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

status: Public on Sep 23 2024

first: Ting

last: Zhang

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 represented here is a part of the bulk tissue direct gene expression study.

overall_design: 110 individual samples in total were profiled. 98 individual samples from Frontal, midbrain, pons and basal ganglia are listed in this part.

first: Michael

last: Bailey


title: Protocol for detecting m5C RNA modification at single-base resolution using m5C-TAC-seq

status: Public on Oct 01 2024

city: Hangzhou

first: Xiaoyu

last: Li

state: Zhejiang

address: 866 Yuhangtang Road

department: SCHOOL OF BASIC MEDICAL SCIENCES

country: China

institute: Zhejiang University

type: Expression profiling by high throughput sequencing

summary: Here we report m5C-TAC-seq, a base-resolution sequencing method to directly detect m5C sites without affecting unmodified C. In m5C-seq, we combined TET-mediated oxidation of RNA m5C to f5C with the selective chemical labeling reaction of f5C, enabling both pre-enrichment of m5C-containing RNA and a m5C-to-T transition in reverse transcription. m5C-seq identifies 2,500 sites in the transcriptome of HeLa and 768 sites in the transcriptome-wide of HEK293T. In addition, taking advantage of barcoding and pooling strategy, m5C-seq detected differential m5C sites upon specific methyltransferases depletion in mESCs and dynamically regulated m5C sites under cell fate transition. Moreover, we also detected 215 sites in chromatin-associated RNAs, demonstrating that portion of m5C sites can be co-transcriptionally catalyzed and the existence of m5C methylations in repeat RNAs.

overall_design:
To explore m5C distribution in mRNA,we build a TET2-assisted m5C single base solution detect method
*** Please note that multiplexed raw files are designed to a protocol to repeat the data and, therefore, have been uploaded to SRA with special exception.

first: Xiaoting

first: Liang

last: Lu


title: Effect of miR-33 supression in hepatocytes in NAFLD and NASH

city: New Haven

first: PABLO

last: FERNANDEZ-TUSSY

state: CT

address: 10 amistad street, 420C

department: Comparative Medicine

country: USA

institute: Yale University

summary: We perform sc-RNAseq in NASH  livers from WT and miR-33-AlbCRE  conditional knock-out mice. Liver were isolated from mice after 6 months of feeding a choline deficient high fat diet to analyze the effect of miR-33 deficiency specifically in hepatocytes and the crosstalk between hepatocytes and other cell types in the liver.

overall_design: Liver single cell suspension from WT and mir-33 HKO mice after 6 months of CD-HFD feeding to indunce NASH.

first: Pablo

last: Fernández-Tussy

first: Carlos

last: Fernández-Hernando


title: Mitochondrial metabolism is a key determinant of chemotherapy sensitivity in Colorectal Cancer

status: Public on Sep 18 2024

city: Belfast

first: Deborah

middle: Y.

last: Moss

address: 97 Lisburn Road

department: Patrick G. Johnston Centre for Cancer Research

country: United Kingdom

institute: Queen's University Belfast

summary: Therapy resistance is attributed to over 80% of cancer deaths per year emphasizing the urgent need to overcome this challenge for improved patient outcomes. Despite its widespread use in colorectal cancer (CRC) treatment, resistance to 5-fluorouracil (5FU) remains poorly understood. Here, we investigate the transcriptional responses of CRC cells to 5FU treatment, revealing significant metabolic reprogramming towards heightened mitochondrial activity. Utilizing CRC models, we demonstrate sustained enhancement of mitochondrial biogenesis and function following 5FU treatment, leading to resistance in both in vitro and in vivo settings. Furthermore, we show that targeting mitochondrial metabolism, specifically by inhibiting Complex I (CI), sensitizes CRC cells to 5FU, resulting in delayed tumour growth and prolonged survival in preclinical models. Additionally, our analysis of patient data suggests that oxidative metabolism signatures may predict responses to 5FU-based chemotherapy. These findings shed light on mechanisms underlying 5FU resistance and propose a rational strategy for combination therapy in CRC, emphasizing the potential clinical benefit of targeting mitochondrial metabolism to overcome resistance and enhance patient outcomes.

overall_design: To investigate transcriptional differences between colorectal cancer organoids carrying Apcnull/Krasmutant/p53null genotype that are either sensitive (AKPV_PAR) or resistant (AKPV_5FURES) to 5-Fluorouracil (5FU)

middle: Y

first: Emma

middle: M

last: Kerr

first: Christopher

last: McCann

first: Simon

last: McDade

first: Emily

last: Rogan

first: Rachel

last: McCole


title: Multiomic single-cell sequencing of skin and blister fluid from patients with severe cutaneous adverse drug reactions.

city: Perth

first: Andrew

last: Gibson

state: Western Australia

address: Building 390, Discovery Way, Murdoch University

country: Australia

institute: Murdoch University

summary: Severe cutaneous adverse reactions (SCAR) are rare but life-threatening drug reactions mediated by human leukocyte antigen (HLA) class I-restricted CD8+ T-cells. To obtain an unbiased assessment of SCAR cellular immunopathogenesis, we performed single-cell (sc) transcriptome, surface proteome, and TCR sequencing (5' scRNA-TCR-CITE-seq, 10x Genomics) on unaffected skin, affected skin, and blister fluid from diverse SCAR patients.

overall_design: 5' scRNA-TCR-CITE-seq, 10x Genomics

first: Elizabeth

last: Phillips


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

status: Public on Sep 24 2024

city: Los Angeles

state: CA

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 presented here is a part of the Nanostring GeoMx DSP study.

overall_design:
319 ROIs are profiled. GeoMx DSP results of 79 ROIs in the midbrain (substaintia nigra, red nucleus, cerebral peduncle and periaqueduct grey matter)

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

first: Liuliu

last: Pan

first: Kathy

last: Ton


title: Targeting YAP/TAZ-TEAD as a precision therapy approach in head and neck squamous cell carcinoma

city: La Jolla

first: Kuniaki

last: Sato

address: 3855 Health Sciences Dr Room 2345

department: Moores Cancer Center

institute: University of California San Diego

summary: Dysregulation of the Hippo pathway and the consequent activation of its downstream targets, the transcriptional co-activators YAP and TAZ (YAP/TAZ), drives oncogenic transcriptional programs upon binding TEAD transcription factors in multiple human malignancies. The recent development of small molecule TEAD inhibitors (smTEADi) provides an opportunity to therapeutically target Hippo pathway dysregulation in cancer. In this regard, HPV-negative head and neck squamous cell carcinoma (HNSCC) harbor multiple genetic alterations that promote YAP/TAZ hyperactivation, raising the possibility that HNSCC cells might be dependent on YAP/TAZ-TEAD driven oncogenic transcriptional programs. To test this hypothesis, we examined the antitumor activity of the novel smTEADi, SW-682 and genetically encoded TEAD inhibitor peptide (pTEADi) in Cal33 HPV-negative HNSCC cell line-derived xenograft model. To elucidate the transcriptomic changes upon YAP/TAZ-TEAD inhibition, RNA extracted from xenograft tumors treated with SW-682 or pTEADi, as well as control, was subjected to RNA sequencing.

overall_design: Total RNA extracted from xenograft tumor tissues was subjected to paired-end 150bp sequencing on the Illumina NovaSeq6000 sequencer at Novogene Co., Ltd.. Sequencing reads were aligned to GRCh38 human reference genome by STAR v2.7.9 using Gencode v38 annotations. Read count data was generated by RSEM v1.3.1.

first: Lei

last: Chen

first: Ramiro

last: Iglesias-Bartolome

first: Silvio

last: Gutkind


title: Mitochondrial metabolism is a key determinant of chemotherapy sensitivity in Colorectal Cancer (HCT116)

overall_design: To investigate transcriptional response to treatment with 5-Fluorouracil (5FU) at two timepoints in human CRC cell line, HCT116


title: Deep learning of enhancer codes highlights similarities between mammalian and avian telencephalon cell types [stereoseq]

status: Public on Sep 16 2024

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

summary: Combinations of transcription factors govern the identity of cell types, which is reflected by genomic enhancer codes. We utilized deep learning to characterize these enhancer codes and devised three novel metrics to compare cell types in the telencephalon between mammals and birds. To this end, we generated single-cell multiome and spatially-resolved transcriptomics data of the chicken telencephalon. Enhancer codes of orthologous non-neuronal and GABAergic cell types show a high degree of similarity across vertebrates, while excitatory neurons of the mammalian neocortex and avian pallium exhibit varying degrees of similarity. Enhancer codes of avian mesopallial neurons are most similar to those of mammalian deep layer neurons. With this study, we present generally applicable deep learning approaches to characterize and compare cell types solely based on genomic sequences.

overall_design: 15 days domestic chicken (broiler) were used for the experiments. A coronal section of the telencephalon was dissected and analyzed with Stereo-seq spatial transcriptomics.

first: Nikolai

last: Hecker

first: Niklas

last: Kempynck

first: David

last: Mauduit

first: Darina

last: Abaffyova

first: Ioannis

last: Sarropoulus

first: Sam

last: Dieltens

first: Carmen

last: Bravo Gonzalez-Blas

first: Roel

last: Vandepoel

first: Elke

last: Leysen

first: Lynette

last: Lim

first: Joris

last: De Wit

first: Valerie

last: Christiaens

first: Suresh

last: Poovathingal

first: Aerts

last: Stein


title: Deciphering mRNA binding determinants of RBPs

status: Public on Sep 30 2024

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: We created mutliple sequence mutants of several RNA binding proteins. We thenmeasured the in-vivo RNA target specificity of them and the corresponidng (and more) wild type strains using a RNA tagging approach

overall_design: Pup2-tagged strains were generated and grown too exponential phase, when RNA was extracted for library construction

first: Inbal

last: Zigdon

first: Felix

last: Jonas

first: Miri

last: Carmi


title: Identifying the target genes of the arginine transcription factor ArgR

status: Public on Sep 15 2024

city: Haikou City, Hainan Province

first: Chaolun

last: Liu

address: 58 Minlan Road, Haikou City, Hainan Province, China

institute: Hainan University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To elucidate the target genes of ArgR in Aeromonas veronii, we engineered an Aeromonas veronii strain that expresses the ArgR protein fused to a 3× FLAG tag, and  FLAG antibodies were employed for the immunoprecipitation of DNA-protein complexes.

