title: A potent HDAC inhibitor blocks Toxoplasma gondii tachyzoite growth and profoundly disrupts parasite gene expression.

city: Lille

first: Mathieu

last: Gissot

address: 1, rue du Pr. calmette

institute: CNRS

summary: Toxoplasmosis is a major health issue worldwide especially for immune-deficient individuals and the offspring of newly infected mothers. It is caused by a unicellular intracellular parasite called Toxoplasma gondii. Although the drugs commonly used to treat toxoplasmosis are efficient, they present serious side effects and adverse events are common. Therefore, there is a need for the discovery of new compounds with potent anti-T. gondii activity. We have tested compounds designed to target enzymes that are involved in the epigenetic regulation of gene expression. Among the most active compounds, we identified a HDAC inhibitor that shows an IC50 of around 30 nM with a selectivity index of more than 100. MC1742 is active at inhibiting the growth of the parasite in vitro but also at preventing the consequences of the acute disease in vivo. This compound induces a hyper-acetylation of histones while acetylated tubulin level remains unchanged. After MC1742 treatment, the parasite expression profile is profoundly changed with the activation of genes preferentially expressed in the sexual stages that are normally repressed at the tachyzoite stage. These findings suggest that this compound disturbs the T. gondii gene expression program, inducing parasite death.

overall_design: Three biological replicate of theparasite T. gondii tachyzoites treated with DMSO or MC1742. mRNA profiles were generated by high throughput sequencing using HiSeq 2500 system (Illumina).

last: GISSOT

first: Thomas

last: Mouveaux


title: LKB1 prevents ILC2 exhaustion and lung cancer metastasis

status: Public on May 21 2024

city: Shanghai

first: Hongshen

last: Niu

state: Shanghai

address: south chongqing road 280

department: shanghai institute of immunology

country: China

institute: Shanghai jiao tong university school of medicine

type: Expression profiling by high throughput sequencing

summary: Group 2 innate lymphoid cells (ILC2s) mediate type 2 immune responses involved in anti-helminth immunity, allergic inflammation, and metabolic homeostasis. Recently, they have emerged as key players in regulating tumor immunity. The tumor suppressor liver kinase B1 (LKB1) inactivating mutations is associated with a variety of human cancers, but the role of LKB1 in ILC2 function and ILC2-mediated tumor immunity remains unknown. Here, we show that LKB1 is required for mature ILC2 survival. Ablation of LKB1 in ILC2s results in impaired proliferation and a marked decrease in type 2 cytokine production upon activation, accompanied with the expression of exhaustion signature genes and reduced cellular metabolism, which promote the development of lung melanoma metastasis. In addition, LKB1 deficiency leads to a marked increase of programmed cell death protein-1 (PD-1) expression in ILC2s through activation of nuclear factor of activated T cells (NFAT) pathway. Blockade of PD-1 can restore type 2 cytokine production in LKB1-deficient ILC2 and reverse its exhaustion state, leading to enhanced antitumor immune responses in vivo. Together, our results reveal that LKB1 retrains ILC2 exhaustion state to maintain immune homeostasis and their antitumor immunity.

overall_design: lung ILC2s mRNA profiles of IL-33 treated R5/+ (WT) and R5/+LKB1f/f (KO) mice

first: Lei

last: Shen

first: Huasheng

last: Zhang


title: Reanalysis of peripheral blood gene expression of IFIH1 rs1990760 variants in critically-ill COVID-19 patients [third-party re-analysis of GSE168400]

status: Public on May 22 2024

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

state: CA

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

country: USA

institute: University of California San Diego

summary: Peripheral blood gene expression analysis of IFIH1 rs1990760 variants in critically-ill COVID-19 patients

relation:
Reanalysis of: GSM5137947
Reanalysis of: GSM5137948
Reanalysis of: GSM5137949
Reanalysis of: GSM5137950
Reanalysis of: GSM5137951
Reanalysis of: GSM5137952
Reanalysis of: GSM5137953
Reanalysis of: GSM5137954
Reanalysis of: GSM5137955
Reanalysis of: GSM5137956
Reanalysis of: GSM5137957
Reanalysis of: GSM5137958
Reanalysis of: GSM5137959
Reanalysis of: GSM5137960
Reanalysis of: GSM5137961
Reanalysis of: GSM5137962
Reanalysis of: GSM5137963
Reanalysis of: GSM5137964
Reanalysis of: GSM5137965
Reanalysis of: GSM5137966
Reanalysis of: GSM5137967
Reanalysis of: GSM5137968
Reanalysis of: GSM5137969
Reanalysis of: GSM5137970
Reanalysis of: GSM5137971
Reanalysis of: GSM5137972
Reanalysis of: GSM5137973
Reanalysis of: GSM5137974
Reanalysis of: GSM5137975
Reanalysis of: GSM5137976
Reanalysis of: GSM5137977
Reanalysis of: GSM5137978
Reanalysis of: GSM5137979
Reanalysis of: GSM5137980
Reanalysis of: GSM5137981
Reanalysis of: GSM5137982
Reanalysis of: GSM5137983
Reanalysis of: GSM5137984
Reanalysis of: GSM5137985
Reanalysis of: GSM5137986
Reanalysis of: GSM5137987
Reanalysis of: GSM5137988

overall_design:
Re-analysis of GSE168400
data processing step:
Basecalling was performed using the default Ion Torrent software trimming was performed using the fastp software v0.20.1 and the parameters -f 3, -r, -M 15 Counts were calculated using the pseudoalignment tool salmon v1.4.0 with the default parameters for mapping-based quantification and the hg38 salmon partial index (genome build: hg38 (GRCh38)). Reads were loaded in R using the tximport library. the 42n_expr.txt includes log2 of TPM values


title: Deciphering lineage specification during early embryogenesis in mouse gastruloids using integrative multi-layered proteomics

city: Nijmegen

first: Suzan

last: Stelloo

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: m6A-mRNA&lncRNA Epitranscriptomic Microarray analysis for human liver tissues of healthy, HBV-infected with and without cirrhosis donors.

city: Xi'an

first: Chao

last: Fan

address: #169, Changle Road, Xincheng District

institute: The Fourth Military Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: The samples of human liver tissues from the healthy donors, the HBV-infected patients without cirrhosis, and the HBV-infected patients with cirrhosis were collected. The tissues were then analyzed by the m6A-mRNA&lncRNA Epitranscriptomic miroarray. The Goal of this experiment was to determine the different of gene expression and m6a methylation of liver tissues among the healthy donors, the HBV-infected patients with and without cirrhosis.

overall_design: a total of 9 liver tissues from different donors were collected, including 3 from healthy donors, 3 from HBV-infected patients without cirrohsis, and 3 from HBV-infected patients with cirrhosis. The total RNA were extracted from the tissues within 24h at 4 °C and ahead of microarray analysis. Ethical approval for this study was provided by the Ethical Committee of the Second Affiliated Hospital of Air Force Military Medical University, Xi’an, China on 24 February 2016. All research was conducted in accordance with both the Declarations of Helsinki and Istanbul. Written consent was given in writing by all subjects.

middle: J


title: Deciphering lineage specification during early embryogenesis in mouse gastruloids using integrative multi-layered proteomics [ChIP-seq]

summary: Gastrulation is a critical stage of embryonic development during which the three germ layers are established. Deciphering the molecular mechanisms underlying this proces from a protein perspective remains a significant challenge. To address this, we employed a multilayered mass spectrometry-based proteomics approach to investigate the global dynamics of (phospho)protein expression during differentiation of ESCs towards gastruloids – an in vitro model of gastrulation-stage embryogenesis. Our findings revealed that many proteins exhibited temporal expression with unique expression profiles corresponding to the three germ layers. Additionally, we profiled enhancer interaction landscapes in ESCs and gastruloids using p300 proximity labeling, which revealed numerous gastruloid-specific transcription factors and chromatin remodelers. Subsequent degron based perturbations combined with scRNA-seq revealed a critical role for Zeb2 in regulating mouse and human somitogenesis. Overall, this study provides a rich resource for developmental and synthetic biology communities endeavoring to understand mammalian embryogenesis.

overall_design: mouse gastruloids were generated as previously described (Protoc. Exch. https://doi.org/10.1038/protex.2018.094). ChIP-seq was performed on undifferentiated mESCs and 120h gastruloids.

first: Michiel

last: Vermeulen


title: Differential in vivo roles of Mpl cytoplasmic tyrosine residues in murine hematopoiesis and myeloproliferative disease

city: Parkville

first: Carolyn

middle: A

last: de Graaf

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

summary: Thrombopoietin (Tpo), which binds to its specific receptor, the Mpl protein, is the major cytokine regulator of megakaryopoiesis and circulating platelet number. Produced primarily in the liver, Tpo binds to Mpl on the surface of target cells triggering activation of Janus kinase 2 (Jak2) and phosphorylation of the receptor, as well as activation of several intracellular signalling cascades that mediate cellular responses. Three tyrosine (Y) residues in the C-terminal region of the Mpl intracellular domain have been implicated as sites of phosphorylation required for the activation and regulation of major Tpo-stimulated signalling pathways: Mpl-Y565, Mpl-Y599 and Mpl-Y604. Here, we have introduced mutations in the mouse germline to define the roles of Mpl receptor intracellular domains and tyrosine residues in steady-state and pathophysiological actions of Tpo/Mpl signalling. We report a consistent physiological requirement for Mpl-Y599, absence of which resulted in thrombocytopenia, deficient megakaryopoiesis, low hematopoietic stem cell (HSC) number and function, and attenuated responses to myelosuppression caused by administration of 5-fluorouracil (5-FU). We further show that in models of myeloproliferative neoplasms (MPN) driven by mutations in Jak2 or hCalr, where Mpl is required for pathogenesis, thrombocytosis was dependent on intact Mpl-Y599. In contrast, Mpl-Y565 was required for negative regulation of Tpo responses; mutation of this residue resulted in excess megakaryopoiesis at steady-state and in response to 5-FU, and exacerbated mutant Jak2 and hCalr-driven thrombocytosis.

overall_design: LSK cells (Lin- Sca+ Kit+) Hematopoetic stem cells from mice with mutations in the tyrosine residues of the Mpl receptor

first: Kira

last: Behrens

first: Maria

last: Kauppi

first: Liam

last: Salleh

first: Warren

middle: S

last: Alexander


title: Neoantigen identification for 1956 and F244 murine MCA-sarcomas

status: Public on May 20 2024

city: Saint Louis

first: Robert

middle: D

last: Schreiber

state: MO

address: 425 South Euclid

department: Department of Pathology and Immunology

institute: Washington University in St. Louis

summary: This study was to predict neoantigens in 1956 and F244 murine MCA-sarcomas (female C57BL/6N and male 129S6 lines, respectively). Mutations were called by comparing tumor versus normal whole exome sequencing (WES) data, and filtered for expressing mutations using RNA-seq data. Out of expressing mutations, MHC class I or II neoantigens were predicted and screened by T cell reactivities (IFN-gamma ELISPOT and tetramer staining). Therapeutic vaccine confirmed an M50I mutation in Psmd6 and an R144S mutation in Cs to be the major MHC class I (H-2Kb) and II (I-Ab) neoantigens for 1956; and a G122A in Pex14 and a D2944Y mutation in Plec to be the major class I (H-2Kb) and class II (I-Ab) neoantigens for F244.

