Onco最新文献

{"title":"Gene Screening in High-Throughput Right-Censored Lung Cancer Data.","authors":"Chenlu Ke,&nbsp;Dipankar Bandyopadhyay,&nbsp;Mario Acunzo,&nbsp;Robert Winn","doi":"10.3390/onco2040017","DOIUrl":"https://doi.org/10.3390/onco2040017","url":null,"abstract":"<p><strong>Background: </strong>Advances in sequencing technologies have allowed collection of massive genome-wide information that substantially advances lung cancer diagnosis and prognosis. Identifying influential markers for clinical endpoints of interest has been an indispensable and critical component of the statistical analysis pipeline. However, classical variable selection methods are not feasible or reliable for high-throughput genetic data. Our objective is to propose a model-free gene screening procedure for high-throughput right-censored data, and to develop a predictive gene signature for lung squamous cell carcinoma (LUSC) with the proposed procedure.</p><p><strong>Methods: </strong>A gene screening procedure was developed based on a recently proposed independence measure. The Cancer Genome Atlas (TCGA) data on LUSC was then studied. The screening procedure was conducted to narrow down the set of influential genes to 378 candidates. A penalized Cox model was then fitted to the reduced set, which further identified a 6-gene signature for LUSC prognosis. The 6-gene signature was validated on datasets from the Gene Expression Omnibus.</p><p><strong>Results: </strong>Both model-fitting and validation results reveal that our method selected influential genes that lead to biologically sensible findings as well as better predictive performance, compared to existing alternatives. According to our multivariable Cox regression analysis, the 6-gene signature was indeed a significant prognostic factor (<i>p</i>-value < 0.001) while controlling for clinical covariates.</p><p><strong>Conclusions: </strong>Gene screening as a fast dimension reduction technique plays an important role in analyzing high-throughput data. The main contribution of this paper is to introduce a fundamental yet pragmatic model-free gene screening approach that aids statistical analysis of right-censored cancer data, and provide a lateral comparison with other available methods in the context of LUSC.</p>","PeriodicalId":74339,"journal":{"name":"Onco","volume":"2 4","pages":"305-318"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10100230/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9323816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ERBB1/EGFR and JAK3 Tyrosine Kinases as Potential Therapeutic Targets in High-Risk Multiple Myeloma.","authors":"Fatih M Uckun, Sanjive Qazi","doi":"10.3390/onco2040016","DOIUrl":"10.3390/onco2040016","url":null,"abstract":"<p><p>Our main objective was to identify abundantly expressed tyrosine kinases in multiple myeloma (MM) as potential therapeutic targets. We first compared the transcriptomes of malignant plasma cells from newly diagnosed MM patients who were risk-categorized based on the patient-specific EMC-92/SKY-92 gene expression signature values vs. normal plasma cells from healthy volunteers using archived datasets from the HOVON65/GMMG-HD4 randomized Phase 3 study evaluating the clinical efficacy of bortezomib induction/maintenance versus classic cytotoxic drugs and thalidomide maintenance. In particular, ERBB1/EGFR was significantly overexpressed in MM cells in comparison to normal control plasma cells, and it was differentially overexpressed in MM cells from high-risk patients. Amplified expression of EGFR/ERBB1 mRNA in MM cells was positively correlated with increased expression levels of mRNAs for several DNA binding proteins and transcription factors with known upregulating activity on EGFR/ERBB1 gene expression. MM patients with the highest ERBB1/EGFR expression level had significantly shorter PFS and OS times than patients with the lowest ERBB1/EGFR expression level. High expression levels of EGFR/ERBB1 were associated with significantly increased hazard ratios for unfavorable PFS and OS outcomes in both univariate and multivariate Cox proportional hazards models. The impact of high EGFR/ERBB1 expression on the PFS and OS outcomes remained significant even after accounting for the prognostic effects of other covariates. These results regarding the prognostic effect of EGFR/ERBB1 expression were validated using the MMRF-CoMMpass RNAseq dataset generated in patients treated with more recently applied drug combinations included in contemporary induction regimens. Our findings provide new insights regarding the molecular mechanism and potential clinical significance of upregulated EGFR/ERBB1 expression in MM.