1
|
Luo M, Wong D, Zelley K, Wu J, Schubert J, Denenberg EH, Fanning EA, Chen J, Gallo D, Golenberg N, Patel M, Conlin LK, Maxwell KN, Wertheim GB, Surrey LF, Zhong Y, Brodeur GM, MacFarland SP, Li MM. Identification of TP53 germline variants in pediatric patients undergoing tumor testing: strategy and prevalence. J Natl Cancer Inst 2024:djae102. [PMID: 38702830 DOI: 10.1093/jnci/djae102] [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: 01/08/2024] [Revised: 04/08/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND TP53 alterations are common in certain pediatric cancers, making identification of putative germline variants through tumor genomic profiling crucial for patient management. METHODS We analyzed TP53 alterations in 3123 tumors from 2788 pediatric patients sequenced using tumor-only or tumor-normal paired panels. Germline confirmatory testing was performed when indicated. Somatic and germline variants were classified following published guidelines. RESULTS In 248 tumors from 222 patients, 284 Tier 1/2 TP53 sequence and small copy number variants were detected. Following germline classification, 73.9% of 142 unique variants were pathogenic/likely pathogenic (P/LP). Confirmatory testing on 118 patients revealed germline TP53 variants in 28 patients (23 P/LP and 5 uncertain significance), suggesting a minimum Li-Fraumeni syndrome (LFS) incidence of 0.8% (23/2788) in this cohort, 10.4% (23/222) in patients with TP53 variant-carrying tumors, and 19.5% (23/118) with available normal samples. About 25% (7/28) of patients with germline TP53 variants did not meet LFS diagnostic/testing criteria while 20.9% (28/134) with confirmed or inferred somatic origins did. TP53 biallelic inactivation occurred in 75% of germline carrier tumors and was also prevalent in other groups, causing an elevated tumor-observed variant allelic fraction (VAF). However, somatic evidence including low VAF correctly identified only 27.8% (25/90) of patients with confirmed somatic TP53 variants. CONCLUSION The high incidence and variable phenotype of LFS in this cohort highlights the importance of assessing germline status of TP53 variants identified in all pediatric tumors. Without clear somatic evidence, distinguishing somatic from germline origins is challenging. Classifying germline and somatic variants should follow appropriate guidelines.
Collapse
Affiliation(s)
- Minjie Luo
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Derek Wong
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kristin Zelley
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jinhua Wu
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jeffery Schubert
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elizabeth H Denenberg
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elizabeth A Fanning
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jiani Chen
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daniel Gallo
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Netta Golenberg
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maha Patel
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura K Conlin
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kara N Maxwell
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael Crescenz Veterans Affairs Medical Center, Philadelphia, PA, USA
| | - Gerald B Wertheim
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lea F Surrey
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yiming Zhong
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Garrett M Brodeur
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Suzanne P MacFarland
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marilyn M Li
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
2
|
Lin F, Cao K, Chang F, Oved JH, Luo M, Fan Z, Schubert J, Wu J, Zhong Y, Gallo DJ, Denenberg EH, Chen J, Fanning EA, Lambert MP, Paessler ME, Surrey LF, Zelley K, MacFarland S, Kurre P, Olson TS, Li MM. Uncovering the Genetic Etiology of Inherited Bone Marrow Failure Syndromes Using a Custom-Designed Next-Generation Sequencing Panel. J Mol Diagn 2024; 26:191-201. [PMID: 38103590 DOI: 10.1016/j.jmoldx.2023.11.010] [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] [Received: 05/20/2023] [Revised: 09/13/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023] Open
Abstract
Inherited bone marrow failure syndromes (IBMFS) are a group of heterogeneous disorders that account for ∼30% of pediatric cases of bone marrow failure and are often associated with developmental abnormalities and cancer predisposition. This article reports the laboratory validation and clinical utility of a large-scale, custom-designed next-generation sequencing panel, Children's Hospital of Philadelphia (CHOP) IBMFS panel, for the diagnosis of IBMFS in a cohort of pediatric patients. This panel demonstrated excellent analytic accuracy, with 100% sensitivity, ≥99.99% specificity, and 100% reproducibility on validation samples. In 269 patients with suspected IBMFS, this next-generation sequencing panel was used for identifying single-nucleotide variants, small insertions/deletions, and copy number variations in mosaic or nonmosaic status. Sixty-one pathogenic/likely pathogenic variants (54 single-nucleotide variants/insertions/deletions and 7 copy number variations) and 24 hypomorphic variants were identified, resulting in the molecular diagnosis of IBMFS in 21 cases (7.8%) and exclusion of IBMFS with a diagnosis of a blood disorder in 10 cases (3.7%). Secondary findings, including evidence of early hematologic malignancies and other hereditary cancer-predisposition syndromes, were observed in 9 cases (3.3%). The CHOP IBMFS panel was highly sensitive and specific, with a significant increase in the diagnostic yield of IBMFS. These findings suggest that next-generation sequencing-based panel testing should be a part of routine diagnostics in patients with suspected IBMFS.
Collapse
Affiliation(s)
- Fumin Lin
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kajia Cao
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Fengqi Chang
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Joseph H Oved
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zhiqian Fan
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jeffrey Schubert
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jinhua Wu
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Yiming Zhong
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Daniel J Gallo
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elizabeth H Denenberg
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jiani Chen
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elizabeth A Fanning
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michele P Lambert
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Pediatric Comprehensive Bone Marrow Failure Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michele E Paessler
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kristin Zelley
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Suzanne MacFarland
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Peter Kurre
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Pediatric Comprehensive Bone Marrow Failure Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Timothy S Olson
- Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Pediatric Comprehensive Bone Marrow Failure Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| |
Collapse
|
3
|
Newman H, Clark ME, Wong D, Wu J, Brodeur GM, Hunger SP, Tasian SK, Olson T, Warren JT, Teachey DT, Bona K, Schubert J, Golenberg N, Patel M, Denenberg EH, Fanning EA, Chen J, Luke T, Charles S, Gallo D, Cao K, Fu W, Fan Z, Surrey LF, Wertheim G, Luo M, MacFarland SP, Li MM, Zhong Y. Genomic profiling of pediatric hematologic malignancies and diagnosis of cancer predisposition syndromes: tumor-only versus paired tumor-normal sequencing. Haematologica 2024. [PMID: 38385299 DOI: 10.3324/haematol.2023.284855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Indexed: 02/23/2024] Open
Abstract
Not available.
Collapse
Affiliation(s)
- Haley Newman
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Mary Egan Clark
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Derek Wong
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jinhua Wu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Garrett M Brodeur
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Stephen P Hunger
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Sarah K Tasian
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Timothy Olson
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Julia T Warren
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - David T Teachey
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kira Bona
- Department of Pediatric Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA
| | - Jeffrey Schubert
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Netta Golenberg
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Maha Patel
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Elizabeth H Denenberg
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Elizabeth A Fanning
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jiani Chen
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Tamara Luke
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Sarah Charles
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Daniel Gallo
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kajia Cao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Weixuan Fu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Zhiqian Fan
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Lea F Surrey
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Gerald Wertheim
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Minjie Luo
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Suzanne P MacFarland
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Marilyn M Li
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Yiming Zhong
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.
| |
Collapse
|
4
|
Hruby Weston A, Li MM, Huang X, Campos LM, Prestegaard-Wilson JM, Pilonero T, Budde A, Hanigan MD. Effects of dietary starch and ruminally undegraded protein on glucogenic precursors in lactating dairy cows. Animal 2023; 17 Suppl 5:100893. [PMID: 37468351 DOI: 10.1016/j.animal.2023.100893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/21/2023] Open
Abstract
Gluconeogenesis is a large contributor to the blood supply of glucose carbons. The impact of varying dietary starch and ruminally degraded protein (RDP) on glucose entry, and the contributions of propionate and lactate to total plasma glucose entry were evaluated. Six cannulated, lactating, Holstein cows were fed one of four treatment diets arranged as a 2 × 2 factorial within a 4 × 4 partially replicated Latin Square design: (1) 8% RDP (LRDP) and 16% starch (LSt), (2) LRDP and 30% starch (HSt), (3) 11% RDP (HRDP) and LSt, or (4) HRDP and HSt. On d 12 of each period, 2-[13C]-sodium propionate (0.15 g/h) was ruminally infused for 4 h; on d 13, 1,2-[13C2]-glucose (0.2 g/h) was infused into the jugular vein for 1 h followed by 1-[13C]-lactate (0.1 g/h) for 1 h. Blood samples were serially collected starting prior to the infusions, and analyzed for plasma glucose, propionate, and lactate isotopic ratios. A one-compartment, glucose carbon model with inputs from lactate, propionate, and other glucogenic precursors (Oth, primarily absorbed glucose plus amino acids) was fitted to the isotope ratio data to derive glucose entry rates and conversion of the precursors to glucose. Milk protein production additively increased when HSt and HRDP were fed (P = 0.05 and P = 0.02, respectively). Plasma glucose and propionate concentrations increased with HSt (P = 0.04 and P = 0.01, respectively) and LRDP (P = 0.02 and P < 0.01, respectively). Total glucose and Oth entry increased (P = 0.03 and P = 0.03, respectively) with HSt, indicating greater glucose absorption from the small intestine or conversion of amino acids to glucose in the liver. However, neither entry rate was affected by RDP. The lack of an RDP effect suggests the increase in microbial outflow in response to RDP did not significantly alter glucose precursor supplies. Entry rates of propionate and lactate carbon to glucose carbon were not affected by treatment suggesting that neither starch nor RDP significantly affected fermentation or lactate production. Derivation of absolute entry rates and contributions to glucose using isotopic tracers is complicated by single carbon removals in the pentose phosphate (PPP), tri-carboxylic acid (TCA), and gluconeogenic pathways, and label randomization with the PPP and TCA pathways. Multiple tracers must be used to avoid assumptions regarding the proportional entries. These results provide insights on glucose supply and contributors, and draw attention to significant label cycling when utilizing isotope techniques.
Collapse
Affiliation(s)
- A Hruby Weston
- School of Animal Sciences, Virginia Tech, Blacksburg, VA 24060, USA.
| | - M M Li
- School of Animal Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - X Huang
- School of Animal Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - L M Campos
- School of Animal Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | | | - T Pilonero
- School of Animal Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - A Budde
- School of Animal Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - M D Hanigan
- School of Animal Sciences, Virginia Tech, Blacksburg, VA 24060, USA.
| |
Collapse
|
5
|
Ang Z, Paruzzo L, Hayer KE, Schmidt C, Torres Diz M, Xu F, Zankharia U, Zhang Y, Soldan S, Zheng S, Falkenstein CD, Loftus JP, Yang SY, Asnani M, King Sainos P, Pillai V, Chong E, Li MM, Tasian SK, Barash Y, Lieberman PM, Ruella M, Schuster SJ, Thomas-Tikhonenko A. Alternative splicing of its 5'-UTR limits CD20 mRNA translation and enables resistance to CD20-directed immunotherapies. Blood 2023; 142:1724-1739. [PMID: 37683180 PMCID: PMC10667349 DOI: 10.1182/blood.2023020400] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 03/08/2023] [Revised: 08/04/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
Aberrant skipping of coding exons in CD19 and CD22 compromises the response to immunotherapy in B-cell malignancies. Here, we showed that the MS4A1 gene encoding human CD20 also produces several messenger RNA (mRNA) isoforms with distinct 5' untranslated regions. Four variants (V1-4) were detected using RNA sequencing (RNA-seq) at distinct stages of normal B-cell differentiation and B-lymphoid malignancies, with V1 and V3 being the most abundant. During B-cell activation and Epstein-Barr virus infection, redirection of splicing from V1 to V3 coincided with increased CD20 positivity. Similarly, in diffuse large B-cell lymphoma, only V3, but not V1, correlated with CD20 protein levels, suggesting that V1 might be translation-deficient. Indeed, the longer V1 isoform contained upstream open reading frames and a stem-loop structure, which cooperatively inhibited polysome recruitment. By modulating CD20 isoforms with splice-switching morpholino oligomers, we enhanced CD20 expression and anti-CD20 antibody rituximab-mediated cytotoxicity in a panel of B-cell lines. Furthermore, reconstitution of CD20-knockout cells with V3 mRNA led to the recovery of CD20 positivity, whereas V1-reconstituted cells had undetectable levels of CD20 protein. Surprisingly, in vitro CD20-directed chimeric antigen receptor T cells were able to kill both V3- and V1-expressing cells, but the bispecific T-cell engager mosunetuzumab was only effective against V3-expressing cells. To determine whether CD20 splicing is involved in immunotherapy resistance, we performed RNA-seq on 4 postmosunetuzumab follicular lymphoma relapses and discovered that in 2 of them, the downregulation of CD20 was accompanied by a V3-to-V1 shift. Thus, splicing-mediated mechanisms of epitope loss extend to CD20-directed immunotherapies.
Collapse
Affiliation(s)
- Zhiwei Ang
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Luca Paruzzo
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katharina E. Hayer
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Carolin Schmidt
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Manuel Torres Diz
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Feng Xu
- Division of Genomic Diagnostic, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Urvi Zankharia
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA
| | - Yunlin Zhang
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Samantha Soldan
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA
| | - Sisi Zheng
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Joseph P. Loftus
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Scarlett Y. Yang
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Mukta Asnani
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Vinodh Pillai
- Division of Hematopathology, Children's Hospital of Philadelphia, Philadelphia, PA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Emeline Chong
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Marilyn M. Li
- Division of Genomic Diagnostic, Children's Hospital of Philadelphia, Philadelphia, PA
- Division of Hematopathology, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Sarah K. Tasian
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Paul M. Lieberman
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA
| | - Marco Ruella
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Stephen J. Schuster
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| |
Collapse
|
6
|
Gu GX, Ran MZ, Li MM. [Research advances on mental disorders in patients with extensive burns]. Zhonghua Shao Shang Yu Chuang Mian Xiu Fu Za Zhi 2023; 39:994-998. [PMID: 37899567 DOI: 10.3760/cma.j.cn501225-20221116-00490] [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] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
Extensive burns can cause nonnegligible acute and chronic damage to central nervous system of patients. The damage of central nervous system may have a profound impact on patients, including neurobehavioral changes such as post-traumatic stress disorder, depression, anxiety, and sleep disorder. These changes may persist after injury, greatly affecting patients' integration into society and return to work. This paper systematically reviewed the clinical manifestations, pathogenesis, and current intervention methods of mental disorders in patients with extensive burns, aiming to provide a basis for further understanding, prevention, and treatment of patients with mental disorders after burns.
