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Miéville R, Marquis R, Mazzella W. Discrimination between right- and left-handed writers based on sister lines. J Forensic Sci 2024; 69:959-965. [PMID: 38362955 DOI: 10.1111/1556-4029.15489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/17/2024]
Abstract
Forensic document examiners are often confronted with questioned documents written with ballpoint pens. Depending on the force applied (or pressure) as well as the angle between the pen and the surface, sister lines running parallel to the inked strokes can be left by the lip of the housing ball. In a real case, sister lines were observed on the left side of inked strokes of a questioned signature. To assess whether the writer of that signature was a left-handed or a right-handed writer based on this result, an experimental study was carried out. Handwritten samples and signatures from 182 right-handed and 18 left-handed writers were collected with different ballpoint pens. For every writer, the presence or absence of sister lines was recorded. Sister lines were observed in 49% of the writers of the studied population (in 50% of the right-handed and ca. 39% of the left-handed writers). Most individuals who left sister lines showed a writing angle of 50°-55°. The location of sister lines was tabulated to inform probabilities of observing sister lines at a given location, if the writer is a right-handed or left-handed writer. In the case at hand, a likelihood ratio of 48 was obtained in support of the proposition of a left-handed writer, rather than a right-handed writer. Applying Bayes' theorem, such value moves the prior probability of 15% that the writer of the questioned signature is left-handed to a posterior probability of 89%.
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Affiliation(s)
- Roxane Miéville
- School of Criminal Justice, University of Lausanne, Lausanne, Switzerland
| | - Raymond Marquis
- School of Criminal Justice, University of Lausanne, Lausanne, Switzerland
| | - Williams Mazzella
- School of Criminal Justice, University of Lausanne, Lausanne, Switzerland
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Yang Y, More S, De Smet F, De Vleeschouwer S, Agostinis P. Antioxidant network-based signatures cluster glioblastoma into distinct redox-resistant phenotypes. Front Immunol 2024; 15:1342977. [PMID: 38698847 PMCID: PMC11063242 DOI: 10.3389/fimmu.2024.1342977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
Introduction Aberrant reactive oxygen species (ROS) production is one of the hallmarks of cancer. During their growth and dissemination, cancer cells control redox signaling to support protumorigenic pathways. As a consequence, cancer cells become reliant on major antioxidant systems to maintain a balanced redox tone, while avoiding excessive oxidative stress and cell death. This concept appears especially relevant in the context of glioblastoma multiforme (GBM), the most aggressive form of brain tumor characterized by significant heterogeneity, which contributes to treatment resistance and tumor recurrence. From this viewpoint, this study aims to investigate whether gene regulatory networks can effectively capture the diverse redox states associated with the primary phenotypes of GBM. Methods In this study, we utilized publicly available GBM datasets along with proprietary bulk sequencing data. Employing computational analysis and bioinformatics tools, we stratified GBM based on their antioxidant capacities and evaluated the distinctive functionalities and prognostic values of distinct transcriptional networks in silico. Results We established three distinct transcriptional co-expression networks and signatures (termed clusters C1, C2, and C3) with distinct antioxidant potential in GBM cancer cells. Functional analysis of each cluster revealed that C1 exhibits strong antioxidant properties, C2 is marked with a discrepant inflammatory trait and C3 was identified as the cluster with the weakest antioxidant capacity. Intriguingly, C2 exhibited a strong correlation with the highly aggressive mesenchymal subtype of GBM. Furthermore, this cluster holds substantial prognostic importance: patients with higher gene set variation analysis (GSVA) scores of the C2 signature exhibited adverse outcomes in overall and progression-free survival. Conclusion In summary, we provide a set of transcriptional signatures that unveil the antioxidant potential of GBM, offering a promising prognostic application and a guide for therapeutic strategies in GBM therapy.
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Affiliation(s)
- Yihan Yang
- Research Group Experimental Neurosurgery and Neuroanatomy, Department of Neurosciences, KU Leuven, Leuven, Belgium
- Laboratory of Cell Death Research & Therapy, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- Vlaams Instituut voor Biotechnologie (VIB) Center for Cancer Biology Research, Leuven, Belgium
| | - Sanket More
- Laboratory of Cell Death Research & Therapy, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- Vlaams Instituut voor Biotechnologie (VIB) Center for Cancer Biology Research, Leuven, Belgium
| | - Frederik De Smet
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- Leuven Institute for Single-Cell Omics (LISCO), Leuven, Belgium
| | - Steven De Vleeschouwer
- Research Group Experimental Neurosurgery and Neuroanatomy, Department of Neurosciences, KU Leuven, Leuven, Belgium
- Department of Neurosurgery, University Hospitals Leuven, Leuven, Belgium
- Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Patrizia Agostinis
- Laboratory of Cell Death Research & Therapy, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- Vlaams Instituut voor Biotechnologie (VIB) Center for Cancer Biology Research, Leuven, Belgium
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Hopper MA, Wenzl K, Hartert KT, Krull JE, Dropik AR, Novak JP, Manske MK, Serres MR, Sarangi V, Larson MC, Maurer MJ, Yang ZZ, Paludo J, McPhail ED, Habermann TM, Link BK, Rimsza LM, Ansell SM, Cerhan JR, Jevremovic D, Novak AJ. Molecular classification and identification of an aggressive signature in low-grade B-cell lymphomas. Hematol Oncol 2023; 41:644-654. [PMID: 37254453 PMCID: PMC10592585 DOI: 10.1002/hon.3187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/04/2023] [Accepted: 05/12/2023] [Indexed: 06/01/2023]
Abstract
Non-follicular low-grade B-cell lymphomas (LGBCL) are biologically diverse entities that share clinical and histologic features that make definitive pathologic categorization challenging. While most patients with LGBCL have an indolent course, some experience aggressive disease, highlighting additional heterogeneity across these subtypes. To investigate the potential for shared biology across subtypes, we performed RNA sequencing and applied machine learning approaches that identified five clusters of patients that grouped independently of subtype. One cluster was characterized by inferior outcome, upregulation of cell cycle genes, and increased tumor immune cell content. Integration of whole exome sequencing identified novel LGBCL mutations and enrichment of TNFAIP3 and BCL2 alterations in the poor survival cluster. Building on this, we further refined a transcriptomic signature associated with early clinical failure in two independent cohorts. Taken together, this study identifies unique clusters of LGBCL defined by novel gene expression signatures and immune profiles associated with outcome across diagnostic subtypes.
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Affiliation(s)
| | | | | | | | | | - Joseph P. Novak
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | | | | | | | - Melissa C. Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Matthew J. Maurer
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | | | - Jonas Paludo
- Division of Hematology, Mayo Clinic, Rochester, MN
| | | | | | - Brian K. Link
- Division of Hematology, Oncology, and Bone & Marrow Transplantation, University of Iowa, Iowa City, IA
| | - Lisa M. Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, AZ
| | | | - James R. Cerhan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Dragan Jevremovic
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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Mendelsohn SC, Verhage S, Mulenga H, Scriba TJ, Hatherill M. Systematic review of diagnostic and prognostic host blood transcriptomic signatures of tuberculosis disease in people living with HIV. Gates Open Res 2023; 7:27. [PMID: 37123047 PMCID: PMC10133453.2 DOI: 10.12688/gatesopenres.14327.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 05/09/2023] Open
Abstract
Background HIV-associated tuberculosis (TB) has high mortality; however, current triage and prognostic tools offer poor sensitivity and specificity, respectively. We conducted a systematic review of diagnostic and prognostic host-blood transcriptomic signatures of TB in people living with HIV (PLHIV). Methods We systematically searched online databases for studies published in English between 1990-2020. Eligible studies included PLHIV of any age in test or validation cohorts, and used microbiological or composite reference standards for TB diagnosis. Inclusion was not restricted by setting or participant age. Study selection, quality appraisal using the QUADAS-2 tool, and data extraction were conducted independently by two reviewers. Thereafter, narrative synthesis of included studies, and comparison of signatures performance, was performed. Results We screened 1,580 records and included 12 studies evaluating 31 host-blood transcriptomic signatures in 10 test or validation cohorts of PLHIV that differentiated individuals with TB from those with HIV alone, latent Mycobacterium tuberculosis infection, or other diseases (OD). Two (2/10; 20%) cohorts were prospective (29 TB cases; 51 OD) and 8 (80%) case-control (353 TB cases; 606 controls) design. All cohorts (10/10) were recruited in Sub-Saharan Africa and 9/10 (90%) had a high risk of bias. Ten signatures (10/31; 32%) met minimum WHO Target Product Profile (TPP) criteria for TB triage tests. Only one study (1/12; 8%) evaluated prognostic performance of a transcriptomic signature for progression to TB in PLHIV, which did not meet the minimum WHO prognostic TPP. Conclusions Generalisability of reported findings is limited by few studies enrolling PLHIV, limited geographical diversity, and predominantly case-control design, which also introduces spectrum bias. New prospective cohort studies are needed that include PLHIV and are conducted in diverse settings. Further research exploring the effect of HIV clinical, virological, and immunological factors on diagnostic performance is necessary for development and implementation of TB transcriptomic signatures in PLHIV.
