title: Change in prostate tissue gene expression following finasteride or doxazosin administration in the Medical Therapy for Prostatic Symptoms (MTOPS) Study

city: Memphis

first: Hyo Young

last: Choi

state: TN

address: 66 N. Pauline Street

department: Preventive Medicine

institute: University of Tennessee Health Science Center

summary: Benign prostatic hyperplasia (BPH) may decrease patient quality of life and often leads to acute urinary retention and surgical intervention. While effective treatments are available, many BPH patients do not respond or develop resistance to treatment. To understand molecular determinants of BPH treatment resistance, we investigated gene expression profiles before and after treatments in the prostate transitional zone of 108 participants in the Medical Therapy of Prostatic Symptoms (MTOPS) Trial. Unsupervised clustering revealed molecular subgroups characterized by expression changes in a large set of genes associated with resistance to finasteride, a 5α-reductase inhibitor. Pathway analyses within this gene cluster found finasteride administration induced changes in fatty acid metabolism, amino acid metabolism, immune response, steroid hormone metabolism, and kinase activity within the transitional zone. We found that patients without this transcriptional response were highly likely to develop drug resistance, which is expected in 33% of finasteride-treated patients. Importantly, a patient’s transcriptional response to finasteride was associated with their pre-treatment kinase expression. Further, we identified novel expression signatures of finasteride resistance among the transcriptionally responded patients. These patients showed different gene expression profiles at baseline and increased prostate transitional zone volume compared to the patients who responded to the treatment. Our work suggests molecular mechanisms of resistance to finasteride treatment that could be potentially helpful for personalized BPH treatment as well as new drug development to increase patients drug response.

overall_design: We defined a case as a patient that resisted treatment and had clinical progression. We defined a control as a patient responsive to treatment and without clinical progression during the trial. We randomly selected 1 responsive control for each resistant case within each treatment arm from within the tissue sub-study. Tissue at baseline and follow-up were from the same side of the TZ. We also selected responsive controls such that the distributions for age (± 3 yrs) and baseline AUA-SI score (± 3 pts) were similar to that of identified resistant cases. We considered individually matching controls to cases, rather than simply matching distributions across groups but determined that any added precision might be small as our focus is on within-individual change in gene expression and MTOPS imposed eligibility constraints on age, clinical characteristics, data collection protocols, and duration of follow-up across all participants. The final study population consisted of 108 MTOPS participants with adequate specimens available in the archive for both baseline and follow-up specimens and with successful RNA extraction and sequencing for both specimens across doxazosin, finasteride, combination, and placebo. RNA was extracted from frozen TZ biopsies at baseline and follow-up. Prior to extraction, excess OCT from each biopsy sample was physically removed on an aluminum block surrounded by dry ice to ensure the tissue does not thaw. Frozen tissue was sectioned to 20 µM slices QIAzol ensuring that the sample is submerged in the liquid and stored at -80C. RNA extraction used the miRNAeasy kit from QIAgen (Item # 69989) following manufacturer instructions. RNA samples were sequenced at Novagene in a blinded manner by Illumina HiSeq 2500 and subjected to quality control using FastQC. RNA reads were aligned to the hg19 genome assembly using TopHat followed by quantification of gene-level raw reads counts using the HTseq.

first: HyoYoung

first: Kathleen

last: Torkko

first: M

last: Lucia

first: Khyobeni

last: Mozhui

first: Won-Young

first: Peter

last: Clark

first: Jay

middle: H

last: Fowke


title: Spatiotemporal transcriptomic mapping of regenerative inflammation in skeletal muscle reveals a dynamic multilayered tissue architecture

status: Public on Aug 28 2024

city: New York

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

country: USA

institute: Mount Sinai Icahn School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Tissue regeneration is orchestrated by macrophages that clear damaged cells and promote regenerative inflammation. How macrophages spatially adapt and diversify their functions to support the architectural requirements of actively regenerating tissue remains unknown. In this study, we reconstructed the dynamic trajectories of myeloid cells isolated from acutely injured and early-stage dystrophic muscles. We identified divergent subsets of monocytes/macrophages and dendritic cells (DCs) and validated markers (e.g., GPNMB) and transcriptional regulators associated with defined functional states. In dystrophic muscle, specialized repair-associated subsets exhibited distinct macrophage diversity and reduced DC heterogeneity. Integrating spatial transcriptomics analyses with immunofluorescence uncovered the ordered distribution of subpopulations and multilayered regenerative inflammation zones (RIZs) where distinct macrophage subsets are organized in functional zones around damaged myofibers supporting all phases of regeneration. Importantly, intermittent glucocorticoid treatment disrupted the RIZs. Our findings suggest that macrophage subtypes mediated the development of the highly ordered architecture of regenerative tissues, unveiling the principles of the structured yet dynamic nature of regenerative inflammation supporting effective tissue repair.

overall_design: ATAC-seq and H3K27Ac ChIP-seq timecourse of sorted Ly6Chigh circulating monocytes and muscle infiltrating macrophage at Day 1 (Ly6C high F4/80-) and Day 4 (Ly6C low F4/80 high) after CTX injury.

first: Andreas

last: Patsalos

first: Petros

last: Tzerpos

first: Gergely

last: Nagy


title: The 16S RNA-seq data in riboflavin-treated  alcoholic liver disease

city: Harbin

first: Yanan

last: Jiang

state: Heilongjiang Province

address: Health Road Street

country: China

institute: Harbin medical university

summary: Alcoholic liver disease (ALD) is a kind of liver disease that will result in liver cancer and some other high death rate liver disease. The study results show that riboflavin could protect the mouse against ALD. Then the study divides the C57BL/6 mice into the three groups including Control (C), Alcohol, Alcohol with riboflavin (AR) groups respectively. And the study makes the mouse stool samples 16S RNA sequencing (RNA-seq) to find the  differential itestinal microbiota homeostasis among three groups futher and does the related analysis in riboflavin-treated alcoholic liver disease.

overall_design: The study divides the C57BL/6 mice into the three groups including Control (C), Alcohol, Alcohol with riboflavin (AR) groups respectively. And the study makes the mouse stool samples 16S RNA sequencing (RNA-seq) to find the  differential itestinal microbiota homeostasis among three groups.

first: Xiuyun

last: Shen


title: Tauroursodeoxycholic acid ameliorates renal injury induced by COL4A3 mutation

city: Shanghai

first: shuwen

last: Yu

state: Shanghai

address: 197, Ruijin Er Road

institute: Shanghai Jiao Tong University Schoo

type: Expression profiling by high throughput sequencing

summary: COL4A3/A4/A5 mutations have been identified as critical causes of Alport syndrome and other genetic chronic kidney diseases. However, the underlying pathogenesis remains unclear, and specific treatments are lacking. Here, we constructed a transgenic Alport syndrome mouse model by generating a mutation (Col4a3 p.G799R) identified previously from one large Alport syndrome family into mice. We observed that the mutation caused a pathological decrease in intracellular and secreted collagen IV α3α4α5 heterotrimers. The mutant collagen IV α3 chains abnormally accumulated in the endoplasmic reticulum and exhibited defective secretion, leading to persistent endoplasmic reticulum stress in vivo and in vitro. RNA-seq analysis revealed that the MyD88/p38 MAPK pathway plays key roles in mediating subsequent inflammation and apoptosis signaling activation. Treatment with tauroursodeoxycholic acid, a chemical chaperone drug that functions as an endoplasmic reticulum stress inhibitor, effectively suppressed endoplasmic reticulum stress, promoted secretion of the α3 chains, and inhibited the activation of the MyD88/p38 MAPK pathway. Tauroursodeoxycholic acid treatment significantly improved renal function in vivo. These results partly clarified the pathogenesis of renal injuries associated with Alport syndrome, especially in glomeruli, and suggested that tauroursodeoxycholic acid might be useful for the early clinical treatment of Alport syndrome.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Col4a3 p.G799R mutant mice and  Col4a3 wild-type  mice

first: Jingyuan

last: Xie

first: Yuanmeng

last: Jin

first: Shuwen

first: Xiangchen

last: Gu


title: Halting Multiple Myeloma with MALT1 Inhibition: Suppressing BCMA-Induced NF-κB and Inducing Immunogenic Cell Death

city: Xuzhou

first: Yao

last: Yao

state: Jiangsu

address: #84 Huaihai west RD

institute: Associate professor, Xuzhou Medical University

summary: As multiple myeloma (MM) poses a formidable therapeutic challenge despite recent progress, exploring novel targets is crucial. Mucosa-associated lymphoid tissue lymphoma translocation protein-1 (MALT1) emerges as a promising paracaspase with druggable potential, especially unexplored in MM. Our study provided compelling evidence demonstrating a statistically significant elevation of MALT1 expression in human primary MM cells. Moreover, elevated MALT1 expression was associated with a poorer prognosis in MM. Genetic deletion of MALT1 reduced cell growth, colony formation, and tumor growth in vivo. Pharmacological inhibition with 1 μM Mi-2 effectively inhibited cell growth, inducing mitochondria-dependent apoptotic cell death. Mechanistically, MALT1 inhibition disrupted diverse signal transduction pathways, notably impeding nuclear factor κB (NF-κB). Significantly, the inhibition of MALT1 demonstrated a substantial suppression of NF-κB activation by elevating IκB, disrupting the nuclear localization of p65 and C-Rel. This effect was observed in both the basal state and when stimulated by BCMA, highlighting the pivotal role of MALT1 inhibition in influencing MM cell survival. It was noteworthy that Mi-2 induces properties associated with immunogenic cell death (ICD), as evidenced by increased calreticulin (CRT), ATP release, and high-mobility group protein B1 (HMGB1) upregulation, consequently triggering ICD-associated immune activation and enhancing CD8+ T-cell cytotoxicity in vitro. In conclusion, our research highlights MALT1 as a promising druggable target for therapeutic interventions in MM, providing insights into its molecular mechanisms in MM progression.

overall_design: H929 cells were treated with MALT1 inhibitor Mi-2 or DMSO (solvent) for 24 hours. A total of 6 samples in triplicate were analyzed.

first: Mei

last: Yuan

first: Min

last: Shi

first: Wenyu

last: Li

first: Yuqian

last: Sha

first: Yan

last: Zhang

first: Canli

first: Jianping

last: Luo

first: Zhenyu

first: Chengcheng

last: Liao

first: Kailin

last: Xu

first: Mingshan

last: Niu


title: REPURPOSED AT9283 TRIGGERS ANTI-TUMORAL EFFFECTS BY TARGETING MKK3 ONCOGENIC FUNCTIONS IN COLORECTAL CANCER

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

summary:
Background
Colorectal cancer (CRC) is the third most common type of cancer and the second leading cause of cancer-related deaths worldwide, with a survival rate near to 10% when diagnosed at an advanced stage. The lack of clinical improvements for advanced-stage CRC require essential the identification of new molecular targets to design more selective and efficient therapies. The Mitogen activated protein kinase kinase 3 (MKK3) may be a novel and efficient therapeutic target, albeit selective inhibitors are currently unavailable.
Methods
Transcriptomic based drug repurposing approach identified the multitargeted kinase inhibitor AT9283 as a putative compound with MKK3 depletion-mimicking activity. AT9283 effects were investigate with CRC lines, colonocytes and CRC patient-derived organoids through in vitro and in vivo studies.
Results
AT9283, like MKK3 silencing, promotes autophagy and cell death and reduces cell migration and invasion in tested CRC lines and patient-derived organoids (PDOs). AT9283 inhibits tumor growth in preclinical models. Interestingly, AT9283 did not affect the growth or survival of primary colonocytes. Mechanistically, results demonstrated that AT9283 abrogates phospho- and total-MKK3 protein levels mainly through the inhibition of aurora kinase A (AURKA), uncovering the relevance of MKK3/AURKA crosstalk in sustaining their own protein stability and activity.
Conclusion
Overall, we demonstrated that the anti-tumoral effects triggered by AT9283 treatment recapitulated the MKK3 depletion effects in all tested CRC cell lines, suggesting that AT9283 is a repurposed drug. According to its good tolerance when tested with primary colonocytes (CCD-18CO), AT9283 is a promising drug for the development of novel therapeutic strategies to target MKK3 oncogenic functions in late-stage and metastatic CRC patients.

