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Wise A, Li J, Yamakawa M, Loureiro J, Peterson B, Worringer K, Sivasankaran R, Palma JA, Mitic L, Heuer HW, Lario-Lago A, Staffaroni AM, Clark A, Taylor J, Ljubenkov PA, Vandevrede L, Grinberg LT, Spina S, Seeley WW, Miller BL, Boeve BF, Dickerson BC, Grossman M, Litvan I, Pantelyat A, Tartaglia MC, Zhang Z, Wills AMA, Rexach J, Rojas JC, Boxer AL. CSF Proteomics in Patients With Progressive Supranuclear Palsy. Neurology 2024; 103:e209585. [PMID: 38959435 PMCID: PMC11226322 DOI: 10.1212/wnl.0000000000209585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 05/15/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Identification of fluid biomarkers for progressive supranuclear palsy (PSP) is critical to enhance therapeutic development. We implemented unbiased DNA aptamer (SOMAmer) proteomics to identify novel CSF PSP biomarkers. METHODS This is a cross-sectional study in original (18 clinically diagnosed PSP-Richardson syndrome [PSP-RS], 28 cognitively healthy controls]), validation (23 PSP-RS, 26 healthy controls), and neuropathology-confirmed (21 PSP, 52 non-PSP frontotemporal lobar degeneration) cohorts. Participants were recruited through the University of California, San Francisco, and the 4-Repeat Neuroimaging Initiative. The original and neuropathology cohorts were analyzed with the SomaScan platform version 3.0 (5026-plex) and the validation cohort with version 4.1 (7595-plex). Clinical severity was measured with the PSP Rating Scale (PSPRS). CSF proteomic data were analyzed to identify differentially expressed targets, implicated biological pathways using enrichment and weighted consensus gene coexpression analyses, diagnostic value of top targets with receiver-operating characteristic curves, and associations with disease severity with linear regressions. RESULTS A total of 136 participants were included (median age 70.6 ± 8 years, 68 [50%] women). One hundred fifty-five of 5,026 (3.1%), 959 of 7,595 (12.6%), and 321 of 5,026 (6.3%) SOMAmers were differentially expressed in PSP compared with controls in original, validation, and neuropathology-confirmed cohorts, with most of the SOMAmers showing reduced signal (83.1%, 95.1%, and 73.2%, respectively). Three coexpression modules were associated with PSP across cohorts: (1) synaptic function/JAK-STAT (β = -0.044, corrected p = 0.002), (2) vesicle cytoskeletal trafficking (β = 0.039, p = 0.007), and (3) cytokine-cytokine receptor interaction (β = -0.032, p = 0.035) pathways. Axon guidance was the top dysregulated pathway in PSP in original (strength = 1.71, p < 0.001), validation (strength = 0.84, p < 0.001), and neuropathology-confirmed (strength = 0.78, p < 0.001) cohorts. A panel of axon guidance pathway proteins discriminated between PSP and controls in original (area under the curve [AUC] = 0.924), validation (AUC = 0.815), and neuropathology-confirmed (AUC = 0.932) cohorts. Two inflammatory proteins, galectin-10 and cytotoxic T lymphocyte-associated protein-4, correlated with PSPRS scores across cohorts. DISCUSSION Axon guidance pathway proteins and several other molecular pathways are downregulated in PSP, compared with controls. Proteins in these pathways may be useful targets for biomarker or therapeutic development.
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Affiliation(s)
- Amy Wise
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Jingyao Li
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Mai Yamakawa
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Joseph Loureiro
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Brant Peterson
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Kathleen Worringer
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Rajeev Sivasankaran
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Jose-Alberto Palma
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Laura Mitic
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Hilary W Heuer
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Argentina Lario-Lago
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Adam M Staffaroni
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Annie Clark
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Jack Taylor
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Peter A Ljubenkov
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Lawren Vandevrede
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Lea T Grinberg
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Salvatore Spina
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - William W Seeley
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Bruce L Miller
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Bradley F Boeve
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Bradford C Dickerson
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Murray Grossman
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Irene Litvan
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Alexander Pantelyat
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Maria Carmela Tartaglia
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Zihan Zhang
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Anne-Marie A Wills
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Jessica Rexach
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Julio C Rojas
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
| | - Adam L Boxer
- From the Weill Institute for Neurosciences (A.W., L.M., H.W.H., A.L.-L., A.M.S., A.C., J.T., P.A.L., L.V., L.T.G., S.S., W.W.S., B.L.M., J.C.R., A.L.B.), Department of Neurology, Memory and Aging Center, University of California, San Francisco; Novartis Institutes for Biomedical Research, Inc. (J. Li, J. Loureiro, B.P., K.W., R.S., J.-A.P.), Cambridge, MA; Department of Neurology (M.Y., J.R.), University of California, Los Angeles; The Bluefield Project to Cure FTD (L.M.); Department of Neurology (B.F.B.), Mayo Clinic, Rochester, MN; Department of Neurology (B.C.D., A.-M.A.W.), Massachusetts General Hospital and Harvard Medical School, Boston; Department of Neurology (M.G.), University of Pennsylvania, Philadelphia; Department of Neurology (I.L.), University of California, San Diego; Department of Neurology (A.P.), Johns Hopkins University, Baltimore, MD; Department of Neurology (M.C.T.), University of Toronto, Ontario, Canada; and Departments of Mathematics and Statistics (Z.Z.), University of California, Los Angeles
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2
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Dempsey PW, Sandu CM, Gonzalezirias R, Hantula S, Covarrubias-Zambrano O, Bossmann SH, Nagji AS, Veeramachaneni NK, Ermerak NO, Kocakaya D, Lacin T, Yildizeli B, Lilley P, Wen SWC, Nederby L, Hansen TF, Hilberg O. Description of an activity-based enzyme biosensor for lung cancer detection. COMMUNICATIONS MEDICINE 2024; 4:37. [PMID: 38443590 PMCID: PMC10914759 DOI: 10.1038/s43856-024-00461-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/14/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Lung cancer is associated with the greatest cancer mortality as it typically presents with incurable distributed disease. Biomarkers relevant to risk assessment for the detection of lung cancer continue to be a challenge because they are often not detectable during the asymptomatic curable stage of the disease. A solution to population-scale testing for lung cancer will require a combination of performance, scalability, cost-effectiveness, and simplicity. METHODS One solution is to measure the activity of serum available enzymes that contribute to the transformation process rather than counting biomarkers. Protease enzymes modify the environment during tumor growth and present an attractive target for detection. An activity based sensor platform sensitive to active protease enzymes is presented. A panel of 18 sensors was used to measure 750 sera samples from participants at increased risk for lung cancer with or without the disease. RESULTS A machine learning approach is applied to generate algorithms that detect 90% of cancer patients overall with a specificity of 82% including 90% sensitivity in Stage I when disease intervention is most effective and detection more challenging. CONCLUSION This approach is promising as a scalable, clinically useful platform to help detect patients who have lung cancer using a simple blood sample. The performance and cost profile is being pursued in studies as a platform for population wide screening.
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Affiliation(s)
| | | | | | | | | | | | - Alykhan S Nagji
- University of Kansas Medical Center (KUMC), Kansas City, KS, USA
| | | | | | | | | | | | | | - Sara W C Wen
- Vejle Hospital, University Hospital of Southern Denmark, Vejle, Denmark
| | - Line Nederby
- Vejle Hospital, University Hospital of Southern Denmark, Vejle, Denmark
| | - Torben F Hansen
- Vejle Hospital, University Hospital of Southern Denmark, Vejle, Denmark
| | - Ole Hilberg
- Vejle Hospital, University Hospital of Southern Denmark, Vejle, Denmark
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3
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Mohamed E, García Martínez DJ, Hosseini MS, Yoong SQ, Fletcher D, Hart S, Guinn BA. Identification of biomarkers for the early detection of non-small cell lung cancer: a systematic review and meta-analysis. Carcinogenesis 2024; 45:1-22. [PMID: 38066655 DOI: 10.1093/carcin/bgad091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 02/13/2024] Open
Abstract
Lung cancer (LC) causes few symptoms in the earliest stages, leading to one of the highest mortality rates among cancers. Low-dose computerised tomography (LDCT) is used to screen high-risk individuals, reducing the mortality rate by 20%. However, LDCT results in a high number of false positives and is associated with unnecessary follow-up and cost. Biomarkers with high sensitivities and specificities could assist in the early detection of LC, especially in patients with high-risk features. Carcinoembryonic antigen (CEA), cytokeratin 19 fragments and cancer antigen 125 have been found to be highly expressed during the later stages of LC but have low sensitivity in the earliest stages. We determined the best biomarkers for the early diagnosis of LC, using a systematic review of eight databases. We identified 98 articles that focussed on the identification and assessment of diagnostic biomarkers and achieved a pooled area under curve of 0.85 (95% CI 0.82-0.088), indicating that the diagnostic performance of these biomarkers when combined was excellent. Of the studies, 30 focussed on single/antigen panels, 22 on autoantibodies, 31 on miRNA and RNA panels, and 15 suggested the use of circulating DNA combined with CEA or neuron-specific enolase (NSE) for early LC detection. Verification of blood biomarkers with high sensitivities (Ciz1, exoGCC2, ITGA2B), high specificities (CYFR21-1, antiHE4, OPNV) or both (HSP90α, CEA) along with miR-15b and miR-27b/miR-21 from sputum may improve early LC detection. Further assessment is needed using appropriate sample sizes, control groups that include patients with non-malignant conditions, and standardised cut-off levels for each biomarker.
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Affiliation(s)
- Eithar Mohamed
- Centre for Biomedicine, Hull York Medical School, University of Hull, Kingston-upon-Hull, HU6 7RX, UK
| | - Daniel J García Martínez
- Department of Biotechnology, Pozuelo de Alarcón, University Francisco De Vitoria, Madrid, 28223, Spain
| | - Mohammad-Salar Hosseini
- Research Centre for Evidence-Based Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Si Qi Yoong
- Alice Lee Centre for Nursing Studies, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Daniel Fletcher
- Centre for Biomedicine, Hull York Medical School, University of Hull, Kingston-upon-Hull, HU6 7RX, UK
| | - Simon Hart
- Respiratory Medicine, Hull York Medical School, University of Hull, Kingston-upon-Hull, HU6 7RX, UK
| | - Barbara-Ann Guinn
- Centre for Biomedicine, Hull York Medical School, University of Hull, Kingston-upon-Hull, HU6 7RX, UK
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4
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Saputra HA, Jannath KA, Kim KB, Park DS, Shim YB. Conducting polymer composite-based biosensing materials for the diagnosis of lung cancer: A review. Int J Biol Macromol 2023; 252:126149. [PMID: 37582435 DOI: 10.1016/j.ijbiomac.2023.126149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/17/2023]
Abstract
The development of a simple and fast cancer detection method is crucial since early diagnosis is a key factor in increasing survival rates for lung cancer patients. Among several diagnosis methods, the electrochemical sensor is the most promising one due to its outstanding performance, portability, real-time analysis, robustness, amenability, and cost-effectiveness. Conducting polymer (CP) composites have been frequently used to fabricate a robust sensor device, owing to their excellent physical and electrochemical properties as well as biocompatibility with nontoxic effects on the biological system. This review brings up a brief overview of the importance of electrochemical biosensors for the early detection of lung cancer, with a detailed discussion on the design and development of CP composite materials for biosensor applications. The review covers the electrochemical sensing of numerous lung cancer markers employing composite electrodes based on the conducting polyterthiophene, poly(3,4-ethylenedioxythiophene), polyaniline, polypyrrole, molecularly imprinted polymers, and others. In addition, a hybrid of the electrochemical biosensors and other techniques was highlighted. The outlook was also briefly discussed for the development of CP composite-based electrochemical biosensors for POC diagnostic devices.
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Affiliation(s)
- Heru Agung Saputra
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Khatun A Jannath
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Kwang Bok Kim
- Digital Health Care R&D Department, Korea Institute of Industrial Technology, Cheonan 31056, Republic of Korea
| | - Deog-Su Park
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Yoon-Bo Shim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea.
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5
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Ngo D, Pratte KA, Flexeder C, Petersen H, Dang H, Ma Y, Keyes MJ, Gao Y, Deng S, Peterson BD, Farrell LA, Bhambhani VM, Palacios C, Quadir J, Gillenwater L, Xu H, Emson C, Gieger C, Suhre K, Graumann J, Jain D, Conomos MP, Tracy RP, Guo X, Liu Y, Johnson WC, Cornell E, Durda P, Taylor KD, Papanicolaou GJ, Rich SS, Rotter JI, Rennard SI, Curtis JL, Woodruff PG, Comellas AP, Silverman EK, Crapo JD, Larson MG, Vasan RS, Wang TJ, Correa A, Sims M, Wilson JG, Gerszten RE, O’Connor GT, Barr RG, Couper D, Dupuis J, Manichaikul A, O’Neal WK, Tesfaigzi Y, Schulz H, Bowler RP. Systemic Markers of Lung Function and Forced Expiratory Volume in 1 Second Decline across Diverse Cohorts. Ann Am Thorac Soc 2023; 20:1124-1135. [PMID: 37351609 PMCID: PMC10405603 DOI: 10.1513/annalsats.202210-857oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
Rationale: Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by airway obstruction and accelerated lung function decline. Our understanding of systemic protein biomarkers associated with COPD remains incomplete. Objectives: To determine what proteins and pathways are associated with impaired pulmonary function in a diverse population. Methods: We studied 6,722 participants across six cohort studies with both aptamer-based proteomic and spirometry data (4,566 predominantly White participants in a discovery analysis and 2,156 African American cohort participants in a validation). In linear regression models, we examined protein associations with baseline forced expiratory volume in 1 second (FEV1) and FEV1/forced vital capacity (FVC). In linear mixed effects models, we investigated the associations of baseline protein levels with rate of FEV1 decline (ml/yr) in 2,777 participants with up to 7 years of follow-up spirometry. Results: We identified 254 proteins associated with FEV1 in our discovery analyses, with 80 proteins validated in the Jackson Heart Study. Novel validated protein associations include kallistatin serine protease inhibitor, growth differentiation factor 2, and tumor necrosis factor-like weak inducer of apoptosis (discovery β = 0.0561, Q = 4.05 × 10-10; β = 0.0421, Q = 1.12 × 10-3; and β = 0.0358, Q = 1.67 × 10-3, respectively). In longitudinal analyses within cohorts with follow-up spirometry, we identified 15 proteins associated with FEV1 decline (Q < 0.05), including elafin leukocyte elastase inhibitor and mucin-associated TFF2 (trefoil factor 2; β = -4.3 ml/yr, Q = 0.049; β = -6.1 ml/yr, Q = 0.032, respectively). Pathways and processes highlighted by our study include aberrant extracellular matrix remodeling, enhanced innate immune response, dysregulation of angiogenesis, and coagulation. Conclusions: In this study, we identify and validate novel biomarkers and pathways associated with lung function traits in a racially diverse population. In addition, we identify novel protein markers associated with FEV1 decline. Several protein findings are supported by previously reported genetic signals, highlighting the plausibility of certain biologic pathways. These novel proteins might represent markers for risk stratification, as well as novel molecular targets for treatment of COPD.
