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1.
Curr Issues Mol Biol ; 46(5): 4133-4146, 2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38785522

ABSTRACT

Today, colorectal cancer (CRC) diagnosis is performed using colonoscopy, which is the current, most effective screening method. However, colonoscopy poses risks of harm to the patient and is an invasive process. Recent research has proven metabolomics as a potential, non-invasive detection method, which can use identified biomarkers to detect potential cancer in a patient's body. The aim of this study is to develop a machine-learning (ML) model based on chemical descriptors that will recognize CRC-associated metabolites. We selected a set of metabolites found as the biomarkers of CRC, confirmed that they participate in cancer-related pathways, and used them for training a machine-learning model for the diagnostics of CRC. Using a set of selective metabolites and random compounds, we developed a range of ML models. The best performing ML model trained on Stage 0-2 CRC metabolite data predicted a metabolite class with 89.55% accuracy. The best performing ML model trained on Stage 3-4 CRC metabolite data predicted a metabolite class with 95.21% accuracy. Lastly, the best-performing ML model trained on Stage 0-4 CRC metabolite data predicted a metabolite class with 93.04% accuracy. These models were then tested on independent datasets, including random and unrelated-disease metabolites. In addition, six pathways related to these CRC metabolites were also distinguished: aminoacyl-tRNA biosynthesis; glyoxylate and dicarboxylate metabolism; glycine, serine, and threonine metabolism; phenylalanine, tyrosine, and tryptophan biosynthesis; arginine biosynthesis; and alanine, aspartate, and glutamate metabolism. Thus, in this research study, we created machine-learning models based on metabolite-related descriptors that may be helpful in developing a non-invasive diagnosis method for CRC.

2.
FASEB J ; 37(8): e23068, 2023 08.
Article in English | MEDLINE | ID: mdl-37436778

ABSTRACT

In sporadic amyotrophic lateral sclerosis (sALS), IL-17A- and granzyme-positive cytotoxic T lymphocytes (CTL), IL-17A-positive mast cells, and inflammatory macrophages invade the brain and spinal cord. In some patients, the disease starts following a trauma or a severe infection. We examined cytokines and cytokine regulators over the disease course and found that, since the early stages, peripheral blood mononuclear cells (PBMC) exhibit increased expression of inflammatory cytokines IL-12A, IFN-γ, and TNF-α, as well as granzymes and the transcription factors STAT3 and STAT4. In later stages, PBMCs upregulated the autoimmunity-associated cytokines IL-23A and IL-17B, and the chemokines CXCL9 and CXCL10, which attract CTL and monocytes into the central nervous system. The inflammation is fueled by the downregulation of IL-10, TGFß, and the inhibitory T-cell co-receptors CTLA4, LAG3, and PD-1, and, in vitro, by stimulation with the ligand PD-L1. We investigated in two sALS patients the regulation of the macrophage transcriptome by dimethyl fumarate (DMF), a drug approved against multiple sclerosis and psoriasis, and the cyclic GMP-AMP synthase/stimulator of interferon genes (cGAS/STING) pathway inhibitor H-151. Both DMF and H-151 downregulated the expression of granzymes and the pro-inflammatory cytokines IL-1ß, IL-6, IL-15, IL-23A, and IFN-γ, and induced a pro-resolution macrophage phenotype. The eicosanoid epoxyeicosatrienoic acids (EET) from arachidonic acid was anti-inflammatory in synergy with DMF. H-151 and DMF are thus candidate drugs targeting the inflammation and autoimmunity in sALS via modulation of the NFκB and cGAS/STING pathways.


Subject(s)
Amyotrophic Lateral Sclerosis , Cytokines , Humans , Cytokines/metabolism , Interleukin-17 , Dimethyl Fumarate , Leukocytes, Mononuclear/metabolism , Amyotrophic Lateral Sclerosis/drug therapy , Granzymes , Inflammation/drug therapy , Nucleotidyltransferases
3.
J Transl Med ; 21(1): 830, 2023 11 18.
Article in English | MEDLINE | ID: mdl-37978542

ABSTRACT

Advancing personalized medicine in brain cancer relies on innovative strategies, with mRNA vaccines emerging as a promising avenue. While the initial use of mRNA vaccines was in oncology, their stunning success in COVID-19 resulted in widespread attention, both positive and negative. Regardless of politically biased opinions, which relate more to the antigenic source than form of delivery, we feel it is important to objectively review this modality as relates to brain cancer. This class of vaccines trigger robust immune responses through MHC-I and MHC-II pathways, in both prophylactic and therapeutic settings. The mRNA platform offers advantages of rapid development, high potency, cost-effectiveness, and safety. This review provides an overview of mRNA vaccine delivery technologies, tumor antigen identification, combination therapies, and recent therapeutic outcomes, with a particular focus on brain cancer. Combinatorial approaches are vital to maximizing mRNA cancer vaccine efficacy, with ongoing clinical trials exploring combinations with adjuvants and checkpoint inhibitors and even adoptive cell therapy. Efficient delivery, neoantigen identification, preclinical studies, and clinical trial results are highlighted, underscoring mRNA vaccines' potential in advancing personalized medicine for brain cancer. Synergistic combinatorial therapies play a crucial role, emphasizing the need for continued research and collaboration in this area.


