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Employing Multi-Omics Analyses To Understand Changes During Kidney Development In Perinatal Interleukin-6 Animal Model., Ganesh Panzade, Tarak Srivastava, Daniel P. Heruth, Mohammad Rezaiekhaligh, Jianping Zhou, Zhen Lyu, Mukut Sharma, Trupti Joshi Oct 2024

Employing Multi-Omics Analyses To Understand Changes During Kidney Development In Perinatal Interleukin-6 Animal Model., Ganesh Panzade, Tarak Srivastava, Daniel P. Heruth, Mohammad Rezaiekhaligh, Jianping Zhou, Zhen Lyu, Mukut Sharma, Trupti Joshi

Manuscripts, Articles, Book Chapters and Other Papers

Chronic kidney disease (CKD) is a leading cause of morbidity and mortality globally. Maternal obesity during pregnancy is linked to systemic inflammation and elevated levels of the pro-inflammatory cytokine interleukin-6 (IL-6). In our previous work, we demonstrated that increased maternal IL-6 during gestation impacts intrauterine development in mice. We hypothesized that IL-6-induced inflammation alters gene expression in the developing fetus. To test this, pregnant mice were administered IL-6 or saline during mid-gestation. Newborn mouse kidneys were analyzed using mRNA-seq, miRNA-seq and whole-genome bisulfite-seq (WGBS). A multi-omics approach was employed to quantify mRNA gene expression, miRNA expression and DNA methylation, using …

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Il-7rα On Cd4+ T Cells Is Required For Their Survival And The Pathogenesis Of Experimental Autoimmune Encephalomyelitis, Gholamreza Azizi, Bram Van Den Broek, Larissa Ishikawa, Hamed Naziri, Reza Yazdani, Guang-Xian Zhang, Bogoljub Ciric, Mohamad Rostami Oct 2024

Il-7rα On Cd4+ T Cells Is Required For Their Survival And The Pathogenesis Of Experimental Autoimmune Encephalomyelitis, Gholamreza Azizi, Bram Van Den Broek, Larissa Ishikawa, Hamed Naziri, Reza Yazdani, Guang-Xian Zhang, Bogoljub Ciric, Mohamad Rostami

Department of Neurology Faculty Papers

BACKGROUND: The IL-7 receptor alpha (IL-7Rα) binds both IL-7 and thymic stromal lymphopoietin (TSLP). IL-7Rα is essential for the development and survival of naive CD4+ T cells and their differentiation to effector/memory CD4+ T cells. Mice lacking IL-7Rα have severe lymphopenia and are resistant to experimental autoimmune encephalomyelitis (EAE), a model for multiple sclerosis. However, it has been reported that IL-7Rα on peripheral CD4+ T cells is disposable for their maintenance and EAE pathogenesis, which does not align with the body of knowledge on the role of IL-7Rα in the biology of CD4+ T cells. Given that a definitive study …

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Atr Inhibition Radiosensitizes Cells Through Augmented Dna Damage And G2 Cell Cycle Arrest Abrogation, Scott J Bright, Mandira Manandhar, David B Flint, Rishab Kolachina, Mariam Ben Kacem, David Kj Martinus, Broderick X Turner, Ilsa Qureshi, Conor H Mcfadden, Poliana C Marinello, Simona F Shaitelman, Gabriel O Sawakuchi Oct 2024

Atr Inhibition Radiosensitizes Cells Through Augmented Dna Damage And G2 Cell Cycle Arrest Abrogation, Scott J Bright, Mandira Manandhar, David B Flint, Rishab Kolachina, Mariam Ben Kacem, David Kj Martinus, Broderick X Turner, Ilsa Qureshi, Conor H Mcfadden, Poliana C Marinello, Simona F Shaitelman, Gabriel O Sawakuchi

Faculty, Staff and Student Publications

Ataxia telangiectasia and Rad3-related protein (ATR) is a key DNA damage response protein that facilitates DNA damage repair and regulates cell cycle progression. As such, ATR is an important component of the cellular response to radiation, particularly in cancer cells, which show altered DNA damage response and aberrant cell cycle checkpoints. Therefore, ATR's pharmacological inhibition could be an effective radiosensitization strategy to improve radiotherapy. We assessed the ability of an ATR inhibitor, AZD6738, to sensitize cancer cell lines of various histologic types to photon and proton radiotherapy. We found that radiosensitization took place through persistent DNA damage and abrogated G2 …

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Tca Metabolism Regulates Dna Hypermethylation In Lps And Mycobacterium Tuberculosis–Induced Immune Tolerance, Abhimanyu, Santiago Carrero Longlax, Tomoki Nishiguchi, Malik Ladki, Daanish Sheikh, Amera L Martinez, Emily M Mace, Sandra L Grimm, Thaleia Caldwell, Alexandra Portillo Varela, Rajagopal V Sekhar, Anna M Mandalakas, Mandla Mlotshwa, Sibuse Ginidza, Jeffrey D Cirillo, Robert S Wallis, Mihai G Netea, Reinout Van Crevel, Cristian Coarfa, Andrew R Dinardo Oct 2024

Tca Metabolism Regulates Dna Hypermethylation In Lps And Mycobacterium Tuberculosis–Induced Immune Tolerance, Abhimanyu, Santiago Carrero Longlax, Tomoki Nishiguchi, Malik Ladki, Daanish Sheikh, Amera L Martinez, Emily M Mace, Sandra L Grimm, Thaleia Caldwell, Alexandra Portillo Varela, Rajagopal V Sekhar, Anna M Mandalakas, Mandla Mlotshwa, Sibuse Ginidza, Jeffrey D Cirillo, Robert S Wallis, Mihai G Netea, Reinout Van Crevel, Cristian Coarfa, Andrew R Dinardo

Faculty, Staff and Students Publications

Severe and chronic infections, including pneumonia, sepsis, and tuberculosis (TB), induce long-lasting epigenetic changes that are associated with an increase in all-cause postinfectious morbidity and mortality. Oncology studies identified metabolic drivers of the epigenetic landscape, with the tricarboxylic acid (TCA) cycle acting as a central hub. It is unknown if the TCA cycle also regulates epigenetics, specifically DNA methylation, after infection-induced immune tolerance. The following studies demonstrate that lipopolysaccharide and Mycobacterium tuberculosis induce changes in DNA methylation that are mediated by the TCA cycle. Infection-induced DNA hypermethylation is mitigated by inhibitors of cellular metabolism (rapamycin, everolimus, metformin) and the TCA …