</p>","PeriodicalId":74339,"journal":{"name":"Onco","volume":" ","pages":"282-304"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9610889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40656304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Dependence of Compensation Dose on Systematic and Random Interruption Treatment Time in Radiation Therapy","authors":"R. Abolfath, M. Khalili, A. Senejani, Balachandran Kodery, R. Ivker","doi":"10.3390/onco2030015","DOIUrl":"https://doi.org/10.3390/onco2030015","url":null,"abstract":"Introduction: In this work, we develop a multi-scale model to calculate corrections to the prescription dose to predict compensation required for the DNA repair mechanism and the repopulation of the cancer cells due to the occurrence of patient scheduling variabilities and the treatment time-gap in fractionation scheme. Methods: A system of multi-scale, time-dependent birth-death Master equations is used to describe stochastic evolution of double-strand breaks (DSBs) formed on DNAs and post-irradiation intra and inter chromosomes end-joining processes in cells, including repair and mis-repair mechanisms in microscopic scale, with an extension appropriate for calculation of tumor control probability (TCP) in macroscopic scale. Variabilities in fractionation time due to systematic shifts in patient’s scheduling and randomness in inter-fractionation treatment time are modeled. For an illustration of the methodology, we focus on prostate cancer. Results: We derive analytical corrections to linear-quadratic radiobiological indices α and β as a function of variabilities in treatment time and shifts in patient’s scheduling. We illustrate the dependence of the absolute value of the compensated dose on radio-biological sensitivity, α/β, DNA repair half-time, T1/2, tumor cells repopulation rate, and the time-gaps among treatment fractions due to inter-patient variabilities. At a given tumor size, delays between fractions totaling 24 h over the entire course of treatment, in a typical prostate cancer fractionation scheme, e.g., 81 Gy, 1.8 Gy per fraction and 45 treatment days, require up to 10% compensation dose if the sublethal DNA repair half-time, T1/2, spans over 10 h. We show that the contribution of the fast DNA repair mechanisms to the total dose is negligible. Instead, any compensation to the total dose stems from the tumor cell repopulation that may go up to a significant fraction of the original dose for a time gap of up to one week. Conclusions: We recommend implementation of time irregularities in treatment scheduling in the clinic settings to be taken into account. To achieve a clinical endpoint, corrections to the prescription dose must be assessed, in particular, if modern external beam therapy techniques such as IMRT/VMAT are used for the treatment of cancer.","PeriodicalId":74339,"journal":{"name":"Onco","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47421762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Augmented Expression of the IL3RA/CD123 Gene in MLL/KMT2A-Rearranged Pediatric AML and Infant ALL","authors":"S. Qazi, F. Uckun","doi":"10.3390/onco2030014","DOIUrl":"https://doi.org/10.3390/onco2030014","url":null,"abstract":"Here, we evaluated transcript-level IL3RA/CD123 expression in mixed lineage leukemia 1 (MLL) gene/KMT2A-rearranged (MLL-R+) vs. MLL-R− pediatric AML as well as infant ALL by comparing the archived datasets of the transcriptomes of primary leukemic cells from the corresponding patient populations. Our studies provide unprecedented evidence that IL3RA/CD123 expression exhibits transcript-level amplification in MLL-R+ pediatric AML and infant ALL cells. IL3RA was differentially upregulated in MLL-AF10+ (2.41-fold higher, p-value = 4.4 × 10−6) and MLL-AF6+ (1.83-fold higher, p-value = 9.9 × 10−4) but not in MLL-AF9+ cases compared to other pediatric AML cases. We also show that IL3RA/CD123 expression is differentially amplified in MLL-AF4+ (1.76-fold higher, p-value = 2.1 × 10−4) as well as MLL-ENL+ infant ALL (1.43-fold higher, p-value = 0.055). The upregulated expression of IL3RA/CD123 in MLL-R+ pediatric AML and infant ALL suggests that CD123 may be a suitable target for biotherapy in these high-risk leukemias.","PeriodicalId":74339,"journal":{"name":"Onco","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45952757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic and Gene Expression Studies Helped to Define the Heterogeneity of Small-Cell Lung Cancer and Other Lung Neuroendocrine Tumors and to Identify New Therapeutic Targets","authors":"U. Testa, E. Pelosi, G. Castelli","doi":"10.3390/onco2030013","DOIUrl":"https://doi.org/10.3390/onco2030013","url":null,"abstract":"Small-cell lung cancer (SCLC) is a high-grade neuroendocrine carcinoma, corresponding to about 15% of lung cancers, occurring predominantly in smokers and associated with a very poor prognosis. Key genetic alterations very frequently observed in SCLC are represented by the loss of TP53 and RB1, due to mutational events or deletions; frequent