title: Transcriptional profiling of intrahepatic cholangiocarcinoma (iCCA) cell lines transfected with GD3S

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

summary: Glycosphingolipids (GSL), a class of plasma membrane lipids, have been proposed as  markers of cancer stem cells (CSC). In particular, gangliosides (GS), sialic acid-containing GSL, have  been investigated for their role in the malignant phenotype of several cancers and in tumor-stem like  cells, but there are no data about human cholangiocarcinoma (CCA). Our study aims to provide a GSL  and GS profiling of both stem-like subsets and their parental cells in human CCA. Experimentals.  Intrahepatic CCA cells (HUCCT1, CCLP1) were used. Stem-like subset was enriched by sphere culture  (SPH) and compared to parental cells grown as monolayer (MON). CCA GS patterns were determined  by chromatographic analytical procedures, and their molecular species identification was evaluated by    feeding cells with 3H-sphingosine. GS role in modulation of stem features was investigated using D-  threo-1phenyl-2-palmitoylamino-3-N-morpholine-1-propanol (PPMP, glucosylceramide synthase    inhibitor), and CCA GD3S-transfected cells. FACS-sorted GD2+ SPH cells were examined for stem-like  gene expression compared to GD2- SPH. GS biosynthesis enzymes were analyzed by RT-qPCR at  different times of spherogenesis. Results: In both CCA lines, compared to MON, SPH showed drastic  changes in specific sphingolipids (Cer, Gb3, SM), and in the amount of total GS. In contrast to MON,  CCA-SPH shows increase content of GM3, reduction of GM2; among complex GS, strongly increase of  GD1a and appearance of GD2, a finding also corroborated by high levels of GM3 synthase as well as  GD3- and GM2/GD2 synthases expression in CCA-SPH. Notably, sphere-forming ability and expression  of CSC-related genes were affected by PPMP. Importantly it has emerged that the cancer stem features  related on GD2 availability are not due to the ganglioside GD2 synthase enzyme, but depend on the  enzyme GD3S, the synthase that provides the precursor (GD3) of ganglioside GD2. Thus we have stably  transfected both CCLP1 and HUCCT1 cells with the GD3S gene. GD3S-transfected MON (MON  GD3S+) cells showed enhanced sphere-forming ability in vitro, superior invasive properties, as well as  higher drug resistance when treated with cisplatin and oxaliplatin compare to the transfected control. To  better clarify the molecular features and the altered pathways in MON GD3S+ CCA cells, a global  transcriptomic analysis was performed. Likewise, GD2+ SPH cells were enriched with CSC-markers at  protein and gene levels in addition to several genes involved in pluripotency, self-renewal, and EMT,  compare to GD2- SPH. Notably, expression of GM2/GD2 synthases was significantly expressed in tumor  samples compared to paired non-tumoral liver tissue of CCA patients (n=104) and greatly correlated with  presence of satellite nodules, lymph node invasion, and recurrence. Conclusions: We show for the first  time that the CCA stem-like properties may be associated with GSL synthetic pathway and pattern. GSL  and GS synthases could represent potential markers for CCA.

overall_design: Transcriptional profiling of HUCCT1 and CCLP1 intrahepatic cholangiocarcinoma (iCCA) cell lines upon transfection with GD3S versus non transfected cells, analyzed in duplicates.

first: Caterina

last: Peraldo-Neia

first: Chiara

last: Raggi


title: Maternal under-nutrition during pregnancy alters the molecular response to over-nutrition in multiple tissues in juvenile offspring.

status: Public on Jan 08 2025

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

department: Internal Medicine

country: USA

institute: Wake Forest School of Medicine

summary:
This study examined gene expression in liver, fat and skeletal muscle of juvenile baboons to determine the effect of maternal under-nutrition (MUN; dams were fed a diet with 30% reduction in nutrients) during pregnancy on response to consumption of a high-fat, high-carbohydrate, high-salt and sugar drink (HFCS) diet for 7 weeks later in development of MUN offspring.
After dietary challenge, gene expression in the liver, fat and skeletal muscle of MUN juvenile baboons was compared with that of control juvenile baboons (CON; dams were fed a control diet).
Results showed that the number of differentially expressed genes and enriched pathways in these tissues differed between MUN and CON juvenile baboons.

overall_design:
Offspring from mothers fed the CON diet ad libitum were in the CON group, and those from mothers fed a nutrient reduced diet were in the MUN group.
After weaning, offspring consumed the chow diet until 4.5 years of age when they were challenged with the HFCS diet for 7 weeks or remained on the chow diet.
Gene expression in liver, fat and skeletal muscle of animals was measured using gene array from Illumina (HumanHT-12 v4 Expression BeadChips).

first: Laura

middle: A

last: Cox

first: Peter

middle: W

last: Nathanielsz


title: oHSV Drives Tertiary Lymphoid Structure Boosting Oral Cancer Immunotherapy

city: wuhan

first: Meng-Jie

last: Zhang

state: hubei

address: No. 237, Luoyu Road, Hongshan District

country: China

institute: wuhan university

type: Expression profiling by high throughput sequencing

summary: The formation of TLSs induced by oncolytic virus treatment can enhance the anti-tumor response of oral cancer. Therefore, oncolytic virotherapy in vivo is a good strategy. To understand the mechanism of post-treatment changes, we collected oHSV-treated tumors for RNA-seq.

overall_design: 4MOSC1 tumor-bearing mice were treated with oHSV on days 10, 14, and 18, and tumors from control and oHSV treated groups were collected on day 35 for RNA-seq.

first: Wen-Ping

last: Lin

first: Qing

last: Wang

first: Shuo

first: Hao

last: Li

first: Zhi-Jun

last: Sun


title: Chromatin remodeling in HIF-1a deficient B cell during IgA class switching [ChIP-seq]

city: Erlangen

first: Xianyi

last: Meng

address: Glückstr. 6

country: Germany

institute: Department of Medicine 3, Rheumatology and Immunology, University of Erlangen‐Nuremberg

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
The interconnection between metabolic programming and chromatin remodeling during IgA class switching suggest that HIF-1a-dependent glycolytic flux may control the epigenetic modification at α class switching region (Sα) in the Igh locus. To test our hypothesis, histone acetylation was analyzed by chromatin immunoprecipitation sequencing (ChIP-seq) (H3K9ac and H3K27ac) in Hif-1a deficient and control B cell during IgA class switching.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K27ac and H3K9ac in B cell from WT and HIF-1a deficient mice.

overall_design: 6 WT samples and 6 HIF-1a deficient samples for ChIP-seq.

first: Aline

last: Bozec


title: MicroRNA profile of tissue and discharge samples from cervical precancerous lesions

city: Salaya

first: Sarin

last: Chimnaronk

state: Nakhon Pathom

address: 25/25 Phuttamonthon 4 Road

department: Institute of Molecular Biosciences

country: Thailand

institute: Mahidol University

type: Non-coding RNA profiling by high throughput sequencing

summary: Cervical tissue and discharge samples were collected from patients with high-grade squamous intraepithelial lesion (HSIL) and adenocarcinoma in situ (AIS). Normal tissue samples were also collected for miRNA expression comparison. The samples were then sent for small RNA sequencing to obtain the miRNA counts for the miRNA profiles of the samples.

overall_design: A total of 49 cervical tissue samples and 23 discharge samples were collected from 27 patients. The samples were grouped as HSIL (40 tissue and 19 discharge samples), AIS (4 tissue and 4 discharge samples), and normal (5 tissue samples). The samples were then sent for small RNA sequencing to obtain the miRNA counts for the miRNA profiles of each sample.

first: Rooge

last: Suvanasuthi


title: Malaria pigment hemozoin

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

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

overall_design: Refer to individual Series


title: miR-146b-5p downregulates IRAK1 and ADAM19 to suppress trophoblast proliferation, invasion and migration in miscarriage [miRNA profiles]

city: Nanning

first: lihong

last: pang

state: Guangxi

address: NO.6 Shuangyong Road

department: Prenatal Diagnosis and Genetic Diseases

institute: Guangxi Medical University

summary: A large proportion of miscarriages are classified as unexplained miscarriages (UM) since no cause is identified. No reliable biomarkers or treatments are available for these pregnancy losses. While our transcriptomic sequencing has revealed substantial upregulation of miR-146b-5p in UM villous tissues, its role and associated molecular processes have yet to be fully characterized. Our work revealed that relative to samples from normal pregnancy (NP), miR-146b-5p was significantly elevated in villous tissues from UM patients and displayed promising diagnostic potential. Moreover, miR-146b-5p agomir contributed to higher rates of embryonic resorption in ICR mice. When overexpressed in HTR-8/SVneo cells, miR-146b-5p attenuated the proliferative, invasive, and migratory activity of these cells while suppressing the expression of MMP9 and immune inflammation-associated cytokines, including IL1B, IL11, CXCL1, CXCL8, and CXCL12. Conversely, inhibition of its expression enhanced proliferation, migration, and invasion abilities. Mechanistically, IRAK1 (IL-1 receptor-associated kinase-1) and ADAM19 (a disintegrin and metalloproteinase 19) were identified as miR-146b-5p targets regulating trophoblast function, and silencing IRAK1 had similar effects as miR-146b-5p overexpression, while IRAK1 overexpression could partially reverse the inhibitory impact of this miRNA on trophoblasts. miR-146b-5p may inhibit trophoblast proliferation, migration, invasion, and implantation-associated inflammation by downregulating IRAK1 and ADAM19, participating in the pathogenesis of miscarriage and providing a critical biomarker and a promising therapeutic target for UM.

overall_design: Maternal and gestational age-matched placental villus tissues from normal pregnancy (NP, n=5) and recurrent miscarriage (RM, n=5) were collected for RNA-seq of the whole transcriptome (including circRNA, lincRNA, miRNA and mRNA profiles) . To minimize the effect of maternal age and gestational age on miscarriage incidence or gene expression, specific criteria were used to match villus tissues from UM with those from NP. These criteria included a difference in maternal age ≤ 2 years and a difference in gestational age, as determined by ultrasound of ≤ 1 week.


title: Effect of depletion of HIF-1a on gene expression during B cell IgA class switching [RNA-seq]

summary: Investigate the function HIF-1a in the regulation of B cell IgA class switching using WT and HIF-1a conditional knockout mice.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 WT and 3 HIF-1a KO samples during B cell IgA class switching.


title: SARS-CoV-2 infection of human pluripotent stem cell-derived vascular cells reveals smooth muscle cells as key mediators of vascular pathology during infection

city: Cambridge

first: Rudolf

last: Jaenisch

state: MA

address: 455 Main St.

institute: Whitehead Institute for Biomedical Research

summary: Nearly 20% of hospitalized patients diagnosed with severe SARS-CoV-2 infection are at risk for thromboembolic events. We developed a model of SARS-CoV-2 infection using human-induced pluripotent stem cell-derived endothelial cells, pericytes, and smooth muscle cells to recapitulate the vascular pathology associated with SARS-CoV-2 exposure. Our results demonstrate that perivascular cells, particularly smooth muscle cells (SMCs), are a specifically susceptible vascular target for SARS-CoV-2 infection. Utilizing RNA sequencing, we characterized the transcriptomic changes accompanying SARS-CoV-2 infection of SMCs, and endothelial cells (ECs). We observed that infected human SMCs shift to a pro-inflammatory state and increase the expression of key mediators of the coagulation cascade. Further, we showed human ECs exposed to the secretome of infected SMCs produce hemostatic factors that can contribute to vascular dysfunction, despite not being susceptible to direct infection. The findings here recapitulate observations from patient sera in human COVID-19 patients and provide mechanistic insight into the unique vascular implications of SARS-CoV-2 infection at a cellular level.

