bims-drudre Biomed News
on Targeted drug delivery and programmed release mechanisms
Issue of 2022–02–06
fourteen papers selected by
Ceren Kimna, Technical University of Munich
  1. Phase-separating peptides for direct cytosolic delivery and redox-activated release of macromolecular therapeutics.
  2. Biomimetic Design of Artificial Hybrid Nanocells for Boosted Vascular Regeneration in Ischemic Tissues.
  3. Shape-changing DNA-linked nanoparticle films dictated by lateral and vertical patterns.
  4. miR-182 targeting reprograms tumor-associated macrophages and limits breast cancer progression.
  5. Monitoring Clinical-Pathological Grading of Hepatocellular Carcinoma Using MicroRNA-Guided Semiconducting Polymer Dots.
  6. DNA-encoded library versus RNA-encoded library selection enables design of an oncogenic noncoding RNA inhibitor.
  7. Programmable DNA Hydrogels as Artificial Extracellular Matrix.
  8. Programmable allosteric DNA regulations for molecular networks and nanomachines.
  9. Programmable Macroscopic Self-Assembly of DNA-Decorated Hydrogels.
  10. Organoids at the PUB: The Porcine Urinary Bladder serves As A Pancreatic Niche for Advanced Cancer Modelling.
  11. Multiscale engineered artificial tooth enamel.
  12. Reprogramming the piRNA pathway for multiplexed and transgenerational gene silencing in C. elegans.
  13. Urine Microenvironment-Initiated Composite Hydrogel Patch Reconfiguration Propels Scarless Memory Repair and Reinvigoration of Urethra.
  14. The DNA methylome of cervical cells can predict the presence of ovarian cancer.
  1. Nat Chem. 2022 Feb 03.
    Phase-separating peptides for direct cytosolic delivery and redox-activated release of macromolecular therapeutics.
    Yue Sun, Sze Yi Lau, Zhi Wei Lim, Shi Chieh Chang, Farid Ghadessy, Anthony Partridge, Ali Miserez.
      Biomacromolecules are highly promising therapeutic modalities to treat various diseases. However, they suffer from poor cellular membrane permeability, limiting their access to intracellular targets. Strategies to overcome this challenge often employ nanoscale carriers that can get trapped in endosomal compartments. Here we report conjugated peptides that form pH- and redox-responsive coacervate microdroplets by liquid-liquid phase separation that readily cross the cell membrane. A wide range of macromolecules can be quickly recruited within the microdroplets, including small peptides, enzymes as large as 430 kDa and messenger RNAs (mRNAs). The therapeutic-loaded coacervates bypass classical endocytic pathways to enter the cytosol, where they undergo glutathione-mediated release of payload, the bioactivity of which is retained in the cell, while mRNAs exhibit a high transfection efficiency. These peptide coacervates represent a promising platform for the intracellular delivery of a large palette of macromolecular therapeutics that have potential for treating various pathologies (for example, cancers and metabolic diseases) or as carriers for mRNA-based vaccines.
    DOI:  https://doi.org/10.1038/s41557-021-00854-4
  2. Adv Mater. 2022 Feb 02. e2110352
    Biomimetic Design of Artificial Hybrid Nanocells for Boosted Vascular Regeneration in Ischemic Tissues.
    Xiangyun Zhang, Yue Zhang, Ran Zhang, Xinbang Jiang, Adam C Midgley, Qiqi Liu, Helong Kang, Jin Wu, Anila Khalique, Meng Qian, Di An, Jing Huang, Lailiang Ou, Qiang Zhao, Jie Zhuang, Xiyun Yan, Deling Kong, Xinglu Huang.
