title: Investigating the role of NODAL signalling in preimplantation human embryos

status: Public on Nov 03 2024

city: Cambridge

first: Loke CTR

last: Bioinformatics

address: Downing Street

department: Physiology building

institute: Loke Centre for Trophoblast Research

summary: NODAL signalling is required to maintain pluripotency in human embryonic stem cells, by maintaining expression of transcription factor NANOG. We treated human blastocysts with NODAL signalling inhibitor A8301 and performed RNAseq on whole embryos to determine if NANOG expression and pluripotency in human embryos requires NODAL signalling activity.

overall_design: Human blastocysts were treated from 6 dpf for 24h with ACTIVIN/NODAL signalling inhibitor A8301 or volume matched DMSO. Whole blastocysts were collected for cDNA generation and RNA sequencing.

first: A

middle: S

last: Brumm

first: Kathy

last: Niakan

first: Afshan

last: McCarthy

first: Laura

last: Woods


title: Coupling of response biomarkers between tumour and peripheral blood in patients undergoing chemoimmunotherapy II

status: Public on Oct 31 2024

city: Crawley

first: Wee Loong

last: Chin

state: Western Australia

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

type: Expression profiling by high throughput sequencing

summary: Platinum-based chemotherapy in combination with anti-PD-L1 antibodies has shown promising results in mesothelioma. However, the immunological mechanisms underlying its efficacy are not well understood and there are no predictive biomarkers to guide treatment decisions. Here, we combine time-course RNA sequencing of peripheral blood mononuclear cells with pre-treatment tumour transcriptome data from the 54-patient single arm phase II DREAM study. Single cell RNA-seq and TCR-seq reveal CD8+ T effector memory (TEM) cells with stem-like properties are more abundant in peripheral blood of responders and this population expands upon treatment. These peripheral blood changes are linked to the transcriptional state of the tumour microenvironment. Combining information from both compartments, rather than individually, is most predictive of response. Our study highlights the complex, but predictive interactions between the tumour and immune cells in peripheral blood during the response to chemoimmunotherapy.

overall_design:
Peripheral blood samples were drawn at three timepoints. The first was taken at pretreatment baseline prior to dexamethasone pre-medication (Baseline). The subsequent two samples were taken before the second (C2D1) and third cycles (C3D1) of chemoimmunotherapy treatment. A window of up to 7 days was permitted before timepoint 0 bloods, and a window of up to 3 days before treatment administration was permitted before timepoint 1 and timepoint 2 bloods.
----------------------------
Authors state "raw data were not submitted due to patient privacy concerns".

first: Alistair

middle: R

last: Forrest


title: Comparison of the gene expression profile in aorta tissue between C57BL/6J and Apoe-knockout mouse

city: Guangzhou

first: Benrong

last: Liu

state: Guangdong

address: 250 Changgang Dong Road

country: China

institute: Guangzhou Institute of Cardiovascular Disease,the Second Affiliated Hospital, Guangzhou Medical University

summary: The physiological functions other than lipid metabolism of APOE may interfere with the research results of Apoe-knockout mice as atherosclerosis models. The elucidation of the molecular basis of the physiological functions of APOE other than lipid metabolism will help to make rational use of the Apoe-knockout mouse model. Therefore, our aim is to reveal the changes in aortic gene expression profile caused by Apoe-knockout. We used the second generation sequencing to detect the gene mRNA expression level in the aortic tissues of 5 C57BL/6J mice and 4 Apoe knockout mice. This will provide more clues for studying the physiological function of Apoe, and also remind researchers to pay special attention to the possible interference to the results when using Apoe-knockout mice as atherosclerosis models.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C57BL/6J mouse aorta and Apoe-knockout mouse aorta.

first: Shi-Ming

first: Lei

last: Fang

first: Wen-Chao

last: Ou


title: Conserved helical motifs in the Ikaros IDR mediate NuRD corepressor interaction and transcriptional repression [Spike-In ChIPseq]

status: Public on Oct 29 2024

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The transcription factor IKZF1/Ikaros is essential for B cell development, and recurrently mutated in human B-ALL.  Ikaros has been ascribed both activating and repressive functions via interactions with coactivator and corepressor complexes, but the relative abundance of Ikaros-associated coregulatory complexes and their contribution to Ikaros-mediated gene regulation are not well understood. To address this issue, we performed an unbiased identification of Ikaros-interacting proteins in pre-B cells, and found that Ikaros interacts overwhelmingly with corepressors and heterochromatin-associated proteins. Time-resolved analysis of transcription and chromatin state identified transcriptional repression as the immediate response to Ikaros induction. Transcriptional repression preceded transcriptional activation by several hours, and was accompanied by a rapid loss of chromatin accessibility and reduced levels of H3K27ac particularly at enhancers. Functional characterisation of intrinsically disordered regions in the Ikaros protein identified highly conserved helical motifs that mediate Ikaros association with the NuRD corepressor complex and contribute to the silencing of target genes in pre-B cells and antiproliferative functions of Ikaros in human B-ALL.

overall_design: We performed ChIP for KAP1 and H3K9me3 at early timepoints after Ikaros induction in pre-B cells to investigate the early impact of Ikaros induction on the KAP1 and H3K9me3 silencing pathways.

first: Tianyi

last: Zhang

first: Yi-Fang

last: Wang

first: Matthias

last: Merkenschlager


title: Conserved helical motifs in the Ikaros IDR mediate NuRD corepressor interaction and transcriptional repression [ChIP-seq]

overall_design: We performed ChIP for Ikaros, H3K27ac, and CHD4 at early timepoints after Ikaros induction in pre-B cells to investigate the early impact of Ikaros binding on CHD4 recruitment and H3K27ac levels.


title: RNA-seq Analysis of Enterococcus faecalis in Response to Surfactin Treatment

status: Public on Nov 08 2024

city: Taipei

first: KungTa

last: Lee

address: No. 1, Sec. 4, Roosevelt Rd

country: Taiwan

institute: National Taiwan University

summary: We found that biofilm formation ability of E. faecalis was impacted by surfactin. To further understand how E. faecalis responded to surfactin, we searched for differentially expressed genes between E. faecalis treated with or without surfactin using RNA-seq analysis.

overall_design: E. faecalis was cultured with or without surfactin at 37 °C for 1 hours. Their RNA was then extracted and analyzed.

first: Chunyi

last: Wu

first: Kungta


title: Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A

status: Public on Oct 27 2024

city: Chicago

first: Sarah

middle: A

last: Tersey

state: IL

department: Medicine

country: USA

institute: University of Chicago

summary: Prior to type 2 diabetes onset, β cells adapt to insulin resistance through compensation—a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that β cell compensation requires the activity of deoxyhypusine synthase (DHPS), which post-translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for β cell compensation, it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A, we used the following animal and cell-based models: transgenic zebrafish and inducible, β cell-specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS (and accumulate unhypusinated eIF5A) showed stunted exocrine pancreas growth at 3 days post-fertilization. Although, those injected with anti-eIF5A morpholinos (to deplete all eIF5A) showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented, these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly, following 4 weeks of high fat diet feeding and obesity, mice lacking total eIF5A in β cells had improved glucose tolerance compared to mice lacking DHPS in β cells, despite similar weight gain and insulin sensitivity. Taken together, our data provide evidence that DHPS deficiency and obesity conditions impair β cell function, inpart, from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which β cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A.

overall_design: Zebrafish embryos were injected with control, dhps, or eif5a1/2 morpholinos; 24 hours post fertilization embryoes were processed for RNA and sent to sequencing.

first: Raghavendra

last: Mirmira

first: Ryan

last: Anderson

first: Cara


title: RNA sequencing of Streptococcus salivarius strains from oral cavities of Korean subjects

status: Public on Nov 10 2024

city: Seoul

first: Jae-Hyung

address: 26 Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: Kyung Hee University

summary: To investigate the subspecies level differences in the expression profiles of Streptococcus salivarius strains, we conducted the RNA sequencing analysis of Streptococcus salivarius strains.

overall_design: Streptococcus salivarius strains were grown in BHI broth under the same conditions (OD600 = 0.5–0.7, 37°C, anaerobic chamber).

first: Ji-Hoi

last: Moon


title: Modulation of tumor drug sensitivity and inflammatory signaling through CMTM4

status: Public on Nov 07 2024

city: New York

first: Won-Min

last: Song

state: New York

address: One Gustave L. Levy Place, Box 1123

institute: Icahn school of medicine at Mount Sinai

summary: Although the association between inflammation and cancer development has been recognized, how inflammation affects the outcomes of immunotherapy and chemotherapy hasn’t yet been well evaluated. In this study, we found that CKLF-like MARVEL transmembrane domain-containing member 4 (CMTM4) was highly expressed in multiple human and murine cancers. Loss of CMTM4 significantly reduced tumor growth and impaired NFB, mTOR, PI3K/Akt pathway activation. Interestingly, we found that CMTM4 can regulate epidermal growth factor (EGF) signaling post-translationally by promoting EGFR recycling and preventing its degradation through Rab proteins. Consequentially, CMTM4 knockout promoted response sensitivity of human tumor cells to EGFR inhibitors. Importantly, CMTM4 knockout tumors stimulated with EGF significantly decreased their production of inflammatory cytokines including G-CSF, leading to decreased recruitment of polymorphonuclear myeloid-derived suppressor cells and thus, a less suppressive tumor-immune-environment. Therapeutically, siRNA-liposome targeting CMTM4 reduced tumor growth in vivo and prolonged animal survival. Furthermore, CMTM4 knockout enhance immune checkpoint blockade or chemotherapy to reduce tumor growth. These data suggest that CMTM4 represents a novel target to inhibit tumor inflammation and improve immune response and drug sensitivity.

overall_design: To investigate the gene expression profile affected by CMTM4, we generated stable CMTM4 KD cell line with shRNA. Then we perform RNA-seq with control and CMTM4 KD cells.

first: Kyeongah

last: Kang

first: Yuan Shuo

first: Bin

first: Shu-Hsia

last: Chen


title: Injury response of human lens epithelial cells ex-vivo

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

summary: This study investigates the response of human lens epithelial cells to mechanical injury.  Human geriatric lenses obtained from cadaver eyes from donated to an eye bank for research were subject to in-vitro capsulotomy mimicking the injury sustained during cataract surgery. The anterior capsule was dissected using a curvilinear capsulorhexis technique, and central lens epithelial cells attached to the patch of anterior capsule (Rhexis) were immediately stabilized in RNAlater. The fiber cells were then removed, and the cortical fibers were immediately stabilized in RNA later.  The remaining equatorial lens epithelial cells  attached to the capsular bag from one eye were stabilized in RNA later immediately while the equatorial lens epithelial cells from the other eye were cultured for  24 hours then stabilized in RNAlater.

overall_design: 6 Lenses from 3 human donors, each donor provided 2 lenses. For each donor, one lens capsule was analyzed at zero hours (lens "a") and the second lens capsule was analyzed at 24 hours (lens "b").   One patch of anterior capsule (Rhexis), and one sample of cortical fibers were analyzed at 0 hours for each donor, the corresponding lens is marked "a" or "b".