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Affiliation(s)
- Simon C Mendelsohn
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Savannah Verhage
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Humphrey Mulenga
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, Western Cape, 7935, South Africa
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Thomaidou AC, Batsaki P, Adamaki M, Goulielmaki M, Baxevanis CN, Zoumpourlis V, Fortis SP. Promising Biomarkers in Head and Neck Cancer: The Most Clinically Important miRNAs. Int J Mol Sci 2022; 23:ijms23158257. [PMID: 35897831 PMCID: PMC9367895 DOI: 10.3390/ijms23158257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 02/01/2023] Open
Abstract
Head and neck cancers (HNCs) comprise a heterogeneous group of tumors that extend from the oral cavity to the upper gastrointestinal tract. The principal etiologic factors for oral tumors include tobacco smoking and alcohol consumption, while human papillomavirus (HPV) infections have been accused of a high incidence of pharyngeal tumors. Accordingly, HPV detection has been extensively used to categorize carcinomas of the head and neck. The diverse nature of HNC highlights the necessity for novel, sensitive, and precise biomarkers for the prompt diagnosis of the disease, its successful monitoring, and the timely prognosis of patient clinical outcomes. In this context, the identification of certain microRNAs (miRNAs) and/or the detection of alterations in their expression patterns, in a variety of somatic fluids and tissues, could serve as valuable biomarkers for precision oncology. In the present review, we summarize some of the most frequently studied miRNAs (including miR-21, -375, -99, -34a, -200, -31, -125a/b, -196a/b, -9, -181a, -155, -146a, -23a, -16, -29, and let-7), their role as biomarkers, and their implication in HNC pathogenesis. Moreover, we designate the potential of given miRNAs and miRNA signatures as novel diagnostic and prognostic tools for successful patient stratification. Finally, we discuss the currently ongoing clinical trials that aim to identify the diagnostic, prognostic, or therapeutic utility of miRNAs in HNC.
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Affiliation(s)
- Arsinoe C. Thomaidou
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece; (A.C.T.); (M.A.)
| | - Panagiota Batsaki
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, 11522 Athens, Greece; (P.B.); (M.G.); (C.N.B.)
| | - Maria Adamaki
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece; (A.C.T.); (M.A.)
| | - Maria Goulielmaki
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, 11522 Athens, Greece; (P.B.); (M.G.); (C.N.B.)
| | - Constantin N. Baxevanis
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, 11522 Athens, Greece; (P.B.); (M.G.); (C.N.B.)
| | - Vassilis Zoumpourlis
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece; (A.C.T.); (M.A.)
- Correspondence: (V.Z.); (S.P.F.); Tel.: +30-210-727-3730 (V.Z.); +30-210-640-9462 (S.P.F.)
| | - Sotirios P. Fortis
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, 11522 Athens, Greece; (P.B.); (M.G.); (C.N.B.)
- Correspondence: (V.Z.); (S.P.F.); Tel.: +30-210-727-3730 (V.Z.); +30-210-640-9462 (S.P.F.)
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Raj SKS, Routh ED, Chou JW, Votanopoulos KI, Triozzi PL, Miller LD. Prognostic attributes of immune signatures in soft tissue sarcomas show differential dependencies on tumor mutational burden. Cancer 2022; 128:3254-3264. [PMID: 35767280 PMCID: PMC9544607 DOI: 10.1002/cncr.34333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/14/2022] [Accepted: 04/05/2022] [Indexed: 11/11/2022]
Abstract
Background Cellular and intrinsic markers of sarcoma immunogenicity are poorly understood. To gain insight into whether tumor–immune interactions correlate with clinical aggressiveness, the authors examined the prognostic significance of immune gene signatures in combination with tumor mutational burden (TMB) and cancer–testis antigen (CTA) expression. Methods RNA sequencing and clinical data of 259 soft tissue sarcomas from The Cancer Genome Atlas project were used to investigate associations between published immune gene signatures and patient overall survival (OS) in the contexts of TMB, as computed from whole‐exome sequencing data, and CTA gene expression. Multivariate Cox proportional hazards regression models and log‐rank tests were used to assess survival associations. Results Immune signature scores that reflected in part the intratumoral abundance of cytotoxic T cells showed significant positive associations with OS. However, the prognostic power of the T‐cell signatures was highly dependent on TMB‐high status, consistent with protective effects of tumor‐infiltrating T cells in tumors with elevated antigenicity. In TMB‐low tumors, a signature of infiltrating plasma B cells was significantly and positively associated with OS, independent of T‐cell signature status. Although tumor subtypes based on differential expression patterns of CTA genes showed different survival associations within leiomyosarcoma and myxofibrosarcoma histologies, neither CTA nor histologic subtype interacted with the T‐cell–survival association. Conclusions Signatures of T‐cell and plasma B‐cell infiltrates were associated with a survival benefit in soft tissue sarcomas. TMB, but not CTA expression, influenced the prognostic power of T‐cell–associated, but not plasma B‐cell–associated, survival. Lay summary Clinical data and RNA analysis of 259 soft tissue sarcomas from The Cancer Genome Atlas project were used to investigate associations between five published gene immune cell expression signatures and survival in the context of tumor mutations. Activated T cells had a significant positive association with patient survival. Although high tumor mutation burden was associated with good survival, the prognostic power of T‐cell signatures was highly dependent on tumor mutational status, consistent with protective effects of tumor‐infiltrating T cells in tumors with high levels of antigens. In low tumor mutation‐bearing tumors, plasma B cells were positively associated with survival.
Signatures of T‐cell and plasma B‐cell infiltrates are associated with survival benefit in soft tissue sarcomas, and tumor mutational burden (TMB), but not cancer–testis antigen expression, is a tumor‐intrinsic determinant of T‐cell–associated survival, but not plasma B‐cell–associated survival. Although high TMB trended toward an association with good survival, the prognostic power of the T‐cell signatures was highly dependent on TMB‐high status, consistent with the protective effects of tumor‐infiltrating T cells in tumors with elevated antigenicity; however, in TMB‐low tumors, a signature of infiltrating plasma B cells was positively associated with overall survival, independent of T‐cell signature status.
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Affiliation(s)
- Shailaja K S Raj
- Section of Hematology and Oncology, Department of Internal Medicine, Wake Forest Baptist Medical Center, Winston Salem, North Carolina, USA
| | - Eric D Routh
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeff W Chou
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston Salem, North Carolina, USA
| | - Konstantinos I Votanopoulos
- Department of Surgery, Division of Surgical Oncology, Wake Forest Baptist Medical Center, Winston Salem, North Carolina, USA.,Wake Forest Baptist Comprehensive Cancer Center, Winston Salem, North Carolina, USA
| | - Pierre L Triozzi
- Section of Hematology and Oncology, Department of Internal Medicine, Wake Forest Baptist Medical Center, Winston Salem, North Carolina, USA.,Wake Forest Baptist Comprehensive Cancer Center, Winston Salem, North Carolina, USA
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina, USA.,Wake Forest Baptist Comprehensive Cancer Center, Winston Salem, North Carolina, USA
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Schansker G, Ohnishi M, Furutani R, Miyake C. Identification of Twelve Different Mineral Deficiencies in Hydroponically Grown Sunflower Plants on the Basis of Short Measurements of the Fluorescence and P700 Oxidation/Reduction Kinetics. Front Plant Sci 2022; 13:894607. [PMID: 35720579 PMCID: PMC9201956 DOI: 10.3389/fpls.2022.894607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/28/2022] [Indexed: 05/31/2023]
Abstract
The photosynthetic electron transport chain is mineral rich. Specific mineral deficiencies can modify the electron transport chain specifically. Here, it is shown that on the basis of 2 short Chl fluorescence and P700+ measurements (approx. 1 s each), it is possible to discriminate between 10 out of 12 different mineral deficiencies: B, Ca, Cu, Fe, K, Mg, Mn, Mo, N, P, S, and Zn. B- and Mo-deficient plants require somewhat longer measurements to detect the feedback inhibition they induce. Eight out of twelve deficiencies mainly affect PS I and NIR measurements are, therefore, very important for this analysis. In Cu- and P-deficient plants, electron flow from the plastoquinone pool to PS I, is affected. In the case of Cu-deficiency due to the loss of plastocyanin and in the case of P-deficiency probably due to a fast and strong generation of Photosynthetic Control. For several Ca-, K-, and Zn-deficient plant species, higher levels of reactive oxygen species have been measured in the literature. Here, it is shown that this not only leads to a loss of Pm (maximum P700 redox change) reflecting a lower PS I content, but also to much faster P700+ re-reduction kinetics during the I2-P (~30-200 ms) fluorescence rise phase. The different mineral deficiencies affect the relation between the I2-P and P700+ kinetics in different ways and this is used to discuss the nature of the relationship between these two parameters.
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Affiliation(s)
| | - Miho Ohnishi
- Department of Applied Biological Science, Graduate School for Agricultural Science, Kobe University, Kobe, Japan
| | - Riu Furutani
- Department of Applied Biological Science, Graduate School for Agricultural Science, Kobe University, Kobe, Japan
| | - Chikahiro Miyake
- Department of Applied Biological Science, Graduate School for Agricultural Science, Kobe University, Kobe, Japan
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Innocenti F, Yazdani A, Rashid N, Qu X, Ou FS, Van Buren S, Bertagnolli M, Kabbarah O, Blanke CD, Venook AP, Lenz HJ, Vincent BG. Tumor Immunogenomic Features Determine Outcomes in Patients with Metastatic Colorectal Cancer Treated with Standard-of-Care Combinations of Bevacizumab and Cetuximab. Clin Cancer Res 2022; 28:1690-1700. [PMID: 35176136 PMCID: PMC9093780 DOI: 10.1158/1078-0432.ccr-21-3202] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/22/2021] [Accepted: 02/11/2022] [Indexed: 12/16/2022]
Abstract
PURPOSE CALGB/SWOG 80405 was a randomized phase III trial in first-line patients with metastatic colorectal cancer treated with bevacizumab, cetuximab, or both, plus chemotherapy. We tested the effect of tumor immune features on overall survival (OS). EXPERIMENTAL DESIGN Primary tumors (N = 554) were profiled by RNA sequencing. Immune signatures of macrophages, lymphocytes, TGFβ, IFNγ, wound healing, and cytotoxicity were measured. CIBERSORTx scores of naive and memory B cells, plasma cells, CD8+ T cells, resting and activated memory CD4+ T cells, M0 and M2 macrophages, and activated mast cells were measured. RESULTS Increased M2 macrophage score [HR, 6.30; 95% confidence interval (CI), 3.0-12.15] and TGFβ signature expression (HR, 1.35; 95% CI, 1.05-1.77) were associated with shorter OS. Increased scores of plasma cells (HR, 0.55; 95% CI, 0.38-0.87) and activated memory CD4+ T cells (HR, 0.34; 95% CI, 0.16-0.65) were associated with longer OS. Using optimal cutoffs from these four features, patients were categorized as having either 4, 3, 2, or 0-1 beneficial features associated with longer OS, and the median (95% CI) OS decreased from 42.5 (35.8-47.8) to 31.0 (28.8-34.4), 25.2 (20.6-27.9), and 17.7 (13.5-20.4) months respectively (P = 3.48e-11). CONCLUSIONS New immune features can be further evaluated to improve patient response. They provide the rationale for more effective immunotherapy strategies.