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Enhanced Staphylococcus Aureus Protection By Uncoupling Of The Α-Toxin-Adam10 Interaction During Murine Neonatal Vaccination, Kelly L Tomaszewski, Meagan Blanchard, Reuben Olaniyi, Hannah R Brenton, Samantha Hayes, Farheen Fatma, Gaya K Amarasinghe, Byoung-Kyu Cho, Young Ah Goo, Andrea C Dedent, Stephanie A Fritz, Juliane Bubeck Wardenburg Oct 2024

Enhanced Staphylococcus Aureus Protection By Uncoupling Of The Α-Toxin-Adam10 Interaction During Murine Neonatal Vaccination, Kelly L Tomaszewski, Meagan Blanchard, Reuben Olaniyi, Hannah R Brenton, Samantha Hayes, Farheen Fatma, Gaya K Amarasinghe, Byoung-Kyu Cho, Young Ah Goo, Andrea C Dedent, Stephanie A Fritz, Juliane Bubeck Wardenburg

2020-Current year OA Pubs

Staphylococcus aureus remains a leading global cause of bacterial infection-associated mortality and has eluded prior vaccine development efforts. S. aureus α-toxin (Hla) is an essential virulence factor in disease, impairing the T cell response to infection. The anti-Hla antibody response is a correlate of human protective immunity. Here we observe that this response is limited early in human life and design a vaccine strategy to elicit immune protection against Hla in a neonatal mice. By targeted disruption of the interaction of Hla with its receptor ADAM10, we identify a vaccine antigen (Hla

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Clinically Relevant Mouse Models Of Severe Spinal Muscular Atrophy With Respiratory Distress Type 1., Sarah E Holbrook, Amy N Hicks, Paige B Martin, Timothy J Hines, Harold P Castro, Gregory A. Cox Oct 2024

Clinically Relevant Mouse Models Of Severe Spinal Muscular Atrophy With Respiratory Distress Type 1., Sarah E Holbrook, Amy N Hicks, Paige B Martin, Timothy J Hines, Harold P Castro, Gregory A. Cox

Faculty Research 2024

Spinal Muscular Atrophy with Respiratory Distress (SMARD1) is a lethal infantile disease, characterized by the loss of motor neurons leading to muscular atrophy, diaphragmatic paralysis, and weakness in the trunk and limbs. Mutations in IGHMBP2, a ubiquitously expressed DNA/RNA helicase, have been shown to cause a wide spectrum of motor neuron disease. Though mutations in IGHMBP2 are mostly associated with SMARD1, milder alleles cause the axonal neuropathy, Charcot-Marie-Tooth disease type 2S (CMT2S), and some null alleles are potentially a risk factor for sudden infant death syndrome (SIDS). Variant heterogeneity studied using an allelic series can be informative in order to …

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Xenotransplanted Human Organoids Identify Transepithelial Zinc Transport As A Key Mediator Of Intestinal Adaptation, Maame Efua S Sampah, Vered Gazit, Deborah C Rubin, Et Al. Oct 2024

Xenotransplanted Human Organoids Identify Transepithelial Zinc Transport As A Key Mediator Of Intestinal Adaptation, Maame Efua S Sampah, Vered Gazit, Deborah C Rubin, Et Al.

2020-Current year OA Pubs

Short bowel syndrome (SBS) leads to severe morbidity and mortality. Intestinal adaptation is crucial in improving outcomes. To understand the human gene pathways associated with adaptation, we perform single-cell transcriptomic analysis of human small intestinal organoids explanted from mice with experimental SBS. We show that transmembrane ion pathways, specifically the transepithelial zinc transport pathway genes SLC39A4 and SLC39A5, are upregulated in SBS. This discovery is corroborated by an external dataset, bulk RT-qPCR, and Western blots. Oral zinc supplementation is shown to improve survival and weight gain of SBS mice and increase the proliferation of intestinal crypt cells in vitro. Finally, …

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Rescue Of Scn5a Mis-Splicing Does Not Improve The Structural And Functional Heart Defects Of A Dm1 Heart Mouse Model, Larissa Nitschke, Rong-Chi Hu, Andrew N Miller, Thomas A Cooper Oct 2024

Rescue Of Scn5a Mis-Splicing Does Not Improve The Structural And Functional Heart Defects Of A Dm1 Heart Mouse Model, Larissa Nitschke, Rong-Chi Hu, Andrew N Miller, Thomas A Cooper

Faculty, Staff and Students Publications

Myotonic Dystrophy Type 1 (DM1) is an autosomal dominant multisystemic disorder for which cardiac features, including conduction delays and arrhythmias, are the second leading cause of disease mortality. DM1 is caused by expanded CTG repeats in the 3' untranslated region of the DMPK gene. Transcription of the expanded DMPK allele produces mRNAs containing long tracts of CUG repeats, which sequester the Muscleblind-Like family of RNA binding proteins, leading to their loss-of-function and the dysregulation of alternative splicing. A well-characterized mis-regulated splicing event in the DM1 heart is the increased inclusion of SCN5A exon 6A rather than the mutually exclusive exon …

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An Iron-Rich Subset Of Macrophages Promotes Tumor Growth Through A Bach1-Ednrb Axis, Ian W Folkert, William A Molina Arocho, Tsun Ki Jerrick To, Samir Devalaraja, Irene S Molina, Jason Shoush, Hesham Mohei, Li Zhai, Md Naushad Akhtar, Veena Kochat, Emre Arslan, Alexander J Lazar, Khalida Wani, William P Israel, Zhan Zhang, Venkata S Chaluvadi, Robert J Norgard, Ying Liu, Ashley M Fuller, Mai T Dang, Robert E Roses, Giorgos C Karakousis, John T Miura, Douglas L Fraker, T S Karin Eisinger-Mathason, M Celeste Simon, Kristy Weber, Kai Tan, Yi Fan, Kunal Rai, Malay Haldar Oct 2024