overall_design: Chromatin Immunoprecipitation and sequencing (ChIP-seq) for ArgR in Aeromonas veronii

first: Zucheng

last: Wang

first: Zhu


title: Androgen receptor splicing variant 7 (ARv7) promotes DNA damage response in prostate cancer cells

status: Public on Sep 14 2024

city: Changchun

first: Chen

last: Shao

state: Jilin

address: 126 Xinmin ST

institute: Jilin University

summary: In the treatment of patients with locally advanced prostate cancer (PCa), androgen deprivation therapy (ADT) significantly enhances the efficacy of radiotherapy by weakening the DNA damage response (DDR) pathway. Recently, several studies have suggested that androgen receptor splicing variants (ARvs) may mediate a compensatory DDR pathway when canonical androgen receptor (AR) signaling is inhibited, thus contributing to the resistance of some patients to this combinational treatment. However, the specific roles of certain ARvs as well as the detailed mechanism of how ARvs regulate the DDR are not well understood. Here, we demonstrated that AR splicing variant 7 (ARv7), which is the most abundant form of ARvs, significantly promotes the DDR of PCa cells under severe DNA damage independent of its parental AR by using the ionizing radiation (IR) and doxorubicin (Dox)-treated cell models. Mechanistically, ARv7 is sufficient to upregulate both the homologous recombination (HR) and the nonhomologous end joining (NHEJ) pathways by forming a positive regulatory loop with poly ADP-ribose polymerase 1 (PARP1). Moreover, the presence of ARv7 impairs the synergistic effect between AR antagonists and poly ADP-ribose polymerase (PARP) inhibitor, which has been recently shown to be a promising future treatment strategy for metastatic castration resistant prostate cancer (mCRPC). Combined, our data indicate that constitutively active ARv7 not only contributes to radioresistance after ADT, but may also serve as a potential predictive biomarker for assessing the efficacy of novel PARP inhibitor-based therapy in PCa.

overall_design: C4-2 cells stably expressing ARv7 and 22Rv-1 cells with ARv7 depletion were generated by puromycin selection. Then total RNA was extracted to assess the differentially expressed genes after ARv7 levels changes.

first: Haoge

last: Luo


title: 5' RACE (Rapid amplification of cDNA ends) and 3' RACE of U6 or U1-driven Cas13 CRISPR RNAs (crRNAs)

city: Hong Kong

first: S. Chul

last: Kwon

address: L1-05, Laboratory Block, 21 Sassoon Road, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) technologies have evolved rapidly over the past decade with the continuous discovery of new Cas systems. In particular, RNA-targeting CRISPR-Cas13 proteins are promising single-effector systems to regulate target mRNAs without altering genomic DNA, yet the current Cas13 systems are restrained by suboptimal efficiencies. Here, we show that U1 promoter-driven CRISPR RNAs (crRNAs) increase the efficiency of various applications, including RNA knockdown and editing, without modifying the Cas13 protein effector. We confirm that U1-driven crRNAs are exported into the cytoplasm, while conventional U6 promoter-driven crRNAs are mostly confined to the nucleus. Furthermore, we reveal that the end positions of crRNAs expressed by the U1 promoter are consistent regardless of guide sequences and lengths. We also demonstrate that U1-driven crRNAs, but not U6-driven crRNAs, can efficiently repress the translation of target genes in combination with catalytically inactive Cas13 proteins. Finally, we show that U1-driven crRNAs can counteract the inhibitory effect of miRNAs. Our simple and effective engineering enables unprecedented cytosolic RNA-targeting applications.

overall_design: U6 or U1-driven Cas13 crRNAs were expressed in HEK293E cells, and the 5' and 3' end positions of crRNAs were identified using 5' RACE and 3' RACE.

first: Ezra C.K.

last: Cheng


title: Maternal H3.3-Mediated Reprogramming of Parental Genomes during Minor Zygotic Genome Activation [CUT&TAG]

status: Public on Sep 12 2024

city: Harbin

first: Hou

middle: wei

last: bo

state: Heilongjiang

address: Xiangfang District

institute: College of Life Science,Northeast Agricultural University

summary: Zygotic gene activation (ZGA) is the first transcription event in life, and is associated with extensive epigenetic reprogramming, which is involved with dynamic incorporation of histone variant H3.3. H3.3 plays essential roles during mouse pre-implantation development. However, the coexistence of distinct sources of H3.3 in early embryos, including paternal and maternal allele-expressed H3.3 (paH3.3 and maH3.3), complicates our ability to track their individual dynamics, which may have distinct roles in embryonic development. In this study, by taking advantage of our H3.3B-HA-tagged mouse model, we illustrated the paH3.3 and maH3.3 landscapes in mouse early embryos, and described the manner of maternal mRNAs-derived H3.3 (mH3.3) on paternal genome reprogramming. We found the deposition of mH3.3 is required for cleavage development and minor ZGA, mechanistically, by mH3.3S31p-meditated acetylation at lysine 27. And, we propose that the mH3.3K27ac modification displaces the repressive histone modifications, thus enabling the activation of minor ZGA genes. Taken together, we demonstrate the central role of mH3.3 in reprogramming parental genomes by establishment of H3K27ac.

overall_design: We illustrated the paH3.3 and maH3.3 landscapes in mouse early embryos by taking advantage of our H3.3B-HA-tagged mouse model, and described the manner of maternal mRNAs-derived H3.3 (mH3.3) on paternal genome reprogramming. In the ChIP-seq analysis on pre-implantation embryos, 100 embryos were used for per reaction and two or three replicates were performed for each stage.

first: Jiaming

last: Zhang

first: Xuanwen

last: Li

first: Xiaoyu

first: Qingran

last: Kong

first: Duancheng

last: Wen


title: Maternal H3.3-Mediated Reprogramming of Parental Genomes during Minor Zygotic Genome Activation [ChIP-seq]


title: Maternal H3.3-Mediated Reprogramming of Parental Genomes during Minor Zygotic Genome Activation

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

overall_design: Refer to individual Series


title: Effect of glutamine and alphaketoglutarate in gene expression

status: Public on Sep 10 2024

city: Cologne

first: Bruna

last: Martins Garcia

address: Joseph-Stelzmann-Strasse 9B

country: Germany

institute: Max Planck Institute for Biology of Ageing

summary: Glutamine (gln) is an essential and versatile metabolite that feeds different cellular pathways and generates several derivatives. Alpha-ketoglutarate (aKG) is the gln derivative that feeds the TCA cycle, activates cellular growth, and is related to epigenetic changes. Despite gln importance, the specific role of gln – and not its derivatives – in gene expression is not clear. To address this question, U2OS cells were cultured in the presence of gln or its absence +/- aKG for 8 hours.  Gln had an unique effect in the transcriptome of U2OS cells and the addition of aKG was not able to mimic the gln effect. In conclusion, gln affects gene expression independently of its derivative aKG.

overall_design: To assess the role of gln in regulation gene expression, U2OS cells were cultured in the presence of gln or its absence +/- aKG for 8 hours.

first: Tania

last: Mederios

first: Lena

last: Pernas


title: All-defined NGN2 neuron protocol reveals multifaceted signatures of neuronal maturation.

city: South San Francisco

first: Mitchell

last: Rezzonico

address: 1 DNA Way

institute: Genentech


title: Single-cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos

status: Public on Sep 27 2024

city: nantong

first: wang

last: xiaoning

state: jiangsu

address: Qixiu Road 19

institute: Nantong University

summary: Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar-sweetened beverages. Nevertheless, the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently, we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model, we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels, especially intersegmental vessels (ISVs). The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells (ECs) into tip cells. Single-cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs, proliferating ECs, and a series of upregulated proangiogenic genes.

overall_design: Firstly, we isolated the EGFP-positive cells from control and high glucose-treated Tg(fli1ep:EGFP-CAAX) transgenic embryos. Following the proteolytic dissociation of embryos, the EGFP-positive cells were isolated by fluorescence-activated cell sorting (FACS). Around 300~500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large-scale scRNA-seq (10X Genomics) platform.

first: Xiaoning

first: Jinxiang

last: Zhao

first: Jiehuan

last: Xu

first: Bowen

first: Xia

first: Gangcai

last: Xie

first: Xuchu

last: Duan

first: Dong


title: Maternal H3.3-Mediated Reprogramming of Parental Genomes during Minor Zygotic Genome Activation [RNA-seq]

first: Hou

first: Jiaming

first: Xuanwen

last: Liu


title: Spatial Transcriptomics and bulk tissue direct gene expression in the postmortem brains of severe acute COVID19 patients and matched controls

first: Ting


title: CD103+CD56+ ILCs are associated with an immunosuppressed tumour microenvironment

status: Public on Sep 07 2024

city: Toronto

first: Pamela

last: Ohashi

state: Ontario

address: 610 University Ave

country: Canada

institute: Princess Margaret Cancer Centre

summary: Immunotherapies have had unprecedented success for multiple cancer types, albeit with variable response rates. Unravelling the complex network of immune cells within the tumour microenvironment (TME) may provide additional insights to enhance anti-tumour immunity and improve clinical response. Here, we identified a CD103-expressing CD56+ ILC subset that were associated with a poor proliferative capacity of tumour-infiltrating lymphocytes (TILs) in culture. We demonstrate that CD103+CD56+ ILCs isolated directly from tumors represent a distinct ILC population that expressed unique surface markers, transcription factor networks, and transcriptomic profiles compared to CD103-CD56+ NK cells. Using multiple approaches, we found that these CD103+CD56+ ILCs were associated with CD8+ T cells with a reduced expression of GZMB. This study identifies 59 a population of CD103+CD56+ ILCs with potentially inhibitory functions, that are associated with a TME that includes CD8+ T cells with poor anti-tumour activity. Further studies focusing on these potentially inhibitory cells may provide insights into understanding the biology of an inhibitory TME.

overall_design: 3 samples of High Grade Serous Ovarian Cancer, profiled by 10x single cell sequencing scRNA.

first: Chung

last: Douglas

first: Ohashi

last: Pamela


title: Transcription factors associated with regulation of transcriptome in human thigh and calf muscles at baseline and after six days of disuse

status: Public on Sep 08 2024

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

summary: Disuse has a negative impact on the postural muscles of the trunk and legs. Different leg muscles demonstrate a differentiated and conservative response to disuse, in terms of a decrease in muscle mass, strength, aerobic performance, and changes in gene expression. We aimed to identify transcription factors regulating gene expression at baseline and after disuse in human m. soleus – a “slow” muscle with a strong postural function, and “mixed“ m. vastus lateralis. Biopsies were taken from these muscles prior to and after 6 days of strict disuse (dry immersion). The enriched transcription factor binding sites (and corresponding factors) in the individual promoter regions of co-expressed genes were examined using the positional weight matrix approach. The baseline transcriptomic profiles and the disuse-induced changes (RNA-seq) differ significantly between muscles. In particular, the specific and significant response to disuse in m. soleus was found to be strongly related to the suppression of genes regulating the mitochondrial energy metabolism, the activation of the inflammatory response and the ubiquitin-proteasome system. This response is associated with the proinflammatory transcription factors such as families IRF, STAT, and other. The validity of approximately two-thirds of the predicted transcription factors was indirectly confirmed by the analysis of their function described in the literature. These identified transcription factors appear to be promising candidates for future targeted studies that mechanistically investigate gene expression regulation in various muscles at baseline, following disuse or inactivity.