Collapse
Affiliation(s)
- G X Gu
- Graduate School of Jinzhou Medical University, Jinzhou 121000, China
| | - M Z Ran
- Department of Anesthesiology, the Fourth Medical Center of PLA General Hospital, Beijing 100089, China
| | - M M Li
- Department of Anesthesiology, the Fourth Medical Center of PLA General Hospital, Beijing 100089, China
| |
Collapse
|
7
|
Li MM, Tang XH, Wang LM. [Study on the predictive significance of PLR, SII and RPR in ovarian endometriotic cyst]. Zhonghua Fu Chan Ke Za Zhi 2023; 58:672-679. [PMID: 37724384 DOI: 10.3760/cma.j.cn112141-20230504-00200] [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] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Objective: To investigate the predictive value of platelet-to-lymphocyte ratio (PLR), red blood cell distribution width to platelet count ratio (RPR) and systemic immune inflammation index (SII) in the staging and postoperative recurrence of ovarian endometrial cysts. Methods: Retrospective analysis was made on the clinical data of patients who underwent laparoscopic surgery for ovarian cysts in the Affiliated Hospital of Qingdao University from January 2018 to January 2020. The patients with ovarian endometriosis cyst confirmed by pathology after surgery were the observation group (n=350), and the patients with other benign ovarian cyst were the control group (n=150). The preoperative platelet count, platelet distribution width, absolute number of neutrophils, lymphocyte absolute number, absolute number of monocytes, red blood cell distribution width, and serum cancer antigen 125 (CA125) of the patients in two groups were recorded, and PLR, neutrophil-to-lymphocyte ratio (NLR), RPR, SII, and systemic inflammation response index (SIRI) were calculated and analyzed. The general data of all patients and the follow-up data within 2 years after the operation of the observation group were statistically recorded to evaluate the diagnostic value of PLR, RPR and SII for ovarian endometrial cyst, and the predictive value of staging and recurrence within 2 years after the operation. Results: PLR, NLR, SII (median: 147.53, 1.86, and 488.70 respectively) and CA125 (median: 59.41 kU/L) in the observation group were significantly higher than those in the control group, while RPR (median: 0.16) was lower than that in the control group, with significant differences (all P<0.01). There was no significant difference in SIRI between the two groups (P>0.05). The PLR and SII (median: 122.73, 345.00) of the observation group at stage Ⅲ and Ⅳ were higher than those of patients at stage Ⅰ and Ⅱ, and the RPR was lower than that of patients with stage Ⅰ and Ⅱ, with significant differences (all P<0.001). The PLR, NLR, SII, SIRI (median: 179.63, 2.75, 762.96, and 1.06 respectively) and CA125 (median: 108.83 kU/L) in patients with recurrence were significantly higher than those in patients without recurrence 2 years after the operation, and the differences were statistically significant (all P<0.001). The area under curve (AUC) of CA125 in the diagnosis of ovarian endometriosis cyst was 0.951, the sensitivity was 85.7%, and the specificity was 93.0%, which were higher than those of PLR and SII; the AUC of PLR+SII+CA125 in the diagnosis of ovarian endometriosis cyst was 0.952. The AUC of RPR predicting the stage of ovarian endometriosis cyst was 0.713, higher than PLR and SII, lower than CA125; the AUC of RPR+SII+CA125 in predicting the stage of ovarian endometriotic cyst was 0.825, with sensitivity of 68.7% and specificity of 85.7%. The AUC predicted by SII for recurrence of ovarian endometriotic cyst within 2 years after the operation was 0.803, higher than NLR, PLR, SIRI and CA125; the AUC of PLR+SII+CA125, sensitivity, specificity was 0.813, 81.5% and 73.0%, higher than SII. Conclusion: PLR, RPR and SII are related to the staging of ovarian endometriotic cyst, and SII has a certain predictive value for the recurrence of ovarian endometriotic cyst after surgery.
Collapse
Affiliation(s)
- M M Li
- Department of Gynecology, the Affiliated Hospital of Qingdao University, Qingdao 266400, China
| | - X H Tang
- Department of Gynecology, the Affiliated Hospital of Qingdao University, Qingdao 266400, China
| | - L M Wang
- Department of Gynecology, the Affiliated Hospital of Qingdao University, Qingdao 266400, China
| |
Collapse
|
8
|
Ang Z, Paruzzo L, Hayer KE, Schmidt C, Torres Diz M, Xu F, Zankharia U, Zhang Y, Soldan S, Zheng S, Falkenstein CD, Loftus JP, Yang SY, Asnani M, King Sainos P, Pillai V, Chong E, Li MM, Tasian SK, Barash Y, Lieberman PM, Ruella M, Schuster SJ, Thomas-Tikhonenko A. Alternative splicing of its 5'-UTR limits CD20 mRNA translation and enables resistance to CD20-directed immunotherapies. bioRxiv 2023:2023.02.19.529123. [PMID: 37645778 PMCID: PMC10461923 DOI: 10.1101/2023.02.19.529123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Aberrant skipping of coding exons in CD19 and CD22 compromises responses to immunotherapy for B-cell malignancies. Here, we show that the MS4A1 gene encoding human CD20 also produces several mRNA isoforms with distinct 5' untranslated regions (5'-UTR). Four variants (V1-4) were detectable by RNA-seq in distinct stages of normal B-cell differentiation and B-lymphoid malignancies, with V1 and V3 being the most abundant by far. During B-cell activation and Epstein-Barr virus infection, redirection of splicing from V1 to V3 coincided with increased CD20 positivity. Similarly, in diffuse large B-cell lymphoma only V3, but not V1, correlated with CD20 protein levels, suggesting that V1 might be translation-deficient. Indeed, the longer V1 isoform was found to contain upstream open reading frames (uORFs) and a stem-loop structure, which cooperatively inhibited polysome recruitment. By modulating CD20 isoforms with splice-switching Morpholino oligomers, we enhanced CD20 expression and anti-CD20 antibody rituximab-mediated cytotoxicity in a panel of B-cell lines. Furthermore, reconstitution of CD20-knockout cells with V3 mRNA led to the recovery of CD20 positivity, while V1-reconstituted cells had undetectable levels of CD20 protein. Surprisingly, in vitro CD20-directed CAR T cells were able to kill both V3- and V1-expressing cells, but the bispecific T cell engager mosunetuzumab was only effective against V3-expressing cells. To determine whether CD20 splicing is involved in immunotherapy resistance, we performed RNA-seq on four post-mosunetuzumab follicular lymphoma relapses and discovered that in two of them downregulation of CD20 was accompanied by the V3-to-V1 shift. Thus, splicing-mediated mechanisms of epitope loss extend to CD20-directed immunotherapies. Key Points In normal & malignant human B cells, CD20 mRNA is alternatively spliced into four 5'-UTR isoforms, some of which are translation-deficient.The balance between translation-deficient and -competent isoforms modulates CD20 protein levels & responses to CD20-directed immunotherapies. Explanation of Novelty We discovered that in normal and malignant B-cells, CD20 mRNA is alternatively spliced to generate four distinct 5'-UTRs, including the longer translation-deficient V1 variant. Cells predominantly expressing V1 were still sensitive to CD20-targeting chimeric antigen receptor T-cells. However, they were resistant to the bispecific anti-CD3/CD20 antibody mosunetuzumab, and the shift to V1 were observed in CD20-negative post-mosunetuzumab relapses of follicular lymphoma.
Collapse
|
9
|
Ren Z, Li Q, Cao K, Li MM, Zhou Y, Wang K. Correction: Model performance and interpretability of semi-supervised generative adversarial networks to predict oncogenic variants with unlabeled data. BMC Bioinformatics 2023; 23:572. [PMID: 37259034 DOI: 10.1186/s12859-023-05357-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Affiliation(s)
- Zilin Ren
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Quan Li
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, M5G2C1, Canada
| | - Kajia Cao
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Marilyn M Li
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yunyun Zhou
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
10
|
Cheng LY, Yang L, Li MM, Li YG, Zhang YL. [Pregnancy outcome analysis after radiofrequency ablation of monochorionic twin pregnancy in different gestational weeks and psychological intervention]. Zhonghua Yi Xue Za Zhi 2023; 103:1236-1241. [PMID: 37087408 DOI: 10.3760/cma.j.cn112137-20221108-02352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
Abstract
Objective: To investigate the effect of different gestational weeks and psychological intervention on pregnancy outcome in patients with monochorionic twin pregnancy. Methods: The clinical data of 68 patients with monochorionic twin pregnancy in the middle and late pregnancy who were treated with radiofrequency ablation in the First Affiliated Hospital of Zhengzhou University from March 2017 to April 2021 were retrospectively analyzed, including 54 patients with single chorionic and single amniotic sac and 14 patients with single chorionic and double amniotic sac. Patients were divided into three groups according to the gestational weeks:<20 weeks (n=36), 20-23 weeks (n=17) and ≥24 weeks (n=15); and were divided into intervention group (n=40) and control group (n=28) according to the preoperative psychological intervention. The pregnancy outcome of patients with different pregnancy reduction and the effect of psychological intervention on pregnancy outcome was analyzed. Results: The age of 68 patients was (30.2±4.6) years old, the gestational age was (22.2±3.2) weeks, and 60 cases (88.2%) were live births after fetal reduction. There were no significant difference in age [(31.8±4.7),(28.3±5.0),(30.3±4.0) years old] (P=0.098), abortion rate, preterm birth rate, live birth rate, delivery mode, gestational week of preterm birth, gestational week of delivery, and neonatal weight between the two groups at different gestational weeks (all P>0.05). The ages of the intervention group and the control group were (30.6±4.7) and (29.4±4.0) years old (P=0.352). After psychological intervention for 40 patients in the intervention group, the anxiety score after pregnancy reduction was reduced from (54.8±6.8) to (37.3±7.3) (P<0.001), while the depression score decreased from (62.7±7.2) to (33.2±2.4) (P<0.001). Compared with patients in the control group (12.5%, n=5), the proportion of postoperative discomfort in the intervention group was higher (53.6%, n=15) (P<0.001). Compared with the control group, there were no statistically significant difference in the postoperative preterm birth rate, abortion rate, live birth rate, delivery mode, gestational week of preterm birth, gestational week of delivery, and neonatal weight in the intervention group (all P>0.05). Conclusions: Radiofrequency ablation is a safe and effective minimally invasive technique. For complex monochorionic twin pregnancies, early fetal reduction (<20 weeks) and preoperative psychological intervention can provide a solid guarantee for a good postoperative pregnancy outcome.
Collapse
Affiliation(s)
- L Y Cheng
- Reproductive Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - L Yang
- Reproductive Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - M M Li
- Reproductive Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Y G Li
- Reproductive Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Y L Zhang
- Reproductive Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| |
Collapse
|
11
|
Ren Z, Li Q, Cao K, Li MM, Zhou Y, Wang K. Model performance and interpretability of semi-supervised generative adversarial networks to predict oncogenic variants with unlabeled data. BMC Bioinformatics 2023; 24:43. [PMID: 36759776 PMCID: PMC9909865 DOI: 10.1186/s12859-023-05141-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND It remains an important challenge to predict the functional consequences or clinical impacts of genetic variants in human diseases, such as cancer. An increasing number of genetic variants in cancer have been discovered and documented in public databases such as COSMIC, but the vast majority of them have no functional or clinical annotations. Some databases, such as CiVIC are available with manual annotation of functional mutations, but the size of the database is small due to the use of human annotation. Since the unlabeled data (millions of variants) typically outnumber labeled data (thousands of variants), computational tools that take advantage of unlabeled data may improve prediction accuracy. RESULT To leverage unlabeled data to predict functional importance of genetic variants, we introduced a method using semi-supervised generative adversarial networks (SGAN), incorporating features from both labeled and unlabeled data. Our SGAN model incorporated features from clinical guidelines and predictive scores from other computational tools. We also performed comparative analysis to study factors that influence prediction accuracy, such as using different algorithms, types of features, and training sample size, to provide more insights into variant prioritization. We found that SGAN can achieve competitive performances with small labeled training samples by incorporating unlabeled samples, which is a unique advantage compared to traditional machine learning methods. We also found that manually curated samples can achieve a more stable predictive performance than publicly available datasets. CONCLUSIONS By incorporating much larger samples of unlabeled data, the SGAN method can improve the ability to detect novel oncogenic variants, compared to other machine-learning algorithms that use only labeled datasets. SGAN can be potentially used to predict the pathogenicity of more complex variants such as structural variants or non-coding variants, with the availability of more training samples and informative features.
Collapse
Affiliation(s)
- Zilin Ren
- grid.239552.a0000 0001 0680 8770Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Quan Li
- grid.239552.a0000 0001 0680 8770Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA ,grid.17063.330000 0001 2157 2938Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G2C1 Canada
| | - Kajia Cao
- grid.239552.a0000 0001 0680 8770Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Marilyn M. Li
- grid.239552.a0000 0001 0680 8770Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Yunyun Zhou
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
12
|
Li MM, Cottrell CE, Pullambhatla M, Roy S, Temple-Smolkin RL, Turner SA, Wang K, Zhou Y, Vnencak-Jones CL. Assessments of Somatic Variant Classification Using the Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists Guidelines: A Report from the Association for Molecular Pathology. J Mol Diagn 2023; 25:69-86. [PMID: 36503149 DOI: 10.1016/j.jmoldx.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/09/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
To assess the clinical implementation of the 2017 Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists, identify content that may result in classification inconsistencies, and evaluate implementation barriers, an Association for Molecular Pathology Working Group conducted variant interpretation challenges and a guideline implementation survey. A total of 134 participants participated in the variant interpretation challenges, consisting of 11 variants in four cancer cases. Results demonstrate 86% (range, 54% to 94%) of the respondents correctly classified clinically significant variants, variants of uncertain significance, and benign/likely benign variants; however, only 59% (range, 39% to 84%) of responses agreed with the working group's consensus intended responses regarding both tiers and categories of clinical significance. In the implementation survey, 71% (157/220) of respondents have implemented the 2017 guidelines for variant classification and reporting either with or without modifications. Collectively, this study demonstrates that, although they may not yet be optimized, the 2017 guideline recommendations are being adopted for standardized somatic variant classification. The working group identified significant areas for future guideline improvement, including the need for a more granular and comprehensive classification system and education resources to meet the growing needs of both laboratory professionals and medical oncologists.