amplification or overexpression of MYC family genes (MYC, MYCL and MYCN); frequent genetic alterations by mutation/deletion of KMT2D, RB family members p107 (RBL1) and p130 (RBL2), PTEN, NOTCH receptors and CREBBP. The profile of expression of specific transcription factors allowed to differentiate four subtypes of SCLC defined according to levels of ASCL1 (SCLC-A), NEUROD1 (SCLC-N), POUF23 (SCLC-P) or YAP1 (SCLC-Y). A recent study identified the subgroup SCLC-I, characterized by the expression of inflammatory/immune-related genes. Recent studies have characterized at molecular level other lung neuroendocrine tumors, including large cell neuroendocrine cancers (LCNECs) and lung carcinoids. These molecular studies have identified some therapeutic vulnerabilities that can be targeted using specific drugs and some promising biomarkers that can predict the response to this treatment. Furthermore, the introduction of immunotherapy (immune checkpoint blockade) into standard first-line treatment has led to a significant clinical benefit in a limited subset of patients.","PeriodicalId":74339,"journal":{"name":"Onco","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49535508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Role of Liquid Biopsy in the Diagnostic Testing Algorithm for Advanced Lung Cancer","authors":"A. Tan","doi":"10.3390/onco2030012","DOIUrl":"https://doi.org/10.3390/onco2030012","url":null,"abstract":"The discovery of therapeutically targetable oncogenic driver alterations has led to marked improvements in NSCLC outcomes. Targeted agents have been approved for an expanding list of biomarkers. Consequently, the accurate and timely identification of targetable alterations with diagnostic molecular profiling is crucial. The use of multiplexed tissue assays, such as next-generation sequencing (NGS), has increased significantly. However, significant limitations with tissue NGS remain, such as insufficient tissue, scheduling limitations, the need for repeat biopsies, and long turnaround times. Liquid biopsies, using plasma circulating tumor DNA (ctDNA), have the potential to overcome these issues, with simpler sample processing requirements, greater convenience, and better patient acceptability. In particular, an early liquid biopsy may allow patients access to highly effective therapies faster, allow better symptom control and quality of life, prevent rapid clinical deterioration, and reduce patient anxiety at diagnosis. More broadly, it may also allow for the more cost-effective delivery of healthcare to patients.","PeriodicalId":74339,"journal":{"name":"Onco","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44765266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Role of Immune Checkpoint Blockade in Acute Myeloid Leukemia","authors":"Margarida F B Silva, D. Martins, F. Mendes","doi":"10.3390/onco2030011","DOIUrl":"https://doi.org/10.3390/onco2030011","url":null,"abstract":"Immune checkpoint inhibition (ICI) has emerged as a therapeutic option for acute myeloid leukemia (AML) for patients that suffer from relapsed or high-risk disease, or patients ineligible for standard therapy. We aimed to study ICI as monotherapy and/or combined therapy (with chemotherapy (QT), for AML patients. The PRISMA statement was used. The literature used comprised clinical trials, randomized controlled trials, and systematic reviews published within the last 7 years. The blockade of CTLA-4 presented a 42% of complete remission within AML. Nivolumab in high-risk AML showed a median recurrence-free survival (RFS) of 8.48 months. The same drug on relapsed hematologic malignancies after allogenic transplantation shows a 1-year OS of 56%. The use of prophylaxis post allogenic transplantation cyclophosphamide (PTCy), following checkpoint inhibition, demonstrated different baseline disease and transplantation characteristics when compared to no-PCTy patients, being 32% and 10%, respectively. CTLA-4 blockage was a worthy therapeutic approach in relapsed hematologic malignancies, presenting long-lasting responses. The approach to AML and myelodysplastic syndrome patients with ICI before allogenic hematopoietic stem cell transplantation and the use of a graft-versus-host disease prophylaxis have shown improvement in the transplantation outcomes, and therefore AML treatment.","PeriodicalId":74339,"journal":{"name":"Onco","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41393704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fucoxanthinol Promotes Apoptosis in MCF-7 and MDA-MB-231 Cells by Attenuating Laminins–Integrins Axis","authors":"Ayaka Yasuda, Momoka Wagatsuma, Wataru Murase, Atsuhito Kubota, Hiroyuki Kojima, Tohru Ohta, Junichi Hamada, Hayato Maeda, Masaru Terasaki","doi":"10.3390/onco2030010","DOIUrl":"https://doi.org/10.3390/onco2030010","url":null,"abstract":"Fucoxanthinol (FxOH), the main