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Affiliation(s)
- Debby Ngo
- Cardiovascular Research Institute
- Division of Pulmonary, Critical Care, and Sleep Medicine, and
| | | | - Claudia Flexeder
- Institute of Epidemiology and
- Comprehensive Pneumology Center Munich (CPC-M) as member of the German Center for Lung Research (DZL), Munich, Germany
- Institute and Clinic for Occupational, Social, and Environmental Medicine, University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Hans Petersen
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Hong Dang
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yanlin Ma
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | | | - Yan Gao
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi; and
- Institute and Clinic for Occupational, Social, and Environmental Medicine, University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | | | | | | | | | | | | | | | - Hanfei Xu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Claire Emson
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | - Christian Gieger
- Institute of Epidemiology and
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine Qatar, Education City, Doha, Qatar
| | | | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Matthew P. Conomos
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Russell P. Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA (University of California, Los Angeles) Medical Center, Torrance, California
| | - Yongmei Liu
- Division of Cardiology, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina
| | - W. Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Elaine Cornell
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA (University of California, Los Angeles) Medical Center, Torrance, California
| | - George J. Papanicolaou
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA (University of California, Los Angeles) Medical Center, Torrance, California
| | - Steven I. Rennard
- Pulmonary, Critical Care, Allergy, and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | - Prescott G. Woodruff
- Pulmonary, Critical Care, Allergy, and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | | | | | | | - Martin G. Larson
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
| | - Ramachandran S. Vasan
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
- Division of Preventive Medicine and
- Division of Cardiology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Thomas J. Wang
- Department of Medicine, UT (University of Texas) Southwestern Medical Center, Dallas, Texas
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adolfo Correa
- Jackson Heart Study, Department of Medicine, and
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi; and
| | - Mario Sims
- Jackson Heart Study, Department of Medicine, and
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi; and
| | - James G. Wilson
- Cardiovascular Research Institute
- Jackson Heart Study, Department of Medicine, and
| | - Robert E. Gerszten
- Cardiovascular Research Institute
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - George T. O’Connor
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts
- Pulmonary Center, Department of Medicine, Boston University, Boston, Massachusetts
| | - R. Graham Barr
- Department of Medicine and
- Department of Epidemiology, Columbia University, New York, New York
| | - David Couper
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Wanda K. O’Neal
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yohannes Tesfaigzi
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Holger Schulz
- Institute of Epidemiology and
- Comprehensive Pneumology Center Munich (CPC-M) as member of the German Center for Lung Research (DZL), Munich, Germany
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Mackay S, Frazer LC, Bailey GK, Miller CM, Gong Q, Dewitt ON, Singh DK, Good M. Identification of serum biomarkers for necrotizing enterocolitis using aptamer-based proteomics. Front Pediatr 2023; 11:1184940. [PMID: 37325361 PMCID: PMC10264655 DOI: 10.3389/fped.2023.1184940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/10/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction Necrotizing enterocolitis (NEC) is a potentially fatal intestinal disease primarily affecting preterm infants. Early diagnosis of neonates with NEC is crucial to improving outcomes; however, traditional diagnostic tools remain inadequate. Biomarkers represent an opportunity to improve the speed and accuracy of diagnosis, but they are not routinely used in clinical practice. Methods In this study, we utilized an aptamer-based proteomic discovery assay to identify new serum biomarkers of NEC. We compared levels of serum proteins in neonates with and without NEC and identified ten differentially expressed serum proteins between these groups. Results We detected two proteins, C-C motif chemokine ligand 16 (CCL16) and immunoglobulin heavy constant alpha 1 and 2 heterodimer (IGHA1 IGHA2), that were significantly increased during NEC and eight that were significantly decreased. Generation of receiver operating characteristic (ROC) curves revealed that alpha-fetoprotein (AUC = 0.926), glucagon (AUC = 0.860), and IGHA1 IGHA2 (AUC = 0.826) were the proteins that best differentiated patients with and without NEC. Discussion These findings indicate that further investigation into these serum proteins as a biomarker for NEC is warranted. In the future, laboratory tests incorporating these differentially expressed proteins may improve the ability of clinicians to diagnose infants with NEC rapidly and accurately.
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Affiliation(s)
- Stephen Mackay
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, The University of North Carolina at Chapel Hill, NC, United States
| | - Lauren C. Frazer
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, The University of North Carolina at Chapel Hill, NC, United States
| | - Grace K. Bailey
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, The University of North Carolina at Chapel Hill, NC, United States
| | - Claire M. Miller
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, The University of North Carolina at Chapel Hill, NC, United States
| | - Qingqing Gong
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
| | - Olivia N. Dewitt
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
| | - Dhirendra K. Singh
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, The University of North Carolina at Chapel Hill, NC, United States
| | - Misty Good
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, The University of North Carolina at Chapel Hill, NC, United States
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7
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Vanarsa K, Castillo J, Wang L, Lee KH, Pedroza C, Lotan Y, Mohan C. Comprehensive proteomics and platform validation of urinary biomarkers for bladder cancer diagnosis and staging. BMC Med 2023; 21:133. [PMID: 37016361 PMCID: PMC10074794 DOI: 10.1186/s12916-023-02813-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 03/02/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Bladder cancer (BC) is among the most common cancers diagnosed in men in the USA. The current gold standards for the diagnosis of BC are invasive or lack the sensitivity to correctly identify the disease. METHODS An aptamer-based screen analyzed the expression of 1317 proteins in BC compared to urology clinic controls. The top hits were subjected to systems biology analyses. Next, 30 urine proteins were ELISA-validated in an independent cohort of 68 subjects. Three of these proteins were next validated in an independent BC cohort of differing ethnicity. RESULTS Systems biology analysis implicated molecular functions related to the extracellular matrix, collagen, integrin, heparin, and transmembrane tyrosine kinase signaling in BC susceptibility, with HNF4A and NFKB1 emerging as key molecular regulators. STEM analysis of the dysregulated pathways implicated a functional role for the immune system, complement, and interleukins in BC disease progression. Of 21 urine proteins that discriminated BC from urology clinic controls (UC), urine D-dimer displayed the highest accuracy (0.96) and sensitivity of 97%. Furthermore, 8 urine proteins significantly discriminated MIBC from NMIBC (AUC = 0.75-0.99), with IL-8 and IgA being the best performers. Urine IgA and fibronectin exhibited the highest specificity of 80% at fixed sensitivity for identifying advanced BC. CONCLUSIONS Given the high sensitivity (97%) of urine D-dimer for BC, it may have a role in the initial diagnosis or detection of cancer recurrence. On the other hand, urine IL-8 and IgA may have the potential in identifying disease progression during patient follow-up. The use of these biomarkers for initial triage could have a significant impact as the current cystoscopy-based diagnostic and surveillance approach is costly and invasive when compared to a simple urine test.
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Affiliation(s)
- Kamala Vanarsa
- Department Biomedical Engineering, University of Houston, 3517 Cullen Blvd., Room 2027, Houston, TX, 77204-5060, USA
| | - Jessica Castillo
- Department Biomedical Engineering, University of Houston, 3517 Cullen Blvd., Room 2027, Houston, TX, 77204-5060, USA
| | - Long Wang
- Department of Urology, Third Xiangya Hospital of Central South University, Changsha, China
| | - Kyung Hyun Lee
- Center for Clinical Research and Evidence-Based Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Claudia Pedroza
- Center for Clinical Research and Evidence-Based Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yair Lotan
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chandra Mohan
- Department Biomedical Engineering, University of Houston, 3517 Cullen Blvd., Room 2027, Houston, TX, 77204-5060, USA.
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8
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Blatt S, Kämmerer PW, Krüger M, Surabattula R, Thiem DGE, Dillon ST, Al-Nawas B, Libermann TA, Schuppan D. High-Multiplex Aptamer-Based Serum Proteomics to Identify Candidate Serum Biomarkers of Oral Squamous Cell Carcinoma. Cancers (Basel) 2023; 15:cancers15072071. [PMID: 37046731 PMCID: PMC10093013 DOI: 10.3390/cancers15072071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/17/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Improved serological biomarkers are needed for the early detection, risk stratification and treatment surveillance of patients with oral squamous cell carcinoma (OSCC). We performed an exploratory study using advanced, highly specific, DNA-aptamer-based serum proteomics (SOMAscan, 1305-plex) to identify distinct proteomic changes in patients with OSCC pre- vs. post-resection and compared to healthy controls. A total of 63 significantly differentially expressed serum proteins (each p < 0.05) were found that could discriminate between OSCC and healthy controls with 100% accuracy. Furthermore, 121 proteins were detected that were significantly altered between pre- and post-resection sera, and 12 OSCC-associated proteins reversed to levels equivalent to healthy controls after resection. Of these, 6 were increased and 6 were decreased relative to healthy controls, highlighting the potential relevance of these proteins as OSCC tumor markers. Pathway analyses revealed potential pathophysiological mechanisms associated with OSCC. Hence, quantitative proteome analysis using SOMAscan technology is promising and may aid in the development of defined serum marker assays to predict tumor occurrence, progression and recurrence in OSCC, and to guide personalized therapies.
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9
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Louis Sam Titus ASC, Vanarsa K, Soomro S, Patel A, Prince J, Kugathasan S, Mohan C. Resistin, Elastase, and Lactoferrin as Potential Plasma Biomarkers of Pediatric Inflammatory Bowel Disease Based on Comprehensive Proteomic Screens. Mol Cell Proteomics 2023; 22:100487. [PMID: 36549591 PMCID: PMC9918796 DOI: 10.1016/j.mcpro.2022.100487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/10/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Inflammatory bowel disease (IBD) is an immune-mediated chronic inflammation of the intestine, which can present in the form of ulcerative colitis (UC) or as Crohn's disease (CD). Biomarkers are needed for reliable diagnosis and disease monitoring in IBD, especially in pediatric patients. Plasma samples from a pediatric IBD cohort were interrogated using an aptamer-based screen of 1322 proteins. The elevated biomarkers identified using the aptamer screen were further validated by ELISA using an independent cohort of 76 pediatric plasma samples, drawn from 30 CD, 30 UC, and 16 healthy controls. Of the 1322 proteins screened in plasma from IBD patients, 129 proteins were significantly elevated when compared with healthy controls. Of these 15 proteins had a fold change greater than 2 and 28 proteins had a fold change >1.5. Neutrophil and extracellular vesicle signatures were detected among the elevated plasma biomarkers. When seven of these proteins were validated by ELISA, resistin was the only protein that was significantly higher in both UC and CD (p < 0.01), with receiver operating characteristic area under the curve value of 0.82 and 0.77, respectively, and the only protein that exhibited high sensitivity and specificity for both CD and UC. The next most discriminatory plasma proteins were elastase and lactoferrin, particularly for UC, with receiver operating characteristic area under the curve values of 0.74 and 0.69, respectively. We have identified circulating resistin, elastase, and lactoferrin as potential plasma biomarkers of IBD in pediatric patients using two independent diagnostic platforms and two independent patient cohorts.
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Affiliation(s)
| | - Kamala Vanarsa
- Department Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Sanam Soomro
- Department Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Anjali Patel
- Department Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Jarod Prince
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA.
| | - Chandra Mohan
- Department Biomedical Engineering, University of Houston, Houston, Texas, USA.