Collapse
Affiliation(s)
- Marilyn M Li
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
| | - Catherine E Cottrell
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | | | - Somak Roy
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | - Scott A Turner
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Kai Wang
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Yunyun Zhou
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Cindy L Vnencak-Jones
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| |
Collapse
|
13
|
Cao XC, Jiang SY, Li SJ, Han JY, Zhou Q, Li MM, Bai RM, Xia SW, Yang ZM, Ge JF, Zhang BQ, Yang CZ, Yuan J, Pan DD, Shi JY, Hu XF, Lin ZL, Wang Y, Zeng LC, Zhu YP, Wei QF, Guo Y, Chen L, Liu CQ, Jiang SY, Li XY, Sun HQ, Qi YJ, Hei MY, Cao Y. [Status of fungal sepsis among preterm infants in 25 neonatal intensive care units of tertiary hospitals in China]. Zhonghua Er Ke Za Zhi 2023; 61:29-35. [PMID: 36594118 DOI: 10.3760/cma.j.cn112140-20220918-00813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Objective: To analyze the prevalence and the risk factors of fungal sepsis in 25 neonatal intensive care units (NICU) among preterm infants in China, and to provide a basis for preventive strategies of fungal sepsis. Methods: This was a second-analysis of the data from the "reduction of infection in neonatal intensive care units using the evidence-based practice for improving quality" study. The current status of fungal sepsis of the 24 731 preterm infants with the gestational age of <34+0 weeks, who were admitted to 25 participating NICU within 7 days of birth between May 2015 and April 2018 were retrospectively analyzed. These preterm infants were divided into the fungal sepsis group and the without fungal sepsis group according to whether they developed fungal sepsis to analyze the incidences and the microbiology of fungal sepsis. Chi-square test was used to compare the incidences of fungal sepsis in preterm infants with different gestational ages and birth weights and in different NICU. Multivariate Logistic regression analysis was used to study the outcomes of preterm infants with fungal sepsis, which were further compared with those of preterm infants without fungal sepsis. The 144 preterm infants in the fungal sepsis group were matched with 288 preterm infants in the non-fungal sepsis group by propensity score-matched method. Univariate and multivariate Logistic regression analysis were used to analyze the risk factors of fungal sepsis. Results: In all, 166 (0.7%) of the 24 731 preterm infants developed fungal sepsis, with the gestational age of (29.7±2.0) weeks and the birth weight of (1 300±293) g. The incidence of fungal sepsis increased with decreasing gestational age and birth weight (both P<0.001). The preterm infants with gestational age of <32 weeks accounted for 87.3% (145/166). The incidence of fungal sepsis was 1.0% (117/11 438) in very preterm infants and 2.0% (28/1 401) in extremely preterm infants, and was 1.3% (103/8 060) in very low birth weight infants and 1.7% (21/1 211) in extremely low birth weight infants, respectively. There was no fungal sepsis in 3 NICU, and the incidences in the other 22 NICU ranged from 0.7% (10/1 397) to 2.9% (21/724), with significant statistical difference (P<0.001). The pathogens were mainly Candida (150/166, 90.4%), including 59 cases of Candida albicans and 91 cases of non-Candida albicans, of which Candida parapsilosis was the most common (41 cases). Fungal sepsis was independently associated with increased risk of moderate to severe bronchopulmonary dysplasia (BPD) (adjusted OR 1.52, 95%CI 1.04-2.22, P=0.030) and severe retinopathy of prematurity (ROP) (adjusted OR 2.55, 95%CI 1.12-5.80, P=0.025). Previous broad spectrum antibiotics exposure (adjusted OR=2.50, 95%CI 1.50-4.17, P<0.001), prolonged use of central line (adjusted OR=1.05, 95%CI 1.03-1.08, P<0.001) and previous total parenteral nutrition (TPN) duration (adjusted OR=1.04, 95%CI 1.02-1.06, P<0.001) were all independently associated with increasing risk of fungal sepsis. Conclusions: Candida albicans and Candida parapsilosis are the main pathogens of fungal sepsis among preterm infants in Chinese NICU. Preterm infants with fungal sepsis are at increased risk of moderate to severe BPD and severe ROP. Previous broad spectrum antibiotics exposure, prolonged use of central line and prolonged duration of TPN will increase the risk of fungal sepsis. Ongoing initiatives are needed to reduce fungal sepsis based on these risk factors.
Collapse
Affiliation(s)
- X C Cao
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - S Y Jiang
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - S J Li
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - J Y Han
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Q Zhou
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - M M Li
- Department of Neonatology, Women's Hospital of Nanjing Medical University, Nanjing 210004, China
| | - R M Bai
- Department of Neonatology, Northwest Women's and Children's Hospital, Xi'an 200001, China
| | - S W Xia
- Department of Neonatology, Maternal and Child Hospital of Hubei Province, Wuhan 430064, China
| | - Z M Yang
- Department of Neonatology, Suzhou Municipal Hospital, Suzhou 215008, China
| | - J F Ge
- Department of Neonatology, Shanxi Children's Hospital, Taiyuan 030006, China
| | - B Q Zhang
- Department of Neonatology, Fujian Maternity and Child Health Hospital, Fuzhou 350005, China
| | - C Z Yang
- Department of Neonatology, the Affiliated Shenzhen Maternity and Child Healthcare Hospital of Southern Medical University, Shenzhen 518047, China
| | - J Yuan
- Department of Neonatology, Qingdao Women and Children's Hospital, Qingdao 266011, China
| | - D D Pan
- Department of Neonatology, Guiyang Maternal and Child Health Care Hospital, Guiyang Children's Hospital, Guiyang 550002, China
| | - J Y Shi
- Department of Neonatology, Gansu Provincial Maternity and Child-care Hospital, Lanzhou 730050, China
| | - X F Hu
- Department of Neonatology, Shanghai First Maternal and Infant Hospital, Shanghai 201204, China
| | - Z L Lin
- Department of Neonatology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325088, China
| | - Y Wang
- Department of Neonatology, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - L C Zeng
- Department of Neonatology, Jiangxi Provincial Children's Hospital, Nanchang 330006, China
| | - Y P Zhu
- Department of Neonatology, the First Affiliated Hospital of Xinjiang Medical University, Urumchi 830054, China
| | - Q F Wei
- Department of Neonatology, Maternity and Child Health Care of Guangxi Zhuang Autonomous Region, Nanning 530002, China
| | - Y Guo
- Department of Neonatology, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - L Chen
- Department of Neonatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - C Q Liu
- Department of Neonatology, Children's Hospital of Hebei Province, Shijiazhuang 050031, China
| | - S Y Jiang
- Department of Neonatology, Wuxi Maternal and Child Health Care Hospital, Wuxi 214002, China
| | - X Y Li
- Department of Neonatology, Children's Hospital Affiliated to Shandong University, Jinan Children's Hospital, Jinan 250022, China
| | - H Q Sun
- Division of Neonatology, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450018, China
| | - Y J Qi
- Department of Neonatology, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - M Y Hei
- Department of Neonatology, the Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Y Cao
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| |
Collapse
|
14
|
Bosse KR, Giudice AM, Lane MV, McIntyre B, Schürch PM, Pascual-Pasto G, Buongervino SN, Suresh S, Fitzsimmons A, Hyman A, Gemino-Borromeo M, Saggio J, Berko ER, Daniels AA, Stundon J, Friedrichsen M, Liu X, Margolis ML, Li MM, Tierno MB, Oxnard GR, Maris JM, Mossé YP. Serial Profiling of Circulating Tumor DNA Identifies Dynamic Evolution of Clinically Actionable Genomic Alterations in High-Risk Neuroblastoma. Cancer Discov 2022; 12:2800-2819. [PMID: 36108156 PMCID: PMC9722579 DOI: 10.1158/2159-8290.cd-22-0287] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 03/17/2022] [Revised: 07/21/2022] [Accepted: 09/13/2022] [Indexed: 01/12/2023]
Abstract
Neuroblastoma evolution, heterogeneity, and resistance remain inadequately defined, suggesting a role for circulating tumor DNA (ctDNA) sequencing. To define the utility of ctDNA profiling in neuroblastoma, 167 blood samples from 48 high-risk patients were evaluated for ctDNA using comprehensive genomic profiling. At least one pathogenic genomic alteration was identified in 56% of samples and 73% of evaluable patients, including clinically actionable ALK and RAS-MAPK pathway variants. Fifteen patients received ALK inhibition (ALKi), and ctDNA data revealed dynamic genomic evolution under ALKi therapeutic pressure. Serial ctDNA profiling detected disease evolution in 15 of 16 patients with a recurrently identified variant-in some cases confirming disease progression prior to standard surveillance methods. Finally, ctDNA-defined ERRFI1 loss-of-function variants were validated in neuroblastoma cellular models, with the mutant proteins exhibiting loss of wild-type ERRFI1's tumor-suppressive functions. Taken together, ctDNA is prevalent in children with high-risk neuroblastoma and should be followed throughout neuroblastoma treatment. SIGNIFICANCE ctDNA is prevalent in children with neuroblastoma. Serial ctDNA profiling in patients with neuroblastoma improves the detection of potentially clinically actionable and functionally relevant variants in cancer driver genes and delineates dynamic tumor evolution and disease progression beyond that of standard tumor sequencing and clinical surveillance practices. See related commentary by Deubzer et al., p. 2727. This article is highlighted in the In This Issue feature, p. 2711.
Collapse
Affiliation(s)
- Kristopher R. Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA, 19104; USA
| | - Anna Maria Giudice
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Maria V. Lane
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Brendan McIntyre
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Patrick M. Schürch
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Guillem Pascual-Pasto
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Samantha N. Buongervino
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Sriyaa Suresh
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Alana Fitzsimmons
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Adam Hyman
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Maria Gemino-Borromeo
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Jennifer Saggio
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Esther R. Berko
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Alexander A. Daniels
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | - Jennifer Stundon
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | | | - Xin Liu
- Foundation Medicine, Inc. Cambridge, MA 02141; USA
| | | | - Marilyn M. Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and the Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
| | | | | | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA, 19104; USA
| | - Yael P. Mossé
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia; Philadelphia, PA, 19104; USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania; Philadelphia, PA, 19104; USA
| |
Collapse
|
15
|
Guo XY, Li MM, Long DY, Sang CH, Tang RB, Jiang CX, Du X, Dong JZ, Ma CS. [Efficacy and safety of radiofrequency catheter ablation of septal hypertrophy guided by intracardiac echocardiography in hypertrophic obstructive cardiomyopathy]. Zhonghua Yi Xue Za Zhi 2022; 102:3549-3552. [PMID: 36418255 DOI: 10.3760/cma.j.cn112137-20220501-00975] [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] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nine patients identified as hypertrophic obstructive cardiomyopathy (HOCM) in Beijing Anzhen Hopspital who underwent ablation from March to July 2019 were included in the study. All patients had left ventricular outflow tract gradient (LVOTG) over 50 mmHg(1 mmHg=0.133 kPa)with significant symptoms despite not optimal drug therapy. Intracardiac echocardiography (ICE) was used to reconstruct septum and surrounding structures, and monitor the effect of ablation during procedure. Nine patients with HOCM were included,.of which 6 men and 3 women. The average age was (51.7±12.2) years. All patients underwent successful ablation after a mean of procedural time of (152.2±31.9) minutes and ablation time of (838.4±227.3) seconds. Except for one patients, all other patients had significant LVOTG reduction(P=0.001)within 50 mmHg after the procedure. Systolic anterior motion of the mitral valve disappeared in all patients after the procedure without major periprocedural complications. The LVOTG of these patients remained stable during follow-up. Radiofrequency ablation using ICE guidance is feasible in treating HOCM with promising efficacy and safety.
Collapse
Affiliation(s)
- X Y Guo
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing 100029, China
| | - M M Li
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing 100029, China
| | - D Y Long
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing 100029, China
| | - C H Sang
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing 100029, China
| | - R B Tang
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing 100029, China
| | - C X Jiang
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing 100029, China
| | - X Du
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing 100029, China
| | - J Z Dong
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing 100029, China
| | - C S Ma
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing 100029, China
| |
Collapse
|
16
|
Chen HL, Zhou YS, Hao JJ, Zhang JX, Hu J, Song C, Li MM, Li D, Feng Y, Liao LJ, Ruan YH, Xing H, Shao YM. [Effects of pretreatment HIV drug resistance on the virological response of HIV-infected patients after 3-year antiretroviral therapy]. Zhonghua Liu Xing Bing Xue Za Zhi 2022; 43:1778-1783. [PMID: 36444462 DOI: 10.3760/cma.j.cn112338-20220112-00028] [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] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Objective: To investigate the impact of pretreatment drug resistance (PDR) on virological effect among HIV-infected patients having received antiretroviral therapy (ART) after three years. Methods: The baseline survey of PDR among HIV-infected patients was conducted in 2018, with a three-year follow up study. The clinic data and virological laboratory test variables were statistically analyzed. Results: Of the 2 433 participants, 41.6% (1 012/2 433) were aged between 18 and 34, 82.8% (2 015/2 433) were males, 46.9% (1 142/2 433) had education of high school or above, 22.4% (544/2 433) were farmers, 33.8% (823/2 433) were unmarried, 48.1% (1 169/2 433) were infected heterosexually and 41.3% (1 004/2 433) were with CRF07_BC. The prevalence of PDR was 4.5% (109/2 433). The prevalence of virological suppression failure (viral load ≥50 copies/ml) and drug resistance at three years follow up after ART was 8.1%(196/2 433) and 2.5%(60/2 433) respectively. The prevalence of virological suppression failure and drug resistance at three years follow up after ART were 18.3% (20/109) and 7.6% (176/2 324), and 4.6% (5/109) and 2.4% (55/2 324) among participants with PDR and non-PDR, respectively. The results of multivariate logistic regression model showed that illiteracy (aOR=3.26, 95%CI: 1.82-5.86), primary and junior high school education (aOR=1.54, 95%CI: 1.09-2.18), CD4+T lymphocyte count <200/μl (aOR=2.77, 95%CI: 1.75-4.37) and CD4+T lymphocyte count 200-499/μl (aOR=1.55, 95%CI: 1.10-2.18) at a three year follow up visit after ART, missed drugs in the past month (aOR=4.24, 95%CI: 2.92-6.17), and PDR (aOR=2.84, 95%CI: 1.67-4.85) were statistically significant with virological suppression failure on treatment. Conclusions: The prevalence of PDR in China at a low level currently, and the virological suppression failure rate is low after three years of ART. It is necessary to strengthen drug resistance monitoring of HIV-infected patients and pay attention to the influence of PDR on treatment effect.
