scholarly journals Vaxrank: A computational tool for designing personalized cancer vaccines

2017 ◽  
Author(s):  
Alexander Rubinsteyn ◽  
Isaac Hodes ◽  
Julia Kodysh ◽  
Jeffrey Hammerbacher

AbstractTherapeutic vaccines targeting mutant tumor antigens (“neoantigens”) are an increasingly popular form of personalized cancer immunotherapy. Vaxrank is a computational tool for selecting neoantigen vaccine peptides from tumor mutations, tumor RNA data, and patient HLA type. Vaxrank is freely available at www.github.com/openvax/vaxrank under the Apache 2.0 open source license and can also be installed from the Python Package Index.

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Manlio Fusciello ◽  
Flavia Fontana ◽  
Siri Tähtinen ◽  
Cristian Capasso ◽  
Sara Feola ◽  
...  

AbstractVirus-based cancer vaccines are nowadays considered an interesting approach in the field of cancer immunotherapy, despite the observation that the majority of the immune responses they elicit are against the virus and not against the tumor. In contrast, targeting tumor associated antigens is effective, however the identification of these antigens remains challenging. Here, we describe ExtraCRAd, a multi-vaccination strategy focused on an oncolytic virus artificially wrapped with tumor cancer membranes carrying tumor antigens. We demonstrate that ExtraCRAd displays increased infectivity and oncolytic effect in vitro and in vivo. We show that this nanoparticle platform controls the growth of aggressive melanoma and lung tumors in vivo both in preventive and therapeutic setting, creating a highly specific anti-cancer immune response. In conclusion, ExtraCRAd might serve as the next generation of personalized cancer vaccines with enhanced features over standard vaccination regimens, representing an alternative way to target cancer.


Vaccines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 668
Author(s):  
Howard Donninger ◽  
Chi Li ◽  
John W. Eaton ◽  
Kavitha Yaddanapudi

The advent of cancer immunotherapy has revolutionized the field of cancer treatment and offers cancer patients new hope. Although this therapy has proved highly successful for some patients, its efficacy is not all encompassing and several cancer types do not respond. Cancer vaccines offer an alternate approach to promote anti-tumor immunity that differ in their mode of action from antibody-based therapies. Cancer vaccines serve to balance the equilibrium of the crosstalk between the tumor cells and the host immune system. Recent advances in understanding the nature of tumor-mediated tolerogenicity and antigen presentation has aided in the identification of tumor antigens that have the potential to enhance anti-tumor immunity. Cancer vaccines can either be prophylactic (preventative) or therapeutic (curative). An exciting option for therapeutic vaccines is the emergence of personalized vaccines, which are tailor-made and specific for tumor type and individual patient. This review summarizes the current standing of the most promising vaccine strategies with respect to their development and clinical efficacy. We also discuss prospects for future development of stem cell-based prophylactic vaccines.


Author(s):  
Wei Hao Khoong

In this paper, we introduce deboost, a Python library devoted to weighted distance ensembling of predictions for regression and classification tasks. Its backbone resides on the scikit-learn library for default models and data preprocessing functions. It offers flexible choices of models for the ensemble as long as they contain the predict method, like the models available from scikit-learn. deboost is released under the MIT open-source license and can be downloaded from the Python Package Index (PyPI) at https://pypi.org/project/deboost. The source scripts are also available on a GitHub repository at https://github.com/weihao94/DEBoost.


2021 ◽  
Author(s):  
Moataz Dowaidar

Cancer immunotherapy, which attempts to activate or stimulate the immune system to treat cancer, has become the standard of treatment. Although some cancer vaccines are efficiently translated, they have not yet reached the same degree of success as infectious disease immunizations. A primary factor is the low immunogenicity of the tumor and related antigens. Unlike viruses, cancer cells emerge from somatic mutations in patients' healthy tissues, making it harder for the immune system to properly detect tumor cells. Biogenic nanoparticles have recently been highlighted as a solution to address some of the issues with creating anticancer vaccinations. Antigens, medication delivery, and others all benefit from biogenic nanoparticles. Biogenic nanoparticles have long been researched as a vaccine. Biogenic nanoparticles-based platforms, like particular VLPs, inherently activate inflammatory responses and may be increased with TAAs evaluated for antigen-specific antitumor responses to patient malignancies. OMVs and OMV-coated nanoparticles can be multiantigenic and immunostimulative in the box. PAMPs present in OMVs can activate innate immunity while suppressing tumor development. A range of cells, including immune and malignant cells, produce exosomes and play a critical role in cell-to-cell communication. Exosomes may contain interesting materials such as specific drugs, proteins, DNA, and RNA species, and their function depends on host cells. In cancer vaccines, however, these biogenic nanoparticles still have some limitations. Transferring tumor antigens and adjuvants to the secondary lymphoid system is a critical issue for biogenic nanoparticles. OMVs lack tumor antigens. Adjuvants are low in VLPs and exosomes. Furthermore, enhancing the protective response of biogenic nanoparticles, generating protective antigens in these nanoparticles and reducing the toxicity of nanoparticles are all challenges in cancer immunotherapy. There has been a lot of information regarding biogenic nanoparticles created by a variety of bacteria or cells in the area of bacterial vesicle research for a long time, but there has been a dearth of in-depth study focused on identifying molecules crucial to biogenesis or biogenic nanoparticles. Many basic questions remain unanswered here. Which envelope factors release biogenic nanoparticles? What signals and mechanisms regulate biogenic biogenic nanoparticles? Understanding these and other concepts as a cancer immunotherapy delivery technique is vital for the future development of biogenic nanoparticles. Future investigations are anticipated to begin to address these fundamental issues and increase our knowledge.