An Iron-Rich Subset Of Macrophages Promotes Tumor Growth Through A Bach1-Ednrb Axis, Ian W Folkert, William A Molina Arocho, Tsun Ki Jerrick To, Samir Devalaraja, Irene S Molina, Jason Shoush, Hesham Mohei, Li Zhai, Md Naushad Akhtar, Veena Kochat, Emre Arslan, Alexander J Lazar, Khalida Wani, William P Israel, Zhan Zhang, Venkata S Chaluvadi, Robert J Norgard, Ying Liu, Ashley M Fuller, Mai T Dang, Robert E Roses, Giorgos C Karakousis, John T Miura, Douglas L Fraker, T S Karin Eisinger-Mathason, M Celeste Simon, Kristy Weber, Kai Tan, Yi Fan, Kunal Rai, Malay Haldar

Faculty, Staff and Student Publications

We define a subset of macrophages in the tumor microenvironment characterized by high intracellular iron and enrichment of heme and iron metabolism genes. These iron-rich tumor-associated macrophages (iTAMs) supported angiogenesis and immunosuppression in the tumor microenvironment and were conserved between mice and humans. iTAMs comprise two additional subsets based on gene expression profile and location-perivascular (pviTAM) and stromal (stiTAM). We identified the endothelin receptor type B (Ednrb) as a specific marker of iTAMs and found myeloid-specific deletion of Ednrb to reduce tumor growth and vascular density. Further studies identified the transcription factor Bach1 as a repressor of the iTAM transcriptional …

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Alzheimer’S Disease Risk Gene Cd2ap Is A Dose-Sensitive Determinant Of Synaptic Structure And Plasticity, Matea Pavešković, Ruth B De-Paula, Shamsideen A Ojelade, Evelyne K Tantry, Mikhail Y Kochukov, Suyang Bao, Surabi Veeraragavan, Alexandra R Garza, Snigdha Srivastava, Si-Yuan Song, Masashi Fujita, Duc M Duong, David A Bennett, Philip L De Jager, Nicholas T Seyfried, Mary E Dickinson, Jason D Heaney, Benjamin R Arenkiel, Joshua M Shulman Oct 2024

Alzheimer’S Disease Risk Gene Cd2ap Is A Dose-Sensitive Determinant Of Synaptic Structure And Plasticity, Matea Pavešković, Ruth B De-Paula, Shamsideen A Ojelade, Evelyne K Tantry, Mikhail Y Kochukov, Suyang Bao, Surabi Veeraragavan, Alexandra R Garza, Snigdha Srivastava, Si-Yuan Song, Masashi Fujita, Duc M Duong, David A Bennett, Philip L De Jager, Nicholas T Seyfried, Mary E Dickinson, Jason D Heaney, Benjamin R Arenkiel, Joshua M Shulman

Duncan NRI Faculty and Staff Publications

CD2-Associated protein (CD2AP) is a candidate susceptibility gene for Alzheimer's disease, but its role in the mammalian central nervous system remains largely unknown. We show that CD2AP protein is broadly expressed in the adult mouse brain, including within cortical and hippocampal neurons, where it is detected at pre-synaptic terminals. Deletion of Cd2ap altered dendritic branching and spine density, and impaired ubiquitin-proteasome system activity. Moreover, in mice harboring either one or two copies of a germline Cd2ap null allele, we noted increased paired-pulse facilitation at hippocampal Schaffer-collateral synapses, consistent with a haploinsufficient requirement for pre-synaptic release. Whereas conditional Cd2ap knockout in …

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Trβ Activation Confers At2-To-At1 Cell Differentiation And Anti-Fibrosis During Lung Repair Via Klf2 And Cebpa, Xin Pan, Lan Wang, Juntang Yang, Yingge Li, Min Xu, Chenxi Liang, Lulu Liu, Zhongzheng Li, Cong Xia, Jiaojiao Pang, Mengyuan Wang, Meng Li, Saiya Guo, Peishuo Yan, Chen Ding, Ivan O Rosas, Guoying Yu Oct 2024

Trβ Activation Confers At2-To-At1 Cell Differentiation And Anti-Fibrosis During Lung Repair Via Klf2 And Cebpa, Xin Pan, Lan Wang, Juntang Yang, Yingge Li, Min Xu, Chenxi Liang, Lulu Liu, Zhongzheng Li, Cong Xia, Jiaojiao Pang, Mengyuan Wang, Meng Li, Saiya Guo, Peishuo Yan, Chen Ding, Ivan O Rosas, Guoying Yu

Faculty, Staff and Students Publications

Aberrant repair underlies the pathogenesis of pulmonary fibrosis while effective strategies to convert fibrosis to normal regeneration are scarce. Here, we found that thyroid hormone is decreased in multiple models of lung injury but is essential for lung regeneration. Moreover, thyroid hormone receptor α (TRα) promotes cell proliferation, while TRβ fuels cell maturation in lung regeneration. Using a specific TRβ agonist, sobetirome, we demonstrate that the anti-fibrotic effects of thyroid hormone mainly rely on TRβ in mice. Cellularly, TRβ activation enhances alveolar type-2 (AT2) cell differentiation into AT1 cell and constrains AT2 cell hyperplasia. Molecularly, TRβ activation directly regulates the …

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An Iron-Rich Subset Of Macrophages Promotes Tumor Growth Through A Bach1-Ednrb Axis, Ian W Folkert, Mai T Dang, Et Al. Oct 2024

An Iron-Rich Subset Of Macrophages Promotes Tumor Growth Through A Bach1-Ednrb Axis, Ian W Folkert, Mai T Dang, Et Al.