overall_design: Ten males participated in a 7-day dry immersion (DI, ages 25–38 years; median height 1.78 m [interquartile range 1.71–1.79 m]; body mass 70 kg [64–74 kg]; and body mass index 24 kg/m² [21–24 kg/m²]). Muscle samples were taken using a Bergström needle with aspiration under local anesthesia (2 ml of 2% lidocaine) from the medial part of m. vastus lateralis (Vas) and m. soleus (Sol) muscles of the left leg 14 days before the start of DI (prior to any familiarization protocols and physiological tests, which did not included in the paper) and 6 days after the start of 7-day DI (at 10:00, 3 hours after a standardized light breakfast: 5.2 g protein, 2.7 g fat, 55 g carbohydrates, 1253 kJ). Strand-specific RNA libraries were prepared using the NEBNext Ultra II RNA kit (New England Biolabs, USA) and single-end sequencing was done by a NextSeq 550 analyzer (Illumina, USA).

first: Daniil

last: Popov

last: Makhnovskii


title: RGS2 is an innate immune checkpoint for suppressing Gαq mediated IFNγ generation and lung injury

status: Public on Sep 04 2024

city: Chicago

first: Vijay Avin

last: Balaji Ragunathrao

state: IL

address: 835 S Wolcott Ave

department: Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

summary: Infections can trigger the release of IFNγ, a type II interferon, which exacerbates tissue inflammation and may lead to severe acute lung injury (ALI). However, the regulatory mechanisms of IFNγ production in the lungs are not fully understood. In this study, we identified RGS2 as a crucial regulator of IFNγ levels in the lungs during infection. The absence of RGS2 led to persistently elevated IFNγ production in macrophages, resulting in unresolved inflammatory lung damage. Notably, this effect was absent in RGS2-deficient chimeric mice that received wild-type bone marrow or RGS2 expression in alveolar macrophages (AMs), as well as in those treated with an IFNγ-blocking antibody. RGS2 exerts its regulatory role by inhibiting Gαq-mediated IFNγ production and inflammatory signaling in AMs. Consequently, the inhibition of Gαq in RGS2-deficient mice prevented IFNγ production in AMs and shifted their transcriptomic profile from an inflammatory to a reparative state. These findings suggest that the RGS2-Gαq signaling pathway could be a promising therapeutic target for mitigating inflammatory lung injury.

overall_design: In this experiment, RNA sequencing (RNA-seq) was performed to investigate the transcriptomic effects of lipopolysaccharide (LPS)-induced inflammation in the lungs of wild-type (WT) and Rgs2 knockout (KO) mice. Bronchoalveolar lavage (BAL) collected 64 hours after LPS administration from both WT and Rgs2 KO mice, with or without treatment with the Gαq inhibitor (BIM-46187) (three mice per group pooled together). Total RNA was extracted using the RNeasy mini kit (Qiagen USA), and ribosomal RNA was depleted using the RiboMinus™ Eukaryote kit v2 (Thermo Fisher Scientific). RNA libraries were then constructed with the TruSeq RNA library prep kit v2 (Illumina) and sequenced using the NovaSeq 6000 platform with paired-end 150 bp reads.

first: Jagdish Chandra

last: Joshi

first: Bhagwati

first: Cuiping

last: Zhang

first: Somenath

last: Banerjee

first: Vigneshwaran

last: Vellingiri

last: Balaji Raghunathrao

first: Mumtaz

last: Anwar

first: Tejas Pravin

last: Rokade

first: Lianghui

first: Ruhul

last: Amin

first: Yuanlin

last: Song

first: Dolly

last: Mehta


title: Modulation of host gene expression by the zinc finger antiviral protein [CLIP-seq]

status: Public on Sep 01 2024

city: London

first: Daniel

last: Goncalves-Carneiro

address: Sir Alexander Fleming Building, Imperial College Rd

institute: Imperial College London

summary: The zinc finger antiviral protein (ZAP) depletes non-self RNAs through recognition of their elevated CpG dinucleotide content. CpG dinucleotides are sparse in most endogenous mammalian mRNAs, but a subset might potentially be modulated by ZAP. While CpG frequency alone is insufficient to predict ZAP-regulation, we developed an algorithm using experimentally determined compositional features to predict which endogenous mRNAs may be ZAP-regulated. Using ZAP-knockout mice, we demonstrate that levels of many host mRNAs that are algorithmically predicted ZAP targets are indeed increased when ZAP is absent. ZAP is interferon-inducibel and we also identify genes that are downregulated by ZAP during an innate immune response. Many ZAP-regulated gene products are extracellular matrix or of nucleosome components, whose ZAP mediated control is conserved in human cells. Overall, we provide a new tool for the prediction of ZAP target genes and reveal host mRNAs that are ZAP-regulated.

overall_design: The goal of the experiment was to analyze RNA sequences bound by the Zinc Finger Antiviral Protein (ZAP). ZAP:RNA complexes were extracted and purified from MT4 cells, reversed transcribed and analysed by NGS. Two biological replicates are included.

first: Paul

last: Bieniasz


title: Glycerophospholipid remodeling is critical for orthoflavivirus infection

status: Public on Sep 03 2024

city: Gießen

first: Torsten

last: Hain

state: Hessen

address: Schubertstraße 81

department: Institute for Medical Microbiology

institute: Justus-Liebig University

summary: Flavivirus infection is tightly connected to host lipid metabolism. Here, we performed shotgun lipidomics of cells infected with neurotropic Zika, West Nile, and tick-borne encephalitis viruses, as well as dengue and yellow fever virus. Early in infection specific lipids accumulated, e.g., neutral lipids in Zika and some lyso-phospholipids in all infections. Ceramide levels increased following infection with viruses that cause a cytopathic effect. In addition, fatty acid desaturation as well as glycerophospholipid metabolism were significantly altered. Importantly, depletion of enzymes involved in phosphatidylserine metabolism as well as phosphatidylinositol biosynthesis reduced orthoflavivirus titers and cytopathic effects while inhibition of fatty acid monounsaturation only rescued from virus-induced cell death. Interestingly, interfering with ceramide synthesis had opposing effects on virus replication and cytotoxicity depending on the targeted enzyme. Thus, lipid remodeling by orthoflaviviruses includes distinct changes but also common patterns shared by several viruses that are needed for efficient infection and replication.

overall_design: Shotgun lipidomics and transcriptomics of cells infected with neurotropic Zika, West Nile, and tick-borne encephalitis viruses, as well as dengue and yellow fever virus. Early in infection specific lipids accumulated, e.g., neutral lipids in Zika and some lyso-phospholipids in all infections.

first: Julia

last: Hehner

first: Laura

last: Schneider

first: Anna

last: Woitalla

first: Benjamin

last: Ott

first: Anja

last: Schöbel

first: Dominik

last: Schwudke

first: Eva

last: Herker


title: RNA-sequence facilitates analyze changes of P3 Plscr5 knockout mice

status: Public on Aug 31 2024

city: Nanjing

first: Guoqiang

last: Wan

state: Jiangsu

address: Xuefu Road 12

department: Medical School

institute: Nanjing University

summary: We report application of RNA-seq for transcriptomic analyses of cochlear tissues from wildtype and Plscr5 knockout mice to reveal gene expressions altered by Plscr5 knock out

overall_design: Cochlear tissues (3 each genotype) were collected from P3 Plscr5 knockout mice and wildtype mice and subjected to RNA-seq

first: Sihao

last: Gong


title: DNA methylation dynamics in male germline development in Brassica rapa [RNA-seq/Bisulfite-seq]

city: Shanghai

first: Hongbo

last: Gao

address: 800 Dongchuan Rd

department: School of Agriculture and Biology

institute: Shanghai Jiao Tong University

type: Methylation profiling by high throughput sequencing

summary: Cytosine DNA methylation (mC) can silence transposable elements (TEs) and regulate gene expression. However, the mechanism and function of DNA methylation reprogramming during plant development are still largely unknown. To explore the DNA methylation dynamics during the male sexual-lineage development in the Brassicaceae family, we assessed the mC level in meiocyte, microspore and pollen of a Brassica rapa doubled haploid (DH) line by whole genome bisulfite sequencing (WGBS). Analysis of global mC profiles showed that significant reprogramming of CHH methylation occurred in the Brassica rapa male sex cells, similar to that observed in Arabidopsis. Analysis of differential methylation sites identified specific methylation loci in sex cells that can target and possibly regulate gene expression, suggesting a mechanism consistent with that of Arabidopsis. Quite a few long terminal repeat (LTR) transposable elements were activated in meiocyte and microspore, which correlated with reduced DNA methylation. Expression analysis of key genes that affect DNA methylation showed that active methylation and demethylation occurred during male sexual lineage development. These results suggest a conserved DNA methylation reprogramming mechanism during Brassica rapa male sex lineage development. The transcriptome and DNA methylome data obtained will also be useful for other mechanism studies in Brassica rapa.

overall_design: To better understand the DNA methylation reprogramming during male sexual lineage development of Brassica rapa, we analyzed DNA methylome and transcriptome of several male cell types, including meiocyte, microspore and pollen in a DH line ‘K2’ of Non-heading Chinese cabbage (Brassica rapa. ssp. Chinensis), and demonstrated the methylation patterns and the potential influences on transcription across sequence contexts, genic and TEs regions. In addition, we also identified differentially-methylated regions (DMRs), found and analyzed sexual-lineage-specific DNA methylation in Brassica rapa.

first: Jun

last: Zhang

first: Di

last: Wu

first: Yating

first: Xiaoqi

last: Feng


title: Depletion of ABHD17B mRNA in primary human hepatic stellate cells

city: Boston

first: Alan

middle: C.

last: Mullen

state: MA

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

summary: ABHD17B mRNA was depleted in primary human hepatic stellate cells  to evaulate effect on gene expression.