overall_design: Human endothelial cells (ECs), pericytes (PCs), and smooth muscle cells (SMCs) were differentiated from human pluripotent stem cells(hPSCs). hPSC-derived ECs and SMCs were treated with either live SARS-CoV-2, heat-inactivated (HI) SARS-CoV-2 or mock-infected (no virus). We compared the transcriptional changes induced by each of these conditions in both ECs and SMCs. We also compared the transcriptional changes induced by the treatment of ECs with media from SMCs that were infected with SARS-CoV-2 or HI SARS-CoV-2. For the media transfer experiments, ECs were exposed to media from SMCs that had been exposed to live or HI SARS-CoV-2, and then RNA was isolated from the ECs 48 hours after exposure.

first: Alexsia

last: Richards


title: Malaria pigment hemozoin-induced chromatin remodeling of mouse hematopoietic stem and progenitor cells, granulocyte-macrophage progenitors, and bone marrow monocytes

summary: Trained immunity is the phenomenon whereby innate immune cells such as monocytes or macrophages, and their progenitors in the bone-marrow, undergo functional reprogramming after exposure to certain microbial and danger signals, altering their responses to future exposures. In this study, we performed a non-lethal Plasmodium yoelii 17XNL (Py) infection in wild-type C57/BL6J mice to investigate the underlying mechanism of Py-induced myelopoiesis and performed chromatin accessibility analysis on HSPCs, GMPs, and monocytes 6 weeks following exposure.

overall_design: C57/b6 mice were infected with Plasmodium yoelii for 6 weeks and then infected with CLP or left untreated for additional 3 hours. Mice were then sacrificed and bone marrow were harvested for HSPC, GMP or monoctes isolation. Different cells were sorted by BD Aria III with the following surface markers. HSPCs were sorted from Lin- cKit+ CD34+ population. GMPs were sorted from Lin-Ckit+Sca1-Cd16/32+CD34- population. Monocytes were sorted from CD45+CD11b+Ly6Chi Ly6G- population.

first: Shih-Chin

last: Cheng


title: Mechanotransduction inhibition prevents scarring and yields regeneration in a large animal model

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

institute: Stanford University

summary: Inhibiting mechanotransduction (via Yes-associated protein [YAP] inhibition) in mouse wounds yields wound regeneration without scarring. However, rodents are loose-skinned and fail to recapitulate key aspects of human wound repair. We thus sought to elucidate the effects of YAP inhibition in red Duroc pig wounds, the most human-like model of scarring. We show that a single treatment with the YAP inhibitor verteporfin, immediately following wounding, is sufficient to prevent scarring and drive wound regeneration in pigs. By performing scRNA-seq for the first time on porcine wounds in conjunction with spatial protein analysis, we reveal perturbations in fibroblast subpopulation profiles with verteporfin treatment and the presence of putative pro-regenerative and pro-fibrotic fibroblast subsets enriched in regenerating and scarring pig wounds, respectively. Finally, we validate our findings in a human foreskin xenograft wound model, including scRNA-seq of human wound cells. Collectively, our findings provide critical support for the future translation of local mechanotransduction inhibitors to prevent human skin scarring.

sample_organism:
Homo sapiens
Sus scrofa

platform_organism:
Homo sapiens
Sus scrofa

overall_design: scRNA-seq of unsorted cells from pig and human-->mouse xenograft skin wound samples using the 10X Genomics platform

first: Shamik

last: Mascharak

first: Michelle

last: Griffin

first: Heather

middle: E

last: Talbot

first: Jason

middle: L

last: Guo


title: Malaria pigment hemozoin-induced transcriptional remodeling of mouse hematopoietic stem and progenitor cells, granulocyte-macrophage progenitors, and bone marrow monocytes

summary: Trained immunity is the phenomenon whereby innate immune cells such as monocytes or macrophages, and their progenitors in the bone-marrow, undergo functional reprogramming after exposure to certain microbial and danger signals, altering their responses to future exposures. In this study, we performed a non-lethal Plasmodium yoelii 17XNL (Py) infection in wild-type C57/BL6J mice to investigate the underlying mechanism of Py-induced myelopoiesis and performed transcriptomic analysis on HSPCs, GMPs, and monocytes 6 weeks following exposure. Next cecal ligation and puncture (CLP) was used to model sepsis in vivo as a secondary exposure, and the transcriptomes of PBS and Py-exposed monocytes were generated.


title: Repurposing Live Attenuated Trivalent MMR Vaccine as Cost-effective Cancer Immunotherapy

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

summary: Oncolytic viral therapy is an emerging new class of immunotherapy that involves selectively infecting and killing tumor cells. Several oncolytic viruses (OVs) have exhibited promising potential for treating human cancer in animal models and clinical trials, including  hepatocellular carcinoma (HCC). However, despite clinical evidence and benefit for patients, the cost-intensive manufacturing and testing nature of oncolytic viral products makes them far out of reach for most US patients. We propose to develop a cost-effective immunovirotherapy approach that could synergize with other therapies to improve the outcomes for patients with advanced HCC. Specifically, we showed that intratumoral administration of low doses of the live attenuated measles, mumps and rueball viruses (MMR) vaccine effectively activates a robust cytotoxic T cells response, leading to tumor regression and extended survival in the syngeneic HCC model. Using  transcriptomic approach, we showed that mechanistically MMR exerts its anti-tumor activity by priming innate and adaptive anti-tumor immune responses, leading to immunologically coordinated death of cancer cells. The proposed research can impact cancer patients globally, and our multidisciplinary team is uniquely equipped to execute the proposed studies.

overall_design: Anti-tumor mechanism of MMR in hepatocellular cancer

first: Yuguo

last: Zhang

first: Musa

last: Gabere

first: Mika

last: Taylor

first: Camila

middle: C

last: Simoes

first: Chelsae

last: Dumbauld

first: Oumar

last: Barro

first: Jean

last: Chamcheu

first: Steven

middle: R

last: Post

first: Thomas

middle: J

last: Kelly

first: Mitesh

last: Borad

first: Martin

last: Cannon

first: Alexei

last: Basnakian

first: Bolni

middle: M

last: Nagalo


title: Transcriptome profiling of in-vitro challenged monocyte-derived  macrophages during pre- and post infection stages in Indian Ghurrah and Landrance pigs

city: Bareilly

first: AMIT

last: KUMAR

state: Uttar Pradesh

address: Izatnagar

department: Animal Genetics

country: India

institute: Indian Veterinary Research Institute

summary: In this study, the monocyte-derived macrophages (MDMs) were cultured and challenged with CSF virulent virus strain and response was studied at 48 hours post-infection. Transcriptome profiles were generated in the MDMs of 3 Landrace, and 3 indigenous Ghurrah pigs before and 48 hours after challenge with Classical Swine fever virulent virus strain under in-vitro conditions. The piglets were 3 months old and free of maternally derived antibodies against CSF. The sequencing was done on Illumina X-Ten platform, generating  average of 69.78 million paired end reads for each sample.

overall_design: Horizontal and vertical comparisons of MDM transcriptomes were made along challenge (pre- versus post challenge) and breed (Ghurrah versus Landrace).

first: Amit

last: Kumar

first: Harish

first: Sheikh

middle: F

last: Ahmad


title: Glial cell diversity and methamphetamine-induced neuroinflammation in human cerebral organoids

status: Public on Jan 07 2025

city: La Jolla

first: Tariq

last: Rana

state: California

address: 3147 Biomedical Sciences Wy

department: Pediatrics

institute: UC San Diego School of Medicine

summary: Methamphetamine (METH) is a potent stimulant that induces a euphoric state but also causes cognitive impairment, neurotoxicity and neurodevelopmental deficits. Yet, the molecular mechanisms by which METH causes neurodevelopmental defects have remained elusive. Here we utilized human cerebral organoids and single-cell RNA sequencing (scRNA-seq) to study the effects of prenatal METH exposure on fetal brain development. Findings have been reported in Dang et al. 2021, Molecular Psychiatry.

overall_design: We analyzed 20,758 cells from eight untreated and six METH-treated cerebral organoids and found that the organoids developed from embryonic stem cells contained a diverse array of glial and neuronal cell types

first: Jason

last: Dang

first: Shashi

middle: K

last: Tiwari

first: Kriti

last: Agrawal

first: Hui

last: Hui

first: Yue

last: Qin


title: Polydatin protects against DSS-induced ulcerative colitis via Nrf2/Slc7a11/Gpx4-dependent inhibition of ferroptosis signalling activation

city: Guangzhou

first: Ting

last: Zhang

address: 183 Zhongshan Avenue West

institute: the third affiliated hospital of southern medical university

summary: Ulcerative colitis (UC), a form of inﬂammatory bowel disease, is characterized by a Q7 recurrent and persistent nonspeciﬁc inﬂammatory response. Polydatin (PD), a natural stilbenoid polyphenol with potent properties, exhibits unexpected beneﬁcial effects beyond its well-documented anti-inﬂammatory and antioxidant activities. In this study, we presented evidence that PD confers protection against dextran sodium sulfate (DSS)-induced ulcerative colitis. Our ﬁndings demonstrated that PD mitigated the DSS-induced increases in proinﬂammatory  cytokines (IL-6, TNF-α, and IL-1β), alleviated colon length shortening, reduced morphological damage to the intestinal mucosa, and preserved tight junction proteins (TJ) occludin and Zonula occludens-1 (ZO-1) in both Caco-2 cells and murine models of colitis. Results from bulk RNA sequencing and differential gene analysis suggested a potential role for ferroptosis in the protective mechanisms of PD against UC. Further investigations revealed that PD modulated the expression levels of several ferroptosis-related proteins and transcription factors within the DSS-induced colitis model. Notably, treatment with PD enhanced nuclear translocation of Nrf2, which inhibits ferroptosis while ameliorating oxidative stress through upregulation of Slc7a11 and Gpx4 expression. Additionally, erastin—a known inducer of ferroptosis—reversed the protective effects conferred by PD in the DSS-induced colitis model by downregulating Slc7a11 expression. These ﬁndings underscore that PD protects against DSS-induced ulcerative colitis via the Nrf2/ Slc7a11/Gpx4 signaling axis, highlighting its potential as a novel therapeutic agent for UC.

overall_design: The subsequent groups were tested: (1) Control group: the standard incubator became the place where the cells were preserved; (2) DSS group: the cells were treated with 3%DSS at 37°C for 8 h; (3) DSS + PD group: 30 μM PD pre-treatment for 2 h, followed by coprocessing with 3% DSS for 8 h; (4) DSS + PD + Erastin group: with pretreatment, the cells were treated with 5 μM erastin at 37°C for 3 h prior to DSS + PD treatment; (5) DSS + Fer-1 group: the cells were treated with 10 μM Fer-1 at 37°C for 2 h before the DSS treatment. The application of inducers (erastin) and inhibitors (Fer-1) is crucial in the study of ferroptosis and related diseases (Du and Guo, 2022).