first: Samuel

middle: G

last: Novo

first: Adam

middle: P

last: Faranda

first: Mahbubul

middle: H

last: Shihan

first: Yan

first: Justin

last: D'Antin

first: Ralph

last: Michael

middle: K


title: Host-microbiota interaction is regulated by autonomous skin-intrinsic germinal centers [BCR]

status: Public on Oct 23 2024

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

summary: Host symbiosis with its microbiota can represent a liability for the host. Indeed, while these communities of microbes broadly control host physiology, the microbiota can also promote inflammation and represent a source of local and systemic infection. The unique strategies employed by each tissue to maintain and control coexistence with commensal microbes remain largely unclear. Here we uncover that, within the skin, host protection from its microbiota depends on the remarkable ability of the skin to act as an autonomous lymphoid organ. Notably, an encounter with a new skin microbe is associated with two parallel responses both, under the control of Langerhans cells. On one hand, skin commensal promotes the development of classical germinal centers within secondary lymphoid organs leading to IgG1 and IgG3 responses. On the other hand, microbial colonization also leads to the development of tertiary lymphoid organs that can locally sustain and mature IgG2b and IgG2c responses. The ability of the skin to develop as a lymphoid compartment is at least in part mediated by the ability of the local Treg pool to convert into T follicular helper cells accumulating within organized tertiary lymphoid organs surrounding the hair follicles. Remarkably, skin autonomous production of antibodies is sufficient to control both microbial colonization within the skin as well as subsequent infection with the same commensal. Collectively these results reveal a profound compartmentalization of humoral responses between the lymph nodes and the skin. Further, this work uncovers a previously unappreciated function for the skin as a compartment able to develop, in the absence of inflammation, powerful and long-lived antibody responses independently of secondary lymphoid organs.

overall_design: bulk BCR sequencing was performed on samples from skin, spleen, and lymph nodes


title: AgRP neurons shape the sperm small RNA payload

status: Public on Oct 22 2024

city: Barcelona

first: Arnaud

last: Obri

address: C/ del Rosselló, 149

country: Spain

institute: IDIBAPS

type: Non-coding RNA profiling by high throughput sequencing

summary: Dietary habits and obesity in fathers imprint upon progeny through epigenetic signals carried by sperm RNA. By activating hypothalamic AgRP neurons in mice to mimic obesity's effects, we observed significant alterations in sperm tsRNAs, miRNAs, and rsRNAs. These changes, particularly in tsRNAs, mirror those seen with short-term high-fat diets, suggesting a shared upstream regulatory mechanism involving AgRP neurons that influence metabolic epigenetic inheritance.

overall_design: We aimed to replicate the AgRP neuronal state that will occur in obesity. To achieve this, we employed Designer Receptors Exclusively Activated by Designer Drugs (DREADD) .We bilaterally injected an activator DREADD adeno-associated viral (AAV-hM3Dq-mCherry) vector into the arcuate nucleus of the hypothalamus (ARH) in both AgrpCre/+ and Agrp+/+. The DREADD ligand, Clozapine-N-Oxide (CNO), was administered to AgrpCre/+ (activated) and Agrp+/+ (control) mice in the absence of food. Four hours post-administration, mature sperm was harvested from the caudae epididymides, and RNAs were extracted from the sperm. These RNAs were then used to prepare a small non-coding RNA (sncRNA) library, which was subsequently sequenced.

first: Iasim

last: Tahiri

first: Sergio

last: Llana

first: Francisco

last: Díaz-Castro

first: Marc

last: Claret


title: Identification of chromatin states in mouse testicular germ cells using CUT&Tag

status: Public on Oct 21 2024

city: Wuhan

first: Weihua

last: Wang

address: No.8, Sanjiaohu Rd

institute: Jianghan University

summary: Here we describe successful implementation of CUT&Tag sequencing technology for profiling of protein-DNA interactions in mouse testicular germ cells. By performing CUT&Tag sequencing using antibodies against XAP5/XAP5L, we identified numerous common binding sites for both proteins. This work highlights the significant overlap in the genomic targets of XAP5 and XAP5L.

overall_design: CUT&Tag experiments were performed in postnatal day 16 (P16) mouse testicular germ cells for XAP5, and in P56 mouse testicular germ cells for XAP5L, according to the manufacturer’s protocol using Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme).

first: Junqiao

last: Xing

first: Xiqi

last: Zhang


title: Acarbose improves obesity-induced insulin resistance and immune homeostasis by directly regulating gut microbiota and macrophages inflammation

status: Public on Nov 04 2024

city: Beijing

first: Shimeng

last: Zheng

address: Yongan Road

department: Beijing Clinical Research Institute

institute: Beijing Friendship Hospital

summary: Acarbose was reported to alleviate obesity-induced insulin resistance IR and regulate the gut microbiota community; however, the critical microbial signaling metabolites and the host targets associated with the metabolic benefits of acarbose remains unknown. In this study, we reported that acarbose treatment was able to significantly improve high fat diet (HFD) induced IR and inflammation states in adipose tissue and intestine by influencing the survival and pro-inflammatory function of M1 macrophages. Furthermore, we revealed that acarbose exert anti-inflammatory effects partly in a gut-microbiota dependent manner by microbiota clearance experiments. 16S rRNA sequencing and metabolomic researches identified that acarbose could enhance the proliferation of propionic acid (PA)-producing Parasutterella excrementihominis (PARA). As the vital metabolic mediator, PA regulated the pro-inflammatory and anti-inflammatory balance of M1/M2 macrophages by GPR4/NLRP3 signaling pathway. In addition, in vivo studies of NBD fluorescence labeled acarbose verified that acarbose directly inhibited the macrophage inflammatory response in adipose tissue via being captured by intestinal macrophage due to the aggravated intestinal permeability in HFD mice. We also validated this result in bone-marrow derived macrophage (BMDM) and human macrophages in vitro. Mechanistically, acarbose may suppressed mTOR signaling pathway and the following autophagy/mitochondrial function of M1 macrophage by activating GPR120, thereby reducing its survival and the secretion of pro-inflammatory cytokines. In conclusion, these findings presented that acarbose improved obesity-induced IR by maintaining beneficial microbiota and direct inhibited action on M1 macrophages.

overall_design: Control sample: M1 bone-marrow derived macrophage; Exprimental sample: Acarbose treated M1 bone-marrow derived macrophage

first: Xiaohui

last: Li

first: Guangyong

last: Sun

first: Dong


title: Distinct features of a peripheral T-helper subset that drives the B-cell response in dengue virus infection

city: New Delhi,

first: Asgar

last: Ansari

state: Delhi

address: Aruna Asaf Ali Marg, Jawaharlal Nehru University,

country: India

institute: National Institute of Immunology,

summary: Dengue virus-induced humoral immunity can increase the risk of severe disease, but the factors influencing this response are poorly understood. Here, we investigated the contribution of CD4+ T cells to B-cell responses in human dengue-infection. We identified a dominant peripheral PD1+ T-cell subset that accumulated in severe patients and could induce B-cell differentiation via IL21-related pathway. Single-cell RNA-seq analyses was performed to reveal the heterogeneity in PD1+ cells. This subsequently revealed the coexistence of subsets with ‘helper’ (IL21+) or ‘cytotoxic’ characteristics. The IL21+ subset displayed a distinct clonotypic and transcriptomic signature than Tfh-cells and persisted as a memory in lymph-nodes. Notably, we showed that the IL21+ subset seems to majorly drive the extrafollicular B-cell responses in dengue. Our study established the peripheral IL21+ subset as a potential determinant of the humoral response to dengue-virus infection. These findings provide important insights into the T-cell-dependent regulation of humoral responses and can inform the design of effective dengue vaccines.

overall_design: ICOS+CD38+ CD4+ T cells from cryopreserved PBMCs of three adult acute dengue patients were FACS-sorted and processed for single-cell RNAseq and TCRseq analysis using 10x Genomics platform.

first: Shilpa

last: Sachan

first: Jatin

last: Ahuja

first: Sureshkumar

last: Venkadesan

first: Bhushan

last: Nikam

first: Debasisa

last: Mohanty

first: Manish

last: Soneja

first: Nimesh

last: Gupta


title: A CHD8-TRRAP axis facilitates MYC and E2F target gene regulation in human neural stem cells.

status: Public on Nov 06 2024

city: Rotterdam

first: Raymond

last: Poot

address: Wytemaweg 80

department: Cell Biology

country: Netherlands

institute: Erasmus MC

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

overall_design: Refer to individual Series


title: Mapping Decidualization Resistance in Former Severe Preeclampsia Patients at Multi-Omic Levels

status: Public on Oct 16 2024

city: Paterna

first: Raul

last: Pérez-Moraga

state: Valencia

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

institute: Carlos Simon Foundation, INCLIVA Health Research Institute

summary: Endometrial decidualization resistance (DR) is implicated in various gynaecological and obstetric conditions. Employing a multi-omic strategy, we unraveled the cellular and molecular characteristics of DR in patients that have suffered severe preeclampsia (sPE). Morphological analysis unveiled significant glandular anatomical abnormalities, confirmed histologically. Single-cell RNA sequencing (scRNA-seq) of endometrial samples from sPE cases (n=11) and controls (n=12) revealed sPE-associated shifts in cell composition, manifesting as a stromal mosaic state characterized by proliferative stromal cells (MMP11, SFRP1+) alongside IGFBP1+ decidualized cells, with concurrent epithelial mosaicism and a dearth of epithelial-stromal transition associated with decidualization. Cell-cell communication network mapping underscored aberrant crosstalk among specific cell types, implicating crucial pathways such as endoglin and WNT. Spatial transcriptomics in a replication cohort validated DR-associated features. Laser capture microdissection/mass spectrometry in a second replication cohort corroborated several scRNA-seq findings, notably the absence of stromal to epithelial transition at a pathway level, indicating disrupted response to steroid hormones, particularly estrogens. These insights shed light on potential molecular mechanisms underpinning DR pathogenesis in the context of sPE.

overall_design:
A total of 23 non-pregnant women who had a previous pregnancy were enrolled in this study for single-cell RNA-Sequencing analysis. From those, 12 were women with a healthy previous pregnancy as control cases and 11 were women diagnosed with Severe Preeclampsia in their last pregnancy clinically classified based the ACOG guidelines: high blood pressure (systolic > 160 or diastolic > 100 mmHg) or thrombocytopenia, impaired liver function, progressive renal insufficiency, pulmonary edema, or the inset cerebral or visual disturbances. Endometrial biopsies were collected during the late secretory phase of the menstrual cycle (1 to 3 days before menstruation) and tissue were segmented in different portions, one of the were embedded in paraffin to obtain histological sections for the spatial transcriptomics approach, other section were included in OCT for the laser capture and mass spectrometry approach and another portion was processed to obtain the cell isolation that will be used to the single-cell RNA sequencing using 10X genomics technologies. The maternal parameters were recruited in the Supplementary table 1. A two tailed Student’s T-test was applied between sPE and Control variables based on the normal distribution of data.

