title: Neutrophil Extracellular Traps induced by chemotherapy inhibit tumor growth in vivo

status: Public on Jan 12 2024

city: cleveland heights

first: ZHENGHE

last: WANG

state: Ohio

address: 2103 CORNELL Road, WRB 3203

institute: CASE WESTERN RESERVE UNIVERSITY

summary: Neutrophil Extracellular Traps (NETs), a web-like structure of cytosolic and granule proteins assembled on decondensed chromatin, kill pathogens and causes tissue damage in diseases. Whether NETs can kill cancer cells is unexplored. Here, we report that a combination of glutaminase inhibitor CB-839 and 5-FU inhibits the growth of PIK3CA mutant colorectal cancers (CRCs) in xenograft, syngeneic, and genetically engineered mouse models in part through NETs. Disruption of NETs by either DNase I treatment or depletion of neutrophils in CRCs attenuated the efficacy of the drug combination. Moreover, NETs were present in tumor biopsies taken from patients treated with the drug combination in a phase II clinical trial. Increased NET levels in tumors are associated with longer progression-free survival. Mechanistically, the drug combination induced the expression of IL-8 preferentially in PIK3CA mutant CRCs to attract neutrophils into the tumors. Further, the drug combination increased the levels of reactive oxygen species in neutrophils, thereby inducing NETs. Cathepsin G (CTSG), a serine protease localized in NETs, enters CRC cells through the RAGE cell surface protein. The internalized CTSG cleaves 14-3-3 proteins, releases Bax, and triggers apoptosis in CRC cells. Thus, our studies illuminate a previously unrecognized mechanism by which chemotherapy-induced NETs kill cancer cells.

overall_design: To determine how the combination of CB-839 and 5-FU induces NETs. We performed RNA-seq on isogenic DLD1 PIK3CA WT-only and Mut-only cell lines treated with either vehicle or the combination of CB-839 and 5-FU, because the drug combination induced more NETs and tumor-infiltrating neutrophils in PIK3CA Mut-only tumors than the isogenic WT-only tumors

first: Zhenghe

first: Yamu

last: Li

first: Trang

last: Dinh


title: CaSSiDI: Novel single-cell “Cluster Similarity Scoring and Distinction Index” reveals critical functions for PirB and context-dependent Cebpb repression

status: Public on Jan 14 2024

city: Toronto

first: Tak

last: Mak

state: ON

address: 610 University Ave

department: The Campbell Family Institute for Breast Cancer Research

country: Canada

institute: Princess Margaret Cancer Centre, University Health Network

type: Expression profiling by high throughput sequencing

summary: PirB is an inhibitory cell surface receptor particularly prominent on myeloid cells. PirB curtails the phenotypes of activated macrophages during inflammation or tumorigenesis, but its functions in macrophage homeostasis are obscure. To elucidate PirB-related functions in macrophages at steady-state, we generated and compared single-cell RNA-sequencing (scRNAseq) datasets obtained from myeloid cell subsets of wild type (WT) and PirB-deficient knockout (PirB KO) mice. To facilitate this analysis, we developed a novel approach to clustering parameter optimization called “Cluster Similarity Scoring and Distinction Index” (CaSSiDI). Our application of CaSSiDI in this study has revealed previously unknown roles for PirB in myeloid cell populations. In particular, we have discovered homeostatic functions for PirB that are related to Cebpb expression in distinct macrophage subsets. Our results establish the utility of CaSSiDI for single-cell assay analyses and the determination of optimal clustering parameters.

overall_design: Comparative analysis of scRNA-seq data obtained from tissue-derived macrophage subsets to investigate differential cluster formation in WT and PirB-KO samples. A new analysis pipeline "CaSSiDI" was established for the analysis.

first: Robert

last: Nechanitzky

first: Parameswaran

last: Ramachandran

first: Duygu

middle: W


title: Molecular reframing of fibroblasts during resolution of arthritis [scRNA]

status: Public on Jan 16 2024

city: Erlangen

first: Hashem

last: Mohammadian

address: Ulmenweg 18

department: Department of Medicine 3 - Rheumatology and Immunology

country: Germany

institute: University of Erlangen-Nürnberg

summary: Fibroblasts are key orchestrators of inflammation. Little is known whether these cells change phenotype during resolution of inflammation. We adopted a method to visualise fibroblast activation during inflammation in humans in vivo, which is based on a fibroblast activation protein (FAP) tracer detected by positron emission tomography (PET). While tracer accumulation was high in active arthritis, it decreased significantly after TNF- and IL-17A inhibition. Biopsy-based scRNA-seq analyses in experimental arthritis demonstrated that FAP signal reduction reflected a phenotypic switch from pro-inflammatory MMP3+/IL6+ fibroblasts (high FAP internalisation) to pro-resolving CD200+DKK3+ fibroblasts (low FAP internalisation). Spatial transcriptomics of human joints revealed that pro-resolving niches of CD200+DKK3+ fibroblasts clustered with innate lymphoid cells (ILC)2, whereas MMP3+/IL6+ fibroblasts were co-localised with inflammatory immune cells. CD200+DKK3+ fibroblasts stabilised the ILC2 phenotype and induced resolution of arthritis via CD200/CD200R1 pathway. Taken together, these data suggest a dynamic molecular regulation of the mesenchymal compartment during resolution of inflammation.

overall_design: Cells from synovial joints were separated by fluorescence-activated cell sorting from R5 x R26tdTomato mice in either healthy, serum transfer arthritis (STA), or STA treated with Il23mc condition. R5-fatemap ILCs (viable CD45+ tdTomato+ CD3- TCRb- TCRgd-  CD11b- GR-1-) and fibroblasts (viable CD45- GR-1-) were sorted from each animal and analyzed using scRNAseq. Libraries were generated from pooled animals, each of them individually separated by antibody hashes directed against CD45 and B2m.

first: Simon

last: Rauber

first: Mario

last: Angeli

first: Kai-Ting

last: Yang

first: Andreas

last: Ramming


title: Mitf regulates gene expression networks implicated in B cell homeostasis, germinal center responses, and tolerance

status: Public on Jan 10 2024

city: New York

first: Christopher

last: Roman

address: 450 Clarkson Avenue, Brooklyn

department: Department of Cell Biology

country: USA

institute: SUNY-Downstate Health Sciences University

summary: The microphthalmia transcription factor Mitf has been shown to regulate B cell activation and tolerance. However, the underlying B cell-specific mechanisms responsible, and those that distinguish Mitf from closely related Mitf/TFE (MiT) transcription factors Tfe3, Tfeb, and Tfec, remain obscure. Two complementary mouse models of Mitf and MiT deficiency – the Mitfmi-vga9/mi-vga9 systemic loss-of-function mutation, and B-cell specific MiT family inactivation via transgenic expression of a trans-dominant negative (TDN) protein (TDN-B) – were used to identify MiT family candidate target genes and pathways. Both models displayed spontaneous splenomegaly coincident with elevated plasma cell numbers, autoantibody titers, and proteinuria. These abnormalities appeared dependent on T helper cells, but independent of other non-B cell intrinsic effects of systemic Mitf inactivation. MiT inactivation in B cells augmented aspects of lupus-like autoimmune disease on the C57BL/6-Faslpr/lpr background. In both models, RNAseq of ex vivo resting B cells showed transcriptional upregulation of genes that control cell cycle, germinal center responses, and plasma cell differentiation. Among the genes strongly upregulated in both models were Socs6, Isp53 (Baiap1), S1pR2, and IgG2b/c. Mitf null B cells, but not TDN-B cells, showed evidence of type I interferon dysregulation implicating non-autonomous B-lymphocyte mechanisms caused by systemic absence of Mitf. These studies clarify Mitf's role as 1) a key regulator of a B cell intrinsic germinal center program that influences self-tolerance through novel target genes, and 2) a regulator of systemic inflammatory processes that can impact the B cell microenvironment.

overall_design: To investigate the B cell-specific function of Mitf in comparison to other MiT family members, we employed two mouse models: TDN-B, expressing a dominant negative MiT inhibitor solely in B cells, and a germline recessive null Mitf mutation, Mitfmi-vga9/mi-vga9, which does not inhibit other MiT family proteins. To distinguish between B cell abnormalities due to Mitf inactivation and those influenced by T cell function, we utilized TDN transgenic mice (TDN-B/T). These mice express TDN in both B and T cells, leading to impaired T cell function. Subsequently, we performed RNAseq analysis on resting B cells from the different MiT/Mitf-impaired strains mentioned above. This analysis aimed to identify differentially regulated genes that might elucidate underlying mechanisms explaining the common and unique B cell abnormalities observed in each model.

first: Abhimanyu

last: Amarnani

first: Maria

last: Lopez-Ocasioa

first: Ramile

last: Dilshat


title: Deterministic nuclear reprogramming of mammalian nuclei to a totipotency-like state by Amphibian meiotic oocytes for stem cell therapy in humans

city: Cambridge

first: Ming-Hsuan

last: Wen

address: Tennis Court Road

country: United Kingdom

institute: Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge

summary: The ultimate aim of nuclear reprogramming is to provide stem cells or differentiated cells from unrelated cell types as a cell source for regenerative medicine. A popular route towards this is transcription factor induction, and an alternative way is an original procedure of transplanting a single somatic cell nucleus to an unfertilized egg. A third route is to transplant hundreds of cell nuclei into the germinal vesicle (GV) of a non-dividing Amphibian meiotic oocyte, which leads to the activation of silent genes in 24 hours and robustly induces a totipotency-like state in almost all transplanted cells. We apply this third route for potential therapeutic use and describe a procedure by which the differentiated states of cells can be reversed so that totipotency and pluripotency gene expression are regained. Differentiated cells are exposed to GV extracts and are reprogrammed to form embryoid bodies, which shows the maintenance of stemness and could be induced to follow new directions of differentiation. We conclude that much of the reprogramming effect of eggs is already present in meiotic oocytes and does not require cell division or selection of dividing cells. Reprogrammed cells by oocytes could serve as replacements for defective adult cells in humans.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
To investigate the clinical potential of Xenopus meiotic oocytes in reprogramming mammalian cells as novel stem cell resources, we performed nuclear transfer and reprogrammed mammalian cells for different durations.
We evaluated the transcriptional reprogramming of mammalian cells by Xenopus meiotic oocytes. We obtained RNA-seq data from transplanted human and mouse cells: three mouse cell types, embryonic stem cells, embryonic fibroblasts, and myoblasts, and one human cell type, neuroblastoma cells.


title: TP53 knock-down in cultured, starved human adipocytes

city: Graz

last: Prokesch

state: Styria

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology, and Embryology

country: Austria

institute: Medical University Graz

summary: The goal of this cell culture experiment was to validate in vivo data showing adipocyte p53-dependent changes of the immune cell landscape of visceral adipose tissue in obese mice that are interemittently fasted.

overall_design: Therefore, human SGBS preadipocytes were differentiated into mature adipocytes before TP53 was knocked down via siRNA transfection. twentyfour hours before harvest, the cells were switched to starvation medium (HBSS+HEPES). Control cells were transfected with non-targeting siRNA and also starved. Each group contains triplicate measurements.

first: Isabel

last: Reinisch


title: Circadian RNA-seq dataset in nhr-23 knockldown strain.