Subject(s)
Brain Neoplasms , Cancer Vaccines , Neoplasms , Humans , Precision Medicine/methods , Immunotherapy/methods , Brain Neoplasms/therapy , Brain Neoplasms/drug therapy , RNA, Messenger/genetics , Neoplasms/therapy
4.
Nucleic Acids Res ; 49(3): 1235-1246, 2021 02 22.
Article in English | MEDLINE | ID: mdl-33398344

ABSTRACT

We have identified chemical probes that simultaneously inhibit cancer cell progression and an immune checkpoint. Using the computational Site Identification by Ligand Competitive Saturation (SILCS) technology, structural biology and cell-based assays, we identify small molecules that directly and selectively bind to the RNA Recognition Motif (RRM) of hnRNP A18, a regulator of protein translation in cancer cells. hnRNP A18 recognizes a specific RNA signature motif in the 3'UTR of transcripts associated with cancer cell progression (Trx, VEGF, RPA) and, as shown here, a tumor immune checkpoint (CTLA-4). Post-transcriptional regulation of immune checkpoints is a potential therapeutic strategy that remains to be exploited. The probes target hnRNP A18 RRM in vitro and in cells as evaluated by cellular target engagement. As single agents, the probes specifically disrupt hnRNP A18-RNA interactions, downregulate Trx and CTLA-4 protein levels and inhibit proliferation of several cancer cell lines without affecting the viability of normal epithelial cells. These first-in-class chemical probes will greatly facilitate the elucidation of the underexplored biological function of RNA Binding Proteins (RBPs) in cancer cells, including their effects on proliferation and immune checkpoint activation.


Subject(s)
Antineoplastic Agents/pharmacology , RNA-Binding Proteins/antagonists & inhibitors , Animals , Antineoplastic Agents/therapeutic use , CTLA-4 Antigen/genetics , CTLA-4 Antigen/metabolism , Cell Line, Tumor , Humans , Ligands , Mice , Neoplasms/drug therapy , Neoplasms/genetics , Neoplasms/metabolism , Nuclear Magnetic Resonance, Biomolecular , Protein Biosynthesis , RNA/metabolism , RNA Recognition Motif , RNA-Binding Proteins/chemistry , RNA-Binding Proteins/metabolism
5.
Sensors (Basel) ; 23(3)2023 Jan 28.
Article in English | MEDLINE | ID: mdl-36772494

ABSTRACT

The presence of missing values in a time-series dataset is a very common and well-known problem. Various statistical and machine learning methods have been developed to overcome this problem, with the aim of filling in the missing values in the data. However, the performances of these methods vary widely, showing a high dependence on the type of data and correlations within the data. In our study, we performed some of the well-known imputation methods, such as expectation maximization, k-nearest neighbor, iterative imputer, random forest, and simple imputer, to impute missing data obtained from smart, wearable health trackers. In this manuscript, we proposed the use of data binning for imputation. We showed that the use of data binned around the missing time interval provides a better imputation than the use of a whole dataset. Imputation was performed for 15 min and 1 h of continuous missing data. We used a dataset with different bin sizes, such as 15 min, 30 min, 45 min, and 1 h, and we carried out evaluations using root mean square error (RMSE) values. We observed that the expectation maximization algorithm worked best for the use of binned data. This was followed by the simple imputer, iterative imputer, and k-nearest neighbor, whereas the random forest method had no effect on data binning during imputation. Moreover, the smallest bin sizes of 15 min and 1 h were observed to provide the lowest RMSE values for the majority of the time frames during the imputation of 15 min and 1 h of missing data, respectively. Although applicable to digital health data, we think that this method will also find applicability in other domains.