overall_design: Two conditions, sh/MKK3 and sh/scr, were analyzes in biological replicates (three). Gene expression profiles were compared to control (sh/scr). H3, GAPDH, GUSB, RPL19, RNU2 and ACTIN were used as endogenous controls to normalize gene expression. The Affymetrix gene expression data (array HTA_2.0) were background adjusted and quantile normalized. Gene expression values were calculated using the robust multiple-array average (RMA) procedure, and duplicates were averaged. Probes not detected in all the samples were removed. The summarized signals were log2-transformed and quantile normalized. Significantly modulated genes between different conditions were identified with a distribution fold change test (DFC) and a permutation test, adjusting for multiple comparisons.

first: Valentina

last: Piastra

first: Federica

last: Ganci

first: Andrea

last: Sacconi

first: Angelina

last: Pranteda

first: Matteo

last: Allegretti

first: Roberta

last: Bernardini

first: Martina

last: Serra

first: Emanuela

last: Dell’Aquila

first: Gianluigi

last: Ferretti

first: Edoardo

last: Pescarmona

first: Armando

last: Bartolazzi

first: Giovanni

last: Blandino

first: Livio

last: Trusolino

first: Gianluca

last: Bossi


title: Displacement of PDE4D3 with an anchoring disruptor peptide is RGC protective after injury

city: Palo Alto

first: Michael

middle: Seth

last: Kapiloff

state: California

address: 1651 Page Mill Road, Room 2112

institute: Stanford University

summary: Loss of retinal ganglion cells (RGCs) is central to the pathogenesis of optic neuropathies such as glaucoma. Increased cAMP signaling in RGCs is neuroprotective, as has been previously demonstrated in multiple animal models, including optic nerve crush (ONC) injury. We have shown that displacement of the cAMP-specific phosphodiesterase PDE4D3 from an RGC perinuclear compartment by expression of the modified PDE4D3 N-terminal peptide 4D3(E) increases perinuclear protein kinase A activity in cultured neurons and RGC survival in vivo after ONC injury. To explore potential mechanisms by which 4D3(E) expression promotes neuroprotection, mice intravitreally injected with an adeno-associated virus to express an mCherry-tagged 4D3(E) peptide were subjected to ONC injury and analyzed by single cell RNA-sequencing (scRNA-seq) for changes in RGC gene expression. 4D3(E)-mCherry expression was associated with an attenuation of injury-induced changes in gene expression, thereby supporting the hypothesis that enhanced perinuclear PKA signaling promotes neuroprotective RGC gene expression.

overall_design: scRNA-seq was performed using RGCs isolated from C57BL/6J mice 1 day after crush injury. 4-5 week old mice (Jackson Laboratories Strain 000664) of both sexes were injected intravitreally with AAV2.4D3(E)-mCherry or AAV2.mCherry control. 2 weeks after AAV administration, paired cohorts of 8 mice were subjected to optic nerve crush or sham injury. The following day RGCs were isolated by a modified two-step immunopanning protocol and analyzed by scRNA-seq. The entire experiment was performed twice, resulting in biological duplicates for each of the four cohorts.

first: Ying

last: Zhu

first: Ramesh

last: Nair


title: Characterization of open chromatin sensitive to actin polymerization using DSP-MNase-DNA-seq

city: Tianjin

first: Yaxin

last: Li

state: Tianjin

address: Building 24 B3, Tianjin University, No 92 Weijin Road, Nankai District

department: SPST

institute: Tianjin University

summary: Mechanotransduction leads to a variety of biological responses including changes in cell shape, migration, tissue development, immune responses, and gene expression. Dysregulation of mechanotransduction is implicated in the progression of various diseases such as cancer and cardiovascular diseases. The actin cytoskeleton plays a crucial role in transmitting mechanical stimuli. Actin filaments, essential for cell motility and shape changes, respond to mechanical cues by remodeling, influencing gene expression via the LINC complex and mechanosensitive transcription factors. This study employs the DSP-MNase DNA-seq method to explore the relationship between cellular mechanosensing and chromatin architecture.

overall_design: Genome wide examination of trans-acting factor binding regions in human skeleton muscle cell.

first: Fumihiko

last: Nakamura

first: Kangjing


title: SMARCA4 controls state plasticity in small cell lung cancer through regulation of neuroendocrine transcription factors and REST splicing [ChIP-seq]

first: Yingqian

middle: Ada

last: Zhan

state: New York

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

institute: MSKCC

summary: Small Cell Lung Cancer (SCLC) can be classified into transcriptional subtypes with distinct degrees of neuroendocrine (NE) differentiation. Recent evidence supports plasticity among subtypes with a bias toward adoption of low-NE states during disease progression or upon acquired chemotherapy resistance. Here, we identify a role for SMARCA4, the catalytic subunit of the SWI/SNF complex, as a regulator of subtype shift in SCLC. SMARCA4 binds to gene loci encoding NE-lineage transcription factors ASCL1 and NEUROD1 and alters chromatin accessibility, suppressing NE programs. In parallel, SMARCA4 also controls REST, a known suppressor of the NE phenotype, by regulating SRRM4-dependent REST splicing. The SMARCA2/4 inhibitor FHD-286 induces loss of NE features and drives ERBB pathway activation in SCLC, rendering SCLC tumors sensitive to afatinib. This study nominates SMARCA4 as a key regulator of the NE state plasticity and defines a novel therapeutic strategy for SCLC.

overall_design: SMARCA4 ChipSeq in 4 neuroendocrine SCLC PDXs

first: Esther

last: Redin

middle: A

first: Charles

middle: M

last: Rudin


title: SMARCA4 controls state plasticity in small cell lung cancer through regulation of neuroendocrine transcription factors and REST splicing [RNA-seq]

overall_design: To study the role of SMARCA4/2 in regulating the neuroendocrine phenotype in SCLC, we pharmacologically inhibited  this target using FHD-286 and performed gene expression profiling analysis by RNAseq. We treated H146 and H82 cells for 14 days with 100nM of FHD-286. Comparative gene expression profiling of RNAseq data for H82 and H146 treated vs untreated cells.


title: Letrozole in Combination with Standard Therapy in Recurrent High-Grade Gliomas

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: University of Cincinnati, 160 Panzeca Way

institute: University of Cincinnati

summary: High grade gliomas (HGGs) remain highly fatal malignancies with glioblastoma accounting for almost 50% of primary brain malignancies in the elderly.  Unfortunately, despite the use of multiple treatment modalities, the prognosis remains poor in this population.   Our pre-clinical studies suggest that the expression of CYP19A1, that encodes aromatase, is significantly upregulated in HGGs and that letrozole (LTZ), an FDA approved aromatase inhibitor, has marked activity against HGGs.   We conducted a phase 0/I single center clinical trial to assess the tumoral availability, pharmacokinetics (PK), safety and tolerability of LTZ in recurrent HGG patients.  Planned dose cohorts included 2.5, 5, 10, 12.5, 15, 17.5 and 20 mg of LTZ administered daily pre- and post-surgery or biopsy.  Tumor samples were assayed for LTZ content and relevant biomarkers. LTZ caused dose-dependent inhibition of estradiol synthesis and modulated DNA damage pathways in tumor tissues as evident using RNA-seq analysis.

overall_design: Patient tumor samples from 2.5 mg (Group 1), 5 mg (Group 2) and 10 mg (Group 3) dose-cohorts, and three control samples were processed for mRNA isolation via poly-A RNA purification. The mRNA libraries were prepared, indexed, and pooled in order to obtain 50-100 million reads per sample. Sequencing of libraries for 50 bp was performed using the Illumina HiSeq system. Data were de-multiplexed, and appropriate quality control checks were performed before aligning the sequences to the human reference genome (hg19) using TopHat2 aligner.

first: Pankaj

middle: B

last: Desai

first: Aniruddha

last: Karve

first: Trisha

last: Wise-Draper


title: Characterization of ribosome stalling and no-go mRNA decay stimulated by the Fragile X protein, FMRP

city: Columbus

first: Wen

last: Tang

state: Ohio

address: 1060 Carmack Rd

department: Department of Biological Chemistry and Pharmacology

institute: The Ohio State University

summary: Loss of functional fragile X mental retardation protein (FMRP) causes fragile X syndrome (FXS) and is the leading monogenic cause of autism spectrum disorders and intellectual disability. FMRP is most notably a translational repressor and is thought to inhibit translation elongation by stalling ribosomes as FMRP-bound polyribosomes from brain tissue are resistant to puromycin and nuclease treatment. Here, we present data showing that the C-terminal non-canonical RNA-binding domain of FMRP is essential and sufficient to induce puromycin-resistant mRNA•ribosome complexes. Given that stalled ribosomes can stimulate ribosome collisions and no-go mRNA decay (NGD), we tested the ability of FMRP to drive NGD of its target transcripts in neuroblastoma cells. Indeed, FMRP and ribosomal proteins, but not PABPC1, were enriched in isolated nuclease-resistant disomes compared to controls. Using siRNA knockdown and RNA-seq, we identified 16 putative FMRP-mediated NGD substrates, many of which encode proteins involved in neuronal development and function. Increased mRNA stability of the putative substrates was also observed when either FMRP was depleted or NGD was prevented via RNAi. Taken together, these data support that FMRP stalls ribosomes and can stimulate NGD in cells, albeit on a small number of transcripts, revealing an unappreciated role of FMRP that would be misregulated in FXS when FMRP is lost.

overall_design: N2A cells were obtained from ATCC (# CCL-131) and maintained in high glucose DMEM (Thermo # 11995065) supplemented with 10% heat-inactivated FBS and 1% penicillin-streptomycin in standard tissue culture-treated plastics at 37°C with 5% CO2. N2A cells were seeded in 12-well plates 24 hrs prior to knockdown, and then transfected with Silencer Select siRNAs (Thermo) using Lipofectamine RNAiMAX (Thermo # 13778150) following the manufacturer’s recommendation. At the time of transfection, N2A cells were at ~20% confluency. 24 hrs post siRNA transfection, the media was changed. After 72 hr transfection, total RNA or protein was harvested by TRIzol.

