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Mock M, Langmead CJ, Grandsard P, Edavettal S, Russell A. Recent advances in generative biology for biotherapeutic discovery. Trends Pharmacol Sci 2024; 45:255-267. [PMID: 38378385 DOI: 10.1016/j.tips.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/22/2023] [Accepted: 01/05/2024] [Indexed: 02/22/2024]
Abstract
Generative biology combines artificial intelligence (AI), advanced life sciences technologies, and automation to revolutionize the process of designing novel biomolecules with prescribed properties, giving drug discoverers the ability to escape the limitations of biology during the design of next-generation protein therapeutics. Significant hurdles remain, namely: (i) the inherently complex nature of drug discovery, (ii) the bewildering number of promising computational and experimental techniques that have emerged in the past several years, and (iii) the limited availability of relevant protein sequence-function data for drug-like molecules. There is a need to focus on computational methods that will be most practically effective for protein drug discovery and on building experimental platforms to generate the data most appropriate for these methods. Here, we discuss recent advances in computational and experimental life sciences that are most crucial for impacting the pace and success of protein drug discovery.
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Affiliation(s)
- Marissa Mock
- Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | | | - Peter Grandsard
- Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Suzanne Edavettal
- Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Alan Russell
- Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA.
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Chae J, Choi J, Chung J. Polymeric immunoglobulin receptor (pIgR) in cancer. J Cancer Res Clin Oncol 2023; 149:17683-17690. [PMID: 37897659 DOI: 10.1007/s00432-023-05335-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 10/30/2023]
Abstract
BACKGROUND The polymeric immunoglobulin receptor (pIgR) is a transmembrane transporter of polymeric IgA through the intestinal epithelium. Its overexpression has been reported in several cancers, but its role as a diagnostic and prognostic biomarker of oncogenesis is currently unclear. METHOD A literature search was conducted to summarize the functions of pIgR, its expression levels, and its clinical implications. RESULTS pIgR expression has previously been investigated by proteomic analysis, RNA sequencing, and tissue microarray at the level of both RNA and protein in various cancers including pancreatic, esophageal, gastric, lung, and liver. However, studies have reported inconsistent results on how pIgR levels affect clinical outcomes such as survival rate and chemotherapy resistance. Possible explanations include pIgR mRNA levels being minimally correlated with the rate of downstream pIgR protein synthesis, and the diversity of antibodies used in immunohistochemistry studies further magnifying this ambiguity. In ovarian cancer cells, the transcytosis of IgA accompanied a series of transcriptional changes in intracellular inflammatory pathways that inhibit the progression of cancer, including the upregulation of IFN-gamma and downregulation of tumor-promoting ephrins. These findings suggest that both the levels of pIgR and secreted IgA from tumor-infiltrating B cells affect clinical outcomes. CONCLUSION Overall, no direct correlation was observed between the levels of pIgR inside tumor tissue and the clinical features in cancer patients. Measuring pIgR protein levels with a more specific and possibly chemically defined antibody, along with tumoral IgA, is a potential solution to better understand the pathways and consequences of pIgR overexpression in cancer cells.
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Affiliation(s)
- Jisu Chae
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jinny Choi
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.
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Yong J, Mellick AS, Whitelock J, Wang J, Liang K. A Biomolecular Toolbox for Precision Nanomotors. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2205746. [PMID: 36055646 DOI: 10.1002/adma.202205746] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/31/2022] [Indexed: 06/15/2023]
Abstract
The application of nanomotors for cancer diagnosis and therapy is a new and exciting area of research, which when combined with precision nanomedicine, promises to solve many of the issues encountered by previous development of passive nanoparticles. The goal of this article is to introduce nanomotor and nanomedicine researchers to the deep pool of knowledge available regarding cancer cell biology and biochemistry, as well as provide a greater appreciation of the complexity of cell membrane compositions, extracellular surfaces, and their functional consequences. A short description of the nanomotor state-of-art for cancer therapy and diagnosis is first provided, as well as recommendations for future directions of the field. Then, a biomolecular targeting toolbox has been collated for researchers looking to apply their nanomaterial of choice to a biological setting, as well as providing a glimpse into currently available clinical therapies and technologies. This toolbox contains an overview of different classes of targeting molecules available for high affinity and specific targeting and cell surface targets to aid researchers in the selection of a clinical disease model and targeting methodology. It is hoped that this review will provide biological context, inspiration, and direction to future nanomotor and nanomedicine research.
