1
|
Afolabi H, Zhang BM, O'Shaughnessy M, Chertow GM, Lafayette R, Charu V. The Association of Class I and II Human Leukocyte Antigen Serotypes With End-Stage Kidney Disease Due to Membranoproliferative Glomerulonephritis and Dense Deposit Disease. Am J Kidney Dis 2024; 83:79-89. [PMID: 37739026 DOI: 10.1053/j.ajkd.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 09/24/2023]
Abstract
RATIONALE & OBJECTIVE Membranoproliferative glomerulonephritis (MPGN), encompassing several distinct diseases, is a rare but significant cause of kidney failure in the United States. The potential etiologies of MPGN are unclear, but prior studies have suggested dysregulation of the alternative complement pathway and, recently, autoimmunity as potential mechanisms driving MPGN pathogenesis. In this study, we examined HLA associations with end-stage kidney disease (ESKD) due to MPGN and dense deposit disease (DDD) in a large racially and ethnically diverse US-based cohort. STUDY DESIGN Case-control study. SETTING & PARTICIPANTS Using US Renal Data System (USRDS) and United Network for Organ Sharing (UNOS) data, we identified 3,424 patients with kidney failure due to MPGN and 263 due to DDD. We matched patients to kidney donor controls on designated race and ethnicity in a 1:15 ratio. EXPOSURE 58 class I and II HLA serotypes. OUTCOME Case-control status. ANALYTICAL APPROACH For each disease cohort, univariable and multivariable logistic regression analyses were used to investigate associations between the disease and 58 HLA serotypes. In subgroup analyses, we investigated HLA associations in White and Black patients. We also studied antiglomerular basement membrane (anti-GBM) nephritis as a positive-control outcome. We applied a Bonferroni correction to account for multiple comparisons. RESULTS Eighteen serotypes were significantly associated with the odds of having MPGN in univariable analyses, with DR17 having the strongest association (odds ratio [OR], 1.55 [95% CI, 1.44-1.68], P=4.33e-28). No significant associations were found between any HLA serotype and DDD. Designated race-specific analyses showed comparable findings. We recapitulated known HLA associations in anti-GBM nephritis. LIMITATIONS Reliance on HLA serotypes (rather than genotype), lack of biopsy-confirmed diagnoses. CONCLUSIONS HLA-DR17 is associated with ESKD due to MPGN in a racially and ethnically diverse cohort. The strength of association was similar in White and Black patients, suggesting a role in the pathogenesis of MPGN. No HLA associations were observed in patients with DDD. PLAIN-LANGUAGE SUMMARY Prior studies have suggested dysregulation of the alternative complement pathway as a potential etiology of membranoproliferative glomerulonephritis (MPGN), but recent evidence from a British White population has implicated an autoimmune mechanism in MPGN pathogenesis. We investigated HLA associations between MPGN and dense deposit disease (DDD) in a large racially and ethnically diverse cohort of patients. We found that HLA-DR17 is associated with end-stage kidney disease (ESKD) due to MPGN in both White and Black patients. By contrast, no significant HLA associations with ESKD due to DDD were identified. These results suggest a role for autoimmunity in some cases of MPGN and highlight differences in the disease etiology of MPGN compared with DDD.
Collapse
Affiliation(s)
- Halimat Afolabi
- Department of Pathology, Department of Medicine, School of Medicine, Stanford University, Stanford, California
| | - Bing M Zhang
- Department of Pathology, Department of Medicine, School of Medicine, Stanford University, Stanford, California
| | | | - Glenn M Chertow
- Division of Nephrology, Department of Medicine, School of Medicine, Stanford University, Stanford, California
| | - Richard Lafayette
- Division of Nephrology, Department of Medicine, School of Medicine, Stanford University, Stanford, California
| | - Vivek Charu
- Department of Pathology, Department of Medicine, School of Medicine, Stanford University, Stanford, California; Department of Medicine and Quantitative Sciences Unit, Department of Medicine, School of Medicine, Stanford University, Stanford, California.
| |
Collapse
|
2
|
Tsuchiya KD, Funke B, Hegde M, Santani A, Souers RJ, Szelinger S, Halley J, Zhao Q, Mot N, Roy A, Smith VL, Zhang BM, Voelkerding K, Moyer AM. Implementation, Evolution, and Laboratory Performance of Methods-Based Proficiency Testing for Next-Generation Sequencing Detection of Germline Sequence Variants. Arch Pathol Lab Med 2023:496484. [PMID: 37852169 DOI: 10.5858/arpa.2023-0090-cp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2023] [Indexed: 10/20/2023]
Abstract
CONTEXT.— Next-generation sequencing (NGS)-based assays are used for diagnosis of diverse inherited disorders. Limited data are available pertaining to interlaboratory analytical performance of these assays. OBJECTIVE.— To report on the College of American Pathologists (CAP) NGS Germline Program, which is methods based, and explore the evolution in laboratory testing practices. DESIGN.— Results from the NGS Germline Program from 2016-2020 were analyzed for interlaboratory analytical performance. Self-reported laboratory testing practices were also evaluated. RESULTS.— From 2016-2020, a total of 297 laboratories participated in at least 1 program mailing. Of the 289 laboratories that provided information on tests offered, 138 (47.8%) offered only panel testing throughout their enrollment, while 35 (12.1%) offered panels and exome testing, 30 (10.4%) offered only exomes, 9 (3.1%) offered only genomes, and 15 (5.2%) offered panels, exomes, and genomes. The remainder (62 laboratories, 21.4%) changed their test offerings during the 2016-2020 timeframe. Considering each genomic position/interval, the median detection percentage at variant positions across the 2016-2020 mailings ranged from 94.3% to 100%, while at reference positions (no variant detected), the median correct response percentage was 100% across all mailings. When considering performance of individual laboratories, 89.5% (136 of 152) to 98.0% (149 of 152) of laboratories successfully met the detection threshold (≥90% of the variants present), while 94.6% (87 of 92) to 100% (163 of 163) of laboratories met the 95% specificity threshold across mailings. CONCLUSIONS.— Since the inception of this program, laboratories have consistently performed well. The median sensitivity and specificity of detection of sequence variants included in this program (eg, single nucleotide variants, insertions, and deletions) were 100.0%.