Subject(s)
Algorithms , Wearable Electronic Devices , Time Factors , Random Forest
6.
Int Tinnitus J ; 27(1): 40-46, 2023 Dec 04.
Article in English | MEDLINE | ID: mdl-38050883

ABSTRACT

BACKGROUND: Tinnitus is the perception of sound in the absence of external acoustic stimulation. Being one of the most common diseases of the ear, it has a global prevalence ranging from 4.1 to 37.2%. To date, it has been difficult to treat tinnitus as its pathophysiology is poorly understood and there are limited treatment options. OBJECTIVE: To investigate the effect of OKN-007 (also known as HPN-07), a nitrone-based investigational drug, in combination with oral N-acetylcycsteine (NAC), for the treatment of hearing loss and chronic tinnitus under an individual expanded access protocol. PATIENT CASE: We report the case of a patient who presented with left-sided ear fullness, mild tinnitus, and mild high frequency sensorineural hearing loss with 100% word recognition. A large enhancing mass seen on MRI revealed a vestibular schwannoma. He underwent subtotal resection of the tumor resulting in a moderate-to-profound sensorineural hearing loss and catastrophic tinnitus. The patient was treated with intravenous OKN-007 at 60 mg/kg dosed three times per week and oral NAC 2500 mg twice daily. RESULTS: Post-treatment audiometric testing revealed an average of 16.66 dB in hearing threshold improvement in three frequencies (125, 250 and 500 Hz) with residual hearing in the affected left ear. His tinnitus loudness matching improved from 90 dB to 19 dB post-treatment. His Tinnitus Handicap Inventory improved from 86/100 (Catastrophic) to 40/100 (Moderate). He also experienced improvements in sleep, concentration, hearing, and emotional well-being, and reported significantly decreased levels of tinnitusrelated distress. CONCLUSIONS: This case report highlights the feasibility and therapeutic potential of the combination of OKN-007 and NAC in treating hearing loss and tinnitus that warrants further investigation.


Subject(s)
Deafness , Hearing Loss, Sensorineural , Hearing Loss, Unilateral , Hearing Loss , Neuroma, Acoustic , Tinnitus , Male , Humans , Tinnitus/diagnosis , Tinnitus/drug therapy , Tinnitus/etiology , Hearing Loss, Unilateral/diagnosis , Hearing Loss, Unilateral/etiology , Hearing Loss, Unilateral/therapy , Neuroma, Acoustic/complications , Neuroma, Acoustic/diagnosis , Neuroma, Acoustic/surgery , Hearing Loss/complications
7.
Lab Invest ; 102(7): 711-721, 2022 07.
Article in English | MEDLINE | ID: mdl-35013528

ABSTRACT

Glioblastoma (GBM) is still one of the most commonly diagnosed advanced stage primary brain tumors. Current treatments for patients with primary GBM (pGBM) are often not effective and a significant proportion of the patients with pGBM recur. The effective treatment options for recurrent GBM (rGBM) are limited and survival outcomes are poor. This retrospective multicenter pilot study aims to determine potential cell-free microRNAs (cfmiRs) that identify patients with pGBM and rGBM tumors. 2,083 miRs were assessed using the HTG miRNA whole transcriptome assay (WTA). CfmiRs detection was compared in pre-operative plasma samples from patients with pGBM (n = 32) and rGBM (n = 13) to control plasma samples from normal healthy donors (n = 73). 265 cfmiRs were found differentially expressed in plasma samples from pGBM patients compared to normal healthy donors (FDR < 0.05). Of those 193 miRs were also detected in pGBM tumor tissues (n = 15). Additionally, we found 179 cfmiRs differentially expressed in rGBM, of which 68 cfmiRs were commonly differentially expressed in pGBM. Using Random Forest algorithm, specific cfmiR classifiers were found in the plasma of pGBM, rGBM, and both pGBM and rGBM combined. Two common cfmiR classifiers, miR-3180-3p and miR-5739, were found in all the comparisons. In receiving operating characteristic (ROC) curves analysis for rGBM miR-3180-3p showed a specificity of 87.7% and a sensitivity of 100% (AUC = 98.5%); while miR-5739 had a specificity of 79.5% and sensitivity of 92.3% (AUC = 90.2%). This study demonstrated that plasma samples from pGBM and rGBM patients have specific miR signatures. CfmiR-3180-3p and cfmiR-5739 have potential utility in diagnosing patients with pGBM and rGBM tumors using a minimally invasive blood assay.