city: Setagaya-ku

first: Shingo

last: Hiroki

state: Tokyo

address: 2-1-6 Kamikitazawa

country: Japan

institute: Tokyo Metropolitan Instituite of Medical Sciences

summary: C. elegans were cultivated under temperature cycles for circadian entraiment. Then, we depleted NHR-23 using auxin-induced degron system, and sampled worms under constant(CC) condition every 2 h.

overall_design: Circadian transcriptome anaysis of nhr-23 knockdown and control condition, at 12 h time points with 2 replicates.


title: Efect of Rag1 3'-UTR deficiency on TCR repertoire diversity

status: Public on Jan 17 2024

city: Ulm

first: Marcin

last: Lyszkiewicz

address: Eythstr. 24

department: Dpt. of  Pediatrics and Adolescent Medicine

institute: Ulm University Medical Center

summary: To assess the impact of Rag1 3'-UTR deficiency on the TCR repertoire, we generated Rag1 3'-UTR -deficient mice from which we isolated CD4 T cells and subjected them to NGS sequencing.

overall_design: From the spleens of age-matched mice, 8 of which were WT or het and 4 of which were Rag1 3'-UTR KO, 0.7 million CD4 T cells were purified by FACS.   Technical details:  - Library preparation kit: Takara SMARTer Mouse TCR alpha-beta Profiling Kit  - Sample QC method: Qubit and Tapestation  - Library QC method: Qubit and Tapestation  - Instrument: Illumina MiSeq  - Read length: PE300"

first: Taku

last: Kureha

first: Vigo

last: Heissmeyer


title: Cell-type brain-region specific changes in prefrontal cortex of mouse model of alcohol dependence

city: Austin

first: Dayne

last: Mayfield

state: TX

address: 2500 Speedway

institute: The University of Texas at Austin

summary: The prefrontal cortex is a crucial regulator of escalation of alcohol drinking, dependence, and other behavioral criteria associated with AUD. Comprehensive identification of cell-type specific transcriptomic changes in alcohol dependence will improve our understanding of mechanisms mediating the escalation of alcohol use and will refine targets for therapeutic development. We performed single nucleus RNA sequencing (snRNA-seq) on ~150,000 single nuclei from the medial prefrontal cortex (mPFC) obtained from C57BL/6J mice exposed to the chronic intermittent ethanol exposure (CIE) paradigm which models phenotypes associated with alcohol dependence. Gene co-expression network analysis and differential expression analysis identified highly dysregulated co-expression networks in multiple cell types. Here, we present a comprehensive atlas of cell-type specific alcohol dependence related gene expression changes in the mPFC.

overall_design: 8 control samples, 6 alcohol-vapor exposed samples

first: Nihal

middle: A

last: Salem

first: Marisa

last: Roberto

first: R

middle: D


title: Pathogenicity and landscape of differential gene expression in mice orally infected with clinical coxsackievirus A6 (CA6)

city: beijing

first: lihong

last: zhang

address: panjiayuan

country: China

institute: , Chinese Academy of Medical Sciences and Comparative Medicine Center

summary: Hand, foot, and mouth disease (HFMD) is caused by more than 20 pathogenic enteroviruses belonging to the Picornaviridae family and Enterovirus genus. Since the introduction of the EV71 vaccine in 2016, the number of HFMD cases caused by EV71 has decreased. However, cases of infections caused by other enteroviruses, such as coxsackievirus A6 (CA6) and CA10, have been increasing accordingly. In this study, we used a clinical isolate of CA6 to establish an intragastric infection mouse model using 7-day-old mice to mimic the natural transmission route, by which we investigated the differential gene expression profiles associated with virus infection and pathogenicity. After intragastric infection, mice exhibited hind limb paralysis symptoms and weight loss, similar to those reported for EV71 infection in mice. The skeletal muscle was identified as the main site of virus replication, with a peak viral load reaching 2.31 × 107 copies/mg at 5 dpi and increased infiltration of inflammatory cells. RNA sequencing analysis identified differentially expressed genes (DEGs) after CA6 infection. DEGs in the blood, muscle, brain, spleen, and thymus were predominantly enriched in immune system responses, including pathways such as Toll-like receptor signalling and PI3K-Akt signalling. Our study has unveiled the genes involved in the host immune response during CA6 infection, thereby enhancing our comprehension of the pathological mechanism of HFMD.

overall_design: Collect blood, muscle, brain, spleen, and thymus samples from mice infected for 3 dpi, 5 dpi, 7 dpi for RNA-Seq analysis.

first: Lihong

last: Zhang

first: Wanjun

last: Peng

first: Jing

last: Wu

first: Xiaohui

last: Wei

last: Rong

first: Gengxin

first: Hekai

first: Xiaoyue

last: Ding

first: Binbin

last: Zhao

first: Jiangning

last: Liu


title: Effect of Cabergoline on Post-Lactational Involution and Long-Term Mammary Gland Behavior.

city: Salamanca

first: Jesús

last: Pérez Losada

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

summary: The aim of this study is to assess the impact of cabergoline on the intensity of short-term post-lactational involution and to explore long-term alterations in the epithelial dynamics of the glandular component in Brca1/P53-deficient mice. This study also delves into the transcriptomic changes associated with these processes. To further investigate the molecular changes occurring at these temporal points, RNA sequencing (RNA-seq) was conducted 1 day after post-lactation involution and again at 60 days.

overall_design: Multiparous Brca1/P53-deficient mice (Liu et al., 2007) with two pregnancies were administered intraperitoneal (IP) cabergoline at a dose of X on the same day of the second weaning. To study the short-term effect of cabergoline, organoids were generated 24 hours later, RNA was extracted, and RNA-seq (Novogene) was performed. Mice treated with cabergoline were compared with untreated controls. For the long-term effect study, the experiment was repeated in another group of mice. Organoids were generated 60 days post-weaning, including multiparous mice treated and untreated with cabergoline and age-equivalent nulliparous mice.

first: Natalia

last: García-Sancha

first: Roberto

last: Corchado-Cobos

first: Adrián

last: Blanco-Gómez

first: Diego

last: Alonso-López

first: Javier

last: de las Rivas

last: Pérez-Losada


title: Molecular reframing of fibroblasts during resolution of arthritis [scRNA 2]

first: Hashem

last: Mohammadian

overall_design: Cells from synovial joints were separated by fluorescence-activated cell sorting to isolate viable CD45- GR-1 cells or viable CD45- FAP+ Pdpn+ and processed for single-cell RNA sequencing using 10x Genomics Chromium Kits. Three libraries were generated for CD45- cells without enrichment for FAP+ Pdpn+ cells, each containing cells from four individual animals separated by antibody hashes directed against CD45 and B2m. Each of these three libraries contained a healthy wild-type reference (#4) and 3 arthritic hTNFtg197+ animals treated with Il23mc for 9 days (#1-3). Arthritic animals were either untreated or treated with TNF- or IL-17-inhibiting antibodies (one condition per library). An additional library was generated with viable CD45- FAP+ Pdpn+ cells containing five individually hashtag-tagged arthritic hTNFtg197+ animals treated with Il23mc for 9 days.

first: Simon

last: Rauber

first: Mario

last: Angeli

first: Maria

last: Raimondo

first: Hannah

last: Labinsky

first: Kai-Ting

last: Yang

first: Andreas

last: Ramming


title: Molecular reframing of fibroblasts during resolution of arthritis [RNA]

overall_design: Total RNA was isolated from arthroscopic synovial biopsies of patients with rheumatoid arthritis (RA; N=10) and psoriatic arthritis (PsA; N=8) and bulk RNA sequencing was performed.

last: Mohammdian

first: Megan

last: Hanlon

first: Ursula

last: Fearon

first: Douglas

last: Veale


title: RNA-seq PHIKZ-infected cells - early infection

city: Würzburg

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

institute: Würzburg University

summary: The 280-kB giant bacteriophage PHIKZ expresses hundreds of transcripts upon infection of Pseudomonas aeruginosa. To illuminate which transcripts are the very first and abundant ones, we extracted RNA after infection and sequenced the transcripts. The early expressed genes promise to be important for surpassing the host defence systems and to reprogram the host machinery towards phage replication. We discovered a number of transcripts that encode for proteins which we found in an independent study to be associated with large complexes. In essence, early genes represent exciting opportunities to filter for important factors that could also engage in large complexes.

overall_design: Pseudomonas aeruginosa PAO1 was grown in M9 minimal media with 0.4% glucose. Exponentially growing cells were infected at an MOI of 15 with PHIKZ in two replicates. At time points -2, 0, 2, 4, 6, 8, 10 min, we extracted RNA with hot phenol and sequenced the samples.

first: Milan

last: Gerovac


title: MicroRNA expression profiling of urine exosomes in children with congenital cytomegalovirus infection

status: Public on Jan 15 2024

city: Nagoya city

first: Yuka

last: Torii

address: Showa-ku Tsurumai-cho 65

institute: Nagoya University

summary: To investigate the extent of neuronal damage in patients with cCMV, exosomal miRNA expression in the urine obtained in early infancy was investigated in cCMV-infected infants and controls.

overall_design: miRNAs were subjected to microarray analysis in a cohort of 30 infants, including 11 with symptomatic cCMV (ScCMV), seven with asymptomatic cCMV (AScCMV), one with late-onset ScCMV, and 11 healthy controls (HC).

first: Yoshinori

last: Ito


title: Synthetic reversed sequences reveal default genomic states

first: Brendan

middle: R.

last: Camellato

state: New York

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU Langone Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or ‘noise’1,2,3,4. Characterizing default genome states could help understand whether pervasive transcriptional activity has biological meaning. Here we addressed this question by introducing a synthetic 101-kb locus into the genomes of Saccharomyces cerevisiae and Mus musculus and characterizing genomic activity. The locus was designed by reversing but not complementing human HPRT1, including its flanking regions, thus retaining basic features of the natural sequence but ablating evolved coding or regulatory information. We observed widespread activity of both reversed and native HPRT1 loci in yeast, despite the lack of evolved yeast promoters. By contrast, the reversed locus displayed no activity at all in mouse embryonic stem cells, and instead exhibited repressive chromatin signatures. The repressive signature was alleviated in a locus variant lacking CpG dinucleotides; nevertheless, this variant was also transcriptionally inactive. These results show that synthetic genomic sequences that lack coding information are active in yeast, but inactive in mouse embryonic stem cells, consistent with a major difference in ‘default genomic states’ between these two divergent eukaryotic cell types, with implications for understanding pervasive transcription, horizontal transfer of genetic information and the birth of new genes.

sample_organism:
Saccharomyces cerevisiae
Mus musculus

platform_organism:
Saccharomyces cerevisiae
Mus musculus

overall_design: Synthetic loci were characterized in yeast using ATAC-seq, RNA-seq, CAGE-seq, and CUT&RUN for H3K4me3, and in mESCs using ATAC-seq, RNA-seq, and CUT&RUN for H3K4me3, H3K27ac, H3K27me3, and RNAP2. HPRT1 and HPRT1R were characterized in yeast as episomes and following genomic integration. In mESCs, HPRT1 was characterized in mESCs at one integration site on chrX, and HPRT1R and HPRT1RnoCpG were characterized at two integration sites each, on chrX and chr3. Two independent clones were characterized for each synthetic locus integration, and two replicates were performed for each clone.