first: Shi-min

last: Zheng

first: Jian-bin

last: Yin

first: Bing-bing

last: Wang


title: Comparative evaluation of the biological characteristics of a novel retinoid X receptor agonist and bexarotene II

city: Nagoya

first: Makoto

last: Inoue

address: 1-100 Kusumoto-cho, Chikusa-ku, Nagoya

department: School of Pharmacy

country: Japan

institute: Aichi Gakuin University

summary: Retinoid X receptor (RXR) is a crucial and distinctive member of the nuclear receptor superfamily, which is involved in regulating various physiological processes. RXR agonists have the potential to treat Alzheimer’s disease (AD). In this study, we identified a novel RXR agonist superior to existing drugs after extensively exploring the biological properties of 6-hydroxy-3’-propyl-[1,1’-biphenyl]-3-propanoic acid (6OHA), a compound synthesized in our laboratory based on the structure of magnaldehyde B. 6OHA exhibited higher selectivity for RXRα over retinoic acid receptor (RARα) and lower transcriptional activity for RXRg compared to the existing RXR agonist bexarotene (Bex). RNA-sequencing analysis, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggest that 6OHA and Bex exhibit similar gene expression patterns but have distinct transcriptional effects; 6OHA was more closely associated with chemotaxis and response to stimuli compared to Bex. Pharmacokinetic studies revealed that 6OHA exhibited faster intestinal absorption, reached higher concentrations in the brain and liver shortly after oral dministration, and was cleared from the body more rapidly than Bex, subsequently inducing target gene transcription in the brain. Bex increased serum triglyceride and decreased serum thyrotropin and free thyroxine levels, whereas 6OHA did not induce these adverse effects, attributable to the distinct properties of 6OHA as an RXR agonist compared to Bex. Our results highlight 6OHA as a promising RXR agonist for treating AD without any adverse effects.

overall_design:
Mouse microglial MG5 cells were treated with 6OHA or Bex at a concentration of 10 µM for 6 h, followed by extraction of total RNA. We then performed gene expression profiling using RNA-seq data from cells treated with 6OHA or Bex or untreated control (n=3).
Bexarotene (Bex), an established retinoid X receptor (RXR) agonist, has demonstrated neuroprotective and anti-neuroinflammatory effects, suggesting its potential for Alzheimer's disease (AD) treatment. However, concerns remain regarding the serious adverse effects associated with Bex, including hypertriglyceridemia, hypothyroidism, and hepatomegaly. In this study, we investigated the differences in agonist activity between 6OHA, a newly synthesized RXR agonist in our laboratory, and Bex, with the goal of identifying alternative RXR agonists that may be suitable for the treatment or prevention of AD.
Comparative gene expression profiling analysis of RNA-seq data for MG5 cells treated with 6OHA and untreated cells.

first: Koji

last: Tomita

first: Ken-ichi

last: Nakashima

first: Eiji

last: Yamaguchi

first: Akichika

last: Itoh

first: Kaname

last: Tsutsumiuchi


title: RNA-seq analysis of ipsilateral rat TGs on day 14 after CCI-ION or sham operation

city: Suzhou

first: Jin

last: Tao

state: Jiangsu

address: 199 Ren-Ai Road

department: Physiology and Neurobiology

institute: Soochow University

summary: Nerve injury-induced changes in gene expression in primary sensory neurons, such as trigeminal ganglion (TG) neurons, play a critical role in the genesis of neuropathic pain. Therefore, understanding the molecular mechanisms underlying these changes in the TGs following peripheral nerve injury will enable us to develop a new avenue for managing trigeminal-mediated neuropathic pain. Studies have highlighted the involvement of miRNA-mediated modulation in a wide range of diseases, leading to the exploration of miRNA-based therapeutics as a potential treatment strategy. Here, in this RNA-seq database, we have found that microRNA-216a-3p (miR-216a-3p) and miR-32-5p (miR-32-5p), which are downregulated in injured TGs, are novel functional RNAs involved in regulating trigeminal-mediated neuropathic pain. Histone methylation-mediated miRNA downregulation in TG neurons regulates trigeminal neuropathic pain by targeting either STIM1 (H3K27me3/SOX10/miR-216a-3p/STIM1) or Cav3.2 (GR/miR-32-5p/Cav3.2) channels. Moreover, we found that miR-323-3p exhibited the most significant upregulation in the injured TG. Understanding the mechanistic role of the PRMT2/FOXA2/miR-323-3p/Kv2.1 signaling axis in sensory neurons may advance the discovery of novel therapeutic strategies for neuropathic pain.

overall_design: Trigeminal ganglia miRNA profiles in ipsilateral rat TG tissue on day 14 after CCI-ION (n=3) or sham operation (n=3)

first: Reifei

last: Qi

first: Yufang

last: Sun

first: Yu

first: Yuan


title: Barrier formation by primary human airway epithelial cells sets limits to Staphylococcus aureus adhesion, invasion and cytotoxicity

city: Groningen

first: Xiaofang

last: Li

address: Hanzeplein 1

country: Netherlands

institute: University of Groningen


title: Fibronectin and E-cadherin drive collective invasion in drug-resistant ovarian cancer cells

city: Bangalore

first: Ramray

last: Bhat

state: Karnataka

address: CV Raman Rd

department: Developmental Biology & Genetics

institute: Indian Institute of Science

summary: Rapid progression in epithelial ovarian cancer (EOC) is characterized by resistance to platinum-based therapy. We asked if progression kinetics is caused by coevolution of invasiveness with drug resistance. Isogenic carboplatin-resistant counterparts of high grade serous human cancer cells invaded better through, and on, ECM and within murine peritonea. The resistant cell transcriptome was ontologically enriched for signatures of migration, erstwhile reported resistance signatures in patients and mediators of transition between epithelial, mesenchymal, and amoeboid states, which was confirmed through higher expression of fibronectin and E-cadherin. Lower matrix adhesion, weak focal adhesion, and higher translatory dynamics of deformable cell collectives that could clear surrounding mesothelia indicated that resistant cancer cells displayed a unique collective amoeboid-like migration. E-cadherin knockdown partially restored sensitivity to carboplatin and decreased collective integrity, but did not affect migration. In contrast, silencing fibronectin decreased migration but did not affect resistance and integrity. Therefore, unique migrative abilities coevolve with EOC drug-resistance through the upregulation of distinct molecular trait drivers.

overall_design: RNA-seq profiling of wildtype 'OVCAR-3' cells and its isogenic carboplatin resistant variant 'res OVCAR-3' cells at 24 hrs

first: Shyamili

last: Goutham

first: Nivedhya

last: Venas


title: Targeting PARK7: Sodium 4-Phenylbutyrate Shields Endothelial Cells from GSDME-Mediated Pyroptosis in Acute Lung Injury

city: Shanghai

first: Jian

last: Xu

address: 180 Fenglin Road

institute: Zhongshan hospital

summary: Summary Sodium 4-phenylbutyrate (Na-PBA), a histone deacetylase inhibitor, shows potential in mitigating acute lung injury (ALI) by addressing endothelial cell injury. In a lipopolysaccharide (LPS)-induced ALI mouse model, Na-PBA pretreatment reduced lung damage, pulmonary edema, and inflammatory markers, while decreasing oxidative stress and endothelial pyroptosis via the cytochrome c-caspase9-caspase3-GSDME pathway. In vitro studies with human umbilical vein endothelial cells (HUVECs) confirmed that Na-PBA enhanced PARK7 expression, which is crucial for its protective effects against oxidative damage and pyroptosis. The mechanism involves PARK7 stabilizing mitochondria and inhibiting cytochrome c leakage, leading to reduced caspase activation. Na-PBA's effects are mediated through upregulation of PARK7, potentially within a positive feedback loop involving NRF2. These findings identify a novel therapeutic strategy to alleviate endothelial injury in lung diseases.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For primary pulmonary endothelial cells, 6-week to 8-week C57BL/6 mice were administered PBS or 5 mg/kg lipopolysaccharide (LPS) via the trachea, executed 3 days later, and endothelial cells were sorted from lung tissue for RNA-seq. For HUVECs, cells in the treatment group were pre-treated with 0.5 mM Na-PBA, followed by stimulation of injury with LPS and Nigericin in both the treatment and injury groups.


title: Comparative Transcriptomic Analysis of Left-Right Sensory Differences in Haliotis discus hannai

city: Yantai

first: Haifeng

last: Huang

state: Shandong

address: Middle Hongqi Road, Zhifu District

institute: Ludong University

summary: Asymmetric development, in which functional differences occur between left-right symmetrical organs, is widespread in organisms, including fish and mollusks. However, the asymmetry of symmetrical sensory structures in Haliotis discus hannai, a gastropod with a sensitive sensory system, remains unknown. This study analyzed the transcriptomes of three sensory structures (eyestalks, cephalic tentacles, and epipodial tentacles) to explore potential asymmetries in this species. RNA-seq revealed functional differences in sensory ability and sperm-egg recognition between right and left eyestalks, with cephalic tentacles displaying asymmetry in cytoskeletal organization and cell cycle regulation. Epipodial tentacles showed similar asymmetries, including immune response differences. Moreover, the cAMP-protein kinase A (PKA)-CREB-binding protein (CBP) signaling pathway responded asymmetrically, with PKA responding to activators and inhibitors on both sides and CBP showing a stronger response on the right. These findings provide insights into sensory asymmetry in mollusks and guidance for further investigations of the molecular mechanisms underlying asymmetry in symmetrical organs.

overall_design:
This study focuses on the left and right sensory organs (particularly the eyestalks and tentacles) of Haliotis discus hannai, utilizing transcriptome sequencing to analyze the differences in gene expression between the left and right sides. The experimental design includes the following steps:
1. Collecting tissue samples from the left and right eyestalks and tentacles of abalones.
2. Extracting total RNA and performing high-throughput sequencing to obtain 3. comprehensive gene expression profiles.
4. Comparing gene expression differences between left and right tissues to identify key differentially expressed genes.
5. Analyzing the expression patterns of genes related to the cAMP-PKA-CBP and TGF-β signaling pathways in left and right tissues.
6. Validating the expression of key genes using qPCR to ensure data reliability.
This study aims to uncover the molecular regulatory mechanisms underlying the asymmetry of abalone sensory organs and provide new insights into the evolution and adaptation of sensory functions in mollusks.

first: Lintao

last: Tan

first: Lei

last: Wei

first: Hongce

last: Song

first: Wenwen

first: Meiyun

last: Dong

first: Xiaolong

last: Chu

first: Xiaotong


title: Gene expression changes induced by HA-PRCC-TFE3 in HEK293 cells

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 1-1-1 Honjo, Chuo-ku

department: Urology

institute: Kumamoto University

summary: PRCC-TFE3 is an oncogenic chimeric transcription factor identified in human TFE3-rearranged renal cell carcinoma. To analyze gene expression changes driven by PRCC-TFE3, we generated and utilized an HA-tagged PRCC-TFE3-inducible HEK293 cell line, which expresses HA-tagged PRCC-TFE3 in a doxycycline-dependent manner. Cells were cultured with or without doxycycline, and comprehensive gene expression analysis was conducted using Affymetrix arrays .

overall_design: We performed Affymetrix array analysis on HA-PRCC-TFE3 doxycycline-inducible HEK293 cell lines, cultured with or without doxycycline.

first: W

last: Linehan


title: NELFCD: A Crucial Factor in Uveal Melanoma Cell Proliferation and Tumorigenesis

city: shenzhen

first: huan

last: wan

address: huaqiangnan road

institute: shenzhen aier eye hospital

summary: Uveal melanoma is the most common intraocular malignant tumour in adults.Posterior uveal melanoma is highly likely to metastasise to the liver (89%), lungs (29%), bone (17%), skin and subcutaneous tissues (12%), and lymph nodes (11%) and has an extremely high mortality rate.Due to the unclear pathogenesis, there is still no effective treatment for uveal melanoma other than surgery.Thus, it is crucial to investigate the mechanisms of carcinogenesis and proliferation of uveal melanoma.Recent evidence suggests that biomolecular condensates，membrane-free cellular compartments formed by liquid-liquid phase separation (LLPS), plays crucial roles in physiological and tumorigenic processes.The aim of this study was to investigate the role of LLPS in the development of uveal melanoma in order to explore potential therapeutic targets for UM.