overall_design: Gene expression profiling was perfomred in human hepatic stellate cells using two siRNAs that depleted ABHD17B

first: Robert

last: Sparks

first: Cheng

last: Sun

first: Wenyang

last: Li

first: Victor

last: Barrera

first: Shannan

last: Ho Sui

first: Raza

last: Rahman

middle: C


title: RNAseq of WT + pctrl, ∆flaX + pctrl and ∆flaX + pPflaAX in V. cholerae

status: Public on Aug 28 2024

city: Jena

first: Rabea

last: Ghandour

address: Winzerlaer Straße 2

department: Institute of Microbiology

institute: Friedrich Schiller University

summary: Gene regulation at the post-transcriptional level is prevalent in all domains of life. In bacteria, ProQ-like proteins have emerged as important RNA chaperones facilitating RNA stability and RNA duplex formation. In the major human pathogen V. cholerae, post-transcriptional gene regulation is key for virulence, biofilm formation, and antibiotic resistance, yet the role of ProQ has not been studied. Here, we show that ProQ interacts with hundreds of transcripts in V. cholerae, including the highly abundant FlaX small RNA (sRNA). Global analyses of RNA duplex formation using RIL-Seq (RNA interaction by ligation and sequencing) revealed a vast network of ProQ-assisted interactions and identified a role for FlaX in motility regulation. Specifically, FlaX base-pairs with multiple sites on the flaB flagellin mRNA, preventing 30S ribosome binding and translation initiation. V. cholerae cells lacking flaX display impaired motility gene expression, altered flagella composition, and reduced swimming in liquid environments. Our results provide a global view on ProQ-mediated RNA duplex formation and pinpoint the mechanistic and phenotypic consequences associated with ProQ-associated sRNAs in V. cholerae.

overall_design: To investigate the impact of FlaX sRNA on transcriptional changes, V. cholerae WT + pctrl, ∆flaX + pctrl and ∆flaX + pPflaAX were cultivated in LB medium to OD600 of 0.2 and 2.0. Three biological replicates for each condition are provided.

first: Kai

last: Papenfort


title: GATA6 regulates WNT and BMP programs to pattern precardiac mesoderm during the earliest stages of human cardiogenesis (CUT&RUN)

status: Public on Aug 27 2024

city: New York

first: Joseph

middle: A.

last: Bisson

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Haploinsufficiency for GATA6 is associated with congenital heart disease (CHD) with variable comorbidity of pancreatic or diaphragm defects, although the etiology of disease is not well understood. Here, we used cardiac directed differentiation from human embryonic stem cells (hESCs) as a platform to study GATA6 function during early cardiogenesis. GATA6 loss-of-function hESCs had a profound impairment in cardiac progenitor cell (CPC) specification and cardiomyocyte (CM) generation due to early defects during the mesendoderm and lateral mesoderm patterning stages. Profiling by RNA-seq and CUT&RUN identified genes of the WNT and BMP programs regulated by GATA6 during early mesoderm patterning. Furthermore, interactome analysis detected GATA6 binding with developmental transcription factors and chromatin remodelers suggesting cooperative regulation of cardiac lineage gene accessibility. We show that modulating WNT and BMP inputs during the first 48 hours of cardiac differentiation is sufficient to partially rescue CPC and CM defects in GATA6 heterozygous and homozygous mutant hESCs. This study provides evidence of the regulatory functions for GATA6 directing human precardiac mesoderm patterning during the earliest stages of cardiogenesis to further our understanding of haploinsufficiency causing CHD and the co-occurrence of cardiac and other organ defects caused by human GATA6 mutations.

overall_design: CUT&RUN was performed on control H1-GATA6-hESCs (GATA6+/+) using a GATA6 antibody and IgG control antibody at day 2 of in vitro cardiac directed differentiation.


title: Gene expression analysis of cervical cancer cells transfected with siRNAs against either HPV E6 or E6/E7

status: Public on Aug 25 2024

city: Tsukuba

first: Takeo

last: Minaguchi

state: Ibaraki

address: 1-1-1 Tennoudai

country: Japan

institute: University of Tsukuba

summary: The study aimed to explore HPV E7-specific pathways in cervical cancer cells.

overall_design:
CaSki and HeLa cells were transfected with siRNAs against either HPV E6 or E6/E7, control siRNA, or mock. Cells were harvested at 24 hours after transfection.

**The raw and processed data were removed from GSE274812 due to data confidentiality concerns*


title: GATA6 regulates WNT and BMP programs to pattern precardiac mesoderm during the earliest stages of human cardiogenesis (RNA-Seq)

overall_design: RNA-seqeuncing was performed on H1-GATA6-hESCs (GATA6+/+, GATA6+/-, and GATA6-/-) at days 2, 3, and 5 of in vitro cardiac directed differentiation.


title: Effect of Ndrg3-deficiency on gene expression by CD8SP thymocytes

status: Public on Aug 26 2024

city: Freiburg

first: Jeremy

last: Swann

address: Stübeweg 51

department: Developmental Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: The objective of this study was to determine gene expression changes that occur as a result of Ndrg3-deficiency in mature CD8+ thymocytes. Our research has revealed that conditional ablation of Ndrg3 in the T cell lineage causes a significant loss of naive CD8+ T cells, and in order to determine the basis for this defect, we isolated mature, CD8 single-positive thymocytes from control and knockout mice, and subjected them to RNA-seq analysis to identify genes that were dysregulated in the absence of Ndrg3.

overall_design: CD8SP TCRb+MHCIhi thymocytes were isolated by fluorescence-activated cell sorting (FACS) from control and Ndrg3 conditional knockout mice. Total RNA was subsequently extracted from the sorted cells, and subjected to RNA-seq analysis to determine gene expression changes between control and conditional knockout groups. Four biological replicates were performed per group.

first: Julia

last: Komorowska

first: Mirela

last: Balan


title: Effect of YKL-40 on melanoma proliferation in a mouse model.

city: Weifang

first: Yubing

last: WANG

state: Shandong

address: no.7166 Baotong Street, Weicheng

institute: Weifang Medical University

summary: To investigate the effect of YKL-40 on melanoma proliferation in C57BL/6J mice, we established a B16F10 cell line overexpressing YKL-40. Then we used the cells for subcutaneous injection into mice, thereby establishing a tumor model. Finally, we performed gene expression profiling using data obtained from RNA-seq of mouse melanoma tissues.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for melanoma tumor tissue formed subcutaneously in mice by B16F10 cells overexpressing YKL-40

last: Wang

first: Mengqi

last: Shi


title: Rapid in vitro evolution of flucytosine resistance in Candida auris

status: Public on Aug 22 2024

city: Vienna

first: Trinh

last: Phan-Canh

email: phancanht99@univie.ac.at, phancanhtrinh@gmail.com, karl.kuchler@univie.ac.at, karl.kuchler@univie.ac.at

state: Vienna

address: Dr.-Bohr-Gasse 9

department: Max Perutz Labs Vienna, Campus Vienna Biocenter

country: Austria

institute: Medical University of Vienna

summary: Comparative transcriptomic profiling of Candida auris derivative clones collected from 5FC-containing medium in comparison to the Wild-Type Strain

overall_design: RNA Sequencing was conducted on a multidrug resistant Candida auris 1133/P/13R and its derivatives clones after treated with 5FC. The cells were cultivated to the exponential phase in YPD at 37°C with agitation at 200rpm. Subsequently, cultures were harvested, and RNA isolation was performed, followed by the preparation of sequencing libraries for three biological replicates.

first: Karl

last: Kuchler


title: Genome-scale CRISPRi Perturb-seq on both unstimulated and stimulated Jurkat cells reveals regulators of human T-cell signaling

city: Washington

first: Bicna

last: Song

state: DC

address: 7144 13th Pl NW

institute: Children's National Hospital

summary: The goal of the experiment is to identify genes involved in T-cell receptor (TCR) signaling and T-cell activation in human T cells.

overall_design: The Jurkat E6 cell line, engineered to express dCas9-KRAB and transduced with a genome-wide CRISPRi CROP-seq library, was isolated through Fluorescence-activated cell sorting (FACS) based on the percentage of GFP positivity. Subsequently, the isolated cells underwent analysis using single-cell RNA sequencing.

first: Anatoly

last: Vasilyev

first: Adam

last: Krejci

first: Nicole

last: Untermoser

first: Anke

last: Loregger

first: Tilmann

last: Bürckstümmer

first: Wei


title: Enhancing Immunotherapy Outcomes: Spatial Multi-Omics Predictive Models for Non-Small Cell Lung Cancer

city: New Haven

first: Thazin

middle: Nwe

last: Aung

address: 310 Cedar Street

institute: Yale University

summary: Non–small cell lung cancer (NSCLC) has an increasing number of targeted and systemic therapies allowing subsets of patients to achieve long–term durable benefit. Fundamental to understanding responses to a given therapy is comprehensive molecular characterization of the underlying tumor immune microenvironment (TIME). The TIME may inform models to predict immunotherapy outcomes and features to delineate therapeutic responses and clinical endpoints. We hypothesize that an integrated multi–omics approach will uncover interactions within the NSCLC TIME and identify novel biomarkers that are predictive of immunotherapy responses, thus aiding precision oncology. To develop a spatially resolved TIME model for NSCLC immunotherapy, we utilized a multi–omics approach, combining spatial mapping of protein expression at the single–cell resolution by Phenocycler Fusion (PCF) and multi–cellular readout whole transcriptome profiling at cellular compartment resolution by Digital Spatial Profiling (DSP–GeoMx–WTA). This approach facilitated a detailed examination of the TIME in NSCLC samples from patients undergoing first–line immunotherapy. We studied two independent cohorts of advanced NSCLC tissue samples, treated with PD–1–based immunotherapies. We derived gene signatures from cell type signatures to predict treatment outcomes using a multistage Least Absolute Shrinkage and Selection Operator (LASSO) approach. Our spatial proteomic analysis identified three distinct cell types, proliferating tumor cells, granulocytes, and vessels, associated with resistance to immunotherapy. A high proportion of these cell types demonstrated a hazard ratio (HR) of 3.8 (p = 0.004) in the Yale training cohort and 1.8 (p = 0.05) in the UQ validation cohort. In the response cell–type model, higher levels of M1 macrophages, M2 macrophages, and CD4 T cells had an HR of 0.4 (p = 0.019) in the training cohort and 0.49 (p = 0.036) in the validation. In the transcriptomic analysis, gene signatures derived from these cell types predicted outcomes with high accuracy. The resistance gene model, which included 8 genes associated with epithelial–mesenchymal transition (EMT) and cell migration, showed an HR of 5.3 (p < 0.001) in the Yale training cohort, 2.2 (p = 0.036) in the UQ validation cohort, and 1.7 (p = 0.042) in the Greece validation cohort. Conversely, the response gene model, consisting of 8 genes associated with immunomodulation, had an HR of 0.22 (p = 0.005) in the Yale training cohort, 0.38 (p = 0.034) in the UQ validation cohort, and 0.56 (p = 0.041) in the Greece validation cohort. Multivariable analysis, adjusting for age, sex, disease stage, prior chemotherapy, type of immunotherapy, line of immunotherapy, histology, and smoking status, confirmed that the resistance signature remained significantly associated with worse outcomes, while the response signature remained associated with improved outcomes in both the UQ and Greece cohorts. This research highlights the potential of a multi–omics cell typing and gene expression profiling approach in advancing NSCLC treatment toward precision oncology. By offering insights into the TIME and unveiling novel biomarkers, our model seeks to define resistance and to improve prediction of response to treatment.