2020-Current year OA Pubs

We define a subset of macrophages in the tumor microenvironment characterized by high intracellular iron and enrichment of heme and iron metabolism genes. These iron-rich tumor-associated macrophages (iTAMs) supported angiogenesis and immunosuppression in the tumor microenvironment and were conserved between mice and humans. iTAMs comprise two additional subsets based on gene expression profile and location-perivascular (pviTAM) and stromal (stiTAM). We identified the endothelin receptor type B (Ednrb) as a specific marker of iTAMs and found myeloid-specific deletion of Ednrb to reduce tumor growth and vascular density. Further studies identified the transcription factor Bach1 as a repressor of the iTAM transcriptional …

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25-Hydroxycholesterol Promotes Brain Cytokine Production And Leukocyte Infiltration In A Mouse Model Of Lipopolysaccharide-Induced Neuroinflammation, Johnathan Romero, Danira Toral-Rios, Jinsheng Yu, Steven M Paul, Anil G Cashikar Oct 2024

25-Hydroxycholesterol Promotes Brain Cytokine Production And Leukocyte Infiltration In A Mouse Model Of Lipopolysaccharide-Induced Neuroinflammation, Johnathan Romero, Danira Toral-Rios, Jinsheng Yu, Steven M Paul, Anil G Cashikar

2020-Current year OA Pubs

Neuroinflammation has been implicated in the pathogenesis of several neurologic and psychiatric disorders. Microglia are key drivers of neuroinflammation and, in response to different inflammatory stimuli, overexpress a proinflammatory signature of genes. Among these, Ch25h is a gene overexpressed in brain tissue from Alzheimer's disease as well as various mouse models of neuroinflammation. Ch25h encodes cholesterol 25-hydroxylase, an enzyme upregulated in activated microglia under conditions of neuroinflammation, that hydroxylates cholesterol to form 25-hydroxycholesterol (25HC). 25HC can be further metabolized to 7α,25-dihydroxycholesterol, which is a potent chemoattractant of leukocytes. We have previously shown that 25HC increases the production and secretion of …

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Cd28 Costimulation Augments Car Signaling In Nk Cells Via The Lck/Cd3Ζ/Zap70 Signaling Axis, Sunil Acharya, Rafet Basar, May Daher, Hind Rafei, Ping Li, Nadima Uprety, Emily Ensley, Mayra Shanley, Bijender Kumar, Pinaki P Banerjee, Luciana Melo Garcia, Paul Lin, Vakul Mohanty, Kun H Kim, Xianli Jiang, Yuchen Pan, Ye Li, Bin Liu, Ana K Nunez Cortes, Chenyu Zhang, Mohsen Fathi, Ali Rezvan, Melisa J Montalvo, Sophia L Cha, Francia Reyes-Silva, Rejeena Shrestha, Xingliang Guo, Kiran Kundu, Alexander Biederstädt, Luis Muniz-Feliciano, Gary M Deyter, Mecit Kaplan, Xin R Jiang, Enli Liu, Antrix Jain, Janos Roszik, Natalie W Fowlkes, Luisa M Solis Soto, Maria G Raso, Joseph D Khoury, Pei Lin, Francisco Vega, Navin Varadarajan, Ken Chen, David Marin, Elizabeth J Shpall, Katayoun Rezvani Oct 2024

Cd28 Costimulation Augments Car Signaling In Nk Cells Via The Lck/Cd3Ζ/Zap70 Signaling Axis, Sunil Acharya, Rafet Basar, May Daher, Hind Rafei, Ping Li, Nadima Uprety, Emily Ensley, Mayra Shanley, Bijender Kumar, Pinaki P Banerjee, Luciana Melo Garcia, Paul Lin, Vakul Mohanty, Kun H Kim, Xianli Jiang, Yuchen Pan, Ye Li, Bin Liu, Ana K Nunez Cortes, Chenyu Zhang, Mohsen Fathi, Ali Rezvan, Melisa J Montalvo, Sophia L Cha, Francia Reyes-Silva, Rejeena Shrestha, Xingliang Guo, Kiran Kundu, Alexander Biederstädt, Luis Muniz-Feliciano, Gary M Deyter, Mecit Kaplan, Xin R Jiang, Enli Liu, Antrix Jain, Janos Roszik, Natalie W Fowlkes, Luisa M Solis Soto, Maria G Raso, Joseph D Khoury, Pei Lin, Francisco Vega, Navin Varadarajan, Ken Chen, David Marin, Elizabeth J Shpall, Katayoun Rezvani

Faculty, Staff and Student Publications

Multiple factors in the design of a chimeric antigen receptor (CAR) influence CAR T-cell activity, with costimulatory signals being a key component. Yet, the impact of costimulatory domains on the downstream signaling and subsequent functionality of CAR-engineered natural killer (NK) cells remains largely unexplored. Here, we evaluated the impact of various costimulatory domains on CAR-NK cell activity, using a CD70-targeting CAR. We found that CD28, a costimulatory molecule not inherently present in mature NK cells, significantly enhanced the antitumor efficacy and long-term cytotoxicity of CAR-NK cells both in vitro and in multiple xenograft models of hematologic and solid tumors. Mechanistically, …

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Cell Type-Specific Epigenetic Priming Of Gene Expression In Nucleus Accumbens By Cocaine, Philipp Mews, Yentl Van Der Zee, Ashik Gurung, Molly Estill, Rita Futamura, Hope Kronman, Aarthi Ramakrishnan, Meagan Ryan, Abner A Reyes, Benjamin A Garcia, Caleb J Browne, Simone Sidoli, Li Shen, Eric J Nestler Oct 2024

Cell Type-Specific Epigenetic Priming Of Gene Expression In Nucleus Accumbens By Cocaine, Philipp Mews, Yentl Van Der Zee, Ashik Gurung, Molly Estill, Rita Futamura, Hope Kronman, Aarthi Ramakrishnan, Meagan Ryan, Abner A Reyes, Benjamin A Garcia, Caleb J Browne, Simone Sidoli, Li Shen, Eric J Nestler

2020-Current year OA Pubs

A hallmark of addiction is the ability of drugs of abuse to trigger relapse after periods of prolonged abstinence. Here, we describe an epigenetic mechanism whereby chronic cocaine exposure causes lasting chromatin and downstream transcriptional modifications in the nucleus accumbens (NAc), a critical brain region controlling motivation. We link prolonged withdrawal from cocaine to the depletion of the histone variant H2A.Z, coupled with increased genome accessibility and latent priming of gene transcription, in D1 dopamine receptor-expressing medium spiny neurons (D1 MSNs) that relate to aberrant gene expression upon drug relapse. The histone chaperone ANP32E removes H2A.Z from chromatin, and we …

