ≥ 0.35 kU/L following the Chinese Guidelines for the Diagnosis and Treatment of Allergic Rhinitis criteria were enrolled. Each patient received detailed information on the study procedures, the treatments, the potential risks and benefits, and the fundamental rights in the clinical trial. To evaluate the efficacy and safety of ribavirin spray for AR treatment, ribavirin (12 mg daily) or placebo was given twice a day, one spray per nostril for 4 weeks.  We obtained nasal swab samples from enrolled patients with allergic rhinitis for metatranscriptomic sequencing, with sampling time points before medication and four weeks after commencing treatment. Simultaneously, to assess whether there is a significant difference in the abundance of nasal commensal viruses between healthy individuals and patients with allergic rhinitis, we collected nasal swabs from healthy individuals without allergic rhinitis as controls for metatranscriptomic sequencing. All patients provided written informed consent.The clinical trial was registered at Chinese Clinical Trial Registry (ChiCTR2400082642).

first: Jin

last: Hou


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

city: Qingdao

first: WEI

last: WANG

state: Shandong

address: 23 Hongkong east road haier building G zone

institute: Ocean University of China

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

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

first: Wei

last: Wang

first: Lionel

last: Christiaen


title: Transcriptional profiling of tumor infiltrating and ciculating T lymphocytes of mice harboring MOC1 tumors

city: Bethesda

first: Cem

last: Sievers

address: 10 Center Drive

institute: NIH

summary: Combination TGF-β neutralization and PD-L1 immune checkpoint blockade promotes anti-tumoral systemic immunity by enhancing tumor egress of CD8+ TILs. This enhanced egress associated with reduced expression of the tissue residency marker Itgae and its upstream regulator Znf683, with the circulating CD8+ T cells expressing higher Cxcr3, an observation made as well in samples from patients treated with dual TGF- neutralization and ICB.

overall_design: Tumor tissues from five individual mice were processed and cell suspensions were stained with anti-mouse TCR-β and T cells were sorted to >99% purity. Two captures per treatment of 10,000 cells each were performed. Cells were mixed with barcoded gel beads and 5’ GEM Kit v3 reagents and single cell capture was performed (10X Genomics). Following reverse transcription, cDNA and murine TCRs were amplified, and gene expression and TCR sequencing libraries were re-constructed. Each DNA library was loaded into a sequencing lane on a NovaSeq system. Spleens and tumor draining lymph nodes from individual mice were processed and T cells were isolated using the EasySep Mouse T cell Isolation Kit from StemCell Technologies. RNA was extracted from all sorted samples using the RNEasy Mini Kit and deep TCR sequencing was performed using the SMARTer Mouse TCR Profiling Kit from MiLaboratories.

first: Xinping

first: Magdalena

last: Fay

first: Marco

last: Craveiro


title: Dynamic regulation of tissue fluidity controls skin repair during wound healing [ATAC]

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

summary: During wounding healing, different pools of stem cells (SCs) During homeostasis, different compartments of the epidermis are sustained by distinct pools of stem cells (SC) whereas, upon wounding, these different SCs contribute to skin repair. However, how SCs become activated and drive the tissue remodeling essential for skin repair is still poorly understood. Here, by developing a mouse model allowing lineage tracing and basal cell lineage ablation while leaving the basic organization of the skin intact, we monitor SC fate and tissue dynamics during regeneration using confocal and intravital imaging. Analysis of basal cell rearrangements shows dynamic transitions from a solid-like homeostatic state to a fluid-like state allowing tissue remodelling during repair, as predicted by a minimal mathematical modelling of the spatiotemporal dynamics and fate behaviour of the basal cells population. The basal cell layer progressively returns to a solid-like state with re-epithelialization and the restoration of barrier function. Bulk, single-cell RNA and epigenetic profiling of SCs together with functional experiments uncover a common regenerative state regulated by the EGFR/AP1 axis activated during tissue fluidization that is essential for skin SC activation and tissue repair.

overall_design: To investigate the chromatin remdelling and epigenetic lanscape behind the clonal expansion and tissue fluidity we isolated basal epidermal cells in control and ablation condition from K14 tracing and performed ATAC sequencing.