first: MaKenzie

middle: R

last: Scarpitti

first: Benjamin

last: Pastore

middle: G

last: Kearse


title: PHLDA1-PRDM1 mediates the effect of lentiviral vectors on fate-determination of human retinal progenitor cells

city: guangzhou

first: yuhua

last: xiao

state: guangdong province

address: jinsui load

department: zhongshan Ophthalmic  center

institute: Sun Yat-sen University

summary: Lentiviral vectors have markedly enhanced gene therapy efficiency in treating congenital diseases, but its long-term safety remains controversial. Most gene therapies for congenital eye diseases need to be carried out at early ages, yet the assessment of related risks to ocular development posed by lentiviral vectors is challenging. Utilizing single-cell transcriptomic profiling on human retinal organoids, this study explored the impact of lentiviral vectors on the retinal development and found that lentiviral vectors can cause retinal precursor cells to shift toward photoreceptor fate through the up-regulation of key fate-determining genes such as PRDM1. Further investigation demonstrated that the intron and intergenic region of PRDM1 was bound by PHLDA1, which was also upregulated by lentiviral vector exposure. Importantly, knockdown of PHLDA1 successfully suppressed the lentivirus-induced differentiation bias of photoreceptor cells. The findings also suggest that while lentiviral vectors may disrupt the fate determination of retinal precursor cells, posing risks in early-stage retinal gene therapy, these risks could potentially be reduced by inhibiting the PHLDA1-PRDM1 signaling axis.

overall_design: This study aims to investigate the genomic and transcriptomic alterations in Y79 retinoblastoma cell lines upon lentivirus infection. We employ Cleavage Under Targets & Tagmentation (CUT&Tag) technology to probe PHLDA1 protein interactions and RNA sequencing (RNA-seq) to assess gene expression changes.

first: Xing

last: Hu

first: Jia

last: Chen

first: Wangxuan

last: Dai

first: Yuhua

last: Xiao


title: SMARCA4 controls state plasticity in small cell lung cancer through regulation of neuroendocrine transcription factors and REST splicing [ATAC-seq]

overall_design: To study the role of SMARCA4/2 in regulating the neuroendocrine phenotype in SCLC, we pharmacologically inhibited  this target using FHD-286 and performed ATAseq. We treated H146 and H82 cells for 14 days with 100nM of FHD-286.


title: BAFF neutralization impairs the clearance of dead adipocytes and promotes insulin resistance in obese mice

city: Greenville

first: Akshaya

middle: K

last: Meher

address: 600 N. Moye Blvd.

institute: East Carolina University

summary: B cell-activating factor (BAFF) is critical for the survival and maturation of B2 cells. However, excess BAFF breaks the peripheral tolerance of B2-cells leading to the production of autoantibodies that cause autoimmune diseases. During obesity, BAFF is predominantly produced by white adipose tissue (WAT), and IgG autoantibodies against adipocytes are identified in the WAT of obese humans. However, it remains to be determined if the autoantibodies formed during obesity affect WAT remodeling and systemic insulin resistance. Here, we show that IgGs from high-fat diet (HFD)-induced obese mice bind to apoptotic adipocytes and promote their clearance by macrophages. Next, using murine models of obesity in which the gonadal WAT undergoes remodeling, unexpectedly we found that BAFF neutralization increased the number of dead adipocytes and exacerbated WAT inflammation and insulin resistance despite depletion of IgG autoantibodies. RNA sequencing of the stromal vascular fraction from the WAT revealed impaired B cell activation and phagocytosis pathways. In-vitro, the clearance of apoptotic adipocytes by macrophages was attenuated in the presence of IgGs from BAFF-neutralized mice compared to the control mice. Altogether, our study suggests a beneficial role of BAFF and IgG autoantibodies in WAT remodeling in obesity and the regulation of systemic insulin resistance.

overall_design: Effect of BAFF neutralization in the stromal vascular fraction of gonadal white adipose tissue of high-fat diet-induced obese male C57BL6J mice undergoing diet intervention: Six-week-old male C57BL/6J mice were placed on a high-fat diet (60% calories from fat) for 12 weeks to induce insulin resistance and two experimental groups were determined based on a glucose tolerance test. Mice were then simultaneously switched from the high-fat diet to a normal chow diet (16% calories from fat) and given an injection of 2 mg/kg of anti-BAFF antibody (Sandy-2, AdipoGen) or an isotype control antibody (IgG1k, BioX Cell) every 2 weeks for a total of 6 weeks. At the end of the experiment, which was week 18, mice were euthanized, one of the gonadal fat pads was isolated, minced, and digested for 1 hour in Hanks Balanced Salt Solution (Gibco) with 2% bovine serum albumin (BSA) and 2 mg/ml of collagenase type I shaking at 37 °C. After digestion, tissue was filtered through a 500 μM nylon mesh strainer and washed with HBSS with 2% BSA. The cells were centrifuged (450xg for 5 min) to allow the stromal vascular cells (SVF) to separate with the adipocytes floating on the top of the buffer. The SVF pellet was collected, and red blood cells were lysed. SVF cells were washed, centrifuged, and resuspended in TRIZOL and sent to SingulOmics (Bronx, New York) for bulk RNA sequencing.

first: Melissa

last: Lempicki

first: Jake

last: Gray


title: Comparative Analysis of Host Responses Between Sepsis and COVID-19: A Prospective Observational Study of Whole Blood Transcriptome (RNA-Seq)

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: This prospective observational study conducted at Osaka University Graduate School of Medicine aimed to compare host responses in sepsis and COVID-19 patients by analyzing mRNA and miRNA profiles. They included 22 sepsis patients, 35 COVID-19 patients, and 15 healthy subjects. Sepsis was diagnosed using Sepsis-3 criteria, while COVID-19 was confirmed through SARS-CoV-2 RT-PCR testing and chest CT scans for pneumonia assessment.                    For RNA sequencing, 14,500 mRNAs, 1121 miRNAs, and 2556 miRNA-targeted mRNAs were available for analysis in sepsis patients. Numbers of genes showing upregulated:downregulated gene expression (false discovery rate <0.05, |log2 fold change| >1.5) were 256:2887 for mRNA, 53:5 for miRNA, and 49:2507 for miRNA-targeted mRNA. Similarly, in COVID-19 patients, 14,500 mRNAs, 1121 miRNAs, and 327 miRNA-targeted mRNAs were analyzed, with numbers of genes exhibiting upregulated:downregulated gene expression of 672:1147 for mRNA, 3:4 for miRNA, and 165:162 for miRNA-targeted mRNA.  Sepsis patients had a greater number of upregulated and downregulated genes and pathways compared to COVID-19 patients, indicating a dynamic change in gene expression and pathway activation in sepsis.

overall_design: We performed the single RNA-seq analysis using whole blood from 22 sepsis patients and 35 COVID-19 patients admitted to our department, as well as 15 healthy subjects.

first: A

last: Muratsu

first: D

last: Okuzaki

first: H

last: Matsumoto


title: Comparative Analysis of Host Responses Between Sepsis and COVID-19: A Prospective Observational Study of Whole Blood Transcriptome (miRNA-Seq)

type: Non-coding RNA profiling by high throughput sequencing

overall_design: We performed the single miRNA-seq analysis using whole blood from 22 sepsis patients and 35 COVID-19 patients admitted to our department, as well as 15 healthy subjects.


title: Generation of human region-specific brain organoids with medullary spinal trigeminal nuclei [scRNA-seq]

first: Jinkui

last: Zhu

address: 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China.

department: School of Life Science and Technology

institute: ShanghaiTech University

summary: Brain organoids with nucleus-specific identities provide unique platforms for studying human brain development and diseases at a finer resolution. Despite its essential role in vital body functions, the medulla of the hindbrain has seen a lack of in vitro models, let alone models resembling specific medullary nuclei, including the crucial spinal trigeminal nucleus (SpV) that relays peripheral sensory signals to the thalamus. Here, we report a method to differentiate human pluripotent stem cells into region-specific brain organoids resembling the dorsal domain of the medullary hindbrain. Importantly, organoids specifically recapitulated the development of SpV derived from the dorsal medulla. We also developed an organoid system to create the trigeminothalamic projections between the SpV and the thalamus by fusing these organoids, namely human medullary SpV-like organoids (hmSpVOs), with organoids representing the thalamus (hThOs). Our study provides a platform for understanding SpV development, nucleus-based circuit organizations, and related disorders in the human brain.

overall_design: Organoids generated from embryonic stem cells (H9) on days 30 and 62 of differentiation were used for single-cell RNA sequencing.

first: Wei

last: Pang

first: Yangfei

last: Xiang


title: Interleukin-27 Gene Delivery Targeting IL-6Rα-Expressing Cells as a Stress Response Therapy

city: West Lafayette

first: Sagar

last: Utturkar

state: IN

address: 201 S University St

department: Institute for Cancer Research

institute: Purdue University

summary: Interleukin-27 (IL-27) has shown promise in halting tumor growth and mediating tumor regression in several models, including prostate cancer. We describe our findings on the effects of IL-27 on the gene expression changes of TC2R prostate adenocarcinoma cells. We utilized RNAseq to assess profile differences between empty vector control, vector delivering IL-27 modified at its C-terminus with a non-specific peptide, and IL-27 modified at the C-terminus with a peptide targeting the IL-6-Rα. The targeted IL-27 had higher bioactivity and activity in vivo in a recent study by our group, but the mechanisms underlying this effect had not been characterized in detail at the gene expression level on tumor cells. In the present work, we sought to examine potential mechanisms for targeted IL-27 enhanced activity directly on tumor cells. The targeted IL-27 appeared to modulate several changes that would be consistent with an anti-tumor effect, including upregulation in the Interferon (IFN) and Interferon regulatory factor (IRF), oxidative phosphorylation, Janus kinase/Signal transducers and activators of transcription (JAK/STAT), and eukaryotic initiation factor 2 (EIF2) signaling. Of these signaling changes predicted by ingenuity pathway analyses (IPA), the novel form also with the highest significance (-log(Benjamini–Hochberg (B-H))p-value) was the EIF2 signaling upregulation. We validated this predicted change by assaying for eukaryotic initiation factor 2 alpha (eIF2α), or phosphorylated eIF2α (p-eIF2α), and caspase-3 levels. We detected an increase in the phosphorylated form of eIF2α and in the cleaved caspase-3 fraction, indicating that the EIF2 signaling pathway was upregulated in these prostate tumor cells following targeted IL-27 gene delivery. This approach of targeting cytokines to enhance their activity against cancer cells is a novel approach to help augment IL-27′s bioactivity and efficacy against prostate tumors and could be extended to other conditions where it could help interfere with the EIF2α pathway and promote caspase-3 activation.

overall_design: Prostate cancer cells TRAMPC2-Ras (TC2R) were transfected with control empty vector (plasmid DNA pcDNA3.1), or the same backbone vector containing control IL-27 with a non-specific peptide, or the targeted form of IL-27 (IL-27pepL, targeted to the IL-6Rα).

first: Marxa

middle: L

last: Figueiredo

first: Hiroki

last: Yokota


title: Generation of human region-specific brain organoids with medullary spinal trigeminal nuclei [RNA-seq]

overall_design: Organoids derived from embryonic stem cells (H9) on day 30 of differentiation were used for bulk RNA sequencing.