overall_design: WES was performed for DNA extracted from in vitro cultured 1956 or F244 cells (n=1 per line); or a tail of a female C57BL/6N or male 129S6 mouse (normal controls for 1956 and F244, respectively; n=1 per strain). RNA-seq was performed for RNA extracted from in vitro cultured 1956 or F244 cells (n=1 per line).

first: Takeuchi

last: Yoshiko

first: Ward

middle: P

last: Jeffrey

first: Meng

last: Wei

first: Sultan

last: Hussein

first: Arthur

last: Cora

first: Mardis

middle: R

last: Elaine

first: Artyomov

middle: N

last: Maxim

first: Lichti

middle: F

last: Cheryl

first: Schreiber

last: Robert


title: Impaired signaling pathways on Berardinelli–Seip congenital lipodystrophy macrophages during Leishmania infantum infection

city: Natal

first: Selma

middle: MB

last: Jeronimo

state: Rio Grande do Norte

address: 655 Av Passeio dos Girassois, Capim Macio

department: Tropical Medicine Institute (IMT-RN)

country: Brazil

institute: Federal University of Rio Grande do Norte (UFRN)

summary: This was an in vitro experimental study of monocytes-derived macrophages from blood samples of BSCL individuals (type I - AGPAT2, type II - BSCL2, and heterozygous - BSCL2), and healthy controls (WT). Samples were infected with L. infantum. In the control group, there are monocytes-derived macrophages from individuals WT with and without a history of visceral leishmaniasis (VL). RNA-seq was done to identify the different group responses to the infection.

overall_design: Monocyte-derived macrophage samples from BSCL individuals (type I and II, and type II heterozygous) and wild type (WT with and without an LV history) were infected with L. infantum. Both infected and non-infected mRNA samples were sequenced, each containing three experimental replicates (with the exception of participant 6, who has only an experimental duplicate in the infected sample).

first: Viviane

middle: B

last: Nogueira

first: Carolina

middle: O

last: Mendes-Aguiar

first: Josivan

middle: G

last: Lima


title: Single-cell RNA-sequencing of human cytomegalovirus-infected humanized mice

city: Wuhan

first: Xiaoxu

last: Zhu

address: Jinlong Street

institute: WUHAN INSTITUTE OF VIROLOGY,  CENTER FOR BIOSAFETY  MEGA SCIENCE, CAS

summary: Human cytomegalovirus (HCMV) is a common herpesvirus that persistently infects a large portion of the world's population. Despite the robust host immune response, HCMV is able to replicate, evade host defenses, and establish latency throughout the lifespan by developing multiple immunomodulatory strategies, making the studies on the interaction between HCMV infection and host response particularly important. HCMV has a strict host specificity that specifically infects humans. Therefore, most of the in vivo researches of HCMV rely on clinical samples. Fortunately, the establishment of humanized mouse models allows for convenient in-lab animal experiments involving HCMV infection. Single-cell RNA sequencing(scRNA-seq) enables the study of the relationship between viral and host gene expressions at the single-cell level within host cells. In this study, we assessed the gene expression alterations of PBMCs at the single-cell level within HCMV-infected humanized mice, which sheds light onto the virus-host interactions in the context of HCMV infecton of humanized mice and provides a valuable dataset for the related researches.

overall_design: To delineate the single-cell dynamics of peripheral blood mononuclear cells (PBMCs) during latent and reactivated HCMV infection, we procured PBMCs from the peripheral blood of humanized mice. These were categorized into two groups: two wild-type (Mock), and two HCMV-infected (HCMV). Initially, NHDF cells harboring HCMV were introduced into the peritoneal cavity of NOD-scid IL2Rgcnull mice. Following a 4-week period peripheral blood was harvested and partitioned from each mouse group

first: An

last: Wang

first: Yuanyuan

last: Bie

first: Bowen

last: Zhang

first: Wenting

last: Ji

first: Jing

last: Lou

first: Muhan

last: Huang

first: Xi

last: Zhou

first: Yujie

last: Ren


title: Cut & Tag sequencing exhibited the chromosome binding regions of transcription factor IRF5 within murine bone marrow derived macrophages

city: Hangzhou

first: Zhejun

last: Cai

state: Zhejiang

address: 88 Jiefang Road

department: Department of Cardiology, The Second Affiliated Hospital

institute: Zhejiang University School of Medicine

summary: CUT&Tag technology represents a cutting-edge method for investigating protein-DNA interactions. Utilizing a hyperactive novel fusion enzyme (Hyperactive pG-Tn5 / pA-Tn5 Transposase), this technique, under antibody guidance, specifically targets and cleaves DNA sequences near target proteins. It boasts several advantages over traditional ChIP-Seq, including lower cell input requirements, enhanced signal-to-noise ratio, and improved repeatability. Employing this innovative approach, we examined the binding strength of interferon regulatory factor 5 in bone marrow-derived macrophages, and analyzed the biological behaviors of IRF5 following stimulation of these cells.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) for the IRF5 binding regions (using anti-IRF5 antibody (abcam ab21689) in the murine bone marrow derived macrophages stimulated with CpG or control


title: Glycolysis involved in transcription dysregulation through histone lactylation in T-lineage acute lymphoblastic leukemia II

first: Wu

last: Wenyan

address: 1678 Dongfang Road, Pudong New District, Shanghai

institute: Shanghai Children's Medical Center

summary: Tumor cells are known for excessive lactate production, due to Warburg effect, and transcriptional dysregulation. However, how lactate influences the epigenetic modifications at a genome-wide level and its impact on gene transcription in tumor cell remains unclear. Addressing this gap, we analyzed genome-wide modification of H3K18 lactylation (H3K18la) in T-cell acute lymphoblastic leukemia (T-ALL). Integrated analysis with histone modifications with established functions show the H3K18la is mainly involved in active regulation of gene transcription. We report increased lactate and H3K18la modification levels in T-ALL as compared to normal T cells. We observe clusters of H3K18la modifications in patterns reminiscent of super-enhancers. We show a notable shift of genome-wide H3K18la modification from T cell immunity in normal T cells to leukemogenesis in T-ALL, correlating with altered gene transcription profiles. By disrupting H3K18la modification, we uncover both synergetic and divergent changes between H3K18la and H3K27ac modifications, suggesting the H3K18la and H3K27ac modifications may have specific regulation mechanisms correspondingly. These findings expand our understanding of metabolic disruptions involvement in transcription dysregulation through epigenetic changes in T-ALL, and emphasize the collective importance of histone modifications in maintaining oncogenic epigenetic stability.

overall_design: To explore the effects of H3K18la modifications on transcriptional regulation, we subjected JURKAT cells to RNA sequencing (RNA-Seq) across three experimental conditions: control (untreated), oxamate treatment, and combined oxamate and lactate treatment.

first: Wenyan

last: Wu

first: Huiying

last: Sun

first: Han

first: Xiaoyu

last: Cui

first: Shuang

last: Zhao

first: Rongrong

last: Fan

first: Ronghua

first: Ying

last: Zhong

first: Kefei

first: Xiaoxiao

last: Chen

first: Liang

last: Zheng

first: Shuhong

last: shen

first: Meng

last: Yin

first: Yu

last: Liu


title: Gene expression profile at single cell level of non-malignant cells in KRAS syngeniec mouse tumor models harboring STK11 and/or KEAP1 co-muation

city: Houston

last: Qian

address: 1515 Holcombe blvd

institute: MDACC

summary: STK11/LKB1 and KEAP1 mutations are associated with immunotherapy resistance. We employed KRAS syngeneic mouse cells (K) and generated KEAP1 loss (KK) or STK11/KEAP1 loss (KLK) by CRISPR/KO. Then we injected these tumor cells and collected the tumor for single-cell RNA-seq. Our aim is to analyze the impact of STK11 and/or KEAP1 deficiency on the immune microenvironment.

overall_design: LKR13K, LKR13KK and LKR13KLK tumor cells were injected into 129SV mice. The tumors were collected and performed scRNAseq at the Univerisity of Texas MD Anderson Cancer Center Sequencing Core.

first: Ferdinandos

last: Skoulidis

first: John

middle: V

last: Heymach


title: Age-related differences in the mouse corneal epithelial transcriptome and their impact on corneal wound healing

first: Cintia

middle: S.

last: de Paiva

state: TX

address: 6565 Fannin Street NC505G

department: Ophthalmology

institute: Baylor College of Medicine

summary: RNA from corneal epithelium from C57BL/6 mice of different ages were collected, RNA extracted and bulk RNA sequencing was performed.

overall_design: Corneal epithelium of female C57BL/6J (B6) mice of different ages [2, 12, 18, and 24 months, M] was collected, RNA extracted, and bulk RNA sequencing performed.

first: Anmar

last: Abu-Romman

first: Kaitlin

middle: K

last: Scholand

first: Gowthaman

last: Govindarajan

first: Zhiyuan

last: Yu

first: Sonali

last: Pal-Ghosh

first: Mary

last: Stepp


title: CRISPR/Cas9 regulates EphA2-CDH1 axis to inhibit the migration of castration-resistant prostate cancer cells

city: Suzhou

first: Chaogang

last: Wei

address: 1055 Sanxiang Road, Suzhou 215004, Jiangsu, China

institute: The Second Affiliated Hospital of Soochow University

summary: We ued CRISPR/Cas9 to knock out EphA2 gene in PC3 cells, and overexpress EphA2 gene in Du145 cells with overexpressed plasmids to explore the underlying mechanisms of EphA2 function in castration-resistant prostate cancer(CRPC) and clinical relevance, providing more evidence for EphA2 as a potential therapeutic target for CRPC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PC3-EphA2-KO and control cells, DU145-EphA2-OE and control cells.

first: Song

last: Yan

first: Xiaojing

last: Li

first: Yiting

first: Peng

last: Pan

first: Ningfan

last: Hu

first: Lanyi

first: Yue

last: Xiao

first: Li


title: Mast Cells Control Lung Type 2 Inflammation via Prostaglandin E2-Driven Soluble ST2.

city: Boston

first: Daniel

last: Dwyer

state: MA

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

summary: Severe asthma and sinus disease is a consequence of Type 2 inflammation (T2I), mediated by IL-33 signaling through its membrane-bound receptor, ST2. Soluble (s)ST2 reduces available IL-33 and limits T2I, but little is known about its regulation. We demonstrate that prostaglandin E2 (PGE2) drives production of sST2 to limit features of lung T2I. PGE2 deficient mice display diminished sST2. In humans with severe respiratory T2I, urinary PGE2 metabolites correlate with serum sST2. In mice, PGE2 enhanced sST2 secretion by mast cells (MCs). Mice lacking MCs, ST2 expression by MCs or EP2 receptors by MCs showed reduced sST2 lung concentrations and strong T2I. Recombinant sST2 reduced T2I in mice lacking PGE2 or ST2 expression by MCs back to control levels. PGE2 deficiency also reversed the hyperinflammatory phenotype in mice lacking ST2 expression by MCs. PGE2 thus suppresses T2I through MC-derived sST2, explaining the severe T2I observed in low PGE2 states.

overall_design: RNA-seq analysis of Mouse Bone Marrow MCs were stimulated with 10 ng/mL of IL-33 and/or 1 µM of PGE2 for 24 hours

first: Kinan

last: Alhallak

first: Joshua

last: Boyce


title: Deciphering lineage specification during early embryogenesis in mouse gastruloids using integrative multi-layered proteomics [RNA]

first: Suzan

last: Stelloo

overall_design: Somitic gastruloids were generated as previously described (Protoc. Exch. https://doi.org/10.1038/protex.2018.094, van den Brink et al., Nature 2020). RNA-seq was performed on somitic gastruloids expressing Zeb2-degron tag.