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Identification Of An Ionic Mechanism For Erα-Mediated Rapid Excitation In Neurons, Meng Yu, Na Yin, Bing Feng, Peiyu Gao, Kaifan Yu, Hesong Liu, Hailan Liu, Yongxiang Li, Olivia Z Ginnard, Kristine M Conde, Mengjie Wang, Xing Fang, Longlong Tu, Jonathan C Bean, Qingzhuo Liu, Yue Deng, Yuxue Yang, Junying Han, Sanika V Jossy, Megan L Burt, Huey Zhong Wong, Yongjie Yang, Benjamin R Arenkiel, Yang He, Shaodong Guo, Pierre Gourdy, Jean-Francois Arnal, Francoise Lenfant, Zhao Wang, Chunmei Wang, Yanlin He, Yong Xu Oct 2024

Identification Of An Ionic Mechanism For Erα-Mediated Rapid Excitation In Neurons, Meng Yu, Na Yin, Bing Feng, Peiyu Gao, Kaifan Yu, Hesong Liu, Hailan Liu, Yongxiang Li, Olivia Z Ginnard, Kristine M Conde, Mengjie Wang, Xing Fang, Longlong Tu, Jonathan C Bean, Qingzhuo Liu, Yue Deng, Yuxue Yang, Junying Han, Sanika V Jossy, Megan L Burt, Huey Zhong Wong, Yongjie Yang, Benjamin R Arenkiel, Yang He, Shaodong Guo, Pierre Gourdy, Jean-Francois Arnal, Francoise Lenfant, Zhao Wang, Chunmei Wang, Yanlin He, Yong Xu

Faculty, Staff and Students Publications

The major female ovarian hormone, 17β-estradiol (E2), can alter neuronal excitability within milliseconds to regulate a variety of physiological processes. Estrogen receptor-α (ERα), classically known as a nuclear receptor, exists as a membrane-bound receptor to mediate this rapid action of E2, but the ionic mechanisms remain unclear. Here, we show that a membrane channel protein, chloride intracellular channel protein-1 (Clic1), can physically interact with ERα with a preference to the membrane-bound ERα. Clic1-mediated currents can be enhanced by E2 and reduced by its depletion. In addition, Clic1 currents are required to mediate the E2-induced rapid excitations in multiple brain ERα …

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Arid1a-Baf Coordinates Zic2 Genomic Occupancy For Epithelial-To-Mesenchymal Transition In Cranial Neural Crest Specification., Samantha M Barnada, Aida Giner De Gracia, Cruz Morenilla-Palao, Maria Teresa López-Cascales, Chiara Scopa, Francis J Waltrich, Harald M M Mikkers, Maria Elena Cicardi, Jonathan Karlin, Davide Trotti, Kevin A Peterson, Samantha A Brugmann, Gijs W E Santen, Steven B Mcmahon, Eloísa Herrera, Marco Trizzino Oct 2024

Arid1a-Baf Coordinates Zic2 Genomic Occupancy For Epithelial-To-Mesenchymal Transition In Cranial Neural Crest Specification., Samantha M Barnada, Aida Giner De Gracia, Cruz Morenilla-Palao, Maria Teresa López-Cascales, Chiara Scopa, Francis J Waltrich, Harald M M Mikkers, Maria Elena Cicardi, Jonathan Karlin, Davide Trotti, Kevin A Peterson, Samantha A Brugmann, Gijs W E Santen, Steven B Mcmahon, Eloísa Herrera, Marco Trizzino

Faculty Research 2024

The BAF chromatin remodeler regulates lineage commitment including cranial neural crest cell (CNCC) specification. Variants in BAF subunits cause Coffin-Siris syndrome (CSS), a congenital disorder characterized by coarse craniofacial features and intellectual disability. Approximately 50% of individuals with CSS harbor variants in one of the mutually exclusive BAF subunits, ARID1A/ARID1B. While Arid1a deletion in mouse neural crest causes severe craniofacial phenotypes, little is known about the role of ARID1A in CNCC specification. Using CSS-patient-derived ARID1A[thorn]/ induced pluripotent stem cells to model CNCC specification, we discovered that ARID1A- haploinsufficiency impairs epithelial-to-mesenchymal transition (EMT), a process necessary for CNCC delamination and migration …

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Arid1a-Baf Coordinates Zic2 Genomic Occupancy For Epithelial-To-Mesenchymal Transition In Cranial Neural Crest Specification, Samantha M. Barnada, Aida Giner De Gracia, Cruz Morenilla-Palao, Maria Teresa López-Cascales, Chiara Scopa, Francis J. Waltrich, Harald M.M. Mikkers, Maria Elena Cicardi, Jonathan Karlin, Davide Trotti, Kevin A. Peterson, Samantha A. Brugmann, Gijs W.E. Santen, Steven B. Mcmahon, Eloísa Herrera, Marco Trizzino Oct 2024

Arid1a-Baf Coordinates Zic2 Genomic Occupancy For Epithelial-To-Mesenchymal Transition In Cranial Neural Crest Specification, Samantha M. Barnada, Aida Giner De Gracia, Cruz Morenilla-Palao, Maria Teresa López-Cascales, Chiara Scopa, Francis J. Waltrich, Harald M.M. Mikkers, Maria Elena Cicardi, Jonathan Karlin, Davide Trotti, Kevin A. Peterson, Samantha A. Brugmann, Gijs W.E. Santen, Steven B. Mcmahon, Eloísa Herrera, Marco Trizzino

Department of Biochemistry and Molecular Biology Faculty Papers

The BAF chromatin remodeler regulates lineage commitment including cranial neural crest cell (CNCC) specification. Variants in BAF subunits cause Coffin-Siris syndrome (CSS), a congenital disorder characterized by coarse craniofacial features and intellectual disability. Approximately 50% of individuals with CSS harbor variants in one of the mutually exclusive BAF subunits, ARID1A/ARID1B. While Arid1a deletion in mouse neural crest causes severe craniofacial phenotypes, little is known about the role of ARID1A in CNCC specification. Using CSS-patient-derived ARID1A induced pluripotent stem cells to model CNCC specification, we discovered that ARID1A-haploinsufficiency impairs epithelial-to-mesenchymal transition (EMT), a process necessary for CNCC delamination and migration from …