title: RNAseq analysis for tails, and ears from Ikbkb mut/mut and Ikbkb wt/wt mice

status: Public on Jan 09 2024

city: Acton

first: Zhi-Ping

last: Feng

state: ACT

address:
131 Garran Road, John Curtin School Of Medical Research Building (Level 3, Stage 1)
, The Australian National University

country: Australia

institute: JCSMR

summary: Loss-of-function mutations have provided crucial insights into the immunoregulatory actions of Foxp3+ regulatory T cells (Tregs). By contrast, we know very little about the consequences of defects that amplify aspects of Treg function or differentiation. We report that mice heterozygous for an Ikbkb gain-of-function (GoF) mutation develop psoriasis. Doubling the gene dose (IkbkbGoF/GoF) results in dactylitis, spondylitis, and characteristic nail changes, which are features of psoriatic arthritis. IkbkbGoF mice exhibit a selective expansion of Foxp3+ CD25+ Tregs of which a subset express IL-17. These modified Tregs were enriched at the inflamed tissues and spleen, and their transfer was sufficient to induce disease without conventional T cells. Single-cell transcriptional and phenotyping analyses of isolated Tregs revealed expansion of non-lymphoid tissue (tissue-resident) Tregs expressing Th17-related genes, Helios, tissue-resident markers including CD103 and CD69, and a prominent NF-kB transcriptome. Thus, IKK2 regulates tissue-resident Treg differentiation, and overactivity drives dose-dependent skin and systemic inflammation.

overall_design: By comparing transcriptome of tissues from Ikbkbmut/mut and Ikbkb+/+ mice, it revealed that tail and ear tissues from Ikbkbmut/mut mice with inflammation had the upregulation of psoriasis markers. By contrast, atopic dermatitis were lowly expressed and/or not significantly differentially expressed.

first: Chelisa

last: Cardinez

first: Yuwei

last: Hao

first: Bahar

last: Miraghazadeh

first: Matthew

middle: C

last: Cook


title: Differential gene expression at tick bite site

city: Chapel Hill

first: Shailesh

middle: Kumar

last: Choudhary

state: NC

address: 3300 Thurston Bldg., CB#7280

department: Medicine

institute: University of North Carolina at Chapel Hill

summary: Alpha-gal syndrome (AGS) is a delayed allergic response to red meat caused by the production of alpha-gal-specific IgE following certain tick bites. We designed this study to characterize the underlying immune response to tick bites associated with AGS. Our results suggest that Amblyomma americanum bites direct mouse immunity toward Th2 following the initial burst of proinflammatory response and facilitate host sensitization to the α-gal antigen.

overall_design: Tick bite site biopsies from sensitized and non-sensitized mice were subjected to mRNA gene expression analysis to assess the host immune response.

first: Scott

last: Commins

first: Shahid

last: Karim

first: Surendra

last: Sharma


title: Chromatin-enriched RNAs expression profiling by high-throughput sequencing of T47D-MTVL human breast cancer cells

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

institute: IBMB-CSIC

summary: Chromatin-enriched RNAs expression of T47D-MTVL human breast cancer cells expressing Dox-inducible shRNAs against multiple histone H1 variants (multiH1sh).

overall_design: Stable breast cancer-derived cell lines expressing an shRNA against multiple H1 variants in response to doxycycline (Dox) were grown for six days in the absence of Dox, RNA extracted, and high-throughput sequenced. Cell lines used: inducible shRNA against multiple H1 variants under Untreated conditions (i.e. no Dox-induced depletion of any H1).

first: A

first: M

last: Salinas

first: N

last: Serna


title: Cystatin from the helminth Ascaris lumbricoides (Al-CPI) upregulates mevalonate and cholesterol biosynthesis pathways and immunomodulatory genes in human monocyte-derived dendritic cells (moDC)

city: Stockholm

first: David

last: Brodin

address: Hälsovägen 7-9

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

summary: Background: Ascaris lumbricoides cystatin (Al-CPI) prevents development of allergic airway inflammation and colitis in mice models. It has been suggested that helminth derived cystatins inhibit cathepsins in dendritic cells (DC), but their immunomodulatory mechanisms are unclear. We aimed to analyze the transcriptional profile of human monocyte derived DC (moDC) upon stimulation with Al-CPI to elucidate target genes and pathways of parasite immunomodulation. Methods: moDC were generated from peripheral blood monocytes from six healthy human donors of Denmark, stimulated with 1 μM of Al-CPI and cultured for 5 hours at 37°C. RNA was sequenced using TrueSeq RNA libraries and the NextSeq 550 v2.5 (75 cycles) sequencing kit (Illumina, Inc). After QC, reads were aligned to the human GRCh38 genome using STAR. Differential expression was calculated by DESEq2 and expressed in fold changes (FC). Cell surface markers and cytokine production by moDC were evaluated by flow cytometry. Results: Compared to unstimulated cells, Al‐CPI stimulated moDC showed differential expression of 444 transcripts (|FC| ≥1.3). The top significant differences were in kruppel like factor 10 (KLF10, FC 3.3, PBH = 3 x 10-136 ), palladin (FC 2, PBH = 3 x 10-41 ) and the low-density lipoprotein receptor (LDLR, FC 2.6, PBH = 5 x 10-41 ). Upregulated genes were enriched in regulation of cholesterol biosynthesis by sterol regulatory element-binding proteins (SREBP) signaling pathways. Several genes in the cholesterol biosynthetic pathway showed significantly increased expression upon Al-CPI stimulation, even in the presence of LPS. Regarding the pathway of negative regulation of immune response, we found significant decrease in cell surface expression of CD86, HLA-DR and PD-L1 upon stimulation with 1 μM Al-CPI. Conclusion: Al-CPI modifies the transcriptome of moDC, increasing several transcripts encoding enzymes involved in cholesterol biosynthesis and SREBP signaling. Moreover, Al-CPI target several transcripts in the TNF-alpha signaling pathway influencing cytokine release by moDC. Several SMADs, members of the TGF-beta and the IL-10 families, including KLF10 were also This is a provisional file, not the final typeset article modified by Al-CPI stimulation. The regulation of the mevalonate pathway and cholesterol biosynthesis suggests new mechanisms involved in DC responses to helminth immunomodulatory molecules.

overall_design: To identify immunomodulatory mechanisms of Ascaris lumbricoides cystatin, we analyzed differentially expressed genes in human monocyte-derived dendritic cells stimulated with Al-CPI 0.1 uM, Al-CPI 1 uM, LPS, LPS + Al-CPI 0.1 uM, Al-CPI + LPS 1 uM, or LPS + ABF (n = 6 biological replicates per condition). moDCs grown in culture medium only was used as negative control.

first: Nathalie

last: Acevedo

first: Ana

last: Lozano

first: Josefina

last: Zakzuk

first: Kevin

last: Llinás-Caballero

first: Peter

last: Nejsum

first: Andrew

middle: R

last: Williams

first: Luis

last: Caraballo


title: Crosstalk between CD64+MHCII+ macrophages and CD4+ T cells mediates joint pathology during chikungunya

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary: Communications between immune cells are essential to ensure appropriate coordination of their activities. Here, we observed the infiltration of activated macrophages into the joint-footpads of chikungunya virus (CHIKV)-infected animals. Large numbers of CD64+MHCII+ and CD64+MHCII- macrophages were present in the joint-footpad, preceded by the recruitment of their CD11b+Ly6C+ inflammatory monocyte precursors. Regulation of these myeloid subsets was highly dependent on IFNγ and GM-CSF secreted by CHIKV-specific CD4+ T cells. Transcriptomic and gene ontology analyses of CD64+MHCII+ and CD64+MHCII- macrophages revealed 89 differentially expressed genes, including genes involved in T cell proliferation and differentiation pathways. Depletion of CD64+MHCII+ macrophages from CHIKV-infected mice reduced disease pathology, demonstrating that these cells play a pro-inflammatory role in CHIKV infection. Together, these results highlight the synergistic dynamics of immune cell crosstalk in driving CHIKV immunopathogenesis. This study provides new insights in the disease mechanism and offers opportunities for development of novel anti-CHIKV therapeutics.

overall_design: 10 samples, 5 samples per group. No reference control.

first: Fok-Moon

last: Lum

first: Yi-Hao

last: Chan

first: Teck-Hui

last: Teo

first: Etienne

last: Becht

first: Siti

last: Amrun

first: Karen

last: Teng

first: Siddesh

middle: V

last: Hartimah

middle: K

last: Yeo

first: Wearn-Xin

last: Yee

first: Anthony

middle: M

last: Torres-Ruesta

first: Siew-Wai

last: Fong

first: Julian

last: L Goggi

first: Evan

last: Newell

first: Laurent

last: Renia

first: Guillaume

last: Carissimo

first: Lisa

middle: F

last: Ng


title: Gene expression profiling by high-throughput sequencing of T47D-MTVL human breast cancer cells upon H1X knock-down

first: Albert

last: Jordan

type: Non-coding RNA profiling by high throughput sequencing

summary: Gene expression of T47D-MTVL human breast cancer cells expressing Dox-inducible shRNAs against histone H1X (H1Xsh).

overall_design: Stable breast cancer-derived cell lines expressing an shRNA against H1X in response to doxycycline (Dox) were grown for six days in the presence or absence of Dox, RNA extracted, and high-throughput sequenced. Cell lines used: inducible shRNA against H1X histone H1 variant.

first: A

first: M

last: Salinas

first: N

last: Serna


title: PD-L1 is an IFNγ-independent maturation marker on tumor-associated macrophages and associates with good clinical outcome in human breast cancer

status: Public on Jan 08 2024

city: Duarte

first: Peter

middle: P

last: Lee

state: CA

address: 1500 E. Duarte Rd.

department: Immuno-Oncology

institute: Beckman Research Institute at City of Hope

summary: ER+ breast cancer is an immune cold cancer. We utilized single-cell RNA-sequencing to learn the cell heterogeneity in ER+ breast tumor microenvironment.

overall_design: 4 primary ER+ breast tumors were collected and analyzed by single-cell RNA sequencing.

first: Weihua

last: Guo

first: Colt

last: Egelston

first: Raditya

last: Utama


title: Single-cell RNA sequencing of IkbkbV203I Tregs from spleen and bone marrow

first: Zhi-Ping

last: Feng

summary: Foxp3+ regulatory T cells (Tregs) typically suppress immune responses to prevent autoimmunity and aberrant inflammatory responses. In addition, tissue resident Tregs contribute to homeostasis and repair of non-lymphoid parenchyma. We generated a mouse model of a human inborn error of immunity arising from a gain-of-function missense mutation inIkbkband observed cell-intrinsic expansion of Tregs that maintained expression of Foxp3 and CD25. Remarkably, a subset of Tregs in this model expressed IL-17. We show by scRNA seq that NF-kB regulates specifically the expansion of a subset tissue Tregs, previously names skin NLT. Mice homozygous for theIkbkbmutation developed psoriasis, while homozygous mice also developed features of psoriatic arthritis. Skin NLTs were enriched at sites of pathology, and disease was dependent on the presence of pathological Tregs. Thus, we identify canonical NF-kB as a regulator tissue Treg differentiation and that this pathway can explain aberrant tissue healing responses that underpin psoriasis and psoriatic arthritis.