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Affiliation(s)
| | - Akram Yazdani
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Naim Rashid
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Fang-Shu Ou
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN
| | - Scott Van Buren
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | - Alan P. Venook
- University of California at San Francisco, San Francisco, CA
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Abstract
Within certain cancers, extensive copy number alterations (CNAs) contribute to a complex and heterogenic genomic profile. This makes it difficult to understand and unravel the distinct molecular dynamics shaping the disease while preventing clinically effective patient stratification. CNA signature analysis represents a novel genomic stratification tool for probing this complexity, offering an intricate framework for deriving CNA patterns at the molecular level. This allows the underlying genomic mechanisms of specific cancers to be revealed, leading to the potential identification of therapeutic targets and prognostic associations. This review outlines the molecular and methodological basis of CNA signatures and focuses on recent advances highlighting their clinical utility, limitations and prospective future as novel diagnostic and prognostic cancer biomarkers.
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Affiliation(s)
- Conor Giles Doran
- UCD Conway Institute, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stephen R Pennington
- UCD Conway Institute, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
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Sapra D, Kaur H, Dhall A, Raghava GPS. ProCanBio: A Database of Manually Curated Biomarkers for Prostate Cancer. J Comput Biol 2021; 28:1248-1257. [PMID: 34898255 DOI: 10.1089/cmb.2021.0348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Prostate cancer (PCa) is the second lethal malignancy in men worldwide. In the past, numerous research groups investigated the omics profiles of patients and scrutinized biomarkers for the diagnosis and prognosis of PCa. However, information related to the biomarkers is widely scattered across numerous resources in complex textual format, which poses hindrance to understand the tumorigenesis of this malignancy and scrutinization of robust signature. To create a comprehensive resource, we collected all the relevant literature on PCa biomarkers from the PubMed. We scrutinize the extensive information about each biomarker from a total of 412 unique research articles. Each entry of the database incorporates PubMed ID, biomarker name, biomarker type, biomolecule, source, subjects, validation status, and performance measures such as sensitivity, specificity, and hazard ratio (HR). In this study, we present ProCanBio, a manually curated database that maintains detailed data on 2053 entries of potential PCa biomarkers obtained from 412 publications in user-friendly tabular format. Among them are 766 protein-based, 507 RNA-based, 157 genomic mutations, 260 miRNA-based, and 122 metabolites-based biomarkers. To explore the information in the resource, a web-based interactive platform was developed with searching and browsing facilities. To the best of the authors' knowledge, there is no resource that can consolidate the information contained in all the published literature. Besides this, ProCanBio is freely available and is compatible with most web browsers and devices. Eventually, we anticipate this resource will be highly useful for the research community involved in the area of prostate malignancy.
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Affiliation(s)
- Dikscha Sapra
- Department of Computational Biology, Indraprastha Institute of Information Technology Delhi, New Delhi, India
| | - Harpreet Kaur
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Anjali Dhall
- Department of Computational Biology, Indraprastha Institute of Information Technology Delhi, New Delhi, India
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology Delhi, New Delhi, India
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Gliddon HD, Kaforou M, Alikian M, Habgood-Coote D, Zhou C, Oni T, Anderson ST, Brent AJ, Crampin AC, Eley B, Heyderman R, Kern F, Langford PR, Ottenhoff THM, Hibberd ML, French N, Wright VJ, Dockrell HM, Coin LJ, Wilkinson RJ, Levin M. Identification of Reduced Host Transcriptomic Signatures for Tuberculosis Disease and Digital PCR-Based Validation and Quantification. Front Immunol 2021; 12:637164. [PMID: 33763081 PMCID: PMC7982854 DOI: 10.3389/fimmu.2021.637164] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
Recently, host whole blood gene expression signatures have been identified for diagnosis of tuberculosis (TB). Absolute quantification of the concentrations of signature transcripts in blood have not been reported, but would facilitate diagnostic test development. To identify minimal transcript signatures, we applied a transcript selection procedure to microarray data from African adults comprising 536 patients with TB, other diseases (OD) and latent TB (LTBI), divided into training and test sets. Signatures were further investigated using reverse transcriptase (RT)-digital PCR (dPCR). A four-transcript signature (GBP6, TMCC1, PRDM1, and ARG1) measured using RT-dPCR distinguished TB patients from those with OD (area under the curve (AUC) 93.8% (CI95% 82.2-100%). A three-transcript signature (FCGR1A, ZNF296, and C1QB) differentiated TB from LTBI (AUC 97.3%, CI95%: 93.3-100%), regardless of HIV. These signatures have been validated across platforms and across samples offering strong, quantitative support for their use as diagnostic biomarkers for TB.
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Affiliation(s)
- Harriet D Gliddon
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom.,National Public Health Speciality Training Programme, South West, United Kingdom
| | - Myrsini Kaforou
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Mary Alikian
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom.,Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Dominic Habgood-Coote
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Chenxi Zhou
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Tolu Oni
- School of Public Health and Family Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Suzanne T Anderson
- Brighton and Sussex Medical School, Brighton, United Kingdom.,Brighton and Malawi Liverpool Wellcome Trust Unit, Blantyre, Malawi
| | - Andrew J Brent
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Amelia C Crampin
- Malawi Epidemiology and Intervention Research Unit, Chilumba, Malawi.,London School of Hygiene & Tropical Medicine, London, United Kingdom.,Karonga Prevention Study, Chilumba, Malawi
| | - Brian Eley
- Paediatric Infectious Diseases Unit, Red Cross War Memorial Children's Hospital, Cape Town, South Africa.,Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Robert Heyderman
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Florian Kern
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom.,Brighton and Sussex University Hospitals National Health Service (NHS) Trust, Brighton, United Kingdom
| | - Paul R Langford
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Neil French
- Tropical and Infectious Disease Unit, Royal Liverpool and Broadgreen University Hospitals National Health Service (NHS) Trust, Liverpool, United Kingdom.,Centre for Global Vaccine Research, Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Victoria J Wright
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Hazel M Dockrell
- Department of Immunology and Infection, and Tuberculosis (TB) Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lachlan J Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Robert J Wilkinson
- The Francis Crick Institute, London, United Kingdom.,Department of Medicine, Imperial College London, London, United Kingdom.,Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Michael Levin
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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12
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Chao-yang G, Rong T, Yong-qiang S, Tai-cong L, Kai-sheng Z, Wei N, Hai-hong Z. Prognostic Signatures of Metabolic Genes and Metabolism-Related Long Non-coding RNAs Accurately Predict Overall Survival for Osteosarcoma Patients. Front Cell Dev Biol 2021; 9:644220. [PMID: 33708772 PMCID: PMC7940372 DOI: 10.3389/fcell.2021.644220] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
In this study, we identified eight survival-related metabolic genes in differentially expressed metabolic genes by univariate Cox regression analysis based on the therapeutically applicable research to generate effective treatments (n = 84) data set and genotype tissue expression data set (n = 396). We also constructed a six metabolic gene signature to predict the overall survival of osteosarcoma (OS) patients using least absolute shrinkage and selection operator (Lasso) Cox regression analysis. Our results show that the six metabolic gene signature showed good performance in predicting survival of OS patients and was also an independent prognostic factor. Stratified correlation analysis showed that the metabolic gene signature accurately predicted survival outcomes in high-risk and low-risk OS patients. The six metabolic gene signature was also verified to perform well in predicting survival of OS patients in an independent cohort (GSE21257). Then, using univariate Cox regression and Lasso Cox regression analyses, we identified an eight metabolism-related long noncoding RNA (lncRNA) signature that accurately predicts overall survival of OS patients. Gene set variation analysis showed that the apical surface and bile acid metabolism, epithelial mesenchymal transition, and P53 pathway were activated in the high-risk group based on the eight metabolism-related lncRNA signature. Furthermore, we constructed a competing endogenous RNA (ceRNA) network and conducted immunization score analysis based on the eight metabolism-related lncRNA signature. These results showed that the six metabolic gene signature and eight metabolism-related lncRNA signature have good performance in predicting the survival outcomes of OS patients.