*** Submitter states "we are unable to upload the raw sequences to a public database, as they originate from living donors. Once the publication is approved for release, we will proceed to upload the raw sequence data to a managed access database"***

first: Irene

last: Muñoz-Blat

first: Raúl

first: Nerea

last: Castillo-Marco

first: Teresa

last: Cordero

first: Ana

last: Ochando

first: Sheila

last: Ortega

first: Marcos

last: Parrás

first: Rogelio

last: Monfort

first: Elena

last: Satorres-Perez

first: Blanca

last: Novillo

first: Alfredo

last: Perales

first: Matthew

last: Gormley

first: Beatriz

last: Roson

first: Susan

last: Fisher

first: Carlos

last: Simón

first: Tamara

last: Garrido-Gómez


title: An obesogenic FTO allele causes accelerated development, growth and insulin resistance in human skeletal muscle cells

status: Public on Oct 15 2024

first: lu

last: guang

address: 1 Beichen West Road

department: Institute of Zoology

institute: Chinese Academy of Sciences

summary: Human GWAS have shown that obesogenic FTO polymorphisms correlate with lean mass, but the mechanisms have remained unclear. It is counterintuitive because lean mass is inversely correlated with obesity and metabolic diseases. Here, we use CRISPR to knock-in FTOrs9939609-A into hESC-derived tissue models, to elucidate potentially hidden roles of FTO during development. We find that among human tissues , FTOrs9939609-A most robustly affect human muscle progenitors’ proliferation, differentiation, senescence, thereby accelerating muscle developmental and metabolic aging. An edited FTOrs9939609-A allele over-stimulates insulin/IGF signaling via increased muscle-specific enhancer H3K27ac, FTO expression and m6A demethylation of H19 lncRNA and IGF2 mRNA, with excessive insulin/IGF signaling leading to insulin resistance upon replicative aging or exposure to high fat diet. This FTO-m6A-H19/IGF2 circuit may explain paradoxical GWAS findings linking FTOrs9939609-A to both leanness and obesity. Our results provide a proof-of-principle that CRISPR-hESC-tissue platforms can be harnessed to resolve puzzles in human metabolism.

overall_design: To model the influence of FTOrs9939609-A on human developmental fates, we used CRISPR/Cas9-based prime editing of FTOrs9939609-TT hESCs, followed by induction of their differentiation into myotubes.

first: Lu

last: Guang

first: Shilin

last: Ma

first: Ziyue

last: Yao

first: Dan

last: Song


title: Coupling of response biomarkers between tumour and peripheral blood in patients undergoing chemoimmunotherapy

first: Wee Loong

last: Chin

overall_design:
Peripheral blood samples were drawn at three timepoints. The first was taken at pretreatment baseline prior to dexamethasone pre-medication (Baseline). The subsequent two samples were taken before the second (C2D1) and third cycles (C3D1) of chemoimmunotherapy treatment. A window of up to 7 days was permitted before timepoint 0 bloods, and a window of up to 3 days before treatment administration was permitted before timepoint 1 and timepoint 2 bloods.

***************************************************************
raw data were not submitted due to patient privacy concerns.
***************************************************************

first: Lesterhuis

last: W Joost

first: Cook

last: Alistair


title: KLF13 promotes SLE Pathogenesis by modifying chromatin accessibility of key proinflammatory cytokine genes [RNA-seq]

city: dallas

first: Shaheen

last: Khan

state: texas

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Although significant progress has been achieved in elucidating the genetic architecture of systemic lupus erythematosus (SLE), identifying genes underlying the pathogenesis has been challenging. The NZM2410-derived lupus susceptibility Sle3 locus is associated with T cell hyperactivity and activated myeloid cells. However, candidate genes associated with these phenotypes have not been identified. Here, we narrow the Sle3 locus to a smaller genomic segment (Sle3k) and show that mice carrying Sle3k and Sle1 loci developed lupus nephritis. We identify Klf13 as the primary candidate gene upregulated in Sle3k mice and demonstrate that Klf13 upregulation is associated with genome-wide transcription changes resulting in higher levels of proinflammatory cytokines, enhanced T cell activation, and hyperresponsiveness of myeloid cells. Correspondingly, Klf13 –/– mice display striking repression of genes involved in mediating immune activation, including key proinflammatory cytokines/chemokines. Furthermore, Klf13 –/– mice show profound dysregulation in cytokine signaling pathways in myeloid cells in response to toll receptor ligands, thus revealing a key role of KLF13 in modulating myeloid cell function. Klf13 upregulation is associated with increased production of RANTES, a key chemokine in lupus nephritis, in activated T cells and the kidneys of lupus-prone mice. In sum, our findings reveal Klf13 as a key gene in the Sle3 interval in mediating lupus pathogenesis that may have implications in the rational design of new therapies for SLE and other autoimmune/inflammatory diseases.

overall_design: We isolated CD4 T cells, Bone marrow derived macrophages (BMDMs) and Bone marrow derived dendritic cells (BMDCs) from different mouse strains and performed RNA-seq analysis to compare genome-wide expression changes.

first: Edward

last: Wakeland


title: Immune microenvironment of premenopausal estrogen receptor-positive/HER2-negative advanced breast cancer in response to treatment of Pembrolizumab, exemestane, and leuprolide

status: Public on Oct 28 2024

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

institute: National Taiwan University Hospital

summary: We evaluated the efficacy of combining pembrolizumab (anti-PD1 antibody), exemestane (nonsteroidal aromatase inhibitor), and leuprolide (gonadotropin-releasing hormone agonist) for 15 patients with ER+/HER2− premenopausal MBC who had failed one to two lines of hormone therapy without chemotherapy.

overall_design: We profiled the immune-related genes from pre- and post-treatment samples.

first: I-Chun

last: Chen

first: Yen-Shen

last: Lu


title: Conserved helical motifs in the Ikaros IDR mediate NuRD corepressor interaction and transcriptional repression [bulk RNAseq]

first: LMS

last: Bioinformatics Core

overall_design: To investigate the role of Ikaros in transcriptional regulation, we performed a nascent chromatin-associated RNA-seq timecourse over 24h following Ikaros induction in pre-B cells.

first: Tianyi

last: Zhang

first: Yi-Fang

last: Wang

first: Matthias

last: Merkenschlager


title: Conserved helical motifs in the Ikaros IDR mediate NuRD corepressor interaction and transcriptional repression [ATACseq]

overall_design: To investigate the impact of the TF Ikaros on chromatin accessibility in pre-B cells, we performed a timecourse of ATAC-seq before and at early timepoints (30m,1h,2) after Ikaros induction.


title: Sequence determinants of intron-mediated enhancement learned from thousands of random introns

city: Cambridge

first: Emma

middle: Joanna Katharina

last: Kowal

email: emmajkkowal@gmail.com, ejkk@mit.edu

state: MA

address: 21 St Mary Road Apt 2

department: Biology

institute: MIT

summary: Spliceosomal introns are a ubiquitous feature of eukaryotic genes, whose presence often boosts the expression of their host gene, a phenomenon known as intron-mediated enhancement (IME). IME has been noted across diverse genes and organisms, but remains mysterious in many respects. For example, how does intron sequence affect the magnitude of IME? In this study, we performed a massively parallel reporter assay (MPRA) to assess the effect of varying intron sequence on gene expression in a high-throughput manner, using tens of thousands of synthetic introns with natural splice sites and randomized internal sequence. We observe that most random introns splice efficiently and enhance gene expression as well as or better than fully natural introns. Nearly all introns stimulate gene expression ~eight-fold above an intronless control, at both mRNA and protein levels, suggesting that the primary mechanism acts to increase mRNA levels. IME strength is positively associated with splicing efficiency and with the intronic content of poly-uridine stretches, which we confirm using reporter experiments. In sum, this work elucidates sequence determinants of IME from tens of thousands of random introns.

overall_design:
We constructed a plasmid library with two reporter genes, GFP and dTomato, in which the GFP carries a single intron in its 5'UTR, comprising natural splice sites flanking 160nt of random nucleotide sequence. We also included an intron-specific barcode in the downstream exon of GFP as well as in the dTomato in order to normalize GFP expression to dTomato expression from each barcode. We integrated this library into the genome of a specialized HEK293T cell line with a recombinase landing pad (Khandelia et al 2011) to create a stable transgenic pool of cells.
From these cells we extracted total RNA and generated an amplicon library of GFP and dTomato 5'UTRs using gene-specific RT-PCR, which we sequence to measure steady-state mRNA abundance and splicing status, in ten biological replicates.
We also measure effects on protein expression via GFP and dTomato fluorescence intensity by iteratively selecting cells with the most extreme fluorescence ratios and performing the same RNA-seq protocol on these subpopulations to identify which introns they contain. This was done for the top 10% most green and most red cells, in three successive stages, in two replicate trajectories.
Finally, we synthesized and tested a second smaller library with mutated versions of introns from the original library to validate the effect of polyU content on intron-mediated enhancement.

middle: J

first: Yuta

last: Sakai

first: Michael

last: McGurk

first: Zoe

last: Pasetzky

first: Christopher

middle: B

last: Burge


title: Protective effects of red filtered light during IVF: transcriptomic analysis of murine embryos and embryo-derived EVs

city: Budapest

first: Bence

last: Nagy

state: Pest

address: Nagyvárad tér 4

department: Institute of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

summary: Background: Light exposure of embryos during assisted reproduction affects embryo quality and implantation capacity in a wavelength dependent manner. We investigated the molecular mechanism of these light-induced changes through the comparative analysis of gene expression and regulatory miRNA profile of murine embryos cultured in dark environment and those exposed to white- or red filtered light. miRNA sequencing was used to assess the role of embryo-derived extracellular vesicles in the endometrium-embryo dialogue. Methods: In vitro cultured mouse embryos (3.5 dpc) were exposed to white or red filtered light. After 24 hours mRNA and miRNA content of the embryos as well as the miRNA content of embryo-derived extracellular vesicles were isolated and RNA-sequencing was performed. Differential expression analysis and functional enrichment analysis were used for evaluating the transcriptome results.Results: Light exposure caused transcriptomic changes in the embryos. White light upregulated apoptotic pathways, while red filtered light gave rise to the activation of regeneration pathways, including DNA repair mechanisms. Embryo-derived extracellular vesicles enclosed wavelength dependently unique miRNA cargos the target genes of which play a role in embryo implantation. In conclusion: white light upregulates apoptotic pathways, at both the transcriptome and regulatory miRNAs levels. Red filtration partially counterbalances these negative effects by shifting the cellular processes towards regeneration, including DNA repair mechanisms. Extracellular vesicles of light exposed embryos play a role in blastocyst-decidua communication through the horizontal transfer of regulatory miRNAs. Our data prove that light exposure during in vitro fertilization modifies cell function that might affect the outcome of implantation.

overall_design:
To investigate the effect of light exposure on the transcriptome of murine embryos, we have estabilished three treatment groups, embryos treated with white light, filtered red light and control.
We have sequenced the mRNA and miRNA isolated from the embryos and miRNA isolated from the embryo derived extracellular vesicles
We have performed differential expression analysis on the samples and functional enrichment to identify the significantly changed molecular pathways.