      Restoration of sufficient blood supply for the treatment of ischemia remains a significant scientific and clinical challenge. Here, we introduce a cell-like nanoparticle delivery technology that is capable of recapitulating multiple cell functions for the spatiotemporal triggering of vascular regeneration. Specifically, a copper-containing protein was successfully prepared using a recombinant protein scaffold based on a de novo design strategy, which facilitated the timely release of nitric oxide (NO) and improved accumulation of particles within ischemic tissues. Through closely mimicking physiological cues, we demonstrated the benefits of bioactive factors secreted from hypoxic stem cells on promoting angiogenesis. Following this cell-mimicking manner, artificial hybrid nano-sized cells (Hynocell) were constructed by integrating the hypoxic stem cell secretome into nanoparticles with surface coatings of cell membranes fused with copper-containing protein. The Hynocell, hybridized with different cell-derived components, provided synergistic effects on targeting ischemic tissues and promoting vascular regeneration in acute hindlimb ischemia and acute myocardial infarction models. This study offers new insights into the utilization of nanotechnology to potentiate the development of cell-free therapeutics. This article is protected by copyright. All rights reserved.
    Keywords:  cell-like delivery; ferritin; ischemic diseases; nitric oxide; vascular regeneration
    DOI:  https://doi.org/10.1002/adma.202110352
  3. Adv Mater. 2022 Feb 04. e2109091
    Shape-changing DNA-linked nanoparticle films dictated by lateral and vertical patterns.
    Jongwook Kim, Sunghee Lee, Jisu Choi, Kyungnae Baek, Tae Soup Shim, Jerome Kartham Hyun, So-Jung Park.
      xxxx. This article is protected by copyright. All rights reserved.
    Keywords:  DNA-directed self-assembly; Plasmonic; gold nanoparticle; patterning; stimuli-responsive
    DOI:  https://doi.org/10.1002/adma.202109091
  4. Proc Natl Acad Sci U S A. 2022 Feb 08. pii: e2114006119. [Epub ahead of print]119(6):
    miR-182 targeting reprograms tumor-associated macrophages and limits breast cancer progression.
    Chengxin Ma, Dasa He, Pu Tian, Yuan Wang, Yunfei He, Qiuyao Wu, Zhenchang Jia, Xue Zhang, Peiyuan Zhang, Hao Ying, Zi-Bing Jin, Guohong Hu.
      The protumor roles of alternatively activated (M2) tumor-associated macrophages (TAMs) have been well established, and macrophage reprogramming is an important therapeutic goal. However, the mechanisms of TAM polarization remain incompletely understood, and effective strategies for macrophage targeting are lacking. Here, we show that miR-182 in macrophages mediates tumor-induced M2 polarization and can be targeted for therapeutic macrophage reprogramming. Constitutive miR-182 knockout in host mice and conditional knockout in macrophages impair M2-like TAMs and breast tumor development. Targeted depletion of macrophages in mice blocks the effect of miR-182 deficiency in tumor progression while reconstitution of miR-182-expressing macrophages promotes tumor growth. Mechanistically, cancer cells induce miR-182 expression in macrophages by TGFβ signaling, and miR-182 directly suppresses TLR4, leading to NFκb inactivation and M2 polarization of TAMs. Importantly, therapeutic delivery of antagomiR-182 with cationized mannan-modified extracellular vesicles effectively targets macrophages, leading to miR-182 inhibition, macrophage reprogramming, and tumor suppression in multiple breast cancer models of mice. Overall, our findings reveal a crucial TGFβ/miR-182/TLR4 axis for TAM polarization and provide rationale for RNA-based therapeutics of TAM targeting in cancer.
    Keywords:  RNAi therapeutics; breast cancer; extracellular vesicle; miR-182; tumor-associated macrophage
    DOI:  https://doi.org/10.1073/pnas.2114006119
  5. ACS Appl Mater Interfaces. 2022 Feb 03.
    Monitoring Clinical-Pathological Grading of Hepatocellular Carcinoma Using MicroRNA-Guided Semiconducting Polymer Dots.
    Ze Zhang, Yuyang Wu, Nan Lin, Shengyan Yin, Zihui Meng.