Subject(s)
Brain Neoplasms , Circulating MicroRNA , Glioblastoma , MicroRNAs , Biomarkers, Tumor/genetics , Brain Neoplasms/diagnosis , Brain Neoplasms/genetics , Glioblastoma/diagnosis , Glioblastoma/genetics , Humans , MicroRNAs/genetics , Pilot Projects , Transcriptome
8.
J Transl Med ; 20(1): 620, 2022 12 26.
Article in English | MEDLINE | ID: mdl-36572880

ABSTRACT

Glioblastoma is the most lethal form of brain tumor with a recurrence rate of almost 90% and a survival time of only 15 months post-diagnosis. It is a highly heterogeneous, aggressive, and extensively studied tumor. Multiple studies have proposed therapeutic approaches to mitigate or improve the survival for patients with glioblastoma. In this article, we review the loss of the 5'-methylthioadenosine phosphorylase (MTAP) gene as a potential therapeutic approach for treating glioblastoma. MTAP encodes a metabolic enzyme required for the metabolism of polyamines and purines leading to DNA synthesis. Multiple studies have explored the loss of this gene and have shown its relevance as a therapeutic approach to glioblastoma tumor mitigation; however, other studies show that the loss of MTAP does not have a major impact on the course of the disease. This article reviews the contrasting findings of MTAP loss with regard to mitigating the effects of glioblastoma, and also focuses on multiple aspects of MTAP loss in glioblastoma by providing insights into the known findings and some of the unexplored areas of this field where new approaches can be imagined for novel glioblastoma therapeutics.


Subject(s)
Glioblastoma , Humans , Glioblastoma/genetics , Glioblastoma/therapy , Purine-Nucleoside Phosphorylase/genetics , Purine-Nucleoside Phosphorylase/metabolism
9.
Future Oncol ; 18(29): 3245-3254, 2022 Sep.
Article in English | MEDLINE | ID: mdl-35950603

ABSTRACT

AdAPT-001 is an investigational therapy consisting of a replicative type 5 adenovirus armed with a TGF-ß receptor-immunoglobulin Fc fusion trap, designed to neutralize isoforms 1 and 3 of the profibrotic and immunosuppressive cytokine, TGF-ß. In preclinical studies with an immunocompetent mouse model, AdAPT-001 eradicated directly treated 'cold' tumors as well as distant untreated tumors, and, from its induction of systemic CD8+ T cell-mediated antitumor immunity, protected the mice from rechallenge with tumor cells. AdAPT-001 also sensitized resistant tumors to checkpoint blockade. This manuscript describes the rationale and design of the first-in-human phase I, dose-escalation and dose-expansion study of AdAPT-001 alone and in combination with a checkpoint inhibitor in adults with treatment-refractory superficially accessible solid tumors.


The purpose of this study is to find out more about the experimental oncolytic virus called AdAPT-001 that has been designed to selectively eliminate cancer cells. The virus is also designed to make a particular protein called a TGF-ß trap, which neutralizes TGF-ß, an overproduced chemical in cancer cells that puts the immune system into a comatose state. This article discusses a clinical trial called BETA PRIME for patients with no other standard treatment options. The trial will explore different doses of AdAPT-001 both alone and in combination with an approved checkpoint inhibitor or another immunotherapy, which blocks the 'off' signal on immune cells, to determine the safest and best dose. Clinical Trial Registration: NCT04673942 (ClinicalTrials.gov).


Subject(s)
Neoplasms , Oncolytic Virotherapy , Animals , Cell Line, Tumor , Clinical Trials, Phase I as Topic , Cytokines , Humans , Immunoglobulins , Immunotherapy , Mice , Neoplasms/drug therapy , Receptors, Transforming Growth Factor beta , Transforming Growth Factor beta
10.
Sensors (Basel) ; 22(3)2022 Jan 19.
Article in English | MEDLINE | ID: mdl-35161502

ABSTRACT

Wearable devices use sensors to evaluate physiological parameters, such as the heart rate, pulse rate, number of steps taken, body fat and diet. The continuous monitoring of physiological parameters offers a potential solution to assess personal healthcare. Identifying outliers or anomalies in heart rates and other features can help identify patterns that can play a significant role in understanding the underlying cause of disease states. Since anomalies are present within the vast amount of data generated by wearable device sensors, identifying anomalies requires accurate automated techniques. Given the clinical significance of anomalies and their impact on diagnosis and treatment, a wide range of detection methods have been proposed to detect anomalies. Much of what is reported herein is based on previously published literature. Clinical studies employing wearable devices are also increasing. In this article, we review the nature of the wearables-associated data and the downstream processing methods for detecting anomalies. In addition, we also review supervised and un-supervised techniques as well as semi-supervised methods that overcome the challenges of missing and un-annotated healthcare data.


Subject(s)
Data Analysis , Wearable Electronic Devices , Algorithms , Heart Rate
11.
BMC Neurol ; 21(1): 231, 2021 Jun 23.
Article in English | MEDLINE | ID: mdl-34162346

ABSTRACT

BACKGROUND: Gliosarcoma (GS) refers to the presence of mesenchymal differentiation (as seen using light microscopy) in the setting of glioblastoma (GB, an astrocytoma, WHO Grade 4). Although the same approach to treatment is typically adopted for GS and GB, there remains some debate as to whether GS should be considered a discrete pathological entity. Differences between these tumors have not been clearly established at the molecular level. METHODS: Patients with GS (n=48) or GB (n=1229) underwent molecular profiling (MP) with a pan-cancer panel of tests as part of their clinical care. The methods employed included next-generation sequencing (NGS) of DNA and RNA, copy number variation (CNV) of DNA and immunohistochemistry (IHC). The MP comprised 1153 tests in total, although results for each test were not available for every tumor profiled. We analyzed this data retrospectively in order to determine if our results were in keeping with what is known about the pathogenesis of GS by contrast with GB. We also sought novel associations between the MP and GS vs. GB which might improve our understanding of pathogenesis of GS. RESULTS: Potentially meaningful associations (p<0.1, Fisher's exact test (FET)) were found for 14 of these tests in GS vs. GB. A novel finding was higher levels of proteins mediating immuno-evasion (PD-1, PD-L1) in GS. All of the differences we observed have been associated with epithelial-to-mesenchymal transition (EMT) in other tumor types. Many of the changes we saw in GS are novel in the setting of glial tumors, including copy number amplification in LYL1 and mutations in PTPN11. CONCLUSIONS: GS shows certain characteristics of EMT, by contrast with GB. Treatments targeting immuno-evasion may be of greater therapeutic value in GS relative to GB.


Subject(s)
Glioblastoma/pathology , Gliosarcoma/pathology , Adolescent , Adult , Aged , Aged, 80 and over , Basic Helix-Loop-Helix Transcription Factors/genetics , Basic Helix-Loop-Helix Transcription Factors/metabolism , Brain Neoplasms/genetics , Brain Neoplasms/metabolism , Brain Neoplasms/pathology , Child , Child, Preschool , DNA Copy Number Variations , Epithelial-Mesenchymal Transition , Female , Glioblastoma/genetics , Glioblastoma/metabolism , Gliosarcoma/genetics , Gliosarcoma/metabolism , Humans , Male , Middle Aged , Neoplasm Grading , Neoplasm Proteins/genetics , Neoplasm Proteins/metabolism , Protein Tyrosine Phosphatase, Non-Receptor Type 11/genetics , Protein Tyrosine Phosphatase, Non-Receptor Type 11/metabolism , Retrospective Studies , Young Adult
12.
Int J Mol Sci ; 22(16)2021 Aug 05.
Article in English | MEDLINE | ID: mdl-34445128

ABSTRACT

The WNT (Wingless/Integrated) signaling pathway is implicated in various stages of glioblastoma, which is an aggressive brain tumor for which therapeutic options are limited. WNT has been recognized as a hallmark of therapeutic challenge due to its context-dependent role and critical function in healthy tissue homeostasis. In this review, we deeply scrutinize the WNT signaling pathway and its involvement in the genesis of glioblastoma as well as its acquired therapy resistance. We also provide an analysis of the WNT pathway in terms of its therapeutic importance in addition to an overview of the current targeted therapies under clinical investigation.


Subject(s)
Brain Neoplasms/genetics , Glioblastoma/genetics , Wnt Signaling Pathway/genetics , Animals , Humans
13.
J Transl Med ; 17(1): 271, 2019 08 19.
Article in English | MEDLINE | ID: mdl-31426803

ABSTRACT

BACKGROUND: ACAM2000, a thymidine kinase (TK)-positive strain of vaccinia virus, is the current smallpox vaccine in the US. Preclinical testing demonstrated potent oncolytic activity of ACAM2000 against several tumor types. This Phase I clinical trial of ACAM2000 delivered by autologous adipose stromal vascular fraction (SVF) cells was conducted to determine the safety and feasibility of such a treatment in patients with advanced solid tumors or acute myeloid leukemia (AML). METHODS: Twenty-four patients with solid tumors and two patients with AML participated in this open-label, non-randomized dose-escalation trial. All patients were treated with SVF derived from autologous fat and incubated for 15 min to 1 h with ACAM2000 before application. Six patients received systemic intravenous application only, one patient received intra-tumoral application only, 15 patients received combination intravenous with intra-tumoral deployment, 3 patients received intravenous and intra-peritoneal injection and 1 patient received intravenous, intra-tumoral and intra-peritoneal injections. Safety at each dose level of ACAM2000 (1.4 × 106 plaque-forming units (PFU) to 1.8 × 107 PFU) was evaluated. Blood samples for PK assessments, flow cytometry and cytokine analysis were collected at baseline and 1 min, 1 h, 1 day, 1 week, 1 month, 3 months and 6 months following treatment. RESULTS: No serious toxicities (> grade 2) were reported. Seven patients reported an adverse event (AE) in this study: self-limiting skin rashes, lasting 7 to 18 days-an expected adverse reaction to ACAM2000. No AEs leading to study discontinuation were reported. Viral DNA was detected in all patients' blood samples immediately following treatment. Interestingly, in 8 patients viral DNA disappeared 1 day and re-appeared 1 week post treatment, suggesting active viral replication at tumor sites, and correlating with longer survival of these patients. No major increase in cytokine levels or correlation between cytokine levels and skin rashes was noted. We were able to assess some initial efficacy signals, especially when the ACAM2000/SVF treatment was combined with checkpoint inhibition. CONCLUSIONS: Treatment with ACAM2000/SVF in patients with advanced solid tumors or AML is safe and well tolerated, and several patients had signals of an anticancer effect. These promising initial clinical results merit further investigation of therapeutic utility. Trial registration Retrospectively registered (ISRCTN#10201650) on October 22, 2018.


Subject(s)
Adipose Tissue/blood supply , Adipose Tissue/cytology , Oncolytic Viruses/physiology , Thymidine Kinase/metabolism , Vaccinia virus/physiology , Adult , Aged , Aged, 80 and over , Cell Line, Tumor , DNA, Viral/blood , Female , Humans , Kaplan-Meier Estimate , Male , Middle Aged , Oncolytic Virotherapy/adverse effects , Stromal Cells/metabolism , Treatment Outcome , Young Adult
14.
Int J Cancer ; 143(11): 3019-3026, 2018 12 01.
Article in English | MEDLINE | ID: mdl-29923182

ABSTRACT

We sought to compare the tumor profiles of brain metastases from common cancers with those of primary tumors and extracranial metastases in order to identify potential targets and prioritize rational treatment strategies. Tumor samples were collected from both the primary and metastatic sites of nonsmall cell lung cancer, breast cancer and melanoma from patients in locations worldwide, and these were submitted to Caris Life Sciences for tumor multiplatform analysis, including gene sequencing (Sanger and next-generation sequencing with a targeted 47-gene panel), protein expression (assayed by immunohistochemistry) and gene amplification (assayed by in situ hybridization). The data analysis considered differential protein expression, gene amplification and mutations among brain metastases, extracranial metastases and primary tumors. The analyzed population included: 16,999 unmatched primary tumor and/or metastasis samples: 8,178 nonsmall cell lung cancers (5,098 primaries; 2,787 systemic metastases; 293 brain metastases), 7,064 breast cancers (3,496 primaries; 3,469 systemic metastases; 99 brain metastases) and 1,757 melanomas (660 primaries; 996 systemic metastases; 101 brain metastases). TOP2A expression was increased in brain metastases from all 3 cancers, and brain metastases overexpressed multiple proteins clustering around functions critical to DNA synthesis and repair and implicated in chemotherapy resistance, including RRM1, TS, ERCC1 and TOPO1. cMET was overexpressed in melanoma brain metastases relative to primary skin specimens. Brain metastasis patients may particularly benefit from therapeutic targeting of enzymes associated with DNA synthesis, replication and/or repair.


Subject(s)
Brain Neoplasms/genetics , Brain Neoplasms/pathology , Neoplasm Metastasis/genetics , Neoplasm Metastasis/pathology , Aged , Female , Gene Expression/genetics , Humans , Male , Middle Aged , Mutation/genetics
15.
Cancer ; 124(6): 1288-1296, 2018 03 15.
Article in English | MEDLINE | ID: mdl-29211306

ABSTRACT

BACKGROUND: Telomerase reverse transcriptase (TERT) promoter mutations that may affect telomerase activity have recently been described in human malignancies. The purpose of this study was to investigate the clinical correlates of TERT promoter abnormalities in a large cohort of patients with diverse cancers. METHODS: This study analyzed TERT promoter alterations and clinical characteristics of 423 consecutive patients for whom molecular testing by next-generation sequencing was performed between August 2014 and July 2015. RESULTS: Of the 423 patients, 61 (14.4%) had TERT promoter mutations, and this placed TERT promoter alterations among the most prevalent aberrations after tumor protein 53 (TP53; 39%) and KRAS and cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) alterations (15% each) in this population. TERT promoter alterations were more frequent in men (P = .031) and were associated with brain cancers (P = .001), skin cancers/melanoma (P = .001), and a higher number of aberrations (P = .0001). A co-alteration analysis found that TERT promoter alterations were significantly correlated with CDKN2A/B (P = .001) and BRAF abnormalities (P = .0003). Patients harboring TERT promoter alterations or TP53 or CDKN2A/B alterations and those with 4 or more alterations demonstrated shorter survival (hazard ratio for normal TERT promoters vs aberrant ones, 0.44; P = .017). However, only a higher number of alterations remained significant in the multivariate analysis. CONCLUSIONS: Overall, TERT promoter alterations were among the most prevalent aberrations in this population, with very high rates in brain cancers (48% of patients) and melanomas (56% of patients). These aberrations frequently coexist with a high number of other aberrations, with the latter feature also significantly associated with poorer overall survival. Therapeutic options for targeting tumors with TERT promoter mutations are currently limited, although a variety of novel approaches are under development. Cancer 2018;124:1288-96. © 2017 American Cancer Society.