Collapse
Affiliation(s)
- H L Chen
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Y S Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - J J Hao
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - J X Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - J Hu
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - C Song
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - M M Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - D Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Y Feng
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - L J Liao
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Y H Ruan
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - H Xing
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Y M Shao
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| |
Collapse
|
17
|
Saliba J, Church AJ, Danos A, Furtado LV, Laetsch T, Zhang L, Nardi V, Lin WH, Ritter D, Li MM, Griffith OL, Griffith M, Raca G, Roy A. 115. Standardized assessment of Oncogenicity and clinical significance of NTRK fusions. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2022.10.118] [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: 11/28/2022]
|
18
|
Saliba J, Raca G, Roy A, King I, Selvarajah S, Xu X, Kanagal-Shamanna R, Satgunaseelan L, Meredith D, Mullighan C, Krysiak K, Evans MG, Akkari Y, Terraf P, Church AJ, Kovach A, Williams H, Lin WH, Kesserwan C, Ritter DI, Danos A, Reshmi SC, Li MM, Sonkin D, Berg JS, Plon SE, Rehm HL, Wagner AH, Kulkarni S, Govindan R, Griffith OL, Griffith M, on behalf of the ClinGen Somatic Working Group. 22. Reimagining and enhancing the Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2022.10.025] [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: 11/28/2022]
|
19
|
Leibowitz MS, Zelley K, Adams D, Brodeur GM, Fox E, Li MM, Mattei P, Pogoriler J, MacFarland SP. Neuroblastoma and cutaneous angiosarcoma in a child with PTEN hamartoma tumor syndrome. Pediatr Blood Cancer 2022; 69:e29656. [PMID: 35278038 DOI: 10.1002/pbc.29656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/26/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Michael S Leibowitz
- Division of Oncology, Department of Pediatrics, Children's Hospital of Phialdelphia, Philadelphia, Pennsylvania, USA
| | - Kristin Zelley
- Division of Oncology, Department of Pediatrics, Children's Hospital of Phialdelphia, Philadelphia, Pennsylvania, USA
| | - Denise Adams
- Division of Oncology, Department of Pediatrics, Children's Hospital of Phialdelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Garrett M Brodeur
- Division of Oncology, Department of Pediatrics, Children's Hospital of Phialdelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Elizabeth Fox
- Department of Oncology, St. Jude's Children's Research Hospital, Memphis, Tennessee, USA
| | - Marilyn M Li
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelpiha, Philadelphia, Pennsylvania, USA
| | - Peter Mattei
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA.,Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jennifer Pogoriler
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelpiha, Philadelphia, Pennsylvania, USA
| | - Suzanne P MacFarland
- Division of Oncology, Department of Pediatrics, Children's Hospital of Phialdelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| |
Collapse
|
20
|
Pugh TJ, Bell JL, Bruce JP, Doherty GJ, Galvin M, Green MF, Hunter-Zinck H, Kumari P, Lenoue-Newton ML, Li MM, Lindsay J, Mazor T, Ovalle A, Sammut SJ, Schultz N, Yu TV, Sweeney SM, Bernard B. AACR Project GENIE: 100,000 Cases and Beyond. Cancer Discov 2022; 12:2044-2057. [PMID: 35819403 PMCID: PMC9437568 DOI: 10.1158/2159-8290.cd-21-1547] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/20/2022] [Accepted: 07/07/2022] [Indexed: 01/26/2023]
Abstract
The American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE) is an international pan-cancer registry with the goal to inform cancer research and clinical care worldwide. Founded in late 2015, the milestone GENIE 9.1-public release contains data from >110,000 tumors from >100,000 people treated at 19 cancer centers from the United States, Canada, the United Kingdom, France, the Netherlands, and Spain. Here, we demonstrate the use of these real-world data, harmonized through a centralized data resource, to accurately predict enrollment on genome-guided trials, discover driver alterations in rare tumors, and identify cancer types without actionable mutations that could benefit from comprehensive genomic analysis. The extensible data infrastructure and governance framework support additional deep patient phenotyping through biopharmaceutical collaborations and expansion to include new data types such as cell-free DNA sequencing. AACR Project GENIE continues to serve a global precision medicine knowledge base of increasing impact to inform clinical decision-making and bring together cancer researchers internationally. SIGNIFICANCE AACR Project GENIE has now accrued data from >110,000 tumors, placing it among the largest repository of publicly available, clinically annotated genomic data in the world. GENIE has emerged as a powerful resource to evaluate genome-guided clinical trial design, uncover drivers of cancer subtypes, and inform real-world use of genomic data. This article is highlighted in the In This Issue feature, p. 2007.
Collapse
Affiliation(s)
- Trevor J. Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,University of Toronto, Toronto, Ontario, Canada.,Corresponding Authors: Trevor J. Pugh, Princess Margaret Cancer Centre, University Health Network, MaRS Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada. Phone: 416-946-2000; E-mail: ; and Brady Bernard, 4805 NE Glisan Street, Suite 2N35, Portland, OR 97213. Phone: 503-215-6588; E-mail:
| | | | - Jeff P. Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Gary J. Doherty
- Cancer Research United Kingdom (CRUK) Cambridge Centre, Cambridge, United Kingdom.,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Matthew Galvin
- Earle A. Chiles Research Institute, Portland, Oregon.,Providence Cancer Institute, Portland, Oregon
| | | | | | - Priti Kumari
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michele L. Lenoue-Newton
- Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Marilyn M. Li
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - Tali Mazor
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Stephen-John Sammut
- Cancer Research United Kingdom (CRUK) Cambridge Centre, Cambridge, United Kingdom.,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | | | | | - Shawn M. Sweeney
- American Association for Cancer Research, Philadelphia, Pennsylvania
| | - Brady Bernard
- Earle A. Chiles Research Institute, Portland, Oregon.,Providence Cancer Institute, Portland, Oregon.,Corresponding Authors: Trevor J. Pugh, Princess Margaret Cancer Centre, University Health Network, MaRS Centre, 101 College Street, Toronto, Ontario M5G 1L7, Canada. Phone: 416-946-2000; E-mail: ; and Brady Bernard, 4805 NE Glisan Street, Suite 2N35, Portland, OR 97213. Phone: 503-215-6588; E-mail:
| | | |
Collapse
|
21
|
Newman H, Long JM, Zelley K, Baldino S, Li MM, Maxwell KN, MacFarland SP. Looking closely at overgrowth: Constitutional mosaicism in PTEN hamartoma tumor syndrome. Clin Genet 2022; 102:557-559. [PMID: 35923098 DOI: 10.1111/cge.14202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Haley Newman
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jessica M Long
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kristin Zelley
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Sarah Baldino
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kara N Maxwell
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Suzanne P MacFarland
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
22
|
Schubert J, Wu J, Li MM, Cao K. Best Practice for Clinical Somatic Variant Interpretation and Reporting. Clin Lab Med 2022; 42:423-434. [DOI: 10.1016/j.cll.2022.04.006] [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: 11/03/2022]
|
23
|
Xu F, Viaene AN, Ruiz J, Schubert J, Wu J, Chen J, Cao K, Fu W, Bagatell R, Fan Z, Long A, Pagliaroli L, Zhong Y, Luo M, Kreiger PA, Surrey LF, Wertheim GB, Cole KA, Li MM, Santi M, Storm PB. Novel ATXN1/ATXN1L::NUTM2A fusions identified in aggressive infant sarcomas with gene expression and methylation patterns similar to CIC-rearranged sarcoma. Acta Neuropathol Commun 2022; 10:102. [PMID: 35836290 PMCID: PMC9281131 DOI: 10.1186/s40478-022-01401-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/22/2022] [Indexed: 11/10/2022] Open
Abstract
CIC-rearranged sarcomas are newly defined undifferentiated soft tissue tumors with CIC-associated fusions, and dismal prognosis. CIC fusions activate PEA3 family genes, ETV1/4/5, leading to tumorigenesis and progression. We report two high-grade CNS sarcomas of unclear histological diagnosis and one disseminated tumor of unknown origin with novel fusions and similar gene-expression/methylation patterns without CIC rearrangement. All three patients were infants with aggressive diseases, and two experienced rapid disease deterioration and death. Whole-transcriptome sequencing identified an ATXN1-NUTM2A fusion in the two CNS tumors and an ATXN1L-NUTM2A fusion in case 3. ETV1/4/5 and WT1 overexpression were observed in all three cases. Methylation analyses predicted CIC-rearranged sarcoma for all cases. Retrospective IHC staining on case 2 demonstrated ETV4 and WT1 overexpression. ATXN1 and ATXN1L interact with CIC forming a transcription repressor complex. We propose that ATXN1/ATXN1L-associated fusions disrupt their interaction with CIC and decrease the transcription repressor complex, leading to downstream PEA3 family gene overexpression. These three cases with novel ATXN1/ATXN1L-associated fusions and features of CIC-rearranged sarcomas may further expand the scope of "CIC-rearranged" sarcomas to include non-CIC rearrangements. Additional cases are needed to demonstrate if ATXN1/ATXN1L-NUTM2A fusions are associated with younger age and more aggressive diseases.
Collapse
Affiliation(s)
- Feng Xu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Angela N Viaene
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jenny Ruiz
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jeffrey Schubert
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jinhua Wu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jiani Chen
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kajia Cao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Weixuan Fu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rochelle Bagatell
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhiqian Fan
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ariel Long
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Luca Pagliaroli
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yiming Zhong
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Portia A Kreiger
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gerald B Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristina A Cole
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Phillip B Storm
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
24
|
Li MM, Yuan DF, Liu YX, Liu YB, Wang B. [Meta analysis on mumps virus seroprevalence and evaluation of immunization effect in Chinese healthy population]. Zhonghua Yu Fang Yi Xue Za Zhi 2022; 56:994-1003. [PMID: 35899355 DOI: 10.3760/cma.j.cn112150-20220402-00313] [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] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Objective: To systematically analyze the IgG seroprevalence of mumps virus (MuV) in Chinese healthy population, and evaluate the immune effect based on the immunization strategy and the incidence of mumps in China. Methods: The databases of Wanfang data knowledge service platform, China National Knowledge Infrastructure, SinoMed, PubMed, and Web of Science were searched to retrieve literature about the level of MuV IgG antibody in Chinese healthy population from January 1, 2000, to March 31, 2022. The quality of eligible papers was appraised by using the cross-sectional study evaluation tool from Joanna Briggs Institute. Data analysis, including the stratified analysis of the IgG seroprevalence in different generations, regions, gender, immunization status, and age groups, was performed using R 4.1.2 and Stata 16.0. Results: A total of 69 papers (66 in Chinese and 3 in English) were included, involving 97 034 people in 26 administrative regions across China. The results showed that the MuV IgG seroprevalence in Chinese healthy population was 74.87% (95%CI: 71.41%-78.17%) and increased over time according to the cumulative Meta-analysis. The geometric mean concentration of antibody was 177.83 U/ml. The subgroup analysis showed that the positive rate of MuV IgG antibody increased with the age and vaccination doses. The positive rate of antibody in children aged from 0 to 17 months was only 32.42% (95%CI: 25.96%-38.88%). The highest positive rate was reported in North China, about 81.45% (95%CI: 75.76%-87.14%). In addition, the positive rate of MuV IgG antibody in urban population was higher than that in rural population (P<0.01) and the positive rate of MuV IgG antibody in women was higher than that in men (P<0.01). Conclusion: Since the vaccine was included in the expanded immunization program, the positive rate of mumps antibody in China has increased, and the antibody level varies in different regions and populations. It is still necessary to improve the MuV antibody level in Chinese healthy population, so as to better prevent and control the mumps epidemic in the future.
Collapse
Affiliation(s)
- M M Li
- Department of Epidemiology and Health Statistics, Southeast University School of Public Health, Nanjing 210009, China
| | - D F Yuan
- Department of Epidemiology and Health Statistics, Southeast University School of Public Health, Nanjing 210009, China
| | - Y X Liu
- Department of Epidemiology and Health Statistics, Southeast University School of Public Health, Nanjing 210009, China
| | - Y B Liu
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Bei Wang
- Department of Epidemiology and Health Statistics, Southeast University School of Public Health, Nanjing 210009, China
| |
Collapse
|
25
|
Li MM, Tayoun AA, DiStefano M, Pandya A, Rehm HL, Robin NH, Schaefer AM, Yoshinaga-Itano C. Clinical evaluation and etiologic diagnosis of hearing loss: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2022; 24:1392-1406. [PMID: 35802133 DOI: 10.1016/j.gim.2022.03.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/26/2022] Open
Abstract
Hearing loss is a common and complex condition that can occur at any age, can be inherited or acquired, and is associated with a remarkably wide array of etiologies. The diverse causes of hearing loss, combined with the highly variable and often overlapping presentations of different forms of hearing loss, challenge the ability of traditional clinical evaluations to arrive at an etiologic diagnosis for many deaf and hard-of-hearing individuals. However, identifying the etiology of hearing loss may affect clinical management, improve prognostic accuracy, and refine genetic counseling and assessment of the likelihood of recurrence for relatives of deaf and hard-of-hearing individuals. Linguistic and cultural identities associated with being deaf or hard-of-hearing can complicate access to and the effectiveness of clinical care. These concerns can be minimized when genetic and other health care services are provided in a linguistically and culturally sensitive manner. This clinical practice resource offers information about the frequency, causes, and presentations of hearing loss and suggests approaches to the clinical and genetic evaluation of deaf and hard-of-hearing individuals aimed at identifying an etiologic diagnosis and providing informative and effective patient education and genetic counseling.