overall_design: The experiment was set up with three groups of control cells and three groups of cells knocking down NELFCD.


title: Gene expression changes induced by ARID2 knockout in UOK124 cells.

summary: TFE3-rearranged Renal Cell Carcinoma (TFE3-RCC) is an aggressive RCC subtype characterized by Xp11.2 rearrangements, resulting in TFE3 fusion proteins with oncogenic potential. To investigate the role of ARID2, a component of the SWI/SNF chromatin remodeling complex, in TFE3-RCC, we knocked out the ARID2 gene in a TFE3-RCC cell line, UOK124, which is derived from human TFE3-RCC with the PRCC-TFE3 fusion gene. UOK124 parental cells (UOK124-WT) and UOK124-ARID2_KO cells were cultured, and comprehensive gene expression analysis was performed using RNA-seq.

overall_design: UOK124-WT and UOK124-ARID2_KO cells were cultured under normal conditions in triplicate, and RNA-seq analysis was performed on these samples.

first: Jinglong

last: Tang


title: CA-125 as a Biomarker in Renal Medullary Carcinoma: Integrated Molecular Profiling, Functional Characterization, and Prospective Clinical Validation [ChIP-Seq cell lines]

city: Houston

first: Amrit

last: Koirala

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: Purpose: Renal medullary carcinoma (RMC) is a highly aggressive malignancy defined by the loss of the SMARCB1 tumor suppressor. It mainly affects young individuals of African descent with sickle cell trait, and it is resistant to conventional therapies used for other renal cell carcinomas. This study aimed to identify potential biomarkers for early detection and disease monitoring of RMC. Experimental Design: Integrated profiling of primary untreated RMC tumor tissues and paired adjacent kidney controls was performed using RNA-sequencing (RNA-seq) and histone Chromatin Immunoprecipitation Sequencing (ChIP-seq). The expression of serum cancer antigen 125 (CA-125), was prospectively evaluated in 47 patients with RMC. Functional studies were conducted in RMC cell lines to assess the effects of SMARCB1 re-expression and MUC16 knockdown. Results: MUC16, encoding for CA-125, was identified as one of the top upregulated genes in RMC tissues, with concomitant enrichment of active histone marks H3K4me3 and H3K27ac at its promoter. Elevated serum CA-125 levels were found in 31 of 47 (66%) RMC patients and correlated significantly with metastatic tumor burden (p = 0.03). SMARCB1 re-expression significantly reduced MUC16 expression in RMC cell lines. Functional studies in RMC cell lines demonstrated that SMARCB1 re-expression significantly reduced MUC16 expression, and that MUC16 knockdown induced apoptosis and reduced cell proliferation. Conclusions: The correlation between serum CA-125 levels and metastatic burden suggests that CA-125 is a clinically relevant biomarker for RMC. These findings support further exploration of CA-125 for disease monitoring and targeted therapeutics in RMC.

overall_design: Cell lines derived from Renal medullary carcinoma (RMC) were transfected with either empty vector or SNF5 (SMARCB1) constructs and treated with doxycycline to express SNF5 (SMARCB1).

first: Pavlos

last: Msaouel

first: Cristian

last: Coarfa

first: Sandra

last: Grimm

first: Menuka

last: Karki


title: The fungicide propiconazole induces hepatic steatosis and activates PXR in a mouse model of diet-induced obesity

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Propiconazole is a triazole fungicide previously shown to induce triglyceride accumulation in human liver HepaRG cells, potentially via activation of the Pregnane X Receptor (PXR). However, whether propiconazole can disrupt hepatic and whole-body metabolism in vivo is currently unknown. Therefore, we aimed to examine the metabolic effects of propiconazole in the context of metabolic dysfunction-associated steatotic liver disease (MASLD), obesity, and insulin resistance. To this end, male C57BL/6J mice were fed a high-fat diet for 20 weeks. During the last 10 weeks, mice additionally received vehicle, 0.04, 30, or 100 mg/kg body weight (bw)/day propiconazole via oral gavage. High-dose propiconazole, but not low or intermediate dose, reduced body weight gain and adipose tissue weight in obese mice. Mice receiving high-dose propiconazole displayed improved glucose tolerance and reduced levels of plasma triglycerides and cholesterol. Propiconazole dose-dependently increased liver weight and triglyceride levels and at high dose caused signs of hepatic inflammation. RNA sequencing on the liver revealed that propiconazole mainly induced PXR target genes. At intermediate and high-dose, propiconazole induced pathways related to cell-cell interactions and inflammation, while oxidative phosphorylation was repressed by propiconazole. Comparison of gene regulation in wildtype and PXR knockout primary hepatocytes as well as gene reporter assays confirmed the activation of PXR by propiconazole. All in all, our data underscore the capacity of propiconazole to activate PXR in the liver and thereby promote the development of hepatic steatosis in vivo.

overall_design: Livers were obtained from mice fed a high-fat diet that were treated with either vehicle or three doses of propiconazole (0.04, 30 or 100 mg/kg BW) through oral gavage for 10 weeks. Gene expression was profiled by RNA-sequencing.

first: Brecht

last: Attema

first: Sander

last: Kersten


title: PRCC-TFE3 Function and the Role of HIF1α and HIF2α in TFE3-Rearranged Renal Cell Carcinoma Development

summary: PRCC-TFE3 is an oncogenic chimeric transcription factor identified in human TFE3-rearranged renal cell carcinoma. To investigate the function of PRCC-TFE3 in vivo, we generated PRCC-TFE3 knock-in (KI) mice by inserting a loxP-STOP-loxP-PRCC-TFE3 cassette into the Rosa26 locus. When PRCC-TFE3 KI mice were crossed with Cadherin 16-Cre transgenic mice (KSP-Cre), the resulting mice developed TFE3-RCC in the kidney. Our findings revealed that hypoxia-inducible factors HIF1α and HIF2α are directly upregulated by PRCC-TFE3. To clarify the roles of HIF1α and HIF2α in TFE3-RCC development, we further crossed PRCC-TFE3 KI mice with HIF1α flox and/or HIF2α flox mice.

overall_design: We performed RNA-seq analysis on kidney samples from Cre(-) control mice, PRCC-TFE3 KI/KSP-Cre mice, PRCC-TFE3 KI/HIF1α flox/KSP-Cre mice, PRCC-TFE3 KI/HIF2α flox/KSP-Cre mice, and PRCC-TFE3 KI/HIF1α/HIF2α flox/KSP-Cre mice.

first: Wenjuan

last: Ma

first: Akira

last: Nishiyama


title: CA-125 as a Biomarker in Renal Medullary Carcinoma: Integrated Molecular Profiling, Functional Characterization, and Prospective Clinical Validation [ChIP-Seq tumors]

overall_design: Renal medullary carcinoma (RMC) kidney tumors or adjacent normal tissue from untreated patients were used for Chromatin immunoprecipitation against four histone marks (H3K27ac, H3K4me1, H3K4me3, H3K27me3).


title: ac4C transcriptomes of Zebrafish and Worm

city: Fuzhou

first: lele

last: Yang

address: Fujian Medical University, 1 Xuefubei Road, Minhou, Fuzhou, Fujian province, China

institute: Fujian Medical University

summary: ac4C modification appears in mutilple model organisms including Zebrafish and Worm

sample_organism:
Caenorhabditis elegans
Danio rerio

platform_organism:
Caenorhabditis elegans
Danio rerio

overall_design: To investigate whether ac4C modification is involved in evolution, we performed ac4C-RIP-seq on Zebrafish and Worm.

first: Zekai

last: Wu

first: An

last: Zhu

first: Kunqi

last: Chen


title: MVA-based SARS-CoV-2 vaccine candidates encoding different spike protein conformations induce distinct early transcriptional responses which may impact subsequent adaptive immunity

city: Hamburg

first: Michael

last: Spohn

address: Martinistr. 52

department: Bioinformatics Core

institute: UKE Hamburg

summary: Introduction: Vaccine platforms such as viral vectors and mRNA can accelerate vaccine development in response to newly emerging pathogens, as demonstrated during the COVID-19 pandemic. However, the differential effects of platform and antigen insert on vaccine immunogenicity remain incompletely understood. Innate immune responses induced by viral vector vaccines are suggested to have an adjuvant effect for subsequent adaptive immunity. Integrating data on both innate and adaptive immunity, systems vaccinology approaches can improve the understanding of vaccine-induced immune mechanisms. Methods: Two vaccine candidates against SARS-CoV-2, both based on the viral vector Modified Vaccinia virus Ankara (MVA) and encoding the native (MVA SARS-2-S) or prefusion-stabilized spike protein (MVA-SARS-2-ST), were evaluated in phase 1 clinical trials (ClinicalTrials.gov: NCT04569383, NCT04895449). Longitudinal dynamics of innate and early adaptive immune responses induced by vaccination in SARS-CoV-2-naïve individuals were analyzed based on transcriptome and flow cytometry data, in comparison to the licensed ChAd and mRNA vaccines. Results: Compared to MVA-SARS-2-S, MVA-SARS-2-ST (encoding the prefusion-stabilized spike protein) induced a stronger transcriptional activation early after vaccination, as well as higher virus neutralizing antibodies. Positive correlations were observed between innate and adaptive immune responses induced by a second MVA-SARS-2-ST vaccination. MVA-, ChAd- and mRNA-based vaccines induced distinct immune signatures, with the overall strongest transcriptional activation as well as monocyte and T follicular helper cell responses induced by ChAd. Discussion: Our findings suggest a potential impact of the spike protein conformation not only on adaptive but also on innate immune responses. As indicated by positive correlations between several immune parameters induced by MVA-SARS-2-ST, the distinct transcriptional activation early after vaccination may be linked to the induction of classical monocytes and activation of cTFH1 cells, which may in turn result in the superior adaptive immunogenicity of MVA-SARS-2-ST, compared to MVA-SARS-2-S. Overall, our data demonstrate that both the vaccine platform and antigen insert can affect innate immune responses and subsequent vaccine immunogenicity in humans.

overall_design:
We collected whole blood for RNA-seq from participants who received 2 vaccinations (V1 and V2), before each vaccination (Day 0, D0) and on Day 1, 3 and 7 (D1, D3 and D7) after each vaccination. 12 participants (MVA-S cohort) received 2 MVA-SARS-2-S vaccinations (low dose, LD, or high dose, HD), 15 participants (MVA-ST cohort) received 2 MVA-SARS-2-ST vaccinations (low dose, LD, or middle dose, MD), 10 participants (mRNA cohort) received 2 mRNA (BNT162b2) vaccinations and 8 participants (ChAd/mRNA cohort) received one ChAdOx1 nCoV-19 and one mRNA (BNT162b2 or mRNA-1273) vaccination. We compared the transciptional profile of each time point post vaccination to V1D0, and between the cohorts.