Collapse
Affiliation(s)
- Karen D Tsuchiya
- From the Department of Laboratory Medicine and Pathology, University of Washington, Seattle (Tsuchiya)
| | | | | | - Avni Santani
- Center for Applied Genomics, Children's Hospital of Philadelphia, Pennsylvania (Santani)
- LetsGetChecked, Monrovia, California (Santani)
| | - Rhona J Souers
- Biostatistics Department (Souers) and Proficiency Testing (Szelinger, Halley, Zhao, Mot), College of American Pathologists, Northfield, Illinois
| | - Szabolcs Szelinger
- Biostatistics Department (Souers) and Proficiency Testing (Szelinger, Halley, Zhao, Mot), College of American Pathologists, Northfield, Illinois
| | - Jaimie Halley
- Biostatistics Department (Souers) and Proficiency Testing (Szelinger, Halley, Zhao, Mot), College of American Pathologists, Northfield, Illinois
| | - Qin Zhao
- Biostatistics Department (Souers) and Proficiency Testing (Szelinger, Halley, Zhao, Mot), College of American Pathologists, Northfield, Illinois
| | - Nicole Mot
- Biostatistics Department (Souers) and Proficiency Testing (Szelinger, Halley, Zhao, Mot), College of American Pathologists, Northfield, Illinois
| | - Angshumoy Roy
- the Departments of Pathology & Immunology and Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston (Roy)
| | - Vanessa L Smith
- the Department of Pathology, Duke University School of Medicine, Durham, North Carolina (Smith)
| | - Bing M Zhang
- the Department of Pathology, Stanford University School of Medicine, Stanford, California (Zhang)
| | | | - Ann M Moyer
- the Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota (Moyer)
| |
Collapse
|
3
|
Han J, Moayedi Y, Henricksen EJ, Waddell K, Valverde-Twiggs J, Kim D, Luikart H, Zhang BM, Teuteberg J, Khush KK. Primary Graft Dysfunction Is Associated With Development of Early Cardiac Allograft Vasculopathy, but Not Other Immune-mediated Complications, After Heart Transplantation. Transplantation 2023; 107:1624-1629. [PMID: 36801852 DOI: 10.1097/tp.0000000000004551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
BACKGROUND We investigated associations between primary graft dysfunction (PGD) and development of acute cellular rejection (ACR), de novo donor-specific antibodies (DSAs), and cardiac allograft vasculopathy (CAV) after heart transplantation (HT). METHODS A total of 381 consecutive adult HT patients from January 2015 to July 2020 at a single center were retrospectively analyzed. The primary outcome was incidence of treated ACR (International Society for Heart and Lung Transplantation grade 2R or 3R) and de novo DSA (mean fluorescence intensity >500) within 1 y post-HT. Secondary outcomes included median gene expression profiling score and donor-derived cell-free DNA level within 1 y and incidence of cardiac allograft vasculopathy (CAV) within 3 y post-HT. RESULTS When adjusted for death as a competing risk, the estimated cumulative incidence of ACR (PGD 0.13 versus no PGD 0.21; P = 0.28), median gene expression profiling score (30 [interquartile range, 25-32] versus 30 [interquartile range, 25-33]; P = 0.34), and median donor-derived cell-free DNA levels was similar in patients with and without PGD. After adjusting for death as a competing risk, estimated cumulative incidence of de novo DSA within 1 y post-HT in patients with PGD was similar to those without PGD (0.29 versus 0.26; P = 0.10) with a similar DSA profile based on HLA loci. There was increased incidence of CAV in patients with PGD compared with patients without PGD (52.6% versus 24.8%; P = 0.01) within the first 3 y post-HT. CONCLUSIONS During the first year after HT, patients with PGD had a similar incidence of ACR and development of de novo DSA, but a higher incidence of CAV when compared with patients without PGD.