overall_design: We utilized a multi-omics approach, combining CODEX for spatial mapping of protein expressions at the single-cell level and DSP-WTA for comprehensive transcriptomic insights from the cell types identified by CODEX. This methodology facilitated a detailed examination of the TIME in NSCLC samples from patients undergoing first-line immunotherapy.

middle: N

first: Jonathan

middle: H

last: Warrell

first: David

middle: L

last: Rimm

first: Arutha

last: Kulasinghe


title: Single-cell CRISPR Screen for HIV Host Dependency Factors Involved in Latency Reversal

summary: Perturb-seq reveals intrinsic and extrinsic biological factors that regulate gene functions in laten HIV expression.

overall_design: We used a Jurkat HIV cell model that we previously established for pooled CRISPR screening, where cells stably expresses Cas9 and are latently infected with HIV-GFP viral vectors. We performed Perturb-seq experiments on three different conditions, including stimulated Jurkat (by PMA/I) followed by GFP expression sorting (GFP+ or GFP-), or unstimulated cells.

first: Weiwei

last: Dai

first: Natalie

last: McMyn

first: Hao

last: Zhang

first: Jenet

last: Siliciano

first: Robert

last: Li


title: Dynamic promoter-enhancer contacts contribute to spatiotemporal gene expression during mouse fetal development

status: Public on Sep 02 2024

city: Cleveland

first: Ming

last: Hu

state: OH

address: 9500 Euclid Avenue

institute: Cleveland Clinic

summary: While a rich set of putative cis-regulatory sequences involved in mouse fetal development has been annotated recently based on chromatin accessibility and histone modification patterns, delineating their roles in developmentally regulated gene expression continues to be challenging due to a lack of information regarding their putative target genes. To fill this gap, we examined the tissue-to-tissue variability and developmental dynamics of chromatin contacts between gene promoters and distal sequences genome-wide in mouse embryos. Among the 248,620 long-range chromatin interactions centered at 14,138 protein-coding genes, many occur between promoters and putative enhancers located hundreds of kilobases away. More than 75% of the chromatin interactions coincide with the binding of CTCF at one or both anchors, underscoring a broad role for this chromatin organizer in developmentally regulated 3D chromatin conformation. The predicted target genes of 15,098 candidate enhancers demonstrate highly tissue-specific and developmental stage restricted expression patterns, and may facilitate the annotation of noncoding risk variants associated with human diseases.

overall_design: We performed H3K4me3 PLAC-seq and CTCF ChIP-seq across twelve tissues and developmental stages in mouse embryos to investigate the promoter-centered interactomes during fetal development.

first: Miao

last: Yu

first: Nathan

middle: R

last: Zemke

first: Ziyin

last: Chen

first: Ivan

last: Juric

first: Rong

first: Ramya

last: Raviram

first: Armen

last: Abnousi

first: Rongxin

last: Fang

first: Yanxiao

middle: U

last: Gorkin

first: Yang

first: Yuan

last: Zhao

first: Lindsay

last: Lee

first: Anthony

middle: D

last: Schmitt

first: Yunjiang

last: Qiu

first: Diane

middle: E

last: Dickel

first: Axel

last: Visel

first: Len

middle: A

last: Penacchio

first: Bing

last: Ren


title: Reconstitution of SPO11-dependent double-strand break formation

status: Public on Aug 20 2024

first: Meret

last: Arter

address: 430 E 67th Street

institute: Memorial Sloan Kettering Cancer Center

summary: Homologous meiotic recombination starts with DNA double-strand breaks (DSBs) generated by SPO11 protein. SPO11 is critical for meiosis in most species but the DSBs it makes are also dangerous because of their mutagenic and gametocidal potential, so cells must foster beneficial functions of SPO11 while minimizing its risks. SPO11 mechanism and regulation remain poorly understood. Here we report reconstitution of DNA cleavage in vitro with purified recombinant mouse SPO11 bound to its essential partner TOP6BL. Similar to their yeast orthologs, SPO11–TOP6BL complexes are monomeric (1:1) in solution and bind tightly to DNA. Unlike in yeast, however, dimeric (2:2) assemblies of mouse SPO11–TOP6BL cleaves DNA to form covalent 5 prime attachments requiring SPO11 active site residues, divalent metal ions, and SPO11 dimerization. Surprisingly, SPO11 can also manifest topoisomerase activity by relaxing supercoils and resealing DNA that it has nicked. Structure modeling with AlphaFold3 illuminates the protein-DNA interface and suggests that DNA is bent prior to cleavage. Deep sequencing of in vitro cleavage products reveals a rotationally symmetric base composition bias that partially explains DSB site preferences in vivo. Cleavage is inefficient on complex DNA substrates, partly because SPO11 is readily trapped in DSB-incompetent (presumably monomeric) binding states that exchange slowly. However, cleavage is improved by using substrates that favor DSB-competent dimer assembly, or by fusing SPO11 to an artificial dimerization module. Our results inform a model in which intrinsically feeble dimerization restrains SPO11 activity in vivo, making it exquisitely dependent on accessory proteins that focus and control DSB formation so that it happens only at the right time and the right places.

sample_organism:
Escherichia coli
Saccharomyces cerevisiae
Mus musculus
Cloning vector pUC19

overall_design: Detection of DNA double strand break ends generated by mSPO11 in vitro and in vivo

first: Shintaro

last: Yamada

first: Scott

last: Keeney


title: Pancreatic Differentiation Clones and Pooled Single-cell RNA-seq

first: Bicna

last: Song

summary: scRNA-seq identifies novel cell-type dependent gene functions in regulating pancreatic cell differentiation.

overall_design: Transcriptional profiling of WT and HHEX KO, FOXA1 KO, OTUD5 KO, CCDC6 KO hESC-derived cells at different stages of pancreatic differentiation.

first: Dingyu

last: Liu

first: Dapeng

last: Yang

first: Danwei

last: Huangfu

first: Wei

last: Li


title: Decoding Heterogenous Single-cell Perturbation Responses

status: Public on Aug 21 2024

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

overall_design: Refer to individual Series


title: Transcriptome analysis of callus tissues generated from pnet1 mutant, PNET1 overexpression line, and wild-type Arabidopsis

city: Berkeley

first: Yangnan

last: Gu

state: California

address: 371A Koshland Hall

department: Plant & Microbial Biology

institute: UC Berkeley

summary: Purpose: To understand the changes in cell cycle related genes in the callus tissues when PNET1 is ectopically expressed. we performed the whole genome transcriptome analysis on callus induced from the hypocotyls of WT, pnet1 mutant, and PNET1 overexpression line using RNA-seq. Conclusions: Most cell cycle related genes were downregulated in pnet1 mutant but upregulated in PNET1 overexpression line.

overall_design: mRNA profiles of 10-day old callus of wild type (Col-0), pnet1 mutant, and PNET1 overexpression line were generated by deep sequencing, in triplicate, using Illumina HiSeq PE-150.

first: Yiling

last: Fang


title: A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin [ChIPseq]

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Transcription factors (TFs) are key regulators of gene expression, yet many of their targets and modes of action remain unknown. In Schizosaccharomyces pombe, one-third of TFs are solely homology-predicted, with few experimentally validated. We created a comprehensive library of 89 endogenously tagged S. pombe TFs, mapping their protein and chromatin interactions using immunoprecipitation mass-spectrometry and chromatin immunoprecipitation sequencing. Our study identified protein interactors for half the TFs, with over a quarter potentially forming stable complexes. We discovered DNA binding sites for most TFs across 2,027 unique genomic regions, revealing motifs for 38 TFs and uncovering a complex regulatory network of extensive TF cross- and autoregulation. Characterization of the largest TF family revealed conserved DNA sequence preferences but diverse binding patterns, and identified a repressive heterodimer, Ntu1/Ntu2, linked to perinuclear gene localization. Our TFexplorer webtool makes all data interactively accessible, offering new insights into TF interactions and regulatory mechanisms with broad biological relevance.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for endogenously tagged transcription factors in vegetatively growing Schizosaccharomyces pombe cells.

first: Merle

last: Skribbe

first: Charlotte

last: Soneson

first: Michael

middle: B

last: Stadler

first: Michaela

last: Schwaiger

first: Vishnu

last: Suma Sreechakram

first: Vytautas

last: Iesmantavicius

first: Daniel

last: Hess

first: Eliza

last: Pandini Figueiredo Moreno

first: Sigurd

last: Braun

first: Jan

last: Seebacher

first: Sebastien

last: Smallwood

first: Marc

last: Bühler


title: Spatial transcriptomics profile at single cell level of murine glioblastomas treated with and without anti-CSF-1R inhibitors.

status: Public on Aug 10 2024

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: Anti-CSF-1R treatment results in rapid regression of murne proneural glioblastoma models. However, the microenvironment response to treatment results in fibrosis that can promote tumor recurrence. We investigated the single-cell transcriptional profile of murine glioblastomas before and after treatment with an anti-CSF-1R inhibitor to determine the cause of fibrotic treatment response.

overall_design: Gliobastomas were induced in mice using the RCAS model system at 5-weeks of age. Mice were monitored by MRI over the next 6 weeks until tumors developed that were at least 30 mm3 in volume. 3 mice were sacraficed prior to the initiation of treatment. 9 mice were treated daily with 200 mg/kg BLZ945 (Novartis), 3 were sacraficed 7-days post treatment, 3 at 28-days, 3 after rebound. All brain tumor samples were harvested and immediately embedded for cryosectioning for In Situ spatial transcriptomics using the 10X Genomics Xenium platform.

first: Spencer

last: Watson

first: Anoek

last: Zomer

first: Johanna

last: Joyce


title: Gene expression profile at single cell level of murine glioblastomas treated with and without anti-CSF-1R inhibitors

overall_design: Gliobastomas were induced in mice using the RCAS model system at 5-weeks of age. Mice were monitored by MRI over the next 6 weeks until tumors developed that were at least 30 mm3 in volume. 3 mice were sacraficed at this time point prior to the initiation of treatment. 6 mice were treated daily with 200 mg/kg BLZ945 (Novartis), 3 were sacraficed 7-days post treatment, 3 at 14-days. All tumors were harvested from brain tissue and immediately dissociated with collagenase/dispase and gentle mechanical agitation, then single-cell barcoded cDNA libraries were created using the 10X Chormium workflow. Once all libraries were collected, samples were submited for next-generation sequencing at Genewiz.