first: Michiel

last: Vermeulen


title: Single-cell profiles of peripheral blood mononuclear cell (PBMC) and bone marrow mononuclear cell (BMMC) from pneumosepsis mice

city: Xiamen

first: Qiuyue

last: Long

state: Fujian

address: Xiang‘an east Road 2000

institute: Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University

summary: Immune disorder is a major pathological feature of sepsis, and its complex mechanisms have not been clarified so far. With the help of single-cell transcriptomics technology,we propose to explore the disregulated mechanisms of heterogeneous immune cells in the periphery and bone marrow of peumosepsis hosts.

overall_design: PBMC and BMMC were isolated from klebsiella-pneumoniae-induced pneumosepsis mice at 0 hour (Control), 12 hours (KP1), 36 hours (KP2), and 90 hours (KP3), which represented four progressive status of the healthy, local pneumonia, distant spread, and ultimate sepsis, respectively.

first: Jiwei

first: Yali

last: Zheng

first: Zhancheng

last: Gao


title: Aberrant CHCHD2-Associated Mitochondrial Abnormality in Kii ALS/PDC Astrocytes

city: Tokyo

first: Nicolas

last: Leventoux

state: Tokyo

address: 35, Shinanomachi

department: Physiology

country: Japan

institute: Keio University

summary: The Amyotrophic Lateral Sclerosis/Parkinsonism-Dementia Complex (Kii ALS/PDC), a rare and complex neurological disorder, is predominantly observed in the Western Pacific islands, including regions of Japan, Guam, and Papua. This enigmatic condition continues to capture medical attention due to patients displaying symptoms that parallel those seen in either classical amyotrophic lateral sclerosis (ALS) or Parkinson's Disease (PD). Distinctly, post-mortem examinations of the brains of affected individuals have shown concurrent hallmarks: the presence of α-synuclein aggregates, which are a signature of PD, and TDP-43, associated with classical ALS. These observations are further complicated by the detection of phosphorylated tau, accentuating the multifaceted proteinopathic nature of Kii ALS/PDC. The etiological foundations of this disease remain undetermined, and genetic investigations have yet to provide conclusive answers. However, emerging evidence has cast a spotlight on astrocytes, cells pivotal for maintaining brain health. These astrocytes are likely to play a significant role in the pathogenesis of Kii ALS/PDC. Leveraging advanced iPSC technology, our team cultivated multiple astrocyte lines to probe the disease further. CHCHD2 emerged as asignificantly dysregulated gene when disease astrocytes were compared to healthy controls. Our analyses also unveiled imbalances in specific pathways: those associated with astrocytic cilium dysfunction, known to have ties with neurodegeneration, and those related to major neurological disorders, including classical ALS and PD. Further in-depth examinations revealed abnormalities in the mitochondrial morphology and metabolic processes of the affected astrocytes. A particularly striking observation was the reduced expression of CHCHD2 in a patient’s spinal cord. In sum, our findings suggest a potential compromise in the support Kii ALS/PDC astrocytes provide to neurons, emphasizing the need to explore the role of CHCHD2 in maintaining mitochondrial health and its implications for the disease.

overall_design: To question the contribution of astrocytes to the Kii-ALS/PDC disease, we established five iPS cell lines from patients and differentiated them into astrocytes (iPasts). We then performed gene expression profiling by RNA sequencing, including two control-iPasts from healthy donors.

first: Satoru

last: Morimoto

first: Chris

last: Kato

first: Hideyuki

last: Okano


title: Genome wide analysis of the upper lumbar spinal cord at 4 days after T9 hemisection injury

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: The goal of this study is to elucidate the influence of hemisection injury at thoracic spinal cord (T9) on the upper transcriptome of the upper lumbar spinal cord at acute phase. mRNA profiles of spinal cord at 4 days-post injury and before injury were generated. 72 Differentially Expressed Genes (DEGs) were observed. Our study represents the detailed analysis of transcriptomes of spinal cord distal to the hemisected lesion at acute phase, with biologic replicates, generated by RNA-seq technology.

overall_design: The effect of spinal cord injury on the transcriptome of intact upper spinal cord was investigated.

first: Kazu

last: Kobayakawa

first: Reggie

last: Edgerton

first: Akihito

last: Harada

first: Jumpei

last: Nogami


title: Genome wide analysis of the lower lumbar spinal cord at 4 days after T9 hemisection injury

summary: The goal of this study is to elucidate the influence of hemisection injury at thoracic spinal cord (T9) on the transcriptome of the lower lumbar spinal cord at acute phase. mRNA profiles of spinal cord at 4 days-post injury and before injury were generated. 72 Differentially Expressed Genes (DEGs) were observed. Our study represents the detailed analysis of transcriptomes of spinal cord distal to the hemisected lesion at acute phase, with biologic replicates, generated by RNA-seq technology.

overall_design: The effect of spinal cord injury on the transcriptome of intact lower spinal cord was investigated.


title: Mina53 regulates the neural stem cell pool by acting as an arginine demethylase

first: Jie

last: Sun

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: To investigate the function Mina53 in the regulation of neural stem cells proliferation and differentiation, we collect neural stem cells which Mina53 has been knocked down by shRNA.

overall_design: We performed CUT&Tag in ctrl and Mina53-knockdown aNSCs to profile the distributions of H4R3me2a.

first: Wen

last: Yi


title: CSF single cell transcriptomic changes associated with post-acute sequelae of SARS CoV 2 infection

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary: Natural history and mechanisms for persistent cognitive symptoms (also known as “brain fog”) following acute and often mild COVID-19 are unknown.  In a large prospective cohort of people who recovered from acute COVID-19 in the New York City/New Jersey area, we found the presence of cognitive dysfunction to closely associate with fatigue symptoms and, in some people, brain imaging abnormalities.  In a smaller subset of people who underwent cerebrospinal fluid analysis at a median of 9 months after their initial infection, there was no evidence to suggest changes related to Alzheimer’s disease or neurodegeneration.  However, single cell gene expression analysis of immune cells (T cells, border associated macrophages, microglia-like myeloid cells, myeloid dendritic cells) from the cerebrospinal fluid showed many changes seen in models of acute SARS-CoV-2 infection.  Longitudinal follow-up additionally showed recovery from cognitive dysfunction to be very slow, and associate with greater – not less – activation of interferon-related inflammatory processes in both single cell transcriptomic and targeted fluid proteomic studies.  These findings suggest persistent brain fog following COVID-19 to resemble more viral infection than autoimmune disorders.

overall_design:
We performed a cross-sectional comparison between people who are healthy control (HC) subjects and people who developed cognitive symptoms after COVID-19 with (PASC with Cognitive Impairment, PASC-CI) or without (PASC with Subjective Cognitive Concerns, PASC-SCC) objective cognitive deficits.
We further compared CSF scRNASeq between people with PASC-CI who later recovered and people with  PASC-CI whose deficits persisted.

first: William

last: Hu

first: Milota

last: Kaluzova

first: Alice

last: Dawson

first: Victor

last: Sotelo

first: Julia

last: Papas

first: Carol

last: Shu

first: Mini

last: Jomartin

first: Ashima

last: Nayyar

first: Sabiha

last: Hussain


title: Establishment and characterization of six canine hepatocellular carcinoma cell lines (Transcriptional changes induced by drug treatment with toceranib or sorafenib)

city: Seoul

first: Jayoung

last: Lee

address: 120, Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea

country: South Korea

institute: Konkuk University

summary: Hepatocellular carcinoma (HCC) is the most common malignant liver tumor in dogs. Although surgical resection is a major treatment option for canine HCC, there are no distinct strategies for unresectable tumor subtypes or adjuvant chemotherapy for tumors with positive margins. We aimed to establish and characterize novel HCC cell lines from canine patients. The cellular morphology, general growth features and tumorigenicity of the established cell lines were evaluated. We also examined the sensitivity of the cell lines to multi-target tyrosine kinase inhibitors (TKIs). Toceranib, a veterinary TKI that targets vascular endothelial growth factor (VEGFR)/platelet-derived growth factor receptor (PDGFR)/c-kit, effectively inhibited the mitogen-activated protein kinase pathway and induced apoptosis. The established canine HCC cell lines showed greater sensitivity to toceranib than to sorafenib, a first-line treatment for human HCC targeting RAF/VEGFR/PDGFR. Sorafenib showed improved anti-tumor effects when co-treated with SCH772984, an extracellular signal-regulated kinase inhibitor. Our study suggests new therapeutic strategies for canine HCC, and these cell lines are valuable research materials for understanding HCC tumor biology in both humans and dogs.

overall_design: We established canine HCC cell lines from hepatic tumors of six canine patients.To investigate the transcriptional changes induced by drug treatment in the cell lines, the cells were treated with toceranib (15μM) or sorefenib (30μM) for 24hrs. The cells treated with vehicle (sorafenib-DMSO, toceranib-DPBS) were used as control. Gene Ontology Biological Processes (GO-BP) enrichment analysis was performed using data obtained from RNA-seq of 4 different cell lines.


title: Genome wide analysis of lower spinal cords with training after spinal cord hemisection injury

first: Yasuyuki

last: Ohkawa

summary: The goal of this study is to elucidate the influence of treadmill training on transcriptome of the lower lumbar spinal cord after thoracic spinal cord hemisection. mRNA profiles of spinal cords at 23 days-post injury with/without treadmill training were generated. The expression levels of 650 genes in the trained animal were increased ( > 2-fold) compared to untrained animals. Our study represents the detailed analysis of transcriptomes of spinal cord distal to the hemisected lesion after treadmill training, with biologic replicates, generated by RNA-seq technology.

overall_design: The effect of training after spinal cord injury (T9) on the transcriptome of intact lower spinal cord was investigated.

first: Kazu

last: Kobayakawa


title: Single-cell RNA sequencing of human various osteosarcoma tissues

city: Nanning

first: Wenyu

last: Feng

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

summary: We performed the scRNA-seq analysis of 2 primary osteosarcoma tissues ,2 osteosarcoma lymphoid tissues, 4 adjacent tissues of osteosarcoma based on the 10X Genomics platform.

overall_design: Primary osteosarcoma tissues,osteosarcoma lymphoid tissues and  adjacent tissues of osteosarcoma from 4 patients were used for single cell RNA sequencing by 10X Genomics

first: Yun

last: Liu

first: Mingwei

last: He

first: Tianyu

last: Xie

first: Haijun

last: Tang

first: Qingjun

last: Wei


title: Mina53 regulates the neural stem cell pool by acting as an argnine demethlysae

first: Jie

last: Sun

overall_design: Comparative gene expression profiling analysis of RNA-seq data for nerual stem cells and its KD derivatives (shMina53).

first: Wen

last: Yi


title: Diurnal gene expression profiles in mouse brain tissues constituting the central dopamine system

first: Soo Hyun

last: Kim

address: Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu

institute: Ewha Womans University

summary: The circadian regulation of gene expression underlies orchestrated daily rhythms in physiology, metabolism, and behavior. The central dopamine (DA) system arising from DA neurons in the ventral midbrain has been implicated in a wide range of brain functions. Growing evidence suggests that DA transmission follows daily oscillations at multiple regulatory steps, and its dysfunction is closely related to the onset of various neuropsychiatric diseases. We examined diurnal gene expression profiles across key brain areas constituting the central DA pathways in mice by use of microarray analyses to identify rhythmically expressed genes according to the time of day (TOD).