Collapse
Affiliation(s)
- Jiho Han
- Section of Cardiology, University of Chicago Medical Center, Chicago, IL
| | - Yasbanoo Moayedi
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON, Canada
| | | | - Kian Waddell
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA
| | - Julien Valverde-Twiggs
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA
| | - Daniel Kim
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA
| | - Helen Luikart
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA
| | - Bing M Zhang
- Department of Pathology, Stanford University, Stanford, CA
| | - Jeffrey Teuteberg
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA
| | - Kiran K Khush
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA
| |
Collapse
|
4
|
Malik A, Sayed AA, Han P, Tan MMH, Watt E, Constantinescu-Bercu A, Cocker ATH, Khoder A, Saputil RC, Thorley E, Teklemichael A, Ding Y, Hart ACJ, Zhang H, Mitchell WA, Imami N, Crawley JTB, Salles-Crawley II, Bussel JB, Zehnder JL, Adams S, Zhang BM, Cooper N. The role of CD8+ T-cell clones in immune thrombocytopenia. Blood 2023; 141:2417-2429. [PMID: 36749920 PMCID: PMC10329190 DOI: 10.1182/blood.2022018380] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 02/09/2023] Open
Abstract
Immune thrombocytopenia (ITP) is traditionally considered an antibody-mediated disease. However, a number of features suggest alternative mechanisms of platelet destruction. In this study, we use a multidimensional approach to explore the role of cytotoxic CD8+ T cells in ITP. We characterized patients with ITP and compared them with age-matched controls using immunophenotyping, next-generation sequencing of T-cell receptor (TCR) genes, single-cell RNA sequencing, and functional T-cell and platelet assays. We found that adults with chronic ITP have increased polyfunctional, terminally differentiated effector memory CD8+ T cells (CD45RA+CD62L-) expressing intracellular interferon gamma, tumor necrosis factor α, and granzyme B, defining them as TEMRA cells. These TEMRA cells expand when the platelet count falls and show no evidence of physiological exhaustion. Deep sequencing of the TCR showed expanded T-cell clones in patients with ITP. T-cell clones persisted over many years, were more prominent in patients with refractory disease, and expanded when the platelet count was low. Combined single-cell RNA and TCR sequencing of CD8+ T cells confirmed that the expanded clones are TEMRA cells. Using in vitro model systems, we show that CD8+ T cells from patients with ITP form aggregates with autologous platelets, release interferon gamma, and trigger platelet activation and apoptosis via the TCR-mediated release of cytotoxic granules. These findings of clonally expanded CD8+ T cells causing platelet activation and apoptosis provide an antibody-independent mechanism of platelet destruction, indicating that targeting specific T-cell clones could be a novel therapeutic approach for patients with refractory ITP.
Collapse
Affiliation(s)
- Amna Malik
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Anwar A. Sayed
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Department of Medical Microbiology and Immunology, Taibah University, Medina, Saudi Arabia
| | - Panpan Han
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
- Department of Hematology, Shandong Province Hospital, Shandong First Medical University, Jinan, China
| | - Michelle M. H. Tan
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Eleanor Watt
- Specialist Integrated Haematology and Malignancy Diagnostic Service–Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Adela Constantinescu-Bercu
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | | | - Ahmad Khoder
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Rocel C. Saputil
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Emma Thorley
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Ariam Teklemichael
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Yunchuan Ding
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Alice C. J. Hart
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Haiyu Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Wayne A. Mitchell
- Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Nesrina Imami
- Centre for Immunology and Vaccinology, Imperial College London, London, United Kingdom
| | - James T. B. Crawley
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Isabelle I. Salles-Crawley
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
- Vascular Biology Research Centre, Molecular and Clinical Sciences Research Institute, St. George’s, University of London, London, United Kingdom
| | - James B. Bussel
- Department of Pediatrics, Weill Cornell Medicine, New York, NY
| | - James L. Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Stuart Adams
- Specialist Integrated Haematology and Malignancy Diagnostic Service–Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Bing M. Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Nichola Cooper
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| |
Collapse
|
5
|
Reddi HV, Wand H, Funke B, Zimmermann MT, Lebo MS, Qian E, Shirts BH, Zou YS, Zhang BM, Rose NC, Abu-El-Haija A. Laboratory perspectives in the development of polygenic risk scores for disease: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100804. [PMID: 36971772 DOI: 10.1016/j.gim.2023.100804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 03/29/2023] Open
Affiliation(s)
- Honey V Reddi
- Department of Pathology & Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Hannah Wand
- Division of Cardiovascular Medicine, Department of Medicine, Stanford Medicine, Stanford, CA
| | | | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Mass General Brigham, Cambridge, MA
| | - Emily Qian
- Department of Genetics, Yale University, New Haven, CT
| | - Brian H Shirts
- Department of Laboratory Medicine & Pathology, UW Medicine, University of Washington, Seattle, WA
| | - Ying S Zou
- Department of Genomic Medicine and Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Bing M Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Nancy C Rose
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Utah Health, Salt Lake City, UT
| | - Aya Abu-El-Haija
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA; Harvard Medical School, Boston, MA
| |
Collapse
|
6
|
Tung JK, Jangam D, Ho CC, Fung E, Khodadoust MS, Kim YH, Zehnder JL, Stehr H, Zhang BM. Minimal/Measurable Residual Disease (MRD) Monitoring in Patients with Lymphoid Neoplasms by High-Throughput Sequencing of the T-Cell Receptor. J Mol Diagn 2023; 25:331-341. [PMID: 36870603 DOI: 10.1016/j.jmoldx.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 03/06/2023] Open
Abstract
High-throughput sequencing of the T-cell receptor beta (TRB) and gamma (TRG) loci is increasingly utilized due to its high sensitivity, specificity, and versatility in the diagnosis of various T-cell malignancies. Application of these technologies for tracking disease burden can be valuable in detecting recurrence, determining response to therapy, guiding future management of patients, and establishing endpoints for clinical trials. In this study, the performance of the commercially available LymphoTrack high-throughput sequencing assay was assessed for determining residual disease burden in patients with various T-cell malignancies seen at the authors' institution. A custom bioinformatics pipeline and database was also developed to facilitate minimal/measurable residual disease analysis and clinical reporting. This assay demonstrated excellent test performance characteristics, achieving a sensitivity of 1 of 100,000 T-cell equivalents for the DNA inputs evaluated and high concordance with orthogonal testing methods. This assay was further utilized to correlate disease burden in several patients, demonstrating its potential utility for monitoring patients with T-cell malignancies.