overall_design: FACS-sorted FOXP3-GFP+ Tregs from bone marrow and spleen of wild type and IkbkbV203I homozygous mice. Single gene expression libraries were preprared by the Biomolecular Resource Facility at JCSMR, ANU using Chromium Next GEM Single cell 5' kit v2 Dual Index (10X Genomics) according to manufacturer's instructions. The library was sequenced in S1 Flowcell with 2x50bp paired-end reads by NovaSeq 6000 sequencer (Illumina). The 10X Cell ranger package (10X Genomics, v6.0.1) was used to process data and align to mouse genome (mm10).

first: Chelisa

last: Cardinez

first: Matthew

last: Cook


title: Capturing the dynamic interactions between tumor and immune components of the tumor micro-environment is important for determining efficacy of anti-PD1 treatment [TBL]

city: Bangalore

first: Nandini

middle: Pal

last: Basak

state: Karnataka

address: Hosur road

department: R&D

country: India

institute: Farcast Biosciences

summary: RNA of tumor samples from 14 patients with  head and neck squamous cell carcinoma treated anti-PD1 was analyzed on the nCounter system using the Pan cancer IO360 panel

overall_design: Investigating baseline signature of anti-PD1 treated samples through ex vivo human TruTrumor histoculture platform.

last: Pal Basak

first: Biswajit

last: Das


title: Capturing the dynamic interactions between tumor and immune components of the tumor micro-environment is important for determining efficacy of anti-PD1 treatment

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

overall_design: Refer to individual Series


title: Human cytomegalovirus modulates mTORC1 to redirect protein translation within quiescently infected monocytes

city: Syracuse

first: Gary

last: Chan

state: NY

address: 750 East Adams Street

institute: SUNY Upstate Medical University

summary: Human cytomegalovirus (HCMV) has profound effect on gene expression during infection of monocytes. We performed RNA-seq and RIBO-seq to analyze the extend to which HCMV reshapes the transciptome and translatome of infected monocytes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCMV-infected, GMCSF, or MCSF treated monocytes of total mRNA and polysome-assoacted mRNA

first: Michael

middle: J

last: Miller


title: CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone mRNA processing

status: Public on Jan 06 2024

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited effective treatment options, potentiating the importance of uncovering novel drug targets. Here, we target Cleavage and Polyadenylation Specificity Factor 3 (CPSF3), the 3’ endonuclease that catalyzes mRNA cleavage during polyadenylation and histone mRNA processing. We find that CPSF3 is highly expressed in PDAC and is associated with poor prognosis. CPSF3 knockdown blocks PDAC cell proliferation and colony formation in vitro and tumor growth in vivo. Chemical inhibition of CPSF3 by the small molecule JTE-607 also attenuates PDAC cell proliferation and colony formation, while it has no effect on cell proliferation of non-transformed immortalized control pancreatic cells. Mechanistically, JTE-607 induces transcriptional read-through in replication-dependent histones, reduces core histone expression, destabilizes chromatin structure and arrests cells in the S-phase of the cell cycle. Therefore, CPSF3 represents a potential therapeutic target for the treatment of PDAC.

overall_design: For the knockdown experiment, Panc1 cells were infected with lentivirus harboring pLKO.1-shNTC (non-targeting control) and pLKO.1-shCPSF3 at 40% confluency. Polybrene was used to increase the efficacy of infection. After 72 hours, cells were selected with 2.5μg/ml puromycin. Cells were then collected for RNAseq.For drug treatment, Panc1 cells were treated with DMSO control or 10uM of JTE-607 for 24 hours then cells were collected for RNAseq.3 biological replicates were used for each condition.

first: Abdulrahman

last: Alahmari

first: Aditi

middle: H

last: Chaubey

first: Venkata

middle: S

last: Jonnakuti

first: Arwen

last: Tisdale

first: Carla

last: Schwarz

first: Abigail

last: Cornwell

first: Kathryn

middle: E

last: Maraszek

first: Emily

last: Paterson

first: Minsuh

last: Kim

first: Swati

last: Venkat

last: Cortes Gomez

first: Jianmin

last: Wang

first: Katerina

last: Gurova

first: Hari

last: Yalamanchili

last: Feigin


title: NINJ1 mediates inflammatory cell death, PANoptosis, and drives lethality during heat stress

status: Public on Jan 05 2024

city: Memphis

first: Thirumala-Devi

last: Kanneganti

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

summary: Innate immunity provides the first line of defense through key mechanisms, including pyrogen and cytokine production and cell death. While elevated body temperature during infection is beneficial, heat stress (HS) can lead to inflammation and pathology. Links between HS, cytokine release, and inflammation have been observed, but fundamental innate immune mechanisms driving pathology during HS remain unclear. Here, we use diverse genetic approaches to elucidate innate immune pathways in HS. Our results show that bacteria and LPS robustly increase inflammatory cell death, PANoptosis, during HS. NINJ1 is the key executioner of this cell death to release inflammatory molecules, independent of other pore-forming executioners. In an in vivo HS model, mortality is reduced by deleting NINJ1 and fully rescued by deleting key PANoptosis molecules. Our findings suggest that therapeutic strategies blocking NINJ1 or its upstream regulators to prevent PANoptosis may reduce the release of inflammatory mediators and benefit patients experiencing HS.

overall_design: The Mouse Brie CRISPR KO library carrying four gRNAs for each gene to cover the entire genome was a gift from David Root and John Doench (Addgene #73632 and #73633). The plasmid library was amplified and validated in the Center for Advanced Genome Engineering (CAGE) at St. Jude as described in the Broad GPP protocol, the only exception being the use of Endura DUOs electrocompetent E. coli cells. The St. Jude Hartwell Center Genome Sequencing Facility provided all NGS sequencing. Single end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina). Validation to check gRNA presence and representation was performed using calc_auc_v1.1.py (https://github.com/mhegde/) and count_spacers.py84. Viral particles were produced by the St. Jude Vector Development and Production laboratory using co-transfection of the lentiviral packaging plasmids along with the Brie library in the 293T cells. CRISPR KO screens were analyzed using Mageck-Vispr v0.5.7.  Cas9-expressing iBMDMs were generated from Cas9-GFP knock-in mice. A total of 300 × 10^6 Cas9-iBMDMs were distributed across twelve 15 cm2 tissue culture dishes at 25 × 10^6 cells per dish and infected with the Brie library of lentiviral particles, which carry four gRNAs for each gene to cover the entire genome, at an MOI of 0.3 in 25 ml of complete DMEM (DMEM supplemented with 10% heat-inactivated fetal bovine serum (HI-FBS; S1620, Biowest)) with 100 ml of LentiBOOST transduction reagent (SB-P-LV-101-02, Lentivirus Transduction Enhancer Solution, Siron Biotech). After infection, the iBMDMs were incubated for 24 h for efﬁcient transduction. These transduced cells were expanded with intermittent passaging to avoid overcrowding of the cells and to generate a sufﬁcient number of cells for the downstream whole-genome CRISPR screens. Two replicates of an adequate number of cells were used as control to obtain a representation (screen depth) of > 500 cells for each sgRNA of the library, and a similar number of cells from the same batch of virus preparation were stimulated with LPS priming for 2 h, then incubated at 43 °C for 1 h to induce heat shock (HS). After 24 h, the media was removed, and cells in the unstimulated and stimulated conditions were washed with PBS to remove the non-adherent dead cells, leaving only the adherent surviving cells for downstream analyses. The surviving cells from the unstimulated and LPS plus HS-treated samples were then subjected to CRISPR screen enrichment analysis. Total genomic DNA was isolated using NucleoSpin® Blood kits (Takara Bio Inc., USA; 740954 and 740950) and the concentrations of the isolated gDNA samples were measured using NanoDrop (Thermo Fisher Scientific, USA).  Next-generation sequencing (NGS) of the PCR-amplified, barcoded gRNAs was performed to quantitatively identify gRNAs that were enriched in the surviving pool of cells. Because the presence of a gRNA should delete the corresponding gene in that cell, enriched gRNAs were expected to represent genes where deletion rescues the cells from LPS plus HS-mediated cell death, suggesting they are positive regulators of the cell death..

first: Joo-Hui

last: Han

first: Rajendra

last: Karki

first: R

last: Malireddi

first: Raghvendra

last: Mall

first: Roman

last: Sarkar

first: Bhesh

last: Sharma

first: Jonathon

last: Klein

first: Harmut

last: Berns

first: Harshan

last: Pisharath

first: Shondra

last: Pruett-Miller

first: Sung-Jin

last: Bae


title: Th17 cells secrete TWEAK to trigger epithelial-mesenchymal transition and promote colorectal cancer liver metastasis (scRNA-seq)

city: Guangzhou

first: Lixia

last: Xu

address: 58 Zhongshan Road 2

institute: Sun Yat-sen University First Affiliated Hospital

summary: Liver metastasis is the leading cause of mortality in patients with colorectal cancer (CRC). Given the significance of both epithelial-mesenchymal transition (EMT) of tumor cells and the immune microenvironment in CRC liver metastasis (CRLM), the interplay between them could hold the key for developing improved treatment options. We employed multi-omics analysis of 130 samples from 18 synchronous CRLM patients integrated with external datasets to comprehensively evaluate the interaction between immune cells and EMT of tumor cells in liver metastasis. Single-cell RNA sequencing analysis revealed distinct distributions of non-malignant cells between primary tumors from patients with metastatic CRC (mCRC) and non-metastatic CRC, showing that Th17 cells were predominantly enriched in the primary lesion of mCRC. TWEAK, a cytokine secreted by Th17 cells, promoted EMT by binding to receptor Fn14 on tumor cells, and the TWEAK-Fn14 interaction enhanced tumor migration and invasion. In mouse models, targeting Fn14 using CRISPR-induced knockout or lipid-nanoparticle-encapsulated siRNA alleviated metastasis and prolonged survival. Mice lacking Il17a or Tnfsf12 (encoding TWEAK) exhibited fewer metastases compared to wild-type mice, while co-transfer of Th17 with tumor cells promoted liver metastasis. Higher TWEAK expression was associated with a worse prognosis in CRC patients. Additionally, CD163L1+ macrophages interacted with Th17 cells, recruiting Th17 via the CCL4-CCR5 axis. Collectively, this study unveils the role of immune cells in the EMT process and identifies TWEAK secreted by Th17 as a driver of CRLM.

overall_design:
In this study, single-cell analysis of more than 160,000 cells isolated from primary and metastatic colorectal cancer tissues, enabled us to unveil the interaction between tumor and immune cells in the context of liver metastasis in colorectal cancer.