title: RNA difference in superficial temporal artery between moyamoya disease and normal control

city: Hefei

first: Chengyu

last: Xia

address: 17 Lujiang Road, Hefei City, Anhui Province, China

institute: USTC

summary: We collected the Superficial temporal artery (STA) tissues from patients with Moyamoya disease who underwent combined direct and indirect bypass surgery and patients with brain trauma requiring craniotomy in the Department of Neurosurgery, First Affiliated Hospital of USTC (Anhui Provincial Hospital). One part was fixed in 10% neutral formalin solution, and the other part was stored in a refrigerator at -80 ℃. All protocols using human specimens were approved by the ethics committee of the First Affiliated Hospital of USTC (Anhui Provincial Hospital). Written informed consent was obtained from all patients. All protocols were approved by the Institutional Review Board of the First Affiliated Hospital of USTC (Anhui Provincial Hospital).Total RNA was extracted from the STA tissues using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. The integrity and concentration of RNA were detected using an Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, Calif., USA), enriched and purified with Oligo (dT) -bearing magnetic beads. RNA sequencing was performed by Anoroad (Beijing, China).

overall_design: To explore the difference of gene expression in patients with moyamoya disease


title: Targeting SWI/SNF ATPases reduces cell invasiveness and plasticity in core transcription factors-addicted neuroblastoma [RNA-seq]

city: Bethesda

first: Zhihui

last: Liu

state: Maryland

address: 9000 rockville pike

institute: National Cancer Institute

summary: Neuroblastoma (NB) comprises mesenchymal (MES) and adrenergic (ADRN) subtypes, and the cell identity is determined by core transcription factors (TFs). However, the binding mechanism of these TFs to DNA and the epigenetic mechanisms governing NB plasticity remain unclear. In this study, we investigated the impact of targeting SWI/SNF ATPases with SMARCA2/4 dual degraders on NB cells. Our results revealed that depletion of SWI/SNF ATPases compacted cis-regulatory elements, diminished enhancer activity, and displaced core TFs (MYCN, HAND2, PHOX2B, and GATA3) from DNA, suppressing transcriptional programs linked to plasticity and invasiveness. These findings underscore the pivotal role of SWI/SNF ATPases in driving NB progression, positioning them as promising therapeutic targets.

overall_design: To investigate the effect of SWI/SNF ATPases depletion on gene expression in NB cells, we treated different NB cell lines with or without ACBI1 for 8, 24 or 96 hours, or transfected NB cells with control siRNA (siCtrl) or two different SMARCA4 siRNAs (siSMA4-5, siSMA5-7) for 48 hours. RNA-seq was performed for gene expression profiling analysis.

first: Man

last: Xu

first: Jason

middle: J

last: Hong

first: Carol

last: Thiele


title: Targeting SWI/SNF ATPases reduces neuroblastoma cell plasticity

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

overall_design: Refer to individual Series


title: RNA-seq of cardiac lineage cells (day 3 of cardiac differentiation) derived from human embryonic stem cells (hESCs) overexpressed with Monkeypox virus-protein revealed the effects of H3L and A29L in human cardiac development.

city: Guangzhou

first: Juli

state: Guangdong

address: Zhongshan 2nd road No. 106, Yuexiu District, Guangzhou, Guangdong, China

institute: Guangdong Provincial People's Hospital

summary: Monkeypox virus (MPV) can infect human cells and induces injuries in human. However, whether and how MPV affect the function of human cells remain to be elucidated. Here, we overexpressed H3L and A29L in hESCs, separately. We appliced RNA-seq on cardiac lineage cells (day 3 of cardiac differentiation) derived from human embryonic stem cells (hESCs) overexpressed with Monkeypox virus-proteins (Control, H3L and A29L) and want to know gene expression patterns of control and overexpression cell lines. Subsequent data analyses will help us to know whether and how H3L and A29L affect human cardiac development.

overall_design: The stable hESCs overexpressed with H3L or A29L were rotinely maintained in mTesR1 medium in 6-well plate. For cardiac differentiation, STEMdiff™ Ventricular Cardiomyocyte Differentiation Kit (STEMCELL Technologies) was used according to the manual. The hESCs were differentiated into cardiac lineage cells. Then, the cardiac lineage cells  on day 3 post differentiation were collected for bulk RNA-seq. Total RNAs were extracted and purified with RNeasy Mini Kit (Qiagen). Two biological replicates were applied for RNA-seq.

first: JULI

last: LIU

first: SHAOXIAN

last: CHEN

first: GUIPING

last: HUANG


title: ChIP-seq of human embryonic stem cells (hESCs) overexpressed with Monkeypox viral proteins H3L and A29L

summary: We found that Monkeypox viral proteins H3L and A29L caused injuries in human cells. Whether they can bind chromatin and  re-model chromation is unclear. Here, we applied ChIP-seq on hESCs to evaluate whether and how they are involved in chromatin regulation.

overall_design: ChIP was conducted using anti-myc tag, anti-H3K4me4 or anti-H3K27me3 on human embryonic stem cells (hESCs) overexpressed with Monkeypox viral proteins H3L and A29L. Then chromatin DNAs were purifed for sequencing.

first: Shaoxian

last: Chen

first: Guiping

last: Huang


title: The synthetic opioid fentanyl increases HIV replication expression in macrophages

first: Mario

last: Medvedovic

summary: The illicit use of synthetic opioids such as fentanyl has led to a serious public health crisis in the US. People with opioid use disorder are more likely to contract infections such as HIV and viral hepatitis and experience more severe disease. While several drugs of abuse are known to enhance viral replication and to suppress immunologic responses, the effects of synthetic opioids on HIV pathogenesis have not been investigated thoroughly. Thus, we examined the impact of fentanyl on macrophage cell line U937 and monocyte derived macrophage cells and chemokine receptor expression in vitro.

overall_design: U937 cells were exposed to varying concentrations of fentanyl. Expression levels of the CXCR4 and CCR5 chemokine receptors were measured in cell lysates. HIV p24 antigen was quantified in culture supernatants by ELISA, and HIV proviral DNA was quantified in cells using SYBR real-time PCR targeting the pol gene. RNAseq was performed to characterize cellular gene regulation in the presence of fentanyl.

first: Janani

last: Madhuravasal Krishnan

middle: T

last: Blackard


title: Comparative Analysis of Host Responses Between Sepsis and COVID-19: A Prospective Observational Study of Whole Blood Transcriptome

first: Daisuke

last: Motooka


title: RNA-seq of mosue heart tissues overexpressed with Monkeypox virus (MPV) proteins  H3L or A29L.

summary: Here, we overexpressed Monkeypox virus (MPV) proteins H3L and A29L in mouse hearts, separately. We appliced bulk RNA-seq on heart muscle tissues (2 months after overexpression) and want to know gene expression patterns in control group and overexpression groups. Subsequent data analyses will help us to know whether and how H3L and A29L affect mosue heart.

overall_design: Total RNAs were extracted and purified with miRNeasy Mini Kit (Qiagen). Three biological replicates were applied for the bulk RNA-seq.


title: NR4a knock-down in HER2 CAR-T cells improves T cell longevity and promotes  solid tumor eradication [RNA-Seq]

city: Shinjuku-ku

first: Taeko

last: Hayakawa

state: Tokyo

address: 35 Shinanomachi

department: Division of Tumor Immunology, Institute for Advanced Medical Research

institute: Keio University School of Medicine

summary: Chimeric antigen receptor (CAR)-T cell therapy targeting human CD19 have demonstrated clinical efficacy against B-cell malignancies. However, CAR-T cell therapy's efficacy against solid tumors is limited due to factors like low tumor-associated antigens, infiltration rate, and T cell exhaustion. We have shown that deleting NR4a genes in CAR-T cells prevents T cell exhaustion and improved their therapeutic effects on solid tumors in a mouse model. To further explore this for human, we deleted all three NR4a family factors in CAR-T cells that recognize Epidermal Growth Factor Receptor type 2 (HER2) using the CRISPR/Cas9 system. These modified CAR-T cells (NR4a-TKO CAR-T) exhibited resistance to exhaustion, increased tumor-killing activity, and higher efficacy in tumor regression and survival rate in a human lung carcinoma model in mice. The enhanced therapeutic effects were associated with increased cytokine expression, reduced exhaustion-related gene expression, and improved persistence within tumors. We propose that targeting NR4a could be a promising strategy for developing superior CAR-T cells against solid tumors.

overall_design: Primary human T cells were isolated from PBMC derived from healthy donors and activated with anti-CD3/CD28 Dynabeads in AIM-V medium supplemented with IL-2 (10ng/mL). After 24 hours, the anti-HER2 CAR-Transgene was transduced with a Lentivirus into the T cells using RetroNectin (Takara Bio). On day 3, Dynabeads were magnetically removed, and CAR-T cells were electroporated with Cas9-RNPs.

first: Kensuke

last: Nakagawara

first: Akihiko

last: Yoshimura


title: Targeting SWI/SNF ATPases reduces cell invasiveness and plasticity in core transcription factors-addicted neuroblastoma [ATAC-seq]

overall_design: ATAC-seq was performed in IMR32 cells or BE(2)C cells treated with DMSO (as a vehicle control) or ACBI1 for 24 hours, as well as in IMR5 cells transfected with control siRNA (siCtrl) or SMARCA4 siRNA (siSMARCA4) for 48 hours.


title: Increased copy-number variant load of associated risk genes in sporadic cases of amyotrophic lateral sclerosis

city: Catania

first: Sebastiano

last: Cavallaro

address: Via Paolo Gaifami, 18

institute: IRIB-CNR

summary: Amyotrophic lateral sclerosis (ALS) is an age-related neurodegenerative disease characterized by selective loss of motor neurons in the brainstem and spinal cord. Several genetic factors have been associated to ALS, ranging from causal genes and potential risk factors to disease modifiers. Here, we applied an exon-centric aCGH method to investigate, in sporadic ALS patients, the load of CNVs in 131 genes previously associated to ALS. Our approach revealed that CNV load, defined as the total number of CNVs or their length, was significantly higher in ALS cases.

overall_design: A total of 32 Southern Italian patients (17 males and 15 females), with a diagnosis of sALS according to the EL Escorial criteria (21), and 20 controls of Southern Italian patients affected by neurological disorders without diagnosis of ALS, were analysed by using an 8x60K custom exon-centric NeuroArray platform v. 2.0 (Agilent Technologies, Santa Clara, CA), tailored to detect single/multi-exon deletions and duplications in a large panel of ALS-related genes. DNA test and a reference of the same sex (Euro Reference, Agilent Technologies, Santa Clara, CA) were processed according to the manufacturer’s protocol (Agilent Technologies, Santa Clara, CA). sALS patient DNAs were labeled with Cy5-dUTP and reference DNAs for reference DNAs. Arrays were scanned at 3 µm resolution using an Agilent G4900DA SureScan Microarray Scanner System and aCGH image data were processed using Agilent’s Feature Extraction software. Feature extracted raw data was normalized, analyzed and visualized using Agilent CytoGenomics v. 4.0.3.12 and Genomic Workbench v. 7.0.4.0 software (Agilent Technologies, Santa Clara, CA, USA). GC correction with a window size of 2 kb and Diploid Peak Centralization were used for normalization. The Centralization Normalization Algorithm with a threshold of 6.0 and a bin size of 10 was also used for detecting aberrant regions or regions of constant CNVs. Aberrations were detected by the Aberration Detection Method II algorithm (ADM-2), with a sensitivity threshold of 6.0 and moving average window of 2Mb. Human reference sequence hg19 assembly was used to define the genomic coordinates of detected CNVs.