overall_design: Male C57BL/6 mice were entrained to a 12-h light-dark (LD) photoperiod, and sacrificed from the Zeitgeber time 11 (ZT11) at 4-h intervals for 2 successive days. Four brain tissues including the substantia nigra and ventral tegmental area of the ventral midbrain (SN/VTA), prefrontal cortex (PFC), striatum (STR), and habenula (HAB), were bilaterally dissected from 1-mm-thick brain slices, which were coronally sectioned in a brain matrix chilled on ice. A total of 48 RNA samples were analyzed by use of Affymetrix GeneChip Mouse Gene 2.0 ST Array (Affymetirx, Santa Clara, CA, USA).

first: Sooyoung

last: Chung

first: Eun

first: Soo

middle: H

first: Seongsik

last: Yun

first: Yunmi

first: Jihyun

first: Hyo

last: Cha

first: Joo

middle: Y

last: Oh

first: Hyun

first: Kyungjin

first: Gi

last: Son


title: Small RNAseq using tumor-derived extracellular vesicles

city: Suita

first: Kentaro

last: Jingushi

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

institute: Osaka University

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA modifications play important roles in cellular processes, and their dysregulation has been linked to various diseases, including cancer. As extracellular vesicles (EVs) contain various RNAs, it is assumed that these can be modified. However, the presence of such modified transcripts has not been determined due to the small amount of RNAs in EVs. Herein, we successfully detected 22 RNA modifications in EVs using a proprietary ultra-high performance liquid chromatography tandem mass spectrometry system and identified reduced levels of N6-methyladenosine (m6A) in EVs derived from colon cancer tissues, which correlated with cancer recurrence. Increasing m6A modification levels in colorectal cancer EVs via m6A demethylase Alkbh5 knockout suppressed the tumor-promoting effect of colorectal cancer EVs. Mechanistically, colorectal cancer-derived EVs increased tumor necrotic factor a and interleukin-6 secretion by macrophages via toll-like receptor 8 in an m6A-dependent manner and promoted cancer cell proliferation. RNA-seq analysis showed that 5’-tRF-GlyGCC were enriched in colorectal cancer EVs, and m6A levels on 5’-tRF-GlyGCC were decreased in colorectal cancer EVs compared with those in normal colon EVs. Cancer-derived EVs containing 5’-tRF-GlyGCC significantly promoted tumor growth, and the effect was impeded through macrophage depletion. These data provide evidence that cancer-specific RNA modifications are present in EVs, promoting tumor progression by regulating immune cells.

overall_design: To investigate the colon cancer-charachteristic small RNA in EVs, we analyzed EV-RNA from colon cancer-tissue derived EVs (small EVs=6, large EVs=6) and adjacent norrmal colon-tissue derived EVs (small EVs=6, large EVs=6).

first: Yuya

last: Monoe

first: Yoshiaki

last: Takano

first: Kensuke

last: Hirosuna

first: Kohei

last: Taniguchi

first: Kazumasa

last: Komura

first: Sang-Woong

last: Lee

first: Kazutake

last: Tsujikawa


title: Targeting of lncRNA Morrbid inhibits abdominal aortic aneurysm by regulating macrophage-mediated vascular inflammation.

city: guang zhou

first: CaiYun

last: He

address: Yingdong Building, No 96, Dongchuan Road, Yuexiu District, Guangzhou, 510080, People's Republic of China.

institute: Guangdong Provincial People's Hospital

summary: To investigate the possible target gene of morrbid, we detected the mRNA expression in bone marrow derived macrophages(BMDMs) with deletion of Morrbid by RNA-seq.

overall_design: We performed gene expression profiling analysis of  RNA-seq data of  BMDMs originating from myeloid-specific Morrbid knockout mice and control mice.

first: Caiyun

first: Fan

last: Yang


title: Sperm transcriptional state associated with paternal transmission of stress phenotypes

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Paternal stress can induce long-lasting changes in germ cells potentially propagating heritable changes across generations. To date, no studies have investigated differences in transmission patterns between stress-resilient and -susceptible mice. We tested the hypothesis that transcriptional alterations in sperm during chronic social defeat stress (CSDS) transmit increased susceptibility to stress phenotypes to the next generation. We demonstrate differences in offspring from stressed fathers that depend upon paternal category (resilient vs susceptible) and offspring sex. Importantly, artificial insemination reveals that sperm mediates some of the behavioral phenotypes seen in offspring. Using RNA-sequencing we report substantial and distinct changes in the transcriptomic profiles of sperm following CSDS in susceptible vs resilient fathers, with alterations in long noncoding RNAs (lncRNAs) predominating especially in susceptibility. Correlation analysis revealed that these alterations were accompanied by a loss of regulation of protein-coding genes by lncRNAs in sperm of susceptible males. We also identify several co-expression gene modules that are enriched in differentially expressed genes in sperm from either resilient or susceptible fathers. Taken together, these studies advance our understanding of intergenerational epigenetic transmission of behavioral experience.

overall_design: Control vs Defeat mice sperm sequenced

first: Ashley

middle: M

last: Cunningham

first: Deena

last: Walker

first: Li

last: Shen

first: Eric

middle: J

last: Nestler


title: Choline intake in pregnancy and lactation modifies liver transcriptome profile in the offspring of female rats with nonalcoholic fatty liver disease

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

summary: The aim of the study was to analyze the impact of choline intake during pregnancy and/or lactation on histological alternation and gene expression profile in the liver of NAFLD dam progeny. We hypothesized that offspring of mothers suffering from non-alcoholic fatty liver (NAFLD) is more prone to develop fatty liver, because of suboptimal intrauterine environment.  The performed analyses included histological examination of liver tissue obtained from 24-day-old male rats, which were offspring of dams with fatty liver: provided with proper choline amount during pregnancy and lactation (NN), fed a choline-deficient diet during these both periods (DD), deprived with choline only during pregnancy (DN) or only during lactation (ND). The global gene expression profile was analyzed by using microarray approach (Affymetrix® Rat Gene 2.1 ST Array Strip).

overall_design: Thirty-four animals were included in the study: seventeen dams and seventeen male offspring. Eighteen female and nine male rats eight weeks old were obtained from Charles River Laboratories (Germany). Animals were housed at the Laboratory of the Department of Human Nutrition and Dietetics, Poznań University of Life Sciences under standard conditions (12/12 h light/dark cycle, 21 ± 1 °C, humidity 55 %–65 %,) and were kept in pairs/in threes within the same sex in stainless steel cages coated with metal-free enamel. After a five-day adaptation period, when animals have been fed standard maintenance diet Labofeed B (Morawski, Poland), females started to be fed with the AIN-93 M diet deficient in choline (D group, n=17, one dam was excluded from the study because of malocclusion) for 16 weeks to establish a fatty liver model. Next, dams were mated with healthy Wistar males fed with the standard AIN-93 M diet. A vaginal plug was the evidence of mating. Pregnant dams with fatty liver were randomized to two subgroups: one was still fed the diet deficient in choline (D group, n=9); the second one started to receive proper choline amounts in the diet (standard AIN-93 G diet; N group, n=8). Three days before expected delivery, dams started to be kept in a single cage. After delivery, the animals from the D group were randomized once again into two subgroups, which were still fed the diets deficient in choline (DD group, n=4) or with the standard AIN-93 G diet (DN group, n=5). The same was done with animals from the N group – one subgroup was still fed standard AIN-93 G diet (NN group, n=4) and the second started to be fed diet deficient in choline (ND group, n=4). This feeding method in the DD, DN, ND and NN groups were continued till 24. day after delivery, when one male from each litter was sacrificed for tissue collection.

first: Joanna

last: Mikołajczyk-Stecyna

first: Ewelina

last: Żuk

first: Agata

last: Chmurzynska

first: Małgorzata

last: Blatkiewicz

first: Karol

last: Jopek


title: A promising clinical treatment for EGFRI-induced rash by targeting the early pathological alteration revealed by transcriptome analysis

city: Shanghai

first: qing

last: you

address: 800 Dongchuan

institute: Shanghai Jiao Tong University

summary: In order to investigate the early pathological alteration of EGFRI-induced rash, we treated rat with vehicle or afatinib for 3 days. We then performed gene expression profiling analysis using data obtained from RNA-Seq of 3 different rat skins in each group

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control rat skins (vehicle treated) and afatinib-treated rat skins, in triplicate.

first: Shiyi

last: Zhang

first: Qing

last: You

first: Leying

last: Chen

first: Liangyong

last: Xia


title: Cell-in-Cell Structure Mediates In-Cell Killing Suppressed by CD44

city: Beijing

first: Qiang

last: Sun

state: Beijing

address: 20 Dongda Street

department: Laboratory of Cell Engineering

institute: Institute of Biotechnology

summary: Penetration of immune cells into tumor cells was believed to be immune-suppressive via cell-in-cell (CIC) mediated death of the internalized immune cells. We unexpectedly found that CIC formation largely led to the death of the host tumor cells, but not the internalized immune cells, manifesting typical features of death executed by NK cells, which we called “in-cell killing” that demonstrates efficacy superior to the canonical way of “kiss killing” from outside. By expression profiling of isogenic cells, CD44 on tumor cells was identified as a negative regulator of “in-cell killing” via inhibiting CIC formation. CD44 functions to antagonize NK cell internalization by reducing N-cadherin-mediated intercellular adhesion and enhancing Rho GTPase-regulated cellular stiffness as well. Remarkably, antibody-mediated blockade of CD44 signaling potentiated the suppressive effects of NK cells on tumor growth associated with increased heterotypic CIC formation. Together, we identified CIC-mediated “in-cell killing” as a promising strategy for cancer immunotherapy.

overall_design: Examination of genes associated to cell-in-cell formation in liver tumor cells.

first: Jie

last: Fan

first: Jianqing

last: Liang

first: Yan

last: Su


title: m6A-Seq analysis for the  methylated RNA of primate prefrontal cortex after sevoflurane exposure

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: We thus isolated prefrontal cotex from rhesus macaques and performed m6A-Seq analysis.MeRIP libraries using eluted RNA were constructed using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian User Manual according to the manufacturer’s instructions.

overall_design: two groups（Ctrl；Sevoflurane）, two male macaques and four female macaques were included in group Ctrl; two male macaques and three female macaques were included in group sevoflurane. Additionally, two male macaques  in group Ctrl, marked as A and B, respectively, were named Ctrl-M, two male macaques  in group sevoflurane marked as D and S1, respectively, were named SEV-M, four female macaques  in group Ctrl, marked as C, C1, C2, and C3, respectively, were named Ctrl-F, three female macaques  in group sevoflurane, marked as F, S2, and S3, respectively, were named SEV-F.