Subject(s)
Biomarkers, Tumor/genetics , High-Throughput Nucleotide Sequencing/methods , Mutation , Neoplasms/genetics , Promoter Regions, Genetic , Telomerase/genetics , Female , Follow-Up Studies , Gene Expression Regulation, Neoplastic , Humans , Male , Middle Aged , Neoplasms/classification , Neoplasms/pathology , Prognosis , Retrospective Studies , Survival Rate
16.
J Transl Med ; 16(1): 212, 2018 07 27.
Article in English | MEDLINE | ID: mdl-30053821

ABSTRACT

Mesenchymal stem cell (MSC) therapy offers great potential for treatment of disease through the multifunctional and responsive ability of these cells. In numerous contexts, MSC have been shown to reduce inflammation, modulate immune responses, and provide trophic factor support for regeneration. While the most commonly used MSC source, the bone marrow provides relatively little starting material for cellular expansion, and requires invasive extraction means, fibroblasts are easily harvested in large numbers from various biological wastes. Additionally, in vitro expansion of fibroblasts is significantly easier given the robustness of these cells in tissue culture and shorter doubling time compared to typical MSC. In this paper we put forward the concept that in some cases, fibroblasts may be utilized as a more practical, and potentially more effective cell therapy than mesenchymal stem cells. Anti-inflammatory, immune modulatory, and regenerative properties of fibroblasts will be discussed in the context of regenerative medicine.


Subject(s)
Fibroblasts/cytology , Mesenchymal Stem Cells/cytology , Animals , Cell Differentiation , Clinical Trials as Topic , Humans , Immunomodulation
17.
J Transl Med ; 16(1): 242, 2018 08 31.
Article in English | MEDLINE | ID: mdl-30170620

ABSTRACT

Tumor necrosis factor (TNF)-alpha was originally identified in the 1970s as the serum mediator of innate immunity capable of inducing hemorrhagic necrosis in tumors. Today, a wide spectrum of biological activities have been attributed to this molecule, and clinical translation has mainly occurred not in using it to treat cancer, but rather to inhibit its effects to treat autoimmunity. Clinical trials utilizing systemic TNF-alpha administration have resulted in an unacceptable level of toxicities, which blocked its development. In contrast, localized administration of TNF-alpha in the form of isolated limb perfusion have yielded excellent results in soft tissue sarcomas. Here we describe a novel approach to leveraging the potent antineoplastic activities of TNF-alpha by enhancing activity of locally produced TNF-alpha through extracorporeal removal of soluble TNF-alpha receptors. Specifically, it is known that cancerous tissues are infiltrated with monocytes, T cells, and other cells capable of producing TNF-alpha. It is also known that tumors, as well as cells in the tumor microenvironment produce soluble TNF-alpha receptors. The authors believe that by selectively removing soluble TNF-alpha receptors local enhancement of endogenous TNF-alpha activity may provide for enhanced tumor cell death without associated systemic toxicities.


Subject(s)
Immunotherapy/methods , Sarcoma/therapy , Soft Tissue Neoplasms/therapy , Tumor Necrosis Factor-alpha/therapeutic use , Animals , Antineoplastic Agents, Alkylating/therapeutic use , Humans , Mice , Receptors, Tumor Necrosis Factor, Type I/metabolism , Receptors, Tumor Necrosis Factor, Type II/metabolism , Sarcoma/pathology , Soft Tissue Neoplasms/pathology , Tumor Microenvironment
18.
J Transl Med ; 16(1): 57, 2018 03 09.
Article in English | MEDLINE | ID: mdl-29523171