first: Maria

last: Guarnaccia

first: Giovanna

last: Morello

first: Valentina

last: La Cognata


title: Targeting SWI/SNF ATPases reduces cell invasiveness and plasticity in core transcription factors-addicted neuroblastoma [ChIP-seq]

first: Zhihui

last: Liu

overall_design: Chromatin immunoprecipitation DNA seqeuncing (ChIP-seq) for HAND2, PHOX2B, GATA3, MYCN and H3K27ac in IMR32 cells treated with DMSO (as a vehicle control) or ACBI1 for 24 hours, or transfected with control siRNA (siCtrl) or SMARCA4 siRNA (siSMARCA4) for 72 hours.

first: Man

last: Xu

first: Jason

last: Hong

first: Carol

last: Thiele


title: The effects of serotonin by Tph1 and Htr2b on skeletal muscle

status: Public on Aug 29 2024

city: Buk-gu, Gwangju

first: Suhyeon

last: Park

state: Gwangju

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호

country: South Korea

institute: GIST

summary: It is known that reducing circulating serotonin by inhibiting Tph1 increases the sensitivity of BAT cells and this drives thermogenesis by fat and glucose oxidation. In our results inhibiting Tph1 in muscle showed activation of SIRT1/LKB1/AMPK pathway in skeletal muscle cells and increased p-ACC. Also, it's known that inhibiting adipose Htr2b signaling ameliorates HFD-induced systemic insulin resistance. Here we report insulin sensitivity changes by regulating serotonin in skeletal muscle by Htr2b. Inhibiting Htr2b increases AMPK activity, glucose uptake, and myofiber size and decreases lipid droplet accumulation in HFD mice skeletal muscle. These results indicate improved insulin resistance and myosteatosis in skeletal muscle by lack of Serotonin by Tph1/Htr2b on skeletal muscle.

overall_design: Non-pathogenic mouse strains on a C57BL/6 background; expressing Acta1 cre recombinase under the Htr2b promoter in which the exon 2,3 of the Htr2b gene is floxed.

first: Chang-Myung

last: Oh


title: RNA-seq of Monkeypox virus-protein overexpression in human embryonic stem cells (hESCs) revealed the effects of H3L, A29L, A35R and I1L in human

first: Juli

address: Zhongshan 2nd road

department: Medical Research Center

institute: Guangdong provincial people's hospital

summary: Monkeypox virus (MPV) can infect human cells and induces injuries in human. However, whether and how MPV affect the function of human cells remain to be elucidated. Here, we overexpressed H3L, A29L, A35R and I1L in hESCs, separately. We appliced RNA-seq on these hESCs and want to know gene expression patterns of control and Overexpression hESCs. Subsequent data analyses will help us to know whether and how H3L, A29L, A35R or I1L affect cells in human.

overall_design: We separately cloned DNA seqeunces of H3L, A29L, A35R and I1L into lentivirus and infected hESCs, follwed with puro screening. The stable cell lines were rotinely maintained in mTesR1 medium in 6-well plate. Stable cell lines were collected for RNA purification and RNA-seq. Lenti-virus control cell line (control hESCs) did not express any protein. Total RNAs were extracted and purified with RNeasy Mini Kit (Qiagen). 4 biological replicates were applied for each overexpression cell line.

first: JULI

last: LIU

first: SHAOXIAN

last: CHEN

first: GUIPING

last: HUANG


title: Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds

city: RTP

first: Monique

last: Hazemi

state: NC

address: 109 T.W. Alexander Dr

institute: US EPA

summary: The per-and polyfluoroalkyl substances (PFAS) are of significant global concern due to their highly ubiquitous and persistent nature, bioaccumulation in organisms, and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However, little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active, in addition to the toxicity endpoints that best reflect chemical hazard. In this study, zebrafish (Danio rerio) were exposed to a 0.33% DMSO vehicle control, 1uM chlorpyrifos (CAS 2921-88-2) positive control, and eight concentrations (0-100 uM, half-log dilutions) of three environmentally relevant PFAS compounds in concentration-response: PFOS (CAS 1763-21-1), PFOA (CAS 45285-51-6), and PFHxS (CAS 355-46-4). There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure (tPOD; a benchmark dose/concentration -based treatment level below which a concerted gene expression response is not observed) estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short-term embryo/larval plate-based high-throughput toxicity tests, tPODs were determined across seven distinct developmental windows (6-24 hours post fertilization (hpf), 6-48 hpf, 24-48 hpf, 6-120 hpf, 24-120 hpf, 48-120 hpf, 96-120 hpf) to assess how common experimental design variables (e.g., different exposure durations, exposure at different developmental stages) affect point of departure estimates.

overall_design: Zebrafish (Danio rerio) embryos were exposed to eight concentrations of three different per- or polyfluoroalkyl substances (PFAS), perfluorooctanesulfonic acid (PFOS; DTXSID3031864); perfluorooctanoic acid (PFOA; DTXSID8031865); and perfluorohexane sulfonate (PFHxS; DTXSID90892476) in concentration-response (0-100 uM, half-log dilutions), and then whole body gene expression was determined using RNA sequencing. Embryos were exposed to each of the three PFAS over seven distinct exposure periods (6 hours post fertilization [hpf]-120 hpf; 6 hpf-48 hpf; 6 hpf-24 hpf; 24 hpf – 120 hpf; 48 hpf-120 hpf; and 96 hpf-120 hpf) with the goal of determining how much the tPOD varies as a function of the developmental window over which the organisms were exposed. Zebrafish were also exposed to 0.33% DMSO (vehicle control) and 1uM chlorpyrifos (transcription positive control).  Each PFAS chemical concentration was included on two of the three 96-well plates (n=5 individuals/plate), and DMSO (n=8 individuals/plate) and chlorpyrifos (n=3 individuals/plate) were included on all three plates.

first: Prarthana

last: Shankar

first: Dan

last: Villeneuve

first: Mary

last: See

first: Meagan

last: Bell

first: Jenna

last: Cavallin

first: Kevin

last: Flynn

first: Carlie

last: LaLone

first: Sara

last: Vliet


title: Engineering oncogenic hotspot mutations on SF3B1 via CRISPR-directed PRECIS mutagenesis

city: Monrovia

first: Lili

last: Wang

state: CALIFORNIA

address: 1218 South Fifth Ave.

department: Systems biology

institute: City of Hope

summary: To engineer novel SF3B1 mutant cell lines, we developed a methodology called PRECIS to install the pathogenic K700E mutation. We used this method to engineer CLL cell lines HG-3 and MEC-1 with the SF3B1 K700E mutation and then carried out RNA-seq.

overall_design: RNA-seq analysis of isogenic HG-3 and MEC-1 SF3B1 WT or K700E mutant cell lines in triplicates.


title: Chinmo maintains adult stem cell sex identity by directly regulating Doublesex and Insulin signaling [scRNA-seq]

city: Shenzhen

first: Qing

last: Ma

address: 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, P.R.China

institute: Shenzhen Institutes of Advanced Technology

summary: After sex specification during development, inappropriate sex maintenance in adults can lead to numerous defects and pathologies across many species. The molecular and cellular signals involved remain unknown. In the adult Drosophila testis, removing the JAK-STAT downstream effector Chinmo from adult somatic cyst stem cells (CySCs) causes their feminization, such that the sex-concordant interactions between male germ cells and the adjacent somatic cells are disrupted, causing gradual formation of testis germ cell tumors (GCT). Here we use single cell RNA-Seq to characterize cell-type specific transcriptional profiles for chinmo mutant testes undergoing sex transformation. This revealed both expected and novel mutant-specific cell populations and the full repertoire of transcriptomic changes accompanying sex transformation. Cell-cell communication networks were computed among all major cell types, revealing that feminized CySCs have reduced outgoing signaling to themselves and hub cells but elevated outgoing signaling including insulin signaling to germline stem cells (GSCs) /spermatogonia. Using Chinmo CUT & Tag, we identified Chinmo’s direct targets including the sex determination factor dsx and members of the insulin signaling pathway. We also found that Chinmo mainly functions as an activator in CySCs. By functional assays, we found ectopic expression of insulin pathway members in GSCs/spermatogonia phenocopies feminized chinmo mutant testes. In addition, knocking down insulin signaling in germ cells partially rescues the chinmo mutant phenotype. Altogether, we uncovered that Chinmo directly regulates canonical sex determination signals, as well as insulin signaling, to drive sex conversion of CySCs and germline tumorigenesis.

overall_design: Single cell RNA-seq of wild-type and chinmoST testes across three timepoints (3–5, 6–8 and 9–11 days of adulthood) using 10x Genomics Chromium Single Cell 3ʹ Reagent Kits v3

first: Rui

last: Zhang

first: Peiyu

last: Shi

first: Shuyang

last: Xu


title: Epigenome analysis  of  Sorafenib-resistant huh7 cell lines

city: Xiamen

first: Chunli

last: Mo

state: fujian

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District

institute: School of Life Sciences, Xiamen University

summary: Genome-wide DNA methylation profiling of 3 Sorafenib-resistant huh7 cell lines. The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from  cell lines

overall_design: Bisulphite converted DNA from the cells were hybridised to the Illumina Infinium 850K Human MethylationEPIC Beadchip


title: Disturbed glycolipid metabolism activates CXCL13-CXCR5 axis in senescent TSCs to promote heterotopic ossification formation

first: Yuyu

last: Chen

address: Zhongshan II road, 74th

summary: Heterotopic ossification (HO) occurs as a common complication after injury, while its risk factor and mechanism remain unclear yet, which restricts the development of pharmacological treatment. Clinical research suggested that diabetes mellitus (DM) patients were prone to develop HO in tendon, but the solid evidence and mechanical research are still needed. Here, we combined the clinical samples and DM mice model to identify that disordered glycolipid metabolism aggravates the senescence of tendon derived stem cells (TSCs) and promotes their osteogenic differentiation. Then, combining the RNA-seq results of aging tendon, we detected the abnormally activated autocrine CXCL13-CXCR5 axis in TSCs cultured in high fat high glucose (HFHG) environment and also in aged tendon. Genetic inhibition of CXCL13 successfully alleviates the HO formation in DM mice, providing a potential therapeutical target for suppressing HO formation in DM patients after trauma or surgery.