***************************************************************
Please note that raw data have been deposited in the Genome Sequence Archive for Human under accession HRA005549
***************************************************************

first: Xin

last: Liu

first: Qingxia

last: Yang

first: Xinming

last: Song

first: Fang


title: Augmentation of a neuroprotective myeloid state by hematopoietic cell transplantation: Control Cohort

status: Public on Jan 04 2024

city: Stanford

first: Marius

middle: Marc-Daniel

last: Mader

address: 265 Campus Drive

institute: Stanford University

summary: Multiple sclerosis (MS) is an autoimmune disease associated with inflammatory demyelination in the central nervous system (CNS). Autologous hematopoietic cell transplantation (HCT) is under investigation as a promising therapy for treatment-refractory MS. Here we identify a reactive myeloid state in chronic experimental autoimmune encephalitis (EAE) that is surprisingly associated with neuroprotection and immune suppression. HCT in EAE mice leads to an enhancement of this myeloid state, as well as clinical improvement, reduction of demyelinated lesions, decrease in effector T cells, and amelioration of reactive astrogliosis reflected in reduced expression of EAE-associated gene signatures in oligodendrocytes and astrocytes. Further enhancement of myeloid cell incorporation into the CNS following a modified HCT protocol results in an even more consistent therapeutic effect corroborated by additional amplification of HCT-induced transcriptional changes, hence underlining myeloid-derived beneficial effects in the chronic phase of EAE. Replacement or manipulation of CNS myeloid cells thus represents an intriguing therapeutic direction for inflammatory demyelinating disease.

overall_design:
Single-nuclei RNA transcriptomes of spinal cords obtained from C57BL/6JN mice injected either with phosphate-buffered saline (PBS) or Complete Freund's Adjuvant (CFA) using 10x Genomics Drop-seq (v3.1).
Per library (PBS and CFA), 4 biological samples were pooled and each sample was hashtagged with oligos. The gex library has the RNAseq information, hto the oligo sequence information (needed for demultiplexing). Thus, the *.tar.gz processed data files are generated from both GEX and HTO raw files, and  are linked to the corresponding GEX sample records.

first: Alan

last: Napole

first: Danwei

last: Wu

first: Alexa

last: Scavetti

first: Olver

last: Hahn

first: Micaiah

last: Atkins

first: Aulden

middle: G

last: Foltz

first: Yohei

last: Shibuya

first: Tony

last: Wyss-Coray

first: Lawrence

last: Steinman

last: Wernig


title: Augmentation of a neuroprotective myeloid state by hematopoietic cell transplantation

summary: Multiple sclerosis (MS) is an autoimmune disease associated with inflammatory demyelination in the central nervous system (CNS). Autologous hematopoietic cell transplantation (HCT) is under investigation as a promising therapy for treatment-refractory MS. Here we show that the enhancement of a reactive myeloid response following HCT is neuroprotective in chronic experimental autoimmune encephalitis (EAE). Myeloid cells are the CNS population with the strongest transcriptional changes in chronic EAE, which are further promoted by HCT. HCT leads to clinical improvement, reduction in demyelinated lesions, and amelioration of reactive astrogliosis reflected in reduced expression of EAE-associated gene signatures in oligodendrocytes and astrocytes. Enhanced incorporation of circulation-derived myeloid cells into the CNS results in a more consistent therapeutic effect corroborated by additional amplification of HCT-induced transcriptional changes, underlining myeloid-derived beneficial effects in the chronic phase of EAE. Replacement or manipulation of CNS myeloid cells thus represents an intriguing therapeutic direction for inflammatory demyelinating disease.

overall_design: Single-nuclei RNA transcriptomes of spinal cords obtained from healthy control (control) or mice with experimental autoimmune encephalomyelitis (EAE) using 10x Genomics Drop-seq (v3.1). EAE mice were further divided in experimental groups with either no treatment, bone marrow transplantation, or bone marrow transplantation in combination with CSF1R inhibitor (PLX)

first: Oliver

first: Yongjin

last: Yoo

first: Ron

last: Danziger

first: Christina

last: Tan


title: Single-cell analysis of fetal human gonads (male and female) using 10X genomics

status: Public on Jan 02 2024

city: Leiden

first: Susana

last: Chuva de Sousa Lopes

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: Leiden University Medical Center

summary: Single cell transcriptomic analyses are increasingly being employed to study human developmental processes in the gonad to advance our understanding of human gametogenesis. However, to date, these analyses have primarily focused on germ cells, while the somatic niche has been largely overlooked. Moreover, a comparative transcriptomic analysis of both female and male early gonad development on the single cell level is currently lacking. We performed single cell RNA-Seq on whole human fetal gonads from first and second trimester, both from male and female. We define gene expression profiles, which include novel marker genes, of major gonadal somatic cell types and validate them on the protein level. We identify the genetic signature of early human male rete cells, both in male and in female gonads. Overall, our study provides an in-depth molecular characterization of both male and female somatic cell types in early fetal gonads.

overall_design: Four samples from 6 fetal gonads and one mesonephros sample from 3 male donors were used for single cell cluster analysis.

first: S

first: I

last: Moustakas

first: J

last: Taelman

last: Czukiewska

first: X

last: Fan


title: Single-cell Circle-seq unveils diversity and cell specificity of circular DNA in single cells

first: Jinxin

middle: Phaedo

last: Chen

address: Tomtebodavägen 23

department: MTC

institute: Karolinska Institutet

summary: Circular DNAs have been reported for decades and have been linked to tumorigenesis in humans. Previous sequencing-based genomic approaches capture circular DNA and average their readout over millions of cells, thereby losing insight into intercellular variation. Here, we introduce single-cell Circle-seq and show that the occurrence of most circular DNA species is stochastic, with some oncogene-containing large circular DNAs observed relatively frequently among different single cells. Despite this stochasticity, circular DNA is cell type-specific, which is concordant with H3K9me3 and H3K4me3 chromatin modification specificity of the corresponding cell lines. Moreover, we identify a cell type-specific circular DNA signature in cancer cells, which, we believe holds potential for early cancer diagnosis. In sum, our novel method single-cell Circle-seq dissects the randomness and cell type-specificity of circular DNAs at the single-cell level and uncovers the potential clinical application of circular DNA.

overall_design: Colo320DM, PC3, HeLa, K562 and HEK293T cells are mouth-pippeted into single tubes and subjected to scCircle-seq protocol.


title: On the genetic basis of tail-loss evolution in humans and apes [RNA-seq]

status: Public on Jan 01 2024

city: Cambridge

first: Bo

last: Xia

state: MA

address: 415 Main Street

institute: Broad institute

summary: The loss of the tail is one of the main anatomical evolutionary changes to have occurred along the lineage leading to humans and to the “anthropomorphous apes”. This morphological evolution in the ancestral hominoids has long been considered to have accommodated a characteristic style of locomotion and contributed to the evolution of bipedalism in humans. Yet, the genetic mechanism that facilitated tail-loss evolution in hominoids remains unknown. Primate genome sequencing projects have made possible the inference of causal links between genotypic and phenotypic changes, and enabled the search for hominoid-specific genetic elements controlling tail development. Here, we present evidence that an individual Alu element insertion in the genome of the hominoid ancestor may have contributed to tail-loss evolution. We demonstrate that this Alu element – inserted into an intron of the TBXT gene (also called T or Brachyury ) – pairs with a neighboring ancestral Alu element encoded in the reverse genomic orientation and leads to a hominoid-specific alternative splicing event. To study the effect of this splicing event, we generated multiple mouse models that express both full length and exon-skipped isoforms of mouse Tbxt, mimicking expression pattern of its hominoid ortholog TBXT. We found that mice expressing both Tbxt isoforms can exhibit a complete absence of the tail or a shortened tail, depending on the relative abundance of Tbxt isoforms expressed at the embryonic tail bud, supporting the notion that the exon-skipped transcript is sufficient to induce a tail-loss phenotype. We further noted that mice expressing the exon-skipped Tbxt isoform – both in heterozygous and homozygous forms – may develop a neural tube defect condition, which affects ~1/1,000 human neonates. We speculate that tail loss evolution along the hominoid lineage may be associated with an adaptive cost of potential neural tube defects that may continue to affect human health today.

overall_design: Total RNA isolated from day-1 in vitro differentiated mESC lines across wild-type, TbxtinsASAY/insASAY, TbxtΔexon6/+, and TbxtΔexon6/Δexon6 genotypes was used for bulk RNA-seq. Each genotype has two replicates. WT mESC lines are controls.

first: Weimin

last: Zhang

first: Guisheng

last: Zhao

first: Xinru

first: Jiangshan

last: Bai

first: Ran

last: Brosh

first: Aleksandra

last: Wudzinska

first: Emily

last: Huang

first: Hannah

last: Ashe

first: Gwen

last: Ellis

first: Maayan

last: Pour

first: Yu

first: Camila

last: Coelho

first: Yinan

last: Zhu

first: Alexander

last: Miller

first: Jeremy

last: Dasen

first: Matthew

middle: T

last: Maurano

first: Sang

middle: Y

last: Kim

first: Jef

middle: D

last: Boeke

first: Itai

last: Yanai


title: On the genetic basis of tail-loss evolution in humans and apes [Capture-seq]

first: Bo

last: Xia

summary: The loss of the tail is among the notable anatomical changes to have occurred along the evolutionary lineage leading to humans and to the “anthropomorphous apes”, with a hypothesized role in contributing to human bipedalism. Yet, the genetic mechanism that facilitated tail-loss evolution in hominoids remains unknown. Here, we present evidence that an individual insertion of an Alu element in the genome of the hominoid ancestor may have contributed to tail-loss evolution. We demonstrate that this Alu element – inserted into an intron of the TBXT gene – pairs with a neighboring ancestral Alu element encoded in the reverse genomic orientation and leads to a hominoid-specific alternative splicing event. To study the effect of this splicing event, we generated multiple mouse models that express both full-length and exon-skipped isoforms of mouse Tbxt, mimicking the expression pattern of its hominoid ortholog TBXT. We found that mice expressing both Tbxt isoforms can exhibit a complete absence of the tail or a shortened tail, depending on the relative abundance of Tbxt isoforms expressed at the embryonic tail bud, supporting the notion that the exon-skipped transcript is sufficient to induce a tail-loss phenotype. We further noted that mice expressing the exon-skipped Tbxt isoform may develop neural tube defects, a condition that affects ~1/1,000 neonates in human. Thus tail-loss evolution may have been associated with an adaptive cost of the potential for neural tube defects, which continue to affect human health today.

overall_design: The samples are designed to perform region-specific genomic DNA sequencing for genotyping the related cell lines and mouse models. The goal is to verify whether the specific genotype was correct, and whether any off target events occurred in the samples.

first: Weimin

last: Zhang

first: Guisheng

first: Xinru


title: On the genetic basis of tail-loss evolution in humans and apes


title: tsRNA sequencing of 3 primary tumor tissues and 3 metastastic tumor tissues of pancreatic cancer

city: sichuan

first: Qunli

last: Xiong

state: State...

address: sichuan

institute: sichuan university

summary: To identify and characterize differentially expressed tsRNA, we collected 3 primary tissues and 3 liver metastasis tissues in pancreatic cancer, and compared the tsRNA expression profiles between primary tissues and liver metastasis tissues in pancreatic cancer using tsRNA sequencing.

overall_design: We used 3 primary tissues of pancreatic cancer as control, and  3 liver metastasis tissues of pancreatic cancer as the *experimental group.


title: CLCF1/NF-κB signaling pathway regulates macrophage efferocytosis to ameliorate neurological damage and cognitive dysfunction following CO poisoning

city: Jinan

first: Xudong

last: Zhou

address: 4655 University Road, University Science and Technology Park, Changqing District, Jinan City, Shandong Province, China

department: First Clinical College

institute: Shandong University of Traditional Chinese Medicine

summary: Severe carbon monoxide (CO) poisoning can induce structural damage to the nervous system, leading to long-term cognitive dysfunction in patients. The proper termination of the inflammatory response caused by neuronal cell damage is a prerequisite for tissue repair. Macrophages can clear cell corpses/fragments caused by brain injury through efferocytosis and produce cytokines to coordinate immune responses, thereby promoting neuronal repair and regeneration. However, in the microenvironment of the nervous system affected by CO poisoning, the function of macrophages is inhibited. Our study found that CLCF1 can regulate the secretion of cytokines such as TNF-α, IL-1β, and IL-10 through the NF-κB signaling pathway, thereby affecting neuronal cell repair and regeneration.