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Affiliation(s)
- Gong Chao-yang
- Lanzhou University Second Hospital, Lanzhou, China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, China
| | - Tang Rong
- Department of Anesthesiology, Lanzhou University Second Hospital, Lanzhou, China
| | - Shi Yong-qiang
- Lanzhou University Second Hospital, Lanzhou, China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, China
| | - Liu Tai-cong
- Lanzhou University Second Hospital, Lanzhou, China
- Orthopaedics Key Laboratory of Gansu Province, Lanzhou, China
| | | | - Nan Wei
- Lanzhou University Second Hospital, Lanzhou, China
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13
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Doultsinos D, Mills IG. Derivation and Application of Molecular Signatures to Prostate Cancer: Opportunities and Challenges. Cancers (Basel) 2021; 13:495. [PMID: 33525365 PMCID: PMC7865812 DOI: 10.3390/cancers13030495] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/15/2022] Open
Abstract
Prostate cancer is a high-incidence cancer that requires improved patient stratification to ensure accurate predictions of risk and treatment response. Due to the significant contributions of transcription factors and epigenetic regulators to prostate cancer progression, there has been considerable progress made in developing gene signatures that may achieve this. Some of these are aligned to activities of key drivers such as the androgen receptor, whilst others are more agnostic. In this review, we present an overview of these signatures, the strategies for their derivation, and future perspectives on their continued development and evolution.
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Affiliation(s)
- Dimitrios Doultsinos
- Nuffield Department of Surgical Sciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK;
| | - Ian G. Mills
- Nuffield Department of Surgical Sciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK;
- Patrick G Johnston Centre for Cancer Research, Queen’s University of Belfast, Belfast BT9 7AE, UK
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14
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Abou Khouzam R, Brodaczewska K, Filipiak A, Zeinelabdin NA, Buart S, Szczylik C, Kieda C, Chouaib S. Tumor Hypoxia Regulates Immune Escape/Invasion: Influence on Angiogenesis and Potential Impact of Hypoxic Biomarkers on Cancer Therapies. Front Immunol 2021; 11:613114. [PMID: 33552076 PMCID: PMC7854546 DOI: 10.3389/fimmu.2020.613114] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/30/2020] [Indexed: 01/19/2023] Open
Abstract
The environmental and metabolic pressures in the tumor microenvironment (TME) play a key role in molding tumor development by impacting the stromal and immune cell fractions, TME composition and activation. Hypoxia triggers a cascade of events that promote tumor growth, enhance resistance to the anti-tumor immune response and instigate tumor angiogenesis. During growth, the developing angiogenesis is pathological and gives rise to a haphazardly shaped and leaky tumor vasculature with abnormal properties. Accordingly, aberrantly vascularized TME induces immunosuppression and maintains a continuous hypoxic state. Normalizing the tumor vasculature to restore its vascular integrity, should hence enhance tumor perfusion, relieving hypoxia, and reshaping anti-tumor immunity. Emerging vascular normalization strategies have a great potential in achieving a stable normalization, resulting in mature and functional blood vessels that alleviate tumor hypoxia. Biomarkers enabling the detection and monitoring of tumor hypoxia could be highly advantageous in aiding the translation of novel normalization strategies to clinical application, alone, or in combination with other treatment modalities, such as immunotherapy.
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Affiliation(s)
- Raefa Abou Khouzam
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Klaudia Brodaczewska
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, Warsaw, Poland
| | - Aleksandra Filipiak
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Nagwa Ahmed Zeinelabdin
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Stephanie Buart
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, Faulty. De médecine Univ. Paris-Sud, University Paris-Saclay, Villejuif, France
| | - Cezary Szczylik
- Centre of Postgraduate Medical Education, Department of Oncology, European Health Centre, Otwock, Warsaw, Poland
| | - Claudine Kieda
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, Warsaw, Poland.,Centre for Molecular Biophysics, UPR CNRS 4301, Orléans, France
| | - Salem Chouaib
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates.,INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, EPHE, Faulty. De médecine Univ. Paris-Sud, University Paris-Saclay, Villejuif, France
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15
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Leboyer M, Godin O, Terro E, Boukouaci W, Lu CL, Andre M, Aouizerate B, Berna F, Barau C, Capdevielle D, Clauss-Kobayashi J, Chereau I, D Amato T, Dubertret C, Dubreucq J, Fond G, Laouamri H, Leignier S, Lancon C, Llorca PM, Mallet J, Le Corvoisier P, Misdrahi D, Passerieux C, Rey R, Pignon B, Urbach M, Szoke A, Schürhoff F, Tamouza R. Immune Signatures of Treatment-Resistant Schizophrenia: A FondaMental Academic Centers of Expertise for Schizophrenia (FACE-SZ) Study. Schizophr Bull Open 2021; 2:sgab012. [PMID: 34901861 PMCID: PMC8650073 DOI: 10.1093/schizbullopen/sgab012] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Treatment-resistant schizophrenia (TRS) affects around 30% of patients with schizophrenia (SZ) resulting in poor functioning, relapses, and reduced quality of life. Convergent findings show that inflammation could contribute to resistance. We thus search for immune signatures of patients with TRS/ultra TRS (UTRS) in a sample of community-dwelling outpatients with SZ. In total, 195 stabilized SZ patients (mean age = 31.2 years, 73% male gender) were consecutively included in the network of the FondaMental Expert Centers for Schizophrenia in France and received a thorough clinical assessment. At inclusion, psychotic symptomatology was evaluated by the Positive and Negative Syndrome Scale (PANSS) for schizophrenia. Circulating serum/plasma levels of a large panel of markers reflecting the main inflammatory pathways were evaluated. TRS was defined by current treatment by clozapine (CLZ) and UTRS by current CLZ treatment + PANSS total score ≥ 70. The frequency of TRS and UTRS patients was, respectively, 20% and 7.7% and was defined using multivariable analysis elevated by high levels of interleukin (IL)-12/IL-23p40, IL-17A, IL-10, and beta 2 microglobulin (B2M) and IL-12/IL-23p40, IL-17A, IL-6, IL-10, IFNγ, and B2M, respectively. These observations suggest that resistance and ultra resistance to CLZ treatment are underpinned by pro-inflammatory molecules mainly belonging to the T helper 17 pathway, a finding making sense given the interplay between inflammation and antipsychotic treatment responses. If confirmed, our findings may allow us to consider IL-23/IL-17 pathway as a therapeutic target for patients with resistance to antipsychotics.
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Affiliation(s)
- Marion Leboyer
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, DMU IMPACT, Fondation FondaMental, F-94010, Créteil, France.,AP-HP, Hôpitaux Universitaires Henri Mondor, Département Médico-Universitaire de Psychiatrie et d'Addictologie (DMU IMPACT), Fédération Hospitalo-Universitaire de Médecine de Précision en Psychiatrie (FHU ADAPT) F-94010, France.,Fondation FondaMental, Créteil, France
| | - Ophélia Godin
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, DMU IMPACT, Fondation FondaMental, F-94010, Créteil, France.,Fondation FondaMental, Créteil, France
| | | | - Wahid Boukouaci
- AP-HP, Hôpitaux Universitaires Henri Mondor, Département Médico-Universitaire de Psychiatrie et d'Addictologie (DMU IMPACT), Fédération Hospitalo-Universitaire de Médecine de Précision en Psychiatrie (FHU ADAPT) F-94010, France.,Fondation FondaMental, Créteil, France
| | - Ching-Lieng Lu
- AP-HP, Hôpitaux Universitaires Henri Mondor, Département Médico-Universitaire de Psychiatrie et d'Addictologie (DMU IMPACT), Fédération Hospitalo-Universitaire de Médecine de Précision en Psychiatrie (FHU ADAPT) F-94010, France.,Fondation FondaMental, Créteil, France
| | - Myrtille Andre
- Fondation FondaMental, Créteil, France.,Service Universitaire de Psychiatrie Adulte, Hôpital la Colombière, CHRU Montpellier, Université Montpellier 1, INSERM 1061, Montpellier, France
| | - Bruno Aouizerate
- Fondation FondaMental, Créteil, France.,Centre Hospitalier Charles Perrens, Université de Bordeaux, Bordeaux F-33076, France.,INRAE, NutriNeuro, University of Bordeaux, U1286, Bordeaux F-33076, France
| | - Fabrice Berna
- Fondation FondaMental, Créteil, France.,Hôpitaux Universitaires de Strasbourg, Université de Strasbourg, INSERM U1114, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Caroline Barau
- INSERM, Centre Investigation Clinique 1430, AP-HP, Hôpitaux Universitaires Henri Mondor, Université Paris Est Créteil, F94010 Créteil, France
| | - Delphine Capdevielle
- Fondation FondaMental, Créteil, France.,Service Universitaire de Psychiatrie Adulte, Hôpital la Colombière, CHRU Montpellier, Université Montpellier 1, INSERM 1061, Montpellier, France
| | - Julie Clauss-Kobayashi
- Fondation FondaMental, Créteil, France.,Hôpitaux Universitaires de Strasbourg, Université de Strasbourg, INSERM U1114, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Isabelle Chereau
- Fondation FondaMental, Créteil, France.,CHU Clermont-Ferrand, Department of Psychiatry, University of Clermont Auvergne, EA 7280, Clermont-Ferrand, France
| | - Thierry D Amato
- INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, Université Claude Bernard Lyon 1, Equipe PSYR2, Centre Hospitalier Le Vinatier, Pole Est, Bron, France
| | - Caroline Dubertret
- Fondation FondaMental, Créteil, France.,Université de Paris, INSERM UMR1266, AP-HP, Groupe Hospitalo-Universitaire AP-HP Nord, Service de Psychiatrie et Addictologie. Hôpital Louis Mourier, Colombes, France
| | - Julien Dubreucq
