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Miele E, Anghileri E, Calatozzolo C, Lazzarini E, Patrizi S, Ciolfi A, Pedace L, Patanè M, Abballe L, Paterra R, Maddaloni L, Barresi S, Mastronuzzi A, Petruzzi A, Tramacere I, Farinotti M, Gurrieri L, Pirola E, Scarpelli M, Lombardi G, Villani V, Simonelli M, Merli R, Salmaggi A, Tartaglia M, Silvani A, DiMeco F, Calistri D, Lamperti E, Locatelli F, Indraccolo S, Pollo B. Clinicopathological and molecular landscape of 5-year IDH-wild-type glioblastoma survivors: A multicentric retrospective study. Cancer Lett 2024; 588:216711. [PMID: 38423245 DOI: 10.1016/j.canlet.2024.216711] [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: 10/24/2023] [Revised: 01/19/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Five-year glioblastoma (GBM) survivors (LTS) are the minority of the isocitrate dehydrogenase (IDH)-wild-type GBM patients, and their molecular fingerprint is still largely unexplored. This multicenter retrospective study analyzed a large LTS-GBM cohort from nine Italian institutions and molecularly characterized a subgroup of patients by mutation, DNA methylation (DNAm) and copy number variation (CNV) profiling, comparing it to standard survival GBM. Mutation scan allowed the identification of pathogenic variants in most cases, showing a similar mutational spectrum in both groups, and highlighted TP53 as the most commonly mutated gene in the LTS group. We confirmed DNAm as a valuable tool for GBM classification with a diagnostic refinement by using brain tumor classifier v12.5. LTS were more heterogeneous with more cases classified as diffuse pediatric high-grade glioma subtypes and having peculiar CNVs. We observed a global higher methylation in CpG islands and in gene promoters of LTS with methylation levels of distinct gene promoters correlating with prognosis.
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Affiliation(s)
- Evelina Miele
- Department of Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Elena Anghileri
- Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta (FINCB), Milan, Italy.
| | - Chiara Calatozzolo
- Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Elisabetta Lazzarini
- Basic and Translational Oncology Unit, Istituto Oncologico Veneto (IOV)-IRCCS, Padua, Italy
| | - Sara Patrizi
- Department of Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lucia Pedace
- Department of Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Monica Patanè
- Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Luana Abballe
- Department of Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rosina Paterra
- Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta (FINCB), Milan, Italy
| | - Luisa Maddaloni
- Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta (FINCB), Milan, Italy
| | - Sabina Barresi
- Pathology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Angela Mastronuzzi
- Department of Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alessandra Petruzzi
- Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta (FINCB), Milan, Italy
| | - Irene Tramacere
- Department of Research and Clinical Development, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Mariangela Farinotti
- Neuroepidemiology-Brain Cancer Registry, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Lorena Gurrieri
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) Dino Amadori, Meldola, Italy
| | - Elena Pirola
- Department of Neurosurgery Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Mauro Scarpelli
- Neurology Unit, Azienda Ospedaliera Universitaria Integrata Verona, Italy
| | - Giuseppe Lombardi
- Medical Oncology Unit 1, Istituto Oncologico Veneto IOV-IRCCS, Padua, Italy
| | - Veronica Villani
- Neuro-Oncology Unit, IRCCS Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | - Matteo Simonelli
- Department of Oncology and Hematology Unit, IRCCS Humanitas Research Hospital, Rozzano, Italy; Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Rossella Merli
- Neurosurgery Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | | | - Marco Tartaglia
- Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Silvani
- Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta (FINCB), Milan, Italy
| | - Francesco DiMeco
- Department of Neurosurgery, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy; Department of Neurological Surgery, John Hopkins Medical School, Baltimore, MD, USA
| | - Daniele Calistri
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Elena Lamperti
- Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta (FINCB), Milan, Italy
| | - Franco Locatelli
- Department of Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Life Sciences and Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - Stefano Indraccolo
- Basic and Translational Oncology Unit, Istituto Oncologico Veneto (IOV)-IRCCS, Padua, Italy; Department of Surgery Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Bianca Pollo
- Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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Wu J, Zhang Y, Qin T, Xu Z, Qu S, Pan L, Li B, Jia Y, Li C, Wang H, Gao Q, Cai W, Gong J, Zhao S, Li F, Gale RP, Xiao Z. IPSS-M has greater survival predictive accuracy compared with IPSS-R in persons ≥ 60 years with myelodysplastic syndromes. Exp Hematol Oncol 2022; 11:73. [PMID: 36253799 PMCID: PMC9578211 DOI: 10.1186/s40164-022-00328-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