overall_design: In a series of experiments, we first conducted knockdown or overexpression experiments on the CLCF1 gene, selecting two effective targets (Target a-126 and Target b-266) from three shRNAs designed for CLCF1. CLCF1 cDNA sequence was inserted into a lentiviral vector, transformed into DH5α E. coli, and plasmids were extracted using the EndoFree Plasmid Maxi Kit. Subsequently, a mixture of psPAX2, pMD2.G, and the transfer vector in OPTIMEM was transfected into 293T cells using PEI MAX. After 48 hours, lentiviruses were harvested by centrifuging at 800g for 10 minutes and then used to treat BMDM for 48 hours to assess the efficiency of knockdown or overexpression. Next, an acute CO poisoning model in rats was prepared using the method described by Li et al., where rats inhaled 1000 ppm of CO gas for 40 minutes followed by 3000 ppm for 20 minutes. The successful model was indicated by confusion and high HbCO concentration (>60%). Post-modelling, blood was drawn from the femoral artery and HbCO concentration was measured using a blood gas analyzer. In the lipid injection experiment in rats, chloroquine phosphate liposomes and PBS liposomes (control) were equilibrated to 25°C, and 0.5 mL of liposomes were drawn into a 3 mL syringe, adjusting the dosage according to body weight, and injected through the tail vein or retro-orbital sinus after anesthesia with isoflurane. Finally, in macrophage reconstitution, two days post chloroquine phosphate liposome treatment, rats were reconstituted with BMDM. Cells were detached using trypsin-EDTA, washed with PBS, resuspended, and then slowly injected into the rats through the tail vein or retro-orbital sinus.

first: Huiping

last: Song

first: Jingjing

last: He

first: Wei

last: Han

first: Qin

last: Li


title: Inflammation-dependent differentiation of two distinct regulatory T cell populations in the visceral adipose tissue shapes systemic metabolism [RNA-seq I]

city: Clayton

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

institute: Monash University

summary: Visceral adipose tissue (VAT) is an endocrine organ critical for energy storage and metabolic homeostasis. Its function, at least in part, is controlled by immune cells, including Foxp3+ regulatory T (Treg) cells, which restrain VAT inflammation and glucose intolerance. Here we uncover that the VAT harbours two distinct Treg cell populations, prototypical ST2+ Treg cells, that are enriched in males and depend on the cytokine IL-33 and the transcription factor PPAR and a previously uncharacterized population of VAT Treg cells that express the chemokine receptor CXCR3+, are enriched in females and depend on the transcription factor T-bet. We further show that the transcription factor GATA3 promoted differentiation of ST2+ VAT Treg cells and together with PPAR and IL-33 repressed the differentiation of CXCR3+ Treg cells. CXCR3+ VAT Treg cells developed from naïve Treg cells in a cytokine IFN- dependent manner. Finally, we demonstrate that ST2+ Treg cells promoted glucose tolerance, while CXCR3+ Treg cells limited VAT inflammation in a sex specific manner. This study for the first time establishes how inflammation determines the developmental trajectories of two functionally and molecularly distinct Treg cell types in the VAT.

overall_design: RNA sequencing of total VAT obtained from 27-33 week old male and female mice

first: Santiago

last: Valle Torres

first: Tarek

last: Elmzzahi

first: Melanie

last: Prout

first: Caitlin

last: Abbot

first: David

last: Chisanga

first: Teisha

last: Mason

first: Vanessa

last: Haynes

first: Kevin

last: Man

first: Joanna

last: Groom

first: Shaun

last: McColl

last: Watt

first: Graham

last: LeGros

first: Marc

last: Beyer

first: Ajithkumar

last: Vasanthakumar

first: Axel

last: Kallies


title: PRAMEL7 and CUL2 decrease NuRD stability to establish ground-state pluripotency

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

summary: Pluripotency is established in E4.5 preimplantation epiblast. Embryonic stem cells (ESCs) represent the immortalization of pluripotency, however, they only partially resemble the gene expression signature of developmental ground-state. Induced PRAMEL7 expression, a protein highly expressed in the ICM but lowly expressed in ESCs, reprograms developmentally advanced ESC+serum into ground-state pluripotency by inducing a gene expression signature close to developmental ground-state. However, how PRAMEL7 reprograms gene expression remains elusive. Here we show that PRAMEL7 associates with Cullin2 (CUL2) and this interaction is required to establish ground-state gene expression. PRAMEL7 recruits CUL2 to chromatin and targets for proteasomal degradation regulators of repressive chromatin, including NuRD complex. PRAMEL7 antagonizes NuRD-mediated repression of genes implicated in pluripotency by decreasing NuRD stability and promoter association in a CUL2-dependent manner. Our data link proteasome degradation pathways to ground-state gene expression, offering insights to generate in vitro models to reproduce the in vivo ground-state pluripotency.

overall_design:
RNA seq in mouse ESC

CHD4 ChIP seq in mouse ESC WT or everexpressing Pramel7 WT and Pramel7 DN.

first: Meneka

last: Rupasinghe

first: Cristiana

last: Bersaglieri

first: Deena

last: Pedrioli

first: Patrick

first: Martina

last: Panatta

first: Michael

middle: O

last: Hottiger

first: Paolo

last: Cinelli


title: Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF

first: Indranil

last: Sinha

address: The Wenner-Gren Institute

department: Department of Molecular Biosciences

institute: Stockholm University

summary: Stroma provides tissues with structural integrity and organization, but its capacity to shape myeloid cells is poorly understood. Here we quantify stromal response to inflammation in pediatric inflammatory bowel disease (IBD) and reveal subset-specific inflammatory responses across colon segments and intestinal layers. Using data from a murine dynamic gut injury model and human ex vivo transcriptomic/protein/spatial analysis, we found that PDGFRA+CD142-/low fibroblasts and monocytes/macrophages co-localize in the intestine. Primary human fibroblast-monocyte co-cultures showed that intestinal PDGFRA+CD142-/low fibroblasts foster monocyte transition to CCR2+CD206+ macrophages through granulocyte-macrophage colony-stimulating factor (GM-CSF). Monocyte-derived CCR2+CD206+ cells from co-cultures had a phenotype similar to intestinal CCR2+CD206+ macrophages from newly diagnosed pediatric IBD patients, with higher levels of PD-L1 and lower levels of GM-CSF receptor. The study depicts subset-specific changes in stromal response to inflammation and demonstrates the stromal potential to guide intestinal macrophage differentiation.

overall_design: Bulk seq on FACS sorted intestinal stromal cells, three different populations (X1-X3).

first: Egle

last: Kvedaraite

first: Magda

last: Lourda

first: Natalia

last: Mouratidou

first: Jan

middle: I

last: Henter

first: Mattias

last: Svensson


title: RNA-seq of Multilineage differentiating stress-enduring enriched cells (MECs) derived from MenSCs

city: Xinxiang

first: Han

last: Li

address: 601 Jinsui Road, Hongqi District, Xinxiang City, Henan Province

institute: Xinxiang Medical University

summary: The increasing interest in multilineage differentiating stress-enduring (Muse) cells within the field of regenerative medicine is attributed to their exceptional homing capabilities, prolonged viability in adverse conditions, and enhanced three-germ-layer differentiate ability, surpassing their parent mesenchymal stem cells. Given their abundant sources, non-invasive collection procedure, and periodic availability, human menstrual blood-derived endometrium stem cells (MenSCs) have been extensively investigated as a potential resource for stem cell-based therapies. However, there is no established modality to isolate Muse cells from MenSCs and disparity in gene expression profiles between Muse cells and MenSCs remain unknown. In this study, Muse cells were isolated from MenSCs by long-time trypsin incubation method. Muse cells expressed pluripotency markers and could realize trilineage differentiation in vitro. Compared with MenSCs, Muse cells showed enhanced homing ability and superior therapeutic efficacy in animal models of acute liver injury (ALI) and intracerebral hemorrhage (ICH). Furthermore, the RNA-seq analysis offers insights into the mechanism underlying the disparity in trypsin resistance and migration ability between Muse and MenSCs cells. This research offers a significant foundation for further exploration of cell-based therapies using MenSCs-derived Muse cells in the context of various human diseases, highlighting their promising application in the field of regenerative medicine.

overall_design: RNA was isolated from three batches of MenSCs and MECs and mRNA high-throughput sequencing was performed to detect the differential mRNA expression profiling of MenSCs and MECs.

first: Jinghui

last: Wei

first: Juntang

last: Lin


title: Seizure-induced LIN28A disrupts pattern separation via aberrant hippocampal neurogenesis

city: Seoul

first: Kyung-Ok

middle: for Aging and Metabolic

last: Cho

state: --- Select One ---

address: 222 Banpo-daero, Seocho-gu

department: Department of Pharmacology

country: South Korea

institute: The Catholic University of Korea

summary: Prolonged seizures can disrupt stem cell behavior in the adult hippocampus, an important brain structure for spatial memory. Here, using a mouse model of pilocarpine-induced status epilepticus (SE), we characterized spatiotemporal expression of Lin28a mRNA and proteins after SE. Unlike Lin28a transcripts, induction of LIN28A protein after SE was detected mainly in the subgranular zone, where immunoreactivity was found in progenitors, neuroblasts, and immature and mature granule neurons. To investigate roles of LIN28A in epilepsy, we generated Nestin-Cre::Lin28aloxP/loxP (cKO) and Nestin-Cre::Lin28a+/+ (WT) mice to block LIN28A upregulation in all neuronal lineages after acute seizure. Adult-generated neuron- and hippocampus-associated cognitive impairments were absent in epileptic LIN28A cKO mice as evaluated by pattern separation and contextual fear conditioning tests, respectively, while sham-manipulated WT and cKO animals showed comparable memory function. Moreover, numbers of hilar PROX1-expressing ectopic granule cells (EGCs), together with PROX1/NEUN+ mature EGCs, were significantly reduced in epileptic cKO mice. Transcriptomic analysis and immunohistochemical validation at 3 d post-pilocarpine provided potential LIN28A downstream targets such as serotonin receptor 4. Collectively, our findings indicate that LIN28A is a novel target for regulation of newborn neuron-associated memory dysfunction in epilepsy by modulating seizure-induced aberrant neurogenesis.

overall_design: To investigate the function of LIN28A in epilepsy-associated cognitive impairment, we generated Nestin-Cre::LIN28A loxP wildtype and conditional knockout mice. We then subjected these mice to sham- or pilocarpine-induced status epilepticus.


title: Capturing the dynamic interactions between tumor and immune components of the tumor micro-environment is important for determining efficacy of anti-PD1 treatment [Post Culture_Metadata]

first: Nandini

last: Basak

summary: RNA extracted from the post 72 hour cultured tumor samples from 31 patients with head and neck squamous cell carcinoma treated Nivolumab and Nivolumab+Ipilimumab was analyzed on the nCounter system using the Pan cancer IO360 panel.

overall_design: Investigating on-treatment signature of anti-PD1 treated samples and evaluating the effect of different drug treatments through ex-vivo human TruTrumor histoculture platform.