first: Zoltán

last: Bognár

first: Tímea-judit

last: Csabai

first: Nóra

last: Fekete

first: Edit-Irén

last: Buzás

first: Árpád-Ferenc

last: Kovács

first: Júlia

last: Szekeres-Barthó

first: Éva

last: Pállinger


title: Coupling of response biomarkers between tumour and peripheral blood in mesothelioma patients undergoing chemoimmunotherapy

city: Crawley

first: Wee Loong

last: Chin

address: 35 Stirling Hwy

institute: University of Western Australia

summary: Platinum-based chemotherapy in combination with anti-PD-L1 antibodies has shown promising results in mesothelioma. However, the immunological mechanisms underlying its efficacy are not well understood and there are no predictive biomarkers of clinical outcomes to guide treatment decisions. Here, we combine time-course RNA sequencing of peripheral blood mononuclear cells with pre-treatment tumour transcriptome data from the 54-patient cohort in the single arm phase II DREAM study. The identified immunological correlates are predictive of response and provide further evidence for the additive nature of the interaction between platinum-based chemotherapy and PD-L1 antibodies. Our study highlights the complex, but predictive interactions between the tumour and immune cells in peripheral blood during the response to chemoimmunotherapy.

overall_design: Fifty-four participants were recruited to the DREAM clinical trial of durvalumab plus chemotherapy in malignant mesothelioma. Tumour biopsy tissue and matched bloods were collected. To analyse tumour tissue, archival FFPE tissue (blocks or slides) was obtained from participating hospital sites and mRNA was extracted. We retrieved mRNA of sufficient quantity and quality to perform gene expression analysis using the nanoString nCounter platform from 46 of these patients. The nanoString PanCancer IO 360 kit provided gene expression data for 770 immune-oncology related genes. Differential expression of genes were compared between two patient groups based on Progression at 6 months (PFS6) for the purpose of identifying predictive biomarkers. Samples were run as a single replicate, with each nCounter casette containing a manufacturer's QC Standard sample plus up to 11 experimental samples.

first: Alistair

middle: M

last: Cook


title: Conserved helical motifs in the Ikaros IDR mediate NuRD corepressor interaction and transcriptional repression.

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

institute: MRC London Institute of Medical Sciences


title: EZH2-mediated macrophage-to-myofibroblast transition contributes to calcium oxalate crystal-induced kidney fibrosis

status: Public on Oct 26 2024

first: Fan

last: Cheng

state: China

address: Wuhan ,Hubei,China

institute: Department of Urology, Renmin Hospital of Wuhan University

summary: Long-term nephrocalcinosis leads to kidney injury, fibrosis, and even chronic kidney disease (CKD). Reports have proved macrophages can transition into myofibroblasts(MMT), leading to collagen deposition and fibrosis in CKD. However, the effect of MMT in calcium oxalate (CaOx) crystal-induced kidney fibrosis remains unclear. This study demonstrated that histone methyltransferase EZH2-mediated MMT contributes to CaOx crystal-induced fibrosis. We identified abundant MMT cells by immunofluorescence and flow cytometry in kidney tissues of patients with CaOx-related CKD, CaOx nephrocalcinosis mouse model, and CaOx-treated RAW264.7 macrophage cells. A high level of MMT cell infiltration was associated with a decline in the glomerular filtration rate in CaOx nephrocalcinosis patients. Clodronate Liposomes-mediated macrophage depletion attenuates calcium oxalate crystal-induced fibrosis in mice. Subsequently, transcriptomic and single-cell sequencing revealed that EZH2 was highly expressed in kidneys with CaOx deposition, especially in macrophages. Further study demonstrated that EZH2 inducible knock-out or pharmacological inhibition by GSK-126 attenuated MMT and renal fibrosis in vivo and in vitro. Mechanistically, ChIP and transcriptomic sequencing showed that EZH2 inhibition reduced the enrichment of H3K27me3 on the DUSP23 gene promoter and elevated DUSP23 expression. The Co-IP and molecular docking analysis showed that DUSP23 mediated the dephosphorylation of pSMAD3 (S423/425), the key regulator of MMT. In addition, DUSP23 over-expression could alleviate SMAD3-mediated MMT. Thus, our study found that EZH2 promotes kidney fibrosis by meditating MMT via the DUSP23/SMAD3 pathway in nephrocalcinosis.

overall_design: To explore the differentially expressed genes between kidney stone mice and the control mice, RNA-Seq was performed. Male C57BL/6 mice were treated with 120 mg/kg of glyoxylic acid intraperitoneal injection once a day for 12 days to construct the CaOx kidney stone model. The control mice were treated with equal volume of saline. The kidney tissues were harvested. Differential expression genes were identified between the two groups.

first: Weimin

last: Yu

first: Ting

last: Rao

first: Xiangjun

last: Zhou

first: Yuqi

last: Xia

first: Zehua

last: Ye


title: Double and single stranded detection of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore sequencing

city: Bath

first: Adele

last: Murrell

address: Claverton Down

department: Life Sciences Department

institute: University of Bath

type: Methylation profiling by high throughput sequencing

summary: 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are modified versions of cytosine in DNA with roles in regulating gene expression. Using whole genomic DNA from mouse cerebellum, we have benchmarked 5mC and 5hmC detection by Oxford Nanopore Technologies sequencing against other standard techniques. In addition, we assessed the ability of duplex base-calling to study strand asymmetric modification. Nanopore detection of 5mC and 5hmC is accurate relative to compared techniques and opens new means of studying these modifications. Strand asymmetric modification is widespread across the genome but reduced at imprinting control regions and CTCF binding sites in mouse cerebellum. This study demonstrates the unique ability of nanopore sequencing to improve the resolution and detail of cytosine modification mapping.

overall_design: Cerebellum tissues were obtained from two 8-week-old female C57BL/6J mice, from which high molecular weight genomic DNA was extracted using the QIAGEN MagAttract HMW DNA Kit (QIAGEN, 67563). Cerebellar gDNA was sheared using a Covaris g-TUBE (Covaris, 520079) to a target length of 8 kb. Whole genome sequencing (WGS) libraries were prepared in duplicate for each biological replicate, using the Ligation Sequencing Kit V14 standard protocol (Oxford Nanopore Technologies, SQK-LSK114) with reagents from the NEBNext Companion Module for Oxford Nanopore Technologies Ligation Sequencing (New England Biolabs, E7180S). 150 ng of each sample was loaded onto PromethION (Oxford Nanopore Technologies, PRO-SEQ048) flow cells (Oxford Nanopore Technologies, FLO-PRO114HD). All sequencing runs were manually stopped after 72 hours.

first: Dominic Oliver

last: Halliwell

first: Floris

last: Honig

first: Stefan

last: Bagby

first: Sandipan

last: Roy


title: KLF13 promotes SLE Pathogenesis by modifying chromatin accessibility of key proinflammatory cytokine genes [ATAC-seq]

first: Shaheen

last: Khan

overall_design: We isolated CD4 T cells, Bone marrow derived macrophages (BMDMs) and Bone marrow derived dendritic cells (BMDCs) from different mouse strains and performed ATAC-seq  analysis

first: Edward

last: Wakeland


title: The translational repair pathway is a frequent synthetic lethal target in cancer

status: Public on Oct 14 2024

city: South San Francisco

first: Sarah

last: Kongpachith

state: CA

address: 1000 Gateway Blvd

institute: AbbVie

summary: Synthetic lethality exploits the genetic vulnerabilities of cancer cells enabling, a targeted, precision approach to treat cancer. Synthetic lethal discovery approaches have led to clinical successes of PARP inhibitors and the progression of several next-generation therapeutic targets such as WRN, USP1, PKMYT1, POLQ, and PRMT5 into the clinic. To date, however, most discovery efforts in the synthetic lethal space have focused on DNA repair.  Here, we show, for the first time in humans, a frequent synthetic lethal interaction between two complexes of the translational repair pathway, PELO/HBS1L and the superkiller (SKI) complex. In distinct genetic contexts, either in 9p21.3 (FOCAD) deleted or MSI-H tumors, we found that phenotypically destabilized SKI complex leads to dependence on the PELO/HBS1L ribosomal rescue complex. We estimate that 20% of all tumors have a destabilized SKI complex. The concomitant loss of PELO in a SKI destabilized tumor drives an unfolded protein stress response, cell cycle arrest, and robust tumor growth inhibition. Furthermore, we demonstrate that the loss of HBS1L phenocopies PELO loss, presenting a second potential therapeutic target within the rescue complex. Our results indicate that PELO/HBS1L represent novel therapeutic targets whose dependence converges upon SKI complex destabilization, a common phenotypic biomarker in diverse genetic contexts and a significant patient population.

overall_design: To understand the impact of PELO or HBS1L loss in SKI destabilized lines, we performed RNAseq on MIAPACA2 PELO and HBS1L dox-inducible knockout systems. Samples were prepped in triplicate at 48 and 96 hours post induction of PELO or HBS1L knockout.

first: Vivian

last: Prindle

first: Adam

last: Richardson

first: Kimberly

last: Sher

first: Kaitlin

last: Kentala

first: Dong

last: Chen

first: Deborah

last: Widomski

first: Phuong

last: Le

first: Sakina

last: Petiwala

first: Maricel

last: Torrent

first: Anlu

first: Diya

last: Mitra

first: Vlasios

last: Manaves

first: Charles

last: Lu

first: Stephanie

last: Sandoval

first: Greg

last: Buchanan

first: Daniel

last: Verduzco

first: Brian

last: Bierie

first: Jonathan

last: Meulbroek

first: William

middle: N

last: Pappano

first: Joshua

last: Plotnik


title: Effect of knockdown of KAT7 on gene expression in HCT116 cell line.

status: Public on Oct 13 2024

first: 萌

last: 王

state: beijing

address: peking university

institute: Peking university

summary: Accurate centriole formation is critical for cell replication. However, the holistic transcriptional regulatory mechanisms involved in this process remain elusive.We report here that KAT7 histone acetyltransferase is a key regulatory molecule that regulates centriole replication. Knockdown of KAT7 leads to reduced levels of histone H3K14 acetylation and reduced enrichment of H3K14ac in the promoter region of centriole formation-related genes, resulting in blocked centriole formation. Our data provide a new insight for the role of histone modifying factors in centriole replication-related pathways.

overall_design: To investigate the role of KAT7 in gene transcription, we transfected non-specific siRNA and KAT siRNA into HCT116 cells, respectively.We then performed gene expression profiling analysis and comparative gene expression profiling analysis using data from RNA-seq of KAT knockdown and control.