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10
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Feng X, Duan Y, Lv X, Li Q, Liang B, Ou X. The Impact of Lung Cancer in Patients with Combined Pulmonary Fibrosis and Emphysema (CPFE). J Clin Med 2023; 12:jcm12031100. [PMID: 36769748 PMCID: PMC9917551 DOI: 10.3390/jcm12031100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/20/2023] [Accepted: 01/22/2023] [Indexed: 02/02/2023] Open
Abstract
Given the high risk of lung cancer (LC) in patients with combined pulmonary fibrosis and emphysema (CPFE), and the difficulty of early diagnosis, it is important to understand the impact of LC in these patients. The effect of LC on the development of acute exacerbation (AE) as a natural course of CPFE is still unknown. We retrospectively reviewed medical records of patients at the West China Hospital and enrolled 59 patients with CPFE combined with LC and 68 CPFE patients without LC for initial diagnosis matched in the same period. We compared the clinical characteristics and imaging features of CPFE patients with LC and without LC, and analyzed the associated factors for the prevalence of LC using binary logistic regression. Cox proportional hazards regression analysis was performed to explore risk factors of AE as a natural course of CPFE. Patients with CPFE combined with LC were more common among elderly male smokers. The most common pathological type of tumor was adenocarcinoma (24/59, 40.7%) and squamous cell carcinoma (18/59, 30.5%). Compared with those in the without LC group, the proportions of men, and ex- or current smokers, and the levels of smoking pack-years, serum CRP, IL-6, fibrinogen, complement C3 and C4 in patients with LC were significantly higher (p < 0.05). There was no significant difference in the proportion of natural-course-related AE (10.2% vs. 16.2%, p > 0.05) between the two groups. Logistic regression analysis demonstrated that pack-years ≥ 20 (OR: 3.672, 95% CI: 1.165-11.579), family history of cancer (OR: 8.353, 95% CI: 2.368-10.417), the level of fibrinogen > 4.81 g/L (OR: 3.628, 95% CI: 1.403-9.385) and serum C3 > 1.00 g/L (OR: 5.299, 95% CI: 1.727-16.263) were independently associated with LC in patients with CPFE. Compared to those without AE, CPFE patients with AE had significantly higher levels of PLR and serum CRP, with obviously lower DLCO and VC. The obviously increased PLR (HR: 3.731, 95% CI: 1.288-10.813), and decreased DLCO%pred (HR: 0.919, 95% CI: 0.863-0.979) and VC%pred (HR: 0.577, 95% CI: 0.137-0.918) rather than the presence of LC independently contributed to the development of natural-course-related AE in patients with CPFE. Pack-years, family history of cancer, the levels of fibrinogen and serum C3 were independently associated with LC in patients with CPFE. The presence of LC did not significantly increase the risk of AE as a natural course of CPFE. Clinicians should give high priority to CPFE patients, especially those with more severe fibrosis and systemic inflammation, in order to be alert for the occurrence of AE.
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Affiliation(s)
- Xiaoyi Feng
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yishan Duan
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xiafei Lv
- Department of Radiology, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Qinxue Li
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Binmiao Liang
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xuemei Ou
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
- Correspondence:
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11
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Liquid Biopsy for Lung Cancer: Up-to-Date and Perspectives for Screening Programs. Int J Mol Sci 2023; 24:ijms24032505. [PMID: 36768828 PMCID: PMC9917347 DOI: 10.3390/ijms24032505] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 01/31/2023] Open
Abstract
Lung cancer is the deadliest cancer worldwide. Tissue biopsy is currently employed for the diagnosis and molecular stratification of lung cancer. Liquid biopsy is a minimally invasive approach to determine biomarkers from body fluids, such as blood, urine, sputum, and saliva. Tumor cells release cfDNA, ctDNA, exosomes, miRNAs, circRNAs, CTCs, and DNA methylated fragments, among others, which can be successfully used as biomarkers for diagnosis, prognosis, and prediction of treatment response. Predictive biomarkers are well-established for managing lung cancer, and liquid biopsy options have emerged in the last few years. Currently, detecting EGFR p.(Tyr790Met) mutation in plasma samples from lung cancer patients has been used for predicting response and monitoring tyrosine kinase inhibitors (TKi)-treated patients with lung cancer. In addition, many efforts continue to bring more sensitive technologies to improve the detection of clinically relevant biomarkers for lung cancer. Moreover, liquid biopsy can dramatically decrease the turnaround time for laboratory reports, accelerating the beginning of treatment and improving the overall survival of lung cancer patients. Herein, we summarized all available and emerging approaches of liquid biopsy-techniques, molecules, and sample type-for lung cancer.
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12
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Huang H, Yang Y, Zhu Y, Chen H, Yang Y, Zhang L, Li W. Blood protein biomarkers in lung cancer. Cancer Lett 2022; 551:215886. [PMID: 35995139 DOI: 10.1016/j.canlet.2022.215886] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022]
Abstract
Lung cancer has consistently ranked first as the cause of cancer-associated mortality. The 5-year survival rate has risen slowly, and the main obstacle to improving the prognosis of patients has been that lung cancer is usually diagnosed at an advanced or incurable stage. Thus, early detection and timely intervention are the most effective ways to reduce lung cancer mortality. Tumor-specific molecules and cellular elements are abundant in circulation, providing real-time information in a noninvasive and cost-effective manner during lung cancer development. These circulating biomarkers are emerging as promising tools for early detection of lung cancer and can be used to supplement computed tomography screening, as well as for prognosis prediction and treatment response monitoring. Serum and plasma are the main sources of circulating biomarkers, and protein biomarkers have been most extensively studied. In this review, we summarize the research progress on three most common types of blood protein biomarkers (tumor-associated antigens, autoantibodies, and exosomal proteins) in lung cancer. This review will potentially guide researchers toward a more comprehensive understanding of candidate lung cancer protein biomarkers in the blood to facilitate their translation to the clinic.
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Affiliation(s)
- Hong Huang
- Institute of Clinical Pathology, Key Laboratory of Transplantation Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Yongfeng Yang
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China; Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Yihan Zhu
- Institute of Clinical Pathology, Key Laboratory of Transplantation Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Hongyu Chen
- Institute of Clinical Pathology, Key Laboratory of Transplantation Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Ying Yang
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Li Zhang
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China; Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Weimin Li
- Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China; Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China; Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China; The Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, Chengdu, 610041, China.
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13
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Kussrow A, Kammer MN, Massion PP, Webster R, Bornhop DJ. Assay Performance of a Label-Free, Solution-Phase CYFRA 21-1 Determination. ACS OMEGA 2022; 7:31916-31923. [PMID: 36120008 PMCID: PMC9476196 DOI: 10.1021/acsomega.2c02763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
CYFRA 21.1, a cytokeratin fragment of epithelial origin, has long been a valuable blood-based biomarker. As with most biomarkers, the clinical diagnostic value of CYFRA 21.1 is dependent on the quantitative performance of the assay. Looking toward translation, it is shown here that a free-solution assay (FSA) coupled with a compensated interferometric reader (CIR) can be used to provide excellent analytical performance in quantifying CYFRA 21.1 in patient serum samples. This report focuses on the analytical performance of the high-sensitivity (hs)-CYFRA 21.1 assay in the context of quantifying the biomarker in two indeterminate pulmonary nodule (IPN) patient cohorts totaling 179 patients. Each of the ten assay calibrations consisted of 6 concentrations, each run as 7 replicates (e.g., 10 × 6 × 7 data points) and were performed on two different instruments by two different operators. Coefficients of variation (CVs) for the hs-CYFRA 21.1 analytical figures of merit, limit of quantification (LOQ) of ca. 60 pg/mL, B max, initial slope, probe-target binding affinity, and reproducibility of quantifying an unknown were found to range from 2.5 to 8.3%. Our results demonstrate the excellent performance of our FSA-CIR hs-CYFRA 21-1 assay and a proof of concept for potentially redefining the performance characteristics of this existing important candidate biomarker.
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Affiliation(s)
- Amanda
K. Kussrow
- Department
of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Michael N. Kammer
- Division
of Allergy, Pulmonary and Critical Care Medicine and Vanderbilt-Ingram
Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Pierre P. Massion
- Division
of Allergy, Pulmonary and Critical Care Medicine and Vanderbilt-Ingram
Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Rebekah Webster
- Department
of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Darryl J. Bornhop
- Department
of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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Vandghanooni S, Sanaat Z, Farahzadi R, Eskandani M, Omidian H, Omidi Y. Recent progress in the development of aptasensors for cancer diagnosis: Focusing on aptamers against cancer biomarkers. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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15
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Li H, Vanarsa K, Zhang T, Soomro S, Cicalese PA, Duran V, Dasari S, Lee KH, Pedroza C, Kisiel JB, Qin H, Bresalier RS, Chia N, Mohan C. Comprehensive aptamer-based screen of 1317 proteins uncovers improved stool protein markers of colorectal cancer. J Gastroenterol 2021; 56:659-672. [PMID: 34117903 DOI: 10.1007/s00535-021-01795-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND To screen and validate novel stool protein biomarkers of colorectal cancer (CRC). METHODS A novel aptamer-based screen of 1317 proteins was used to uncover elevated proteins in the stool of patients with CRC, as compared to healthy controls (HCs) in a discovery cohort. Selected biomarker candidates from the discovery cohort were ELISA validated in three independent cross-sectional cohorts comprises 76 CRC patients, 15 adenoma patients, and 63 healthy controls, from two different ethnicities. The expression of the potential stool biomarkers within CRC tissue was evaluated using single-cell RNA-seq datasets. RESULTS A total of 92 proteins were significantly elevated in CRC samples as compared to HCs in the discovery cohort. Among Caucasians, the 5 most discriminatory proteins among the 16 selected proteins, ordered by their ability to distinguish CRC from adenoma and healthy controls, were MMP9, haptoglobin, myeloperoxidase, fibrinogen, and adiponectin. Except myeloperoxidase, the others were significantly associated with depth of tumor invasion. The 8 stool proteins with the highest AUC values were also discriminatory in a second cohort of Indian CRC patients. Several of the stool biomarkers elevated in CRC were also expressed within CRC tissue, based on the single-cell RNA-seq analysis. CONCLUSIONS Stool MMP9, fibrinogen, myeloperoxidase, and haptoglobin emerged as promising CRC stool biomarkers, outperforming stool Hemoglobin. Longitudinal studies are warranted to assess the clinical utility of these novel biomarkers in early diagnosis of CRC.
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Affiliation(s)
- Hao Li
- Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Biomedical Engineering, University of Houston, Houston, USA
| | - Kamala Vanarsa
- Department of Biomedical Engineering, University of Houston, Houston, USA
| | - Ting Zhang
- Department of Biomedical Engineering, University of Houston, Houston, USA
| | - Sanam Soomro
- Department of Biomedical Engineering, University of Houston, Houston, USA
| | | | - Valeria Duran
- Department of Biomedical Engineering, University of Houston, Houston, USA
| | - Shobha Dasari
- Department of Biomedical Engineering, University of Houston, Houston, USA
| | - Kyung Hyun Lee
- Center for Clinical Research and Evidence-Based Medicine, McGovern Medical School, UT Health Science Center At Houston, Houston, USA
| | - Claudia Pedroza
- Center for Clinical Research and Evidence-Based Medicine, McGovern Medical School, UT Health Science Center At Houston, Houston, USA
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, USA
| | - Huanlong Qin
- Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Robert S Bresalier
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Nicholas Chia
- Department of Surgical Research, Mayo Clinic, Rochester, USA
| | - Chandra Mohan
- Department of Biomedical Engineering, University of Houston, Houston, USA.
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16
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Shimada YJ, Raita Y, Liang LW, Maurer MS, Hasegawa K, Fifer MA, Reilly MP. Comprehensive Proteomics Profiling Reveals Circulating Biomarkers of Hypertrophic Cardiomyopathy. Circ Heart Fail 2021; 14:e007849. [PMID: 34192899 DOI: 10.1161/circheartfailure.120.007849] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Hypertrophic cardiomyopathy (HCM) is caused by mutations in the genes coding for proteins essential in normal myocardial contraction. However, it remains unclear through which molecular pathways gene mutations mediate the development of HCM. The objectives were to determine plasma protein biomarkers of HCM and to reveal molecular pathways differentially regulated in HCM. METHODS We conducted a multicenter case-control study of cases with HCM and controls with hypertensive left ventricular hypertrophy. We performed plasma proteomics profiling of 1681 proteins. We performed a sparse partial least squares discriminant analysis to develop a proteomics-based discrimination model with data from 1 institution (ie, the training set). We tested the discriminative ability in independent samples from the other institution (ie, the test set). As an exploratory analysis, we executed pathway analysis of significantly dysregulated proteins. Pathways with false discovery rate <0.05 were declared positive. RESULTS The study included 266 cases and 167 controls (n=308 in the training set; n=125 in the test set). Using the proteomics-based model derived from the training set, the area under the receiver operating characteristic curve was 0.89 (95% CI, 0.83-0.94) in the test set. Pathway analysis revealed that the Ras-MAPK (mitogen-activated protein kinase) pathway, along with its upstream and downstream pathways, was upregulated in HCM. Pathways involved in inflammation and fibrosis-for example, the TGF (transforming growth factor)-β pathway-were also upregulated. CONCLUSIONS This study serves as the largest-scale investigation with the most comprehensive proteomics profiling in HCM, revealing circulating biomarkers and exhibiting both novel (eg, Ras-MAPK) and known (eg, TGF-β) pathways differentially regulated in HCM.
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Affiliation(s)
- Yuichi J Shimada
- Division of Cardiology, Department of Medicine (Y.J.S., L.W.L., M.S.M., M.P.R.), Columbia University Irving Medical Center, New York, NY.,Cardiology Division, Department of Medicine (Y.J.S., M.A.F.), Massachusetts General Hospital, Harvard Medical School, Boston
| | - Yoshihiko Raita
- Department of Emergency Medicine (Y.R., K.H.), Massachusetts General Hospital, Harvard Medical School, Boston
| | - Lusha W Liang
- Division of Cardiology, Department of Medicine (Y.J.S., L.W.L., M.S.M., M.P.R.), Columbia University Irving Medical Center, New York, NY
| | - Mathew S Maurer
- Division of Cardiology, Department of Medicine (Y.J.S., L.W.L., M.S.M., M.P.R.), Columbia University Irving Medical Center, New York, NY
| | - Kohei Hasegawa
- Department of Emergency Medicine (Y.R., K.H.), Massachusetts General Hospital, Harvard Medical School, Boston
| | - Michael A Fifer
- Cardiology Division, Department of Medicine (Y.J.S., M.A.F.), Massachusetts General Hospital, Harvard Medical School, Boston
| | - Muredach P Reilly
- Division of Cardiology, Department of Medicine (Y.J.S., L.W.L., M.S.M., M.P.R.), Columbia University Irving Medical Center, New York, NY.,Irving Institute for Clinical and Translational Research (M.P.R.), Columbia University Irving Medical Center, New York, NY
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Soomro S, Venkateswaran S, Vanarsa K, Kharboutli M, Nidhi M, Susarla R, Zhang T, Sasidharan P, Lee KH, Rosh J, Markowitz J, Pedroza C, Denson LA, Hyams J, Kugathasan S, Mohan C. Predicting disease course in ulcerative colitis using stool proteins identified through an aptamer-based screen. Nat Commun 2021; 12:3989. [PMID: 34183667 PMCID: PMC8239008 DOI: 10.1038/s41467-021-24235-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/04/2021] [Indexed: 12/19/2022] Open
Abstract
In the search for improved stool biomarkers for inflammatory bowel disease (IBD), an aptamer-based screen of 1129 stool proteins was conducted using stool samples from an IBD cohort. Here we report that of the 20 proteins subsequently validated by ELISA, stool Ferritin, Fibrinogen, Haptoglobin, Hemoglobin, Lipocalin-2, MMP-12, MMP-9, Myeloperoxidase, PGRP-S, Properdin, Resistin, Serpin A4, and TIMP-1 are significantly elevated in both ulcerative colitis (UC) and Crohn's disease (CD) compared to controls. When tested in a longitudinal cohort of 50 UC patients at 4 time-points, fecal Fibrinogen, MMP-8, PGRP-S, and TIMP-2 show the strongest positive correlation with concurrent PUCAI and PGA scores and are superior to fecal calprotectin. Unlike fecal calprotectin, baseline stool Fibrinogen, MMP-12, PGRP-S, TIMP-1, and TIMP-2 can predict clinical remission at Week-4. Here we show that stool proteins identified using the comprehensive aptamer-based screen are superior to fecal calprotectin alone in disease monitoring and prediction in IBD.