      MicroRNAs (miRNAs) are a class of small, noncoding RNAs involved in nearly all genetic central dogma processes and human biological behavior, which also play a significant role in the pathological activity of tumors, such as gene transcription, protein translation, and exosome secretion. Therefore, through the navigation of certain specific miRNAs, we can trace the specific physiological processes or image some specific tissues. Designing and accurately positioning microRNA (miRNA)-sensitive fluorescent nanoprobes with benign specificity and recognition in cells or tissues are a challenging research field. To solve the difficulties, we introduce four semiconducting polymer dots (Pdots) as nanoprobes linked by specific miRNA antisense sequences for monitoring the pathological grading by the variation in miRNA expression. Based on the base pairing principle, these miRNA-sensitive Pdots could bind to specific miRNAs within the cancerous cells. As impacted by the background of different pathology gradings, the proportions of the four hepatocellular carcinoma (HCC)-specific miRNAs within the cancerous cell are different, and the pathological grading of the patient tissues can be determined by comparing the palette combinations. The short single-stranded RNA-functionalized Pdots, which have excellent microRNA sensitivity, are observed in an experimental cell model and a series of tissue specimens from HCC patients for the first time. Using the Förster (or fluorescence) resonance energy transfer (FRET) model of Pdots and Cy3dt tag to simulate in vivo miRNA detection, the superior sensitivity and specificity of these nanoprobes are verified. The interference of subjective factors in traditional single/bis-dye emission intensity detection is abandoned, and multiple label staining is used to enhance sensitivity further and reduce the false-positive rate. The feasibility exhibited by this novel staining method is verified in normal hepatocellular HCC cell lines and 16 frozen ultrathin tissue sections, which are employed to quantify pathological grading-related color presentation systems for clinical doctors and pathologists' use. The intelligently designed miRNA-guided Pdots will emerge as an ideal platform with promising biological imaging.
    Keywords:  hepatocellular carcinoma; microRNA; pathological grading diagnosis; prognosis; semiconducting polymer dots
    DOI:  https://doi.org/10.1021/acsami.1c24191
  6. Proc Natl Acad Sci U S A. 2022 Feb 08. pii: e2114971119. [Epub ahead of print]119(6):
    DNA-encoded library versus RNA-encoded library selection enables design of an oncogenic noncoding RNA inhibitor.
    Raphael I Benhamou, Blessy M Suresh, Yuquan Tong, Wesley G Cochrane, Valerie Cavett, Simon Vezina-Dawod, Daniel Abegg, Jessica L Childs-Disney, Alexander Adibekian, Brian M Paegel, Matthew D Disney.
      Nature evolves molecular interaction networks through persistent perturbation and selection, in stark contrast to drug discovery, which evaluates candidates one at a time by screening. Here, nature's highly parallel ligand-target search paradigm is recapitulated in a screen of a DNA-encoded library (DEL; 73,728 ligands) against a library of RNA structures (4,096 targets). In total, the screen evaluated ∼300 million interactions and identified numerous bona fide ligand-RNA three-dimensional fold target pairs. One of the discovered ligands bound a 5'GAG/3'CCC internal loop that is present in primary microRNA-27a (pri-miR-27a), the oncogenic precursor of microRNA-27a. The DEL-derived pri-miR-27a ligand was cell active, potently and selectively inhibiting pri-miR-27a processing to reprogram gene expression and halt an otherwise invasive phenotype in triple-negative breast cancer cells. By exploiting evolutionary principles at the earliest stages of drug discovery, it is possible to identify high-affinity and selective target-ligand interactions and predict engagements in cells that short circuit disease pathways in preclinical disease models.
    Keywords:  RNA; RNA folding; drug design; nucleic acids
    DOI:  https://doi.org/10.1073/pnas.2114971119
  7. Small. 2022 Feb 04. e2107640
    Programmable DNA Hydrogels as Artificial Extracellular Matrix.
    Yuhan Wei, Kaizhe Wang, Shihua Luo, Fan Li, Xiaolei Zuo, Chunhai Fan, Qian Li.