first: Rahul

last: Sarate

first: Cédric

last: Blanpain


title: Valproic acid targets IDH1 mutants through alteration of lipid metabolism [2022]

first: Riki

last: Kawaguchi

summary: Histone deacetylases (HDACs) have a wide range of targets and can rewire both the chromatin and lipidome of cancer cells. In this study, we show that valproic acid (VPA), a brain penetrant anti-epilepticseizure medication and histone deacetylase inhibitor, inhibits the growth of IDH1 mutant tumors in vivo and in vitro, with at least some selectivity over IDH1 wild-type tumors. Surprisingly, genes upregulated by VPA showed no change inenhanced chromatin accessibility at the promoter, but there was a correlation between VPA-downregulated genes and diminished promoter chromatin accessibility. VPA inhibited the transcription of lipogenic genes and these lipogenic genes showed significant decreases in promoter chromatin accessibility only in the IDH1 MT glioma cell lines tested. VPA inhibited the mTOR pathway and a key lipogenic gene, fatty acid synthase (FASN). Both VPA and a selective FASN inhibitor TVB-2640 rewired the lipidome and promoted apoptosis in an IDH1 MT but not in an IDH1 WT glioma cell line. We further find that HDACs are involved in the regulation of lipogenic genes and HDAC6 is particularly important for the regulation of FASN in IDH1 MT glioma. Finally, we show that FASN knockdown alone and VPA in combination with FASN knockdown significantly improved the survival of mice in an IDH1 MT primary orthotopic xenograft model in vivo. We conclude that targeting fatty acid metabolism through HDAC inhibition and/or FASN inhibition may be a novel therapeutic opportunity in IDH1 mutant gliomas.

overall_design: Primary GBM cell lines were treated with Control(DMSO), TVB-2640 1µM) (FASNi),  palmitate (50µM) or both for 4 days, cell pellet collected for RNA extraction

first: Lubayna

last: Elahi

last: Qin

first: Harley

last: Kornblum


summary: To elucidate the potential role of commensal viruses in the etiology of AR, we performed a metagenomic analysis of nasal lavage fluid (NLF) to identify commensal viruses in the nose of mice colonizing in the specific pathogen-free (SPF) circumstances (Vehicle group). To evaluate the potential role of these commensal viruses, we reduced them in the nose of mice by administrating intranasal drops of broad-spectrum antiviral drug ribavirin daily, starting at 4-week-old and lasting for three weeks (Ribavirin group).

overall_design: Nasal lavage fluid (NLF) was obtained from mice that were administered intranasal drops of either vehicle (n=7) or ribavirin (n=7) daily, starting at 4 weeks old and lasting for three weeks. The NLF samples were then subjected to metatranscriptomic sequencing to assess the abundance of viruses.

first: Ye

last: Zhou


title: Isolation and identification of patient-derived liver cancer stem cells and development of personalized treatment strategies

city: Guang Zhou

first: Tingting

last: Guo

state: Guang Dong

address: University Town Campus (South Campus): 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre,

institute: South China University of Technology

summary: Liver cancer is a devastating disease characterized by its molecular complexity and the insidious behavior of liver cancer stem cells (LCSCs), which drive the metastasis and recurrence. However, the heterogeneity of molecular markers of LCSCs has hindered the development of effective methods to isolate them. This study introduced a pioneering approach to isolate and culture LCSCs from primary tumor tissues, leveraging mouse embryonic fibroblasts (MEFs) as a feeder cell to provide the niche in conjunction with using defined medium, which stands in stark contrast to traditional techniques, and promised to revolutionize our understanding of LCSCs. Total seventeen cell strains were directly isolated from 24 patients’ tissues without sorting, seven of which could be maintained long-term culture as colony growth on MEFs, which is unique characteristics of stem cells. Cloned cells formed a round packed morphology on MEFs and could be cryopreserved and re-cultured. Even 10 of cloned cells could form xenografts of human liver cancers in immunodeficient mice, indicating high tumorigenicity. Thus, cloned cells could be designated as liver cancer stem cells. Our further investigation found that reported putative liver cancer stem cell markers were all expressed in cloned cells, and stemness of cancer stem cells could well maintained under our developed culture conditions when compared to those under traditional suspension conditions. Furthermore, our findings revealed a distinct molecular landscape within hepatocellular carcinomas (HCCs), pinpointing a C2 subtype with profound implications for personalized medicine and the development of targeted therapies. By illuminating the unique responses of this subtype to chemotherapeutic agents, our research not only advances the frontiers of liver cancer biology but also charts a course for more effective, patient-specific treatment strategies.