There are considerable new data on mutation topography in persons with myelodysplastic syndromes (MDS). These data have been used to update conventional risk models such as the Revised International Prognostic Scoring System (IPSS-R). Whether the molecular IPSS (IPSS-M) which includes these data improves survival prediction accuracy is untested. To answer this question, we compared survival prediction accuracies of the IPSS-R and IPSS-M in 852 consecutive subjects with de novo MDS. Concordance statistics (C-statistics) of the IPSS-R and IPSS-M in the entire cohort were similar, 0.67 (95% Confidence Interval [CI] 0.64, 0.71) and 0.68 (0.64, 0.71). Average numbers of mutations and of IPSS-M related mutations were greater in persons ≥ 60 years (2.0 [Interquartile Range [IQR], 1, 3] vs. 1.6 [0, 2], P = 0.003; 1.6 [0, 2] vs. 1.3 [0, 2], P = 0.006). Subjects ≥ 60 years had a higher incidence of mutations in RUNX1, TP53, TET2, SRSF2, DNMT3A, STAG2, EZH2 and DDX41. In contrast, mutations in U2AF1 were more common in persons < 60 years. Next we tested survival prediction accuracy based on age < or ≥ 60 years. C-statistics of the IPSS-R and IPSS-M in subjects ≥ 60 years were 0.66 (0.61, 0.71) and 0.69 (0.64, 0.73) whereas in subjects < 60 years they were 0.67 (0.61, 0.72) and 0.65 (0.59, 0.71). These data indicate an advantage for the IPSS-M over the IPSS-R in subjects ≥ 60 years but not in those < 60 years probably because of a great frequency of mutations correlated with survival in those ≥ 60 years.
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Affiliation(s)
- Junying Wu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Yudi Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Tiejun Qin
- MDS and MPN Centre, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Zefeng Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,MDS and MPN Centre, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Shiqiang Qu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,MDS and MPN Centre, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Lijuan Pan
- MDS and MPN Centre, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Bing Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,MDS and MPN Centre, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Yujiao Jia
- Hematologic Pathology Centre, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Chengwen Li
- Hematologic Pathology Centre, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Huijun Wang
- Hematologic Pathology Centre, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Qingyan Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,MDS and MPN Centre, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Wenyu Cai
- Hematologic Pathology Centre, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jingye Gong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Songyang Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Fuhui Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Robert Peter Gale
- Centre for Hematology, Department of Immunology and Inflammation, Imperial College of Science, Technology and Medicine, London, UK
| | - Zhijian Xiao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China. .,MDS and MPN Centre, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China. .,Hematologic Pathology Centre, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
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Li SS, Zhai XH, Liu HL, Liu TZ, Cao TY, Chen DM, Xiao LX, Gan XQ, Cheng K, Hong WJ, Huang Y, Lian YF, Xiao J. Whole-exome sequencing analysis identifies distinct mutational profile and novel prognostic biomarkers in primary gastrointestinal diffuse large B-cell lymphoma. Exp Hematol Oncol 2022; 11:71. [PMID: 36243813 PMCID: PMC9569083 DOI: 10.1186/s40164-022-00325-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 05/21/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
Background Diffuse large B-cell lymphoma (DLBCL) is the most common aggressive non-Hodgkin lymphoma, and about 10% of DLBCL cases primarily occur in the gastrointestinal tract. Previous reports have revealed that primary gastrointestinal-DLBCL (pGI-DLBCL) harbors different genetic mutations from other nodal or extranodal DLBCL. However, the exonic mutation profile of pGI-DLBCL has not been fully addressed. Methods We performed whole-exome sequencing of matched tumor tissues and blood samples from 53 pGI-DLBCL patients. The exonic mutation profiles were screened, and the correlations between genetic mutations and clinicopathological characteristics were analyzed. Results A total of 6,588 protein-altering events were found and the five most frequent mutated genes in our pGI-DLBCL cohort were IGLL5 (47%), TP53 (42%), BTG2 (28%), P2RY8 (26%) and PCLO (23%). Compared to the common DLBCL, significantly less or absence of MYD88 (0%), EZH2 (0%), BCL2 (2%) or CD79B (8%) mutations were identified in pGI-DLBCL. The recurrent potential driver genes were mainly enriched in pathways related to signal transduction, infectious disease and immune regulation. In addition, HBV infection had an impact on the mutational signature in pGI-DLBCL, as positive HBsAg was significantly associated with the TP53 and LRP1B mutations, two established tumor suppressor genes in many human cancers. Moreover, IGLL5 and LRP1B mutations were significantly correlated with patient overall survival and could serve as two novel prognostic biomarkers in pGI-DLBCL. Conclusions Our study provides a comprehensive view of the exonic mutation profile of the largest pGI-DLBCL cohort to date. The results could facilitate the clinical development of novel therapeutic and prognostic biomarkers for pGI-DLBCL. Supplementary Information The online version contains supplementary material available at 10.1186/s40164-022-00325-7.