      The cell microenvironment plays a crucial role in regulating cell behavior and fate in physiological and pathological processes. As the fundamental component of the cell microenvironment, extracellular matrix (ECM) typically possesses complex ordered structures and provides essential physical and chemical cues to the cells. Hydrogels have attracted much attention in recapitulating the ECM. Compared to natural and synthetic polymer hydrogels, DNA hydrogels have unique programmable capability, which endows the material precise structural customization and tunable properties. This review focuses on recent advances in programmable DNA hydrogels as artificial extracellular matrix, particularly the pure DNA hydrogels. It introduces the classification, design, and assembly of DNA hydrogels, and then summarizes the state-of-the-art achievements in cell encapsulation, cell culture, and tissue engineering with DNA hydrogels. Ultimately, the challenges and prospects for cellular applications of DNA hydrogels are delivered.
    Keywords:  DNA hydrogels; cell microenvironment; extracellular matrix; programmability
    DOI:  https://doi.org/10.1002/smll.202107640
  8. Sci Adv. 2022 Feb 04. 8(5): eabl4589
    Programmable allosteric DNA regulations for molecular networks and nanomachines.
    Cheng Zhang, Xueying Ma, Xuedong Zheng, Yonggang Ke, Kuiting Chen, Dongsheng Liu, Zuhong Lu, Jing Yang, Hao Yan.
      Structure-based molecular regulations have been widely adopted to modulate protein networks in cells and recently developed to control allosteric DNA operations in vitro. However, current examples of programmable allosteric signal transmission through integrated DNA networks are stringently constrained by specific design requirements. Developing a new, more general, and programmable scheme for establishing allosteric DNA networks remains challenging. Here, we developed a general strategy for programmable allosteric DNA regulations that can be finely tuned by varying the dimensions, positions, and number of conformational signals. By programming the allosteric signals, we realized fan-out/fan-in DNA gates and multiple-layer DNA cascading networks, as well as expanding the approach to long-range allosteric signal transmission through tunable DNA origami nanomachines ~100 nm in size. This strategy will enable programmable and complex allosteric DNA networks and nanodevices for nanoengineering, chemical, and biomedical applications displaying sense-compute-actuate molecular functionalities.
    DOI:  https://doi.org/10.1126/sciadv.abl4589
  9. J Am Chem Soc. 2022 Jan 31.
    Programmable Macroscopic Self-Assembly of DNA-Decorated Hydrogels.
    Vyankat A Sontakke, Yohei Yokobayashi.
      The precise and predictable formation of double-helical structures from complementary DNA sequences has made DNA an extremely versatile tool for programming self-assembled structures from the nanometer to micrometer scale. While a number of supramolecular interactions have been shown to drive self-assembly of macroscopic building blocks of the millimeter scale, DNA-driven self-assembly of macroscopic objects has not been well-established. In this work, we developed a postpolymerization coupling strategy to conjugate short DNA sequences to polyacrylamide-based hydrogel blocks. We observed sequence-specific self-assembly of DNA-decorated hydrogels with 1-2 mm edges in aqueous solution. Furthermore, selective disassembly of hydrogels upon addition of a DNA strand was demonstrated by exploiting a strand displacement reaction. These results lay the foundation for adaptation of various DNA functions to macroscopic self-assembly, for example, molecular recognition, molecular computation, and chemical catalysis.
    DOI:  https://doi.org/10.1021/jacs.1c10308
  10. Adv Healthc Mater. 2022 Feb 03. e2102345
    Organoids at the PUB: The Porcine Urinary Bladder serves As A Pancreatic Niche for Advanced Cancer Modelling.
    Michael Karl Melzer, Markus Breunig, Frank Arnold, Felix Wezel, Anca Azoitei, Elodie Roger, Jana Krüger, Jessica Merkle, Lena Schütte, Viktor Zehe, Friedemann Zengerling, Ninel Azoitei, Lukas Klein, Frederike Penz, Shiv Singh, Thomas Seufferlein, Meike Hohwieler, Christian Bolenz, Cagatay Günes, Johann Gout, Alexander Kleger.