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Ilka

last: Grewe

first: Monika

last: Friedrich

first: Marie-Louise

last: Dieck

first: My

last: Ly

first: Verena

last: Krähling

first: Leonie

last: Mayer

first: Sibylle

last: Mellinghoff

last: Rottstegge

first: Rebekka

last: Kraemer

first: Asisa

last: Volz

first: Stephan

last: Becker

first: Anahita

last: Fathi

first: Christine

last: Dahlke

last: Weskamm

first: Marylyn

last: Addo


title: Single-cell RNA sequencing of chronic idiopathic erythroderma defines disease-specific markers

city: Vienna

first: Natalia

last: Alkon

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

summary:
Background: Chronic erythroderma is a potentially life-threatening condition that can be caused by a variety of diseases, but approximately 30% of cases remain idiopathic, often with insufficient treatment options.

Objective: To establish a molecular disease map of chronic idiopathic erythroderma.

Methods: We performed single-cell RNA sequencing combined with T-cell receptor sequencing of blood and skin from 5 chronic idiopathic erythroderma (CIE) patients and compared results with 8 cases of erythrodermic cutaneous T-cell lymphoma (eCTCL), 15 moderate-to-severe atopic dermatitis (AD), 10 psoriasis and 20 healthy control (HC) individuals.

Results: In erythrodermic CTCL, we found strong expansion of CD4+ malignant clones with a CCR7+SELL+ central memory phenotype. By contrast, CIE exhibited a pattern of low-level, but consistent expansion of CD8A+KLRK1+ T-cell clones, both in blood and skin. KLRK1 was also expressed by CCR10+FUT7+ skin-homing CIE blood T-cells that had increased proliferation rates and were absent in all other conditions. While CIE and CTCL patients lacked the strong type 2 or type 17 immune skewing typically found in AD or psoriasis, respectively, they were characterized by upregulation of MHC II genes (HLA-DRB1, HLA-DRA, CD74) in keratinocytes and fibroblasts, most likely in an IFNG-dependent fashion. However, we found strongest upregulation of type 1 immune mediators in CIE samples, both in the expanded CD8A+ clones, as well as in the tissue microenvironment.

Conclusion: Despite the notion that CIE might be a mere bundle of various yet uncharacterized disease processes, we found specific pathogenic signatures in these patients, that were different from other forms of erythroderma. These data might help to improve our pathogenic understanding of the blood and skin compartments of CIE, aiding in discovery of future treatment targets.

overall_design:
Comparison of skin cells obtained from chronic idiopathic erythroderma (CIE), erythrodermic cutaneous T-cell lymphoma (CTCL), atopic dermatitis (AD) and healthy controls (HC).

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Submitter states that missing raw files are due to patient privacy concerns.
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first: Sumanth

last: Chennareddy

first: Katharina

last: Rindler

first: Shannon

last: Meledathu

first: Malini

middle: P

last: Naidu

first: John

last: Ruggiero

first: Lisa

last: Szmolyan

first: Wolfgang

last: Weninger

last: Bauer

first: Johannes

last: Griss

first: Constanze

last: Jonak

first: Patrick

last: Brunner


title: RAGE is a key regulator of ductular reaction-mediated fibrosis during cholestasis

city: Tübingen

first: Morgana

last: Barroso Oquendo

address: Otfried-Müller-Straße 37

department: Quantitative Biology Center (QBiC)

institute: University of Tuebingen

summary: Ductular reaction (DR) is the hallmark of cholestatic diseases manifested in the proliferation of bile ductules lined by biliary epithelial cells (BECs). It is commonly associated with increased risk of fibrosis and liver failure. The Receptor for Advanced Glycation End Products (RAGE) was identified as a critical mediator of DR during chronic injury. Yet, the direct link between RAGE-mediated DR and fibrosis as well as the mode of interaction between BECs and hepatic stellate cells (HSCs) to drive fibrosis remains elusive. In this study, we aimed to delineate the specific function of RAGE on BECs during DR and its potential association with fibrosis in the context of cholestasis. Employing a biliary lineage tracing cholestatic liver injury mouse model, combined with whole transcriptome sequencing and in vitro analyses, we revealed the central role of BEC-specific Rage activity in fostering a pro-fibrotic milieu. RAGE is predominantly expressed in BECs and contributes to DR. Notch ligand Jagged1 is secreted from activated BECs in a Rage-dependent manner and signals HSCs in trans, eventually enhancing fibrosis during cholestasis.

overall_design: A mouse line harboring a biliary lineage tracing reporter gene and generated R26TomHnf1b-CreRagefl/fl mice with BEC-specific deletion of Rage (RageΔBEC) was employed. Cholestasis was induced in vivo by the ad libitum Choline-deficient Ethionine-supplemented (CDE) diet. Whole transcriptome sequencing was performed on FACS-sorted primary BECs from CDE-challenged mice to identify Rage-dependent signaling pathways during cholestasis. Using this genetic mouse model, combined with immunohistological analyses, co-culture assays and mass spectrometry analysis, the interplay between BECs and hepatic stellate cells (HSCs) during chronic liver damage was evaluated.

first: Wai-Ling

last: Lam

first: Gisela

last: Gabernet

first: Tanja

last: Poth

first: Melanie

last: Sator-Schmitt

first: Bettina

last: Kast

first: Sabrina

last: Lohr

first: Aurora

last: de Ponti

first: Lena

last: Weiß

first: Martin

last: Schneider

first: Dominic

last: Helm

first: Karin

last: Müller-Decker

first: Peter

last: Schirmacher

first: Mathias

last: Heikenwälder

first: Ursula

last: Klingmüller

first: Fabian

last: Geisler

first: Doris

last: Schneller

first: Sven

last: Nahnsen

last: Angel


title: Dysregulation of synaptic transcripts underlies network abnormalities in ALS patient-derived motor neurons

city: Trondheim

first: Anna

middle: Mikalsen

last: Kollstrøm

address: Edvard Griegs gate 8

department: Department of Neuromedicine and Movement Science

country: Norway

institute: NTNU

summary: Amyotrophic lateral sclerosis (ALS) is characterized by dysfunction and loss of upper and lower motor neurons. Several studies have identified structural and functional alterations in the motor neurons before the manifestation of symptoms, yet the underlying cause of such alterations and how they contribute to the progressive degeneration of affected motor neuron networks remain unclear. Importantly, the short and long-term spatiotemporal dynamics of neuronal network activity make it challenging to discern how ALS-related network reconfigurations emerge and evolve. To address this, we systematically monitored the structural and functional dynamics of motor neuron networks with a confirmed endogenous C9orf72 mutation. We show that ALS patient-derived motor neurons display time-dependent neural network dysfunction, specifically reduced firing rate and spike amplitude, impaired bursting, but higher overall synchrony in network activity. These changes coincided with altered neurite outgrowth and branching within the networks. Moreover, transcriptional analyses revealed dysregulation of molecular pathways involved in synaptic development and maintenance, neurite outgrowth and cell adhesion, suggesting impaired synaptic stabilization. This study identifies early synaptic dysfunction as a contributing mechanism resulting in network-wide structural and functional compensation, which may over time render the networks vulnerable to neurodegeneration.

overall_design: To investigate the underlying molecular mechanisms contributing to network dysfunction in ALS, we conducted mRNA  sequencing of healthy and ALS patient hiPSC-derived motor neurons at three different time points: 18 days in vitro (DIV), 38 DIV and 52 DIV.

first: Nicholas

last: Christiansen

first: Axel

last: Sandvig

first: Ioanna


title: METTL3 Aggravates Intimal Hyperplasia by Facilitating the m6A-YTHDC1-dependent SGK1 Gene Transcription in VSMCs

city: Beijing

first: Jiaqi

last: Huang

address: Xueyuan Road 38

institute: Peking University

type: Methylation profiling by high throughput sequencing

summary:
Rationale: Neointima formation is a common pathological feature of atherosclerosis and restenosis after angioplasty and involves the proliferation and migration of vascular smooth muscle cells (VSMCs). N6-methyladenosine (m6A), the most prevalent mRNA internal modification and being proposed to be primarily produced by RNA methyltransferase METTL3, plays a vital role in post-transcriptional regulations. Nevertheless, the role of RNA m6A modification in VSMCs and neointima formation remains disputable and undetermined.
Objective: To determine the role of METTL3 and its produced RNA modification m6A in VSMCs and neointima formation after vascular injury.
Methods and Results: We examined the expression of m6A writers and erasers in the carotid artery collected from human carotid endarterectomy (CEA) as well as in that of mice and unanimously found that METTL3 expression is increased significantly after vascular injury. Then, VSMC-confined METLL3 knockout mice (Myh11CreERT2 METTL3flox/flox) were generated, and carotid artery injury was induced. METTL3 knockout markedly attenuated artery neointima formation induced by wire injury. Moreover, we discovered that METTL3 deficiency repressed both ex vivo and in vivo proliferation of VSMCs. Through a joint analysis of the data from bulk RNA and m6A sequencing, serum- and glucocorticoid-inducible kinase 1 (SGK1) was identified due to its well-documented role in promoting VSMC proliferation and migration. Mechanistically, METTL3-mediated SGK1 mRNA methylation (A146 and A210) was proposed to facilitate SGK1 transcription by recruiting the m6A reader YTHDC1, as shown by well-designed experiments involving methylation site mapping, m6A RNA immunoprecipitation (m6A-RIP), chromatin immunoprecipitation quantitative PCR (ChIP-qPCR) and reporter gene analysis. As anticipated, VSMC proliferation and intimal hyperplasia that had already been mitigated by METTL3 ablation were both restored by SGK1 overexpression.
Conclusions: Our findings suggest that METTL3 promotes SGK1 expression via mRNA methylation-mediated facilitation of its own transcription, thus predisposing VSMCs to a proliferative state and contributing to neointima formation after vascular injury, underscoring the essential role METTL3 plays in vascular remodeling.

overall_design: MeRIP (m6A immunoprecipitation) for control or Mettl3-overexpressing rat primary VSMCs

first: Yihan

last: Liu

first: Qianqian

last: Feng


title: Anti-aging Metabolite-Based Polymeric Microparticles for Intracellular Drug Delivery and Bone Regeneration

status: Public on Jan 06 2025

city: Iowa City

first: Erliang

last: Zeng

state: IOWA

address: 801 Newton Rd, DSB N101-9, College of Dentistry

institute: University of Iowa

summary: In this study, we compared the gene expression profiles of mouse MC3T3-E1 cells treated with PAKG MPs to those of the control group.

overall_design: mouse MC3T3-E1 cells were treated with PAKG–8diol–PEG(S) MPs (30 μg mL−1) for 2 days before cell harvested for total RNAs isolation. The cells without MPs treatment and cultured in the same OC medium were served as control group. Poly(A) RNA-sequencing library construction and sequencing, transcripts assembly, and different expression analysis were performed.

first: Zhuozhi

last: Wang

first: Jue

last: Hu

first: Jeffrey

last: Marschall

first: Ling

last: Yang

first: Shaoping

last: Zhang

first: Hongli

last: Sun


title: Induction of differentiation from hiPSCs into Leydig-like cells

city: Kobe

first: Katsuya

last: Sato

address: 7-5-2, Kusunoki-cho, Chuo-ku

institute: Kobe University

summary: We generated Leydig-like cells by the forced expression of NR5A1 in hiPSCs and by switching from 3D culture to adherent culture.

overall_design: Total RNA was extracted at each time point of differentiation induction and analyzed for comprehensive gene expression using a next-generation sequencer.