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Affiliation(s)
- Shan-Shan Li
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Xiao-Hui Zhai
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Hai-Ling Liu
- Department of Pathology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Ting-Zhi Liu
- Department of Hematology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Tai-Yuan Cao
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Dong-Mei Chen
- Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Le-Xin Xiao
- Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Xiao-Qin Gan
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Ke Cheng
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Wan-Jia Hong
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Yan Huang
- Department of Pathology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China. .,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
| | - Yi-Fan Lian
- Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
| | - Jian Xiao
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China. .,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
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Meena JP, Pathak N, Gupta AK, Bakhshi S, Gupta R, Makkar H, Seth R. Molecular evaluation of gene mutation profiles and copy number variations in pediatric acute myeloid leukemia. Leuk Res 2022; 122:106954. [PMID: 36162216 DOI: 10.1016/j.leukres.2022.106954] [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: 05/23/2022] [Revised: 08/19/2022] [Accepted: 09/17/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND The objectives of this study were to investigate the mutation profiles of targeted genes and copy number variations (CNVs) in normal cytogenetics (CN) pediatric acute myeloid leukemia (AML). METHODS This prospective study was conducted from October 2018 to December 2020. The next-generation sequencing (NGS) and chromosomal microarray analyses (CMA) were performed in pediatric CN-AML patients. RESULTS Out of 94 children (aged ≤18 years), 70 patients with AML (24 excluded) underwent conventional karyotyping/cytogenetic analyses. Forty-five (64.3%) of patients had abnormal/ recurrent cytogenetic abnormalities and 25 (35.7%) had normal cytogenetics. Twenty-three out of 25 CN-AML were further processed for gene mutation profile and CNVs using NGS and CMA, respectively. Twenty-two out of 23 (95.7%) patients were detected to have mutations in various genes. The common mutations were: NRAS, NPM1, CEBPA, KRAS, KIT, RUNX1, NOTCH1, WT1, GATA1, GATA2, FLT3, KMT2D, FLT3-TKD, and PHF6. Copy number variations (CNVs) were detected in nine patients (39%), and eight (34.8%) had a long contiguous stretch of homozygosity (LCSH) /loss of heterozygosity (LOH). An LCSH was detected on chromosomes 5, 7, 11, and 19. The gains were more common than losses (8 vs 2). The gains were observed on chromosomes 8, 9, 14, 19, 21, and 22, and the losses were detected on chromosomes 7 and 10. Monosomy was observed in three patients. Three patients (monosomy7, n = 2, and FLT-ITD, n = 1) were reclassified into the high-risk category. Post-induction, complete remission was achieved in all evaluable patients. CONCLUSION CN-AML patients have genetic abnormalities that can be detected by more advanced techniques like NGS and CMA. These genetic abnormalities play a role in risk stratification that may remain hidden in otherwise CN-AML.
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Affiliation(s)
- Jagdish Prasad Meena
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Nivedita Pathak
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Aditya Kumar Gupta
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Sameer Bakhshi
- Department of Medical Oncology, Dr. B.R.A. IRCH, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. B.R.A. IRCH, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Harshita Makkar
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Rachna Seth
- Division of Pediatric Oncology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi 110029, India.