title: A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin [RNAseq]

first: Fabio

last: Mohn

overall_design: mRNA extraction and sequencing (mRNA-seq) from wildtype and Ntu1 or Ntu2 knockout Schizosaccharomyces pombe cells.


title: Spatial and scRNAseq profiling of murine glioblastomas treated with and without anti-CSF-1R inhibitors


title: A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin


title: Elucidating the human tRNA transcriptome dependent upon the TRMT1 and TRMT1L paralogs for modification, stability, and function

status: Public on Aug 09 2024

city: Santa Cruz

first: Todd

last: Lowe

state: CA

address: 1156 High Street

department: Biomolecular Engineering and Bioinformatics

institute: University of California Santa Cruz

summary: The tRNA methyltransferase 1 (TRMT1) enzyme catalyzes the formation of dimethylguanosine (m2,2G) in tRNAs. Loss-of-function mutations in TRMT1 lead to intellectual disability disorders in humans. In addition to TRMT1, vertebrates encode a tRNA methyltransferase 1-like (TRMT1L) paralog. Here, we use a comprehensive tRNA sequencing approach to decipher the landscape of tRNAs that are modified by human TRMT1 and TRMT1L. We find that TRMT1 modifies a single position in more than half of all cytoplasmic tRNAs and a subset of mitochondrial tRNAs. Notably, TRMT1 and TRMT1L catalyze m2,2G formation at distinct positions in tyrosine tRNAs that are each required for the efficient installation of additional modifications. Moreover, we identify a role for m2,2G modification in the stability of tyrosine and serine tRNAs that is abrogated in human patient cells homozygous for pathogenic TRMT1 variants. Human cells deficient in TRMT1 and/or TRMT1L exhibit reduced translation of specific codons, indicating that m2,2G modifications are necessary for maintaining functional levels of certain tRNAs. These findings uncover key roles for the m2,2G modification, and pinpoint tRNAs that are dysregulated in neurodevelopmental disorders caused by tRNA modification deficiency.

overall_design: CRISPR editing was performed by transfecting px333 plasmids containing guide RNAs targeting TRMT1, TRMT1L, or a scramble sequence (SCR) into HEK293T cells. PNK-treated RNA was used for Ordered Two Template Relay to generate small RNA libraries in biological triplicate. Sequencing data was analyzed by tRNA expression analysis (tRAX) software for accurate tRNA mapping and downstream analyses.

first: Kejia

last: Zhang

first: Aidan

last: Manning

first: Jenna

last: Lentini

first: Jonathan

last: Howard

first: Patricia

middle: P

last: Chan

first: Hayley

last: Chang

first: Dragony

last: Fu


title: Dissection of in vivo fasting on pancreatic ILC2 function and migration [scRNA-Seq]

status: Public on Aug 05 2024

city: Lisbon

first: Miguel

middle: Alves

last: Rendas

address: Avenida Brasília, 1400-038 Lisbon

department: Physiology and Cancer

country: Portugal

institute: Champalimaud Foundation

summary: Recent studies showed that ILC2 are important regulators of glucose homeostasis. Yet, to date it is not known if fasting influence function and migration of pancreatic ILC2 to help to maintain glucose homeostasis. In this study we showed that enteric sympathetic-ILC2 units respond to low body energy levels, setting an ILC2 gut-pancreatic migration route, leading to increased pancreatic glucagon and maintenance of glucose homeostasis.

overall_design: Expression profiling of genes associated with ILC2 function and identity.

first: Marko

last: Šestan

first: Bruno

last: Raposo

first: David

last: Brea

first: Roksana

last: Pirzgalska

first: Ana

last: Rasteiro

first: Maria

last: Aliseychik

first: Inês

last: Godinho

first: Hélder

last: Ribeiro

first: Tânia

last: Carvalho

first: Stephan

last: Wueest

first: Daniel

last: Konrad

first: Henrique

last: Veiga-Fernandes


title: Dissection of in vivo fasting on pancreatic ILC2 function [RNA-Seq]

summary: Recent studies showed that ILC2 are important regulators of glucose homeostasis. Yet, to date it is not known if fasting influence function of pancreatic ILC2 to help to maintain glucose homeostasis. In this study we showed that enteric sympathetic-ILC2 units respond to low body energy levels, setting an ILC2 gut-pancreatic migration route, leading to increased pancreatic glucagon and maintenance of glucose homeostasis.

overall_design: Expression profiling of genes associated with ILC2 function.


title: TCF4 is a key mediator of cell identity in neuroblastoma and vulnerable to protein degradation by multiple epigenetic factors [ChIP-seq]

city: Memphis

first: Kevin

last: Freeman

address: 19 S. Manassas

department: GGI

institute: UTHSC

summary: Neuroblastomas (NBs) are aggressive pediatric tumors that are responsible for up to 15% of all pediatric cancer deaths. Two differentiation states exist in NB tumors, a majority of more committed ADRN tumor cells and a minority of neural crest cell (MES/NCC)-like cells. The transition between identity states is governed by different sets of master TFs that collectively form core regulatory circuitries (CRC) that drive high expression of downstream lineage-specific genes. In this study we aim to discover new lineage dependency factors in NB. Here, we identified the E-box transcription factor TCF4 (E2-2) not previously reported in NB to be a critical factor shared across both NB states and play important role in driving NB oncogenesis. We performed multiple functional and high-throughput analysis to delineate the unrecognized function of TCF4 in NB

overall_design: To determine the consequences of TCF4 knockdown, we transduced two representatives NB cell lines Kelly (ADRN) and SK-N-AS (MES) with three doxycycline-inducible shRNA expression vectors targeting TCF4 KD (#2 and #3). we first performed RNA-seq analysis after TCF4 KD in Kelly and SK-N-AS cells to identify TCF4-regulated genes. We next examined the genome-wide occupancy of TCF4 by chromatin immunoprecipitation sequencing (ChIP-seq) analysis in Kelly and SK-N-AS cells. To identify TCF4 direct targets, we integrated the ChIP-seq and RNA-seq data for TCF4 KD in both NB cells

first: Nour

last: Aljouda

middle: W


title: TCF4 is a key mediator of cell identity in neuroblastoma and vulnerable to protein degradation by multiple epigenetic factors [RNA-seq]


title: TCF4 is a key mediator of cell identity in neuroblastoma and vulnerable to protein degradation by multiple epigenetic factors


title: Extraction of a Stromal Metastatic Gene Signature in Breast Cancer via Spatial Profiling

status: Public on Aug 04 2024

city: Palermo

first: Claudio

last: Tripodo

address: Corso Tukory 211

department: PROMISE

country: Italy

institute: Univerisity of Palermo

summary: The identification of molecular characteristics that define metastatic disease is a primary research focus across numerous types of malignancies. Understanding the mechanisms that drive metastatic foci, which diverge significantly from the biology of primary tumors, and identifying new biomarkers specifically associated with metastatic disease, is of critical importance in oncology. Consequently, the characterization of the stroma associated with metastatic foci has been largely unexplored and remains an area requiring significant investigation. We identified a detailed transcriptional profile of the stromal compartment within primary tumors and corresponding metastatic foci using spatially resolved approaches. The identified stromal Met signature may serve as a prognostic biomarker and provide insights into the molecular mechanisms underlying the metastatic potential of the tumor microenvironment.

overall_design: 1x105 4T1 cells were resuspended in PBS and injected in the mammary fat pad of 8-week- old BALB/c mice. After 28 days from the inoculum, mice were sacrificed, and tumors and lungs were collected for histopathologicand spatial transcriptomical analyses.  Four micrometer-thick FFPE sections  were sliced and mounted on a Visium glass slide before undergoing HE staining.

first: Valeria

last: Cancila

first: Giorgio

last: Bertolazzi


title: A small protein encoded by lncRNA PCBP1-AS1 promotes the replication of influenza virus via regulating the expression of proviral effectors

status: Public on Aug 03 2024

city: Fuzhou

first: Song

last: Wang

state: Fujian

address: Cangshan District

institute: Fujian Agriculture and Forestry University

summary: Many annotated long noncoding RNAs (lncRNAs) contain small open reading frames (sORFs), some of which have been demonstrated to encode small proteins or micropeptides with fundamental biological importance. While the small proteins or micropeptides hidden in lncRNA are gradually being revealed, their functions in influenza virus infection remain largely unexplored. Here, we identified and characterized a small 110-amino acid protein named PAESP that is encoded by the putative lncRNA PCBP1-AS1. We found that both PCBP1-AS1 and PAESP were upregulated by influenza virus infection as well as type I interferon treatment. Overexpression of PCBP1-AS1 or PAESP enhanced influenza virus replication. Conversely, knockdown of PCBP1-AS1 or knockout of PAESP inhibited viral production. In addition, loss-of-function experiment demonstrated that PAESP is essential for PCBP1-AS1 to facilitate influenza virus replication. More importantly, the overexpression of PAESP increases the mRNA level of several genes such as IFIT2 and IFIT3, which have been proved to be retasked by influenza virus from canonical antiviral factors into proviral effectors. Interestingly, when IFIT2 or IFIT3 expression was knocked down in PAESP-overexpressed cells, the virus titers significantly decreased compared to control cells. These findings reveal a novel lncRNA-derived small protein that is exploited by influenza virus and provide new insights into the virus-host regulatory network.

overall_design: To identify lncRNAs that play important roles in  influenza virus infection, we infected A549 cells with or without PR8 influenza virus for 12h, and performed RNA-seq to find differently expressed lncRNA .

first: Xiaojuan

last: Chi

first: Ji-Long

last: Chen


title: Decoding spatial gene activity changes in multiple sclerosis lesion progression

city: Groningen

first: Astrid

last: Alsema

address: Antonius Deusinglaan 1

department: Biomedical Sciences of Cells and Systems

country: Netherlands

institute: University Medical Center Groningen

summary: Multiple sclerosis (MS) is an inflammatory disease of the central nervous system characterised by myelin loss and progressive neurodegeneration. To better understand MS lesion initiation and progression, we generated spatial gene activity maps of white (WM) and grey matter (GM) MS lesions. In different MS lesion types, we detected novel transcriptional domains, including an identifiable rim around active WM lesions. These active lesion rims were characterised by changes in astrocytic, oligodendrocytic, and microglial gene activity. Furthermore, we identified three novel WM lesion trajectories, predicting how normal appearing WM could progress into WM lesions, with lesion rims, active lesion cores, and mixed active/inactive lesion cores as potential outcomes. Our findings offer new insights into MS lesion progression, and the dynamic molecular and cellular processes that underlie MS.

overall_design:
Visium ST profiling was performed on snap-frozen samples containing 3 control grey matter samples (from 3 donors), 3 normal-appearing grey matter samples (from 3 donors), 5 subpial lesions (from 5 donors), 2 control white matter samples (from 2 donors), 3 normal-appearing white matter samples (from 3 donors), 4 active lesions (from 3 donors), 6 mixed active/inactive lesions (from 6 donors). GeoMx Digital Spatial Profiling was performed on FFPE samples containing 3 active lesions (from 2 donors) and 3 mixed active/inactive lesions (from 3 donors).