Collapse
Affiliation(s)
- Jack K Tung
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Diwash Jangam
- Molecular Pathology Laboratory, Stanford Health Care, Stanford, California
| | - Chandler C Ho
- Molecular Pathology Laboratory, Stanford Health Care, Stanford, California
| | - Eula Fung
- Molecular Pathology Laboratory, Stanford Health Care, Stanford, California
| | - Michael S Khodadoust
- Department of Dermatology, Stanford University School of Medicine, Stanford, California; Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, California
| | - Youn H Kim
- Department of Dermatology, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Bing M Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
| |
Collapse
|
7
|
McAtee J, Zhang BM. A Retrospective Analysis to Identify Barriers in Allogeneic Hematopoietic Stem Cell Transplantation with Ethnically Diverse Population. Transplant Cell Ther 2023. [DOI: 10.1016/s2666-6367(23)00538-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
8
|
Sigurjonsdottir VK, Purington N, Chaudhuri A, Zhang BM, Fernandez-Vina M, Palsson R, Kambham N, Charu V, Piburn K, Maestretti L, Shah A, Gallo A, Concepcion W, Grimm PC. Complement-Binding Donor-Specific Anti-HLA Antibodies: Biomarker for Immunologic Risk Stratification in Pediatric Kidney Transplantation Recipients. Transpl Int 2022; 35:10158. [PMID: 35992747 PMCID: PMC9386741 DOI: 10.3389/ti.2021.10158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/27/2021] [Indexed: 01/09/2023]
Abstract
Antibody-mediated rejection is a common cause of early kidney allograft loss but the specifics of antibody measurement, therapies and endpoints have not been universally defined. In this retrospective study, we assessed the performance of risk stratification using systematic donor-specific antibody (DSA) monitoring. Included in the study were children who underwent kidney transplantation between January 1, 2010 and March 1, 2018 at Stanford, with at least 12-months follow-up. A total of 233 patients were included with a mean follow-up time of 45 (range, 9–108) months. Median age at transplant was 12.3 years, 46.8% were female, and 76% had a deceased donor transplant. Fifty-two (22%) formed C1q-binding de novo donor-specific antibodies (C1q-dnDSA). After a standardized augmented immunosuppressive protocol was implemented, C1q-dnDSA disappeared in 31 (58.5%). Graft failure occurred in 16 patients at a median of 54 (range, 5–83) months, of whom 14 formed dnDSA. The 14 patients who lost their graft due to rejection, all had persistent C1q-dnDSA. C1q-binding status improved the individual risk assessment, with persistent; C1q binding yielding the strongest independent association of graft failure (hazard ratio, 45.5; 95% confidence interval, 11.7–177.4). C1q-dnDSA is more useful than standard dnDSA as a noninvasive biomarker for identifying patients at the highest risk of graft failure.
Collapse
Affiliation(s)
- Vaka K. Sigurjonsdottir
- Division of Nephrology, Department of Pediatrics, Stanford University, Palo Alto, CA, United States
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Division of Nephrology, Internal Medicine and Emergency Services, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
- *Correspondence: Vaka K. Sigurjonsdottir,
| | - Natasha Purington
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA, United States
| | - Abanti Chaudhuri
- Division of Nephrology, Department of Pediatrics, Stanford University, Palo Alto, CA, United States
| | - Bing M. Zhang
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Stanford University, Palo Alto, CA, United States
| | - Marcelo Fernandez-Vina
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Stanford University, Palo Alto, CA, United States
| | - Runolfur Palsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Division of Nephrology, Internal Medicine and Emergency Services, Landspitali–The National University Hospital of Iceland, Reykjavik, Iceland
| | - Neeraja Kambham
- Department of Pathology, Stanford University, Palo Alto, CA, United States
| | - Vivek Charu
- Department of Pathology, Stanford University, Palo Alto, CA, United States
| | - Kim Piburn
- Division of Nephrology, Department of Pediatrics, Stanford University, Palo Alto, CA, United States
| | - Lynn Maestretti
- Division of Nephrology, Department of Pediatrics, Stanford University, Palo Alto, CA, United States
| | - Anika Shah
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Stanford University, Palo Alto, CA, United States
| | - Amy Gallo
- Division of Nephrology, Department of Pediatrics, Stanford University, Palo Alto, CA, United States
- Division of Abdominal Transplantation, Department of Surgery, Stanford University, Palo Alto, CA, United States
| | - Waldo Concepcion
- Transplantation Services, Mohamed Bin Rashid University, Dubai, United Arab Emirates
| | - Paul C. Grimm
- Division of Nephrology, Department of Pediatrics, Stanford University, Palo Alto, CA, United States
| |
Collapse
|
9
|
Ho CC, Tung JK, Zehnder JL, Zhang BM. Validation of a Next-Generation Sequencing-Based T-Cell Receptor Gamma Gene Rearrangement Diagnostic Assay: Transitioning from Capillary Electrophoresis to Next-Generation Sequencing. J Mol Diagn 2021; 23:805-815. [PMID: 33892183 DOI: 10.1016/j.jmoldx.2021.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 03/15/2021] [Accepted: 03/25/2021] [Indexed: 01/23/2023] Open
Abstract
Assessment of T-cell receptor γ gene (TRG) rearrangements is an importants consideration in the diagnostic workup of lymphoproliferative diseases. Although fragment analysis by PCR and capillary electrophoresis (CE) is the current standard of such assessment in clinical molecular diagnostic laboratories, it does not provide sequence information and is only semi-quantitative. Next-generation sequencing (NGS)-based assays are an attractive alternative to the conventional fragment size-based methods, given that they generate results with specific clonotype sequence information and allow for more accurate quantitation. The present study evaluated various test parameters and performance characteristics of a commercially available NGS-based TRG gene-rearrangement assay by testing 101 clinical samples previously characterized by fragment analysis. The NGS TRG assay showed an overall accuracy of 83% and an analytical specificity of 100%. The concordance rates were 88% to 95% in the Vγ1-8, Vγ10, and Vγ11 gene families, but lower in the Vγ9 gene family. This difference was mostly attributed to the incomplete polyclonal symmetry resulting from the two-tube CE assay versus the one-tube design of the NGS assay. The NGS assay also demonstrated strengths in distinguishing clonotypes of the same fragment size. This clinical validation demonstrated robust performance of the NGS-based TRG assay and identified potential pitfalls associated with CE assay design that are important for understanding the observed discrepancies with the CE-based assay.