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5
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Paul D, Pyne N, Paul S. Mutation profile of SARS-CoV-2 spike protein and identification of potential multiple epitopes within spike protein for vaccine development against SARS-CoV-2. Virusdisease 2021; 32:703-726. [PMID: 34754886 PMCID: PMC8569294 DOI: 10.1007/s13337-021-00747-7] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 09/28/2021] [Indexed: 12/20/2022] Open
Abstract
The COVID-19 pandemic worldwide has resulted in over 176 million cases and roughly 3.8 million deaths so far. We could analyze mutation dynamics across the genome from countries such as the USA, Italy, the UK, France, Brazil, and India considering the rapid mutations of the SARS-CoV-2 genome. The analysis would help us to understand the genome diversity, the implications of the mutations in protein stability, and viral transmission. Among the 11 genes, surface glycoprotein (S) was singled out because of its crucial function associated with the entry of virion into the human cell upon binding with the hACE2 receptor. 749 S protein sequences from India were retrieved from the NCBI database for our study. The S protein is an important antigenic component responsible for inducing host immune responses, neutralizing antibodies, and providing protective immunity against viral infection. During an epitope prediction from a mutation-prone S-protein region, it is necessary to ascertain how new mutations significantly change the S protein, such that our vaccine is effective against all the mutated strains as well. The S1 region of the S protein had been our prime focus for identifying immune epitopes against SARS-COV-2. Antigenic B- cell epitopes were YYPDKVF from NTD and LFRKSNLKP from RBD. Cytotoxic T-cell epitopes WTAGAAAYY (within NTD) and CVADYSVLY (within RBD) exhibited binding with a maximum number of MHC I alleles. The T-cell epitopes which showed a maximum affinity for MHC II alleles were FLPFFSNVT within NTD and YFPLQSYGF within RBD. Furthermore, the best epitopes were characterized in terms of their physicochemical properties to establish their potentiality.
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Affiliation(s)
- Debadrita Paul
- Laboratory of Cell and Molecular Biology, Department of Botany, Centre of Advanced Study, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019 India
| | - Nibedita Pyne
- Laboratory of Cell and Molecular Biology, Department of Botany, Centre of Advanced Study, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019 India
| | - Santanu Paul
- Laboratory of Cell and Molecular Biology, Department of Botany, Centre of Advanced Study, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019 India
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6
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Páramo JA, Marcos-Jubilar M, Lecumberri R. Impact of the mutation profile on thrombotic risk in cancer patients. Rev Clin Esp 2021; 222:93-99. [PMID: 34548256 DOI: 10.1016/j.rceng.2021.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/16/2021] [Indexed: 10/20/2022]
Abstract
Patients with cancer present with an elevated risk of thrombosis, which entails high morbidity and mortality. Various predictive scales that incorporate clinical and biological data have been developed to identify those at high risk of thrombosis, but, in general, they do not allow for the optimal selection of subjects who are candidates for thromboprophylaxis. Recent studies have demonstrated that the mutation profile has a high impact on the risk of thrombosis; this will facilitate developing new predictive models of thrombosis in patients with cancer.
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Affiliation(s)
- J A Páramo
- Servicio de Hematología, Clínica Universidad de Navarra, Pamplona, Spain.
| | - M Marcos-Jubilar
- Servicio de Hematología, Clínica Universidad de Navarra, Pamplona, Spain
| | - R Lecumberri
- Servicio de Hematología, Clínica Universidad de Navarra, Pamplona, Spain
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7
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Mohiuddin S, Maraka S, Usman Baig M, Gupta S, Muzzafar T, Valyi-Nagy T, Lindsay H, Moody K, Razvi S, Paulino A, Slavin K, Gondi V, McCutcheon I, Zaky W, Khatua S. Case series of diffuse extraneural metastasis in H3F3A mutant high-grade gliomas: Clinical, molecular phenotype and literature review. J Clin Neurosci 2021; 89:405-411. [PMID: 34053821 DOI: 10.1016/j.jocn.2021.05.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 12/16/2020] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 11/19/2022]
Abstract
H3K27M and H3.3G34R/V mutations have been identified in pediatric high-grade gliomas (pHGG), though extraneural metastases are rarely reported and poorly characterized. Three pHGG patients from two institutions were identified with extraneural metastasis, harboring histone mutations. Their clinical, imaging and molecular characteristics are reported here. A 17-year old female presented with supratentorial H3.3G34R-mutant glioma with metastatic osseous lesions in the spine, pelvis, bone marrow, pleural effusion and soft tissue of pelvis. Bone marrow biopsy and soft tissue of pelvis biopsy showed neoplastic cells positive for P53. A 20-year old female was diagnosed with H3F3A H3K27M-mutant thalamic glioma. She developed diffuse sclerotic osseous lesions. Biopsy of an osseous lesion was non-diagnostic. A 17-year old female presented with a H3F3A H3K27M-mutant diffuse midline glioma with diffuse spinal cord metastasis. She further developed multifocal chest lymphadenopathy, pleural effusions, and a soft tissue mass in the abdominal wall. The latter was positive for H3K27M mutation. We present the first case series of pHGG with H3F3A mutation and diffuse extraneural dissemination, describing their clinical and molecular profile.