- Fondation FondaMental, Créteil, France.,Centre Référent de Réhabilitation Psychosociale et de Remédiation Cognitive (C3R), CH Alpes Isère, France
| | - Guillaume Fond
- Fondation FondaMental, Créteil, France.,AP-HM, Aix-Marseille Univ, School of medicine - La Timone Medical Campus, EA 3279: CEReSS - Health Service Research and Quality of Life Center, 13005 Marseille, France
| | | | - Sylvain Leignier
- Fondation FondaMental, Créteil, France.,Centre Référent de Réhabilitation Psychosociale et de Remédiation Cognitive (C3R), CH Alpes Isère, France
| | - Christophe Lancon
- Fondation FondaMental, Créteil, France.,AP-HM, Aix-Marseille Univ, School of medicine - La Timone Medical Campus, EA 3279: CEReSS - Health Service Research and Quality of Life Center, 13005 Marseille, France
| | - Pierre-Michel Llorca
- Fondation FondaMental, Créteil, France.,CHU Clermont-Ferrand, Department of Psychiatry, University of Clermont Auvergne, EA 7280, Clermont-Ferrand, France
| | - Jasmina Mallet
- Fondation FondaMental, Créteil, France.,Université de Paris, INSERM UMR1266, AP-HP, Groupe Hospitalo-Universitaire AP-HP Nord, Service de Psychiatrie et Addictologie. Hôpital Louis Mourier, Colombes, France
| | - Philippe Le Corvoisier
- INSERM, Centre Investigation Clinique 1430, AP-HP, Hôpitaux Universitaires Henri Mondor, Université Paris Est Créteil, F94010 Créteil, France
| | - David Misdrahi
- Fondation FondaMental, Créteil, France.,Department of Adult Psychiatry, Charles Perrens Hospital, University of Bordeaux, CNRS UMR 5287-INCIA "Neuroimagerie et cognition humaine," Bordeaux, France
| | - Christine Passerieux
- Fondation FondaMental, Créteil, France.,Service Universitaire de psychiatrie et d'addictologie du Centre Hospitalier de Versailles, INSERM UMR1018, CESP, Team "DevPsy," Université de Versailles Saint-Quentin-en-Yvelines, Paris - Saclay, France
| | - Romain Rey
- Fondation FondaMental, Créteil, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, Université Claude Bernard Lyon 1, Equipe PSYR2, Centre Hospitalier Le Vinatier, Pole Est, Bron, France
| | - Baptiste Pignon
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, DMU IMPACT, Fondation FondaMental, F-94010, Créteil, France.,AP-HP, Hôpitaux Universitaires Henri Mondor, Département Médico-Universitaire de Psychiatrie et d'Addictologie (DMU IMPACT), Fédération Hospitalo-Universitaire de Médecine de Précision en Psychiatrie (FHU ADAPT) F-94010, France.,Fondation FondaMental, Créteil, France
| | - Mathieu Urbach
- Fondation FondaMental, Créteil, France.,Service Universitaire de psychiatrie et d'addictologie du Centre Hospitalier de Versailles, INSERM UMR1018, CESP, Team "DevPsy," Université de Versailles Saint-Quentin-en-Yvelines, Paris - Saclay, France
| | - Andrei Szoke
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, DMU IMPACT, Fondation FondaMental, F-94010, Créteil, France.,AP-HP, Hôpitaux Universitaires Henri Mondor, Département Médico-Universitaire de Psychiatrie et d'Addictologie (DMU IMPACT), Fédération Hospitalo-Universitaire de Médecine de Précision en Psychiatrie (FHU ADAPT) F-94010, France.,Fondation FondaMental, Créteil, France
| | - Franck Schürhoff
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, DMU IMPACT, Fondation FondaMental, F-94010, Créteil, France.,AP-HP, Hôpitaux Universitaires Henri Mondor, Département Médico-Universitaire de Psychiatrie et d'Addictologie (DMU IMPACT), Fédération Hospitalo-Universitaire de Médecine de Précision en Psychiatrie (FHU ADAPT) F-94010, France.,Fondation FondaMental, Créteil, France
| | - Ryad Tamouza
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, DMU IMPACT, Fondation FondaMental, F-94010, Créteil, France.,AP-HP, Hôpitaux Universitaires Henri Mondor, Département Médico-Universitaire de Psychiatrie et d'Addictologie (DMU IMPACT), Fédération Hospitalo-Universitaire de Médecine de Précision en Psychiatrie (FHU ADAPT) F-94010, France.,Fondation FondaMental, Créteil, France
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16
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Zhang Y, Wang Y, Li C, Jiang T. Systemic Analysis of the Prognosis-Associated Alternative Polyadenylation Events in Breast Cancer. Front Genet 2020; 11:590770. [PMID: 33329736 PMCID: PMC7673440 DOI: 10.3389/fgene.2020.590770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/08/2020] [Indexed: 01/22/2023] Open
Abstract
Alternative polyadenylation (APA) is a post-translational modification that occurs during mRNA maturation in humans. Studies suggested that abnormal APA events are associated with the genesis and progression of malignant tumors. Here, we aimed to comprehensively evaluate the prognostic value of APA events involved in breast cancer (BC). Both APA events and clinical information for BC patients were downloaded from The Cancer Genome Atlas (TCGA) database to identify prognosis-related APA events in BC. A total of 462 APA events and 374 APA events were shown to be significantly related to overall survival (OS) and relapse-free survival (RFS), respectively, of BC patients. The TCGA set was randomly divided into a training and a test set. Key prognosis-related APA events were selected by LASSO regression to build prediction signatures for OS and RFS by multivariate Cox regression analysis in the training, test, and whole set. BC patients were stratified into high-risk and low-risk groups based on median risk scores. Kaplan–Meier survival analysis demonstrated that low-risk groups had better OS and RFS than high-risk groups in all three sets. The time-dependent receiver operating characteristic (ROC) curves showed that our signatures had a good predictive ability for survival and recurrence for BC patients in all three sets. The independent prognostic indicators-based nomogram model had excellent performance and considerable net benefit for predicting the OS and RFS in BC. A PPI network was constructed between key prognosis and core regulators associated with APA, consisting of 48 nodes and 244 edges. Functional enrichment analysis also revealed their association with RNA processing and RNA synthesis. Collectively, our data indicate that prognostic signatures based on APA events may be powerful prognostic predictors for OS and RFS in BC.
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Affiliation(s)
- Yi Zhang
- Department of Blood Transfusion, People's Hospital of Deyang City, Deyang, China
| | - Yuzhi Wang
- Department of Laboratory Medicine, People's Hospital of Deyang City, Deyang, China
| | - Chengwen Li
- School of Basic Medical Science, Southwest Medical University, Luzhou, China
| | - Tianhua Jiang
- Department of Blood Transfusion, People's Hospital of Deyang City, Deyang, China
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17
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Abstract
Forged signature threatens the authenticity of personal identity. Here, an effective SERS anti-counterfeiting system is designed for personal signatures. Mixed ligands improve the complexity of Raman spectra and expand the coding capacity. Fourteen distinct combinations are created from mere five ligands, and great expansion is possible with modest expansion of the ligand library. On the other hand, the (Au-aggregate)@Ag@PSPAA nanostructure significantly increases the surface-enhanced Raman scattering (SERS) intensity and stability so that excellent performance is achieved in SERS detection. By integrating these strategies, SERS inks are produced and applied in signature anti-counterfeiting. The resulting spectra are converted to barcodes that are readily detected through a smart phone APP. With these improvements, this work brings SERS one step closer toward practical applications in signature anti-counterfeiting.
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Affiliation(s)
- Yusai Zhou
- Institute of Advanced Synthesis and School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, Jiangsu, P. R. China
| | - Gui Zhao
- Institute of Advanced Synthesis and School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, Jiangsu, P. R. China
| | - Jingming Bian
- Institute of Advanced Synthesis and School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, Jiangsu, P. R. China
| | - Xiaoli Tian
- Institute of Advanced Synthesis and School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, Jiangsu, P. R. China
| | - Xuejun Cheng
- Institute of Advanced Synthesis and School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, Jiangsu, P. R. China
| | - Hong Wang
- Institute of Advanced Synthesis and School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, Jiangsu, P. R. China
| | - Hongyu Chen
- Institute of Advanced Synthesis and School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, Jiangsu, P. R. China
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18
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Zheng M, Hu Y, Gou R, Liu O, Nie X, Li X, Liu Q, Hao Y, Liu J, Lin B. Identification of immune-enhanced molecular subtype associated with BRCA1 mutations, immune checkpoints and clinical outcome in ovarian carcinoma. J Cell Mol Med 2020; 24:2819-2831. [PMID: 31995855 PMCID: PMC7077593 DOI: 10.1111/jcmm.14830] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/26/2019] [Accepted: 11/06/2019] [Indexed: 12/15/2022] Open
Abstract
Ovarian carcinoma has the highest mortality among the malignant tumours in gynaecology, and new treatment strategies are urgently needed to improve the clinical status of ovarian carcinoma patients. The Cancer Genome Atlas (TCGA) cohort were performed to explore the immune function of the internal environment of tumours and its clinical correlation with ovarian carcinoma. Finally, four molecular subtypes were obtained based on the global immune‐related genes. The correlation analysis and clinical characteristics showed that four subtypes were all significantly related to clinical stage; the immune scoring results indicated that most immune signatures were upregulated in C3 subtype, and the majority of tumour‐infiltrating immune cells were upregulated in both C3 and C4 subtypes. Compared with other subtypes, C3 subtype had a higher BRCA1 mutation, higher expression of immune checkpoints, and optimal survival prognosis. These findings of the immunological microenvironment in tumours may provide new ideas for developing immunotherapeutic strategies for ovarian carcinoma.