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A Ligation-Independent Sequencing Method Reveals Trna-Derived Rnas With Blocked 3′ Termini, Alessandro Scacchetti, Emily J Shields, Natalie A Trigg, Grace S Lee, Jeremy E Wilusz, Colin C Conine, Roberto Bonasio Oct 2024

A Ligation-Independent Sequencing Method Reveals Trna-Derived Rnas With Blocked 3′ Termini, Alessandro Scacchetti, Emily J Shields, Natalie A Trigg, Grace S Lee, Jeremy E Wilusz, Colin C Conine, Roberto Bonasio

Faculty, Staff and Students Publications

Despite the numerous sequencing methods available, the diversity in RNA size and chemical modification makes it difficult to capture all RNAs in a cell. We developed a method that combines quasi-random priming with template switching to construct sequencing libraries from RNA molecules of any length and with any type of 3' modifications, allowing for the sequencing of virtually all RNA species. Our ligation-independent detection of all types of RNA (LIDAR) is a simple, effective tool to identify and quantify all classes of coding and non-coding RNAs. With LIDAR, we comprehensively characterized the transcriptomes of mouse embryonic stem cells, neural progenitor …

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Inflammation-Induced Epigenetic Imprinting Regulates Intestinal Stem Cells, Dongchang Zhao, Visweswaran Ravikumar, Tyler J Leach, Daniel Kraushaar, Emma Lauder, Lu Li, Yaping Sun, Katherine Oravecz-Wilson, Evan T Keller, Fengju Chen, Laure Maneix, Robert R Jenq, Robert Britton, Katherine Y King, Ana E Santibanez, Chad J Creighton, Arvind Rao, Pavan Reddy Oct 2024

Inflammation-Induced Epigenetic Imprinting Regulates Intestinal Stem Cells, Dongchang Zhao, Visweswaran Ravikumar, Tyler J Leach, Daniel Kraushaar, Emma Lauder, Lu Li, Yaping Sun, Katherine Oravecz-Wilson, Evan T Keller, Fengju Chen, Laure Maneix, Robert R Jenq, Robert Britton, Katherine Y King, Ana E Santibanez, Chad J Creighton, Arvind Rao, Pavan Reddy

Faculty, Staff and Students Publications

It remains unknown whether, and how intestinal stem cells (ISC) adapt to inflammatory exposure, and if the adaptation leaves scars will affect their subsequent regeneration. We investigated the consequences of inflammation on Lgr5+ISCs in well-defined clinically relevant models of gastrointestinal acute graft-versus-host disease (GI GVHD). Utilizing single cell transcriptomics, organoid, metabolic, epigenomic and in vivo models we found that Lgr5+ISCs undergo metabolic changes that lead to accumulation of succinate, which reprograms its epigenome. These changes reduced the ability of ISCs to differentiate and regenerate ex vivo in serial organoid cultures and also in vivo following serial transplantation. Furthermore, ISCs demonstrated …

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Synergic Activity Of Fgfr2 And Mek Inhibitors In The Treatment Of Fgfr2-Amplified Cancers Of Unknown Primary, Andrea Cavazzoni, Irene Salamon, Claudia Fumarola, Giulia Gallerani, Noemi Laprovitera, Francesco Gelsomino, Mattia Riefolo, Karim Rihawi, Elisa Porcellini, Tania Rossi, Martina Mazzeschi, Maria Naddeo, Salvatore Serravalle, Elisabetta Broseghini, Federico Agostinis, Olivier Deas, Roberta Roncarati, Giorgio Durante, Ilaria Pace, Mattia Lauriola, Ingrid Garajova, George A Calin, Massimiliano Bonafè, Antonia D'Errico, Pier Giorgio Petronini, Stefano Cairo, Andrea Ardizzoni, Gabriele Sales, Manuela Ferracin Oct 2024

Synergic Activity Of Fgfr2 And Mek Inhibitors In The Treatment Of Fgfr2-Amplified Cancers Of Unknown Primary, Andrea Cavazzoni, Irene Salamon, Claudia Fumarola, Giulia Gallerani, Noemi Laprovitera, Francesco Gelsomino, Mattia Riefolo, Karim Rihawi, Elisa Porcellini, Tania Rossi, Martina Mazzeschi, Maria Naddeo, Salvatore Serravalle, Elisabetta Broseghini, Federico Agostinis, Olivier Deas, Roberta Roncarati, Giorgio Durante, Ilaria Pace, Mattia Lauriola, Ingrid Garajova, George A Calin, Massimiliano Bonafè, Antonia D'Errico, Pier Giorgio Petronini, Stefano Cairo, Andrea Ardizzoni, Gabriele Sales, Manuela Ferracin

Faculty, Staff and Student Publications

Patients with cancer of unknown primary (CUP) carry the double burden of an aggressive disease and reduced access to therapies. Experimental models are pivotal for CUP biology investigation and drug testing. We derived two CUP cell lines (CUP#55 and #96) and corresponding patient-derived xenografts (PDXs), from ascites tumor cells. CUP cell lines and PDXs underwent histological, immune-phenotypical, molecular, and genomic characterization confirming the features of the original tumor. The tissue-of-origin prediction was obtained from the tumor microRNA expression profile and confirmed by single-cell transcriptomics. Genomic testing and fluorescence in situ hybridization analysis identified FGFR2 gene amplification in both models, in …

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Synergic Activity Of Fgfr2 And Mek Inhibitors In The Treatment Of Fgfr2-Amplified Cancers Of Unknown Primary, Andrea Cavazzoni, Irene Salamon, Claudia Fumarola, Giulia Gallerani, Noemi Laprovitera, Francesco Gelsomino, Mattia Riefolo, Karim Rihawi, Elisa Porcellini, Tania Rossi, Martina Mazzeschi, Maria Naddeo, Salvatore Serravalle, Elisabetta Broseghini, Federico Agostinis, Olivier Deas, Roberta Roncarati, Giorgio Durante, Ilaria Pace, Mattia Lauriola, Ingrid Garajova, George A Calin, Massimiliano Bonafè, Antonia D'Errico, Pier Giorgio Petronini, Stefano Cairo, Andrea Ardizzoni, Gabriele Sales, Manuela Ferracin Oct 2024