overall_design: ALDH-positive HCC2 CSCs were cultured in three different ways: on MEFs, in suspension conditions, and in differentiation conditions using DMEM medium containing 10% FBS.

first: Yuyou

last: Duan


title: Valproic acid targets IDH1 mutants through alteration of lipid metabolism [2020]

overall_design: Primary GBM cell lines were cultured in GBM media (DMEMF12/B27/Penstrep), treated with either DMS0(control) or DRUG(VPA) for 48hrs, collected for RNA extraction

first: Yue


title: Retrospective meningiomas RNA-sequencing data.

city: Toronto

first: Vikas

last: Patil

state: Ontario

address: 610 University Ave.

institute: Princess Margaret Cancer Center

summary: Bulk RNA-sequencing data of multicentre retrospectively colllected meningioma tumors, fresh-frozen samples

overall_design: Meningioma samples n = 994; retrospective data, no technical replicates.

first: Justin

first: Farshad

last: Nassiri

first: Gelareh

last: Zadeh


title: Dynamic regulation of tissue fluidity controls skin repair during wound healing [bulk RNA-seq]

overall_design: To investigate the mechanism behind the clonal expansion and tissue fluidity we isolated basal epidermal cells in control and ablation condition and performed RNA seq.


title: Dynamic regulation of tissue fluidity controls skin repair during wound healing [scRNA-seq]

overall_design: To investigate the mechanism behind the clonal expansion and tissue fluidity we isolated basal epidermal cells in control and ablation condition from K14 and Lrig1 tracing with multiplexing approach and performed scRNA sequencing.


title: Multi-omics study on the effect of moderate intensity exercise on protein of lactylation in mouse muscle tissue

first: Ting

last: Zhang

address: Dongcheng District

institute: Beijing Municipal Key Laboratory of Child Development and Nutriomics

summary: To explore the effects of moderate intensity exercise on protein of lactylation in mouse muscle tissue metabolism. The healthy adult mice running for 6 weeks as exercise model and sedentary mice as control were used to perform transcriptomic, proteomic, lactylation-proteomics, and metabolomics analysis. In addition, correlation analysis between transcriptome and proteome, and proteome and metabolome was conducted as well.

overall_design: To explore the effects of moderate intensity exercise on protein of lactylation in mouse muscle tissue metabolism. The 3 healthy adult mice running for 6 weeks as exercise model and 3 sedentary mice as control were used to perform transcriptomic, proteomic, lactylation-proteomics, and metabolomics analysis.