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Affiliation(s)
- Mingjun Zheng
- Department of Gynaecology and Obstetrics, Shengjing Hospital Affiliated to China Medical University, Shenyang, China.,Key Laboratory Of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China.,Department of Obstetrics and Gynecology, University Hospital, LMU Munich, Munich, Germany
| | - Yuexin Hu
- Department of Gynaecology and Obstetrics, Shengjing Hospital Affiliated to China Medical University, Shenyang, China.,Key Laboratory Of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Rui Gou
- Department of Gynaecology and Obstetrics, Shengjing Hospital Affiliated to China Medical University, Shenyang, China.,Key Laboratory Of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Ouxuan Liu
- Department of Gynaecology and Obstetrics, Shengjing Hospital Affiliated to China Medical University, Shenyang, China.,Key Laboratory Of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Xin Nie
- Department of Gynaecology and Obstetrics, Shengjing Hospital Affiliated to China Medical University, Shenyang, China.,Key Laboratory Of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Xiao Li
- Department of Gynaecology and Obstetrics, Shengjing Hospital Affiliated to China Medical University, Shenyang, China.,Key Laboratory Of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Qing Liu
- Department of Gynaecology and Obstetrics, Shengjing Hospital Affiliated to China Medical University, Shenyang, China.,Key Laboratory Of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Yingying Hao
- Department of Gynaecology and Obstetrics, Shengjing Hospital Affiliated to China Medical University, Shenyang, China.,Key Laboratory Of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Juanjuan Liu
- Department of Gynaecology and Obstetrics, Shengjing Hospital Affiliated to China Medical University, Shenyang, China.,Key Laboratory Of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Bei Lin
- Department of Gynaecology and Obstetrics, Shengjing Hospital Affiliated to China Medical University, Shenyang, China.,Key Laboratory Of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
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19
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Massmann C. Identification of factors influencing hydrologic model performance using a top-down approach in a large number of U.S. catchments. Hydrol Process 2020; 34:4-20. [PMID: 32001949 PMCID: PMC6973287 DOI: 10.1002/hyp.13566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/24/2019] [Indexed: 06/10/2023]
Abstract
Investigating the performance that can be achieved with different hydrological models across catchments with varying characteristics is a requirement for identifying an adequate model for any catchment, gauged or ungauged, just based on information about its climate and catchment properties. As parameter uncertainty increases with the number of model parameters, it is important not only to identify a model achieving good results but also to aim at the simplest model still able to provide acceptable results. The main objective of this study is to identify the climate and catchment properties determining the minimal required complexity of a hydrological model. As previous studies indicate that the required model complexity varies with the temporal scale, the study considers the performance at the daily, monthly, and annual timescales. In agreement with previous studies, the results show that catchments located in arid areas tend to be more difficult to model. They therefore require more complex models for achieving an acceptable performance. For determining which other factors influence model performance, an analysis was carried out for four catchment groups (snowy, arid, and eastern and western catchments). The results show that the baseflow and aridity indices are the most consistent predictors of model performance across catchment groups and timescales. Both properties are negatively correlated with model performance. Other relevant predictors are the fraction of snow in the annual precipitation (negative correlation with model performance), soil depth (negative correlation with model performance), and some other soil properties. It was observed that the sign of the correlation between the catchment characteristics and model performance varies between clusters in some cases, stressing the difficulties encountered in large sample analyses. Regarding the impact of the timescale, the study confirmed previous results indicating that more complex models are needed for shorter timescales.
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Affiliation(s)
- Carolina Massmann
- Institute for Hydrology and Water Management (HyWa)University of Natural Resources and Life SciencesViennaAustria
- Department of Civil EngineeringUniversity of BristolBristolUK
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20
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Cooper DJ, Schürer S. Improving the Utility of the Tox21 Dataset by Deep Metadata Annotations and Constructing Reusable Benchmarked Chemical Reference Signatures. Molecules 2019; 24:E1604. [PMID: 31018579 DOI: 10.3390/molecules24081604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 02/03/2023] Open
Abstract
The Toxicology in the 21st Century (Tox21) project seeks to develop and test methods for high-throughput examination of the effect certain chemical compounds have on biological systems. Although primary and toxicity assay data were readily available for multiple reporter gene modified cell lines, extensive annotation and curation was required to improve these datasets with respect to how FAIR (Findable, Accessible, Interoperable, and Reusable) they are. In this study, we fully annotated the Tox21 published data with relevant and accepted controlled vocabularies. After removing unreliable data points, we aggregated the results and created three sets of signatures reflecting activity in the reporter gene assays, cytotoxicity, and selective reporter gene activity, respectively. We benchmarked these signatures using the chemical structures of the tested compounds and obtained generally high receiver operating characteristic (ROC) scores, suggesting good quality and utility of these signatures and the underlying data. We analyzed the results to identify promiscuous individual compounds and chemotypes for the three signature categories and interpreted the results to illustrate the utility and re-usability of the datasets. With this study, we aimed to demonstrate the importance of data standards in reporting screening results and high-quality annotations to enable re-use and interpretation of these data. To improve the data with respect to all FAIR criteria, all assay annotations, cleaned and aggregate datasets, and signatures were made available as standardized dataset packages (Aggregated Tox21 bioactivity data, 2019).
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21
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Seborova K, Vaclavikova R, Soucek P, Elsnerova K, Bartakova A, Cernaj P, Bouda J, Rob L, Hruda M, Dvorak P. Association of ABC gene profiles with time to progression and resistance in ovarian cancer revealed by bioinformatics analyses. Cancer Med 2019; 8:606-616. [PMID: 30672151 PMCID: PMC6382717 DOI: 10.1002/cam4.1964] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/07/2018] [Accepted: 12/18/2018] [Indexed: 12/31/2022] Open
Abstract
Introduction Ovarian cancer (OC) represents a serious disease with high mortality and lack of efficient predictive and prognostic biomarkers. ATP‐binding cassette (ABC) proteins constitute a large family dedicated to active transmembrane transport including transport of xenobiotics. Materials and methods mRNA level was measured by quantitative RT‐PCR in tumor tissues from OC patients. Bioinformatics analyses were applied to two gene expression datasets (60 primary tumors and 29 peritoneal metastases). Two different approaches of expression data normalization were applied in parallel, and their results were compared. Data from publically available cancer datasets were checked to further validate our conclusions. Results The results showed significant connections between ABC gene expression profiles and time to progression (TTP), chemotherapy resistance, and metastatic progression in OC. Two consensus ABC gene profiles with clinical meaning were documented. (a) Downregulation of ABCC4, ABCC10, ABCD3, ABCE1, ABCF1, ABCF2, and ABCF3 was connected with the best sensitivity to chemotherapy and TTP. (b) Oppositely, downregulation of ABCB11 and upregulation of ABCB1 and ABCG2 were connected with the worst sensitivity to chemotherapy and TTP. Results from publicly available online databases supported our conclusions. Conclusion This study stressed the connection between two well‐documented ABC genes and clinicopathological features—ABCB1 and ABCG2. Moreover, we showed a comparable connection also for several other ABC genes—ABCB11, ABCC4, ABCC10, ABCD3,ABCE1, ABCF1, ABCF2, and ABCF3. Our results add new clinically relevant information to this oncology field and can stimulate further exploration.
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Affiliation(s)
- Karolina Seborova
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic.,Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Radka Vaclavikova
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic.,Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Pavel Soucek
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic.,Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Katerina Elsnerova
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic.,Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Alena Bartakova
- Department of Gynecology and Obstetrics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Petr Cernaj
- Department of Gynecology and Obstetrics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Jiri Bouda
- Department of Gynecology and Obstetrics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Lukas Rob
- Department of Gynecology and Obstetrics, Third Faculty of Medicine and Faculty Hospital Kralovske Vinohrady, Charles University, Prague, Czech Republic
| | - Martin Hruda
- Department of Gynecology and Obstetrics, Third Faculty of Medicine and Faculty Hospital Kralovske Vinohrady, Charles University, Prague, Czech Republic
| | - Pavel Dvorak
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Department of Biology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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22
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Cafiso V, Stracquadanio S, Lo Verde F, Gabriele G, Mezzatesta ML, Caio C, Pigola G, Ferro A, Stefani S. Colistin Resistant A. baumannii: Genomic and Transcriptomic Traits Acquired Under Colistin Therapy. Front Microbiol 2019; 9:3195. [PMID: 30666237 PMCID: PMC6330354 DOI: 10.3389/fmicb.2018.03195] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/10/2018] [Indexed: 12/31/2022] Open
Abstract
Even though colistin-based treatment represents the antimicrobial-regimen backbone for the management of multidrug-resistant Gram-negative infections, colistin resistance is still rare, at least as a full resistance, in Acinetobacter baumannii (Ab). We investigated the genomics and transcriptomics of two clinical Extensively Drug Resistance (XDR) colistin-susceptible/resistant (COL-S/R) Ab strain-pairs in which COL-resistance was developed after exposure to colistin therapy. The molecular characterization of the strains showed that all strains belonged to PFGE-A, ST-281, OXA-23 producers, Global Clone-II, and were resistant to imipenem, meropenem, ampicillin/sulbactam, ciprofloxacin, gentamicin, amikacin, trimethoprim/sulfamethoxazole, and susceptible to tigecycline, in agreement with NGS-acquired resistome. COL-R vs. COL-S Ab comparative genomics, mapping on Ab ATCC 17978 and Ab ACICU Reference Genomes, revealed a closely related genomic phylogeny, especially between strain-pair isolates, and distinctive common genomic non-synonymous SNPs (nsSNPs) in COL-R Ab strains. Furthermore, pmrB and pmrC nsSNPs were found. Notably we recovered, for the first time, lpxC and lpxD nsSNPs previously described only in "in-vitro" mutants and associated with colistin resistance in a clinical COL-R Ab. COL-R vs. COL-S Ab comparative transcriptomics evidenced a strain-dependent response to the colistin resistance onset highly variable among the single COL-R strains vs. their COL-S parents and merely seven common over-expressed transcripts, i.e. the PgaB lipoprotein for biofilm-matrix production, the diacylglycerol kinase for the lipid recycling in the membrane-derived oligosaccharide cycle, a membrane non-ribosomal peptide synthetase, the Lipid A phosphoethanol aminotransferase PmrC, and three hypothetical proteins. The transcript analysis of the "COL-R related genes" and the RNA-seq data confirmed pmrCAB over-expression responsible for a greater positive net cell-charge, and lpxACD under-expression in COL-R causing a decreased LPS production, as main mechanisms of colistin resistance. Our study reports the COL-R Ab genomic and transcriptomic signatures reflecting the interplay between several direct and indirect potential adaptations to antimicrobial pressure, including the occurrence of SNP accumulation hotspot loci in genes related to intrinsic or adaptive colistin resistance, surface adhesion proteins and porins, and over-expressed genes involved in different pathways, i.e. biofilm production, oxidative stress response, extensive drug and COL resistance.