Synergic Activity Of Fgfr2 And Mek Inhibitors In The Treatment Of Fgfr2-Amplified Cancers Of Unknown Primary, Andrea Cavazzoni, Irene Salamon, Claudia Fumarola, Giulia Gallerani, Noemi Laprovitera, Francesco Gelsomino, Mattia Riefolo, Karim Rihawi, Elisa Porcellini, Tania Rossi, Martina Mazzeschi, Maria Naddeo, Salvatore Serravalle, Elisabetta Broseghini, Federico Agostinis, Olivier Deas, Roberta Roncarati, Giorgio Durante, Ilaria Pace, Mattia Lauriola, Ingrid Garajova, George A Calin, Massimiliano Bonafè, Antonia D'Errico, Pier Giorgio Petronini, Stefano Cairo, Andrea Ardizzoni, Gabriele Sales, Manuela Ferracin

Faculty, Staff and Student Publications

Patients with cancer of unknown primary (CUP) carry the double burden of an aggressive disease and reduced access to therapies. Experimental models are pivotal for CUP biology investigation and drug testing. We derived two CUP cell lines (CUP#55 and #96) and corresponding patient-derived xenografts (PDXs), from ascites tumor cells. CUP cell lines and PDXs underwent histological, immune-phenotypical, molecular, and genomic characterization confirming the features of the original tumor. The tissue-of-origin prediction was obtained from the tumor microRNA expression profile and confirmed by single-cell transcriptomics. Genomic testing and fluorescence in situ hybridization analysis identified FGFR2 gene amplification in both models, in …

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Novel Ox40 And 4–1bb Derived Spacers Enhance Cd30 Car Activity And Safety In Cd30 Positive Lymphoma Models, Lindsay Kua, Chee Hoe Ng, Jin Wei Tan, Hwee Ching Tan, Cheah Chen Seh, Fiona Wong, Richard Ong, Cliona M Rooney, Joel Tan, Qingfeng Chen, Ivan D Horak, Kar Wai Tan, Lionel Low Oct 2024

Novel Ox40 And 4–1bb Derived Spacers Enhance Cd30 Car Activity And Safety In Cd30 Positive Lymphoma Models, Lindsay Kua, Chee Hoe Ng, Jin Wei Tan, Hwee Ching Tan, Cheah Chen Seh, Fiona Wong, Richard Ong, Cliona M Rooney, Joel Tan, Qingfeng Chen, Ivan D Horak, Kar Wai Tan, Lionel Low

Faculty, Staff and Students Publications

The chimeric antigen receptor (CAR) derived from the CD30 specific murine antibody, HRS-3, has produced promising clinical efficacy with a favorable safety profile in the treatment of relapsed or refractory CD30-positive lymphomas. However, persistence of the autologous CAR-T cells was brief, and many patients relapsed a year after treatment. The lack of persistence may be attributed to the use of a wild-type immunoglobulin (Ig)G1 spacer that can associate with Fc receptors. We first identified the cysteine-rich domain (CRD) 5 of CD30 as the primary binding epitope of HRS-3 and armed with this insight, attempted to improve the HRS-3 CAR functionality …

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Dietary Restriction Impacts Health And Lifespan Of Genetically Diverse Mice., Andrea Di Francesco, Andrew Deighan, Lev Litichevskiy, Zhenghao Chen, Alison Luciano, Laura Robinson, Gaven Garland, Hannah J Donato, Matthew J Vincent, William H. Schott, Kevin M Wright, Anil Raj, G V Prateek, Martin Mullis, Warren G Hill, Mark L Zeidel, Luanne L. Peters, Fiona Harding, David Botstein, Ron Korstanje, Christoph A Thaiss, Adam Freund, Gary Churchill Oct 2024

Dietary Restriction Impacts Health And Lifespan Of Genetically Diverse Mice., Andrea Di Francesco, Andrew Deighan, Lev Litichevskiy, Zhenghao Chen, Alison Luciano, Laura Robinson, Gaven Garland, Hannah J Donato, Matthew J Vincent, William H. Schott, Kevin M Wright, Anil Raj, G V Prateek, Martin Mullis, Warren G Hill, Mark L Zeidel, Luanne L. Peters, Fiona Harding, David Botstein, Ron Korstanje, Christoph A Thaiss, Adam Freund, Gary Churchill

Faculty Research 2024

Caloric restriction extends healthy lifespan in multiple species. Intermittent fasting, an alternative form of dietary restriction, is potentially more sustainable in humans, but its effectiveness remains largely unexplored. Identifying the most efficacious forms of dietary restriction is key for developing interventions to improve human health and longevity. Here we performed an extensive assessment of graded levels of caloric restriction (20% and 40%) and intermittent fasting (1 and 2 days fasting per week) on the health and survival of 960 genetically diverse female mice. We show that caloric restriction and intermittent fasting both resulted in lifespan extension in proportion to the …

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Longitudinal Fragility Phenotyping Contributes To The Prediction Of Lifespan And Age-Associated Morbidity In C57bl/6 And Diversity Outbred Mice., Alison Luciano, Laura Robinson, Gaven Garland, Bonnie Lyons, Ron Korstanje, Andrea Di Francesco, Gary Churchill Oct 2024

Longitudinal Fragility Phenotyping Contributes To The Prediction Of Lifespan And Age-Associated Morbidity In C57bl/6 And Diversity Outbred Mice., Alison Luciano, Laura Robinson, Gaven Garland, Bonnie Lyons, Ron Korstanje, Andrea Di Francesco, Gary Churchill

Faculty Research 2024

Aging studies in mammalian models often depend on natural lifespan data as a primary outcome. Tools for lifespan prediction could accelerate these studies and reduce the need for veterinary intervention. Here, we leveraged large-scale longitudinal frailty and lifespan data on two genetically distinct mouse cohorts to evaluate noninvasive strategies to predict life expectancy in mice. We applied a modified frailty assessment, the Fragility Index, derived from existing frailty indices with additional deficits selected by veterinarians. We developed an ensemble machine learning classifier to predict imminent mortality (95% proportion of life lived [95PLL]). Our algorithm represented improvement over previous predictive criteria …