first: Jiahui

last: Chang

first: Wanyu

last: Wu

first: Ping

last: Qian

first: Zhaoxu

last: Lu

first: Xuejia

last: He

first: Fang

last: Wang


title: MicroRNA-19b exacerbates systemic sclerosis through promoting Th9 cells

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

summary: Systemic sclerosis (SSc) is a chronic autoimmune disease characterized with fibrosis of skin and multiple vital organs, but the immunological pathogenesis of SSc remains largely unknown. We show here that microRNA-19b (miR-19b) promotes IL-9-producing CD4+ T cells (Th9) that exacerbate SSc. Specifically, TGF-b plus IL-4 induced expression of TNF receptor associated factor 6 (TRAF6) through phosphorylated Smad3 linker region site Serine 213 (p-Smad3L-Ser213) and activated it through K63 ubiquitination by suppressing the leucine-rich-repeat-containing protein 3 (NLRC3). TRAF6 consequently formed complex with and activated TGF-b activated kinase 1 (TAK1). TAK1 promoted nuclear factor kappa B (NFκB) p65 activation, which then specifically upregulated miR-19b. miR-19b activated Il9 gene expression and promoted Th9 differentiation by directly targeting and suppressing atypical E2F family member E2f8 gene, a repressor for Il9 gene transcription. Importantly, Th9 cells played a critical role in the development and pathogenesis of experimental SSc by promoting the fibrosis in mice induced with Bleomycin. miR-19b and IL-9 were increased in CD4+ T cells in experimental SSc in mice and also in patients with SSc. Strikingly, inhibition of miR-19b resulted in fewer Th9 cells and attenuated fibrotic manifestations and ameliorated the disease in SSc mice. Our study identifies miR-19b as a key factor of Th9 cells that are involved in the pathogenesis of SSc. Our findings should have clinical implications for patients with SSc.

overall_design:
Study of new molecular mechanism for Th9 differentiation
CD4 primary cells treated with CTRL, TGF, IL4, TGF+IL4.

first: Yun-Ji

last: Lim

first: Sang-A

last: Park

first: Dandan

first: Wenwen

last: Jin

first: Wai

last: Ku

first: Dunfang

first: WanJun

last: Chen


title: miR-876 is a tumor suppressor on 9p21 that is inactivated in melanoma and targets ERK

city: Cincinnati

first: Nathan

last: Salomonis

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: While melanomas commonly harbor losses of 9p21, on which CDKN2A resides, the presence of additional tumor suppressor elements at this locus is incompletely characterized. Here we assess the expression levels and functional role of microRNA-876 (miR-876), whose gene also maps to 9p21.

overall_design: The consequences of regulation of miR-876 expression were assessed on melanoma cell colony formation, migration, invasion, apoptosis, cell cycle progression, and drug sensitivity in culture, and on in vivo tumor growth in a xenograft model. Genome-wide transcriptomic changes induced by miR-876 overexpression were determined using RNA sequencing (RNA-Seq).

first: Vladimir

last: Bezrookove

first: Imran

last: Khan

first: Mehdi

last: Nosrati

first: Mohammed

last: Kashani-Sabet


title: Molecular classification of meningioma predicts the response to surgical resection and adjuvant radiotherapy.

first: Vikas

last: Patil

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

overall_design: Refer to individual Series


title: Members of an array of zinc finger proteins specify distict Hox chromatin boundaries [ChIP-seq]

city: Miami

first: Danny

last: Reinberg

state: Florida

address: 1501 NW 10th Ave

department: Sylvester Cancer Center/Human Genetics

institute: University of Miami

summary: In this experiment, we sought to identify how the distribution of RAD21 and ZNF263 change in WT, PATZ1 KO, and ZNF263 KO cells during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs).

overall_design: Examination of RAD21 and ZNF263 binding in embryonic stem cells and cervical motor neurons using ChIP-seq, by status of PATZ1 KO or ZNF263 KO in the cells: WT, ZNF263 KO, and PATZ1 KO


title: Members of an array of zinc finger proteins specify distict Hox chromatin boundaries [Micro-C]

summary: In this experiment, we sought to identify how genome organization change in WT versus PATZ1 KO cells during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs).

overall_design: Examination of genome organization in embryonic stem cells and cervical motor neurons using Micro-C sequencing, by status of PATZ1 KO in the cells: WT and PATZ1 KO


title: Meningioma methylation data

summary:
Methylation analysis of meningioma cases
Genomic DNA isolated directly from human meningioma samples

first: Justin

first: Farshad

last: Nassiri

first: Gelareh

last: Zadeh


title: Spatially resolved whole-transcriptomic and proteomic profiling of lung cancer and immune-microenvironment according to PD-L1 expression

