Towards precision oncology discovery: four less known genes and their unknown interactions as highest-performed biomarkers for colorectal cancer

npj Precision Oncology, Journal Year: 2024, Volume and Issue: 8(1)

Published: Jan. 20, 2024

Abstract The goal of this study was to use a new interpretable machine-learning framework based on max-logistic competing risk factor models identify parsimonious set differentially expressed genes (DEGs) that play pivotal role in the development colorectal cancer (CRC). Transcriptome data from nine public datasets were analyzed, and Chinese cohort collected validate findings. discovered four critical DEGs - CXCL8, PSMC2, APP, SLC20A1 exhibit highest accuracy detecting CRC diverse populations ethnicities. Notably, PSMC2 CXCL8 appear central CRC, alone could potentially serve as an early-stage marker for CRC. This work represents pioneering effort applying model human malignancies, interpretability reproducibility results across suggests identified can provide comprehensive description transcriptomic features practical implications research include potential personalized assessment precision diagnosis tailored treatment plans patients.

Language: Английский

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Five Critical Gene-Based Biomarkers With Optimal Performance for Hepatocellular Carcinoma

Cancer Informatics, Journal Year: 2023, Volume and Issue: 22

Published: Jan. 1, 2023

Hepatocellular carcinoma (HCC) is one of the most fatal cancers in world. There an urgent need to understand molecular background HCC facilitate identification biomarkers and discover effective therapeutic targets. Published transcriptomic studies have reported a large number genes that are individually significant for HCC. However, reliable remain be determined. In this study, built on max-linear competing risk factor models, we developed machine learning analytical framework analyze data identify miniature set differentially expressed (DEGs). By analyzing 9 public whole-transcriptome datasets (containing 1184 samples 672 nontumor controls), identified 5 critical (DEGs) (ie, CCDC107, CXCL12, GIGYF1, GMNN, IFFO1) between control samples. The classifiers these DEGs reached nearly perfect performance was further validated US Caucasian cohort collected 17 with paired tissue). conceptual advance our work lies modeling gene-gene interactions correcting batch effect analytic framework. demonstrated clear signature patterns results interpretable, robust, reproducible across diverse cohorts/populations various disease etiologies, indicating intrinsic variables can describe overall features at genomic level. applied study may pave new way improving transcriptome profiling analysis human cancers.

Language: Английский

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The Existence of at Least Three Genomic Signature Patterns and at Least Seven Subtypes of COVID-19 and the End of the Disease

Vaccines, Journal Year: 2022, Volume and Issue: 10(5), P. 761 - 761

Published: May 11, 2022

Hoping to find genomic clues linked COVID-19 and end the pandemic has driven scientists' tremendous efforts try all kinds of research. Signs progress have been achieved but are still limited. This paper intends prove existence at least three signature patterns seven subtypes by five critical genes (the smallest subset genes) using blood-sampled datasets. These signatures provide crucial information in diagnosis (including ICU patients), research focuses, treatment methods. Unlike existing approaches focused on gene fold-changes pathways, gene-gene nonlinear competing interactions driving forces finding subtypes. Furthermore, method leads high accuracy with hospitalized patients, showing biological mathematical equivalences between status a methodological advantage over other methods that cannot lead accuracy. As result, as new biomarkers, findings can be much more informative than for interpreting mechanisms, developing second (third) generation vaccines, antiviral drugs, methods, eventually bringing hopes an pandemic.

Language: Английский

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The Initial COVID-19 Reliable Interactive DNA Methylation Markers and Biological Implications

Biology, Journal Year: 2024, Volume and Issue: 13(4), P. 245 - 245

Published: April 7, 2024

Earlier research has established the existence of reliable interactive genomic biomarkers. However, DNA methylation biomarkers, not to mention interactivity, have yet be identified at epigenetic level. This study, drawing from 865,859 sites, discovered two miniature sets Infinium MethylationEPIC each having eight CpG sites (genes) interact with other and disease subtypes. They led nearly perfect (96.87–100% accuracy) prediction COVID-19 patients diseases or healthy controls. These can jointly explain some post-COVID-19-related conditions. optimally performing biomarkers reported in literature become potential druggable targets. Among these cg16785077 (gene MX1), cg25932713 PARP9), cg22930808 PARP9) levels indicate that initial SARS-CoV-2 virus may better treated as a transcribed viral into RNA virus, i.e., an concerned scientists field. Such discovery significantly change scientific thinking knowledge viruses.

Language: Английский

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Genomic Biomarker Heterogeneities between SARS-CoV-2 and COVID-19

Vaccines, Journal Year: 2022, Volume and Issue: 10(10), P. 1657 - 1657

Published: Oct. 2, 2022

Genes functionally associated with SARS-CoV-2 infection and genes related to the COVID-19 disease can be different, whose distinction will become first essential step for successfully fighting against pandemic. Unfortunately, this has not been completed in all biological medical research. Using a newly developed max-competing logistic classifier, two genes, ATP6V1B2 IFI27, stand out critical transcriptional response differential expressions derived from NP/OP swab PCR. This finding is evidenced by combining these another gene predicting status achieve better-indicating accuracy than existing classifiers same number of genes. In addition, three other form five-gene classifier outperforms ten or more These pandemic as new focus direction their exceptional accuracy. Comparing functional effects 100% identified tested blood samples our earlier work, on infection, signature patterns antibodies, are significantly different. We use total fourteen cohort studies (including breakthrough infections omicron variants) 1481 justify results. Such significant findings help explore causal pathological links between disease, fight targeted vaccines, antiviral drugs, therapies.