Collapse
Affiliation(s)
- Marilyn M Li
- Department of Pathology and Laboratory Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children's Specialty Hospital, Mohammed Bin Rashid University, Dubai, United Arab Emirates
| | | | - Arti Pandya
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Nathaniel H Robin
- Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - Amanda M Schaefer
- Department of Otolaryngology-Head & Neck Surgery, Molecular Otolaryngology and Renal Research Laboratories, University of Iowa, Iowa City, IA
| | | |
Collapse
|
26
|
Gao Y, Li MM, Yu HB, Xu GQ, Xu BG, Wu M, Wang N, Liang YC, Wang YL, Han Y. [The success rate of His-Purkinje system pacing in patients with various sites of atrioventricular block]. Zhonghua Xin Xue Guan Bing Za Zhi 2022; 50:543-548. [PMID: 35705462 DOI: 10.3760/cma.j.cn112148-20220403-00238] [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] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Objective: To evaluate the success rate of His-Purkinje system pacing (HPSP) in patients with various sites of atrioventricular block (AVB) and provide clinical evidence for the selection of HPSP in patients with AVB. Methods: This is a retrospective case analysis. 637 patients with AVB who underwent permanent cardiac pacemaker implantation and requiring high proportion of ventricular pacing from March 2016 to September 2021 in the Department of Cardiology, General Hospital of Northern Theater Command were enrolled. The site of AVB was determined by electrophysiological examination. His bundle pacing (HBP) was performed in the first 130 patients (20.4%) who were classified as the HBP group and HPSP included HBP and/or left bundle branch pacing (LBBP) was performed in later 507 patients (79.6%) and these patients were classified as the HPSP group. The basic clinical information such as age and sex of the two groups was compared, and the success rates of HBP or HPSP in patients with different sites of AVB and QRS intervals were analyzed. Results: The age of HBP group was (66.4±15.9) years with 75 males (57.7%). The age of HPSP group was (66.8±13.6) years with 288 (56.8%) males. Among 637 patients, 63.0% (401/637) had atrioventricular node block; 22.9% (146/637) had intra-His block; 14.1% (90/637) had distal or inferior His bundle block. Totally, the success rate of HPSP was higher than that of HBP [93.9% (476/507) vs. 86.9% (113/130), P<0.05]. In each group of patients with various AVB sites, the success rate of HPSP was higher than that of HBP respectively and both success rates of HBP and HPSP showed a declining trend with the distant AVB site. The success rate of HBP in patients with atrioventricular node block and intra-His block was higher than that in patients with distal or inferior His bundle block [95.2% (79/83) vs. 47.1% (8/17), P<0.001; 86.7% (26/30) vs. 47.1% (8/17), P=0.010]. The success rate of HPSP was higher than that of HBP in patients with distal or inferior His bundle block [87.7% (64/73) vs 47.1% (8/17), P=0.001]. In patients with QRS<120 ms, 94.9% (520/548) of AVB sites were in atrioventricular node or intra-His, and HBP had a similar high success rate with HPSP [95.6% (109/114) vs. 96.3% (418/434), P=0.943] in these patients. In patients with QRS ≥ 120 ms, 69.7% (62/89) of AVB sites were at distal or inferior His bundle, and the success rate of HBP was only 25.0% (4/16), while the success rate of HPSP was as high as 79.5% (58/73), P<0.001. Conclusions: In patients with QRS<120 ms and atrioventricular node block or intra-His block, success rates of HBP and HPSP are similarly high and HBP might be considered as the first choice. In patients with QRS ≥ 120 ms and AVB site at distal or inferior His bundle, the success rate of HPSP is higher than that of HBP, suggesting LBBP should be considered as the first-line treatment option.
Collapse
Affiliation(s)
- Y Gao
- Department of Cardiology, General Hospital of Northern Theater Command, Shenyang 110016, China
| | - M M Li
- The Graduate School, Dalian Medical University, Dalian 116044, China
| | - H B Yu
- Department of Cardiology, General Hospital of Northern Theater Command, Shenyang 110016, China
| | - G Q Xu
- Department of Cardiology, General Hospital of Northern Theater Command, Shenyang 110016, China
| | - B G Xu
- Department of Cardiology, General Hospital of Northern Theater Command, Shenyang 110016, China
| | - M Wu
- Department of Cardiology, General Hospital of Northern Theater Command, Shenyang 110016, China
| | - N Wang
- Department of Cardiology, General Hospital of Northern Theater Command, Shenyang 110016, China
| | - Y C Liang
- Department of Cardiology, General Hospital of Northern Theater Command, Shenyang 110016, China
| | - Y L Wang
- Department of Cardiology, General Hospital of Northern Theater Command, Shenyang 110016, China
| | - Yaling Han
- Department of Cardiology, General Hospital of Northern Theater Command, Shenyang 110016, China
| |
Collapse
|
27
|
Saliba J, Raca G, Roy A, King I, Selvarajah S, Xu X, Kanagal-Shamanna R, Satgunaseelan L, Meredith D, Evans M, Church A, Terraf P, Akkari Y, Williams HE, Lin WH, Kesserwan C, Ritter DI, Krysiak K, Danos A, Wagner A, Li MM, Sonkin D, Berg JS, Plon SE, Rehm HL, Kulkarni S, Govindan R, Griffith OL, Griffith M. Abstract 1192: The Clinical Genome Resource (ClinGen) somatic cancer clinical domain working group. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1192] [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] [Indexed: 11/16/2022]
Abstract
Abstract
Interpretation of the clinical significance of somatic gene variants in cancer remains a major challenge in cancer diagnosis, prognosis and treatment response prediction. We will report on progress and plans of the Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group (CDWG). The CDWG membership consists of over 150 multi-disciplinary experts in cancer biology, oncology, pathology, genetics, genomics and informatics. The mission of the ClinGen Somatic Cancer CDWG is to facilitate the development of data curation guidelines and standards to determine the clinical significance of somatic alterations in cancer, thereby enhancing the usability, dissemination and implementation of cancer somatic changes in the ClinGen resource and other knowledgebases including CIViC, ClinVar, and the Variant Interpretation for Cancer Consortium (VICC) MetaKB. Our goal is to create high-quality assertions of the clinical significance of specific somatic variants in cancer by leveraging the CIViC curation interface, adapting the germline procedures of ClinGen to somatic variant interpretation, and implementing the interoperability standards of the Global Alliance for Genomics and Health (GA4GH). The ClinGen Somatic effort is overseen by the Somatic CDWG and reports progress to the overall ClinGen consortium. There are Somatic Cancer subdomains focused on particular clinically important domains of cancer variant interpretation including three Task Forces (covering Pediatric Cancer, Hematologic Cancer, and Solid Tumors) and a growing number of Somatic Cancer Variant Curation Expert Panels (SC-VCEPs). To improve quality and consistency of clinical interpretations, each candidate somatic cancer VCEP must complete a four step approval process adapted from ClinGen’s work in Germline disease domains. The Somatic CDWG works to ensure that each group is aware of available training materials and detailed standard operating procedures. Each SC-VCEP also coordinates with the ClinGen Cancer Variant Interpretation Committee (CVI) whose goal is to support development of granular specifications for the AMP/ASCO/CAP guidelines for somatic variant interpretation. New SC-VCEPs are anticipated to focus on specific clinically relevant genes, pathways, disease entities, variant classes or treatment modalities. Currently, three SC-VCEPs have begun to work through the four step process (focused on FGFR mutations, NTRK fusions, and FLT3 mutations respectively), and two more SC-VCEPs are in the planning stage (Histone H3 and Ph-like ALL). To date, ClinGen Somatic groups have contributed 619 evidence lines into CIViC from 353 published papers and 21 assertions of clinical significance. Input from the AACR community is critical for the establishment of new SC-VCEPs that address areas of variant interpretation with the greatest need.
Citation Format: Jason Saliba, Gordana Raca, Angshumoy Roy, Ian King, Shamini Selvarajah, Xinjie Xu, Rashmi Kanagal-Shamanna, Laveniya Satgunaseelan, David Meredith, Mark Evans, Alanna Church, Panieh Terraf, Yassmine Akkari, Heather E. Williams, Wan-Hsin Lin, Chimene Kesserwan, Deborah I. Ritter, Kilannin Krysiak, Arpad Danos, Alex Wagner, Marilyn M. Li, Dmitriy Sonkin, Jonathan S. Berg, Sharon E. Plon, Heidi L. Rehm, Shashikant Kulkarni, Ramaswamy Govindan, Obi L. Griffith, Malachi Griffith, on behalf of the ClinGen Somatic CDWG. The Clinical Genome Resource (ClinGen) somatic cancer clinical domain working group [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1192.
Collapse
Affiliation(s)
- Jason Saliba
- 1Washington University School of Medicine, St. Louis, MO
| | - Gordana Raca
- 2Children's Hospital Los Angeles, Los Angeles, CA
| | | | - Ian King
- 4University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Shamini Selvarajah
- 4University Health Network and University of Toronto, Toronto, Ontario, Canada
| | | | | | | | - David Meredith
- 8Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Mark Evans
- 6The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alanna Church
- 9Boston Children’s Hospital and Harvard Medical School, Boston, MA
| | - Panieh Terraf
- 10Memorial Sloan Kettering Cancer Center, New York City, NY
| | | | | | | | | | | | | | - Arpad Danos
- 1Washington University School of Medicine, St. Louis, MO
| | - Alex Wagner
- 15Nationwide Children's Hospital, Columbus, OH
| | - Marilyn M. Li
- 16Children’s Hospital of Philadelphia, Philadelphia, PA
| | | | - Jonathan S. Berg
- 18University of North Carolina School of Medicine, Chapel Hill, NC
| | | | - Heidi L. Rehm
- 19Massachusetts General Hospital and Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | | |
Collapse
|
28
|
Wu J, Schubert J, Xu F, Long A, Patel M, Golenberg N, Fu W, Cao K, Chen J, Denenberg EH, Fanning EA, Bagatell R, Laetsch TW, Resnick A, Santi M, Storm PJB, Luo M, Surrey LF, Zhong Y, Li MM. Abstract 5268: The spectrum of FGFR mutations in pediatric and young adult solid tumor. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5268] [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] [Indexed: 11/16/2022]
Abstract
Abstract
Fibroblast growth factor receptors (FGFRs) are a family of receptor tyrosine kinases expressed on the cell membrane that play crucial roles in cellular lineage commitment, differentiation, proliferation, and apoptosis. Deregulated FGFR signaling is observed in a subset of tumors across various histologies, making FGFRs ideal therapeutic targets. We sought to determine the genetic landscape of FGFR-family variations in a cohort of pediatric and young adult patients with solid tumors. The CHOP Comprehensive Solid Tumor Panel was performed on 1,420 patients. The panel covers 238 cancer genes and screens for single nucleotide variants (SNVs), indels, copy number alterations, and 117 fusion gene partners interrogating over 700 exons for known and novel fusions. Identified variants were categorized and reported according to the AMP/ASCO/CAP guidelines. Fifty-six patients (4.1%), including 47 children and 9 young adults, were found to carry at least one FGFR alteration in their tumors. CNS tumors accounted for most of the cases (51 total, 87.9%), with pilomyxoid astrocytoma/pilocytic astrocytoma and dysembryoplastic neuroepithelial tumor the most common (13 and 12 patients, respectively). Non-CNS solid tumors included rhabdomyosarcoma (4 patients), neuroblastoma/ganglioneuroblastoma (2), and follicular thyroid carcinoma (1). FGFR somatic alterations were found in 56 tumors including 41 SNVs and small indels, 6 internal tandem duplications (ITDs), and 15 fusions genes. The most common SNVs observed were hotspot mutations p.K656E and p.N546K of FGFR1. Sequence alterations in FGFR1 contained 35 SNVs and small indels, mostly gain of function mutations located in the kinase domain, and 6 kinase domain ITDs. One SNV was identified in FGFR2 in the immunoglobulin domain. Two SNVs were reported in FGFR3, both of which were in the fibroblast growth factor receptor family domain, and 3 SNVs were identified in FGFR4, all occurring at the p.V550 codon located on the kinase domain. Companion mutations in non-FGFR genes were detected in 27 tumors, predominantly involving RAS signaling pathway genes including NF1 (14 variants), PIK3CA (8), PTPN11 (6) and PIK3R1 (4). Among fusion variants, FGFR1-TACC1 fusions were found in 5 patients, mostly in pediatric patients. One FGFR3-TACC3 fusion was identified in one young adult patient. Seven pediatric patients tested positive for FGFR2 fusions; all with different 3’ partners. The detection of an FGFR alteration defined or changed the histologic diagnosis for 22 patients. Our results reveal that FGFR alterations account for 4.1% (56/1420) of the patients with solid tumors tested in our laboratory. The majority of the FGFR-positive tumors are low-grade CNS tumors. Further, the identification of FGFR alterations can significantly improve the tumor diagnosis and provide genomic evidence for potential targeted treatment with FGFR inhibitors.
Citation Format: Jinhua Wu, Jeffrey Schubert, Feng Xu, Ariel Long, Maha Patel, Netta Golenberg, Weixuan Fu, Kajia Cao, Jiani Chen, Elizabeth H. Denenberg, Elizabeth A. Fanning, Rochelle Bagatell, Theodore W. Laetsch, Adam Resnick, Mariarita Santi, Phillip Jay B. Storm, Minjie Luo, Lea F. Surrey, Yiming Zhong, Marilyn M. Li. The spectrum of FGFR mutations in pediatric and young adult solid tumor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5268.
Collapse
Affiliation(s)
- Jinhua Wu
- 1Children’s Hospital of Philadelphia, Philadelphia, PA
| | | | - Feng Xu
- 1Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Ariel Long
- 1Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Maha Patel
- 1Children’s Hospital of Philadelphia, Philadelphia, PA
| | | | - Weixuan Fu
- 1Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Kajia Cao
- 1Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Jiani Chen
- 1Children’s Hospital of Philadelphia, Philadelphia, PA
| | | | | | | | | | - Adam Resnick
- 1Children’s Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Minjie Luo
- 1Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Lea F. Surrey
- 1Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Yiming Zhong
- 1Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Marilyn M. Li
- 1Children’s Hospital of Philadelphia, Philadelphia, PA
| |
Collapse
|
29
|
Li MM, Drilon A, Laetsch TW. Editorial. Cancer Genet 2022; 266-267:37-38. [PMID: 35728328 DOI: 10.1016/j.cancergen.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Marilyn M Li
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Department of Pathology and Laboratory Medicine, Department of Pediatrics and Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Alexander Drilon
- Early Drug Development Service, Division of Solid Tumor Oncology, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, USA
| | - Theodore W Laetsch
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and Department of Pediatrics and Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
30
|
Yeo KK, Alexandrescu S, Cotter JA, Vogelzang J, Bhave V, Li MM, Ji J, Benhamida JK, Rosenblum MK, Bale TA, Bouvier N, Kaneva K, Rosenberg T, Lim-Fat MJ, Ghosh H, Martinez M, Aguilera D, Smith A, Goldman S, Diamond EL, Gavrilovic I, MacDonald TJ, Wood MD, Nazemi KJ, Truong A, Cluster A, Ligon KL, Cole K, Bi WL, Margol AS, Karajannis MA, Wright KD. Multi-institutional study of the frequency, genomic landscape, and outcome of IDH-mutant glioma in pediatrics. Neuro Oncol 2022; 25:199-210. [PMID: 35604410 PMCID: PMC9825351 DOI: 10.1093/neuonc/noac132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The incidence and biology of IDH1/2 mutations in pediatric gliomas are unclear. Notably, current treatment approaches by pediatric and adult providers vary significantly. We describe the frequency and clinical outcomes of IDH1/2-mutant gliomas in pediatrics. METHODS We performed a multi-institutional analysis of the frequency of pediatric IDH1/2-mutant gliomas, identified by next-generation sequencing (NGS). In parallel, we retrospectively reviewed pediatric IDH1/2-mutant gliomas, analyzing clinico-genomic features, treatment approaches, and outcomes. RESULTS Incidence: Among 851 patients with pediatric glioma who underwent NGS, we identified 78 with IDH1/2 mutations. Among patients 0-9 and 10-21 years old, 2/378 (0.5%) and 76/473 (16.1%) had IDH1/2-mutant tumors, respectively. Frequency of IDH mutations was similar between low-grade glioma (52/570, 9.1%) and high-grade glioma (25/277, 9.0%). Four tumors were graded as intermediate histologically, with one IDH1 mutation. Outcome: Seventy-six patients with IDH1/2-mutant glioma had outcome data available. Eighty-four percent of patients with low-grade glioma (LGG) were managed observantly without additional therapy. For low-grade astrocytoma, 5-year progression-free survival (PFS) was 42.9% (95%CI:20.3-63.8) and, despite excellent short-term overall survival (OS), numerous disease-related deaths after year 10 were reported. Patients with high-grade astrocytoma had a 5-year PFS/OS of 36.8% (95%CI:8.8-66.4) and 84% (95%CI:50.1-95.6), respectively. Patients with oligodendroglioma had excellent OS. CONCLUSIONS A subset of pediatric gliomas is driven by IDH1/2 mutations, with a higher rate among adolescents. The majority of patients underwent upfront observant management without adjuvant therapy. Findings suggest that the natural history of pediatric IDH1/2-mutant glioma may be similar to that of adults, though additional studies are needed.