first: Guanqun

last: Mu

first: Meng

last: Wang


title: Nuclear Translocation of SIRT4 Mediates Deacetylation of U2AF2 to Modulate Renal Fibrosis Through Alternative Splicing-mediated Upregulation of CCN2

status: Public on Oct 11 2024

city: Shenzhen

first: Shu

last: Yang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

institute: shenzhen people's hospital

summary: TGF-β stimulates CCN2 expression which in turn amplifies TGF-β signaling. This process promotes extracellular matrix production and accelerates the pathological progression of fibrotic diseases. Alternative splicing plays an important role in multiple disease development, while U2 small nuclear RNA auxiliary factor 2 (U2AF2) is an essential factor in the early steps of pre-mRNA splicing. However, the molecular mechanism underlying abnormal CCN2 expression upon TGF-β stimulation remains unclear. This study elucidates that SIRT4 acts as a master regulator for CCN2 expression in response to TGF-β by modulating U2AF2-mediated alternative splicing. Analyses of renal biopsy specimens from patients with CKD and mouse fibrotic kidney tissues revealed marked nuclear accumulation of SIRT4. The tubulointerstitial fibrosis was alleviated by global deletion or tubular epithelial cell (TEC)-specific knockout of Sirt4, and aggravated by adeno-associated virus-mediated SIRT4 overexpression in TECs. Furthermore, SIRT4 was found to translocate from the mitochondria to the cytoplasm through the BAX/BAK pore under TGF-β stimulation. In the cytoplasm, TGF-β activated the ERK pathway and induced the phosphorylation of SIRT4 at Ser36, which further promoted its interaction with importin α1 and subsequent nuclear translocation. In the nucleus, SIRT4 was found to deacetylate U2AF2 at K413, facilitating the splicing of CCN2 pre-mRNA to promote CCN2 protein expression. Importantly, exosomes containing anti-SIRT4 antibodies were found to effectively mitigate the UUO-induced kidney fibrosis in mice. Collectively, these findings indicated that SIRT4 plays a role in kidney fibrosis by regulating CCN2 expression via the pre-mRNA splicing.

overall_design: Hence, we hypothesized that the SIRT4-mediated deacetylation of U2AF2 participates in the regulation of these processes. RNA-sequencing was performed to identify the changes in gene expression and alternative splicing in adenovirus-mediated SIRT4OE-transfected cells or adenovirus-Ctrl-transfected cells after TGF-β1 stimulation (Fig. 6A). Surprisingly, SIRT4 stimulation upregulated several genes (P < 0.01; Table EV1) that are involved in mRNA processing and the TGF-β signaling pathway. A total of 142 differentially expressed genes (P < 0.0005) were identified (Fig. 6A). Meanwhile, 248 genes showed differential intron retention (FDR < 0.05; Table EV2) (Fig. 6A). This analysis revealed four genes that were common between the differentially expressed genes and the differentially spliced genes (Fig. 6A). Ccn2, one of these four genes, ranked third among the all upregulated genes (P < 0.0005) after SIRT4 overexpression.

first: Guangyan

first: Jiaqing

last: Xiang

first: Xiaoxiao

first: Lin

last: Kang

first: Zhen

last: Liang


title: Distinct effects of sacituzumab govitecan and berzosertib on DNA damage response in ovarian cancer

first: Jayakumar

last: Nair

state: MD

address: 10 center drive

department: Women malignancies Branch

institute: National Cancer Institute

summary: Antibody-drug conjugates (ADCs) have become an important class of anticancer drugs in solid tumors including drug-resistant gynecologic malignancies. TROP2 is a cell surface antigen that is highly expressed in ovarian carcinoma (OC) but minimally expressed in normal ovarian tissues. In this study, we aimed to identify how TROP2-specific ADC, sacituzumab govitecan (SG), modulates DNA damage response pathways in drug-resistant OC. We found that SG induces G2/M arrest, increases RPA1 foci, and decreases replication fork speed, resulting in replication stress in TROP2-positive cells while these were less evident in TROP2-negative cells. In OC in vitro and in vivo models, SN-38 sensitivity and TROP2 expression play key roles in response to either ATR inhibitor or SG alone, or in combination. Additionally, inhibition of translesion DNA synthesis enhances SG and PARP inhibitor (PARPi) sensitivity in PARPi-resistant OC cells. These findings provide mechanistic insights for clinical development of SG in drug-resistant OC.

overall_design: RNA sequencing (RNAseq) data were obtained from total RNA from fresh frozen tumor biopsy samples from 15 BRCAmut HGSOC patients and 20 BRCAwt HGSOC patients  enrolled in the clinical trial at the National Cancer Institute (ClinicalTrials.gov, NCT02203513). RNAseq was performed using a HiSeq4000 sequencing system (Illumina) at the CCR Sequencing Facility/NCI.  Paired-end sequencing was done.  Quartile normalization and log-transformation prior to analysis were performed on datasets.

first: Tzu-Ting

last: Huang

first: Anu

last: Sunkara

first: Margaret

last: Pruitt

first: Kristen

last: Ibanez

first: Chih-Yuan

last: Chiang

first: Ken

middle: C

last: Cheng

first: Kelli

last: Wilson

first: Thomas

last: Cardillo

first: Scott

last: Hofsess

first: Jung-Min

last: Lee


title: Implantation of engineered adipocytes that outcompete tumors for resources suppresses cancer progression

status: Public on Oct 17 2024

city: San Francisco

first: Hai

middle: Phi

last: Nguyen

department: Bioengineering

institute: UCSF

summary: Tumors acquire an increased ability to obtain and metabolize nutrients. Here, we engineered adipocytes to outcompete tumors for nutrients and show that they can substantially reduce cancer progression. Growing cells from several cancers (breast, colon, pancreas, prostate) with engineered human adipocytes or xenografts alongside adipose organoids significantly suppresses cancer progression and reduces hypoxia and angiogenesis. Transplanting modulated adipocyte organoids in pancreatic or breast cancer genetic mouse models significantly suppressed their growth and decreased angiogenesis and hypoxia. To further showcase therapeutic potential, we demonstrate that co-culturing engineered patient-derived adipocytes with tumor organoids from dissected human breast cancers significantly reduces cancer growth and reduces proliferation of organoids from donors with BRCA1/2 mutations. In addition, inducing adipose organoids to outcompete tumors via tetracycline or placing them in an integrated cell-scaffold delivery platform and implanting them next to the tumor, both significantly suppress cancer growth. Finally, to display how this approach can be customized for different tumor-associated metabolic programs, we show that upregulating UPP1 in adipose organoids can outcompete a uridine-dependent pancreatic ductal adenocarcinoma for resources and suppress its growth. Combined, our results introduce a novel cancer therapeutic approach, termed adipose modulation transplantation (AMT), that can be utilized for a broad range of cancers.

overall_design: RNA samples isolated MCF7 xenograft tumors that were co-implanted with either UCP1-CRISRPa modualted-  or dCas9-VP64 (control) treated- adipose organoids in SCID micce fed with chow, high-fet diet, or 15% glucose water

first: Kelly

last: An

first: Yusuke

last: Ito

first: Bhushan

last: Kharbikar

first: Rory

last: Sheng

first: Breanna

last: Paredes

first: Elizabeth

last: Murray

first: Kimberly

last: Pham

first: Michael

last: Bruck

first: Xuija

last: Zhou

first: Cassidy

last: Biellak

first: Aki

last: Ushiki

first: Daniel

last: Bernards

first: Filipa

last: Lynce

first: Deborah

last: Dillon

first: Mark

last: Magbanua

first: Laura

last: Huppert

first: Heinz

last: Hammerlindl

last: Esserman

first: Tejal

last: Desai

first: Sook

middle: W

last: Yee

first: Jennifer

last: Rosenbluth

first: Nadav

last: Ahituv


title: Subclonal evolution revealed by single-cell profiles of expressed mutations identifies adaptation mechanisms to immunotherapy in melanoma.

first: Maxwell

last: Lee

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

overall_design: Refer to individual Series


title: Protocadherin 8 and transcription factor Dbx1 regulate the formation of developing cerebral cortex

city: paris

first: Frederic

last: Causeret

address: 24 bd de montparnasse

department: Imagine Institute

country: France

institute: Inserm

summary: Normal development of the mammalian central nervous system requires correct tissue patterning, production of the appropriate cell types and establishment of functional neuronal circuits. Transcription factors (TFs) play essential roles in these processes, regulating the expression of target genes responsible for neuronal subtypes specific features. Cell adhesion molecules are key components of neuronal identities that control cell sorting, migration, neurite outgrowth/guidance and synaptogenesis. So far, the link between cell adhesion and cell fate is not known TFs are known to control neuronal adhesion but not the opposite.   Here, using acute gain- and loss-of-function experiments by in utero electroporation in the developing mouse telencephalon we demonstrate that ectopic expression of Dbx1, a homeodomain TF acting as a cell fate determinant, leads to increased expression of Protocadherin 8 (Pcdh8) and cell aggregation, together with the induction of neuronal fate markers Nr4a2 (Nurr1)   and Pax6. These effects were are modulated depending on the region and timing of electroporation. Furthermore, we found that Pcdh8 expression is required for Dbx1-induced fate specification. Surprisingly, Pcdh8 overexpression also proved sufficient to induce Dbx1 expression as well as a complete reorganisation of the apico-basal polarity and dorso-ventral patterning. Finally, we present evidence that these effects are mediated through regulation of the expression of Notch ligands and promotion of cell cycle exit. Altogether, our work therefore points to cell adhesion molecules as unexpectedimportant, yet unexpected important, players in the regulation of cell identity and, in particular, Pcdh8 through its bidirectional action crossregulation  with the Dbx1 transcription factor.

overall_design:
Explants encompassing the septum were dissected from eight PGKCre ; Rosa26YFP E11.5 mouse embryos originating from two distinct litters and four Dbx1Cre ; Rosa26tdTomato E12.5 embryos from two litters. Cells were dissociated, pooled and a Single Cell 3′ Kit v2 library was produced.
The telencephalic vesicle was dissected from three wild-type E12 mouse embryos originating from two distinct litters. Cells were dissociated, pooled and a Single Cell 3' Kit v3.1 library was produced.

first: Matthieu

middle: X

last: Moreau

first: Frédéric


title: LA-CB1, a novel Abemaciclib derivative induces apoptosis in breast cancer cells by inhibiting the CDK4/6-Cyclin D-Rb-E2F pathway path

city: lianyungang

first: He

last: Jingliang

address: tongguan

institute: Jiangsu Ocean University

summary: Triple-negative breast cancer (TNBC) is a subtype of breast cancer (BC) characterized by deletion of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor (Her-2). It accounts for 10.0% to 20.8% of all pathological types of BC, has specific biological behavior and clinicopathological features, and has a worse prognosis than other types. TNBC usually has a high mortality and recurrence rate, and a poor prognosis after surgery, radiation, chemotherapy, and endocrine therapy. There are no conventional and effective treatments to control its progression. Therefore, we designed and developed a derivative based on Abemaciclib, named LA-CB1. To investigate the influence of LA-CB1 on biological function of TNBC. We use the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide test (MTT) to detect the viability of breast cancer cells. Evaluation of drug effects on cell migration and invasion by Transwell assays. Cell clone formation assay detects cell proliferation ability after drug addition. Subsequently, we determined the clinical significance and functional role of LA-CB1 through chick embryo experiments. Then, transcriptome sequencing technology (RNA-Seq) and bioinformatics methods were used to study the main pathway of LA-CB1 action on MDA-MB-231 cells. Western Blot assay verified the effect of LA-CB1 on the expression of CDK4/6-CyclinD1-Rb-E2F pathway protein. The compound LA-CB1 can inhibit the proliferation, colony formation, migration and invasion of TNBC cells. Effect of compound LA-CB1 on apoptosis and cell cycle detected by flow cytometry. The expression levels of CDK4, CDK6, CyclinD1, E2F1 and p-Rb proteins were positively correlated with LA-CB1 concentration. In summary, LA-CB1 showed a good anti-tumor cell proliferation effect, showing potential anti-TNBC drug candidate properties. This study provides new ideas and possibilities for TNBC treatment.