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Affiliation(s)
- Sanam Soomro
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Suresh Venkateswaran
- Department of Pediatrics, Emory University School of Medicine and Children Health Care of Atlanta, Atlanta, GA, USA
| | - Kamala Vanarsa
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Marwa Kharboutli
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Malavika Nidhi
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Ramya Susarla
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Ting Zhang
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | | | - Kyung Hyun Lee
- Center for Clinical Research and Evidence-based Medicine, McGovern Medical School, UT Health Science Center at Houston, Houston, TX, USA
| | - Joel Rosh
- Division of Gastroenterology, Hepatology, and Nutrition, Goryeb Children's Hospital, Atlantic Health, Morristown, NJ, USA
| | - James Markowitz
- Division of Gastroenterology, Hepatology, and Nutrition, Cohen Children's Medical Center Of New York, New Hyde Park, NY, USA
| | - Claudia Pedroza
- Center for Clinical Research and Evidence-based Medicine, McGovern Medical School, UT Health Science Center at Houston, Houston, TX, USA
| | - Lee A Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jeffrey Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, CT, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine and Children Health Care of Atlanta, Atlanta, GA, USA.
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
| | - Chandra Mohan
- Department Biomedical Engineering, University of Houston, Houston, TX, USA.
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Tonry C, Finn S, Armstrong J, Pennington SR. Clinical proteomics for prostate cancer: understanding prostate cancer pathology and protein biomarkers for improved disease management. Clin Proteomics 2020; 17:41. [PMID: 33292167 PMCID: PMC7678104 DOI: 10.1186/s12014-020-09305-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
Following the introduction of routine Prostate Specific Antigen (PSA) screening in the early 1990's, Prostate Cancer (PCa) is often detected at an early stage. There are also a growing number of treatment options available and so the associated mortality rate is generally low. However, PCa is an extremely complex and heterogenous disease and many patients suffer disease recurrence following initial therapy. Disease recurrence commonly results in metastasis and metastatic PCa has an average survival rate of just 3-5 years. A significant problem in the clinical management of PCa is being able to differentiate between patients who will respond to standard therapies and those who may benefit from more aggressive intervention at an earlier stage. It is also acknowledged that for many men the disease is not life threatenting. Hence, there is a growing desire to identify patients who can be spared the significant side effects associated with PCa treatment until such time (if ever) their disease progresses to the point where treatment is required. To these important clinical needs, current biomarkers and clinical methods for patient stratification and personlised treatment are insufficient. This review provides a comprehensive overview of the complexities of PCa pathology and disease management. In this context it is possible to review current biomarkers and proteomic technologies that will support development of biomarker-driven decision tools to meet current important clinical needs. With such an in-depth understanding of disease pathology, the development of novel clinical biomarkers can proceed in an efficient and effective manner, such that they have a better chance of improving patient outcomes.
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Affiliation(s)
- Claire Tonry
- UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Stephen Finn
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin 8, Ireland
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Chemical Modification of Aptamers for Increased Binding Affinity in Diagnostic Applications: Current Status and Future Prospects. Int J Mol Sci 2020; 21:ijms21124522. [PMID: 32630547 PMCID: PMC7350236 DOI: 10.3390/ijms21124522] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Aptamers are short single stranded DNA or RNA oligonucleotides that can recognize analytes with extraordinary target selectivity and affinity. Despite their promising properties and diagnostic potential, the number of commercial applications remains scarce. In order to endow them with novel recognition motifs and enhanced properties, chemical modification of aptamers has been pursued. This review focuses on chemical modifications, aimed at increasing the binding affinity for the aptamer's target either in a non-covalent or covalent fashion, hereby improving their application potential in a diagnostic context. An overview of current methodologies will be given, thereby distinguishing between pre- and post-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) modifications.
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20
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Stanley S, Vanarsa K, Soliman S, Habazi D, Pedroza C, Gidley G, Zhang T, Mohan S, Der E, Suryawanshi H, Tuschl T, Buyon J, Putterman C, Mok CC, Petri M, Saxena R, Mohan C. Comprehensive aptamer-based screening identifies a spectrum of urinary biomarkers of lupus nephritis across ethnicities. Nat Commun 2020; 11:2197. [PMID: 32366845 PMCID: PMC7198599 DOI: 10.1038/s41467-020-15986-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 04/02/2020] [Indexed: 02/08/2023] Open
Abstract
Emerging urinary biomarkers continue to show promise in evaluating lupus nephritis (LN). Here, we screen urine from active LN patients for 1129 proteins using an aptamer-based platform, followed by ELISA validation in two independent cohorts comprised of 127 inactive lupus, 107 active LN, 67 active non-renal lupus patients and 74 healthy controls, of three different ethnicities. Urine proteins that best distinguish active LN from inactive disease are ALCAM, PF-4, properdin, and VCAM-1 among African-Americans, sE-selectin, VCAM-1, BFL-1 and Hemopexin among Caucasians, and ALCAM, VCAM-1, TFPI and PF-4 among Asians. Most of these correlate significantly with disease activity indices in the respective ethnic groups, and surpass conventional metrics in identifying active LN, with better sensitivity, and negative/positive predictive values. Several elevated urinary molecules are also expressed within the kidneys in LN, based on single-cell RNAseq analysis. Longitudinal studies are warranted to assess the utility of these biomarkers in tracking lupus nephritis.
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Affiliation(s)
- Samantha Stanley
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Kamala Vanarsa
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Samar Soliman
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
- Rheumatology and Rehabilitation Department, Faculty of Medicine, Minia University, Minya, Egypt
| | - Deena Habazi
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Claudia Pedroza
- Center for Clinical Research and Evidence-Based Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Gabriel Gidley
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Ting Zhang
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Shree Mohan
- Department Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Evan Der
- Department of Rheumatology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hemant Suryawanshi
- Department of Molecular Biology, Rockefeller University, New York, NY, USA
| | - Thomas Tuschl
- Department of Molecular Biology, Rockefeller University, New York, NY, USA
| | - Jill Buyon
- Department of Rheumatology, New York University, New York, NY, USA
| | - Chaim Putterman
- Department of Rheumatology, Albert Einstein College of Medicine, Bronx, NY, USA
- Azrieli Faculty of Medicine, Bar-Ilan University, Zefat, Israel
- Research Institute, Galilee Medical Center, Nahariya, Israel
| | - Chi Chiu Mok
- Department of Medicine, Tuen Mun Hospital, New Territories, Hong Kong, China
| | - Michelle Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ramesh Saxena
- University Hospital Kidney & Liver Clinic, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chandra Mohan
- Department Biomedical Engineering, University of Houston, Houston, TX, USA.
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21
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Pisani LF, Moriggi M, Gelfi C, Vecchi M, Pastorelli L. Proteomic insights on the metabolism in inflammatory bowel disease. World J Gastroenterol 2020; 26:696-705. [PMID: 32116417 PMCID: PMC7039832 DOI: 10.3748/wjg.v26.i7.696] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/02/2020] [Accepted: 02/09/2020] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic and relapsing inflammatory conditions of the gut that include Crohn's disease and ulcerative colitis. The pathogenesis of IBD is not completely unraveled, IBD are multi-factorial diseases with reported alterations in the gut microbiota, activation of different immune cell types, changes in the vascular endothelium, and alterations in the tight junctions’ structure of the colonic epithelial cells. Proteomics represents a useful tool to enhance our biological understanding and to discover biomarkers in blood and intestinal specimens. It is expected to provide reproducible and quantitative data that can support clinical assessments and help clinicians in the diagnosis and treatment of IBD. Sometimes a differential diagnosis of Crohn's disease and ulcerative colitis and the prediction of treatment response can be deducted by finding meaningful biomarkers. Although some non-invasive biomarkers have been described, none can be considered as the “gold standard” for IBD diagnosis, disease activity and therapy outcome. For these reason new studies have proposed an “IBD signature”, which consists in a panel of biomarkers used to assess IBD. The above described approach characterizes “omics” and in this review we will focus on proteomics.
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Affiliation(s)
- Laura Francesca Pisani
- Gastroenterology and Digestive Endoscopy Unit, IRCCS Policlinico San Donato, San Donato Milanese 20097, Italy
| | - Manuela Moriggi
- Gastroenterology and Digestive Endoscopy Unit, IRCCS Policlinico San Donato, San Donato Milanese 20097, Italy
| | - Cecilia Gelfi
- Department of Biomedical Science for Health, University of the Study of Milan, IRCCS Istituto Ortopedico Galeazzi, Milan 20122, Italy
| | - Maurizio Vecchi
- Gastroenterology and Endoscopy Unit, IRCCS Ca' Granda Foundation, Policlinico Hospital, University of the Study of Milan, Milan 20122, Italy
| | - Luca Pastorelli
- Gastroenterology and Digestive Endoscopy Unit, IRCCS Policlinico San Donato, San Donato Milanese 20097, Italy
- Department of Biomedical Science for Health, University of the Study of Milan, Milan 20122, Italy
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22
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Abstract
Abstract
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. This can be achieved by leveraging omics information for accurate molecular characterization of tumors. Tumor tissue biopsies are currently the main source of information for molecular profiling. However, biopsies are invasive and limited in resolving spatiotemporal heterogeneity in tumor tissues. Alternative non-invasive liquid biopsies can exploit patient’s body fluids to access multiple layers of tumor-specific biological information (genomes, epigenomes, transcriptomes, proteomes, metabolomes, circulating tumor cells, and exosomes). Analysis and integration of these large and diverse datasets using statistical and machine learning approaches can yield important insights into tumor biology and lead to discovery of new diagnostic, predictive, and prognostic biomarkers. Translation of these new diagnostic tools into standard clinical practice could transform oncology, as demonstrated by a number of liquid biopsy assays already entering clinical use. In this review, we highlight successes and challenges facing the rapidly evolving field of cancer biomarker research.
Lay Summary
Precision oncology aims to tailor clinical decisions specifically to patients with the objective of improving treatment outcomes. The discovery of biomarkers for precision oncology has been accelerated by high-throughput experimental and computational methods, which can inform fine-grained characterization of tumors for clinical decision-making. Moreover, advances in the liquid biopsy field allow non-invasive sampling of patient’s body fluids with the aim of analyzing circulating biomarkers, obviating the need for invasive tumor tissue biopsies. In this review, we highlight successes and challenges facing the rapidly evolving field of liquid biopsy cancer biomarker research.
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23
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Wang Z, Maschera B, Lea S, Kolsum U, Michalovich D, Van Horn S, Traini C, Brown JR, Hessel EM, Singh D. Airway host-microbiome interactions in chronic obstructive pulmonary disease. Respir Res 2019; 20:113. [PMID: 31170986 PMCID: PMC6555748 DOI: 10.1186/s12931-019-1085-z] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 05/28/2019] [Indexed: 12/31/2022] Open
Abstract
Background Little is known about the interactions between the lung microbiome and host response in chronic obstructive pulmonary disease (COPD). Methods We performed a longitudinal 16S ribosomal RNA gene-based microbiome survey on 101 sputum samples from 16 healthy subjects and 43 COPD patients, along with characterization of host sputum transcriptome and proteome in COPD patients. Results Dysbiosis of sputum microbiome was observed with significantly increased relative abundance of Moraxella in COPD versus healthy subjects and during COPD exacerbations, and Haemophilus in COPD ex-smokers versus current smokers. Multivariate modeling on sputum microbiome, host transcriptome and proteome profiles revealed that significant associations between Moraxella and Haemophilus, host interferon and pro-inflammatory signaling pathways and neutrophilic inflammation predominated among airway host-microbiome interactions in COPD. While neutrophilia was positively correlated with Haemophilus, interferon signaling was more strongly linked to Moraxella. Moreover, while Haemophilus was significantly associated with host factors both in stable state and during exacerbations, Moraxella-associated host responses were primarily related to exacerbations. Conclusions Our study highlights a significant airway host-microbiome interplay associated with COPD inflammation and exacerbations. These findings indicate that Haemophilus and Moraxella influence different components of host immune response in COPD, and that novel therapeutic strategies should consider targeting these bacteria and their associated host pathways in COPD. Electronic supplementary material The online version of this article (10.1186/s12931-019-1085-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhang Wang
- Computational Biology, Human Genetics, Research and Development (R&D), GlaxoSmithKline (GSK), 1250 S. Collegeville Road, Collegeville, PA, 19426-0989, USA.,Present Address: School of Life Sciences, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Barbara Maschera
- Refractory Respiratory Inflammation Discovery Performance Unit, Respiratory Therapy Area, R&D, GSK, Stevenage, SG1 2NY, UK
| | - Simon Lea
- University of Manchester and University Hospital of South Manchester, Manchester, M23 9QZ, UK
| | - Umme Kolsum
- University of Manchester and University Hospital of South Manchester, Manchester, M23 9QZ, UK
| | - David Michalovich
- Refractory Respiratory Inflammation Discovery Performance Unit, Respiratory Therapy Area, R&D, GSK, Stevenage, SG1 2NY, UK
| | - Stephanie Van Horn
- Functional Genomics, Medicinal Science and Technology, R&D, GSK, Collegeville, PA, 19426, USA
| | - Christopher Traini
- Functional Genomics, Medicinal Science and Technology, R&D, GSK, Collegeville, PA, 19426, USA
| | - James R Brown
- Computational Biology, Human Genetics, Research and Development (R&D), GlaxoSmithKline (GSK), 1250 S. Collegeville Road, Collegeville, PA, 19426-0989, USA.