city: Seoul

first: Jaemoon

last: Koh

address: 101, Daehak-ro Jongno-gu

department: Department of Pathology

institute: Seoul National University Hospital

summary: The expression of PD-L1 on tumor cells (TCs) is used as an immunotherapy biomarker in lung cancer, but heterogeneous intratumoral expression is often observed. Using a Digital Spatial Profiler, we performed proteomic and whole-transcriptomic analyses of TCs and immune cells (ICs) in spatially matched areas according to tumor PD-L1 expression and the status of the immune microenvironment. Several findings were validated using immunohistochemistry, The Cancer Genome Atlas, and immunotherapy cohorts. ICs in areas with high PD-L1 expression showed more features indicative of immunosuppression and exhaustion than ICs in areas with low PD-L1 expression. TCs highly expressing PD-L1 within immune-inflamed (IF) areas show up-regulation of pro-inflammatory processes, whereas TCs highly expressing PD-L1 within immune-deficient (ID) areas show up-regulation of various metabolic processes. Using differentially expressed genes of TCs between the IF and ID areas, we identified a novel prognostic gene signature for lung cancer. In addition, the high ratio of CD8+ cells to M2 macrophages was found to predict favorable outcomes in patients with PD-L1-expressing lung cancer after immune checkpoint inhibitor therapy. This study demonstrates that TCs and ICs have distinct spatial features within the tumor microenvironment that are related to tumoral PD-L1 expression and IC infiltration.

overall_design: Total 95 areas of interest from 8 Lung Adenocarcinomas were sequenced using Nanostring GeoMX Digital Spatial Profiling (DSP) with (v1.0) Human NGS Whole Transcriptome Atlas RNA Probeset.

first: Dongjoo

last: Lee


title: Maternal obesity induces the meiotic defects and epigenetic alterations during fetal oocyte development [BiSulfite-seq]

city: Nanjing

first: Qiuzhen

address: 101 Longmian Rd, Nanjing, Jiangsu, 211166 China

institute: Nanjing Medical University

type: Methylation profiling by high throughput sequencing

summary: It has been widely reported that obesity adversely impacts reproductive performance of females. However, the effects of maternal obesity on fetal germ cells remain poorly understood. In the present study, by employing a high-fat diet (HFD)-based mouse model, we found that maternal obesity disrupts the chromosomal synapsis and homologous recombination during fetal oogenesis. Moreover, transcriptomic profiling revealed the potential molecular network controlling this process. Of note, the global hypermethylation of genomic DNA in fetal oocytes from obese mouse was detected. Importantly, time-restricted feeding (TRF) of obese mice not only ameliorated the meiotic defects, but also partly restored the epigenetic remodeling in fetal oocytes. In sum, we provide the evidence showing the deficit fetal oogenesis in obese mother, implicating a mechanism underlying the intergenerational effects of environmental insults. TRF may represent a potentially effective approach for mitigating fertility issues in obese patients.

overall_design: Genome-Wide Bisulfite sequencing (WGBS) was used for base-resolution methylome analysis. Fetal oocytes from both ND and HFD mice were collected at E13.5 and E18.5.

first: Shoubin

last: Tang

first: Jiashuo

last: Li

first: Xi

last: Wang

first: Qiang


title: Tho2-mediated escort of Nrd1 regulates gene expression for lifespan maintenance

city: Ansan

first: Yan

last: Liu

state: Gyeonggi-do

address: 55 Hanyangdeahak-ro

department: Department of Molecular and Life Science

institute: Hanyang University

summary: The relationship between aging and RNA biogenesis and trafficking is attracting growing interest, yet the precise mechanisms are unknown. The THO complex is crucial for mRNA cotranscriptional maturation and export. Herein, we report that the THO complex is closely linked to maintaining a normal lifespan. Deficiencies in Hpr1 and Tho2, components of the THO complex, reduced replicative lifespan (RLS) and are linked to a novel Sir2-independent RLS control pathway. Although transcript sequestration in hpr1Δ or tho2Δ mutants was countered by exosome component Rrp6, loss of this failed to mitigate RLS defects in hpr1Δ. However, RLS impairment in tho2Δ was counteracted by Nrd1-specific mutants that interacted with Rrp6. This effect relied on the interaction of Nrd1, a transcriptional regulator of aging-related genes, including ribosome biogenesis or RNA metabolism genes, with RNA polymerase II.  Nrd1 overexpression reduced RLS in a Tho2-dependent pathway. Intriguingly, THO2 deletion mirrored Nrd1 overexpression effects by inducing arbitrary Nrd1 chromatin binding. Taken together, these findings underscore the importance of Tho2-mediated Nrd1 escorting in maintaining a normal lifespan by transcriptional regulation of aging-related genes.