Collapse
Affiliation(s)
- Chandler C Ho
- Molecular Pathology Laboratory, Stanford Health Care, Stanford, California
| | - Jack K Tung
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Bing M Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
| |
Collapse
|
10
|
Zhang BM, Keegan A, Li P, Lindeman NI, Nagarajan R, Routbort MJ, Vasalos P, Kim AS, Merker JD. An Overview of Characteristics of Clinical Next-Generation Sequencing-Based Testing for Hematologic Malignancies. Arch Pathol Lab Med 2021; 145:1110-1116. [PMID: 33450747 DOI: 10.5858/arpa.2019-0661-cp] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2020] [Indexed: 11/06/2022]
Abstract
CONTEXT.— With the increasing integration of molecular alterations into the evaluation of hematologic malignancies (HM), somatic mutation profiling by next-generation sequencing (NGS) has become a common clinical testing strategy. Limited data are available about the characteristics of these assays. OBJECTIVE.— To describe assay characteristics, specimen requirements, and reporting practices for NGS-based HM testing using College of American Pathologists proficiency testing survey data. DESIGN.— The College of American Pathologists NGS Hematologic Malignancies Survey (NGSHM) results from 78 laboratories were used to determine laboratory practices in NGS-based HM testing. RESULTS.— The majority of laboratories performed tumor-only (88.5% [69 of 78]), targeted sequencing of cancer genes or mutation hotspots (98.7% [77 of 78]); greater than 90% performed testing on fresh bone marrow and peripheral blood. The majority of laboratories reported a 5% lower limit of detection for single-nucleotide variants (73.1% [57 of 78]) and small insertions and deletions (50.6% [39 of 77]). A majority of laboratories used benchtop sequencers and custom enrichment approaches. CONCLUSIONS.— This manuscript summarizes the characteristics of clinical NGS-based testing for the detection of somatic variants in HM. These data may be broadly useful to inform laboratory practice and quality management systems, regulation, and oversight of NGS testing, and precision medicine efforts using a data-driven approach.
Collapse
Affiliation(s)
- Bing M Zhang
- From the Department of Pathology, Stanford University School of Medicine, Stanford, California (Zhang)
| | - Alissa Keegan
- the Department of Pathology, Brigham and Women's Hospital, Harvard University, Boston, Massachusetts (Keegan, Lindeman, Kim).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Peng Li
- ARUP Laboratories, Department of Pathology, University of Utah, Salt Lake City, Utah (Li)
| | - Neal I Lindeman
- the Department of Pathology, Brigham and Women's Hospital, Harvard University, Boston, Massachusetts (Keegan, Lindeman, Kim).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Rakesh Nagarajan
- PierianDx, St Louis, Missouri (Nagarajan).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Mark J Routbort
- the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Routbort).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Patricia Vasalos
- Proficiency Testing, College of American Pathologists, Northfield, Illinois (Vasalos).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Annette S Kim
- the Department of Pathology, Brigham and Women's Hospital, Harvard University, Boston, Massachusetts (Keegan, Lindeman, Kim).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Jason D Merker
- the Departments of Pathology and Laboratory Medicine & Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill (Merker).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| |
Collapse
|
11
|
Hou Y, Shao L, Zhou H, Liu Y, Fisk DG, Spiteri E, Zehnder JL, Peng J, Zhang BM, Hou M. Identification of a pathogenic TUBB1 variant in a Chinese family with congenital macrothrombocytopenia through whole genome sequencing. Platelets 2021; 32:1108-1112. [PMID: 33400601 DOI: 10.1080/09537104.2020.1869714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Congenital macrothrombocytopenia is a genetically heterogeneous group of rare disorders. We herein report a large Chinese family presented with phenotypic variability involving thrombocytopenia and/or giant platelets. Whole genome sequencing (WGS) of the proband and one of his affected brothers identified a potentially pathogenic c.952 C > T heterozygous variant in the TUBB1 gene. This p.R318W β1-tubulin variant was also identified in three additional siblings and five members of the next generation. These findings were consistent with an autosomal dominant inheritance with incomplete penetrance. Moreover, impaired platelet agglutination in response to ristocetin was detected in the patient's brother. Half of the family members harboring the p.R318W mutation displayed significantly decreased external release of p-selectin by stimulated platelets. The p.R318W β1-tubulin mutation was identified for the first time in a Chinese family with congenital macrothrombocytopenia using WGS as an unbiased sequencing approach. Affected individuals within the family demonstrated impaired platelet aggregation and/or release functions.