| | - Edith M Hessel
- Refractory Respiratory Inflammation Discovery Performance Unit, Respiratory Therapy Area, R&D, GSK, Stevenage, SG1 2NY, UK
| | - Dave Singh
- University of Manchester and University Hospital of South Manchester, Manchester, M23 9QZ, UK
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24
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Zhao P, Wu J, Lu F, Peng X, Liu C, Zhou N, Ying M. The imbalance in the complement system and its possible physiological mechanisms in patients with lung cancer. BMC Cancer 2019; 19:201. [PMID: 30841875 PMCID: PMC6404310 DOI: 10.1186/s12885-019-5422-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 02/28/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The clinical and experimental evidences for complement-cancer relationships are solid, whereas an epidemiological study reporting the imbalance of complement system in patients is still lacking. METHODS Using publicly available databases, we jointly compared the levels of complement components in plasma and lung cancer tissues. With iTRAQ proteomics, quantitative RT-PCR and western blotting, we analysed the differences in complement levels in lung cancer tissues and normal control tissues. Complement components are mainly synthesized by the liver and secreted into the blood. Using paired co-cultures of human normal QSG-7701 hepatocytes with lung cancer cells (A549, LTEP-α-2 or NCI-H1703) or human normal bronchial epithelial (HBE) cells, we examined the effects of lung cancer cells on complement synthesis and secretion in QSG-7701 hepatocytes. RESULTS An integrated analysis of transcriptome and proteome datasets from 43 previous studies revealed lower mRNA and protein levels of 25 complement and complement-related components in lung cancer tissues than those in normal control tissues; conversely, higher levels of complement proteins were detected in plasma from patients than those in healthy subjects. Our iTRAQ proteome study identified decreased and increased levels of 31 and 2 complement and complement-related proteins, respectively, in lung cancer tissues, of which the reduced levels of 10 components were further confirmed using quantitative RT-PCR and western blotting. Paired co-cultures of QSG-7701 hepatocytes with A549, LTEP-α-2, NCI-H1703 or HBE cells indicated that lung cancer cells increased complement synthesis and secretion in QSG-7701 cells compared to HBE cells. CONCLUSIONS The opposite associations between the levels of complement and complement-related components in lung cancer tissues and plasma from patients that have been repeatedly reported by independent publications may indicate the prevalence of an imbalance in the complement system of lung cancer patients. The possible mechanism of the imbalance may be associated not only with the decreased complement levels in lung cancer tissues but also the concurrent lung cancer tissue-induced increase in hepatocyte complement synthesis and plasma secretion in patients. And the imbalance should be accompanied by a suppression of complement-dependent immunity in lung cancer tissues coupled with a burden of complement immunity in the circulation of patients.
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Affiliation(s)
- Ping Zhao
- Department of Molecular Biology and Biochemistry, Basic Medical College of Nanchang University, Nanchang, People’s Republic of China
| | - Jun Wu
- Department of Molecular Biology and Biochemistry, Basic Medical College of Nanchang University, Nanchang, People’s Republic of China
| | - Feiteng Lu
- Department of Molecular Biology and Biochemistry, Basic Medical College of Nanchang University, Nanchang, People’s Republic of China
| | - Xuan Peng
- Department of Molecular Biology and Biochemistry, Basic Medical College of Nanchang University, Nanchang, People’s Republic of China
| | - Chenlin Liu
- Department of Molecular Biology and Biochemistry, Basic Medical College of Nanchang University, Nanchang, People’s Republic of China
| | - Nanjin Zhou
- Institute of Molecular Medicine, Jiangxi Academy of Medical Sciences, Bayi Road 603, Nanchang, 330006 People’s Republic of China
| | - Muying Ying
- Department of Molecular Biology and Biochemistry, Basic Medical College of Nanchang University, Nanchang, People’s Republic of China
- Institute of Molecular Medicine, Jiangxi Academy of Medical Sciences, Bayi Road 603, Nanchang, 330006 People’s Republic of China
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Jung YJ, Oh IJ, Kim Y, Jung JH, Seok M, Lee W, Park CK, Lim JH, Kim YC, Kim WS, Choi CM. Clinical Validation of a Protein Biomarker Panel for Non-Small Cell Lung Cancer. J Korean Med Sci 2018; 33:e342. [PMID: 30595683 PMCID: PMC6306327 DOI: 10.3346/jkms.2018.33.e342] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/09/2018] [Indexed: 12/19/2022] Open
Abstract
We validated the diagnostic performance of a previously developed blood-based 7-protein biomarker panel, AptoDetect™-Lung (Aptamer Sciences Inc., Pohang, Korea) using modified aptamer-based proteomic technology for lung cancer detection. Non-small cell lung cancer (NSCLC), 200 patients and benign nodule controls, 200 participants were enrolled. In a high-risk population corresponding to ≥ 55 years of age and ≥ 30 pack-years, the diagnostic performance was improved, showing 73.3% sensitivity and 90.5% specificity with an area under the curve of 0.88. AptoDetect™-Lung (Aptamer Sciences Inc.) offers the best validated performance to discriminate NSCLC from benign nodule controls in a high-risk population and could play a complementary role in lung cancer screening.
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Affiliation(s)
- Young Ju Jung
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Health Promotion Center, Asan Medical Center, Seoul, Korea
| | - In-Jae Oh
- Department of Internal Medicine, Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | | | | | | | - Woochang Lee
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Cheol Kyu Park
- Department of Internal Medicine, Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Jung-Hwan Lim
- Department of Internal Medicine, Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Young-Chul Kim
- Department of Internal Medicine, Lung and Esophageal Cancer Clinic, Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Woo-Sung Kim
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Chang-Min Choi
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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Norman KC, Moore BB, Arnold KB, O’Dwyer DN. Proteomics: Clinical and research applications in respiratory diseases. Respirology 2018; 23:993-1003. [PMID: 30105802 PMCID: PMC6234509 DOI: 10.1111/resp.13383] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/05/2018] [Accepted: 07/19/2018] [Indexed: 12/27/2022]
Abstract
The proteome is the study of the protein content of a definable component of an organism in biology. However, the tissue-specific expression of proteins and the varied post-translational modifications, splice variants and protein-protein complexes that may form, make the study of protein a challenging yet vital tool in answering many of the unanswered questions in medicine and biology to date. Indeed, the spatial, temporal and functional composition of proteins in the human body has proven difficult to elucidate for many years. Given the effect of microRNA and epigenetic regulation on silencing and enhancing gene transcription, the study of protein arguably provides more accurate information on homeostasis and perturbation in health and disease. There have been significant advances in the field of proteomics in recent years, with new technologies and platforms available to the research community. In this review, we briefly discuss some of these new technologies and developments in the context of respiratory disease. We also discuss the types of data science approaches to analyses and interpretation of the large volumes of data generated in proteomic studies. We discuss the application of these technologies with regard to respiratory disease and highlight the potential for proteomics in generating major advances in the understanding of respiratory pathophysiology into the future.
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Affiliation(s)
- Katy C. Norman
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
| | - Bethany B. Moore
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, USA
| | - Kelly B. Arnold
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
| | - David N. O’Dwyer
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, USA
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Patel V, Dwivedi AK, Deodhar S, Mishra I, Cistola DP. Aptamer-based search for correlates of plasma and serum water T 2: implications for early metabolic dysregulation and metabolic syndrome. Biomark Res 2018; 6:28. [PMID: 30237882 PMCID: PMC6142358 DOI: 10.1186/s40364-018-0143-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 08/29/2018] [Indexed: 12/13/2022] Open
Abstract
Background Metabolic syndrome is a cluster of abnormalities that increases the risk for type 2 diabetes and atherosclerosis. Plasma and serum water T2 from benchtop nuclear magnetic resonance relaxometry are early, global and practical biomarkers for metabolic syndrome and its underlying abnormalities. In a prior study, water T2 was analyzed against ~ 130 strategically selected proteins and metabolites to identify associations with insulin resistance, inflammation and dyslipidemia. In the current study, the analysis was broadened ten-fold using a modified aptamer (SOMAmer) library, enabling an unbiased search for new proteins correlated with water T2 and thus, metabolic health. Methods Water T2 measurements were recorded using fasting plasma and serum from non-diabetic human subjects. In parallel, plasma samples were analyzed using a SOMAscan assay that employed modified DNA aptamers to determine the relative concentrations of 1310 proteins. A multi-step statistical analysis was performed to identify the biomarkers most predictive of water T2. The steps included Spearman rank correlation, followed by principal components analysis with variable clustering, random forests for biomarker selection, and regression trees for biomarker ranking. Results The multi-step analysis unveiled five new proteins most predictive of water T2: hepatocyte growth factor, receptor tyrosine kinase FLT3, bone sialoprotein 2, glucokinase regulatory protein and endothelial cell-specific molecule 1. Three of the five strongest predictors of water T2 have been previously implicated in cardiometabolic diseases. Hepatocyte growth factor has been associated with incident type 2 diabetes, and endothelial cell specific molecule 1, with atherosclerosis in subjects with diabetes. Glucokinase regulatory protein plays a critical role in hepatic glucose uptake and metabolism and is a drug target for type 2 diabetes. By contrast, receptor tyrosine kinase FLT3 and bone sialoprotein 2 have not been previously associated with metabolic conditions. In addition to the five most predictive biomarkers, the analysis unveiled other strong correlates of water T2 that would not have been identified in a hypothesis-driven biomarker search. Conclusions The identification of new proteins associated with water T2 demonstrates the value of this approach to biomarker discovery. It provides new insights into the metabolic significance of water T2 and the pathophysiology of metabolic syndrome. Electronic supplementary material The online version of this article (10.1186/s40364-018-0143-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vipulkumar Patel
- 1Nanoparticle Diagnostics Laboratory, Institute for Cardiovascular & Metabolic Diseases, University of North Texas Health Science Center, Fort Worth, TX 76107 USA.,2Center of Emphasis in Diabetes & Metabolism, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905 USA
| | - Alok K Dwivedi
- 3Division of Biostatistics & Epidemiology, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905 USA
| | - Sneha Deodhar
- 1Nanoparticle Diagnostics Laboratory, Institute for Cardiovascular & Metabolic Diseases, University of North Texas Health Science Center, Fort Worth, TX 76107 USA
| | - Ina Mishra
- 1Nanoparticle Diagnostics Laboratory, Institute for Cardiovascular & Metabolic Diseases, University of North Texas Health Science Center, Fort Worth, TX 76107 USA.,2Center of Emphasis in Diabetes & Metabolism, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905 USA
| | - David P Cistola
- 1Nanoparticle Diagnostics Laboratory, Institute for Cardiovascular & Metabolic Diseases, University of North Texas Health Science Center, Fort Worth, TX 76107 USA.,2Center of Emphasis in Diabetes & Metabolism, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905 USA
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Lee PY, Chin SF, Low TY, Jamal R. Probing the colorectal cancer proteome for biomarkers: Current status and perspectives. J Proteomics 2018; 187:93-105. [PMID: 29953962 DOI: 10.1016/j.jprot.2018.06.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/13/2018] [Accepted: 06/23/2018] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide. Biomarkers that can facilitate better clinical management of CRC are in high demand to improve patient outcome and to reduce mortality. In this regard, proteomic analysis holds a promising prospect in the hunt of novel biomarkers for CRC and in understanding the mechanisms underlying tumorigenesis. This review aims to provide an overview of the current progress of proteomic research, focusing on discovery and validation of diagnostic biomarkers for CRC. We will summarize the contributions of proteomic strategies to recent discoveries of protein biomarkers for CRC and also briefly discuss the potential and challenges of different proteomic approaches in biomarker discovery and translational applications.
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Affiliation(s)
- Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia.
| | - Siok-Fong Chin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
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29
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Mu H, Sun J, Li L, Yin J, Hu N, Zhao W, Ding D, Yi L. Ionizing radiation exposure: hazards, prevention, and biomarker screening. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:15294-15306. [PMID: 29705904 DOI: 10.1007/s11356-018-2097-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/20/2018] [Indexed: 06/08/2023]
Abstract
Radiation is a form of energy derived from a source that is propagated through material in space. It consists of ionizing radiation or nonionizing radiation. Ionizing radiation is a feature of the environment and an important tool in medical treatment, but it can cause serious damage to organisms. A number of protective measures and standards of protection have been proposed to protect against radiation. There is also a need for biomarkers to rapidly assess individual doses of radiation, which can not only estimate the dose of radiation but also determine its effects on health. Proteomics, genomics, metabolomics, and lipidomics have been widely used in the search for such biomarkers. These topics are discussed in depth in this review.
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Affiliation(s)
- Hongxiang Mu
- Institute of Cytology and Genetics, College of pharmaceutical and biological science, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Jing Sun
- Institute of Cytology and Genetics, College of pharmaceutical and biological science, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Linwei Li
- Institute of Cytology and Genetics, College of pharmaceutical and biological science, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Jie Yin
- Institute of Cytology and Genetics, College of pharmaceutical and biological science, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Nan Hu
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Weichao Zhao
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Dexin Ding
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Lan Yi
- Institute of Cytology and Genetics, College of pharmaceutical and biological science, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China.