overall_design: RNA-seq using RNA extracted from TSCs cultured in HFHG medium or LG medium

first: Hang

last: Zhou


title: E14 cells knockdown with shRNA

first: Linlin

last: Hou

address: No. 66, Gongchang Road, Guangming District

institute: School of Medicine, Sun Yat-Sen University

summary: Transcription factors are considered to be the master switches that determine the state and fate of cells. Sox2 is an important transcription factor necessary for the pluripotency and self-renewal of embryonic stem cells. Sox2 is generally considered to play a role in the initiation of transcription, but recent studies have shown that Sox2 may influence the alternative splicing of pluripotent genes with the assistance of proteins associated with RNA metabolism, suggesting that Sox2 may be regulated in a novel way during the maintenance of pluripotency in embryonic stem cells. Using mouse embryonic stem cell model, this project focused on Sox2 and proteins related to RNA metabolism to explore their mode of action and the mechanism of regulating the maintenance of pluripotency of embryonic stem cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for E14 cells and its KD derivatives (shCdk9, shHnrnpk, and shSox2).

first: Qiang

last: Cao

first: Yanlan

last: Huang


title: Spatiotemporal transcriptomic mapping of regenerative inflammation in skeletal muscle reveals a dynamic multilayered tissue architecture

city: New York

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

institute: Mount Sinai Icahn School of Medicine

summary: Tissue regeneration is orchestrated by macrophages that clear damaged cells and promote regenerative inflammation. How macrophages spatially adapt and diversify their functions to support the architectural requirements of actively regenerating tissue remains unknown. In this study, we reconstructed the dynamic trajectories of myeloid cells isolated from acutely injured and early-stage dystrophic muscles. We identified divergent subsets of monocytes/macrophages and dendritic cells (DCs) and validated markers (e.g., GPNMB) and transcriptional regulators associated with defined functional states. In dystrophic muscle, specialized repair-associated subsets exhibited distinct macrophage diversity and reduced DC heterogeneity. Integrating spatial transcriptomics analyses with immunofluorescence uncovered the ordered distribution of subpopulations and multilayered regenerative inflammation zones (RIZs) where distinct macrophage subsets are organized in functional zones around damaged myofibers supporting all phases of regeneration. Importantly, intermittent glucocorticoid treatment disrupted the RIZs. Our findings suggest that macrophage subtypes mediated the development of the highly ordered architecture of regenerative tissues, unveiling the principles of the structured yet dynamic nature of regenerative inflammation supporting effective tissue repair.

overall_design: Single-cell trancriptomic profiling of C57 mouse CD45+ cells from TA, after one (D1), two (D2) and four days (D4 - see GSE161467) after CTX-induced acute sterile muscle injury and CD45+ cells from 2 month old D2.mdx GAST using high throughput sequencing (scRNA-seq, 10x Chromium V3 chemistry). Spatial trancriptomic profiling of D4 and D8 post-CTX TA muscles from WT and DBA2/J as well as 2 month old Vehicle and Prednisone-treated GAST from D2.mdx (stRNA-seq 10x Visium).

first: Andreas

last: Patsalos

last: Nagy


title: Single-Cell Transcriptome Sequencing for investigating tumor microenvironment remodeling mediated by a chimeric oncolytic adenovirus combined with PD-1 antibody

city: Shanghai

first: Changqing

last: Su

state: China

address: 225 Changhai Road, Yangpu District

department: Molecular Oncology

institute: National Center for Liver Cancer

summary: We constructed a chimeric oncolytic adenovirus which is a novel broad-spectrum anticancer product with multiple mechanisms of synergistic and potentiated immunotherapy

overall_design: Examination of 4 xenografted tumors of murine MC38 cells from different treated groups.

first: Yinghan

first: Jiang

last: Li

first: Lunxiu

last: Qin


title: Chinmo maintains adult stem cell sex identity by directly regulating Doublesex and Insulin signaling [CUT&Tag]

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) for Chinmo in drosophila wild-type and chinmoST testes


title: Gene expression of CD14+ peripheral blood monocytes in different phases of chronic HBV infection

city: New Delhi

first: Pramod

last: Upadhyay

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

summary: To identify gene biomarkers for different phases of chronic HBV infection, we performed RNA-seq of CD14+ monocytes from pateints in each of the phases, which was then analyzed for differntial gene expression and validated by qRT-PCR in individual samples

overall_design: CD14+ monocytes were isolated by MACS from blood of HBV patients in Immune-tolerant (IT), Immune-clearance (IC) or inactive carrier (IN) and Healthy control (HC) and RNA was isolated from these cells. 1 sample from each of IT, IC, IN and HC were sequenced as single sample, while 5 samples of IT, IC and HC were pooled repectively, hence 7 sequenced samples. Differential gene expression compared to HC was generated after RNA-seq data analysis, hence 5 total lists of differntially expressed genes, which was shortlisted for PCR validation and analyzed.

first: Prakriti

last: Sinha

first: Vaishali

last: Bhardwaj

first: Abaranjita

last: Muniyasamy

first: K

middle: V

last: Mohan

first: Kshama

last: Jain

first: Kiran

last: Chaudhary


title: Extracellular Vesicle contents of mouse trophoblast cells and their predicted influence on fetal brain development

city: Ames

first: Geetu

last: Tuteja

email: arnstrm@iastate.edu, geetu@iastate.edu

state: IA

address: 2437 PAMMEL DR

department: Genetics Development & Cell Biology

institute: Iowa State University

summary: Current work characterizes mRNA expression derived from mouse neural cortical stem cells incubated with and without EVs derived from either mouse parietal trophoblast giant cells or mouse trophoblast stem cells

overall_design: Four replicates each for three different treatments, total of 12 samples and 3 conditions (1 control).

first: Jessica

last: Kinkade

first: Arun

middle: S

last: Seetharam

first: Shrikesh

last: Sachdev

first: Nathan

last: Bivens

first: Brett

last: Phinney

first: Gabriela

last: Grigorean

first: R

last: Roberts

first: Cheryl

last: Rosenfeld


title: Targeting heterogeneous tumor microenvironments in pancreatic cancer mouse models of metastasis by TGFB depletion

status: Public on Aug 27 2024

city: Baltimore

first: Heng Chung

last: Kung

address: 1650 Orleans Street

department: Department of Oncology

institute: Johns Hopkins University School of Medicine

summary: The dual tumor-suppressive and promoting function of TGFB signaling has made its targeting challenging. We hereby examined the effects of TGFB depletion by AVID200/BMS-986416(TGFB-TRAP), a TGFB ligand trap, on the tumor microenvironment of pancreatic ductal adenocarcinoma (PDAC) murine models with different organ-specific metastasis using single-nuclear RNA-sequencing (snRNA-seq)

overall_design: Frozen mouse orthotopic KPC PDAC tumors were homogenized and isolated into single nuclei, modified from a previously described 10x Genomics protocol. Frozen mouse orthotopic KPC PDAC tumors were mechanically homogenized into powder form using mortar and pestle in liquid nitrogen. Lysis buffer containing 0.1% Triton-X (Sigma-Aldrich), 0.2 U/mL NxGen RNase inhibitor (Lucigen), and sucrose density buffer was added to the homogenized tissue and let sit for 3 min on ice. Following lysis, the crude homogenate was pipetted over a 100 mm cell strainer, washed with sucrose density buffer, and centrifuged at 400 rcf for 5 min at 4°C on low brake setting. The supernatant was aspirated, and the pellet was resuspended in resuspension buffer containing PBS + 1% BSA (Sigma-Aldrich) and 0.2 U/mL RNase inhibitor (Lucigen) over a 35 mm filter flow tube. Amplified cDNA was generated from RNA from each single nuclei using the Chromium Next GEM Single Cell V(D)J Reagent Kits v.1.1, per the manufacturer’s instructions.

first: Zheng

last: Lei

first: Chen

last: Sophia

first: Kung

last: Heng-Chung

first: Espinoza

last: Birginia


title: ALDH1A1 Promotes Immune Escape of Tumor Cells through ZBTB7B-Glycolysis Pathway

city: Zhuzhou

first: Huan

last: Chen

state: Hunan

address: No.116, Changjiang South Road, Tianyuan District, Zhuzhou, China

institute: Zhuzhou Central Hospital

summary: Background The primary impediment to the success of immunotherapy lies in the immune evasion orchestrated by tumors, contributing to the suboptimal overall response rates observed. Despite this recognition, the intricacies of the underlying mechanisms remain incompletely understood. Methods and Results Through preliminary detection of clinical patient tissues, we have found that ALDH1A1 was a key gene for the prognosis of cancer patients and tumor glycolysis. In vitro experiments and tumor formation in nude mice suggested that targeting ALDH1A1 could inhibit tumor growth. Through further analysis of xenograft tumor models in immune-normal mice and flow cytometry, we found that deficiency in ALDH1A1 could promote immune system suppression of tumors in vivo. Specifically, RNA-seq analysis, combined with qPCR and western blot, identified the transcription factor ZBTB7B as downstream of ALDH1A1. The binding sites of the transcription factor ZBTB7B on the LDHA promoter region, which is responsible for regulating the rate-limiting enzyme gene LDHA in glycolysis, were determined using luciferase reporter gene detection and Chip-qPCR, respectively. In addition, the increased SUMOylation of ZBTB7B stabilized its transcriptional activity. Further in vivo and in vitro experiments confirmed that the combination of targeting ALDH1A1 and ZBTB7B with immune checkpoint inhibitors could synergistically inhibit tumors in vivo. Finally, after conducting additional verification of patient tissue and clinical data, we have confirmed the potential translational value of targeting ALDH1A1 and ZBTB7B for tumor immunotherapy. Conclusions These results emphasize the potential translational significance of targeting ALDH1A1 and ZBTB7B in the realm of tumor immunotherapy. The convergence of ALDH1A1 inhibition and immune checkpoint blockade, particularly with PD-L1/PD-1 mAb, presents a compelling avenue for curtailing tumor immune escape.

overall_design: To investigating the combination of targeting ALDH1A1 and ZBTB7B with immune checkpoint inhibitors whether or not synergistically inhibit tumors in vivo


title: Extracellular vesicle contents of mouse trophoblast cells and their predicted influence on fetal brain development

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

summary: Current work characterizes small RNA within EVs derived from culture media of undifferentiated mouse trophoblast stem cells (mTSC), and mTSC differentiated into pTGCs

overall_design: Four replicates each for two different cell types, total of 8 samples for 2 conditions.


title: Single-cell transcriptomics reveals tissue architecture in ovarian carcinosarcoma

city: Hangzhou

first: Junfen

last: Xu

state: Other (Non U.S.)

address: No.1 Xueshi Road

department: Department of Gynecologic Oncology

institute: Women’s Hospital, Zhejiang University School of Medicine

summary: Ovarian carcinosarcoma (OCS) is one of rarest and most challenging histologic subtype of ovarian cancer. It features remarkable cellular heterogeneity. Using single-cell RNA sequencing, we characterize the cellular composition of the OCS and identify their molecular characteristics.

overall_design: landscape of  OCS


title: HIV Induces RSAD2/Viperin To Promote Sustained Infection of Monocyte-Derived Macrophages