overall_design: Yeast strains WT and tho2Δ were grown in 5 mL of YPD until mid-log phase. mRNA profiles of them were generated by sequencing, in duplicate, using Illumina NovaSeq 6000.

first: Suji

last: Lim

first: Jeong-Min

last: Park

first: Ruxin

last: Duan

first: Byung-Ho

last: Rhie

first: Soo

middle: Y

last: Cho

first: Hong-Yeoul

last: Ryu

first: Seong

middle: H

last: Ahn


title: Secreted factors from M1 macrophages drive prostate cancer stem cell plasticity by upregulating NANOG, SOX2 and CD44 through NFκB signaling

city: Kuopio

first: Einari

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland


title: The RPD3L deacetylation complex is required for facultative heterochromatin repression in Neurospora crassa [ChIP-seq]

city: Sapporo

first: Hideki

last: Tanizawa

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

department: Institute for Genetic Medicine

institute: Hokkaido University

summary: Repression of facultative heterochromatin is essential for developmental processes in numerous organisms.  Methylation of histone H3 lysine 27 (H3K27) by Polycomb repressive complex 2 is a prominent feature of facultative heterochromatin in both fungi and higher eukaryotes.  Although this methylation is frequently crucial for silencing, the detailed mechanism of repression remains poorly understood.  We utilized a forward genetics approach to identify three previously uncharacterized genes required to maintain silencing at facultative heterochromatin genes in Neurospora crassa: sds3 (NCU01599), rlp1 (RPD3L protein 1; NCU09007) and rlp2 (RPD3L protein 2; NCU02898).  We found that SDS3, RLP1, and RLP2 associate with N. crassa homologs of the Saccharomyces cerevisiae RPD3L complex and are required for repression of a subset of H3K27-methylated genes.  Loss of these genes does not lead to loss of H3K27 methylation but increases acetylation of histone H3 lysine 14 at upregulated genes, and SDS3 binding levels are highest at genes derepressed upon loss of sds3, rlp1, and rlp2, implying that RPD3L-driven deacetylation is a previously undescribed factor required for silencing of facultative heterochromatin in N. crassa.

overall_design: To analyze levels of histone modifications in RPD3L and RPD3S mutants, we performed ChIP-seq in ∆sds3, ∆rlp1, ∆rlp2, ∆eaf-3, and strain N6279 treated with TSA with antibodies against H3K27me2me3, H3K9ac, and H3K14ac.

first: Colleen

middle: C

last: Mumford

first: Elizabeth

last: Wiles

first: Kevin

last: McNaught

first: Kirsty

last: Jamieson

first: Kenta

last: Tsukamoto

first: Eric

middle: U

last: Selker


title: The RPD3L deacetylation complex is required for facultative heterochromatin repression in Neurospora crassa [RNA-seq]

overall_design: To determine the global effects on transcription in RPD3L and RPD3S mutants, we performed mRNA-seq in wild type and strains bearing deletions of sds3, rlp1, rlp2, and eaf-3, or mycelium treated with Trichostatin A (TSA).


title: SFRP4 promotes autophagy and blunts FSH responsiveness through inhibition of AKT signaling in ovarian granulosa cells