first: Lei


title: Histone lactylation-mediated NSUN2 transcriptional activation dictates choroidal neovascularization through promoting AKAP2 mRNA expression [CUT&Tag]

status: Public on May 19 2024

first: Sipeng

last: Zuo

address: No. 12, Lane 833, Zhizaoju Road, Huangpu District

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

summary:
Background: As a widespread post-transcriptional RNA modification, N5-methylcytosine (m5C) is implicated in a variety of cellular responses and processes that regulate RNA metabolism. Despite this, a clear understanding of m5C modification’s role and mechanism in angiogenesis is still lacking.
Methods: Single-cell RNA sequencing data was analyzed to determine expression of m5C methylase NSUN2. m5C levels were determined by mRNA isolation and anti-m5C dot blot in both hypoxia-induced endothelial cells (ECs) and laser-induced choroidal neovascularization (CNV). In addition, endothelial cell and endothelium‐specific NSUN2‐knockout mouse model were used to investigate the effect of NSUN2 silence on angiogenic phenotype. Genome-wide multiomics analyses were performed to identify the functional target of NSUN2, including proteomic analysis, transcriptome screening and m5C-methylated RNA immunoprecipitation sequencing (m5C-meRIP-seq). CUT&Tag sequencing was performed to test the histone lactylation signal in the promoter region of NSUN2. Finally, AAV-mediated short hairpin RNAi knockdown of NSUN2 gene expression (AAV-shNSUN2) was constructed to investigate the effect of inhibiting CNV.
Results: First, we discovered that m5C methylase NSUN2 expression level and mRNA m5C level were significantly higher in CNV-ECs than in normal ECs. NSUN2 knockdown in ECs inhibited proliferative, migration, and tube formation activities of ECs. Moreover, compared with EC NSUN2flox/flox mice, EC-specific NSUN2-deficient (EC NSUN2-/-) mice displayed less retinal vascular leakage after laser induction. Through multiomics analyses, we subsequently identified A-kinase anchoring protein 2 (AKAP2), a scaffolding protein which isolate Protein kinase A (PKA) to specific subcellular locations through binding to its regulatory subunit, as a downstream candidate target of NSUN2 in ECs. Overexpression of exogenous AKAP2 markedly reversed the inhibitory phenotypes in NSUN2-deficient ECs. Interestingly, laser induced NSUN2 up-regulation was driven by lactate-mediated lactylation on histone H3K18. In CNV models, AAV-mediated repression of NSUN2 modulated highly retinal vascular leakage and choroidal thickness.
Conclusion: Overall, our findings indicate that NSUN2 is a novel therapeutic target for choroidal neovascularization.

overall_design: CUT&Tag-seq data related to gene NSUN2 in human umbilical vein endothelial cell

first: Lin

last: Li

first: Linna

last: Lu

first: Xianqun


title: Faecalibacterium prausnitzii-derived extracellular vesicles alleviate chronic colitis-related intestinal fibrosis by macrophage metabolic reprogramming II

city: Shenzhen

first: Ying

last: Wang

address: xinan

department: Shenzhen hospital

institute: southern mecical university

summary: Faecalibacterium prausnitzii (F. prausnitzii) has been recognized for its various intestinal and extraintestinal benefits to human. And reduction of F. prausnitzii has been linked to an increased risk of intestinal fibrosis in patients of Crohn’s disease (CD). In this study, oral administration of either live F. prausnitzii or its extracellular vesicles (FEVs) can markedly mitigate the severity of fibrosis in mice induced by repetitive administration of DSS. In vitro experiment revealed that FEVs were capable of directing the polarization of peripheral blood mononuclear cells (PBMCs) towards an M2b macrophage phenotype, which has been associated with anti-fibrotic activities. This effect of FEV was found to be stable under various conditions that promote the development of pro-fibrotic M1/M2a/M2c macrophages. Proteomics and RNA sequencing were performed to uncover the molecular modulation of macrophages by FEVs. Notably, we found that FEVs reprogramed every metabolism of macrophages by damaging the mitochondria, and inhibited oxidative phosphorylation and glycolysis. Moreover, FEV-treated macrophages showed a decreased expression of PPARγ and an altered lipid processing phenotype characterized by decreased cholesterol efflux, which may promote energy reprogramming. Taken together, these findings identify FEV as a driver of macrophage reprogramming, suggesting that triggering M2b macrophage polarization by oral admiration of FEV may serve as strategy to alleviate hyperfibrotic intestine conditions in CD.

overall_design: To test the underlying mechanisms of the anti-fibrotic effects of FEVs, LPMCs from three FEV-treated mice or three saline-treated control donors were isolated, followed by RNA isolation and RNA-seq analysis

first: Linjie

first: Shuze

first: Ye


title: WWP2 MEDIATES THE METABOLIC REPROGRAMMING OF RENAL MYOFIBROBLASTS TO PROMOTE KIDNEY FIBROSIS [ChIP-Seq]

city: Singapore

first: Jing

last: Guo

state: State...

address: 8 Collage Road, DUKE-NUS Medical School, level 5

department: Center for Computational Biology

country: Singapore

institute: Duke-NUS Medical School

summary: Renal fibrosis is a common pathological endpoint that is challenging to reverse in chronic kidney disease (CKD) independently of the underlying causes. Although myofibroblasts are mainly responsible for the accumulation of a fibrillar collagen-rich extracellular matrix (ECM), recent reports revealed their heterogeneity in proliferative and fibrotic activities, mirroring specific metabolic states that drive fibrosis. Here, we investigate the role of E3 ubiquitin-protein ligase WWP2 in the metabolic reprogramming of renal myofibroblasts in fibrosis. The tubulointerstitial expression of WWP2 contributes to the progression of fibrosis in CKD patients and in pre-clinical models of CKD. WWP2 deficiency leads to increased fatty acid oxidation, boosting mitochondrial respiration, promoting myofibroblast proliferation and arresting pro-fibrotic activation, thus ameliorating kidney fibrosis. Specifically, WWP2 suppresses the transcription of PGC-1α, which mediates the metabolic and proliferative changes in fibrotic myofibroblasts. Pharmacological intervention targeting PGC-1α reverses the pro-fibrotic effect of WWP2. These findings reveal a previously unappreciated WWP2-PGC-1α axis underlying the metabolic reprogramming of myofibroblasts during renal fibrosis, which could provide a new target for therapeutic intervention in CKD.

overall_design: Chromatin immuno-precipitation (ChIP) of WWP2 from wildtype mouse kidney fibroblast treated with TGFβ1 for 24 hours

first: Huimei

first: Enrico

last: G Petretto


title: Histone lactylation-mediated NSUN2 transcriptional activation dictates choroidal neovascularization through promoting AKAP2 mRNA expression [RNA-seq]

overall_design: RNA-seq data related to gene NSUN2 in human umbilical vein endothelial cell


title: Tumor macrophages treated with exosomes

city: La Jolla

first: Jack

last: Bui

address: 9500 Gilman Dr

institute: UC San Diego

summary: Macrophages treated with exosomes containing high levels of MEK1 express chemokines

overall_design: Gene differential expression analysis on tumor macrophages treated with either MEK1-hi or MEK1-low exosomes in vitro

first: Jarrod

last: Yee


title: The role of CD4 T cells in tumor-specific CD8 T cell reprogramming [RNA-Seq]

first: Andrea

last: Schietinger

state: NY

address: 1275 York Avenue

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: RNA-seq analysis of tumor-specific CD8 T cells from tumors with and without tumor-specific CD4 T cells

overall_design: T cells were sorted by flow cytometry and RNA-seq was performed.

first: Gabriel

last: Espinosa Carrasco

first: Paul

last: Zumbo


title: Gene expression profiling of RKO cells with or without SQLE knockdown.

first: Xinxiang

address: #270 Dongan Road, Xuhui District

institute: Fudan University Shanghai Cancer Center

summary: RKO cells (WT or SQLE knockdown) were harvested and mRNA were extracted for high-throughput sequencing.

overall_design: WT v.s. SQLE knockdown, in duplicate

first: Qi

last: Liu


title: Tumor macrophages from rejecting and growing tumors

summary: Macrophages in rejecting tumors have IFNg gene signature

overall_design: Gene differential expression analysis on ex vivo tumor macrophages from 9609 MEK1-hi and MEK1-low exosome tumors


title: Dual SMAD inhibition enhances the longevity of human epididymis epithelial cells

city: Cleveland

first: Ann

last: Harris

state: OH

address: 2109 Adelbert Rd

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Primary human epididymis epithelial (HEE) cells are valuable reagents for functional studies on the human epididymis. We used them previously to determine the transcriptional networks that establish cell identity along the length of the epididymis from caput, corpus and cauda. These studies on HEE cells and organoids derived from them revealed important cellular properties. However, similar to other primary cells, HEE cells undergo replicative senescence and de-differentiation in culture. A cocktail of small molecules was shown elsewhere to extend longevity of epithelial basal cells.  The components included transforming growth factor β (TGF-β)/bone morphogenetic protein (BMP) antagonists, WNT agonist and Rho-associated and coiled-coil containing protein kinase (ROCK) inhibitor (ROCKi), which together prevented the senescence-related upregulation of TGF-β signaling pathway members. Here we treat HEE cells with the same cocktail and observed enhanced replicative potential and prolonged expression of markers of HEE differentiation. This treatment expands the differentiated HEE cell population available from individual epididymis tissue samples that can be used for molecular, cellular and functional studies.

overall_design: 12 RNA-seq datasets, 3 replicates between 4 groups

first: Giuliana

last: Castello Coatti

first: Shih-Hsing

last: Leir

first: Alekh

last: Paranjapye


title: The role of CD4 T cells in tumor-specific CD8 T cell reprogramming  [ATAC-Seq]

summary: ATAC-seq analysis of tumor-specific CD8 T cells from tumors with and without tumor-specific CD4 T cells

overall_design: T cells were sorted by flow cytometry and ATAC-seq was performed.


title: Transcriptomics in the nucleus accumbens shell reveal sex- and reinforcer-specific signatures associated with morphine and sucrose craving

city: Philadelphia

first: Mathieu

last: Wimmer

state: PA

address: 1701 N 13th Street

institute: Temple University

summary: RNA-sequencing was performed using nucleus accumbens tissue from male and female rats following 1 or 30 days of morphine self-admininstration or sucrose self-adminnistration.

overall_design: A total of 101 samples were analyzed. The groups included male morphine (saline: 11, Day 1: 10, Day 30: 11), female morphine (saline: 8, Day 1: 7, Day 30: 8), male sucrose (cue-only: 5, Day 1: 7, Day 30: 8), and female sucrose (cue-only: 8, Day 1: 8, Day 30: 80)

first: Mayberry

last: Hannah

first: Bavley

last: Charlotte

first: Karbalaei

last: Reza

first: Peterson

last: Drew

first: Bongiovanni

last: Angela

first: Ellis

last: Alexandra

first: Downey

last: Sara

first: Toussaint

last: Andre

first: Wimmer

last: Mathieu


title: Microorganism-mediated denitrogenation of aquaculture systems provoked by poly-β-hydroxybutyrate (PHB)

status: Public on May 18 2024

city: Guangzhou

first: Yarong

state: Guangzhou/Guangdong

address: No. 1 Xingyu Road

department: Aquaculture and Nutrition Research Lab

institute: Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences

summary: The biodegradable polymer poly-β-hydroxybutyrate (PHB) is a promising carbon source for biological mitigation of nitrogen pollution, a significant problem in aquaculture that physical and chemical methods have not provided a comprehensive solution. Here we investigated the impact of PHB on the zero-water-change largemouth bass culture by 30- and 40-day experiments. PHB loaded into the filter circulation pump at 4g L-1, optimum value determined by the first experiment, significantly reduced the levels of nitrate by 99.65%, nitrite by 95.96%, and total nitrogen by 85.22% compared to the control without PHB. PHB also significantly increased denitrifying bacteria (e.g., Proteobacteria and Fusobacteria) and expression of denitrification genes (e.g., nirK and nirS) in the microbial community, improving growth and health parameters of largemouth bass. While the impact may vary in other culture systems, PHB thus demonstrated its remarkable utility in aquaculture, highlighting ecological assessment and application to larger aquaculture operations as future considerations.