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: HIV establishes long-term latent infection in memory CD4+ T cells, but also establishes sustained long-term productive infection in macrophages, especially in the CNS.  To better understand how HIV sustains infection in macrophages, we performed RNAseq analysis after infection of human-monocyte derived macrophages (MDMs) with the brain-derived HIV-1 strain YU2 and compared this with acute infection of CD4+ T cells. HIV infection in MDM and CD4+ T-cells altered many gene transcripts, but with few overlaps between these different cell types. We found interferon pathways upregulated in both MDM and CD4+ T-cells, but with different gene signatures.  The interferon-stimulated gene RSAD2/Viperin was among the most upregulated genes following HIV infection in MDMs, but not in CD4+ T-cells.  RSAD2/Viperin was induced early after infection with various HIV strains, was sustained over time, and remained elevated in established MDM infection even if new rounds of infection were blocked by antiretroviral treatment.  Immunofluorescence microscopy revealed that RSAD2/Viperin was induced strongly in HIV infected cells, as well as in some uninfected neighboring cells, and was frequently localized at junctions between cells.  Knockdown of RSAD2/Viperin following establishment of infection in MDMs reduced production of HIV transcripts and viral p24 antigen.  This correlated with reduction in the number of multinucleated giant cells, and changes in the histone modifications at the HIV LTR, including loss of histone H3K7ac and H3K9me3, epigenetic marks that we have found associated with HIV in MDMs.  RNA-seq transcriptomic analysis of RSAD2/Viperin knockdown during HIV infection of MDMs revealed activation of interferon alpha and gamma pathways and inactivation of Rho GTPase pathways. Taken together, these results suggest that RSAD2/Viperin supports HIV infection in macrophages through multiple mechanisms, potentially including the attenuation of the interferon response.

overall_design: We knocked down RSAD2 in HIV infected MDMs using siRNA (siRSAD2 or siControl) and then studied the effect of knockdown on MDM transcriptomic response by RNA-seq.

first: Urvi

last: Zankharia

first: Yanjie

last: Yi

first: Fang

last: Lu

first: Olga

last: Vladimirova

first: Andrew

last: Kossenkov

first: Jayamanna

first: Paul

last: Lieberman

first: Ronald

last: Collman


title: Spatial transcriptome for investigating tumor microenvironment remodeling mediated by a chimeric oncolytic adenovirus combined with PD-1 antibody

first: Changqing

last: Su

first: Yinghan

first: Jiang

last: Li

first: Lunxiu

last: Qin


title: GCN2 drives diurnal patterns in the hepatic integrated stress response and maintains circadian rhythms in whole body metabolism during amino acid insufficiency

city: New Brunswick

first: Tracy

last: Anthony

state: NJ

address: 59 Dudley rd

department: Nutritional Sciences

institute: Rutgers University

summary: Disruptions in circadian rhythms are associated with increased risk of developing metabolic diseases. General control nonderepressible 2 (GCN2), a primary sensor of amino acid insufficiency and activator of the integrated stress response (ISR), has emerged as a conserved regulator of the circadian clock in multiple organisms. The objective of this study was to examine diurnal patterns in hepatic ISR activation in the liver and whole-body rhythms in metabolism. We hypothesized that GCN2 activation cues hepatic ISR signaling over a natural 24 h feeding fasting cycle. To address our objective, wild type (WT) and whole body Gcn2 knockout (GCN2 KO) mice were housed in metabolic cages and provided free access to either a Control or leucine-devoid diet (LeuD) for 8-days in total darkness. On the last day, blood and livers were collected at circadian time (CT) 3 and CT15. In livers of WT mice, GCN2 phosphorylation followed a diurnal pattern that was guided by intracellular branched chain amino acid concentrations (r2=0.93). Feeding LeuD to WT mice increased hepatic ISR activation at CT15 only. Diurnal oscillation in hepatic ISR signaling, the hepatic transcriptome including lipid metabolic genes, and triglyceride concentrations were substantially reduced or absent in GCN2 KO mice. Further, mice lacking GCN2 were unable to maintain circadian rhythms in whole body energy expenditure, respiratory exchange ratio and physical activity when fed LeuD. In conclusion, GCN2 activation functions to maintain diurnal ISR activation in the liver and has a vital role in the mechanisms by which nutrient stress affects whole-body metabolism.

overall_design: For this study, liver tissue was collected from WT and whole body GCN2 KO mice fed a Control or LeuD diet and killed at CT03 or CT15. Our comparisons look at the impact of GCN2 deletion, LeuD feeding and their interaction on diurnal patterns in the hepatic transcriptome. For this experiment we compare the differential expression of transcripts between the two time points within our various treatment groups. In addition, to observe the time dependent impact of LeuD feeding on the hepatic transcriptome, we compare the differential gene expression of Control and LeuD fed WT mice at the CT03 and CT15 time points.

first: Jordan

last: Levy

first: Emily

last: Mirek

first: Esther

last: Rodriguez

first: Maria

last: Tolentino

first: Brian

last: Zalma

first: Troy

last: Roepke

middle: C

last: Wek

first: Rufeing

last: Cao


title: Maternal immune cell gene expression associates with maternal gut microbiome, milk composition and infant gut microbiome

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

summary: Background - Prepregnancy overweight and obesity promote deleterious health impacts on both mothers during pregnancy and the offspring. Significant changes in the maternal peripheral blood mononuclear cells (PBMCs) gene expression due to obesity are well-known. However, during pregnancy the impact of overweight on immune cell gene expression and its association with maternal and infant outcomes is not well explored. Methods – Blood samples were collected from healthy normal weight (NW, BMI 18.5-24.9) or overweight (OW, BMI 25-29.9) 2nd parity pregnant women at 12, 24 and 36 weeks of pregnancy. PBMCs were isolated from the blood and subjected to mRNA sequencing. Maternal and infant microbiota were analyzed by 16S rRNA gene sequencing. Integrative multi-omics data analysis was performed to evaluate the association of gene expression with maternal diet, gut microbiota, milk composition, and infant gut microbiota.  Results - Gene expression analysis revealed that 453 genes were differentially expressed in the OW women compared to NW women at 12 weeks of pregnancy, out of which 354 were upregulated and 99 were downregulated. Several up-regulated genes in the OW group were enriched in inflammatory, chemokine-mediated signaling and regulation of interleukin-8 production-related pathways. At 36 weeks of pregnancy healthy eating index score was positively associated with several genes that include, DTD1, ELOC, GALNT8, ITGA6-AS1, KRT17P2, NPW, POT1-AS1 and RPL26. In addition, at 36 weeks of pregnancy, genes involved in adipocyte functions, such as NG2 and SMTNL1, were negatively correlated to human milk 2’FL and total fucosylated oligosaccharides content collected at 1 month postnatally. Furthermore, infant Akkermansia was positively associated with maternal PBMC anti-inflammatory genes that include CPS1 and RAB7B, at 12 and 36 weeks of pregnancy. Conclusions – These findings suggest that prepregnancy overweight impacts the immune cell gene expression profile, particularly at 12 weeks of pregnancy. Further, deciphering the complex association of PBMC’s gene expression levels with maternal gut microbiome and milk composition and infant gut microbiome may aid in developing strategies to mitigate obesity-mediated effects.

overall_design:
Mother-child dyads who were enrolled in the Growing Life, Optimizing Wellness study (Glowing, ClinicalTrials.gov ID:NCT01131117) at Arkansas Children's Nutrition Center were included in the study. Healthy women of 2nd parity, without any pre-existing conditions and who were with either normal weight (NW, BMI 18.5-24.9, n = 9-10) or with overweight (OW, BMI 25-29.9, n = 9-10) were enrolled in the study. Blood samples from the participants were collected at 12, 24, and 36 weeks of gestation for peripheral blood mononuclear cells. PBMCs were isolated using FICO/Lite-LyphoH density gradient method. Maternal dietary factors, gut microbiota at 36 weeks of gestaion, milk components (cytokines and macronutrients) at postnatal 2 weeks, 4 weeks, 2 months and 3 months, milk HMOs at postnatal 2 months and infant microbiome at 1 month of age published previously for the GLOWING study was used to associate with PBMC mRNA gene expression.
Differential gene expression between NW and OW was determined using DESeq2 and pathway analysis was performed using DAVID.
Association between gene expression and maternal and infant factors was calculated using integrative multi-omics and cross-omic analyses, emplyoing sparse partial least square regression-based modeling.

first: Manoj

last: Gurung

first: Bharath

last: K Mulakala

first: Brent

last: T Schlegel

first: Kartik

last: Shankar

first: Lars

last: Bode

first: Meghan

last: L Ruebel

first: Clark

last: Sims

first: Audrey

last: Martinez

first: Aline

last: Andres

first: Laxmi

last: Yeruva


title: Targeting S6K1 and S6K2 by siRNA and sgRNA in LN229 GBM cells

city: Cincinnati

first: David

middle: R.

last: Plas

state: OH

address: 3125 Eden Ave.

department: Department of Cancer Biology

institute: University of Cincinnati

summary: To systematically identify the function of S6K1 and S6K2 in glioblastoma cells, LN229 cells were stably transduced with Cas9, control non-targeting sgRNA (sgNT), or sgRNAs targeting S6K1 or S6K2.  The cells were then transiently transfected with non-targeting siRNAs (siNT), or siRNA pools targeting S6K1 or S6K2.  RNA sequencing was performed to compare cellular responses to inactivation of single or combination S6 kinases.

overall_design: RNA-seq of LN229 GBM cells treated with either siS6K1, siS6K2, sgS6K1, sgS6K2, siS6K1 + sgS6K2, siS6K2 + sgS6K1


title: A multidimensional analysis reveals distinct immune phenotypes and tertiary lymphoid structure-like aggregates in pediatric acute myeloid leukemia.

city: Utrecht

first: Joost

last: Koedijk

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

summary: Because of the low mutational burden, children with acute myeloid leukemia (AML) are thought to have a ‘cold’ tumor microenvironment and consequently, a low likelihood of response to T cell-directed immunotherapies. Here, we provide a multidimensional overview of the tumor immune microenvironment in newly diagnosed pediatric AML. On a cohort level, we demonstrate wide variation in T cell infiltration with nearly one-third of cases harboring an immune-infiltrated bone marrow. These immune-infiltrated cases are characterized by a decreased abundance of M2-like macrophages, which we find to be associated with response to T cell-directed immunotherapy in adult AML. On an organizational level, we reveal the composition of spatially organized immune aggregates in pediatric AML, and show that in the adult setting such aggregates in post-treatment bone marrow and extramedullary sites associate with response to ipilimumab-based therapy. Altogether, our study provides immune correlates of response to T cell-directed immunotherapies and indicates starting points for further investigations into immunomodulatory mechanisms in AML.

overall_design:
The aim of this spatial transcriptomics experiment was to compare the gene expression profiles of immune aggregates (large T cell networks that colocalized with a dense network of B cells; called Aggregate-regions) with mixed regions (containing AML cells and other microenvironmental populations; called MIXED1 in case this mixed region was from a biopsy that contained immune aggregates, and MIXED2 if the mixed region was from a biopsy that did not contain immune aggregates) and control regions (regions from non-leukemic control samples). In total, we sequenced regions from 4 AML biopsies with immune aggregates, 2 AML biopsies without immune aggregates, and 2 non-leukemic control biopsies. The number of regions successfully sequenced and for further details, we refer to our preprint on medRxiv: https://www.medrxiv.org/content/10.1101/2023.03.03.23286485v3.