Collapse
Affiliation(s)
- Yu Hou
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Linlin Shao
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hai Zhou
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yanfeng Liu
- Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Dianna G Fisk
- Clinical Genomics Program, Stanford Health Care, Palo Alto, United States
| | - Elizabeth Spiteri
- Clinical Genomics Program, Stanford Health Care, Palo Alto, United States.,Department of Pathology, Stanford University School of Medicine, Palo Alto, United States
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, Palo Alto, United States
| | - Jun Peng
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Bing M Zhang
- Department of Pathology, Stanford University School of Medicine, Palo Alto, United States
| | - Ming Hou
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Shandong Provincial Key Laboratory of Immunohematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Leading Research Group of Scientific Innovation, Department of Science and Technology of Shandong Province, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| |
Collapse
|
12
|
Shyr DC, Zhang BM, Saini G, Madani ND, Schultz LM, Patel S, Kristovich K, Fernandez-Vina M, Bertaina A. HLA-haplotype loss after TCRαβ/CD19-depleted haploidentical HSCT. Bone Marrow Transplant 2020; 56:733-737. [PMID: 33070150 DOI: 10.1038/s41409-020-01081-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/29/2020] [Indexed: 11/09/2022]
Affiliation(s)
- David C Shyr
- Department of Pediatrics, Division of Stem Cell Transplant and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Bing M Zhang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gopin Saini
- Department of Pediatrics, Division of Stem Cell Transplant and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Nahid D Madani
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Liora M Schultz
- Department of Pediatrics, Division of Hematology and Oncology, Stanford University, Stanford, CA, USA
| | - Shabnum Patel
- Department of Medicine, Cancer Institute, Stanford University, Stanford, CA, USA
| | - Karen Kristovich
- Department of Pediatrics, Division of Stem Cell Transplant and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | | | - Alice Bertaina
- Department of Pediatrics, Division of Stem Cell Transplant and Regenerative Medicine, Stanford University, Stanford, CA, USA.
| |
Collapse
|
13
|
Sharma D, Egidio C, Grskovic M, Viña MAF, Zhang BM. Chimerism Monitoring with Highly Sensitive and Precise Next-Generation Sequencing Assay in Patients Post-Allogeneic Hematopoietic Stem Cell Transplantation. Biol Blood Marrow Transplant 2020. [DOI: 10.1016/j.bbmt.2019.12.412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
14
|
Zhang H, Zhang BM, Guo X, Xu L, You X, West RB, Bussel JB, Zehnder JL. Blood transcriptome and clonal T-cell correlates of response and non-response to eltrombopag therapy in a cohort of patients with chronic immune thrombocytopenia. Haematologica 2019; 105:e129-e132. [PMID: 31296576 DOI: 10.3324/haematol.2019.226688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Haiyu Zhang
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Bing M Zhang
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Xiangqian Guo
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.,Department of Preventive Medicine, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Liwen Xu
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Xiaoqing You
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Robert B West
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - James B Bussel
- Platelet Disorders Center, Department of Pediatrics, Weill-Cornell Medicine, New York, NY, USA
| | - James L Zehnder
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| |
Collapse
|
15
|
Zhu MW, Wei JM, Chen W, Yang X, Cui HY, Zhu SN, Zhang PP, Xiong J, Zheng DF, Song HJ, Liang XY, Zhang L, Xu WY, Wang HB, Su GQ, Feng LJ, Chen T, Wu YD, Li H, Sun JQ, Shi Y, Tong BD, Zhou SM, Wang XY, Huang YH, Zhang BM, Xu J, Zhang HY, Chang GL, Jia ZY, Chen SF, Hu J, Zhang XW, Wang H, Li ZD, Gao YY, Gui B. [Dynamic investigation of nutritional risk in patients with malignant tumor during hospitalization]. Zhonghua Yi Xue Za Zhi 2018; 98:1093-1098. [PMID: 29690722 DOI: 10.3760/cma.j.issn.0376-2491.2018.14.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To prospectively investigate the changes in nutritional status of patients with malignant tumors during hospitalization by using nutritional risk screening (NRS2002), and to analyze the correlation between the nutritional status and clinical outcomes . Methods: This was a prospective and parallel research done by multi-center collaboration from 34 hospitals in China from June to September 2014.Hospitalized patients with malignant tumors inthese departments (Department of Gastroenterology, respiratory medicine, oncology, general surgery, thoracic surgery and geriatrics)were investigated. Only the patients with age≥ 18 years and hospitalization time between 7-30 days were included. During hospitalization, the physical indexes of human bodywere measured, and the NRS 2002 scores, and monitored the nutritional support at the time points of admission and 24 hours before discharge were recorded.And whether there was a nutritional risk in hospitalized patients and its association with clinical outcomes were investigated. Results: A total of 2 402 patients with malignancies were enrolled in this study. Seventy fourpatients who did not complete NRS2002 were eliminated, and 2 328 patients were included. The number of the main diseases was the top five, including 587 cases of colorectal cancer, 567 cases of lung cancer, 564 cases of gastric cancer, 146 cases of esophageal cancer, and 119 cases of liver tumor. At the time of discharge, compared with admission, the BMI, body weight, grip and calf circumferences of patients with malignant tumor were significantly decreased (P<0.05). The total protein, albumin, prealbumin and hemoglobin were significantly lower than those at admission (P<0.05). In 2 328 patients who were completed nutritional risk screening, the rate of malnutrition at admission was 11.1% (BMI =18.5, 258/2 328) and the rate of malnutrition at discharge was 10.9% (BMI =18.5, 254/2 328), there were no significant differences (χ(2)=0.019 7, P=0.888). There were 1 204 patients with nutritional risk at admission (51.7%, NRS2002 score≥3)and 1 352 patients with nutritional risk at discharge (58.1%, NRS2002 score≥3), with significant differences (χ(2)=49.9, P<0.001). The incidence of nutritional risk in patients with colorectal, stomach, and lung tumors at discharge was significantly higher than that at admission (P<0.05). The infective complications and other complications of patients with nutritional risk were significantly greater than those without nutritional risk at admission and at discharge.ICU hospitalization stay of patients with nutritional risk was increased significantly than those without nutritional risk at admission(P=0.042). Hospitalization expenses of patients with nutritional risk was increased significantly than those of patients without nutritional risk at discharge(P<0.01). Conclusion: The patients with malignant tumor have a higher incidence rate of malnutrition at both admission and discharge and malnutritionhas correlation with adverse clinical outcomes.The aboveindicators did not improve significantly at discharge.Doctors should pay more attention to the nutritional status (screening and evaluation)of patients before discharge and use appropriate and adequate nutrition support in order to prevent the weight loss and improve the life quality of patients.