Small ◽  
2018 ◽  
Vol 14 (38) ◽  
pp. 1801372 ◽  
Author(s):  
Binghua Wang ◽  
Jingyi An ◽  
Huifang Zhang ◽  
Shudong Zhang ◽  
Huijuan Zhang ◽  
...  

2019 ◽  
Vol 27 (S2) ◽  
Author(s):  
K. Esfahani ◽  
L. Roudaia ◽  
N. Buhlaiga ◽  
S.V. Del Rincon ◽  
N. Papneja ◽  
...  

Compared with previous standards of care (including chemotherapy, radiotherapy, and surgery), cancer immunotherapy has brought significant improvements for patients in terms of survival and quality of life. Immunotherapy has now firmly established itself as a novel pillar of cancer care, from the metastatic stage to the adjuvant and neoadjuvant settings in numerous cancer types. In this review article, we highlight how the history of cancer immunotherapy paved the way for discoveries that are now part of the standard of care. We also highlight the current pitfalls and limitations of cancer checkpoint immunotherapy and how novel research in the fields of personalized cancer vaccines, autoimmunity, the microbiome, the tumour microenvironment, and metabolomics is aiming to solve those challenges.


Vaccines ◽  
2018 ◽  
Vol 6 (3) ◽  
pp. 52 ◽  
Author(s):  
Angelika Terbuch ◽  
Juanita Lopez

Dramatic success in cancer immunotherapy has been achieved over the last decade with the introduction of checkpoint inhibitors, leading to response rates higher than with chemotherapy in certain cancer types. These responses are often restricted to cancers that have a high mutational burden and show pre-existing T-cell infiltrates. Despite extensive efforts, therapeutic vaccines have been mostly unsuccessful in the clinic. With the introduction of next generation sequencing, the identification of individual mutations is possible, enabling the production of personalized cancer vaccines. Combining immune check point inhibitors to overcome the immunosuppressive microenvironment and personalized cancer vaccines for directing the host immune system against the chosen antigens might be a promising treatment strategy.


Cancers ◽  
2021 ◽  
Vol 13 (15) ◽  
pp. 3667
Author(s):  
Yi Yao ◽  
Chunmei Fu ◽  
Li Zhou ◽  
Qing-Sheng Mi ◽  
Aimin Jiang

As the initiators of adaptive immune responses, DCs play a central role in regulating the balance between CD8 T cell immunity versus tolerance to tumor antigens. Exploiting their function to potentiate host anti-tumor immunity, DC-based vaccines have been one of most promising and widely used cancer immunotherapies. However, DC-based cancer vaccines have not achieved the promised success in clinical trials, with one of the major obstacles being tumor-mediated immunosuppression. A recent discovery on the critical role of type 1 conventional DCs (cDC1s) play in cross-priming tumor-specific CD8 T cells and determining the anti-tumor efficacy of cancer immunotherapies, however, has highlighted the need to further develop and refine DC-based vaccines either as monotherapies or in combination with other therapies. DC-derived exosomes (DCexos) have been heralded as a promising alternative to DC-based vaccines, as DCexos are more resistance to tumor-mediated suppression and DCexo vaccines have exhibited better anti-tumor efficacy in pre-clinical animal models. However, DCexo vaccines have only achieved limited clinical efficacy and failed to induce tumor-specific T cell responses in clinical trials. The lack of clinical efficacy might be partly due to the fact that all current clinical trials used peptide-loaded DCexos from monocyte-derived DCs. In this review, we will focus on the perspective of expanding current DCexo research to move DCexo cancer vaccines forward clinically to realize their potential in cancer immunotherapy.


2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Lei Miao ◽  
Yu Zhang ◽  
Leaf Huang

AbstractmRNA vaccines have become a promising platform for cancer immunotherapy. During vaccination, naked or vehicle loaded mRNA vaccines efficiently express tumor antigens in antigen-presenting cells (APCs), facilitate APC activation and innate/adaptive immune stimulation. mRNA cancer vaccine precedes other conventional vaccine platforms due to high potency, safe administration, rapid development potentials, and cost-effective manufacturing. However, mRNA vaccine applications have been limited by instability, innate immunogenicity, and inefficient in vivo delivery. Appropriate mRNA structure modifications (i.e., codon optimizations, nucleotide modifications, self-amplifying mRNAs, etc.) and formulation methods (i.e., lipid nanoparticles (LNPs), polymers, peptides, etc.) have been investigated to overcome these issues. Tuning the administration routes and co-delivery of multiple mRNA vaccines with other immunotherapeutic agents (e.g., checkpoint inhibitors) have further boosted the host anti-tumor immunity and increased the likelihood of tumor cell eradication. With the recent U.S. Food and Drug Administration (FDA) approvals of LNP-loaded mRNA vaccines for the prevention of COVID-19 and the promising therapeutic outcomes of mRNA cancer vaccines achieved in several clinical trials against multiple aggressive solid tumors, we envision the rapid advancing of mRNA vaccines for cancer immunotherapy in the near future. This review provides a detailed overview of the recent progress and existing challenges of mRNA cancer vaccines and future considerations of applying mRNA vaccine for cancer immunotherapies.


Small ◽  
2018 ◽  
Vol 14 (38) ◽  
pp. 1870173 ◽  
Author(s):  
Binghua Wang ◽  
Jingyi An ◽  
Huifang Zhang ◽  
Shudong Zhang ◽  
Huijuan Zhang ◽  
...  

Sign in / Sign up

Export Citation Format

Share Document