Collapse
Affiliation(s)
- Kee Kiat Yeo
- Corresponding Author: Kee Kiat Yeo, MD, Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, 450 Brookline Ave, Boston, MA 02215, USA ()
| | | | | | - Jayne Vogelzang
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, Boston, MA, USA
| | | | - Marilyn M Li
- Division of Genomic Diagnostics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jianling Ji
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA,USA
| | - Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc K Rosenblum
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tejus A Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nancy Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kristiyana Kaneva
- Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, USA,Tempus Labs, Inc., Chicago, IL, USA
| | - Tom Rosenberg
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Mary Jane Lim-Fat
- Department of Medical Oncology, Dana-Farber/Brigham and Women’s Hospital Cancer Center, Boston, MA, USA
| | - Hia Ghosh
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Migdalia Martinez
- Department of Pediatrics, Arnold Palmer Hospital for Children, Orlando, FL, USA
| | - Dolly Aguilera
- Department of Pediatrics, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Amy Smith
- Department of Pediatrics, Arnold Palmer Hospital for Children, Orlando, FL, USA
| | - Stewart Goldman
- Department of Child Health, Phoenix Children’s Hospital, University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Eli L Diamond
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Igor Gavrilovic
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tobey J MacDonald
- Department of Pediatrics, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Matthew D Wood
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Kellie J Nazemi
- Department of Pediatrics, Doernbecher Children’s Hospital, Portland, OR, USA
| | - AiLien Truong
- Department of Pediatrics, Doernbecher Children’s Hospital, Portland, OR, USA
| | - Andrew Cluster
- Department of Pediatrics, St. Louis Children’s Hospital, St. Louis, MO, USA
| | - Keith L Ligon
- Department of Pathology, Dana-Farber/Brigham and Women’s Hospital Cancer Center, Boston, MA, USA
| | - Kristina Cole
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Ashley S Margol
- Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | | | - Karen D Wright
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorder Center, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| |
Collapse
|
31
|
Hao N, Zhou J, Li MM, Luo WW, Zhang HZ, Qi QW, Jiang YL, Zhou XY, Yang K, Chen H, Pan HJ, Zhu JT, Liu J. [Efficacy and initial clinical evaluation of optical genome mapping in the diagnosis of structural variations]. Zhonghua Yu Fang Yi Xue Za Zhi 2022; 56:632-639. [PMID: 35644979 DOI: 10.3760/cma.j.cn112150-20220212-00131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
To investigate the efficacy and value of optical genome mapping (OGM) in detecting chromosomal structural variations. In a clinical study about high-precision analysis of genomic structural variation for complex genetic diseases, a retrospective study was performed on the cases with karyotyping at the department of Obstetrics and Gynecology, and Endocrinology of Peking Union Medical College Hospital from January to December 2021. Ten cases with abnormal karyotype was detected by OGM. Partial cases were verified by fluorescence in situ hybridization (FISH), SNP array or CNV-seq. Results of ten cases, nine were detected with abnormality by OGM, including unbalanced chromosomal rearrangements (n=3), translocation (n=5) and paracentric inversion (n=1), and the results were in concordance with other standard assays. However, one case with breakpoint and reconnected at centromere has not been detected. In conclusion, ten samples were comprehensively analyzed by karyotyping, FISH, SNP array or CNV-seq, and OGM, and results demonstrated that optical genome mapping as a new technology can not only detect unbalanced rearrangements such as copy number variants as well as balanced translocations and inversions, but more importantly, it can refine breakpoints and orientation of duplicated segments or insertions. So it can contribute to the diagnosis of genetic diseases and prevent birth defect. However, the current technology is not yet capable of detecting breakpoints of balanced structural variations lying within unmapped regions.
Collapse
Affiliation(s)
- N Hao
- Department of Obstetrics and Gynecology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing 100730, China
| | - J Zhou
- Department of Obstetrics and Gynecology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing 100730, China
| | - M M Li
- Department of Obstetrics and Gynecology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing 100730, China
| | - W W Luo
- Department of Obstetrics and Gynecology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing 100730, China
| | - H Z Zhang
- Department of Obstetrics and Gynecology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing 100730, China
| | - Q W Qi
- Department of Obstetrics and Gynecology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing 100730, China
| | - Y L Jiang
- Department of Obstetrics and Gynecology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing 100730, China
| | - X Y Zhou
- Department of Obstetrics and Gynecology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing 100730, China
| | - K Yang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, State Key Laboratory of Complex Severe and Rare Diseases, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - H Chen
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, State Key Laboratory of Complex Severe and Rare Diseases, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - H J Pan
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, State Key Laboratory of Complex Severe and Rare Diseases, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - J T Zhu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, State Key Laboratory of Complex Severe and Rare Diseases, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100730, China
| | - Juntao Liu
- Department of Obstetrics and Gynecology, Chinese Academy of Medical Sciences & Peking Union Medical College, National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing 100730, China
| |
Collapse
|
32
|
Li Q, Ren Z, Cao K, Li MM, Wang K, Zhou Y. CancerVar: An artificial intelligence-empowered platform for clinical interpretation of somatic mutations in cancer. Sci Adv 2022; 8:eabj1624. [PMID: 35544644 PMCID: PMC9075800 DOI: 10.1126/sciadv.abj1624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 03/21/2022] [Indexed: 05/12/2023]
Abstract
Several knowledgebases are manually curated to support clinical interpretations of thousands of hotspot somatic mutations in cancer. However, discrepancies or even conflicting interpretations are observed among these databases. Furthermore, many previously undocumented mutations may have clinical or functional impacts on cancer but are not systematically interpreted by existing knowledgebases. To address these challenges, we developed CancerVar to facilitate automated and standardized interpretations for 13 million somatic mutations based on the AMP/ASCO/CAP 2017 guidelines. We further introduced a deep learning framework to predict oncogenicity for these variants using both functional and clinical features. CancerVar achieved satisfactory performance when compared to several independent knowledgebases and, using clinically curated datasets, demonstrated practical utility in classifying somatic variants. In summary, by integrating clinical guidelines with a deep learning framework, CancerVar facilitates clinical interpretation of somatic variants, reduces manual work, improves consistency in variant classification, and promotes implementation of the guidelines.
Collapse
Affiliation(s)
- Quan Li
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON M5G2C1, Canada
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Zilin Ren
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kajia Cao
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Marilyn M. Li
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yunyun Zhou
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| |
Collapse
|
33
|
Franco AT, Ricarte-Filho JC, Isaza A, Jones Z, Jain N, Mostoufi-Moab S, Surrey L, Laetsch TW, Li MM, DeHart JC, Reichenberger E, Taylor D, Kazahaya K, Adzick NS, Bauer AJ. Fusion Oncogenes Are Associated With Increased Metastatic Capacity and Persistent Disease in Pediatric Thyroid Cancers. J Clin Oncol 2022; 40:1081-1090. [PMID: 35015563 PMCID: PMC8966969 DOI: 10.1200/jco.21.01861] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [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: 07/31/2021] [Revised: 10/07/2021] [Accepted: 12/09/2021] [Indexed: 12/15/2022] Open
Abstract
PURPOSE In 2014, data from a comprehensive multiplatform analysis of 496 adult papillary thyroid cancer samples reported by The Cancer Genome Atlas project suggested that reclassification of thyroid cancer into molecular subtypes, RAS-like and BRAF-like, better reflects clinical behavior than sole reliance on pathologic classification. The aim of this study was to categorize the common oncogenic variants in pediatric differentiated thyroid cancer (DTC) and investigate whether mutation subtype classification correlated with the risk of metastasis and response to initial therapy in pediatric DTC. METHODS Somatic cancer gene panel analysis was completed on DTC from 131 pediatric patients. DTC were categorized into RAS-mutant (H-K-NRAS), BRAF-mutant (BRAF p.V600E), and RET/NTRK fusion (RET, NTRK1, and NTRK3 fusions) to determine differences between subtype classification in regard to pathologic data (American Joint Committee on Cancer TNM) as well as response to therapy 1 year after initial treatment had been completed. RESULTS Mutation-based subtype categories were significant in most variables, including age at diagnosis, metastatic behavior, and the likelihood of remission at 1 year. Patients with RET/NTRK fusions were significantly more likely to have advanced lymph node and distant metastasis and less likely to achieve remission at 1 year than patients within RAS- or BRAF-mut subgroups. CONCLUSION Our data support that genetic subtyping of pediatric DTC more accurately reflects clinical behavior than sole reliance on pathologic classification with patients with RET/NTRK fusions having worse outcomes than those with BRAF-mutant disease. Future trials should consider inclusion of molecular subtype into risk stratification.
Collapse
Affiliation(s)
- Aime T Franco
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Julio C Ricarte-Filho
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Amber Isaza
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Zachary Jones
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA
- Deceased
| | - Neil Jain
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Sogol Mostoufi-Moab
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Lea Surrey
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Theodore W Laetsch
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Erin Reichenberger
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ken Kazahaya
- Division of Pediatric Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA
| | - N Scott Adzick
- Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Andrew J Bauer
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA
| |
Collapse
|
34
|
Saliba J, Church AJ, Rao S, Danos A, Furtado LV, Laetsch T, Zhang L, Nardi V, Lin WH, Ritter D, Madhavan S, Li MM, Griffith OL, Griffith M, Raca G, Roy A. Standardized Evidence-Based Approach for Assessment of Oncogenic and Clinical Significance of NTRK Fusions. Cancer Genet 2022; 264-265:50-59. [DOI: 10.1016/j.cancergen.2022.03.001] [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] [Received: 10/18/2021] [Revised: 02/13/2022] [Accepted: 03/07/2022] [Indexed: 11/17/2022]
|
35
|
Xu F, Aref-Eshghi E, Wu J, Schubert J, Wertheim G, Bhatti T, Pogoriler J, Patel M, Cao K, Long A, Fan Z, Denenberg E, Fanning E, Wilmoth D, Luo M, Conlin L, Dain AS, Baldino S, Zelley K, Balamuth NJ, Macfarland S, Li MM, Zhong Y. A Novel TP53 Tandem Duplication in a Child with Li-Fraumeni Syndrome. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006181. [PMID: 35232817 PMCID: PMC9059784 DOI: 10.1101/mcs.a006181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/18/2022] [Indexed: 11/24/2022] Open
Abstract
Li–Fraumeni syndrome (LFS) is one of the most common cancer predisposition syndromes that affects both children and adults. Individuals with LFS are at an increased risk of developing various types of cancer over their lifetime including soft tissue sarcomas, osteosarcomas, breast cancer, leukemia, brain tumors, and adrenocortical carcinoma. Heterozygous germline pathogenic variants in the tumor suppressor gene TP53 are the known causal genetic defect for LFS. Single-nucleotide variants (SNVs) including missense substitutions that occur in the highly conserved DNA binding domain of the protein are the most common alterations, followed by nonsense and splice site variants. Gross copy-number changes in TP53 are rare and account for <1% of all variants. Using next-generation sequencing (NGS) panels, we identified a paternally inherited germline intragenic duplication of TP53 in a child with metastatic osteosarcoma who later developed acute myeloid leukemia (AML). Transcriptome sequencing (RNA-seq) demonstrated the duplication was tandem, encompassing exons 2–6 and 28 nt of the untranslated region (UTR) upstream of the start codon in exon 2. The inclusion of the 28 nt is expected to result in a frameshift with a stop codon 18 codons downstream from the exon 6, leading to a loss-of-function allele. This case highlights the significance of simultaneous identification of both significant copy-number variants as well as SNVs/indels using NGS panels.
