Evaluation of cytosine base editing and adenine base editing as a potential treatment for alpha-1 antitrypsin deficiency

Molecular therapy : the journal of the American Society of Gene Therapy

2022 Feb 02

Packer, MS;Chowdhary, V;Lung, G;Cheng, LI;Aratyn-Schaus, Y;Leboeuf, D;Smith, S;Shah, A;Chen, D;Zieger, M;Cafferty, BJ;Yan, B;Ciaramella, G;Gregoire, FM;Mueller, C;
PMID: 35121111 | DOI: 10.1016/j.ymthe.2022.01.040

Alpha-1 antitrypsin deficiency (AATD) is a rare autosomal codominant disease caused by mutations within the SERPINA1 gene. The most prevalent variant in patients is PiZ SERPINA1, containing a single G > A transition mutation. PiZ alpha-1 antitrypsin (AAT) is prone to misfolding, leading to the accumulation of toxic aggregates within hepatocytes. In addition, the abnormally low level of AAT secreted into circulation provides insufficient inhibition of neutrophil elastase within the lungs, eventually causing emphysema. Cytosine and adenine base editors enable the programmable conversion of C⋅G to T⋅A and A⋅T to G⋅C base pairs, respectively. In this study, two different base editing approaches were developed: use of a cytosine base editor to install a compensatory mutation (p.Met374Ile) and use of an adenine base editor to mediate the correction of the pathogenic PiZ mutation. After treatment with lipid nanoparticles formulated with base editing reagents, PiZ-transgenic mice exhibited durable editing of SERPINA1 in the liver, increased serum AAT, and improved liver histology. These results indicate that base editing has the potential to address both lung and liver disease in AATD.

Causes and functional intricacies of inter- and intratumor heterogeneity of primary liver cancers

Advances in Cancer Research

2022 Feb 24

Khatib, S;Wang, X;
| DOI: 10.1016/bs.acr.2022.01.006

Tumor heterogeneity is a major feature of primary liver cancers. Defined as the unique genotypic and phenotypic differences of cancer cells within a single tumor (intratumor) or amongst different patients (intertumor), tumor heterogeneity has consistently been linked to worse clinical outcomes in most, if not all, solid tumor types. In particular, liver cancer heterogeneity has been associated with altered immune infiltration, resistance to therapeutics, and worse overall patient survival. Current advancements in single-cell omic technologies have allowed for a deeper understanding and appreciation of the intricate composition and relationships between individual cells within a tumor. These observations have led to the discovery of new cell types in liver cancer, potential new mechanisms of therapy resistance and tumor progression, and new insights into the evolutionary patterns of liver cancer. To better understand the tumor biology of liver cancers and their heterogeneous features, we will begin this chapter on a brief background of liver cancer and then discuss the various etiologies of this disease and how each one can contribute to diverse genomic, transcriptomic, proteomic, and spatial architecture observations. Next, we will go into the specific causes and implications of tumor heterogeneity and end with how understanding the spatial architecture of liver tumors can provide us with new insights and ideas for tumor diversity and therapeutic development.

The Perspective of DMPK on Recombinant Adeno-Associated Virus-Based Gene Therapy: Past Learning, Current Support, and Future Contribution

The AAPS journal

2022 Jan 31

Chen, N;Sun, K;Chemuturi, NV;Cho, H;Xia, CQ;
PMID: 35102450 | DOI: 10.1208/s12248-021-00678-7

Given the recent success of gene therapy modalities and the growing number of cell and gene-based therapies in clinical development across many different therapeutic areas, it is evident that this evolving field holds great promise for the unmet medical needs of patients. The recent approvals of Luxturna and Zolgensma prove that recombinant adeno-associated virus (rAAV)-based gene therapy is a transformative modality that enables curative treatment for genetic disorders. Over the last decade, Takeda has accumulated significant experience with rAAV-based gene therapies, especially in the early stage of development. In this review, based on the learnings from Takeda and publicly available information, we aim to provide a guiding perspective on Drug Metabolism and Pharmacokinetics (DMPK) substantial role in advancing therapeutic gene therapy modalities from nonclinical research to clinical development, in particular the characterization of gene therapy product biodistribution, elimination (shedding), immunogenicity assessment, multiple platform bioanalytical assays, and first-in-human (FIH) dose projection strategies. Graphical abstract.