overall_design: To investigate the role of LA-CB1 in breast cancer and its mechanism, we treated and did not treat MDA-MB-231 cells with LA-CB1. Then, we performed gene expression profiling using RNA-seq data from MDA-MB-231_LA-CB1 and MDA-MB-231_DMSO cells.

first: Jingliang

last: He

first: Bin

last: Liu


title: Dlk1 is a novel adrenocortical stem/progenitor cell marker that predicts malignancy in adrenocortical carcinoma

first: James

last: Pittaway

address: Charterhouse Square

department: Centre for Endocrinology

institute: Queen Mary University of London

summary: Adrenocortical carcinoma (ACC) is characterized by disruption of tissue development and homeostatic pathways. Here, using genetic fate mapping and murine ACC models, we have identified a population of adrenocortical stem cells that express Delta-like non-canonical Notch ligand 1 (DLK1). These cells are active during development, near dormant postnatally but are re-expressed in ACC. DLK1 expression is widespread in human ACC samples and independently influences recurrence-free survival. Spatial transcriptomic analysis has identified DLK1 positive ACC cells to have increased steroidogenic potential, a finding also observed in both human and murine ACC cell lines. Additionally, the cleavable DLK1 ectodomain is detectable in patients’ serum and effectively distinguishes ACC from other adrenal pathologies, offering potential diagnostic and follow-up utility for ACC patients. These data demonstrate a prognostic role for DLK1 in ACC, elucidate its hierarchical expression in homeostasis and cancer and suggest its utility as a biomarker in this malignancy.

overall_design: To investigate the spatial trascriptomic differences between DLK1 positive and negative tumour areas of 5 human adenocortical carcinoma samples. In tissue sections 1 and 2, 9 positive and 9 negative regions of interest were selected. In tissue sections 3-5, 6 postive and 6 negative regions of interst were selected.

first: Katia

last: Marineillo

first: Leonardo

last: Guasti


title: Unraveling Epigenetic and Immune Mechanisms Underlying Cystogenesis in Autosomal Dominant Polycystic Kidney Disease

status: Public on Oct 10 2024

city: Tianjin

first: Jiayuan

last: Chen

state: State...

address: Heping

institute: Tianjin Medical University

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


title: Characterization and bioinformatic filtering of ambient gRNAs in single-cell CRISPR screens using CLEANSER [CRISPR]

status: Public on Oct 08 2024

city: Durham

first: Charles

last: Gersbach

state: NC

address: 2127 Campus Drive

institute: Duke University

summary: Recent technological developments in single-cell RNA-seq CRISPR screens enable high-throughput investigation of the genome. Through transduction of a gRNA library to a cell population followed by transcriptomic profiling by scRNA-seq, it is possible to characterize the effects of thousands of genomic perturbations on global gene expression. A major source of noise in scRNA-seq CRISPR screens are ambient gRNAs, which are contaminating gRNAs that likely originate from other cells. If not properly filtered, ambient gRNAs can result in an excess of false positive gRNA assignments. Here, we utilize CRISPR barnyard assays to characterize ambient gRNA noise in single-cell CRISPR screens. We use these datasets to develop and train CLEANSER, a mixture model that identifies and filters ambient gRNA noise. This model takes advantage of the bimodal distribution between native and ambient gRNAs and includes both gRNA and cell-specific normalization parameters, correcting for confounding technical factors that affect individual gRNAs and cells. The output of CLEANSER is the probability that a gRNA-cell assignment is in the native distribution over the ambient distribution. We find that ambient gRNA filtering methods impact differential gene expression analysis outcomes and that CLEANSER outperforms alternate approaches by increasing gRNA-cell assignment accuracy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: gRNA library transduction: HEK293T dCas9KRAB cells were seeded at a density of 5x104 cells/cm2 and NIH3T3 dCas9KRAB cells were seeded at a density of 1.25x104 cells/cm2 on 6-well plates in one biological replicate each. The cells were transduced with lentivirus using 8 μg/mL polybrene at a multiplicity of infection (MOI) of ~10 as determined by titration. Two days post-transduction, cells were treated with either 500 (HEK293T dCas9KRAB + non-targeting library #1 cells) or 1000 (NIH3T3 dCas9KRAB + non-targeting library #2 cells) ng/mL puromycin or 20 (HEK293T dCas9KRAB cells + non-targeting library #1) or 80 (NIH3T3 dCas9KRAB cells + non-targeting library #2) μg/mL blasticidin and were selected for 10 days. 7 days post-transduction, cells were trypsinized and seeded on 6-well plates in three conditions: 1) HEK293T dCas9KRAB + non-targeting library #1 cells at a density of 3.9 x 104 cells/cm2 2) NIH3T3 dCas9KRAB + non-targeting library #2 cells at a density of 1.5 x 104 cells/cm2 3) HEK293T dCas9KRAB + non-targeting library #1 cells at a density of 2.0 x 104 cells/cm2 and NIH3T3 dCas9KRAB + non-targeting library #2 cells at a density of 2.0 x 104 cells/cm2. Genomic DNA isolation and NGS: Genomic DNA was isolated from cells using the Purelink Genomic DNA mini kit (Thermo Fisher)

first: Siyan

first: Marisa

last: Hamilton

first: Thomas

last: Cowart

first: Alejandro

last: Barrera

first: Lexi

last: Bounds

first: Alexander

last: Nelson

first: Richard

last: Doty

first: Andrew

middle: S

last: Allen

first: Gregory

middle: E

last: Crawford

first: William

last: Majoros


title: KLF13 promotes SLE Pathogenesis by modifying chromatin accessibility of key proinflammatory cytokine genes

first: Shaheen

last: Khan

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center


title: The microglial response to inhibition of Colony-Stimulating-Factor-1 Receptor by PLX3397 differs by sex in adult mice

status: Public on Oct 06 2024

city: Rochester

first: Ania

last: Majewska

state: NY

address: 601 Elmwood Ave

department: Department of Neuroscience

institute: University of Rochester Medical Center

summary: Microglia, the resident macrophage of the brain, are derived from the yolk sac and colonize the brain before the blood-brain barrier forms. Once established, they expand locally and require Colony-stimulating factor 1 receptor (CSF1R) signaling for their development and maintenance. CSF1R inhibitors have been used extensively to deplete microglia in the healthy and diseased brain. In this study, we demonstrated sex-dependent differences in the microglial response to the CSF1R inhibitor PLX3397. Male mice exhibited greater microglial depletion compared to females. Transcriptomic and flow cytometry analysis revealed sex-specific differences in the remaining microglia population, with female microglia upregulating autophagy and proteostasis pathways while male microglia increased mitobiogenesis. Furthermore, manipulating key microglial receptors by using different transgenic mouse lines resulted in changes in depletion efficacies that were also sex-dependent. These findings suggest sex-dependent microglial survival mechanisms, which might contribute to the well-documented sex differences in various neurological disorders.

overall_design: To investigate the underlying mechanisms that gave rise to the sex-dependent disparity in PLX-induced microglial depletion, microglia from young male and female mice treated with either PLX or control chow were isolated by Fluorescence activated cell sorting (FACS), their total RNA were sequenced and subsequently analyzed.

first: Le

last: Linh

first: Eliseeva

last: Sophia

first: Plunk

last: Elizabeth

first: Kara-Pabani

last: Kallam

first: Li

last: Herman

first: Yarovinsky

middle: O

last: Felix

first: Majewska

last: Ania


title: Myeloid-derived IL1B drives epithelial and stromal cell remodeling during chronic rhinosinusitis and nasal polyps [scRNA-seq]

status: Public on Oct 03 2024

city: Jinan

first: Xinyu

last: Xie

address: Wenhua West Road

institute: Shandong University

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the function of IL1B in the nasal mucosa.

overall_design:
33 bioptic samples from human inferior turbinates, middle turbinates, and nasal polyps were collected from healthy donors or CRSwNP patients.

***************************************************************
Submitter states that missing raw files are due to patient privacy concerns.
***************************************************************


title: Characterization and bioinformatic filtering of ambient gRNAs in single-cell CRISPR screens using CLEANSER [scRNA-seq]

first: Charles

last: Gersbach

overall_design: gRNA library transduction: HEK293T dCas9KRAB cells were seeded at a density of 5x104 cells/cm2 and NIH3T3 dCas9KRAB cells were seeded at a density of 1.25x104 cells/cm2 on 6-well plates in one biological replicate each. The cells were transduced with lentivirus using 8 μg/mL polybrene at a multiplicity of infection (MOI) of ~10 as determined by titration. Two days post-transduction, cells were treated with either 500 (HEK293T dCas9KRAB + non-targeting library #1 cells) or 1000 (NIH3T3 dCas9KRAB + non-targeting library #2 cells) ng/mL puromycin or 20 (HEK293T dCas9KRAB cells + non-targeting library #1) or 80 (NIH3T3 dCas9KRAB cells + non-targeting library #2) μg/mL blasticidin and were selected for 10 days. 7 days post-transduction, cells were trypsinized and seeded on 6-well plates in three conditions: 1) HEK293T dCas9KRAB + non-targeting library #1 cells at a density of 3.9 x 104 cells/cm2 2) NIH3T3 dCas9KRAB + non-targeting library #2 cells at a density of 1.5 x 104 cells/cm2 3) HEK293T dCas9KRAB + non-targeting library #1 cells at a density of 2.0 x 104 cells/cm2 and NIH3T3 dCas9KRAB + non-targeting library #2 cells at a density of 2.0 x 104 cells/cm2  CRISPR barnyard single-cell RNA-seq: 10 days post transduction, cells were washed three times, trypsinized, and strained through a 40 µm cell strainer. The cells were diluted to 1K cells/µL and a fourth condition of HEK293T dCas9KRAB + non-targeting library #1 and NIH3T3 dCas9KRAB cells + non-targeting library #2 were mixed. Eight lanes were loaded for single-cell transcriptome profiling, with one lane per condition for each CROP-seq and modified direct capture perturb-seq vector. Approximately 10,000 cells were captured per lane of a 10x Chromium chip (Next GEM Chip G) using Chromium Next GEM Single Cell 3ʹ HT Reagent Kits v3.1 with Feature Barcoding technology for CRISPR Screening (10x Genomics, Inc, Document number CG000418, Rev D). CROP-seq protospacer sequences were amplified from barcoded cDNA as described previously.   CRISPR barnyard single-cell RNA-seq library sequencing: Final libraries were pooled and sequenced on a NovaSeq S4 flow cell (R1:28 I1:10, I2:10, R2:90) aiming for ~15,000 reads per cell for gene expression libraries and ~5,000 reads per cell for gRNA libraries

first: Siyan

last: Liu

first: Marisa

last: Hamilton

first: Thomas

last: Cowart

first: Alejandro

last: Barrera

middle: R

middle: A


title: ATV-TfR and ATV-CD98hc biodistribution in the mouse brain

status: Public on Oct 02 2024

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: We evaluated the distributions of transferrin receptor (TfR)- and CD98 heavy chain (CD98hc)-targeting antibody transport vehicles (ATVs) in mouse brain using systemically injected fluorescently tagged ATVs. Combining FACS sorting with scRNA-seq, we report the localization of ATV-TfR and ATV-CD98hc on brain endothelial cells and their unique distribution across parenchymal brain cells.