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Affiliation(s)
- Sana Mohiuddin
- Department of Pediatrics Patient Care, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stefania Maraka
- Department of Neurology and Rehabilitation, University of Illinois at Chicago, Chicago, IL, USA; Department of Neuro-oncology, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Muhammad Usman Baig
- Department of Pediatrics Patient Care, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sumit Gupta
- Department of Pediatrics Patient Care, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tariq Muzzafar
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tibor Valyi-Nagy
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, USA
| | - Holly Lindsay
- Department of Pediatrics, Division of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Karen Moody
- Department of Pediatrics Patient Care, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shehla Razvi
- Department of Pediatrics Patient Care, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Arnold Paulino
- Department of Radiation Oncology, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Konstantin Slavin
- Department of Neurosurgery, University of Illinois at Chicago, Chicago, IL, USA
| | - Vinai Gondi
- Northwestern Medicine Chicago Proton Center, Warrenville, IL, USA
| | - Ian McCutcheon
- Department of Neurosurgery, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Wafik Zaky
- Department of Pediatrics Patient Care, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Soumen Khatua
- Department of Hematology-Oncology, Mayo Clinic, Rochester, MN.
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8
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Zhang J, Xiang C, Han Y, Teng H, Li X, Shao J, Zhu L, Han-Zhang H, Ye J, Yu K. Differential diagnosis of pulmonary enteric adenocarcinoma and metastatic colorectal carcinoma with the assistance of next-generation sequencing and immunohistochemistry. J Cancer Res Clin Oncol 2018; 145:269-279. [PMID: 30415301 DOI: 10.1007/s00432-018-2788-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 06/08/2018] [Accepted: 11/02/2018] [Indexed: 12/27/2022]
Abstract
PURPOSE Pulmonary enteric adenocarcinoma (PEAC), defined as tumors with an enteric component exceeding 50% and a histological morphology similar to colorectal cancer (CRC) and metastatic colorectal carcinoma (MCC), is an extremely rare primary lung adenocarcinoma, which was recently recognized by World Health Organization (WHO). Adenocarcinomas with intestinal differentiation have also been described in other anatomic sites, including paranasal sinuses, extrahepatic biliary tree, uterine and cervix, ovary. The morphologic spectrum and immunohistochemical profiles of PEAC overlap with those of colonic adenocarcinomas, the diagnosis of PEAC remains challenging. Currently, colonoscopy has to be performed to confirm the diagnosis, resulting in low compliance due to its invasiveness. Due to the rareness of PEAC, its molecular signature has not been comprehensively examined. METHODS In this study, we investigated the molecular signatures associated with PEAC and its histological counterparts, CRC and MCC using capture-based targeted sequencing. RESULTS We revealed that 12/13 (92.31%) PEAC patients harbored mutations in well-established driver genes for non-small cell lung cancer and none of them had mutations unique to CRC. Furthermore, 13/15 (86.7%) of MCC harbored mutations that are frequently seen in CRC. CONCLUSION Collectively, our study showed that PEAC, exhibiting a similar mutational profile with NSCLC, showed a distinctive signature from CRC and MCC. Furthermore, we derived a classification model, intergrading both IHC markers and genetic signature, to accurately diagnose PEAC.
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Affiliation(s)
- Jie Zhang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Chan Xiang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yuchen Han
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Haohua Teng
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xiaojing Li
- Department of Pathology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Jinchen Shao
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Lei Zhu
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | | | - Junyi Ye
- Burning Rock Biotech, Guangzhou, 510000, China
| | - Keke Yu
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China.
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