metabolite of the marine carotenoid fucoxanthin, exerts anti-cancer effects. However, fragmentary information is available on the growth-inhibiting effects of FxOH on breast cancer (BC). We investigated the growth-inhibiting effects of FxOH on human BC cells (MCF-7 and MDA-MB-231 cells), and the underlying mechanisms, differently from previous studies, by using comprehensive transcriptome analysis. The molecular mechanisms of FxOH were evaluated using flow cytometry, microarray, Western blotting, and gene knockdown analyses. FxOH (20 μM) significantly induced apoptosis in MCF-7 and MDA-MB-231 cells. Transcriptome analysis revealed that FxOH modulated the following 12 signaling pathways: extracellular matrix (ECM), adhesion, cell cycle, chemokine and cytokine, PI3K/AKT, STAT, TGF-β, MAPK, NF-κB, RAS/Rho, DNA repair, and apoptosis signals. FxOH downregulated the levels of laminin β1, integrin α5, integrin β1, integrin β4, cyclin D1, Rho A, phosphorylated (p)paxillin (Tyr31), pSTAT3(Ser727), and pSmad2(Ser465/467), which play critical roles in the 12 signaling pathways mentioned above. Additionally, FxOH upregulated the levels of pERK1/2(Thr202/Tyr204) and active form of caspase-3. Integrin β1 or β4 knockdown significantly inhibited the growth of MCF7 and MDA-MB-231 cells. These results suggest that FxOH induces apoptosis in human BC cells through some core signals, especially the ECM–integrins axis, and the downstream of cell cycle, STAT, TGF-β, RAS/Rho, MAPK, and/or DNA repair signals.","PeriodicalId":74339,"journal":{"name":"Onco","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41973617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole Genome Variant Dataset for Enriching Studies across 18 Different Cancers.","authors":"John Torcivia, Kawther Abdilleh, Fabian Seidl, Owais Shahzada, Rebecca Rodriguez, David Pot, Raja Mazumder","doi":"10.3390/onco2020009","DOIUrl":"10.3390/onco2020009","url":null,"abstract":"<p><p>Whole genome sequencing (WGS) has helped to revolutionize biology, but the computational challenge remains for extracting valuable inferences from this information. Here, we present the cancer-associated variants from the Cancer Genome Atlas (TCGA) WGS dataset. This set of data will allow cancer researchers to further expand their analysis beyond the exomic regions of the genome to the entire genome. A total of 1342 WGS alignments available from the consortium were processed with VarScan2 and deposited to the NCI Cancer Cloud. The sample set covers 18 different cancers and reveals 157,313,519 pooled (non-unique) cancer-associated single-nucleotide variations (SNVs) across all samples. There was an average of 117,223 SNVs per sample, with a range from 1111 to 775,470 and a standard deviation of 163,273. The dataset was incorporated into BigQuery, which allows for fast access and cross-mapping, which will allow researchers to enrich their current studies with a plethora of newly available genomic data.</p>","PeriodicalId":74339,"journal":{"name":"Onco","volume":"2 2","pages":"129-144"},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10571071/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Profiling of the Prognostic Role of Extracellular Matrix-Related Genes in Neuroblastoma Using Databases and Integrated Bioinformatics","authors":"L. Jahangiri","doi":"10.3390/onco2020007","DOIUrl":"https://doi.org/10.3390/onco2020007","url":null,"abstract":"A complex interaction occurs between cancer cells and the extracellular matrix (ECM) in the tumour microenvironment (TME). In this study, the expressions and mutational profiles of 964 ECM-related genes and their correlations with patient overall survival (OS) in neuroblastoma, an aggressive paediatric malignancy, were investigated using cBioPortal and PCAT databases. Furthermore, extended networks comprising protein-protein, protein-long non-coding RNA (lncRNA), and protein-miRNA of 12 selected ECM-related genes were established. The higher expressions of 12 ECM-related genes, AMBN, COLQ, ELFN1, HAS3, HSPE1, LMAN1, LRP5, MUC6, RAMP2, RUVBL2, SSBP1 and UMOD in neuroblastoma patients displayed a significant correlation with patient OS, while similar associations with neuroblastoma patient risk groups, histology and MYCN amplification were obtained. Furthermore, extended gene networks formed by these 12 ECM-related genes were established using Cytoscape, STRING, MSigDB/BioGRID, GeneMANIA and Omicsnet. Finally, the implications of the 12 ECM-related genes in other cancers were revealed using GEPIA2 and the Human Pathology Atlas databases. This meta-analysis showed the significance of these 12 ECM-related genes as putative prognostic predictors in neuroblastoma and other cancers.","PeriodicalId":74339,"journal":{"name":"Onco","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42641203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}