Collapse
Affiliation(s)
- Feng Xu
- Children's Hospital of Philadelphia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marilyn M Li
- Children's Hospital of Philadelphia; University of Pennsylvania
| | | |
Collapse
|
36
|
Li TY, Zhang J, Li MM, An N, Pan Q. [Diabetes insipidus as the onset manifestation of IgG 4-related disease: a case report]. Zhonghua Nei Ke Za Zhi 2022; 61:324-326. [PMID: 35263976 DOI: 10.3760/cma.j.cn112138-20210615-00422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- T Y Li
- Graduate School of Peking Union Medical College, Department of Endocrinology, Beijing Hospital, Beijing 100730, China Department of Endocrinology,Beijing Hospital,National Center of Gerontology,Institute of Geriatric Medicine,Chinese Academy of Medical Sciences, Beijing 100730, China
| | - J Zhang
- Department of Endocrinology,Beijing Hospital,National Center of Gerontology,Institute of Geriatric Medicine,Chinese Academy of Medical Sciences, Beijing 100730, China
| | - M M Li
- Graduate School of Peking Union Medical College, Department of Endocrinology, Beijing Hospital, Beijing 100730, China Department of Endocrinology,Beijing Hospital,National Center of Gerontology,Institute of Geriatric Medicine,Chinese Academy of Medical Sciences, Beijing 100730, China
| | - N An
- Department of Endocrinology,Beijing Hospital,National Center of Gerontology,Institute of Geriatric Medicine,Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Q Pan
- Graduate School of Peking Union Medical College, Department of Endocrinology, Beijing Hospital, Beijing 100730, China Department of Endocrinology,Beijing Hospital,National Center of Gerontology,Institute of Geriatric Medicine,Chinese Academy of Medical Sciences, Beijing 100730, China
| |
Collapse
|
37
|
Bruehl FK, Kim AS, Li MM, Lindeman NI, Moncur JT, Souers RJ, Vasalos P, Voelkerding KV, Xian RR, Surrey LF. Tiered Somatic Variant Classification Adoption Has Increased Worldwide With Some Practice Differences Based on Location and Institutional Setting. Arch Pathol Lab Med 2022; 146:822-832. [PMID: 34979564 DOI: 10.5858/arpa.2021-0179-cp] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The 2017 Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists (CAP) tier classification guideline provides a framework to standardize interpretation and reporting of somatic variants. OBJECTIVE.— To evaluate the adoption and performance of the 2017 guideline among laboratories performing somatic next-generation sequencing (NGS). DESIGN.— A survey was distributed to laboratories participating in NGS CAP proficiency testing for solid tumors (NGSST) and hematologic malignancies (NGSHM). RESULTS.— Worldwide, 64.4% (152 of 236) of NGSST and 66.4% (87 of 131) of NGSHM participants used tier classification systems, of which the 2017 guideline was used by 84.9% (129 of 152) of NGSST and 73.6% (64 of 87) of NGSHM participants. The 2017 guideline was modified by 24.4% (30 of 123) of NGSST and 21.7% (13 of 60) of NGSHM laboratories. Laboratories implementing the 2017 guideline were satisfied or very satisfied (74.2% [89 of 120] NGSST and 69.5% [41 of 59] NGSHM), and the impression of tier classification reproducibility was high (mean of 3.9 [NGSST] and 3.6 [NGSHM] on a 5-point scale). Of nonusers, 35.2% (38 of 108) of NGSST and 39.4% (26 of 66) of NGSHM laboratories were planning implementation. For future guideline revisions, respondents favored including variants to monitor disease (63.9% [78 of 122] NGSST, 80.0% [48 of 60] NGSHM) and germline variants (55.3% [63 of 114] NGSST, 75.0% [45 of 60] NGSHM). Additional subtiers were not favored by academic laboratories compared to nonacademic laboratories (P < .001 NGSST and P = .02 NGSHM). CONCLUSIONS.— The 2017 guideline has been implemented by more than 50.0% of CAP laboratories. While most laboratories using the 2017 guideline report satisfaction, thoughtful guideline modifications may further enhance the quality, reproducibility, and clinical utility of the 2017 guideline for tiered somatic variant classification.
Collapse
Affiliation(s)
- Frido K Bruehl
- From Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio (Bruehl)
| | - Annette S Kim
- The Departments of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts (Kim, Lindeman)
| | - Marilyn M Li
- The Department of Pathology and Laboratory Medicine, Perelman School of Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (Li, Surrey)
| | - Neal I Lindeman
- The Departments of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts (Kim, Lindeman)
| | - Joel T Moncur
- The Joint Pathology Center, Office of the Director, Silver Spring, Maryland (Moncur), College of American Pathologists, Northfield, Illinois
| | - Rhona J Souers
- Biostatistics Department (Souers), College of American Pathologists, Northfield, Illinois
| | - Patricia Vasalos
- Proficiency Testing (Vasalos), College of American Pathologists, Northfield, Illinois
| | | | - Rena R Xian
- The Department of Pathology and Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland (Xian)
| | - Lea F Surrey
- The Department of Pathology and Laboratory Medicine, Perelman School of Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (Li, Surrey)
| |
Collapse
|
38
|
Felix CA, Slater DJ, Davenport JW, Yu X, Gregory BD, Li MM, Rappaport EF, Cheung NKV. KMT2A-MAML2 rearrangement emerged and regressed during neuroblastoma therapy without leukemia after 12.8-year follow-up. Pediatr Blood Cancer 2022; 69:e29344. [PMID: 34550633 PMCID: PMC9616630 DOI: 10.1002/pbc.29344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/09/2021] [Accepted: 08/19/2021] [Indexed: 01/03/2023]
Abstract
Twelvepatients without therapy-related leukemia were studied after completing TOP2 poison chemotherapy in a high-risk neuroblastoma regimen. One patient harbored an inv(11) that was a KMT2A rearrangement. The KMT2A-MAML2 transcript was expressed at low level. The patient was prospectively followed. The inv(11) was undetectable in ensuing samples. Leukemia never developed after a 12.8-year follow-up period. Enriched etoposide-induced TOP2A cleavage in the relevant MAML2 genomic region supports a TOP2A DNA damage mechanism. After completing TOP2 poison chemotherapies, covert KMT2A-R clones may occur in a small minority of patients; however, not all KMT2A rearrangements herald a therapy-related leukemia diagnosis.
Collapse
Affiliation(s)
- Carolyn A. Felix
- Division of Oncology, The Children’s Hospital of Philadelphia, Center for Childhood Cancer Research, Philadelphia, PA 19104,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104,Corresponding Author: Carolyn A. Felix, M.D., Professor of Pediatrics, Joshua Kahan Endowed Chair in Pediatric Leukemia Research, Division of Oncology, The Children’s Hospital of Philadelphia, Colket Translational Research Building, Room 4006, 3501 Civic Center Blvd., Philadelphia, PA 19104-4318, (215) 590-2831,
| | - Diana J. Slater
- Division of Oncology, The Children’s Hospital of Philadelphia, Center for Childhood Cancer Research, Philadelphia, PA 19104,Nucleic Acids and PCR Core Facility, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - James W. Davenport
- Division of Oncology, The Children’s Hospital of Philadelphia, Center for Childhood Cancer Research, Philadelphia, PA 19104
| | - Xiang Yu
- Biology Department, University of Pennsylvania, Philadelphia, PA 19104
| | - Brian D. Gregory
- Biology Department, University of Pennsylvania, Philadelphia, PA 19104
| | - Marilyn M. Li
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104,Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104,Division of Genomic Diagnostics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104,Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104
| | - Eric F. Rappaport
- Nucleic Acids and PCR Core Facility, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Nai-Kong V. Cheung
- Department of Pediatrics, Memorial Sloan-Kettering Cancer Center, New York, NY 10021
| |
Collapse
|
39
|
Bride KL, Hu H, Tikhonova A, Fuller TJ, Vincent TL, Shraim R, Li MM, Carroll WL, Raetz EA, Aifantis I, Teachey DT. Rational drug combinations with CDK4/6 inhibitors in acute lymphoblastic Leukemia. Haematologica 2021; 107:1746-1757. [PMID: 34937317 PMCID: PMC9335101 DOI: 10.3324/haematol.2021.279410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 11/09/2022] Open
Abstract
Despite improvements in outcomes for children with B and T-cell acute lymphoblastic leukemia (B-ALL and T-ALL), patients with resistant or relapsed disease fare poorly. Previous studies have demonstrated the essential role of cyclin D3 in T-ALL disease initiation and progression and that targeting of the CDK4/6-cyclin D complex can suppress T-ALL proliferation, leading to efficient cell death in animal models. Studies in leukemia and other malignancies, suggest that schedule is important when combining CDK4/6 inhibitors (CDKis) with cytotoxic agents. Based on these observations, we broadened evaluation of two CDKis, palbociclib (PD-0332991, Pfizer) and ribociclib (LEE011, Novartis) in B and T-ALL as single agent and in combination with conventional cytotoxic chemotherapy, using different schedules in preclinical models. As monotherapy, CDKis caused cell cycle arrest with a significant decrease in S phase entry and were active in vivo across a broad number of patient-derived xenograft samples. Prolonged monotherapy induces resistance, for which we identified a potential novel mechanism using transcriptome profiling. Importantly, simultaneous but not sequential treatment of CDKis with conventional chemotherapy (dexamethasone, L-asparaginase and vincristine) led to improved efficacy compared to monotherapy in vivo. We provide novel evidence that combining CDKis and conventional chemotherapy can be safe and effective. These results led to the rational design of a clinical trial.
Collapse
Affiliation(s)
- Karen L Bride
- Department of Pediatrics, Division of Hematology/Oncology and Cellular Therapy, Cohen Children's Medical Center, New Hyde Park
| | - Hai Hu
- Perlmutter Cancer Center and Department of Pediatrics, NYU Langone Health, NY, NY
| | | | - Tori J Fuller
- Children's Hospital of Philadelphia; Philadelphia, PA
| | | | - Rawan Shraim
- Children's Hospital of Philadelphia; Philadelphia, PA
| | - Marilyn M Li
- Children's Hospital of Philadelphia; Philadelphia, PA
| | - William L Carroll
- Perlmutter Cancer Center and Department of Pediatrics, NYU Langone Health, NY, NY
| | - Elizabeth A Raetz
- Perlmutter Cancer Center and Department of Pediatrics, NYU Langone Health, NY, NY
| | - Iannis Aifantis
- Perlmutter Cancer Center and Department of Pediatrics, NYU Langone Health, NY, NY
| | | |
Collapse
|
40
|
Kotch C, Fisher MJ, Lin F, Zhong Y, Gallo D, Fan Z, Chen J, Santi M, Li MM. Atypical teratoid rhabdoid tumor in a child with neurofibromatosis type 2: A novel dual diagnosis. Cancer Genet 2021; 262-263:1-4. [PMID: 34972035 DOI: 10.1016/j.cancergen.2021.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 09/24/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022]
Abstract
Neurofibromatosis type 2 (NF2) is a genetic disorder characterized by the development of tumors of the nervous system and is associated with NF2 gene alterations. Atypical teratoid rhabdoid tumor (ATRT) is a malignant central nervous system tumor that occurs primarily in children less than 3 years of age. The majority of cases of ATRT demonstrate genomic alterations of SMARCB1, a core member of the SWI/SNF chromatin-remodeling complex and tumor suppressor gene. SMARCB1 inactivation in ATRT is occasionally associated with somatic NF2 deletion; however, concurrent germline NF2 mutations have not been reported. Herein, we describe the case of a 3-year-old patient who presented with an intracranial mass. Next generation sequencing analysis of tumor identified homozygous deletions of the entire SMARCB1 gene and exon 7 to exon 14 of NF2 gene with whole chromosome 22 loss of heterozygosity (LOH). Multiplex Ligation-dependent Probe Amplification (MLPA) assay performed on blood identified a germline heterozygous intragenic deletion of NF2 exon 7 to exon 14; a somatic chromosome 22 LOH led to the homozygous deletion. SMARCB1 MLPA assay of blood showed no deletion. This cascade represents a novel, "four-hit" mechanism of SMARCB1 inactivation resulting in ATRT and the first known dual diagnosis of NF2 and ATRT.
Collapse
Affiliation(s)
- Chelsea Kotch
- Department of Pediatrics, Division of Oncology, Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Philadelphia, PA 19104, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| | - Michael J Fisher
- Department of Pediatrics, Division of Oncology, Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Philadelphia, PA 19104, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Yiming Zhong
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Dan Gallo
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Zhiqian Fan
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jiani Chen
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Mariarita Santi
- Division of Anatomic Pathology, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Marilyn M Li
- Department of Pediatrics, Division of Oncology, Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Philadelphia, PA 19104, United States; Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| |
Collapse
|
41
|
Aref-Eshghi E, Lin F, Li MM, Zhong Y. The oncogenic roles of NTRK fusions and methods of molecular diagnosis. Cancer Genet 2021; 258-259:110-119. [PMID: 34710798 DOI: 10.1016/j.cancergen.2021.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/23/2021] [Accepted: 10/16/2021] [Indexed: 10/20/2022]
Abstract
The NTRK gene family is composed of NTRK1, NTRK2, and NTRK3, which encode three tropomyosin-receptor kinases, belonging to a class of tyrosine kinase receptors. These proteins are known to play roles in cell proliferation, differentiation, apoptosis, and survival. Fusions involving the NTRK genes are long known as drivers in many tumors. Although they occur in less than 5% of all malignancies, their occurrence in a great diversity of tumors has been documented. Several rare tumors including infantile fibrosarcoma, secretory breast carcinoma, and mammary analogue secretory carcinoma are accompanied by NTRK fusions in more than 90% of cases, demonstrating a diagnostic value for the NTRK fusion testing in these tumors. More recently, the development of effective targeted therapies has created a demand for their detection in all malignancies. A variety of approaches are available for testing including immunohistochemistry, fluorescence in situ hybridization (FISH), reverse transcription polymerase chain reaction (RT-PCR), and DNA- and RNA-based next-generation sequencing (NGS). This article reviews the molecular biology and tumorigenesis of NTRK fusions, their prevalence and clinical significance with a focus on available methods for fusion detection. The advantages and limitations of different technologies, the best practice algorithms for NTRK fusion detection, and the future direction of NTRK testing are also discussed.
Collapse
Affiliation(s)
- Erfan Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Yiming Zhong
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| |
Collapse
|
42
|
Strait AM, Bridge JA, Iafrate AJ, Li MM, Xu F, Tsongalis GJ, Linos K. Mammary-type Myofibroblastoma with Leiomyomatous Differentiation: A Rare Variant with Potential Pitfalls. Int J Surg Pathol 2021; 30:200-206. [PMID: 34338561 DOI: 10.1177/10668969211031309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Myofibroblastoma is a rare, benign stromal tumor with a diverse morphologic spectrum. Mammary-type myofibroblastoma (MTMF) is the extra-mammary counterpart of this neoplasm and its occurrence throughout the body has become increasingly recognized. Similar morphologic variations of MTMF have now been described which mirror those seen in the breast. We describe a case of intra-abdominal MTMF composed of short fascicles of eosinophilic spindle cells admixed with mature adipose tissue. The spindle cells stained diffusely positive for CD34, desmin, smooth muscle actin, and h-caldesmon by immunohistochemistry. Concurrent loss of RB1 (13q14) and 13q34 loci were confirmed by fluorescence in situ hybridization whereas anchored multiplex PCR and whole transcriptome sequencing did not reveal any pathognomonic fusions suggesting an alternative diagnosis. To the best of our knowledge this is the first documented case of leiomyomatous variant of MTMF.