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Affiliation(s)
- Viviana Cafiso
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Stefano Stracquadanio
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Flavia Lo Verde
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Giacoma Gabriele
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Maria Lina Mezzatesta
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Carla Caio
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Giuseppe Pigola
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
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23
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Krishnan G, Hofmann H. Adapting the Chumbley Score to Match Striae on Land Engraved Areas (LEAs) of Bullets. J Forensic Sci 2018; 64:728-740. [PMID: 30444940 DOI: 10.1111/1556-4029.13950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/08/2018] [Accepted: 10/18/2018] [Indexed: 11/28/2022]
Abstract
The same-source problem remains a major challenge in forensic toolmark and firearm examination. Here, we investigate the applicability of the Chumbley method (J Forensic Sci, 2018, 63, 849; J Forensic Sci, 2010, 55, 953) (10,12), developed for screwdriver markings, for same-source identification of striations on bullet LEAs. The Hamby datasets 44 and 252 measured by NIST and CSAFE (high-resolution scans) are used here. We provide methods to identify parameters that minimize error rates for matching of LEAs, and a remedial algorithm to alleviate the problem of failed tests, while increasing the power of the test and reducing error rates. For 85,491 land-to-land comparisons (84,235 known nonmatches and 1256 known matches), the adapted test does not provide a result in 176 situations (originally more than 500). The Type I and Type II error rates are 7.2% (6105 out of 84,235) and 21.4% (271 out of 1256), respectively. This puts the proposed method on similar footing as other single-feature matching approaches in the literature.
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Affiliation(s)
- Ganesh Krishnan
- Department of Statistics, Iowa State University and CSAFE (Center for Statistics and Applications in Forensic Evidence), Iowa State University, 195 Durham, 613 Morril Road, Ames, IA, 50010, United States
| | - Heike Hofmann
- Department of Statistics, Iowa State University and CSAFE (Center for Statistics and Applications in Forensic Evidence), Iowa State University, 195 Durham, 613 Morril Road, Ames, IA, 50010, United States
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24
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Bagwell CE, Noble PA, Milliken CE, Li D, Kaplan DI. Amplicon Sequencing Reveals Microbiological Signatures in Spent Nuclear Fuel Storage Basins. Front Microbiol 2018; 9:377. [PMID: 29593667 PMCID: PMC5854691 DOI: 10.3389/fmicb.2018.00377] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/19/2018] [Indexed: 11/18/2022] Open
Abstract
Water quality is an important determinant for the structural integrity of alloy cladded fuels and assemblies during long-term wet storage. Detailed characterization of a water filled storage basin for spent nuclear reactor fuel was performed following the formation and proliferation of an amorphous white flocculent. White precipitant was sampled throughout the storage basin for chemical and spectroscopic characterization, and environmental DNA was extracted for 454 pyrosequencing of bacterial 16S rRNA gene diversity. Accordingly, spectroscopic analyses indicated the precipitant to be primarily amorphous to crystalline aluminum (oxy) hydroxides with minor associated elemental components including Fe, Si, Ti, and U. High levels of organic carbon were co-localized with the precipitant relative to bulk dissolved organic concentrations. Bacterial densities were highly variable between sampling locations and with depth within the water filled storage basin; cell numbers ranged from 4 × 103to 4 × 104 cells/mL. Bacterial diversity that was physically associated with the aluminum (oxy) hydroxide complexes exceeded an estimated 4,000 OTUs/amplicon library (3% cutoff) and the majority of sequences were aligned to the families Burkholderiaceae (23%), Nitrospiraceae (23%), Hyphomicrobiaceae (17%), and Comamonadaceae (6%). We surmise that episodic changes in the physical and chemical properties of the basin contribute to the polymerization of aluminum (oxy) hydroxides, which in turn can chemisorb nutrients, carbon ligands and bacterial cells from the surrounding bulk aqueous phase. As such, these precipitants should establish favorable microhabitats for bacterial colonization and growth. Comparative analyses of 16S rRNA gene amplicon libraries across a selection of natural and engineered aquatic ecosystems were performed and microbial community and taxonomic signatures unique to the spent nuclear fuel (SNF) storage basin environment were revealed. These insights could spur the development of tractable bio-indicators that are specific of and diagnostic for water quality at discrete locations and finer scales of resolution, marking an important contribution for improved water quality and management of SNF storage facilities.
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Affiliation(s)
- Christopher E Bagwell
- Earth Systems Science Division, Pacific Northwest National Laboratory, United States Department of Energy, Richland, WA, United States
| | - Peter A Noble
- Department of Periodontics, University of Washington, Seattle, WA, United States
| | - Charles E Milliken
- Environmental Sciences and Biotechnology, Savannah River National Laboratory, United States Department of Energy, Aiken, SC, United States
| | - Dien Li
- Environmental Sciences and Biotechnology, Savannah River National Laboratory, United States Department of Energy, Aiken, SC, United States
| | - Daniel I Kaplan
- Environmental Sciences and Biotechnology, Savannah River National Laboratory, United States Department of Energy, Aiken, SC, United States
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25
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Modelska A, Quattrone A, Re A. Molecular portraits: the evolution of the concept of transcriptome-based cancer signatures. Brief Bioinform 2015; 16:1000-7. [PMID: 25832647 PMCID: PMC4652618 DOI: 10.1093/bib/bbv013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Indexed: 12/13/2022] Open
Abstract
Cancer results from dysregulation of multiple steps of gene expression programs. We review how transcriptome profiling has been widely explored for cancer classification and biomarker discovery but resulted in limited clinical impact. Therefore, we discuss alternative and complementary omics approaches.
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26
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Abstract
Although it has been >30 years since the eradication of smallpox, the unearthing of well-preserved tissue material in which the virus may reside has called into question the viability of variola virus decades or centuries after its original occurrence. Experimental data to address the long-term stability and viability of the virus are limited. There are several instances of well-preserved corpses and tissues that have been examined for poxvirus viability and viral DNA. These historical specimens cause concern for potential exposures, and each situation should be approached cautiously and independently with the available information. Nevertheless, these specimens provide information on the history of a major disease and vaccination against it.
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27
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McCollum AM, Li Y, Wilkins K, Karem KL, Davidson WB, Paddock CD, Reynolds MG, Damon IK. Poxvirus viability and signatures in historical relics. Emerg Infect Dis 2014; 20:177-84. [PMID: 24447382 DOI: 10.3201/eid2002/131098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Although it has been >30 years since the eradication of smallpox, the unearthing of well-preserved tissue material in which the virus may reside has called into question the viability of variola virus decades or centuries after its original occurrence. Experimental data to address the long-term stability and viability of the virus are limited. There are several instances of well-preserved corpses and tissues that have been examined for poxvirus viability and viral DNA. These historical specimens cause concern for potential exposures, and each situation should be approached cautiously and independently with the available information. Nevertheless, these specimens provide information on the history of a major disease and vaccination against it.
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28
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Caligiuri MP, Kim C, Landy KM. Kinematics of signature writing in healthy aging. J Forensic Sci 2014; 59:1020-4. [PMID: 24673648 DOI: 10.1111/1556-4029.12437] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 05/19/2013] [Accepted: 06/08/2013] [Indexed: 11/28/2022]
Abstract
Forensic document examiners (FDE) called upon to distinguish a genuine from a forged signature of an elderly person are often required to consider the question of age-related deterioration and whether the available exemplars reliably capture the natural effects of aging of the original writer. An understanding of the statistical relationship between advanced age and handwriting movements can reduce the uncertainty that may exist in an examiner's approach to questioned signatures formed by elderly writers. The primary purpose of this study was to systematically examine age-related changes in signature kinematics in healthy writers. Forty-two healthy subjects between the ages of 60-91 years participated in this study. Signatures were recorded using a digitizing tablet, and commercial software was used to examine the temporal and spatial stroke kinematics and pen pressure. Results indicated that vertical stroke duration and dysfluency increased with age, whereas vertical stroke amplitude and velocity decreased with age. Pen pressure decreased with age. We found that a linear model characterized the best-fit relationship between advanced age and handwriting movement parameters for signature formation. Male writers exhibited stronger age effects than female writers, especially for pen pressure and stroke dysfluency. The present study contributes to an understanding of how advanced age alters signature formation in otherwise healthy adults.