      Despite intensive research and recent progress in personalized medicine including advanced organoid technologies, pancreatic ductal adenocarcinoma remains one of the deadliest and most difficult to treat cancer entities. Pancreatic duct-like organoids (PDLOs) derived from human pluripotent stem cells (PSCs) or pancreatic cancer patient-derived organoids (PDOs) provide unique tools to study both early and late state dysplasia and to foster personalized medicine. However, such advanced systems are neither rapidly nor easily accessible and require an in vivo niche to study tumor formation, progression, and interaction with the stroma. Here, we reveal the establishment of the porcine urinary bladder (PUB) as an advanced organ culture model for shaping a novel ex vivo pancreatic niche. This model allows pancreatic progenitor cells to enter the ductal and endocrine lineages, while PSC-derived PDLOs further mature into duct-like tissue. Accordingly, the PUB offers an ex vivo platform for earliest pancreatic dysplasia and cancer if PDLOs feature oncogenic KRASG12D mutations. Finally, we demonstrate that PDOs-on-PUB (i) resemble primary pancreatic cancer morphology, (ii) preserve molecular cancer subtypes, (iii) enable the study of niche epithelial crosstalk by spiking in pancreatic stellate and peripheral blood mononuclear cells into the grafts and finally (iv) also allow ex vivo drug testing. In sum, the PUB advances and extends the existing pancreatic cancer models by adding feasibility, complexity, and customization at low cost and high flexibility. This article is protected by copyright. All rights reserved.
    Keywords:  Pancreatic cancer; organ culture models; stem cell differentiation; urinary bladder
    DOI:  https://doi.org/10.1002/adhm.202102345
  11. Science. 2022 Feb 04. 375(6580): 551-556
    Multiscale engineered artificial tooth enamel.
    Hewei Zhao, Shaojia Liu, Yan Wei, Yonghai Yue, Mingrui Gao, Yangbei Li, Xiaolong Zeng, Xuliang Deng, Nicholas A Kotov, Lin Guo, Lei Jiang.
      Tooth enamel, renowned for its high stiffness, hardness, and viscoelasticity, is an ideal model for designing biomimetic materials, but accurate replication of complex hierarchical organization of high-performance biomaterials in scalable abiological composites is challenging. We engineered an enamel analog with the essential hierarchical structure at multiple scales through assembly of amorphous intergranular phase (AIP)-coated hydroxyapatite nanowires intertwined with polyvinyl alcohol. The nanocomposite simultaneously exhibited high stiffness, hardness, strength, viscoelasticity, and toughness, exceeding the properties of enamel and previously manufactured bulk enamel-inspired materials. The presence of AIP, polymer confinement, and strong interfacial adhesion are all needed for high mechanical performance. This multiscale design is suitable for scalable production of high-performance materials.
    DOI:  https://doi.org/10.1126/science.abj3343
  12. Nat Methods. 2022 Feb 03.
    Reprogramming the piRNA pathway for multiplexed and transgenerational gene silencing in C. elegans.
    Monika Priyadarshini, Julie Zhouli Ni, Amhed M Vargas-Velazquez, Sam Guoping Gu, Christian Frøkjær-Jensen.
      Single-guide RNAs can target exogenous CRISPR-Cas proteins to unique DNA locations, enabling genetic tools that are efficient, specific and scalable. Here we show that short synthetic guide Piwi-interacting RNAs (piRNAs) (21-nucleotide sg-piRNAs) expressed from extrachromosomal transgenes can, analogously, reprogram the endogenous piRNA pathway for gene-specific silencing in the hermaphrodite germline, sperm and embryos of Caenorhabditis elegans. piRNA-mediated interference ('piRNAi') is more efficient than RNAi and can be multiplexed, and auxin-mediated degradation of the piRNA-specific Argonaute PRG-1 allows conditional gene silencing. Target-specific silencing results in decreased messenger RNA levels, amplification of secondary small interfering RNAs and repressive chromatin modifications. Short (300 base pairs) piRNAi transgenes amplified from arrayed oligonucleotide pools also induce silencing, potentially making piRNAi highly scalable. We show that piRNAi can induce transgenerational epigenetic silencing of two endogenous genes (him-5 and him-8). Silencing is inherited for four to six generations after target-specific sg-piRNAs are lost, whereas depleting PRG-1 leads to essentially permanent epigenetic silencing.