first: Michiyo

last: Koyanagi-Aoi

first: Takashi

last: Aoi


title: A single-cell transcriptomic atlas characterizes the kidney in the diabetic kidney disease

city: Jinan

first: jinxiu

address: jingwuweiqi

institute: Shandong Provincial Hospital

summary: Diabetic kidney disease (DKD), a common and devastating microvascular complication of diabetes, is the leading cause of end-stage renal disease (ESRD). Since mechanisms of kidney injury in DKD were largely unknown, we performed single-cell RNA sequencing (scRNA-seq) on human kidneys collected from 3 DKD and 3 normal samples using 10×Genomics. In our study, a total of 51315 cells were enrolled for analyses and nine kidney cell types and seven immune cell types were identified. The cell-type-specific changes in gene expression and signaling pathways of podocyte, mesangial cells, endothelial cells, proximal tubule and macrophages indicate abnormal regulation associated with inflammation, apoptosis, oxidative stress, extracelluar matrix accumulation, and immune activation. In particular, we show that podocytes and renal tubular epithelial cells have a tremendous capacity to regenerate, which is involved in the repairment of injury. And extracellular vesicles, an important mediator of intercellular communication, might play a vital role for this progress. Besides, we identified new candidate transcription factors responsible for the progression of DKD. We also revealed a M1-M2 hybrid pattern, in which M1 and M2 are coupled activation in macrophages of DKD. Furthermore, we demonstrated a complex intercellular interaction between kidney cells and kidney cells or kidney cells and immune cells. Thus, our study will further the understanding of DKD pathogenesis and provide novel therapeutic targets for its treatment in the future.

overall_design: Fresh kidney samples were isolated and sequenced using scRNAseq.

first: L

middle: V

last: Zhimei

first: Wang

last: Rong


title: Gene expression analysis of frozen skin from B6 mouse models of Cutaneous Lupus Erythematosus and Primary Cicatricial Alopecia

city: North Grafton

first: Jillian

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

summary: OT1 CD8 T cells or OT2 Th2 T cells were injected into rtTA+K5TGO+TLR9KO recipients or littermate controls. A portion of the skin was frozen and saved for RNA analysis at the first presentation of disease (approximately 3-4 weeks). OT2 recipient skin was also harvested at flare (approximately 10-12 weeks). All extracted RNA samples were analyzed using NanoString mouse Cancer Immunology panel (C3400).

first: Ümmügülsüm

last: Yıldız-Altay


title: Induction of differentiation from hiPSCs into Leydig-like cells (scRNA-Seq)

overall_design: We performed single-cell RNA sequencing (scRNA-seq) using the BD Rhapsody Express Single-Cell Analysis System


title: Transcriptomic Analysis of Asthma from The Asthma BioRepository for Integrative Genomic Exploration (Asthma BRIDGE) Project

city: Boston

first: Benjamin

last: Raby

address: 300 Longwood Avenue

department: Division of Pulmonary Medicine

institute: BOSTON CHILDREN'S HOSPITAL

summary: Microarray gene expression analysis of various cell types was performed. Gene expressions were compared between patients with asthma and the control groups.

overall_design: RNA were extracted from whole blood (n = 954), peripheral blood CD4+ T lymphocytes (n = 411), induced sputum alveolar macrophages (n = 84), bronchoalveolar cells (n = 42), and bronchial epithelial cells (n = 44).

first: Vincent

last: Carey


title: Lactylated histone promotes rheumatoid arthritis progression by increasing NFATc2 expression and the production of anti-lactylated histone autoantibodies [II]

city: Wenzhou

first: Wu

last: Gan

address: Chashan Street, Ouhai District

institute: Wenzhou Medical University

summary: The elevated lactate in the joint microenvironment of patients with rheumatoid arthritis (RA) is crucial for disease progression, although the underlying mechanism remains to be elucidated. In this study, we observed significantly increased global lactylation levels within fibroblast-like synoviocytes (FLS) of RA patients compared to HC (healthy controls), and lactylated proteins were enriched in histones. Furthermore, we found that anti-lactated histone antibodies were detected in almost RA patients and positively correlated with Disease Activity Score 28 (DAS28). Then we identified NFATc2 as a key target gene regulated by histone H3 lysine 9 lactylation (H3K9la) using CUT&Tag combined with RNA-seq. Functional studies revealed that NFATc2 promotes migration of RA-FLSs. Additionally, using server combined immune-deficiency (SCID) and collagen-induced arthritis (CIA) mouse models, we demonstrated that NFATc2 exacerbates RA disease progression through enhanced FLS cartilage invasion function. Collectively, our findings suggest that upregulated target gene NFATc2 by lactate-dependent histone lactylation, can be used as a potential therapeutic target for intervention, anti-lactated histone autoantibodies is promising as a diagnostic marker for RA.

overall_design: RNA-seq profiling of wildtyp and NFATc2 knockdown fibroblast-like synoviocytes (FLS) from RA patients.


title: Lactylated histone promotes rheumatoid arthritis progression by increasing NFATc2 expression and the production of anti-lactylated histone autoantibodies [CUT&Tag]

overall_design: CUT&Tag of the histone modification H3K9la in fibroblast-like synoviocytes (FLS) from RA patients and healthy controls

first: Gan

last: Wu


title: Gene expression changes induced by HA-PRCC-TFE3 in HK-2 cells

first: Masaya

last: Baba

summary: PRCC-TFE3 is an oncogenic chimeric transcription factor identified in human TFE3-rearranged renal cell carcinoma. To analyze gene expression changes driven by PRCC-TFE3, we generated and utilized an HA-tagged PRCC-TFE3-inducible HK-2 cell line, which expresses HA-tagged PRCC-TFE3 in a doxycycline-dependent manner. Cells were cultured with or without doxycycline, and comprehensive gene expression analysis was conducted using RNA-seq.

overall_design: We performed RNA-seq analysis on HA-PRCC-TFE3 doxycycline-inducible HK-2 cell lines, cultured with or without doxycycline.

first: Wenjuan

last: Ma

first: Yorifumi

last: Satou

first: Marston

last: Linehan


title: Transcriptomic analysis of pancreatic cyst fluid in patients with pancreatic cysts reveals novel biomarkers of pancreatic cancer risk

city: Dublin

first: Laura

last: Kane

state: Dublin

address: Trinity St. James's Cancer Institute

department: Department of Surgery

country: Ireland

institute: Trinity College Dublin

summary: Integration of multi-omic data for the purposes of biomarker discovery can provide novel and robust panels across multiple biological compartments. Appropriate analytical methods are key to ensuring accurate and meaningful outputs in the multi-omic setting. Here, we extensively profile the proteome and transcriptome of patient pancreatic cyst fluid (PCF) (n=32) and serum (n=68), before integrating matched omic and biofluid data, to identify biomarkers of pancreatic cancer risk. Differential expression analysis, feature reduction, multi-omic data integration, unsupervised hierarchical clustering, principal component analysis, spearman correlations and leave-one-out cross-validation were performed using RStudio and CombiROC software. An 11-feature multi-omic panel in PCF [PIGR, S100A8, REG1A, LGALS3, TCN1, LCN2, PRSS8, MUC6, SNORA66, miR-216a-5p, miR-216b-5p] generated an AUC=0.80. A 13-feature multi-omic panel in serum [SHROOM3, IGHV3-72, IGJ, IGHA1, PPBP, APOD, SFN, IGHG1, miR-197-5p, miR-6741-5p, miR-3180, miR-3180-3p, miR-6782-5p] produced an AUC=0.824. Integration of the strongest performing biomarkers generated a 10-feature cross-biofluid multi-omic panel [S100A8, LGALS3, SNORA66, miR-216b-5p, IGHV3-72, IGJ, IGHA1, PPBP, miR-3180, miR-3180-3p] with an AUC=0.970. Multi-omic profiling provides an abundance of potential biomarkers. Integration of data from different omic compartments, and across biofluids, produced a biomarker panel that performs with high accuracy, showing promise for the risk stratification of these patients.

overall_design:
Neat pancreatic cyst fluid samples, obtained during endoscope-guided fine-needle aspiration from patients with pancreatic cystic lesions (n=30), were processed for HTG Molecular miRNA Whole Transcriptome Sequencing by HTG Molecular. Patients were separated into low-risk (n=15) and high-risk (n=15) of pancreatic cancer categories using the 2018 European evidence-based guidlines of cyctic neoplasms. Differential expression analysis, downstream bioinformatic interrogation and multi-omic integration was used to identify novel biomarkers of pancreatic cancer risk.

***************************************************************
These data were generated with HTG Molecular Diagnostics Inc. using their proprietary quantitative nuclease protection assay (qNPA) chemistry with a next generation sequencing platform. The data raw datafiles generated cannot be analysed with standard RNA-seq analysis tools.
***************************************************************

first: Gregory

middle: S

last: Mellotte

first: Eimear

last: Mylod

first: Paul

last: Dowling

first: Simone

last: Marcone

first: Caitriona

last: Scaife

first: Elaine

last: Kenny

first: Michael

last: Henry

first: Paula

last: Meleady

last: Ridgway

first: Finbar

last: MacCarthy

first: Kevin

last: Conlon

first: Barbara

last: Ryan

first: Stephen

middle: G

last: Maher


title: Expression profiling of primary and metastatic oral squamous cell carcinoma identifies progression-associated transcriptome changes and therapeutic vulnerabilities

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

summary: Oral squamous cell carcinoma (OSCC) constitutes a subset of head and neck squamous cell carcinoma primarily caused by the excessive consumption of alcohol, tobacco, and areca nut. According to the latest estimates of the global burden of cancer (GLOBOCAN 2022), cancers of the lip and oral cavity account for 389,485 new cancer cases and 188,230 deaths annually. Despite significant progress in OSCC diagnosis and therapy only about 65% of patients survive five years or longer. This poor prognosis is mainly due to the fact that about half of OSCC patients are diagnosed with advanced disease. Hence, a better understanding of the molecular mechanisms responsible for the development and metastatic progression of OSCC is needed in order to identify novel biomarkers and therapeutic targets. We isolated RNA from 87 primary tumours and 21 lymph node metastases from a total of 72 OSCC patients. The RNA was subjected to next-generation sequencing (~62 Mio. reads per sample) upon depletion of ribosomal RNA. Comprehensive transcriptome-wide expression and correlation analyses were performed in order to identify expression subtypes, disease-associated genes and isoforms. The functional and therapeutic relevance of selected candidates was further investigated in vitro using gain- and loss-of-function analyses. Unsupervised clustering of primary tumours identified three clusters (C1-C3) that show different overall survival (OS) probabilities, especially for C3. Furthermore, gene-level analyses identified SHMT2 as a prognostic biomarker associated with poor OS. Importantly, targeting of SHMT2 using siRNAs or a small molecule inhibitor (SHIN1/RZ-2994) decreased cell proliferation and induced apoptosis in a panel of OSCC cell lines and establish SHMT2 as a promising therapeutic target. Comparison of primary tumours and their matched lymph node metastases identified additional druggable metastasis-associated genes as well as several isoform switches. For example, the canonical full-length isoform of WNT5A was higher expressed in metastases and its overexpression in SAS enhanced cell invasion capacity. Our profiling study provides a valuable resource for the community that will foster functional analyses to gain insights into the molecular mechanisms of OSCC progression, and it will help to identify novel biomarkers and therapeutic targets in the future.

overall_design: total RNA-seq of 87 primary OSCC tumours and 21 lymph node metastasies

first: Jonas

last: Pyko

first: Julia

last: Rosemann

first: Jana

last: Macho

first: Matthias

last: Kappler

first: Sarah

last: Qasem

first: Alexander

last: Eckert

first: Stefan

last: Hüttelmaier

first: Monika

last: Haemmerle

first: Tony

last: Gutschner


title: Human enteric glia diversity in health and disease: new avenues for the treatment of Hirschsprung disease

city: Rotterdam

first: Maria

last: Alves

address: Wytemaweg 80

department: Departments of Clinical Genetics and Pediatric Surgery

institute: Erasmus University Medical Center-Sophia Children’s Hospital

summary: This study brings new insight into the heterogeneity of human enteric glia, contributing to our understanding of enteric glial diversity in health and disease.