Collapse
Affiliation(s)
| | - Julia A Bridge
- 12284University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Marilyn M Li
- The Children's Hospital of Philadelphia, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA, USA
| | - Feng Xu
- The Children's Hospital of Philadelphia, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA, USA
| | - Gregory J Tsongalis
- 22916Dartmouth-Hitchcock Medical Center Lebanon, NH, USA.,12285Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Konstantinos Linos
- 22916Dartmouth-Hitchcock Medical Center Lebanon, NH, USA.,12285Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| |
Collapse
|
43
|
Tomás-Velázquez A, Surrey LF, Miele E, Li MM, Alaggio R, Goitz RJ, Reyes-Múgica M, Salgado CM. Mesenchymal PLAG1 Tumor With PCMTD1-PLAG1 Fusion in an Infant: A New Type of "Plagoma". Am J Dermatopathol 2021; 44:54-57. [PMID: 34291746 DOI: 10.1097/dad.0000000000001978] [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] [Indexed: 11/25/2022]
Abstract
ABSTRACT In the past decade, there have been major advances in knowledge related to mesenchymal tumors, and new genetic alterations are being delineated. We report a mesenchymal spindle cell neoplasm harboring a novel gene fusion in an infant. Histopathologically, the neoplasm shared some features with sclerosing perineurioma, but immunohistochemically, EMA was negative, whereas GLUT1, NK1-C3, and BCOR were positive. Next-generation sequencing revealed a PCMTD1-pleomorphic adenoma gene 1 (PLAG1) fusion. PLAG1 contributes to the expression of a variety of genes implicated in regulating cell proliferation, and PCMTD1 has been related to the development of certain carcinomas. Recently, other soft tissue tumors in young children associated with PLAG1 fusion variants have been reported. Perhaps, mesenchymal neoplasms presenting PLAG1 fusions with different genes would confirm a specific group (PLAG mesenchymal tumours or "plagomas") in the near future.
Collapse
Affiliation(s)
- Alejandra Tomás-Velázquez
- Department of Dermatology, University Clinic of Navarra, School of Medicine, University of Navarra, Pamplona, Spain; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; Department of Pediatric Hematology/Oncology, IRCCS Bambino Gesù Children's Hospital, Roma, Italy; Department of Pathology, Ospedale Bambino Gesù, Roma, Italy; Orthopedic Division, University of Pittsburgh Medical Center, Pittsburgh, PA; and Department of Pathology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Morales AG, Vibart RE, Li MM, Jonker A, Pacheco D, Hanigan MD. Evaluation of Molly model predictions of ruminal fermentation, nutrient digestion, and performance by dairy cows consuming ryegrass-based diets. J Dairy Sci 2021; 104:9676-9702. [PMID: 34127259 DOI: 10.3168/jds.2020-19740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 04/20/2021] [Indexed: 11/19/2022]
Abstract
Several studies have been conducted to improve grazing management and supplementation in pasture-based systems. However, it is necessary to develop tools that integrate the available information linking the representation of biological processes with animal performance for use in decision making. The objective of this study was to evaluate the precision and accuracy of the Molly cow model predictions of ruminal fermentation, nutrient digestion, and animal performance by cows consuming pasture-based diets to identify model strengths and weaknesses, and to derive new digestive parameters when relevant. Model modifications for adipose tissue, protein synthesis in lean body mass and viscera representation were included. Data used for model evaluations were collected from 25 publications containing 115 treatment means sourced from studies conducted with lactating dairy cattle. The inclusion criteria were that diets contained ≥45% perennial ryegrass (Lolium perenne L.), and that dry matter intake, dietary ingredient composition, and nutrient digestion observations were reported. Animal performance and N excretion variables were also included if they were reported. Model performance was assessed before and after model reparameterization of selected digestive parameters, global sensitivity analysis was conducted after reparameterization, and a 5-fold cross evaluation was performed. Although rumen fermentation predictions were not significantly improved, rumen volatile fatty acids absorption rates were recalculated, which improved the concordance correlation coefficient (CCC) for rumen propionate and ammonia concentration predictions but decreased CCC for acetate predictions. Similar degradation rates of crude protein were observed for grass and total mixed ration diets, but rumen-undegradable protein predictions seemed to be affected by the solubility of the protein source as was the intestinal digestibility coefficient. Ruminal fiber degradation was greater after reparameterization, driven primarily by hemicellulose degradation. Predictions of ruminal and fecal outflow of neutral detergent fiber and acid detergent fiber, as well as total fecal output predictions, improved significantly after reparameterization. Blood urea N and urinary N excretion predictions resulted in similar accuracy using both sets of model parameters, whereas fecal N excretion predictions were significantly improved after reparameterization. Body weight and body condition score predictions were greatly improved after model modifications and reparameterization. Before reparameterization, yield predictions for daily milk, milk fat, milk protein, and milk lactose were greatly overestimated (mean bias of 61.0, 58.7, 73.7, and 64.6% of mean squared error, respectively). Although this problem was partially addressed by model modifications and reparameterization (mean bias of 3.2, 1.1, 1.7, and 0.4% of mean squared error, respectively), CCC values were still small. The ability of the model to predict grass digestion and animal performance in dairy cows consuming pasture-based diets was improved, demonstrating the applicability of this model to these productive systems. However, the failure to predict grass digestion based on standard model inputs without reparameterization indicates there are still fundamental challenges in characterizing feeds for this model.
Collapse
Affiliation(s)
- A G Morales
- Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg 24061; Animal Science Institute, Universidad Austral de Chile, Valdivia 5110566, Chile
| | - R E Vibart
- AgResearch, Grasslands Research Centre, Tennent Drive, Palmerston North 4442, New Zealand
| | - M M Li
- Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg 24061
| | - A Jonker
- AgResearch, Grasslands Research Centre, Tennent Drive, Palmerston North 4442, New Zealand
| | - D Pacheco
- AgResearch, Grasslands Research Centre, Tennent Drive, Palmerston North 4442, New Zealand
| | - M D Hanigan
- Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg 24061.
| |
Collapse
|
45
|
Jain P, Surrey LF, Straka J, Russo P, Womer R, Li MM, Storm PB, Waanders AJ, Hogarty MD, Resnick AC, Picarsic J. BRAF fusions in pediatric histiocytic neoplasms define distinct therapeutic responsiveness to RAF paradox breakers. Pediatr Blood Cancer 2021; 68:e28933. [PMID: 33565241 DOI: 10.1002/pbc.28933] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 01/12/2021] [Indexed: 01/26/2023]
Abstract
Pediatric histiocytic neoplasms are hematopoietic disorders frequently driven by the BRAF-V600E mutation. Here, we identified two BRAF gene fusions (novel MTAP-BRAF and MS4A6A-BRAF) in two aggressive histiocytic neoplasms. In contrast to previously described BRAF fusions, MTAP-BRAF and MS4A6A-BRAF do not respond to the paradox breaker RAF inhibitor (RAFi) PLX8394 due to stable fusion dimerization mediated by the N-terminal fusion partners. This highlights a significant and clinically relevant shift from the current dogma that BRAF-fusions respond similarly to BRAF-inhibitors. As an alternative, we show suppression of fusion-driven oncogenic growth with the pan-RAFi LY3009120 and MEK inhibition.
Collapse
Affiliation(s)
- Payal Jain
- Center for Data Driven Discovery in Biomedicine (D3B), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Joshua Straka
- Center for Data Driven Discovery in Biomedicine (D3B), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Pierre Russo
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Richard Womer
- Department of Pediatrics, Division of Hematology and Oncology, Children's Hospital of Philadelphia (CHOP), Philadelphia, Pennsylvania, USA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Phillip B Storm
- Center for Data Driven Discovery in Biomedicine (D3B), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Neurosurgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Angela J Waanders
- Department of Pediatrics, Feinberg School of Medicine Northwestern University, Chicago, Illinois, USA
| | - Michael D Hogarty
- Department of Pediatrics, Division of Hematology and Oncology, Children's Hospital of Philadelphia (CHOP), Philadelphia, Pennsylvania, USA
| | - Adam C Resnick
- Center for Data Driven Discovery in Biomedicine (D3B), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jennifer Picarsic
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| |
Collapse
|
46
|
Lalonde E, Rentas S, Wertheim G, Cao K, Surrey LF, Lin F, Zhao X, Obstfeld A, Aplenc R, Luo M, Li MM. Clinical impact of genomic characterization of 15 patients with acute megakaryoblastic leukemia-related malignancies. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a005975. [PMID: 33832921 PMCID: PMC8040732 DOI: 10.1101/mcs.a005975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/26/2021] [Indexed: 01/30/2023] Open
Abstract
Acute megakaryoblastic leukemia (AMKL) is a rare subtype of acute myeloid leukemia but is approximately 500 times more likely to develop in children with Down syndrome (DS) through transformation of transient abnormal myelopoiesis (TAM). This study investigates the clinical significance of genomic heterogeneity of AMKL in children with and without DS and in children with TAM. Genomic evaluation of nine patients with DS-related TAM or AMKL, and six patients with non-DS AMKL, included conventional cytogenetics and a comprehensive next-generation sequencing panel for single-nucleotide variants/indels and copy-number variants in 118 genes and fusions involving 110 genes. Recurrent gene fusions were found in all patients with non-DS, including two individuals with complex genomes and either a NUP98–KDM5A or a KMT2A–MLLT6 fusion, and the remaining harbored a CBFA2T3–GLIS2 fusion, which arose from both typical and atypical cytogenetic mechanisms. These fusions guided treatment protocols and resulted in a change in diagnosis in two patients. The nine patients with DS had constitutional trisomy 21 and somatic GATA1 mutations, and those with DS-AMKL had two to four additional clinically significant somatic mutations. Comprehensive genomic characterization provides critical information for diagnosis, risk stratification, and treatment decisions for patients with AMKL. Continued genetic and clinical characterization of these rare cancers will aid in improving patient management.
Collapse
Affiliation(s)
- Emilie Lalonde
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Stefan Rentas
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Gerald Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kajia Cao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Xiaonan Zhao
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Amrom Obstfeld
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Richard Aplenc
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
47
|
Zhao X, Kotch C, Fox E, Surrey LF, Wertheim GB, Baloch ZW, Lin F, Pillai V, Luo M, Kreiger PA, Pogoriler JE, Linn RL, Russo PA, Santi M, Resnick AC, Storm PB, Hunger SP, Bauer AJ, Li MM. NTRK Fusions Identified in Pediatric Tumors: The Frequency, Fusion Partners, and Clinical Outcome. JCO Precis Oncol 2021; 1:PO.20.00250. [PMID: 34036219 PMCID: PMC8140782 DOI: 10.1200/po.20.00250] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/26/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022] Open
Abstract
Neurotrophic tyrosine receptor kinase (NTRK) fusions have been described as
oncogenic drivers in a variety of tumors. However, little is known about the
overall frequency of NTRK fusion in unselected pediatric tumors. Here, we
assessed the frequency, fusion partners, and clinical course in pediatric
patients with NTRK fusion–positive tumors.
Collapse
Affiliation(s)
- Xiaonan Zhao
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Chelsea Kotch
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth Fox
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Lea F Surrey
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gerald B Wertheim
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Zubair W Baloch
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Vinodh Pillai
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Portia A Kreiger
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jennifer E Pogoriler
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Rebecca L Linn
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Pierre A Russo
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Adam C Resnick
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Phillip B Storm
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Stephen P Hunger
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Andrew J Bauer
- Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| |
Collapse
|
48
|
Viaene AN, Pu C, Perry A, Li MM, Luo M, Santi M. Congenital tumors of the central nervous system: an institutional review of 64 cases with emphasis on tumors with unique histologic and molecular characteristics. Brain Pathol 2021; 31:45-60. [PMID: 32681571 PMCID: PMC8018134 DOI: 10.1111/bpa.12885] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
Congenital brain tumors are rare accounting for 0.5%-1.9% of all pediatric brain tumors. While different criteria have been used to classify a tumor as congenital, those diagnosed prior to 6 months of age are considered to be "probably" congenital in origin. We performed an institutional review of all central nervous system (CNS) tumors (surgical and autopsy specimens from 1990 to 2019) in patients less than 6 months old. Sixty-four unique cases were identified, and these accounted for 2.0% of all CNS tumor specimens at our institution. The most common tumor types were high-grade gliomas, low-grade gliomas and medulloblastomas. Atypical teratoid rhabdoid tumors, choroid plexus tumors and germ cell tumors also accounted for a significant portion of the cohort. Seven tumors were diagnosed prenatally. The most common clinical presentation at diagnosis was increased head circumference. At the conclusion of the study, over half of the patients were alive including all patients with WHO grade I and II tumors. Ninety-two percent of cases were classifiable using the 2016 WHO system, and when available, molecular findings supported the histologic diagnoses. However, several gliomas had unusual histologic features and did not correspond to a well-defined entity. Molecular testing was essential for accurate classification of a subset of these tumors, and several high-grade gliomas exhibited fusions considered unique to infantile gliomas, including those involving the MET, ALK and NTRK genes. To our knowledge, this cohort represents the largest single-institution study of congenital CNS tumors and highlights many ways in which congenital CNS tumors are distinct from CNS tumors of older pediatric patients and adults.
Collapse
Affiliation(s)
- Angela N. Viaene
- Department of Pathology and Laboratory MedicineChildren’s Hospital of PhiladelphiaUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
| | - Cunfeng Pu
- Department of Pathology and Laboratory MedicinePenn State College of MedicineHersheyPAUSA
| | - Arie Perry
- Department of PathologyUniversity of CaliforniaSan FranciscoCAUSA
- Department of Neurological SurgeryUniversity of CaliforniaSan FranciscoCAUSA
| | - Marilyn M. Li
- Department of Pathology and Laboratory MedicineChildren’s Hospital of PhiladelphiaUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
| | - Minjie Luo
- Department of Pathology and Laboratory MedicineChildren’s Hospital of PhiladelphiaUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
| | - Mariarita Santi
- Department of Pathology and Laboratory MedicineChildren’s Hospital of PhiladelphiaUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPAUSA
| |
Collapse
|
49
|
Zhong Y, Xu F, Wu J, Schubert J, Li MM. Application of Next Generation Sequencing in Laboratory Medicine. Ann Lab Med 2021; 41:25-43. [PMID: 32829577 PMCID: PMC7443516 DOI: 10.3343/alm.2021.41.1.25] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.
Collapse
Affiliation(s)
- Yiming Zhong
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
| | - Feng Xu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jinhua Wu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jeffrey Schubert
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Marilyn M. Li
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| |
Collapse
|
50
|
Zeng Q, Li MM, Hu GH. [Use of larynx-preservation strategies in the treatment of laryngeal cancer]. Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2020; 55:1186-1190. [PMID: 33342139 DOI: 10.3760/cma.j.cn115330-20200914-00743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Q Zeng
- Department of Otolaryngology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016 China
| | - M M Li
- Department of Oncology, the First Affiliated Hospital of Chongqing Medical University Chongqing 400016 China
| | - G H Hu
- Department of Otolaryngology, the First Affiliated Hospital of Chongqing Medical University, Chongqing 400016 China
| |
Collapse
|