GABAergic neuronal IL-4R mediates T cell effect on memory

Neuron

2021 Nov 17

Herz, J;Fu, Z;Kim, K;Dykstra, T;Wall, M;Li, H;Salvador, AF;Zou, B;Yan, N;Blackburn, SM;Andrews, PH;Goldman, DH;Papadopoulos, Z;Smirnov, I;Xie, XS;Kipnis, J;
PMID: 34793707 | DOI: 10.1016/j.neuron.2021.10.022

Mechanisms governing how immune cells and their derived molecules impact homeostatic brain function are still poorly understood. Here, we elucidate neuronal mechanisms underlying T cell effects on synaptic function and episodic memory. Depletion of CD4 T cells led to memory deficits and impaired long-term potentiation. Severe combined immune-deficient mice exhibited amnesia, which was reversible by repopulation with T cells from wild-type but not from IL-4-knockout mice. Behaviors impacted by T cells were mediated via IL-4 receptors expressed on neurons. Exploration of snRNA-seq of neurons participating in memory processing provided insights into synaptic organization and plasticity-associated pathways regulated by immune cells. IL-4Rα knockout in inhibitory (but not in excitatory) neurons was sufficient to impair contextual fear memory, and snRNA-seq from these mice pointed to IL-4-driven regulation of synaptic function in promoting memory. These findings provide new insights into complex neuroimmune interactions at the transcriptional and functional levels in neurons under physiological conditions.

A census of the lung: CellCards from LungMAP

Developmental cell

2021 Dec 20

Sun, X;Perl, AK;Li, R;Bell, SM;Sajti, E;Kalinichenko, VV;Kalin, TV;Misra, RS;Deshmukh, H;Clair, G;Kyle, J;Crotty Alexander, LE;Silva, JM;Kitzmiller, JA;Wikenheiser-Brokamp, KA;Deutsch, G;Guo, M;Du, Y;Morley, MP;Valdez, MJ;Yu, HV;Jin, K;Bardes, EE;Zepp, JA;Neithamer, T;Basil, MC;Zacharias, WJ;Verheyden, J;Young, R;Bandyopadhyay, G;Lin, S;Ansong, C;Adkins, J;Salomonis, N;Aronow, BJ;Xu, Y;Pryhuber, G;Whitsett, J;Morrisey, EE;NHLBI LungMAP Consortium, ;
PMID: 34936882 | DOI: 10.1016/j.devcel.2021.11.007

The human lung plays vital roles in respiration, host defense, and basic physiology. Recent technological advancements such as single-cell RNA sequencing and genetic lineage tracing have revealed novel cell types and enriched functional properties of existing cell types in lung. The time has come to take a new census. Initiated by members of the NHLBI-funded LungMAP Consortium and aided by experts in the lung biology community, we synthesized current data into a comprehensive and practical cellular census of the lung. Identities of cell types in the normal lung are captured in individual cell cards with delineation of function, markers, developmental lineages, heterogeneity, regenerative potential, disease links, and key experimental tools. This publication will serve as the starting point of a live, up-to-date guide for lung research at https://www.lungmap.net/cell-cards/. We hope that Lung CellCards will promote the community-wide effort to establish, maintain, and restore respiratory health.

IL-1β Promotes Expansion of IL-33+ Lung Epithelial Stem Cells Following RSV Infection During Infancy

American journal of respiratory cell and molecular biology

2021 Dec 03

Vu, LD;Phan, ATQ;Hijano, DR;Siefker, DT;Tillman, H;Cormier, SA;
PMID: 34861136 | DOI: 10.1165/rcmb.2021-0313OC

Respiratory syncytial virus (RSV)-induced immunopathogenesis and disease severity in neonatal mice and human infants have been related to elevated pulmonary IL-33. Thus, targeting IL-33 has been suggested as a potential therapy for respiratory viral infections. Yet, the regulatory mechanisms on IL-33 during early life remain unclear. Here, using a neonatal mouse model of RSV, we demonstrate that IL-1β positively regulates but is not required for RSV-induced expression of pulmonary IL-33 in neonatal mice early after the initial infection. Exogenous IL-1β upregulates RSV-induced IL-33 expression by promoting the proliferation of IL-33pos lung epithelial stem/progenitor cells (EpiSPC). These cells are exclusively detected in RSV-infected neonatal rather than adult mice, partially explaining the IL-1β-independent IL-33 expression in RSV-infected adult mice. Furthermore, IL-1β aggravates IL-33 mediated Th2 biased immunopathogenesis upon reinfection. Collectively, our study demonstrates that IL-1β exacerbates IL-33 mediated RSV immunopathogenesis by promoting the proliferation of IL-33pos EpiSPC in early life.