overall_design: PHB was added at 0 g L-1 and 4 g L-1 to the triplicate control (T2-1-T2-3) and experimental (C2-1-C2-3) groups,.

first: Yun

last: Xia


title: Developmental trajectory of unconventional T cells of the cynomolgus macaque thymus

first: Jaeil

last: Lee

address: 103 Daehak-ro, Jongno-gu

institute: Seoul National University

summary: We profiled the differentiation pathways and heterogeneity of thymocytes in the young cynomolgus monkey thymus using single-cell RNA sequencing.

overall_design: Using DEG analysis and trajectory analysis, we temporally distinguished the conventional selection pathway and the agonist selection pathway of thymocytes and inferred the association between agonist selection and various unconventional T-cell lineages.

first: Sung

last: Choi

first: Kyeong

middle: C

last: Jung

first: Jae

middle: I


title: miRNAs analysis in early pregnancy

city: TauYau

first: Yun-Shien

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

summary:
A prFunctional embryo-maternal interactions occur during the embryo implantation and placentation. Extracellular vesicles with microRNA (miRNA) between cells have been considered of crtital importance for embro implantation and programming of human pregnancy
We used microarrays to investigate miRNAs expression during early pregnancy

overall_design: to examine miRNA different human decidaul stromal cells from noraml pregnancy and spontaneous miscarriage

first: Hsien-Ming

last: Wu


title: RNA sequencing of NPM1cA/SMC+/- mouse myeloid sarcoma and whole bone marrow

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8797 Watertown Plank Rd

department: Stem Cell Transriptional Regulation

institute: Versiti Blood Research Institte

summary: This study was designed to investigate the RNA sequencing profile of mouse myeloid sarcomas in comparison to their matched whole bone marrow acute myeloid leukemia specimens. The goal was to determine gene set profiles that are different between the two phenotypes in the same primary genetic driver of AML mutation in mice to further investigate the results demonstrated in the patient derived specimens.

overall_design: Samples includes were mouse myeloid sarcomas (AML tumors) and mouse whole bone marrow specimens (infiltrated with AML). All but one pair were NPM1cA mutated in combination with heterozygous SMC3 (SMC3+/-) and one sample was NPM1cA mutated but wild type SMC3.

first: Kristin

middle: E

last: Zorn

first: Alison

last: Meyer

first: George

last: Vassiliou


title: Transcriptomic analysis of human vascular endothelial cell line (EA.hy926) exposed to okadaic acid

city: Incheon

first: Jeong-In

last: Park

address: 119, Academy-ro

institute: Incheon National University

summary: As the climate changes due to global warming, the frequency of appearance of marine-derived toxins increases. In particular, the need to investigate marine-derived toxins for which toxicity has not yet been identified is emerging. Blood vessels are passageways through which compounds entering the body move to various organs and are the sites first exposed to compounds. Therefore, it is important to know the effects of compounds on blood vessels when they enter the body. In this study, the human vascular endothelial cell line EA.hy926 was exposed to the marine toxins OA (IC20; 42.9 nM) and the mechanism of toxicity was investigated at the transcriptome level. Quantseq 3' mRNA sequencing was performed by extracting RNA from EA.hy926 cells exposed to the toxins. Differentially expressed genes were determined based on fold change ≥ 1.5 and P value < 0.05.

overall_design: Cell culture The EA.hy926 cell line (human vascular endothelial cell line) was cultured in Dulbecco's Modified Eagle Medium (DMEM; Gibco®, USA) supplemented with 10% fetal bovine serum (FBS; Gibco®, USA), 1% Penicillin/Streptomycin (P/S; Gibco®, USA), 3.7 g/L sodium bicarbonate (Sigma-Aldrich, USA), 1 mM sodium pyruvate (Gibco®, USA) and maintained at 37℃ under 5% CO2. The cells were grown in a 100 mm culture dish and subcultured every 3 d by detaching with 0.25% (w/v) trypsin-EDTA (Gibco®, USA) at a split ratio of approximately 1:3.  Cell viability assay The 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT; Sigma-Aldrich, USA) assay is based on the principle that the yellow MTT solution is reduced to purple by the dehydrogenase of living cells that exhibit mitochondrial activity. EA.hy926 cells were seeded at a density of 20×104 cells per well in 96-well plates and incubated for 24 h. Cells were exposed to OA (National Research Council, Canada) at concentrations of 4.0625–1040 nM, respectively. DMEM was used as a solvent for OA. After 24 h of exposure, the medium was removed, 200 μL of MTT solution was dispensed into each well and incubated in the dark at 37°C for 3 h. Afterward, the medium was removed and 200 μL of DMSO was dispensed to dissolve the formazan crystals. Absorbance value were measured at a wavelength of 570 nm using a spectrophotometer (Varioskan LUX Multimode Microplate Reader, Thermo Fisher, USA). Cell viability of the control group was set to 100%, and the survival of the exposure group was calculated accordingly. IC20 was defined as the concentration that reduced cell viability by 20% compared to that in the control group. IC20 values were determined using linear-dose curves.  Total RNA isolation EA.hy926 cells were treated with OA at IC20 concentration for 24 h, and total RNA was extracted using TRIzol™ reagent (Invitrogen, USA). Total RNA was purified using the RNeasy Mini Kit (Qiagen, USA). The RNase-free Kit (Qiagen, USA) was used to remove genomic DNA during RNA purification. The RNA integrity number was confirmed using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). RNA quantification was performed using an ND-2000 spectrophotometer (Thermo Fisher, USA).  Library preparation and sequencing  To obtain gene information, Quant sequencing was performed using EA.hy926 cells exposed to OA (IC20). Sequencing was conducted using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Austria). Two micrograms of total RNA were prepared and oligo dT primers containing Illumina-compatible sequences at the 5' end were hybridized to RNA and reverse transcription carried out. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5' end. The double-stranded library was purified by using magnetic beads to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library was purified from the PCR components. High-throughput sequencing was performed as single-end 75 sequencing using NextSeq 500 (Illumina, USA).   Data analysis of RNA-seq QuantSeq 3’ mRNA sequencing reads were aligned using Bowtie2 (Langmead and Salzberg, 2012). Bowtie2 indices were either generated from the genome assembly sequence or the representative transcript sequences for aligning to the genome and transcriptome. The alignment file was used for assembling transcripts, estimating their abundances, and detecting differential expression of genes. DEGs were determined based on counts from unique and multiple alignments based on coverage, in Bedtools (Quinlan and Hall, 2010). The Read count (RC) were processed based on the quantile normalization method using the EdgeR tool in R (Robinson and Mccarthy and Smyth, 2010) using the Bioconductor package (Gentleman et al., 2004). Gene classification was based on searches performed by DAVID Bioinformatics Resources (http://david.abcc.ncifcrf.gov/) and Medline databases (http://www.ncbi.nlm.nih.gov/). Data mining and graphic visualization were performed using ExDEGA v5.1.1.4 (Ebiogen Inc., Korea).

first: Jong

last: Kim

first: Youn-Jung


title: Identification of functional genetic variants in transformed Ba/F3 cells expressing U2AF35(S34F)

city: Worcester

first: Jennifer

last: Benanti

address: 364 Plantation St. LRB525

department: Molecular, Cell & Cancer Biology

institute: UMass Medical School

summary: Exome and transcriptome sequencing analysis of murine transformed cells identifies loss of potential tumor suppressor

overall_design: Genomic and transcriptomic profiles of parental (U2AF35-WT) and transformed Ba/F3 cell lines (U2AF35-S34F) were generated by deep sequencing.

first: Haibo

last: Liu

first: Julie

last: Zhu

first: Michael

middle: R

last: Green


title: Faecalibacterium prausnitzii-derived extracellular vesicles alleviate chronic colitis-related intestinal fibrosis by macrophage metabolic reprogramming

status: Public on May 17 2024

first: Ying

last: Wang

overall_design: To investigate the role of FEVs on innate macrophages, PBMCs isolated from healthy donors were stimulated with FEVs at a concentration of 10 µg/ml. There are two groups in this study, including FEV-treated group and saline-treated control group.

first: Linjie

last: Li

first: Shuze

last: Chen

first: Ye


title: Single-cell gene expression profile of intra-islet immune cell populations in WT NOD and NOD.Cxcl16-/- mice

city: St Louis

first: Tiandao

state: MO

address: 4444 Forest Park Ave

institute: Washington University

summary: We examined how Cxcl16 deficiency may alter autoimmune responses targeting pancreatic islets, with a focus on changes in islet-infiltrating CD4 and CD8 T cells.

overall_design: Pancreatic islets were isolated and handpicked from 12-week-old female NOD and NOD.Cxcl16-/- mice. The islets were dispersed by a non-enzymatic approach and the dispersed islet cells of either strain were used for FACS-sorting CD45+ immune cells for single-cell RNA-seq analysis.

first: Neetu

last: Srivastava

first: Bo

last: Zhang

first: Xiaoxiao

last: Wan


title: Genome-wide methylation studies in nasal epithelial cells using a custom Asthma&Allergy DNAm array

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58th Street, CLSC 501

department: Human Genetics

institute: The University of Chicago

type: Methylation profiling by genome tiling array

summary: We performed an epigenome-wide association study (EWAS) of allergic sensitization using nasal epithelial cell DNA from 474 subjects.

overall_design:
Nasal epithelial cell methylation patterns were assessed in 474 children ages 5-7 with allergic sensitization as a quantitative trait.
Latent factors were estimated in order to account for unobserved variation in the DNA methylation data. The citation for the R package used for latent factor analysis is listed below.
FALCO: Factor AnaLysis in COrrelated data
McKennan, Chris; https://arxiv.org/abs/2009.11134

first: William

last: Wentworth-Sheilds


title: Ubiquitination of hepatic APOC3 by GM47544 prevents hypertriglyceridemia and ameliorates atherosclerosis

city: Wuhan

first: Qianqian

last: Xiao

address: 1095# Jiefang Ave., Wuhan 430030 People’s Rep. of China

department: Departments of Internal Medicine

institute: Tongji Hospital

summary:
To investigate the function of lnc GM47544 in the regulation of triglyceride, we established AML-12 cell lines in which lnc GM47544 has been stably overexpressed by lentivirus.
We then performed gene expression profiling analysis using data obtained from RNA-seq of AML-12-pLKO.1 (control) and AML-12-GM47544 (O/E).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AML-12-pLKO.1 (control) and AML-12-GM47544 (O/E).

first: Hu

last: Ding


title: Transcriptome changes after overexpression, knockdown and condItional knockout of UXT in mice