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Affiliation(s)
- Joel Yong
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Kensington, New South Wales, 2052, Australia
| | - Albert S Mellick
- Graduate School of Biomedical Engineering, The University of New South Wales, Kensington, New South Wales, 2052, Australia
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, 2170, Australia
| | - John Whitelock
- Graduate School of Biomedical Engineering, The University of New South Wales, Kensington, New South Wales, 2052, Australia
| | - Joseph Wang
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kang Liang
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Kensington, New South Wales, 2052, Australia
- Graduate School of Biomedical Engineering, The University of New South Wales, Kensington, New South Wales, 2052, Australia
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Transcriptome Analysis Reveals Effect of Dietary Probiotics on Immune Response Mechanism in Southern Catfish ( Silurus meridionalis) in Response to Plesiomonas shigelloides. Animals (Basel) 2023; 13:ani13030449. [PMID: 36766339 PMCID: PMC9913393 DOI: 10.3390/ani13030449] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
To explore whether a probiotic complex composed of Lactobacillus rhamnosus, Lactobacillus plantarum, and Lactobacillus casei can prevent or inhibit the inflammatory response caused by the invasion of Plesiomonas shigelloides in the southern catfish, we screened differentially expressed genes and enriched inflammation-related pathways among a control and three experimental groups and conducted analysis by transcriptome sequencing after a 21-day breeding experiment. Compared with those in the PS (Plesiomonas shigelloides) group, southern catfish in the L-PS (Lactobacillus-Plesiomonas shigelloides) group had no obvious haemorrhages or ulcerations. The results also showed that inflammation-related genes, such as mmp9, cxcr4, nfkbia, socs3, il-8, pigr, tlr5, and tnfr1, were significantly upregulated in the PS group compared with those in the L-PS groups. In addition, we verified six DEGs (mmp9, cxcr4, nfkbia, socs3, rbp2, and calr) and three proteins (CXCR4, NFKBIA, and CALR) by qRT-PCR and ELISA, respectively. Our results were consistent with the transcriptome data. Moreover, significantly downregulated genes (p < 0.05) were enriched in inflammation-related GO terms (lymphocyte chemotaxis and positive regulation of inflammatory response) and immune-related pathways (intestinal immune network for IgA production and IL-17 signalling pathway) in the L-PS vs. the PS group. Our results indicate that the infection of P. shigelloides can produce an inflammatory response, and probiotics could inhibit the inflammatory response caused by P. shigelloides to some extent.
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White I, Tamot N, Doddareddy R, Ho J, Jiao Q, Harvilla PB, Yang TY, Geist B, Borrok MJ, Truppo MD, Ganesan R, Chowdhury P, Zwolak A. Bifunctional molecules targeting SARS-CoV-2 spike and the polymeric Ig receptor display neutralization activity and mucosal enrichment. MAbs 2021; 13:1987180. [PMID: 34693867 PMCID: PMC8547864 DOI: 10.1080/19420862.2021.1987180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
The global health crisis and economic tolls of COVID-19 necessitate a panoply of strategies to treat SARS-CoV-2 infection. To date, few treatment options exist, although neutralizing antibodies against the spike glycoprotein have proven to be effective. Because infection is initiated at the mucosa and propagates mainly at this site throughout the course of the disease, blocking the virus at the mucosal milieu should be effective. However, administration of biologics to the mucosa presents a substantial challenge. Here, we describe bifunctional molecules combining single-domain variable regions that bind to the polymeric Ig receptor (pIgR) and to the SARS-CoV-2 spike protein via addition of the ACE2 extracellular domain (ECD). The hypothesis behind this design is that pIgR will transport the molecule from the circulation to the mucosal surface where the ACE ECD would act as a decoy receptor for the nCoV2. The bifunctional molecules bind SARS-Cov-2 spike glycoprotein in vitro and efficiently transcytose across the lung epithelium in human tissue-based analyses. Designs featuring ACE2 tethered to the C-terminus of the Fc do not induce antibody-dependent cytotoxicity against pIgR-expressing cells. These molecules thus represent a potential therapeutic modality for systemic administration of neutralizing anti-SARS-CoV-2 molecules to the mucosa.
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Affiliation(s)
- Ian White
- Janssen Biotherapeutics, Janssen R&D LLC, Spring House, PA, USA
| | - Ninkka Tamot
- Janssen Biotherapeutics, Janssen R&D LLC, Spring House, PA, USA
| | | | - Jason Ho
- Janssen Biotherapeutics, Janssen R&D LLC, Spring House, PA, USA
| | - Qun Jiao
- Janssen Biotherapeutics, Janssen R&D LLC, Spring House, PA, USA
| | | | - Tong-Yuan Yang
- Janssen Biotherapeutics, Janssen R&D LLC, Spring House, PA, USA
| | - Brian Geist
- Janssen Biotherapeutics, Janssen R&D LLC, Spring House, PA, USA
| | - M. Jack Borrok
- Janssen Biotherapeutics, Janssen R&D LLC, Spring House, PA, USA
| | - Matthew D. Truppo
- Active Pharmaceutical Ingredient Development, Janssen R&D LLC, Spring House, PA, USA
| | - Rajkumar Ganesan
- Biologics Discovery, Alector, Inc., South San Francisco, CA, USA
| | | | - Adam Zwolak
- Janssen Biotherapeutics, Janssen R&D LLC, Spring House, PA, USA
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