Selective FGFR/FGF pathway inhibitors: inhibition strategies, clinical activities, resistance mutations, and future directions

Expert review of clinical pharmacology

2021 Oct 01

Repetto, M;Crimini, E;Giugliano, F;Morganti, S;Belli, C;Curigliano, G;
PMID: 34591728 | DOI: 10.1080/17512433.2021.1947246

Introduction: Fibroblast growth factor receptor (FGFR)/fibroblast growth factor (FGF) is a pathway characterized by recurring alterations in cancer. Its dysregulations enhance cancer cell proliferation, survival, migration and invasion, as well as angiogenesis and immune evasion.Areas covered: FGFR/FGF selective inhibitors belong to a broad class of drugs with some being approved for specific indications and others under investigation in ongoing phase I and II clinical trials. In this review, all available clinical data from trials on selective FGFR/FGF inhibitors as well as described resistance mutations and mechanisms are presented. FGFR/FGF pathway inhibitors are classified according to the mechanism they employ to dampen/suppress signaling and to the preferred FGFR binding mode when X-ray crystal structure is available.Expert opinion: Data presented suggests the general actionability of FGFR1,2,3 mutations and fusions across histologies, whereas FGFR1,2,3 amplifications alone are poor predictors of response to tyrosine kinase inhibitors. Overexpression on immunohistochemistry (IHC) of FGF19, the stimulatory ligand of FGFR4, can predict response to FGFR selective inhibitors in hepatocellular carcinoma. Whereas IHC overexpression of FGFR1,2,3 is not sufficient to predict benefit from FGFR inhibitors across solid tumors. FGFR1,2,3 mRNA overexpression can predict response even in absence of structural alteration. Data on resistance mutations suggests the need for new inhibitors to overcome gatekeeper mutations.

Norrie disease protein is essential for cochlear hair cell maturation

Proceedings of the National Academy of Sciences of the United States of America

2021 Sep 28

Hayashi, Y;Chiang, H;Tian, C;Indzhykulian, AA;Edge, ASB;
PMID: 34544869 | DOI: 10.1073/pnas.2106369118

Mutations in the gene for Norrie disease protein (Ndp) cause syndromic deafness and blindness. We show here that cochlear function in an Ndp knockout mouse deteriorated with age: At P3-P4, hair cells (HCs) showed progressive loss of Pou4f3 and Gfi1, key transcription factors for HC maturation, and Myo7a, a specialized myosin required for normal function of HC stereocilia. Loss of expression of these genes correlated to increasing HC loss and profound hearing loss by 2 mo. We show that overexpression of the Ndp gene in neonatal supporting cells or, remarkably, up-regulation of canonical Wnt signaling in HCs rescued HCs and cochlear function. We conclude that Ndp secreted from supporting cells orchestrates a transcriptional network for the maintenance and survival of HCs and that increasing the level of β-catenin, the intracellular effector of Wnt signaling, is sufficient to replace the functional requirement for Ndp in the cochlea.

CONSEQUENCES OF mTOR INHIBITION ON AAV HEPATIC TRANSDUCTION EFFICACY

Human gene therapy

2021 Sep 24

Perez-Iturralde, A;Carte, B;Aldabe, R;
PMID: 34555962 | DOI: 10.1089/hum.2021.171

The efficiency of recombinant Adeno-associated virus vectors (AAV) transducing host cells is very low, limiting their therapeutic potential in patients. There are several cellular pathways interacting and interfering with the journey of the AAV from the cell surface to the nucleus, opening the possibility to enhance AAV transduction by modifying these interactions. In this study, we explored the results of AAV hepatic transduction when different mTOR inhibitors.- rapamycin, MLN0128, RapaLink-1 -were used in preconditioned juvenile and adult mice. We confirmed rapamycin as an AAV hepatic transduction enhancer in juvenile and adult mice; however, RapaLink-1, a stronger mTOR inhibitor and a clear hepatic autophagy inducer, had no positive effect. Moreover, MLN0128 reduced AAV hepatic transduction. Therefore, our results show a complex interaction between the mTOR pathway and AAV-mediated hepatic transduction and indicate that mTOR inhibition is not a straightforward strategy for improving AAV transduction. More studies are necessary to elucidate the molecular mechanisms involve in the positive and negative effects of mTOR inhibitors on AAV transduction efficiency.

A Comparison of the Cellular and Molecular Atlases of the Macaque and Mouse Dorsal Horns

SSRN Electronic Journal

2021 Sep 18

Arokiaraj, C;Kleyman, M;Chamessian, A;Shiers, S;Kang, B;Kennedy, M;Patterson, R;Lewis, D;Qadri, Y;Levine, A;Price, T;Pfenning, A;Seal, R;
| DOI: 10.2139/ssrn.3924596

The spinal dorsal horn transforms incoming somatosensory information and transmits it supraspinally to generate modality-specific sensory percepts. Understanding precisely how neurons in this region process somatosensory information in rodents, and in higher-order species such as primates, has been hampered by the incomplete identification of individual cell types. In this study, we generate a comprehensive classification scheme for molecularly defined cell types across species-from mouse to primate by performing single nucleus RNA-sequencing of the Rhesus macaque dorsal horn and comparing it to a mouse meta-analysis. A comparison of the laminar distributions of these cell types across species lends further support to this classification. Despite the high conservation, we also identify species-specific differences in the expression of key genes. The study thus provides an essential resource for the functional interrogation of neural circuits underlying somatosensory processing within the dorsal horn and across species as well as for the validation of therapeutic targets.