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

summary: Ubiquitously expressed transcript (UXT)  has been shown to play a role in regulating the process of autophagy. Here, we investigated roles of UXT in the innnate immune responses after  overexpression, knockdown and condItional knockout of UXT in mice

overall_design: Total RNA in mouse MEF cells  after overexpression and knockdown of UXT was isolated and sequenced by deep sequencing using Illumina HiSeq 2500; Total RNA in mouse BMDM cells  of myeloid-cell-specific UXT conditional knockout mice was isolated and sequenced by deep sequencing using Illumina HiSeq 2500;

last: HU

first: Mingyu

last: Pan


title: Lack of TREM2 during anti-PD-1 therapy reprograms intestinal macrophages and microbiota to enhance tumor rejection

city: St. Louis

first: Marco

last: Colonna

address: 660 S. Euclid Ave

department: Immunology&Pathology

institute: Washington University in St. Louis

summary: The gut microbiota and tumor-associated macrophages (TAM) impact anti-PD-1 checkpoint blockade. Reprogramming TAM by either blocking or deleting the macrophage receptor TREM2 attenuates tumor growth, and lack of functional TREM2 enhances tumor elimination by anti-PD-1. Here, we found that anti-PD-1 combined with TREM2 deficiency induces proinflammatory programs in intestinal macrophages and a concomitant expansion of Ruminococcus gnavus (R. gnavus) in the gut microbiota. Gavage of wild-type mice with R. gnavus recapitulated enhancement of anti-PD-1-mediated tumor elimination occurring in the absence of TREM2. The intestinal proinflammatory environment coincided with expansion, increased circulation and migration of TNF-producing CD4+ T cells to the tumor bed. Thus, TREM2 remotely controls anti-PD-1 checkpoint blockade through modulation of the intestinal immune environment and microbiota, with R. gnavus emerging as a potential probiotic agent for increasing responsiveness to anti-PD-1.

overall_design:
We performed single-cell RNA sequencing on intestinal myeloid cells , as well as bulk RNA-seq on total colonic tissue, from WT and TREM2-deficient mice treated or not with anti-PD-1. We also performed single-cell RNA sequencing on tumor immune cells from WT mice treated or not with Ruminococcus gnavus.
Details for HTO Antibodies:
HTO: Barcode Sequence: Hashtagged sample
TotalSeq™-B0301 anti-mouse Hashtag 1 Antibody: ACCCACCAGTAAGAC: First biological sample harvasted from WT mice either treated or not with Ruminococcus gnavus gavage.
TotalSeq™-B0302 anti-mouse Hashtag 2 Antibody: GGTCGAGAGCATTCA: Second biological sample harvasted from WT mice either treated or not with Ruminococcus gnavus gavage.
TotalSeq™-B0303 anti-mouse Hashtag 3 Antibody: CTTGCCGCATGTCAT: Third biological sample harvasted from WT mice either treated or not with Ruminococcus gnavus gavage.
TotalSeq™-B0303 anti-mouse Hashtag 4 Antibody: AAAGCATTCTTCACG: Forth biological sample harvasted from WT mice either treated or not with Ruminococcus gnavus gavage.

first: Blanda

last: Di Luccia

first: Martina

last: Molgora

first: Darya

last: Khantakova


title: DPSCs Regulate Epithelial-T Cell Interactions in Oral Submucous Fibrosis

city: Xi‘an

first: sy

last: w

address: Changle West Road 145

institute: fmmu

summary:
Background: Oral submucous fibrosis (OSF) is a precancerous lesion characterized by fibrous tissue deposition, the incidence of which correlates positively with the frequency of betel nut chewing. Prolonged betel nut chewing can damage the integrity of the oral mucosal epithelium, leading to chronic inflammation and local immunological derangement. However, currently, the underlying cellular events driving fibrogenesis and dysfunction are incompletely understood, such that OSF has few treatment options with limited therapeutic effectiveness. Dental pulp stem cells (DPSCs) have been recognized for their anti-inflammatory and anti-fibrosis capabilities, making them promising candidates to treat a range of immune, inflammatory, and fibrotic diseases. However, the application of DPSCs in OSF is inconclusive. Therefore, this study aimed to explore the pathogenic mechanism of OSF and, based on this, to explore new treatment options.
Methods: A human cell atlas of oral mucosal tissues was compiled using single-cell RNA sequencing to delve into the underlying mechanisms. Epithelial cells were reclustered to observe the heterogeneity of OSF epithelial cells and their communication with immune cells. The results were validated in vitro, in clinicopathological sections, and in animal models. In vivo, the therapeutic effect and mechanism of DPSCs were characterized by histological staining, immunohistochemical staining, scanning electron microscopy, and atomic force microscopy.
Results: A unique epithelial cell population, Epi1.2, with proinflammatory and profibrotic functions, was predominantly found in OSF. Epi1.2 cells also induced the fibrotic process in fibroblasts by interacting with T cells through receptor-ligand crosstalk between macrophage migration inhibitory factor (MIF)-CD74 and C-X-C motif chemokine receptor 4 (CXCR4). Furthermore, we developed OSF animal models and simulated the clinical local injection process in the rat buccal mucosa using DPSCs to assess their therapeutic impact and mechanism. In the OSF rat model, DPSCs demonstrated superior therapeutic effects compared with the positive control (glucocorticoids), including reducing collagen deposition and promoting blood vessel regeneration. DPSCs mediated immune homeostasis primarily by regulating the numbers of KRT19+MIF+ epithelial cells and via epithelial-stromal crosstalk.
Conclusions: Given the current ambiguity surrounding the cause of OSF and the limited treatment options available, our study reveals that epithelial cells and their crosstalk with T cells play an important role in the mechanism of OSF and suggests the therapeutic promise of DPSCs.

overall_design: We performed scRNA-seq analysis with oral mucosa tissues from OSF patients and controls.

first: Kai

last: Jiao


title: Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation

city: Bethesda

first: Octavio

last: Mondragon Palomino

address: 4 MEMORIAL DR

institute: National Institutes of Health

summary: Background: Parasitic helminths influence the composition of the gut microbiome. However, the microbiomes of individuals living in helminth-endemic regions are understudied. The Orang Asli, an indigenous population in Malaysia with high burdens of the helminth Trichuris trichiura, display microbiotas enriched in Clostridiales, an order of spore-forming obligate anaerobes with immunogenic properties. We previously isolated novel Clostridiales that were enriched in these individuals and found that a subset promoted the Trichuris life cycle. In this study, we aimed to further characterize the functional properties of these bacteria.Results: Clostridiales isolates were profiled for their ability to perform 57 enzymatic reactions and produce short chain fatty acids (SCFAs) and hydrogen sulfide, revealing that these bacteria were capable of a range of activities associated with metabolism and host response. Consistent with this finding, monocolonization of mice with individual isolates identified bacteria that were potent inducers of regulatory T cell (Treg) differentiation in the colon. Comparisons between variables revealed by these studies identified enzymatic properties correlated with Treg induction and Trichuris egg hatching.

overall_design: R. hominis-OA6 is unable to induce Tregs despite its taxonomic relationship to the other two Peptostreptococcaceae isolates, the Treg-inducing R. hominis-OA2 and P. sordellii-OA8. To better characterize the host response to the three Peptostreptococcaceae isolates, we performed RNAseq on colonic tissue from mice monocolonized with these three bacteria, as well as GF mice (Figure S3). Principal coordinate analysis (PCA) showed that the four conditioned mainly separated on the PC1 axis, with R. hominis-OA2 the farthest from GF controls, and R. hominis-OA6 and P. sordellii-OA8 in-between (Figure S3a).

first: Shushan

last: Sargsian

last: Mondragon-Palomino

first: Defne

last: Ercelen


title: Synthetic trimeric Interleukin-6 receptor complexes with a STAT3 phosphorylation dominated activation profile

city: Düsseldorf

first: Christiane

last: Seibel

address: Universitätstraße 1

country: Germany

institute: Heinrich-Heine-Universität

summary: In Interleukin (IL)-6 signalling, IL-6 site I binds to the IL-6 receptor (IL-6R) first, following by IL-6 site II interaction to domain 2/3 of gp130 to form premature trimeric IL-6:IL‑6R:gp130 receptor complexes. Formation of the mature hexameric receptor complex is then facilitated by the inter-trimeric interaction of IL-6 site III with domain 1 of the opposing gp130. The two gp130-associated Janus kinases (JAKs) trans-phosphorylate when their spatiotemporal pairing is correct, which causes the activation of STAT, ERK, and AKT pathways in a balanced manner. Since the intracellular domain (ICD) of IL-6R is not needed for STAT/ERK/AKT phosphorylation, we investigated the conditions under which a chimeric IL-6RECD-gp130TMD/ICD receptor protein confers biological activity. For IL‑6RECD‑gp130TMD/ICD, the extracellular domain (ECD) of IL-6R was fused to the transmembrane domain (TMD) and ICD of gp130. Co-expression of IL‑6RECD‑gp130TMD/ICD with signalling-deficient gp130 variants did not induce IL-6 signalling, suggesting that the assembly of hexameric complexes failed to dimerize the IL-6R-associated JAKs correctly. By mimicking the premature trimeric receptor complex, IL-6-mediated dimerization of IL-6RECD-gp130TMD/ICD with the single-cytokine-binding variant gp130DD1 induced signalling. Of note, IL-6 signalling via these synthetic gp130DD1:IL-6RECD-gp130TMD/ICD complexes resulted predominantly in STAT3 phosphorylation. A STAT3-dominated profile was also observed after IL-6-induced signalling mediated by a JAK-deficient IL‑6RECD‑gp130TMD/ICDDJAK variant in complex with the JAK-proficient but STAT/ERK/AKT-deficient gp130JAKDICD variant. Our data showed that effective ERK/AKT signalling could not be executed after intracellular domain swapping from gp130 to the IL-6R. Taken together, the chimeric IL-6R/gp130 receptor may be helpful in the creation of customized synthetic IL-6 signalling.

overall_design: Expression profiling by high throughput sequencing


title: AP-1 regulates heterogeneous cellular dormancy in TNBC

city: Shanghai

first: Yang

last: Dong

state: 上海

address: Shanghai

institute: Tongji University

summary: Slow-cycling cells (SCCs) are a heterogeneous subpopulation of tumor cells. They pre-exist in tumor tissues and evade killing by chemotherapeutics that target mitosis due to their dormant nature. We here utilized varieties of fluorescent dyes or proteins (Claret, H2BeGFP, and Violet) retaining method to label and isolate SCCs, and RNA-seq was performed to understand the gene expression characteristics of subpopulations of SCCs.

overall_design: Here we reported that SCCs subgroups share similar gene expression profiles. Up-regulations of AP-1 subunits regulate triple negative breast cancer (TNBC) dormancy by up-regulating the expression of CDKN1A and GADD45 family as transcription factors.

first: Dean

last: Tang


title: Transthyretin orchestrates vitamin B12-induced stress resilience [II]

city: Jena

first: Konstantin

last: Riege

address: Beutenbergstraße 11

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

summary: Background: Chronic stress significantly contributes to mood- and anxiety disorders. Previous data suggest a correlative connection between vitamin B12 supplementation, depression, and stress resilience. However, the underlying mechanisms are still poorly understood.  Methods: Using the chronic variable stress mouse model coupled with RNA-sequencing, we determined vitamin B12-induced transcriptional changes related to stress resilience. By viral-mediated gene transfer and in vivo epigenome editing, we reveal a functional pathway linking vitamin B12, DNA methylation, and depressive-like symptoms. Results: We identified Transthyretin (Ttr) as a sex-specific key target of vitamin B12 action in chronic stress. Accordingly, TTR expression was increased postmortem in the prefrontal cortex of male, but not female, depressed patients. Virally altered Ttr in the prefrontal cortex functionally contributed to stress- and depression-related behaviors, changes in dendritic spine morphology, and gene expression. In stressed mice, vitamin B12 reduced DNAme in the Ttr promoter region. Importantly, using in vivo epigenome editing to alter DNAme in the brains of living mice for the first time, we establish a direct causal link between DNAme on Ttr and stress-associated behaviors.  Discussion: In summary, using state-of-the-art techniques, this study uncovers a mechanistic link between cobalamin supplementation, Ttr, and markers of chronic stress and depression, encouraging further studies into dietary interventions for mood disorders.