overall_design: This study includes 12-week old mice from three different genotypes: C57BL/6J, TfR mu/hu KI, and CD98hcmu/hu KI (on a C57Bl6J background). For each genotype, two male and two female animals included.

first: Nathalie

last: El Khoury

first: David

last: Tatarakis

first: Joy

last: Zuchero


title: Terminal differentiation and persistence of effector regulatory T cells essential for the prevention of intestinal inflammation [scMultiomics]

status: Public on Oct 01 2024

city: La Jolla

first: Stanislav

last: Dikiy

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

summary: Regulatory T (Treg) cells represent a specialized CD4+ T cell lineage with essential anti-inflammatory functions. Recent studies of the adaptations of Treg cells to non-lymphoid tissues which enable their specialized immunosuppressive and tissue supportive functions raise questions about the underlying mechanisms of these adaptations and whether they represent stable differentiation or reversible activation states. Using novel genetic tools, we characterized the transcriptional programs of distinct colonic effector Treg cell types. We found that attenuated T cell receptor (TCR) signaling and acquisition of substantial TCR independent functionality appears to facilitate the terminal differentiation of a population of colonic effector Treg cells distinguished by stable expression of immunomodulatory cytokine interleukin-10 (IL-10). Functional studies revealed that this subset of effector Treg cells, but not their expression of IL-10, was indispensable for preventing colitis. These findings suggest core features of terminal differentiation of effector Treg cells in non-lymphoid tissues and their function therein.

overall_design: We performed scRNA-seq on total Treg cells from large intestine and small intestine in order to identify potential subpopulations within each as well as to gain insight into relationships between and potential differentiation  trajectories of Il10 expressing and non Il10 expressing Treg cell subsets within each tissue.

first: Aazam

middle: P

last: Ghelani

first: Andrew

middle: G

last: Levine

first: Stephen

last: Martis

first: Paolo

last: Giovanelli

first: Zhong-Min

last: Wang

first: Giorgi

last: Beroshvili

first: Yuri

last: Pritykin

first: Chirag

last: Krishna

first: Xiao

last: Huang

first: Ariella

last: Glasner

first: Benjamin

middle: D

last: Greenbaum

first: Christina

last: Leslie

first: Alexander

middle: Y

last: Rudensky


title: Histone Deacetylase 1 (HDAC1) maintains the transcriptome of embryonic stem cells through regulating acetylation at crucial genomic sites [ATAC-seq]

city: Leicester

first: Shaun

last: Cowley

address: Henry Wellcome Building, Lancaster Road

department: Molecular and Cell Biology

institute: University of Leicester

summary: Histone Deacetylase 1 (HDAC1) removes acetyl groups from lysine residues on the core histones, balancing histone acetyltransferase (HAT) activity. Despite this apparent repressive function, suppression of HDAC activity causes both up and downregulation of gene expression. Here we exploit the degradation tag (dTAG) system to rapidly degrade HDAC1 in embryonic stem cells (ESCs) lacking the paralog, HDAC2. Unlike HDAC inhibitors that lack isoform specificity the dTAG system allowed specific HDAC1 targeting and completely removed HDAC1 100x faster than genetic knockouts. HDAC1 degradation caused rapid increases in histone acetylation, with H2BK5 and H2BK11 most sensitive. The majority of differentially expressed genes following 2 hours of HDAC1 degradation were upregulated (275 genes up vs 15 down) with increased proportions of downregulated genes at 6 (1153 up vs 443 down) and 24 hours (1146 up vs 967 down). Upregulated genes showed increased H2BK5ac and H3K27ac around their transcriptional start site (TSS). In contrast, decreased acetylation of super-enhancers (SEs) was linked to the most strongly downregulated genes, leading to a collapse of the core pluripotency-associated gene network. These findings suggest that HDAC1 plays a crucial role in regulating the ESC gene expression network by maintaining the correct acetylation levels at key genomic sites.

overall_design: To investigate the consequences of HDAC1 removal in mouse embryonic stem cells we stably expressed a HDAC1-FKBP12F36V-Flag construct in conditional Hdac1/2 double knockout ESCs so that we could degrade the HDAC1-FKBP12F36V-Flag protein in the absence of endogenous HDAC1/2 and assay the consequences. We performed ATAC-seq following 2, 6 or 24 hours of HDAC1-FKBP12F36V-Flag degradation against a control treated with DMSO for 24 hours. Analysis allowed determination of genomic sites that show changes in accessibility following the degradation of HDAC1-FKBP12F36V.

last: English

first: Khadija

last: Sabat

first: Samuel

last: Lee

first: India

last: Baker

first: Trong

last: Khoa Pham

first: Mark

last: Collins


title: PBAF associates with repressed chromatin to enable REST occupancy

city: New York

first: Elena

last: Grossi

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai


title: PBAF associates with repressed chromatin to enable REST occupancy (ChIP-seq)

summary: Multimeric SWI/SNF chromatin remodelers assemble in distinct conformations, with individual functions difficult to dissect. Importantly, mutations in specific SWI/SNF genes are enriched in distinct cancers, as the PBAF-specific component ARID2 in melanoma. Through comprehensive epigenomic profiling of SWI/SNF complexes and their associated chromatin states in melanoma and melanocytes, we found that a subset of PBAF-exclusive regions unexpectedly coexists with PRC2 and repressed chromatin. Time-resolved approaches revealed that PBAF regions are generally less sensitive to ATPase-mediated remodeling compared to BAF sites. Notably, PBAF/PRC2-bound loci are enriched for REST, a transcription factor that represses neuronal genes. In turn, absence of ARID2 and consequent PBAF loss hinders REST ability to bind and inactivate its targets, leading to upregulation of neuronal and synaptic transcripts, a gene signature also associated with ARID2 mutations in melanoma patients. In sum, we demonstrate a unique role for PBAF in generating accessibility for a silencing transcription factor at repressed chromatin.

overall_design: Chromatin Immunoprecipitation sequencing (ChIP-seq) of different SWI/SNF components and transcription factors in melanoma 113/6-4L cells (4L) and normal human epithelial melanocytes (NHEM)

first: Emily

last: Bernstein


title: Protein arginine methyltransferase 7 is linked to schizophrenia by regulating the function of neural progenitor cell

city: Changsha

first: Ting

last: Shen

address: Tongzhipo Road 172

institute: Central South University

summary: Schizophrenia (SCZ) is a severe mental disorder with strong heritability and complex inheritance, which affects about 1% of populations worldwide. In this study, we prioritized protein arginine methyltransferase 7 (PRMT7) for SCZ susceptibility. Next, we explored the cellular and molecular infrastructures conferring PRMT7 to SCZ risk. Down-regulation of PRMT7 in neural progenitor cells (NPCs) caused decreased proliferation and increased neuronal differentiation. Additionally, the differentiated neurons derived from these NPCs displayed longer neurites compared to controls. Conversely, Over-expression of PRMT7 led to enhanced NPC proliferation and reduced neuronal differentiation. Moreover, in 3D cerebral organoids, the similar NPC phenotypic changes were observed following PRMT7 depletion. Mechanistically, the expression of genes related to cell cycle and neuronal functions were under regulation of PRMT7 via depositing H4R3me2s on their promoter regions. Disease enrichment analysis revealed that these PRMT7-regulated genes were more strongly associated with SCZ compared to other mental disorders. In summary, this study uncovers that PRMT7 is a functional gene at 16q22.1 contributing to the etiology of SCZ by impacting the proliferation and differentiation of NPCs as an epigenetic regulator.

overall_design: To uncover the mechanism of PRMT7 contributing to SCZ risk, we establisded NPC models with PRMT7 downregulation via two different shRNAs.

first: Jing

last: Yu

first: Bin

last: Xie

first: Cuiping

first: Jingjie

last: Cui

first: Kefu

last: Liu

first: Chunyu

first: Chao

last: Chen


title: Molecular Connectomics Reveals a Glucagon-Like Peptide 1 Sensitive Neural Circuit for Satiety

status: Public on Oct 07 2024

city: Charlottesville

first: John

last: Campbell

state: VA

address: 485 MCCORMICK RD, GILMER HALL ROOM 229 PO BOX 400328

institute: University of Virginia

summary: Liraglutide and other agonists of the glucagon-like peptide 1 receptor (GLP-1RAs) are effective weight-loss drugs, but how they suppress appetite remains unclear. One potential mechanism is by activating neurons which inhibit hunger-promoting Agouti-related peptide (AgRP) neurons of the arcuate hypothalamus (Arc). To identify these afferents, we developed a method combining rabies-based connectomics with single-nuclei transcriptomics. Applying this method to AgRP neurons predicted at least 21 afferent subtypes in the mouse mediobasal and paraventricular hypothalamus. Among these are Trh+ Arc neurons (TrhArc), inhibitory neurons which express the Glp1r gene and are activated by the GLP-1RA liraglutide. Activating TrhArc neurons inhibits AgRP neurons and feeding, likely in an AgRP neuron-dependent manner. Silencing TrhArc neurons causes over-eating and weight gain and attenuates liraglutide’s effect on body weight. Our results demonstrate a widely applicable method for molecular connectomics, comprehensively identify local inputs to AgRP neurons, and reveal a circuit through which GLP-1RAs suppress appetite.

overall_design: We profiled gene expression in single cell nuclei of  mouse hypothalamus after performing Cre-sepcific monosynaptic rabies tracing in AgRP-Cre mice, using the 10X Chromium Single Cell 3' Gene Expression system

first: Addison

last: Webster


title: Identification of EV-responsive transcripts in the planarian Schmidtea mediterranea

city: Oklahoma

first: David

middle: J

last: Forsthoefel

state: OK

address: 825 NE 13th St

department: Genes and Human Disease Research Program

institute: Oklahoma Medical Research Foundation

summary: The roles of extracellular vesicles in animal models of regeneration are poorly characterized. The goal of this study was to identify differentially expressed transcripts in planarian flatworms after injection of buffer only or extracellular vesicles compared to uninjected animals.

overall_design: Total RNA was isolated from planarian tail fragments (postpharyngeal region excluding ~10% of the posterior-most tail tip) 24 hours after EV injection, buffer injection, or no injection (5 tail fragments per replicate, 4 biological replicates per condition). Library generation (IDT xGen RNA library prep kit with NEB poly-A selection) and RNA sequencing (2x150bp paired-end, Illumina NovaSeq X Plus) were conducted by the Oklahoma Medical Research Foundation Clinical Genomics Core. Bioinformatic analysis was conducted using BBDuk, Bowtie2, and edgeR.