Astrocyte-derived neurons provide excitatory input to the adult striatal circuitry

Proceedings of the National Academy of Sciences of the United States of America

2021 Aug 17

Dorst, MC;Díaz-Moreno, M;Dias, DO;Guimarães, EL;Holl, D;Kalkitsas, J;Silberberg, G;Göritz, C;
PMID: 34389674 | DOI: 10.1073/pnas.2104119118

Astrocytes have emerged as a potential source for new neurons in the adult mammalian brain. In mice, adult striatal neurogenesis can be stimulated by local damage, which recruits striatal astrocytes into a neurogenic program by suppression of active Notch signaling (J. P. Magnusson et al., Science 346, 237-241 [2014]). Here, we induced adult striatal neurogenesis in the intact mouse brain by the inhibition of Notch signaling in astrocytes. We show that most striatal astrocyte-derived neurons are confined to the anterior medial striatum, do not express established striatal neuronal markers, and exhibit dendritic spines, which are atypical for striatal interneurons. In contrast to striatal neurons generated during development, which are GABAergic or cholinergic, most adult astrocyte-derived striatal neurons possess distinct electrophysiological properties, constituting the only glutamatergic striatal population. Astrocyte-derived neurons integrate into the adult striatal microcircuitry, both receiving and providing synaptic input. The glutamatergic nature of these neurons has the potential to provide excitatory input to the striatal circuitry and may represent an efficient strategy to compensate for reduced neuronal activity caused by aging or lesion-induced neuronal loss.

Deciphering the Mechanisms of COVID-19 Induced Anosmia

SSRN Electronic Journal

2021 Aug 14

Zazhytska, M;Kodra, A;Hoagland, D;Fullard, J;Shayya, H;Moeller, R;Uhl, S;Omer, A;Firestein, S;Gong, Q;Canoll, P;Goldman, J;Rousos, P;tenOever, B;Overdevest, J;Lomvardas, S;
| DOI: 10.2139/ssrn.3900127

SARS-CoV-2 infects less than 1% of cells in the human body, yet it can cause severe damage in a variety of organs. Thus, deciphering the non-cell autonomous effects of SARS-CoV-2 infection is imperative for understanding the cellular and molecular disruption it elicits. Neurological and cognitive defects are among the least understood symptoms of COVID-19 patients, with olfactory dysfunction being their most common sensory deficit. Here, we show that both in humans and hamsters SARS-CoV-2 infection causes widespread downregulation of olfactory receptors (OR) and of their signaling components. This non-cell autonomous effect coincides with a dramatic reorganization of the neuronal nuclear architecture, which results in dissipation of genomic OR compartments and elimination of genomic contact domains genomewide. Our data provide a novel mechanism by which SARS-CoV-2 infection alters the cellular morphology and the transcriptome of cells it cannot infect, providing insight to its systemic effects in the nervous system and beyond.

Pages

	Description
sense Example: Hs-LAG3-sense	Standard probes for RNA detection are in antisense. Sense probe is reverse complent to the corresponding antisense probe.
Intron# Example: Mm-Htt-intron2	Probe targets the indicated intron in the target gene, commonly used for pre-mRNA detection
Pool/Pan Example: Hs-CD3-pool (Hs-CD3D, Hs-CD3E, Hs-CD3G)	A mixture of multiple probe sets targeting multiple genes or transcripts
No-XSp Example: Hs-PDGFB-No-XMm	Does not cross detect with the species (Sp)
XSp Example: Rn-Pde9a-XMm	designed to cross detect with the species (Sp)
O# Example: Mm-Islr-O1	Alternative design targeting different regions of the same transcript or isoforms
CDS Example: Hs-SLC31A-CDS	Probe targets the protein-coding sequence only
EnEm	Probe targets exons n and m
En-Em	Probe targets region from exon n to exon m
Retired Nomenclature
tvn Example: Hs-LEPR-tv1	Designed to target transcript variant n
ORF Example: Hs-ACVRL1-ORF	Probe targets open reading frame
UTR Example: Hs-HTT-UTR-C3	Probe targets the untranslated region (non-protein-coding region) only
5UTR Example: Hs-GNRHR-5UTR	Probe targets the 5' untranslated region only
3UTR Example: Rn-Npy1r-3UTR	Probe targets the 3' untranslated region only
Pan Example: Pool	A mixture of multiple probe sets targeting multiple genes or transcripts

Search form

Probes for INS

Content for comparison

Gene

Product

Research area

Category

Pages

Advanced Cell Diagnostics

Bio-Techne

Advanced Cell Diagnostics China