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China.
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30
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Duo J, Chiriac C, Huang RYC, Mehl J, Chen G, Tymiak A, Sabbatini P, Pillutla R, Zhang Y. Slow Off-Rate Modified Aptamer (SOMAmer) as a Novel Reagent in Immunoassay Development for Accurate Soluble Glypican-3 Quantification in Clinical Samples. Anal Chem 2018; 90:5162-5170. [PMID: 29605994 DOI: 10.1021/acs.analchem.7b05277] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Accurate quantification of soluble glypican-3 in clinical samples using immunoassays is challenging, because of the lack of appropriate antibody reagents to provide a full spectrum measurement of all potential soluble glypican-3 fragments in vivo. Glypican-3 SOMAmer (slow off-rate modified aptamer) is a novel reagent that binds, with high affinity, to a far distinct epitope of glypican-3, when compared to all available antibody reagents generated in-house. This paper describes an integrated analytical approach to rational selection of key reagents based on molecular characterization by epitope mapping, with the focus on our work using a SOMAmer as a new reagent to address development challenges with traditional antibody reagents for the soluble glypican-3 immunoassay. A qualified SOMAmer-based assay was developed and used for soluble glypican-3 quantification in hepatocellular carcinoma (HCC) patient samples. The assay demonstrated good sensitivity, accuracy, and precision. Data correlated with those obtained using the traditional antibody-based assay were used to confirm the clinically relevant soluble glypican-3 forms in vivo. This result was reinforced by a liquid chromatography tandem mass spectrometry (LC-MS/MS) assay quantifying signature peptides generated from trypsin digestion. The work presented here offers an integrated strategy for qualifying aptamers as an alternative affinity platform for immunoassay reagents that can enable speedy assay development, especially when traditional antibody reagents cannot meet assay requirements.
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Affiliation(s)
- Jia Duo
- Translational Medicine , Bristol-Myers Squibb Co. , Princeton , New Jersey 08543 , United States
| | - Camelia Chiriac
- Translational Medicine , Bristol-Myers Squibb Co. , Princeton , New Jersey 08543 , United States
| | - Richard Y-C Huang
- Pharmaceutical Candidate Optimization , Bristol-Myers Squibb Co. , Princeton , New Jersey 08543 , United States
| | - John Mehl
- Pharmaceutical Candidate Optimization , Bristol-Myers Squibb Co. , Princeton , New Jersey 08543 , United States
| | - Guodong Chen
- Pharmaceutical Candidate Optimization , Bristol-Myers Squibb Co. , Princeton , New Jersey 08543 , United States
| | - Adrienne Tymiak
- Pharmaceutical Candidate Optimization , Bristol-Myers Squibb Co. , Princeton , New Jersey 08543 , United States
| | - Peter Sabbatini
- Translational Medicine , Bristol-Myers Squibb Co. , Princeton , New Jersey 08543 , United States
| | - Renuka Pillutla
- Translational Medicine , Bristol-Myers Squibb Co. , Princeton , New Jersey 08543 , United States
| | - Yan Zhang
- Translational Medicine , Bristol-Myers Squibb Co. , Princeton , New Jersey 08543 , United States
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31
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Bayramoglu G, Ozalp VC, Dincbal U, Arica MY. Fast and Sensitive Detection of Salmonella in Milk Samples Using Aptamer-Functionalized Magnetic Silica Solid Phase and MCM-41-Aptamer Gate System. ACS Biomater Sci Eng 2018; 4:1437-1444. [DOI: 10.1021/acsbiomaterials.8b00018] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Gulay Bayramoglu
- Biochemical Processing and Biomaterial Research Laboratory, Gazi University, 06500 Teknikokullar, Ankara, Turkey
- Department of Chemistry, Faculty of Sciences, Gazi University, 06500 Ankara, Turkey
| | - V. Cengiz Ozalp
- Konya Food and Agriculture University, Bioengineering, 42080 Konya, Turkey
- Research and Development Center for Diagnostic Kits (KIT-ARGEM), Konya Food and Agriculture University, 42080 Konya, Turkey
| | - Uguray Dincbal
- Biochemical Processing and Biomaterial Research Laboratory, Gazi University, 06500 Teknikokullar, Ankara, Turkey
| | - M. Yakup Arica
- Biochemical Processing and Biomaterial Research Laboratory, Gazi University, 06500 Teknikokullar, Ankara, Turkey
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32
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Sullivan KD, Evans D, Pandey A, Hraha TH, Smith KP, Markham N, Rachubinski AL, Wolter-Warmerdam K, Hickey F, Espinosa JM, Blumenthal T. Trisomy 21 causes changes in the circulating proteome indicative of chronic autoinflammation. Sci Rep 2017; 7:14818. [PMID: 29093484 PMCID: PMC5665944 DOI: 10.1038/s41598-017-13858-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/02/2017] [Indexed: 12/11/2022] Open
Abstract
Trisomy 21 (T21) causes Down syndrome (DS), but the mechanisms by which T21 produces the different disease spectrum observed in people with DS are unknown. We recently identified an activated interferon response associated with T21 in human cells of different origins, consistent with overexpression of the four interferon receptors encoded on chromosome 21, and proposed that DS could be understood partially as an interferonopathy. However, the impact of T21 on systemic signaling cascades in living individuals with DS is undefined. To address this knowledge gap, we employed proteomics approaches to analyze blood samples from 263 individuals, 165 of them with DS, leading to the identification of dozens of proteins that are consistently deregulated by T21. Most prominent among these proteins are numerous factors involved in immune control, the complement cascade, and growth factor signaling. Importantly, people with DS display higher levels of many pro-inflammatory cytokines (e.g. IL-6, MCP-1, IL-22, TNF-α) and pronounced complement consumption, resembling changes seen in type I interferonopathies and other autoinflammatory conditions. Therefore, these results are consistent with the hypothesis that increased interferon signaling caused by T21 leads to chronic immune dysregulation, and justify investigations to define the therapeutic value of immune-modulatory strategies in DS.
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Affiliation(s)
- Kelly D Sullivan
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Donald Evans
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Ahwan Pandey
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | | | - Keith P Smith
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Neil Markham
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Angela L Rachubinski
- JFK Partners/Developmental Pediatrics, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Kristine Wolter-Warmerdam
- Anna and John J. Sie Center for Down Syndrome, Children's Hospital Colorado, Aurora, Colorado, 80045, USA
| | - Francis Hickey
- Anna and John J. Sie Center for Down Syndrome, Children's Hospital Colorado, Aurora, Colorado, 80045, USA
| | - Joaquin M Espinosa
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA. .,Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA. .,Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80203, USA.
| | - Thomas Blumenthal
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA. .,Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80203, USA. .,Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA.
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Abstract
SOMAscan is an aptamer-based proteomics assay capable of measuring 1,305 human protein analytes in serum, plasma, and other biological matrices with high sensitivity and specificity. In this work, we present a comprehensive meta-analysis of performance based on multiple serum and plasma runs using the current 1.3 k assay, as well as the previous 1.1 k version. We discuss normalization procedures and examine different strategies to minimize intra- and interplate nuisance effects. We implement a meta-analysis based on calibrator samples to characterize the coefficient of variation and signal-over-background intensity of each protein analyte. By incorporating coefficient of variation estimates into a theoretical model of statistical variability, we also provide a framework to enable rigorous statistical tests of significance in intervention studies and clinical trials, as well as quality control within and across laboratories. Furthermore, we investigate the stability of healthy subject baselines and determine the set of analytes that exhibit biologically stable baselines after technical variability is factored in. This work is accompanied by an interactive web-based tool, an initiative with the potential to become the cornerstone of a regularly updated, high quality repository with data sharing, reproducibility, and reusability as ultimate goals.
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34
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Erez O, Romero R, Maymon E, Chaemsaithong P, Done B, Pacora P, Panaitescu B, Chaiworapongsa T, Hassan SS, Tarca AL. The prediction of late-onset preeclampsia: Results from a longitudinal proteomics study. PLoS One 2017; 12:e0181468. [PMID: 28738067 PMCID: PMC5524331 DOI: 10.1371/journal.pone.0181468] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/30/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Late-onset preeclampsia is the most prevalent phenotype of this syndrome; nevertheless, only a few biomarkers for its early diagnosis have been reported. We sought to correct this deficiency using a high through-put proteomic platform. METHODS A case-control longitudinal study was conducted, including 90 patients with normal pregnancies and 76 patients with late-onset preeclampsia (diagnosed at ≥34 weeks of gestation). Maternal plasma samples were collected throughout gestation (normal pregnancy: 2-6 samples per patient, median of 2; late-onset preeclampsia: 2-6, median of 5). The abundance of 1,125 proteins was measured using an aptamers-based proteomics technique. Protein abundance in normal pregnancies was modeled using linear mixed-effects models to estimate mean abundance as a function of gestational age. Data was then expressed as multiples of-the-mean (MoM) values in normal pregnancies. Multi-marker prediction models were built using data from one of five gestational age intervals (8-16, 16.1-22, 22.1-28, 28.1-32, 32.1-36 weeks of gestation). The predictive performance of the best combination of proteins was compared to placental growth factor (PIGF) using bootstrap. RESULTS 1) At 8-16 weeks of gestation, the best prediction model included only one protein, matrix metalloproteinase 7 (MMP-7), that had a sensitivity of 69% at a false positive rate (FPR) of 20% (AUC = 0.76); 2) at 16.1-22 weeks of gestation, MMP-7 was the single best predictor of late-onset preeclampsia with a sensitivity of 70% at a FPR of 20% (AUC = 0.82); 3) after 22 weeks of gestation, PlGF was the best predictor of late-onset preeclampsia, identifying 1/3 to 1/2 of the patients destined to develop this syndrome (FPR = 20%); 4) 36 proteins were associated with late-onset preeclampsia in at least one interval of gestation (after adjustment for covariates); 5) several biological processes, such as positive regulation of vascular endothelial growth factor receptor signaling pathway, were perturbed; and 6) from 22.1 weeks of gestation onward, the set of proteins most predictive of severe preeclampsia was different from the set most predictive of the mild form of this syndrome. CONCLUSIONS Elevated MMP-7 early in gestation (8-22 weeks) and low PlGF later in gestation (after 22 weeks) are the strongest predictors for the subsequent development of late-onset preeclampsia, suggesting that the optimal identification of patients at risk may involve a two-step diagnostic process.
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Affiliation(s)
- Offer Erez
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Maternity Department “D” and Obstetrical Day Care Center, Division of Obstetrics and Gynecology, Soroka University Medical Center, School of Medicine, Faculty of Heath Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Roberto Romero
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, United States of America
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
- * E-mail: (RR); (ALT)
| | - Eli Maymon
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Piya Chaemsaithong
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
| | - Bogdan Done
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
| | - Percy Pacora
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Bogdan Panaitescu
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Sonia S. Hassan
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Adi L. Tarca
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland, and Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- Department of Computer Science, Wayne State University College of Engineering, Detroit, Michigan, United States of America
- * E-mail: (RR); (ALT)
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Birse CE, Tomic JL, Pass HI, Rom WN, Lagier RJ. Clinical validation of a blood-based classifier for diagnostic evaluation of asymptomatic individuals with pulmonary nodules. Clin Proteomics 2017; 14:25. [PMID: 28694742 PMCID: PMC5498919 DOI: 10.1186/s12014-017-9158-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/10/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The number of pulmonary nodules detected in the US is expected to increase substantially following recent recommendations for nationwide CT-based lung cancer screening. Given the low specificity of CT screening, non-invasive adjuvant methods are needed to differentiate cancerous lesions from benign nodules to help avoid unnecessary invasive procedures in the asymptomatic population. We have constructed a serum-based multi-biomarker panel and assessed its clinical accuracy in a retrospective analysis of samples collected from participants with suspicious radiographic findings in the Prostate, Lung, Chest and Ovarian (PLCO) cancer screening trial. METHODS Starting with a set of 9 candidate biomarkers, we identified 8 that exhibited limited pre-analytical variability with increasing clotting time, a key pre-analytical variable associated with the collection of serum. These 8 biomarkers were evaluated in a training study consisting of 95 stage I NSCLC patients and 186 smoker controls where a 5-biomarker pulmonary nodule classifier (PNC) was selected. The clinical accuracy of the PNC was determined in a blinded study of asymptomatic individuals comprising 119 confirmed malignant nodule cases and 119 benign nodule controls selected from the PLCO screening trial. RESULTS A PNC comprising 5 biomarkers: CEA, CYFRA 21-1, OPN, SCC, and TFPI, was selected in the training study. In an independent validation study, the PNC resolved lung cancer cases from benign nodule controls with an AUC of 0.653 (p < 0.0001). CEA and CYFRA 21-1, two of the markers included in the PNC, also accurately distinguished malignant lesions from benign controls. CONCLUSIONS A 5-biomarker blood test has been developed for the diagnostic evaluation of asymptomatic individuals with solitary pulmonary nodules.