first: Priscilla

last: Avalos

first: Lily

middle: L

last: Wong


title: Understanding the early molecular changes associated with radiation therapy – a preliminary bulk RNA sequencing study

status: Public on Sep 27 2024

city: Salt Lake City

first: Sujee

last: Jeyapalina

state: Utah

address: 500 Foothill Dr

institute: Department of Veteran Affairs

summary:
Introduction
Cancer is the second leading cause of death in the United States, with breast cancer being the most commonly diagnosed new cancer in women. Radiation therapy provides well-documented survival and recurrence benefits; however, it can lead to significant adverse effects, such as radiation-induced fibrosis (RIF), which can cause pain and result in poor aesthetic outcomes. The biological mechanisms underlying RIF are not entirely understood and require further investigation to identify potential intervention avenues. In this study, we investigated the biological response to radiotherapy by analyzing non-irradiated and irradiated tissues from breast cancer patients.
Materials and methods
We collected tissue from breast cancer patients who underwent unilateral radiation and bilateral breast reconstruction. At the time of final reconstruction (post-radiation), samples were collected from both non-irradiated and irradiated reconstruction sites. These samples were analyzed using bulk RNA sequencing, histology, and immunohistochemistry (IHC).
Results
In fibrous tissue capsules, CLCA2, COL4A5, and COL6A6 were differentially expressed and may be related to reduced micro-vascularization. CXCL9 and PTCHD4 were upregulated within the skin, possibly conferring an increased immune response, while multiple keratin-related genes (KRT6B, KRT17, KRT25, KRT28, and KRT75) were downregulated. In irradiated muscle tissue, there was increased expression of CXCL10 and downregulation of DCD. These results were confirmed using IHC.
Conclusions
This study highlights the utility of bulk RNA sequencing studies in conjunction with IHC to identify target genes and biological processes responsible for RIF in tissues at final breast reconstruction. Due to the sample size limitation, further research is warranted to understand the role of keratin and collagen genes in regulating epidermal changes, vascularity, and fibrosis.

overall_design: Patients diagnosed with breast cancer were enrolled in the current study. Each patient underwent a double mastectomy, unilateral radiation therapy of the affected breast, and bilateral breast reconstruction. At bilateral breast reconstruction, skin, muscle, and capsular tissues were collected from each side (6 samples/patient).

first: Andrew

last: Miller

first: Henning

last: De May

last: Rou

first: Jayant

last: Agarwal


title: RNA-seq Analysis of Prmt3f/f and Prmt3LKO Mouse Tumor Transcriptomes

status: Public on Sep 24 2024

city: Sanya

first: yan

middle: fang

last: zhi

address: No. 80 Jianglin Road, Haitang District, Sanya City, Hainan Province, CHINA

department: tropical medicine

institute: Chinese Hainan Hospital, General Hospital of the People's Liberation Army

summary: To investigate the role of PRMT3 in regulating the progression of hepatocellular carcinoma (HCC), we established a mouse liver model by administering DEN-CCL4 to both Prmt3f/f and Prmt3LKO mice. Tumors from these mice were performed to RNA-seq for gene expression profiling.

overall_design: To induce a mouse liver tumor model, two-week-old Prmt3f/f and Prmt3LKO mice were administrated with DEN (25mg/kg) via intraperitoneal injection, followed by intraperitoneal injection with 10% CCl4 (dissolved in oil, 0.5 ml/kg) twice weekly at the age of 6 weeks. The mice were then sacrificed at 26 weeks, respectively. The tumors derived from Prmt3f/f and Prmt3HKO mouse liver were administrated to RNA-seq.

first: Chen H

last: Ding

first: Bo N

last: Xu

first: Xin

last: Zhang

first: Wei F


title: Disease-associated variant in LACC1, a Crohn’s risk gene, acts in T cells to alter gene expression, metabolism and T cell function

status: Public on Sep 30 2024

first: Gabriel

last: Ascui

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: Genome wide association studies (GWAS) identify a site near the metabolism gene laccase domain containing 1 (LACC1) as a risk for Crohn’s disease (CD). We previously found the Crohn’s disease risk allele near LACC1 correlates with decreased T lymphocyte LACC1 expression. Despite this, proof of this allelic effect, the mechanism by which gene expression is affected, and links to T cell function and inflammatory disease, remained unknown. Here we identified sites in a promoter region in a haploblock that influenced LACC1 gene expression. Direct association of disease-risk variants with lower LACC1 mRNA was confirmed by comparing transcripts from each allele in LACC1 heterozygous human CD4+ T cells. Using gene editing, we validated the role of this promoter region in LACC1 expression in T cells. Human CD4+ T cells with LACC1 gene knockdown showed altered metabolism, including a reduced oxygen consumption rate, and reduced regulatory T cell differentiation. Therefore, our study provides a mechanism for this disease GWAS hit by linking promoter region alterations to changes in T cell metabolism and function.

overall_design: To investigate how LACC1 deciciency influence the transcriptome of human Th0 and iTreg cells, we knocked down LACC1 by lentiviral shRNA in these CD4 cells. Then we performed bulk RNA-seq on empty vector (EV) and LACC1 knockdown (KD) transuced Th0 and iTreg cells, 4 or 5 human donors were used.

first: Yingcong

last: Li

first: Martina

last: Dicker

first: Thomas

last: Riffelmacher

first: Vivek

last: Chandra

first: Benjamin

last: Schmiedel

first: Ting-Fang

last: Chou

first: Pandurangan

last: Vijayanand

first: Mitchell

last: Kronenberg


title: Bulk tissue direct gene expression in the postmortem brains of severe acute COVID19 patients and matched controls II

city: Los Angeles

first: Ting

address: 2506 Gonda Bldg, 695 Charles E.Young Dr. South

department: Pathology and laboratory medicine

institute: University of California, Los Angeles

summary:
Understanding the pathological basis of the neurological symptoms observed following SARS-CoV2 infection is essential to optimizing outcomes and developing therapeutics. To date, small sample sizes and narrow molecular profiling limit the generalizability of findings. We profiled multiple cortical and subcortical regions in postmortem COVID-19 patient brains and controls (total n=42) with spatial transcriptomics in the frontal cortex, midbrain and pons, bulk RNA expression in frontal cortex, midbrain, basal ganglia, and pons, and proteomics in the 8 regions (frontal cortex, temporal cortex, occipital cortex, midbrain, pons, hippocampus, thalamus and basal ganglia). We observed a multi-regional antiviral response in the absence of direct active SARS-CoV2 infection. We identified dysregulation of mitochondrial and synaptic pathways in deep-layer excitatory neurons and up-regulation of neuroinflammation in glia, in both mRNA and protein. Remarkably, these alterations overlapped substantially with changes in various age-related neurodegenerative diseases, such as Parkinson’s disease (PD) and Alzheimer’s disease (AD). Our work, combining multiple experimental and analytical methods, demonstrates the brain-wide impact of severe COVID-19, involving both cortical and subcortical regions, shedding light on potential therapeutic targets within pathways typically associated with pathological aging.
The data prresented here is a part of the bulk tissue direct gene expression study.

overall_design: 110 individual samples in total were profiled.12 individual samples from basal ganglia are listed in this part.

first: Emmanuelle

last: Faure


title: Spatial transcriptomics n the postmortem brains of severe acute COVID19 [FGWM]

summary:
Understanding the pathological basis of the neurological symptoms observed following SARS-CoV2 infection is essential to optimizing outcomes and developing therapeutics. To date, small sample sizes and narrow molecular profiling limit the generalizability of findings. We profiled multiple cortical and subcortical regions in postmortem COVID-19 patient brains and controls (total n=42) with spatial transcriptomics in the frontal cortex, midbrain and pons, bulk RNA expression in frontal cortex, midbrain, basal ganglia, and pons, and proteomics in the 8 regions (frontal cortex, temporal cortex, occipital cortex, midbrain, pons, hippocampus, thalamus and basal ganglia). We observed a multi-regional antiviral response in the absence of direct active SARS-CoV2 infection. We identified dysregulation of mitochondrial and synaptic pathways in deep-layer excitatory neurons and up-regulation of neuroinflammation in glia, in both mRNA and protein. Remarkably, these alterations overlapped substantially with changes in various age-related neurodegenerative diseases, such as Parkinson’s disease (PD) and Alzheimer’s disease (AD). Our work, combining multiple experimental and analytical methods, demonstrates the brain-wide impact of severe COVID-19, involving both cortical and subcortical regions, shedding light on potential therapeutic targets within pathways typically associated with pathological aging.
The data presented here is a part of the Nanostring GeoMx DSP study.

overall_design:
319 ROIs are profiled. GeoMx DSP results of 121 ROIs in the Frontal Grey matter and white matter are listed here.

>>>Submitter states that raw data are not available due to patient privacy concerns.<<<

first: Liuliu

last: Pan

first: Kathy

last: Ton


title: Spatial transcriptomics in the postmortem brains of severe acute COVID19 [Pons]

overall_design:
319 ROIs are profiled. GeoMx DSP results of 119 ROIs in the Pons (Corticospinal Tract, Pontocerebellar Tract, Pontine Nuclei, and Tegmentum)

>>>Submitter states that raw data are not available due to patient privacy concerns.<<<


title: Dynamic properties of transcriptional condensates modulate CRISPRa-mediated gene activation

status: Public on Oct 05 2024

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

summary: Purpose: To identify differential expressed genes upon CRISPRa activation. Methods:  293T cells were activated by different CRISPRa systems and then collected for RNA sequencing at 48 hpf (hours post CRISPRa activation).

overall_design: Comparison of tanscriptome between control and activation group at 48 hpf.

last: Cheng

first: Yujuan

last: Fu


title: Structural and functional dissection of Pacinian corpuscle reveals a multicellular mechanism of touch detection independent of the outer core

city: New Haven

first: Luke

last: Ziolkowski

state: CT

address: 333 Cedar Street SHM B146

department: Cellular & Molecular Physiology

institute: Yale University School of Medicine

summary: Lamellated corpuscles are rapidly adapting mechanoreceptors that detect transient touch and high-frequency vibration in many vertebrates. It the prevailing model, these properties are determined by outer core, which acts as a mechanical filter that limits static and low-frequency stimuli from reaching afferent terminal—the sole site of touch detection in corpuscles. Using focused ion beam scanning electron microscopy and single corpuscle electrophysiology, we determine the detailed architecture of corpuscular components and reveal their contribution to touch detection. We show that outer core is dispensable for rapid adaptation and frequency tuning. Instead, these properties are encoded within inner core, composed of gap junction-coupled syncytium formed by lamellar Schwann cells (LCS) around afferent terminal. By acting as additional touch sensors, LSCs potentiate mechanosensitivity of the terminal, which detects touch via fast-inactivating ion channels. Our findings support a model in which lamellated corpuscle function is mediated by a bicellular mechanism within inner core.

overall_design: Gene expression analysis and differential transcriptomics of single inner cores of Pacinian corpuscles (n = 7 biological replicates) compared to bill epidermis (n=6 biological replicates) in duck.

middle: H

first: Yury

last: Nikolaev

first: Akitoshi

last: Chikamoto

first: Mai

last: Oda

first: Viktor

middle: V

last: Feketa

first: David

last: Monedero-Alonso

first: Serafima

last: Ardasheva

first: Samuel

last: Bae

first: C

last: Xu

first: Song

last: Pang

first: Elena

last: Gracheva

first: Sviatoslav

middle: N

last: Bagriantsev