Collapse
Affiliation(s)
- M W Zhu
- Department of General Surgery, Beijing Hospital, Beijing 100730, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Affiliation(s)
- Bing M Zhang
- Stanford University School of Medicine, Stanford, CA
| | | | - Chieh Y Lin
- Stanford University School of Medicine, Stanford, CA
| | - James Ford
- Stanford University School of Medicine, Stanford, CA
| | | | | |
Collapse
|
17
|
|
18
|
Wang SX, Zhang BM, Wakelee H, Diehn M, Kunder CA, Neal JW. PS01.67: Case Series of MET Exon 14 Skipping Mutation-Positive Non–Small Cell Lung Cancers and Response to Crizotinib. J Thorac Oncol 2016. [DOI: 10.1016/j.jtho.2016.09.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
19
|
Xu L, You X, Zheng P, Zhang BM, Gupta PK, Lavori P, Meyer E, Zehnder JL. Methodologic Considerations in the Application of Next-Generation Sequencing of Human TRB Repertoires for Clinical Use. J Mol Diagn 2016; 19:72-83. [PMID: 27815002 DOI: 10.1016/j.jmoldx.2016.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/24/2016] [Accepted: 07/28/2016] [Indexed: 01/08/2023] Open
Abstract
Next-generation sequencing (NGS) of immune receptors has become a standard tool to assess minimal residual disease (MRD) in patients treated for lymphoid malignancy, and it is being used to study the T-cell repertoire in many clinical settings. To better understanding the potential clinical utility and limitations of this application outside of MRD, we developed a BIOMED-2 primer-based NGS method and characterized its performance in controls and patients with graft-versus-host disease (GVHD) after allogeneic hematopoietic transplant. For controls and patients with GVHD, replicate sequencing of the same T-cell receptor β (TRB) libraries was highly reproducible. Higher variability was observed in sequencing of different TRB libraries made from the same DNA stock. Variability was increased in patients with GVHD compared with controls; patients with GVHD also had lower diversity than controls. In the T-cell repertoire of a healthy person, approximately 99.6% of the CDR3 clones were in low abundance, with frequency <10-3. A single library could identify >93% of the clones with frequency ≥10-3 in the repertoire. Sequencing in duplicate increased the average detection rate to >97%. This work demonstrates that NGS reliably and robustly characterizes TRB populations in healthy individuals and patients with GVHD with frequency ≥10-3 and provides a methodologic framework for applying NGS immune repertoire methods to clinical testing applications beyond MRD.
Collapse
Affiliation(s)
- Liwen Xu
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - Xiaoqing You
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - PingPing Zheng
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - Bing M Zhang
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - Puja K Gupta
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - Philip Lavori
- Department of Biomedical Data Science, Stanford School of Medicine, Stanford University, Stanford, California
| | - Everett Meyer
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California.
| |
Collapse
|
20
|
Huo Y, Wang F, Sun B, Yin LR, Zhang PP, Zhang YJ, Zhang BM. [Prokaryotic expression and purification of antimicrobial peptide LL-37 and the inhibiting effect against Candida albicans]. Zhonghua Fu Chan Ke Za Zhi 2016; 51:120-5. [PMID: 26917481 DOI: 10.3760/cma.j.issn.0529-567x.2016.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To study the inhibitory effect of antimicrobial peptide LL-37 on Candida albicans through its ability to promote the secretion of immune factors by vaginal epithelial cells. METHODS (1) LL-37 prokaryotic expression vector pET-Duet/LL-37 was constructed and its expression was induced in Escherichia coli M15. The expressed LL-37 fusion protein was purified and identified by western blot. Antifungal activity of the purified protein was initially identified by Kirby-Bauer (K-B) method. (2) Purified LL-37 protein was added to human vaginal epithelial cells co-cultured with Candida, and inhibitory effect on Candida growth was determined by the glucose consumption method. Interferon γ (IFN-γ), interleukin 10 (IL-10) concentration and IFN-γ/IL-10 ratio were measured by ELISA at different time points. RESULTS (1) LL-37 fusion protein was purified to 96% purity at a concentration of 433.92 μg/ml, and was shown to possess anti-fungal activity confirmed by the K-B method. (2) A Candida-vaginal epithelial cells co-culture system was successfully constructed. LL-37 recombinant protein inhibited the growth of Candida with absorbance values significantly higher in the treatment group compared to the control group at all measured time points (12-hour: 3.008±0.003 versus 2.967±0.003, 24-hour: 2.941±0.003 versus 2.601±0.003, 48-hour: 2.893 ± 0.004 versus 2.409 ± 0.003; all P<0.01). Furthermore, the rate of decrease was also much slower compared to the control group. In both control and experimental groups, IFN-γ and IL-10 secretion levels were observed to rise at first peaking at 24 hours and subsequently decrease. For each time period, IFN-γ concentration in the experimental group was significantly higher at 24 hours compared to the control group [(104.00 ± 1.07) versus (85.17 ± 0.28) pg/ml,P<0.01]. In contrast, IL-10 concentrations were significantly lower than the control group at all time points (P<0.01). IFN-γ/IL-10 ratio was also observed to be significantly higher than the control group at all measured time points (P<0.01). CONCLUSIONS (1) Recombinant protein LL-37 could significantly inhibit the growth of Candida. (2) By influencing the secretion of immune factors such as IFN-γ, IL-10, etc, recombinant protein LL-37 is able to adjust vaginal epithelial cells local immunity, and enhance resistance to Candida infection.
Collapse
Affiliation(s)
- Y Huo
- Department of Family Planning, the Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | | | | | | | | | | | | |
Collapse
|
21
|
Zhang BM, Kohli V, Adachi R, López JA, Udden MM, Sullivan R. Calmodulin binding to the C-terminus of the small-conductance Ca2+-activated K+ channel hSK1 is affected by alternative splicing. Biochemistry 2001; 40:3189-95. [PMID: 11258935 DOI: 10.1021/bi001675h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We identified three splice variants of hSK1 whose C-terminal structures are determined by the independent deletion of two contiguous nucleotide sequences. The upstream sequence extends 25 bases in length, is initiated by a donor splice site within exon 8, and terminates at the end of the exon. The downstream sequence consists of nine bases that compose exon 9. When the upstream sequence (hSK1(-)(25b)) or both sequences (hSK1(-)(34b)) are deleted, truncated proteins are encoded in which the terminal 118 amino acids are absent. The binding of calmodulin to these variants is diminished, particularly in the absence of Ca2+ ions. The first 20 amino acids of the segment deleted from hSK1(-)(25b) and hSK1(-)(34b) contain a 1-8-14 Ca2+ calmodulin binding motif, and synthetic oligopeptides based on this region bind calmodulin better in the presence than absence of Ca2+ ions. When the downstream sequence (hSK1(-)(9b)) alone is deleted, only the three amino acids A452, Q453, and K454 are removed, and calmodulin binding is not reduced. On the basis of the relative abundance of mRNA encoding each of the four isoforms, the full-length variant appears to account for most hSK1 in the human hippocampus, while hSK1(-)(34b) predominates in reticulocytes, and hSK1(-)(9b) is especially abundant in human erythroleukemia cells in culture. We conclude that the binding of calmodulin by hSK1 can be modulated through alternative splicing.
Collapse
Affiliation(s)
- B M Zhang
- Department of Medicine, Baylor College of Medicine, and Research Department, VA Medical Center, Houston, Texas 77030, USA
| | | | | | | | | | | |
Collapse
|
22
|
McCutcheon IE, Friend KE, Gerdes TM, Zhang BM, Wildrick DM, Fuller GN. Intracranial injection of human meningioma cells in athymic mice: an orthotopic model for meningioma growth. J Neurosurg 2000; 92:306-14. [PMID: 10659019 DOI: 10.3171/jns.2000.92.2.0306] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECT Although human meningioma cells have been heterotopically implanted in nude mice, introducing these cells into intracranial locations seems more likely to reproduce normal patterns of tumor growth. To provide an orthotopic xenograft model of meningioma, the authors implanted a controlled quantity of meningioma cells at subdural and intracerebral sites in athymic mice. METHODS Malignant (one tumor), atypical (two tumors), or benign (three tumors) meningiomas were placed into primary cell cultures. Cells (10(6)/10 microl) from these cultures and from an immortalized malignant meningioma cell line, IOMM-Lee, were injected with stereotactic guidance into the frontal white matter or subdural space of athymic mice. Survival curves were plotted for mice receiving tumor cells of each histological type and according to injection site. Other mice were killed at intervals and their heads were sectioned whole. Hematoxylin and eosin staining of these sections revealed the extent of tumor growth. CONCLUSIONS The median length of survival for mice with malignant, atypical, or benign tumors was 19, 42, or longer than 84 days, respectively. Atypical and malignant tumors were invasive, but did not metastasize extracranially. Malignant tumors uniformly showed leptomeningeal dissemination and those implanted intracerebrally grew locally and spread noncontiguously to the ventricles, choroid plexus, convexities, and skull base. Tumors formed in only 50% of mice injected with benign meningioma cells, whereas injection of more aggressive cells was uniformly successful at tumor production. The three types of human meningiomas grown intracranially in athymic mice maintained their relative positions in the spectrum of malignancy. However, atypical meningiomas became more aggressive after xenografting and acquired malignant features, implying that there had been immune constraint in the original host. Tumor cells injected into brain parenchyma migrated to more optimal environments and grew best there. This model provides insights into the biology of meningiomas and may be useful for testing new therapies.
Collapse
Affiliation(s)
- I E McCutcheon
- Department of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston 77030, USA.
| | | | | | | | | | | |
Collapse
|
23
|
Zhang BM, Song XR. [Comparative study of the effect of wei-yan-ning and furazolidone in the treatment of gastritis and gastric ulcer caused by pyloric Campylobacter]. Zhong Xi Yi Jie He Za Zhi 1989; 9:599-600, 581. [PMID: 2605737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Wei-Yan-Ning and Furazolidone were used separately in the treatment of 62 cases of gastritis and gastric ulcer caused by pyloric campylobacteria. The examinations one month later proved, through the gastrofiberscopy and pathological test as well as the urease test, that, among the 40 cases of Wei-Yan-Ning group, there were 25 cures (62.5%), prominent effect for 9 cases (22.5%), improvement for 3 cases (7.5%). The total effective rate was 92.5%. Among the 22 cases of the Furazolidone group, there were 7 cures (31.8%), prominent effect for 5 cases (22.7%), improvement for 4 cases (18.2%). The total effective rate was 72.7%. As for the improvement of symptom, the average time for the Wei-Yan-Ning group was 12.5 +/- 8.12 days; and the Furazolidone group was 21.63 +/- 7.87 days. Therefore, the effect of Wei-Yan-Ning group was superior to that of the Furazolidone group (P less than 0.05).
Collapse
|