overall_design: Full-thickness intestinal resection material from pediatric controls and HSCR patients was collected, dissociated and enriched for the ENS population through fluorescence-activated cell sorting. Single-cell RNA sequencing was performed to uncover the transcriptomic diversity of the ENS in HSCR patients and controls.

first: J

middle: D

last: Windster

first: N

last: Kakiailatu

first: L

last: Kuil

first: A

last: Antanaviciute

last: Sacchetti

first: K

last: MacKenzie

last: Peulen-Zink

first: T

last: Kan

first: E

last: Bindels

last: de Pater

first: M

last: Doukas

last: van den Bosch

first: S

last: Yousefi

last: Barakat

first: C

last: Meeussen

last: Sloots

first: R

last: Wijnen

last: Parikh

first: W

last: Boesmans

first: V

last: Melotte

last: Hofstra

last: Simmons


title: Gut epithelium modifies enteric behaviors during nutritional adversity via distinct peptidergic signaling axes

city: New York

first: Surojit

last: Sural

state: NY

address: 1212 Amsterdam Avenue

department: Biological Sciences

institute: Howard Hughes Medical Institute, Columbia University

summary: Interorgan signaling events are emerging as key regulators of behavioral plasticity. The foregut and hindgut circuits of the C. elegans enteric nervous system (ENS) control feeding and defecation behavior, respectively. Here we show that epithelial cells in the midgut integrate feeding state information to control these behavioral outputs via releasing distinct neuropeptidergic signals. In favorable conditions, insulin and non-insulin peptides released from midgut epithelia activate foregut and hindgut enteric neurons, respectively, to sustain normal feeding and defecation behavior. During food scarcity, altered insulin signaling from sensory neurons activates the transcription factor DAF-16/FoxO in midgut epithelia, which blocks both peptidergic signaling axes to the ENS via transcriptionally shutting down the intestinal neuropeptide secretion machinery. Our findings demonstrate that midgut epithelial cells act as integrators to relay internal state information to distinct parts of the enteric nervous system to control animal behavior.

overall_design: RNA-seq profiling of dauer stage animals in which DAF-16/FoxO is specifically depleted from the intestinal epithelial cells using the AID2 system.

first: Zion

last: Walker

first: Oliver

last: Hobert


title: Lateral olivocochlear neurons modulate cochlear responses to noise exposure

first: Lisa

last: Goodrich

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

summary: The sense of hearing originates in the cochlea, which detects sounds across dynamic sensory environments. Like other peripheral organs, the cochlea is subjected to environmental insults, including loud, damage-inducing sounds. In response to internal and external stimuli, the central nervous system directly modulates cochlear function through olivocochlear neurons (OCNs), which are located in the brainstem and innervate the cochlear sensory epithelium. One population of OCNs, the lateral olivocochlear (LOC) neurons, target spiral ganglion neurons (SGNs), the primary sensory neurons of the ear. LOCs alter their transmitter expression for days to weeks in response to noise exposure (NE), suggesting that they are well-positioned to tune SGN excitability over long time periods in response to auditory experience. To examine how LOCs affect auditory function after NE, we characterized the transcriptional profiles of OCNs and found that LOCs exhibit transient changes in gene expression after NE, including upregulation of multiple neuropeptide-encoding genes.

overall_design: Single nuclei were collected from animals 1 day or 7 days after exposure to a 110 dB, 8–16 kHz octave-band noise or from unexposed littermate controls, which remained in the vivarium. Samples were enriched for cholinergic olivocochlear neurons by dissecting the ventral brainstem of ChatCre{delta}Neo;Rosa26LSL-Sun1-GFP animals and using fluorescence-activated cell sorting to isolate GFP+ cells prior to encapsulation with the 10x Genomics 3’ Single-Cell Kit (v. 3.1). Each round of single-nucleus sequencing included pooled tissue from 3–5 ChatCre{delta}Neo;Rosa26LSL-Sun1-GFP mice of both sexes between 6–10 weeks of age. In each case, tissue from noise-exposed animals and unexposed littermate controls was collected simultaneously and run on parallel lanes of the same 10x Genomics microfluidic chip. Two independent collections for the 1 day post-exposure timepoint included a total of 8 unexposed (5 male, 3 female) and 9 noise-exposed mice (6 male, 3 female). Four collections for the 7 day post-exposure timepoint included 14 unexposed (7 male, 7 female) and 15 noise-exposed mice (8 male, 7 female).

first: Austen

last: Sitko

first: Michelle

last: Frank

first: Gabriel

last: Romero


title: A mutant ASXL1-EHMT complex contributes to heterochromatin dysfunction in clonal hematopoiesis and chronic monomyelocytic leukemia [RNAseq_human]

city: La Jolla

first: Zhen

last: Dong

address: 9420 Athena Circle

department: Department of Signaling and Gene Expression

institute: La Jolla Institute for Immunology

summary: RNA-seq libraries from normal Peripheral blood mononuclear cells were generated to compare them against RNA-seq samples from patients with Chronic myelomonocytic leukemia (CMML).

overall_design: Peripheral blood mononuclear cells were isolated from blood donated of healthy unidentified individuals

first: Jenna

last: Fernandez

first: Leo

last: Josue Arteaga

first: Hugo

last: Sepulveda

first: Mrinal

last: Patnaik

first: Anjana

last: Rao


title: A mutant ASXL1-EHMT complex contributes to heterochromatin dysfunction in clonal hematopoiesis and chronic monomyelocytic leukemia [Cut & Run]

summary: ASXL1 is one of the three most frequently mutated genes in age-related clonal hematopoiesis (CH), with the others being DNMT3A and TET2. CH can progress to myeloid malignancies including chronic monomyelocytic leukemia (CMML), and is also strongly associated with inflammatory cardiovascular disease and all-cause mortality in humans. DNMT3A and TET2 regulate DNA methylation and demethylation pathways respectively, and DNMT3A and TET2 loss-of-function mutations in CH reduce DNA methylation in heterochromatin, allowing de-repression of silenced elements in heterochromatin. In contrast, the mechanisms that connect mutant ASXL1 and CH are not yet fully understood. CH/CMML-associated ASXL1 mutations encode C-terminally truncated proteins that enhance the deubiquitinase activity of the ASXL-BAP1 “PR-DUB” deubiquitinase complex, which removes mono-ubiquitin from H2AK119Ub. Here we show that ASXL1 mutant proteins interact with the EHMT1-EHMT2 methyltransferase complex, which generates H3K9me1 and me2, the latter a repressive modification in constitutive heterochromatin. Compared to cells from age-matched wildtype mice, we found that expanded myeloid cells from old Asxl1tm/+ mice, a heterozygous knock-in mouse model of CH, display genome-wide decreases of H3K9me2, H3K9me3 and H2AK119Ub as well as an associated increase in expression of transposable elements (TEs) and satellite repeats. Increased TE expression was also observed in monocytes from ASXL1-mutant CMML patients compared to monocytes from healthy control individuals. Our data suggest that mutant ASXL1 proteins compromise the integrity of both constitutive and facultative heterochromatin in an age-dependent manner, by reducing the levels of H3K9me2/3 and H2AK119Ub respectively. The resulting increase in TE expression can alter the expression of nearby genes and promote the expression of inflammation-associated and interferon-inducible genes (ISGs).

overall_design:
To study the functions of ASXL1 mutant proteins in clonal hematopoiesis and chronic monomyelocytic leukemia (CMML), we isolated myeloid cells (CD11b+) and hematopoietic progenitor or stem cells (LK+) from mice.
We performed Cut&Run followed by NGS-sequencing to map histone modifications at the genome, including H2AK119ub, H3K9me2/me3, H3K4me3, and H3K27me3.


title: Targeting the 3D genome by anthracyclines for chemotherapeutic effects

city: Chapel Hill

first: Marielle

last: Bond

state: NC

address: 116 Manning Dr

department: Genetics

institute: UNC Chapel Hill

summary: The chromatins are folded into three-dimensional (3D) structures inside cells, which coordinates the regulation of gene transcription by the non-coding regulatory elements. Aberrant chromatin 3D folding has been shown in many diseases, such as acute myeloid leukemia (AML), and may contribute to tumorigenesis. The anthracycline topoisomerase II inhibitors can induce histone eviction and DNA damage. We performed genome-wide high-resolution mapping of the chemotherapeutic effects of various clinically used anthracycline drugs. ATAC-seq was used to profile the histone eviction effects of different anthracyclines. TOP2A ChIP-seq was used to profile the potential DNA damage regions. Integrated analyses show that different anthracyclines have distinct target selectivity on epigenomic regions, based on their respective ATAC-seq and ChIP-seq profiles. We identified the underlying molecular mechanism that unique anthracycline variants selectively target chromatin looping anchors via disrupting CTCF binding, suggesting an additional potential therapeutic effect on the 3D genome. We further performed Hi-C experiments, and data from K562 cells treated with the selective anthracycline drugs indicate that the 3D chromatin organization is disrupted. Furthermore, AML patients receiving anthracycline drugs showed altered chromatin structures around potential looping anchors of, which linked to distinct clinical outcomes. Our data indicate that anthracyclines are potent and selective epigenomic targeting drugs and can target the 3D genome for anticancer therapy, which could be used for personalized medicine to treat tumors with aberrant 3D chromatin structures

overall_design: Hi-C of K562 cells treated with DMSO, daunorubicin, or aclarubicin for 2h.

first: Minkang

last: Tan

first: Shengnan

last: Sun

first: Yuchen

last: Liu

first: Andrea

last: Perreault

first: Douglas

middle: H

last: Phanstiel

first: Liping

last: Dou

first: Baoxu

last: Pang


title: Hypoxia-mediated high expression of TRIM15 promotes malignant progression of high-grade serous ovarian cancer (HGSOC) through activation of AKT signaling pathway by K63 ubiquitination

city: Dalian

first: Ning

last: Wang

address: 467 Zhongshan Road, Dalian, P.R.

institute: the Second Hospital of Dalian Medical University

summary: To analyze the gene expression patterns of ovary in 4 patients with high-grade serous ovarian cancer (HGSOC) and 4 normal individuals.

overall_design: Ovarian tissue samples was collected from 4 patients with high-grade serous ovarian cancer (HGSOC) and 4 normal individuals for mRNA-seq.


title: Gene regulation linked to plasticity in queen weight and behavior reveals candidates for supergene-mediated genetic accommodation in the fire ant

city: Griffin

first: Brendan

last: Hunt

state: GA

address: 1109 Experiment St

department: Entomology

institute: University of Georgia

summary: In the fire ant Solenopsis invicta, a chromosomal inversion-derived supergene predicts gyne (pre-reproductive queen) weight and corresponding colony founding behavior. Inversion-carrying gynes are lightweight and depend on assistance from workers, meaning they must initiate reproduction in an already existing social group. Gynes that lack the inversion supergene are heavier and found colonies from scratch, relying on their own nutrient reserves to feed an initial brood. However, plasticity in gyne weight and life history also exists in fire ants, such as queen replacement, an alternative mode of dependent reproduction determined by gyne overwintering status. Like inversion-carrying gynes, overwintered gynes without the inversion supergene exhibit a lightweight phenotype and worker dependence. In gyne brains and ovaries, we compared transcriptional profiles of overwintered and non-overwintered gynes to reveal the gene regulatory changes associated with overwintering. We observed functional enrichment for several biological processes related to metabolism and behavior among these plasticity-associated differentially expressed genes. A comparison to genes differentially expressed by supergene genotype revealed significantly greater overlap than expected by chance in ovarian tissues. Moreover, some plasticity-associated genes were found to exhibit fixed allelic differences between inverted and non-inverted supergene variants that may contribute to observed differences in gene expression and physiology. Overall, our results are consistent with the hypothesis that a supergene modulates variation in social organization, in part, through increased genetic regulation of ancestrally plastic traits.