    DOI:  https://doi.org/10.1038/s41592-021-01369-z
  13. Adv Mater. 2022 Feb 04. e2109522
    Urine Microenvironment-Initiated Composite Hydrogel Patch Reconfiguration Propels Scarless Memory Repair and Reinvigoration of Urethra.
    Ming Yang, Yang Zhang, Chao Fang, Li Song, Ying Wang, Lu Lu, Ranxing Yang, Zhaoting Bu, Xiayi Liang, Kun Zhang, Qiang Fu.
      Harsh urine microenvironment (UME) as an inherent hurdle endangers and renders urethral repair unreachable. Innovatively, we utilized the unfavorable UME as the design source to construct a UME-responsive 3D-printed hydrogel patch for realizing scarless memory repair, wherein laser-excited reactive oxygen species (ROS) production and mechanical strength elevation using chemically-crosslinked silicon quantum dots (SiQDs) are accessible. Intriguingly, the proposed composite scaffolds can respond to Ca2+ in urine, cause structure reconfiguration, and repress swelling to further enhance scaffold stiffness. Systematic experiments validate that ROS birth and unexpected stiffness elevation in such UME-responsive scaffolds can realize scarless memory repair of urethra in vivo. Comprehensive mechanism explorations uncover that the activations of cell proliferation and collagen-related genes (e.g., MMP-1 and COL3A1) and the dampening of fibrosis-related (e.g., TGF-β/Smad) and mechanosensitive genes (e.g., YAP/TAZ) are responsible for the scarless memory repair of such UME-responsive scaffolds via enhancing collagen deposition, recalling mechanical memory, decreasing fibrosis and inflammation and accelerating angiogenesis. The design rationales (e.g., UME-initiated structure reconfiguration and anti-swelling) can serve as an instructive and general approach for urethra repair. This article is protected by copyright. All rights reserved.
    Keywords:  Anti-swelling; Mechanical strength; Scarless memory repair; Structure reconfiguration; Urine microenvironment
    DOI:  https://doi.org/10.1002/adma.202109522
  14. Nat Commun. 2022 Feb 01. 13(1): 448
    The DNA methylome of cervical cells can predict the presence of ovarian cancer.
    James E Barrett, Allison Jones, Iona Evans, Daniel Reisel, Chiara Herzog, Kantaraja Chindera, Mark Kristiansen, Olivia C Leavy, Ranjit Manchanda, Line Bjørge, Michal Zikan, David Cibula, Martin Widschwendter.
      The vast majority of epithelial ovarian cancer arises from tissues that are embryologically derived from the Müllerian Duct. Here, we demonstrate that a DNA methylation signature in easy-to-access Müllerian Duct-derived cervical cells from women with and without ovarian cancer (i.e. referred to as the Women's risk IDentification for Ovarian Cancer index or WID-OC-index) is capable of identifying women with an ovarian cancer in the absence of tumour DNA with an AUC of 0.76 and women with an endometrial cancer with an AUC of 0.81. This and the observation that the cervical cell WID-OC-index mimics the epigenetic program of those cells at risk of becoming cancerous in BRCA1/2 germline mutation carriers (i.e. mammary epithelium, fallopian tube fimbriae, prostate) further suggest that the epigenetic misprogramming of cervical cells is an indicator for cancer predisposition. This concept has the potential to advance the field of risk-stratified cancer screening and prevention.
    DOI:  https://doi.org/10.1038/s41467-021-26615-y
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