city: Saint-Hyacinthe

first: Michael

last: Bérubé

state: QC

address: 3200, Sicotte street

institute: University of Montreal

summary:
Background: Secreted frizzled-related proteins (SFRPs) comprise a family of WNT signaling antagonists whose roles in the ovary are poorly understood. Sfrp4-null mice were previously found to be hyperfertile due to an enhanced granulosa cell response to gonadotropins, leading to decreased antral follicle atresia and enhanced ovulation rates.  The present study aimed to elucidate the mechanisms whereby Sfrp4 antagonizes FSH action.
Methods: Primary cultures of granulosa cells from wild-type mice were treated with FSH and/or SFRP4, and effects of treatment on gene expression were evaluated by RT-qPCR and RNAseq.  Bioinformatic analyses were conducted to analyse the effects of SFRP4 on the transcriptome, and compare them to those of FSH or a constitutively active mutant of FOXO1.  Additional granulosa cell cultures from wild-type or Sfrp4-null mice, some pretreated with pharmacologic inhibitors of specific signaling effectors, were used to examine the effects of FSH and/or SFRP4 on signaling pathways, autophagy and apoptosis by western blotting and TUNEL.
Results: Treatment of cultured granulosa cells with recombinant SFRP4 was found to decrease basal and FSH-stimulated mRNA levels of FSH target genes.  Unexpectedly, this effect was found to occur neither via a canonical (CTNNB1-dependent) nor non-canonical WNT signaling mechanism, but was found to be GSK3β-dependent.  Rather, SFRP4 was found to antognize AKT activity via a mechanism involving AMPK.  This lead to the hypophosphorylation of FOXO1 and a decrease in the expression of a portion of the FSH and FOXO1 transcriptomes.  Conversely, FSH-stimulated AMPK, AKT and FOXO1 phosphorylation levels were found to be increased in the granulosa cells of Sfrp4-null mice relative to wild-type controls.  SFRP4 treatement of granulosa cells also induced autophagy, both by signaling via AKT-mTORC1-ULK1 and by transcriptional regulation of autophagy-related genes.  SFRP4 further induced granulosa cell apoptosis in an autophagy-independent manner.
Conclusions: This study identifies a novel GSK3β-AMPK-AKT signaling mechanism through which SFPR4 antagonizes FSH action, and further identifies SFRP4 as a novel regulator of granulosa cell autophagy.  These findings provide a mechanistic basis for the phenotypic changes previously observed in Sfrp4-null mice, and broaden our understanding of the physiological roles of WNT signaling processes in the ovary.

overall_design: Primary culture of mouse preovulatory granulosa cells treated or not with exogenous SFRP4 protein

first: Atefeh

last: Abedini

first: Evelyne

last: Lapointe

first: Samuel

last: Gusscott

first: Julie

last: Brind’Amour

first: Gustavo

last: Zamberlam

first: Derek

last: Boerboom


title: Inherited mitochondrial dysfunction triggered by OPA1 mutation impacts the sensory innervation fibre identity, functionality and regenerative potential in the cornea

city: Montpellier

first: Frederic

last: Michon

address: 80, rue Augustin Fliche

department: Institute for Neurosciences of Montpellier

country: France

institute: Inserm

summary: Mitochondrial dysfunctions are detrimental to organ metabolism. The cornea, transparent outmost layer of the eye, is prone to environmental aggressions, such as UV light, and therefore dependent on adequate mitochondrial function. While several reports have linked corneal defects to mitochondrial dysfunction, the impact of OPA1 mutation, known to induce such dysfunction, has never been studied in this context. We used the mouse line carrying OPA1delTTAG mutation to investigate its impact on corneal biology. To our surprise, neither the tear film composition nor the corneal epithelial transcriptomic signature were altered upon OPA1 mutation. However, when analyzing the corneal innervation, we discovered an undersensitivity of the cornea upon the mutation, but an increased innervation volume at 3 months. Furthermore, the fibre identity changed with a decrease of the SP+ axons. Finally, we demonstrated that the innervation regeneration was less efficient and less functional in OPA1+/- corneas. Altogether, our study describes the resilience of the corneal epithelial biology, reflecting the mitohormesis induced by the OPA1 mutation, and the adaptation of the corneal innervation to maintain its functionality despite its morphogenesis defects. These findings will participate to a better understanding of the mitochondrial dysfunction on peripheral innervation.

overall_design: We compared the transcriptomic signatures of murine corneas at 3 and 6 months in OPA1+/+ and OPA1+/- animals

first: Lena

last: Meneux


title: Identification and characterization of metastasis-initiating cells in esophageal squamous cell carcinoma in a pulmonary metastasis mouse model

city: Hong Kong

first: Ching Ngar

last: Wong

state: Hong Kong

address: Lab Block, 21 Sassoon Road,

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong