21 results on '"Barros LRC"'
Search Results
2. CARTmath - A Mathematical Model of CAR-T Immunotherapy in Preclinical Models
- Author
-
Paixão Ea, Naozuka Gt, Barros Lrc, Almeida Rcc, Fassoni Ac, and Valli Amp
- Subjects
business.industry ,medicine.medical_treatment ,medicine ,biochemistry ,Long term immunity ,Computational biology ,Immunotherapy ,Car t cells ,business - Abstract
Immunotherapy has gained great momentum with chimeric antigen receptor T cell (CAR-T) therapy, in which patient’s T lymphocytes are genetically manipulated to recognize tumor-specific antigens increasing tumor elimination efficiency. In the last years, CAR-T cell immunotherapy for hematological malignancies achieved a great response rate on patients and is a very promising therapy for several other malignancies. Each new CAR design requires a preclinical proof-of-concept experiment using immunodeficient mouse models. The absence of a functional immune system in these mice makes them simple and suitable to be mathematically modeled. In this work, we developed a three population mathematical model to describe tumor response to CAR-T cell immunotherapy in immunodeficient mouse models, encompassing interactions between a non-solid tumor and CAR-T cells (effector and long-term memory). We account for several phenomena, such as tumor-induced immunosuppression, memory pool formation, and conversion of memory into effector CAR-T cells in the presence of new tumor cells. Individual donor and tumor specificities were considered as uncertainties in the model parameters. Our model is able to reproduce several CAR-T cell immunotherapy scenarios, with different CAR receptors and tumor targets reported in the literature. We found that therapy effectiveness mostly depends on some specific parameters such as the differentiation of effector to memory CAR-T cells, CAR-T cytotoxic capacity, tumor growth rate, and tumor-induced immunosuppression. In summary, our model can contribute to reduce and optimize the number of in vivo experiments with in silico tests to select specific scenarios that could be tested in experimental research. Such in silico laboratory was made available in a Shiny R-based platform called CARTmath. It is an open-source, easy to run simulator, available at github.com/tmglncc/CARTmath or directly on the webpage cartmath.lncc.br, containing this manuscript results as examples and documentation. The developed model, together with the CARTmath platform, provides potential use for assessing different CAR-T cell immunotherapy protocols and associated efficacy, becoming an accessory towards in silico trials.
- Published
- 2021
3. Prevalence of germline variants in Brazilian pancreatic carcinoma patients.
- Author
-
Rodrigues LM, Maistro S, Katayama MLH, Rocha VM, Lopez RVM, Lopes EFDT, Gonçalves FT, Fridman C, Serio PAMP, Barros LRC, Leite LAS, Segatelli V, Estevez-Diz MDP, Guindalini RSC, Ribeiro Junior U, and Folgueira MAAK
- Subjects
- Humans, Brazil epidemiology, Male, Middle Aged, Female, Aged, Cross-Sectional Studies, Adult, Prevalence, Aged, 80 and over, Adenocarcinoma genetics, Pancreatic Neoplasms genetics, Pancreatic Neoplasms epidemiology, Germ-Line Mutation, Genetic Predisposition to Disease
- Abstract
We evaluated the prevalence of pathogenic/likely pathogenic germline variants (PGV) in Brazilian pancreatic adenocarcinoma (PC) patients, that represent a multiethnic population, in a cross-sectional study. We included 192 PC patients unselected for family history of cancer. We evaluated a panel of 113 cancer genes, through genomic DNA sequencing and 46 ancestry-informative markers, through multiplex PCR. The median age was 61 years; 63.5% of the patients presented disease clinical stages III or IV; 8.3% reported personal history of cancer; 4.7% and 16.1% reported first-degree relatives with PC or breast and/or prostate cancer, respectively. Although the main ancestry was European, there was considerable genetic composition admixture. Twelve patients (6.25%) were PGV carriers in PC predisposition genes (ATM, BRCA1, BRCA2, CDKN2A, MSH2, PALB2) and another 25 (13.0%) were PGV carriers in genes with a limited association or not previously associated with PC (ACD, BLM, BRIP1, CHEK2, ERCC4, FANCA, FANCE, FANCM, GALNT12, MITF, MRE11, MUTYH, POLE, RAD51B, RAD51C, RECQL4, SDHA, TERF2IP). The most frequently affected genes were CHEK2, ATM and FANC. In tumor samples from PGV carriers in ACD, BRIP1, MRE11, POLE, SDHA, TERF2IP, which were examined through exome sequencing, the main single base substitutions (SBS) mutational signature was SBS1+5+18, probably associated with age, tobacco smoking and reactive oxygen species. SBS3 associated with homologous repair deficiency was also represented, but on a lower scale. There was no difference in the frequency of PGV carriers between: (a) patients with or without first-degree relatives with cancer; and (b) patients with admixed ancestry versus those with predominantly European ancestry. Furthermore, there was no difference in overall survival between PGV carriers and non-carriers. Therefore, genetic testing should be offered to all Brazilian pancreatic cancer patients, regardless of their ancestry. Genes with limited or previously unrecognized associations with pancreatic cancer should be further investigated to clarify their role in cancer risk., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
4. Protocol for the establishment of a serine integrase-based platform for functional validation of genetic switch controllers in eukaryotic cells.
- Author
-
de Oliveira MA, Florentino LH, Sales TT, Lima RN, Barros LRC, Limia CG, Almeida MSM, Robledo ML, Barros LMG, Melo EO, Bittencourt DM, Rehen SK, Bonamino MH, and Rech E
- Subjects
- Humans, Plasmids genetics, Serine metabolism, Gene Editing methods, Integrases metabolism, Integrases genetics, Eukaryotic Cells metabolism
- Abstract
Serine integrases (Ints) are a family of site-specific recombinases (SSRs) encoded by some bacteriophages to integrate their genetic material into the genome of a host. Their ability to rearrange DNA sequences in different ways including inversion, excision, or insertion with no help from endogenous molecular machinery, confers important biotechnological value as genetic editing tools with high host plasticity. Despite advances in their use in prokaryotic cells, only a few Ints are currently used as gene editors in eukaryotes, partly due to the functional loss and cytotoxicity presented by some candidates in more complex organisms. To help expand the number of Ints available for the assembly of more complex multifunctional circuits in eukaryotic cells, this protocol describes a platform for the assembly and functional screening of serine-integrase-based genetic switches designed to control gene expression by directional inversions of DNA sequence orientation. The system consists of two sets of plasmids, an effector module and a reporter module, both sets assembled with regulatory components (as promoter and terminator regions) appropriate for expression in mammals, including humans, and plants. The complete method involves plasmid design, DNA delivery, testing and both molecular and phenotypical assessment of results. This platform presents a suitable workflow for the identification and functional validation of new tools for the genetic regulation and reprogramming of organisms with importance in different fields, from medical applications to crop enhancement, as shown by the initial results obtained. This protocol can be completed in 4 weeks for mammalian cells or up to 8 weeks for plant cells, considering cell culture or plant growth time., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 de Oliveira et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2024
- Full Text
- View/download PDF
5. Not Only RET but NF1 and Chromosomal Instability Are Seen in Young Patients with Sporadic Medullary Thyroid Carcinoma.
- Author
-
Castroneves LA, Mangone FRR, Lerario AM, da Cunha Mercante AM, Batista RL, Barros LRC, Ferreira CV, Farias EC, Vanderlei FAB, Maia AL, Nagai MA, Jorge AAL, and Hoff AO
- Abstract
Context: Genetic analysis of sporadic medullary thyroid carcinoma (MTC) has revealed somatic variants in RET , RAS , and occasionally other genes. However, around 20% of patients with sporadic MTC lack a known genetic driver., Objective: To uncover potential new somatic or germline drivers, we analyze a distinct cohort of patients with sporadic, very early-onset, and aggressive MTC., Methods: Germline and somatic DNA exome sequencing was performed in 19 patients, previously tested negative for germline RET variants., Results: Exome sequencing of 19 germline samples confirmed the absence of RET and identified an NF1 pathogenic variant in 1 patient. Somatic sequencing was successful in 15 tumors revealing RET variants in 80%, predominantly p.Met918Thr, which was associated with disease aggressiveness. In RET -negative tumors, pathogenic variants were found in HRAS and NF1 . The NF1 germline and somatic variants were observed in a patient without a prior clinical diagnosis of neurofibromatosis type 1, demonstrating that the loss of heterozygosity of NF1 functions as a potential MTC driver. Somatic copy number alterations analysis revealed chromosomal alterations in 53.3% of tumors, predominantly in RET -positive cases, with losses in chromosomes 9 and 22 being the most prevalent., Conclusion: This study reveals that within a cohort of early-onset nonhereditary MTC, RET remains the major driver gene. In RET -negative tumors, NF1 and RAS are drivers of sporadic MTC. In addition, in young patients without a RET germline mutation, a careful clinical evaluation with a consideration of germline NF1 gene analysis is ideal to exclude Neurofibromatosis type 1 (NF1)., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Endocrine Society.)
- Published
- 2024
- Full Text
- View/download PDF
6. A systematic review of clinical trials for gene therapies for β-hemoglobinopathy around the world.
- Author
-
Rós FA, Couto SCF, Milhomens J, Ovider I, Maio KT, Jennifer V, Ramos RN, Picanço-Castro V, Kashima S, Calado RT, Barros LRC, and Rocha V
- Subjects
- Humans, Cell- and Tissue-Based Therapy, China, Genetic Therapy, Hemoglobinopathies genetics, Hemoglobinopathies therapy, Anemia, Sickle Cell genetics, Anemia, Sickle Cell therapy
- Abstract
Background Aims: Amidst the success of cell therapy for the treatment of onco-hematological diseases, the first recently Food and Drug Administration-approved gene therapy product for patients with transfusion-dependent β-thalassemia (TDT) indicates the feasibility of gene therapy as curative for genetic hematologic disorders. This work analyzed the current-world scenario of clinical trials involving gene therapy for β-hemoglobinopathies., Methods: Eighteen trials for patients with sickle cell disease (SCD) and 24 for patients with TDT were analyzed., Results: Most are phase 1 and 2 trials, funded by the industry and are currently recruiting volunteers. Treatment strategies for both diseases are fetal hemoglobin induction (52.4%); addition of wild-type or therapeutic β-globin gene (38.1%) and correction of mutations (9,5%). Gene editing (52.4%) and gene addition (40.5%) are the two most used techniques. The United States and France are the countries with the greatest number of clinical trials centers for SCD, with 83.1% and 4.2%, respectively. The United States (41.1%), China (26%) and Italy (6.8%) lead TDT trials centers., Conclusions: Geographic trial concentration indicates the high costs of this technology, logistical issues and social challenges that need to be overcome for gene therapy to reach low- and middle-income countries where SCD and TDT are prevalent and where they most impact the patient's health., Competing Interests: Declaration of Competing Interest The authors have no commercial, proprietary or financial interest in the products or companies described in this article., (Copyright © 2023 International Society for Cell & Gene Therapy. Published by Elsevier Inc. All rights reserved.)
- Published
- 2023
- Full Text
- View/download PDF
7. Modeling Patient-Specific CAR-T Cell Dynamics: Multiphasic Kinetics via Phenotypic Differentiation.
- Author
-
Paixão EA, Barros LRC, Fassoni AC, and Almeida RC
- Abstract
Chimeric Antigen Receptor (CAR)-T cell immunotherapy revolutionized cancer treatment and consists of the genetic modification of T lymphocytes with a CAR gene, aiming to increase their ability to recognize and kill antigen-specific tumor cells. The dynamics of CAR-T cell responses in patients present multiphasic kinetics with distribution, expansion, contraction, and persistence phases. The characteristics and duration of each phase depend on the tumor type, the infused product, and patient-specific characteristics. We present a mathematical model that describes the multiphasic CAR-T cell dynamics resulting from the interplay between CAR-T and tumor cells, considering patient and product heterogeneities. The CAR-T cell population is divided into functional (distributed and effector), memory, and exhausted CAR-T cell phenotypes. The model is able to describe the diversity of CAR-T cell dynamical behaviors in different patients and hematological cancers as well as their therapy outcomes. Our results indicate that the joint assessment of the area under the concentration-time curve in the first 28 days and the corresponding fraction of non-exhausted CAR-T cells may be considered a potential marker to classify therapy responses. Overall, the analysis of different CAR-T cell phenotypes can be a key aspect for a better understanding of the whole CAR-T cell dynamics.
- Published
- 2022
- Full Text
- View/download PDF
8. COVID-19 impact on anxiety and depression in head and neck cancer patients: A cross-sectional study.
- Author
-
Rodrigues-Oliveira L, Kauark-Fontes E, Alves CGB, Tonaki JO, Gueiros LA, Moutinho K, Marta GN, Barros LRC, Santos-Silva AR, Brandão TB, and Prado-Ribeiro AC
- Subjects
- Humans, Cross-Sectional Studies, Depression epidemiology, Anxiety, Surveys and Questionnaires, Stress, Psychological, COVID-19, Head and Neck Neoplasms complications, Head and Neck Neoplasms therapy
- Abstract
Objective: To evaluate whether the coronavirus disease 2019 has increased anxiety, depression, and distress levels in head and neck cancer (HNC) patients undergoing radiotherapy (RT)., Methods: In this cross-sectional study, RT-HNC patients were surveyed using the Hospital Anxiety and Depression Scale (HADS) for anxiety and depression and the distress thermometer (DT) for distress. HADS scores were compared with data pre-COVID-19. Additionally, we evaluated the COVID-19 impact on daily routines, treatment, and cancer care through a questionnaire., Results: Fifty patients were included. The HADS mean score and estimated rates were 4.34 (±4.06)/22% for anxiety and 5.08 (±4.82)/22% for depression; in comparison, our historical control had 4.04 (±3.59)/20% for anxiety (p = .79) and 4.03 (±3.62)/17% for depression (p = .49). Mean DT score was 3.68 (±2.77). Responders were aware of COVID-19, afraid of having medical complications, believed it was life-threatening, did not miss appointments, believed their treatment was not impacted, and felt safe at the hospital amid the pandemic., Conclusion: This study suggests that anxiety, depression, and distress levels found in RT-HNC patients did not increase during the pandemic. Patients were afraid of being infected by COVID-19; however, they complied with their cancer treatment., (© 2021 Wiley Periodicals LLC.)
- Published
- 2022
- Full Text
- View/download PDF
9. Systematic Review of Available CAR-T Cell Trials around the World.
- Author
-
Barros LRC, Couto SCF, da Silva Santurio D, Paixão EA, Cardoso F, da Silva VJ, Klinger P, Ribeiro PDAC, Rós FA, Oliveira TGM, Rego EM, Ramos RN, and Rocha V
- Abstract
In this systematic review, we foresee what could be the approved scenario in the next few years for CAR-T cell therapies directed against hematological and solid tumor malignancies. China and the USA are the leading regions in numbers of clinical studies involving CAR-T. Hematological antigens CD19 and BCMA are the most targeted, followed by mesothelin, GPC3, CEA, MUC1, HER2, and EGFR for solid tumors. Most CAR constructs are second-generation, although third and fourth generations are being largely explored. Moreover, the benefit of combining CAR-T treatment with immune checkpoint inhibitors and other drugs is also being assessed. Data regarding product formulation and administration, such as cell phenotype, transfection technique, and cell dosage, are scarce and could not be retrieved. Better tracking of trials' status and results on the ClinicalTrials.gov database should aid in a more concise and general view of the ongoing clinical trials involving CAR-T cell therapy.
- Published
- 2022
- Full Text
- View/download PDF
10. A Stochastic Binary Model for the Regulation of Gene Expression to Investigate Responses to Gene Therapy.
- Author
-
Giovanini G, Barros LRC, Gama LR, Tortelli TC Jr, and Ramos AF
- Abstract
In this manuscript, we use an exactly solvable stochastic binary model for the regulation of gene expression to analyze the dynamics of response to a treatment aiming to modulate the number of transcripts of a master regulatory switching gene. The challenge is to combine multiple processes with different time scales to control the treatment response by a switching gene in an unavoidable noisy environment. To establish biologically relevant timescales for the parameters of the model, we select the RKIP gene and two non-specific drugs already known for changing RKIP levels in cancer cells. We demonstrate the usefulness of our method simulating three treatment scenarios aiming to reestablish RKIP gene expression dynamics toward a pre-cancerous state: (1) to increase the promoter's ON state duration; (2) to increase the mRNAs' synthesis rate; and (3) to increase both rates. We show that the pre-treatment kinetic rates of ON and OFF promoter switching speeds and mRNA synthesis and degradation will affect the heterogeneity and time for treatment response. Hence, we present a strategy for reaching increased average mRNA levels with diminished heterogeneity while reducing drug dosage by simultaneously targeting multiple kinetic rates that effectively represent the chemical processes underlying the regulation of gene expression. The decrease in heterogeneity of treatment response by a target gene helps to lower the chances of emergence of resistance. Our approach may be useful for inferring kinetic constants related to the expression of antimetastatic genes or oncogenes and for the design of multi-drug therapeutic strategies targeting the processes underpinning the expression of master regulatory genes.
- Published
- 2022
- Full Text
- View/download PDF
11. Abnormal Long Non-Coding RNAs Expression Patterns Have the Potential Ability for Predicting Survival and Treatment Response in Breast Cancer.
- Author
-
Pavanelli AC, Mangone FR, Barros LRC, Machado-Rugolo J, Capelozzi VL, and Nagai MA
- Subjects
- Antineoplastic Agents therapeutic use, Biomarkers, Tumor metabolism, Breast Neoplasms drug therapy, Breast Neoplasms pathology, Docetaxel therapeutic use, Female, Humans, RNA, Long Noncoding metabolism, Survival Analysis, Transcriptome, Biomarkers, Tumor genetics, Breast Neoplasms genetics, Drug Resistance, Neoplasm, RNA, Long Noncoding genetics
- Abstract
Abnormal long non-coding RNAs (lncRNAs) expression has been documented to have oncogene or tumor suppressor functions in the development and progression of cancer, emerging as promising independent biomarkers for molecular cancer stratification and patients' prognosis. Examining the relationship between lncRNAs and the survival rates in malignancies creates new scenarios for precision medicine and targeted therapy. Breast cancer (BRCA) is a heterogeneous malignancy. Despite advances in its molecular classification, there are still gaps to explain in its multifaceted presentations and a substantial lack of biomarkers that can better predict patients' prognosis in response to different therapeutic strategies. Here, we performed a re-analysis of gene expression data generated using cDNA microarrays in a previous study of our group, aiming to identify differentially expressed lncRNAs (DELncRNAs) with a potential predictive value for response to treatment with taxanes in breast cancer patients. Results revealed 157 DELncRNAs (90 up- and 67 down-regulated). We validated these new biomarkers as having prognostic and predictive value for breast cancer using in silico analysis in public databases. Data from TCGA showed that compared to normal tissue, MIAT was up-regulated, while KCNQ1OT1, LOC100270804, and FLJ10038 were down-regulated in breast tumor tissues. KCNQ1OT1, LOC100270804, and FLJ10038 median levels were found to be significantly higher in the luminal subtype. The ROC plotter platform results showed that reduced expression of these three DElncRNAs was associated with breast cancer patients who did not respond to taxane treatment. Kaplan-Meier survival analysis revealed that a lower expression of the selected lncRNAs was significantly associated with worse relapse-free survival (RFS) in breast cancer patients. Further validation of the expression of these DELncRNAs might be helpful to better tailor breast cancer prognosis and treatment.
- Published
- 2021
- Full Text
- View/download PDF
12. CART math -A Mathematical Model of CAR-T Immunotherapy in Preclinical Studies of Hematological Cancers.
- Author
-
Barros LRC, Paixão EA, Valli AMP, Naozuka GT, Fassoni AC, and Almeida RC
- Abstract
Immunotherapy has gained great momentum with chimeric antigen receptor T cell (CAR-T) therapy, in which patient's T lymphocytes are genetically manipulated to recognize tumor-specific antigens, increasing tumor elimination efficiency. In recent years, CAR-T cell immunotherapy for hematological malignancies achieved a great response rate in patients and is a very promising therapy for several other malignancies. Each new CAR design requires a preclinical proof-of-concept experiment using immunodeficient mouse models. The absence of a functional immune system in these mice makes them simple and suitable for use as mathematical models. In this work, we develop a three-population mathematical model to describe tumor response to CAR-T cell immunotherapy in immunodeficient mouse models, encompassing interactions between a non-solid tumor and CAR-T cells (effector and long-term memory). We account for several phenomena, such as tumor-induced immunosuppression, memory pool formation, and conversion of memory into effector CAR-T cells in the presence of new tumor cells. Individual donor and tumor specificities are considered uncertainties in the model parameters. Our model is able to reproduce several CAR-T cell immunotherapy scenarios, with different CAR receptors and tumor targets reported in the literature. We found that therapy effectiveness mostly depends on specific parameters such as the differentiation of effector to memory CAR-T cells, CAR-T cytotoxic capacity, tumor growth rate, and tumor-induced immunosuppression. In summary, our model can contribute to reducing and optimizing the number of in vivo experiments with in silico tests to select specific scenarios that could be tested in experimental research. Such an in silico laboratory is an easy-to-run open-source simulator, built on a Shiny R-based platform called CART math . It contains the results of this manuscript as examples and documentation. The developed model together with the CART math platform have potential use in assessing different CAR-T cell immunotherapy protocols and its associated efficacy, becoming an accessory for in silico trials., Competing Interests: The authors declare no conflicts of interest.
- Published
- 2021
- Full Text
- View/download PDF
13. In Search of an Ideal CAR-T Cell Antigen Target.
- Author
-
Barros LRC
- Subjects
- Antigens, CD19, Antigens, Neoplasm, Humans, Immunotherapy, Adoptive, Receptors, Antigen, T-Cell, T-Lymphocytes, Receptors, Chimeric Antigen genetics
- Abstract
Chimeric antigen receptor T (CAR-T) cells are proving their value in hematological cancers such as B cell acute lymphoid leukemia (B-ALL). This success is in great part due to the chosen target antigen, the lineage marker CD19, that is expressed by leukemia blasts and B lymphocytes, which are not crucial. For solid tumors, the challenge is greater because antigen expression is highly heterogeneous within the tumor and even an efficient CAR-T strategy would not kill all tumor cells. Also, many antigens are shared between solid tumors and healthy cells, causing off-target cell lysis and dangerous collateral damage. New antigen sources are emerging as targets, such as viruses, endogenous viruses, and immune checkpoint molecules. New technologies are in search of the ideal target, with antigen combinations the leading candidates.
- Published
- 2021
- Full Text
- View/download PDF
14. High infiltration of B cells in tertiary lymphoid structures, TCR oligoclonality, and neoantigens are part of esophageal squamous cell carcinoma microenvironment.
- Author
-
Barros LRC, Souza-Santos PT, Pretti MAM, Vieira GF, Bragatte MAS, Mendes MFA, De Freitas MV, Scherer NM, De Oliveira IM, Rapozo DCM, Fernandes PV, Simão TA, Soares-Lima SC, Boroni M, Ribeiro Pinto LF, and Bonamino MH
- Subjects
- B-Lymphocytes pathology, Esophageal Neoplasms pathology, Esophageal Squamous Cell Carcinoma pathology, Female, Humans, Lymphocytes, Tumor-Infiltrating pathology, Male, RNA-Seq, Tertiary Lymphoid Structures pathology, Antigens, Neoplasm immunology, B-Lymphocytes immunology, Esophageal Neoplasms immunology, Esophageal Squamous Cell Carcinoma immunology, Lymphocytes, Tumor-Infiltrating immunology, Receptors, Antigen, T-Cell immunology, Tertiary Lymphoid Structures immunology, Tumor Microenvironment immunology
- Abstract
Esophageal squamous cell carcinoma (ESCA) exhibits high intratumoral molecular heterogeneity posing a challenge to cancer therapy. Immune checkpoint blockade therapy has been approved for this disease, but with modest results. RNA-Seq data from paired tumor and surrounding nonmalignant tissue from 14 patients diagnosed with ESCA without previous treatment and from The Cancer Genome Atlas-ESCA cohort were analyzed. Herein, we investigated ESCA immune landscape including mutation-derived neoantigens and immune cell subpopulations. Tumor-associated antigen expression was determined by in silico analyses and confirmed by immunohistochemistry showing that PRAME, CEACAM4, and MAGEA11 proteins are expressed on tumors. Immune checkpoint molecules gene expression was higher in the tumor compared with surrounding nonmalignant tissue, but its expression varies greatly among patients. TCR repertoire and BCR transcripts analysis evidenced low clonal diversity with one TCR clone predicted to be specific for a MAGEA11-derived peptide. A high number of B-cell clones infiltrating the tumors and the abundance of these cells in tertiary lymphoid structures observed in ESCA tumors support B cells as a potential immune modulator in this tumor., (©2020 Society for Leukocyte Biology.)
- Published
- 2020
- Full Text
- View/download PDF
15. A comparative analysis of noise properties of stochastic binary models for a self-repressing and for an externally regulating gene.
- Author
-
Giovanini G, Sabino AU, Barros LRC, and Ramos AF
- Subjects
- Models, Genetic, Probability, Stochastic Processes, Gene Expression Regulation, Proteins
- Abstract
This manuscript presents a comparison of noise properties exhibited by two stochastic binary models for: (i) a self-repressing gene; (ii) a repressed or activated externally regulating one. The stochastic models describe the dynamics of probability distributions governing two random variables, namely, protein numbers and the gene state as ON or OFF. In a previous work, we quantify noise in protein numbers by means of its Fano factor and write this quantity as a function of the covariance between the two random variables. Then we show that distributions governing the number of gene products can be super-Fano, Fano or sub-Fano if the covariance is, respectively, positive, null or negative. The latter condition is exclusive for the self-repressing gene and our analysis shows the conditions for which the Fano factor is a sufficient classifier of fluctuations in gene expression. In this work, we present the conditions for which the noise on the number of gene products generated from a self-repressing gene or an externally regulating one are quantitatively similar. That is important for inference of gene regulation from noise in gene expression quantitative data. Our results contribute to a classification of noise function in biological systems by theoretically demonstrating the mechanisms underpinning the higher precision in expression of a self-repressing gene in comparison with an externally regulated one.
- Published
- 2020
- Full Text
- View/download PDF
16. Genetic switches designed for eukaryotic cells and controlled by serine integrases.
- Author
-
Gomide MS, Sales TT, Barros LRC, Limia CG, de Oliveira MA, Florentino LH, Barros LMG, Robledo ML, José GPC, Almeida MSM, Lima RN, Rehen SK, Lacorte C, Melo EO, Murad AM, Bonamino MH, Coelho CM, and Rech E
- Subjects
- Animals, Cattle, Humans, Integrases metabolism, Leukocytes, Mononuclear enzymology, Promoter Regions, Genetic, Serine metabolism, Arabidopsis enzymology, Fibroblasts enzymology, Integrases genetics, Plasmids genetics, Protoplasts enzymology, Recombination, Genetic, Serine genetics
- Abstract
Recently, new serine integrases have been identified, increasing the possibility of scaling up genomic modulation tools. Here, we describe the use of unidirectional genetic switches to evaluate the functionality of six serine integrases in different eukaryotic systems: the HEK 293T cell lineage, bovine fibroblasts and plant protoplasts. Moreover, integrase activity was also tested in human cell types of therapeutic interest: peripheral blood mononuclear cells (PBMCs), neural stem cells (NSCs) and undifferentiated embryonic stem (ES) cells. The switches were composed of plasmids designed to flip two different genetic parts driven by serine integrases. Cell-based assays were evaluated by measurement of EGFP fluorescence and by molecular analysis of attL/attR sites formation after integrase functionality. Our results demonstrate that all the integrases were capable of inverting the targeted DNA sequences, exhibiting distinct performances based on the cell type or the switchable genetic sequence. These results should support the development of tunable genetic circuits to regulate eukaryotic gene expression.
- Published
- 2020
- Full Text
- View/download PDF
17. Distinct pattern of one-carbon metabolism, a nutrient-sensitive pathway, in invasive breast cancer: A metabolomic study.
- Author
-
Santos JR, Waitzberg DL, da Silva IDCG, Junior TCT, Barros LRC, Canuto GAB, Faccio AT, Yamaguchi LF, Kato MJ, Tavares MFM, Martinez AC, Logullo ÂF, Torrinhas RSMM, and Ravacci G
- Abstract
Altered cell metabolism is a hallmark of cancer and critical for its development. Particularly, activation of one-carbon metabolism in tumor cells can sustain oncogenesis while contributing to epigenetic changes and metabolic adaptation during tumor progression. We assessed whether increased one-carbon metabolism activity is a metabolic feature of invasive ductal carcinoma (IDC). Differences in the metabolic profile between biopsies from IDC ( n = 47) and its adjacent tissue ( n = 43) and between biopsies from different breast cancer subtypes were assessed by gas spectrometry in targeted (Biocrates Life Science
® ) and untargeted approaches, respectively. The metabolomics data were statistically treated using MetaboAnalyst 4.0, SIMCA P+ (version 12.01), Statistica 10 software and t test with p < 0.05. The Cancer Genome Atlas breast cancer dataset was also assessed to validate the metabolomic profile of IDC. Our targeted metabolomics analysis showed distinct metabolomics profiles between IDC and adjacent tissue, where IDC displayed a comparative enrichment of metabolites involved in one-carbon metabolism (serine, glycine, threonine, and methionine) and a predicted increase in the activity of pathways that receive and donate carbon units (i.e., folate, methionine, and homocysteine). In addition, the targeted and untargeted metabolomics analyses showed similar metabolomics profiles between breast cancer subtypes. The gene set enrichment analysis identified different transcription-related functions between IDC and non-tumor tissues that involved one-carbon metabolism. Our data suggest that one-carbon metabolism may be a central pathway in IDC and even in general breast tumors, representing a potential target for its treatment and prevention., Competing Interests: CONFLICTS OF INTEREST The authors have no conflicts of interest to declare., (Copyright: © 2020 Santos et al.)- Published
- 2020
- Full Text
- View/download PDF
18. Development of CAR-T cell therapy for B-ALL using a point-of-care approach.
- Author
-
de Macedo Abdo L, Barros LRC, Saldanha Viegas M, Vieira Codeço Marques L, de Sousa Ferreira P, Chicaybam L, and Bonamino MH
- Subjects
- Animals, Cell Line, Tumor, Cell- and Tissue-Based Therapy, Humans, Mice, Xenograft Model Antitumor Assays, Immunotherapy, Adoptive, Leukemia, B-Cell therapy, Point-of-Care Systems, Receptors, Chimeric Antigen genetics
- Abstract
Recently approved by the FDA and European Medicines Agency, CAR-T cell therapy is a new treatment option for B-cell malignancies. Currently, CAR-T cells are manufactured in centralized facilities and face bottlenecks like complex scaling up, high costs, and logistic operations. These difficulties are mainly related to the use of viral vectors and the requirement to expand CAR-T cells to reach the therapeutic dose. In this paper, by using Sleeping Beauty-mediated genetic modification delivered by electroporation, we show that CAR-T cells can be generated and used without the need for ex vivo activation and expansion, consistent with a point-of-care (POC) approach. Our results show that minimally manipulated CAR-T cells are effective in vivo against RS4;11 leukemia cells engrafted in NSG mice even when inoculated after only 4 h of gene transfer. In an effort to better characterize the infused CAR-T cells, we show that 19BBz T lymphocytes infused after 24 h of electroporation (where CAR expression is already detectable) can improve the overall survival and reduce tumor burden in organs of mice engrafted with RS4;11 or Nalm-6 B cell leukemia. A side-by-side comparison of POC approach with a conventional 8-day expansion protocol using Transact beads demonstrated that both approaches have equivalent antitumor activity in vivo . Our data suggest that POC approach is a viable alternative for the generation and use of CAR-T cells, overcoming the limitations of current manufacturing protocols. Its use has the potential to expand CAR immunotherapy to a higher number of patients, especially in the context of low-income countries., (© 2020 The Author(s). Published with license by Taylor & Francis Group, LLC.)
- Published
- 2020
- Full Text
- View/download PDF
19. 4T1 Mammary Carcinoma Colonization of Metastatic Niches Is Accelerated by Obesity.
- Author
-
Evangelista GCM, Salvador PA, Soares SMA, Barros LRC, Xavier FHDC, Abdo LM, Gualberto ACM, Macedo GC, Clavijo-Salomon MA, and Gameiro J
- Abstract
Breast cancer (BC) remains the leading cause of cancer-related deaths among women, and the chances to develop it are duplicated by obesity. Still, the impact of obesity during BC progression remains less understood. We investigated the role of obesity in tumor progression using the murine model of 4T1 mammary carcinoma in BALB/c female mice, previously high-fat-diet (HFD) fed. HFD induced obesity, metabolic impairment, and high serum and fat leptin levels. After injection of 4T1-cells, HFD-mice accelerated tumor progression and metastasis. 4T1-cells found within HFD-mice metastatic niches presented higher clonogenic potential. 4T1-cells treated in vitro with fat-conditioned medium derived from HFD-mice, increased migration capacity through CXCL12 and CCL25 gradients. In HFD-mice, the infiltration and activation of immune cells into tumor-sentinel lymph nodes was overall reduced, except for activated CD4
+ T cells expressing low CD25 levels. Within the bone marrow, the levels of haematopoiesis-related IL-6 and TNF-α decreased after 4T1-cells injection in HFD-mice whereas increased in the controls, suggesting that upregulation of both cytokines, regardless of the tumor, is disrupted by obesity. Finally, the expression of genes for leptin, CXCR4, and CCR9 (receptors of CXCL12 and CCL25, respectively) was negatively correlated with the infiltration of CD8 T cells in human triple-negative BC tumors from obese patients compared to non-obese. Together, our data present early evidence of systemic networks triggered by obesity that promote BC progression to the metastatic niches. Targeting these pathways might be useful to prevent the rapid BC progression observed among obese patients., (Copyright © 2019 Evangelista, Salvador, Soares, Barros, Xavier, Abdo, Gualberto, Macedo, Clavijo-Salomon and Gameiro.)- Published
- 2019
- Full Text
- View/download PDF
20. CAR T Cells Generated Using Sleeping Beauty Transposon Vectors and Expanded with an EBV-Transformed Lymphoblastoid Cell Line Display Antitumor Activity In Vitro and In Vivo.
- Author
-
Chicaybam L, Abdo L, Carneiro M, Peixoto B, Viegas M, de Sousa P, Fornazin MC, Spago MC, Albertoni Laranjeira AB, de Campos-Lima PO, Nowill A, Barros LRC, and Bonamino MH
- Subjects
- Animals, Cell Line, Transformed, Cell Line, Tumor, Disease Models, Animal, Female, Gene Expression, Genetic Vectors administration & dosage, Humans, Immunologic Memory, Mice, Neoplasms genetics, Neoplasms immunology, Neoplasms metabolism, Neoplasms therapy, Receptors, Antigen, T-Cell genetics, Receptors, Chimeric Antigen genetics, T-Lymphocyte Subsets immunology, T-Lymphocyte Subsets metabolism, Xenograft Model Antitumor Assays, DNA Transposable Elements, Genetic Vectors genetics, Immunotherapy, Adoptive, Receptors, Antigen, T-Cell metabolism, Receptors, Chimeric Antigen metabolism, T-Lymphocytes immunology, T-Lymphocytes metabolism
- Abstract
Chimeric antigen receptor (CAR) T cell immunotherapy for the treatment of cancer is now an approved treatment for B cell malignancies. However, the use of viral vectors to provide long-term CAR expression is associated with high production costs and cumbersome quality controls, impacting the final cost of CAR T cell therapies. Nonviral integrative vectors, such as Sleeping Beauty (SB) transposons, provide an alternative to modify primary T cells. Therefore, we developed a protocol to expand SB-transfected 19BBζ CAR T cells using a lymphoblastoid cell line, and evaluated T cell phenotype as well as function along the T cell expansion. Electroporation of PBMCs with transposon plasmid decreased cell viability on day 1 but had a minor impact on the frequency of memory subpopulations when compared to mock condition. CAR+ lymphocytes showed increased proliferation compared to mock control and high cytotoxic activity towards CD19+ cells without significant differences in exhaustion markers expression. Moreover, CAR+ lymphocytes showed an increased frequency by the end of the stimulation cycle compared with day 1, suggesting that CAR expression confers a selective proliferation advantage. Immunodeficient NOD scid gamma chain knockout (NSG) mice engrafted with the human pre-B leukemic cell line RS4;11 and treated with 19BBζ CAR T cells showed improved overall survival when compared to mock T cells treated animals. The results showed that electroporation using the SB system is a simple and affordable method for inducing long-term CAR expression in T lymphocytes. Expansion of gene-modified T cells with the lymphoblastoid cell line provided up to 2 cycles of stimulations, generating effective T cells against leukemia in vitro and in vivo.
- Published
- 2019
- Full Text
- View/download PDF
21. Transcriptional characterization of immunological infiltrates and their relation with glioblastoma patients overall survival.
- Author
-
Pereira MB, Barros LRC, Bracco PA, Vigo A, Boroni M, Bonamino MH, and Lenz G
- Abstract
Introduction : Several cell populations from the peripheral immune system interact to create a complex immunologic status during glioblastoma growth and response to therapy. The aim of this study was to integrate the impact of different immune cell populations present in glioblastoma tumor microenvironment on overall survival. Methodology : Gene expression and clinical data were generated by The Cancer Genome Atlas and previously reported meta-signatures representing cells of the immune system were used. The relationship between meta-signatures was evaluated through Pearson's correlation analyses. Survival analyses were performed through Kaplan-Meier plots and Cox regression model. Results and discussion : Meta-signatures corresponding to infiltrating immune cells with immunosuppressive roles, such as macrophages, NK and NK T cells, MDSCs and Tregs, correlated with poorer patient prognosis. Meta-signatures related to CD8+ T cells predicted improved survival only in patients with low immunosuppressive meta-signatures. By clustering the meta-signatures we found that the cluster containing high meta-signatures of macrophages, MDSCs and Tregs demonstrated the worst prognosis. Conclusion : Integrating the information provided by transcriptional signatures of immunological aspects is fundamental in understanding the impact of the immune system on patient survival. We found a predictive impact on survival with positive role for CD8 and negative roles for macrophages, MDSC, Tregs, NK and NK-T in glioblastoma patients. Understanding these regulatory and stimulatory factors of patients' immune system is essential to delineate an effective strategy to increase the anti-tumor immune response and to generate potential clinical benefits.
- Published
- 2018
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.