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Submitter states that missing raw data are being made available for controlled access in EGA.
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first: Olaf

last: Heidenreich


title: Metabolic Reprogramming of Iron Endows the Function of ISCA2-TET Interaction During Peri-implantation Development

first: Xinyu

last: Wang

address: Siping Road 1239

institute: Tongji University

summary: Metabolic reprogramming plays important roles in embryo development. However, the metabolic network has still not been systematically investigated during the processes. In this study, we develop MFE, a metabolites flux estimation tool, to predict metabolite abundances and their regulons, highlighting the role of Fe(II) and its regulon-ISCA2, in the inner cell mass (ICM) of human and mouse blastocysts. By introducing Isca2-/-, Isca2G77S/G77S and Isca2C144S/C144S mice, we find ISCA2 binding with iron, but not Fe-S cluster, is indispensable for mouse peri-implantation development. Mechanistically, nuclear ISCA2 interacts with TET, and Fe(II) is important for the interaction by triggering the enzymatic activity of TET. The partnership safeguards promoters of epiblast-specific genes from hypermethylation and is essential for epiblast development in mouse peri-implantation embryos. The study provides insights into how iron metabolism modulates embryo development, and suggests a manner of Fe(II)-dependentenzymes to achieve activity under physiological conditions.

overall_design: RNA-seq, small RNA-seq, EM-seq of mouse Isca2 WT and KO pre-implantation embryos. To collected pre-implantation embryos, Isca2+/- female mouse intraperitoneal with 6.5 international unit of pregnant mares’ serum gonadotropin and, 45 to 47 h later, with 5 IU of human chorionic gonadotropin and crossed to Isca2+/- males.

first: Jiaming

last: Zhang

first: Weibo

last: Hou

first: Qingran

last: Kong


title: Mitochondrial activity dictates definitive hematopoietic stem cell production and lympho-myeloid lineage segregation during mouse mouse embryogenesis [bulkRNAseq]

city: Bengaluru

first: Maneesha

last: Inamdar

state: Karnataka

address: JNCASR, Jakkur

department: MBGU

institute: JNCASR

summary: Mitochondrial metabolism determines bone marrow hematopoietic stem cell (HSC) heterogeneity, and influences long-term blood repopulation potential.Self-renewal and multilineage engraftment capacity of hematopoietic stem cells (HSCs) are key properties leveraged for their clinical use in bone marrow transplantation. Variations in long-term blood reconstitution ability are partly attributed to the functional heterogeneity in HSCs, which is influenced by the dynamic mitochondrial metabolic state, in addition to differences in gene expression. However, when and how this mitochondrial regulation of definitive HSCs originates is unexplored.  Whether metabolic variation is an outcome of the diverse HSC milieu, or an inherent property of the emergent HSCs, is not known. Here, Wwe show that dynamic changes in mitochondrial activity during endothelial to hematopoietic transition (EHT) drives the production of mature HSCs in the mouse embryo. Pharmacological and genetic manipulations show that  hematopoietic emergence during the endothelial to hematopoietic transition (EHT) in the aorta-gonad-mesonephros (AGM) region involves mitochondrial remodelling. reduced mitochondrial activity activates Wnt signalling to promote expansion of mature HSCs in the AGM. Further, single cell transcriptomics and functional assays uncovered mitochondrial membrane potential (MMP) driven functional heterogeneity within the mature HSC pool. MMPlow HSCs are myeloid-biased and exhibit enhanced differentiation potential. Contrarily, MMPhigh HSCs are lymphoid-biased with diminished differentiation potential. Mechanistically, low mitochondrial activity upregulates PI3K signalling to fuel embryonic HSC differentiation. We provide insights into the metabolic regulation of HSC origin and function, that can be leveraged to direct HSC fate decisions for clinical interventions.

overall_design: To investigate the mechanims of how mitochondrial activity regulates embryonic HSC maturation, E10.5 AGM was treated with CCCP and bulk-RNA transcriptome analysis was carried out in control and CCCP treated c-kit+ HSCs.

first: Aishwarya

last: Prakash


title: Mitochondrial activity dictates definitive hematopoietic stem cell production and lympho-myeloid lineage segregation during mouse embryogenesis [scRNAseq]

summary: Mitochondrial metabolism determines bone marrow hematopoietic stem cell (HSC) heterogeneity, and influences long-term blood repopulation potential. However, when and how this mitochondrial regulation of definitive HSCs originates is unexplored. We show that dynamic changes in mitochondrial activity during endothelial to hematopoietic transition (EHT) drives the production of mature HSCs in the mouse embryo. Pharmacological and genetic manipulations show that reduced mitochondrial activity activates Wnt signalling to promote expansion of mature HSCs in the AGM. Further, single cell transcriptomics and functional assays uncovered mitochondrial membrane potential (MMP) driven functional heterogeneity within the mature HSC pool. MMPlow HSCs are myeloid-biased and exhibit enhanced differentiation potential. Contrarily, MMPhigh HSCs are lymphoid-biased with diminished differentiation potential. Mechanistically, low mitochondrial activity upregulates PI3K signalling to fuel embryonic HSC differentiation. We provide insights into the metabolic regulation of HSC origin and function, that can be leveraged to direct HSC fate decisions for clinical interventions.

overall_design: To understand the transcriptional basis of mitochondrial activity mediated segregation of HSC function, scRNA sequencing analysis was performed on E11.5 AGM cells sorted on the basis of mitochondrial activity levels.


title: Transcriptome expression changes after knockdown of ALDH1A1 in human colon cancer cells HT29

city: Changsha, Hunan, China

first: Xi

last: Li

address: No.87 Xiangya Road

institute: Xiangya Hospital, Central South University

summary: Firstly, shRNA (GCCAAATCATTCCTTGGAATT) was used to knock down ALDH1A1 in HT29 cells, and the knockdown effect was verified by western blot. Then the shALDH1A1 HT29 cells were compared with parental HT29 cells by RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for shALDH1A1 HT29 cells and parental HT29 cells.

first: Mingyuan


title: Notch signaling suppresses neuroendocrine differentiation and alters the tumor immune microenvironment in advanced prostate cancer

city: Boston

first: Sheng-Yu

last: Ku

state: MA

address: 44 Binney St, Dana Building, DA1422, MA 02215

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: Neuroendocrine prostate cancer (NEPC) is an aggressive, androgen-independent variant of prostate cancer (PCa) that most commonly develops in patients as a mechanism of therapeutic resistance. The underlying mechanisms driving PCa lineage plasticity and trans-differentiation to a neuroendocrine lineage are not fully understood. Here, we identify Notch signaling as a key suppressor of neuroendocrine differentiation in PCa. Restoration of Notch signaling in NEPC models results in phenotypic conversion towards a non-neuroendocrine state with expression of prostate luminal cell markers and immunologic changes including up-regulation of MHC Class I and II and type I interferon signaling that correlate with changes in the tumor immune microenvironment. Overall, these data provide new insights into how Notch signaling influences PCa lineage plasticity and points to new therapeutic avenues to modulate it.

overall_design:
To investigate the role of ASCL1 in neuroendocrine prostate cancer, we knocked out ASCL1 using CRISPR-Cas9 in NEPC organoids, WCM154, and inoculated organoids in vivo to investigate the tumor phenotype.
We performed RNA-seq on control (sgGFP) and ASCL1 knockout (sgASCL1) tumors from three independent mice per condition. Differential expresesion analysis was then performed to illuminate gene expression.

first: Kei

last: Muzino

first: Himisha

last: Beltran


title: Senescent fibroblasts in the tumor stroma rewire lung cancer metabolism and plasticity

city: San Francisco

first: Tien

last: Peng

state: California

address: 513 Parnassus Avenue

department: medicine

institute: UCSF

summary: Our study identified a druggable component of the tumor stroma that fulfills the metabolic requirement of tumor cells to acquire a more aggressive phenotype.

overall_design: The p16INK4a+ and p16INK4a- lung fibroblasts and tdTomato+ LUAD cells of KPTI mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence of eGFP signal and analyzed using scRNAseq. tdTomato+ tumor cells were isolated by FACS after digestion of tumor organoids. KPTI mouse lung sections and human LUAD sections were analyzed by Xenium for spatial transcriptomics data.

first: Jinyoung

last: Lee


title: ST2+ T-regulatory Cells in Renal Inflammation and Fibrosis following Ischemic Kidney Injury

city: Charlottesville

first: Vikram

last: Sabapathy

state: Virginia

address: 1340 Jefferson Park Ave., Pinn Hall, Room No: 4043

department: Center for Immunity, Inflammation and Regenerative Medicine

institute: University of Virginia

summary: The role of IL-33 and its receptor ST2 in kidney injury is not well understood. This study demonstrates the importance of ST2 expression on the T-regulatory cells (Tregs) for the resolution of renal injury by suppressing inflammation and fibrosis. Treg-specific deletion of  ST2, detrimentally impacted late outcomes of renal injury worsening the impairment of kidney function, inflammation, and fibrosis.

overall_design: To delineate the role of kidney-specific ST2+ Tregs, we utilized single-cell RNA sequencing platform.  Post unilateral IRI CD4 T cells were sorted from digested kidneys of Il1rl1fl/fl and  Il1rl1fl/fl Foxp3YFP-Cre mice respectively using flow cytometry. The samples from Il1rl1fl/fl mice, IRIWT1 (10,146 cells) and IRIWT2 (9,573 cells) were merged as IRIWT, and  Il1rl1fl/fl Foxp3YFP-Cre mice, IRIKO1 (4,580 cells), IRIKO2 (10,899 cells) and IRIKO3 (5,580 cells) were merged as IRIKO respectively.

first: Rahul

last: Sharma


title: Histone demethylase JMJ4 interacts with transcription factor BLH3 to modulate jasmonate biosynthesis in tomato response to cold stress [RNA-seq]

first: Chenxu

last: Liu

state: Zhejiang

address: Xihu District, No.866 Yuhangtang Road

department: Horticulture

institute: Zhejiang university

summary: To investigate the difference of gene expression regulated by JMJ4, we performed RNA-seq assay of jmj4 mutant and wild type plants under control and cold treatment conditions.

overall_design: For RNA-seq, jmj4 mutant and wild type plants were both subjected to 25 degree and 4 degree treatment for 12h, then leaf samples were collected for high-throughput sequencing.

first: Tong

last: Xu

first: Jie

last: Zhou


title: Epigenome analysis of anterior capsular membrane of lens in healthy and cataract patients

city: Mudanjiang City

first: Xiaoya

last: Chen

state: Heilongjiang Province

address: No.4 Tongxiang Street, Aimin District, Mudanjiang City, Heilongjiang Province

institute: 牡丹江医学院

summary:
DNA methylation levels were analyzed by MethylationEPIC BeadChip (850K) in ARC patients and normal controls. Compared with the control group, a total of 52705 differentially methylated site (DMS) were detected in the ARC group, of which 13858 were hypermethylated and 38847 were hypomethylated.
Our study revealed that the whole-genome DNA methylation patterns and gene expression profiles in ARC and identifified molecular markers of methylation may aid in the prevention, diagnosis, treatment, and prognosis of ARC.

overall_design: NOR group (There are three groups of two samples per group) and ARC group (There are three groups of two samples per group)

first: Shanshan

last: Hu