GeoMx Digital Spatial Profiling was performed on FFPE samples containing active (n=3 lesions from 2 donors) and act/inact (n=3 lesions from 3 donors) lesions.

middle: M

first: Marion

last: Wijering

first: Anneke

last: Miedema

first: Janssen

last: Kotah

first: Mirjam

last: Koster

first: Merel

last: Rijnsburger

first: Hilmar

last: van Weering

first: Helga

last: de Vries

first: Wia

last: Baron

first: Susanne

last: Kooistra

first: Bart

last: Eggen


title: A hidden mark of a troubled past: neuroimaging and transcriptomic analyses reveal interactive effects of maternal immune activation and adolescent THC exposure in the absence of overt behavioural disruptions

status: Public on Aug 01 2024

city: Madrid

first: Alejandro

last: Higuera-Matas

state: Madrid

address: Calle Juan del Rosal 10

department: Psychobiology

country: Spain

institute: Universidad Nacional de Educación a Distancia (UNED)

summary: Maternal exposure to infections during gestation has been shown to predispose individuals to develop schizophrenia. In addition, clinical data suggest that cannabis use could trigger disease onset in vulnerable individuals. However, the question of causality remains unclear. To shed light on this issue, we used a rat model of maternal immune activation combined with exposure to increasing doses of THC during adolescence in animals of both sexes. We studied several behaviours at adulthood that resemble specific symptoms of schizophrenia (working memory impairments, sensorimotor gating deficits, alterations in social behaviour, anhedonia, and potential alterations in implicit learning). In addition, we performed positron emission tomography on two time points to search for affected brain regions and then obtained brain samples of one of these affected regions (the orbitofrontal cortex) to carry out RNAseq analyses, which were also performed in peripheral blood mononuclear cells. Strikingly, while there were no overt behavioural disruptions, our PET scans revealed several brain alterations that relied on the combination of both hits. Maternal immune activation affected glutamatergic and serotoninergic genes, and the combination with THC shifted their expression from down-regulation to up-regulation. In the peripheral cells, interactive effects were observed on inflammatory pathways and some genes are proposed as biomarkers of the disease. These results suggest that the combination of these two vulnerability factors leaves a lingering mark on the body which could predispose to the disease, even before behavioural alterations manifest.

overall_design: We studied the effects of maternal exposure to LPS/saline,  adolescent exposute to increasing doses of THC (or vehicle) and the sex of the animals.  Samples are blood peripheral mononuclear cells RNA or orbitofrontal cortex RNA 17:33from rats extracted with RNAeasy Qiagen kit.

first: Mario

last: Moreno-Fernández


title: Nuclear Argonaute protein NRDE-3 switches small RNA binding partners during embryogenesis coincident with the formation of SIMR granules

status: Public on Jul 31 2024

city: Los Angeles

first: Carolyn

middle: Marie

last: Phillips

address: 1050 Childs Way, RRI 201

department: Biological Sciences

institute: University of Southern California

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA interference (RNAi) is a conserved gene regulation mechanism that utilizes the Argonaute protein and their associated small RNAs to exert regulatory function on complementary transcripts. While the majority of germline-expressed RNAi pathway components reside in perinuclear germ granules, it is unknown whether and how RNAi pathways are spatially organized in other cell types. Here we find that the small RNA biogenesis machinery is spatially and temporally organized during embryogenesis. Specifically, the RNAi factor, SIMR-1, forms visible concentrates during mid-embryogenesis that contain an RNA-dependent RNA polymerase, a poly-UG polymerase, and the unloaded nuclear Argonaute protein, NRDE-3. Further, we observe that many other RNAi factors form foci in embryonic cells distinct from SIMR granules, including the Argonaute protein CSR-1, underscoring a potential role for cytoplasmic concentrates of RNAi factors to promote gene regulation in embryos.  Curiously, coincident with the appearance of the “SIMR granules”, the small RNAs bound to NRDE-3 switch from predominantly CSR-class 22G-RNAs to ERGO-dependent 22G-RNAs. Thus, our study defines two separable roles for NRDE-3, targeting germline-expressed genes during early embryogenesis and switching later in embryogenesis to repress recently duplicated genes and retrotransposons in somatic cells, highlighting the plasticity of Argonaute proteins and the need for more precise temporal characterization of Argonaute-small RNA interactions.

overall_design: FLAG::NRDE-3 immunoprecipitation from whole C. elegans embryo extract followed by small RNA purification, library preparation, and sequencing

first: Shihui


title: THAP1 is a master regulator of zinc finger transcription factors guiding gastrulation of murine embryos [scRNA-seq_rat]

city: Tuebingen

first: Fubo

last: Cheng

address: Calwerstrasse 7

department: Institute of Medical Genetics and Applied Genomics

institute: University of Tuebingen

summary: Gastrulation and early organogenesis are remarkable processes of early embryonic development. Our previous study showed that deletion of DYT6 gene product THAP1 leads to embryonic lethality at the stage of gastrulation and early organogenesis. However, the function of THAP1 in regulating gene expression, as well as its role in regulating embryo gastrulation and early organogenesis are not well characterized. In this study, we used different in vitro and in vivo models to characterize the function of THAP1 in regulating gene expression and in controlling embryonic development, which could help us to understand pathogenesis of THAP1-associated disorders and provide data to characterize the transcription regulation of gastrulation of murine embryo.

overall_design: Rat embryos at E10.5 and E11.5 days were carefully dissected, the single cell were isolated for scRNA-seq analysis.

first: Olaf

last: Riess

first: Wenxu

last: Zheng


title: Genome-wide deciphering the OCT4-RNA interactome in vivo by HITS-CLIP

status: Public on Jul 24 2024

city: Hangzhou

first: Yingjie

last: Wang

state: Zhejiang

address: Research Center C701,School of Medicine,Zhejiang University,866 Yuhangtang Road

department: Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine

country: China

institute: Zhejiang University

summary: We set out to systematically decipher the OCT4-RNA interactome by HITS-CLIP.

overall_design: We utilized a CRISPR/Cas9-edited H1 cell line in which a TAP (Tandem Affinity Purification) tag was knocked in to the endogenous POU5F1 locus to facilitate the isolation and enrichment of OCT4-RNA complexes.

first: Bo

last: Kang


title: A strain of Streptococcus mitis inhibits biofilm formation of caries pathogens via abundant hydrogen peroxide production

status: Public on Aug 02 2024

city: Columbus

first: Justin

middle: Ray

last: Kaspar

address: 305 W 12th Ave

department: Biosciences

country: USA

institute: The Ohio State University

summary: Our group recently transcriptomically characterized coculture growth between Streptococcus mutans and several species of commensal streptococci (Rose et al, 2023; Choi et al 2024). One interaction that stood out was with Streptococcus mitis ATCC 49456, which completely inhibited the growth of S. mutans during biofilm formation. This is due to abudant hydrogen peroxide production by S. mitis ATCC 49456, 3-5x higher than other oral commensal streptococci we have worked with. To understand how the transcriptome of S. mutans is modified in coculture with a high hydrogen peroxide producer, we evaluated the transcriptome during monoculture or coculture growth between the two strains. Our results show differential gene expression (DEGs) in S. mutans that follows other trends we have documented previously with other commensal Streptococcus species, as well as DEGs specific to the interaction with S. mitis.

sample_organism:
Streptococcus mutans
Streptococcus mitis

overall_design: Streptococcus mutans UA159 and Streptococcus mitis ATCC49456 were grown either as monocultures or cocultures, inoculated 1:1. All samples were grown in TYG. Cultures were harvested during mid exponential growth phase (OD600 nm = 0.4). Resulting comparisions included differentially expressed genes (DEGs) between monoculture and coculture growth for each strain.

first: Isabella

last: Williams

first: Jacob

last: Tuckerman

first: Daniel

last: Peters


title: The fork protection complex promotes symmetric histone recycling to maintain heterochromatin

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

summary:
The inheritance of parental histones across the replication fork is thought to mediate epigenetic memory. Here, we reveal that fission yeast Mrc1 (Claspin in humans) binds H3-H4 tetramers and operates as a central coordinator of symmetric parental histone inheritance. Mrc1 mutants in a key connector domain disrupted segregation of parental histones to the lagging strand comparable to Mcm2 histone-binding mutants. Both mutants showed clonal and asymmetric loss of H3K9me-mediated gene silencing. AlphaFold predicted co-chaperoning of H3-H4 tetramers by Mrc1 and Mcm2, with the Mrc1 connector domain bridging histone and Mcm2 binding. Biochemical and functional analysis validated this model and revealed a duality in Mrc1 function: disabling histone binding in the connector domain disrupted lagging strand recycling while another histone-binding mutation impaired leading strand recycling. We propose Mrc1 toggles histones between the lagging and leading strand recycling pathways, in part by intra-replisome co-chaperoning, to ensure epigenetic transmission to both daughter cells.