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Affiliation(s)
- Charles E. Birse
- Quest Diagnostics, Research and Development, 33608 Ortega Highway, San Juan Capistrano, CA 92675 USA
| | - Jennifer L. Tomic
- Quest Diagnostics, Research and Development, 33608 Ortega Highway, San Juan Capistrano, CA 92675 USA
- Grifols Diagnostic Solutions, 4560 Horton St., Emeryville, CA 94608 USA
| | - Harvey I. Pass
- Department of Cardiothoracic Surgery, NYU Langone Medical Center, 530 First Avenue, New York, NY 10016 USA
| | - William N. Rom
- Division of Pulmonary, Critical Care, and Sleep Medicine, NYU School of Medicine, New York, NY 10016 USA
| | - Robert J. Lagier
- Quest Diagnostics, Research and Development, 33608 Ortega Highway, San Juan Capistrano, CA 92675 USA
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36
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Romero R, Erez O, Maymon E, Chaemsaithong P, Xu Z, Pacora P, Chaiworapongsa T, Done B, Hassan SS, Tarca AL. The maternal plasma proteome changes as a function of gestational age in normal pregnancy: a longitudinal study. Am J Obstet Gynecol 2017; 217:67.e1-67.e21. [PMID: 28263753 PMCID: PMC5813489 DOI: 10.1016/j.ajog.2017.02.037] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/10/2017] [Accepted: 02/23/2017] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Pregnancy is accompanied by dramatic physiological changes in maternal plasma proteins. Characterization of the maternal plasma proteome in normal pregnancy is an essential step for understanding changes to predict pregnancy outcome. The objective of this study was to describe maternal plasma proteins that change in abundance with advancing gestational age and determine biological processes that are perturbed in normal pregnancy. STUDY DESIGN A longitudinal study included 43 normal pregnancies that had a term delivery of an infant who was appropriate for gestational age without maternal or neonatal complications. For each pregnancy, 3 to 6 maternal plasma samples (median, 5) were profiled to measure the abundance of 1125 proteins using multiplex assays. Linear mixed-effects models with polynomial splines were used to model protein abundance as a function of gestational age, and the significance of the association was inferred via likelihood ratio tests. Proteins considered to be significantly changed were defined as having the following: (1) >1.5-fold change between 8 and 40 weeks of gestation; and (2) a false discovery rate-adjusted value of P < .1. Gene ontology enrichment analysis was used to identify biological processes overrepresented among the proteins that changed with advancing gestation. RESULTS The following results were found: (1) Ten percent (112 of 1125) of the profiled proteins changed in abundance as a function of gestational age; (2) of the 1125 proteins analyzed, glypican-3, sialic acid-binding immunoglobulin-type lectin-6, placental growth factor, C-C motif-28, carbonic anhydrase 6, prolactin, interleukin-1 receptor 4, dual-specificity mitogen-activated protein kinase 4, and pregnancy-associated plasma protein-A had more than a 5-fold change in abundance across gestation (these 9 proteins are known to be involved in a wide range of both physiological and pathological processes, such as growth regulation, embryogenesis, angiogenesis immunoregulation, inflammation etc); and (3) biological processes associated with protein changes in normal pregnancy included defense response, defense response to bacteria, proteolysis, and leukocyte migration (false discovery rate, 10%). CONCLUSION The plasma proteome of normal pregnancy demonstrates dramatic changes in both the magnitude of changes and the fraction of the proteins involved. Such information is important to understand the physiology of pregnancy and the development of biomarkers to differentiate normal vs abnormal pregnancy and determine the response to interventions.
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Affiliation(s)
- Roberto Romero
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI; Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI.
| | - Offer Erez
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
| | - Eli Maymon
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
| | - Piya Chaemsaithong
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
| | - Zhonghui Xu
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI
| | - Percy Pacora
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
| | - Bogdan Done
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI
| | - Sonia S Hassan
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
| | - Adi L Tarca
- Perinatology Research Branch, Program for Perinatal Research and Obstetrics, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, and Detroit, MI; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI.
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DeBoer EM, Kroehl ME, Wagner BD, Accurso FJ, Harris JK, Lynch DA, Sagel SD, Deterding RR. Proteomic profiling identifies novel circulating markers associated with bronchiectasis in cystic fibrosis. Proteomics Clin Appl 2017; 11. [DOI: 10.1002/prca.201600147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/20/2017] [Accepted: 04/25/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Emily M. DeBoer
- Department of Pediatrics; University of Colorado Anschutz Medical Campus and Children's Hospital Colorado; USA
| | - Miranda E. Kroehl
- Department of Biostatistics and Informatics; University of Colorado School of Public Health; USA
| | - Brandie D. Wagner
- Department of Pediatrics; University of Colorado Anschutz Medical Campus and Children's Hospital Colorado; USA
- Department of Biostatistics and Informatics; University of Colorado School of Public Health; USA
| | - Frank J. Accurso
- Department of Pediatrics; University of Colorado Anschutz Medical Campus and Children's Hospital Colorado; USA
| | - J. Kirk Harris
- Department of Pediatrics; University of Colorado Anschutz Medical Campus and Children's Hospital Colorado; USA
| | - David A. Lynch
- Department of Radiology; National Jewish Health; Denver USA
| | - Scott D. Sagel
- Department of Pediatrics; University of Colorado Anschutz Medical Campus and Children's Hospital Colorado; USA
| | - Robin R. Deterding
- Department of Pediatrics; University of Colorado Anschutz Medical Campus and Children's Hospital Colorado; USA
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Pfeiffer F, Rosenthal M, Siegl J, Ewers J, Mayer G. Customised nucleic acid libraries for enhanced aptamer selection and performance. Curr Opin Biotechnol 2017; 48:111-118. [PMID: 28437710 DOI: 10.1016/j.copbio.2017.03.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 03/28/2017] [Accepted: 03/30/2017] [Indexed: 12/24/2022]
Abstract
Aptamers are short single-stranded oligo(deoxy)nucleotides that are selected to bind to target molecules with high affinity and specificity. Because of their sophisticated characteristics and versatile applicability, aptamers are thought to become universal molecular probes in biotechnological and therapeutic applications. However, the variety of possible interactions with a putative target molecule is limited by the chemical repertoire of the natural nucleobases. Consequently, many desired targets are not addressable by aptamers. This obstacle is overcome by broadening the chemical diversity of aptamers, mainly achieved by nucleobase-modifications and the introduction of novel bases or base pairs. We discuss these achievements and the characteristics of the respective modified aptamers, reflected by SOMAmers (slow off-rate modified aptamers), clickmers, and aptamers bearing an expanded genetic alphabet.
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Affiliation(s)
- Franziska Pfeiffer
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Malte Rosenthal
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Julia Siegl
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Jörg Ewers
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany; Center of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany.
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Wang DL, Xiao C, Fu G, Wang X, Li L. Identification of potential serum biomarkers for breast cancer using a functional proteomics technology. Biomark Res 2017; 5:11. [PMID: 28293426 PMCID: PMC5348793 DOI: 10.1186/s40364-017-0092-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/06/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Cancer is a genetic disease; its development and metastasis depend on the function of many proteins. Human serum contains thousands of proteins; it is a window for the homeostasis of individual's health. Many of the proteins found in the human serum could be potential biomarkers for cancer early detection and drug efficacy evaluation. METHODS In this study, a functional proteomics technology was used to systematically monitor metabolic enzyme and protease activities from resolved serum proteins produced by a modified 2-D gel separation and subsequent Protein Elution Plate, a method collectively called PEP. All the experiments were repeated at least twice to ensure the validity of the findings. RESULTS For the first time, significant differences were found between breast cancer patient serum and normal serum in two families of enzymes known to be involved in cancer development and metastasis: metabolic enzymes and proteases. Multiple enzyme species were identified in the serum assayed directly or after enrichment. Both qualitative and quantitative differences in the metabolic enzyme and protease activity were detected between breast cancer patient and control group, providing excellent biomarker candidates for breast cancer diagnosis and drug development. CONCLUSIONS This study identified several potential functional protein biomarkers from breast cancer patient serum. It also demonstrated that the functional proteomics technology, PEP, can be applied to the analysis of any functional proteins in human serum which contains thousands of proteins. The study indicated that the functional domain of the human serum could be unlocked with the PEP technology, pointing to a novel alternative for the development of diagnosis biomarkers for breast cancer and other diseases.
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Affiliation(s)
- David L. Wang
- Department of Biology, Vanderbilt University, Nashville, TN USA
| | | | - Guofeng Fu
- Array Bridge Inc., 4320 Forest Park Ave, Suite 303, St. Louis, MO 63108 USA
| | - Xing Wang
- Array Bridge Inc., 4320 Forest Park Ave, Suite 303, St. Louis, MO 63108 USA
| | - Liang Li
- Zibo Central Hospital, Zibo, China
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Zhang L, Wan S, Jiang Y, Wang Y, Fu T, Liu Q, Cao Z, Qiu L, Tan W. Molecular Elucidation of Disease Biomarkers at the Interface of Chemistry and Biology. J Am Chem Soc 2017; 139:2532-2540. [PMID: 28121431 PMCID: PMC5519284 DOI: 10.1021/jacs.6b10646] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Disease-related biomarkers are objectively measurable molecular signatures of physiological status that can serve as disease indicators or drug targets in clinical diagnosis and therapy, thus acting as a tool in support of personalized medicine. For example, the prostate-specific antigen (PSA) biomarker is now widely used to screen patients for prostate cancer. However, few such biomarkers are currently available, and the process of biomarker identification and validation is prolonged and complicated by inefficient methods of discovery and few reliable analytical platforms. Therefore, in this Perspective, we look at the advanced chemistry of aptamer molecules and their significant role as molecular probes in biomarker studies. As a special class of functional nucleic acids evolved from an iterative technology termed Systematic Evolution of Ligands by Exponential Enrichment (SELEX), these single-stranded oligonucleotides can recognize their respective targets with selectivity and affinity comparable to those of protein antibodies. Because of their fast turnaround time and exceptional chemical properties, aptamer probes can serve as novel molecular tools for biomarker investigations, particularly in assisting identification of new disease-related biomarkers. More importantly, aptamers are able to recognize biomarkers from complex biological environments such as blood serum and cell surfaces, which can provide direct evidence for further clinical applications. This Perspective highlights several major advancements of aptamer-based biomarker discovery strategies and their potential contribution to the practice of precision medicine.
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Affiliation(s)
- Liqin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Shuo Wan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Ying Jiang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Yanyue Wang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Ting Fu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
| | - Zhijuan Cao
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
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Jung YJ, Katilius E, Ostroff RM, Kim Y, Seok M, Lee S, Jang S, Kim WS, Choi CM. Development of a Protein Biomarker Panel to Detect Non-Small-Cell Lung Cancer in Korea. Clin Lung Cancer 2016; 18:e99-e107. [PMID: 27836219 DOI: 10.1016/j.cllc.2016.09.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 09/06/2016] [Accepted: 09/06/2016] [Indexed: 11/26/2022]
Abstract
BACKGROUND Lung cancer screening using low-dose computed tomography reduces lung cancer mortality. However, the high false-positive rate, cost, and potential harms highlight the need for complementary biomarkers. We compared the diagnostic performance of modified aptamer-based protein biomarkers with Cyfra 21-1. PATIENTS AND METHODS Participants included 100 patients diagnosed with lung cancer, and 100 control subjects from Asan Medical Center (Seoul, Korea). We investigated candidate biomarkers with new modified aptamer-based proteomic technology and developed a 7-protein panel that discriminates lung cancer from controls. A naive Bayesian classifier was trained using sera from 75 lung cancers and 75 controls. An independent set of 25 cases and 25 controls was used to verify performance of this classifier. The panel results were compared with Cyfra 21-1 to evaluate the diagnostic accuracy for lung nodules detected by computed tomography. RESULTS We derived a 7-protein biomarker classifier from the initial train set comprising: EGFR1, MMP7, CA6, KIT, CRP, C9, and SERPINA3. This classifier distinguished lung cancer cases from controls with an area under the curve (AUC) of 0.82 in the train set and an AUC of 0.77 in the verification set. The 7-marker naive Bayesian classifier resulted in 91.7% specificity with 75.0% sensitivity for the subset of individuals with lung nodules. The AUC of the classifier for lung nodules was 0.88, whereas Cyfra 21-1 had an AUC of 0.72. CONCLUSION We have developed a protein biomarker panel to identify lung cancers from controls with a high accuracy. This integrated noninvasive approach to the evaluation of lung nodules deserves further prospective validation among larger cohorts of patients with lung nodules in screening strategy.
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Affiliation(s)
- Young Ju Jung
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea; Health Promotion Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | | | | | | | | | - Sujin Lee
- Aptamer Sciences Inc., Pohang, Korea
| | - Seongsoo Jang
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Woo Sung Kim
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Chang-Min Choi
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
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Proteomic study of hepatocellular carcinoma using a novel modified aptamer-based array (SOMAscan™) platform. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:434-443. [PMID: 27663888 DOI: 10.1016/j.bbapap.2016.09.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/17/2016] [Accepted: 09/19/2016] [Indexed: 12/12/2022]
Abstract
Vascular invasion is a pathological hallmark of hepatocellular carcinoma (HCC), associated with poor prognosis; it is strongly related to the early recurrence and poor survival after curative resection. In order to determine the proteomic backgrounds of HCC carcinogenesis and vascular invasion, we employed a novel modified aptamer-based array (SOMAscan) platform. SOMAscan is based on the Slow Off-rate Modified Aptamers (SOMAmers), which rely on the natural 3D folding of single-stranded DNA-based protein affinity reagents. Currently, the expression level of 1129 proteins can be assessed quantitatively. Correlation matrix analysis showed that the overall proteomic features captured by SOMAscan differ between tumor and non-tumor tissues. Non-tumor tissues were shown to have more homogeneous proteome backgrounds than tumor tissues. A comparative study identified 68 proteins with differential expression between tumor and non-tumor tissues, together with eight proteins associated with vascular invasion. Gene Ontology analysis showed that the extracellular space and extracellular region proteins were predominantly detected. Network analysis revealed the linkage of seven proteins, AKT1, MDM2, PTEN, FGF1, MAPK8, PRKCB, and FN1, which were categorized as the components of "Pathways in cancer" in pathway analysis. The results of SOMAscan analysis were not concordant with those obtained by western blotting; only the determined FN1 levels were concordant between the two platforms. We demonstrated that the proteome captured by SOMAscan includes the proteins relevant to carcinogenesis and vascular invasion in HCC. The identified proteins may serve as candidates for the future studies of disease mechanisms and clinical applications.