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Affiliation(s)
- Michael P Caligiuri
- Department of Psychiatry, University of California at San Diego, La Jolla, CA
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29
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Gowrishankar B, Ibragimova I, Zhou Y, Slifker MJ, Devarajan K, Al-Saleem T, Uzzo RG, Cairns P. MicroRNA expression signatures of stage, grade, and progression in clear cell RCC. Cancer Biol Ther 2013; 15:329-41. [PMID: 24351440 DOI: 10.4161/cbt.27314] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Clear cell RCC is the most common, and more likely to metastasize, of the three main histological types of RCC. Pathologic stage is the most important prognostic indicator and nuclear grade can predict outcome within stages of localized RCC. Epithelial tumors are thought to accumulate a series of genetic and epigenetic changes as they progress through well-defined clinical and histopathological changes. MicroRNAs (miRNAs) are involved in the regulation of mRNA expression from many human genes and miRNA expression is dysregulated in cancer. To better understand the contribution of dysregulated miRNA expression to the progression and biology of ccRCC, we examined the differences in expression levels of 723 human miRNAs through a series of analyses by stage, grade, and disease progression status in a large series of 94 ccRCC. We found a consistent signature that included significant upregulation of miR-21-5p, 142-3p, let-7g-5p, let-7i-5p and 424-5p, as well as downregulation of miR-204-5p, to be associated with ccRCC of high stage, or high grade, or progression. Discrete signatures associated with each of stage, grade, or progression were also identified. The let-7 family was significantly downregulated in ccRCC compared with normal renal parenchyma. Expression of the 6 most significantly differentially expressed miRNAs between ccRCC was verified by stem-loop qRT-PCR. Pathways predicted as targets of the most significantly dysregulated miRNAs included signaling, epithelial cancers, metabolism, and epithelial to mesenchymal transition. Our studies help to further elucidate the biology underlying the progression of ccRCC and identify miRNAs for potential translational application.
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Affiliation(s)
| | - Ilsiya Ibragimova
- Cancer Epigenetics Program; Fox Chase Cancer Center; Philadelphia, PA USA
| | - Yan Zhou
- Biostatistics and Bioinformatics; Fox Chase Cancer Center; Philadelphia, PA USA
| | - Michael J Slifker
- Biostatistics and Bioinformatics; Fox Chase Cancer Center; Philadelphia, PA USA
| | - Karthik Devarajan
- Biostatistics and Bioinformatics; Fox Chase Cancer Center; Philadelphia, PA USA
| | - Tahseen Al-Saleem
- Kidney Cancer Keystone Program; Fox Chase Cancer Center; Philadelphia, PA USA; Department of Pathology; Fox Chase Cancer Center; Philadelphia, PA USA
| | - Robert G Uzzo
- Kidney Cancer Keystone Program; Fox Chase Cancer Center; Philadelphia, PA USA; Department of Surgery; Fox Chase Cancer Center; Philadelphia, PA USA
| | - Paul Cairns
- Cancer Epigenetics Program; Fox Chase Cancer Center; Philadelphia, PA USA; Kidney Cancer Keystone Program; Fox Chase Cancer Center; Philadelphia, PA USA
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30
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van den Kerkhof TLGM, Feenstra KA, Euler Z, van Gils MJ, Rijsdijk LWE, Boeser-Nunnink BD, Heringa J, Schuitemaker H, Sanders RW. HIV-1 envelope glycoprotein signatures that correlate with the development of cross-reactive neutralizing activity. Retrovirology 2013; 10:102. [PMID: 24059682 PMCID: PMC3849187 DOI: 10.1186/1742-4690-10-102] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 09/12/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Current HIV-1 envelope glycoprotein (Env) vaccines are unable to induce cross-reactive neutralizing antibodies. However, such antibodies are elicited in 10-30% of HIV-1 infected individuals, but it is unknown why these antibodies are induced in some individuals and not in others. We hypothesized that the Envs of early HIV-1 variants in individuals who develop cross-reactive neutralizing activity (CrNA) might have unique characteristics that support the induction of CrNA. RESULTS We retrospectively generated and analyzed env sequences of early HIV-1 clonal variants from 31 individuals with diverse levels of CrNA 2-4 years post-seroconversion. These sequences revealed a number of Env signatures that coincided with CrNA development. These included a statistically shorter variable region 1 and a lower probability of glycosylation as implied by a high ratio of NXS versus NXT glycosylation motifs. Furthermore, lower probability of glycosylation at position 332, which is involved in the epitopes of many broadly reactive neutralizing antibodies, was associated with the induction of CrNA. Finally, Sequence Harmony identified a number of amino acid changes associated with the development of CrNA. These residues mapped to various Env subdomains, but in particular to the first and fourth variable region as well as the underlying α2 helix of the third constant region. CONCLUSIONS These findings imply that the development of CrNA might depend on specific characteristics of early Env. Env signatures that correlate with the induction of CrNA might be relevant for the design of effective HIV-1 vaccines.
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Affiliation(s)
- Tom L G M van den Kerkhof
- Department of Experimental Immunology and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - K Anton Feenstra
- Center for Integrative Bioinformatics VU (IBIVU) and Amsterdam Institute for Molecules, Medicine and Systems (AIMMS), VU University Amsterdam, 1081 HV Amsterdam, the Netherlands
- Netherlands Bioinformatics Center (NBIC), 6525 GA Nijmegen, the Netherlands
| | - Zelda Euler
- Department of Experimental Immunology and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Marit J van Gils
- Department of Experimental Immunology and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Linda W E Rijsdijk
- Center for Integrative Bioinformatics VU (IBIVU) and Amsterdam Institute for Molecules, Medicine and Systems (AIMMS), VU University Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Brigitte D Boeser-Nunnink
- Department of Experimental Immunology and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Jaap Heringa
- Center for Integrative Bioinformatics VU (IBIVU) and Amsterdam Institute for Molecules, Medicine and Systems (AIMMS), VU University Amsterdam, 1081 HV Amsterdam, the Netherlands
- Netherlands Bioinformatics Center (NBIC), 6525 GA Nijmegen, the Netherlands
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Hanneke Schuitemaker
- Department of Experimental Immunology and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
- Crucell Holland BV, 2333 CN Leiden, the Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
- Department of Microbiology and Immunology, Weill Medical College, Cornell University, New York, NY 10065 USA
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Stoney DA, Bowen AM, Stoney PL. Inferential Source Attribution from Dust: Review and Analysis. Forensic Sci Rev 2013; 25:107-142. [PMID: 26226853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The analysis of dust allows inference of exposures to geographical areas, environments, activities, and processes. This activity of inferential source attribution is distinguished from that of comparative source attribution, where the focus is on the degree of correspondence between two sources in relation to other possible sources. Review of source attribution efforts in the forensic and broader scientific literature shows that most efforts are limited in one or more of four principal ways, which are classified as: (a) methods based on attribution by direct comparison; (b) methods based on closed-set item classification; (c) analysis using restricted methods and characteristics, and (d) requirement of a large sample size. These limitations provide the context for the requirements of more generalized inferential source attribution. Occurring much more rarely, and almost exclusively in the forensic literature, are individual source attribution case reports that have a microscopical, multidisciplinary perspective. Collectively these are an excellent illustration of potential and their common features demonstrate that (a) a diversity of laboratory expertise and methodology is required in order for source attribution to be successful; (b) different tools need to be applied in different cases, and (c) a process must be in place that allows a facile choice among this diversity of tools, in response to the particular investigative problem and the specifics of the samples that are available. Alternative collaborative mechanisms are considered and recommendations are made for related research and programmatic application.
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Affiliation(s)
- D A Stoney
- Stoney Forensics, Inc., Chantilly, VA, USA.
| | - A M Bowen
- Stoney Forensics, Inc., Chantilly, VA, USA
| | - P L Stoney
- Stoney Forensics, Inc., Chantilly, VA, USA
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Bose J, Pottosin II, Shabala SS, Palmgren MG, Shabala S. Calcium efflux systems in stress signaling and adaptation in plants. Front Plant Sci 2011; 2:85. [PMID: 22639615 PMCID: PMC3355617 DOI: 10.3389/fpls.2011.00085] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 11/04/2011] [Indexed: 05/18/2023]
Abstract
Transient cytosolic calcium ([Ca(2+)](cyt)) elevation is an ubiquitous denominator of the signaling network when plants are exposed to literally every known abiotic and biotic stress. These stress-induced [Ca(2+)](cyt) elevations vary in magnitude, frequency, and shape, depending on the severity of the stress as well the type of stress experienced. This creates a unique stress-specific calcium "signature" that is then decoded by signal transduction networks. While most published papers have been focused predominantly on the role of Ca(2+) influx mechanisms to shaping [Ca(2+)](cyt) signatures, restoration of the basal [Ca(2+)](cyt) levels is impossible without both cytosolic Ca(2+) buffering and efficient Ca(2+) efflux mechanisms removing excess Ca(2+) from cytosol, to reload Ca(2+) stores and to terminate Ca(2+) signaling. This is the topic of the current review. The molecular identity of two major types of Ca(2+) efflux systems, Ca(2+)-ATPase pumps and Ca(2+)/H(+) exchangers, is described, and their regulatory modes are analyzed in detail. The spatial and temporal organization of calcium signaling networks is described, and the importance of existence of intracellular calcium microdomains is discussed. Experimental evidence for the role of Ca(2+) efflux systems in plant responses to a range of abiotic and biotic factors is summarized. Contribution of Ca(2+)-ATPase pumps and Ca(2+)/H(+) exchangers in shaping [Ca(2+)](cyt) signatures is then modeled by using a four-component model (plasma- and endo-membrane-based Ca(2+)-permeable channels and efflux systems) taking into account the cytosolic Ca(2+) buffering. It is concluded that physiologically relevant variations in the activity of Ca(2+)-ATPase pumps and Ca(2+)/H(+) exchangers are sufficient to fully describe all the reported experimental evidence and determine the shape of [Ca(2+)](cyt) signatures in response to environmental stimuli, emphasizing the crucial role these active efflux systems play in plant adaptive responses to environment.
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Affiliation(s)
- Jayakumar Bose
- School of Agricultural Science, University of TasmaniaHobart, TAS, Australia
| | - Igor I. Pottosin
- Centro Universitario de Investigaciones Biomédicas, Universidad de ColimaColima, México
| | | | | | - Sergey Shabala
- School of Agricultural Science, University of TasmaniaHobart, TAS, Australia
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