overall_design: PolyA selected mRNA sequenced for 16 brain (prefrontal cortex) samples from 10 weeks old, male mice in four groups: under naive condition or after 21 days of induced chronic variable stress and saline (control) or vitamin B12 injected afterwards.

first: Gregor

last: Stein

first: Janine

middle: S

last: Aly

first: Annamaria

last: Manzolillo

first: Lisa

last: Lange

first: Iqra

last: Hussain

first: Elizabeth

middle: A

last: Heller

first: Susana

last: Cubillos

first: Thomas

last: Ernst

first: Christian

last: Hübner

first: Gustavo

last: Turecki

first: Steve

last: Hoffmann

first: Olivia

last: Engmann


title: PLPP1-deficiency-mediated ferroptosis induced by PD-1 signaling impairs antitumor activity of intratumoral CD8+ T cells III.

city: Zhengzhou

first: Jiqi

last: Shan

state: Henan

address: 1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

institute: The First Affiliated Hospital of Zhengzhou University, Zhengzhou,

summary: Metabolic programming plays a crucial role in T-cell activation. Herein, we describe how phospholipid metabolism regulates CD8+ T-cell function in patients with cancer. We found that phosphatidylcholine (PC) and phosphatidyl ethanolamine (PE) levels were lower in intratumoral CD8+ T cells than in circulating CD8+ T cells. The expression of phospholipid phosphatase 1 (PLPP1), an enzyme that catalyzes PE and PC synthesis, was also downregulated in CD8+ T cells upon infiltrating tumors. Moreover, unsaturated fatty acid-mediated ferroptosis was a major factor impairing the antitumor function of PLPP1-deficient CD8+ T cells infiltrated in tumors, accompanied by enhanced reactive oxygen species production and lipid peroxidation. The activation of programmed cell death 1 (PD-1) signaling in CD8+ T cells suppressed the PLPP1 expression by increasing GATA1 binding to the promoter region of PLPP1. PLPP1 expression was upregulated after anti-PD-1 therapy. Our findings revealed therapeutic potential of enhancing PLPP1 levels to restore CD8+ T-cell function.

overall_design: PLPP1fl/fl and Lckcre-PLPP1fl/fl CD8+ T cells infiltrated in B16 tumors after anti-PD-1 therapy were isolated for single cell RNA-seq (scRNA-seq). scRNA-seq of CD8+ T cells was performed by Analytical Biosciences Beijing Limited

first: Yu

last: Ping


title: Profiling of circRNA Expression in Human Ovarian Clear Cell Carcinoma (OCCC)

city: Suita

first: Tadashi

last: Oride

address: 2-15 Yamadaoka

department: Obstetrics and Gynecology

institute: Osaka university

summary: To identify highly expressed circular RNAs (circRNAs) in OCCC and elucidate their function, we performed a circRNA microarray analysis using two OCCC clinical samples and their corresponding normal ovarian tissues from the opposite side, screening 13,617 circRNAs.

overall_design: In this study, we identified highly expressed circRNAs in OCCCs compared to normal ovaries and elucidated their function in the processes of carcinogenesis and progression

first: T

first: M

last: Yamamoto

first: Y

last: Oi

first: K

last: Sawada


title: Therapeutic targeting ERRγ suppresses metastasis via extracellular matrix remodeling in small cell lung cancer

first: Hong

last: Wang

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-sen University

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

overall_design: Refer to individual Series


title: Gene expression and T cell repertoire profile at single cell level of peripheral blood T cells after treatment with a personalized neoantigen vaccine (GNOS-PV02) and Pembrolizumab for advanced hepatocellular carcinoma.

city: Philadelphia

first: Renzo

last: Perales-Linares

address: 3675 Market Street, Suite 200

department: Research and Development

institute: Geneos Therapeutics

summary: To further characterize the T cell response to the neoantigen vaccine, we performed single-cell RNA and T cell receptor (scRNA/TCR-seq) of peripheral blood T cells at the 12-week post-vaccination time point.

overall_design:
T cells were isolated and enriched from the week 12 post-treatment PBMC of 3 patients (#6, 7, and 8) using the Miltenyi human Pan T Cell Isolation Kit and analyzed using scRNA/TCR-seq.
***Submitter declares that the raw data will be deposited in dbGap due to due to IRB restrictions***

first: Daniel

last: Shu

last: Perales


title: Multi-Omics molecular subtyping based on commensal microbiome predicts molecular characteristics and therapeutic response in Triple-Negative Breast Cancer [scRNA-seq]

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

summary: We thoroughly analyzed the molecular subtyping of Triple-Negative Breast Cancer and its different manifestations, and located T cells and Tumor cells related to the survival of breast cancer through single cell sequencing and space transcriptome according to our score, and finally investigated their relationship with the therapeutic efficacy, providing a scientific basis for the treatment of triple negative breast cancer.

overall_design: 10x Single-cell Transcriptome sequencing were used to obtain the characteristics of  2 TNBC samples, and 10x Spatial Transcriptome sequencing were used to obtain the characteristics of 4 TNBC samples.

first: Feng

last: Qi

first: Jia

last: Li

last: Gao

first: Wenxing

last: Qin


title: Transciptomic changes in Mycobacterium tuberculosis (Mtb) infected hepatocytes at early and late time points of infection

city: New Delhi

first: Debasisa

last: Mohanty

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Imunology

summary: Mycobacterium tuberculosis (Mtb), although primarily a pulmonary pathogen, can disseminate to various other organs of the body causing extra pulmonary tuberculosis (EPTB). In the present study, we have shown that hepatocytes, the major parenchyma cells of the liver, get robustly infected by Mtb. Using a combination of in-vitro, ex-vivo and animal models; we demonstrate that Mtb utilizes hepatocytes as a replicative niche, modulates its various biological functions like lipid metabolism and shields itself against the common anti-TB drugs. Hepatocytes, being a key cell type having both immune and metabolic functions, controls and coordinates various aspects of the physiology in both health and disease. In case of a multifactorial chronic infection like TB, we are curious to know whether hepatocyte infection plays any major role in the systemic outcome of this age-old disease.

overall_design: HepG2 cell lines were infected with Mtb-H37Rv-mCherry at a multiplicity of infection of 10 (MOI:10) . Two time points were selected:- early time point of 0 hour post infection ( i.e., 5 hours of incubating the cells with Mtb) and late time point of 48 hours post infection (i.e., 48 hours ). After infection, a single cell suspension was made and only the mCherry positive HepG2 cells (infected) were sorted.

first: Rajesh

last: Gokhale

first: Vinay

last: Nandicoori

first: Binayak

last: Sarkar

first: Jyotsna

last: Singh


title: Circadian tumor infiltration and function of CD8+ T cells dictate a temporal response to immunotherapy

city: Genève

first: Christoph

last: Scheiermann

address: 1, rue Michel Servet

country: Switzerland

institute: UNIGE

summary: The quantity and quality of tumor-infiltrating lymphocytes (TILs), particularly CD8+ T cells, are parameters linked to tumor control and response to immunotherapy. Yet, it is unknown whether these parameters are controlled in a circadian manner. Here, we show in murine and human cancers that the phenotype and number of TILs show time-of-day differences, which are driven by rhythmic leukocyte infiltration and depend on the circadian clock machinery. These rhythms can be harnessed therapeutically: chimeric antigen receptor (CAR) T cells or immune checkpoint blockers produce significant antitumor benefits when administered at the optimal time of the day, but have little effect when administered at other times. Furthermore, time-of-day-dependent T cell signatures in murine tumor models predict overall survival in melanoma patients and correlate with response to anti-PD-1 therapy. Our data provide unexpected evidence of circadian dynamics in the tumor microenvironment (TME), and suggest the importance of exploiting them in prospective clinical trials.

overall_design: Tumors were harvested at different times of the day and tumor infiltrating leukocytes were isolated by fluorescence activated cell sorting: live CD45+ cells. Tumor infiltrating leukocytes were sequenced by scRNA-seq and analyzed.

first: Chen

first: Qun

last: Zeng

first: Zeynep

last: Gul

first: Sisi

first: Robert

last: Pick

first: Phil

last: Cheng

first: Ruben

last: Bill

first: Yan

last: Wu

first: Stefan

last: Naulaerts

first: Coline

last: Barnoud

first: Pei-Chun

last: Hsueh

first: Sofie

last: Moller

first: Mara

last: Cenerenti

first: Mengzhu

last: Sun

first: Ziyang

last: Su

first: Stéphane

last: Jemelin

first: Volodymyr

last: Petrenko

first: Charna

last: Dibner

first: Stéphanie

last: Hugues

first: Camilla

last: Jandus

first: Zhongwu

first: Olivier

last: Michielin

first: Ping-Chih

last: Ho

first: Abhishek

middle: D

last: Garg

first: Federico

last: Simonetta

first: Mikaël

last: Pittet


title: Single-cell transcriptomic analysis of decidual immune cell landscape in the occurrence of adverse pregnancy outcomes induced by Toxoplasma gondii infection

first: Zhidan

last: Li

address: Ruijin er road 207

institute: NIPD

summary: Toxoplasma gondii (T. gondii) is an obligate intracellular parasite that can lead to adverse pregnancy outcomes, particularly in early pregnancy. Previous studies have illustrated the landscape of decidual immune cells. However, the landscape of decidual immune cells in the maternal–fetal microenvironment during T. gondii infection remains unknown. In this study, we employed single-cell RNA sequencing to analyze the changes in human decidual immune cells following T. gondii infection. Our results showed that the proportion of 17 decidual immune cell clusters and the expression levels of 21 genes were changed after T. gondii infection. Differential gene analysis demonstrated that T. gondii infection induced the differential expression of 279, 312, and 380 genes in decidual NK, dMφ, and dT cells, respectively. Our findings first revealed that several previously unknown molecules in decidual immune cells changed following T. gondii infection. This result revealed that the function of maternal–fetal immune tolerance declined, whereas the killing ability of decidual immune cells enhanced, eventually contributing to the occurrence of adverse pregnancy outcomes. The results of this study provide a valuable resource for uncovering several novel molecules that play an important role in the occurrence of abnormal pregnancy outcomes induced by T. gondii infection.

overall_design: In the present study, human decidual tissues from seven healthy pregnant women during first trimester were collected and then purified mononuclear cells. The purified cells were infected with T. gondii and analyzed with scRNA-seq.

first: Tianyi

last: Fu

first: Xiaohui

last: Wang

first: Xuemei

last: Hu


title: Multi-Omics molecular subtyping based on commensal microbiome predicts molecular characteristics and therapeutic response in Triple-Negative Breast Cancer [Spatial Transcriptome seq]

first: Zhang

last: hua

overall_design: 10x Single-cell Transcriptome sequencing were used to obtain the characteristics of  2 TNBC samples , and 10x Spatial Transcriptome sequencing were used to obtain the characteristics of 4 TNBC samples.

first: Feng

last: Qi

first: Jia

last: Gao

first: Wenxing

last: Qin