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Shi T, Song E, Nie S, Rodland KD, Liu T, Qian WJ, Smith RD. Advances in targeted proteomics and applications to biomedical research. Proteomics 2016; 16:2160-82. [PMID: 27302376 PMCID: PMC5051956 DOI: 10.1002/pmic.201500449] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 05/09/2016] [Accepted: 06/10/2016] [Indexed: 12/17/2022]
Abstract
Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074-1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ehwang Song
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Song Nie
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karin D Rodland
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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Sullivan KD, Lewis HC, Hill AA, Pandey A, Jackson LP, Cabral JM, Smith KP, Liggett LA, Gomez EB, Galbraith MD, DeGregori J, Espinosa JM. Trisomy 21 consistently activates the interferon response. eLife 2016; 5:e16220. [PMID: 27472900 PMCID: PMC5012864 DOI: 10.7554/elife.16220] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 07/28/2016] [Indexed: 12/12/2022] Open
Abstract
Although it is clear that trisomy 21 causes Down syndrome, the molecular events acting downstream of the trisomy remain ill defined. Using complementary genomics analyses, we identified the interferon pathway as the major signaling cascade consistently activated by trisomy 21 in human cells. Transcriptome analysis revealed that trisomy 21 activates the interferon transcriptional response in fibroblast and lymphoblastoid cell lines, as well as circulating monocytes and T cells. Trisomy 21 cells show increased induction of interferon-stimulated genes and decreased expression of ribosomal proteins and translation factors. An shRNA screen determined that the interferon-activated kinases JAK1 and TYK2 suppress proliferation of trisomy 21 fibroblasts, and this defect is rescued by pharmacological JAK inhibition. Therefore, we propose that interferon activation, likely via increased gene dosage of the four interferon receptors encoded on chromosome 21, contributes to many of the clinical impacts of trisomy 21, and that interferon antagonists could have therapeutic benefits.
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Affiliation(s)
- Kelly D Sullivan
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, United States
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, United States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - Hannah C Lewis
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, United States
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, United States
| | - Amanda A Hill
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, United States
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, United States
| | - Ahwan Pandey
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, United States
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, United States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - Leisa P Jackson
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, United States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - Joseph M Cabral
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, United States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - Keith P Smith
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, United States
| | - L Alexander Liggett
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, United States
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, United States
| | - Eliana B Gomez
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, United States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - Matthew D Galbraith
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, United States
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, United States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
| | - James DeGregori
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, United States
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, United States
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, United States
- Integrated Department of Immunology, University of Colorado School of Medicine, Aurora, United States
- Section of Hematology, University of Colorado School of Medicine, Aurora, United States
- Department of Medicine, University of Colorado School of Medicine, Aurora, United States
| | - Joaquín M Espinosa
- Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, United States
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, United States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
- Howard Hughes Medical Institute, Chevy Chase, United States
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Tonry CL, Leacy E, Raso C, Finn SP, Armstrong J, Pennington SR. The Role of Proteomics in Biomarker Development for Improved Patient Diagnosis and Clinical Decision Making in Prostate Cancer. Diagnostics (Basel) 2016; 6:E27. [PMID: 27438858 PMCID: PMC5039561 DOI: 10.3390/diagnostics6030027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/28/2016] [Accepted: 07/07/2016] [Indexed: 02/06/2023] Open
Abstract
Prostate Cancer (PCa) is the second most commonly diagnosed cancer in men worldwide. Although increased expression of prostate-specific antigen (PSA) is an effective indicator for the recurrence of PCa, its intended use as a screening marker for PCa is of considerable controversy. Recent research efforts in the field of PCa biomarkers have focused on the identification of tissue and fluid-based biomarkers that would be better able to stratify those individuals diagnosed with PCa who (i) might best receive no treatment (active surveillance of the disease); (ii) would benefit from existing treatments; or (iii) those who are likely to succumb to disease recurrence and/or have aggressive disease. The growing demand for better prostate cancer biomarkers has coincided with the development of improved discovery and evaluation technologies for multiplexed measurement of proteins in bio-fluids and tissues. This review aims to (i) provide an overview of these technologies as well as describe some of the candidate PCa protein biomarkers that have been discovered using them; (ii) address some of the general limitations in the clinical evaluation and validation of protein biomarkers; and (iii) make recommendations for strategies that could be adopted to improve the successful development of protein biomarkers to deliver improvements in personalized PCa patient decision making.
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Affiliation(s)
- Claire L Tonry
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Emma Leacy
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Cinzia Raso
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Stephen P Finn
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland.
| | | | - Stephen R Pennington
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
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Widlak P, Pietrowska M, Polanska J, Marczyk M, Ros-Mazurczyk M, Dziadziuszko R, Jassem J, Rzyman W. Serum mass profile signature as a biomarker of early lung cancer. Lung Cancer 2016; 99:46-52. [PMID: 27565913 DOI: 10.1016/j.lungcan.2016.06.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 05/12/2016] [Accepted: 06/11/2016] [Indexed: 01/10/2023]
Abstract
OBJECTIVES Circulating molecular biomarkers of lung cancer may allow the pre-selection of candidates for computed tomography screening or increase its efficacy. We aimed to identify features of serum mass profile distinguishing individuals with early lung cancer from healthy participants of the lung cancer screening program. METHODS Blood samples were collected during a low-dose computed tomography (LD-CT) screening program performed by one institution (Medical University of Gdansk, Poland). MALDI-ToF mass spectrometry was used to characterize the low-molecular-weight (1000-14,000Da) serum fraction. The analysis comprised 95 patients with early stage lung cancer (including 30 screen-detected cases) and a matched group of 285 healthy controls. The cases were split into two independent cohorts (discovery and validation), analyzed separately 6 months apart. RESULTS Several molecular components of serum (putatively components of endogenous peptidome) discriminating patients with early lung cancer from controls were identified in a discovery cohort. This allowed building an effective cancer classifier as a model tuned to maximize negative predictive value, with an area under the curve (AUC) of 0.88, a negative predictive value of 100%, and a positive predictive value of 48%. However, the classifier performed worse in a validation cohort including independent sample sets (AUC 0.73, NPV 88% and PPV 30%). CONCLUSIONS We developed a serum mass profile-based signature identifying patients with early lung cancer. Although this marker has insufficient value as a stand-alone preselecting tool for LD-CT screening, its potential clinical usefulness in evaluation of indeterminate pulmonary nodules deserves further investigation.
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Affiliation(s)
- Piotr Widlak
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Wybrzeże Armii Krajowej 15, 44-100 Gliwice, Poland.
| | - Monika Pietrowska
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Wybrzeże Armii Krajowej 15, 44-100 Gliwice, Poland.
| | - Joanna Polanska
- Silesian University of Technology, ul. Akademicka 16, 44-100 Gliwice, Poland.
| | - Michal Marczyk
- Silesian University of Technology, ul. Akademicka 16, 44-100 Gliwice, Poland.
| | - Malgorzata Ros-Mazurczyk
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, ul. Wybrzeże Armii Krajowej 15, 44-100 Gliwice, Poland.
| | | | - Jacek Jassem
- Medical University of Gdańsk, ul. Dębinki 7, 80-211 Gdańsk, Poland.
| | - Witold Rzyman
- Medical University of Gdańsk, ul. Dębinki 7, 80-211 Gdańsk, Poland.
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Sun Z, Chen X, Wang G, Li L, Fu G, Kuruc M, Wang X. Identification of functional metabolic biomarkers from lung cancer patient serum using PEP technology. Biomark Res 2016; 4:11. [PMID: 27252855 PMCID: PMC4888258 DOI: 10.1186/s40364-016-0065-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/12/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Reprogrammed metabolism is a new hallmark of cancer. In many types of cancer, most of the genes in the glycolytic pathway are overexpressed, reflecting an essential shift of metabolism during cancer development. The reprogrammed metabolism contributes to cancer development in multiple ways, from supplying the elevated energy requirement to creating a microenvironment suitable for tumor growth and suppressing the human immune surveillance system. METHOD In this study, a functional proteomics top-down approach was used to systematically monitor metabolic enzyme activities in resolved serum proteins produced by a modified 2-D gel separation and subsequent Protein Elution Plate, a method collectively called PEP. RESULTS We found that the enrichment of low abundance proteins with a bead based product called AlbuVoid™(,) is important to increase the number of observable features and to increase the level of signal achievable from the assay used. From our methods, significant metabolic enzyme activities were detected in both normal and lung cancer patient sera in many fractions after the elution of the 2-D gel separated proteins to the Protein Elution Plate (PEP). Eighteen fractions with the most dramatic metabolic enzyme activity difference between the normal and lung cancer patient sera were submitted for mass spectrometry protein identification. Proteins from the glycolytic metabolic pathway, such as GAPDH along with other proteins not previously annotated to the glycolytic pathway were identified. Further verification with commercially purified GAPDH showed that the addition of purified GAPDH to the metabolic enzyme assay system employed enhanced the enzyme activity, demonstrating that proteins identified from the PEP technology and mass spectrometry could be further verified with biological assay. CONCLUSION This study identified several potential functional enzyme biomarkers from lung cancer patient serum, it provides an alternative and complementary approach to sequence annotation for the discovery of biomarkers in human diseases.
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Affiliation(s)
- Zhenyu Sun
- />The Third Hospital Affiliated to Nantong University School of Medicine, Wuxi, China
| | - Xiaofeng Chen
- />Shanghai Huashan Hospital, Fudan University School of Medicine, Shanghai, China
| | - Gan. Wang
- />Institute of Environmental Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201 USA
| | - Liang Li
- />Zibo Central Hospital, Zibo, China
| | | | - Matthew Kuruc
- />Biotech Support Group, LLC, Monmouth Junction, NJ USA
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Petek LM, Rickard AM, Budech C, Poliachik SL, Shaw D, Ferguson MR, Tawil R, Friedman SD, Miller DG. A cross sectional study of two independent cohorts identifies serum biomarkers for facioscapulohumeral muscular dystrophy (FSHD). Neuromuscul Disord 2016; 26:405-13. [PMID: 27185459 PMCID: PMC4912392 DOI: 10.1016/j.nmd.2016.04.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/07/2016] [Accepted: 04/14/2016] [Indexed: 11/18/2022]
Abstract
Measuring the severity and progression of facioscapulohumeral muscular dystrophy (FSHD) is particularly challenging because muscle weakness progresses over long periods of time and can be sporadic. Biomarkers are essential for measuring disease burden and testing treatment strategies. We utilized the sensitive, specific, high-throughput SomaLogic proteomics platform of 1129 proteins to identify proteins with levels that correlate with FSHD severity in a cross-sectional study of two independent cohorts. We discovered biomarkers that correlate with clinical severity and disease burden measured by magnetic resonance imaging. Sixty-eight proteins in the Rochester cohort (n = 48) and 51 proteins in the Seattle cohort (n = 30) had significantly different levels in FSHD-affected individuals when compared with controls (p-value ≤ .005). A subset of these varied by at least 1.5 fold and four biomarkers were significantly elevated in both cohorts. Levels of creatine kinase MM and MB isoforms, carbonic anhydrase III, and troponin I type 2 reliably predicted the disease state and correlated with disease severity. Other novel biomarkers were also discovered that may reveal mechanisms of disease pathology. Assessing the levels of these biomarkers during clinical trials may add significance to other measures of quantifying disease progression or regression.
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Affiliation(s)
- Lisa M Petek
- Department of Pediatrics, Div. of Genetic Med., University of Washington, Seattle, WA, USA
| | - Amanda M Rickard
- Department of Pediatrics, Div. of Genetic Med., University of Washington, Seattle, WA, USA
| | | | | | - Dennis Shaw
- Department of Radiology, Seattle Children's Hospital, Seattle, WA, USA
| | - Mark R Ferguson
- Department of Radiology, Seattle Children's Hospital, Seattle, WA, USA
| | - Rabi Tawil
- Department of Neurology, University of Rochester, Rochester, NY, USA
| | - Seth D Friedman
- Department of Radiology, Seattle Children's Hospital, Seattle, WA, USA
| | - Daniel G Miller
- Department of Pediatrics, Div. of Genetic Med., University of Washington, Seattle, WA, USA.
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Abstract
Noninvasive molecular biomarkers are becoming attractive tools to monitor disease progression, aid drug development programs and use as surrogate outcome measures in clinical trials. Cutting edge proteomic methods to assay biomarkers in body fluids have been developed in the past few years, but transitioning them to clinical practice has been slow and depends on the qualification of both the method and the biomarker.
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Affiliation(s)
- Yetrib Hathout
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, USA
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Veronesi G, Bianchi F, Infante M, Alloisio M. The challenge of small lung nodules identified in CT screening: can biomarkers assist diagnosis? Biomark Med 2016; 10:137-43. [DOI: 10.2217/bmm.15.122] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Various biomarkers have been developed as noninvasive tests to indicate the presence of lung cancer in asymptomatic persons, and in particular to provide evidence as to whether indeterminate lung nodules detected by screening are malignant. We performed an overview of the range of biomarkers reported in the literature and described those that can complement low-dose computed tomography screening. Several have promising sensitivity and specificity. However to our knowledge, only three techniques have reached the prospective screening phase (phase 4) of the five-phase biomarker development process. Two miRNA signatures (the miR-Test for serum and the miRNA signature classifier test for plasma) are being assessed in prospective screening trials, as is the EarlyCDT-Lung test based on autoantibodies. All will need to undergo prospective studies to determine their ability to improve outcomes before they can become an established adjunct to lung cancer control strategies.
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Affiliation(s)
- Giulia Veronesi
- Division of Thoracic Surgery, Istituto Clinico Humanitas, 20089 Rozzano MI, Italy
| | - Fabrizio Bianchi
- Molecular Medicin Lab, European Institute of Oncology, 20129, Milan, Italy
| | - Maurizio Infante
- Division of Thoracic Surgery, Istituto Clinico Humanitas, 20089 Rozzano MI, Italy
| | - Marco Alloisio
- Division of Thoracic Surgery, Istituto Clinico Humanitas, 20089 Rozzano MI, Italy
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