first: Biswajit

last: Das


title: G-quadruplex on Chromosomal DNA Negatively Regulates Topoisomerase 1 Activity [ChIP-seq]

city: Changsha

first: Ke-wei

last: Zheng

address: Lushan Road (S), Yuelu District

department: School of Medical Sciences

institute: Hunan University

summary: Human DNA topoisomerase 1 (Top1) is a crucial enzyme responsible for alleviating torsional stress on DNA during transcription and replication, thereby maintaining genome stability. Previous researches had found that non-working Top1 interacted extensively with chromosomal DNA in human cells. However, the reason for its retention on chromosomal DNA remained unclear. In this study, we discovered a close association between Top1 and chromosomal DNA, specifically linked to the presence of G-quadruplex (G4) structures. G4 structures, formed during transcription, trap Top1 and hinder its ability to relax neighboring DNAs. Disruption of the Top1-G4 interaction using G4 ligand relieved the inhibitory effect of G4 on Top1 activity, resulting in a further reduction of R-loop levels in cells. Additionally, the activation of Top1 through the use of a G4 ligand enhanced the toxicity of Top1 inhibitors towards cancer cells. Our study uncovers a negative regulation mechanism of human Top1 and highlights a novel pathway for activating Top1.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for G4P (an artificial G-quadruplex binding protein) in HCT116 cells.

first: Huiting

last: Liang

first: Jiangyu

last: Yan

first: Haojun

last: Yao

first: Zhiming

last: Xing

first: Lin

last: Liu

first: Yaoqing

last: Chen

first: Guorui

first: Jing

last: Huang

first: Yide

last: He

first: Kewei


title: G-quadruplex on Chromosomal DNA Negatively Regulates Topoisomerase 1 Activity [CUT&Tag]

overall_design: Cleavage under targets and tagmentation (CUT&Tag) for Topoisomerase 1 and R-loop in HCT116 cells.


title: G-quadruplex on Chromosomal DNA Negatively Regulates Topoisomerase 1 Activity

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

overall_design: Refer to individual Series


title: Single-cell and spatial profiling identify three response trajectories to pembrolizumab and radiation therapy in triple negative breast cancer

city: West Hollywood

first: Simon

last: Knott

state: California

address: 8687 Melrose Ave

department: BFG

institute: Cedars Sinai

summary: Cancer immunotherapy trials have produced encouraging results, but resistance remains a problem necessitating strategies to identify patients that benefit from immunotherapy alone or who require additional combinations like chemotherapy or radiotherapy. Here we employ single-cell transcriptomics and spatial proteomics to profile triple negative breast cancer biopsies taken before and after one cycle of pembrolizumab and after a second cycle of pembrolizumab given with radiotherapy. Non-responders lack immune infiltrate before and after therapy and exhibit minimal therapy-induced immune changes. Responding tumors form two groups that are distinguishable by a classifier prior to therapy, with one showing high MHC expression, evidence of tertiary lymphoid structures and displaying anti-tumor immunity before treatment. The other responder group resembles non-responders at baseline and mounts a maximal immune response after the combination therapy, which is characterized by cytotoxic T cell and antigen presenting myeloid cell interactions and is mirrored in murine breast tumors only after radiation.

overall_design: From November 2017 through June 2021, we enrolled 50 patients in our phase Ib/II trial entitled “Preoperative Combination of Pembrolizumab and Radiation Therapy in Patients with Operable Breast Cancer”03366844, clinicaltrials.gov). Patients with tumors greater than 2 cm with any nodal status as determined by imaging without metastatic disease were eligible for the trial. Patients received pembrolizumab at a dose of 200 mg, administered intravenously, on Day 1 and 21 and received three daily fractions of 8 Gray (Gy) stereotactic radiation to the breast tumor only between Day 21 and 28. Biopsies were taken prior to each treatment and patients were consented to analysis of the biopsies which included, but were not limited to, sequencing and immunohistochemistry. We utilized the E0771 orthotopic murine model of TNBC and performed a four-arm study consisting of control IgG treatment, anti-PD1 treatment, control IgG + radiation therapy, or anti-PD1 + radiation therapy. We then performed single-cell RNA-sequencing on CD45-positive cells isolated from tumors (n=2, with 2 mice pooled per replicate) from each of the arms.

middle: R

first: Stephen

middle: L

last: Shiao

first: Kenneth

last: Gouin III

first: Aagam

middle: B

last: Shah


title: Integrated analysis of lncRNA, miRNA and mRNA expression profiles reveal regulatory pathways associated with pig testis function

city: Yunnan Kunming

first: Huo

last: Jinlong

address: Jinhei Road 95

institute: Yunnan Agricultural University

summary: To investigate the the differences in expression and function of Diannan small-ear pigs,Duroc and Large white pigs testis.

overall_design: RNA-seq and small RNA-seq of Chinese indigenous Diannan small-ear (DSE) pigs and introduced Western Duroc (DU) and Large white (LW) pigs.

first: Jinlong

last: Huo

first: Yu

last: Sun

first: Pei

last: Wang

first: Zhipeng


title: RNA-sequencing of C2C12 myotubes after electrical stimulation under 5% O2 and 1% O2 and their non-stimulated controls

city: Lausanne

first: Chris

last: Donnelly

address: Quartier UNIL Centre

department: Institute of Sport Sciences

institute: University of Lausanne

summary: To investigate the effect of acute hypoxic exposure on the response of transcripts to electrically-evoked contractions in C2C12 myotubes

overall_design: RNA-seq


title: Inflammation-dependent differentiation of two distinct regulatory T cell populations in the visceral adipose tissue shapes systemic metabolism

first: Wei

last: Shi


title: Effect of methionine/choline deficient diet on liver and suprachiasmatic nucleus circadian transcriptome.

city: Manchester

first: Jean-Michel

last: Fustin

state: England

address: Faculty of Biology, Medicine and Health, , Oxford road

department: Centre for Biological Timing

institute: University of Manchester

summary: The feeding/fasting cycles controlled by our circadian clock impose great daily metabolic and physiological changes, and yet investigations into the consequences of metabolic deficiencies, either dietary or genetic, have often ignored the time of day or the circadian time of the animals or subjects. In addition, these deficiencies may themselves disrupt our circadian clock, causing secondary metabolic, physiological and behavioural disorders. Dietary methionine/choline deficiency in rodents is a common model for human non-alcoholic steatohepatitis, but methionine and choline are nutrients essential for many other processes beyond fatty acid synthesis in the liver, including biological methylations and 1-carbon metabolism, regulation of translation notably via the mTOR pathway, phospholipid synthesis, polyamine pathway and glutathione synthesis. We have previously shown that circadian rhythms in many organisms are highly sensitive to deficiency or excesses of 1-carbon metabolites. Using a methionine/choline deficient diet in mice, we illustrate the nutrigenomic crosstalk between circadian rhythms and 1-carbon metabolism. We show not only that circadian locomotor activity behaviour is profoundly, rapidly and reversibly affected by methionine/choline deficiency, but also that the effects of methionine/choline deficiency on gene expression and 1-carbon metabolites are dependent on circadian time, illustrating the importance of considering circadian rhythms in metabolic studies. This study also highlights the impact of what we eat, or don't, on our behaviour and biological rhythms.

overall_design: Raw RNA-seq reads from cDNA libraries prepared from liver and suprachiasmatic nucleus samples extracted every 4 hours during 24 hours from mice fed ad libitum with control or a methionine/choline free diet for 11 days. 2 male mice and 1 female mouse were used as three replicate for each time point.

first: Benjamin

last: Saer

first: Bharath

last: Ananthasubramaniam

first: Andrew

last: Hayes


title: Trophoblast syncytialization maintains the placenta-heart axis

first: In-Jeoung

last: Baek

address: 88, Olympic-ro 43-gil, Songpa-gu

institute: Asan Institute for Life Sciences

summary: The developmental connection between the placenta and certain embryonic organs, such as the heart, is associated with normal pregnancy and complications, but how the placenta governs embryonic cardiogenesis is poorly understood. Trophoblasts fuse into a multinucleated syncytiotrophoblast (SynT) layer, primarily consisting of a placental materno-fetal interface. We identify that endogenous progesterone immunomodulatory binding factor 1 (PIBF1) is essential for trophoblast differentiation and fusion into SynT in human trophoblasts and mouse placentas. Moreover, SynT-derived PIBF1 enables the communication between SynT and adjacent vascular cells to develop the vascular network in the primary placenta and further impacts the early development of the embryonic cardiovascular system in an endocrine manner. Thus, SynT-derived factors and SynT itself in the placenta may play crucial roles in the proper organogenesis of other organs in the embryo.

overall_design: To verify the effect of rsPIBF on the development of hHO, on day 8 (one day after hHO induction), cells were cultured in the hHO medium (control group), or hHO medium containing 200 ng/ml sPIBF (sPIBF group), with the medium replaced every two days until day 19-21.

first: Jong

last: Lee

first: Jung-Min

last: Yon

first: Globinna

last: Kim


title: Chromatin remodeler CHD8 is required for spermatogonial proliferation and early meiotic progression

status: Public on Dec 31 2023

city: Kanazawa

first: Kenta

last: Nitahara

state: Ishikawa

address: 13-1, Takaramachi

department: Department of Histology and Cellular Biology

institute: Kanazawa Univeristy

summary: Meiosis is a key step during germ cell differentiation, accompanied by the activation of thousands of genes through germline-specific chromatin reorganization. The chromatin remodeling mechanisms underpinning early meiotic stages remain poorly understood. Here we focus on the function of one of the major autism genes, CHD8, in spermatogenesis, based on the epidemiological association between autism and low fertility rates. Specific ablation of Chd8 in germ cells results in gradual depletion of undifferentiated spermatogonia as well as failure of meiotic double strand formation followed by arrest at meiotic prophase I and cell death. Transcriptional analyses demonstrate that CHD8 is required for extensive activation of spermatogenic genes in spermatogonia, necessary for spermatogonial proliferation and meiosis. CHD8 directly binds to promoters of genes crucial for meiosis, including H3K4me3 histone methyltransferase genes, meiotic cohesin genes, HORMA domain containing genes, synaptonemal complex genes, and DNA damage response genes. Through transcriptionally regulating the interaction of these meiosis-related genes, we argue that CHD8 contributes to meiotic double strand break formation and subsequent meiotic progression. Our study uncovers an essential role of CHD8 for the proliferation of undifferentiated spermatogonia and the successful progression of meiotic prophase I.

overall_design: RNA-seq analysis in Thy1+ and c-Kit+ spermatogonia from mice at 10 dpp (triplicate; Chd8 Ctrl vs. CKO), ChIP-seq analysis with antibody to CHD8 in unsorted testicular cells from mice at 12 dpp (triplicate; WT) and in Thy1+ and c-Kit+ spermatogonia from mice at 10 dpp (duplicate; Chd8 Ctrl vs. CKO), ChIP-seq analysis with antibody to H3K4me3 in c-Kit+ spermatogonia from mice at 10 dpp (duplicate; Chd8 Ctrl vs. CKO).