Language: Английский

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Genomic Transcriptome Benefits and Potential Harms of COVID-19 Vaccines Indicated from Optimized Genomic Biomarkers

Vaccines, Journal Year: 2022, Volume and Issue: 10(11), P. 1774 - 1774

Published: Oct. 22, 2022

COVID-19 vaccines can be the tugboats for preventing SARS-CoV-2 infections when they are practical and, more importantly, without adverse effects. However, reality is that may result in short-term or long-term impacts on COVID-19-related diseases and even trigger formation of new variants SARS-CoV-2. Using published data, we use a set optimized-performance genomic biomarkers (MND1, CDC6, ZNF282) to study benefits effects BNT162b2 vaccine. We found vaccine lowered expression values genes MND1 CDC6 while heightening ZNF282 individuals who naïve, which expected satisfies biological equivalence between disease signature patterns established literature. also COVID-19-convalescent octogenarians responded reversely. The heightened CDC6. In addition, it ZNF282. Such raise outstanding concerns about whether not should take current it. These findings at level provide insights into developing next-generation vaccines, antiviral drugs, pandemic management guidance.

Language: Английский

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Role of miRNAs to control the progression of Chronic Myeloid Leukemia by their expression levels

Medical Oncology, Journal Year: 2024, Volume and Issue: 41(2)

Published: Jan. 12, 2024

Language: Английский

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Omicron’s intrinsic gene-gene interactions jumped away from earlier SARS-CoV-2 variants and gene homologs between humans and animals

Advances in Biomarker Sciences and Technology, Journal Year: 2023, Volume and Issue: 5, P. 105 - 123

Published: Jan. 1, 2023

Omicron and its subvariants have become the predominant SARS-CoV-2 variants worldwide. The Omicron's basic reproduction number (R0) has been close to 20 or higher. However, it is not known what caused such an extremely high R0 whether intrinsic gene-gene interactions are different from earlier variants. Find explanation for infection. Max-linear competing logistic regression classifier. We found that jumped away which can be fully described by a miniature set of genes reported in our work. gene PTAFR (Platelet Activating Factor Receptor) highly correlated with variants, so CCNI (Cyclin I), conserved chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, frog. combination lead 100% accuracy differentiating COVID-19 infection negative. hypothesize were potentially COVID-19-infected animals back humans. In addition, there also several other two-gene interactions, besides CCNI, accuracy. Such observations explain Omicron"s fast-spread capability as either those infection, i.e., multiplication R0s leads much higher R0. At genomic level, PTAFR, identified this work rise druggable targets antiviral drugs existing drugs.

Language: Английский

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The Existence of At Least Three Genomic Signature Patterns and At Least Seven Subtypes of COVID-19 and the End of the Disease

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Jan. 25, 2022

Abstract Hoping to find genomic clues linked COVID-19 and end the pandemic has driven scientists’ tremendous efforts try all kinds of research. Signs progress have been achieved but are still limited. This paper intends prove existence at least three signature patterns seven subtypes by five critical genes (the smallest subset genes). These signatures provide crucial information in diagnosis (including ICU patients), research focuses, treatment methods. Unlike existing approaches focused on gene fold-changes pathways, gene-gene nonlinear competing interactions driving forces finding subtypes. Furthermore, method leads 100% accuracy, which shows biological mathematical equivalences between status a methodological advantage over other methods that cannot lead accuracy. As result, as new biomarkers, findings can be much more informative than for interpreting mechanisms, developing second (third) generation vaccines, antiviral drugs, methods, eventually bringing hopes an pandemic.

Language: Английский

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Genomic Benefits and Potential Harms of COVID-19 Vaccines Indicated from High-Performance Genomic Biomarkers

Research Square (Research Square), Journal Year: 2022, Volume and Issue: unknown

Published: Aug. 15, 2022

Abstract COVID-19 vaccines can be the tugboats of preventing SARS-CoV-2 infections when they are practical and, more importantly, without adverse effects. However, reality is that may result in short-term or long-term impacts on COVID-19-related diseases and even trigger formation new variants SARS-CoV-2. Using published data, we use a set high-performance genomic biomarkers (MND1, CDC6, ZNF282) to study benefits effects BNT162b2 vaccine. We found vaccine lowered expression values genes MND1 CDC6 while heightening ZNF282 individuals with SARS-CoV-2-naive, which expected satisfies biological equivalence between disease signature patterns established literature. also adversely affected convalescent octogenarians. It heightened CDC6. In addition, it ZNF282. Such raise outstanding concerns about whether not should take current it. These findings at level provide insights into developing next-generation vaccines, antiviral drugs, pandemic management guidance.

Language: Английский

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