This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Schizosaccharomyces pombe
Mus musculus

platform_organism:
Schizosaccharomyces pombe
Mus musculus

overall_design: Refer to individual Series

first: Sebastian

middle: J

last: Charlton

first: Valentin

last: Flury

first: Yutaka

last: Kanoh

first: Aitana

middle: V

last: Genzor

first: Leonie

last: Kollenstart

first: Wantong

last: Ao

first: Peter

last: Brøgger

first: Melanie

last: Weisser

first: Marek

last: Adamus

first: Nicolas

last: Alcaraz

first: Charlotte

last: Delvaux de Fenffe

first: Francesca

last: Mattiroli

first: Guillermo

last: Montoya

first: Hisao

last: Masai

first: Geneviève

last: Thon


title: Sequences within and upstream of the mouse Ets1 gene drive high level expression in B cells, but are not sufficient for consistent expression in T cells

city: Buffalo

first: Lee

middle: Ann

last: Garrett-Sinha

address: 955 Main St, Room 5124

department: Biochemistry

institute: University at Buffalo

summary: The levels of transcription factor Ets1 are high in resting B and T cells, but are downregulated by signaling through antigen receptors and Toll-like receptors (TLRs). Loss of Ets1 in mice leads to excessive immune cell activation and development of an autoimmune syndrome and reduced Ets1 expression has been observed in human PBMCs in the context of autoimmune diseases. In B cells, Ets1 serves to prevent premature activation and differentiation to antibody-secreting cells. Given these important roles for Ets1 in the immune response, stringent control of Ets1 gene expression levels is required for homeostasis. However, the genetic regulatory elements that control expression of the Ets1 gene remain relatively unknown. Here we identify a topologically-associating domain (TAD) in the chromatin of B cells that includes the mouse Ets1 gene locus and describe an interaction hub that extends over 100 kb upstream and into the gene body. Additionally, we compile epigenetic datasets to find several putative regulatory elements within the interaction hub by identifying regions of high DNA accessibility and enrichment of active enhancer histone marks. Using reporter constructs, we determine that DNA sequences within this interaction hub are sufficient to direct reporter gene expression in lymphoid tissues of transgenic mice. Further analysis indicates that the reporter construct drives faithful expression of the reporter gene in mouse B cells, but variegated expression in T cells, suggesting the existence of T cell regulatory elements outside this region. To investigate how the downregulation of Ets1 transcription is associated with alterations in the epigenetic landscape of stimulated B cells, we performed ATAC-seq in resting and BCR-stimulated primary B cells and identified four regions within and upstream of the Ets1 locus that undergo changes in chromatin accessibility that correlate to Ets1 gene expression. Interestingly, functional analysis of several putative Ets1 regulatory elements using luciferase constructs suggested a high level of functional redundancy. Taken together our studies reveal a complex network of regulatory elements and transcription factors that coordinate the B cell-specific expression of  Ets1.

overall_design: B cells were isolated from two wild type C57BL/6 mouse spleens (numbers 1060 and 1062) using the EasySep Mouse B Cell Isolation Kit (Stem Cell Technologies) and cultured in RPMI-1640 media with 10% fetal calf serum, penicillin/streptomycin, glutamax and 50 micromolar beta-mercaptoethanol at 37°C in a tissue culture incubator. For each mouse number, cells were either left unstimulated (no treatment, NT) or stimulated (stim) via the BCR with goat F(ab')₂ fragment of goat anti-mouse IgM, µ chain specific antibody (Jackson ImmunoResearch) for two hours. 100,000 cells from each sample were pelleted and stored frozen prior to Assay for transposase accessible chromatin followed by sequencing (ATAC-seq). Reads were aligned to the mm10 version of the mouse genome.

first: Alyssa

last: Kearly

first: Prontip

last: Saelee

first: Jonathan

last: Bard

first: Satrajit

last: Sinha

first: Anne

last: Satterthwaite


title: ALS molecular subtypes are a combination of cellular and pathological features learned by deep multiomics classifiers (snRNA-seq)

status: Public on Jul 19 2024

city: New York

first: Oliver

middle: H

last: Tam

state: New York

address: 435 E 30th St

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

summary: Amyotrophic Lateral Sclerosis (ALS) is a complex syndrome with multiple genetic causes and wide variation in disease presentation. Despite this general heterogeneity, several common factors have been identified. For example, nearly all patients show pathological accumulations of phosphorylated TDP-43 protein in affected regions of the motor cortex and spinal cord. Moreover, large patient cohort studies have revealed that most patient samples can be grouped into a small number of ALS subtypes, as defined by their transcriptomic profiles. These ALS molecular subtypes can be grouped by whether postmortem motor cortex samples display signatures of: mitochondrial dysfunction and oxidative stress (ALS-Ox), microglial activation and neuroinflammation (ALS-Glia), or dense TDP-43 pathology and associated transposable element de-silencing (ALS-TE).  In this study, we have built a deep layer ALS neural network classifier (DANcer) that has learned to accurately assign patient samples to these ALS subtypes, and which can be run on either bulk or single-cell datasets. Upon applying this classifier to an expanded ALS patient cohort from the NYGC ALS Consortium, we show that ALS Molecular Subtypes are robust across clinical centers, with no new subtypes appearing in a cohort that has quadrupled in size. Signatures from two of these molecular subtypes strongly correlate with disease duration: ALS-TE signatures in cortex and ALS-Glia signatures in spinal cord, revealing molecular correlates of clinical features. Finally, we use single nucleus RNA sequencing to reveal the cell type-specific contributions to ALS subtype, as determined by our single-cell classifier (scDANCer). Single-cell transcriptomes reveal that ALS molecular subtypes are recapitulated in neurons and glia, with both ALS-wide shared alterations in each cell type as well as ALS subtype-specific alterations.  In summary, ALS molecular subtypes: (1) are robust across large cohorts of sporadic and familial ALS patient samples, (2) represent a combination of cellular, genetic, and pathological features, and (3) correlate with clinical features of ALS.

overall_design: Nuclei were extracted from frozen post-mortem motor cortex tissue of ALS and unaffected individuals via homogenization & FACS, and analyzed via single-nuclei RNA-seq.

first: Kathryn

last: O'Neill

first: Regina

last: Shaw

first: John

last: Ravits

first: Molly

last: Gale Hammell


title: Somatic embryogensis of Vitis vinifera exhibits a transcriptomic hourglass pattern

status: Public on Jul 23 2024

city: Zagreb

first: Tomislav

last: Domazet-Loso

state: Grad Zagreb

address: Bijenička cesta 54

department: Division of Molecular Biology

country: Croatia

institute: Institut Rudjer Bošković

summary: The objective of the study was to uncover the developmental dynamics in the artificially induced  somatic embryogenesis of Vitis vinifera on the transcriptome level.

overall_design:
Comparative gene expression profiling of RNA-seq data and evolutionary analysis for 12 developmental stages of Vitis vinifera obtained by artificialy induced direct somatic embryogenesis.
Samples were collected for early induction stage (EI), preglobular stage (PG), globular stage 1 (G1), globular stage 2 (G2), heart stage (H), torpedo stage 1 (T1), torpedo stage 2 (T2), cotiledonary stage 1 (C1), cotiledonary stage 2 (C2), seedling stage (S), seedling with epicotyl stage (EP), juvenile plant stage (JP).

first: Sara

last: Koska

first: Dunja

last: Leljak-Levanić

first: Nenad

last: Malenica

first: Kian

last: Bigović Villi

first: Momir

last: Futo

first: Nina

last: Čorak

first: Mateja

last: Jagić

first: Mirjana

last: Domazet-Lošo

first: Kristian

last: Vlahoviček


title: ALS molecular subtypes are a combination of cellular and pathological features learned by deep multiomics classifiers (postmortem spinal cord)

summary: Amyotrophic Lateral Sclerosis (ALS) is a complex syndrome with multiple genetic causes and wide variation in disease presentation. Despite this general heterogeneity, several common factors have been identified. For example, nearly all patients show pathological accumulations of phosphorylated TDP-43 protein in affected regions of the motor cortex and spinal cord. Moreover, large patient cohort studies have revealed that most patient samples can be grouped into a small number of ALS subtypes, as defined by their transcriptomic profiles. These ALS molecular subtypes can be grouped by whether postmortem motor cortex samples display signatures of: mitochondrial dysfunction and oxidative stress (ALS-Ox), microglial activation and neuroinflammation (ALS-Glia), or dense TDP-43 pathology and associated transposable element de-silencing (ALS-TE). In this study, we have built a deep layer ALS neural network classifier (DANcer) that has learned to accurately assign patient samples to these ALS subtypes, and which can be run on either bulk or single-cell datasets. Upon applying this classifier to an expanded ALS patient cohort from the NYGC ALS Consortium, we show that ALS Molecular Subtypes are robust across clinical centers, with no new subtypes appearing in a cohort that has quadrupled in size. Signatures from two of these molecular subtypes strongly correlate with disease duration: ALS-TE signatures in cortex and ALS-Glia signatures in spinal cord, revealing molecular correlates of clinical features. Finally, we use single nucleus RNA sequencing to reveal the cell type-specific contributions to ALS subtype, as determined by our single-cell classifier (scDANCer). Single-cell transcriptomes reveal that ALS molecular subtypes are recapitulated in neurons and glia, with both ALS-wide shared alterations in each cell type as well as ALS subtype- specific alterations. In summary, ALS molecular subtypes: (1) are robust across large cohorts of sporadic and familial ALS patient samples, (2) represent a combination of cellular, genetic, and pathological features, and (3) correlate with clinical features of ALS.

overall_design: To identify the ALS molecular subtypes of post-mortem spinal cord samples through transcriptomic analysis of genes and TE, and correlate with molecular and clinical features

first: Hemali

last: Phatnani

last: Gale-Hammel


title: CD11c-expressing microglia are transient, driven by interactions with apoptotic cells

status: Public on Jul 17 2024

city: Salt Lake City

first: Monica

middle: L.

last: Vetter

state: UT

department: Neurobiology & Anatomy

institute: University of Utah

summary: Microglia, the parenchymal macrophage of the central nervous system serve crucial remodeling functions throughout development in response to developmental cues. Microglia are transcriptionally heterogenous, suggesting that distinct microglial states confer distinct roles. Currently, little is known about how dynamic these states are, the cues that promote them, or how they impact microglial function. In the developing retina, we previously found a significant proportion of microglia that express CD11c (Integrin αX, complement receptor 4, Itgax). which has also been reported in other developmental and disease contexts. Here, we sought to understand the regulation and function of CD11c+ microglia by examining the developmental contexts and dynamics for the emergence of CD11c+ microglia. We find that microglial CD11c expression tracks with prominent waves of neuronal apoptosis in postnatal retina. Using genetic fate mapping, we provide evidence that microglia transition out of the CD11c state to return to homeostasis. We show that CD11c+ microglia have elevated lysosomal content and contribute to the clearance of apoptotic neurons, and found that acquisition of CD11c expression is, in part, dependent upon the TAM receptor Axl. Using selective ablation, we find similar effects on apoptotic cell clearance with depletion of CD11c+ versus non-CD11c microglia, suggesting that CD11c+ microglia are not uniquely critical for phagocytic clearance. Together, our data suggests CD11c+ microglia are a transient state induced in response to developmental apoptosis rather than a specialized subset mediating phagocytic elimination.

overall_design: Bulk RNA-seq of sorted Cd11+ and Cd11c lineage-traced retinal microglia from postnatal day 5 mouse.

first: Nathaniel

last: Ghena

first: Sarah

last: Anderson

first: Jacqueline

last: Roberts

first: Emmalyn

last: Irvin

first: Joon

last: Schwakopf

first: Alejandra

last: Bosco

middle: L