first: K

first: M

last: Nishiyama


title: ALKBH5 SUMOylation-mediated FBXW7 m6A modification regulates epithelial cells senescence during 1-nitropyrene-induced pulmonary fibrosis

city: hefei

first: Se

middle: Ruo

last: Li

state: anhui

address: furong road 678

department: Respiratory and Critical Care Medicine

institute: The Second Affiliated Hospital of Anhui Medical University


title: Methylation of histone H3 lysine 36 is a barrier for therapeutic interventions of head and neck squamous cell carcinomas

city: Maiami

first: Yuichiro

last: Nakata

address: 1501 NW 10th Ave

institute: University of Miami

summary: We show that  head and neck squamous cell carcinomas models with deficient H3K36me, induced by H3K36M expression, lead to epigenetic dysregulation.

overall_design: RNA-seq, ChIP-seq and Cut/Run in head and neck squamous cell carcinomas, such as FaDU, SCC25, Detroit562 and primary gingival keratinocytes.

first: Lucas

last: Caeiro

first: Mengsheng

last: Zha

first: Liliana

last: Garcia-Martinez

first: Stephanie

last: Stransky

first: Tong

last: Liu

first: Ho

last: Chan

first: John

last: Brabson

first: Diana

last: Domínguez

first: Yusheng

last: Zhang

first: Salvador

last: Aznar-Benitah

first: Peter

middle: W

last: Lewis

first: Luisa

last: Cimmino

first: Daniel

last: Bilbao

first: Simone

last: Sidoli

first: Zheng

first: Ramiro

last: Verdun

first: Lluis

last: Morey


title: ALKBH5 SUMOylation-mediated FBXW7 m6A modification regulates epithelial cells senescence during 1-nitropyrene-induced pulmonary fibrosis [Ribo-seq]

first: Se

last: Li

summary: Abstract：Our previous study found that 1-nitropyrene (1-NP) exposure evoked pulmonary fibrosis in mice. However, the exact mechanism remained elusive. We found that 1-NP induced telomere damage and cellular senescence in mice lungs and MLE-12 cells. Further research showed that 1-NP downregulated telomere repeat binding factor 2 (TRF2), and upregulated FBXW7. Mechanistically, 1-NP-caused TRF2 ubiquitination and proteasomal degradation depended on E3 ubiquitin ligase activity of FBXW7. Moreover, 1-NP upregulated FBXW7 m6A modification via an ALKBH5-YTHDF1-dependent manner. Further analysis found 1-NP promoted ALKBH5 SUMOylation and subsequent proteasomal degradation. Additionally, 1-NP evoked mitochondrial reactive oxygen species (mtROS) overproduction. Mito-TEMPO, a mitochondrial-targeted antioxidant, mitigated 1-NP-caused mtROS overproduction, ALKBH5 SUMOylation, FBXW7 m6A modification, TRF2 degradation and cellular senescence. Taken together, mtROS-initiated ALKBH5 SUMOylation and subsequent FBXW7 m6A modification is indispensable in TRF2 degradation and cellular senescence in pulmonary epithelial cells during 1-NP-induced pulmonary fibrosis. Our study provides target intervention measures towards 1-NP-evoked pulmonary fibrosis.

overall_design: The immortalized mouse lung epithelial (MLE)-12 cells, also known as AEC2 cells were from American Type Culture Collection (USA). MLE-12 cells were incubated using 4 mL of medium comprising 10% fetal bovine serum obtained from Thermo Scientific (MA, USA) in an incubator with 5% CO2. To investigate the influence of 1-nitropyrene (5 μM) on FBXW7 mRNA translation, the MLE-12 cells were cultured with or without 1-nitropyrene for 12h.


title: ALKBH5 SUMOylation-mediated FBXW7 m6A modification regulates epithelial cells senescence during 1-nitropyrene-induced pulmonary fibrosis [RNA-seq]


title: Gene expression profiles of cerebral cortice from sham- and X-ray-irradiated mice after photothrombotic strokes

city: Hong Kong

first: MA

last: Chi Him Eddie

address: Tat Chee Avenue, Kowloon, Hong Kong

department: Department of Neuroscience

country: Hong Kong

institute: City University of Hong Kong

summary: Current study aims to study the gene expression change after photothrombotic strokes, and the potential beneficial effects of whole-body X-ray irradiation on stroke mice

overall_design: Photothrombotic strokes were induced in the right hemisphere, and the cerebral cortices were harvested for RNA-seq from both sham- and X-ray-irradiated mice at day 1, 3 and 7 post-stroke

first: Chi

middle: H

last: Ma

first: Ngan

middle: P

last: Au

first: Tan

last: Wu

first: Xin

last: Wang


title: Gene expression of injured DRGs from WT and Fmn2-/- mice

summary: Current study aimed to identify the gene expression change that are unique in injured Fmn2-/- DRGs compared with WT mice.

overall_design: Sciatic nerve transection was performed on both WT and Fmn2-/- mice. Injured lumbar 4 and 5 (L4/5) DRGs directly supplying the sciatic nerve were harvested 5 days after injury from both genotypes for RNA-seq. A total of 12 samples were analyzed.

first: Ma

first: Au

last: Ngan Pan Bennett


title: Differential T-cell and monocyte responses in hepatocellular carcinoma treated with regorafenib plus nivolumab: an integrated clinical and biomarker analysis of the phase 2 RENOBATE trial

city: Seocho-gu

first: June-Young

last: Koh

state: Seoul

address: 2575 Nambusunhwan-ro,

institute: GENOME INSIGHT

summary: Regorafenib has anti-tumor activity in patients with unresectable hepatocellular carcinoma (uHCC) with potential immunomodulatory effects, suggesting that its combination with immune checkpoint inhibitor may have clinically meaningful benefits in patients with uHCC. The multicenter, single-arm, phase 2 RENOBATE trial tested regorafenib-nivolumab as front-line treatment for uHCC. Forty-two patients received nivolumab 480 mg every 4 weeks and regorafenib 80 mg daily (3-weeks-on/1-week-off schedule). The primary endpoint was the investigator-assessed objective response rate (ORR) per Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1. The secondary endpoints included safety, progression-free survival (PFS) and overall survival (OS). ORR per RECIST version 1.1 was 31.0%, meeting the primary endpoint. The most common adverse events were palmar-plantar erythrodysesthesia syndrome (38.1%), alopecia (26.2%) and skin rash (23.8%). Median PFS was 7.38 months. The 1-year OS rate was 80.5%, and the median OS was not reached. Exploratory single-cell RNA sequencing analyses of peripheral blood mononuclear cells showed that long-term responders exhibited T cell receptor repertoire diversification, enrichment of genes representing immunotherapy responsiveness in MKI67+ proliferating CD8+ T cells and a higher probability of M1-directed monocyte polarization. Our data support further clinical development of the regorafenib-nivolumab combination as front-line treatment for uHCC and provide preliminary insights on immune biomarkers of response. ClinicalTrials.gov identifier: NCT04310709 .

overall_design: Single-cell RNA sequencing was performed using peripheral blood mononuclear cells from early progressors (progressively increased tumor burden) and long-term responders (response/stable disease for ≥10 months) in RENOBATE trial.

first: Hyung-Don

last: Kim

first: Seyoung

last: Jung

first: Ho

last: Lim

first: Baek-Yeol

last: Ryoo

first: Min-Hee

last: Ryu

first: Hong

middle: J

last: Chon

first: Beodeul

last: Kang

first: Jung

last: Hong

first: Han

middle: C

last: Lee

first: Deok-Bog

last: Moon

first: Ki-Hoon

first: Tae

first: Jeong

middle: S

first: Richard

last: Finn

first: Changhoon

last: Yoo


title: MeDIP-seq profiles of mouse  ApcDHep hepatocytes   at day 6 vs wt hepatocytes

city: Paris

first: Angelique

last: Gougelet

address: 15 rue de l'école de médecine

country: France

institute: INSERM U1138

type: Methylation profiling by high throughput sequencing

summary: We analyzed the level of DNA methylation by MeDIPseq in hepatocytes isolated by collagenase perfusion from  Apclox/loxlivers, six days after injection of 2mg tamoxifen vs wt hepatocytes. Our aims was to study the impact of the beta-catenin on DNA methylation during the early steps of liver tumorigenesis

overall_design: DNA isolated from mouse ApcDHep hepatocytes  at day 6 vs wt hepatocytes by Phenol/chloroform  technique was immunoprecipitated by anti-5-methylcytosine (Active motif)

first: Angélique

first: Sabine

last: Colnot


title: METTL14-mediated N6-methyladenosine modification of Col17a1/Itgα6/Itgβ4 governs epidermal homeostasis

city: Shanghai

first: Qirui

last: Wang

state: Shanghai

address: 639 Zhi Zao Ju Road

department: Department of Plastic and Reconstructive Surgery

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


title: Functional annotation of genetic variants   using locally haploid human pluripotent stem cells

city: Berkeley

first: Dirk

last: Hockemeyer

address: 400 Li Ka Shing Center

department: Department of Molecular & Cell Biology

institute: University of California, Berkeley

summary: Mutations in the BRCA2 gene are associated with sporadic and familial cancer, cause genomic instability, and sensitize cancer cells to PARP inhibition. We have developed a human primary cell system to annotate variants in BRCA2 and to test the variants’ sensitivities to PARP inhibition. We engineered locally haploid human pluripotent stem cells (loHAPs) that contain a localized deletion encompassing one copy of BRCA2. Next, we characterized essential regions of the BRCA2 gene to identify permissive and loss-of-function mutations in hPSCs and differentiated fibroblasts, using CRISPR-Cas9 editing of the functional allele. Additionally, we used gene editing to directly test the function of individual amino acids, including clinical variants of uncertain significance in BRCA2, and identify alleles that are sensitive PARP inhibitors, a standard of care in BRCA2-deficient cancers. Collectively, our analysis demonstrates that loHAPs can facilitate detailed structure-function analysis of genes and the rapid functional evaluation of clinically-observed mutations.

overall_design: The CRISPR-mediated mutation tiling experients were designed to evaluate the scale and resolution that loHAPs can be employed to annotate BRCA2 function. Each sgRNA was individually delivered into 1 million hPSCs as RNP. After nucleofection, cells were combined into different pools by the position of sgRNA they received (6 sgRNAs in exon 2, 22 sgRNA in exon 27), then each cell pool was seeded onto three 15cm MEF dishes as biological triplicates. At least 0.3 million cells were replated for expansion or collected as genomic DNA every 7 days for 3 weeks. Drug sensitivity screening was started on day 21 with at least 0.3 million cells were used in each replicate, and cells were collected on day 28. At least 2µg phenol-chloroform extracted genomic DNA from each sample was used as a template in PCR amplification of the mutagenized region, then amplicons were purified, barcoded, and NGS-sequenced at depth >1 million reads per sample on PE250 NovaSeq or PE150 NextSeq2000. NGS reads were first processed using CRISPResso2 to trim off adapter sequences, aligned to a provided reference sequence, and filtered by quality.

first: Hanqin

last: Li


title: Identification a lncRNA/circRNA-miRNA-mRNA ceRNA network in Nasopharyngeal Carcinoma by deep sequencing and bioinformatics analysis

first: Pengfei

last: Zhang

address: Xiangya Road 87

institute: Xiangya Hospital, Central South University

summary: The study was designed to explore the ceRNA network in Nasopharyngeal Carcinoma

overall_design: Next-generation deep sequencing was performed in 7 cases of NPC tissues and 7 cases of normal tissues

first: Shilei

last: Liu