overall_design: To identify gene candidates regulating plasticity in queen weight, we compared gene expression profiles of overwintered and spring-reared fire ant gynes. We compared this set of genes to those associated with differential expression via the fire ant supergene to identify possible mediators of genetic accommodation.

first: Alex

last: Waugh

first: Catto

last: Michael

first: Arsenault

last: Samuel

first: Sasha

last: Kay

first: Ross

last: Kenneth


title: Differential regulation of brain microvessel transcriptome and brain metabolome by Western and heart-healthy dietary patterns in Ossabaw pig

city: Beltsville

first: Gloria

last: Solano-Aguilar

state: MD

address: 10300 Baltimore Ave

institute: USDA-ARS

summary: Diet is a potentially modifiable neurodegenerative disease risk factor. We studied the effects of a typical Western diet (WD) relative to a heart-healthy diet (HHD) on microvessel transcriptomics and metabolomics of the brain temporal region in Ossabaw minipigs. Thirty-two pigs (16 male and 16 females) were randomized to the WD or HHD starting at the age of 4 months and were fed the assigned diet for the following 6 months. The WD and HHD were isocaloric and had the same macronutrient content but differed in macronutrient quality. Within each dietary group, half of the pigs also received a statin. Relative to HHD-fed pigs, WD-fed pigs had 2,172 genes differentially expressed (FDR<0.05) by diet, 796 upregulated and 1,376 downregulated. Gene Set Enrichment Analysis identified 22 gene sets enriched in WD, comprising pathways related to inflammation, angiogenesis, and apoptosis, and 53 gene sets enriched in the HHD, including cell energetics, neurotransmission, and inflammation resolution pathways. Enrichment in arginine, tyrosine, and lysine was observed in WD-fed pigs and enrichment in ergothioneine and S-adenosyl methionine in HHD-fed pigs. Statin treatment had very modest effects on brain vessel transcriptome. Our study suggests a likely contribution of diet to brain pathologies characterized by neuroinflammation and neurodegeneration.

overall_design: This study was designed to compare the effects of a Western Diet (WD) to a Heart-Healthy Diet (HHD), with or without a statin (S), on cardiovascular disease in Ossabaw minipigs. Thirty two pigs were randomized to four groups in a 2 x 2 factorial design: WD, WD+statin, HHD, HHD+statin. Differential gene expression analysis was performed using RNAseq on RNA samples from blood microvessels that were isolated from the right brain temporal region and purified to contain neurovascular units which comprise small blood vessel and associated pericytes and perivascular astrocyte end-feet. Differential gene expression analysis of the diet effect was assessed by comparing animals fed a WD (WD and WD+statin groups) to those fed a HHD (HHD and HHD+statin groups). Statin effects were assessed by comparing animals treated with statin (WD+statin and HHD+statin groups) to no statin (WD and HHD groups)

first: Gregory

last: Matuszek

first: Nirupa

last: Matthan

first: Alice

last: Lichtenstein

first: Xuedi

first: Sukla

last: Lakshman

first: Kathryn

last: Barger

first: Joseph

last: Urban

first: Aleksey

last: Molokin

first: Rachel

last: Bennett

first: Bradley

middle: T

last: Hyman

first: Stefania

last: Lamon-Fava


title: Transcriptomic analysis of serum in patients with pancreatic cysts reveals novel biomarkers of pancreatic cancer risk

first: Laura

last: Kane

overall_design:
Neat serum samples from patients with pancreatic cystic lesions (n=30) were processed for HTG Molecular miRNA Whole Transcriptome Sequencing by HTG Molecular. Patients were separated into low-risk (n=15) and high-risk (n=15) of pancreatic cancer categories using the 2018 European evidence-based guidlines of cyctic neoplasms. Differential expression analysis, downstream bioinformatic interrogation and multi-omic integration was used to identify novel biomarkers of pancreatic cancer risk.

***************************************************************
These data were generated with HTG Molecular Diagnostics Inc. using their proprietary quantitative nuclease protection assay (qNPA) chemistry with a next generation sequencing platform. The data raw datafiles generated cannot be analysed with standard RNA-seq analysis tools.
***************************************************************

last: Mellotte

first: Eimear

last: Mylod

first: Paul

last: Dowling

first: Simone

last: Marcone

first: Caitriona

last: Scaife

first: Elaine

last: Kenny

first: Michael

last: Henry

first: Paula

last: Meleady

last: Ridgway

first: Finbar

last: MacCarthy

first: Kevin

last: Conlon

first: Barbara

last: Ryan

first: Stephen

last: Maher


title: scRNA-seq reveals the impact of dysfunction on meibomian gland population dynamics

city: Irvine

first: Julie

last: Wiedemann

address: Sprague Hall

institute: UCI

summary: While meibomian gland dysfunction (MGD) is widely recognized as a major cause of evaporative dry eye disease, little is known about normal gland differentiation and lipid synthesis or the mechanism underlying gland atrophy and abnormal lipid secretion. In this study, we used single-cell and spatial transcriptomics to probe changes in cell composition, differentiation, and gene expression associated with two murine models of MGD: age-related gland atrophy in wild-type mice and altered meibum quality in acyl-CoA wax alcohol acyltransferase 2 (Awat2) knockout (KO) mice. We identified the stratified expression of lipogenic genes during meibocyte differentiation, which may control the progressive synthesis of meibum lipids; an age-related decrease in meibocytes; and increased immune cell infiltration. Additionally, we detected unique immune cell populations in the Awat2 KO mouse suggesting the activation of psoriasis-like, inflammatory pathways associated with the synthesis of altered meibum quality causing ductal dilation and hyperplasia of the duct. Together these findings support novel mechanism controlling gland function and dysfunction.

overall_design: For the first run of scRNA-seq, meibomian gland WT replicates 1 and 2, we used six WT, 6-month-old, male C57Bl/6 mice, which were pooled into two groups of three. For the second run, we used eight mice, including four 6-month-old, male Awat2 KO mice and four WT, C57Bl/6 litter mates, which were pooled to create the meibomian gland WT 3 and meibomian gland AWAT2 KO samples.

first: Bogi

last: Andersen

first: James

last: Jester


title: Cancer Cell’s Seven Achilles Heels: Considerations for design of anti-cancer drug combinations.

city: Saskatoon

first: Franco

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

summary:
Loss of function screens using shRNA and CRISPR are routinely used to identify genes that modulate responses of tumor cells to anti-cancer drugs. Here, by integrating GSEA and CMAP analyses of multiple published shRNA screens, we identified a core set of pathways that affect responses to multiple drugs with diverse mechanisms of action. This suggests that these pathways represent “weak points” or “Achilles heels”, whose mild disturbance should make cancer cells vulnerable to a variety of treatments. These “weak points” include proteasome, protein synthesis, RNA splicing, RNA synthesis, cell cycle, Akt-mTOR, and tight junction-related pathways. Therefore, inhibitors of these pathways are expected to sensitize cancer cells to a variety of drugs. This hypothesis was tested by analyzing the diversity of drugs that synergize with FDA-approved inhibitors of the proteasome, RNA synthesis, and Akt-mTOR pathways. Indeed, the quantitative evaluation indicates that inhibitors of any of these signaling pathways can synergize with a more diverse set of pharmaceuticals, compared to compounds inhibiting targets distinct from the “weak points” pathways. Our findings described here imply that inhibitors of the “weak points” pathways should be considered as primary candidates in a search for synergistic drug combinations.
We used microarray to identify genetic interaction partners of 2 drugs

overall_design: Samples were collected at different time points after infection with the 90k shRNA libraries and probes were prepared to hybridize to microarray chips to identify GI partners of 2 drugs.

first: Frederick

first: Keith

last: Bonham

first: Meena

last: Sakharkar

first: Andrew

last: Freywald


title: RNA-seq of T-47D cells treated with 17-beta-estradiol and/or APOBEC3B-targeting siRNA

city: London

first: Chi

last: Zhang

address: 15 Cotswold Road

department: Division of Cancer Therapeutics

country: United Kingdom

institute: The Institute of Cancer Research

summary: Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3B, A3B) is a key molecular driver inducing mutations in multiple human cancer.  A3B belongs to the APOBEC3 enzyme family, which consists seven closely related DNA deaminases that catalyse cytosine-to-uracil (C>U) editing of single-stranded DNA (ssDNA). Here, we used RNA-seq technology to study the effect of A3B knockdown on the effect of estradiol induction in T-47D cells.

overall_design: T-47D cells were treated with non-targeting or A3B-targeting siRNA, before treated with DMSO or 17-beta-estradiol. RNA-seq experiments were conducted using samples from these cells.

first: Yu-jing

last: Lu

first: Jianbin

last: Yan

first: Bingjie

last: Chen

first: Konstantinos

last: Mitsopoulos

first: Marcello

last: Totoricci

first: Olivia

last: Rossanese

first: Paul

middle: A

last: Clarke

last: Workman


title: ChIP-seq of TDRD3, CARM1 and H3R17me2a in T-47D cells

summary: Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3B, A3B) is a key molecular driver inducing mutations in multiple human cancer.  A3B belongs to the APOBEC3 enzyme family, which consists seven closely related DNA deaminases that catalyse cytosine-to-uracil (C>U) editing of single-stranded DNA (ssDNA). By using mass-spec proteomics, we identified TDRD3, a ‘reader’ of asymmetrically methylated arginine marks, as the binding partner of A3B.

overall_design: Genomic occupancy of TDRD3, CARM1 and H3R17me2a was investigated using ChIP-seq in T-47D cells.


title: DNA methylation analysis of HepG2 cells overexpressing DNMT3A

city: Shenzhen

first: Aixia

last: Zhai

state: Guangdong

address: 92 Fuhua Road, Futian District

department: The Eighth Affiliated Hospital

institute: Sun Yat-sen University

summary: Chronic hepatitis B virus (HBV) infection is the main etiology of liver fibrosis (LF), leading to cirrhosis and liver tumors.  DNA methylation caused by HBV protein changes the liver microenvironment and activates hepatic stellate cells, which is an important mechanism of liver fibrosis. However, the exact mechanism remains unclear. DNA methyltransferase 3A (DNMT3A) is a major enzyme that promotes DNA methylation. HBV infection promotes the expression of DNMT3A. To determine the specific roles of DNMT3A, we used lentivirus to overexpress DNMT3A in hepatocellular carcinoma cell line (HepG2). And the changes of epigenome were analysed by RRBS.

overall_design: To explore the changes of epigenome by DNMT3A, HepG2 cells were divided into two groups: cells infected with control lentivirus and cells infected with DNMT3A-overexpressing lentivirus. RRBS profiling the control and  DNMT3A overexpression HepG2 cells.

first: Yang

last: Liu

first: Xumeng

last: Wang

first: Yuetong

last: Li

first: Xin

last: Yu

first: Yanping

first: Changlong

last: Bi