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Enhanced Isradipine Sensitivity In Vascular Smooth Muscle Cells Due To Hypoxia-Induced Ca, Charlene Priscilla Poore, Jialei Yang, Shunhui Wei, Chee Kong Fhu, Zoë Bichler, Juejin Wang, Tuck Wah Soong, Ping Liao Oct 2024

Enhanced Isradipine Sensitivity In Vascular Smooth Muscle Cells Due To Hypoxia-Induced Ca, Charlene Priscilla Poore, Jialei Yang, Shunhui Wei, Chee Kong Fhu, Zoë Bichler, Juejin Wang, Tuck Wah Soong, Ping Liao

Faculty Research 2024

Calcium influx via the L-type voltage-gated Cav 1.2 calcium channel in
smooth muscle cells regulates vascular contraction. Calcium channel
blockers (CCBs) are widely used to treat hypertension by inhibiting Cav 1.2
channels. Using the vascular smooth muscle cell line, A7r5 and primary cul-
ture of cerebral vascular smooth muscle cells, we found that the expression
and function of Cav 1.2 channels are downregulated during hypoxia. Further-
more, hypoxia induces structural changes in Cav1.2 channels via alternative
splicing. The expression of exon 9* is upregulated, whereas exon 33 is down-
regulated. Such structural alterations of Cav1.2 channels are caused by the …

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Proteins Required For Stereocilia Elongation During Mammalian Hair Cell Development Ensure Precise And Steady Heights During Adult Life., Elli I Hartig, Matthew Day, Amandine Jarysta, Basile Tarchini Oct 2024

Proteins Required For Stereocilia Elongation During Mammalian Hair Cell Development Ensure Precise And Steady Heights During Adult Life., Elli I Hartig, Matthew Day, Amandine Jarysta, Basile Tarchini

Faculty Research 2024

Mammalian auditory hair cells (HCs) are not naturally regenerative and must preserve their elaborate structure to ensure lifelong hearing. Stereocilia, the actin-based projections at the HC surface that detect sound vibration, are particularly vulnerable to damage incurred from noise and aging. We show that the tip-localized protein module GPSM2–GNAI required for stereocilia development is also involved in stereocilia maintenance in mature cells. Inactivating Gpsm2 in adult mouse HCs results in low-frequency hearing deficits and stereocilia height reduction proportional to the region reported to turn over actin at the distal tip. Molecular insight into how actin exchange ensures stable height in …

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Loss Of Sting Impairs Lactogenic Differentiation., Ramiah R Vickers, Garhett L Wyatt, Lilia Sanchez, Jordyn J Vanportfliet, A Phillip West, Weston W Porter Oct 2024

Loss Of Sting Impairs Lactogenic Differentiation., Ramiah R Vickers, Garhett L Wyatt, Lilia Sanchez, Jordyn J Vanportfliet, A Phillip West, Weston W Porter

Faculty Research 2024

Heightened energetic and nutrient demand during lactogenic differentiation of the mammary gland elicits upregulation of various stress responses to support cellular homeostasis. Here, we identify the stimulator of interferon genes (STING) as an immune supporter of the functional development of mouse mammary epithelial cells (MECs). An in vitro model of MEC differentiation revealed that STING is activated in a cGAS-independent manner to produce both type I interferons and proinflammatory cytokines in response to the accumulation of mitochondrial reactive oxygen species. Induction of STING activity was found to be dependent on the breast tumor suppressor gene single-minded 2 (SIM2). Using mouse …

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Presynaptic Nrxn3 Is Essential For Ribbon-Synapse Maturation In Hair Cells., Alma Jukic, Zhengchang Lei, Elizabeth R Cebul, Katherine Pinter, Yommi Tadesse, Amandine Jarysta, Sandeep David, Natalie Mosqueda, Basile Tarchini, Katie Kindt Oct 2024

Presynaptic Nrxn3 Is Essential For Ribbon-Synapse Maturation In Hair Cells., Alma Jukic, Zhengchang Lei, Elizabeth R Cebul, Katherine Pinter, Yommi Tadesse, Amandine Jarysta, Sandeep David, Natalie Mosqueda, Basile Tarchini, Katie Kindt

Faculty Research 2024

Hair cells of the inner ear and lateral-line system rely on specialized ribbon synapses to transmit sensory information to the central nervous system. The molecules required to assemble these synapses are not fully understood. We show that Nrxn3, a presynaptic adhesion molecule, is crucial for ribbon-synapse maturation in hair cells. In both mouse and zebrafish models, the loss of Nrxn3 results in significantly fewer intact ribbon synapses. We show in zebrafish that, initially, Nrxn3 loss does not alter pre- and postsynapse numbers but, later, synapses fail to pair, leading to postsynapse loss. We also demonstrate that Nrxn3 subtly influences synapse …

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Machine-Guided Design Of Cell-Type-Targeting Cis-Regulatory Elements., Sager J Gosai, Rodrigo Castro, Natalia Fuentes, John C Butts, Kousuke Mouri, Michael Alasoadura, Susan Kales, Thanh Thanh L Nguyen, Ramil R Noche, Arya S Rao, Mary T Joy, Pardis C Sabeti, Steven K Reilly, Ryan Tewhey Oct 2024

Machine-Guided Design Of Cell-Type-Targeting Cis-Regulatory Elements., Sager J Gosai, Rodrigo Castro, Natalia Fuentes, John C Butts, Kousuke Mouri, Michael Alasoadura, Susan Kales, Thanh Thanh L Nguyen, Ramil R Noche, Arya S Rao, Mary T Joy, Pardis C Sabeti, Steven K Reilly, Ryan Tewhey

Faculty Research 2024

Cis-regulatory elements (CREs) control gene expression, orchestrating tissue identity, developmental timing and stimulus responses, which collectively define the thousands of unique cell types in the body1–3 . While there is great potential for strategically incorporating CREs in therapeutic or biotechnology applications that require tissue specificity, there is no guarantee that an optimal CRE for these intended purposes has arisen naturally. Here we present a platform to engineer and validate synthetic CREs capable of driving gene expression with programmed cell-type specificity. We take advantage of innovations in deep neural network modelling of CRE activity across three cell types, efficient in silico …

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