ABSTRACT

BACKGROUND: Multiple sclerosis (MS) is a progressively debilitating neurological condition in which the immune system abnormally erodes the myelin sheath insulating the nerves. Mesenchymal stem cells (MSC) have been used in the last decade to safely treat certain immune and inflammatory conditions. METHODS: A safety and feasibility study was completed on the use of umbilical cord MSC (UCMSC) as a treatment for MS. In this 1-year study, consenting subjects received seven intravenous infusions of 20 × 106 UCMSC over 7 days. Efficacy was assessed at baseline, 1 month and 1 year after treatment, including magnetic resonance imaging (MRI) scans, Kurtzke Expanded Disability Status Scale (EDSS), Scripps Neurological Rating Scale, Nine-Hole Peg Test, 25-Foot Walk Test, and RAND Short Form-36 quality of life questionnaire. RESULTS: Twenty subjects were enrolled in this study. No serious adverse events were reported. Of the mild AEs denoted as possibly related to treatment, most were headache or fatigue. Symptom improvements were most notable 1 month after treatment. Improvements were seen in EDSS scores (p < 0.03), as well as in bladder, bowel, and sexual dysfunction (p < 0.01), in non-dominant hand average scores (p < 0.01), in walk times (p < 0.02) and general perspective of a positive health change and improved quality of life. MRI scans of the brain and the cervical spinal cord showed inactive lesions in 15/18 (83.3%) subjects after 1 year. CONCLUSIONS: Treatment with UCMSC intravenous infusions for subjects with MS is safe, and potential therapeutic benefits should be further investigated. Trial registration ClinicalTrials.gov NCT02034188. Registered Jan 13, 2014. https://clinicaltrials.gov/ct2/show/NCT02034188.


Subject(s)
Mesenchymal Stem Cell Transplantation , Mesenchymal Stem Cells/cytology , Multiple Sclerosis/therapy , Umbilical Cord/cytology , Adult , Feasibility Studies , Female , Humans , Magnetic Resonance Imaging , Male , Middle Aged , Multiple Sclerosis/diagnostic imaging , Treatment Outcome , Young Adult
19.
J Transl Med ; 16(1): 142, 2018 05 29.
Article in English | MEDLINE | ID: mdl-29843811

ABSTRACT

BACKGROUND: Standard therapy for glioblastoma includes surgery, radiotherapy, and temozolomide. This Phase 3 trial evaluates the addition of an autologous tumor lysate-pulsed dendritic cell vaccine (DCVax®-L) to standard therapy for newly diagnosed glioblastoma. METHODS: After surgery and chemoradiotherapy, patients were randomized (2:1) to receive temozolomide plus DCVax-L (n = 232) or temozolomide and placebo (n = 99). Following recurrence, all patients were allowed to receive DCVax-L, without unblinding. The primary endpoint was progression free survival (PFS); the secondary endpoint was overall survival (OS). RESULTS: For the intent-to-treat (ITT) population (n = 331), median OS (mOS) was 23.1 months from surgery. Because of the cross-over trial design, nearly 90% of the ITT population received DCVax-L. For patients with methylated MGMT (n = 131), mOS was 34.7 months from surgery, with a 3-year survival of 46.4%. As of this analysis, 223 patients are ≥ 30 months past their surgery date; 67 of these (30.0%) have lived ≥ 30 months and have a Kaplan-Meier (KM)-derived mOS of 46.5 months. 182 patients are ≥ 36 months past surgery; 44 of these (24.2%) have lived ≥ 36 months and have a KM-derived mOS of 88.2 months. A population of extended survivors (n = 100) with mOS of 40.5 months, not explained by known prognostic factors, will be analyzed further. Only 2.1% of ITT patients (n = 7) had a grade 3 or 4 adverse event that was deemed at least possibly related to the vaccine. Overall adverse events with DCVax were comparable to standard therapy alone. CONCLUSIONS: Addition of DCVax-L to standard therapy is feasible and safe in glioblastoma patients, and may extend survival. Trial registration Funded by Northwest Biotherapeutics; Clinicaltrials.gov number: NCT00045968; https://clinicaltrials.gov/ct2/show/NCT00045968?term=NCT00045968&rank=1 ; initially registered 19 September 2002.


Subject(s)
Brain Neoplasms/immunology , Brain Neoplasms/therapy , Cancer Vaccines/immunology , Dendritic Cells/immunology , Glioblastoma/immunology , Glioblastoma/therapy , Adult , Aged , Brain Neoplasms/diagnosis , Cancer Vaccines/adverse effects , Endpoint Determination , Female , Glioblastoma/diagnosis , Humans , Male , Middle Aged , Prognosis , Survival Analysis , Treatment Outcome , Young Adult
20.
J Transl Med ; 16(1): 179, 2018 06 29.
Article in English | MEDLINE | ID: mdl-29958537

ABSTRACT

Following publication of the original article [1], the authors reported an error in the spelling of one of the author names. In this Correction the incorrect and correct author names are indicated and the author name has been updated in the original publication. The authors also reported an error in the Methods section of the original article. In this Correction the incorrect and correct versions of the affected sentence are indicated. The original article has not been updated with regards to the error in the Methods section.

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